Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 49 of 59
Found at i:17610517 original size:17 final size:19
Alignment explanation
Indices: 17610490--17610524 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17610480 TTTTGTTTCT
17610490 TTTTTCTTTTCTT-TTTGA
1 TTTTTCTTTTCTTATTTGA
17610508 TTTTTC-TTTCTTATTTG
1 TTTTTCTTTTCTTATTTG
17610525 TTTCTTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.06, C:0.11, G:0.06, T:0.77
Consensus pattern (19 bp):
TTTTTCTTTTCTTATTTGA
Found at i:17610641 original size:14 final size:14
Alignment explanation
Indices: 17610622--17610669 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
17610612 GTAGCCTACA
17610622 ATCAATTTTCGTTC
1 ATCAATTTTCGTTC
**
17610636 ATCAATCATCGTTC
1 ATCAATTTTCGTTC
*
17610650 ATCAATTGTT-GGTC
1 ATCAATT-TTCGTTC
17610664 ATCAAT
1 ATCAAT
17610670 CATCAACTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 27 0.96
15 1 0.04
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (14 bp):
ATCAATTTTCGTTC
Found at i:17612617 original size:23 final size:23
Alignment explanation
Indices: 17612587--17612631 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
17612577 TACTAAGTCA
*
17612587 GATAAACGTTGGAGTAAAACTAG
1 GATAAACGTTGGAGCAAAACTAG
17612610 GATAAACGTTGGAGCAAAACTA
1 GATAAACGTTGGAGCAAAACTA
17612632 AGAGAACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.20
Consensus pattern (23 bp):
GATAAACGTTGGAGCAAAACTAG
Found at i:17624555 original size:24 final size:25
Alignment explanation
Indices: 17624522--17624569 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
17624512 GAGCCGCAAC
*
17624522 TTTGACTTTTTT-TATTTTTTTTAT
1 TTTGACTTTTTTGAATTTTTTTTAT
*
17624546 TTTGATTTTTTTGAATTTTTTTTA
1 TTTGACTTTTTTGAATTTTTTTTA
17624570 AACCAATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (25 bp):
TTTGACTTTTTTGAATTTTTTTTAT
Found at i:17632524 original size:13 final size:13
Alignment explanation
Indices: 17632506--17632530 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17632496 GAAAAGGAAC
17632506 AAAAAGAAGAAAG
1 AAAAAGAAGAAAG
17632519 AAAAAGAAGAAA
1 AAAAAGAAGAAA
17632531 ATAATGAAAG
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGAAAG
Found at i:17635001 original size:28 final size:29
Alignment explanation
Indices: 17634960--17635019 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
17634950 GTCTATGGGC
*
17634960 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCAGTTTTAGGGGGCAAAAATGT
* * *
17634988 AATTTTTGATTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAGTTTTA-GGGGGCAAAAATGT
17635018 AA
1 AA
17635020 ATATCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (29 bp):
AATTTTTCAGTTTTAGGGGGCAAAAATGT
Found at i:17637626 original size:15 final size:15
Alignment explanation
Indices: 17637577--17637627 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
17637567 TTTAAAGATC
*
17637577 AAAGATTTTGATTTT
1 AAAGTTTTTGATTTT
* * *
17637592 AAAGCTTTGGATTTC
1 AAAGTTTTTGATTTT
17637607 AAAGTTTTTGATTTT
1 AAAGTTTTTGATTTT
17637622 AAAGTT
1 AAAGTT
17637628 GTTTTAAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (15 bp):
AAAGTTTTTGATTTT
Found at i:17637672 original size:5 final size:5
Alignment explanation
Indices: 17637662--17637701 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
17637652 TGCGTGGCCC
* *
17637662 AAGTT AAGTT AAGTT AAG-T AAGTC AAGTT AAGTT AGGTT A
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT A
17637702 TATCGAGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.35
Consensus pattern (5 bp):
AAGTT
Found at i:17640129 original size:28 final size:29
Alignment explanation
Indices: 17640088--17640147 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
17640078 GTCTATGGGC
*
17640088 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCAGTTTTAGGGGGCAAAAATGT
* * *
17640116 AATTTTTGATTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAGTTTTA-GGGGGCAAAAATGT
17640146 AA
1 AA
17640148 ATATCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (29 bp):
AATTTTTCAGTTTTAGGGGGCAAAAATGT
Found at i:17646595 original size:21 final size:20
Alignment explanation
Indices: 17646543--17646599 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
17646533 ATTGAAGAAC
* **
17646543 ATCTATCGATAGATTGACCT
1 ATCTATCGATAGATAGACAA
* *
17646563 ATTTATCAATAGATGAGACAA
1 ATCTATCGATAGAT-AGACAA
17646584 ATCTATCGATAGATAG
1 ATCTATCGATAGATAG
17646600 CAACTCGAGA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
ATCTATCGATAGATAGACAA
Found at i:17649693 original size:37 final size:37
Alignment explanation
Indices: 17649640--17649756 Score: 189
Period size: 37 Copynumber: 3.2 Consensus size: 37
17649630 TGATGTTGGG
*
17649640 TGATGATGATAAAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGATAGAGTGTGCGAGTAGGGAGTGCACACA
* *
17649677 TGATGATGATGGAGTGTGCGAGTAGGGAGTGCACACG
1 TGATGATGATAGAGTGTGCGAGTAGGGAGTGCACACA
* *
17649714 TGATGATGACAGAGTGTGCAAGTAGGGAGTGCACACA
1 TGATGATGATAGAGTGTGCGAGTAGGGAGTGCACACA
17649751 TGATGA
1 TGATGA
17649757 CGATGTATGT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.30, C:0.11, G:0.38, T:0.21
Consensus pattern (37 bp):
TGATGATGATAGAGTGTGCGAGTAGGGAGTGCACACA
Found at i:17653022 original size:168 final size:168
Alignment explanation
Indices: 17652761--17653064 Score: 457
Period size: 168 Copynumber: 1.8 Consensus size: 168
17652751 AATGGGTCTC
* *** * * *
17652761 AAGCCTATCAACTAAATCATCAATAGTGGGAGCTTAACTCAAGACTTATGGTTGACTTGTAAGTC
1 AAGCCTATCAACTAAATCACCAATAGTAAAAGCTCAACTCAAGACTTATGGCTGACTTGCAAGTC
* * * *
17652826 TTGAGTATTGACCATTTCACCGCATGGATGATTGCAAGCATTGATTTATTTTTTCCATCCCAAGG
66 TTGAGCATTGACCATTTCACCACATGGATGATTGCAAGCACTAATTTATTTTTTCCATCCCAAGG
17652891 TATAAAGTGTTTGGTTCCTTTCAAGAAAGATGGATGTT
131 TATAAAGTGTTTGGTTCCTTTCAAGAAAGATGGATGTT
* *
17652929 AAGCCTATCAACTAAATCACCAATGGTAAAAGCTCAACTTAACG-CTTATGGCTGACTTGCAAGT
1 AAGCCTATCAACTAAATCACCAATAGTAAAAGCTCAACTCAA-GACTTATGGCTGACTTGCAAGT
*
17652993 CTTGAGCATTGACCATTTCATCACATGGATGATTGCAAGCACTAATTTATTTTTTCCATCCCAAG
65 CTTGAGCATTGACCATTTCACCACATGGATGATTGCAAGCACTAATTTATTTTTTCCATCCCAAG
*
17653058 GTGTAAA
130 GTATAAA
17653065 ATGCTTAGTT
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
168 119 0.99
169 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (168 bp):
AAGCCTATCAACTAAATCACCAATAGTAAAAGCTCAACTCAAGACTTATGGCTGACTTGCAAGTC
TTGAGCATTGACCATTTCACCACATGGATGATTGCAAGCACTAATTTATTTTTTCCATCCCAAGG
TATAAAGTGTTTGGTTCCTTTCAAGAAAGATGGATGTT
Found at i:17658156 original size:19 final size:20
Alignment explanation
Indices: 17658132--17658171 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
17658122 CCATTTGACT
17658132 TATTGGAGTATGATTT-AAG
1 TATTGGAGTATGATTTGAAG
17658151 TATTGGAGTATGATTTGAAG
1 TATTGGAGTATGATTTGAAG
17658171 T
1 T
17658172 TTAGAAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (20 bp):
TATTGGAGTATGATTTGAAG
Found at i:17658180 original size:20 final size:19
Alignment explanation
Indices: 17658132--17658180 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
17658122 CCATTTGACT
*
17658132 TATTGGAGTATGATTTAAG
1 TATTGAAGTATGATTTAAG
*
17658151 TATTGGAGTATGATTTGAAG
1 TATTGAAGTATGATTT-AAG
17658171 T-TTAGAAGTA
1 TATT-GAAGTA
17658181 AAAAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.41
Consensus pattern (19 bp):
TATTGAAGTATGATTTAAG
Found at i:17659280 original size:13 final size:13
Alignment explanation
Indices: 17659262--17659286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17659252 GGAAAATGAG
17659262 ATTTTATAAAATA
1 ATTTTATAAAATA
17659275 ATTTTATAAAAT
1 ATTTTATAAAAT
17659287 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:17659724 original size:116 final size:117
Alignment explanation
Indices: 17659509--17659741 Score: 414
Period size: 116 Copynumber: 2.0 Consensus size: 117
17659499 GATTATAAAA
*
17659509 TGGGCACTGCAGTGACGGGGGTTCCGTGGGCCACCCTAATTAGAGGGGCACGGTTCTCAATTATT
1 TGGGCACTGCAGTGACGGGGGTTCCGTGGGCCACCCTAATTAGAGGGGCACGGTTCCCAATTATT
*
17659574 GAGCTTGCCTCGATTGGAGAGGCACGTAGAATAACTCCCGAGGTAGGATTTG
66 GAGCTTACCTCGATTGGAGAGGCACGTAGAATAACTCCCGAGGTAGGATTTG
*
17659626 TGGGCACT-CAGTGACGGGGGTTCCGTGGGCCAGCCTAATTAGAGGGGCACGGTTCCCAATTATT
1 TGGGCACTGCAGTGACGGGGGTTCCGTGGGCCACCCTAATTAGAGGGGCACGGTTCCCAATTATT
* *
17659690 GAGCTTACCTCGATTGGAGAGGCGCGTAGGATAACTCCCGAGGTAGGATTTG
66 GAGCTTACCTCGATTGGAGAGGCACGTAGAATAACTCCCGAGGTAGGATTTG
17659742 AGTACACTTC
Statistics
Matches: 111, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
116 103 0.93
117 8 0.07
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (117 bp):
TGGGCACTGCAGTGACGGGGGTTCCGTGGGCCACCCTAATTAGAGGGGCACGGTTCCCAATTATT
GAGCTTACCTCGATTGGAGAGGCACGTAGAATAACTCCCGAGGTAGGATTTG
Found at i:17671913 original size:2 final size:2
Alignment explanation
Indices: 17671893--17671949 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
17671883 TTTAGGCAAT
* * *
17671893 TA TA TA CA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17671935 TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA
17671950 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:17671990 original size:2 final size:2
Alignment explanation
Indices: 17671983--17672036 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
17671973 NNNNNNNNNN
17671983 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
17672024 AT AT AT AT TT AT A
1 AT AT AT AT AT AT A
17672037 ATCTAGTACC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:17678390 original size:16 final size:17
Alignment explanation
Indices: 17678369--17678411 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
17678359 TGGATTAAAT
17678369 TCTAATATACATCC-AA
1 TCTAATATACATCCAAA
*
17678385 TCTAATTTACATCCAAA
1 TCTAATATACATCCAAA
17678402 TCTAGATATA
1 TCTA-ATATA
17678412 GATAACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 13 0.57
17 6 0.26
18 4 0.17
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (17 bp):
TCTAATATACATCCAAA
Found at i:17680156 original size:2 final size:2
Alignment explanation
Indices: 17680149--17680199 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
17680139 TNATAATAAC
17680149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17680191 TA TA TA TA T
1 TA TA TA TA T
17680200 CACTAGTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17682730 original size:26 final size:27
Alignment explanation
Indices: 17682701--17682853 Score: 90
Period size: 26 Copynumber: 6.0 Consensus size: 27
17682691 TTACGACATT
17682701 CATCCATTTTTTG-TGGTAAAATTATC
1 CATCCATTTTTTGATGGTAAAATTATC
* *
17682727 CATCCA-TTTCTGGT-GTCAAAATTATC
1 CATCCATTTTTTGATGGT-AAAATTATC
* ** *
17682753 C-T-TAGATTTTGATGCTAAAATTATC
1 CATCCATTTTTTGATGGTAAAATTATC
* *
17682778 CATCCA-TTTCTGATGGTAAAATTATT
1 CATCCATTTTTTGATGGTAAAATTATC
* ** * * *
17682804 C-T-TAAATTCTAATAGTAAAATTATC
1 CATCCATTTTTTGATGGTAAAATTATC
* *
17682829 CATCCACTTCTT-ATGGTAAAATTAT
1 CATCCATTTTTTGATGGTAAAATTAT
17682854 TCTTAGAATT
Statistics
Matches: 96, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
24 2 0.02
25 41 0.43
26 49 0.51
27 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (27 bp):
CATCCATTTTTTGATGGTAAAATTATC
Found at i:17682778 original size:25 final size:24
Alignment explanation
Indices: 17682716--17682829 Score: 75
Period size: 25 Copynumber: 4.5 Consensus size: 24
17682706 ATTTTTTGTG
* ** *
17682716 GTAAAATTATCCATCCATTTCTGGT
1 GTAAAATTATCCTTAAATTT-TGAT
*
17682741 GTCAAAATTATCCTTAGATTTTGAT
1 GT-AAAATTATCCTTAAATTTTGAT
* **
17682766 GCTAAAATTATCCATCCATTTCTGAT
1 G-TAAAATTATCCTTAAATTT-TGAT
* * *
17682792 GGTAAAATTATTCTTAAATTCTAAT
1 -GTAAAATTATCCTTAAATTTTGAT
17682817 AGTAAAATTATCC
1 -GTAAAATTATCC
17682830 ATCCACTTCT
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
25 35 0.50
26 34 0.49
27 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (24 bp):
GTAAAATTATCCTTAAATTTTGAT
Found at i:17682783 original size:51 final size:50
Alignment explanation
Indices: 17682716--17682863 Score: 181
Period size: 51 Copynumber: 2.9 Consensus size: 50
17682706 ATTTTTTGTG
* *
17682716 GTAAAATTATCCATCCATTTCTGGT-GTCAAAATTATCCTTAGATTTTGAT
1 GTAAAATTATCCATCCATTTCTGATGGT-AAAATTATCCTTAAATTTTGAT
* * *
17682766 GCTAAAATTATCCATCCATTTCTGATGGTAAAATTATTCTTAAATTCTAAT
1 G-TAAAATTATCCATCCATTTCTGATGGTAAAATTATCCTTAAATTTTGAT
* * *
17682817 AGTAAAATTATCCATCCACTTCTTATGGTAAAATTATTCTTAGAATT
1 -GTAAAATTATCCATCCATTTCTGATGGTAAAATTATCCTTA-AATT
17682864 AAAATAGTAA
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
50 1 0.01
51 79 0.91
52 7 0.08
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (50 bp):
GTAAAATTATCCATCCATTTCTGATGGTAAAATTATCCTTAAATTTTGAT
Found at i:17685716 original size:28 final size:29
Alignment explanation
Indices: 17685658--17685721 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
17685648 GCAAATTTTA
** *
17685658 AAAAATTACACTTTTACCCCCGTAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
* *
17685687 AAAAATTATATTTTTA-CCCCAAAAACTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
17685715 AAAAATT
1 AAAAATT
17685722 GCCCATAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAACTG
Found at i:17689469 original size:67 final size:67
Alignment explanation
Indices: 17689361--17689493 Score: 230
Period size: 67 Copynumber: 2.0 Consensus size: 67
17689351 TGTACTTGTT
* *
17689361 TCTCCTTTCATTCTTGTGTTAGTGAATCCTCATTTAGCCTAAAGCATATTTAAGTGGAACCAGAC
1 TCTCCTTTCATTCCTGTGTTAGTAAATCCTCATTTAGCCTAAAGCATATTTAAGTGGAACCAGAC
17689426 TA
66 TA
* *
17689428 TCTCCTTTCATTCCTGTGTTAGTAAATCCTCTTTTAGCCTAAAGCATATTTAAGTGGAATCAGAC
1 TCTCCTTTCATTCCTGTGTTAGTAAATCCTCATTTAGCCTAAAGCATATTTAAGTGGAACCAGAC
17689493 T
66 T
17689494 TTTGCAATTC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (67 bp):
TCTCCTTTCATTCCTGTGTTAGTAAATCCTCATTTAGCCTAAAGCATATTTAAGTGGAACCAGAC
TA
Found at i:17693971 original size:25 final size:25
Alignment explanation
Indices: 17693943--17693994 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
17693933 TATCAAATCG
** *
17693943 CATATGCATTTATACGTACAAAGTA
1 CATATGCACATATAAGTACAAAGTA
17693968 CATATGCACATATAAGTACAAAGTA
1 CATATGCACATATAAGTACAAAGTA
17693993 CA
1 CA
17693995 GTGCTGTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (25 bp):
CATATGCACATATAAGTACAAAGTA
Found at i:17696908 original size:22 final size:22
Alignment explanation
Indices: 17696883--17696938 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
17696873 AATAATAATT
*
17696883 AATTATAAATAATATA-TTATAA
1 AATTATAAATAATA-ACTAATAA
*
17696905 AATT-TAAAGTGATAACTAATAA
1 AATTATAAA-TAATAACTAATAA
17696927 AATTATTAAATA
1 AATTA-TAAATA
17696939 TAATCATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
21 5 0.19
22 17 0.63
23 1 0.04
24 4 0.15
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
AATTATAAATAATAACTAATAA
Found at i:17697165 original size:21 final size:20
Alignment explanation
Indices: 17697114--17697165 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
17697104 CTATCATATA
* *
17697114 TTATAATATTAACATATAACT
1 TTATAAT-TTAAAATATAAAT
*
17697135 TATATCATTTAAAATATATAAT
1 T-TATAATTTAAAATATA-AAT
17697157 TTATAATTT
1 TTATAATTT
17697166 CATATTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATAATTTAAAATATAAAT
Found at i:17697440 original size:23 final size:23
Alignment explanation
Indices: 17697413--17697467 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
17697403 ACCAACCAAA
17697413 AAACCAATTAGACTAAATATTTT
1 AAACCAATTAGACTAAATATTTT
17697436 AAACCAATTAGACTAAATATTTT
1 AAACCAATTAGACTAAATATTTT
17697459 AAACCAATT
1 AAACCAATT
17697468 GATCCAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.33
Consensus pattern (23 bp):
AAACCAATTAGACTAAATATTTT
Found at i:17705723 original size:19 final size:18
Alignment explanation
Indices: 17705703--17705754 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 18
17705693 GTAAAATATA
17705703 AAATAAATTTTTATTTAT
1 AAATAAATTTTTATTTAT
17705721 AAAT--ATTTTT-TTTATT
1 AAATAAATTTTTATTTA-T
*
17705737 TAATAAAATTTTTATTTA
1 AAAT-AAATTTTTATTTA
17705755 GATCAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
15 4 0.14
16 10 0.36
18 4 0.14
19 6 0.21
20 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AAATAAATTTTTATTTAT
Found at i:17705742 original size:20 final size:18
Alignment explanation
Indices: 17705710--17705754 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 18
17705700 ATAAAATAAA
17705710 TTTTTATTTATAAATATTT
1 TTTTTATTTATAAA-ATTT
17705729 TTTTTATTTAATAAAATTT
1 TTTTTATTT-ATAAAATTT
17705748 TTATTTA
1 TT-TTTA
17705755 GATCAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTATTTATAAAATTT
Found at i:17706809 original size:17 final size:18
Alignment explanation
Indices: 17706787--17706832 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
17706777 AATTAAAAAA
17706787 ATTTAAATAATTATAATT
1 ATTTAAATAATTATAATT
* * *
17706805 A-TTAAAGAGTTATATTT
1 ATTTAAATAATTATAATT
17706822 ATTTAAATAAT
1 ATTTAAATAAT
17706833 AAAAGTTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (18 bp):
ATTTAAATAATTATAATT
Found at i:17709848 original size:79 final size:79
Alignment explanation
Indices: 17709717--17709872 Score: 206
Period size: 79 Copynumber: 2.0 Consensus size: 79
17709707 CTTGAGCTGG
* * * * * *
17709717 AAGCTCACTTTGTAAAAGCTTGGTGAAAGCTATTAATTTCACTAGTTTTAGTGAAGTTGGATTGA
1 AAGCTCACTTTATAAAAACTTGGTGAAAACTATTAATTCCACTAGCTTTAGTGAAGTTGGATTAA
17709782 AAATCTTAGATTAA
66 AAATCTTAGATTAA
* * *
17709796 AAGCTCATTTTATAAAAACTTGGTGAAAACTGTTAATTCCA-TTGACTTTAGTGAAGTTGGATTA
1 AAGCTCACTTTATAAAAACTTGGTGAAAACTATTAATTCCACTAG-CTTTAGTGAAGTTGGATTA
*
17709860 AAAATCTTTGATT
65 AAAATCTTAGATT
17709873 GGGAATATTA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
78 2 0.03
79 64 0.97
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (79 bp):
AAGCTCACTTTATAAAAACTTGGTGAAAACTATTAATTCCACTAGCTTTAGTGAAGTTGGATTAA
AAATCTTAGATTAA
Found at i:17717585 original size:75 final size:74
Alignment explanation
Indices: 17717501--17717650 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 74
17717491 GCTGCATAGA
17717501 TGTCCTTGTTTCATCTCATATTGATTTCTGTTCCCTGCATCACATTTTGACTTACATTTACATTT
1 TGTCCTTGTTTCATCTCATATTGATTTCTGTTCCCTGCATCACATTTTGACTTACATTTACATTT
17717566 TGTAGCTTT
66 TGTAGCTTT
17717575 TNGTCCTTGTTTCATCTCATATTGATTTCTGTTCCCTGCATCACATTTTGACTTACATTTACATT
1 T-GTCCTTGTTTCATCTCATATTGATTTCTGTTCCCTGCATCACATTTTGACTTACATTTACATT
17717640 TTGTAGCTTT
65 TTGTAGCTTT
17717650 T
1 T
17717651 TATGTGGCCA
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 1 0.01
75 74 0.99
ACGTcount: A:0.17, C:0.21, G:0.11, T:0.50
Consensus pattern (74 bp):
TGTCCTTGTTTCATCTCATATTGATTTCTGTTCCCTGCATCACATTTTGACTTACATTTACATTT
TGTAGCTTT
Found at i:17722493 original size:2 final size:2
Alignment explanation
Indices: 17722486--17722534 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
17722476 ACATAAATAC
17722486 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17722528 AT AT AT A
1 AT AT AT A
17722535 AAATCAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17731232 original size:27 final size:28
Alignment explanation
Indices: 17731202--17731260 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
17731192 GTAAAAGCTT
17731202 ATTTGATTCAAAATAA-AAAAAATAAAG
1 ATTTGATTCAAAATAATAAAAAATAAAG
* ** *
17731229 ATTTGATTGAACGTAATAAAAAATAAAT
1 ATTTGATTCAAAATAATAAAAAATAAAG
17731257 ATTT
1 ATTT
17731261 ATTTTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.32
Consensus pattern (28 bp):
ATTTGATTCAAAATAATAAAAAATAAAG
Found at i:17737583 original size:26 final size:26
Alignment explanation
Indices: 17737554--17737605 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
17737544 AATATGCTAG
17737554 AATTAATGTTAAGAATTA-TGTTTGGA
1 AATT-ATGTTAAGAATTATTGTTTGGA
* *
17737580 AATTTTGTTGAGAATTATTGTTTGGA
1 AATTATGTTAAGAATTATTGTTTGGA
17737606 TTTTCAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (26 bp):
AATTATGTTAAGAATTATTGTTTGGA
Found at i:17737668 original size:13 final size:13
Alignment explanation
Indices: 17737650--17737688 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
17737640 TAAACATTAA
17737650 GAATTATGTTTGG
1 GAATTATGTTTGG
*
17737663 GAATTATG-TTGA
1 GAATTATGTTTGG
17737675 GAATTATTGTTTGG
1 GAATTA-TGTTTGG
17737689 ATTTTCAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 9 0.41
13 10 0.45
14 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (13 bp):
GAATTATGTTTGG
Found at i:17737682 original size:84 final size:84
Alignment explanation
Indices: 17737526--17737980 Score: 696
Period size: 84 Copynumber: 5.4 Consensus size: 84
17737516 AAGAAACTGA
* * ** * *
17737526 TCAATTAAAATTATTGGTAATATGCTAGAATT-AATGTTAAGAATTATGTTTGGAAATTTTGTTG
1 TCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
17737590 AGAATTATTGTTTGGATTT
66 AGAATTATTGTTTGGATTT
*
17737609 TCAATTAAAATGATTGGCAATATGCTTGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
1 TCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
17737674 AGAATTATTGTTTGGATTT
66 AGAATTATTGTTTGGATTT
* *
17737693 TCAATTAAAATGATTAGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTAGGTTG
1 TCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
17737758 AGAATTATTGTTTGGATTT
66 AGAATTATTGTTTGGATTT
* * * *
17737777 TCAATTAAAATGATTGGTAATATGCTAGAACTAAACATTAAAAATTATGTTTAGGAATTAATGTT
1 TCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATT-ATGTT
* *
17737842 TAGAATTATTGTTTGAATTT
65 GAGAATTATTGTTTGGATTT
* * *
17737862 TCAATTAAAATAATTGGCAATATGTTAGAATTAAACATTAAGAATTATGTTTGAGAATTAATGTT
1 TCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATT-ATGTT
* *
17737927 TAGAATTATTATTTGGATTT
65 GAGAATTATTGTTTGGATTT
*
17737947 TCAATTACAATGATTGGCAATATGCTAGAATTAA
1 TCAATTAAAATGATTGGCAATATGCTAGAATTAA
17737981 TGATTGGAAT
Statistics
Matches: 340, Mismatches: 30, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
83 29 0.09
84 182 0.54
85 129 0.38
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (84 bp):
TCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
AGAATTATTGTTTGGATTT
Found at i:17737847 original size:13 final size:13
Alignment explanation
Indices: 17737819--17737860 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
17737809 AAACATTAAA
17737819 AATT-ATGTTTAGG
1 AATTAATGTTTA-G
17737832 AATTAATGTTTAG
1 AATTAATGTTTAG
*
17737845 AATTATTGTTT-G
1 AATTAATGTTTAG
17737857 AATT
1 AATT
17737861 TTCAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 5 0.19
13 15 0.56
14 7 0.26
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (13 bp):
AATTAATGTTTAG
Found at i:17737925 original size:14 final size:13
Alignment explanation
Indices: 17737902--17737934 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
17737892 TTAAACATTA
17737902 AGAATT-ATGTTT
1 AGAATTAATGTTT
17737914 GAGAATTAATGTTT
1 -AGAATTAATGTTT
17737928 AGAATTA
1 AGAATTA
17737935 TTATTTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (13 bp):
AGAATTAATGTTT
Found at i:17740692 original size:25 final size:25
Alignment explanation
Indices: 17740664--17740717 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
17740654 CTTTTGAAAC
17740664 TAATGTTTATTTATT-ATATAAAGAT
1 TAATGTTTATTTATTGA-ATAAAGAT
*
17740689 TAATGTTTATTTATTGAATGAAGAT
1 TAATGTTTATTTATTGAATAAAGAT
17740714 TAAT
1 TAAT
17740718 ATTATTAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (25 bp):
TAATGTTTATTTATTGAATAAAGAT
Found at i:17744856 original size:18 final size:18
Alignment explanation
Indices: 17744833--17744871 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
17744823 GTGAACCATT
17744833 TTTAAATGGAAGTAAATA
1 TTTAAATGGAAGTAAATA
17744851 TTTAAATGGAAGTAAATA
1 TTTAAATGGAAGTAAATA
17744869 TTT
1 TTT
17744872 CTTGCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (18 bp):
TTTAAATGGAAGTAAATA
Found at i:17763333 original size:17 final size:18
Alignment explanation
Indices: 17763311--17763351 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
17763301 ATAGAAATAG
17763311 AATAAAATGAAATA-AAT
1 AATAAAATGAAATATAAT
*
17763328 AATAAAATTAAATATTAAT
1 AATAAAATGAAATA-TAAT
17763347 AATAA
1 AATAA
17763352 TATAAATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.62
19 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AATAAAATGAAATATAAT
Found at i:17763473 original size:1 final size:1
Alignment explanation
Indices: 17763469--17763514 Score: 83
Period size: 1 Copynumber: 46.0 Consensus size: 1
17763459 AAAAATTAAA
*
17763469 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17763515 AATTTATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.02, C:0.00, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:17763519 original size:10 final size:10
Alignment explanation
Indices: 17763468--17763519 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
17763458 AAAAAATTAA
17763468 ATTTTTTTTT
1 ATTTTTTTTT
17763478 -TTTTTTTTT
1 ATTTTTTTTT
17763487 -TTTTTTTTT
1 ATTTTTTTTT
*
17763496 TTTTTTTTTT
1 ATTTTTTTTT
*
17763506 ATTTTTTTTA
1 ATTTTTTTTT
17763516 ATTT
1 ATTT
17763520 ATTAATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
9 18 0.46
10 21 0.54
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:17771760 original size:28 final size:28
Alignment explanation
Indices: 17771720--17771794 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
17771710 TCGGGTGTGT
* **
17771720 AAAATTACAATTTTGCCCCTAGAATCAC
1 AAAATTACCATTTTAACCCTAGAATCAC
* ***
17771748 AAAATTACCATTTTAATCCTAGAATGGT
1 AAAATTACCATTTTAACCCTAGAATCAC
17771776 AAAATTACCATTTT-ACCCT
1 AAAATTACCATTTTAACCCT
17771795 TATGCTCCGA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 4 0.10
28 35 0.90
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (28 bp):
AAAATTACCATTTTAACCCTAGAATCAC
Found at i:17771866 original size:19 final size:19
Alignment explanation
Indices: 17771842--17771879 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17771832 ACTTCTCAAC
17771842 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
17771861 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
17771880 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:17774792 original size:26 final size:26
Alignment explanation
Indices: 17774763--17774814 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
17774753 AATATGCTAG
17774763 AATTAATGTTAAGAATTA-TGTTTGGA
1 AATT-ATGTTAAGAATTATTGTTTGGA
* *
17774789 AATTTTGTTGAGAATTATTGTTTGGA
1 AATTATGTTAAGAATTATTGTTTGGA
17774815 TTTTCAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (26 bp):
AATTATGTTAAGAATTATTGTTTGGA
Found at i:17774877 original size:13 final size:13
Alignment explanation
Indices: 17774859--17774897 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
17774849 TAAACATTAA
17774859 GAATTATGTTTGG
1 GAATTATGTTTGG
*
17774872 GAATTATG-TTGA
1 GAATTATGTTTGG
17774884 GAATTATTGTTTGG
1 GAATTA-TGTTTGG
17774898 ATTTTCAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 9 0.41
13 10 0.45
14 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (13 bp):
GAATTATGTTTGG
Found at i:17774891 original size:84 final size:84
Alignment explanation
Indices: 17774735--17775181 Score: 601
Period size: 84 Copynumber: 5.4 Consensus size: 84
17774725 AAGAAACTGA
* * ** * *
17774735 TCAATTAAAATTATTGGTAATATGCTAGAATT-AATGTTAAGAATTATGTTTGGAAATTTTGTTG
1 TCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
17774799 AGAATTATTGTTTGGATTT
66 AGAATTATTGTTTGGATTT
*
17774818 TCAATTAAAATGATTGGCAATATGCTTGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
1 TCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
17774883 AGAATTATTGTTTGGATTT
66 AGAATTATTGTTTGGATTT
* *
17774902 TCAATTAAAATGATTAGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTAGGTTG
1 TCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
17774967 AGAATTATTGTTTGGATTT
66 AGAATTATTGTTTGGATTT
* *
17774986 TCAATTAAAATGATTGGTAATATGCTAGAATT-AACATT----A-TA--TTTAGGAATTAATGTT
1 TCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATT-ATG-T
* * *
17775043 TAGA-ATTA-TTGTTTGAATTT
64 T-GAGAATTATTGTTTGGATTT
* * *
17775063 TCAATTAAAATAATTGGCAATATGTTAGAATTAAACATTAAGAATTATGTTTGAGAATTAATGTT
1 TCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATT-ATGTT
* *
17775128 TAGAATTATTATTTGGATTT
65 GAGAATTATTGTTTGGATTT
*
17775148 TCAATTACAATGATTGGCAATATGCTAGAATTAA
1 TCAATTAAAATGATTGGCAATATGCTAGAATTAA
17775182 TGATTGGAAT
Statistics
Matches: 320, Mismatches: 30, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
76 9 0.03
77 42 0.13
78 12 0.04
79 3 0.01
82 1 0.00
83 38 0.12
84 162 0.51
85 53 0.17
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (84 bp):
TCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
AGAATTATTGTTTGGATTT
Found at i:17775019 original size:168 final size:162
Alignment explanation
Indices: 17774735--17775181 Score: 630
Period size: 161 Copynumber: 2.7 Consensus size: 162
17774725 AAGAAACTGA
* * ** * *
17774735 TCAATTAAAATTATTGGTAATATGCTAGAATT-AATGTTAAGAATTATGTTTGGAAATTTTGTTG
1 TCAATTAAAATAATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
*
17774799 AGAATTATTGTTTGGATTTTCAATTAAAATGATTGGCAATATGCTTGAATTAAACATTAAGAATT
66 AGAATTATTGTTTGGATTTTCAATTAAAATGATTGGCAATATGCTAGAATTAAACATT----A-T
* *
17774864 ATGTTTGGGAATT-ATGTTGAGAATTATTGTTTGGATTT
126 A--TTTAGGAATTAATGTTGAGAATTATTGTTTGAATTT
* * *
17774902 TCAATTAAAATGATTAGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTAGGTTG
1 TCAATTAAAATAATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
*
17774967 AGAATTATTGTTTGGATTTTCAATTAAAATGATTGGTAATATGCTAGAATT-AACATTATATTTA
66 AGAATTATTGTTTGGATTTTCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTATATTTA
*
17775031 GGAATTAATGTTTAGAATTATTGTTTGAATTT
131 GGAATTAATGTTGAGAATTATTGTTTGAATTT
* *
17775063 TCAATTAAAATAATTGGCAATATGTTAGAATTAAACATTAAGAATTATGTTTGAGAATTAATGTT
1 TCAATTAAAATAATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATT-ATGTT
* * *
17775128 TAGAATTATTATTTGGATTTTCAATTACAATGATTGGCAATATGCTAGAATTAA
65 GAGAATTATTGTTTGGATTTTCAATTAAAATGATTGGCAATATGCTAGAATTAA
17775182 TGATTGGAAT
Statistics
Matches: 254, Mismatches: 22, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
160 9 0.04
161 78 0.31
162 54 0.21
163 2 0.01
167 35 0.14
168 76 0.30
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (162 bp):
TCAATTAAAATAATTGGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAATTATGTTG
AGAATTATTGTTTGGATTTTCAATTAAAATGATTGGCAATATGCTAGAATTAAACATTATATTTA
GGAATTAATGTTGAGAATTATTGTTTGAATTT
Found at i:17775065 original size:77 final size:77
Alignment explanation
Indices: 17774945--17775102 Score: 228
Period size: 77 Copynumber: 2.1 Consensus size: 77
17774935 AACATTAAGA
* * * * *
17774945 ATTATGTTTGGGAATTAGGTTGAGAATTATTGTTTGGATTTTCAATTAAAATGATTGGTAATATG
1 ATTATATTTAGGAATTAGGTTGAGAATTATTGTTTGAATTTTCAATTAAAATAATTGGCAATATG
17775010 CTAGAATT-AAC
66 CTAGAATTAAAC
* *
17775021 ATTATATTTAGGAATTAATGTTTAGAATTATTGTTTGAATTTTCAATTAAAATAATTGGCAATAT
1 ATTATATTTAGGAATT-AGGTTGAGAATTATTGTTTGAATTTTCAATTAAAATAATTGGCAATAT
*
17775086 GTTAGAATTAAAC
65 GCTAGAATTAAAC
17775099 ATTA
1 ATTA
17775103 AGAATTATGT
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
76 14 0.19
77 51 0.71
78 7 0.10
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.43
Consensus pattern (77 bp):
ATTATATTTAGGAATTAGGTTGAGAATTATTGTTTGAATTTTCAATTAAAATAATTGGCAATATG
CTAGAATTAAAC
Found at i:17775126 original size:14 final size:13
Alignment explanation
Indices: 17775103--17775135 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
17775093 TTAAACATTA
17775103 AGAATT-ATGTTT
1 AGAATTAATGTTT
17775115 GAGAATTAATGTTT
1 -AGAATTAATGTTT
17775129 AGAATTA
1 AGAATTA
17775136 TTATTTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (13 bp):
AGAATTAATGTTT
Found at i:17777874 original size:25 final size:25
Alignment explanation
Indices: 17777846--17777899 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
17777836 CTTTTGAAAC
17777846 TAATGTTTATTTATT-ATATAAAGAT
1 TAATGTTTATTTATTGA-ATAAAGAT
*
17777871 TAATGTTTATTTATTGAATGAAGAT
1 TAATGTTTATTTATTGAATAAAGAT
17777896 TAAT
1 TAAT
17777900 ATTATTAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (25 bp):
TAATGTTTATTTATTGAATAAAGAT
Found at i:17781015 original size:31 final size:30
Alignment explanation
Indices: 17780983--17781087 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 30
17780973 CTGCAAGAAG
* *
17780983 TCAGCGTGTCACGCCACAAGTCTGCGTTAAG
1 TCAGCGTGTCACGCCATAAGTCTGC-TTAAC
* * * *
17781014 TCAACGTGTCACGTCATAAGTTTGAATTAAC
1 TCAGCGTGTCACGCCATAAGTCTG-CTTAAC
* * *
17781045 TCAGCGTGTCAAGCCATAATTCTGCTTGCAC
1 TCAGCGTGTCACGCCATAAGTCTGCTT-AAC
17781076 TCAGCGTGTCAC
1 TCAGCGTGTCAC
17781088 CGCAATTGGC
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
30 2 0.03
31 56 0.97
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.28
Consensus pattern (30 bp):
TCAGCGTGTCACGCCATAAGTCTGCTTAAC
Found at i:17784625 original size:31 final size:31
Alignment explanation
Indices: 17784579--17784821 Score: 339
Period size: 31 Copynumber: 7.8 Consensus size: 31
17784569 TTTGTCAGTC
* *
17784579 ATGTTGTTACACGCCATGCATATAATGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
17784610 ATGTAGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* *
17784641 ATG-TGCTAACACGCCATGCAAATAACATAAA
1 ATGTTG-TAACACGCCATGCATATAACGTAAA
17784672 ATGTTGTAACACGCCATGCATAT-ACTGTAAA
1 ATGTTGTAACACGCCATGCATATAAC-GTAAA
* *
17784703 ATGTGGTAACACGCCATGCATATAACGGAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* *
17784734 ATG-TGATAACATGCCATGCATATAACGTTAA
1 ATGTTG-TAACACGCCATGCATATAACGTAAA
* *
17784765 ATGTTGTAACACACCATGCATATCACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
17784796 ATGTTGTAACACGCCATGCATATAAC
1 ATGTTGTAACACGCCATGCATATAAC
17784822 CAATGTCGTG
Statistics
Matches: 186, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
30 4 0.02
31 176 0.95
32 6 0.03
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (31 bp):
ATGTTGTAACACGCCATGCATATAACGTAAA
Found at i:17791021 original size:87 final size:87
Alignment explanation
Indices: 17790932--17791095 Score: 192
Period size: 87 Copynumber: 1.9 Consensus size: 87
17790922 ATAAAAATGA
* * *
17790932 AAAAAGAAAATATACAAA-ACAAGAAATTAAATTAAAA-ATAACATGATATTAA-A-TTTAATAA
1 AAAAAGAAAATAGACAAATACAA-AAA--AAATTAAAATAAAACATCATATTAATATTTTAATAA
* *
17790993 AAATGAAATTGAAAGAGATGAACGG
63 AAAAGAAATTAAAAGAGATGAACGG
* * * *
17791018 AAAATGAAAATAGATAAATACAAAAAAGATTAAAATAAAATATCATATTAATATTTTAATAAAAA
1 AAAAAGAAAATAGACAAATACAAAAAAAATTAAAATAAAACATCATATTAATATTTTAATAAAAA
17791083 AGAAATTAAAAGA
66 AGAAATTAAAAGA
17791096 TAAAAAATGA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
84 8 0.12
85 12 0.18
86 19 0.29
87 26 0.40
ACGTcount: A:0.63, C:0.04, G:0.09, T:0.24
Consensus pattern (87 bp):
AAAAAGAAAATAGACAAATACAAAAAAAATTAAAATAAAACATCATATTAATATTTTAATAAAAA
AGAAATTAAAAGAGATGAACGG
Found at i:17793825 original size:8 final size:8
Alignment explanation
Indices: 17793812--17793836 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17793802 ATAAATTTTT
17793812 TCTTTTAA
1 TCTTTTAA
17793820 TCTTTTAA
1 TCTTTTAA
17793828 TCTTTTAA
1 TCTTTTAA
17793836 T
1 T
17793837 AAAACACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TCTTTTAA
Found at i:17794348 original size:29 final size:30
Alignment explanation
Indices: 17794305--17794366 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
17794295 TTTTTATTTT
*
17794305 TTTTCCTTAACTTCAATAAAAAAAATCTCA
1 TTTTCCTTAACTTCAATAAAAAAAATATCA
* *
17794335 TTTT-CTTAATTTCAATAAAAAATATATCA
1 TTTTCCTTAACTTCAATAAAAAAAATATCA
17794364 TTT
1 TTT
17794367 GAATATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (30 bp):
TTTTCCTTAACTTCAATAAAAAAAATATCA
Found at i:17799245 original size:20 final size:20
Alignment explanation
Indices: 17799204--17799245 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
17799194 TATATTAATT
* *
17799204 TTTATATATTTTTAATATAA
1 TTTATATATTATTAATAAAA
17799224 TTTATTATATTATT-ATAAAA
1 TTTA-TATATTATTAATAAAA
17799244 TT
1 TT
17799246 ATGAATTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATATATTATTAATAAAA
Found at i:17806045 original size:307 final size:308
Alignment explanation
Indices: 17805443--17806051 Score: 1060
Period size: 307 Copynumber: 2.0 Consensus size: 308
17805433 ACTTAAAAAC
17805443 AATAATTTCTAACTTTTAATACTTAGAAGATAAATTCATTTAATATTTATCAGTTACAATTTAAT
1 AATAATTTCTAACTTTTAATACTTAGAAGATAAATTCATTTAATATTTATCAGTTACAATTTAAT
*
17805508 ATTATTTTTTATCTATATTTTTTTATTCTGCATGAACCTGAATCTAGAGTAAATAGATATATCTT
66 ATTATTTTTTATCTATATTTTTTTATTCTGCATGAACCTGAATCTAGAATAAATAGATATATCTT
*
17805573 TTATACTTAAATGTTTAAATTTCAATAAATATCCATACAATTCATTATATAAAAGTAAGATAATT
131 TTATACTTAAATATTTAAATTTCAATAAATATCCATACAATTCATTATATAAAAGTAAGATAATT
* * *
17805638 GATTGGGTTAATCGATTGACATTTGTCATTCTTAATTAAATTAATTTTTTTTACACTTTATGTCA
196 GATTGGGTCAATAGATTGACATTTGTCATTCTTAATTAAATTAATTTTTTTTACACCTTATGTCA
*
17805703 AAACTACATTATTTTTGACATTTGAAGGGTTTTTTT-TTTTTACTTTT
261 AAACTACATTATTTTTGACATTTAAAGGGTTTTTTTCTTTTTACTTTT
* *
17805750 AATAATTTCTAACTTTTAATACTTAGAAGATAGATTCATTTAATCTTTATCAGTTACAATTTAAT
1 AATAATTTCTAACTTTTAATACTTAGAAGATAAATTCATTTAATATTTATCAGTTACAATTTAAT
* * * *
17805815 ATTATTTTTTATCTATATTTTTTTATTTTGCATGAACCTGAATCTATAATAAATAGATATTTTTT
66 ATTATTTTTTATCTATATTTTTTTATTCTGCATGAACCTGAATCTAGAATAAATAGATATATCTT
*
17805880 TTATACTTAAATATTTAAATTTCAATAAATATCCATCCAATTCATTATATAAAAGTAAGATAATT
131 TTATACTTAAATATTTAAATTTCAATAAATATCCATACAATTCATTATATAAAAGTAAGATAATT
17805945 GATTGGGTCAATAGATTGACATTTGTCATTCTTAATTAAATTAA-TTTTTTTACACCTTATGTCA
196 GATTGGGTCAATAGATTGACATTTGTCATTCTTAATTAAATTAATTTTTTTTACACCTTATGTCA
* *
17806009 AAACTACATTGTTTTTGACATTTAAAAGGTTTTTTTTCTTTTT
261 AAACTACATTATTTTTGACATTT-AAAGGGTTTTTTTCTTTTT
17806052 TATTTTTATT
Statistics
Matches: 285, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
306 41 0.14
307 239 0.84
308 5 0.02
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (308 bp):
AATAATTTCTAACTTTTAATACTTAGAAGATAAATTCATTTAATATTTATCAGTTACAATTTAAT
ATTATTTTTTATCTATATTTTTTTATTCTGCATGAACCTGAATCTAGAATAAATAGATATATCTT
TTATACTTAAATATTTAAATTTCAATAAATATCCATACAATTCATTATATAAAAGTAAGATAATT
GATTGGGTCAATAGATTGACATTTGTCATTCTTAATTAAATTAATTTTTTTTACACCTTATGTCA
AAACTACATTATTTTTGACATTTAAAGGGTTTTTTTCTTTTTACTTTT
Found at i:17821667 original size:13 final size:13
Alignment explanation
Indices: 17821649--17821673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17821639 TATCAGTCTC
17821649 AACAAATAAAACG
1 AACAAATAAAACG
17821662 AACAAATAAAAC
1 AACAAATAAAAC
17821674 AATAGTCCAT
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:0.72, C:0.16, G:0.04, T:0.08
Consensus pattern (13 bp):
AACAAATAAAACG
Found at i:17823420 original size:1 final size:1
Alignment explanation
Indices: 17823414--17823439 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
17823404 AAAACAATTG
17823414 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
17823440 AAAANNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:17826797 original size:28 final size:28
Alignment explanation
Indices: 17826757--17826811 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
17826747 CTTTGGTAAA
*
17826757 AGTCTTGAAAGAGGGATTTAGTTCTAAC
1 AGTCTTGAAAGAGGGATTTAATTCTAAC
17826785 AGTCTTGAAAGAGGGATTTAATTCTAA
1 AGTCTTGAAAGAGGGATTTAATTCTAA
17826812 ACTCCTATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.33
Consensus pattern (28 bp):
AGTCTTGAAAGAGGGATTTAATTCTAAC
Found at i:17828381 original size:62 final size:62
Alignment explanation
Indices: 17828305--17828427 Score: 201
Period size: 62 Copynumber: 2.0 Consensus size: 62
17828295 TGGTTGAGTT
* * * *
17828305 TGCTATCCTGCTCACTTTTTAAGCTAGCCTTGAGCTCCACTACCCTTATAAAATTTCAGCTC
1 TGCTATCCTGCTCACTTTGTAAGCTAACCTTGAGCTCCACTAACCTTATAAAAATTCAGCTC
*
17828367 TGCTATCCTGCTCACTTTGTAAGCTAACCTTGAGCTCCACTAACCTTGTAAAAATTCAGCT
1 TGCTATCCTGCTCACTTTGTAAGCTAACCTTGAGCTCCACTAACCTTATAAAAATTCAGCT
17828428 TTTTCTGTGC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.34
Consensus pattern (62 bp):
TGCTATCCTGCTCACTTTGTAAGCTAACCTTGAGCTCCACTAACCTTATAAAAATTCAGCTC
Found at i:17834713 original size:5 final size:5
Alignment explanation
Indices: 17834698--17834735 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
17834688 TAAAATTTAT
17834698 TATATA TATAA TATAA TATAA TATAA TATAA TATAA TA
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TA
17834736 ACTTTGTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:17847551 original size:13 final size:13
Alignment explanation
Indices: 17847520--17847561 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
17847510 CATAACAACC
17847520 TTTTCTTCTATT-T
1 TTTTCTTCT-TTCT
*
17847533 TCTTCTTCTTTCT
1 TTTTCTTCTTTCT
17847546 TTTTC-TCTTTCT
1 TTTTCTTCTTTCT
17847558 TTTT
1 TTTT
17847562 TTGGCTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 13 0.50
13 13 0.50
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTCTTTCT
Found at i:17847929 original size:17 final size:17
Alignment explanation
Indices: 17847882--17847930 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
17847872 ACAGCATTAA
* *
17847882 TTAAGTTTTTAGCTTTT
1 TTAATTTTTTAGGTTTT
*
17847899 TTAATTTTTCAGGTTTT
1 TTAATTTTTTAGGTTTT
17847916 TTAATTTTTTAGGTT
1 TTAATTTTTTAGGTT
17847931 ATCTTTGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.18, C:0.04, G:0.12, T:0.65
Consensus pattern (17 bp):
TTAATTTTTTAGGTTTT
Found at i:17848706 original size:12 final size:12
Alignment explanation
Indices: 17848691--17848732 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
17848681 AAAAAATGAT
17848691 AATAAAATATAA
1 AATAAAATATAA
17848703 AATATAAA-ATAA
1 AATA-AAATATAA
17848715 AATAAAATATAA
1 AATAAAATATAA
17848727 AA-AAAA
1 AATAAAA
17848733 AGAGAGAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.25
12 18 0.64
13 3 0.11
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AATAAAATATAA
Found at i:17848733 original size:17 final size:17
Alignment explanation
Indices: 17848683--17848733 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
17848673 TCTAAAACAA
* *
17848683 AAAATGATAATAAAATAT
1 AAAAT-ATAAAAAAAAAT
*
17848701 AAAATATAAAATAAAAT
1 AAAATATAAAAAAAAAT
17848718 AAAATATAAAAAAAAA
1 AAAATATAAAAAAAAA
17848734 GAGAGAGGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 24 0.83
18 5 0.17
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (17 bp):
AAAATATAAAAAAAAAT
Found at i:17850330 original size:23 final size:22
Alignment explanation
Indices: 17850286--17850331 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
17850276 AAAACTGAAA
17850286 AATATAAAAAAAATAATGATAAT
1 AATATAAAAAAAATAA-GATAAT
17850309 AATAGTAAAAATAAATAA-ATAAT
1 AATA-TAAAAA-AAATAAGATAAT
17850332 CCAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 9 0.43
24 6 0.29
25 6 0.29
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (22 bp):
AATATAAAAAAAATAAGATAAT
Found at i:17862226 original size:59 final size:59
Alignment explanation
Indices: 17862015--17862551 Score: 670
Period size: 59 Copynumber: 9.0 Consensus size: 59
17862005 CATTTATGAA
* * * *
17862015 TTAAATAGAACCTGTTTTGAGATAGGTCGAGCCTAGATTAAGT-TTGAGAATTTTAATCT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAG-GAATTTTAATTT
* * * * * *
17862074 TGAAATCGAACTTGTTTGTGAGATAGGTC-ATGCCTAAATTAAGTTTAGGGATTTCAATTTTGT
1 TTAAATCGAACCTG-TTGTGAGATAGGTCGA-GCCTAGATTAAGTCTAGGAATTTTAA--TT-T
* *
17862137 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGCCTAGGAATTTCAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTT
*
17862196 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA-TT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTT
* * * *
17862254 TTAAATTGAACCTGTTGTGAGATAGGTCGAACCTAGATCAAGTTTAGGAATTTTAATTTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAA-TTT
*
17862314 TTAAATCGAACCTGTTTGTGAGAT-GGATCGAGCCTA-AGTCAAGTCTAGGAATTTTAATTT
1 TTAAATCGAACCTG-TTGTGAGATAGG-TCGAGCCTAGA-TTAAGTCTAGGAATTTTAATTT
* *
17862374 TTAAATCGAACATGTTGTGAGATAGGTTGAGCCTAGATTAAGTCTAGGAATTTTAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTT
* * * *
17862433 TTAAATTGAACCTGTTGTGAGATAGGTCAAGCCTAAATTAAGTTTAGGAATTTTAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAA--TT-T
* * * *
17862495 TTAAATCAAACCTATTATGAGATAGGTCGAGCCTAGATGAAGTCTAGGAATTTTAAT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAAT
17862552 CGAATTTGTT
Statistics
Matches: 420, Mismatches: 41, Indels: 33
0.85 0.08 0.07
Matches are distributed among these distances:
58 53 0.13
59 156 0.37
60 72 0.17
61 39 0.09
62 86 0.20
63 14 0.03
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (59 bp):
TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTT
Found at i:17862410 original size:237 final size:241
Alignment explanation
Indices: 17862015--17862551 Score: 723
Period size: 237 Copynumber: 2.2 Consensus size: 241
17862005 CATTTATGAA
* *
17862015 TTAAATAGAACCTGTTTTGAGATAGGTCGAGCCTAGATTAAGTTT-GAGAATTTTAA-TCTTGAA
1 TTAAATAGAACCTGTTATGAGATAGGTCGAGCCTAGATCAAGTTTAG-GAATTTTAATTCTTGAA
* * * *
17862078 ATCGAACTTGTTTGTGAGATAGGTCATGCCTAAATTAAGTTTAGGGATTTCAATTTTGTTTAAAT
65 ATCGAACCTGTTTGTGAGATAGGTCATGCCTAAATCAAGTCTAGGAATTTCAA-TTTGTTTAAAT
*
17862143 CGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGCCTAGGAATTTCAATTTTTAAATCGAACC
129 CGAACATGTTGTGAGATAGGTCGAGCCTAGATTAAGCCTAGGAATTTCAATTTTTAAATCGAACC
* *
17862208 TGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA-T-T
194 TGTTGTGAGATAGGTCAAGCCTAAATTAAGTCTAGGAATTTCAATTGT
* * * * *
17862254 TTAAATTGAACCTGTTGTGAGATAGGTCGAACCTAGATCAAGTTTAGGAATTTTAATTTTTTAAA
1 TTAAATAGAACCTGTTATGAGATAGGTCGAGCCTAGATCAAGTTTAGGAATTTTAATTCTTGAAA
* *
17862319 TCGAACCTGTTTGTGAGAT-GGATCGA-GCCTAAGTCAAGTCTAGGAATTTTAA-TT-TTTAAAT
66 TCGAACCTGTTTGTGAGATAGG-TC-ATGCCTAAATCAAGTCTAGGAATTTCAATTTGTTTAAAT
* * * *
17862380 CGAACATGTTGTGAGATAGGTTGAGCCTAGATTAAGTCTAGGAATTTTAATTTTTAAATTGAACC
129 CGAACATGTTGTGAGATAGGTCGAGCCTAGATTAAGCCTAGGAATTTCAATTTTTAAATCGAACC
* *
17862445 TGTTGTGAGATAGGTCAAGCCTAAATTAAGTTTAGGAATTTTAATTTTGT
194 TGTTGTGAGATAGGTCAAGCCTAAATTAAGTCTAGGAATTTCAA--TTGT
* * *
17862495 TTAAATCA-AACCTATTATGAGATAGGTCGAGCCTAGATGAAGTCTAGGAATTTTAAT
1 TTAAAT-AGAACCTGTTATGAGATAGGTCGAGCCTAGATCAAGTTTAGGAATTTTAAT
17862552 CGAATTTGTT
Statistics
Matches: 262, Mismatches: 27, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
237 107 0.41
238 2 0.01
239 52 0.20
240 49 0.19
241 52 0.20
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (241 bp):
TTAAATAGAACCTGTTATGAGATAGGTCGAGCCTAGATCAAGTTTAGGAATTTTAATTCTTGAAA
TCGAACCTGTTTGTGAGATAGGTCATGCCTAAATCAAGTCTAGGAATTTCAATTTGTTTAAATCG
AACATGTTGTGAGATAGGTCGAGCCTAGATTAAGCCTAGGAATTTCAATTTTTAAATCGAACCTG
TTGTGAGATAGGTCAAGCCTAAATTAAGTCTAGGAATTTCAATTGT
Found at i:17862589 original size:113 final size:114
Alignment explanation
Indices: 17862344--17862614 Score: 273
Period size: 121 Copynumber: 2.3 Consensus size: 114
17862334 AGATGGATCG
* * * * *
17862344 AGCCTAAGTCAAGTCTAGGAATTTTAA--TT-TTTAAATCGAACATGTTGTGAGATAGGTTGAGC
1 AGCCTAA-TCAAGTTTAGGAATTTTAATTTTGTTTAAATCAAACATATTATGAGATAGGTCGAGC
* * * *
17862406 CTAGATTAAGTCTAGGAATTTTAATTTTTAAATTGAACCTGTTGTGAGATAGGTCA
65 CTAGATGAAGTCTAGGAATTTTAA--TTCAAATT--A--TGTTCTAAGATAGGTCA
* *
17862462 AGCCTAAATTAAGTTTAGGAATTTTAATTTTGTTTAAATCAAACCTATTATGAGATAGGTCGAGC
1 AGCCT-AATCAAGTTTAGGAATTTTAATTTTGTTTAAATCAAACATATTATGAGATAGGTCGAGC
* * *
17862527 CTAGATGAAGTCTAGGAATTTTAA-TCGAATT-TGTTCTAATATGGGTCA
65 CTAGATGAAGTCTAGGAATTTTAATTCAAATTATGTTCTAAGATAGGTCA
* * *
17862575 AGCCTAGATCAAGTTTAGCAATTTCAATTTTGCTTAAATC
1 AGCCTA-ATCAAGTTTAGGAATTTTAATTTTGTTTAAATC
17862615 GAACTTTTTT
Statistics
Matches: 130, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
112 1 0.01
113 47 0.36
118 27 0.21
119 2 0.02
120 2 0.02
121 51 0.39
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (114 bp):
AGCCTAATCAAGTTTAGGAATTTTAATTTTGTTTAAATCAAACATATTATGAGATAGGTCGAGCC
TAGATGAAGTCTAGGAATTTTAATTCAAATTATGTTCTAAGATAGGTCA
Found at i:17862778 original size:18 final size:18
Alignment explanation
Indices: 17862755--17862814 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
17862745 TAGACACCTC
*
17862755 TAAAATAAAAA-ATGATAA
1 TAAAATAAAAATAT-AAAA
17862773 TAAAATATAAAATATAAAA
1 TAAAATA-AAAATATAAAA
17862792 TAAAATAAAATATATAAAA
1 TAAAATAAAA-ATATAAAA
17862811 -AAAA
1 TAAAA
17862815 AGAGGAATAG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
18 14 0.37
19 22 0.58
20 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
TAAAATAAAAATATAAAA
Found at i:17862813 original size:12 final size:12
Alignment explanation
Indices: 17862755--17862805 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
17862745 TAGACACCTC
*
17862755 TAAAATAAAAAA
1 TAAAATAAAATA
*
17862767 TGATAATAAAATA
1 T-AAAATAAAATA
17862780 TAAAATATAAA-A
1 TAAAATA-AAATA
17862792 TAAAATAAAATA
1 TAAAATAAAATA
17862804 TA
1 TA
17862806 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.09
12 17 0.52
13 13 0.39
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (12 bp):
TAAAATAAAATA
Found at i:17862813 original size:17 final size:17
Alignment explanation
Indices: 17862756--17862813 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
17862746 AGACACCTCT
*
17862756 AAAATAAAAAATGATAATA
1 AAAATAAAATAT-ATAA-A
17862775 AAATATAAAATATA-AAA
1 AAA-ATAAAATATATAAA
17862792 TAAAATAAAATATATAAA
1 -AAAATAAAATATATAAA
17862810 AAAA
1 AAAA
17862814 AAGAGGAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 15 0.43
18 8 0.23
19 4 0.11
20 8 0.23
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (17 bp):
AAAATAAAATATATAAA
Found at i:17863171 original size:24 final size:22
Alignment explanation
Indices: 17863139--17863182 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
17863129 TAGCCACAAG
17863139 AACAAAAGATCAAAAATCAAAACA
1 AACAAAAGA-CAAAAA-CAAAACA
*
17863163 AACACAAGACAAAAACAAAA
1 AACAAAAGACAAAAACAAAA
17863183 AAAGAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.73, C:0.18, G:0.05, T:0.05
Consensus pattern (22 bp):
AACAAAAGACAAAAACAAAACA
Found at i:17878539 original size:16 final size:17
Alignment explanation
Indices: 17878509--17878541 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
17878499 TATTGATTGG
*
17878509 CCAAATTTGGTCCAAAC
1 CCAAATTTGGCCCAAAC
17878526 CCAAA-TTGGCCCAAAC
1 CCAAATTTGGCCCAAAC
17878542 TTTTAGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.33, G:0.12, T:0.18
Consensus pattern (17 bp):
CCAAATTTGGCCCAAAC
Found at i:17886912 original size:16 final size:17
Alignment explanation
Indices: 17886888--17886922 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
17886878 GATTTTACAC
*
17886888 AATAGTTAAAT-ATATA
1 AATAATTAAATAATATA
17886904 AATAATTAAATAATATA
1 AATAATTAAATAATATA
17886921 AA
1 AA
17886923 AAAAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AATAATTAAATAATATA
Found at i:17887286 original size:2 final size:2
Alignment explanation
Indices: 17887281--17887360 Score: 96
Period size: 2 Copynumber: 42.0 Consensus size: 2
17887271 TTATATCAAT
* * *
17887281 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA NA AA TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
17887321 TA T- TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17887361 CACTAATTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
1 4 0.06
2 65 0.94
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17887505 original size:4 final size:4
Alignment explanation
Indices: 17887496--17887522 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
17887486 CATAATACTA
17887496 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
17887523 ATTACCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:17887963 original size:67 final size:67
Alignment explanation
Indices: 17887855--17887986 Score: 239
Period size: 67 Copynumber: 2.0 Consensus size: 67
17887845 TCTCCCTTAA
17887855 TTGACTTAACCTATAAAATTTTTAATTTATTTAATGAGTTAAGGTTTGAGGAGAAAGATCCAAAT
1 TTGACTTAACCTATAAAATTTTTAATTTATTTAATGAGTTAAGGTTTGAGGAGAAAGATCCAAAT
17887920 CT
66 CT
*
17887922 TTGACTTAACCGT-TAAAATTTTTAATTTATTTAATGAGTTAAGGTTTGAGGAGAAAGATTCAAA
1 TTGACTTAACC-TATAAAATTTTTAATTTATTTAATGAGTTAAGGTTTGAGGAGAAAGATCCAAA
17887986 T
65 T
17887987 TTTAACGAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
67 62 0.98
68 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (67 bp):
TTGACTTAACCTATAAAATTTTTAATTTATTTAATGAGTTAAGGTTTGAGGAGAAAGATCCAAAT
CT
Found at i:17897720 original size:62 final size:61
Alignment explanation
Indices: 17897644--17897768 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 61
17897634 GAAAATTCCC
* *
17897644 ATTATTTTTCTAGGCTTATAATTCATCATTATTCATTATAATTCCTCAAATAAACATCAAG
1 ATTATTTTTCTAGGCTCATAATTCATCATTATTCATCATAATTCCTCAAATAAACATCAAG
17897705 NATTATTTTTCTAGGCTCATAATTCATCATTATTCATCATAATTCCTCAAATAAACATCAAG
1 -ATTATTTTTCTAGGCTCATAATTCATCATTATTCATCATAATTCCTCAAATAAACATCAAG
17897767 AT
1 AT
17897769 CAGCAGCCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 2 0.03
62 59 0.97
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (61 bp):
ATTATTTTTCTAGGCTCATAATTCATCATTATTCATCATAATTCCTCAAATAAACATCAAG
Found at i:17906423 original size:2 final size:2
Alignment explanation
Indices: 17906416--17906446 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17906406 GCGAGCCTTG
*
17906416 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17906447 GTCTTCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17911101 original size:25 final size:23
Alignment explanation
Indices: 17911060--17911107 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 23
17911050 AAATAATAAG
17911060 TATAAAAAAGAAAAAAATTAAAT
1 TATAAAAAAGAAAAAAATTAAAT
17911083 TATAATAAAAGAAATAAAATTAAAT
1 TATAA-AAAAGAAA-AAAATTAAAT
17911108 ATGTAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.22
24 8 0.35
25 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (23 bp):
TATAAAAAAGAAAAAAATTAAAT
Found at i:17911102 original size:20 final size:18
Alignment explanation
Indices: 17911070--17911108 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
17911060 TATAAAAAAG
*
17911070 AAAAAAATTAAATTATAAT
1 AAAAAAATAAAATTA-AAT
17911089 AAAAGAAATAAAATTAAAT
1 AAAA-AAATAAAATTAAAT
17911108 A
1 A
17911109 TGTAATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAAAATAAAATTAAAT
Found at i:17912388 original size:115 final size:115
Alignment explanation
Indices: 17912179--17912411 Score: 358
Period size: 115 Copynumber: 2.0 Consensus size: 115
17912169 ATGATGTTTT
* *
17912179 TTTTCAATTTGTCTCATAACCATTGGATGTCATTTTACTAAGAGATATAGCCATTCACATTAAAA
1 TTTTCAATTTGTCTCATAAACATTGGATGTCATTTTACCAAGAGATATAGCCATTCACATTAAAA
*
17912244 ACCTACCTACAATCCAATAGCAACACTATATCACTTTATGTGACATAACC
66 ACCTACCTACAATCCAATAGCAACACTATATCACTTTATGTAACATAACC
*
17912294 TTTTCAATTTGTCTCATAAACATTGGATGTGATTTTACCAAGAGATATAGCCATTCACATTAAAA
1 TTTTCAATTTGTCTCATAAACATTGGATGTCATTTTACCAAGAGATATAGCCATTCACATTAAAA
** * ** * * *
17912359 ATGTGCCTGTAATCTAATAGCCACTCTATATCACTTTATGTAACATAACC
66 ACCTACCTACAATCCAATAGCAACACTATATCACTTTATGTAACATAACC
17912409 TTT
1 TTT
17912412 GAGTTAAGAT
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
115 106 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (115 bp):
TTTTCAATTTGTCTCATAAACATTGGATGTCATTTTACCAAGAGATATAGCCATTCACATTAAAA
ACCTACCTACAATCCAATAGCAACACTATATCACTTTATGTAACATAACC
Found at i:17919438 original size:20 final size:22
Alignment explanation
Indices: 17919401--17919440 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
17919391 TATTTAACTA
17919401 TTTATATTTTATGTATTATAGT
1 TTTATATTTTATGTATTATAGT
17919423 TTTATA-TTTA-GTATTATA
1 TTTATATTTTATGTATTATA
17919441 AGTTCGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (22 bp):
TTTATATTTTATGTATTATAGT
Found at i:17920067 original size:20 final size:20
Alignment explanation
Indices: 17920031--17920084 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
17920021 GAGGAGCAAA
* * *
17920031 AAAAAAAAGAAAGAAAGTGTG
1 AAAAAAAGGAAA-AAAGAGAG
17920052 AAAAAAAGGAAAAAAGAGAG
1 AAAAAAAGGAAAAAAGAGAG
*
17920072 AAAAGAAGGAAAA
1 AAAAAAAGGAAAA
17920085 TGAACAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (20 bp):
AAAAAAAGGAAAAAAGAGAG
Found at i:17925462 original size:15 final size:18
Alignment explanation
Indices: 17925430--17925464 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17925420 ATTCAGCCCT
17925430 ACTCATCATAAGATAATA
1 ACTCATCATAAGATAATA
*
17925448 ACTCATCATAAAATAAT
1 ACTCATCATAAGATAAT
17925465 TTTTTATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.29
Consensus pattern (18 bp):
ACTCATCATAAGATAATA
Found at i:17928067 original size:59 final size:59
Alignment explanation
Indices: 17928001--17928118 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
17927991 AATTGTCTGA
* *
17928001 ACTTTGATTGAGGCAATGGTGATAAAATGTTGAAAGAATAAAATTGGGTGAATGTGGTT
1 ACTTTGATTGAGGCAATGGTGATAAAATGTTGAAAGAATAAAATGGGGTGAACGTGGTT
17928060 ACTTTGATTGAGGCAATGGTGATAAAATGTTGAAAGAATAAAATGGGGTGAACGTGGTT
1 ACTTTGATTGAGGCAATGGTGATAAAATGTTGAAAGAATAAAATGGGGTGAACGTGGTT
17928119 TGGATGGGAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.36, C:0.04, G:0.30, T:0.31
Consensus pattern (59 bp):
ACTTTGATTGAGGCAATGGTGATAAAATGTTGAAAGAATAAAATGGGGTGAACGTGGTT
Found at i:17929600 original size:34 final size:34
Alignment explanation
Indices: 17929560--17929663 Score: 111
Period size: 34 Copynumber: 3.0 Consensus size: 34
17929550 TTTGCTATCA
*
17929560 GATTGTGAAGGACAAAGGGAGCTTTGTGCTGTC-
1 GATTGTGAAGGACAAAGGGAGCTTTGTGCTGCCG
* * ** * *
17929593 GATTTGTGCAGGAAAAATAGAGGTTGTTTGCTGCCG
1 GA-TTGTGAAGGACAAAGGGAGCTT-TGTGCTGCCG
*
17929629 GATTGTGAAGGACAAAGGGGGCTTTGTGCTGCCG
1 GATTGTGAAGGACAAAGGGAGCTTTGTGCTGCCG
17929663 G
1 G
17929664 TTTTTTAGGG
Statistics
Matches: 54, Mismatches: 14, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
33 2 0.04
34 27 0.50
35 23 0.43
36 2 0.04
ACGTcount: A:0.23, C:0.12, G:0.38, T:0.27
Consensus pattern (34 bp):
GATTGTGAAGGACAAAGGGAGCTTTGTGCTGCCG
Found at i:17929625 original size:35 final size:35
Alignment explanation
Indices: 17929506--17929640 Score: 87
Period size: 35 Copynumber: 3.9 Consensus size: 35
17929496 GGTGAGAAAG
* * * *
17929506 AGAGGTTGTGTTGCTGTTGGTTTGTGTAGGAAAAGT
1 AGAGGTTGT-TTGCTGTCGATTTGTGAAGGAAAAAT
* * * * * *
17929542 GGAGGCTATTTGCTATCAGA-TTGTGAAGGACAAAG
1 AGAGGTTGTTTGCTGTC-GATTTGTGAAGGAAAAAT
* * * *
17929577 GGAGCTT-TGTGCTGTCGATTTGTGCAGGAAAAAT
1 AGAGGTTGTTTGCTGTCGATTTGTGAAGGAAAAAT
*
17929611 AGAGGTTGTTTGCTGCCGGA-TTGTGAAGGA
1 AGAGGTTGTTTGCTGTC-GATTTGTGAAGGA
17929641 CAAAGGGGGC
Statistics
Matches: 73, Mismatches: 22, Indels: 9
0.70 0.21 0.09
Matches are distributed among these distances:
33 2 0.03
34 24 0.33
35 38 0.52
36 9 0.12
ACGTcount: A:0.24, C:0.09, G:0.36, T:0.32
Consensus pattern (35 bp):
AGAGGTTGTTTGCTGTCGATTTGTGAAGGAAAAAT
Found at i:17929790 original size:13 final size:13
Alignment explanation
Indices: 17929772--17929822 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
17929762 AAAAGGAGAG
*
17929772 AGAAAGAAGGAAA
1 AGAAAGAAGAAAA
17929785 AGAAAG--GAAAA
1 AGAAAGAAGAAAA
*
17929796 AGAGAGAAGAAAA
1 AGAAAGAAGAAAA
* *
17929809 AAAAAGAATAAAA
1 AGAAAGAAGAAAA
17929822 A
1 A
17929823 TAAAATGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
11 9 0.29
13 22 0.71
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (13 bp):
AGAAAGAAGAAAA
Found at i:17930566 original size:19 final size:19
Alignment explanation
Indices: 17930538--17930575 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17930528 CCATTTAACT
* *
17930538 TATTGGAGTATGATTTGAG
1 TATTGAAGTATAATTTGAG
17930557 TATTGAAGTATAATTTGAG
1 TATTGAAGTATAATTTGAG
17930576 GGTTTGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (19 bp):
TATTGAAGTATAATTTGAG
Found at i:17937039 original size:13 final size:12
Alignment explanation
Indices: 17937004--17937041 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
17936994 AGTAAAAGTC
17937004 AATTA-AAAGAG
1 AATTAGAAAGAG
17937015 AATTAGAAAGAG
1 AATTAGAAAGAG
*
17937027 AATTTAGATAGAG
1 AA-TTAGAAAGAG
17937040 AA
1 AA
17937042 GCTCCAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 5 0.21
12 8 0.33
13 11 0.46
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (12 bp):
AATTAGAAAGAG
Found at i:17937624 original size:35 final size:36
Alignment explanation
Indices: 17937558--17937626 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
17937548 CTTTACTTAT
* *
17937558 TCTAATTGTTCTACGTTGAAGTAGCGTTTCACTTGA
1 TCTAATTGTTCTACGATGAAGTAGCGCTTCACTTGA
17937594 TCTAATTGTTCTAC-ATGAAGTAG-GACTTCACTT
1 TCTAATTGTTCTACGATGAAGTAGCG-CTTCACTT
17937627 ATTTTAGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 1 0.03
35 15 0.50
36 14 0.47
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (36 bp):
TCTAATTGTTCTACGATGAAGTAGCGCTTCACTTGA
Found at i:17939201 original size:12 final size:12
Alignment explanation
Indices: 17939173--17939219 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
17939163 AAATAAATCA
17939173 ATAATACAAAAAT
1 ATAATA-AAAAAT
17939186 ATATATTAAAAAAT
1 ATA-A-TAAAAAAT
*
17939200 ATAATAAAAATT
1 ATAATAAAAAAT
17939212 ATAATAAA
1 ATAATAAA
17939220 GTTTGATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 15 0.48
13 4 0.13
14 10 0.32
15 2 0.06
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAATAAAAAAT
Found at i:17946587 original size:13 final size:13
Alignment explanation
Indices: 17946569--17946593 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17946559 TTTCAGAAAA
17946569 TTTATAAAATCAT
1 TTTATAAAATCAT
17946582 TTTATAAAATCA
1 TTTATAAAATCA
17946594 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:17959280 original size:23 final size:23
Alignment explanation
Indices: 17959253--17959297 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
17959243 GTACACAGAA
*
17959253 AGAAAAAATTAAGAAGAGAAAAT
1 AGAAAAAAATAAGAAGAGAAAAT
* *
17959276 AGAAAAAAATAGGGAGAGAAAA
1 AGAAAAAAATAAGAAGAGAAAA
17959298 CAATTAGGGA
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:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (23 bp):
AGAAAAAAATAAGAAGAGAAAAT
Found at i:17966622 original size:9 final size:9
Alignment explanation
Indices: 17966608--17966642 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
17966598 AATGAACCTA
*
17966608 TTAATTTTT
1 TTAATTATT
17966617 TTAATTATT
1 TTAATTATT
*
17966626 TTACTTATT
1 TTAATTATT
17966635 TTAATTAT
1 TTAATTAT
17966643 AACACCACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (9 bp):
TTAATTATT
Found at i:17974274 original size:20 final size:19
Alignment explanation
Indices: 17974222--17974264 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
17974212 AATTATATTG
*
17974222 AAAATATATA-AAAATTAA
1 AAAATATATATAAAAGTAA
17974240 AAAATATATATAAAAGTAA
1 AAAATATATATAAAAGTAA
17974259 AAAATA
1 AAAATA
17974265 ATTAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAATATATATAAAAGTAA
Found at i:17976959 original size:30 final size:31
Alignment explanation
Indices: 17976919--17976981 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
17976909 CTATTTTTAA
*
17976919 TTGTAACTTATT-TGTCTAGATTATGTAAGC
1 TTGTAACTTATTATATCTAGATTATGTAAGC
*
17976949 TTGTAGCTTATTATATCTAGATTATGTAAGC
1 TTGTAACTTATTATATCTAGATTATGTAAGC
17976980 TT
1 TT
17976982 ATCTTATCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.48
Consensus pattern (31 bp):
TTGTAACTTATTATATCTAGATTATGTAAGC
Found at i:17978142 original size:35 final size:35
Alignment explanation
Indices: 17978103--17978212 Score: 139
Period size: 35 Copynumber: 3.1 Consensus size: 35
17978093 ATTCCATACG
* * *
17978103 AAATAATACTCCACTTATTCTAATTATTCTACATA
1 AAATAACACTTCACTTATTCTAATTATTCTACGTA
* * **
17978138 AAATAGCACTTCACGTATTCTAATTATTCTGTGTA
1 AAATAACACTTCACTTATTCTAATTATTCTACGTA
* *
17978173 AAATAACACTTCATTTATTTTAATTATTCTACGTA
1 AAATAACACTTCACTTATTCTAATTATTCTACGTA
17978208 AAATA
1 AAATA
17978213 GTACTTTAGT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (35 bp):
AAATAACACTTCACTTATTCTAATTATTCTACGTA
Found at i:17978166 original size:70 final size:70
Alignment explanation
Indices: 17978088--17978218 Score: 163
Period size: 70 Copynumber: 1.9 Consensus size: 70
17978078 GTACTTGTAT
* *
17978088 TAATTATTCCATACGAAATAATACTCCACTTATTCTAATTATTCTACATAAAATAGCACTTCACG
1 TAATTATTCCATACAAAATAACACTCCACTTATTCTAATTATTCTACATAAAATAGCACTTCACG
17978153 TATTC
66 TATTC
** ** * * * * *
17978158 TAATTATTCTGTGTAAAATAACACTTCATTTATTTTAATTATTCTACGTAAAATAGTACTT
1 TAATTATTCCATACAAAATAACACTCCACTTATTCTAATTATTCTACATAAAATAGCACTT
17978219 TAGTGATTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
70 50 1.00
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (70 bp):
TAATTATTCCATACAAAATAACACTCCACTTATTCTAATTATTCTACATAAAATAGCACTTCACG
TATTC
Found at i:17978228 original size:35 final size:34
Alignment explanation
Indices: 17978118--17978237 Score: 123
Period size: 35 Copynumber: 3.4 Consensus size: 34
17978108 ATACTCCACT
* *
17978118 TATTCTAATTATTCTACATAAAATAGCACTTCACG
1 TATTTTAATTATTCTACGTAAAATAGCACTTCA-G
* ** * *
17978153 TATTCTAATTATTCTGTGTAAAATAACACTTCATT
1 TATTTTAATTATTCTACGTAAAATAGCACTTCA-G
* *
17978188 TATTTTAATTATTCTACGTAAAATAGTACTTTAG
1 TATTTTAATTATTCTACGTAAAATAGCACTTCAG
*
17978222 TGATTTTGATTATTCT
1 T-ATTTTAATTATTCT
17978238 TTATATAATA
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
34 1 0.01
35 69 0.99
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.46
Consensus pattern (34 bp):
TATTTTAATTATTCTACGTAAAATAGCACTTCAG
Found at i:17982371 original size:23 final size:25
Alignment explanation
Indices: 17982340--17982389 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
17982330 ACGTTGATTG
*
17982340 ATTTCAACAA-ACACATCTCTTAAA
1 ATTTCAACAAGACACATCTATTAAA
*
17982364 ATTT-AACAAGACACGTCTATTAAA
1 ATTTCAACAAGACACATCTATTAAA
17982388 AT
1 AT
17982390 AAATTAGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (25 bp):
ATTTCAACAAGACACATCTATTAAA
Found at i:17983384 original size:11 final size:12
Alignment explanation
Indices: 17983347--17983384 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
17983337 GACAAACCTT
17983347 TAAGAAAAATGA
1 TAAGAAAAATGA
17983359 TAAGAAAAATGA
1 TAAGAAAAATGA
17983371 TAAGAAAAAT-A
1 TAAGAAAAATGA
17983382 TAA
1 TAA
17983385 ATTGTTTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.18
Consensus pattern (12 bp):
TAAGAAAAATGA
Found at i:17986767 original size:24 final size:24
Alignment explanation
Indices: 17986735--17986781 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
17986725 TTTTTATGTT
17986735 AAATAGCCTCATTCTAGAATATTC
1 AAATAGCCTCATTCTAGAATATTC
*
17986759 AAATAGCCTCGTTCTAGAATATT
1 AAATAGCCTCATTCTAGAATATT
17986782 TAGTATGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (24 bp):
AAATAGCCTCATTCTAGAATATTC
Found at i:17987260 original size:17 final size:17
Alignment explanation
Indices: 17987223--17987270 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
17987213 CAGATATATT
*
17987223 TATTCAAATTAAAGTGAC
1 TATTTAAATT-AAGTGAC
*
17987241 TATTTAAATTAAGTGTC
1 TATTTAAATTAAGTGAC
*
17987258 TATTTACATTAAG
1 TATTTAAATTAAG
17987271 ACATGACTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (17 bp):
TATTTAAATTAAGTGAC
Found at i:17990851 original size:30 final size:30
Alignment explanation
Indices: 17990811--17990874 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
17990801 ATCAAACCAG
17990811 TATACTTTTATTTTGAACCAAATAAGCCAT
1 TATACTTTTATTTTGAACCAAATAAGCCAT
* * *
17990841 TATATTTTTATTTTGAATCAAATAAGCCTT
1 TATACTTTTATTTTGAACCAAATAAGCCAT
17990871 TATA
1 TATA
17990875 ACTAATGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (30 bp):
TATACTTTTATTTTGAACCAAATAAGCCAT
Found at i:17997054 original size:16 final size:16
Alignment explanation
Indices: 17997035--17997065 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17997025 CTGTTAATAC
*
17997035 TTTATTATGTTGGTAA
1 TTTATTATGCTGGTAA
17997051 TTTATTATGCTGGTA
1 TTTATTATGCTGGTA
17997066 TTAATCTAAT
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:0.23, C:0.03, G:0.19, T:0.55
Consensus pattern (16 bp):
TTTATTATGCTGGTAA
Found at i:18004485 original size:2 final size:2
Alignment explanation
Indices: 18004478--18004543 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
18004468 ACCCTAATGT
18004478 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
18004520 TC TC TC TG TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC
18004544 ATTTTTTTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
TC
Found at i:18005772 original size:27 final size:27
Alignment explanation
Indices: 18005719--18005773 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
18005709 CAAAATCACG
* *
18005719 TGTTGAAAAAAATATTGTTGCACGCCA
1 TGTTGAAAAAAATATTATTACACGCCA
*
18005746 TGTTGAAAAAAATATTATTACATGCCA
1 TGTTGAAAAAAATATTATTACACGCCA
18005773 T
1 T
18005774 TTTTTTTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (27 bp):
TGTTGAAAAAAATATTATTACACGCCA
Found at i:18006222 original size:29 final size:29
Alignment explanation
Indices: 18006185--18006252 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
18006175 TAAAAAATGT
*
18006185 TGTTGTTACACG-TCATATTCAAAAAAAAA
1 TGTTATTACACGCT-ATATTCAAAAAAAAA
* * *
18006214 TTTTATTACACGCTATTTTGAAAAAAAAA
1 TGTTATTACACGCTATATTCAAAAAAAAA
*
18006243 TGTTGTTACA
1 TGTTATTACA
18006253 TGTAGACATG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (29 bp):
TGTTATTACACGCTATATTCAAAAAAAAA
Found at i:18006239 original size:141 final size:139
Alignment explanation
Indices: 18005979--18006252 Score: 313
Period size: 141 Copynumber: 1.9 Consensus size: 139
18005969 AAGGTGTTTA
*
18005979 ACTCTAAGAGTTTATGTCTAATAAAATACAAAGATAGAGACCAAGTTACACGCCATGTTAAAAAA
1 ACTCTAAGAGTTTATGTCTAATAAAATACAAAG--AGAGA-CAAGTTACACACCATGTTAAAAAA
* * * *
18006044 TATTGTTACTACATGTCATGTTAAAAAAAATGTTGGTGCACACCATGTTGAAAAAAAA-GTTGTT
63 TATTGTTACTACACGTCATATTAAAAAAAATGTTAGTACACACCATGTTGAAAAAAAATGTTGTT
18006108 ACACGTTATTTG
128 ACACGTTATTTG
*
18006120 ACTCTAAGAGTTTATGT-TATAGTAAAATACAAAG-GAG-CAAGTTACACACCATATTTAAAAAA
1 ACTCTAAGAGTTTATGTCTA-A-TAAAATACAAAGAGAGACAAGTTACACACCAT-GTTAAAAAA
* ** * * * * *
18006182 TGTTGTTGTTACACGTCATATTCAAAAAAAAATTTTATTACACGCTATTTTGAAAAAAAAATGTT
63 TATTGTTACTACACGTCATATT--AAAAAAAATGTTAGTACACACCATGTTG-AAAAAAAATGTT
18006247 GTTACA
125 GTTACA
18006253 TGTAGACATG
Statistics
Matches: 112, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
137 14 0.12
138 25 0.22
139 3 0.03
140 23 0.21
141 26 0.23
142 21 0.19
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.32
Consensus pattern (139 bp):
ACTCTAAGAGTTTATGTCTAATAAAATACAAAGAGAGACAAGTTACACACCATGTTAAAAAATAT
TGTTACTACACGTCATATTAAAAAAAATGTTAGTACACACCATGTTGAAAAAAAATGTTGTTACA
CGTTATTTG
Found at i:18007146 original size:116 final size:116
Alignment explanation
Indices: 18006942--18007152 Score: 305
Period size: 116 Copynumber: 1.8 Consensus size: 116
18006932 AAAACTCAAC
* *
18006942 ACCAATAAACCCAAGAACATGTTGATACTCACCATACCCTGCTCTTTGGTTTGTAAATCGACGAT
1 ACCAATAAACCCAAGAACATGTTGATACCCACCATACCCTGCTCTTTGGTCTGTAAATCGACGAT
18007007 GATATGACAAGATGATGAGAGATAGACAGAGAAAAAGTTTTGTGAATGTAA
66 GATATGACAAGATGATGAGAGATAGACAGAGAAAAAGTTTTGTGAATGTAA
* ** **** * *
18007058 ACCAATAAACCCAAGAACATGTTGTTACCCGTCATGTTTTGCTCTTTGGTCTGTAGATTGACGAT
1 ACCAATAAACCCAAGAACATGTTGATACCCACCATACCCTGCTCTTTGGTCTGTAAATCGACGAT
* *
18007123 GATATGGCAAGATGGTGAGAGATAGACAGA
66 GATATGACAAGATGATGAGAGATAGACAGA
18007153 AAGAAATAGT
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
116 82 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (116 bp):
ACCAATAAACCCAAGAACATGTTGATACCCACCATACCCTGCTCTTTGGTCTGTAAATCGACGAT
GATATGACAAGATGATGAGAGATAGACAGAGAAAAAGTTTTGTGAATGTAA
Found at i:18013812 original size:85 final size:85
Alignment explanation
Indices: 18013653--18013823 Score: 204
Period size: 85 Copynumber: 2.0 Consensus size: 85
18013643 AGTGGGCTTC
* * * *
18013653 CAGAGTTAACCACGTGGAGGGCAGAGAGAGTGAAACGGAAAAAATGCTGAAGCAAAGAGAGAGAA
1 CAGAGTTAACCACGTGAAGGGCAAAGAGAGAGAAACGGAAAAAATGCTGAAGCAAAGAGAGACAA
*
18013718 AGAGAGGGGTGCAAAGGGGT
66 AGAGAGGGGTGCAAAGAGGT
* * * **
18013738 CAGAGTTAACCGCGTGAAGGGCAAATAGAGAGAAA-GAGAAAAAGATGTTGAAGCAAA-TTAG-C
1 CAGAGTTAACCACGTGAAGGGCAAAGAGAGAGAAACG-GAAAAA-ATGCTGAAGCAAAGAGAGAC
18013800 AAAGAGAGGGGGTGCAAAGAGGT
64 AAAGAGA-GGGGTGCAAAGAGGT
18013823 C
1 C
18013824 CCGTGTGTTG
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 8 0.11
85 53 0.73
86 12 0.16
ACGTcount: A:0.42, C:0.11, G:0.36, T:0.11
Consensus pattern (85 bp):
CAGAGTTAACCACGTGAAGGGCAAAGAGAGAGAAACGGAAAAAATGCTGAAGCAAAGAGAGACAA
AGAGAGGGGTGCAAAGAGGT
Done.