Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 74 of 213
Found at i:20094262 original size:19 final size:20
Alignment explanation
Indices: 20094219--20094268 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
20094209 TTTCTTCATT
* *
20094219 TTTTTTATACTTTATCATAA
1 TTTTTTATATTTTATCAGAA
*
20094239 TTTTTTATATTTTGTCAGAA
1 TTTTTTATATTTTATCAGAA
20094259 -TTTTTATATT
1 TTTTTTATATT
20094269 CCTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTTTATATTTTATCAGAA
Found at i:20094346 original size:19 final size:19
Alignment explanation
Indices: 20094322--20094362 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
20094312 AAAACGAGGA
20094322 TTTCGTACTATATATAGAT
1 TTTCGTACTATATATAGAT
20094341 TTTCGTACTATATATAGAT
1 TTTCGTACTATATATAGAT
20094360 TTT
1 TTT
20094363 GAGTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (19 bp):
TTTCGTACTATATATAGAT
Found at i:20094800 original size:17 final size:18
Alignment explanation
Indices: 20094753--20094806 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
20094743 GATTCTTTTA
*
20094753 TTTTGTT-AGGTTCAGGGG
1 TTTTGTTAAGGTTTA-GGG
20094771 TTTTGTTAAGG-TTAGGG
1 TTTTGTTAAGGTTTAGGG
20094788 TTTT-TTAAGGGTTTAGGG
1 TTTTGTTAA-GGTTTAGGG
20094806 T
1 T
20094807 CAGAGCTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.12
17 9 0.28
18 16 0.50
19 3 0.09
ACGTcount: A:0.15, C:0.02, G:0.35, T:0.48
Consensus pattern (18 bp):
TTTTGTTAAGGTTTAGGG
Found at i:20102273 original size:21 final size:20
Alignment explanation
Indices: 20102230--20102274 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
20102220 TCCCTTGTAA
*
20102230 TTTTGGTACTTCCTTATATT
1 TTTTGGTACTTCCTCATATT
20102250 TTTTGGTA-TTCTCTCATAATT
1 TTTTGGTACTTC-CTCAT-ATT
20102271 TTTT
1 TTTT
20102275 ATACATACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 12 0.55
21 7 0.32
ACGTcount: A:0.16, C:0.13, G:0.09, T:0.62
Consensus pattern (20 bp):
TTTTGGTACTTCCTCATATT
Found at i:20102354 original size:40 final size:40
Alignment explanation
Indices: 20102287--20102387 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 40
20102277 ACATACTCAA
* * * *
20102287 TACTTCCTCAGATTTCTTCGTATTCCCTCAGAA-TTTTTGG
1 TACTTCCTCATATTTTTTGGTACTCCCTCA-AATTTTTTGG
* *
20102327 TATTTCCTCATATTTTTTGGTACTCCCTCAAATTTTTTTTG
1 TACTTCCTCATATTTTTTGGTACTCCCTCAAA-TTTTTTGG
20102368 TACTTCCTCATAATTTTTTG
1 TACTTCCTCAT-ATTTTTTG
20102388 TATTGTTTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
39 2 0.04
40 25 0.49
41 16 0.31
42 8 0.16
ACGTcount: A:0.18, C:0.22, G:0.09, T:0.51
Consensus pattern (40 bp):
TACTTCCTCATATTTTTTGGTACTCCCTCAAATTTTTTGG
Found at i:20102364 original size:20 final size:20
Alignment explanation
Indices: 20102287--20102387 Score: 89
Period size: 20 Copynumber: 5.0 Consensus size: 20
20102277 ACATACTCAA
* * *
20102287 TACTTCCTCAGATTTCTTCG
1 TACTTCCTCAAATTTTTTGG
20102307 TA-TTCCCTCAGAA-TTTTTGG
1 TACTT-CCTCA-AATTTTTTGG
* *
20102327 TATTTCCTCATATTTTTTGG
1 TACTTCCTCAAATTTTTTGG
* *
20102347 TACTCCCTCAAATTTTTTTTG
1 TACTTCCTCAAA-TTTTTTGG
20102368 TACTTCCTCATAATTTTTTG
1 TACTTCCTCA-AATTTTTTG
20102388 TATTGTTTCA
Statistics
Matches: 65, Mismatches: 10, Indels: 11
0.76 0.12 0.13
Matches are distributed among these distances:
19 3 0.05
20 35 0.54
21 25 0.38
22 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.09, T:0.51
Consensus pattern (20 bp):
TACTTCCTCAAATTTTTTGG
Found at i:20102367 original size:22 final size:22
Alignment explanation
Indices: 20102332--20102386 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
20102322 TTTGGTATTT
*
20102332 CCTCAT-A-TTTTTTGGTACTC
1 CCTCATAATTTTTTTTGTACTC
*
20102352 CCTCA-AATTTTTTTTGTACTT
1 CCTCATAATTTTTTTTGTACTC
20102373 CCTCATAATTTTTT
1 CCTCATAATTTTTT
20102387 GTATTGTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 6 0.20
21 16 0.53
22 8 0.27
ACGTcount: A:0.18, C:0.22, G:0.05, T:0.55
Consensus pattern (22 bp):
CCTCATAATTTTTTTTGTACTC
Found at i:20102878 original size:20 final size:21
Alignment explanation
Indices: 20102855--20102910 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
20102845 TCCTTCGTAA
*
20102855 TTTTTTGTATATCCTCAATTTT
1 TTTTTTGTATATCCTCAA-TCT
*
20102877 TTTTTTGTA-ATTCTTCAA-CT
1 TTTTTTGTATA-TCCTCAATCT
20102897 TTTTTTGTAT-TCCT
1 TTTTTTGTATATCCT
20102911 TTATAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 3 0.10
20 10 0.34
21 1 0.03
22 15 0.52
ACGTcount: A:0.16, C:0.14, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTTTGTATATCCTCAATCT
Found at i:20102880 original size:22 final size:22
Alignment explanation
Indices: 20102855--20102902 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20102845 TCCTTCGTAA
*
20102855 TTTTTTGT-ATATCCTCAATTTT
1 TTTTTTGTAAT-TCCTCAACTTT
*
20102877 TTTTTTGTAATTCTTCAACTTT
1 TTTTTTGTAATTCCTCAACTTT
20102899 TTTT
1 TTTT
20102903 GTATTCCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.17, C:0.12, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTTTGTAATTCCTCAACTTT
Found at i:20102920 original size:20 final size:19
Alignment explanation
Indices: 20102817--20103097 Score: 110
Period size: 20 Copynumber: 14.1 Consensus size: 19
20102807 TCCCATATAC
*
20102817 TTTTTTGAATTCCCTCAT--
1 TTTTTTGTATT-CCTCATAA
* *
20102835 TTTTTGGTATTCCTTCGTAA
1 TTTTTTGTATTCC-TCATAA
**
20102855 TTTTTTGTATATCCTCAATTTT
1 TTTTTTGTAT-TCCTC-A-TAA
* *
20102877 TTTTTTGTAATTCTTCA-ACT
1 TTTTTTGT-ATTCCTCATA-A
*
20102897 TTTTTTGTATTCCTTTATAA
1 TTTTTTGTATTCC-TCATAA
* *
20102917 TTTTTGGTACTTGCTCAT-A
1 TTTTTTGTA-TTCCTCATAA
20102936 TTTTTTGGTATTCCCTCATAA
1 TTTTTT-GTATT-CCTCATAA
** *
20102957 TTTTTTACATT-TTCATAA
1 TTTTTTGTATTCCTCATAA
*
20102975 TTTTTGGTACTTCCTCA-AA
1 TTTTTTGTA-TTCCTCATAA
* **
20102994 TTTTTTTATATTTTTTTCAT-A
1 -TTTTTTGTA--TTCCTCATAA
* * *
20103015 TTTTTTTTATACATTCTCATAT
1 TTTTTTGTAT---TCCTCATAA
20103037 TTTTTTGTTATTCCTCAT-A
1 TTTTTTG-TATTCCTCATAA
20103056 TTTTTTGGTACTTCCTCATAA
1 TTTTTT-GTA-TTCCTCATAA
* * *
20103077 TTCTTGGTACTCCTCATAA
1 TTTTTTGTATTCCTCATAA
20103096 TT
1 TT
20103098 ATTGGTATTA
Statistics
Matches: 198, Mismatches: 38, Indels: 53
0.69 0.13 0.18
Matches are distributed among these distances:
17 2 0.01
18 25 0.13
19 35 0.18
20 80 0.40
21 32 0.16
22 19 0.10
23 5 0.03
ACGTcount: A:0.19, C:0.16, G:0.07, T:0.58
Consensus pattern (19 bp):
TTTTTTGTATTCCTCATAA
Found at i:20103010 original size:11 final size:11
Alignment explanation
Indices: 20102994--20103025 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
20102984 CTTCCTCAAA
20102994 TTTTTTTATAT
1 TTTTTTTATAT
*
20103005 TTTTTTCATAT
1 TTTTTTTATAT
20103016 TTTTTTTATA
1 TTTTTTTATA
20103026 CATTCTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTATAT
Found at i:20103060 original size:21 final size:21
Alignment explanation
Indices: 20102985--20103061 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
20102975 TTTTTGGTAC
*
20102985 TTCCTCAAATTTTTTTATATT-
1 TTCCTCATATTTTTTT-TATTA
** *
20103006 TTTTTCATATTTTTTTTATACA
1 TTCCTCATATTTTTTTTAT-TA
*
20103028 TT-CTCATA-TTTTTTTGTTA
1 TTCCTCATATTTTTTTTATTA
20103047 TTCCTCATATTTTTT
1 TTCCTCATATTTTTT
20103062 GGTACTTCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 3 0.07
20 17 0.38
21 23 0.51
22 2 0.04
ACGTcount: A:0.19, C:0.13, G:0.01, T:0.66
Consensus pattern (21 bp):
TTCCTCATATTTTTTTTATTA
Found at i:20103095 original size:19 final size:20
Alignment explanation
Indices: 20103047--20103104 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
20103037 TTTTTTGTTA
* *
20103047 TTCCTCATATTTTTTGGTAC
1 TTCCTCATAATTATTGGTAC
*
20103067 TTCCTCATAATTCTTGGTAC
1 TTCCTCATAATTATTGGTAC
20103087 -TCCTCATAATTATTGGTA
1 TTCCTCATAATTATTGGTA
20103105 TTATTATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (20 bp):
TTCCTCATAATTATTGGTAC
Found at i:20103312 original size:18 final size:18
Alignment explanation
Indices: 20103271--20103312 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
20103261 TATATTTCAC
*
20103271 AATAATTTTAAAAAATAT
1 AATAAATTTAAAAAATAT
20103289 AA-AAATTTAAATAAATA-
1 AATAAATTTAAA-AAATAT
20103306 AATAAAT
1 AATAAAT
20103313 AAAAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATTTAAAAAATAT
Found at i:20103540 original size:20 final size:20
Alignment explanation
Indices: 20103517--20103617 Score: 98
Period size: 20 Copynumber: 5.1 Consensus size: 20
20103507 GCATTCTTTT
*
20103517 ATAATTTTTGGTACATCCTC
1 ATAATTTTTAGTACATCCTC
* *
20103537 ATAATTTTTAGTACTTCCAC
1 ATAATTTTTAGTACATCCTC
* * *
20103557 AAAATTTTT-CTACTTCCTC
1 ATAATTTTTAGTACATCCTC
* *
20103576 ATATTTTTTAGTATATCCTC
1 ATAATTTTTAGTACATCCTC
*
20103596 ATAATTTTTGGTA-ATCCCTC
1 ATAATTTTTAGTACAT-CCTC
20103616 AT
1 AT
20103618 GTTTTTTTGG
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
19 17 0.26
20 49 0.74
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.48
Consensus pattern (20 bp):
ATAATTTTTAGTACATCCTC
Found at i:20103602 original size:39 final size:38
Alignment explanation
Indices: 20103461--20103624 Score: 134
Period size: 39 Copynumber: 4.2 Consensus size: 38
20103451 TTTCTAATAA
*
20103461 ATTTTTT-GTATTCCTTCATAATGTTTGGTACTTCCTCAT
1 ATTTTTTAGTATTCC-TCATAAT-TTTTGTACTTCCTCAT
* * * * *
20103500 -TTTTTTGGCATTCTTTTATAATTTTTGGTACATCCTCAT
1 ATTTTTTAGTATTC-CTCATAATTTTT-GTACTTCCTCAT
* * * *
20103539 AATTTTTAGTACTTCCACAAAATTTTTCTACTTCCTCAT
1 ATTTTTTAGTA-TTCCTCATAATTTTTGTACTTCCTCAT
* *
20103578 ATTTTTTAGTATATCCTCATAATTTTTGGTAATCCCTCAT
1 ATTTTTTAGTAT-TCCTCATAATTTTT-GTACTTCCTCAT
*
20103618 GTTTTTT
1 ATTTTTT
20103625 TGGTACTTTC
Statistics
Matches: 97, Mismatches: 21, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
38 10 0.10
39 54 0.56
40 30 0.31
41 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.08, T:0.53
Consensus pattern (38 bp):
ATTTTTTAGTATTCCTCATAATTTTTGTACTTCCTCAT
Found at i:20103623 original size:20 final size:20
Alignment explanation
Indices: 20103461--20103629 Score: 68
Period size: 20 Copynumber: 8.6 Consensus size: 20
20103451 TTTCTAATAA
20103461 ATTTTTT-GTAT-TCCTTCAT
1 ATTTTTTGGTATATCC-TCAT
* *
20103480 AATGTTTGGTACT-TCCTCAT
1 ATTTTTTGGTA-TATCCTCAT
* * *
20103500 -TTTTTTGGCAT-TCTTTTAT
1 ATTTTTTGGTATATC-CTCAT
* *
20103519 AATTTTTGGTACATCCTCAT
1 ATTTTTTGGTATATCCTCAT
* * * *
20103539 AATTTTTAGTACT-TCCACAA
1 ATTTTTTGGTA-TATCCTCAT
* *
20103559 AATTTTT-CTACT-TCCTCAT
1 ATTTTTTGGTA-TATCCTCAT
*
20103578 ATTTTTTAGTATATCCTCAT
1 ATTTTTTGGTATATCCTCAT
*
20103598 AATTTTTGGTA-ATCCCTCAT
1 ATTTTTTGGTATAT-CCTCAT
*
20103618 GTTTTTTTGGTA
1 -ATTTTTTGGTA
20103630 CTTTCTTATA
Statistics
Matches: 115, Mismatches: 25, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
18 3 0.03
19 33 0.29
20 64 0.56
21 15 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (20 bp):
ATTTTTTGGTATATCCTCAT
Found at i:20103711 original size:20 final size:20
Alignment explanation
Indices: 20103683--20103745 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
20103673 ATTTTTTGGC
* *
20103683 ATTCTCTCATAATTTATGGT
1 ATTCCCTCATAATTTATAGT
*
20103703 ATTCCCTCA-ACATTTTTAGT
1 ATTCCCTCATA-ATTTATAGT
*
20103723 ACTT-CCTCATAATTTTTAGT
1 A-TTCCCTCATAATTTATAGT
20103743 ATT
1 ATT
20103746 ACCTTAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.08
20 31 0.84
21 3 0.08
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.49
Consensus pattern (20 bp):
ATTCCCTCATAATTTATAGT
Found at i:20103758 original size:19 final size:20
Alignment explanation
Indices: 20103688--20103743 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
20103678 TTGGCATTCT
* *
20103688 CTCATAATTTATGGTA-TTCC
1 CTCATAATTTTTAGTACTT-C
20103708 CTCA-ACATTTTTAGTACTTC
1 CTCATA-ATTTTTAGTACTTC
20103728 CTCATAATTTTTAGTA
1 CTCATAATTTTTAGTA
20103744 TTACCTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 1 0.03
20 27 0.87
21 3 0.10
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (20 bp):
CTCATAATTTTTAGTACTTC
Found at i:20104004 original size:20 final size:19
Alignment explanation
Indices: 20103979--20104032 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
20103969 GTACACCCTC
*
20103979 ATAATTTTTGGTATTTTCTT
1 ATAATTTTTGGTATCTT-TT
*
20103999 ATAATTTTTGGTACACTTTT
1 ATAATTTTTGGTA-TCTTTT
20104019 ATAATTTTTGGTAT
1 ATAATTTTTGGTAT
20104033 AGTCCTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.24, C:0.06, G:0.11, T:0.59
Consensus pattern (19 bp):
ATAATTTTTGGTATCTTTT
Found at i:20104724 original size:37 final size:37
Alignment explanation
Indices: 20104683--20104753 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
20104673 GAATTCTTGT
*
20104683 TTGGCTTTGTTTGTACTAGAATGGTTCACCACTCTTA
1 TTGGCTTTGTTTGTACTAGAACGGTTCACCACTCTTA
*
20104720 TTGGCTTTGTTTGTACTAGGACGGTTCACCACTC
1 TTGGCTTTGTTTGTACTAGAACGGTTCACCACTC
20104754 AACTTGTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (37 bp):
TTGGCTTTGTTTGTACTAGAACGGTTCACCACTCTTA
Found at i:20111287 original size:68 final size:67
Alignment explanation
Indices: 20111131--20111288 Score: 208
Period size: 67 Copynumber: 2.3 Consensus size: 67
20111121 TATCGGACGT
* * * *
20111131 CATAGCCCAACTATGGTCTTACATAGTATAAACCCATGTTTAATGTCTTGGCGACTCCACATATT
1 CATAGCCTAACTATGGTCTTACACAATATAAACCCATGTTTAATGTCTTGGAGACTCCACATATT
20111196 GC
66 GC
* * * * * *
20111198 CATACCCTAATTACGGTCTTACACAATATAAACCCTTGTTTAATGTCTTGGAGAACTCCATATGT
1 CATAGCCTAACTATGGTCTTACACAATATAAACCCATGTTTAATGTCTTGGAG-ACTCCACATAT
*
20111263 TTC
65 TGC
20111266 CATAGCCTAACTATGGTCTTACA
1 CATAGCCTAACTATGGTCTTACA
20111289 TATTGTGAAT
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
67 45 0.59
68 31 0.41
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (67 bp):
CATAGCCTAACTATGGTCTTACACAATATAAACCCATGTTTAATGTCTTGGAGACTCCACATATT
GC
Found at i:20111626 original size:73 final size:73
Alignment explanation
Indices: 20111495--20111635 Score: 194
Period size: 73 Copynumber: 1.9 Consensus size: 73
20111485 AATATCGCCT
* * *
20111495 TTGTAGTGTCATTCCATCAAATCGATAGATCATCATCACAATGTCACTCTAACGAGCCAGTAAAA
1 TTGTAGTGTCACTCCATCAAATCGATAGATCATCATCACAATGTCACTCTAACAAGCCAATAAAA
20111560 AACTGTTG
66 AACTGTTG
* * * * *
20111568 TTGTAGTGTCACTCCAT-AGAGTCGATAGATCATCGTCACAGTGTCACTCTAGCAAGCCAATCAA
1 TTGTAGTGTCACTCCATCA-AATCGATAGATCATCATCACAATGTCACTCTAACAAGCCAATAAA
20111632 AAAC
65 AAAC
20111636 CACCATCGTA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
72 1 0.02
73 58 0.98
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (73 bp):
TTGTAGTGTCACTCCATCAAATCGATAGATCATCATCACAATGTCACTCTAACAAGCCAATAAAA
AACTGTTG
Found at i:20111647 original size:73 final size:73
Alignment explanation
Indices: 20111497--20111668 Score: 193
Period size: 73 Copynumber: 2.4 Consensus size: 73
20111487 TATCGCCTTT
* * *
20111497 GTAGTGTCATTCCATCA-AATCGATAGATCATCATCACAATGTCACTCTAACGAGCCAGTAAAAA
1 GTAGTGTCACTCCAT-AGAATCGATAGATCATCATCACAATGTCACTCTAACAAGCCAATAAAAA
***** *
20111561 ACTGTTGTT
65 ACCACCATC
* * * * *
20111570 GTAGTGTCACTCCATAGAGTCGATAGATCATCGTCACAGTGTCACTCTAGCAAGCCAATCAAAAA
1 GTAGTGTCACTCCATAGAATCGATAGATCATCATCACAATGTCACTCTAACAAGCCAATAAAAAA
20111635 CCACCATC
66 CCACCATC
*
20111643 GTAGTGTCACTCCTTAGAATCGATAG
1 GTAGTGTCACTCCATAGAATCGATAG
20111669 GCCGTTGATA
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
72 1 0.01
73 81 0.99
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (73 bp):
GTAGTGTCACTCCATAGAATCGATAGATCATCATCACAATGTCACTCTAACAAGCCAATAAAAAA
CCACCATC
Found at i:20114418 original size:28 final size:28
Alignment explanation
Indices: 20114370--20114423 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
20114360 TGAAATTAAA
* *
20114370 AAAAATTATCAGATTAGGCCATTTTTTG
1 AAAAATTATCAGACTAGGCCAATTTTTG
*
20114398 AAAAATTA-CAGGACTATGCCAATTTT
1 AAAAATTATCA-GACTAGGCCAATTTT
20114424 CAAAAAACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 2 0.09
28 20 0.91
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (28 bp):
AAAAATTATCAGACTAGGCCAATTTTTG
Found at i:20116078 original size:15 final size:15
Alignment explanation
Indices: 20116058--20116105 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
20116048 AACAAAACAG
20116058 AAAGAAAAAGAAAGA
1 AAAGAAAAAGAAAGA
20116073 AAAGAAAAAGGGGAAAG-
1 AAAGAAAAA---GAAAGA
20116090 AAAGAAAGAAGAAAGA
1 AAAGAAA-AAGAAAGA
20116106 CAAGGCTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 14 0.50
17 7 0.25
18 7 0.25
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAAGA
Found at i:20117055 original size:37 final size:40
Alignment explanation
Indices: 20116998--20117106 Score: 116
Period size: 41 Copynumber: 2.8 Consensus size: 40
20116988 CTTTGAGTCA
* *
20116998 ATGAGGCACTAGGTGCCAATTTA-A-TTCAG-TTTAATCG
1 ATGAGACACTAGGTGTCAATTTACACTTCAGATTTAATCG
* ** *
20117035 ATGAGACACTGGGTGTCAATTTACTACTTTGGATTTATTCG
1 ATGAGACACTAGGTGTCAATTTAC-ACTTCAGATTTAATCG
*
20117076 ATGAGACACTAGGTGTTAATTTACTACTTCA
1 ATGAGACACTAGGTGTCAATTTAC-ACTTCA
20117107 AATTATTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
37 20 0.34
39 1 0.02
40 3 0.05
41 34 0.59
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (40 bp):
ATGAGACACTAGGTGTCAATTTACACTTCAGATTTAATCG
Found at i:20117079 original size:41 final size:41
Alignment explanation
Indices: 20117027--20117104 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
20117017 TTTAATTCAG
*
20117027 TTTAATCGATGAGACACTGGGTGTCAATTTACTACTTTGGA
1 TTTAATCGATGAGACACTAGGTGTCAATTTACTACTTTGGA
* *
20117068 TTTATTCGATGAGACACTAGGTGTTAATTTACTACTT
1 TTTAATCGATGAGACACTAGGTGTCAATTTACTACTT
20117105 CAAATTATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (41 bp):
TTTAATCGATGAGACACTAGGTGTCAATTTACTACTTTGGA
Found at i:20120182 original size:9 final size:9
Alignment explanation
Indices: 20120160--20120224 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
20120150 CTTATTCTTT
20120160 AAAAAATAGCC
1 AAAAAA-AG-C
20120171 AAAAAAAGC
1 AAAAAAAGC
**
20120180 AAAAAGCGC
1 AAAAAAAGC
20120189 AAAAAAACAGC
1 -AAAAAA-AGC
20120200 AAAAAAAGC
1 AAAAAAAGC
**
20120209 AAAAAGCGC
1 AAAAAAAGC
20120218 AAAAAAA
1 AAAAAAA
20120225 AAGTTGCCTA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 23 0.52
10 13 0.30
11 8 0.18
ACGTcount: A:0.71, C:0.15, G:0.12, T:0.02
Consensus pattern (9 bp):
AAAAAAAGC
Found at i:20120194 original size:11 final size:10
Alignment explanation
Indices: 20120170--20120224 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 10
20120160 AAAAAATAGC
20120170 CAAAAAAA-G
1 CAAAAAAACG
*
20120179 C-AAAAAGCG
1 CAAAAAAACG
20120188 CAAAAAAACAG
1 CAAAAAAAC-G
20120199 CAAAAAAA-G
1 CAAAAAAACG
*
20120208 C-AAAAAGCG
1 CAAAAAAACG
20120217 CAAAAAAA
1 CAAAAAAA
20120225 AAGTTGCCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
8 10 0.27
9 7 0.19
10 11 0.30
11 9 0.24
ACGTcount: A:0.71, C:0.16, G:0.13, T:0.00
Consensus pattern (10 bp):
CAAAAAAACG
Found at i:20120202 original size:29 final size:30
Alignment explanation
Indices: 20120160--20120224 Score: 114
Period size: 29 Copynumber: 2.2 Consensus size: 30
20120150 CTTATTCTTT
*
20120160 AAAAAATAGCCAAAAAAAGCAAAAAGCGCA
1 AAAAAACAGCCAAAAAAAGCAAAAAGCGCA
20120190 AAAAAACAG-CAAAAAAAGCAAAAAGCGCA
1 AAAAAACAGCCAAAAAAAGCAAAAAGCGCA
20120219 AAAAAA
1 AAAAAA
20120225 AAGTTGCCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 26 0.76
30 8 0.24
ACGTcount: A:0.71, C:0.15, G:0.12, T:0.02
Consensus pattern (30 bp):
AAAAAACAGCCAAAAAAAGCAAAAAGCGCA
Found at i:20120210 original size:20 final size:19
Alignment explanation
Indices: 20120160--20120213 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
20120150 CTTATTCTTT
*
20120160 AAAAAATAGCCAAAAAAAGC
1 AAAAAA-AGCAAAAAAAAGC
**
20120180 AAAAAGCGCAAAAAAACAGC
1 AAAAAAAGCAAAAAAA-AGC
20120200 AAAAAAAGCAAAAA
1 AAAAAAAGCAAAAA
20120214 GCGCAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.72, C:0.15, G:0.11, T:0.02
Consensus pattern (19 bp):
AAAAAAAGCAAAAAAAAGC
Found at i:20130444 original size:5 final size:5
Alignment explanation
Indices: 20130436--20130479 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
20130426 TGCGTTTTCA
* * *
20130436 TTTAT TTTAT TCTAT CTTAT TTTAT TTTAT TTTTT GTTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTT
20130480 CTACAATCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:20131506 original size:17 final size:20
Alignment explanation
Indices: 20131462--20131507 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
20131452 GCATGCTTAC
20131462 ATATATTTTTATATTACATA
1 ATATATTTTTATATTACATA
*
20131482 AT-T-TTTTT-TAATACA-A
1 ATATATTTTTATATTACATA
20131498 ATATATTTTT
1 ATATATTTTT
20131508 TCTTTTCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 3 0.13
17 7 0.30
18 10 0.43
19 1 0.04
20 2 0.09
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATATTTTTATATTACATA
Found at i:20144069 original size:44 final size:44
Alignment explanation
Indices: 20144006--20144109 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 44
20143996 AAACCTTATC
** * *
20144006 CCCTGAAGTTGCAGTGGAGCAGGTTGAATATAC-AAGTCTTACTT
1 CCCTGAAGTTGCAGTGGAGCAGACTGAAGATACTAA-TCCTACTT
*
20144050 CCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACTAATCCTACTT
1 CCCTGAAGTTGCAGTGGAGCAGACTGAAGATACTAATCCTACTT
*
20144094 CCCTGAAGTTACAGTG
1 CCCTGAAGTTGCAGTG
20144110 AAGCGGATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 51 0.96
45 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (44 bp):
CCCTGAAGTTGCAGTGGAGCAGACTGAAGATACTAATCCTACTT
Found at i:20149534 original size:96 final size:96
Alignment explanation
Indices: 20149297--20149539 Score: 405
Period size: 96 Copynumber: 2.5 Consensus size: 96
20149287 AGCCCCTTAA
* ** **
20149297 GCCAAAACCACCGAAAGAAGAGGAATCACCTGTAACAAGGGAACGACCTCCACCACTTAAATTGC
1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
*
20149362 CACCGCCAGTTGTTAAGCCCCCGACACCAGT
66 CACCGCCAGTTATTAAGCCCCCGACACCAGT
*
20149393 GTCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
20149458 CACCGCCAGTTATTAAGCCCCCGACACCAGT
66 CACCGCCAGTTATTAAGCCCCCGACACCAGT
* *
20149489 GCCAAAACCACCGACACAAGAGGAATCACCTATAACAAGGGAACGGTCTCC
1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCC
20149540 GCCAGTTATT
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 137 1.00
ACGTcount: A:0.36, C:0.33, G:0.19, T:0.13
Consensus pattern (96 bp):
GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
CACCGCCAGTTATTAAGCCCCCGACACCAGT
Found at i:20149589 original size:78 final size:78
Alignment explanation
Indices: 20149460--20149617 Score: 271
Period size: 78 Copynumber: 2.0 Consensus size: 78
20149450 AAAATTGCCA
* *
20149460 CCGCCAGTTATTAAGCCCCCGACACCAGTGCCAAAACCACCGACACAAGAGGAATCACCTATAAC
1 CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC
20149525 AAGGGAACGGTCT
66 AAGGGAACGGTCT
* * *
20149538 CCGCCAGTTATTAAGCCCCCGCCACCAGTGGAAAAACCACCGAAACAAGAGGAATCACCTGTAAC
1 CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC
20149603 AAGGGAACGGTCT
66 AAGGGAACGGTCT
20149616 CC
1 CC
20149618 ACCACCAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.34, C:0.33, G:0.20, T:0.13
Consensus pattern (78 bp):
CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC
AAGGGAACGGTCT
Found at i:20149688 original size:24 final size:24
Alignment explanation
Indices: 20149661--20149707 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
20149651 CCCGACACTA
20149661 CCAGTCCACTCTCCACCACCACCT
1 CCAGTCCACTCTCCACCACCACCT
20149685 CCAGTCCACTCTCCACCACCACC
1 CCAGTCCACTCTCCACCACCACC
20149708 ACCAATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.60, G:0.04, T:0.15
Consensus pattern (24 bp):
CCAGTCCACTCTCCACCACCACCT
Found at i:20149724 original size:24 final size:24
Alignment explanation
Indices: 20149660--20149731 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
20149650 CCCCGACACT
* *
20149660 ACCAGTCCACTCTCCACCACCACC
1 ACCAATCCACTCACCACCACCACC
* * *
20149684 TCCAGTCCACTCTCCACCACCACC
1 ACCAATCCACTCACCACCACCACC
* * *
20149708 ACCAATTCATTCACCACCTCCACC
1 ACCAATCCACTCACCACCACCACC
20149732 TGTTCACTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.25, C:0.56, G:0.03, T:0.17
Consensus pattern (24 bp):
ACCAATCCACTCACCACCACCACC
Found at i:20149751 original size:21 final size:21
Alignment explanation
Indices: 20149727--20149770 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
20149717 TTCACCACCT
* * *
20149727 CCACCTGTTCACTCTCCTCCA
1 CCACCAGTGCACTCTCCGCCA
*
20149748 CCACCAGTGCATTCTCCGCCA
1 CCACCAGTGCACTCTCCGCCA
20149769 CC
1 CC
20149771 TCTTTCTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.09, T:0.23
Consensus pattern (21 bp):
CCACCAGTGCACTCTCCGCCA
Found at i:20152086 original size:20 final size:21
Alignment explanation
Indices: 20152054--20152094 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
20152044 TATAAAAAGC
20152054 TAAAAGTGAATAATAA-ATAA
1 TAAAAGTGAATAATAAGATAA
20152074 TAAAA-TGATATAATAAGATAA
1 TAAAAGTGA-ATAATAAGATAA
20152095 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 12 0.63
21 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (21 bp):
TAAAAGTGAATAATAAGATAA
Found at i:20152133 original size:22 final size:22
Alignment explanation
Indices: 20152108--20152154 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
20152098 TATATATAAT
*
20152108 TAAAA-ATAAACAAATAAACAAA
1 TAAAATATAAA-AAATAAAAAAA
*
20152130 TAAAATATAAAATATAAAAAAA
1 TAAAATATAAAAAATAAAAAAA
20152152 TAA
1 TAA
20152155 TGCAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (22 bp):
TAAAATATAAAAAATAAAAAAA
Found at i:20152245 original size:13 final size:13
Alignment explanation
Indices: 20152062--20152239 Score: 56
Period size: 13 Copynumber: 13.3 Consensus size: 13
20152052 GCTAAAAGTG
20152062 AATAATAAATAAT
1 AATAATAAATAAT
*
20152075 AA-AATGATATAAT
1 AATAAT-AAATAAT
*
20152088 AA-GATAAATATAT
1 AATAATAAATA-AT
20152101 ATATAATTAAA-AAT
1 A-ATAA-TAAATAAT
* *
20152115 AAACAAATAAACAAAT
1 -AA-TAATAAA-TAAT
20152131 AA-AATATAA-AAT
1 AATAATA-AATAAT
20152143 -ATAA-AAA-AAT
1 AATAATAAATAAT
20152153 AATGCAA-AAATAATT
1 AAT--AATAAATAA-T
20152168 CATATAATAATATAAT
1 -A-ATAATAA-ATAAT
*
20152184 AATAATGAATAGAT
1 AATAATAAATA-AT
**
20152198 AGATAA-AAGGAA-
1 A-ATAATAAATAAT
20152210 AATAA-AAACTAAT
1 AATAATAAA-TAAT
20152223 AATAATAAATAAT
1 AATAATAAATAAT
20152236 AATA
1 AATA
20152240 TCAAATTTAT
Statistics
Matches: 129, Mismatches: 11, Indels: 50
0.68 0.06 0.26
Matches are distributed among these distances:
10 5 0.04
11 10 0.08
12 15 0.12
13 41 0.32
14 26 0.20
15 15 0.12
16 11 0.09
17 6 0.05
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.26
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:20153305 original size:21 final size:22
Alignment explanation
Indices: 20153268--20153308 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20153258 TGGTTTTGTA
20153268 TTGGGCTTCGAATTTGGGCTTG
1 TTGGGCTTCGAATTTGGGCTTG
*
20153290 TTGGGCTT-GCATTTGGGCT
1 TTGGGCTTCGAATTTGGGCT
20153309 GGTCTGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.07, C:0.15, G:0.37, T:0.41
Consensus pattern (22 bp):
TTGGGCTTCGAATTTGGGCTTG
Found at i:20153868 original size:44 final size:44
Alignment explanation
Indices: 20153700--20154290 Score: 393
Period size: 45 Copynumber: 13.0 Consensus size: 44
20153690 AAGATCGGTA
* * * * *
20153700 ATTTATAGTTTTAATCTGTTCCACTGCAACTTCAAGGAAATAAG
1 ATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* * * * *
20153744 ATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAAATAAG
1 ATTTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* * *
20153789 ATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
1 ATTTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* * *
20153834 GTTTGTGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAG
1 ATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
*
20153878 ATTTGTAGCCTGTCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAG
1 ATTTGTAG-C--T-TT-AATCTGCTCCACTGCAACTTCAGGGAGATAAG
* ** * * * * *
20153927 ATTGTTTATTTTTAACCTTCTCCACTGTAACTTCCGTGAGATAAG
1 ATT-TGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* * * *
20153972 GTTTG-A---TAAGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCAATA
1 ATTTGTAGCTTTA-ATCTGCTCCACTGCAACTTCAG-G-G---AGAT-AA-G
* * *
20154020 ATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAG
1 ATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* * * * *
20154064 ATTCGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAG
1 ATTTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* * * * *
20154109 ACTCGTTATGGTAGATTTAATCTGAC-CTACTGCAACTTCAGAGATATAGG
1 A----TT-T-GTAGCTTTAATCTG-CTCCACTGCAACTTCAGGGAGATAAG
* * * * * ** *
20154159 ATTTATCGTTTTAATCCGCTCCAATGCAACTTCAAAGAGATAGG
1 ATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
** *
20154203 ATTAATAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
1 ATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* ** **
20154247 ATTGGTATTTTTAA-CTTGCTCCGTTGCAACTTCAGGGAGATAAG
1 ATTTGTAGCTTTAATC-TGCTCCACTGCAACTTCAGGGAGATAAG
20154291 GTTGGTTATC
Statistics
Matches: 434, Mismatches: 84, Indels: 58
0.75 0.15 0.10
Matches are distributed among these distances:
40 2 0.00
41 17 0.04
43 4 0.01
44 148 0.34
45 149 0.34
46 11 0.03
47 4 0.01
48 5 0.01
49 37 0.09
50 33 0.08
51 22 0.05
52 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
ATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
Found at i:20153918 original size:93 final size:90
Alignment explanation
Indices: 20153712--20154290 Score: 317
Period size: 94 Copynumber: 6.4 Consensus size: 90
20153702 TTATAGTTTT
* * * * * *
20153712 AATCTGTTCCACTGCAACTTCAAGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTACTCCACTGCAACTT
20153777 CAAGGAAATAAGATTTGCTATCTTC
66 CAAGGAAATAAGATTTGCTATCTTC
* * * *
20153802 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG-TGGCTTTAATCTACTCCACTGCAACTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTACTCCACTGCAACTT
* * *
20153866 CAGGGAGATAAGATTTGTAGCCTGTCTTC
66 CAAGGAAATAAGA-TT-T-G-CTATCTTC
* * ** * * * *
20153895 AATCTGCTCCACTGTAACTTCAGGGAGATAAGA-TTGTTTATTTTTAACCTTCTCCACTGTAACT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-CTAGCTTCAATCTACTCCACTGCAACT
* * * *
20153959 TC-CGTGAGATAAGGTTTG--A---TA
65 TCAAG-GAAATAAGATTTGCTATCTTC
* * ** * **
20153980 AGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCAATAATTTATAGCTTTAATCTGTTCCACT
1 A-ATCTGCTCCACTGCAACTTCAGGGAGATAAG----AT--TTGCTAGCTTCAATCTACTCCACT
* *
20154045 GCAACTTCAGGGAAATAAGATTCGCTATCTTC
59 GCAACTTCAAGGAAATAAGATTTGCTATCTTC
* * * * * *
20154077 AGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTCGTTATGGTAGATTTAATCTGAC-CTACTG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA----TT-TGCTAGCTTCAATCT-ACTCCACTG
* * *
20154141 CAACTTC-AGAGATATAGGA-TT--TATCGTTTT
60 CAACTTCAAG-GAAATAAGATTTGCTATC--TTC
* * ** * ** *
20154171 AATCCGCTCCAATGCAACTTCAAAGAGATAGGA-TTAATAGCTTCAATCTGCTCCACTGCAACTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTACTCCACTGCAACTT
* * * * *
20154235 CAGGGAGATAAGA-TTGGTATTTTT
66 CAAGGAAATAAGATTTGCTATCTTC
**
20154259 AA-CTTGCTCCGTTGCAACTTCAGGGAGATAAG
1 AATC-TGCTCCACTGCAACTTCAGGGAGATAAG
20154291 GTTGGTTATC
Statistics
Matches: 374, Mismatches: 80, Indels: 72
0.71 0.15 0.14
Matches are distributed among these distances:
85 2 0.01
86 28 0.07
87 2 0.01
88 59 0.16
89 35 0.09
90 38 0.10
91 2 0.01
92 42 0.11
93 43 0.11
94 62 0.17
95 31 0.08
96 28 0.07
97 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (90 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTACTCCACTGCAACTT
CAAGGAAATAAGATTTGCTATCTTC
Found at i:20154105 original size:137 final size:137
Alignment explanation
Indices: 20153749--20154108 Score: 386
Period size: 137 Copynumber: 2.6 Consensus size: 137
20153739 ATAAGATTTG
* *
20153749 CTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAAATAAGATTTGCTATCTTCAGTCTGCTCCAC
1 CTATCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TTGCTATCTTCAGTCTGCTCCAC
* * *
20153814 TGCAACTTCAGGGAGATAAGGTTTGTGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGA
65 TGCAACTTCAGGGAGATAAGGTTTGTGGCATAAATCTACTCCACTGCAACTTCAGAGAGATAAGA
*** *
20153879 TTTGTAGC
130 TCAATAAC
* * * * * * ** *
20153887 CTGTCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGTTTATTTTTAACCTTCTCCAC
1 CTATCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTG-CTATCTTCAGTCTGCTCCAC
* * * * *
20153952 TGTAACTTCCGTGAGATAAGG-TT-T-G-ATAAGATCTGCTCTACTGCAACTTCAGAGAGATAAG
65 TGCAACTTCAGGGAGATAAGGTTTGTGGCATAA-ATCTACTCCACTGCAACTTCAGAGAGATAAG
*
20154013 ATCAATAAT
129 ATCAATAAC
* * *
20154022 TTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCC
1 CTAT--CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATT-GCTATCTTCAGTCTGCTCC
*
20154087 ACTGCAACTTTAGGGAGATAAG
63 ACTGCAACTTCAGGGAGATAAG
20154109 ACTCGTTATG
Statistics
Matches: 177, Mismatches: 40, Indels: 11
0.78 0.18 0.05
Matches are distributed among these distances:
134 2 0.01
135 35 0.20
136 1 0.01
137 70 0.40
138 69 0.39
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (137 bp):
CTATCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTGCTATCTTCAGTCTGCTCCACT
GCAACTTCAGGGAGATAAGGTTTGTGGCATAAATCTACTCCACTGCAACTTCAGAGAGATAAGAT
CAATAAC
Found at i:20154243 original size:320 final size:315
Alignment explanation
Indices: 20153632--20154293 Score: 821
Period size: 320 Copynumber: 2.1 Consensus size: 315
20153622 TCTGCCCCAT
* * ** * * *
20153632 TGCAACTTTAGGGAGATTAGACTTGTTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCG
1 TGCAACTTCAGGGAGATAAGGTTTGATAAGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCA
* * *
20153697 GTAATTTATAGTTTTAATCTGTTCCACTGCAACTTCAAGGAAATAAGATTTGCTATCTTCAGTCT
66 ATAATTTATAGCTTTAATCTGTTCCACTGCAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCT
** *
20153762 GCTCCACTGCAACTTCAAGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGG
131 GCTCCACTGCAACTTCAAGGAAATAAGATTTGCTAGATTCAATCTGCTCCACTGCAACTTCA-GG
* * * * ** **
20153827 AGATAAGGTTTGTGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCCTGTC
195 AGATAAGGTTTATCGCTTTAATCCACTCCAATGCAACTTCAAAGAGATAAGATTAATA--C-GTC
* *
20153892 TTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGTTTATTTTTAACCTT-CTCCAC
257 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTG-GTATTTTTAA-CTTGCTCCAC
* * *
20153952 TGTAACTTCCGTGAGATAAGGTTTGATAAGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCA
1 TGCAACTTCAGGGAGATAAGGTTTGATAAGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCA
*
20154017 ATAATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCT
66 ATAATTTATAGCTTTAATCTGTTCCACTGCAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCT
* * * * * *
20154082 GCTCCACTGCAACTTTAGGGAGATAAGACTCGTTATGGTAGATTTAATCTGAC-CTACTGCAACT
131 GCTCCACTGCAACTTCAAGGAAATAAGA----TT-TGCTAGATTCAATCTG-CTCCACTGCAACT
* * *
20154146 TCA-GAGATATAGGATTTATCGTTTTAATCCGCTCCAATGCAACTTCAAAGAGATAGGATTAATA
190 TCAGGAGATA-AGG-TTTATCGCTTTAATCCACTCCAATGCAACTTCAAAGAGATAAGATTAATA
**
20154210 -G-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATTTTTAACTTGCTCCGT
253 CGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATTTTTAACTTGCTCCAC
20154271 TGCAACTTCAGGGAGATAAGGTT
1 TGCAACTTCAGGGAGATAAGGTT
20154294 GGTTATCTTC
Statistics
Matches: 292, Mismatches: 41, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
318 3 0.01
319 33 0.11
320 180 0.62
321 1 0.00
323 6 0.02
324 5 0.02
325 63 0.22
326 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (315 bp):
TGCAACTTCAGGGAGATAAGGTTTGATAAGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCA
ATAATTTATAGCTTTAATCTGTTCCACTGCAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCT
GCTCCACTGCAACTTCAAGGAAATAAGATTTGCTAGATTCAATCTGCTCCACTGCAACTTCAGGA
GATAAGGTTTATCGCTTTAATCCACTCCAATGCAACTTCAAAGAGATAAGATTAATACGTCTTCA
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATTTTTAACTTGCTCCAC
Found at i:20155901 original size:12 final size:13
Alignment explanation
Indices: 20155884--20155916 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
20155874 TTTCTTTTTC
20155884 CTTTTTTTCTCTT
1 CTTTTTTTCTCTT
*
20155897 CTTTTTTTCTTTT
1 CTTTTTTTCTCTT
20155910 CTTTTTT
1 CTTTTTT
20155917 CATCATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
CTTTTTTTCTCTT
Found at i:20155954 original size:21 final size:21
Alignment explanation
Indices: 20155928--20155969 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20155918 ATCATTTTCA
*
20155928 TTTTTTT-GAGATATTTTGAT
1 TTTTTTTAAAGATATTTTGAT
*
20155948 TTTTTTTAAATATATTTTGAT
1 TTTTTTTAAAGATATTTTGAT
20155969 T
1 T
20155970 GGATCTGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TTTTTTTAAAGATATTTTGAT
Found at i:20155960 original size:19 final size:19
Alignment explanation
Indices: 20155921--20155960 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20155911 TTTTTTCATC
*
20155921 ATTTTCATTTTTTTGAGAT
1 ATTTTCATTTTTTTGAAAT
* *
20155940 ATTTTGATTTTTTTTAAAT
1 ATTTTCATTTTTTTGAAAT
20155959 AT
1 AT
20155961 ATTTTGATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (19 bp):
ATTTTCATTTTTTTGAAAT
Found at i:20161376 original size:20 final size:21
Alignment explanation
Indices: 20161344--20161384 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
20161334 TATAAAAAGC
20161344 TAAAAGTGAATAATAA-ATAA
1 TAAAAGTGAATAATAAGATAA
20161364 TAAAA-TGATATAATAAGATAA
1 TAAAAGTGA-ATAATAAGATAA
20161385 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 12 0.63
21 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (21 bp):
TAAAAGTGAATAATAAGATAA
Found at i:20161453 original size:41 final size:41
Alignment explanation
Indices: 20161383--20161479 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 41
20161373 ATAATAAGAT
*
20161383 AAATAT-ATATATAAAATTAAAAATTAAAAATAA-ACAAATA
1 AAATATAATATATAAAA-TAAAAATCAAAAATAATACAAATA
* *
20161423 AAATATAATATATAAAA-AAATAATGCAAAAATAATTCATATA
1 AAATATAATATATAAAATAAA-AAT-CAAAAATAATACAAATA
20161465 ATAATATAATA-ATAA
1 A-AATATAATATATAA
20161480 TGAATAGATA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
39 3 0.06
40 9 0.18
41 18 0.37
42 10 0.20
43 9 0.18
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (41 bp):
AAATATAATATATAAAATAAAAATCAAAAATAATACAAATA
Found at i:20161536 original size:13 final size:13
Alignment explanation
Indices: 20161352--20161530 Score: 56
Period size: 13 Copynumber: 13.3 Consensus size: 13
20161342 GCTAAAAGTG
20161352 AATAATAAATAAT
1 AATAATAAATAAT
*
20161365 AA-AATGATATAAT
1 AATAAT-AAATAAT
*
20161378 AA-GATAAATATAT
1 AATAATAAATA-AT
* *
20161391 ATATAA-AATTAAA
1 A-ATAATAAATAAT
20161404 AATTAA-AAATAA-
1 AA-TAATAAATAAT
20161416 ACA-AATAAA-ATAT
1 A-ATAATAAATA-AT
*
20161429 AATATATAAAAAAAT
1 AATA-AT-AAATAAT
20161444 AATGCAA-AAATAATT
1 AAT--AATAAATAA-T
20161459 CATATAATAATATAAT
1 -A-ATAATAA-ATAAT
*
20161475 AATAATGAATAGAT
1 AATAATAAATA-AT
**
20161489 AGATAA-AAGGAA-
1 A-ATAATAAATAAT
20161501 AATAA-AAACTAAT
1 AATAATAAA-TAAT
20161514 AATAATAAATAAT
1 AATAATAAATAAT
20161527 AATA
1 AATA
20161531 TCAAATTTAT
Statistics
Matches: 127, Mismatches: 14, Indels: 50
0.66 0.07 0.26
Matches are distributed among these distances:
11 9 0.07
12 17 0.13
13 45 0.35
14 26 0.20
15 17 0.13
16 6 0.05
17 7 0.06
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.27
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:20164557 original size:54 final size:54
Alignment explanation
Indices: 20164499--20164601 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
20164489 TATAATATAA
* * * *
20164499 GGTCACACGGCCGTGTGGCCAGGCTGTGTAAC-TCTCTATGATCGTGTGGCTCAG
1 GGTCACACGACCATGTCGCCAGGCCGTGT-ACTTCTCTATGATCGTGTGGCTCAG
* * *
20164553 GGTCACACGACTATGTCTCCAGGCCGTGTACTTCTCTATGCTCGTGTGG
1 GGTCACACGACCATGTCGCCAGGCCGTGTACTTCTCTATGATCGTGTGG
20164602 ATTGACCTGC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 2 0.05
54 39 0.95
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (54 bp):
GGTCACACGACCATGTCGCCAGGCCGTGTACTTCTCTATGATCGTGTGGCTCAG
Found at i:20173847 original size:13 final size:13
Alignment explanation
Indices: 20173829--20173854 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20173819 AATATTTACA
20173829 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
20173842 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
20173855 GGAGTGATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:20174404 original size:43 final size:43
Alignment explanation
Indices: 20174335--20174416 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
20174325 ATTGTATCTA
** *
20174335 CATTTTAAAGCTGATTTCTTATTACCTATAGGAAAGACCCAGT
1 CATTTTAAAGCTGACATCTTACTACCTATAGGAAAGACCCAGT
*
20174378 CATTTTAAAGCTGACATCTTGCTACCTATAGGAAAGACC
1 CATTTTAAAGCTGACATCTTACTACCTATAGGAAAGACC
20174417 AAGAACATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (43 bp):
CATTTTAAAGCTGACATCTTACTACCTATAGGAAAGACCCAGT
Found at i:20176315 original size:2 final size:2
Alignment explanation
Indices: 20176308--20176334 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20176298 GAAAGGATTT
20176308 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20176335 CCATCAAGTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20181546 original size:16 final size:17
Alignment explanation
Indices: 20181514--20181546 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20181504 TATATATGTA
20181514 TAATAAATATATAAAAT
1 TAATAAATATATAAAAT
*
20181531 TAATAATTAT-TAAAAT
1 TAATAAATATATAAAAT
20181547 AAAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATATATAAAAT
Found at i:20194694 original size:18 final size:19
Alignment explanation
Indices: 20194660--20194700 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
20194650 TCTCATTGCA
20194660 TCATTTTATATTTCATTTC
1 TCATTTTATATTTCATTTC
20194679 TCATTTTATA-TTCATTTC
1 TCATTTTATATTTCATTTC
20194697 TCAT
1 TCAT
20194701 ATTTGCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (19 bp):
TCATTTTATATTTCATTTC
Found at i:20195945 original size:11 final size:11
Alignment explanation
Indices: 20195929--20195971 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
20195919 TTTCTATTTC
*
20195929 TTTTATTATGT
1 TTTTATTATAT
20195940 TTTTATTATAT
1 TTTTATTATAT
20195951 TTATTATTATAT
1 TT-TTATTATAT
*
20195963 TATTATTAT
1 TTTTATTAT
20195972 TAACCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (11 bp):
TTTTATTATAT
Found at i:20201516 original size:58 final size:58
Alignment explanation
Indices: 20201417--20201530 Score: 165
Period size: 58 Copynumber: 2.0 Consensus size: 58
20201407 CTACAAACAG
* * * **
20201417 ACAAGGACTAATTTGGAACAGTTCTAAAAGTTTTAGCGCAATATTTAAAATACCTAAA
1 ACAAAGACTAATTTGGAAAAATTCTAAAAGTTTTAGCGCAATATAAAAAATACCTAAA
* *
20201475 ACAAAGACTAATTTGGAAAAATTCTAAAAGTTTTAGGGCAATCTAAAAAATACCTA
1 ACAAAGACTAATTTGGAAAAATTCTAAAAGTTTTAGCGCAATATAAAAAATACCTA
20201531 GAAATAAGGG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (58 bp):
ACAAAGACTAATTTGGAAAAATTCTAAAAGTTTTAGCGCAATATAAAAAATACCTAAA
Found at i:20216210 original size:35 final size:35
Alignment explanation
Indices: 20216171--20216243 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
20216161 TGCGCATACT
20216171 TTTGTTGCAACATAGAACCTGAATTTGTGCATGTA
1 TTTGTTGCAACATAGAACCTGAATTTGTGCATGTA
20216206 TTTGTTGCAACATAGAACCTGAATTTGTGCATGTA
1 TTTGTTGCAACATAGAACCTGAATTTGTGCATGTA
20216241 TTT
1 TTT
20216244 TGTGAAGTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (35 bp):
TTTGTTGCAACATAGAACCTGAATTTGTGCATGTA
Found at i:20222823 original size:19 final size:18
Alignment explanation
Indices: 20222762--20222812 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
20222752 TGTGACGAGC
*
20222762 ATAAATTAA-AAAAATTT
1 ATAAATTAATAAAAATAT
* *
20222779 AAAAATCT-TTAAAAATAT
1 ATAAAT-TAATAAAAATAT
20222797 ATAAATTAATAAAAAT
1 ATAAATTAATAAAAAT
20222813 GAGTATAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAATTAATAAAAATAT
Found at i:20222871 original size:17 final size:18
Alignment explanation
Indices: 20222841--20222889 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
20222831 CAGGTTAACA
20222841 TTTAAAAGTTTATA-ATTT
1 TTTAAAA-TTTATATATTT
20222859 TTTAAAATTTATATATTT
1 TTTAAAATTTATATATTT
20222877 TTT-AAATTTATAT
1 TTTAAAATTTATAT
20222890 TTATCACGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTAAAATTTATATATTT
Found at i:20223026 original size:3 final size:3
Alignment explanation
Indices: 20223018--20223058 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
20223008 ACATATTAAT
20223018 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20223059 TTCCAACTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20225382 original size:23 final size:23
Alignment explanation
Indices: 20225354--20225447 Score: 125
Period size: 23 Copynumber: 4.1 Consensus size: 23
20225344 ATGTGTGTAT
*
20225354 CTTTTCATATTCAAGCCTCTTAA
1 CTTTTCATATTCAAGCCTCTTCA
*
20225377 CTTTTCATCTTCAAGCCTCTTCA
1 CTTTTCATATTCAAGCCTCTTCA
* ** *
20225400 CTATTCATATTCAAGTTTTTTCA
1 CTTTTCATATTCAAGCCTCTTCA
*
20225423 CTTTTCATATTCAAGTCTCTTCA
1 CTTTTCATATTCAAGCCTCTTCA
20225446 CT
1 CT
20225448 CTTCTAACTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.22, C:0.27, G:0.04, T:0.47
Consensus pattern (23 bp):
CTTTTCATATTCAAGCCTCTTCA
Found at i:20229888 original size:23 final size:23
Alignment explanation
Indices: 20229860--20229953 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
20229850 ATGTGTGTAT
* *
20229860 CTTTTCATATTCAAGCCTCTTAA
1 CTTTTCATATTCAAGTCTCTTCA
*
20229883 CTTTTCATCTTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
* * *
20229906 CTATTCATATTCAAGTTTTTTCA
1 CTTTTCATATTCAAGTCTCTTCA
20229929 CTTTTCATATTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
20229952 CT
1 CT
20229954 CTTCTAACTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.22, C:0.26, G:0.04, T:0.48
Consensus pattern (23 bp):
CTTTTCATATTCAAGTCTCTTCA
Found at i:20231348 original size:10 final size:10
Alignment explanation
Indices: 20231308--20231354 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
20231298 AAAATTTTGG
*
20231308 ATTTTTTTAT
1 ATTTTTATAT
20231318 ATTTTTA-AGT
1 ATTTTTATA-T
*
20231328 TTTTTTATAT
1 ATTTTTATAT
20231338 ATTTTTATAT
1 ATTTTTATAT
20231348 AATTTTT
1 -ATTTTT
20231355 TGAGATGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 1 0.03
10 23 0.74
11 7 0.23
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:20240878 original size:26 final size:25
Alignment explanation
Indices: 20240826--20240879 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
20240816 AATTCTATTT
20240826 TTTTATATTTTTACAACTTTTAATAA
1 TTTTATATTTTTACAACTTTT-ATAA
*
20240852 TTTTATAATTTTTATAACATTTT-TAA
1 TTTTAT-ATTTTTACAAC-TTTTATAA
20240878 TT
1 TT
20240880 ATATCTAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 11 0.44
27 10 0.40
28 4 0.16
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTTATATTTTTACAACTTTTATAA
Found at i:20255862 original size:8 final size:9
Alignment explanation
Indices: 20255835--20255866 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
20255825 TTTTCATGAA
20255835 TAATCAATT
1 TAATCAATT
20255844 TAATCAATT
1 TAATCAATT
20255853 TAAT-AATT
1 TAATCAATT
20255861 T-ATCAA
1 TAATCAA
20255867 ATATGATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 2 0.09
8 7 0.32
9 13 0.59
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (9 bp):
TAATCAATT
Found at i:20256078 original size:44 final size:44
Alignment explanation
Indices: 20256015--20256105 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
20256005 AACTCTGTTT
* * *
20256015 TTAGTTTCCCATTTAAACTCTGATTAGTGTAGGCTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTGATTAGTATAAGCTATTTTAATA
* *
20256059 TTAGTTTCTCACTTAAACTCTGATTAGTATAAGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTGATTAGTATAAGCTATTTTAATA
20256103 TTA
1 TTA
20256106 TTTGACCTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACTCTGATTAGTATAAGCTATTTTAATA
Found at i:20258024 original size:44 final size:44
Alignment explanation
Indices: 20257961--20258051 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
20257951 AACTCTGTTT
*
20257961 TTAGTTTCTCACTTAAACTTTGATTAGGGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTTTGATTAGGGTAGGTTATTTTAATA
*
20258005 TTAGTTTCCCACTTAAACTTTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTTTGATTAGGGTAGGTTATTTTAATA
20258049 TTA
1 TTA
20258052 TTTAACTCAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.48
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACTTTGATTAGGGTAGGTTATTTTAATA
Found at i:20261380 original size:78 final size:79
Alignment explanation
Indices: 20261094--20261393 Score: 335
Period size: 78 Copynumber: 3.9 Consensus size: 79
20261084 AATTGTATTC
* * * * *
20261094 TGTTTCAAACAGAAATTCAATTGAACAATCCTGTTTCAAGA-TTTATTCCTGCCGTTTAACAGGA
1 TGTTTCAAACAGAAAATCAATTGAACAATCTTGTTTCAGGATTTTATTCCTGTCGTTTAACAGTA
* *
20261158 CTTGTTTAATTTTT
66 TTTGTTTGATTTTT
* * * *
20261172 TG-TTCAAACAGAAAATCAATTGAACAATCTTGTTTTAGGATTTTATTTCTGACGTCTAACA-TG
1 TGTTTCAAACAGAAAATCAATTGAACAATCTTGTTTCAGGATTTTATTCCTGTCGTTTAACAGT-
20261235 ATTTGTTTGA-TTTT
65 ATTTGTTTGATTTTT
* * * *
20261249 TGTTTCGAACAGAAAATCAATTGAATAATTTTGTTTCAGGATTTTATTTCTGTCGTTTAACAGTA
1 TGTTTCAAACAGAAAATCAATTGAACAATCTTGTTTCAGGATTTTATTCCTGTCGTTTAACAGTA
*
20261314 TTTTTTTGATTTTT
66 TTTGTTTGATTTTT
* * * * * *
20261328 TGTTTCAAACA-AAAATCAACTGAATAATTTTCTTTCAGGATTCTT-TTCCTGTCATTCAACAG-
1 TGTTTCAAACAGAAAATCAATTGAACAATCTTGTTTCAGGATT-TTATTCCTGTCGTTTAACAGT
20261390 ATTT
65 ATTT
20261394 TATTCAATTT
Statistics
Matches: 193, Mismatches: 23, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
77 44 0.23
78 132 0.68
79 17 0.09
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (79 bp):
TGTTTCAAACAGAAAATCAATTGAACAATCTTGTTTCAGGATTTTATTCCTGTCGTTTAACAGTA
TTTGTTTGATTTTT
Found at i:20264389 original size:98 final size:98
Alignment explanation
Indices: 20264215--20264424 Score: 366
Period size: 98 Copynumber: 2.1 Consensus size: 98
20264205 CTACAGGGGT
* * *
20264215 CACATGGCCGTGTGGGCATTCAAAATAGGGACACACGGCCGTGTCCTAGCCTGTGTCCGTGCCCT
1 CACACGGCCGTGTGGGCATTCAAAATAGGGACACACGGCCGTGTCCCAGCCTGTGCCCGTGCCCT
20264280 TGTAACTCACTGACTTGGGTCACACGGCCAAGC
66 TGTAACTCACTGACTTGGGTCACACGGCCAAGC
*
20264313 CACACGGCCGTGTGGGCATTCAAAATAGGGACACACGGTCGTGTCCCAGCCTGTGCCCGTGCCCT
1 CACACGGCCGTGTGGGCATTCAAAATAGGGACACACGGCCGTGTCCCAGCCTGTGCCCGTGCCCT
20264378 TGTAACTCACTGACTTGGGTCACACGGCCAAGC
66 TGTAACTCACTGACTTGGGTCACACGGCCAAGC
**
20264411 CACACACCCGTGTG
1 CACACGGCCGTGTG
20264425 TTAGGCCATG
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 106 1.00
ACGTcount: A:0.20, C:0.32, G:0.27, T:0.20
Consensus pattern (98 bp):
CACACGGCCGTGTGGGCATTCAAAATAGGGACACACGGCCGTGTCCCAGCCTGTGCCCGTGCCCT
TGTAACTCACTGACTTGGGTCACACGGCCAAGC
Found at i:20265490 original size:39 final size:39
Alignment explanation
Indices: 20265436--20265547 Score: 161
Period size: 39 Copynumber: 2.9 Consensus size: 39
20265426 ATACACCGGC
* *
20265436 ACACAACCTGCTAGGCACATAGCCCGAATAATCACCAGT
1 ACACAGCCTGCTAGGCACATAGCCTGAATAATCACCAGT
*
20265475 ACACAGCCTGCTAGGCACATAGCCTGAATAATCATCAGT
1 ACACAGCCTGCTAGGCACATAGCCTGAATAATCACCAGT
* * * *
20265514 AGACAGCCTACTAGGCATATAGCCTAAATAATCA
1 ACACAGCCTGCTAGGCACATAGCCTGAATAATCA
20265548 GCCTGCTAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 66 1.00
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.19
Consensus pattern (39 bp):
ACACAGCCTGCTAGGCACATAGCCTGAATAATCACCAGT
Found at i:20265559 original size:29 final size:29
Alignment explanation
Indices: 20265517--20265576 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
20265507 CATCAGTAGA
* *
20265517 CAGCCTACTAGGCATATAGCCTAAATAAT
1 CAGCCTACTAGGCACATAGCCCAAATAAT
* *
20265546 CAGCCTGCTAGGCACATAGCCCGAATAAT
1 CAGCCTACTAGGCACATAGCCCAAATAAT
20265575 CA
1 CA
20265577 CCAGCACACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (29 bp):
CAGCCTACTAGGCACATAGCCCAAATAAT
Found at i:20265588 original size:68 final size:68
Alignment explanation
Indices: 20265478--20265615 Score: 206
Period size: 68 Copynumber: 2.0 Consensus size: 68
20265468 CACCAGTACA
* * * * *
20265478 CAGCCTGCTAGGCACATAGCCTGAATAATCATCAGTAGACAGCCTACTAGGCATATAGCCTA-AA
1 CAGCCTGCTAGGCACATAGCCCGAATAATCACCAGCACACAGCCTACTAGGCACATAGCC-AGAA
20265542 TAAT
65 TAAT
*
20265546 CAGCCTGCTAGGCACATAGCCCGAATAATCACCAGCACACAGCCTGCTAGGCACATAGCCAGAAT
1 CAGCCTGCTAGGCACATAGCCCGAATAATCACCAGCACACAGCCTACTAGGCACATAGCCAGAAT
20265611 AAT
66 AAT
20265614 CA
1 CA
20265616 CCGGATTTCT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 1 0.02
68 62 0.98
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.18
Consensus pattern (68 bp):
CAGCCTGCTAGGCACATAGCCCGAATAATCACCAGCACACAGCCTACTAGGCACATAGCCAGAAT
AAT
Found at i:20269783 original size:113 final size:113
Alignment explanation
Indices: 20269583--20269800 Score: 312
Period size: 113 Copynumber: 1.9 Consensus size: 113
20269573 TGCAGTCGTG
* * * *
20269583 CTACTGTCGTGTTCATCTTGTTGTTGAATCCTGGGAGACAGTCGACCAACATTTCTCCATCACCA
1 CTACTGTCGTGCTCATCTTGTTGTTGAATCCTGGCAGACAATCGACCAACATTTCTCCAACACCA
* * *
20269648 TAGGAGCAACCGAATCTGTCTTAAGGAAACTGTGAAAACATGCCCCAA
66 TAGGAACAACCGAATCTATCTTAAGGAAACTATGAAAACATGCCCCAA
* *
20269696 CTACTGTCGTGCTCATCTTGTTGTT-ATATCTTGGCAGACAATCGACCAACGTTTCTCCAACACC
1 CTACTGTCGTGCTCATCTTGTTGTTGA-ATCCTGGCAGACAATCGACCAACATTTCTCCAACACC
** *
20269760 ATAGGAACGGCCGAATTTATCTTAAGGAAACTATGAAAACA
65 ATAGGAACAACCGAATCTATCTTAAGGAAACTATGAAAACA
20269801 GACCTCAAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
112 1 0.01
113 91 0.99
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (113 bp):
CTACTGTCGTGCTCATCTTGTTGTTGAATCCTGGCAGACAATCGACCAACATTTCTCCAACACCA
TAGGAACAACCGAATCTATCTTAAGGAAACTATGAAAACATGCCCCAA
Found at i:20272295 original size:19 final size:20
Alignment explanation
Indices: 20272271--20272315 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
20272261 ATTTTTATAT
20272271 ATATGTATAC-ATTATTTTA
1 ATATGTATACTATTATTTTA
20272290 ATATG--TACTATTATTTTA
1 ATATGTATACTATTATTTTA
*
20272308 AAATGTAT
1 ATATGTAT
20272316 GTATATACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 3 0.14
18 13 0.59
19 5 0.23
20 1 0.05
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (20 bp):
ATATGTATACTATTATTTTA
Found at i:20272765 original size:27 final size:27
Alignment explanation
Indices: 20272723--20272784 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
20272713 GCCACTGATA
*
20272723 GGCGGCACCAAAGGTGTCATTCCCATG
1 GGCGGCACCAAAGGTGCCATTCCCATG
*
20272750 GGCGGCACCAATGGTGCCATTCCCATG
1 GGCGGCACCAAAGGTGCCATTCCCATG
*
20272777 GGCAGCAC
1 GGCGGCAC
20272785 TGCCCTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.21, C:0.32, G:0.31, T:0.16
Consensus pattern (27 bp):
GGCGGCACCAAAGGTGCCATTCCCATG
Found at i:20272849 original size:3 final size:3
Alignment explanation
Indices: 20272841--20272964 Score: 59
Period size: 3 Copynumber: 42.3 Consensus size: 3
20272831 AGGAGAGGGA
* *
20272841 AAG AAG AAG AAAG AAAG AAAG AAA AAG AAG GA- AAG AA- AACG AAAG
1 AAG AAG AAG -AAG -AAG -AAG AAG AAG AAG AAG AAG AAG AA-G -AAG
* * * *
20272886 GAG AAG AAG AA- AA- AAG AAAG AAA AAG AAG GA- AAG AA- AAG GA-
1 AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
20272927 AAG GAG AAG -AG AA- AAA AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
20272965 GGGGAGGAAG
Statistics
Matches: 94, Mismatches: 15, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
2 15 0.16
3 62 0.66
4 15 0.16
5 2 0.02
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20272854 original size:10 final size:10
Alignment explanation
Indices: 20272839--20272962 Score: 77
Period size: 10 Copynumber: 12.3 Consensus size: 10
20272829 GAAGGAGAGG
20272839 GAAAGAAGAA
1 GAAAGAAGAA
20272849 GAAAGAAAGAAA
1 GAAAG-AAG-AA
20272861 GAAA-AAGAA
1 GAAAGAAGAA
20272870 GGAAAGAA-AA
1 -GAAAGAAGAA
20272880 CGAAAGGAGAAGAA
1 -G-AA--AGAAGAA
*
20272894 GAAAAAAGAAA
1 GAAAGAAG-AA
20272905 GAAA-AAGAA
1 GAAAGAAGAA
20272914 GGAAAGAA-AA
1 -GAAAGAAGAA
*
20272924 GGAAAGGAGAA
1 -GAAAGAAGAA
20272935 G--AGAA-AA
1 GAAAGAAGAA
20272942 -AAAGAAGAA
1 GAAAGAAGAA
20272951 G-AAGAAGAA
1 GAAAGAAGAA
20272960 GAA
1 GAA
20272963 GAGGGGAGGA
Statistics
Matches: 93, Mismatches: 4, Indels: 34
0.71 0.03 0.26
Matches are distributed among these distances:
7 2 0.02
8 7 0.08
9 15 0.16
10 37 0.40
11 17 0.18
12 8 0.09
13 5 0.05
14 2 0.02
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (10 bp):
GAAAGAAGAA
Found at i:20272899 original size:20 final size:20
Alignment explanation
Indices: 20272842--20272959 Score: 87
Period size: 24 Copynumber: 5.5 Consensus size: 20
20272832 GGAGAGGGAA
*
20272842 AGAAGAAGAAAGAAAGAAAGA
1 AGAAGAAGAAA-AAAGAAAGG
*
20272863 AAAAGAAGGAAAGAAAACGAAAGG
1 AGAAGAA-G-AA-AAAA-GAAAGG
*
20272887 AGAAGAAGAAAAAAGAAAGA
1 AGAAGAAGAAAAAAGAAAGG
*
20272907 AAAAGAAGGAAAGAAAAGGAAAGG
1 AGAAGAA-G-AA-AAAA-GAAAGG
*
20272931 AGAAG-AGAAAAAA-AGAAGA
1 AGAAGAAGAAAAAAGA-AAGG
20272950 AGAAGAAGAA
1 AGAAGAAGAA
20272960 GAAGAGGGGA
Statistics
Matches: 79, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
18 1 0.01
19 8 0.10
20 19 0.24
21 13 0.16
22 6 0.08
23 11 0.14
24 21 0.27
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (20 bp):
AGAAGAAGAAAAAAGAAAGG
Found at i:20272916 original size:44 final size:44
Alignment explanation
Indices: 20272842--20272957 Score: 182
Period size: 44 Copynumber: 2.6 Consensus size: 44
20272832 GGAGAGGGAA
20272842 AGAAGAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAACGAAAGG
1 AGAAGAAGAAA-AAAGAAAGAAAAAGAAGGAAAGAAAACGAAAGG
*
20272887 AGAAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
1 AGAAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAACGAAAGG
*
20272931 AGAAG-AGAAAAAA-AGAAGAAGAAGAAG
1 AGAAGAAGAAAAAAGA-AAGAAAAAGAAG
20272958 AAGAAGAGGG
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
42 1 0.01
43 19 0.28
44 37 0.54
45 11 0.16
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (44 bp):
AGAAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAACGAAAGG
Found at i:20273273 original size:15 final size:15
Alignment explanation
Indices: 20273255--20273288 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20273245 ATATGTGTAA
*
20273255 GAAAACAAAAAATAC
1 GAAAACAAAAAAAAC
*
20273270 GAAAAGAAAAAAAAC
1 GAAAACAAAAAAAAC
20273285 GAAA
1 GAAA
20273289 CTTGTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.09, G:0.12, T:0.03
Consensus pattern (15 bp):
GAAAACAAAAAAAAC
Found at i:20273897 original size:287 final size:287
Alignment explanation
Indices: 20273376--20274330 Score: 1625
Period size: 287 Copynumber: 3.3 Consensus size: 287
20273366 AAAGTAAAAA
* * *
20273376 TATAAAATTAGAAATTATGAAATTTTTTAAAGTAATAAAATGTAGAG-AAAAAATCCGAAGAAAT
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCAGAGAAAAAAATACGAAGAAAT
* * *
20273440 GGCCGAGGTAAGAGTGTTTTACAAAATTTTTAAAAAATTTAGAAATAATTAATACAATTATTTGA
66 GGCCGAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGA
20273505 AACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTA
131 AACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTA
* *
20273570 ATAAAATTAGGGAAAATAATATGAGCAAATGGCGGGAATAAGGGTTTTTTTTACACTAAATTAAT
196 ATAAAATTAGGGAAAATAATACGAGCAAATGACGGGAATAAGGGTTTTTTTTACACTAAATTAAT
*
20273635 TTAAAAAACACACTAAAATAATAAATT
261 TTAAAAAACACACTAAATTAATAAATT
*
20273662 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCAGAGAAAAAAATACGAAGAAAT
* *
20273727 AGCCGAGGTAAGAGTGTTTTACAAATTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGA
66 GGCCGAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGA
20273792 AACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTA
131 AACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTA
* *
20273857 ATAAAATTTGGGAAAATAATACGAGCAAATGACAGGAATAAGGG-TTTTTTTACACTAAATTAAT
196 ATAAAATTAGGGAAAATAATACGAGCAAATGACGGGAATAAGGGTTTTTTTTACACTAAATTAAT
20273921 TT-AAAAACACACTAAATTAATAAATT
261 TTAAAAAACACACTAAATTAATAAATT
*
20273947 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGC-GAAGAAAAAAATACAAAGAAA
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCAG-AGAAAAAAATACGAAGAAA
*
20274011 TGGCCGAGGTAAGAGTGTTTTACAAAATGTTTTAAAAATTCAGAAATAATTAATACAAATATTTG
65 TGGCCGAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTG
*
20274076 AAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTAGTGAAAGT
130 AAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGT
* * *
20274141 AATAAAATTCA-GGAAAATAATACTAGCAAATGGA-GGGAATAATGGTTTTCTTTACACTAAATT
195 AATAAAATT-AGGGAAAATAATACGAGCAAAT-GACGGGAATAAGGGTTTTTTTTACACTAAATT
20274204 AATTTAAAAAACACACTAAATTAATAAATT
258 AATTTAAAAAACACACTAAATTAATAAATT
* *
20274234 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCAGAGAAAAAGATAGGAAGAAAT
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCAGAGAAAAAAATACGAAGAAAT
* *
20274299 GGCCGAGGTAAGAGTGTTTTACTAACTTTTTT
66 GGCCGAGGTAAGAGTGTTTTACAAAATTTTTT
20274331 TTCAACATGC
Statistics
Matches: 632, Mismatches: 30, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
284 1 0.00
285 247 0.39
286 89 0.14
287 294 0.47
288 1 0.00
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.31
Consensus pattern (287 bp):
TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCAGAGAAAAAAATACGAAGAAAT
GGCCGAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGA
AACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTA
ATAAAATTAGGGAAAATAATACGAGCAAATGACGGGAATAAGGGTTTTTTTTACACTAAATTAAT
TTAAAAAACACACTAAATTAATAAATT
Found at i:20278847 original size:18 final size:18
Alignment explanation
Indices: 20278808--20278849 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20278798 CCAATGATCG
*
20278808 CCACCACCTTCTTCAACG
1 CCACCACCTTCTTCAACA
**
20278826 CCACCACCTTCTTCTTCA
1 CCACCACCTTCTTCAACA
20278844 CCACCA
1 CCACCA
20278850 ACCATATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.52, G:0.02, T:0.24
Consensus pattern (18 bp):
CCACCACCTTCTTCAACA
Found at i:20279808 original size:10 final size:10
Alignment explanation
Indices: 20279780--20279816 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
20279770 AAATACCTTT
20279780 TTTTTCTCTTC
1 TTTTTCTC-TC
*
20279791 TCTTTCTCTC
1 TTTTTCTCTC
20279801 TTTTTCTCTC
1 TTTTTCTCTC
20279811 TTTTTC
1 TTTTTC
20279817 CGTAGCAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:20285188 original size:9 final size:9
Alignment explanation
Indices: 20285169--20285213 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
20285159 AATATATTTC
20285169 AAAAAGAAAG
1 AAAAAG-AAG
20285179 AAAAAGAAG
1 AAAAAGAAG
*
20285188 AAGAAGAAG
1 AAAAAGAAG
*
20285197 AAGAAGAAG
1 AAAAAGAAG
20285206 AAAAAGAA
1 AAAAAGAA
20285214 AATGAGAGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:20285190 original size:3 final size:3
Alignment explanation
Indices: 20285176--20285213 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
20285166 TTCAAAAAGA
* *
20285176 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
20285214 AATGAGAGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20286893 original size:131 final size:131
Alignment explanation
Indices: 20286564--20287157 Score: 861
Period size: 131 Copynumber: 4.5 Consensus size: 131
20286554 TATTGGCAGC
* *
20286564 GAAGCAGATTTAAGCCACCAG-CCTTATCTCCCTGAGCAGCAGTGGAGTAAGTTGAAGATTGCAA
1 GAAGCAGATTTAAGCCACCAGTCC-TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAG
* * * *
20286628 ATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGT
65 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGT
20286693 AGG
130 A-G
* * *
20286696 GAAGCAAATTTAAGCCACCAG-CCTTATCCCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGCAG
1 GAAGCAGATTTAAGCCACCAGTCC-TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAG
* * * *
20286760 ATCTTATCTCCCTAAGCAGTAGTGGAGAAGATCGAAAACAGCGAATCTTATCTTCCTGAGATAGT
65 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGT
20286825 AG
130 AG
* * *
20286827 GAAGCATATTTAAGCCACTAGTCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAGATT-CTAG
1 GAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGC-AG
* *
20286891 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATTTTATCTTCCCGAGATAGT
65 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGT
20286956 AG
130 AG
* * * *
20286958 AAAGCAGATTTTAGCCACCAGTCTTATCTGCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGA
1 GAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGA
* ** * *
20287023 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGATGAATCTTATATTCCCGAGAAAGTA
66 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTA
20287088 G
131 G
* * *
20287089 GAAGCAGATTTAAGCCACCAGTCCTATCTTCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGA
1 GAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGA
20287154 TCTT
66 TCTT
20287158 GTCTTCCTGT
Statistics
Matches: 415, Mismatches: 44, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
130 1 0.00
131 294 0.71
132 120 0.29
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (131 bp):
GAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGA
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTA
G
Found at i:20287157 original size:87 final size:85
Alignment explanation
Indices: 20287026--20287278 Score: 226
Period size: 86 Copynumber: 2.9 Consensus size: 85
20287016 TTGCAGATCT
* * *
20287026 TATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGA-CG-ATGAATCTTATATTCCCG-A-GAAAGT
1 TATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCA-G-ATCTTATATTCCCGTACGAAAGT
***
20287087 AGGAAGCAGATTTAAGCCACCAGTCC
64 --GAAGCAGA--TAAAAAACCAGTCC
* * * * **
20287113 TATCTTCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTGTCTTCCTGTACTGGCAGTG
1 TATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTATATTCCCGTAC-GAAAGTG
*
20287178 AAGCAGATAAAAAACTAGTCC
65 AAGCAGATAAAAAACCAGTCC
* * * * **
20287199 TATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTGTCTTCCTGTACTGGCAGTG
1 TATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTATATTCCCGTAC-GAAAGTG
20287264 AAGCAGATCAAAAAA
65 AAGCAGAT-AAAAAA
20287279 ATGGTCAAAG
Statistics
Matches: 145, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
86 81 0.56
87 48 0.33
88 11 0.08
89 1 0.01
90 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (85 bp):
TATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTATATTCCCGTACGAAAGTGA
AGCAGATAAAAAACCAGTCC
Found at i:20287165 original size:44 final size:44
Alignment explanation
Indices: 20286586--20287251 Score: 165
Period size: 44 Copynumber: 15.2 Consensus size: 44
20286576 AGCCACCAGC
* * * *
20286586 CTTATCTCCCTGAGCAGCAGTGGAGTA-AGTTGAAGATTGCAAAT
1 CTTATCTTCCTAAGCAGTAGTGGAGTAGA-TTGAAGATTGCAGAT
* * * * *
20286630 CTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTG-A-AT
1 CTTATCTTCCTAAGCAGTAGTGGAGTAGATTGAAGA--TTGCAGAT
* * * * * **** *
20286674 CTTATCTTCCCAAGGTAGTAG-GGAAGCAAATTTAAGCCACCAG-C
1 CTTATCTTCCTAA-GCAGTAGTGG-AGTAGATTGAAGATTGCAGAT
** * * * *
20286718 CTTATCCCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGCAGAT
1 CTTATCTTCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAGAT
* * * * **
20286762 CTTATCTCCCTAAGCAGTAGTGGAGAAGATCGAAAACAGC-GAAT
1 CTTATCTTCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAG-AT
* * * * *
20286806 CTTATCTTCCTGAG-A-TAGTAGGAAGCATATTTAAGCCACT--AG-T
1 CTTATCTTCCTAAGCAGTAGT-GG-AGTAGATTGAAG--ATTGCAGAT
* * * * * *
20286849 CCTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAGATT-CTAGAT
1 CTTATCTTCCTAAGCAGTAGTGGAGTAGATTGAAGATTGC-AGAT
* * * *
20286893 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC-GAAT
1 CTTATCTTCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAG-AT
* ** * * ** ****
20286937 TTTATCTTCCCGAG-A-TAGTAGAAAGCAGATTTTAGCCACCAG-T
1 CTTATCTTCCTAAGCAGTAGT-G-GAGTAGATTGAAGATTGCAGAT
* * * *
20286980 CTTATCTGCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGAT
1 CTTATCTTCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAGAT
* * *
20287024 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGA-CG-ATGAAT
1 CTTATCTTCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCA-G-AT
* ** * * * * ****
20287068 CTTATATTCCCGAGAAAGTAG-GAAGCAGATTTAAGCCACCAG-T
1 CTTATCTTCCTAAG-CAGTAGTGGAGTAGATTGAAGATTGCAGAT
* *
20287111 CCTATCTTCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGAT
1 CTTATCTTCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAGAT
* * * * * * ** * *
20287155 CTTGTCTTCCTGTA-CTGGCAGTGAAGCAGATAAAAAACT--AG-T
1 CTTATCTTCCT-AAGC-AGTAGTGGAGTAGATTGAAGATTGCAGAT
* * * *
20287197 CCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGCAGAT
1 CTTATCTTCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAGAT
*
20287241 CTTGTCTTCCT
1 CTTATCTTCCT
20287252 GTACTGGCAG
Statistics
Matches: 431, Mismatches: 150, Indels: 82
0.65 0.23 0.12
Matches are distributed among these distances:
41 17 0.04
42 24 0.06
43 99 0.23
44 239 0.55
45 47 0.11
46 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (44 bp):
CTTATCTTCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAGAT
Found at i:20287225 original size:86 final size:87
Alignment explanation
Indices: 20287108--20287278 Score: 317
Period size: 86 Copynumber: 2.0 Consensus size: 87
20287098 TTAAGCCACC
*
20287108 AGTCCTATCTTCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTGTCTTCCTGTACTGG
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTGTCTTCCTGTACTGG
20287173 CAGTGAAGCAGAT-AAAAAACT
66 CAGTGAAGCAGATCAAAAAACT
*
20287194 AGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTGTCTTCCTGTACTGG
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTGTCTTCCTGTACTGG
20287259 CAGTGAAGCAGATCAAAAAA
66 CAGTGAAGCAGATCAAAAAA
20287279 ATGGTCAAAG
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
86 76 0.93
87 6 0.07
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (87 bp):
AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTGTCTTCCTGTACTGG
CAGTGAAGCAGATCAAAAAACT
Found at i:20289029 original size:10 final size:10
Alignment explanation
Indices: 20289014--20289041 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
20289004 TTATTAATCA
20289014 TATATTTTTT
1 TATATTTTTT
20289024 TATATTTTTT
1 TATATTTTTT
20289034 TATATTTT
1 TATATTTT
20289042 CATTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TATATTTTTT
Found at i:20289131 original size:3 final size:3
Alignment explanation
Indices: 20289123--20289220 Score: 85
Period size: 3 Copynumber: 33.0 Consensus size: 3
20289113 ATTTAAGCTC
*
20289123 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT GTT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * * *
20289169 AGA ATT ATA ATAT ATT ATT ATC AGT ATT ATA ATT -TT ATT ATGT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
*
20289215 AAT ATT
1 ATT ATT
20289221 TTAAGTTTCT
Statistics
Matches: 76, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
2 6 0.08
3 65 0.86
4 5 0.07
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:20289257 original size:23 final size:23
Alignment explanation
Indices: 20289193--20289261 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 23
20289183 TTATTATCAG
* * *
20289193 TATTATAATTTTATTATGTATTAA
1 TATT-TAATTTCATCATATATTAA
*
20289217 TATTTTAAGTTTCTTCATATATTAA
1 TA-TTTAA-TTTCATCATATATTAA
20289242 TATTTAATTTCATCATATAT
1 TATTTAATTTCATCATATAT
20289262 CATCTTATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 12 0.32
24 10 0.26
25 16 0.42
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.57
Consensus pattern (23 bp):
TATTTAATTTCATCATATATTAA
Found at i:20296748 original size:17 final size:17
Alignment explanation
Indices: 20296726--20296758 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20296716 TTCACTTGAT
20296726 CATATAGGCTCACATGG
1 CATATAGGCTCACATGG
*
20296743 CATATAGGCTCGCATG
1 CATATAGGCTCACATG
20296759 CACCTAGGGA
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:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (17 bp):
CATATAGGCTCACATGG
Found at i:20296889 original size:29 final size:28
Alignment explanation
Indices: 20296746--20296886 Score: 138
Period size: 29 Copynumber: 4.9 Consensus size: 28
20296736 CACATGGCAT
** * *
20296746 ATAGGCTCGCATGCACCTAGGGATTTTAT
1 ATAGGCTCGCATGTTCCTAGGG-TTTCAC
** * *
20296775 ATAGGCTTTCAAGTTTCTAGGGTTTTCAC
1 ATAGGCTCGCATGTTCCTAGGG-TTTCAC
*
20296804 ATAGGCTCGCATGTTACTAGGGTTCTCAC
1 ATAGGCTCGCATGTTCCTAGGGTT-TCAC
* * *
20296833 ATAAGCTCACATGTTCCTCGGGTTTGCAC
1 ATAGGCTCGCATGTTCCTAGGGTTT-CAC
20296862 ATAGGCTCGCATGTTCCTAGGGTTT
1 ATAGGCTCGCATGTTCCTAGGGTTT
20296887 GCATATCACA
Statistics
Matches: 90, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
28 3 0.03
29 87 0.97
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (28 bp):
ATAGGCTCGCATGTTCCTAGGGTTTCAC
Found at i:20304570 original size:16 final size:17
Alignment explanation
Indices: 20304530--20304573 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
20304520 ATTACGCAAT
20304530 ATATATAAAAATAACATA
1 ATATA-AAAAATAACATA
*
20304548 ATATAAAAAATTACA-A
1 ATATAAAAAATAACATA
*
20304564 ATTTAAAAAA
1 ATATAAAAAA
20304574 GGGTTGGTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 9 0.38
18 5 0.21
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
ATATAAAAAATAACATA
Found at i:20315012 original size:15 final size:15
Alignment explanation
Indices: 20315003--20315035 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
20314993 CAAATGCTAT
20315003 AATAATAAATACAAC
1 AATAATAAATACAAC
*
20315018 AATAATAAATACATC
1 AATAATAAATACAAC
20315033 AAT
1 AAT
20315036 GACATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:20315069 original size:21 final size:20
Alignment explanation
Indices: 20315039--20315085 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
20315029 CATCAATGAC
* *
20315039 ATAA-AAATAATATAAACAA
1 ATAATAAATAAAATAAAAAA
20315058 ATGAATAAATAAAATAAAAAA
1 AT-AATAAATAAAATAAAAAA
20315079 ATAATAA
1 ATAATAA
20315086 TCCATGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 7 0.29
21 15 0.62
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (20 bp):
ATAATAAATAAAATAAAAAA
Found at i:20315416 original size:22 final size:22
Alignment explanation
Indices: 20315391--20315434 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
20315381 ATATACATAT
*
20315391 AAATATGAAAATATTCATTAAA
1 AAATAGGAAAATATTCATTAAA
*
20315413 AAATAGGAAAATATTCGTTAAA
1 AAATAGGAAAATATTCATTAAA
20315435 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (22 bp):
AAATAGGAAAATATTCATTAAA
Found at i:20315759 original size:21 final size:23
Alignment explanation
Indices: 20315734--20315777 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
20315724 AAAAGTTTAA
20315734 ATATATA-TATTATAT-AAGAAG
1 ATATATATTATTATATCAAGAAG
20315755 ATATATATTTATTATATCAAGAA
1 ATATATA-TTATTATATCAAGAA
20315778 AATGCACGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (23 bp):
ATATATATTATTATATCAAGAAG
Found at i:20315867 original size:15 final size:15
Alignment explanation
Indices: 20315849--20315886 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
20315839 AATCACAGTG
*
20315849 ATAATATTAACAATA
1 ATAATAATAACAATA
20315864 ATAATAATAACAATA
1 ATAATAATAACAATA
*
20315879 CTAATAAT
1 ATAATAAT
20315887 TATATTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAATAATAACAATA
Found at i:20316497 original size:4 final size:4
Alignment explanation
Indices: 20316490--20316553 Score: 51
Period size: 4 Copynumber: 15.8 Consensus size: 4
20316480 ATTTAGGCAA
* * *
20316490 AAAT AAAT AAAT AAAT AAAT AGAGA- AAAT AAAA AAAT AAAAT ATAT ATAT
1 AAAT AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT AAAT -AAAT AAAT AAAT
*
20316540 AAAT GAA- AAAT AAA
1 AAAT AAAT AAAT AAA
20316554 AGAACGATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
3 3 0.06
4 39 0.80
5 6 0.12
6 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:20318495 original size:26 final size:27
Alignment explanation
Indices: 20318466--20318521 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
20318456 TCAACTTCTC
20318466 TTTTAAGTTTATA-AA-TTCTCTTTGAG
1 TTTTAAGTTTA-AGAATTTCTCTTTGAG
**
20318492 TTTTATTTTTAAGAATTTCTCTTTGAG
1 TTTTAAGTTTAAGAATTTCTCTTTGAG
20318519 TTT
1 TTT
20318522 GTTTTAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 1 0.04
26 11 0.42
27 14 0.54
ACGTcount: A:0.23, C:0.07, G:0.11, T:0.59
Consensus pattern (27 bp):
TTTTAAGTTTAAGAATTTCTCTTTGAG
Found at i:20318532 original size:27 final size:27
Alignment explanation
Indices: 20318481--20318532 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
20318471 AGTTTATAAA
**
20318481 TTCTCTTTGAGTTTTATTTTTAAGAAT
1 TTCTCTTTGAGTTTTATTTAGAAGAAT
20318508 TTCTCTTTGAGTTTGT-TTTAGAAGA
1 TTCTCTTTGAGTTT-TATTTAGAAGA
20318533 GTTTTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (27 bp):
TTCTCTTTGAGTTTTATTTAGAAGAAT
Found at i:20320683 original size:45 final size:45
Alignment explanation
Indices: 20320611--20320761 Score: 178
Period size: 45 Copynumber: 3.4 Consensus size: 45
20320601 ATATGTCAAT
20320611 ATGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGATAAAA
1 ATGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGATAAAA
* * ** * *
20320656 ATGAATAAGACCCTAGCTGAAAA-ATGTTATGGCATCAAAACATAA
1 ATGAGTAAGACCATAGCT-AAAAGATGTTATGGCATCATGATAAAA
* * * *
20320701 ATGAGTAAGACCATGGCTAAAAGACGTTATGGCATCATGGTAAAC
1 ATGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGATAAAA
* *
20320746 AGGACTAAGACCATAG
1 ATGAGTAAGACCATAG
20320762 TTGAAAGACT
Statistics
Matches: 85, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
44 4 0.05
45 77 0.91
46 4 0.05
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.22
Consensus pattern (45 bp):
ATGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGATAAAA
Found at i:20320988 original size:27 final size:27
Alignment explanation
Indices: 20320929--20320990 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
20320919 GCATCATAGT
*
20320929 TAGTCCAACGGGACATTAAACATAAGA
1 TAGTCCGACGGGACATTAAACATAAGA
* *
20320956 TCGTCCGACGGGACATTAAACA-AGGGA
1 TAGTCCGACGGGACATTAAACATA-AGA
20320983 TAGTCCGA
1 TAGTCCGA
20320991 TAAGACGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (27 bp):
TAGTCCGACGGGACATTAAACATAAGA
Found at i:20330274 original size:19 final size:19
Alignment explanation
Indices: 20330230--20330276 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
20330220 TTCAATAAAT
* **
20330230 TTTTTACAATTTTTTTTTA
1 TTTTTATAATTTTTTCATA
20330249 TTTTTATAATTTTTTCATA
1 TTTTTATAATTTTTTCATA
20330268 TTTTTATAA
1 TTTTTATAA
20330277 AATTTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTATAATTTTTTCATA
Found at i:20331354 original size:48 final size:47
Alignment explanation
Indices: 20331300--20331407 Score: 114
Period size: 48 Copynumber: 2.3 Consensus size: 47
20331290 TTTTTGTAAA
*
20331300 TTTTAATATTTTA-TAATTATTTTGGCAA-TTTTATAAT-TTCTTTTCTAT
1 TTTTAATATTTTATTAA--ATTTT-GCAATTTTTA-AATATTCTTTTATAT
* * *
20331348 TTTTAATAATTTATTAACTTTTGTAATTTTTAAATAATTCTTTTATAT
1 TTTTAATATTTTATTAAATTTTGCAATTTTTAAAT-ATTCTTTTATAT
20331396 TTTTAATATTTT
1 TTTTAATATTTT
20331408 TTGTAATATT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
46 6 0.12
47 9 0.18
48 33 0.65
49 3 0.06
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.63
Consensus pattern (47 bp):
TTTTAATATTTTATTAAATTTTGCAATTTTTAAATATTCTTTTATAT
Found at i:20331416 original size:21 final size:22
Alignment explanation
Indices: 20331366--20331420 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
20331356 ATTTATTAAC
*
20331366 TTTTGTAAT-TTTTAAATAATT
1 TTTTGTAATATTTTTAATAATT
*
20331387 CTTT-T-ATATTTTTAAT-ATT
1 TTTTGTAATATTTTTAATAATT
20331406 TTTTGTAATATTTTT
1 TTTTGTAATATTTTT
20331421 TTTTCTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 8 0.29
20 9 0.32
21 11 0.39
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTGTAATATTTTTAATAATT
Found at i:20332691 original size:19 final size:19
Alignment explanation
Indices: 20332651--20332692 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
20332641 CAACGTCAAC
* *
20332651 AAATAATTTAAAAACTATA
1 AAATAATTTAAAAAATAAA
*
20332670 AAATATTTTAAAAAATAAA
1 AAATAATTTAAAAAATAAA
20332689 AAAT
1 AAAT
20332693 TCAAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATAATTTAAAAAATAAA
Found at i:20332975 original size:16 final size:17
Alignment explanation
Indices: 20332954--20332985 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20332944 AATTTATTAC
20332954 ATTTTTTGAAA-ATTTA
1 ATTTTTTGAAACATTTA
20332970 ATTTTTTGAAACATTT
1 ATTTTTTGAAACATTT
20332986 TAGGTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
ATTTTTTGAAACATTTA
Found at i:20333441 original size:37 final size:37
Alignment explanation
Indices: 20333382--20333462 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
20333372 ATTCTATAGA
*
20333382 GTCTGTGGCGAGATCCCAGATTGACTACTGATGGTCAT
1 GTCT-TGGCGAGATCCCAGATTGACTACTGACGGTCAT
* * *
20333420 GTCTTGGCGAGATCTCGGATTGACTGCTGACGGTCAT
1 GTCTTGGCGAGATCCCAGATTGACTACTGACGGTCAT
20333457 GTCTTG
1 GTCTTG
20333463 TTGATCAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 35 0.90
38 4 0.10
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (37 bp):
GTCTTGGCGAGATCCCAGATTGACTACTGACGGTCAT
Found at i:20337616 original size:28 final size:30
Alignment explanation
Indices: 20337554--20337617 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
20337544 CCAACGTGAA
20337554 TATATTATGTTATAAAAAATATTATATTAAT
1 TATA-TATGTTATAAAAAATATTATATTAAT
* * *
20337585 TATATATGTTA-AATAAGTATTATA-TATT
1 TATATATGTTATAAAAAATATTATATTAAT
20337613 TATAT
1 TATAT
20337618 TAAATCACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 8 0.27
29 11 0.37
30 7 0.23
31 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (30 bp):
TATATATGTTATAAAAAATATTATATTAAT
Found at i:20337765 original size:39 final size:40
Alignment explanation
Indices: 20337721--20337810 Score: 119
Period size: 39 Copynumber: 2.2 Consensus size: 40
20337711 AAAAAATATA
**
20337721 TTTAATATAATAAAATATTTATTATATTTAT-TTGTGTTT
1 TTTAATATAATAAAATATTTATTATATTTATGTAATGTTT
* * *
20337760 TTTAATGTAATGAAATATTTATTATGTTTATGGTAATGTTT
1 TTTAATATAATAAAATATTTATTATATTTAT-GTAATGTTT
20337801 TTTAATATAA
1 TTTAATATAA
20337811 ATATTTTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 28 0.65
41 15 0.35
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (40 bp):
TTTAATATAATAAAATATTTATTATATTTATGTAATGTTT
Found at i:20340362 original size:42 final size:42
Alignment explanation
Indices: 20340300--20340450 Score: 124
Period size: 42 Copynumber: 3.6 Consensus size: 42
20340290 ATTGAAGCAT
* * * * * *
20340300 CATACTGACACGTAGGTGCATCATCTGATGTACTGAAGAAAA
1 CATACTGGCCCGTAAGTGCATCATCAGATATACCGAAGAAAA
*
20340342 CATATTGGCCCGTAAGTGCATCATCAGATATACCGAAGAAAA
1 CATACTGGCCCGTAAGTGCATCATCAGATATACCGAAGAAAA
* * * * ** * * *
20340384 CATACTGGCACATGAGTGCATAATTGGACATACCAAAGTAATA
1 CATACTGGCCCGTAAGTGCATCATCAGATATACCGAAG-AAAA
* *
20340427 -ATACTGGCACGTAAATGCATCATC
1 CATACTGGCCCGTAAGTGCATCATC
20340451 GGCTACATCG
Statistics
Matches: 86, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
42 83 0.97
43 3 0.03
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (42 bp):
CATACTGGCCCGTAAGTGCATCATCAGATATACCGAAGAAAA
Done.