Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 140 of 318
Found at i:43425556 original size:29 final size:30
Alignment explanation
Indices: 43425517--43425595 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
43425507 CTTAATAATC
43425517 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
43425547 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
43425576 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
43425596 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:43429322 original size:47 final size:47
Alignment explanation
Indices: 43429258--43429519 Score: 225
Period size: 47 Copynumber: 5.6 Consensus size: 47
43429248 ATCCATAAGT
43429258 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
* * * * * * * * *
43429305 GAACTCGGACTCAACTCAACAAGTTCAGACG-TTCGCATCCA--TAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TTACATTTCA-C
* * *
43429351 GAACTCAGACTCAACTCAACGACTTCGAATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
* * * * * * *
43429398 AAATTCAGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--TTCA-C
43429444 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
* *
43429491 GAACTCGGACTCAACTTAACAAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
43429520 CGTTCGCATC
Statistics
Matches: 163, Mismatches: 38, Indels: 28
0.71 0.17 0.12
Matches are distributed among these distances:
42 2 0.01
43 4 0.02
44 1 0.01
45 4 0.02
46 56 0.34
47 85 0.52
48 4 0.02
49 1 0.01
50 4 0.02
51 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:43429345 original size:93 final size:93
Alignment explanation
Indices: 43429211--43429561 Score: 551
Period size: 93 Copynumber: 3.8 Consensus size: 93
43429201 CGCCCATAAG
** * *
43429211 CGAACTCGGACTCAACTCAATGAGCTT-GGGCATTCGTATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACAAG-TTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
43429275 AACGAGTTCGGATGCCTAGTTACATTTCA
65 AACGAGTTCGGATGCCTAGTTACATTTCA
* * *
43429304 CGAACTCGGACTCAACTCAACAAGTTCAGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
43429369 ACGACTTCGAATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
* * * *
43429397 CAAATTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
43429462 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
* *
43429490 CGAACTCGGACTCAACTTAACAAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
43429555 ACGAGTT
66 ACGAGTT
43429562 TGGAAGCCCA
Statistics
Matches: 233, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
92 2 0.01
93 231 0.99
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:43429472 original size:46 final size:46
Alignment explanation
Indices: 43429204--43429561 Score: 238
Period size: 46 Copynumber: 7.7 Consensus size: 46
43429194 TGTAACCCGC
* * *
43429204 CCATAAGCGAACTCGGACTCAACTCAATGAGCTT-GGGCATTCGTAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCAT
* *
43429250 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * * * *
43429300 --TTCA-CGAACTCGGACTCAACTCAACAAGTTCAGACGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * * *
43429343 CCATAAGTGAACTCAGACTCAACTCAACGACTTC-GA-ATGC-CTAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--T
* * * * *
43429389 ACATTTCA-CAAATTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
43429436 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * * * *
43429486 --TTCA-CGAACTCGGACTCAACTTAACAAGTTCGGACGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
43429529 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTT
43429562 TGGAAGCCCA
Statistics
Matches: 238, Mismatches: 46, Indels: 56
0.70 0.14 0.16
Matches are distributed among these distances:
42 4 0.02
43 7 0.03
44 5 0.02
45 10 0.04
46 106 0.45
47 80 0.34
48 8 0.03
49 6 0.03
50 8 0.03
51 4 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:43429505 original size:186 final size:186
Alignment explanation
Indices: 43429219--43429558 Score: 610
Period size: 186 Copynumber: 1.8 Consensus size: 186
43429209 AGCGAACTCG
* * *
43429219 GACTCAACTCAATGAGCTTGGGCATTCGTATCCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 GACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTC
43429284 GGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACAAGTTCAGACGTTCGCATCCATAA
66 GGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACAAGTTCAGACGTTCGCATCCATAA
43429349 GTGAACTCAGACTCAACTCAACGACTTCGAATGCCTAGTTACATTTCACAAATTCA
131 GTGAACTCAGACTCAACTCAACGACTTCGAATGCCTAGTTACATTTCACAAATTCA
43429405 GACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
1 GACTCAACTCAACGAGCTT-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
* *
43429469 CGGATGCCTAGTTACATTTCACGAACTCGGACTCAACTTAACAAGTTCGGACGTTCGCATCCATA
65 CGGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACAAGTTCAGACGTTCGCATCCATA
*
43429534 AGTGAACTCGGACTCAACTCAACGA
130 AGTGAACTCAGACTCAACTCAACGA
43429559 GTTTGGAAGC
Statistics
Matches: 147, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
185 2 0.01
186 145 0.99
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (186 bp):
GACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTC
GGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACAAGTTCAGACGTTCGCATCCATAA
GTGAACTCAGACTCAACTCAACGACTTCGAATGCCTAGTTACATTTCACAAATTCA
Found at i:43451953 original size:4 final size:4
Alignment explanation
Indices: 43451944--43451973 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
43451934 AAGGGAGCGT
43451944 GGCA GGCA GGCA GGCA GGCA GGCA GGCA GG
1 GGCA GGCA GGCA GGCA GGCA GGCA GGCA GG
43451974 TTCGTCACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.53, T:0.00
Consensus pattern (4 bp):
GGCA
Found at i:43456992 original size:43 final size:43
Alignment explanation
Indices: 43456931--43457016 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
43456921 TCCATGTCGC
*
43456931 AACACCACATCTGTAAAGTCATGACATTGAAACTGGACAATCA
1 AACACCACATCTGTAAAGTCAAGACATTGAAACTGGACAATCA
43456974 AACACCACATCTGTAAAGTCAAGACATTGAAACTGGACAATCA
1 AACACCACATCTGTAAAGTCAAGACATTGAAACTGGACAATCA
43457017 CTTGGGACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (43 bp):
AACACCACATCTGTAAAGTCAAGACATTGAAACTGGACAATCA
Found at i:43458956 original size:46 final size:45
Alignment explanation
Indices: 43458893--43459057 Score: 159
Period size: 46 Copynumber: 3.5 Consensus size: 45
43458883 CTAATTGTTT
* *
43458893 TGTAGGTTCAACCCTTACGAGTGATTAGACACTATTATCCGATTTG
1 TGTAGGTTCAACCCTTACG-GTGACTAGACACTATTATACGATTTG
* ** * **
43458939 TGTAGGTTCAACCCTTACGGTTGACCAGGGACTATGATTTATTATTTG
1 TGTAGGTTCAACCCTTACGG-TGACTAGACACTAT--TATACGATTTG
* * * * *
43458987 TGTAGGTTTAACCCTTATGGGTGACTAGACAGTATTATTCGATTCG
1 TGTAGGTTCAACCCTTA-CGGTGACTAGACACTATTATACGATTTG
43459033 TGTAGGTTCAACCCTTACGTGTGAC
1 TGTAGGTTCAACCCTTACG-GTGAC
43459058 CAAGAATTAT
Statistics
Matches: 93, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
45 2 0.02
46 56 0.60
48 33 0.35
49 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (45 bp):
TGTAGGTTCAACCCTTACGGTGACTAGACACTATTATACGATTTG
Found at i:43459058 original size:94 final size:94
Alignment explanation
Indices: 43458893--43459117 Score: 281
Period size: 94 Copynumber: 2.4 Consensus size: 94
43458883 CTAATTGTTT
* * * * *
43458893 TGTAGGTTCAACCCTTACGAGTGATTAGACACTATTATCCGATTTGTGTAGGTTCAACCCTTACG
1 TGTAGGTTTAACCCTTATGGGTGACTAGACACTATTATCCGATTCGTGTAGGTTCAACCCTTACG
* * *
43458958 GTTGACCAGGGACTATGATTTATTATTTG
66 GTTGACCAAGAACTATGATTCATTATTTG
* *
43458987 TGTAGGTTTAACCCTTATGGGTGACTAGACAGTATTATTCGATTCGTGTAGGTTCAACCCTTAC-
1 TGTAGGTTTAACCCTTATGGGTGACTAGACACTATTATCCGATTCGTGTAGGTTCAACCCTTACG
*
43459051 GTGTGACCAAGAATTATGATTCATTATTTG
66 GT-TGACCAAGAACTATGATTCATTATTTG
* ** * * *
43459081 TTTAGGTTTAACCCAAATGGGTAACCAGACATTATTA
1 TGTAGGTTTAACCCTTATGGGTGACTAGACACTATTA
43459118 CTTTTACCTA
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
93 2 0.02
94 111 0.98
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (94 bp):
TGTAGGTTTAACCCTTATGGGTGACTAGACACTATTATCCGATTCGTGTAGGTTCAACCCTTACG
GTTGACCAAGAACTATGATTCATTATTTG
Found at i:43459115 original size:48 final size:48
Alignment explanation
Indices: 43458934--43459115 Score: 163
Period size: 48 Copynumber: 3.8 Consensus size: 48
43458924 CTATTATCCG
* * * ** * *
43458934 ATTTGTGTAGGTTCAACCCTTACGGTTGACCAGGGACTATGATTTATT
1 ATTTGTGTAGGTTTAACCCTTATGGGTGACCAGACATTATGATTCATT
* * * *
43458982 ATTTGTGTAGGTTTAACCCTTATGGGTGACTAGACAGTATTATTC--G
1 ATTTGTGTAGGTTTAACCCTTATGGGTGACCAGACATTATGATTCATT
* * * *
43459028 ATTCGTGTAGGTTCAACCCTTACGTGTGACCAAGA-ATTATGATTCATT
1 ATTTGTGTAGGTTTAACCCTTATGGGTGACC-AGACATTATGATTCATT
* ** *
43459076 ATTTGTTTAGGTTTAACCCAAATGGGTAACCAGACATTAT
1 ATTTGTGTAGGTTTAACCCTTATGGGTGACCAGACATTAT
43459116 TACTTTTACC
Statistics
Matches: 104, Mismatches: 26, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
46 34 0.33
47 6 0.06
48 64 0.62
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (48 bp):
ATTTGTGTAGGTTTAACCCTTATGGGTGACCAGACATTATGATTCATT
Found at i:43461658 original size:24 final size:24
Alignment explanation
Indices: 43461610--43461659 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
43461600 CGATGTACTA
* **
43461610 TCAGTCTAATCATTCACATTTATG
1 TCAGTCTAATCAATCACATCCATG
43461634 TCAGTCTAATCAATCACATCCATG
1 TCAGTCTAATCAATCACATCCATG
43461658 TC
1 TC
43461660 TTTATTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (24 bp):
TCAGTCTAATCAATCACATCCATG
Found at i:43469299 original size:44 final size:43
Alignment explanation
Indices: 43469155--43469313 Score: 164
Period size: 43 Copynumber: 3.7 Consensus size: 43
43469145 AGCTCGTACA
* ** *
43469155 ATGCCAAAGTCCCAGACGCGGTCTTACATGT-AATCAAATATCA
1 ATGCCAACGTCCCAGACATGGTCTTACATGTAAATCAAATAT-G
* * *
43469198 ATGCC-ACTATCCCAGACAGGGTCTTACACG-AAATCAAATATG
1 ATGCCAAC-GTCCCAGACATGGTCTTACATGTAAATCAAATATG
* *
43469240 ATGCCGATGTCCCAGACATGGTCTTACATGTAAATCATAAGT-TG
1 ATGCCAACGTCCCAGACATGGTCTTACATGTAAATCA-AA-TATG
*
43469284 ATGCCAACGTCCCAGACGTGGTCTTACATG
1 ATGCCAACGTCCCAGACATGGTCTTACATG
43469314 ATAACACATA
Statistics
Matches: 97, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
42 25 0.26
43 40 0.41
44 31 0.32
45 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACATGTAAATCAAATATG
Found at i:43474087 original size:43 final size:42
Alignment explanation
Indices: 43473999--43474087 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 42
43473989 CATGCAATTA
* * * *
43473999 GGGACATTGGCATCATATTTGATTTCGTGTAAGACCCTGTTT
1 GGGACAGTGGCATCATATTTGATTACATGTAAGACCCTGTCT
43474041 GGGACAGTGGCATCAATATTTGATTACATGTAAGACCAC-GTCT
1 GGGACAGTGGCATC-ATATTTGATTACATGTAAGACC-CTGTCT
43474084 GGGA
1 GGGA
43474088 TGTTGGCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
42 13 0.32
43 27 0.66
44 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (42 bp):
GGGACAGTGGCATCATATTTGATTACATGTAAGACCCTGTCT
Found at i:43481716 original size:13 final size:13
Alignment explanation
Indices: 43481667--43481704 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
43481657 TTAATATTAA
43481667 TATTATTATATTAT
1 TATTATTAT-TTAT
43481681 TATTATTATTTAT
1 TATTATTATTTAT
43481694 TATTATTATTT
1 TATTATTATTT
43481705 GTATATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:43481733 original size:3 final size:3
Alignment explanation
Indices: 43481652--43481716 Score: 64
Period size: 3 Copynumber: 21.7 Consensus size: 3
43481642 AGTAGCTTTT
* *
43481652 TTA TT- TTA ATA TTA ATA TTA TTA -TA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
43481696 TTA TTA TT- TGTA TATA TTA TT
1 TTA TTA TTA T-TA T-TA TTA TT
43481717 CATACTATCA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
2 5 0.10
3 40 0.77
4 7 0.13
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:43494302 original size:76 final size:75
Alignment explanation
Indices: 43494148--43494662 Score: 261
Period size: 78 Copynumber: 6.5 Consensus size: 75
43494138 TTCTGTTTTC
* ** * * * *
43494148 AAAAATTAACTCATATTATGAGAGGCGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGACACGCTGAGGTATTTTCAATTT-
** *
43494213 TGT-CTTTTGAA
65 T-TACTCATCAA
**
43494224 AAAAATTGACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGACACGCTGAGGTAATTTT-AATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGACACGCTGAGGT-ATTTTCAATTT
43494288 TTACTCATCAA
65 TTACTCATCAA
* ** *
43494299 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAG-CCTTGGCTCACGTGCTGAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGG-ACAC--GCTGAGGTATTTTCAAT
* * *
43494363 TTCTATTCGTCAA
63 TTTTACTCATCAA
* * * * * * *
43494376 AAGAAATCAACTCATATTGCTAGAAGTGAGTTGAGTCTCAGGCCACATGCCGAGG-ACTTTTTAA
1 AA-AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGG--ACACGCTGAGGTA--TTTTCA
*
43494440 ATTCTATTTTAAATTCTATTTTTCAA
61 A---T-TTTT--ACTC-A----TCAA
* * * *
43494466 AAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGTCACATG-TCGAGGTATTTTCAA
1 A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGG--ACACGCT-GAGGTATTTTC--
* *
43494530 AACCTTCTTTTAAGT-TTC-A
60 AA---T-TTTT-ACTCATCAA
* * * *
43494549 AAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTGAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGACACGCTGAGGTATTTTCAA-TT-
** **
43494614 TGTTTTTCAAAAA
64 T-TTACTCATCAA
* * *
43494627 AAAAATCAACTCATATTGCAAAAGATGAGTTGAGCC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
43494663 TCGGGCCACA
Statistics
Matches: 351, Mismatches: 56, Indels: 62
0.75 0.12 0.13
Matches are distributed among these distances:
74 5 0.01
75 41 0.12
76 60 0.17
77 31 0.09
78 70 0.20
79 9 0.03
80 17 0.05
81 1 0.00
82 41 0.12
83 5 0.01
84 2 0.01
85 4 0.01
89 4 0.01
90 52 0.15
91 9 0.03
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGACACGCTGAGGTATTTTCAATTTT
TACTCATCAA
Found at i:43494451 original size:12 final size:12
Alignment explanation
Indices: 43494434--43494461 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
43494424 GCCGAGGACT
43494434 TTTTAAATTCTA
1 TTTTAAATTCTA
43494446 TTTTAAATTCTA
1 TTTTAAATTCTA
43494458 TTTT
1 TTTT
43494462 TCAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTAAATTCTA
Found at i:43494520 original size:90 final size:86
Alignment explanation
Indices: 43494379--43495037 Score: 446
Period size: 90 Copynumber: 7.6 Consensus size: 86
43494369 TCGTCAAAAG
* * * * * * *
43494379 AAATCAACTCATATTGCTAGAAGTGAGTTGAGTCTCAGGCCACATGCCGAGG-ACTTTTTAAATT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTA-TTTTCAAATT
43494443 CTATTTTAAATTCTATTTTTCAAAAA
65 CT-TTTT-AATTCTATTTTTC--AAA
* *
43494469 AAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAAA-AC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAAATTC
* * **
43494533 CTTCT--TT-TAAGTTTCAAA
66 TTTTTAATTCTATTTTTCAAA
* * * *
43494551 AAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGG--ACACG-CTGAGGTATTTTGAATTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTC-GAGGTATTTTCAAATT
* ***
43494613 CTGTTT--TTC-A---AAAAAA
65 CTTTTTAATTCTATTTTTCAAA
* * * *
43494629 AAATCAACTCATATTGCAAAAGATGAGTTGAGCCTCGGGCCACATGTCGAGGTATTTTCAAAATT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTC-AAA-T
* *
43494694 TCGTTTTTCAATTTCTGTTTCTTCCAA
64 TC-TTTTT-AA-TTCTATTT-TTCAAA
* *
43494721 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTTGAGGTATTTTCAATTGA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAA---A
*
43494786 TGT-TTTTTCAGTT-TATGCTTTTC-AA
63 T-TCTTTTT-AATTCTAT--TTTTCAAA
* *
43494811 AAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATG-CAGAGGTATTTTCAAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTC-GAGGTATTTTCAAATT
**
43494875 CTGTTTTGCAAATTCT-GCTTTC-AA
65 CT-TTTT---AATTCTATTTTTCAAA
* ** * * * *
43494899 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTAGCTCACGTG-CTGAGCTATTTTCAATTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTC-GAGGTATTTTCAAATT
*
43494963 CTATTTTTAATGTCTAGTTTT-AAA
65 C--TTTTTAAT-TCTATTTTTCAAA
* * * * ** * *
43494987 GAGTCAATTCATATTACGAGAAATGAGTTGAG-CTCAGGATCACATGCCGAG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGTCACATGTCGAG
43495038 TAAAGAATAA
Statistics
Matches: 459, Mismatches: 72, Indels: 78
0.75 0.12 0.13
Matches are distributed among these distances:
78 38 0.08
79 1 0.00
80 30 0.07
81 9 0.02
82 45 0.10
83 4 0.01
84 6 0.01
85 2 0.00
86 4 0.01
87 10 0.02
88 111 0.24
89 6 0.01
90 117 0.25
91 9 0.02
92 64 0.14
93 1 0.00
94 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (86 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAAATTC
TTTTTAATTCTATTTTTCAAA
Found at i:43494658 original size:250 final size:251
Alignment explanation
Indices: 43494298--43494781 Score: 651
Period size: 250 Copynumber: 1.9 Consensus size: 251
43494288 TTACTCATCA
* * *
43494298 AAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGGTATTTTCAAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACG-GCTGAGGTATTTTCAAT
* * *
43494363 TTCTATTCGTCAAAAGAAATCAACTCATATTGCTAGAAGTGAGTTGAGTCTCAGGCCACATGCCG
65 TTCTATTCGTCAAAAAAAATCAACTCATATTGCTAAAAGTGAGTTGAGCCTCAGGCCACATGCCG
* *
43494428 AGG-ACTTTT-TAAA-TTC-TATTTT-AAATTCTATTT-TTCAAAAAAAATCAACTCATGTTGCG
130 AGGTA-TTTTCAAAATTTCGT-TTTTCAAATTCTATTTCTTC--AAAAAATCAACTCATATTGCG
*
43494487 AGAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAAAACCTTCTTTTAAGTTTC
191 AGAGGTGAGTTGAGCCTCGGCTCACATGTCGAGGTATTTTCAAAACCTTCTTTTAAGTTTC
* * *
43494548 AAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGACAC-GCTGAGGTATTTTGAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGGCTGAGGTATTTTCAATT
* ** * *
43494612 TCTGTTTTTCAAAAAAAAAATCAACTCATATTGC-AAAAGATGAGTTGAGCCTCGGGCCACATGT
66 TCTATTCGTC--AAAAAAAATCAACTCATATTGCTAAAAG-TGAGTTGAGCCTCAGGCCACATGC
* * *
43494676 CGAGGTATTTTCAAAATTTCGTTTTTCAATTTCTGTTTCTTCCAAAAATCAACTCATATTGCGAG
128 CGAGGTATTTTCAAAATTTCGTTTTTCAAATTCTATTTCTTCAAAAAATCAACTCATATTGCGAG
*
43494741 AGGTGAGTTGAGCCTCGGCTCACATGTTGAGGTATTTTCAA
193 AGGTGAGTTGAGCCTCGGCTCACATGTCGAGGTATTTTCAA
43494782 TTGATGTTTT
Statistics
Matches: 204, Mismatches: 21, Indels: 16
0.85 0.09 0.07
Matches are distributed among these distances:
248 24 0.12
249 4 0.02
250 92 0.45
251 4 0.02
252 67 0.33
253 10 0.05
254 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (251 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGGCTGAGGTATTTTCAATT
TCTATTCGTCAAAAAAAATCAACTCATATTGCTAAAAGTGAGTTGAGCCTCAGGCCACATGCCGA
GGTATTTTCAAAATTTCGTTTTTCAAATTCTATTTCTTCAAAAAATCAACTCATATTGCGAGAGG
TGAGTTGAGCCTCGGCTCACATGTCGAGGTATTTTCAAAACCTTCTTTTAAGTTTC
Found at i:43494734 original size:92 final size:89
Alignment explanation
Indices: 43494627--43494933 Score: 340
Period size: 92 Copynumber: 3.4 Consensus size: 89
43494617 TTTTCAAAAA
*
43494627 AAAAATCAACTCATATTGCAAAAGATGAGTTGAGCCTCGGGCCACATGTCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTCGGGCCACATGTCGAGGTATTTTCAAAA
43494692 TTTCGTTTTTCAATTTCTGTTTCTTCC
66 TTT-GTTTTTCAATTTCTG-TTCTT-C
* * *
43494719 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGTTGAGGTATTTTC--A
1 AAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTCGGGC-CACATGTCGAGGTATTTTCAAA
* *
43494781 ATTGATGTTTTTTCAGTTTATGCTT-TTC
65 ATT--TG-TTTTTCAATTTCTG-TTCTTC
* * * *
43494809 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATG-CAGAGGTATTTTCAAA
1 AAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTCGGGCCACATGTC-GAGGTATTTTCAAA
* * * *
43494873 ATCTGTTTTGCAAATTCTGCT-TTC
65 ATTTGTTTTTCAATTTCTGTTCTTC
*
43494897 AAAAATCAACTCATATTGCGAGAA-GTGAGTTGAGCCT
1 AAAAATCAACTCATATTGC-AAAAGGTGAGTTGAGCCT
43494934 TAGCTCACGT
Statistics
Matches: 186, Mismatches: 20, Indels: 22
0.82 0.09 0.10
Matches are distributed among these distances:
88 35 0.19
89 11 0.06
90 61 0.33
91 8 0.04
92 71 0.38
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (89 bp):
AAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTCGGGCCACATGTCGAGGTATTTTCAAAA
TTTGTTTTTCAATTTCTGTTCTTC
Found at i:43494999 original size:88 final size:87
Alignment explanation
Indices: 43494627--43495033 Score: 337
Period size: 88 Copynumber: 4.6 Consensus size: 87
43494617 TTTTCAAAAA
* *
43494627 AAAAATCAACTCATATTGC-AAAAGATGAGTTGAGCCTCGGGC-CACATG-TCGAGGTATTTTCA
1 AAAAATCAACTCATATTACGAGAAG-TGAGTTGAGCCTC-GGCTCACATGCT-GAGGTATTTTC-
* * *
43494689 AAATTTCGTTTTTCAATTTCT-GTTTCTT
62 -AATTTC-TTTTTTAATGTCTAGCTT-TT
* * *
43494717 CCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTTGAGGTATTTTCAA
1 --AAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAA
* * *
43494782 TTGATGTTTTTTCA-GTTTATGCTTTT
64 TT--TCTTTTTTAATGTCTA-GCTTTT
* * * *
43494808 CAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCAGAGGTATTTTCAAA
1 -AAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAAT
* * *
43494873 ATCTGTTTTGCAAAT-TCT-GCTTTC
65 TTCT-TTTT--TAATGTCTAGCTTTT
* ** * *
43494897 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATT
43494962 TCTATTTTTAATGTCTAG-TTTT
66 TCT-TTTTTAATGTCTAGCTTTT
* * * *
43494984 AAAGAGTCAATTCATATTACGAGAAATGAGTTGAG-CTCAGGATCACATGC
1 AAA-AATCAACTCATATTACGAGAAGTGAGTTGAGCCTC-GGCTCACATGC
43495034 CGAGTAAAGA
Statistics
Matches: 260, Mismatches: 40, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
86 3 0.01
87 11 0.04
88 100 0.38
89 9 0.03
90 66 0.25
91 14 0.05
92 53 0.20
93 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (87 bp):
AAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATT
TCTTTTTTAATGTCTAGCTTTT
Found at i:43496183 original size:28 final size:28
Alignment explanation
Indices: 43496151--43496213 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
43496141 TCCCATATTA
43496151 ATGGGGTATAGGAAAAGTTTCATAACTT
1 ATGGGGTATAGGAAAAGTTTCATAACTT
* *
43496179 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTATAGGAAAAGTTTCATAACTT
43496207 ATGGGGT
1 ATGGGGT
43496214 TGATAATGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGTTTCATAACTT
Found at i:43501607 original size:28 final size:28
Alignment explanation
Indices: 43501567--43501629 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
43501557 TCCTATATTA
43501567 ATGGGGTATAGGAAAAGTCCCATAACTT
1 ATGGGGTATAGGAAAAGTCCCATAACTT
* ***
43501595 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTATAGGAAAAGTCCCATAACTT
43501623 ATGGGGT
1 ATGGGGT
43501630 TGATAATGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGTCCCATAACTT
Found at i:43502869 original size:44 final size:42
Alignment explanation
Indices: 43502818--43502981 Score: 136
Period size: 42 Copynumber: 3.9 Consensus size: 42
43502808 ATATGTGTTA
*
43502818 TCGTGTAAGACCACGTTTGAGACATTGGCATCG-ACTTATGATT
1 TCGTGTAAGACCACGTCTGAGACATTGGCATCGTA-TT-TGATT
* *
43502861 TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATT
1 T-CGTGTAAGACCACGTCTGAGACATTGGCATCGTATTTGATT
* ** * *
43502904 TCATGTAAGACCTTGTCT-AGGATAGTGGCATCGATATTTGATT
1 TCGTGTAAGACCACGTCTGA-GACATTGGCATCG-TATTTGATT
* * * * * *
43502947 ACATGTAAGATCAC-TCTGGGACGTTGGCATTGTAT
1 TCGTGTAAGACCACGTCTGAGACATTGGCATCGTAT
43502982 GAGCTTTCTG
Statistics
Matches: 99, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
41 3 0.03
42 38 0.38
43 26 0.26
44 31 0.31
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (42 bp):
TCGTGTAAGACCACGTCTGAGACATTGGCATCGTATTTGATT
Found at i:43502921 original size:42 final size:42
Alignment explanation
Indices: 43502821--43502956 Score: 141
Period size: 42 Copynumber: 3.2 Consensus size: 42
43502811 TGTGTTATCG
* * *
43502821 TGTAAGACCACGT-TTGAGACATTGGCATCG-ACTTATGATTTACG
1 TGTAAGACCATGTCTAG-GACATTGGCATCGTA-TT-TGATTT-CA
*
43502865 TGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTTCA
1 TGTAAGACCATGTCTAGGACATTGGCATCGTATTTGATTTCA
* * * *
43502907 TGTAAGACCTTGTCTAGGATAGTGGCATCGATATTTGATTACA
1 TGTAAGACCATGTCTAGGACATTGGCATCG-TATTTGATTTCA
43502950 TGTAAGA
1 TGTAAGA
43502957 TCACTCTGGG
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
42 27 0.33
43 24 0.30
44 27 0.33
45 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (42 bp):
TGTAAGACCATGTCTAGGACATTGGCATCGTATTTGATTTCA
Found at i:43506491 original size:40 final size:40
Alignment explanation
Indices: 43506447--43506557 Score: 143
Period size: 40 Copynumber: 2.8 Consensus size: 40
43506437 TCGAGAATTA
* *
43506447 AAAGTGAATAGGATCTATTCTTGATTCACTA-AAAGAAACT
1 AAAGTGAATAGGATTTATTCCTGATTCACTAGAAAGAAA-T
* * *
43506487 AAAGTGAATAGGATTTATTCCTGATGCACTAGAAATATAT
1 AAAGTGAATAGGATTTATTCCTGATTCACTAGAAAGAAAT
* *
43506527 AAAGTGGATAGGATTTGTTCCTGATTCACTA
1 AAAGTGAATAGGATTTATTCCTGATTCACTA
43506558 TGGTAACTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 57 0.92
41 5 0.08
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (40 bp):
AAAGTGAATAGGATTTATTCCTGATTCACTAGAAAGAAAT
Found at i:43510333 original size:47 final size:47
Alignment explanation
Indices: 43510279--43510410 Score: 158
Period size: 47 Copynumber: 2.8 Consensus size: 47
43510269 TCGCAATTGA
*
43510279 TAAGTACCTATACCATGACCCGTAGCCAAATCAAGGTAACTTATCCC
1 TAAGTACCTATACCATGACCCGTAGCCAAATCAAGGTAACTCATCCC
* * * * *
43510326 TAAGTACCTATACTATGGCCCGTAACCAAATCAAGGTAACTCCTCTC
1 TAAGTACCTATACCATGACCCGTAGCCAAATCAAGGTAACTCATCCC
* * * *
43510373 AAAATACCTATATCAT-AGCCCATAGCCAAATCAAGGTA
1 TAAGTACCTATACCATGA-CCCGTAGCCAAATCAAGGTA
43510411 TTATTCACAC
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.23
Consensus pattern (47 bp):
TAAGTACCTATACCATGACCCGTAGCCAAATCAAGGTAACTCATCCC
Found at i:43527121 original size:40 final size:40
Alignment explanation
Indices: 43527059--43527265 Score: 303
Period size: 40 Copynumber: 5.2 Consensus size: 40
43527049 CGGATGATAA
* * *
43527059 CCGGGCCAAGTCCCGAAGGCATTTGTGCGAGTGACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
43527099 CTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
43527139 CCGGGCTAAGTCCCGAAGGTA-TTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
43527178 CCGGGCTAAGTCCCGAAGACATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
43527218 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
43527258 CC-GGCTAA
1 CCGGGCTAA
43527266 AATCCGAAGG
Statistics
Matches: 151, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 44 0.29
40 107 0.71
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:43527191 original size:79 final size:80
Alignment explanation
Indices: 43527055--43527265 Score: 311
Period size: 79 Copynumber: 2.7 Consensus size: 80
43527045 TATTCGGATG
* * * * *
43527055 ATAACCGGGCCAAGTCCCGAAGGCATTTGTGCGAGTGACTATTTCTGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGACA
*
43527120 TTTGTGCTAGTTACT
66 TTTGTGCGAGTTACT
* *
43527135 ATATCCGGGCTAAGTCCCGAAGGTA-TTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGACA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGACA
43527199 TTTGTGCGAGTTACT
66 TTTGTGCGAGTTACT
*
43527214 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC-GGCTAA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAA
43527266 AATCCGAAGG
Statistics
Matches: 118, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
79 80 0.68
80 38 0.32
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGACA
TTTGTGCGAGTTACT
Found at i:43535312 original size:40 final size:40
Alignment explanation
Indices: 43535250--43535467 Score: 323
Period size: 40 Copynumber: 5.5 Consensus size: 40
43535240 CGGATGATAA
* * * *
43535250 CCGGGCCAAGTCCCAAAGGCATTTGTGCGAGTGACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
43535290 CCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTCTAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
43535330 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
43535370 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
43535410 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
43535450 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
43535468 TACTTGGTTT
Statistics
Matches: 164, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 16 0.10
40 148 0.90
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:43545887 original size:33 final size:33
Alignment explanation
Indices: 43545847--43545923 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
43545837 TGGCCAGGTA
* * *
43545847 GGCTGTGT-GTGACACATAGGCTGGACTGATTTT
1 GGCTGTGTAG-GACACACAGGCTAGACTGATTTG
* *
43545880 GGTTGTGTAGGCCACACAGGCTAGACTGATTTG
1 GGCTGTGTAGGACACACAGGCTAGACTGATTTG
43545913 GGCTGTGTAGG
1 GGCTGTGTAGG
43545924 TCATACGAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 36 0.97
34 1 0.03
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (33 bp):
GGCTGTGTAGGACACACAGGCTAGACTGATTTG
Found at i:43546043 original size:17 final size:18
Alignment explanation
Indices: 43546017--43546052 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
43546007 CAAATAGGGC
*
43546017 CGTGTGGGCCA-CACGGG
1 CGTGTAGGCCAGCACGGG
43546034 CGTGTAGGCCAGCACGGG
1 CGTGTAGGCCAGCACGGG
43546052 C
1 C
43546053 AGGCCACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.14, C:0.31, G:0.44, T:0.11
Consensus pattern (18 bp):
CGTGTAGGCCAGCACGGG
Found at i:43551530 original size:29 final size:28
Alignment explanation
Indices: 43551478--43551626 Score: 172
Period size: 29 Copynumber: 5.1 Consensus size: 28
43551468 GTATAGACGC
* *
43551478 CCATCGAATATGAAAAGGGTTGGTTTCA
1 CCATCAAATATGAAAAGGGATGGTTTCA
* **
43551506 TCTATCAAATATGAAAAGGGATGGTGACGA
1 -CCATCAAATATGAAAAGGGATGGTTTC-A
*
43551536 CCATCAAATAAGAAAAGGGATGGTTTCAA
1 CCATCAAATATGAAAAGGGATGGTTTC-A
* **
43551565 CCATCGAATATGAAAAGGGATGGTGACGA
1 CCATCAAATATGAAAAGGGATGGTTTC-A
43551594 CCATCAAATATGAAAAGGGATGGTTTCAA
1 CCATCAAATATGAAAAGGGATGGTTTC-A
43551623 CCAT
1 CCAT
43551627 TGATTAAAGA
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
29 99 0.99
30 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (28 bp):
CCATCAAATATGAAAAGGGATGGTTTCA
Found at i:43551554 original size:58 final size:58
Alignment explanation
Indices: 43551473--43551626 Score: 245
Period size: 58 Copynumber: 2.7 Consensus size: 58
43551463 ATGAAGTATA
* * * * *
43551473 GACGCCCATCGAATATGAAAAGGGTTGGTTTCATCTATCAAATATGAAAAGGGATGGT
1 GACGACCATCAAATATGAAAAGGGATGGTTTCAACCATCAAATATGAAAAGGGATGGT
* *
43551531 GACGACCATCAAATAAGAAAAGGGATGGTTTCAACCATCGAATATGAAAAGGGATGGT
1 GACGACCATCAAATATGAAAAGGGATGGTTTCAACCATCAAATATGAAAAGGGATGGT
43551589 GACGACCATCAAATATGAAAAGGGATGGTTTCAACCAT
1 GACGACCATCAAATATGAAAAGGGATGGTTTCAACCAT
43551627 TGATTAAAGA
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 88 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (58 bp):
GACGACCATCAAATATGAAAAGGGATGGTTTCAACCATCAAATATGAAAAGGGATGGT
Found at i:43551626 original size:87 final size:88
Alignment explanation
Indices: 43551478--43551655 Score: 225
Period size: 87 Copynumber: 2.0 Consensus size: 88
43551468 GTATAGACGC
* ** * *
43551478 CCATCGAATATGAAAAGGGTTGGTTTCATCTATCAAATATGAAAAGGGATGGTGACGACCATCAA
1 CCATCGAATATGAAAAGGGATGGTGACATCCATCAAATATGAAAAGGGATGGTGACAACCATCAA
* *
43551543 AT-AAGAAAAGGGATGGTTTCAA
66 ATAAAGAAAAGAGATAGTTTCAA
** **
43551565 CCATCGAATATGAAAAGGGATGGTGACGA-CCATCAAATATGAAAAGGGATGGTTTCAACCATTG
1 CCATCGAATATGAAAAGGGATGGTGAC-ATCCATCAAATATGAAAAGGGATGGTGACAACCATCA
*
43551629 ATTAAAGAAAAGAGATAGTTTCAA
65 AATAAAGAAAAGAGATAGTTTCAA
43551653 CCA
1 CCA
43551656 CCATTTAGCA
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
87 55 0.71
88 22 0.29
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (88 bp):
CCATCGAATATGAAAAGGGATGGTGACATCCATCAAATATGAAAAGGGATGGTGACAACCATCAA
ATAAAGAAAAGAGATAGTTTCAA
Found at i:43557583 original size:27 final size:27
Alignment explanation
Indices: 43557529--43557588 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
43557519 AATATAATAT
*
43557529 AATTATAAAATAATTAAATTGTACTTA
1 AATTATAAAATAATTAAATTGTAATTA
*
43557556 AATTATAAACAT-ATTAAATTTTAATTA
1 AATTATAAA-ATAATTAAATTGTAATTA
*
43557583 ATTTAT
1 AATTAT
43557589 TAATAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (27 bp):
AATTATAAAATAATTAAATTGTAATTA
Found at i:43561602 original size:9 final size:9
Alignment explanation
Indices: 43561560--43561600 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
43561550 GTTAATTTCA
43561560 GTTAAATTG
1 GTTAAATTG
43561569 GTTAAATTG
1 GTTAAATTG
43561578 GTTAAATTG
1 GTTAAATTG
*
43561587 ATT-AATTCG
1 GTTAAATT-G
43561596 GTTAA
1 GTTAA
43561601 TTTTTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 4 0.14
9 23 0.82
10 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (9 bp):
GTTAAATTG
Found at i:43561837 original size:21 final size:20
Alignment explanation
Indices: 43561806--43561851 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
43561796 TTTTTGCTTT
* * *
43561806 TAAAATTTTATGTCTTTTTA
1 TAAAATTTTATATATATTTA
43561826 TAAAACTTTTATATATATTTA
1 TAAAA-TTTTATATATATTTA
43561847 TAAAA
1 TAAAA
43561852 AGATTTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (20 bp):
TAAAATTTTATATATATTTA
Found at i:43562864 original size:20 final size:21
Alignment explanation
Indices: 43562841--43562880 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43562831 AAATAACGAA
*
43562841 AAAATAGTA-AAAAAAACAAG
1 AAAATAATATAAAAAAACAAG
*
43562861 AAAATAATATAACAAAACAA
1 AAAATAATATAAAAAAACAA
43562881 AAATTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAATAATATAAAAAAACAAG
Found at i:43565942 original size:46 final size:48
Alignment explanation
Indices: 43565857--43565958 Score: 127
Period size: 46 Copynumber: 2.1 Consensus size: 48
43565847 TAGTAAAACT
* * *
43565857 ATGGTCTTACACATAGTCATATATCACACACTGAAGCCATAGCCCAGCC
1 ATGGTCTTACACAGAGTCACATAT-ACACACTGAAGCCATAGCCCAGAC
* * *
43565906 ATGGTCTTACACAGA-TCACATAT-CACACTGATGCCATATCCCAGAT
1 ATGGTCTTACACAGAGTCACATATACACACTGAAGCCATAGCCCAGAC
43565952 ATGGTCT
1 ATGGTCT
43565959 ATATTGAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
46 26 0.55
48 7 0.15
49 14 0.30
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.25
Consensus pattern (48 bp):
ATGGTCTTACACAGAGTCACATATACACACTGAAGCCATAGCCCAGAC
Found at i:43566979 original size:22 final size:24
Alignment explanation
Indices: 43566952--43567055 Score: 110
Period size: 25 Copynumber: 4.4 Consensus size: 24
43566942 CACTAATGAA
43566952 CAGAGAGCACTGA-AGTGCT-ATA-
1 CAGAGAGCACTGACA-TGCTAATAT
** **
43566974 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGACATGCTAATAT
43566996 CAGAGAGCACTGACATGCTAAATAT
1 CAGAGAGCACTGACATGCT-AATAT
43567021 CAGAGAGCACTGACATGCTAAATAT
1 CAGAGAGCACTGACATGCT-AATAT
43567046 CAGAGAGCAC
1 CAGAGAGCAC
43567056 AAATGTTATA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.01
22 31 0.44
24 1 0.01
25 37 0.53
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.17
Consensus pattern (24 bp):
CAGAGAGCACTGACATGCTAATAT
Found at i:43567052 original size:27 final size:25
Alignment explanation
Indices: 43566994--43567055 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
43566984 AAATGTGCTA
43566994 ATCAGAGAGCACTGACATGCTAAAT
1 ATCAGAGAGCACTGACATGCTAAAT
43567019 ATCAGAGAGCACTGACATGCTAAAT
1 ATCAGAGAGCACTGACATGCTAAAT
43567044 ATCAGAGAGCAC
1 ATCAGAGAGCAC
43567056 AAATGTTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (25 bp):
ATCAGAGAGCACTGACATGCTAAAT
Found at i:43570344 original size:110 final size:115
Alignment explanation
Indices: 43570187--43570406 Score: 288
Period size: 110 Copynumber: 2.0 Consensus size: 115
43570177 GCAAATATTT
* * * ** *
43570187 CATGTACCATGATCTGCCAATTTGATTTACGCATCATTGAAGGCTACACCATG-A-A-T-ATATA
1 CATGTACCAAGATCTGCCAATTTGATTTACACAACAGCGAAGGCTACACCATGAACATTCATAAA
* *
43570248 TACA-AACATATCATGCCATGGGTCATAACCACATGGTTTTACACACATC
66 AACATAACATATCATGCCATGGGTCATAACCACATGGTCTTACACACATC
* *
43570297 CATGTATCAAGATTTGCCAATTTGATTTACACAACAGCGAAGGCTACACCATGAACATTCATAAA
1 CATGTACCAAGATCTGCCAATTTGATTTACACAACAGCGAAGGCTACACCATGAACATTCATAAA
* **
43570362 AACATATCATATCATGCCATGGGTTTTAACCACATGGTCTTACAC
66 AACATAACATATCATGCCATGGGTCATAACCACATGGTCTTACAC
43570407 TCATTTTTAA
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
110 46 0.50
111 1 0.01
112 1 0.01
113 1 0.01
114 7 0.08
115 36 0.39
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (115 bp):
CATGTACCAAGATCTGCCAATTTGATTTACACAACAGCGAAGGCTACACCATGAACATTCATAAA
AACATAACATATCATGCCATGGGTCATAACCACATGGTCTTACACACATC
Found at i:43574554 original size:24 final size:24
Alignment explanation
Indices: 43574507--43574554 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
43574497 CATAAAATCA
* * **
43574507 GACATAACAGTAGATGTAGCCACT
1 GACATAAAAGTAGAAGTAAACACT
43574531 GACATAAAAGTAGAAGTAAACACT
1 GACATAAAAGTAGAAGTAAACACT
43574555 AACGTAGAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.19
Consensus pattern (24 bp):
GACATAAAAGTAGAAGTAAACACT
Found at i:43579781 original size:11 final size:11
Alignment explanation
Indices: 43579765--43579797 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
43579755 CTTAGAACAG
43579765 ATCCCTTAGTA
1 ATCCCTTAGTA
43579776 ATCCCTTAGTA
1 ATCCCTTAGTA
43579787 AGT-CCTTAGTA
1 A-TCCCTTAGTA
43579798 CTCTTGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 20 0.95
12 1 0.05
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCCCTTAGTA
Found at i:43581508 original size:46 final size:46
Alignment explanation
Indices: 43581453--43581573 Score: 172
Period size: 46 Copynumber: 2.6 Consensus size: 46
43581443 TTTTGCATGA
* *
43581453 TGCCATAGTGTCTTTCAACTATAGTCTTATTCATTTCCCGTCATAT
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCCATCATAT
* * *
43581499 TTCCATAGTGTCTTTCAAAC-ATGGTCTTATTCATTTCCTATCATGT
1 TGCCATAGTGTCTTTC-AACTATGGTCTTATTCATTTCCCATCATAT
*
43581545 TGCCGTAGTGTCTTTCAACTATGGTCTTA
1 TGCCATAGTGTCTTTCAACTATGGTCTTA
43581574 CACGTTTAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
45 3 0.05
46 60 0.91
47 3 0.05
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (46 bp):
TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCCATCATAT
Found at i:43581605 original size:45 final size:45
Alignment explanation
Indices: 43581448--43581758 Score: 166
Period size: 45 Copynumber: 6.9 Consensus size: 45
43581438 TTATTTTTTG
** * * ***
43581448 CATGATGCCATAGTGTCTTTCAACTATAGTCTTATTCATTTCCCGT
1 CATGATGCCATAACGTCTTTCAACTATGGTCTTACTCATTT-AAAT
* ** * **
43581494 CAT-ATTTCCATAGTGTCTTTCAAAC-ATGGTCTTATTCATTTCCTAT
1 CATGA-TGCCATAACGTCTTTC-AACTATGGTCTTACTCATTT-AAAT
* * ** * * *
43581540 CATGTTGCCGTAGTGTCTTTCAACTATGGTCTTACACGTTTAAGT
1 CATGATGCCATAACGTCTTTCAACTATGGTCTTACTCATTTAAAT
* * *
43581585 CATGATGCCATAACGTCTTTCAGCTATCGTCTTACTTATTTAAAT
1 CATGATGCCATAACGTCTTTCAACTATGGTCTTACTCATTTAAAT
** ** *
43581630 CATGATATCAT-ACTGTCTTT--TTTATGGTCTTACTCATCTAAAT
1 CATGATGCCATAAC-GTCTTTCAACTATGGTCTTACTCATTTAAAT
* * * ** ***
43581673 CGTGATGTCATAACGTCTTTCAATTATGGTCTTACTTGTTTTTGGT
1 CATGATGCCATAACGTCTTTCAACTATGGTCTTAC-TCATTTAAAT
* ** *
43581719 -ATGGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTT
1 CATGATGCCATAACGTCTTTCAACTATGGTCTTACTCATTT
43581759 TCCGGTATAG
Statistics
Matches: 208, Mismatches: 48, Indels: 20
0.75 0.17 0.07
Matches are distributed among these distances:
43 33 0.16
44 8 0.04
45 94 0.45
46 70 0.34
47 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (45 bp):
CATGATGCCATAACGTCTTTCAACTATGGTCTTACTCATTTAAAT
Found at i:43581781 original size:46 final size:45
Alignment explanation
Indices: 43581687--43581804 Score: 166
Period size: 46 Copynumber: 2.6 Consensus size: 45
43581677 ATGTCATAAC
* * * *
43581687 GTCTTTCAATTATGGTCTTACTT-GTTTTTGGTATGGTGCCATAGT
1 GTCTTTCAACTATGGTCTTA-TTCATTTTCGGTATAGTGCCATAGT
43581732 GTCTTTCAACTATGGTCTTATTCATTTTCCGGTATAGTGCCATAGT
1 GTCTTTCAACTATGGTCTTATTCATTTT-CGGTATAGTGCCATAGT
*
43581778 GTCTTTCAACTATGGTCTTAATCATTT
1 GTCTTTCAACTATGGTCTTATTCATTT
43581805 CCTTAGTGTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 2 0.03
45 23 0.35
46 41 0.62
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.47
Consensus pattern (45 bp):
GTCTTTCAACTATGGTCTTATTCATTTTCGGTATAGTGCCATAGT
Found at i:43581812 original size:34 final size:34
Alignment explanation
Indices: 43581774--43581842 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
43581764 TATAGTGCCA
43581774 TAGTGTCTTTCAACTATGGTCTTAATCATTTCCT
1 TAGTGTCTTTCAACTATGGTCTTAATCATTTCCT
43581808 TAGTGTCTTTCAACTATGGTCTTAATCATTTCCT
1 TAGTGTCTTTCAACTATGGTCTTAATCATTTCCT
43581842 T
1 T
43581843 CAAGCCAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (34 bp):
TAGTGTCTTTCAACTATGGTCTTAATCATTTCCT
Found at i:43586944 original size:30 final size:30
Alignment explanation
Indices: 43586903--43586968 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
43586893 TTTTTGGCTT
43586903 AGGGACTAAATTGAATAAAAGTAAAATTTTA
1 AGGG-CTAAATTGAATAAAAGTAAAATTTTA
*
43586934 AGGGCTAAATTGAATAAATGTAAAATTTTA
1 AGGGCTAAATTGAATAAAAGTAAAATTTTA
*
43586964 GGGGC
1 AGGGC
43586969 AATTTTGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (30 bp):
AGGGCTAAATTGAATAAAAGTAAAATTTTA
Found at i:43586983 original size:30 final size:29
Alignment explanation
Indices: 43586903--43586990 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 29
43586893 TTTTTGGCTT
*
43586903 AGGGACTAAATTGAATAAAAGTAAAATTTTA
1 AGGG-CTAAATTGAA-AAATGTAAAATTTTA
43586934 AGGGCTAAATTGAATAAATGTAAAATTTTA
1 AGGGCTAAATTGAA-AAATGTAAAATTTTA
* *
43586964 GGGGC-AATTTTGTAAAAATGTCAAAAT
1 AGGGCTAA-ATTG-AAAAATGT-AAAAT
43586991 GACCAAATTC
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.04
30 38 0.75
31 11 0.22
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.31
Consensus pattern (29 bp):
AGGGCTAAATTGAAAAATGTAAAATTTTA
Found at i:43587486 original size:25 final size:25
Alignment explanation
Indices: 43587456--43587561 Score: 88
Period size: 25 Copynumber: 4.2 Consensus size: 25
43587446 GTTTCAACCC
43587456 ACAGCTCGTGTGAACATA-CTGATTT
1 ACAGCTCGTGTGAACATATC-GATTT
*
43587481 ACAGCTCGTGTGAGCATATCGATTT
1 ACAGCTCGTGTGAACATATCGATTT
* * ** * * *
43587506 ATAGCTCATAAGAGCATATCAATCT
1 ACAGCTCGTGTGAACATATCGATTT
** * *
43587531 ACAGCTCAAGTGAGCATATCGATTC
1 ACAGCTCGTGTGAACATATCGATTT
43587556 ACAGCT
1 ACAGCT
43587562 TATATGAGCA
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
25 65 0.98
26 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (25 bp):
ACAGCTCGTGTGAACATATCGATTT
Found at i:43587569 original size:25 final size:25
Alignment explanation
Indices: 43587476--43587573 Score: 92
Period size: 25 Copynumber: 3.9 Consensus size: 25
43587466 TGAACATACT
* * *
43587476 GATTTACAGCTCGTGTGAGCATATC
1 GATTCACAGCTCATATGAGCATATC
* * *
43587501 GATTTATAGCTCATAAGAGCATATC
1 GATTCACAGCTCATATGAGCATATC
*
43587526 -AATCTACAGCTCA-AGTGAGCATATC
1 GATTC-ACAGCTCATA-TGAGCATATC
*
43587551 GATTCACAGCTTATATGAGCATA
1 GATTCACAGCTCATATGAGCATA
43587574 CATGTACTGG
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
24 3 0.05
25 52 0.88
26 4 0.07
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (25 bp):
GATTCACAGCTCATATGAGCATATC
Found at i:43588693 original size:20 final size:20
Alignment explanation
Indices: 43588660--43588698 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
43588650 GCCATATGGT
43588660 TTGGCTTGTGTTATGGTATC
1 TTGGCTTGTGTTATGGTATC
43588680 TTGG-TTGTGATTATGGTAT
1 TTGGCTTGTG-TTATGGTAT
43588699 TTTCAACGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.05, G:0.31, T:0.51
Consensus pattern (20 bp):
TTGGCTTGTGTTATGGTATC
Found at i:43590763 original size:25 final size:25
Alignment explanation
Indices: 43590735--43590800 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 25
43590725 CGATATATGT
43590735 CTCTTTAGAGCTTCCCAATTAAAGG
1 CTCTTTAGAGCTTCCCAATTAAAGG
* *
43590760 CTCTTCTATAAGCTTCCCAATTAATGG
1 CTCTT-TA-GAGCTTCCCAATTAAAGG
* *
43590787 CTCTCTGGAGCTTC
1 CTCTTTAGAGCTTC
43590801 TCGATATTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 11 0.32
26 3 0.09
27 20 0.59
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (25 bp):
CTCTTTAGAGCTTCCCAATTAAAGG
Found at i:43590813 original size:24 final size:24
Alignment explanation
Indices: 43590784--43590872 Score: 90
Period size: 24 Copynumber: 3.7 Consensus size: 24
43590774 TCCCAATTAA
43590784 TGGCTCTCTGGAGCTTCTCGATAT
1 TGGCTCTCTGGAGCTTCTCGATAT
* * *
43590808 TGGCTCGCTTGAACTTCTCGATAT
1 TGGCTCTCTGGAGCTTCTCGATAT
* * * *
43590832 TGGCTCATATGG-GCTTCCCGTTAA
1 TGGCTC-TCTGGAGCTTCTCGATAT
*
43590856 TGGCTCTCCGGAGCTTC
1 TGGCTCTCTGGAGCTTC
43590873 CTGTTACATA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
23 3 0.06
24 46 0.90
25 2 0.04
ACGTcount: A:0.13, C:0.27, G:0.25, T:0.35
Consensus pattern (24 bp):
TGGCTCTCTGGAGCTTCTCGATAT
Found at i:43598512 original size:24 final size:25
Alignment explanation
Indices: 43598480--43598544 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 25
43598470 TGGAAGAGTG
*
43598480 TCCCGTTAT-TAACTCTCATGAGCT
1 TCCCATTATATAACTCTCATGAGCT
** **
43598504 TCCCATTATATAGTTCTTGTGAGCT
1 TCCCATTATATAACTCTCATGAGCT
*
43598529 TCCCATTA-ATAGCTCT
1 TCCCATTATATAACTCT
43598545 TCGAAGCATC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 15 0.44
25 19 0.56
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (25 bp):
TCCCATTATATAACTCTCATGAGCT
Found at i:43598545 original size:24 final size:25
Alignment explanation
Indices: 43598498--43598545 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
43598488 TTAACTCTCA
*
43598498 TGAGCTTCCCATTATATAGTTCTTG
1 TGAGCTTCCCATTATATAGCTCTTG
43598523 TGAGCTTCCCATTA-ATAGCTCTT
1 TGAGCTTCCCATTATATAGCTCTT
43598546 CGAAGCATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (25 bp):
TGAGCTTCCCATTATATAGCTCTTG
Found at i:43598648 original size:25 final size:26
Alignment explanation
Indices: 43598620--43598686 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
43598610 CACAAAATAT
43598620 GGCTCTTC-GGAGCTTCCCGATTAAA
1 GGCTCTTCAGGAGCTTCCCGATTAAA
* *
43598645 GGCTCTTTCATGAGCTTCCCGATTAAT
1 GGCTC-TTCAGGAGCTTCCCGATTAAA
*
43598672 GGCT-TTCTGGAGCTT
1 GGCTCTTCAGGAGCTT
43598687 TCAATTAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 14 0.39
26 3 0.08
27 19 0.53
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.34
Consensus pattern (26 bp):
GGCTCTTCAGGAGCTTCCCGATTAAA
Found at i:43602073 original size:20 final size:21
Alignment explanation
Indices: 43602048--43602090 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
43602038 ATTTTAGATA
*
43602048 TTTATGTATTTTTGT-TTTAT
1 TTTATGTATTTATGTATTTAT
43602068 TTTATGTATTTATGTATTTAT
1 TTTATGTATTTATGTATTTAT
43602089 TT
1 TT
43602091 ATCTTATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (21 bp):
TTTATGTATTTATGTATTTAT
Found at i:43604824 original size:43 final size:44
Alignment explanation
Indices: 43604773--43604963 Score: 205
Period size: 43 Copynumber: 4.4 Consensus size: 44
43604763 TATTGAGATG
*
43604773 TGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
* * * **
43604817 TG-TTACATGTAAGACCATGTTTGAGACATTGGAAAGGTATTGA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
*
43604860 -GATTACATGTAAGACCATGTCTGGGACATTGGCATCG--TTAA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
* * * * *
43604901 TCGATTTCGTATAAGACCCTGTCTGGGACAGTGGCATCG-ATATG-
1 T-GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT-TGA
*
43604945 TGATAACATGTAAGACCAT
1 TGATTACATGTAAGACCAT
43604964 ATTTGGCATA
Statistics
Matches: 120, Mismatches: 22, Indels: 11
0.78 0.14 0.07
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 111 0.93
44 4 0.03
45 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (44 bp):
TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
Found at i:43608417 original size:37 final size:37
Alignment explanation
Indices: 43608367--43608479 Score: 190
Period size: 37 Copynumber: 3.1 Consensus size: 37
43608357 TTTTAGCTCA
* *
43608367 GACAAAATCTCCACACGAAGTTATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
43608404 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
* *
43608441 GACATAATCTCCACGCGTAGTCATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
43608478 GA
1 GA
43608480 ATATATTTCC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (37 bp):
GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
Found at i:43608750 original size:48 final size:49
Alignment explanation
Indices: 43608626--43608836 Score: 295
Period size: 50 Copynumber: 4.3 Consensus size: 49
43608616 GCACATCGCC
* *
43608626 TACATATTTCACACT-AGCCATTCGGCTTTGCCACATATACATATCTCATA
1 TACATATTTCACATTGA-CCATTCGGCTTTACCACATATACATATCTCA-A
* * *
43608676 TATATATTTCACATTGACCATTCGGCTGTACCACATATGCATATCTC-A
1 TACATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCAA
43608724 TACATATTTCACATT-AGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTGA-CCATTCGGCTTTACCACATATACATATCTCA-A
* *
43608774 TATATATTTCACATTGACCATTCGGCTTTACCACATATGCATATCTC-A
1 TACATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCAA
43608822 TACATATTTCACATT
1 TACATATTTCACATT
43608837 CACATTCATC
Statistics
Matches: 145, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
47 1 0.01
48 58 0.40
50 84 0.58
51 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (49 bp):
TACATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCAA
Found at i:43608835 original size:98 final size:98
Alignment explanation
Indices: 43608626--43608836 Score: 395
Period size: 98 Copynumber: 2.2 Consensus size: 98
43608616 GCACATCGCC
* *
43608626 TACATATTTCACACTAGCCATTCGGCTTTGCCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
43608691 GACCATTCGGCTGTACCACATATGCATATCTCA
66 GACCATTCGGCTGTACCACATATGCATATCTCA
43608724 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
*
43608789 GACCATTCGGCTTTACCACATATGCATATCTCA
66 GACCATTCGGCTGTACCACATATGCATATCTCA
43608822 TACATATTTCACATT
1 TACATATTTCACATT
43608837 CACATTCATC
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 110 1.00
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (98 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
GACCATTCGGCTGTACCACATATGCATATCTCA
Found at i:43622130 original size:25 final size:25
Alignment explanation
Indices: 43622096--43622149 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
43622086 CAAAAGTCTG
43622096 CCTTCATAATTAACCCTTAGTGATC
1 CCTTCATAATTAACCCTTAGTGATC
43622121 CCTTCATAATTAACCCTTAGTGATC
1 CCTTCATAATTAACCCTTAGTGATC
43622146 CCTT
1 CCTT
43622150 TTGAGTGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (25 bp):
CCTTCATAATTAACCCTTAGTGATC
Found at i:43629602 original size:28 final size:26
Alignment explanation
Indices: 43629546--43629659 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 26
43629536 CAGCATGGCT
* * *
43629546 ACCAGAATAGATAATGTGACAGAGTC
1 ACCAGAACAGATAATGTGGCAGAGCC
43629572 ACCAGATACAGATAATCGTGGCAGAGCC
1 ACCAGA-ACAGATAAT-GTGGCAGAGCC
43629600 ACCAGAACAGATATATGTGGCAGAGCC
1 ACCAGAACAGATA-ATGTGGCAGAGCC
* * *
43629627 ACTAGATCAGATAATTTGTGGCATAGCC
1 ACCAGAACAGATAA--TGTGGCAGAGCC
43629655 ACCAG
1 ACCAG
43629660 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
26 7 0.09
27 37 0.49
28 32 0.42
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (26 bp):
ACCAGAACAGATAATGTGGCAGAGCC
Found at i:43629655 original size:55 final size:54
Alignment explanation
Indices: 43629546--43629659 Score: 149
Period size: 55 Copynumber: 2.1 Consensus size: 54
43629536 CAGCATGGCT
* *
43629546 ACCAGAATAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCC
1 ACCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCC
* * * *
43629600 ACCAGAACAGATATATGTGGCAGAGCCACTAGAT-CAGATAATTTGTGGCATAGCC
1 ACCAGAACAGATA-ATGTGACAGAGCCACCAGATACAGATAA-TCGTGGCAGAGCC
43629655 ACCAG
1 ACCAG
43629660 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
54 19 0.37
55 33 0.63
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (54 bp):
ACCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCC
Found at i:43639793 original size:43 final size:43
Alignment explanation
Indices: 43639745--43640080 Score: 345
Period size: 43 Copynumber: 7.8 Consensus size: 43
43639735 ATCGAGATGT
43639745 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
* * * * *
43639788 GATTACATGTAAGACCATGTCTAGGACATTGGAAATGTGTGGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
**
43639831 GATTATGTGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
* * *
43639874 GATTACATGTAAGACCATGTCTGGGACATTGGCAATGTGTGGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
** * * *
43639917 GATTATGTGTAAGACCATGTCTGGGACATTGGCAATGTGTGGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
** * * * *
43639960 GATTATGTGTAAGACCATGTCTGGGACATTAGCATCGTTAAT-C
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTG-TATTGA
* * * * * * *
43640003 GATTTCGTATAAGACCCTGTCTGGGACAGTGGCATCG-ATATGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT-TGA
* * * *
43640046 GATAACATGTAAGACCATATTTGGGATA-TGGCATT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATT
43640081 AACGAGCTTT
Statistics
Matches: 247, Mismatches: 43, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
41 1 0.00
42 7 0.03
43 238 0.96
44 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
Found at i:43639890 original size:86 final size:86
Alignment explanation
Indices: 43639752--43639989 Score: 413
Period size: 86 Copynumber: 2.8 Consensus size: 86
43639742 TGTGATTACA
*
43639752 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTAGGACAT
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
43639817 TGGAAATGTGTGGAGATTATG
66 TGGAAATGTGTGGAGATTATG
43639838 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
*
43639903 TGGCAATGTGTGGAGATTATG
66 TGGAAATGTGTGGAGATTATG
* * * **
43639924 TGTAAGACCATGTCTGGGACATTGGCAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
43639989 T
66 T
43639990 AGCATCGTTA
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 145 1.00
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (86 bp):
TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
TGGAAATGTGTGGAGATTATG
Found at i:43639975 original size:129 final size:129
Alignment explanation
Indices: 43639745--43640063 Score: 428
Period size: 129 Copynumber: 2.5 Consensus size: 129
43639735 ATCGAGATGT
* *
43639745 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCAATGTATGGAGATTACATGTAAGACCATGTCT
*
43639810 AGGACATTGGAAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
66 AGGACATTGGAAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTAGCATTGTATTGA
* **
43639874 GATTACATGTAAGACCATGTCTGGGACATTGGCAATGTGTGGAGATTATGTGTAAGACCATGTCT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCAATGTATGGAGATTACATGTAAGACCATGTCT
* * * * *
43639939 GGGACATTGGCAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTAGCATCGTTAAT-C
66 AGGACATTGGAAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTAGCATTG-TATTGA
* * * * * * *
43640003 GATTTCGTATAAGACCCTGTCTGGGACAGTGGC-ATCGATAT-GTGATAACATGTAAGACCAT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCAAT-G-TATGGAGATTACATGTAAGACCAT
43640064 ATTTGGGATA
Statistics
Matches: 166, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
128 2 0.01
129 159 0.96
130 5 0.03
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (129 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCAATGTATGGAGATTACATGTAAGACCATGTCT
AGGACATTGGAAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTAGCATTGTATTGA
Found at i:43640016 original size:86 final size:85
Alignment explanation
Indices: 43639752--43640063 Score: 398
Period size: 86 Copynumber: 3.6 Consensus size: 85
43639742 TGTGATTACA
*
43639752 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTAGGACAT
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
*
43639817 TGGAAATGTGTGGAGATTATG
66 TGG-CATGTGTGGAGATTATG
43639838 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
43639903 TGGCAATGTGTGGAGATTATG
66 TGGC-ATGTGTGGAGATTATG
* * * **
43639924 TGTAAGACCATGTCTGGGACATTGGCAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
* *
43639989 TAGCATCGT-T-AATCGATT-TCG
66 TGGCAT-GTGTGGA--GATTAT-G
* * * * * *
43640010 TATAAGACCCTGTCTGGGACAGTGGCATCG-ATATGTGATAACATGTAAGACCAT
1 TGTAAGACCATGTCTGGGACATTGGCATTGTAT-TGAGATTACATGTAAGACCAT
43640064 ATTTGGGATA
Statistics
Matches: 200, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
84 1 0.00
85 5 0.03
86 194 0.97
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (85 bp):
TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
TGGCATGTGTGGAGATTATG
Found at i:43643751 original size:27 final size:27
Alignment explanation
Indices: 43643721--43643898 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
43643711 ATATTGAGTC
* * * *
43643721 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
43643748 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
43643775 CGCACACTTAGTGCTACATAGTCGAACT
1 CGCACACTTAGTGCTACATAGTC-AAAT
** * *
43643803 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
43643830 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
43643857 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43643884 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43643899 GTACAATTCA
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:43643860 original size:82 final size:81
Alignment explanation
Indices: 43643742--43643897 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
43643732 TGCTATATAA
* * *
43643742 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCGAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTC-AAATCGCA
43643807 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
43643824 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
43643888 CACTTAGTGC
65 CACTTAGTGC
43643898 TGTACAATTC
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:43643910 original size:82 final size:83
Alignment explanation
Indices: 43643721--43643910 Score: 212
Period size: 82 Copynumber: 2.3 Consensus size: 83
43643711 ATATTGAGTC
* * * * *
43643721 CGCACACTCAGTGCTATATAA-TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTA
1 CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
* *
43643785 GTGCTACATAGTCGAACT
66 GTGCAACATAGTCGAAAT
* * **
43643803 CGCACACTTAGTGCCG--C-ATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACAC
1 CGCACACTTAGTGCTGTACAAT--TCAATTCGCACACTTAGTGCTA-CATAATCAAATCGCACAC
43643864 TTAGTGCAACATAGTC-AAAT
63 TTAGTGCAACATAGTCGAAAT
43643884 CGCACACTTAGTGCTGTACAATTCAAT
1 CGCACACTTAGTGCTGTACAATTCAAT
43643911 CCCGCGCACT
Statistics
Matches: 89, Mismatches: 12, Indels: 14
0.77 0.10 0.12
Matches are distributed among these distances:
79 1 0.01
81 19 0.21
82 66 0.74
83 1 0.01
84 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (83 bp):
CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
GTGCAACATAGTCGAAAT
Found at i:43651819 original size:27 final size:27
Alignment explanation
Indices: 43651789--43651966 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
43651779 ATATTGAGTC
* * * *
43651789 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* * *
43651816 CGCACACTTACTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43651843 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
43651871 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
43651898 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
43651925 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43651952 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43651967 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:43653849 original size:14 final size:14
Alignment explanation
Indices: 43653830--43653860 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
43653820 GAATTACATG
43653830 TTAGAATAGTATCA
1 TTAGAATAGTATCA
43653844 TTAGAATAGTATCA
1 TTAGAATAGTATCA
43653858 TTA
1 TTA
43653861 AAAAATGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (14 bp):
TTAGAATAGTATCA
Found at i:43672329 original size:27 final size:27
Alignment explanation
Indices: 43672280--43672352 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
43672270 TTGGCTATGG
* * * *
43672280 AAACATAAGG-AGTCCATCAGGACAGT
1 AAACATAGGGTAGCCCACCAGGACAAT
43672306 AAACAT-GGGATAGCCCACCAGGACAAT
1 AAACATAGGG-TAGCCCACCAGGACAAT
*
43672333 AAACATAGGGTAGTCCACCA
1 AAACATAGGGTAGCCCACCA
43672353 AGACGGTAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.05
26 6 0.15
27 28 0.72
28 3 0.08
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.14
Consensus pattern (27 bp):
AAACATAGGGTAGCCCACCAGGACAAT
Found at i:43685477 original size:39 final size:38
Alignment explanation
Indices: 43685416--43685554 Score: 215
Period size: 39 Copynumber: 3.6 Consensus size: 38
43685406 GAATTTAAGC
* *
43685416 CCGGATATAATTCCAGCTCATAGCCTGCTGATCTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGA-CTGAAGT
* *
43685455 CCAGATATAATCCCAGCACATAGCCTGCGGACCTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGA-CTGAAGT
43685494 CCGGATATAATTCCAGCACATAGCCTGCGGACTTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGAC-TGAAGT
43685533 CCGGATATAATTCCAGCACATA
1 CCGGATATAATTCCAGCACATA
43685555 CAATTATGAT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
38 1 0.01
39 91 0.99
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (38 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACTGAAGT
Found at i:43693763 original size:39 final size:39
Alignment explanation
Indices: 43693702--43693840 Score: 233
Period size: 39 Copynumber: 3.6 Consensus size: 39
43693692 GAATTTAAGC
* * *
43693702 CCGGATATAATTCCAGCTCATAGCTTGCGGATCTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
**
43693741 CTTGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
43693780 CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
43693819 CCGGATATAATTCCAGCACATA
1 CCGGATATAATTCCAGCACATA
43693841 CAATTATGAT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 93 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
Found at i:43697274 original size:30 final size:30
Alignment explanation
Indices: 43697238--43697299 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
43697228 ACTTATATTA
43697238 TTGTTAATTCTGTTATTATTTTAAAGGCAT
1 TTGTTAATTCTGTTATTATTTTAAAGGCAT
* * **
43697268 TTGTTAATTTTTTTATTATTTTAGCGGCAT
1 TTGTTAATTCTGTTATTATTTTAAAGGCAT
43697298 TT
1 TT
43697300 ACTTGTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (30 bp):
TTGTTAATTCTGTTATTATTTTAAAGGCAT
Found at i:43719933 original size:5 final size:5
Alignment explanation
Indices: 43719925--43719949 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
43719915 TTAAAAATAA
43719925 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
43719950 GCAAGAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:43723676 original size:27 final size:27
Alignment explanation
Indices: 43723646--43723915 Score: 267
Period size: 27 Copynumber: 10.1 Consensus size: 27
43723636 CGCCAAGAAT
* * *
43723646 GCATTCCTTTCACAGTAAGCCATAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
** * *
43723673 GCATTTATTTTAGAGTACGCCAC-AA-
1 GCATTCCTTTCAGAGTATGCCACAAAG
* *
43723698 GCATTTCTTTTAGAGTATGCCACAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
* * *
43723725 GCATTACTTTTAGAGTACGCCACAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
*
43723752 GCATTCCTTTCAGTGTATGCCACAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
* * * * **
43723779 GCATTCTTTTCAGAATATGCAATAATT
1 GCATTCCTTTCAGAGTATGCCACAAAG
*
43723806 GCATTCCTTTCAGAGTATGCTACAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
* * * *
43723833 GAATTCCTTTCACAGTATGCTAAAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
* *
43723860 GCACTT-CTTTTAGAGTACGCCACAAAG
1 GCA-TTCCTTTCAGAGTATGCCACAAAG
*
43723887 GCATTTCTTTCAGAGTATGCCACAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
43723914 GC
1 GC
43723916 TAACACGATG
Statistics
Matches: 201, Mismatches: 38, Indels: 8
0.81 0.15 0.03
Matches are distributed among these distances:
25 21 0.10
26 6 0.03
27 172 0.86
28 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (27 bp):
GCATTCCTTTCAGAGTATGCCACAAAG
Found at i:43723821 original size:81 final size:81
Alignment explanation
Indices: 43723646--43723915 Score: 294
Period size: 81 Copynumber: 3.4 Consensus size: 81
43723636 CGCCAAGAAT
* * * ** * * *
43723646 GCATTCCTTTCACAGTAAGCCATAAAGGCATTTATTTTAGAGTACGCCAC-AA-GCATTTCTTTT
1 GCATTCCTTTCAGAGTATGCCACAAAGGCATTCCTTTCAGAGTATGCCACAAAGGCACTTCTTTT
43723709 AGAGTATGCCACAAAG
66 AGAGTATGCCACAAAG
* * * *
43723725 GCATTACTTTTAGAGTACGCCACAAAGGCATTCCTTTCAGTGTATGCCACAAAGGCA-TTCTTTT
1 GCATTCCTTTCAGAGTATGCCACAAAGGCATTCCTTTCAGAGTATGCCACAAAGGCACTTCTTTT
* * * **
43723789 CAGAATATGCAATAATT
66 -AGAGTATGCCACAAAG
* * * * *
43723806 GCATTCCTTTCAGAGTATGCTACAAAGGAATTCCTTTCACAGTATGCTAAAAAGGCACTTCTTTT
1 GCATTCCTTTCAGAGTATGCCACAAAGGCATTCCTTTCAGAGTATGCCACAAAGGCACTTCTTTT
*
43723871 AGAGTACGCCACAAAG
66 AGAGTATGCCACAAAG
*
43723887 GCATTTCTTTCAGAGTATGCCACAAAGGC
1 GCATTCCTTTCAGAGTATGCCACAAAGGC
43723916 TAACACGATG
Statistics
Matches: 154, Mismatches: 33, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
79 40 0.26
80 9 0.06
81 98 0.64
82 7 0.05
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (81 bp):
GCATTCCTTTCAGAGTATGCCACAAAGGCATTCCTTTCAGAGTATGCCACAAAGGCACTTCTTTT
AGAGTATGCCACAAAG
Found at i:43731109 original size:21 final size:21
Alignment explanation
Indices: 43731079--43731129 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
43731069 TGTAAAAAGG
43731079 AATGCATAAGTATTATGACAT
1 AATGCATAAGTATTATGACAT
*
43731100 AATGCGTAAGTATTATGACAT
1 AATGCATAAGTATTATGACAT
*
43731121 GATGCATAA
1 AATGCATAA
43731130 TTAGTTTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (21 bp):
AATGCATAAGTATTATGACAT
Found at i:43738495 original size:27 final size:28
Alignment explanation
Indices: 43738411--43738508 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
43738401 CATGAGATTG
* * * *
43738411 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
43738440 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
43738468 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
43738495 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
43738509 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:43738519 original size:27 final size:27
Alignment explanation
Indices: 43738439--43738521 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
43738429 TAAATTGTAC
* *
43738439 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
43738467 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
43738494 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
43738521 A
1 A
43738522 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:43738522 original size:29 final size:27
Alignment explanation
Indices: 43738411--43738522 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
43738401 CATGAGATTG
** * *
43738411 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
43738440 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
43738468 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
43738495 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
43738523 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:43746524 original size:27 final size:28
Alignment explanation
Indices: 43746438--43746537 Score: 139
Period size: 27 Copynumber: 3.6 Consensus size: 28
43746428 ATCATGAGAT
* * *
43746438 TAGCACTAAGTGTGCGGGTTTAAATTGTA
1 TAGCACTAAGTGTGCGAGTTT-GATTATA
*
43746467 CAGCACTAAGTGTGCGAGTTTGATTATA
1 TAGCACTAAGTGTGCGAGTTTGATTATA
43746495 TAGCACTAAGTGTGCGAG-TTGATTATA
1 TAGCACTAAGTGTGCGAGTTTGATTATA
*
43746522 TAGCACTGAGTGTGCG
1 TAGCACTAAGTGTGCG
43746538 GACTTAATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 24 0.37
28 22 0.34
29 19 0.29
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGCACTAAGTGTGCGAGTTTGATTATA
Found at i:43746548 original size:27 final size:27
Alignment explanation
Indices: 43746468--43746550 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
43746458 TAAATTGTAC
* *
43746468 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
43746496 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
43746523 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
43746550 A
1 A
43746551 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:43746551 original size:29 final size:27
Alignment explanation
Indices: 43746438--43746551 Score: 102
Period size: 28 Copynumber: 4.0 Consensus size: 27
43746428 ATCATGAGAT
** *
43746438 TAGCACTAAGTGTGCGGGTTTAAATTGTA
1 TAGCACTAAGTGTGC-GACTT-AATTATA
* * *
43746467 CAGCACTAAGTGTGCGAGTTTGATTATA
1 TAGCACTAAGTGTGCGA-CTTAATTATA
* *
43746495 TAGCACTAAGTGTGCGAGTTGATTATA
1 TAGCACTAAGTGTGCGACTTAATTATA
*
43746522 TAGCACTGAGTGTGCGGACTTAATATATA
1 TAGCACTAAGTGTGC-GACTTAAT-TATA
43746551 T
1 T
43746552 TTTTGAATCA
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.38
29 22 0.30
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGACTTAATTATA
Found at i:43749535 original size:25 final size:25
Alignment explanation
Indices: 43749507--43749558 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
43749497 TAAGTTATAT
43749507 GTTTTTATATTATAAGAATGAACAG
1 GTTTTTATATTATAAGAATGAACAG
43749532 GTTTTTATATTATAAGAATGAACAG
1 GTTTTTATATTATAAGAATGAACAG
43749557 GT
1 GT
43749559 ATTAGTATTT
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:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (25 bp):
GTTTTTATATTATAAGAATGAACAG
Found at i:43749567 original size:25 final size:25
Alignment explanation
Indices: 43749511--43749567 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
43749501 TTATATGTTT
*
43749511 TTATATTATAAGAATGAACAGGTTT
1 TTATATTATAAGAATGAACAGGTTA
43749536 TTATATTATAAGAATGAACAGG-TA
1 TTATATTATAAGAATGAACAGGTTA
43749560 TTAGTATT
1 TTA-TATT
43749568 TGGGATAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (25 bp):
TTATATTATAAGAATGAACAGGTTA
Found at i:43749791 original size:16 final size:16
Alignment explanation
Indices: 43749770--43749808 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
43749760 ATATATTTTT
*
43749770 TTATAAATGCTATATA
1 TTATAAATGATATATA
*
43749786 TTATAAATTATATATA
1 TTATAAATGATATATA
43749802 TTATAAA
1 TTATAAA
43749809 ATTATTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (16 bp):
TTATAAATGATATATA
Found at i:43755571 original size:17 final size:17
Alignment explanation
Indices: 43755549--43755587 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
43755539 GCAGTCTCTA
*
43755549 TCAGTTTTGCTACAGTC
1 TCAGTTTTACTACAGTC
*
43755566 TCAGTTTTACTACAGTT
1 TCAGTTTTACTACAGTC
43755583 TCAGT
1 TCAGT
43755588 ATACATTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (17 bp):
TCAGTTTTACTACAGTC
Found at i:43755733 original size:35 final size:35
Alignment explanation
Indices: 43755687--43755765 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
43755677 GTTTCAGAAT
*
43755687 ACATAC-AAGATCGACACCGGAGACTCGGTGTACC
1 ACATACTAAGATCGACACCGAAGACTCGGTGTACC
*
43755721 ACATACTAAGATCGGCACCGAAGACTCGGTGTACC
1 ACATACTAAGATCGACACCGAAGACTCGGTGTACC
43755756 ACATACTAAG
1 ACATACTAAG
43755766 TTAAATCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
34 6 0.14
35 36 0.86
ACGTcount: A:0.34, C:0.28, G:0.22, T:0.16
Consensus pattern (35 bp):
ACATACTAAGATCGACACCGAAGACTCGGTGTACC
Found at i:43756512 original size:35 final size:35
Alignment explanation
Indices: 43756446--43756512 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
43756436 GTAGCAGTTT
* * * *
43756446 GGGCCTTAGCCTAGTTCAGTATCAGTTATGCACTA
1 GGGCCTTAGCCCAGTTCAATAACAGTCATGCACTA
43756481 GGGCCTTAGCCCA-TTACAATAACAGTCATGCA
1 GGGCCTTAGCCCAGTT-CAATAACAGTCATGCA
43756513 TACAGTAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.07
35 25 0.93
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (35 bp):
GGGCCTTAGCCCAGTTCAATAACAGTCATGCACTA
Found at i:43766689 original size:29 final size:32
Alignment explanation
Indices: 43766657--43766717 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 32
43766647 AAAAATTTAA
43766657 AATTTAG-TCTTTAC-ATTTTTAT-TTTCAAG
1 AATTTAGTTCTTTACTATTTTTATATTTCAAG
*
43766686 AATTTAGTTTCTTTACTTTTTTTATATTTCAA
1 AATTTAG-TTCTTTACTATTTTTATATTTCAA
43766718 AATCCAAGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 7 0.26
31 7 0.26
32 7 0.26
33 6 0.22
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.59
Consensus pattern (32 bp):
AATTTAGTTCTTTACTATTTTTATATTTCAAG
Found at i:43769279 original size:190 final size:187
Alignment explanation
Indices: 43768909--43769286 Score: 419
Period size: 189 Copynumber: 2.0 Consensus size: 187
43768899 GTCATTGAAA
43768909 AAAAAAAATGAGTCTAACCATCATCAACCATACAAGAAAAATAAAGAGAAATAAAAAAGAAATAA
1 AAAAAAAATGAGTCTAACCATCATCAACCATACAAGAAAAATAAAGAGAAATAAAAAAGAAATAA
*
43768974 AAGATTAAGGTTTATTTTAGTATTAAGAAACATATATATATTGAAAAGTAGAAAACATTGAAAAA
66 AAGATTAAGGTTTATTTTA-TATTAAGAAAAATATATATATTGAAAAGTAGAAAACATTGAAAAA
* * *
43769039 CATGTATAGTTGAATTTTTTAAAAATATTTTTTTGAAAATTTAAAATATATGAAAATTT
130 CATGTATAGTTGAATTTTTTAAAAATA-TTTTTTAAAAAATTAAAATATATAAAAATTT
* * * * * *
43769098 AAAAAAATTGAGTTTCACCATCATCAACCATACAAG-AAAATAGAA-AGAATTAAAGAAGAATTA
1 AAAAAAAATGAGTCTAACCATCATCAACCATACAAGAAAAATA-AAGAGAAATAAAAAAGAAATA
* * * * * *
43769161 CAAA-TTTAAGGTTT-TTTCT-TATTGCAGGAAAAATATATTATTTTTTAAACGTAGAAATCATT
65 -AAAGATTAAGGTTTATTT-TATATT--AAGAAAAATATA-TA-TATTGAAAAGTAGAAAACATT
* * * *
43769223 GAAAAACGTTTTTGGTTGAAAGTTTTTT-AAAATA-TTTTTAAAAAATTAATAATATATAAAAAT
124 GAAAAACATGTATAGTTG-AA-TTTTTTAAAAATATTTTTTAAAAAATTAA-AATATATAAAAAT
43769286 T
186 T
43769287 AGAAAATAAT
Statistics
Matches: 159, Mismatches: 20, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
186 4 0.03
187 3 0.02
188 41 0.26
189 53 0.33
190 44 0.28
191 8 0.05
192 6 0.04
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.33
Consensus pattern (187 bp):
AAAAAAAATGAGTCTAACCATCATCAACCATACAAGAAAAATAAAGAGAAATAAAAAAGAAATAA
AAGATTAAGGTTTATTTTATATTAAGAAAAATATATATATTGAAAAGTAGAAAACATTGAAAAAC
ATGTATAGTTGAATTTTTTAAAAATATTTTTTAAAAAATTAAAATATATAAAAATTT
Found at i:43769283 original size:17 final size:17
Alignment explanation
Indices: 43769263--43769301 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
43769253 AATATTTTTA
*
43769263 AAAAATTA-ATAATATAT
1 AAAAATTAGAAAATA-AT
43769280 AAAAATTAGAAAATAAT
1 AAAAATTAGAAAATAAT
43769297 AAAAA
1 AAAAA
43769302 ATATGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAATTAGAAAATAAT
Found at i:43769284 original size:18 final size:18
Alignment explanation
Indices: 43769261--43769303 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
43769251 AAAATATTTT
*
43769261 TAAAAAATTA-ATAAT-A
1 TAAAAAATTAGAAAATAA
43769277 TATAAAAATTAGAAAATAA
1 TA-AAAAATTAGAAAATAA
43769296 TAAAAAAT
1 TAAAAAAT
43769304 ATGTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.09
17 8 0.35
18 10 0.43
19 3 0.13
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
TAAAAAATTAGAAAATAA
Found at i:43773135 original size:20 final size:20
Alignment explanation
Indices: 43773097--43773135 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43773087 TTCTTAGATT
*
43773097 TTTAACCCAACACATTATTA
1 TTTAACCCAACACAATATTA
* *
43773117 TTTAATCCAACTCAATATT
1 TTTAACCCAACACAATATT
43773136 TGTTTTCTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAACCCAACACAATATTA
Found at i:43773361 original size:14 final size:13
Alignment explanation
Indices: 43773315--43773367 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
43773305 TCATAATGAC
43773315 TAATTAATTTAATT
1 TAATT-ATTTAATT
* *
43773329 TCATTATTGAATT
1 TAATTATTTAATT
43773342 TCAATTATTTAATT
1 T-AATTATTTAATT
*
43773356 ATAATTACTTAA
1 -TAATTATTTAA
43773368 ATAATAATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 8 0.25
14 23 0.72
15 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.53
Consensus pattern (13 bp):
TAATTATTTAATT
Found at i:43774676 original size:22 final size:22
Alignment explanation
Indices: 43774648--43774689 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
43774638 GTAGGATATG
43774648 AATCTGTATCTGTTATGCATGT
1 AATCTGTATCTGTTATGCATGT
43774670 AATCTGTATCTGTTATGCAT
1 AATCTGTATCTGTTATGCAT
43774690 TGATGTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (22 bp):
AATCTGTATCTGTTATGCATGT
Found at i:43779546 original size:22 final size:23
Alignment explanation
Indices: 43779504--43779555 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
43779494 AACCTAAAAT
43779504 TTTTAATTCTAATTATTTAA-TA
1 TTTTAATTCTAATTATTTAATTA
43779526 TTTT-ATT-TAATTATTCCTAATTA
1 TTTTAATTCTAATTATT--TAATTA
43779549 -TTTAATT
1 TTTTAATT
43779556 ATCTAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 8 0.31
21 3 0.12
22 10 0.38
23 5 0.19
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTAATTCTAATTATTTAATTA
Found at i:43782634 original size:40 final size:40
Alignment explanation
Indices: 43782574--43782796 Score: 297
Period size: 40 Copynumber: 5.6 Consensus size: 40
43782564 TATTCGAATG
* ** *
43782574 ATATCCGGGCTAAGTCCCGAAGGTTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
43782614 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
*
43782654 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
*
43782694 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
43782734 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
*
43782774 ATATCCGAGCTAAGACCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGG
43782797 TCTTGTGCGA
Statistics
Matches: 164, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 161 0.98
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:43782707 original size:80 final size:80
Alignment explanation
Indices: 43782574--43782833 Score: 323
Period size: 80 Copynumber: 3.3 Consensus size: 80
43782564 TATTCGAATG
** * *
43782574 ATATCCGGGCTAAGTCCCGAAGGTTTTTATGCTAGTGACTATATCCGGACTAAGATCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
*
43782639 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTCGCT
* * *
43782654 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGACTATATCCGGGCTAAGACCCGAAGGC
*
43782718 ATTTGTGCTAG-CGACT
65 ATTTGTGCGAGTCG-CT
* *
43782734 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACCATATCCGAGCTAAGACCCGAAGG--
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
43782797 TCTTGTGCGAGTGGTT
66 T-TTGTGCGAGTCGCT
* *
43782813 ATATCC-GGCTAAATCCTGAAG
1 ATATCCGGGCTAAGTCCCGAAG
43782834 ATACTTGGGT
Statistics
Matches: 156, Mismatches: 19, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
78 14 0.09
79 18 0.12
80 122 0.78
81 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTCGCT
Found at i:43782787 original size:120 final size:119
Alignment explanation
Indices: 43782574--43782824 Score: 330
Period size: 120 Copynumber: 2.1 Consensus size: 119
43782564 TATTCGAATG
* ** *
43782574 ATATCCGGGCTAAGTCCCGAAGGTTTTTATGCTAGTGACTATATCCGGACTAAGATCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGATCCGAAGGCA
* * * *
43782639 TTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGG-CATTTGTGCGAGTTGCT
66 TTTATGCGAGTTGCCATATCCGAGCTAAGACCCGAAGGTC--TTGTGCGAGTGGCT
* *
43782694 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAG-TCCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGAT-CCGAAGGC
* *
43782758 ATTTATGCTAG-TGACCATATCCGAGCTAAGACCCGAAGGTCTTGTGCGAGTGGTT
65 ATTTATGCGAGTTG-CCATATCCGAGCTAAGACCCGAAGGTCTTGTGCGAGTGGCT
43782813 ATATCC-GGCTAA
1 ATATCCGGGCTAA
43782825 ATCCTGAAGA
Statistics
Matches: 116, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
118 6 0.05
119 21 0.18
120 88 0.76
121 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (119 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGATCCGAAGGCA
TTTATGCGAGTTGCCATATCCGAGCTAAGACCCGAAGGTCTTGTGCGAGTGGCT
Found at i:43790115 original size:35 final size:35
Alignment explanation
Indices: 43790069--43790139 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
43790059 GAAGTGCAAA
*
43790069 TGTTAGTATTTGATTACTAGTGTATATATGTGTAT
1 TGTTAGTATTTGATTACTAGTGTATATATATGTAT
*
43790104 TGTTAGTATTTGATTGCTAGTGTATATATATGTAT
1 TGTTAGTATTTGATTACTAGTGTATATATATGTAT
43790139 T
1 T
43790140 AGCCGAGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.25, C:0.03, G:0.20, T:0.52
Consensus pattern (35 bp):
TGTTAGTATTTGATTACTAGTGTATATATATGTAT
Found at i:43790930 original size:40 final size:40
Alignment explanation
Indices: 43790870--43791052 Score: 230
Period size: 40 Copynumber: 4.6 Consensus size: 40
43790860 TATTCGAATG
*
43790870 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
43790910 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * *
43790950 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
43790990 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
43791030 ATATCCGGGCTAAGA-CTCGAAGG
1 ATATCCGGGCTAAGATC-CGAAGG
43791053 TCTTGTGCGA
Statistics
Matches: 125, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.02
40 120 0.96
41 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:43797776 original size:47 final size:47
Alignment explanation
Indices: 43797706--43797800 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 47
43797696 GTTGGAGAAA
* *
43797706 AACCATATTTCCACTAATTGTCCGTGTACTTGGAGAAACAAAATAAC
1 AACCATATTTCCACTAATAGTCCGTGTACCTGGAGAAACAAAATAAC
** *
43797753 AACCATATTTCTGCTAATAGTCCGTGTACCTGGAGGAACAAAATAAC
1 AACCATATTTCCACTAATAGTCCGTGTACCTGGAGAAACAAAATAAC
43797800 A
1 A
43797801 CGAAGTAAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (47 bp):
AACCATATTTCCACTAATAGTCCGTGTACCTGGAGAAACAAAATAAC
Found at i:43799261 original size:22 final size:22
Alignment explanation
Indices: 43799222--43799264 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43799212 TGTGGCGAGG
* * *
43799222 GCGATGACTGTGGCAGATGACA
1 GCGATGACGGTAGAAGATGACA
43799244 GCGATGACGGTAGAAGATGAC
1 GCGATGACGGTAGAAGATGAC
43799265 GGCGGAAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.37, T:0.16
Consensus pattern (22 bp):
GCGATGACGGTAGAAGATGACA
Found at i:43808630 original size:14 final size:15
Alignment explanation
Indices: 43808607--43808636 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
43808597 AAATCAAAAT
43808607 AAAATCAAAAATAAA
1 AAAATCAAAAATAAA
43808622 AAAAT-AAAAATAAA
1 AAAATCAAAAATAAA
43808636 A
1 A
43808637 TAAGACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAATCAAAAATAAA
Found at i:43813016 original size:40 final size:40
Alignment explanation
Indices: 43812956--43813137 Score: 278
Period size: 40 Copynumber: 4.6 Consensus size: 40
43812946 TATTCGGATG
* *
43812956 ATATTCGGGCTAAGTCCCGAAGGCCTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
43812996 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
43813036 ATATCCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
43813076 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
43813116 ATATCC-GGCTAATTCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
43813138 TACTTGGGTT
Statistics
Matches: 131, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 14 0.11
40 115 0.88
41 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:43817574 original size:39 final size:40
Alignment explanation
Indices: 43817531--43817698 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
43817521 CTCGTTCAAG
* * * *
43817531 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
43817570 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
43817610 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
43817650 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
43817690 TGCCTTCGG
1 TGCCTTCGG
43817699 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:43817711 original size:40 final size:40
Alignment explanation
Indices: 43817568--43817698 Score: 201
Period size: 40 Copynumber: 3.3 Consensus size: 40
43817558 TAACTCATAC
* *
43817568 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
43817608 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
43817648 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
43817688 AATGCCTTCGG
1 AATGCCTTCGG
43817699 ATCTTAGTCC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 3 0.04
40 79 0.96
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:43817711 original size:80 final size:80
Alignment explanation
Indices: 43817531--43817751 Score: 229
Period size: 80 Copynumber: 2.8 Consensus size: 80
43817521 CTCGTTCAAG
* * * * * * * *
43817531 TGCCTTCGGGACATAGCCCGGTTATAGTAACTCA-TACAATGCCTTCGGGACTTAACCCGGATTT
1 TGCCTTCGGGACTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGATAT
*
43817595 TAAAACTCGCACGAA
66 TAAAACTCGCACAAA
*
43817610 TGCCTTCGGGACTTAACCCGGA-ATTAGT-A-TCTCGCACAAAGGCCTTCGGGACTTAACCCGGA
1 TGCCTTCGGGACTTAACCCGGATA-TAGTCACT-TAGCACAAA-GCCTTCGGGACTTAACCCGGA
43817672 -ATTAATAACTCGCACAAA
63 TATTAA-AACTCGCACAAA
** * *
43817690 TGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAGAGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
43817752 CAGCATTCAA
Statistics
Matches: 119, Mismatches: 14, Indels: 17
0.79 0.09 0.11
Matches are distributed among these distances:
77 1 0.01
78 2 0.02
79 34 0.29
80 72 0.61
81 9 0.08
82 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (80 bp):
TGCCTTCGGGACTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGATAT
TAAAACTCGCACAAA
Found at i:43832265 original size:42 final size:42
Alignment explanation
Indices: 43832187--43832295 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 42
43832177 GCCCTGTTTT
* * * *
43832187 CACACAGCCTG-TGACACAGGCGTGTCGGTGGCCGTGTGATG
1 CACACGGCCTGTTGACACGGGCATGTCGGTGGCCGTGTGAGG
43832228 CACACGG-CT-TATGACACGGGCATGTCTGGTGGCCGTGTGAGG
1 CACACGGCCTGT-TGACACGGGCATGTC-GGTGGCCGTGTGAGG
*
43832270 CACACGGCCTGTTTACACGGGCATGT
1 CACACGGCCTGTTGACACGGGCATGT
43832296 GACCCTTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
40 2 0.03
41 19 0.33
42 21 0.36
43 15 0.26
44 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.21
Consensus pattern (42 bp):
CACACGGCCTGTTGACACGGGCATGTCGGTGGCCGTGTGAGG
Found at i:43832544 original size:23 final size:23
Alignment explanation
Indices: 43832514--43832559 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
43832504 CCTATTCTGG
43832514 CAACGGATACGGGTTAGGGGTGT
1 CAACGGATACGGGTTAGGGGTGT
43832537 CAACGGATACGGGTTAGGGGTGT
1 CAACGGATACGGGTTAGGGGTGT
43832560 TACACACCAA
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:0.22, C:0.13, G:0.43, T:0.22
Consensus pattern (23 bp):
CAACGGATACGGGTTAGGGGTGT
Found at i:43833489 original size:34 final size:34
Alignment explanation
Indices: 43833451--43833520 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
43833441 ATCATTTAAG
43833451 TATAAATCTTTTATATGATCAAACCTTAAGACTT
1 TATAAATCTTTTATATGATCAAACCTTAAGACTT
43833485 TATAAATCTTTTATATGATCAAACCTTAAGACTT
1 TATAAATCTTTTATATGATCAAACCTTAAGACTT
43833519 TA
1 TA
43833521 GCATTTAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (34 bp):
TATAAATCTTTTATATGATCAAACCTTAAGACTT
Found at i:43835635 original size:29 final size:29
Alignment explanation
Indices: 43835593--43835652 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
43835583 GAGGTTTCAA
*
43835593 AGCCTCTTCATATTCTTCCTCATCATCAT
1 AGCCTCTTCATATTCTTCATCATCATCAT
43835622 AGCCTCTTCATATTCTTCATCATCATCAT
1 AGCCTCTTCATATTCTTCATCATCATCAT
43835651 AG
1 AG
43835653 TCATAAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.32, G:0.05, T:0.40
Consensus pattern (29 bp):
AGCCTCTTCATATTCTTCATCATCATCAT
Done.