Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold109
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: 1855911
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.34
Warning! 69956 characters in sequence are not A, C, G, or T
File 12 of 13
Found at i:1653160 original size:18 final size:19
Alignment explanation
Indices: 1653124--1653165 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
1653114 AGATATAATA
*
1653124 ATTTATATATTTATATTAT
1 ATTTAAATATTTATATTAT
1653143 ATTTAAATATTT-TATTAT
1 ATTTAAATATTTATATTAT
1653161 ATTTA
1 ATTTA
1653166 TAATTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTAAATATTTATATTAT
Found at i:1653198 original size:30 final size:29
Alignment explanation
Indices: 1653120--1653198 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 29
1653110 TTTTAGATAT
*
1653120 AATAATTTATATATTTAT-ATTATATTTA
1 AATATTTTATATATTTATAATTATATTTA
1653148 AATATTTTATTATATTTATAATTATATTTA
1 AATATTTTA-TATATTTATAATTATATTTA
1653178 AACTATTTTATAT-TTATATAA
1 AA-TATTTTATATATT-TATAA
1653199 ATTTTAAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
28 8 0.17
29 11 0.24
30 20 0.43
31 7 0.15
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
AATATTTTATATATTTATAATTATATTTA
Found at i:1653798 original size:20 final size:23
Alignment explanation
Indices: 1653768--1653810 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 23
1653758 TTTAAAAATA
1653768 AATATAAATAAT-TT-TATTTTT
1 AATATAAATAATATTATATTTTT
1653789 AATA-AAATAATATTATATTTTT
1 AATATAAATAATATTATATTTTT
1653811 TAGTTGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 6 0.30
22 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATATAAATAATATTATATTTTT
Found at i:1655994 original size:19 final size:20
Alignment explanation
Indices: 1655949--1655994 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1655939 TTTTTAATAA
*
1655949 ATAAAATATTACAAAGTATT
1 ATAAAATATTACAAAGAATT
*
1655969 ATAAAATATTTCAAA-AATT
1 ATAAAATATTACAAAGAATT
*
1655988 ATTAAAT
1 ATAAAAT
1655995 TTTTTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
ATAAAATATTACAAAGAATT
Found at i:1667272 original size:21 final size:20
Alignment explanation
Indices: 1667248--1667292 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1667238 TTTATCTTTT
1667248 AATTTAAAAAAATTACTACTC
1 AATTTAAAAAAATTACT-CTC
1667269 AA-TTAAAAAAATTACTCTC
1 AATTTAAAAAAATTACTCTC
*
1667288 TATTT
1 AATTT
1667293 TTTTAACTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 16 0.73
21 2 0.09
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTAAAAAAATTACTCTC
Found at i:1672523 original size:429 final size:430
Alignment explanation
Indices: 1671723--1672582 Score: 1496
Period size: 429 Copynumber: 2.0 Consensus size: 430
1671713 GAGGTAAACA
1671723 CTACATCTGAACCTATTTTTGAAATAGATACTAATCTTTATCTACTAATTGCCTTAAGGAAAAAA
1 CTACATCTGAACCTATTTTTGAAATAGATACTAATCTTTATCTACTAATTGCCTTAAGGAAAAAA
*
1671788 CCTAGAGAATGTACTAAACACCCTTTATATCCAATATCAAATTTTGTGTCTTTTGATAAATTTTT
66 CCTAGAGAATGTACTAAACACCCTTTATATCCAATATCAAATTTTGTGTCTTTTGATAAATTTTC
* *
1671853 CTCATCTTATAAGGCATTTCTTTTGAGCCTAAATACTATCTCGATTCCTAAAACTTTATCTAAAG
131 CTCATCCTATAAGGCATTTCTTTTGAGCCTAAATACTATCTCGATTCCTAAAACTTTACCTAAAG
* * * *
1671918 CATTGTTCAAAGAAGAGTGGAGGGAAGCTATGAGAGTAGAAATGGAGGCATTAGAGAAAAATAGA
196 CATTGTTCAAAGAAGAGTGGAGGGAAGCCATGAGAGTAGAAATAGAGGCATTAGAGAAAAACAAA
1671983 ACTCGGGAAATTGTAAAACTACTAAAAAGAAAAAAACCAGTAAGTTGTAAATGGCTTTTCTCAGT
261 ACTCGGGAAATTGTAAAACTACTAAAAAGAAAAAAACCAGTAAGTTGTAAATGGCTTTTCTCAGT
*
1672048 GAAGTATAAGGTAGATGGTAAACTAGAGAGATATAAAACTAGGCTGGTAGCTAAGAGTTACACTC
326 GAAGTATAAGGCAGATGGTAAACTAGAGAGATATAAAACTAGGCTGGTAGCTAAGAGTTACACTC
1672113 AAACTTGTAGGGTAGACTACCAA-GAAACCTTTGCCCCAAT
391 AAACTTGTAGGGTAGACTA-CAAGGAAACCTTTGCCCCAAT
*
1672153 CTACATCTGAACCTATTTTTGAAATAGATACTGATCTTTATCTACTAATTGCCTTAAGGAAAAAA
1 CTACATCTGAACCTATTTTTGAAATAGATACTAATCTTTATCTACTAATTGCCTTAAGG-AAAAA
*
1672218 ACCTAGAGAATGTACTAAACACCCTTTATATCTAATATCAAA-TTT-TGTCTTTTGATAAATTTT
65 ACCTAGAGAATGTACTAAACACCCTTTATATCCAATATCAAATTTTGTGTCTTTTGATAAATTTT
1672281 CCTCATCCTAT-AGGACATTTCTTTTGAGCCTAAATACTATCTCGATTCCTAAAACTTTACCTAA
130 CCTCATCCTATAAGG-CATTTCTTTTGAGCCTAAATACTATCTCGATTCCTAAAACTTTACCTAA
1672345 AGCATTGTTCAAAGAAGAGTGGAGGGAAGCCATGAGAGTA-AAACTAGAGGCATTAGAGAAAAAC
194 AGCATTGTTCAAAGAAGAGTGGAGGGAAGCCATGAGAGTAGAAA-TAGAGGCATTAGAGAAAAAC
* * * *
1672409 AAAACTTGGGAAATTGTAGAACTACTAAAAGGAAAAAAACCAGTAGGTTGTAAATGGCTTTTCTC
258 AAAACTCGGGAAATTGTAAAACTACTAAAAAGAAAAAAACCAGTAAGTTGTAAATGGCTTTTCTC
*
1672474 AGTGAAGTATAAGGCAGATGGTAAACTAGAGAGATATAAAGCTAGGCTGGTAGCTAAGAGTTACA
323 AGTGAAGTATAAGGCAGATGGTAAACTAGAGAGATATAAAACTAGGCTGGTAGCTAAGAGTTACA
* *
1672539 CTCAAACTTGTGGGGTAGACTACAAGGAAACCTTTGTCCCAAT
388 CTCAAACTTGTAGGGTAGACTACAAGGAAACCTTTGCCCCAAT
1672582 C
1 C
1672583 GCAAAATTAA
Statistics
Matches: 409, Mismatches: 17, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
428 9 0.02
429 293 0.72
430 61 0.15
431 46 0.11
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (430 bp):
CTACATCTGAACCTATTTTTGAAATAGATACTAATCTTTATCTACTAATTGCCTTAAGGAAAAAA
CCTAGAGAATGTACTAAACACCCTTTATATCCAATATCAAATTTTGTGTCTTTTGATAAATTTTC
CTCATCCTATAAGGCATTTCTTTTGAGCCTAAATACTATCTCGATTCCTAAAACTTTACCTAAAG
CATTGTTCAAAGAAGAGTGGAGGGAAGCCATGAGAGTAGAAATAGAGGCATTAGAGAAAAACAAA
ACTCGGGAAATTGTAAAACTACTAAAAAGAAAAAAACCAGTAAGTTGTAAATGGCTTTTCTCAGT
GAAGTATAAGGCAGATGGTAAACTAGAGAGATATAAAACTAGGCTGGTAGCTAAGAGTTACACTC
AAACTTGTAGGGTAGACTACAAGGAAACCTTTGCCCCAAT
Found at i:1672858 original size:43 final size:43
Alignment explanation
Indices: 1672797--1672882 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
1672787 CCAAGGGCTT
*
1672797 AGTTTGGGAAGTTTACAAAGGTAATGATAACCAACGGATGCAA
1 AGTTTGGAAAGTTTACAAAGGTAATGATAACCAACGGATGCAA
1672840 AGTTTGGAAAGTTTACAAAGGTAATGATAACCAACGGATGCAA
1 AGTTTGGAAAGTTTACAAAGGTAATGATAACCAACGGATGCAA
1672883 CCAAAAGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (43 bp):
AGTTTGGAAAGTTTACAAAGGTAATGATAACCAACGGATGCAA
Found at i:1673819 original size:18 final size:17
Alignment explanation
Indices: 1673795--1673832 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1673785 ATTCGTGTTT
1673795 GTATTATT-T-TTTAAG
1 GTATTATTATATTTAAG
*
1673810 TTATTATTATATTTAAG
1 GTATTATTATATTTAAG
1673827 GTATTA
1 GTATTA
1673833 AATTTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 7 0.37
16 1 0.05
17 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (17 bp):
GTATTATTATATTTAAG
Found at i:1674313 original size:20 final size:18
Alignment explanation
Indices: 1674288--1674325 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 18
1674278 TATTTTTCTA
1674288 ATAACAATATATATATATAT
1 ATAAC-ATATA-ATATATAT
1674308 ATAACATATAATATATAT
1 ATAACATATAATATATAT
1674326 TGGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 5 0.28
20 5 0.28
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAACATATAATATATAT
Found at i:1675145 original size:20 final size:20
Alignment explanation
Indices: 1675122--1675168 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1675112 CTAATATTAA
*
1675122 TTTATTATTAAAATTATATT
1 TTTAATATTAAAATTATATT
*
1675142 TTTAATATTTAAATTATA-T
1 TTTAATATTAAAATTATATT
1675161 TTTAATAT
1 TTTAATAT
1675169 AATTGATCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAATATTAAAATTATATT
Found at i:1675808 original size:21 final size:22
Alignment explanation
Indices: 1675786--1675854 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
1675776 CGTTCAATTT
1675786 AATAAATTTAATTTAAATTTTA
1 AATAAATTTAATTTAAATTTTA
*
1675808 AATAAA---AATTTATAAATTTA
1 AATAAATTTAATTTA-AATTTTA
* * *
1675828 AATTAATTTAATTTAATTTTTC
1 AATAAATTTAATTTAAATTTTA
1675850 AATAA
1 AATAA
1675855 TAAAAAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
19 6 0.16
20 11 0.30
22 14 0.38
23 6 0.16
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAAATTTAATTTAAATTTTA
Found at i:1675839 original size:42 final size:46
Alignment explanation
Indices: 1675781--1675883 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 46
1675771 TTATCCGTTC
*
1675781 AATTT-AATAAATTTAATTTAAATTTT-A-AAT-AAAAAT-TTATA
1 AATTTAAATTAATTTAATTTAAATTTTAATAATAAAAAATATTATA
* *
1675822 AATTTAAATTAATTTAATTTAATTTTTCAATAATAAAAAATATTTTA
1 AATTTAAATTAATTTAATTTAAATTTT-AATAATAAAAAATATTATA
1675869 AATTTAAATTTAATT
1 AATTTAAA-TTAATT
1675884 ATAAAAATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
41 5 0.10
42 19 0.37
44 1 0.02
45 3 0.06
46 6 0.12
47 12 0.23
48 6 0.12
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (46 bp):
AATTTAAATTAATTTAATTTAAATTTTAATAATAAAAAATATTATA
Found at i:1676379 original size:5 final size:5
Alignment explanation
Indices: 1676369--1676404 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
1676359 TATTATTTTC
1676369 TTTAA TTTAA -TT-A TTTAA TTTAA TTTAA TTT-A TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
1676405 TCGTGTATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
3 1 0.04
4 8 0.29
5 19 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:1676383 original size:18 final size:18
Alignment explanation
Indices: 1676369--1676404 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
1676359 TATTATTTTC
1676369 TTTAATTTAATTATTTAA
1 TTTAATTTAATTATTTAA
1676387 TTTAATTTAATTTATTTA
1 TTTAATTTAA-TTATTTA
1676405 TCGTGTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAATTTAATTATTTAA
Found at i:1676387 original size:13 final size:13
Alignment explanation
Indices: 1676369--1676393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1676359 TATTATTTTC
1676369 TTTAATTTAATTA
1 TTTAATTTAATTA
1676382 TTTAATTTAATT
1 TTTAATTTAATT
1676394 TAATTTATTT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTAATTTAATTA
Found at i:1677956 original size:38 final size:35
Alignment explanation
Indices: 1677914--1678034 Score: 101
Period size: 32 Copynumber: 3.5 Consensus size: 35
1677904 ATTATGGTGT
1677914 TATAAATATAATATAAAATTAATTAAAATATAATATAA
1 TATAAATAT-ATATAAAATT-ATTAAAAT-TAATATAA
* *
1677952 TATAAATATATA-AATATT-TTAAAATTTATATAA
1 TATAAATATATATAAAATTATTAAAATTAATATAA
* * * *
1677985 TTTAAAT-TATA-AATA-TATCAAAATTTATATAA
1 TATAAATATATATAAAATTATTAAAATTAATATAA
*
1678017 TTATAAA-ATATATTAAAT
1 -TATAAATATATATAAAAT
1678035 ATAATTATAA
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
31 1 0.01
32 22 0.31
33 22 0.31
34 9 0.13
36 5 0.07
37 3 0.04
38 9 0.13
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (35 bp):
TATAAATATATATAAAATTATTAAAATTAATATAA
Found at i:1677964 original size:8 final size:8
Alignment explanation
Indices: 1677937--1678066 Score: 62
Period size: 8 Copynumber: 16.0 Consensus size: 8
1677927 TAAAATTAAT
1677937 TAAA-ATA
1 TAAATATA
1677944 TAATATAATA
1 TAA-AT-ATA
1677954 TAAATATA
1 TAAATATA
*
1677962 TAAATATTT
1 TAAATA-TA
*
1677971 TAAAATTTA
1 T-AAATATA
1677980 TATAAT-T-
1 TA-AATATA
1677987 TAAAT-TA
1 TAAATATA
1677994 TAAATATA
1 TAAATATA
*
1678002 TCAAAATTTA
1 T--AAATATA
1678012 TATAAT-TA
1 TA-AATATA
1678020 TAAAATATA
1 T-AAATATA
*
1678029 TTAA-ATA
1 TAAATATA
1678036 T-AAT-TA
1 TAAATATA
1678042 TAACAT-TA
1 TAA-ATATA
1678050 TAAAATATA
1 T-AAATATA
1678059 TAAATATA
1 TAAATATA
1678067 ATATAAACAC
Statistics
Matches: 100, Mismatches: 5, Indels: 35
0.71 0.04 0.25
Matches are distributed among these distances:
6 9 0.09
7 15 0.15
8 38 0.38
9 21 0.21
10 17 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (8 bp):
TAAATATA
Found at i:1678008 original size:32 final size:33
Alignment explanation
Indices: 1677946--1678037 Score: 123
Period size: 32 Copynumber: 2.7 Consensus size: 33
1677936 TTAAAATATA
* * *
1677946 ATATAATATAAATATATAAATATTTTAAAATTT
1 ATATAATTTAAATATATAAATATATCAAAATTT
1677979 ATATAATTTAAAT-TATAAATATATCAAAATTT
1 ATATAATTTAAATATATAAATATATCAAAATTT
1678011 ATATAATTATAAAATATATTAAATATA
1 ATATAATT-T-AAATATA-TAAATATA
1678038 ATTATAACAT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
32 25 0.48
33 13 0.25
34 4 0.08
35 2 0.04
36 8 0.15
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
ATATAATTTAAATATATAAATATATCAAAATTT
Found at i:1678015 original size:20 final size:19
Alignment explanation
Indices: 1677992--1678073 Score: 59
Period size: 17 Copynumber: 4.3 Consensus size: 19
1677982 TAATTTAAAT
*
1677992 TATAAATATATCAAAATTTA
1 TATAAATATAT-AAAATATA
1678012 TAT-AAT-TATAAAATATA
1 TATAAATATATAAAATATA
1678029 T-TAAATATAATTATAACAT-TA
1 TATAAATAT-A-TA-AA-ATATA
1678050 TA-AAATATAT-AAATATAA
1 TATAAATATATAAAATAT-A
1678068 TATAAA
1 TATAAA
1678074 CACACTAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 21
0.70 0.01 0.29
Matches are distributed among these distances:
16 3 0.06
17 14 0.27
18 7 0.14
19 8 0.16
20 6 0.12
21 11 0.22
22 2 0.04
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
TATAAATATATAAAATATA
Found at i:1678036 original size:22 final size:21
Alignment explanation
Indices: 1678011--1678058 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
1678001 ATCAAAATTT
*
1678011 ATATAATTATAAAATATATTAA
1 ATATAATTATAAAAT-TATAAA
*
1678033 ATATAATTATAACATTATAAA
1 ATATAATTATAAAATTATAAA
1678054 ATATA
1 ATATA
1678059 TAAATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATAATTATAAAATTATAAA
Found at i:1678050 original size:30 final size:29
Alignment explanation
Indices: 1677916--1678073 Score: 115
Period size: 30 Copynumber: 5.6 Consensus size: 29
1677906 TATGGTGTTA
*
1677916 TAAATATAA-TATAAAATTAATTAAAATATAA
1 TAAATATAATTAT-AAATT-A-TAAAATATAT
* *
1677947 TATAATATAAATATATAAATATTTTAAA-AT-T
1 TA-AATAT-AAT-TATAAAT-TATAAAATATAT
1677978 T--ATATAATT-TAAATTAT-AAATATAT
1 TAAATATAATTATAAATTATAAAATATAT
*
1678003 CAAA-AT--TTATATAATTATAAAATATAT
1 TAAATATAATTATA-AATTATAAAATATAT
1678030 TAAATATAATTATAACATTATAAAATATA-
1 TAAATATAATTATAA-ATTATAAAATATAT
1678059 TAAATATAA-TATAAA
1 TAAATATAATTATAAA
1678074 CACACTAATT
Statistics
Matches: 105, Mismatches: 6, Indels: 36
0.71 0.04 0.24
Matches are distributed among these distances:
23 3 0.03
24 6 0.06
25 8 0.08
26 9 0.09
27 16 0.15
28 11 0.10
29 10 0.10
30 18 0.17
31 3 0.03
32 7 0.07
33 6 0.06
34 4 0.04
35 4 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAATATAATTATAAATTATAAAATATAT
Found at i:1678232 original size:11 final size:10
Alignment explanation
Indices: 1678212--1678305 Score: 63
Period size: 9 Copynumber: 9.6 Consensus size: 10
1678202 GATAATTTTA
*
1678212 AATATGATATT
1 AATATAATA-T
1678223 AATATAATAT
1 AATATAATAT
* *
1678233 ATTATAAAAAT
1 AATAT-AATAT
*
1678244 ATTATAATA-
1 AATATAATAT
1678253 AATATAATAT
1 AATATAATAT
*
1678263 -ATTTAAATAT
1 AATAT-AATAT
1678273 AAT-TAATAT
1 AATATAATAT
*
1678282 AA-ATAACAT
1 AATATAATAT
*
1678291 AATAT-ATTT
1 AATATAATAT
1678300 AATATA
1 AATATA
1678306 CGTATCATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
9 32 0.48
10 16 0.24
11 19 0.28
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (10 bp):
AATATAATAT
Found at i:1678258 original size:30 final size:30
Alignment explanation
Indices: 1678218--1678301 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 30
1678208 TTTAAATATG
*
1678218 ATATTAATATAATATATTATAAAAAT-ATT-
1 ATATAAATATAATATATT-TAAAAATAATTA
*
1678247 ATAATAAATATAATATATTTAAATATAATTA
1 AT-ATAAATATAATATATTTAAAAATAATTA
1678278 ATATAAATAACATAATATATTTAA
1 ATATAAAT---ATAATATATTTAA
1678302 TATACGTATC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
29 8 0.17
30 24 0.51
31 2 0.04
33 13 0.28
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (30 bp):
ATATAAATATAATATATTTAAAAATAATTA
Found at i:1678815 original size:21 final size:19
Alignment explanation
Indices: 1678789--1678833 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1678779 AATCTGAAAT
1678789 TTAAAAAACATATGAAAAAAA
1 TTAAAAAACAT-TG-AAAAAA
*
1678810 TTAAAAAATATTGAAAAAA
1 TTAAAAAACATTGAAAAAA
1678829 TTAAA
1 TTAAA
1678834 TATAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
20 2 0.09
21 10 0.43
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (19 bp):
TTAAAAAACATTGAAAAAA
Found at i:1679265 original size:14 final size:15
Alignment explanation
Indices: 1679218--1679265 Score: 73
Period size: 14 Copynumber: 3.3 Consensus size: 15
1679208 AATTTTTTTA
1679218 TTTTTATAAATAAAT
1 TTTTTATAAATAAAT
*
1679233 TTTTTATAAA-ATAT
1 TTTTTATAAATAAAT
1679247 TTTTTA-AAATAAAT
1 TTTTTATAAATAAAT
1679261 TTTTT
1 TTTTT
1679266 TTATGGCTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 3 0.10
14 17 0.57
15 10 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTTATAAATAAAT
Found at i:1679266 original size:15 final size:15
Alignment explanation
Indices: 1679218--1679266 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
1679208 AATTTTTTTA
1679218 TTTTTATAAATAAATT
1 TTTTTA-AAATAAATT
1679234 TTTTATAAAAT--A-T
1 TTTT-TAAAATAAATT
1679247 TTTTTAAAATAAATT
1 TTTTTAAAATAAATT
1679262 TTTTT
1 TTTTT
1679267 TATGGCTACG
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 6 0.21
13 5 0.17
14 2 0.07
15 6 0.21
16 8 0.28
17 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTAAAATAAATT
Found at i:1679655 original size:117 final size:116
Alignment explanation
Indices: 1679442--1679719 Score: 290
Period size: 117 Copynumber: 2.4 Consensus size: 116
1679432 AATTTTTTAA
* * *
1679442 TAAAAATAATATCTAATTAACTTTAAAAAGATTCACATTAATAAATTAAAATATTCATTATTTTT
1 TAAAAATAATATCTAATTAACTTTAAAAAAATTCACATTAACAAATTAAAATATTAATTATTTTT
* *
1679507 TAAAATAAAAATTAAATTAAAAAAGTTTATTATTATTATTTTTTAATAAAAT
66 T-AAATAAAAATAAAAGTAAAAAAGTTTATTATTATTATTTTTTAATAAAAT
* *
1679559 TAAAAATAATATTTAATTAAGTTTAAAAAAATT-ACATTAACAAATTAAAATATTAATTATATGT
1 TAAAAATAATATCTAATTAACTTTAAAAAAATTCACATTAACAAATTAAAATATTAATTAT-T-T
* *
1679623 TTT-TATAAAAATAAAAAGT-----A-TTTATTATTATTA-TTATTAAT-AAAT
64 TTTAAATAAAAAT-AAAAGTAAAAAAGTTTATTATTATTATTTTTTAATAAAAT
** * * * *
1679668 TATCTAATAATAT-TAAATTAAATTTTAAAAAATTTACATTAATAAATTAAAA
1 TA-AAAATAATATCT-AATTAACTTTAAAAAAATTCACATTAACAAATTAAAA
1679720 AAATAGCATT
Statistics
Matches: 141, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
109 7 0.05
110 32 0.23
111 29 0.21
112 1 0.01
116 33 0.23
117 35 0.25
118 4 0.03
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (116 bp):
TAAAAATAATATCTAATTAACTTTAAAAAAATTCACATTAACAAATTAAAATATTAATTATTTTT
TAAATAAAAATAAAAGTAAAAAAGTTTATTATTATTATTTTTTAATAAAAT
Found at i:1679715 original size:111 final size:113
Alignment explanation
Indices: 1679442--1679719 Score: 309
Period size: 111 Copynumber: 2.4 Consensus size: 113
1679432 AATTTTTTAA
* *
1679442 TAAAAATAATATCTAATTAACTTTAAAAAGATTCACATTAATAAATTAAAATATTCATTATTTTT
1 TAAAAATAATAT-TAATTAACTTTAAAAA-ATTTACATTAATAAATTAAAATATTAATTATTTTT
*
1679507 TAAAATAAAAATTAAATTAAAAAAGTTTATTATTATTATTTTTTAATAAAAT
64 T-AAATAAAAATTAAA-TAAAAAAGTTTATTATTATTATTTATTAATAAAAT
* * *
1679559 TAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATATGTT
1 TAAAAATAATA-TTAATTAACTTTAAAAAATTTACATTAATAAATTAAAATATTAATTAT-T-TT
* **
1679624 TT-TATAAAAA-T-AA-AAAGTA-TTTATTATTATTA-TTATTAAT-AAAT
63 TTAAATAAAAATTAAATAAAAAAGTTTATTATTATTATTTATTAATAAAAT
** *
1679668 TATCTAATAATATTAAATTAAATTTTAAAAAATTTACATTAATAAATTAAAA
1 TA-AAAATAATATT-AATT-AACTTTAAAAAATTTACATTAATAAATTAAAA
1679720 AAATAGCATT
Statistics
Matches: 141, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
109 8 0.06
110 18 0.13
111 42 0.30
112 4 0.03
114 2 0.01
115 1 0.01
116 34 0.24
117 27 0.19
118 5 0.04
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (113 bp):
TAAAAATAATATTAATTAACTTTAAAAAATTTACATTAATAAATTAAAATATTAATTATTTTTTA
AATAAAAATTAAATAAAAAAGTTTATTATTATTATTTATTAATAAAAT
Found at i:1679744 original size:111 final size:111
Alignment explanation
Indices: 1679532--1679746 Score: 247
Period size: 111 Copynumber: 1.9 Consensus size: 111
1679522 ATTAAAAAAG
* *
1679532 TTTATTATTATTATTTTTTAATAAAATTAAAAATAATATTTAATTAAGTTTAAAAAAATTACATT
1 TTTATTATTATTATTTATTAATAAAATTAAAAATAATATTAAATTAAGTTTAAAAAAATTACATT
* * * ***
1679597 AACAAATTAAAATATTAATTATATGTTTTTATAAAAATAAAAAGTA
66 AACAAATTAAAAAAATAATTATAAGGAATTATAAAAATAAAAAGTA
** * *
1679643 TTTATTATTATTA-TTATTAAT-AAATTATCTAATAATATTAAATTAAATTTTAAAAAATTTACA
1 TTTATTATTATTATTTATTAATAAAATTA-AAAATAATATTAAATT-AAGTTTAAAAAAATTACA
* *
1679706 TTAATAAATTAAAAAAATAGCATT-TAAGGAATTAAAAAAAT
64 TTAACAAATTAAAAAAATA--ATTATAAGGAATTATAAAAAT
1679747 TTATCATTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
109 6 0.07
110 20 0.23
111 45 0.52
112 12 0.14
113 3 0.03
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (111 bp):
TTTATTATTATTATTTATTAATAAAATTAAAAATAATATTAAATTAAGTTTAAAAAAATTACATT
AACAAATTAAAAAAATAATTATAAGGAATTATAAAAATAAAAAGTA
Found at i:1680248 original size:108 final size:110
Alignment explanation
Indices: 1680069--1680298 Score: 351
Period size: 108 Copynumber: 2.1 Consensus size: 110
1680059 TTAATTTAAA
* *
1680069 TTTTTTA-TTTTA-AAAACATAATAATTAATATTCTAATTTGTTAATGTAAATTTTTTCAACGTA
1 TTTTTTATTTTTATAAAACATAATAATTAATATTCTAATTTATTAATGTAAATTTTTTAAACGTA
* *
1680132 ATTAAATATTATTTTTTATTTTATTAAAAATTATAATAAAAAACC
66 ATTAAATATTATTTTTAATTTTATTAAAAATAATAATAAAAAACC
* * *
1680177 TTTTTTATTTTTATAAATCATAATAATTAA-ATTTTAATTTATTAATGT-AATTTTTTAAACTTA
1 TTTTTTATTTTTATAAAACATAATAATTAATATTCTAATTTATTAATGTAAATTTTTTAAACGTA
*
1680240 ATTAAATATTATTTTTAATTTTATTAAAAATAATAATAATAAACC
66 ATTAAATATTATTTTTAATTTTATTAAAAATAATAATAAAAAACC
*
1680285 CTTTTTATTTTTAT
1 TTTTTTATTTTTAT
1680299 TTAAATTTTT
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
108 75 0.68
109 21 0.19
110 15 0.14
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (110 bp):
TTTTTTATTTTTATAAAACATAATAATTAATATTCTAATTTATTAATGTAAATTTTTTAAACGTA
ATTAAATATTATTTTTAATTTTATTAAAAATAATAATAAAAAACC
Found at i:1680711 original size:39 final size:38
Alignment explanation
Indices: 1680647--1680737 Score: 92
Period size: 38 Copynumber: 2.4 Consensus size: 38
1680637 TTTAAAGTTA
* * * *
1680647 ATTAAAATCTAAAAGATATGGGTAATACATAAATTTTTT
1 ATTAGAATTTAAAAGATATGAGTAAT-CATAAATTATTT
* * * * *
1680686 ATTATATTTTAAAAGATATTAGTAATTATAGATTATTT
1 ATTAGAATTTAAAAGATATGAGTAATCATAAATTATTT
1680724 ATTAGAATTTAAAA
1 ATTAGAATTTAAAA
1680738 AAAGTGACTA
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
38 21 0.50
39 21 0.50
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (38 bp):
ATTAGAATTTAAAAGATATGAGTAATCATAAATTATTT
Found at i:1680735 original size:38 final size:39
Alignment explanation
Indices: 1680647--1680771 Score: 94
Period size: 39 Copynumber: 3.2 Consensus size: 39
1680637 TTTAAAGTTA
* * *
1680647 ATTAAAATCTAAAAGATATGGGTAATACATAAATTTTTT
1 ATTAAAATTTAAAAGATATGAGTAATACATAAATTATTT
* * * * *
1680686 ATTATATTTTAAAAGATATTAGTAAT-TATAGATTATTT
1 ATTAAAATTTAAAAGATATGAGTAATACATAAATTATTT
* * * *
1680724 ATTAGAATTTAAAA-AAAGTGACTAATATATAAAATT-TTT
1 ATTAAAATTTAAAAGATA-TGAGTAATACAT-AAATTATTT
*
1680763 ATTCAAATT
1 ATTAAAATT
1680772 CCAAGATATG
Statistics
Matches: 67, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
37 2 0.03
38 27 0.40
39 34 0.51
40 4 0.06
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (39 bp):
ATTAAAATTTAAAAGATATGAGTAATACATAAATTATTT
Found at i:1681277 original size:43 final size:42
Alignment explanation
Indices: 1681156--1681277 Score: 101
Period size: 43 Copynumber: 2.9 Consensus size: 42
1681146 ACATGTATTA
* * *
1681156 TTTTTATTAAAATTAATTAATATTGTGCATGTATTATTAATTT
1 TTTTTATTAAAATTAATTAATATTTTACAT-TATTATCAATTT
* *
1681199 TTATTTA-T--AATTACTTTTAATTTATTTATAAATTA-TA-CAATTT
1 TT-TTTATTAAAATTA--ATTAA--TATTT-TACATTATTATCAATTT
1681242 TTTTTATTAAAATTAATTAATATTTTACATTATTAT
1 TTTTTATTAAAATTAATTAATATTTTACATTATTAT
1681278 TTTTATAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 23
0.67 0.08 0.25
Matches are distributed among these distances:
40 6 0.10
41 12 0.20
42 4 0.07
43 19 0.31
44 6 0.10
45 11 0.18
46 3 0.05
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (42 bp):
TTTTTATTAAAATTAATTAATATTTTACATTATTATCAATTT
Found at i:1685004 original size:94 final size:92
Alignment explanation
Indices: 1684718--1685009 Score: 309
Period size: 90 Copynumber: 3.2 Consensus size: 92
1684708 ATCTTTCAAC
* * *** * *
1684718 TATGATATTTACAATCAATCAACTTTTCAGCTTTTCTATAAAAAAGAATCTGATTCTCAATTATA
1 TATGATATTTATAATCAACCAACTTTTCTTTTTTTTTATAAAAAAGAATCTGATTCTCAATTACA
* * * *
1684783 ATTTATGCATTATTATAATCTTTGCAG
66 ATTCATGCATTAGTCTAATCCTTGCAG
* * * * * *
1684810 TATCATACTTATAATCAACCAGCTTTTCTTTTTTTTT-CAAAAGA-AATCTGATTCTCATTTACA
1 TATGATATTTATAATCAACCAACTTTTCTTTTTTTTTATAAAAAAGAATCTGATTCTCAATTACA
*
1684873 ATTCATGCATTAGTCTAATCCTTGCAA
66 ATTCATGCATTAGTCTAATCCTTGCAG
* * ** *
1684900 TCTGACATTTATAATCAGTCAACTTTTCTTTTTTTTTTTATAAAAAAGAATCTGATTCTCAAATA
1 TATGATATTTATAATCAACCAACTTTTC--TTTTTTTTTATAAAAAAGAATCTGATTCTCAATTA
* *
1684965 GAATTCATGCATTAGTCTAATCCTCGCAG
64 CAATTCATGCATTAGTCTAATCCTTGCAG
* *
1684994 TTTGATATTTACAATC
1 TATGATATTTATAATC
1685010 GATTCTCAGA
Statistics
Matches: 161, Mismatches: 35, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
90 60 0.37
91 5 0.03
92 37 0.23
93 5 0.03
94 54 0.34
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (92 bp):
TATGATATTTATAATCAACCAACTTTTCTTTTTTTTTATAAAAAAGAATCTGATTCTCAATTACA
ATTCATGCATTAGTCTAATCCTTGCAG
Found at i:1685041 original size:57 final size:57
Alignment explanation
Indices: 1684948--1685065 Score: 175
Period size: 57 Copynumber: 2.1 Consensus size: 57
1684938 TATAAAAAAG
* *
1684948 AATCTGATTCTCAAATAGAATTCATGCATTAGTCTAATCCTCGCAGTTTGATATTTAC
1 AATCTGATTCTCAAATAGAATTCATGCATTAATCTAATCCTCGCAGTTT-ACATTTAC
* * *
1685006 AATC-GATTCTCAGATATAATTCATGCATTAATCTAATCCTTGCAGTTTACATTTAC
1 AATCTGATTCTCAAATAGAATTCATGCATTAATCTAATCCTCGCAGTTTACATTTAC
1685062 AATC
1 AATC
1685066 AATAAACTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
56 11 0.20
57 40 0.73
58 4 0.07
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.38
Consensus pattern (57 bp):
AATCTGATTCTCAAATAGAATTCATGCATTAATCTAATCCTCGCAGTTTACATTTAC
Found at i:1685128 original size:146 final size:151
Alignment explanation
Indices: 1684854--1685155 Score: 371
Period size: 146 Copynumber: 2.0 Consensus size: 151
1684844 TTTCAAAAGA
** * * *
1684854 AATCTGATTCTCATTTACAATTCATGCATTAGTCTAATCCTTGCAATCTGACATTTATAATCAGT
1 AATCTGATTCTCAGATACAATTCATGCATTAATCTAATCCTTGCAATCTGACATTTACAATCAAT
* * * ** *
1684919 CAACTTTTCTTTTTTTTTTTATAAAAAAGAATCTGATTCTCAAATAGAATTCATGCATTAGTCTA
66 AAAC-TTTCTTTTTCTCTCAATAAAAAAGAATCTGATTCTCAAATAGAATTCATACATTAGTCTA
* *
1684984 ATCCTCGCAGTTTGATATTTAC
130 ATCCTCGCAGTCTGACATTTAC
* * *
1685006 AATC-GATTCTCAGATATAATTCATGCATTAATCTAATCCTTGCAGT-TTACATTTACAATCAAT
1 AATCTGATTCTCAGATACAATTCATGCATTAATCTAATCCTTGCAATCTGACATTTACAATCAAT
** *
1685069 AAAC-TT-TTTTTCTCTCAATAAAAAAGAAT-TGATTCTCTGATATAATTCATACATTAGTCTAA
66 AAACTTTCTTTTTCTCTCAATAAAAAAGAATCTGATTCTCAAATAGAATTCATACATTAGTCTAA
* *
1685131 TCTTTGCAGTCTGACATTTAC
131 TCCTCGCAGTCTGACATTTAC
1685152 AATC
1 AATC
1685156 AATCAACTTT
Statistics
Matches: 129, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
146 50 0.39
147 19 0.15
148 2 0.02
150 17 0.13
151 37 0.29
152 4 0.03
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.41
Consensus pattern (151 bp):
AATCTGATTCTCAGATACAATTCATGCATTAATCTAATCCTTGCAATCTGACATTTACAATCAAT
AAACTTTCTTTTTCTCTCAATAAAAAAGAATCTGATTCTCAAATAGAATTCATACATTAGTCTAA
TCCTCGCAGTCTGACATTTAC
Found at i:1686439 original size:20 final size:19
Alignment explanation
Indices: 1686395--1686443 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
1686385 AAAGTTAGGT
*
1686395 AAAAAAGAAAGAAAGAAGAT
1 AAAAAAGAAAGAAAGAA-AA
*
1686415 GAAAAAGAAAGAAAGAAAA
1 AAAAAAGAAAGAAAGAAAA
1686434 AAAAAAGAAA
1 AAAAAAGAAA
1686444 AAATATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (19 bp):
AAAAAAGAAAGAAAGAAAA
Found at i:1686834 original size:14 final size:14
Alignment explanation
Indices: 1686815--1686847 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1686805 TTATTTTATT
1686815 TATATGTATATATA
1 TATATGTATATATA
1686829 TATATGTATATATA
1 TATATGTATATATA
*
1686843 CATAT
1 TATAT
1686848 TTTGAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (14 bp):
TATATGTATATATA
Found at i:1689487 original size:50 final size:49
Alignment explanation
Indices: 1689430--1689575 Score: 151
Period size: 50 Copynumber: 3.0 Consensus size: 49
1689420 ATAAAAAGGG
*
1689430 TTTATTATTATTTTTTTAATAAAATTAAAAATAATATTTAATTAAGTTT
1 TTTATTATTATATTTTTAATAAAATTAAAAATAATATTTAATTAAGTTT
* * * *
1689479 TTTAATTATTATGTTTTT-ATAAAAATAATAAAT--T-TTAAAATAAAAGGTTT
1 TTT-ATTATTATATTTTTAATAAAATTAA-AAATAATATT-TAAT-TAA-GTTT
*
1689529 TTTATTA-TA-ATTTTTAATAAAATAAAAAATAATATTTAATTAAGTTT
1 TTTATTATTATATTTTTAATAAAATTAAAAATAATATTTAATTAAGTTT
1689576 AAAAAAATTT
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
47 15 0.19
48 16 0.20
49 22 0.28
50 26 0.33
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (49 bp):
TTTATTATTATATTTTTAATAAAATTAAAAATAATATTTAATTAAGTTT
Found at i:1689488 original size:47 final size:46
Alignment explanation
Indices: 1689429--1689575 Score: 138
Period size: 49 Copynumber: 3.1 Consensus size: 46
1689419 AATAAAAAGG
*
1689429 GTTTATTATTATTTTTTTAATAAAATTAAAAATAATATTTAATTAA
1 GTTTTTTATTATTTTTTTAATAAAATTAAAAATAATATTTAATTAA
* * * *
1689475 GTTTTTTAATTATTATGTTTTTATAAAAATAATAAAT--T-TTAAAATAAAA
1 GTTTTTT-ATTATT-T-TTTTAATAAAATTAA-AAATAATATT-TAAT-TAA
* *
1689524 GGTTTTTTATTATAATTTTTAATAAAATAAAAAATAATATTTAATTAA
1 -GTTTTTTATTAT-TTTTTTAATAAAATTAAAAATAATATTTAATTAA
1689572 GTTT
1 GTTT
1689576 AAAAAAATTT
Statistics
Matches: 79, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
46 6 0.08
47 16 0.20
48 19 0.24
49 25 0.32
50 13 0.16
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (46 bp):
GTTTTTTATTATTTTTTTAATAAAATTAAAAATAATATTTAATTAA
Found at i:1689981 original size:23 final size:23
Alignment explanation
Indices: 1689955--1690044 Score: 92
Period size: 23 Copynumber: 3.8 Consensus size: 23
1689945 ATAATGATAA
*
1689955 ATTTTTTTAATTTCTTAAATGTT
1 ATTTTTTTAATTTATTAAATGTT
* *
1689978 ATTTTTTTAATTTGTT-AATGTAA
1 ATTTTTTTAATTTATTAAATGT-T
* *
1690001 ATTTTTTAAAATTTAATTAAATATT
1 ATTTTTT-TAATTT-ATTAAATGTT
*
1690026 ATTTTTTTATTTTATTAAA
1 ATTTTTTTAATTTATTAAA
1690045 AATAATAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
22 5 0.09
23 28 0.51
24 9 0.16
25 9 0.16
26 4 0.07
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (23 bp):
ATTTTTTTAATTTATTAAATGTT
Found at i:1690028 original size:48 final size:47
Alignment explanation
Indices: 1689946--1690043 Score: 126
Period size: 48 Copynumber: 2.1 Consensus size: 47
1689936 TTTATTTGAA
* * * *
1689946 TAATGATAAATTTTTTTAATTTCTTAAATGTTATTTTTTTAATTTGT
1 TAATGATAAATTTTTTAAATTTATTAAATATTATTTTTTTAATTTAT
*
1689993 TAATG-TAAATTTTTTAAAATTTAATTAAATATTATTTTTTTATTTTAT
1 TAATGATAAATTTTTT-AAATTT-ATTAAATATTATTTTTTTAATTTAT
1690041 TAA
1 TAA
1690044 AAATAATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
46 10 0.23
47 10 0.23
48 24 0.55
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (47 bp):
TAATGATAAATTTTTTAAATTTATTAAATATTATTTTTTTAATTTAT
Found at i:1690157 original size:109 final size:109
Alignment explanation
Indices: 1689982--1690253 Score: 293
Period size: 113 Copynumber: 2.4 Consensus size: 109
1689972 AATGTTATTT
* * *
1689982 TTTTAATTTGTTAATGTAAATTTTTTAAAATTTAATTAAATATTATTTTTTTATTTTATTAAAAA
1 TTTTAATTTGTTAATGT-AATTTTTT-AAACTTAATTAAATATTA--TTTTAATCTTATTAAAAA
*
1690047 TAATAATAAAAAATATTT-TTT-A-TTTTTA-TAAAACATATAATTAGTA
62 TAATAATAAAAAATATTTATTTAATTTTTTATTAAAA-A-ATAATTAATA
1690093 TTTTAATTTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTAATCTTATTAAAAA-AAT
1 TTTTAATTTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTAATCTTATTAAAAATAAT
* * *
1690157 AATAATAAACCCTTTTTAATTTAATTTTTTATTTTAAAAATAATTAATA
66 AATAA-AAA--ATATTT-ATTTAATTTTTTA-TTAAAAAATAATTAATA
* ** * *
1690206 TTTTAATTTATTAATAAAAATTTTTTGAAGTTAATTAAATATTATTTT
1 TTTTAATTTGTTAAT-GTAATTTTTTAAACTTAATTAAATATTATTTT
1690254 TATTAAAAAT
Statistics
Matches: 139, Mismatches: 12, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
106 8 0.06
107 19 0.14
109 21 0.15
110 8 0.06
111 20 0.14
112 1 0.01
113 29 0.21
114 29 0.21
115 4 0.03
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (109 bp):
TTTTAATTTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTAATCTTATTAAAAATAAT
AATAAAAAATATTTATTTAATTTTTTATTAAAAAATAATTAATA
Found at i:1690304 original size:64 final size:68
Alignment explanation
Indices: 1690182--1690307 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 68
1690172 TTAATTTAAT
** * *
1690182 TTTTTATTTTAAAAATAATTAATATTTTAATTTATTAATAAAAATTTTTTGAAGTTAATTAAATA
1 TTTTTATTAAAAAAATAATTAATATATTAATTTATTAATAAAAATTTTTTAAAGTTAATTAAATA
1690247 TTA
66 TTA
* *
1690250 TTTTTATTAAAAATAATAATTAATATATT-A-TTATT-AT-TAAA-TTTTTAAATTTAATTAA
1 TTTTTATTAAAAA-AATAATTAATATATTAATTTATTAATAAAAATTTTTTAAAGTTAATTAA
1690308 TTTATAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
64 15 0.29
65 3 0.06
66 2 0.04
67 5 0.10
68 12 0.24
69 14 0.27
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (68 bp):
TTTTTATTAAAAAAATAATTAATATATTAATTTATTAATAAAAATTTTTTAAAGTTAATTAAATA
TTA
Found at i:1693013 original size:178 final size:177
Alignment explanation
Indices: 1692685--1693662 Score: 1071
Period size: 176 Copynumber: 5.4 Consensus size: 177
1692675 TCTTTACAGT
* *
1692685 CTTTTTTTTCTTATAAAAAAGAATTCGATTCTCAGATATAATTCATACATTAGTCTAATCCTTGC
1 CTTTTTTTTC-TATAAAAAA-AATT-GATTCTCAGATATAATTCATGCATTAGTCTAATCCTTAC
* * * * *
1692750 AGTCTGACACTTACAATCAATTAGTCTTTTTTTTTTTTTTCTATAAAAAAGATTTCGATTCTCAG
63 AGTCTGACATTTACAATCAATCA-AC-TTTTCTTTTTTTTC-ATAAAAAAGA-ATCGATTCTCAG
* * **
1692815 ATATAATTCATGAATTAGTCTAATCTTTGCAGTCTCACATTTACAATGGATCAA
124 ATATAATTCATGCATTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAA
* * * *
1692869 CTTTTTTTTCTATAAAAAAAATTGATTCTCATATATAATTTATGCATTAGTTTAATCCTTACTGT
1 CTTTTTTTTCTATAAAAAAAATTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
* * *
1692934 CTGACATTTATAATCAGTCAACTTTTATTTTTTTTCATAAAAAAGAATCCGATTCTCAGATATAA
66 CTGACATTTACAATCAATCAACTTTTCTTTTTTTTCATAAAAAAGAAT-CGATTCTCAGATATAA
* *
1692999 TTCATGCATTAGTCTAATTTTTGCCGTCTGACATTTACAATCAATCAA
130 TTCATGCATTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAA
* *
1693047 TCTTTCTTTTTTTCTATAAAAAAAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATACTT
1 -C--T-TTTTTTTCTATAAAAAAAAT-TGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
** * * * *
1693112 GTAGTTTGACATTTACAATCAGTTAA-----C-TTTTTTT-ATAAAAAAGAATCCGATTCTTAGA
61 ACAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTTTCATAAAAAAGAAT-CGATTCTCAGA
* * * * *
1693170 TATAATTCATGCATTAGTCTAATCCTTGTAGTATGATATTTACAATCAGTCAA
125 TATAATTCATGCATTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAA
* * * * *
1693223 TTTTTCTTTTATTCTATAGAAAAGAAATCGATTCTCAAATAT-ATTCATGCATTAGTCTATTCTT
1 --CTT-TTTT-TTCTATA-AAAA-AAATTGATTCTCAGATATAATTCATGCATTAGTCTAATCCT
* * * * *
1693287 TAGAGTCAGACATTTACAATCAATCAATTTTTCTTTTTTCTCTATAAAAAAGAATTGATTCTCAG
60 TACAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTTTC-ATAAAAAAGAATCGATTCTCAG
* * *
1693352 ATACAATTCATGCATTAGTTTAATCTTTACAGTCTGACATTTACAATCAATCAA
124 ATATAATTCATGCATTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAA
* * * * *
1693406 CTTTTTTTTC-ATTAAAAAAATCTGATTCTTAGATATAATTCATGCATAAGTCTAATCTTTGCAG
1 CTTTTTTTTCTATAAAAAAAAT-TGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAG
* * * *
1693470 TTTGACATTTACAATCAATCAACTTTTCTTTTTTTT--TAATAAAAAAATTGATTCTTAGATATA
65 TCTGACATTTACAATCAATCAACTTTTCTTTTTTTTCATAA-AAAAGAATCGATTCTCAGATATA
* * *
1693533 ATTCATGCATTAGTCTAATCATTGCAGTTTGACATTTACAATTAATCAA
129 ATTCATGCATTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAA
* * * * *
1693582 CTTTTATTTT-TCATAAAAAAAATTCGATTCTCATATATAATCCATACATTAGTCTATTTCTTAC
1 CTTTT-TTTTCT-ATAAAAAAAATT-GATTCTCAGATATAATTCATGCATTAGTCTAATCCTTAC
1693646 AGTCTGACATTTACAAT
63 AGTCTGACATTTACAAT
1693663 TTATATATTA
Statistics
Matches: 675, Mismatches: 93, Indels: 58
0.82 0.11 0.07
Matches are distributed among these distances:
174 1 0.00
175 8 0.01
176 189 0.28
177 46 0.07
178 185 0.27
179 17 0.03
180 5 0.01
181 56 0.08
182 30 0.04
183 116 0.17
184 22 0.03
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (177 bp):
CTTTTTTTTCTATAAAAAAAATTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
CTGACATTTACAATCAATCAACTTTTCTTTTTTTTCATAAAAAAGAATCGATTCTCAGATATAAT
TCATGCATTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAA
Found at i:1693231 original size:176 final size:172
Alignment explanation
Indices: 1692686--1693662 Score: 960
Period size: 178 Copynumber: 5.5 Consensus size: 172
1692676 CTTTACAGTC
*
1692686 TTTTTTTTCTTATAAAAAAGAATTCGATTCTCAGATATAATTCATACATTAGTCTAATCCTTGCA
1 TTTTTTTTC-TATAAAAAA-AA-TCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCA
* * * *
1692751 GTCTGACACTTACAATCAATTAGTCTTTTTTTTTTTTTTCTATAAAAAAGATTTCGATTCTCAGA
63 GTCTGACATTTACAATCAATCA-AC-------TTTTTTT-TATAAAAAAGA-ATCGATTCTCAGA
* * ** *
1692816 TATAATTCATGAATTAGTCTAATCTTTGCAGTCTCACATTTACAATGGATCAA-C
118 TATAATTCATGCATTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAATT
* * * * * *
1692870 TTTTTTTTCTATAAAAAAAATTGATTCTCATATATAATTTATGCATTAGTTTAATCCTTACTGTC
1 TTTTTTTTCTATAAAAAAAATCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGTC
* *
1692935 TGACATTTATAATCAGTCAACTTTTATTTTTTTTCATAAAAAAGAATCCGATTCTCAGATATAAT
66 TGACATTTACAATCAATCAAC-----TTTTTTTT-ATAAAAAAGAAT-CGATTCTCAGATATAAT
* *
1693000 TCATGCATTAGTCTAATTTTTGCCGTCTGACATTTACAATCAATCAATCTT
124 TCATGCATTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAA--TT
* *
1693051 TCTTTTTTTCTATAAAAAAAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATACTTGTAG
1 T-TTTTTTTCTATAAAAAAAAT-CGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAG
* * * *
1693116 TTTGACATTTACAATCAGTTAAC-TTTTTTTATAAAAAAGAATCCGATTCTTAGATATAATTCAT
64 TCTGACATTTACAATCAATCAACTTTTTTTTATAAAAAAGAAT-CGATTCTCAGATATAATTCAT
* * * * *
1693180 GCATTAGTCTAATCCTTGTAGTATGATATTTACAATCAGTCAATTT
128 GCATTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAA-TT
* * *
1693226 TTCTTTTATTCTATAGAAAAGAAATCGATTCTCAAATAT-ATTCATGCATTAGTCTATTCTTTAG
1 TT-TTTT-TTCTATA-AAAA-AAATCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT-G
* *
1693290 -AGTCAGACATTTACAATCAATCAATTTTTCTTTTTTCTCTATAAAAAAGAATTGATTCTCAGAT
61 CAGTCTGACATTTACAATCAATCAA-----CTTTTTT-T-TATAAAAAAGAATCGATTCTCAGAT
* * * *
1693354 ACAATTCATGCATTAGTTTAATCTTTACAGTCTGACATTTACAATCAATCAA-C
119 ATAATTCATGCATTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAATT
* * * *
1693407 TTTTTTTTC-ATTAAAAAAATCTGATTCTTAGATATAATTCATGCATAAGTCTAATCTTTGCAGT
1 TTTTTTTTCTATAAAAAAAATC-GATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGT
* * * * *
1693471 TTGACATTTACAATCAATCAACTTTTCTTTTTTTTTAATAAAAAAATTGATTCTTAGATATAATT
65 CTGACATTTACAATCAATCAAC---T-TTTTTTTATAA-AAAAGAATCGATTCTCAGATATAATT
* * *
1693536 CATGCATTAGTCTAATCATTGCAGTTTGACATTTACAATTAATCAACTT
125 CATGCATTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAA-TT
* * * * * * *
1693585 TTATTTTTC-ATAAAAAAAATTCGATTCTCATATATAATCCATACATTAGTCTATTTCTTACAGT
1 TTTTTTTTCTATAAAAAAAA-TCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGT
1693649 CTGACATTTACAAT
65 CTGACATTTACAAT
1693663 TTATATATTA
Statistics
Matches: 673, Mismatches: 89, Indels: 68
0.81 0.11 0.08
Matches are distributed among these distances:
173 1 0.00
174 1 0.00
175 11 0.02
176 187 0.28
177 48 0.07
178 191 0.28
179 5 0.01
180 5 0.01
181 57 0.08
182 27 0.04
183 118 0.18
184 22 0.03
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (172 bp):
TTTTTTTTCTATAAAAAAAATCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGTC
TGACATTTACAATCAATCAACTTTTTTTTATAAAAAAGAATCGATTCTCAGATATAATTCATGCA
TTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAATT
Found at i:1693333 original size:268 final size:268
Alignment explanation
Indices: 1692687--1693662 Score: 1160
Period size: 268 Copynumber: 3.6 Consensus size: 268
1692677 TTTACAGTCT
* * *
1692687 TTTTTTTCTTATAAAAAAGAATTCGATTCTCAGATATAATTCATACATTAGTCTAATCCTTGCAG
1 TTTTTTTC-TATAAAAAAGAAATCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTTGCAG
* * * * *
1692752 TCTGACACTTACAATCAATTAGTCTTTTTTTTTTTTTTCTATAAAAAAGATTTCGATTCTCAGAT
65 TCTGACATTTACAATCAATCAATC---TTTCTTTTTTTCTATAAAAAAGAATTCGATTCTCAGAT
* * *
1692817 ATAATTCATGAATTAGTCTAATCTTTGCAGTCTCACATTTACAAT-GGATCAACTTTTTTTTCTA
127 ATAATTCATGCATTAGTCTAATC-TTGCAGTCTGACATTTACAATCAG-TCAAC-TTTTTTT-TA
* * * * * *
1692881 TAAAAAAAAT-TGATTCTCATATATAATTTATGCATTAGTTTAATCCTTACT-GTCTGACATTTA
188 TAAAAAAAATCTGATTCTTAGATATAATTCATGCATTAGTCTAATCCTT-GTAGTATGACATTTA
*
1692944 TAATCAGTCAACTTTTAT-
252 CAATCAGTCAA-TTTT-TC
* *
1692962 TTTTTTTC-ATAAAAAAG-AATCCGATTCTCAGATATAATTCATGCATTAGTCTAATTTTTGCCG
1 TTTTTTTCTATAAAAAAGAAAT-CGATTCTCAGATATAATTCATGCATTAGTCTAATCTTTGCAG
*
1693025 TCTGACATTTACAATCAATCAATCTTTCTTTTTTTCTATAAAAAA-AATCCGATTCTCAGATATA
65 TCTGACATTTACAATCAATCAATCTTTCTTTTTTTCTATAAAAAAGAATTCGATTCTCAGATATA
* * *
1693089 ATTCATGCATTAGTCTAATACTTGTAGTTTGACATTTACAATCAGTTAAC-TTTTTTTATAAAAA
130 ATTCATGCATTAGTCTAAT-CTTGCAGTCTGACATTTACAATCAGTCAACTTTTTTTTATAAAAA
* *
1693153 AGAATCCGATTCTTAGATATAATTCATGCATTAGTCTAATCCTTGTAGTATGATATTTACAATCA
194 A-AATCTGATTCTTAGATATAATTCATGCATTAGTCTAATCCTTGTAGTATGACATTTACAATCA
1693218 GTCAATTTTTC
258 GTCAATTTTTC
* * * *
1693229 TTTTATTCTATAGAAAAGAAATCGATTCTCAAATAT-ATTCATGCATTAGTCTATTCTTTAG-AG
1 TTTTTTTCTATAAAAAAGAAATCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTT-GCAG
* * *
1693292 TCAGACATTTACAATCAATCAATTTTTCTTTTTTCTCTATAAAAAAGAATT-GATTCTCAGATAC
65 TCTGACATTTACAATCAATCAATCTTTCTTTTTT-TCTATAAAAAAGAATTCGATTCTCAGATAT
* * * *
1693356 AATTCATGCATTAGTTTAATCTTTACAGTCTGACATTTACAATCAATCAACTTTTTTTTCATTAA
129 AATTCATGCATTAGTCTAATC-TTGCAGTCTGACATTTACAATCAGTCAACTTTTTTTT-ATAAA
* * * *
1693421 AAAAATCTGATTCTTAGATATAATTCATGCATAAGTCTAATCTTTGCAGTTTGACATTTACAATC
192 AAAAATCTGATTCTTAGATATAATTCATGCATTAGTCTAATCCTTGTAGTATGACATTTACAATC
* *
1693486 AATCAACTTTTC
257 AGTCAATTTTTC
* * *
1693498 TTTTTTT-T-TAATAAAA-AAATTGATTCTTAGATATAATTCATGCATTAGTCTAATCATTGCAG
1 TTTTTTTCTATAA-AAAAGAAATCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTTGCAG
* * * *
1693560 TTTGACATTTACAATTAATCAA-CTTT-TATTTTTC-ATAAAAAA-AATTCGATTCTCATATATA
65 TCTGACATTTACAATCAATCAATCTTTCTTTTTTTCTATAAAAAAGAATTCGATTCTCAGATATA
* * * *
1693621 ATCCATACATTAGTCTATTTCTTACAGTCTGACATTTACAAT
130 ATTCATGCATTAGTCTA-ATCTTGCAGTCTGACATTTACAAT
1693663 TTATATATTA
Statistics
Matches: 612, Mismatches: 69, Indels: 51
0.84 0.09 0.07
Matches are distributed among these distances:
263 4 0.01
264 55 0.09
265 4 0.01
266 15 0.02
267 97 0.16
268 188 0.31
269 142 0.23
270 29 0.05
272 2 0.00
273 68 0.11
275 8 0.01
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (268 bp):
TTTTTTTCTATAAAAAAGAAATCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTTGCAGT
CTGACATTTACAATCAATCAATCTTTCTTTTTTTCTATAAAAAAGAATTCGATTCTCAGATATAA
TTCATGCATTAGTCTAATCTTGCAGTCTGACATTTACAATCAGTCAACTTTTTTTTATAAAAAAA
ATCTGATTCTTAGATATAATTCATGCATTAGTCTAATCCTTGTAGTATGACATTTACAATCAGTC
AATTTTTC
Found at i:1694150 original size:124 final size:128
Alignment explanation
Indices: 1693948--1694209 Score: 392
Period size: 124 Copynumber: 2.1 Consensus size: 128
1693938 AAATATTAAT
*
1693948 TATTTTT-TAAAAATAAAAAATTTAAATAAAAATAAAAAGGGTTTACTGTTATTATTTTTTTAAT
1 TATTTTTATAAAAATAAAAAATTT--ATAAAAATAAAAAGGGTTTA-TGTTATTATATTTTTAAT
* * *
1694012 AAAATTAAAAATAATATTTAATTAAGTTTAAAAAATTACATTAACAAATTAAAATATTAATTATT
63 AAAATAAAAAATAATATTTAATTAAATTTAAAAAATTACATTAACAAATTAAAATATTAATTATG
1694077 A
128 A
* *
1694078 TGTTTTTATAAAAATAAAAAATTT-T-AAAGTAAAAA-GGTTT-T-TTATTATAATTTTTAATAA
1 TATTTTTATAAAAATAAAAAATTTATAAAAATAAAAAGGGTTTATGTTATTAT-ATTTTTAATAA
1694138 AATAAAAAATAATATTTAATTAAATTTAAAAAATTACATTAACAAATTAAAATATTAATTATGA
65 AATAAAAAATAATATTTAATTAAATTTAAAAAATTACATTAACAAATTAAAATATTAATTATGA
1694202 TATTTTTA
1 TATTTTTA
1694210 GCATAATATA
Statistics
Matches: 123, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
123 7 0.06
124 79 0.64
126 5 0.04
127 9 0.07
128 1 0.01
130 6 0.05
131 16 0.13
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (128 bp):
TATTTTTATAAAAATAAAAAATTTATAAAAATAAAAAGGGTTTATGTTATTATATTTTTAATAAA
ATAAAAAATAATATTTAATTAAATTTAAAAAATTACATTAACAAATTAAAATATTAATTATGA
Found at i:1694155 original size:22 final size:24
Alignment explanation
Indices: 1694124--1694171 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
1694114 GTTTTTTATT
*
1694124 ATAATTTTTAA-TAAA-ATAAAAA
1 ATAATATTTAATTAAATATAAAAA
*
1694146 ATAATATTTAATTAAATTTAAAAA
1 ATAATATTTAATTAAATATAAAAA
1694170 AT
1 AT
1694172 TACATTAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.45
23 4 0.18
24 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAATATTTAATTAAATATAAAAA
Found at i:1694664 original size:9 final size:9
Alignment explanation
Indices: 1694641--1694695 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
1694631 TTTTAATATT
*
1694641 TATACTATA
1 TATATTATA
1694650 -ATATTATA
1 TATATTATA
*
1694658 TATATTATG
1 TATATTATA
*
1694667 TATATGATA
1 TATATTATA
*
1694676 TAAATTATA
1 TATATTATA
1694685 TA-ATGTATA
1 TATAT-TATA
1694694 TA
1 TA
1694696 AATATAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
8 9 0.24
9 29 0.76
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (9 bp):
TATATTATA
Found at i:1694676 original size:23 final size:23
Alignment explanation
Indices: 1694658--1694703 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1694648 TAATATTATA
*
1694658 TATATTATGTATATGATATAAAT
1 TATATAATGTATATGATATAAAT
*
1694681 TATATAATGTATATAAATATAAA
1 TATATAATGTATAT-GATATAAA
1694704 AATAATATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (23 bp):
TATATAATGTATATGATATAAAT
Found at i:1694696 original size:18 final size:18
Alignment explanation
Indices: 1694654--1694724 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 18
1694644 ACTATAATAT
* *
1694654 TATATATATTATGTATATG
1 TATATAAATTATATA-ATG
1694673 -ATATAAATTATATAATG
1 TATATAAATTATATAATG
*
1694690 TATATAAA-TATAAAAAT-
1 TATATAAATTAT-ATAATG
* *
1694707 AATATACATTATATAATG
1 TATATAAATTATATAATG
1694725 AAAAACGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
17 16 0.38
18 26 0.62
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (18 bp):
TATATAAATTATATAATG
Found at i:1697077 original size:16 final size:16
Alignment explanation
Indices: 1697047--1697099 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1697037 TGACCCGAGC
* *
1697047 TTAAAATGGTCCGAAT
1 TTAAAATGATTCGAAT
1697063 TTAAAATGATTCGAAT
1 TTAAAATGATTCGAAT
* * * *
1697079 CTGAAATAATTCGAAC
1 TTAAAATGATTCGAAT
1697095 TTAAA
1 TTAAA
1697100 TTAAATATTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Consensus pattern (16 bp):
TTAAAATGATTCGAAT
Found at i:1703484 original size:15 final size:17
Alignment explanation
Indices: 1703466--1703500 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1703456 AAATAATATT
1703466 TATTAAA-ATT-TTAAA
1 TATTAAATATTATTAAA
1703481 TATTAAATATTATTAAA
1 TATTAAATATTATTAAA
1703498 TAT
1 TAT
1703501 ATATAGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 3 0.17
17 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTAAATATTATTAAA
Found at i:1703664 original size:3 final size:3
Alignment explanation
Indices: 1703658--1703691 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
1703648 CATCATCATC
1703658 ATT ATT ATT ATT ATT ATT ATT ATT AATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT A
1703692 CAAATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1704167 original size:28 final size:30
Alignment explanation
Indices: 1704104--1704168 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
1704094 TTTTAATTTT
* *
1704104 AATTTGTATTTATTCTATTAAAATTAAGTA
1 AATTTATATTTATTCTATTAAAATTAAATA
** *
1704134 TGTTTATATTTA-T-TATTTAAATTAAATA
1 AATTTATATTTATTCTATTAAAATTAAATA
1704162 AATTTAT
1 AATTTAT
1704169 TCGTAAATAC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 18 0.64
29 1 0.04
30 9 0.32
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (30 bp):
AATTTATATTTATTCTATTAAAATTAAATA
Found at i:1704246 original size:22 final size:23
Alignment explanation
Indices: 1704212--1704257 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1704202 ATAATTGAGC
* *
1704212 ATATTCATTAACAATTAA-AAAT
1 ATATTCATAAACAATAAACAAAT
*
1704234 ATATTTATAAACAATAAACAAAT
1 ATATTCATAAACAATAAACAAAT
1704257 A
1 A
1704258 AATCTAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATTCATAAACAATAAACAAAT
Found at i:1704396 original size:42 final size:43
Alignment explanation
Indices: 1704305--1704404 Score: 120
Period size: 43 Copynumber: 2.3 Consensus size: 43
1704295 TTAGTTTTAA
*
1704305 ATATAAAATAATAAAACACAAATATTATTAATTATAACTATTT
1 ATATAAAATAATAAAACACAAATATTATTAATTATAACTATAT
1704348 ATAT-AAATAACTAAAACACAAATAATAATATTAATTAT-A-T-TAT
1 ATATAAAATAA-TAAAACACAAAT-AT--TATTAATTATAACTATAT
1704391 A-ATAAAATAATAAA
1 ATATAAAATAATAAA
1704405 TGAAATTTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
42 12 0.24
43 25 0.49
44 3 0.06
45 1 0.02
46 10 0.20
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (43 bp):
ATATAAAATAATAAAACACAAATATTATTAATTATAACTATAT
Found at i:1704945 original size:26 final size:27
Alignment explanation
Indices: 1704891--1704961 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 27
1704881 AATAATATTT
*
1704891 AAAAAATTTTAAAAA-TAAAAATAATG
1 AAAAAATTTTAAAAATTAAAAATAAGG
**
1704917 AAAAAATTTTAAAAATTTCAAAT-AGG
1 AAAAAATTTTAAAAATTAAAAATAAGG
1704943 -AAAAA-TTTAAAAATTAAAA
1 AAAAAATTTTAAAAATTAAAA
1704962 TAAATAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
24 12 0.31
25 5 0.13
26 17 0.44
27 5 0.13
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAAAATTTTAAAAATTAAAAATAAGG
Found at i:1707065 original size:22 final size:22
Alignment explanation
Indices: 1707040--1707095 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1707030 AAAAATTATT
* *
1707040 ATTTTATATTAATATTTATAT-A
1 ATTTTTTATTAA-ATTTAAATAA
1707062 ATTTTTTAATTAAATTTAAATAA
1 ATTTTTT-ATTAAATTTAAATAA
1707085 ATTTTTTATTA
1 ATTTTTTATTA
1707096 GATGAGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTTTTATTAAATTTAAATAA
Found at i:1707073 original size:23 final size:24
Alignment explanation
Indices: 1707041--1707093 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
1707031 AAAATTATTA
*
1707041 TTTTATATTAATATTTATAT-AATT
1 TTTTATATTAA-ATTTAAATAAATT
1707065 TTTTA-ATTAAATTTAAATAAATT
1 TTTTATATTAAATTTAAATAAATT
1707088 TTTTAT
1 TTTTAT
1707094 TAGATGAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 7 0.27
23 14 0.54
24 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATATTAAATTTAAATAAATT
Found at i:1707243 original size:9 final size:10
Alignment explanation
Indices: 1707223--1707264 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1707213 ACTAATTTAA
1707223 TTTTATATAT
1 TTTTATATAT
1707233 TTTTATA-AT
1 TTTTATATAT
1707242 TTTTATATGAT
1 TTTTATAT-AT
* *
1707253 TTATATTTAT
1 TTTTATATAT
1707263 TT
1 TT
1707265 AATTTAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 9 0.32
10 11 0.39
11 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTATATAT
Found at i:1707255 original size:18 final size:18
Alignment explanation
Indices: 1707220--1707257 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1707210 AGAACTAATT
*
1707220 TAATTTTATATATTTTTA
1 TAATTTTATATATATTTA
1707238 TAATTTT-TATATGATTTA
1 TAATTTTATATAT-ATTTA
1707256 TA
1 TA
1707258 TTTATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TAATTTTATATATATTTA
Found at i:1707738 original size:22 final size:22
Alignment explanation
Indices: 1707713--1707756 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1707703 AAACATAATT
*
1707713 AAATATTC-TTTATATAAGAATA
1 AAATATTCATGTATATAA-AATA
1707735 AAATATTCATGTATATAAAATA
1 AAATATTCATGTATATAAAATA
1707757 CACGTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (22 bp):
AAATATTCATGTATATAAAATA
Found at i:1708781 original size:2 final size:2
Alignment explanation
Indices: 1708774--1708808 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1708764 TCGGTTGTTT
1708774 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1708809 GCTTGTGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1719928 original size:18 final size:18
Alignment explanation
Indices: 1719905--1719939 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1719895 AATATGTCTC
* *
1719905 TTATATGTGTATATATAT
1 TTATATATGTAAATATAT
1719923 TTATATATGTAAATATA
1 TTATATATGTAAATATA
1719940 AATTTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
TTATATATGTAAATATAT
Found at i:1720443 original size:13 final size:13
Alignment explanation
Indices: 1720425--1720450 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1720415 CATGTTGAGG
1720425 AAAGAGGGAAATC
1 AAAGAGGGAAATC
1720438 AAAGAGGGAAATC
1 AAAGAGGGAAATC
1720451 GATTGTAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.31, T:0.08
Consensus pattern (13 bp):
AAAGAGGGAAATC
Found at i:1722729 original size:28 final size:24
Alignment explanation
Indices: 1722678--1722741 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 24
1722668 CAAATAGATA
*
1722678 TTTATTTTTATAAAAATTACAATT
1 TTTATTTTTTTAAAAATTACAATT
1722702 CCTTTATTTTTTTAAATATTATTA-AATT
1 --TTTATTTTTTTAAA-A--ATTACAATT
*
1722730 TTTATATTTTTA
1 TTTATTTTTTTA
1722742 TAAGATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 24 0.73
27 1 0.03
28 4 0.12
29 4 0.12
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTATTTTTTTAAAAATTACAATT
Found at i:1722969 original size:32 final size:33
Alignment explanation
Indices: 1722933--1723005 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
1722923 AAAATGACCC
* * *
1722933 AAATTTGAAGTAACTTGAACTT-AAAATAATTT
1 AAATTTAAAATAACTTAAACTTGAAAATAATTT
* *
1722965 AAATTTAAAATAATTTAAACTTGAAAATGATTT
1 AAATTTAAAATAACTTAAACTTGAAAATAATTT
1722998 AAAATTTA
1 -AAATTTA
1723006 GGACTCGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 18 0.53
33 9 0.26
34 7 0.21
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (33 bp):
AAATTTAAAATAACTTAAACTTGAAAATAATTT
Found at i:1722997 original size:17 final size:16
Alignment explanation
Indices: 1722950--1723000 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
1722940 AAGTAACTTG
1722950 AACTTAAAATAATTTA
1 AACTTAAAATAATTTA
*
1722966 AATTTAAAATAATTTA
1 AACTTAAAATAATTTA
*
1722982 AACTTGAAAATGATTTA
1 AACTT-AAAATAATTTA
1722999 AA
1 AA
1723001 ATTTAGGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
16 19 0.61
17 12 0.39
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (16 bp):
AACTTAAAATAATTTA
Found at i:1728075 original size:18 final size:17
Alignment explanation
Indices: 1728047--1728088 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
1728037 GAATATGAGC
*
1728047 AAAAGAGAGAGAAAGAA
1 AAAAGAAAGAGAAAGAA
*
1728064 AGAAAGAAAGAGAATGAA
1 A-AAAGAAAGAGAAAGAA
1728082 AAAAGAA
1 AAAAGAA
1728089 TATGAGCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (17 bp):
AAAAGAAAGAGAAAGAA
Found at i:1732773 original size:2 final size:2
Alignment explanation
Indices: 1732762--1732794 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1732752 TTTTTTCTTT
*
1732762 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1732795 GAAAGTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1733058 original size:44 final size:44
Alignment explanation
Indices: 1732996--1733124 Score: 231
Period size: 44 Copynumber: 2.9 Consensus size: 44
1732986 ATAACACGAG
*
1732996 AATTAATTAATTCTTTGATTTTGCATTGATTTGTGGTGGGATAT
1 AATTAATTAATTCTTTGATTTTGTATTGATTTGTGGTGGGATAT
*
1733040 AATTAATTAACTCTTTGATTTTGTATTGATTTGTGGTGGGATAT
1 AATTAATTAATTCTTTGATTTTGTATTGATTTGTGGTGGGATAT
*
1733084 AATTAATTAATTCTTTGATTTGGTATTGATTTGTGGTGGGA
1 AATTAATTAATTCTTTGATTTTGTATTGATTTGTGGTGGGA
1733125 CATACTTCAA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 81 1.00
ACGTcount: A:0.25, C:0.04, G:0.22, T:0.50
Consensus pattern (44 bp):
AATTAATTAATTCTTTGATTTTGTATTGATTTGTGGTGGGATAT
Found at i:1733556 original size:14 final size:14
Alignment explanation
Indices: 1733537--1733569 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1733527 CCCGCTCATA
*
1733537 TTATTTTATTTATT
1 TTATTTTATTAATT
1733551 TTATTTTATTAATT
1 TTATTTTATTAATT
1733565 TTATT
1 TTATT
1733570 AGCTTTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTTATTAATT
Found at i:1734914 original size:27 final size:28
Alignment explanation
Indices: 1734884--1734958 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 28
1734874 TATATAATTA
*
1734884 TTAAATAAGT-CGAGTC-AAGCTCGAACT
1 TTAAA-AAGTACGAGTCAAAGCTAGAACT
*
1734911 TT-AAAAGTAGGAGTCAAAGCTAGAACT
1 TTAAAAAGTACGAGTCAAAGCTAGAACT
*
1734938 TT-AAAAGTAAGAGTCAAAGCT
1 TTAAAAAGTACGAGTCAAAGCT
1734959 TGGCCTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 4 0.09
26 7 0.16
27 32 0.74
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (28 bp):
TTAAAAAGTACGAGTCAAAGCTAGAACT
Found at i:1734925 original size:26 final size:26
Alignment explanation
Indices: 1734895--1734954 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
1734885 TAAATAAGTC
* *
1734895 GAGTCAAGCTCGAACTTTAAAAGTAG
1 GAGTCAAGCTAGAACTTTAAAAGTAA
1734921 GAGTCAAAGCTAGAACTTTAAAAGTAA
1 GAGTC-AAGCTAGAACTTTAAAAGTAA
1734948 GAGTCAA
1 GAGTCAA
1734955 AGCTTGGCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (26 bp):
GAGTCAAGCTAGAACTTTAAAAGTAA
Found at i:1735552 original size:24 final size:23
Alignment explanation
Indices: 1735508--1735552 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1735498 TATGAAATGG
*
1735508 TATTTATAATTCTTATACAATTA
1 TATTTATAATTATTATACAATTA
1735531 TATTTAATAACTTATTAT-CAAT
1 TATTT-ATAA-TTATTATACAAT
1735553 AACAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 8 0.42
25 6 0.32
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTATAATTATTATACAATTA
Found at i:1737131 original size:17 final size:17
Alignment explanation
Indices: 1737111--1737149 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1737101 ATGATTACAT
1737111 ATTTAAAATGTATAAAA
1 ATTTAAAATGTATAAAA
* * *
1737128 ATTTTAAATTTATAAAT
1 ATTTAAAATGTATAAAA
1737145 ATTTA
1 ATTTA
1737150 TAGGTAATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
ATTTAAAATGTATAAAA
Found at i:1738039 original size:19 final size:19
Alignment explanation
Indices: 1738015--1738078 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
1738005 TTTCAACGAT
1738015 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1738034 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
1738048 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1738066 TTGTATCGATACA
1 TTGTATCGATACA
1738079 ATGTATCGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 24 0.62
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1738052 original size:32 final size:32
Alignment explanation
Indices: 1738016--1738144 Score: 198
Period size: 32 Copynumber: 4.2 Consensus size: 32
1738006 TTCAACGATT
1738016 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1738048 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1738080 TGTATCGATAC--AA----TGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
1738106 TGTATCGATACATAAATTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1738138 TGTATCG
1 TGTATCG
1738145 CTACGAAGCT
Statistics
Matches: 91, Mismatches: 0, Indels: 12
0.88 0.00 0.12
Matches are distributed among these distances:
26 24 0.26
28 2 0.02
30 2 0.02
32 63 0.69
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1738053 original size:13 final size:13
Alignment explanation
Indices: 1738035--1738117 Score: 112
Period size: 13 Copynumber: 5.9 Consensus size: 13
1738025 ACATAAGTGT
1738035 TGTATCGATACAA
1 TGTATCGATACAA
1738048 TGTATCGATACATAA
1 TGTATCGATAC--AA
1738063 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1738080 TGTATCGATACAA
1 TGTATCGATACAA
1738093 TGTATCGATACAA
1 TGTATCGATACAA
1738106 TGTATCGATACA
1 TGTATCGATACA
1738118 TAAATTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
13 49 0.77
15 2 0.03
17 2 0.03
19 11 0.17
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1738128 original size:58 final size:58
Alignment explanation
Indices: 1738035--1738144 Score: 202
Period size: 58 Copynumber: 1.9 Consensus size: 58
1738025 ACATAAGTGT
*
1738035 TGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACAA
1 TGTATCGATACAATGTATCGATACATAAATGTTGTATCGATACAATGTATCGATACAA
*
1738093 TGTATCGATACAATGTATCGATACATAAATTTTGTATCGATACAATGTATCG
1 TGTATCGATACAATGTATCGATACATAAATGTTGTATCGATACAATGTATCG
1738145 CTACGAAGCT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (58 bp):
TGTATCGATACAATGTATCGATACATAAATGTTGTATCGATACAATGTATCGATACAA
Found at i:1738389 original size:21 final size:21
Alignment explanation
Indices: 1738363--1738407 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1738353 GGTCAGGATT
1738363 CATGTCAAAACTCAATTGCCA
1 CATGTCAAAACTCAATTGCCA
1738384 CATGTCAAAACTCAATTGCCA
1 CATGTCAAAACTCAATTGCCA
1738405 CAT
1 CAT
1738408 ACCAAAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.09, T:0.24
Consensus pattern (21 bp):
CATGTCAAAACTCAATTGCCA
Found at i:1738413 original size:21 final size:21
Alignment explanation
Indices: 1738368--1738415 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1738358 GGATTCATGT
**
1738368 CAAAACTCAATTGCCACATGT
1 CAAAACTCAATTGCCACATAC
1738389 CAAAACTCAATTGCCACATAC
1 CAAAACTCAATTGCCACATAC
1738410 CAAAAC
1 CAAAAC
1738416 ACATTTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19
Consensus pattern (21 bp):
CAAAACTCAATTGCCACATAC
Found at i:1739397 original size:13 final size:13
Alignment explanation
Indices: 1739379--1739403 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1739369 CATAAAATGT
1739379 TGTATCGATACAA
1 TGTATCGATACAA
1739392 TGTATCGATACA
1 TGTATCGATACA
1739404 TATTTTTTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1739401 original size:33 final size:32
Alignment explanation
Indices: 1739359--1739427 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
1739349 TTCAACGATT
*
1739359 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACAT-AAATGTTATATCGATACAA
** *
1739392 TGTATCGATACATATTTTTTATATCGATACAA
1 TGTATCGATACATAAATGTTATATCGATACAA
1739424 TGTA
1 TGTA
1739428 AGCTACTGCC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATAAATGTTATATCGATACAA
Found at i:1739486 original size:13 final size:13
Alignment explanation
Indices: 1739468--1739492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1739458 ATTACTCACA
1739468 TGTATCGATACAT
1 TGTATCGATACAT
1739481 TGTATCGATACA
1 TGTATCGATACA
1739493 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1739557 original size:52 final size:52
Alignment explanation
Indices: 1739501--1739625 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1739491 CACTGATCTT
*
1739501 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1739553 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1739605 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1739626 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1743815 original size:17 final size:17
Alignment explanation
Indices: 1743795--1743830 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1743785 TCACATCATG
1743795 ATCATCCTTGTATCTCC
1 ATCATCCTTGTATCTCC
1743812 ATCATCCTTGTATCTCC
1 ATCATCCTTGTATCTCC
1743829 AT
1 AT
1743831 AGATTGCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.33, G:0.06, T:0.42
Consensus pattern (17 bp):
ATCATCCTTGTATCTCC
Found at i:1746552 original size:13 final size:12
Alignment explanation
Indices: 1746533--1746599 Score: 66
Period size: 12 Copynumber: 5.4 Consensus size: 12
1746523 AAAGGTGATA
1746533 AAAAAAACAAAC
1 AAAAAAACAAAC
*
1746545 AAACAAAAAAAAC
1 AAA-AAAACAAAC
*
1746558 ACACAAAAAAAAAC
1 A-A-AAAAACAAAC
1746572 AAAAAAACAAA-
1 AAAAAAACAAAC
1746583 AAAAAACACAAA-
1 AAAAAA-ACAAAC
1746595 AAAAA
1 AAAAA
1746600 TGCAAAGGCA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
11 6 0.12
12 21 0.43
13 10 0.20
14 11 0.22
15 1 0.02
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAC
Found at i:1746555 original size:18 final size:17
Alignment explanation
Indices: 1746532--1746588 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
1746522 AAAAGGTGAT
*
1746532 AAAAAAAACAAACAAAC
1 AAAAAAAACAAACAAAA
*
1746549 AAAAAAAACACACAAAA
1 AAAAAAAACAAACAAAA
*
1746566 AAAAACAAAAAAACAAAA
1 AAAAA-AAACAAACAAAA
1746584 AAAAA
1 AAAAA
1746589 CACAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
17 20 0.57
18 15 0.43
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAACAAACAAAA
Found at i:1746556 original size:31 final size:31
Alignment explanation
Indices: 1746532--1746599 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
1746522 AAAAGGTGAT
*
1746532 AAAAAAAACAAACAAACAAAAAAAACACACA
1 AAAAAAAACAAAAAAACAAAAAAAACACACA
1746563 AAAAAAAACAAAAAAACAAAAAAAA-ACACA
1 AAAAAAAACAAAAAAACAAAAAAAACACACA
1746593 AAAAAAA
1 AAAAAAA
1746600 TGCAAAGGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 12 0.33
31 24 0.67
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (31 bp):
AAAAAAAACAAAAAAACAAAAAAAACACACA
Found at i:1746605 original size:11 final size:11
Alignment explanation
Indices: 1746532--1746599 Score: 76
Period size: 10 Copynumber: 6.6 Consensus size: 11
1746522 AAAAGGTGAT
1746532 AAAAAAA-AC-
1 AAAAAAACACA
*
1746541 AAACAAACA-A
1 AAAAAAACACA
1746551 AAAAAACACACA
1 AAAAAA-ACACA
1746563 AAAAAAA-AC-
1 AAAAAAACACA
1746572 AAAAAAACA-A
1 AAAAAAACACA
1746582 AAAAAAACACA
1 AAAAAAACACA
1746593 AAAAAAA
1 AAAAAAA
1746600 TGCAAAGGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
9 13 0.26
10 18 0.36
11 12 0.24
12 7 0.14
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACACA
Found at i:1746856 original size:13 final size:12
Alignment explanation
Indices: 1746838--1746889 Score: 68
Period size: 13 Copynumber: 4.2 Consensus size: 12
1746828 TCTTTTCCAA
1746838 AAAAAAACAAAAC
1 AAAAAAA-AAAAC
1746851 AAAAAAAAAAAC
1 AAAAAAAAAAAC
*
1746863 AAAGAAAAAAGAC
1 AAA-AAAAAAAAC
*
1746876 AAAAAAAAGAAC
1 AAAAAAAAAAAC
1746888 AA
1 AA
1746890 CCCCTTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
12 17 0.49
13 18 0.51
ACGTcount: A:0.85, C:0.10, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:1746860 original size:11 final size:11
Alignment explanation
Indices: 1746839--1746889 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 11
1746829 CTTTTCCAAA
1746839 AAAAAACAAAAC
1 AAAAAA-AAAAC
1746851 AAAAAAAAAAAC
1 -AAAAAAAAAAC
1746863 AAAGAAAAAAGAC
1 AAA-AAAAAA-AC
1746876 AAAAAAAAGAAC
1 AAAAAAAA-AAC
1746888 AA
1 AA
1746890 CCCCTTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.09
12 20 0.57
13 12 0.34
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:1746871 original size:17 final size:17
Alignment explanation
Indices: 1746836--1746886 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
1746826 GTTCTTTTCC
1746836 AAAAAAAAACAAA-ACAA
1 AAAAAAAAACAAAGA-AA
1746853 AAAAAAAAACAAAGAAA
1 AAAAAAAAACAAAGAAA
1746870 AAAGACAAAAA-AAAGAA
1 AAA-A-AAAAACAAAGAA
1746887 CAACCCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 18 0.58
18 8 0.26
19 5 0.16
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (17 bp):
AAAAAAAAACAAAGAAA
Found at i:1747871 original size:31 final size:31
Alignment explanation
Indices: 1747833--1747977 Score: 179
Period size: 31 Copynumber: 4.7 Consensus size: 31
1747823 ATACCTTTTT
1747833 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
* *
1747864 AAAGTCCACGACTTAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
1747895 AAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
*
1747925 AAAGTCCACGACTCAGTGGC-ATCCTTTTCTTC
1 AAAGTCCACGACTCAGTGGCAAT-CTCTTC-TC
* * *
1747957 AAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
1747978 CACTCTGTGG
Statistics
Matches: 101, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.02
30 27 0.27
31 50 0.50
32 22 0.22
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTC
Found at i:1748078 original size:35 final size:33
Alignment explanation
Indices: 1747979--1748541 Score: 597
Period size: 35 Copynumber: 16.5 Consensus size: 33
1747969 TCCGTGGCAC
* *
1747979 ACTCTGTGGCACATTTTTTCTTTTAAAGCCCACA
1 ACTCCGTGGCAC-CTTTTTCTTTTAAAGCCCACA
*
1748013 ACTCCATGGCACCTTTTTCTTTTAAAGCCCACA
1 ACTCCGTGGCACCTTTTTCTTTTAAAGCCCACA
*
1748046 ACTCTGTGGCACACTTTTTCTTTTTAAAGCCCACA
1 ACTCCGTGGCAC-CTTTTTC-TTTTAAAGCCCACA
**
1748081 ACTTTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACA
1 ACTCCGTGGCAC-CTTTTT--CTTTT-AAAGCCCACA
* *
1748118 ACTCTGTGGCACCTTTTTCTTTTTAAAGCTCACA
1 ACTCCGTGGCACCTTTTTC-TTTTAAAGCCCACA
1748152 ACTCCGTGGCACTCTTTTTCCCTTTTTAAAGCCCACA
1 ACTCCGTGGCAC-CTTTTT--C-TTTTAAAGCCCACA
*
1748189 ACTCCGTGGCACCTTCTTTTCCTTCT-AAGCCCACA
1 ACTCCGTGGCACC-T-TTTT-CTTTTAAAGCCCACA
* *
1748224 ACTCCGTGGCACC-----CTTTT-AAGTCCACG
1 ACTCCGTGGCACCTTTTTCTTTTAAAGCCCACA
*
1748251 ACTCCGTGGCA-CTCTTTTCCTTTAAAGCCCACA
1 ACTCCGTGGCACCT-TTTTCTTTTAAAGCCCACA
* * *
1748284 ACTACGTGGCA-CTCTTTTCCTTCAAAGCCCACA
1 ACTCCGTGGCACCT-TTTTCTTTTAAAGCCCACA
*
1748317 ACTCTGTGGCACACTTTTTCTTTTTAAAGCCCACA
1 ACTCCGTGGCAC-CTTTTTC-TTTTAAAGCCCACA
**
1748352 ACTTTGTGGCACTCTTTTTCCCTTTTTAAAAGCCCACA
1 ACTCCGTGGCAC-CTTTTT--C-TTTT-AAAGCCCACA
1748390 ACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACA
1 ACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACA
*
1748424 ACTCTGTGGCACACTTTTTCTTTTAAAGCCCACA
1 ACTCCGTGGCAC-CTTTTTCTTTTAAAGCCCACA
*
1748458 ACTCCGTGGCACTTTTTTCTTTTAAAGCCCACA
1 ACTCCGTGGCACCTTTTTCTTTTAAAGCCCACA
*
1748491 ACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCCACA
1 ACTCCGTGGCAC-CTTTTT--CTTTTAAAGCCCACA
*
1748526 ACTCCGTGGCATCTTT
1 ACTCCGTGGCACCTTT
1748542 CTCCCTTCCT
Statistics
Matches: 466, Mismatches: 34, Indels: 58
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.00
27 22 0.05
32 4 0.01
33 109 0.23
34 98 0.21
35 125 0.27
36 19 0.04
37 64 0.14
38 24 0.05
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.35
Consensus pattern (33 bp):
ACTCCGTGGCACCTTTTTCTTTTAAAGCCCACA
Found at i:1748249 original size:27 final size:27
Alignment explanation
Indices: 1748209--1748268 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1748199 ACCTTCTTTT
*
1748209 CCTTCTAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
* *
1748236 CCTTTTAAGTCCACGACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
*
1748263 TCTTTT
1 CCTTTT
1748269 CCTTTAAAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.38, G:0.15, T:0.28
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCGTGGCAC
Found at i:1748564 original size:106 final size:102
Alignment explanation
Indices: 1747998--1748541 Score: 608
Period size: 106 Copynumber: 5.3 Consensus size: 102
1747988 CACATTTTTT
** * * *
1747998 CTTTTAAAGCCCACAACTCCATGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACACTTT
1 CTTTT-AAGCCCACAACTCTGTGGCAACTTTTTCTTTTAAAGCCCACAACTCCGTGGCAC-TTTT
**
1748063 TTCTTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTCC
64 TTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
* *
1748102 CTTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTTAAAGCTCACAACTCCGTGGCACTCT
1 CTTTT--AAGCCCACAACTCTGTGGCAACTTTTTC-TTTTAAAGCCCACAACTCCGTGGCACT-T
*
1748167 TTTTCCCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTCTTTTC
62 TTTT--CTTTTTAAAGCCCACAACTCCGTGGCACTCTT-TTTCC
* * * * * *
1748210 CTTCTAAGCCCACAACTCCGTGGC-AC----CCTTTT-AAGTCCACGACTCCGTGGCACTCTTTT
1 CTTTTAAGCCCACAACTCTGTGGCAACTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTTTTTT
* *
1748269 C-CTTTAAAGCCCACAACTACGTGGCACTC-TTTT-C
66 CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
** **
1748303 CTTCAAAGCCCACAACTCTGTGGCACACTTTTTCTTTTTAAAGCCCACAACTTTGTGGCACTCTT
1 CTTTTAAGCCCACAACTCTGTGGCA-ACTTTTTC-TTTTAAAGCCCACAACTCCGTGGCACT-TT
*
1748368 TTTCCCTTTTTAAAAGCCCACAACTCCGTGGCAC-CTTTTTCT
63 TTT--CTTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCC
* *
1748410 GTTTAAAGCCCACAACTCTGTGGCACACTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTTTTT
1 CTTTTAAGCCCACAACTCTGTGGCA-ACTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTTTTT
1748475 TC-TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
65 TCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
* * *
1748512 CTTTTAAGTCCACAACTCCGTGGCATCTTT
1 CTTTTAAGCCCACAACTCTGTGGCAACTTT
1748542 CTCCCTTCCT
Statistics
Matches: 378, Mismatches: 39, Indels: 49
0.81 0.08 0.11
Matches are distributed among these distances:
93 23 0.06
94 3 0.01
95 27 0.07
96 2 0.01
98 4 0.01
99 20 0.05
100 8 0.02
101 45 0.12
102 36 0.10
103 1 0.00
104 6 0.02
105 37 0.10
106 97 0.26
107 35 0.09
108 34 0.09
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.35
Consensus pattern (102 bp):
CTTTTAAGCCCACAACTCTGTGGCAACTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTTTTTT
CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
Found at i:1748589 original size:33 final size:34
Alignment explanation
Indices: 1748546--1748610 Score: 123
Period size: 33 Copynumber: 1.9 Consensus size: 34
1748536 ATCTTTCTCC
1748546 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
1748580 CTTCC-AAAGCCCACACAAGTCGGTGGCAACC
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACC
1748611 CTTTTAAGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.28, C:0.37, G:0.18, T:0.17
Consensus pattern (34 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
Found at i:1748722 original size:43 final size:45
Alignment explanation
Indices: 1748613--1749686 Score: 1146
Period size: 43 Copynumber: 23.1 Consensus size: 45
1748603 TGGCAACCCT
* *
1748613 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TC-TC
* *
1748662 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C-C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTC
*
1748705 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-----T-C-TC
* * *
1748757 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----TCTC
*
1748806 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CT-
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTC
* *
1748849 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TC-TC
*
1748898 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CT-
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTC
* *
1748941 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TC-TC
*
1748990 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTC
*
1749033 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-----T-C-TC
* * *
1749085 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----TCTC
*
1749134 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CT-
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTC
* *
1749177 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TC-TC
*
1749226 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CT-
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTC
* *
1749269 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TC-TC
*
1749318 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CT-
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTC
* *
1749361 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TC-TC
* *
1749410 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C-C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTC
* *
1749453 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TC-TC
*
1749502 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTC
1749545 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C-C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTC
*
1749588 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-----T-C-TC
* * * *
1749640 CTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATC-C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTC
1749684 TTT
1 TTT
1749687 TTCTCATTTT
Statistics
Matches: 893, Mismatches: 69, Indels: 131
0.82 0.06 0.12
Matches are distributed among these distances:
43 390 0.44
44 8 0.01
45 7 0.01
46 1 0.00
47 7 0.01
48 5 0.01
49 349 0.39
50 3 0.00
51 8 0.01
52 115 0.13
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (45 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTC
Found at i:1748914 original size:92 final size:90
Alignment explanation
Indices: 1748804--1749682 Score: 1018
Period size: 92 Copynumber: 9.5 Consensus size: 90
1748794 GGCACCTTTA
* * *
1748804 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-T-TTTAAGTCCAATATCGC
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCATCTTTAAGTCCAATGTAGC
*
1748866 TGGCCTTGAATCAGCATATTGGCACCTTC
66 TGGCCTTGAATCAGCACATTGGCA----C
* * *
1748895 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-T-TTTAAGTCCAATATCG
1 -TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCATCTTTAAGTCCAATGTAG
*
1748957 CTGGCCTTGAATCAGCATATTGGCACCTTC
65 CTGGCCTTGAATCAGCACATTGGCA----C
* *
1748987 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--CTTTAAGTCCAATATAG
1 -TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCATCTTTAAGTCCAATGTAG
*
1749049 CTGGCCTTGAATCAGCATATTGGCACCTTTTCC
65 CTGGCCTTGAATCAGCACATTGGCA-------C
* * *
1749082 ATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCCAATG
1 -TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TCATCTTTAAGTCCAATG
1749147 TAGCTGGCCTTGAATCAGCACATTGGCAC
62 TAGCTGGCCTTGAATCAGCACATTGGCAC
* *
1749176 T-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TCATCTTTAAGTCCAATGT
1749240 AGCTGGCCTTGAATCAGCACATTGGCAC
63 AGCTGGCCTTGAATCAGCACATTGGCAC
* *
1749268 T-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TCATCTTTAAGTCCAATGT
1749332 AGCTGGCCTTGAATCAGCACATTGGCAC
63 AGCTGGCCTTGAATCAGCACATTGGCAC
* *
1749360 T-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TCATCTTTAAGTCCAATGT
*
1749424 AGCTGGCCTTGACTCAGCACATTGGCAC
63 AGCTGGCCTTGAATCAGCACATTGGCAC
* *
1749452 -CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TCATCTTTAAGTCCAATGT
1749516 AGCTGGCCTTGAATCAGCACATTGGCAC
63 AGCTGGCCTTGAATCAGCACATTGGCAC
*
1749544 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C--CTTTAAGTCCAATATAGC
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCATCTTTAAGTCCAATGTAGC
*
1749605 TGGCCTTGAATCAGCATATTGGCACC
66 TGGCCTTGAATCAGCACATTGGCA-C
* * *
1749631 TTTTCCATCCTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATC
1 ---T-C-T--TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATC
1749683 CTTTTTCTCA
Statistics
Matches: 743, Mismatches: 23, Indels: 38
0.92 0.03 0.05
Matches are distributed among these distances:
86 40 0.05
87 1 0.00
88 1 0.00
92 575 0.77
93 2 0.00
94 1 0.00
95 82 0.11
96 1 0.00
101 40 0.05
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (90 bp):
TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCATCTTTAAGTCCAATGTAGC
TGGCCTTGAATCAGCACATTGGCAC
Found at i:1749208 original size:328 final size:331
Alignment explanation
Indices: 1748611--1750006 Score: 1970
Period size: 328 Copynumber: 4.2 Consensus size: 331
1748601 GGTGGCAACC
* *
1748611 CTTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CTTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
*
1748676 AGCTGGCCTTGACTCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAT
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAT
1748741 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATC
131 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATC
*
1748806 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-T-TTTAAGTCCAATATCGCTG
196 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCATCTTTAAGTCCAATATAGCTG
1748868 GCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
261 GCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
1748933 TTGGCA
326 TTGGCA
*
1748939 CTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CTTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1749004 AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAT
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAT
1749069 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATC
131 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATC
*
1749134 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-T-TTTAAGTCCAATATCGCTG
196 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCATCTTTAAGTCCAATATAGCTG
1749196 GCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
261 GCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
1749261 TTGGCA
326 TTGGCA
*
1749267 CTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CTTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
* *
1749332 AGCTGGCCTTGAATCAGCACATTGGCACTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAT
*
1749397 TGGCA--TCTT-CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C-----C
131 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATC
* * * *
1749453 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAG
196 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---TCATCTTTAAGTCCAATATAG
* *
1749518 CTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
258 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
1749577 ACATTGGCA
323 ACATTGGCA
* * *
1749586 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCCTTAAGTTCAA
1 CTTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAA
* ** *
1749651 TGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATTTTTAAGTCCAATAGCGTTGGC
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA--------C-C---TTTAAGTCCAATATAGCTGGC
* * *
1749716 CGTGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCATCTTTAAGTCCAATATAGCTG
116 CTTGAATCAGCATATTGG---C---A-C-C--TT-T--TC--CATCTTTAAGTCCAATGTAGCTG
* * *
1749781 GCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACA
166 GCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
* *
1749846 TTGGCACCTTCATCTTTAAGTCCAGTATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
231 TTGGCA---TCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
1749911 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA
293 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
*
1749950 CCTTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 ----C-T-TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1750007 ATCTTTAAAA
Statistics
Matches: 970, Mismatches: 41, Indels: 75
0.89 0.04 0.07
Matches are distributed among these distances:
319 123 0.13
321 3 0.00
322 42 0.04
323 1 0.00
324 2 0.00
325 83 0.09
326 3 0.00
328 457 0.47
330 1 0.00
334 35 0.04
337 1 0.00
340 1 0.00
346 1 0.00
347 1 0.00
349 1 0.00
352 42 0.04
353 1 0.00
358 83 0.09
364 40 0.04
367 4 0.00
368 3 0.00
370 42 0.04
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (331 bp):
CTTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAT
TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATC
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCATCTTTAAGTCCAATATAGCTG
GCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
TTGGCA
Found at i:1749546 original size:21 final size:21
Alignment explanation
Indices: 1749522--1749589 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1749512 ATGTAGCTGG
1749522 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* * *
1749543 CCTTTAAGTC--CA-ATATAGCTGG
1 CCTTGAA-TCAGCACAT-TGGC--A
1749565 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
1749586 CCTT
1 CCTT
1749590 TAAGTCCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:1749565 original size:24 final size:24
Alignment explanation
Indices: 1749538--1749608 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 24
1749528 ATCAGCACAT
1749538 TGGCACCTTTAAGTCCAATATAGC
1 TGGCACCTTTAAGTCCAATATAGC
* ** * *
1749562 TGG--CCTTGAA-T-CAGCACA-T
1 TGGCACCTTTAAGTCCAATATAGC
1749581 TGGCACCTTTAAGTCCAATATAGC
1 TGGCACCTTTAAGTCCAATATAGC
1749605 TGGC
1 TGGC
1749609 CTTGAATCAG
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 7 0.22
23 4 0.12
24 7 0.22
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (24 bp):
TGGCACCTTTAAGTCCAATATAGC
Found at i:1749568 original size:22 final size:22
Alignment explanation
Indices: 1749543--1749611 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
1749533 CACATTGGCA
1749543 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
* * *
1749565 CCTTGAA-TCAGCACAT-TGGC--A
1 CCTTTAAGTC--CA-ATATAGCTGG
1749586 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
1749608 CCTT
1 CCTT
1749612 GAATCAGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
CCTTTAAGTCCAATATAGCTGG
Found at i:1749724 original size:55 final size:51
Alignment explanation
Indices: 1749587--1749724 Score: 136
Period size: 52 Copynumber: 2.6 Consensus size: 51
1749577 ACATTGGCAC
* *
1749587 CTTTAAGTCCAATATAGC-TGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCC-A-ATAGCGTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
* *
1749639 CCTTAAGTTCAATGTAGC-TGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAA--TAGCGTGGCCTTGAATCAGCACATTGACA-CC-TTTTC-CAT
* *
1749694 TTTTAAGTCCAATAGCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATAGCG-TGGCCTTGAATCA
1749725 ACATATTGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 34 0.48
53 6 0.08
54 5 0.07
55 24 0.34
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.35
Consensus pattern (51 bp):
CTTTAAGTCCAATAGCGTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
Found at i:1749785 original size:174 final size:164
Alignment explanation
Indices: 1749587--1749908 Score: 457
Period size: 174 Copynumber: 1.9 Consensus size: 164
1749577 ACATTGGCAC
*
1749587 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCCTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCCTTAAGTCCAAT
*
1749652 GTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATTTTTAAGTCCA-ATAGCGTTGGC
63 GTAGCTGGCCTTGAATCAGCACATTGACA-CC----T-TCATCTTTAAGTCCAGATAGC--TGGC
*
1749716 CGTGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
120 CGTGAATCAACATATTGGCACCTTTATCACTTTTCTCATCTTCAT
*
1749761 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCCTTAAGTCCAATGTA
* * * *
1749826 GCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAGTATAGCTGGCCTTGAATCAG
66 GCTGGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCAG-ATAGCTGGCCGTGAATCAA
1749891 CATATTGGCACCTTTATC
130 CATATTGGCACCTTTATC
1749909 TTTAAGTCCA
Statistics
Matches: 138, Mismatches: 8, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
165 43 0.31
166 1 0.01
167 5 0.04
170 2 0.01
171 40 0.29
173 3 0.02
174 44 0.32
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (164 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCCTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCAGATAGCTGGCCGTGAATCAAC
ATATTGGCACCTTTATCACTTTTCTCATCTTCAT
Found at i:1749831 original size:49 final size:49
Alignment explanation
Indices: 1749755--1750006 Score: 414
Period size: 49 Copynumber: 5.1 Consensus size: 49
1749745 CTTTTCTCAT
1749755 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
* * * *
1749804 CTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
*
1749853 CTTCATCTTTAAGTCCAGTATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
* * * *
1749902 CTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
*
1749951 CTTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1750000 CTTCATC
1 CTTCATC
1750007 ATCTTTAAAA
Statistics
Matches: 184, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 184 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (49 bp):
CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:1749924 original size:98 final size:98
Alignment explanation
Indices: 1749755--1750002 Score: 478
Period size: 98 Copynumber: 2.5 Consensus size: 98
1749745 CTTTTCTCAT
1749755 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCC
1749820 AATGTAGCTGGCCTTGACTCAGCACATTGGCAC
66 AATGTAGCTGGCCTTGACTCAGCACATTGGCAC
*
1749853 CTTCATCTTTAAGTCCAGTATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCC
1749918 AATGTAGCTGGCCTTGACTCAGCACATTGGCAC
66 AATGTAGCTGGCCTTGACTCAGCACATTGGCAC
*
1749951 CTTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTT
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
1750003 CATCATCTTT
Statistics
Matches: 147, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 147 1.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (98 bp):
CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCC
AATGTAGCTGGCCTTGACTCAGCACATTGGCAC
Found at i:1750843 original size:13 final size:13
Alignment explanation
Indices: 1750825--1750849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1750815 CATAAAATGT
1750825 TGTATCGATACAA
1 TGTATCGATACAA
1750838 TGTATCGATACA
1 TGTATCGATACA
1750850 TATTTTTTTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1750847 original size:33 final size:33
Alignment explanation
Indices: 1750805--1750874 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1750795 TTCAACGATT
*
1750805 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTATATCGATACAA
*** *
1750838 TGTATCGATACATATTTTTTTATATCGATACAA
1 TGTATCGATACATAAAATGTTATATCGATACAA
1750871 TGTA
1 TGTA
1750875 AGCTACTGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTATATCGATACAA
Found at i:1750933 original size:13 final size:13
Alignment explanation
Indices: 1750915--1750939 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1750905 ATTACTCACA
1750915 TGTATCGATACAT
1 TGTATCGATACAT
1750928 TGTATCGATACA
1 TGTATCGATACA
1750940 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1751004 original size:52 final size:52
Alignment explanation
Indices: 1750948--1751072 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1750938 CACTGATCTT
* *
1750948 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
*
1751000 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
*
1751052 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1751073 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
Found at i:1757140 original size:57 final size:58
Alignment explanation
Indices: 1757124--1757350 Score: 183
Period size: 58 Copynumber: 3.9 Consensus size: 58
1757114 AAAATGGTCT
1757124 TAAAATGCATGAAATTACATAAAAATCCATAAAACATGAAAAATGACTAAAATAACTC
1 TAAAATGCATGAAATTACATAAAAATCCATAAAACATGAAAAATGACTAAAATAACTC
* * * * * *
1757182 TAAAATGCATGAAATTATATAAATAATCC-TAAAACATGACAAATTACTAGAATGACCC
1 TAAAATGCATGAAATTACATAAA-AATCCATAAAACATGAAAAATGACTAAAATAACTC
* * ** * * * * *
1757240 TAAAATACATGAGAA-TGCATAAATGGTTC-TAAATCATGAAAATTTA-TAAAAATAACTT
1 TAAAATGCATGA-AATTACATAAA-AATCCATAAAACATGAAAAATGACT-AAAATAACTC
* * * * ** * *
1757298 TAAAGTGCATGAAATAACATAAAAGTCCCTAAGTCATGAAAAATAATTAAAAT
1 TAAAATGCATGAAATTACATAAAAATCCATAAAACATGAAAAATGACTAAAAT
1757351 GCATGAAATG
Statistics
Matches: 135, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
57 6 0.04
58 121 0.90
59 8 0.06
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.26
Consensus pattern (58 bp):
TAAAATGCATGAAATTACATAAAAATCCATAAAACATGAAAAATGACTAAAATAACTC
Found at i:1757156 original size:29 final size:28
Alignment explanation
Indices: 1757124--1757215 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
1757114 AAAATGGTCT
1757124 TAAAATGCATGAAATTACATAAAAATCC
1 TAAAATGCATGAAATTACATAAAAATCC
* *
1757152 ATAAAA--CATGAAAAATGAC-TAAAATAACTC
1 -TAAAATGCATG--AAATTACATAAAA-ATC-C
*
1757182 TAAAATGCATGAAATTATATAAATAATCC
1 TAAAATGCATGAAATTACATAAA-AATCC
1757211 TAAAA
1 TAAAA
1757216 CATGACAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
27 4 0.08
28 5 0.10
29 29 0.58
30 7 0.14
31 5 0.10
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.25
Consensus pattern (28 bp):
TAAAATGCATGAAATTACATAAAAATCC
Found at i:1757196 original size:58 final size:58
Alignment explanation
Indices: 1757124--1757320 Score: 202
Period size: 58 Copynumber: 3.4 Consensus size: 58
1757114 AAAATGGTCT
*
1757124 TAAAATGCATGAAATTACATAAA-AATCCATAAAACATGAAAAATGACTAAAATAACTC
1 TAAAATGCATGAAATTACATAAATAATCC-TAAAACATGAAAAATTACTAAAATAACTC
* * * * *
1757182 TAAAATGCATGAAATTATATAAATAATCCTAAAACATGACAAATTACTAGAATGACCC
1 TAAAATGCATGAAATTACATAAATAATCCTAAAACATGAAAAATTACTAAAATAACTC
* * ** * * * *
1757240 TAAAATACATGAGAA-TGCATAAATGGTTCTAAATCATGAAAATTTA-TAAAAATAACTT
1 TAAAATGCATGA-AATTACATAAATAATCCTAAAACATGAAAAATTACT-AAAATAACTC
* *
1757298 TAAAGTGCATGAAATAACATAAA
1 TAAAATGCATGAAATTACATAAA
1757321 AGTCCCTAAG
Statistics
Matches: 112, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
57 3 0.03
58 102 0.91
59 7 0.06
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (58 bp):
TAAAATGCATGAAATTACATAAATAATCCTAAAACATGAAAAATTACTAAAATAACTC
Found at i:1757225 original size:29 final size:28
Alignment explanation
Indices: 1757096--1757227 Score: 78
Period size: 29 Copynumber: 4.6 Consensus size: 28
1757086 TAATAGTCTT
* ** *
1757096 TAAAACATTGAAAATGATA-AAATGGTCT
1 TAAAACA-TGAAAATTATATAAATAATCC
*
1757124 TAAAATGCATG-AAATTACATAAA-AATCC
1 TAAAA--CATGAAAATTATATAAATAATCC
*
1757152 ATAAAACATGAAAAATGACTA-AAATAA-CTC
1 -TAAAACATG-AAAATTA-TATAAATAATC-C
1757182 TAAAATGCATG-AAATTATATAAATAATCC
1 TAAAA--CATGAAAATTATATAAATAATCC
1757211 TAAAACATGACAAATTA
1 TAAAACATGA-AAATTA
1757228 CTAGAATGAC
Statistics
Matches: 81, Mismatches: 8, Indels: 29
0.69 0.07 0.25
Matches are distributed among these distances:
27 8 0.10
28 15 0.19
29 47 0.58
30 7 0.09
31 4 0.05
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (28 bp):
TAAAACATGAAAATTATATAAATAATCC
Found at i:1758101 original size:12 final size:12
Alignment explanation
Indices: 1758076--1758110 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1758066 CTTTCCATTT
1758076 TCTTTTGTTCTTTC
1 TCTTTT-TT-TTTC
1758090 TCTTTTTTTTTC
1 TCTTTTTTTTTC
1758102 TCTTTTTTT
1 TCTTTTTTT
1758111 CTCTAGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 13 0.62
13 2 0.10
14 6 0.29
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (12 bp):
TCTTTTTTTTTC
Done.