Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 31 of 75
Found at i:9729485 original size:28 final size:27
Alignment explanation
Indices: 9729454--9729508 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
9729444 AAAATAATTA
*
9729454 AAAATTCAA-TATATTAATAATTTAAGTG
1 AAAATT-AATTAT-TTAATAATTAAAGTG
*
9729482 AAAATTAATTATTTTATAATTAAAGTG
1 AAAATTAATTATTTAATAATTAAAGTG
9729509 TGAATTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (27 bp):
AAAATTAATTATTTAATAATTAAAGTG
Found at i:9733928 original size:26 final size:25
Alignment explanation
Indices: 9733875--9733935 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
9733865 CAATAATTTT
**
9733875 ATATATTATATAATAAAACCCATGC
1 ATATATTATATAATAAAACCCACAC
* *
9733900 ATATATGTATATAGTAAGACCCACAC
1 ATATAT-TATATAATAAAACCCACAC
*
9733926 ATATAATATA
1 ATATATTATA
9733936 ATTTATGTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.31
Consensus pattern (25 bp):
ATATATTATATAATAAAACCCACAC
Found at i:9735882 original size:31 final size:31
Alignment explanation
Indices: 9735847--9735913 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
9735837 GACAGTTTTC
9735847 CTTTTCCTTCAAAGTATTTCTTTAATTCTTT
1 CTTTTCCTTCAAAGTATTTCTTTAATTCTTT
*
9735878 CTTTTCTTTCAAAGTATTTCTTTAATTCTTT
1 CTTTTCCTTCAAAGTATTTCTTTAATTCTTT
9735909 CTTTT
1 CTTTT
9735914 TCTTAAGTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.18, G:0.03, T:0.61
Consensus pattern (31 bp):
CTTTTCCTTCAAAGTATTTCTTTAATTCTTT
Found at i:9736905 original size:20 final size:21
Alignment explanation
Indices: 9736859--9736906 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
9736849 TTTTGTTAGT
*
9736859 CTTTGTGGCATTCTGATACGGC
1 CTTTGTGGCATTCTGATAC-AC
*
9736881 CTTTGTGGCATTCTGTTA-AC
1 CTTTGTGGCATTCTGATACAC
9736901 CTTTGT
1 CTTTGT
9736907 AACATTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
22 17 0.71
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (21 bp):
CTTTGTGGCATTCTGATACAC
Found at i:9744408 original size:13 final size:13
Alignment explanation
Indices: 9744389--9744420 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
9744379 AGGTAGGCAA
9744389 CTTTTTTTTTGCG
1 CTTTTTTTTTGCG
*
9744402 GTTTTTTTTTGCG
1 CTTTTTTTTTGCG
9744415 CTTTTT
1 CTTTTT
9744421 GCTTTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (13 bp):
CTTTTTTTTTGCG
Found at i:9744437 original size:30 final size:30
Alignment explanation
Indices: 9744403--9744466 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
9744393 TTTTTTGCGG
9744403 TTTTTTTTT-GCGCTTTT-TGCTTTTTCTT
1 TTTTTTTTTGGCGCTTTTGTGCTTTTTCTT
***
9744431 TTTTTTTTTGGTTTTTTTGTGCTTTTTCTT
1 TTTTTTTTTGGCGCTTTTGTGCTTTTTCTT
9744461 TTTTTT
1 TTTTTT
9744467 AAAGAATAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 9 0.29
29 5 0.16
30 17 0.55
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (30 bp):
TTTTTTTTTGGCGCTTTTGTGCTTTTTCTT
Found at i:9744444 original size:39 final size:36
Alignment explanation
Indices: 9744389--9744463 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
9744379 AGGTAGGCAA
9744389 CTTTTTTTTTGCGGTTTTTTTTTGCGCTTTTTGCTTTTT
1 CTTTTTTTTTGCGG--TTTTTTTGCGCTTTTT-CTTTTT
** *
9744428 CTTTTTTTTTTTGGTTTTTTTGTGCTTTTTCTTTTT
1 CTTTTTTTTTGCGGTTTTTTTGCGCTTTTTCTTTTT
9744464 TTTAAAGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 6 0.18
37 15 0.45
39 12 0.36
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.76
Consensus pattern (36 bp):
CTTTTTTTTTGCGGTTTTTTTGCGCTTTTTCTTTTT
Found at i:9753235 original size:22 final size:23
Alignment explanation
Indices: 9753176--9753260 Score: 59
Period size: 22 Copynumber: 3.8 Consensus size: 23
9753166 TCTTCTTTCG
* * *
9753176 GAGAATATTCACTGTTCATGTTG
1 GAGAATATTCACTGTTCAAGCTA
***
9753199 GAGAAT-TTTGTTGTTCAAGCTA
1 GAGAATATTCACTGTTCAAGCTA
* *
9753221 GAGAAT-TTTACTGTTCATCGC-A
1 GAGAATATTCACTGTTCA-AGCTA
*
9753243 GAGAATCTTCACTGTTCA
1 GAGAATATTCACTGTTCA
9753261 TTCTCATTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
22 32 0.64
23 18 0.36
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (23 bp):
GAGAATATTCACTGTTCAAGCTA
Found at i:9757062 original size:24 final size:24
Alignment explanation
Indices: 9757034--9757091 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
9757024 AAAATTAAAA
9757034 GAAAAGAAAAATAAT-GAAGAAGAG
1 GAAAAGAAAAAT-ATCGAAGAAGAG
* *
9757058 GAAAAAGAAAAGTATCGAAGAAGAT
1 G-AAAAGAAAAATATCGAAGAAGAG
*
9757083 GAGAAGAAA
1 GAAAAGAAA
9757092 CTAAGGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.64, C:0.02, G:0.26, T:0.09
Consensus pattern (24 bp):
GAAAAGAAAAATATCGAAGAAGAG
Found at i:9767482 original size:17 final size:17
Alignment explanation
Indices: 9767444--9767476 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9767434 CACTAACATG
*
9767444 AAAATGTAATGACAATA
1 AAAATGCAATGACAATA
9767461 AAAATGCAATGACAAT
1 AAAATGCAATGACAAT
9767477 GTAAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:9778872 original size:17 final size:17
Alignment explanation
Indices: 9778811--9778876 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
9778801 TTCATGCATA
* * *
9778811 ATAATAGTTCACTCTAT
1 ATAATAATTCATTCAAT
*
9778828 ATAA-AAGTTCATACAAT
1 ATAATAA-TTCATTCAAT
* * *
9778845 GTAACAGTTCATTCAAT
1 ATAATAATTCATTCAAT
9778862 ATAATAATTCATTCA
1 ATAATAATTCATTCA
9778877 TACAACATCG
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
16 1 0.03
17 35 0.95
18 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAATAATTCATTCAAT
Found at i:9779529 original size:18 final size:18
Alignment explanation
Indices: 9779506--9779545 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
9779496 CTCACAATAC
9779506 ACAGTTTGACAAATTAAT
1 ACAGTTTGACAAATTAAT
* *
9779524 ACAGTTTGCCATATTAAT
1 ACAGTTTGACAAATTAAT
9779542 ACAG
1 ACAG
9779546 ATCACCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (18 bp):
ACAGTTTGACAAATTAAT
Found at i:9779557 original size:18 final size:18
Alignment explanation
Indices: 9779515--9779558 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
9779505 CACAGTTTGA
* **
9779515 CAAATTAATACAGTTTGC
1 CAAATTAATACAGATCAC
*
9779533 CATATTAATACAGATCAC
1 CAAATTAATACAGATCAC
9779551 CAAATTAA
1 CAAATTAA
9779559 CACAATTTGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (18 bp):
CAAATTAATACAGATCAC
Found at i:9783210 original size:42 final size:42
Alignment explanation
Indices: 9783150--9783229 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
9783140 TTTTAGAAAT
* *
9783150 AAACGCCTCTAAAGGTCATGACTTTTAGCCGCGCTTTTATAA
1 AAACGCCTCTAAAAGTCATGACCTTTAGCCGCGCTTTTATAA
*
9783192 AAACGCCGT-TAAAAGTCATGACCTTTAGCGGCGCTTTT
1 AAACGCC-TCTAAAAGTCATGACCTTTAGCCGCGCTTTT
9783230 TCCACAAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (42 bp):
AAACGCCTCTAAAAGTCATGACCTTTAGCCGCGCTTTTATAA
Found at i:9783258 original size:43 final size:43
Alignment explanation
Indices: 9783150--9783304 Score: 154
Period size: 43 Copynumber: 3.6 Consensus size: 43
9783140 TTTTAGAAAT
* * * * *
9783150 AAACGCCTCTAAAGGTCATGACTTTTAGCCGCGCTTTTAT--AA
1 AAACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTT-TCCAC
* * *
9783192 AAACGCCGTTAAAAGTCATGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTTCCAC
* * * *
9783235 AAACGCCGCTAAAGGCCAGGACCTTTCGCGGTGC-TTTTCACGC
1 AAACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTTC-CAC
*
9783278 AAACGCCGCTAAAGGCCAAGACCTTTA
1 AAACGCCGCTAAAGGCCATGACCTTTA
9783305 AAAAATTTAA
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.01
42 38 0.40
43 56 0.59
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTTCCAC
Found at i:9785895 original size:11 final size:11
Alignment explanation
Indices: 9785879--9785904 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9785869 ATTGTAGAAC
9785879 AAAACAAAAAG
1 AAAACAAAAAG
9785890 AAAACAAAAAG
1 AAAACAAAAAG
9785901 AAAA
1 AAAA
9785905 ATGAGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAG
Found at i:9787108 original size:7 final size:7
Alignment explanation
Indices: 9787098--9787153 Score: 67
Period size: 7 Copynumber: 8.0 Consensus size: 7
9787088 CTCTTAATCT
*
9787098 CTAACCT
1 CTAACCC
9787105 CTAACCC
1 CTAACCC
9787112 CTAACCC
1 CTAACCC
*
9787119 CAAACCC
1 CTAACCC
9787126 CTAACCC
1 CTAACCC
*
9787133 TTAACCC
1 CTAACCC
*
9787140 TTAACCC
1 CTAACCC
*
9787147 TTAACCC
1 CTAACCC
9787154 TTAAACATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.30, C:0.50, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAACCC
Found at i:9787154 original size:7 final size:7
Alignment explanation
Indices: 9787106--9787157 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
9787096 CTCTAACCTC
*
9787106 TAACCCC
1 TAACCCT
*
9787113 TAACCCC
1 TAACCCT
* *
9787120 AAACCCC
1 TAACCCT
9787127 TAACCCT
1 TAACCCT
9787134 TAACCCT
1 TAACCCT
9787141 TAACCCT
1 TAACCCT
9787148 TAACCCT
1 TAACCCT
9787155 TAA
1 TAA
9787158 ACATTATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (7 bp):
TAACCCT
Found at i:9787157 original size:14 final size:14
Alignment explanation
Indices: 9787084--9787153 Score: 70
Period size: 14 Copynumber: 5.0 Consensus size: 14
9787074 CCTTAAATCA
* * *
9787084 CTAACTCTTAATCT
1 CTAACCCTTAACCC
9787098 CTAA-CCTCTAACCC
1 CTAACCCT-TAACCC
**
9787112 CTAACCCCAAACCC
1 CTAACCCTTAACCC
9787126 CTAACCCTTAACCC
1 CTAACCCTTAACCC
*
9787140 TTAACCCTTAACCC
1 CTAACCCTTAACCC
9787154 TTAAACATTA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
13 2 0.04
14 42 0.91
15 2 0.04
ACGTcount: A:0.30, C:0.46, G:0.00, T:0.24
Consensus pattern (14 bp):
CTAACCCTTAACCC
Found at i:9787834 original size:41 final size:41
Alignment explanation
Indices: 9787744--9787935 Score: 246
Period size: 41 Copynumber: 4.7 Consensus size: 41
9787734 AAATTTTTTT
* *
9787744 GCGGCGCTTTTTCAAAAATGCCGC-AAATCTC-GAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
* * *
9787783 GCGGCTCTTTTCCAAAATA-GCCGCTAAAGCTCTGAGCGTTA
1 GCGGCGCTTTTTCAAAA-ACGCCGCTAAAGCTCTGAGCATTA
* *
9787824 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCTCTAAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
* * *
9787865 GCAGCACTTTTTCAAAAATGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
* *
9787906 GCGGTGCTTTTTCAAAAACGTCGCTAAAGC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGC
9787936 CTCGAAAGGT
Statistics
Matches: 132, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
39 20 0.15
40 8 0.06
41 104 0.79
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
Found at i:9788021 original size:39 final size:39
Alignment explanation
Indices: 9787972--9788067 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 39
9787962 TGGGCTTAGG
* *
9787972 TTTTTTGCGGCGCTTTTCTA-AACAACACCGCTAATGCT-A
1 TTTTTAGCGGCGTTTTTC-AGAA-AACACCGCTAATGCTCA
* *
9788011 TTTTTAGCGGCGTTTTTCAGAAAGCACCGCTAATTCTCGA
1 TTTTTAGCGGCGTTTTTCAGAAAACACCGCTAATGCTC-A
*
9788051 TCTTTAGCGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
9788068 TATCCAAACG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
38 14 0.29
39 18 0.37
40 17 0.35
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.39
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTCAGAAAACACCGCTAATGCTCA
Found at i:9790316 original size:20 final size:20
Alignment explanation
Indices: 9790272--9790398 Score: 69
Period size: 21 Copynumber: 6.2 Consensus size: 20
9790262 CTTTTATGGC
* * *
9790272 GCATTTTGTTAGCCTTTTTT
1 GCATTTTATTAGCCTTTGTG
*
9790292 TCATTTTATTAGCCTTTGTG
1 GCATTTTATTAGCCTTTGTG
**
9790312 GCATTTT-GGACGACCTTTGTG
1 GCATTTTATTA-G-CCTTTGTG
* *
9790333 GCATTCTATTAACCTTTTGTG
1 GCATTTTATTAGCC-TTTGTG
* * * *
9790354 ACATTTTGATATGGCTTTTATG
1 GCATTTT-AT-TAGCCTTTGTG
* *
9790376 GCATTCTATTA-ACTTTGTG
1 GCATTTTATTAGCCTTTGTG
9790395 GCAT
1 GCAT
9790399 ACTCTGTATA
Statistics
Matches: 78, Mismatches: 23, Indels: 13
0.68 0.20 0.11
Matches are distributed among these distances:
19 10 0.13
20 26 0.33
21 27 0.35
22 13 0.17
23 2 0.03
ACGTcount: A:0.17, C:0.16, G:0.18, T:0.49
Consensus pattern (20 bp):
GCATTTTATTAGCCTTTGTG
Found at i:9790343 original size:41 final size:41
Alignment explanation
Indices: 9790293--9790398 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 41
9790283 GCCTTTTTTT
* *
9790293 CATTTTATTAGCCTTTGTGGCATTTTG-GACGACCTTTGTGG
1 CATTCTATTA-CCTTTGTGGCATTTTGAGACGACCTTTATGG
* * * * *
9790334 CATTCTATTAACCTTTTGTGACATTTTGATATGGCTTTTATGG
1 CATTCTATT-ACC-TTTGTGGCATTTTGAGACGACCTTTATGG
*
9790377 CATTCTATTAACTTTGTGGCAT
1 CATTCTATTACCTTTGTGGCAT
9790399 ACTCTGTATA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
41 19 0.36
42 16 0.30
43 18 0.34
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.46
Consensus pattern (41 bp):
CATTCTATTACCTTTGTGGCATTTTGAGACGACCTTTATGG
Found at i:9790351 original size:21 final size:20
Alignment explanation
Indices: 9790327--9790398 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 20
9790317 TTGGACGACC
9790327 TTTGTGGCATTCTATTAACCT
1 TTTGTGGCATTCTATTAA-CT
* * **
9790348 TTTGTGACATTTTGATATGGCT
1 TTTGTGGCATTCT-AT-TAACT
*
9790370 TTTATGGCATTCTATTAAC-
1 TTTGTGGCATTCTATTAACT
9790389 TTTGTGGCAT
1 TTTGTGGCAT
9790399 ACTCTGTATA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
19 9 0.23
20 2 0.05
21 13 0.33
22 14 0.36
23 1 0.03
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (20 bp):
TTTGTGGCATTCTATTAACT
Found at i:9793719 original size:19 final size:20
Alignment explanation
Indices: 9793692--9793734 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
9793682 CATTTTATAA
*
9793692 ATAAAATAT-TATCACTTTT
1 ATAAAATATAAATCACTTTT
* *
9793711 ATAACATATAAATCATTTTT
1 ATAAAATATAAATCACTTTT
9793731 ATAA
1 ATAA
9793735 TAAACTCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAAATATAAATCACTTTT
Found at i:9793838 original size:119 final size:120
Alignment explanation
Indices: 9793702--9793942 Score: 475
Period size: 119 Copynumber: 2.0 Consensus size: 120
9793692 ATAAAATATT
9793702 ATCACTTTTATAACATATAAATCATTTTTATAATAAACTCCTTAACCATAGCTTTAAAAAAATAT
1 ATCACTTTTATAACATATAAATCATTTTTATAATAAACTCCTTAACCATAGCTTTAAAAAAATAT
9793767 TTAAATAATATAATTTTTTGTTATAACTTTATAAAATACACAAATT-TTATTATA
66 TTAAATAATATAATTTTTTGTTATAACTTTATAAAATACACAAATTATTATTATA
9793821 ATCACTTTTATAACATATAAATCATTTTTATAATAAACTCCTTAACCATAGCTTTAAAAAAATAT
1 ATCACTTTTATAACATATAAATCATTTTTATAATAAACTCCTTAACCATAGCTTTAAAAAAATAT
9793886 TTAAATAATATAATTTTTTGTTATAACTTTATAAAATACACAAATTATTATTATA
66 TTAAATAATATAATTTTTTGTTATAACTTTATAAAATACACAAATTATTATTATA
9793941 AT
1 AT
9793943 ATAATTTTTT
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
119 111 0.92
120 10 0.08
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.43
Consensus pattern (120 bp):
ATCACTTTTATAACATATAAATCATTTTTATAATAAACTCCTTAACCATAGCTTTAAAAAAATAT
TTAAATAATATAATTTTTTGTTATAACTTTATAAAATACACAAATTATTATTATA
Found at i:9793910 original size:58 final size:58
Alignment explanation
Indices: 9793729--9793911 Score: 142
Period size: 58 Copynumber: 3.1 Consensus size: 58
9793719 TAAATCATTT
9793729 TTATAATAAACTCCTTAACCATAGCTTTAAAAAAATATTTAAATAATATAATTTTTTG
1 TTATAATAAACTCCTTAACCATAGCTTTAAAAAAATATTTAAATAATATAATTTTTTG
** *** ** ** * * **
9793787 TTATAACTTTA-T-AAAATACACA-AATTTTATTATAATCACTTTTATAA-CATATAAATCATTT
1 TTATAA-TAAACTCCTTA-AC-CATAGCTTTAAAAAAAT-A--TTTA-AATAATAT-AATTTTTT
9793848 -
58 G
9793848 TTATAATAAACTCCTTAACCATAGCTTTAAAAAAATATTTAAATAATATAATTTTTTG
1 TTATAATAAACTCCTTAACCATAGCTTTAAAAAAATATTTAAATAATATAATTTTTTG
9793906 TTATAA
1 TTATAA
9793912 CTTTATAAAA
Statistics
Matches: 86, Mismatches: 26, Indels: 26
0.62 0.19 0.19
Matches are distributed among these distances:
57 9 0.10
58 32 0.37
59 5 0.06
60 5 0.06
61 26 0.30
62 9 0.10
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (58 bp):
TTATAATAAACTCCTTAACCATAGCTTTAAAAAAATATTTAAATAATATAATTTTTTG
Found at i:9806585 original size:15 final size:16
Alignment explanation
Indices: 9806562--9806617 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
9806552 TTTTTATGTT
*
9806562 TTATATATATTATTTTA
1 TTATATATA-TATTATA
*
9806579 TTATATAATATAATATA
1 TTATAT-ATATATTATA
*
9806596 TTATAT-TGTATTATA
1 TTATATATATATTATA
9806611 TTATATA
1 TTATATA
9806618 AATTAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 13 0.39
17 17 0.52
18 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTATATATATATTATA
Found at i:9806594 original size:27 final size:27
Alignment explanation
Indices: 9806566--9806618 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
9806556 TATGTTTTAT
9806566 ATATATTAT-TT-TATTATATAATATA
1 ATATATTATATTGTATTATATAATATA
*
9806591 ATATATTATATTGTATTATATTATATA
1 ATATATTATATTGTATTATATAATATA
9806618 A
1 A
9806619 ATTAAATAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.36
26 2 0.08
27 14 0.56
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
ATATATTATATTGTATTATATAATATA
Found at i:9806601 original size:5 final size:5
Alignment explanation
Indices: 9806562--9806616 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
9806552 TTTTTATGTT
* *
9806562 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA TTATA TTGTA TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
9806611 TTATA T
1 TTATA T
9806617 AAATTAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.20
5 28 0.68
7 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:9807333 original size:24 final size:23
Alignment explanation
Indices: 9807292--9807338 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
9807282 TACTCATGGG
9807292 ACATTTAAAGTAAGGTAAGTAATA
1 ACATTTAAAGTAAGGTAAG-AATA
*
9807316 ACATTTGAAATTAA-GTAAGAATA
1 ACATTT-AAAGTAAGGTAAGAATA
9807339 TGTGTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (23 bp):
ACATTTAAAGTAAGGTAAGAATA
Found at i:9809305 original size:14 final size:14
Alignment explanation
Indices: 9809268--9809313 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
9809258 CCAAGCTGGA
9809268 AAGGACCTTATGTGG
1 AAGG-CCTTATGTGG
*
9809283 AAGACCCTTATGTGG
1 AAG-GCCTTATGTGG
*
9809298 AAGGCCTTATTTGG
1 AAGGCCTTATGTGG
9809312 AA
1 AA
9809314 AAGCGTCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (14 bp):
AAGGCCTTATGTGG
Found at i:9810833 original size:44 final size:44
Alignment explanation
Indices: 9810785--9811011 Score: 127
Period size: 44 Copynumber: 5.2 Consensus size: 44
9810775 AGACACTAGC
**
9810785 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGCATTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* ** * * * * * * *
9810829 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAG-C
1 CTTGCCTCCCTGCATTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
* ** * * *
9810873 CTTGCCTCCCAGGTTTGGAGTGGAGCAGGTTAAAAATTGCAGAT
1 CTTGCCTCCCTGCATTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* ** * * ** * * * *
9810917 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAG-C
1 CTTGCCTCCCTGCATTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
* *
9810961 CTTGCCTCCCTG-AGTTGTAGCGGAGTAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGCA-TTGCAGCGGAGCAGGTTAAAAATAGCAGAT
9811005 CTTGCCT
1 CTTGCCT
9811012 TCCTACACCG
Statistics
Matches: 120, Mismatches: 58, Indels: 10
0.64 0.31 0.05
Matches are distributed among these distances:
43 33 0.28
44 53 0.44
45 34 0.28
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.22
Consensus pattern (44 bp):
CTTGCCTCCCTGCATTGCAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:9811237 original size:88 final size:88
Alignment explanation
Indices: 9810639--9811225 Score: 789
Period size: 88 Copynumber: 6.7 Consensus size: 88
9810629 AGCAGATCAG
* * * * *
9810639 TAAAGATAACAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAACCTTGCTT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
9810704 CCCTGGGTTGTAGCGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* * * * *
9810727 TAAAAATAGTAGATCTTGCCCTCCTACACCGACAGCAAAGCAGATCGAAGACACTAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
9810792 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
*
9810815 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
9810880 CCCAGGTTTGGAGTGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
*
9810903 TAAAAATTGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * * *
9810968 CCCTGAGTTGTAGCGGAGTAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* * ** * *
9810991 TAAAAATAGCAGATCTTGCCTTCCTACACCGACAACGAAATAAATCGAAGACACCAACCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
9811056 CCCTGGGTTGTAGTGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* * * *
9811079 TAAAAATAACAGATTTTGCCTTCCTGCATCGACAGAGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
9811144 CCCTGGGTAGCAGTGGAGTAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* * * * * *
9811167 TAAAAATAGAAAATCTTGCCTTCCTGCACCGA-AGGTGAAGCAAATCGATGACCCCAGCC
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACA-GCGAAGCAGATCGAAGACACCAGCC
9811226 CTATCTCCCT
Statistics
Matches: 437, Mismatches: 61, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
87 1 0.00
88 436 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGTGGAGCAGGT
Found at i:9811293 original size:44 final size:43
Alignment explanation
Indices: 9811225--9811346 Score: 147
Period size: 44 Copynumber: 2.8 Consensus size: 43
9811215 TGACCCCAGC
*
9811225 CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAATATTGT-AAGT
1 CCTATCTCCCTGG-CAGCAGTGGAATAGGTTGAAGATTGTGAA-T
* * *
9811269 TCTATCTCCCTGGTCAGCATTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGG-CAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
9811313 CCTATCTCCCTGAGCAACAGTGGAGTAGGTTGAA
1 CCTATCTCCCTG-GCAGCAGTGGAATAGGTTGAA
9811347 AATAGCAGAT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
44 63 0.95
45 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (43 bp):
CCTATCTCCCTGGCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:9811470 original size:50 final size:50
Alignment explanation
Indices: 9811416--9811514 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
9811406 CGCCTTGACG
* *
9811416 TTGCAATGGAAAAGATTGAAGCCACAACGGCGAATCTTATTTCCCTGGCA
1 TTGCAACGGAAAAGATTGAAGCCACAACGGCGAATCTTATCTCCCTGGCA
* ** * *
9811466 TTGCAGCGGAGTAGATTGAAGCCACGACGGTGAATCTTATCTCCCTGGC
1 TTGCAACGGAAAAGATTGAAGCCACAACGGCGAATCTTATCTCCCTGGC
9811515 GTTAAGGCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.24
Consensus pattern (50 bp):
TTGCAACGGAAAAGATTGAAGCCACAACGGCGAATCTTATCTCCCTGGCA
Found at i:9811765 original size:44 final size:44
Alignment explanation
Indices: 9811710--9812172 Score: 219
Period size: 44 Copynumber: 10.7 Consensus size: 44
9811700 GAAGATGATG
*
9811710 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAC
* * * * * *
9811754 AATCCTATCTCCCTAAAGTCGCAGTGGAGCGGATTAAA-ATCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAC
* * * *** *
9811797 AGATCTTATCTCTCTGAAATTGCAG-AGAGCAGATCGCATCT-A-
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAC
* **
9811839 GA-CTTATCTCCCTGAAGTTGCAGTGGAGCAGGCT-AAG-TAAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAA-C
* * * * * **
9811881 AAGCCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGC
1 AA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAGCTAAC
* * *
9811926 GAATCTTATCTCCCTGAAGTTGCAGTTGAGCAGATTAAAGCCAAT
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAC
* * ** * *
9811971 AATCATATCTCTCTGAAGTTGCAGTGGAGTGGATTAAA-ATCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAC
* * * *
9812014 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAG----ACGC-ATC
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAC
** * * *
9812053 GGGTACTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAATC
1 -AAT-CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAA-C
* * * *
9812099 AAGTCTTATCCCCCTAAAATTGCAGTGCG-GCAGACTAAA--TAAAC
1 AA-TCTTATCTCCCTGAAGTTGCAGTG-GAGCAGATTAAAGCT-AAC
* * *
9812143 AAATCTCATCTCCCTAAAGTTGTAGTGGAG
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAG
9812173 TGGATTAGAA
Statistics
Matches: 313, Mismatches: 75, Indels: 62
0.70 0.17 0.14
Matches are distributed among these distances:
39 4 0.01
40 41 0.13
41 13 0.04
42 1 0.00
43 22 0.07
44 155 0.50
45 68 0.22
46 9 0.03
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAC
Found at i:9811959 original size:45 final size:44
Alignment explanation
Indices: 9811841--9811959 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 44
9811831 CGCATCTAGA
* *
9811841 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGCAAGC
1 CTTATCTCCCTGAAGTTGCAGTTGAGCAGACTAAGTAAGCAAGC
* * *
9811885 CTTATC-CTCCTGAAGTTGTAG-TGAGGCAGACTGAAG-ATGGCGAA-T
1 CTTATCTC-CCTGAAGTTGCAGTTGA-GCAGACT-AAGTA-AGC-AAGC
9811930 CTTATCTCCCTGAAGTTGCAGTTGAGCAGA
1 CTTATCTCCCTGAAGTTGCAGTTGAGCAGA
9811960 TTAAAGCCAA
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
43 3 0.05
44 25 0.40
45 28 0.45
46 6 0.10
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTTGAGCAGACTAAGTAAGCAAGC
Found at i:9812070 original size:217 final size:218
Alignment explanation
Indices: 9811695--9812172 Score: 676
Period size: 217 Copynumber: 2.2 Consensus size: 218
9811685 GCAATTTAAA
* * *
9811695 AGACTGAAGATGATGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAATAATCCT
1 AGACTGAAGATGACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCAT
9811760 ATCTCCCTAAAGTCGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAATTGCAGAGA
66 ATCTCCCTAAAGTCGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAATTGCAGAGA
* * *
9811825 GCAGATCGCATCTAGACTTATCTCCCTGAAGTTGCAGTGGAGCAGGCT-AAGTAAGCAAGCCTTA
131 GCAGATCGCATCGAGACTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGCCTTA
* * * *
9811889 TCCTCCTGAAGTTGTAGTGAGGC
196 TCCCCCTAAAATTGCAGTGAGGC
* *
9811912 AGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTTGAGCAGATTAAAGCCAATAATCAT
1 AGACTGAAGATGACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCAT
* * * * *
9811977 ATCTCTCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGA
66 ATCTCCCTAAAGTCGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAATTGCAGAGA
* * *
9812042 GCAGA-CGCATCGGGTACTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCAAGTCTT
131 GCAGATCGCATCGAG-ACTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGCCTT
*
9812106 ATCCCCCTAAAATTGCAGTGCGGC
195 ATCCCCCTAAAATTGCAGTGAGGC
* * * * *
9812130 AGACT-AA-ATAAACAAATCTCATCTCCCTAAAGTTGTAGTGGAG
1 AGACTGAAGAT-GACGAATCTTATCTCCCTGAAGTTGCAGTGGAG
9812173 TGGATTAGAA
Statistics
Matches: 230, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
216 9 0.04
217 185 0.80
218 36 0.16
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (218 bp):
AGACTGAAGATGACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCAT
ATCTCCCTAAAGTCGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAATTGCAGAGA
GCAGATCGCATCGAGACTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGCCTTA
TCCCCCTAAAATTGCAGTGAGGC
Found at i:9812707 original size:19 final size:19
Alignment explanation
Indices: 9812683--9812755 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
9812673 AATCTTCAAG
9812683 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
9812702 GATATGCAGTCTTAGATAT
1 GATATGCAATCTTAGATAT
*
9812721 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
9812740 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
9812756 AGTTATAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:9813006 original size:23 final size:23
Alignment explanation
Indices: 9812962--9813006 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
9812952 TCTTATTTTG
* *
9812962 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
9812985 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
9813007 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:9818389 original size:15 final size:14
Alignment explanation
Indices: 9818362--9818389 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9818352 AATTAGTGTT
9818362 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
9818376 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
9818390 TGGGGGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
GAAAACTAAAAAAA
Found at i:9819222 original size:41 final size:41
Alignment explanation
Indices: 9819112--9819249 Score: 143
Period size: 42 Copynumber: 3.4 Consensus size: 41
9819102 GATGCTAACG
* * * * * * *
9819112 GAAAAACGCTACGATAGGTAAAGCAGTAGCGGGGTTTATGA
1 GAAAAACGCCACAAAAGGTCAAGCATTAGCGGCGTTTATAA
* **
9819153 GAAAAACAACTGCAAAAGGTCAAGCATTAGCGGCGTTTATAA
1 GAAAAAC-GCCACAAAAGGTCAAGCATTAGCGGCGTTTATAA
* *
9819195 GAAAAACGCCACAAAAGGTCAAGCATTAGCAGCG-CTATAA
1 GAAAAACGCCACAAAAGGTCAAGCATTAGCGGCGTTTATAA
*
9819235 GAAAAACGCCGCAAA
1 GAAAAACGCCACAAA
9819250 GTATCATTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
40 19 0.23
41 30 0.37
42 33 0.40
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (41 bp):
GAAAAACGCCACAAAAGGTCAAGCATTAGCGGCGTTTATAA
Found at i:9819306 original size:19 final size:19
Alignment explanation
Indices: 9819282--9819320 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
9819272 ACGGCATCTT
9819282 TTTGCTCTGCTCAGTTTTA
1 TTTGCTCTGCTCAGTTTTA
9819301 TTTGCTCTGCTCAGTTTTA
1 TTTGCTCTGCTCAGTTTTA
9819320 T
1 T
9819321 CCCCAACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.21, G:0.15, T:0.54
Consensus pattern (19 bp):
TTTGCTCTGCTCAGTTTTA
Found at i:9821464 original size:41 final size:39
Alignment explanation
Indices: 9821419--9821546 Score: 114
Period size: 39 Copynumber: 3.2 Consensus size: 39
9821409 AGCGGTATTT
**
9821419 TTAGCGGCG-TTTGGACAAAAAACGCCGCTAAAAATTGAGCA
1 TTAGCGGCGCTTT-GA-AAAAAACGCCGCT-AAAATACAGCA
* **
9821460 TTAGCGGCGCTTTTAGGAAAACGCCGCTAAAATACAGCA
1 TTAGCGGCGCTTTGAAAAAAACGCCGCTAAAATACAGCA
* *** * * *
9821499 TTAGCGGCACTTTTTGAAAAATGCTGCTAAAATAGAGCA
1 TTAGCGGCGCTTTGAAAAAAACGCCGCTAAAATACAGCA
9821538 TTAGCGGCG
1 TTAGCGGCG
9821547 TTTTCCAAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
39 50 0.68
40 11 0.15
41 10 0.14
42 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (39 bp):
TTAGCGGCGCTTTGAAAAAAACGCCGCTAAAATACAGCA
Found at i:9821503 original size:39 final size:39
Alignment explanation
Indices: 9821436--9821550 Score: 151
Period size: 39 Copynumber: 2.9 Consensus size: 39
9821426 CGTTTGGACA
*
9821436 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTTAG
1 AAAAACGCCGCT-AAAATAGAGCATTAGCGGCGCTTTTAG
* * * *
9821476 GAAAACGCCGCTAAAATACAGCATTAGCGGCACTTTTTG
1 AAAAACGCCGCTAAAATAGAGCATTAGCGGCGCTTTTAG
* *
9821515 AAAAATGCTGCTAAAATAGAGCATTAGCGGCG-TTTT
1 AAAAACGCCGCTAAAATAGAGCATTAGCGGCGCTTTT
9821551 CCAAGAAGCG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 4 0.06
39 50 0.77
40 11 0.17
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (39 bp):
AAAAACGCCGCTAAAATAGAGCATTAGCGGCGCTTTTAG
Found at i:9821795 original size:41 final size:41
Alignment explanation
Indices: 9821609--9821808 Score: 137
Period size: 41 Copynumber: 4.9 Consensus size: 41
9821599 CTTTTGAGGA
*
9821609 TTTAGCGGCG-TTTT-AAAAATGCG-TCGCTAATGAT-TGGGCC
1 TTTAGCGGCGTTTTTCAAAAA-GCGCT-GCTAATGCTCTGGG-C
** *
9821649 TTTAGCGATGTTTTTCAAAAAGCG-T-CAAGAATGCT-TGGGGC
1 TTTAGCGGCGTTTTTCAAAAAGCGCTGC--TAATGCTCT-GGGC
* * * * *
9821690 TTTAGCGGCATTTTACAAAAAACGCCGCGAATGCTC-GGGAC
1 TTTAGCGGCGTTTTTCAAAAAGCGCTGCTAATGCTCTGGG-C
* ** *
9821731 TTAAGCGGCGTTTCCCAATAAGCGCTGCTAATGCTCTGGGC
1 TTTAGCGGCGTTTTTCAAAAAGCGCTGCTAATGCTCTGGGC
* **
9821772 TTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCT
1 TTTAGCGGCGTTTTTCAAAAAGCGCTGCTAATGCTCT
9821809 ATTTTTAGCG
Statistics
Matches: 125, Mismatches: 25, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
39 1 0.01
40 11 0.09
41 101 0.81
42 11 0.09
43 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTCAAAAAGCGCTGCTAATGCTCTGGGC
Found at i:9822076 original size:14 final size:14
Alignment explanation
Indices: 9822057--9822261 Score: 105
Period size: 14 Copynumber: 13.9 Consensus size: 14
9822047 TATCACTATA
*
9822057 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
9822071 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* *
9822085 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
*
9822099 GTTTAGGTGTTACCAT-
1 GTTTAGG-GTT--TATG
*
9822115 -TTTAAGGTTTATG
1 GTTTAGGGTTTATG
*
9822128 GATTATGGGTTTATAG
1 GTTTA-GGGTTTAT-G
*
9822144 G-TTATGGTTTATG
1 GTTTAGGGTTTATG
*
9822157 GTTTATGGTTTATG
1 GTTTAGGGTTTATG
*
9822171 GTTTAAAGGCTGGTATTTAAG
1 GTTT--A-G--GG--TTTATG
9822192 GTTTAGAGG-TTATG
1 GTTTAG-GGTTTATG
* *
9822206 TGTTAAGGGTTTAGG
1 -GTTTAGGGTTTATG
*
9822221 GTTTTAGGGTTTTAAG
1 G-TTTAGGG-TTTATG
9822237 GTTTA-GGTTTATG
1 GTTTAGGGTTTATG
*
9822250 GTTTAGGATTTA
1 GTTTAGGGTTTA
9822262 GATTAACTAG
Statistics
Matches: 148, Mismatches: 23, Indels: 40
0.70 0.11 0.19
Matches are distributed among these distances:
12 2 0.01
13 12 0.08
14 72 0.49
15 37 0.25
16 9 0.06
17 3 0.02
18 1 0.01
19 3 0.02
21 9 0.06
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.47
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:9822102 original size:7 final size:7
Alignment explanation
Indices: 9822057--9822175 Score: 82
Period size: 7 Copynumber: 16.7 Consensus size: 7
9822047 TATCACTATA
*
9822057 GTTTAGG
1 GTTTATG
*
9822064 GTTTTTG
1 GTTTATG
*
9822071 GTTTAGG
1 GTTTATG
*
9822078 GTATATG
1 GTTTATG
9822085 GTTTA-G
1 GTTTATG
*
9822091 AGTTTAAG
1 -GTTTATG
9822099 GTTTA-G
1 GTTTATG
**
9822105 GTGTTACCA
1 GT-TTA-TG
* *
9822114 TTTTAAG
1 GTTTATG
9822121 GTTTATG
1 GTTTATG
*
9822128 GATTATGG
1 GTTTAT-G
9822136 GTTTATAG
1 GTTTAT-G
9822144 G-TTATG
1 GTTTATG
9822150 GTTTATG
1 GTTTATG
9822157 GTTTATG
1 GTTTATG
9822164 GTTTATG
1 GTTTATG
9822171 GTTTA
1 GTTTA
9822176 AAGGCTGGTA
Statistics
Matches: 89, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
6 6 0.07
7 70 0.79
8 12 0.13
9 1 0.01
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (7 bp):
GTTTATG
Found at i:9822152 original size:29 final size:27
Alignment explanation
Indices: 9822120--9822173 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
9822110 ACCATTTTAA
9822120 GGTTTATGGATTATGGGTTTATAGGTTAT
1 GGTTTATGGATTAT-GGTTTAT-GGTTAT
*
9822149 GGTTTATGGTTTATGGTTTATGGTT
1 GGTTTATGGATTATGGTTTATGGTT
9822174 TAAAGGCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.17
28 7 0.29
29 13 0.54
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (27 bp):
GGTTTATGGATTATGGTTTATGGTTAT
Found at i:9822221 original size:7 final size:7
Alignment explanation
Indices: 9822211--9822262 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
9822201 TTATGTGTTA
9822211 AGGGTTT
1 AGGGTTT
9822218 AGGGTTTT
1 AGGG-TTT
9822226 AGGGTTTT
1 AGGG-TTT
*
9822234 AAGGTTT
1 AGGGTTT
9822241 A-GGTTT
1 AGGGTTT
*
9822247 ATGGTTT
1 AGGGTTT
*
9822254 AGGATTT
1 AGGGTTT
9822261 AG
1 AG
9822263 ATTAACTAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
6 6 0.15
7 20 0.50
8 14 0.35
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
AGGGTTT
Found at i:9822231 original size:15 final size:14
Alignment explanation
Indices: 9822211--9822262 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
9822201 TTATGTGTTA
9822211 AGGGTTTAGGGTTTT
1 AGGGTTTAGGG-TTT
*
9822226 AGGGTTTTAAGGTTT
1 AGGG-TTTAGGGTTT
*
9822241 A-GGTTTATGGTTT
1 AGGGTTTAGGGTTT
*
9822254 AGGATTTAG
1 AGGGTTTAG
9822263 ATTAACTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 10 0.32
14 7 0.23
15 8 0.26
16 6 0.19
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (14 bp):
AGGGTTTAGGGTTT
Found at i:9822328 original size:7 final size:7
Alignment explanation
Indices: 9822307--9822474 Score: 52
Period size: 7 Copynumber: 23.7 Consensus size: 7
9822297 TTAATTATCA
*
9822307 TTATAGT
1 TTATGGT
*
9822314 TTAGGGT
1 TTATGGT
9822321 TTATGGT
1 TTATGGT
*
9822328 TTAAGGT
1 TTATGGT
*
9822335 ATATGGT
1 TTATGGT
*
9822342 TTAGGGT
1 TTATGGT
*
9822349 TTAAGGT
1 TTATGGT
*
9822356 TTA-GGAG
1 TTATGG-T
***
9822363 TTACTACC
1 TTA-TGGT
*
9822371 TTAAGGT
1 TTATGGT
*
9822378 TTATGGA
1 TTATGGT
*
9822385 TTATGGA
1 TTATGGT
*
9822392 TTATGGA
1 TTATGGT
9822399 TTATGGTT
1 TTATGG-T
* *
9822407 TTAAGGG
1 TTATGGT
*
9822414 TTAGGGT
1 TTATGGT
*
9822421 TTAAGG-
1 TTATGGT
*
9822427 TTATGGG
1 TTATGGT
*
9822434 TTAGGGGT
1 TTA-TGGT
* *
9822442 TAAGGGT
1 TTATGGT
* *
9822449 TAAGGGT
1 TTATGGT
*
9822456 TTATAGT
1 TTATGGT
*
9822463 TTATGTT
1 TTATGGT
9822470 TTATG
1 TTATG
9822475 ATTTTGGGTT
Statistics
Matches: 121, Mismatches: 34, Indels: 12
0.72 0.20 0.07
Matches are distributed among these distances:
6 7 0.06
7 102 0.84
8 12 0.10
ACGTcount: A:0.23, C:0.02, G:0.31, T:0.44
Consensus pattern (7 bp):
TTATGGT
Found at i:9822329 original size:14 final size:14
Alignment explanation
Indices: 9822307--9822360 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
9822297 TTAATTATCA
*
9822307 TTATAGTTTAGGGT
1 TTATGGTTTAGGGT
*
9822321 TTATGGTTTAAGGT
1 TTATGGTTTAGGGT
*
9822335 ATATGGTTTAGGGT
1 TTATGGTTTAGGGT
*
9822349 TTAAGGTTTAGG
1 TTATGGTTTAGG
9822361 AGTTACTACC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
TTATGGTTTAGGGT
Found at i:9822432 original size:35 final size:36
Alignment explanation
Indices: 9822392--9822467 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 36
9822382 GGATTATGGA
**
9822392 TTATGGATTATGGTTTTAAGGGTT-AGGGTTTA-AGG
1 TTATGGATTA-GGGGTTAAGGGTTAAGGGTTTATAGG
* *
9822427 TTATGGGTTAGGGGTTAAGGGTTAAGGGTTTATAGT
1 TTATGGATTAGGGGTTAAGGGTTAAGGGTTTATAGG
9822463 TTATG
1 TTATG
9822468 TTTTATGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 11 0.31
35 17 0.49
36 7 0.20
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.42
Consensus pattern (36 bp):
TTATGGATTAGGGGTTAAGGGTTAAGGGTTTATAGG
Found at i:9822436 original size:20 final size:21
Alignment explanation
Indices: 9822407--9822456 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
9822397 GATTATGGTT
*
9822407 TTAAGGGTTAGGGTTTAA-GG
1 TTAAGGGTTAGGGGTTAAGGG
*
9822427 TTATGGGTTAGGGGTTAAGGG
1 TTAAGGGTTAGGGGTTAAGGG
9822448 TTAAGGGTT
1 TTAAGGGTT
9822457 TATAGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (21 bp):
TTAAGGGTTAGGGGTTAAGGG
Found at i:9822617 original size:19 final size:17
Alignment explanation
Indices: 9822592--9822627 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
9822582 TAGATCAATT
9822592 TTATATATATTAAATGG
1 TTATATATATTAAATGG
9822609 TTATATATATTAAATGG
1 TTATATATATTAAATGG
9822626 TT
1 TT
9822628 TAGGATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (17 bp):
TTATATATATTAAATGG
Found at i:9826946 original size:43 final size:43
Alignment explanation
Indices: 9826898--9827013 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
9826888 ATAGTGGCGC
* *
9826898 TTGTGGTAGACGCGTCACTAAAGGTCATGATTTTTAGCGGAGT
1 TTGTGGTAGAAGCGTCACTAAAGGTCATGATCTTTAGCGGAGT
*
9826941 TTGTGGTAGAAGCGTCGCTAAAGGTCATGATCTTTAGCGGCA-T
1 TTGTGGTAGAAGCGTCACTAAAGGTCATGATCTTTAGCGG-AGT
* * * * *
9826984 TTGCGGAAGAAGCGCCGCTAAAGGCCATGA
1 TTGTGGTAGAAGCGTCACTAAAGGTCATGA
9827014 GTTAGTGGCG
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 64 0.98
44 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (43 bp):
TTGTGGTAGAAGCGTCACTAAAGGTCATGATCTTTAGCGGAGT
Found at i:9827307 original size:35 final size:35
Alignment explanation
Indices: 9827262--9827328 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
9827252 AAATTTAAAG
*
9827262 ATGATAATCATAACTTATATAAACATTTAAAGTTT
1 ATGATAATCATAACTTACATAAACATTTAAAGTTT
* *
9827297 ATGATTATCATAATTTACATAAACATTTAAAG
1 ATGATAATCATAACTTACATAAACATTTAAAG
9827329 AGTAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (35 bp):
ATGATAATCATAACTTACATAAACATTTAAAGTTT
Found at i:9827403 original size:56 final size:56
Alignment explanation
Indices: 9827339--9827455 Score: 198
Period size: 56 Copynumber: 2.1 Consensus size: 56
9827329 AGTAAAAAAA
** *
9827339 AACTTTGGACCATAACTTATTTAACTTACATAATACATAATTATATATCATATCAT
1 AACTTTGGACCATAACTTACATAACTTACATAATACATAAATATATATCATATCAT
*
9827395 AACTTTGGATCATAACTTACATAACTTACATAATACATAAATATATATCATATCAT
1 AACTTTGGACCATAACTTACATAACTTACATAATACATAAATATATATCATATCAT
9827451 AACTT
1 AACTT
9827456 ACATAAAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (56 bp):
AACTTTGGACCATAACTTACATAACTTACATAATACATAAATATATATCATATCAT
Found at i:9833529 original size:43 final size:43
Alignment explanation
Indices: 9833468--9833626 Score: 124
Period size: 43 Copynumber: 3.7 Consensus size: 43
9833458 TTTCCACAAA
* * * *
9833468 CGCCGCCAAAGAACATGACTTTTATCGGCGCTTTTAGTAAAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAGGAAAAG
* * *
9833511 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTGGGGAAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAGGAAAAG
* * ** * *
9833554 CACCGCTAAAGGTA-ATGTTCTTTAGCGGC-ATTTGTAGGGAAAG
1 CGCCGCTAAA-GAACATGACCTTTAGCGGCGCTTT-TAGGAAAAG
* * * **
9833597 CGCAGCCAAAGGACATGTTCTTTAGCGGCG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCG
9833627 TTTGTGTGAG
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
42 5 0.05
43 88 0.93
44 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (43 bp):
CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAGGAAAAG
Found at i:9833631 original size:43 final size:43
Alignment explanation
Indices: 9833507--9833631 Score: 153
Period size: 43 Copynumber: 2.9 Consensus size: 43
9833497 GCTTTTAGTA
* ** * *
9833507 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTGGGG
1 AAAGCGCCGCTAAAGGACATGTTCTTTAGCGGCGTTTGTAGGG
* *
9833550 AAAGCACCGCTAAAGGTA-ATGTTCTTTAGCGGCATTTGTAGGG
1 AAAGCGCCGCTAAAGG-ACATGTTCTTTAGCGGCGTTTGTAGGG
* *
9833593 AAAGCGCAGCCAAAGGACATGTTCTTTAGCGGCGTTTGT
1 AAAGCGCCGCTAAAGGACATGTTCTTTAGCGGCGTTTGT
9833632 GTGAGAAGTG
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 1 0.01
43 67 0.97
44 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGGACATGTTCTTTAGCGGCGTTTGTAGGG
Found at i:9842235 original size:16 final size:18
Alignment explanation
Indices: 9842200--9842237 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
9842190 GATATTAATA
9842200 ATTCATTCCAAATATTTT
1 ATTCATTCCAAATATTTT
*
9842218 ATTCA-TCCAACT-TTTT
1 ATTCATTCCAAATATTTT
9842234 ATTC
1 ATTC
9842238 TCTCCCTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTCATTCCAAATATTTT
Found at i:9846870 original size:19 final size:19
Alignment explanation
Indices: 9846846--9846884 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9846836 ATGTCAAAAT
9846846 TTTCAAGTATCCAAAT-TGA
1 TTTCAAGTAT-CAAATGTGA
*
9846865 TTTCAATTATCAAATGTGA
1 TTTCAAGTATCAAATGTGA
9846884 T
1 T
9846885 AAATCAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (19 bp):
TTTCAAGTATCAAATGTGA
Found at i:9856488 original size:92 final size:90
Alignment explanation
Indices: 9856201--9856550 Score: 384
Period size: 91 Copynumber: 3.8 Consensus size: 90
9856191 ATAACACATC
* * *
9856201 AGATGCACATAGTGCAAAGCCCGTAGGCTAAAAATTCTCCAC-CAATAACACGCCAGTTAGCTCA
1 AGATGCACATAGTGCAAAGCCCGTAGGCTAAATATT-TCC-CTCAATAACATGCCAGTTTGCTCA
* * *
9856265 TAAAAGCTATTCCAACCGATATCACACT
64 TAAGAGCTATTCCAA-CGATAACACGCT
* * *
9856293 AGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTTCCCCCAATAACACT-TCAGATTGCTCAT
1 AGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTTCCCTCAATAACA-TGCCAGTTTGCTCAT
9856357 AAGAGCTATTCCAACTGATAA-ATCGCT
65 AAGAGCTATTCCAAC-GATAACA-CGCT
** * * *
9856384 AGATGCACATAGTGCAAA-CCAAATAGGCTAAATATTCTCCCTCGATAACATGCCAGTTTTCTCG
1 AGATGCACATAGTGCAAAGCC-CGTAGGCTAAATATT-TCCCTCAATAACATGCCAGTTTGCTCA
* *
9856448 TAAGAGTTATTCCAATCGATAACACGCC
64 TAAGAGCTATTCCAA-CGATAACACGCT
* * * * * *
9856476 AAATACACATAGTACAAAGCTCGTAGGCTAAATATTTCCCTCGATAACATGCCAGTTTACTCATA
1 AGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTTCCCTCAATAACATGCCAGTTTGCTCATA
*
9856541 ATAGCTATTC
66 AGAGCTATTC
9856551 AAACCAATAT
Statistics
Matches: 220, Mismatches: 28, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
90 5 0.02
91 108 0.49
92 104 0.47
93 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (90 bp):
AGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTTCCCTCAATAACATGCCAGTTTGCTCATA
AGAGCTATTCCAACGATAACACGCT
Found at i:9856503 original size:183 final size:183
Alignment explanation
Indices: 9856201--9856550 Score: 436
Period size: 183 Copynumber: 1.9 Consensus size: 183
9856191 ATAACACATC
**
9856201 AGATGCACATAGTGCAAAGCCCGTAGGCTAAAAATTCTCCACCAATAACACGCCAGTTAGCTCAT
1 AGATGCACATAGTGCAAAGCCAATAGGCTAAAAATTCTCCACCAATAACACGCCAGTTAGCTCAT
* * * * *
9856266 AAAAGCTATTCCAACCGATATCACACTAGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTTC
66 AAAAGCTATTCCAACCGATAACACACCAAATACACATAGTACAAAGCCCGTAGGCTAAATATTTC
* *
9856331 CCCCAATAACACT-TCAGATTGCTCATAAGAGCTATTCCAACTGATAAATCGCT
131 CCCCAATAACA-TGCCAGATTACTCATAAGAGCTATTCCAACTGATAAATCGCT
* * * **
9856384 AGATGCACATAGTGCAAA-CCAAATAGGCTAAATATTCTCC-CTCGATAACATGCCAGTTTTCTC
1 AGATGCACATAGTGCAAAGCC-AATAGGCTAAAAATTCTCCAC-CAATAACACGCCAGTTAGCTC
* * * * * *
9856447 GTAAGAGTTATTCCAATCGATAACACGCCAAATACACATAGTACAAAGCTCGTAGGCTAAATATT
64 ATAAAAGCTATTCCAACCGATAACACACCAAATACACATAGTACAAAGCCCGTAGGCTAAATATT
* * * *
9856512 TCCCTCGATAACATGCCAGTTTACTCATAATAGCTATTC
129 TCCCCCAATAACATGCCAGATTACTCATAAGAGCTATTC
9856551 AAACCAATAT
Statistics
Matches: 140, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
182 4 0.03
183 136 0.97
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (183 bp):
AGATGCACATAGTGCAAAGCCAATAGGCTAAAAATTCTCCACCAATAACACGCCAGTTAGCTCAT
AAAAGCTATTCCAACCGATAACACACCAAATACACATAGTACAAAGCCCGTAGGCTAAATATTTC
CCCCAATAACATGCCAGATTACTCATAAGAGCTATTCCAACTGATAAATCGCT
Found at i:9862176 original size:69 final size:71
Alignment explanation
Indices: 9862050--9862180 Score: 185
Period size: 69 Copynumber: 1.9 Consensus size: 71
9862040 GTTCTGGACA
* * *
9862050 TTGTTTTGATAGTCTGCTGGAAAATGTTATTTTAGTTTGTTAGTGAGTAGAAGATGAAACTGTTG
1 TTGTTTTGATAGTCTGCTGGAAAATGTTACTTGAGTTTGTTAGTCAGTAGAAGATGAAACTGTTG
9862115 TGGCAG
66 TGGCAG
* ** *
9862121 TTGTTTTGATTGTCTGCTGGAACTTGTT-CTTGA-TTTGTTAGTCAGTAGAATATGAAACTG
1 TTGTTTTGATAGTCTGCTGGAAAATGTTACTTGAGTTTGTTAGTCAGTAGAAGATGAAACTG
9862181 GAACTTTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
69 25 0.47
70 3 0.06
71 25 0.47
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.43
Consensus pattern (71 bp):
TTGTTTTGATAGTCTGCTGGAAAATGTTACTTGAGTTTGTTAGTCAGTAGAAGATGAAACTGTTG
TGGCAG
Found at i:9868846 original size:16 final size:16
Alignment explanation
Indices: 9868819--9868877 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
9868809 ATTTTTATTT
9868819 TTATTT-TTATTTTTC
1 TTATTTCTTATTTTTC
*
9868834 TTATTTCTTATTTCTTT
1 TTATTTCTTATTT-TTC
*
9868851 TTCATTTTCTTTGTTTTTC
1 TT-A-TTTC-TTATTTTTC
9868870 TT-TTTCTT
1 TTATTTCTT
9868878 GACTTTTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
15 8 0.22
16 10 0.28
17 4 0.11
18 1 0.03
19 8 0.22
20 5 0.14
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.78
Consensus pattern (16 bp):
TTATTTCTTATTTTTC
Found at i:9868859 original size:6 final size:6
Alignment explanation
Indices: 9868792--9868832 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
9868782 TTCCTTCTTC
9868792 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
9868833 CTTATTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:9868873 original size:6 final size:6
Alignment explanation
Indices: 9868789--9868877 Score: 74
Period size: 6 Copynumber: 14.8 Consensus size: 6
9868779 ATGTTCCTTC
* * * * * *
9868789 TTCTTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTCTTAT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTT-T
* *
9868838 TTCTTAT TTCTTT TTCATT TTC--T TTGTTT TTCTTT TTCTT
1 TTCTT-T TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTT
9868878 GACTTTTGAT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
4 3 0.04
6 59 0.79
7 13 0.17
ACGTcount: A:0.10, C:0.09, G:0.01, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:9873246 original size:9 final size:9
Alignment explanation
Indices: 9873232--9873315 Score: 107
Period size: 9 Copynumber: 9.4 Consensus size: 9
9873222 TTTGGTTAAA
9873232 AATTAACCG
1 AATTAACCG
9873241 AATTAACC-
1 AATTAACCG
* *
9873249 AAATACCCG
1 AATTAACCG
9873258 AATTAACCG
1 AATTAACCG
9873267 AATTAACCG
1 AATTAACCG
*
9873276 AATTACCCG
1 AATTAACCG
*
9873285 AATTAACCA
1 AATTAACCG
*
9873294 AATTAACCA
1 AATTAACCG
*
9873303 AATTAACCA
1 AATTAACCG
9873312 AATT
1 AATT
9873316 GAATCACTAC
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
8 6 0.09
9 61 0.91
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:9873306 original size:27 final size:27
Alignment explanation
Indices: 9873232--9873307 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
9873222 TTTGGTTAAA
9873232 AATTAACCGAATTAACCAAA-TACCCG
1 AATTAACCGAATTAACCAAATTACCCG
*
9873258 AATTAACCGAATTAACCGAATTACCCG
1 AATTAACCGAATTAACCAAATTACCCG
*
9873285 AATTAACCAAATTAACCAAATTA
1 AATTAACCGAATTAACCAAATTA
9873308 ACCAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 19 0.41
27 27 0.59
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (27 bp):
AATTAACCGAATTAACCAAATTACCCG
Found at i:9873315 original size:27 final size:27
Alignment explanation
Indices: 9873231--9873315 Score: 118
Period size: 27 Copynumber: 3.2 Consensus size: 27
9873221 TTTTGGTTAA
9873231 AAATTAACCGAATTAACCAAA-TACCC
1 AAATTAACCGAATTAACCAAATTACCC
* *
9873257 GAATTAACCGAATTAACCGAATTACCC
1 AAATTAACCGAATTAACCAAATTACCC
* * *
9873284 GAATTAACCAAATTAACCAAATTAACC
1 AAATTAACCGAATTAACCAAATTACCC
9873311 AAATT
1 AAATT
9873316 GAATCACTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 19 0.37
27 33 0.63
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.22
Consensus pattern (27 bp):
AAATTAACCGAATTAACCAAATTACCC
Found at i:9873462 original size:18 final size:18
Alignment explanation
Indices: 9873422--9873465 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
9873412 TAATTTTATG
**
9873422 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
9873440 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
9873458 CTTGGGTT
1 ATTGGGTT
9873466 TAGATTGCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:9877578 original size:92 final size:91
Alignment explanation
Indices: 9877359--9877664 Score: 405
Period size: 92 Copynumber: 3.3 Consensus size: 91
9877349 CTCCAGATTA
* * ** * *
9877359 CTCATAAGAGTTATTCCCACCAATAACACATCAGATGCACACAGTACAAAGCCTGTAGGCTAAAT
1 CTCATAAGAGCTATTCCAACCAATAACACGCCAGATGCACATAGTACAAAGCCCGTAGGCTAAAT
9877424 ATTCTCCCCGGTAACACGTCAGTTTT
66 ATTCTCCCCGGTAACACGTCAGTTTT
* * *
9877450 CTCATAAGAGCTATTCCAACCAATATCACGCCAGATGCACATAGTACAAAGCCCATAGGATAAAT
1 CTCATAAGAGCTATTCCAACCAATAACACGCCAGATGCACATAGTACAAAGCCCGTAGGCTAAAT
** *
9877515 ATTCTCATTCGGTAACACGTCAGTTTG
66 ATTCTC-CCCGGTAACACGTCAGTTTT
* ** **
9877542 CTCATAAGAGCTATTCCAACCGATAACACGTTAGATGCACATAGTGTAAAGCCCGTAGGCTAAAT
1 CTCATAAGAGCTATTCCAACCAATAACACGCCAGATGCACATAGTACAAAGCCCGTAGGCTAAAT
* *
9877607 ATTCTCCCCCGATAACACGTCATTTTT
66 ATTCT-CCCCGGTAACACGTCAGTTTT
* *
9877634 CTCATAAGAACTATTCCAACCAATATCACGC
1 CTCATAAGAGCTATTCCAACCAATAACACGC
9877665 TAGAACCTCC
Statistics
Matches: 184, Mismatches: 29, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
91 62 0.34
92 121 0.66
93 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (91 bp):
CTCATAAGAGCTATTCCAACCAATAACACGCCAGATGCACATAGTACAAAGCCCGTAGGCTAAAT
ATTCTCCCCGGTAACACGTCAGTTTT
Found at i:9878838 original size:48 final size:52
Alignment explanation
Indices: 9878784--9878884 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 52
9878774 GAAGGCTTGT
* * * *
9878784 ATAATATTTCTCCTG-TAAA-AAAAAA-A-AGATACTAATTAAATTGTTATA
1 ATAATATTTCTCCAGAAAAATAAAAAATATAGAAACTAATTAAAATGTTATA
9878832 ATAATATTTCTCCAGAAAAATAAAAAATATAGAAACTAATTAAAATGTTATA
1 ATAATATTTCTCCAGAAAAATAAAAAATATAGAAACTAATTAAAATGTTATA
9878884 A
1 A
9878885 GTTTTCAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
48 14 0.31
49 3 0.07
50 6 0.13
51 1 0.02
52 21 0.47
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (52 bp):
ATAATATTTCTCCAGAAAAATAAAAAATATAGAAACTAATTAAAATGTTATA
Found at i:9879542 original size:11 final size:11
Alignment explanation
Indices: 9879526--9879558 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
9879516 GAGAGAAGTG
9879526 ATTTATACTTA
1 ATTTATACTTA
9879537 ATTTATACTTA
1 ATTTATACTTA
9879548 A--TATACTTA
1 ATTTATACTTA
9879557 AT
1 AT
9879559 AAAATAAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
11 12 0.57
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTATACTTA
Found at i:9892574 original size:398 final size:399
Alignment explanation
Indices: 9891838--9892637 Score: 1566
Period size: 398 Copynumber: 2.0 Consensus size: 399
9891828 TTGATTTACG
9891838 AATCTCCATTTCGTGTTGTACGTTATTCCTCTATTGTTTTATTTATTCAAAAGATTACGTTTCAT
1 AATCTCCATTTCGTGTTGTACGTTATTCCTCTATTGTTTTATTTATTCAAAAGATTACGTTTCAT
9891903 ATCATTTAAATGTCAAAAGCGTTTTTATCCAAAAAAAGCTCTCAAATAACGCGGCACTCGGAATT
66 ATCATTTAAATGTCAAAAGCGTTTTTATCCAAAAAAAGCTCTCAAATAACGCGGCACTCGGAATT
9891968 GGGGATCCTCGAAAAGATTGTGTCCTAACTTACTGGATTCCAATCTTCCTCGGGATCTAAGAAAC
131 GGGGATCCTCGAAAAGATTGTGTCCTAACTTACTGGATTCCAATCTTCCTCGGGATCTAAGAAAC
9892033 CGAATATCCCTTTTAATCAACACACAAATAAAAAACTCATTCTCGGGAATTCGACACGTTGTGCC
196 CGAATATCCCTTTTAATCAACACACAAATAAAAAACTCATTCTCGGGAATTCGACACGTTGTGCC
9892098 CTAACGCATTGGATGTGACATGTCGTTTTCTCAAGACGAGGATTCTTCTAACAAATGAAAATAAA
261 CTAACGCATTGGATGTGACATGTCGTTTTCTCAAGACGAGGATTCTTCTAACAAATGAAAATAAA
9892163 GGCAATATTTGATGTTTAGGGATTTTGTGAAATCAAACCCTAACTTACTGGGTTTGATTTTCTCA
326 GGCAATATTTGATGTTTAGGGATTTTGTGAAATCAAACCCTAACTTACTGGGTTTGATTTTCTCA
9892228 -TTAACCCA
391 TTTAACCCA
9892236 AATCTCCATTTCGTGTTGTACGTTATTCCTCTATTGTTTTATTTATTCAAAAGATTACGTTTCAT
1 AATCTCCATTTCGTGTTGTACGTTATTCCTCTATTGTTTTATTTATTCAAAAGATTACGTTTCAT
9892301 ATCATTTAAATGTCAAAAGCGTTTTTATCCAAAAAAAGCTCTCAAATAACGCGGCACTCGGAATT
66 ATCATTTAAATGTCAAAAGCGTTTTTATCCAAAAAAAGCTCTCAAATAACGCGGCACTCGGAATT
9892366 GGGGATCCTCGAAAAGATTGTGTCCTAACTTACTGGATTCCAATCTTCCTCGGGATCTAAGAAAC
131 GGGGATCCTCGAAAAGATTGTGTCCTAACTTACTGGATTCCAATCTTCCTCGGGATCTAAGAAAC
9892431 CGAATATCCCTTTTAATCAACACACAAATAAAAAACTCATTCTCGGGAATTCGACACGTTGTGCC
196 CGAATATCCCTTTTAATCAACACACAAATAAAAAACTCATTCTCGGGAATTCGACACGTTGTGCC
**
9892496 CTAACGCATTGGATGTGACATGTCGTTTTCTTGAGACGAGGATTCTTCTAACAAATGAAAATAAA
261 CTAACGCATTGGATGTGACATGTCGTTTTCTCAAGACGAGGATTCTTCTAACAAATGAAAATAAA
*
9892561 GGCAATATTTGATGTTTAGGGATTTTGTGAAATCGAACCCTAACTTACTGGGTTTGATTTTCTCA
326 GGCAATATTTGATGTTTAGGGATTTTGTGAAATCAAACCCTAACTTACTGGGTTTGATTTTCTCA
9892626 TTTAACCCA
391 TTTAACCCA
9892635 AAT
1 AAT
9892638 GATCAGATAC
Statistics
Matches: 398, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
398 387 0.97
399 11 0.03
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (399 bp):
AATCTCCATTTCGTGTTGTACGTTATTCCTCTATTGTTTTATTTATTCAAAAGATTACGTTTCAT
ATCATTTAAATGTCAAAAGCGTTTTTATCCAAAAAAAGCTCTCAAATAACGCGGCACTCGGAATT
GGGGATCCTCGAAAAGATTGTGTCCTAACTTACTGGATTCCAATCTTCCTCGGGATCTAAGAAAC
CGAATATCCCTTTTAATCAACACACAAATAAAAAACTCATTCTCGGGAATTCGACACGTTGTGCC
CTAACGCATTGGATGTGACATGTCGTTTTCTCAAGACGAGGATTCTTCTAACAAATGAAAATAAA
GGCAATATTTGATGTTTAGGGATTTTGTGAAATCAAACCCTAACTTACTGGGTTTGATTTTCTCA
TTTAACCCA
Found at i:9893780 original size:21 final size:23
Alignment explanation
Indices: 9893737--9893783 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
9893727 AAAATTTTCA
9893737 AAAATTGAAAACAAAAATCTTTT
1 AAAATTGAAAACAAAAATCTTTT
9893760 AAAATT-AAAA-AAAAAGT-TTTT
1 AAAATTGAAAACAAAAA-TCTTTT
9893781 AAA
1 AAA
9893784 CACTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.52
22 5 0.22
23 6 0.26
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAATTGAAAACAAAAATCTTTT
Found at i:9900889 original size:20 final size:20
Alignment explanation
Indices: 9900846--9900885 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9900836 NNNNNNNNNC
* *
9900846 ATATGTATATAGATATATAG
1 ATATGTATATAAATATATAA
9900866 ATATGTATATAAAT-TATAA
1 ATATGTATATAAATATATAA
9900885 A
1 A
9900886 ATATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
ATATGTATATAAATATATAA
Found at i:9902509 original size:25 final size:25
Alignment explanation
Indices: 9902476--9902637 Score: 89
Period size: 25 Copynumber: 6.6 Consensus size: 25
9902466 CTCTTTCGAT
* *
9902476 CCATTTAACGGGAAGCTCATGTGAG
1 CCATATAACGGGAAGCTCATATGAG
* * * *
9902501 CCATGTAACGGGAAGCTTATCTGGG
1 CCATATAACGGGAAGCTCATATGAG
** *
9902526 CTGTATAACGGGAAGCTCATAAGAG
1 CCATATAACGGGAAGCTCATATGAG
* ** **
9902551 CCATAT-TCAAGAAGCTCATGCGAG
1 CCATATAACGGGAAGCTCATATGAG
* * ** *
9902575 CCA-ATAACGCGTAGCTCCGAAGAG
1 CCATATAACGGGAAGCTCATATGAG
**
9902599 CCAT-TAACGGGAAGCTCCGGAT-AG
1 CCATATAACGGGAAGCT-CATATGAG
*
9902623 CCATATATCGGGAAG
1 CCATATAACGGGAAG
9902638 TTCAAGCAAG
Statistics
Matches: 102, Mismatches: 31, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
23 2 0.02
24 45 0.44
25 55 0.54
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (25 bp):
CCATATAACGGGAAGCTCATATGAG
Found at i:9902624 original size:24 final size:24
Alignment explanation
Indices: 9902572--9902637 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
9902562 AAGCTCATGC
* * *
9902572 GAGCCAATAACGCGTAGCTCCGAA
1 GAGCCATTAACGGGAAGCTCCGAA
*
9902596 GAGCCATTAACGGGAAGCTCCGGA
1 GAGCCATTAACGGGAAGCTCCGAA
* *
9902620 TAGCCATATATCGGGAAG
1 GAGCCAT-TAACGGGAAG
9902638 TTCAAGCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 26 0.74
25 9 0.26
ACGTcount: A:0.32, C:0.24, G:0.29, T:0.15
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCCGAA
Found at i:9903894 original size:15 final size:16
Alignment explanation
Indices: 9903866--9903896 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9903856 TTGAAATAGC
9903866 ATTAAAACAATAACTA
1 ATTAAAACAATAACTA
9903882 ATTAAAA-AATAACTA
1 ATTAAAACAATAACTA
9903897 TTCACACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTAAAACAATAACTA
Found at i:9904977 original size:20 final size:21
Alignment explanation
Indices: 9904938--9904979 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9904928 ACAAAATTAT
*
9904938 AAAATATAAAAATATTCATAA
1 AAAATATAAAAATATACATAA
9904959 AAAATATAAAAATA-ACATAA
1 AAAATATAAAAATATACATAA
9904979 A
1 A
9904980 GTACATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATATAAAAATATACATAA
Found at i:9917175 original size:25 final size:25
Alignment explanation
Indices: 9917142--9917303 Score: 89
Period size: 25 Copynumber: 6.6 Consensus size: 25
9917132 CTCTTTCGAT
* *
9917142 CCATTTAACGGGAAGCTCATGTGAG
1 CCATATAACGGGAAGCTCATATGAG
* * * *
9917167 CCATGTAACGGGAAGCTTATCTGGG
1 CCATATAACGGGAAGCTCATATGAG
** *
9917192 CTGTATAACGGGAAGCTCATAAGAG
1 CCATATAACGGGAAGCTCATATGAG
* ** **
9917217 CCATAT-TCAAGAAGCTCATGCGAG
1 CCATATAACGGGAAGCTCATATGAG
* * ** *
9917241 CCA-ATAACGCGTAGCTCCGAAGAG
1 CCATATAACGGGAAGCTCATATGAG
**
9917265 CCAT-TAACGGGAAGCTCCGGAT-AG
1 CCATATAACGGGAAGCT-CATATGAG
*
9917289 CCATATATCGGGAAG
1 CCATATAACGGGAAG
9917304 TTCAAGCAAG
Statistics
Matches: 102, Mismatches: 31, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
23 2 0.02
24 45 0.44
25 55 0.54
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (25 bp):
CCATATAACGGGAAGCTCATATGAG
Found at i:9917290 original size:24 final size:24
Alignment explanation
Indices: 9917238--9917303 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
9917228 AAGCTCATGC
* * *
9917238 GAGCCAATAACGCGTAGCTCCGAA
1 GAGCCATTAACGGGAAGCTCCGAA
*
9917262 GAGCCATTAACGGGAAGCTCCGGA
1 GAGCCATTAACGGGAAGCTCCGAA
* *
9917286 TAGCCATATATCGGGAAG
1 GAGCCAT-TAACGGGAAG
9917304 TTCAAGCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 26 0.74
25 9 0.26
ACGTcount: A:0.32, C:0.24, G:0.29, T:0.15
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCCGAA
Found at i:9918560 original size:15 final size:16
Alignment explanation
Indices: 9918532--9918562 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9918522 TTGAAATAGC
9918532 ATTAAAACAATAACTA
1 ATTAAAACAATAACTA
9918548 ATTAAAA-AATAACTA
1 ATTAAAACAATAACTA
9918563 TTCACACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTAAAACAATAACTA
Found at i:9919643 original size:20 final size:21
Alignment explanation
Indices: 9919604--9919645 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9919594 ACAAAATTAT
*
9919604 AAAATATAAAAATATTCATAA
1 AAAATATAAAAATATACATAA
9919625 AAAATATAAAAATA-ACATAA
1 AAAATATAAAAATATACATAA
9919645 A
1 A
9919646 GTACATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATATAAAAATATACATAA
Found at i:9925528 original size:4 final size:4
Alignment explanation
Indices: 9925519--9925570 Score: 54
Period size: 4 Copynumber: 13.0 Consensus size: 4
9925509 AGGAGAATAA
* *
9925519 AAAT AAAT AACAA AAAT AAAT AAAT AAAT -AA- AAAT AAAC AAAT AAATT
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T
9925567 AAAT
1 AAAT
9925571 CGAAAAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
3 4 0.10
4 29 0.73
5 7 0.17
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:9925535 original size:13 final size:12
Alignment explanation
Indices: 9925517--9925565 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
9925507 TAAGGAGAAT
9925517 AAAAATAAATAA
1 AAAAATAAATAA
9925529 CAAAAATAAATAA
1 -AAAAATAAATAA
*
9925542 ATAAATAAAAATAA
1 A-AAA-ATAAATAA
*
9925556 ACAAATAAAT
1 AAAAATAAAT
9925566 TAAATCGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 6 0.19
13 17 0.55
14 8 0.26
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAATAAATAA
Found at i:9925553 original size:18 final size:18
Alignment explanation
Indices: 9925519--9925565 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
9925509 AGGAGAATAA
*
9925519 AAATAAAT-AACAAAAAT
1 AAATAAATAAATAAAAAT
9925536 AAATAAATAAATAAAAAT
1 AAATAAATAAATAAAAAT
*
9925554 AAACAAATAAAT
1 AAATAAATAAAT
9925566 TAAATCGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATAAATAAATAAAAAT
Found at i:9926066 original size:19 final size:19
Alignment explanation
Indices: 9926023--9926062 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
9926013 GATTAAGGAG
9926023 AATAAAAATAACAAAAATA
1 AATAAAAATAACAAAAATA
*
9926042 AATAAAAATAA-ACAAATA
1 AATAAAAATAACAAAAATA
9926060 AAT
1 AAT
9926063 TAAATCGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (19 bp):
AATAAAAATAACAAAAATA
Found at i:9926463 original size:496 final size:496
Alignment explanation
Indices: 9925530--9926508 Score: 1780
Period size: 496 Copynumber: 2.0 Consensus size: 496
9925520 AATAAATAAC
*
9925530 AAAAATAAATAAATAAATAAAAATAAACAAATAAATTAAATCGAAAAACCAATAAGGAAGATTAA
1 AAAAATAAAAAAATAAATAAAAATAAACAAATAAATTAAATCGAAAAACCAATAAGGAAGATTAA
* *
9925595 CTCGCTTCAGGGTTTGTAACTAACTTCAGATTAGAGTTTTAGAGTGGATTAGTAATCGATTAACT
66 CTCGCTTAAGGGTTTGTAACTAACTTCAGATTAGAGTTTTACAGTGGATTAGTAATCGATTAACT
* *
9925660 AATTATTAGCTCCCGGCCTCAAATTAACGAGTAAATTGGTTGATACTCGCTTATCTCCCGACCTC
131 AATTATTACCTCCCGACCTCAAATTAACGAGTAAATTGGTTGATACTCGCTTATCTCCCGACCTC
*
9925725 ACTTTCTCAACCCAAATAAATTACAATTTACTTAGTTCGACTTATCTTTCGAACTCATCTAACCT
196 ACTTTCTCAACCCAAATAAATTACAATTTACTTAGTTCGACTTATCTTCCGAACTCATCTAACCT
*
9925790 ATGATAACTTATTAGGGTTGTGAAGCCTAACAATTTAAAAACACATAATTTATACCAACTAATCC
261 ATGATAACTTATTAGGGTTGTGAAGACTAACAATTTAAAAACACATAATTTATACCAACTAATCC
* * *
9925855 TTCTCGAGAAACCCTAAATCCTCCGTTAATCTCATCCCCATCCACTTGTTAATTTCCCTTAAGGG
326 TTCTCGAGAAACCCCAAATCCGCCATTAATCTCATCCCCATCCACTTGTTAATTTCCCTTAAGGG
9925920 ATTTAGCCACTCATGTTATTCATAATCTCAATTTCAATTGAATAAACTATGTGAGAAACACGATC
391 ATTTAGCCACTCATGTTATTCATAATCTCAATTTCAATTGAATAAACTATGTGAGAAACACGATC
9925985 GTTTCGGAGAAAAAAGGAGATTTGAATAGATTAAGGAGAAT
456 GTTTCGGAGAAAAAAGGAGATTTGAATAGATTAAGGAGAAT
9926026 AAAAATAACAAAAATAAATAAAAATAAACAAATAAATTAAATCGAAAAACCAATAAGGAAGATTA
1 AAAAATAA-AAAAATAAATAAAAATAAACAAATAAATTAAATCGAAAAACCAATAAGGAAGATTA
*
9926091 ACTTGCTTAAGGGTTTGTAACTAACTTCAGATTAGAGTTTTACAGTGGATTAGTAATCGATTAAC
65 ACTCGCTTAAGGGTTTGTAACTAACTTCAGATTAGAGTTTTACAGTGGATTAGTAATCGATTAAC
9926156 TAATTATTACCTCCCGACCTCAAATTAACGAGTAAATTGGTTGATACTCGCTTATCT-CCGACCT
130 TAATTATTACCTCCCGACCTCAAATTAACGAGTAAATTGGTTGATACTCGCTTATCTCCCGACCT
* *
9926220 CACTTTCTCAACGCAAATAAATTACAATTTACTTAGTTCGACTTATCTTCCGACCTCATCTAACC
195 CACTTTCTCAACCCAAATAAATTACAATTTACTTAGTTCGACTTATCTTCCGAACTCATCTAACC
*
9926285 TATGATAACTTATTAGGGTTGTGAAGACTAACAATTTAAGAACACATAATTTATACCAACTAATC
260 TATGATAACTTATTAGGGTTGTGAAGACTAACAATTTAAAAACACATAATTTATACCAACTAATC
*
9926350 CTTCTCGAGAAACCCCAAATCCGCCATTAATCTCATCCTCATCCACTTGTTAATTTCCCTTAAGG
325 CTTCTCGAGAAACCCCAAATCCGCCATTAATCTCATCCCCATCCACTTGTTAATTTCCCTTAAGG
9926415 GATTTAGCCACTCATGTTATTCATAATCTCAATTTCAATTGAATAAACTATGTGAGAAACACGAT
390 GATTTAGCCACTCATGTTATTCATAATCTCAATTTCAATTGAATAAACTATGTGAGAAACACGAT
* * *
9926480 CGTTTTGGAGAGAAAATGAGATTTGAATA
455 CGTTTCGGAGAAAAAAGGAGATTTGAATA
9926509 ATTGTGGATT
Statistics
Matches: 464, Mismatches: 18, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
496 292 0.63
497 172 0.37
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.31
Consensus pattern (496 bp):
AAAAATAAAAAAATAAATAAAAATAAACAAATAAATTAAATCGAAAAACCAATAAGGAAGATTAA
CTCGCTTAAGGGTTTGTAACTAACTTCAGATTAGAGTTTTACAGTGGATTAGTAATCGATTAACT
AATTATTACCTCCCGACCTCAAATTAACGAGTAAATTGGTTGATACTCGCTTATCTCCCGACCTC
ACTTTCTCAACCCAAATAAATTACAATTTACTTAGTTCGACTTATCTTCCGAACTCATCTAACCT
ATGATAACTTATTAGGGTTGTGAAGACTAACAATTTAAAAACACATAATTTATACCAACTAATCC
TTCTCGAGAAACCCCAAATCCGCCATTAATCTCATCCCCATCCACTTGTTAATTTCCCTTAAGGG
ATTTAGCCACTCATGTTATTCATAATCTCAATTTCAATTGAATAAACTATGTGAGAAACACGATC
GTTTCGGAGAAAAAAGGAGATTTGAATAGATTAAGGAGAAT
Found at i:9928178 original size:2 final size:2
Alignment explanation
Indices: 9928171--9928197 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9928161 AAACACGCAA
9928171 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9928198 GAAACTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9931819 original size:48 final size:48
Alignment explanation
Indices: 9931699--9931820 Score: 129
Period size: 48 Copynumber: 2.5 Consensus size: 48
9931689 TTGTCTGTGG
* * * *
9931699 TTAAATGATTGATTTGCCCGTGATGTAAATAAATGATTTGTCCTAGAT
1 TTAAATGACTGATTTGTCTGTGATTTAAATAAATGATTTGTCCTAGAT
* * * * * **
9931747 GTAAATGACTGTTTTATCTGTGATTTAAATGATTGATTTGTTTGTA-AT
1 TTAAATGACTGATTTGTCTGTGATTTAAATAAATGATTTG-TCCTAGAT
9931795 TTAAATGACTGATTTGTCTGTGATTT
1 TTAAATGACTGATTTGTCTGTGATTT
9931821 GTATGACTTA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
48 56 0.95
49 3 0.05
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (48 bp):
TTAAATGACTGATTTGTCTGTGATTTAAATAAATGATTTGTCCTAGAT
Found at i:9931828 original size:24 final size:24
Alignment explanation
Indices: 9931688--9931820 Score: 117
Period size: 24 Copynumber: 5.6 Consensus size: 24
9931678 TCTGAATACT
* *
9931688 TTTGTCTGTG-GTTAAATGATTGA
1 TTTGTCTGTGATTTAAATGACTGA
* * * * *
9931711 TTTGCCCGTGATGTAAATAAATGA
1 TTTGTCTGTGATTTAAATGACTGA
* * *
9931735 TTTGTCCT-AGATGTAAATGACTGT
1 TTTGT-CTGTGATTTAAATGACTGA
* *
9931759 TTTATCTGTGATTTAAATGATTGA
1 TTTGTCTGTGATTTAAATGACTGA
* *
9931783 TTTGTTTGTAATTTAAATGACTGA
1 TTTGTCTGTGATTTAAATGACTGA
9931807 TTTGTCTGTGATTT
1 TTTGTCTGTGATTT
9931821 GTATGACTTA
Statistics
Matches: 84, Mismatches: 23, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
23 10 0.12
24 73 0.87
25 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.47
Consensus pattern (24 bp):
TTTGTCTGTGATTTAAATGACTGA
Found at i:9931934 original size:27 final size:27
Alignment explanation
Indices: 9931896--9931958 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
9931886 ATAGAGAAAG
9931896 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTGGCT-TGGCCACATA
9931921 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
9931949 TACTGTTACT
1 TACTGTTACT
9931959 AGCAGCTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 1 0.03
26 5 0.15
27 26 0.76
28 2 0.06
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.33
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:9931966 original size:27 final size:27
Alignment explanation
Indices: 9931914--9931966 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
9931904 TGGTGGCTCT
* **
9931914 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAATCACTGTTACTAGCAGCTTG
9931941 GCCACATAT-ACTGTTACTAGCAGCTT
1 GCCACA-ATCACTGTTACTAGCAGCTT
9931967 TGCTGCGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTGTTACTAGCAGCTTG
Found at i:9936045 original size:27 final size:27
Alignment explanation
Indices: 9936012--9936078 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
9936002 GCAATATACG
* *
9936012 AAAGGAATGCCTTCATGGCAAACTTTA
1 AAAGGAATGCCTTCATGACAAACTCTA
*
9936039 AAGGGAATGCCTTCATGACAAACTCTA
1 AAAGGAATGCCTTCATGACAAACTCTA
9936066 AAAGGAATGCCTT
1 AAAGGAATGCCTT
9936079 GACGGCGTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (27 bp):
AAAGGAATGCCTTCATGACAAACTCTA
Found at i:9958258 original size:39 final size:39
Alignment explanation
Indices: 9958203--9958382 Score: 209
Period size: 39 Copynumber: 4.6 Consensus size: 39
9958193 AACATGTTTT
* * *
9958203 TGAGTATTGTGGTATATGTTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
9958242 TGAGTATTGTGATATATGCCTGAATGTTATGTGATTGTA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* ** *
9958281 TGAGTATTGTTATATATGCTTAAACATTATGTAATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
9958320 TGAGTATTGTGATATATGCATAAAGGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
9958359 T-ATGTAATGTGATACATGTTTAAA
1 TGA-GTATTGTGATATATGCTTAAA
9958383 AGTGATTATC
Statistics
Matches: 120, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
38 1 0.01
39 119 0.99
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.44
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:9959153 original size:42 final size:42
Alignment explanation
Indices: 9959103--9959197 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
9959093 TTTCCCAGTG
9959103 GTATCGATACCACTTGAGAGAATTACTAACACCATTT-TTATA
1 GTATCGATACCACTTGAGAGAATTACTAACACC-TTTGTTATA
* * *
9959145 GTATCGATACCACTTGAGAGAATTATTGATACCTTTGTTATA
1 GTATCGATACCACTTGAGAGAATTACTAACACCTTTGTTATA
9959187 GTATCGATACC
1 GTATCGATACC
9959198 TACATAATTG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
41 3 0.06
42 46 0.94
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (42 bp):
GTATCGATACCACTTGAGAGAATTACTAACACCTTTGTTATA
Found at i:9960255 original size:18 final size:18
Alignment explanation
Indices: 9960232--9960266 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
9960222 TTGAAAATTT
9960232 GGATTTGAGTAGAAAAGG
1 GGATTTGAGTAGAAAAGG
9960250 GGATTTGAGTAGAAAAG
1 GGATTTGAGTAGAAAAG
9960267 CATCCAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.37, T:0.23
Consensus pattern (18 bp):
GGATTTGAGTAGAAAAGG
Found at i:9961445 original size:73 final size:73
Alignment explanation
Indices: 9961344--9961490 Score: 267
Period size: 73 Copynumber: 2.0 Consensus size: 73
9961334 TTATATCATG
9961344 AGCAAAGTTTCCTTTCCTAAATACACCACCACACAAGGTTAGTAGGTGTATAGATAAGCATATAA
1 AGCAAAGTTTCCTTTCCTAAATACACCACCACACAAGGTTAGTAGGTGTATAGATAAGCATATAA
9961409 ATCCAACC
66 ATCCAACC
* * *
9961417 AGCAAAGTTTCCTTTCCTAAATACACCACCATACAAGGTTAGTAGGTGTATAGGTAAGCATCTAA
1 AGCAAAGTTTCCTTTCCTAAATACACCACCACACAAGGTTAGTAGGTGTATAGATAAGCATATAA
9961482 ATCCAACC
66 ATCCAACC
9961490 A
1 A
9961491 ATTTGTGAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (73 bp):
AGCAAAGTTTCCTTTCCTAAATACACCACCACACAAGGTTAGTAGGTGTATAGATAAGCATATAA
ATCCAACC
Found at i:9962331 original size:39 final size:39
Alignment explanation
Indices: 9962259--9962334 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
9962249 TTTCTTTATC
*
9962259 TAAATAGTAATTTTATTCAATTAATACTATTCCAACACT
1 TAAATAGTAATTTTATTCAATTAATACCATTCCAACACT
*
9962298 TAAATAAGTAATTTTATAT-AATTAAT-CCCTTCCAACA
1 TAAAT-AGTAATTTTAT-TCAATTAATACCATTCCAACA
9962335 TTATTTTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 14 0.42
40 18 0.55
41 1 0.03
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (39 bp):
TAAATAGTAATTTTATTCAATTAATACCATTCCAACACT
Found at i:9971235 original size:11 final size:11
Alignment explanation
Indices: 9971219--9971245 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
9971209 AATCCCGTAG
9971219 ATAATAAAATA
1 ATAATAAAATA
9971230 ATAATAAAATA
1 ATAATAAAATA
9971241 ATAAT
1 ATAAT
9971246 TTACTAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAATAAAATA
Found at i:9971415 original size:18 final size:19
Alignment explanation
Indices: 9971381--9971418 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
9971371 AAATCTTGTT
9971381 ATTAAACTTGGTGATGTGA
1 ATTAAACTTGGTGATGTGA
9971400 ATTAAA-TTGGAT-ATGTGA
1 ATTAAACTTGG-TGATGTGA
9971418 A
1 A
9971419 CACTTAACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (19 bp):
ATTAAACTTGGTGATGTGA
Found at i:9979646 original size:18 final size:18
Alignment explanation
Indices: 9979619--9979655 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
9979609 ATTGAGTAAG
*
9979619 AAAAGTGATTAATTTTAT
1 AAAAGCGATTAATTTTAT
9979637 AAAAGCGATTAATTTTAT
1 AAAAGCGATTAATTTTAT
9979655 A
1 A
9979656 TGCTCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.41
Consensus pattern (18 bp):
AAAAGCGATTAATTTTAT
Found at i:9981725 original size:3 final size:3
Alignment explanation
Indices: 9981717--9981773 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
9981707 GCATTAATGG
9981717 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
9981765 TAA AAA TAA
1 TAA TAA TAA
9981774 AATGACTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:9981774 original size:6 final size:6
Alignment explanation
Indices: 9981721--9981825 Score: 57
Period size: 6 Copynumber: 16.0 Consensus size: 6
9981711 TAATGGTAAT
* * * * * * *
9981721 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
*
9981769 AATAAA ATGACTAAA AATAAA TAGCATAAA AATAAA GAAAATAA AATAATA
1 AATAAA A--A-TAAA AATAAA -A--ATAAA AATAAA -AATA-AA AATAA-A
9981820 AATAAA
1 AATAAA
9981826 TAAATAAGAA
Statistics
Matches: 87, Mismatches: 3, Indels: 18
0.81 0.03 0.17
Matches are distributed among these distances:
6 59 0.68
7 14 0.16
8 4 0.05
9 10 0.11
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (6 bp):
AATAAA
Found at i:9981832 original size:15 final size:13
Alignment explanation
Indices: 9981717--9981824 Score: 85
Period size: 12 Copynumber: 8.8 Consensus size: 13
9981707 GCATTAATGG
9981717 TAAT-AATAATAA
1 TAATAAATAATAA
9981729 TAAT-AATAATAA
1 TAATAAATAATAA
9981741 TAAT-AATAATAA
1 TAATAAATAATAA
9981753 TAAT-AATAATAA
1 TAATAAATAATAA
9981765 TAA-AAATAA-AA
1 TAATAAATAATAA
*
9981776 TGACTAAA-AATAAA
1 T-AATAAATAAT-AA
9981790 TAGCATAAA-AATAA
1 TA--ATAAATAATAA
9981804 -AGA-AAATAA-AA
1 TA-ATAAATAATAA
9981815 TAATAAATAA
1 TAATAAATAA
9981825 ATAAATAAGA
Statistics
Matches: 83, Mismatches: 3, Indels: 20
0.78 0.03 0.19
Matches are distributed among these distances:
11 9 0.11
12 57 0.69
13 5 0.06
14 5 0.06
15 7 0.08
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (13 bp):
TAATAAATAATAA
Found at i:9993035 original size:26 final size:26
Alignment explanation
Indices: 9992989--9993038 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
9992979 TGCATTTCCC
*
9992989 CTAATGCAAAAGAAAACTAAAAACTA
1 CTAATGCAAAAGAAAAATAAAAACTA
*
9993015 CTAATG-AAAATAAAGAATAAAAAC
1 CTAATGCAAAAGAAA-AATAAAAAC
9993039 ATAAAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.64, C:0.12, G:0.08, T:0.16
Consensus pattern (26 bp):
CTAATGCAAAAGAAAAATAAAAACTA
Found at i:10004481 original size:27 final size:27
Alignment explanation
Indices: 10004449--10004505 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
10004439 AACACGTCAA
* *
10004449 GAAAGAAAATCCTTTATGGCTTAATAT
1 GAAAGAAAAGCCTTTATGGCGTAATAT
* *
10004476 GAAAGAAAAGCCTTTTTGGCGTGATAT
1 GAAAGAAAAGCCTTTATGGCGTAATAT
10004503 GAA
1 GAA
10004506 TGATTAGCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.30
Consensus pattern (27 bp):
GAAAGAAAAGCCTTTATGGCGTAATAT
Found at i:10007726 original size:6 final size:6
Alignment explanation
Indices: 10007715--10007755 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
10007705 CGAGTATGTA
* *
10007715 TATATG TATATG TATATA TATATG TATATA TATATG TATAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATAT
10007756 AATGCTCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:10007730 original size:12 final size:12
Alignment explanation
Indices: 10007709--10007756 Score: 78
Period size: 12 Copynumber: 3.8 Consensus size: 12
10007699 AAGGTACGAG
10007709 TATGTATATATGTA
1 TATGTATATA--TA
10007723 TATGTATATATA
1 TATGTATATATA
10007735 TATGTATATATA
1 TATGTATATATA
10007747 TATGTATATA
1 TATGTATATA
10007757 ATGCTCGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 24 0.71
14 10 0.29
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:10007773 original size:2 final size:2
Alignment explanation
Indices: 10007713--10007756 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
10007703 TACGAGTATG
* * * *
10007713 TA TA TA TG TA TA TG TA TA TA TA TA TG TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10007755 TA
1 TA
10007757 ATGCTCGAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10008568 original size:69 final size:70
Alignment explanation
Indices: 10008478--10008633 Score: 199
Period size: 69 Copynumber: 2.2 Consensus size: 70
10008468 TTTGAAGAAC
* * * **
10008478 ATGTATATACATTTGGTGATAATACTTGTTAGGC-ATATGTATATATGCATTCAGCTATTCATG-
1 ATGTATATACATTCGATGATAATACTTGTTAAGCAATATGTATATACACATTCAGCTATTCATGT
10008541 TTTAA
66 TTTAA
* *
10008546 AGTGTATATACATTCGATGATAATATTTGTTAAGCATATATGTATATACACATTCGGCTATTCAT
1 A-TGTATATACATTCGATGATAATACTTGTTAAGCA-ATATGTATATACACATTCAGCTATTCAT
10008611 GTTTTAA
64 GTTTTAA
*
10008618 ATAGTATATGCATTCG
1 AT-GTATATACATTCG
10008634 GTTTTAAGTG
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
68 1 0.01
69 29 0.39
71 27 0.36
72 18 0.24
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (70 bp):
ATGTATATACATTCGATGATAATACTTGTTAAGCAATATGTATATACACATTCAGCTATTCATGT
TTTAA
Found at i:10014613 original size:41 final size:41
Alignment explanation
Indices: 10014566--10014971 Score: 573
Period size: 41 Copynumber: 9.9 Consensus size: 41
10014556 TAAGTTTTTT
* *
10014566 GGGCCTTTAGCGGCGTTTTAGAAAAAGCGCCGCTAATGCTG
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
**
10014607 GGGCCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
10014648 GGGCCTTTAGCGTCGTTTTT-AACAAAGCGCCGCTAATGC-C
1 GGGCCTTTAGCGGCGTTTTTGAA-AAAGCGCCGCTAATGCTC
* * *
10014688 GGGCCTTTAGCGGCGTTTGTGAAGAAGCGCCGCTAATGCTG
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
10014729 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * * *
10014770 GAGCCTTTTAGCGGCGTTTCTGAAGAAGCGCCGCTAATTCTC
1 GGGCC-TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
10014812 GTGCCTTTAGCGGCGTTTTTGATAAAGCGCCGCTAGTGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
10014853 TGGCCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * * *
10014894 CGGTCTTTAGCGGCGCTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
10014935 TGGTCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
10014972 AATAACAAAA
Statistics
Matches: 324, Mismatches: 37, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
40 35 0.11
41 252 0.78
42 37 0.11
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:10015610 original size:7 final size:7
Alignment explanation
Indices: 10015598--10015659 Score: 63
Period size: 7 Copynumber: 8.9 Consensus size: 7
10015588 TAAATAAGGT
10015598 TTAGGGG
1 TTAGGGG
10015605 TTAGGGG
1 TTAGGGG
*
10015612 TTAGAGG
1 TTAGGGG
10015619 TTAGGGG
1 TTAGGGG
*
10015626 CT-GGGG
1 TTAGGGG
*
10015632 TTATGGG
1 TTAGGGG
*
10015639 TTATGGGT
1 TTA-GGGG
*
10015647 TTAGGGT
1 TTAGGGG
10015654 TTAGGG
1 TTAGGG
10015660 TTTTAAGGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
6 5 0.11
7 36 0.78
8 5 0.11
ACGTcount: A:0.15, C:0.02, G:0.50, T:0.34
Consensus pattern (7 bp):
TTAGGGG
Found at i:10015660 original size:7 final size:7
Alignment explanation
Indices: 10015595--10015693 Score: 60
Period size: 7 Copynumber: 14.0 Consensus size: 7
10015585 TATTAAATAA
10015595 GGTTTAG
1 GGTTTAG
*
10015602 GGGTTAG
1 GGTTTAG
*
10015609 GGGTTAG
1 GGTTTAG
10015616 AGG-TTAG
1 -GGTTTAG
**
10015623 GGGCT-G
1 GGTTTAG
*
10015629 GGGTTATG
1 GGTTTA-G
10015637 GG-TTATG
1 GGTTTA-G
10015644 GGTTTAG
1 GGTTTAG
10015651 GGTTTAG
1 GGTTTAG
*
10015658 GGTTTTAA
1 GG-TTTAG
*
10015666 GGTTTAA
1 GGTTTAG
*
10015673 GGTTAAG
1 GGTTTAG
*
10015680 GGTTCAG
1 GGTTTAG
10015687 GGTTTAG
1 GGTTTAG
10015694 AATTTAAGGG
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
6 7 0.09
7 57 0.73
8 14 0.18
ACGTcount: A:0.17, C:0.02, G:0.44, T:0.36
Consensus pattern (7 bp):
GGTTTAG
Found at i:10015845 original size:21 final size:21
Alignment explanation
Indices: 10015811--10015872 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
10015801 ATTGGGGTAA
10015811 TTAGGG-TTATGAGTTTGGGA-
1 TTAGGGTTTA-GAGTTTGGGAT
* *
10015831 TTAGAGGTTTAGAGTTAGAGAT
1 TTAG-GGTTTAGAGTTTGGGAT
10015853 TTAGGGTTTAGAGATTTGGG
1 TTAGGGTTTAGAG-TTTGGG
10015873 GTCGAGTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 4 0.12
21 19 0.56
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (21 bp):
TTAGGGTTTAGAGTTTGGGAT
Done.