Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 7 of 352
Found at i:2221779 original size:18 final size:18
Alignment explanation
Indices: 2221738--2221779 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2221728 CACTACCACT
*
2221738 ACCACCTCCATGTCCACC
1 ACCACCTCCATGTCCAAC
* *
2221756 AGCACCTCCATTTCCAAC
1 ACCACCTCCATGTCCAAC
2221774 ACCACC
1 ACCACC
2221780 ACCTTCTCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.52, G:0.05, T:0.17
Consensus pattern (18 bp):
ACCACCTCCATGTCCAAC
Found at i:2221797 original size:129 final size:126
Alignment explanation
Indices: 2221489--2221778 Score: 361
Period size: 129 Copynumber: 2.3 Consensus size: 126
2221479 CACCACCCTT
** * * * * * *
2221489 ACCTCCACCTCCACCACCTCCTCCATTTCCAGCTCCACTACCAGCTCCACCTCCTTCACCACCTC
1 ACCTCCATGTCCACCAGCACCTCCATATCCACCACCACTACCAGCTCCACCTCCTTCACCAACTC
*
2221554 CACTTCCATACCCAGAAGCTCCACCTGCACTACCTCCGCCACCACCATTACCACCACCTCCTCC
66 CACTTCCATACCCAGAAGCTCCACCTGCACTACCTCCGCCACCACC--TACCACCACCT-CACC
* * * **
2221618 TCCTCCATGTCCACCTGCTCCTCCATATCCGGCACCACTACCAGCTCCACCTCCTTCACCAACTC
1 ACCTCCATGTCCACCAGCACCTCCATATCCACCACCACTACCAGCTCCACCTCCTTCACCAACTC
* * *
2221683 CACTTCCATATCCAGAAGCTCCACCTGCACTACCTCCGCCTCCACC-ACTACCA-CT-ACC
66 CACTTCCATACCCAGAAGCTCCACCTGCACTACCTCCGCCACCACCTACCACCACCTCACC
* *
2221741 ACCTCCATGTCCACCAGCACCTCCATTTCCAACACCAC
1 ACCTCCATGTCCACCAGCACCTCCATATCCACCACCAC
2221779 CACCTTCTCC
Statistics
Matches: 142, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
123 34 0.24
125 2 0.01
126 6 0.04
129 100 0.70
ACGTcount: A:0.22, C:0.52, G:0.06, T:0.20
Consensus pattern (126 bp):
ACCTCCATGTCCACCAGCACCTCCATATCCACCACCACTACCAGCTCCACCTCCTTCACCAACTC
CACTTCCATACCCAGAAGCTCCACCTGCACTACCTCCGCCACCACCTACCACCACCTCACC
Found at i:2221813 original size:24 final size:22
Alignment explanation
Indices: 2221751--2221813 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 22
2221741 ACCTCCATGT
* *
2221751 CCACCAGCACCTCCATTTCCAA
1 CCACCACCACCTCCATATCCAA
*
2221773 -CACCACCACCT---TCTCCACTA
1 CCACCACCACCTCCATATCCA--A
2221793 CCACCACCACCTCCATATCCA
1 CCACCACCACCTCCATATCCA
2221814 GCACTAGCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
18 5 0.16
20 1 0.03
21 21 0.66
24 5 0.16
ACGTcount: A:0.27, C:0.54, G:0.02, T:0.17
Consensus pattern (22 bp):
CCACCACCACCTCCATATCCAA
Found at i:2221818 original size:27 final size:24
Alignment explanation
Indices: 2221788--2221857 Score: 59
Period size: 27 Copynumber: 2.8 Consensus size: 24
2221778 CCACCTTCTC
2221788 CACTACCACCACCACCTCCATATCCAG
1 CACTACCACCACCACCTCCA-A-CC-G
* * * *
2221815 CACTAGCACCTCCTCCTACAACCG
1 CACTACCACCACCACCTCCAACCG
**
2221839 CAGAACCACCACCACCTCC
1 CACTACCACCACCACCTCC
2221858 TGAACCGCCT
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
24 14 0.42
25 2 0.06
26 1 0.03
27 16 0.48
ACGTcount: A:0.29, C:0.53, G:0.06, T:0.13
Consensus pattern (24 bp):
CACTACCACCACCACCTCCAACCG
Found at i:2232044 original size:31 final size:31
Alignment explanation
Indices: 2232009--2232070 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2231999 TCTGACTACA
**
2232009 CTTGCTTAAAA-ATTACTCCCTTTGCCACATG
1 CTTGC-TAAAATATTACTCAATTTGCCACATG
2232040 CTTGCTAAAATATTACTCAATTTGCCACATG
1 CTTGCTAAAATATTACTCAATTTGCCACATG
2232071 TATCTATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (31 bp):
CTTGCTAAAATATTACTCAATTTGCCACATG
Found at i:2232706 original size:12 final size:12
Alignment explanation
Indices: 2232691--2232763 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
2232681 TATAAAAATA
2232691 TATATTATATAT
1 TATATTATATAT
2232703 TATATTA-AT-T
1 TATATTATATAT
2232713 TAATATT-TAAGTAT
1 T-ATATTAT-A-TAT
*
2232727 TA-A-TATATAA
1 TATATTATATAT
2232737 TATA-T-TATAT
1 TATATTATATAT
2232747 TATATTATATAT
1 TATATTATATAT
*
2232759 AATAT
1 TATAT
2232764 ATAAAACATA
Statistics
Matches: 49, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
10 14 0.29
11 12 0.24
12 19 0.39
13 2 0.04
14 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (12 bp):
TATATTATATAT
Found at i:2232758 original size:24 final size:24
Alignment explanation
Indices: 2232698--2232765 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
2232688 ATATATATTA
*
2232698 TATATTATATTA-ATTTAATAT-T
1 TATATTATATTATATATAATATAT
* *
2232720 TA-AGTAT-TAATATATAATATAT
1 TATATTATATTATATATAATATAT
2232742 TATATTATATTATATATAATATAT
1 TATATTATATTATATATAATATAT
2232766 AAAACATAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 2 0.05
21 12 0.32
22 5 0.14
23 4 0.11
24 14 0.38
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
TATATTATATTATATATAATATAT
Found at i:2232766 original size:7 final size:7
Alignment explanation
Indices: 2232687--2232767 Score: 60
Period size: 7 Copynumber: 11.3 Consensus size: 7
2232677 TTTATATAAA
2232687 AATATAT
1 AATATAT
*
2232694 ATTATAT
1 AATATAT
*
2232701 ATTATATT
1 AATATA-T
2232709 AAT-T-T
1 AATATAT
*
2232714 AATATTT
1 AATATAT
2232721 AAGTAT-T
1 AA-TATAT
2232728 AATATAT
1 AATATAT
2232735 AATATATT
1 AATATA-T
2232743 ATATTATAT
1 A-A-TATAT
*
2232752 TATATAT
1 AATATAT
2232759 AATATAT
1 AATATAT
2232766 AA
1 AA
2232768 AACATAAGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
5 4 0.06
6 4 0.06
7 39 0.63
8 9 0.15
9 2 0.03
10 4 0.06
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (7 bp):
AATATAT
Found at i:2233950 original size:22 final size:22
Alignment explanation
Indices: 2233910--2233977 Score: 93
Period size: 22 Copynumber: 3.0 Consensus size: 22
2233900 TGTACTATTA
*
2233910 TTAGCACGTTAAGTGCTCTCTGT
1 TTAGCAC-TTTAGTGCTCTCTGT
2233933 TTAGCACATTT-GTGCTCTCTGT
1 TTAGCAC-TTTAGTGCTCTCTGT
*
2233955 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACTTTAGTGCTCTCTGT
2233977 T
1 T
2233978 CGTTTGTGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.08
22 28 0.70
23 9 0.22
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (22 bp):
TTAGCACTTTAGTGCTCTCTGT
Found at i:2235727 original size:19 final size:18
Alignment explanation
Indices: 2235699--2235737 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
2235689 ATTTTTATTT
2235699 TAAAAAATTAAAATTAAA
1 TAAAAAATTAAAATTAAA
*
2235717 TAAAAATATTAAAATTTAA
1 TAAAAA-ATTAAAATTAAA
2235736 TA
1 TA
2235738 TGAAATTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAAATTAAAATTAAA
Found at i:2235752 original size:19 final size:19
Alignment explanation
Indices: 2235730--2235769 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2235720 AAATATTAAA
2235730 ATTTAATATGAAATTACTG
1 ATTTAATATGAAATTACTG
* *
2235749 ATTTAATATTAAATTATTG
1 ATTTAATATGAAATTACTG
2235768 AT
1 AT
2235770 AATAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (19 bp):
ATTTAATATGAAATTACTG
Found at i:2244724 original size:41 final size:41
Alignment explanation
Indices: 2244669--2244907 Score: 299
Period size: 41 Copynumber: 5.8 Consensus size: 41
2244659 GAATGTAATA
* *
2244669 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
2244710 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
2244751 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
2244792 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* * *
2244833 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAAT
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT--TT
* * **
2244874 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
2244908 ATCTGTTTAA
Statistics
Matches: 181, Mismatches: 10, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
39 3 0.02
40 8 0.04
41 168 0.93
42 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:2252355 original size:41 final size:41
Alignment explanation
Indices: 2252305--2252530 Score: 291
Period size: 41 Copynumber: 5.5 Consensus size: 41
2252295 GACGTTACGT
2252305 TAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTTTAAGTC
1 TAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTTTAAGTC
2252346 TAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAAGTC
1 TAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAAGTC
* *
2252387 TAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAAGTC
* *
2252428 TAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAAGTC
* * *
2252469 TAGCAGGC-TAAGTGCCGGTG-TAC-TGAATCAGGCTTTAAGCC
1 TAGCAGGCTTAA-TGCCGGTGATACAT--TTCAGACTTTAAGTC
**
2252510 TAGCAGGCAAAATGCCGGTGA
1 TAGCAGGCTTAATGCCGGTGA
2252531 ATCTGTTTAA
Statistics
Matches: 170, Mismatches: 8, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
39 3 0.02
40 8 0.05
41 157 0.92
42 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAAGTC
Found at i:2260346 original size:23 final size:23
Alignment explanation
Indices: 2260292--2260348 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
2260282 TTTTAAATAT
**
2260292 TTTTTAAAGTAATTATTTTATTTTA
1 TTTTT-AA-TAATTATTTTATTAAA
* *
2260317 GTATTAATAATTATTTTATTAAA
1 TTTTTAATAATTATTTTATTAAA
2260340 TTTTTAATA
1 TTTTTAATA
2260349 TAATTATCTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 21 0.81
24 2 0.08
25 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTAATAATTATTTTATTAAA
Found at i:2262647 original size:13 final size:13
Alignment explanation
Indices: 2262631--2262655 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2262621 AAAGAACAAA
2262631 TATAATAAAATTT
1 TATAATAAAATTT
2262644 TATAATAAAATT
1 TATAATAAAATT
2262656 AATGTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATAATAAAATTT
Found at i:2274813 original size:18 final size:17
Alignment explanation
Indices: 2274779--2274817 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2274769 CTTTACTAAC
2274779 TAAAAATTATAAAAATA
1 TAAAAATTATAAAAATA
2274796 TAAAAA-TATAATATAATA
1 TAAAAATTATAA-A-AATA
2274814 TAAA
1 TAAA
2274818 TTAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 7 0.35
18 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAATTATAAAAATA
Found at i:2274815 original size:10 final size:8
Alignment explanation
Indices: 2274779--2274817 Score: 51
Period size: 8 Copynumber: 4.5 Consensus size: 8
2274769 CTTTACTAAC
2274779 TAAAAATTA
1 TAAAAA-TA
2274788 TAAAAATA
1 TAAAAATA
2274796 TAAAAATA
1 TAAAAATA
2274804 TAATATAATA
1 TAA-A-AATA
2274814 TAAA
1 TAAA
2274818 TTAATTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 13 0.46
9 8 0.29
10 7 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
TAAAAATA
Found at i:2275044 original size:23 final size:24
Alignment explanation
Indices: 2275008--2275055 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2274998 ATAAATAATT
* *
2275008 TAAAATTTATAAAATATTTAAAAA
1 TAAAATTTAAAAAATATATAAAAA
2275032 TAAAA-TTAAAAAATATATAAAAA
1 TAAAATTTAAAAAATATATAAAAA
2275055 T
1 T
2275056 TTAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAAATTTAAAAAATATATAAAAA
Found at i:2275074 original size:23 final size:23
Alignment explanation
Indices: 2275009--2275075 Score: 56
Period size: 23 Copynumber: 3.1 Consensus size: 23
2274999 TAAATAATTT
*
2275009 AAAATTTATAAAAT-ATT-TAAAA
1 AAAATTTA-AAAATAATTATAATA
*
2275031 ATAAAATT-AAAA-AA-TAT-ATA
1 A-AAATTTAAAAATAATTATAATA
2275051 AAAATTTAAAAATAATTATAATA
1 AAAATTTAAAAATAATTATAATA
2275074 AA
1 AA
2275076 GTATACGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 13
0.69 0.06 0.25
Matches are distributed among these distances:
19 5 0.14
20 8 0.23
21 8 0.23
22 4 0.11
23 10 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATTTAAAAATAATTATAATA
Found at i:2277214 original size:97 final size:93
Alignment explanation
Indices: 2277096--2277274 Score: 270
Period size: 97 Copynumber: 1.9 Consensus size: 93
2277086 CTTGTTTTTC
2277096 TTTATTTTCCATTCTACTCTACTTCTCTCTCTGTTTTCCCCTATTTTCCATTTCTTTTAATACAG
1 TTTATTTTCCATTCTACTCTACTTCTCTCTCTG--TTCCCC-ATTTTCCATTTCTTTTAATACAG
*
2277161 TTTTTTTTATGTTTTCCATTTATTAAAATTAG
63 -TTTTTCTATGTTTTCCATTTATTAAAATTAG
* * *
2277193 TTTATTTTCCATTC-CCTTCTACTTCTCTCTCTGTTCTCCATTTTCCATTTCTTTTAATTCAGTT
1 TTTATTTTCCATTCTAC-TCTACTTCTCTCTCTGTTCCCCATTTTCCATTTCTTTTAATACAGTT
2277257 TTTCTATGTTTTCCATTT
65 TTTCTATGTTTTCCATTT
2277275 GTTAGGGAGA
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
93 19 0.25
94 22 0.29
95 5 0.06
96 1 0.01
97 30 0.39
ACGTcount: A:0.16, C:0.23, G:0.04, T:0.58
Consensus pattern (93 bp):
TTTATTTTCCATTCTACTCTACTTCTCTCTCTGTTCCCCATTTTCCATTTCTTTTAATACAGTTT
TTCTATGTTTTCCATTTATTAAAATTAG
Found at i:2278761 original size:17 final size:19
Alignment explanation
Indices: 2278725--2278761 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
2278715 AATACATCTC
*
2278725 AAAAATGAATTTACAGAAG
1 AAAAATGAAATTACAGAAG
2278744 AAAAA-GAAATTA-AGAAG
1 AAAAATGAAATTACAGAAG
2278761 A
1 A
2278762 GAGCTAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.65, C:0.03, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAAATGAAATTACAGAAG
Found at i:2280149 original size:29 final size:27
Alignment explanation
Indices: 2280102--2280170 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 27
2280092 CGTATTATTT
*
2280102 TTTAAAAAAATTATTATATAAAATAAA
1 TTTAAAAAAATTAATATATAAAATAAA
* *
2280129 TTTAAAAAATATATAATATATCAAATATA
1 TTTAAAAAA-AT-TAATATATAAAATAAA
*
2280158 -TTAAAAATATTAA
1 TTTAAAAAAATTAA
2280171 AATAAATGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 3 0.08
27 11 0.31
28 9 0.25
29 13 0.36
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
TTTAAAAAAATTAATATATAAAATAAA
Found at i:2289638 original size:3 final size:3
Alignment explanation
Indices: 2289630--2289655 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2289620 ATTCTCCTCT
2289630 TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TG
2289656 TTCCTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.35, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:2296643 original size:18 final size:18
Alignment explanation
Indices: 2296602--2296643 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2296592 AACTGATAAT
*
2296602 AATTAATTCGAATAATTA
1 AATTAATTAGAATAATTA
**
2296620 TCTTAATTAGAATAATTA
1 AATTAATTAGAATAATTA
2296638 AATTAA
1 AATTAA
2296644 CAAAAAAATA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (18 bp):
AATTAATTAGAATAATTA
Found at i:2302500 original size:20 final size:20
Alignment explanation
Indices: 2302450--2302515 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
2302440 AAAATTATTT
*
2302450 AAATTTTTTTAT-AATTTTAA
1 AAATTTTTATATAAATTTT-A
** *
2302470 AAAAATATATATAAATTTTA
1 AAATTTTTATATAAATTTTA
*
2302490 AAATTTTTATA-AATATTTTG
1 AAATTTTTATATAA-ATTTTA
2302510 AAATTT
1 AAATTT
2302516 AAAAATTATT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.06
20 28 0.78
21 6 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AAATTTTTATATAAATTTTA
Found at i:2307107 original size:41 final size:40
Alignment explanation
Indices: 2307062--2307167 Score: 119
Period size: 39 Copynumber: 2.6 Consensus size: 40
2307052 AAAAAGGTTT
2307062 TTAGCGGCGTTTTGAATAAAAACGCCACTAAAGAGT-GAGCA
1 TTAGCGGCGTTTT-AATAAAAACGCCACTAAAGA-TCGAGCA
* * *
2307103 TTAGCGGCGTTTCT-A-AAAAACGCCGCTAAAGATCGATCT
1 TTAGCGGCGTTT-TAATAAAAACGCCACTAAAGATCGAGCA
*
2307142 TTAGCGGCGTTTTTAATAAAAGCGCC
1 TTAGCGGCG-TTTTAATAAAAACGCC
2307168 GCTATAGGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
38 1 0.02
39 29 0.52
40 5 0.09
41 20 0.36
42 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (40 bp):
TTAGCGGCGTTTTAATAAAAACGCCACTAAAGATCGAGCA
Found at i:2307186 original size:41 final size:39
Alignment explanation
Indices: 2307061--2307191 Score: 99
Period size: 41 Copynumber: 3.3 Consensus size: 39
2307051 AAAAAAGGTT
* * *
2307061 TTTAGCGGCGTTTTGAATAAAAACGCCACTAAAGAGTGAGCA
1 TTTAGCGGCGTTTTTAAT-AAAACGCCGCT-AAG-GTCAGCA
* * *
2307103 -TTAGCGGCGTTTCTAA-AAAACGCCGCTAAAGATCGATC-
1 TTTAGCGGCGTTTTTAATAAAACGCCGCT-AAGGTC-AGCA
2307141 TTTAGCGGCGTTTTTAATAAAAGCGCCGCTATAGGTTCA-CA
1 TTTAGCGGCGTTTTTAATAAAA-CGCCGCTA-AGG-TCAGCA
*
2307182 TTTAGTGGCG
1 TTTAGCGGCG
2307192 CTTCAAGAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 15
0.75 0.09 0.15
Matches are distributed among these distances:
38 1 0.01
39 31 0.42
40 6 0.08
41 33 0.45
42 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (39 bp):
TTTAGCGGCGTTTTTAATAAAACGCCGCTAAGGTCAGCA
Found at i:2307925 original size:21 final size:22
Alignment explanation
Indices: 2307899--2307939 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2307889 GGTACTTTAC
*
2307899 GGTTTAGGGTATATG-GTTAAG
1 GGTTTAAGGTATATGAGTTAAG
*
2307920 GGTTTAAGGTTTATGAGTTA
1 GGTTTAAGGTATATGAGTTA
2307940 TTATTTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.41
Consensus pattern (22 bp):
GGTTTAAGGTATATGAGTTAAG
Found at i:2308370 original size:14 final size:13
Alignment explanation
Indices: 2308324--2308375 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
2308314 AGGGTTTAGA
*
2308324 GTTTATGTGTAAG
1 GTTTATGTTTAAG
*
2308337 GTTTATGGTTTTAG
1 GTTTAT-GTTTAAG
2308351 GTTTTAGTGTTTAAG
1 G-TTTA-TGTTTAAG
2308366 GTTTAATGTT
1 GTTT-ATGTT
2308376 AATAAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 6 0.19
14 13 0.41
15 12 0.38
16 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (13 bp):
GTTTATGTTTAAG
Found at i:2308602 original size:13 final size:14
Alignment explanation
Indices: 2308578--2308612 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
2308568 GAAAAAAATG
2308578 AAATTATTTAGATT
1 AAATTATTTAGATT
2308592 AAATT-TTTAGATT
1 AAATTATTTAGATT
2308605 AAATTATT
1 AAATTATT
2308613 GAAGAGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (14 bp):
AAATTATTTAGATT
Found at i:2312408 original size:13 final size:14
Alignment explanation
Indices: 2312392--2312420 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2312382 TTCTAAATAT
2312392 TTATAATT-TTTAA
1 TTATAATTGTTTAA
2312405 TTATAATTGTTTAA
1 TTATAATTGTTTAA
2312419 TT
1 TT
2312421 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:2312854 original size:15 final size:16
Alignment explanation
Indices: 2312829--2312859 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2312819 GCAACAACTT
2312829 AGAGTGGAGGCAGCAG
1 AGAGTGGAGGCAGCAG
2312845 AGAG-GGAGGCAGCAG
1 AGAGTGGAGGCAGCAG
2312860 CAGCAGCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.13, G:0.52, T:0.03
Consensus pattern (16 bp):
AGAGTGGAGGCAGCAG
Found at i:2312929 original size:42 final size:42
Alignment explanation
Indices: 2312835--2312931 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
2312825 ACTTAGAGTG
* *
2312835 GAGGCAGCAGAGAGGGAGGCAGCAGCAGCAGCAAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCAGAAGCAGCAGCAAGGGAGGCA
* *
2312877 GCGGCAGCAGCGAGGGAGGCAGAAGCA-CGAGCGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCAGAAGCAGC-AGCAAGGGAGGCA
2312919 GAGGCAGCAGCGA
1 GAGGCAGCAGCGA
2312932 TGGCAGCAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 1 0.02
42 48 0.98
ACGTcount: A:0.31, C:0.21, G:0.48, T:0.00
Consensus pattern (42 bp):
GAGGCAGCAGCGAGGGAGGCAGAAGCAGCAGCAAGGGAGGCA
Found at i:2312941 original size:42 final size:40
Alignment explanation
Indices: 2312835--2312948 Score: 131
Period size: 42 Copynumber: 2.8 Consensus size: 40
2312825 ACTTAGAGTG
* * *
2312835 GAGGCAGCAGAGAGGGAGGCAGCAGCAGCAGCAAGGGAGGCA
1 GAGGCAGCAGCGAGGCAGGCAG-AGCAG-AGCGAGGGAGGCA
* *
2312877 GCGGCAGCAGCGAGGGAGGCAGAAGCACGAGCGAGGGAGGCA
1 GAGGCAGCAGCGAGGCAGGCAG-AGCA-GAGCGAGGGAGGCA
2312919 GAGGCAGCAGCGATGGCA-GCAGAGCAGAGC
1 GAGGCAGCAGCGA-GGCAGGCAGAGCAGAGC
2312949 AAAAAGTACG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
40 4 0.06
41 4 0.06
42 52 0.81
43 4 0.06
ACGTcount: A:0.31, C:0.21, G:0.47, T:0.01
Consensus pattern (40 bp):
GAGGCAGCAGCGAGGCAGGCAGAGCAGAGCGAGGGAGGCA
Found at i:2312942 original size:21 final size:21
Alignment explanation
Indices: 2312835--2312931 Score: 126
Period size: 21 Copynumber: 4.6 Consensus size: 21
2312825 ACTTAGAGTG
*
2312835 GAGGCAGCAGAGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCA
*
2312856 GCA-GCAGCAGCAAGGGAGGCA
1 G-AGGCAGCAGCGAGGGAGGCA
*
2312877 GCGGCAGCAGCGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCA
*
2312898 GAAGCA-CGAGCGAGGGAGGCA
1 GAGGCAGC-AGCGAGGGAGGCA
2312919 GAGGCAGCAGCGA
1 GAGGCAGCAGCGA
2312932 TGGCAGCAGA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 62 0.95
22 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.48, T:0.00
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGGAGGCA
Found at i:2313356 original size:43 final size:44
Alignment explanation
Indices: 2313294--2313400 Score: 148
Period size: 43 Copynumber: 2.5 Consensus size: 44
2313284 CAAATCTGCT
2313294 ATGGCTTTTAGCGGCGCTTTTCCC-ACAAACGCCACTAAAAG-C
1 ATGGCTTTTAGCGGCGCTTTTCCCAACAAACGCCACTAAAAGCC
* *
2313336 AGTGGCTTTTAGCGGCGC-TTTCCCAATAAACGCCGCTAAAAGCC
1 A-TGGCTTTTAGCGGCGCTTTTCCCAACAAACGCCACTAAAAGCC
* *
2313380 ATGACTTTCAGCGGCGCTTTT
1 ATGGCTTTTAGCGGCGCTTTT
2313401 TTAAATAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
42 7 0.12
43 45 0.79
44 5 0.09
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.26
Consensus pattern (44 bp):
ATGGCTTTTAGCGGCGCTTTTCCCAACAAACGCCACTAAAAGCC
Found at i:2315117 original size:23 final size:23
Alignment explanation
Indices: 2315085--2315128 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2315075 ACTACCGTTT
2315085 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
2315108 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
2315129 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:2315121 original size:13 final size:11
Alignment explanation
Indices: 2315089--2315131 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2315079 CCGTTTTCTA
*
2315089 AATAAAATAAT
1 AATAAAATATT
2315100 AAT-AAATATCT
1 AATAAAATAT-T
2315111 AAGTAAAATATT
1 AA-TAAAATATT
2315123 AATAAAATA
1 AATAAAATA
2315132 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:2317786 original size:22 final size:24
Alignment explanation
Indices: 2317732--2317786 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
2317722 TATATAACTG
2317732 ATAATAT-TA-AAATATATACATA
1 ATAATATATATAAATATATACATA
* *
2317754 ATATTATATATAAAT-TATTCAT-
1 ATAATATATATAAATATATACATA
2317776 ATAATATATAT
1 ATAATATATAT
2317787 TTAAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.57
23 8 0.29
24 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATATATATAAATATATACATA
Found at i:2317968 original size:3 final size:3
Alignment explanation
Indices: 2317960--2317989 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2317950 ACAAGGATAT
2317960 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2317990 TTGAAACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2318105 original size:9 final size:9
Alignment explanation
Indices: 2318092--2318146 Score: 76
Period size: 9 Copynumber: 6.0 Consensus size: 9
2318082 TAATGGACAA
2318092 TAATAACTA-
1 TAATAA-TAT
2318101 TAATAATAT
1 TAATAATAT
*
2318110 TAATAATAA
1 TAATAATAT
2318119 TAATAAATAT
1 TAAT-AATAT
2318129 TAATAATAT
1 TAATAATAT
2318138 TAATAATAT
1 TAATAATAT
2318147 GAAAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
8 2 0.05
9 32 0.76
10 8 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (9 bp):
TAATAATAT
Found at i:2318106 original size:3 final size:3
Alignment explanation
Indices: 2318090--2318145 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
2318080 ACTAATGGAC
* *
2318090 AAT AAT AACT -AT AAT AAT ATT AAT AAT AAT AAT AAAT ATT AAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
*
2318136 ATT AAT AAT A
1 AAT AAT AAT A
2318146 TGAAAATAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 1 0.02
3 39 0.89
4 4 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:2319036 original size:35 final size:35
Alignment explanation
Indices: 2318990--2319058 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
2318980 GGGTGTGTGA
2318990 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
2319025 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
2319059 AGAGGCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.51, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:2319828 original size:76 final size:74
Alignment explanation
Indices: 2319660--2320157 Score: 576
Period size: 74 Copynumber: 6.7 Consensus size: 74
2319650 CTCAACTCAT
* * *
2319660 TCAGCGTGTCCTGAGGCTCAATTCACCTCTCGCAATATGAGTTGA--TTTTTGAAACATACAAAA
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-AT---AGA
*
2319723 AATTGACAA-TACC
62 AATT-AAAATTACC
* ** ** * * * * *
2319736 TAAGTATGTCTTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGACAACACAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
*
2319801 GAAATTACC
66 AAAATTACC
**
2319810 TCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAATAGAAA
1 TCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAA
2319873 TTGAAAA-TACC
64 TT-AAAATTACC
* ** * * * *
2319884 TCAACGTGTCTTGAGGCTCAATTAATCTCTCGCAATATGAGTTGATTTTTTTAAAAAAATAGAAA
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT--GAAAATAGAAA
2319949 TTAAAATTACC
64 TTAAAATTACC
* *
2319960 TCAGCGTGTCCCGAGGCTCAATTCATCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
2320025 AAAATTACC
66 AAAATTACC
*
2320034 TCATCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
2320099 AAAATTACC
66 AAAATTACC
* ** * *
2320108 TCAGCGTGTCCCGAGGCTCAACCCATTTCTCGCAATATAAGTTGAATTTT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
2320158 GAAAACGGAA
Statistics
Matches: 363, Mismatches: 48, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
72 33 0.09
73 2 0.01
74 177 0.49
75 7 0.02
76 135 0.37
77 1 0.00
78 8 0.02
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (74 bp):
TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
AAAATTACC
Found at i:2319974 original size:148 final size:146
Alignment explanation
Indices: 2319660--2320162 Score: 634
Period size: 148 Copynumber: 3.4 Consensus size: 146
2319650 CTCAACTCAT
* * *
2319660 TCAGCGTGTCCTGAGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTTGAAACATACAAAAAA
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA-AT---AGAAA
* * *
2319725 TTGACAATACCT-AA-GTATGTCTTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTT
62 TTGAAAATACCTCAACG--TGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
* * * *
2319788 GACAACACAAATTGAAATTACC
125 GAAAATAGAAATTAAAATTACC
**
2319810 TCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAGAAATT
1 TCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAGAAATT
* * * *
2319875 GAAAATACCTCAACGTGTCTTGAGGCTCAATTAATCTCTCGCAATATGAGTTGATTTTTTTAAAA
64 GAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT--GA
2319940 AAATAGAAATTAAAATTACC
127 AAATAGAAATTAAAATTACC
* *
2319960 TCAGCGTGTCCCGAGGCTCAATTCATCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAATAGAAATT
* **
2320025 -AAAATTACCTCATCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
64 GAAAA-TACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
2320089 AATAGAAATTAAAATTACC
128 AATAGAAATTAAAATTACC
* ** * *
2320108 TCAGCGTGTCCCGAGGCTCAACCCATTTCTCGCAATATAAGTTGAATTTTGAAAA
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
2320163 CGGAAGTAAC
Statistics
Matches: 312, Mismatches: 32, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
146 9 0.03
148 154 0.49
149 6 0.02
150 96 0.31
151 2 0.01
152 45 0.14
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (146 bp):
TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAGAAATTGA
AAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAT
AGAAATTAAAATTACC
Found at i:2320087 original size:224 final size:223
Alignment explanation
Indices: 2319664--2320161 Score: 630
Period size: 224 Copynumber: 2.2 Consensus size: 223
2319654 ACTCATTCAG
*
2319664 CGTGTCCTGAGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTTGAAACATACAAAAAATTGA
1 CGTGTCCTGAGGCTCAATTCATCTCTCGCAATATGAGTTGATTTTTGAAACATACAAAAAATTGA
* * ** * *
2319729 CAATACCTAAGTATGTCTTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGACAAC
66 AAATACCTAAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAAAAC
*
2319794 ACAAATTGAAATTACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
131 ACAAATTAAAATTACCTCAGCA-GTGAACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
2319859 TTTGAAAATAGAAATTGAAAA-TACCTCAA
195 TTTGAAAATAGAAATT-AAAATTACCTCAA
* * *
2319888 CGTGTCTTGAGGCTCAATTAATCTCTCGCAATATGAGTTGATTTTTTTAAA-A-A-AATAGAAAT
1 CGTGTCCTGAGGCTCAATTCATCTCTCGCAATATGAGTTGA-TTTTTGAAACATACAA-A-AAAT
* * * * *
2319950 T-AAAATTACCTCAGCGTGTCCCGAGGCTCAATTCATCTCTCGCAATATGAGTTGATTTTTTTGA
63 TGAAAA-TACCTAAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGA
* * * **
2320014 AAATAGAAATTAAAATTACCTCATC-GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
127 AAACACAAATTAAAATTACCTCAGCAGTGAACCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
2320078 ATTTTTTTGAAAATAGAAATTAAAATTACCTCAG
192 A--TTTTTGAAAATAGAAATTAAAATTACCTCAA
* ** * * *
2320112 CGTGTCCCGAGGCTCAACCCATTTCTCGCAATATAAGTTGAATTTTGAAA
1 CGTGTCCTGAGGCTCAATTCATCTCTCGCAATATGAGTTGATTTTTGAAA
2320162 ACGGAAGTAA
Statistics
Matches: 236, Mismatches: 31, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
222 40 0.17
223 16 0.07
224 172 0.73
225 8 0.03
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (223 bp):
CGTGTCCTGAGGCTCAATTCATCTCTCGCAATATGAGTTGATTTTTGAAACATACAAAAAATTGA
AAATACCTAAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAAAAC
ACAAATTAAAATTACCTCAGCAGTGAACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TTGAAAATAGAAATTAAAATTACCTCAA
Found at i:2332702 original size:22 final size:24
Alignment explanation
Indices: 2332648--2332702 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
2332638 TATATAACTG
2332648 ATAATAT-TA-AAATATATACATA
1 ATAATATATATAAATATATACATA
* *
2332670 ATATTATATATAAAT-TATTCAT-
1 ATAATATATATAAATATATACATA
2332692 ATAATATATAT
1 ATAATATATAT
2332703 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.57
23 8 0.29
24 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATATATATAAATATATACATA
Found at i:2333927 original size:35 final size:35
Alignment explanation
Indices: 2333881--2333949 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
2333871 GGGTGTGTGA
*
2333881 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGAAGAGTGGGAG
2333916 TGGTGCTGGTGGCAGACAGCATGGAAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGAAGAGTGGGA
2333950 AGAGGCAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.22, C:0.12, G:0.49, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGAAGAGTGGGAG
Found at i:2335734 original size:38 final size:38
Alignment explanation
Indices: 2335638--2335787 Score: 165
Period size: 38 Copynumber: 3.9 Consensus size: 38
2335628 CGAGGTATAA
* * * *
2335638 AACCCGAACATAACACCAGCACGAAGCCTACGGGACTTT
1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGA-TTT
*** * *
2335677 AAACTTAGATATAATACCAGCACTAGGCCTGCGGGATTT
1 -AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
2335716 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
* * **
2335754 AACCCGGATATAATTCTAGCATAAAGCCTGCGGG
1 AACCCGGATATAATACCAGCACGAAGCCTGCGGG
2335788 TCTCTAAGCC
Statistics
Matches: 92, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
38 63 0.68
39 3 0.03
40 26 0.28
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (38 bp):
AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
Found at i:2335803 original size:78 final size:78
Alignment explanation
Indices: 2335638--2335787 Score: 180
Period size: 78 Copynumber: 1.9 Consensus size: 78
2335628 CGAGGTATAA
* * ** *
2335638 AACCCGAACATAACACCAGCACGAAGCCTACGGGACTTTAAACTTAGATATAATACCAGCACTAG
1 AACCCGGATATAACACCAGCACGAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACTAA
2335703 GCCTGCGGGATTT
66 GCCTGCGGGATTT
* * * * *
2335716 AACCCGGATATAATACCAGCACGAAGCCTGCGGGA-TTT-AACCCGGATATAATTCTAGCA-TAA
1 AACCCGGATATAACACCAGCACGAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACT-A
2335778 AGCCTGCGGG
65 AGCCTGCGGG
2335788 TCTCTAAGCC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
75 1 0.02
76 26 0.43
77 3 0.05
78 31 0.51
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (78 bp):
AACCCGGATATAACACCAGCACGAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACTAA
GCCTGCGGGATTT
Found at i:2351984 original size:39 final size:40
Alignment explanation
Indices: 2351936--2352033 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
2351926 GCTCTGATGA
*
2351936 GCTTCAGTTAGCC-TTCGGGCTTCCGTTTAGTACTTATGT
1 GCTTCAGTTAGCCTTTCGGGCTTCCGTTTAGCACTTATGT
* * *
2351975 GGTTCAGTTAGCCTTTGGGGCTTCCGTTTAGCACTTTTGT
1 GCTTCAGTTAGCCTTTCGGGCTTCCGTTTAGCACTTATGT
*
2352015 GCTTCAGTTAG-ATTTCGGG
1 GCTTCAGTTAGCCTTTCGGG
2352034 TATTAGATCA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 18 0.35
40 33 0.65
ACGTcount: A:0.12, C:0.20, G:0.27, T:0.41
Consensus pattern (40 bp):
GCTTCAGTTAGCCTTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:2352018 original size:21 final size:21
Alignment explanation
Indices: 2351954--2352019 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2351944 TAGCCTTCGG
* *
2351954 GCTTCCGTTTAGTACTTATGT
1 GCTTCCGTTTAGCACTTTTGT
* * * *
2351975 GGTTCAG-TTAGC-CTTTGGG
1 GCTTCCGTTTAGCACTTTTGT
2351994 GCTTCCGTTTAGCACTTTTGT
1 GCTTCCGTTTAGCACTTTTGT
2352015 GCTTC
1 GCTTC
2352020 AGTTAGATTT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
19 9 0.27
20 9 0.27
21 15 0.45
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.44
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTTTGT
Found at i:2365170 original size:19 final size:19
Alignment explanation
Indices: 2365146--2365183 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2365136 TTATTAATAA
2365146 ATTTA-TATTTTAATCAATT
1 ATTTATTATTTTAAT-AATT
2365165 ATTTATTATTTTAATAATT
1 ATTTATTATTTTAATAATT
2365184 TTAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTATTATTTTAATAATT
Found at i:2365447 original size:22 final size:23
Alignment explanation
Indices: 2365395--2365447 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
2365385 TTTCATTTAG
*
2365395 ATATTTT-ATAATTTATAAAATT
1 ATATTTTAATAATTAATAAAATT
* **
2365417 TTAAATTAATAA-TAATAAAATT
1 ATATTTTAATAATTAATAAAATT
2365439 ATATTTTAA
1 ATATTTTAA
2365448 CCTCAAAATA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTTTAATAATTAATAAAATT
Found at i:2366172 original size:6 final size:6
Alignment explanation
Indices: 2366161--2366187 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2366151 ATAATTTAAT
2366161 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
2366188 ACATATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:2366230 original size:18 final size:18
Alignment explanation
Indices: 2366207--2366248 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
2366197 TTTATACAAA
2366207 TAATTC-AGTTAATTTGAG-
1 TAATTCAAG-TAATTT-AGT
2366225 TAATTCAAGTAATTTAGT
1 TAATTCAAGTAATTTAGT
2366243 TAATTC
1 TAATTC
2366249 GACTAATTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.09
18 18 0.82
19 2 0.09
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (18 bp):
TAATTCAAGTAATTTAGT
Found at i:2369716 original size:18 final size:15
Alignment explanation
Indices: 2369682--2369714 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2369672 TTTAATCCTT
2369682 TAAAAATTATAAAAA
1 TAAAAATTATAAAAA
*
2369697 TAAAAATTATTAAAA
1 TAAAAATTATAAAAA
2369712 TAA
1 TAA
2369715 TATAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAATTATAAAAA
Found at i:2371548 original size:27 final size:27
Alignment explanation
Indices: 2371513--2371565 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
2371503 ATACCTATAA
2371513 GGTTTTGTTGAGCAGCAAATAATCAAG
1 GGTTTTGTTGAGCAGCAAATAATCAAG
2371540 GGTTTTGTTGAGCAGCAAATAATCAA
1 GGTTTTGTTGAGCAGCAAATAATCAA
2371566 TCAACAACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (27 bp):
GGTTTTGTTGAGCAGCAAATAATCAAG
Found at i:2373655 original size:13 final size:13
Alignment explanation
Indices: 2373637--2373663 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2373627 GAGAACATGA
2373637 AGGCGAGTTCAAC
1 AGGCGAGTTCAAC
2373650 AGGCGAGTTCAAC
1 AGGCGAGTTCAAC
2373663 A
1 A
2373664 TGCATTGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.30, T:0.15
Consensus pattern (13 bp):
AGGCGAGTTCAAC
Found at i:2374438 original size:58 final size:59
Alignment explanation
Indices: 2374348--2374468 Score: 165
Period size: 58 Copynumber: 2.1 Consensus size: 59
2374338 AATATAACAT
*
2374348 TTTGTACCTGAACTTAACACCTTTTTCTAATTTGGTACGTAAAATTTTTTTAGCTT-AA
1 TTTGTACCTGAACTTAACACCTTTTTCTAATTTGGTACCTAAAATTTTTTTAGCTTCAA
* * * * *
2374406 TTTGTACTTGAATTTGACA-CTTTTTACTAATTTGGTACCTAAACTTTTTTTAGGTTCAA
1 TTTGTACCTGAACTTAACACCTTTTT-CTAATTTGGTACCTAAAATTTTTTTAGCTTCAA
2374465 TTTG
1 TTTG
2374469 ATTCTTAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 6 0.11
58 43 0.78
59 6 0.11
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.49
Consensus pattern (59 bp):
TTTGTACCTGAACTTAACACCTTTTTCTAATTTGGTACCTAAAATTTTTTTAGCTTCAA
Found at i:2382707 original size:16 final size:17
Alignment explanation
Indices: 2382675--2382707 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2382665 TTTATACGTA
*
2382675 TATATCAATCGTTTCAT
1 TATATCAATCATTTCAT
2382692 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
2382708 GTTTCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:2383312 original size:46 final size:46
Alignment explanation
Indices: 2382993--2383307 Score: 407
Period size: 46 Copynumber: 6.8 Consensus size: 46
2382983 TTTGACATGA
* * * *
2382993 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCACGT
* *
2383039 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
* **
2383085 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
* **
2383131 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
* * * *
2383177 TGCCATGGTATCTTTCAACCACGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
* * * *
2383223 TGCCATGGTATCTTTCAACCACGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
** *
2383269 TGCCATAATATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
2383308 ATCAGATGGC
Statistics
Matches: 249, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 4 0.02
46 245 0.98
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
Found at i:2396671 original size:11 final size:11
Alignment explanation
Indices: 2396638--2396690 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
2396628 TATGTTACTA
2396638 TTTT-TTATTG
1 TTTTGTTATTG
* *
2396648 TTTTGTCAGTG
1 TTTTGTTATTG
*
2396659 TTTTTTTATTG
1 TTTTGTTATTG
*
2396670 TTTTGTTATTA
1 TTTTGTTATTG
*
2396681 TTTCGTTATT
1 TTTTGTTATT
2396691 ATATTGCTAC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
10 4 0.12
11 30 0.88
ACGTcount: A:0.11, C:0.04, G:0.13, T:0.72
Consensus pattern (11 bp):
TTTTGTTATTG
Found at i:2396834 original size:26 final size:25
Alignment explanation
Indices: 2396805--2396859 Score: 92
Period size: 26 Copynumber: 2.2 Consensus size: 25
2396795 TTTTAGTGTT
*
2396805 TTTTAAATATATATTTTTTTAAAAAA
1 TTTTAAATATATATATTTTT-AAAAA
2396831 TTTTAAATATATATATTTTTAAAAA
1 TTTTAAATATATATATTTTTAAAAA
2396856 TTTT
1 TTTT
2396860 CATTTATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTAAATATATATATTTTTAAAAA
Found at i:2398301 original size:39 final size:39
Alignment explanation
Indices: 2398240--2398350 Score: 177
Period size: 39 Copynumber: 2.8 Consensus size: 39
2398230 TCATGATCTA
* *
2398240 AAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACAG
1 AAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACAG
* * *
2398279 AAGCCCGGAGGCTAACTAAAGCACATAAGTGCTAAACGG
1 AAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACAG
2398318 AAGCCCGAAGGCTAACTGAAGCACATAAGTGCT
1 AAGCCCGAAGGCTAACTGAAGCACATAAGTGCT
2398351 GAACTGAAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.14
Consensus pattern (39 bp):
AAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACAG
Found at i:2408433 original size:39 final size:39
Alignment explanation
Indices: 2408379--2408456 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
2408369 CTTTAATCAC
2408379 CCCAGATGATTTAAACTCGAAACACAGAAAAAAAATTAA
1 CCCAGATGATTTAAACTCGAAACACAGAAAAAAAATTAA
2408418 CCCAGATGATTTAAACTCGAAACACAGAAAAAAAATTAA
1 CCCAGATGATTTAAACTCGAAACACAGAAAAAAAATTAA
2408457 AGGAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.54, C:0.18, G:0.10, T:0.18
Consensus pattern (39 bp):
CCCAGATGATTTAAACTCGAAACACAGAAAAAAAATTAA
Found at i:2417852 original size:30 final size:31
Alignment explanation
Indices: 2417803--2417866 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
2417793 AGTTTAAATT
*
2417803 ATTTTATAAAATTCTAAAAT-ATATAATAATAA
1 ATTTTATAAAAGTCTAAAATAATAT-ATAA-AA
2417835 ATTTTA-AAAAGTC-AAAATAATATATAAAA
1 ATTTTATAAAAGTCTAAAATAATATATAAAA
2417864 ATT
1 ATT
2417867 GAAAATTGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.17
30 9 0.30
31 10 0.33
32 6 0.20
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (31 bp):
ATTTTATAAAAGTCTAAAATAATATATAAAA
Found at i:2418120 original size:12 final size:12
Alignment explanation
Indices: 2418089--2418126 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
2418079 TATTTCTAGA
2418089 TTATATATTTA-
1 TTATATATTTAT
2418100 TTATATATTTAT
1 TTATATATTTAT
*
2418112 TTCTATATTTTAT
1 TTATATA-TTTAT
2418125 TT
1 TT
2418127 TTTTAACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 11 0.46
12 6 0.25
13 7 0.29
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATATATTTAT
Found at i:2422482 original size:14 final size:14
Alignment explanation
Indices: 2422463--2422494 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2422453 CTCAATCACC
2422463 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
2422477 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
2422491 GGGC
1 GGGC
2422495 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:2427603 original size:14 final size:14
Alignment explanation
Indices: 2427584--2427615 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2427574 TCAAATCACC
2427584 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
2427598 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
2427612 GGGC
1 GGGC
2427616 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:2432464 original size:14 final size:14
Alignment explanation
Indices: 2432441--2432474 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2432431 GAAAAAATCG
2432441 AAAAAA-TAAAGAT
1 AAAAAATTAAAGAT
2432454 AAAAAATTAAAGAT
1 AAAAAATTAAAGAT
2432468 AAAAAAT
1 AAAAAAT
2432475 CGTGACTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (14 bp):
AAAAAATTAAAGAT
Found at i:2435854 original size:20 final size:20
Alignment explanation
Indices: 2435809--2435855 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2435799 AGGAAGTTAC
* *
2435809 TTAAATAAAAAATTATTTAT
1 TTAATTAAAAAATTATTAAT
2435829 TT-ATTAAATAAATT-TTAAT
1 TTAATTAAA-AAATTATTAAT
2435848 TTAATTAA
1 TTAATTAA
2435856 TATTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATTAAAAAATTATTAAT
Found at i:2438647 original size:6 final size:6
Alignment explanation
Indices: 2438636--2438660 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2438626 AGCTAAGGAA
2438636 GAAGCT GAAGCT GAAGCT GAAGCT G
1 GAAGCT GAAGCT GAAGCT GAAGCT G
2438661 CGACTGCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (6 bp):
GAAGCT
Found at i:2439265 original size:20 final size:20
Alignment explanation
Indices: 2439240--2439279 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2439230 TAATATTAAC
2439240 TCTTAAATATTTATTATTTG
1 TCTTAAATATTTATTATTTG
2439260 TCTTAAATATTTATTATTTG
1 TCTTAAATATTTATTATTTG
2439280 AATCTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (20 bp):
TCTTAAATATTTATTATTTG
Found at i:2443461 original size:46 final size:46
Alignment explanation
Indices: 2443393--2443484 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
2443383 AAATATATTT
* *
2443393 ACTTTTAGAGACTTAACTATATATATAAAGTTTTTTCATCGACTTC
1 ACTTTTAGAGACTTAACAATATATATAAAATTTTTTCATCGACTTC
2443439 ACTTTTAGAGACTTAACAATATATATAAAATTTTTTCATCGACTTC
1 ACTTTTAGAGACTTAACAATATATATAAAATTTTTTCATCGACTTC
2443485 TACTGTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (46 bp):
ACTTTTAGAGACTTAACAATATATATAAAATTTTTTCATCGACTTC
Found at i:2449110 original size:21 final size:21
Alignment explanation
Indices: 2449084--2449123 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2449074 GATGTGGCAA
*
2449084 GTTAACTTGCCACATCAGCTG
1 GTTAACTTGCAACATCAGCTG
*
2449105 GTTAACTTGTAACATCAGC
1 GTTAACTTGCAACATCAGC
2449124 AATCCCGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (21 bp):
GTTAACTTGCAACATCAGCTG
Found at i:2452493 original size:15 final size:16
Alignment explanation
Indices: 2452462--2452496 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2452452 TAATATTATA
2452462 TATATATTAATTGTTT
1 TATATATTAATTGTTT
*
2452478 TATATTTTAA-TGTTT
1 TATATATTAATTGTTT
2452493 TATA
1 TATA
2452497 AAGGTAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (16 bp):
TATATATTAATTGTTT
Found at i:2454898 original size:3 final size:3
Alignment explanation
Indices: 2454890--2454942 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
2454880 TCCACAAAGA
* * * *
2454890 ATT ATT ATT ATT ATT ATT ACT ATT ACT ATT ACT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2454938 ATT AT
1 ATT AT
2454943 GGTCCTTAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:2465593 original size:21 final size:21
Alignment explanation
Indices: 2465551--2465589 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2465541 TACGGATTAA
2465551 TTTTTAATAATAAAAATTATT
1 TTTTTAATAATAAAAATTATT
*
2465572 TTTTTAATAA-AAAGATTA
1 TTTTTAATAATAAAAATTA
2465590 ATTTACTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
TTTTTAATAATAAAAATTATT
Found at i:2465730 original size:24 final size:24
Alignment explanation
Indices: 2465685--2465730 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2465675 AAAAGTCTTC
**
2465685 ATAAAAATTAACTAATTTTAATTT
1 ATAAAAATTAACTAATAATAATTT
2465709 ATAAATAATTAA-TAATAATAAT
1 ATAAA-AATTAACTAATAATAAT
2465731 AAATTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAAAAATTAACTAATAATAATTT
Found at i:2466258 original size:24 final size:23
Alignment explanation
Indices: 2466231--2466276 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2466221 AATCATTTTC
*
2466231 TTTATCCATTTAAAAATAAATAAT
1 TTTATACATTT-AAAATAAATAAT
* *
2466255 TTTATATATTTAAATTAAATAA
1 TTTATACATTTAAAATAAATAA
2466277 ATAATCCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTATACATTTAAAATAAATAAT
Found at i:2481311 original size:19 final size:19
Alignment explanation
Indices: 2481289--2481325 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2481279 AATAATATAT
*
2481289 ATTTTTATCATTTTTAATA
1 ATTTTAATCATTTTTAATA
*
2481308 ATTTTAATGATTTTTAAT
1 ATTTTAATCATTTTTAAT
2481326 TCTTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTTAATCATTTTTAATA
Found at i:2485502 original size:47 final size:48
Alignment explanation
Indices: 2485422--2485561 Score: 149
Period size: 58 Copynumber: 2.7 Consensus size: 48
2485412 ATTTAAAACA
*
2485422 TAAATATTAATCTAAAAATAACAT-ATAATAAATAGTGAAACATATTATT
1 TAAA-ATTAATC-AATAATAACATAATAATAAATAGTGAAACATATTATT
2485471 TAAAATTAATCAATAATAACATAATAAAAATAGGGAATAAATAGTGAAACATATTATT
1 TAAAATTAATCAATAATAAC---AT---AAT----AATAAATAGTGAAACATATTATT
2485529 TAAAATTAATCAATAATAACATAATAA-AAATAG
1 TAAAATTAATCAATAATAACATAATAATAAATAG
2485562 GGAGGAGAGC
Statistics
Matches: 79, Mismatches: 1, Indels: 24
0.76 0.01 0.23
Matches are distributed among these distances:
47 14 0.18
48 9 0.11
49 4 0.05
50 2 0.03
52 3 0.04
54 2 0.03
55 2 0.03
58 43 0.54
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (48 bp):
TAAAATTAATCAATAATAACATAATAATAAATAGTGAAACATATTATT
Found at i:2485513 original size:58 final size:58
Alignment explanation
Indices: 2485448--2485564 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
2485438 AATAACATAT
2485448 AATAAATAGTGAAACATATTATTTAAAATTAATCAATAATAACATAATAAAAATAGGG
1 AATAAATAGTGAAACATATTATTTAAAATTAATCAATAATAACATAATAAAAATAGGG
2485506 AATAAATAGTGAAACATATTATTTAAAATTAATCAATAATAACATAATAAAAATAGGG
1 AATAAATAGTGAAACATATTATTTAAAATTAATCAATAATAACATAATAAAAATAGGG
2485564 A
1 A
2485565 GGAGAGCATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.29
Consensus pattern (58 bp):
AATAAATAGTGAAACATATTATTTAAAATTAATCAATAATAACATAATAAAAATAGGG
Found at i:2494218 original size:23 final size:25
Alignment explanation
Indices: 2494174--2494220 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2494164 ATTTAATAAC
*
2494174 TTTAAAATATATTAATATTTAAAAG
1 TTTAAAATATATTAATAATTAAAAG
*
2494199 TTTAAAATAT-TT-TTAATTAAAA
1 TTTAAAATATATTAATAATTAAAA
2494221 TAAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTAAAATATATTAATAATTAAAAG
Found at i:2495567 original size:23 final size:24
Alignment explanation
Indices: 2495539--2495591 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
2495529 ACAAGGTTTT
* * *
2495539 TTCTTTCTTTTTTGAA-CAATTTA
1 TTCTTTATTTTTCGAATCAATATA
*
2495562 TTCTTTATTTTTCGAATGAATATA
1 TTCTTTATTTTTCGAATCAATATA
2495586 TTCTTT
1 TTCTTT
2495592 TAAATTGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (24 bp):
TTCTTTATTTTTCGAATCAATATA
Found at i:2507124 original size:13 final size:13
Alignment explanation
Indices: 2507106--2507131 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2507096 ATTTAACTCT
2507106 TTTTCAATATATC
1 TTTTCAATATATC
2507119 TTTTCAATATATC
1 TTTTCAATATATC
2507132 AAGCACATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTCAATATATC
Found at i:2508218 original size:93 final size:88
Alignment explanation
Indices: 2508063--2508234 Score: 245
Period size: 93 Copynumber: 1.9 Consensus size: 88
2508053 TTGAAAGAAA
* * *
2508063 ATATACAATATAATTAAAAATATTAATTTTTTTAAAAAAAACTAGTTATCATCACCTGACCTTCC
1 ATATACAATACAATTAAAAATATTAAATTTTTTAAAAAAAACTAGTTATCATCACCTAACCTTCC
2508128 ATTTTATATAACTTTAAAAAAAT
66 ATTTTATATAACTTTAAAAAAAT
* * *
2508151 ATATACAATACAATTAAAAATATTGATGCAATTTTTTAAAAATGAATTATTTATCATCACCTAAC
1 ATATACAATACAATTAAAAATATT-A---AATTTTTTAAAAA-AAACTAGTTATCATCACCTAAC
2508216 CTTCCATTTTATATAACTT
61 CTTCCATTTTATATAACTT
2508235 CATTGAAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
88 23 0.32
89 1 0.01
92 12 0.16
93 37 0.51
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (88 bp):
ATATACAATACAATTAAAAATATTAAATTTTTTAAAAAAAACTAGTTATCATCACCTAACCTTCC
ATTTTATATAACTTTAAAAAAAT
Found at i:2511472 original size:39 final size:40
Alignment explanation
Indices: 2511417--2511495 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
2511407 TTACAATAAA
*
2511417 TTATTTTAATTCCC-TTTTAAAAAATGGGCCCATTTTAGG
1 TTATTTTAATTCCCTTTTTAAAAAATGGACCCATTTTAGG
* *
2511456 TTATTTTAATTTCCTTTTTTAAGAAATGGACCCATTTTAG
1 TTATTTTAA-TTCCCTTTTTAAAAAATGGACCCATTTTAG
2511496 CTTTAATAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 9 0.26
40 4 0.11
41 22 0.63
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (40 bp):
TTATTTTAATTCCCTTTTTAAAAAATGGACCCATTTTAGG
Found at i:2514969 original size:25 final size:27
Alignment explanation
Indices: 2514941--2514993 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2514931 ACATTTTGTA
*
2514941 TATTT-AGATTTTAGT-TCCCTACTTT
1 TATTTAAGAATTTAGTCTCCCTACTTT
*
2514966 TATTTAAGAATTTAGTCTCTCTACTTT
1 TATTTAAGAATTTAGTCTCCCTACTTT
2514993 T
1 T
2514994 TGAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 9 0.38
27 10 0.42
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.55
Consensus pattern (27 bp):
TATTTAAGAATTTAGTCTCCCTACTTT
Found at i:2523807 original size:22 final size:19
Alignment explanation
Indices: 2523780--2523830 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2523770 TATGAGAAAC
2523780 ATATATAATATTTTTTATGA
1 ATATATAATATTTTTTAT-A
*
2523800 ATAAAT-ATATTATTTTTATA
1 ATATATAATA-T-TTTTTATA
2523820 ATATATAATAT
1 ATATATAATAT
2523831 GAGTTATGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
ATATATAATATTTTTTATA
Found at i:2526014 original size:19 final size:20
Alignment explanation
Indices: 2525950--2526007 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
2525940 TAATTACTTT
2525950 AAATTTCTTCAAGTTTTTAA
1 AAATTTCTTCAAGTTTTTAA
2525970 AAATTTCTTCAAGTTTTTAA
1 AAATTTCTTCAAGTTTTTAA
2525990 AAATTTCTTCAAGTTTTT
1 AAATTTCTTCAAGTTTTT
2526008 GAAATTTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (20 bp):
AAATTTCTTCAAGTTTTTAA
Found at i:2527033 original size:16 final size:16
Alignment explanation
Indices: 2527012--2527044 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2527002 TACCTGGTAT
2527012 TTTATCCTTTTGCCTG
1 TTTATCCTTTTGCCTG
2527028 TTTATCCTTTTGCCTG
1 TTTATCCTTTTGCCTG
2527044 T
1 T
2527045 GAAATGTTAC
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:0.06, C:0.24, G:0.12, T:0.58
Consensus pattern (16 bp):
TTTATCCTTTTGCCTG
Found at i:2528913 original size:45 final size:45
Alignment explanation
Indices: 2528860--2529452 Score: 510
Period size: 45 Copynumber: 13.5 Consensus size: 45
2528850 GAATAGTTTG
** * ** * *
2528860 GCTGAGAAGGCGAACAAAGAGATGGCCTCGACAGTGAATAGCTCA
1 GCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCTCA
* ** *
2528905 GCTGAGAAGATGAAGAACGAGATGGCCATGACAGTAAATAGCTCCA
1 GCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCT-CA
* * * *
2528951 -CTGAGGAGATGAA-AAGAGAGACA-AC-T-ACAATAAAGAGCTCA
1 GCTGAGAAGATGAAGAA-AGAGACAGCCTTGACAGTAAATAGCTCA
* * * * *
2528992 GCGGAGAAGATGAACAAAGAGACAGCCTTGAAAATAAATAACTCA
1 GCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCTCA
* *
2529037 GCTGAGAAGATGAAGAAAGA-A-A--CAT--CATTAAATAGCTCA
1 GCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCTCA
* * *
2529076 GCTGAGAAGATG-AGACAAGAGACAG-C-T-ACAGAAAATGGTTCA
1 GCTGAGAAGATGAAGA-AAGAGACAGCCTTGACAGTAAATAGCTCA
* *
2529118 GCTGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAATATCTCA
1 GCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCTCA
* * * *
2529163 GCTGAAAAGATGAACAAAGAGACAGCCTTGACAATAAATAACTCA
1 GCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCTCA
** ** *
2529208 GCTGAGAAGATGAAGAAAGAGATGGCCAGGACAGTGAATAGCTCA
1 GCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCTCA
* * *
2529253 GCTGAGAAGATG-AGACAAGAGACAG-C-T-ACAGTTAATGGCTCG
1 GCTGAGAAGATGAAGA-AAGAGACAGCCTTGACAGTAAATAGCTCA
* *
2529295 GCTGAGAAGATGAAGAAAGAGACGGCCTTGACAGTAAAGAGCTCGA
1 GCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCTC-A
* * * *
2529341 AC-GAGAAGGTGAAGAAAGAAACAGCCTTGACAGTAAATAACTCA
1 GCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCTCA
* * * * *
2529385 GCTGAGAAGGTTAAGAAAGAGATC-G-CTTCACAAGTGAATGGCTCA
1 GCTGAGAAGATGAAGAAAGAGA-CAGCCTTGAC-AGTAAATAGCTCA
*
2529430 GCTGAGAAGATGAAAAAAGAGAC
1 GCTGAGAAGATGAAGAAAGAGAC
2529453 CACTGTGGCA
Statistics
Matches: 449, Mismatches: 74, Indels: 51
0.78 0.13 0.09
Matches are distributed among these distances:
38 3 0.01
39 27 0.06
40 1 0.00
41 6 0.01
42 92 0.20
43 13 0.03
44 19 0.04
45 284 0.63
46 4 0.01
ACGTcount: A:0.43, C:0.16, G:0.27, T:0.15
Consensus pattern (45 bp):
GCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCTCA
Found at i:2529105 original size:126 final size:126
Alignment explanation
Indices: 2528939--2529182 Score: 316
Period size: 126 Copynumber: 1.9 Consensus size: 126
2528929 GCCATGACAG
* *
2528939 TAAATAGCTCCACTGAGGAGATGAAAAGAGAGACAACTACA-ATAAA-GAGCTCAGCGGAGAAGA
1 TAAATAGCTCCACTGAGAAGATGAAAAGAGAGACAACTACAGA-AAATG-GCTCAGCGGAAAAGA
* *
2529002 TGAACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAGAAGATGAAGAAAGAAACATCAT
64 TGAACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAAAAGATGAACAAAGAAACATCAT
* * * *
2529065 TAAATAGCT-CAGCTGAGAAGATGAGACA-AGAGACAGCTACAGAAAATGGTTCAGCTGAAAAGA
1 TAAATAGCTCCA-CTGAGAAGATGA-AAAGAGAGACAACTACAGAAAATGGCTCAGCGGAAAAGA
* * * *
2529128 TGAAGAAAGAGACAGCCTTGACAGTAAATATCTCAGCTGAAAAGATGAACAAAGA
64 TGAACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAAAAGATGAACAAAGA
2529183 GACAGCCTTG
Statistics
Matches: 102, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
125 2 0.02
126 96 0.94
127 4 0.04
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.15
Consensus pattern (126 bp):
TAAATAGCTCCACTGAGAAGATGAAAAGAGAGACAACTACAGAAAATGGCTCAGCGGAAAAGATG
AACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAAAAGATGAACAAAGAAACATCAT
Found at i:2529284 original size:132 final size:135
Alignment explanation
Indices: 2528988--2529452 Score: 354
Period size: 132 Copynumber: 3.5 Consensus size: 135
2528978 CAATAAAGAG
* * * * * * *
2528988 CTCAGCGGAGAAGATGAACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAGAAGATGAAGA
1 CTCAGCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAAAAGATGAACA
* * * * * *
2529053 AAGAAACATCATT-A-AAT--AG--CTC-AGCTGAGAAGATG-AGACAAGAGACAG-C--TACAG
66 AAGAGACAGCCTTGACAATAAAGAACTCGAAC-GAGAAGATGAAGA-AAGAAACAGCCAGGACAG
* **
2529107 AAAATGG
129 TAAATAA
* * *
2529114 TTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAATATCTCAGCTGAAAAGATGAACA
1 CTCAGCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAAAAGATGAACA
* * * **
2529179 AAGAGACAGCCTTGACAATAAATAACTC-AGCTGAGAAGATGAAGAAAGAGATGGCCAGGACAGT
66 AAGAGACAGCCTTGACAATAAAGAACTCGAAC-GAGAAGATGAAGAAAGAAACAGCCAGGACAGT
* *
2529243 GAATAG
130 AAATAA
* * * * *
2529249 CTCAGCTGAGAAGATG-AGACAAGAGACAG-C-T-ACAGTTAATGGCTCGGCTGAGAAGATGAAG
1 CTCAGCTGAGAAGATGAAGA-AAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAAAAGATGAAC
* * * * **
2529310 AAAGAGACGGCCTTGACAGTAAAGAGCTCGAACGAGAAGGTGAAGAAAGAAACAGCCTTGACAGT
65 AAAGAGACAGCCTTGACAATAAAGAACTCGAACGAGAAGATGAAGAAAGAAACAGCCAGGACAGT
2529375 AAATAA
130 AAATAA
* * * * * *
2529381 CTCAGCTGAGAAGGTTAAGAAAGAGATC-G-CTTCACAAGTGAATGGCTCAGCTGAGAAGATGAA
1 CTCAGCTGAGAAGATGAAGAAAGAGA-CAGCCTTGAC-AGTAAATAGCTCAGCTGAAAAGATGAA
*
2529444 AAAAGAGAC
64 CAAAGAGAC
2529453 CACTGTGGCA
Statistics
Matches: 277, Mismatches: 45, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
126 66 0.24
127 1 0.00
128 3 0.01
130 1 0.00
132 124 0.45
133 12 0.04
134 6 0.02
135 64 0.23
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.15
Consensus pattern (135 bp):
CTCAGCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAAAAGATGAACA
AAGAGACAGCCTTGACAATAAAGAACTCGAACGAGAAGATGAAGAAAGAAACAGCCAGGACAGTA
AATAA
Found at i:2529325 original size:177 final size:174
Alignment explanation
Indices: 2528860--2529452 Score: 641
Period size: 177 Copynumber: 3.4 Consensus size: 174
2528850 GAATAGTTTG
** * * *
2528860 GCTGAGAAGGCGAACAAAGAGATGGCCTCGACAGTGAATAGCTCAGCTGAGAAGATGAAGA-ACG
1 GCTGAGAAGATGAAGAAAGAGATGGCC-AGACAGTGAATAGCTCAGCTGAGAAGATG-AGACAAG
** * * ** *
2528924 AGATGGCCATGACAGTAAATAGCTCCA-CTGAGGAGATGAA-AAGAGAGACAAC-T-ACAATAAA
64 AGACAG-C-T-ACAGTAAATGGCT-CAGCTGAGAAGATGAAGAA-AGAGACGCCTTGACAGTAAA
*
2528985 GAGCTCAGCGGAGAAGATGAACAAAGAGACAGCCTTGAAAATAAATAACTCA
124 GAGCTCAGC-GAGAAGATGAACAAAGAGACAGCCTTGACAATAAATAACTCA
* * * *
2529037 GCTGAGAAGATGAAGAAAGA-A---ACA-TCATTAAATAGCTCAGCTGAGAAGATGAGACAAGAG
1 GCTGAGAAGATGAAGAAAGAGATGGCCAGACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGAG
* * * * *
2529097 ACAGCTACAGAAAATGGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAATATCTC
66 ACAGCTACAGTAAATGGCTCAGCTGAGAAGATGAAGAAAGAGAC-GCCTTGACAGTAAAGAGCTC
*
2529162 AGCTGAAAAGATGAACAAAGAGACAGCCTTGACAATAAATAACTCA
130 AGC-GAGAAGATGAACAAAGAGACAGCCTTGACAATAAATAACTCA
2529208 GCTGAGAAGATGAAGAAAGAGATGGCCAGGACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGA
1 GCTGAGAAGATGAAGAAAGAGATGGCCA-GACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGA
* *
2529273 GACAGCTACAGTTAATGGCTCGGCTGAGAAGATGAAGAAAGAGACGGCCTTGACAGTAAAGAGCT
65 GACAGCTACAGTAAATGGCTCAGCTGAGAAGATGAAGAAAGAGAC-GCCTTGACAGTAAAGAGCT
* * * * *
2529338 CGAACGAGAAGGTGAAGAAAGAAACAGCCTTGACAGTAAATAACTCA
129 C-AGCGAGAAGATGAACAAAGAGACAGCCTTGACAATAAATAACTCA
* * * * * * *
2529385 GCTGAGAAGGTTAAGAAAGAGATCGCTTCACA-AGTGAATGGCTCAGCTGAGAAGATGAAAAAAG
1 GCTGAGAAGATGAAGAAAGAGATGGC--CAGACAGTGAATAGCTCAGCTGAGAAGATGAGACAAG
2529449 AGAC
64 AGAC
2529453 CACTGTGGCA
Statistics
Matches: 352, Mismatches: 49, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
167 2 0.01
168 27 0.08
169 4 0.01
170 5 0.01
171 104 0.30
172 1 0.00
173 1 0.00
175 2 0.01
176 1 0.00
177 200 0.57
178 3 0.01
179 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.27, T:0.15
Consensus pattern (174 bp):
GCTGAGAAGATGAAGAAAGAGATGGCCAGACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGAG
ACAGCTACAGTAAATGGCTCAGCTGAGAAGATGAAGAAAGAGACGCCTTGACAGTAAAGAGCTCA
GCGAGAAGATGAACAAAGAGACAGCCTTGACAATAAATAACTCA
Found at i:2530212 original size:32 final size:32
Alignment explanation
Indices: 2530171--2530231 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
2530161 AAAGAATGTC
2530171 GTACCATTTACTTTACCGAAAATGGTTATGCT
1 GTACCATTTACTTTACCGAAAATGGTTATGCT
*
2530203 GTACCATTTACTTTATCGAAAATGGTTAT
1 GTACCATTTACTTTACCGAAAATGGTTAT
2530232 CTTTTTTCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (32 bp):
GTACCATTTACTTTACCGAAAATGGTTATGCT
Found at i:2537902 original size:22 final size:22
Alignment explanation
Indices: 2537854--2537902 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2537844 GCTATTTTAT
* * **
2537854 AAAAATTAATGATAAAATTTAA
1 AAAAAATAATAATAAAAGCTAA
*
2537876 CAAAAATAATAATAAAAGCTAA
1 AAAAAATAATAATAAAAGCTAA
2537898 AAAAA
1 AAAAA
2537903 TACACATTAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAAAATAATAATAAAAGCTAA
Found at i:2541487 original size:30 final size:30
Alignment explanation
Indices: 2541451--2541513 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2541441 ACTTATTTTA
2541451 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
2541481 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
2541511 TTG
1 TTG
2541514 CTTGTTAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:2542692 original size:148 final size:147
Alignment explanation
Indices: 2542496--2542793 Score: 555
Period size: 149 Copynumber: 2.0 Consensus size: 147
2542486 TCCTCTCTCC
2542496 ATTCCACATCCTTAATTAATAACATGCACAAGTAACATTATCAATAATTTCACTATTTACTTAT-
1 ATTCCACATCCTTAATTAATAACATGCACAAGTAACATTATCAATAATTTCACTATTTACTTATG
2542560 TATATTCAAAACTATCCATTTGCGTCATAGTCACTAAATTATTTATATATTAAGCT-AATAACTC
66 TATATTCAAAACTATCCATTTGCGTCATAGTCACTAAATTATTTATATATTAAGCTAAATAACTC
2542624 AAAATTAAGATCTGCTA
131 AAAATTAAGATCTGCTA
2542641 ATTCCACATCCTTAATTTATATAACATGCAACAAGTAACATTATCAATAATTTCACTATTTACTT
1 ATTCCACATCCTTAA-TTA-ATAACATGC-ACAAGTAACATTATCAATAATTTCACTATTTACTT
2542706 ATGTATATTCAAAACTATCCATTTGCGTCATAGTCACTAAATTATTTATATATTAAGCTAAATAA
63 ATGTATATTCAAAACTATCCATTTGCGTCATAGTCACTAAATTATTTATATATTAAGCTAAATAA
2542771 CTCAAAATTAAGATCTGCTA
128 CTCAAAATTAAGATCTGCTA
2542791 ATT
1 ATT
2542794 TTCCCTGAAA
Statistics
Matches: 148, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
145 15 0.10
146 3 0.02
147 9 0.06
148 37 0.25
149 56 0.38
150 28 0.19
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (147 bp):
ATTCCACATCCTTAATTAATAACATGCACAAGTAACATTATCAATAATTTCACTATTTACTTATG
TATATTCAAAACTATCCATTTGCGTCATAGTCACTAAATTATTTATATATTAAGCTAAATAACTC
AAAATTAAGATCTGCTA
Found at i:2544448 original size:23 final size:21
Alignment explanation
Indices: 2544419--2544483 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 21
2544409 TTTCGCATTA
2544419 AAAATATTTCACATATAAACAT
1 AAAATATTTCACATATAAA-AT
* * * *
2544441 AAAGATATTTGAAATAATTAATT
1 AAA-ATATTTCACAT-ATAAAAT
2544464 AAAATATTTCACATATAAAA
1 AAAATATTTCACATATAAAA
2544484 ATATTTGAAG
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
21 4 0.12
22 12 0.36
23 13 0.39
24 4 0.12
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (21 bp):
AAAATATTTCACATATAAAAT
Found at i:2544766 original size:25 final size:27
Alignment explanation
Indices: 2544710--2544764 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
2544700 AATATGTTTA
*
2544710 AAAGAGGAGAAATTGAACCTTAGACTC
1 AAAGAGGAGAAATCGAACCTTAGACTC
2544737 AAAGA-GAGAAATCGAA-CTTAGGACTC
1 AAAGAGGAGAAATCGAACCTTA-GACTC
2544763 AA
1 AA
2544765 GAACAAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 17 0.65
27 5 0.19
ACGTcount: A:0.47, C:0.15, G:0.22, T:0.16
Consensus pattern (27 bp):
AAAGAGGAGAAATCGAACCTTAGACTC
Found at i:2551426 original size:13 final size:13
Alignment explanation
Indices: 2551410--2551439 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2551400 TAAACCAAGC
2551410 TTTTCAAAAGCAT
1 TTTTCAAAAGCAT
*
2551423 TTTTCATAAGCAT
1 TTTTCAAAAGCAT
2551436 TTTT
1 TTTT
2551440 TTGCAGCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:2553551 original size:22 final size:21
Alignment explanation
Indices: 2553498--2553552 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
2553488 AATTTTGAAG
2553498 CACGAAA-TTTTTTTTTAAAA
1 CACGAAATTTTTTTTTTAAAA
* *
2553518 AATGAAAGTTTTTTTTTTAAAA
1 CACGAAA-TTTTTTTTTTAAAA
2553540 CACGAGAATTTTT
1 CACGA-AATTTTT
2553553 AAACACGGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.18
22 21 0.75
23 2 0.07
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.45
Consensus pattern (21 bp):
CACGAAATTTTTTTTTTAAAA
Found at i:2553602 original size:18 final size:18
Alignment explanation
Indices: 2553581--2553644 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
2553571 AACACGAAAA
2553581 TTTTTAAAACACGACATT
1 TTTTTAAAACACGACATT
* * *
2553599 TTTTTGAAACACGAGA-A
1 TTTTTAAAACACGACATT
*
2553616 TTTTTAAAACAAGACATT
1 TTTTTAAAACACGACATT
2553634 TTTTATAAAAC
1 TTTT-TAAAAC
2553645 GATTTTTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
17 13 0.35
18 18 0.49
19 6 0.16
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (18 bp):
TTTTTAAAACACGACATT
Found at i:2553691 original size:18 final size:18
Alignment explanation
Indices: 2553668--2553917 Score: 183
Period size: 18 Copynumber: 13.8 Consensus size: 18
2553658 ATCACCGGAG
2553668 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
2553686 TCTTTG-AAACACCG-AAA
1 TTTTTGAAAACA-CGAAAA
2553703 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
2553721 TTTTTG-AAACACGAAATT
1 TTTTTGAAAACACGAAA-A
* *
2553739 TTTTTGAAAATACGAAGA
1 TTTTTGAAAACACGAAAA
*** *
2553757 TTTTTTTTAACACGGAAA
1 TTTTTGAAAACACGAAAA
***
2553775 TTTTTG-AAACACGGTCATTT
1 TTTTTGAAAACAC-G--AAAA
2553795 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* **
2553813 TTTTTGAAAGACATG-ATT
1 TTTTTGAAA-ACACGAAAA
* *
2553831 TTTTTGAAAATACGGAAA
1 TTTTTGAAAACACGAAAA
*
2553849 TTTAT-AAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
2553866 TTTTTTCTGAAAACAAGAAAA
1 --TTTT-TGAAAACACGAAAA
* *
2553887 TTTTTG-AAACACTAGAA
1 TTTTTGAAAACACGAAAA
2553904 -TTTTGAAAACACGA
1 TTTTTGAAAACACGA
2553918 TTTTTCTTTA
Statistics
Matches: 179, Mismatches: 37, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
16 5 0.03
17 58 0.32
18 72 0.40
19 19 0.11
20 8 0.04
21 17 0.09
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:2553742 original size:17 final size:17
Alignment explanation
Indices: 2553530--2553898 Score: 146
Period size: 17 Copynumber: 20.8 Consensus size: 17
2553520 TGAAAGTTTT
*
2553530 TTTTTTAAAACACGAGAA
1 TTTTTTGAAACACGA-AA
2553548 -TTTTT-AAACACGGAAA
1 TTTTTTGAAACAC-GAAA
***
2553564 -TTTCAAAAACACGAAA
1 TTTTTTGAAACACGAAA
* * *
2553580 ATTTTTAAAACACGACAT
1 TTTTTTGAAACACGA-AA
2553598 TTTTTTGAAACACGAGAA
1 TTTTTTGAAACACGA-AA
* * *
2553616 -TTTTTAAAACAAGACA
1 TTTTTTGAAACACGAAA
* **
2553632 TTTTTT-ATAAAACGATT
1 TTTTTTGA-AACACGAAA
* *
2553649 TTTTTTAAAATCACCG-GA
1 TTTTTTGAAA-CA-CGAAA
*
2553667 GTTTTTGAAAACACGAAA
1 TTTTTTG-AAACACGAAA
* *
2553685 ATCTTTGAAACACCGAAA
1 TTTTTTGAAACA-CGAAA
2553703 -TTTTTGAAAACACGAAA
1 TTTTTTG-AAACACGAAA
*
2553720 ATTTTTGAAACACGAAA
1 TTTTTTGAAACACGAAA
*
2553737 TTTTTTTGAAAATACGAAGA
1 -TTTTTTG-AAACACGAA-A
**
2553757 TTTTTTTTAACACGGAAA
1 TTTTTTGAAACAC-GAAA
**
2553775 -TTTTTGAAACACGGTCATT
1 TTTTTTGAAACAC-G--AAA
2553794 TTTTTTGAAAACACGAAA
1 TTTTTTG-AAACACGAAA
* * *
2553812 ATTTTTGAAAGAC-ATGAT
1 TTTTTTGAAACACGA--AA
*
2553830 TTTTTTGAAAATACGGAAA
1 TTTTTTG-AAACAC-GAAA
* *
2553849 -TTTATAAAACACGAAAA
1 TTTTTTGAAACACG-AAA
*
2553866 TTTTTTCTGAAAACAAGAAA
1 -TTTTT-TG-AAACACGAAA
*
2553886 ATTTTTGAAACAC
1 TTTTTTGAAACAC
2553899 TAGAATTTTG
Statistics
Matches: 269, Mismatches: 50, Indels: 65
0.70 0.13 0.17
Matches are distributed among these distances:
16 19 0.07
17 112 0.42
18 77 0.29
19 36 0.13
20 12 0.04
21 13 0.05
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (17 bp):
TTTTTTGAAACACGAAA
Found at i:2553776 original size:54 final size:56
Alignment explanation
Indices: 2553711--2553817 Score: 155
Period size: 56 Copynumber: 1.9 Consensus size: 56
2553701 AATTTTTGAA
* *
2553711 AACACGAAAATTTTTGAAACAC-G-AAATTTTTTTGAAAATACGAAGATTTTTTTT
1 AACACGAAAATTTTTGAAACACGGTAAATTTTTTTGAAAACACGAAAATTTTTTTT
* * *
2553765 AACACGGAAATTTTTGAAACACGGTCATTTTTTTTGAAAACACGAAAATTTTT
1 AACACGAAAATTTTTGAAACACGGTAAATTTTTTTGAAAACACGAAAATTTTT
2553818 GAAAGACATG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 21 0.46
55 1 0.02
56 24 0.52
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (56 bp):
AACACGAAAATTTTTGAAACACGGTAAATTTTTTTGAAAACACGAAAATTTTTTTT
Found at i:2553780 original size:36 final size:34
Alignment explanation
Indices: 2553530--2553870 Score: 192
Period size: 35 Copynumber: 9.7 Consensus size: 34
2553520 TGAAAGTTTT
* *
2553530 TTTTTTAAAACACGAGAATTTTT-AAACACGGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACAC-GAAA
** * *
2553564 -TTTCAAAAACACGAAAATTTTTAAAACACGACATT
1 TTTTTGAAAACACGAAAATTTTTGAAACACGA-A-A
* * * *
2553599 TTTTTG-AAACACGAGAATTTTTAAAACAAGACA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAAA
* *** * * *
2553632 TTTTTTATAAA-ACGATTTTTTTTAAAATCACCGGAG
1 TTTTTGA-AAACACGAAAATTTTTGAAA-CA-CGAAA
*
2553668 TTTTTGAAAACACGAAAATCTTTGAAACACCGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACA-CGAAA
2553703 TTTTTGAAAACACGAAAATTTTTGAAACACGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAAA
* * **
2553737 TTTTTTTGAAAATACGAAGATTTTTTTTAACACGGAAA
1 --TTTTTGAAAACACGAA-AATTTTTGAAACAC-GAAA
***
2553775 TTTTTG-AAACACGGTCATTTTTTTTGAAAACACGAAAA
1 TTTTTGAAAACAC-G--AAAATTTTTG-AAACACG-AAA
* ** *
2553813 TTTTTGAAAGACATG-ATTTTTTTGAAAATACGGAAA
1 TTTTTGAAA-ACACGAAAATTTTTG-AAACAC-GAAA
*
2553849 TTTAT-AAAACACGAAAATTTTT
1 TTTTTGAAAACACGAAAATTTTT
2553871 TCTGAAAACA
Statistics
Matches: 242, Mismatches: 43, Indels: 43
0.74 0.13 0.13
Matches are distributed among these distances:
33 26 0.11
34 29 0.12
35 79 0.33
36 64 0.26
37 19 0.08
38 19 0.08
39 3 0.01
40 3 0.01
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (34 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACGAAA
Found at i:2553834 original size:38 final size:36
Alignment explanation
Indices: 2553688--2553895 Score: 126
Period size: 38 Copynumber: 5.7 Consensus size: 36
2553678 CACGAAAATC
* ***
2553688 TTTG-AAACACCG-AAATTTTTGAAAACACGAAAATT
1 TTTGAAAACA-CGAAAATTTTTGAAAACATGATTTTT
* *
2553723 TTTG-AAACACGAAATTTTTTTGAAAATACGAAGATTTTT
1 TTTGAAAACACGAAA-ATTTTTG-AAA-AC-ATGATTTTT
* * *
2553762 TTT---AACACGGAAATTTTTGAAACACGGTCATTTTT
1 TTTGAAAACACGAAAATTTTTGAAA-AC-ATGATTTTT
2553797 TTTGAAAACACGAAAATTTTTGAAAGACATGA-TTTT
1 TTTGAAAACACGAAAATTTTTGAAA-ACATGATTTTT
* * * *
2553833 TTTGAAAATACGGAAATTTAT-AAAACACGAAAATTTTT
1 TTTGAAAACACGAAAATTTTTGAAAACATG---ATTTTT
* *
2553871 TCTGAAAACAAGAAAATTTTTGAAA
1 TTTGAAAACACGAAAATTTTTGAAA
2553896 CACTAGAATT
Statistics
Matches: 136, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
34 6 0.04
35 29 0.21
36 34 0.25
37 14 0.10
38 42 0.31
39 11 0.08
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (36 bp):
TTTGAAAACACGAAAATTTTTGAAAACATGATTTTT
Found at i:2553846 original size:74 final size:73
Alignment explanation
Indices: 2553548--2553895 Score: 203
Period size: 74 Copynumber: 4.9 Consensus size: 73
2553538 AACACGAGAA
**
2553548 TTTTTAAACACGGAAATTTCA-AAAACACGAAAA---TTTTT-AAAACACGACATTTTTTTGAAA
1 TTTTTAAACACGGAAATTT-ATAAAACACGAAAATTTTTTTTGAAAACACGA-AAATTTTTGAAA
* *
2553608 CACG-AGAAT
64 GACGAAGATT
* * * * * *
2553617 TTTTAAAACA-AGACATTTTTTATAAA-ACG---ATTTTTTTT-AAAATCACCG-GAGTTTTTGA
1 TTTTTAAACACGGA-AATTTATA-AAACACGAAAATTTTTTTTGAAAA-CA-CGAAAATTTTTG-
* *
2553675 AAACACGAA-AAT
61 AAAGACGAAGATT
* * * * *
2553687 CTTTGAAACACCGAAATTTTTGAAAACACGAAAA---TTTTTG-AAACACGAAATTTTTTTGAAA
1 TTTTTAAACACGGAAATTTAT-AAAACACGAAAATTTTTTTTGAAAACACGAAA-ATTTTTG-AA
*
2553748 ATACGAAGATT
63 AGACGAAGATT
* * * ***
2553759 TTTTTTAACACGGAAATTTTTGAAACACGGTCATTTTTTTTGAAAACACGAAAATTTTTGAAAGA
1 TTTTTAAACACGGAAATTTATAAAACACGAAAATTTTTTTTGAAAACACGAAAATTTTTGAAAGA
*
2553824 C-ATGATT
66 CGAAGATT
* * *
2553831 TTTTTGAAAATACGGAAATTTATAAAACACGAAAATTTTTTCTGAAAACAAGAAAATTTTTGAAA
1 TTTTT--AAACACGGAAATTTATAAAACACGAAAATTTTTTTTGAAAACACGAAAATTTTTGAAA
2553896 CACTAGAATT
Statistics
Matches: 218, Mismatches: 35, Indels: 47
0.73 0.12 0.16
Matches are distributed among these distances:
66 1 0.00
68 2 0.01
69 34 0.16
70 35 0.16
71 40 0.18
72 29 0.13
73 5 0.02
74 62 0.28
75 10 0.05
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (73 bp):
TTTTTAAACACGGAAATTTATAAAACACGAAAATTTTTTTTGAAAACACGAAAATTTTTGAAAGA
CGAAGATT
Found at i:2553871 original size:92 final size:92
Alignment explanation
Indices: 2553674--2553870 Score: 244
Period size: 92 Copynumber: 2.2 Consensus size: 92
2553664 GGAGTTTTTG
* * **
2553674 AAAACACGAAAATCTTTGAAACACCG--A-AATTTTTGAAAACACGAAAATTTTTGAAACACGAA
1 AAAACACGAAAATTTTTGAAACACGGTCATTTTTTTTGAAAACACGAAAATTTTTGAAACACGAA
*
2553736 ATTTTTTTGAAAATACGAAGATTTTTT
66 ATTTTTTTGAAAATACGAAGATTTTAT
** * *
2553763 TTAACACGGAAATTTTTGAAACACGGTCATTTTTTTTGAAAACACGAAAATTTTTGAAAGAC-AT
1 AAAACACGAAAATTTTTGAAACACGGTCATTTTTTTTGAAAACACGAAAATTTTTGAAACACGA-
*
2553827 GATTTTTTTGAAAATACGGAA-A-TTTAT
65 AATTTTTTTGAAAATAC-GAAGATTTTAT
2553854 AAAACACGAAAATTTTT
1 AAAACACGAAAATTTTT
2553871 TCTGAAAACA
Statistics
Matches: 90, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
89 21 0.23
91 20 0.22
92 46 0.51
93 3 0.03
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (92 bp):
AAAACACGAAAATTTTTGAAACACGGTCATTTTTTTTGAAAACACGAAAATTTTTGAAACACGAA
ATTTTTTTGAAAATACGAAGATTTTAT
Found at i:2553891 original size:92 final size:89
Alignment explanation
Indices: 2553569--2553922 Score: 243
Period size: 92 Copynumber: 4.0 Consensus size: 89
2553559 GGAAATTTCA
* * ** * *
2553569 AAAACACGAAAATTTT-TAAAACACGACATTTTTTTGAAACAC-G-AGAATTTTT-AAAACAAGA
1 AAAATACGAAGATTTTATAAAACACGA-AAATTTTTGAAACACAGCAAAATTTTTGAAAACACGA
* * * *
2553630 CATTTTTTATAAAAC-GATTTTTTTT
65 AAATTTTT-GAAAACAGATTTTTTTG
* * *
2553655 AAAATCACCGGAG-TTTT-TGAAAACACGAAAATCTTTGAAACAC--CGAAATTTTTGAAAACAC
1 AAAAT-A-CGAAGATTTTAT-AAAACACGAAAATTTTTGAAACACAGCAAAATTTTTGAAAACAC
*
2553716 GAAAATTTTTGAAACACGAAATTTTTTTG
63 GAAAATTTTTGAAA-AC-AGATTTTTTTG
* ** * * ***
2553745 AAAATACGAAGATTTTTTTTAACACGGAAATTTTTGAAACACGGTCATTTTTTTTGAAAACACGA
1 AAAATACGAAGATTTTATAAAACACGAAAATTTTTGAAACACAG-CAAAATTTTTGAAAACACGA
2553810 AAATTTTTGAAAGACATGATTTTTTTG
65 AAATTTTTGAAA-ACA-GATTTTTTTG
2553837 AAAATACGGAA-A-TTTATAAAACACGAAAATTTTTTCTGAAA-ACAAG-AAAATTTTTG-AAAC
1 AAAATAC-GAAGATTTTATAAAACACGAAAA--TTTT-TGAAACAC-AGCAAAATTTTTGAAAAC
* *
2553897 ACTAGAA-TTTTGAAAACACGATTTTT
61 ACGAAAATTTTTGAAAACA-GATTTTT
2553923 CTTTAACAAA
Statistics
Matches: 213, Mismatches: 36, Indels: 35
0.75 0.13 0.12
Matches are distributed among these distances:
86 4 0.02
87 28 0.13
88 32 0.15
89 35 0.16
90 22 0.10
91 23 0.11
92 54 0.25
93 9 0.04
94 6 0.03
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (89 bp):
AAAATACGAAGATTTTATAAAACACGAAAATTTTTGAAACACAGCAAAATTTTTGAAAACACGAA
AATTTTTGAAAACAGATTTTTTTG
Found at i:2554514 original size:11 final size:11
Alignment explanation
Indices: 2554498--2554524 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2554488 GTTTTTATTT
2554498 TTTTTAATTAC
1 TTTTTAATTAC
2554509 TTTTTAATTAC
1 TTTTTAATTAC
2554520 TTTTT
1 TTTTT
2554525 TTCTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTAATTAC
Found at i:2554535 original size:10 final size:10
Alignment explanation
Indices: 2554522--2554575 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
2554512 TTAATTACTT
2554522 TTTTTCTTTC
1 TTTTTCTTTC
2554532 TTTTTCTTTC
1 TTTTTCTTTC
2554542 TCTTTT-TTTC
1 T-TTTTCTTTC
*
2554552 TTTCTTTTTTC
1 TTT-TTCTTTC
*
2554563 TTCTTCTCTTC
1 TTTTTCT-TTC
2554574 TT
1 TT
2554576 CTTGTCTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 2 0.05
10 21 0.55
11 15 0.39
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:2554541 original size:14 final size:13
Alignment explanation
Indices: 2554520--2554572 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 13
2554510 TTTTAATTAC
2554520 TTTT-TTTCTTTCT
1 TTTTCTTTCTTT-T
2554533 TTTTCTTTCTCTTT
1 TTTTCTTTCT-TTT
2554547 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
2554560 TTCTTCTTCTCTT
1 TT-TTCTT-TCTT
2554573 CTTCTTGTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.25
14 21 0.58
15 6 0.17
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTCTTTT
Found at i:2555164 original size:29 final size:30
Alignment explanation
Indices: 2555131--2555248 Score: 107
Period size: 30 Copynumber: 3.9 Consensus size: 30
2555121 TGTAATTTTT
*
2555131 AGAAAATTT-AGGATTAAAATGAAATTTAA
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * *
2555160 TGAAAGTTTAAGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTAAGGGT-TAAAATGAAATTTAA
* *
2555190 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * *
2555219 GGAAAAGTTTAGGGGTCAAAATGCAAATTT
1 AGAAAA-TTTAAGGGTTAAAATG-AAATTT
2555249 TATTTTTTAA
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
29 12 0.16
30 55 0.74
31 7 0.09
ACGTcount: A:0.46, C:0.03, G:0.21, T:0.30
Consensus pattern (30 bp):
AGAAAATTTAAGGGTTAAAATGAAATTTAA
Found at i:2555186 original size:30 final size:30
Alignment explanation
Indices: 2555146--2555248 Score: 136
Period size: 30 Copynumber: 3.4 Consensus size: 30
2555136 ATTTAGGATT
*
2555146 AAAATGAAATTTAATGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
2555176 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
2555206 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
2555236 AAAATGCAAATTT
1 AAAATG-AAATTT
2555249 TATTTTTTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
29 2 0.03
30 56 0.88
31 6 0.09
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:2555705 original size:54 final size:54
Alignment explanation
Indices: 2555520--2555831 Score: 510
Period size: 54 Copynumber: 5.9 Consensus size: 54
2555510 CACGTGAGCC
* *
2555520 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT--AA
*
2555575 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAG--A--AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
2555625 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
2555679 AAGGCTCAACTCACCTCTCGCAATATG-GTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
2555732 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
2555786 AAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTGAAAAACA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
2555832 AAAACTGAAA
Statistics
Matches: 244, Mismatches: 7, Indels: 13
0.92 0.03 0.05
Matches are distributed among these distances:
50 48 0.20
52 1 0.00
53 51 0.21
54 100 0.41
55 38 0.16
56 6 0.02
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
Done.