Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 101 of 410
Found at i:29718780 original size:7 final size:7
Alignment explanation
Indices: 29718770--29718794 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29718760 TCATCACCAC
29718770 AACATCA
1 AACATCA
29718777 AACATCA
1 AACATCA
29718784 AACATCA
1 AACATCA
29718791 AACA
1 AACA
29718795 AGAAGACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (7 bp):
AACATCA
Found at i:29725725 original size:27 final size:28
Alignment explanation
Indices: 29725695--29725794 Score: 121
Period size: 27 Copynumber: 3.5 Consensus size: 28
29725685 ATAGTGAGTC
29725695 CGCACACTTAGTGCTATAAAATC-AACT
1 CGCACACTTAGTGCTATAAAATCAAACT
* *
29725722 CGCACACCTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
29725750 CGCACACTTAGTGCTGTACAAATTTAAAACC
1 CGCACACTTAGTGCTATA-AAA--TCAAACT
29725781 CGCACACTTAGTGC
1 CGCACACTTAGTGC
29725795 AATCTCATGA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
27 21 0.34
28 20 0.32
29 2 0.03
31 19 0.31
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:29726646 original size:7 final size:7
Alignment explanation
Indices: 29726636--29726660 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29726626 TCATCACCAC
29726636 AACATCA
1 AACATCA
29726643 AACATCA
1 AACATCA
29726650 AACATCA
1 AACATCA
29726657 AACA
1 AACA
29726661 AGAAGACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (7 bp):
AACATCA
Found at i:29728179 original size:91 final size:91
Alignment explanation
Indices: 29728014--29728199 Score: 264
Period size: 91 Copynumber: 2.0 Consensus size: 91
29728004 TCGGAGATTA
* * ** * *
29728014 TGGCGTGTTATCGGTTGGAAAGCTCTTATGAGCAATATGACGTGTTATCGGGGGAGAATATTTAG
1 TGGCATGTTATCGATTACAAAGCTCTTATGAGCAATATGACATGTTATCAGGGGAGAATATTTAG
*
29728079 CCTATGGGCTTTGCACTATATGCATC
66 CCTACGGGCTTTGCACTATATGCATC
* * *
29728105 TGGCATGTTATCGATTACAAAGCTCTTATGAGTAATTTGACATGTTATCAGTGGAGAATATTTAG
1 TGGCATGTTATCGATTACAAAGCTCTTATGAGCAATATGACATGTTATCAGGGGAGAATATTTAG
* *
29728170 CCTACGGGCTTTGCATTATGTGCATC
66 CCTACGGGCTTTGCACTATATGCATC
29728196 TGGC
1 TGGC
29728200 GTATTATTAG
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (91 bp):
TGGCATGTTATCGATTACAAAGCTCTTATGAGCAATATGACATGTTATCAGGGGAGAATATTTAG
CCTACGGGCTTTGCACTATATGCATC
Found at i:29734242 original size:213 final size:213
Alignment explanation
Indices: 29733875--29734512 Score: 974
Period size: 213 Copynumber: 3.0 Consensus size: 213
29733865 GTCCCTTTGC
* *
29733875 CTCAAAGATGAAACACTACAACAAGAAATCAATTTGTAGCCTACTATCGA-AAGAGTCATGACAC
1 CTCAAAGATGCAACACTACAACAAGAAATCAACTTGTAGCCTACTATCGAGAA-AGTCATGACAC
* * * *
29733939 CAAGCCCGAAGTCACAATATTGAGCCTCTGAGGTCGTGATATTCCTAATGGTGTTGAAGTGAAGA
65 CAAGCCCGAAGTCGCGATATTGAGCCTCTGAGGTCGTGATATCCCTAATAGTGTTGAAGTGAAGA
* * *
29734004 AATTATGGTCACCACAAGTGATGTCGCGACACCGAGAACCCCCAAAACCATGAGTGTACCATTAT
130 AATTGTGGTCACCACAAGTGATGTCGCGACACCGAGAACCCCCAAAACCATGAGTGCACCACTAT
* *
29734069 CAAAGGTGTCATGACATCT
195 CAAAGGTGTCATGACACCG
* * *
29734088 CTCAAAGAAGCAACACTACAATAAGAAATCAACTTGTAGCCTACTATCGAGAAAGTCTTGACACC
1 CTCAAAGATGCAACACTACAACAAGAAATCAACTTGTAGCCTACTATCGAGAAAGTCATGACACC
* *
29734153 AAGCCCGAAGTCGCGATATTGAGCCTCTAAGGTCGTGATATCCCTTATAGTGTTGAAGTGAAGAA
66 AAGCCCGAAGTCGCGATATTGAGCCTCTGAGGTCGTGATATCCCTAATAGTGTTGAAGTGAAGAA
* *
29734218 ATTGTGGTCACCACAAGTGATGTCGCGACACCGAGAACCCCCAAAACCACGAGTGCACAACTATC
131 ATTGTGGTCACCACAAGTGATGTCGCGACACCGAGAACCCCCAAAACCATGAGTGCACCACTATC
*
29734283 AAAGGTGTCGTGACACCG
196 AAAGGTGTCATGACACCG
* *
29734301 CTCAAAGATGCAACACTACAACAAGAAATCAACTTGTAGCCTACTATCGAGAGAGTCGTGACACC
1 CTCAAAGATGCAACACTACAACAAGAAATCAACTTGTAGCCTACTATCGAGAAAGTCATGACACC
* * * *
29734366 AAGCCCGAAGTCGCGACATTGAGCCTTTGAGGTCATGATAACCCTAATA-TGTTGAAGTGAAGAA
66 AAGCCCGAAGTCGCGATATTGAGCCTCTGAGGTCGTGATATCCCTAATAGTGTTGAAGTGAAGAA
* * * * *
29734430 ATTGTGGTCACCACAAGTGATGCCGCGACACTGAAAACCCTCAAAACTATGAGTGCACCACTATC
131 ATTGTGGTCACCACAAGTGATGTCGCGACACCGAGAACCCCCAAAACCATGAGTGCACCACTATC
*
29734495 AAAGGTGTCATGGCACCG
196 AAAGGTGTCATGACACCG
29734513 AAGTCTAGGT
Statistics
Matches: 386, Mismatches: 38, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
212 89 0.23
213 295 0.76
214 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (213 bp):
CTCAAAGATGCAACACTACAACAAGAAATCAACTTGTAGCCTACTATCGAGAAAGTCATGACACC
AAGCCCGAAGTCGCGATATTGAGCCTCTGAGGTCGTGATATCCCTAATAGTGTTGAAGTGAAGAA
ATTGTGGTCACCACAAGTGATGTCGCGACACCGAGAACCCCCAAAACCATGAGTGCACCACTATC
AAAGGTGTCATGACACCG
Found at i:29738891 original size:188 final size:188
Alignment explanation
Indices: 29738568--29738915 Score: 554
Period size: 188 Copynumber: 1.9 Consensus size: 188
29738558 TCTGTTATGA
**
29738568 AATCTCTTAATATGGTACTTCTATTTTGAAAATGGTTATATTAGTATCTACACTTTCAATTTATT
1 AATCTCTTAATATGGTACTTCTATTTTGAAAATAATTATATTAGTATCTACACTTTCAATTTATT
* * * *
29738633 TGGTACCAATCAATAGACCATATTTCAATCAATACTGACAAAATCAATTGGTATGAACGGTACCA
66 TAGTACCAACCAATACACCATATTTCAATCAATACTGACAAAATCAACTGGTATGAACGGTACCA
29738698 ATCGAAATTTACACCAAAACT-GAACCTAAAGTTTGTTGTTCTGATTTACTACCAGAAC
131 ATCGAAATTTACACCAAAACTGGAA-CTAAAGTTTGTTGTTCTGATTTACTACCAGAAC
* * *
29738756 AATCTTTTAATATGGTACTTCTATTTTGAATATAATTATATTAGTATCTACACTTTCAATTTCTT
1 AATCTCTTAATATGGTACTTCTATTTTGAAAATAATTATATTAGTATCTACACTTTCAATTTATT
* * * *
29738821 TAGTACCAACCGATACACCATATTTCAATCAATATTGATAAAATCAACTGGTATGAATGGTACCA
66 TAGTACCAACCAATACACCATATTTCAATCAATACTGACAAAATCAACTGGTATGAACGGTACCA
*
29738886 ATCGAAATTTACTCCAAAACTGGAACTAAA
131 ATCGAAATTTACACCAAAACTGGAACTAAA
29738916 ATTTATTATT
Statistics
Matches: 145, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
188 142 0.98
189 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (188 bp):
AATCTCTTAATATGGTACTTCTATTTTGAAAATAATTATATTAGTATCTACACTTTCAATTTATT
TAGTACCAACCAATACACCATATTTCAATCAATACTGACAAAATCAACTGGTATGAACGGTACCA
ATCGAAATTTACACCAAAACTGGAACTAAAGTTTGTTGTTCTGATTTACTACCAGAAC
Found at i:29744686 original size:18 final size:18
Alignment explanation
Indices: 29744651--29744709 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 18
29744641 AAACGCCGCT
*
29744651 AAATCATAAAAT-TTAAA
1 AAATAATAAAATATTAAA
29744668 AAATAATAAAATATTAAA
1 AAATAATAAAATATTAAA
* *
29744686 AAATTATGAAAAATATAAAA
1 AAATAAT--AAAATATTAAA
29744706 AAAT
1 AAAT
29744710 TTAAAATTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.31
18 11 0.31
20 14 0.39
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATAATAAAATATTAAA
Found at i:29746418 original size:29 final size:29
Alignment explanation
Indices: 29746376--29746459 Score: 159
Period size: 29 Copynumber: 2.9 Consensus size: 29
29746366 TTTATACCGG
29746376 AATAACATTGACTACATTAAAAAATTCTA
1 AATAACATTGACTACATTAAAAAATTCTA
*
29746405 AATAACATTGACTACATTAAAAAATTCTG
1 AATAACATTGACTACATTAAAAAATTCTA
29746434 AATAACATTGACTACATTAAAAAATT
1 AATAACATTGACTACATTAAAAAATT
29746460 GCTGAAATCA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (29 bp):
AATAACATTGACTACATTAAAAAATTCTA
Found at i:29749850 original size:21 final size:21
Alignment explanation
Indices: 29749826--29749901 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
29749816 AAAATACTAA
*
29749826 TTAA-CCTAAACCTTAAACCTC
1 TTAACCCTAAACCATAAACC-C
**
29749847 TTAACCCCTATCCCATAAACCC
1 TTAA-CCCTAAACCATAAACCC
* *
29749869 TAAACCCTAAACCCTAAACCC
1 TTAACCCTAAACCATAAACCC
*
29749890 TTAACCCCAAAC
1 TTAACCCTAAAC
29749902 TTTTACACCT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 28 0.64
22 4 0.09
23 12 0.27
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (21 bp):
TTAACCCTAAACCATAAACCC
Found at i:29749874 original size:7 final size:7
Alignment explanation
Indices: 29749830--29749901 Score: 65
Period size: 7 Copynumber: 10.0 Consensus size: 7
29749820 TACTAATTAA
29749830 CCTAAAC
1 CCTAAAC
*
29749837 CTTAAAC
1 CCTAAAC
*
29749844 CTCTTAACC
1 C-C-TAAAC
*
29749853 CCT-ATC
1 CCTAAAC
29749859 CCATAAAC
1 CC-TAAAC
29749867 CCTAAAC
1 CCTAAAC
29749874 CCTAAAC
1 CCTAAAC
29749881 CCTAAAC
1 CCTAAAC
*
29749888 CCTTAAC
1 CCTAAAC
*
29749895 CCCAAAC
1 CCTAAAC
29749902 TTTTACACCT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
6 4 0.08
7 39 0.74
8 5 0.09
9 5 0.09
ACGTcount: A:0.38, C:0.43, G:0.00, T:0.19
Consensus pattern (7 bp):
CCTAAAC
Found at i:29750020 original size:14 final size:14
Alignment explanation
Indices: 29749989--29750040 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
29749979 AATTAACTCC
* *
29749989 TAAACCTTAAACCC
1 TAAACCATAAACCT
* *
29750003 TAAACCATATATCT
1 TAAACCATAAACCT
29750017 TAAACCATAAACCT
1 TAAACCATAAACCT
*
29750031 TAAACTATAA
1 TAAACCATAA
29750041 TGATAATTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCATAAACCT
Found at i:29750274 original size:41 final size:40
Alignment explanation
Indices: 29750210--29750362 Score: 130
Period size: 41 Copynumber: 3.8 Consensus size: 40
29750200 GACTTTTAGT
** * *
29750210 GGCGTTTTAGCA-AAAGCACCGCTAGTGCTCTGGTATTTAAT
1 GGCGTTTTA-CAGAAAGTGCCGCTAATGCTCTGGT-TTTAAC
** * * *
29750251 GGCGTTTTATTGAAAGTGTCGCTAATGCTATGGTTTTTAGC
1 GGCGTTTTACAGAAAGTGCCGCTAATGCTCTGG-TTTTAAC
* * *
29750292 GGCGTTTTACAGAAAGTGCCTCTAATGCTCTGGTTTTTAG
1 GGCGTTTTACAGAAAGTGCCGCTAATGCTCTGGTTTTAAC
* *
29750332 GGCGTTTT-CAGTAAAATGCCGCTATTGCTCT
1 GGCGTTTTACAG-AAAGTGCCGCTAATGCTCT
29750363 ATTTTTAGCC
Statistics
Matches: 89, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.03
40 28 0.31
41 57 0.64
42 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (40 bp):
GGCGTTTTACAGAAAGTGCCGCTAATGCTCTGGTTTTAAC
Found at i:29750477 original size:16 final size:16
Alignment explanation
Indices: 29750456--29750486 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29750446 TAGTGTATTG
*
29750456 TTTTAATATTAAATAT
1 TTTTAAGATTAAATAT
29750472 TTTTAAGATTAAATA
1 TTTTAAGATTAAATA
29750487 ATATTAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTTAAGATTAAATAT
Found at i:29751941 original size:3 final size:3
Alignment explanation
Indices: 29751929--29751976 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
29751919 ACATGAAAGT
*
29751929 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATC ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29751976 A
1 A
29751977 GTAACAAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:29761102 original size:3 final size:3
Alignment explanation
Indices: 29761094--29761186 Score: 186
Period size: 3 Copynumber: 31.0 Consensus size: 3
29761084 TAATATATGT
29761094 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29761142 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29761187 AAGAATAAAA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:29766572 original size:22 final size:22
Alignment explanation
Indices: 29766543--29766610 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
29766533 TGCACAAACG
29766543 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
29766565 TACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
*
29766587 AACAGAGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
29766610 A
1 A
29766611 TAATAGAACG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.74
23 8 0.21
24 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:29772371 original size:124 final size:124
Alignment explanation
Indices: 29772149--29772373 Score: 326
Period size: 124 Copynumber: 1.8 Consensus size: 124
29772139 GAATTATGTG
* * * * * * *
29772149 AAATGAAATATGGATGTGTATTGATTATTGATTTATGTGTGTATGAGTATTTGAATGATACCCGG
1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
* **
29772214 GCTAAGTCCCGAAGGCGATTATGCTAGTGATTATATTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA
*
29772273 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATATCCGG
1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
*
29772338 GCTAAGTCCCGAAGACG-TTATTGCTGGAAATTATAT
66 GCTAAGTCCCGAAGACGATTA-TGCTAGAAATTATAT
29772374 CCGGGTTAAG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 3 0.03
124 85 0.97
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (124 bp):
AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA
Found at i:29772495 original size:40 final size:40
Alignment explanation
Indices: 29772368--29772497 Score: 156
Period size: 40 Copynumber: 3.2 Consensus size: 40
29772358 TTGCTGGAAA
* * * *
29772368 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGA
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
29772408 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
29772448 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
29772488 TTATATCCGG
1 TTATATCCGG
29772498 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:29775040 original size:31 final size:31
Alignment explanation
Indices: 29775005--29775067 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
29774995 AACCATCCAG
* *
29775005 TGATTTGAAT-AAAAACTTTCAAATAATTTAA
1 TGATTTAAATGAAAAA-TTTCAAATAAATTAA
*
29775036 TGATTTAAATGAAAAATTTTAAATAAATTAA
1 TGATTTAAATGAAAAATTTCAAATAAATTAA
29775067 T
1 T
29775068 AATTATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (31 bp):
TGATTTAAATGAAAAATTTCAAATAAATTAA
Found at i:29777181 original size:13 final size:14
Alignment explanation
Indices: 29777161--29777201 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
29777151 ATATGAAGAA
29777161 TATTATTTAAAATT
1 TATTATTTAAAATT
29777175 T-TTATTTTTAAAATT
1 TATTA--TTTAAAATT
29777190 TATTA-TTAAAAT
1 TATTATTTAAAAT
29777202 AAAATTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 10 0.42
16 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTATTTAAAATT
Found at i:29777186 original size:15 final size:17
Alignment explanation
Indices: 29777161--29777197 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
29777151 ATATGAAGAA
29777161 TATTATTTAAAATTT-T
1 TATTATTTAAAATTTAT
29777177 TATT-TTTAAAATTTAT
1 TATTATTTAAAATTTAT
29777193 TATTA
1 TATTA
29777198 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTTAAAATTTAT
Found at i:29777247 original size:19 final size:20
Alignment explanation
Indices: 29777209--29777247 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29777199 AATAAAATTG
* *
29777209 AAATATTAAATAATTTATTA
1 AAATAATAAATAAATTATTA
29777229 AAATAATAAA-AAATTATTA
1 AAATAATAAATAAATTATTA
29777248 TATGACTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATAATAAATAAATTATTA
Found at i:29779296 original size:109 final size:110
Alignment explanation
Indices: 29778987--29780492 Score: 1757
Period size: 109 Copynumber: 13.7 Consensus size: 110
29778977 AAAACCTGAA
* * * * *
29778987 TACTGATTCTACTG-AAGTACTC-AATGAGCAATATCTACTGATACTACTGAAAGTGCTTAACGA
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
*
29779050 GCAATATCTACTGATCCTACTAAATGTGCTCAAACGAGCAATGTC
66 GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
* * * * * * * * *
29779095 TATTGATTCTACTTAAAGTTCTCAAACAAACAATATCTACTGATACCACTGAAAATGCTCAACGA
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
*
29779160 GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGTAATGTC
66 GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
*
29779205 TACTGATTCTACTGAAAGTGCTC-AACGAGCAATATCTACTGGTTCTACTGAAAGTGCTTAACG-
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
* * *
29779268 GACAATATCTATTGATCCAACTGAATGTGCTCAAACGAGTAATGTC
66 G-CAATATCTACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
* ** *
29779314 TACTGATTCTACTGAAAGTGCTCAAATGAGCAATATCTACTAATTCTATTG-AAGTGCTCAACGA
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
* * *
29779378 GCAATATCTTCTGATCCTACTGAATGTGCTTAAACGAGAAATGTC
66 GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
* * * * *
29779423 TATTGATTCTACTG-AAGTGGTC-AATGAGCAATATCTATTGGTTCTACTGAAAGTGCTCAATGA
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
* * * *
29779486 GCAATATTTACTGATCCTATTAAATGTGCTCAAACGAGTAATGTC
66 GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
*
29779531 TACTGATTCTAGTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
* * * *
29779596 GCAATATCTATTAATCCTACTAAATGTGCTCAAACCAGCAATGTC
66 GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
* * * * * *
29779641 TACTGGTTCTACTG-AAGTGCTCAAACGAGCAATATCTATTGATACCACTGAAAATGCTCAACGA
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
*
29779705 GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGAAATGTC
66 GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
* * * * *
29779750 TGCTGATTCTACTGAAAGTGCTC-AACAAACAATATCTACTGGTTCTACTGAAAGTGCTTAACTA
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
* * *
29779814 GCAATATCTATTGATCCTACTAAATGTGCTCAAACGAGTAATGTC
66 GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
* * ** *
29779859 TACTGATTCTACTGAAAATGCTCAAATGAGCAATATCTACTAATTCTATTG-AAGTGCTCAACGA
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
** * * * * *
29779923 GTTATAGCTTCTGATCCTACTGAATATGCTCAAACGAGAAATGTT
66 GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
* * * * *
29779968 TATTGATTCTACTG-AAGTTCTCAATC-AGCAATATCTATTGGTTCTACTGAAAGTGCTCAATGA
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
* * *
29780031 GCAATATCTACTGGTCCTACTGAATGTACTCAAATGAGCAATGTC
66 GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
* * * * * *
29780076 TGCTGATTCTAGTGAAAGTGCTTAAACGAGCAATATCTATTGGTTCTATTAAAAGTGCTCAACGA
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
* * *
29780141 GCAATATCTATTAATCCTACTAAATGTGCTCAAATC-AGCAATGTC
66 GCAATATCTACTGATCCTACTGAATGTGCTCAAA-CGAGCAATGTC
* * * *
29780186 TACTGGTTCTACTG-AAGTGCTCAAACGAGCAATATCTATTGATTCTACCGAAAGTGCTCAACGA
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
* * *
29780250 TCAATATCTACTGATCCTACTGAATGTGCCCAAACGAGCAATGTT
66 GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
* * *
29780295 TAATGATTCTACTG-AAGTGCTCAAACGAGCAATATTTATTGGTTCTACTGAATAGTTGCTCAAA
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAA-AG-TGCTC-AA
* * * ** * **
29780359 TGAG-AATATCCATTGATTATACTGAATGTTTGCTCAAATGAGCAATACC
63 CGAGCAATATCTACTGATCCTACTGAATG--TGCTCAAACGAGCAATGTC
* * * * * * * * * *
29780408 CACTGATTATACTGAATGTTTGCTCAAACAAGCGATATCCAATGATTATACTGAATGCATGCTCA
1 TACTGATTCTACTGAAAG--TGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAG--TGCTC-
* *
29780473 AACGAGCCATATCCACTGAT
61 AACGAGCAATATCTACTGAT
29780493 TACGTGAAAT
Statistics
Matches: 1189, Mismatches: 184, Indels: 41
0.84 0.13 0.03
Matches are distributed among these distances:
107 42 0.04
108 150 0.13
109 565 0.48
110 325 0.27
111 25 0.02
112 4 0.00
113 25 0.02
114 2 0.00
115 1 0.00
116 39 0.03
117 11 0.01
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (110 bp):
TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
GCAATATCTACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
Found at i:29780076 original size:545 final size:545
Alignment explanation
Indices: 29778987--29780346 Score: 2152
Period size: 545 Copynumber: 2.5 Consensus size: 545
29778977 AAAACCTGAA
* * * * * *
29778987 TACTGATTCTACTG-AAGTACTC-AATGAGCAATATCTACTGATACTACTGAAAGTGCTTAACGA
1 TACTGATTCTAGTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
* * * * * * *
29779050 GCAATATCTACTGATCCTACTAAATGTGCTCAAACGAGCAATGTCTATTGATTCTACTTAAAGTT
66 GCAATATCTATTAATCCTACTAAATGTGCTCAAACCAGCAATGTCTACTGGTTCTAC-TGAAGTG
* * *
29779115 CTCAAACAAACAATATCTACTGATACCACTGAAAATGCTCAACGAGCAATATCTACTGATCCTAC
130 CTCAAACGAGCAATATCTATTGATACCACTGAAAATGCTCAACGAGCAATATCTACTGATCCTAC
*
29779180 TGAATGTGCTCAAACGAGTAATGTCTACTGATTCTACTGAAAGTGCTCAACGAGCAATATCTACT
195 TGAATGTGCTCAAACGAGAAATGTCTACTGATTCTACTGAAAGTGCTCAACGAGCAATATCTACT
* *
29779245 GGTTCTACTGAAAGTGCTTAACGGACAATATCTATTGATCCAACTGAATGTGCTCAAACGAGTAA
260 GGTTCTACTGAAAGTGCTTAACAGACAATATCTATTGATCCAACTAAATGTGCTCAAACGAGTAA
*
29779310 TGTCTACTGATTCTACTGAAAGTGCTCAAATGAGCAATATCTACTAATTCTATTGAAGTGCTCAA
325 TGTCTACTGATTCTACTGAAAATGCTCAAATGAGCAATATCTACTAATTCTATTGAAGTGCTCAA
* * *
29779375 CGAGCAATATCTTCTGATCCTACTGAATGTGCTTAAACGAGAAATGTCTATTGATTCTACTGAAG
390 CGAGCAATAGCTTCTGATCCTACTGAATATGCTCAAACGAGAAATGTCTATTGATTCTACTGAAG
* * *
29779440 TGGTCAATGAGCAATATCTATTGGTTCTACTGAAAGTGCTCAATGAGCAATATTTACTGATCCTA
455 TGCTCAATCAGCAATATCTATTGGTTCTACTGAAAGTGCTCAATGAGCAATATCTACTGATCCTA
* * *
29779505 TTAAATGTGCTCAAACGAGTAATGTC
520 CTAAATGTACTCAAACGAGCAATGTC
29779531 TACTGATTCTAGTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
1 TACTGATTCTAGTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
29779596 GCAATATCTATTAATCCTACTAAATGTGCTCAAACCAGCAATGTCTACTGGTTCTACTGAAGTGC
66 GCAATATCTATTAATCCTACTAAATGTGCTCAAACCAGCAATGTCTACTGGTTCTACTGAAGTGC
29779661 TCAAACGAGCAATATCTATTGATACCACTGAAAATGCTCAACGAGCAATATCTACTGATCCTACT
131 TCAAACGAGCAATATCTATTGATACCACTGAAAATGCTCAACGAGCAATATCTACTGATCCTACT
* * *
29779726 GAATGTGCTCAAACGAGAAATGTCTGCTGATTCTACTGAAAGTGCTCAACAAACAATATCTACTG
196 GAATGTGCTCAAACGAGAAATGTCTACTGATTCTACTGAAAGTGCTCAACGAGCAATATCTACTG
*
29779791 GTTCTACTGAAAGTGCTTAACTAG-CAATATCTATTGATCCTACTAAATGTGCTCAAACGAGTAA
261 GTTCTACTGAAAGTGCTTAAC-AGACAATATCTATTGATCCAACTAAATGTGCTCAAACGAGTAA
29779855 TGTCTACTGATTCTACTGAAAATGCTCAAATGAGCAATATCTACTAATTCTATTGAAGTGCTCAA
325 TGTCTACTGATTCTACTGAAAATGCTCAAATGAGCAATATCTACTAATTCTATTGAAGTGCTCAA
** *
29779920 CGAGTTATAGCTTCTGATCCTACTGAATATGCTCAAACGAGAAATGTTTATTGATTCTACTGAAG
390 CGAGCAATAGCTTCTGATCCTACTGAATATGCTCAAACGAGAAATGTCTATTGATTCTACTGAAG
* *
29779985 TTCTCAATCAGCAATATCTATTGGTTCTACTGAAAGTGCTCAATGAGCAATATCTACTGGTCCTA
455 TGCTCAATCAGCAATATCTATTGGTTCTACTGAAAGTGCTCAATGAGCAATATCTACTGATCCTA
* *
29780050 CTGAATGTACTCAAATGAGCAATGTC
520 CTAAATGTACTCAAACGAGCAATGTC
* * * * *
29780076 TGCTGATTCTAGTGAAAGTGCTTAAACGAGCAATATCTATTGGTTCTATTAAAAGTGCTCAACGA
1 TACTGATTCTAGTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
*
29780141 GCAATATCTATTAATCCTACTAAATGTGCTCAAATCAGCAATGTCTACTGGTTCTACTGAAGTGC
66 GCAATATCTATTAATCCTACTAAATGTGCTCAAACCAGCAATGTCTACTGGTTCTACTGAAGTGC
* * * * *
29780206 TCAAACGAGCAATATCTATTGATTCTACCGAAAGTGCTCAACGATCAATATCTACTGATCCTACT
131 TCAAACGAGCAATATCTATTGATACCACTGAAAATGCTCAACGAGCAATATCTACTGATCCTACT
* * * * * *
29780271 GAATGTGCCCAAACGAGCAATGTTTAATGATTCTACTG-AAGTGCTCAAACGAGCAATATTTATT
196 GAATGTGCTCAAACGAGAAATGTCTACTGATTCTACTGAAAGTGCTC-AACGAGCAATATCTACT
29780335 GGTTCTACTGAA
260 GGTTCTACTGAA
29780347 TAGTTGCTCA
Statistics
Matches: 752, Mismatches: 60, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
544 21 0.03
545 641 0.85
546 90 0.12
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (545 bp):
TACTGATTCTAGTGAAAGTGCTCAAACGAGCAATATCTACTGGTTCTACTGAAAGTGCTCAACGA
GCAATATCTATTAATCCTACTAAATGTGCTCAAACCAGCAATGTCTACTGGTTCTACTGAAGTGC
TCAAACGAGCAATATCTATTGATACCACTGAAAATGCTCAACGAGCAATATCTACTGATCCTACT
GAATGTGCTCAAACGAGAAATGTCTACTGATTCTACTGAAAGTGCTCAACGAGCAATATCTACTG
GTTCTACTGAAAGTGCTTAACAGACAATATCTATTGATCCAACTAAATGTGCTCAAACGAGTAAT
GTCTACTGATTCTACTGAAAATGCTCAAATGAGCAATATCTACTAATTCTATTGAAGTGCTCAAC
GAGCAATAGCTTCTGATCCTACTGAATATGCTCAAACGAGAAATGTCTATTGATTCTACTGAAGT
GCTCAATCAGCAATATCTATTGGTTCTACTGAAAGTGCTCAATGAGCAATATCTACTGATCCTAC
TAAATGTACTCAAACGAGCAATGTC
Found at i:29780423 original size:39 final size:39
Alignment explanation
Indices: 29779012--29780494 Score: 301
Period size: 36 Copynumber: 40.5 Consensus size: 39
29779002 AGTACTCAAT
* * *
29779012 GAGCAATATCTACTGA-TACTACTGAAAG--TGCT-TAAC
1 GAGCAATATCCACTGATTA-TACTGAATGTTTGCTCAAAC
* ** *
29779048 GAGCAATATCTACTGATCCTACTAAATG--TGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * * *
29779085 GAGCAATGTCTATTGATTCTACTTAAAG-TT-CTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * **
29779122 AAACAATATCTACTGA-TACCACTGAA--AATGCTC-AAC
1 GAGCAATATCCACTGATTA-TACTGAATGTTTGCTCAAAC
* **
29779158 GAGCAATATCTACTGATCCTACTGAATG--TGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * *
29779195 GAGTAATGTCTACTGATTCTACTGAAAG--TGCTC-AAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * *
29779231 GAGCAATATCTACTGGTTCTACTGAAAG--TGCT-TAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * *
29779267 G-GACAATATCTATTGATCCA-ACTGAATG--TGCTCAAAC
1 GAG-CAATATCCACTGAT-TATACTGAATGTTTGCTCAAAC
* * * * * *
29779304 GAGTAATGTCTACTGATTCTACTGAAAG--TGCTCAAAT
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * *
29779341 GAGCAATATCTACTAATTCTATTGAA-G--TGCTC-AAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
** ** *
29779376 GAGCAATATCTTCTGATCCTACTGAATG--TGCTTAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * * * *
29779413 GAGAAATGTCTATTGATTCTACTGAA-G--TGGTC-AAT
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * * *
29779448 GAGCAATATCTATTGGTTCTACTGAAAG--TGCTC-AAT
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
** ** * *
29779484 GAGCAATATTTACTGATCCTATTAAATG--TGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * * *
29779521 GAGTAATGTCTACTGATTCTAGTGAAAG--TGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * *
29779558 GAGCAATATCTACTGGTTCTACTGAAAG--TGCTC-AAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * ** *
29779594 GAGCAATATCTATTAATCCTACTAAATG--TGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * *
29779631 CAGCAATGTCTACTGGTTCTACTGAA-G--TGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * **
29779667 GAGCAATATCTATTGA-TACCACTGAA--AATGCTC-AAC
1 GAGCAATATCCACTGATTA-TACTGAATGTTTGCTCAAAC
* **
29779703 GAGCAATATCTACTGATCCTACTGAATG--TGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * ** * *
29779740 GAGAAATGTCTGCTGATTCTACTGAAAG--TGCTC-AAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * * * *
29779776 AAACAATATCTACTGGTTCTACTGAAAG--TGCT-TAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * ** *
29779812 TAGCAATATCTATTGATCCTACTAAATG--TGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * ** *
29779849 GAGTAATGTCTACTGATTCTACTGAA--AATGCTCAAAT
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * *
29779886 GAGCAATATCTACTAATTCTATTGAA-G--TGCTC-AAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
** * ** ** *
29779921 GAGTTATAGCTTCTGATCCTACTGAA--TATGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * ** * * *
29779958 GAGAAATGTTTATTGATTCTACTGAA-G-TT-CTCAATC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * * *
29779994 -AGCAATATCTATTGGTTCTACTGAAAG--TGCTC-AAT
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * ** * *
29780029 GAGCAATATCTACTGGTCCTACTGAATG--TACTCAAAT
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* ** * * * *
29780066 GAGCAATGTCTGCTGATTCTAGTGAAAG--TGCTTAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * * * *
29780103 GAGCAATATCTATTGGTTCTATTAAAAG--TGCTC-AAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * ** *
29780139 GAGCAATATCTATTAATCCTACTAAATG--TGCTCAAATC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAA-C
* * * *
29780177 -AGCAATGTCTACTGGTTCTACTGAA-G--TGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * * *
29780212 GAGCAATATCTATTGATTCTACCGAAAG--TGCTC-AAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * ** *
29780248 GATCAATATCTACTGATCCTACTGAATG--TGCCCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* ** * *
29780285 GAGCAATGTTTAATGATTCTACTGAA-G--TGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
** * * * *
29780321 GAGCAATATTTATTGGTTCTACTGAATAG-TTGCTCAAAT
1 GAGCAATATCCACTGATTATACTGAAT-GTTTGCTCAAAC
* *
29780360 GAG-AATATCCATTGATTATACTGAATGTTTGCTCAAAT
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
*
29780398 GAGCAATACCCACTGATTATACTGAATGTTTGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
* * * **
29780437 AAGCGATATCCAATGATTATACTGAATGCATGCTCAAAC
1 GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
*
29780476 GAGCCATATCCACTGATTA
1 GAGCAATATCCACTGATTA
29780495 CGTGAAATGA
Statistics
Matches: 1168, Mismatches: 228, Indels: 99
0.78 0.15 0.07
Matches are distributed among these distances:
35 96 0.08
36 480 0.41
37 464 0.40
38 36 0.03
39 92 0.08
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (39 bp):
GAGCAATATCCACTGATTATACTGAATGTTTGCTCAAAC
Found at i:29785383 original size:19 final size:20
Alignment explanation
Indices: 29785351--29785391 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
29785341 GAATGAAATT
29785351 GAGAGAACAAACAAAGAAAA
1 GAGAGAACAAACAAAGAAAA
29785371 GAGAGAA-AAACAAAGAAAA
1 GAGAGAACAAACAAAGAAAA
29785390 GA
1 GA
29785392 AAGTGAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.71, C:0.07, G:0.22, T:0.00
Consensus pattern (20 bp):
GAGAGAACAAACAAAGAAAA
Found at i:29789782 original size:2 final size:2
Alignment explanation
Indices: 29789775--29789805 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29789765 GATTTGGTTG
29789775 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
29789806 GCAAATGGCC
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:29790106 original size:12 final size:12
Alignment explanation
Indices: 29790089--29790113 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29790079 AATGCCTATT
29790089 TGTGCCATTTTG
1 TGTGCCATTTTG
29790101 TGTGCCATTTTG
1 TGTGCCATTTTG
29790113 T
1 T
29790114 TTGGTGTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.24, T:0.52
Consensus pattern (12 bp):
TGTGCCATTTTG
Found at i:29797162 original size:2 final size:2
Alignment explanation
Indices: 29797155--29797182 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29797145 TTCAAAAATA
29797155 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
29797183 TTTGGATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29797627 original size:2 final size:2
Alignment explanation
Indices: 29797616--29797653 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
29797606 TAAATCAACA
29797616 AT AT -T AT AT AT 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 AT AT AT AT AT AT A
29797654 GTTGATAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29798235 original size:27 final size:28
Alignment explanation
Indices: 29798205--29798257 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
29798195 TTGATTTCTA
*
29798205 AAAATATTTTTTA-TTTTCATTTTTTAG
1 AAAATAGTTTTTATTTTTCATTTTTTAG
*
29798232 AAAATAGTTTTTATTTTTTATTTTTT
1 AAAATAGTTTTTATTTTTCATTTTTT
29798258 TAAAAAGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (28 bp):
AAAATAGTTTTTATTTTTCATTTTTTAG
Found at i:29798263 original size:28 final size:26
Alignment explanation
Indices: 29798203--29798263 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
29798193 GTTTGATTTC
*
29798203 TAAAAATATTTTTTATTTTCATTTTT
1 TAAAAATAGTTTTTATTTTCATTTTT
*
29798229 TAGAAAATAGTTTTTATTTTTTATTTTTT
1 TA-AAAATAGTTTTTA-TTTTCA-TTTTT
29798258 TAAAAA
1 TAAAAA
29798264 GCATTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 2 0.07
27 12 0.40
28 9 0.30
29 7 0.23
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (26 bp):
TAAAAATAGTTTTTATTTTCATTTTT
Found at i:29799203 original size:24 final size:24
Alignment explanation
Indices: 29799188--29799239 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
29799178 AATCAATGTC
*
29799188 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
29799212 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
29799236 AAAT
1 AAAT
29799240 CTTCTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:29803297 original size:24 final size:23
Alignment explanation
Indices: 29803269--29803334 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
29803259 AGTAGATACA
* *
29803269 TAAAAGAACCATAACTGTTTTTCT
1 TAAAAGAAACACAACTG-TTTTCT
* *
29803293 TAAAATAAACACAATTGTTTTCT
1 TAAAAGAAACACAACTGTTTTCT
* *
29803316 TAAAATAAACACAATTGTT
1 TAAAAGAAACACAACTGTT
29803335 AAAACTACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
23 25 0.66
24 13 0.34
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (23 bp):
TAAAAGAAACACAACTGTTTTCT
Found at i:29803317 original size:23 final size:23
Alignment explanation
Indices: 29803287--29803334 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
29803277 CCATAACTGT
29803287 TTTTCTTAAAATAAACACAATTG
1 TTTTCTTAAAATAAACACAATTG
29803310 TTTTCTTAAAATAAACACAATTG
1 TTTTCTTAAAATAAACACAATTG
29803333 TT
1 TT
29803335 AAAACTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (23 bp):
TTTTCTTAAAATAAACACAATTG
Found at i:29810714 original size:70 final size:70
Alignment explanation
Indices: 29810638--29810772 Score: 225
Period size: 70 Copynumber: 1.9 Consensus size: 70
29810628 TAGTTTATTA
* * * * *
29810638 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTG
1 CTAATTAATATGCTGCTGTAATACTATAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
29810703 CTTAG
66 CTTAG
29810708 CTAATTAATATGCTGCTGTAATACTATAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
1 CTAATTAATATGCTGCTGTAATACTATAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
29810773 TTATGTGCTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTATAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
CTTAG
Found at i:29811602 original size:43 final size:43
Alignment explanation
Indices: 29811545--29811714 Score: 191
Period size: 43 Copynumber: 4.0 Consensus size: 43
29811535 TATCGAAATG
*
29811545 TGATAT-AGAGCTTCGGGCCTAGTAGGCTATAATGCCGGTGAAA
1 TGATATCAG-GCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
* * *
29811588 TGATATCAGGCTTCGGCCCTAGCAGGCTATAATGCTGGTGAGA
1 TGATATCAGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
* * * * *
29811631 TAATATCGGGCCTCGGGCCTAACAGGCTATAATGCCCGTGAAA
1 TGATATCAGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
* ** * *
29811674 TGATATCGGGCTTCAAGCCTAGCAGGC-AAAATGTCGGTGAA
1 TGATATCAGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAA
29811715 TGAATTCAGA
Statistics
Matches: 106, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
42 11 0.10
43 93 0.88
44 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.24
Consensus pattern (43 bp):
TGATATCAGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
Found at i:29816975 original size:17 final size:17
Alignment explanation
Indices: 29816952--29816995 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
29816942 CAATTTGAGC
29816952 CGTGTGGGCCACAC-GAG
1 CGTGTGGGCCACACAG-G
*
29816969 TGTGTGGGCCACACAGG
1 CGTGTGGGCCACACAGG
29816986 CGTGTGGGCC
1 CGTGTGGGCC
29816996 CAAACGGGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.14, C:0.27, G:0.43, T:0.16
Consensus pattern (17 bp):
CGTGTGGGCCACACAGG
Found at i:29819425 original size:32 final size:32
Alignment explanation
Indices: 29819382--29819445 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
29819372 TTGATCTTAT
29819382 TCTGCAACTTATAGCACTCAGACTTAATGTGC
1 TCTGCAACTTATAGCACTCAGACTTAATGTGC
*
29819414 TCTGCATCTTATAGCACTCAGACTTAATGTGC
1 TCTGCAACTTATAGCACTCAGACTTAATGTGC
29819446 CCTTTCTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (32 bp):
TCTGCAACTTATAGCACTCAGACTTAATGTGC
Found at i:29820441 original size:24 final size:25
Alignment explanation
Indices: 29820426--29820477 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
29820416 AATAAATGTC
29820426 AAATATATTAT-GCTAATAAATACT
1 AAATATATTATAGCTAATAAATACT
*
29820450 AAATATATTATAG-TAATAAATAAT
1 AAATATATTATAGCTAATAAATACT
29820474 AAAT
1 AAAT
29820478 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (25 bp):
AAATATATTATAGCTAATAAATACT
Found at i:29832258 original size:57 final size:58
Alignment explanation
Indices: 29832157--29832306 Score: 151
Period size: 57 Copynumber: 2.6 Consensus size: 58
29832147 CGATCCACAT
* *
29832157 ATCATATTACAGGATTACCAATCCAGGCTAAATCCATTATGTAACGTATGCTCAAAAGAG
1 ATCATA-T-CAGGATTACCAATCCAGGCTAAATCCATAATGTAACATATGCTCAAAAGAG
* * * * * *
29832217 ATCA-ATTAGGATTACCAGTCTAGGCTAAA-CCCTAATCGTAACATATGCTCGAGAGAG
1 ATCATATCAGGATTACCAATCCAGGCTAAATCCATAAT-GTAACATATGCTCAAAAGAG
* * * *
29832274 ATTATATCAGGATTACCCATCCAAGCTCAATCC
1 ATCATATCAGGATTACCAATCCAGGCTAAATCC
29832307 TTTCTATAAT
Statistics
Matches: 72, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
56 5 0.07
57 40 0.56
58 20 0.28
59 3 0.04
60 4 0.06
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (58 bp):
ATCATATCAGGATTACCAATCCAGGCTAAATCCATAATGTAACATATGCTCAAAAGAG
Found at i:29833902 original size:24 final size:24
Alignment explanation
Indices: 29833852--29833902 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
29833842 TTTTGCACAT
* *
29833852 AAACAAGCCATAACAAGGCATTCA
1 AAACAAGCCAAAACAAGGCATTAA
*
29833876 AAACAAGCCAAAATCAAGTC-TTAA
1 AAACAAGCCAAAA-CAAGGCATTAA
29833900 AAA
1 AAA
29833903 TAAAATATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.55, C:0.22, G:0.10, T:0.14
Consensus pattern (24 bp):
AAACAAGCCAAAACAAGGCATTAA
Found at i:29834651 original size:25 final size:25
Alignment explanation
Indices: 29834623--29834727 Score: 97
Period size: 25 Copynumber: 4.2 Consensus size: 25
29834613 ATGCTCATGT
*
29834623 GAGCTATGAATCGGTATGCTC-TCAC
1 GAGCTATGAATCGGTAAGCTCAT-AC
*
29834648 GAGCTATGAACCGGTAAGCTCATAC
1 GAGCTATGAATCGGTAAGCTCATAC
* *
29834673 GAGCTATAAATCGAG-AAGCTCAAAC
1 GAGCTATGAATCG-GTAAGCTCATAC
*** * *
29834698 GAGCTGCAAATCGGGAAGCTCATAT
1 GAGCTATGAATCGGTAAGCTCATAC
29834723 GAGCT
1 GAGCT
29834728 GTGGTGTGTC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.01
25 65 0.96
26 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (25 bp):
GAGCTATGAATCGGTAAGCTCATAC
Found at i:29838346 original size:20 final size:20
Alignment explanation
Indices: 29838308--29838348 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
29838298 TTTTTATTTC
*
29838308 TTTCCTATTTTTCCTTTCTT
1 TTTCCTATTTTTCATTTCTT
29838328 TTTCC-ATTTTTCATATTCTT
1 TTTCCTATTTTTCAT-TTCTT
29838348 T
1 T
29838349 CTTTTTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTCCTATTTTTCATTTCTT
Found at i:29838349 original size:18 final size:18
Alignment explanation
Indices: 29838298--29838349 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
29838288 CATTTTTTTC
29838298 TTTTT-ATTTCTTTCCTA
1 TTTTTCATTTCTTTCCTA
*
29838315 TTTTTCCTTTCTTTTTCC-A
1 TTTTTCATTTC--TTTCCTA
29838334 TTTTTCATATTCTTTC
1 TTTTTCAT-TTCTTTC
29838350 TTTTTCCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 5 0.17
18 8 0.28
19 8 0.28
20 8 0.28
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTCATTTCTTTCCTA
Found at i:29847095 original size:6 final size:6
Alignment explanation
Indices: 29847084--29847155 Score: 60
Period size: 6 Copynumber: 12.2 Consensus size: 6
29847074 AACACCGAAC
* * *
29847084 AAATAT AAATAT AAATAT AAATATT AAATAC AAGATCT GAA-AT AAA-AT
1 AAATAT AAATAT AAATAT AAATA-T AAATAT AA-ATAT AAATAT AAATAT
* *
29847132 -AATAT AAATAT ATATAT ATATAT A
1 AAATAT AAATAT AAATAT AAATAT A
29847156 GATTTATGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
4 2 0.04
5 7 0.13
6 37 0.67
7 9 0.16
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (6 bp):
AAATAT
Found at i:29847647 original size:25 final size:25
Alignment explanation
Indices: 29847619--29847670 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
29847609 AGTAGCCTTT
* *
29847619 AAATCAATTTGAATAAAATTAAATC
1 AAATCAATTGGAATAAAATCAAATC
** *
29847644 AAATTGATTGGAATCAAATCAAATC
1 AAATCAATTGGAATAAAATCAAATC
29847669 AA
1 AA
29847671 GATATATGTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.29
Consensus pattern (25 bp):
AAATCAATTGGAATAAAATCAAATC
Found at i:29852298 original size:82 final size:81
Alignment explanation
Indices: 29852159--29852353 Score: 239
Period size: 82 Copynumber: 2.4 Consensus size: 81
29852149 GTTGAACTGC
* * * *
29852159 AGGATTAAATCTCGAAA-AAAATTATTTAATTAAATCTGTTTGGAAACAAAATAAAAATCGAATA
1 AGGAATAAATCCCAAAACAAAATTATTCAATTAAATCTGTTTGGAAACAAAATAAAAATCGAATA
29852223 AAATCTGTTAAACGGT
66 AAATCTGTTAAACGGT
* * * * *
29852239 GGGAATAAATCCCAAAACAAAATTATTCAGTTAATTCTCGTTTGGAAACAAAATCAAAATGGAAT
1 AGGAATAAATCCCAAAACAAAATTATTCAATTAAATCT-GTTTGGAAACAAAATAAAAATCGAAT
*
29852304 AAAATCTGTTGAACGGT
65 AAAATCTGTTAAACGGT
* ** *
29852321 AGGAATAAATTCTGAAACAAATTTTATTCAATT
1 AGGAATAAATCCCAAAACAAA-ATTATTCAATT
29852354 TTAATTTTTA
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
80 13 0.14
81 17 0.18
82 57 0.59
83 9 0.09
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (81 bp):
AGGAATAAATCCCAAAACAAAATTATTCAATTAAATCTGTTTGGAAACAAAATAAAAATCGAATA
AAATCTGTTAAACGGT
Found at i:29852575 original size:51 final size:51
Alignment explanation
Indices: 29852495--29852592 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
29852485 ATTATAGACA
* *
29852495 AGATTTGAAATAAAATAATATAAAAAAATATTTATATTTATGTAAAACACC
1 AGATTTAAAATAAAAAAATATAAAAAAATATTTATATTTATGTAAAACACC
* *
29852546 AGATTTAAAATAAAACAAAT-TAAACAAATATTTATATTTATTTAAAA
1 AGATTTAAAATAAAA-AAATATAAAAAAATATTTATATTTATGTAAAA
29852593 ACGTCAGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 39 0.93
52 3 0.07
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (51 bp):
AGATTTAAAATAAAAAAATATAAAAAAATATTTATATTTATGTAAAACACC
Found at i:29860283 original size:43 final size:42
Alignment explanation
Indices: 29860215--29860327 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
29860205 AATGCCATAT
* ** *
29860215 CCCAGATATGGTCTTACATGTAATCTTGTATCGATACTAATAG
1 CCCAGATATGGTCTTACACGTAATCTCATATAGAT-CTAATAG
* * * * *
29860258 CCCAGCTATGGTCTTACACGAAATCTCATATAGATGTCATAT
1 CCCAGATATGGTCTTACACGTAATCTCATATAGATCTAATAG
29860300 CCCAGATATGGTCTTACACGTAATCTCA
1 CCCAGATATGGTCTTACACGTAATCTCA
29860328 GTGAACTTAA
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
42 30 0.51
43 29 0.49
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (42 bp):
CCCAGATATGGTCTTACACGTAATCTCATATAGATCTAATAG
Found at i:29860317 original size:42 final size:43
Alignment explanation
Indices: 29860210--29860327 Score: 148
Period size: 43 Copynumber: 2.8 Consensus size: 43
29860200 GTACCAATGC
* ** *
29860210 CATATCCCAGATATGGTCTTACATGTAATCTTGTATCGATACT
1 CATATCCCAGATATGGTCTTACACGTAATCTCATATAGATACT
* * * * *
29860253 AATAGCCCAGCTATGGTCTTACACGAAATCTCATATAGAT-GT
1 CATATCCCAGATATGGTCTTACACGTAATCTCATATAGATACT
29860295 CATATCCCAGATATGGTCTTACACGTAATCTCA
1 CATATCCCAGATATGGTCTTACACGTAATCTCA
29860328 GTGAACTTAA
Statistics
Matches: 62, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 30 0.48
43 32 0.52
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (43 bp):
CATATCCCAGATATGGTCTTACACGTAATCTCATATAGATACT
Found at i:29865254 original size:42 final size:43
Alignment explanation
Indices: 29865170--29865297 Score: 188
Period size: 43 Copynumber: 3.0 Consensus size: 43
29865160 TCATATTTCA
* *
29865170 TTTCTCATCTCATAATCATTCCTCATATTTGT-CATTTTAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTT-TCCATTTCAATAT
29865213 TTTCTCATCTCATAATCATTTCTC-TATTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
* * *
29865255 TTTCTCATCTCATATTCATTTTTCATCTTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
29865298 CAATTACATA
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
41 1 0.01
42 37 0.47
43 40 0.51
ACGTcount: A:0.23, C:0.23, G:0.01, T:0.53
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
Found at i:29866012 original size:19 final size:18
Alignment explanation
Indices: 29865969--29866012 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
29865959 ATTAATATTA
* *
29865969 TATATTTCAATTTCACAT
1 TATATTTAAATTTCACAC
*
29865987 TAAATTTAAATTTTCACAC
1 TATATTTAAA-TTTCACAC
29866006 TATATTT
1 TATATTT
29866013 TGCTTATTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (18 bp):
TATATTTAAATTTCACAC
Found at i:29871821 original size:27 final size:27
Alignment explanation
Indices: 29871783--29871836 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
29871773 TCAATCCACC
*
29871783 TTTATTTGTAACTTTATATATATGATT
1 TTTATTTATAACTTTATATATATGATT
29871810 TTTATTTATAACTTTATATATATGATT
1 TTTATTTATAACTTTATATATATGATT
29871837 CCCGAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (27 bp):
TTTATTTATAACTTTATATATATGATT
Found at i:29873712 original size:34 final size:33
Alignment explanation
Indices: 29873670--29873734 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 33
29873660 CTTTTATTTA
29873670 TTTAAAAATGTAAA-AT-AAAAATTAACATAAATT
1 TTTAAAAA--TAAATATGAAAAATTAACATAAATT
*
29873703 TTTATAAAATAAATTTGAAAAATTAACATAAA
1 TTTA-AAAATAAATATGAAAAATTAACATAAA
29873735 AATATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 4 0.14
33 5 0.18
34 19 0.68
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (33 bp):
TTTAAAAATAAATATGAAAAATTAACATAAATT
Found at i:29877223 original size:22 final size:22
Alignment explanation
Indices: 29877197--29877250 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
29877187 ATATCTAAAT
**
29877197 AATAATAACAAAATAGTAGTAA
1 AATAATAACAAAATAGTAACAA
* * *
29877219 TATAACAGCAAAATAGTAACAA
1 AATAATAACAAAATAGTAACAA
29877241 AATAATAACA
1 AATAATAACA
29877251 TAACAACAAC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.63, C:0.09, G:0.07, T:0.20
Consensus pattern (22 bp):
AATAATAACAAAATAGTAACAA
Found at i:29882164 original size:18 final size:18
Alignment explanation
Indices: 29882141--29882180 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
29882131 ATTGCACATA
29882141 GTTCCACTATTTACTCTT
1 GTTCCACTATTTACTCTT
29882159 GTTCCACTATTTACTCTT
1 GTTCCACTATTTACTCTT
29882177 GTTC
1 GTTC
29882181 ATCTCAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.28, G:0.07, T:0.50
Consensus pattern (18 bp):
GTTCCACTATTTACTCTT
Found at i:29883099 original size:51 final size:51
Alignment explanation
Indices: 29883022--29883169 Score: 244
Period size: 51 Copynumber: 2.9 Consensus size: 51
29883012 CGGATACCCG
* *
29883022 GTGGCCTTCACATAGTACCACCCTTGTAG-CCAAAACTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAAA
*
29883073 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
*
29883124 GTGGCCTTTACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
29883170 CTAAGGTTCA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
50 1 0.01
51 90 0.99
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
Found at i:29884905 original size:23 final size:24
Alignment explanation
Indices: 29884857--29884913 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
29884847 TCGTTGCTTG
* *
29884857 TTTATTTTTATTTTCTATTTGTAA
1 TTTATGTTTATTTTCTAATTGTAA
*
29884881 TTTATGTTTCTTTT-TAATTGTAA
1 TTTATGTTTATTTTCTAATTGTAA
29884904 TTCTA-GTTTA
1 TT-TATGTTTA
29884914 GTTTATTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (24 bp):
TTTATGTTTATTTTCTAATTGTAA
Found at i:29891756 original size:40 final size:40
Alignment explanation
Indices: 29891686--29891911 Score: 217
Period size: 40 Copynumber: 5.7 Consensus size: 40
29891676 CCGCACCAAG
* * *
29891686 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATCACGATTTGCACAAAT
29891726 GCCTTCGGGTCTTAGCCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATCACGATTTGCACAAAT
** * * * *
29891766 GCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATCACGATTTGCACAAAT
* * * * *
29891806 GCCTTCGGGTCTTAGCCCGGATGT-AGCCACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATCA-CGATTTGCACAAAT
* * *
29891846 GCCTTCGGGTCTTAACCCGGTTAT-A--ATTTCCAGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATCACGATTTGCA-CA-AA-T
* *
29891886 GTCTTCGGGGCTTAGCCCGGATATCA
1 GCCTTCGGGTCTTAGCCCGGATATCA
29891912 TTCAATTTCT
Statistics
Matches: 154, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
37 4 0.03
38 2 0.01
39 2 0.01
40 145 0.94
41 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATCACGATTTGCACAAAT
Found at i:29899892 original size:40 final size:40
Alignment explanation
Indices: 29899822--29900047 Score: 217
Period size: 40 Copynumber: 5.7 Consensus size: 40
29899812 CCGCACCAAG
* * *
29899822 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATCACGATTTGCACAAAT
29899862 GCCTTCGGGTCTTAGCCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATCACGATTTGCACAAAT
** * * * *
29899902 GCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATCACGATTTGCACAAAT
* * * * *
29899942 GCCTTCGGGTCTTAGCCCGGATGT-AGCCACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATCA-CGATTTGCACAAAT
* * *
29899982 GCCTTCGGGTCTTAACCCGGTTAT-A--ATTTCCAGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATCACGATTTGCA-CA-AA-T
* *
29900022 GTCTTCGGGGCTTAGCCCGGATATCA
1 GCCTTCGGGTCTTAGCCCGGATATCA
29900048 TTCAATTTCT
Statistics
Matches: 154, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
37 4 0.03
38 2 0.01
39 2 0.01
40 145 0.94
41 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATCACGATTTGCACAAAT
Found at i:29912339 original size:25 final size:25
Alignment explanation
Indices: 29912311--29912388 Score: 129
Period size: 25 Copynumber: 3.1 Consensus size: 25
29912301 CTAATAGATA
*
29912311 AGCACTAACGTGCTAATAATCAGAG
1 AGCACCAACGTGCTAATAATCAGAG
* *
29912336 AGCACCAACGTGCTAATAATTAGAT
1 AGCACCAACGTGCTAATAATCAGAG
29912361 AGCACCAACGTGCTAATAATCAGAG
1 AGCACCAACGTGCTAATAATCAGAG
29912386 AGC
1 AGC
29912389 GCACTAAGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (25 bp):
AGCACCAACGTGCTAATAATCAGAG
Found at i:29914210 original size:27 final size:28
Alignment explanation
Indices: 29914154--29914223 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
29914144 AAACTTGTAC
29914154 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
29914182 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
29914209 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
29914224 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:29914234 original size:27 final size:27
Alignment explanation
Indices: 29914154--29914235 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
29914144 AAACTTGTAC
* *
29914154 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
29914182 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
29914209 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
29914236 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.61
28 18 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:29923704 original size:28 final size:27
Alignment explanation
Indices: 29923645--29923710 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 27
29923635 TGAGTCCGCG
29923645 CACTTAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTATATAATCAACTCGCA
*
29923672 CACTTAGTGCTATATGATCAAACTCGCA
1 CACTTAGTGCTATATAATC-AACTCGCA
29923700 CACTTAGTGCT
1 CACTTAGTGCT
29923711 GTACAAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 18 0.49
28 19 0.51
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (27 bp):
CACTTAGTGCTATATAATCAACTCGCA
Found at i:29924838 original size:2 final size:2
Alignment explanation
Indices: 29924831--29924859 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29924821 TCATGACATG
29924831 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 T
29924860 GACTAGTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29926290 original size:20 final size:21
Alignment explanation
Indices: 29926253--29926292 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
29926243 ATTTATTGTT
29926253 TTGAATATTTATTCTTTATTC
1 TTGAATATTTATTCTTTATTC
29926274 TTGAAT-TTTATAT-TTTATT
1 TTGAATATTTAT-TCTTTATT
29926293 TATATTTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (21 bp):
TTGAATATTTATTCTTTATTC
Found at i:29927456 original size:32 final size:31
Alignment explanation
Indices: 29927372--29927456 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 31
29927362 AATAGGATTG
29927372 TTATTAAATATAATTTAATAAAAAATAGTAAA
1 TTATTAAATATAATTTAAT-AAAAATAGTAAA
* *
29927404 TTATTTAATCAT-ATTTAA-ATATAAT--T--A
1 TTATTAAAT-ATAATTTAATA-AAAATAGTAAA
29927431 TTATTAAATATAATTTAATAAAAATA
1 TTATTAAATATAATTTAATAAAAATA
29927457 ATATAATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
26 2 0.05
27 19 0.43
28 1 0.02
29 1 0.02
30 1 0.02
31 4 0.09
32 14 0.32
33 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (31 bp):
TTATTAAATATAATTTAATAAAAATAGTAAA
Found at i:29927506 original size:10 final size:10
Alignment explanation
Indices: 29927491--29927535 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
29927481 ATAATTATTT
29927491 TTATATTAAA
1 TTATATTAAA
29927501 TTATATTAAA
1 TTATATTAAA
29927511 --ATATT--A
1 TTATATTAAA
29927517 -TATATTAAA
1 TTATATTAAA
29927526 TTATATTAAA
1 TTATATTAAA
29927536 ATGTTTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 1 0.03
7 5 0.16
8 5 0.16
9 1 0.03
10 19 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TTATATTAAA
Found at i:29934581 original size:30 final size:30
Alignment explanation
Indices: 29934547--29934607 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29934537 TCCTTAACTC
29934547 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
29934577 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
29934607 A
1 A
29934608 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:29938252 original size:101 final size:101
Alignment explanation
Indices: 29938125--29938327 Score: 406
Period size: 101 Copynumber: 2.0 Consensus size: 101
29938115 TTCAAATTGT
29938125 AATAAATCTTTCTTTCCATACTTTCTTAACTGTTTTAATAGGTAATTAGGCCAATATTTCTTTTC
1 AATAAATCTTTCTTTCCATACTTTCTTAACTGTTTTAATAGGTAATTAGGCCAATATTTCTTTTC
29938190 ACTCATAACTGATAAATCACAATTCAAATGAACAAC
66 ACTCATAACTGATAAATCACAATTCAAATGAACAAC
29938226 AATAAATCTTTCTTTCCATACTTTCTTAACTGTTTTAATAGGTAATTAGGCCAATATTTCTTTTC
1 AATAAATCTTTCTTTCCATACTTTCTTAACTGTTTTAATAGGTAATTAGGCCAATATTTCTTTTC
29938291 ACTCATAACTGATAAATCACAATTCAAATGAACAAC
66 ACTCATAACTGATAAATCACAATTCAAATGAACAAC
29938327 A
1 A
29938328 TTTACTATCT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (101 bp):
AATAAATCTTTCTTTCCATACTTTCTTAACTGTTTTAATAGGTAATTAGGCCAATATTTCTTTTC
ACTCATAACTGATAAATCACAATTCAAATGAACAAC
Found at i:29942897 original size:46 final size:47
Alignment explanation
Indices: 29942826--29942954 Score: 178
Period size: 46 Copynumber: 2.8 Consensus size: 47
29942816 GGTGGTATGT
29942826 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATT-ATGA-A
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-CATTGA-GACA
*
29942873 -AGCCAGTGTAAGACATGTCAGGGACATGCATCGG--CATTGAGACGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCCATTGAGAC-A
*
29942918 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCC
29942955 TCGAGATATA
Statistics
Matches: 73, Mismatches: 3, Indels: 11
0.84 0.03 0.13
Matches are distributed among these distances:
43 6 0.08
44 1 0.01
45 1 0.01
46 65 0.89
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (47 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCCATTGAGACA
Found at i:29946555 original size:2 final size:2
Alignment explanation
Indices: 29946548--29946575 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29946538 AATGATTTTC
29946548 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
29946576 TTTCCATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29948466 original size:43 final size:42
Alignment explanation
Indices: 29948381--29948569 Score: 263
Period size: 43 Copynumber: 4.4 Consensus size: 42
29948371 TTGAATTTGA
*
29948381 GGCACTAAGTGTGCGATAAATGAAATAG-CTACGGCTAATTAATT
1 GGCACTAAGTGTGCGATAAAT--TATAGCCT-CGGCTAATTAATT
*
29948425 GGCACTAAATGTGCGATACAATTATAGCCTCGGCTAATTAATT
1 GGCACTAAGTGTGCGATA-AATTATAGCCTCGGCTAATTAATT
29948468 GGCACTAAGTGTGCGATAAAATTATAGCCTCGGCTAATTAATT
1 GGCACTAAGTGTGCGAT-AAATTATAGCCTCGGCTAATTAATT
* * * *
29948511 GGAACTAAGTGTGTGATATAATTATAGCTTCAGCTAATTAATT
1 GGCACTAAGTGTGCGATA-AATTATAGCCTCGGCTAATTAATT
29948554 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
29948570 GTTCGTTGAA
Statistics
Matches: 132, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
42 1 0.01
43 108 0.82
44 20 0.15
45 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (42 bp):
GGCACTAAGTGTGCGATAAATTATAGCCTCGGCTAATTAATT
Found at i:29948744 original size:89 final size:89
Alignment explanation
Indices: 29948626--29948899 Score: 503
Period size: 89 Copynumber: 3.1 Consensus size: 89
29948616 ATTGGAGTGA
* *
29948626 TAAATGTGATAGATAAGAACATAGTGGTACAGGTGTGTACGAAACCTATGTGCTTAATGATGTTA
1 TAAATGTGATAGA-AAGAACATAATGGTACAGGTATGTACGAAACCTATGTGCTTAATGATGTTA
29948691 AGTATGAAGTAGATGAAAAATTATG
65 AGTATGAAGTAGATGAAAAATTATG
*
29948716 TAAATGTGATAGAAAGAACATAATGGTACAGGTATGTACAAAACCTATGTGCTTAATGATGTTAA
1 TAAATGTGATAGAAAGAACATAATGGTACAGGTATGTACGAAACCTATGTGCTTAATGATGTTAA
29948781 GTATGAAGTAGATGAAAAATTATG
66 GTATGAAGTAGATGAAAAATTATG
*
29948805 TAAATGTGATAGAAAGAACATAATGGTACAGGTATGTACGAAACCTATGTGGTTAATGATGTTAA
1 TAAATGTGATAGAAAGAACATAATGGTACAGGTATGTACGAAACCTATGTGCTTAATGATGTTAA
29948870 GTATGAAGTAGATGAAAAATTATG
66 GTATGAAGTAGATGAAAAATTATG
29948894 TAAATG
1 TAAATG
29948900 AATGATGAAA
Statistics
Matches: 179, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
89 166 0.93
90 13 0.07
ACGTcount: A:0.41, C:0.06, G:0.23, T:0.30
Consensus pattern (89 bp):
TAAATGTGATAGAAAGAACATAATGGTACAGGTATGTACGAAACCTATGTGCTTAATGATGTTAA
GTATGAAGTAGATGAAAAATTATG
Found at i:29950013 original size:20 final size:20
Alignment explanation
Indices: 29949979--29950018 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29949969 AGAGAATGAA
*
29949979 TATGAAATTGGTTGATGATAT
1 TATGAAATTGATTGAT-ATAT
29950000 TATG-AATTGATTGATATAT
1 TATGAAATTGATTGATATAT
29950019 GTTTGGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (20 bp):
TATGAAATTGATTGATATAT
Found at i:29950423 original size:17 final size:18
Alignment explanation
Indices: 29950401--29950436 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
29950391 GTGACCTTTA
29950401 TAAC-TTAGAAAAATTTT
1 TAACTTTAGAAAAATTTT
29950418 TAACTTTTAGAAAAATTTT
1 TAAC-TTTAGAAAAATTTT
29950437 GTATGTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
19 13 0.76
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (18 bp):
TAACTTTAGAAAAATTTT
Found at i:29953298 original size:10 final size:10
Alignment explanation
Indices: 29953283--29953307 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29953273 AAATTTCTTG
29953283 CCATATTCGA
1 CCATATTCGA
29953293 CCATATTCGA
1 CCATATTCGA
29953303 CCATA
1 CCATA
29953308 AACTTGTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.28
Consensus pattern (10 bp):
CCATATTCGA
Found at i:29953691 original size:39 final size:40
Alignment explanation
Indices: 29953586--29953788 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
29953576 TCGAATGATG
* *
29953586 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATA
*
29953626 TCCGGACTAAGAT-CCGAAGGCA-TTGTGCGAGTTACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA
*
29953664 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* *
29953704 TCCGGGTTAAGTCCCGAAGGCATTTATGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* * **
29953744 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATA
29953784 TCCGG
1 TCCGG
29953789 TTAAATTCCG
Statistics
Matches: 141, Mismatches: 14, Indels: 16
0.82 0.08 0.09
Matches are distributed among these distances:
38 10 0.07
39 44 0.31
40 86 0.61
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:29953791 original size:79 final size:77
Alignment explanation
Indices: 29953587--29953802 Score: 226
Period size: 79 Copynumber: 2.7 Consensus size: 77
29953577 CGAATGATGT
* *
29953587 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAG-TCCGAAGGCATT
* *
29953650 GTGCGAGTTACTAATT
62 ATGCGAGTTACTAATA
*
29953666 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATATCC-GGTTAAGT-CCGAAGGCA-TT
29953729 ATGCGAGTTACT-ATAA
62 ATGCGAGTTACTAAT-A
* ** *
29953745 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTT-AAGTCCGAAGG
29953803 TACGTGATTC
Statistics
Matches: 117, Mismatches: 10, Indels: 20
0.80 0.07 0.14
Matches are distributed among these distances:
77 1 0.01
78 33 0.28
79 55 0.47
80 28 0.24
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (77 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGTCCGAAGGCATTATGC
GAGTTACTAATA
Found at i:29961782 original size:39 final size:40
Alignment explanation
Indices: 29961686--29961866 Score: 174
Period size: 40 Copynumber: 4.5 Consensus size: 40
29961676 ATGATGTCCG
* * * *
29961686 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATTC-
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCA
* *
29961725 GGACTAAGAT-CCGAAGGCAATTGTGCGAGTTACTAATTCCA
1 GG-CTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCA
* *
29961766 GGCTAAG-CCCGAAGGCATTTGTGCTAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCA
* * *
29961805 GGTTAAGTCCCGAAGGCATTTATGCGAGTTACTATAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCA
* *
29961845 GGCTATGTCCCGAAGGCGTTTG
1 GGCTAAGTCCCGAAGGCATTTG
29961867 AACGAGTAGC
Statistics
Matches: 118, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
39 35 0.30
40 72 0.61
41 11 0.09
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCA
Found at i:29961820 original size:79 final size:80
Alignment explanation
Indices: 29961686--29961866 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 80
29961676 ATGATGTCCG
* * *
29961686 GGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATTCGGACTAAGATCCGAAGGCAATTGTGC
1 GGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCAATTATGC
29961751 GAGTTACTAATTCCA
66 GAGTTACTAATTCCA
* ** *
29961766 GGCTAAG-CCCGAAGGCATTTGTGCT-AGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTAT
1 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCAATTAT
* *
29961828 GCGAGTTACT-ATAACCG
64 GCGAGTTACTAAT-TCCA
*
29961845 GGCTATGTCCCGAAGGCGTTTG
1 GGCTAAGTCCCGAAGGC-TTTG
29961867 AACGAGTAGC
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 55 0.64
80 28 0.33
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (80 bp):
GGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCAATTATGC
GAGTTACTAATTCCA
Found at i:29961888 original size:79 final size:79
Alignment explanation
Indices: 29961735--29961899 Score: 174
Period size: 79 Copynumber: 2.1 Consensus size: 79
29961725 GGACTAAGAT
* * ** *
29961735 CCGAAGGCAATTGTGCGAGTTACTAATTCCAGGCTAAGCCCGAAGGCATTTGTGCTAGTTACTAA
1 CCGAAGGCAATTATGCGAGTTACTAATACCAGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
29961800 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * * *
29961814 CCGAAGGCATTTATGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCGTTTGAACGAG-TAGC
1 CCGAAGGCAATTATGCGAGTTACTAAT-ACCAGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
29961877 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
29961893 CCGAAGG
1 CCGAAGG
29961900 TACGTGATTT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.65
80 23 0.32
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (79 bp):
CCGAAGGCAATTATGCGAGTTACTAATACCAGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:29964162 original size:40 final size:40
Alignment explanation
Indices: 29964104--29964454 Score: 557
Period size: 40 Copynumber: 8.8 Consensus size: 40
29964094 TGAATGATAC
* * *
29964104 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
29964144 CCGGGCTAAGACCTGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * * *
29964184 TCAGGCTAAGACCCGAAGGCATTCGTGCCAGTTGTGATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
29964224 TCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
29964264 CCGGGCTAAGACCCGAAGGCATTAGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
29964304 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
29964344 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
29964384 -CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
29964423 CCGGGCTAAGACCCGAAGGCA-TT-TGCGAGTTG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
29964455 CTATCCGGCT
Statistics
Matches: 290, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
38 9 0.03
39 40 0.14
40 239 0.82
41 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:29972469 original size:40 final size:40
Alignment explanation
Indices: 29972414--29972727 Score: 408
Period size: 40 Copynumber: 8.2 Consensus size: 40
29972404 TGAATGATAC
* * *
29972414 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
29972454 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
29972494 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
29972534 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
29972574 CCGGGCTAAGACCCGAAGGCA-TTGTGCGA---GTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
29972610 CC--G-TAAGACCCGAAGGCA-TTGTGC------TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* *
29972640 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * ** *
29972680 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
29972720 CC-GGCTAA
1 CCGGGCTAA
29972728 ATTCCGAAGA
Statistics
Matches: 248, Mismatches: 15, Indels: 23
0.87 0.05 0.08
Matches are distributed among these distances:
30 8 0.03
32 1 0.00
33 36 0.15
34 7 0.03
36 9 0.04
39 13 0.05
40 172 0.69
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:29976758 original size:36 final size:36
Alignment explanation
Indices: 29976711--29976782 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
29976701 AAGAGAGACC
29976711 TTATATCTTCATCTTATTGATTTACCAAATCCAACA
1 TTATATCTTCATCTTATTGATTTACCAAATCCAACA
29976747 TTATATCTTCATCTTATTGATTTACCAAATCCAACA
1 TTATATCTTCATCTTATTGATTTACCAAATCCAACA
29976783 GACTTACTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (36 bp):
TTATATCTTCATCTTATTGATTTACCAAATCCAACA
Found at i:29978069 original size:16 final size:16
Alignment explanation
Indices: 29978050--29978082 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29978040 TATAAATAAG
29978050 AATGAAAATAAAATTT
1 AATGAAAATAAAATTT
29978066 AATGAAAATAAAATTT
1 AATGAAAATAAAATTT
29978082 A
1 A
29978083 CCTTTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
AATGAAAATAAAATTT
Found at i:29982985 original size:31 final size:31
Alignment explanation
Indices: 29982947--29983024 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
29982937 GCTTGTGGGC
* *
29982947 CACACAGGCGTGTGGGCTCATACGGGTGTTT
1 CACACAGGTGTGTGGGCCCATACGGGTGTTT
29982978 CACACAGGTGTGTGGGCCCATACGGGTGTTT
1 CACACAGGTGTGTGGGCCCATACGGGTGTTT
29983009 CACACAGGTGTGTGGG
1 CACACAGGTGTGTGGG
29983025 TTGTTGGCCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.17, C:0.22, G:0.37, T:0.24
Consensus pattern (31 bp):
CACACAGGTGTGTGGGCCCATACGGGTGTTT
Found at i:29986277 original size:348 final size:347
Alignment explanation
Indices: 29985641--29986328 Score: 1286
Period size: 348 Copynumber: 2.0 Consensus size: 347
29985631 ACTTGGGAGA
29985641 ACTTCGCTCTTGAGAGCACTTCTAGTGAGATAATTGTACTGAGTCCGTTGAGGCAGTTTGTCCAG
1 ACTTCGCTCTTGAGAGCACTTCTAGTGAGATAATTGTACTGAGTCCGTTGAGGCAGTTTGTCCAG
* *
29985706 GTTAGTAAACTCTGTAGGGATGTTCCATTAGAGGTGCAAGGCACTATTTTGTGGCAAATCTGATG
66 GTTAGTAAACTCTATAGGGATGTTCCATTAGAGGTGCAAGGCACTATTTTCTGGCAAATCTGATG
* *
29985771 GAGCTTTCGTTTGGGGAGTTTGACTTAATTCTGGGCATGGATTGGTTGGTCAAGCACTGAGTTAG
131 GAGCTTTCGTTTGGGGAGTTCGACTTAATTCTGGGCATGGATTGGTTCGTCAAGCACTGAGTTAG
29985836 TTTGGACTGTATGACTAAAAGGGTCGTTTTAAGGACTGAAGATGATAAGGAGGTGGTTGTGATTG
196 TTTGGACTGTATGACTAAAAGGGTCGTTTTAAGGACTGAAGATGATAAGGAGGTGGTTGTGATTG
*
29985901 GCGAGCATCTAGATTACTTGTCTAATGTGATTTTCGCTCTTGTGGCTGAGAAATTGGTTTTGAAA
261 GCGAGCATCTAGATTACTTGTCTAATGTGATTTTCGCTCTTGTGGCTGAGAAATTGGTTTAGAAA
29985966 AGGTGTGAGGCGTACAAGGCGT
326 AGGTGTGAGGCGTACAAGGCGT
*
29985988 ACTTCGCTCTTGAGAGCACTTCTAGTGAGATAATTGTACTGAGTCCGTTGGGGCAGTTTGTCCAG
1 ACTTCGCTCTTGAGAGCACTTCTAGTGAGATAATTGTACTGAGTCCGTTGAGGCAGTTTGTCCAG
*
29986053 GTTAGTAAACTCTATAGGGATGTTCCATTAGAGGTGCAAGGCACTATTTTTCTGGCAGATCTGAT
66 GTTAGTAAACTCTATAGGGATGTTCCATTAGAGGTGCAAGGCACTA-TTTTCTGGCAAATCTGAT
*
29986118 GGAGCTTTCGTTTGGGGAGTTCGACTTAATTCTTGGCATGGATTGGTTCGTCAAGCACTGAGTTA
130 GGAGCTTTCGTTTGGGGAGTTCGACTTAATTCTGGGCATGGATTGGTTCGTCAAGCACTGAGTTA
29986183 GTTTGGACTGTATGACTAAAAGGGTCGTTTTAAGGACTGAAGATGATAAGGAGGTGGTTGTGATT
195 GTTTGGACTGTATGACTAAAAGGGTCGTTTTAAGGACTGAAGATGATAAGGAGGTGGTTGTGATT
29986248 GGCGAGCATCTAGATTACTTGTCTAATGTGATTTTCGCTCTTGTGGCTGAGAAATTGGTTTAGAA
260 GGCGAGCATCTAGATTACTTGTCTAATGTGATTTTCGCTCTTGTGGCTGAGAAATTGGTTTAGAA
*
29986313 AGGGTGTGAGGCGTAC
325 AAGGTGTGAGGCGTAC
29986329 TTGGCTTACG
Statistics
Matches: 331, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
347 109 0.33
348 222 0.67
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (347 bp):
ACTTCGCTCTTGAGAGCACTTCTAGTGAGATAATTGTACTGAGTCCGTTGAGGCAGTTTGTCCAG
GTTAGTAAACTCTATAGGGATGTTCCATTAGAGGTGCAAGGCACTATTTTCTGGCAAATCTGATG
GAGCTTTCGTTTGGGGAGTTCGACTTAATTCTGGGCATGGATTGGTTCGTCAAGCACTGAGTTAG
TTTGGACTGTATGACTAAAAGGGTCGTTTTAAGGACTGAAGATGATAAGGAGGTGGTTGTGATTG
GCGAGCATCTAGATTACTTGTCTAATGTGATTTTCGCTCTTGTGGCTGAGAAATTGGTTTAGAAA
AGGTGTGAGGCGTACAAGGCGT
Found at i:30002268 original size:46 final size:46
Alignment explanation
Indices: 30002200--30002382 Score: 285
Period size: 46 Copynumber: 4.0 Consensus size: 46
30002190 TATATATACA
* * * *
30002200 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
30002246 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
30002292 CATCTCATACACATTTCGCATTAGACATTTGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
30002338 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
30002383 ATACACTTCC
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.35
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:30002427 original size:47 final size:47
Alignment explanation
Indices: 30002356--30002525 Score: 243
Period size: 47 Copynumber: 3.6 Consensus size: 47
30002346 ACACATTTCG
* * * * * *
30002356 CATTAGCCATTCGGCTTTACCACATATATACACT-TCCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCA-TATTCACATTCATCA
* *
30002403 CATTGGCCATTCTGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATATTCACATTCATCA
30002450 CATTGGCCATTCGGCCTTATCACATATATGCATATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATATTCACATTCATCA
*
30002497 CATTGGCCATTCGGCCTTATCACACATAT
1 CATTGGCCATTCGGCCTTATCACATATAT
30002526 TGTGACAGCC
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
46 1 0.01
47 111 0.99
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATATTCACATTCATCA
Found at i:30002474 original size:22 final size:22
Alignment explanation
Indices: 30002446--30002520 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
30002436 GTTCACATTC
30002446 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * * *
30002468 ATCACATATATGCATATTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
30002492 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
30002515 ATCACA
1 ATCACA
30002521 CATATTGTGA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 17 0.43
23 6 0.15
24 6 0.15
25 11 0.28
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:30002496 original size:25 final size:25
Alignment explanation
Indices: 30002421--30002499 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
30002411 ATTCTGCCTT
*
30002421 ATCACATATATGCATGTTCACATTC
1 ATCACATATATGCATATTCACATTC
* * * *
30002446 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATGCATATTC-ACATTC
30002468 ATCACATATATGCATATTCACATTC
1 ATCACATATATGCATATTCACATTC
30002493 ATCACAT
1 ATCACAT
30002500 TGGCCATTCG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 10 0.25
23 6 0.15
24 6 0.15
25 18 0.45
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (25 bp):
ATCACATATATGCATATTCACATTC
Found at i:30004212 original size:39 final size:39
Alignment explanation
Indices: 30004158--30004340 Score: 294
Period size: 39 Copynumber: 4.7 Consensus size: 39
30004148 GAATGTTCGA
*
30004158 GTGATATCTGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
30004197 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* * *
30004236 GTGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
30004275 ATGATATCCAGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
30004314 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
30004341 CTTTGAGCGG
Statistics
Matches: 131, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 122 0.93
40 9 0.07
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:30005823 original size:22 final size:22
Alignment explanation
Indices: 30005798--30005916 Score: 59
Period size: 22 Copynumber: 5.1 Consensus size: 22
30005788 GTTCACATTC
30005798 ATCACATTGGCCATTCAGCCTT
1 ATCACATTGGCCATTCAGCCTT
*
30005820 ATCACACATAT-G-CATGTTCA-CATT
1 AT--CACAT-TGGCCA--TTCAGCCTT
*
30005844 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCAGCCTT
* *
30005867 ATCACATATATG-CATGTTCA-CATT
1 ATCACAT-T-GGCCA--TTCAGCCTT
*
30005891 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCAGCCTT
30005914 ATC
1 ATC
30005917 TCACATATGC
Statistics
Matches: 72, Mismatches: 9, Indels: 32
0.64 0.08 0.28
Matches are distributed among these distances:
22 19 0.26
23 18 0.25
24 18 0.25
25 17 0.24
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCAGCCTT
Found at i:30005845 original size:47 final size:47
Alignment explanation
Indices: 30005776--30005992 Score: 344
Period size: 47 Copynumber: 4.6 Consensus size: 47
30005766 TTCGGGTGTT
*
30005776 ACACATATGCATGTTCACATTCATCACATTGGCCATTCAGCCTTATC
1 ACACATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATC
30005823 ACACATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATC
1 ACACATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATC
*
30005870 ACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATC
1 ACACATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATC
* * *
30005917 TCACATATGCATGTTCACATTCATCACATTTGCCATTCGGCCTTAAC
1 ACACATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATC
* * * **
30005964 TCATATATACACATTCACATTCATCACAT
1 ACACATATGCATGTTCACATTCATCACAT
30005993 AAAATCCTAA
Statistics
Matches: 160, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 160 1.00
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (47 bp):
ACACATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATC
Found at i:30007677 original size:2 final size:2
Alignment explanation
Indices: 30007670--30007695 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30007660 TTCATTATTA
30007670 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
30007696 CTAAACACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30015821 original size:37 final size:37
Alignment explanation
Indices: 30015768--30015889 Score: 226
Period size: 37 Copynumber: 3.3 Consensus size: 37
30015758 TATAAAAGAA
*
30015768 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
30015805 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
30015842 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
30015879 GTCTCACCCGG
1 GTCTTACCCGG
30015890 AACATATTCC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:30016046 original size:49 final size:49
Alignment explanation
Indices: 30015991--30016107 Score: 216
Period size: 49 Copynumber: 2.4 Consensus size: 49
30015981 TTTTGCATTA
30015991 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
30016040 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
30016089 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
30016108 CATATATGTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 66 1.00
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:30019672 original size:29 final size:29
Alignment explanation
Indices: 30019636--30019862 Score: 409
Period size: 29 Copynumber: 7.8 Consensus size: 29
30019626 TATTGAAAAA
* *
30019636 CTCGCACACACAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
30019665 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
30019694 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
30019723 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
*
30019752 CTCGCACACATAGTGCCCCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
30019781 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
*
30019810 CTCGCACACATAGTGCCCCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
*
30019839 CTCGTACACATAGTGCCTCGATTA
1 CTCGCACACATAGTGCCTCGATTA
30019863 ACGAAATTTG
Statistics
Matches: 191, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 191 1.00
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (29 bp):
CTCGCACACATAGTGCCTCGATTACTGAT
Found at i:30021993 original size:37 final size:37
Alignment explanation
Indices: 30021940--30022061 Score: 226
Period size: 37 Copynumber: 3.3 Consensus size: 37
30021930 TATAAAAGAA
*
30021940 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
30021977 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
30022014 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
30022051 GTCTCACCCGG
1 GTCTTACCCGG
30022062 AACATATTCC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:30022218 original size:49 final size:49
Alignment explanation
Indices: 30022163--30022279 Score: 216
Period size: 49 Copynumber: 2.4 Consensus size: 49
30022153 TTTTGCATTA
30022163 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
30022212 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
30022261 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
30022280 CATATATGTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 66 1.00
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:30029417 original size:42 final size:42
Alignment explanation
Indices: 30029311--30029418 Score: 137
Period size: 43 Copynumber: 2.5 Consensus size: 42
30029301 GTACCAATGT
* * *
30029311 CATATCCTAGATATGGTCTTACATGAAATCTCGTATCGATGC
1 CATATCCCAGATATGGTCTTACATGAAATCTCATATCGATAC
* * *
30029353 CA-ATTGCCCAGCTATGGTCTTACATGAAGTCTCATATTGATAC
1 CATA-T-CCCAGATATGGTCTTACATGAAATCTCATATCGATAC
30029396 CATATCCCAGATATGGTCTTACA
1 CATATCCCAGATATGGTCTTACA
30029419 CGTTATCTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
41 1 0.02
42 20 0.36
43 34 0.61
44 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (42 bp):
CATATCCCAGATATGGTCTTACATGAAATCTCATATCGATAC
Found at i:30035645 original size:27 final size:27
Alignment explanation
Indices: 30035615--30035690 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 27
30035605 AAAACCCTAG
*
30035615 TTTGTAAAATTATCAAAATACCCCCAA
1 TTTGTAAAATTACCAAAATACCCCCAA
* **
30035642 TTTGTAAAATTACCAAAATA-TCCCTG
1 TTTGTAAAATTACCAAAATACCCCCAA
30035668 TTTGTAAAATTACCAAAATACCC
1 TTTGTAAAATTACCAAAATACCC
30035691 TTGTCGTGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.53
27 20 0.47
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (27 bp):
TTTGTAAAATTACCAAAATACCCCCAA
Found at i:30035678 original size:26 final size:25
Alignment explanation
Indices: 30035608--30035705 Score: 106
Period size: 27 Copynumber: 3.7 Consensus size: 25
30035598 GGTCGTTAAA
*
30035608 ACCCTAGTTTGTAAAATTATCAAAAT
1 ACCCT-GTTTGTAAAATTACCAAAAT
**
30035634 ACCCCCAATTTGTAAAATTACCAAAAT
1 A--CCCTGTTTGTAAAATTACCAAAAT
30035661 ATCCCTGTTTGTAAAATTACCAAAAT
1 A-CCCTGTTTGTAAAATTACCAAAAT
*
30035687 ACCCTTGTCGTGTAAAATT
1 ACCC-TGT-TTGTAAAATT
30035706 TCCGAAACAC
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
25 3 0.05
26 27 0.44
27 28 0.46
28 3 0.05
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
ACCCTGTTTGTAAAATTACCAAAAT
Found at i:30037982 original size:40 final size:40
Alignment explanation
Indices: 30037927--30038151 Score: 263
Period size: 40 Copynumber: 5.6 Consensus size: 40
30037917 TATTCGGATG
* * *
30037927 ATATCCGGGCTAAGTCTCGAAGGCATTTGCGCGAGTTCCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
30037967 ATATCCGAGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
30038007 ATATCCGGGCGAAGTCCCGAAGGCATTTGTACTAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC--G-AGTTACT
* * * *
30038050 ATACCCGGGCTAAATCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
30038090 ATATCCGGGCTAAGACCCGAAGGCATTTGTGAGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
30038130 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
30038152 TACTTGGGTT
Statistics
Matches: 154, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
39 14 0.09
40 107 0.69
43 33 0.21
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:30038080 original size:83 final size:81
Alignment explanation
Indices: 30037927--30038151 Score: 330
Period size: 83 Copynumber: 2.8 Consensus size: 81
30037917 TATTCGGATG
* * * * *
30037927 ATATCCGGGCTAAGTCTCGAAGGCATTTG-CGCGAGTTCCTATATCCGAGCTAAGTCCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTCGAGAGTTGCTATATCCGGGCTAAATCCCGAAGGC
30037991 ATTTGTGCTAGTGACT
66 ATTTGTGCTAGTGACT
* * *
30038007 ATATCCGGGCGAAGTCCCGAAGGCATTTGTACTAGTAGTTGCTATACCCGGGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGT-CGAG-AGTTGCTATATCCGGGCTAAATCCCGAAG
30038072 GCATTTGTGCTAGTGACT
64 GCATTTGTGCTAGTGACT
*
30038090 ATATCCGGGCTAAGACCCGAAGGCATTTGT-GAGAGTTGCTATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTCGAGAGTTGCTATATCCGGGCTAAATCCCGAAGG
30038152 TACTTGGGTT
Statistics
Matches: 130, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
79 16 0.12
80 39 0.30
81 2 0.02
82 2 0.02
83 71 0.55
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (81 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTCGAGAGTTGCTATATCCGGGCTAAATCCCGAAGGC
ATTTGTGCTAGTGACT
Found at i:30043260 original size:27 final size:28
Alignment explanation
Indices: 30043230--30043299 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
30043220 ATAATAAGTC
*
30043230 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
30043257 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
30043285 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30043300 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:30051191 original size:27 final size:28
Alignment explanation
Indices: 30051161--30051230 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
30051151 ATAATAAGTC
*
30051161 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
30051188 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
30051216 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30051231 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:30057146 original size:20 final size:20
Alignment explanation
Indices: 30057121--30057172 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
30057111 GAGGCAAAAC
30057121 ACACGCCTGTGTGCTTAGGG
1 ACACGCCTGTGTGCTTAGGG
30057141 ACACG-CTCGTGTGCTTAGGG
1 ACACGCCT-GTGTGCTTAGGG
30057161 ACACGCCTGTGT
1 ACACGCCTGTGT
30057173 CCCTCGCCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.15, C:0.27, G:0.33, T:0.25
Consensus pattern (20 bp):
ACACGCCTGTGTGCTTAGGG
Found at i:30066219 original size:284 final size:284
Alignment explanation
Indices: 30065703--30066277 Score: 954
Period size: 284 Copynumber: 2.0 Consensus size: 284
30065693 ATGTTGTCCC
* * **
30065703 TAAAACAAACCTACAAGGCCTAAAACATGCATTGGAAGTGGTTTGGGACTAAACCGAGAATTTAG
1 TAAAATAAACCTACAAGGCCCAAAACATGCATTGGAAGTGGTTCAGGACTAAACCGAGAATTTAG
30065768 AAAATTCTACAACACTTAGAAAATTTTTCATCAAAACAGGTAACAAGCCCGTGTGGCTTGGAACA
66 AAAATTCTACAACACTTAGAAAATTTTTCATCAAAACAGGTAACAAGCCCGTGTGGCTTGGAACA
* *
30065833 CGCTCGTATGTGTTGGCTATGTGGTCACACACACCCGTGTCTTTAACCCATGTAACTCTCAGTTT
131 CGCTCGTATGTGTTGGCCATGTGGTCACACACACCCGTGTCCTTAACCCATGTAACTCTCAGTTT
* *
30065898 ATGACATCATGCAACAAAAGAAGTCACACAGCCAAGTTACACGCCCGTGTGCTAGGCTGTGTGGT
196 ATGACATCATGCAACAAAAGAAGTCACACAGCCAAGTTACACGCCCGTGTGCTAGGCCGTGTGGC
*
30065963 TAATATAATTTTCAAAATTTTTCA
261 GAATATAATTTTCAAAATTTTTCA
* * *
30065987 TAAAATAAACCTACGATGCCCAAAACATGCATTGGAGGTGGTTCAGGACTAAACCGAGAATTTAG
1 TAAAATAAACCTACAAGGCCCAAAACATGCATTGGAAGTGGTTCAGGACTAAACCGAGAATTTAG
* *
30066052 AAAATTCTACAACACTTAGAAATTTTTTCATCAAAACAGGTAACAAGCCCGTGTGGCTTGGGACA
66 AAAATTCTACAACACTTAGAAAATTTTTCATCAAAACAGGTAACAAGCCCGTGTGGCTTGGAACA
* * * * * *
30066117 CGCTCGTGTAG-GTTGGCCGTGTGGTCACACACGCCTGTGTCCTTAACCCGTGTAACTCTCTGTT
131 CGCTCGTAT-GTGTTGGCCATGTGGTCACACACACCCGTGTCCTTAACCCATGTAACTCTCAGTT
30066181 TATGACATCATGCAACAAAAGAAGTCACACAGCCAAGTTACACGCCCGTGTGCTAGGCCGTGTGG
195 TATGACATCATGCAACAAAAGAAGTCACACAGCCAAGTTACACGCCCGTGTGCTAGGCCGTGTGG
30066246 CGAATATAATTTTCAAAATTTTTCA
260 CGAATATAATTTTCAAAATTTTTCA
30066271 TAAAATA
1 TAAAATA
30066278 GGTGCAGACT
Statistics
Matches: 270, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
284 269 1.00
285 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (284 bp):
TAAAATAAACCTACAAGGCCCAAAACATGCATTGGAAGTGGTTCAGGACTAAACCGAGAATTTAG
AAAATTCTACAACACTTAGAAAATTTTTCATCAAAACAGGTAACAAGCCCGTGTGGCTTGGAACA
CGCTCGTATGTGTTGGCCATGTGGTCACACACACCCGTGTCCTTAACCCATGTAACTCTCAGTTT
ATGACATCATGCAACAAAAGAAGTCACACAGCCAAGTTACACGCCCGTGTGCTAGGCCGTGTGGC
GAATATAATTTTCAAAATTTTTCA
Found at i:30070697 original size:19 final size:20
Alignment explanation
Indices: 30070668--30070705 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
30070658 CAATATTCAT
*
30070668 ATATTCTTTTATTTTTCAAC
1 ATATTCTTTTATTTATCAAC
30070688 ATATTC-TTTATTTATCAA
1 ATATTCTTTTATTTATCAA
30070706 TATTTTCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTCTTTTATTTATCAAC
Found at i:30071136 original size:19 final size:19
Alignment explanation
Indices: 30071112--30071148 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
30071102 CTTAAATATT
30071112 CAAAATCACTTGTTCTTCC
1 CAAAATCACTTGTTCTTCC
30071131 CAAAATCACTTGTTCTTC
1 CAAAATCACTTGTTCTTC
30071149 TCTTCTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (19 bp):
CAAAATCACTTGTTCTTCC
Found at i:30080449 original size:50 final size:50
Alignment explanation
Indices: 30080374--30080726 Score: 420
Period size: 50 Copynumber: 7.0 Consensus size: 50
30080364 AGTCACGTGC
30080374 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGT
1 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGT
*
30080424 GTAGTACTAAGTGCAGGCTACTACGTGTACCATATTGATAGGTCGCATGT
1 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGT
* * ** * * * * * *
30080474 GTAGTACTAAGTGTAGGCTACTATGCATACCCG-TTAACTTCGATCACGTGT
1 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGA--TAGGTCGCATGT
** * ** * * * * *
30080525 GTAGTACTAAGTATAGGCTACTACGTGTATCAGACGGTTAAGTCACGTAT
1 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGT
*
30080575 GTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGATAGGTCGCATGT
1 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGT
* * * * ***
30080625 GTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAAGTCATGTGT
1 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGT
30080675 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGT
1 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGT
30080725 GT
1 GT
30080727 TAGAATTAAG
Statistics
Matches: 248, Mismatches: 52, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
49 3 0.01
50 210 0.85
51 35 0.14
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGT
Found at i:30080643 original size:151 final size:151
Alignment explanation
Indices: 30080366--30080647 Score: 438
Period size: 151 Copynumber: 1.9 Consensus size: 151
30080356 TCATTGTGAG
* ** * * *
30080366 TCACGTGCGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGTAC
1 TCACGTGCGTAGTACTAAGTACAGGCTACTACGTGTACCAGACGGATAAGTCACATATGTAGTAC
* * *
30080431 TAAGTGCAGGCTACTACGTGTACCATATTGATAGGTCGCATGTGTAGTACTAAGTGTAGGCTACT
66 TAAGTGCAGGCTACTACATGTACCAGATTGATAGGTCGCATGTGTAGTACTAAGTGCAGGCTACT
30080496 ATGCATACCCGTTAACTTCGA
131 ATGCATACCCGTTAACTTCGA
* * * * *
30080517 TCACGTGTGTAGTACTAAGTATAGGCTACTACGTGTATCAGACGGTTAAGTCACGTATGTAGTAC
1 TCACGTGCGTAGTACTAAGTACAGGCTACTACGTGTACCAGACGGATAAGTCACATATGTAGTAC
30080582 TAAGTGCAGGCTACTACATGTACCAGATTGATAGGTCGCATGTGTAGTACTAAGTGCAGGCTACT
66 TAAGTGCAGGCTACTACATGTACCAGATTGATAGGTCGCATGTGTAGTACTAAGTGCAGGCTACT
30080647 A
131 A
30080648 CGTGTATCAG
Statistics
Matches: 117, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
151 117 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (151 bp):
TCACGTGCGTAGTACTAAGTACAGGCTACTACGTGTACCAGACGGATAAGTCACATATGTAGTAC
TAAGTGCAGGCTACTACATGTACCAGATTGATAGGTCGCATGTGTAGTACTAAGTGCAGGCTACT
ATGCATACCCGTTAACTTCGA
Found at i:30080654 original size:100 final size:100
Alignment explanation
Indices: 30080364--30080726 Score: 471
Period size: 100 Copynumber: 3.6 Consensus size: 100
30080354 ATTCATTGTG
* *
30080364 AGTCACGTGCGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGT
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGATAGGTCGCATGTGTAGT
* * * *
30080429 ACTAAGTGCAGGCTACTACGTGTACCATATTGATA
66 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTTA
* * * * * * * * * *
30080464 GGTCGCATGTGTAGTACTAAGTGTAGGCTACT--ATGCATACCCG-TTAACTTCGATCACGTGTG
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATG--TACCAGATTGA--TAGGTCGCATGTG
** *
30080526 TAGTACTAAGTATAGGCTACTACGTGTATCAGACGGTTA
62 TAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTA
*
30080565 AGTCACGTATGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGATAGGTCGCATGTGTAGT
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGATAGGTCGCATGTGTAGT
30080630 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTTA
66 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTTA
* *
30080665 AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGT
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGATAGGTCGCATGTGT
30080727 TAGAATTAAG
Statistics
Matches: 220, Mismatches: 36, Indels: 14
0.81 0.13 0.05
Matches are distributed among these distances:
98 2 0.01
99 3 0.01
100 136 0.62
101 73 0.33
102 3 0.01
103 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (100 bp):
AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGATAGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTACGTGTATCAGATGGTTA
Found at i:30081046 original size:5 final size:5
Alignment explanation
Indices: 30081036--30081063 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
30081026 ATATGTGTTC
30081036 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
30081064 TTTACAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:30087192 original size:14 final size:14
Alignment explanation
Indices: 30087170--30087201 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
30087160 AAGAAAGAGG
30087170 GGTACGAATGAAAT
1 GGTACGAATGAAAT
*
30087184 GGTAGGAATGAAAT
1 GGTACGAATGAAAT
30087198 GGTA
1 GGTA
30087202 TGAACAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.34, T:0.22
Consensus pattern (14 bp):
GGTACGAATGAAAT
Found at i:30091652 original size:16 final size:15
Alignment explanation
Indices: 30091611--30091654 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
30091601 CTTTTCACTC
30091611 TCTTTTGTTTTCTTTT
1 TCTTTTGTTTT-TTTT
* *
30091627 TCTTAT-TTTTTTCT
1 TCTTTTGTTTTTTTT
30091641 TCTTTTGTTTTTTT
1 TCTTTTGTTTTTTT
30091655 ACAATCTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 8 0.35
15 10 0.43
16 5 0.22
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.82
Consensus pattern (15 bp):
TCTTTTGTTTTTTTT
Found at i:30102916 original size:2 final size:2
Alignment explanation
Indices: 30102909--30102940 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30102899 AAGGAAAAAC
30102909 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
30102941 CCTAAGCAAA
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
Done.