Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 42 of 172
Found at i:13460183 original size:10 final size:10
Alignment explanation
Indices: 13460168--13460199 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
13460158 TAAATATATT
13460168 TAATTAAAGA
1 TAATTAAAGA
13460178 TAATTAAAGA
1 TAATTAAAGA
13460188 TAATTAAA-A
1 TAATTAAAGA
13460197 TAA
1 TAA
13460200 AATCCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (10 bp):
TAATTAAAGA
Found at i:13460244 original size:15 final size:15
Alignment explanation
Indices: 13460224--13460253 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13460214 ATAATCCTAA
*
13460224 TAATTATCTTAATAT
1 TAATTATCCTAATAT
13460239 TAATTATCCTAATAT
1 TAATTATCCTAATAT
13460254 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:13462394 original size:15 final size:14
Alignment explanation
Indices: 13462351--13462395 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
13462341 GTTCTTTTTG
*
13462351 TTTTTCCTTC-CTT
1 TTTTTCTTTCTCTT
13462364 TTTTTCTTTCTCTT
1 TTTTTCTTTCTCTT
13462378 TTCTTTCTTT-TCTT
1 TT-TTTCTTTCTCTT
13462392 TTTT
1 TTTT
13462396 CCCCTTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 11 0.38
14 11 0.38
15 7 0.24
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTCTTTCTCTT
Found at i:13462396 original size:16 final size:15
Alignment explanation
Indices: 13462361--13462393 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
13462351 TTTTTCCTTC
13462361 CTTTT-TTTCTTTCT
1 CTTTTCTTTCTTTCT
13462375 CTTTTCTTTCTTT-T
1 CTTTTCTTTCTTTCT
13462389 CTTTT
1 CTTTT
13462394 TTCCCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTCTTTCTTTCT
Found at i:13462396 original size:23 final size:24
Alignment explanation
Indices: 13462352--13462396 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
13462342 TTCTTTTTGT
13462352 TTTTCCTTCCTTTTTTTCTTTCTC
1 TTTTCCTTCCTTTTTTTCTTTCTC
*
13462376 TTTT-CTTTCTTTTCTTT-TTTC
1 TTTTCCTTCCTTTT-TTTCTTTC
13462397 CCCTTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTCCTTCCTTTTTTTCTTTCTC
Found at i:13467397 original size:15 final size:15
Alignment explanation
Indices: 13467377--13467406 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13467367 GTCACGTCAC
13467377 AAAAATTGGGTTAGT
1 AAAAATTGGGTTAGT
13467392 AAAAATTGGGTTAGT
1 AAAAATTGGGTTAGT
13467407 GGCCCGAGAG
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:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (15 bp):
AAAAATTGGGTTAGT
Found at i:13469265 original size:20 final size:20
Alignment explanation
Indices: 13469240--13469277 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13469230 ACCAATGTCA
* *
13469240 GATTTTTTTAGTTTAAAAGT
1 GATTTTTTAAATTTAAAAGT
13469260 GATTTTTTAAATTTAAAA
1 GATTTTTTAAATTTAAAA
13469278 TTAAAATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTTTAAATTTAAAAGT
Found at i:13473526 original size:53 final size:52
Alignment explanation
Indices: 13473459--13473620 Score: 200
Period size: 53 Copynumber: 3.1 Consensus size: 52
13473449 CTTTCTCAAT
* * *
13473459 AATAAAAAAAAATTAAACTATTTTGTTCAAGATCGACAATATTGGGTCTTACA
1 AATAAAACATAATTAAACTATTTTGTTCAAGA-CGACAATATTGTGTCTTACA
* * *
13473512 AATAATACATAATTAAA-TGATTTTGTTCAAGACCGACAACATTCTGTCTTACA
1 AATAAAACATAATTAAACT-ATTTTGTTCAAGA-CGACAATATTGTGTCTTACA
* * *
13473565 AATAAAAGATAATTAAACGATTTTGTTCAAGACTGACAGTATTGTGTCTTACA
1 AATAAAACATAATTAAACTATTTTGTTCAAGAC-GACAATATTGTGTCTTACA
13473618 AAT
1 AAT
13473621 TGAAAAATAC
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
52 2 0.02
53 91 0.98
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (52 bp):
AATAAAACATAATTAAACTATTTTGTTCAAGACGACAATATTGTGTCTTACA
Found at i:13474287 original size:94 final size:85
Alignment explanation
Indices: 13474110--13474300 Score: 231
Period size: 94 Copynumber: 2.1 Consensus size: 85
13474100 GCCAAAGAGA
* * *
13474110 ATGACTCTACCAAATAAAATATCAATTTTAATTTAAATTAAAAAACACATTTAAAAAAAATCTGA
1 ATGACTCCACCAAATAAAATATCAATTTTAATTTAAATAAAAAAACACATTTAAAAAAAAACTGA
*
13474175 CAGTGGTGGCACCATTCTCT
66 AAGTGGTGGCACCATTCTCT
*
13474195 ATGGCTCCACCAAATAAAATATCAATTTTATATTTAAAATGAAAAAAACAC-TTATAAAAAAAGG
1 ATGACTCCACCAAATAAAATATCAATTTTA-ATTT-AAAT-AAAAAAACACATT-TAAAAAAA--
*
13474259 TGACACATTAAAGTGGTGGCACCATTCTCT
60 --A-AC-TGAAAGTGGTGGCACCATTCTCT
13474289 ATGACTCCACCA
1 ATGACTCCACCA
13474301 CCATTATTTT
Statistics
Matches: 89, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
85 28 0.31
86 4 0.04
87 6 0.07
88 17 0.19
92 1 0.01
93 1 0.01
94 32 0.36
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (85 bp):
ATGACTCCACCAAATAAAATATCAATTTTAATTTAAATAAAAAAACACATTTAAAAAAAAACTGA
AAGTGGTGGCACCATTCTCT
Found at i:13487800 original size:20 final size:21
Alignment explanation
Indices: 13487777--13487823 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
13487767 TATGTTCTTG
13487777 ATTAAAT-TGA-ATTATACATA
1 ATTAAATGTGATA-TATACATA
*
13487797 ATTAAGTGTGATGATATACATA
1 ATTAAATGTGAT-ATATACATA
13487819 ATTAA
1 ATTAA
13487824 GTGATCTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 3 0.13
22 13 0.57
23 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (21 bp):
ATTAAATGTGATATATACATA
Found at i:13490195 original size:39 final size:41
Alignment explanation
Indices: 13490152--13490228 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
13490142 TTATATATTT
*
13490152 TATTATATA-TATATT-TATT-CTGTTTTTTTATATGTAATA
1 TATTATATACTAT-TTATATTACTGTATTTTTATATGTAATA
*
13490191 TATTATATACTATTTATGTTACTGTATTTTTATATGTA
1 TATTATATACTATTTATATTACTGTATTTTTATATGTA
13490229 GAATACTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 11 0.33
40 6 0.18
41 16 0.48
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (41 bp):
TATTATATACTATTTATATTACTGTATTTTTATATGTAATA
Found at i:13490469 original size:26 final size:26
Alignment explanation
Indices: 13490440--13490501 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
13490430 ATTATTTTCC
*
13490440 TATATTATTTCATATTTATA-TA-TTAT
1 TATATTATTT-AT-TTTAAATTACTTAT
*
13490466 TATATTGTTTATTTTAAATTACTTAT
1 TATATTATTTATTTTAAATTACTTAT
*
13490492 TATATAATTT
1 TATATTATTT
13490502 TTAAAATTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 5 0.17
25 4 0.13
26 21 0.70
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (26 bp):
TATATTATTTATTTTAAATTACTTAT
Found at i:13490470 original size:16 final size:16
Alignment explanation
Indices: 13490417--13490471 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 16
13490407 ATATAAACCT
13490417 TATTTATTATATTATTA
1 TATTTA-TATATTATTA
*
13490434 T-TTTCCTATATTATTTCA
1 TATTT-ATATATTA-TT-A
13490452 TATTTATATATTATTA
1 TATTTATATATTATTA
13490468 TATT
1 TATT
13490472 GTTTATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 15 0.47
17 5 0.16
18 9 0.28
19 3 0.09
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTATATATTATTA
Found at i:13490594 original size:23 final size:22
Alignment explanation
Indices: 13490568--13490612 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
13490558 GCTATAAAAA
* *
13490568 ATTTATCTTTTATTATATATACT
1 ATTTATATTATATTAT-TATACT
13490591 ATTTATATTATATTATTATACT
1 ATTTATATTATATTATTATACT
13490613 TGACTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTATATTATATTATTATACT
Found at i:13492519 original size:6 final size:6
Alignment explanation
Indices: 13492498--13492538 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
13492488 AAGGAGGAAG
13492498 AAATGAA AAATAAA AAATAA AAATAA AAATAA AAATAA AAA
1 AAAT-AA AAAT-AA AAATAA AAATAA AAATAA AAATAA AAA
13492539 GAGAAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 23 0.70
7 10 0.30
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:13492545 original size:12 final size:12
Alignment explanation
Indices: 13492502--13492547 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
13492492 AGGAAGAAAT
13492502 GAAAAATAAAAAA
1 GAAAAAT-AAAAA
*
13492515 TAAAAATAAAAA
1 GAAAAATAAAAA
*
13492527 TAAAAATAAAAA
1 GAAAAATAAAAA
*
13492539 GAGAAATAA
1 GAAAAATAA
13492548 TGTAAAGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 24 0.80
13 6 0.20
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (12 bp):
GAAAAATAAAAA
Found at i:13492545 original size:18 final size:18
Alignment explanation
Indices: 13492502--13492547 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
13492492 AGGAAGAAAT
13492502 GAAAAATAAAAAATAAAAA
1 GAAAAAT-AAAAATAAAAA
*
13492521 TAAAAATAAAAATAAAAA
1 GAAAAATAAAAATAAAAA
*
13492539 GAGAAATAA
1 GAAAAATAA
13492548 TGTAAAGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (18 bp):
GAAAAATAAAAATAAAAA
Found at i:13493946 original size:20 final size:24
Alignment explanation
Indices: 13493904--13493954 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
13493894 ATTTAATTAA
13493904 ATTTAAATAAAATTATTAATATTT-
1 ATTTAAATAAAATTATT-ATATTTC
13493928 ATTTAAATAAAA-TA-T-TATTTC
1 ATTTAAATAAAATTATTATATTTC
13493949 ATTTAA
1 ATTTAA
13493955 TTACGTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.19
21 6 0.23
22 1 0.04
23 2 0.08
24 12 0.46
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTAAATAAAATTATTATATTTC
Found at i:13504272 original size:46 final size:45
Alignment explanation
Indices: 13504205--13504379 Score: 208
Period size: 46 Copynumber: 3.8 Consensus size: 45
13504195 TGTAACCCGC
13504205 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGTAT
* *
13504251 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGT-T
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGTAT
* *** * * *
13504297 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGTAT
*
13504344 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
13504380 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
45 1 0.01
46 71 0.65
47 35 0.32
48 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGTAT
Found at i:13504325 original size:93 final size:93
Alignment explanation
Indices: 13504213--13504383 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
13504203 GCCCATAAGT
* * *
13504213 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
13504278 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
13504306 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
13504371 CGAGTTCGGATGC
66 CGAGCTCGGATGC
13504384 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:13505053 original size:56 final size:56
Alignment explanation
Indices: 13504967--13505079 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
13504957 TTATGTTTTA
13504967 TGACATGCTGATCATTTTTCCCTTCTATGGCAACATTAAATTCTCACTCTAACATG
1 TGACATGCTGATCATTTTTCCCTTCTATGGCAACATTAAATTCTCACTCTAACATG
13505023 TGACATGCTGATCATTTTTCCCTTCTATGGCAACATTAAATTCTCACTCTAACATG
1 TGACATGCTGATCATTTTTCCCTTCTATGGCAACATTAAATTCTCACTCTAACATG
13505079 T
1 T
13505080 ACTTATGACT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (56 bp):
TGACATGCTGATCATTTTTCCCTTCTATGGCAACATTAAATTCTCACTCTAACATG
Found at i:13506933 original size:30 final size:30
Alignment explanation
Indices: 13506889--13506977 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
13506879 CAAAGATAAT
13506889 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* * *
13506918 GAGAAACCCAGAATAAAGAGATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * * *
13506948 AAGAGATCTAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
13506978 CGATATTATG
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
29 9 0.19
30 36 0.77
31 2 0.04
ACGTcount: A:0.56, C:0.15, G:0.18, T:0.11
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:13506945 original size:15 final size:15
Alignment explanation
Indices: 13506889--13506968 Score: 74
Period size: 15 Copynumber: 5.4 Consensus size: 15
13506879 CAAAGATAAT
*
13506889 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
13506903 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
13506918 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
*
13506933 AAGAGATCCAGAATA
1 AAGAAATCCAGAATA
* * *
13506948 AAGAGATCTAGGATA
1 AAGAAATCCAGAATA
13506963 AAGAAA
1 AAGAAA
13506969 CCCAAGATAC
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
14 9 0.17
15 44 0.81
16 1 0.02
ACGTcount: A:0.57, C:0.12, G:0.19, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:13506977 original size:15 final size:15
Alignment explanation
Indices: 13506900--13506977 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
13506890 AGAAAACCGA
13506900 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
13506915 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
*
13506929 AATAAAGAGATCC-AG
1 -ATAAAGAAATCCAAG
* * *
13506944 AATAAAGAGATCTAGG
1 -ATAAAGAAATCCAAG
*
13506960 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
13506975 ATA
1 ATA
13506978 CGATATTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 4 0.08
15 43 0.86
16 3 0.06
ACGTcount: A:0.55, C:0.14, G:0.18, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:13510057 original size:46 final size:45
Alignment explanation
Indices: 13509914--13510057 Score: 120
Period size: 46 Copynumber: 3.1 Consensus size: 45
13509904 CCCGCCCATA
*
13509914 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTA-CATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATC-CT
* * *
13509963 --CGAACTCGGACTCAACTCAACGAGTTC--A-GACATTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCA-AC-CATCC-T
13510006 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCATCCT
13510053 AGTGA
1 AGTGA
13510058 CATGTCACTT
Statistics
Matches: 78, Mismatches: 7, Indels: 23
0.72 0.06 0.21
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 6 0.08
44 2 0.03
45 1 0.01
46 31 0.40
47 26 0.33
48 6 0.08
49 2 0.03
50 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCCT
Found at i:13512329 original size:7 final size:7
Alignment explanation
Indices: 13512317--13512343 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
13512307 TCTAATATTC
13512317 AAATTTA
1 AAATTTA
13512324 AAATTTA
1 AAATTTA
13512331 AAATTTA
1 AAATTTA
13512338 AAATTT
1 AAATTT
13512344 TCATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:13518550 original size:42 final size:42
Alignment explanation
Indices: 13518504--13518584 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
13518494 TGGAATAAAT
13518504 TAAATTAATTGAGTTAGTGAATTTTAGTTAAAGTCAACTAAC
1 TAAATTAATTGAGTTAGTGAATTTTAGTTAAAGTCAACTAAC
13518546 TAAATTAATTGAGTTAGTGAATTTTAGTTAAAGTCAACT
1 TAAATTAATTGAGTTAGTGAATTTTAGTTAAAGTCAACT
13518585 CAAATAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (42 bp):
TAAATTAATTGAGTTAGTGAATTTTAGTTAAAGTCAACTAAC
Found at i:13518594 original size:42 final size:42
Alignment explanation
Indices: 13518499--13518591 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
13518489 TTTGCTGGAA
13518499 TAAATTAAATTAATTGAGTTAGTGAATTTTAGTTAAAGTCAAC
1 TAAA-TAAATTAATTGAGTTAGTGAATTTTAGTTAAAGTCAAC
*
13518542 TAACTAAATTAATTGAGTTAGTGAATTTTAGTTAAAGTCAAC
1 TAAATAAATTAATTGAGTTAGTGAATTTTAGTTAAAGTCAAC
13518584 TCAAATAA
1 T-AAATAA
13518592 TTAGTTTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 39 0.83
43 8 0.17
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (42 bp):
TAAATAAATTAATTGAGTTAGTGAATTTTAGTTAAAGTCAAC
Found at i:13518895 original size:143 final size:143
Alignment explanation
Indices: 13518637--13518952 Score: 535
Period size: 143 Copynumber: 2.2 Consensus size: 143
13518627 TTAATTAAAG
* *
13518637 TTTAATGTGTCTTTAGTTAGGACAAATTAATTCCATGATAAAAATTAATTCTAGCCGAATTTAAT
1 TTTAAAGTGTCTTTAGTTAGGACAAATTAATTCCATGATAAAAATTAATTCTAGCAGAATTTAAT
* *
13518702 TTGTTTTCTTAATCTATGACATGTTTTAATGTGTCTTAGTAAGTACATAGAATCAATGTGTCTGA
66 TTGTTGTCTTAATCTATGACATGTTTTAATGTGTCCTAGTAAGTACATAGAATCAATGTGTCTGA
13518767 ATTAATACATGCA
131 ATTAATACATGCA
* *
13518780 TTTAAAGTGTCTTTAGTTAGGACAAATTAGTTTCATGATAAAAATTAATTCTAGCAGAATTTAAT
1 TTTAAAGTGTCTTTAGTTAGGACAAATTAATTCCATGATAAAAATTAATTCTAGCAGAATTTAAT
*
13518845 TTGTTGTCTTAATCTATGACATGTTTTAATGTGTCCTAGTAAGTATATAGAATCAATGTGTCTGA
66 TTGTTGTCTTAATCTATGACATGTTTTAATGTGTCCTAGTAAGTACATAGAATCAATGTGTCTGA
13518910 ATTAATACATGCA
131 ATTAATACATGCA
* *
13518923 TTTAAAGTGTCCTAAGCTTA-GACAAATTAA
1 TTTAAAGTGTCTTTAG-TTAGGACAAATTAA
13518953 ACAAGCTATT
Statistics
Matches: 162, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
143 159 0.98
144 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (143 bp):
TTTAAAGTGTCTTTAGTTAGGACAAATTAATTCCATGATAAAAATTAATTCTAGCAGAATTTAAT
TTGTTGTCTTAATCTATGACATGTTTTAATGTGTCCTAGTAAGTACATAGAATCAATGTGTCTGA
ATTAATACATGCA
Found at i:13530001 original size:40 final size:40
Alignment explanation
Indices: 13529910--13530079 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
13529900 TCCTCGTTCA
* * * * *
13529910 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
13529949 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
13529989 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
13530029 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
13530069 AAGGCCTTCGG
1 AATGCCTTCGG
13530080 ATCTTAGTCC
Statistics
Matches: 112, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 32 0.29
40 80 0.71
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:13532599 original size:22 final size:22
Alignment explanation
Indices: 13532574--13532621 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
13532564 TACACATATC
*
13532574 AAATCAAT-AAAATATTCATAAA
1 AAATCAATCAAAATA-TAATAAA
* *
13532596 AAATTAATCTAAATATAATAAA
1 AAATCAATCAAAATATAATAAA
13532618 AAAT
1 AAAT
13532622 TATTTTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATCAATCAAAATATAATAAA
Found at i:13533855 original size:130 final size:129
Alignment explanation
Indices: 13533600--13533953 Score: 354
Period size: 130 Copynumber: 2.7 Consensus size: 129
13533590 TTCTAACAAT
* * * * *
13533600 ACAATTTGTTGTTGTAAATTATTAATAAAATGTATAACGACTAAATAAATTGTTGT-TAAACATT
1 ACAATTTGTTGTTATGAATTATTAATAAAATTTATAACTACAAAATAAATT-TT-TATAAACATT
* * * * * * * * *
13533664 AAAATAATAATAACAACTTTAAAACGTCATTATATAATTTATTTTTTTCTTATTAAAAGCAATGA
64 AAAATATTAACAACAACTTTAAAATGTTATTACATAATTAATTTTCTACTTAGTAAAAGCAATGA
13533729 C
129 C
* **
13533730 ACAATTTGTTGTTATGAATTATTAATAAAATTTATAACTA-AAAATTAAGTTTTTATAAATGTTA
1 ACAATTTGTTGTTATGAATTATTAATAAAATTTATAACTACAAAA-TAAATTTTTATAAACATTA
* * * *
13533794 AAATATTAACACCAACTTTAAAATATTATTACATAATTAAGTTTTCTACTTAGTAATAGCAATGG
65 AAATATTAACAACAACTTTAAAATGTTATTACATAATTAA-TTTTCTACTTAGTAAAAGCAATGA
13533859 C
129 C
** * ** * ** *
13533860 ATGATTAGTCATTTTGAATTATTAATAAAATTTGCAA-TGACAAAATAAATTGTTACTAAACATT
1 ACAATTTGTTGTTATGAATTATTAATAAAATTTATAACT-ACAAAATAAATTTTTA-TAAACATT
*
13533924 AAAATATTAGCAACAACTTTAAAATGTTAT
64 AAAATATTAACAACAACTTTAAAATGTTAT
13533954 GTATTTTAAT
Statistics
Matches: 182, Mismatches: 36, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
128 1 0.01
129 45 0.25
130 99 0.54
131 37 0.20
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (129 bp):
ACAATTTGTTGTTATGAATTATTAATAAAATTTATAACTACAAAATAAATTTTTATAAACATTAA
AATATTAACAACAACTTTAAAATGTTATTACATAATTAATTTTCTACTTAGTAAAAGCAATGAC
Found at i:13534656 original size:21 final size:20
Alignment explanation
Indices: 13534613--13534656 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
13534603 AACCGTAACA
* * *
13534613 AAACATTTTAAAAAAGAATT
1 AAACAATTTAAAAAAAAAAT
13534633 AAACAATTTAAAAAAAACAAT
1 AAACAATTTAAAAAAAA-AAT
13534654 AAA
1 AAA
13534657 TATAATTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (20 bp):
AAACAATTTAAAAAAAAAAT
Found at i:13541582 original size:49 final size:49
Alignment explanation
Indices: 13541528--13541707 Score: 261
Period size: 49 Copynumber: 3.7 Consensus size: 49
13541518 CTGGTACGCA
*
13541528 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
*
13541577 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
* * ** * * *
13541626 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACGCG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCGGTACACG
*
13541676 TAGTAGCCTGCATTTAGTACTACACATGCGAC
1 TAGTAGCCTGCACTTAGTACTACACATGCGAC
13541708 TTCACAATAG
Statistics
Matches: 119, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 79 0.66
50 40 0.34
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
Found at i:13546139 original size:46 final size:46
Alignment explanation
Indices: 13546089--13546261 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
13546079 TGGTTGAGCA
*
13546089 TCCGAACTCGTTGAGTTGAGTCCTAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
13546135 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* **
13546180 CATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
13546228 CCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
13546262 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 58 0.57
47 28 0.27
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:13546245 original size:93 final size:93
Alignment explanation
Indices: 13546086--13546256 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
13546076 GGATGGTTGA
* * ***
13546086 GCATCCGAACTCGTTGAGTTGAGTCCTAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
13546151 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
13546179 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTTGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
13546244 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
13546257 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:13547955 original size:13 final size:13
Alignment explanation
Indices: 13547937--13547968 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
13547927 GCTCGCGTGA
13547937 GCCACACAGGCTG
1 GCCACACAGGCTG
*
13547950 GCCACACGGGCTG
1 GCCACACAGGCTG
13547963 GCCACA
1 GCCACA
13547969 TGCCTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.41, G:0.31, T:0.06
Consensus pattern (13 bp):
GCCACACAGGCTG
Found at i:13548546 original size:57 final size:57
Alignment explanation
Indices: 13548476--13548588 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
13548466 TTAAAATGAA
*
13548476 TTAAAAACAAAATTAAAAGCCAATTTTTGTCCATCTTCTTCATTAGGCCGAAATTTT
1 TTAAAAACAAAATTAAAAGCCAATTTTTGTCCATCTTATTCATTAGGCCGAAATTTT
13548533 TTAAAAACAAAATTAAAAGCCAATTTTTGTCCATCTTATTCATTAGGCCGAAATTT
1 TTAAAAACAAAATTAAAAGCCAATTTTTGTCCATCTTATTCATTAGGCCGAAATTT
13548589 CAAGGGTTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (57 bp):
TTAAAAACAAAATTAAAAGCCAATTTTTGTCCATCTTATTCATTAGGCCGAAATTTT
Found at i:13549574 original size:46 final size:46
Alignment explanation
Indices: 13549521--13549696 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
13549511 TGGTTGAGCA
*
13549521 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
13549567 TCTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
13549612 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
13549660 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
13549697 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 60 0.57
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:13549677 original size:93 final size:93
Alignment explanation
Indices: 13549518--13549689 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
13549508 GGATGGTTGA
* * * *
13549518 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
13549583 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
13549611 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
13549676 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
13549690 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:13552193 original size:45 final size:45
Alignment explanation
Indices: 13552120--13552209 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
13552110 ATAAGAAGCA
* *
13552120 AAATGTGGGTCCTAAATCCCAGACTACTTCGGCAGCCAGTGTAGG
1 AAATGTGGGTCCTAAATCCCAGAATACTTCGGCAGCCAATGTAGG
* * *
13552165 AAATGTGGGTCTTAAATCTCAGAATACTTCTGCAGCCAATGTAGG
1 AAATGTGGGTCCTAAATCCCAGAATACTTCGGCAGCCAATGTAGG
13552210 GAACTCGAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (45 bp):
AAATGTGGGTCCTAAATCCCAGAATACTTCGGCAGCCAATGTAGG
Found at i:13557242 original size:46 final size:46
Alignment explanation
Indices: 13557192--13557367 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
13557182 TGGTTGAGCA
13557192 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
13557238 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * * *
13557283 CATCCGAACTCGTTGTGTTGAGTCCGAGTTCAGTTATGGATACGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
13557331 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
13557368 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 28 0.26
48 4 0.04
50 3 0.03
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:13557348 original size:93 final size:93
Alignment explanation
Indices: 13557189--13557360 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
13557179 GGATGGTTGA
* * *
13557189 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
13557254 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
13557282 GCATCCGAACTCGTTGTGTTGAGTCCGAGTTCAGTTATGGATACGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
13557347 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
13557361 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:13565507 original size:91 final size:91
Alignment explanation
Indices: 13565383--13565552 Score: 259
Period size: 91 Copynumber: 1.9 Consensus size: 91
13565373 AATGATAAAT
* * *
13565383 ATATTGGTGGATGAATCATCCATCTATGTAGATAAAAGTTGCTAATATGTTGTGGATAAACCACT
1 ATATTGGTGGATGAACCATCCATCTATGCAGATAAAAGTTGCTAATATGTTGTGGAGAAACCACT
* *
13565448 TGTTGAGCATATGATTGTCAACTAGA
66 GGTCGAGCATATGATTGTCAACTAGA
* * * *
13565474 ATATTGGTGGATGAACCATTCATTTGTGCAGATAAAAGTTGCTAATATGTTGTGGAGAAACCAGT
1 ATATTGGTGGATGAACCATCCATCTATGCAGATAAAAGTTGCTAATATGTTGTGGAGAAACCACT
13565539 GGTCGAGCATATGA
66 GGTCGAGCATATGA
13565553 ACTACCAGTT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 70 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (91 bp):
ATATTGGTGGATGAACCATCCATCTATGCAGATAAAAGTTGCTAATATGTTGTGGAGAAACCACT
GGTCGAGCATATGATTGTCAACTAGA
Found at i:13568443 original size:18 final size:18
Alignment explanation
Indices: 13568420--13568456 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
13568410 TTACATACAA
13568420 AGGTCAATAACCTTCAAT
1 AGGTCAATAACCTTCAAT
13568438 AGGTCAATAACCTTCAAT
1 AGGTCAATAACCTTCAAT
13568456 A
1 A
13568457 TTTGAAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.27
Consensus pattern (18 bp):
AGGTCAATAACCTTCAAT
Found at i:13570603 original size:27 final size:26
Alignment explanation
Indices: 13570566--13570675 Score: 148
Period size: 27 Copynumber: 4.1 Consensus size: 26
13570556 GCATGGCTGT
* *
13570566 CAGAACAGATAATGTGACAGAGTCAC
1 CAGAACAGATAATGTGGCAGAGCCAC
13570592 CAGATACAGATAATCGTGGCAGAGCCAC
1 CAGA-ACAGATAAT-GTGGCAGAGCCAC
13570620 CAGAACAGATATATGTGGCAGAGCCAC
1 CAGAACAGATA-ATGTGGCAGAGCCAC
* *
13570647 CAGATCAGATAATTGTGGCATAGCCAC
1 CAGAACAGATAA-TGTGGCAGAGCCAC
13570674 CA
1 CA
13570676 AGACGCTTCC
Statistics
Matches: 76, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
26 5 0.07
27 54 0.71
28 17 0.22
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (26 bp):
CAGAACAGATAATGTGGCAGAGCCAC
Found at i:13570656 original size:54 final size:54
Alignment explanation
Indices: 13570566--13570675 Score: 168
Period size: 54 Copynumber: 2.0 Consensus size: 54
13570556 GCATGGCTGT
*
13570566 CAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCAC
1 CAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCAC
* * *
13570620 CAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCAC
1 CAGAACAGATA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCAC
13570674 CA
1 CA
13570676 AGACGCTTCC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (54 bp):
CAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCAC
Found at i:13571907 original size:12 final size:12
Alignment explanation
Indices: 13571886--13571922 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
13571876 AGAAGTTGAT
13571886 AAAGAGAGAAAAA
1 AAAGA-AGAAAAA
*
13571899 AAAGAAGAAAAG
1 AAAGAAGAAAAA
13571911 AAAGAAGAAAAA
1 AAAGAAGAAAAA
13571923 GGAAGAATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAGAAGAAAAA
Found at i:13571910 original size:21 final size:22
Alignment explanation
Indices: 13571867--13571929 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
13571857 GACAGACAAG
**
13571867 AAGAAGAAAAGAAGTTGATAAAGA
1 AAGAAGAAAA-AAGAAGA-AAAGA
*
13571891 GAGAA-AAAAAAGAAGAAAAGA
1 AAGAAGAAAAAAGAAGAAAAGA
*
13571912 AAGAAGAAAAAGGAAGAA
1 AAGAAGAAAAAAGAAGAA
13571930 TGGTCAGGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 9 0.27
22 16 0.48
23 4 0.12
24 4 0.12
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (22 bp):
AAGAAGAAAAAAGAAGAAAAGA
Found at i:13571922 original size:13 final size:13
Alignment explanation
Indices: 13571886--13571929 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
13571876 AGAAGTTGAT
13571886 AAAGAGAGAAAAA-
1 AAAGA-AGAAAAAG
13571899 AAAGAAG-AAAAG
1 AAAGAAGAAAAAG
13571911 AAAGAAGAAAAAG
1 AAAGAAGAAAAAG
*
13571924 GAAGAA
1 AAAGAA
13571930 TGGTCAGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 4 0.14
12 9 0.32
13 15 0.54
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAG
Found at i:13578819 original size:4 final size:4
Alignment explanation
Indices: 13578810--13578834 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
13578800 GCACTAAAGC
13578810 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
13578835 AGAAACAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:13582559 original size:40 final size:40
Alignment explanation
Indices: 13582515--13582593 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 40
13582505 TAATTATAGA
* * * * *
13582515 ATTGTTTTGAGTACTGAATTGAATTGTGAAGTTATTGAAT
1 ATTGTTATGACTACTGAATTGAACTGTGAAATTACTGAAT
* *
13582555 ATTGTTATGTCTACTGCATTGAACTGTGAAATTACTGAA
1 ATTGTTATGACTACTGAATTGAACTGTGAAATTACTGAA
13582594 GCAATGAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (40 bp):
ATTGTTATGACTACTGAATTGAACTGTGAAATTACTGAAT
Found at i:13582851 original size:45 final size:46
Alignment explanation
Indices: 13582801--13582909 Score: 168
Period size: 45 Copynumber: 2.4 Consensus size: 46
13582791 ACTACTGTTT
*
13582801 CTGTTACCGTTACTGTTACCA-ATTCGACACTTTGTGTGTCGAATA
1 CTGTTACCGTTACTGTTACCAGATTCAACACTTTGTGTGTCGAATA
* *
13582846 CTGTTACCGTTACTATTA-CAGATTCAACACTTTGTGTGTTGAATA
1 CTGTTACCGTTACTGTTACCAGATTCAACACTTTGTGTGTCGAATA
*
13582891 CTGTTACTGTTACTGTTAC
1 CTGTTACCGTTACTGTTAC
13582910 TGTTATTGCT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
44 2 0.04
45 55 0.96
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (46 bp):
CTGTTACCGTTACTGTTACCAGATTCAACACTTTGTGTGTCGAATA
Found at i:13582858 original size:51 final size:51
Alignment explanation
Indices: 13582784--13582914 Score: 150
Period size: 45 Copynumber: 2.7 Consensus size: 51
13582774 CAGGCACTTA
* * *
13582784 TGTGTCGACTACTGTTTCTGTTACCGTTACTGTTACCA-ATTCGACACTTTG
1 TGTGTCGAATACTGTTACTGTTACCGTTACTGTTA-CAGATTCAACACTTTG
*
13582835 TGTGTCG-A-A----TACTGTTACCGTTACTATTACAGATTCAACACTTTG
1 TGTGTCGAATACTGTTACTGTTACCGTTACTGTTACAGATTCAACACTTTG
* *
13582880 TGTGTTGAATACTGTTACTGTTACTGTTACTGTTA
1 TGTGTCGAATACTGTTACTGTTACCGTTACTGTTA
13582915 TTGCTACTGT
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
44 2 0.03
45 36 0.55
46 1 0.02
47 1 0.02
49 1 0.02
51 25 0.38
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (51 bp):
TGTGTCGAATACTGTTACTGTTACCGTTACTGTTACAGATTCAACACTTTG
Found at i:13582900 original size:6 final size:6
Alignment explanation
Indices: 13582889--13582938 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
13582879 GTGTGTTGAA
* *
13582889 TACTGT TACTGT TACTGT TACTGT TATTGC TACTGT TACTGAT TACTGT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT
13582938 T
1 T
13582939 TAGGTACTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 33 0.85
7 6 0.15
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (6 bp):
TACTGT
Found at i:13582946 original size:24 final size:24
Alignment explanation
Indices: 13582895--13582957 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
13582885 TGAATACTGT
*
13582895 TACTGTTACTGTTACTGTTATTGC
1 TACTGTTACTGTTACTGTTATAGC
*
13582919 TACTGTTACTGATTACTGTT-TAGG
1 TACTGTTACTG-TTACTGTTATAGC
*
13582943 TACTGTGTACCGTTA
1 TACTGT-TACTGTTA
13582958 AGGTACGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 22 0.65
25 12 0.35
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.46
Consensus pattern (24 bp):
TACTGTTACTGTTACTGTTATAGC
Found at i:13583516 original size:28 final size:29
Alignment explanation
Indices: 13583452--13583516 Score: 107
Period size: 28 Copynumber: 2.3 Consensus size: 29
13583442 CAAGTCTAAG
*
13583452 AATTATAACGAAAGAAGTTTATCCATTTC
1 AATTATAATGAAAGAAGTTTATCCATTTC
13583481 -ATTATAATGAAAGAAGTTTATCCATTTC
1 AATTATAATGAAAGAAGTTTATCCATTTC
13583509 AATT-TAAT
1 AATTATAAT
13583517 TAGTACATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 31 0.91
29 3 0.09
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (29 bp):
AATTATAATGAAAGAAGTTTATCCATTTC
Found at i:13589189 original size:13 final size:14
Alignment explanation
Indices: 13589171--13589208 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
13589161 ATAAGAAGTT
13589171 AATAAAATAAAAG-
1 AATAAAATAAAAGA
* *
13589184 AATAAAAGAAATGA
1 AATAAAATAAAAGA
13589198 AATAAAATAAA
1 AATAAAATAAA
13589209 GTAAAGAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:13590021 original size:40 final size:40
Alignment explanation
Indices: 13589973--13590059 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
13589963 AATTATAGAA
* * * *
13589973 TACTGAATATTGTTTTGAGTATTGAATTGAATTGTGAAGT
1 TACTGAATATTGTTATGAGTACTGAATTGAACTGTGAAAT
* * *
13590013 TATTGAATATTGTTATGTGTACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATGAGTACTGAATTGAACTGTGAAAT
13590053 TACTGAA
1 TACTGAA
13590060 GCAATGAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.43
Consensus pattern (40 bp):
TACTGAATATTGTTATGAGTACTGAATTGAACTGTGAAAT
Found at i:13590319 original size:45 final size:45
Alignment explanation
Indices: 13590262--13590370 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
13590252 ACTACTGTTT
* * *
13590262 CTGTTATCGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAATA
1 CTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTATGTCGAATA
* * * *
13590307 TTGTTGCCGTTACTATTACAGATTCAGCACTTTGTATGTTGAATA
1 CTGTTACCGTTACTGTTACAGATTCAGCACTTTGTATGTCGAATA
*
13590352 CTGTTACTGTTACTGTTAC
1 CTGTTACCGTTACTGTTAC
13590371 TGCTACTGCT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
45 51 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (45 bp):
CTGTTACCGTTACTGTTACAGATTCAGCACTTTGTATGTCGAATA
Found at i:13590361 original size:6 final size:6
Alignment explanation
Indices: 13590350--13590399 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
13590340 GTATGTTGAA
* * *
13590350 TACTGT TACTGT TACTGT TACTGC TACTGC TACTGT TATTGAT TACTGT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT
13590399 T
1 T
13590400 TAGGTACTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 34 0.87
7 5 0.13
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:13597944 original size:12 final size:12
Alignment explanation
Indices: 13597927--13597951 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13597917 GCCGATTACT
13597927 GTTACTGTTATC
1 GTTACTGTTATC
13597939 GTTACTGTTATC
1 GTTACTGTTATC
13597951 G
1 G
13597952 ATACGACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (12 bp):
GTTACTGTTATC
Found at i:13613506 original size:12 final size:12
Alignment explanation
Indices: 13613481--13613515 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
13613471 CTTGGTTTTT
* *
13613481 GGACACGGGTGA
1 GGACATGGGCGA
13613493 GGACATGGGCGA
1 GGACATGGGCGA
13613505 GGACATGGGCG
1 GGACATGGGCG
13613516 TGTCTAGGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.51, T:0.09
Consensus pattern (12 bp):
GGACATGGGCGA
Found at i:13620615 original size:44 final size:43
Alignment explanation
Indices: 13620567--13620779 Score: 110
Period size: 44 Copynumber: 4.8 Consensus size: 43
13620557 AGATTCGTTG
13620567 TCTTCGATCTGCTCCACTGCTGCTCAGGGAGATAAGATTTACAA
1 TCTTC-ATCTGCTCCACTGCTGCTCAGGGAGATAAGATTTACAA
* * ****
13620611 TCTTCAGTCTGCTCC-CTTGCTACTTCAGGAAGATAAGA-TTGGTG
1 TCTTCA-TCTGCTCCAC-TGCTGC-TCAGGGAGATAAGATTTACAA
* * * * * * * * *
13620655 GCTTAAATCTACTCCCCTACTACCTC-GAGAAGATAAGATTCACCA
1 TCTT-CATCTGCTCCACTGCT-GCTCAG-GGAGATAAGATTTACAA
* * * * *
13620700 TCTTCGATCTACTCCATTACTGCTTCA-AGAGATAAGATCTACAA
1 TCTTC-ATCTGCTCCACTGCTGC-TCAGGGAGATAAGATTTACAA
* *
13620744 TCTTCAGCCTGCTCCACTGTTGCTCAGGGAGATAAG
1 TCTTCA-TCTGCTCCACTGCTGCTCAGGGAGATAAG
13620780 GCTAGTGGCT
Statistics
Matches: 124, Mismatches: 32, Indels: 26
0.68 0.18 0.14
Matches are distributed among these distances:
43 7 0.06
44 82 0.66
45 35 0.28
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
TCTTCATCTGCTCCACTGCTGCTCAGGGAGATAAGATTTACAA
Found at i:13620624 original size:133 final size:130
Alignment explanation
Indices: 13620487--13620960 Score: 519
Period size: 133 Copynumber: 3.6 Consensus size: 130
13620477 AATTTCACCT
13620487 TGCTCCACTGCAGCTCTAGGGAGATAAGGCTAGTGGCTTCAAAT-TGCTCCCCTACTACCTCAGG
1 TGCTCCACTGCAGCTC-AGGGAGATAAGGCTAGTGGCTT-AAATCTGCTCCCCTACTACCTC-GG
***
13620551 AAGATAAGATTCGTTGTCTTCGATCTGCTCCACTGCTGCTCAGGGAGATAAGATTTACAATCTTC
63 AAGATAAGATTCACCGTCTTCGATCTGCTCCACTGCTGCTCAGGGAGATAAGATTTACAATCTTC
13620616 AGTC
128 AG-C
* ** * *
13620620 TGCTCC-CTTGCTA-CTTCAGGAAGATAAGATTGGTGGCTTAAATCTACTCCCCTACTACCTCGA
1 TGCTCCAC-TGC-AGC-TCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTCCCCTACTACCTCG-
* * * * * *
13620683 GAAGATAAGATTCACCATCTTCGATCTACTCCATTACTGCTTCA-AGAGATAAGATCTACAATCT
62 GAAGATAAGATTCACCGTCTTCGATCTGCTCCACTGCTGC-TCAGGGAGATAAGATTTACAATCT
13620747 TCAGCC
126 TCAG-C
** *
13620753 TGCTCCACTGTTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCTGGAA
1 TGCTCCACTGCAGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTCCCCTACTACCTC-GGAA
* *
13620818 GATAAGATTCACCGTCTTTGATCTGCTCCACTGCTGCTCAGGGAGA-AA-ATTTCTACAATCTTT
65 GATAAGATTCACCGTCTTCGATCTGCTCCACTGCTGCTCAGGGAGATAAGA-TT-TACAATCTTC
13620881 AGC
128 AGC
* ** * * * * *
13620884 TTACTCCACTGTTGCTCAGGGAGACAAGGCTACTGACTTAAAATCTGCTCCCATACTACCTTGGG
1 -TGCTCCACTGCAGCTCAGGGAGATAAGGCTAGTGGCTT-AAATCTGCTCCCCTACTACC-TCGG
13620949 AAGATAAGATTC
63 AAGATAAGATTC
13620961 GTCACTTTCG
Statistics
Matches: 288, Mismatches: 38, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
130 1 0.00
131 7 0.02
132 130 0.45
133 142 0.49
134 8 0.03
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (130 bp):
TGCTCCACTGCAGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTCCCCTACTACCTCGGAAG
ATAAGATTCACCGTCTTCGATCTGCTCCACTGCTGCTCAGGGAGATAAGATTTACAATCTTCAGC
Found at i:13621132 original size:177 final size:177
Alignment explanation
Indices: 13620922--13621458 Score: 597
Period size: 177 Copynumber: 3.0 Consensus size: 177
13620912 GCTACTGACT
*
13620922 TAAAATCTGCTCCCATACTACCTTGGGAAGATAAGATTCGTCACTTTCGATCTTTCCCACTACTA
1 TAAAATCTGCTCCCATACTACCTTGGGAAGATAAGATTCG-CACTTTCGATCTTCCCCACTACTA
* * * * *
13620987 TCTTGAAGAGACCAA-ATCT-GAATCATCAGTCTACTCCCTTGCTACCTCAAGAAGATAATACTA
65 TCTTGAGGAGA-CAAGATCTACAATCATCAGTCTACTCCCTTGCTACCTTAGGAAGATAAGACTA
*
13621050 CAATCTTCAGCCTGTTCCCTTGCTACCTCAGGGAAATAAGGCTGGTGGC
129 CAATCTTCAGCCTGCTCCCTTGCTACCTCAGGGAAATAAGGCTGGTGGC
* * * * *
13621099 TAAAATCTGCTCCCCTAC-AACTTCGGGAAGATAAGATTCGCTATCTTT-GATCTGCTCCACTGC
1 TAAAATCTGCTCCCATACTACCTT-GGGAAGATAAGATTCGC-A-CTTTCGATCTTCCCCACTAC
* * * * ** *
13621162 TATC-TCAGGGAGATAAGATCTACAATCTTCAATCTACTTTCTTGCTACCTTAGGAAGATAAGAG
63 TATCTTGA-GGAGACAAGATCTACAATCATCAGTCTACTCCCTTGCTACCTTAGGAAGATAAGAC
* * * *
13621226 TACAATCTTCGGCCTGCTCCTTTACTACCTCA-GGAAGATAAGGCAGGTGGC
127 TACAATCTTCAGCCTGCTCCCTTGCTACCTCAGGGAA-ATAAGGCTGGTGGC
* * * * *
13621277 T-AAATCTGCT-CCATTGCTACCTTGGAAAGATAAGATTCGCCATTTTCAATCTACCCCACTACT
1 TAAAATCTGCTCCCA-TACTACCTTGGGAAGATAAGATTCG-CACTTTCGATCTTCCCCACTACT
* * * * *
13621340 ATCTCGAGGAGACAAGATCTACAATCCTCAGTCTTCTCCCTTGCTACCTTAGGAAGGTAAGGCTA
64 ATCTTGAGGAGACAAGATCTACAATCATCAGTCTACTCCCTTGCTACCTTAGGAAGATAAGACTA
* * *
13621405 CAATCTTCAGCTTGCTCCCTTGCTACCCCAGAGAGAA-AAGGCTGGTGGC
129 CAATCTTCAGCCTGCTCCCTTGCTACCTCAGGGA-AATAAGGCTGGTGGC
13621454 TAAAA
1 TAAAA
13621459 CCTACGCCCT
Statistics
Matches: 295, Mismatches: 50, Indels: 29
0.79 0.13 0.08
Matches are distributed among these distances:
176 14 0.05
177 189 0.64
178 91 0.31
179 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (177 bp):
TAAAATCTGCTCCCATACTACCTTGGGAAGATAAGATTCGCACTTTCGATCTTCCCCACTACTAT
CTTGAGGAGACAAGATCTACAATCATCAGTCTACTCCCTTGCTACCTTAGGAAGATAAGACTACA
ATCTTCAGCCTGCTCCCTTGCTACCTCAGGGAAATAAGGCTGGTGGC
Found at i:13621446 original size:44 final size:44
Alignment explanation
Indices: 13621358--13621447 Score: 103
Period size: 44 Copynumber: 2.0 Consensus size: 44
13621348 GAGACAAGAT
** **
13621358 CTACAATCCTCAGTCTTCTCCCTTGCTACCTTAGGAAGGTAAGG
1 CTACAATCCTCAGTCTTCTCCCTTGCTACCCCAGGAAGAAAAGG
*
13621402 CTACAATCTTCAG-CTTGCTCCCTTGCTACCCCA-GAGAGAAAAGG
1 CTACAATCCTCAGTCTT-CTCCCTTGCTACCCCAGGA-AGAAAAGG
13621446 CT
1 CT
13621448 GGTGGCTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
43 5 0.13
44 34 0.87
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (44 bp):
CTACAATCCTCAGTCTTCTCCCTTGCTACCCCAGGAAGAAAAGG
Found at i:13621469 original size:44 final size:44
Alignment explanation
Indices: 13621421--13621519 Score: 171
Period size: 44 Copynumber: 2.2 Consensus size: 44
13621411 TCAGCTTGCT
13621421 CCCTTGCTACCCCAGAGAGAAAAGGCTGGTGGCTAAAACCTACG
1 CCCTTGCTACCCCAGAGAGAAAAGGCTGGTGGCTAAAACCTACG
* *
13621465 CCCTTGCTACCCTAGAGAGAAAAGGCTGGTGGCTAAAACCTACT
1 CCCTTGCTACCCCAGAGAGAAAAGGCTGGTGGCTAAAACCTACG
*
13621509 CCCTTACTACC
1 CCCTTGCTACC
13621520 TCGGAAAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.19
Consensus pattern (44 bp):
CCCTTGCTACCCCAGAGAGAAAAGGCTGGTGGCTAAAACCTACG
Found at i:13621642 original size:44 final size:44
Alignment explanation
Indices: 13621575--13621754 Score: 218
Period size: 44 Copynumber: 4.1 Consensus size: 44
13621565 TCGAGGAGAC
* * * *
13621575 AAGATCTACAATCCTCAGTCTGCTCCCTTGTTACCTCAGAAAGAT
1 AAGA-CTACAATCTTTAGCCTGCTCCCTTGCTACCTCAGAAAGAT
*
13621620 AAGACTACAATCTTTAGCCTGCTCCCTTGCTACCTCAGGAAGAT
1 AAGACTACAATCTTTAGCCTGCTCCCTTGCTACCTCAGAAAGAT
* * *
13621664 AAGACTATAAT-TTTCAGCCTGTTCCCTTGCTACCTCAGAGAGAT
1 AAGACTACAATCTTT-AGCCTGCTCCCTTGCTACCTCAGAAAGAT
* ** * *
13621708 AAGGCTACAATCTTTAGTATGCTCCTTTGCTACCTCAGAGAGAT
1 AAGACTACAATCTTTAGCCTGCTCCCTTGCTACCTCAGAAAGAT
13621752 AAG
1 AAG
13621755 CTAGTGGCTA
Statistics
Matches: 118, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
43 3 0.03
44 108 0.92
45 7 0.06
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (44 bp):
AAGACTACAATCTTTAGCCTGCTCCCTTGCTACCTCAGAAAGAT
Found at i:13621693 original size:222 final size:221
Alignment explanation
Indices: 13621149--13621713 Score: 627
Period size: 222 Copynumber: 2.5 Consensus size: 221
13621139 CTATCTTTGA
* ** ** * ** *
13621149 TCTGCTCCAC-TGCTATCTCAGGGAGATAAGATCTACAATCTTCAATCTACTTTCTTGCTACCTT
1 TCTGCTCC-CTTGCTACCTCAGAAAGATAAGA-CTACAATCTTCAGCCTGCTCCCTTGCTACCTC
* * * * * *
13621213 AGGAAGATAAGAGTACAATCTTCGGCCTGCTCCTTTACTACCTCAG-GAAGATAAGGCAGGTGGC
64 AGGAAGATAAGACTATAATCTTCAGCCTGCTCCCTTGCTACCTCAGAG-AGATAAGGCTGGTGGC
* * * * *
13621277 TAAATCTGCTCCATTGCTACCTTGGAAAGATAAGATTCGCCATTTTCAATCTACCCCACTACTAT
128 TAAACCTACTCCATTACTACCTCGGAAAGATAAGATTCACCATTTTCAATCTACCCCACTACTAT
13621342 CTCGAGGAGACAAGATCTACAATCCTCAG
193 CTCGAGGAGACAAGATCTACAATCCTCAG
* * * * * * *
13621371 TCTTCTCCCTTGCTACCTTAGGAAGGTAAGGCTACAATCTTCAGCTTGCTCCCTTGCTACCCCA-
1 TCTGCTCCCTTGCTACCTCAGAAAGATAAGACTACAATCTTCAGCCTGCTCCCTTGCTACCTCAG
* * * ** ** * * * *
13621435 GAGAGAAAAGGCTGGT-GGCTAAAACCTACGCCCTTGCTACC-CTAGAGAGAAAAGGCTGGTGGC
66 GA-AGATAAGACT-ATAATCTTCAGCCTGCTCCCTTGCTACCTC-AGAGAGATAAGGCTGGTGGC
* * *
13621498 TAAAACCTACTCCCTTACTACCTCGGAAAGATAAGATTCATCATTTTCGATCTACCCCACTACTA
128 T-AAACCTACTCCATTACTACCTCGGAAAGATAAGATTCACCATTTTCAATCTACCCCACTACTA
13621563 TCTCGAGGAGACAAGATCTACAATCCTCAG
192 TCTCGAGGAGACAAGATCTACAATCCTCAG
* *
13621593 TCTGCTCCCTTGTTACCTCAGAAAGATAAGACTACAATCTTTAGCCTGCTCCCTTGCTACCTCAG
1 TCTGCTCCCTTGCTACCTCAGAAAGATAAGACTACAATCTTCAGCCTGCTCCCTTGCTACCTCAG
* *
13621658 GAAGATAAGACTATAATTTTCAGCCTGTTCCCTTGCTACCTCAGAGAGATAAGGCT
66 GAAGATAAGACTATAATCTTCAGCCTGCTCCCTTGCTACCTCAGAGAGATAAGGCT
13621714 ACAATCTTTA
Statistics
Matches: 273, Mismatches: 61, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
220 3 0.01
221 66 0.24
222 201 0.74
223 3 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (221 bp):
TCTGCTCCCTTGCTACCTCAGAAAGATAAGACTACAATCTTCAGCCTGCTCCCTTGCTACCTCAG
GAAGATAAGACTATAATCTTCAGCCTGCTCCCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAA
ACCTACTCCATTACTACCTCGGAAAGATAAGATTCACCATTTTCAATCTACCCCACTACTATCTC
GAGGAGACAAGATCTACAATCCTCAG
Found at i:13621701 original size:88 final size:88
Alignment explanation
Indices: 13621589--13621754 Score: 244
Period size: 88 Copynumber: 1.9 Consensus size: 88
13621579 TCTACAATCC
* * *
13621589 TCAGTCTGCTCCCTTGTTACCTCAGAAAGATAAGACTACAATCTTTAGCCTGCTCCCTTGCTACC
1 TCAGCCTGCTCCCTTGCTACCTCAGAAAGATAAGACTACAATCTTTAGCATGCTCCCTTGCTACC
13621654 TCAG-GAAGATAAGACTATAATTT
66 TCAGAG-AGATAAGACTATAATTT
* * * * *
13621677 TCAGCCTGTTCCCTTGCTACCTCAGAGAGATAAGGCTACAATCTTTAGTATGCTCCTTTGCTACC
1 TCAGCCTGCTCCCTTGCTACCTCAGAAAGATAAGACTACAATCTTTAGCATGCTCCCTTGCTACC
13621742 TCAGAGAGATAAG
66 TCAGAGAGATAAG
13621755 CTAGTGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
88 68 0.99
89 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (88 bp):
TCAGCCTGCTCCCTTGCTACCTCAGAAAGATAAGACTACAATCTTTAGCATGCTCCCTTGCTACC
TCAGAGAGATAAGACTATAATTT
Found at i:13623206 original size:18 final size:18
Alignment explanation
Indices: 13623185--13623241 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
13623175 TTTTGTTTTG
13623185 TTTTTATTATTTTTAATT
1 TTTTTATTATTTTTAATT
13623203 TTTTTAATT-TTTTTAATT
1 TTTTT-ATTATTTTTAATT
*
13623221 TTTTTA--ATTTTTGATT
1 TTTTTATTATTTTTAATT
13623237 TTTTT
1 TTTTT
13623242 TGGGTCTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
16 13 0.36
17 1 0.03
18 19 0.53
19 3 0.08
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTATTATTTTTAATT
Found at i:13623240 original size:27 final size:25
Alignment explanation
Indices: 13623164--13623242 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 25
13623154 TCTTTCTTCC
*
13623164 TTTTTATTATTTTTTGTTTTGTTTTTA
1 TTTTT-TTAATTTTTGTTTT-TTTTTA
13623191 TTATTTTTAATTTTT-TTAATTTTTTTAA
1 TT-TTTTTAATTTTTGTT--TTTTTTT-A
*
13623219 TTTTTTTAATTTTTGATTTTTTTT
1 TTTTTTTAATTTTTGTTTTTTTTT
13623243 GGGTCTCAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
26 9 0.20
27 27 0.60
28 9 0.20
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (25 bp):
TTTTTTTAATTTTTGTTTTTTTTTA
Found at i:13623241 original size:9 final size:9
Alignment explanation
Indices: 13623185--13623232 Score: 80
Period size: 9 Copynumber: 5.3 Consensus size: 9
13623175 TTTTGTTTTG
13623185 TTTTT-ATT
1 TTTTTAATT
13623193 ATTTTTAATT
1 -TTTTTAATT
13623203 TTTTTAATT
1 TTTTTAATT
13623212 TTTTTAATT
1 TTTTTAATT
13623221 TTTTTAATT
1 TTTTTAATT
13623230 TTT
1 TTT
13623233 GATTTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
9 35 0.92
10 3 0.08
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTAATT
Found at i:13623243 original size:10 final size:9
Alignment explanation
Indices: 13623164--13623242 Score: 63
Period size: 9 Copynumber: 8.9 Consensus size: 9
13623154 TCTTTCTTCC
*
13623164 TTTTTATTA
1 TTTTTTTTA
13623173 TTTTTTGTT-
1 TTTTTT-TTA
*
13623182 TTGTTTTTA
1 TTTTTTTTA
*
13623191 TTATTTTTA
1 TTTTTTTTA
*
13623200 ATTTTTTTA
1 TTTTTTTTA
*
13623209 ATTTTTTTA
1 TTTTTTTTA
*
13623218 ATTTTTTTA
1 TTTTTTTTA
* *
13623227 -ATTTTTGA
1 TTTTTTTTA
13623235 TTTTTTTT
1 TTTTTTTT
13623243 GGGTCTCAAG
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
8 8 0.14
9 48 0.83
10 2 0.03
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:13623813 original size:15 final size:14
Alignment explanation
Indices: 13623775--13623813 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
13623765 TTCCATGATC
13623775 TTTTTTTTTTTACT
1 TTTTTTTTTTTACT
*
13623789 TTTTACTTTTTTACT
1 TTTT-TTTTTTTACT
*
13623804 TTTGTTTTTT
1 TTTTTTTTTT
13623814 CTTTTTGGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTTTACT
Found at i:13628550 original size:17 final size:18
Alignment explanation
Indices: 13628530--13628573 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
13628520 ATGAAATTTT
13628530 AAAATATAA-CAAA-TAAA
1 AAAATA-AACCAAATTAAA
13628547 AAAATAAACCAAATTAAA
1 AAAATAAACCAAATTAAA
13628565 ATAAATAAA
1 A-AAATAAA
13628574 ATGTGATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 10 0.42
18 5 0.21
19 7 0.29
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAATAAACCAAATTAAA
Found at i:13628969 original size:12 final size:12
Alignment explanation
Indices: 13628952--13628976 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13628942 ACCCAAAACC
13628952 CTTAGCCCAAAA
1 CTTAGCCCAAAA
13628964 CTTAGCCCAAAA
1 CTTAGCCCAAAA
13628976 C
1 C
13628977 ACTAACCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CTTAGCCCAAAA
Found at i:13629753 original size:12 final size:12
Alignment explanation
Indices: 13629736--13629784 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
13629726 TTTTTTGTTG
*
13629736 TTTATATTTTTA
1 TTTATATTATTA
13629748 TTTATATTATTA
1 TTTATATTATTA
13629760 -TTATTATTATTA
1 TTTA-TATTATTA
13629772 -TTATTATTATTA
1 TTTA-TATTATTA
13629784 T
1 T
13629785 CTCCGTGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 3 0.09
12 31 0.91
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:13629822 original size:19 final size:17
Alignment explanation
Indices: 13629797--13629834 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
13629787 CCGTGACTAT
*
13629797 TATTATTATT-TTGTTA
1 TATTACTATTATTGTTA
13629813 TATTACTATTATTGTTA
1 TATTACTATTATTGTTA
13629830 TATTA
1 TATTA
13629835 TCACTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (17 bp):
TATTACTATTATTGTTA
Found at i:13629842 original size:20 final size:21
Alignment explanation
Indices: 13629817--13629856 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
13629807 TTGTTATATT
*
13629817 ACTATTATTGTTA-TATTATC
1 ACTATTATTCTTACTATTATC
*
13629837 ACTATTTTTCTTACTATTAT
1 ACTATTATTCTTACTATTAT
13629857 TATTACTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57
Consensus pattern (21 bp):
ACTATTATTCTTACTATTATC
Found at i:13629876 original size:3 final size:3
Alignment explanation
Indices: 13629752--13629861 Score: 73
Period size: 3 Copynumber: 36.7 Consensus size: 3
13629742 TTTTTATTTA
* * *
13629752 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CTCCGT GAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -T--AT TAT TAT TAT
* * * * * *
13629800 TAT TAT T-T TGT TA- TAT TAC TAT TAT TGT TA- TAT TAT CAC TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
13629845 TCT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
13629862 CTACAACTAT
Statistics
Matches: 81, Mismatches: 20, Indels: 12
0.72 0.18 0.11
Matches are distributed among these distances:
2 6 0.07
3 73 0.90
4 1 0.01
6 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:13630019 original size:21 final size:21
Alignment explanation
Indices: 13629972--13630020 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
13629962 TTTTTCTCTG
13629972 TTTTATTACTATTATTAATAT
1 TTTTATTACTATTATTAATAT
** **
13629993 CATTATTACTATTATTTTTAT
1 TTTTATTACTATTATTAATAT
13630014 TTTTATT
1 TTTTATT
13630021 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATTACTATTATTAATAT
Found at i:13630169 original size:15 final size:15
Alignment explanation
Indices: 13630145--13630175 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13630135 TATTATTTTC
13630145 TATTTATTACTATTA
1 TATTTATTACTATTA
*
13630160 TATTTGTTACTATTA
1 TATTTATTACTATTA
13630175 T
1 T
13630176 TATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (15 bp):
TATTTATTACTATTA
Found at i:13630192 original size:18 final size:18
Alignment explanation
Indices: 13630155--13630192 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
13630145 TATTTATTAC
*
13630155 TATTATATTTGTTACTAT
1 TATTATATTTGTTACCAT
13630173 TATTATATTT-TTACCCAT
1 TATTATATTTGTTA-CCAT
13630191 TA
1 TA
13630193 CTCTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (18 bp):
TATTATATTTGTTACCAT
Found at i:13633847 original size:15 final size:15
Alignment explanation
Indices: 13633827--13633857 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13633817 TTTACTTTCC
*
13633827 AGAGAGGTAGAAAAG
1 AGAGAGGTAAAAAAG
13633842 AGAGAGGTAAAAAAG
1 AGAGAGGTAAAAAAG
13633857 A
1 A
13633858 AAATCTAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.06
Consensus pattern (15 bp):
AGAGAGGTAAAAAAG
Found at i:13642139 original size:205 final size:205
Alignment explanation
Indices: 13641787--13642371 Score: 917
Period size: 205 Copynumber: 2.9 Consensus size: 205
13641777 GTAATAGGCC
* *
13641787 ACACATAGCAGATCTCACCTTCAGATGATTTCGCTGAAGTAGATCCAAGATGGTTTGGCATCCTT
1 ACACATAGCAGATCTCACCTTCAGATGATTTCACTGAAGCAGATCCAAGATGGTTTGGCATCCTT
*
13641852 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATG-AAGCAA
66 GTGTTTACAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTAC-ATGAAAGCAA
13641916 ATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG
130 ATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG
13641981 ATGGAGAGCAG
195 ATGGAGAGCAG
* *
13641992 ACACATAGCAGATCTCGCCTTCAGACGATTTCACTGAAGCAGATCCAAGATGGTTTGGCATCCTT
1 ACACATAGCAGATCTCACCTTCAGATGATTTCACTGAAGCAGATCCAAGATGGTTTGGCATCCTT
*
13642057 GTGTTTACAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTACAAGAAAGCAAA
66 GTGTTTACAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTACATGAAAGCAAA
*
13642122 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
131 TCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
13642187 TGGAGAGCAG
196 TGGAGAGCAG
* *
13642197 ACACATAGCAGATCTCACCTTCGGATG-TTT-ATGCTGAAGCGGATCCAAGATGGTTTGGCATCC
1 ACACATAGCAGATCTCACCTTCAGATGATTTCA--CTGAAGCAGATCCAAGATGGTTTGGCATCC
* * * * * * * *
13642260 TTATGCTTATAAGGAGCAAATCGAA-TCATAGTTGATTTGGCTTTCACGTGCTTACGTTAAAGCA
64 TTGTGTTTACAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTACATGAAAGCA
* * * * *
13642324 AATCTAAGATGATTTGGCATCTCTGTATTGCCAGGGAACAAATCGAAG
129 AATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAG
13642372 AAATAGATCT
Statistics
Matches: 351, Mismatches: 26, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
203 1 0.00
204 81 0.23
205 269 0.77
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (205 bp):
ACACATAGCAGATCTCACCTTCAGATGATTTCACTGAAGCAGATCCAAGATGGTTTGGCATCCTT
GTGTTTACAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTACATGAAAGCAAA
TCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
TGGAGAGCAG
Found at i:13642507 original size:13 final size:13
Alignment explanation
Indices: 13642489--13642524 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
13642479 GTGTTTATGG
13642489 GGAACAGATCGAA
1 GGAACAGATCGAA
13642502 GGAACAGATCGAA
1 GGAACAGATCGAA
13642515 -GAAGCAGATC
1 GGAA-CAGATC
13642525 AAGAACTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.44, C:0.17, G:0.31, T:0.08
Consensus pattern (13 bp):
GGAACAGATCGAA
Found at i:13642729 original size:12 final size:12
Alignment explanation
Indices: 13642712--13642736 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13642702 ACCCAAAACC
13642712 CTTAGCCCAAAA
1 CTTAGCCCAAAA
13642724 CTTAGCCCAAAA
1 CTTAGCCCAAAA
13642736 C
1 C
13642737 ACTAACCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CTTAGCCCAAAA
Found at i:13643517 original size:12 final size:12
Alignment explanation
Indices: 13643500--13643549 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
13643490 TTTTTTGTTG
*
13643500 TTTATATTTTTA
1 TTTATATTATTA
13643512 TTTATATTATTA
1 TTTATATTATTA
13643524 -TTAGTATTATTA
1 TTTA-TATTATTA
13643536 -TTATTATTATTA
1 TTTA-TATTATTA
13643548 TT
1 TT
13643550 ATTATTATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 3 0.09
12 30 0.88
13 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:13643595 original size:19 final size:17
Alignment explanation
Indices: 13643570--13643607 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
13643560 CCGTGATTAT
*
13643570 TATTATTATT-TTGTTA
1 TATTACTATTATTGTTA
13643586 TATTACTATTATTGTTA
1 TATTACTATTATTGTTA
13643603 TATTA
1 TATTA
13643608 TCACTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (17 bp):
TATTACTATTATTGTTA
Found at i:13643608 original size:22 final size:22
Alignment explanation
Indices: 13643504--13643608 Score: 68
Period size: 24 Copynumber: 4.6 Consensus size: 22
13643494 TTGTTGTTTA
* *
13643504 TATTTTTAT-TTATATTATTAT
1 TATTATTATATTATATTACTAT
* *
13643525 TAGTATTATTATTATTATTATTAT
1 TATTATTA-TATTA-TATTACTAT
* ** *
13643549 TATTATTATCTCCGTGATTATTAT
1 TATTATTATAT-TAT-ATTACTAT
* *
13643573 TATTATTTTGTTATATTACTAT
1 TATTATTATATTATATTACTAT
*
13643595 TATTGTTATATTAT
1 TATTATTATATTAT
13643609 CACTATTTTT
Statistics
Matches: 65, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
21 6 0.09
22 19 0.29
23 7 0.11
24 33 0.51
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.63
Consensus pattern (22 bp):
TATTATTATATTATATTACTAT
Found at i:13643615 original size:20 final size:21
Alignment explanation
Indices: 13643590--13643629 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
13643580 TTGTTATATT
*
13643590 ACTATTATTGTTA-TATTATC
1 ACTATTATTCTTACTATTATC
*
13643610 ACTATTTTTCTTACTATTAT
1 ACTATTATTCTTACTATTAT
13643630 TATTACTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57
Consensus pattern (21 bp):
ACTATTATTCTTACTATTATC
Found at i:13643649 original size:3 final size:3
Alignment explanation
Indices: 13643516--13643634 Score: 91
Period size: 3 Copynumber: 39.7 Consensus size: 3
13643506 TTTTTATTTA
* *
13643516 TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CTCCGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -T--AT
* * * *
13643564 GAT TAT TAT TAT TAT T-T TGT TA- TAT TAC TAT TAT TGT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
13643609 CAC TAT TTT TCT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
13643635 CTACAACTAT
Statistics
Matches: 90, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
2 6 0.07
3 82 0.91
4 1 0.01
6 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:13643817 original size:21 final size:21
Alignment explanation
Indices: 13643770--13643818 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
13643760 TTTTTCTCTG
13643770 TTTTATTACTATTATTAATAT
1 TTTTATTACTATTATTAATAT
** **
13643791 CATTATTACTATTATTTTTAT
1 TTTTATTACTATTATTAATAT
13643812 TTTTATT
1 TTTTATT
13643819 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATTACTATTATTAATAT
Found at i:13643967 original size:15 final size:15
Alignment explanation
Indices: 13643943--13643973 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13643933 TATTATTTTC
13643943 TATTTATTACTATTA
1 TATTTATTACTATTA
*
13643958 TATTTGTTACTATTA
1 TATTTATTACTATTA
13643973 T
1 T
13643974 TATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (15 bp):
TATTTATTACTATTA
Found at i:13643990 original size:18 final size:18
Alignment explanation
Indices: 13643953--13643990 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
13643943 TATTTATTAC
*
13643953 TATTATATTTGTTACTAT
1 TATTATATTTGTTACCAT
13643971 TATTATATTT-TTACCCAT
1 TATTATATTTGTTA-CCAT
13643989 TA
1 TA
13643991 CTCTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (18 bp):
TATTATATTTGTTACCAT
Found at i:13647645 original size:15 final size:15
Alignment explanation
Indices: 13647625--13647655 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13647615 TTTACTTTCC
*
13647625 AGAGAGGTAGAAAAG
1 AGAGAGGTAAAAAAG
13647640 AGAGAGGTAAAAAAG
1 AGAGAGGTAAAAAAG
13647655 A
1 A
13647656 AAATCTAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.06
Consensus pattern (15 bp):
AGAGAGGTAAAAAAG
Found at i:13655943 original size:205 final size:206
Alignment explanation
Indices: 13655585--13656374 Score: 1252
Period size: 205 Copynumber: 3.9 Consensus size: 206
13655575 GTAATAGGCC
* *
13655585 ACACATAGCAGATCTCACCTTCAGATGATTT-CGCTGAAGTAGATCCAAGATGGTTTGGCATCCT
1 ACACATAGCAGATCTCACCTTCAGATGATTTATGCTGAAGCAGATCCAAGATGGTTTGGCATCCT
* *
13655649 TGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACATGATTACGATGAAGCAA
66 TGTGTTTACAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTACGATGAAGCAA
*
13655714 ATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG
131 ATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG
13655779 ATGGAGAGCAG
196 ATGGAGAGCAG
* * * * *
13655790 ACTCATAGCAGATCTGACCGTCAGATG-TTTATGCTGAAACAGATCCAAGATGGTTGGGCATCCT
1 ACACATAGCAGATCTCACCTTCAGATGATTTATGCTGAAGCAGATCCAAGATGGTTTGGCATCCT
*
13655854 TGTGTTTATAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTACGATGAAGCAA
66 TGTGTTTACAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTACGATGAAGCAA
13655919 ATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG
131 ATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG
13655984 ATGGAGAGCAG
196 ATGGAGAGCAG
* *
13655995 ACACATAGCAGATCTCGCCTTCAGACGATTTCA--CTGAAGCAGATCCAAGATGGTTTGGCATCC
1 ACACATAGCAGATCTCACCTTCAGATGATTT-ATGCTGAAGCAGATCCAAGATGGTTTGGCATCC
*
13656058 TTGTGTTTACAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTAC-AAGAAAGC
65 TTGTGTTTACAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTACGATG-AAGC
*
13656122 AAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTT
129 AAATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTT
13656187 TGATGGAGAGCAG
194 TGATGGAGAGCAG
* *
13656200 ACACATAGCAGATCTCACCTTCGGATG-TTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCT
1 ACACATAGCAGATCTCACCTTCAGATGATTTATGCTGAAGCAGATCCAAGATGGTTTGGCATCCT
* * * * * * * *
13656264 TATGCTTATAAGGAGCAAATCGAA-TCATAGTTGATTTGGCTTTCACGTGCTTACGTTAAAGCAA
66 TGTGTTTACAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTACGATGAAGCAA
* * * *
13656328 ATCTAAGATGATTTGGCATCTCTGTATTGCCAGGGAACAAATCGAAG
131 ATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGAACGAATCGAAG
13656375 AAATAGATCT
Statistics
Matches: 539, Mismatches: 39, Indels: 15
0.91 0.07 0.03
Matches are distributed among these distances:
203 1 0.00
204 84 0.16
205 450 0.83
206 3 0.01
207 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (206 bp):
ACACATAGCAGATCTCACCTTCAGATGATTTATGCTGAAGCAGATCCAAGATGGTTTGGCATCCT
TGTGTTTACAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTACGATGAAGCAA
ATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG
ATGGAGAGCAG
Found at i:13656510 original size:13 final size:13
Alignment explanation
Indices: 13656492--13656527 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
13656482 GTGTTTATGG
13656492 GGAACAGATCGAA
1 GGAACAGATCGAA
13656505 GGAACAGATCGAA
1 GGAACAGATCGAA
13656518 -GAAGCAGATC
1 GGAA-CAGATC
13656528 AAGAACTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.44, C:0.17, G:0.31, T:0.08
Consensus pattern (13 bp):
GGAACAGATCGAA
Found at i:13656732 original size:12 final size:12
Alignment explanation
Indices: 13656715--13656739 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13656705 ACCCAAAACC
13656715 CTTAGCCCAAAA
1 CTTAGCCCAAAA
13656727 CTTAGCCCAAAA
1 CTTAGCCCAAAA
13656739 C
1 C
13656740 ACTAACCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CTTAGCCCAAAA
Found at i:13661853 original size:14 final size:15
Alignment explanation
Indices: 13661829--13661857 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13661819 AAATGTATAC
13661829 AAAAATAATTTTTTT
1 AAAAATAATTTTTTT
13661844 AAAAAT-ATTTTTTT
1 AAAAATAATTTTTTT
13661858 CAACATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAAAATAATTTTTTT
Found at i:13663565 original size:23 final size:23
Alignment explanation
Indices: 13663539--13663632 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
13663529 AAGTTAGAAG
13663539 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
13663562 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
13663585 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
13663608 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
13663631 AG
1 AG
13663633 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:13668072 original size:23 final size:23
Alignment explanation
Indices: 13668046--13668139 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
13668036 AAGTTAGAAG
13668046 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
13668069 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
13668092 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
13668115 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
13668138 AG
1 AG
13668140 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:13673683 original size:21 final size:21
Alignment explanation
Indices: 13673644--13673687 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13673634 TAGCACATGG
13673644 CCATGTGATAGAGGCACACGC
1 CCATGTGATAGAGGCACACGC
*
13673665 CCATGTGA-AGCAGGGACACGC
1 CCATGTGATAG-AGGCACACGC
13673686 CC
1 CC
13673688 GTATGAGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.27, C:0.32, G:0.30, T:0.11
Consensus pattern (21 bp):
CCATGTGATAGAGGCACACGC
Found at i:13674357 original size:5 final size:5
Alignment explanation
Indices: 13674349--13674386 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
13674339 TTCACTTCCA
*
13674349 AAAAT AAAAT -ACA- AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
13674387 CTAAAACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:13674365 original size:13 final size:14
Alignment explanation
Indices: 13674347--13674386 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
13674337 ACTTCACTTC
13674347 CAAAAATAAAAT-A
1 CAAAAATAAAATAA
13674360 CAAAAATAAAATAA
1 CAAAAATAAAATAA
*
13674374 AATAAAATAAAAT
1 CA-AAAATAAAAT
13674387 CTAAAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 2 0.08
15 10 0.42
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (14 bp):
CAAAAATAAAATAA
Found at i:13676661 original size:12 final size:12
Alignment explanation
Indices: 13676644--13676670 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13676634 TTAATATGGT
13676644 AAATGATAATTA
1 AAATGATAATTA
13676656 AAATGATAATTA
1 AAATGATAATTA
13676668 AAA
1 AAA
13676671 CAAAACTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (12 bp):
AAATGATAATTA
Found at i:13676948 original size:21 final size:20
Alignment explanation
Indices: 13676911--13676950 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13676901 TAACCATGAG
*
13676911 TTTTGAAGTTTCTTGATAGA
1 TTTTGAAGTTTCATGATAGA
*
13676931 TTTTGAATGTTTGATGATAG
1 TTTTGAA-GTTTCATGATAG
13676951 TTATACAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.25, C:0.03, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTTGAAGTTTCATGATAGA
Found at i:13682423 original size:31 final size:31
Alignment explanation
Indices: 13682366--13682448 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
13682356 TATCATTTAG
* *
13682366 ATTTGCATA-TTATACCATGTGATCTATCAT
1 ATTTGCATATTTATACCATGTAATCTATCAC
* * *
13682396 ATTTTCATATTTGTACCTTGTAATCTATCAC
1 ATTTGCATATTTATACCATGTAATCTATCAC
*
13682427 ATTTGCATATTTATACCCTGTA
1 ATTTGCATATTTATACCATGTA
13682449 CTCTCACAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 8 0.18
31 36 0.82
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (31 bp):
ATTTGCATATTTATACCATGTAATCTATCAC
Found at i:13695715 original size:30 final size:31
Alignment explanation
Indices: 13695679--13695758 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
13695669 CAAGAAAACC
* *
13695679 GAATAAAGAAATCCAAGATAGAGA-ATCCCG
1 GAATAAAGAAATCCAAGATAAAGAGATCCAG
*
13695709 GAATAAAGAAATCC-AGAATAAAGAGATCTAG
1 GAATAAAGAAATCCAAG-ATAAAGAGATCCAG
*
13695740 G-ATAAAGAAACCCAAGATA
1 GAATAAAGAAATCCAAGATA
13695759 CGATACTATG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
29 2 0.05
30 34 0.79
31 7 0.16
ACGTcount: A:0.54, C:0.14, G:0.19, T:0.14
Consensus pattern (31 bp):
GAATAAAGAAATCCAAGATAAAGAGATCCAG
Found at i:13695758 original size:15 final size:15
Alignment explanation
Indices: 13695681--13695758 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
13695671 AGAAAACCGA
13695681 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
13695696 ATAGAG-AATCCCGG
1 ATAAAGAAATCCAAG
13695710 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* * *
13695725 AATAAAGAGATCTAGG
1 -ATAAAGAAATCCAAG
*
13695741 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
13695756 ATA
1 ATA
13695759 CGATACTATG
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
14 6 0.12
15 36 0.75
16 6 0.12
ACGTcount: A:0.54, C:0.14, G:0.18, T:0.14
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:13698790 original size:93 final size:93
Alignment explanation
Indices: 13698681--13698853 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
13698671 CGCCCATAAG
* *
13698681 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
13698746 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* * * *
13698774 CGAACTCATACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
13698839 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
13698854 CAAATATCCC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:13698849 original size:46 final size:46
Alignment explanation
Indices: 13698674--13698849 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
13698664 TGTAACCCGC
* * *
13698674 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACATTTGCAT
* * *
13698720 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* * *
13698770 -C-TCA-CGAACTCATACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACATTTGCAT
* * *
13698813 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA
13698850 TGCCCAAATA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 61 0.57
47 27 0.25
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:13702361 original size:131 final size:131
Alignment explanation
Indices: 13702127--13702380 Score: 445
Period size: 131 Copynumber: 1.9 Consensus size: 131
13702117 ATGGATGGAT
* * *
13702127 TGACTCCTAATTGTCTCTGGTTAATTTATAATGAATTTCCAAAGTCGGAACAGGAAATCCAGAAA
1 TGACTCCTAATTATCTCTGGTTAATTTATAATGAATTTCCAAACTCGAAACAGGAAATCCAGAAA
*
13702192 CCATTCTGGCCCTGTCTCACAAGAACCTGAATATCTCTTAACATACTGTCCGTATGATTGTTTGC
66 CCATTCTGGCCCTGTCTCACAAGAACCTGAATATCTCTTAACATACTGTCCATATGATTGTTTGC
13702257 A
131 A
*
13702258 TGACTCCTAATTATCTCTGGTTAATTTATAATGAATTTCCAAACTCGAAACAGGGAATCCAGAAA
1 TGACTCCTAATTATCTCTGGTTAATTTATAATGAATTTCCAAACTCGAAACAGGAAATCCAGAAA
* *
13702323 CCGTTCTGGCCCTGTCTCACGAGAACCTGAATATCTCTTAACATACTGTCCATATGAT
66 CCATTCTGGCCCTGTCTCACAAGAACCTGAATATCTCTTAACATACTGTCCATATGAT
13702381 AATTTCGTTA
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
131 116 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.31
Consensus pattern (131 bp):
TGACTCCTAATTATCTCTGGTTAATTTATAATGAATTTCCAAACTCGAAACAGGAAATCCAGAAA
CCATTCTGGCCCTGTCTCACAAGAACCTGAATATCTCTTAACATACTGTCCATATGATTGTTTGC
A
Found at i:13703366 original size:79 final size:81
Alignment explanation
Indices: 13703249--13703429 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 81
13703239 GCTACTCGTT
* *
13703249 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
13703313 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* * **
13703329 CAAATGCCTTCGGG-CTTAGCTCGGA-ATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
13703392 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
13703409 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
13703430 TGGACATCAT
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
78 4 0.05
79 54 0.63
80 28 0.33
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:13703427 original size:40 final size:40
Alignment explanation
Indices: 13703249--13703429 Score: 217
Period size: 40 Copynumber: 4.5 Consensus size: 40
13703239 GCTACTCGTT
* *
13703249 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
13703289 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
13703329 CAAATGCCTTCGGG-CTTAGCTCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
13703368 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
13703409 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
13703430 TGGACATCAT
Statistics
Matches: 120, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.02
39 31 0.26
40 75 0.62
41 12 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:13704108 original size:100 final size:100
Alignment explanation
Indices: 13703935--13704131 Score: 376
Period size: 100 Copynumber: 2.0 Consensus size: 100
13703925 TGCAACACCA
*
13703935 ATCTCCTTCCTATGGCCGAATATGCATGTCTATGTTGGGGCCGATTTCAACACTTAATACATTCT
1 ATCTCCTTCCTATGGCCGAATATGCATGTCTATGTTGGGGCCGATTGCAACACTTAATACATTCT
13704000 ACAAGTATGGTCACTTGTATTGACTAAACACCCTT
66 ACAAGTATGGTCACTTGTATTGACTAAACACCCTT
*
13704035 ATCTCCTTCCTATGGCCGAATATGCATGTCTATGTTGGGGCCGATTGCAACACTTAGTACATTCT
1 ATCTCCTTCCTATGGCCGAATATGCATGTCTATGTTGGGGCCGATTGCAACACTTAATACATTCT
13704100 ACAAGTATGGTCACTTGTATTGACTAAACACC
66 ACAAGTATGGTCACTTGTATTGACTAAACACC
13704132 ATTTTGTTTC
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 95 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (100 bp):
ATCTCCTTCCTATGGCCGAATATGCATGTCTATGTTGGGGCCGATTGCAACACTTAATACATTCT
ACAAGTATGGTCACTTGTATTGACTAAACACCCTT
Found at i:13705308 original size:25 final size:25
Alignment explanation
Indices: 13705275--13705606 Score: 132
Period size: 25 Copynumber: 13.3 Consensus size: 25
13705265 CATCAACAAT
13705275 CTTTCCATACAATATGCCACAATA-G
1 CTTTCCATACAATATGCCACAA-AGG
*
13705300 CTTTGCATA-AGAT-TAGCCACAAAGG
1 CTTTCCATACA-ATAT-GCCACAAAGG
* *
13705325 CTTTCCAGACAATACGCCACAAAGG
1 CTTTCCATACAATATGCCACAAAGG
* *
13705350 C-TTCTC-T-TAATATTAGCGACAAAGG
1 CTTTC-CATACAATA-T-GCCACAAAGG
* * * *
13705375 CTTTCTAGATAATACGCCACAAAGG
1 CTTTCCATACAATATGCCACAAAGG
* * * *
13705400 CTTTCTAGATAATAAGCCACAAAGG
1 CTTTCCATACAATATGCCACAAAGG
* * * *
13705425 ATTTACATATAATACGCCACAAAGAG
1 CTTTCCATACAATATGCCACAAAG-G
* *
13705451 -TTTTCATA-AGAT-TAGCCATAAAGG
1 CTTTCCATACA-ATAT-GCCACAAAGG
* * *
13705475 CTTTCCAAATAATATGCCATAAAGG
1 CTTTCCATACAATATGCCACAAAGG
* *
13705500 TTTTTCATA-AGAT-TAGCCACAAAGG
1 CTTTCCATACA-ATAT-GCCACAAAGG
* ** *
13705525 CTTTCCAGACAATACACCACAAAAG
1 CTTTCCATACAATATGCCACAAAGG
* * *
13705550 CTTTTCATA-AGAT-TAACTACAAAGG
1 CTTTCCATACA-ATAT-GCCACAAAGG
* * * * *
13705575 CTTTCTAGATATTATGGCACAAAGG
1 CTTTCCATACAATATGCCACAAAGG
13705600 CTTTCCA
1 CTTTCCA
13705607 GTTAATCCGT
Statistics
Matches: 236, Mismatches: 46, Indels: 50
0.71 0.14 0.15
Matches are distributed among these distances:
23 4 0.02
24 11 0.05
25 206 0.87
26 10 0.04
27 5 0.02
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (25 bp):
CTTTCCATACAATATGCCACAAAGG
Found at i:13705365 original size:50 final size:50
Alignment explanation
Indices: 13705275--13705603 Score: 335
Period size: 50 Copynumber: 6.6 Consensus size: 50
13705265 CATCAACAAT
* * * *
13705275 CTTTCCATACAATATGCCACAATA-GCTTTGCATAAGATTAGCCACAAAGG
1 CTTTCCAGATAATACGCCACAA-AGGCTTTTCATAAGATTAGCCACAAAGG
* * * * *
13705325 CTTTCCAGACAATACGCCACAAAGGCTTCTCTTAATATTAGCGACAAAGG
1 CTTTCCAGATAATACGCCACAAAGGCTTTTCATAAGATTAGCCACAAAGG
*
13705375 CTTTCTAGATAATACGCCACAAAGGC-TTTC-T-AGATAATAAGCCACAAAGG
1 CTTTCCAGATAATACGCCACAAAGGCTTTTCATAAGAT--T-AGCCACAAAGG
* * * *
13705425 ATTTACATATAATACGCCACAAAGAG-TTTTCATAAGATTAGCCATAAAGG
1 CTTTCCAGATAATACGCCACAAAG-GCTTTTCATAAGATTAGCCACAAAGG
* * * *
13705475 CTTTCCAAATAATATGCCATAAAGGTTTTTCATAAGATTAGCCACAAAGG
1 CTTTCCAGATAATACGCCACAAAGGCTTTTCATAAGATTAGCCACAAAGG
* * * * *
13705525 CTTTCCAGACAATACACCACAAAAGCTTTTCATAAGATTAACTACAAAGG
1 CTTTCCAGATAATACGCCACAAAGGCTTTTCATAAGATTAGCCACAAAGG
* * * *
13705575 CTTTCTAGATATTATGGCACAAAGGCTTT
1 CTTTCCAGATAATACGCCACAAAGGCTTT
13705604 CCAGTTAATC
Statistics
Matches: 231, Mismatches: 39, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
47 3 0.01
48 1 0.00
49 6 0.03
50 210 0.91
51 6 0.03
52 1 0.00
53 4 0.02
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (50 bp):
CTTTCCAGATAATACGCCACAAAGGCTTTTCATAAGATTAGCCACAAAGG
Done.