Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 53 of 344
Found at i:17499045 original size:37 final size:36
Alignment explanation
Indices: 17499003--17499170 Score: 133
Period size: 37 Copynumber: 4.6 Consensus size: 36
17498993 TATGATGAGG
* *
17499003 GTTGAAGCAAGAAGGAAGAAAGTATGGAGCTTAAAAA
1 GTTGAAGCAAGAGGGAAGAAAGTA-GGAGCTTGAAAA
* * * *
17499040 GTTGAAAG-AATTA-GGAATAAACTAGGAAGCTCGAAAA
1 GTTG-AAGCAA-GAGGGAAGAAAGTAGG-AGCTTGAAAA
* * * **
17499077 GTTGAAGGAATAGGGAAGAAAGTCAGCAGCTTGAAGG
1 GTTGAAGCAAGAGGGAAGAAAGT-AGGAGCTTGAAAA
* ** *
17499114 GTTGAAGGAAGAGGGAAGAAAGTAGGGAATTTGAAGA
1 GTTGAAGCAAGAGGGAAGAAAGTA-GGAGCTTGAAAA
17499151 GTTGAAGCAAGAGGGAAGAA
1 GTTGAAGCAAGAGGGAAGAA
17499171 CATAGGGATC
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
36 8 0.07
37 93 0.87
38 6 0.06
ACGTcount: A:0.45, C:0.05, G:0.34, T:0.16
Consensus pattern (36 bp):
GTTGAAGCAAGAGGGAAGAAAGTAGGAGCTTGAAAA
Found at i:17499192 original size:37 final size:34
Alignment explanation
Indices: 17499107--17499215 Score: 94
Period size: 37 Copynumber: 3.0 Consensus size: 34
17499097 AGTCAGCAGC
*
17499107 TTGAAGGGTTGAAGGAAGAGGGAAGAAAGTAGGGAAT
1 TTGAA-GGTTGAAGCAAGAGGGAAGAAA-TAGGG-AT
17499144 TTGAAGAGTTGAAGCAAGAGGGAAGAACATAGGGAT
1 TTGAAG-GTTGAAGCAAGAGGGAAGAA-ATAGGGAT
* **
17499180 CTTTAATGGTTGAATTAA-ATGGGAAGAAAATAGGGA
1 -TTGAA-GGTTGAAGCAAGA-GGGAAG-AAATAGGGA
17499216 GCTTCAAGGG
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
36 4 0.06
37 54 0.87
38 4 0.06
ACGTcount: A:0.41, C:0.03, G:0.36, T:0.20
Consensus pattern (34 bp):
TTGAAGGTTGAAGCAAGAGGGAAGAAATAGGGAT
Found at i:17500393 original size:37 final size:36
Alignment explanation
Indices: 17500349--17500696 Score: 283
Period size: 37 Copynumber: 9.4 Consensus size: 36
17500339 ATGGGATGAT
*
17500349 AAGGGTTGAAGGAAGAGGTAAAAAAGTAGGGACCTTG
1 AAGGGTTGAAGGAAGAGG-AAAAAAGTAGGGAGCTTG
* * * * * *
17500386 AAAGGTTGAAGGAACCGA-GAATAAATTAGGAAGATCG
1 AAGGGTTGAAGGAA--GAGGAAAAAAGTAGGGAGCTTG
* *
17500423 AAGGGTTGAAGGAAGTAGGAAGAAAGTAGGGAGTTTG
1 AAGGGTTGAAGGAAG-AGGAAAAAAGTAGGGAGCTTG
* * * * *
17500460 AAGGGTTGAAGCAAGAGGGAAGAATGTAGGGATCTTC
1 AAGGGTTGAAGGAAGA-GGAAAAAAGTAGGGAGCTTG
* * * *
17500497 AAGGGTTGAATGAATTG-GGAAGAAAGTAGAGAGCTTC
1 AAGGGTTGAAGGAA--GAGGAAAAAAGTAGGGAGCTTG
* * * **
17500534 AAGGATTGAAGGAAAATGAAAGATTGTAGGGAGCTTG
1 AAGGGTTGAAGGAAGAGGAAA-AAAGTAGGGAGCTTG
* *
17500571 AAGGGTTGAAGGAAAAGGAAAGATTA-TAGGGAGCTTG
1 AAGGGTTGAAGGAAGAGGAAA-A-AAGTAGGGAGCTTG
*
17500608 AAGTGTTGAAGGAATTGA-GAAGAAAA-TAGGGAGCTTG
1 AAGGGTTGAAGGAA--GAGGAA-AAAAGTAGGGAGCTTG
*
17500645 AAGGGTTGAAGGAAGAGGGAAAAACGTAGGGAGCTTG
1 AAGGGTTGAAGGAAGA-GGAAAAAAGTAGGGAGCTTG
*
17500682 AAGGGCTGAAGGAAG
1 AAGGGTTGAAGGAAG
17500697 GCGTGCGATT
Statistics
Matches: 254, Mismatches: 41, Indels: 32
0.78 0.13 0.10
Matches are distributed among these distances:
35 3 0.01
36 8 0.03
37 232 0.91
38 6 0.02
39 5 0.02
ACGTcount: A:0.40, C:0.05, G:0.38, T:0.18
Consensus pattern (36 bp):
AAGGGTTGAAGGAAGAGGAAAAAAGTAGGGAGCTTG
Found at i:17500693 original size:111 final size:108
Alignment explanation
Indices: 17500349--17500695 Score: 338
Period size: 111 Copynumber: 3.1 Consensus size: 108
17500339 ATGGGATGAT
* ** * *
17500349 AAGGGTTGAAGGAAGAGGTAAA-AA-AGTAGGGACCTTGAAAGGTTGAAGGAACCGAGAATAAAT
1 AAGGGTTGAAGGAAAAGG-AAAGAATA-TAGGGACCTTG-AAGGTTGAAGGAATTGAGAAGAAAA
* * * *
17500412 TAGGAAGATCGAAGGGTTGAAGGAAGTAGGAAGAAAGTAGGGAGTTTG
63 TAGGGAGCTTGAAGGGTTGAAGGAAG-AGGAA-AAAGTAGGGAGCTTG
* * * * * * * * *
17500460 AAGGGTTGAAGCAAGAGGGAAGAATGTAGGGATCTTCAAGGGTTGAATGAATTGGGAAGAAAGTA
1 AAGGGTTGAAGGAAAAGGAAAGAATATAGGGACCTTGAA-GGTTGAAGGAATTGAGAAGAAAATA
* * * * * *
17500525 GAGAGCTTCAAGGATTGAAGGAAAATGAAAGATTGTAGGGAGCTTG
65 GGGAGCTTGAAGGGTTGAAGGAAGAGGAAA-A-AGTAGGGAGCTTG
* *
17500571 AAGGGTTGAAGGAAAAGGAAAGATTATAGGGAGCTTGAAGTGTTGAAGGAATTGAGAAGAAAATA
1 AAGGGTTGAAGGAAAAGGAAAGAATATAGGGACCTTGAAG-GTTGAAGGAATTGAGAAGAAAATA
17500636 GGGAGCTTGAAGGGTTGAAGGAAGAGGGAAAAACGTAGGGAGCTTG
65 GGGAGCTTGAAGGGTTGAAGGAAGA-GGAAAAA-GTAGGGAGCTTG
*
17500682 AAGGGCTGAAGGAA
1 AAGGGTTGAAGGAA
17500696 GGCGTGCGAT
Statistics
Matches: 190, Mismatches: 38, Indels: 16
0.78 0.16 0.07
Matches are distributed among these distances:
109 1 0.01
110 10 0.05
111 175 0.92
112 4 0.02
ACGTcount: A:0.40, C:0.05, G:0.37, T:0.18
Consensus pattern (108 bp):
AAGGGTTGAAGGAAAAGGAAAGAATATAGGGACCTTGAAGGTTGAAGGAATTGAGAAGAAAATAG
GGAGCTTGAAGGGTTGAAGGAAGAGGAAAAAGTAGGGAGCTTG
Found at i:17501773 original size:37 final size:37
Alignment explanation
Indices: 17501720--17501986 Score: 180
Period size: 37 Copynumber: 7.2 Consensus size: 37
17501710 GATGATGAGC
* * **
17501720 GTTGAAGGAAAAGGGAAGAAAATAGGAAGATTGAAAA
1 GTTGAAGGAATAGGGAAGAAAATAGGAAGCTTGAAGG
* * * * *
17501757 GTTGAAGGAATCGGGAATAAACTAAGAAGCTCGAAGG
1 GTTGAAGGAATAGGGAAGAAAATAGGAAGCTTGAAGG
* * * * *
17501794 GTTGATGGAGTTGGGAAGAAAGTAGAAAGCTTGAAGG
1 GTTGAAGGAATAGGGAAGAAAATAGGAAGCTTGAAGG
* * *
17501831 GTTGAAGGAAGAGGGAAGAAAGTA-GAGAGTTTGAAGG
1 GTTGAAGGAATAGGGAAGAAAATAGGA-AGCTTGAAGG
* * * * * * * *
17501868 GTTGAAGCAAGAGGAAAGAACATAGGGATCTTAAAGA
1 GTTGAAGGAATAGGGAAGAAAATAGGAAGCTTGAAGG
* * * *
17501905 GTTGAATGAATTGGAAAGAAAGTATGG-AGCTTGAAGG
1 GTTGAAGGAATAGGGAAGAAAATA-GGAAGCTTGAAGG
*** * *
17501942 GTTGAAGGAATTTAGAAGAAAGTAAGG-AGTTTGAAGG
1 GTTGAAGGAATAGGGAAGAAAAT-AGGAAGCTTGAAGG
17501979 GTTGAAGG
1 GTTGAAGG
17501987 GTTGAAGAAA
Statistics
Matches: 180, Mismatches: 46, Indels: 8
0.77 0.20 0.03
Matches are distributed among these distances:
36 1 0.01
37 175 0.97
38 4 0.02
ACGTcount: A:0.42, C:0.03, G:0.36, T:0.19
Consensus pattern (37 bp):
GTTGAAGGAATAGGGAAGAAAATAGGAAGCTTGAAGG
Found at i:17512475 original size:24 final size:24
Alignment explanation
Indices: 17512443--17512533 Score: 146
Period size: 24 Copynumber: 3.8 Consensus size: 24
17512433 CAAGCCCATT
*
17512443 TTCACAACTCGTGTGAGCATTATA
1 TTCACAACTCATGTGAGCATTATA
17512467 TTCACAACTCATGTGAGCATTATA
1 TTCACAACTCATGTGAGCATTATA
*
17512491 TTCACAGCTCATGTGAGCATTATA
1 TTCACAACTCATGTGAGCATTATA
* *
17512515 TTCACATCTCGTGTGAGCA
1 TTCACAACTCATGTGAGCA
17512534 CTTCTATCCC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (24 bp):
TTCACAACTCATGTGAGCATTATA
Found at i:17513390 original size:24 final size:24
Alignment explanation
Indices: 17513362--17513412 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
17513352 CATACATTAC
17513362 TAAACCTTATCTACATGCCACTTA
1 TAAACCTTATCTACATGCCACTTA
17513386 TAAACCTTATCTACATGCCACTTA
1 TAAACCTTATCTACATGCCACTTA
17513410 TAA
1 TAA
17513413 CTGAGCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.33
Consensus pattern (24 bp):
TAAACCTTATCTACATGCCACTTA
Found at i:17513848 original size:13 final size:13
Alignment explanation
Indices: 17513825--17513932 Score: 71
Period size: 13 Copynumber: 8.1 Consensus size: 13
17513815 TTCATGATCT
17513825 ATTTCCATATAACC
1 ATTT-CATATAACC
17513839 GA-TTCATATAACC
1 -ATTTCATATAACC
* *
17513852 ATTTCATATATCT
1 ATTTCATATAACC
17513865 ATTTCCATATAA--
1 ATTT-CATATAACC
17513877 ATGATTCATATAACC
1 AT--TTCATATAACC
** *
17513892 ATTTCATATGTCT
1 ATTTCATATAACC
*
17513905 ATTTCCATATAATC
1 ATTT-CATATAACC
17513919 -TATTCATATAACC
1 AT-TTCATATAACC
17513932 A
1 A
17513933 AGATATATTC
Statistics
Matches: 73, Mismatches: 11, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
12 3 0.04
13 50 0.68
14 17 0.23
15 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTCATATAACC
Found at i:17513869 original size:40 final size:40
Alignment explanation
Indices: 17513811--17513932 Score: 183
Period size: 40 Copynumber: 3.1 Consensus size: 40
17513801 ATCCAATATT
* *
17513811 CCATTTCAT-GATCTATTTCCATATAACCGATTCATATAA
1 CCATTTCATATATCTATTTCCATATAAACGATTCATATAA
*
17513850 CCATTTCATATATCTATTTCCATATAAATGATTCATATAA
1 CCATTTCATATATCTATTTCCATATAAACGATTCATATAA
* * *
17513890 CCATTTCATATGTCTATTTCCATATAATCTATTCATATAA
1 CCATTTCATATATCTATTTCCATATAAACGATTCATATAA
17513930 CCA
1 CCA
17513933 AGATATATTC
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
39 9 0.12
40 66 0.88
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.41
Consensus pattern (40 bp):
CCATTTCATATATCTATTTCCATATAAACGATTCATATAA
Found at i:17514428 original size:21 final size:21
Alignment explanation
Indices: 17514373--17514415 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
17514363 TTCCATGCTT
17514373 AAATTTACCTTTCAAACCATA
1 AAATTTACCTTTCAAACCATA
17514394 AAATTTACCTTTCAAACCATA
1 AAATTTACCTTTCAAACCATA
17514415 A
1 A
17514416 TTTTTCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATTTACCTTTCAAACCATA
Found at i:17519065 original size:22 final size:21
Alignment explanation
Indices: 17519035--17519093 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
17519025 ATGAATTCAC
17519035 AAATATAGGAGCACATAAATGCT
1 AAAT-TAGGAGCACA-AAATGCT
* *
17519058 AAATTAGGAGAACCAAAGTGCT
1 AAATTAGGAGCA-CAAAATGCT
*
17519080 AAATTCTGGAGCAC
1 AAATT-AGGAGCAC
17519094 CAAAGTGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.20
Consensus pattern (21 bp):
AAATTAGGAGCACAAAATGCT
Found at i:17519095 original size:23 final size:23
Alignment explanation
Indices: 17519054--17519131 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
17519044 AGCACATAAA
* *
17519054 TGCTAAATT-AGGAGAACCAAAG
1 TGCTAAATTCTGGAGCACCAAAG
17519076 TGCTAAATTCTGGAGCACCAAAG
1 TGCTAAATTCTGGAGCACCAAAG
* * * * *
17519099 TG-TTAGTTTTAGGAACACCGAAG
1 TGCTAAATTCT-GGAGCACCAAAG
17519122 TGCTAAATTC
1 TGCTAAATTC
17519132 ACGAGCACGC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 14 0.33
23 25 0.58
24 4 0.09
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (23 bp):
TGCTAAATTCTGGAGCACCAAAG
Found at i:17519555 original size:32 final size:32
Alignment explanation
Indices: 17519519--17519585 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
17519509 CTTATTTTCC
*
17519519 CTTATCTAGACCCCTTCTATCTTCTTCCTTCT
1 CTTATCTACACCCCTTCTATCTTCTTCCTTCT
*
17519551 CTTATCTACACCCCTTCTGTCTTCTTCCTTCT
1 CTTATCTACACCCCTTCTATCTTCTTCCTTCT
17519583 CTT
1 CTT
17519586 TCTCTTCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.10, C:0.39, G:0.03, T:0.48
Consensus pattern (32 bp):
CTTATCTACACCCCTTCTATCTTCTTCCTTCT
Found at i:17520695 original size:8 final size:8
Alignment explanation
Indices: 17520616--17520699 Score: 55
Period size: 8 Copynumber: 10.0 Consensus size: 8
17520606 TTAAATTTAT
*
17520616 TAAAAATT
1 TAAAAATA
17520624 TAAAAA-A
1 TAAAAATA
17520631 TAAAAATA
1 TAAAAATA
*
17520639 -AAAAAAA
1 TAAAAATA
*
17520646 TGAAAACTTAA
1 T-AAAA-AT-A
17520657 TAAGAAATA
1 TAA-AAATA
*
17520666 TTAAAATTA
1 -TAAAAATA
*
17520675 TATAAATTA
1 TA-AAAATA
17520684 TAAAAATA
1 TAAAAATA
17520692 TAAAAATA
1 TAAAAATA
17520700 CATTTTTCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
7 12 0.20
8 22 0.36
9 17 0.28
10 6 0.10
11 4 0.07
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.27
Consensus pattern (8 bp):
TAAAAATA
Found at i:17521408 original size:12 final size:12
Alignment explanation
Indices: 17521391--17521415 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17521381 AACATGTTAA
17521391 AATATAATTATT
1 AATATAATTATT
17521403 AATATAATTATT
1 AATATAATTATT
17521415 A
1 A
17521416 TTTAGTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATATAATTATT
Found at i:17521628 original size:35 final size:35
Alignment explanation
Indices: 17521560--17521630 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
17521550 AAAAATGTAC
**
17521560 CTTAAATTTTATTTAAACTCATTTTTCGGATTTTA
1 CTTAAATTTTATTTAAACTCATTTTTCAAATTTTA
*
17521595 CTTAAATTTTATTTAAACTCATTTTTTAAATTTTA
1 CTTAAATTTTATTTAAACTCATTTTTCAAATTTTA
17521630 C
1 C
17521631 ATTTTGTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.55
Consensus pattern (35 bp):
CTTAAATTTTATTTAAACTCATTTTTCAAATTTTA
Found at i:17521803 original size:21 final size:21
Alignment explanation
Indices: 17521778--17521818 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17521768 GTAAAATAAA
17521778 AAGAAATAATCATA-ATTTTTT
1 AAGAAA-AATCATATATTTTTT
*
17521799 AAGAAAAATTATATATTTTT
1 AAGAAAAATCATATATTTTT
17521819 ATAAATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
AAGAAAAATCATATATTTTTT
Found at i:17521866 original size:25 final size:26
Alignment explanation
Indices: 17521807--17521866 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
17521797 TTAAGAAAAA
17521807 TTATATATTTTTATAAATTTTCCTTTT
1 TTATAT-TTTTTATAAATTTTCCTTTT
* *
17521834 TGAT-TTTTTTGTAAA-TTT-CTATTT
1 TTATATTTTTTATAAATTTTCCT-TTT
17521858 TTATATTTT
1 TTATATTTT
17521867 AAATTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
23 2 0.07
24 9 0.32
25 13 0.46
26 1 0.04
27 3 0.11
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.68
Consensus pattern (26 bp):
TTATATTTTTTATAAATTTTCCTTTT
Found at i:17535960 original size:15 final size:15
Alignment explanation
Indices: 17535926--17535982 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
17535916 TTTTAAGGTT
*
17535926 AGAGAAAAAGAAAAA
1 AGAGGAAAAGAAAAA
*
17535941 AGA--AAAA-AAAGA
1 AGAGGAAAAGAAAAA
17535953 AGAGGAAAAGAAAAA
1 AGAGGAAAAGAAAAA
* *
17535968 GGAGGAAAGGAAAAA
1 AGAGGAAAAGAAAAA
17535983 TGGAGATGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 7 0.20
13 4 0.11
14 4 0.11
15 20 0.57
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
AGAGGAAAAGAAAAA
Found at i:17535982 original size:16 final size:15
Alignment explanation
Indices: 17535954--17535987 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
17535944 AAAAAAAGAA
17535954 GAGGAAAAGAAAAAG
1 GAGGAAAAGAAAAAG
*
17535969 GAGGAAAGGAAAAATG
1 GAGGAAAAGAAAAA-G
17535985 GAG
1 GAG
17535988 ATGCCTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (15 bp):
GAGGAAAAGAAAAAG
Found at i:17536381 original size:36 final size:36
Alignment explanation
Indices: 17536341--17536416 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
17536331 AATATTGTTG
*
17536341 CTGGTATATTGTTGCTTATGTTGTTATACATGGCTA
1 CTGGTATATTATTGCTTATGTTGTTATACATGGCTA
17536377 CTGGTATATTATTGCTTATGTTGTTATACATGGCTA
1 CTGGTATATTATTGCTTATGTTGTTATACATGGCTA
17536413 CTGG
1 CTGG
17536417 CATACATGGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.46
Consensus pattern (36 bp):
CTGGTATATTATTGCTTATGTTGTTATACATGGCTA
Found at i:17537161 original size:21 final size:21
Alignment explanation
Indices: 17537120--17537161 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17537110 ATCTTTTTGG
*
17537120 TGAGTTAGGGCAGCTTACTGA
1 TGAGTTAGGGCAGCCTACTGA
* *
17537141 TGAGTTGGGGCAGCCTGCTGA
1 TGAGTTAGGGCAGCCTACTGA
17537162 GTTAGGGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.38, T:0.26
Consensus pattern (21 bp):
TGAGTTAGGGCAGCCTACTGA
Found at i:17538041 original size:25 final size:26
Alignment explanation
Indices: 17538007--17538067 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
17537997 GCATGCATAT
*
17538007 TATTAAAAAATACTCACT-GCATGTA
1 TATTAAAAAATACTCAATAGCATGTA
*
17538032 TATTAAAAAATAGTCAATAGCATGTA
1 TATTAAAAAATACTCAATAGCATGTA
17538058 TATTAAAAAA
1 TATTAAAAAA
17538068 AAAGCCATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
25 16 0.48
26 17 0.52
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (26 bp):
TATTAAAAAATACTCAATAGCATGTA
Found at i:17538054 original size:26 final size:25
Alignment explanation
Indices: 17537999--17538067 Score: 95
Period size: 26 Copynumber: 2.8 Consensus size: 25
17537989 CAATCATTGC
*
17537999 ATGCATAT-TATTAAAAAATACTCA
1 ATGCATGTATATTAAAAAATACTCA
* *
17538023 CTGCATGTATATTAAAAAATAGTCA
1 ATGCATGTATATTAAAAAATACTCA
17538048 ATAGCATGTATATTAAAAAA
1 AT-GCATGTATATTAAAAAA
17538068 AAAGCCATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.15
25 16 0.41
26 17 0.44
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (25 bp):
ATGCATGTATATTAAAAAATACTCA
Found at i:17538103 original size:96 final size:95
Alignment explanation
Indices: 17537895--17538191 Score: 459
Period size: 96 Copynumber: 3.1 Consensus size: 95
17537885 TAAAAAGCAG
* *
17537895 TCACTACATGCATATTATTAAAAAAAATACTTACTGCATGCATATTAAAAAATAGTCAACAACAT
1 TCACTACATGCATATTATT--AAAAAATACTCACTGCATGCATATTAAAAAATAGTCAATAACAT
**
17537960 GTATATTAAAAAACAGTCATACACACTGACAA
64 GTATATTAAAAAACAGTCATACACACCAACAA
* * * *
17537992 TCATTGCATGCATATTATTAAAAAATACTCACTGCATGTATATTAAAAAATAGTCAATAGCATGT
1 TCACTACATGCATATTATTAAAAAATACTCACTGCATGCATATTAAAAAATAGTCAATAACATGT
* *
17538057 ATATTAAAAAAAAAGCCATACACACCAACAA
66 ATATT-AAAAAACAGTCATACACACCAACAA
*
17538088 TCACTACATGTATATTATTAAAAAATACTCACTGCATGCATATTAAAAAATAGTCAATAACATGT
1 TCACTACATGCATATTATTAAAAAATACTCACTGCATGCATATTAAAAAATAGTCAATAACATGT
17538153 ATATTAAAAAACAGTCATACACACCAACAA
66 ATATTAAAAAACAGTCATACACACCAACAA
*
17538183 TCAATACAT
1 TCACTACAT
17538192 ATTAAAAAAA
Statistics
Matches: 181, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
95 78 0.43
96 86 0.48
97 17 0.09
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (95 bp):
TCACTACATGCATATTATTAAAAAATACTCACTGCATGCATATTAAAAAATAGTCAATAACATGT
ATATTAAAAAACAGTCATACACACCAACAA
Found at i:17538137 original size:25 final size:26
Alignment explanation
Indices: 17538103--17538163 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
17538093 ACATGTATAT
* *
17538103 TATTAAAAAATACTCACT-GCATGCA
1 TATTAAAAAATACTCAATAACATGCA
* *
17538128 TATTAAAAAATAGTCAATAACATGTA
1 TATTAAAAAATACTCAATAACATGCA
17538154 TATTAAAAAA
1 TATTAAAAAA
17538164 CAGTCATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 16 0.52
26 15 0.48
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (26 bp):
TATTAAAAAATACTCAATAACATGCA
Found at i:17538151 original size:26 final size:25
Alignment explanation
Indices: 17538103--17538173 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
17538093 ACATGTATAT
* * *
17538103 TATTAAAAAATACTCACTGCATGCA
1 TATTAAAAAATAGTCAATACATGCA
*
17538128 TATTAAAAAATAGTCAATAACATGTA
1 TATTAAAAAATAGTCAAT-ACATGCA
*
17538154 TATTAAAAAACAGTC-ATACA
1 TATTAAAAAATAGTCAATACA
17538174 CACCAACAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
24 3 0.08
25 18 0.45
26 19 0.47
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (25 bp):
TATTAAAAAATAGTCAATACATGCA
Found at i:17543069 original size:15 final size:15
Alignment explanation
Indices: 17543051--17543080 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17543041 CTTTCAGCTG
17543051 CATCACTACCAGACA
1 CATCACTACCAGACA
17543066 CATCACTACCAGACA
1 CATCACTACCAGACA
17543081 TTTCTTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.40, G:0.07, T:0.13
Consensus pattern (15 bp):
CATCACTACCAGACA
Found at i:17543261 original size:61 final size:61
Alignment explanation
Indices: 17543183--17543319 Score: 195
Period size: 62 Copynumber: 2.2 Consensus size: 61
17543173 GCATTTTTGT
* * *
17543183 CAGATAATAACCGATAC-AAAATAATTTAATACAAACGCAACCATTTCTGTTATGCACATGA
1 CAGA-AATAACCAATACAAAAATAATTTAATACAAACACAACCATTTCTGTCATGCACATGA
* *
17543244 CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTTTGTCATGCACATGG
1 CAGA-AATAACCAATACAAAAATAATTTAATACAAACACAACCATTTCTGTCATGCACATGA
17543306 CAGGAAATAACCAA
1 CA-GAAATAACCAA
17543320 ACATTTTAAC
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
61 15 0.22
62 51 0.75
63 2 0.03
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.23
Consensus pattern (61 bp):
CAGAAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTCTGTCATGCACATGA
Found at i:17543650 original size:6 final size:6
Alignment explanation
Indices: 17543641--17543698 Score: 80
Period size: 6 Copynumber: 9.7 Consensus size: 6
17543631 ATCAGAATAG
* * **
17543641 AAATCA AAATTA AAACCA AAATCA AAATCA AAATCA AAATCA AAATTG
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
17543689 AAATCA AAAT
1 AAATCA AAAT
17543699 TGAAATCGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.66, C:0.14, G:0.02, T:0.19
Consensus pattern (6 bp):
AAATCA
Found at i:17543660 original size:12 final size:12
Alignment explanation
Indices: 17543641--17543710 Score: 86
Period size: 12 Copynumber: 5.8 Consensus size: 12
17543631 ATCAGAATAG
17543641 AAATCAAAATTA
1 AAATCAAAATTA
* *
17543653 AAACCAAAATCA
1 AAATCAAAATTA
*
17543665 AAATCAAAATCA
1 AAATCAAAATTA
*
17543677 AAATCAAAATTG
1 AAATCAAAATTA
*
17543689 AAATCAAAATTG
1 AAATCAAAATTA
*
17543701 AAATCGAAAT
1 AAATCAAAAT
17543711 AACCCAAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 52 1.00
ACGTcount: A:0.63, C:0.13, G:0.04, T:0.20
Consensus pattern (12 bp):
AAATCAAAATTA
Found at i:17543662 original size:18 final size:18
Alignment explanation
Indices: 17543641--17543698 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
17543631 ATCAGAATAG
*
17543641 AAATCAAAATTAAAACCA
1 AAATCAAAATTAAAATCA
*
17543659 AAATCAAAATCAAAATCA
1 AAATCAAAATTAAAATCA
*
17543677 AAATCAAAATTGAAATCA
1 AAATCAAAATTAAAATCA
17543695 AAAT
1 AAAT
17543699 TGAAATCGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.66, C:0.14, G:0.02, T:0.19
Consensus pattern (18 bp):
AAATCAAAATTAAAATCA
Found at i:17543704 original size:18 final size:18
Alignment explanation
Indices: 17543641--17543710 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
17543631 ATCAGAATAG
** *
17543641 AAATCAAAATTAAAACCA
1 AAATCAAAATCGAAATCA
*
17543659 AAATCAAAATCAAAATCA
1 AAATCAAAATCGAAATCA
*
17543677 AAATCAAAATTGAAATCA
1 AAATCAAAATCGAAATCA
**
17543695 AAATTGAAATCGAAAT
1 AAATCAAAATCGAAAT
17543711 AACCCAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.63, C:0.13, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATCAAAATCGAAATCA
Found at i:17543734 original size:16 final size:16
Alignment explanation
Indices: 17543715--17543752 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
17543705 CGAAATAACC
17543715 CAAAATAACCCTAAAT
1 CAAAATAACCCTAAAT
17543731 CAAAATAACCCTAAAT
1 CAAAATAACCCTAAAT
17543747 CTAAAA
1 C-AAAA
17543753 AATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.58, C:0.24, G:0.00, T:0.18
Consensus pattern (16 bp):
CAAAATAACCCTAAAT
Found at i:17547322 original size:19 final size:20
Alignment explanation
Indices: 17547298--17547335 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
17547288 CTAATTGTGG
*
17547298 AATTAAAAATTAAA-AAAAT
1 AATTAAAAAATAAACAAAAT
17547317 AATTAAAAAATAAACAAAA
1 AATTAAAAAATAAACAAAA
17547336 CTCATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (20 bp):
AATTAAAAAATAAACAAAAT
Found at i:17548212 original size:39 final size:39
Alignment explanation
Indices: 17548158--17548240 Score: 166
Period size: 39 Copynumber: 2.1 Consensus size: 39
17548148 ATCTTAATTG
17548158 ATAAATTTATTAAAATAAACAAATGAAAGTTATTATAAC
1 ATAAATTTATTAAAATAAACAAATGAAAGTTATTATAAC
17548197 ATAAATTTATTAAAATAAACAAATGAAAGTTATTATAAC
1 ATAAATTTATTAAAATAAACAAATGAAAGTTATTATAAC
17548236 ATAAA
1 ATAAA
17548241 AAAGTGAGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (39 bp):
ATAAATTTATTAAAATAAACAAATGAAAGTTATTATAAC
Found at i:17548234 original size:20 final size:20
Alignment explanation
Indices: 17548172--17548234 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
17548162 ATTTATTAAA
17548172 ATAAACAAATGAAAGTTATT
1 ATAAACAAATGAAAGTTATT
*
17548192 AT-AAC--AT-AAATTTATT
1 ATAAACAAATGAAAGTTATT
17548208 AAAATAAACAAATGAAAGTTATT
1 ---ATAAACAAATGAAAGTTATT
17548231 ATAA
1 ATAA
17548235 CATAAAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
16 8 0.24
17 2 0.06
19 5 0.15
20 9 0.26
22 2 0.06
23 8 0.24
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.32
Consensus pattern (20 bp):
ATAAACAAATGAAAGTTATT
Found at i:17548703 original size:7 final size:7
Alignment explanation
Indices: 17548691--17548743 Score: 52
Period size: 7 Copynumber: 7.0 Consensus size: 7
17548681 AGACTAGAAC
17548691 AATAATA
1 AATAATA
17548698 AATAATA
1 AATAATA
17548705 AATAATA
1 AATAATA
17548712 AATATATTA
1 AATA-A-TA
*
17548721 AATTATTA
1 AA-TAATA
*
17548729 AATATTAA
1 AATAAT-A
17548737 AATAATA
1 AATAATA
17548744 TATATTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 23 0.57
8 11 0.28
9 4 0.10
10 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AATAATA
Found at i:17548752 original size:16 final size:16
Alignment explanation
Indices: 17548691--17548759 Score: 65
Period size: 15 Copynumber: 4.5 Consensus size: 16
17548681 AGACTAGAAC
*
17548691 AATAATAAATA-AT-A
1 AATAATAAATATTTAA
17548705 AATAATAAATATATTAA
1 AATAATAAATAT-TTAA
* *
17548722 ATTATTAAATA-TTAA
1 AATAATAAATATTTAA
*
17548737 AATAATATATATTTAA
1 AATAATAAATATTTAA
17548753 AA-AATAA
1 AATAATAA
17548760 TATGAACAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
14 11 0.25
15 16 0.36
16 7 0.16
17 10 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAATAAATATTTAA
Found at i:17567278 original size:16 final size:16
Alignment explanation
Indices: 17567259--17567289 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17567249 CTTCTTCACT
17567259 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
17567275 TACTTACTTACTTAA
1 TACTCACTTACTTAA
17567290 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:17567295 original size:20 final size:20
Alignment explanation
Indices: 17567256--17567295 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17567246 AAACTTCTTC
* *
17567256 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
17567276 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
17567296 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:17567610 original size:53 final size:54
Alignment explanation
Indices: 17567481--17567732 Score: 275
Period size: 55 Copynumber: 4.7 Consensus size: 54
17567471 ACACATGTAC
* * * * *
17567481 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTA----T-CCTTTTGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCTTTGCCTTATGAAA
* * *
17567530 CTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCTTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCTTTGCCTTATGAAA
* * * * *
17567583 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCTTTGCCTTAT-GAAA
* * *
17567638 CTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCTTTGCCTTATGAAA
*
17567691 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATC
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATC
17567733 CTTAAACCCT
Statistics
Matches: 171, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
49 34 0.20
53 49 0.29
54 14 0.08
55 74 0.43
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.35
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCTTTGCCTTATGAAA
Found at i:17567672 original size:108 final size:110
Alignment explanation
Indices: 17567528--17567728 Score: 327
Period size: 108 Copynumber: 1.8 Consensus size: 110
17567518 ATCCTTTTGA
* *
17567528 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCTTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTA-GAAACCTCACCAA
17567591 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * *
17567636 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTCACCAAT
17567701 TGCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
17567729 TATCCTTAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 7 0.08
110 28 0.33
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:17572107 original size:24 final size:24
Alignment explanation
Indices: 17572080--17572195 Score: 124
Period size: 24 Copynumber: 4.8 Consensus size: 24
17572070 GTTCCGACCC
* *
17572080 ACAGCTCTTAAGAGCATACCGATT
1 ACAGCTCGTGAGAGCATACCGATT
*
17572104 ACAGCTCGTGAGAGCATATCGATT
1 ACAGCTCGTGAGAGCATACCGATT
* * *
17572128 ATAGCTCGTGAGAGTATACCAATT
1 ACAGCTCGTGAGAGCATACCGATT
* * *
17572152 ATAGCTTGTGAGAGCATACTGATTT
1 ACAGCTCGTGAGAGCATACCGA-TT
* *
17572177 ACAACTCGTGTGAGCATAC
1 ACAGCTCGTGAGAGCATAC
17572196 ATGTACAGGA
Statistics
Matches: 76, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
24 59 0.78
25 17 0.22
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (24 bp):
ACAGCTCGTGAGAGCATACCGATT
Found at i:17572549 original size:23 final size:23
Alignment explanation
Indices: 17572523--17572568 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
17572513 TATTATTTGC
17572523 CTAAAGAGTAAGCTATATTCTAT
1 CTAAAGAGTAAGCTATATTCTAT
17572546 CTAAAGAGTAAGCTATATTCTAT
1 CTAAAGAGTAAGCTATATTCTAT
17572569 GTTATATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
CTAAAGAGTAAGCTATATTCTAT
Found at i:17576810 original size:21 final size:22
Alignment explanation
Indices: 17576784--17576850 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 22
17576774 CATGTGGAGG
17576784 GAGGCACACGGCCGTGTGGAA-
1 GAGGCACACGGCCGTGTGGAAC
*
17576805 GAGGCACACGCCCGTGT-GAAC
1 GAGGCACACGGCCGTGTGGAAC
* *
17576826 TAGGGACACGGCCGTGT-GAAC
1 GAGGCACACGGCCGTGTGGAAC
17576847 -AGGC
1 GAGGC
17576851 CGTGTAACTC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
20 6 0.15
21 34 0.85
ACGTcount: A:0.24, C:0.27, G:0.39, T:0.10
Consensus pattern (22 bp):
GAGGCACACGGCCGTGTGGAAC
Found at i:17578591 original size:34 final size:34
Alignment explanation
Indices: 17578548--17578616 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
17578538 TTTAGAAAAC
17578548 GAACACAAAATAAATACAAAAATCTACATTTCTA
1 GAACACAAAATAAATACAAAAATCTACATTTCTA
17578582 GAACACAAAATAAATACAAAAATCTACATTTCTA
1 GAACACAAAATAAATACAAAAATCTACATTTCTA
17578616 G
1 G
17578617 TATCACAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.55, C:0.17, G:0.04, T:0.23
Consensus pattern (34 bp):
GAACACAAAATAAATACAAAAATCTACATTTCTA
Found at i:17580919 original size:18 final size:19
Alignment explanation
Indices: 17580896--17580931 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17580886 GAACATAAGG
*
17580896 AAAAGAAGCAGA-GAGAAA
1 AAAAGAAGAAGAGGAGAAA
17580914 AAAAGAAGAAGAGGAGAA
1 AAAAGAAGAAGAGGAGAA
17580932 TGTCTAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.67, C:0.03, G:0.31, T:0.00
Consensus pattern (19 bp):
AAAAGAAGAAGAGGAGAAA
Found at i:17585108 original size:2 final size:2
Alignment explanation
Indices: 17585101--17585127 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17585091 TTCAGGTTCT
17585101 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
17585128 ACATGTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:17586741 original size:24 final size:24
Alignment explanation
Indices: 17586696--17586741 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
17586686 GATCACTCAA
* *
17586696 TGTACAAAGGGCACCAGGTATTCT
1 TGTACAAAGAGCACCAGATATTCT
17586720 TGTACAAAAGAGCA-CAGATATT
1 TGTAC-AAAGAGCACCAGATATT
17586742 TGCTGCTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (24 bp):
TGTACAAAGAGCACCAGATATTCT
Found at i:17590066 original size:16 final size:15
Alignment explanation
Indices: 17590045--17590081 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
17590035 AACATCTTAC
17590045 TTTTAAATTATTTTAT
1 TTTTAAATTATTTT-T
*
17590061 TTTTAATTTATTTTT
1 TTTTAAATTATTTTT
17590076 TTTTAA
1 TTTTAA
17590082 TTAATAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTAAATTATTTTT
Found at i:17590068 original size:15 final size:14
Alignment explanation
Indices: 17590045--17590084 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
17590035 AACATCTTAC
*
17590045 TTTTAAATTATTTT
1 TTTTTAATTATTTT
17590059 ATTTTTAATTTATTTT
1 -TTTTTAA-TTATTTT
17590075 TTTTTAATTA
1 TTTTTAATTA
17590085 ATAACTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 3 0.13
15 13 0.57
16 7 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTAATTATTTT
Found at i:17590153 original size:21 final size:21
Alignment explanation
Indices: 17590129--17590172 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
17590119 TATGTAATTA
17590129 TATGATGAAAATATATTTAAT
1 TATGATGAAAATATATTTAAT
* * *
17590150 TATGTTTAAAATATTTTTAAT
1 TATGATGAAAATATATTTAAT
17590171 TA
1 TA
17590173 ATAACTCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TATGATGAAAATATATTTAAT
Found at i:17590434 original size:35 final size:32
Alignment explanation
Indices: 17590391--17590465 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 32
17590381 ATTAAATAAT
*
17590391 TATTTCAAACATCATTATTATTTTTATATGTAAAA
1 TATTTCAAACATCATTATT-TTTATATATG--AAA
**
17590426 TATTTCAAATGTCATTATTTTTATATATGAAA
1 TATTTCAAACATCATTATTTTTATATATGAAA
17590458 TATTTCAA
1 TATTTCAA
17590466 TTAATTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 11 0.30
34 9 0.24
35 17 0.46
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (32 bp):
TATTTCAAACATCATTATTTTTATATATGAAA
Found at i:17590475 original size:30 final size:32
Alignment explanation
Indices: 17590407--17590475 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
17590397 AAACATCATT
* *
17590407 ATTATTTTTATATGTAAAATATTTCAAATGTC
1 ATTATTTTTATATATAAAATATTTCAAATGTA
*
17590439 ATTATTTTTATATATGAAATATTTC-AAT-TA
1 ATTATTTTTATATATAAAATATTTCAAATGTA
17590469 ATTATTT
1 ATTATTT
17590476 CAAATACCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 8 0.24
31 3 0.09
32 23 0.68
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (32 bp):
ATTATTTTTATATATAAAATATTTCAAATGTA
Found at i:17590477 original size:45 final size:45
Alignment explanation
Indices: 17590426--17590527 Score: 150
Period size: 45 Copynumber: 2.3 Consensus size: 45
17590416 ATATGTAAAA
** * *
17590426 TATTTCAAATGTCATTATTTTTATATATGAAATATTTCAATTAAT
1 TATTTCAAATACCATTATGTTTATATATGAAATATTTCAAATAAT
* *
17590471 TATTTCAAATACCATTATGTTTATATGTTAAATATTTCAAATAAT
1 TATTTCAAATACCATTATGTTTATATATGAAATATTTCAAATAAT
17590516 TATTTCAAATAC
1 TATTTCAAATAC
17590528 ACATACAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (45 bp):
TATTTCAAATACCATTATGTTTATATATGAAATATTTCAAATAAT
Found at i:17590692 original size:109 final size:108
Alignment explanation
Indices: 17590577--17590818 Score: 262
Period size: 105 Copynumber: 2.2 Consensus size: 108
17590567 TGATATGGAT
* * * *
17590577 TGAAAAAATAAATATTTCACATATAAAAATTATATTTACTAAAAT-TAATGATATTTGAAATAAT
1 TGAAAAAATAAATATTTGACATATAAAAATTACATATA--AAAATACAATGATATTTGAAATAAT
* *
17590641 TAATTAATTTTATAATATTAGAATTTATCATACCCACAATGTAGA
64 TAATTAATTTTATAATATTAGAAATCATCATACCCACAATGTAGA
**
17590686 TGAAAAAA-ATAATATTTGA-A-AT--ATTTTACATATAAAAATAACAATGATATTTGAAATAAT
1 TGAAAAAATA-AATATTTGACATATAAAAATTACATATAAAAAT-ACAATGATATTTGAAATAAT
* * * * *
17590746 TATTTTATTTTATAATATTAGAAATCATCATACTCACCATGTAGG
64 TAATTAATTTTATAATATTAGAAATCATCATACCCACAATGTAGA
* *
17590791 TGGAGAAATTAAATATTTGACATATAAA
1 T-GAAAAAATAAATATTTGACATATAAA
17590819 TATATATAAA
Statistics
Matches: 109, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
103 5 0.05
105 65 0.60
106 14 0.13
107 4 0.04
108 4 0.04
109 16 0.15
110 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (108 bp):
TGAAAAAATAAATATTTGACATATAAAAATTACATATAAAAATACAATGATATTTGAAATAATTA
ATTAATTTTATAATATTAGAAATCATCATACCCACAATGTAGA
Found at i:17590824 original size:105 final size:106
Alignment explanation
Indices: 17590623--17590829 Score: 265
Period size: 105 Copynumber: 2.0 Consensus size: 106
17590613 TACTAAAATT
* *
17590623 AATGATATTTGAAATAATTAATTAATTTTATAATATTAGAATTTATCATACCCACAATGTAGATG
1 AATGATATTTGAAATAATTAATTAATTTTATAATATTAGAAATCATCATACCCACAATGTAGATG
**
17590688 AAAAAAATAATATTTGAAATATTTTACATATA-AAAATAAC
66 AAAAAAATAATATTTGAAATATTAAACATATATAAAATAAC
* * * * *
17590728 AATGATATTTGAAATAATTATTTTATTTTATAATATTAGAAATCATCATACTCACCATGTAGGTG
1 AATGATATTTGAAATAATTAATTAATTTTATAATATTAGAAATCATCATACCCACAATGTAGATG
* * * * *
17590793 GAGAAATTAAATATTTGACATA-TAAATATATATAAAA
66 AAAAAAAT-AATATTTGAAATATTAAACATATATAAAA
17590830 AATAGTTGAT
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
105 70 0.81
106 16 0.19
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (106 bp):
AATGATATTTGAAATAATTAATTAATTTTATAATATTAGAAATCATCATACCCACAATGTAGATG
AAAAAAATAATATTTGAAATATTAAACATATATAAAATAAC
Found at i:17590974 original size:93 final size:92
Alignment explanation
Indices: 17590869--17591043 Score: 228
Period size: 93 Copynumber: 1.9 Consensus size: 92
17590859 TATTTAACAC
* *
17590869 AATGATAAATATAAAAAATATTTTTTATTATATAATT-ATAATTATTA-ATTTATTTATATAAAT
1 AATGATAAATATAAAAAATA-TATTT-TTATATAATTAATAATTATTATA-TTATTTATATAAAG
* *
17590932 AAAGGATTTATTAATTAAAAATATTTTTAT
63 AAAAGAGTTATTAATTAAAAATATTTTTAT
* * * *
17590962 AATGATATATATAAAATATATATTTTTATATAATTACATATTTATTATATTGTTTATATAAAGAA
1 AATGATAAATATAAAAAATATATTTTTATATAATTA-ATAATTATTATATTATTTATATAAAGAA
17591027 AAGAGTTATTAATTAAA
65 AAGAGTTATTAATTAAA
17591044 GAGATGATTA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
91 10 0.14
92 4 0.06
93 56 0.79
94 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.47
Consensus pattern (92 bp):
AATGATAAATATAAAAAATATATTTTTATATAATTAATAATTATTATATTATTTATATAAAGAAA
AGAGTTATTAATTAAAAATATTTTTAT
Found at i:17591096 original size:13 final size:13
Alignment explanation
Indices: 17591078--17591102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17591068 ATAATATATT
17591078 TATTAATTAAAAA
1 TATTAATTAAAAA
17591091 TATTAATTAAAA
1 TATTAATTAAAA
17591103 TTTTTTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:17591387 original size:28 final size:29
Alignment explanation
Indices: 17591328--17591388 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
17591318 TAATCAAAAT
* * *
17591328 TTTGGCCTATATCCTTAATTTTTTCTTGAA
1 TTTGGCATATATCCTTAATTTTGTC-TAAA
*
17591358 TTTGGCATATATCGTTAATTTTGTC-AAA
1 TTTGGCATATATCCTTAATTTTGTCTAAA
17591386 TTT
1 TTT
17591389 TTATTTTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 5 0.19
30 22 0.81
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.52
Consensus pattern (29 bp):
TTTGGCATATATCCTTAATTTTGTCTAAA
Found at i:17595310 original size:5 final size:5
Alignment explanation
Indices: 17595296--17595343 Score: 62
Period size: 5 Copynumber: 9.6 Consensus size: 5
17595286 AAATAGAAAG
* *
17595296 ATTTT ATTTT GTTTT ATTTT ATTTTT ATTTT -TATT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT A-TTTT ATTTT ATTTT ATTTT ATTTT ATT
17595344 AATTTAGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 3 0.08
5 29 0.78
6 5 0.14
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:17595332 original size:20 final size:21
Alignment explanation
Indices: 17595297--17595340 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
17595287 AATAGAAAGA
*
17595297 TTTTATTTTGTTTTATTTTAT
1 TTTTATTTTGTATTATTTTAT
17595318 TTTTATTTT-TATTATTTTAT
1 TTTTATTTTGTATTATTTTAT
17595338 TTT
1 TTT
17595341 ATTAATTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (21 bp):
TTTTATTTTGTATTATTTTAT
Found at i:17595342 original size:13 final size:13
Alignment explanation
Indices: 17595307--17595349 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
17595297 TTTTATTTTG
17595307 TTTTATTTTA-T-
1 TTTTATTTTATTA
17595318 TTTTATTTTTATTA
1 TTTTA-TTTTATTA
17595332 TTTTATTTTATTA
1 TTTTATTTTATTA
*
17595345 ATTTA
1 TTTTA
17595350 GGTTAGGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 5 0.18
12 5 0.18
13 13 0.46
14 5 0.18
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:17595860 original size:12 final size:12
Alignment explanation
Indices: 17595843--17595882 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
17595833 CCACTCTAGC
17595843 CACGACCCTTGA
1 CACGACCCTTGA
* * *
17595855 CACGACTCTAGC
1 CACGACCCTTGA
17595867 CACGACCCTTGA
1 CACGACCCTTGA
17595879 CACG
1 CACG
17595883 GCATTCTGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.25, C:0.42, G:0.17, T:0.15
Consensus pattern (12 bp):
CACGACCCTTGA
Found at i:17595865 original size:24 final size:24
Alignment explanation
Indices: 17595835--17595882 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
17595825 CCCTACTACC
17595835 ACTCTAGCCACGACCCTTGACACG
1 ACTCTAGCCACGACCCTTGACACG
17595859 ACTCTAGCCACGACCCTTGACACG
1 ACTCTAGCCACGACCCTTGACACG
17595883 GCATTCTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.42, G:0.17, T:0.17
Consensus pattern (24 bp):
ACTCTAGCCACGACCCTTGACACG
Found at i:17604296 original size:16 final size:16
Alignment explanation
Indices: 17604260--17604311 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
17604250 AATAGGCCTA
* * *
17604260 TAATAGAATAGAGCTG
1 TAATGGAATAAAGTTG
17604276 TAATGGAATAAAGTTG
1 TAATGGAATAAAGTTG
*
17604292 TAATGTAATAGAA-TTG
1 TAATGGAATA-AAGTTG
17604308 TAAT
1 TAAT
17604312 CAATAATTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 29 0.94
17 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (16 bp):
TAATGGAATAAAGTTG
Found at i:17604574 original size:26 final size:25
Alignment explanation
Indices: 17604487--17604574 Score: 65
Period size: 26 Copynumber: 3.5 Consensus size: 25
17604477 ATAGGATTAT
*
17604487 TATTAAATATAATTTAAT-AAAA-AA
1 TATT-AATTTAATTTAATAAAAATAA
* * * *
17604511 -ATTAATTATATTTTAATATAATTAT
1 TATTAATT-TAATTTAATAAAAATAA
*
17604536 TATTAAATATAATTTAATAAAAATAA
1 TATT-AATTTAATTTAATAAAAATAA
17604562 TATATAATTTAAT
1 TAT-TAATTTAAT
17604575 AACATTCTTA
Statistics
Matches: 47, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
22 3 0.06
23 11 0.23
24 2 0.04
25 1 0.02
26 26 0.55
27 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTAATTTAATTTAATAAAAATAA
Found at i:17607378 original size:11 final size:11
Alignment explanation
Indices: 17607330--17607378 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
17607320 TGTTTTCTCC
17607330 TTATTTTGCTA
1 TTATTTTGCTA
** *
17607341 CCATTTTACTA
1 TTATTTTGCTA
*
17607352 TTATGTTGCTA
1 TTATTTTGCTA
*
17607363 TTATTTTGCTG
1 TTATTTTGCTA
17607374 TTATT
1 TTATT
17607379 GTTTGGATAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.18, C:0.12, G:0.10, T:0.59
Consensus pattern (11 bp):
TTATTTTGCTA
Found at i:17613981 original size:45 final size:45
Alignment explanation
Indices: 17613930--17614067 Score: 165
Period size: 45 Copynumber: 3.1 Consensus size: 45
17613920 ATGAGGAAGA
* * * *
17613930 ATTGGTGGCTTCTTCTACAACCTACATGGCAGCTTGTCTGCGAAT
1 ATTGGTGGCTTCTTCCACAACCTACATGGAAGCTTGTCTACAAAT
* *
17613975 ATTGGTGGCTTCATCCACAACCTACATGAAAGCTTGTCTACAAAT
1 ATTGGTGGCTTCTTCCACAACCTACATGGAAGCTTGTCTACAAAT
* * *
17614020 ATTGGTAG-TT-TATCCACAACTTACATGGTAGCTTGTCTACAAAT
1 ATTGGTGGCTTCT-TCCACAACCTACATGGAAGCTTGTCTACAAAT
17614064 -TTGG
1 ATTGG
17614068 AGTGTCTGGA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
43 4 0.05
44 31 0.38
45 46 0.57
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (45 bp):
ATTGGTGGCTTCTTCCACAACCTACATGGAAGCTTGTCTACAAAT
Found at i:17614061 original size:23 final size:23
Alignment explanation
Indices: 17613943--17614061 Score: 57
Period size: 23 Copynumber: 5.3 Consensus size: 23
17613933 GGTGGCTTCT
* *
17613943 TCTACAACCTACATGGCAGCTTG
1 TCTACAACATACATGGTAGCTTG
* * * * *
17613966 TCTGCGA-ATA-TTGGTGGCTTCA
1 TCTACAACATACATGGTAGCTT-G
* * **
17613988 TCCACAACCTACATGAAAGCTTG
1 TCTACAACATACATGGTAGCTTG
* * *
17614011 TCTACAA-ATA-TTGGTAGTTTA
1 TCTACAACATACATGGTAGCTTG
* *
17614032 TCCACAACTTACATGGTAGCTTG
1 TCTACAACATACATGGTAGCTTG
17614055 TCTACAA
1 TCTACAA
17614062 ATTTGGAGTG
Statistics
Matches: 62, Mismatches: 29, Indels: 10
0.61 0.29 0.10
Matches are distributed among these distances:
21 19 0.31
22 10 0.16
23 27 0.44
24 6 0.10
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (23 bp):
TCTACAACATACATGGTAGCTTG
Found at i:17616241 original size:16 final size:15
Alignment explanation
Indices: 17616216--17616245 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17616206 CAATTTGATT
17616216 AAAAAAAAGAAGAAG
1 AAAAAAAAGAAGAAG
17616231 AAAAGAAAAGAAGAA
1 AAAA-AAAAGAAGAA
17616246 TTTAAAGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAGAAG
Found at i:17616781 original size:26 final size:27
Alignment explanation
Indices: 17616747--17616800 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
17616737 ATATAAATAT
* *
17616747 TAAATATATATA-TATAAAAATAGAAA
1 TAAATATATAAATTATAAAAATAAAAA
17616773 TAAATATATAAATTATAAAAATAAAAA
1 TAAATATATAAATTATAAAAATAAAAA
17616800 T
1 T
17616801 TACATAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (27 bp):
TAAATATATAAATTATAAAAATAAAAA
Found at i:17616791 original size:7 final size:8
Alignment explanation
Indices: 17616736--17616791 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
17616726 TTATCAAATG
17616736 TATATAAA
1 TATATAAA
17616744 TAT-TAAA
1 TATATAAA
*
17616751 TATATATA
1 TATATAAA
*
17616759 TATAAAAA
1 TATATAAA
*
17616767 TAGAAATAAA
1 T--ATATAAA
17616777 TATATAAA
1 TATATAAA
17616785 T-TATAAA
1 TATATAAA
17616792 AATAAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
7 13 0.33
8 20 0.51
10 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (8 bp):
TATATAAA
Found at i:17617538 original size:22 final size:22
Alignment explanation
Indices: 17617509--17617557 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
17617499 ACAATTTTTT
*
17617509 ATTTTTTTTAA-AAATTTACAA
1 ATTTTTTTTAACAAATTTAAAA
*
17617530 ATTTTTTTTAACAATTTTAAAA
1 ATTTTTTTTAACAAATTTAAAA
17617552 ATTTTT
1 ATTTTT
17617558 AATATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTTTTTAACAAATTTAAAA
Found at i:17617649 original size:11 final size:11
Alignment explanation
Indices: 17617617--17617657 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
17617607 TATATACCGG
*
17617617 ATTTTTTGTAT
1 ATTTTTTTTAT
*
17617628 TTTTATTTTTAT
1 ATTT-TTTTTAT
17617640 ATTTTTTTTAT
1 ATTTTTTTTAT
17617651 ATTTTTT
1 ATTTTTT
17617658 CTAGATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (11 bp):
ATTTTTTTTAT
Found at i:17623040 original size:35 final size:35
Alignment explanation
Indices: 17623013--17623139 Score: 164
Period size: 35 Copynumber: 3.5 Consensus size: 35
17623003 CATGGAAAAG
*
17623013 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
17623048 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
17623083 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
**
17623123 TAAGAAATGTAGGTATG
1 TGTGAAATGTAGGTATG
17623140 ATATTTCCCA
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
35 51 0.63
38 3 0.04
40 27 0.33
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:17623132 original size:75 final size:75
Alignment explanation
Indices: 17623013--17623183 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
17623003 CATGGAAAAG
** *
17623013 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGATATT-TC
**
17623072 CCATACTGAGC
65 CCATACCAAGC
17623083 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGATATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGATATTTCC
*
17623148 CATACCAAGT
66 CATACCAAGC
**
17623158 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
17623184 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.34
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGATATTTCC
CATACCAAGC
Found at i:17623151 original size:35 final size:35
Alignment explanation
Indices: 17623016--17623181 Score: 158
Period size: 35 Copynumber: 4.6 Consensus size: 35
17623006 GGAAAAGTGT
* **
17623016 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
17623051 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
17623086 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* **
17623126 GAAATGTAGGTATGATATTTCCCATACCAAGTTGAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTT-AA
17623162 -AAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
17623182 AATGAGGAAA
Statistics
Matches: 115, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
35 82 0.71
36 2 0.02
39 2 0.02
40 29 0.25
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.34
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:17626275 original size:19 final size:18
Alignment explanation
Indices: 17626237--17626281 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
17626227 GATGATAATT
*
17626237 TTTTAATTATTTTTCTTC
1 TTTTAATTATTTTTCATC
17626255 TTCTTAATTATTTGTT-ATC
1 TT-TTAATTATTT-TTCATC
17626274 TTTTAATT
1 TTTTAATT
17626282 TAGTGATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 14 0.58
20 2 0.08
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTAATTATTTTTCATC
Found at i:17630422 original size:46 final size:46
Alignment explanation
Indices: 17630355--17630529 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
17630345 TGTAACCCGC
* *
17630355 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
17630401 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCACAT
* * * * * *
17630451 CTCA-CA---AACTCGGGCTCAACTCAACGAGTTCGGACGCTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
* *
17630494 CCATAAATGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
17630530 ATGCCCAAAT
Statistics
Matches: 108, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
42 4 0.04
43 5 0.05
44 1 0.01
46 60 0.56
47 25 0.23
48 1 0.01
49 1 0.01
50 6 0.06
51 5 0.05
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
Found at i:17630495 original size:93 final size:93
Alignment explanation
Indices: 17630364--17630534 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
17630354 CCCATAAGCG
* * * *
17630364 AACTCGGACTCAACTCAATGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACGCTCACATCCATAAATGAACTCGGACTCAACTCAAC
17630429 GAGCTCGGATGCCTAGTTACATCTCACA
66 GAGCTCGGATGCCTAGTTACATCTCACA
* * *
17630457 AACTCGGGCTCAACTCAACGAGTTCGGACGCTCGCATCCATAAATGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACGCTCACATCCATAAATGAACTCGGACTCAACTCAAC
*
17630522 GAGTTCGGATGCC
66 GAGCTCGGATGCC
17630535 CAAATATCCT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.20
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCGGACGCTCACATCCATAAATGAACTCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCACA
Found at i:17632332 original size:53 final size:53
Alignment explanation
Indices: 17632269--17632376 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
17632259 CTACTTTTTG
*
17632269 TAAGTATTTGTAGGACAAATTTATGAGATTATAATTGCACTTTCCTTGACAAT
1 TAAGTATTTGTAGGACAAATTTATGAGATTATAATTGCACTGTCCTTGACAAT
* *
17632322 TAAGTATTTGTAGGACAAATTTGTGAGATTATAATTGCACTGTCCTTGGCAAT
1 TAAGTATTTGTAGGACAAATTTATGAGATTATAATTGCACTGTCCTTGACAAT
17632375 TA
1 TA
17632377 TAATTCAAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (53 bp):
TAAGTATTTGTAGGACAAATTTATGAGATTATAATTGCACTGTCCTTGACAAT
Found at i:17632996 original size:18 final size:19
Alignment explanation
Indices: 17632961--17632995 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17632951 AAATGAAAAT
17632961 AAATATAAAAATAATTTTA
1 AAATATAAAAATAATTTTA
17632980 AAATA-AAAAAT-ATTTT
1 AAATATAAAAATAATTTT
17632996 TTTTCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 6 0.38
19 5 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATAAAAATAATTTTA
Found at i:17633505 original size:18 final size:19
Alignment explanation
Indices: 17633482--17633522 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
17633472 TTTTCTTAAG
17633482 TTTTTGAAAATTTTAT-AT
1 TTTTTGAAAATTTTATAAT
17633500 TTTTTGAAAATTTTATAAT
1 TTTTTGAAAATTTTATAAT
17633519 TTTT
1 TTTT
17633523 CATTTATCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTTTGAAAATTTTATAAT
Found at i:17633527 original size:26 final size:25
Alignment explanation
Indices: 17633490--17633541 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
17633480 AGTTTTTGAA
* *
17633490 AATTTTATATTTTTTGAAAATTTTAT
1 AATTTTATATTTATCG-AAATTTTAT
17633516 AATTTT-TCATTTATCGAAATTTTAT
1 AATTTTAT-ATTTATCGAAATTTTAT
17633541 A
1 A
17633542 CATAGGGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (25 bp):
AATTTTATATTTATCGAAATTTTAT
Found at i:17637061 original size:6 final size:7
Alignment explanation
Indices: 17637044--17637070 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
17637034 TGAGAGAAGT
17637044 TTTTTTC
1 TTTTTTC
17637051 TTTTTTC
1 TTTTTTC
17637058 TTTTTTC
1 TTTTTTC
17637065 TTTTTT
1 TTTTTT
17637071 GGGTTTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:17638962 original size:61 final size:61
Alignment explanation
Indices: 17638867--17638993 Score: 236
Period size: 61 Copynumber: 2.1 Consensus size: 61
17638857 GAATATTGAC
*
17638867 TTCAAGGGTATCAATAACCCTGAGCTAGGTATTGGTACCTAAGTGCAGGACAGACTAAAAA
1 TTCAAGGGTATCAATAACCCTGAGCTAGGTATTGGTACCTAAATGCAGGACAGACTAAAAA
*
17638928 TTCAAGGGTATCAATAACCCTGAGCTAGGTATTGGTACCTAAATGTAGGACAGACTAAAAA
1 TTCAAGGGTATCAATAACCCTGAGCTAGGTATTGGTACCTAAATGCAGGACAGACTAAAAA
17638989 TTCAA
1 TTCAA
17638994 CTCAAACACT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (61 bp):
TTCAAGGGTATCAATAACCCTGAGCTAGGTATTGGTACCTAAATGCAGGACAGACTAAAAA
Found at i:17639607 original size:23 final size:23
Alignment explanation
Indices: 17639581--17639627 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
17639571 TTACGATTCC
17639581 TATTAAGGTTTCATTTGTAGCCT
1 TATTAAGGTTTCATTTGTAGCCT
17639604 TATTAAGGTTTCATTTGTAGCCT
1 TATTAAGGTTTCATTTGTAGCCT
17639627 T
1 T
17639628 TAGTATACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (23 bp):
TATTAAGGTTTCATTTGTAGCCT
Found at i:17641067 original size:8 final size:8
Alignment explanation
Indices: 17641054--17641100 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
17641044 TATAATATTG
17641054 TTATAAAA
1 TTATAAAA
17641062 TTATAAAA
1 TTATAAAA
*
17641070 -TATATAA
1 TTATAAAA
17641077 TTAT-AAA
1 TTATAAAA
*
17641084 TTTTAAAA
1 TTATAAAA
*
17641092 TTTTAAAA
1 TTATAAAA
17641100 T
1 T
17641101 AATATATAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 11 0.32
8 23 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TTATAAAA
Found at i:17641078 original size:15 final size:15
Alignment explanation
Indices: 17641055--17641101 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
17641045 ATAATATTGT
17641055 TATAAAATTATAAAA
1 TATAAAATTATAAAA
* *
17641070 TATATAATTATAAAT
1 TATAAAATTATAAAA
* *
17641085 TTTAAAATTTTAAAA
1 TATAAAATTATAAAA
17641100 TA
1 TA
17641102 ATATATAAGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAAAATTATAAAA
Found at i:17641114 original size:21 final size:21
Alignment explanation
Indices: 17641088--17641139 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 21
17641078 TATAAATTTT
17641088 AAAATTTTAAAATAATATATA
1 AAAATTTTAAAATAATATATA
* ** *
17641109 AGAA--TTAAAATTTTTTATA
1 AAAATTTTAAAATAATATATA
17641128 AAAATTTTAAAA
1 AAAATTTTAAAA
17641140 AAAGTATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
19 15 0.62
21 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAATTTTAAAATAATATATA
Found at i:17641233 original size:23 final size:23
Alignment explanation
Indices: 17641187--17641238 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
17641177 TTTAAAAACT
** *
17641187 TTTTAGAATTTTATAATTATATA
1 TTTTAGAATTTTATAAAAAAATA
17641210 TTTTAGAATTTTATAAAAAAATA
1 TTTTAGAATTTTATAAAAAAATA
17641233 TATTTA
1 T-TTTA
17641239 AACCTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTTAGAATTTTATAAAAAAATA
Found at i:17641348 original size:16 final size:15
Alignment explanation
Indices: 17641330--17641397 Score: 50
Period size: 15 Copynumber: 4.4 Consensus size: 15
17641320 AATTATCCTT
*
17641330 TTTTTGTAAATTTTA
1 TTTTTATAAATTTTA
17641345 TTTTTATAAATTTTTTA
1 TTTTTATAAA--TTTTA
* *
17641362 TAATTTATATA-TTTA
1 T-TTTTATAAATTTTA
*
17641377 TTTTTAT-ATTTTATA
1 TTTTTATAAATTT-TA
17641392 TTTTTA
1 TTTTTA
17641398 ATGTATATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
14 7 0.17
15 22 0.52
17 6 0.14
18 7 0.17
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (15 bp):
TTTTTATAAATTTTA
Found at i:17641377 original size:8 final size:7
Alignment explanation
Indices: 17641357--17641395 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
17641347 TTTATAAATT
17641357 TTTTATA
1 TTTTATA
*
17641364 ATTTATA
1 TTTTATA
17641371 TATTTAT-
1 T-TTTATA
17641378 TTTTATA
1 TTTTATA
17641385 TTTTATA
1 TTTTATA
17641392 TTTT
1 TTTT
17641396 TAATGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 5 0.18
7 18 0.64
8 5 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTATA
Found at i:17641393 original size:19 final size:21
Alignment explanation
Indices: 17641356--17641397 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17641346 TTTTATAAAT
17641356 TTTTTATAATTTATATATTTA
1 TTTTTATAATTTATATATTTA
* *
17641377 TTTTTATATTTTATATTTTTA
1 TTTTTATAATTTATATATTTA
17641398 ATGTATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATAATTTATATATTTA
Found at i:17642321 original size:20 final size:21
Alignment explanation
Indices: 17642288--17642328 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
17642278 AAAAAAATAA
17642288 AAAGATAATTTGTA-TCATAT
1 AAAGATAATTTGTATTCATAT
17642308 AAAGA-AATTATGTATTCATAT
1 AAAGATAATT-TGTATTCATAT
17642329 GGAGATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (21 bp):
AAAGATAATTTGTATTCATAT
Found at i:17652738 original size:17 final size:18
Alignment explanation
Indices: 17652714--17652749 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
17652704 ATGTTATACA
*
17652714 TATATATATATGTTATTTT
1 TATATAT-TATGTAATTTT
17652733 TATATATTATGTAATTT
1 TATATATTATGTAATTT
17652750 ATAACACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
TATATATTATGTAATTTT
Found at i:17654444 original size:30 final size:31
Alignment explanation
Indices: 17654396--17654461 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
17654386 TTCATTTTAG
*
17654396 TCACTCAACTTTAGAAAAA-TAACAAAACAA
1 TCACTCAACTTTACAAAAAGTAACAAAACAA
* *
17654426 TCACT-AACTTTATCAAAAAGTGACAAATCAA
1 TCACTCAACTTTA-CAAAAAGTAACAAAACAA
17654457 TCACT
1 TCACT
17654462 TATTAACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 7 0.23
30 10 0.32
31 14 0.45
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (31 bp):
TCACTCAACTTTACAAAAAGTAACAAAACAA
Found at i:17655101 original size:38 final size:38
Alignment explanation
Indices: 17655050--17655196 Score: 171
Period size: 38 Copynumber: 4.0 Consensus size: 38
17655040 ACCATGTGCA
17655050 TGATGTTGTGTATGTCATGTTTATTGTTTGTATCAAAC
1 TGATGTTGTGTATGTCATGTTTATTGTTTGTATCAAAC
*
17655088 TGATGTTGTGTATGTCAAGTTTATTGTTTGTATCAAAC
1 TGATGTTGTGTATGTCATGTTTATTGTTTGTATCAAAC
* * ** ** *
17655126 TAATGTTGTGTATGTCGTGTGCATGTGCATGT-GC--A-
1 TGATGTTGTGTATGTCATGTTTAT-TGTTTGTATCAAAC
17655161 TGATGTTGTG--TGTCATGTTTATTGTTTGTATCAAAC
1 TGATGTTGTGTATGTCATGTTTATTGTTTGTATCAAAC
17655197 AATATCAAGT
Statistics
Matches: 88, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
32 5 0.06
33 10 0.11
35 10 0.11
36 1 0.01
38 57 0.65
39 5 0.06
ACGTcount: A:0.20, C:0.09, G:0.24, T:0.47
Consensus pattern (38 bp):
TGATGTTGTGTATGTCATGTTTATTGTTTGTATCAAAC
Found at i:17655105 original size:20 final size:20
Alignment explanation
Indices: 17655082--17655141 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
17655072 ATTGTTTGTA
*
17655082 TCAAACTGATGTTGTGTATG
1 TCAAACTAATGTTGTGTATG
** *
17655102 TCAAGTTTATTGTT-TGTA--
1 TCAA-ACTAATGTTGTGTATG
17655120 TCAAACTAATGTTGTGTATG
1 TCAAACTAATGTTGTGTATG
17655140 TC
1 TC
17655142 GTGTGCATGT
Statistics
Matches: 29, Mismatches: 7, Indels: 8
0.66 0.16 0.18
Matches are distributed among these distances:
17 6 0.21
18 8 0.28
20 10 0.34
21 5 0.17
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (20 bp):
TCAAACTAATGTTGTGTATG
Found at i:17655123 original size:18 final size:18
Alignment explanation
Indices: 17655068--17655123 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
17655058 TGTATGTCAT
17655068 GTTTATTGTTTGTATCAA
1 GTTTATTGTTTGTATCAA
** *
17655086 ACTGA-TGTTGTGTATGTCAA
1 GTTTATTGTT-TGTA--TCAA
17655106 GTTTATTGTTTGTATCAA
1 GTTTATTGTTTGTATCAA
17655124 ACTAATGTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
17 4 0.14
18 10 0.36
20 10 0.36
21 4 0.14
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.50
Consensus pattern (18 bp):
GTTTATTGTTTGTATCAA
Found at i:17655543 original size:15 final size:15
Alignment explanation
Indices: 17655524--17655583 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
17655514 TGTTTGATTT
17655524 TGATGTGTCTGATAG
1 TGATGTGTCTGATAG
* * * *
17655539 CGATGTGTTTGTTAA
1 TGATGTGTCTGATAG
*
17655554 TGATGTATCTGATAG
1 TGATGTGTCTGATAG
*
17655569 TGATGTGTCTAATAG
1 TGATGTGTCTGATAG
17655584 GATAATGGTT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (15 bp):
TGATGTGTCTGATAG
Found at i:17662956 original size:17 final size:17
Alignment explanation
Indices: 17662931--17662965 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17662921 AATTAAAAAT
*
17662931 ATATATTATTGTTATAA
1 ATATATTATTATTATAA
*
17662948 ATATTTTATTATTATAA
1 ATATATTATTATTATAA
17662965 A
1 A
17662966 AATGAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATATTATTATTATAA
Found at i:17662968 original size:19 final size:21
Alignment explanation
Indices: 17662924--17662968 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
17662914 AATGCTTAAT
*
17662924 TAAAAATATATATTATTGTTA
1 TAAAAATATATATTATTATTA
17662945 T--AAATAT-T-TTATTATTA
1 TAAAAATATATATTATTATTA
17662962 TAAAAAT
1 TAAAAAT
17662969 GAATTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
17 9 0.43
18 1 0.05
19 10 0.48
21 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TAAAAATATATATTATTATTA
Found at i:17665164 original size:51 final size:51
Alignment explanation
Indices: 17665088--17665209 Score: 190
Period size: 51 Copynumber: 2.4 Consensus size: 51
17665078 CGGATCACAT
* *
17665088 TTATCACTTGTCACCTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAATGTAGCTAAAGCTACCAC
* * *
17665139 TTATCACTTGTCACTTGTCACTGATCAGATAAATGTAGCTGAGGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAATGTAGCTAAAGCTACCAC
*
17665190 TTATCACTTGTCACTGATCA
1 TTATCACTTGTCACTTATCA
17665210 GAAGTACTCA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Consensus pattern (51 bp):
TTATCACTTGTCACTTATCACTGATCAGATAAATGTAGCTAAAGCTACCAC
Found at i:17674824 original size:14 final size:16
Alignment explanation
Indices: 17674784--17674827 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
17674774 TTTTCAACAT
*
17674784 AAATTAAACTTAATTCA
1 AAATTAAA-TAAATTCA
17674801 AAATTAAATAAATT-A
1 AAATTAAATAAATTCA
17674816 AAA-TAAATAAAT
1 AAATTAAATAAAT
17674828 ATAGGTTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.35
15 4 0.15
16 5 0.19
17 8 0.31
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTAAATAAATTCA
Found at i:17678778 original size:22 final size:22
Alignment explanation
Indices: 17678745--17678795 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
17678735 TCTCTCCAGG
17678745 ATGTCTTCACAAAAGAAGTAG-A
1 ATGT-TTCACAAAAGAAGTAGCA
17678767 AGTGTTTCACAAAAGAAGTAGCA
1 A-TGTTTCACAAAAGAAGTAGCA
17678790 ATGTTT
1 ATGTTT
17678796 TCATAGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (22 bp):
ATGTTTCACAAAAGAAGTAGCA
Found at i:17684353 original size:109 final size:109
Alignment explanation
Indices: 17684222--17684550 Score: 604
Period size: 109 Copynumber: 3.0 Consensus size: 109
17684212 AAAATATAAA
17684222 AATTTATATTAATATTAATTTCTAAAATTAAAATTAAATATAAAATATTTTTTTATTATTTTTAA
1 AATTTATATTAATATTAATTTCTAAAATTAAAATTAAATATAAAATATTTTTTTATTATTTTTAA
17684287 ATAGGAATGGTCTAGTCGAGCGAAACCAACTCAAAGAAATTTTT
66 ATAGGAATGGTCTAGTCGAGCGAAACCAACTCAAAGAAATTTTT
17684331 AATTTATATTAATATTAATTTCTAAAATTAAAATTAAATATAAAATATTTTTTTATTATTTTTAA
1 AATTTATATTAATATTAATTTCTAAAATTAAAATTAAATATAAAATATTTTTTTATTATTTTTAA
17684396 ATAGGAATGGTCTAGTCGAGCGAAACCAACTCAAAGAAATTTTT
66 ATAGGAATGGTCTAGTCGAGCGAAACCAACTCAAAGAAATTTTT
*
17684440 AATTTATATTAATATTAATTTCTAAAATTAAAATTAAATATAAAATGTTTTTTTAATTATTTTTA
1 AATTTATATTAATATTAATTTCTAAAATTAAAATTAAATATAAAATATTTTTTT-ATTATTTTTA
* * *
17684505 AATAGGAAATGGTCTATTCTAGCGAAACCAACTCAAAGAATTTTTT
65 AATAGG-AATGGTCTAGTCGAGCGAAACCAACTCAAAGAAATTTTT
17684551 TAAATTGGAC
Statistics
Matches: 214, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
109 162 0.76
110 16 0.07
111 36 0.17
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (109 bp):
AATTTATATTAATATTAATTTCTAAAATTAAAATTAAATATAAAATATTTTTTTATTATTTTTAA
ATAGGAATGGTCTAGTCGAGCGAAACCAACTCAAAGAAATTTTT
Found at i:17686069 original size:16 final size:15
Alignment explanation
Indices: 17686043--17686077 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
17686033 TGATGTGAAT
17686043 AATATAAAATATTAA
1 AATATAAAATATTAA
*
17686058 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
17686074 AATA
1 AATA
17686078 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:17686322 original size:29 final size:29
Alignment explanation
Indices: 17686282--17686348 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
17686272 TATAATTAAA
*
17686282 ATATATACATAAGATAACATGTAAA-ATAT
1 ATATATAAATAAGATAACAT-TAAAGATAT
* **
17686311 ATATATAAATAATATAGTATTAAAGATAT
1 ATATATAAATAAGATAACATTAAAGATAT
*
17686340 ATACATAAA
1 ATATATAAA
17686349 ATAGTATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (29 bp):
ATATATAAATAAGATAACATTAAAGATAT
Found at i:17686339 original size:25 final size:25
Alignment explanation
Indices: 17686227--17686440 Score: 105
Period size: 25 Copynumber: 8.9 Consensus size: 25
17686217 TACGTGATAA
* *
17686227 TATTAAAAATATGTACATAATATAG
1 TATTAAAGATATATACATAATATAG
* * *
17686252 T-GTAAAAAGTACATACATAATATA-
1 TATTAAAGA-TATATACATAATATAG
* *
17686276 -ATTAAA-ATATATACATAAGATAA
1 TATTAAAGATATATACATAATATAG
* * *
17686299 CATGTAAAATATATATATAAATAATATAG
1 TAT-T--AA-AGATATATACATAATATAG
*
17686328 TATTAAAGATATATACATAAAATAG
1 TATTAAAGATATATACATAATATAG
* *
17686353 TA-TAATATATATATACGTAATATAG
1 TATTAA-AGATATATACATAATATAG
* * *
17686378 AATT-TAGA-ATATACCT-A-ATA-
1 TATTAAAGATATATACATAATATAG
* *
17686398 TATTAAA-A-ATATATATAATATAA
1 TATTAAAGATATATACATAATATAG
*
17686421 TATT-AAGAAATATA-ATAATA
1 TATTAAAGATATATACATAATA
17686441 ACAAAAAAAA
Statistics
Matches: 148, Mismatches: 24, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
20 10 0.07
21 5 0.03
22 19 0.13
23 19 0.13
24 22 0.15
25 50 0.34
26 3 0.02
27 2 0.01
28 2 0.01
29 16 0.11
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (25 bp):
TATTAAAGATATATACATAATATAG
Found at i:17686438 original size:23 final size:23
Alignment explanation
Indices: 17686397--17686440 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
17686387 TATACCTAAT
17686397 ATATTAAAAATATATATAATATA
1 ATATTAAAAATATATATAATATA
17686420 ATATTAAGAAATATA-ATAATA
1 ATATTAA-AAATATATATAATA
17686441 ACAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATTAAAAATATATATAATATA
Found at i:17696271 original size:21 final size:21
Alignment explanation
Indices: 17696245--17696285 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17696235 AGACGAGCAA
* *
17696245 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
17696266 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
17696286 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:17700337 original size:29 final size:26
Alignment explanation
Indices: 17700301--17700377 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 26
17700291 TATTTAAAAA
*
17700301 ATACATAATAATATTAAAGAATACGTAC
1 ATACATAATAATATT-AAGAATA-ATAC
*
17700329 ATACTATAAT-ATAATAAGAA-AATAC
1 ATAC-ATAATAATATTAAGAATAATAC
17700354 ATACAATATATAATATTAAGAATA
1 ATAC-ATA-ATAATATTAAGAATA
17700378 TATATATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
25 10 0.24
26 3 0.07
27 14 0.34
28 9 0.22
29 5 0.12
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (26 bp):
ATACATAATAATATTAAGAATAATAC
Found at i:17700373 original size:27 final size:26
Alignment explanation
Indices: 17700301--17700391 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 26
17700291 TATTTAAAAA
*
17700301 ATACATA-ATAATATTAA-AGAATAC
1 ATACATATATAATATTAAGAAAATAC
*
17700325 GTACATACTATAATATAATAAGAAAATAC
1 ATACATA-TATAATAT--TAAGAAAATAC
* *
17700354 ATACAATATATAATATTAAGAATATAT
1 ATAC-ATATATAATATTAAGAAAATAC
*
17700381 ATATATATATA
1 ATACATATATA
17700392 TGAATAGTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
24 6 0.11
26 14 0.25
27 12 0.22
28 3 0.05
29 17 0.31
30 3 0.05
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (26 bp):
ATACATATATAATATTAAGAAAATAC
Found at i:17700811 original size:22 final size:23
Alignment explanation
Indices: 17700753--17700811 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
17700743 ATATACAAAA
*
17700753 ATATAACATTAA-AAATATATAT
1 ATATAATATTAAGAAATATATAT
* *
17700775 ATGTAATATACAAGAAATATATAT
1 ATATAATAT-TAAGAAATATATAT
*
17700799 A-ATAGTATTAAGA
1 ATATAATATTAAGA
17700812 CTATAAACAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 11 0.38
23 7 0.24
24 11 0.38
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (23 bp):
ATATAATATTAAGAAATATATAT
Found at i:17701691 original size:17 final size:17
Alignment explanation
Indices: 17701669--17701701 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17701659 CAGCGCCGTC
*
17701669 TATTTTTTTGTTTTTTT
1 TATTTTTTTATTTTTTT
17701686 TATTTTTTTATTTTTT
1 TATTTTTTTATTTTTT
17701702 GGTATTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (17 bp):
TATTTTTTTATTTTTTT
Found at i:17703207 original size:19 final size:20
Alignment explanation
Indices: 17703183--17703222 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
17703173 AGGGGAAAAG
* *
17703183 TAGGAGAGAGTAAAAA-TTT
1 TAGGAGAAAATAAAAAGTTT
17703202 TAGGAGAAAATAAAAAGTTT
1 TAGGAGAAAATAAAAAGTTT
17703222 T
1 T
17703223 GAGGGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.28
Consensus pattern (20 bp):
TAGGAGAAAATAAAAAGTTT
Found at i:17703443 original size:9 final size:9
Alignment explanation
Indices: 17703425--17703461 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
17703415 TATAGTTTGA
*
17703425 TATTCAAAT
1 TATTCGAAT
17703434 TATTCGAAT
1 TATTCGAAT
*
17703443 TATTCGAGT
1 TATTCGAAT
17703452 TATTCGAAT
1 TATTCGAAT
17703461 T
1 T
17703462 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Done.