Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 10 of 109
Found at i:3223748 original size:107 final size:107
Alignment explanation
Indices: 3223560--3223759 Score: 337
Period size: 107 Copynumber: 1.9 Consensus size: 107
3223550 TTACAATCAT
* *
3223560 ATCTACCAGTCCAGCTTTCATCTTACTAGAGGCATCACCATGAGTGTTTTTATATCATATTATGC
1 ATCTACCAGTCCAACTTTCATCTTACTAGAGGCATCACCATGAGTGTCTTTATATCATATTATGC
* * *
3223625 CATGGGTCTCAGCCACATGGACTTACACATTCTCATGTGGTG
66 CAAGGGTCTCAACCACATAGACTTACACATTCTCATGTGGTG
*
3223667 ATCTACCAGTCCAACTTTCATCTTACTAGAGGCATCACCATGAGTGTCTTTATATTATATTATGC
1 ATCTACCAGTCCAACTTTCATCTTACTAGAGGCATCACCATGAGTGTCTTTATATCATATTATGC
*
3223732 CAAGGGTCTCAACCACATAGCCTTACAC
66 CAAGGGTCTCAACCACATAGACTTACAC
3223760 TTATTTTTGT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 86 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (107 bp):
ATCTACCAGTCCAACTTTCATCTTACTAGAGGCATCACCATGAGTGTCTTTATATCATATTATGC
CAAGGGTCTCAACCACATAGACTTACACATTCTCATGTGGTG
Found at i:3224898 original size:40 final size:40
Alignment explanation
Indices: 3224812--3224956 Score: 173
Period size: 41 Copynumber: 3.6 Consensus size: 40
3224802 AACCTTTCGG
* * * * *
3224812 GGCTTTAGCGGCGTTTTTTAAAAAGCGCTGCTATTGCTTA
1 GGCTTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCTCA
*
3224852 GAGCTTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCGCA
1 G-GCTTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCTCA
*
3224893 GGCTTTTAGCGGCAGTTTTAAAAAAGCGCCGCTAATGCTCA
1 GGC-TTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCTCA
* * * *
3224934 GGATTTAGCTGCGTTTTTGAAAA
1 GGCTTTAGCGGCATTTTTAAAAA
3224957 TGTGCCGCAA
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 19 0.21
41 71 0.79
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (40 bp):
GGCTTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCTCA
Found at i:3225441 original size:7 final size:7
Alignment explanation
Indices: 3225429--3225454 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3225419 ACAGTAAGGC
3225429 GTTAGGG
1 GTTAGGG
3225436 GTTAGGG
1 GTTAGGG
3225443 GTTAGGG
1 GTTAGGG
3225450 GTTAG
1 GTTAG
3225455 AGATTAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (7 bp):
GTTAGGG
Found at i:3225575 original size:13 final size:13
Alignment explanation
Indices: 3225550--3225587 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
3225540 TATTAAATAA
3225550 GGTTTAGGGGTTAG
1 GGTTTA-GGGTTAG
3225564 GGATTT-GGGTTAG
1 GG-TTTAGGGTTAG
3225577 GGTTTAGGGTT
1 GGTTTAGGGTT
3225588 TAGATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 14 0.64
14 2 0.09
15 3 0.14
ACGTcount: A:0.13, C:0.00, G:0.47, T:0.39
Consensus pattern (13 bp):
GGTTTAGGGTTAG
Found at i:3225585 original size:74 final size:76
Alignment explanation
Indices: 3225498--3225641 Score: 202
Period size: 74 Copynumber: 1.9 Consensus size: 76
3225488 TCGGTATCAA
* * *
3225498 GTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAA-TT-TATATTAAATAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
3225561 TAGGGATTTGG
66 TAGGGATTTGG
* * * **
3225572 GTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
3225637 TAGGG
66 TAGGG
3225642 GTTAGGGGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 31 0.52
75 2 0.03
76 27 0.45
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.44
Consensus pattern (76 bp):
GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
TAGGGATTTGG
Found at i:3225641 original size:7 final size:7
Alignment explanation
Indices: 3225629--3225659 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3225619 TAAAGAAGGT
3225629 TTAGGGG
1 TTAGGGG
3225636 TTAGGGG
1 TTAGGGG
3225643 TTAGGGG
1 TTAGGGG
*
3225650 TTAGAGG
1 TTAGGGG
3225657 TTA
1 TTA
3225660 AGAATTAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:3228990 original size:42 final size:43
Alignment explanation
Indices: 3228908--3229085 Score: 198
Period size: 43 Copynumber: 4.2 Consensus size: 43
3228898 TGTTTTTAGT
* * * * *
3228908 GGCGTTTTTTGCAAGAAGCGTCGCTAAAGGT-TTGTTCTATAAC
1 GGCGTTTGTGGCAA-AAGCGCCGCTAAAGGTCCTGATCTATAAC
3228951 GGCGTTTGT-GCAAAAGCGCCGCTAAAGGTCCTGATCTATAAC
1 GGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCCTGATCTATAAC
* * * * *
3228993 GGCGTTTGTGGAAAAAGTGCTGCTAAAGGTCCTGAACTATAGC
1 GGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCCTGATCTATAAC
* * * * *
3229036 GACGTTTGTGGGAAAAGTGCCGCTAAAGGTCATGGTCTATAAC
1 GGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCCTGATCTATAAC
3229079 GGCGTTT
1 GGCGTTT
3229086 ATTTCTAAAA
Statistics
Matches: 116, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
41 15 0.13
42 23 0.20
43 78 0.67
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (43 bp):
GGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCCTGATCTATAAC
Found at i:3229023 original size:43 final size:43
Alignment explanation
Indices: 3228929--3229085 Score: 201
Period size: 43 Copynumber: 3.7 Consensus size: 43
3228919 CAAGAAGCGT
* * * *
3228929 CGCTAAAGGT-TTGTTCTATAACGGCGTTTGT-GCAAAAGCGC
1 CGCTAAAGGTCCTGATCTATAACGGCGTTTGTGGAAAAAGTGC
3228970 CGCTAAAGGTCCTGATCTATAACGGCGTTTGTGGAAAAAGTGC
1 CGCTAAAGGTCCTGATCTATAACGGCGTTTGTGGAAAAAGTGC
* * * * *
3229013 TGCTAAAGGTCCTGAACTATAGCGACGTTTGTGGGAAAAGTGC
1 CGCTAAAGGTCCTGATCTATAACGGCGTTTGTGGAAAAAGTGC
* *
3229056 CGCTAAAGGTCATGGTCTATAACGGCGTTT
1 CGCTAAAGGTCCTGATCTATAACGGCGTTT
3229086 ATTTCTAAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 10 0.10
42 19 0.19
43 70 0.71
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (43 bp):
CGCTAAAGGTCCTGATCTATAACGGCGTTTGTGGAAAAAGTGC
Found at i:3231102 original size:13 final size:13
Alignment explanation
Indices: 3231086--3231110 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3231076 ATTAAGGTTG
3231086 TAAATATTTTTAT
1 TAAATATTTTTAT
3231099 TAAATATTTTTA
1 TAAATATTTTTA
3231111 GAGTCGTAAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTTTAT
Found at i:3234051 original size:23 final size:23
Alignment explanation
Indices: 3234025--3234076 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
3234015 AGAATTAGTT
*
3234025 AATTGCATGAAATTATTATTCTA
1 AATTGAATGAAATTATTATTCTA
3234048 AATTGAATGAAATTATTATTCTA
1 AATTGAATGAAATTATTATTCTA
*
3234071 GATTGA
1 AATTGA
3234077 GAATAAGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (23 bp):
AATTGAATGAAATTATTATTCTA
Found at i:3235239 original size:6 final size:6
Alignment explanation
Indices: 3235224--3235253 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3235214 AGTTCATGCC
*
3235224 TTTCAT TTTCAA TTTCAA TTTCAA TTTCAA
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
3235254 ACCACAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTCAA
Found at i:3235468 original size:21 final size:21
Alignment explanation
Indices: 3235442--3235500 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
3235432 CGACACGTAA
3235442 GTGCCTGAAACGACACACGAG
1 GTGCCTGAAACGACACACGAG
3235463 GTGCCTGAAACGACACACGAG
1 GTGCCTGAAACGACACACGAG
*
3235484 GTGCCTGATACGACACA
1 GTGCCTGAAACGACACA
3235501 TAAAATGCGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.32, C:0.29, G:0.27, T:0.12
Consensus pattern (21 bp):
GTGCCTGAAACGACACACGAG
Found at i:3235545 original size:23 final size:22
Alignment explanation
Indices: 3235430--3235558 Score: 86
Period size: 21 Copynumber: 6.0 Consensus size: 22
3235420 CTGATTAGTA
*
3235430 TACGACACGT-AAGTGCCTGA-
1 TACGACACATAAAGTGCCTGAG
* ** *
3235450 AACGACACACGAGGTGCCTGA-
1 TACGACACATAAAGTGCCTGAG
* ** *
3235471 AACGACACACGAGGTGCCTGA-
1 TACGACACATAAAGTGCCTGAG
* *
3235492 TACGACACATAAAATGCGTGAG
1 TACGACACATAAAGTGCCTGAG
*
3235514 ATACAACACATAAAGTGCCTGATG
1 -TACGACACATAAAGTGCCTGA-G
* *
3235538 TACGACACTTAAAGTGTCTGA
1 TACGACACATAAAGTGCCTGA
3235559 TCGGCAAAGC
Statistics
Matches: 89, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
20 7 0.08
21 45 0.51
23 36 0.40
24 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (22 bp):
TACGACACATAAAGTGCCTGAG
Found at i:3235829 original size:36 final size:38
Alignment explanation
Indices: 3235749--3235847 Score: 91
Period size: 36 Copynumber: 2.7 Consensus size: 38
3235739 ACCAACACAT
* * *
3235749 ACTTTCAAATTCACATTTCAATTC-AATTTCACTTTTTC
1 ACTTTC-AAGTCACAATTCAATTCAAATTTCAATTTTTC
3235787 ACTTTCAA-TCACAATTCAATTCAAATTT-AA-TTTTC
1 ACTTTCAAGTCACAATTCAATTCAAATTTCAATTTTTC
* *
3235822 TATTTTCAAGTCA-ATATTCATTTCAA
1 -ACTTTCAAGTCACA-ATTCAATTCAA
3235848 TTCCATACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
35 5 0.09
36 22 0.42
37 20 0.38
38 6 0.11
ACGTcount: A:0.33, C:0.20, G:0.01, T:0.45
Consensus pattern (38 bp):
ACTTTCAAGTCACAATTCAATTCAAATTTCAATTTTTC
Found at i:3237040 original size:18 final size:20
Alignment explanation
Indices: 3237005--3237042 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
3236995 AGATAAAAAA
3237005 AAAACTTTAAATACCAAATT
1 AAAACTTTAAATACCAAATT
3237025 AAAA-TTTAAA-ACCAAATT
1 AAAACTTTAAATACCAAATT
3237043 CAAGTACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 6 0.33
20 4 0.22
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAACTTTAAATACCAAATT
Found at i:3246792 original size:40 final size:42
Alignment explanation
Indices: 3246737--3246848 Score: 140
Period size: 40 Copynumber: 2.7 Consensus size: 42
3246727 TAAATATATT
*
3246737 TATTTTTTT-AATTTTAAAATATTTTTTACATAC-TTTTTAA
1 TATTTTTTTAAATTTTAAAATATTTTTTAAATACTTTTTTAA
*
3246777 -ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 TATTTTTTTAAATTTTAAAATATTTTTTAAATAC-TTTTTTAA
* *
3246819 TTTTTTTTTTAATTTTTAAAATAATTTTTT
1 -TATTTTTTTAAATTTTAAAAT-ATTTTTT
3246849 GGTATTTATT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
39 8 0.13
40 22 0.36
42 7 0.11
44 18 0.30
45 6 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (42 bp):
TATTTTTTTAAATTTTAAAATATTTTTTAAATACTTTTTTAA
Found at i:3246803 original size:18 final size:18
Alignment explanation
Indices: 3246740--3246805 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 18
3246730 ATATATTTAT
*
3246740 TTTTTTAATTTTAAAATA
1 TTTTTAAATTTTAAAATA
* *
3246758 TTTTTTACATACTTTTTAAATT
1 -TTTTTA-A-A-TTTTAAAATA
3246780 TTTTTAAATTTTAAAATA
1 TTTTTAAATTTTAAAATA
3246798 TTTTTAAA
1 TTTTTAAA
3246806 ATACTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 16 0.41
19 6 0.15
20 2 0.05
21 7 0.18
22 8 0.21
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTAAATTTTAAAATA
Found at i:3246825 original size:12 final size:12
Alignment explanation
Indices: 3246810--3246835 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3246800 TTTAAAATAC
3246810 TTTTTTTAATTT
1 TTTTTTTAATTT
3246822 TTTTTTTAATTT
1 TTTTTTTAATTT
3246834 TT
1 TT
3246836 AAAATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTAATTT
Found at i:3247137 original size:21 final size:21
Alignment explanation
Indices: 3247098--3247137 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3247088 TGAATTTTTT
* *
3247098 TTTCTTCTCCCTCTGTTTTCC
1 TTTCTTCTCCATCTCTTTTCC
*
3247119 TTTCTTCTCCATTTCTTTT
1 TTTCTTCTCCATCTCTTTT
3247138 AACGTAGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.33, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTCTTCTCCATCTCTTTTCC
Found at i:3247245 original size:20 final size:21
Alignment explanation
Indices: 3247222--3247270 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
3247212 TTCTTTTTTT
3247222 ATTTTCTTTTTCT-TCTTCCC
1 ATTTTCTTTTTCTCTCTTCCC
* *
3247242 A-TTTATTTTTCTCTCTTCTC
1 ATTTTCTTTTTCTCTCTTCCC
*
3247262 ATATTCTTT
1 ATTTTCTTT
3247271 ACTGCAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 10 0.43
20 8 0.35
21 5 0.22
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTCTTTTTCTCTCTTCCC
Found at i:3251119 original size:19 final size:19
Alignment explanation
Indices: 3251092--3251138 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3251082 GGACTAATTT
3251092 GAAACAAAATAGAAAATTTTA
1 GAAA-AAAAT-GAAAATTTTA
* *
3251113 GAAAAAAATTAAAATTTTG
1 GAAAAAAATGAAAATTTTA
3251132 GAAAAAA
1 GAAAAAA
3251139 GGGTTACACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.62
20 5 0.21
21 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (19 bp):
GAAAAAAATGAAAATTTTA
Found at i:3267537 original size:56 final size:56
Alignment explanation
Indices: 3267476--3267626 Score: 221
Period size: 56 Copynumber: 2.7 Consensus size: 56
3267466 ATTGCGATAC
*
3267476 ATGAATGTTTATAAGACCATGTGGTTAAGACCCATGGCAAGATATGAAATGACTGA
1 ATGAATGTTTGTAAGACCATGTGGTTAAGACCCATGGCAAGATATGAAATGACTGA
* * * * *
3267532 ATGAATGTTTGTAAGACCATATGGTTAATATCTATGGCAAGATATGAAATGATTGA
1 ATGAATGTTTGTAAGACCATGTGGTTAAGACCCATGGCAAGATATGAAATGACTGA
* * *
3267588 ATGAATGTATGTAAGACCATGAGATTAAGACCCATGGCA
1 ATGAATGTTTGTAAGACCATGTGGTTAAGACCCATGGCA
3267627 TCTTCTGTGA
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 82 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (56 bp):
ATGAATGTTTGTAAGACCATGTGGTTAAGACCCATGGCAAGATATGAAATGACTGA
Found at i:3272924 original size:20 final size:19
Alignment explanation
Indices: 3272901--3272952 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
3272891 CTCCGATGCC
3272901 TCTGTTTGCACTTTGGTGCT
1 TCTGTTTGCACTTTGGTG-T
* *
3272921 TCTGTATACACTTTGGTGT
1 TCTGTTTGCACTTTGGTGT
*
3272940 CCTTGTTTGCACT
1 TC-TGTTTGCACT
3272953 ACGATGCCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.48
Consensus pattern (19 bp):
TCTGTTTGCACTTTGGTGT
Found at i:3273778 original size:23 final size:23
Alignment explanation
Indices: 3273746--3273789 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3273736 ACTACCATTT
3273746 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
3273769 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
3273790 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:3273782 original size:13 final size:11
Alignment explanation
Indices: 3273750--3273792 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
3273740 CCATTTTCTA
*
3273750 AATAAAATAAT
1 AATAAAATATT
3273761 AAT-AAATATCT
1 AATAAAATAT-T
3273772 AAGTAAAATATT
1 AA-TAAAATATT
3273784 AATAAAATA
1 AATAAAATA
3273793 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:3277587 original size:40 final size:40
Alignment explanation
Indices: 3277543--3277622 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
3277533 TGTATCCTCC
3277543 ACATTTACTTGTACCTTGTCTACAGCTACAACTAGCTCTA
1 ACATTTACTTGTACCTTGTCTACAGCTACAACTAGCTCTA
3277583 ACATTTACTTGTACCTTGTCTACAGCTACAACTAGCTCTA
1 ACATTTACTTGTACCTTGTCTACAGCTACAACTAGCTCTA
3277623 CCTTCATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (40 bp):
ACATTTACTTGTACCTTGTCTACAGCTACAACTAGCTCTA
Found at i:3282362 original size:17 final size:17
Alignment explanation
Indices: 3282336--3282368 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3282326 AACCCATATC
*
3282336 AATCATATATCAATCAG
1 AATCACATATCAATCAG
3282353 AATCACATATCAATCA
1 AATCACATATCAATCA
3282369 TATTCATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.27
Consensus pattern (17 bp):
AATCACATATCAATCAG
Found at i:3288262 original size:30 final size:30
Alignment explanation
Indices: 3288221--3288306 Score: 111
Period size: 30 Copynumber: 2.9 Consensus size: 30
3288211 TACGAGATAA
*
3288221 ATTGCTCACACAAGCTGACAGTATATTAGGT
1 ATTGCTCACACAAGCTGACATTATATTA-GT
* * *
3288252 -TTGTTCACACAAGTTGACATTATAATAGT
1 ATTGCTCACACAAGCTGACATTATATTAGT
*
3288281 ATTGCTCACACAATCTGACATTATAT
1 ATTGCTCACACAAGCTGACATTATAT
3288307 CGAAATTACC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 2 0.04
30 44 0.96
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34
Consensus pattern (30 bp):
ATTGCTCACACAAGCTGACATTATATTAGT
Found at i:3291529 original size:3 final size:3
Alignment explanation
Indices: 3291516--3291577 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
3291506 CACTTCAACT
* *
3291516 GAA GGA GAA GAA GAA GAA GAA GAA GTA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3291564 GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GA
3291578 GGGCAGTGTC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:3291806 original size:19 final size:18
Alignment explanation
Indices: 3291773--3291812 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3291763 AAAAACCCTA
3291773 ATTATTATTTTAGTTAGT
1 ATTATTATTTTAGTTAGT
* *
3291791 ATTATTGTTGTTAGTTATT
1 ATTATTATT-TTAGTTAGT
3291810 ATT
1 ATT
3291813 GTTAGTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (18 bp):
ATTATTATTTTAGTTAGT
Found at i:3291899 original size:60 final size:59
Alignment explanation
Indices: 3291738--3291923 Score: 194
Period size: 57 Copynumber: 3.2 Consensus size: 59
3291728 TAGTTTAGTT
* *
3291738 ATTATTGTTAGTTATTAAGATTAATAAAAACCCTAATTATTATTTTAG----TTAGTATT
1 ATTATTGTTAGTTATTAAGATTAATAAAAA-CCTAATTATTATTTTAGTATTTTTGTATA
* * * * *
3291794 ATTGTTGTTAGTTATTATTG-TTAGT--TAA--TAATTATTTTTACTTAGTATTTTTGTATA
1 ATTATTGTTAGTTATTA-AGATTAATAAAAACCTAATTATTATT--TTAGTATTTTTGTATA
3291851 ATTATTGTTAGTTATTAAGATTAATAAAAACCGTAATTATTATTTTAGTATTTTTGTATA
1 ATTATTGTTAGTTATTAAGATTAATAAAAACC-TAATTATTATTTTAGTATTTTTGTATA
3291911 ATTATT-TTAGTTA
1 ATTATTGTTAGTTA
3291924 GTATAACTAT
Statistics
Matches: 105, Mismatches: 12, Indels: 23
0.75 0.09 0.16
Matches are distributed among these distances:
51 10 0.10
53 4 0.04
54 2 0.02
56 21 0.20
57 27 0.26
59 9 0.09
60 22 0.21
62 10 0.10
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.53
Consensus pattern (59 bp):
ATTATTGTTAGTTATTAAGATTAATAAAAACCTAATTATTATTTTAGTATTTTTGTATA
Found at i:3291917 original size:22 final size:22
Alignment explanation
Indices: 3291889--3291953 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 22
3291879 AACCGTAATT
3291889 ATTATTTTAGTATTTTTGTATA
1 ATTATTTTAGTATTTTTGTATA
*
3291911 ATTATTTTAG----TTAGTATA
1 ATTATTTTAGTATTTTTGTATA
*
3291929 ACTATTGTTAGTTATTTTTGTATA
1 ATTATT-TTAG-TATTTTTGTATA
3291953 A
1 A
3291954 GTTTAGTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
18 12 0.35
19 4 0.12
22 10 0.29
24 8 0.24
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.58
Consensus pattern (22 bp):
ATTATTTTAGTATTTTTGTATA
Found at i:3291972 original size:155 final size:154
Alignment explanation
Indices: 3291801--3292308 Score: 538
Period size: 155 Copynumber: 3.3 Consensus size: 154
3291791 ATTATTGTTG
*
3291801 TTAGTTATTATTGTTAGTTAATAATTATTTTTACTTAGTATTTTTGTATAATTATTGTTAGTTAT
1 TTAGTTATTATTGTTAGTTAATAATTATTGTTACTTAGTATTTTTGTATAATTATTGTTAGTTAT
3291866 TAAGATTAATAAAAACCGTAATTATTATTTTAGTATTTTTGTATAATTATTTTAGTTAGTATAAC
66 TAAGATTAATAAAAACCGTAATTATTATTTT-GTATTTTTGTATAATTATTTTAGTTAGTATAAC
3291931 TATTGTTAGTTATTTTTGTATAAGT
130 TATTGTTAGTTATTTTTGTATAAGT
3291956 TTAGTTATTATTGTTAGTTAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATT
1 TTAGTTATTATTGTTAGTTAATAATTATTGTTACTTAGTA-T-TT-TT-G--------T-ATA--
* * * * *
3292021 ATTATTATGGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTATTTT-TA-GTTAGTAT-A-T
51 ATTA-T-T-GTTAGTTATTAAGATTAATAAAAACCGTAATTATTATTTTGTATTTTTGTATAATT
* * *
3292082 -TGTTAGTT--T-TTAC-ATT-ATA-TTATTGTTTGT-T-A--
113 ATTTTAGTTAGTATAACTATTGTTAGTTATT-TTTGTATAAGT
* * * *
3292114 TTA-TT-TT-TAGTTA-ATAATTATTGTT---ACTTAGTATTTTTGTATAATTATTGTTAGTTAT
1 TTAGTTATTATTGTTAGTTAATAATTATTGTTACTTAGTATTTTTGTATAATTATTGTTAGTTAT
*
3292172 TAAGATTAATAAAAACCGTAATTATTATTTTTGTATTTTTGTATAATTATTTTAATTAGTATAAC
66 TAAGATTAATAAAAACCGTAATTATTA-TTTTGTATTTTTGTATAATTATTTTAGTTAGTATAAC
3292237 TATTGTTAGTTATTTTTGTATAAGT
130 TATTGTTAGTTATTTTTGTATAAGT
*
3292262 TTAGTTATTATTGTTAGTTAATAATTATTGTTACTTAGTATTATTGT
1 TTAGTTATTATTGTTAGTTAATAATTATTGTTACTTAGTATTTTTGT
3292309 TAGTAAAAAA
Statistics
Matches: 284, Mismatches: 27, Indels: 84
0.72 0.07 0.21
Matches are distributed among these distances:
133 33 0.12
134 5 0.02
135 3 0.01
136 10 0.04
137 1 0.00
138 4 0.01
139 7 0.02
141 1 0.00
142 3 0.01
143 3 0.01
144 7 0.02
145 6 0.02
146 1 0.00
147 1 0.00
148 5 0.02
149 4 0.01
150 3 0.01
151 13 0.05
152 9 0.03
154 9 0.03
155 58 0.20
156 3 0.01
157 4 0.01
158 5 0.02
159 1 0.00
160 1 0.00
161 6 0.02
162 7 0.02
163 3 0.01
164 3 0.01
165 1 0.00
167 8 0.03
168 4 0.01
169 1 0.00
170 10 0.04
171 3 0.01
172 1 0.00
173 37 0.13
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (154 bp):
TTAGTTATTATTGTTAGTTAATAATTATTGTTACTTAGTATTTTTGTATAATTATTGTTAGTTAT
TAAGATTAATAAAAACCGTAATTATTATTTTGTATTTTTGTATAATTATTTTAGTTAGTATAACT
ATTGTTAGTTATTTTTGTATAAGT
Found at i:3292040 original size:42 final size:41
Alignment explanation
Indices: 3291974--3292088 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 41
3291964 TATTGTTAGT
* * *
3291974 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAA-AC
1 TAATTATTATTTTTAGTTAGTATTATTGTTAGTAAAAACAC
* * *
3292014 TAA-TATTATTATTATGGTTAGTTATTA-GGATTAGTAAAAACCC
1 TAATTATTATT-TT-TAGTTAG-TATTATTG-TTAGTAAAAACAC
3292057 TAATTATTATTTTTAGTTAGTA-TATTGTTAGT
1 TAATTATTATTTTTAGTTAGTATTATTGTTAGT
3292089 TTTTACATTA
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
39 6 0.10
40 11 0.18
41 9 0.15
42 21 0.35
43 6 0.10
44 7 0.12
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (41 bp):
TAATTATTATTTTTAGTTAGTATTATTGTTAGTAAAAACAC
Found at i:3292135 original size:30 final size:27
Alignment explanation
Indices: 3292100--3292173 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 27
3292090 TTTACATTAT
*
3292100 ATTATTGTTTGTTATTATTTTTAGTTAATA
1 ATTATTGTTAGTTATTATTTTT-G-T-ATA
* *
3292130 ATTATTGTTACTTAGTATTTTTGTATA
1 ATTATTGTTAGTTATTATTTTTGTATA
3292157 ATTATTGTTAGTTATTA
1 ATTATTGTTAGTTATTA
3292174 AGATTAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 18 0.46
28 1 0.03
29 1 0.03
30 19 0.49
ACGTcount: A:0.27, C:0.01, G:0.11, T:0.61
Consensus pattern (27 bp):
ATTATTGTTAGTTATTATTTTTGTATA
Found at i:3292139 original size:151 final size:159
Alignment explanation
Indices: 3291851--3292384 Score: 447
Period size: 173 Copynumber: 3.4 Consensus size: 159
3291841 TTTTTGTATA
* * * * * *
3291851 ATTATTGTTAGTTATTAAGATTAATAAAAACCGTAATTATTATTTTAGTATTTTTGTATAATTAT
1 ATTATGGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTATTTT--TA-GTTAGTATAATTAT
* * * *
3291916 TTTAGTTAGTATAACTATTGTTAGTTATTTTTGTATAAGTTTAGTTATTATTGTTAGTTAATAAT
63 GTTAATTA-TATAACTATTGATAGTTA------T-T--GTTT-GTTATTATTTTTAGTTAATAAT
3291981 TATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATT
117 TATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATT
3292024 ATTATGGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTATTTTTAGTTAGTAT-A-T-TGTT
1 ATTATGGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTATTTTTAGTTAGTATAATTATGTT
* *
3292086 AGTT-T-TTAC-ATT-ATA-TTATTGTTTGTTATTATTTTTAGTTAATAATTATTGTTACTTAGT
66 AATTATATAACTATTGATAGTTATTGTTTGTTATTATTTTTAGTTAATAATTATTGTTACTTAGT
3292146 A-T-TT-TT-G--------T-ATA--ATT
131 ATTATTGTTAGTAAAAAACTAATATTATT
* * * * *
3292160 A-T-T-GTTAGTTATTAAGATTAATAAAAACCGTAATTATTATTTTTGTATTTTTGTATAATTAT
1 ATTATGGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTA-TTTT-TA-GTTAGTATAATTAT
* * *
3292222 TTTAATTAGTATAACTATTGTTAGTTATTTTTGTATAAGTTTAGTTATTATTGTTAGTTAATAAT
63 GTTAATTA-TATAACTATTGATAGTTA------T-T--GTTT-GTTATTATTTTTAGTTAATAAT
3292287 TATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATT
117 TATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATT
3292330 ATTATGGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTA-TTTTAGTTAGTAT
1 ATTATGGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTATTTTTAGTTAGTAT
3292385 GAATGAAAAA
Statistics
Matches: 296, Mismatches: 25, Indels: 84
0.73 0.06 0.21
Matches are distributed among these distances:
133 33 0.11
134 5 0.02
135 3 0.01
136 10 0.03
137 1 0.00
138 4 0.01
139 7 0.02
141 1 0.00
142 3 0.01
143 3 0.01
144 2 0.01
145 3 0.01
147 1 0.00
148 2 0.01
149 2 0.01
150 1 0.00
151 37 0.12
152 5 0.02
154 5 0.02
155 37 0.12
156 1 0.00
157 2 0.01
158 2 0.01
159 1 0.00
161 3 0.01
162 2 0.01
163 3 0.01
164 3 0.01
165 1 0.00
167 8 0.03
168 4 0.01
169 7 0.02
170 12 0.04
171 6 0.02
172 1 0.00
173 75 0.25
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.52
Consensus pattern (159 bp):
ATTATGGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTATTTTTAGTTAGTATAATTATGTT
AATTATATAACTATTGATAGTTATTGTTTGTTATTATTTTTAGTTAATAATTATTGTTACTTAGT
ATTATTGTTAGTAAAAAACTAATATTATT
Found at i:3292290 original size:17 final size:16
Alignment explanation
Indices: 3292267--3292312 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
3292257 TAAGTTTAGT
3292267 TATTATTGTTAGTTAA
1 TATTATTGTTAGTTAA
* *
3292283 TAATTATTGTTACTTAG
1 T-ATTATTGTTAGTTAA
3292300 TATTATTGTTAGT
1 TATTATTGTTAGT
3292313 AAAAAACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (16 bp):
TATTATTGTTAGTTAA
Found at i:3292357 original size:306 final size:305
Alignment explanation
Indices: 3291793--3292384 Score: 1121
Period size: 306 Copynumber: 1.9 Consensus size: 305
3291783 TAGTTAGTAT
* *
3291793 TATTGTTGTTAGTTATTATTGTTAGTTAATAATTATTTTTACTTAGTATTTTTGTATAATTATTG
1 TATTATTGTTAGTTATTATTGTTAGTTAATAATTATTGTTACTTAGTATTTTTGTATAATTATTG
*
3291858 TTAGTTATTAAGATTAATAAAAACCGTAATTATTATTTTAGTATTTTTGTATAATTATTTTAGTT
66 TTAGTTATTAAGATTAATAAAAACCGTAATTATTATTTTAGTATTTTTGTATAATTATTTTAATT
3291923 AGTATAACTATTGTTAGTTATTTTTGTATAAGTTTAGTTATTATTGTTAGTTAATAATTATTGTT
131 AGTATAACTATTGTTAGTTATTTTTGTATAAGTTTAGTTATTATTGTTAGTTAATAATTATTGTT
3291988 ACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTATTAGGATTAGTAAAA
196 ACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTATTAGGATTAGTAAAA
3292053 ACCCTAATTATTATTTTTAGTTAGTATATTGTTAGTTTTTACATTA
261 ACCCTAATTATTA-TTTTAGTTAGTATATTGTTAGTTTTTACATTA
* *
3292099 TATTATTGTTTGTTATTATTTTTAGTTAATAATTATTGTTACTTAGTATTTTTGTATAATTATTG
1 TATTATTGTTAGTTATTATTGTTAGTTAATAATTATTGTTACTTAGTATTTTTGTATAATTATTG
*
3292164 TTAGTTATTAAGATTAATAAAAACCGTAATTATTATTTTTGTATTTTTGTATAATTATTTTAATT
66 TTAGTTATTAAGATTAATAAAAACCGTAATTATTATTTTAGTATTTTTGTATAATTATTTTAATT
3292229 AGTATAACTATTGTTAGTTATTTTTGTATAAGTTTAGTTATTATTGTTAGTTAATAATTATTGTT
131 AGTATAACTATTGTTAGTTATTTTTGTATAAGTTTAGTTATTATTGTTAGTTAATAATTATTGTT
3292294 ACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTATTAGGATTAGTAAAA
196 ACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTATTAGGATTAGTAAAA
3292359 ACCCTAATTATTATTTTAGTTAGTAT
261 ACCCTAATTATTATTTTAGTTAGTAT
3292385 GAATGAAAAA
Statistics
Matches: 280, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
305 13 0.05
306 267 0.95
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.53
Consensus pattern (305 bp):
TATTATTGTTAGTTATTATTGTTAGTTAATAATTATTGTTACTTAGTATTTTTGTATAATTATTG
TTAGTTATTAAGATTAATAAAAACCGTAATTATTATTTTAGTATTTTTGTATAATTATTTTAATT
AGTATAACTATTGTTAGTTATTTTTGTATAAGTTTAGTTATTATTGTTAGTTAATAATTATTGTT
ACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTATTAGGATTAGTAAAA
ACCCTAATTATTATTTTAGTTAGTATATTGTTAGTTTTTACATTA
Found at i:3295222 original size:8 final size:8
Alignment explanation
Indices: 3295209--3295251 Score: 77
Period size: 8 Copynumber: 5.4 Consensus size: 8
3295199 AATTGTTATG
*
3295209 TGTAATAT
1 TGTAATGT
3295217 TGTAATGT
1 TGTAATGT
3295225 TGTAATGT
1 TGTAATGT
3295233 TGTAATGT
1 TGTAATGT
3295241 TGTAATGT
1 TGTAATGT
3295249 TGT
1 TGT
3295252 TGTAAGACCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (8 bp):
TGTAATGT
Found at i:3295230 original size:16 final size:16
Alignment explanation
Indices: 3295194--3295251 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
3295184 GAGCTTATGC
* *
3295194 TGTAAAATTGTTATG-
1 TGTAATATTGTAATGT
3295209 TGTAATATTGTAATGT
1 TGTAATATTGTAATGT
*
3295225 TGTAATGTTGTAATGT
1 TGTAATATTGTAATGT
*
3295241 TGTAATGTTGT
1 TGTAATATTGT
3295252 TGTAAGACCC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
15 13 0.33
16 26 0.67
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (16 bp):
TGTAATATTGTAATGT
Found at i:3295243 original size:24 final size:23
Alignment explanation
Indices: 3295201--3295251 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
3295191 TGCTGTAAAA
*
3295201 TTGTTATGTGTAATATTGTAATG
1 TTGTAATGTGTAATATTGTAATG
*
3295224 TTGTAATGTTGTAATGTTGTAATG
1 TTGTAATG-TGTAATATTGTAATG
3295248 TTGT
1 TTGT
3295252 TGTAAGACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (23 bp):
TTGTAATGTGTAATATTGTAATG
Found at i:3298214 original size:22 final size:22
Alignment explanation
Indices: 3298167--3298211 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
3298157 ATACAATCTT
*
3298167 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATATTAGA
* *
3298189 AGATATGATTTTGTAATATTAGA
1 AGATATGA-TATGCAATATTAGA
3298212 GATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATATTAGA
Found at i:3298396 original size:18 final size:19
Alignment explanation
Indices: 3298373--3298413 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3298363 CAAATTTCTG
*
3298373 TTTCTGTTGC-GTTCTTAT
1 TTTCTGTGGCTGTTCTTAT
3298391 TTTCTGTGGCTTGTTCTTAT
1 TTTCTGTGGC-TGTTCTTAT
3298411 TTT
1 TTT
3298414 GTTGGTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.05, C:0.15, G:0.17, T:0.63
Consensus pattern (19 bp):
TTTCTGTGGCTGTTCTTAT
Found at i:3300449 original size:302 final size:302
Alignment explanation
Indices: 3299903--3300508 Score: 1212
Period size: 302 Copynumber: 2.0 Consensus size: 302
3299893 GTATTTTATT
3299903 TCTTCATAAACATATTTTTCAGTATTTTATTTTTAATGCTATTTTTTGTAAAAAAAAACTCATTA
1 TCTTCATAAACATATTTTTCAGTATTTTATTTTTAATGCTATTTTTTGTAAAAAAAAACTCATTA
3299968 CAACATGCTAAATAAATTCATAAAAAATATATCTAATCAACATAGAATGTACATAACATTAGTTT
66 CAACATGCTAAATAAATTCATAAAAAATATATCTAATCAACATAGAATGTACATAACATTAGTTT
3300033 TTTACATGCTAAATAAATTTCATAAAAATTTTATACTAAATAAAATAATAAAACATATAATATAC
131 TTTACATGCTAAATAAATTTCATAAAAATTTTATACTAAATAAAATAATAAAACATATAATATAC
3300098 ATAACATGAGTTTTTTACACAAATTATATAAAAAAATTAAAATAATACCAAAAAAAATTACCTTC
196 ATAACATGAGTTTTTTACACAAATTATATAAAAAAATTAAAATAATACCAAAAAAAATTACCTTC
3300163 CTTTTTTTTTCTTTCTTTTTCCTTCCCTCCCTCTTCTTCTTC
261 CTTTTTTTTTCTTTCTTTTTCCTTCCCTCCCTCTTCTTCTTC
3300205 TCTTCATAAACATATTTTTCAGTATTTTATTTTTAATGCTATTTTTTGTAAAAAAAAACTCATTA
1 TCTTCATAAACATATTTTTCAGTATTTTATTTTTAATGCTATTTTTTGTAAAAAAAAACTCATTA
3300270 CAACATGCTAAATAAATTCATAAAAAATATATCTAATCAACATAGAATGTACATAACATTAGTTT
66 CAACATGCTAAATAAATTCATAAAAAATATATCTAATCAACATAGAATGTACATAACATTAGTTT
3300335 TTTACATGCTAAATAAATTTCATAAAAATTTTATACTAAATAAAATAATAAAACATATAATATAC
131 TTTACATGCTAAATAAATTTCATAAAAATTTTATACTAAATAAAATAATAAAACATATAATATAC
3300400 ATAACATGAGTTTTTTACACAAATTATATAAAAAAATTAAAATAATACCAAAAAAAATTACCTTC
196 ATAACATGAGTTTTTTACACAAATTATATAAAAAAATTAAAATAATACCAAAAAAAATTACCTTC
3300465 CTTTTTTTTTCTTTCTTTTTCCTTCCCTCCCTCTTCTTCTTC
261 CTTTTTTTTTCTTTCTTTTTCCTTCCCTCCCTCTTCTTCTTC
3300507 TC
1 TC
3300509 CTTCTCTTTC
Statistics
Matches: 304, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
302 304 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.40
Consensus pattern (302 bp):
TCTTCATAAACATATTTTTCAGTATTTTATTTTTAATGCTATTTTTTGTAAAAAAAAACTCATTA
CAACATGCTAAATAAATTCATAAAAAATATATCTAATCAACATAGAATGTACATAACATTAGTTT
TTTACATGCTAAATAAATTTCATAAAAATTTTATACTAAATAAAATAATAAAACATATAATATAC
ATAACATGAGTTTTTTACACAAATTATATAAAAAAATTAAAATAATACCAAAAAAAATTACCTTC
CTTTTTTTTTCTTTCTTTTTCCTTCCCTCCCTCTTCTTCTTC
Found at i:3300548 original size:3 final size:3
Alignment explanation
Indices: 3300540--3300566 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3300530 CGCCTCCTTC
3300540 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
3300567 TCCTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:3305669 original size:9 final size:9
Alignment explanation
Indices: 3305655--3305691 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
3305645 TATAGTTTGA
3305655 TATTCGAAT
1 TATTCGAAT
3305664 TATTCGAAT
1 TATTCGAAT
*
3305673 TATTCGAGT
1 TATTCGAAT
3305682 TATTCGAAT
1 TATTCGAAT
3305691 T
1 T
3305692 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:3305763 original size:9 final size:9
Alignment explanation
Indices: 3305746--3305776 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3305736 TCGAGTTGAT
3305746 TCGAATAAC
1 TCGAATAAC
*
3305755 TCGATTAAC
1 TCGAATAAC
3305764 TCGAATAAC
1 TCGAATAAC
3305773 TCGA
1 TCGA
3305777 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:3306214 original size:20 final size:19
Alignment explanation
Indices: 3306189--3306235 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
3306179 ATTAATTATT
3306189 TATAAAATTTAATTAGAATA
1 TATAAAATTTAATTA-AATA
* * *
3306209 TATAAACTATATTTAAATA
1 TATAAAATTTAATTAAATA
3306228 TA-AAAATT
1 TATAAAATT
3306236 AAATATTTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TATAAAATTTAATTAAATA
Found at i:3308032 original size:19 final size:19
Alignment explanation
Indices: 3307990--3308039 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
3307980 CTGAGTTTTG
* *
3307990 AAGTAAATTAAGATCACTG
1 AAGTGAATTAAGATCACTA
*
3308009 AAGTGAATTAGGATCACTA
1 AAGTGAATTAAGATCACTA
*
3308028 AAGTGAGTTAAG
1 AAGTGAATTAAG
3308040 TTCCTGCCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (19 bp):
AAGTGAATTAAGATCACTA
Found at i:3313396 original size:39 final size:39
Alignment explanation
Indices: 3313353--3313430 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
3313343 AATGCCTAAG
3313353 GAATTAGGTTCATGTATTAATTGGATGGAAATCCATATT
1 GAATTAGGTTCATGTATTAATTGGATGGAAATCCATATT
3313392 GAATTAGGTTCATGTATTAATTGGATGGAAATCCATATT
1 GAATTAGGTTCATGTATTAATTGGATGGAAATCCATATT
3313431 CTTACTCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (39 bp):
GAATTAGGTTCATGTATTAATTGGATGGAAATCCATATT
Found at i:3321999 original size:94 final size:96
Alignment explanation
Indices: 3321834--3322006 Score: 251
Period size: 94 Copynumber: 1.8 Consensus size: 96
3321824 CTTTTTTTTA
* * *
3321834 TTATTGTTTGTTTTATAATATTTTAAATATATATATTTTTTGGAGGAGTCATTCTAAATTGTGCC
1 TTATTATTTGTTTTATAATATTTTAAATATATATATTTTTTGGAGGAGTCATTCTAAATGGCGCC
* *
3321899 CCCAGTTTATTTAATTTTTTTAAAAATTTGT
66 ACCAGTTCATTTAATTTTTTTAAAAATTTGT
* * *
3321930 TTATTATTTGTTTTATAATATTTTAAA-GT-TATATTTTTTGGTGGAGTCATTCTAAATGGCGTC
1 TTATTATTTGTTTTATAATATTTTAAATATATATATTTTTTGGAGGAGTCATTCTAAATGGCGCC
*
3321993 ATCAGTTCATTTAA
66 ACCAGTTCATTTAA
3322007 ACATTTTTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
94 41 0.60
95 1 0.01
96 26 0.38
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.52
Consensus pattern (96 bp):
TTATTATTTGTTTTATAATATTTTAAATATATATATTTTTTGGAGGAGTCATTCTAAATGGCGCC
ACCAGTTCATTTAATTTTTTTAAAAATTTGT
Found at i:3322049 original size:22 final size:22
Alignment explanation
Indices: 3322001--3322047 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3321991 TCATCAGTTC
** *
3322001 ATTTAAACATTTTTTAAATTAT
1 ATTTAAACATTTTAAAAATAAT
3322023 ATTTAAA-ATTTTAAAAATAAT
1 ATTTAAACATTTTAAAAATAAT
3322044 ATTT
1 ATTT
3322048 TATTTGGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTAAACATTTTAAAAATAAT
Found at i:3322348 original size:28 final size:27
Alignment explanation
Indices: 3322316--3322378 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3322306 AGATTCCACC
* *
3322316 AAATAAAAAATTATTTTTTAAAAAT-TTT
1 AAATAAAAAA--AATTTTAAAAAATGTTT
3322344 AAATATAAAAAAATTTTAAAAAATGTTT
1 AAATA-AAAAAAATTTTAAAAAATGTTT
3322372 AAATAAA
1 AAATAAA
3322379 CTGATGGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 13 0.42
28 13 0.42
29 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
AAATAAAAAAAATTTTAAAAAATGTTT
Found at i:3323275 original size:21 final size:21
Alignment explanation
Indices: 3323250--3323289 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3323240 TTAGAATTTA
*
3323250 ATTTAATTTATTTGAATTATT
1 ATTTAATTAATTTGAATTATT
*
3323271 ATTTAATTAATTTTAATTA
1 ATTTAATTAATTTGAATTA
3323290 AATAATTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
ATTTAATTAATTTGAATTATT
Found at i:3323458 original size:23 final size:23
Alignment explanation
Indices: 3323431--3323476 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3323421 AGAAAATAAT
3323431 TTAATTGAAATAAAT-TATTTTAA
1 TTAATTG-AATAAATATATTTTAA
3323454 TTAATTGAATAAATAGTATTTTA
1 TTAATTGAATAAATA-TATTTTA
3323477 TATAAAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 7 0.33
24 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (23 bp):
TTAATTGAATAAATATATTTTAA
Found at i:3324751 original size:17 final size:17
Alignment explanation
Indices: 3324731--3324763 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3324721 ATTTAATATA
3324731 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
3324748 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
3324764 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:3325181 original size:16 final size:16
Alignment explanation
Indices: 3325160--3325213 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
3325150 TTTGGTTCGC
*
3325160 TGTAATGAAATAAAGG
1 TGTAATGAAATAGAGG
* *
3325176 TGTAATGGAATAGATG
1 TGTAATGAAATAGAGG
* *
3325192 CGTAATGTAATAGAGG
1 TGTAATGAAATAGAGG
3325208 TGTAAT
1 TGTAAT
3325214 AGGTAATCCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.41, C:0.02, G:0.28, T:0.30
Consensus pattern (16 bp):
TGTAATGAAATAGAGG
Found at i:3325285 original size:44 final size:46
Alignment explanation
Indices: 3325195--3325288 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 46
3325185 ATAGATGCGT
* * * *
3325195 AATGTAATAGAGGTGTAATAGGTAATCCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATCCTTGTGTTTAGTTGAATGG
*
3325241 AATGGAATAGAGGCGTAATA-GT-ATTCTTGTGTTTAGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATCCTTGTGTTTAGTTGAATGG
3325285 AATG
1 AATG
3325289 ATGTTATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 23 0.53
45 2 0.05
46 18 0.42
ACGTcount: A:0.30, C:0.04, G:0.29, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATCCTTGTGTTTAGTTGAATGG
Found at i:3329946 original size:68 final size:62
Alignment explanation
Indices: 3329888--3330004 Score: 227
Period size: 62 Copynumber: 1.9 Consensus size: 62
3329878 ATTTAATGGG
3329888 TAATGGGTTTC-ATATACTATAATTTTATAGGTATGAAGCATAAATAAAAAGTTTTCGAATT
1 TAATGGGTTTCAATATACTATAATTTTATAGGTATGAAGCATAAATAAAAAGTTTTCGAATT
3329949 TAATGGGTTTCAATATACTATAATTTTATAGGTATGAAGCATAAATAAAAAGTTTT
1 TAATGGGTTTCAATATACTATAATTTTATAGGTATGAAGCATAAATAAAAAGTTTT
3330005 ACTTTAACGA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 11 0.20
62 44 0.80
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.39
Consensus pattern (62 bp):
TAATGGGTTTCAATATACTATAATTTTATAGGTATGAAGCATAAATAAAAAGTTTTCGAATT
Found at i:3330232 original size:26 final size:26
Alignment explanation
Indices: 3330185--3330234 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3330175 TAAACTAAGG
*
3330185 TAAAATCGAAGAAATTAATTTAAAAT
1 TAAAATCGAAGAAAATAATTTAAAAT
*
3330211 TAAAATCGAA-ATAAATATTTTAAA
1 TAAAATCGAAGA-AAATAATTTAAA
3330235 TAAAACCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (26 bp):
TAAAATCGAAGAAAATAATTTAAAAT
Found at i:3331020 original size:15 final size:15
Alignment explanation
Indices: 3331000--3331030 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3330990 CCTTCAAAGA
3331000 TAAAGCATGCCACTT
1 TAAAGCATGCCACTT
3331015 TAAAGCATGCCACTT
1 TAAAGCATGCCACTT
3331030 T
1 T
3331031 CTTGGATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (15 bp):
TAAAGCATGCCACTT
Found at i:3335427 original size:2 final size:2
Alignment explanation
Indices: 3335420--3335454 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3335410 AAGTACATAT
3335420 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3335455 GTATGTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3341892 original size:23 final size:24
Alignment explanation
Indices: 3341866--3341911 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
3341856 TAAAGAACAA
*
3341866 ATCAA-CCTTCTATTAAAAATTCT
1 ATCAATCCTACTATTAAAAATTCT
*
3341889 ATCAATTTCTACTATTAAAAATT
1 ATCAA-TCCTACTATTAAAAATT
3341912 GATTTTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
25 14 0.74
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (24 bp):
ATCAATCCTACTATTAAAAATTCT
Found at i:3355275 original size:6 final size:6
Alignment explanation
Indices: 3355264--3355308 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
3355254 AAACATAAAG
* * *
3355264 GAAGCT GAAGCT GATGCT GATGCT GAAGCT GATGCT GAAGCT GAA
1 GAAGCT GAAGCT GAAGCT GAAGCT GAAGCT GAAGCT GAAGCT GAA
3355309 AGAGAAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (6 bp):
GAAGCT
Found at i:3355288 original size:12 final size:12
Alignment explanation
Indices: 3355264--3355307 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
3355254 AAACATAAAG
*
3355264 GAAGCTGAAGCT
1 GAAGCTGATGCT
*
3355276 GATGCTGATGCT
1 GAAGCTGATGCT
3355288 GAAGCTGATGCT
1 GAAGCTGATGCT
3355300 GAAGCTGA
1 GAAGCTGA
3355308 AAGAGAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.27, C:0.16, G:0.34, T:0.23
Consensus pattern (12 bp):
GAAGCTGATGCT
Found at i:3355290 original size:18 final size:18
Alignment explanation
Indices: 3355264--3355308 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
3355254 AAACATAAAG
3355264 GAAGCTGAAGCTGATGCT
1 GAAGCTGAAGCTGATGCT
*
3355282 GATGCTGAAGCTGATGCT
1 GAAGCTGAAGCTGATGCT
3355300 GAAGCTGAA
1 GAAGCTGAA
3355309 AGAGAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (18 bp):
GAAGCTGAAGCTGATGCT
Found at i:3366354 original size:312 final size:312
Alignment explanation
Indices: 3365788--3366416 Score: 954
Period size: 312 Copynumber: 2.0 Consensus size: 312
3365778 ATCTTTGCCT
** ** *
3365788 TCAGAATTGACTGTCGAGAACCTAAAGTGTGGAGCTGAGGCCAATGAAAAAGAGGAAGAAAAGGT
1 TCAGAATTGACTGAAGAGAACCTAAAGCATGGAGCTGAGGCCAATGAAAAAGAGGAAGAAAAGGA
* * *
3365853 GAAGGAAGTGGAAATTCTCGAAAAGGAAAGACCTCAGGAGCCTGAAGCTGTTATGGATCAAGAAA
66 GAAGGAAGTGGAAATTCTAGAAAAGGAAAGACCTCAGGAGCCTAAAGCTGTTATAGATCAAGAAA
* * *
3365918 CCATTATAGTTCAGGCTTCAATAACAGAAGGATCACAAGAGATTGAAGCAAACGAAGAGAAAAGG
131 CCATTATAGCTCAGGCTTCAATAACAGAAGGATCACAAGAGATTGAAGCAAACAAAGAAAAAAGG
* * * *
3365983 AAAGAAGCCAAAAAGCTTGACGATGGGAACCGTGAAGACTCGTCAGCTGGAGAAACAGAAAAGCT
196 AAAGAAACCAAAAAGCTTCACGATGGGAACCATGAAGACTCATCAGCTGGAGAAACAGAAAAGCT
* * * *
3366048 AAATGAGCTTCAATTAGTTACTAGAGAAGAAATTGCTTCTGGTCAGTCTTCC
261 AAATGAGCTTCAATTAGTTACAAAAAAAGAAATTGCTTCTGCTCAGTCTTCC
* * * **
3366100 TCAGAATTGACTGAAGAGAGCCTAAAGCATGGAGCTGGGGCCAATGAAGAAGAGGGGGAAAAGGA
1 TCAGAATTGACTGAAGAGAACCTAAAGCATGGAGCTGAGGCCAATGAAAAAGAGGAAGAAAAGGA
* *
3366165 GAAGGAAGTGGAACTTCTAGAAAAGGAAGGACCTCAGGAGCCTAAAGCTGTTATAGATCAAGAAA
66 GAAGGAAGTGGAAATTCTAGAAAAGGAAAGACCTCAGGAGCCTAAAGCTGTTATAGATCAAGAAA
* *
3366230 CCATTATTGCTCAGGCTTCATTAACAG-AGGAATCACAAGAGATTGAAGCAAACAAAGAAAAAAG
131 CCATTATAGCTCAGGCTTCAATAACAGAAGG-ATCACAAGAGATTGAAGCAAACAAAGAAAAAAG
* * *
3366294 GAAAGAAACCGAAAAGCTTCACGATGGGAACCATGAAGACTCATCAGCTGGAGTAACAGAAGAGC
195 GAAAGAAACCAAAAAGCTTCACGATGGGAACCATGAAGACTCATCAGCTGGAGAAACAGAAAAGC
*
3366359 TAAATGAGCTTCAGTTAGTTACAAAAAAAGAAATTGCTTCTGCTCAGTCTTCC
260 TAAATGAGCTTCAATTAGTTACAAAAAAAGAAATTGCTTCTGCTCAGTCTTCC
3366412 TCAGA
1 TCAGA
3366417 GAAGCAACTT
Statistics
Matches: 284, Mismatches: 32, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
311 3 0.01
312 281 0.99
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.18
Consensus pattern (312 bp):
TCAGAATTGACTGAAGAGAACCTAAAGCATGGAGCTGAGGCCAATGAAAAAGAGGAAGAAAAGGA
GAAGGAAGTGGAAATTCTAGAAAAGGAAAGACCTCAGGAGCCTAAAGCTGTTATAGATCAAGAAA
CCATTATAGCTCAGGCTTCAATAACAGAAGGATCACAAGAGATTGAAGCAAACAAAGAAAAAAGG
AAAGAAACCAAAAAGCTTCACGATGGGAACCATGAAGACTCATCAGCTGGAGAAACAGAAAAGCT
AAATGAGCTTCAATTAGTTACAAAAAAAGAAATTGCTTCTGCTCAGTCTTCC
Found at i:3379788 original size:24 final size:24
Alignment explanation
Indices: 3379760--3379808 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3379750 CAAAAAACAG
3379760 TTAGCAAAAGTAGCAACTAACTGC
1 TTAGCAAAAGTAGCAACTAACTGC
*
3379784 TTAGCAAAAGTAGTAACTAACTGC
1 TTAGCAAAAGTAGCAACTAACTGC
3379808 T
1 T
3379809 ACCTGATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (24 bp):
TTAGCAAAAGTAGCAACTAACTGC
Found at i:3380710 original size:27 final size:27
Alignment explanation
Indices: 3380678--3380733 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
3380668 TATTTTTCCC
*
3380678 TATTTCTTTCTCCTT-TTT-TTTCATTTT
1 TATTTC-TTATCCTTCTTTCTTT-ATTTT
3380705 TATTTCTTATCCTTCTTTCTTTATTTT
1 TATTTCTTATCCTTCTTTCTTTATTTT
3380732 TA
1 TA
3380734 GTAACTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 7 0.27
27 16 0.62
28 3 0.12
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (27 bp):
TATTTCTTATCCTTCTTTCTTTATTTT
Found at i:3384447 original size:20 final size:20
Alignment explanation
Indices: 3384422--3384466 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
3384412 TAAATTCAAA
3384422 TAATTAAAAC-AAGACAC-AAT
1 TAATT-AAACTAAGAC-CTAAT
3384442 TAATTAAACTAAGACCTAAT
1 TAATTAAACTAAGACCTAAT
3384462 TAATT
1 TAATT
3384467 CGGTTAGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (20 bp):
TAATTAAACTAAGACCTAAT
Found at i:3390021 original size:280 final size:281
Alignment explanation
Indices: 3389508--3390070 Score: 1119
Period size: 280 Copynumber: 2.0 Consensus size: 281
3389498 ATAGATGGTT
3389508 AATAAAAAGTATTAGTTTGTTATTTAATTTACAGCATAGGAAATGCAATCTGACTAGCAATTTTC
1 AATAAAAAGTATTAGTTTGTTATTTAATTTACAGCATAGGAAATGCAATCTGACTAGCAATTTTC
3389573 ACGATACTTTTATCGAATTTAAAGGATTTTTGATGTGAAATGAGTCAAATTAAAGTAGTGTTTCC
66 ACGATACTTTTATCGAATTTAAAGGATTTTTGATGTGAAATGAGTCAAATTAAAGTAGTGTTTCC
3389638 CATTGCAACCAGTTGGAATTATTGAATCATTCTTCAAATCCGCATTTATATGTCAGGTAAGGATA
131 CATTGCAACCAGTTGGAATTATTGAATCATTCTTCAAATCCGCATTTATATGTCAGGTAAGGATA
3389703 TGGAACATTGAAAACAAGTATTGCTCCACCTCAAGATCATCTAGCATCCGAAGAAGAGTAAATGC
196 TGGAACATTGAAAACAAGTATTGCTCCACCTCAAGATCATCTAGCATCCGAAGAAGAGTAAATGC
3389768 GATTCCAAGTTCAGAAAGTAG
261 GATTCCAAGTTCAGAAAGTAG
3389789 AATAAAAAGTA-TAGTTTGTTATTTAATTTACAGCATAGGAAATGCAATCTGACTAGCAATTTTC
1 AATAAAAAGTATTAGTTTGTTATTTAATTTACAGCATAGGAAATGCAATCTGACTAGCAATTTTC
3389853 ACGATACTTTTATCGAATTTAAAGGATTTTTGATGTGAAATGAGTCAAATTAAAGTAGTGTTTCC
66 ACGATACTTTTATCGAATTTAAAGGATTTTTGATGTGAAATGAGTCAAATTAAAGTAGTGTTTCC
3389918 CATTGCAACCAGTTGGAATTATTGAATCATTCTTCAAATCCGCATTTATATGTCAGGTAAGGATA
131 CATTGCAACCAGTTGGAATTATTGAATCATTCTTCAAATCCGCATTTATATGTCAGGTAAGGATA
3389983 TGGAACATTGAAAACAAGTATTGCTCCACCTCAAGATCATCTAGCATCCGAAGAAGAGTAAATGC
196 TGGAACATTGAAAACAAGTATTGCTCCACCTCAAGATCATCTAGCATCCGAAGAAGAGTAAATGC
3390048 GATTCCAAGTTCAGAAAGTAG
261 GATTCCAAGTTCAGAAAGTAG
3390069 AA
1 AA
3390071 AAGTTTTGAT
Statistics
Matches: 282, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
280 271 0.96
281 11 0.04
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (281 bp):
AATAAAAAGTATTAGTTTGTTATTTAATTTACAGCATAGGAAATGCAATCTGACTAGCAATTTTC
ACGATACTTTTATCGAATTTAAAGGATTTTTGATGTGAAATGAGTCAAATTAAAGTAGTGTTTCC
CATTGCAACCAGTTGGAATTATTGAATCATTCTTCAAATCCGCATTTATATGTCAGGTAAGGATA
TGGAACATTGAAAACAAGTATTGCTCCACCTCAAGATCATCTAGCATCCGAAGAAGAGTAAATGC
GATTCCAAGTTCAGAAAGTAG
Found at i:3391097 original size:15 final size:14
Alignment explanation
Indices: 3391062--3391122 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
3391052 ATTTTGCTAA
*
3391062 AATTTTAATATTTGT
1 AATTTTAAT-TTTTT
3391077 -ATTTTAATTTGTTT
1 AATTTTAATTT-TTT
3391091 AATTTTAATTTTTT
1 AATTTTAATTTTTT
*
3391105 --TTGT-ATTTTTT
1 AATTTTAATTTTTT
3391116 AATTTTA
1 AATTTTA
3391123 GTTTGATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
11 7 0.18
12 3 0.08
13 5 0.13
14 13 0.34
15 10 0.26
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (14 bp):
AATTTTAATTTTTT
Found at i:3391131 original size:19 final size:19
Alignment explanation
Indices: 3391093--3391131 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3391083 ATTTGTTTAA
*
3391093 TTTTAATTTTTTTTGTATT
1 TTTTAATTTTGTTTGTATT
3391112 TTTTAATTTTAGTTTG-ATT
1 TTTTAATTTT-GTTTGTATT
3391131 T
1 T
3391132 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (19 bp):
TTTTAATTTTGTTTGTATT
Found at i:3397291 original size:6 final size:6
Alignment explanation
Indices: 3397280--3397332 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
3397270 CTATAAAAAT
3397280 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
3397328 ATATT
1 ATATT
3397333 TTAATATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
ATATTA
Found at i:3397347 original size:18 final size:20
Alignment explanation
Indices: 3397280--3397358 Score: 98
Period size: 18 Copynumber: 4.2 Consensus size: 20
3397270 CTATAAAAAT
3397280 ATATTAATATTAATA--TTA
1 ATATTAATATTAATATTTTA
3397298 ATATTAATATTAATA--TTA
1 ATATTAATATTAATATTTTA
3397316 ATATTAATATTAATATTTTA
1 ATATTAATATTAATATTTTA
*
3397336 ATA-TAATA-TAATTTTTTTA
1 ATATTAATATTAA-TATTTTA
3397355 ATAT
1 ATAT
3397359 ATTTTATTTA
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
18 36 0.64
19 14 0.25
20 6 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTAATATTAATATTTTA
Found at i:3407907 original size:194 final size:193
Alignment explanation
Indices: 3407384--3407972 Score: 866
Period size: 194 Copynumber: 3.0 Consensus size: 193
3407374 GCCTAGAATG
* * *
3407384 AACATAAACTGAAAACCTATTCTCTTCTCCCTGCAAAAAATAAATAAATAAA-AAGA-AAAAAAA
1 AACAT-AACTGAAAACCTGTTCTCTTCTCCCTGC-AAAAATAAATTAATAAAGAATATAAAAAAA
*
3407447 GATTAACAAAAACACTTCATGATTATTATGATCAAGATCATAATTCAGAAAGAGGCATAATAATT
64 GATTAACAAAAACACTTCATGATTATGATGATCAAGATCATAATTCAGAAAGAGGCATAATAATT
3407512 TCTCTAATTTTCAAATC--TA-AAATATTTAGTAACTAATTTAAGGAAAATGTAGCT-AAAAGAA
129 TCTCTAATTTTCAAATCTATAGAAATATTTAGTAACTAATTTAAGGAAAATGTAGCTAAAAAGAA
* * * * * **
3407573 AAGATAACTGAAAACTTGTTCTCTTCTCCCGGCAAAATTAAATTAACAAAGAATATTTTTTAAAA
1 AACATAACTGAAAACCTGTTCTCTTCTCCCTGCAAAAATAAATTAATAAAGAATA---TAAAAAA
* * * *
3407638 AGATTAACAAAAACAATTCGTAATTATGATAATCAAGATCATAATTCAGAAAGAGGCATAATAAT
63 AGATTAACAAAAACACTTCATGATTATGATGATCAAGATCATAATTCAGAAAGAGGCATAATAAT
* *
3407703 TTCTCTAATTTTCAAATCTATAGAAAGATTTAGTAACTAATTTAAGGAAAATTTAGCTAAAAAGA
128 TTCTCTAATTTTCAAATCTATAGAAATATTTAGTAACTAATTTAAGGAAAATGTAGCTAAAAAGA
3407768 A
193 A
*
3407769 AACATAACTGAAAACCTGTTCACTTCTCCCTGCAAAAATAAATTAATAAAGAATATAAAAAAGAG
1 AACATAACTGAAAACCTGTTCTCTTCTCCCTGCAAAAATAAATTAATAAAGAATATAAAAAA-AG
* *
3407834 ATTAACAGAAACACTTCATGATTATGATGATCAAGATCATAATTCAGAAAGAGGCATAGTAATTT
65 ATTAACAAAAACACTTCATGATTATGATGATCAAGATCATAATTCAGAAAGAGGCATAATAATTT
*
3407899 CTCTAATTTTCAAATCTATAGAAATATTTAGTAACTAATTTAAGATAAAAATGTAGCTAAAAAGA
130 CTCTAATTTTCAAATCTATAGAAATATTTAGTAACTAATTTAAG--GAAAATGTAGCTAAAAAGA
3407964 A
193 A
*
3407965 AAGATAAC
1 AACATAAC
3407973 AAACTTTATC
Statistics
Matches: 353, Mismatches: 35, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
187 14 0.04
188 28 0.08
189 4 0.01
192 82 0.23
193 5 0.01
194 106 0.30
195 33 0.09
196 81 0.23
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (193 bp):
AACATAACTGAAAACCTGTTCTCTTCTCCCTGCAAAAATAAATTAATAAAGAATATAAAAAAAGA
TTAACAAAAACACTTCATGATTATGATGATCAAGATCATAATTCAGAAAGAGGCATAATAATTTC
TCTAATTTTCAAATCTATAGAAATATTTAGTAACTAATTTAAGGAAAATGTAGCTAAAAAGAA
Found at i:3412618 original size:31 final size:32
Alignment explanation
Indices: 3412592--3412651 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
3412582 TAATAGCTTG
*
3412592 ATGACTTAAGTGAAAA-TTTTCAAATAGTTCA
1 ATGACTTAAATGAAAACTTTTCAAATAGTTCA
*
3412623 ATGACTTAAATGAAAACTTTT-GAATAGTT
1 ATGACTTAAATGAAAACTTTTCAAATAGTT
3412652 TAGTGACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (32 bp):
ATGACTTAAATGAAAACTTTTCAAATAGTTCA
Found at i:3420850 original size:21 final size:20
Alignment explanation
Indices: 3420821--3420860 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3420811 ACAAGAGAAC
3420821 AAGGAGAGCCATGCGAGGTGA
1 AAGGAGAG-CATGCGAGGTGA
* *
3420842 AAGGCGAGCATGTGAGGTG
1 AAGGAGAGCATGCGAGGTG
3420861 GTGAAGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.30, C:0.12, G:0.45, T:0.12
Consensus pattern (20 bp):
AAGGAGAGCATGCGAGGTGA
Found at i:3426271 original size:19 final size:19
Alignment explanation
Indices: 3426247--3426294 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
3426237 ATTTTGTGTT
3426247 TGAATAGAAATGAACAGAA
1 TGAATAGAAATGAACAGAA
*
3426266 TGAATAAAAATGAACAGAA
1 TGAATAGAAATGAACAGAA
3426285 TGAATAGAAA
1 TGAATAGAAA
3426295 AAGAGAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.60, C:0.04, G:0.19, T:0.17
Consensus pattern (19 bp):
TGAATAGAAATGAACAGAA
Found at i:3437212 original size:14 final size:14
Alignment explanation
Indices: 3437193--3437220 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3437183 ATATGAAATT
3437193 CTCTTGCTTACACC
1 CTCTTGCTTACACC
3437207 CTCTTGCTTACACC
1 CTCTTGCTTACACC
3437221 ATTTCTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.43, G:0.07, T:0.36
Consensus pattern (14 bp):
CTCTTGCTTACACC
Found at i:3437640 original size:51 final size:53
Alignment explanation
Indices: 3437563--3437683 Score: 187
Period size: 52 Copynumber: 2.4 Consensus size: 53
3437553 CGGTGACCTG
*
3437563 CACATAGTACCACC-CTTGTAGCCAAAGCTA-CCTTCTTCACAAAGTGGCCTT
1 CACATAGTACCACCACTTGTAGACAAAGCTATCCTTCTTCACAAAGTGGCCTT
* *
3437614 CACATAGTACCACCACTTGT-GACAAAGCTATCTTTCTTCACAAAGTGGCTTT
1 CACATAGTACCACCACTTGTAGACAAAGCTATCCTTCTTCACAAAGTGGCCTT
3437666 CACATAGTACCA-CACTTG
1 CACATAGTACCACCACTTG
3437684 AGTCACTAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
51 29 0.45
52 36 0.55
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (53 bp):
CACATAGTACCACCACTTGTAGACAAAGCTATCCTTCTTCACAAAGTGGCCTT
Found at i:3442272 original size:10 final size:11
Alignment explanation
Indices: 3442256--3442284 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
3442246 GCCTAGGATG
3442256 TGAATTGAATA
1 TGAATTGAATA
3442267 -GAATTGAATA
1 TGAATTGAATA
3442277 TGAATTGA
1 TGAATTGA
3442285 TGTTAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (11 bp):
TGAATTGAATA
Found at i:3442862 original size:24 final size:24
Alignment explanation
Indices: 3442835--3442888 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3442825 TTTCCGACAT
* *
3442835 ATGGCTATTTAGAGCTTCCCGTTA
1 ATGGCTATTCAGAGCTACCCGTTA
* *
3442859 ATGGCTCTTCGGAGCTACCCGTTA
1 ATGGCTATTCAGAGCTACCCGTTA
*
3442883 TTGGCT
1 ATGGCT
3442889 CGCATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (24 bp):
ATGGCTATTCAGAGCTACCCGTTA
Found at i:3445607 original size:17 final size:18
Alignment explanation
Indices: 3445585--3445618 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3445575 CAATATGATT
3445585 AAATAAAT-TATTAAAAG
1 AAATAAATGTATTAAAAG
3445602 AAATAAATGTATTAAAA
1 AAATAAATGTATTAAAA
3445619 TATTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AAATAAATGTATTAAAAG
Found at i:3449524 original size:18 final size:18
Alignment explanation
Indices: 3449498--3449535 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3449488 TTTCTCTCAA
3449498 TTTTCTATTTT-ATAATCT
1 TTTTCTATTTTCATAA-CT
*
3449516 TTTTTTATTTTCATAACT
1 TTTTCTATTTTCATAACT
3449534 TT
1 TT
3449536 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTCTATTTTCATAACT
Found at i:3458083 original size:14 final size:14
Alignment explanation
Indices: 3458064--3458091 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3458054 AGAATAGATT
3458064 TTTAATTAATTAAA
1 TTTAATTAATTAAA
3458078 TTTAATTAATTAAA
1 TTTAATTAATTAAA
3458092 AATTTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:3460269 original size:23 final size:24
Alignment explanation
Indices: 3460216--3460268 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
3460206 TTTTTAAATA
3460216 AAAAAATTAAAAAATAACATGTGT
1 AAAAAATTAAAAAATAACATGTGT
*
3460240 AAAAAATTAAAAAATAACATGTGC
1 AAAAAATTAAAAAATAACATGTGT
3460264 AAAAA
1 AAAAA
3460269 TAACGAGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.66, C:0.06, G:0.08, T:0.21
Consensus pattern (24 bp):
AAAAAATTAAAAAATAACATGTGT
Found at i:3461303 original size:23 final size:23
Alignment explanation
Indices: 3461276--3461322 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3461266 ACATGCTTGT
3461276 TGCCTAATCCACAGTCTACCTCA
1 TGCCTAATCCACAGTCTACCTCA
3461299 TGCCTAATCCACAGTCTACCTCA
1 TGCCTAATCCACAGTCTACCTCA
3461322 T
1 T
3461323 ACTTCTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.38, G:0.09, T:0.28
Consensus pattern (23 bp):
TGCCTAATCCACAGTCTACCTCA
Found at i:3465050 original size:23 final size:24
Alignment explanation
Indices: 3465024--3465082 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 24
3465014 CTAAAATCTA
* *
3465024 ATTAAATAAAAAT-TTATATTAAT
1 ATTAAATAAAAATAGTATACTAAT
3465047 ATTAAATAAAAATAAGTATACTAAT
1 ATTAAATAAAAAT-AGTATACTAAT
3465072 ATTAAATAAAA
1 ATTAAATAAAA
3465083 TACAAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 13 0.41
25 19 0.59
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
ATTAAATAAAAATAGTATACTAAT
Found at i:3468168 original size:18 final size:18
Alignment explanation
Indices: 3468147--3468181 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3468137 CTGGGGTAGG
3468147 TTTGGG-TTTAAGTTTGGT
1 TTTGGGCTTT-AGTTTGGT
3468165 TTTGGGCTTTAGTTTGG
1 TTTGGGCTTTAGTTTGG
3468182 GTACTAGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.09, C:0.03, G:0.34, T:0.54
Consensus pattern (18 bp):
TTTGGGCTTTAGTTTGGT
Found at i:3469349 original size:21 final size:21
Alignment explanation
Indices: 3469325--3469366 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3469315 AGCCCAGATT
* *
3469325 GTGTGTCTATTCCACACGCCC
1 GTGTGGCTACTCCACACGCCC
*
3469346 GTGTGGCTACTCCACATGCCC
1 GTGTGGCTACTCCACACGCCC
3469367 ATGTACTTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.38, G:0.21, T:0.26
Consensus pattern (21 bp):
GTGTGGCTACTCCACACGCCC
Found at i:3471409 original size:18 final size:18
Alignment explanation
Indices: 3471372--3471439 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
3471362 ACCATTATAA
*
3471372 TAATAAAATATAAGAATAG
1 TAATAAAA-ATAAAAATAG
* *
3471391 TAATAGAAATAGAAATAG
1 TAATAAAAATAAAAATAG
3471409 TAATAAAAATAAAAATA-
1 TAATAAAAATAAAAATAG
*
3471426 AAATATAAAATAAA
1 TAATA-AAAATAAA
3471440 GTATTATAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
17 4 0.10
18 31 0.74
19 7 0.17
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (18 bp):
TAATAAAAATAAAAATAG
Found at i:3471435 original size:12 final size:12
Alignment explanation
Indices: 3471367--3471439 Score: 53
Period size: 12 Copynumber: 5.9 Consensus size: 12
3471357 ATATCACCAT
3471367 TATAATAATAAAA
1 TATAA-AATAAAA
*
3471380 TATAAGAATAGTAA
1 TATAA-AATA-AAA
*
3471394 TA-GAAATAGAAA
1 TATAAAATA-AAA
*
3471406 TAGTAATA-AAAA
1 TA-TAAAATAAAA
3471418 TA-AAAATAAAA
1 TATAAAATAAAA
3471429 TATAAAATAAA
1 TATAAAATAAA
3471440 GTATTATAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
10 3 0.06
11 6 0.12
12 22 0.46
13 11 0.23
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (12 bp):
TATAAAATAAAA
Found at i:3483642 original size:19 final size:19
Alignment explanation
Indices: 3483581--3483632 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3483571 TATACACATT
**
3483581 AAAAA-ATATAAAAATGGA
1 AAAAATATATAAAAATTCA
3483599 AATAAATATATAAAAATTCA
1 AA-AAATATATAAAAATTCA
3483619 AAAAATATATAAAA
1 AAAAATATATAAAA
3483633 TCTAGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 15 0.50
20 13 0.43
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (19 bp):
AAAAATATATAAAAATTCA
Found at i:3483973 original size:15 final size:15
Alignment explanation
Indices: 3483948--3483986 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3483938 NNNNNNNNNN
*
3483948 ATATT-TATTTTTAT
1 ATATTATATTTTTAA
3483962 ATATTATATTTTTAA
1 ATATTATATTTTTAA
3483977 ATATTTATAT
1 ATA-TTATAT
3483987 ACATTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 11 0.50
16 6 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATATTATATTTTTAA
Found at i:3487296 original size:15 final size:16
Alignment explanation
Indices: 3487265--3487298 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3487255 AGATAATTAT
3487265 ATAAAAAATTTCAATAA
1 ATAAAAAATTT-AATAA
3487282 ATAAAAAATTT-ATAA
1 ATAAAAAATTTAATAA
3487297 AT
1 AT
3487299 TTATTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
17 11 0.65
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAAAAATTTAATAA
Found at i:3488985 original size:14 final size:15
Alignment explanation
Indices: 3488966--3488994 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3488956 CTTGCACAAT
3488966 TTTGCAGA-AAATGG
1 TTTGCAGACAAATGG
3488980 TTTGCAGACAAATGG
1 TTTGCAGACAAATGG
3488995 ATATTAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (15 bp):
TTTGCAGACAAATGG
Found at i:3492589 original size:41 final size:41
Alignment explanation
Indices: 3492519--3492634 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 41
3492509 GGCACTAACG
* * * * *
3492519 GAAAAACGCCGCAATAGGTAAAGCAGTAGCGGTGTTTATAA
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCGCTTACAA
* * *
3492560 GAAAAATGCCGCAAAAGGTCAAGCGGTAGCGGCGCTTACGA
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCGCTTACAA
* * * *
3492601 GAAAAACGCTGCAAAAAGTCAAGTATTAGCGGCG
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCG
3492635 TTTATCAAAA
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.38, C:0.18, G:0.28, T:0.16
Consensus pattern (41 bp):
GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCGCTTACAA
Found at i:3492739 original size:34 final size:34
Alignment explanation
Indices: 3492698--3492790 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 34
3492688 TACTATGCTA
* *
3492698 AAAATCTCTTATTTTCCCCCTAAACCATAACCCT
1 AAAATCTCTTATTTTACCCCTAAACCATAACCCC
*
3492732 AAAATCTCTTATTTTATCCCTAAACCATAACCCC
1 AAAATCTCTTATTTTACCCCTAAACCATAACCCC
* *
3492766 AAAATCCCTTATTTTTTCCCCTAAA
1 AAAATCTCTTA-TTTTACCCCTAAA
3492791 AATTGGAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 41 0.79
35 11 0.21
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.34
Consensus pattern (34 bp):
AAAATCTCTTATTTTACCCCTAAACCATAACCCC
Found at i:3494071 original size:5 final size:5
Alignment explanation
Indices: 3494063--3494087 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3494053 CTCTTCTCTC
3494063 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
3494088 CTCTGAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:3494369 original size:29 final size:29
Alignment explanation
Indices: 3494336--3494391 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
3494326 ATAATCATAT
3494336 TTTTA-AACAATAATTTTAATTTGATAAGC
1 TTTTATAAC-ATAATTTTAATTTGATAAGC
* *
3494365 TTTTATAACATATTTTTAATTTTATAA
1 TTTTATAACATAATTTTAATTTGATAA
3494392 ATATTTTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (29 bp):
TTTTATAACATAATTTTAATTTGATAAGC
Found at i:3498243 original size:5 final size:5
Alignment explanation
Indices: 3498233--3498257 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3498223 AGTTTTGGCA
3498233 TGTAT TGTAT TGTAT TGTAT TGTAT
1 TGTAT TGTAT TGTAT TGTAT TGTAT
3498258 ACTAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TGTAT
Found at i:3502497 original size:42 final size:43
Alignment explanation
Indices: 3502429--3502532 Score: 113
Period size: 42 Copynumber: 2.4 Consensus size: 43
3502419 TTCTGAGGTG
* *
3502429 TGATTTCGTGTAAGACTATGTATGGGACATTGGCATCG-TATA
1 TGATTTCGTGTAAGACCATGTATGGGACAGTGGCATCGATATA
* *
3502471 TGATTTCGTGTAAGACCCA-GTCTGGGATAGTGGCATCGATATA
1 TGATTTCGTGTAAGA-CCATGTATGGGACAGTGGCATCGATATA
* ** *
3502514 TTATAACATGTAAGACCAT
1 TGATTTCGTGTAAGACCAT
3502533 ATCTTAGATA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 34 0.67
43 17 0.33
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (43 bp):
TGATTTCGTGTAAGACCATGTATGGGACAGTGGCATCGATATA
Found at i:3504717 original size:6 final size:6
Alignment explanation
Indices: 3504706--3504741 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
3504696 TAGCGGATTA
3504706 ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT
1 ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT
3504742 TAGTGTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATTAGT
Found at i:3504749 original size:18 final size:18
Alignment explanation
Indices: 3504708--3504751 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
3504698 GCGGATTAAT
*
3504708 TAGTATTAGTATTAGTAT
1 TAGTATTAGTATTAGTAG
3504726 TAGTATTAGTATTAGTTAG
1 TAGTATTAGTATTAG-TAG
3504745 T-GTATTA
1 TAGTATTA
3504752 CAAAGGGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (18 bp):
TAGTATTAGTATTAGTAG
Found at i:3506846 original size:43 final size:43
Alignment explanation
Indices: 3506784--3506962 Score: 173
Period size: 43 Copynumber: 4.2 Consensus size: 43
3506774 CACAAACGCC
** **
3506784 GCTAAAGAACATGGA-CTTTAGCGGCGCTTTTATTAAAAATGTT
1 GCTAAAGAACAT-GACCTTTAGCGGCGCTTTTACCAAAAATGCA
* * * *
3506827 GCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTTACCAAAAATGCA
* * * *
3506870 GCTATAGAACATGACCTTTAGTGGCTCTTTT-CTCACAAATGCA
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTTAC-CAAAAATGCA
* * * * *
3506913 GCTAAAGAACATGACATTTAACGGCGCTTTTACTAAAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTTACCAAAAATGCA
3506956 GCTAAAG
1 GCTAAAG
3506963 GTCATGTTCT
Statistics
Matches: 112, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
42 3 0.03
43 108 0.96
44 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (43 bp):
GCTAAAGAACATGACCTTTAGCGGCGCTTTTACCAAAAATGCA
Found at i:3506879 original size:86 final size:86
Alignment explanation
Indices: 3506768--3506962 Score: 257
Period size: 86 Copynumber: 2.3 Consensus size: 86
3506758 GTTAGTGGTA
* **
3506768 TTTTCCCACAAACGCCGCTAAAGAACATGGA-CTTTAGCGGCGCTTTTATTAAAAATGTTGCTAA
1 TTTTCCCACAAACGCCGCTAAAGAACAT-GACCTTTAGCGGCGCTTTTATCAAAAATGCAGCTAA
* *
3506832 AGAACATGACCTTTAGCGGCGC
65 AGAACATGACATTTAACGGCGC
* * * * *
3506854 TTTTCCCACAAACGCCGCTATAGAACATGACCTTTAGTGGCTCTTTTCTCACAAATGCAGCTAAA
1 TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAAAAATGCAGCTAAA
3506919 GAACATGACATTTAACGGCGC
66 GAACATGACATTTAACGGCGC
* * *
3506940 TTTTACTAAAAACGCCGCTAAAG
1 TTTTCCCACAAACGCCGCTAAAG
3506963 GTCATGTTCT
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 2 0.02
86 92 0.98
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (86 bp):
TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAAAAATGCAGCTAAA
GAACATGACATTTAACGGCGC
Found at i:3507071 original size:43 final size:41
Alignment explanation
Indices: 3506949--3507071 Score: 111
Period size: 43 Copynumber: 2.9 Consensus size: 41
3506939 CTTTTACTAA
* * *
3506949 AAACGCCGCTAAAGGTCATGTTCTATAGCGCCATTTTTAGT
1 AAACGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTTTAGG
* * * * *** *
3506990 AAAAGCATCGCTACAGGTAATGTTCTTTATAAGTGTTTTTATGGG
1 AAACGC--CGCTAAAGGTCATGTTCTATAGCGGCGTTTTTA--GG
3507035 AAACGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTT
1 AAACGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTT
3507072 CTCACATAAA
Statistics
Matches: 59, Mismatches: 19, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
41 5 0.08
43 48 0.81
45 6 0.10
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (41 bp):
AAACGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTTTAGG
Found at i:3507946 original size:123 final size:123
Alignment explanation
Indices: 3507727--3507975 Score: 462
Period size: 123 Copynumber: 2.0 Consensus size: 123
3507717 TAGCCTAAGT
3507727 TGCCATCTCTTCACTATCGGGCCAACCAGGCTTCAATCTGACAGGCTTCTCCAATATCTCTTTGA
1 TGCCATCTCTTCACTATCGGGCCAACCAGGCTTCAATCTGACAGGCTTCTCCAATATCTCTTTGA
3507792 ATCGGGCCAGTTCTTGTGGGCCAAATGATCCCCATCTGAGCAACAGACCTCCATTGGA
66 ATCGGGCCAGTTCTTGTGGGCCAAATGATCCCCATCTGAGCAACAGACCTCCATTGGA
* * *
3507850 TGCCATCTCTTTATTATCGGGCCAACCAGGCTTCAATCTGACAGGCTTGTCCAATATCTCTTTGA
1 TGCCATCTCTTCACTATCGGGCCAACCAGGCTTCAATCTGACAGGCTTCTCCAATATCTCTTTGA
*
3507915 ATCGGGCCAGTTCTTGTGGGCTAAATGATCCCCATCTGAGCAACAGACCTCCATTGGA
66 ATCGGGCCAGTTCTTGTGGGCCAAATGATCCCCATCTGAGCAACAGACCTCCATTGGA
3507973 TGC
1 TGC
3507976 ATTTGGTGCG
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 122 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.28
Consensus pattern (123 bp):
TGCCATCTCTTCACTATCGGGCCAACCAGGCTTCAATCTGACAGGCTTCTCCAATATCTCTTTGA
ATCGGGCCAGTTCTTGTGGGCCAAATGATCCCCATCTGAGCAACAGACCTCCATTGGA
Found at i:3516298 original size:3 final size:3
Alignment explanation
Indices: 3516292--3516323 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3516282 GTTGTTCTTC
3516292 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
3516324 CCTGTCTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:3517325 original size:128 final size:129
Alignment explanation
Indices: 3517097--3517353 Score: 507
Period size: 128 Copynumber: 2.0 Consensus size: 129
3517087 AATGTTTGTT
3517097 TTGCAAAAAAAAAAGGGTTATACTAATGGTTTATAAAGGCTTGAGATTAAGTTTCTATATGGGCC
1 TTGCAAAAAAAAAAGGGTTATACTAATGGTTTATAAAGGCTTGAGATTAAGTTTCTATATGGGCC
3517162 CCCTTTTTTTTTTCCTTATTTATTTATGTTATAATAATATAAAAATAAAAAT-AATAAGAAAAG
66 CCCTTTTTTTTTTCCTTATTTATTTATGTTATAATAATATAAAAATAAAAATAAATAAGAAAAG
3517225 TTGCAAAAAAAAAAGGGTTATACTAATGGTTTATAAAGGCTTGAGATTAAGTTTCTATATGGGCC
1 TTGCAAAAAAAAAAGGGTTATACTAATGGTTTATAAAGGCTTGAGATTAAGTTTCTATATGGGCC
3517290 CCCTTTTTTTTTTCCTTATTTATTTATGTTATAATAATATAAAAATAAAAATAAATAAGAAAAG
66 CCCTTTTTTTTTTCCTTATTTATTTATGTTATAATAATATAAAAATAAAAATAAATAAGAAAAG
3517354 GGTTTGAAAT
Statistics
Matches: 128, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 117 0.91
129 11 0.09
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (129 bp):
TTGCAAAAAAAAAAGGGTTATACTAATGGTTTATAAAGGCTTGAGATTAAGTTTCTATATGGGCC
CCCTTTTTTTTTTCCTTATTTATTTATGTTATAATAATATAAAAATAAAAATAAATAAGAAAAG
Found at i:3522505 original size:3 final size:3
Alignment explanation
Indices: 3522497--3522762 Score: 532
Period size: 3 Copynumber: 88.7 Consensus size: 3
3522487 GAATTGGTCC
3522497 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3522545 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3522593 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3522641 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3522689 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3522737 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
3522763 CCTATTTATT
Statistics
Matches: 263, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 263 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3528170 original size:55 final size:55
Alignment explanation
Indices: 3528098--3528206 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
3528088 GATAGAAGCA
* * * *
3528098 GGAGAAAGTACTAAAAGGTCGGCTCCAAGGAAAAAGGAACATGAGATAAACAATG
1 GGAGAAAGTACTAAAAGGTCAGCACCAAGAAAAAAAGAACATGAGATAAACAATG
*
3528153 GGAGAAAGTACTAAAAGGTCAGCACCAAGAAAAAAAGAGCATGAGATAAACAAT
1 GGAGAAAGTACTAAAAGGTCAGCACCAAGAAAAAAAGAACATGAGATAAACAAT
3528207 ACAAGCATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.50, C:0.13, G:0.25, T:0.12
Consensus pattern (55 bp):
GGAGAAAGTACTAAAAGGTCAGCACCAAGAAAAAAAGAACATGAGATAAACAATG
Found at i:3557132 original size:16 final size:15
Alignment explanation
Indices: 3557096--3557134 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3557086 ATATTTCACT
*
3557096 TGAAAAAAGGGGCAT
1 TGAAAAAAGGGGCAC
*
3557111 TCAAAAAAGGGGGCAC
1 TGAAAAAA-GGGGCAC
3557127 TGAAAAAA
1 TGAAAAAA
3557135 AAAAGAGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.51, C:0.10, G:0.28, T:0.10
Consensus pattern (15 bp):
TGAAAAAAGGGGCAC
Found at i:3558584 original size:50 final size:49
Alignment explanation
Indices: 3558450--3558886 Score: 246
Period size: 50 Copynumber: 8.9 Consensus size: 49
3558440 AAACCATAGT
* * * *
3558450 TTGCAATTTAAAAGACCGAAGCCACAACGGCGAATCTTACTTC-CAGGCGA
1 TTGCAATTTAAAAGATC-AAGCCACAACGGCGAATCTCACTTCTCCGAC-A
**** * * * *
3558500 -TGCAGCGGAACAGATTGAAGCTACAACGGTGAATCTCACTTCTCCGACA
1 TTGCAATTTAAAAGA-TCAAGCCACAACGGCGAATCTCACTTCTCCGACA
* * *
3558549 TTGCAATTTAAAAGATCAATGCCACAACGGCGAATCTTACTTC-CAGGCGA
1 TTGCAATTTAAAAGATCAA-GCCACAACGGCGAATCTCACTTCTCCGAC-A
**** * * * * *
3558599 -TGCAGCGGAACAGATTGAAGCTACAACGACGAATCTCACTTCTCCGATA
1 TTGCAATTTAAAAGA-TCAAGCCACAACGGCGAATCTCACTTCTCCGACA
* *
3558648 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCT--GGCGA
1 TTGCAATTTAAAAGATC-AAGCCACAACGGCGAATCTCACTTCTCCGAC-A
*** * *
3558697 -TGC-AGCGAAACAGATTGAAGCTACAACGGCGAATCTCACTTCTCCGACA
1 TTGCAATTTAAA-AGA-TCAAGCCACAACGGCGAATCTCACTTCTCCGACA
* * * **
3558746 TTGCAATTTAAAAGATCGAAGCCATAACGGCGAATCTTACTTCT-GGTGA
1 TTGCAATTTAAAAGATC-AAGCCACAACGGCGAATCTCACTTCTCCGACA
* ** * * * * * * *
3558795 -TGCAGTGGAACAGATTGAAGCTACAATGGCGAGTCTCGCTTCCCCGACA
1 TTGCAATTTAAAAGA-TCAAGCCACAACGGCGAATCTCACTTCTCCGACA
* * *
3558844 TTACAATTTAAAAGATCGAAGCCACAACGGTGAATCTTACTTC
1 TTGCAATTTAAAAGATC-AAGCCACAACGGCGAATCTCACTTC
3558887 CAGGCGACAC
Statistics
Matches: 276, Mismatches: 90, Indels: 42
0.68 0.22 0.10
Matches are distributed among these distances:
47 4 0.01
48 60 0.22
49 79 0.29
50 129 0.47
51 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (49 bp):
TTGCAATTTAAAAGATCAAGCCACAACGGCGAATCTCACTTCTCCGACA
Found at i:3558749 original size:98 final size:99
Alignment explanation
Indices: 3558450--3558929 Score: 750
Period size: 98 Copynumber: 4.9 Consensus size: 99
3558440 AAACCATAGT
*
3558450 TTGCAATTTAAAAGACCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGAT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGAT
*
3558515 TGAAGCTACAACGGTGAATCTCACTTCTCCGACA
66 TGAAGCTACAACGGCGAATCTCACTTCTCCGACA
3558549 TTGCAATTTAAAAGATC-AATGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
1 TTGCAATTTAAAAGATCGAA-GCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
* *
3558613 TTGAAGCTACAACGACGAATCTCACTTCTCCGATA
65 TTGAAGCTACAACGGCGAATCTCACTTCTCCGACA
* *
3558648 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTT-CTGGCGATGCAGCGAAACAGAT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGAT
3558712 TGAAGCTACAACGGCGAATCTCACTTCTCCGACA
66 TGAAGCTACAACGGCGAATCTCACTTCTCCGACA
* * * *
3558746 TTGCAATTTAAAAGATCGAAGCCATAACGGCGAATCTTACTT-CTGGTGATGCAGTGGAACAGAT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGAT
* * * *
3558810 TGAAGCTACAATGGCGAGTCTCGCTTCCCCGACA
66 TGAAGCTACAACGGCGAATCTCACTTCTCCGACA
* * **
3558844 TTACAATTTAAAAGATCGAAGCCACAACGGTGAATCTTACTTCCAGGCGACACAGCGGAACAGAT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGAT
**
3558909 TGAAGCCGCAACGGCGAATCT
66 TGAAGCTACAACGGCGAATCT
3558930 TATTTCCTCG
Statistics
Matches: 350, Mismatches: 28, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
98 183 0.52
99 165 0.47
100 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (99 bp):
TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGAT
TGAAGCTACAACGGCGAATCTCACTTCTCCGACA
Found at i:3558786 original size:197 final size:197
Alignment explanation
Indices: 3558450--3558929 Score: 748
Period size: 197 Copynumber: 2.4 Consensus size: 197
3558440 AAACCATAGT
*
3558450 TTGCAATTTAAAAGACCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGAT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGAT
*
3558515 TGAAGCTACAACGGTGAATCTCACTTCTCCGACATTGCAATTTAAAAGATCAATGCCACAACGGC
66 TGAAGCTACAACGGCGAATCTCACTTCTCCGACATTGCAATTTAAAAGATCAATGCCACAACGGC
*
3558580 GAATCTTACTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGACGAATCTCACTTCTCCG
131 GAATCTTACTT-CAGGCGATGCAGCGGAACAGATTGAAGCTACAACGACGAATCTCACTTCCCCG
*
3558645 ATA
195 ACA
* *
3558648 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTT-CTGGCGATGCAGCGAAACAGAT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGAT
*
3558712 TGAAGCTACAACGGCGAATCTCACTTCTCCGACATTGCAATTTAAAAGATCGAA-GCCATAACGG
66 TGAAGCTACAACGGCGAATCTCACTTCTCCGACATTGCAATTTAAAAGATC-AATGCCACAACGG
* * * * * * *
3558776 CGAATCTTACTTCTGGTGATGCAGTGGAACAGATTGAAGCTACAATGGCGAGTCTCGCTTCCCCG
130 CGAATCTTACTTCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGACGAATCTCACTTCCCCG
3558841 ACA
195 ACA
* * **
3558844 TTACAATTTAAAAGATCGAAGCCACAACGGTGAATCTTACTTCCAGGCGACACAGCGGAACAGAT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGAT
**
3558909 TGAAGCCGCAACGGCGAATCT
66 TGAAGCTACAACGGCGAATCT
3558930 TATTTCCTCG
Statistics
Matches: 258, Mismatches: 22, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
196 87 0.34
197 128 0.50
198 43 0.17
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (197 bp):
TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGAT
TGAAGCTACAACGGCGAATCTCACTTCTCCGACATTGCAATTTAAAAGATCAATGCCACAACGGC
GAATCTTACTTCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGACGAATCTCACTTCCCCGA
CA
Found at i:3559796 original size:17 final size:17
Alignment explanation
Indices: 3559762--3559796 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3559752 TCTTTTCCTG
*
3559762 TTTCTTTTTTTATTTTT
1 TTTCTTTTTTTATCTTT
*
3559779 TTTCTTTTTTTCTCTTT
1 TTTCTTTTTTTATCTTT
3559796 T
1 T
3559797 CATTAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTCTTTTTTTATCTTT
Found at i:3560233 original size:3 final size:3
Alignment explanation
Indices: 3560225--3560292 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
3560215 GAATTGGTCC
3560225 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3560273 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
3560293 CCTATTTATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3562332 original size:29 final size:30
Alignment explanation
Indices: 3562268--3562334 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
3562258 ATTTGATCTT
* * *
3562268 ATTTGATTCTTTTTAATAATATAATGACTAA
1 ATTTGA-TCTATTTAATAATAGAAGGACTAA
*
3562299 A-TTGATCTATTTAATAATAGAGGGAC-AA
1 ATTTGATCTATTTAATAATAGAAGGACTAA
3562327 ATTTGATC
1 ATTTGATC
3562335 CAGCCCCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 3 0.10
29 23 0.74
30 4 0.13
31 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (30 bp):
ATTTGATCTATTTAATAATAGAAGGACTAA
Done.