Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 254 of 290
Found at i:87538572 original size:6 final size:6
Alignment explanation
Indices: 87538561--87538832 Score: 258
Period size: 6 Copynumber: 44.8 Consensus size: 6
87538551 AACCAAAATG
*
87538561 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* *
87538609 AGTAA-C AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* *
87538658 AGAATC AGTAA-C AGAATC AGAATC AGAATC AGTATT AGTAA-C AGAATC
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC
* *
87538706 AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC AGAATC AGTAA-C
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC AG-AATC
* *
87538755 AGAATC AGAATC AGAATC AGTATT AGTAA-C AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC
* *
87538803 AGAATT ACGTGA-C AGAATC AGAATC AGAAT
1 AGAATC A-G-AATC AGAATC AGAATC AGAAT
87538833 GTGAATGCAA
Statistics
Matches: 221, Mismatches: 22, Indels: 46
0.76 0.08 0.16
Matches are distributed among these distances:
5 16 0.07
6 186 0.84
7 15 0.07
8 4 0.02
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:87538576 original size:30 final size:30
Alignment explanation
Indices: 87538561--87538832 Score: 363
Period size: 30 Copynumber: 9.4 Consensus size: 30
87538551 AACCAAAATG
*
87538561 AGAATCAGAATCAGAATCAGTAACAGAATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
87538591 AGAATCAGAATCA-ATATTAGTAACAGAATC
1 AGAATCAGAATCAGA-ATTAGTAACAGAATC
87538621 AGAATCAGAATCAGAATTAGGT----G-A-C
1 AGAATCAGAATCAGAATTA-GTAACAGAATC
*
87538646 AGAATCAGAATCAGAATCAGTAACAGAATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
*
87538676 AGAATCAGAATCAGTATTAGTAACAGAATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
87538706 AGAATCAGAATCAGAATTAGGT----G-A-C
1 AGAATCAGAATCAGAATTA-GTAACAGAATC
*
87538731 AGAATCAGAATCAGAATCAGTAACAGAATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
*
87538761 AGAATCAGAATCAGTATTAGTAACAGAATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
*
87538791 AGAATCAGAATCAGAATTACGTGACAGAATC
1 AGAATCAGAATCAGAATTA-GTAACAGAATC
87538822 AGAATCAGAAT
1 AGAATCAGAAT
87538833 GTGAATGCAA
Statistics
Matches: 215, Mismatches: 10, Indels: 33
0.83 0.04 0.13
Matches are distributed among these distances:
24 4 0.02
25 38 0.18
26 2 0.01
27 2 0.01
28 2 0.01
29 3 0.01
30 138 0.64
31 26 0.12
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (30 bp):
AGAATCAGAATCAGAATTAGTAACAGAATC
Found at i:87538661 original size:85 final size:85
Alignment explanation
Indices: 87538561--87538832 Score: 526
Period size: 85 Copynumber: 3.2 Consensus size: 85
87538551 AACCAAAATG
*
87538561 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
87538626 CAGAATCAGAATTAGGTGAC
66 CAGAATCAGAATTAGGTGAC
87538646 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
87538711 CAGAATCAGAATTAGGTGAC
66 CAGAATCAGAATTAGGTGAC
87538731 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
*
87538796 CAGAATCAGAATTACGTGAC
66 CAGAATCAGAATTAGGTGAC
87538816 AGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAT
87538833 GTGAATGCAA
Statistics
Matches: 185, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 185 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (85 bp):
AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
CAGAATCAGAATTAGGTGAC
Found at i:87538987 original size:27 final size:26
Alignment explanation
Indices: 87538950--87539015 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
87538940 AGCATGGCTG
*
87538950 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
87538976 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
87539003 CCAGAATCAGATA
1 CCAGAA-CAGATA
87539016 ATGTGGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:87539020 original size:27 final size:27
Alignment explanation
Indices: 87538950--87539023 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
87538940 AGCATGGCTG
* *
87538950 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
*
87538976 CCAG-ATACAGATATTGTGGCAGAGCCA
1 CCAGAAT-CAGATAATGTGGCAGAGCCA
87539003 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
87539024 AACCCACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.10
27 32 0.80
28 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:87539030 original size:27 final size:27
Alignment explanation
Indices: 87538974--87539031 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
87538964 GTGACAGAGT
* * *
87538974 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
87539001 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
87539028 CACC
1 CACC
87539032 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:87539236 original size:22 final size:22
Alignment explanation
Indices: 87539188--87539246 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
87539178 GTAAATACGT
*
87539188 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
87539210 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
87539232 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
87539247 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:87539413 original size:27 final size:26
Alignment explanation
Indices: 87539334--87539416 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
87539324 TCTAGCGGTC
* * *
87539334 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
87539360 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
87539387 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
87539414 AAC
1 AAC
87539417 GCTTCCTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.16
27 43 0.84
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:87539645 original size:27 final size:27
Alignment explanation
Indices: 87539615--87539856 Score: 367
Period size: 27 Copynumber: 9.0 Consensus size: 27
87539605 GGGGCAAAAT
* * * *
87539615 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
87539642 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
87539669 GATATTTCTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
87539696 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
87539723 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
87539750 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
87539777 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
87539804 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
87539831 GGTAATTCTACCCTACAGGGGTATTT
1 GGTAATTCTACCCTACAGGGGTATTT
87539857 TAGTAATTTC
Statistics
Matches: 195, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 195 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:87539759 original size:81 final size:81
Alignment explanation
Indices: 87539616--87539864 Score: 408
Period size: 81 Copynumber: 3.1 Consensus size: 81
87539606 GGGCAAAATG
* * * * *
87539616 GTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGATATTTCTACC
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
*
87539681 CTACAAGGGTATTTTA
66 CTACAGGGGTATTTTA
* * *
87539697 GTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACC
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
*
87539762 CTACAGGGGTATTTCA
66 CTACAGGGGTATTTTA
87539778 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
87539843 CTACAGGGGTATTTTA
66 CTACAGGGGTATTTTA
87539859 GTAATT
1 GTAATT
87539865 TCACAATCAA
Statistics
Matches: 154, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 154 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (81 bp):
GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
CTACAGGGGTATTTTA
Found at i:87539899 original size:27 final size:27
Alignment explanation
Indices: 87539869--87540143 Score: 376
Period size: 27 Copynumber: 10.2 Consensus size: 27
87539859 GTAATTTCAC
* *
87539869 AATCAAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
87539896 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
87539923 AA-CTGAGGGTAAACCAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * **
87539950 AATCAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
87539977 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
87540004 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
87540031 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
**
87540058 AATCGAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
87540085 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
*
87540112 AATCGAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
87540139 AATCG
1 AATCG
87540144 GGAGTACTTT
Statistics
Matches: 217, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
26 3 0.01
27 211 0.97
28 3 0.01
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:87546072 original size:43 final size:42
Alignment explanation
Indices: 87546004--87546125 Score: 154
Period size: 43 Copynumber: 2.9 Consensus size: 42
87545994 ACATGTACCG
* * * *
87546004 CATCCATTATGAACTCGGACGACTCAACGAGCTCGGATGCTCT
1 CATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGC-CA
*
87546047 CATCCATAATGAGCTCAGACCACTCAACGAGCTCGGATGCCA
1 CATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGCCA
** * *
87546089 CATATATCATGAACTCAGACCACTCAACGAGTTCGGA
1 CATCCATAATGAACTCAGACCACTCAACGAGCTCGGA
87546126 CTTCTTAATT
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
42 33 0.48
43 36 0.52
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.20
Consensus pattern (42 bp):
CATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGCCA
Found at i:87546119 original size:42 final size:43
Alignment explanation
Indices: 87546012--87546125 Score: 149
Period size: 42 Copynumber: 2.7 Consensus size: 43
87546002 CGCATCCATT
* * * *
87546012 ATGAACTCGGACGACTCAACGAGCTCGGATGCTCTCATCCATA
1 ATGAACTCAGACCACTCAACGAGCTCGGATGCTCACATACATA
* * *
87546055 ATGAGCTCAGACCACTCAACGAGCTCGGATGC-CACATATATC
1 ATGAACTCAGACCACTCAACGAGCTCGGATGCTCACATACATA
*
87546097 ATGAACTCAGACCACTCAACGAGTTCGGA
1 ATGAACTCAGACCACTCAACGAGCTCGGA
87546126 CTTCTTAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
42 33 0.53
43 29 0.47
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (43 bp):
ATGAACTCAGACCACTCAACGAGCTCGGATGCTCACATACATA
Found at i:87548725 original size:23 final size:23
Alignment explanation
Indices: 87548694--87548738 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
87548684 AAGAACTTTA
* *
87548694 ATCAAGAAGCTCTCGAAGAGCCT
1 ATCAAGAAGCTCACAAAGAGCCT
*
87548717 ATCAGGAAGCTCACAAAGAGCC
1 ATCAAGAAGCTCACAAAGAGCC
87548739 GTAATAGGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.13
Consensus pattern (23 bp):
ATCAAGAAGCTCACAAAGAGCCT
Found at i:87549252 original size:21 final size:21
Alignment explanation
Indices: 87549228--87549275 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
87549218 ATATAAATGA
87549228 ATTT-AATCATCAATTTAATTC
1 ATTTCAATC-TCAATTTAATTC
*
87549249 ATTTCATTCTCAATTTAATTC
1 ATTTCAATCTCAATTTAATTC
*
87549270 AATTCA
1 ATTTCA
87549276 CATTCTAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTCAATCTCAATTTAATTC
Found at i:87553456 original size:29 final size:29
Alignment explanation
Indices: 87553418--87553524 Score: 126
Period size: 29 Copynumber: 3.7 Consensus size: 29
87553408 GTTAAAATGG
*
87553418 AAGCCTTTGTGGTAATCTCTGTTATAAGA
1 AAGCCTTTGTGGCAATCTCTGTTATAAGA
** * *
87553447 AAGCGC-TTGTGGTGATTTCTATTATAAGA
1 AAGC-CTTTGTGGCAATCTCTGTTATAAGA
* * *
87553476 AAGCCTTTGTGGCAATATCTGTTAAAAGG
1 AAGCCTTTGTGGCAATCTCTGTTATAAGA
87553505 AAGCCTTTGTGGCAATCTCT
1 AAGCCTTTGTGGCAATCTCT
87553525 ACTGAAAGGA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
28 1 0.02
29 64 0.97
30 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (29 bp):
AAGCCTTTGTGGCAATCTCTGTTATAAGA
Found at i:87553532 original size:29 final size:29
Alignment explanation
Indices: 87553476--87553547 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
87553466 TATTATAAGA
**
87553476 AAGCCTTTGTGGCAATATCTGTTAAAAGG
1 AAGCCTTTGTGGCAATATCTACTAAAAGG
* *
87553505 AAGCCTTTGTGGCAATCTCTACTGAAAGG
1 AAGCCTTTGTGGCAATATCTACTAAAAGG
*
87553534 AATGCCTCTGTGGC
1 AA-GCCTTTGTGGC
87553548 GCAATAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 27 0.73
30 10 0.27
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (29 bp):
AAGCCTTTGTGGCAATATCTACTAAAAGG
Found at i:87555751 original size:48 final size:48
Alignment explanation
Indices: 87555694--87555824 Score: 212
Period size: 48 Copynumber: 2.8 Consensus size: 48
87555684 CTTGCACAAT
*
87555694 AAGTACCTATACCATGGCCTGAAGCCAAATCAAGGTAACTTATCTCCG
1 AAGTACCTATACCATGGCCTGAAGCCAAATCAAGGTAACTCATCTCCG
* *
87555742 GAGTACCTATACCATGGCCTGAAGCCAAATCAAGGTGACTCATCTCCG
1 AAGTACCTATACCATGGCCTGAAGCCAAATCAAGGTAACTCATCTCCG
*
87555790 AAATACCTATACCATGG-C-GAAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCTGAAGCCAAATCAAGGTA
87555825 TGACTCGCAC
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
46 16 0.21
47 1 0.01
48 60 0.78
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCTGAAGCCAAATCAAGGTAACTCATCTCCG
Found at i:87560803 original size:43 final size:43
Alignment explanation
Indices: 87560739--87560936 Score: 211
Period size: 43 Copynumber: 4.6 Consensus size: 43
87560729 ATGCCACTAT
* *
87560739 AGAACATGACCTTTAGCGGTGCTTTTCTCACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGTGCTTTTCCCACAAACACCGCTAA
* * * * *
87560782 ATAACATGACCTTTAGTGGTGC-TTTCCCATAAACGCTGCTAA
1 AGAACATGACCTTTAGCGGTGCTTTTCCCACAAACACCGCTAA
* *** * *
87560824 AGAATATGACCTTTAGCGACAC-TTTCCCAACAAACAACTCTAA
1 AGAACATGACCTTTAGCGGTGCTTTTCCC-ACAAACACCGCTAA
* * * * *
87560867 AGAATATGACCTTTAGTGGCGCTTTCCCCACAAACATCGCTAA
1 AGAACATGACCTTTAGCGGTGCTTTTCCCACAAACACCGCTAA
87560910 AGAACATGACCTTTAGCGGTGCTTTTC
1 AGAACATGACCTTTAGCGGTGCTTTTC
87560937 TCAAAAACCT
Statistics
Matches: 127, Mismatches: 26, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
42 39 0.31
43 83 0.65
44 5 0.04
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (43 bp):
AGAACATGACCTTTAGCGGTGCTTTTCCCACAAACACCGCTAA
Found at i:87582499 original size:71 final size:72
Alignment explanation
Indices: 87582415--87582622 Score: 224
Period size: 71 Copynumber: 2.9 Consensus size: 72
87582405 AGAATAAATG
*
87582415 GTTCCACTTAATATCAAAACTCAATAAGTTGAACTAAATTAACCTTTTTAAAAATTCATAATTAA
1 GTTCCACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAATTCATAATTAA
87582480 ACAAAC-
66 ACAAACA
* ** ** * ** * * * *
87582486 TTTTTACTTAATATCAAATTTCAAAAAATCAAACTAGATTAAGC-TTTTGAAAATGT-ATAACTA
1 GTTCCACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAAT-TCATAATTA
*
87582549 AATAAACA
65 AACAAACA
* * **
87582557 GTTCCACTTAATATCAAAACTTAATAAATTGAAGTAAATTAACCTTTTTAAAAACACATAATTAA
1 GTTCCACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAATTCATAATTAA
87582622 A
66 A
87582623 TAAATGATTT
Statistics
Matches: 103, Mismatches: 30, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
70 21 0.20
71 66 0.64
72 16 0.16
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (72 bp):
GTTCCACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAATTCATAATTAA
ACAAACA
Found at i:87584628 original size:22 final size:22
Alignment explanation
Indices: 87584603--87584648 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
87584593 AACATATAAT
*
87584603 TAAATTAA-TCAAAATTTACAAA
1 TAAA-TAATTCAAAAATTACAAA
*
87584625 TAAATAATTCAAAAATTGCAAA
1 TAAATAATTCAAAAATTACAAA
87584647 TA
1 TA
87584649 GCAGCACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAATAATTCAAAAATTACAAA
Found at i:87589689 original size:11 final size:11
Alignment explanation
Indices: 87589673--87589711 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
87589663 GAAAGAGAGG
87589673 TTGATTTTTGC
1 TTGATTTTTGC
*
87589684 TTGATTTTAGC
1 TTGATTTTTGC
*
87589695 TTGATTCTTGC
1 TTGATTTTTGC
87589706 TTGATT
1 TTGATT
87589712 GAAGCAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.13, C:0.10, G:0.18, T:0.59
Consensus pattern (11 bp):
TTGATTTTTGC
Found at i:87590563 original size:35 final size:35
Alignment explanation
Indices: 87590478--87590563 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 35
87590468 ATACTCAGTC
* * *
87590478 AGATACAGATACAAATTCGCGCTTATGCCCATTAA
1 AGATACAGATACAGATTCGCGCCTAAGCCCATTAA
* * *
87590513 AGATACAGATGCAGATTCGGGCCTAAGCCCATCTCA
1 AGATACAGATACAGATTCGCGCCTAAGCCCAT-TAA
*
87590549 A-ATATAGATACAGAT
1 AGATACAGATACAGAT
87590564 GTACAATCAG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 39 0.93
36 3 0.07
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (35 bp):
AGATACAGATACAGATTCGCGCCTAAGCCCATTAA
Found at i:87599788 original size:19 final size:21
Alignment explanation
Indices: 87599755--87599794 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
87599745 CCAATCATTA
*
87599755 AAACTTTTTATTTTTC-CCCT
1 AAACTTTTTACTTTTCACCCT
87599775 AAAC-TTTTACTTTTCACCCT
1 AAACTTTTTACTTTTCACCCT
87599795 TTACCCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50
Consensus pattern (21 bp):
AAACTTTTTACTTTTCACCCT
Found at i:87602491 original size:29 final size:29
Alignment explanation
Indices: 87602429--87602495 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
87602419 AATCAACCGT
87602429 GCACACTTAGTGCCATGCACTTTAAACTC
1 GCACACTTAGTGCCATGCACTTTAAACTC
* **
87602458 ACACACTTAGTGCCATGCA-TTTCAAGTTC
1 GCACACTTAGTGCCATGCACTTT-AAACTC
87602487 GCACACTTA
1 GCACACTTA
87602496 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.28
Consensus pattern (29 bp):
GCACACTTAGTGCCATGCACTTTAAACTC
Found at i:87602609 original size:174 final size:174
Alignment explanation
Indices: 87602317--87602644 Score: 611
Period size: 174 Copynumber: 1.9 Consensus size: 174
87602307 AACTCAAGGT
* *
87602317 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
87602382 GAAAATATATATTGGGTACGCACACATAGTGCTTAATAATCAACCGTGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTACGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
87602447 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
87602491 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
87602556 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTACGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
87602621 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
87602645 TGTACAATTT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 149 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTACGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:87602636 original size:29 final size:29
Alignment explanation
Indices: 87602597--87602675 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
87602587 CTTAATAATC
* *
87602597 AACCGCGCACACTTAGTGCCATGCACTTTA
1 AACC-CGCACACTTAGTGCCATACAATTTA
* **
87602627 AACTCGCACACTTAGTGCTGTACAATTTA
1 AACCCGCACACTTAGTGCCATACAATTTA
87602656 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
87602676 ATCTCATGAC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 38 0.93
30 3 0.07
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATACAATTTA
Found at i:87619247 original size:39 final size:39
Alignment explanation
Indices: 87619183--87619453 Score: 436
Period size: 39 Copynumber: 7.0 Consensus size: 39
87619173 AAGACACTGA
*
87619183 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
87619222 AAATGTATCTGGGCTAAAGTCCCGCAGGCTTCGTGCTGA
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
87619261 AAATATATCCGGGCTAAAGTCCCGCA-GCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
87619299 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
87619338 AAATGTATCCGGACTAAAGTCCAGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
87619377 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
87619416 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
87619454 ATAATATAAT
Statistics
Matches: 214, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
38 36 0.17
39 178 0.83
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:87619387 original size:116 final size:117
Alignment explanation
Indices: 87619183--87619453 Score: 445
Period size: 116 Copynumber: 2.3 Consensus size: 117
87619173 AAGACACTGA
* * *
87619183 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCTGGGCTAAAGTCCCGCA
1 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGACTAAAGTCCAGCA
*
87619248 GGCTTCGTGCTGAAAATATATCCGGGCTAAAGTCCCGCA-GCTTCGTGCTGG
66 GGCTTCGTGCTGAAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
*
87619299 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGACTAAAGTCCAGCA
1 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGACTAAAGTCCAGCA
* *
87619364 GGCTTCGTGCTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
66 GGCTTCGTGCTGAAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
* * *
87619416 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
87619454 ATAATATAAT
Statistics
Matches: 143, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
116 97 0.68
117 46 0.32
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (117 bp):
AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGACTAAAGTCCAGCA
GGCTTCGTGCTGAAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:87623302 original size:39 final size:39
Alignment explanation
Indices: 87623248--87623480 Score: 376
Period size: 39 Copynumber: 6.0 Consensus size: 39
87623238 AAGACACTGA
* *
87623248 AAATGTATCCGGGCTAAAGTCCCCCAGGCATCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
87623287 AAATGTATCCGGGCTAAAGTCCCGCAGGTTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
87623326 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
87623365 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
87623404 AAATGTCTCCGGACTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
87623443 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
87623481 ATAATATAAT
Statistics
Matches: 180, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 180 1.00
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.23
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:87623603 original size:86 final size:86
Alignment explanation
Indices: 87623458--87623623 Score: 332
Period size: 86 Copynumber: 1.9 Consensus size: 86
87623448 TATCCGGGCC
87623458 AAAGTCCCGCAGGCTTTGTGCTGATAATATAATTTCAGGTTTTATACCTAGTGGGCCAAGTGCCG
1 AAAGTCCCGCAGGCTTTGTGCTGATAATATAATTTCAGGTTTTATACCTAGTGGGCCAAGTGCCG
87623523 ATGAATTTGATAAAATAGGTT
66 ATGAATTTGATAAAATAGGTT
87623544 AAAGTCCCGCAGGCTTTGTGCTGATAATATAATTTCAGGTTTTATACCTAGTGGGCCAAGTGCCG
1 AAAGTCCCGCAGGCTTTGTGCTGATAATATAATTTCAGGTTTTATACCTAGTGGGCCAAGTGCCG
87623609 ATGAATTTGATAAAA
66 ATGAATTTGATAAAA
87623624 GTATACAATT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (86 bp):
AAAGTCCCGCAGGCTTTGTGCTGATAATATAATTTCAGGTTTTATACCTAGTGGGCCAAGTGCCG
ATGAATTTGATAAAATAGGTT
Found at i:87633646 original size:30 final size:33
Alignment explanation
Indices: 87633602--87633665 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 33
87633592 TTATTTTATG
*
87633602 TATATACTTCCTTTTAAATCTATTTAT-ATTTA
1 TATATACTTCCTTTTAAATCTATATATAATTTA
87633634 TATATA-TT-CTTTTAAATCTATATATAATTTA
1 TATATACTTCCTTTTAAATCTATATATAATTTA
87633665 T
1 T
87633666 CTTTTAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 16 0.53
31 8 0.27
32 6 0.20
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (33 bp):
TATATACTTCCTTTTAAATCTATATATAATTTA
Found at i:87637843 original size:12 final size:12
Alignment explanation
Indices: 87637828--87637861 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
87637818 ATGCAAAAGG
87637828 AGATGCAAGAAC
1 AGATGCAAGAAC
*
87637840 AGATGCAAGCAC
1 AGATGCAAGAAC
*
87637852 AAATGCAAGA
1 AGATGCAAGA
87637862 GCCATTGGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.18, G:0.24, T:0.09
Consensus pattern (12 bp):
AGATGCAAGAAC
Found at i:87638157 original size:83 final size:84
Alignment explanation
Indices: 87638001--87638161 Score: 211
Period size: 83 Copynumber: 1.9 Consensus size: 84
87637991 TGAATGATAA
* * * *
87638001 TGAAGATCCTCTCTACACCCCTAGTTTCACCCTGAAAAATGCTTAAACACAACCCGAGATGCACA
1 TGAAAATCCTCTCTACACCCCTAGTTTCACCCTCAAAAATGCTCAAACACAACCCGAGATCCACA
**
87638066 TGCAAAGGCCATCTGTTAC
66 CACAAAGGCCATCTGTTAC
*
87638085 TGAAAATCCTCTCTAC-CCCCTGGTTTCACCC-CAACAAATGCTCAAA-AGCAACCCGAGATCCA
1 TGAAAATCCTCTCTACACCCCTAGTTTCACCCTCAA-AAATGCTCAAACA-CAACCCGAGATCCA
*
87638147 CACACGAAGGCCATC
64 CACACAAAGGCCATC
87638162 CATTATAATC
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
82 3 0.04
83 49 0.73
84 15 0.22
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (84 bp):
TGAAAATCCTCTCTACACCCCTAGTTTCACCCTCAAAAATGCTCAAACACAACCCGAGATCCACA
CACAAAGGCCATCTGTTAC
Found at i:87646285 original size:45 final size:44
Alignment explanation
Indices: 87646181--87646485 Score: 212
Period size: 45 Copynumber: 6.8 Consensus size: 44
87646171 ATGGAGAATA
* * *
87646181 TTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCCATA--AGTC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAG--ATAGCAATC
*
87646225 TTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGC-AATC
* * * *
87646270 TTATTTCTCTGAAGTTGTAGTGGAACAGATTGAAGCTATAAATAAACAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAG------AT-AGCA-ATC
* * * * * *
87646322 TTATCTCTCTGAAGTTACAGTAGAGCAGA-T---CATAGCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGC-AATC
* * * *
87646363 TTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTA--AAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCAA-TC
* * * *
87646406 TTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCGAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGC-AATC
* *
87646451 TTATTTCCCTGAAGTTGTAGTGGAACAGATTGAAG
1 TTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAG
87646486 CTATAAATAA
Statistics
Matches: 207, Mismatches: 34, Indels: 39
0.74 0.12 0.14
Matches are distributed among these distances:
41 30 0.14
42 9 0.04
43 34 0.16
44 32 0.15
45 68 0.33
46 1 0.00
51 4 0.02
52 29 0.14
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCAATC
Found at i:87646396 original size:93 final size:92
Alignment explanation
Indices: 87646223--87646578 Score: 323
Period size: 93 Copynumber: 3.8 Consensus size: 92
87646213 AAGCCATAAG
* * * * * * * *
87646223 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCGAATCTTATTTCTCTGAAGTTGT
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T---CATAGCAAACCTTATCTCCCTGAAGTTGT
87646288 AGTGGAACAGATTGAAGCTATAAATAAACAGA
62 AGTGGAACAGATTGAAGCTATAAATAAA-AGA
* * *
87646320 TCTTATCTCTCTGAAGTTACAGTAGAGCAGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTA
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCCTGAAGTTGTAGTG
* *
87646385 GAGCAGGTTGAAG---T---T-AAAG-
66 GAACAGATTGAAGCTATAAATAAAAGA
* * ** * ** *
87646404 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCGAGTCTTATTTCCCTGAAGTTGT
1 TCTTATCTCTCTGAAGTTGCAGTAGAGC--A--GATCATAGCAAACCTTATCTCCCTGAAGTTGT
87646469 AGTGGAACAGATTGAAGCTATAAATAAATAGA
62 AGTGGAACAGATTGAAGCTATAAATAAA-AGA
* * * *
87646501 TCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCATAGCAAACCTTATCTCCTTGAAATTGTAGAG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCCTGAAGTTGTAGTG
* *
87646566 GAGCAGACTGAAG
66 GAACAGATTGAAG
87646579 ATAGCAGATC
Statistics
Matches: 206, Mismatches: 40, Indels: 30
0.75 0.14 0.11
Matches are distributed among these distances:
84 25 0.12
85 2 0.01
86 3 0.01
87 1 0.00
88 39 0.19
90 1 0.00
91 1 0.00
93 75 0.36
94 1 0.00
95 3 0.01
96 3 0.01
97 52 0.25
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (92 bp):
TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCCTGAAGTTGTAGTG
GAACAGATTGAAGCTATAAATAAAAGA
Found at i:87646419 original size:43 final size:41
Alignment explanation
Indices: 87646319--87646706 Score: 141
Period size: 41 Copynumber: 8.8 Consensus size: 41
87646309 AAATAAACAG
* *
87646319 ATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCATAGCAA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCATAGCAA
* * * *
87646360 ACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGA-AGTTAA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCA-GATCATAG-CAA
* ** *
87646402 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCGA
1 A-TCTTATCTCCCTGAAGTTGCAGTAGAGC--A--GATCATAGCAA
* * * * * **
87646448 GTCTTATTTCCCTGAAGTTGTAGTGGAACAGATTGAAGCTATAAATAAATA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-T----C-AT--A-GCA-A
* *
87646499 GATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCATAGCAA
1 -ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCATAGCAA
* * * * * *
87646541 ACCTTATCTCCTTGAAATTGTAG-AGGAGCAGACTGAAGATAGCAG
1 ATCTTATCTCCCTGAAGTTGCAGTA-GAGCAGA-T---CATAGCAA
* * * * *
87646586 ATCTTATCTCCTTGAAGTTGCAATGGAGCAAATCGTAGCCACCA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCATAG-CA--A
* * * * *
87646630 TTCTTATCTCTCTGAAGTTGCAATAGAGCAGGATAAAAATACACAA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCA-GAT---CATA-GCAA
* * *
87646676 ACCTTATCTCCCTGAAGTTGTAGTGGAGCAG
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAG
87646707 GTTGAAGTTA
Statistics
Matches: 257, Mismatches: 58, Indels: 60
0.69 0.15 0.16
Matches are distributed among these distances:
40 1 0.00
41 60 0.23
42 10 0.04
43 28 0.11
44 28 0.11
45 60 0.23
46 31 0.12
47 5 0.02
48 4 0.02
49 1 0.00
51 2 0.01
52 27 0.11
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (41 bp):
ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCATAGCAA
Found at i:87646455 original size:181 final size:182
Alignment explanation
Indices: 87646181--87646617 Score: 662
Period size: 181 Copynumber: 2.4 Consensus size: 182
87646171 ATGGAGAATA
* ** *
87646181 TTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCCATAAGTCTTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGTAGTAGAGCAGATTGAAGATAGAAGTCTTATCTCCCTGAAGTTGCAGT
* * *
87646246 GGAACAGACTGAAGATAGCGAATCTTATTTCTCTGAAGTTGTAGTGGAACAGATTGAAGCTATAA
66 GGAGCAAACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGTAGTGGAACAGATTGAAGCTATAA
87646311 ATAAACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCATAGCAAACC
131 ATAAACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCATAGCAAACC
* * *
87646363 TTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTA-AAGTCTTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGTAGTAGAGCAGATTGAAGATAGAAGTCTTATCTCCCTGAAGTTGCAGT
*
87646427 GGAGCAAACTGAAGATAGCGAGTCTTATTTCCCTGAAGTTGTAGTGGAACAGATTGAAGCTATAA
66 GGAGCAAACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGTAGTGGAACAGATTGAAGCTATAA
* **
87646492 ATAAATAGATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCATAGCAAACC
131 ATAAACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCATAGCAAACC
* * * * *
87646544 TTATCTCCTTGAAATTGTAG-AGGAGCAGACTGAAGATAGCAGATCTTATCTCCTTGAAGTTGCA
1 TTATCTCCCTGAAGTTGTAGTA-GAGCAGATTGAAGATAGAAG-TCTTATCTCCCTGAAGTTGCA
*
87646608 ATGGAGCAAA
64 GTGGAGCAAA
87646618 TCGTAGCCAC
Statistics
Matches: 231, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
180 1 0.00
181 166 0.72
182 35 0.15
183 29 0.13
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (182 bp):
TTATCTCCCTGAAGTTGTAGTAGAGCAGATTGAAGATAGAAGTCTTATCTCCCTGAAGTTGCAGT
GGAGCAAACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGTAGTGGAACAGATTGAAGCTATAA
ATAAACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCATAGCAAACC
Found at i:87646713 original size:135 final size:130
Alignment explanation
Indices: 87646501--87646739 Score: 316
Period size: 135 Copynumber: 1.8 Consensus size: 130
87646491 AATAAATAGA
* * * * *
87646501 TCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCATAGCAAACCTTATCTCCTTGAAATTGTAGAG
1 TCTTATCTCTCTGAAGTTGCAATAGAGCAGATAATAACAAACCTTATCTCCCTGAAATTGTAGAG
*
87646566 GAGCAGACTGAAGATAGCAGATCTTATCTCCTTGAAGTTGCAATGGAGCAAATCGTAGCCACCAT
66 GAGCAGACTGAAGATACCAGATCTTATCTCCTTGAAGTTGCAATGGAGCAAATCGTAGCCACCAT
*
87646631 TCTTATCTCTCTGAAGTTGCAATAGAGCAGGATAAAAATACACAAACCTTATCTCCCTGAAGTTG
1 TCTTATCTCTCTGAAGTTGCAATAGAGCA-GAT---AATA-ACAAACCTTATCTCCCTGAAATTG
* ** * * *
87646696 TAGTGGAGCAGGTTGAAGTTACCAGTTCTTATCTCCTTTAAGTT
61 TAGAGGAGCAGACTGAAGATACCAGATCTTATCTCCTTGAAGTT
87646740 CCAGCGGAGT
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
130 27 0.30
131 3 0.03
134 3 0.03
135 58 0.64
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (130 bp):
TCTTATCTCTCTGAAGTTGCAATAGAGCAGATAATAACAAACCTTATCTCCCTGAAATTGTAGAG
GAGCAGACTGAAGATACCAGATCTTATCTCCTTGAAGTTGCAATGGAGCAAATCGTAGCCACCAT
Found at i:87646780 original size:135 final size:135
Alignment explanation
Indices: 87646538--87646780 Score: 299
Period size: 135 Copynumber: 1.8 Consensus size: 135
87646528 CAGATCATAG
* *
87646538 CAAACCTTATCTCCTTGAAATTGTAGAGGAGCAGACTGAAGATAGCAGATCTTATCTCCTTGAAG
1 CAAACCTTATCTCCCTGAAATTGTAGAGGAGCAGACTGAAGATACCAGATCTTATCTCCTTGAAG
* * * * * *
87646603 TTGCAATGGAGCAAATCGTAGCCACCATTCTTATCTCTCTGAAGTTGCAATAGAGCAGGATAAAA
66 TTCCAACGGAGCAAATCATAGCCACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGGATAAAA
87646668 ATACA
131 ATACA
* * ** * * *
87646673 CAAACCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGTTACCAGTTCTTATCTCCTTTAAG
1 CAAACCTTATCTCCCTGAAATTGTAGAGGAGCAGACTGAAGATACCAGATCTTATCTCCTTGAAG
* * * *
87646738 TTCCAGCGGAGTAGATCATAGCTACAAATCTCT-TCTCCCTGAA
66 TTCCAACGGAGCAAATCATAGCCACAAATCT-TATCTCCCTGAA
87646781 ATTACATTGG
Statistics
Matches: 88, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
135 87 0.99
136 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (135 bp):
CAAACCTTATCTCCCTGAAATTGTAGAGGAGCAGACTGAAGATACCAGATCTTATCTCCTTGAAG
TTCCAACGGAGCAAATCATAGCCACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGGATAAAA
ATACA
Found at i:87647425 original size:13 final size:13
Alignment explanation
Indices: 87647407--87647436 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
87647397 AATAGAAAAA
87647407 CTTTTATTTTTTT
1 CTTTTATTTTTTT
87647420 CTTTTATTTTTTT
1 CTTTTATTTTTTT
87647433 CTTT
1 CTTT
87647437 CGGCTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (13 bp):
CTTTTATTTTTTT
Found at i:87648553 original size:30 final size:30
Alignment explanation
Indices: 87648519--87648578 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
87648509 TTGCGTATTA
*
87648519 TTATATGTATATGCTTCT-TTTTAAATCTAT
1 TTATATGTATAT-ATTCTCTTTTAAATCTAT
* *
87648549 TTATATTTATATATTTTCTTTTAAATCTAT
1 TTATATGTATATATTCTCTTTTAAATCTAT
87648579 ATGTAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.60
Consensus pattern (30 bp):
TTATATGTATATATTCTCTTTTAAATCTAT
Found at i:87658665 original size:49 final size:49
Alignment explanation
Indices: 87658397--87659538 Score: 2078
Period size: 49 Copynumber: 23.6 Consensus size: 49
87658387 CCCTTCGGGA
* * * * *
87658397 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
87658444 CCTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
87658491 CTTATCAC--ATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
87658538 CTTATCAC--ATGTATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87658585 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87658632 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87658681 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87658730 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87658779 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87658828 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87658877 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87658926 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87658975 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87659024 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87659073 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87659122 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87659171 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87659220 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87659269 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87659318 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87659367 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
87659416 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
87659465 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
87659512 CTTATCAC--ATATATACACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
87659539 TATTCAAATA
Statistics
Matches: 1073, Mismatches: 18, Indels: 8
0.98 0.02 0.01
Matches are distributed among these distances:
46 1 0.00
47 243 0.23
49 829 0.77
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:87664135 original size:39 final size:39
Alignment explanation
Indices: 87664072--87664347 Score: 435
Period size: 39 Copynumber: 7.1 Consensus size: 39
87664062 AATTTTATTA
*
87664072 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
* *
87664111 CCAACACAAAGCCTGGGGGTCTTTAGCCCGGATACATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
* * * *
87664150 CCAGCACGAAGCCTGCGAGTCTTTGGCCCGGATATATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
*
87664189 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
87664228 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
* * * *
87664267 CCAGCACGAAGCCTGTGGGTCTTTGGCCCGGATATATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
*
87664306 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATATATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
87664345 CCA
1 CCA
87664348 TACACATTTC
Statistics
Matches: 215, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 215 1.00
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (39 bp):
CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
Found at i:87664278 original size:117 final size:117
Alignment explanation
Indices: 87664067--87664353 Score: 502
Period size: 117 Copynumber: 2.4 Consensus size: 117
87664057 CCCGAAATTT
* *
87664067 TATTACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAACACAAAGCCTGGGGGTC
1 TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAACACAAAGCCTGCGGGTC
87664132 TTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGAGTCTTTGGCCCGGATA
66 TTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGAGTCTTTGGCCCGGATA
*
87664184 TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACAAAGCCTGCGGGTC
1 TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAACACAAAGCCTGCGGGTC
* *
87664249 TTTAGCCCGGATACATTTCCAGCACGAAGCCTGTGGGTCTTTGGCCCGGATA
66 TTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGAGTCTTTGGCCCGGATA
* *
87664301 TATTTCCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATATATTTCCATACACA
1 TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCA-ACACA
87664354 TTTCGTCTTC
Statistics
Matches: 161, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
117 157 0.98
118 4 0.02
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (117 bp):
TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAACACAAAGCCTGCGGGTC
TTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGAGTCTTTGGCCCGGATA
Found at i:87682639 original size:20 final size:20
Alignment explanation
Indices: 87682602--87682639 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
87682592 AGCCCAGCAT
87682602 AGTATCAACAACAGAAATAC
1 AGTATCAACAACAGAAATAC
*
87682622 AGTATTCAATAACA-AAAT
1 AGTA-TCAACAACAGAAAT
87682640 CCTACCCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.55, C:0.16, G:0.08, T:0.21
Consensus pattern (20 bp):
AGTATCAACAACAGAAATAC
Found at i:87686947 original size:20 final size:20
Alignment explanation
Indices: 87686919--87686988 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
87686909 TACAATTTGG
*
87686919 TATCAATACCATTTAAAAAA
1 TATCGATACCATTTAAAAAA
*
87686939 TATCGATA-CTTTTATAAAAA
1 TATCGATACCATTTA-AAAAA
*
87686959 TATTGATACTCA--TAACAAAA
1 TATCGATAC-CATTTAA-AAAA
*
87686979 TATTGATACC
1 TATCGATACC
87686989 TCTGGGTGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
19 7 0.17
20 34 0.81
22 1 0.02
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.34
Consensus pattern (20 bp):
TATCGATACCATTTAAAAAA
Found at i:87692327 original size:25 final size:23
Alignment explanation
Indices: 87692297--87692361 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
87692287 AATAAAAAAT
*
87692297 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
87692322 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
*
87692343 -TTAAAACA-AGAAACAAATA
1 TTTAAAACATAAAAACAAATA
87692362 AAAAATGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 1 0.03
23 5 0.14
24 3 0.08
25 11 0.30
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.25
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:87692358 original size:19 final size:20
Alignment explanation
Indices: 87692323--87692361 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
87692313 TCAAATACAT
87692323 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
*
87692343 TTAAAACA-AGAAACAAATA
1 TTAAAACATAAAAACAAATA
87692362 AAAAATGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.18
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:87698235 original size:5 final size:5
Alignment explanation
Indices: 87698225--87698255 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
87698215 TAAAGTATTA
87698225 AAAAT AAAAT AAAAT AAAAT AAAAT CAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT
87698256 CAATCCAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:87698848 original size:20 final size:21
Alignment explanation
Indices: 87698803--87698850 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
87698793 TTTGAAACAA
*
87698803 CTTTAAAATCAAGTTAAAATG
1 CTTTTAAATCAAGTTAAAATG
*
87698824 ATTTTAAAT-AAGTTAAAA-G
1 CTTTTAAATCAAGTTAAAATG
87698843 TCTTTTAA
1 -CTTTTAA
87698851 CAAATCTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 15 0.65
21 7 0.30
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
CTTTTAAATCAAGTTAAAATG
Found at i:87698917 original size:21 final size:20
Alignment explanation
Indices: 87698892--87698943 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
87698882 TCCAGGCTAA
87698892 AAAGTATTGATACCTCTTTG
1 AAAGTATTGATACCTCTTTG
*
87698912 ACAAGTATTGATA--TTTTTG
1 A-AAGTATTGATACCTCTTTG
87698931 AAA-TATTGATACC
1 AAAGTATTGATACC
87698944 CTTCAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 8 0.29
18 2 0.07
19 6 0.21
20 1 0.04
21 11 0.39
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (20 bp):
AAAGTATTGATACCTCTTTG
Found at i:87700137 original size:24 final size:23
Alignment explanation
Indices: 87700094--87700150 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 23
87700084 TAACAAATAA
87700094 TTAAATTAAAAATTTTATTTAAG
1 TTAAATTAAAAATTTTATTTAAG
*
87700117 TTAAATCTATAAAA-TTTATTTAAT
1 TTAAAT-TA-AAAATTTTATTTAAG
87700141 TTAAATTAAA
1 TTAAATTAAA
87700151 TAGGAAAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 2 0.06
23 8 0.26
24 17 0.55
25 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAAATTAAAAATTTTATTTAAG
Found at i:87701217 original size:131 final size:131
Alignment explanation
Indices: 87700982--87701218 Score: 325
Period size: 131 Copynumber: 1.8 Consensus size: 131
87700972 AAAATAAATT
* * * **
87700982 TTAATATTACCAGTATATTTAAAATTTTTATCTTCATCTTCTACTTCAACCCATCATTCTTGTTA
1 TTAATATTACAAGTATATTTAAAATTTCTATCTTCATCTTCTACTTCAACCCATCATTCTCGACA
*
87701047 TCATCTTCCATATTGGATCTTCTTCTTCAATCTATATCATCATCTAAAATCTATATTTTTTGAAT
66 TCATCTTCCATATTGGATCTTCTTCTACAATCTATATCATCATCTAAAATCTATATTTTTTGAAT
87701112 A
131 A
* * * * *
87701113 TTAATATTACAAGTATATTT-AAATTCTCTATTTTGATCTTTTGCTTTAACCCATCATTCTCGAC
1 TTAATATTACAAGTATATTTAAAATT-TCTATCTTCATCTTCTACTTCAACCCATCATTCTCGAC
* *
87701177 ATCATCTTTCATCTT-GATCTTCTTCTACAATCTATCATCATC
65 ATCATCTTCCATATTGGATCTTCTTCTACAATCTAT-ATCATC
87701219 TAGATCTACT
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
130 24 0.26
131 67 0.74
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.47
Consensus pattern (131 bp):
TTAATATTACAAGTATATTTAAAATTTCTATCTTCATCTTCTACTTCAACCCATCATTCTCGACA
TCATCTTCCATATTGGATCTTCTTCTACAATCTATATCATCATCTAAAATCTATATTTTTTGAAT
A
Found at i:87718210 original size:43 final size:43
Alignment explanation
Indices: 87718162--87718243 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
87718152 AAAGCTCGTA
* ** *
87718162 CAATGCCAATGTCCCAGACGTGGTCTAACATGTAATCAAATAT
1 CAATGCCAATGTCCCAAACAAGGTCTAACATGAAATCAAATAT
* *
87718205 CAATGCCACTGTCCCAAACAAGGTCTTACATGAAATCAA
1 CAATGCCAATGTCCCAAACAAGGTCTAACATGAAATCAA
87718244 GTATGATGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.23
Consensus pattern (43 bp):
CAATGCCAATGTCCCAAACAAGGTCTAACATGAAATCAAATAT
Found at i:87732006 original size:42 final size:42
Alignment explanation
Indices: 87731892--87732058 Score: 131
Period size: 43 Copynumber: 3.9 Consensus size: 42
87731882 CAAAAAGCTC
* * * **
87731892 GTACAATGCCAATGTCCCAGACGTGGTCTAACATGTAATCAA
1 GTACGATGCCAATGTCCCAGATGTGGTCTTACATAAAATCAA
* * *
87731934 ATATCGATGCCACTGTCCCAGACAG-GGTCTTACATAAAATCAA
1 GTA-CGATGCCAATGTCCCAGA-TGTGGTCTTACATAAAATCAA
* * **
87731977 GTACGATGCCAATGTCCTAGATGTAGTCTTACACGCAAATCATAA
1 GTACGATGCCAATGTCCCAGATGTGGTCTTACA-TAAAATC--AA
** * *
87732022 GT-CGATGCCAACATCCGAGATGTGGTCTTACACAAAA
1 GTACGATGCCAATGTCCCAGATGTGGTCTTACATAAAA
87732059 ACACATATCG
Statistics
Matches: 99, Mismatches: 20, Indels: 11
0.76 0.15 0.08
Matches are distributed among these distances:
41 1 0.01
42 26 0.26
43 41 0.41
44 27 0.27
45 4 0.04
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (42 bp):
GTACGATGCCAATGTCCCAGATGTGGTCTTACATAAAATCAA
Found at i:87741893 original size:43 final size:42
Alignment explanation
Indices: 87741745--87741912 Score: 159
Period size: 43 Copynumber: 4.0 Consensus size: 42
87741735 ATATCATACA
* * *
87741745 ATGCCAACGTCCCAGACGTGGTCCTTACATGCAATCACATATCG
1 ATGCC-ACATCCCAGACGTGGT-CTTACACGTAATCACATATCG
* * *
87741789 ATGCCACTATCTCAAACAG-GGTCTTACACG-AATCAAATA-CG
1 ATGCCAC-ATCCCAGAC-GTGGTCTTACACGTAATCACATATCG
** * *
87741830 ATGCCA-AT--GGGACATGGTCTTACACGTAATCACATATCC
1 ATGCCACATCCCAGACGTGGTCTTACACGTAATCACATATCG
87741869 ATGCCAACATCCCAGACGTGGTCTTACACGTAATCACATATCG
1 ATGCC-ACATCCCAGACGTGGTCTTACACGTAATCACATATCG
87741912 A
1 A
87741913 AAATCCTATG
Statistics
Matches: 100, Mismatches: 15, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
37 13 0.13
38 8 0.08
39 8 0.08
40 1 0.01
41 10 0.10
42 8 0.08
43 37 0.37
44 14 0.14
45 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.23
Consensus pattern (42 bp):
ATGCCACATCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:87747600 original size:20 final size:21
Alignment explanation
Indices: 87747528--87747604 Score: 61
Period size: 26 Copynumber: 3.5 Consensus size: 21
87747518 AAACGTTCAT
87747528 TTATTAAAACATACTCATGAAATAAA
1 TTATTAAAACATACT--TG--A-AAA
87747554 TTATTAAAACATACTTGAAAA
1 TTATTAAAACATACTTGAAAA
* *
87747575 AT-TTAAAA-AT-TTTGAGAAA
1 TTATTAAAACATACTTGA-AAA
87747594 TTATTAAAACA
1 TTATTAAAACA
87747605 AAGTAATGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
18 4 0.09
19 6 0.13
20 12 0.27
21 5 0.11
22 1 0.02
24 2 0.04
26 15 0.33
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (21 bp):
TTATTAAAACATACTTGAAAA
Found at i:87750525 original size:13 final size:13
Alignment explanation
Indices: 87750507--87750534 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
87750497 ACAAAATAAG
87750507 AACCTTCATCACT
1 AACCTTCATCACT
87750520 AACCTTCATCACT
1 AACCTTCATCACT
87750533 AA
1 AA
87750535 TAATAGGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (13 bp):
AACCTTCATCACT
Found at i:87757324 original size:49 final size:49
Alignment explanation
Indices: 87757226--87757324 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
87757216 GTTTACAGCT
* *
87757226 ACATGGCCGCACATTTGCCATCATACGACAGTGTCTCCCCCCCAACCAC
1 ACATGGCCGCACATTTGCCATCATACGACAGTGTCTCCCACACAACCAC
* *
87757275 ACATGGCCGCACATTTGCCATCATACGACAGTGTCTCGCACACAGCCAC
1 ACATGGCCGCACATTTGCCATCATACGACAGTGTCTCCCACACAACCAC
87757324 A
1 A
87757325 ACTTTGACAG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.26, C:0.39, G:0.16, T:0.18
Consensus pattern (49 bp):
ACATGGCCGCACATTTGCCATCATACGACAGTGTCTCCCACACAACCAC
Found at i:87761969 original size:31 final size:30
Alignment explanation
Indices: 87761934--87761995 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
87761924 TCCTTAAATC
87761934 AAACTTTTGAAAAAATTACAATTTTGCCCCT
1 AAACTTTTG-AAAAATTACAATTTTGCCCCT
* * * *
87761965 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
87761995 A
1 A
87761996 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACAATTTTGCCCCT
Found at i:87769254 original size:30 final size:29
Alignment explanation
Indices: 87769218--87769277 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 29
87769208 ATGTTTTGGT
87769218 AAGAGTTGATAAATTTATTTTTCCTGCTG
1 AAGAGTTGATAAATTTATTTTTCCTGCTG
87769247 NAAGAGTTGATAAATTTATTTTTCCTGCTG
1 -AAGAGTTGATAAATTTATTTTTCCTGCTG
87769277 A
1 A
87769278 TTCCATTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.43
Consensus pattern (29 bp):
AAGAGTTGATAAATTTATTTTTCCTGCTG
Found at i:87776504 original size:26 final size:27
Alignment explanation
Indices: 87776488--87776623 Score: 109
Period size: 27 Copynumber: 5.0 Consensus size: 27
87776478 TATTGAAATG
*
87776488 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCTAGTTTATAAAATTACCAAAATAC
*
87776515 CCCTAGTTTATAAAATTACCGAAATAC
1 CCCTAGTTTATAAAATTACCAAAATAC
*** * * * *
87776542 AATTGGTTTGTGAAATTACCGAAATA-
1 CCCTAGTTTATAAAATTACCAAAATAC
*
87776568 CCCTCA-ATTAGTAAAATTACCAAAATAC
1 CCCT-AGTTTA-TAAAATTACCAAAATAC
*
87776596 CCCT-GATTTACAAAATTA-CAGAAATAC
1 CCCTAG-TTTATAAAATTACCA-AAATAC
87776623 C
1 C
87776624 TTTGACTTTT
Statistics
Matches: 85, Mismatches: 18, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
26 5 0.06
27 73 0.86
28 7 0.08
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.29
Consensus pattern (27 bp):
CCCTAGTTTATAAAATTACCAAAATAC
Found at i:87776523 original size:27 final size:27
Alignment explanation
Indices: 87776488--87776599 Score: 118
Period size: 27 Copynumber: 4.1 Consensus size: 27
87776478 TATTGAAATG
87776488 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCTAGTTTGTAAAATTACCAAAATAC
* *
87776515 CCCTAGTTTATAAAATTACCGAAATAC
1 CCCTAGTTTGTAAAATTACCAAAATAC
*** * * *
87776542 AATTGGTTTGTGAAATTACCGAAATA-
1 CCCTAGTTTGTAAAATTACCAAAATAC
* *
87776568 CCCTCAATTAGTAAAATTACCAAAATAC
1 CCCT-AGTTTGTAAAATTACCAAAATAC
87776596 CCCT
1 CCCT
87776600 GATTTACAAA
Statistics
Matches: 67, Mismatches: 16, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
26 1 0.01
27 62 0.93
28 4 0.06
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.29
Consensus pattern (27 bp):
CCCTAGTTTGTAAAATTACCAAAATAC
Found at i:87776558 original size:54 final size:54
Alignment explanation
Indices: 87776493--87776595 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
87776483 AAATGCCCTA
* *
87776493 GTTTGTAAAATTACCAAAATACCC-CTAGTTTA-TAAAATTACCGAAATACAATTG
1 GTTTGTAAAATTACCAAAATACCCTC-A-ATTAGTAAAATTACCAAAATACAATTG
* *
87776547 GTTTGTGAAATTACCGAAATACCCTCAATTAGTAAAATTACCAAAATAC
1 GTTTGTAAAATTACCAAAATACCCTCAATTAGTAAAATTACCAAAATAC
87776596 CCCTGATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
53 3 0.07
54 39 0.91
55 1 0.02
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (54 bp):
GTTTGTAAAATTACCAAAATACCCTCAATTAGTAAAATTACCAAAATACAATTG
Found at i:87776675 original size:27 final size:26
Alignment explanation
Indices: 87776632--87776686 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
87776622 CCTTTGACTT
87776632 TTTAAAAATTATAGAAATACCATTGG
1 TTTAAAAATTATAGAAATACCATTGG
* *
87776658 TTTACAAAATTATTGAAATACCCTTGG
1 TTTA-AAAATTATAGAAATACCATTGG
87776685 TT
1 TT
87776687 CGTAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (26 bp):
TTTAAAAATTATAGAAATACCATTGG
Found at i:87777656 original size:25 final size:23
Alignment explanation
Indices: 87777618--87777695 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 23
87777608 AGGAAGTGCT
*
87777618 AAAAGGGTTCTGCCCCAGTTTACTG
1 AAAAGGGTT-TGCCCCAGTTTA-TC
87777643 AAAAGGGCTTTGCCCCAGTTTATC
1 AAAAGGG-TTTGCCCCAGTTTATC
* *
87777667 AGAAAGGGGTTTGCCCTAG-TTATT
1 A-AAA-GGGTTTGCCCCAGTTTATC
87777691 AAAAG
1 AAAAG
87777696 AGGCTAGGCT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
22 1 0.02
23 3 0.06
24 7 0.15
25 31 0.66
26 5 0.11
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (23 bp):
AAAAGGGTTTGCCCCAGTTTATC
Found at i:87777894 original size:42 final size:42
Alignment explanation
Indices: 87777835--87777926 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
87777825 TAGTCTCCCC
* *
87777835 AAATGGGCTTGCCTACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
87777877 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
87777919 AAATGGGC
1 AAATGGGC
87777927 CTAAGGGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:87777985 original size:31 final size:31
Alignment explanation
Indices: 87777950--87778033 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
87777940 TGTTTATAGT
87777950 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
87777981 AAAGGCTTCGGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
87778012 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
87778034 TCAAGACTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 5 0.10
31 47 0.90
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:87779772 original size:27 final size:27
Alignment explanation
Indices: 87779738--87779901 Score: 188
Period size: 27 Copynumber: 6.1 Consensus size: 27
87779728 TATTGAAATG
*
87779738 CCCTAGTTTGTAATATTACCAAAATAC
1 CCCTAGTTTGTAAAATTACCAAAATAC
87779765 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCTAGTTTGTAAAATTACCAAAATAC
*
87779792 CCCTAGTTTGTAAAATTACCGAAATAC
1 CCCTAGTTTGTAAAATTACCAAAATAC
** * * *
87779819 CATTGGTTTGTGAAATTACCGAAATAC
1 CCCTAGTTTGTAAAATTACCAAAATAC
* * *
87779846 CCTTAATTTGTAAAATTACCAAAAAAC
1 CCCTAGTTTGTAAAATTACCAAAATAC
**
87779873 CCCT-GATTTACAAAATTA-CAGAAATAC
1 CCCTAG-TTTGTAAAATTACCA-AAATAC
87779900 CC
1 CC
87779902 TTGAATTTTT
Statistics
Matches: 118, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.02
27 116 0.98
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
CCCTAGTTTGTAAAATTACCAAAATAC
Found at i:87779837 original size:81 final size:81
Alignment explanation
Indices: 87779743--87779900 Score: 221
Period size: 81 Copynumber: 2.0 Consensus size: 81
87779733 AAATGCCCTA
* * **
87779743 GTTTGTAATATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCT-AGTTTGTAAAA
1 GTTTGTAATATTACCAAAATACCCCTAATTTGTAAAATTACCAAAAAACCCCTGA-TTTACAAAA
*
87779807 TTACCGAAATACCATTG
65 TTACAGAAATACCATTG
* *
87779824 GTTTGTGAA-ATTACCGAAATACCCTTAATTTGTAAAATTACCAAAAAACCCCTGATTTACAAAA
1 GTTTGT-AATATTACCAAAATACCCCTAATTTGTAAAATTACCAAAAAACCCCTGATTTACAAAA
87779888 TTACAGAAATACC
65 TTACAGAAATACC
87779901 CTTGAATTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
81 65 0.96
82 3 0.04
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (81 bp):
GTTTGTAATATTACCAAAATACCCCTAATTTGTAAAATTACCAAAAAACCCCTGATTTACAAAAT
TACAGAAATACCATTG
Found at i:87779902 original size:54 final size:55
Alignment explanation
Indices: 87779744--87779960 Score: 192
Period size: 54 Copynumber: 4.0 Consensus size: 55
87779734 AATGCCCTAG
* * ** * *
87779744 TTTGTAATATTACCAAAATACCCCT-AGTTTGTAAAATTACCA-AAATACCCCTAG
1 TTTGTAAAATTACCAAAATACCACTGAGTTTACAAAATTA-CAGAAATACCCTTAA
* * *** *
87779798 TTTGTAAAATTACCGAAATACCATTG-GTTTGTGAAATTACCGAAATACCCTTAA
1 TTTGTAAAATTACCAAAATACCACTGAGTTTACAAAATTACAGAAATACCCTTAA
* *
87779852 TTTGTAAAATTACCAAAAAACCCCTGA-TTTACAAAATTACAGAAATACCCTTGAA
1 TTTGTAAAATTACCAAAATACCACTGAGTTTACAAAATTACAGAAATACCCTT-AA
* * * * *
87779907 TTTTTAAAAATTA-TAGAAATACCATTGATTTTACAAAATTACTGAAATACCCTT
1 TTTGT-AAAATTACCA-AAATACCACTGAGTTTACAAAATTACAGAAATACCCTT
87779961 GGTTTGTAGA
Statistics
Matches: 134, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
53 1 0.01
54 86 0.64
55 7 0.05
56 16 0.12
57 24 0.18
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (55 bp):
TTTGTAAAATTACCAAAATACCACTGAGTTTACAAAATTACAGAAATACCCTTAA
Found at i:87779924 original size:29 final size:28
Alignment explanation
Indices: 87779871--87779961 Score: 107
Period size: 28 Copynumber: 3.2 Consensus size: 28
87779861 TTACCAAAAA
* *
87779871 ACCCCTGA-TTTACAAAATTACAGAAAT
1 ACCCTTGATTTTACAAAATTATAGAAAT
87779898 ACCCTTGAATTTTTA-AAAATTATAGAAAT
1 ACCCTTG-A-TTTTACAAAATTATAGAAAT
*
87779927 ACCATTGATTTTACAAAATTACT-GAAAT
1 ACCCTTGATTTTACAAAATTA-TAGAAAT
87779955 ACCCTTG
1 ACCCTTG
87779962 GTTTGTAGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 11 0.20
28 20 0.36
29 20 0.36
30 4 0.07
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.33
Consensus pattern (28 bp):
ACCCTTGATTTTACAAAATTATAGAAAT
Found at i:87779938 original size:28 final size:29
Alignment explanation
Indices: 87779879--87779957 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
87779869 AAACCCCTGA
* *
87779879 TTTACAAAATTACAGAAATACCCTTGAATT
1 TTTACAAAATTATAGAAATACCATTGAA-T
87779909 TTTA-AAAATTATAGAAATACCATTG-AT
1 TTTACAAAATTATAGAAATACCATTGAAT
87779936 TTTACAAAATTACT-GAAATACC
1 TTTACAAAATTA-TAGAAATACC
87779958 CTTGGTTTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.11
28 16 0.36
29 20 0.44
30 4 0.09
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (29 bp):
TTTACAAAATTATAGAAATACCATTGAAT
Found at i:87782926 original size:27 final size:27
Alignment explanation
Indices: 87782892--87783055 Score: 188
Period size: 27 Copynumber: 6.1 Consensus size: 27
87782882 TATTGAAATG
*
87782892 CCCTAGTTTGTAATATTACCAAAATAC
1 CCCTAGTTTGTAAAATTACCAAAATAC
87782919 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCTAGTTTGTAAAATTACCAAAATAC
*
87782946 CCCTAGTTTGTAAAATTACCGAAATAC
1 CCCTAGTTTGTAAAATTACCAAAATAC
** * * *
87782973 CATTGGTTTGTGAAATTACCGAAATAC
1 CCCTAGTTTGTAAAATTACCAAAATAC
* * *
87783000 CCTTAATTTGTAAAATTACCAAAAAAC
1 CCCTAGTTTGTAAAATTACCAAAATAC
**
87783027 CCCT-GATTTACAAAATTA-CAGAAATAC
1 CCCTAG-TTTGTAAAATTACCA-AAATAC
87783054 CC
1 CC
87783056 TTGACTTTTT
Statistics
Matches: 118, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.02
27 116 0.98
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
CCCTAGTTTGTAAAATTACCAAAATAC
Found at i:87782991 original size:81 final size:81
Alignment explanation
Indices: 87782897--87783054 Score: 221
Period size: 81 Copynumber: 2.0 Consensus size: 81
87782887 AAATGCCCTA
* * **
87782897 GTTTGTAATATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCT-AGTTTGTAAAA
1 GTTTGTAATATTACCAAAATACCCCTAATTTGTAAAATTACCAAAAAACCCCTGA-TTTACAAAA
*
87782961 TTACCGAAATACCATTG
65 TTACAGAAATACCATTG
* *
87782978 GTTTGTGAA-ATTACCGAAATACCCTTAATTTGTAAAATTACCAAAAAACCCCTGATTTACAAAA
1 GTTTGT-AATATTACCAAAATACCCCTAATTTGTAAAATTACCAAAAAACCCCTGATTTACAAAA
87783042 TTACAGAAATACC
65 TTACAGAAATACC
87783055 CTTGACTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
81 65 0.96
82 3 0.04
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (81 bp):
GTTTGTAATATTACCAAAATACCCCTAATTTGTAAAATTACCAAAAAACCCCTGATTTACAAAAT
TACAGAAATACCATTG
Found at i:87783072 original size:29 final size:28
Alignment explanation
Indices: 87782957--87783114 Score: 98
Period size: 27 Copynumber: 5.8 Consensus size: 28
87782947 CCTAGTTTGT
* * * *
87782957 AAAATTACCGAAATACCATTGGTTTGT-
1 AAAATTACAGAAATACCCTTGATTTTTA
* * * *
87782984 GAAATTACCGAAATACCCTTAATTTGT-
1 AAAATTACAGAAATACCCTTGATTTTTA
* *
87783011 AAAATTACCA-AAAAACCCCTGA--TTTA
1 AAAATTA-CAGAAATACCCTTGATTTTTA
87783037 CAAAATTACAGAAATACCCTTGACTTTTTA
1 -AAAATTACAGAAATACCCTTGA-TTTTTA
* * *
87783067 AAAATTATAGAAATACCATTG--GTTTA
1 AAAATTACAGAAATACCCTTGATTTTTA
87783093 CAAAATTACTA-AAATACCCTTG
1 -AAAATTAC-AGAAATACCCTTG
87783115 GTTTGTAGAT
Statistics
Matches: 105, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
25 2 0.02
26 6 0.06
27 72 0.69
28 2 0.02
29 19 0.18
30 4 0.04
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (28 bp):
AAAATTACAGAAATACCCTTGATTTTTA
Found at i:87783098 original size:56 final size:55
Alignment explanation
Indices: 87782930--87783114 Score: 173
Period size: 54 Copynumber: 3.4 Consensus size: 55
87782920 CCTAGTTTGT
* * * **
87782930 AAAATTACCA-AAATACCCCT-AGTTTGTAAAATTACCGAAATACCATTGGTTTGT
1 AAAATTA-CAGAAATACCCTTGAATTTGTAAAATTACAGAAATACCATTGGTTTAC
* * * ** *
87782984 GAAATTACCGAAATACCCTT-AATTTGTAAAATTACCA-AAAAACCCCTGATTTAC
1 AAAATTACAGAAATACCCTTGAATTTGTAAAATTA-CAGAAATACCATTGGTTTAC
* * *
87783038 AAAATTACAGAAATACCCTTGACTTTTTAAAAATTATAGAAATACCATTGGTTTAC
1 AAAATTACAGAAATACCCTTGAATTTGT-AAAATTACAGAAATACCATTGGTTTAC
87783094 AAAATTACTA-AAATACCCTTG
1 AAAATTAC-AGAAATACCCTTG
87783115 GTTTGTAGAT
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 57 0.54
55 7 0.07
56 39 0.37
57 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (55 bp):
AAAATTACAGAAATACCCTTGAATTTGTAAAATTACAGAAATACCATTGGTTTAC
Found at i:87784083 original size:25 final size:24
Alignment explanation
Indices: 87784045--87784114 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
87784035 AGGAAGTGCT
* *
87784045 AAAAAGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
* *
87784069 GAAAAGGGCTTTGCCCCATTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
*
87784094 AGAAAGGGCTTTGCCCTAGTT
1 A-AAAGGGCTTTGCCCCAGTT
87784115 ATTAAAAGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 1 0.03
25 37 0.97
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:87784127 original size:24 final size:24
Alignment explanation
Indices: 87784070--87784127 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
87784060 CAGTTTACCG
*
87784070 AAAAGGGCTTTGCCCCATTTTATC
1 AAAAGGGCTTTGCCCCATGTTATC
* *
87784094 AGAAAGGGCTTTGCCCTA-GTTATT
1 A-AAAGGGCTTTGCCCCATGTTATC
87784118 AAAAGAGGCT
1 AAAAG-GGCT
87784128 AGGCCTCCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 15 0.52
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCATGTTATC
Found at i:87784351 original size:42 final size:42
Alignment explanation
Indices: 87784262--87784560 Score: 568
Period size: 42 Copynumber: 7.2 Consensus size: 42
87784252 TAGTCTCCCC
*
87784262 AAATGGGCTTGCATACATTCATTGACATT--A-GTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
87784301 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
87784343 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
87784385 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
87784427 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
87784469 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
87784511 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
87784553 AAATGGGC
1 AAATGGGC
87784561 CTAAGGGCCA
Statistics
Matches: 256, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
39 28 0.11
41 1 0.00
42 227 0.89
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:87784619 original size:31 final size:31
Alignment explanation
Indices: 87784584--87784698 Score: 205
Period size: 31 Copynumber: 3.7 Consensus size: 31
87784574 CGTTTACAGT
87784584 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
87784615 AAAGGCTTCGACCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
87784646 AAAGGCTTCGGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
87784677 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
87784699 TCAAGACTAA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
30 5 0.06
31 76 0.94
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:87787991 original size:29 final size:29
Alignment explanation
Indices: 87787939--87788000 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
87787929 CGGGCGTGCA
*
87787939 CCATAGCCGTGTTAAAAAGACAGTGTTGT
1 CCATAGCCGTGTTAAAAAGACAGTGTTGC
* * * *
87787968 CCATGGCCGTGTTGATAAGTCAGTGTTGC
1 CCATAGCCGTGTTAAAAAGACAGTGTTGC
87787997 CCAT
1 CCAT
87788001 TGCTAAAGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (29 bp):
CCATAGCCGTGTTAAAAAGACAGTGTTGC
Found at i:87793390 original size:20 final size:20
Alignment explanation
Indices: 87793365--87793405 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
87793355 ATTGAAGACC
*
87793365 AAGTCAACCTAAATTCAGCT
1 AAGTCAACCCAAATTCAGCT
*
87793385 AAGTCAACCCAAATTCGGCT
1 AAGTCAACCCAAATTCAGCT
87793405 A
1 A
87793406 CACATGGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (20 bp):
AAGTCAACCCAAATTCAGCT
Found at i:87821778 original size:28 final size:28
Alignment explanation
Indices: 87821741--87821831 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 28
87821731 TACATACATG
* * *
87821741 CATATAGCCCACTAGGCCCAATCTCATT
1 CATATGGCCCATTAGGCCAAATCTCATT
*
87821769 CATATGGCCCATTAGGACCAAATCAT-GTT
1 CATATGGCCCATTAGG-CCAAATC-TCATT
* *
87821798 CGTATGGCCCATTAGGCCTAAATCACATT
1 CATATGGCCCATTAGGCC-AAATCTCATT
87821827 CATAT
1 CATAT
87821832 ACATGCTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
28 16 0.31
29 34 0.67
30 1 0.02
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (28 bp):
CATATGGCCCATTAGGCCAAATCTCATT
Found at i:87836159 original size:27 final size:27
Alignment explanation
Indices: 87836077--87836149 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
87836067 GTCGTTAAGA
87836077 CCCTAGTTTGTAAAATTACTGAAATAC
1 CCCTAGTTTGTAAAATTACTGAAATAC
* *
87836104 CCCTAATTTGTAAAATTATTGAAATAC
1 CCCTAGTTTGTAAAATTACTGAAATAC
*
87836131 CCCTGGTTTGTAAAATTAC
1 CCCTAGTTTGTAAAATTAC
87836150 CTAATTACCC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (27 bp):
CCCTAGTTTGTAAAATTACTGAAATAC
Found at i:87836185 original size:27 final size:29
Alignment explanation
Indices: 87836080--87836192 Score: 114
Period size: 27 Copynumber: 4.1 Consensus size: 29
87836070 GTTAAGACCC
87836080 TAGTTTGTAAAATTA-CTGAAATACCCC--
1 TAGTTTGTAAAATTATC-GAAATACCCCTG
* *
87836107 TAATTTGTAAAATTATTGAAATACCCCTG
1 TAGTTTGTAAAATTATCGAAATACCCCTG
* * * *
87836136 --GTTTGTAAAATTACCTAATTACCCTTG
1 TAGTTTGTAAAATTATCGAAATACCCCTG
87836163 TAG-TT-TAAAATTATCGAAATACCCCTG
1 TAGTTTGTAAAATTATCGAAATACCCCTG
87836190 TAG
1 TAG
87836193 GGTAAAATGA
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
27 66 0.96
28 2 0.03
29 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (29 bp):
TAGTTTGTAAAATTATCGAAATACCCCTG
Found at i:87840523 original size:30 final size:31
Alignment explanation
Indices: 87840463--87840523 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
87840453 TTTTACGAGC
* **
87840463 CTAGGGGCAAAATTATAATTTTTGTGAAAGT
1 CTAGGGGCAAAATGATAATTTTTGCCAAAGT
*
87840494 CTAGGGGCAAAATGGTAA-TTTTGCCAAAGT
1 CTAGGGGCAAAATGATAATTTTTGCCAAAGT
87840524 TTGAATTGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (31 bp):
CTAGGGGCAAAATGATAATTTTTGCCAAAGT
Found at i:87844350 original size:50 final size:49
Alignment explanation
Indices: 87844227--87844411 Score: 194
Period size: 50 Copynumber: 3.7 Consensus size: 49
87844217 TGAGGTCGCA
* * * *
87844227 TGTGTAGTACTAAGTGCAGGCTACTATGAGTACCCGAAAACTAT-GATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CC--AAACTGTAGGTCACG
* ** *
87844278 TGTGTAGTACTAAGTGCGGGCTACTACGTGTATTAGA-TGGTGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAACT-GT-AGGTCACG
* * *
87844328 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAACTGTTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAACTGTAGGTCACG
* *
87844377 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
87844412 GATAGCTTCG
Statistics
Matches: 113, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
47 1 0.01
48 3 0.03
49 38 0.34
50 41 0.36
51 30 0.27
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAACTGTAGGTCACG
Found at i:87847440 original size:15 final size:15
Alignment explanation
Indices: 87847420--87847484 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
87847410 GTGTCTTGGG
87847420 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
87847435 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
87847450 TTT-TTCTA-TCTTGGA
1 TTTCTT-TATTC-TGGA
*
87847465 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
87847479 TTTCTT
1 TTTCTT
87847485 GTTATCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 12 0.28
15 27 0.63
16 4 0.09
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:87847452 original size:30 final size:31
Alignment explanation
Indices: 87847416--87847484 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
87847406 TATTGTGTCT
87847416 TGGGTTTCTT-TAT-TCTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCT-TGGATTTCTTTATTC
87847446 TGGGTTT-TTCTATCTTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCTTGGATTTCTTTATTC
*
87847476 -GGTTTTCTT
1 TGGGTTTCTT
87847485 GTTATCTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 7 0.20
30 27 0.77
31 1 0.03
ACGTcount: A:0.09, C:0.13, G:0.17, T:0.61
Consensus pattern (31 bp):
TGGGTTTCTTCTATCTTGGATTTCTTTATTC
Found at i:87849328 original size:49 final size:50
Alignment explanation
Indices: 87849146--87849332 Score: 164
Period size: 50 Copynumber: 3.7 Consensus size: 50
87849136 ATGATCTATT
* * * ** **
87849146 GTGAGGTCACATCTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAA
1 GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAG-ATG
* * * ** *
87849197 CTGTGATCATGTGTGTAGTACTAAGTGC-GGTCTACTACGTGTATTAGATG
1 GTGAGGTCACATGTGTAGTACTAAGTGCAGG-CTACTACGTGTACTAGATG
* *
87849247 GTGAGGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACTAGACT-
1 GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGA-TG
* * *
87849297 GT-TGGTCGCATGTGTAGTAATAAGTGCAGGCTACTA
1 GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
87849333 TGCGTACCAG
Statistics
Matches: 109, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
49 29 0.27
50 44 0.40
51 36 0.33
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (50 bp):
GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATG
Found at i:87855056 original size:30 final size:30
Alignment explanation
Indices: 87855020--87855118 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 30
87855010 TACATGTATT
** *
87855020 AGTTATGTAAGTTGTTATGTACGTTATGTG
1 AGTTATGTAAGTTGTTATGTAAATTATGTA
87855050 AGTTATGTAAGTTGTTATGTAAATTATGTA
1 AGTTATGTAAGTTGTTATGTAAATTATGTA
* * *
87855080 AGTTA--TATG-AGTTATGTAAGTTATGTA
1 AGTTATGTAAGTTGTTATGTAAATTATGTA
* *
87855107 ATTTATTTAAGT
1 AGTTATGTAAGT
87855119 AATGATCAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
27 20 0.34
28 3 0.05
29 3 0.05
30 32 0.55
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.47
Consensus pattern (30 bp):
AGTTATGTAAGTTGTTATGTAAATTATGTA
Found at i:87855066 original size:21 final size:21
Alignment explanation
Indices: 87855042--87855101 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
87855032 TGTTATGTAC
87855042 GTTATGTGAGTTATGTAAGTT
1 GTTATGTGAGTTATGTAAGTT
* *
87855063 GTTATGTAAATTATGTAA---
1 GTTATGTGAGTTATGTAAGTT
*
87855081 GTTATATGAGTTATGTAAGTT
1 GTTATGTGAGTTATGTAAGTT
87855102 ATGTAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 15 0.48
21 16 0.52
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (21 bp):
GTTATGTGAGTTATGTAAGTT
Found at i:87855107 original size:9 final size:9
Alignment explanation
Indices: 87855033--87855118 Score: 82
Period size: 9 Copynumber: 9.2 Consensus size: 9
87855023 TATGTAAGTT
*
87855033 GTTATGTAC
1 GTTATGTAA
*
87855042 GTTATGTGA
1 GTTATGTAA
87855051 GTTATGTAA
1 GTTATGTAA
87855060 GTTGTTATGTAA
1 ---GTTATGTAA
*
87855072 ATTATGTAA
1 GTTATGTAA
* *
87855081 GTTATATGA
1 GTTATGTAA
87855090 GTTATGTAA
1 GTTATGTAA
87855099 GTTATGTAA
1 GTTATGTAA
* *
87855108 TTTATTTAA
1 GTTATGTAA
87855117 GT
1 GT
87855119 AATGATCAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
9 53 0.85
12 9 0.15
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.48
Consensus pattern (9 bp):
GTTATGTAA
Found at i:87855961 original size:23 final size:23
Alignment explanation
Indices: 87855935--87855984 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
87855925 GTTCAAGTTT
87855935 ATTTAAAGGGCTGCAATTCATAC
1 ATTTAAAGGGCTGCAATTCATAC
87855958 ATTTAAAGGGCTGCAATTCATAC
1 ATTTAAAGGGCTGCAATTCATAC
87855981 ATTT
1 ATTT
87855985 GATTAATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
ATTTAAAGGGCTGCAATTCATAC
Found at i:87859412 original size:13 final size:13
Alignment explanation
Indices: 87859394--87859427 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
87859384 TTAGGGTTAG
87859394 GGGGAAAATTTTA
1 GGGGAAAATTTTA
*
87859407 GGGGAAAGTTTTA
1 GGGGAAAATTTTA
87859420 GGGGAAAA
1 GGGGAAAA
87859428 ACACTTAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (13 bp):
GGGGAAAATTTTA
Found at i:87859970 original size:18 final size:18
Alignment explanation
Indices: 87859936--87859970 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
87859926 TTGATTTATT
*
87859936 TAATATATAATTTAAAAA
1 TAATATATAATTAAAAAA
87859954 TAATATA-AATTAAAAAA
1 TAATATATAATTAAAAAA
87859971 CAATCAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAATATATAATTAAAAAA
Found at i:87860113 original size:26 final size:27
Alignment explanation
Indices: 87860084--87860158 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 27
87860074 AAGAATTAGA
*
87860084 TAAAATTTGAAATATTGAAAATTATT-
1 TAAAATTTGAAATCTTGAAAATTATTC
*
87860110 TAAAATTTGAAATCTTGAAATTTATTC
1 TAAAATTTGAAATCTTGAAAATTATTC
*
87860137 T-AAATTTGAAATCTTTAAAATT
1 TAAAATTTGAAATCTTGAAAATT
87860159 TTAAATTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 43 0.98
27 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (27 bp):
TAAAATTTGAAATCTTGAAAATTATTC
Found at i:87860615 original size:29 final size:28
Alignment explanation
Indices: 87860549--87860638 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
87860539 TAATTAAATC
* * *
87860549 CCTT-AACCCCTAACCCATATCCCTTTAA
1 CCTTAAACCCATAACCCATA-ACCATTAA
*
87860577 CCATTAAACCCATAACCCATGACCATTAA
1 CC-TTAAACCCATAACCCATAACCATTAA
* *
87860606 TCCTTAAACCCATAATCCATAACCCTTAA
1 -CCTTAAACCCATAACCCATAACCATTAA
87860635 CCTT
1 CCTT
87860639 TACCCACTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
28 6 0.12
29 31 0.60
30 15 0.29
ACGTcount: A:0.34, C:0.38, G:0.01, T:0.27
Consensus pattern (28 bp):
CCTTAAACCCATAACCCATAACCATTAA
Found at i:87860632 original size:22 final size:22
Alignment explanation
Indices: 87860574--87860634 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
87860564 CATATCCCTT
*
87860574 TAACCATTAAACCCAT-AACCCA
1 TAACCATT-AACCCTTAAACCCA
* *
87860596 TGACCATTAATCCTTAAACCCA
1 TAACCATTAACCCTTAAACCCA
87860618 TAATCCA-TAACCCTTAA
1 TAA-CCATTAACCCTTAA
87860635 CCTTTACCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 5 0.16
22 24 0.75
23 3 0.09
ACGTcount: A:0.41, C:0.33, G:0.02, T:0.25
Consensus pattern (22 bp):
TAACCATTAACCCTTAAACCCA
Found at i:87861045 original size:28 final size:29
Alignment explanation
Indices: 87861005--87861059 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
87860995 AATAAATTGT
*
87861005 ATTTTAATCAATATAA-ATATAAATAAACC
1 ATTTAAATCAATA-AATATATAAATAAACC
*
87861034 ATTTAAAT-AATAAATATATACATAAA
1 ATTTAAATCAATAAATATATAAATAAA
87861060 ATACTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 14 0.61
29 7 0.30
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (29 bp):
ATTTAAATCAATAAATATATAAATAAACC
Found at i:87861481 original size:39 final size:39
Alignment explanation
Indices: 87861353--87861484 Score: 119
Period size: 40 Copynumber: 3.3 Consensus size: 39
87861343 TTGAGCAGTT
* *
87861353 GCGGTGTTTTTTATAAAAGCGCCGCTAATGCTCGATA-TATA
1 GCGGCGTTTTTTAGAAAA-CGCCGCTAATGCT-GA-ACTATA
* * *
87861394 GCGGCG-CTTTTAGAAAAACGCTGCTAATGTCCT-ATCTATA
1 GCGGCGTTTTTTAG-AAAACGCCGCTAATG--CTGAACTATA
*
87861434 GTGGCGTTTGTTTAG-AAACGCCGCTAATGCTGAACTATA
1 GCGGCGTTT-TTTAGAAAACGCCGCTAATGCTGAACTATA
87861473 GCGGCGTTTTTT
1 GCGGCGTTTTTT
87861485 GTTCAAACGA
Statistics
Matches: 74, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
38 5 0.07
39 14 0.19
40 38 0.51
41 10 0.14
42 7 0.09
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (39 bp):
GCGGCGTTTTTTAGAAAACGCCGCTAATGCTGAACTATA
Found at i:87870646 original size:30 final size:30
Alignment explanation
Indices: 87870603--87870696 Score: 172
Period size: 30 Copynumber: 3.2 Consensus size: 30
87870593 CAAGTAACCG
87870603 AAGCTAG-TTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
87870632 AAGCTAGTTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
*
87870662 AAGCTAGTTTAAATCGTACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
87870692 AAGCT
1 AAGCT
87870697 TCCGATTCAT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
29 7 0.11
30 56 0.89
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (30 bp):
AAGCTAGTTTAAATCGCACACTTAGTGCCA
Found at i:87872117 original size:45 final size:46
Alignment explanation
Indices: 87872053--87872161 Score: 148
Period size: 45 Copynumber: 2.3 Consensus size: 46
87872043 AGATCCTGTT
*
87872053 TGTTGGACATGGCATCGACATTGAT-CGAAAGCCAGCGTAAGACCA
1 TGTTGGACATGGCATCGACATGGATACGAAAGCCAGCGTAAGACCA
* * * *
87872098 TGTTGGACATGGCATCGACATGGATACGAGAGCTAGTGTAATACCA
1 TGTTGGACATGGCATCGACATGGATACGAAAGCCAGCGTAAGACCA
87872144 TGTCTGGGACATGGCATC
1 TGT-T-GGACATGGCATC
87872162 AGCCTCGACA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
45 24 0.43
46 19 0.34
47 1 0.02
48 12 0.21
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (46 bp):
TGTTGGACATGGCATCGACATGGATACGAAAGCCAGCGTAAGACCA
Found at i:87880172 original size:40 final size:40
Alignment explanation
Indices: 87880114--87880295 Score: 260
Period size: 40 Copynumber: 4.6 Consensus size: 40
87880104 AACCCAAGTA
* *
87880114 CCTTCGGGAATTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * * *
87880153 CCTTCAGGTCTTAGACCGGATACAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
87880193 CCTTCGGGACTTAGCCCGGATGTAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
87880233 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
87880273 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
87880296 CATCCGAATA
Statistics
Matches: 127, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 11 0.09
40 115 0.91
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:87889005 original size:31 final size:31
Alignment explanation
Indices: 87888962--87889040 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
87888952 TTTAACGGTT
*
87888962 ACTGGGCTGAAGCCTTTCCATAAATCATATC
1 ACTGGGCCGAAGCCTTTCCATAAATCATATC
*
87888993 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTCCATAAATCATATC
*
87889024 ATTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
87889041 ACTGTAAACG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTCCATAAATCATATC
Found at i:87889330 original size:26 final size:26
Alignment explanation
Indices: 87889246--87889407 Score: 242
Period size: 26 Copynumber: 6.3 Consensus size: 26
87889236 CTGGAGGCCT
87889246 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
** *
87889270 AGCCCTTTTCGGTAAACTAGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
87889295 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
87889321 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
87889347 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
87889373 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
87889399 AGCCCTTTT
1 AGCCCTTTT
87889408 GCACTTCCTC
Statistics
Matches: 125, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
23 5 0.04
24 5 0.04
25 31 0.25
26 84 0.67
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:87890241 original size:27 final size:26
Alignment explanation
Indices: 87890205--87890286 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
87890195 AGGGCATATT
* *
87890205 CGTCATTTTACCATACAGGGG-TATTA
1 CGTCACTTTACCCTACAGGGGCT-TTA
87890231 CAGTCACTTTACCCTACAGGGGCTTTA
1 C-GTCACTTTACCCTACAGGGGCTTTA
*
87890258 CGATCTCTTTACCCTACAGGGGCTTTA
1 CG-TCACTTTACCCTACAGGGGCTTTA
87890285 CG
1 CG
87890287 GTATTTTTAC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 2 0.04
27 47 0.94
28 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (26 bp):
CGTCACTTTACCCTACAGGGGCTTTA
Found at i:87890306 original size:27 final size:27
Alignment explanation
Indices: 87890237--87890297 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
87890227 ATTACAGTCA
*
87890237 CTTTACCCTACAGGGGCTTTACGATCT
1 CTTTACCCTACAGGGGCTTTACGATAT
*
87890264 CTTTACCCTACAGGGGCTTTACGGTAT
1 CTTTACCCTACAGGGGCTTTACGATAT
*
87890291 TTTTACC
1 CTTTACC
87890298 TAATAGGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (27 bp):
CTTTACCCTACAGGGGCTTTACGATAT
Found at i:87890464 original size:27 final size:27
Alignment explanation
Indices: 87890330--87890687 Score: 221
Period size: 27 Copynumber: 13.2 Consensus size: 27
87890320 TCATCCTACA
* * * * *
87890330 AGGGTGTTTTGGTAAATCTACAAACCA
1 AGGGTATTTTGGTAATTTTACAAATCT
** ** * *
87890357 AGGGTATTTCAGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTTTACAAATCT
* ** * *
87890384 ATGGTATTTTCATAATTTTTAGAAAGTCA
1 AGGGTATTTTGGTAA-TTTTACAAA-TCT
* **
87890413 AGGGTATTTCT-GTAACTTTGTAAATC-
1 AGGGTATTT-TGGTAATTTTACAAATCT
*
87890439 AGGAGTATTTTGATAATTTTACAAAT-T
1 AGG-GTATTTTGGTAATTTTACAAATCT
* *
87890466 GAGGGTATTTCGGTAATTTCACAAA-CT
1 -AGGGTATTTTGGTAATTTTACAAATCT
87890493 AGTGGTATTTTGGTAATTTTACAAA-CT
1 AG-GGTATTTTGGTAATTTTACAAATCT
87890520 AGGGGTATTTTTGGTAATTTTACAAAT-T
1 A-GGGTA-TTTTGGTAATTTTACAAATCT
* * * *
87890548 GGGGGTATTTTAGTAATTTTACAAACCA
1 -AGGGTATTTTGGTAATTTTACAAATCT
* * *
87890576 AGGGTATTTTAGCAATTTTACAGA-CT
1 AGGGTATTTTGGTAATTTTACAAATCT
** *
87890602 A-GGTATTTTGGTAATTTTACTGATCA
1 AGGGTATTTTGGTAATTTTACAAATCT
**
87890628 AGGGTATTTTGGTAATTTTGTAAA-CT
1 AGGGTATTTTGGTAATTTTACAAATCT
* ** *
87890654 GAGGGTATTTTAGTAATTTTGTAAATCG
1 -AGGGTATTTTGGTAATTTTACAAATCT
87890682 AGGGTA
1 AGGGTA
87890688 AAATAGTAAT
Statistics
Matches: 266, Mismatches: 47, Indels: 36
0.76 0.13 0.10
Matches are distributed among these distances:
25 19 0.07
26 11 0.04
27 180 0.68
28 42 0.16
29 13 0.05
30 1 0.00
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTACAAATCT
Found at i:87890542 original size:82 final size:78
Alignment explanation
Indices: 87890443--87890673 Score: 273
Period size: 82 Copynumber: 2.9 Consensus size: 78
87890433 TAAATCAGGA
* * * *
87890443 GTATTTTGATAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACTAGTGGTATTTTGGTA
1 GTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTTACAAACTAG-GGTATTTTAGTA
87890508 ATTTTACAAACTAGGG
65 ATTTTACAAACTA--G
* * * *
87890524 GTATTTTTGGTAATTTTACAAATTGGGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTAGC
1 GTA-TTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTTACAAA-CTAGGGTATTTTAGT
*
87890589 AATTTTACAGACTAG
64 AATTTTACAAACTAG
** ** **
87890604 GTATTTTGGTAATTTTACTGATCAAGGGTATTTTGGTAATTTTGTAAACTGAGGGTATTTTAGTA
1 GTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTTACAAACT-AGGGTATTTTAGTA
87890669 ATTTT
65 ATTTT
87890674 GTAAATCGAG
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
79 55 0.43
80 4 0.03
81 3 0.02
82 62 0.48
83 3 0.02
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.43
Consensus pattern (78 bp):
GTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTTACAAACTAGGGTATTTTAGTAA
TTTTACAAACTAG
Found at i:87890686 original size:54 final size:53
Alignment explanation
Indices: 87890330--87890687 Score: 244
Period size: 54 Copynumber: 6.6 Consensus size: 53
87890320 TCATCCTACA
* * * * * ** ** *
87890330 AGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACCA
1 AGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAA-CT
* * *
87890384 ATGGTATTTTCA-TAATTTTTAGAAAGTCAAGGGTATTTCT-GTAACTTTGTA-AATC-
1 AGGGTATTTT-AGTAA-TTTTACAAA-TCAAGGGTATTT-TGGTAA-TTT-TACAAACT
** * *
87890439 AGGAGTATTTT-GATAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACT
1 AGG-GTATTTTAG-TAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACT
* * *
87890493 AGTGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTTGGTAATTTTACAAATT
1 AG-GGTATTTTAGTAATTTTACAAATC-AAGGGTA-TTTTGGTAATTTTACAAACT
* * * * *
87890548 GGGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTAGCAATTTTACAGACT
1 -AGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACT
* ** **
87890602 A-GGTATTTTGGTAATTTTACTGATCAAGGGTATTTTGGTAATTTTGTAAACT
1 AGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACT
** *
87890654 GAGGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 -AGGGTATTTTAGTAATTTTACAAATCAAGGGTA
87890688 AAATAGTAAT
Statistics
Matches: 238, Mismatches: 46, Indels: 40
0.73 0.14 0.12
Matches are distributed among these distances:
52 43 0.18
53 7 0.03
54 92 0.39
55 62 0.26
56 28 0.12
57 5 0.02
58 1 0.00
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (53 bp):
AGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACT
Found at i:87890694 original size:27 final size:27
Alignment explanation
Indices: 87890665--87890795 Score: 163
Period size: 27 Copynumber: 4.9 Consensus size: 27
87890655 AGGGTATTTT
* *
87890665 AGTAATTTTGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
87890692 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
87890719 ATTAATTCTATAAATTGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
87890746 GGTAATTCTTTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
87890773 GGTAATTCTATAAATTGAGGGTA
1 AGTAATTCTGTAAATCGAGGGTA
87890796 CTTTGGTAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 91 1.00
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:87890806 original size:54 final size:54
Alignment explanation
Indices: 87890665--87890795 Score: 181
Period size: 54 Copynumber: 2.4 Consensus size: 54
87890655 AGGGTATTTT
* * * **
87890665 AGTAATTTTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTATAAATTGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
* * *
87890719 ATTAATTCTATAAATTGAGGGTAAAACGGTAATTCTTTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATTGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
*
87890773 GGTAATTCTATAAATTGAGGGTA
1 AGTAATTCTATAAATTGAGGGTA
87890796 CTTTGGTAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (54 bp):
AGTAATTCTATAAATTGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
Found at i:87893022 original size:13 final size:13
Alignment explanation
Indices: 87893004--87893029 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
87892994 TTTGGGTGTA
87893004 AAGGAAAGCTAAG
1 AAGGAAAGCTAAG
87893017 AAGGAAAGCTAAG
1 AAGGAAAGCTAAG
87893030 CCCAAGGTTT
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:0.54, C:0.08, G:0.31, T:0.08
Consensus pattern (13 bp):
AAGGAAAGCTAAG
Found at i:87896245 original size:40 final size:40
Alignment explanation
Indices: 87896171--87896471 Score: 500
Period size: 40 Copynumber: 7.6 Consensus size: 40
87896161 AACCCAAGTA
* *
87896171 CCTTCGGGAATTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
87896210 CCTTTGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
87896250 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAAT-
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
87896289 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
87896329 CCTTCGGGACTGAGCCCGGATATAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
87896369 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
87896409 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
87896449 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
87896472 CATCCGAATA
Statistics
Matches: 246, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
39 49 0.20
40 196 0.80
41 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:87898721 original size:14 final size:14
Alignment explanation
Indices: 87898702--87898728 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
87898692 CATAATCGAT
87898702 AAAATTTTCATATC
1 AAAATTTTCATATC
87898716 AAAATTTTCATAT
1 AAAATTTTCATAT
87898729 GGCATTTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTTTCATATC
Found at i:87906749 original size:46 final size:46
Alignment explanation
Indices: 87906682--87906859 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
87906672 TGTAACCCGC
*
87906682 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
* * * *
87906728 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG-TTCGCAT
* *** * * **
87906774 ACATCTCTCGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
* *
87906821 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG
87906860 CCCAAACATC
Statistics
Matches: 104, Mismatches: 25, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
46 71 0.68
47 33 0.32
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
Found at i:87906802 original size:93 final size:93
Alignment explanation
Indices: 87906690--87906861 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
87906680 GCCCATAAGT
* ***
87906690 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
87906755 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
87906783 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
* *
87906848 TGAGTTCGGATGCC
66 CGAGCTCGGATGCC
87906862 CAAACATCCT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Done.