Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 61 of 153
Found at i:19635546 original size:49 final size:49
Alignment explanation
Indices: 19635375--19635599 Score: 252
Period size: 49 Copynumber: 4.5 Consensus size: 49
19635365 TGAGGTCGCA
* * * * *
19635375 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCACG
* ** **
19635426 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCACG
* * *
19635476 TGTGTAGTACTAAGTGTAGGCTATTACATGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
* * *
19635525 TGTGTAGTACAAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
* * *
19635574 TGTGTAGTACTATGTTCAAGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
19635600 TGCGTACCAG
Statistics
Matches: 146, Mismatches: 27, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
49 73 0.50
50 41 0.28
51 32 0.22
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
Found at i:19635552 original size:99 final size:101
Alignment explanation
Indices: 19635375--19635556 Score: 269
Period size: 99 Copynumber: 1.8 Consensus size: 101
19635365 TGAGGTCGCA
** *
19635375 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGTGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACACGTACCCGAAAACTGTGATCACGTGTGTAGTACAAAG
19635440 TGCAGGCTACTACGTGTATCAAATGGTTAGGTCACG
66 TGCAGGCTACTACGTGTATCAAATGGTTAGGTCACG
* * * * * *
19635476 TGTGTAGTACTAAGTGTAGGCTATTACATGTACCGGATAA-T-TGGTCACGTGTGTAGTACAAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACACGTACCCGAAAACTGTGATCACGTGTGTAGTACAAAG
19635539 TGCAGGCTACTACGTGTA
66 TGCAGGCTACTACGTGTA
19635557 CCGGATAATT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 38 0.53
100 1 0.01
101 33 0.46
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (101 bp):
TGTGTAGTACTAAGTGCAGGCTACTACACGTACCCGAAAACTGTGATCACGTGTGTAGTACAAAG
TGCAGGCTACTACGTGTATCAAATGGTTAGGTCACG
Found at i:19643957 original size:35 final size:35
Alignment explanation
Indices: 19643891--19644299 Score: 311
Period size: 35 Copynumber: 11.6 Consensus size: 35
19643881 CATGGCAAAG
* *
19643891 TGTGAAATGTAGGTATGGTATGATCAAATCCATATTGAGT
1 TGTGAAACGTAGGTATGG--T-ATC--ATCCATACTGAGT
** *
19643931 TAAGAAACGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * *
19643966 TGTGAAATGTAGGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* *
19644001 TGTGAAATGTAGGTATGGTATCATCCATACGGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * *
19644036 TGTGAAACGTAGGTATGGTATTAACCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * * * *
19644071 TGTGAAACATAGGTATGGTATTAACCATACTAAGC
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * *
19644106 TGTGAAACGTAGGTATGGTAT-TTCCATACCGAGC
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* *** * * * *
19644140 TATGAAACGTAGGTATGACGTCGTCCATATTGTGC
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * * *
19644175 TATGATACGTAGGTATGGCATCGTCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* ** **
19644210 TATGAAATATAGGTATGGTATTTTCCATA-TCGAG-
1 TGTGAAACGTAGGTATGGTATCATCCATACT-GAGT
** * * * ** * * *
19644244 CATGAAAAGTAGGTGTGGTGTTTTTCATGCCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
19644279 TGTGAAACGTAGGTATGGTAT
1 TGTGAAACGTAGGTATGGTAT
19644300 TTCAATGAGG
Statistics
Matches: 305, Mismatches: 60, Indels: 13
0.81 0.16 0.03
Matches are distributed among these distances:
34 52 0.17
35 234 0.77
37 3 0.01
38 1 0.00
40 15 0.05
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.32
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
Found at i:19644084 original size:105 final size:105
Alignment explanation
Indices: 19643891--19644156 Score: 354
Period size: 105 Copynumber: 2.5 Consensus size: 105
19643881 CATGGCAAAG
** * *
19643891 TGTGAAATGTAGGTATGGTATGATCAAATCCATATTGAGTTAAGAAACGTAGGTATGGTATCATC
1 TGTGAAATGTAGGTATGG--T-ATC--ATCCATACCGAGTTATGAAACGTAGGTATGGTATCAAC
** * *
19643956 CATACCGAGTTGTGAAATGTAGGTATGGTATTAACCATACTGAGT
61 CATACCGAGTTGTGAAACATAGGTATGGTATTAACCATACTAAGC
* * *
19644001 TGTGAAATGTAGGTATGGTATCATCCATACGGAGTTGTGAAACGTAGGTATGGTATTAACCATAC
1 TGTGAAATGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATCAACCATAC
19644066 CGAGTTGTGAAACATAGGTATGGTATTAACCATACTAAGC
66 CGAGTTGTGAAACATAGGTATGGTATTAACCATACTAAGC
* * *
19644106 TGTGAAACGTAGGTATGGTAT-TTCCATACCGAGCTATGAAACGTAGGTATG
1 TGTGAAATGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATG
19644157 ACGTCGTCCA
Statistics
Matches: 141, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
104 26 0.18
105 93 0.66
107 3 0.02
108 1 0.01
110 18 0.13
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (105 bp):
TGTGAAATGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATCAACCATAC
CGAGTTGTGAAACATAGGTATGGTATTAACCATACTAAGC
Found at i:19648467 original size:142 final size:142
Alignment explanation
Indices: 19648208--19648492 Score: 516
Period size: 142 Copynumber: 2.0 Consensus size: 142
19648198 GTCGAGCTCG
19648208 AGCCCCAAATGAAATTCCTAGCAAGCTTCTCAATCTCCAGACAGATCAAAATTGGCACTTGGGTC
1 AGCCCCAAATGAAATTCCTAGCAAGCTTCTCAATCTCCAGACAGATCAAAATTGGCACTTGGGTC
*
19648273 TTACACATGAAATAATTCAATATGACAAGCAGCACAGACCATGCCACATTATTTTACCCACCAAA
66 ATACACATGAAATAATTCAATATGACAAGCAGCACAGACCATGCCACATTATTTTACCCACCAAA
19648338 GAAAGTCGACGC
131 GAAAGTCGACGC
* *
19648350 AGCCCCAAATGAAATTCCTAGCAAGCTTCTCAATCTCTAGACAGATCGAAATTGGCACTTGGGTC
1 AGCCCCAAATGAAATTCCTAGCAAGCTTCTCAATCTCCAGACAGATCAAAATTGGCACTTGGGTC
* **
19648415 ATACACATGAAATAATTCAATATGACAAGCAGCACAGATCATGCCATGTTATTTTACCCACCAAA
66 ATACACATGAAATAATTCAATATGACAAGCAGCACAGACCATGCCACATTATTTTACCCACCAAA
19648480 GAAAGTCGACGC
131 GAAAGTCGACGC
19648492 A
1 A
19648493 CATGCCATCT
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 137 1.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.22
Consensus pattern (142 bp):
AGCCCCAAATGAAATTCCTAGCAAGCTTCTCAATCTCCAGACAGATCAAAATTGGCACTTGGGTC
ATACACATGAAATAATTCAATATGACAAGCAGCACAGACCATGCCACATTATTTTACCCACCAAA
GAAAGTCGACGC
Found at i:19648751 original size:16 final size:17
Alignment explanation
Indices: 19648724--19648756 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19648714 TAATAGTTAC
*
19648724 AATTATATAAAATAATT
1 AATTATATAAAAAAATT
19648741 AATTA-ATAAAAAAATT
1 AATTATATAAAAAAATT
19648757 TCTCCACCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTATATAAAAAAATT
Found at i:19649262 original size:17 final size:17
Alignment explanation
Indices: 19649222--19649276 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
19649212 AATACTTTTG
*
19649222 TAAAAATTAAAAAAAACT
1 TAAAAATT-AAAAAAATT
19649240 TATAAAATATAAAAAAATT
1 TA-AAAAT-TAAAAAAATT
*
19649259 TAAAAATTAATAAAATT
1 TAAAAATTAAAAAAATT
19649276 T
1 T
19649277 TTTAAAAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 10 0.30
18 7 0.21
19 15 0.45
20 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAATTAAAAAAATT
Found at i:19649280 original size:20 final size:20
Alignment explanation
Indices: 19649217--19649417 Score: 69
Period size: 20 Copynumber: 10.2 Consensus size: 20
19649207 ATGATAATAC
*
19649217 TTTTGTAAAAATTAAAAAAAA
1 TTTT-TAAAAATTAATAAAAA
* *
19649238 CTTAT-AAAATATAA-AAAAA
1 TTTTTAAAAAT-TAATAAAAA
*
19649257 --TTTAAAAATTAATAAAAT
1 TTTTTAAAAATTAATAAAAA
* *
19649275 TTTTTAAAAGTTATTAAAAA
1 TTTTTAAAAATTAATAAAAA
* * * *
19649295 TTTCTAAAAAATATTAAAGCA
1 TTTTTAAAAATTAATAAA-AA
* * *
19649316 -TATTAAAAAGCT-GTAAAAA
1 TTTTTAAAAA-TTAATAAAAA
* *
19649335 TATTTAAAAATT-CTAAAAA
1 TTTTTAAAAATTAATAAAAA
* ** *
19649354 CTATTTAAAAATTTGTGAAAA
1 -TTTTTAAAAATTAATAAAAA
* * *
19649375 TTATTAAAAATGATTAAAAA
1 TTTTTAAAAATTAATAAAAA
* * *
19649395 -TTGTAAAAAGT-ATAAGAA
1 TTTTTAAAAATTAATAAAAA
19649413 TTTTT
1 TTTTT
19649418 TTAAAAAATA
Statistics
Matches: 134, Mismatches: 35, Indels: 24
0.69 0.18 0.12
Matches are distributed among these distances:
17 5 0.04
18 14 0.10
19 28 0.21
20 78 0.58
21 9 0.07
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (20 bp):
TTTTTAAAAATTAATAAAAA
Found at i:19649312 original size:10 final size:10
Alignment explanation
Indices: 19649223--19649394 Score: 52
Period size: 10 Copynumber: 17.3 Consensus size: 10
19649213 ATACTTTTGT
19649223 AAAA-ATTAA
1 AAAATATTAA
* *
19649232 AAAAAACTTAT
1 AAAATA-TTAA
*
19649243 AAAATATAAA
1 AAAATATTAA
19649253 AAAAT-TTAA
1 AAAATATTAA
* *
19649262 AAATTAATAA
1 AAAATATTAA
** *
19649272 AATTTTTTAA
1 AAAATATTAA
**
19649282 AAGTTATT-A
1 AAAATATTAA
*
19649291 AAAATTTCTAA
1 AAAATAT-TAA
19649302 AAAATATTAA
1 AAAATATTAA
**
19649312 AGCATATTAA
1 AAAATATTAA
* *
19649322 AAAGCT-GT-A
1 AAA-ATATTAA
*
19649331 AAAATATTTA
1 AAAATATTAA
19649341 AAAAT-TCTAA
1 AAAATAT-TAA
* *
19649351 AAACTATTTA
1 AAAATATTAA
* *
19649361 AAAATTTGTGA
1 AAAATAT-TAA
*
19649372 AAATTATT-A
1 AAAATATTAA
19649381 AAAATGATTAA
1 AAAAT-ATTAA
19649392 AAA
1 AAA
19649395 TTGTAAAAAG
Statistics
Matches: 117, Mismatches: 33, Indels: 24
0.67 0.19 0.14
Matches are distributed among these distances:
8 1 0.01
9 27 0.23
10 61 0.52
11 28 0.24
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.33
Consensus pattern (10 bp):
AAAATATTAA
Found at i:19655812 original size:47 final size:47
Alignment explanation
Indices: 19655759--19656124 Score: 563
Period size: 47 Copynumber: 7.7 Consensus size: 47
19655749 TTAGGATTCT
* *
19655759 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
* *
19655806 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
19655853 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCA
* * * *
19655902 ATGTGATGAATGTGAAAGTGTATATATATGATAGGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
*
19655949 ATGTGATGAATGTGAAAGTGTATATATATGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
*
19655996 ATGTGATGAATGTGAAAGTGTATATATATGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
* *
19656043 ATGTGATGAATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG-GCCGAATGGCCA
* * *
19656090 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
19656125 TCCCGAAGGG
Statistics
Matches: 299, Mismatches: 16, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
46 2 0.01
47 250 0.84
48 2 0.01
49 45 0.15
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
Found at i:19655911 original size:143 final size:141
Alignment explanation
Indices: 19655759--19656124 Score: 590
Period size: 143 Copynumber: 2.6 Consensus size: 141
19655749 TTAGGATTCT
19655759 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* *
19655824 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
66 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATA--TGATAA
19655889 GGCCGAATGGCCA
129 GGCCGAATGGCCA
* *
19655902 ATGTGATGAATGTGAAAGTGTATATATATGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
19655967 TGTATATATATGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGATAAGG
66 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGATAAGG
19656032 CCGAATGGCCA
131 CCGAATGGCCA
* * * * * *
19656043 ATGTGATGAATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGGATGTGAAA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATGAATGTGAAA
*
19656107 GTGTATAAATGTGATAAG
65 GTGTATATATGTGATAAG
19656125 TCCCGAAGGG
Statistics
Matches: 207, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
140 1 0.00
141 89 0.43
143 117 0.57
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (141 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGATAAGG
CCGAATGGCCA
Found at i:19660493 original size:6 final size:6
Alignment explanation
Indices: 19660478--19660511 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
19660468 TTTGTAAGTT
*
19660478 ATAT-G ATATGG ATATGG ATATGG ATATGT ATATG
1 ATATGG ATATGG ATATGG ATATGG ATATGG ATATG
19660512 CACGTTTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.38
Consensus pattern (6 bp):
ATATGG
Found at i:19661218 original size:12 final size:14
Alignment explanation
Indices: 19661201--19661232 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
19661191 GTTTGCTAAG
19661201 AAAAATA-GAAA-A
1 AAAAATAGGAAATA
19661213 AAAAATAGGAAATA
1 AAAAATAGGAAATA
19661227 AAAAAT
1 AAAAAT
19661233 TAATTACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 4 0.22
14 7 0.39
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (14 bp):
AAAAATAGGAAATA
Found at i:19662931 original size:23 final size:23
Alignment explanation
Indices: 19662904--19662949 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
19662894 TTATTTATCT
19662904 CTATCTTAAAAGTGTTATCCTGA
1 CTATCTTAAAAGTGTTATCCTGA
19662927 CTATCTTAAAAGTGTTATCCTGA
1 CTATCTTAAAAGTGTTATCCTGA
19662950 TACCATCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (23 bp):
CTATCTTAAAAGTGTTATCCTGA
Found at i:19669668 original size:22 final size:24
Alignment explanation
Indices: 19669640--19669695 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
19669630 GCTGTTAAAA
19669640 TTAGTACAATGT-AA-TCATTCAT
1 TTAGTACAATGTAAATTCATTCAT
*
19669662 TTAGTAC-ATGTGAAATTCATTCTT
1 TTAGTACAATGT-AAATTCATTCAT
19669686 TGTAGTACAA
1 T-TAGTACAA
19669696 CTTCCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.14
22 7 0.25
23 2 0.07
24 8 0.29
25 6 0.21
26 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (24 bp):
TTAGTACAATGTAAATTCATTCAT
Found at i:19685430 original size:21 final size:20
Alignment explanation
Indices: 19685392--19685436 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
19685382 TTTTCCTAAT
*
19685392 ATGTGAATTGAATGAAATTGA
1 ATGTGAATTGAATCAAATT-A
**
19685413 ATGTGAATTTTATCAAATTA
1 ATGTGAATTGAATCAAATTA
19685433 ATGT
1 ATGT
19685437 TAAATTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (20 bp):
ATGTGAATTGAATCAAATTA
Found at i:19688395 original size:62 final size:63
Alignment explanation
Indices: 19688319--19688446 Score: 197
Period size: 62 Copynumber: 2.0 Consensus size: 63
19688309 TCTTTTACTC
* * *
19688319 CATTGATTATAGATAAGATAATAATCA-T-TTTTTTATATACTAAAAAAAGTTAATATTTATTA
1 CATTAATTATAGATAAGATAATAATCATTGTTTTTTATATACT-AAAAAAGTTAATATGTATCA
*
19688381 CATTAATTATAGATAAGGTAATAATCATTGTTTTTTATATACTAAAAAAGTTAATATGTATCA
1 CATTAATTATAGATAAGATAATAATCATTGTTTTTTATATACTAAAAAAGTTAATATGTATCA
19688444 CAT
1 CAT
19688447 CATGCCATGC
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
62 25 0.42
63 22 0.37
64 13 0.22
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (63 bp):
CATTAATTATAGATAAGATAATAATCATTGTTTTTTATATACTAAAAAAGTTAATATGTATCA
Found at i:19691677 original size:301 final size:294
Alignment explanation
Indices: 19691141--19691727 Score: 739
Period size: 301 Copynumber: 2.0 Consensus size: 294
19691131 TTTTTAATAT
*
19691141 ATACAATTGATAAAGATAATAAATTGTGCATATTAAAATAAAAATGTATAAAAATATCAAAATGA
1 ATACAATTGATAAAGATAATAAATTGTACATATTAAAATAAAAATGTATAAAAATATCAAAATGA
** * * *
19691206 AGTTTTGCTTGAGTGGTAAAATTGAGGTTTTATTAATCTAATTTGTGTAGGTTCAAATCTCACTA
66 AACTTTGCTTGAGTGGTAAAATTAAGGTTTTATTAATCTAATTGGTGTAGATTCAAATCTCACTA
* * *
19691271 TATATATCTTTATTGGTTTTTAAATAAAAAGACTAAAATACCCTTGAATAATGTAACTTATTTTA
131 TATATATCTTTATTGGTTTTTAAATAAAAAGAC-AAAATAACCTTGAATAATATAACTTATATTA
*** * ** *
19691336 ATTATGGAAGGATATTTTTGTAATTTTCCTAACTGAGTTGGTTCTCGATTGACTT-GTGACACCA
195 ATTACAAAAAGATATTTTCATAATTTTCCTAACTGAGTTGGTGCTCGATTGA-TTCGTGACACCA
19691400 ACTAAATCAGGAGCTTAAATAATAGTAAGTATAGAG
259 ACTAAATCAGGAGCTTAAATAATAGTAAGTATAGAG
** * * *
19691436 ATACAATTGATGGAGATAATAATTTGTACATATTAATATAAAAATGTATAAAATATATTAAAATG
1 ATACAATTGATAAAGATAATAAATTGTACATATTAAAATAAAAATGTATAAAA-ATATCAAAATG
* *
19691501 AAACTTTGGTTGAGTGGTAAAATTAAGGTTTTATTAATCTAATTGGTGTAGATTTAAATC-CTAC
65 AAACTTTGCTTGAGTGGTAAAATTAAGGTTTTATTAATCTAATTGGTGTAGATTCAAATCTC-AC
* * * *
19691565 TATTTGCGTATTTTTATTGGTTTTTTGTTAAAATGAAAAGAC-AAATAACCTTGAATAATATAAC
129 TATAT--ATATCTTTATTGG---TTT-TT-AAATAAAAAGACAAAATAACCTTGAATAATATAAC
* * *
19691629 TTATATTAATTACAAAAATATATTTTCATAATTTTCCTAATTGAGTTGGTGCTCGGTTGATTCGT
187 TTATATTAATTACAAAAAGATATTTTCATAATTTTCCTAACTGAGTTGGTGCTCGATTGATTCGT
* * * * *
19691694 GATACTAACTCAGTCAGTAGCTTAAATAATAGTA
252 GACACCAACTAAATCAGGAGCTTAAATAATAGTA
19691728 TAGATATACA
Statistics
Matches: 247, Mismatches: 35, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
295 49 0.20
296 69 0.28
298 11 0.04
300 2 0.01
301 103 0.42
302 2 0.01
303 11 0.04
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (294 bp):
ATACAATTGATAAAGATAATAAATTGTACATATTAAAATAAAAATGTATAAAAATATCAAAATGA
AACTTTGCTTGAGTGGTAAAATTAAGGTTTTATTAATCTAATTGGTGTAGATTCAAATCTCACTA
TATATATCTTTATTGGTTTTTAAATAAAAAGACAAAATAACCTTGAATAATATAACTTATATTAA
TTACAAAAAGATATTTTCATAATTTTCCTAACTGAGTTGGTGCTCGATTGATTCGTGACACCAAC
TAAATCAGGAGCTTAAATAATAGTAAGTATAGAG
Found at i:19696443 original size:46 final size:43
Alignment explanation
Indices: 19696392--19696512 Score: 136
Period size: 46 Copynumber: 2.7 Consensus size: 43
19696382 GACGAGAGCT
19696392 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTAAGCC
1 AGTGTAAGACATGTCT-GGACATGCATCGG-CTACGAG-T-TAAGCC
* * *
19696438 AGTGTAAGACATGTCTAAGACATGCATCGGCTATGAGTTAAGCT
1 AGTGTAAGACATGTCT-GGACATGCATCGGCTACGAGTTAAGCC
19696482 AGTGTAAGACCATGTTCTGGACATGGCATCG
1 AGTGTAAGA-CATG-TCTGGACAT-GCATCG
19696513 ACATCTTATC
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
44 14 0.21
45 12 0.18
46 40 0.61
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (43 bp):
AGTGTAAGACATGTCTGGACATGCATCGGCTACGAGTTAAGCC
Found at i:19699332 original size:13 final size:13
Alignment explanation
Indices: 19699314--19699344 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19699304 ACAACTTGAA
19699314 CTGAAAATAAAAT
1 CTGAAAATAAAAT
19699327 CTGAAAATAAAAT
1 CTGAAAATAAAAT
*
19699340 TTGAA
1 CTGAA
19699345 CTAACAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (13 bp):
CTGAAAATAAAAT
Found at i:19699531 original size:19 final size:19
Alignment explanation
Indices: 19699504--19699545 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
19699494 TTTTATAATG
*
19699504 TTTTTTATTGCGAT-TTTAA
1 TTTTATATTGC-ATGTTTAA
*
19699523 TTTTATATTTCATGTTTAA
1 TTTTATATTGCATGTTTAA
19699542 TTTT
1 TTTT
19699546 TAGTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTTATATTGCATGTTTAA
Found at i:19705484 original size:46 final size:46
Alignment explanation
Indices: 19705417--19705508 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
19705407 ACGGGGTTCT
*
19705417 GCTTTTGGCGGCAACATGCTATGGGGTGGTGGTCCCGCTTATGGGG
1 GCTTTTGGCAGCAACATGCTATGGGGTGGTGGTCCCGCTTATGGGG
*
19705463 GCTTTTGGCAGCAACATGCTATGGGGTGGTGGTCCCGTTTATGGGG
1 GCTTTTGGCAGCAACATGCTATGGGGTGGTGGTCCCGCTTATGGGG
19705509 TCAAATCAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.12, C:0.18, G:0.40, T:0.29
Consensus pattern (46 bp):
GCTTTTGGCAGCAACATGCTATGGGGTGGTGGTCCCGCTTATGGGG
Found at i:19705931 original size:14 final size:14
Alignment explanation
Indices: 19705912--19705949 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
19705902 AAGATTCGTT
19705912 ATAGTTGACTGTAA
1 ATAGTTGACTGTAA
19705926 ATAGTTGACTGTAA
1 ATAGTTGACTGTAA
19705940 ATAGTTGACT
1 ATAGTTGACT
19705950 AGAATTGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (14 bp):
ATAGTTGACTGTAA
Found at i:19706812 original size:6 final size:6
Alignment explanation
Indices: 19706801--19706844 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
19706791 TTTTCCATTC
19706801 TATTAG TATTAG -ATTAG TATTAG --TTAG -ATTAG -ATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
19706844 T
1 T
19706845 TAGTGATCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.11
5 14 0.40
6 17 0.49
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (6 bp):
TATTAG
Found at i:19706818 original size:11 final size:11
Alignment explanation
Indices: 19706802--19706848 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
19706792 TTTCCATTCT
19706802 ATTAGTATTAG
1 ATTAGTATTAG
19706813 ATTAGTATTAG
1 ATTAGTATTAG
19706824 -TTAG-ATTAG
1 ATTAGTATTAG
19706833 ATTAGTATTAG
1 ATTAGTATTAG
19706844 -TTAGT
1 ATTAGT
19706849 GATCCCGACT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.15
10 13 0.38
11 16 0.47
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:19706833 original size:20 final size:21
Alignment explanation
Indices: 19706803--19706848 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
19706793 TTCCATTCTA
19706803 TTAGTATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
19706824 TTAG-ATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
19706844 TTAGT
1 TTAGT
19706849 GATCCCGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (21 bp):
TTAGTATTAGATTAGTATTAG
Found at i:19706847 original size:15 final size:14
Alignment explanation
Indices: 19706809--19706838 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
19706799 TCTATTAGTA
19706809 TTAGATTAGTATTAG
1 TTAGATTAG-ATTAG
19706824 TTAGATTAGATTAG
1 TTAGATTAGATTAG
19706838 T
1 T
19706839 ATTAGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (14 bp):
TTAGATTAGATTAG
Found at i:19709519 original size:73 final size:73
Alignment explanation
Indices: 19709427--19709605 Score: 277
Period size: 73 Copynumber: 2.5 Consensus size: 73
19709417 CCAAGGCATA
* *
19709427 CCAACCCACACGCCCGTGTGCTAGGCCGTGTGAGCATACTGACTTGCAATATTAAGGTACAGGGG
1 CCAAGCCACACACCCGTGTGCTAGGCCGTGTGAGCATACTGACTTGCAATATTAAGGTACAGGGG
* *
19709492 TCCCATGG
66 TCACACGG
* * * *
19709500 CCAAGCCACACTCCCGTGTGCTAGGTCATGTGAGCATACTGACTTGCAATATTAAGGTGCAGGGG
1 CCAAGCCACACACCCGTGTGCTAGGCCGTGTGAGCATACTGACTTGCAATATTAAGGTACAGGGG
19709565 TCACACGG
66 TCACACGG
*
19709573 CCAAGCCACACACTCGTGTGCTAGGCCGTGTGA
1 CCAAGCCACACACCCGTGTGCTAGGCCGTGTGA
19709606 AAATTTTTGA
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 95 1.00
ACGTcount: A:0.23, C:0.28, G:0.27, T:0.21
Consensus pattern (73 bp):
CCAAGCCACACACCCGTGTGCTAGGCCGTGTGAGCATACTGACTTGCAATATTAAGGTACAGGGG
TCACACGG
Found at i:19709939 original size:14 final size:15
Alignment explanation
Indices: 19709920--19709952 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
19709910 AACCTATATG
*
19709920 CATATT-TCTCAAAT
1 CATATTATCTCAAAC
19709934 CATATTATCTCAAAC
1 CATATTATCTCAAAC
19709949 CATA
1 CATA
19709953 CATTATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.36
Consensus pattern (15 bp):
CATATTATCTCAAAC
Found at i:19710646 original size:26 final size:25
Alignment explanation
Indices: 19710617--19710698 Score: 96
Period size: 26 Copynumber: 3.2 Consensus size: 25
19710607 ACATGTAAAT
19710617 GGGAAGCTCTTTCGAGCCATATAACA
1 GGGAAGCTCTTTCGAGCCAT-TAACA
*
19710643 GGGAAGCTCATGT-GAGCCATGTAACA
1 GGGAAGCTC-TTTCGAGCCAT-TAACA
* *
19710669 -GGAAGCTCATTCGAGCCATTAATA
1 GGGAAGCTCTTTCGAGCCATTAACA
19710693 GGGAAG
1 GGGAAG
19710699 TTCAAGCGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
24 5 0.10
25 20 0.42
26 21 0.44
27 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.21
Consensus pattern (25 bp):
GGGAAGCTCTTTCGAGCCATTAACA
Found at i:19710678 original size:25 final size:26
Alignment explanation
Indices: 19710617--19710698 Score: 107
Period size: 25 Copynumber: 3.2 Consensus size: 26
19710607 ACATGTAAAT
*
19710617 GGGAAGCTCTTTCGAGCCATATAACA
1 GGGAAGCTCATTCGAGCCATATAACA
*
19710643 GGGAAGCTCATGT-GAGCCATGTAACA
1 GGGAAGCTCAT-TCGAGCCATATAACA
*
19710669 -GGAAGCTCATTCGAGCCAT-TAATA
1 GGGAAGCTCATTCGAGCCATATAACA
19710693 GGGAAG
1 GGGAAG
19710699 TTCAAGCGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
24 5 0.10
25 22 0.44
26 22 0.44
27 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.21
Consensus pattern (26 bp):
GGGAAGCTCATTCGAGCCATATAACA
Found at i:19710708 original size:25 final size:26
Alignment explanation
Indices: 19710617--19710711 Score: 104
Period size: 25 Copynumber: 3.7 Consensus size: 26
19710607 ACATGTAAAT
* *
19710617 GGGAAGCTCTTTCGAGCCATATAACA
1 GGGAAGCTCATGCGAGCCATATAACA
* *
19710643 GGGAAGCTCATGTGAGCCATGTAACA
1 GGGAAGCTCATGCGAGCCATATAACA
* *
19710669 -GGAAGCTCATTCGAGCCAT-TAATA
1 GGGAAGCTCATGCGAGCCATATAACA
* *
19710693 GGGAAGTTCAAGCGAGCCA
1 GGGAAGCTCATGCGAGCCA
19710712 ATATTGGGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
24 4 0.07
25 32 0.55
26 22 0.38
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.20
Consensus pattern (26 bp):
GGGAAGCTCATGCGAGCCATATAACA
Found at i:19714173 original size:56 final size:57
Alignment explanation
Indices: 19714054--19714188 Score: 145
Period size: 57 Copynumber: 2.4 Consensus size: 57
19714044 AGGTGTCACT
19714054 GATGTGTCAAGTGGCATCAGTGTTAGATTTAAAAAAAATATTTTTTATTGTGCTGATA
1 GATGTGTCAAGTGGCA-CAGTGTTAGATTTAAAAAAAATATTTTTTATTGTGCTGATA
* * * * *
19714112 G-TGTGTCAAGTAGCACATTTGTTAGATTT-TAAAAAATGATTTTTT-TTGT-ATCG-TC
1 GATGTGTCAAGTGGCACA-GTGTTAGATTTAAAAAAAAT-ATTTTTTATTGTGCT-GATA
19714167 GATGTGTCAAGTGGCACCAGTG
1 GATGTGTCAAGTGGCA-CAGTG
19714189 ATCCCGCGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
55 3 0.05
56 29 0.45
57 32 0.49
58 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (57 bp):
GATGTGTCAAGTGGCACAGTGTTAGATTTAAAAAAAATATTTTTTATTGTGCTGATA
Found at i:19723755 original size:11 final size:11
Alignment explanation
Indices: 19723739--19723769 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
19723729 AAAAGTGAGG
*
19723739 ATTCCTTTAGA
1 ATTCCTCTAGA
19723750 ATTCCTCTAGA
1 ATTCCTCTAGA
19723761 ATTCCTCTA
1 ATTCCTCTA
19723770 AGGCACCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (11 bp):
ATTCCTCTAGA
Found at i:19740779 original size:38 final size:37
Alignment explanation
Indices: 19740732--19740834 Score: 163
Period size: 38 Copynumber: 2.8 Consensus size: 37
19740722 TAAAATTGTG
*
19740732 AAAATGTGGCATATAATTGATGGTTTTAGAGTAAAAAA
1 AAAAAGTGGCATATAATTGATGGTTTTAGAGT-AAAAA
19740770 AAAAAGTGGCATATAATTGATGGTTTTAGAGTAAAAA
1 AAAAAGTGGCATATAATTGATGGTTTTAGAGTAAAAA
* *
19740807 AAAAA-TGCCATATAATTGATGGTGTTAG
1 AAAAAGTGGCATATAATTGATGGTTTTAG
19740835 TGAGTAACAT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 21 0.34
37 10 0.16
38 31 0.50
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (37 bp):
AAAAAGTGGCATATAATTGATGGTTTTAGAGTAAAAA
Found at i:19741743 original size:32 final size:33
Alignment explanation
Indices: 19741688--19741753 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
19741678 TTCCTATAAA
19741688 TAGCCAAGCAAAACCCCCAGTCATTTGTTCATT
1 TAGCCAAGCAAAACCCCCAGTCATTTGTTCATT
19741721 TAGCCAAGCAAAA-CCCCAGTCATTTGTTCATT
1 TAGCCAAGCAAAACCCCCAGTCATTTGTTCATT
19741753 T
1 T
19741754 GCCCCCCTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 20 0.61
33 13 0.39
ACGTcount: A:0.30, C:0.29, G:0.12, T:0.29
Consensus pattern (33 bp):
TAGCCAAGCAAAACCCCCAGTCATTTGTTCATT
Found at i:19746520 original size:25 final size:25
Alignment explanation
Indices: 19746486--19746537 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
19746476 TGTAATTATA
19746486 TTCCACAAATTCTATGGAATCATTT
1 TTCCACAAATTCTATGGAATCATTT
19746511 TTCCACAAATTCTATGGAATCATTT
1 TTCCACAAATTCTATGGAATCATTT
19746536 TT
1 TT
19746538 TTAAGAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (25 bp):
TTCCACAAATTCTATGGAATCATTT
Found at i:19750481 original size:77 final size:77
Alignment explanation
Indices: 19750354--19750507 Score: 281
Period size: 77 Copynumber: 2.0 Consensus size: 77
19750344 TTGAGACTTG
* *
19750354 GATAATACTAAAATACAAAAGGAAAAAAGAAAATCATATTCATATTCAACTGCAACTAATTTTAA
1 GATAATACTAAAATACAAAAGGAAAAAAGAAAACCATACTCATATTCAACTGCAACTAATTTTAA
19750419 AAGCTAACCACA
66 AAGCTAACCACA
*
19750431 GATAATACTAAAATACAAAAGGAAAAAGGAAAACCATACTCATATTCAACTGCAACTAATTTTAA
1 GATAATACTAAAATACAAAAGGAAAAAAGAAAACCATACTCATATTCAACTGCAACTAATTTTAA
19750496 AAGCTAACCACA
66 AAGCTAACCACA
19750508 CATGAATTAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.22
Consensus pattern (77 bp):
GATAATACTAAAATACAAAAGGAAAAAAGAAAACCATACTCATATTCAACTGCAACTAATTTTAA
AAGCTAACCACA
Found at i:19753368 original size:24 final size:25
Alignment explanation
Indices: 19753341--19753395 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
19753331 AATATTTTTA
*
19753341 ATTTTATTAAATTTA-TCTCTAAAT
1 ATTTTATTAAACTTATTCTCTAAAT
* * * *
19753365 ATTTAATTTAACTTATTTTTTAAAT
1 ATTTTATTAAACTTATTCTCTAAAT
19753390 ATTTTA
1 ATTTTA
19753396 AATGATATAG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTTTATTAAACTTATTCTCTAAAT
Found at i:19756204 original size:20 final size:20
Alignment explanation
Indices: 19756159--19756204 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
19756149 GCCACATCAA
*
19756159 TATTCTTATCCTGAATTTTAG
1 TATT-TTATCCTGAATTTAAG
*
19756180 GATTTTATCCTGAATTTAAG
1 TATTTTATCCTGAATTTAAG
19756200 TATTT
1 TATTT
19756205 CAATTTGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (20 bp):
TATTTTATCCTGAATTTAAG
Found at i:19756337 original size:2 final size:2
Alignment explanation
Indices: 19756330--19756354 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19756320 ATCCTTTCTC
19756330 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19756355 AACCCAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19766668 original size:15 final size:15
Alignment explanation
Indices: 19766645--19766676 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19766635 CATTTCACTG
*
19766645 TTATGTCTTTTGTAT
1 TTATATCTTTTGTAT
19766660 TTATATCTTTTGTAT
1 TTATATCTTTTGTAT
19766675 TT
1 TT
19766677 TGAATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATATCTTTTGTAT
Found at i:19778472 original size:6 final size:6
Alignment explanation
Indices: 19778461--19778491 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
19778451 CTATTTTTCC
19778461 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
19778492 CTTTCTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:19778500 original size:18 final size:18
Alignment explanation
Indices: 19778454--19778500 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
19778444 CAAAACCCTA
19778454 TTTTTC-CTTTCTTTTTC
1 TTTTTCTCTTTCTTTTTC
*
19778471 TTTTTCTTTTTCTTTTTC
1 TTTTTCTCTTTCTTTTTC
19778489 TTTCTT-TCTTTC
1 TTT-TTCTCTTTC
19778501 CCTGCTCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 6 0.23
18 18 0.69
19 2 0.08
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTCTCTTTCTTTTTC
Found at i:19778610 original size:16 final size:17
Alignment explanation
Indices: 19778589--19778620 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19778579 TAACATATAT
19778589 ATTATTAT-ATTATTAA
1 ATTATTATAATTATTAA
19778605 ATTATTATAATTATTA
1 ATTATTATAATTATTA
19778621 TTTCTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTATTATAATTATTAA
Found at i:19785870 original size:136 final size:136
Alignment explanation
Indices: 19785724--19785970 Score: 424
Period size: 136 Copynumber: 1.8 Consensus size: 136
19785714 AATAAAAAAG
*
19785724 AAAAAG-AAAAAGAAAATGTAGTTTTAATAAAAATAAAAAAATATTAAAAACATAAAATAATAAA
1 AAAAAGAAAAAAGAAAAAGTAGTTTTAATAAAAAT-AAAAAATATTAAAAACATAAAATAATAAA
19785788 TAAATATTTTTAAATATCTTCATCACTGGATGGTTAGCGAGGTGGGATTGGTGATGAGATAAAAT
65 TAAATATTTTTAAATATCTTCATCACTGGATGGTTAGCGAGGTGGGATTGGTGATGAGATAAAAT
19785853 CTGCTAA
130 CTGCTAA
* * *
19785860 AAAAATAAAAAAGAAAAAGTAGTTTTACTAAAAATTAAAAATATTAAAAACATAAAATAATAAAT
1 AAAAAGAAAAAAGAAAAAGTAGTTTTAATAAAAATAAAAAATATTAAAAACATAAAATAATAAAT
* *
19785925 AAATATTTTTAAATATCTTCATCGCTGGATGGTTTGCGAGGTGGGA
66 AAATATTTTTAAATATCTTCATCACTGGATGGTTAGCGAGGTGGGA
19785971 CTGGCATTGA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
136 78 0.75
137 26 0.25
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (136 bp):
AAAAAGAAAAAAGAAAAAGTAGTTTTAATAAAAATAAAAAATATTAAAAACATAAAATAATAAAT
AAATATTTTTAAATATCTTCATCACTGGATGGTTAGCGAGGTGGGATTGGTGATGAGATAAAATC
TGCTAA
Found at i:19793748 original size:31 final size:31
Alignment explanation
Indices: 19793713--19793775 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
19793703 TGTATTATTT
19793713 CTTAGGTATTGTCTTAAGTCAATCGATTTTC
1 CTTAGGTATTGTCTTAAGTCAATCGATTTTC
19793744 CTTAGGTATTGTCTTAAGTCAATCGATTTTC
1 CTTAGGTATTGTCTTAAGTCAATCGATTTTC
19793775 C
1 C
19793776 CAAAAAGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (31 bp):
CTTAGGTATTGTCTTAAGTCAATCGATTTTC
Found at i:19799334 original size:25 final size:25
Alignment explanation
Indices: 19799265--19799337 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
19799255 CATAGCTCTT
* * * **
19799265 ATGAGCTTCTCAATACTCAGCTTGC
1 ATGAGCTTCCCATTACTTAGCTCAC
*
19799290 ATGAGCTTCCCATTATTTAGCTCAC
1 ATGAGCTTCCCATTACTTAGCTCAC
**
19799315 ATGAGCTTCCTGTTACTTAGCTC
1 ATGAGCTTCCCATTACTTAGCTC
19799338 GGAGGAGCTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (25 bp):
ATGAGCTTCCCATTACTTAGCTCAC
Found at i:19805573 original size:27 final size:26
Alignment explanation
Indices: 19805529--19805580 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
19805519 CTCGCTGCAA
*
19805529 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
19805556 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
19805581 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:19805648 original size:26 final size:27
Alignment explanation
Indices: 19805619--19805678 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
19805609 CCACATATAT
*
19805619 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
19805645 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
19805672 ATATCTG
1 ATATCTG
19805679 ACAGCTTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:19809187 original size:17 final size:18
Alignment explanation
Indices: 19809167--19809200 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19809157 AAGTGAATTG
19809167 AAATTGC-GAAATTAAAT
1 AAATTGCTGAAATTAAAT
19809184 AAATTGCTGAAATTAAA
1 AAATTGCTGAAATTAAA
19809201 ATGAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (18 bp):
AAATTGCTGAAATTAAAT
Found at i:19809937 original size:10 final size:10
Alignment explanation
Indices: 19809918--19809977 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
19809908 TGAAATTCTA
19809918 AAAGATAAAT
1 AAAGATAAAT
19809928 ACAA-ATAAAT
1 A-AAGATAAAT
*
19809938 AAAGATAATT
1 AAAGATAAAT
19809948 AAAGATAAAT
1 AAAGATAAAT
19809958 AAAGATAAAT
1 AAAGATAAAT
19809968 GAAA-ATAAAT
1 -AAAGATAAAT
19809978 CCTAAAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:19811600 original size:17 final size:16
Alignment explanation
Indices: 19811578--19811609 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
19811568 TAATAAAATA
19811578 AAAAGAAAAAAGAAAAG
1 AAAAG-AAAAAGAAAAG
19811595 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
19811610 ATTAAGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAG
Found at i:19817255 original size:17 final size:19
Alignment explanation
Indices: 19817230--19817268 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
19817220 ATTTAAAGTG
19817230 AAATGAAATTGCA-AAATT
1 AAATGAAATTGCAGAAATT
*
19817248 AAAT-AAATTGTAGAAATT
1 AAATGAAATTGCAGAAATT
19817266 AAA
1 AAA
19817269 ATGAGGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (19 bp):
AAATGAAATTGCAGAAATT
Found at i:19818004 original size:10 final size:10
Alignment explanation
Indices: 19817985--19818044 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
19817975 TGAAATTCTA
19817985 AAAGATAAAT
1 AAAGATAAAT
19817995 ACAA-ATAAAT
1 A-AAGATAAAT
*
19818005 AAAGATAATT
1 AAAGATAAAT
19818015 AAAGATAAAT
1 AAAGATAAAT
19818025 AAAGATAAAT
1 AAAGATAAAT
19818035 GAAA-ATAAAT
1 -AAAGATAAAT
19818045 CCTAAAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:19818928 original size:9 final size:9
Alignment explanation
Indices: 19818899--19818928 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
19818889 TGAATTTTAC
19818899 AATTTGAAT
1 AATTTGAAT
*
19818908 AACTTGAAT
1 AATTTGAAT
19818917 AATTTGAAT
1 AATTTGAAT
19818926 AAT
1 AAT
19818929 AGATTGATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (9 bp):
AATTTGAAT
Found at i:19826362 original size:15 final size:16
Alignment explanation
Indices: 19826335--19826364 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19826325 TCATAAAGGG
19826335 TTAAAAATAATTTTTT
1 TTAAAAATAATTTTTT
19826351 TTAAAAAT-ATTTTT
1 TTAAAAATAATTTTT
19826365 AAAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAAAATAATTTTTT
Found at i:19830853 original size:26 final size:27
Alignment explanation
Indices: 19830823--19830874 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
19830813 TACACATTTC
*
19830823 ATCATAATTCATATCAT-TACTCAAAA
1 ATCATAATTCATATCATGTAATCAAAA
* *
19830849 ATCATAGTTCATTTCATGTAATCAAA
1 ATCATAATTCATATCATGTAATCAAA
19830875 TACCCTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (27 bp):
ATCATAATTCATATCATGTAATCAAAA
Found at i:19831269 original size:20 final size:20
Alignment explanation
Indices: 19831237--19831310 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
19831227 CATCATAGAT
19831237 GTGTAAA-AGAGGCACCAAA
1 GTGTAAATAGAGGCACCAAA
*
19831256 GTGTAGATAGAGGCA-CAAA
1 GTGTAAATAGAGGCACCAAA
* *
19831275 -TGTACAATCAAAGGCACCATA
1 GTGTA-AAT-AGAGGCACCAAA
*
19831296 GTGCAAATAGAGGCA
1 GTGTAAATAGAGGCA
19831311 GAGGCACCGA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 4 0.09
19 12 0.27
20 19 0.43
21 6 0.14
22 3 0.07
ACGTcount: A:0.43, C:0.16, G:0.26, T:0.15
Consensus pattern (20 bp):
GTGTAAATAGAGGCACCAAA
Found at i:19834024 original size:31 final size:31
Alignment explanation
Indices: 19833986--19834046 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
19833976 AACCATCACA
19833986 TGTTCATTTAATATTTAACATCTTTATTTCT
1 TGTTCATTTAATATTTAACATCTTTATTTCT
19834017 TGTTCATTTAATATTTAACATCTTTATTTC
1 TGTTCATTTAATATTTAACATCTTTATTTC
19834047 AAGTATTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.57
Consensus pattern (31 bp):
TGTTCATTTAATATTTAACATCTTTATTTCT
Found at i:19834161 original size:13 final size:13
Alignment explanation
Indices: 19834083--19834164 Score: 51
Period size: 13 Copynumber: 6.2 Consensus size: 13
19834073 CACATGTTTA
* *
19834083 TCATATACATATT
1 TCATATATACATT
* *
19834096 TCATATAAACACT
1 TCATATATACATT
*
19834109 TCATATA-ATCGTT
1 TCATATATA-CATT
19834122 TCATATAT-CTATT
1 TCATATATAC-ATT
* *
19834135 AACATATAAACATT
1 -TCATATATACATT
*
19834149 TCATATATCCATT
1 TCATATATACATT
19834162 TCA
1 TCA
19834165 GATTACCATT
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
12 2 0.04
13 41 0.77
14 9 0.17
15 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.01, T:0.41
Consensus pattern (13 bp):
TCATATATACATT
Found at i:19836978 original size:26 final size:26
Alignment explanation
Indices: 19836942--19836999 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
19836932 ACATCTCGTA
*
19836942 TGAGCAGGCCCATTTCACAACTCATG
1 TGAGCAAGCCCATTTCACAACTCATG
***
19836968 TGAGCAAGCCCATTTCATTGCTCATG
1 TGAGCAAGCCCATTTCACAACTCATG
19836994 TGAGCA
1 TGAGCA
19837000 TTATAGAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (26 bp):
TGAGCAAGCCCATTTCACAACTCATG
Found at i:19839266 original size:37 final size:37
Alignment explanation
Indices: 19839225--19839400 Score: 298
Period size: 37 Copynumber: 4.8 Consensus size: 37
19839215 TTTGAGTACT
19839225 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
19839262 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
19839299 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
19839336 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
19839373 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
19839401 TAGCTTCAGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:19839472 original size:45 final size:46
Alignment explanation
Indices: 19839363--19839486 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
19839353 GTGATAAGTG
* *
19839363 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
19839409 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
19839454 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
19839487 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:19846965 original size:37 final size:37
Alignment explanation
Indices: 19846924--19847099 Score: 298
Period size: 37 Copynumber: 4.8 Consensus size: 37
19846914 TTTGAGTACT
19846924 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
19846961 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
19846998 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
19847035 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
19847072 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
19847100 TAGCTTCAGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:19847171 original size:45 final size:46
Alignment explanation
Indices: 19847062--19847185 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
19847052 GTGATAAGTG
* *
19847062 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
19847108 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
19847153 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
19847186 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:19850373 original size:20 final size:21
Alignment explanation
Indices: 19850336--19850379 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19850326 TAAAAACTTG
*
19850336 AAAAGAAGAAAAAGAAATTCA
1 AAAAAAAGAAAAAGAAATTCA
*
19850357 AAAAAAAGAAAGA-AAATTCA
1 AAAAAAAGAAAAAGAAATTCA
19850377 AAA
1 AAA
19850380 TAATCTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.75, C:0.05, G:0.11, T:0.09
Consensus pattern (21 bp):
AAAAAAAGAAAAAGAAATTCA
Found at i:19850955 original size:17 final size:17
Alignment explanation
Indices: 19850929--19850971 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
19850919 AAATGATTTC
*
19850929 ATTTAGTTTTATGTTTT
1 ATTTATTTTTATGTTTT
19850946 ATTTATTTTTATGTTTT
1 ATTTATTTTTATGTTTT
19850963 ATTTATTTT
1 ATTTATTTT
19850972 ATTATGCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (17 bp):
ATTTATTTTTATGTTTT
Found at i:19854368 original size:27 final size:27
Alignment explanation
Indices: 19854338--19854392 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
19854328 GGAAGTACTA
*
19854338 TACTAGTGACTATGTCACATTCACTGT
1 TACTAGTGACTATGCCACATTCACTGT
* * *
19854365 TACTAGTGGCTTTGCCACATTTACTGT
1 TACTAGTGACTATGCCACATTCACTGT
19854392 T
1 T
19854393 TCTGGCAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (27 bp):
TACTAGTGACTATGCCACATTCACTGT
Found at i:19855560 original size:20 final size:20
Alignment explanation
Indices: 19855478--19855561 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
19855468 CTTCAGTAAT
* *
19855478 AACAGTAATTTATCCATATC
1 AACAGTAATTCATCCATTTC
*
19855498 AATAGTAATTCATCC-TTATC
1 AACAGTAATTCATCCATT-TC
* * *
19855518 GATAGTAATTCATTCATTTC
1 AACAGTAATTCATCCATTTC
19855538 AACAGTAATTCATCCATTTC
1 AACAGTAATTCATCCATTTC
19855558 AACA
1 AACA
19855562 TAGCTCATTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.02
20 51 0.94
21 2 0.04
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (20 bp):
AACAGTAATTCATCCATTTC
Found at i:19855761 original size:23 final size:23
Alignment explanation
Indices: 19855729--19855840 Score: 106
Period size: 23 Copynumber: 4.9 Consensus size: 23
19855719 TCTGATAAAT
19855729 AGTAAGCTCTATTGAGCTGAAAC
1 AGTAAGCTCTATTGAGCTGAAAC
*
19855752 -GATAAGCTCTATCGAGCTG-AAC
1 AG-TAAGCTCTATTGAGCTGAAAC
* *
19855774 AGTAAGCTC-ATACGAGCTGAATC
1 AGTAAGCTCTAT-TGAGCTGAAAC
* * *
19855797 GGTAAGCTCCAATGAGCTGAAAAC
1 AGTAAGCTCTATTGAGCTG-AAAC
19855821 AGTAAGCTCTTATT-AGCTGA
1 AGTAAGCTC-TATTGAGCTGA
19855841 TATATCGGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.03
22 18 0.25
23 34 0.47
24 17 0.23
25 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (23 bp):
AGTAAGCTCTATTGAGCTGAAAC
Found at i:19855791 original size:45 final size:46
Alignment explanation
Indices: 19855729--19855830 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 46
19855719 TCTGATAAAT
* *
19855729 AGTAAGCTCTATTGAGCTGAAACGATAAGCT-CTATCGAGCTG-AAC
1 AGTAAGCTCTATCGAGCTGAAACGATAAGCTCCAAT-GAGCTGAAAC
* *
19855774 AGTAAGCTC-ATACGAGCTGAATCGGTAAGCTCCAATGAGCTGAAAAC
1 AGTAAGCTCTAT-CGAGCTGAAACGATAAGCTCCAATGAGCTG-AAAC
19855821 AGTAAGCTCT
1 AGTAAGCTCT
19855831 TATTAGCTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
44 2 0.04
45 31 0.65
46 3 0.06
47 12 0.25
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23
Consensus pattern (46 bp):
AGTAAGCTCTATCGAGCTGAAACGATAAGCTCCAATGAGCTGAAAC
Found at i:19857208 original size:27 final size:28
Alignment explanation
Indices: 19857178--19857232 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
19857168 TTTATAATTT
*
19857178 CACAATTG-ATTGAGATTCGATTGATGA
1 CACAATTGAATTGAGATTCGAGTGATGA
19857205 CACAATTGAATTGAGATTCGAGTGATGA
1 CACAATTGAATTGAGATTCGAGTGATGA
19857233 ATACTAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (28 bp):
CACAATTGAATTGAGATTCGAGTGATGA
Found at i:19863741 original size:16 final size:16
Alignment explanation
Indices: 19863711--19863740 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19863701 AAGAAAACAA
19863711 AAAGAAAGAATAAAAG
1 AAAGAAAGAATAAAAG
19863727 AAAGAAA-AATAAAA
1 AAAGAAAGAATAAAA
19863741 ACAAAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (16 bp):
AAAGAAAGAATAAAAG
Found at i:19875605 original size:262 final size:262
Alignment explanation
Indices: 19875158--19875645 Score: 782
Period size: 262 Copynumber: 1.9 Consensus size: 262
19875148 TGGGAGAGTA
* * * *
19875158 AAAGAAAGAAAAACAAAAAGAAACTGATAAATGGTAAAATAGAAACGTGGGAGAATAAGGGAGAG
1 AAAGAAAAAAAAAAAAAAAGAAACTGATAAATGGAAAAATAGAAACATGGGAGAATAAGGGAGAG
* *
19875223 GAAAAAGTGGAATATTTTACCAAATATTTTAAAATTTAAAATAATAAAACTATTTTTAATAAATC
66 GAAAAAGTGGAATAATTTACCAAATATTTTAAAATTTAAAATAATAAAAATATTTTTAATAAATC
** * *
19875288 ACTAAATCCTCTCCAAACAACCTTTAACCACTTAACCATTTATCCAAGTAATTGGATCAAACTCA
131 ACTAAATCCTCTCCAAACAACCCCTAACCACTCAACCATTTATCCAAGCAATTGGATCAAACTCA
19875353 ATTTCAAACAATG-AAACAATACAAACGTGGTAATTTAGAAAAAATAAACCGGTAAGAGAGTAAA
196 ATTTCAAACAATGAAAACAATACAAACGTGGTAATTTAGAAAAAATAAACCGGTAAGAGAGTAAA
19875417 CG
261 CG
*
19875419 AAAGAAAAACAAAAAAAAAAGAAACTGATAAAT-GAAAAATTAGAAACATGGGAGAGTAAGGGAG
1 AAAGAAAAA-AAAAAAAAAAGAAACTGATAAATGGAAAAA-TAGAAACATGGGAGAATAAGGGAG
*
19875483 AGGAAAAAGTGGAATAATTTACCAAATATTTTAAATTTTAAAATAATAAAAATATTTTTAATAAA
64 AGGAAAAAGTGGAATAATTTACCAAATATTTTAAAATTTAAAATAATAAAAATATTTTTAATAAA
* * *
19875548 TCACTAAATCCTCTCCAAACAACCCCTGACCACTCAACCATTTATTCAAGCAATTGGATCAAATT
129 TCACTAAATCCTCTCCAAACAACCCCTAACCACTCAACCATTTATCCAAGCAATTGGATCAAACT
* * *
19875613 CAATTTCAAACATTGAAAACAGTACAAGCGTGG
194 CAATTTCAAACAATGAAAACAATACAAACGTGG
19875646 AAAATTAGCA
Statistics
Matches: 206, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
261 13 0.06
262 178 0.86
263 15 0.07
ACGTcount: A:0.50, C:0.14, G:0.13, T:0.24
Consensus pattern (262 bp):
AAAGAAAAAAAAAAAAAAAGAAACTGATAAATGGAAAAATAGAAACATGGGAGAATAAGGGAGAG
GAAAAAGTGGAATAATTTACCAAATATTTTAAAATTTAAAATAATAAAAATATTTTTAATAAATC
ACTAAATCCTCTCCAAACAACCCCTAACCACTCAACCATTTATCCAAGCAATTGGATCAAACTCA
ATTTCAAACAATGAAAACAATACAAACGTGGTAATTTAGAAAAAATAAACCGGTAAGAGAGTAAA
CG
Found at i:19877266 original size:17 final size:19
Alignment explanation
Indices: 19877229--19877268 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
19877219 CATTTTAGAG
19877229 TTAAAATAAAATTACTTTT
1 TTAAAATAAAATTACTTTT
* *
19877248 TTAAAA-AATATTATTTTT
1 TTAAAATAAAATTACTTTT
19877266 TTA
1 TTA
19877269 CTTTGCTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAAATAAAATTACTTTT
Found at i:19878115 original size:6 final size:6
Alignment explanation
Indices: 19878093--19878131 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
19878083 CACTGATTCT
* * *
19878093 GATTTT GATTTT GATTTC AATTTC GATTTC GATTTC GAT
1 GATTTC GATTTC GATTTC GATTTC GATTTC GATTTC GAT
19878132 CTCAATCTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (6 bp):
GATTTC
Found at i:19878572 original size:62 final size:64
Alignment explanation
Indices: 19878320--19878645 Score: 426
Period size: 64 Copynumber: 5.2 Consensus size: 64
19878310 GATTTTGATG
* * * *
19878320 TGTTTGTATCTGCCATTGTATGAATGTCATTATCAAACTAATATTTATTGTGTGTATCTGCCAT
1 TGTTTGTATCTGCCATTGTATGAATGACATTATCAAACTGATGTTTATTGTGTATATCTGCCAT
** * *
19878384 TGTTTGTATCTATCATTGTATGAATGCCATTATCAAACTGATATTTATTGTGTATATCTGCCAT
1 TGTTTGTATCTGCCATTGTATGAATGACATTATCAAACTGATGTTTATTGTGTATATCTGCCAT
* *
19878448 TGTTTGTATCTGCCATTGTATGAATGTCATTATCAAATTGATGTTTATTGTGTATATCTGCCAT
1 TGTTTGTATCTGCCATTGTATGAATGACATTATCAAACTGATGTTTATTGTGTATATCTGCCAT
** * * *
19878512 TGTTTGTATCTGCCATTAAAT-TAT-ACATTATTAAACTGATGTTTATTGTGTATATTTGCCAT
1 TGTTTGTATCTGCCATTGTATGAATGACATTATCAAACTGATGTTTATTGTGTATATCTGCCAT
* ** * * **
19878574 TGTTTGTATCTTCCATTAAAT-TAT-ACATTATTAAACTGATGTTTATTGTGTATATCTATCAT
1 TGTTTGTATCTGCCATTGTATGAATGACATTATCAAACTGATGTTTATTGTGTATATCTGCCAT
19878636 TGTTTGTATC
1 TGTTTGTATC
19878646 CAGGCTCCTA
Statistics
Matches: 241, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
62 102 0.42
63 2 0.01
64 137 0.57
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.48
Consensus pattern (64 bp):
TGTTTGTATCTGCCATTGTATGAATGACATTATCAAACTGATGTTTATTGTGTATATCTGCCAT
Found at i:19878950 original size:15 final size:15
Alignment explanation
Indices: 19878930--19878974 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
19878920 TGAAGAAAAC
19878930 GTGTCTGGTAGTGAT
1 GTGTCTGGTAGTGAT
*
19878945 GTGTCTGGTAGTGAA
1 GTGTCTGGTAGTGAT
19878960 GTGTCTGGTAGTGAT
1 GTGTCTGGTAGTGAT
19878975 AGTGATGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.16, C:0.07, G:0.40, T:0.38
Consensus pattern (15 bp):
GTGTCTGGTAGTGAT
Found at i:19880667 original size:43 final size:43
Alignment explanation
Indices: 19880618--19880799 Score: 274
Period size: 43 Copynumber: 4.2 Consensus size: 43
19880608 TTGCTGATCA
* *
19880618 CATGCAATGATTGTTGGAAAGCTATTGACTTTTTTTTAATATG
1 CATGCAATGATTATTGGAAAGCTATTGACTATTTTTTAATATG
* * *
19880661 TATGCAATGATTATTGGAAAGTTGTTGACTATTTTTTAATATG
1 CATGCAATGATTATTGGAAAGCTATTGACTATTTTTTAATATG
* *
19880704 CATGCAATGATTGTTGGAAAGCTATTGACTTTTTTTTAATATG
1 CATGCAATGATTATTGGAAAGCTATTGACTATTTTTTAATATG
* * *
19880747 TATGCAATGATTATTGGAAAGTTGTTGACTATTTTTTAATATG
1 CATGCAATGATTATTGGAAAGCTATTGACTATTTTTTAATATG
19880790 CATGCAATGA
1 CATGCAATGA
19880800 GTTTTTTTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 123 1.00
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.44
Consensus pattern (43 bp):
CATGCAATGATTATTGGAAAGCTATTGACTATTTTTTAATATG
Found at i:19880745 original size:86 final size:86
Alignment explanation
Indices: 19880618--19880799 Score: 364
Period size: 86 Copynumber: 2.1 Consensus size: 86
19880608 TTGCTGATCA
19880618 CATGCAATGATTGTTGGAAAGCTATTGACTTTTTTTTAATATGTATGCAATGATTATTGGAAAGT
1 CATGCAATGATTGTTGGAAAGCTATTGACTTTTTTTTAATATGTATGCAATGATTATTGGAAAGT
19880683 TGTTGACTATTTTTTAATATG
66 TGTTGACTATTTTTTAATATG
19880704 CATGCAATGATTGTTGGAAAGCTATTGACTTTTTTTTAATATGTATGCAATGATTATTGGAAAGT
1 CATGCAATGATTGTTGGAAAGCTATTGACTTTTTTTTAATATGTATGCAATGATTATTGGAAAGT
19880769 TGTTGACTATTTTTTAATATG
66 TGTTGACTATTTTTTAATATG
19880790 CATGCAATGA
1 CATGCAATGA
19880800 GTTTTTTTTA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 96 1.00
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.44
Consensus pattern (86 bp):
CATGCAATGATTGTTGGAAAGCTATTGACTTTTTTTTAATATGTATGCAATGATTATTGGAAAGT
TGTTGACTATTTTTTAATATG
Found at i:19880834 original size:27 final size:26
Alignment explanation
Indices: 19880778--19880837 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
19880768 TTGTTGACTA
*
19880778 TTTTTTAATATGCATGCAATGAGTTT
1 TTTTTTAATATGCATGCAATGAGTTC
* *
19880804 TTTTTATAATATGCATGTAGTGA-TTGC
1 TTTTT-TAATATGCATGCAATGAGTT-C
19880831 TTTTTTA
1 TTTTTTA
19880838 GGGGGGTGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 9 0.31
27 20 0.69
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.53
Consensus pattern (26 bp):
TTTTTTAATATGCATGCAATGAGTTC
Found at i:19881484 original size:21 final size:21
Alignment explanation
Indices: 19881460--19881508 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
19881450 TGTCCGAACC
*
19881460 CAGCAAGAGACTACCCCAAGT
1 CAGCAAGAGACTACCCCAACT
**
19881481 CAGCAAGAGGGTACCCCAACT
1 CAGCAAGAGACTACCCCAACT
*
19881502 CAACAAG
1 CAGCAAG
19881509 GTGCCCCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.33, G:0.20, T:0.08
Consensus pattern (21 bp):
CAGCAAGAGACTACCCCAACT
Found at i:19882287 original size:3 final size:3
Alignment explanation
Indices: 19882272--19882322 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
19882262 CCATTTTTCC
* *
19882272 TCT TCT CCT TCT TCT TCT TC- TCT TCCT GCT TC- TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT
19882316 TCT TCT T
1 TCT TCT T
19882323 TTTTTCCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.85
4 2 0.05
ACGTcount: A:0.00, C:0.37, G:0.02, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:19882297 original size:26 final size:26
Alignment explanation
Indices: 19882268--19882318 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
19882258 ATATCCATTT
19882268 TTCCT-CTTCTCCTTCTTCTTCTTCTC
1 TTCCTGCTTCT-CTTCTTCTTCTTCTC
19882294 TTCCTGCTTCTCTTCTTCTTCTTCT
1 TTCCTGCTTCTCTTCTTCTTCTTCT
19882319 TCTTTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.00, C:0.39, G:0.02, T:0.59
Consensus pattern (26 bp):
TTCCTGCTTCTCTTCTTCTTCTTCTC
Found at i:19883893 original size:7 final size:7
Alignment explanation
Indices: 19883883--19883915 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
19883873 TAGAGTGTTG
19883883 TAAAAAA
1 TAAAAAA
19883890 TAAAAAA
1 TAAAAAA
19883897 TAAAAAA
1 TAAAAAA
19883904 TATAAAAA
1 TA-AAAAA
19883912 TAAA
1 TAAA
19883916 TGTGACACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAAAAA
Found at i:19884289 original size:13 final size:12
Alignment explanation
Indices: 19884267--19884311 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 12
19884257 TCGTTATATA
*
19884267 AAAAAGTAAAAT
1 AAAAATTAAAAT
19884279 ACAAAATTAAAACT
1 A-AAAATTAAAA-T
19884293 AAAAATCTAAAAT
1 AAAAAT-TAAAAT
19884306 AAAAAT
1 AAAAAT
19884312 ATTAATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 1 0.03
13 21 0.72
14 7 0.24
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (12 bp):
AAAAATTAAAAT
Found at i:19885253 original size:25 final size:26
Alignment explanation
Indices: 19885224--19885272 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
19885214 TAATTATAAT
19885224 TTAATTAA-TATTATATTT-AATAAGA
1 TTAATTAATTATTAT-TTTGAATAAGA
19885249 TTAATTAATTATTATTTTGAATAA
1 TTAATTAATTATTATTTTGAATAA
19885273 TGTTACTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
TTAATTAATTATTATTTTGAATAAGA
Found at i:19895344 original size:6 final size:6
Alignment explanation
Indices: 19895333--19895368 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
19895323 ATTATAGTCA
19895333 CCCTCC CCCTCC CCCTCC CCCTCC CCCTCC CCCTCC
1 CCCTCC CCCTCC CCCTCC CCCTCC CCCTCC CCCTCC
19895369 TACTCTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.83, G:0.00, T:0.17
Consensus pattern (6 bp):
CCCTCC
Found at i:19910576 original size:38 final size:38
Alignment explanation
Indices: 19910525--19910609 Score: 127
Period size: 38 Copynumber: 2.2 Consensus size: 38
19910515 GTAAAAGAAG
*
19910525 AAATCCGGACTTAAAGTCCGCAGGCTATA-TGCTGGAAT
1 AAATCCGGACTTAAAGTCCGCAGGCTA-AGTGCTGGAAA
*
19910563 AAATCCGGACTTAAAGTCTGCAGGCTAAGTGCTGGAAA
1 AAATCCGGACTTAAAGTCCGCAGGCTAAGTGCTGGAAA
19910601 AATATCCGG
1 AA-ATCCGG
19910610 GTTAAGGACC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
37 1 0.02
38 36 0.84
39 6 0.14
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (38 bp):
AAATCCGGACTTAAAGTCCGCAGGCTAAGTGCTGGAAA
Found at i:19921276 original size:18 final size:18
Alignment explanation
Indices: 19921253--19921296 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
19921243 AGACCGAGTT
19921253 TGCTTAAGGATAAGCAAA
1 TGCTTAAGGATAAGCAAA
19921271 TGCTTAAGGATAAGCAAA
1 TGCTTAAGGATAAGCAAA
19921289 TGCTTAAG
1 TGCTTAAG
19921297 TGTGGGGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (18 bp):
TGCTTAAGGATAAGCAAA
Found at i:19921499 original size:282 final size:282
Alignment explanation
Indices: 19920989--19921526 Score: 959
Period size: 282 Copynumber: 1.9 Consensus size: 282
19920979 TTGAGGATTT
*
19920989 TGCTTGAGGATAAGCAAACGCTTAAGTGTGGGGCTATTTGATAAGTCGTAATTTATACATATTTT
1 TGCTTAAGGATAAGCAAACGCTTAAGTGTGGGGCTATTTGATAAGTCGTAATTTATACATATTTT
*
19921054 TACCCTAAGCTTAGCACATTTTTGGATGATTTATCCTTAGATTTGGTGAATTCGATGTTCCTAAT
66 TACCCCAAGCTTAGCACATTTTTGGATGATTTATCCTTAGATTTGGTGAATTCGATGTTCCTAAT
* *
19921119 CCTTTAATTTCATGTTTTATACTTAGATGAGCATAGGAGAGTAAAAAGAGCGAGAAACAGGCCGA
131 CCTTTAATTTCATGTTTTATACTTAGATGAGCATAAGAGAGTAAAAAGAGCGAGAAACAAGCCGA
**
19921184 AAATGGAGAAAATGGGCCAACGTGGGAAATCAACACTGCCTGGACTTCCTCAAACAGGTAGACCG
196 AAACAGAGAAAATGGGCCAACGTGGGAAATCAACACTGCCTGGACTTCCTCAAACAGGTAGACCG
19921249 AGTTTGCTTAAGGATAAGCAAA
261 AGTTTGCTTAAGGATAAGCAAA
* *
19921271 TGCTTAAGGATAAGCAAATGCTTAAGTGTGGGGGTATTTGATAAGTCGTAATTTATACATATTTT
1 TGCTTAAGGATAAGCAAACGCTTAAGTGTGGGGCTATTTGATAAGTCGTAATTTATACATATTTT
* *
19921336 TACCCCATGCTTAGCACATTTTTGGATGATTTATCTTTAGATTTGGTGAATTCGATGTTCCTAAT
66 TACCCCAAGCTTAGCACATTTTTGGATGATTTATCCTTAGATTTGGTGAATTCGATGTTCCTAAT
*
19921401 CCTTTAATTTCATGTTTTATACTTAGATGAGCATAAGAGAGTAAAAAGAGCGAGAAATAAGCCGA
131 CCTTTAATTTCATGTTTTATACTTAGATGAGCATAAGAGAGTAAAAAGAGCGAGAAACAAGCCGA
* *
19921466 AAACAGAGAAAATGGGCCAACGTGGGAAATCAACACTGCCTTGACTTCCTCAAATAGGTAG
196 AAACAGAGAAAATGGGCCAACGTGGGAAATCAACACTGCCTGGACTTCCTCAAACAGGTAG
19921527 GCCACACTAT
Statistics
Matches: 243, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
282 243 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (282 bp):
TGCTTAAGGATAAGCAAACGCTTAAGTGTGGGGCTATTTGATAAGTCGTAATTTATACATATTTT
TACCCCAAGCTTAGCACATTTTTGGATGATTTATCCTTAGATTTGGTGAATTCGATGTTCCTAAT
CCTTTAATTTCATGTTTTATACTTAGATGAGCATAAGAGAGTAAAAAGAGCGAGAAACAAGCCGA
AAACAGAGAAAATGGGCCAACGTGGGAAATCAACACTGCCTGGACTTCCTCAAACAGGTAGACCG
AGTTTGCTTAAGGATAAGCAAA
Found at i:19922766 original size:48 final size:48
Alignment explanation
Indices: 19922714--19922835 Score: 145
Period size: 48 Copynumber: 2.5 Consensus size: 48
19922704 AATGCCGATA
* * ** *
19922714 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACATTGTTAATG
1 CCATGTCCCAGACATGGTCTTACACTGACTCTCATAACATGGCCAACG
* * * * *
19922762 CCATGTTCCAAACATGGTCTTACACTGACTCTCATATCGTGGCCGACG
1 CCATGTCCCAGACATGGTCTTACACTGACTCTCATAACATGGCCAACG
*
19922810 CCATGTCCTAGACATGGTCTTACACT
1 CCATGTCCCAGACATGGTCTTACACT
19922836 AGCACACATA
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 61 1.00
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (48 bp):
CCATGTCCCAGACATGGTCTTACACTGACTCTCATAACATGGCCAACG
Found at i:19930326 original size:18 final size:18
Alignment explanation
Indices: 19930303--19930346 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
19930293 AGACCGAGTT
19930303 TGCTTAAGGATAAGCAAA
1 TGCTTAAGGATAAGCAAA
19930321 TGCTTAAGGATAAGCAAA
1 TGCTTAAGGATAAGCAAA
19930339 TGCTTAAG
1 TGCTTAAG
19930347 TGTGGGGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (18 bp):
TGCTTAAGGATAAGCAAA
Found at i:19930549 original size:282 final size:282
Alignment explanation
Indices: 19930039--19930576 Score: 959
Period size: 282 Copynumber: 1.9 Consensus size: 282
19930029 TTGAGGATTT
*
19930039 TGCTTGAGGATAAGCAAACGCTTAAGTGTGGGGCTATTTGATAAGTCGTAATTTATACATATTTT
1 TGCTTAAGGATAAGCAAACGCTTAAGTGTGGGGCTATTTGATAAGTCGTAATTTATACATATTTT
*
19930104 TACCCTAAGCTTAGCACATTTTTGGATGATTTATCCTTAGATTTGGTGAATTCGATGTTCCTAAT
66 TACCCCAAGCTTAGCACATTTTTGGATGATTTATCCTTAGATTTGGTGAATTCGATGTTCCTAAT
* *
19930169 CCTTTAATTTCATGTTTTATACTTAGATGAGCATAGGAGAGTAAAAAGAGCGAGAAACAGGCCGA
131 CCTTTAATTTCATGTTTTATACTTAGATGAGCATAAGAGAGTAAAAAGAGCGAGAAACAAGCCGA
**
19930234 AAATGGAGAAAATGGGCCAACGTGGGAAATCAACACTGCCTGGACTTCCTCAAACAGGTAGACCG
196 AAACAGAGAAAATGGGCCAACGTGGGAAATCAACACTGCCTGGACTTCCTCAAACAGGTAGACCG
19930299 AGTTTGCTTAAGGATAAGCAAA
261 AGTTTGCTTAAGGATAAGCAAA
* *
19930321 TGCTTAAGGATAAGCAAATGCTTAAGTGTGGGGGTATTTGATAAGTCGTAATTTATACATATTTT
1 TGCTTAAGGATAAGCAAACGCTTAAGTGTGGGGCTATTTGATAAGTCGTAATTTATACATATTTT
* *
19930386 TACCCCATGCTTAGCACATTTTTGGATGATTTATCTTTAGATTTGGTGAATTCGATGTTCCTAAT
66 TACCCCAAGCTTAGCACATTTTTGGATGATTTATCCTTAGATTTGGTGAATTCGATGTTCCTAAT
*
19930451 CCTTTAATTTCATGTTTTATACTTAGATGAGCATAAGAGAGTAAAAAGAGCGAGAAATAAGCCGA
131 CCTTTAATTTCATGTTTTATACTTAGATGAGCATAAGAGAGTAAAAAGAGCGAGAAACAAGCCGA
* *
19930516 AAACAGAGAAAATGGGCCAACGTGGGAAATCAACACTGCCTTGACTTCCTCAAATAGGTAG
196 AAACAGAGAAAATGGGCCAACGTGGGAAATCAACACTGCCTGGACTTCCTCAAACAGGTAG
19930577 GCCACACTAT
Statistics
Matches: 243, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
282 243 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (282 bp):
TGCTTAAGGATAAGCAAACGCTTAAGTGTGGGGCTATTTGATAAGTCGTAATTTATACATATTTT
TACCCCAAGCTTAGCACATTTTTGGATGATTTATCCTTAGATTTGGTGAATTCGATGTTCCTAAT
CCTTTAATTTCATGTTTTATACTTAGATGAGCATAAGAGAGTAAAAAGAGCGAGAAACAAGCCGA
AAACAGAGAAAATGGGCCAACGTGGGAAATCAACACTGCCTGGACTTCCTCAAACAGGTAGACCG
AGTTTGCTTAAGGATAAGCAAA
Found at i:19931816 original size:48 final size:48
Alignment explanation
Indices: 19931764--19931885 Score: 145
Period size: 48 Copynumber: 2.5 Consensus size: 48
19931754 AATGCCGATA
* * ** *
19931764 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACATTGTTAATG
1 CCATGTCCCAGACATGGTCTTACACTGACTCTCATAACATGGCCAACG
* * * * *
19931812 CCATGTTCCAAACATGGTCTTACACTGACTCTCATATCGTGGCCGACG
1 CCATGTCCCAGACATGGTCTTACACTGACTCTCATAACATGGCCAACG
*
19931860 CCATGTCCTAGACATGGTCTTACACT
1 CCATGTCCCAGACATGGTCTTACACT
19931886 AGCACACATA
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 61 1.00
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (48 bp):
CCATGTCCCAGACATGGTCTTACACTGACTCTCATAACATGGCCAACG
Found at i:19933822 original size:18 final size:19
Alignment explanation
Indices: 19933783--19933824 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
19933773 CAACACAAAA
19933783 TAATAA-AAAAATCCTAAG
1 TAATAAGAAAAATCCTAAG
*
19933801 -AATAAGAAAAAT-GTAAG
1 TAATAAGAAAAATCCTAAG
19933818 TAATAAG
1 TAATAAG
19933825 GTAAAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.21
Consensus pattern (19 bp):
TAATAAGAAAAATCCTAAG
Found at i:19933991 original size:19 final size:20
Alignment explanation
Indices: 19933963--19934003 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
19933953 TGTGGTGCGC
*
19933963 AAGGGTGAGA-AGAGGGGAG
1 AAGGGAGAGAGAGAGGGGAG
19933982 AAGGGAGAGAGAGAGGGGAG
1 AAGGGAGAGAGAGAGGGGAG
19934002 AA
1 AA
19934004 AAATGAAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.56, T:0.02
Consensus pattern (20 bp):
AAGGGAGAGAGAGAGGGGAG
Found at i:19938870 original size:18 final size:19
Alignment explanation
Indices: 19938839--19938874 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19938829 ATTGTTATTG
19938839 ATATGGGCTAAGGCCCAGC
1 ATATGGGCTAAGGCCCAGC
*
19938858 ATAT-GGCTTAGGCCCAG
1 ATATGGGCTAAGGCCCAG
19938875 GAAGCTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.19
Consensus pattern (19 bp):
ATATGGGCTAAGGCCCAGC
Found at i:19942742 original size:20 final size:20
Alignment explanation
Indices: 19942705--19942742 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19942695 TGATGTGGAA
*
19942705 AGTTAACTGCTACAGTGGCC
1 AGTTAACTGCCACAGTGGCC
19942725 AGTTAACTTGCCAC-GTGG
1 AGTTAAC-TGCCACAGTGG
19942743 GATGTCCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (20 bp):
AGTTAACTGCCACAGTGGCC
Found at i:19947245 original size:24 final size:24
Alignment explanation
Indices: 19947213--19947262 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
19947203 CACACTAAAA
*
19947213 TATAGGTGGGGGTGAATAGAACCT
1 TATAGGTGGGGGCGAATAGAACCT
19947237 TATAGGTGGGGGCGAATAGAACCT
1 TATAGGTGGGGGCGAATAGAACCT
19947261 TA
1 TA
19947263 AAGAAAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.10, G:0.36, T:0.24
Consensus pattern (24 bp):
TATAGGTGGGGGCGAATAGAACCT
Found at i:19947432 original size:33 final size:33
Alignment explanation
Indices: 19947360--19947438 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
19947350 CTTATTTCTT
* *
19947360 TATTAAAATTTATTTCAAATGTATAACAATATA
1 TATTATAATTTATTACAAATGTATAACAATATA
*
19947393 TATTATAATTTATTACATAATGT-TTACAATATA
1 TATTATAATTTATTACA-AATGTATAACAATATA
19947426 GT-TTATATATTTA
1 -TATTATA-ATTTA
19947439 AATTAAGCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
33 29 0.73
34 11 0.28
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (33 bp):
TATTATAATTTATTACAAATGTATAACAATATA
Found at i:19949816 original size:6 final size:6
Alignment explanation
Indices: 19949805--19949841 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
19949795 AAACCTAGAG
*
19949805 AAAACT AAAACT AAAACT AAAACT AAACCT -AAACT AA
1 AAAACT AAAACT AAAACT AAAACT AAAACT AAAACT AA
19949842 TGTGTGTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAACT
Found at i:19950363 original size:51 final size:51
Alignment explanation
Indices: 19950300--19950403 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
19950290 AAAATAAAGA
*
19950300 AAATAAAAAAAAACTATACTAAATTCTATTTTGCTCGAGAAAAAGCTCCTT
1 AAATAAAAAAAAACTATACTAAACTCTATTTTGCTCGAGAAAAAGCTCCTT
19950351 AAATAAAAAAAAACTATACTAAACTCTATTTTGCTCGAGAAAAAGCTCCTT
1 AAATAAAAAAAAACTATACTAAACTCTATTTTGCTCGAGAAAAAGCTCCTT
19950402 AA
1 AA
19950404 GTGTATCGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (51 bp):
AAATAAAAAAAAACTATACTAAACTCTATTTTGCTCGAGAAAAAGCTCCTT
Found at i:19951668 original size:2 final size:2
Alignment explanation
Indices: 19951661--19951694 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19951651 TATCCATTCC
19951661 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19951695 CATTCTCCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19952170 original size:5 final size:5
Alignment explanation
Indices: 19952160--19952202 Score: 50
Period size: 5 Copynumber: 7.8 Consensus size: 5
19952150 ATCCTTATTT
19952160 AAATA AAATA AAGTGATA AAATA AAATA AAATA AAAGTA AAAT
1 AAATA AAATA AA---ATA AAATA AAATA AAATA AAA-TA AAAT
19952203 CCATATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 24 0.71
6 5 0.15
8 5 0.15
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:19952270 original size:21 final size:21
Alignment explanation
Indices: 19952244--19952284 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
19952234 TTAGAATAAG
19952244 GTTTTTTAAACCTTATTAAAA
1 GTTTTTTAAACCTTATTAAAA
19952265 GTTTTTTAAACCTTATTAAA
1 GTTTTTTAAACCTTATTAAA
19952285 CTCTATCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.49
Consensus pattern (21 bp):
GTTTTTTAAACCTTATTAAAA
Found at i:19956712 original size:16 final size:18
Alignment explanation
Indices: 19956677--19956714 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19956667 ATCTTTATTT
*
19956677 AAATAAAATACAGTAGTA
1 AAATAAAATACAGAAGTA
19956695 AAATAAAATA-A-AAGTA
1 AAATAAAATACAGAAGTA
19956711 AAAT
1 AAAT
19956715 CCATATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAGAAGTA
Found at i:19963792 original size:21 final size:22
Alignment explanation
Indices: 19963756--19963797 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
19963746 TGCTATATTA
*
19963756 TATGATGAAATGATGATTTGAG
1 TATGATGAAATGATGAATTGAG
*
19963778 TATGAT-AAATTATGAATTGA
1 TATGATGAAATGATGAATTGA
19963798 ATCATATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (22 bp):
TATGATGAAATGATGAATTGAG
Found at i:19967239 original size:18 final size:18
Alignment explanation
Indices: 19967211--19967256 Score: 83
Period size: 18 Copynumber: 2.5 Consensus size: 18
19967201 CAAAGAAGGG
19967211 GGAGAATGAGTTGATAAGA
1 GGAG-ATGAGTTGATAAGA
19967230 GGAGATGAGTTGATAAGA
1 GGAGATGAGTTGATAAGA
19967248 GGAGATGAG
1 GGAGATGAG
19967257 GGGGAGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (18 bp):
GGAGATGAGTTGATAAGA
Found at i:19969969 original size:15 final size:15
Alignment explanation
Indices: 19969949--19969999 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
19969939 TCATATTTAA
19969949 AAAAATAAAAATTTT
1 AAAAATAAAAATTTT
* *
19969964 AAAAATTATAATTCTT
1 AAAAATAAAAATT-TT
19969980 -AAAATAAAAACTATTT
1 AAAAATAAAAA-T-TTT
19969996 AAAA
1 AAAA
19970000 TTCAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 19 0.68
16 5 0.18
17 4 0.14
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAATAAAAATTTT
Found at i:19970031 original size:25 final size:24
Alignment explanation
Indices: 19969980--19970031 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
19969970 TATAATTCTT
* *
19969980 AAAATAAAAACTATTTAAAATTCA
1 AAAATAAAAAATATTTAAAATACA
*
19970004 AAAATAAAAAATATTTTAAAATAGA
1 AAAATAAAAAATA-TTTAAAATACA
19970029 AAA
1 AAA
19970032 TTTCTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAATAAAAAATATTTAAAATACA
Found at i:19970041 original size:16 final size:17
Alignment explanation
Indices: 19969999--19970041 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
19969989 ACTATTTAAA
*
19969999 ATTCAAAAATAAAAAAT
1 ATTCTAAAATAAAAAAT
* *
19970016 ATTTTAAAATAGAAAAT
1 ATTCTAAAATAAAAAAT
19970033 -TTCTAAAAT
1 ATTCTAAAAT
19970042 TTAGTGTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (17 bp):
ATTCTAAAATAAAAAAT
Found at i:19972093 original size:18 final size:18
Alignment explanation
Indices: 19972070--19972111 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
19972060 TTTATACAAA
*
19972070 TAATTCGGTTAATTTGAG
1 TAATTCGGGTAATTTGAG
*
19972088 TAATTCGGGTAATTTGGG
1 TAATTCGGGTAATTTGAG
19972106 TAATTC
1 TAATTC
19972112 AGATAATTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (18 bp):
TAATTCGGGTAATTTGAG
Found at i:19972127 original size:9 final size:9
Alignment explanation
Indices: 19972070--19972146 Score: 57
Period size: 9 Copynumber: 8.6 Consensus size: 9
19972060 TTTATACAAA
19972070 TAATTCGGT
1 TAATTCGGT
*
19972079 TAATTTGAG-
1 TAATTCG-GT
*
19972088 TAATTCGGG
1 TAATTCGGT
* *
19972097 TAATTTGGG
1 TAATTCGGT
* *
19972106 TAATTCAGA
1 TAATTCGGT
19972115 TAATTCGGT
1 TAATTCGGT
* *
19972124 TAATTTGAT
1 TAATTCGGT
*
19972133 TAATCCGGT
1 TAATTCGGT
19972142 TAATT
1 TAATT
19972147 TTATACTTAT
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
8 1 0.02
9 50 0.96
10 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.43
Consensus pattern (9 bp):
TAATTCGGT
Found at i:19974434 original size:14 final size:14
Alignment explanation
Indices: 19974400--19974426 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19974390 GCTACTATTT
19974400 TACTATTATGTTGA
1 TACTATTATGTTGA
19974414 TACTATTATGTTG
1 TACTATTATGTTG
19974427 TTATTATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (14 bp):
TACTATTATGTTGA
Found at i:19974919 original size:15 final size:15
Alignment explanation
Indices: 19974899--19974928 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19974889 CCCTTTTTTC
19974899 TTCTTTTTTTCTCTT
1 TTCTTTTTTTCTCTT
19974914 TTCTTTTTTTCTCTT
1 TTCTTTTTTTCTCTT
19974929 AACTCTAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTCTTTTTTTCTCTT
Found at i:19976088 original size:21 final size:19
Alignment explanation
Indices: 19976055--19976098 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
19976045 TGAAATAATA
19976055 ATAAAACAATAATTGAAAT
1 ATAAAACAATAATTGAAAT
19976074 ATAAAATCAAATAATTGAAAT
1 ATAAAA-C-AATAATTGAAAT
19976095 -TAAA
1 ATAAA
19976099 TTGGTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 12 0.52
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
ATAAAACAATAATTGAAAT
Found at i:19984309 original size:25 final size:24
Alignment explanation
Indices: 19984265--19984319 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 24
19984255 GTTCCTCTTT
19984265 TTTTTTCATTTTTATTAATTTG-A
1 TTTTTTCATTTTTATTAATTTGAA
19984288 TTTTTT-ATTTTTTAGTTCAATTTGAA
1 TTTTTTCA-TTTTTA-TT-AATTTGAA
19984314 TTTTTT
1 TTTTTT
19984320 TTTAAATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 1 0.04
23 12 0.43
24 2 0.07
25 6 0.21
26 7 0.25
ACGTcount: A:0.20, C:0.04, G:0.05, T:0.71
Consensus pattern (24 bp):
TTTTTTCATTTTTATTAATTTGAA
Found at i:19990043 original size:41 final size:40
Alignment explanation
Indices: 19989986--19990146 Score: 155
Period size: 41 Copynumber: 3.9 Consensus size: 40
19989976 TAAACAGATT
** * *
19989986 CACCGGCATTTTGCCTGCTAGGCTTAAAGCCTGATTCAGTA
1 CACCGGCATTAAGCCTGCTAGACTTAAAGTCTGATT-AGTA
* * *
19990027 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGA-AATGTA
1 CACCGGCA-TTAAGCCTGCTAGACTTAAAGTCTGATTA-GTA
* *
19990067 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTACTT
1 -CACCGGCATTAAGCCTGCTAGACTTAAAGTCTG-ATTAGTA
* *
19990109 CACCGGCATTAAGCCTGCTAGACGTAACGTCTGTATTA
1 CACCGGCATTAAGCCTGCTAGACTTAAAGTCTG-ATTA
19990147 TATTCAATCA
Statistics
Matches: 100, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
39 1 0.01
40 5 0.05
41 89 0.89
42 4 0.04
43 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACTTAAAGTCTGATTAGTA
Done.