Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 129 of 222
Found at i:41645339 original size:81 final size:80
Alignment explanation
Indices: 41645225--41645574 Score: 307
Period size: 81 Copynumber: 4.3 Consensus size: 80
41645215 GGGGTATAAT
* * *
41645225 AGTCGTTTTACCCTATAGGGGTATTTC-AGTCATTTTACCCTATAGGGCTAATTCAATCATTTTA
1 AGTCATTTTACCCTATAGGGGTATTTCGA-TCATTTTACCCTATAGGG-TATTTCGATCATTTTA
* *
41645289 CCCTATGGGGGTAATTC
64 ACCTATGGGGGTATTTC
* * * * * *
41645306 ATTCATTTTACCCTATGGGGGTATTTCGATCATTTCACCCGT-TGGGGATATTTCGGTCATTCT-
1 AGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCC-TATAGGG-TATTTCGATCATTTTA
* *
41645369 ACCATATGAGAGTATTTC
64 ACC-TATGGGGGTATTTC
* * * * * * *
41645387 GGTCATTTTACCTTTTGGGGGTATTTCGATCATTTTGCCTTATGGGGGTATTTCGATCATTTTAA
1 AGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTAT-AGGGTATTTCGATCATTTTAA
41645452 CCTATGGGGGGTATTTC
65 CCTAT-GGGGGTATTTC
* * * * * * *
41645469 -GATTATTCTACCCTATAGAGGTATTTCGGTCATTTTACCTTATGAGGGTATTTTGGTCATTTTA
1 AG-TCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTAT-AGGGTATTTCGATCATTTTA
*
41645533 ACCTATGGGGGT-TTTT
64 ACCTATGGGGGTATTTC
* *
41645549 GGTCATTCTACCCTAT-GGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
41645575 AGTGCAGACA
Statistics
Matches: 221, Mismatches: 39, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
79 9 0.04
80 19 0.09
81 118 0.53
82 75 0.34
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.41
Consensus pattern (80 bp):
AGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATAGGGTATTTCGATCATTTTAAC
CTATGGGGGTATTTC
Found at i:41646213 original size:24 final size:24
Alignment explanation
Indices: 41646188--41646234 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41646178 CCCAAATCCC
41646188 AATATTCTCTCCTCAAATCTCTCCA
1 AATA-TCTCTCCTCAAATCTCTCCA
* *
41646213 AATATCTCTTCTCAATTCTCTC
1 AATATCTCTCCTCAAATCTCTC
41646235 TACGACTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (24 bp):
AATATCTCTCCTCAAATCTCTCCA
Found at i:41647779 original size:26 final size:26
Alignment explanation
Indices: 41647673--41647779 Score: 144
Period size: 26 Copynumber: 4.1 Consensus size: 26
41647663 AACATACCAA
* *
41647673 TATCGCAACAAAGCTACCAGTAATAG
1 TATCGCAGCAAAGCTACCAGTAACAG
*
41647699 TGA-CGCAGCAAAGCTACCAATAACAG
1 T-ATCGCAGCAAAGCTACCAGTAACAG
*
41647725 TAACGCAGCAAAGCTACCAGTAACAG
1 TATCGCAGCAAAGCTACCAGTAACAG
* *
41647751 TATCGCAGCAAAGCTGCTAGTAACAG
1 TATCGCAGCAAAGCTACCAGTAACAG
41647777 TAT
1 TAT
41647780 ACTTCCTCCA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
25 1 0.01
26 70 0.97
27 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (26 bp):
TATCGCAGCAAAGCTACCAGTAACAG
Found at i:41647954 original size:27 final size:27
Alignment explanation
Indices: 41647924--41648275 Score: 304
Period size: 27 Copynumber: 13.1 Consensus size: 27
41647914 AGGGTATAAT
* *
41647924 AGTCGTTTTACCCTATAGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTC
* * *
41647951 AGTCATTTTACCCTATAGGGCTAATTC
1 AGTCATTTTACCCTATGGGGGTATTTC
* *
41647978 AATCATTTTACCCTATGGGGGTAATTC
1 AGTCATTTTACCCTATGGGGGTATTTC
*
41648005 ATTCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTC
* *
41648032 -GATCATTTCACCCGT-TGGGGATATTTC
1 AG-TCATTTTACCC-TATGGGGGTATTTC
* * * * *
41648059 GGTCATTCTACCATATGAGAGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTC
* * *
41648086 GGTCATTTTACCTTTTGGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTC
* *
41648113 -GATCATTTTGCCTTATGGGGGTATTTC
1 AG-TCATTTTACCCTATGGGGGTATTTC
*
41648140 -GATCATTTTAACCTATGGGGGTATTTC
1 AG-TCATTTTACCCTATGGGGGTATTTC
* * *
41648167 -GATCATTCTACCCTATAGAGGTATTTC
1 AG-TCATTTTACCCTATGGGGGTATTTC
* * * *
41648194 GGTCATTTTACCTTATGAGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTC
* * *
41648221 GGTCATTTTAACCTATGGGGGT-TTTT
1 AGTCATTTTACCCTATGGGGGTATTTC
* * *
41648247 GGTCGTTCTACCCTAT-GGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTC
41648273 AGT
1 AGT
41648276 GCAGACATTG
Statistics
Matches: 273, Mismatches: 45, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
25 5 0.02
26 24 0.09
27 241 0.88
28 3 0.01
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (27 bp):
AGTCATTTTACCCTATGGGGGTATTTC
Found at i:41652948 original size:15 final size:15
Alignment explanation
Indices: 41652928--41652956 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41652918 GTATTGTTGC
41652928 TTGATAACATGGTGA
1 TTGATAACATGGTGA
41652943 TTGATAACATGGTG
1 TTGATAACATGGTG
41652957 TGTGTGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (15 bp):
TTGATAACATGGTGA
Found at i:41661679 original size:15 final size:15
Alignment explanation
Indices: 41661659--41661689 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41661649 GTTGCTATAG
*
41661659 AAATAAAATAAATAA
1 AAATAAAAGAAATAA
41661674 AAATAAAAGAAATAA
1 AAATAAAAGAAATAA
41661689 A
1 A
41661690 GTGAGTGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (15 bp):
AAATAAAAGAAATAA
Found at i:41663882 original size:51 final size:51
Alignment explanation
Indices: 41663822--41664012 Score: 237
Period size: 51 Copynumber: 3.8 Consensus size: 51
41663812 CCGGTTCACA
*
41663822 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATACACG
* * * *
41663873 TAGTAGCCTGCACATAGTACTACACACGTGATCA-AAGCTATCC-AGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCA-CTATCCGA-TACACG
* ** * *
41663924 TAGTAGCCTGCACATAGTACTACACATGCAACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGATACACG
41663974 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
41664013 TTCACTGTCA
Statistics
Matches: 117, Mismatches: 17, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
49 4 0.03
50 39 0.33
51 72 0.62
52 1 0.01
53 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATACACG
Found at i:41663997 original size:101 final size:102
Alignment explanation
Indices: 41663820--41664004 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
41663810 TACCGGTTCA
**
41663820 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCAACCATCACTATCCGATACACGTAGTAGCCTGCA
41663885 CATAGTACTACACACGTGATCAAAGCTATCCAGTACG
66 CATAGTACTACACACGTGATCAAAGCTATCCAGTACG
* *
41663922 CATAGTAGCCTGCACATAGTACTACACATGCAACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCAACC-ATCACTATCCGATACACGTAGTAGCCTGC
41663985 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
41664005 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
101 40 0.51
102 34 0.44
103 4 0.05
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCAACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCAAAGCTATCCAGTACG
Found at i:41664027 original size:101 final size:101
Alignment explanation
Indices: 41663817--41664042 Score: 296
Period size: 101 Copynumber: 2.2 Consensus size: 101
41663807 TGATACCGGT
**
41663817 TCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCT
1 TCACATAGTAGCCTGCACATAGTACTACACATGCAACCATCACTATCCGATACACGTAGTAGCCT
*
41663882 GCACATAGTACTACACACGTGATCAAAGCTATCCAG
66 GCACATAGTACTACACACGTGACCAAAGCTATCCAG
* * *
41663918 TACGCATAGTAGCCTGCACATAGTACTACACATGCAACCTATCA-T-TCTGGTACACGTAGTAGC
1 T-CACATAGTAGCCTGCACATAGTACTACACATGCAACC-ATCACTATCCGATACACGTAGTAGC
* * *
41663981 CTGCACATAGTACTACACACGTGACCATCA-CTTTCACTG
64 CTGCACATAGTACTACACACGTGACCA-AAGCTATC-CAG
* *
41664020 TCACATAGTCGCCTACACATAGT
1 TCACATAGTAGCCTGCACATAGT
41664043 CCATGCCACA
Statistics
Matches: 109, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
101 66 0.61
102 39 0.36
103 4 0.04
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.24
Consensus pattern (101 bp):
TCACATAGTAGCCTGCACATAGTACTACACATGCAACCATCACTATCCGATACACGTAGTAGCCT
GCACATAGTACTACACACGTGACCAAAGCTATCCAG
Found at i:41669105 original size:31 final size:32
Alignment explanation
Indices: 41669049--41669133 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 32
41669039 TTATATACTA
*
41669049 AATAAAATAATAAAATATCTCATTAAA-ATATT
1 AATAAAATAATAAAATATCTAATTAAATA-ATT
**
41669081 AATAAAATAAT-ATTTATCTAATTAAATAATT
1 AATAAAATAATAAAATATCTAATTAAATAATT
41669112 -ATAAAATATCATCAAAATATCT
1 AATAAAATA--AT-AAAATATCT
41669134 CTAATATCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
30 8 0.19
31 15 0.35
32 14 0.33
34 6 0.14
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (32 bp):
AATAAAATAATAAAATATCTAATTAAATAATT
Found at i:41672206 original size:11 final size:11
Alignment explanation
Indices: 41672190--41672214 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41672180 GGCGAGAGAA
41672190 GTGGATATAAG
1 GTGGATATAAG
41672201 GTGGATATAAG
1 GTGGATATAAG
41672212 GTG
1 GTG
41672215 TTTCTGCCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.40, T:0.28
Consensus pattern (11 bp):
GTGGATATAAG
Found at i:41673443 original size:25 final size:25
Alignment explanation
Indices: 41673381--41673493 Score: 70
Period size: 25 Copynumber: 4.5 Consensus size: 25
41673371 GTACATGTAT
* * *
41673381 GCTCATACGAGCTATGAATCGGTAT
1 GCTCATACGAGCTATAAATCAGTAA
* *
41673406 GCTC-TCACAAGCTGTAAATCAGTAA
1 GCTCAT-ACGAGCTATAAATCAGTAA
**
41673431 GCTCATACGAGCTA-AGAATTGGTAA
1 GCTCATACGAGCTATA-AATCAGTAA
* * * *
41673456 GCTCTTACGAACTA-AGTATCATTAA
1 GCTCATACGAGCTATA-AATCAGTAA
*
41673481 GCTCATATGAGCT
1 GCTCATACGAGCT
41673494 GAGAATCGGT
Statistics
Matches: 67, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
24 2 0.03
25 64 0.96
26 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTATAAATCAGTAA
Found at i:41673482 original size:50 final size:49
Alignment explanation
Indices: 41673381--41673504 Score: 135
Period size: 50 Copynumber: 2.5 Consensus size: 49
41673371 GTACATGTAT
* *
41673381 GCTCATACGAGCTATGAATCGGTATGCTCTCACAAGCTGTAAATCAGTAA
1 GCTCATACGAGCTAAGAATCGGTAAGCTCTCACAAGCTGT-AATCAGTAA
* * *
41673431 GCTCATACGAGCTAAGAATTGGTAAGCTCTTACGAA-CTAAGT-ATCATTAA
1 GCTCATACGAGCTAAGAATCGGTAAGCTCTCAC-AAGCT--GTAATCAGTAA
* *
41673481 GCTCATATGAGCTGAGAATCGGTA
1 GCTCATACGAGCTAAGAATCGGTA
41673505 GTCCCTAATG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
50 59 0.94
51 2 0.03
52 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (49 bp):
GCTCATACGAGCTAAGAATCGGTAAGCTCTCACAAGCTGTAATCAGTAA
Found at i:41683772 original size:58 final size:58
Alignment explanation
Indices: 41683682--41683920 Score: 322
Period size: 58 Copynumber: 4.1 Consensus size: 58
41683672 GCACCGACAC
* *
41683682 CCATCAAATATGAAAAGGGATGGTGACAACCATCGAATATGAAAAA-GACTGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTGACGACCATCGAATATGAAAAAGGA-TGGTTTCGA
41683740 CCATCGAATATGAAAAGGGATGGTGACGACCATCGAATAT-AAAAAGGGATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTGACGACCATCGAATATGAAAAA-GGATGGTTTCGA
* * * *
41683798 CCATCGAATATGAAAACGGATGGTGAAGACCATCGAATATGAAAAAGGATGGTGAT-AA
1 CCATCGAATATGAAAAGGGATGGTGACGACCATCGAATATGAAAAAGGATGGT-TTCGA
* ** ** *
41683856 CCATCGAATATAAAAAAAGATGGTGGTGACCATCTAATATGAAAAAGGATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTGACGACCATCGAATATGAAAAAGGATGGTTTCGA
41683914 CCATCGA
1 CCATCGA
41683921 TTAAAGAAAA
Statistics
Matches: 162, Mismatches: 14, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
57 6 0.04
58 148 0.91
59 8 0.05
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (58 bp):
CCATCGAATATGAAAAGGGATGGTGACGACCATCGAATATGAAAAAGGATGGTTTCGA
Found at i:41683915 original size:29 final size:29
Alignment explanation
Indices: 41683682--41683949 Score: 283
Period size: 29 Copynumber: 9.2 Consensus size: 29
41683672 GCACCGACAC
* * * *
41683682 CCATCAAATATGAAAAGGGATGGTGACAA
1 CCATCGAATATGAAAAAGGATGGTGTCGA
*
41683711 CCATCGAATATGAAAAA-GACTGGTTTCGA
1 CCATCGAATATGAAAAAGGA-TGGTGTCGA
* *
41683740 CCATCGAATATGAAAAGGGATGGTGACGA
1 CCATCGAATATGAAAAAGGATGGTGTCGA
*
41683769 CCATCGAATAT-AAAAAGGGATGGTTTCGA
1 CCATCGAATATGAAAAA-GGATGGTGTCGA
* **
41683798 CCATCGAATATGAAAACGGATGGTGAAGA
1 CCATCGAATATGAAAAAGGATGGTGTCGA
*
41683827 CCATCGAATATGAAAAAGGATGGTGAT-AA
1 CCATCGAATATGAAAAAGGATGGTG-TCGA
* *
41683856 CCATCGAATATAAAAAAAGATGGTGGT-GA
1 CCATCGAATATGAAAAAGGATGGT-GTCGA
* *
41683885 CCATCTAATATGAAAAAGGATGGTTTCGA
1 CCATCGAATATGAAAAAGGATGGTGTCGA
* * * *
41683914 CCATCGATTAAAGAAAAATGATGGTTTCGA
1 CCATCGAAT-ATGAAAAAGGATGGTGTCGA
41683944 CCATCG
1 CCATCG
41683950 TTTAGCACAC
Statistics
Matches: 202, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.03
29 164 0.81
30 31 0.15
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (29 bp):
CCATCGAATATGAAAAAGGATGGTGTCGA
Found at i:41688588 original size:33 final size:33
Alignment explanation
Indices: 41688546--41688611 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
41688536 AAAAAAAAAT
41688546 ATTGTTATTTTATATACATACTTCCAGCCATCC
1 ATTGTTATTTTATATACATACTTCCAGCCATCC
41688579 ATTGTTATTTTATATACATACTTCCAGCCATCC
1 ATTGTTATTTTATATACATACTTCCAGCCATCC
41688612 TTTCTTCGAA
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:0.27, C:0.24, G:0.06, T:0.42
Consensus pattern (33 bp):
ATTGTTATTTTATATACATACTTCCAGCCATCC
Found at i:41697267 original size:146 final size:148
Alignment explanation
Indices: 41697063--41697346 Score: 394
Period size: 146 Copynumber: 1.9 Consensus size: 148
41697053 TTAGATAGAA
* * *
41697063 TGAAGGTTTTAAAAACAATTTAAAATCATTTAAAATTGGTTCAAAGTTGACCAAAACTTAGAATG
1 TGAAGGCTTTAAAAACAATTTAAAATCATTTAAAATTAGTTCAAAGTTGACCAAAACTTAAAATG
** * * * *
41697128 AGCCCCAAAAGG-ACGAAAA-GCTCCAAATAGTGTAGTATGTTAAACCCTACATTGTGGTATCAG
66 AGCCCCAAAAGGAAAAAAAAGGCTCAAAATAGTGCAGTAGGTTAAACCCTACATTGTGGTATCAA
41697191 TACAAGTAAGGATATGAT
131 TACAAGTAAGGATATGAT
* * *
41697209 TGAAGGCTTT-AAAACAAATTTAAAATCATTTAAAATTAGTTCAAAGTTTATCAGAACTTAAAAT
1 TGAAGGCTTTAAAAAC-AATTTAAAATCATTTAAAATTAGTTCAAAGTTGACCAAAACTTAAAAT
* * *
41697273 GGGCCTCACAAGGAAAAAAAAAGGCTCAAAATAGTGCAGTAGGTTAAACCCTACATTGTGGTATC
65 GAGCCCCAAAAGG-AAAAAAAAGGCTCAAAATAGTGCAGTAGGTTAAACCCTACATTGTGGTATC
41697338 AATACAAGT
129 AATACAAGT
41697347 GAAGAGATGT
Statistics
Matches: 119, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
145 5 0.04
146 62 0.52
148 5 0.04
149 47 0.39
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (148 bp):
TGAAGGCTTTAAAAACAATTTAAAATCATTTAAAATTAGTTCAAAGTTGACCAAAACTTAAAATG
AGCCCCAAAAGGAAAAAAAAGGCTCAAAATAGTGCAGTAGGTTAAACCCTACATTGTGGTATCAA
TACAAGTAAGGATATGAT
Found at i:41702586 original size:37 final size:37
Alignment explanation
Indices: 41702536--41702614 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41702526 TTATTATGAA
* * *
41702536 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
41702573 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
41702610 GTCTT
1 GTCTT
41702615 TAGAGCTCGA
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:41702811 original size:47 final size:47
Alignment explanation
Indices: 41702733--41703089 Score: 588
Period size: 47 Copynumber: 7.6 Consensus size: 47
41702723 CCCTTCGGGA
* * * * * *
41702733 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41702780 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41702827 CTTATCACATATATACACTTTCACATTCATCACATAGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41702874 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41702921 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41702968 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41703015 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41703064 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
41703090 CACAATTATC
Statistics
Matches: 292, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 245 0.84
49 47 0.16
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41710697 original size:22 final size:23
Alignment explanation
Indices: 41710672--41710731 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
41710662 AGTAAAATAA
*
41710672 AAAAATATGATAATTATACA-TT
1 AAAAATATAATAATTATACATTT
* *
41710694 AAAAAGATAATTATTATACATTT
1 AAAAATATAATAATTATACATTT
*
41710717 AAAAATATTATAATT
1 AAAAATATAATAATT
41710732 TAATTCACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (23 bp):
AAAAATATAATAATTATACATTT
Found at i:41722455 original size:67 final size:67
Alignment explanation
Indices: 41722375--41722605 Score: 268
Period size: 67 Copynumber: 3.5 Consensus size: 67
41722365 GGGGTTAATA
* *
41722375 TGTAAGACTATAGCTCGACTATGGAAACATAGAGAGTTTGCCAGGACATTAAACATGGGGTATAT
1 TGTAAGACCATAGCTCGACTATGGAAACATAGAGAGTTTGCCAGGACATTAAACATGAGGTATAT
41722440 TG
66 TG
* *** * * * * * *
41722442 TGTAAGACCATAGCTTGACTATATCAATATAAAGAGTCT-ACATGACATTAAACATGTGGTATAT
1 TGTAAGACCATAGCTCGACTATGGAAACATAGAGAGTTTGCCAGGACATTAAACATGAGGTATAT
*
41722506 TA
66 TG
* *
41722508 TGTAAGACCATAGGTCGACTATGGCAACATAGAGAGTTTGCCAGGACATTAAACATGAGGTATGA
1 TGTAAGACCATAGCTCGACTATGGAAACATAGAGAGTTTGCCAGGACATTAAACATGAGGTAT-A
41722573 -TG
65 TTG
* * * *
41722575 TGTAAAACCATATCTCAACTATGGAAGCATA
1 TGTAAGACCATAGCTCGACTATGGAAACATA
41722606 TGGAGTCAAC
Statistics
Matches: 133, Mismatches: 29, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
66 55 0.41
67 77 0.58
68 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (67 bp):
TGTAAGACCATAGCTCGACTATGGAAACATAGAGAGTTTGCCAGGACATTAAACATGAGGTATAT
TG
Found at i:41722820 original size:19 final size:20
Alignment explanation
Indices: 41722772--41722822 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
41722762 AGGAATCCGC
*
41722772 CGAAAAAGGAAAAAGTAATA
1 CGAAAATGGAAAAAGTAATA
*
41722792 -G-AAATGGGAAAAAGT-CTA
1 CGAAAAT-GGAAAAAGTAATA
41722810 CGAAAATGGAAAA
1 CGAAAATGGAAAA
41722823 CAGGGAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.59, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
CGAAAATGGAAAAAGTAATA
Found at i:41723716 original size:20 final size:20
Alignment explanation
Indices: 41723675--41723716 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
41723665 TCTGGAAAGA
*
41723675 AGTTGCGAATCGTATCCGCC
1 AGTTGCGAATCGTATCCACC
*
41723695 AGTTGCGAATCGTATCTACC
1 AGTTGCGAATCGTATCCACC
41723715 AG
1 AG
41723717 GTAACACTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (20 bp):
AGTTGCGAATCGTATCCACC
Found at i:41729427 original size:20 final size:21
Alignment explanation
Indices: 41729402--41729445 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
41729392 AAAATGTTTA
41729402 AATTGATTG-TCTTCTATTTG
1 AATTGATTGTTCTTCTATTTG
*
41729422 AATTGATTGTTTTTCTATTTG
1 AATTGATTGTTCTTCTATTTG
41729443 AAT
1 AAT
41729446 CAATTCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.23, C:0.07, G:0.14, T:0.57
Consensus pattern (21 bp):
AATTGATTGTTCTTCTATTTG
Found at i:41729522 original size:21 final size:21
Alignment explanation
Indices: 41729494--41729583 Score: 69
Period size: 21 Copynumber: 4.4 Consensus size: 21
41729484 TGGAATATGC
**
41729494 TTCT-TTTAAATTGATTGTCT
1 TTCTATTTAAATCAATTGTCT
* *
41729514 TTCTATTTAAATAAATTGT-G
1 TTCTATTTAAATCAATTGTCT
* *
41729534 TT-TATGTTAAATCGATTGACT
1 TTCTAT-TTAAATCAATTGTCT
* * *
41729555 TTCTGTTTGAATCAATTGTTT
1 TTCTATTTAAATCAATTGTCT
41729576 TTCTATTT
1 TTCTATTT
41729584 GAACCGATTC
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
19 3 0.06
20 16 0.30
21 32 0.60
22 2 0.04
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.56
Consensus pattern (21 bp):
TTCTATTTAAATCAATTGTCT
Found at i:41736803 original size:30 final size:31
Alignment explanation
Indices: 41736764--41736823 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
41736754 AGAGGTGGGA
*
41736764 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
41736795 TGGG-AGGGAGTAAAAATTTTTGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
41736824 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:41758193 original size:45 final size:44
Alignment explanation
Indices: 41758100--41758227 Score: 138
Period size: 44 Copynumber: 2.9 Consensus size: 44
41758090 AATCCACTCT
* * * *
41758100 ACTGCAACCTTAGGGAGATAAGATTTAG-GTCTTCAGTCTGCTCC
1 ACTGCAACCTTAGGGAGATAAGACTT-GCATCTTCAATCTGCCCC
41758144 ACTGCAACCTTAGGGAGATAAGA-TTCGCCATCTTCAATCTGCCCC
1 ACTGCAACCTTAGGGAGATAAGACTT-G-CATCTTCAATCTGCCCC
*
41758189 ACTGCAA-CTTCA-GGAGATAAGACTTGCTATCTTCGATCT
1 ACTGCAACCTT-AGGGAGATAAGACTTGC-ATCTTCAATCT
41758228 ACCTTACTGC
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
43 4 0.05
44 47 0.64
45 23 0.31
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (44 bp):
ACTGCAACCTTAGGGAGATAAGACTTGCATCTTCAATCTGCCCC
Found at i:41758345 original size:88 final size:88
Alignment explanation
Indices: 41758218--41758670 Score: 712
Period size: 88 Copynumber: 5.1 Consensus size: 88
41758208 AGACTTGCTA
* * * *
41758218 TCTTCGATCTACCTT-ACTGCCAATATAGGAAGATAAGATCTGCTATTTTCAACCTACTCCACTA
1 TCTTCGATCTA-CTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
* *
41758282 CTGCCCAAGGAGACAAGGTTG-GTG
65 CTGCCCAGGGAGACAAGGCTGAG-G
* * * **
41758306 TATTCGATCTAGTTCGATGCCAACACAGGTTGACAAGATCTGCTATTTTCAACCTACTCCACTAC
1 TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
*
41758371 TGCCCAGGGAGACAATGCTGAGG
66 TGCCCAGGGAGACAAGGCTGAGG
*
41758394 TCTTTGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
1 TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
41758459 TGCCCAGGGAGACAAGGCTGAGG
66 TGCCCAGGGAGACAAGGCTGAGG
* *
41758482 TCTTCAATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTAC
1 TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
41758547 TGCCCAGGGAGACAAGGCTGAGG
66 TGCCCAGGGAGACAAGGCTGAGG
* * *
41758570 TCTTCAATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTGAACTTACTCCACTAC
1 TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
41758635 TGCCCAGGGAGACAAGGCTGAGG
66 TGCCCAGGGAGACAAGGCTGAGG
41758658 TCTTCGATCTACT
1 TCTTCGATCTACT
41758671 ACAACCTTAG
Statistics
Matches: 337, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
87 2 0.01
88 334 0.99
89 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (88 bp):
TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
TGCCCAGGGAGACAAGGCTGAGG
Found at i:41758773 original size:44 final size:45
Alignment explanation
Indices: 41758672--41758795 Score: 123
Period size: 44 Copynumber: 2.8 Consensus size: 45
41758662 CGATCTACTA
* * * * *
41758672 CAACCTTAGGGAGATAAGATTTAG--GTCTTCAGTCTGCTCCACTG
1 CAACATTAGGGAGATAAGACTT-GCCATCTTCAATCTGCCCCACTG
41758716 CAACATTAGGGAGATAAGA-TTCGCCATCTTCAATCTGCCCCACTG
1 CAACATTAGGGAGATAAGACTT-GCCATCTTCAATCTGCCCCACTG
* *
41758761 CAAC-TTCA-GGAGATAAGACTTGCTATCTTCGATCT
1 CAACATT-AGGGAGATAAGACTTGCCATCTTCAATCT
41758796 ACCTTACTGC
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.04
44 42 0.61
45 24 0.35
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (45 bp):
CAACATTAGGGAGATAAGACTTGCCATCTTCAATCTGCCCCACTG
Found at i:41758805 original size:44 final size:45
Alignment explanation
Indices: 41758710--41758824 Score: 112
Period size: 44 Copynumber: 2.6 Consensus size: 45
41758700 TCAGTCTGCT
*
41758710 CCACTGCAACATTAGGGAGATAAGATTCGCCATCTTCAATCTGCC
1 CCACTGCAACATTAGGGAGATAAGATTCGCCATCTTCAATCTACC
* *
41758755 CCACTGCAAC-TTCA-GGAGATAAGACTT-GCTATCTTCGATCTACC
1 CCACTGCAACATT-AGGGAGATAAGA-TTCGCCATCTTCAATCTACC
** * *
41758799 TTACTGCCA-ATATAGGAAGATAAGAT
1 CCACTGCAACAT-TAGGGAGATAAGAT
41758825 CTGTTATTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
44 35 0.60
45 23 0.40
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (45 bp):
CCACTGCAACATTAGGGAGATAAGATTCGCCATCTTCAATCTACC
Found at i:41758913 original size:88 final size:88
Alignment explanation
Indices: 41758786--41759490 Score: 1112
Period size: 88 Copynumber: 8.0 Consensus size: 88
41758776 AGACTTGCTA
* * * * *
41758786 TCTTCGATCTACCTT-ACTGCCAATATAGGAAGATAAGATCTGTTATTTTCAACCTACTCCACTA
1 TCTTCGATCTA-CTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
* *
41758850 CTGCCCAAGGAGACAAGGTTG-GTG
65 CTGCCCAGGGAGACAAGGCTGAG-G
* * * **
41758874 TATTCGATCTAGTTCGATGCCAACACAGGTTGACAAGATCTGCTATTTTCAACCTACTCCACTAC
1 TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
*
41758939 TGCCCAGGGAGACAATGCTGAGG
66 TGCCCAGGGAGACAAGGCTGAGG
*
41758962 TCTTTGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
1 TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
41759027 TGCCCAGGGAGACAAGGCTGAGG
66 TGCCCAGGGAGACAAGGCTGAGG
* *
41759050 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTAC
1 TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
41759115 TGCCCAGGGAGACAAGGCTGAGG
66 TGCCCAGGGAGACAAGGCTGAGG
* *
41759138 TCTTCAATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACTTACTCCACTAC
1 TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
41759203 TGCCC-GGGAGACAAGGCTGAGG
66 TGCCCAGGGAGACAAGGCTGAGG
* * * *
41759225 TCTTCGATCTACTTCGCTACCAACACAGGAAGACAAGATCTGCTATTTTCAACTTGCTCCATTAC
1 TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
41759290 TGCCCAGGGAGACAAGGCTGAGG
66 TGCCCAGGGAGACAAGGCTGAGG
* * *
41759313 TCTTCGATCTACTTCGCTGCCCACACAAGAAGACAAGATCTTCTATTTTCAACCTACTCCACTAC
1 TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
41759378 TGCCCAGGGAGACAAGGCTGAGG
66 TGCCCAGGGAGACAAGGCTGAGG
* * *
41759401 TCTTCGATCTACTTCGCTGCCCACACTGGAAGACAAGATCTGCTATTTTCAACCTACT-CACTAT
1 TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
41759465 TGCCCAGGGAGACAAGGCTGAGG
66 TGCCCAGGGAGACAAGGCTGAGG
41759488 TCT
1 TCT
41759491 GCGGCTTGTT
Statistics
Matches: 572, Mismatches: 42, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
87 116 0.20
88 455 0.80
89 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (88 bp):
TCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTAC
TGCCCAGGGAGACAAGGCTGAGG
Found at i:41759180 original size:568 final size:567
Alignment explanation
Indices: 41758097--41759237 Score: 2219
Period size: 568 Copynumber: 2.0 Consensus size: 567
41758087 TTTAATCCAC
* *
41758097 TCTACTGCAACCTTAGGGAGATAAGATTTAGGTCTTCAGTCTGCTCCACTGCAACCTTAGGGAGA
1 TCTACTACAACCTTAGGGAGATAAGATTTAGGTCTTCAGTCTGCTCCACTGCAACATTAGGGAGA
41758162 TAAGATTCGCCATCTTCAATCTGCCCCACTGCAACTTCAGGAGATAAGACTTGCTATCTTCGATC
66 TAAGATTCGCCATCTTCAATCTGCCCCACTGCAACTTCAGGAGATAAGACTTGCTATCTTCGATC
41758227 TACCTTACTGCCAATATAGGAAGATAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAAGG
131 TACCTTACTGCCAATATAGGAAGATAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAAGG
41758292 AGACAAGGTTGGTGTATTCGATCTAGTTCGATGCCAACACAGGTTGACAAGATCTGCTATTTTCA
196 AGACAAGGTTGGTGTATTCGATCTAGTTCGATGCCAACACAGGTTGACAAGATCTGCTATTTTCA
41758357 ACCTACTCCACTACTGCCCAGGGAGACAATGCTGAGGTCTTTGATCTACTTCGCTGCCAACACAG
261 ACCTACTCCACTACTGCCCAGGGAGACAATGCTGAGGTCTTTGATCTACTTCGCTGCCAACACAG
41758422 GAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGAGGTCTTC
326 GAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGAGGTCTTC
41758487 AATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTACTGCCC
391 AATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTACTGCCC
41758552 AGGGAGACAAGGCTGAGGTCTTCAATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATT
456 AGGGAGACAAGGCTGAGGTCTTCAATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATT
*
41758617 TTGAACTTACTCCACTACTGCCCAGGGAGACAAGGCTGAGGTCTTCGA
521 TTCAACTTACTCCACTACTGCCC-GGGAGACAAGGCTGAGGTCTTCGA
41758665 TCTACTACAACCTTAGGGAGATAAGATTTAGGTCTTCAGTCTGCTCCACTGCAACATTAGGGAGA
1 TCTACTACAACCTTAGGGAGATAAGATTTAGGTCTTCAGTCTGCTCCACTGCAACATTAGGGAGA
41758730 TAAGATTCGCCATCTTCAATCTGCCCCACTGCAACTTCAGGAGATAAGACTTGCTATCTTCGATC
66 TAAGATTCGCCATCTTCAATCTGCCCCACTGCAACTTCAGGAGATAAGACTTGCTATCTTCGATC
*
41758795 TACCTTACTGCCAATATAGGAAGATAAGATCTGTTATTTTCAACCTACTCCACTACTGCCCAAGG
131 TACCTTACTGCCAATATAGGAAGATAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAAGG
41758860 AGACAAGGTTGGTGTATTCGATCTAGTTCGATGCCAACACAGGTTGACAAGATCTGCTATTTTCA
196 AGACAAGGTTGGTGTATTCGATCTAGTTCGATGCCAACACAGGTTGACAAGATCTGCTATTTTCA
41758925 ACCTACTCCACTACTGCCCAGGGAGACAATGCTGAGGTCTTTGATCTACTTCGCTGCCAACACAG
261 ACCTACTCCACTACTGCCCAGGGAGACAATGCTGAGGTCTTTGATCTACTTCGCTGCCAACACAG
41758990 GAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGAGGTCTTC
326 GAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGAGGTCTTC
* *
41759055 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTACTGCCC
391 AATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTACTGCCC
41759120 AGGGAGACAAGGCTGAGGTCTTCAATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATT
456 AGGGAGACAAGGCTGAGGTCTTCAATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATT
41759185 TTCAACTTACTCCACTACTGCCCGGGAGACAAGGCTGAGGTCTTCGA
521 TTCAACTTACTCCACTACTGCCCGGGAGACAAGGCTGAGGTCTTCGA
41759232 TCTACT
1 TCTACT
41759238 TCGCTACCAA
Statistics
Matches: 567, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
567 30 0.05
568 537 0.95
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (567 bp):
TCTACTACAACCTTAGGGAGATAAGATTTAGGTCTTCAGTCTGCTCCACTGCAACATTAGGGAGA
TAAGATTCGCCATCTTCAATCTGCCCCACTGCAACTTCAGGAGATAAGACTTGCTATCTTCGATC
TACCTTACTGCCAATATAGGAAGATAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAAGG
AGACAAGGTTGGTGTATTCGATCTAGTTCGATGCCAACACAGGTTGACAAGATCTGCTATTTTCA
ACCTACTCCACTACTGCCCAGGGAGACAATGCTGAGGTCTTTGATCTACTTCGCTGCCAACACAG
GAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGAGGTCTTC
AATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTACTGCCC
AGGGAGACAAGGCTGAGGTCTTCAATCTACTTCGCTGCCAACACAGGAAGACAAGATCTGCTATT
TTCAACTTACTCCACTACTGCCCGGGAGACAAGGCTGAGGTCTTCGA
Found at i:41759332 original size:263 final size:264
Alignment explanation
Indices: 41758786--41759490 Score: 1132
Period size: 263 Copynumber: 2.7 Consensus size: 264
41758776 AGACTTGCTA
* * *
41758786 TCTTCGATCTACCTT-ACTGCCAATATAGGAAGATAAGATCTGTTATTTTCAACCTACTCCACTA
1 TCTTCGATCTA-CTTCGCTGCCAATACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTA
* * * * * **
41758850 CTGCCCAAGGAGACAAGGTTG-GTGTATTCGATCTAGTTCGATGCCAACACAGGTTGACAAGATC
65 CTGCCCAGGGAGACAAGGCTGAG-GTCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATC
* *
41758914 TGCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAATGCTGAGGTCTTTGATCTACTTCGC
129 TGCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGAGGTCTTCGATCTACTTCGC
*
41758979 TGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGG
194 TACCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGG
41759044 CTGAGG
259 CTGAGG
41759050 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTAC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTAC
*
41759115 TGCCCAGGGAGACAAGGCTGAGGTCTTCAATCTACTTCGCTGCCAACACAGGAAGACAAGATCTG
66 TGCCCAGGGAGACAAGGCTGAGGTCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTG
*
41759180 CTATTTTCAACTTACTCCACTACTGCCC-GGGAGACAAGGCTGAGGTCTTCGATCTACTTCGCTA
131 CTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGAGGTCTTCGATCTACTTCGCTA
* * *
41759244 CCAACACAGGAAGACAAGATCTGCTATTTTCAACTTGCTCCATTACTGCCCAGGGAGACAAGGCT
196 CCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCT
41759309 GAGG
261 GAGG
* * *
41759313 TCTTCGATCTACTTCGCTGCCCACACAAGAAGACAAGATCT-TCTATTTTCAACCTACTCCACTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGT-TATTTTCAACCTACTCCACTA
* *
41759377 CTGCCCAGGGAGACAAGGCTGAGGTCTTCGATCTACTTCGCTGCCCACACTGGAAGACAAGATCT
65 CTGCCCAGGGAGACAAGGCTGAGGTCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCT
*
41759442 GCTATTTTCAACCTACT-CACTATTGCCCAGGGAGACAAGGCTGAGGTCT
130 GCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGAGGTCT
41759491 GCGGCTTGTT
Statistics
Matches: 411, Mismatches: 26, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
262 11 0.03
263 259 0.63
264 140 0.34
265 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (264 bp):
TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTAC
TGCCCAGGGAGACAAGGCTGAGGTCTTCGATCTACTTCGCTGCCAACACAGGAAGACAAGATCTG
CTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGAGGTCTTCGATCTACTTCGCTA
CCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCT
GAGG
Found at i:41769276 original size:3 final size:3
Alignment explanation
Indices: 41769268--41769308 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
41769258 ATATATAGGT
* *
41769268 ATA ATA ATA TTA ATA CTTA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA A
41769309 CAAACAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.94
4 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:41771911 original size:27 final size:28
Alignment explanation
Indices: 41771881--41771940 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
41771871 TATTTTTAAT
**
41771881 TTTTTGTAATTTTCT-AAAATTTTGTCA
1 TTTTTGTAATTTTCTGAAAATTTAATCA
*
41771908 TTTTTGTAATTTTTTGAAAATTTAATCA
1 TTTTTGTAATTTTCTGAAAATTTAATCA
41771936 TTTTT
1 TTTTT
41771941 ATTTTCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.62
Consensus pattern (28 bp):
TTTTTGTAATTTTCTGAAAATTTAATCA
Found at i:41772706 original size:18 final size:18
Alignment explanation
Indices: 41772670--41772704 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41772660 TATTTTGAAA
41772670 ATATTTATAACAATTTTT
1 ATATTTATAACAATTTTT
*
41772688 ATATTTTTAA-AATTTTT
1 ATATTTATAACAATTTTT
41772705 TAAAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTTATAACAATTTTT
Found at i:41775942 original size:21 final size:21
Alignment explanation
Indices: 41775892--41775942 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
41775882 TAAAGACAAT
*
41775892 GAAAAAT-AAAGAAGAAAAAA
1 GAAAAATAAAAGAACAAAAAA
* * *
41775912 GAACATTAAAAGAACATAAAA
1 GAAAAATAAAAGAACAAAAAA
41775933 GAAAAATAAA
1 GAAAAATAAA
41775943 TTAAATTGCT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.75, C:0.04, G:0.12, T:0.10
Consensus pattern (21 bp):
GAAAAATAAAAGAACAAAAAA
Found at i:41778191 original size:9 final size:9
Alignment explanation
Indices: 41778169--41778206 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
41778159 ATAAAAGTTG
*
41778169 AAAAGATAA
1 AAAAAATAA
*
41778178 GAAAAATAA
1 AAAAAATAA
41778187 AAAAAATAA
1 AAAAAATAA
41778196 AAAAAATAA
1 AAAAAATAA
41778205 AA
1 AA
41778207 CGTATGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (9 bp):
AAAAAATAA
Found at i:41778368 original size:12 final size:12
Alignment explanation
Indices: 41778321--41778369 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
41778311 AATAGAAGTG
*
41778321 ATAACAATAATT
1 ATAACAATAATA
*
41778333 ACAACAATAATA
1 ATAACAATAATA
* *
41778345 ATAATATTAATA
1 ATAACAATAATA
*
41778357 ATAACAAAAATA
1 ATAACAATAATA
41778369 A
1 A
41778370 AAATAAAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAACAATAATA
Found at i:41779019 original size:21 final size:20
Alignment explanation
Indices: 41778980--41779023 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
41778970 TTCACAAAAC
*
41778980 AAATGAAAAGAAAAAAGAAT
1 AAATAAAAAGAAAAAAGAAT
*
41779000 AAATAAAAATGAAAATAGAAT
1 AAATAAAAA-GAAAAAAGAAT
41779021 AAA
1 AAA
41779024 CGCGAATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (20 bp):
AAATAAAAAGAAAAAAGAAT
Found at i:41779169 original size:17 final size:17
Alignment explanation
Indices: 41779147--41779185 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
41779137 CTTAGAGAAG
*
41779147 AAAATAAAATAAA-AATA
1 AAAATAAAA-AAATAACA
41779164 AAAATAAAAAAATAACA
1 AAAATAAAAAAATAACA
41779181 AAAAT
1 AAAAT
41779186 CTAATTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAATAAAAAAATAACA
Found at i:41780062 original size:89 final size:89
Alignment explanation
Indices: 41779955--41781212 Score: 1957
Period size: 89 Copynumber: 14.1 Consensus size: 89
41779945 ACCAATACAT
* * * * *
41779955 GAAGACAAGATCTTTTATCTTTGATCTACCTCATGCCAATACATGAAGACAAGATATGCTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
41780020 CGATCTACTTCGCCACCAGTATGG
66 CGATCTACTTCGCCACCAGTATGG
* *
41780044 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT-ATTTTTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
*
41780108 CCGATCTACTTCGCCACCGGTATGG
66 -CGATCTACTTCGCCACCAGTATGG
* *
41780133 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
*
41780198 CGATCTACTTCGCCACCAATATGG
66 CGATCTACTTCGCCACCAGTATGG
* * *
41780222 GAAGACAAGATCTGTTATCTTCGATCTACTTCACGTCAGTACATGAAGACAAGATCTGCTTTTTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
*
41780287 CGATCTACTTCGCCACCAGTATAG
66 CGATCTACTTCGCCACCAGTATGG
* * *
41780311 GAAGACAAGATCTGGTATCTTTGATCTACCTT-ATGCCAATACATGAAGACAAGATCTGCTTTCT
1 GAAGACAAGATCTGTTATCTTTGATCTA-CTTCACGCCAGTACATGAAGACAAGATCTGCTTTCT
41780375 TCGATCTACTTCGCCACCAGTATGG
65 TCGATCTACTTCGCCACCAGTATGG
** *
41780400 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTTTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* *
41780465 CGATCTACTTCTCCACCGGTATGG
66 CGATCTACTTCGCCACCAGTATGG
* *
41780489 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
*
41780554 CGATCTACTTCGCCACCAATATGG
66 CGATCTACTTCGCCACCAGTATGG
* * *
41780578 GAAGACAAGATCTGTTATCTTCGATCTACTTCACGTCAGTACATGAAGACAAGATCTGCTTTTTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
*
41780643 CGATCTACTTCGCCACCAGTATAG
66 CGATCTACTTCGCCACCAGTATGG
* * * * *
41780667 GAAGACAAGATCTGGTATCTTTGATCTACCTCATGCCAATACATGAAGACAAGATCTACTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
41780732 CGATCTACTTCGCCACCAGTATGG
66 CGATCTACTTCGCCACCAGTATGG
* * *
41780756 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATAT-ATTTTTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* *
41780820 CCGATCTACTTGGCCACCCGTATGG
66 -CGATCTACTTCGCCACCAGTATGG
*
41780845 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
*
41780910 CGATCTACTTCGCCATCAGTATGG
66 CGATCTACTTCGCCACCAGTATGG
* * *
41780934 GAAGACAAGATCTGGTATTTTTGATCTACTTCATGCCAGTACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* *
41780999 CGATCTTACTTCGCCACTAGTATGA
66 CGATC-TACTTCGCCACCAGTATGG
* * *
41781024 GAAGACAAGATATGTTATCTTTGATCTACTTCACACTAGTACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* *
41781089 CGATCTATTTCGCCACCAGTATAG
66 CGATCTACTTCGCCACCAGTATGG
* *
41781113 GAATACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTT-TT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
41781177 CTGATCTACTTCGCCACCAGTATGG
66 C-GATCTACTTCGCCACCAGTATGG
41781202 GAAGACAAGAT
1 GAAGACAAGAT
41781213 ATTCTGCTAC
Statistics
Matches: 1065, Mismatches: 96, Indels: 16
0.90 0.08 0.01
Matches are distributed among these distances:
88 16 0.02
89 955 0.90
90 94 0.09
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (89 bp):
GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
CGATCTACTTCGCCACCAGTATGG
Found at i:41782514 original size:7 final size:7
Alignment explanation
Indices: 41782495--41782536 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
41782485 TTAGCCTCTC
41782495 CATTTTT
1 CATTTTT
41782502 -ATTTTTT
1 CA-TTTTT
41782509 CATTTTT
1 CATTTTT
41782516 CA-TTTT
1 CATTTTT
41782522 CATCTTTT
1 CAT-TTTT
41782530 CATTTTT
1 CATTTTT
41782537 TCACATCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 7 0.23
7 16 0.52
8 8 0.26
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:41782514 original size:14 final size:15
Alignment explanation
Indices: 41782495--41782539 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
41782485 TTAGCCTCTC
41782495 CATTTTT-ATTTTTT
1 CATTTTTCATTTTTT
41782509 CATTTTTCA--TTTT
1 CATTTTTCATTTTTT
41782522 CATCTTTTCATTTTTT
1 CAT-TTTTCATTTTTT
41782538 CA
1 CA
41782540 CATCACTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 7 0.26
14 13 0.48
15 1 0.04
16 6 0.22
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (15 bp):
CATTTTTCATTTTTT
Found at i:41782519 original size:21 final size:21
Alignment explanation
Indices: 41782495--41782536 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41782485 TTAGCCTCTC
* *
41782495 CATTTTTATTTTTTCATTTTT
1 CATTTTCATCTTTTCATTTTT
41782516 CATTTTCATCTTTTCATTTTT
1 CATTTTCATCTTTTCATTTTT
41782537 TCACATCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (21 bp):
CATTTTCATCTTTTCATTTTT
Found at i:41785456 original size:32 final size:31
Alignment explanation
Indices: 41785411--41785506 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
41785401 CTTAGATAAT
41785411 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
41785442 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
41785474 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
41785505 TT
1 TT
41785507 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:41786094 original size:27 final size:28
Alignment explanation
Indices: 41786051--41786165 Score: 100
Period size: 27 Copynumber: 4.2 Consensus size: 28
41786041 TTAAATAAAA
* *
41786051 GCAAAAAAAAAGTAAAAAG-TAAAAAGC
1 GCAAAAAAAAAGCAAAAAGCAAAAAAGC
41786078 GCAAAAAAAACA-CAAAAAGCAAAAAAGC
1 GCAAAAAAAA-AGCAAAAAGCAAAAAAGC
* * *
41786106 GC---AAAAAAG-AGAGAG-TAAAAAGC
1 GCAAAAAAAAAGCAAAAAGCAAAAAAGC
41786129 GCAAAAAAAAGAGAGCAAAAAGCAAAAAAGC
1 GC-AAAAAAA-A-AGCAAAAAGCAAAAAAGC
41786160 GCAAAA
1 GCAAAA
41786166 GCGCAAAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
23 9 0.13
24 5 0.07
25 5 0.07
27 20 0.29
28 11 0.16
29 2 0.03
30 8 0.12
31 9 0.13
ACGTcount: A:0.68, C:0.12, G:0.17, T:0.03
Consensus pattern (28 bp):
GCAAAAAAAAAGCAAAAAGCAAAAAAGC
Found at i:41786129 original size:23 final size:23
Alignment explanation
Indices: 41786099--41786158 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
41786089 ACAAAAAGCA
*
41786099 AAAAAGCGCAAAAAAGAGAGAGT
1 AAAAAGCGCAAAAAAGAGAGAGC
*
41786122 AAAAAGCGCAAAAAAAAGAGAGC
1 AAAAAGCGCAAAAAAGAGAGAGC
41786145 AAAAA--GCAAAAAAG
1 AAAAAGCGCAAAAAAG
41786159 CGCAAAAGCG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 8 0.24
23 26 0.76
ACGTcount: A:0.67, C:0.10, G:0.22, T:0.02
Consensus pattern (23 bp):
AAAAAGCGCAAAAAAGAGAGAGC
Found at i:41789259 original size:32 final size:31
Alignment explanation
Indices: 41789214--41789309 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
41789204 CTTAGATAAT
41789214 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
41789245 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
41789277 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
41789308 TT
1 TT
41789310 GTAATTTGCA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:41790030 original size:19 final size:19
Alignment explanation
Indices: 41789990--41790031 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
41789980 GAGGTGTTTG
* *
41789990 ATGCATATGATGTAATGTA
1 ATGCAAATGATGAAATGTA
41790009 ATGCAAATGCATGAAATG-A
1 ATGCAAATG-ATGAAATGTA
41790028 ATGC
1 ATGC
41790032 GAAAAGAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (19 bp):
ATGCAAATGATGAAATGTA
Found at i:41790495 original size:16 final size:16
Alignment explanation
Indices: 41790474--41790507 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
41790464 TTCTATAATG
41790474 AAATGCCATGCAGTCA
1 AAATGCCATGCAGTCA
41790490 AAATGCCATGCAGTCA
1 AAATGCCATGCAGTCA
41790506 AA
1 AA
41790508 GTGAAACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (16 bp):
AAATGCCATGCAGTCA
Found at i:41792029 original size:32 final size:33
Alignment explanation
Indices: 41791965--41792041 Score: 104
Period size: 32 Copynumber: 2.3 Consensus size: 33
41791955 AAATGAAAAT
* *
41791965 ATAAAAAATATGTATATGTATATATATTTATAAC
1 ATAAAAAATATGTATATG-ATATATATCTATAAA
41791999 ATAAAAGAA-ATGTATATG-TATATATCTATAAA
1 ATAAAA-AATATGTATATGATATATATCTATAAA
41792031 ATAAAAAATAT
1 ATAAAAAATAT
41792042 ATAAAAGTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 2 0.05
32 20 0.51
34 15 0.38
35 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (33 bp):
ATAAAAAATATGTATATGATATATATCTATAAA
Found at i:41792074 original size:9 final size:9
Alignment explanation
Indices: 41792028--41792089 Score: 63
Period size: 9 Copynumber: 7.0 Consensus size: 9
41792018 ATATATCTAT
41792028 AAAATAAAA
1 AAAATAAAA
* *
41792037 AATAT-ATA
1 AAAATAAAA
* *
41792045 AAAGTTAAA
1 AAAATAAAA
* *
41792054 AAGATAAGA
1 AAAATAAAA
41792063 AAAATAAAA
1 AAAATAAAA
41792072 AAAATAAAA
1 AAAATAAAA
41792081 AAAATAAAA
1 AAAATAAAA
41792090 CGTATGTAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
8 5 0.12
9 36 0.88
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (9 bp):
AAAATAAAA
Found at i:41792894 original size:21 final size:20
Alignment explanation
Indices: 41792855--41792898 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
41792845 TTCACAAAGC
*
41792855 AAATGAAAAGAAAAAAGAAT
1 AAATAAAAAGAAAAAAGAAT
*
41792875 AAATAAAAATGAAAATAGAAT
1 AAATAAAAA-GAAAAAAGAAT
41792896 AAA
1 AAA
41792899 CGCGGTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (20 bp):
AAATAAAAAGAAAAAAGAAT
Found at i:41798726 original size:36 final size:36
Alignment explanation
Indices: 41798653--41798727 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
41798643 AATAGCATAA
* * * *
41798653 GAAGAAGAAATTCATACAAGTAATATATTATTAAAT
1 GAAGAAGAAATTCATACAAGGAAGACATTACTAAAT
* * *
41798689 GAAGGAGAAATTCATACAAGGAAGGCATTACTGAAT
1 GAAGAAGAAATTCATACAAGGAAGACATTACTAAAT
41798725 GAA
1 GAA
41798728 CAAAGTGTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (36 bp):
GAAGAAGAAATTCATACAAGGAAGACATTACTAAAT
Found at i:41814089 original size:108 final size:106
Alignment explanation
Indices: 41813903--41814099 Score: 306
Period size: 108 Copynumber: 1.8 Consensus size: 106
41813893 AAAATTCAAG
*
41813903 AGGATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGAGCATGTTCCTCGAA
1 AGGATATTTACCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGAGCATGTTCCTCGAA
41813968 TTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGGA
66 TTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGGA
* * * * *
41814009 AGGATATTTACCTATTTGGTTTAACGAGAAAAATCGACA-CCAGCACCTTAGGGCATGTTTTCTC
1 AGGATATTTACCAATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGAGCATG-TTCCTC
41814073 GAATTTCCAAACGCAAAACATTGCCTT
63 GAATTTCCAAACGCAAAACATTGCCTT
41814100 TATTATTTTT
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
106 25 0.30
107 17 0.21
108 40 0.49
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (106 bp):
AGGATATTTACCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGAGCATGTTCCTCGAA
TTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGGA
Found at i:41814374 original size:4 final size:4
Alignment explanation
Indices: 41814365--41814398 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
41814355 AATATAATGG
41814365 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
41814399 GTATCAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:41816039 original size:33 final size:33
Alignment explanation
Indices: 41815997--41816065 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
41815987 TATTATACAA
41815997 AATATTAGAAGTCATAATAATAATAGTTTAGAG
1 AATATTAGAAGTCATAATAATAATAGTTTAGAG
*
41816030 AATATTAGAAGTCATAATTATAATAGTTTAGAG
1 AATATTAGAAGTCATAATAATAATAGTTTAGAG
41816063 AAT
1 AAT
41816066 TTGCAATTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.35
Consensus pattern (33 bp):
AATATTAGAAGTCATAATAATAATAGTTTAGAG
Found at i:41821545 original size:41 final size:39
Alignment explanation
Indices: 41821492--41821605 Score: 173
Period size: 41 Copynumber: 2.9 Consensus size: 39
41821482 TAAAGTGGAT
41821492 TTTTAAATTGAGTTCGGATTTGAAAATAATTTAGAAAATAAA
1 TTTT-AATTGAGTTCGGATTTGAAAATAATTTAGAAAAT--A
41821534 TTTTAATTGAGTTCGGATTTGAAAATAATTTAGAAAATA
1 TTTTAATTGAGTTCGGATTTGAAAATAATTTAGAAAATA
41821573 ----AATTGAGTTCGGATTTGAAAATAATTTAGAAAA
1 TTTTAATTGAGTTCGGATTTGAAAATAATTTAGAAAA
41821606 ATGGAAGAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
35 33 0.46
39 1 0.01
41 34 0.47
42 4 0.06
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.38
Consensus pattern (39 bp):
TTTTAATTGAGTTCGGATTTGAAAATAATTTAGAAAATA
Found at i:41821584 original size:35 final size:35
Alignment explanation
Indices: 41821495--41821605 Score: 168
Period size: 35 Copynumber: 3.0 Consensus size: 35
41821485 AGTGGATTTT
41821495 TAAATTGAGTTCGGATTTGAAAATAATTTAGAAAA
1 TAAATTGAGTTCGGATTTGAAAATAATTTAGAAAA
41821530 TAAATTTTAATTGAGTTCGGATTTGAAAATAATTTAGAAAA
1 T--A----AATTGAGTTCGGATTTGAAAATAATTTAGAAAA
41821571 TAAATTGAGTTCGGATTTGAAAATAATTTAGAAAA
1 TAAATTGAGTTCGGATTTGAAAATAATTTAGAAAA
41821606 ATGGAAGAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
35 34 0.49
37 1 0.01
39 1 0.01
41 34 0.49
ACGTcount: A:0.45, C:0.03, G:0.16, T:0.36
Consensus pattern (35 bp):
TAAATTGAGTTCGGATTTGAAAATAATTTAGAAAA
Found at i:41828154 original size:24 final size:24
Alignment explanation
Indices: 41828139--41828190 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41828129 AATCAAATTC
41828139 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
41828163 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
41828187 AAAT
1 AAAT
41828191 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:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:41831411 original size:24 final size:24
Alignment explanation
Indices: 41831395--41831446 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41831385 AATCAAAGTC
41831395 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
41831419 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
41831443 AAAT
1 AAAT
41831447 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:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:41842363 original size:22 final size:22
Alignment explanation
Indices: 41842338--41842401 Score: 128
Period size: 22 Copynumber: 2.9 Consensus size: 22
41842328 AAAGATGATG
41842338 GGGAAAGGTTATGAAGCTTATA
1 GGGAAAGGTTATGAAGCTTATA
41842360 GGGAAAGGTTATGAAGCTTATA
1 GGGAAAGGTTATGAAGCTTATA
41842382 GGGAAAGGTTATGAAGCTTA
1 GGGAAAGGTTATGAAGCTTA
41842402 CTTAGCCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.27
Consensus pattern (22 bp):
GGGAAAGGTTATGAAGCTTATA
Found at i:41856984 original size:20 final size:20
Alignment explanation
Indices: 41856959--41856998 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41856949 GACTAAATTG
* * *
41856959 GAAAATGATAGAATTTTTCA
1 GAAAATAATAAAAATTTTCA
41856979 GAAAATAATAAAAATTTTCA
1 GAAAATAATAAAAATTTTCA
41856999 AAACTGTAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (20 bp):
GAAAATAATAAAAATTTTCA
Found at i:41858473 original size:25 final size:25
Alignment explanation
Indices: 41858439--41858524 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
41858429 ACATATATGT
*
41858439 TCACAAGAGCTATGAATCAGAATGC
1 TCACACGAGCTATGAATCAGAATGC
** ** **
41858464 TCACACGAGCTGTAAAAATGGGCCTGC
1 TCACACGAGC--TATGAATCAGAATGC
* *
41858491 TCACACGAGCTTTGAATCAAAATGC
1 TCACACGAGCTATGAATCAGAATGC
41858516 TCACACGAG
1 TCACACGAG
41858525 TTGTGGGTCG
Statistics
Matches: 44, Mismatches: 15, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
25 25 0.57
27 19 0.43
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (25 bp):
TCACACGAGCTATGAATCAGAATGC
Found at i:41868236 original size:3 final size:3
Alignment explanation
Indices: 41868228--41868264 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
41868218 GTTAATAAAT
41868228 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
41868265 AAGATGCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:41870230 original size:30 final size:30
Alignment explanation
Indices: 41870169--41870230 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
41870159 TTATTTATAA
* *
41870169 TTAATTATATGTAAATAAAGTTATTAGTAT
1 TTAATTATATGTAAATAAAGTCATTACTAT
* *
41870199 TTAATTATAAT-TAAATTAAGTCGTTACTAT
1 TTAATTAT-ATGTAAATAAAGTCATTACTAT
41870229 TT
1 TT
41870231 TTTTATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (30 bp):
TTAATTATATGTAAATAAAGTCATTACTAT
Found at i:41879778 original size:45 final size:45
Alignment explanation
Indices: 41879623--41879784 Score: 175
Period size: 45 Copynumber: 3.6 Consensus size: 45
41879613 GTGTACTGAG
* **
41879623 TATCATTGATTATAAAGGTGGTTGATATGTGTTGATTCCACCGGT
1 TATCATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACCGAA
* * * *
41879668 TACCGTTGATTATAAAGGTGGTTGCTATGTGCTGACTCCACCGGAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACC-GAA
* * ** *
41879714 -GTCATTAAAAATAAAGGTGGTTGCTATGTGTTGATTCCATCGAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACCGAA
* *
41879758 TATAATTGATTATAAGGGTGG-TGCTAT
1 TATCATTGATTATAAAGGTGGTTGCTAT
41879785 ATGCTGATCC
Statistics
Matches: 93, Mismatches: 22, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
44 9 0.10
45 83 0.89
46 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (45 bp):
TATCATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACCGAA
Found at i:41879778 original size:90 final size:88
Alignment explanation
Indices: 41879634--41879796 Score: 227
Period size: 90 Copynumber: 1.8 Consensus size: 88
41879624 ATCATTGATT
** ** *
41879634 ATAAAGGTGGTTGATATGTGTTGATTCCACCGGTTACCGTTGATTATAAAGGTGGTTGCTATGTG
1 ATAAAGGTGGTTGATATGTGTTGATTCCACCGAATACAATTGATTATAAAGGTGG-TGCTATATG
41879699 CTGACTCCACCGGAAGTCATTAAAA
65 CTGA-TCCACCGGAAGTCATTAAAA
* * * *
41879724 ATAAAGGTGGTTGCTATGTGTTGATTCCATCGAATATAATTGATTATAAGGGTGGTGCTATATGC
1 ATAAAGGTGGTTGATATGTGTTGATTCCACCGAATACAATTGATTATAAAGGTGGTGCTATATGC
41879789 TGATCCAC
66 TGATCCAC
41879797 TGTGTAACGG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
88 5 0.08
89 12 0.19
90 47 0.73
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (88 bp):
ATAAAGGTGGTTGATATGTGTTGATTCCACCGAATACAATTGATTATAAAGGTGGTGCTATATGC
TGATCCACCGGAAGTCATTAAAA
Found at i:41880151 original size:29 final size:29
Alignment explanation
Indices: 41880109--41880167 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
41880099 AAAAATAGAG
41880109 TAAGCAAAAGGGTTATATATTTTGAGATA
1 TAAGCAAAAGGGTTATATATTTTGAGATA
*
41880138 TAAGCACAAGGGTTATATATTTTGAGATA
1 TAAGCAAAAGGGTTATATATTTTGAGATA
41880167 T
1 T
41880168 TTGAATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (29 bp):
TAAGCAAAAGGGTTATATATTTTGAGATA
Found at i:41886055 original size:21 final size:20
Alignment explanation
Indices: 41886011--41886052 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
41886001 AAATCAAAGG
*
41886011 ATAAATAAGTAAATTAATAA
1 ATAAATAAGTAAATAAATAA
41886031 ATAAACTAAGTGAAATAAATAA
1 ATAAA-TAAGT-AAATAAATAA
41886053 TAACAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 5 0.26
22 9 0.47
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.26
Consensus pattern (20 bp):
ATAAATAAGTAAATAAATAA
Found at i:41889046 original size:50 final size:50
Alignment explanation
Indices: 41888949--41889047 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
41888939 GTTATGAAAT
* * **
41888949 GTCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACTGAGATGAGAG
1 GTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGAGAG
* * *
41888999 GTCCCCCGTAAGACTATGTCTGGGACATGGCATGGGCACCAATATGAGA
1 GTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGAGA
41889048 ACTCTCATAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
GTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGAGAG
Found at i:41896716 original size:48 final size:48
Alignment explanation
Indices: 41896653--41896749 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
41896643 CACCATGTTG
*
41896653 AACTAGCTTTATTATGCATGTTTTAGGTATATTTTGAAGCTTGAAATT
1 AACTAGCTTTATTATGAATGTTTTAGGTATATTTTGAAGCTTGAAATT
41896701 AACTAGCTTTATTATGAATGTTTTAGGTATATTTTGAAGCTTGAAATT
1 AACTAGCTTTATTATGAATGTTTTAGGTATATTTTGAAGCTTGAAATT
41896749 A
1 A
41896750 TGTGCAAATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.45
Consensus pattern (48 bp):
AACTAGCTTTATTATGAATGTTTTAGGTATATTTTGAAGCTTGAAATT
Found at i:41899616 original size:27 final size:27
Alignment explanation
Indices: 41899572--41899623 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
41899562 TTGTTTTTGG
**
41899572 TTTTTTTATTTTTTA-TTTTAAAGTAA
1 TTTTTTTATTTTCAATTTTTAAAGTAA
41899598 TTTTTTTATCTTTCAATTTTTAAAGT
1 TTTTTTTAT-TTTCAATTTTTAAAGT
41899624 GCTTCTAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 4 0.18
28 9 0.41
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (27 bp):
TTTTTTTATTTTCAATTTTTAAAGTAA
Found at i:41899975 original size:30 final size:30
Alignment explanation
Indices: 41899907--41899996 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 30
41899897 GATTAAATCA
* *
41899907 AAATTAAAGTTTCAAGTATATATTTGA-ACC
1 AAATTAAAATTTCAAGTATATAATT-ACACC
* *
41899937 ACAATTAAAATTTCACGTGTATAATTACACC
1 A-AATTAAAATTTCAAGTATATAATTACACC
41899968 AAATTAAAATTTCATA-TATATAATTACAC
1 AAATTAAAATTTCA-AGTATATAATTACAC
41899997 ATTAAACCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
30 27 0.53
31 24 0.47
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.36
Consensus pattern (30 bp):
AAATTAAAATTTCAAGTATATAATTACACC
Found at i:41902681 original size:29 final size:28
Alignment explanation
Indices: 41902621--41902684 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
41902611 TCCGAAGACG
41902621 AAAAATTTATGCAAATTGCTATAAACGA
1 AAAAATTTATGCAAATTGCTATAAACGA
*
41902649 AAAAATTTATGCAAATTGCTATATACGA
1 AAAAATTTATGCAAATTGCTATAAACGA
41902677 AAAAATTT
1 AAAAATTT
41902685 TATAATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.31
Consensus pattern (28 bp):
AAAAATTTATGCAAATTGCTATAAACGA
Found at i:41905810 original size:91 final size:91
Alignment explanation
Indices: 41905663--41905944 Score: 341
Period size: 91 Copynumber: 3.0 Consensus size: 91
41905653 TTGATTTTAG
* *
41905663 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-ATTTTATTATAAAGAATTTTATGAAATTATATATTATTATTAAATTAT
*
41905728 ATTTAATATTAATTATTTTAAATTGTA
65 ATTTAATATTAATTATTTTAAATTATA
* *
41905755 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAATTTTATTATAAAGAATTTTATGAAATTATATATTATTATTAAATTATA
* *
41905820 TGTAATAATAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
* * * *
41905846 CAAATTCATATAAGATAATTATTAGTTATAATTATTTTAAATTTTATTAAATCATATATT-TTAA
1 TAAATTCATATAAGA-AATT-TTA-TTATAA--A----GAATTTTATGAAATTATATATTATT-A
* *
41905910 TTAAAATATATTTAATATTAATTATTTCAAATTAT
56 TTAAATTATATTTAATATTAATTATTTTAAATTAT
41905945 CTTTTATAGT
Statistics
Matches: 164, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
91 83 0.51
92 19 0.12
93 3 0.02
94 5 0.03
96 1 0.01
99 2 0.01
100 51 0.31
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (91 bp):
TAAATTCATATAAGAAATTTTATTATAAAGAATTTTATGAAATTATATATTATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:41905839 original size:26 final size:28
Alignment explanation
Indices: 41905785--41905845 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
41905775 TATTATCAAG
* *
41905785 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
41905813 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
41905839 AATTATA
1 AATTATA
41905846 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:41905845 original size:44 final size:43
Alignment explanation
Indices: 41905703--41905845 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
41905693 GAATTTTATG
* *
41905703 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
41905747 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
41905794 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
41905838 AAATTATA
1 AAATTATA
41905846 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:41906001 original size:120 final size:120
Alignment explanation
Indices: 41905885--41906417 Score: 978
Period size: 120 Copynumber: 4.4 Consensus size: 120
41905875 AATTATTTTA
* * * * *
41905885 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTT
41905949 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
41906005 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTGTGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
41906070 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
41906125 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
41906190 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
41906245 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
41906310 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
41906365 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
41906418 TAAATATGAT
Statistics
Matches: 404, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
120 402 1.00
121 2 0.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:41906045 original size:15 final size:15
Alignment explanation
Indices: 41906010--41906051 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41906000 TTAAGAATTT
*
41906010 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41906024 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41906038 TATTTAATAATAAT
1 TATTTAATTATAAT
41906052 TGTGTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41906165 original size:15 final size:15
Alignment explanation
Indices: 41906130--41906181 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41906120 TTAAGAATTT
*
41906130 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41906144 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41906158 TATTTAATAATAAT-
1 TATTTAATTATAATA
41906172 TATGTTAATT
1 TAT-TTAATT
41906182 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41906285 original size:15 final size:15
Alignment explanation
Indices: 41906250--41906301 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41906240 TTAAGAATTT
*
41906250 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41906264 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41906278 TATTTAATAATAAT-
1 TATTTAATTATAATA
41906292 TATGTTAATT
1 TAT-TTAATT
41906302 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41906400 original size:16 final size:16
Alignment explanation
Indices: 41906379--41906420 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41906369 TTATTAAATT
*
41906379 ATATATTTTAATTATA
1 ATATATTTTAATAATA
41906395 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
41906410 AT-TATGTTTAA
1 ATATAT-TTTAA
41906421 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:41906405 original size:15 final size:15
Alignment explanation
Indices: 41906370--41906411 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41906360 TTAAGAATTT
*
41906370 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41906384 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41906398 TATTTAATAATAAT
1 TATTTAATTATAAT
41906412 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41911437 original size:23 final size:23
Alignment explanation
Indices: 41911409--41911455 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
41911399 TAATATTGTT
41911409 AGATTTAATTATATAACTTTTTA
1 AGATTTAATTATATAACTTTTTA
41911432 AGATTTAATTATATAACTTTTTA
1 AGATTTAATTATATAACTTTTTA
41911455 A
1 A
41911456 AATTAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (23 bp):
AGATTTAATTATATAACTTTTTA
Found at i:41913659 original size:11 final size:11
Alignment explanation
Indices: 41913643--41913667 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41913633 GTGTATAAAT
41913643 TGTGAAATTGA
1 TGTGAAATTGA
41913654 TGTGAAATTGA
1 TGTGAAATTGA
41913665 TGT
1 TGT
41913668 AATAATAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (11 bp):
TGTGAAATTGA
Found at i:41917312 original size:34 final size:34
Alignment explanation
Indices: 41917269--41917337 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
41917259 TATAGGCAAA
*
41917269 ATACAAGAGTAATTGAACCCTAATAAAATTCTTT
1 ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
41917303 ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
1 ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
41917337 A
1 A
41917338 AAATTATCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (34 bp):
ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
Found at i:41918949 original size:42 final size:43
Alignment explanation
Indices: 41918859--41919036 Score: 184
Period size: 43 Copynumber: 4.2 Consensus size: 43
41918849 GCGTCACTAA
* ** * * * *
41918859 CTTTAGCGGCGCTTTTCTAAAAAACGTCGCTAAAGACCATGAT
1 CTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGAACATGAC
* * *
41918902 CTTTAGCGGCGCTTTCCCCACAAACACC-CTAAAGAGTCGT-AC
1 CTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGA-ACATGAC
* *
41918944 TTTTAGCGGCGCTTTGCCCACAAACGCCGCTAAAGAACATGAC
1 CTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGAACATGAC
* *
41918987 CTTTAGCGGCGC-TTCACCCACAAACGCCGCTAAA-AATATGAT
1 CTTTAGCGGCGCTTTC-CCCACAAACGCCGCTAAAGAACATGAC
41919029 CTTTAGCG
1 CTTTAGCG
41919037 ACACATTTTT
Statistics
Matches: 113, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
42 51 0.45
43 62 0.55
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.24
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGAACATGAC
Found at i:41919007 original size:85 final size:86
Alignment explanation
Indices: 41918860--41919020 Score: 227
Period size: 85 Copynumber: 1.9 Consensus size: 86
41918850 CGTCACTAAC
* * * * *
41918860 TTTAGCGGCGCTTTTCTAAAAAACGTCGCTAAAGACCATGATCTTTAGCGGCGCTTTCCCCACAA
1 TTTAGCGGCGCTTTGCCAAAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCACAA
41918925 ACACC-CTAAAGAGTCGTACT
66 ACACCGCTAAAGAGTCGTACT
* *
41918945 TTTAGCGGCGCTTTGCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC-TTCACCCACA
1 TTTAGCGGCGCTTTGCCAAAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTC-CCCACA
*
41919009 AACGCCGCTAAA
65 AACACCGCTAAA
41919021 AATATGATCT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 3 0.05
85 58 0.88
86 5 0.08
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (86 bp):
TTTAGCGGCGCTTTGCCAAAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCACAA
ACACCGCTAAAGAGTCGTACT
Found at i:41923358 original size:14 final size:14
Alignment explanation
Indices: 41923325--41923351 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41923315 TTGTTGAAAT
41923325 ATCTTTCCCCCCTC
1 ATCTTTCCCCCCTC
41923339 ATCTTTCCCCCCT
1 ATCTTTCCCCCCT
41923352 TTTCTTTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.56, G:0.00, T:0.37
Consensus pattern (14 bp):
ATCTTTCCCCCCTC
Found at i:41924137 original size:22 final size:22
Alignment explanation
Indices: 41924089--41924139 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
41924079 ATCATAAAAT
*
41924089 ATAAACCCCTAACCCCTAAACT
1 ATAAACCCCTAACCCCTAAACC
*
41924111 TTAAACCCCTAACCCCTAAACC
1 ATAAACCCCTAACCCCTAAACC
41924133 ATAAACC
1 ATAAACC
41924140 TTAATTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.18
Consensus pattern (22 bp):
ATAAACCCCTAACCCCTAAACC
Found at i:41924725 original size:41 final size:41
Alignment explanation
Indices: 41924650--41924983 Score: 454
Period size: 41 Copynumber: 8.1 Consensus size: 41
41924640 TAGATTATTT
* ** *
41924650 TAAATCCCTGAGCATTAGCGGCGCTTAACAAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
* *
41924691 TAAAGCCCTAAGCATTAGCGGCGCTTTCCCAAAAATGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
*
41924732 TAAAGCCCTGAGCATTAGCGGCGCTTTACCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
* *
41924773 TAAATCCCTGAGCATTAGCGGCGC-TTCCATAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCC-CAAAAACGCCGC
*
41924814 TAAAGCCCTGAGCATTAGAGGCGCTTTCCCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
* * *
41924855 TAAATCCCAGAGCATTAGCGGCGCTTTCCCACAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
* * *
41924896 TAAAGGCCTGAGCATTAGTGGCGCTTTCCCAAAAGCGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
* * **
41924937 TAAAGCCCTAATCATTAGCGGCGCGTTTGCAAAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGC-TTT-CCCAAAAACGCCGC
41924980 TAAA
1 TAAA
41924984 ACCCCGAAAT
Statistics
Matches: 257, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
40 3 0.01
41 232 0.90
42 7 0.03
43 15 0.06
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (41 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
Found at i:41934177 original size:23 final size:22
Alignment explanation
Indices: 41934125--41934177 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
41934115 TCCTTGTCTT
*
41934125 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
* *
41934147 CTTATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTCT-TTCTTT-TTCTAA
41934170 TTTCTTTT
1 TTTCTTTT
41934178 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:41934191 original size:18 final size:18
Alignment explanation
Indices: 41934170--41934209 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41934160 CTTTCTTCAA
* * *
41934170 TTTCTTTTTCACTTTTCT
1 TTTCTGTTTCACATTCCT
41934188 TTTCTGTTTCACATTCCT
1 TTTCTGTTTCACATTCCT
41934206 TTTC
1 TTTC
41934210 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.25, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTCTGTTTCACATTCCT
Found at i:41937135 original size:50 final size:50
Alignment explanation
Indices: 41937028--41937152 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 50
41937018 GATGAGTTCT
* * * * *
41937028 CATGTAAGACCATATCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATATCTGGGATATGGCATGGGCACCAAGATGAGAGCTCC
** * * * *
41937078 CCCGTAAGACCATGTCTGGGATATGGCATGGGCACCAATATGAGATCTTC
1 CATGTAAGACCATATCTGGGATATGGCATGGGCACCAAGATGAGAGCTCC
*
41937128 CATGTAAGACCATATCTAGGATATG
1 CATGTAAGACCATATCTGGGATATG
41937153 ACATTTGCAG
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
CATGTAAGACCATATCTGGGATATGGCATGGGCACCAAGATGAGAGCTCC
Found at i:41938851 original size:26 final size:27
Alignment explanation
Indices: 41938790--41938865 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 27
41938780 TGTGTAAATT
*
41938790 AAGATAATTAGAAGTTTAAATTATATT
1 AAGATAATTAGAAGTTTAAATTATATG
* * *
41938817 ATGAAAATTA-AAGTTTTAATT-TAGTG
1 AAGATAATTAGAAGTTTAAATTATA-TG
* *
41938843 AAGATAATTAGAAATATAAATTA
1 AAGATAATTAGAAGTTTAAATTA
41938866 ATAGGTTAGA
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
25 2 0.05
26 19 0.51
27 16 0.43
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (27 bp):
AAGATAATTAGAAGTTTAAATTATATG
Found at i:41939263 original size:13 final size:13
Alignment explanation
Indices: 41939247--41939280 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
41939237 ACCTCTGAAG
41939247 GGTTCCTCAAAGA
1 GGTTCCTCAAAGA
*
41939260 GGTTCCTCAGAGA
1 GGTTCCTCAAAGA
41939273 GGTATCCT
1 GGT-TCCT
41939281 TACATGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (13 bp):
GGTTCCTCAAAGA
Found at i:41939909 original size:23 final size:23
Alignment explanation
Indices: 41939883--41939949 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
41939873 TTGCTAGCTT
*
41939883 TATTGTGAAAATATTGTA-AATAG
1 TATTGTAAAAATATTG-AGAATAG
*
41939906 TATTGTAAAAATAATGAGAATAG
1 TATTGTAAAAATATTGAGAATAG
* * *
41939929 TGTTGCAAAAATATTGCGAAT
1 TATTGTAAAAATATTGAGAAT
41939950 TGTACCGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (23 bp):
TATTGTAAAAATATTGAGAATAG
Found at i:41940212 original size:54 final size:54
Alignment explanation
Indices: 41940043--41940501 Score: 377
Period size: 54 Copynumber: 8.4 Consensus size: 54
41940033 ATTGAAAACT
* * *
41940043 GCAAGATTCTAG-AAATCTTGTAAGTATAAGGCTGGGATCTTAAAT-GGCGAGCC
1 GCAAGATTC-AGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
* * * * ** *
41940096 ACAAGATTCATAAAATCTTGCAAGTATAAGGCAGGTTGCGATCTTAAATTGGTGAGCA
1 GCAAGATTCAGAAAATCTTGTAAGTAT-A---AGGTTGCGATCTTAAATCGGCAAGCC
* ** * * *
41940154 ACAAGATTTGGAAAATCTTGTAAGTATAAGGTTGAGATCTTAAATCGGTAACCC
1 GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
* * * * * * * *
41940208 ACAAGATTCAAAAAATCTTATAAGTATAATGTTTCGATCTTAAATCAGCGAGCT
1 GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
** **
41940262 GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGAAAAATC
1 GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
* *** *
41940316 GCAAGATTCAGAAAATCCTGTAAGTATAAGGCAACGATCTTAAATCGGCCAGCC
1 GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
* * * ** * *
41940370 GCAAGATTTAAAAAATCTTATAAGTATAAGGTTGCGATCTTAAATTAGCAAACT
1 GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
* * * * * ** *
41940424 GTAAGA-TCGGGAAAATCCTGTAAGTATAAGGTTGAGATATTAAATTAGCCAGCC
1 GCAAGATTC-AGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
* *
41940478 GTAAGACT-AGAAAAATCTTGTAAG
1 GCAAGATTCAG-AAAATCTTGTAAG
41940502 CAGCGAATTG
Statistics
Matches: 323, Mismatches: 74, Indels: 17
0.78 0.18 0.04
Matches are distributed among these distances:
52 1 0.00
53 24 0.07
54 252 0.78
55 1 0.00
57 16 0.05
58 29 0.09
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (54 bp):
GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
Found at i:41940340 original size:162 final size:161
Alignment explanation
Indices: 41940044--41940468 Score: 433
Period size: 162 Copynumber: 2.6 Consensus size: 161
41940034 TTGAAAACTG
* * * * * * ** *
41940044 CAAGATTCTAGAAATCTTGTAAGTATAAGGCTGGGATCTTAAATGGCGAGCCACAAGATTCATAA
1 CAAGATTCAAAAAATCTTATAAGTATAAGGTTGCGATCTTAAATAGCGAGCTGCAAGATTCAGAA
* * *** ** *
41940109 AATCTTGCAAGTATAAGGCAGGTTGCGATCTTAAATTGGTGAGCAACAAGATTTGGAAAATCTTG
66 AATCTTGTAAGTAT-A---AGGTTGCGATCTTAAATCGAAAAGCAACAAGATTCAGAAAATCCTG
** *
41940174 TAAGTATAAGGTTGA-GATCTTAAATCGGTAACCCA
127 TAAGTATAAGG-CAACGATCTTAAATCGGCAACCCA
* *
41940209 CAAGATTCAAAAAATCTTATAAGTATAATGTTTCGATCTTAAATCAGCGAGCTGCAAGATTCAGA
1 CAAGATTCAAAAAATCTTATAAGTATAAGGTTGCGATCTTAAAT-AGCGAGCTGCAAGATTCAGA
* *
41940274 AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGAAAAATC-GCAAGATTCAGAAAATCCTGTA
65 AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCG-AAAAGCAACAAGATTCAGAAAATCCTGTA
* * *
41940338 AGTATAAGGCAACGATCTTAAATCGGCCAGCCG
129 AGTATAAGGCAACGATCTTAAATCGGCAACCCA
* * * * *
41940371 CAAGATTTAAAAAATCTTATAAGTATAAGGTTGCGATCTTAAATTAGCAAACTGTAAGA-TCGGG
1 CAAGATTCAAAAAATCTTATAAGTATAAGGTTGCGATCTTAAA-TAGCGAGCTGCAAGATTC-AG
* * *
41940435 AAAATCCTGTAAGTATAAGGTTGAGATATTAAAT
64 AAAATCTTGTAAGTATAAGGTTGCGATCTTAAAT
41940469 TAGCCAGCCG
Statistics
Matches: 218, Mismatches: 37, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
161 3 0.01
162 144 0.66
163 3 0.01
165 38 0.17
166 30 0.14
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (161 bp):
CAAGATTCAAAAAATCTTATAAGTATAAGGTTGCGATCTTAAATAGCGAGCTGCAAGATTCAGAA
AATCTTGTAAGTATAAGGTTGCGATCTTAAATCGAAAAGCAACAAGATTCAGAAAATCCTGTAAG
TATAAGGCAACGATCTTAAATCGGCAACCCA
Found at i:41945485 original size:16 final size:17
Alignment explanation
Indices: 41945457--41945488 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41945447 TAAAAATATG
41945457 TATATATGTATATAAAT
1 TATATATGTATATAAAT
41945474 TATATA-GTATATAAA
1 TATATATGTATATAAA
41945489 AATGTAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TATATATGTATATAAAT
Found at i:41946395 original size:21 final size:21
Alignment explanation
Indices: 41946370--41946411 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41946360 TGAAACAAAC
41946370 AAAAATAAAAGAAAAGAAAAAG
1 AAAAAT-AAAGAAAAGAAAAAG
*
41946392 AAAAATAAAGAAAATAAAAA
1 AAAAATAAAGAAAAGAAAAA
41946412 ACGCAAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (21 bp):
AAAAATAAAGAAAAGAAAAAG
Found at i:41946411 original size:16 final size:15
Alignment explanation
Indices: 41946371--41946412 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
41946361 GAAACAAACA
*
41946371 AAAATAAAAGAAAAG
1 AAAATAAAAAAAAAG
41946386 AAAA-AGAAAAATAAAG
1 AAAATA-AAAAA-AAAG
41946402 AAAATAAAAAA
1 AAAATAAAAAA
41946413 CGCAAGAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 8 0.35
16 13 0.57
17 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
AAAATAAAAAAAAAG
Found at i:41946412 original size:22 final size:22
Alignment explanation
Indices: 41946370--41946412 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41946360 TGAAACAAAC
*
41946370 AAAAATAAAAGAAAAGAAAAAG
1 AAAAATAAAAGAAAAAAAAAAG
41946392 AAAAAT-AAAGAAAATAAAAAA
1 AAAAATAAAAGAAAA-AAAAAA
41946413 CGCAAGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (22 bp):
AAAAATAAAAGAAAAAAAAAAG
Found at i:41955618 original size:29 final size:29
Alignment explanation
Indices: 41955586--41955663 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
41955576 AAAATATTAG
* *
41955586 TTAAACTAATTAAATTACTTAAACTAAAA
1 TTAACCTAATTAAATTAATTAAACTAAAA
* *
41955615 TTAACCTAATTGAATTAATTAATCTAAAA
1 TTAACCTAATTAAATTAATTAAACTAAAA
*
41955644 -TAACCTAATGAAATTAATTA
1 TTAACCTAATTAAATTAATTA
41955664 GTCTAAGGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 18 0.42
29 25 0.58
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (29 bp):
TTAACCTAATTAAATTAATTAAACTAAAA
Found at i:41955675 original size:28 final size:27
Alignment explanation
Indices: 41955598--41955669 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
41955588 AAACTAATTA
* *
41955598 AATTACTTAAACTAAAATTAACCTAATTG
1 AATTAATTAATCTAAAA-TAACCTAA-TG
41955627 AATTAATTAATCTAAAATAACCTAATG
1 AATTAATTAATCTAAAATAACCTAATG
*
41955654 AAATTAATTAGTCTAA
1 -AATTAATTAATCTAA
41955670 GGTAACTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.05
28 22 0.56
29 15 0.38
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.35
Consensus pattern (27 bp):
AATTAATTAATCTAAAATAACCTAATG
Found at i:41956302 original size:37 final size:37
Alignment explanation
Indices: 41956252--41956325 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
41956242 AAATTACAAA
41956252 GAAAAATAAAATAAAACTATTTAATTGTCTAGCTATC
1 GAAAAATAAAATAAAACTATTTAATTGTCTAGCTATC
41956289 GAAAAATAAAATAAAACTATTTAATTGTCTAGCTATC
1 GAAAAATAAAATAAAACTATTTAATTGTCTAGCTATC
41956326 AACAACCAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (37 bp):
GAAAAATAAAATAAAACTATTTAATTGTCTAGCTATC
Found at i:41961263 original size:29 final size:29
Alignment explanation
Indices: 41961213--41961290 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
41961203 AAAATATTAG
* * *
41961213 TTAAACTAATTAATTTACTTAACCTAAAA
1 TTAACCTAATTAAATTAATTAACCTAAAA
* *
41961242 TTAACCTAATTAAATCAATTAATCTAAAA
1 TTAACCTAATTAAATTAATTAACCTAAAA
*
41961271 -TAACCTAATGAAATTAATTA
1 TTAACCTAATTAAATTAATTA
41961291 GTCTAAGATA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 18 0.43
29 24 0.57
ACGTcount: A:0.50, C:0.13, G:0.01, T:0.36
Consensus pattern (29 bp):
TTAACCTAATTAAATTAATTAACCTAAAA
Found at i:41961284 original size:28 final size:28
Alignment explanation
Indices: 41961231--41961307 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
41961221 ATTAATTTAC
* *
41961231 TTAACCTAAAATTAACCTAATTAAATCAA
1 TTAATCTAAAA-TAACCTAATGAAATCAA
*
41961260 TTAATCTAAAATAACCTAATGAAATTAA
1 TTAATCTAAAATAACCTAATGAAATCAA
* *
41961288 TTAGTCTAAGATAA-CTAATG
1 TTAATCTAAAATAACCTAATG
41961308 GAATTTCCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 6 0.14
28 27 0.63
29 10 0.23
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.32
Consensus pattern (28 bp):
TTAATCTAAAATAACCTAATGAAATCAA
Found at i:41963036 original size:33 final size:33
Alignment explanation
Indices: 41962999--41963094 Score: 84
Period size: 33 Copynumber: 3.2 Consensus size: 33
41962989 TGAGTTAATG
41962999 CATGACTTAATTTAATAATGCAAACTTAACTAA
1 CATGACTTAATTTAATAATGCAAACTTAACTAA
* *
41963032 CATGA---AAGTTACATAAT------TAAACTAA
1 CATGACTTAATTTA-ATAATGCAAACTTAACTAA
* *
41963057 CATGACTTAGTTTAATGATGCAAACTTAACTAA
1 CATGACTTAATTTAATAATGCAAACTTAACTAA
41963090 CATGA
1 CATGA
41963095 AAGTTACATA
Statistics
Matches: 47, Mismatches: 6, Indels: 20
0.64 0.08 0.27
Matches are distributed among these distances:
25 12 0.26
27 4 0.09
28 4 0.09
30 5 0.11
31 5 0.11
33 17 0.36
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (33 bp):
CATGACTTAATTTAATAATGCAAACTTAACTAA
Found at i:41976669 original size:7 final size:7
Alignment explanation
Indices: 41976657--41976713 Score: 96
Period size: 7 Copynumber: 8.1 Consensus size: 7
41976647 GATAAATTTC
41976657 AGAATTG
1 AGAATTG
41976664 AGAATTG
1 AGAATTG
*
41976671 AGGATTG
1 AGAATTG
*
41976678 AGGATTG
1 AGAATTG
41976685 AGAATTG
1 AGAATTG
41976692 AGAATTG
1 AGAATTG
41976699 AGAATTG
1 AGAATTG
41976706 AGAATTG
1 AGAATTG
41976713 A
1 A
41976714 TGATTAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (7 bp):
AGAATTG
Found at i:41976679 original size:14 final size:14
Alignment explanation
Indices: 41976660--41976763 Score: 102
Period size: 14 Copynumber: 7.4 Consensus size: 14
41976650 AAATTTCAGA
41976660 ATTGAGAATTGAGG
1 ATTGAGAATTGAGG
* *
41976674 ATTGAGGATTGAGA
1 ATTGAGAATTGAGG
*
41976688 ATTGAGAATTGAGA
1 ATTGAGAATTGAGG
*
41976702 ATTGAGAATTGATG
1 ATTGAGAATTGAGG
* * *
41976716 ATTAAAAATTGAAG
1 ATTGAGAATTGAGG
*
41976730 ATTGA-AGATTTAGG
1 ATTGAGA-ATTGAGG
* *
41976744 ATTGAGGATTGAGT
1 ATTGAGAATTGAGG
41976758 ATTGAG
1 ATTGAG
41976764 TTGAAAAGAA
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
13 1 0.01
14 73 0.99
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (14 bp):
ATTGAGAATTGAGG
Found at i:41976686 original size:21 final size:21
Alignment explanation
Indices: 41976657--41976763 Score: 108
Period size: 21 Copynumber: 5.1 Consensus size: 21
41976647 GATAAATTTC
41976657 AGAATTGAGAATTGAGGATTG
1 AGAATTGAGAATTGAGGATTG
* *
41976678 AGGATTGAGAATTGAGAATTG
1 AGAATTGAGAATTGAGGATTG
* *
41976699 AGAATTGAGAATTGATGATTA
1 AGAATTGAGAATTGAGGATTG
* * *
41976720 AAAATTGA-AGATTGAAGATTT
1 AGAATTGAGA-ATTGAGGATTG
* * *
41976741 AGGATTGAGGATTGAGTATTG
1 AGAATTGAGAATTGAGGATTG
41976762 AG
1 AG
41976764 TTGAAAAGAA
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 1 0.01
21 68 0.99
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.31
Consensus pattern (21 bp):
AGAATTGAGAATTGAGGATTG
Found at i:41976756 original size:7 final size:7
Alignment explanation
Indices: 41976660--41976763 Score: 91
Period size: 7 Copynumber: 14.9 Consensus size: 7
41976650 AAATTTCAGA
*
41976660 ATTGAGA
1 ATTGAGG
41976667 ATTGAGG
1 ATTGAGG
41976674 ATTGAGG
1 ATTGAGG
*
41976681 ATTGAGA
1 ATTGAGG
*
41976688 ATTGAGA
1 ATTGAGG
*
41976695 ATTGAGA
1 ATTGAGG
*
41976702 ATTGAGA
1 ATTGAGG
*
41976709 ATTGATG
1 ATTGAGG
* **
41976716 ATTAAAA
1 ATTGAGG
*
41976723 ATTGAAG
1 ATTGAGG
*
41976730 ATTGAAG
1 ATTGAGG
*
41976737 ATTTAGG
1 ATTGAGG
41976744 ATTGAGG
1 ATTGAGG
*
41976751 ATTGAGT
1 ATTGAGG
41976758 ATTGAG
1 ATTGAG
41976764 TTGAAAAGAA
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 84 1.00
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (7 bp):
ATTGAGG
Found at i:41985444 original size:14 final size:14
Alignment explanation
Indices: 41985425--41985456 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
41985415 TCCAATCACC
41985425 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
41985439 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
41985453 GGGC
1 GGGC
41985457 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:41990570 original size:14 final size:14
Alignment explanation
Indices: 41990551--41990582 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
41990541 TCCAATCACC
41990551 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
41990565 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
41990579 GGGC
1 GGGC
41990583 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:41996697 original size:95 final size:94
Alignment explanation
Indices: 41996533--41996813 Score: 375
Period size: 95 Copynumber: 3.0 Consensus size: 94
41996523 GTACTGGTGG
* * * * * *
41996533 TGGATACCTCACCGATGGCTAAGATCCTGCATATATTACGGATTCTTCACAGCTCGTGTGGGTAA
1 TGGATACCTTACTGATGGTTAAGATCCTGCATATATTA-AGATTCTTCACAGCTCGTGTGAGCAA
*
41996598 CATCGTGTAATAGTTAATGTCTCGATTTAC
65 CATCGTGTAATGGTTAATGTCTCGATTTAC
*
41996628 TGGATACCTTACTGATGGTTAAGATCCTGCATATATTAAGAATTCTTCACAGCTCGTGTGAGCAG
1 TGGATACCTTACTGATGGTTAAGATCCTGCATATATTAAG-ATTCTTCACAGCTCGTGTGAGCAA
* *
41996693 CATCGTGTAATGGTTAATGTCCCGATTTTC
65 CATCGTGTAATGGTTAATGTCTCGATTTAC
* * * * * *
41996723 TGGATACCTTACTGATGGTTAAGATTCTGCATGTGTTGCAGATTCTTCATAGCTCGTGTGAGGAA
1 TGGATACCTTACTGATGGTTAAGATCCTGCATATATT-AAGATTCTTCACAGCTCGTGTGAGCAA
*
41996788 CATTGTGTAATGGTTAATGTCT-GATT
65 CATCGTGTAATGGTTAATGTCTCGATT
41996814 CACAGCTCAT
Statistics
Matches: 165, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
94 5 0.03
95 158 0.96
96 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (94 bp):
TGGATACCTTACTGATGGTTAAGATCCTGCATATATTAAGATTCTTCACAGCTCGTGTGAGCAAC
ATCGTGTAATGGTTAATGTCTCGATTTAC
Found at i:41999805 original size:27 final size:26
Alignment explanation
Indices: 41999735--41999805 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
41999725 CACGTTGGGG
*
41999735 AAGAAAGCCTTTGTGG-TGTAATATGA
1 AAGAAAGCCTTTGTGGCAG-AATATGA
41999761 AAGAAAGCCTTTGTGGCAGAATATGA
1 AAGAAAGCCTTTGTGGCAGAATATGA
* *
41999787 AAGGTAAGTCTTTGTGGCA
1 AA-GAAAGCCTTTGTGGCA
41999806 AACTCTGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 25 0.62
27 15 0.38
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (26 bp):
AAGAAAGCCTTTGTGGCAGAATATGA
Found at i:42003925 original size:96 final size:96
Alignment explanation
Indices: 42003770--42003951 Score: 240
Period size: 96 Copynumber: 1.9 Consensus size: 96
42003760 TATTGTCCCA
** * *
42003770 ACCAACATTTTGTATTAAATGAAGAAGGTTTTTAATGTCATTTTTTTAGTAATTGAACTTCCAAG
1 ACCAACATTTTGTATTAAAT--AGAAGGTTTTTAATGTCATTAATTCAGCAATTGAACTTCCAAG
* *
42003835 TGCATCGATCATGTTTATTTTTGGAAGTATGGCG
64 TCCATCAATCAT-TTTATTTTTGGAAGTATGGCG
* * *
42003869 ACCAACATTTTGTATTAAAT-GAAGGTTTTTAATGTTATTAATTCAGCGATTGAACTTCCAATTC
1 ACCAACATTTTGTATTAAATAGAAGGTTTTTAATGTCATTAATTCAGCAATTGAACTTCCAAGTC
*
42003933 CATCAATCATTTTTTTTTT
66 CATCAATCATTTTATTTTT
42003952 AGTATGACGT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
95 8 0.11
96 45 0.62
99 20 0.27
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (96 bp):
ACCAACATTTTGTATTAAATAGAAGGTTTTTAATGTCATTAATTCAGCAATTGAACTTCCAAGTC
CATCAATCATTTTATTTTTGGAAGTATGGCG
Done.