Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 66 of 126
Found at i:19281796 original size:19 final size:19
Alignment explanation
Indices: 19281772--19281808 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19281762 TAAACGCCAC
*
19281772 TAATGCTCTGATCTTTAGG
1 TAATGCTCTGACCTTTAGG
19281791 TAATGCTCTGACCTTTAG
1 TAATGCTCTGACCTTTAG
19281809 CGGCGCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (19 bp):
TAATGCTCTGACCTTTAGG
Found at i:19281848 original size:41 final size:40
Alignment explanation
Indices: 19281791--19281977 Score: 142
Period size: 41 Copynumber: 4.6 Consensus size: 40
19281781 GATCTTTAGG
* * *
19281791 TAATGCTCTGACCTTTAGCGGCGCTTTCCTATCAACGCGGC
1 TAATGCTCTGACCTTTAGCGGCGCTTTCCGA-AAACGCCGC
* **
19281832 TAATGCTCTTACCTTTAGCGGCGCTTATGGGAAAACGCCGC
1 TAATGCTCTGACCTTTAGCGGCGCTT-TCCGAAAACGCCGC
* * * * *
19281873 TAATGCTCTGACCTTTAGCGGCGTTTTCCCATAAGCGTCGT
1 TAATGCTCTGACCTTTAGCGGCGCTTTCCGA-AAACGCCGC
* * * * * *
19281914 TAATGCCCTGACTTTTACCGGCGTTTTTCCTATAAACGCCGT
1 TAATGCTCTGACCTTTAGCGGCG-CTTTCCGA-AAACGCCGC
* * *
19281956 TATTGCT-TTACCTTTTGCGGCG
1 TAATGCTCTGACCTTTAGCGGCG
19281978 TTTATGGAAA
Statistics
Matches: 117, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
40 2 0.02
41 93 0.79
42 22 0.19
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (40 bp):
TAATGCTCTGACCTTTAGCGGCGCTTTCCGAAAACGCCGC
Found at i:19281978 original size:41 final size:40
Alignment explanation
Indices: 19281932--19282021 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
19281922 TGACTTTTAC
* * *
19281932 CGGCGTTTTTCCTATAAACGCCGTTATTGCTTTACCTTTTG
1 CGGCGTTTTT-CGAAAAACACCGTTATTGCTTTACCTTTTG
* *
19281973 CGGCGTTTATGGAAAAACACCGTTATTGCTTTACCTTTTG
1 CGGCGTTTTTCGAAAAACACCGTTATTGCTTTACCTTTTG
19282013 CGGCGTTTT
1 CGGCGTTTT
19282022 CTGTCCAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 34 0.79
41 9 0.21
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (40 bp):
CGGCGTTTTTCGAAAAACACCGTTATTGCTTTACCTTTTG
Found at i:19287656 original size:34 final size:33
Alignment explanation
Indices: 19287609--19287702 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 33
19287599 TATTTTTTAG
*
19287609 AAACAACCCAAATATTTAATTATTTAATTACTAA
1 AAACAACCTAAATATTTAATTATTTAATTA-TAA
*
19287643 AATCAACCTAAATATTTAATTCAAAATATTTAATTATAA
1 AAACAACCTAAATATTTAA-T-----TATTTAATTATAA
19287682 AAACAACCTAAATATTTAATT
1 AAACAACCTAAATATTTAATT
19287703 TAAAATATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
33 1 0.02
34 17 0.33
35 1 0.02
38 1 0.02
39 21 0.41
40 10 0.20
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (33 bp):
AAACAACCTAAATATTTAATTATTTAATTATAA
Found at i:19287689 original size:39 final size:39
Alignment explanation
Indices: 19287629--19287718 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 39
19287619 AATATTTAAT
*
19287629 TATTTAATTACTAAAATCAACCTAAATATTTAATTCAAAA
1 TATTTAATTA-TAAAAACAACCTAAATATTTAATTCAAAA
*
19287669 TATTTAATTATAAAAACAACCTAAATATTTAATTTAAAA
1 TATTTAATTATAAAAACAACCTAAATATTTAATTCAAAA
19287708 TATTTAATTAT
1 TATTTAATTAT
19287719 TTAATTATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 38 0.79
40 10 0.21
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (39 bp):
TATTTAATTATAAAAACAACCTAAATATTTAATTCAAAA
Found at i:19287705 original size:5 final size:5
Alignment explanation
Indices: 19287695--19287758 Score: 50
Period size: 5 Copynumber: 13.6 Consensus size: 5
19287685 CAACCTAAAT
**
19287695 ATTTA ATTTA AAAT- ATTTA A-TT- ATTTA A-TT- ATTTA A-TTA TATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA -ATTTA
19287740 ATTTA ATTTA ATTTTA ATT
1 ATTTA ATTTA A-TTTA ATT
19287759 ATTAAAAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
3 2 0.04
4 13 0.28
5 24 0.51
6 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:19287721 original size:8 final size:8
Alignment explanation
Indices: 19287708--19287863 Score: 67
Period size: 8 Copynumber: 19.5 Consensus size: 8
19287698 TAATTTAAAA
19287708 TATTTAAT
1 TATTTAAT
19287716 TATTTAAT
1 TATTTAAT
19287724 TATTTAATT
1 TATTTAA-T
19287733 ATATTTAATT
1 -TATTTAA-T
19287743 TAATTTAA-
1 T-ATTTAAT
19287751 T-TTTAAT
1 TATTTAAT
* *
19287758 TATTAAAAAC
1 TATT--TAAT
* * *
19287768 AATCTAAA
1 TATTTAAT
19287776 TATTTAAT
1 TATTTAAT
19287784 TATTT-A-
1 TATTTAAT
19287790 -A-TTAAT
1 TATTTAAT
*
19287796 TATTTAAA
1 TATTTAAT
19287804 TATTTAAT
1 TATTTAAT
* *
19287812 TATTAAAAA
1 TATT-TAAT
* *
19287821 TAGCTTAAA
1 TA-TTTAAT
*
19287830 AATTTAA-
1 TATTTAAT
* *
19287837 T-TTAAAA
1 TATTTAAT
19287844 TATTTAAT
1 TATTTAAT
19287852 TATTTAAT
1 TATTTAAT
19287860 TATT
1 TATT
19287864 AAAAAAACCC
Statistics
Matches: 112, Mismatches: 21, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
4 2 0.02
5 2 0.02
6 9 0.08
7 4 0.04
8 65 0.58
9 10 0.09
10 20 0.18
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.53
Consensus pattern (8 bp):
TATTTAAT
Found at i:19287739 original size:10 final size:9
Alignment explanation
Indices: 19287708--19287753 Score: 60
Period size: 10 Copynumber: 5.1 Consensus size: 9
19287698 TAATTTAAAA
19287708 TATTTAA-T
1 TATTTAATT
19287716 TATTTAA-T
1 TATTTAATT
19287724 TATTTAATT
1 TATTTAATT
19287733 ATATTTAATT
1 -TATTTAATT
19287743 TAATTTAATT
1 T-ATTTAATT
19287753 T
1 T
19287754 TAATTATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 15 0.43
9 2 0.06
10 18 0.51
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:19287836 original size:80 final size:82
Alignment explanation
Indices: 19287659--19287843 Score: 193
Period size: 80 Copynumber: 2.3 Consensus size: 82
19287649 CCTAAATATT
* *
19287659 TAATTCAAAATATTTAATTATAAAAACAACCTAAATATTTAATTTAAAATATTTAATTATTTAAT
1 TAATT-AAAA-ATTTAATTATAAAAACAACCTAAATATTTAATTTAAAATAATTAATTATTTAAA
* **
19287724 TATTTAATTATATTTAATT
64 TATTTAATTATATTAAAAA
* * * **
19287743 TAATT-TAATTTTAATTATTAAAAACAATCTAAATATTTAA-TT-ATTTAATTAATTATTTAAAT
1 TAATTAAAAATTTAATTA-TAAAAACAACCTAAATATTTAATTTAAAATAATTAATTATTTAAAT
19287805 ATTTAA-T-TATTAAAAA
65 ATTTAATTATATTAAAAA
*
19287821 TAGCTTAAAAATTTAATT-TAAAA
1 TA-ATTAAAAATTTAATTATAAAA
19287844 TATTTAATTA
Statistics
Matches: 85, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
78 13 0.15
79 3 0.04
80 31 0.36
81 10 0.12
82 23 0.27
84 5 0.06
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.47
Consensus pattern (82 bp):
TAATTAAAAATTTAATTATAAAAACAACCTAAATATTTAATTTAAAATAATTAATTATTTAAATA
TTTAATTATATTAAAAA
Found at i:19293190 original size:12 final size:12
Alignment explanation
Indices: 19293172--19293201 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19293162 ATTACTTTTG
19293172 AATTTATTTATT
1 AATTTATTTATT
*
19293184 TATTTATTTATT
1 AATTTATTTATT
19293196 AATTTA
1 AATTTA
19293202 AATCATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
AATTTATTTATT
Found at i:19293519 original size:43 final size:44
Alignment explanation
Indices: 19293472--19293563 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
19293462 ACGTTTGTGA
* * *
19293472 GAAAAACGTTGCT-AAAGATCACATTTTTTAGTGGCATTTGTTG
1 GAAAAACGTCGCTAAAAAATCACATTCTTTAGTGGCATTTGTTG
** * **
19293515 GAAAAGTGTCGCTAAAAAATCACGTTCTTTAGTGGGGTTTGTTG
1 GAAAAACGTCGCTAAAAAATCACATTCTTTAGTGGCATTTGTTG
19293559 GAAAA
1 GAAAA
19293564 GCACCGTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 10 0.25
44 30 0.75
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (44 bp):
GAAAAACGTCGCTAAAAAATCACATTCTTTAGTGGCATTTGTTG
Found at i:19293860 original size:36 final size:37
Alignment explanation
Indices: 19293792--19293869 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 37
19293782 GATGAGATGA
*
19293792 GAGAGAAAGAAAGATATATGAGATAAAAATAAAGGGAC
1 GAGAGAAAGAAAGATATATGAGA-AAAAATAAAAGGAC
* *
19293830 GAGAGAAA-AAGAGATATGTGAG-AAAGATAAAAGGAC
1 GAGAGAAAGAA-AGATATATGAGAAAAAATAAAAGGAC
19293866 GAGA
1 GAGA
19293870 AAGGGAAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 16 0.44
37 2 0.06
38 18 0.50
ACGTcount: A:0.56, C:0.03, G:0.29, T:0.12
Consensus pattern (37 bp):
GAGAGAAAGAAAGATATATGAGAAAAAATAAAAGGAC
Found at i:19297178 original size:13 final size:14
Alignment explanation
Indices: 19297141--19297178 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
19297131 TTGTTATTAA
19297141 ATTTTAATAATATT
1 ATTTTAATAATATT
*
19297155 ATTTTTA-AATA-T
1 ATTTTAATAATATT
19297167 ATTTTAATAATA
1 ATTTTAATAATA
19297179 ATAAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 7 0.33
13 8 0.38
14 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTAATAATATT
Found at i:19297190 original size:29 final size:29
Alignment explanation
Indices: 19297141--19297263 Score: 89
Period size: 26 Copynumber: 4.3 Consensus size: 29
19297131 TTGTTATTAA
*
19297141 ATTTTAATAAT-AT-TAT-TTTTAAATAT
1 ATTTTAATAATAATATATAATTTAAATAT
*
19297167 ATTTTAATAATAATAAATAATTT-AATCAT
1 ATTTTAATAATAATATATAATTTAAAT-AT
* * *
19297196 ATTTTAA-CATAAT-TATTA-TTAAATAC
1 ATTTTAATAATAATATATAATTTAAATAT
* *
19297222 AATTTAATAAAATAATATATAATTTAAAAAAT
1 ATTTTAAT--AATAATATATAATTT-AAATAT
19297254 ATTCTTAATA
1 ATT-TTAATA
19297264 TAAATTTTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
26 20 0.27
27 8 0.11
28 10 0.14
29 17 0.23
30 4 0.05
31 3 0.04
32 6 0.08
33 5 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTTTAATAATAATATATAATTTAAATAT
Found at i:19297293 original size:60 final size:57
Alignment explanation
Indices: 19297152--19297277 Score: 141
Period size: 55 Copynumber: 2.2 Consensus size: 57
19297142 TTTTAATAAT
* * * **
19297152 ATTATTTTTAAATATATTTTAAT--AATAATAAATAATTTAATCATATTTTAACATA
1 ATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAAAAATATTTTAACATA
* *
19297207 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAAAAAATATTCTTAATATAA
1 ATTATTATTAAATACAATTTAATAAAATAATAAATAATTT-AAAAATATT-TTAACAT-A
19297267 ATT-TTATTAAA
1 ATTATTATTAAA
19297278 ATATGAATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
55 20 0.34
57 14 0.24
58 7 0.12
59 14 0.24
60 4 0.07
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (57 bp):
ATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAAAAATATTTTAACATA
Found at i:19298225 original size:11 final size:11
Alignment explanation
Indices: 19298209--19298242 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
19298199 ACAAGAATAA
19298209 TAGATGAGAAT
1 TAGATGAGAAT
19298220 TAGATGAGAAT
1 TAGATGAGAAT
* *
19298231 AAGAAGAGAAT
1 TAGATGAGAAT
19298242 T
1 T
19298243 TGTAATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (11 bp):
TAGATGAGAAT
Found at i:19298409 original size:34 final size:34
Alignment explanation
Indices: 19298364--19298466 Score: 161
Period size: 34 Copynumber: 3.0 Consensus size: 34
19298354 AGAATATGAA
*
19298364 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAGGG
1 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
* *
19298398 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAAGG
1 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
*
19298432 AAGTTAAGGAAGATGGAAGGTTAAAAGATGAAAGG
1 AAGTTAAGGAAGATGGAAGGTT-AAAGATCAAAGG
19298467 TTGAACATCC
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
34 52 0.84
35 10 0.16
ACGTcount: A:0.45, C:0.02, G:0.36, T:0.17
Consensus pattern (34 bp):
AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
Found at i:19298418 original size:17 final size:17
Alignment explanation
Indices: 19298366--19298468 Score: 90
Period size: 17 Copynumber: 6.2 Consensus size: 17
19298356 AATATGAAAA
19298366 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
* ** * *
19298383 GTTAAAGATCAAGGGAG
1 GTTAAGGAAGATGGAAG
19298400 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
19298417 GTTAAAGGTCAA-A-GGAA-
1 GTT-AAGG--AAGATGGAAG
19298434 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
*
19298451 GTTAA--AAGATGAAAG
1 GTTAAGGAAGATGGAAG
19298466 GTT
1 GTT
19298469 GAACATCCAT
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
14 2 0.03
15 13 0.19
16 8 0.12
17 35 0.51
18 8 0.12
19 1 0.01
20 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.36, T:0.19
Consensus pattern (17 bp):
GTTAAGGAAGATGGAAG
Found at i:19300633 original size:29 final size:28
Alignment explanation
Indices: 19300533--19300687 Score: 150
Period size: 30 Copynumber: 5.2 Consensus size: 28
19300523 TTTCGAAAGT
**
19300533 TTTAGGGTCAAAAATAG-AATTTTTCAAAG
1 TTTAGGGT-AAAAAT-GTAATTTTTGGAAG
*
19300562 TTTTAGGGTCAAAAATGGAATTTTTGGAAG
1 -TTTAGGGT-AAAAATGTAATTTTTGGAAG
*
19300592 TTTCAAGGTTAAAAATGTAATTTTTGGAAG
1 TTT--AGGGTAAAAATGTAATTTTTGGAAG
* *
19300622 TTTAGAGGTAAAAATGTAATTTGTAGAAG
1 TTTAG-GGTAAAAATGTAATTTTTGGAAG
* *
19300651 TTTGGGGGTAAAAATGTAATTTTTGAATAG
1 TTT-AGGGTAAAAATGTAATTTTTGGA-AG
19300681 TTTAGGG
1 TTTAGGG
19300688 ACCTTTAATG
Statistics
Matches: 107, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
28 2 0.02
29 48 0.45
30 53 0.50
31 4 0.04
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (28 bp):
TTTAGGGTAAAAATGTAATTTTTGGAAG
Found at i:19301802 original size:19 final size:19
Alignment explanation
Indices: 19301774--19301822 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
19301764 ATTAATACTG
*
19301774 CATTTGTTATTATTAAAAA
1 CATTTATTATTATTAAAAA
*
19301793 CATTTATTATTGTTAAAAA
1 CATTTATTATTATTAAAAA
*
19301812 TATTTATTATT
1 CATTTATTATT
19301823 TTTACTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (19 bp):
CATTTATTATTATTAAAAA
Found at i:19302530 original size:6 final size:6
Alignment explanation
Indices: 19302506--19302578 Score: 55
Period size: 6 Copynumber: 12.5 Consensus size: 6
19302496 TTTGGACATT
* * *
19302506 AATTTA ATTTTA AATTTTA AATTTA TAA--TA AATTTA AATTT- TATGTA
1 AATTTA AATTTA AA-TTTA AATTTA -AATTTA AATTTA AATTTA AATTTA
* *
19302553 AATTTA AATTCA AA-ATA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AAT
19302579 ACTATTGGGC
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
4 2 0.04
5 8 0.16
6 33 0.65
7 8 0.16
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:19302543 original size:17 final size:17
Alignment explanation
Indices: 19302516--19302578 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
19302506 AATTTAATTT
19302516 TAAATTTTAAATTTATAA
1 TAAA-TTTAAATTTATAA
*
19302534 TAAATTTAAATTT-TATG
1 TAAATTTAAATTTATA-A
* *
19302551 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTATAA
19302568 TAAATTTAAAT
1 TAAATTTAAAT
19302579 ACTATTGGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
16 2 0.05
17 32 0.82
18 5 0.13
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:19303257 original size:206 final size:204
Alignment explanation
Indices: 19302899--19303701 Score: 1067
Period size: 206 Copynumber: 3.9 Consensus size: 204
19302889 TCTGGTTTCA
* * * ** * ** *
19302899 TTGACTTGGTCTTCTTTTCAGTGTCTTATCAGGAAGACAACCGCGTCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
* * * * * * *
19302964 TTCTGT-TTTCAACAGGAAGACG-ATTCTGGTTCACTTCTCTGTGTCTCATCAGGAAGCTAACAA
66 CTCTGTATCTCATCAGGAAGACGAATT-TGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* *
19303027 CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGGTTCGAAGATTTGCTCAT
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGGTTCGAAGATTTGCTCAT
19303092 ATCGAGCATGGT
194 ATCGAGC-TGGT
* * *
19303104 TTGATTTGGTCTTCTTCTCAGTATCTGATCAGGAAGATGACCGCATCGCTTGTTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
* * *
19303169 CTCTGTATCTCATCAGGAAGACAAATTTGATCCACTTCTCAGTATCTCATCAGGAATCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * **
19303234 TATATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTACTCGCAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
19303299 CGAG-T-G-
196 CGAGCTGGT
* * * * * * * *
19303305 TTGAGTTAGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
* *
19303370 CTCTGTATCTTATCAGGAAGAGGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * *
19303435 TTTATTGCTTCGACCTACTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGGTTTGCTCATAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
*
19303500 TGAGCGTGGGT
196 CGAGC-T-GGT
**
19303511 TTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
* * *
19303576 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATTAGGAACCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
19303641 TTTATCGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTC
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
19303702 GCATTGAGCA
Statistics
Matches: 520, Mismatches: 71, Indels: 13
0.86 0.12 0.02
Matches are distributed among these distances:
201 176 0.34
202 1 0.00
203 2 0.00
205 82 0.16
206 256 0.49
207 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (204 bp):
TTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
CGAGCTGGT
Found at i:19303731 original size:407 final size:406
Alignment explanation
Indices: 19302976--19303765 Score: 1233
Period size: 407 Copynumber: 1.9 Consensus size: 406
19302966 CTGTTTTCAA
* * *
19302976 CAGGAAGACGATTCTGGTTCACTTCTCTGTGTCTCATCAGGAAGCTAACAACTTTATTGCTTCGA
1 CAGGAAGACGATTCTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACAACTTTATTGCTTCGA
*
19303041 CCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGGTTCGAAGATTTGCTCATATCGAGCATGGTTT
66 CCTACTTCTCAGTATCTCATCAAGAAGCTGGGGGTTCGAAGATTTGCTCATATCGAGCATGGTTT
*
19303106 GATTTGGTCTTCTTCTCAGTATCTGATCAGGAAGATGACCGCATCGCTTGTTTCAATTCGCTTCT
131 GATTTGGTCTTCTTCTCAGTATCTGATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCT
* *
19303171 CTGTATCTCATCAGGAAGACAAATTTGATCCACTTCTCAGTATCTCATCAGGAATCTAACCATTA
196 CTGTATCTCATCAGGAAGACAAATTTGATCCACTTCTCAATATCTCATCAGGAACCTAACCATTA
*
19303236 TATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTACTCGCATCG
261 TATCGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTACTCGCATCG
** * * *
19303301 AGTGTTGAGTTAGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTC
326 AGCATCGAGTTAGCATACTTCTCTGTATCTCATCACGAAGATGACCGCCTCAC-TGTTTCAATTC
19303366 GCTTCTCTGTATCTTAT
390 GCTTCTCTGTATCTTAT
* * *
19303383 CAGGAAGAGGAATT-TGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
1 CAGGAAGACG-ATTCTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACAACTTTATTGCTTCG
* * * * * *
19303447 ACCTACTTCTCAGTGTCTCATCAGGAAGCT-GGGGTTTGAAGGTTTGCTCATATTGAGCGTGGGT
65 ACCTACTTCTCAGTATCTCATCAAGAAGCTGGGGGTTCGAAGATTTGCTCATATCGAGCAT-GGT
* *
19303511 TTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
129 TTGATTTGGTCTTCTTCTCAGTATCTGATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
* * *
19303576 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATTAGGAACCTAACCAT
194 CTCTGTATCTCATCAGGAAGACAAATTTGATCCACTTCTCAATATCTCATCAGGAACCTAACCAT
* * * *
19303641 TTTATCGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTCGCAT
259 TATATCGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTACTCGCAT
* * *
19303706 TGAGCATCGAGTTGGCATACTTCTCTGTATCTCATCACGAAGATGATCGCCTCACTGTTT
324 CGAGCATCGAGTTAGCATACTTCTCTGTATCTCATCACGAAGATGACCGCCTCACTGTTT
19303766 GTGGATAATC
Statistics
Matches: 347, Mismatches: 34, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
406 31 0.09
407 313 0.90
408 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (406 bp):
CAGGAAGACGATTCTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACAACTTTATTGCTTCGA
CCTACTTCTCAGTATCTCATCAAGAAGCTGGGGGTTCGAAGATTTGCTCATATCGAGCATGGTTT
GATTTGGTCTTCTTCTCAGTATCTGATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCT
CTGTATCTCATCAGGAAGACAAATTTGATCCACTTCTCAATATCTCATCAGGAACCTAACCATTA
TATCGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTACTCGCATCG
AGCATCGAGTTAGCATACTTCTCTGTATCTCATCACGAAGATGACCGCCTCACTGTTTCAATTCG
CTTCTCTGTATCTTAT
Found at i:19313397 original size:11 final size:11
Alignment explanation
Indices: 19313381--19313433 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
19313371 ATTTCTAAAA
*
19313381 TTAAATTTACT
1 TTAAATTTAAT
*
19313392 TTAAATTTAAA
1 TTAAATTTAAT
* *
19313403 TTCATTTTAAAT
1 TTAAATTT-AAT
*
19313415 TTAAATTTAGT
1 TTAAATTTAAT
19313426 TTAAATTT
1 TTAAATTT
19313434 GAAATAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
11 25 0.76
12 8 0.24
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:19313400 original size:6 final size:6
Alignment explanation
Indices: 19313376--19313438 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
19313366 GATTTATTTC
* * * *
19313376 TAAAAT TAAATT T-ACTT TAAATT TAAA-T TCATTT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
19313422 T-AGTT TAAATT TGAAAT
1 TAAATT TAAATT T-AAAT
19313439 AATTTTAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
5 11 0.25
6 29 0.66
7 4 0.09
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:19313401 original size:17 final size:17
Alignment explanation
Indices: 19313362--19313449 Score: 97
Period size: 17 Copynumber: 5.1 Consensus size: 17
19313352 TAAAATGGAT
*
19313362 TTTAGATTTATTTCTAAA
1 TTTAAATTTATTT-TAAA
* *
19313380 ATTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
*
19313397 TTTAAATTCATTTTAAA
1 TTTAAATTTATTTTAAA
*
19313414 TTTAAATTTAGTTTAAA
1 TTTAAATTTATTTTAAA
*
19313431 TTTGAAA-TAATTTTAAA
1 TTT-AAATTTATTTTAAA
19313448 TT
1 TT
19313450 AAAACTAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
17 46 0.78
18 13 0.22
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:19314181 original size:22 final size:23
Alignment explanation
Indices: 19314133--19314189 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
19314123 TAAATGGCAT
19314133 TAATAATAATATTTATTTACTAAA
1 TAATAATAATATTTA-TTACTAAA
*
19314157 TAATAATAATATTTA-TAGTAAA
1 TAATAATAATATTTATTACTAAA
*
19314179 TAATAGTAATA
1 TAATAATAATA
19314190 AATAGCATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 16 0.52
24 15 0.48
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
TAATAATAATATTTATTACTAAA
Found at i:19314225 original size:20 final size:20
Alignment explanation
Indices: 19314197--19314238 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
19314187 ATAAATAGCA
*
19314197 TTAATAATAATAAATATTTT
1 TTAACAATAATAAATATTTT
*
19314217 TTAACAATAATAAATGTTTT
1 TTAACAATAATAAATATTTT
19314237 TT
1 TT
19314239 TGGTAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TTAACAATAATAAATATTTT
Found at i:19315382 original size:29 final size:29
Alignment explanation
Indices: 19315305--19315467 Score: 145
Period size: 29 Copynumber: 5.7 Consensus size: 29
19315295 TATTGCCCCC
* *
19315305 AAAAATTATATTTTGACCCCCAAACTTCT
1 AAAAATTACATTTTGACCCTCAAACTTCT
* *
19315334 CCAAAATTACATTTTGACCCTAAAACTTCT
1 -AAAAATTACATTTTGACCCTCAAACTTCT
* * *
19315364 AAAAATTACATTTTTACCCTCGAACTTCC
1 AAAAATTACATTTTGACCCTCAAACTTCT
* * * *
19315393 AAATATTACATTTTGA-CCTCGAAGTTCC
1 AAAAATTACATTTTGACCCTCAAACTTCT
**
19315421 AAAAATTTTATTTTTGACCC-CAAAC-TCT
1 AAAAATTACA-TTTTGACCCTCAAACTTCT
*
19315449 CAAAATTACCATTTT-ACCC
1 AAAAATTA-CATTTTGACCC
19315468 CCGAATGTCC
Statistics
Matches: 109, Mismatches: 21, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
27 4 0.04
28 30 0.28
29 48 0.44
30 27 0.25
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCTCAAACTTCT
Found at i:19315479 original size:57 final size:58
Alignment explanation
Indices: 19315303--19315483 Score: 180
Period size: 57 Copynumber: 3.1 Consensus size: 58
19315293 TTTATTGCCC
**
19315303 CCAAAAATTATA-TTTTGACCCCCAAACTTCTCCAAAATTACATTTTGACCCTAAAACT-T
1 CCAAAAATTATATTTTTGA-CCCCAAAC-TCTCCAAAATTACATTTTGACCCTCGAA-TGT
* * *
19315362 CTAAAAATTACATTTTT-ACCCTCGAACT-TCCAAATATTACATTTTGA-CCTCGAA-GTT
1 CCAAAAATTATATTTTTGACCC-CAAACTCTCCAAA-ATTACATTTTGACCCTCGAATG-T
* *
19315419 CCAAAAATTTTATTTTTGACCCCAAACTCT-CAAAATTACCATTTT-ACCCCCGAATGT
1 CCAAAAATTATATTTTTGACCCCAAACTCTCCAAAATTA-CATTTTGACCCTCGAATGT
19315476 CCAAAAAT
1 CCAAAAAT
19315484 CCCATTTTTG
Statistics
Matches: 102, Mismatches: 10, Indels: 22
0.76 0.07 0.16
Matches are distributed among these distances:
56 5 0.05
57 56 0.55
58 22 0.22
59 15 0.15
60 4 0.04
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (58 bp):
CCAAAAATTATATTTTTGACCCCAAACTCTCCAAAATTACATTTTGACCCTCGAATGT
Found at i:19315602 original size:28 final size:28
Alignment explanation
Indices: 19315568--19315627 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
19315558 AATTTTTCCT
19315568 AAAATTACCATTTTACCCTCGAAAATCC
1 AAAATTACCATTTTACCCTCGAAAATCC
* * *
19315596 AAAATTACCATTTTACTCTCGGACATCC
1 AAAATTACCATTTTACCCTCGAAAATCC
19315624 AAAA
1 AAAA
19315628 GGTCTCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.27, G:0.05, T:0.28
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTCGAAAATCC
Found at i:19315625 original size:146 final size:146
Alignment explanation
Indices: 19315449--19315760 Score: 371
Period size: 146 Copynumber: 2.1 Consensus size: 146
19315439 CCCAAACTCT
** *
19315449 CAAAATTACCATTTTACCCCCGAATGTCCAAAA-ATCCCATTTTTGATCAC-AATTTTTCTAAAA
1 CAAAATTACCATTTTACCCCCGAACATCCAAAAGATCCCATTTTTGATC-CTAATTCTTCTAAAA
* * * * *
19315512 ATTACCGTTTTACCCT-TGA-TTGTCTAAAATGTCATTGATAACCCTAAATTTTTCCTAAAATTA
65 ATTACCATTTTACCCTCAGACAT-T-TAAAATATCATTGATAACCCTAAA-TTTTCCCAAAATTA
19315575 CCATTTTACCCTCGAAAATC
127 CCATTTTACCCTCGAAAATC
* * * * * * *
19315595 CAAAATTACCATTTTACTCTCGGACATCCAAAAGGTCTCATTTTTTATCCTGATTCTTCTAAAAA
1 CAAAATTACCATTTTACCCCCGAACATCCAAAAGATCCCATTTTTGATCCTAATTCTTCTAAAAA
**
19315660 TTACCATTTTACCCTCAGACATTTAAAATATCATTTCTAACCCTAAATTTTCCCAAAATTACCAT
66 TTACCATTTTACCCTCAGACATTTAAAATATCATTGATAACCCTAAATTTTCCCAAAATTACCAT
* * *
19315725 TTTTCCCTCGAGAGTC
131 TTTACCCTCGAAAATC
*
19315741 TAAAATTACCATTTTACCCC
1 CAAAATTACCATTTTACCCC
19315761 GGGTATTCAA
Statistics
Matches: 139, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
146 76 0.55
147 59 0.42
148 3 0.02
149 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.37
Consensus pattern (146 bp):
CAAAATTACCATTTTACCCCCGAACATCCAAAAGATCCCATTTTTGATCCTAATTCTTCTAAAAA
TTACCATTTTACCCTCAGACATTTAAAATATCATTGATAACCCTAAATTTTCCCAAAATTACCAT
TTTACCCTCGAAAATC
Found at i:19328319 original size:92 final size:92
Alignment explanation
Indices: 19327895--19328910 Score: 1574
Period size: 92 Copynumber: 11.0 Consensus size: 92
19327885 AGATCAAAAT
*
19327895 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTAAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
*
19327960 TTGTAGTAAGAGCAAGATAAAGC-TCCA
66 TTGTAGTAAGAGCAAGATGAAGCAT-CA
* * *
19327987 AACATTAATTCTTATCCTTTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
* * *
19328052 AAGTATAGTAAGAGCAAGATAAAGCATCA
66 --TTGTAGTAAGAGCAAGATGAAGCATCA
*
19328081 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGTAAGTCTTTATCTCTCTATAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTC--T-G
*
19328146 TAGTGTAGTAGTAAGAGCAAGATGAAGC-TCCA
63 AAGT-T-GTAGTAAGAGCAAGATGAAGCAT-CA
* *
19328178 AACATCAAATCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGAAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
* * * * **
19328243 TTGTACTAAGAGTAAGGTAAAGTTTCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
19328270 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
19328335 TTGTAGTAAGAGCAAGATGAAGC-TCCA
66 TTGTAGTAAGAGCAAGATGAAGCAT-CA
19328362 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
* *
19328427 TTGTACTAAGAGTAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* *
19328454 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGTAAGTCTTTATCTCTCTAAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
* *
19328519 TTGTAGTAAAAGCAAAATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* * *
19328546 AACATCAATTCCTGTCCTCTTGAAGCTCTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
*
19328611 TTGTAGTAAGAGTAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* *
19328638 AACATCAATTCCTATCCTCTTGAAGCTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCAGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
19328703 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
19328730 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTC-TTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
* *
19328794 TTGTAGTAAGAACAAGATGAAGCTTCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* *
19328821 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAATTGGATAGC-AGATTTTTATCTCTCTCTG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAG-TCTTTA--TCTCTCTG
19328885 AAGTTGTAGTAAGAGCAAGATGAAGC
63 AAGTTGTAGTAAGAGCAAGATGAAGC
19328911 CTCGACATCA
Statistics
Matches: 852, Mismatches: 56, Indels: 30
0.91 0.06 0.03
Matches are distributed among these distances:
90 2 0.00
91 84 0.10
92 560 0.66
93 3 0.00
94 116 0.14
95 2 0.00
96 3 0.00
97 82 0.10
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (92 bp):
AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
TTGTAGTAAGAGCAAGATGAAGCATCA
Found at i:19329234 original size:17 final size:17
Alignment explanation
Indices: 19329193--19329293 Score: 62
Period size: 17 Copynumber: 5.5 Consensus size: 17
19329183 TTTAAAATGG
* *
19329193 AATTTAGATTTATTTCTA
1 AATTTAAATTTACTT-TA
*
19329211 AAATTAAATTTACTTTA
1 AATTTAAATTTACTTTA
19329228 AATTTAAATTTAAATTCATTTTTA
1 AATTTAAATTT--A--C---TTTA
*
19329252 AATTTAAATTTAGTTTA
1 AATTTAAATTTACTTTA
19329269 AATTTGAAATATT--TTTA
1 AATTT-AAAT-TTACTTTA
19329286 AATTTAAA
1 AATTTAAA
19329294 ACTAAAAGCC
Statistics
Matches: 69, Mismatches: 5, Indels: 20
0.73 0.05 0.21
Matches are distributed among these distances:
16 3 0.04
17 30 0.43
18 16 0.23
19 3 0.04
21 1 0.01
22 1 0.01
24 15 0.22
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTACTTTA
Found at i:19329253 original size:18 final size:17
Alignment explanation
Indices: 19329230--19329293 Score: 78
Period size: 17 Copynumber: 3.7 Consensus size: 17
19329220 TTACTTTAAA
19329230 TTTAAATTTAAATTCATT
1 TTTAAATTTAAATT-ATT
*
19329248 TTTAAATTTAAATT-TAG
1 TTTAAATTTAAATTAT-T
19329265 TTTAAATTTGAAA-TATT
1 TTTAAATTT-AAATTATT
19329282 TTTAAATTTAAA
1 TTTAAATTTAAA
19329294 ACTAAAAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
16 4 0.10
17 19 0.46
18 18 0.44
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAAATTATT
Found at i:19329253 original size:35 final size:33
Alignment explanation
Indices: 19329214--19329292 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 33
19329204 ATTTCTAAAA
*
19329214 TTAAATTTACTTTAAATTTAAATTT-AAATTCATTT
1 TTAAATTTAATTT-AATTTAAATTTGAAA-T-ATTT
*
19329249 TTAAATTTAAATTTAGTTTAAATTTGAAATATTT
1 TTAAATTT-AATTTAATTTAAATTTGAAATATTT
19329283 TTAAATTTAA
1 TTAAATTTAA
19329293 AACTAAAAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
33 2 0.05
34 12 0.30
35 19 0.47
36 7 0.17
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (33 bp):
TTAAATTTAATTTAATTTAAATTTGAAATATTT
Found at i:19329293 original size:6 final size:6
Alignment explanation
Indices: 19329169--19329278 Score: 64
Period size: 6 Copynumber: 18.5 Consensus size: 6
19329159 ACTTTGGGTT
* * * ** * * *
19329169 AATTTT AATTTA AGTTTA AAATGG AATTTA GATTT- ATTTCTA AAATTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATT-TA AATTTA
* * **
19329217 AATTT- ACTTTA AATTTA AATTTA AATTCA TTTTTA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
19329263 AGTTTA AATTTGA AAT
1 AATTTA AATTT-A AAT
19329279 ATTTTTAAAT
Statistics
Matches: 74, Mismatches: 25, Indels: 9
0.69 0.23 0.08
Matches are distributed among these distances:
5 10 0.14
6 58 0.78
7 6 0.08
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:19331315 original size:29 final size:29
Alignment explanation
Indices: 19331229--19331407 Score: 139
Period size: 29 Copynumber: 6.1 Consensus size: 29
19331219 CTCTGAAGGT
* * * *
19331229 CCCTAAACTGTCTAAAAATTATATTTTGAC
1 CCCTAAACT-TCCAAAAATTACATTTTTAA
* * *
19331259 CCCTGAACTTCTCCAAAATTATATTTTTAA
1 CCCTAAACTTC-CAAAAATTACATTTTTAA
*
19331289 CCCTAAACTTTCAAAAATTACATTTTT-A
1 CCCTAAACTTCCAAAAATTACATTTTTAA
* * *
19331317 CCCTCGAACTTCCAAACATTACATTTTT-G
1 CCCT-AAACTTCCAAAAATTACATTTTTAA
* * * *
19331346 CTCCCAAACTTCCAAAAGTTTCA-TTTTAG
1 C-CCTAAACTTCCAAAAATTACATTTTTAA
* *
19331375 CCCTTGAACTTCCAAAAATTTCATTTTTAA
1 CCC-TAAACTTCCAAAAATTACATTTTTAA
19331405 CCC
1 CCC
19331408 CAAAACTCAC
Statistics
Matches: 121, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
28 11 0.09
29 69 0.57
30 41 0.34
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTAA
Found at i:19331410 original size:58 final size:58
Alignment explanation
Indices: 19331233--19331411 Score: 175
Period size: 58 Copynumber: 3.1 Consensus size: 58
19331223 GAAGGTCCCT
* * * * * *
19331233 AAACTGTCTAAAAATTATATTTTGACCCCTGAACTTCTCCAAAATTAT-ATTTTTAACCCT
1 AAACT-TCCAAAAATTACATTTTTACCCTTGAACTTC-CAAAAATT-TCATTTTTAACCCC
* * * * *
19331293 AAACTTTCAAAAATTACATTTTTACCCTCGAACTTCCAAACATTACATTTTT-GCTCCC
1 AAACTTCCAAAAATTACATTTTTACCCTTGAACTTCCAAAAATTTCATTTTTAAC-CCC
* *
19331351 AAACTTCCAAAAGTTTCA-TTTTAGCCCTTGAACTTCCAAAAATTTCATTTTTAACCCC
1 AAACTTCCAAAAATTACATTTTTA-CCCTTGAACTTCCAAAAATTTCATTTTTAACCCC
19331409 AAA
1 AAA
19331412 ACTCACGAAA
Statistics
Matches: 97, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
57 6 0.06
58 60 0.62
59 26 0.27
60 5 0.05
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (58 bp):
AAACTTCCAAAAATTACATTTTTACCCTTGAACTTCCAAAAATTTCATTTTTAACCCC
Found at i:19331717 original size:145 final size:147
Alignment explanation
Indices: 19331456--19331726 Score: 404
Period size: 146 Copynumber: 1.9 Consensus size: 147
19331446 AAAAATCCCA
* ** **
19331456 TTTTTATCACGATTTTTCTAACAATTATCGTTTTACCCTCGATTATCTAAAATGTCATTTCTAAC
1 TTTTTATCACGATTTTTCTAAAAATTATCCATTTACCCTCGAACATCTAAAATGTCATTTCTAAC
*
19331521 CTTAAATTTTTCCTAAAATTACCATTTTGCCATCGAAAGTCTATAATTACCATTTTACCCCCGAA
66 CTTAAATTTTTCCTAAAATTACCATTTTGCCATCGAAAGTCTAAAATTACCATTTTACCCCCGAA
19331586 CATCCAAAAGGTTTCAT
131 CATCCAAAAGGTTTCAT
* *
19331603 TTTTTATCCCGATTCTTTC-AAAAATTA-CCATTTACCCTCGAACATTTAAAATGTCATTTCTAA
1 TTTTTATCACGATT-TTTCTAAAAATTATCCATTTACCCTCGAACATCTAAAATGTCATTTCTAA
* * * *
19331666 CCTTAAATTTTTCC-AAAATTACCATTTTGCCCTTGAGAGTTTAAAATTACCATTTTACCCC
65 CCTTAAATTTTTCCTAAAATTACCATTTTGCCATCGAAAGTCTAAAATTACCATTTTACCCC
19331727 ATGTATCCAA
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
145 42 0.38
146 45 0.41
147 20 0.18
148 4 0.04
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (147 bp):
TTTTTATCACGATTTTTCTAAAAATTATCCATTTACCCTCGAACATCTAAAATGTCATTTCTAAC
CTTAAATTTTTCCTAAAATTACCATTTTGCCATCGAAAGTCTAAAATTACCATTTTACCCCCGAA
CATCCAAAAGGTTTCAT
Found at i:19335296 original size:29 final size:29
Alignment explanation
Indices: 19335243--19335315 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
19335233 CCCGAAAAGC
*
19335243 AAAATGGTAATTTT-GGACTCTTGGGGGCA
1 AAAATGG-AATTTTGGGAATCTTGGGGGCA
**
19335272 AAAATGGAATTTTGGGAAATC-TGGGGTTA
1 AAAATGGAATTTTGGG-AATCTTGGGGGCA
19335301 AAAAT-GATATTTTGG
1 AAAATGGA-ATTTTGG
19335316 ATATCCAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.21
29 27 0.71
30 3 0.08
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTGGGAATCTTGGGGGCA
Found at i:19335419 original size:29 final size:28
Alignment explanation
Indices: 19335369--19335457 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
19335359 AAAATAGAGT
* *
19335369 TTTTGGACA-TTTGGGGGTAAAATGGTAA
1 TTTTGGAAAGTTTCGGGGTAAAAT-GTAA
*
19335397 TTTT-GAAAGTTTCGGGGTCAAAAATGAAA
1 TTTTGGAAAGTTTCGGGGT--AAAATGTAA
* **
19335426 TTTTGGGAAGTTTTAGGGTAAAATGTAA
1 TTTTGGAAAGTTTCGGGGTAAAATGTAA
19335454 TTTT
1 TTTT
19335458 TAGATAGTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
27 3 0.06
28 24 0.48
29 7 0.14
30 16 0.32
ACGTcount: A:0.31, C:0.03, G:0.27, T:0.38
Consensus pattern (28 bp):
TTTTGGAAAGTTTCGGGGTAAAATGTAA
Found at i:19335466 original size:29 final size:27
Alignment explanation
Indices: 19335383--19335471 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 27
19335373 GGACATTTGG
**
19335383 GGGTAAAATGGTAA-TTTTGAAAGTTTCG
1 GGGTAAAAT-GTAATTTTTG-AAGTTTTA
* *
19335411 GGGTCAAAAATGAAATTTTGGGAAGTTTTA
1 GGGT--AAAATGTAATTTT-TGAAGTTTTA
19335441 GGGTAAAATGTAATTTTTAGATAG-TTTA
1 GGGTAAAATGTAATTTTT-GA-AGTTTTA
19335469 GGG
1 GGG
19335472 ACCTTTAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
28 25 0.51
29 5 0.10
30 18 0.37
31 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (27 bp):
GGGTAAAATGTAATTTTTGAAGTTTTA
Found at i:19336601 original size:19 final size:19
Alignment explanation
Indices: 19336577--19336630 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
19336567 ATTATTACTG
19336577 CATTTATTATTATTAAAAA
1 CATTTATTATTATTAAAAA
* *
19336596 CATTTATTATTGTTGAAAA
1 CATTTATTATTATTAAAAA
*
19336615 CGTTTATTATTATTAA
1 CATTTATTATTATTAA
19336631 TATTAATACT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (19 bp):
CATTTATTATTATTAAAAA
Found at i:19341978 original size:34 final size:34
Alignment explanation
Indices: 19341931--19342033 Score: 136
Period size: 34 Copynumber: 3.0 Consensus size: 34
19341921 AGAATATGAA
*
19341931 AAGTTAAGAAAGATGGAAGGTTAAAAATCAATGG
1 AAGTTAAGAAAGATGGAAGGTTAAAAATCAAAGG
* **
19341965 AGGTTAA-AGAAGATGGAAGGTTAAAGGTCAAAGG
1 AAGTTAAGA-AAGATGGAAGGTTAAAAATCAAAGG
*
19341999 AAGTTAAGAAAGATGGAAGGTTAAAAGATGAAAGG
1 AAGTTAAGAAAGATGGAAGGTTAAAA-ATCAAAGG
19342034 TTGAATATCC
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
33 1 0.02
34 50 0.86
35 7 0.12
ACGTcount: A:0.49, C:0.02, G:0.31, T:0.18
Consensus pattern (34 bp):
AAGTTAAGAAAGATGGAAGGTTAAAAATCAAAGG
Found at i:19341985 original size:17 final size:17
Alignment explanation
Indices: 19341940--19342035 Score: 64
Period size: 17 Copynumber: 5.8 Consensus size: 17
19341930 AAAGTTAAGA
19341940 AAGATGGAAGGTTAAA-
1 AAGATGGAAGGTTAAAG
*
19341956 AATCAATGG-AGGTTAAAG
1 AA--GATGGAAGGTTAAAG
19341974 AAGATGGAAGGTTAAAGG
1 AAGATGGAAGGTTAAA-G
19341992 TCAA-A-GGAA-GTT-AAG
1 --AAGATGGAAGGTTAAAG
19342007 AAAGATGGAAGGTT-AA-
1 -AAGATGGAAGGTTAAAG
*
19342023 AAGATGAAAGGTT
1 AAGATGGAAGGTT
19342036 GAATATCCAT
Statistics
Matches: 66, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
14 2 0.03
15 14 0.21
16 12 0.18
17 24 0.36
18 11 0.17
19 1 0.02
20 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.31, T:0.20
Consensus pattern (17 bp):
AAGATGGAAGGTTAAAG
Found at i:19342890 original size:20 final size:20
Alignment explanation
Indices: 19342861--19342917 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 20
19342851 TTGTAAAAAT
19342861 AATA-TTTTATAAGATAATA
1 AATATTTTTATAAGATAATA
19342880 AATATTTTTAT-A-A-AATA
1 AATATTTTTATAAGATAATA
* *
19342897 AATTTTTTTACAAGATAATA
1 AATATTTTTATAAGATAATA
19342917 A
1 A
19342918 TTTACATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 13 0.41
18 2 0.06
19 6 0.19
20 11 0.34
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
AATATTTTTATAAGATAATA
Found at i:19346113 original size:24 final size:24
Alignment explanation
Indices: 19346081--19346135 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
19346071 AAACTTCAAG
19346081 TTTGCATTTATGTTTTATGGTAAA
1 TTTGCATTTATGTTTTATGGTAAA
19346105 TTTGCATTTATGTTTTATGGTAAA
1 TTTGCATTTATGTTTTATGGTAAA
19346129 TTTGCAT
1 TTTGCAT
19346136 CAATGGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (24 bp):
TTTGCATTTATGTTTTATGGTAAA
Found at i:19352725 original size:82 final size:80
Alignment explanation
Indices: 19352596--19352867 Score: 293
Period size: 84 Copynumber: 3.3 Consensus size: 80
19352586 CATAGTTCCG
* * * *
19352596 TCAATTCATGGCACCTAGTGCCTAGTGGATAAACCGCAATAAGTGAGCCCACCTCAAGTTGGATT
1 TCAATTCCTGGCACCTAGTGCCTAGCGGATAAACCG--ATAAGTGAGCCCAACTCTAGTTGGATT
19352661 AACCAACGGTAGTTTCA
64 AACCAACGGTAGTTTCA
*
19352678 TCAATTCCTGGCACCTAGTGCCTAGCGGATAAATCACGATAAGTGAGCCCAGAGTTCTAGTTGGA
1 TCAATTCCTGGCACCTAGTGCCTAGCGGATAAA-C-CGATAAGTGAGCCCA-A-CTCTAGTTGGA
19352743 TTAACCAA-GGATAGTTTCA
62 TTAACCAACGG-TAGTTTCA
* * * **
19352762 TCAATT-CTAGGCACCCAGTGCCTAGAGGATAAACCGTAATAAGTGAGCACAACTCTAGTTAAAT
1 TCAATTCCT-GGCACCTAGTGCCTAGCGGATAAACCG--ATAAGTGAGCCCAACTCTAGTTGGAT
* * *
19352826 TAACCAAC--AAATCT-A
63 TAACCAACGGTAGTTTCA
*
19352841 TCAATTCCTGGCACGTAGTGCCTAGCG
1 TCAATTCCTGGCACCTAGTGCCTAGCG
19352868 ATCAATTCCT
Statistics
Matches: 163, Mismatches: 17, Indels: 23
0.80 0.08 0.11
Matches are distributed among these distances:
79 22 0.13
80 5 0.03
82 62 0.38
83 7 0.04
84 67 0.41
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (80 bp):
TCAATTCCTGGCACCTAGTGCCTAGCGGATAAACCGATAAGTGAGCCCAACTCTAGTTGGATTAA
CCAACGGTAGTTTCA
Found at i:19352782 original size:84 final size:83
Alignment explanation
Indices: 19352587--19352833 Score: 268
Period size: 82 Copynumber: 3.0 Consensus size: 83
19352577 TTGTCGTAAC
* * * *
19352587 ATAGTTCCGTCAATTC-ATGGCACCTAGTGCCTAGTGGATAAACCGCAATAAGTGAGCCCACCTC
1 ATAGTTTCATCAATTCTA-GGCACCTAGTGCCTAGAGGATAAACCACAATAAGTGAGCCCACCTC
19352651 AAGTTGGATTAACCAACGG
65 AAGTTGGATTAACCAACGG
* * * **
19352670 -TAGTTTCATCAATTCCT-GGCACCTAGTGCCTAGCGGATAAATCACGATAAGTGAGCCCAGAGT
1 ATAGTTTCATCAATT-CTAGGCACCTAGTGCCTAGAGGATAAACCACAATAAGTGAGCCC--ACC
*
19352733 TCTAGTTGGATTAACCAA-GG
63 TCAAGTTGGATTAACCAACGG
* ** * * *
19352753 ATAGTTTCATCAATTCTAGGCACCCAGTGCCTAGAGGATAAACCGTAATAAGTGAGCACAACTCT
1 ATAGTTTCATCAATTCTAGGCACCTAGTGCCTAGAGGATAAACCACAATAAGTGAGCCCACCTCA
**
19352818 AGTTAAATTAACCAAC
66 AGTTGGATTAACCAAC
19352834 AAATCTATCA
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
82 66 0.48
83 5 0.04
84 66 0.48
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (83 bp):
ATAGTTTCATCAATTCTAGGCACCTAGTGCCTAGAGGATAAACCACAATAAGTGAGCCCACCTCA
AGTTGGATTAACCAACGG
Found at i:19352880 original size:28 final size:28
Alignment explanation
Indices: 19352840--19352895 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
19352830 CAACAAATCT
*
19352840 ATCAATTCCTGGCACGTAGTGCCTAGCG
1 ATCAATTCCTGGCACCTAGTGCCTAGCG
19352868 ATCAATTCCTGGCACCTAGTGCCTAGCG
1 ATCAATTCCTGGCACCTAGTGCCTAGCG
19352896 GATAAACTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.25
Consensus pattern (28 bp):
ATCAATTCCTGGCACCTAGTGCCTAGCG
Found at i:19360554 original size:82 final size:82
Alignment explanation
Indices: 19360413--19360707 Score: 284
Period size: 82 Copynumber: 3.6 Consensus size: 82
19360403 AGCCGAATTC
* * * *
19360413 CGTCAATTCATGGCACCTAGTGCCTAGC-AAGTAAACCGCAATAAGTGAGCCCAGCTCTAGTTGG
1 CGTCAATTCTTAGCACCTAGTGCCAAGCGGA-TAAACCGCAATAAGTGAGCCCAGCTCTAGTTGG
*
19360477 ATTAATCAATCG-TTGTTT
65 ATTAATCAA-CGATAGTTT
* * * *
19360495 CGTCAATT-TCTAGCA-CTCATTGCCAAGTGGATAAACTGCAATAAGTGAGCCCAGTTCTAGTTG
1 CGTCAATTCT-TAGCACCT-AGTGCCAAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTG
19360558 GATTAATCAACGATAGTTT
64 GATTAATCAACGATAGTTT
* * * *
19360577 CGTCAATTCTTGGCACCTAGTGCCTAGCGGATAAACCGTAATAAGTGAGCCCTA-CTCTAGTTAG
1 CGTCAATTCTTAGCACCTAGTGCCAAGCGGATAAACCGCAATAAGTGAGCCC-AGCTCTAGTTGG
* * *
19360641 ATTAACCAAC-A-A-ATC
65 ATTAATCAACGATAGTTT
* * * * **
19360656 CATCAATTCTTGGCACCTAGTGCCTAGTGGATAAATTGCAA-AAGTGAGCCCA
1 CGTCAATTCTTAGCACCTAGTGCCAAGCGGATAAACCGCAATAAGTGAGCCCA
19360708 ACTTTAGTCA
Statistics
Matches: 181, Mismatches: 25, Indels: 19
0.80 0.11 0.08
Matches are distributed among these distances:
77 1 0.01
78 10 0.06
79 37 0.20
80 1 0.01
81 5 0.03
82 122 0.67
83 5 0.03
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (82 bp):
CGTCAATTCTTAGCACCTAGTGCCAAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGA
TTAATCAACGATAGTTT
Found at i:19367432 original size:32 final size:32
Alignment explanation
Indices: 19367395--19367459 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
19367385 TTCAACGGGT
*
19367395 AAGAAAAGGTCAATTGAAAGGTATGTATAAAA
1 AAGAAAAGGTCAATGGAAAGGTATGTATAAAA
*
19367427 AAGAAAAGGTCAATGGAATGGTATGTATAAAA
1 AAGAAAAGGTCAATGGAAAGGTATGTATAAAA
19367459 A
1 A
19367460 CTTAATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.22
Consensus pattern (32 bp):
AAGAAAAGGTCAATGGAAAGGTATGTATAAAA
Found at i:19372647 original size:36 final size:36
Alignment explanation
Indices: 19372597--19372666 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
19372587 AATAGGAAAT
*
19372597 CTACTCCTAGTCGCCCTCTACT-TCTTATAATATAAA
1 CTACTCATAGTCGCCCTCTACTCTC-TATAATATAAA
*
19372633 CTACTCATATTCGCCCTCTACTCTCTATAATATA
1 CTACTCATAGTCGCCCTCTACTCTCTATAATATA
19372667 GAAAACTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 29 0.94
37 2 0.06
ACGTcount: A:0.27, C:0.31, G:0.04, T:0.37
Consensus pattern (36 bp):
CTACTCATAGTCGCCCTCTACTCTCTATAATATAAA
Found at i:19377472 original size:21 final size:21
Alignment explanation
Indices: 19377441--19377494 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
19377431 GGAGTTTTTA
* *
19377441 GTATTGGTAGAAG-CATGACTT
1 GTATCGGTAGAAGTCA-CACTT
*
19377462 GTTTCGGTAGAAGTCACACTT
1 GTATCGGTAGAAGTCACACTT
19377483 GTATCGGTAGAA
1 GTATCGGTAGAA
19377495 CTATCTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCACACTT
Found at i:19390704 original size:33 final size:32
Alignment explanation
Indices: 19390660--19390722 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
19390650 TAGATTGCTC
* *
19390660 CCCTTTAATAAAAGA-CATTTTGAATTTAAGCT
1 CCCTTTAATAAAA-ATCATCTTCAATTTAAGCT
19390692 CCCTTTATATAAAAATCATCTTCAATTTAAG
1 CCCTTTA-ATAAAAATCATCTTCAATTTAAG
19390723 GCATAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 8 0.30
33 19 0.70
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (32 bp):
CCCTTTAATAAAAATCATCTTCAATTTAAGCT
Found at i:19391952 original size:23 final size:22
Alignment explanation
Indices: 19391926--19391969 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
19391916 AAAATATTTC
*
19391926 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
19391949 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
19391970 TTATTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:19395246 original size:20 final size:21
Alignment explanation
Indices: 19395217--19395268 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
19395207 TTGAAGCTGT
*
19395217 GGTATAGATACCTGAT-AAAA
1 GGTATCGATACCTGATGAAAA
* **
19395237 GGTATCGATACTTTTTGAAAA
1 GGTATCGATACCTGATGAAAA
19395258 GGTATCGATAC
1 GGTATCGATAC
19395269 TTTTTGTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (21 bp):
GGTATCGATACCTGATGAAAA
Found at i:19395259 original size:21 final size:21
Alignment explanation
Indices: 19395233--19395274 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
19395223 GATACCTGAT
19395233 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
19395254 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
19395275 TCATTGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (21 bp):
AAAAGGTATCGATACTTTTTG
Found at i:19396704 original size:28 final size:27
Alignment explanation
Indices: 19396647--19396705 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
19396637 AGAGATAACA
*
19396647 AATAAATAAAATACAAAAAAATCAATG
1 AATAAATAAAATACAAAAAAAGCAATG
19396674 AATAAATAAAA-ATCAAATAAAAGGCAA-G
1 AATAAATAAAATA-CAAA-AAAA-GCAATG
19396702 AATA
1 AATA
19396706 TAAATGGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 1 0.04
27 15 0.54
28 9 0.32
29 3 0.11
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (27 bp):
AATAAATAAAATACAAAAAAAGCAATG
Found at i:19396729 original size:7 final size:7
Alignment explanation
Indices: 19396714--19396784 Score: 58
Period size: 7 Copynumber: 9.9 Consensus size: 7
19396704 TATAAATGGC
19396714 ATAAAAA
1 ATAAAAA
*
19396721 ATAACAA
1 ATAAAAA
19396728 ATAAATAA
1 ATAAA-AA
19396736 ATATAAAA
1 ATA-AAAA
*
19396744 ATAATAA
1 ATAAAAA
19396751 AT---AA
1 ATAAAAA
19396755 ATAAAATA
1 ATAAAA-A
19396763 ATACAAATA
1 ATA-AAA-A
19396772 ATAAAAA
1 ATAAAAA
19396779 ATAAAA
1 ATAAAA
19396785 GGGACTAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
4 4 0.07
7 23 0.43
8 17 0.31
9 10 0.19
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (7 bp):
ATAAAAA
Found at i:19396735 original size:4 final size:4
Alignment explanation
Indices: 19396714--19396783 Score: 53
Period size: 4 Copynumber: 18.2 Consensus size: 4
19396704 TATAAATGGC
*
19396714 ATAA A-AA AT-A ACAA ATAA ATAA ATATA A-AA AT-A ATAA ATAA ATAAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA ATAA ATAA AT-AA
*
19396760 ATAA TACAA AT-A ATAA A-AA ATAA A
1 ATAA -ATAA ATAA ATAA ATAA ATAA A
19396784 AGGGACTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
3 16 0.30
4 28 0.53
5 9 0.17
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:19396743 original size:23 final size:24
Alignment explanation
Indices: 19396717--19396783 Score: 93
Period size: 23 Copynumber: 2.8 Consensus size: 24
19396707 AAATGGCATA
*
19396717 AAAAATAACAAATAAATAAAT-AT
1 AAAAATAATAAATAAATAAATAAT
19396740 AAAAATAATAAATAAATAAAATAAT
1 AAAAATAATAAATAAAT-AAATAAT
*
19396765 ACAAATAATAAA-AAATAAA
1 AAAAATAATAAATAAATAAA
19396784 AGGGACTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.47
24 8 0.20
25 13 0.32
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (24 bp):
AAAAATAATAAATAAATAAATAAT
Found at i:19396751 original size:19 final size:18
Alignment explanation
Indices: 19396727--19396782 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
19396717 AAAAATAACA
19396727 AATAAATAAATATAAAAAT
1 AATAAATAAATA-AAAAAT
19396746 AATAAATAAATAAAATAAT
1 AATAAATAAATAAAA-AAT
*
19396765 -ACAAAT-AATAAAAAAT
1 AATAAATAAATAAAAAAT
19396781 AA
1 AA
19396783 AAGGGACTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
16 3 0.09
17 8 0.24
18 8 0.24
19 15 0.44
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AATAAATAAATAAAAAAT
Found at i:19396774 original size:28 final size:27
Alignment explanation
Indices: 19396726--19396783 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
19396716 AAAAAATAAC
* *
19396726 AAATAAATAAATATAAAAATAATAAAT
1 AAATAAATAAATACAAAAATAAAAAAT
19396753 AAATAAA-ATAATACAAATAATAAAAAAT
1 AAATAAATA-AATACAAA-AATAAAAAAT
19396781 AAA
1 AAA
19396784 AGGGACTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 1 0.04
27 14 0.52
28 12 0.44
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (27 bp):
AAATAAATAAATACAAAAATAAAAAAT
Found at i:19396909 original size:30 final size:30
Alignment explanation
Indices: 19396875--19396933 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
19396865 AGGACTAAAT
* *
19396875 TAAAAAT-GAAAATATATTAAAAGTACAAAC
1 TAAAAATAG-AAATAAAATAAAAGTACAAAC
*
19396905 TAAAAATAGAAATAAAATAAAATTACAAA
1 TAAAAATAGAAATAAAATAAAAGTACAAA
19396934 GACCAAAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (30 bp):
TAAAAATAGAAATAAAATAAAAGTACAAAC
Found at i:19397058 original size:30 final size:31
Alignment explanation
Indices: 19397024--19397092 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
19397014 TAAAGCAATT
* *
19397024 AAAATTAAAA-GACGAAATAAAAATAAATAA
1 AAAATGAAAAGGACGAAATAAAAACAAATAA
* * *
19397054 AAAATGAAAAGGACTAAATTAAAACAAATTA
1 AAAATGAAAAGGACGAAATAAAAACAAATAA
19397085 AAAATGAA
1 AAAATGAA
19397093 GATCCCAGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 9 0.27
31 24 0.73
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (31 bp):
AAAATGAAAAGGACGAAATAAAAACAAATAA
Found at i:19398327 original size:18 final size:19
Alignment explanation
Indices: 19398276--19398328 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
19398266 TTTATATTGT
19398276 GAACC-ATGTTAATTTGGC
1 GAACCTATGTTAATTTGGC
* * *
19398294 GAA-TTATATTATTTTGG-
1 GAACCTATGTTAATTTGGC
19398311 GAACCTATGTTAATTTGG
1 GAACCTATGTTAATTTGG
19398329 TGATATATAC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (19 bp):
GAACCTATGTTAATTTGGC
Found at i:19401171 original size:32 final size:32
Alignment explanation
Indices: 19401135--19401223 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 32
19401125 GTTTTGATAT
19401135 ATATATATATATATATATGGGTTATG-TTATAC
1 ATATATATATATATATATGGGTT-TGATTATAC
** * *
19401167 ATATA-ATATATATGCATGGGTCTTGATTGTAT
1 ATATATATATATATATATGGGT-TTGATTATAC
*
19401199 ATATAATATATATGTATATGGGTTT
1 ATAT-ATATATATATATATGGGTTT
19401224 TGTAATGTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
31 16 0.35
32 14 0.30
33 3 0.07
34 13 0.28
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (32 bp):
ATATATATATATATATATGGGTTTGATTATAC
Found at i:19401172 original size:67 final size:66
Alignment explanation
Indices: 19401089--19401222 Score: 173
Period size: 67 Copynumber: 2.0 Consensus size: 66
19401079 ACTAAAAAGG
* * *
19401089 TATGTGTATATATATAATATATATACATGTGTGCGTG-TTTTGATATATATATATATATATATAT
1 TATGTGTATACATATAATATATATACATGGGT-CGTGATTGT-ATATATA-ATATATATATATAT
19401153 GGGT
63 GGGT
* * *
19401157 TATGT-TATACATATAATATATATGCATGGGTCTTGATTGTATATATAATATATATGTATATGGG
1 TATGTGTATACATATAATATATATACATGGGTCGTGATTGTATATATAATATATATATATATGGG
19401221 T
66 T
19401222 T
1 T
19401223 TTGTAATGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
65 18 0.31
66 10 0.17
67 26 0.44
68 5 0.08
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (66 bp):
TATGTGTATACATATAATATATATACATGGGTCGTGATTGTATATATAATATATATATATATGGG
T
Found at i:19403053 original size:276 final size:274
Alignment explanation
Indices: 19402562--19403103 Score: 1012
Period size: 276 Copynumber: 2.0 Consensus size: 274
19402552 CTCGGGATAA
19402562 TATGATTCTTCGATTTGATTCGATCTCCCATCTACCAAAACAAATCTATAAAACAAGGACAAGAC
1 TATGATTCTTCGATTTGATTCGATCTCCCATCTACCAAAACAAATCTATAAAACAAGGACAAGAC
*
19402627 ACGAGTAAGTTTACGAAAGCTTGTAAGTTCGTTCATTAATCAAATAATGAAATATAGAATCAGCC
66 ACGAGTAAGTTTACGAAAGCTTATAAGTTCGTTCATTAATCAAATAATGAAATATAGAATCAGCC
*
19402692 TTGTCAAACACAGCTCACAACGGTGAGTATTGCTATTACAAGTAACATGAATCAATTCTACATTT
131 TTGTCAAAAACAGCTCACAACGGTGAGTATTGCTATTACAAGTAACATGAATCAATTCTACATTT
*
19402757 CTATTAACTTTCAGAGATCATTTAAATAATGTCGATAAGCGATTAGTGGATGTGAGTACACAGTT
196 CTATTAACTTTCAGAGATCATTTAAATAATGTCGATAAGCGATTAGTGGATGTGAGTACACAATT
19402822 AACCATACAAGTAT
261 AACCATACAAGTAT
19402836 TATGATTCTTCGATTTGATTCGATCTCCCATCTACCAAAACAAAATCTATAAAACAAGGACAAGA
1 TATGATTCTTCGATTTGATTCGATCTCCCATCTACCAAAAC-AAATCTATAAAACAAGGACAAGA
19402901 CACGAGTAAGTTTACGAAAGCTTAATAAGTTCGTTCATTAATCAAATAATGAAATATAGAATCAG
65 CACGAGTAAGTTTACGAAAGCTT-ATAAGTTCGTTCATTAATCAAATAATGAAATATAGAATCAG
* *
19402966 TCTTGTCAAAAACAGCTCATAACGGTGAGTATTGCTATTACAAGTAACATGAATCAATTCTACAT
129 CCTTGTCAAAAACAGCTCACAACGGTGAGTATTGCTATTACAAGTAACATGAATCAATTCTACAT
*
19403031 TTCTATTAACTTTCAGAGATCATTTAAATAATGTCGATGAGCGATTAGTGGATGTGAGTACACAA
194 TTCTATTAACTTTCAGAGATCATTTAAATAATGTCGATAAGCGATTAGTGGATGTGAGTACACAA
19403096 TTAACCAT
259 TTAACCAT
19403104 CCAACACATC
Statistics
Matches: 260, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
274 41 0.16
275 46 0.18
276 173 0.67
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (274 bp):
TATGATTCTTCGATTTGATTCGATCTCCCATCTACCAAAACAAATCTATAAAACAAGGACAAGAC
ACGAGTAAGTTTACGAAAGCTTATAAGTTCGTTCATTAATCAAATAATGAAATATAGAATCAGCC
TTGTCAAAAACAGCTCACAACGGTGAGTATTGCTATTACAAGTAACATGAATCAATTCTACATTT
CTATTAACTTTCAGAGATCATTTAAATAATGTCGATAAGCGATTAGTGGATGTGAGTACACAATT
AACCATACAAGTAT
Found at i:19403174 original size:34 final size:32
Alignment explanation
Indices: 19403136--19403251 Score: 108
Period size: 34 Copynumber: 3.4 Consensus size: 32
19403126 GAGTCAATCA
19403136 ATCCAACACACCAAGCACTTGTAAGAGCTAGTCC
1 ATCCAACACACCAAG--CTTGTAAGAGCTAGTCC
*
19403170 ATCCAACACACCATATGCTCGTAAGAGCTAGTCC
1 ATCCAACACACCA-A-GCTTGTAAGAGCTAGTCC
* * * *
19403204 CTCCAACGCACC-AGGTGCTGATAAGAGCTAATCC
1 ATCCAACACACCAAGCT--TG-TAAGAGCTAGTCC
*
19403238 AACCAACACACCAA
1 ATCCAACACACCAA
19403252 ATACACTGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
31 2 0.03
32 1 0.01
33 1 0.01
34 60 0.90
35 2 0.03
36 1 0.01
ACGTcount: A:0.35, C:0.34, G:0.15, T:0.16
Consensus pattern (32 bp):
ATCCAACACACCAAGCTTGTAAGAGCTAGTCC
Found at i:19405178 original size:17 final size:17
Alignment explanation
Indices: 19405137--19405178 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
19405127 ATTATTATGC
*
19405137 ATGAACTATTATTTCAT
1 ATGAACTGTTATTTCAT
*
19405154 ATGAACTGTTATTTTAT
1 ATGAACTGTTATTTCAT
*
19405171 CTGAACTG
1 ATGAACTG
19405179 CATATTCTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
ATGAACTGTTATTTCAT
Found at i:19418522 original size:110 final size:110
Alignment explanation
Indices: 19418320--19418544 Score: 362
Period size: 110 Copynumber: 2.0 Consensus size: 110
19418310 TTAGTGATTT
*
19418320 GTTAATCTTTTTACAATAAATAATTTTATGAAAAAAGGCAAGAATAAATTCTAAGTGATAAGATA
1 GTTAATCTGTTTACAATAAATAATTTTATGAAAAAAGGCAAGAATAAATTC------ATAAGATA
*
19418385 GAAGTTTATATATTTATTTTTAATGCTTTTAAAGTTATTAATTAATTTATC
60 GAAGTTTATATATTTATTTTTAATGCTTTTAAAATTATTAATTAATTTATC
19418436 GTTAATCTGTTTACAATAAATAATTTTATGAAAAAAAGGCAAGAATAAATTC-TAAGATAGAAGT
1 GTTAATCTGTTTACAATAAATAATTTTATG-AAAAAAGGCAAGAATAAATTCATAAGATAGAAGT
19418500 TTATATATTTATTTTTAATGCTTTTAAAATTATTAATTAATTTAT
65 TTATATATTTATTTTTAATGCTTTTAAAATTATTAATTAATTTAT
19418545 TAATGATATG
Statistics
Matches: 106, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
110 56 0.53
116 29 0.27
117 21 0.20
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (110 bp):
GTTAATCTGTTTACAATAAATAATTTTATGAAAAAAGGCAAGAATAAATTCATAAGATAGAAGTT
TATATATTTATTTTTAATGCTTTTAAAATTATTAATTAATTTATC
Found at i:19428123 original size:158 final size:158
Alignment explanation
Indices: 19427830--19428152 Score: 452
Period size: 158 Copynumber: 2.0 Consensus size: 158
19427820 ATTTTGGGAT
* * * * *
19427830 TTACATGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGACTGAGATCTGACATTTGTTGCG
1 TTACATGTTATAAGGATGCTGGTATTAGATGTCCTACAGATGACTAAGATCTGACATTTGTTGCG
* *
19427895 GATTCTCCATAGCTCGTGTGAGCAACATCGTGTAGCTTAACATCTTGACCTACAGCTAGTGTGAG
66 GATTCTCCACAGCTCGTGTGAGCAACATCGTGTAGCTTAACATCTCGACCTACAGCTAGTGTGAG
19427960 CAGGCCCACTTCACAACTCGTGTAAGCA
131 CAGGCCCACTTCACAACTCGTGTAAGCA
* * *
19427988 TTACATGTTATAAGGATGCTGGTATTAGATGT-TTAACAGATGGCTAAGAT-TCGGCATTTGTTG
1 TTACATGTTATAAGGATGCTGGTATTAGATGTCCT-ACAGATGACTAAGATCT-GACATTTGTTG
* * *
19428051 CGGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTTAACATCTCGACCTGCAGCTCGTGTG
64 CGGATTCTCCACAGCTCGTGTGAGCAACATCGTGTAGCTTAACATCTCGACCTACAGCTAGTGTG
* * * *
19428116 AGTAGGCCCATTTCACAGCTCGTGTGAGCA
129 AGCAGGCCCACTTCACAACTCGTGTAAGCA
*
19428146 ATACATG
1 TTACATG
19428153 ATACAGGAAT
Statistics
Matches: 145, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
157 2 0.01
158 143 0.99
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (158 bp):
TTACATGTTATAAGGATGCTGGTATTAGATGTCCTACAGATGACTAAGATCTGACATTTGTTGCG
GATTCTCCACAGCTCGTGTGAGCAACATCGTGTAGCTTAACATCTCGACCTACAGCTAGTGTGAG
CAGGCCCACTTCACAACTCGTGTAAGCA
Found at i:19430137 original size:18 final size:18
Alignment explanation
Indices: 19430114--19430148 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19430104 AACAATGGTG
*
19430114 CTCCAAGGGCGGCAACAC
1 CTCCAAGGGCGACAACAC
*
19430132 CTCCAATGGCGACAACA
1 CTCCAAGGGCGACAACA
19430149 AAGAGATCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.37, G:0.23, T:0.09
Consensus pattern (18 bp):
CTCCAAGGGCGACAACAC
Found at i:19432897 original size:13 final size:15
Alignment explanation
Indices: 19432879--19432912 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19432869 TCTTTCTTCA
19432879 TTCTTTTC-TC-TTT
1 TTCTTTTCTTCTTTT
19432892 TTCTTTTCTTCTTTT
1 TTCTTTTCTTCTTTT
19432907 TTCTTT
1 TTCTTT
19432913 ATAGGTGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 2 0.11
15 9 0.47
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTCTTTTCTTCTTTT
Found at i:19445025 original size:24 final size:24
Alignment explanation
Indices: 19444973--19445027 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
19444963 TCTTTTAGTT
* *
19444973 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTAGTTGTTTCAATC
* * *
19444997 GAACTCTGTTTAGTTGTTTGAGTC
1 AAACTCTGTTTAGTTGTTTCAATC
19445021 AAACTCT
1 AAACTCT
19445028 TATTAGTCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.47
Consensus pattern (24 bp):
AAACTCTGTTTAGTTGTTTCAATC
Found at i:19446965 original size:24 final size:24
Alignment explanation
Indices: 19446937--19446999 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
19446927 AGAAATAATC
* *
19446937 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAGTTA
*
19446961 TTTCAATTAAACTCTGTTTAGTTA
1 TTTCAGTTAAACTCTGTTTAGTTA
* *
19446985 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
19447000 TATTAGTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAGTTA
Found at i:19447887 original size:22 final size:21
Alignment explanation
Indices: 19447862--19447909 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 21
19447852 AGTACGGAAT
19447862 ATAATTATATTG-TTTGATAAAA
1 ATAATTATATTGATTT--TAAAA
19447884 ATAA--ATATTGATTTTAAAA
1 ATAATTATATTGATTTTAAAA
19447903 ATAATTA
1 ATAATTA
19447910 ATTTTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 9 0.39
20 6 0.26
21 4 0.17
22 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (21 bp):
ATAATTATATTGATTTTAAAA
Found at i:19451536 original size:20 final size:21
Alignment explanation
Indices: 19451511--19451556 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
19451501 ATTTTCATTT
19451511 TGAAAAAAATCAAATTC-AAA
1 TGAAAAAAATCAAATTCAAAA
* * *
19451531 TGAAAATACTGAAATTCAAAA
1 TGAAAAAAATCAAATTCAAAA
19451552 TGAAA
1 TGAAA
19451557 TTGATGATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.22
Consensus pattern (21 bp):
TGAAAAAAATCAAATTCAAAA
Found at i:19451935 original size:2 final size:2
Alignment explanation
Indices: 19451928--19451971 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
19451918 ATTGAAATGA
19451928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19451970 AT
1 AT
19451972 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19458993 original size:48 final size:49
Alignment explanation
Indices: 19458908--19459003 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
19458898 TTCAATTTTA
* *
19458908 ATTATATGTTTTGTTTGATTAAATGCATCTTTGTTT-AATGTTCTGCATC
1 ATTATATGTTTTGTTTGATCAAATGCATCTTTCTTTAAATGTT-TGCATC
*
19458957 ATTATGTGTTTTGTTTG-TCAAATGCATCTTTCTTTAAATGTTTGCAT
1 ATTATATGTTTTGTTTGATCAAATGCATCTTTCTTTAAATGTTTGCAT
19459004 TAATACAGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
48 21 0.49
49 22 0.51
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.53
Consensus pattern (49 bp):
ATTATATGTTTTGTTTGATCAAATGCATCTTTCTTTAAATGTTTGCATC
Found at i:19459023 original size:59 final size:59
Alignment explanation
Indices: 19458956--19459069 Score: 169
Period size: 59 Copynumber: 1.9 Consensus size: 59
19458946 TGTTCTGCAT
* *
19458956 CATTATGTGTTTTGTTT-GTCAAATGCATCTTTCTTTAAATGT-TTGCATTAATACAGTTG
1 CATTATGTGTCTTGTTTAGT-AAATGCATCTTTATTT-AATGTCTTGCATTAATACAGTTG
*
19459015 CATTATGTGTCTTGTTTAGTGAATGCATCTTTATTTAATGTCTTGCATTAATACA
1 CATTATGTGTCTTGTTTAGTAAATGCATCTTTATTTAATGTCTTGCATTAATACA
19459070 TTAGCATCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 5 0.10
59 43 0.86
60 2 0.04
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (59 bp):
CATTATGTGTCTTGTTTAGTAAATGCATCTTTATTTAATGTCTTGCATTAATACAGTTG
Found at i:19460262 original size:25 final size:23
Alignment explanation
Indices: 19460198--19460288 Score: 67
Period size: 25 Copynumber: 3.8 Consensus size: 23
19460188 AGAGATCTTG
* *
19460198 AATTCAAAGAAAAAAAGAAA-AA
1 AATTCAAATAAAAAAAAAAAGAA
** *
19460220 AATTCGAAATATTGAAAAAAAAGCA
1 AATTC-AAATA-AAAAAAAAAAGAA
* * *
19460245 AATTCGAAGTTAAAAAAAGAAGGAA
1 AATTC-AA-ATAAAAAAAAAAAGAA
19460270 AATTCAAATAAAAAAAAAA
1 AATTCAAATAAAAAAAAAA
19460289 TTCCTTCCAA
Statistics
Matches: 52, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
22 5 0.10
23 14 0.27
24 9 0.17
25 22 0.42
26 2 0.04
ACGTcount: A:0.68, C:0.05, G:0.11, T:0.15
Consensus pattern (23 bp):
AATTCAAATAAAAAAAAAAAGAA
Found at i:19464622 original size:80 final size:80
Alignment explanation
Indices: 19464414--19464635 Score: 284
Period size: 80 Copynumber: 2.8 Consensus size: 80
19464404 TAACCAGTAA
* *
19464414 ACGATGTTGCTCACACAAGCTGTCAAGAAACAGCAACATATACAGGATC-CTAGCCATCAATACA
1 ACGATGTTGCTCACACAAGCTGTCAAGAAACAGCAACATATGCAGGATCTC-AGCCATC-GTACA
19464478 ATCCATATTACCCACTC
64 ATCCATATTACCCACTC
* * * **
19464495 ACAATGTTGCTCACACAAGCTGTCAAGAATCGGCAACATATGCAGGATCTCAGCCATCGTACGGT
1 ACGATGTTGCTCACACAAGCTGTCAAGAAACAGCAACATATGCAGGATCTCAGCCATCGTACAAT
* *
19464560 CCATGTTACCCGCTC
66 CCATATTACCCACTC
* * * ** *
19464575 ACGATGCTGCTCACACAAGCTATCAAGAAACTGCAATGTATGTAGGATCTCAGCCATCGTA
1 ACGATGTTGCTCACACAAGCTGTCAAGAAACAGCAACATATGCAGGATCTCAGCCATCGTA
19464636 GGGGTCCTTA
Statistics
Matches: 123, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
80 70 0.57
81 52 0.42
82 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.22
Consensus pattern (80 bp):
ACGATGTTGCTCACACAAGCTGTCAAGAAACAGCAACATATGCAGGATCTCAGCCATCGTACAAT
CCATATTACCCACTC
Found at i:19466335 original size:29 final size:30
Alignment explanation
Indices: 19466282--19466635 Score: 391
Period size: 30 Copynumber: 12.0 Consensus size: 30
19466272 TTCTAGTCCC
*
19466282 TAAAC-TTTCCAAATATCACATTTTAACCCT
1 TAAACTTTTCCAAA-ATTACATTTTAACCCT
* * *
19466312 TAAATTTTTCTAAAATTACA-TTTAACCCC
1 TAAACTTTTCCAAAATTACATTTTAACCCT
*
19466341 TAAACTTTTTCAAAATTACATTTTAACCCT
1 TAAACTTTTCCAAAATTACATTTTAACCCT
* *
19466371 TAAACTTTTCCAAAATCACATTTTCACCC-
1 TAAACTTTTCCAAAATTACATTTTAACCCT
* * * *
19466400 TAAACTTTTTCAAAATCACATCTTAACCCC
1 TAAACTTTTCCAAAATTACATTTTAACCCT
*
19466430 TAAACTTTTCCAAAATCACA-TTTAACCCT
1 TAAACTTTTCCAAAATTACATTTTAACCCT
* * * *
19466459 AAAACTTTCCCAAAATTACATTTTGACCAT
1 TAAACTTTTCCAAAATTACATTTTAACCCT
* * *
19466489 AAAACTTTTCCAAAATTATATTTTAACTCT
1 TAAACTTTTCCAAAATTACATTTTAACCCT
*
19466519 TAAACTTCTT-CAAAATTACATTTTGACCCT
1 TAAACTT-TTCCAAAATTACATTTTAACCCT
* * *
19466549 TAAAC-CTTCTCGAAATCACATTTTAACCC-
1 TAAACTTTTC-CAAAATTACATTTTAACCCT
* * *
19466578 TAAACTTTCCCAAAATTACATTTTTA-CCA
1 TAAACTTTTCCAAAATTACATTTTAACCCT
19466607 TAAACTTTTCCAAAATTACATTTTAACCC
1 TAAACTTTTCCAAAATTACATTTTAACCC
19466636 GAATTCTCTG
Statistics
Matches: 272, Mismatches: 42, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
28 4 0.01
29 117 0.43
30 142 0.52
31 9 0.03
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.37
Consensus pattern (30 bp):
TAAACTTTTCCAAAATTACATTTTAACCCT
Found at i:19466344 original size:59 final size:59
Alignment explanation
Indices: 19466279--19466635 Score: 377
Period size: 59 Copynumber: 6.0 Consensus size: 59
19466269 ATATTCTAGT
* * * *
19466279 CCCTAAACTTTCCAAATATCACATTTTAACCCTTAAATTTTTCTAAAATTACA-TTTAAC
1 CCCTAAACTTTCCAAA-ATTACATTTTAACCCTTAAACTTTTCCAAAATCACATTTTAAC
* *
19466338 CCCTAAACTTTTTCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCACATTTTCA-
1 CCCTAAAC-TTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCACATTTTAAC
* * * *
19466397 CCCTAAACTTTTTCAAAATCACATCTTAACCCCTAAACTTTTCCAAAATCACA-TTTAA-
1 CCCTAAAC-TTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCACATTTTAAC
* * * * *
19466455 CCCTAAAACTTTCCCAAAATTACATTTTGACCATAAAACTTTTCCAAAATTATATTTTAAC
1 CCCT-AAACTTT-CCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCACATTTTAAC
* * * * * *
19466516 TCTTAAACTTCTTCAAAATTACATTTTGACCCTTAAAC-CTTCTCGAAATCACATTTTAA-
1 CCCTAAACTT-TCCAAAATTACATTTTAACCCTTAAACTTTTC-CAAAATCACATTTTAAC
* * *
19466575 CCCTAAACTTTCCCAAAATTACATTTTTA-CCATAAACTTTTCCAAAATTACATTTTAAC
1 CCCTAAACTTT-CCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCACATTTTAAC
19466634 CC
1 CC
19466636 GAATTCTCTG
Statistics
Matches: 251, Mismatches: 36, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
58 33 0.13
59 157 0.63
60 58 0.23
61 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.37
Consensus pattern (59 bp):
CCCTAAACTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCACATTTTAAC
Found at i:19466347 original size:89 final size:85
Alignment explanation
Indices: 19466282--19466635 Score: 368
Period size: 89 Copynumber: 4.0 Consensus size: 85
19466272 TTCTAGTCCC
* *
19466282 TAAACTTTCCAAATATCACATTTTAACCCTTAAATTTTTCTAAAATTACATTTAACCCCTAAACT
1 TAAACTTTCCAAA-ATCACATTTTAACCC-TAAACTTTTCCAAAATTACATTTAACCCCTAAAC-
*
19466347 TTTTCAAAATTACATTTTAACCCT
63 TTTTCAAAATCACA-TTTAACCCT
* * *
19466371 TAAACTTTTCCAAAATCACATTTTCACCCTAAACTTTTTCAAAATCACATCTTAACCCCTAAACT
1 TAAAC-TTTCCAAAATCACATTTTAACCCTAAACTTTTCCAAAATTACAT-TTAACCCCTAAACT
19466436 TTTCCAAAATCACATTTAACCCT
64 TTT-CAAAATCACATTTAACCCT
* * * * * * *
19466459 AAAACTTTCCCAAAATTACATTTTGACCATAAAACTTTTCCAAAATTATATTTTAACTCTTAAAC
1 TAAACTTT-CCAAAATCACATTTTAACCCT-AAACTTTTCCAAAATTACA-TTTAACCCCTAAAC
* *
19466524 TTCTTCAAAATTACATTTTGACCCT
63 TT-TTCAAAATCACA-TTTAACCCT
* * * * *
19466549 TAAACCTTCTCGAAATCACATTTTAACCCTAAACTTTCCCAAAATTACATTTTTA-CCATAAACT
1 TAAACTTTC-CAAAATCACATTTTAACCCTAAACTTTTCCAAAATTACA-TTTAACCCCTAAACT
*
19466613 TTTCCAAAATTACATTTTAACCC
64 TTT-CAAAATCACA-TTTAACCC
19466636 GAATTCTCTG
Statistics
Matches: 226, Mismatches: 29, Indels: 21
0.82 0.11 0.08
Matches are distributed among these distances:
87 5 0.02
88 78 0.35
89 102 0.45
90 41 0.18
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.37
Consensus pattern (85 bp):
TAAACTTTCCAAAATCACATTTTAACCCTAAACTTTTCCAAAATTACATTTAACCCCTAAACTTT
TCAAAATCACATTTAACCCT
Found at i:19469145 original size:41 final size:41
Alignment explanation
Indices: 19469088--19469492 Score: 416
Period size: 41 Copynumber: 9.9 Consensus size: 41
19469078 GATGCGGCGA
** *
19469088 AAGCGCCGCTAAAGGTCAGATCAATAGCGGCCCTTATGGGC
1 AAGCGCCGCTAAAGGTCAGAGAAATAGCGGCGCTTATGGGC
* ** * *
19469129 AAGCGCCGCTAAAGGTCATATCAATAGTGGCGCTTATGGGA
1 AAGCGCCGCTAAAGGTCAGAGAAATAGCGGCGCTTATGGGC
* *
19469170 AAGCGCCGCT-AAGGTCAGAGCAATAGCGGCGCTTATGGGA
1 AAGCGCCGCTAAAGGTCAGAGAAATAGCGGCGCTTATGGGC
*** **
19469210 AAGCATTGCTAAAGGTCAGAGAAATAGCGATGCTTATGGGC
1 AAGCGCCGCTAAAGGTCAGAGAAATAGCGGCGCTTATGGGC
* * *
19469251 AAGCACCGCTAAAGGTCAGAGAAATAACGGCGCTTATAGGC
1 AAGCGCCGCTAAAGGTCAGAGAAATAGCGGCGCTTATGGGC
* * * *
19469292 AAGCGCTGCTAAAGGTTAGAGAAATAGCAGCGCTTATGGGG
1 AAGCGCCGCTAAAGGTCAGAGAAATAGCGGCGCTTATGGGC
* * * * *
19469333 AAGCGTCGTTAAAGGTCAGAGAAATAGAGGCGATTATGGGA
1 AAGCGCCGCTAAAGGTCAGAGAAATAGCGGCGCTTATGGGC
* * * *
19469374 AAGTGTCGCTAAAGGTTAGAGAAATAGCGGTGCTTATGGGC
1 AAGCGCCGCTAAAGGTCAGAGAAATAGCGGCGCTTATGGGC
* * * * * *
19469415 AAGCACCGCTAAAGGTCAAAGCAATAGTGGTGCTTATGGGT
1 AAGCGCCGCTAAAGGTCAGAGAAATAGCGGCGCTTATGGGC
* ** * * *
19469456 AAACGCAACGAAAGGTCAGAGCACTAGCGGCGCTTAT
1 AAGCGCCGCTAAAGGTCAGAGAAATAGCGGCGCTTAT
19469493 CTGAAAAATG
Statistics
Matches: 304, Mismatches: 59, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
40 34 0.11
41 270 0.89
ACGTcount: A:0.32, C:0.18, G:0.31, T:0.19
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCAGAGAAATAGCGGCGCTTATGGGC
Found at i:19471303 original size:12 final size:12
Alignment explanation
Indices: 19471286--19471328 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
19471276 TTAAATGAAG
19471286 TATTATATCACA
1 TATTATATCACA
*
19471298 TATTATAACGA-A
1 TATTATATC-ACA
19471310 GTATTATATCACA
1 -TATTATATCACA
19471323 TATTAT
1 TATTAT
19471329 GGTATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (12 bp):
TATTATATCACA
Found at i:19475533 original size:50 final size:50
Alignment explanation
Indices: 19475464--19476136 Score: 517
Period size: 50 Copynumber: 13.6 Consensus size: 50
19475454 AAGATATGAA
*
19475464 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGACGATGTAAT
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTAAT
** * *
19475514 GGGAAAGGTTGAGTTCGCAACAGTGAACCCGGTACCATAGAAGATGTAAT
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTAAT
* * * * * *
19475564 GGGAAAGGTTGAGGTCGAAACGATGAATCCGGTACCAT-GAAGATTTGAA-
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGT-AAT
* * *** * * * * *
19475613 AGG-AAGGATTGAGGCCGTAACAACGAATCTGATACCAT-GAAGATTTGAA-
1 GGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGT-AAT
* * * * * *
19475662 AGG-AAGAATTAAGGCCGCGACGGTGAATCCGGTACCTTAGAAGATGTGAT
1 GGGAAAG-GTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTAAT
* * *** * * *
19475712 GAGAAAGGTTGAGGCTGCAACAACGAACTCGGTACCATA-AAGATTTGAA-
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGT-AAT
* * * * *
19475761 GGG-AAGGATTGAGGTCGCGACGGTGAATCCGGTACCTTAGAAGATATGAT
1 GGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTAAT
* ** * *
19475811 GGGAAAGGTTGAGGCCGTAACGGCAAACCCGGTACCAT-GAAGATTTGAA-
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGT-AAT
* * * *
19475860 GGG-AAGGATTGAGGTCGCGACGGTGAATCTGGTACCTTAGAAGATGTAAT
1 GGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTAAT
* * * *
19475910 GGGAAAGGTTGAGGCCACAACGGTAAACCCGGTACCTAAGAAGATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTAAT
** * * * *
19475960 GGGAAAGGTTGAGGTTGCAACGGCGAACCCGATACCTAAGAAGATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTAAT
** *
19476010 GGGAAAGGTTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGATGCAAT
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTAAT
* * * * * * * * *
19476060 GGGAAAGATTGAGGCTGCCACGGCGAATCCGATACCAT-GAAGATATAAA
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTAAT
* * *
19476109 GGGAAAGATTGAGGCCGTAACGGCGAAC
1 GGGAAAGGTTGAGGCCGCAACGGTGAAC
19476137 TTAGAACCTT
Statistics
Matches: 494, Mismatches: 113, Indels: 33
0.77 0.18 0.05
Matches are distributed among these distances:
48 12 0.02
49 169 0.34
50 302 0.61
51 11 0.02
ACGTcount: A:0.33, C:0.16, G:0.32, T:0.19
Consensus pattern (50 bp):
GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTAAT
Found at i:19475825 original size:198 final size:199
Alignment explanation
Indices: 19475423--19476026 Score: 672
Period size: 198 Copynumber: 3.0 Consensus size: 199
19475413 ACAGGGAAGA
* ** * * * * *
19475423 TTGAGGCCGCAACGGCAAATCTAATACCCTGAAGATATGAAGGGAA-AGGTTGAGGCCGCAACGG
1 TTGAGGCCGTAACAACAAATCTGATACCATGAAGATTTGAAGGGAAGA-ATTGAGGCCGCGACGG
* * * **
19475487 TGAACCCGGTACCTTAGACGATGTAATGGGAAAGGTTGA-GTTCGCAACAGTGAACCCGGTACCA
65 TGAATCCGGTACCTTAGAAGATGTAATGGGAAAGGTTGAGGCT-GCAACAACGAACCCGGTACCA
* * * * **
19475551 TAGAAGATGT-AATGGGAAAGGTTGAGGTCGAAACGATGAATCCGGTACCAT-GAAGATTTGAAA
129 TAGAAGATGTGAA-GGGAAAGGTTGAGGTCGCAACGGTGAATCCGGTACCTTAGAAGATATGATG
19475614 GG-AAGG
193 GGAAAGG
* * *
19475620 ATTGAGGCCGTAACAACGAATCTGATACCATGAAGATTTGAAAGGAAGAATTAAGGCCGCGACGG
1 -TTGAGGCCGTAACAACAAATCTGATACCATGAAGATTTGAAGGGAAGAATTGAGGCCGCGACGG
* * *
19475685 TGAATCCGGTACCTTAGAAGATGTGATGAGAAAGGTTGAGGCTGCAACAACGAACTCGGTACCAT
65 TGAATCCGGTACCTTAGAAGATGTAATGGGAAAGGTTGAGGCTGCAACAACGAACCCGGTACCAT
* *
19475750 A-AAGATTTGAAGGG-AAGGATTGAGGTCGCGACGGTGAATCCGGTACCTTAGAAGATATGATGG
130 AGAAGATGTGAAGGGAAAGG-TTGAGGTCGCAACGGTGAATCCGGTACCTTAGAAGATATGATGG
19475813 GAAAGG
194 GAAAGG
** * * * * *
19475819 TTGAGGCCGTAACGGCAAACCCGGTACCATGAAGATTTGAAGGGAAGGATTGAGGTCGCGACGGT
1 TTGAGGCCGTAACAACAAATCTGATACCATGAAGATTTGAAGGGAAGAATTGAGGCCGCGACGGT
*
19475884 GAATCTGGTACCTTAGAAGATGTAATGGGAAAGGTTGAGGC--C-ACAACGGTAAACCCGGTACC
66 GAATCCGGTACCTTAGAAGATGTAATGGGAAAGGTTGAGGCTGCAACAAC-G--AACCCGGTACC
* * * * * * *
19475946 -TAAGAAGATGTGATGGGAAAGGTTGAGGTTGCAACGGCGAACCCGATACCTAAGAAGATGTGAT
128 AT-AGAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGGTGAATCCGGTACCTTAGAAGATATGAT
19476010 GGGAAAGG
192 GGGAAAGG
19476018 TTGAGGCCG
1 TTGAGGCCG
19476027 CAACGGTGAA
Statistics
Matches: 344, Mismatches: 50, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
195 5 0.01
196 6 0.02
197 36 0.10
198 223 0.65
199 70 0.20
200 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.32, T:0.19
Consensus pattern (199 bp):
TTGAGGCCGTAACAACAAATCTGATACCATGAAGATTTGAAGGGAAGAATTGAGGCCGCGACGGT
GAATCCGGTACCTTAGAAGATGTAATGGGAAAGGTTGAGGCTGCAACAACGAACCCGGTACCATA
GAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGGTGAATCCGGTACCTTAGAAGATATGATGGGA
AAGG
Found at i:19476083 original size:100 final size:99
Alignment explanation
Indices: 19475423--19476169 Score: 530
Period size: 99 Copynumber: 7.5 Consensus size: 99
19475413 ACAGGGAAGA
* * ** * * * *
19475423 TTGAGGCCGCAACGGCAAATCTAATACCCT-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGG
1 TTGAGGCCGCAACGGCGAACCTGGTACCTTAGAAGAT-TGAAGGGAAAGATTGAGGTCGCGACGG
* * * * *
19475487 TGAACCCGGTACCTTAGACGATGTAATGGGAAAGG
65 CGAATCCGATACCTTAGAAGATGTGATGGGAAAGG
** * * * * * **
19475522 TTGAGTTCGCAACAGTGAACCCGGTACCATAGAAGA-TGTAATGGGAAAGGTTGAGGTCGAAACG
1 TTGAGGCCGCAACGGCGAACCTGGTACCTTAGAAGATTG-AA-GGGAAAGATTGAGGTCGCGACG
** * * * **
19475586 ATGAATCCGGTACCAT-GAAGATTTGAAAGG-AAGG
64 GCGAATCCGATACCTTAGAAGATGTGATGGGAAAGG
* ** * * * * * *
19475620 ATTGAGGCCGTAACAACGAATCTGATACCAT-GAAGATTTGAAAGG-AAGAATTAAGGCCGCGAC
1 -TTGAGGCCGCAACGGCGAACCTGGTACCTTAGAAGA-TTGAAGGGAAAG-ATTGAGGTCGCGAC
* * *
19475683 GGTGAATCCGGTACCTTAGAAGATGTGATGAGAAAGG
63 GGCGAATCCGATACCTTAGAAGATGTGATGGGAAAGG
* ** * *
19475720 TTGAGGCTGCAACAACGAA-CTCGGTACCATA-AAGATTTGAAGGGAAGGATTGAGGTCGCGACG
1 TTGAGGCCGCAACGGCGAACCT-GGTACCTTAGAAGA-TTGAAGGGAAAGATTGAGGTCGCGACG
* * *
19475783 GTGAATCCGGTACCTTAGAAGATATGATGGGAAAGG
64 GCGAATCCGATACCTTAGAAGATGTGATGGGAAAGG
* * * * *
19475819 TTGAGGCCGTAACGGCAAACCCGGTACCAT-GAAGATTTGAAGGGAAGGATTGAGGTCGCGACGG
1 TTGAGGCCGCAACGGCGAACCTGGTACCTTAGAAGA-TTGAAGGGAAAGATTGAGGTCGCGACGG
* * * *
19475883 TGAATCTGGTACCTTAGAAGATGTAATGGGAAAGG
65 CGAATCCGATACCTTAGAAGATGTGATGGGAAAGG
* ** * * * * * *
19475918 TTGAGGCCACAACGGTAAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGTTGCAACGG
1 TTGAGGCCGCAACGGCGAACCTGGTACCTTAGAAGAT-TGAAGGGAAAGATTGAGGTCGCGACGG
* *
19475983 CGAACCCGATACCTAAGAAGATGTGATGGGAAAGG
65 CGAATCCGATACCTTAGAAGATGTGATGGGAAAGG
* * *
19476018 TTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGA-TGCAATGGGAAAGATTGAGG-CTGCCAC
1 TTGAGGCCGCAACGGCGAACCTGGTACCTTAGAAGATTG-AA-GGGAAAGATTGAGGTC-GCGAC
* * * * *
19476081 GGCGAATCCGATACCAT-GAAGATATAAAGGGAAAGA
63 GGCGAATCCGATACCTTAGAAGATGTGATGGGAAAGG
* * * * * *
19476117 TTGAGGCCGTAACGGCGAACTTAGAACCTTAGAA-ACATGACGGGAAAGATTGA
1 TTGAGGCCGCAACGGCGAACCTGGTACCTTAGAAGA-TTGAAGGGAAAGATTGA
19476170 AGTCACAATA
Statistics
Matches: 532, Mismatches: 95, Indels: 43
0.79 0.14 0.06
Matches are distributed among these distances:
97 3 0.01
98 54 0.10
99 308 0.58
100 167 0.31
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (99 bp):
TTGAGGCCGCAACGGCGAACCTGGTACCTTAGAAGATTGAAGGGAAAGATTGAGGTCGCGACGGC
GAATCCGATACCTTAGAAGATGTGATGGGAAAGG
Found at i:19476840 original size:15 final size:16
Alignment explanation
Indices: 19476822--19476851 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19476812 ATAAACAAAA
19476822 TTTAAA-TTAAAATGC
1 TTTAAATTTAAAATGC
19476837 TTTAAATTTAAAATG
1 TTTAAATTTAAAATG
19476852 TCCCTTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (16 bp):
TTTAAATTTAAAATGC
Found at i:19478377 original size:30 final size:30
Alignment explanation
Indices: 19478342--19478837 Score: 315
Period size: 30 Copynumber: 16.8 Consensus size: 30
19478332 AAATGTTTTA
** * *
19478342 AAAATCATATTTTGGTCTCTAAACTTTTCA
1 AAAATCATATTTTGAACCCTAAACTTTTCC
*
19478372 AAAATCATATTTTG-ACCCTCAAACTTTTTC
1 AAAATCATATTTTGAACCCT-AAACTTTTCC
*
19478402 AAAACTC-TATTTTG-ACCCTCAAAATTTTCC
1 AAAA-TCATATTTTGAACCCT-AAACTTTTCC
* * *
19478432 AAAAT-TTCATTTTG-ACCTTAAAATTTTCC
1 AAAATCAT-ATTTTGAACCCTAAACTTTTCC
* * *
19478461 ACAATTATATTTTGATCCCTAAACTTTTCC
1 AAAATCATATTTTGAACCCTAAACTTTTCC
* *
19478491 AAAATCACATTTT-AACCCTCAAAATTTTCC
1 AAAATCATATTTTGAACCCT-AAACTTTTCC
* *
19478521 AAAATCACATTTT-CACCCTAAACTTTTCC
1 AAAATCATATTTTGAACCCTAAACTTTTCC
* * * *
19478550 AAAATCACATCTTGATCCCTAAACTTTCCC
1 AAAATCATATTTTGAACCCTAAACTTTTCC
* * *
19478580 AAAATCACATTTT-AACCTTAAAACTTTCCC
1 AAAATCATATTTTGAACCCT-AAACTTTTCC
**
19478610 AAAATCATATTTTG-A-CCTCAAAAATTTCC
1 AAAATCATATTTTGAACCCT-AAACTTTTCC
* * * * *
19478639 AAAATTACA-TTTCAACCACTAAACTTCTCT
1 AAAATCATATTTTGAACC-CTAAACTTTTCC
* * * * * * *
19478669 AAAATTACAATTTAAATCTTAAAC-CTTCTC
1 AAAATCATATTTTGAACCCTAAACTTTTC-C
* * * *
19478699 AAAATCACATTTTG-ACCCCAAACTTCTCT
1 AAAATCATATTTTGAACCCTAAACTTTTCC
* *
19478728 AAAATTATATTTT-AACCCTAAACTTCTT-T
1 AAAATCATATTTTGAACCCTAAACTT-TTCC
* * * *
19478757 AAAATTACATTTTG-AGCCTAAACTTTCCC
1 AAAATCATATTTTGAACCCTAAACTTTTCC
* * * *
19478786 AAAATTATATTTTTACCCCTAAACTTTTCT
1 AAAATCATATTTTGAACCCTAAACTTTTCC
*
19478816 AAAATTATATTTT-AACCCTAAA
1 AAAATCATATTTTGAACCCTAAA
19478838 TTCTTCAAAA
Statistics
Matches: 376, Mismatches: 69, Indels: 43
0.77 0.14 0.09
Matches are distributed among these distances:
28 4 0.01
29 144 0.38
30 218 0.58
31 10 0.03
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAATCATATTTTGAACCCTAAACTTTTCC
Found at i:19478472 original size:89 final size:88
Alignment explanation
Indices: 19478361--19478650 Score: 309
Period size: 89 Copynumber: 3.3 Consensus size: 88
19478351 TTTTGGTCTC
* * * * * *
19478361 TAAACTTTTCAAAAATCATATTTTGA-CCCTCAAACTTTTTCAAAACTC-TATTTTGACCCTCAA
1 TAAAATTTTCCAAAATTACATTTTGATCCCT-AAACTTTTCCAAAA-TCACATTTT-ACCCTCAA
*
19478424 AATTTTCCAAAATTTCATTTTGACCT
63 AATTTTCCAAAATATCATTTTGACCT
* *
19478450 TAAAATTTTCCACAATTATATTTTGATCCCTAAACTTTTCCAAAATCACATTTTAACCCTCAAAA
1 TAAAATTTTCCAAAATTACATTTTGATCCCTAAACTTTTCCAAAATCACATTTT-ACCCTCAAAA
* *
19478515 TTTTCCAAAATCA-CATTTTCACCC
65 TTTTCCAAAAT-ATCATTTTGACCT
* * * * * *
19478539 TAAACTTTTCCAAAATCACATCTTGATCCCTAAACTTTCCCAAAATCACATTTTAACCTTAAAAC
1 TAAAATTTTCCAAAATTACATTTTGATCCCTAAACTTTTCCAAAATCACATTTTACCCTCAAAA-
*
19478604 TTTCCCAAAATCAT-ATTTTGACCT
65 TTTTCCAAAAT-ATCATTTTGACCT
* *
19478628 CAAAAATTTCCAAAATTACATTT
1 TAAAATTTTCCAAAATTACATTT
19478651 CAACCACTAA
Statistics
Matches: 170, Mismatches: 26, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
88 10 0.06
89 156 0.92
90 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.37
Consensus pattern (88 bp):
TAAAATTTTCCAAAATTACATTTTGATCCCTAAACTTTTCCAAAATCACATTTTACCCTCAAAAT
TTTCCAAAATATCATTTTGACCT
Found at i:19478490 original size:59 final size:59
Alignment explanation
Indices: 19478342--19478856 Score: 288
Period size: 59 Copynumber: 8.7 Consensus size: 59
19478332 AAATGTTTTA
* * * * * *
19478342 AAAATCATATTTTGGTCTCTAAACTTTTCAAAAATCAT-ATTTTGACCCTCAAACTTTTTC
1 AAAATTATATTTT-GACCCTAAACTTTTCCAAAAT-ATCATTTTGACCCTCAAAATTTTCC
* * * * *
19478402 AAAACTCTATTTTGACCCTCAAAATTTTCCAAAATTTCATTTTGA-CCTTAAAATTTTCC
1 AAAATTATATTTTGACCCT-AAACTTTTCCAAAATATCATTTTGACCCTCAAAATTTTCC
* *
19478461 ACAATTATATTTTGATCCCTAAACTTTTCCAAAATCA-CATTTTAACCCTCAAAATTTTCC
1 AAAATTATATTTTGA-CCCTAAACTTTTCCAAAAT-ATCATTTTGACCCTCAAAATTTTCC
* * * * * *
19478521 AAAATCACATTTTCACCCTAAACTTTTCCAAAATCA-CATCTTGATCCCT-AAACTTTCCC
1 AAAATTATATTTTGACCCTAAACTTTTCCAAAAT-ATCATTTTGA-CCCTCAAAATTTTCC
* * * * * *
19478580 AAAATCACATTTTAACCTTAAAACTTTCCCAAAATCAT-ATTTTGA-CCTCAAAAATTTCC
1 AAAATTATATTTTGACCCT-AAACTTTTCCAAAAT-ATCATTTTGACCCTCAAAATTTTCC
* ** * * * * ** * **
19478639 AAAATTACATTTCAACCACTAAACTTCTCTAAAAT-TACAATTTAAATCT-TAAACCTTCTC
1 AAAATTATATTTTGACC-CTAAACTTTTCCAAAATAT-CATTTTGACCCTCAAAATTTTC-C
* * * * * * * *
19478699 AAAATCACATTTTGACCCCAAACTTCTCTAAAATTAT-ATTTTAACCCT-AAACTTCTT-T
1 AAAATTATATTTTGACCCTAAACTTTTCCAAAA-TATCATTTTGACCCTCAAAATT-TTCC
* * * * * *
19478757 AAAATTACATTTTGAGCCTAAACTTTCCCAAAATTAT-ATTTTTACCC-CTAAACTTTTCT
1 AAAATTATATTTTGACCCTAAACTTTTCCAAAA-TATCATTTTGACCCTC-AAAATTTTCC
* *
19478816 AAAATTATATTTTAACCCTAAA-TTCTT-CAAAACATCATTTT
1 AAAATTATATTTTGACCCTAAACTT-TTCCAAAATATCATTTT
19478857 CAGCCCCGTT
Statistics
Matches: 364, Mismatches: 69, Indels: 46
0.76 0.14 0.10
Matches are distributed among these distances:
57 3 0.01
58 57 0.16
59 198 0.54
60 105 0.29
61 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (59 bp):
AAAATTATATTTTGACCCTAAACTTTTCCAAAATATCATTTTGACCCTCAAAATTTTCC
Found at i:19478661 original size:89 final size:86
Alignment explanation
Indices: 19478430--19478856 Score: 331
Period size: 89 Copynumber: 4.8 Consensus size: 86
19478420 TCAAAATTTT
** * * * * *
19478430 CCAAAATTTCATTTTGACCTTAAAATTTTCCACAATTATATTTTGATCCCTAAACTTTTCCAAAA
1 CCAAAATCACATTTTGACC-CAAAATTTTCCAAAATTACA-TTTGAACCCTAAACTTCTCCAAAA
* * *
19478495 TCACATTTTAACCCTCAAAATTTT
64 TCACATTTTAA-CCTTAAACTTTC
* * * *
19478519 CCAAAATCACATTTTCACCCTAAACTTTTCCAAAATCACATCTTGATCCCTAAACTT-TCCCAAA
1 CCAAAATCACATTTTGACCC-AAAATTTTCCAAAATTACAT-TTGAACCCTAAACTTCT-CCAAA
19478583 ATCACATTTTAACCTTAAAACTTTC
63 ATCACATTTTAACCTT-AAACTTTC
* * * *
19478608 CCAAAATCATATTTTGACCTCAAAAATTTCCAAAATTACATTTCAACCACTAAACTTCTCTAAAA
1 CCAAAATCACATTTTGACC-CAAAATTTTCCAAAATTACATTTGAACC-CTAAACTTCTCCAAAA
* * * *
19478673 TTACAATTTAAATCTTAAACCTTC
64 TCAC-ATTTTAACCTTAAACTTTC
* * * * * * **
19478697 TCAAAATCACATTTTGACCCCAAACTTCTCTAAAATTATATTTTAACCCTAAACTTCTTTAAAAT
1 CCAAAATCACATTTTGA-CCCAAAATTTTCCAAAATTACATTTGAACCCTAAACTTCTCCAAAAT
* *
19478762 TACATTTTGAGCC-TAAACTTTC
65 CACATTTT-AACCTTAAACTTTC
* * * * * * * *
19478784 CCAAAATTATATTTTTACCCCTAAACTTTTCTAAAATTATATTTTAACCCTAAA-TTCTTCAAAA
1 CCAAAATCACATTTTGA-CCC-AAAATTTTCCAAAATTACATTTGAACCCTAAACTTCTCCAAAA
19478848 -CATCATTTT
64 TCA-CATTTT
19478857 CAGCCCCGTT
Statistics
Matches: 283, Mismatches: 43, Indels: 26
0.80 0.12 0.07
Matches are distributed among these distances:
86 1 0.00
87 44 0.16
88 62 0.22
89 163 0.58
90 13 0.05
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (86 bp):
CCAAAATCACATTTTGACCCAAAATTTTCCAAAATTACATTTGAACCCTAAACTTCTCCAAAATC
ACATTTTAACCTTAAACTTTC
Found at i:19481100 original size:14 final size:14
Alignment explanation
Indices: 19481083--19481112 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19481073 TTTAAACTCT
*
19481083 AAAAGATAAATCTA
1 AAAAGATAAATATA
19481097 AAAAGATAAATATA
1 AAAAGATAAATATA
19481111 AA
1 AA
19481113 TAATATCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (14 bp):
AAAAGATAAATATA
Found at i:19486694 original size:20 final size:20
Alignment explanation
Indices: 19486669--19486707 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19486659 TAATGCGTTG
*
19486669 GATCACCTCTTCTGGTAGTT
1 GATCACCTCTTCTGATAGTT
19486689 GATCACCTCTTCTGATAGT
1 GATCACCTCTTCTGATAGT
19486708 CACACTCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (20 bp):
GATCACCTCTTCTGATAGTT
Found at i:19487660 original size:13 final size:13
Alignment explanation
Indices: 19487639--19487671 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
19487629 ATATAAATAT
*
19487639 ATATTTAAAACTA
1 ATATATAAAACTA
19487652 ATATATAAAACTA
1 ATATATAAAACTA
19487665 ATA-ATAA
1 ATATATAA
19487672 TAACATCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (13 bp):
ATATATAAAACTA
Found at i:19489865 original size:17 final size:17
Alignment explanation
Indices: 19489845--19489877 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19489835 TTTAAGGACT
19489845 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
19489862 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
19489878 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:19490120 original size:47 final size:49
Alignment explanation
Indices: 19490059--19490156 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 49
19490049 GTGCATTATG
* *
19490059 TAATGACATCCATTAACT-C-T-CATGATTAGTTAAGTTTGCATCATAAA
1 TAATGACATCCATTAACTACTTACATG-TTAGTTAAATATGCATCATAAA
* *
19490106 TAATGACATGCATTAAGTAACTTACATGTTAGTTAAATATGCATCATAAA
1 TAATGACATCCATTAACT-ACTTACATGTTAGTTAAATATGCATCATAAA
19490156 T
1 T
19490157 CCTATCATGC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
47 16 0.37
49 1 0.02
50 22 0.51
51 4 0.09
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (49 bp):
TAATGACATCCATTAACTACTTACATGTTAGTTAAATATGCATCATAAA
Found at i:19490151 original size:50 final size:50
Alignment explanation
Indices: 19490072--19490192 Score: 145
Period size: 50 Copynumber: 2.4 Consensus size: 50
19490062 TGACATCCAT
* * *
19490072 TAACTCTCATGATTAGTTAAGTTTGCATCATAAATAATGA-CATGCATTAAG
1 TAACTCACATG-TTAGTTAAATATGCATCATAAATAAT-ATCATGCATTAAG
* ** *
19490123 TAACTTACATGTTAGTTAAATATGCATCATAAATCCTATCATGCATTATG
1 TAACTCACATGTTAGTTAAATATGCATCATAAATAATATCATGCATTAAG
*
19490173 TAACTCCCATGTTAGTTAAA
1 TAACTCACATGTTAGTTAAA
19490193 GTTTGCTTCT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
49 1 0.02
50 50 0.83
51 9 0.15
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAATATGCATCATAAATAATATCATGCATTAAG
Found at i:19494552 original size:17 final size:16
Alignment explanation
Indices: 19494489--19494549 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 16
19494479 TACATTGAAC
19494489 ATTTTT-ATATAAATT
1 ATTTTTAATATAAATT
*
19494504 ATTTTTAAGAT-AATT
1 ATTTTTAATATAAATT
**
19494519 ATTCTTCTTTTAT-AATT
1 ATT-TT-TAATATAAATT
19494536 ATTTTTAATATAAA
1 ATTTTTAATATAAA
19494550 ATTTCAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
15 17 0.47
16 9 0.25
17 10 0.28
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (16 bp):
ATTTTTAATATAAATT
Found at i:19495221 original size:18 final size:19
Alignment explanation
Indices: 19495182--19495223 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
19495172 AAAAGCATGC
*
19495182 AAATATCATAGTTTTAACT
1 AAATATCATAGTTTTAAAT
19495201 AAATATCAT-G-TTTAATAT
1 AAATATCATAGTTTTAA-AT
19495219 AAATA
1 AAATA
19495224 AGCTAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 7 0.33
19 9 0.43
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (19 bp):
AAATATCATAGTTTTAAAT
Found at i:19497291 original size:22 final size:21
Alignment explanation
Indices: 19497258--19497308 Score: 84
Period size: 22 Copynumber: 2.4 Consensus size: 21
19497248 ACAAAACATT
19497258 ATGTTTGTAACTCTCCTCATA
1 ATGTTTGTAACTCTCCTCATA
*
19497279 ATGTTTAGTAACTCTCCTCATT
1 ATGTTT-GTAACTCTCCTCATA
19497301 ATGTTTGT
1 ATGTTTGT
19497309 TTTAAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.47
Consensus pattern (21 bp):
ATGTTTGTAACTCTCCTCATA
Found at i:19497399 original size:29 final size:29
Alignment explanation
Indices: 19497366--19497537 Score: 143
Period size: 29 Copynumber: 5.9 Consensus size: 29
19497356 TTGCACTTAG
* *
19497366 GGGTTCACACATGTAGGGTTTACACCTAA
1 GGGTTCACACATGTAGGGTTCACACATAA
* * * * *
19497395 GGGTTCGCACATCTTGGATT-GCACATACA
1 GGGTTCACACATGTAGGGTTCACACATA-A
* ** *
19497424 TGGTT--CGTATTTAGGGGTTCACACATATA
1 GGGTTCACACATGTA-GGGTTCACACATA-A
**
19497453 GGGTTCACACATGTAGGGTTCACACATCT
1 GGGTTCACACATGTAGGGTTCACACATAA
* **
19497482 GGGCTCACACATGTAGGGTTCACACATCT
1 GGGTTCACACATGTAGGGTTCACACATAA
*
19497511 GGGTTCACACATGTATGGTTCACACAT
1 GGGTTCACACATGTAGGGTTCACACAT
19497538 CTGGCTTCGC
Statistics
Matches: 115, Mismatches: 23, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
27 4 0.03
28 9 0.08
29 85 0.74
30 12 0.10
31 5 0.04
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (29 bp):
GGGTTCACACATGTAGGGTTCACACATAA
Found at i:19497458 original size:15 final size:15
Alignment explanation
Indices: 19497438--19497537 Score: 141
Period size: 15 Copynumber: 6.8 Consensus size: 15
19497428 TCGTATTTAG
*
19497438 GGGTTCACACATATA
1 GGGTTCACACATGTA
19497453 GGGTTCACACATGTA
1 GGGTTCACACATGTA
*
19497468 GGGTTCACACATCT-
1 GGGTTCACACATGTA
*
19497482 GGGCTCACACATGTA
1 GGGTTCACACATGTA
*
19497497 GGGTTCACACATCT-
1 GGGTTCACACATGTA
19497511 GGGTTCACACATGTA
1 GGGTTCACACATGTA
*
19497526 TGGTTCACACAT
1 GGGTTCACACAT
19497538 CTGGCTTCGC
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
14 25 0.33
15 50 0.67
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (15 bp):
GGGTTCACACATGTA
Found at i:19497534 original size:44 final size:44
Alignment explanation
Indices: 19497438--19497537 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
19497428 TCGTATTTAG
*
19497438 GGGTTCACACATATAGGGTTCACACATGTAGGGTTCACACATCT
1 GGGTTCACACATATAGGGTTCACACATCTAGGGTTCACACATCT
* * *
19497482 GGGCTCACACATGTAGGGTTCACACATCT-GGGTTCACACATGT
1 GGGTTCACACATATAGGGTTCACACATCTAGGGTTCACACATCT
*
19497525 ATGGTTCACACAT
1 -GGGTTCACACAT
19497538 CTGGCTTCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 13 0.27
44 36 0.73
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (44 bp):
GGGTTCACACATATAGGGTTCACACATCTAGGGTTCACACATCT
Found at i:19497538 original size:29 final size:29
Alignment explanation
Indices: 19497438--19497551 Score: 174
Period size: 29 Copynumber: 3.9 Consensus size: 29
19497428 TCGTATTTAG
*
19497438 GGGTTCACACATATAGGGTTCACACATGTA
1 GGGTTCACACATCT-GGGTTCACACATGTA
*
19497468 GGGTTCACACATCTGGGCTCACACATGTA
1 GGGTTCACACATCTGGGTTCACACATGTA
19497497 GGGTTCACACATCTGGGTTCACACATGTA
1 GGGTTCACACATCTGGGTTCACACATGTA
* * *
19497526 TGGTTCACACATCTGGCTTCGCACAT
1 GGGTTCACACATCTGGGTTCACACAT
19497552 ACAAGGTTTG
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 65 0.83
30 13 0.17
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (29 bp):
GGGTTCACACATCTGGGTTCACACATGTA
Found at i:19499863 original size:30 final size:30
Alignment explanation
Indices: 19499787--19499928 Score: 160
Period size: 30 Copynumber: 4.8 Consensus size: 30
19499777 CTAAAAATTC
* * * *
19499787 AAGGGTCGAAATATAATTTTAGGAAAGTTC
1 AAGGGTCAAAATATGATTTTGGGAAAGTTT
* * * *
19499817 GATGGTTAAAATGTGATTTTGGGAAAGTTT
1 AAGGGTCAAAATATGATTTTGGGAAAGTTT
* ** *
19499847 AGGGGTCAAAACGTGATTTT-AGAAAGTTT
1 AAGGGTCAAAATATGATTTTGGGAAAGTTT
*
19499876 AAGGGTCAAAATATGATTTTGGAAAAGTTT
1 AAGGGTCAAAATATGATTTTGGGAAAGTTT
19499906 AAGGGTCAAAATATGATTTTGGG
1 AAGGGTCAAAATATGATTTTGGG
19499929 GTAAAACAGG
Statistics
Matches: 91, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
29 25 0.27
30 66 0.73
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (30 bp):
AAGGGTCAAAATATGATTTTGGGAAAGTTT
Found at i:19501399 original size:17 final size:17
Alignment explanation
Indices: 19501360--19501400 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
19501350 ATTGTATTGG
19501360 ATATTTAAATTTAAAAT
1 ATATTTAAATTTAAAAT
* *
19501377 AAATTTAAATTTAGAAT
1 ATATTTAAATTTAAAAT
*
19501394 TTATTTA
1 ATATTTA
19501401 TTAATTTGGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
ATATTTAAATTTAAAAT
Found at i:19516010 original size:23 final size:23
Alignment explanation
Indices: 19515984--19516110 Score: 112
Period size: 23 Copynumber: 5.4 Consensus size: 23
19515974 AGTGCTGGAT
*
19515984 AACAGAGAGCACATACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * * *
19516007 AACAGAGAGTACACAAATTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
19516030 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
***
19516053 CTTAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
19516077 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
*
19516101 AACAAAGAGC
1 AACAGAGAGC
19516111 GCGCTAGTGT
Statistics
Matches: 84, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
23 65 0.77
24 2 0.02
25 14 0.17
26 3 0.04
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:19516110 original size:48 final size:46
Alignment explanation
Indices: 19515938--19516110 Score: 111
Period size: 46 Copynumber: 3.7 Consensus size: 46
19515928 ATACGGAACA
* * * * *
19515938 AACAGAGAGTATCAAA-GTACT-AACAAAGAGTACATAAGTGCTGGAT
1 AACAGAGAGCA-CAAACGTGCTAAACAAAGAGCACACAAGTGCT-AAT
* * * * *
19515984 AACAGAGAGCACATACAGTGCTAAACAGAGAGTACACAAAT--TACT
1 AACAGAGAGCACAAAC-GTGCTAAACAAAGAGCACACAAGTGCTAAT
* *** *
19516029 AATCAGAGAGCACACAAAGTGCTACTTAGAGAGCACACACAGTGCTAAT
1 AA-CAGAGAGCACA-AACGTGCTAAACAAAGAGCACACA-AGTGCTAAT
*
19516078 AACAGAGAGCACGAGACGTGCTAAACAAAGAGC
1 AACAGAGAGCAC-AAACGTGCTAAACAAAGAGC
19516111 GCGCTAGTGT
Statistics
Matches: 96, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
45 6 0.06
46 39 0.41
47 7 0.07
48 38 0.40
49 6 0.06
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (46 bp):
AACAGAGAGCACAAACGTGCTAAACAAAGAGCACACAAGTGCTAAT
Found at i:19518123 original size:18 final size:18
Alignment explanation
Indices: 19518065--19518126 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
19518055 GGGTATCCTC
* *
19518065 AAAATGCATAATGTTTTT
1 AAAATGGATAATGGTTTT
*
19518083 AAAAGGAAGAATAATGTGTTTT
1 AAAATG--G-ATAATG-GTTTT
19518105 AAAATGGATAATGGTTTT
1 AAAATGGATAATGGTTTT
19518123 AAAA
1 AAAA
19518127 GATCATACAC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 14 0.39
19 6 0.17
20 1 0.03
21 6 0.17
22 9 0.25
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (18 bp):
AAAATGGATAATGGTTTT
Found at i:19522597 original size:13 final size:13
Alignment explanation
Indices: 19522579--19522603 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19522569 CAATATATTT
19522579 ATTAATTAAAAAC
1 ATTAATTAAAAAC
19522592 ATTAATTAAAAA
1 ATTAATTAAAAA
19522604 TAAAAAATGC
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:19525398 original size:42 final size:42
Alignment explanation
Indices: 19525319--19525667 Score: 311
Period size: 42 Copynumber: 8.4 Consensus size: 42
19525309 CCGAGTCAAA
*
19525319 AGTCTTCCTTTAAACAT-A----ATGCTCATCCTGAATCACG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCTGAGTCACG
* * * *
19525356 AGTCTTCCTTTAAACATATTCTCATGGTCTTTCTGAGTCACG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCTGAGTCACG
* * ** ** *
19525398 AGTTTTCCTTTTAAACATAATCTCTTGCTCATCCCCAAACATG
1 AGTCTTCC-TTTAAACATAATCTCATGCTCATCCTGAGTCACG
* *
19525441 AGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGCCACG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCTGAGTCACG
* ** *
19525483 AGTCTTCCTTTAAACATATTCTCATGCTC-TTTTCGAGTCACA
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCT-GAGTCACG
* * *
19525525 AGTCTTCCTTTTAAATATAATCTCATGC-CTAT-CTCGAGACATG
1 AGTCTTCC-TTTAAACATAATCTCATGCTC-ATCCT-GAGTCACG
* ** *
19525568 A-TCTTCCTTTAAACATAATCTAATGCTCATCCCAAGTCACA
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCTGAGTCACG
* * * * *
19525609 AGTCTTCCTTTAAACATATTCTCATGCTTATCCCGAGACATG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCTGAGTCACG
*
19525651 AGTCTTCCTTTATACAT
1 AGTCTTCCTTTAAACAT
19525668 CAAGGGATTC
Statistics
Matches: 250, Mismatches: 49, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
37 17 0.07
41 25 0.10
42 151 0.60
43 56 0.22
44 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (42 bp):
AGTCTTCCTTTAAACATAATCTCATGCTCATCCTGAGTCACG
Done.