Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 62 of 153
Found at i:19991995 original size:21 final size:21
Alignment explanation
Indices: 19991975--19992020 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
19991965 TATTCAAATA
19991975 ATTATC-GAACATATTATAAT
1 ATTATCAGAACATATTATAAT
* * *
19991995 ATAATCATAATATATTATAAT
1 ATTATCAGAACATATTATAAT
19992016 ATTAT
1 ATTAT
19992021 AATATTATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTATCAGAACATATTATAAT
Found at i:19992019 original size:8 final size:8
Alignment explanation
Indices: 19991985--19992030 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
19991975 ATTATCGAAC
19991985 ATATTATA
1 ATATTATA
* *
19991993 ATATAATC
1 ATATTATA
19992001 ATA--AT-
1 ATATTATA
19992006 ATATTATA
1 ATATTATA
19992014 ATATTATA
1 ATATTATA
19992022 ATATTATA
1 ATATTATA
19992030 A
1 A
19992031 CTGAAGCAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 2 0.06
8 26 0.79
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (8 bp):
ATATTATA
Found at i:19992029 original size:21 final size:21
Alignment explanation
Indices: 19991985--19992029 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19991975 ATTATCGAAC
*
19991985 ATATTATAATATAATCATAAT
1 ATATTATAATATAATAATAAT
* *
19992006 ATATTATAATATTATAATATT
1 ATATTATAATATAATAATAAT
19992027 ATA
1 ATA
19992030 ACTGAAGCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTATAATATAATAATAAT
Found at i:19997886 original size:14 final size:14
Alignment explanation
Indices: 19997869--19997905 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
19997859 AATTTTATTG
19997869 AATTGAATTTAGAA
1 AATTGAATTTAGAA
*
19997883 AATTAAATTTAGAA
1 AATTGAATTTAGAA
19997897 AATTGAATT
1 AATTGAATT
19997906 GAATGAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (14 bp):
AATTGAATTTAGAA
Found at i:19998359 original size:38 final size:39
Alignment explanation
Indices: 19998257--19998359 Score: 102
Period size: 38 Copynumber: 2.6 Consensus size: 39
19998247 ACTTCAACCT
**
19998257 CAATGAGACACTGGGTGTCATACTGTTACTTCGGATAGATT
1 CAATGAGACACTGGGTGTCA-ACT-TTACTTCGGATAGAGC
* ** * *
19998298 CGATGAGGTACTGGGTG-CCACTTTACTTCGGCTAG-GC
1 CAATGAGACACTGGGTGTCAACTTTACTTCGGATAGAGC
*
19998335 CAATGAGACACTGTGTGTCAACTTT
1 CAATGAGACACTGGGTGTCAACTTT
19998360 GTTTCGAACT
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
37 13 0.27
38 18 0.37
39 3 0.06
40 1 0.02
41 14 0.29
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (39 bp):
CAATGAGACACTGGGTGTCAACTTTACTTCGGATAGAGC
Found at i:20000540 original size:43 final size:43
Alignment explanation
Indices: 20000428--20000550 Score: 212
Period size: 42 Copynumber: 2.9 Consensus size: 43
20000418 CCAGATAACG
*
20000428 ATGCCAATGTCCCAGACATGGTCTTACACGTATTTACAATACA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTATTCACAATACA
20000471 ATGCCAAT-TCCCAGACATGGTCTTACACGTATTCACAATACA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTATTCACAATACA
* *
20000513 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTATTCACA
20000551 TCTCGGTAAC
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
42 41 0.54
43 35 0.46
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTATTCACAATACA
Found at i:20004554 original size:170 final size:170
Alignment explanation
Indices: 20004255--20004588 Score: 512
Period size: 170 Copynumber: 2.0 Consensus size: 170
20004245 GATTTAGTCT
*
20004255 TTTTTCTCAAATTAAGCTATTAAACGATAAAATTAGCTCACGAAATTTTCACACATATATATTCA
1 TTTTTCTCAAATTAAGCTATTAAACGATAAAATTAACTCACGAAATTTTCACACATATATATTCA
20004320 CATGCTGTAAACACCAAAAATAATATAAAATAAATTTTCAACCTCAGATTTATGGTCCCGAAACC
66 CATGCTGTAAACACCAAAAATAATATAAAATAAATTTTCAACCTCAGATTTATGGTCCCGAAACC
* *
20004385 ACTGTTCCGATTTAACTAAAACCGGACTGTTACATAATCC
131 ACAGTTCCGATTTAACTAAAACCGGACTATTACATAATCC
*
20004425 TTTTTCTCAAATTGAGCTATTAAACGATAAAATTAACTCACGAAATTTTCACACATATATATTCA
1 TTTTTCTCAAATTAAGCTATTAAACGATAAAATTAACTCACGAAATTTTCACACATATATATTCA
* * * * **
20004490 TATGCTGTAAACACCAGAAATAATATTAAAAT-AATTTT-ATGATCTCA-ATTTTTGGTTTCGAA
66 CATGCTGTAAACACCAAAAATAATA-TAAAATAAATTTTCA--ACCTCAGATTTATGGTCCCGAA
* *
20004552 ACCACAGTTCCGATTTAGCTAAAACCGGGCTATTACA
128 ACCACAGTTCCGATTTAACTAAAACCGGACTATTACA
20004589 CGTGTGGAAT
Statistics
Matches: 149, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
169 1 0.01
170 137 0.92
171 11 0.07
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.33
Consensus pattern (170 bp):
TTTTTCTCAAATTAAGCTATTAAACGATAAAATTAACTCACGAAATTTTCACACATATATATTCA
CATGCTGTAAACACCAAAAATAATATAAAATAAATTTTCAACCTCAGATTTATGGTCCCGAAACC
ACAGTTCCGATTTAACTAAAACCGGACTATTACATAATCC
Found at i:20008059 original size:31 final size:31
Alignment explanation
Indices: 20008024--20008087 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
20008014 TAATCCTTAA
*
20008024 AACATGTTTTTCCCTGATCTTAAACTAAATT
1 AACATGTTTTTCCCCGATCTTAAACTAAATT
*
20008055 AACATGTTTTTCCCCGATCTTGAACTAAATT
1 AACATGTTTTTCCCCGATCTTAAACTAAATT
20008086 AA
1 AA
20008088 TAATTTCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (31 bp):
AACATGTTTTTCCCCGATCTTAAACTAAATT
Found at i:20009745 original size:30 final size:31
Alignment explanation
Indices: 20009693--20009751 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
20009683 CACCCTTAAA
* *
20009693 ATATTTACACTATTAGTCCTTCAACTTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTTC
20009724 ATATTTACACT-TTAATCCTTCAAATTTT
1 ATATTTACACTATTAATCCTTCAAATTTT
20009752 GAGTATTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.49
Consensus pattern (31 bp):
ATATTTACACTATTAATCCTTCAAATTTTTC
Found at i:20019585 original size:38 final size:38
Alignment explanation
Indices: 20019538--20019611 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
20019528 CAAGATTGGT
* *
20019538 ACATTTTGTTCATATGGGAACCA-TTTGTTGATAAGAGA
1 ACATCTTGTTCACATGGGAA-CATTTTGTTGATAAGAGA
* *
20019576 ACATCTTGTTTACATTGGAACATTTTGTTGATAAGA
1 ACATCTTGTTCACATGGGAACATTTTGTTGATAAGA
20019612 TGCATTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.06
38 29 0.94
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (38 bp):
ACATCTTGTTCACATGGGAACATTTTGTTGATAAGAGA
Found at i:20020236 original size:4 final size:4
Alignment explanation
Indices: 20020227--20020269 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
20020217 TAAACAAATT
* **
20020227 TAAA TAAA TAAA TAAA TTAA -AAA TATG TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
20020270 ATTAAAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 2 0.06
4 30 0.94
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:20020246 original size:27 final size:27
Alignment explanation
Indices: 20020209--20020279 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
20020199 AAGAAACCAT
*
20020209 AATAAACTTAAACAA-ATTTAAATAAATA
1 AATAAA-TTAAA-AATATGTAAATAAATA
20020237 AATAAATTAAAAATATGTAAATAAATA
1 AATAAATTAAAAATATGTAAATAAATA
20020264 AATAAAATTAAAAATA
1 AAT-AAATTAAAAATA
20020280 CAACTTCCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
26 2 0.05
27 20 0.50
28 18 0.45
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (27 bp):
AATAAATTAAAAATATGTAAATAAATA
Found at i:20020634 original size:14 final size:15
Alignment explanation
Indices: 20020592--20020634 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
20020582 AAATATTATT
*
20020592 AAAT-ATCAAATAATA
1 AAATAATCAAA-ATTA
20020607 AAATAATCAAAATTA
1 AAATAATCAAAATTA
20020622 AAATAAT-AAAATT
1 AAATAATCAAAATT
20020635 GGATATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 6 0.23
15 14 0.54
16 6 0.23
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAATCAAAATTA
Found at i:20021072 original size:2 final size:2
Alignment explanation
Indices: 20021065--20021089 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20021055 AATAAAAACT
20021065 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20021090 GTAAATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20021902 original size:30 final size:30
Alignment explanation
Indices: 20021868--20021941 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
20021858 ATTTTATATA
20021868 TTTATAATTTTTGAAAGA-TTAAAATA-AATT
1 TTTATAATTTTT-AAAGAGTTAAAATATAA-T
*
20021898 TTTATTATTTTTAAAGAGTTAAAATATAAT
1 TTTATAATTTTTAAAGAGTTAAAATATAAT
*
20021928 TTTATAATTATTAA
1 TTTATAATTTTTAA
20021942 TTTAAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 5 0.13
30 32 0.82
31 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (30 bp):
TTTATAATTTTTAAAGAGTTAAAATATAAT
Found at i:20022440 original size:20 final size:20
Alignment explanation
Indices: 20022408--20022446 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20022398 CATTTGAAAC
*
20022408 TTCTATAAATATATTTATAA
1 TTCTATAAATATATATATAA
20022428 TTCTA-AAATTATATATATA
1 TTCTATAAA-TATATATATA
20022447 TATATGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TTCTATAAATATATATATAA
Found at i:20034855 original size:41 final size:44
Alignment explanation
Indices: 20034805--20034927 Score: 135
Period size: 44 Copynumber: 2.9 Consensus size: 44
20034795 CGAAGTAAAC
* * * *
20034805 AGTAGTAGTACGATAC-T-TAGTACCTCATCGAATTAAACT-GA
1 AGTAATAGTACGACACATATAGTGCCTCATCGAATCAAACTCGA
* * * *
20034846 AGTAATAGTACGACACATATGGTGCCTCATCGACTCGAAGTCGA
1 AGTAATAGTACGACACATATAGTGCCTCATCGAATCAAACTCGA
* *
20034890 AGTAATAGTACGACACTTATAGTGCCTCATCGACTCAA
1 AGTAATAGTACGACACATATAGTGCCTCATCGAATCAA
20034928 GGTCGAAGCA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 14 0.21
42 1 0.01
43 16 0.24
44 37 0.54
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (44 bp):
AGTAATAGTACGACACATATAGTGCCTCATCGAATCAAACTCGA
Found at i:20034894 original size:44 final size:44
Alignment explanation
Indices: 20034844--20034935 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
20034834 GAATTAAACT
*
20034844 GAAGTAATAGTACGACACATATGGTGCCTCATCGACTCGAA-GTC
1 GAAGTAATAGTACGACACATATAGTGCCTCATCGACTC-AAGGTC
*
20034888 GAAGTAATAGTACGACACTTATAGTGCCTCATCGACTCAAGGTC
1 GAAGTAATAGTACGACACATATAGTGCCTCATCGACTCAAGGTC
20034932 GAAG
1 GAAG
20034936 CATCCCTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 2 0.04
44 43 0.96
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (44 bp):
GAAGTAATAGTACGACACATATAGTGCCTCATCGACTCAAGGTC
Found at i:20035082 original size:13 final size:13
Alignment explanation
Indices: 20035064--20035095 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
20035054 TTCACAATAA
20035064 TAAAACCCTAATT
1 TAAAACCCTAATT
20035077 TAAAACCCTAATT
1 TAAAACCCTAATT
20035090 TAAAAC
1 TAAAAC
20035096 TTCTTTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAAACCCTAATT
Found at i:20035391 original size:17 final size:18
Alignment explanation
Indices: 20035365--20035398 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
20035355 CTAATTTCTC
20035365 CTTTTATTTTCTTTCTTT
1 CTTTTATTTTCTTTCTTT
20035383 CTTTT-TTTTCTTTCTT
1 CTTTTATTTTCTTTCTT
20035399 CTGTTTCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (18 bp):
CTTTTATTTTCTTTCTTT
Found at i:20035488 original size:3 final size:3
Alignment explanation
Indices: 20035480--20035509 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
20035470 TTTATTAACT
*
20035480 TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20035510 ATATCTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:20035776 original size:20 final size:20
Alignment explanation
Indices: 20035753--20035795 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
20035743 TTAATTTATT
20035753 TTTAATAATA-ATAATCATAA
1 TTTAATAATATA-AATCATAA
*
20035773 TTTAATAATATAAATTATAA
1 TTTAATAATATAAATCATAA
20035793 TTT
1 TTT
20035796 GATAGAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAATAATATAAATCATAA
Found at i:20043103 original size:18 final size:17
Alignment explanation
Indices: 20043080--20043116 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
20043070 GCTTCTGTTG
*
20043080 TTCTTTCTTTCATTTTCT
1 TTCTTTATTTCA-TTTCT
20043098 TTCTTTATTTCATTTCT
1 TTCTTTATTTCATTTCT
20043115 TT
1 TT
20043117 TATTCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (17 bp):
TTCTTTATTTCATTTCT
Found at i:20043113 original size:13 final size:14
Alignment explanation
Indices: 20043080--20043116 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
20043070 GCTTCTGTTG
20043080 TTCTTTCTTTCATT
1 TTCTTTCTTTCATT
20043094 TTCTTTCTTT-A-T
1 TTCTTTCTTTCATT
20043106 TTCATTTCTTT
1 TTC-TTTCTTT
20043117 TATTCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 8 0.36
14 10 0.45
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCTTTCTTTCATT
Found at i:20043146 original size:3 final size:3
Alignment explanation
Indices: 20043138--20043182 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
20043128 TTTATTAACT
20043138 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20043183 ATATCTTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20043400 original size:18 final size:17
Alignment explanation
Indices: 20043377--20043413 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
20043367 GCTTCTGTTG
*
20043377 TTCTTTCTTTCATTTTCT
1 TTCTTTATTTCA-TTTCT
20043395 TTCTTTATTTCATTTCT
1 TTCTTTATTTCATTTCT
20043412 TT
1 TT
20043414 TATTCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (17 bp):
TTCTTTATTTCATTTCT
Found at i:20043410 original size:13 final size:14
Alignment explanation
Indices: 20043377--20043413 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
20043367 GCTTCTGTTG
20043377 TTCTTTCTTTCATT
1 TTCTTTCTTTCATT
20043391 TTCTTTCTTT-A-T
1 TTCTTTCTTTCATT
20043403 TTCATTTCTTT
1 TTC-TTTCTTT
20043414 TATTCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 8 0.36
14 10 0.45
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCTTTCTTTCATT
Found at i:20043443 original size:3 final size:3
Alignment explanation
Indices: 20043435--20043479 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
20043425 TTTATTAACT
20043435 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20043480 ATATCTTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20043504 original size:297 final size:297
Alignment explanation
Indices: 20043031--20043626 Score: 1192
Period size: 297 Copynumber: 2.0 Consensus size: 297
20043021 GTTTCTCTTT
20043031 TAATTTTCTTTCTTTCTTTTCTTTCCTCTGTTTCAAAATGCTTCTGTTGTTCTTTCTTTCATTTT
1 TAATTTTCTTTCTTTCTTTTCTTTCCTCTGTTTCAAAATGCTTCTGTTGTTCTTTCTTTCATTTT
20043096 CTTTCTTTATTTCATTTCTTTTATTCTTTTACTTTATTAACTTAATAATAATAATAATAATAATA
66 CTTTCTTTATTTCATTTCTTTTATTCTTTTACTTTATTAACTTAATAATAATAATAATAATAATA
20043161 ATAATAATAATAATAATAATAAATATCTTATCTATTAACAAATATATATATTACGCTTGCCTATT
131 ATAATAATAATAATAATAATAAATATCTTATCTATTAACAAATATATATATTACGCTTGCCTATT
20043226 ATCATCATCCTCCAATTGTCCTTATTTTATTTATTTTATATAATTTAATATTTTAATATAATAAA
196 ATCATCATCCTCCAATTGTCCTTATTTTATTTATTTTATATAATTTAATATTTTAATATAATAAA
20043291 AATATTTTTACTTAAATAAAAAGTAATTAAATAAATA
261 AATATTTTTACTTAAATAAAAAGTAATTAAATAAATA
20043328 TAATTTTCTTTCTTTCTTTTCTTTCCTCTGTTTCAAAATGCTTCTGTTGTTCTTTCTTTCATTTT
1 TAATTTTCTTTCTTTCTTTTCTTTCCTCTGTTTCAAAATGCTTCTGTTGTTCTTTCTTTCATTTT
20043393 CTTTCTTTATTTCATTTCTTTTATTCTTTTACTTTATTAACTTAATAATAATAATAATAATAATA
66 CTTTCTTTATTTCATTTCTTTTATTCTTTTACTTTATTAACTTAATAATAATAATAATAATAATA
20043458 ATAATAATAATAATAATAATAAATATCTTATCTATTAACAAATATATATATTACGCTTGCCTATT
131 ATAATAATAATAATAATAATAAATATCTTATCTATTAACAAATATATATATTACGCTTGCCTATT
20043523 ATCATCATCCTCCAATTGTCCTTATTTTATTTATTTTATATAATTTAATATTTTAATATAATAAA
196 ATCATCATCCTCCAATTGTCCTTATTTTATTTATTTTATATAATTTAATATTTTAATATAATAAA
20043588 AATATTTTTACTTAAATAAAAAGTAATTAAATAAATA
261 AATATTTTTACTTAAATAAAAAGTAATTAAATAAATA
20043625 TA
1 TA
20043627 TTACAAATGT
Statistics
Matches: 299, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
297 299 1.00
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.51
Consensus pattern (297 bp):
TAATTTTCTTTCTTTCTTTTCTTTCCTCTGTTTCAAAATGCTTCTGTTGTTCTTTCTTTCATTTT
CTTTCTTTATTTCATTTCTTTTATTCTTTTACTTTATTAACTTAATAATAATAATAATAATAATA
ATAATAATAATAATAATAATAAATATCTTATCTATTAACAAATATATATATTACGCTTGCCTATT
ATCATCATCCTCCAATTGTCCTTATTTTATTTATTTTATATAATTTAATATTTTAATATAATAAA
AATATTTTTACTTAAATAAAAAGTAATTAAATAAATA
Found at i:20043768 original size:16 final size:16
Alignment explanation
Indices: 20043723--20043772 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
20043713 AGTCCTAATT
*
20043723 TAATAAT-ATAAATTA
1 TAATAATGATAAATAA
*
20043738 TAAT-TTGATAGAATAA
1 TAATAATGATA-AATAA
20043754 TAATAATGATAAATAA
1 TAATAATGATAAATAA
20043770 TAA
1 TAA
20043773 ATATCTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.03
15 7 0.24
16 16 0.55
17 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
TAATAATGATAAATAA
Found at i:20043913 original size:10 final size:10
Alignment explanation
Indices: 20043898--20043928 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
20043888 CTTATAATAT
20043898 AATTATTTTA
1 AATTATTTTA
20043908 AATTATTTTA
1 AATTATTTTA
*
20043918 AATTAATTTA
1 AATTATTTTA
20043928 A
1 A
20043929 CATAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
AATTATTTTA
Found at i:20048524 original size:20 final size:20
Alignment explanation
Indices: 20048499--20048544 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
20048489 GTTGGGCCTT
20048499 GCCCATATTAAC-ACAGTTGG
1 GCCCATATTAACTACAGTT-G
*
20048519 GCCCAT-TTCACTACAGTTG
1 GCCCATATTAACTACAGTTG
20048538 GCCCATA
1 GCCCATA
20048545 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTAACTACAGTTG
Found at i:20051399 original size:34 final size:35
Alignment explanation
Indices: 20051346--20051412 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
20051336 CCTAGCTACA
*
20051346 GTCTCAGTCTTCTAAAGTTTTCAGT-TTTCCCTATT
1 GTCTCAGTCTTCTAAAG-TTTCAGTATTACCCTATT
*
20051381 GTCTCAGT-TTCTACAGTTTCAGTATTACCCTA
1 GTCTCAGTCTTCTAAAGTTTCAGTATTACCCTA
20051413 ACTACAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 7 0.24
34 14 0.48
35 8 0.28
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.45
Consensus pattern (35 bp):
GTCTCAGTCTTCTAAAGTTTCAGTATTACCCTATT
Found at i:20052587 original size:61 final size:61
Alignment explanation
Indices: 20052468--20052587 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 61
20052458 CTATTCAGAA
* *
20052468 ATCAGAGTTAATTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGT
1 ATCAGAGTTAATTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGT
* * * *
20052529 ATCAGAG-TATATTGGGCC-TAGCCCATATCAGTGTCAATCTGGGCCGTATCCCTATTACA
1 ATCAGAGTTA-ATTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACA
20052588 AGTCGAGATA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
60 31 0.61
61 20 0.39
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (61 bp):
ATCAGAGTTAATTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGT
Found at i:20061633 original size:70 final size:69
Alignment explanation
Indices: 20061559--20061700 Score: 171
Period size: 69 Copynumber: 2.0 Consensus size: 69
20061549 GCACTGGGTA
* * * *
20061559 CAACTTCTGTCAATTTATCTGACTAGCAT-TTGGGTACAACCATCGTCT-GTTATTCGATTAGCG
1 CAACTTCTGTCAATTTATCTGACTAG--TGCTGGGCACAACCATCGT-TGGTTATCCGACTAGCG
20061622 CTGGACG
63 CTGGACG
* * *
20061629 CAACTTTTGTTAATTTATTTGACTAGTGCTGGGCACAACCATCGTTGGTTATCCGACTAGCGCTG
1 CAACTTCTGTCAATTTATCTGACTAGTGCTGGGCACAACCATCGTTGGTTATCCGACTAGCGCTG
*
20061694 GGCG
66 GACG
20061698 CAA
1 CAA
20061701 AACATTGTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
68 2 0.03
69 37 0.60
70 23 0.37
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (69 bp):
CAACTTCTGTCAATTTATCTGACTAGTGCTGGGCACAACCATCGTTGGTTATCCGACTAGCGCTG
GACG
Found at i:20065277 original size:13 final size:13
Alignment explanation
Indices: 20065259--20065284 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20065249 AAAAAAGTTC
20065259 AAAATAATAGGTT
1 AAAATAATAGGTT
20065272 AAAATAATAGGTT
1 AAAATAATAGGTT
20065285 TTTTTTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
AAAATAATAGGTT
Found at i:20066189 original size:4 final size:4
Alignment explanation
Indices: 20066182--20066208 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20066172 AATAAAAATC
20066182 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
20066209 TGTTGTATTG
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:20070219 original size:23 final size:23
Alignment explanation
Indices: 20070189--20070232 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
20070179 ACAAAAGTAT
20070189 AATAGTGATGACACCACGTTTTA
1 AATAGTGATGACACCACGTTTTA
20070212 AATAGTGATGACACCACGTTT
1 AATAGTGATGACACCACGTTT
20070233 CTCATCTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (23 bp):
AATAGTGATGACACCACGTTTTA
Found at i:20072958 original size:100 final size:100
Alignment explanation
Indices: 20072785--20072980 Score: 374
Period size: 100 Copynumber: 2.0 Consensus size: 100
20072775 TATCCTCATG
*
20072785 CAATACACCAATGATGATGAAGCTCTTCAACATTGGCCTCAAGAAATCAAGTGAGATACATAAGT
1 CAATACACCAATGATGATGAAGCTCTTCAACATTGGCCTCAAGAAATCAAGTGAGATACATAAAT
*
20072850 TAATTGCTGCTTGTCTATTTGACCCTTTTATATGT
66 TAATTGCTGCTTATCTATTTGACCCTTTTATATGT
20072885 CAATACACCAATGATGATGAAGCTCTTCAACATTGGCCTCAAGAAATCAAGTGAGATACATAAAT
1 CAATACACCAATGATGATGAAGCTCTTCAACATTGGCCTCAAGAAATCAAGTGAGATACATAAAT
20072950 TAATTGCTGCTTATCTATTTGACCCTTTTAT
66 TAATTGCTGCTTATCTATTTGACCCTTTTAT
20072981 GTGTTTTCTT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 94 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (100 bp):
CAATACACCAATGATGATGAAGCTCTTCAACATTGGCCTCAAGAAATCAAGTGAGATACATAAAT
TAATTGCTGCTTATCTATTTGACCCTTTTATATGT
Found at i:20074380 original size:19 final size:19
Alignment explanation
Indices: 20074347--20074385 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20074337 TTTTTTATTT
20074347 ATTATTATATACAAAAATA
1 ATTATTATATACAAAAATA
*
20074366 ATTA-TATATATCAAATATA
1 ATTATTATATA-CAAAAATA
20074385 A
1 A
20074386 AAATAATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTATTATATACAAAAATA
Found at i:20074754 original size:25 final size:23
Alignment explanation
Indices: 20074726--20074778 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
20074716 TGATGTAATA
*
20074726 ATTTTTTAAAATTTTAAATTTTTTG
1 ATTTTTTAAAATATT--ATTTTTTG
*
20074751 ATTTTTTAAAATATTATTTTTTT
1 ATTTTTTAAAATATTATTTTTTG
20074774 ATTTT
1 ATTTT
20074779 AAGTTAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 12 0.46
25 14 0.54
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
ATTTTTTAAAATATTATTTTTTG
Found at i:20078140 original size:12 final size:12
Alignment explanation
Indices: 20078125--20078155 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20078115 TTCTCTTTTA
20078125 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
20078137 TTTTTCTTTCTC
1 TTTTTCTTTCCC
20078149 TTTTTCT
1 TTTTTCT
20078156 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:20078256 original size:16 final size:16
Alignment explanation
Indices: 20078235--20078265 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20078225 TTTATTATTT
20078235 TATTAACATAATATAA
1 TATTAACATAATATAA
*
20078251 TATTAATATAATATA
1 TATTAACATAATATA
20078266 TTAAAATATC
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:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:20078540 original size:15 final size:14
Alignment explanation
Indices: 20078522--20078552 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
20078512 TTAATTTATT
20078522 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
20078537 TAATAATAATCTAA
1 TAATAATAATCTAA
20078551 TA
1 TA
20078553 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:20078563 original size:21 final size:20
Alignment explanation
Indices: 20078539--20078607 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
20078529 AATGCTAATA
20078539 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
20078560 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
20078579 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
20078600 ATAATAAT
1 ATAATAAT
20078608 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:20085801 original size:12 final size:12
Alignment explanation
Indices: 20085786--20085815 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
20085776 TTCTCTTTTA
20085786 TTTTTCTTTC-C
1 TTTTTCTTTCTC
20085797 TTTTTCTTTCTC
1 TTTTTCTTTCTC
20085809 TTTTTCT
1 TTTTTCT
20085816 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTCTTTCTC
Found at i:20087476 original size:3 final size:3
Alignment explanation
Indices: 20087468--20087553 Score: 50
Period size: 3 Copynumber: 28.0 Consensus size: 3
20087458 TGGGTAAAAT
* * *
20087468 ATA ATA ATA ATA ATA AT- ATA ATA GTA GTA ATA ATA ATGA GGTA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A -ATA AT-A
* * * * *
20087515 ATA ATA ATG GTA ATA GTA ATA CTA CT- ATA AGTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
20087554 TAAATGGATA
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
2 3 0.05
3 53 0.82
4 8 0.12
5 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20087535 original size:18 final size:19
Alignment explanation
Indices: 20087469--20087535 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 19
20087459 GGGTAAAATA
* **
20087469 TAATAATAATAATAATATAA
1 TAATAGTAATAATAATA-GG
*
20087489 TAGTAGTAATAATAATGAGG
1 TAATAGTAATAATAAT-AGG
20087509 TAATA--AATAATAAT-GG
1 TAATAGTAATAATAATAGG
20087525 TAATAGTAATA
1 TAATAGTAATA
20087536 CTACTATAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
16 7 0.18
18 13 0.33
20 18 0.46
21 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (19 bp):
TAATAGTAATAATAATAGG
Found at i:20090762 original size:43 final size:43
Alignment explanation
Indices: 20090699--20090816 Score: 125
Period size: 43 Copynumber: 2.7 Consensus size: 43
20090689 GTGGAAAAAT
* * * *
20090699 GTCGCTATAGAACATAACCTTTAGC-GACGCTTAACCTACAGAC
1 GTCGCTAAAGAACATGACCTTTAGCTG-CGCTTAACCCACAAAC
* *
20090742 GTCGCTAAAGAACATGACCTTTAGCTGCGCTTATCCCACAAAT
1 GTCGCTAAAGAACATGACCTTTAGCTGCGCTTAACCCACAAAC
*
20090785 G-CTGCTAAAGAACATGACTTTTAG-TGGCGCTT
1 GTC-GCTAAAGAACATGACCTTTAGCT-GCGCTT
20090817 TTCCTAAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
42 2 0.03
43 62 0.95
44 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (43 bp):
GTCGCTAAAGAACATGACCTTTAGCTGCGCTTAACCCACAAAC
Found at i:20090836 original size:43 final size:43
Alignment explanation
Indices: 20090745--20090837 Score: 100
Period size: 43 Copynumber: 2.2 Consensus size: 43
20090735 TACAGACGTC
* **
20090745 GCTAAAGAACATGACCTTTAGCTGCGCTTATCCCACAAATGCT
1 GCTAAAGAACATGACCTTTAGCTGCGCTTATCCCAAAAAACCT
* * *
20090788 GCTAAAGAACATGACTTTTAG-TGGCGCTTTTCCTAAAAACACCT
1 GCTAAAGAACATGACCTTTAGCT-GCGCTTATCCCAAAAA-ACCT
20090832 -CTAAAG
1 GCTAAAG
20090838 GTCATGTTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
42 1 0.02
43 39 0.93
44 2 0.05
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (43 bp):
GCTAAAGAACATGACCTTTAGCTGCGCTTATCCCAAAAAACCT
Found at i:20095401 original size:20 final size:20
Alignment explanation
Indices: 20095364--20095401 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20095354 ATATTTTTTG
* *
20095364 AAAAATTAAGTAATATTTAA
1 AAAAATTAAATAAAATTTAA
20095384 AAAAATTAAATAAAATTT
1 AAAAATTAAATAAAATTT
20095402 GAAATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAAATTAAATAAAATTTAA
Found at i:20095621 original size:17 final size:18
Alignment explanation
Indices: 20095588--20095621 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20095578 TATCTCTTAA
20095588 ATAATTTAAACTATATTG
1 ATAATTTAAACTATATTG
*
20095606 ATAATTTTAA-TATATT
1 ATAATTTAAACTATATT
20095622 AAAATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATAATTTAAACTATATTG
Found at i:20099621 original size:43 final size:43
Alignment explanation
Indices: 20099551--20099633 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
20099541 ATATTCTAGA
* * *
20099551 AAGGAAAGAAATCAACTAAAGTGAAATCGCAATAGAGAAACCT
1 AAGGAAAGAAATCAACTAAAATAAAATCACAATAGAGAAACCT
* *
20099594 AAGGAAAGAAATCAATTAAAATAAAATCACAATCGAGAAA
1 AAGGAAAGAAATCAACTAAAATAAAATCACAATAGAGAAA
20099634 TCTACTGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (43 bp):
AAGGAAAGAAATCAACTAAAATAAAATCACAATAGAGAAACCT
Found at i:20101712 original size:21 final size:19
Alignment explanation
Indices: 20101684--20101722 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
20101674 GAGCTCGACT
*
20101684 AAAATAAGATCTTAATCAAG
1 AAAATAAG-CCTTAATCAAG
20101704 AAAACTAAGCCTTAATCAA
1 AAAA-TAAGCCTTAATCAA
20101723 AATTAGTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (19 bp):
AAAATAAGCCTTAATCAAG
Found at i:20105309 original size:19 final size:19
Alignment explanation
Indices: 20105285--20105323 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
20105275 TCTCATGACT
20105285 TCTTGCACAAGGTTTAAAG
1 TCTTGCACAAGGTTTAAAG
20105304 TCTTGCACAAGGTTTAAAG
1 TCTTGCACAAGGTTTAAAG
20105323 T
1 T
20105324 TGGTAGGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (19 bp):
TCTTGCACAAGGTTTAAAG
Found at i:20105417 original size:78 final size:79
Alignment explanation
Indices: 20105304--20105555 Score: 371
Period size: 79 Copynumber: 3.2 Consensus size: 79
20105294 AGGTTTAAAG
* * * *
20105304 TCTTGCACAAGGTTTAAAGTTGGTAGGTTGCCAATGAGGTACATTGGTGCTCCTTTTGTTTCTCG
1 TCTTGCACAAGGTTTAAAGTTGGTAGGCTACCAATGAGGTACATTGGTGCTCCTCTTGTTTCTTG
*
20105369 GAAGCTTTCTCACT
66 GAAGCTGTCTCACT
* *
20105383 TCTTGCACAAGGTTT-AAGTTGGTAGGCTACCAATGAGGTACCTTGGTGCACCTCTTGTTTCTTG
1 TCTTGCACAAGGTTTAAAGTTGGTAGGCTACCAATGAGGTACATTGGTGCTCCTCTTGTTTCTTG
20105447 GAAGCTGTCTCACT
66 GAAGCTGTCTCACT
* * * * * *
20105461 TCTTGCATAAGGTTTAAAGTCGGTAGGCTACTAGTGAGGTACTTTGGTGTTCCTCTTGTTTCTTG
1 TCTTGCACAAGGTTTAAAGTTGGTAGGCTACCAATGAGGTACATTGGTGCTCCTCTTGTTTCTTG
20105526 GAAGCTGTCTCACT
66 GAAGCTGTCTCACT
*
20105540 TCTTGCACGAGGTTTA
1 TCTTGCACAAGGTTTA
20105556 GTTCCTCTTG
Statistics
Matches: 156, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
78 70 0.45
79 86 0.55
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (79 bp):
TCTTGCACAAGGTTTAAAGTTGGTAGGCTACCAATGAGGTACATTGGTGCTCCTCTTGTTTCTTG
GAAGCTGTCTCACT
Found at i:20108200 original size:21 final size:21
Alignment explanation
Indices: 20108175--20108239 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 21
20108165 TAGCCTTCGG
20108175 GCTTCCGTTTAGCACTTGTGT
1 GCTTCCGTTTAGCACTTGTGT
**
20108196 GCTT-CAATTAGC-CTTCG-G-
1 GCTTCCGTTTAGCACTT-GTGT
**
20108214 GCTTCCGTTTAGCACTCATGT
1 GCTTCCGTTTAGCACTTGTGT
20108235 GCTTC
1 GCTTC
20108240 AGCTAGACTT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
18 4 0.12
19 10 0.30
20 10 0.30
21 9 0.27
ACGTcount: A:0.12, C:0.28, G:0.22, T:0.38
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTGTGT
Found at i:20108207 original size:39 final size:39
Alignment explanation
Indices: 20108157--20108257 Score: 157
Period size: 39 Copynumber: 2.6 Consensus size: 39
20108147 GCTCTGATGA
**
20108157 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTCATGT
*
20108196 GCTTCAATTAGCCTTCGGGCTTCCGTTTAGCACTCATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTCATGT
* *
20108235 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
20108258 AGATCACGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.13, C:0.28, G:0.24, T:0.36
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTCATGT
Found at i:20110625 original size:46 final size:46
Alignment explanation
Indices: 20110567--20110694 Score: 238
Period size: 46 Copynumber: 2.8 Consensus size: 46
20110557 ATTTAGGCAT
*
20110567 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
20110613 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
*
20110659 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGG
20110695 GCGGGTTACA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.26
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
Found at i:20124501 original size:3 final size:3
Alignment explanation
Indices: 20124493--20124655 Score: 97
Period size: 3 Copynumber: 53.0 Consensus size: 3
20124483 CTTTATTAAA
* * * *
20124493 TAT TAT TAT TAT TAT T-T CTAA TAT TAT TAA TAT TAT TAC TAT TGT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
20124538 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAGT GTA- TAT TTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T -TAT TAT TAT TAT TAT
* * *
20124584 ATAT GTA- TAT ATATT TAT ATAT T-T ATAT ATAG TAT TAT TTT TAAT TAC
1 -TAT -TAT TAT -TA-T TAT -TAT TAT -TAT -TAT TAT TAT TAT T-AT TAT
*
20124632 T-T TAT T-T TAA TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
20124656 ATTTGCTTTT
Statistics
Matches: 125, Mismatches: 19, Indels: 32
0.71 0.11 0.18
Matches are distributed among these distances:
2 11 0.09
3 92 0.74
4 19 0.15
5 3 0.02
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:20124845 original size:24 final size:22
Alignment explanation
Indices: 20124818--20124875 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
20124808 CATTATTTTT
*
20124818 TATTATTATTTTCTTTATTGTGAA
1 TATTATTATTTT-TTTATTCT-AA
*
20124842 TATTATTGTTATTTTTATTCTAA
1 TATTATTATT-TTTTTATTCTAA
20124865 TATTA-TATTTT
1 TATTATTATTTT
20124876 AATATTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 2 0.07
22 3 0.10
23 7 0.23
24 16 0.53
25 2 0.07
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (22 bp):
TATTATTATTTTTTTATTCTAA
Found at i:20136857 original size:153 final size:152
Alignment explanation
Indices: 20136672--20137114 Score: 651
Period size: 153 Copynumber: 2.9 Consensus size: 152
20136662 GGTATTCTGA
*
20136672 TATTTTTA-TTTCTATTTTT-AAAAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAT
1 TATTTTTAGTTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAT
* *
20136735 CACGCACTGAGGTATTTTCAATTTATGTTTAAAAAAAATCAACTCAAATTGCTAGAGGTGAGTTG
66 CACACACTGAGGTATTTTCAATTTATGTTTAAAAAAAATCAACTCATATTGCTAGAGGTGAGTTG
20136800 AGCCTCGGGTCACACGCTGAGG
131 AGCCTCGGGTCACACGCTGAGG
*
20136822 TATTTTTAGTTCCTATTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA
1 TATTTTTAGTTTCTATTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA
* * * *
20136887 TCACAAACTAAGGTATTTTCAATTTCTGTTTCAAAAAAATCAACTCATATTG-TGAGAGGTGAGT
65 TCACACACTGAGGTATTTTCAATTTATGTTTAAAAAAAATCAACTCATATTGCT-AGAGGTGAGT
20136951 TGAGCCTCGGGTCACACGCTGAGG
129 TGAGCCTCGGGTCACACGCTGAGG
* *
20136975 TATTTTTAGTTTCTATTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGA
1 TATTTTTAGTTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGA
* * * *
20137040 -CACACGCTGAGGTATTTTCAATTTATGTTTTTTCAAAAAAAAATCGACTCATATTGCGAGAAGT
65 TCACACACTGAGGTATTTTCAATTTATG---TTT--AAAAAAAATCAACTCATATTGCTAGAGGT
*
20137104 GAGTTAAGCCT
125 GAGTTGAGCCT
20137115 TTTAGTTTCT
Statistics
Matches: 262, Mismatches: 20, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
150 8 0.03
151 10 0.04
152 63 0.24
153 144 0.55
155 3 0.01
157 34 0.13
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (152 bp):
TATTTTTAGTTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAT
CACACACTGAGGTATTTTCAATTTATGTTTAAAAAAAATCAACTCATATTGCTAGAGGTGAGTTG
AGCCTCGGGTCACACGCTGAGG
Found at i:20136996 original size:77 final size:76
Alignment explanation
Indices: 20136672--20137114 Score: 534
Period size: 75 Copynumber: 5.8 Consensus size: 76
20136662 GGTATTCTGA
* * * *
20136672 TATTTTTATTTCTATTTTT-AAAAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATC
1 TATTTTCATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
* *
20136736 ACGCACTGAGG
66 ACACGCTGAGG
* * * * *
20136747 TATTTTCAATT-TATGTTTAAAAAAAATCAACTCAAATTGCTAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTCATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
20136811 ACACGCTGAGG
66 ACACGCTGAGG
* * * *
20136822 TATTTTTAGTTCCTATTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA
1 TATTTTCA-TTTCTATTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
** *
20136887 TCACAAACTAAGG
64 TCACACGCTGAGG
* *
20136900 TATTTTCAATTTC--TGTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGT
1 TATTTTC-ATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
20136963 CACACGCTGAGG
65 CACACGCTGAGG
* * *
20136975 TATTTTTAGTTTCTATTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGA
1 TATTTTCA-TTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
20137040 CACACGCTGAGG
65 CACACGCTGAGG
* * * * *
20137052 TATTTTCAATTTATGTTTTTTCAAAAAAAAATCGACTCATATTGCGAGAAGTGAGTTAAGCCT
1 TATTTTC-ATTTCT-ATTTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
20137115 TTTAGTTTCT
Statistics
Matches: 313, Mismatches: 43, Indels: 19
0.83 0.11 0.05
Matches are distributed among these distances:
74 7 0.02
75 125 0.40
76 6 0.02
77 74 0.24
78 65 0.21
79 1 0.00
80 35 0.11
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (76 bp):
TATTTTCATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
ACACGCTGAGG
Found at i:20138959 original size:3 final size:3
Alignment explanation
Indices: 20138951--20139089 Score: 62
Period size: 3 Copynumber: 46.0 Consensus size: 3
20138941 CTTTATTAAA
* * *
20138951 TAT TAT TAT TAT T-T CTAA TAT TAT TAA TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
20138996 TAT TAGT GTA- TAT TTT TAT TAT ATAT GTA- TAT ATATT TAT ATAT T-T
1 TAT TA-T -TAT TAT TAT TAT TAT -TAT -TAT TAT -TA-T TAT -TAT TAT
* * *
20139042 ATAT ATAG TAT TAT T-T T-T TAT TAC T-T TAT T-T TAA TAT TAT TA-
1 -TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20139084 TAT TAT
1 TAT TAT
20139090 ATTTGCTTTT
Statistics
Matches: 105, Mismatches: 15, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
2 15 0.14
3 70 0.67
4 17 0.16
5 3 0.03
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:20138972 original size:9 final size:9
Alignment explanation
Indices: 20138943--20139000 Score: 64
Period size: 9 Copynumber: 6.3 Consensus size: 9
20138933 TTTCGTTTCT
20138943 TTATTAAATA
1 TTATT-AATA
*
20138953 TTATTATTA
1 TTATTAATA
20138962 TT-TCTAATA
1 TTAT-TAATA
20138971 TTATTAATA
1 TTATTAATA
*
20138980 TTATTACTA
1 TTATTAATA
*
20138989 TTATTATTA
1 TTATTAATA
20138998 TTA
1 TTA
20139001 GTGTATATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
8 1 0.02
9 35 0.83
10 6 0.14
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (9 bp):
TTATTAATA
Found at i:20138972 original size:18 final size:18
Alignment explanation
Indices: 20138943--20139089 Score: 80
Period size: 18 Copynumber: 8.2 Consensus size: 18
20138933 TTTCGTTTCT
20138943 TTATTAAATATTATTATTA
1 TTATT-AATATTATTATTA
*
20138962 TT-TCTAATATTATTAATA
1 TTAT-TAATATTATTATTA
*
20138980 TTATTACTATTATTATTA
1 TTATTAATATTATTATTA
*
20138998 TTAGTGT-ATATTTTTATTA
1 TTA-T-TAATATTATTATTA
20139017 TATATGT-ATA-TA-TATTTA
1 T-TAT-TAATATTATTA-TTA
* *
20139035 TATATTTATATATAGTATTA
1 T-TATTAATAT-TATTATTA
* *
20139055 TT-TT-TTATTACT-TTA
1 TTATTAATATTATTATTA
20139070 TT-TTAATATTATTA-TA
1 TTATTAATATTATTATTA
20139086 TTAT
1 TTAT
20139090 ATTTGCTTTT
Statistics
Matches: 105, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
15 7 0.07
16 13 0.12
17 7 0.07
18 44 0.42
19 23 0.22
20 9 0.09
21 2 0.02
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (18 bp):
TTATTAATATTATTATTA
Found at i:20139256 original size:14 final size:15
Alignment explanation
Indices: 20139239--20139267 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20139229 TTATTAGAAC
20139239 ATTATTTT-TTTATT
1 ATTATTTTCTTTATT
20139253 ATTATTTTCTTTATT
1 ATTATTTTCTTTATT
20139268 GTGAATACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTATTTTCTTTATT
Found at i:20145778 original size:15 final size:15
Alignment explanation
Indices: 20145754--20145787 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20145744 TTAAAAGAAT
* *
20145754 TTAAATTTCAAAATC
1 TTAAAATTCAAAAGC
20145769 TTAAAATTCAAAAGC
1 TTAAAATTCAAAAGC
20145784 TTAA
1 TTAA
20145788 TTAATCATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (15 bp):
TTAAAATTCAAAAGC
Found at i:20146315 original size:3 final size:3
Alignment explanation
Indices: 20146307--20146372 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
20146297 CGCATGAAAG
20146307 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20146355 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
20146373 AGAGGATAGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20151523 original size:29 final size:30
Alignment explanation
Indices: 20151481--20151540 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
20151471 TTATGGAAGA
* *
20151481 GATGGAGAACTTGTTCGTTG-AGAGTTCGT
1 GATGAAGAACTTGTTCGTTGAAGAATTCGT
*
20151510 GATGAAGAACTTGTTTGTTGAAGAATTCGT
1 GATGAAGAACTTGTTCGTTGAAGAATTCGT
20151540 G
1 G
20151541 TCAAGGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.25, C:0.08, G:0.32, T:0.35
Consensus pattern (30 bp):
GATGAAGAACTTGTTCGTTGAAGAATTCGT
Found at i:20151843 original size:13 final size:13
Alignment explanation
Indices: 20151825--20151861 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
20151815 AATCTGTGTG
20151825 TTCTTTATTTTTT
1 TTCTTTATTTTTT
20151838 TTCTTTA-TTTTT
1 TTCTTTATTTTTT
*
20151850 TTCTTTCTTTTT
1 TTCTTTATTTTT
20151862 CTTTGCGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (13 bp):
TTCTTTATTTTTT
Found at i:20155929 original size:224 final size:225
Alignment explanation
Indices: 20155539--20155983 Score: 820
Period size: 224 Copynumber: 2.0 Consensus size: 225
20155529 CTAGTCGTTG
*
20155539 GACTTGAGCTTTAGGATGCTACAATAATTAACGGAACAGTATTATGCAAATCTAAAACCAAAAGT
1 GACTTGAGCTATAGGATGCTACAATAATTAACGGAACAGTATTATGCAAATCTAAAACCAAAAGT
* *
20155604 TCAATTAAACATCGGATGATCTCAAACATTTATACAAAATCATGTTTTGCAAACAAAATCAAGTT
66 TCAATTAAACATCGGATGATCTCAAACATTTACACAAAATCATGCTTTGCAAACAAAATCAAGTT
* *
20155669 TAAATTGAGCCTACGAAAGCTCTAAAGTTGACCCAAAATCAAGCAATGACTAATTTGACACTTTT
131 TAAATTGAGCCTACGAAAGCTCTAAAGTTCACCCAAAATCAAGCAATGACTAATTTGAAACTTTT
*
20155734 ACAAAATGAAAGG-CAAAAATGCAAACAGA
196 ACAAAATGAAAGGAAAAAAATGCAAACAGA
20155763 GACTTGAGCTATAGGATGCTACAATAATTAACGGAACAGTATTATGCAAATCTAAAACCAAAAGT
1 GACTTGAGCTATAGGATGCTACAATAATTAACGGAACAGTATTATGCAAATCTAAAACCAAAAGT
20155828 TCAATTAAACATCGGATGATCTCAAACATTTACACAAAATCATGCTTTGCAAACAAAATCAAGTT
66 TCAATTAAACATCGGATGATCTCAAACATTTACACAAAATCATGCTTTGCAAACAAAATCAAGTT
*
20155893 TAAATTGAGCTTACGAAAGCTCTAAAGTTCACCCAAAATCAAGCAATGACTAATTTGAAACTTTT
131 TAAATTGAGCCTACGAAAGCTCTAAAGTTCACCCAAAATCAAGCAATGACTAATTTGAAACTTTT
20155958 ACAAAATGAAAGGAAAAAAATGCAAA
196 ACAAAATGAAAGGAAAAAAATGCAAA
20155984 ACAGGGGTCA
Statistics
Matches: 213, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
224 202 0.95
225 11 0.05
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (225 bp):
GACTTGAGCTATAGGATGCTACAATAATTAACGGAACAGTATTATGCAAATCTAAAACCAAAAGT
TCAATTAAACATCGGATGATCTCAAACATTTACACAAAATCATGCTTTGCAAACAAAATCAAGTT
TAAATTGAGCCTACGAAAGCTCTAAAGTTCACCCAAAATCAAGCAATGACTAATTTGAAACTTTT
ACAAAATGAAAGGAAAAAAATGCAAACAGA
Found at i:20160600 original size:40 final size:41
Alignment explanation
Indices: 20160550--20160626 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
20160540 AAAATTAAAA
*
20160550 AATGTGTAAGTTTATTATATAATA-TATAAT-ATAAAATCTT
1 AATGTGTAAGTATA-TATATAATATTATAATAATAAAATCTT
* *
20160590 AATGTTTAAGTATATATATTATATTATAATAATAAAA
1 AATGTGTAAGTATATATATAATATTATAATAATAAAA
20160627 CAAGTAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 8 0.25
40 18 0.56
41 6 0.19
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.44
Consensus pattern (41 bp):
AATGTGTAAGTATATATATAATATTATAATAATAAAATCTT
Found at i:20163437 original size:28 final size:26
Alignment explanation
Indices: 20163419--20163503 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 26
20163409 TTCTTACGAC
20163419 TTTATAAAATTTTAT-ATTTTTTTACA
1 TTTATAAAATTTTATGA-TTTTTTACA
* *
20163445 TTTCTATATATTTTATGATTTTTTACTA
1 TTTATA-AAATTTTATGATTTTTTAC-A
** *
20163473 TTTTTATAAAATTTTACAATTTTTTATA
1 --TTTATAAAATTTTATGATTTTTTACA
20163501 TTT
1 TTT
20163504 CTTTACGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
26 8 0.17
27 16 0.34
28 3 0.06
29 15 0.32
30 5 0.11
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.64
Consensus pattern (26 bp):
TTTATAAAATTTTATGATTTTTTACA
Found at i:20163477 original size:19 final size:18
Alignment explanation
Indices: 20163455--20163525 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 18
20163445 TTTCTATATA
*
20163455 TTTTATGATTTTTTACTAT
1 TTTTAT-ATTTTTTACAAT
**
20163474 TTTTATAAAATTTTACAATT
1 TTTTAT-ATTTTTTACAA-T
*
20163494 TTTTATATTTCTTTACGAT
1 TTTTATATTT-TTTACAAT
20163513 TTTTATATTTTTT
1 TTTTATATTTTTT
20163526 CTAATTTTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
18 3 0.07
19 27 0.63
20 13 0.30
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTATATTTTTTACAAT
Found at i:20163524 original size:56 final size:56
Alignment explanation
Indices: 20163381--20163533 Score: 168
Period size: 56 Copynumber: 2.7 Consensus size: 56
20163371 TTTTAAGAAA
* * * *
20163381 TTTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTATATTTT
1 TTTATATTTCTTTACATTTT-TATAATTTT-TTACTATTTTATAAAATTTTACAATTT
* * * *
20163439 TTTACATTTCTATATA-TTTTATGATTTTTTACTATTTTTATAAAATTTTACAATTT
1 TTTATATTTCTTTACATTTTTATAATTTTTTACTA-TTTTATAAAATTTTACAATTT
20163495 TTTATATTTCTTTACGATTTTTAT-ATTTTTT-CTAATTTT
1 TTTATATTTCTTTAC-ATTTTTATAATTTTTTACT-ATTTT
20163534 CAATAAAAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
55 5 0.06
56 44 0.55
57 12 0.15
58 19 0.24
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.63
Consensus pattern (56 bp):
TTTATATTTCTTTACATTTTTATAATTTTTTACTATTTTATAAAATTTTACAATTT
Found at i:20163677 original size:340 final size:339
Alignment explanation
Indices: 20163315--20163979 Score: 1260
Period size: 340 Copynumber: 2.0 Consensus size: 339
20163305 AAAATAAAAT
20163315 AAAATTTATAGAAAAATTATAAAATATTTCTTTTGGTATGATAATTTTTATAATTTTTTTAAGAA
1 AAAATTTATAGAAAAATTATAAAATATTTCTTTTGGTATGATAATTTTTATAATTTTTTTAAGAA
20163380 ATTTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTATATTTTTTTACA
66 ATTTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTATA-TTTTTTACA
20163445 TTTCTATATATTTTATGATTTTTTACTATTTTTATAAAATTTTACAATTTTTTATATTTCTTTAC
130 TTTCTATATATTTTATGATTTTTTACTATTTTTATAAAATTTTACAATTTTTTATATTTCTTTAC
20163510 GATTTTTATATTTTTTCTAATTTTCAATAAAAATTTAATATTTAAATTTTTATTAAAATTTAATA
195 GATTTTTATA-TTTTTCTAATTTTCAATAAAAATTTAATATTTAAATTTTTATTAAAATTTAATA
20163575 ATATTTATAGCTTTTTTATTTTAATTTTTTGTAA-TTTTTTTGTAATTTTTAATAAAAGCAGAGG
259 ATATTTATAGCTTTTTTATTTTAATTTTTTGTAATTTTTTTTGTAATTTTTAATAAAAGCAGAGG
20163639 TAATTTTTATAATAAA
324 TAATTTTTATAATAAA
*
20163655 AAAATTTATAGAAAAATTATAAAATGTTTCTTTTGGTATGATAATTTTTATAATTTTTTTAAGAA
1 AAAATTTATAGAAAAATTATAAAATATTTCTTTTGGTATGATAATTTTTATAATTTTTTTAAGAA
20163720 ATTTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTATATTTTTTACAT
66 ATTTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTATATTTTTTACAT
* *
20163785 TTCTATATATTTTATGATTTTTTACTATTTTTATAAAATTTTACAATTTTTTATATTTTTTTATG
131 TTCTATATATTTTATGATTTTTTACTATTTTTATAAAATTTTACAATTTTTTATATTTCTTTACG
* *
20163850 ATTTTTATATTTTTCTAATTTTCAATAAAATTTTAATGTTTAAATTTTTATTAAAATTTAATAAT
196 ATTTTTATATTTTTCTAATTTTCAATAAAAATTTAATATTTAAATTTTTATTAAAATTTAATAAT
20163915 ATTTATAGCTTTTTTATTTTAATTTTTTGTAATTTTTTTTGTAATTTTTAATAAAAGCAGAGGTA
261 ATTTATAGCTTTTTTATTTTAATTTTTTGTAATTTTTTTTGTAATTTTTAATAAAAGCAGAGGTA
20163980 TGATTGGCTT
Statistics
Matches: 319, Mismatches: 5, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
338 86 0.27
339 114 0.36
340 119 0.37
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (339 bp):
AAAATTTATAGAAAAATTATAAAATATTTCTTTTGGTATGATAATTTTTATAATTTTTTTAAGAA
ATTTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTATATTTTTTACAT
TTCTATATATTTTATGATTTTTTACTATTTTTATAAAATTTTACAATTTTTTATATTTCTTTACG
ATTTTTATATTTTTCTAATTTTCAATAAAAATTTAATATTTAAATTTTTATTAAAATTTAATAAT
ATTTATAGCTTTTTTATTTTAATTTTTTGTAATTTTTTTTGTAATTTTTAATAAAAGCAGAGGTA
ATTTTTATAATAAA
Found at i:20163781 original size:19 final size:19
Alignment explanation
Indices: 20163759--20163835 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
20163749 TTCTTACGAC
20163759 TTTATAAAATTTTA-TATT
1 TTTATAAAATTTTACTATT
*
20163777 TTT-T-ACATTTCTA-TATAT
1 TTTATAAAATTT-TACTAT-T
* **
20163795 TTTATGATTTTTTACTATT
1 TTTATAAAATTTTACTATT
*
20163814 TTTATAAAATTTTACAATT
1 TTTATAAAATTTTACTATT
20163833 TTT
1 TTT
20163836 TATATTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
16 5 0.11
17 6 0.13
18 7 0.15
19 22 0.47
20 7 0.15
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTATAAAATTTTACTATT
Found at i:20163807 original size:10 final size:9
Alignment explanation
Indices: 20163768--20163863 Score: 63
Period size: 9 Copynumber: 10.3 Consensus size: 9
20163758 CTTTATAAAA
20163768 TTTTATATT
1 TTTTATATT
*
20163777 TTTTACA-T
1 TTTTATATT
* *
20163785 TTCTATATA
1 TTTTATATT
20163794 TTTTATGATT
1 TTTTAT-ATT
20163804 TTTTACTA-T
1 TTTTA-TATT
**
20163813 TTTTATAAAA
1 TTTTAT-ATT
*
20163823 TTTTACAATT
1 TTTTA-TATT
20163833 TTTTATATT
1 TTTTATATT
20163842 TTTT-TATGAT
1 TTTTATAT--T
20163852 TTTTATATT
1 TTTTATATT
20163861 TTT
1 TTT
20163864 CTAATTTTCA
Statistics
Matches: 67, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
8 10 0.15
9 29 0.43
10 24 0.36
11 4 0.06
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTATATT
Found at i:20163845 original size:19 final size:19
Alignment explanation
Indices: 20163794--20163863 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
20163784 TTTCTATATA
* *
20163794 TTTTATGATTTTTTACTAT
1 TTTTATAATTTTTTACAAT
**
20163813 TTTTATAAAATTTTACAATT
1 TTTTATAATTTTTTACAA-T
* **
20163833 TTTTATATTTTTTTATGAT
1 TTTTATAATTTTTTACAAT
20163852 TTTTAT-ATTTTT
1 TTTTATAATTTTT
20163864 CTAATTTTCA
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
18 5 0.12
19 21 0.52
20 14 0.35
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:20163853 original size:28 final size:27
Alignment explanation
Indices: 20163774--20163854 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
20163764 AAAATTTTAT
* * **
20163774 ATTTTTTACATTTCTATATATTTTATG
1 ATTTTTTATATTTTTATATATTTTACA
*
20163801 ATTTTTTACTATTTTTATAAAATTTTACA
1 ATTTTTTA-TATTTTTAT-ATATTTTACA
*
20163830 ATTTTTTATATTTTTTTATGATTTT
1 ATTTTTTATATTTTTATAT-ATTTT
20163855 TATATTTTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 9 0.20
28 20 0.45
29 15 0.34
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (27 bp):
ATTTTTTATATTTTTATATATTTTACA
Found at i:20163963 original size:11 final size:12
Alignment explanation
Indices: 20163937--20163963 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20163927 TTTATTTTAA
20163937 TTTTTTGTAATT
1 TTTTTTGTAATT
20163949 TTTTTTGTAATT
1 TTTTTTGTAATT
20163961 TTT
1 TTT
20163964 AATAAAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTGTAATT
Found at i:20169591 original size:30 final size:30
Alignment explanation
Indices: 20169551--20169607 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
20169541 TTTTATAAAT
20169551 AATTAATATTT-AT-TACTTAAATATATTTAA
1 AATTAATATTTCATATA-TTAAA-ATATTTAA
*
20169581 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
20169608 AACAACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 15 0.62
31 7 0.29
32 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:20171066 original size:24 final size:24
Alignment explanation
Indices: 20171039--20171086 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
20171029 ACACTTCTGA
20171039 CCCTGAATACATCATTACTTATAG
1 CCCTGAATACATCATTACTTATAG
20171063 CCCTGAATACATCATTACTTATAG
1 CCCTGAATACATCATTACTTATAG
20171087 TCACAAATTC
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:0.33, C:0.25, G:0.08, T:0.33
Consensus pattern (24 bp):
CCCTGAATACATCATTACTTATAG
Found at i:20174502 original size:27 final size:27
Alignment explanation
Indices: 20174472--20174531 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
20174462 CGATGCACTT
*
20174472 AGCCGAAA-AATGGAATTTGCAATGATA
1 AGCC-AAACAATGGAATTTGCAACGATA
*
20174499 AGCCAAACTATGGAATTTGCAACGATA
1 AGCCAAACAATGGAATTTGCAACGATA
20174526 AGCCAA
1 AGCCAA
20174532 CCGAGAGTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.10
27 27 0.90
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (27 bp):
AGCCAAACAATGGAATTTGCAACGATA
Found at i:20181284 original size:14 final size:15
Alignment explanation
Indices: 20181261--20181293 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20181251 TTATAAAATG
20181261 ATTAAATTC-AATAT
1 ATTAAATTCAAATAT
*
20181275 ATTAATTTCAAATAT
1 ATTAAATTCAAATAT
20181290 ATTA
1 ATTA
20181294 TCAAACTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAAATTCAAATAT
Found at i:20184716 original size:42 final size:42
Alignment explanation
Indices: 20184635--20184716 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
20184625 TCGTTTTTTC
** ** *
20184635 GATGCCATAGTTCAACTATGGTCTTACACATCTTTACATAAT
1 GATGCCATAGCCCAACTATGGTCTTACACATAATCACATAAT
*
20184677 GATGCCATAGCCCAACTATGGTCTTACACGTAATCACATA
1 GATGCCATAGCCCAACTATGGTCTTACACATAATCACATA
20184717 TCTCACTGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.30
Consensus pattern (42 bp):
GATGCCATAGCCCAACTATGGTCTTACACATAATCACATAAT
Found at i:20184744 original size:47 final size:47
Alignment explanation
Indices: 20184677--20184983 Score: 492
Period size: 47 Copynumber: 6.5 Consensus size: 47
20184667 TTTACATAAT
* * * * * *
20184677 GATGCCATAGCCCA-ACTATGGTCTTACAC-GTAATCACATATCTCACT
1 GATGCCATATCCCAGA-TATGGTCTTATACAGT-AGCATATATCACACC
* *
20184724 GATGTCATATCCCAGATATGGTCTTATACAGTAGCATATAACACACC
1 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACC
*
20184771 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATAACACACC
1 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACC
20184818 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACC
1 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACC
20184865 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACC
1 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACC
*
20184912 GATGCCATATCCCAGATATGGTCTTATAAAGTAGCATATATCACACC
1 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACC
20184959 GATGCCATATCCCAGATATGGTCTT
1 GATGCCATATCCCAGATATGGTCTT
20184984 GTACGGAAAT
Statistics
Matches: 247, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
47 244 0.99
48 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (47 bp):
GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACC
Found at i:20189319 original size:32 final size:32
Alignment explanation
Indices: 20189278--20189342 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
20189268 TTAATGCTTG
20189278 GATTAACAACATCTTTGAGAATAATTCTTTAA
1 GATTAACAACATCTTTGAGAATAATTCTTTAA
20189310 GATTAACAACATCTTTGAGAATAATTCTTTAA
1 GATTAACAACATCTTTGAGAATAATTCTTTAA
20189342 G
1 G
20189343 TCAGGGGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (32 bp):
GATTAACAACATCTTTGAGAATAATTCTTTAA
Found at i:20190797 original size:28 final size:28
Alignment explanation
Indices: 20190751--20190806 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
20190741 ACAATTCAAC
20190751 CATTCAAACACATTCCCTTAATGATACT
1 CATTCAAACACATTCCCTTAATGATACT
20190779 CATTCAAACACAATT-CCTTAATGATACT
1 CATTCAAACAC-ATTCCCTTAATGATACT
20190807 TACACATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.32
Consensus pattern (28 bp):
CATTCAAACACATTCCCTTAATGATACT
Found at i:20190817 original size:28 final size:29
Alignment explanation
Indices: 20190755--20190818 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
20190745 TTCAACCATT
**
20190755 CAAACAC-ATTCCCTTAATGATACTCATT
1 CAAACACAATTCCCTTAATGATACTCACA
*
20190783 CAAACACAATT-CCTTAATGATACTTACA
1 CAAACACAATTCCCTTAATGATACTCACA
*
20190811 CATACACA
1 CAAACACA
20190819 CTCATCTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 28 0.90
29 3 0.10
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.28
Consensus pattern (29 bp):
CAAACACAATTCCCTTAATGATACTCACA
Found at i:20203960 original size:28 final size:28
Alignment explanation
Indices: 20203920--20203996 Score: 82
Period size: 36 Copynumber: 2.5 Consensus size: 28
20203910 TAAAATAAAA
20203920 TAAATTTAATAAAACATTGTAACAGATC
1 TAAATTTAATAAAACATTGTAACAGATC
20203948 TAAATTTAATAAAGAGAAATAACATTGTAACAGATC
1 TAAATTTAAT-------AA-AACATTGTAACAGATC
20203984 TAAATTTAATAAA
1 TAAATTTAATAAA
20203997 GTATGATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
28 11 0.27
29 2 0.05
35 2 0.05
36 26 0.63
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (28 bp):
TAAATTTAATAAAACATTGTAACAGATC
Found at i:20204291 original size:24 final size:24
Alignment explanation
Indices: 20204258--20204305 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
20204248 GCAAAAACAA
*
20204258 AAGATGAATAACCAGAACCAATGG
1 AAGATAAATAACCAGAACCAATGG
20204282 AAGATAAATAACCAGAACCAATGG
1 AAGATAAATAACCAGAACCAATGG
20204306 GTAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.17, G:0.19, T:0.12
Consensus pattern (24 bp):
AAGATAAATAACCAGAACCAATGG
Found at i:20205711 original size:117 final size:117
Alignment explanation
Indices: 20205517--20205984 Score: 857
Period size: 117 Copynumber: 4.0 Consensus size: 117
20205507 AATTCTTCTA
*
20205517 AACTGGGACAACCCGGAAACAGGAATTGCCAAGCTAAATGTTGATGGAAGCTGGAATCAAAGAGA
1 AACTGGGACAACCTGGAAACAGGAATTGCCAAGCTAAATGTTGATGGAAGCTGGAATCAAAGAGA
20205582 ATGGAAGGCATGAACAGGCAGTCTATTCAAAGGAGAATGGGAAATTTGGACG
66 ATGGAAGGCATGAACAGGCAGTCTATTCAAAGGAGAATGGGAAATTTGGACG
20205634 AACTGGGACAACCTGGAAACAGGAATTGCCAAGCTAAATGTTGATGGAAGCTGGAATCAAAGAGA
1 AACTGGGACAACCTGGAAACAGGAATTGCCAAGCTAAATGTTGATGGAAGCTGGAATCAAAGAGA
20205699 ATGGAAGGCATGAACAGGCAGTCTATTCAAAGGAGAATGGGAAATTTGGACG
66 ATGGAAGGCATGAACAGGCAGTCTATTCAAAGGAGAATGGGAAATTTGGACG
20205751 AACTGGGACAACCTGGAAACAGGAATTGCCAAGCTAAATGTTGATGGAAGCTGGAATCAAAGAGA
1 AACTGGGACAACCTGGAAACAGGAATTGCCAAGCTAAATGTTGATGGAAGCTGGAATCAAAGAGA
20205816 ATGGAAGGCATGAACAGGCAGTCTATTCAAAGGAGAATGGGAAATTTGGACG
66 ATGGAAGGCATGAACAGGCAGTCTATTCAAAGGAGAATGGGAAATTTGGACG
*
20205868 AACTGGGACAACCTGGAAACAGGAATTGCCAAGCTAAATGTTGATGGAAGCTGGAATAAAAGAGA
1 AACTGGGACAACCTGGAAACAGGAATTGCCAAGCTAAATGTTGATGGAAGCTGGAATCAAAGAGA
* * * * * *
20205933 ATGAAAGGCATGAAC-GGGAGTCTATTCAGAGGAGAACGGGAAAATCGGACG
66 ATGGAAGGCATGAACAGGCAGTCTATTCAAAGGAGAATGGGAAATTTGGACG
20205984 A
1 A
20205985 TTGGATACTT
Statistics
Matches: 343, Mismatches: 8, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
116 32 0.09
117 311 0.91
ACGTcount: A:0.39, C:0.14, G:0.30, T:0.17
Consensus pattern (117 bp):
AACTGGGACAACCTGGAAACAGGAATTGCCAAGCTAAATGTTGATGGAAGCTGGAATCAAAGAGA
ATGGAAGGCATGAACAGGCAGTCTATTCAAAGGAGAATGGGAAATTTGGACG
Found at i:20214775 original size:23 final size:23
Alignment explanation
Indices: 20214745--20214792 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
20214735 CAAAACGATG
*
20214745 AAATCTTAATA-ACATTTTATTTT
1 AAATCTTAATATA-ATTATATTTT
20214768 AAATCTTAATATAATTATATTTT
1 AAATCTTAATATAATTATATTTT
20214791 AA
1 AA
20214793 TAGTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATCTTAATATAATTATATTTT
Found at i:20215414 original size:21 final size:21
Alignment explanation
Indices: 20215389--20215428 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
20215379 GCAAAAATTA
20215389 GAAAAATTTT-TGAAATTTTGC
1 GAAAAATTTTCT-AAATTTTGC
20215410 GAAAAATTTTCTAAATTTT
1 GAAAAATTTTCTAAATTTT
20215429 CGATTGAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (21 bp):
GAAAAATTTTCTAAATTTTGC
Found at i:20216469 original size:62 final size:62
Alignment explanation
Indices: 20216350--20216470 Score: 188
Period size: 62 Copynumber: 2.0 Consensus size: 62
20216340 AAACCATGCC
* *
20216350 TGTAACACCCCGTACCCGAGACCGTTACCGGAGTCGAACACGAGGTATTTACGGACTTATTT
1 TGTAACACCCCGTACCCGAGACCGTTACCGGAGTCGAACACGAGGGATTTACAGACTTATTT
* * * *
20216412 TGTAACACCCCGTACCCGAGACCGTTGCCGGAGTCGGACACGAGGGGTTTGCAGACTTA
1 TGTAACACCCCGTACCCGAGACCGTTACCGGAGTCGAACACGAGGGATTTACAGACTTA
20216471 AATCACTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.21
Consensus pattern (62 bp):
TGTAACACCCCGTACCCGAGACCGTTACCGGAGTCGAACACGAGGGATTTACAGACTTATTT
Found at i:20235365 original size:19 final size:18
Alignment explanation
Indices: 20235341--20235386 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
20235331 CTTTCTTTCT
*
20235341 TTTGCATTCATTCCATGCA
1 TTTGCATTCATTACAT-CA
*
20235360 TTTGCATAGCATTACATCA
1 TTTGCAT-TCATTACATCA
20235379 TTTGCATT
1 TTTGCATT
20235387 AGATTTTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (18 bp):
TTTGCATTCATTACATCA
Found at i:20239870 original size:45 final size:46
Alignment explanation
Indices: 20239813--20239909 Score: 153
Period size: 45 Copynumber: 2.2 Consensus size: 46
20239803 AGTTGTAGGA
* *
20239813 AGCAGA-CTGAAAATTGCAGATCTTATCTCCATGTATCGGCTATGG
1 AGCAGATCTGAAAATGGCAAATCTTATCTCCATGTATCGGCTATGG
*
20239858 AGCAGATC-GAAAATGGCAAATCTTATTTCCATGTATCGGCTATGG
1 AGCAGATCTGAAAATGGCAAATCTTATCTCCATGTATCGGCTATGG
20239903 AGCAGAT
1 AGCAGAT
20239910 TTTAGCCACC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
45 47 0.98
46 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (46 bp):
AGCAGATCTGAAAATGGCAAATCTTATCTCCATGTATCGGCTATGG
Found at i:20239906 original size:177 final size:177
Alignment explanation
Indices: 20239681--20240216 Score: 880
Period size: 177 Copynumber: 3.0 Consensus size: 177
20239671 GTAGCAAGGA
* *
20239681 AGCAGA-CTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAG
1 AGCAGATC-GAAAATGACAAATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAG
20239745 CCTTATCTCTCTGAGGTAGCAAGAGAACAGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGTA
65 CCTTATCTCTCTGAGGTAGCAAGAGAACAGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGTA
*
20239810 GGAAGCAGACTGAAAATTGCAGATCTTATCTCCATGTATCGGCTATGG
130 GGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGG
* * *
20239858 AGCAGATCGAAAATGGCAAATCTTATTTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGT
1 AGCAGATCGAAAATGACAAATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGC
* *
20239923 CTTATCTCTCTAAGGTAGCAAGAGAACAAGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGTAG
66 CTTATCTCTCTGAGGTAGCAAGAGAACAGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGTAG
* * *
20239988 GAAGCAGATTGAAAATTAAAGATCATATCTCCATGTATCGGCTATGG
131 GAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGG
* * * * *
20240035 AGCAAATCGAAAATGACGAGTCTTATCTCCATGTATCGGCTATAGAGCGGATTTTAGCCACCAGC
1 AGCAGATCGAAAATGACAAATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGC
* *
20240100 CTTATCTCTCTGAGGTAGCAGGAGAACAGGTTGAAGATACAAGTCTTATCTT-CTGAAGTTGCAG
66 CTTATCTCTCTGAGGTAGCAAGAGAACAGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGTAG
20240164 GAAGCAGACTG-AAATTACAGATCTTATCTCCATGTATCGGCTATGG
131 GAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGG
20240210 AGCAGAT
1 AGCAGAT
20240217 TTTAGCCACC
Statistics
Matches: 331, Mismatches: 27, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
175 39 0.12
176 21 0.06
177 270 0.82
178 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (177 bp):
AGCAGATCGAAAATGACAAATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGC
CTTATCTCTCTGAGGTAGCAAGAGAACAGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGTAG
GAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGG
Found at i:20240218 original size:130 final size:132
Alignment explanation
Indices: 20240055--20240348 Score: 484
Period size: 130 Copynumber: 2.2 Consensus size: 132
20240045 AAATGACGAG
* * *
20240055 TCTTATCTCCATGTATCGGCTATAGAGCGGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCA
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCA
* * * *
20240120 GGAGAACAGGTTGAAGATACAAGTCTTATCTT-CTGAAGTTGCAGGAAGCAGACT-GAAATTACA
66 AGAGAACAAGTTAAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTAAAAATTACA
20240183 GA
131 GA
20240185 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCA
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCA
* **
20240250 AGAGAACAAGTTAAAGATACAAGTCTTATCTTCCTGAAGTTGTAGGAAGCAGACTAAAAATTGTA
66 AGAGAACAAGTTAAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTAAAAATTACA
20240315 GA
131 GA
20240317 TCTTATCTCCATGTATCGGCTATGGAGCAGAT
1 TCTTATCTCCATGTATCGGCTATGGAGCAGAT
20240349 CGAAAATGGT
Statistics
Matches: 152, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
130 91 0.60
131 21 0.14
132 40 0.26
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (132 bp):
TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCA
AGAGAACAAGTTAAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTAAAAATTACA
GA
Found at i:20240236 original size:307 final size:310
Alignment explanation
Indices: 20239877--20240504 Score: 1055
Period size: 307 Copynumber: 2.0 Consensus size: 310
20239867 AAAATGGCAA
* *
20239877 ATCTTATTTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGTCTTATCTCTCTAAGGTAGC
1 ATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGC
* * *
20239942 AAGAGAACAAGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGTAGGAAGCAGATTGAAAATTAA
66 AAGAGAACAAGTTAAAGATACAAGTCTTATCTTCCTGAAGTTGTAGGAAGCAGACTAAAAATTAA
*
20240007 AGATCATATCTCCATGTATCGGCTATGGAGCAAATCGAAAATGACGAGTCTTATCTCCATGTATC
131 AGATCATATCTCCATGTATCGGCTATGGAGCAAATCGAAAATGACAAGTCTTATCTCCATGTATC
* * *
20240072 GGCTATAGAGCGGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAGGAGAACAGGTTGAAGA
196 GGCTATAGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAACAGGTTAAAGA
20240137 TACAA-GTCTTATCTTC-TGAAGTTGCAGGAAGCAGACTGAAA-TTACAG
261 TACAATGTCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAAAGTTACAG
20240184 ATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGC
1 ATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGC
**
20240249 AAGAGAACAAGTTAAAGATACAAGTCTTATCTTCCTGAAGTTGTAGGAAGCAGACTAAAAATTGT
66 AAGAGAACAAGTTAAAGATACAAGTCTTATCTTCCTGAAGTTGTAGGAAGCAGACTAAAAATTAA
* * ** *
20240314 AGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGTAAGTCTTATTTCCATGTATC
131 AGATCATATCTCCATGTATCGGCTATGGAGCAAATCGAAAATGACAAGTCTTATCTCCATGTATC
* * * *
20240379 GGTTATGGAGCAGATTTTAGCCACCAGTCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTAAAGA
196 GGCTATAGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAACAGGTTAAAGA
20240444 TACAATGTCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAAAGTTACAG
261 TACAATGTCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAAAGTTACAG
20240494 ATCTTATCTCC
1 ATCTTATCTCC
20240505 CTAAACAGTA
Statistics
Matches: 298, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
307 245 0.82
308 11 0.04
309 25 0.08
310 17 0.06
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (310 bp):
ATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGC
AAGAGAACAAGTTAAAGATACAAGTCTTATCTTCCTGAAGTTGTAGGAAGCAGACTAAAAATTAA
AGATCATATCTCCATGTATCGGCTATGGAGCAAATCGAAAATGACAAGTCTTATCTCCATGTATC
GGCTATAGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAACAGGTTAAAGA
TACAATGTCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAAAGTTACAG
Found at i:20240395 original size:177 final size:178
Alignment explanation
Indices: 20240185--20240504 Score: 525
Period size: 177 Copynumber: 1.8 Consensus size: 178
20240175 AAATTACAGA
20240185 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCA
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCA
* **
20240250 AGAGAACAAGTTAAAGATACAA-GTCTTATCTTCCTGAAGTTGTAGGAAGCAGACTAAAAATTGT
66 AGAGAACAAGTTAAAGATACAATGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTAAAAATTAC
20240314 AGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGTAAG
131 AGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGTAAG
* * * *
20240362 TCTTATTTCCATGTATCGGTTATGGAGCAGATTTTAGCCACCAGTCTTATCTCTCTGAGGTAGCA
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCA
* * * * *
20240427 AGAGAGCAGGTTAAAGATACAATGTCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAAAGTTAC
66 AGAGAACAAGTTAAAGATACAATGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTAAAAATTAC
20240492 AGATCTTATCTCC
131 AGATCTTATCTCC
20240505 CTAAACAGTA
Statistics
Matches: 130, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
177 81 0.62
178 49 0.38
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (178 bp):
TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCA
AGAGAACAAGTTAAAGATACAATGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTAAAAATTAC
AGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGTAAG
Found at i:20240523 original size:44 final size:44
Alignment explanation
Indices: 20240475--20240696 Score: 142
Period size: 44 Copynumber: 5.1 Consensus size: 44
20240465 AGTTGCAGGA
* * *
20240475 AGCAGACT-GAAAGTTACAGATCTTATCTCCCTAAACAGTAGTGG
1 AGCAGACTCG-AAGATACAGATCTTATCCCCCTAAGCAGTAGTGG
** * *
20240519 AGCAGA-TCGAAGATAGTGAGCCTTAACCCCCTAAGCAGTAG-GG
1 AGCAGACTCGAAGATACAGA-TCTTATCCCCCTAAGCAGTAGTGG
* * * * *
20240562 TAACAGGCTAGAAAATACAGATC---T-CCCCTAAACAGTAGTGG
1 -AGCAGACTCGAAGATACAGATCTTATCCCCCTAAGCAGTAGTGG
* * *
20240603 AGCAGA-TCGAAGACA-ATGAGCCTTATCCCCCTATGCAGTAG-GG
1 AGCAGACTCGAAGATACA-GA-TCTTATCCCCCTAAGCAGTAGTGG
* * *
20240646 AAACAGACT-GAAGATTACAGATCATATCTCCCTAAGCAGTAGTGG
1 -AGCAGACTCGAAGA-TACAGATCTTATCCCCCTAAGCAGTAGTGG
20240691 AGCAGA
1 AGCAGA
20240697 TTGAAGCAAC
Statistics
Matches: 131, Mismatches: 31, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
38 1 0.01
39 8 0.06
40 18 0.14
41 2 0.02
43 13 0.10
44 73 0.56
45 15 0.11
46 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (44 bp):
AGCAGACTCGAAGATACAGATCTTATCCCCCTAAGCAGTAGTGG
Found at i:20240607 original size:84 final size:84
Alignment explanation
Indices: 20240499--20240702 Score: 268
Period size: 84 Copynumber: 2.4 Consensus size: 84
20240489 TACAGATCTT
* * *
20240499 ATCT-CCCTAAACAGTAGTGGAGCAGATCGAAGATAGTGAGCCTTAACCCCCTAAGCAGTAGGGT
1 ATCTCCCCTAAACAGTAGTGGAGCAGATCGAAGACAATGAGCCTTAACCCCCTAAGCAGTAGGGA
*
20240563 AACAGGCTAGAA-AATACAG
66 AACAGACT-GAAGAATACAG
* *
20240582 ATCTCCCCTAAACAGTAGTGGAGCAGATCGAAGACAATGAGCCTTATCCCCCTATGCAGTAGGGA
1 ATCTCCCCTAAACAGTAGTGGAGCAGATCGAAGACAATGAGCCTTAACCCCCTAAGCAGTAGGGA
*
20240647 AACAGACTGAAGATTACAG
66 AACAGACTGAAGAATACAG
* *
20240666 ATCATATCTCCCTAAGCAGTAGTGGAGCAGATTGAAG
1 ATC---TC-CCCTAAACAGTAGTGGAGCAGATCGAAG
20240703 CAACAATTTC
Statistics
Matches: 106, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
83 7 0.07
84 71 0.67
87 2 0.02
88 26 0.25
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (84 bp):
ATCTCCCCTAAACAGTAGTGGAGCAGATCGAAGACAATGAGCCTTAACCCCCTAAGCAGTAGGGA
AACAGACTGAAGAATACAG
Found at i:20242977 original size:22 final size:22
Alignment explanation
Indices: 20242949--20242993 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
20242939 AACTTACGAA
20242949 TAATTCACAATTAATATAACAT
1 TAATTCACAATTAATATAACAT
*
20242971 TAATTCATAATTAATATAACAT
1 TAATTCACAATTAATATAACAT
20242993 T
1 T
20242994 CATAGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATTCACAATTAATATAACAT
Found at i:20243928 original size:29 final size:27
Alignment explanation
Indices: 20243878--20243945 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
20243868 CAGATTCCAT
* *
20243878 CCAAACACACTAGAATATTATAAATCCTC
1 CCAAACACACCAGAATA--ATATATCCTC
** *
20243907 CGTAACACACCAGTATAATATATCCTC
1 CCAAACACACCAGAATAATATATCCTC
20243934 CCAAACACACCA
1 CCAAACACACCA
20243946 ATAAGGCATT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
27 19 0.59
29 13 0.41
ACGTcount: A:0.43, C:0.32, G:0.04, T:0.21
Consensus pattern (27 bp):
CCAAACACACCAGAATAATATATCCTC
Found at i:20244564 original size:51 final size:52
Alignment explanation
Indices: 20244488--20244610 Score: 169
Period size: 51 Copynumber: 2.4 Consensus size: 52
20244478 TCCCAAACTT
* * * *
20244488 ACTTCATACTTCATCCGGA-ATTATTACTTTGTTGTTCTGGCTTCAACAAGA
1 ACTTCATATTTCATCCGGATATTATTACTTTATTGCTCTAGCTTCAACAAGA
*
20244539 ACTTCATATTTCATCCGGATA-TATTACTTTATTGCTCTAGTTTCAACAAGA
1 ACTTCATATTTCATCCGGATATTATTACTTTATTGCTCTAGCTTCAACAAGA
* *
20244590 GCTTCATATTTCATCCAGATA
1 ACTTCATATTTCATCCGGATA
20244611 ACTTAGTTCT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
51 63 0.98
52 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (52 bp):
ACTTCATATTTCATCCGGATATTATTACTTTATTGCTCTAGCTTCAACAAGA
Found at i:20245506 original size:16 final size:16
Alignment explanation
Indices: 20245468--20245517 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
20245458 TCTATAATTC
*
20245468 ATATTATAATTTAAATA
1 ATATAATAA-TTAAATA
* *
20245485 AAATAATAATTATATA
1 ATATAATAATTAAATA
*
20245501 ATATAATAATTTAATA
1 ATATAATAATTAAATA
20245517 A
1 A
20245518 AGTAAGAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAATAATTAAATA
Found at i:20246515 original size:20 final size:19
Alignment explanation
Indices: 20246492--20246529 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
20246482 TTAAGGACTT
*
20246492 TTTAATTTAATTAAGTTTTA
1 TTTAAATTAA-TAAGTTTTA
20246512 TTTAAATTAATAAGTTTT
1 TTTAAATTAATAAGTTTT
20246530 CATATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTAAATTAATAAGTTTTA
Found at i:20246855 original size:9 final size:9
Alignment explanation
Indices: 20246837--20246899 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
20246827 TTTATTTAAG
20246837 TTAA-GTGT
1 TTAATGTGT
20246845 TTAATGTGT
1 TTAATGTGT
20246854 TT--TGTGT
1 TTAATGTGT
20246861 TTAATAAGTGT
1 TTAAT--GTGT
*
20246872 TTAATATG-
1 TTAATGTGT
20246880 TT--TGT-T
1 TTAATGTGT
20246886 TTAATGTGT
1 TTAATGTGT
20246895 TTAAT
1 TTAAT
20246900 TGCAGGTGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 17
0.70 0.03 0.27
Matches are distributed among these distances:
6 4 0.09
7 7 0.16
8 9 0.20
9 15 0.34
11 9 0.20
ACGTcount: A:0.24, C:0.00, G:0.19, T:0.57
Consensus pattern (9 bp):
TTAATGTGT
Found at i:20246868 original size:27 final size:25
Alignment explanation
Indices: 20246838--20246899 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 25
20246828 TTATTTAAGT
*
20246838 TAAGTGTTTAATGTGTTTTGTGTTTAA
1 TAAGTGTTTAATATG-TTTGT-TTTAA
20246865 TAAGTGTTTAATATGTTTGTTTTAA
1 TAAGTGTTTAATATGTTTGTTTTAA
20246890 T--GTGTTTAAT
1 TAAGTGTTTAAT
20246900 TGCAGGTGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 9 0.26
25 6 0.18
26 5 0.15
27 14 0.41
ACGTcount: A:0.24, C:0.00, G:0.19, T:0.56
Consensus pattern (25 bp):
TAAGTGTTTAATATGTTTGTTTTAA
Found at i:20255943 original size:104 final size:104
Alignment explanation
Indices: 20255763--20255986 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
20255753 TGTATATAAA
** * *
20255763 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
20255828 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
20255867 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
20255931 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
20255971 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
20255987 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:20256038 original size:71 final size:72
Alignment explanation
Indices: 20255905--20256056 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
20255895 TCATTGGTGG
* *
20255905 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
20255970 GAGGGGT
66 GAGGGGT
***
20255977 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
20256041 GAGGGGT
66 GAGGGGT
20256048 TGCTAAGTG
1 TGCTAAGTG
20256057 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:20262253 original size:14 final size:15
Alignment explanation
Indices: 20262223--20262252 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20262213 CGAAAATGTC
20262223 TACTTAAATTTTTTT
1 TACTTAAATTTTTTT
20262238 TACTTAAATTTTTTT
1 TACTTAAATTTTTTT
20262253 AGAGGTGCAA
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:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TACTTAAATTTTTTT
Found at i:20262612 original size:41 final size:40
Alignment explanation
Indices: 20262557--20262643 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 40
20262547 TCAAATACAT
* *
20262557 TTAAAATAAATATTAAAATAAGAAACAAATAAAAAATTATA
1 TTAAAACAAATATTAAAACAAGAAACAAATAAAAAA-TATA
* * * *
20262598 TTAAAACAATTATTAAAACAATACACAAATTAAAAATATA
1 TTAAAACAAATATTAAAACAAGAAACAAATAAAAAATATA
*
20262638 ATAAAA
1 TTAAAA
20262644 AGTGATTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 9 0.23
41 30 0.77
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.26
Consensus pattern (40 bp):
TTAAAACAAATATTAAAACAAGAAACAAATAAAAAATATA
Found at i:20262694 original size:27 final size:26
Alignment explanation
Indices: 20262626--20262697 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 26
20262616 CAATACACAA
* *
20262626 ATTAAAAATATAATAAAAAGTGATTAT
1 ATTAAAAATA-AATAAAAAGTAAATAT
* *
20262653 ATTAAAATTAAAAATAAAATGTAAATAT
1 ATTAAAA--ATAAATAAAAAGTAAATAT
20262681 GATTAAAAATAAATAAA
1 -ATTAAAAATAAATAAA
20262698 TATATATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
27 15 0.41
28 13 0.35
29 9 0.24
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (26 bp):
ATTAAAAATAAATAAAAAGTAAATAT
Found at i:20262699 original size:20 final size:22
Alignment explanation
Indices: 20262659--20262700 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
20262649 TTATATTAAA
20262659 ATTAAAAATAAAATGTAAATATG
1 ATTAAAAATAAAA-GTAAATATG
20262682 ATTAAAAAT-AAA-TAAATAT
1 ATTAAAAATAAAAGTAAATAT
20262701 ATATATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
22 3 0.16
23 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
ATTAAAAATAAAAGTAAATATG
Found at i:20266950 original size:17 final size:17
Alignment explanation
Indices: 20266925--20266963 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
20266915 AAAAATTTTA
*
20266925 AATTTGTTATGTGATTT
1 AATTAGTTATGTGATTT
20266942 AATTAGTTATGTGATTT
1 AATTAGTTATGTGATTT
20266959 AATTA
1 AATTA
20266964 TTTTAGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (17 bp):
AATTAGTTATGTGATTT
Found at i:20272605 original size:20 final size:20
Alignment explanation
Indices: 20272577--20272614 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20272567 CAGTAAGATT
* *
20272577 TATTTTAGTATCAAATTTGA
1 TATTGTAGTATAAAATTTGA
20272597 TATTGTAGTATAAAATTT
1 TATTGTAGTATAAAATTT
20272615 TAATATAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50
Consensus pattern (20 bp):
TATTGTAGTATAAAATTTGA
Done.