Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 88 of 290
Found at i:29493219 original size:6 final size:6
Alignment explanation
Indices: 29493210--29493239 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
29493200 TCCATTTCTC
*
29493210 CATTTT CATTTT CATTTT CATTCT CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT
29493240 GGATAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (6 bp):
CATTTT
Found at i:29493227 original size:12 final size:12
Alignment explanation
Indices: 29493205--29493239 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
29493195 ATGTTTCCAT
29493205 TTCTCCATTTTCA
1 TTCT-CATTTTCA
*
29493218 TTTTCATTTTCA
1 TTCTCATTTTCA
29493230 TTCTCATTTT
1 TTCTCATTTT
29493240 GGATAAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 17 0.85
13 3 0.15
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTCATTTTCA
Found at i:29493241 original size:69 final size:73
Alignment explanation
Indices: 29493142--29493294 Score: 192
Period size: 73 Copynumber: 2.1 Consensus size: 73
29493132 TTCCAAATGA
* *
29493142 TTTCATTTCTCCATTTTTATTTTCATTTTGG-T-AAA-A-ACCATAATCATTTCCAAATG-TTTC
1 TTTCATTT-TCCATTTTCATTCTCATTTTGGATAAAACATACCATAATCATTTCCAAATGATTT-
29493202 CATTTCTCCAT
64 C-TTTCTCCAT
* *
29493213 TTTCATTTT-CATTTTCATTCTCATTTTGGATAAAATCATATCATAATCATTTCCTAATGATTTC
1 TTTCATTTTCCATTTTCATTCTCATTTTGGATAAAA-CATACCATAATCATTTCCAAATGATTTC
29493277 TTTCTCCAT
65 TTTCTCCAT
29493286 TTTCATTTT
1 TTTCATTTT
29493295 TGAGAAAAGC
Statistics
Matches: 72, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
69 18 0.25
70 2 0.03
71 11 0.15
73 19 0.26
74 19 0.26
75 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.52
Consensus pattern (73 bp):
TTTCATTTTCCATTTTCATTCTCATTTTGGATAAAACATACCATAATCATTTCCAAATGATTTCT
TTCTCCAT
Found at i:29495690 original size:54 final size:54
Alignment explanation
Indices: 29495621--29495728 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 54
29495611 AAAAATGATC
* * *
29495621 GGAATAATGAGTTTAT-GTTATTGGACTGTTTTGAAGCCCAAAAATGAAAATAAA
1 GGAAGAATGAATTTATGGTT-TTCGACTGTTTTGAAGCCCAAAAATGAAAATAAA
*
29495675 GGAAGAATGAATTTATGGTTTTCGACTGTTTTGAAGCCCGAAAATGAAAATAAA
1 GGAAGAATGAATTTATGGTTTTCGACTGTTTTGAAGCCCAAAAATGAAAATAAA
29495729 CTCTTCGGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 46 0.94
55 3 0.06
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (54 bp):
GGAAGAATGAATTTATGGTTTTCGACTGTTTTGAAGCCCAAAAATGAAAATAAA
Found at i:29497825 original size:27 final size:26
Alignment explanation
Indices: 29497777--29497962 Score: 223
Period size: 27 Copynumber: 6.9 Consensus size: 26
29497767 GTGAGGCTGC
* *
29497777 CAGATATTGTGAC-GAAGTCACCAGAT
1 CAGATATTGTGGCAG-AGCCACCAGAT
* *
29497803 ACAGATATTGTGGCAGAGGCACCAGAA
1 -CAGATATTGTGGCAGAGCCACCAGAT
29497830 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
*
29497857 CAGATATATGTGGCAGAGCCACCAGGT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
*
29497884 CAGATAATTGTGGCATAGCCACCAGGA-
1 CAGAT-ATTGTGGCAGAGCCACCA-GAT
29497911 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
*
29497938 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
29497963 GACGCTTCCT
Statistics
Matches: 142, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
26 11 0.08
27 125 0.88
28 6 0.04
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAT
Found at i:29497855 original size:54 final size:55
Alignment explanation
Indices: 29497795--29497962 Score: 254
Period size: 54 Copynumber: 3.1 Consensus size: 55
29497785 GTGACGAAGT
* * *
29497795 CACCAGATACAGATAT-TGTGGCAGAGGCACCAGAACAGAT-ATATGTGGCAGAGC
1 CACCAGATACAGATATATGTGGCAGAGCCACCAGATCAGATAAT-TGTGGCATAGC
*
29497849 CACCAGAT-CAGATATATGTGGCAGAGCCACCAGGTCAGATAATTGTGGCATAGC
1 CACCAGATACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGC
*
29497903 CACCAG-GACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGC
1 CACCAGATACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGC
29497957 CACCAG
1 CACCAG
29497963 GACGCTTCCT
Statistics
Matches: 105, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
53 7 0.07
54 96 0.91
55 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (55 bp):
CACCAGATACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGC
Found at i:29497914 original size:81 final size:81
Alignment explanation
Indices: 29497795--29497963 Score: 261
Period size: 81 Copynumber: 2.1 Consensus size: 81
29497785 GTGACGAAGT
* *
29497795 CACCAGATACAGATATTGTGGCAGAGGCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAG
1 CACCAGGTACAGATATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAG
29497860 AT-ATATGTGGCAGAGC
66 ATAAT-TGTGGCAGAGC
* *
29497876 CACCAGGT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAGATCA
1 CACCAGGTACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCA
*
29497940 GATAATTGTGGCATAGC
65 GATAATTGTGGCAGAGC
29497957 CACCAGG
1 CACCAGG
29497964 ACGCTTCCTC
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
80 5 0.06
81 74 0.91
82 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (81 bp):
CACCAGGTACAGATATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAG
ATAATTGTGGCAGAGC
Found at i:29505738 original size:25 final size:25
Alignment explanation
Indices: 29505703--29505768 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
29505693 CTTTTACATA
29505703 TATGCTCACACGAGCTATGAATAAG
1 TATGCTCACACGAGCTATGAATAAG
* * *
29505728 TATGCTTACACGAGTTCTGAATAAG
1 TATGCTCACACGAGCTATGAATAAG
29505753 TATGCTCACACGAGCT
1 TATGCTCACACGAGCT
29505769 GTGGGTCGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (25 bp):
TATGCTCACACGAGCTATGAATAAG
Found at i:29510486 original size:21 final size:21
Alignment explanation
Indices: 29510458--29510649 Score: 78
Period size: 21 Copynumber: 9.3 Consensus size: 21
29510448 TGTACTTCGA
29510458 TACCCCTGAATTGCACATATG
1 TACCCCTGAATTGCACATATG
* * * * **
29510479 TGCCCCTG-TTTGTACTTCGG
1 TACCCCTGAATTGCACATATG
* *
29510499 TACCCCTTAATTGCACATACG
1 TACCCCTGAATTGCACATATG
* * *
29510520 -ACCCCCT-ATTTGTAC-TTTGG
1 TA-CCCCTGAATTGCACATAT-G
29510540 TACCCCTGAATTGCACATATG
1 TACCCCTGAATTGCACATATG
* * **
29510561 TGCCCCTG--TT-CTTACTTCGG
1 TACCCCTGAATTGC--ACATATG
* *
29510581 TACCCTTGAATTGCACAAATG
1 TACCCCTGAATTGCACATATG
* * *
29510602 TACCCCTG-TTTGTAC-TTTGG
1 TACCCCTGAATTGCACATAT-G
*
29510622 TACCCCTGAATTGCACAAATG
1 TACCCCTGAATTGCACATATG
*
29510643 TGCCCCT
1 TACCCCT
29510650 ATTTGTACTT
Statistics
Matches: 117, Mismatches: 40, Indels: 28
0.63 0.22 0.15
Matches are distributed among these distances:
18 1 0.01
19 4 0.03
20 50 0.43
21 56 0.48
22 5 0.04
23 1 0.01
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.33
Consensus pattern (21 bp):
TACCCCTGAATTGCACATATG
Found at i:29510488 original size:41 final size:41
Alignment explanation
Indices: 29510441--29510666 Score: 310
Period size: 41 Copynumber: 5.5 Consensus size: 41
29510431 CCCATACATA
*
29510441 CCCTGTTTGTACTTCGATACCCCTGAATTGCACATATGTGC
1 CCCTGTTTGTACTTCGGTACCCCTGAATTGCACATATGTGC
* * **
29510482 CCCTGTTTGTACTTCGGTACCCCTTAATTGCACATACGACC
1 CCCTGTTTGTACTTCGGTACCCCTGAATTGCACATATGTGC
* *
29510523 CCCTATTTGTACTTTGGTACCCCTGAATTGCACATATGTGC
1 CCCTGTTTGTACTTCGGTACCCCTGAATTGCACATATGTGC
* * *
29510564 CCCTGTTCT-TACTTCGGTACCCTTGAATTGCACAAATGTAC
1 CCCTGTT-TGTACTTCGGTACCCCTGAATTGCACATATGTGC
* *
29510605 CCCTGTTTGTACTTTGGTACCCCTGAATTGCACAAATGTGC
1 CCCTGTTTGTACTTCGGTACCCCTGAATTGCACATATGTGC
* *
29510646 CCCTATTTGTACTTTGGTACC
1 CCCTGTTTGTACTTCGGTACC
29510667 ACTGGATGTA
Statistics
Matches: 163, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
40 1 0.01
41 161 0.99
42 1 0.01
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.35
Consensus pattern (41 bp):
CCCTGTTTGTACTTCGGTACCCCTGAATTGCACATATGTGC
Found at i:29510660 original size:123 final size:123
Alignment explanation
Indices: 29510441--29510666 Score: 346
Period size: 123 Copynumber: 1.8 Consensus size: 123
29510431 CCCATACATA
* *
29510441 CCCTGTTTGTACTTCGATACCCCTGAATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCT
1 CCCTGTTTGTACTTCGATACCCCTGAATTGCACAAATGTACCCCTGTTTGTACTTCGGTACCCCT
* *
29510506 TAATTGCACATACGACCCCCTATTTGTACTTTGGTACCCCTGAATTGCACATATGTGC
66 GAATTGCACAAACGACCCCCTATTTGTACTTTGGTACCCCTGAATTGCACATATGTGC
* * *
29510564 CCCTGTTCT-TACTTCGGTACCCTTGAATTGCACAAATGTACCCCTGTTTGTACTTTGGTACCCC
1 CCCTGTT-TGTACTTCGATACCCCTGAATTGCACAAATGTACCCCTGTTTGTACTTCGGTACCCC
* **
29510628 TGAATTGCACAAATGTGCCCCTATTTGTACTTTGGTACC
65 TGAATTGCACAAACGACCCCCTATTTGTACTTTGGTACC
29510667 ACTGGATGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
123 91 0.99
124 1 0.01
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.35
Consensus pattern (123 bp):
CCCTGTTTGTACTTCGATACCCCTGAATTGCACAAATGTACCCCTGTTTGTACTTCGGTACCCCT
GAATTGCACAAACGACCCCCTATTTGTACTTTGGTACCCCTGAATTGCACATATGTGC
Found at i:29512181 original size:10 final size:10
Alignment explanation
Indices: 29512166--29512190 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29512156 CCATTTTCAC
29512166 CATTTCTATT
1 CATTTCTATT
29512176 CATTTCTATT
1 CATTTCTATT
29512186 CATTT
1 CATTT
29512191 GATTTAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (10 bp):
CATTTCTATT
Found at i:29517154 original size:20 final size:22
Alignment explanation
Indices: 29517115--29517156 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
29517105 TCGTTTTCTA
29517115 TATTTTTCTATGCTTTGAATTT
1 TATTTTTCTATGCTTTGAATTT
*
29517137 TATTTTT-TATTC-TTGAATTT
1 TATTTTTCTATGCTTTGAATTT
29517157 CTTCGTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 4 0.21
22 7 0.37
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (22 bp):
TATTTTTCTATGCTTTGAATTT
Found at i:29517697 original size:8 final size:9
Alignment explanation
Indices: 29517661--29517694 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
29517651 TTAATTGAAA
29517661 AATTAATTT
1 AATTAATTT
*
29517670 AGTTAATTT
1 AATTAATTT
29517679 AATTAA-TT
1 AATTAATTT
29517687 AATTAATT
1 AATTAATT
29517695 AATATTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
AATTAATTT
Found at i:29537803 original size:16 final size:17
Alignment explanation
Indices: 29537767--29537805 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
29537757 CAACTTGGGC
*
29537767 CGTGTGGGCCACACGGG
1 CGTGTGGGCCACACAGG
29537784 CGTGTGGGCC-CACAGG
1 CGTGTGGGCCACACAGG
29537800 CGTGTG
1 CGTGTG
29537806 AGATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.10, C:0.28, G:0.46, T:0.15
Consensus pattern (17 bp):
CGTGTGGGCCACACAGG
Found at i:29538309 original size:38 final size:40
Alignment explanation
Indices: 29538217--29538309 Score: 145
Period size: 41 Copynumber: 2.4 Consensus size: 40
29538207 TTCGGTTCAT
* *
29538217 CATGGTGTGTAGAGATGGGTGGTTCGATATTATCCGTTCAG
1 CATGGTGTGTAGGGATGGGTGGTTCGATATTATCCG-CCAG
29538258 CATGGTGTGTAGGGATGGGTGGTTCGATATTATCC-CCA-
1 CATGGTGTGTAGGGATGGGTGGTTCGATATTATCCGCCAG
29538296 CATGGTGTGTAGGG
1 CATGGTGTGTAGGG
29538310 TTGGATGGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
38 14 0.28
39 2 0.04
41 34 0.68
ACGTcount: A:0.18, C:0.13, G:0.37, T:0.32
Consensus pattern (40 bp):
CATGGTGTGTAGGGATGGGTGGTTCGATATTATCCGCCAG
Found at i:29542710 original size:83 final size:83
Alignment explanation
Indices: 29542568--29542733 Score: 278
Period size: 83 Copynumber: 2.0 Consensus size: 83
29542558 TGTTTATGAG
* *
29542568 AACGCACCGAAGTCCAAGATCACCAACTTTGGTACATCCTACATTGAATCTTAATCACTTCCCCC
1 AACGCACCGAAGTCCAAGATCACCAACTTTGGCACATCCTACATTGAATCTTAACCACTTCCCCC
29542633 CTCACCAACTCATCTGGT
66 CTCACCAACTCATCTGGT
* * * *
29542651 AACGCGCCGAAGTCCACGATCACCAACTTTGGCACATCCTCCATTGAGTCTTAACCACTTCCCCC
1 AACGCACCGAAGTCCAAGATCACCAACTTTGGCACATCCTACATTGAATCTTAACCACTTCCCCC
29542716 CTCACCAACTCATCTGGT
66 CTCACCAACTCATCTGGT
29542734 TCGCTCTATT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.27, C:0.37, G:0.12, T:0.24
Consensus pattern (83 bp):
AACGCACCGAAGTCCAAGATCACCAACTTTGGCACATCCTACATTGAATCTTAACCACTTCCCCC
CTCACCAACTCATCTGGT
Found at i:29554002 original size:44 final size:44
Alignment explanation
Indices: 29553936--29554022 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
29553926 CTATTTTTTA
*
29553936 TTTCCCACTTAAACTCTGATTAGTATAGGTTATTTTAATATTAG
1 TTTCCCACTAAAACTCTGATTAGTATAGGTTATTTTAATATTAG
*
29553980 TTTCCCACTAAAACTCTTATTAGTATAGGTTATTTTAATATTA
1 TTTCCCACTAAAACTCTGATTAGTATAGGTTATTTTAATATTA
29554023 TTTGACTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (44 bp):
TTTCCCACTAAAACTCTGATTAGTATAGGTTATTTTAATATTAG
Found at i:29560250 original size:21 final size:21
Alignment explanation
Indices: 29560226--29560266 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29560216 TTTGAAAAAT
*
29560226 GAATATTA-AATTTTAGATTTA
1 GAAT-TTAGAATTTCAGATTTA
29560247 GAATTTAGAATTTCAGATTT
1 GAATTTAGAATTTCAGATTT
29560267 CTTTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.46
Consensus pattern (21 bp):
GAATTTAGAATTTCAGATTTA
Found at i:29564401 original size:35 final size:35
Alignment explanation
Indices: 29564355--29564427 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
29564345 GAGCTAAGAT
29564355 GGTACATAACATTTAAACTTCAAGATTATATGAAA
1 GGTACATAACATTTAAACTTCAAGATTATATGAAA
29564390 GGTACATAACATTTAAACTTCAAGATTATATGAAA
1 GGTACATAACATTTAAACTTCAAGATTATATGAAA
29564425 GGT
1 GGT
29564428 TAACCTAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (35 bp):
GGTACATAACATTTAAACTTCAAGATTATATGAAA
Found at i:29570863 original size:22 final size:22
Alignment explanation
Indices: 29570838--29570882 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
29570828 TTTAATAAAG
29570838 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
29570860 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
29570882 A
1 A
29570883 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:29576270 original size:28 final size:30
Alignment explanation
Indices: 29576212--29576271 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 30
29576202 TCTCTCTACT
* * *
29576212 TTTTATTTTTAAAAATATTATTTTTATTTA
1 TTTTATTTTTAAAAATATTAGTTCTAGTTA
*
29576242 TTTTA-TTTT-AAAATTTTAGTTCTAGTTA
1 TTTTATTTTTAAAAATATTAGTTCTAGTTA
29576270 TT
1 TT
29576272 ACCACTTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 17 0.65
29 4 0.15
30 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (30 bp):
TTTTATTTTTAAAAATATTAGTTCTAGTTA
Found at i:29580659 original size:279 final size:279
Alignment explanation
Indices: 29580159--29580724 Score: 1062
Period size: 279 Copynumber: 2.0 Consensus size: 279
29580149 GTCAATAATG
*
29580159 TGCTCAATTTAAAGTGCCAAAATGCATATGTGAATCATGTAACATAGCCATTTTAATATCAAATT
1 TGCTCAATTTAAAGTGCCAAAATGCATATGTAAATCATGTAACATAGCCATTTTAATATCAAATT
29580224 AAATCTAGCATACCAATTAACTATTATCAATGTTCATTTATCAATTGAAATATCAACATACCATG
66 AAATCTAGCATACCAATTAACTATTATCAATGTTCATTTATCAATTGAAATATCAACATACCATG
* *
29580289 GACCAAAAACTCTAGCATACTTGCTTAGTTCACCATTATAATCAACCAAATCATGCACATAAAAT
131 GACCAAAAACTCTAACATACTTGCTTAGTTCACCATTATAATCAACCAAATCAAGCACATAAAAT
29580354 CACTAGATGTTCACTTACCAACACTTAACAAAAAATTCATCACTTAAACATATATCAACAATCTT
196 CACTAGATGTTCACTTACCAACACTTAACAAAAAATTCATCACTTAAACATATATCAACAATCTT
29580419 GCAAAATTAACCACCCAAA
261 GCAAAATTAACCACCCAAA
29580438 TGCTCAATTTAAAGTGCCAAAATGCATATGTAAATCATGTAACATAGCCATTTTAATATCAAATT
1 TGCTCAATTTAAAGTGCCAAAATGCATATGTAAATCATGTAACATAGCCATTTTAATATCAAATT
29580503 AAATCTAGCATACCAATTAACTATTATCAATGTTCATTTATCAATTGAAATATCAACATACCATG
66 AAATCTAGCATACCAATTAACTATTATCAATGTTCATTTATCAATTGAAATATCAACATACCATG
* *
29580568 GACCAAAAACTCTAACATACTTGCTTAGTTCTCTATTATAATCAACCAAATCAAGCACATAAAAT
131 GACCAAAAACTCTAACATACTTGCTTAGTTCACCATTATAATCAACCAAATCAAGCACATAAAAT
*
29580633 CACTAGATGTTCACTTACCAACACTTAACAAAAAATTCATCACTTAAACATATATCAATAATCTT
196 CACTAGATGTTCACTTACCAACACTTAACAAAAAATTCATCACTTAAACATATATCAACAATCTT
29580698 GCAAAATTAACCACCCAAA
261 GCAAAATTAACCACCCAAA
*
29580717 -ACTCAATT
1 TGCTCAATT
29580725 AAATATTTGC
Statistics
Matches: 280, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
278 7 0.03
279 273 0.98
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (279 bp):
TGCTCAATTTAAAGTGCCAAAATGCATATGTAAATCATGTAACATAGCCATTTTAATATCAAATT
AAATCTAGCATACCAATTAACTATTATCAATGTTCATTTATCAATTGAAATATCAACATACCATG
GACCAAAAACTCTAACATACTTGCTTAGTTCACCATTATAATCAACCAAATCAAGCACATAAAAT
CACTAGATGTTCACTTACCAACACTTAACAAAAAATTCATCACTTAAACATATATCAACAATCTT
GCAAAATTAACCACCCAAA
Found at i:29581798 original size:69 final size:68
Alignment explanation
Indices: 29581718--29581849 Score: 201
Period size: 69 Copynumber: 1.9 Consensus size: 68
29581708 GGTCACTCCT
* * * *
29581718 ACATTTCCCTTACTTTATCAATTTATCATTTCCCTCCAAAATTTTGAATTTAAAGGTTTATTTNC
1 ACATTTCCCTTACTTTACCAATTGATCATTTCCCTACAAAATTTCGAATTTAAAGGTTTATTT-C
29581783 TCTC
65 TCTC
* *
29581787 ACATTTCCCTTACTTTACCAATTGATCCTTTCCCTACATAATTTCGAATTTAAAGGTTTATTT
1 ACATTTCCCTTACTTTACCAATTGATCATTTCCCTACAAAATTTCGAATTTAAAGGTTTATTT
29581850 GCCAAATAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.45
Consensus pattern (68 bp):
ACATTTCCCTTACTTTACCAATTGATCATTTCCCTACAAAATTTCGAATTTAAAGGTTTATTTCT
CTC
Found at i:29582992 original size:7 final size:6
Alignment explanation
Indices: 29582984--29583052 Score: 77
Period size: 7 Copynumber: 10.8 Consensus size: 6
29582974 GGAAGTTATC
*
29582984 ATTTTT CATTTTT ATTTTGT ATTTTT A-TTTT ATCCTTT ATTTTT CATTTTT
1 ATTTTT -ATTTTT ATTTT-T ATTTTT ATTTTT AT-TTTT ATTTTT -ATTTTT
29583035 ATTTTGT ATTTTT ATTTT
1 ATTTT-T ATTTTT ATTTT
29583053 ATCCTTTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
5 5 0.09
6 21 0.38
7 29 0.53
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (6 bp):
ATTTTT
Found at i:29583007 original size:13 final size:12
Alignment explanation
Indices: 29582984--29583052 Score: 77
Period size: 13 Copynumber: 5.4 Consensus size: 12
29582974 GGAAGTTATC
29582984 ATTTTTCATTTTT
1 ATTTTT-ATTTTT
29582997 ATTTTGTATTTTT
1 ATTTT-TATTTTT
*
29583010 A-TTTTATCCTTT
1 ATTTTTAT-TTTT
29583022 ATTTTTCATTTTT
1 ATTTTT-ATTTTT
29583035 ATTTTGTATTTTT
1 ATTTT-TATTTTT
29583048 ATTTT
1 ATTTT
29583053 ATCCTTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
11 3 0.06
12 7 0.14
13 35 0.71
14 4 0.08
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:29583026 original size:38 final size:38
Alignment explanation
Indices: 29582984--29583064 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
29582974 GGAAGTTATC
29582984 ATTTTTCATTTTTATTTTGTATTTTTATTTTATCCTTT
1 ATTTTTCATTTTTATTTTGTATTTTTATTTTATCCTTT
29583022 ATTTTTCATTTTTATTTTGTATTTTTATTTTATCCTTT
1 ATTTTTCATTTTTATTTTGTATTTTTATTTTATCCTTT
29583060 -TTTTT
1 ATTTTT
29583065 AAATTTCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 5 0.12
38 38 0.88
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.75
Consensus pattern (38 bp):
ATTTTTCATTTTTATTTTGTATTTTTATTTTATCCTTT
Found at i:29583060 original size:13 final size:13
Alignment explanation
Indices: 29583006--29583065 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
29582996 TATTTTGTAT
29583006 TTTTATTTTATCC
1 TTTTATTTTATCC
*
29583019 -TTTATTTT-TCAT
1 TTTTATTTTATC-C
* **
29583031 TTTTATTTTGTAT
1 TTTTATTTTATCC
29583044 TTTTATTTTATCC
1 TTTTATTTTATCC
29583057 TTTT-TTTTA
1 TTTTATTTTA
29583066 AATTTCAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 2 0.05
12 13 0.33
13 23 0.59
14 1 0.03
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTATTTTATCC
Found at i:29583077 original size:38 final size:38
Alignment explanation
Indices: 29582997--29583077 Score: 119
Period size: 38 Copynumber: 2.1 Consensus size: 38
29582987 TTTCATTTTT
* **
29582997 ATTTTGTATTTTTATTTTATCCTTTATTTTTCATTTTT
1 ATTTTGTATTTTTATTTTATCCTTTATTTTTAATTTCA
29583035 ATTTTGTATTTTTATTTTATCCTTT-TTTTTAAATTTCA
1 ATTTTGTATTTTTATTTTATCCTTTATTTTT-AATTTCA
29583073 ATTTT
1 ATTTT
29583078 CTTTCCCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
37 5 0.13
38 34 0.87
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (38 bp):
ATTTTGTATTTTTATTTTATCCTTTATTTTTAATTTCA
Found at i:29594132 original size:21 final size:22
Alignment explanation
Indices: 29594100--29594156 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
29594090 TATAAAAAAA
29594100 TATATTATTTTATTTCTTT-ATT
1 TATATT-TTTTATTTCTTTAATT
*
29594122 TA-AGTTTTTTATTTTTTTAATT
1 TATA-TTTTTTATTTCTTTAATT
29594144 TATATTTTTTATT
1 TATATTTTTTATT
29594157 ATCACCCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 12 0.39
22 18 0.58
23 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TATATTTTTTATTTCTTTAATT
Found at i:29604171 original size:15 final size:16
Alignment explanation
Indices: 29604138--29604201 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
29604128 ATTTTAAGTA
* *
29604138 TTATTT-AATATGAAA
1 TTATTTCAATATTAAT
*
29604153 TTATTTCAATA-TATT
1 TTATTTCAATATTAAT
29604168 TTATTAATCAATATTAAT
1 TTATT--TCAATATTAAT
* *
29604186 TTATTACAATTTTAAT
1 TTATTTCAATATTAAT
29604202 AATCTAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
15 12 0.31
16 13 0.33
17 6 0.15
18 8 0.21
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (16 bp):
TTATTTCAATATTAAT
Found at i:29604180 original size:17 final size:18
Alignment explanation
Indices: 29604158--29604191 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29604148 TGAAATTATT
*
29604158 TCAATA-TATTTTATTAA
1 TCAATATTAATTTATTAA
29604175 TCAATATTAATTTATTA
1 TCAATATTAATTTATTA
29604192 CAATTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
TCAATATTAATTTATTAA
Found at i:29615621 original size:6 final size:6
Alignment explanation
Indices: 29615612--29615641 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
29615602 AAGATGAATT
29615612 TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA
1 TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA
29615642 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.50, T:0.17
Consensus pattern (6 bp):
TGGAGA
Found at i:29615624 original size:18 final size:18
Alignment explanation
Indices: 29615597--29615641 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
29615587 TTGGAAAGGA
* **
29615597 AGATGAAGATGAATTTGG
1 AGATGGAGATGAAGATGG
*
29615615 AGATGGAGATGGAGATGG
1 AGATGGAGATGAAGATGG
29615633 AGATGGAGA
1 AGATGGAGA
29615642 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.20
Consensus pattern (18 bp):
AGATGGAGATGAAGATGG
Found at i:29631798 original size:50 final size:49
Alignment explanation
Indices: 29631671--29631802 Score: 167
Period size: 49 Copynumber: 2.7 Consensus size: 49
29631661 CCATCAAGTC
* * *
29631671 GATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAATTTGAGGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTACCAAATTTCAGGCT
* * * *
29631720 GACGCCATGTCCCAGACATGGTCTTACACT-AGCTCCCACATTTCTGTGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGA-CTACCAAATTTCAG-GCT
*
29631770 GATGCCATGTCCCGGACATGGTCTTACACTGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGAC
29631803 ACATCTCATA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
48 1 0.01
49 38 0.54
50 31 0.44
51 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACTACCAAATTTCAGGCT
Found at i:29631863 original size:46 final size:46
Alignment explanation
Indices: 29631813--29631939 Score: 191
Period size: 46 Copynumber: 2.7 Consensus size: 46
29631803 ACATCTCATA
* *
29631813 GCCGATGCATGTCCCAGACATGTCTTACCCTAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCAAGACATGTCTTACACTAGCTCTCGTCTCAAT
* * *
29631859 GCCGATGCATGTCAAAAACATGTCTTACTCTAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCAAGACATGTCTTACACTAGCTCTCGTCTCAAT
*
29631905 GCCGATGCCATGTCCTAGACATGTCTTACACTAGC
1 GCCGATG-CATGTCCAAGACATGTCTTACACTAGC
29631940 ACACAAATTA
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
46 49 0.68
47 23 0.32
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCAAGACATGTCTTACACTAGCTCTCGTCTCAAT
Found at i:29632661 original size:13 final size:13
Alignment explanation
Indices: 29632643--29632667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29632633 CTAATAATGC
29632643 AAAAATCATCAAG
1 AAAAATCATCAAG
29632656 AAAAATCATCAA
1 AAAAATCATCAA
29632668 AATCACTTAC
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:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATCATCAAG
Found at i:29638483 original size:46 final size:46
Alignment explanation
Indices: 29638428--29638598 Score: 209
Period size: 46 Copynumber: 3.7 Consensus size: 46
29638418 ACATCTTGTA
**
29638428 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTAACATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAG
* * * * * *
29638474 GCCGATGCATGTCCCAAACATGTCTTACTCTAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAG
* *
29638520 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCGAG
*
29638568 GCCGATGCATGTCCCAGACATTTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
29638599 AGCACACAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
46 54 0.51
47 27 0.26
48 23 0.22
49 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.27
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAG
Found at i:29638595 original size:94 final size:92
Alignment explanation
Indices: 29638428--29638601 Score: 251
Period size: 94 Copynumber: 1.9 Consensus size: 92
29638418 ACATCTTGTA
*
29638428 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTAACATCTCGAGGCCGATGCATGTCCCAAAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTAACATATCGAGGCCGATGCATGTCCCAAAC
*
29638493 ATGTCTTACTCTAGCTCTCGTCTCAAT
66 ATGTCTTACACTAGCTCTCGTCTCAAT
** *
29638520 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCATGTCCCA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTAACAT-ATCGAGGCCGATGCATGTCCCA
* *
29638584 GACATTTCTTACACTAGC
63 AACATGTCTTACACTAGC
29638602 ACACAAATAA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
92 7 0.10
93 14 0.19
94 50 0.69
95 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTAACATATCGAGGCCGATGCATGTCCCAAAC
ATGTCTTACACTAGCTCTCGTCTCAAT
Found at i:29639324 original size:13 final size:13
Alignment explanation
Indices: 29639306--29639330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29639296 CTAAAAATGT
29639306 AAAAATCATCAAG
1 AAAAATCATCAAG
29639319 AAAAATCATCAA
1 AAAAATCATCAA
29639331 AATCACTTAC
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:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATCATCAAG
Found at i:29641611 original size:6 final size:6
Alignment explanation
Indices: 29641600--29641628 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29641590 CCTCGCTCCA
29641600 AGATCC AGATCC AGATCC AGATCC AGATC
1 AGATCC AGATCC AGATCC AGATCC AGATC
29641629 TAGTATGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.17
Consensus pattern (6 bp):
AGATCC
Found at i:29646396 original size:36 final size:36
Alignment explanation
Indices: 29646348--29646418 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
29646338 TCTACATGGT
** *
29646348 CTGCAACGTTTCACACGTCTGTGTGCCCCACACGGG
1 CTGCAACGTTTCACACAACCGTGTGCCCCACACGGG
*
29646384 CTGCAA-GATTTCACATAACCGTGTGCCCCACACGG
1 CTGCAACG-TTTCACACAACCGTGTGCCCCACACGG
29646419 CTTGGCCACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 1 0.03
36 29 0.97
ACGTcount: A:0.21, C:0.35, G:0.23, T:0.21
Consensus pattern (36 bp):
CTGCAACGTTTCACACAACCGTGTGCCCCACACGGG
Found at i:29646712 original size:20 final size:20
Alignment explanation
Indices: 29646682--29646719 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29646672 AATAACCACT
29646682 TTCCTTAAAGTAACAATTCAA
1 TTCCTTAAAGTAA-AATTCAA
29646703 TTCC-TAAAGTAAAATTC
1 TTCCTTAAAGTAAAATTC
29646720 GAGTACATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.34
Consensus pattern (20 bp):
TTCCTTAAAGTAAAATTCAA
Found at i:29650901 original size:49 final size:51
Alignment explanation
Indices: 29650845--29650953 Score: 134
Period size: 54 Copynumber: 2.1 Consensus size: 51
29650835 TGAGCTTGGA
*
29650845 TTTCTTAACGTAAATTAGCT-GA-AATGCTAACATGGGTTGCGGA-GTTGTT
1 TTTCTTAACGTAAATTAGCTAGACAATGCTAACATGGGTTGC-AATGTTGTT
* *
29650894 TTTCTTAATGTAAATTGGCTGAAGATCAATGCTAACATGGGTTGCAATGTTGTT
1 TTTCTTAACGTAAATTAGCT--AGA-CAATGCTAACATGGGTTGCAATGTTGTT
29650948 TTTCTT
1 TTTCTT
29650954 TATGCATATC
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
49 18 0.35
52 2 0.04
53 1 0.02
54 30 0.59
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (51 bp):
TTTCTTAACGTAAATTAGCTAGACAATGCTAACATGGGTTGCAATGTTGTT
Found at i:29656129 original size:13 final size:13
Alignment explanation
Indices: 29656111--29656137 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29656101 TCAGCTTTTC
29656111 TCATGTATTTGGA
1 TCATGTATTTGGA
29656124 TCATGTATTTGGA
1 TCATGTATTTGGA
29656137 T
1 T
29656138 GTGTTTTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (13 bp):
TCATGTATTTGGA
Found at i:29661587 original size:40 final size:40
Alignment explanation
Indices: 29661510--29661702 Score: 300
Period size: 40 Copynumber: 4.8 Consensus size: 40
29661500 TATCTAGCAC
* * *
29661510 AGCCTGCAGGTTTTTAA-CCCGGATTC-ATTCCAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
29661548 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
29661588 AGCCTGCGGGTCTTTAAGCCCGGATACAATTTCCAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAA-TTCCAGCACGA
**
29661629 AGCCTGCGGGTCTTTAAGCCCGGATATGATTCCAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
**
29661669 AGCCTGTAGGTCTTTAAGCCCGGATACAATTCCA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCA
29661703 CATCAAATAA
Statistics
Matches: 143, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
38 15 0.10
39 8 0.06
40 82 0.57
41 38 0.27
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
Found at i:29661629 original size:81 final size:81
Alignment explanation
Indices: 29661510--29661699 Score: 305
Period size: 81 Copynumber: 2.4 Consensus size: 81
29661500 TATCTAGCAC
* *
29661510 AGCCTGCAGGTTTTTAA-CCCGGATTC-A-TTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGA
1 AGCCTGCAGGTCTTTAAGCCCGGATACAATTTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGA
29661572 TACAATTCCAGCACGA
66 TACAATTCCAGCACGA
*
29661588 AGCCTGCGGGTCTTTAAGCCCGGATACAATTTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGA
1 AGCCTGCAGGTCTTTAAGCCCGGATACAATTTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGA
**
29661653 TATGATTCCAGCACGA
66 TACAATTCCAGCACGA
*
29661669 AGCCTGTAGGTCTTTAAGCCCGGATACAATT
1 AGCCTGCAGGTCTTTAAGCCCGGATACAATT
29661700 CCACATCAAA
Statistics
Matches: 102, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
78 15 0.15
79 8 0.08
80 1 0.01
81 78 0.76
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
AGCCTGCAGGTCTTTAAGCCCGGATACAATTTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGA
TACAATTCCAGCACGA
Found at i:29667291 original size:42 final size:42
Alignment explanation
Indices: 29667238--29667361 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 42
29667228 ACATGTAATT
* * *
29667238 CAATATCGATGCCTCTGTCCCAGATAGGGTCTTACACGAAAT-
1 CAATA-CGATGCCTATGTCCCAGACATGGTCTTACACGAAATA
*
29667280 CAAATACGATG-CTGATGTCCCAGACATGGTCTTATACGTAAATA
1 C-AATACGATGCCT-ATGTCCCAGACATGGTCTTACACG-AAATA
*
29667324 TCAAT-CGA-GTCCTGTGTCCCAGACATGGTCTTACACGA
1 -CAATACGATG-CCTATGTCCCAGACATGGTCTTACACGA
29667362 TATCTCAGAT
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
41 2 0.03
42 28 0.41
43 33 0.48
44 5 0.07
45 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (42 bp):
CAATACGATGCCTATGTCCCAGACATGGTCTTACACGAAATA
Found at i:29668252 original size:9 final size:9
Alignment explanation
Indices: 29668238--29668273 Score: 72
Period size: 9 Copynumber: 4.0 Consensus size: 9
29668228 CCTTTAAAAA
29668238 TAACCATAT
1 TAACCATAT
29668247 TAACCATAT
1 TAACCATAT
29668256 TAACCATAT
1 TAACCATAT
29668265 TAACCATAT
1 TAACCATAT
29668274 ATTCCACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (9 bp):
TAACCATAT
Found at i:29672045 original size:15 final size:16
Alignment explanation
Indices: 29672021--29672069 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
29672011 AATTAGATTT
*
29672021 ATAATAAAAAATAAC-
1 ATAATTAAAAATAACG
*
29672036 ATAATTAAAAATATCCG
1 ATAATTAAAAATA-ACG
*
29672053 AAAATTAAAAATAACG
1 ATAATTAAAAATAACG
29672069 A
1 A
29672070 ATTACCATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 12 0.43
16 4 0.14
17 12 0.43
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.22
Consensus pattern (16 bp):
ATAATTAAAAATAACG
Found at i:29675181 original size:26 final size:26
Alignment explanation
Indices: 29675122--29675174 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
29675112 CCAATTGAGG
29675122 AGATGACTAGTCTTGGCTATCAGAGT
1 AGATGACTAGTCTTGGCTATCAGAGT
29675148 AGATGACTAGTCTTGGCTATCAGAGT
1 AGATGACTAGTCTTGGCTATCAGAGT
29675174 A
1 A
29675175 TTTGACTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (26 bp):
AGATGACTAGTCTTGGCTATCAGAGT
Found at i:29679901 original size:28 final size:28
Alignment explanation
Indices: 29679773--29679925 Score: 198
Period size: 28 Copynumber: 5.5 Consensus size: 28
29679763 TCGATATTTT
* ** *
29679773 GCACTCTAAGTGCCATATTCAATGTCTC
1 GCACACTAAGTGCCATGCTCGATGTCTC
* ** *
29679801 GCACACTAAGTGTCATATTCAATGTCTC
1 GCACACTAAGTGCCATGCTCGATGTCTC
29679829 GCACACTAAGTGCCATGCTCGATGTCTC
1 GCACACTAAGTGCCATGCTCGATGTCTC
*
29679857 GCACACTAAGTGCCATGCTTGATGTCTC
1 GCACACTAAGTGCCATGCTCGATGTCTC
* *
29679885 GCACACTAAGTGCCATGCTCGATATCTT
1 GCACACTAAGTGCCATGCTCGATGTCTC
*
29679913 GTACACTAAGTGC
1 GCACACTAAGTGC
29679926 TAAACATAGC
Statistics
Matches: 114, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 114 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (28 bp):
GCACACTAAGTGCCATGCTCGATGTCTC
Found at i:29686805 original size:28 final size:28
Alignment explanation
Indices: 29686769--29686835 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
29686759 GATATTTCGT
* *
29686769 ACACTAAGTGCCATACCCACTGTCTCTC
1 ACACTAAGTGCCATACCCAATGTCTCGC
* **
29686797 ACATTAAGTGCCATATTCAATGTCTCGC
1 ACACTAAGTGCCATACCCAATGTCTCGC
29686825 ACACTAAGTGC
1 ACACTAAGTGC
29686836 TAAACATAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.27
Consensus pattern (28 bp):
ACACTAAGTGCCATACCCAATGTCTCGC
Found at i:29689671 original size:10 final size:10
Alignment explanation
Indices: 29689656--29689685 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
29689646 TAACTTACTC
29689656 AAACATACCA
1 AAACATACCA
*
29689666 AAACATAACA
1 AAACATACCA
29689676 AAACATACCA
1 AAACATACCA
29689686 TTGCCTAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.63, C:0.27, G:0.00, T:0.10
Consensus pattern (10 bp):
AAACATACCA
Found at i:29700811 original size:11 final size:11
Alignment explanation
Indices: 29700797--29700823 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
29700787 TACTAATTAA
29700797 ATCATTCAAAT
1 ATCATTCAAAT
29700808 ATCATTCAAAT
1 ATCATTCAAAT
29700819 ATCAT
1 ATCAT
29700824 AAGAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (11 bp):
ATCATTCAAAT
Found at i:29706298 original size:13 final size:13
Alignment explanation
Indices: 29706280--29706304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29706270 AAATAGATAT
29706280 TTATTATTTATCA
1 TTATTATTTATCA
29706293 TTATTATTTATC
1 TTATTATTTATC
29706305 TATCAAATTA
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:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATTTATCA
Found at i:29717176 original size:56 final size:56
Alignment explanation
Indices: 29717080--29717213 Score: 189
Period size: 56 Copynumber: 2.4 Consensus size: 56
29717070 TCCCAGATAG
* * * *
29717080 GGTCTTACTCGGACACA-ATATCGGAGTCACATATCGATGCCAACGTATAAAACGT
1 GGTCTTACTCGCACACATATATCGAAGCCACATATCAATGCCAACGTATAAAACGT
* *
29717135 GGTCTTACTCGCACAAATATATCGAAGCCACATATCAATGCCAACGTATAAAATGT
1 GGTCTTACTCGCACACATATATCGAAGCCACATATCAATGCCAACGTATAAAACGT
* *
29717191 GGTCGTACTCACACACATATATC
1 GGTCTTACTCGCACACATATATC
29717214 AATGCCATAG
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
55 15 0.22
56 54 0.78
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGAAGCCACATATCAATGCCAACGTATAAAACGT
Found at i:29719364 original size:68 final size:68
Alignment explanation
Indices: 29719214--29719371 Score: 169
Period size: 68 Copynumber: 2.3 Consensus size: 68
29719204 CTAGCCAATT
* * *
29719214 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACA
**
29719279 TTTA
65 CATA
* * *
29719283 TCTCTCCCGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTA
29719345 CTACATA
63 C-ACATA
29719352 GTATCTCGTAGCTCTCTTGT
1 -TATCTCGTAGCTCTCTTGT
29719372 ACACATGATG
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
68 36 0.48
69 7 0.09
70 6 0.08
71 26 0.35
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACAC
ATA
Found at i:29719641 original size:77 final size:77
Alignment explanation
Indices: 29719509--29719663 Score: 265
Period size: 77 Copynumber: 2.0 Consensus size: 77
29719499 TTATGATTCA
* *
29719509 AAATCAACTAAAATATATAAAATAGGCTGAAATAAAAAAATGTAAATGAATTTAATGTATTATTT
1 AAATCAACTAAAATATATAAAATAGGCTGAAATAAAAAAATATAAATGAAGTTAATGTATTATTT
*
29719574 ACATGCAAACTT
66 ACATACAAACTT
* *
29719586 AAATCAACTAAAATATATAAAATATGCTGAAATACAAAAATATAAATGAAGTTAATGTATTATTT
1 AAATCAACTAAAATATATAAAATAGGCTGAAATAAAAAAATATAAATGAAGTTAATGTATTATTT
29719651 ACATACAAACTT
66 ACATACAAACTT
29719663 A
1 A
29719664 CATCGGTGCA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (77 bp):
AAATCAACTAAAATATATAAAATAGGCTGAAATAAAAAAATATAAATGAAGTTAATGTATTATTT
ACATACAAACTT
Found at i:29722730 original size:16 final size:16
Alignment explanation
Indices: 29722709--29722758 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
29722699 AAATAGATAT
29722709 TTATTATTTATCATTA
1 TTATTATTTATCATTA
*
29722725 TTATTATTCTATCA-AA
1 TTATTATT-TATCATTA
*
29722741 TTATAATTTAT-ATTA
1 TTATTATTTATCATTA
29722756 TTA
1 TTA
29722759 AATTATAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.03
15 7 0.24
16 16 0.55
17 5 0.17
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTATTTATCATTA
Found at i:29723716 original size:44 final size:44
Alignment explanation
Indices: 29723631--29723722 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
29723621 TGTTCAGGGA
* *
29723631 TACTTCGACCTTGAGTCGATGAGGCACTATAAGTGTGGTACTAT
1 TACTTCGACCTTGAGTCGATAAGGCACTATAAGTGTCGTACTAT
* * *
29723675 TACTTCGACTTTGAGTCGATAAGGCACCT-TATGTGTCGTACTGT
1 TACTTCGACCTTGAGTCGATAAGGCA-CTATAAGTGTCGTACTAT
29723719 TACT
1 TACT
29723723 ATTACTTCAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 40 0.95
45 2 0.05
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (44 bp):
TACTTCGACCTTGAGTCGATAAGGCACTATAAGTGTCGTACTAT
Found at i:29726089 original size:30 final size:30
Alignment explanation
Indices: 29726053--29726111 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
29726043 AAGTAAGTAC
29726053 GCTAGTGAATGGGTCTCGACTGAGGCTGAA
1 GCTAGTGAATGGGTCTCGACTGAGGCTGAA
29726083 GCTAGTGAATGGGTCTCGACTGAGGCTGA
1 GCTAGTGAATGGGTCTCGACTGAGGCTGA
29726112 TATGTACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.24
Consensus pattern (30 bp):
GCTAGTGAATGGGTCTCGACTGAGGCTGAA
Found at i:29728768 original size:49 final size:49
Alignment explanation
Indices: 29728706--29728926 Score: 179
Period size: 49 Copynumber: 4.6 Consensus size: 49
29728696 ACATCAAAGT
*
29728706 CGATGTCATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAAGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAAGC
* ** * * ** *
29728755 CGATGCCGTGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCGGTGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAAGC
* * * * *
29728804 CGATGTCATGTCCTAGACAAGTCTTACACTAAC--ACACA-A-C-AAGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAAGC
* * * * * *
29728848 TGACGCCATGTCCTAGACAGGTCTTACACTAGCTTGT-ATATCTTG-AGAC
1 CGATGCCATGTCCCAGACAGGTCTTACACTAACTT-TCATATATCGAAG-C
*
29728897 CGATG-CATGTCCCAGACATGTCTTACACTA
1 CGATGCCATGTCCCAGACAGGTCTTACACTA
29728927 CCACACATAT
Statistics
Matches: 131, Mismatches: 34, Indels: 15
0.73 0.19 0.08
Matches are distributed among these distances:
44 29 0.22
45 1 0.01
46 3 0.02
47 2 0.02
48 25 0.19
49 71 0.54
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAAGC
Found at i:29746911 original size:46 final size:46
Alignment explanation
Indices: 29746844--29746972 Score: 204
Period size: 46 Copynumber: 2.8 Consensus size: 46
29746834 TGTAACCCGC
** * *
29746844 CCATAAGCAAACTCAGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
29746890 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
29746936 CCATAAATGAACTCGGACTCAACTCAACGAGCTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
29746973 TGCCCAAATA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:29754271 original size:27 final size:27
Alignment explanation
Indices: 29754207--29754265 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 27
29754197 TTTAATTCCA
**
29754207 TAAATATATTTTATCTCGAAAAGTTTTTT
1 TAAATA-A-TTTATCTCGAAAAGTTTAAT
29754236 TAAATAATTTAT-TCGAAAA-TTTAAT
1 TAAATAATTTATCTCGAAAAGTTTAAT
29754261 TAAAT
1 TAAAT
29754266 GAAATTCTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 9 0.32
26 7 0.25
27 5 0.18
28 1 0.04
29 6 0.21
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (27 bp):
TAAATAATTTATCTCGAAAAGTTTAAT
Found at i:29758173 original size:43 final size:42
Alignment explanation
Indices: 29758068--29758232 Score: 267
Period size: 43 Copynumber: 3.9 Consensus size: 42
29758058 GCGTTTATTA
*
29758068 AAAAAAAGCGCCGCTAAAAGTTATGGCCTTTAGCGGCGTTTG
1 AAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTG
29758110 AAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTG
1 AAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTG
*
29758152 AAGAAAAAGCGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTG
1 AA-AAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTG
* * *
29758195 AATAAAAAGTGCCGCTAAAAGTCGTGGCCTTTAACGGC
1 AA-AAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGC
29758233 TTTTTATTTT
Statistics
Matches: 117, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
42 43 0.37
43 74 0.63
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.22
Consensus pattern (42 bp):
AAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTG
Found at i:29758288 original size:43 final size:43
Alignment explanation
Indices: 29758241--29758382 Score: 216
Period size: 43 Copynumber: 3.3 Consensus size: 43
29758231 GCTTTTTATT
*
29758241 TTTAGCGGCGTTTG-AGTAAAAAGCGCCGCTAGAAGTCGTGGCT
1 TTTAGCGGCGTTTGAAG-AAAAAGCGCCGCTAGAAGTCGTGGCC
29758284 TTTAGCGGCGTTTGAAGAGAAAA-CGCCGCTAGAAGTCGTGGCC
1 TTTAGCGGCGTTTGAAGA-AAAAGCGCCGCTAGAAGTCGTGGCC
* * *
29758327 TTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAAAAGTCATAGCC
1 TTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAGAAGTCGTGGCC
29758370 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
29758383 TTCCCACAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
42 4 0.04
43 82 0.89
44 6 0.07
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (43 bp):
TTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAGAAGTCGTGGCC
Found at i:29758288 original size:146 final size:146
Alignment explanation
Indices: 29758096--29758384 Score: 456
Period size: 146 Copynumber: 2.0 Consensus size: 146
29758086 AGTTATGGCC
29758096 TTTAGCGGCGTTTGAAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGAAGA-AAAA
1 TTTAGCGGCGTTTGAAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGAAGAGAAAA
* * * *
29758160 GCGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTGAATAAAAAGTGCCGCTAAAAGTCGTGGCCT
66 -CGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAAAAGTCATAGCCT
29758225 TTAACGGC-TTTTTATT
130 TTAACGGCGTTTTTATT
* * * *
29758241 TTTAGCGGCGTTTGAGTAAAAAGCGCCGCTAGAAGTCGTGGCTTTTAGCGGCGTTTGAAGAGAAA
1 TTTAGCGGCGTTTGA-AAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGAAGAGAAA
*
29758306 ACGCCGCTAGAAGTCGTGGCCTTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAAAAGTCATAGCCT
65 ACGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAAAAGTCATAGCCT
*
29758371 TTAGCGGCGTTTTT
130 TTAACGGCGTTTTT
29758385 CCCACAAACG
Statistics
Matches: 131, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
145 15 0.11
146 107 0.82
147 9 0.07
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (146 bp):
TTTAGCGGCGTTTGAAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGAAGAGAAAA
CGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAAAAGTCATAGCCTT
TAACGGCGTTTTTATT
Found at i:29758320 original size:103 final size:103
Alignment explanation
Indices: 29758138--29758335 Score: 310
Period size: 103 Copynumber: 1.9 Consensus size: 103
29758128 AGTCATGGCC
*
29758138 TTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTGAATAAAAA
1 TTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTGAAGAAAAA
*
29758203 GTGCCGCTAAAAGTCGTGGCCTTTAACGGCTTTTTATT
66 GCGCCGCTAAAAGTCGTGGCCTTTAACGGCTTTTTATT
* *
29758241 TTTAGCGGCGTTTG-AGTAAAAAGCGCCGCTAGAAGTCGTGGCTTTTAGCGGCGTTTGAAGAGAA
1 TTTAGCGGCGTTTGAAG-AAAAAGCGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTGAAGA-AA
* *
29758305 AA-CGCCGCTAGAAGTCGTGGCCTTTAGCGGC
64 AAGCGCCGCTAAAAGTCGTGGCCTTTAACGGC
29758336 GTTTGAAGAA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
102 2 0.02
103 81 0.93
104 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (103 bp):
TTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTGAAGAAAAA
GCGCCGCTAAAAGTCGTGGCCTTTAACGGCTTTTTATT
Found at i:29758781 original size:21 final size:21
Alignment explanation
Indices: 29758755--29758816 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
29758745 TTCCTATGCT
* *
29758755 CTGCCTCCCTCGCTACTGCCG
1 CTGCCTCCCTCACTGCTGCCG
29758776 CTGCCTCCCTCACTGCTGCCG
1 CTGCCTCCCTCACTGCTGCCG
*
29758797 CTGCCTCCCTCTCTGCTGCC
1 CTGCCTCCCTCACTGCTGCC
29758817 TCCGCTCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.03, C:0.53, G:0.18, T:0.26
Consensus pattern (21 bp):
CTGCCTCCCTCACTGCTGCCG
Found at i:29759234 original size:13 final size:13
Alignment explanation
Indices: 29759197--29759235 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
29759187 AATGCAACAT
29759197 AACATTATTGAATTA
1 AACATTA-T-AATTA
29759212 AACAATTATAATTA
1 AAC-ATTATAATTA
29759226 AACATTATAA
1 AACATTATAA
29759236 ATATTTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.30
14 8 0.35
15 4 0.17
16 4 0.17
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (13 bp):
AACATTATAATTA
Found at i:29759439 original size:16 final size:17
Alignment explanation
Indices: 29759402--29759440 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
29759392 AAAATATTAT
*
29759402 TTAATATTAGAAAGTTA
1 TTAATATTAGAAAGTAA
*
29759419 TTAATATTTGAAAG-AA
1 TTAATATTAGAAAGTAA
29759435 TTAATA
1 TTAATA
29759441 AAATTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (17 bp):
TTAATATTAGAAAGTAA
Found at i:29764457 original size:9 final size:9
Alignment explanation
Indices: 29764443--29764632 Score: 107
Period size: 9 Copynumber: 20.6 Consensus size: 9
29764433 TATTTAAGTA
29764443 TTATGTAAG
1 TTATGTAAG
29764452 TTATGTAAG
1 TTATGTAAG
*
29764461 TTATGATATG
1 TTATG-TAAG
* * *
29764471 ATATAT-AT
1 TTATGTAAG
*
29764479 TTATGTAAA
1 TTATGTAAG
* *
29764488 TTATAT-AT
1 TTATGTAAG
*
29764496 TTATCTAAG
1 TTATGTAAG
*
29764505 TTATATAAG
1 TTATGTAAG
29764514 TTATGTAAG
1 TTATGTAAG
*
29764523 TTATGTAAA
1 TTATGTAAG
*
29764532 TTATGATATAAAA
1 TTATG---T-AAG
*
29764545 TATATTTAAG
1 T-TATGTAAG
29764555 TATTATGTAAG
1 --TTATGTAAG
29764566 TTATGTAAG
1 TTATGTAAG
* *
29764575 TTATAT-AT
1 TTATGTAAG
*
29764583 TTATCTAAG
1 TTATGTAAG
*
29764592 TTATATAAG
1 TTATGTAAG
*
29764601 TTATGTACG
1 TTATGTAAG
*
29764610 TTTTGTAAG
1 TTATGTAAG
* *
29764619 TTATATAAA
1 TTATGTAAG
29764628 TTATG
1 TTATG
29764633 ATATCAAATA
Statistics
Matches: 139, Mismatches: 31, Indels: 22
0.72 0.16 0.11
Matches are distributed among these distances:
8 16 0.12
9 98 0.71
10 8 0.06
11 8 0.06
12 2 0.01
13 4 0.03
14 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:29764525 original size:71 final size:69
Alignment explanation
Indices: 29764443--29764605 Score: 202
Period size: 71 Copynumber: 2.3 Consensus size: 69
29764433 TATTTAAGTA
* * * *
29764443 TTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAATTATAT-ATTTATCTAAGTT
1 TTATGTAAGTTATGTAAGTTATGATATAAAATATATTTAAGT--ATTATATAAGTTATCTAAGTT
29764507 ATATAAG
64 ATAT-AG
* * *
29764514 TTATGTAAGTTATGTAAATTATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT
1 TTATGTAAGTTATGTAAGTTATGATATAAAATATATTTAAGTATTATATAAGTTATCTAAGTTAT
*
29764579 ATAT
66 ATAG
* *
29764583 TTATCTAAGTTATATAAGTTATG
1 TTATGTAAGTTATGTAAGTTATG
29764606 TACGTTTTGT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
69 27 0.34
70 15 0.19
71 38 0.47
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (69 bp):
TTATGTAAGTTATGTAAGTTATGATATAAAATATATTTAAGTATTATATAAGTTATCTAAGTTAT
ATAG
Found at i:29764581 original size:87 final size:90
Alignment explanation
Indices: 29764479--29764663 Score: 259
Period size: 96 Copynumber: 2.0 Consensus size: 90
29764469 TGATATATAT
*
29764479 TTATGTAAATTATATATTTATCTAAGTTATATAAG-T-TA-TGTAAGTTATGTAAATTATGATAT
1 TTATGTAAATTATATATTTATCTAAGTTATATAAGTTGTATTGTAAGTTATATAAATTATGATAT
29764541 AAAATATATTTAAGTATTATGTAAG
66 AAAATATATTTAAGTATTATGTAAG
*
29764566 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTACGTTTTGTAAGTTATATAAATTA
1 TTATGTAAATTATATATTTATCTAAGTTATATAAG-T-TGTA----TTGTAAGTTATATAAATTA
* *
29764631 TGATATCAAATATATTTATGTATTATGTAAG
60 TGATATAAAATATATTTAAGTATTATGTAAG
29764662 TT
1 TT
29764664 TTTAATTTCA
Statistics
Matches: 85, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
87 34 0.40
90 1 0.01
91 2 0.02
96 48 0.56
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (90 bp):
TTATGTAAATTATATATTTATCTAAGTTATATAAGTTGTATTGTAAGTTATATAAATTATGATAT
AAAATATATTTAAGTATTATGTAAG
Found at i:29764619 original size:114 final size:114
Alignment explanation
Indices: 29764419--29764632 Score: 290
Period size: 114 Copynumber: 1.9 Consensus size: 114
29764409 ACTAGTTATG
* * * *
29764419 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATG
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATAGTTATA
*
29764484 TAAATTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
66 TAAATTATATATTTATCTAAGTTATATAAATTATGTAAGTTATGTAAAT
* *
29764533 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT-ATAT-TTATCTAAGTTAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATAT-AGTTAT
* * *
29764596 ATAAGTTATGTACGTTT-TGTAAGTTATATAAATTATG
65 ATAAATTATATA--TTTATCTAAGTTATATAAATTATG
29764633 ATATCAAATA
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
112 4 0.05
113 18 0.21
114 62 0.71
115 3 0.03
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.47
Consensus pattern (114 bp):
TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATAGTTATA
TAAATTATATATTTATCTAAGTTATATAAATTATGTAAGTTATGTAAAT
Found at i:29764757 original size:15 final size:15
Alignment explanation
Indices: 29764737--29764792 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
29764727 AAGTAGCGGG
29764737 ATTAAATAATATTTA
1 ATTAAATAATATTTA
29764752 ATTAAATAATATTT-
1 ATTAAATAATATTTA
29764766 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
*
29764781 ATTAAGTAATAT
1 ATTAAATAATAT
29764793 ACATGTCGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.46
16 5 0.14
17 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:29766178 original size:357 final size:358
Alignment explanation
Indices: 29765002--29766240 Score: 2399
Period size: 358 Copynumber: 3.5 Consensus size: 358
29764992 ATAAAACGGA
*
29765002 GAATTTTTTAAGATTCATCATACGCGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
1 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
*
29765067 CTCGATATAAGGCAACCCGTCAAGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
66 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
29765132 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAATTATAACTTTTAAAGAC
131 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAATTATAACTTTTAAAGAC
29765197 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
196 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
29765262 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
261 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
29765327 ATGAGCTTGATAGAACTTTTTTCAAGTCTTTTT
326 ATGAGCTTGATAGAACTTTTTTCAAGTCTTTTT
29765360 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
1 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
29765425 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
66 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
* *
29765490 AAGGTTGGAGAGAAGGTTAGCCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
131 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAATTATAACTTTTAAAGAC
*
29765555 ATTTAGAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
196 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
29765620 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
261 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
*
29765685 ATGAGCTCGATAGAACTTTTTTCAAGTCTTTTT
326 ATGAGCTTGATAGAACTTTTTTCAAGTCTTTTT
*
29765718 GAATTTTTTAAGATTTATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
1 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
29765783 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
66 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
29765848 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAATTATAACTTTTAAAGAC
131 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAATTATAACTTTTAAAGAC
29765913 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGC-AAAAAATAGTAATTTGAATATAA
196 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
29765977 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
261 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
29766042 ATGAGCTTGATAGAACTTTTTTCAAGTCTTTTT
326 ATGAGCTTGATAGAACTTTTTTCAAGTCTTTTT
29766075 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
1 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
29766140 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
66 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
*
29766205 AAGGTTGGAGAGAAGGTCATCCATTGTTGTAATTTT
131 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTT
29766241 AATGGACAAG
Statistics
Matches: 868, Mismatches: 13, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
357 284 0.33
358 584 0.67
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (358 bp):
GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAATTATAACTTTTAAAGAC
ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
ATGAGCTTGATAGAACTTTTTTCAAGTCTTTTT
Found at i:29766484 original size:15 final size:15
Alignment explanation
Indices: 29766464--29766492 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29766454 AGAATTTTGA
29766464 AATAAAACGTACCTT
1 AATAAAACGTACCTT
29766479 AATAAAACGTACCT
1 AATAAAACGTACCT
29766493 GGTCTACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
AATAAAACGTACCTT
Found at i:29767593 original size:420 final size:420
Alignment explanation
Indices: 29766814--29767654 Score: 1673
Period size: 420 Copynumber: 2.0 Consensus size: 420
29766804 GAACCAATAC
29766814 TTTTTTCAAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGA
1 TTTTTTCAAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGA
29766879 TCCATTATATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATC
66 TCCATTATATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATC
29766944 TTTAAAATATTTAAAATAAGGTTGGAGAGAAGGTCATCCATTGTTGTAATTTTAATGGACAAGCA
131 TTTAAAATATTTAAAATAAGGTTGGAGAGAAGGTCATCCATTGTTGTAATTTTAATGGACAAGCA
29767009 AGCTACACTGTAATAAAATTAATTCATACTTATTCATACTTAAGCTGAATCAAATAATAATTAAG
196 AGCTACACTGTAATAAAATTAATTCATACTTATTCATACTTAAGCTGAATCAAATAATAATTAAG
29767074 TTGAACCAAATATTTAAAATTAATTTGGTAACAAAATAGTTTTGCTCCAAACAGAACCAACAATT
261 TTGAACCAAATATTTAAAATTAATTTGGTAACAAAATAGTTTTGCTCCAAACAGAACCAACAATT
29767139 AAATCTTTACAAAATCGCAACCCCAAAATATTAATTTTTCCAAAATCATCATGATAAAACTATTA
326 AAATCTTTACAAAATCGCAACCCCAAAATATTAATTTTTCCAAAATCATCATGATAAAACTATTA
29767204 TTGATTAGAATTTTGAAATAAAACGTACCT
391 TTGATTAGAATTTTGAAATAAAACGTACCT
*
29767234 TTTTTTCAAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTATACCTAGGGAGGA
1 TTTTTTCAAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGA
29767299 TCCATTATATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATC
66 TCCATTATATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATC
29767364 TTTAAAATATTTAAAATAAGGTTGGAGAGAAGGTCATCCATTGTTGTAATTTTAATGGACAAGCA
131 TTTAAAATATTTAAAATAAGGTTGGAGAGAAGGTCATCCATTGTTGTAATTTTAATGGACAAGCA
29767429 AGCTACACTGTAATAAAATTAATTCATACTTATTCATACTTAAGCTGAATCAAATAATAATTAAG
196 AGCTACACTGTAATAAAATTAATTCATACTTATTCATACTTAAGCTGAATCAAATAATAATTAAG
29767494 TTGAACCAAATATTTAAAATTAATTTGGTAACAAAATAGTTTTGCTCCAAACAGAACCAACAATT
261 TTGAACCAAATATTTAAAATTAATTTGGTAACAAAATAGTTTTGCTCCAAACAGAACCAACAATT
29767559 AAATCTTTACAAAATCGCAACCCCAAAATATTAATTTTTCCAAAATCATCATGATAAAACTATTA
326 AAATCTTTACAAAATCGCAACCCCAAAATATTAATTTTTCCAAAATCATCATGATAAAACTATTA
29767624 TTGATTAGAATTTTGAAATAAAACGTACCT
391 TTGATTAGAATTTTGAAATAAAACGTACCT
29767654 T
1 T
29767655 AATAAAACGT
Statistics
Matches: 420, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
420 420 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (420 bp):
TTTTTTCAAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGA
TCCATTATATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATC
TTTAAAATATTTAAAATAAGGTTGGAGAGAAGGTCATCCATTGTTGTAATTTTAATGGACAAGCA
AGCTACACTGTAATAAAATTAATTCATACTTATTCATACTTAAGCTGAATCAAATAATAATTAAG
TTGAACCAAATATTTAAAATTAATTTGGTAACAAAATAGTTTTGCTCCAAACAGAACCAACAATT
AAATCTTTACAAAATCGCAACCCCAAAATATTAATTTTTCCAAAATCATCATGATAAAACTATTA
TTGATTAGAATTTTGAAATAAAACGTACCT
Found at i:29767660 original size:15 final size:15
Alignment explanation
Indices: 29767640--29767668 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29767630 AGAATTTTGA
29767640 AATAAAACGTACCTT
1 AATAAAACGTACCTT
29767655 AATAAAACGTACCT
1 AATAAAACGTACCT
29767669 GGTCTACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
AATAAAACGTACCTT
Found at i:29768178 original size:183 final size:183
Alignment explanation
Indices: 29767870--29768238 Score: 666
Period size: 183 Copynumber: 2.0 Consensus size: 183
29767860 CCTAGAACAG
*
29767870 ATGTAAGATTATAAGAGTAGCATCAAATATATTTCAGTTGAAGCAAATATAAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTGAAGCAAATATAAAAACTTTATCTAT
*
29767935 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
66 ATCAGTACCAAATATCAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
*
29768000 AGCAGGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
131 AGCAGGAAGCAGTAACTGAAACACATACAACATTAATTCACTAATACAGACAC
* *
29768053 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATGAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTGAAGCAAATATAAAAACTTTATCTAT
*
29768118 ATTAGTACCAAATATCAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
66 ATCAGTACCAAATATCAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
* *
29768183 AGCAGGAAGCAGTAACTGAAACATATACAACATTAATTCACTAATATAGACAC
131 AGCAGGAAGCAGTAACTGAAACACATACAACATTAATTCACTAATACAGACAC
29768236 ATG
1 ATG
29768239 GAACTATATC
Statistics
Matches: 178, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 178 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (183 bp):
ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTGAAGCAAATATAAAAACTTTATCTAT
ATCAGTACCAAATATCAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
AGCAGGAAGCAGTAACTGAAACACATACAACATTAATTCACTAATACAGACAC
Found at i:29768328 original size:14 final size:13
Alignment explanation
Indices: 29768309--29768338 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
29768299 CAATATAATT
29768309 TTACTTCATATATA
1 TTACTTCATATA-A
29768323 TTACTTCATATAA
1 TTACTTCATATAA
29768336 TTA
1 TTA
29768339 TTATAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (13 bp):
TTACTTCATATAA
Found at i:29770900 original size:15 final size:15
Alignment explanation
Indices: 29770880--29770928 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
29770870 GGTAAAAATT
29770880 TTGGGGGAGAAGAAG
1 TTGGGGGAGAAGAAG
*
29770895 TT-GGGG-G-A-AAT
1 TTGGGGGAGAAGAAG
29770906 TTGGGGGAGAAGAAG
1 TTGGGGGAGAAGAAG
29770921 TTGGGGGA
1 TTGGGGGA
29770929 AATTGGGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
11 4 0.14
12 5 0.18
13 2 0.07
14 5 0.18
15 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.53, T:0.18
Consensus pattern (15 bp):
TTGGGGGAGAAGAAG
Found at i:29770926 original size:25 final size:26
Alignment explanation
Indices: 29770879--29770937 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
29770869 GGGTAAAAAT
29770879 TTTGGGGGAGAAGAAGTTGGGGGAAA
1 TTTGGGGGAGAAGAAGTTGGGGGAAA
29770905 TTTGGGGGAGAAGAAGTTGGGGGAAA
1 TTTGGGGGAGAAGAAGTTGGGGGAAA
29770931 -TTGGGGG
1 TTTGGGGG
29770938 TAAATCGGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 7 0.21
26 26 0.79
ACGTcount: A:0.27, C:0.00, G:0.53, T:0.20
Consensus pattern (26 bp):
TTTGGGGGAGAAGAAGTTGGGGGAAA
Found at i:29771278 original size:21 final size:21
Alignment explanation
Indices: 29771254--29771309 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
29771244 ACCCCTATAA
* *
29771254 CCTTAATCCCTAAAGTATATC
1 CCTTAAACCCTAAACTATATC
29771275 CCTTAAACCCTAAACTATATC
1 CCTTAAACCCTAAACTATATC
*
29771296 CCTT-AACCATAAAC
1 CCTTAAACCCTAAAC
29771310 CACAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 9 0.28
21 23 0.72
ACGTcount: A:0.38, C:0.32, G:0.02, T:0.29
Consensus pattern (21 bp):
CCTTAAACCCTAAACTATATC
Found at i:29771558 original size:21 final size:22
Alignment explanation
Indices: 29771527--29771570 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
29771517 ATTAACCCCT
*
29771527 AACCCCTAACCCTTAAATCATA
1 AACCCCTAACCCTTAAACCATA
29771549 AACCCC-AACCCTTAAACCATA
1 AACCCCTAACCCTTAAACCATA
29771570 A
1 A
29771571 TACATAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (22 bp):
AACCCCTAACCCTTAAACCATA
Found at i:29771687 original size:41 final size:41
Alignment explanation
Indices: 29771630--29771890 Score: 416
Period size: 41 Copynumber: 6.4 Consensus size: 41
29771620 TAACCTAAAC
* *
29771630 TTTTTAACGACGTTTTACCAAAAGCGCCGCTAATGCTCTTA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
* *
29771671 TTTTTAGCGGTGTTTTACCAAAAGCACCGCTAATGCTCTTA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
**
29771712 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCGA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
*
29771753 TTTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTTA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
29771794 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
* * *
29771835 TTTTTAGCGGTGTTTTACCAAAAGCGCCGCTATTGCTC-TG
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
*
29771875 TTTTTAGCGGTGTTTT
1 TTTTTAGCGGCGTTTT
29771891 TGGTAAAACG
Statistics
Matches: 205, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
40 17 0.08
41 188 0.92
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (41 bp):
TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
Found at i:29771850 original size:123 final size:122
Alignment explanation
Indices: 29771630--29771921 Score: 433
Period size: 123 Copynumber: 2.4 Consensus size: 122
29771620 TAACCTAAAC
* * * *
29771630 TTTTTAACGACGTTTTACCAAAAGCGCCGCTAATGCTCTTATTTTTAGCGGTGTTTTACCAAAAG
1 TTTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTTATTTTTAGCGGCGTTTTACCAAAAG
29771695 CACCGCTAATGCTCTTATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCG
66 CACCGCTAATGCTCTTATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCG
29771752 ATTTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTTATTTTTAGCGGCGTTTTACCAAAA
1 -TTTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTTATTTTTAGCGGCGTTTTACCAAAA
* * * *
29771817 GCGCCGCTAATGCTCTTATTTTTAGCGGTGTTTTACCAAAAGCGCCGCTATTGCTCTG
65 GCACCGCTAATGCTCTTATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCG
* **** *
29771875 TTTTTAGCGGTGTTTTTGGTAAAACGCCGCTATTGCTC-TATGTTTTA
1 TTTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTTAT-TTTTA
29771922 CAATTTTTTG
Statistics
Matches: 154, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
121 3 0.02
122 37 0.24
123 114 0.74
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (122 bp):
TTTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTTATTTTTAGCGGCGTTTTACCAAAAG
CACCGCTAATGCTCTTATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCG
Found at i:29782227 original size:24 final size:24
Alignment explanation
Indices: 29782191--29782236 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
29782181 AAAAAACCTA
*
29782191 AAACCTGCTAGAG-GGAGCAGACAG
1 AAACCTGCCAGAGAGG-GCAGACAG
*
29782215 AAACGTGCCAGAGAGGGCAGAC
1 AAACCTGCCAGAGAGGGCAGAC
29782237 CATTAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.37, C:0.22, G:0.35, T:0.07
Consensus pattern (24 bp):
AAACCTGCCAGAGAGGGCAGACAG
Found at i:29787892 original size:42 final size:42
Alignment explanation
Indices: 29787825--29787949 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 42
29787815 GAGCAAACGG
* * * *
29787825 AAACCCATAAGGGTTAAACAAAAGCTCGTAAGAGCTGAGCAA
1 AAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTGAACAA
* * * **
29787867 AAACTCATAAGAGTTTAACAGAAGCTCGAAAGAGTTGAACGG
1 AAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTGAACAA
* * *
29787909 AAACTCATATGAGTTAAACAGAAGCTTGTAAGAGCTAAACA
1 AAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTGAACA
29787950 GAAAGTAAAA
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (42 bp):
AAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTGAACAA
Found at i:29787899 original size:21 final size:21
Alignment explanation
Indices: 29787875--29787952 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
29787865 AAAAACTCAT
*
29787875 AAGAGTTTAACAGAAGCTCGA
1 AAGAGTTAAACAGAAGCTCGA
* * *
29787896 AAGAGTTGAACGGAAACTC-A
1 AAGAGTTAAACAGAAGCTCGA
* * *
29787916 TATGAGTTAAACAGAAGCTTGT
1 -AAGAGTTAAACAGAAGCTCGA
*
29787938 AAGAGCTAAACAGAA
1 AAGAGTTAAACAGAA
29787953 AGTAAAACAC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
20 1 0.02
21 43 0.98
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (21 bp):
AAGAGTTAAACAGAAGCTCGA
Found at i:29790377 original size:10 final size:9
Alignment explanation
Indices: 29790348--29790373 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
29790338 AGTCCCTAAA
29790348 CATCAAAAT
1 CATCAAAAT
29790357 CATCAAAAT
1 CATCAAAAT
29790366 CATCAAAA
1 CATCAAAA
29790374 ATCACTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (9 bp):
CATCAAAAT
Found at i:29791046 original size:30 final size:30
Alignment explanation
Indices: 29791012--29791071 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
29791002 TATTTTATTA
29791012 TTAATTTTGTTATTATTTTAAAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGTATTTG
*
29791042 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGTATTTG
29791072 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGTATTTG
Found at i:29792272 original size:28 final size:27
Alignment explanation
Indices: 29792208--29792272 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
29792198 ACACAAATTG
* *
29792208 AAAATAAAATAAAAAGTGGTTATATTA
1 AAAATAAAATAAAAAGTAGATATATTA
* *
29792235 AAATTGAAAATAAAATGTAGATATGATTA
1 AAAAT-AAAATAAAAAGTAGATAT-ATTA
29792264 AAAATAAAA
1 AAAATAAAA
29792273 AAATATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 4 0.13
28 19 0.61
29 8 0.26
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.28
Consensus pattern (27 bp):
AAAATAAAATAAAAAGTAGATATATTA
Found at i:29795715 original size:28 final size:28
Alignment explanation
Indices: 29795643--29795717 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
29795633 CCAAAATCAG
* * * *
29795643 GGAAAGTCCACTAAGGACTGTCTTATGT
1 GGAAAGTCTACCAAGGACTGCCTTATGA
* * *
29795671 GGAAAGTTTTCCTAGGACTGCCTTATGA
1 GGAAAGTCTACCAAGGACTGCCTTATGA
29795699 GGAAAGTCTACCAAGGACT
1 GGAAAGTCTACCAAGGACT
29795718 ATCTTGAAGA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (28 bp):
GGAAAGTCTACCAAGGACTGCCTTATGA
Found at i:29799641 original size:16 final size:15
Alignment explanation
Indices: 29799620--29799649 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29799610 AAAATAAAGT
29799620 AATTAAATTCTTAAAA
1 AATTAAATT-TTAAAA
29799636 AATTAAATTTTAAA
1 AATTAAATTTTAAA
29799650 TTAGTGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTAAATTTTAAAA
Found at i:29812537 original size:20 final size:20
Alignment explanation
Indices: 29812494--29812531 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29812484 TTTATCTTTA
29812494 TCTTTTTCTCTTTTATTCTT
1 TCTTTTTCTCTTTTATTCTT
29812514 TCTTTTTCT-TTTT-TTCTT
1 TCTTTTTCTCTTTTATTCTT
29812532 CTTCTTCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 9 0.50
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTTTTCTCTTTTATTCTT
Found at i:29813776 original size:25 final size:23
Alignment explanation
Indices: 29813740--29813785 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
29813730 AAATGGTTAT
29813740 AAAAAATTATTAAAAATTAATAA
1 AAAAAATTATTAAAAATTAATAA
*
29813763 AAAAAATTAAATTATAAATTAAT
1 AAAAAATT--ATTAAAAATTAAT
29813786 TATCATCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
25 12 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAAATTATTAAAAATTAATAA
Found at i:29822148 original size:23 final size:23
Alignment explanation
Indices: 29822045--29822158 Score: 76
Period size: 23 Copynumber: 5.0 Consensus size: 23
29822035 CCGATATATC
*
29822045 AGCTTGAA-AGAGCTTATTGTTTT
1 AGCTT-AATAGAGCTTACTGTTTT
* * * *
29822068 CAGCTCATTGGAGCTTACCGTTTT
1 -AGCTTAATAGAGCTTACTGTTTT
* *
29822092 AGCTCGT-AT-GAACTTACTG-TTC
1 AGCT--TAATAGAGCTTACTGTTTT
29822114 AGCTTGAA-AGAGCTTACTGTTTT
1 AGCTT-AATAGAGCTTACTGTTTT
*
29822137 AGCTTAATAGAGCTTATTGTTT
1 AGCTTAATAGAGCTTACTGTTT
29822159 ATCAGCTCAG
Statistics
Matches: 69, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
20 1 0.01
22 18 0.26
23 33 0.48
24 17 0.25
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (23 bp):
AGCTTAATAGAGCTTACTGTTTT
Found at i:29824274 original size:44 final size:45
Alignment explanation
Indices: 29824167--29824435 Score: 231
Period size: 47 Copynumber: 5.8 Consensus size: 45
29824157 GGGATAAATT
* * * *
29824167 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATATGCA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGC--ACATCTCTGTA
* * *
29824216 TGCTGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCT-TA
1 -GCCGATGCATGTCCCAGACATGTCTTACACTGGCACATCTCTGTA
* * *
29824261 GCCGATGCGTGTCCCAGACACGTCTTACACTGGC-TATCTCTGTCGA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCACATCTCTGT--A
* *
29824307 GGCCGATGCATGTCTCAGACATGTCTTACTCTGGCACTCATCTCTGT-
1 -GCCGATGCATGTCCCAGACATGTCTTACACTGGCA--CATCTCTGTA
* * *
29824354 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCACATC-T-CTGTA
* *
29824402 GCCGAAGCATGTCCCAGCCATGTCTTACACTGGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC
29824436 GCACAAATCA
Statistics
Matches: 183, Mismatches: 24, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
43 5 0.03
44 31 0.17
45 3 0.02
46 27 0.15
47 59 0.32
48 30 0.16
49 14 0.08
50 14 0.08
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCACATCTCTGTA
Found at i:29824412 original size:94 final size:91
Alignment explanation
Indices: 29824165--29824435 Score: 309
Period size: 94 Copynumber: 2.9 Consensus size: 91
29824155 ATGGGATAAA
* *
29824165 TTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATATGCAT-GCTGATGCATGT
1 TTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATG--TGGCCGATGCATGT
*
29824229 CCCAGACATGTCTTACACTAGCACAACTC
63 CCCAGACATGTCTTACACTGGCACAACTC
* * * *
29824258 TTAGCCGATG-CGTGTCCCAGACA-CGTCTTACACTGGCTATCTC-T-GTCGAGGCCGATGCATG
1 TT-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC--TCTCATAAT-GTGGCCGATGCATG
* * *
29824319 TCTCAGACATGTCTTACTCTGGCACTCATCTC
62 TCCCAGACATGTCTTACACTGGCA--CAACTC
*
29824351 TGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCC
1 T-TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCC
*
29824416 CAGCCATGTCTTACACTGGC
65 CAGACATGTCTTACACTGGC
29824436 GCACAAATCA
Statistics
Matches: 148, Mismatches: 18, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
91 32 0.22
92 14 0.09
93 32 0.22
94 56 0.38
95 14 0.09
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (91 bp):
TTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCC
AGACATGTCTTACACTGGCACAACTC
Found at i:29831199 original size:60 final size:59
Alignment explanation
Indices: 29831123--29831254 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 59
29831113 AACTGTGTTA
* *
29831123 ATATGGGCAAAGCCCAATATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAAGCCCAATATACTCT-GA-TATGTAA-AGGGCTACGGCCCAGATTAATACTG
* * * *
29831183 ATATGGGCTAGGCCCAATATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAAGCCCAATATACTCTGATA-TGTAAAGGGCTACGGCCCAGATTAATACTG
29831243 ATATGGGCTAAG
1 ATATGGGCTAAG
29831255 GCTCAGTTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
59 1 0.02
60 53 0.85
61 8 0.13
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (59 bp):
ATATGGGCTAAGCCCAATATACTCTGATATGTAAAGGGCTACGGCCCAGATTAATACTG
Found at i:29836981 original size:54 final size:54
Alignment explanation
Indices: 29836814--29837014 Score: 210
Period size: 54 Copynumber: 3.7 Consensus size: 54
29836804 GGTACCTTTC
* * * * *
29836814 ACCATTGCCATGTCTTGACATGGCCTTACGTGGTATCCTTGCCTTAT-GAACTC
1 ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTT
* * * * **
29836867 ACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTG-CTTATAGTAGTTT
1 ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG-AACTT
* * * *
29836921 ATCAATGCCATGTCC-TGACATGGTCTTACATGATTTCCTTGCCTTGTAGAACTT
1 ACCAATGCCATG-CCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTT
* *
29836975 ACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
29837015 AAACCCTAAT
Statistics
Matches: 119, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
52 5 0.04
53 38 0.32
54 68 0.57
55 8 0.07
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (54 bp):
ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTT
Found at i:29838318 original size:20 final size:20
Alignment explanation
Indices: 29838293--29838338 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
29838283 TGTTTGAATT
29838293 GAACCGGCCAGTCAGATCAA
1 GAACCGGCCAGTCAGATCAA
29838313 GAACCGGCCAGTCAGATCAA
1 GAACCGGCCAGTCAGATCAA
29838333 GAACCG
1 GAACCG
29838339 AAATTGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.30, G:0.26, T:0.09
Consensus pattern (20 bp):
GAACCGGCCAGTCAGATCAA
Found at i:29842652 original size:90 final size:90
Alignment explanation
Indices: 29842494--29842674 Score: 299
Period size: 90 Copynumber: 2.0 Consensus size: 90
29842484 AAAATTAACG
* *
29842494 AGAAAATGATGAACATGTTCACAGGTGAAATAAAACATTCAATAGTTCTGATCAAGCTGTGGATG
1 AGAAAATGATGAACATGTTCACAGGTGAAATAAAACATTCAATAGTTCCGATCAAGCTATGGATG
* *
29842559 ATACAAATACAAACTATCCAGAAGA
66 ATACAAATACAAACCATCCAAAAGA
* *
29842584 AGAAGATGATGAACATGTTCACAGGTGAAGTAAAACATTCAATAGTTCCGATCAAGCTATGGATG
1 AGAAAATGATGAACATGTTCACAGGTGAAATAAAACATTCAATAGTTCCGATCAAGCTATGGATG
*
29842649 ATACAAATACTAACCATCCAAAAGA
66 ATACAAATACAAACCATCCAAAAGA
29842674 A
1 A
29842675 CTCTTGAATA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 84 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (90 bp):
AGAAAATGATGAACATGTTCACAGGTGAAATAAAACATTCAATAGTTCCGATCAAGCTATGGATG
ATACAAATACAAACCATCCAAAAGA
Found at i:29855591 original size:40 final size:43
Alignment explanation
Indices: 29855547--29855644 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 43
29855537 GTTATAAATA
29855547 GCACTAAGTGTGCGA-AATG-GAATAGCTTTGGCTATATG-A-G
1 GCACTAAGTGTGCGATAATGAG-ATAGCTTTGGCTATATGAATG
* * *
29855587 GCACTAAGTGTGCGATACTGAGGTAGCTTTGGCTATTTGAAATG
1 GCACTAAGTGTGCGATAATGAGATAGCTTTGGCTATATG-AATG
29855631 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
29855645 GGATCATTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 15 0.30
41 18 0.36
42 1 0.02
43 1 0.02
44 15 0.30
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.29
Consensus pattern (43 bp):
GCACTAAGTGTGCGATAATGAGATAGCTTTGGCTATATGAATG
Found at i:29860374 original size:81 final size:81
Alignment explanation
Indices: 29860239--29860725 Score: 947
Period size: 81 Copynumber: 6.0 Consensus size: 81
29860229 TGAACTTAAA
* *
29860239 AGGTCAAAATTGAAGATTATGGAGGATGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
1 AGGTCAAAATTGAAGATTATGGGGGACGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
29860304 TAACCATTGATTTTCT
66 TAACCATTGATTTTCT
29860320 AGGTCAAAATTGAAGATTATGGGGGACGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
1 AGGTCAAAATTGAAGATTATGGGGGACGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
29860385 TAACCATTGATTTTCT
66 TAACCATTGATTTTCT
29860401 AGGTCAAAATTGAAGATTATGGGGGACGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
1 AGGTCAAAATTGAAGATTATGGGGGACGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
29860466 TAACCATTGATTTTCT
66 TAACCATTGATTTTCT
29860482 AGGTCAAAATTGAAGATTATGGGGGACGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
1 AGGTCAAAATTGAAGATTATGGGGGACGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
29860547 TAACCATTGATTTTCT
66 TAACCATTGATTTTCT
29860563 AGGTCAAAATTGAAGATTATGGGGGACGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
1 AGGTCAAAATTGAAGATTATGGGGGACGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
29860628 TAACCATTGATTTTCT
66 TAACCATTGATTTTCT
29860644 AGGTCAAAATTGAAGATTATGGGGGACGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
1 AGGTCAAAATTGAAGATTATGGGGGACGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
*
29860709 TAACCATTGATCTTCT
66 TAACCATTGATTTTCT
29860725 A
1 A
29860726 ACACACTTGG
Statistics
Matches: 403, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 403 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (81 bp):
AGGTCAAAATTGAAGATTATGGGGGACGCAAAGCACACCGACTACAAAAACCAACCAAATAGCTT
TAACCATTGATTTTCT
Found at i:29866174 original size:49 final size:49
Alignment explanation
Indices: 29866121--29866218 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
29866111 TCTCGTAAAG
* * *
29866121 AAAAGAGAAATAACATAGATTTTTTACGGGCAGAGAAGAAGAAAATTCA
1 AAAAGAGAAATAACACAGATTTTTTACGGGCAGAAAAAAAGAAAATTCA
* *
29866170 AAAAGAGAAATAATACAGATTTTTTACGGGTAGAAAAAAAGAAAATTCA
1 AAAAGAGAAATAACACAGATTTTTTACGGGCAGAAAAAAAGAAAATTCA
29866219 CTATGTCGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.21
Consensus pattern (49 bp):
AAAAGAGAAATAACACAGATTTTTTACGGGCAGAAAAAAAGAAAATTCA
Found at i:29868886 original size:9 final size:9
Alignment explanation
Indices: 29868810--29868896 Score: 57
Period size: 9 Copynumber: 9.0 Consensus size: 9
29868800 TATTTTTAAA
*
29868810 AATATTTTA
1 AATATTTTT
*
29868819 ACATAATTTCT
1 A-AT-ATTTTT
*
29868830 AATATTATT
1 AATATTTTT
*
29868839 AATATATGCTT
1 AATAT-T-TTT
29868850 AATATTTTT
1 AATATTTTT
*
29868859 AATAATTTAT
1 AAT-ATTTTT
*
29868869 ATTTATTTTT
1 A-ATATTTTT
29868879 AATATTTTT
1 AATATTTTT
*
29868888 AAAATTTTT
1 AATATTTTT
29868897 TAGAATTATT
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
9 30 0.49
10 18 0.30
11 13 0.21
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (9 bp):
AATATTTTT
Found at i:29872694 original size:40 final size:40
Alignment explanation
Indices: 29872631--29872853 Score: 281
Period size: 40 Copynumber: 5.6 Consensus size: 40
29872621 AAGCCAAGTA
* * * * *
29872631 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
29872670 CCTTCGGGACATAGCTCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
29872710 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
29872750 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
29872790 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* *
29872830 CCTTCGAGACTTAGCCCGGTTATA
1 CCTTCGGGACTTAGCCCGGATATA
29872854 TTCCGAATAT
Statistics
Matches: 163, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 13 0.08
40 149 0.91
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:29873468 original size:45 final size:45
Alignment explanation
Indices: 29873404--29873493 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
29873394 GATTGTCTAA
29873404 GCCAAAATAAAAGCATCAATATGCTTGCCTCTAACCGAATACATG
1 GCCAAAATAAAAGCATCAATATGCTTGCCTCTAACCGAATACATG
29873449 GCCAAAATAAAAGCATCAATATGCTTGCCTCTAACCGAATACATG
1 GCCAAAATAAAAGCATCAATATGCTTGCCTCTAACCGAATACATG
29873494 CAACACCAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.22
Consensus pattern (45 bp):
GCCAAAATAAAAGCATCAATATGCTTGCCTCTAACCGAATACATG
Found at i:29880982 original size:41 final size:41
Alignment explanation
Indices: 29880908--29880988 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
29880898 TCAAAAAATA
*
29880908 AAAAATTCCAAAAATATTTTTCGTTTTTGTTTTAATTTTTC
1 AAAAATTCCAAAAATATTTTTCGTTTATGTTTTAATTTTTC
29880949 AAAAA-TCCAAAAATATTTATTAC-TTTCAT-TTTTAATTTTT
1 AAAAATTCCAAAAATATTT-TT-CGTTT-ATGTTTTAATTTTT
29880989 GTTATTGCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
40 13 0.36
41 21 0.58
42 2 0.06
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (41 bp):
AAAAATTCCAAAAATATTTTTCGTTTATGTTTTAATTTTTC
Found at i:29887180 original size:21 final size:21
Alignment explanation
Indices: 29887151--29887207 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
29887141 TGCTAAACAG
*
29887151 AAACCCATAAGGGTTGAATGG
1 AAACCCATAAGGGTTGAATGA
* * * *
29887172 AAGCTCATAAGAGCTGAATGA
1 AAACCCATAAGGGTTGAATGA
29887193 AAACCCATAAGGGTT
1 AAACCCATAAGGGTT
29887208 AAACTGAATC
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.19
Consensus pattern (21 bp):
AAACCCATAAGGGTTGAATGA
Found at i:29887182 original size:42 final size:41
Alignment explanation
Indices: 29887130--29887277 Score: 138
Period size: 42 Copynumber: 3.6 Consensus size: 41
29887120 GGCTACACAA
* * *
29887130 AAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTGAATGG
1 AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAAT-G
* *
29887172 AAGCTCATAAGAGCTGAA-TGAAAACCCATAAGGGTTAAACTG
1 AAGCTCATAAGAGCTAAACAG-AAACCCATAAGGGTTAAA-TG
* * * *
29887214 AATCTCAAAAGAGCTAAACAGAAACCTATTAGGGTTAAATAG
1 AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAAT-G
* * *
29887256 AAACTCATATGAG-TTAACAGAA
1 AAGCTCATAAGAGCTAAACAGAA
29887278 GCTCGTGAGA
Statistics
Matches: 87, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
41 10 0.11
42 75 0.86
43 2 0.02
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.20
Consensus pattern (41 bp):
AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAATG
Found at i:29887920 original size:72 final size:72
Alignment explanation
Indices: 29887827--29887970 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
29887817 ATGCCACCTC
*
29887827 AGCCATCTCTTGTGTGGCAATTTACCCTTTTAGTCCTCTCTTATTTATCACTTGAGCTATTTAAT
1 AGCCATCTCTTGTGTGCCAATTTACCCTTTTAGTCCTCTCTTATTTATCACTTGAGCTATTTAAT
29887892 CATTATT
66 CATTATT
29887899 AGCCATCTCTTGTGTGCCAATTTACCCTTTTAGTCCTCTCTTATTTATCACTTGAGCTATTTAAT
1 AGCCATCTCTTGTGTGCCAATTTACCCTTTTAGTCCTCTCTTATTTATCACTTGAGCTATTTAAT
29887964 CATTATT
66 CATTATT
29887971 TCTTTAATTA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (72 bp):
AGCCATCTCTTGTGTGCCAATTTACCCTTTTAGTCCTCTCTTATTTATCACTTGAGCTATTTAAT
CATTATT
Found at i:29892682 original size:40 final size:40
Alignment explanation
Indices: 29892584--29893566 Score: 1756
Period size: 40 Copynumber: 24.6 Consensus size: 40
29892574 TCCTCGTTCA
* * * * *
29892584 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
29892623 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
29892663 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29892703 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29892743 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29892783 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29892823 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29892863 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29892903 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29892943 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29892983 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29893023 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29893063 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29893103 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29893143 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29893183 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29893223 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29893263 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29893303 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29893343 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29893383 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29893423 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
29893463 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
29893503 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
29893543 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29893567 CAGCATTCAA
Statistics
Matches: 920, Mismatches: 20, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
39 37 0.04
40 875 0.95
41 8 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:29895115 original size:73 final size:73
Alignment explanation
Indices: 29894996--29895141 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
29894986 TCACATTCAA
29894996 ACATTTCGGTGACTCAGTTTAGCGGTCCCGAAACCACTTCCCGACTAGGGTCAACTTTGGGCTGT
1 ACATTTCGGTGACTCAGTTTAGCGGTCCCGAAACCACTTCCCGACTAGGGTCAACTTTGGGCTGT
29895061 CACAACTC
66 CACAACTC
*
29895069 ACATTTCGGTGACTCGGTTTAGCGGTCCCGAAACCACTTCCCGACTAGGGTCAACTTTGGGCTGT
1 ACATTTCGGTGACTCAGTTTAGCGGTCCCGAAACCACTTCCCGACTAGGGTCAACTTTGGGCTGT
29895134 CACAACTC
66 CACAACTC
29895142 TCCCCCACTT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (73 bp):
ACATTTCGGTGACTCAGTTTAGCGGTCCCGAAACCACTTCCCGACTAGGGTCAACTTTGGGCTGT
CACAACTC
Found at i:29904219 original size:844 final size:844
Alignment explanation
Indices: 29902978--29904957 Score: 3156
Period size: 844 Copynumber: 2.3 Consensus size: 844
29902968 GGCTGTCACA
29902978 CATATACCCAAAGAACATGTTTTTAAATTCTTGTTCTTATACCGGAAGAATTGGGACATTACTAC
1 CATATACCCAAAGAACATGTTTTTAAATTCTTGTTCTTATACCGGAAGAATTGGGACATTACTAC
* *
29903043 TTGTCCCATGTTCAGATGTCTATACTCTACTATTGGCCTCATCATGTTTGGCATGTTCAGATCTT
66 TTGTCCCATGTTTAGATGTCTGTACTCTACTATTGGCCTCATCATGTTTGGCATGTTCAGATCTT
29903108 TCTGTCATCTTTACAATCTATAAAAAAACAAGGGTTAGATCTAATCATACACATCACACTATCAC
131 TCTGTCATCTTTACAATCTATAAAAAAACAAGGGTTAGATCTAATCATACACATCACACTATCAC
*
29903173 ATATTTTATATGACATGTATTTCTAGACATTTTACACACTACGTTTATTATGAGAATTAGCTAAA
196 ATATTTTATATGACATGTATTTCTAGACATTTTACACACTACGTTCATTATGAGAATTAGCTAAA
* * * * * *
29903238 CTAAAGCTCTAATACCACTAAGTATAACACCCTTAATCGTTTTTGAAACATGGTTATAGAGCATT
261 CTGAAGCTCTGATACCACTAAGTGTAACACCCTTAATCGTCTCTGAAACAGGGTTATAGAGCATT
* *
29903303 ACTAGACATTTCAGACCAATTACCAATATTTCATATCATTTAATACACATATCAAAAACTAATCA
326 ACTAAACATTTCAAACCAATTACCAATATTTCATATCATTTAATACACATATCAAAAACTAATCA
* *
29903368 CTGATCGTTTTCCTTGAGGCAAGTTAAGAAATTCCCTCTTCTTTTTGCCTAGATACCTCTTGCCA
391 CTGATCGTTTTCCTTGAGGCAAATTAAGAAATTCCCTCTTCTTTTTGCCTAGATAACTCTTGCCA
* * * * *
29903433 ACATATTTTCTTTTAAATTCATTCTGAAAGAATTTCCAAATGATTTTCTCTTTCGGCACTACAAC
456 ACATAGTTTCTTTTAAATTCATTCTAAAAGAATTTCCAAATGATTTTATCTTTCGACACAACAAC
* * * *
29903498 CACTATTATTGACCACCAATTATAAGCTTCTTCTTTCAGTAGTGAAACATCACATCTTAGATAAT
521 CACTATTATTGACCACCAATTATAAGCTTCCTCTTTCAATAATGAAACATCACATCTCAGATAAT
*
29903563 CATCGGGAGAACAAA-ATATTTCTTCAAAAACTCTTATTGCATTCTGAAGCAAATATTCAACTTT
586 CATCGGGAGAA-AAAGATATTTCTTCAAAAACTCTTATTACATTCTGAAGCAAATATTCAACTTT
* * * *
29903627 AACTAAATCATCATCTGACCTACCCTAAAATTATTTGGCCCCACACTTTTTGAGTTTTTCTATTG
650 AACTAAATCATCATCTGACCTACCCCAAAATTATTCGACCCCACACTTTTTGAGTTTTTCTATTA
* * *
29903692 GAGTACGTTTAGTTGATTCAGTCACTTAAGGAGGTGGAGGTGCAATCGGCGTCTCTACAGGTGGT
715 GAGTACGTTTAGTTGATTCAGTCACTGAAGGAGGTAGAGGTGCAATCGGCGTCTCTACAGATGGT
* * *
29903757 ACAATAGGGGGAGGAGGTTGTTGAGT-CATATTTATTTCTTGCATAAATTCACTAAATCATTGGT
780 ACAATAGGAGGAGGAGGTTGTTGA-TCCATATTTATATCTTGCATAAATTCACTAAACCATTGGT
29903821 T
844 T
*
29903822 CATATACCCAAAGAACATGTTTTTAAATTCTTGTTCTTATACCGGAAGAATTGAGACATTACTAC
1 CATATACCCAAAGAACATGTTTTTAAATTCTTGTTCTTATACCGGAAGAATTGGGACATTACTAC
* *
29903887 TTGTCCCATGTTTAGATGTCTGTACTCCACTATTGGCCTTATCATGTTTGGCATGTTCAGATCTT
66 TTGTCCCATGTTTAGATGTCTGTACTCTACTATTGGCCTCATCATGTTTGGCATGTTCAGATCTT
* *
29903952 TCTGTCATCTTTACAATCTATAAAAAAATAAGGGTTAGATCTAATCATACACATCACAGTATCAC
131 TCTGTCATCTTTACAATCTATAAAAAAACAAGGGTTAGATCTAATCATACACATCACACTATCAC
* *
29904017 ATATTTTATGTGACATGTATTTCTAGACATTTTACACACTACGTTCATTATGAGAATCAGCTAAA
196 ATATTTTATATGACATGTATTTCTAGACATTTTACACACTACGTTCATTATGAGAATTAGCTAAA
29904082 CTGAAGCTCTGATACCACTAAGTGTAACACCCTTAATCGTCTCTGAAACAGGGTTATAGAGCATT
261 CTGAAGCTCTGATACCACTAAGTGTAACACCCTTAATCGTCTCTGAAACAGGGTTATAGAGCATT
*
29904147 ACTAAACATTTCAAACCAATTACGAATATTTCATATCATTTAATACACATATCAAAAACTAATCA
326 ACTAAACATTTCAAACCAATTACCAATATTTCATATCATTTAATACACATATCAAAAACTAATCA
* *
29904212 CTGATCGTTTTCCTTGGGGCAAATTAAGAAATTCCCTTTTCTTTTTGCCTAGATAACTCTTGCCA
391 CTGATCGTTTTCCTTGAGGCAAATTAAGAAATTCCCTCTTCTTTTTGCCTAGATAACTCTTGCCA
* * *
29904277 ACATAGTTTCTTTTAAATTCATTCTAAAAGAATTTCCAAGTGATTTTATTTTTCGACACAACAGC
456 ACATAGTTTCTTTTAAATTCATTCTAAAAGAATTTCCAAATGATTTTATCTTTCGACACAACAAC
*
29904342 CACTATTATTGACCACCAATTATAAGCTTCCTCTTTCAATAATGAAACGTCACATCTCAGATAAT
521 CACTATTATTGACCACCAATTATAAGCTTCCTCTTTCAATAATGAAACATCACATCTCAGATAAT
* * * ** * *
29904407 CATTGGGATAAAAAGCTATTTCTTCAAAAACTCTTATTATTTTCTGAAGCCAATATTCAGCTTTA
586 CATCGGGAGAAAAAGATATTTCTTCAAAAACTCTTATTACATTCTGAAGCAAATATTCAACTTTA
* * * * *
29904472 ACTGAATCATCATCTTATCTACCCCGAAATTCTTCGACCCCACACTTTTTGAGTTTTTCTATTAG
651 ACTAAATCATCATCTGACCTACCCCAAAATTATTCGACCCCACACTTTTTGAGTTTTTCTATTAG
29904537 AGTACGTTTAGTTGATTCAGTCACTGAAGGAGGTAGAGGTGCAATCGGCGTCTCTACAGATGGTA
716 AGTACGTTTAGTTGATTCAGTCACTGAAGGAGGTAGAGGTGCAATCGGCGTCTCTACAGATGGTA
* * * *
29904602 CAGTAGGAGGAGGAGGTTGTTGATCCATATTTCTATCTTGCATAAATTTACTGAACCATTGGTT
781 CAATAGGAGGAGGAGGTTGTTGATCCATATTTATATCTTGCATAAATTCACTAAACCATTGGTT
* * * * * *
29904666 TATATACCTAAAGAACATGTTTTTTAATTCTTGTTCTTGTGCCGG-ATAATTGGGACATTACTAC
1 CATATACCCAAAGAACATGTTTTTAAATTCTTGTTCTTATACCGGAAGAATTGGGACATTACTAC
* * * * *
29904730 TTGTCCCATGTTTAGATGTCTGTATTTTACTATTGGTCACATCATGTTCGGCATGTTCAGATCTT
66 TTGTCCCATGTTTAGATGTCTGTACTCTACTATTGGCCTCATCATGTTTGGCATGTTCAGATCTT
** *
29904795 TCTGTCATCTTTACAATCTATAAGAAAAACAAGGGTTAGATCGGATCATACACATCATACTATCA
131 TCTGTCATCTTTACAATCTATAA-AAAAACAAGGGTTAGATCTAATCATACACATCACACTATCA
* * * * * *
29904860 CATATTTTATATGGCATGTATTTCTAGACATTTTACACACTATGTTCGTTCTGATAATTGGCTAA
195 CATATTTTATATGACATGTATTTCTAGACATTTTACACACTACGTTCATTATGAGAATTAGCTAA
*
29904925 ACTGAAGCTCTGATACCACTAAATGTAACACCC
260 ACTGAAGCTCTGATACCACTAAGTGTAACACCC
29904958 CTAACCCTTA
Statistics
Matches: 1042, Mismatches: 91, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
843 102 0.10
844 940 0.90
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (844 bp):
CATATACCCAAAGAACATGTTTTTAAATTCTTGTTCTTATACCGGAAGAATTGGGACATTACTAC
TTGTCCCATGTTTAGATGTCTGTACTCTACTATTGGCCTCATCATGTTTGGCATGTTCAGATCTT
TCTGTCATCTTTACAATCTATAAAAAAACAAGGGTTAGATCTAATCATACACATCACACTATCAC
ATATTTTATATGACATGTATTTCTAGACATTTTACACACTACGTTCATTATGAGAATTAGCTAAA
CTGAAGCTCTGATACCACTAAGTGTAACACCCTTAATCGTCTCTGAAACAGGGTTATAGAGCATT
ACTAAACATTTCAAACCAATTACCAATATTTCATATCATTTAATACACATATCAAAAACTAATCA
CTGATCGTTTTCCTTGAGGCAAATTAAGAAATTCCCTCTTCTTTTTGCCTAGATAACTCTTGCCA
ACATAGTTTCTTTTAAATTCATTCTAAAAGAATTTCCAAATGATTTTATCTTTCGACACAACAAC
CACTATTATTGACCACCAATTATAAGCTTCCTCTTTCAATAATGAAACATCACATCTCAGATAAT
CATCGGGAGAAAAAGATATTTCTTCAAAAACTCTTATTACATTCTGAAGCAAATATTCAACTTTA
ACTAAATCATCATCTGACCTACCCCAAAATTATTCGACCCCACACTTTTTGAGTTTTTCTATTAG
AGTACGTTTAGTTGATTCAGTCACTGAAGGAGGTAGAGGTGCAATCGGCGTCTCTACAGATGGTA
CAATAGGAGGAGGAGGTTGTTGATCCATATTTATATCTTGCATAAATTCACTAAACCATTGGTT
Found at i:29906181 original size:42 final size:42
Alignment explanation
Indices: 29906120--29906223 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
29906110 CCAAAAGCAG
* * * *
29906120 ATAAGTGCTAAATAGAAACCTGTAAAGGTGGAACGGAAGCTC
1 ATAAGAGCTAAATGGAAACCTATAAAGGTGAAACGGAAGCTC
* * * *
29906162 ATAAGAGCTGAATGGAAACCTATAAGGGTTAAACTGAAGCTC
1 ATAAGAGCTAAATGGAAACCTATAAAGGTGAAACGGAAGCTC
* *
29906204 AAAAGAGTTAAATGGAAACC
1 ATAAGAGCTAAATGGAAACC
29906224 CATTAGGGTT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.19
Consensus pattern (42 bp):
ATAAGAGCTAAATGGAAACCTATAAAGGTGAAACGGAAGCTC
Done.