Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 140 of 150
Found at i:42137381 original size:18 final size:19
Alignment explanation
Indices: 42137338--42137382 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
42137328 TTTTAAAAAT
*
42137338 TATATTTTATATTTTTAAA
1 TATATTTTACATTTTTAAA
42137357 -ATGATTTT-CATTTTTAAA
1 TAT-ATTTTACATTTTTAAA
42137375 TATATTTT
1 TATATTTT
42137383 TATATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TATATTTTACATTTTTAAA
Found at i:42143626 original size:2 final size:2
Alignment explanation
Indices: 42143619--42143687 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
42143609 GTTATGTCTC
42143619 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
42143661 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
42143688 ATGCAGATGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:42144797 original size:59 final size:60
Alignment explanation
Indices: 42144724--42144856 Score: 223
Period size: 59 Copynumber: 2.2 Consensus size: 60
42144714 TTCAGAATGC
42144724 TTTAATGCTAAAGTAAATGAAACATTAGAATCTATTG-AAATTTGACCTTTGGAACTCGT
1 TTTAATGCTAAAGTAAATGAAACATTAGAATCTATTGAAAATTTGACCTTTGGAACTCGT
* * * *
42144783 TTTAATGTTGAAGTAAATGAAATATTAGAATCTATTGAAAATTTGACTTTTGGAACTCGT
1 TTTAATGCTAAAGTAAATGAAACATTAGAATCTATTGAAAATTTGACCTTTGGAACTCGT
42144843 TTTAATGCTAAAGT
1 TTTAATGCTAAAGT
42144857 TAATCTCCGA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 34 0.51
60 33 0.49
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (60 bp):
TTTAATGCTAAAGTAAATGAAACATTAGAATCTATTGAAAATTTGACCTTTGGAACTCGT
Found at i:42157601 original size:13 final size:13
Alignment explanation
Indices: 42157583--42157607 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42157573 AGAGAATCCT
42157583 CCAACATTGCTTG
1 CCAACATTGCTTG
42157596 CCAACATTGCTT
1 CCAACATTGCTT
42157608 TTAGGCACCA
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:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (13 bp):
CCAACATTGCTTG
Found at i:42158778 original size:21 final size:21
Alignment explanation
Indices: 42158728--42158776 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
42158718 ATTATATCAA
42158728 CATTCAAACCAGTTCAAAACT
1 CATTCAAACCAGTTCAAAACT
42158749 CATTCAAACCAGTTCAAAACT
1 CATTCAAACCAGTTCAAAACT
42158770 CA-TCAAA
1 CATTCAAA
42158777 ACATACCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.45, C:0.29, G:0.04, T:0.22
Consensus pattern (21 bp):
CATTCAAACCAGTTCAAAACT
Found at i:42160980 original size:20 final size:20
Alignment explanation
Indices: 42160957--42161001 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
42160947 AGAATTTTAC
42160957 CGATACTTGATTAAAGGTAT
1 CGATACTTGATTAAAGGTAT
** *
42160977 CGATACTTTTTTATAGGTAT
1 CGATACTTGATTAAAGGTAT
42160997 CGATA
1 CGATA
42161002 TTCGAACAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (20 bp):
CGATACTTGATTAAAGGTAT
Found at i:42166636 original size:16 final size:17
Alignment explanation
Indices: 42166615--42166647 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
42166605 GTAGACTTAA
*
42166615 ATAAAATTAACT-AAAT
1 ATAAAATAAACTGAAAT
42166631 ATAAAATAAACTGAAAT
1 ATAAAATAAACTGAAAT
42166648 TGTTGGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (17 bp):
ATAAAATAAACTGAAAT
Found at i:42166773 original size:30 final size:29
Alignment explanation
Indices: 42166739--42166796 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
42166729 GAAACTAATC
42166739 TCAATTACTGATTCTTAGGAAATTAGGATA
1 TCAATTACTGATTCTTAGG-AATTAGGATA
42166769 TCAATTACTGATTCTTAGGAATTAGGAT
1 TCAATTACTGATTCTTAGGAATTAGGAT
42166797 TTATTTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (29 bp):
TCAATTACTGATTCTTAGGAATTAGGATA
Found at i:42170602 original size:30 final size:29
Alignment explanation
Indices: 42170568--42170625 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
42170558 GAAACTAATC
42170568 TCAATTACTGATTCTTAGGAAATTAGGATA
1 TCAATTACTGATTCTTAGG-AATTAGGATA
42170598 TCAATTACTGATTCTTAGGAATTAGGAT
1 TCAATTACTGATTCTTAGGAATTAGGAT
42170626 TTATTTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (29 bp):
TCAATTACTGATTCTTAGGAATTAGGATA
Found at i:42179659 original size:29 final size:31
Alignment explanation
Indices: 42179626--42179684 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
42179616 ATCTAAGGTA
42179626 TAATT-TGATACAT-GAACTTTGA-TGTGGTG
1 TAATTATGA-ACATAGAACTTTGATTGTGGTG
42179655 TAATTATGAACATAGAACTTTGATTGTGGT
1 TAATTATGAACATAGAACTTTGATTGTGGT
42179685 TCAAATACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 9 0.33
30 12 0.44
31 6 0.22
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.41
Consensus pattern (31 bp):
TAATTATGAACATAGAACTTTGATTGTGGTG
Found at i:42180974 original size:25 final size:25
Alignment explanation
Indices: 42180946--42180997 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
42180936 AATAAACATA
**
42180946 TTTTAATTTTAAT-TTAATTATAAAT
1 TTTTAATAGTAATATTAA-TATAAAT
*
42180971 TTTTTATAGTAATATTAATATAAAT
1 TTTTAATAGTAATATTAATATAAAT
42180996 TT
1 TT
42180998 GTTTAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTAATAGTAATATTAATATAAAT
Found at i:42181453 original size:24 final size:24
Alignment explanation
Indices: 42181438--42181483 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
42181428 TATTATAACT
42181438 TTTTTATTTACCAATATATATATA
1 TTTTTATTTACCAATATATATATA
* *
42181462 TTTTTATTTACTAAAATATATA
1 TTTTTATTTACCAATATATATA
42181484 AAAAAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTTATTTACCAATATATATATA
Found at i:42182925 original size:14 final size:13
Alignment explanation
Indices: 42182904--42182937 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
42182894 TCCCAATAAA
42182904 ATAATAATACAAT
1 ATAATAATACAAT
*
42182917 ATGAATAATACATT
1 AT-AATAATACAAT
42182931 ATAATAA
1 ATAATAA
42182938 CAACACATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (13 bp):
ATAATAATACAAT
Found at i:42183311 original size:17 final size:16
Alignment explanation
Indices: 42183282--42183320 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
42183272 AAGTATACTG
42183282 AATTAATTTATAAATA
1 AATTAATTTATAAATA
42183298 AATTAATATTATAAATA
1 AATTAAT-TTATAAATA
*
42183315 AGTTAA
1 AATTAA
42183321 AATATTAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTAATTTATAAATA
Found at i:42186808 original size:3 final size:3
Alignment explanation
Indices: 42186802--42186848 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
42186792 ACAACAAAGC
42186802 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
42186849 ACAGAATGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42201310 original size:21 final size:21
Alignment explanation
Indices: 42201284--42201345 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
42201274 TGGTATTTGG
42201284 GAATTGGTACGAAATGGTATA
1 GAATTGGTACGAAATGGTATA
* *
42201305 GAATTGGTATGAAATGGTATG
1 GAATTGGTACGAAATGGTATA
* *
42201326 GTATTTGGTACGAATTGGTA
1 G-AATTGGTACGAAATGGTA
42201346 ATGGTTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (21 bp):
GAATTGGTACGAAATGGTATA
Found at i:42203792 original size:79 final size:79
Alignment explanation
Indices: 42203669--42203814 Score: 256
Period size: 79 Copynumber: 1.8 Consensus size: 79
42203659 CGAATATACG
* *
42203669 AATAGCATGTTTTGATCTATTAACTATATGTGCAACTAGTATGTTCTGATATGTTTTATCTGCAT
1 AATAACATGTTTTGATCTATTAACTATATGTGCAACTAGTATGTTATGATATGTTTTATCTGCAT
42203734 ATAGGTAATATGCC
66 ATAGGTAATATGCC
* *
42203748 AATAACATGTTTTGATCTGTTAATTATATGTGCAACTAGTATGTTATGATATGTTTTATCTGCAT
1 AATAACATGTTTTGATCTATTAACTATATGTGCAACTAGTATGTTATGATATGTTTTATCTGCAT
42203813 AT
66 AT
42203815 GGGCACGTCT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (79 bp):
AATAACATGTTTTGATCTATTAACTATATGTGCAACTAGTATGTTATGATATGTTTTATCTGCAT
ATAGGTAATATGCC
Found at i:42205887 original size:24 final size:24
Alignment explanation
Indices: 42205855--42205906 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
42205845 ATTTTAGGTA
42205855 CACACGGCCTG-GA-ACAGAGACTGT
1 CACACGGCCTGAGACACAG-G-CTGT
42205879 CACACGGCCTGAGACACAGGCTGT
1 CACACGGCCTGAGACACAGGCTGT
42205903 CACA
1 CACA
42205907 TGGCTGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 19 0.73
25 3 0.12
26 4 0.15
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.12
Consensus pattern (24 bp):
CACACGGCCTGAGACACAGGCTGT
Found at i:42206901 original size:37 final size:36
Alignment explanation
Indices: 42206846--42206922 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 36
42206836 TGTTTGATGC
*
42206846 TTAGGTTCCATTTATTGATCAATTCATTAATTTCTAA
1 TTAGATTCCATTTATTGATCAATTCATTAATTTCT-A
*
42206883 TTAGATTCCATTTGTTGATCAATTCATTAATTTCTA
1 TTAGATTCCATTTATTGATCAATTCATTAATTTCTA
42206919 TTAG
1 TTAG
42206923 GTTGTCGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 5 0.13
37 33 0.87
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (36 bp):
TTAGATTCCATTTATTGATCAATTCATTAATTTCTA
Found at i:42223877 original size:33 final size:32
Alignment explanation
Indices: 42223826--42223986 Score: 115
Period size: 33 Copynumber: 4.8 Consensus size: 32
42223816 CAGTGTTTAT
*
42223826 ATGTAAGACCGTAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
* * * * *
42223858 ATGATAAGACCATAACTGGGTTATGGCACTATA
1 ATG-TAAGACCATAGCTGGGCTATGGCATTCTG
* * * * * * *
42223891 ACCGTAAGACCATGGTTGGACCATGGCAATATTTAT
1 A-TGTAAGACCATAGCTGGGCTATGGC-AT-TCT-G
* *
42223927 ATGTAAGACCATAGCCGGGCTATGACATTCTG
1 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
* *
42223959 ATGATAAGACCATAACTGGGTTATGGCA
1 ATG-TAAGACCATAGCTGGGCTATGGCA
42223987 CTACGAATGT
Statistics
Matches: 94, Mismatches: 29, Indels: 11
0.70 0.22 0.08
Matches are distributed among these distances:
32 6 0.06
33 63 0.67
34 4 0.04
35 20 0.21
36 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGCTATGGCATTCTG
Found at i:42223885 original size:101 final size:101
Alignment explanation
Indices: 42223760--42223998 Score: 390
Period size: 101 Copynumber: 2.4 Consensus size: 101
42223750 GAATTGAGGA
* * *
42223760 ATAAGACCATAACTAGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
1 ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATATTTA
* * *
42223825 TATGTAAGACCGTAGCTGGGCTATGGCATTCTGATG
66 TATGTAAGACCATAGCCGGGCTATGACATTCTGATG
42223861 ATAAGACCATAACTGGGTTATGGCACTAT-AACCGTAAGACCATGGTTGGACCATGGCAATATTT
1 ATAAGACCATAACTGGGTTATGGCACTATGAA-CGTAAGACCATGGTTGGACCATGGCAATATTT
42223925 ATATGTAAGACCATAGCCGGGCTATGACATTCTGATG
65 ATATGTAAGACCATAGCCGGGCTATGACATTCTGATG
* *
42223962 ATAAGACCATAACTGGGTTATGGCACTACGAATGTAA
1 ATAAGACCATAACTGGGTTATGGCACTATGAACGTAA
42223999 ATGATGAATT
Statistics
Matches: 128, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
100 2 0.02
101 124 0.97
102 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (101 bp):
ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATATTTA
TATGTAAGACCATAGCCGGGCTATGACATTCTGATG
Found at i:42224043 original size:26 final size:26
Alignment explanation
Indices: 42223992--42224043 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
42223982 TGGCACTACG
* *
42223992 AATGTAAATGATGAATTGACGAAAAA
1 AATGTAAAGGATGAATTGAAGAAAAA
*
42224018 AATGTAAAGGATGAATTGAAGGAAAA
1 AATGTAAAGGATGAATTGAAGAAAAA
42224044 TTACCCAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.54, C:0.02, G:0.23, T:0.21
Consensus pattern (26 bp):
AATGTAAAGGATGAATTGAAGAAAAA
Found at i:42240488 original size:21 final size:21
Alignment explanation
Indices: 42240462--42240510 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
42240452 TTTATTTCTA
* **
42240462 TTAATTTAGTAATTTTTATTT
1 TTAATTTAATAATTTTTAAAT
*
42240483 TTAATTTAATACTTTTTAAAT
1 TTAATTTAATAATTTTTAAAT
42240504 TTAATTT
1 TTAATTT
42240511 TTAAATTCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTAATTTAATAATTTTTAAAT
Found at i:42241843 original size:20 final size:21
Alignment explanation
Indices: 42241820--42241861 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
42241810 AATATCCTAT
42241820 TAATTTAA-TGAATAAAAAAA
1 TAATTTAATTGAATAAAAAAA
*
42241840 TAATTTAATTTAATAAAAAAA
1 TAATTTAATTGAATAAAAAAA
42241861 T
1 T
42241862 CTATCTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TAATTTAATTGAATAAAAAAA
Found at i:42253773 original size:39 final size:39
Alignment explanation
Indices: 42253719--42253795 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
42253709 GACGCCACTT
*
42253719 GATAGTGTCCTGATTGATGTATATGTTTAATAGCAATTC
1 GATAGTGCCCTGATTGATGTATATGTTTAATAGCAATTC
42253758 GATAGTGCCCTGATTGATGTATATGTTTAATAGCAATT
1 GATAGTGCCCTGATTGATGTATATGTTTAATAGCAATT
42253796 TGGTAATTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (39 bp):
GATAGTGCCCTGATTGATGTATATGTTTAATAGCAATTC
Found at i:42270836 original size:20 final size:19
Alignment explanation
Indices: 42270798--42270840 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
42270788 TTTAAAATAA
42270798 ATAAAAAAATTAAAGAATT
1 ATAAAAAAATTAAAGAATT
*
42270817 CATAAAAAATATTACA-AATT
1 -ATAAAAAA-ATTAAAGAATT
42270837 ATAA
1 ATAA
42270841 GTTTCTTCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (19 bp):
ATAAAAAAATTAAAGAATT
Found at i:42271460 original size:27 final size:28
Alignment explanation
Indices: 42271429--42271481 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
42271419 AACATATAAT
42271429 TTATAATA-TATTTATTTTTAAAAAAAA
1 TTATAATATTATTTATTTTTAAAAAAAA
*
42271456 TTATAATATTATTTATTTTTACAAAA
1 TTATAATATTATTTATTTTTAAAAAA
42271482 TTTTTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TTATAATATTATTTATTTTTAAAAAAAA
Found at i:42273713 original size:51 final size:51
Alignment explanation
Indices: 42273599--42273763 Score: 251
Period size: 51 Copynumber: 3.3 Consensus size: 51
42273589 CTTACGTATG
* * * *
42273599 ATCACTTATCACTTGTCCCTAATTAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTGAAGCTACTACTT
* *
42273649 ATCACTTGCCACTTGTCACTTATCAGATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTGAAGCTACTACTT
* *
42273700 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGTTGAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTGAAGCTACTACTT
42273751 ATCACTTGTCACT
1 ATCACTTGTCACT
42273764 GATCAGAAGT
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 33 0.31
51 72 0.69
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTGAAGCTACTACTT
Found at i:42287938 original size:24 final size:24
Alignment explanation
Indices: 42287890--42287951 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
42287880 ATTGTGGAAG
*
42287890 ACAAATGCCTAAAA-TTTAGTCAA
1 ACAAATCCCTAAAATTTTAGTCAA
42287913 ACAAATCCCTAAAATTTTAG-CTAA
1 ACAAATCCCTAAAATTTTAGTC-AA
42287937 ACAAA-CCCTAAAATT
1 ACAAATCCCTAAAATT
42287952 GTGAAAGACA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
23 24 0.67
24 12 0.33
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.26
Consensus pattern (24 bp):
ACAAATCCCTAAAATTTTAGTCAA
Found at i:42289721 original size:16 final size:17
Alignment explanation
Indices: 42289689--42289723 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
42289679 TAGAATTGGG
*
42289689 TTGAGATAATTATTTAA
1 TTGAGATAATTAATTAA
42289706 TTGAGA-AATTAATTAA
1 TTGAGATAATTAATTAA
42289722 TT
1 TT
42289724 TAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (17 bp):
TTGAGATAATTAATTAA
Found at i:42301385 original size:2 final size:2
Alignment explanation
Indices: 42301378--42301409 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42301368 ATATCTTTTA
42301378 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42301410 TGTTAGGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42305643 original size:348 final size:347
Alignment explanation
Indices: 42305000--42305656 Score: 1206
Period size: 348 Copynumber: 1.9 Consensus size: 347
42304990 GACCATTAAA
42305000 ATTTAAAGATCTTTGGGTGTCCTGCATATACTCATGTTGATAATGGAAAATTGGAACCGAGATCT
1 ATTTAAAGATCTTTGGGTGTCCTGCATATACTCATGTTGATAATGGAAAATTGGAACCGAGATCT
*
42305065 ATTAAATATGTTTTTCTTGGTCATAAAACTGGTATAAATGGGTATAAGTTATGGTGTCCTAAAAA
66 ATTAAATATGTTTTTCTTGGTCATAAAACTGGTATAAAGGGGTATAAGTTATGGTGTCCTAAAAA
* *
42305130 TAGAAAATTTATGATTAGCAGAGATATTGTTTTTGATGAAACTATTATGCTACCTAATTTATCTC
131 TAGAAAAGTTATGATTAGCAGAGATATTGTTTTTGATGAAACTATTATGCTACCTAACTTATCTC
42305195 TTAAAGACTCTTCCAATAAAGAAAATCAAAAGCAGGTGGAGCATCAGATTAATCCAGAATCTACA
196 TTAAAGACTCTTCCAATAAAGAAAATCAAAAGCAGGTGGAGCATCAGATTAATCCAGAATCTACA
*
42305260 ATAGAGCCGACTCCTCAAGCCAGTACAAAAATTTAGAATAGAGTTGCTTTTAATAGATCTTTTTA
261 ATAGAGCAGACTCCTCAAGCCAGTACAAAAATTTAGAATAGAGTTGCTTTTAATAGATCTTTTTA
42305325 ATCTACAATGGAACCGAGATCT
326 ATCTACAATGGAACCGAGATCT
* *
42305347 ATTTAATAGATCTTTGGGTGTCCTGCGTATGCTCATGTTGATAATGGAAAATTGGAACCGAGATC
1 ATTTAA-AGATCTTTGGGTGTCCTGCATATACTCATGTTGATAATGGAAAATTGGAACCGAGATC
* *
42305412 TATTAAATATGTTTTTCTTGGTCATAAAGCTGGTGTAAAGGGGTATAAGTTATGGTGTCCTAAAA
65 TATTAAATATGTTTTTCTTGGTCATAAAACTGGTATAAAGGGGTATAAGTTATGGTGTCCTAAAA
* *
42305477 ATAGAAAAGTTATGATTAGCGGAGATATTGTTTTTGATGAAATTATTATGCTACCTAACTTATCT
130 ATAGAAAAGTTATGATTAGCAGAGATATTGTTTTTGATGAAACTATTATGCTACCTAACTTATCT
*
42305542 CTTAAAGACTCTTCCAATAAAGAAAATCAAAAGTAGGTGGAGCATCAGATTAATCCAGAATCTAC
195 CTTAAAGACTCTTCCAATAAAGAAAATCAAAAGCAGGTGGAGCATCAGATTAATCCAGAATCTAC
42305607 AATAGAGCAGACTCCTCAAGCCAGTACAAAAATTTAGAATAGAGTTGCTT
260 AATAGAGCAGACTCCTCAAGCCAGTACAAAAATTTAGAATAGAGTTGCTT
42305657 CTTCACCACA
Statistics
Matches: 298, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
347 6 0.02
348 292 0.98
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (347 bp):
ATTTAAAGATCTTTGGGTGTCCTGCATATACTCATGTTGATAATGGAAAATTGGAACCGAGATCT
ATTAAATATGTTTTTCTTGGTCATAAAACTGGTATAAAGGGGTATAAGTTATGGTGTCCTAAAAA
TAGAAAAGTTATGATTAGCAGAGATATTGTTTTTGATGAAACTATTATGCTACCTAACTTATCTC
TTAAAGACTCTTCCAATAAAGAAAATCAAAAGCAGGTGGAGCATCAGATTAATCCAGAATCTACA
ATAGAGCAGACTCCTCAAGCCAGTACAAAAATTTAGAATAGAGTTGCTTTTAATAGATCTTTTTA
ATCTACAATGGAACCGAGATCT
Found at i:42310538 original size:45 final size:45
Alignment explanation
Indices: 42310475--42310565 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
42310465 ATAAAATATC
* * *
42310475 TCAAATATCATTATTTTTATACT-TGAAGTATTTCAAATAATTATT
1 TCAAATATAATTATTTTTATA-TGGGAAATATTTCAAATAATTATT
42310520 TCAAATATAATTGA-TTTTATATGGGAAATATTTCAAATAATTATT
1 TCAAATATAATT-ATTTTTATATGGGAAATATTTCAAATAATTATT
42310565 T
1 T
42310566 TCAATACACA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
44 1 0.02
45 39 0.95
46 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (45 bp):
TCAAATATAATTATTTTTATATGGGAAATATTTCAAATAATTATT
Found at i:42319107 original size:6 final size:6
Alignment explanation
Indices: 42319096--42319127 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
42319086 AATTACTCCG
42319096 TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA TC
1 TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA TC
42319128 ATTCTCAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.50, G:0.00, T:0.34
Consensus pattern (6 bp):
TCCCTA
Found at i:42320980 original size:2 final size:2
Alignment explanation
Indices: 42320975--42321001 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42320965 GTGTTGAATA
42320975 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
42321002 ATTTACTATC
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:42323586 original size:8 final size:8
Alignment explanation
Indices: 42323575--42323605 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
42323565 AAATTTCATA
*
42323575 ATTAAATT
1 ATTACATT
42323583 ATTACATT
1 ATTACATT
42323591 ATTACATT
1 ATTACATT
42323599 ATTACAT
1 ATTACAT
42323606 GTTTATCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTACATT
Found at i:42329571 original size:6 final size:6
Alignment explanation
Indices: 42329560--42329590 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
42329550 CTAATCATAA
42329560 CCAACT CCAACT CCAACT CCAACT CCAACT C
1 CCAACT CCAACT CCAACT CCAACT CCAACT C
42329591 TTCTGTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (6 bp):
CCAACT
Found at i:42334260 original size:2 final size:2
Alignment explanation
Indices: 42334253--42334286 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42334243 TATTATTTTA
42334253 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42334287 GCACGTAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42335797 original size:42 final size:43
Alignment explanation
Indices: 42335645--42335846 Score: 185
Period size: 43 Copynumber: 4.7 Consensus size: 43
42335635 ATTTCGTACA
* * * * *
42335645 ATGCCAACGTCCCAGACGTGATCTTACATGTAATCAAATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATTAAATAACG
* * * *
42335688 ATGTCACTGTCCCAGACAGGGTCTTACATGTAATTAAATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATTAAATAACG
* * * * *
42335731 ATGCCACTGTCCTAGATAGGGTCTTACACGTAATTATAT-ACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATTAAATAACG
* * *
42335773 ACGCCAATGTCCCAGACCTGGTCTTACACGTAAATCTCAAAT--TG
1 ATGCCAATGTCCCAGACATGGTCTTACACGT-AAT-T-AAATAACG
* *
42335817 ATGCCAATGTCCCAGACGTGATCTTACACG
1 ATGCCAATGTCCCAGACATGGTCTTACACG
42335847 AAATCACATT
Statistics
Matches: 133, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
42 28 0.21
43 73 0.55
44 29 0.22
45 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATTAAATAACG
Found at i:42335842 original size:86 final size:85
Alignment explanation
Indices: 42335645--42335852 Score: 206
Period size: 86 Copynumber: 2.4 Consensus size: 85
42335635 ATTTCGTACA
* * * * *
42335645 ATGCCAACGTCCCAGACGTGATCTTACATGTAATCAAATAACGATGTCACTGTCCCAGACAGGGT
1 ATGCCAATGTCCCAGACGTGATCTTACACGTAATCAAATAACGACGCCAATGTCCCAGACAGGGT
*
42335710 CTTACATGTAATTAAATAACG
66 CTTACACGTAATTAAAT-ACG
* * * * * * **
42335731 ATGCCACTGTCCTAGATAG-GGTCTTACACGTAATTATAT-ACGACGCCAATGTCCCAGACCTGG
1 ATGCCAATGTCCCAGA-CGTGATCTTACACGTAATCAAATAACGACGCCAATGTCCCAGACAGGG
*
42335794 TCTTACACGTAAATCTCAAAT-TG
65 TCTTACACGT-AAT-T-AAATACG
*
42335817 ATGCCAATGTCCCAGACGTGATCTTACACGAAATCA
1 ATGCCAATGTCCCAGACGTGATCTTACACGTAATCA
42335853 CATTTCAGCA
Statistics
Matches: 96, Mismatches: 21, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
85 29 0.30
86 61 0.64
87 2 0.02
88 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (85 bp):
ATGCCAATGTCCCAGACGTGATCTTACACGTAATCAAATAACGACGCCAATGTCCCAGACAGGGT
CTTACACGTAATTAAATACG
Found at i:42336315 original size:23 final size:23
Alignment explanation
Indices: 42336289--42336338 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
42336279 AACTATGCCT
42336289 TAGCCGAATCTTCCTATAGTCCA
1 TAGCCGAATCTTCCTATAGTCCA
42336312 TAGCCGAATCTTCCTATAGTCCA
1 TAGCCGAATCTTCCTATAGTCCA
42336335 TAGC
1 TAGC
42336339 AACCCATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (23 bp):
TAGCCGAATCTTCCTATAGTCCA
Found at i:42346597 original size:14 final size:15
Alignment explanation
Indices: 42346572--42346600 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42346562 TTTGAAAAAA
42346572 ATATTATAATTCATT
1 ATATTATAATTCATT
42346587 ATATT-TAATTCATT
1 ATATTATAATTCATT
42346601 CATTTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTATAATTCATT
Found at i:42347726 original size:24 final size:27
Alignment explanation
Indices: 42347681--42347731 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
42347671 TGGCGGCGGC
42347681 GGCGGCGGCGGAGCAGACAGAGGAGGA
1 GGCGGCGGCGGAGCAGACAGAGGAGGA
42347708 GGCGGCGGCGGAG-A-A-AGAGGAGGA
1 GGCGGCGGCGGAGCAGACAGAGGAGGA
42347732 AACGATGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.38
25 1 0.04
26 1 0.04
27 13 0.54
ACGTcount: A:0.27, C:0.16, G:0.57, T:0.00
Consensus pattern (27 bp):
GGCGGCGGCGGAGCAGACAGAGGAGGA
Found at i:42350524 original size:153 final size:150
Alignment explanation
Indices: 42350227--42350529 Score: 491
Period size: 153 Copynumber: 2.0 Consensus size: 150
42350217 CTCTTGCTAA
*
42350227 TTGGAGTGTGAACAAGTAAACACCACAATCTTGAAATTGAGTTGTTGCCATTTTCAAAGAAAGAA
1 TTGGAGTGTGAACAAGTAAACACCACAATCTTGAAATTGAGTTGCTGCCATTTTCAAAGAAAGAA
** **
42350292 CAAGAATTGAATCTTGTAAAAACTCTCAGAGTAAATTACAAAGCATAGTATCCCATGTATAGACT
66 CAAGAATCAAATCTTGTAAAAACTCTCAGAGTAAATTACAAAGCATAGTATCCCATACATAGACT
*
42350357 TAAGTTACTTGAAAAATAAG
131 TAAGTTACATGAAAAATAAG
* *
42350377 TTGGAGTGTGAAGAAGTAAACACCACTATCTTGAAGATTGAGTTGCTGCCACTTTT-AAAGAAAG
1 TTGGAGTGTGAACAAGTAAACACCACAATCTTGAA-ATTGAGTTGCTGCCA-TTTTCAAAGAAAG
42350441 AACAAGAATCAAATCTTGTAAAAACTCTCAAAGAGTAAATTACAAAGCATAGTATCCCATACATA
64 AACAAGAATCAAATCTTGTAAAAACTCTC--AGAGTAAATTACAAAGCATAGTATCCCATACATA
42350506 GACTTAAGTTACATGAAAAATAAG
127 GACTTAAGTTACATGAAAAATAAG
42350530 GAAACAACCC
Statistics
Matches: 141, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
150 33 0.23
151 49 0.35
152 4 0.03
153 55 0.39
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (150 bp):
TTGGAGTGTGAACAAGTAAACACCACAATCTTGAAATTGAGTTGCTGCCATTTTCAAAGAAAGAA
CAAGAATCAAATCTTGTAAAAACTCTCAGAGTAAATTACAAAGCATAGTATCCCATACATAGACT
TAAGTTACATGAAAAATAAG
Found at i:42358260 original size:21 final size:21
Alignment explanation
Indices: 42358222--42358261 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42358212 CTAACTTGAA
*
42358222 TTTTAAATATTTTTATATTCC
1 TTTTAAATATTTTAATATTCC
42358243 TTTTAAAT-TTTTAAATATT
1 TTTTAAATATTTT-AATATT
42358262 TTTATAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAAATATTTTAATATTCC
Found at i:42358770 original size:40 final size:40
Alignment explanation
Indices: 42358715--42358795 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
42358705 TAATCAGAAG
42358715 TATGAGCAATCAAATCATAACTCTGGGATGCAAATGGTTT
1 TATGAGCAATCAAATCATAACTCTGGGATGCAAATGGTTT
42358755 TATGAGCAATCAAATCATAACTCTGGGATGCAAATGGTTT
1 TATGAGCAATCAAATCATAACTCTGGGATGCAAATGGTTT
42358795 T
1 T
42358796 CCTATCTCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (40 bp):
TATGAGCAATCAAATCATAACTCTGGGATGCAAATGGTTT
Found at i:42363094 original size:25 final size:26
Alignment explanation
Indices: 42363060--42363114 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
42363050 TGGTGATTAA
* *
42363060 AAAAATTAATGGTTTAA-AATTTTATT
1 AAAAATTAATAGTATAATAATTTT-TT
42363086 AAAAA-TAATAGTATAATAATTTTTT
1 AAAAATTAATAGTATAATAATTTTTT
42363111 AAAA
1 AAAA
42363115 TCTTATAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (26 bp):
AAAAATTAATAGTATAATAATTTTTT
Found at i:42366906 original size:16 final size:16
Alignment explanation
Indices: 42366885--42366916 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42366875 CAAGTCAAAG
42366885 TAATTAAATATTTACT
1 TAATTAAATATTTACT
42366901 TAATTAAATATTTACT
1 TAATTAAATATTTACT
42366917 CTGGAAGCAA
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:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTAAATATTTACT
Found at i:42367317 original size:22 final size:22
Alignment explanation
Indices: 42367292--42367334 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
42367282 TACTACTGTT
*
42367292 TTGCTGCCATTTTGTTATTATA
1 TTGCTACCATTTTGTTATTATA
* *
42367314 TTGCTACTATTTTGTTGTTAT
1 TTGCTACCATTTTGTTATTAT
42367335 TATTTGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (22 bp):
TTGCTACCATTTTGTTATTATA
Found at i:42370877 original size:11 final size:11
Alignment explanation
Indices: 42370861--42370890 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
42370851 GTATGGTTGG
42370861 ATTAAAAAATC
1 ATTAAAAAATC
42370872 ATT-AAAAATC
1 ATTAAAAAATC
42370882 ATTAAAAAA
1 ATTAAAAAA
42370891 AACAATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (11 bp):
ATTAAAAAATC
Found at i:42378326 original size:89 final size:89
Alignment explanation
Indices: 42378059--42379987 Score: 1565
Period size: 89 Copynumber: 21.3 Consensus size: 89
42378049 CTGCTGCGCT
* * * * *
42378059 TGATCTACTTCACGCC---A-ATGAAGACAAGGTCTG-TTCTCTTCGATCTACTCCACCACCAGT
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT-TTTTCGATCTGCTTCGCCACCAGT
* * * *
42378119 ATGGGGAGACAAGATCTGTTGTCTT
65 ATGGGAAGGCAAGATCTGTTATCTC
* * * * *
42378144 TGATCTACTTCATGCTAATACATGGAGACAAGATCTGCTTTTTCCTTCGATCTACTTCGCCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC-TTTT--TTCGATCTGCTTCGCCACCA
* * * *
42378209 GTATGGGAAGACAAGATTTGTTACCTT
63 GTATGGGAAGGCAAGATCTGTTATCTC
* * * * *
42378236 TGATATACTTCACGCCAGTACATGAAGACAAGATCT-ATTCTTTTCGATCTACTCCACCACCAGT
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT-TTTTCGATCTGCTTCGCCACCAGT
* * * * *
42378300 ATGGGGAGACAAGATCTTTTGTCTT
65 ATGGGAAGGCAAGATCTGTTATCTC
* * * *
42378325 TGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTCTTCCTTCGATCTACTTCGCTACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT-TT--TTCGATCTGCTTCGCCACCA
* * * *
42378390 GTAT-GGAAGACAAGATTTGTTACCTT
63 GTATGGGAAGGCAAGATCTGTTATCTC
* * * * *
42378416 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATTTGTTTCGCCACTAGTA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTTCGATCTGCTTCGCCACCAGTA
* * *
42378481 TAGGAAGACAAGATCTGTTATCTT
66 TGGGAAGGCAAGATCTGTTATCTC
* *
42378505 TGATCTACTTCACGCCAGTACATGAAGACAATATCTGCTTTCTTT-TATCTGCTTCGCCACCAGT
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTT-TTTCGATCTGCTTCGCCACCAGT
* *
42378569 ATGTGAAGGCAAGATCTGGTATCTC
65 ATGGGAAGGCAAGATCTGTTATCTC
* * *
42378594 TGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGCCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-CTTTT--TTCGATCTGCTTCGCCACCA
42378659 GTATGGGAAGGCAAGATCTGTTATCTC
63 GTATGGGAAGGCAAGATCTGTTATCTC
*
42378686 TGATCTACTTCACGCCAGTACATAAAGACAAGATCTGCTTTCTTT-GATCTGCTTCGCCACCAGT
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTT-TTTCGATCTGCTTCGCCACCAGT
*
42378750 ATGGGAAGGCAAGATCTGGTATCTC
65 ATGGGAAGGCAAGATCTGTTATCTC
42378775 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTCCTTCGATCTGCTTCGCCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC-TTTT--TTCGATCTGCTTCGCCACCA
* *
42378840 GTATAGGAAGGCAAGATCTATTATCTC
63 GTATGGGAAGGCAAGATCTGTTATCTC
42378867 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTT-GATCTGCTTCGCCACCAGT
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTT-TTTCGATCTGCTTCGCCACCAGT
42378931 ATGGGAAGGCAAGATCTGTTATCTC
65 ATGGGAAGGCAAGATCTGTTATCTC
* *
42378956 TGATCTACTTCACGCCAATTCATGAAGACAAGATCTGCTTTCTTT-GATCTGCTTCGCCACCAGT
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTT-TTTCGATCTGCTTCGCCACCAGT
*
42379020 ATGGGAAGGCAAGATCTGGTATCTC
65 ATGGGAAGGCAAGATCTGTTATCTC
* *
42379045 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTTTTCCTTCGATCTGCTTCTCCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-CTTTT--TTCGATCTGCTTCGCCACCA
* *
42379110 GTATGGGAATGCAAGATCTATTATCTC
63 GTATGGGAAGGCAAGATCTGTTATCTC
*
42379137 TGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTT-GATCTGCTTTCTTTGATCT
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTT-TTTCGATCTG----C--T--TC-
* ** * * * * * * *
42379201 GCTTCGCCACCA--GTATGGGAAG-GCAAGATCTGTAATC
56 GC--CACCAGTATGGGAAGGCAAGATC-TG-T-TAT-CTC
* *
42379238 TCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAG
1 T--GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTTCGATCTGCTTCGCCACCAG
** * *
42379303 TATGGGAAGATAAGATCTGGTATCTT
64 TATGGGAAGGCAAGATCTGTTATCTC
*
42379329 TGATCTACTTCACGTCAGTACATGAAGACAAGATCTGCTTTTTCCTTCGATCTGCTTCGCCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC-TTTT--TTCGATCTGCTTCGCCACCA
***********************
42379394 GTATNNNNNNNNNNNNNNNNNNNNNNN
63 GTATGGGAAGGCAAGATCTGTTATCTC
*****************************************************************
42379421 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTTCGATCTGCTTCGCCACCAGTA
************
42379486 NNNNNNNNNNNNATCTGTTATCTC
66 TGGGAAGGCAAGATCTGTTATCTC
42379510 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTT-GATCTGCTTCGCCACCAGT
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTT-TTTCGATCTGCTTCGCCACCAGT
*
42379574 ATGGGAAGGCAAGATCTGGTATCTC
65 ATGGGAAGGCAAGATCTGTTATCTC
* * *
42379599 TGATCTACTTCACGCCAGTACATGAAGGCAAGATCTACTTTCTTCGATCTGCTTCGCCACCAGTA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTTCGATCTGCTTCGCCACCAGTA
*
42379664 TGGGAAGGCAAGATCTGGTATCTC
66 TGGGAAGGCAAGATCTGTTATCTC
*
42379688 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTTTCCTTCGATCTGCTTCGCCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC-TTTT--TTCGATCTGCTTCGCCACCA
*
42379753 GTATGGGAAGGCAAGATCTATTATCTC
63 GTATGGGAAGGCAAGATCTGTTATCTC
42379780 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTT-GATCTGCTTCGCCACCAGT
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTT-TTTCGATCTGCTTCGCCACCAGT
42379844 ATGGGAAGGCAAGATCTGTTATCTC
65 ATGGGAAGGCAAGATCTGTTATCTC
*
42379869 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTT-GATCTGCTTTGCCACCAGT
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTT-TTTCGATCTGCTTCGCCACCAGT
* *
42379933 ATGGAAAGG-AAGATTTGTTATCTC
65 ATGGGAAGGCAAGATCTGTTATCTC
**
42379957 TGATCTACTTCACGCTGGTACATGAAGACAA
1 TGATCTACTTCACGCCAGTACATGAAGACAA
42379988 AAACCGCTAT
Statistics
Matches: 1473, Mismatches: 312, Indels: 115
0.78 0.16 0.06
Matches are distributed among these distances:
85 14 0.01
88 65 0.04
89 760 0.52
90 34 0.02
91 78 0.05
92 439 0.30
93 1 0.00
94 9 0.01
95 4 0.00
97 4 0.00
98 7 0.00
99 2 0.00
100 7 0.00
101 3 0.00
102 2 0.00
103 44 0.03
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.30
Consensus pattern (89 bp):
TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTTCGATCTGCTTCGCCACCAGTA
TGGGAAGGCAAGATCTGTTATCTC
Found at i:42378380 original size:181 final size:182
Alignment explanation
Indices: 42378059--42379397 Score: 1598
Period size: 181 Copynumber: 7.4 Consensus size: 182
42378049 CTGCTGCGCT
* * * *
42378059 TGATCTACTTCACGCC---A-ATGAAGACAAGGTCTG-TTCTCTTCGATCTACTCCACCACCAGT
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTCTTTTCGATCTACTTCGCCACCAGT
* * * * * * * *
42378119 ATGGGGAGACAAGATCTGTTGTCTTTGATCTACTTCATGCTAATACATGGAGACAAGATCTGCTT
66 ATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* * * *
42378184 T-TTCCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATTTGTTACCTT
131 TCTT-CTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTC
* * *
42378236 TGATATACTTCACGCCAGTACATGAAGACAAGATCT-ATTCTTTTCGATCTACTCCACCACCAGT
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTCTTTTCGATCTACTTCGCCACCAGT
* * * * * *
42378300 ATGGGGAGACAAGATCTTTTGTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG-TT
66 ATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* * * * *
42378364 TCTTCCTTCGATCTACTTCGCTACCAGTAT-GGAAGACAAGATTTGTTACCTT
131 TCTT-CTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTC
* * ** *
42378416 TGATCTACTTCACGCCAGTACATGAAGACAAGATCT-ACTT-TCTTCGATTTGTTTCGCCACTAG
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGA-TTCTTTTCGATCTACTTCGCCACCAG
* * * *
42378479 TATAGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAATATCTGCT
65 TATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT
* * *
42378544 TTCTT-TT--ATCTGCTTCGCCACCAGTATGTGAAGGCAAGATCTGGTATCTC
130 TTCTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTC
* * *
42378594 TGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGCCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTCTT--TTCGATCTACTTCGCCACCA
*
42378659 GTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATAAAGACAAGATCTGC
64 GTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* *
42378724 TTTC-T-TT-GATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTC
129 TTTCTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTC
* * *
42378775 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTCCTTCGATCTGCTTCGCCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTCTT--TTCGATCTACTTCGCCACCA
* *
42378840 GTATAGGAAGGCAAGATCTATTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
64 GTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
*
42378905 TTTC-T-TT-GATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTC
129 TTTCTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTC
* * * *
42378956 TGATCTACTTCACGCCAATTCATGAAGACAAGATCTGCTT-TCTTT-GATCTGCTTCGCCACCAG
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTCT-TTTCGATCTACTTCGCCACCAG
* *
42379019 TATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGAT
65 TATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT
* *
42379084 TT-TTCCTTCGATCTGCTTCTCCACCAGTATGGGAATG-CAAGATCTATTATCTC
130 TTCTT-CTTCGATCTGCTTCGCCACCAGTATGGGAA-GACAAGATCTGTTATCTC
* * *
42379137 TGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTGCTTTCTTTGATCTG
1 TGATCTACTTCACGCCAGTACATGAAGACAAGA-------TC--TGAT-T-C-TT-TTCGATCTA
*
42379202 CTTCGCCACCAGTATGGGAAGGCAAGATCTGTAATCTCTGATCTACTTCACGCCAGTACATGAAG
53 CTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAG
* * * *
42379267 ACAAGATCTGC--T-TTCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGGTATCTT
118 ACAAGATCTGCTTTCTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTC
* * * *
42379329 TGATCTACTTCACGTCAGTACATGAAGACAAGATCTGCTTTTTCCTTCGATCTGCTTCGCCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTCTT--TTCGATCTACTTCGCCACCA
42379394 GTAT
64 GTAT
42379398 NNNNNNNNNN
Statistics
Matches: 1049, Mismatches: 76, Indels: 70
0.88 0.06 0.06
Matches are distributed among these distances:
177 33 0.03
178 135 0.13
179 5 0.00
180 143 0.14
181 562 0.54
182 2 0.00
183 3 0.00
185 2 0.00
188 2 0.00
190 3 0.00
191 2 0.00
192 71 0.07
193 4 0.00
194 3 0.00
195 79 0.08
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (182 bp):
TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTCTTTTCGATCTACTTCGCCACCAGT
ATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
TCTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTC
Found at i:42378804 original size:270 final size:271
Alignment explanation
Indices: 42378059--42379987 Score: 1809
Period size: 270 Copynumber: 7.1 Consensus size: 271
42378049 CTGCTGCGCT
* * * *
42378059 TGATCTACTTCACGCC---A-ATGAAGACAAGGTCTG--TTCT-CTTCGATCTACTCCACCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGCCACCA
* * * * * * * *
42378117 GTATGGGGAGACAAGATCTGTTGTCTTTGATCTACTTCATGCTAATACATGGAGACAAGATCTGC
66 GTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * * * * * * *
42378182 TTTTTCCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATTTGTTACCTTTGATATACTTC
131 --TTT-CTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTC
* * * * * *
42378247 ACGCCAGTACATGAAGACAAGATCT--ATTCTTTTCGATCTACTCCACCACCAGTATGGGGAGAC
193 ACGCCAGTACATGAAGACAAGATCTGCTTTCTTTTC-ATCTGCTTCGCCACCAGTATGGGAAGGC
* * *
42378310 AAGATCTTTTGTCTT
257 AAGATCTGTTATCTC
* * *
42378325 TGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTCTTCCTTCGATCTACTTCGCTACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGCCACCA
* * * * *
42378390 GTAT-GGAAGACAAGATTTGTTACCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTAC
66 GTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * * * * * * *
42378454 TTTCTTCGATTTGTTTCGCCACTAGTATAGGAAGACAAGATCTGTTATCTTTGATCTACTTCACG
131 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
* *
42378519 CCAGTACATGAAGACAATATCTGCTTTCTTTT-ATCTGCTTCGCCACCAGTATGTGAAGGCAAGA
196 CCAGTACATGAAGACAAGATCTGCTTTCTTTTCATCTGCTTCGCCACCAGTATGGGAAGGCAAGA
*
42378583 TCTGGTATCTC
261 TCTGTTATCTC
*
42378594 TGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGCCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGCCACCA
*
42378659 GTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATAAAGACAAGATCTGC
66 GTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
42378724 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
131 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
*
42378789 CCAGTACATGAAGACAAGATCTGCTTT-TTCCTTCGATCTGCTTCGCCACCAGTATAGGAAGGCA
196 CCAGTACATGAAGACAAGATCTGCTTTCTT--TTC-ATCTGCTTCGCCACCAGTATGGGAAGGCA
*
42378853 AGATCTATTATCTC
258 AGATCTGTTATCTC
* * *
42378867 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTG--CTTT-CTTTGATCTGCTTCGCCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGCCACCA
* *
42378929 GTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAATTCATGAAGACAAGATCTGC
66 GTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
42378994 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
131 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
* * *
42379059 CCAGTACATGAAGACAAGATCTGATTT-TTCCTTCGATCTGCTTCTCCACCAGTATGGGAATGCA
196 CCAGTACATGAAGACAAGATCTGCTTTCTT--TTC-ATCTGCTTCGCCACCAGTATGGGAAGGCA
*
42379123 AGATCTATTATCTC
258 AGATCTGTTATCTC
* *
42379137 TGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTGCTTTCTTTGATCTG
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTG--TT-TTT--TC--C-TTC---GATCTA
*
42379202 CTTCGCCACCAGTATGGGAAGGCAAGATCTGTAATCTCTGATCTACTTCACGCCAGTACATGAAG
55 CTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAG
* * ** *
42379267 ACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGGTATCTTTGA
120 ACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGA
*
42379332 TCTACTTCACGTCAGTACATGAAGACAAGATCTGCTTT-TTCCTTCGATCTGCTTCGCCACCAGT
185 TCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT--TTC-ATCTGCTTCGCCACCAGT
********************
42379396 AT---NNNNNNNNNNNNNNNNNNNN
247 ATGGGAAGGCAAGATCTGTTATCTC
*****************************************************************
42379418 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGCCACCA
***************
42379483 NNNNNNNNNNNNNNNATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
66 GTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
42379548 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
131 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
* *
42379613 CCAGTACATGAAGGCAAGATCTACTTTC--TTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAG
196 CCAGTACATGAAGACAAGATCTGCTTTCTTTTC-ATCTGCTTCGCCACCAGTATGGGAAGGCAAG
*
42379676 ATCTGGTATCTC
260 ATCTGTTATCTC
** *
42379688 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTTTCCTTCGATCTGCTTCGCCACCA
1 TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGCCACCA
*
42379753 GTATGGGAAGGCAAGATCTATTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
66 GTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
*
42379818 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACG
131 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
* * *
42379883 CCAGTACATGAAGACAAGATCTGCTTTC-TTTGATCTGCTTTGCCACCAGTATGGAAAGG-AAGA
196 CCAGTACATGAAGACAAGATCTGCTTTCTTTTCATCTGCTTCGCCACCAGTATGGGAAGGCAAGA
*
42379946 TTTGTTATCTC
261 TCTGTTATCTC
**
42379957 TGATCTACTTCACGCTGGTACATGAAGACAA
1 TGATCTACTTCACGCCAGTACATGAAGACAA
42379988 AAACCGCTAT
Statistics
Matches: 1327, Mismatches: 303, Indels: 63
0.78 0.18 0.04
Matches are distributed among these distances:
266 16 0.01
267 24 0.02
269 218 0.16
270 708 0.53
271 14 0.01
272 53 0.04
273 97 0.07
275 2 0.00
277 1 0.00
280 1 0.00
281 2 0.00
284 191 0.14
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.30
Consensus pattern (271 bp):
TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGCCACCA
GTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
CCAGTACATGAAGACAAGATCTGCTTTCTTTTCATCTGCTTCGCCACCAGTATGGGAAGGCAAGA
TCTGTTATCTC
Found at i:42379187 original size:14 final size:14
Alignment explanation
Indices: 42379168--42379204 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
42379158 ATGAAGACAA
42379168 GATCTGCTTTCTTT
1 GATCTGCTTTCTTT
42379182 GATCTGCTTTCTTT
1 GATCTGCTTTCTTT
42379196 GATCTGCTT
1 GATCTGCTT
42379205 CGCCACCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.22, G:0.16, T:0.54
Consensus pattern (14 bp):
GATCTGCTTTCTTT
Found at i:42379227 original size:103 final size:103
Alignment explanation
Indices: 42379093--42379289 Score: 340
Period size: 103 Copynumber: 1.9 Consensus size: 103
42379083 TTTTTCCTTC
* * *
42379093 GATCTGCTTCTCCACCAGTATGGGAATGCAAGATCTATTATCTCTGATCTACTTCACACCAGTAC
1 GATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTATAATCTCTGATCTACTTCACACCAGTAC
*
42379158 ATGAAGACAAGATCTGCTTTCTTTGATCTGCTTTCTTT
66 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTTCTTT
* *
42379196 GATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTAATCTCTGATCTACTTCACGCCAGTAC
1 GATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTATAATCTCTGATCTACTTCACACCAGTAC
42379261 ATGAAGACAAGATCTGCTTTCTTCGATCT
66 ATGAAGACAAGATCTGCTTTCTTCGATCT
42379290 ACTTCGCCAC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 88 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (103 bp):
GATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTATAATCTCTGATCTACTTCACACCAGTAC
ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTTCTTT
Found at i:42379273 original size:44 final size:42
Alignment explanation
Indices: 42379219--42379365 Score: 150
Period size: 44 Copynumber: 3.3 Consensus size: 42
42379209 ACCAGTATGG
*
42379219 GAAGGCAAGATCTGTAATCTCTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGT-ATCT-TGATCTACTTCACGCCAGTACAT
* * * ***
42379263 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTG-TATCTT-GATCTACTTC-ACGCCAGTACAT
* *
42379308 GAAGATAAGATCTGGTATCTTTGATCTACTTCACGTCAGTACAT
1 GAAGACAAGATCT-GTATC-TTGATCTACTTCACGCCAGTACAT
42379352 GAAGACAAGATCTG
1 GAAGACAAGATCTG
42379366 CTTTTTCCTT
Statistics
Matches: 82, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
43 2 0.02
44 44 0.54
45 33 0.40
46 3 0.04
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (42 bp):
GAAGACAAGATCTGTATCTTGATCTACTTCACGCCAGTACAT
Found at i:42379318 original size:45 final size:45
Alignment explanation
Indices: 42379182--42379397 Score: 179
Period size: 45 Copynumber: 4.8 Consensus size: 45
42379172 TGCTTTCTTT
* * * *
42379182 GATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAA
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATAGGAAGACAA
* * * * *
42379227 GATCTG-TAATC-TCTGATCTACTTC-ACGCCAGTACATGAAGACAA
1 GATCTGCT-TTCTTC-GATCTACTTCGCCACCAGTATAGGAAGACAA
* *
42379271 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGATAA
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATAGGAAGACAA
* * * * ** * *
42379316 GATCTGGTATCTTTGATCTACTTC-ACGTCAGTACATGAAGACAA
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATAGGAAGACAA
*
42379360 GATCTGCTTTTTCCTTCGATCTGCTTCGCCACCAGTAT
1 GATCTGC--TTT-CTTCGATCTACTTCGCCACCAGTAT
42379398 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 34, Indels: 15
0.72 0.19 0.08
Matches are distributed among these distances:
44 53 0.41
45 55 0.43
46 2 0.02
47 12 0.09
48 6 0.05
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (45 bp):
GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATAGGAAGACAA
Found at i:42379383 original size:195 final size:194
Alignment explanation
Indices: 42378987--42379385 Score: 626
Period size: 195 Copynumber: 2.0 Consensus size: 194
42378977 ATGAAGACAA
42378987 GATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTA
1 GATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTA
* * *
42379052 CTTCACGCCAGTACATGAAGACAAGATCTGATTTTTCCTTCGATCTGCTTCTCCACCAGTATGGG
66 CTTCACGCCAGTACATGAAGACAAGATCTGA-CTTTCCTTCGATCTACTTCGCCACCAGTATGGG
* *
42379117 AATGCAAGATCTATTATCTCTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTT
130 AATGCAAGATCTAGTATCTCTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTC
42379182 GATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCT-GTAATCTCTGATCT
1 GATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGT-ATCTCTGATCT
42379246 ACTTCACGCCAGTACATGAAGACAAGATCTG-CTTT-CTTCGATCTACTTCGCCACCAGTATGGG
65 ACTTCACGCCAGTACATGAAGACAAGATCTGACTTTCCTTCGATCTACTTCGCCACCAGTATGGG
* * * **
42379309 AA-GATAAGATCTGGTATCTTTGATCTACTTCACGTCAGTACATGAAGACAAGATCTGCTTTTTC
130 AATG-CAAGATCTAGTATCTCTGATCTACTTCACACCAGTACATGAAGACAAGATCTGC--TTT-
42379373 CTTC
191 CTTC
42379377 GATCTGCTT
1 GATCTGCTT
42379386 CGCCACCAGT
Statistics
Matches: 189, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
191 1 0.01
192 76 0.40
193 3 0.02
194 5 0.03
195 104 0.55
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (194 bp):
GATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTA
CTTCACGCCAGTACATGAAGACAAGATCTGACTTTCCTTCGATCTACTTCGCCACCAGTATGGGA
ATGCAAGATCTAGTATCTCTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTC
Found at i:42379805 original size:181 final size:178
Alignment explanation
Indices: 42379498--42379987 Score: 829
Period size: 181 Copynumber: 2.7 Consensus size: 178
42379488 NNNNNNNNNN
42379498 ATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTGCT
1 ATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTGCT
* *
42379563 TCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGGC
66 TCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGAC
42379628 AAGATCTACTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAG
131 AAGATCTACTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAG
* * *
42379676 ATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTTTCCTTCGATCT
1 ATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC--TTT-CTTTGATCT
*
42379741 GCTTCGCCACCAGTATGGGAAGGCAAGATCTATTATCTCTGATCTACTTCACGCCAGTACATGAA
63 GCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAA
* *
42379806 GACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAG
128 GACAAGATCTACTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAG
42379857 ATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTGCT
1 ATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTGCT
* * * **
42379922 TTGCCACCAGTATGGAAAGG-AAGATTTGTTATCTCTGATCTACTTCACGCTGGTACATGAAGAC
66 TCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGAC
42379986 AA
131 AA
42379988 AAACCGCTAT
Statistics
Matches: 292, Mismatches: 17, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
177 42 0.14
178 77 0.26
179 3 0.01
180 3 0.01
181 167 0.57
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (178 bp):
ATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTGCT
TCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGAC
AAGATCTACTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAG
Found at i:42391037 original size:18 final size:18
Alignment explanation
Indices: 42391016--42391055 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
42391006 AAAAAATCTT
*
42391016 TAAAATTTCAAAAAATAA
1 TAAAATTTAAAAAAATAA
*
42391034 TAAATTTTAAAAAAATAA
1 TAAAATTTAAAAAAATAA
42391052 -AAAA
1 TAAAA
42391056 GCCCTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAATTTAAAAAAATAA
Found at i:42401327 original size:22 final size:22
Alignment explanation
Indices: 42401299--42401341 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42401289 AGATAGAGAT
*
42401299 AGAAAGAGCTAAGTCTTTTTTC
1 AGAAAGAGCTAACTCTTTTTTC
*
42401321 AGAAAGAGCTAACTTTTTTTT
1 AGAAAGAGCTAACTCTTTTTT
42401342 TTCTTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (22 bp):
AGAAAGAGCTAACTCTTTTTTC
Found at i:42406542 original size:42 final size:43
Alignment explanation
Indices: 42406495--42406593 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
42406485 AAACTAAGAC
* *
42406495 CTTTAGCGGCGCTTTAGTG-GAAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGCTTTAGCGAGAAGCGCCGCTAAAGATCAAGGT
* * * *
42406537 CTTTAGCGGCGTTTTTGCGAGAAGCGTCGCTAAAGATTAAGGT
1 CTTTAGCGGCGCTTTAGCGAGAAGCGCCGCTAAAGATCAAGGT
42406580 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
42406594 CGACCACAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 16 0.33
43 33 0.67
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTAGCGAGAAGCGCCGCTAAAGATCAAGGT
Found at i:42406648 original size:43 final size:42
Alignment explanation
Indices: 42406601--42406699 Score: 103
Period size: 43 Copynumber: 2.3 Consensus size: 42
42406591 CTTCGACCAC
*
42406601 AAACGCCACTAAAGAACCAA-ATCTTTAGCGGAGCTTTTATT-AA
1 AAACGCCACTAAAG-ACCAACACCTTTAGCGGAG-TTTT-TTAAA
* * * *
42406644 AAACGCCGCTAAAGGCCAACACCTTTAGTGGCGTTTTTTAAAA
1 AAACGCCACTAAAGACCAACACCTTTAGCGGAGTTTTTT-AAA
42406687 AAACGCCACTAAA
1 AAACGCCACTAAA
42406700 TTTGGCTGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
41 2 0.04
42 8 0.17
43 37 0.79
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (42 bp):
AAACGCCACTAAAGACCAACACCTTTAGCGGAGTTTTTTAAA
Found at i:42407035 original size:21 final size:21
Alignment explanation
Indices: 42407006--42407065 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
42406996 TTTGACGCTG
*
42407006 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
**
42407027 CTCTACTTCCCTCGCTATAGC
1 CTCTACTTCCCTCGCTGCAGC
* *
42407048 CTCTACTTCTCTTGCTGC
1 CTCTACTTCCCTCGCTGC
42407066 CGCATCTGCT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.08, C:0.43, G:0.13, T:0.35
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCAGC
Found at i:42407198 original size:66 final size:65
Alignment explanation
Indices: 42407067--42407217 Score: 223
Period size: 66 Copynumber: 2.3 Consensus size: 65
42407057 TCTTGCTGCC
*
42407067 GCATCTGCTTTAAGCTGCTGCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCAATGT
1 GCATCTGCTTTAAGTTG-TGCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCAATGT
42407132 T
65 T
* *
42407133 GCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATG
1 GCATCTGCTTTAAGTTGT-GCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCAATG
42407197 TT
64 TT
* *
42407199 GCCTCCGCTTTAAGTTGTG
1 GCATCTGCTTTAAGTTGTG
42407218 TAATTTGCTC
Statistics
Matches: 78, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
65 2 0.03
66 72 0.92
67 4 0.05
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (65 bp):
GCATCTGCTTTAAGTTGTGCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCAATGTT
Found at i:42412663 original size:9 final size:9
Alignment explanation
Indices: 42412614--42412923 Score: 209
Period size: 9 Copynumber: 36.8 Consensus size: 9
42412604 AATTGCACGG
42412614 GTAAGTTAT
1 GTAAGTTAT
42412623 GT-A-TTAT
1 GTAAGTTAT
*
42412630 GTAAGCTAT
1 GTAAGTTAT
*
42412639 GTAAGTTGT
1 GTAAGTTAT
42412648 GT-A-TTAT
1 GTAAGTTAT
42412655 GTAAGTTAT
1 GTAAGTTAT
42412664 -T-A-TTAT
1 GTAAGTTAT
42412670 GTAAGTTAT
1 GTAAGTTAT
*
42412679 GTAAGTAAT
1 GTAAGTTAT
42412688 GT-A-TTAT
1 GTAAGTTAT
*
42412695 GTAAGTTGT
1 GTAAGTTAT
*
42412704 GT-A-TAAT
1 GTAAGTTAT
*
42412711 GTTAGTTAT
1 GTAAGTTAT
**
42412720 CAAAGTTAT
1 GTAAGTTAT
42412729 GT-A-TTAT
1 GTAAGTTAT
42412736 GTAAGTTAT
1 GTAAGTTAT
*
42412745 TTAAGTTAT
1 GTAAGTTAT
*
42412754 GTAAGTTGT
1 GTAAGTTAT
42412763 GT-A-TTAT
1 GTAAGTTAT
42412770 GTAAGTTAT
1 GTAAGTTAT
* *
42412779 GTAGGCTAT
1 GTAAGTTAT
* *
42412788 GTATGTTAA
1 GTAAGTTAT
*
42412797 GTAAGTCAT
1 GTAAGTTAT
42412806 GT-A-TTAT
1 GTAAGTTAT
*
42412813 GTAAGTTGT
1 GTAAGTTAT
*
42412822 GT-A-TAAT
1 GTAAGTTAT
*
42412829 GTTAGTTAT
1 GTAAGTTAT
**
42412838 CAAAGTTAT
1 GTAAGTTAT
42412847 GT-A-TTAT
1 GTAAGTTAT
42412854 GTAAGTTAT
1 GTAAGTTAT
*
42412863 TTAAGTTAT
1 GTAAGTTAT
*
42412872 GTAAGTTGT
1 GTAAGTTAT
42412881 GT-A-TTAT
1 GTAAGTTAT
42412888 GTAAGTTAT
1 GTAAGTTAT
*
42412897 -TATGTTATTAT
1 GTAAG---TTAT
42412908 GTAAGTTAT
1 GTAAGTTAT
*
42412917 GCAAGTT
1 GTAAGTT
42412924 TATATATAAG
Statistics
Matches: 230, Mismatches: 44, Indels: 54
0.70 0.13 0.16
Matches are distributed among these distances:
6 4 0.02
7 53 0.23
8 25 0.11
9 141 0.61
11 4 0.02
12 3 0.01
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:42412669 original size:15 final size:16
Alignment explanation
Indices: 42412636--42412917 Score: 141
Period size: 16 Copynumber: 16.8 Consensus size: 16
42412626 TTATGTAAGC
*
42412636 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
42412652 TATGTAAGTTAT-TAT
1 TATGTAAGTTATGTAT
42412667 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
*
42412685 AATGT-A-TTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
42412701 TGTGT-A-TAATGTTAGT
1 TATGTAAGTTATG-TA-T
**
42412717 TATCAAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
42412733 TATGTAAGTTATTTAAGT
1 TATGTAAGTTATGT-A-T
*
42412751 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
*
42412767 TATGTAAGTTATGTAGGC
1 TATGTAAGTTATGTA--T
* *
42412785 TATGTATGTTAAGTAAGT
1 TATGTAAGTTATGT-A-T
*
42412803 CATGT-A-TTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
42412819 TGTGT-A-TAATGTTAGT
1 TATGTAAGTTATG-TA-T
**
42412835 TATCAAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
42412851 TATGTAAGTTATTTAAGT
1 TATGTAAGTTATGT-A-T
*
42412869 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
42412885 TATGTAAGTTATTATGTTAT
1 TATGTAAG---TTATG-TAT
42412905 TATGTAAGTTATG
1 TATGTAAGTTATG
42412918 CAAGTTTATA
Statistics
Matches: 211, Mismatches: 35, Indels: 39
0.74 0.12 0.14
Matches are distributed among these distances:
15 15 0.07
16 105 0.50
17 19 0.09
18 56 0.27
19 5 0.02
20 11 0.05
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.48
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:42412698 original size:25 final size:25
Alignment explanation
Indices: 42412620--42412923 Score: 134
Period size: 25 Copynumber: 12.0 Consensus size: 25
42412610 ACGGGTAAGT
*
42412620 TATGTATTATGTAAGCTATGTAAGT
1 TATGTATTATGTAAGTTATGTAAGT
*
42412645 TGTGTATTATGTAAGTTAT-T-A-T
1 TATGTATTATGTAAGTTATGTAAGT
*
42412667 TATGTAAGTTATGTAAGTAATGT-A-T
1 TATGT-A-TTATGTAAGTTATGTAAGT
* * *
42412692 TATGTAAGTTGTGT-A-TAATGTTAGT
1 TATGT-A-TTATGTAAGTTATGTAAGT
**
42412717 TATCAAAGTTATGT-A-TTATGTAAGT
1 TAT-GTA-TTATGTAAGTTATGTAAGT
* *
42412742 TATTTAAGTTATGTAAGTTGTGT-A-T
1 TATGT-A-TTATGTAAGTTATGTAAGT
* * *
42412767 TATGTAAGTTATGTAGGCTATGTATGT
1 TATGT-A-TTATGTAAGTTATGTAAGT
* *
42412794 TAAGTAAGTCATGT-A-TTATGTAAGT
1 TATGT-A-TTATGTAAGTTATGTAAGT
* * * **
42412819 TGTGTATAATGTTAGTTATCAAAGT
1 TATGTATTATGTAAGTTATGTAAGT
*
42412844 TATGTATTATGTAAGTTATTTAAGT
1 TATGTATTATGTAAGTTATGTAAGT
*
42412869 TATGTAAGTTGTGT-A-TTATGTAAGTTAT
1 TATGT-A-TTATGTAAGTTATGTAAG---T
*
42412897 TATGTTATTATGTAAGTTATGCAAGT
1 TATG-TATTATGTAAGTTATGTAAGT
42412923 T
1 T
42412924 TATATATAAG
Statistics
Matches: 221, Mismatches: 37, Indels: 41
0.74 0.12 0.14
Matches are distributed among these distances:
22 5 0.02
23 13 0.06
24 17 0.08
25 136 0.62
26 6 0.03
27 28 0.13
28 7 0.03
29 9 0.04
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (25 bp):
TATGTATTATGTAAGTTATGTAAGT
Found at i:42412789 original size:34 final size:33
Alignment explanation
Indices: 42412636--42412904 Score: 152
Period size: 34 Copynumber: 8.6 Consensus size: 33
42412626 TTATGTAAGC
* *
42412636 TATGTAAGTTGTGTA-TTATGTAAGTTAT-TAT
1 TATGTAAGTTATGTAGTTATGTAAGTTGTGTAT
* *
42412667 TATGTAAGTTATGTAAGTAATGT-A-TTATGTAAGT
1 TATGTAAGTTATGT-AGTTATGTAAGTTGTGT-A-T
* * ** *
42412701 TGTGT-A-TAATGTTAGTTATCAAAGTTATGTAT
1 TATGTAAGTTATG-TAGTTATGTAAGTTGTGTAT
*
42412733 TATGTAAGTTATTTAAGTTATGTAAGTTGTGTAT
1 TATGTAAGTTATGT-AGTTATGTAAGTTGTGTAT
*
42412767 TATGTAAGTTATGTAGGCTATGT-A--TGT-TA-
1 TATGTAAGTTATGTA-GTTATGTAAGTTGTGTAT
*
42412796 -A-GTAAGTCATGTA-TTATGTAAGTTGTG---
1 TATGTAAGTTATGTAGTTATGTAAGTTGTGTAT
* ** *
42412823 TA--TAA--TGT-TAGTTATCAAAGTTATGTAT
1 TATGTAAGTTATGTAGTTATGTAAGTTGTGTAT
*
42412851 TATGTAAGTTATTTAAGTTATGTAAGTTGTGTAT
1 TATGTAAGTTATGT-AGTTATGTAAGTTGTGTAT
42412885 TATGTAAGTTAT-TATGTTAT
1 TATGTAAGTTATGTA-GTTAT
42412905 TATGTAAGTT
Statistics
Matches: 184, Mismatches: 26, Indels: 54
0.70 0.10 0.20
Matches are distributed among these distances:
24 2 0.01
25 17 0.09
26 1 0.01
27 14 0.08
28 7 0.04
30 5 0.03
31 20 0.11
32 20 0.11
33 21 0.11
34 77 0.42
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.48
Consensus pattern (33 bp):
TATGTAAGTTATGTAGTTATGTAAGTTGTGTAT
Found at i:42412822 original size:118 final size:115
Alignment explanation
Indices: 42412619--42412898 Score: 465
Period size: 118 Copynumber: 2.4 Consensus size: 115
42412609 CACGGGTAAG
* * * *
42412619 TTATGT-A-TTATGTAAGCTATGTAAGTTGTGTATTATGTAAGTTATTATTATGTAAGTTATGTA
1 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATTACTATGTAAGTTAAGTA
42412682 AGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
66 AGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
*
42412732 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTATGTTAA
1 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTAT-TA--CTATGTAAGTTAA
*
42412797 GTAAGTCATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
63 GTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
42412850 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATTA
1 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATTA
42412899 TGTTATTATG
Statistics
Matches: 156, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
113 6 0.04
114 1 0.01
115 36 0.23
116 2 0.01
117 2 0.01
118 109 0.70
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (115 bp):
TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATTACTATGTAAGTTAAGTA
AGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
Found at i:42413220 original size:40 final size:38
Alignment explanation
Indices: 42413176--42413435 Score: 210
Period size: 40 Copynumber: 6.7 Consensus size: 38
42413166 TATATAAATT
42413176 TTTAA-TATATATATATATAAATTTTAAGTAATGTAATATA
1 TTTAAGTA-ATATATATATAAATTTT-AGTAA-GTAATATA
* *
42413216 TTTAAGTAATGTA-AGTTATAAATTTTTGTAAGTAATATA
1 TTTAAGTAATATATA--TATAAATTTTAGTAAGTAATATA
* *
42413255 TTTAAGTAATGTA-ATAT--ATTTTAGTAAGTAATGTA
1 TTTAAGTAATATATATATAAATTTTAGTAAGTAATATA
** * * *
42413290 AGTAATGTAATATATACT-TTAATTTTAGTAAGTCATGTA
1 TTTAA-GTAATATATA-TATAAATTTTAGTAAGTAATATA
* * *
42413329 TTTAAGTAATATATTTAAGTAAATTCTAGTAAGTAATGTA
1 TTTAAGTAATATATAT-A-TAAATTTTAGTAAGTAATATA
* * *
42413369 TTTAAGTAATATATTTAAGTAAATTTTAGTGATTAATATA
1 TTTAAGTAATATATAT-A-TAAATTTTAGTAAGTAATATA
*
42413409 TTTAAGTAATGTA-AGTTATAAATTTTA
1 TTTAAGTAATATATA--TATAAATTTTA
42413436 AAAATATATA
Statistics
Matches: 187, Mismatches: 20, Indels: 27
0.80 0.09 0.12
Matches are distributed among these distances:
35 19 0.10
36 7 0.04
37 6 0.03
38 10 0.05
39 52 0.28
40 80 0.43
41 13 0.07
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.46
Consensus pattern (38 bp):
TTTAAGTAATATATATATAAATTTTAGTAAGTAATATA
Found at i:42413221 original size:18 final size:18
Alignment explanation
Indices: 42413198--42413286 Score: 101
Period size: 18 Copynumber: 4.8 Consensus size: 18
42413188 ATATATAAAT
42413198 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
42413216 TTTAAGTAATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
**
42413238 TTTTTGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
42413255 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
*
42413273 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
42413287 GTAAGTAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
17 13 0.21
18 30 0.49
19 3 0.05
20 3 0.05
21 4 0.07
22 8 0.13
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:42413281 original size:31 final size:31
Alignment explanation
Indices: 42413200--42413304 Score: 100
Period size: 31 Copynumber: 3.5 Consensus size: 31
42413190 ATATAAATTT
42413200 TAAGTAATGTAATATA--TT--TAAGTAATG
1 TAAGTAATGTAATATATTTTAGTAAGTAATG
* * *
42413227 TAAGT--TATAA-ATTTTTGTAAGTAA-TATATT
1 TAAGTAATGTAATATATTT-T-AGTAAGTA-ATG
42413257 TAAGTAATGTAATATATTTTAGTAAGTAATG
1 TAAGTAATGTAATATATTTTAGTAAGTAATG
42413288 TAAGTAATGTAATATAT
1 TAAGTAATGTAATATAT
42413305 ACTTTAATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
24 2 0.03
25 4 0.07
26 1 0.02
27 6 0.10
29 2 0.03
30 10 0.16
31 24 0.39
32 7 0.11
33 5 0.08
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (31 bp):
TAAGTAATGTAATATATTTTAGTAAGTAATG
Found at i:42413343 original size:13 final size:13
Alignment explanation
Indices: 42413327--42413418 Score: 84
Period size: 13 Copynumber: 6.9 Consensus size: 13
42413317 GTAAGTCATG
42413327 TATTTAAGTAATA
1 TATTTAAGTAATA
42413340 TATTTAAGTAA-A
1 TATTTAAGTAATA
*
42413352 T-TCTAGTAAGTAATG
1 TAT-T--TAAGTAATA
42413367 TATTTAAGTAATA
1 TATTTAAGTAATA
42413380 TATTTAAGTAA-A
1 TATTTAAGTAATA
*
42413392 T-TTTAGTGATTAATA
1 TATTTA---AGTAATA
42413407 TATTTAAGTAAT
1 TATTTAAGTAAT
42413419 GTAAGTTATA
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
11 5 0.08
12 5 0.08
13 35 0.54
14 11 0.17
15 4 0.06
16 5 0.08
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.46
Consensus pattern (13 bp):
TATTTAAGTAATA
Found at i:42414585 original size:22 final size:22
Alignment explanation
Indices: 42414558--42414609 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
42414548 AAGAAAAAAC
42414558 AAGCAAAAG-AGAAAAAGAGAAA
1 AAGCAAAAGAAGAAAAA-AGAAA
*
42414580 GAGC-AAAGAAGAAAAAAGAAA
1 AAGCAAAAGAAGAAAAAAGAAA
*
42414601 AAGGAAAAG
1 AAGCAAAAG
42414610 GGGGGAGAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.71, C:0.04, G:0.25, T:0.00
Consensus pattern (22 bp):
AAGCAAAAGAAGAAAAAAGAAA
Found at i:42414715 original size:10 final size:10
Alignment explanation
Indices: 42414700--42414782 Score: 58
Period size: 10 Copynumber: 7.4 Consensus size: 10
42414690 CTGTCGAAGG
42414700 AGAAGAAAAA
1 AGAAGAAAAA
42414710 AGAAGAAAAA
1 AGAAGAAAAA
* *
42414720 GGAAGAAGAA
1 AGAAGAAAAA
*
42414730 GGAAGAACGAAGA
1 AGAAGAA--AA-A
42414743 AGAAAGAAAAA
1 AG-AAGAAAAA
42414754 AGGGGGAAAGAAAAA
1 A----G-AAGAAAAA
42414769 AGAAGAAAAA
1 AGAAGAAAAA
42414779 AGAA
1 AGAA
42414783 AAAGAATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
10 37 0.61
11 3 0.05
12 3 0.05
13 2 0.03
14 5 0.08
15 11 0.18
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (10 bp):
AGAAGAAAAA
Found at i:42414743 original size:14 final size:14
Alignment explanation
Indices: 42414700--42414750 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
42414690 CTGTCGAAGG
*
42414700 AGAAGAAA-AAAGA
1 AGAAGAAAGAACGA
42414713 AGAA-AAAGGAA-GA
1 AGAAGAAA-GAACGA
*
42414726 AGAAGGAAGAACGA
1 AGAAGAAAGAACGA
42414740 AGAAGAAAGAA
1 AGAAGAAAGAA
42414751 AAAAGGGGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 3 0.09
13 13 0.41
14 16 0.50
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (14 bp):
AGAAGAAAGAACGA
Found at i:42415132 original size:18 final size:19
Alignment explanation
Indices: 42415089--42415134 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
42415079 CCCAGCAGAG
42415089 AGAAAAAAAGAAAGAAAAA
1 AGAAAAAAAGAAAGAAAAA
*
42415108 AG-GAAAAAGAAA-AAAAA
1 AGAAAAAAAGAAAGAAAAA
42415125 AGAAAAAAAG
1 AGAAAAAAAG
42415135 GGTTTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.29
18 15 0.62
19 2 0.08
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AGAAAAAAAGAAAGAAAAA
Found at i:42415321 original size:11 final size:11
Alignment explanation
Indices: 42415290--42415338 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
42415280 GTATTTATAT
42415290 TTTTAATTTAA
1 TTTTAATTTAA
*
42415301 -TTCAATTTTAA
1 TTTTAA-TTTAA
42415312 TTTTAATTT-A
1 TTTTAATTTAA
*
42415322 TTTTAA-ATAA
1 TTTTAATTTAA
42415332 TTTTAAT
1 TTTTAAT
42415339 AAATAAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
9 1 0.03
10 18 0.58
11 8 0.26
12 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:42416533 original size:14 final size:14
Alignment explanation
Indices: 42416514--42416592 Score: 77
Period size: 14 Copynumber: 5.4 Consensus size: 14
42416504 AATCCTAAAT
42416514 CCCTAACTTCTAAC
1 CCCTAACTTCTAAC
*
42416528 CCCTAAATCTTCTAGC
1 CCCT-AA-CTTCTAAC
*
42416544 CCCTAAATTCCTAAC
1 CCCTAACTT-CTAAC
* *
42416559 CCCTAACTCCTAAT
1 CCCTAACTTCTAAC
**
42416573 CCCTAACCCCTAAC
1 CCCTAACTTCTAAC
42416587 CCCTAA
1 CCCTAA
42416593 ACCTTATATC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 28 0.52
15 15 0.28
16 11 0.20
ACGTcount: A:0.29, C:0.44, G:0.01, T:0.25
Consensus pattern (14 bp):
CCCTAACTTCTAAC
Found at i:42416541 original size:16 final size:16
Alignment explanation
Indices: 42416520--42416564 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
42416510 AAATCCCTAA
42416520 CTTCTAACCCCTAAAT
1 CTTCTAACCCCTAAAT
*
42416536 CTTCTAGCCCCTAAAT
1 CTTCTAACCCCTAAAT
*
42416552 -TCCTAACCCCTAA
1 CTTCTAACCCCTAA
42416565 CTCCTAATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.29, C:0.40, G:0.02, T:0.29
Consensus pattern (16 bp):
CTTCTAACCCCTAAAT
Found at i:42416565 original size:7 final size:7
Alignment explanation
Indices: 42416553--42416592 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
42416543 CCCCTAAATT
42416553 CCTAACC
1 CCTAACC
*
42416560 CCTAACT
1 CCTAACC
*
42416567 CCTAATC
1 CCTAACC
42416574 CCTAACC
1 CCTAACC
42416581 CCTAACC
1 CCTAACC
42416588 CCTAA
1 CCTAA
42416593 ACCTTATATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.30, C:0.50, G:0.00, T:0.20
Consensus pattern (7 bp):
CCTAACC
Found at i:42416578 original size:21 final size:21
Alignment explanation
Indices: 42416543--42416592 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
42416533 AATCTTCTAG
*
42416543 CCCCTAAATTCCTAACCCCTAA
1 CCCCT-AATCCCTAACCCCTAA
*
42416565 CTCCTAATCCCTAACCCCTAA
1 CCCCTAATCCCTAACCCCTAA
42416586 CCCCTAA
1 CCCCTAA
42416593 ACCTTATATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.30, C:0.48, G:0.00, T:0.22
Consensus pattern (21 bp):
CCCCTAATCCCTAACCCCTAA
Found at i:42417239 original size:16 final size:16
Alignment explanation
Indices: 42417211--42417246 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
42417201 TCACATCCAC
42417211 AATATATATTTAAATT
1 AATATATATTTAAATT
42417227 AATACTATA-TTAAATT
1 AATA-TATATTTAAATT
42417243 AATA
1 AATA
42417247 ATCANNNNNN
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATATATTTAAATT
Found at i:42417739 original size:42 final size:41
Alignment explanation
Indices: 42417649--42417860 Score: 130
Period size: 41 Copynumber: 5.1 Consensus size: 41
42417639 TATTTTTTTT
*
42417649 GCGGCGCTTCA-ACAAAAACGCCGCT-AAAACCCTAACATTA
1 GCGGCGCTT-ATATAAAAACGCCGCTAAAAACCCTAACATTA
* * * * *
42417689 GCGGCGCTTATCATAGAATCGCCGCTAAAAATCTTAACTTTA
1 GCGGCGCTTAT-ATAAAAACGCCGCTAAAAACCCTAACATTA
* * * * *
42417731 GCGTCGCTTATATAAAAACGCCGCTAGAAGA-CCAAATATTC
1 GCGGCGCTTATATAAAAACGCCGCTA-AAAACCCTAACATTA
* * * *
42417772 GCGGCGCTTCA-A-AGAAATCGCCGCTAAATACCTTAACTTTA
1 GCGGCGCTT-ATATA-AAAACGCCGCTAAAAACCCTAACATTA
* * * * * *
42417813 GCGGTGGTTGAT-TAAAAACGCCACTAAAACCCCCGACCATTA
1 GCGGCGCTT-ATATAAAAACGCCGCTAAAA-ACCCTAACATTA
42417855 GCGGCG
1 GCGGCG
42417861 AGAGCCTAAA
Statistics
Matches: 127, Mismatches: 35, Indels: 18
0.71 0.19 0.10
Matches are distributed among these distances:
39 1 0.01
40 13 0.10
41 74 0.58
42 39 0.31
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTATATAAAAACGCCGCTAAAAACCCTAACATTA
Found at i:42417791 original size:82 final size:82
Alignment explanation
Indices: 42417662--42417844 Score: 214
Period size: 82 Copynumber: 2.2 Consensus size: 82
42417652 GCGCTTCAAC
* * *
42417662 AAAAACGCCGCTAAAACCCTAACATTAGCGGCGCTTATCATAGAATCGCCGCTAAAAATCTTAAC
1 AAAAACGCCGCTAAAACCCAAACATTAGCGGCGCTTATCAAAGAATCGCCGCTAAAAACCTTAAC
42417727 TTTAGCGTCGCTTATAT
66 TTTAGCGTCGCTTATAT
* * *
42417744 AAAAACGCCGCTAGAAGA-CCAAATATTCGCGGCGC-T-TCAAAGAAATCGCCGCTAAATACCTT
1 AAAAACGCCGCTA-AA-ACCCAAACATTAGCGGCGCTTATCAAAG-AATCGCCGCTAAAAACCTT
*
42417806 AACTTTAGCGGT-GGTTGAT-T
63 AACTTTAGC-GTCGCTT-ATAT
*
42417826 AAAAACGCCACTAAAACCC
1 AAAAACGCCGCTAAAACCC
42417845 CCGACCATTA
Statistics
Matches: 87, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
80 1 0.01
81 9 0.10
82 56 0.64
83 20 0.23
84 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (82 bp):
AAAAACGCCGCTAAAACCCAAACATTAGCGGCGCTTATCAAAGAATCGCCGCTAAAAACCTTAAC
TTTAGCGTCGCTTATAT
Found at i:42418388 original size:18 final size:18
Alignment explanation
Indices: 42418365--42418402 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
42418355 AACTTGGTTT
42418365 TTACTTTTATGATTTGAG
1 TTACTTTTATGATTTGAG
42418383 TTACTTTTATGATTTGAG
1 TTACTTTTATGATTTGAG
42418401 TT
1 TT
42418403 CATTATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.16, T:0.58
Consensus pattern (18 bp):
TTACTTTTATGATTTGAG
Found at i:42420367 original size:19 final size:19
Alignment explanation
Indices: 42420326--42420367 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
42420316 GTGGTGGCGT
*
42420326 ATGAATAGGTACATATGAC
1 ATGAATAGGTACATATGAA
*
42420345 ATGAATAGGTGA-ATTTGAA
1 ATGAATAGGT-ACATATGAA
42420364 ATGA
1 ATGA
42420368 TTGAAACTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.29
Consensus pattern (19 bp):
ATGAATAGGTACATATGAA
Found at i:42420853 original size:14 final size:15
Alignment explanation
Indices: 42420828--42420857 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
42420818 ATTATCTCAT
42420828 TAAAATATAATTAAA
1 TAAAATATAATTAAA
42420843 TAAAA-ATAATTAAA
1 TAAAATATAATTAAA
42420857 T
1 T
42420858 TAATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATATAATTAAA
Found at i:42420854 original size:25 final size:24
Alignment explanation
Indices: 42420826--42420875 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
42420816 TCATTATCTC
42420826 ATTAAAAT-ATAATTAAATAAAAATA
1 ATTAAAATAAT-ATTAAA-AAAAATA
*
42420851 ATTAAATTAATATTAAAAAAAATA
1 ATTAAAATAATATTAAAAAAAATA
42420875 A
1 A
42420876 AATTACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 13 0.57
26 2 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
ATTAAAATAATATTAAAAAAAATA
Found at i:42420869 original size:21 final size:19
Alignment explanation
Indices: 42420829--42420880 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
42420819 TTATCTCATT
*
42420829 AAAATATAATTAAATAAAA
1 AAAATAAAATTAAATAAAA
* *
42420848 ATAATTAAATTAATATTAAAA
1 AAAATAAAATTAA-A-TAAAA
42420869 AAAATAAAATTA
1 AAAATAAAATTA
42420881 CCTCTCATCT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 10 0.38
20 1 0.04
21 15 0.58
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATAAAATTAAATAAAA
Found at i:42424602 original size:18 final size:18
Alignment explanation
Indices: 42424575--42424609 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42424565 TTTACTATCA
42424575 TCATCCTTCTTCCCACCT
1 TCATCCTTCTTCCCACCT
*
42424593 TCATCTTTCTTCCCACC
1 TCATCCTTCTTCCCACC
42424610 ATCTTTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.49, G:0.00, T:0.40
Consensus pattern (18 bp):
TCATCCTTCTTCCCACCT
Found at i:42424620 original size:18 final size:17
Alignment explanation
Indices: 42424573--42424612 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
42424563 TTTTTACTAT
42424573 CATCATCCTTCTTCCCAC
1 CATCAT-CTTCTTCCCAC
*
42424591 CTTCATCTTTCTTCCCAC
1 CATCATC-TTCTTCCCAC
42424609 CATC
1 CATC
42424613 TTTCTTCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.15, C:0.47, G:0.00, T:0.38
Consensus pattern (17 bp):
CATCATCTTCTTCCCAC
Found at i:42427201 original size:18 final size:18
Alignment explanation
Indices: 42427178--42427213 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
42427168 TTCATCAAAC
42427178 TGTGTTTTATAAATTAAA
1 TGTGTTTTATAAATTAAA
42427196 TGTGTTTTATAAATTAAA
1 TGTGTTTTATAAATTAAA
42427214 CGCAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (18 bp):
TGTGTTTTATAAATTAAA
Found at i:42448500 original size:2 final size:2
Alignment explanation
Indices: 42448495--42448526 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42448485 ACACATAGAT
42448495 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
42448527 CTCTTTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42449940 original size:63 final size:62
Alignment explanation
Indices: 42449848--42449976 Score: 168
Period size: 63 Copynumber: 2.1 Consensus size: 62
42449838 ATTTTTTTTA
* * * * ***
42449848 TTTTTAGAGTTAGGACTAAATTGATAAATTTTGTAAATGTTGAGGGCCAAATTTATTGAATT
1 TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACAATGAGGGCCAAATTTATTGAATT
* *
42449910 TTTTTAAGAATTAGAACTAAAATGACAAATTTTGTAAACAATGAGGGCTAAATTTGTTGAATT
1 TTTTT-AGAATTAGAACTAAAATGACAAATTTTGTAAACAATGAGGGCCAAATTTATTGAATT
42449973 TTTT
1 TTTT
42449977 ATATTTAGGA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
62 5 0.09
63 52 0.91
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.41
Consensus pattern (62 bp):
TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACAATGAGGGCCAAATTTATTGAATT
Found at i:42459095 original size:2 final size:2
Alignment explanation
Indices: 42459088--42459130 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
42459078 GAAGGCCTTC
42459088 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42459130 T
1 T
42459131 TGATATGACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42469943 original size:30 final size:30
Alignment explanation
Indices: 42469904--42469975 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
42469894 TGTACATATG
*
42469904 AACTTTAATTTGGTGCAATTATACACATAA
1 AACTTTAATTTGGTGCAAATATACACATAA
* * * * *
42469934 AACTCTAATTGTGGTTCAAATGTATACTTAA
1 AACTTTAATT-TGGTGCAAATATACACATAA
42469965 AACTTTAATTT
1 AACTTTAATTT
42469976 TGTTTTAATC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (30 bp):
AACTTTAATTTGGTGCAAATATACACATAA
Found at i:42482423 original size:9 final size:9
Alignment explanation
Indices: 42482409--42482437 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
42482399 TTATTAATTT
42482409 AAAATTTTA
1 AAAATTTTA
42482418 AAAATTTTA
1 AAAATTTTA
42482427 AAAATTTTA
1 AAAATTTTA
42482436 AA
1 AA
42482438 GGGTGTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTTA
Found at i:42489271 original size:16 final size:16
Alignment explanation
Indices: 42489250--42489282 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42489240 CATACTCCTA
42489250 TACCAA-TCGAAAGTTT
1 TACCAATTC-AAAGTTT
42489266 TACCAATTCAAAGTTT
1 TACCAATTCAAAGTTT
42489282 T
1 T
42489283 TCTTCTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (16 bp):
TACCAATTCAAAGTTT
Found at i:42492543 original size:17 final size:17
Alignment explanation
Indices: 42492506--42492553 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
42492496 GAATTTAGAA
*
42492506 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
42492522 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
*
42492539 GAATTTTGTTATTTA
1 GAATTTTGTGATTTA
42492554 AAAAGAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:42493313 original size:14 final size:14
Alignment explanation
Indices: 42493294--42493322 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42493284 CTGTTTAATA
42493294 GTCTAAAATGGTTG
1 GTCTAAAATGGTTG
42493308 GTCTAAAATGGTTG
1 GTCTAAAATGGTTG
42493322 G
1 G
42493323 ATAAGGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.34
Consensus pattern (14 bp):
GTCTAAAATGGTTG
Found at i:42493728 original size:35 final size:35
Alignment explanation
Indices: 42493701--42493770 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
42493691 GATTAGATTA
42493701 TTAGTTCAAATTAAGGGATACGCAAGATTGAGTAC
1 TTAGTTCAAATTAAGGGATACGCAAGATTGAGTAC
42493736 TTAGTTCAAATTAAGGGATACGCAAGATTGAGTAC
1 TTAGTTCAAATTAAGGGATACGCAAGATTGAGTAC
42493771 ATACGTTCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (35 bp):
TTAGTTCAAATTAAGGGATACGCAAGATTGAGTAC
Found at i:42493905 original size:46 final size:46
Alignment explanation
Indices: 42493830--42493919 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
42493820 CATGGCAAAG
* *
42493830 TGTGAAATGTAGGTATGATATTTCAGTGAAGAAAACCATACTGAAT
1 TGTGAAAAGTAGGTATGATATTCCAGTGAAGAAAACCATACTGAAT
* *
42493876 TGTGAAAAGTAGGTATGGTATTCCCGTGAAGAAAACCATACTGA
1 TGTGAAAAGTAGGTATGATATTCCAGTGAAGAAAACCATACTGA
42493920 GTTATAGCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGATATTCCAGTGAAGAAAACCATACTGAAT
Found at i:42502925 original size:92 final size:92
Alignment explanation
Indices: 42502807--42503017 Score: 316
Period size: 92 Copynumber: 2.3 Consensus size: 92
42502797 AACCATCTCT
* * *
42502807 CAAAATACATGCACAATCGGGTGCATGTTCTTCT-TTAAAGTAGCTTCGTTGAATCTGGAAGATA
1 CAAAATTCATGCACAATCGAGTGCATGTTCTT-TATTAAAGTAGCTTCATTGAATCTGGAAGATA
* *
42502871 CATTAATGTCTAGCTAAAAAACAACTCC
65 CATGAATGTCAAGCTAAAAAACAACTCC
42502899 CAAAATTCATGCACAATCGAGTGCATGTTCTTTATTAAAGTAGCTTCATTGAATCTGGAAGATAC
1 CAAAATTCATGCACAATCGAGTGCATGTTCTTTATTAAAGTAGCTTCATTGAATCTGGAAGATAC
* * *
42502964 ATGAATGTCAAGCTGAAAAACAGCTTC
66 ATGAATGTCAAGCTAAAAAACAACTCC
* *
42502991 CAACATTCATGCACAATCGAGTACATG
1 CAAAATTCATGCACAATCGAGTGCATG
42503018 CTCCACATTA
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 1 0.01
92 107 0.99
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (92 bp):
CAAAATTCATGCACAATCGAGTGCATGTTCTTTATTAAAGTAGCTTCATTGAATCTGGAAGATAC
ATGAATGTCAAGCTAAAAAACAACTCC
Found at i:42503064 original size:92 final size:92
Alignment explanation
Indices: 42502807--42503045 Score: 264
Period size: 92 Copynumber: 2.6 Consensus size: 92
42502797 AACCATCTCT
* * * * ** * **
42502807 CAAAATACATGCACAATCGGGTGCATGTTCTTCTTTAAAGTAGCTTCGTTGAATCTGGAAGATAC
1 CAAAATTCATGCACAATCGAGTACATGCTCCACATTAAAGTAGCTTCAATGAATCTGGAAGATAC
* *
42502872 ATTAATGTCTAGCTAAAAAACAACTCC
66 ATGAATGTCAAGCTAAAAAACAACTCC
* * *** *
42502899 CAAAATTCATGCACAATCGAGTGCATGTTCTTTATTAAAGTAGCTTCATTGAATCTGGAAGATAC
1 CAAAATTCATGCACAATCGAGTACATGCTCCACATTAAAGTAGCTTCAATGAATCTGGAAGATAC
* * *
42502964 ATGAATGTCAAGCTGAAAAACAGCTTC
66 ATGAATGTCAAGCTAAAAAACAACTCC
* *
42502991 CAACATTCATGCACAATCGAGTACATGCTCCACATTAATG-AGCTTTCAATGAATC
1 CAAAATTCATGCACAATCGAGTACATGCTCCACATTAAAGTAGC-TTCAATGAATC
42503046 GGCATGGTGC
Statistics
Matches: 128, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
91 3 0.02
92 125 0.98
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (92 bp):
CAAAATTCATGCACAATCGAGTACATGCTCCACATTAAAGTAGCTTCAATGAATCTGGAAGATAC
ATGAATGTCAAGCTAAAAAACAACTCC
Found at i:42503344 original size:13 final size:13
Alignment explanation
Indices: 42503326--42503355 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
42503316 AATAGATTCA
42503326 ATCATCAAAAATC
1 ATCATCAAAAATC
42503339 ATCATCAAAAATC
1 ATCATCAAAAATC
42503352 ATCA
1 ATCA
42503356 GGCATGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
ATCATCAAAAATC
Found at i:42508477 original size:4 final size:4
Alignment explanation
Indices: 42508470--42508521 Score: 50
Period size: 4 Copynumber: 13.0 Consensus size: 4
42508460 CATATATATA
* * * * * *
42508470 TATG TATG TATG CATG CATG TATG TATT TATG TACG TAAG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
42508518 TATG
1 TATG
42508522 ATGCTACCTA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (4 bp):
TATG
Found at i:42516686 original size:5 final size:5
Alignment explanation
Indices: 42516676--42516701 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42516666 TGAGCATTCG
42516676 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
42516702 AATTTTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:42517740 original size:9 final size:9
Alignment explanation
Indices: 42517726--42517762 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42517716 TATAGTTGGA
42517726 TATTCGAAT
1 TATTCGAAT
42517735 TATTCGAAT
1 TATTCGAAT
*
42517744 TATTCGAGT
1 TATTCGAAT
42517753 TATTCGAAT
1 TATTCGAAT
42517762 T
1 T
42517763 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:42517834 original size:9 final size:9
Alignment explanation
Indices: 42517817--42517847 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42517807 TCAAGTTGAT
42517817 TCGAATAAC
1 TCGAATAAC
*
42517826 TCGATTAAC
1 TCGAATAAC
42517835 TCGAATAAC
1 TCGAATAAC
42517844 TCGA
1 TCGA
42517848 TTAGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:42518393 original size:21 final size:21
Alignment explanation
Indices: 42518369--42518408 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
42518359 TACAGCCATC
42518369 AACACACA-TATTTTGACCAGA
1 AACAC-CATTATTTTGACCAGA
42518390 AACACCATTATTTTGACCA
1 AACACCATTATTTTGACCA
42518409 ACCCCAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (21 bp):
AACACCATTATTTTGACCAGA
Found at i:42520369 original size:20 final size:20
Alignment explanation
Indices: 42520344--42520389 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
42520334 CACATATCTG
42520344 TTCTGGCAGCTTGACTGCAA
1 TTCTGGCAGCTTGACTGCAA
** *
42520364 TTCTGGTGGCTTGACTGTAA
1 TTCTGGCAGCTTGACTGCAA
42520384 TTCTGG
1 TTCTGG
42520390 TGGCTTGACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.20, G:0.28, T:0.37
Consensus pattern (20 bp):
TTCTGGCAGCTTGACTGCAA
Found at i:42520390 original size:20 final size:20
Alignment explanation
Indices: 42520352--42520398 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
42520342 TGTTCTGGCA
42520352 GCTTGACTGCAATTCTGGTG
1 GCTTGACTGCAATTCTGGTG
*
42520372 GCTTGACTGTAATTCTGGTG
1 GCTTGACTGCAATTCTGGTG
42520392 GCTTGAC
1 GCTTGAC
42520399 CACACTTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.19, G:0.30, T:0.36
Consensus pattern (20 bp):
GCTTGACTGCAATTCTGGTG
Found at i:42521411 original size:3 final size:3
Alignment explanation
Indices: 42521389--42521461 Score: 92
Period size: 3 Copynumber: 24.3 Consensus size: 3
42521379 ACAATTTAAG
* * * * * *
42521389 AAT AAT ATT AAT ATT CAT AAT AAT GAT GAT GAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42521437 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
42521462 GAAATCTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:42535185 original size:2 final size:2
Alignment explanation
Indices: 42535178--42535208 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42535168 NNNNNNNNNN
42535178 TA TA 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 T
42535209 GAGGGATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42539546 original size:85 final size:85
Alignment explanation
Indices: 42539403--42539573 Score: 306
Period size: 85 Copynumber: 2.0 Consensus size: 85
42539393 TTCTTATGAC
*
42539403 AAGATTTGTTTGGGGTAAAGGATAAAGCTTCTATATGGAACTTAGATGACATAGGTACAAGCTGA
1 AAGATTTGTTTGGGGTAAAGGATAAAGCTTCTATATGAAACTTAGATGACATAGGTACAAGCTGA
42539468 ACATAAAAAATTTTCATCAT
66 ACATAAAAAATTTTCATCAT
* * *
42539488 AAGATTTGTTTGGGGTAAAGGTTGATGCTTCTATATGAAACTTAGATGACATAGGTACAAGCTGA
1 AAGATTTGTTTGGGGTAAAGGATAAAGCTTCTATATGAAACTTAGATGACATAGGTACAAGCTGA
42539553 ACATAAAAAATTTTCATCAT
66 ACATAAAAAATTTTCATCAT
42539573 A
1 A
42539574 TATATAATAG
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (85 bp):
AAGATTTGTTTGGGGTAAAGGATAAAGCTTCTATATGAAACTTAGATGACATAGGTACAAGCTGA
ACATAAAAAATTTTCATCAT
Found at i:42543775 original size:3 final size:3
Alignment explanation
Indices: 42543767--42543798 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42543757 AACTATACAG
42543767 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
42543799 ACTACAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42546639 original size:24 final size:24
Alignment explanation
Indices: 42546597--42546648 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42546587 AATCAAAGTC
** *
42546597 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
42546621 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
42546645 AAAT
1 AAAT
42546649 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:42546870 original size:31 final size:31
Alignment explanation
Indices: 42546812--42546879 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
42546802 CTACAAAATG
*
42546812 GTCACTAAATTATTCAAAAATTTTCATTTAA
1 GTCACTAAATTATTCAAAAATTGTCATTTAA
* * *
42546843 GTCACTAAATTATGT-GAAAGTTGTCATTTGA
1 GTCACTAAATTAT-TCAAAAATTGTCATTTAA
42546874 GTCACT
1 GTCACT
42546880 GAGCTATTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (31 bp):
GTCACTAAATTATTCAAAAATTGTCATTTAA
Done.