Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 205 of 345
Found at i:58891557 original size:46 final size:46
Alignment explanation
Indices: 58891506--58891687 Score: 337
Period size: 46 Copynumber: 4.0 Consensus size: 46
58891496 AGTTAAATAT
58891506 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
58891552 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
*
58891598 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
* *
58891644 ATATATGTGTGGTAAAGCCAAATGGCTAGTATGAAACATGTATG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATG
58891688 AGATGTATAT
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.31
Consensus pattern (46 bp):
ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
Found at i:58891745 original size:47 final size:47
Alignment explanation
Indices: 58891691--58891801 Score: 168
Period size: 47 Copynumber: 2.4 Consensus size: 47
58891681 ATGTATGAGA
* * *
58891691 TGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTCAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
* *
58891738 TGTATATAAGTGATAAGGCCGAATGGCCAATGCGATGAATATGAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
*
58891785 TGTATAAATGTGATAAG
1 TGTATATATGTGATAAG
58891802 TCCCGAGGGG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (47 bp):
TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
Found at i:58901865 original size:43 final size:43
Alignment explanation
Indices: 58901818--58901968 Score: 275
Period size: 43 Copynumber: 3.5 Consensus size: 43
58901808 CATTACGGCA
*
58901818 GCTAGGCACGAAGGCCCGATTACACATCACCGGCATGAAGCCT
1 GCTAGGCACGAAGGCCCGAATACACATCACCGGCATGAAGCCT
*
58901861 GCTAGGCACGAAGGCCCAAATACACATCACCGGCATGAAGCCT
1 GCTAGGCACGAAGGCCCGAATACACATCACCGGCATGAAGCCT
*
58901904 GCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCT
1 GCTAGGCACGAAGGCCCGAATACACATCACCGGCATGAAGCCT
58901947 GCTAGGCACGAAGGCCCGAATA
1 GCTAGGCACGAAGGCCCGAATA
58901969 TAATACCAGC
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 104 1.00
ACGTcount: A:0.30, C:0.32, G:0.26, T:0.11
Consensus pattern (43 bp):
GCTAGGCACGAAGGCCCGAATACACATCACCGGCATGAAGCCT
Found at i:58902009 original size:38 final size:38
Alignment explanation
Indices: 58901961--58902084 Score: 158
Period size: 38 Copynumber: 3.2 Consensus size: 38
58901951 GGCACGAAGG
* * * *
58901961 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
58901999 CCCGGATATAATACTAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
** *
58902037 CCCGGATATTTTACCAGCACGAAGCCTGCGGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA
58902076 GCCCGGATA
1 -CCCGGATA
58902085 CACATCAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
38 62 0.83
39 5 0.07
40 8 0.11
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:58906848 original size:16 final size:16
Alignment explanation
Indices: 58906827--58906858 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
58906817 AGTGTGTTGA
58906827 TTCTCCAATCGTCTTC
1 TTCTCCAATCGTCTTC
*
58906843 TTCTCCAATCTTCTTC
1 TTCTCCAATCGTCTTC
58906859 CAACCTCTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.38, G:0.03, T:0.47
Consensus pattern (16 bp):
TTCTCCAATCGTCTTC
Found at i:58915740 original size:47 final size:48
Alignment explanation
Indices: 58915672--58916040 Score: 257
Period size: 47 Copynumber: 7.8 Consensus size: 48
58915662 TTATTTGTGT
58915672 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGA
* * *
58915718 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAG---CATTGAGACGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT---ATGAGA
* ***
58915766 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGCGATGTA-A
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATG-AGA
* ** * *
58915812 GCTAGTGTAAGA-CATGTCTAGGACATGGTGTC-GACAC-GTAT-AGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGA
* * *** * *
58915856 GGTGTCAGTGTAAGACCATGTCTGGTACATGGCATCAAAACAAATATGTGAGA
1 -G-CT-AGTGTAAGACCATGTCTGGGACATGGCATC-GGCCACAT-TATGAGA
* * * * *
58915909 GCTAGTGTAAGACCATGTCTGGGACATAGCATCAGCCTCGATTTTGATA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATTATGAGA
* * *
58915958 GTTAGTGTAAGACCATGTCTAGGACATGACATC-G--AC-TTGATGGATGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT-AT-GA-GA
*
58916005 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
58916041 ATCATACCCT
Statistics
Matches: 252, Mismatches: 45, Indels: 49
0.73 0.13 0.14
Matches are distributed among these distances:
43 1 0.00
44 3 0.01
45 8 0.03
46 52 0.21
47 71 0.28
48 40 0.16
49 37 0.15
50 33 0.13
51 1 0.00
52 3 0.01
53 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGA
Found at i:58915818 original size:46 final size:46
Alignment explanation
Indices: 58915672--58915838 Score: 203
Period size: 46 Copynumber: 3.6 Consensus size: 46
58915662 TTATTTGTGT
* *
58915672 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGAGA
* * * * *
58915718 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGAGA
*
58915766 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGCGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-AGA
*
58915812 GCTAGTGTAAGACATGTCTAGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
58915839 GTGTCGACAC
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
46 50 0.49
47 29 0.28
48 23 0.22
49 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAGA
Found at i:58926224 original size:23 final size:25
Alignment explanation
Indices: 58926179--58926225 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 25
58926169 TTTAAAATTT
58926179 ATATATTTTAGAATTTTATAAAAAA
1 ATATATTTTAGAATTTTATAAAAAA
*
58926204 ATAT-TTTTA-AACTTT-TAAAAAA
1 ATATATTTTAGAATTTTATAAAAAA
58926226 TTTTCAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 5 0.24
24 5 0.24
25 4 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
ATATATTTTAGAATTTTATAAAAAA
Found at i:58932963 original size:22 final size:24
Alignment explanation
Indices: 58932905--58932964 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 24
58932895 AATTTATTTC
*
58932905 ATAATAAT-ATAAT-ATCAATTAA
1 ATAATTATAATAATAATCAATTAA
*
58932927 ATAA-TATAAACAATAAT-AATT-A
1 ATAATTAT-AATAATAATCAATTAA
58932949 ATAATTATAATAATAA
1 ATAATTATAATAATAA
58932965 ATATCTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 2 0.06
22 16 0.52
23 11 0.35
24 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAATTATAATAATAATCAATTAA
Found at i:58935400 original size:18 final size:18
Alignment explanation
Indices: 58935379--58935422 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
58935369 AATTCCTCTA
58935379 CATATACAAATCCCACCC
1 CATATACAAATCCCACCC
*
58935397 CATATACAAATCCCGCCC
1 CATATACAAATCCCACCC
58935415 CATATACA
1 CATATACA
58935423 GATACAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.41, G:0.02, T:0.18
Consensus pattern (18 bp):
CATATACAAATCCCACCC
Found at i:58936329 original size:13 final size:13
Alignment explanation
Indices: 58936311--58936335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58936301 TTGATAGCGG
58936311 AAAACAAGAAAAC
1 AAAACAAGAAAAC
58936324 AAAACAAGAAAA
1 AAAACAAGAAAA
58936336 GTTTTGGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.12, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAACAAGAAAAC
Found at i:58936364 original size:6 final size:6
Alignment explanation
Indices: 58936355--58936391 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
58936345 AAAAGAAAGA
58936355 AAAATT AAAATT AAAATT AAAATT -AAATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AA
58936392 TAATAATCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:58936384 original size:11 final size:11
Alignment explanation
Indices: 58936356--58936391 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
58936346 AAAGAAAGAA
58936356 AAATTAAAATT
1 AAATTAAAATT
58936367 AAAATTAAAATT
1 -AAATTAAAATT
58936379 AAATTAAAATT
1 AAATTAAAATT
58936390 AA
1 AA
58936392 TAATAATCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATTAAAATT
Found at i:58951767 original size:5 final size:5
Alignment explanation
Indices: 58951752--58951781 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
58951742 CCAAAAATAA
58951752 TATTT TA-TT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT T
58951782 CTGGTTGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:58955078 original size:21 final size:23
Alignment explanation
Indices: 58955052--58955094 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
58955042 GGTCTCCTCC
58955052 TAGGACACA-TTAA-ACAAACAT
1 TAGGACACATTTAACACAAACAT
58955073 TAGGACACATTTAACACAAACA
1 TAGGACACATTTAACACAAACA
58955095 CAAACACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.51, C:0.21, G:0.09, T:0.19
Consensus pattern (23 bp):
TAGGACACATTTAACACAAACAT
Found at i:58958977 original size:19 final size:19
Alignment explanation
Indices: 58958953--58958990 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
58958943 TGAAAAGAAA
* *
58958953 AACTCAAAGAGAATTTGTT
1 AACTCAAAAAGAAGTTGTT
58958972 AACTCAAAAAGAAGTTGTT
1 AACTCAAAAAGAAGTTGTT
58958991 GAATAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (19 bp):
AACTCAAAAAGAAGTTGTT
Found at i:58972122 original size:20 final size:20
Alignment explanation
Indices: 58972099--58972146 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
58972089 AGCTCCGTCT
58972099 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** **
58972119 AGCTCGTTTCAGCTTGTTTG
1 AGCTCAACTCAGCTCATTTG
58972139 AGCTCAAC
1 AGCTCAAC
58972147 CGAGCTTACT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:58972622 original size:156 final size:156
Alignment explanation
Indices: 58972338--58972650 Score: 590
Period size: 156 Copynumber: 2.0 Consensus size: 156
58972328 GTTTAGCTTA
*
58972338 ACATGATATTTATGATGTCTAGTTCATGCTTTTAACATGTTCAGCTGAATATACATTGGGATTTA
1 ACATGATATTTATGATGTCTAGTTCATGCTCTTAACATGTTCAGCTGAATATACATTGGGATTTA
*
58972403 ATGTGTTCATGTTTCTTGTAGGTTCAATCGAATGTATTGAGTACATTTAATGAGATTCATGCACT
66 ATGTGTTCATGTTTCTTGTAGGTTCAATCGAATGTATTGAGTACATTTAATGAGATTCATGCACG
*
58972468 GCTAGGTACATGGAATATAAGAGTTC
131 GCTAGGTACATGAAATATAAGAGTTC
58972494 ACATGATATTTATGATGTCTAGTTCATGCTCTTAACATGTTCAGCTGAATATACATTGGGATTTA
1 ACATGATATTTATGATGTCTAGTTCATGCTCTTAACATGTTCAGCTGAATATACATTGGGATTTA
*
58972559 ATGTGTTCATGTTTCTTGTAGGTTCAGTCGAATGTATTGAGTACATTTAATGAGATTCATGCACG
66 ATGTGTTCATGTTTCTTGTAGGTTCAATCGAATGTATTGAGTACATTTAATGAGATTCATGCACG
58972624 GCTAGGTACATGAAATATAAGAGTTC
131 GCTAGGTACATGAAATATAAGAGTTC
58972650 A
1 A
58972651 TGCATGAACG
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 153 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.38
Consensus pattern (156 bp):
ACATGATATTTATGATGTCTAGTTCATGCTCTTAACATGTTCAGCTGAATATACATTGGGATTTA
ATGTGTTCATGTTTCTTGTAGGTTCAATCGAATGTATTGAGTACATTTAATGAGATTCATGCACG
GCTAGGTACATGAAATATAAGAGTTC
Found at i:58979949 original size:10 final size:10
Alignment explanation
Indices: 58979936--58979964 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
58979926 CTTGGGTTGT
58979936 AAAGAAATTG
1 AAAGAAATTG
58979946 AAAGAAATTG
1 AAAGAAATTG
58979956 AAAGAAATT
1 AAAGAAATT
58979965 CATTTTACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (10 bp):
AAAGAAATTG
Found at i:58987631 original size:23 final size:22
Alignment explanation
Indices: 58987586--58987631 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
58987576 GTATGAAACT
*
58987586 TGAAGATAAATCTGAATTTTTC
1 TGAAGATAAATCTGAATTCTTC
58987608 TGAAGATAAATCTGAAATTCTTC
1 TGAAGATAAATCTG-AATTCTTC
58987631 T
1 T
58987632 TATTCTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (22 bp):
TGAAGATAAATCTGAATTCTTC
Found at i:58997862 original size:21 final size:21
Alignment explanation
Indices: 58997828--58997868 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58997818 CTGCTGTTTT
* *
58997828 TTTTTTATTGTTTTCTTGCTG
1 TTTTTTACTATTTTCTTGCTG
*
58997849 TTTTTTACTATTTTGTTGCT
1 TTTTTTACTATTTTCTTGCT
58997869 ATATATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.10, G:0.12, T:0.71
Consensus pattern (21 bp):
TTTTTTACTATTTTCTTGCTG
Found at i:59011119 original size:3 final size:3
Alignment explanation
Indices: 59011111--59011153 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
59011101 TCTTTTTTAC
59011111 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
59011154 ACCTAAAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:59011399 original size:18 final size:18
Alignment explanation
Indices: 59011359--59011422 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
59011349 TTACTTTCTA
*
59011359 ATATGATTTTAAAATTTT
1 ATATTATTTTAAAATTTT
*
59011377 ATATTATTTTCAAA--TT
1 ATATTATTTTAAAATTTT
*
59011393 AT-TTATTTATAAAATATT
1 ATATTATTT-TAAAATTTT
59011411 AT-TTATTTTAAA
1 ATATTATTTTAAA
59011423 TATGATGTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
15 6 0.15
16 8 0.20
17 4 0.10
18 22 0.55
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
ATATTATTTTAAAATTTT
Found at i:59011400 original size:15 final size:14
Alignment explanation
Indices: 59011375--59011463 Score: 52
Period size: 18 Copynumber: 5.6 Consensus size: 14
59011365 TTTTAAAATT
59011375 TTATATTATTTTCAAA
1 TTAT-TTATTTT-AAA
59011391 TTATTTATTTATAAAATA
1 TTATTTATTT-T--AA-A
59011409 TTATTTATTTTAAA
1 TTATTTATTTTAAA
**
59011423 TATGATGTTCATTTTATT
1 T-T-AT-TT-ATTTTAAA
*
59011441 TTATTTATTTTTAA
1 TTATTTATTTTAAA
*
59011455 GTATTTATT
1 TTATTTATT
59011464 CATCTACTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
14 15 0.25
15 11 0.19
16 9 0.15
17 6 0.10
18 18 0.31
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (14 bp):
TTATTTATTTTAAA
Found at i:59015633 original size:40 final size:40
Alignment explanation
Indices: 59015572--59015808 Score: 152
Period size: 40 Copynumber: 6.0 Consensus size: 40
59015562 CCTTCTAAAA
*
59015572 TGTATGCGCTATTAAGCCATACCTATTGAATCTACTGATT
1 TGTATGCGCTATTAAGCCATACCTACTGAATCTACTGATT
* * * * **
59015612 TGTATGGGCTATTGAGTCATACCTACTGAATTTACTGAAA
1 TGTATGCGCTATTAAGCCATACCTACTGAATCTACTGATT
* * * * * **
59015652 TGTATGTGATATCAAGCCGTACCTACTGATTCTACT-AAG
1 TGTATGCGCTATTAAGCCATACCTACTGAATCTACTGATT
* * * * * * **
59015691 AGTACGCTCTATCAAGCCATACCTATTGAATTTACTGAAA
1 TGTATGCGCTATTAAGCCATACCTACTGAATCTACTGATT
* ** * * * **
59015731 TGTATGCACTATCGAGCCATACCTATTGAATTTACTAAAA
1 TGTATGCGCTATTAAGCCATACCTACTGAATCTACTGATT
* * ** *
59015771 AGTATGCTCTATCGAGCCATACCTACTGATTCTACTGA
1 TGTATGCGCTATTAAGCCATACCTACTGAATCTACTGA
59015809 AAGTTTCTCA
Statistics
Matches: 159, Mismatches: 37, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
39 29 0.18
40 130 0.82
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (40 bp):
TGTATGCGCTATTAAGCCATACCTACTGAATCTACTGATT
Found at i:59015734 original size:79 final size:80
Alignment explanation
Indices: 59015629--59015810 Score: 237
Period size: 79 Copynumber: 2.3 Consensus size: 80
59015619 GCTATTGAGT
* * *
59015629 CATACCTACTGAATTTACTGAAATGTATGTGA-TATCAAGCCGTACCTACTG-ATTCTACT-AAG
1 CATACCTACTGAATTTACTGAAATGTATG-CACTATCAAGCCATACCTACTGAATT-TACTAAAA
59015691 AGTACGCTCTATCAAGC
64 AGTACGCTCTATCAAGC
* * *
59015708 CATACCTATTGAATTTACTGAAATGTATGCACTATCGAGCCATACCTATTGAATTTACTAAAAAG
1 CATACCTACTGAATTTACTGAAATGTATGCACTATCAAGCCATACCTACTGAATTTACTAAAAAG
* *
59015773 TATGCTCTATCGAGC
66 TACGCTCTATCAAGC
59015788 CATACCTACTG-ATTCTACTGAAA
1 CATACCTACTGAATT-TACTGAAA
59015811 GTTTCTCAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 51 0.57
80 38 0.42
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (80 bp):
CATACCTACTGAATTTACTGAAATGTATGCACTATCAAGCCATACCTACTGAATTTACTAAAAAG
TACGCTCTATCAAGC
Found at i:59015796 original size:119 final size:119
Alignment explanation
Indices: 59015580--59015806 Score: 312
Period size: 119 Copynumber: 1.9 Consensus size: 119
59015570 AATGTATGCG
* ** ** * *
59015580 CTATTAAGCCATACCTATTGAATCTACTGATTTGTATGGGCTATTGAGTCATACCTACTGAATTT
1 CTATCAAGCCATACCTATTGAATCTACTGAAATGTATGCACTATCGAGCCATACCTACTGAATTT
* * *
59015645 ACTGAAATGTATGTGATATCAAGCCGTACCTACTGATTCTACTAAGAGTACGCT
66 ACTAAAAAGTATGTGATATCAAGCCATACCTACTGATTCTACTAAGAGTACGCT
* *
59015699 CTATCAAGCCATACCTATTGAATTTACTGAAATGTATGCACTATCGAGCCATACCTATTGAATTT
1 CTATCAAGCCATACCTATTGAATCTACTGAAATGTATGCACTATCGAGCCATACCTACTGAATTT
* *
59015764 ACTAAAAAGTATGCT-CTATCGAGCCATACCTACTGATTCTACT
66 ACTAAAAAGTATG-TGATATCAAGCCATACCTACTGATTCTACT
59015807 GAAAGTTTCT
Statistics
Matches: 93, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
119 92 0.99
120 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (119 bp):
CTATCAAGCCATACCTATTGAATCTACTGAAATGTATGCACTATCGAGCCATACCTACTGAATTT
ACTAAAAAGTATGTGATATCAAGCCATACCTACTGATTCTACTAAGAGTACGCT
Found at i:59024350 original size:26 final size:25
Alignment explanation
Indices: 59024289--59024351 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
59024279 TATTCAGGGC
* * *
59024289 TCCTGATTAATGGCTGTTTGTGAGT
1 TCCTGATTAAAGGCTCTTCGTGAGT
* *
59024314 TTCTAGTTTAAAGGCTCTTCGTGAGCT
1 TCCT-GATTAAAGGCTCTTCGTGAG-T
59024341 TCCTGATTAAA
1 TCCTGATTAAA
59024352 AGTTCTATGT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
25 3 0.10
26 22 0.76
27 4 0.14
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (25 bp):
TCCTGATTAAAGGCTCTTCGTGAGT
Found at i:59027693 original size:27 final size:27
Alignment explanation
Indices: 59027652--59027705 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
59027642 TGTCATGTGA
* *
59027652 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTAATATTACATG
**
59027679 AATTGAATGTTAAATTAATATTACATG
1 AATTGAATGGCAAATTAATATTACATG
59027706 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTAATATTACATG
Found at i:59030482 original size:37 final size:37
Alignment explanation
Indices: 59030429--59030550 Score: 217
Period size: 37 Copynumber: 3.3 Consensus size: 37
59030419 TATAAAAGAA
* *
59030429 GTCTTACCAGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
59030466 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
59030503 GTCTTACCCGGTCATAATCTCCACATGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
59030540 GTCTTACCCGG
1 GTCTTACCCGG
59030551 AACATATTCC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 82 1.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:59030841 original size:27 final size:27
Alignment explanation
Indices: 59030761--59030845 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
59030751 CCATTAGGCC
*
59030761 TCATCACATATACATACACTTTCACAT
1 TCATCACATATACATCCACTTTCACAT
** *** *
59030788 TCATCAC--AT-CGGCCA-TTAGGC-C
1 TCATCACATATACATCCACTTTCACAT
59030810 TCATCACATATACATCCACTTTCACAT
1 TCATCACATATACATCCACTTTCACAT
59030837 TCATCACAT
1 TCATCACAT
59030846 CGGCCATTAG
Statistics
Matches: 40, Mismatches: 13, Indels: 10
0.63 0.21 0.16
Matches are distributed among these distances:
22 7 0.17
23 3 0.08
24 5 0.12
25 6 0.15
26 3 0.08
27 16 0.40
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.31
Consensus pattern (27 bp):
TCATCACATATACATCCACTTTCACAT
Found at i:59031068 original size:49 final size:49
Alignment explanation
Indices: 59030652--59031062 Score: 669
Period size: 49 Copynumber: 8.4 Consensus size: 49
59030642 TTTTGCATTA
59030652 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
59030701 GCCATTAGGCCTTATCACATATACATATACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* *
59030750 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* * *
59030799 GCCATTAGGCCTCATCACATATACATCCACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
59030848 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* * ** *
59030897 ACCATTAGGCCTTATCACATATATACCCACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* *
59030946 GCCATTAGGCTTTATCACATATACATACTCTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* ** *
59030995 GCCATTAGGCCTTATCACATATATACCCACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
59031044 GCCATTAGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
59031063 CATATATGTA
Statistics
Matches: 336, Mismatches: 26, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 336 1.00
ACGTcount: A:0.30, C:0.32, G:0.08, T:0.30
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:59034088 original size:12 final size:12
Alignment explanation
Indices: 59034048--59034081 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
59034038 CAAAACCCTA
*
59034048 TTTTTCCTT-TC
1 TTTTTCTTTCTC
59034059 TTTTTCTTTCTC
1 TTTTTCTTTCTC
59034071 TTTTTCTTTCT
1 TTTTTCTTTCT
59034082 TTCTTTCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCTTTCTC
Found at i:59034187 original size:8 final size:8
Alignment explanation
Indices: 59034151--59034208 Score: 62
Period size: 8 Copynumber: 7.1 Consensus size: 8
59034141 TTATTTTCTT
*
59034151 TATTATTT
1 TATTATTA
59034159 TATTATTA
1 TATTATTA
**
59034167 TAACATATA
1 TATTAT-TA
59034176 TATTATTA
1 TATTATTA
59034184 TATTATTA
1 TATTATTA
*
59034192 AATTATTA
1 TATTATTA
*
59034200 TAATATTA
1 TATTATTA
59034208 T
1 T
59034209 TTCTTATGTA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
8 35 0.85
9 6 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
TATTATTA
Found at i:59036243 original size:19 final size:19
Alignment explanation
Indices: 59036219--59036257 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
59036209 GTATAGGGAC
59036219 TTAGTTTTTCTATGATGGA
1 TTAGTTTTTCTATGATGGA
59036238 TTAGTTTTTCTATGATGGA
1 TTAGTTTTTCTATGATGGA
59036257 T
1 T
59036258 GTTGTTGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.54
Consensus pattern (19 bp):
TTAGTTTTTCTATGATGGA
Found at i:59038020 original size:32 final size:32
Alignment explanation
Indices: 59037953--59038020 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
59037943 ACCTTATTTG
* * *
59037953 TTTTCATATTTGGGAACTAAACAGTCACTTGT
1 TTTTCAGATATGGGAACTAAACAGTCACTTAT
* *
59037985 TTTTCAGATATGGGAACTGAAATAGTGA-TTAT
1 TTTTCAGATATGGGAACT-AAACAGTCACTTAT
59038017 TTTT
1 TTTT
59038021 GGTTTCTCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (32 bp):
TTTTCAGATATGGGAACTAAACAGTCACTTAT
Found at i:59043122 original size:25 final size:25
Alignment explanation
Indices: 59043094--59043142 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
59043084 TTATAATATG
* * *
59043094 AAAAATGACTATTTTGCCCCTAGGT
1 AAAAATGACCATTATACCCCTAGGT
59043119 AAAAATGACCATTATACCCCTAGG
1 AAAAATGACCATTATACCCCTAGG
59043143 GTTTAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (25 bp):
AAAAATGACCATTATACCCCTAGGT
Found at i:59043194 original size:10 final size:10
Alignment explanation
Indices: 59043179--59043216 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
59043169 ATTTTGATAT
59043179 ACATGATTTG
1 ACATGATTTG
59043189 ACATGATTTG
1 ACATGATTTG
*
59043199 ACATGATATG
1 ACATGATTTG
59043209 CACATGAT
1 -ACATGAT
59043217 ATGTATGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 19 0.73
11 7 0.27
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (10 bp):
ACATGATTTG
Found at i:59045398 original size:25 final size:27
Alignment explanation
Indices: 59045361--59045413 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
59045351 TCAAACATGC
59045361 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
59045387 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
59045413 A
1 A
59045414 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:59046921 original size:26 final size:26
Alignment explanation
Indices: 59046891--59046998 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
59046881 TGAAATGCCC
59046891 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
59046917 ATCATGGAATATTAACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
59046943 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
59046969 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
59046995 ATCA
1 ATCA
59046999 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:59052457 original size:25 final size:26
Alignment explanation
Indices: 59052420--59052471 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
59052410 TCAAACATGC
59052420 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* * *
59052446 ATTTCGGT-AATTTATCTCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
59052471 A
1 A
59052472 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:59054003 original size:26 final size:26
Alignment explanation
Indices: 59053947--59054053 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
59053937 TGAAATGCCC
59053947 ATCATGGAACATTTACCTAA-CCATT
1 ATCATGGAACATTTACCTAACCCATT
59053972 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
59053998 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
59054024 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
59054050 ATCA
1 ATCA
59054054 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
25 20 0.26
26 57 0.74
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:59070965 original size:24 final size:21
Alignment explanation
Indices: 59070915--59070965 Score: 57
Period size: 24 Copynumber: 2.3 Consensus size: 21
59070905 TTTCTAACAT
*
59070915 AATTTAGTCTCTATATTTTTA
1 AATTTAGTCTCTATATGTTTA
*
59070936 ATTTTAGTCTCTCTATTATGTTTA
1 AATTTAG--TCTCTA-TATGTTTA
59070960 AATTTA
1 AATTTA
59070966 AAAATTAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 6 0.25
23 6 0.25
24 12 0.50
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (21 bp):
AATTTAGTCTCTATATGTTTA
Found at i:59083762 original size:40 final size:39
Alignment explanation
Indices: 59083713--59083826 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 39
59083703 ATCACGATTT
* *
59083713 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTG
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
* * *
59083753 GCACGAATGCCTTCGGGTGTTAGCCCGGATATAGCTACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
* *
59083793 GCACAATTGCCTTCGGGTCTTAACTCGGATATAA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATATAA
59083827 TTTTCAGCAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.03
40 61 0.97
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
Found at i:59091947 original size:33 final size:33
Alignment explanation
Indices: 59091885--59091948 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
59091875 ACATGCAAAA
* *
59091885 GATGTATCTTTCTATGAGATACCCTTTCATAAG
1 GATGTATCTTTCTATGAGATACACGTTCATAAG
*
59091918 GATGTATCTTT-TAATGAGGTACACGTTCATA
1 GATGTATCTTTCT-ATGAGATACACGTTCATA
59091949 GAATTGTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (33 bp):
GATGTATCTTTCTATGAGATACACGTTCATAAG
Found at i:59093967 original size:9 final size:9
Alignment explanation
Indices: 59093953--59093998 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
59093943 TCATAAACTC
59093953 CATGTAATT
1 CATGTAATT
59093962 CATGTAATT
1 CATGTAATT
59093971 CATGTAACTT
1 CATGTAA-TT
59093981 -A--TAATT
1 CATGTAATT
*
59093987 CATGTAAAT
1 CATGTAATT
59093996 CAT
1 CAT
59093999 ATAGCTCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
6 2 0.06
7 4 0.12
9 24 0.75
10 2 0.06
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (9 bp):
CATGTAATT
Found at i:59094277 original size:23 final size:23
Alignment explanation
Indices: 59094166--59094287 Score: 88
Period size: 23 Copynumber: 5.3 Consensus size: 23
59094156 AAGCTCCTCC
*
59094166 TGAGCTGATAAACAGTAAGCTCCAA
1 TGAGCTG--AAACGGTAAGCTCCAA
* * ***
59094191 AGAGTTG-AACGGTAAGC-CTTG
1 TGAGCTGAAACGGTAAGCTCCAA
**
59094212 TAGAGCTGAAACGGTAAGCTCTTA
1 T-GAGCTGAAACGGTAAGCTCCAA
* *
59094236 CGAGCTGAATCGGTAAGCTCCAA
1 TGAGCTGAAACGGTAAGCTCCAA
*
59094259 TGAGTTGAAACGGTAAGCT-CATA
1 TGAGCTGAAACGGTAAGCTCCA-A
59094282 TGAGCT
1 TGAGCT
59094288 AAGGTGAGTC
Statistics
Matches: 76, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
21 1 0.01
22 16 0.21
23 51 0.67
24 3 0.04
25 5 0.07
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (23 bp):
TGAGCTGAAACGGTAAGCTCCAA
Found at i:59099207 original size:14 final size:14
Alignment explanation
Indices: 59099188--59099237 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
59099178 TAACTTAGGT
59099188 TTAATTTTAGTTAA
1 TTAATTTTAGTTAA
59099202 TTAATTTTA-TT-A
1 TTAATTTTAGTTAA
59099214 TTATTATTTTAGTTTAA
1 TTA--ATTTTAG-TTAA
59099231 TTTAATT
1 -TTAATT
59099238 ATTTATTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
12 4 0.13
13 2 0.07
14 15 0.50
16 5 0.17
17 1 0.03
18 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (14 bp):
TTAATTTTAGTTAA
Found at i:59099243 original size:29 final size:28
Alignment explanation
Indices: 59099191--59099250 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
59099181 CTTAGGTTTA
* *
59099191 ATTTTAGTTAATTAATTTTATTATTATT
1 ATTTTAGTTAATTAATTATATTATTACT
59099219 ATTTTAGTTTAATTTAATTAT-TTATTACT
1 ATTTTAG-TTAA-TTAATTATATTATTACT
59099248 ATT
1 ATT
59099251 GTTTTAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 14 0.50
30 7 0.25
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (28 bp):
ATTTTAGTTAATTAATTATATTATTACT
Found at i:59099256 original size:32 final size:28
Alignment explanation
Indices: 59099191--59099257 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 28
59099181 CTTAGGTTTA
*
59099191 ATTTTAGTTAATTAATTTTATTATTATT
1 ATTTTAGTTAATTAATTTTATTACTATT
59099219 ATTTTAGTTTAATTTAATTATTTATTACTATT
1 ATTTTAG-TTAA-TTAA-T-TTTATTACTATT
*
59099251 GTTTTAG
1 ATTTTAG
59099258 ATATTGCACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 7 0.21
29 4 0.12
30 4 0.12
31 1 0.03
32 17 0.52
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (28 bp):
ATTTTAGTTAATTAATTTTATTACTATT
Found at i:59100250 original size:18 final size:18
Alignment explanation
Indices: 59100209--59100251 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
59100199 TAAATTGGAA
59100209 ATAA-AAATTATTAAAAG
1 ATAATAAATTATTAAAAG
*
59100226 ATGATAAATTATTAAATAG
1 ATAATAAATTATTAAA-AG
59100245 A-AATAAA
1 ATAATAAA
59100252 AATAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 16 0.73
19 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (18 bp):
ATAATAAATTATTAAAAG
Found at i:59123285 original size:48 final size:48
Alignment explanation
Indices: 59123196--59123581 Score: 387
Period size: 48 Copynumber: 8.0 Consensus size: 48
59123186 GATACTAAGG
* * * *
59123196 ATATGTGAGCCAGTGTAAGACCATGTTTGGAACGTGGCATCGGCATTT
1 ATATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCT
* * * * * *
59123244 ATATGAGAGCTAGTGTAAGACTATGTCTGGGACATGTCATCGGCCTCG
1 ATATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCT
* * *
59123292 ATATGTGAGCTAGTGTAAGACCATGTTTGGAACACGGCATCGGCATTT
1 ATATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCT
* * ** * * *
59123340 ATACGAGAGCTAGTGTAAGACCATGTGTGCTACATGGCATCGACCTCG
1 ATATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCT
* * *
59123388 ATATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTT
1 ATATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCT
** * * ** * * *
59123436 ATACAAGAGCTAGCGTAAGACCATGTCTGGGCCATGGCATCAGCCTCA
1 ATATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCT
* * * * *
59123484 ATATGTGGGCTAGTATAAGACCATGTTTGGAACATGGCATCAGCACCGAT
1 ATATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATC--T
* *
59123534 ATATGAGAGCCAGTGTAAGACCATGTCTTGG-ACATGGCATCGACATCT
1 ATATGAGAGCTAGTGTAAGACCATGT-TTGGAACATGGCATCGGCATCT
59123582 TTCCCTTTTG
Statistics
Matches: 265, Mismatches: 70, Indels: 6
0.78 0.21 0.02
Matches are distributed among these distances:
48 226 0.85
50 35 0.13
51 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (48 bp):
ATATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCT
Found at i:59123359 original size:96 final size:96
Alignment explanation
Indices: 59123195--59123575 Score: 528
Period size: 96 Copynumber: 3.9 Consensus size: 96
59123185 TGATACTAAG
* *
59123195 GATATGTGAGCCAGTGTAAGACCATGTTTGGAACGTGGCATCGGCATTTATATGAGAGCTAGTGT
1 GATATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTATACGAGAGCTAGTGT
* *
59123260 AAGACTATGTCTGGGACATGTCATCGGCCTC
66 AAGACCATGTCTGGGACATGGCATCGGCCTC
* *
59123291 GATATGTGAGCTAGTGTAAGACCATGTTTGGAACACGGCATCGGCATTTATACGAGAGCTAGTGT
1 GATATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTATACGAGAGCTAGTGT
* ** *
59123356 AAGACCATGTGTGCTACATGGCATCGACCTC
66 AAGACCATGTCTGGGACATGGCATCGGCCTC
* *
59123387 GATATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTATACAAGAGCTAGCGT
1 GATATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTATACGAGAGCTAGTGT
* *
59123452 AAGACCATGTCTGGGCCATGGCATCAGCCTC
66 AAGACCATGTCTGGGACATGGCATCGGCCTC
* * * * * ** * *
59123483 AATATGTGGGCTAGTATAAGACCATGTTTGGAACATGGCATCAGCACCGATATATGAGAGCCAGT
1 GATATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCA--TTTATACGAGAGCTAGT
*
59123548 GTAAGACCATGTCTTGGACATGGCATCG
64 GTAAGACCATGTCTGGGACATGGCATCG
59123576 ACATCTTTCC
Statistics
Matches: 249, Mismatches: 34, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
96 213 0.86
98 36 0.14
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (96 bp):
GATATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTATACGAGAGCTAGTGT
AAGACCATGTCTGGGACATGGCATCGGCCTC
Found at i:59131840 original size:23 final size:23
Alignment explanation
Indices: 59131814--59131860 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
59131804 TGGGTGCTAG
59131814 GCTCGTACGTCCTACC-AGTGGCT
1 GCTCGTACGTCCTACCGA-TGGCT
59131837 GCTCGTACGTCCTACCGATGGCT
1 GCTCGTACGTCCTACCGATGGCT
59131860 G
1 G
59131861 AGTATACTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.26
Consensus pattern (23 bp):
GCTCGTACGTCCTACCGATGGCT
Found at i:59135904 original size:48 final size:48
Alignment explanation
Indices: 59135827--59135939 Score: 120
Period size: 48 Copynumber: 2.4 Consensus size: 48
59135817 CGATGTCATG
* * *
59135827 TCCCAGACATGGTCTCATACGGGACCTCATATCGATA-CCAATGCCATA
1 TCCCAGATATGGTCTTACACGGGACCTCATATCGA-AGCCAATGCCATA
* * * *
59135875 TCCCAGATATGGTCTTACATGGGATCTCATATTGAAGCTAATGCCATA
1 TCCCAGATATGGTCTTACACGGGACCTCATATCGAAGCCAATGCCATA
** *
59135923 TTTCAAATATGGTCTTA
1 TCCCAGATATGGTCTTA
59135940 TACAGGATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 1 0.02
48 53 0.98
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (48 bp):
TCCCAGATATGGTCTTACACGGGACCTCATATCGAAGCCAATGCCATA
Found at i:59149674 original size:32 final size:32
Alignment explanation
Indices: 59149630--59149694 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
59149620 ATTGGTACTT
*
59149630 TTGAACTTATGGATATATGTAAATATGACATG
1 TTGAACTAATGGATATATGTAAATATGACATG
*
59149662 TTGAACTAATGGATATATGTAAATATGGCATG
1 TTGAACTAATGGATATATGTAAATATGACATG
59149694 T
1 T
59149695 ATAGGCTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (32 bp):
TTGAACTAATGGATATATGTAAATATGACATG
Found at i:59151234 original size:19 final size:19
Alignment explanation
Indices: 59151196--59151234 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
59151186 AACGGACATA
**
59151196 AAAATCTTGACATGGCATG
1 AAAATCTTGACATGAAATG
*
59151215 AAAATCTTGAGATGAAATG
1 AAAATCTTGACATGAAATG
59151234 A
1 A
59151235 TAATGACTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (19 bp):
AAAATCTTGACATGAAATG
Found at i:59158002 original size:2 final size:2
Alignment explanation
Indices: 59157988--59158024 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
59157978 TAAAATACTT
59157988 TA TA TA T- TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59158025 TCAATTGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59170218 original size:22 final size:22
Alignment explanation
Indices: 59170188--59170326 Score: 81
Period size: 22 Copynumber: 6.4 Consensus size: 22
59170178 GAGTATACTC
*
59170188 AAATTAATCCCTCAAGGGATAT
1 AAATAAATCCCTCAAGGGATAT
* * *
59170210 AACTAAATCCC-CTAGGGGATAC
1 AAATAAATCCCTC-AAGGGATAT
** *
59170232 AAAGT-AATCCCTCGTGGTATAT
1 AAA-TAAATCCCTCAAGGGATAT
* * * *
59170254 AACA-CAATCCCTCAAAGCATAC
1 AA-ATAAATCCCTCAAGGGATAT
* *
59170276 GAATTAATCCCTCAAGGGATAT
1 AAATAAATCCCTCAAGGGATAT
*
59170298 AAATTAAT--CTGCAAGGGATAT
1 AAATAAATCCCT-CAAGGGATAT
59170319 AAATAAAT
1 AAATAAAT
59170327 GTTTCATCAC
Statistics
Matches: 89, Mismatches: 21, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
20 2 0.02
21 19 0.21
22 65 0.73
23 3 0.03
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (22 bp):
AAATAAATCCCTCAAGGGATAT
Found at i:59170241 original size:44 final size:44
Alignment explanation
Indices: 59170187--59170299 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 44
59170177 CGAGTATACT
** *
59170187 CAAATTAATCCCTCAAGGGATATAACTA-AATCCC-CTAGGGGATA
1 CAAATTAATCCCTCAAGGGATATAAC-ACAATCCCTC-AAAGCATA
* ** *
59170231 CAAAGTAATCCCTCGTGGTATATAACACAATCCCTCAAAGCATA
1 CAAATTAATCCCTCAAGGGATATAACACAATCCCTCAAAGCATA
*
59170275 CGAATTAATCCCTCAAGGGATATAA
1 CAAATTAATCCCTCAAGGGATATAA
59170300 ATTAATCTGC
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
43 1 0.02
44 53 0.96
45 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (44 bp):
CAAATTAATCCCTCAAGGGATATAACACAATCCCTCAAAGCATA
Found at i:59174570 original size:15 final size:15
Alignment explanation
Indices: 59174550--59174578 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59174540 AGACATAATA
59174550 ATACTAAATATATAC
1 ATACTAAATATATAC
59174565 ATACTAAATATATA
1 ATACTAAATATATA
59174579 TATGCATAAT
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:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
ATACTAAATATATAC
Found at i:59175207 original size:24 final size:23
Alignment explanation
Indices: 59175117--59175234 Score: 68
Period size: 22 Copynumber: 5.1 Consensus size: 23
59175107 AAATATATGC
* *
59175117 ATAAAAATATATATA-TAAGATAGT
1 ATAAAAATATATACACT-A-ATAAT
*
59175141 ATAAAAATATATA-ACT-ATGAT
1 ATAAAAATATATACACTAATAAT
* *
59175162 ACT-AAAGTATATACACGAAATAGTAT
1 A-TAAAAATATATACAC-TAATA--AT
59175188 ATAAAAATATATA-ACTAATAAT
1 ATAAAAATATATACACTAATAAT
* * *
59175210 ATCAAAATATGTACA-TGATAAT
1 ATAAAAATATATACACTAATAAT
59175232 ATA
1 ATA
59175235 TATATAAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 20
0.70 0.10 0.19
Matches are distributed among these distances:
21 13 0.18
22 24 0.32
23 2 0.03
24 20 0.27
25 3 0.04
26 12 0.16
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (23 bp):
ATAAAAATATATACACTAATAAT
Found at i:59175256 original size:24 final size:24
Alignment explanation
Indices: 59175229--59175389 Score: 89
Period size: 24 Copynumber: 6.5 Consensus size: 24
59175219 TGTACATGAT
59175229 AATATATATATA-AAAATATTAGAA
1 AATATATATATATAAAATATTA-AA
* * * *
59175253 AATATATGTACATAATATAATATGAA
1 AATATATATATATAAAAT-AT-TAAA
* *
59175279 AATATATACATAATATAATATT-AA
1 AATATATATAT-ATAAAATATTAAA
* *
59175303 AATATA-ATA-ATACAACATTAAA
1 AATATATATATATAAAATATTAAA
*
59175325 AATATATATGATATATATAATATATAAT
1 AATATATAT-ATATA-A-AATAT-TAAA
* * *
59175353 ATTAAAAGTATATATAACATA-TAAA
1 AAT-ATA-TATATATAAAATATTAAA
59175378 AATATATATATA
1 AATATATATATA
59175390 ATATAATACC
Statistics
Matches: 103, Mismatches: 21, Indels: 27
0.68 0.14 0.18
Matches are distributed among these distances:
21 8 0.08
22 8 0.08
23 10 0.10
24 21 0.20
25 13 0.13
26 14 0.14
27 13 0.13
28 6 0.06
29 7 0.07
30 3 0.03
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (24 bp):
AATATATATATATAAAATATTAAA
Found at i:59175282 original size:13 final size:13
Alignment explanation
Indices: 59175266--59175311 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
59175256 ATATGTACAT
*
59175266 AATATAATATGAA
1 AATATAATATCAA
*
59175279 AATAT-ATA-CAT
1 AATATAATATCAA
*
59175290 AATATAATATTAA
1 AATATAATATCAA
59175303 AATATAATA
1 AATATAATA
59175312 ATACAACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 6 0.22
12 6 0.22
13 15 0.56
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (13 bp):
AATATAATATCAA
Found at i:59175339 original size:55 final size:52
Alignment explanation
Indices: 59175280--59175394 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 52
59175270 TAATATGAAA
59175280 ATATATAC-ATAATATAATATTAAAA-TATAATAATACAACAT-TAAAAATATATAT
1 ATATATACAAT-ATATAATATTAAAAGTAT-AT-AT--AACATATAAAAATATATAT
*
59175334 GATATATATAATATATAATATTAAAAGTATATATAACATATAAAAATATATAT
1 -ATATATACAATATATAATATTAAAAGTATATATAACATATAAAAATATATAT
59175387 ATAATATA
1 AT-ATATA
59175395 ATACCTAAGT
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
52 7 0.13
53 18 0.33
54 2 0.04
55 23 0.42
56 5 0.09
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (52 bp):
ATATATACAATATATAATATTAAAAGTATATATAACATATAAAAATATATAT
Found at i:59175340 original size:9 final size:9
Alignment explanation
Indices: 59175325--59175397 Score: 57
Period size: 9 Copynumber: 8.4 Consensus size: 9
59175315 CAACATTAAA
59175325 AATATATAT
1 AATATATAT
*
59175334 GATATATAT
1 AATATATAT
59175343 -A-ATATAT
1 AATATATAT
*
59175350 AATAT-TAA
1 AATATATAT
59175358 AAGTATATAT
1 AA-TATATAT
*
59175368 AACATATA-
1 AATATATAT
*
59175376 AAAATATAT
1 AATATATAT
59175385 -ATATAATAT
1 AATAT-ATAT
59175394 AATA
1 AATA
59175398 CCTAAGTATA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
7 6 0.12
8 16 0.31
9 22 0.43
10 7 0.14
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (9 bp):
AATATATAT
Found at i:59175354 original size:25 final size:25
Alignment explanation
Indices: 59175229--59175397 Score: 95
Period size: 26 Copynumber: 6.8 Consensus size: 25
59175219 TGTACATGAT
* * * *
59175229 AATATATATATAAAAATATTAGA-A
1 AATATATATATATATATAATATATA
* *
59175253 AATATATGTACATAATATAATATGA-A
1 AATATATATATAT-ATATAATAT-ATA
*
59175279 AATATATACATA-ATATAATAT-TA
1 AATATATATATATATATAATATATA
* * *
59175302 AA-ATATA-ATA-ATACAACATTAAA
1 AATATATATATATATATAATA-TATA
59175325 AATATATATGATATATATAATATAT-
1 AATATATAT-ATATATATAATATATA
* *
59175350 AATAT-TAAAAGTATATATAACATATA
1 AATATAT-ATA-TATATATAATATATA
*
59175376 AAAATATATATATAATATAATA
1 AATATATATATAT-ATATAATA
59175398 CCTAAGTATA
Statistics
Matches: 111, Mismatches: 20, Indels: 26
0.71 0.13 0.17
Matches are distributed among these distances:
21 9 0.08
22 6 0.05
23 6 0.05
24 26 0.23
25 28 0.25
26 29 0.26
27 7 0.06
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (25 bp):
AATATATATATATATATAATATATA
Found at i:59175365 original size:34 final size:34
Alignment explanation
Indices: 59175304--59175385 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
59175294 TAATATTAAA
* * *
59175304 ATATAATAATACAACATTAAAAATATATATGATAT
1 ATATAAT-ATATAACATTAAAAATATATATAACAT
* *
59175339 ATATAATATATAATATTAAAAGTATATATAACAT
1 ATATAATATATAACATTAAAAATATATATAACAT
*
59175373 ATAAAAATATATA
1 AT-ATAATATATA
59175386 TATAATATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
34 24 0.60
35 16 0.40
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (34 bp):
ATATAATATATAACATTAAAAATATATATAACAT
Found at i:59175428 original size:53 final size:53
Alignment explanation
Indices: 59175316--59175431 Score: 134
Period size: 52 Copynumber: 2.2 Consensus size: 53
59175306 ATAATAATAC
* *
59175316 AACAT-TAAAAATATATATGATATATATAATATATAATATTAAAAGTATATAT
1 AACATATAAAAATATATATGATATATATAATACATAATATTAAAAGTACATAT
* *
59175368 AACATATAAAAATATATAT-ATA-ATATAATACCTAAGTA-TACTAAGTACATAT
1 AACATATAAAAATATATATGATATATATAATACATAA-TATTA-AAAGTACATAT
59175420 -ACATATATAAAA
1 AACATATA-AAAA
59175432 GATCCTATAC
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
51 20 0.36
52 23 0.41
53 13 0.23
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.34
Consensus pattern (53 bp):
AACATATAAAAATATATATGATATATATAATACATAATATTAAAAGTACATAT
Found at i:59176894 original size:81 final size:83
Alignment explanation
Indices: 59176798--59177357 Score: 408
Period size: 81 Copynumber: 6.5 Consensus size: 83
59176788 ACGCGTCCTG
* * * *
59176798 AGGCCCAACTCACCTCTCGTAATATGAGTTAATTTTTGAAAA-TAGAAATTGAAAAC-TGAAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATTAAAAACATGAAAAT
* *
59176861 GCCTCGGCATGTGAGCCA
66 ACCTCAGCATGTGAGCCA
* * *
59176879 AGGCTTAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAGCAGAAATTAAAAAACAGGAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATT-AAAAAC----A-T
* * * *
59176944 GAAATTACCTCAGCTTATGA-CCTG
60 GAAAATACCTCAGCATGTGAGCC-A
*
59176968 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAGAAATAGAAATTGAAAAACAGAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAA-AAGTAGAAATT-AAAAAC---A-
* *
59177033 TTTGAAAATACCTCGGCATGTG-GCTCG
59 --TGAAAATACCTCAGCATGTGAGC-CA
* * * *
59177060 AGGCTCAACTCATCTCTCGCAATATGAATTGATTTTTGAAAAGTATAAA-TAAAAA-TTGAAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATTAAAAACATGAAAAT
*
59177123 GCCTCAGCATGTGAGCCA
66 ACCTCAGCATGTGAGCCA
* * *
59177141 AGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGAAAAGCA-AAGATTGAAAAGCAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAGTAGAA-ATT---AA--AAAC
* * *
59177205 ATGAAAATTCCTCAGC--GTG-CCCTG
58 ATGAAAATACCTCAGCATGTGAGCC-A
* *
59177229 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATT-AAAAAC----A-T
* * *
59177294 GAAAATACCTCA--ACGT-ATCCTG
60 GAAAATACCTCAGCATGTGAGCC-A
** * *
59177316 AGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
59177358 ATAAGAACAT
Statistics
Matches: 397, Mismatches: 46, Indels: 66
0.78 0.09 0.13
Matches are distributed among these distances:
81 89 0.22
82 14 0.04
83 18 0.05
84 3 0.01
86 15 0.04
87 62 0.16
88 41 0.10
89 55 0.14
90 27 0.07
91 18 0.05
92 54 0.14
93 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (83 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATTAAAAACATGAAAAT
ACCTCAGCATGTGAGCCA
Found at i:59177150 original size:173 final size:171
Alignment explanation
Indices: 59176534--59177357 Score: 583
Period size: 173 Copynumber: 4.8 Consensus size: 171
59176524 AGCATGTGAT
** * * * * * *
59176534 CCTGAGGCTCAACTCATTTCTCGCAATATGAATTGACTCTTTAAAACAGACATTAAAAATATAAA
1 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAA-AGATA-TAAATA-ACAAA
* * * *
59176599 TTGAAAATAACTCAGCACGTGAGCC-AAGGCTCAACTCATCTCTCGCAATGTGAGTTGGTTTTTG
62 TTGAAAATACCTCAGCACGTGAGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* * * * * *
59176663 AAACT-TAATTTGGAAAGCAGATTTTGAAAATA-CT--GCAGTGTGC
127 AAAATAGAAATTGAAAAACA-A-TTTGAAAATACCTCGGCAGTGAGC
* *
59176706 CCTGAGGCTCAACTCACCTCTCGAAATATGAGTTGAGTTTTG-AAAGATATAAATTGAAAAAACA
1 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGATATAAA-T-----AAC-
* * * * * *
59176770 GAAATTGAAAATACCTCA--ACGCG-TCCTGAGGCCCAACTCACCTCTCGTAATATGAGTTAATT
59 -AAATTGAAAATACCTCAGCACGTGAGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
*
59176832 TTTGAAAATAGAAATTG-AAAAC----TGAAAATGCCTCGGCATGTGAG-
123 TTTGAAAATAGAAATTGAAAAACAATTTGAAAATACCTCGGCA-GTGAGC
* * * * *
59176876 CC-AAGGCTTAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAGCAGAAATTAAAAAACAGG
1 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAA--AGATA-TAAATAACA--
* *** *
59176940 AATTGAAATTACCTCAGCTTATGA-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
60 AATTGAAAATACCTCAGCACGTGAGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
59177004 TGGAAGAAATAGAAATTGAAAAACAGAATTTTGAAAATACCTCGGCATGTG-GC
125 T-G-A-AAATAGAAATTGAAAAAC--AA-TTTGAAAATACCTCGGCA-GTGAGC
* * *
59177057 TC-GAGGCTCAACTCATCTCTCGCAATATGAATTGATTTTTGAAAAG-TATAAATAA-AAATTGA
1 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGATATAAATAACAAATTGA
* * *
59177119 AAATGCCTCAGCATGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGAA
66 AAATACCTCAGCACGTGAGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAA
* * ** * *
59177183 AAGCA-AAGATTGAAAAGCAAAAATGAAAATTCCTCAGC-GT--GC
129 AA-TAGAA-ATTGAAAAAC-AATTTGAAAATACCTCGGCAGTGAGC
59177225 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-ATATAAATTGAAAAACAG
1 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGATATAAA-T----AAC--
* * ** * *
59177289 AAATTGAAAATACCTCA--ACGT-ATCCTGAGGCTCAACTCATTTCTCACAATATGAGTTGAATT
59 AAATTGAAAATACCTCAGCACGTGAGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
59177351 TTGAAAA
124 TTGAAAA
59177358 ATAAGAACAT
Statistics
Matches: 526, Mismatches: 74, Indels: 103
0.75 0.11 0.15
Matches are distributed among these distances:
166 1 0.00
167 7 0.01
168 27 0.05
169 88 0.17
170 47 0.09
171 23 0.04
172 42 0.08
173 132 0.25
174 23 0.04
175 53 0.10
176 6 0.01
177 17 0.03
178 2 0.00
180 4 0.01
181 54 0.10
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (171 bp):
CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGATATAAATAACAAATTGA
AAATACCTCAGCACGTGAGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
TAGAAATTGAAAAACAATTTGAAAATACCTCGGCAGTGAGC
Found at i:59177211 original size:13 final size:14
Alignment explanation
Indices: 59177179--59177211 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
59177169 TTGATTTTTT
*
59177179 TGAAAAGCAAAGAT
1 TGAAAAGCAAAGAA
59177193 TGAAAAGCAAA-AA
1 TGAAAAGCAAAGAA
59177206 TGAAAA
1 TGAAAA
59177212 TTCCTCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.64, C:0.06, G:0.18, T:0.12
Consensus pattern (14 bp):
TGAAAAGCAAAGAA
Found at i:59177283 original size:14 final size:14
Alignment explanation
Indices: 59177264--59177298 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
59177254 GAGTTGATTT
* *
59177264 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
59177278 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
59177292 TTGAAAA
1 TTGAAAA
59177299 TACCTCAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.23
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:59177326 original size:87 final size:87
Alignment explanation
Indices: 59176879--59177360 Score: 464
Period size: 87 Copynumber: 5.5 Consensus size: 87
59176869 ATGTGAGCCA
* * ** * *
59176879 AGGCTTAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAGCAGAAATTAAAAAACAGGAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAACAGAAATT
* *
59176944 GAAATTACCTCAGCTTATGACCTG
66 GAAAATACCTCAGCGTAT--CCTG
59176968 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAGAAATAGAAATTGAAAAACAGAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAA-AAATAGAAATTGAAAAACAGAA-
* * * * *
59177033 TTTGAAAATACCTCGGCATGTGGCTCG
63 ATTGAAAATACCTCAGCGTAT-CCT-G
* * * *
59177060 AGGCTCAACTCATCTCTCGCAATATGAATTGATTTTTG--AAA-AG-TA-T-AAATA-A-AAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAACAGAAATT
* * *
59177117 GAAAATGCCTCAGCATGTGAGCC-A
66 GAAAATACCTCAGC--GT-ATCCTG
* ** *
59177141 AGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGAAAAGCA-AAGATTGAAAAGCA-AA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATAGAA-ATTGAAAAACAGAA
* * **
59177204 AATGAAAATTCCTCAGCGTGCCCTG
63 ATTGAAAATACCTCAGCGTATCCTG
*
59177229 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAACAGAAATT
*
59177294 GAAAATACCTCAACGTATCCTG
66 GAAAATACCTCAGCGTATCCTG
** * *
59177316 AGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTGAAAAATA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATA
59177361 AGAACATCAA
Statistics
Matches: 325, Mismatches: 48, Indels: 42
0.78 0.12 0.10
Matches are distributed among these distances:
81 45 0.14
82 2 0.01
83 9 0.03
84 4 0.01
85 3 0.01
86 23 0.07
87 70 0.22
88 37 0.11
89 38 0.12
90 21 0.06
91 21 0.06
92 52 0.16
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (87 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAACAGAAATT
GAAAATACCTCAGCGTATCCTG
Found at i:59178219 original size:41 final size:42
Alignment explanation
Indices: 59178160--59178239 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 42
59178150 TGTGTTAATC
59178160 AAGACGCCCTTTTCGGGTTTTCACCTTGA-TCCTTTTTTTTT
1 AAGACGCCCTTTTCGGGTTTTCACCTTGATTCCTTTTTTTTT
* * * *
59178201 AAGATGCCCTTTTTGGGTTTTCATCTTGATTTCTTTTTT
1 AAGACGCCCTTTTCGGGTTTTCACCTTGATTCCTTTTTT
59178240 AAACATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 26 0.76
42 8 0.24
ACGTcount: A:0.12, C:0.20, G:0.15, T:0.53
Consensus pattern (42 bp):
AAGACGCCCTTTTCGGGTTTTCACCTTGATTCCTTTTTTTTT
Found at i:59197966 original size:27 final size:26
Alignment explanation
Indices: 59197936--59197992 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
59197926 TAATGGTATT
*
59197936 AAAAGGATAGATATATAATATAATATGA
1 AAAAGG-TAGATACATAATAT-ATATGA
* *
59197964 AAAATGTATATACATAATATATATGA
1 AAAAGGTAGATACATAATATATATGA
59197990 AAA
1 AAA
59197993 CGTAATATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 9 0.35
27 12 0.46
28 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.30
Consensus pattern (26 bp):
AAAAGGTAGATACATAATATATATGA
Found at i:59198000 original size:26 final size:27
Alignment explanation
Indices: 59197950--59198001 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
59197940 GGATAGATAT
*
59197950 ATAATATAATATGAAAAATGTATATAC
1 ATAATATAATATGAAAAACGTATATAC
59197977 ATAATAT-ATATG-AAAACGTAATATA
1 ATAATATAATATGAAAAACGT-ATATA
59198002 GTATTAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
26 10 0.43
27 7 0.30
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.33
Consensus pattern (27 bp):
ATAATATAATATGAAAAACGTATATAC
Found at i:59198179 original size:2 final size:2
Alignment explanation
Indices: 59198174--59198200 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59198164 ACACACACAG
59198174 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
59198201 AACATAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59198557 original size:29 final size:31
Alignment explanation
Indices: 59198481--59198564 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 31
59198471 TACTAAATAT
** * *
59198481 ATATATATGCATAATATAAATAAACATATACA
1 ATATATATTAATAATATTAAT-AACATAGACA
**
59198513 ATATATATTAGGAATATTAATAACATAGA-A
1 ATATATATTAATAATATTAATAACATAGACA
*
59198543 A-ATATATTAATAATAATAATAA
1 ATATATATTAATAATATTAATAA
59198565 ACAAATATAT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
29 18 0.42
30 2 0.05
31 7 0.16
32 16 0.37
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (31 bp):
ATATATATTAATAATATTAATAACATAGACA
Found at i:59199107 original size:47 final size:48
Alignment explanation
Indices: 59199044--59199159 Score: 141
Period size: 48 Copynumber: 2.4 Consensus size: 48
59199034 AAATATATAT
* * * *
59199044 ATAAGATAGTATAAAAATATATAACT-ATGATA-CTAAAGTATATACACG
1 ATAATATA-TATAAAAATATATAACTAATAATATC-AAAATATATACAAG
59199092 A-AATAGTATATAAAAATATATAACTAATAATATCAAAATATATACAAG
1 ATAATA-TATATAAAAATATATAACTAATAATATCAAAATATATACAAG
59199140 ATAATATATATAAAAA-ATAT
1 ATAATATATATAAAAATATAT
59199160 TAGAAAATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
47 24 0.40
48 31 0.52
49 5 0.08
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (48 bp):
ATAATATATATAAAAATATATAACTAATAATATCAAAATATATACAAG
Found at i:59199120 original size:24 final size:23
Alignment explanation
Indices: 59199030--59199159 Score: 74
Period size: 24 Copynumber: 5.5 Consensus size: 23
59199020 AAATATATGC
* *
59199030 ATAAAAATATATATA-TAAGATAGT
1 ATAAAAATATATACACT-A-ATAAT
*
59199054 ATAAAAATATATA-ACT-ATGAT
1 ATAAAAATATATACACTAATAAT
* *
59199075 ACT-AAAGTATATACACGAAATAGTAT
1 A-TAAAAATATATACAC-TAATA--AT
59199101 ATAAAAATATATA-ACTAATAAT
1 ATAAAAATATATACACTAATAAT
* *
59199123 ATCAAAATATATACAAGATAATATAT
1 ATAAAAATATATAC-A-CTAATA-AT
59199149 ATAAAAA-ATAT
1 ATAAAAATATAT
59199160 TAGAAAATAT
Statistics
Matches: 84, Mismatches: 10, Indels: 23
0.72 0.09 0.20
Matches are distributed among these distances:
21 13 0.15
22 17 0.20
23 1 0.01
24 21 0.25
25 12 0.14
26 20 0.24
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (23 bp):
ATAAAAATATATACACTAATAAT
Found at i:59199143 original size:22 final size:22
Alignment explanation
Indices: 59199030--59199147 Score: 80
Period size: 22 Copynumber: 5.1 Consensus size: 22
59199020 AAATATATGC
* *
59199030 ATAAAAATATATATATAAGATAGT
1 ATAAAAATATATA-ACAA-ATAAT
* *
59199054 ATAAAAATATATAAC-TATGAT
1 ATAAAAATATATAACAAATAAT
*
59199075 ACT-AAAGTATATACACGAAATAGTAT
1 A-TAAAAATATATA-AC-AAATA--AT
*
59199101 ATAAAAATATATAACTAATAAT
1 ATAAAAATATATAACAAATAAT
*
59199123 ATCAAAATATAT-ACAAGATAAT
1 ATAAAAATATATAACAA-ATAAT
59199145 ATA
1 ATA
59199148 TATAAAAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
21 16 0.22
22 23 0.31
23 1 0.01
24 19 0.26
25 3 0.04
26 12 0.16
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
ATAAAAATATATAACAAATAAT
Found at i:59199226 original size:21 final size:22
Alignment explanation
Indices: 59199173--59199237 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
59199163 AAAATATGTG
* *
59199173 TACATAATATAATATGAAAATATA
1 TACATAATATAATAT-TAAA-ACA
59199197 TACATAATATAATATTAAAACA
1 TACATAATATAATATTAAAACA
* *
59199219 TA-ATAATACAACATTAAAA
1 TACATAATATAATATTAAAA
59199238 TATATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 15 0.41
22 4 0.11
23 3 0.08
24 15 0.41
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATATAATATTAAAACA
Found at i:59199244 original size:2 final size:2
Alignment explanation
Indices: 59199237--59199309 Score: 50
Period size: 2 Copynumber: 38.5 Consensus size: 2
59199227 CAACATTAAA
*
59199237 AT AT AT AT AT AT GAT AT AT AT A- AT AT AT A- AT AT -T A- AA AGT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
59199277 AT AT AT A- AC AT AT AA AA AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59199310 ATACCTAAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
1 6 0.10
2 50 0.85
3 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (2 bp):
AT
Found at i:59199255 original size:9 final size:8
Alignment explanation
Indices: 59199237--59199309 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 8
59199227 CAACATTAAA
59199237 ATATATAT
1 ATATATAT
59199245 ATATGATAT
1 ATAT-ATAT
59199254 ATATA-AT
1 ATATATAT
59199261 ATATA-AT
1 ATATATAT
*
59199268 AT-TA-AA
1 ATATATAT
59199274 AGTATATAT
1 A-TATATAT
*
59199283 A-ACATAT
1 ATATATAT
* *
59199290 AAAAATAT
1 ATATATAT
59199298 ATATATA-
1 ATATATAT
59199305 ATATA
1 ATATA
59199310 ATACCTAAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
6 4 0.07
7 23 0.43
8 17 0.31
9 10 0.19
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (8 bp):
ATATATAT
Found at i:59208442 original size:20 final size:20
Alignment explanation
Indices: 59208419--59208466 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
59208409 TGCTATGTTT
59208419 TGTTCTGTT-TAGTTTTGCTC
1 TGTTCTGTTCTA-TTTTGCTC
*
59208439 TGTTCTGTTCTATTTTGCTT
1 TGTTCTGTTCTATTTTGCTC
59208459 TGTTCTGT
1 TGTTCTGT
59208467 CATGTTCTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.04, C:0.15, G:0.19, T:0.62
Consensus pattern (20 bp):
TGTTCTGTTCTATTTTGCTC
Found at i:59208460 original size:25 final size:25
Alignment explanation
Indices: 59208409--59208474 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
59208399 AGTTCTCCTC
* * * *
59208409 TGCTATGTTTTGTTCTGTTTAGTTT
1 TGCTCTGTTCTGTTCTATTTAGCTT
*
59208434 TGCTCTGTTCTGTTCTATTTTGCTT
1 TGCTCTGTTCTGTTCTATTTAGCTT
*
59208459 TGTTCTG-TCATGTTCT
1 TGCTCTGTTC-TGTTCT
59208475 GCTCTGTCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 2 0.06
25 32 0.94
ACGTcount: A:0.06, C:0.15, G:0.18, T:0.61
Consensus pattern (25 bp):
TGCTCTGTTCTGTTCTATTTAGCTT
Found at i:59210706 original size:29 final size:29
Alignment explanation
Indices: 59210664--59210878 Score: 215
Period size: 29 Copynumber: 7.4 Consensus size: 29
59210654 ACCTCAGATA
* *
59210664 ATGAAAAAGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGACTATCGAAT
*
59210693 ATGAAAAGGGATAGCTTCGACTATCGACT
1 ATGAAAAGGGATAGCTTCGACTATCGAAT
*
59210722 ATGAAAAGGGATAGCTTC-AGCTATCGATT
1 ATGAAAAGGGATAGCTTCGA-CTATCGAAT
* * * *
59210751 ACGAAAAGGGAT-GGTGACGACCATC-AACT
1 ATGAAAAGGGATAGCT-TCGACTATCGAA-T
* * * *
59210780 ATGAAAAGGGAT-GGTGACGACCATTGAAT
1 ATGAAAAGGGATAGCT-TCGACTATCGAAT
*
59210809 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGACTATCGAAT
*
59210838 GTGAAAAGGGATAGCTTCGACTATC-AATT
1 ATGAAAAGGGATAGCTTCGACTATCGAA-T
*
59210867 ATGAAAAAGGAT
1 ATGAAAAGGGAT
59210879 GATGACGACC
Statistics
Matches: 159, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
28 6 0.04
29 148 0.93
30 5 0.03
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGACTATCGAAT
Found at i:59221175 original size:19 final size:19
Alignment explanation
Indices: 59221133--59221175 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
59221123 TAATTATTTA
59221133 TTAAATTTAATTAGAATAT
1 TTAAATTTAATTAGAATAT
* *
59221152 ATAAATTATATTTA-AATAT
1 TTAAATT-TAATTAGAATAT
59221171 TTAAA
1 TTAAA
59221176 AATAATCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TTAAATTTAATTAGAATAT
Found at i:59222495 original size:30 final size:30
Alignment explanation
Indices: 59222459--59222516 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
59222449 CGGGTGCAAT
59222459 TTAGATCAATGGCCATCCTTGAAACTTTAA
1 TTAGATCAATGGCCATCCTTGAAACTTTAA
59222489 TTAGATCAATGGCCATCCTTGAAACTTT
1 TTAGATCAATGGCCATCCTTGAAACTTT
59222517 CTCAAGCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (30 bp):
TTAGATCAATGGCCATCCTTGAAACTTTAA
Found at i:59223131 original size:72 final size:72
Alignment explanation
Indices: 59222991--59223227 Score: 370
Period size: 72 Copynumber: 3.3 Consensus size: 72
59222981 AATCATATAA
** * *
59222991 AAACAACTATTGATAAAACTA-ATTTA-GTATACATAAGTAGAACATAAATTTAATATCCAAAAA
1 AAACAACTATTGATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATCCAAAAA
*
59223054 TCAAACAT
65 CCAAACAT
* *
59223062 AAACAACTATTGATAAAACTAGATTACACATAAATAAGTAAAATATAAATTCAATATCCAAAAAC
1 AAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAAAC
59223127 CAAACAT
66 CAAACAT
*
59223134 AAACAACCATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAAAC
1 AAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAAAC
59223199 CAAACAT
66 CAAACAT
*
59223206 AAATAACTATTGATAAAACTAG
1 AAACAACTATTGATAAAACTAG
59223228 TTTAGCATTG
Statistics
Matches: 152, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
71 24 0.16
72 128 0.84
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.24
Consensus pattern (72 bp):
AAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAAAC
CAAACAT
Found at i:59223680 original size:18 final size:18
Alignment explanation
Indices: 59223653--59223722 Score: 104
Period size: 18 Copynumber: 3.9 Consensus size: 18
59223643 TGTTTCTATC
*
59223653 AATGTAAACATCATTTGA
1 AATGTGAACATCATTTGA
59223671 AATGTGAACATCATTTGA
1 AATGTGAACATCATTTGA
* * *
59223689 AATCTGGACATCATTTAA
1 AATGTGAACATCATTTGA
59223707 AATGTGAACATCATTT
1 AATGTGAACATCATTT
59223723 CTCACATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (18 bp):
AATGTGAACATCATTTGA
Found at i:59224845 original size:10 final size:11
Alignment explanation
Indices: 59224821--59224860 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
59224811 AGGGAAGTCT
59224821 ATTTATTTCCC
1 ATTTATTTCCC
*
59224832 ATTTA-TTCCT
1 ATTTATTTCCC
59224842 ATTTATTTCCC
1 ATTTATTTCCC
59224853 ATTTATTT
1 ATTTATTT
59224861 TAAATTTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTATTTCCC
Found at i:59224845 original size:21 final size:21
Alignment explanation
Indices: 59224819--59224859 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
59224809 ACAGGGAAGT
59224819 CTATTTATTTCCCATTTATTC
1 CTATTTATTTCCCATTTATTC
59224840 CTATTTATTTCCCATTTATT
1 CTATTTATTTCCCATTTATT
59224860 TTAAATTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.22, G:0.00, T:0.59
Consensus pattern (21 bp):
CTATTTATTTCCCATTTATTC
Found at i:59227315 original size:10 final size:10
Alignment explanation
Indices: 59227300--59227344 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
59227290 AATTTTATCT
*
59227300 TTTATCTTCA
1 TTTATCTTTA
59227310 TTTATCTTTA
1 TTTATCTTTA
*
59227320 ATTATCTTTA
1 TTTATCTTTA
59227330 TTTAT-TTGTA
1 TTTATCTT-TA
59227340 TTTAT
1 TTTAT
59227345 ATTTTAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
9 2 0.06
10 29 0.94
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:59231053 original size:7 final size:7
Alignment explanation
Indices: 59231043--59231156 Score: 102
Period size: 7 Copynumber: 14.4 Consensus size: 7
59231033 TTCTTTTTCT
*
59231043 TTTATTG
1 TTTATTA
59231050 TTTATTA
1 TTTATTA
59231057 TTTATTA
1 TTTATTA
59231064 TTTATTA
1 TTTATTA
59231071 CTTTATTA
1 -TTTATTA
59231079 CTTTATTTTA
1 -TTTA--TTA
59231089 TTTTATTA
1 -TTTATTA
59231097 TTTATTA
1 TTTATTA
59231104 CTTTATTTTA
1 -TTTA--TTA
59231114 TTTTATTA
1 -TTTATTA
59231122 TTTATTA
1 TTTATTA
59231129 CTTTATTTTA
1 -TTTA--TTA
59231139 TTTTATTA
1 -TTTATTA
59231147 TTTATTA
1 TTTATTA
59231154 TTT
1 TTT
59231157 TATTTTGTTT
Statistics
Matches: 94, Mismatches: 4, Indels: 18
0.81 0.03 0.16
Matches are distributed among these distances:
7 44 0.47
8 29 0.31
10 21 0.22
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:59231090 original size:5 final size:5
Alignment explanation
Indices: 59231080--59231162 Score: 73
Period size: 5 Copynumber: 16.6 Consensus size: 5
59231070 ACTTTATTAC
* * * *
59231080 TTTAT TTTAT TTTAT TATT-T ATTAC TTTAT TTTAT TTTAT TATT-T ATTAC
1 TTTAT TTTAT TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT T-TTAT TTTAT
*
59231130 TTTAT TTTAT TTTAT TATT-T ATTAT TTTAT TTT
1 TTTAT TTTAT TTTAT T-TTAT TTTAT TTTAT TTT
59231163 GTTTGGTTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
4 6 0.10
5 50 0.81
6 6 0.10
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:59231126 original size:50 final size:49
Alignment explanation
Indices: 59231037--59231162 Score: 186
Period size: 50 Copynumber: 2.6 Consensus size: 49
59231027 TTTTTTTTCT
* *
59231037 TTTTCTTTTATTGTTTATTATTTA--TTATTTATTACTTTATTACTTTA
1 TTTTATTTTATTATTTATTATTTATTTTATTTATTACTTTATTACTTTA
59231084 TTTTATTTTATTATTTATTACTTTATTTTATTTTATTA-TTTATTACTTTA
1 TTTTATTTTATTATTTATTA-TTTATTTTA-TTTATTACTTTATTACTTTA
59231134 TTTTATTTTATTATTTATTATTTTATTTT
1 TTTTATTTTATTATTTATTA-TTTATTTT
59231163 GTTTGGTTAT
Statistics
Matches: 72, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
47 18 0.25
48 4 0.06
50 43 0.60
51 7 0.10
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (49 bp):
TTTTATTTTATTATTTATTATTTATTTTATTTATTACTTTATTACTTTA
Found at i:59231160 original size:33 final size:30
Alignment explanation
Indices: 59231057--59231156 Score: 120
Period size: 25 Copynumber: 3.3 Consensus size: 30
59231047 TTGTTTATTA
59231057 TTTATTATTTATTACTTTATTACTTTATTTTAT
1 TTTATTATTTATTACTTTA-T--TTTATTTTAT
59231090 TTTATTATTTATTAC-----TTTATTTTAT
1 TTTATTATTTATTACTTTATTTTATTTTAT
59231115 TTTATTATTTATTACTTTATTTTATTTTATT
1 TTTATTATTTATTACTTTATTTTATTTTA-T
59231146 ATTTATTATTT
1 -TTTATTATTT
59231157 TATTTTGTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 15
0.80 0.00 0.20
Matches are distributed among these distances:
25 25 0.42
30 9 0.15
31 1 0.02
32 10 0.17
33 15 0.25
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (30 bp):
TTTATTATTTATTACTTTATTTTATTTTAT
Found at i:59231173 original size:25 final size:25
Alignment explanation
Indices: 59231080--59231162 Score: 157
Period size: 25 Copynumber: 3.3 Consensus size: 25
59231070 ACTTTATTAC
59231080 TTTATTTTATTTTATTATTTATTAC
1 TTTATTTTATTTTATTATTTATTAC
59231105 TTTATTTTATTTTATTATTTATTAC
1 TTTATTTTATTTTATTATTTATTAC
*
59231130 TTTATTTTATTTTATTATTTATTAT
1 TTTATTTTATTTTATTATTTATTAC
59231155 TTTATTTT
1 TTTATTTT
59231163 GTTTGGTTAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTATTTTATTTTATTATTTATTAC
Found at i:59231935 original size:15 final size:15
Alignment explanation
Indices: 59231904--59231932 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59231894 TGTCTACTGA
59231904 GTTAATTATGATTTT
1 GTTAATTATGATTTT
59231919 GTTAATT-TGATTTT
1 GTTAATTATGATTTT
59231933 TGTCTCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (15 bp):
GTTAATTATGATTTT
Found at i:59233150 original size:10 final size:10
Alignment explanation
Indices: 59233135--59233182 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
59233125 ATTTTAGCTA
*
59233135 TTATCTTCAT
1 TTATCTTTAT
*
59233145 TTATCTTTAA
1 TTATCTTTAT
59233155 TTATCTTTAT
1 TTATCTTTAT
59233165 TTAT-TTGTAT
1 TTATCTT-TAT
59233175 TTATCTTT
1 TTATCTTT
59233183 TAGAATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 2 0.06
10 29 0.88
11 2 0.06
ACGTcount: A:0.21, C:0.10, G:0.02, T:0.67
Consensus pattern (10 bp):
TTATCTTTAT
Found at i:59234439 original size:16 final size:16
Alignment explanation
Indices: 59234418--59234464 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
59234408 ATGGAATGCC
59234418 CTATTATGGGTTTATT
1 CTATTATGGGTTTATT
59234434 CTATTATGGGTTTATT
1 CTATTATGGGTTTATT
*
59234450 CTATTATGGGCTTAT
1 CTATTATGGGTTTAT
59234465 GCATGAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.19, C:0.09, G:0.19, T:0.53
Consensus pattern (16 bp):
CTATTATGGGTTTATT
Found at i:59234709 original size:39 final size:39
Alignment explanation
Indices: 59234653--59234727 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
59234643 TAGGTAAACA
* *
59234653 TTTTCTCCCTCTGTTCTTTTCAT-TTTCCTCTTTTTCATT
1 TTTTCTCCCTATGTTCTTTGC-TCTTTCCTCTTTTTCATT
*
59234692 TTTTCTGCCCTAT-TTCTTTGCTCTTTGCTCTTTTTC
1 TTTTCT-CCCTATGTTCTTTGCTCTTTCCTCTTTTTC
59234728 TTCTTTGCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
38 1 0.03
39 25 0.81
40 5 0.16
ACGTcount: A:0.04, C:0.28, G:0.05, T:0.63
Consensus pattern (39 bp):
TTTTCTCCCTATGTTCTTTGCTCTTTCCTCTTTTTCATT
Found at i:59234748 original size:16 final size:16
Alignment explanation
Indices: 59234704--59234748 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
59234694 TTCTGCCCTA
59234704 TTTCTTTGCTCTTTGCT
1 TTTCTTT-CTCTTTGCT
*
59234721 CTT-TTTCTTCTTTGCT
1 TTTCTTTC-TCTTTGCT
59234737 TTTCTTTCTCTT
1 TTTCTTTCTCTT
59234749 AGTAGAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.00, C:0.24, G:0.07, T:0.69
Consensus pattern (16 bp):
TTTCTTTCTCTTTGCT
Found at i:59236723 original size:30 final size:30
Alignment explanation
Indices: 59236689--59236746 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
59236679 TTTTCGAGCA
* *
59236689 TAGGGGTAAAATGGTCATTTTGCCAAAGTC
1 TAGGGGCAAAATGGTCATTTTACCAAAGTC
59236719 TAGGGGCAAAATGGTCATTTTACCAAAG
1 TAGGGGCAAAATGGTCATTTTACCAAAG
59236747 ATGTGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAAGTC
Found at i:59237249 original size:46 final size:47
Alignment explanation
Indices: 59237084--59237251 Score: 182
Period size: 46 Copynumber: 3.6 Consensus size: 47
59237074 ATTTTTGGCT
* * **
59237084 AGTGTAAGACATGTCTGGGACATGTATCGGCCAC-A-TTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACAT-AGAGCC
* * *
59237130 AGTGTAAGACCATGTCTGGGAAATGGCATCGGCATCGAGACA-AGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACATAGAGCC
* * *
59237178 AGTGTAAGACATTTCTAGGATATGCATCGGCCTCGAGACATA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACATAGAGCC
*
59237224 AGTGTAAGACATGTCTGGTACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
59237252 AGCTATGAGA
Statistics
Matches: 101, Mismatches: 16, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
46 52 0.51
47 25 0.25
48 22 0.22
49 1 0.01
50 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACATAGAGCC
Found at i:59241680 original size:16 final size:16
Alignment explanation
Indices: 59241659--59241690 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
59241649 GAATGGTTTG
59241659 GGGTGCATGCTTATGC
1 GGGTGCATGCTTATGC
59241675 GGGTGCATGCTTATGC
1 GGGTGCATGCTTATGC
59241691 AAAAAGGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.38, T:0.31
Consensus pattern (16 bp):
GGGTGCATGCTTATGC
Found at i:59243730 original size:29 final size:29
Alignment explanation
Indices: 59243688--59243771 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 29
59243678 GCCGTATTTT
**
59243688 TTTCCAGCTTGCACACTTAGTGCCAAATA
1 TTTCCAGCACGCACACTTAGTGCCAAATA
*
59243717 TTTCCAGCACGCACACTTAGTGCCATATA
1 TTTCCAGCACGCACACTTAGTGCCAAATA
59243746 TTTCCAGCACGCACACTTAGTGCCAA
1 TTTCCAGCACGCACACTTAGTGCCAA
59243772 TCTCGACACC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.27
Consensus pattern (29 bp):
TTTCCAGCACGCACACTTAGTGCCAAATA
Found at i:59248006 original size:47 final size:46
Alignment explanation
Indices: 59247906--59248013 Score: 114
Period size: 47 Copynumber: 2.3 Consensus size: 46
59247896 GTTATTTTTT
* *
59247906 GCTAGTGTAAGACATGTCTGGGACATACATCGGCCATATGATGAGA
1 GCTAGTGTAAAACATGTCTGGGACATACATCGGCCATATGACGAGA
* *
59247952 GCCAGTGTAAAACCATG-CTGGGACATGGCATCGG-CATCGA-GACGAGA
1 GCTAGTGTAAAA-CATGTCTGGGACAT-ACATCGGCCAT--ATGACGAGA
*
59247999 GCTAGTGTAAGACAT
1 GCTAGTGTAAAACAT
59248014 TTCTAGGATA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
46 25 0.48
47 26 0.50
48 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.20
Consensus pattern (46 bp):
GCTAGTGTAAAACATGTCTGGGACATACATCGGCCATATGACGAGA
Found at i:59249653 original size:46 final size:46
Alignment explanation
Indices: 59249603--59249775 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
59249593 TGGTTGAGCA
*
59249603 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
59249649 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * * *
59249696 TCCGAACTCGTTGAGTTGAGTCCGAGCTCATTTATGAATGCAAACA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
59249742 CCCGAGCTCGTTGAGTTGAGTCCGAGTTTACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
59249776 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:59249759 original size:93 final size:93
Alignment explanation
Indices: 59249600--59249769 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 93
59249590 GGATGGTTGA
* * ***
59249600 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGAATGCAAACACCCGAACTCGTTGAGT
59249665 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
59249693 GCATCCGAACTCGTTGAGTTGAGTCCGAGCTCATTTATGAATGCAAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGAATGCAAACACCCGAACTCGTTGAGT
59249758 TGAGTCCGAGTT
66 TGAGTCCGAGTT
59249770 TACTTAGGGG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGAATGCAAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:59250037 original size:19 final size:20
Alignment explanation
Indices: 59250000--59250037 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
59249990 ATAAGGTGGT
59250000 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
59250020 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
59250038 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:59253657 original size:24 final size:23
Alignment explanation
Indices: 59253608--59253657 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
59253598 TAATGTAGGT
* *
59253608 TATATATTATTTTTATAATATTA
1 TATATATGATTTTTATAATATCA
59253631 TATATTATGATTTTTATTAAT-TCA
1 TATA-TATGATTTTTA-TAATATCA
59253655 TAT
1 TAT
59253658 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 15 0.65
25 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TATATATGATTTTTATAATATCA
Found at i:59253764 original size:58 final size:57
Alignment explanation
Indices: 59253642--59253797 Score: 179
Period size: 58 Copynumber: 2.7 Consensus size: 57
59253632 ATATTATGAT
* * *
59253642 TTTTATT-AATTCATATTTTTAATAATAATTGTATTAAGAATGTTATTAAATTATATATTA
1 TTTTATTAAATT-ATA--TTTAATAATAATTATATTAA-AATATGATTAAATTATATATTA
* * * *
59253702 TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATGATTAAATTATTTGTTA
1 TTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTATATATTA
* *
59253759 TTTTTATTAAATTATATATAATAATAATTTTATTAAAAT
1 -TTTTATTAAATTATATTTAATAATAATTATATTAAAAT
59253798 TTAATAACAA
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
57 18 0.22
58 52 0.63
60 9 0.11
61 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (57 bp):
TTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTATATATTA
Found at i:59253810 original size:25 final size:26
Alignment explanation
Indices: 59253760--59253811 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
59253750 TATTTGTTAT
*
59253760 TTTTATTAAATTATATATAATAATAA
1 TTTTATTAAATTATATATAACAATAA
59253786 TTTTATTAAAATT-TA-ATAACAATAA
1 TTTTATT-AAATTATATATAACAATAA
59253811 T
1 T
59253812 AATAATCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 10 0.42
26 9 0.38
27 5 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTTATTAAATTATATATAACAATAA
Found at i:59255699 original size:28 final size:29
Alignment explanation
Indices: 59255647--59255706 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
59255637 ATATTTAATA
*
59255647 TTTAAAACTTCAAAAAGAATTTAAAAAAT
1 TTTAAAACTTCAAAAAGAATATAAAAAAT
* * *
59255676 TTTAAAATTTTAAAAAG-ATATAAAATAT
1 TTTAAAACTTCAAAAAGAATATAAAAAAT
59255704 TTT
1 TTT
59255707 TTAAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (29 bp):
TTTAAAACTTCAAAAAGAATATAAAAAAT
Found at i:59255707 original size:29 final size:30
Alignment explanation
Indices: 59255643--59255713 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
59255633 ATTAATATTT
* *
59255643 AATA-TTTAAAACTTCAAAAAGAATTTAAA
1 AATATTTTAAAATTTCAAAAAGAATATAAA
*
59255672 AA-ATTTTAAAATTTTAAAAAG-ATATAAA
1 AATATTTTAAAATTTCAAAAAGAATATAAA
*
59255700 ATATTTTTTAAAAT
1 A-ATATTTTAAAAT
59255714 AAAAAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 8 0.23
29 18 0.51
30 9 0.26
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (30 bp):
AATATTTTAAAATTTCAAAAAGAATATAAA
Found at i:59256047 original size:30 final size:30
Alignment explanation
Indices: 59256013--59256073 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
59256003 ATAAGTTTAA
59256013 ATATTCAAATAAA-CTCTTAAATTTTAATTG
1 ATATTCAAATAAATC-CTTAAATTTTAATTG
*
59256043 ATATTCAAATGAATCCTTAAATTTTAATTG
1 ATATTCAAATAAATCCTTAAATTTTAATTG
59256073 A
1 A
59256074 CGCTCAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (30 bp):
ATATTCAAATAAATCCTTAAATTTTAATTG
Found at i:59256113 original size:30 final size:30
Alignment explanation
Indices: 59256079--59256136 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
59256069 ATTGACGCTC
59256079 AAATAAG-TTGTTAATCTTTAATTTATATTT
1 AAATAAGCTT-TTAATCTTTAATTTATATTT
*
59256109 AAATAAGCTTTTAATCTTTTATTTATAT
1 AAATAAGCTTTTAATCTTTAATTTATAT
59256137 CAAAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (30 bp):
AAATAAGCTTTTAATCTTTAATTTATATTT
Done.