Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold42
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: 3911082
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 18191 characters in sequence are not A, C, G, or T
File 9 of 24
Found at i:1219734 original size:2 final size:2
Alignment explanation
Indices: 1219727--1219773 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1219717 TGTGACTAGG
1219727 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1219769 AT AT A
1 AT AT A
1219774 AATAAAAGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1220876 original size:14 final size:14
Alignment explanation
Indices: 1220849--1220972 Score: 68
Period size: 14 Copynumber: 9.1 Consensus size: 14
1220839 TCAAGGTTTA
1220849 ATAATT-TA-AAAT
1 ATAATTATATAAAT
1220861 ATAATTATATAAAT
1 ATAATTATATAAAT
*
1220875 ATAATATATTTAAA-
1 ATAAT-TATATAAAT
*
1220889 AT-ATTAAATAAAT
1 ATAATTATATAAAT
*
1220902 A-ATATGATATAAAT
1 ATA-ATTATATAAAT
*
1220916 ATATATTTTA-AAAT
1 ATA-ATTATATAAAT
1220930 AT-ATGTAATATAAAT
1 ATAAT-T-ATATAAAT
* *
1220945 -TATTTATAT-ATT
1 ATAATTATATAAAT
*
1220957 AAAATTTATATAAAT
1 ATAA-TTATATAAAT
1220972 A
1 A
1220973 AAAGGCATGG
Statistics
Matches: 85, Mismatches: 13, Indels: 25
0.69 0.11 0.20
Matches are distributed among these distances:
12 16 0.19
13 11 0.13
14 37 0.44
15 21 0.25
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
ATAATTATATAAAT
Found at i:1220906 original size:30 final size:30
Alignment explanation
Indices: 1220847--1220912 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1220837 TATCAAGGTT
* *
1220847 TAATA-ATTTAAAATATAATTATATAAATA
1 TAATATATTTAAAATATAAATAAATAAATA
1220876 TAATATATTTAAAATATTAAATAAAT-AATA
1 TAATATATTTAAAATA-TAAATAAATAAATA
*
1220906 TGATATA
1 TAATATA
1220913 AATATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.16
30 20 0.62
31 7 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
TAATATATTTAAAATATAAATAAATAAATA
Found at i:1222839 original size:11 final size:11
Alignment explanation
Indices: 1222817--1222850 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1222807 TTTTGTAATA
1222817 TATATT-TATT
1 TATATTATATT
1222827 TATATTATATT
1 TATATTATATT
1222838 TATATTATTATT
1 TATATTA-TATT
1222850 T
1 T
1222851 TTTATACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.27
11 11 0.50
12 5 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATATTATATT
Found at i:1223824 original size:24 final size:24
Alignment explanation
Indices: 1223797--1223843 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1223787 TACTAATAAT
*
1223797 ATTTAAAT-ATATAAATATATTAAA
1 ATTTAAATAAAATAAA-ATATTAAA
*
1223821 ATTTATATAAAATAAAATATTAA
1 ATTTAAATAAAATAAAATATTAA
1223844 GAAAAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATTTAAATAAAATAAAATATTAAA
Found at i:1224626 original size:18 final size:18
Alignment explanation
Indices: 1224589--1224626 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1224579 CTGTTCAAAC
*
1224589 AAGATGAAAAAGAAGGTT
1 AAGATGAAAAAGAAGATT
1224607 AAGATGAGAAAA-AAGATT
1 AAGATGA-AAAAGAAGATT
1224625 AA
1 AA
1224627 AAAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.16
Consensus pattern (18 bp):
AAGATGAAAAAGAAGATT
Found at i:1224961 original size:18 final size:18
Alignment explanation
Indices: 1224938--1225000 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
1224928 ATTAATAAAT
1224938 AATTTTTTTATTATATTA
1 AATTTTTTTATTATATTA
*
1224956 AATTTTTATTACATTTTATTA
1 AATTTTT-TT--ATTATATTA
* * *
1224977 AATATTTGTATTCTATTA
1 AATTTTTTTATTATATTA
1224995 AATTTT
1 AATTTT
1225001 GTTAATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 20 0.54
19 2 0.05
20 1 0.03
21 14 0.38
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (18 bp):
AATTTTTTTATTATATTA
Found at i:1225072 original size:18 final size:19
Alignment explanation
Indices: 1225046--1225081 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1225036 CCAATTGTTT
*
1225046 TTTTTAAAT-ATTAATAAA
1 TTTTAAAATAATTAATAAA
1225064 TTTTAAAATAATTAATAA
1 TTTTAAAATAATTAATAA
1225082 CGGACAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTAAAATAATTAATAAA
Found at i:1226181 original size:16 final size:16
Alignment explanation
Indices: 1226160--1226206 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1226150 ACATTTTCTA
1226160 TTCAAATATTATTTTT
1 TTCAAATATTATTTTT
* *
1226176 TTCAAA-ATAAATTTT
1 TTCAAATATTATTTTT
1226191 TT-AAATCATTATTTTT
1 TTCAAAT-ATTATTTTT
1226207 ATTTTTACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.12
15 9 0.36
16 13 0.52
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (16 bp):
TTCAAATATTATTTTT
Found at i:1226975 original size:12 final size:12
Alignment explanation
Indices: 1226958--1227033 Score: 57
Period size: 12 Copynumber: 6.1 Consensus size: 12
1226948 AAATATTATA
1226958 TTTATATAAATT
1 TTTATATAAATT
*
1226970 TTTATATATATT
1 TTTATATAAATT
1226982 TTTATATATTATATAT
1 TTTATATA--A-AT-T
*
1226998 TTTATATTATATT
1 TTTATA-TAAATT
* *
1227011 TTAAT-TAATTT
1 TTTATATAAATT
1227022 TTTAT-TAAATT
1 TTTATATAAATT
1227033 T
1 T
1227034 ATATCATATA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
11 14 0.27
12 19 0.37
13 5 0.10
14 2 0.04
15 2 0.04
16 7 0.14
17 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTATATAAATT
Found at i:1226995 original size:19 final size:19
Alignment explanation
Indices: 1226974--1227010 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
1226964 TAAATTTTTA
1226974 TATATATTTT-TA-TATAT
1 TATATATTTTATATTATAT
1226991 TATATATTTTATATTATAT
1 TATATATTTTATATTATAT
1227010 T
1 T
1227011 TTAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 2 0.11
19 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATATATTTTATATTATAT
Found at i:1227002 original size:16 final size:16
Alignment explanation
Indices: 1226953--1227004 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1226943 TATTAAAATA
1226953 TTATAT-TTATATAAATT
1 TTATATATTATAT--ATT
1226970 TT-TATA-TATAT-TT
1 TTATATATTATATATT
1226983 TTATATATTATATATT
1 TTATATATTATATATT
1226999 TTATAT
1 TTATAT
1227005 TATATTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
13 4 0.13
14 4 0.13
15 5 0.16
16 16 0.52
17 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATATTATATATT
Found at i:1228770 original size:18 final size:19
Alignment explanation
Indices: 1228705--1228771 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 19
1228695 ATTATTTTTT
*
1228705 ATAAACTTTA-AT-ATATA
1 ATAAATTTTATATAATATA
*
1228722 ATAAA-TTTATATAATACA
1 ATAAATTTTATATAATATA
* *
1228740 A-GACTTTTATATAAATATA
1 ATAAATTTTATAT-AATATA
1228759 ATAAATTTTATAT
1 ATAAATTTTATAT
1228772 TACAATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
16 4 0.10
17 8 0.21
18 12 0.31
19 6 0.15
20 9 0.23
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (19 bp):
ATAAATTTTATATAATATA
Found at i:1231131 original size:29 final size:28
Alignment explanation
Indices: 1231099--1231161 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
1231089 CATAATACTT
1231099 TAATAAATAAATATT-AATACAATGTA-AAA
1 TAATAAATAAA-ATTGAA-ACAAT-TATAAA
1231128 TAATAAA-AAAATTGAAACAATTATAAA
1 TAATAAATAAAATTGAAACAATTATAAA
1231155 -AATAAAT
1 TAATAAAT
1231162 TTAAAATTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
26 8 0.26
27 11 0.35
28 5 0.16
29 7 0.23
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (28 bp):
TAATAAATAAAATTGAAACAATTATAAA
Found at i:1231350 original size:2 final size:2
Alignment explanation
Indices: 1231343--1231383 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1231333 CACAGAACTA
1231343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1231384 CACACCTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1231706 original size:110 final size:111
Alignment explanation
Indices: 1231576--1231781 Score: 335
Period size: 110 Copynumber: 1.9 Consensus size: 111
1231566 ACAATACCTT
* * *
1231576 TTTTTTTTTTTTTATCATTTTCATTGATTTCCT-ACAACTTTTTATAATCC-AAAGTCATTACCT
1 TTTTTTTTTTTTAATCATTTTCATTGATTT-CTAACAACTTTTTATAATCCAAAAGTCATGACCC
*
1231639 AAAGGCAATAGCTTTTATCTTCGCATCAAACCAAAAATGCCCCCCCC
65 AAAGACAATAGCTTTTATCTTCGCATCAAACCAAAAATGCCCCCCCC
*
1231686 TTTTTTTTTTTTAATCATTTTCATTGATTTTTAACAACTTTTTATAATCCAAAAGTCATGACCCA
1 TTTTTTTTTTTTAATCATTTTCATTGATTTCTAACAACTTTTTATAATCCAAAAGTCATGACCCA
*
1231751 AAGACAATAGCTTTTATCTTCGCGTCAAACC
66 AAGACAATAGCTTTTATCTTCGCATCAAACC
1231782 CCCTTGTATA
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
109 1 0.01
110 46 0.52
111 41 0.47
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (111 bp):
TTTTTTTTTTTTAATCATTTTCATTGATTTCTAACAACTTTTTATAATCCAAAAGTCATGACCCA
AAGACAATAGCTTTTATCTTCGCATCAAACCAAAAATGCCCCCCCC
Found at i:1231854 original size:17 final size:16
Alignment explanation
Indices: 1231832--1231877 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
1231822 GTCAAATCAA
1231832 TTTGTTTATTTTTTATT
1 TTTGTTTATTTTTTA-T
*
1231849 TTTGTTTATTTATTAT
1 TTTGTTTATTTTTTAT
*
1231865 TAT-TTTATTTTTT
1 TTTGTTTATTTTTT
1231878 TACACAACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 9 0.35
16 3 0.12
17 14 0.54
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTGTTTATTTTTTAT
Found at i:1237333 original size:15 final size:15
Alignment explanation
Indices: 1237313--1237344 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1237303 AACCATCAAA
1237313 GATAATGAAGATGAT
1 GATAATGAAGATGAT
*
1237328 GATAATGATGATGAT
1 GATAATGAAGATGAT
1237343 GA
1 GA
1237345 AGTTGAGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (15 bp):
GATAATGAAGATGAT
Found at i:1242040 original size:31 final size:30
Alignment explanation
Indices: 1241977--1242053 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
1241967 AACAATTCAA
*
1241977 TCATCAATTTCATCAAATCTTTTTCAAATT
1 TCATCAATTTCATCAAAACTTTTTCAAATT
**
1242007 TCATCAATTTCACATCAAAAC-TTTTCATTTT
1 TCATCAATTT--CATCAAAACTTTTTCAAATT
**
1242038 TCATCAAAATCATCAA
1 TCATCAATTTCATCAA
1242054 CAAAAACACT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 6 0.15
30 10 0.25
31 16 0.40
32 8 0.20
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (30 bp):
TCATCAATTTCATCAAAACTTTTTCAAATT
Found at i:1245665 original size:20 final size:20
Alignment explanation
Indices: 1245642--1245695 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1245632 CATTTCAAGC
*
1245642 ATGTATCGATACATTCATTT
1 ATGTATCGATACATTCACTT
*
1245662 ATGTATCGATAAATTCACTT
1 ATGTATCGATACATTCACTT
1245682 ATTGTATCGATACA
1 A-TGTATCGATACA
1245696 AATTGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:1250605 original size:22 final size:22
Alignment explanation
Indices: 1250577--1250621 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1250567 GACTATGGAT
* *
1250577 TAGTAATTTATATTAAGGTCAA
1 TAGTAATTTATATCAAGGCCAA
1250599 TAGTAATTTATATCAAGGCCAA
1 TAGTAATTTATATCAAGGCCAA
1250621 T
1 T
1250622 CCATTGGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (22 bp):
TAGTAATTTATATCAAGGCCAA
Found at i:1252840 original size:13 final size:13
Alignment explanation
Indices: 1252822--1252847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1252812 ACATTTTGTG
1252822 ATGTATCGATACA
1 ATGTATCGATACA
1252835 ATGTATCGATACA
1 ATGTATCGATACA
1252848 TATTGTGTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1252842 original size:33 final size:32
Alignment explanation
Indices: 1252800--1252867 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 32
1252790 CGTTACAAGC
*
1252800 CAATGTATCGATACATTTTGTGATGTATCGATA
1 CAATGTATCGATACATATTGTG-TGTATCGATA
1252833 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGTGTGTATCGATA
1252865 CAA
1 CAA
1252868 ATTTAGCTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.38
33 21 0.62
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
CAATGTATCGATACATATTGTGTGTATCGATA
Found at i:1252933 original size:20 final size:20
Alignment explanation
Indices: 1252889--1252940 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1252879 GCCAATGACT
* **
1252889 TGTATTGATACATTTTTTCA
1 TGTATCGATACATTTAGTCA
*
1252909 AGTATCGATACATTTAGTCA
1 TGTATCGATACATTTAGTCA
*
1252929 TGTATCGCTACA
1 TGTATCGATACA
1252941 ATGTATCGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTTAGTCA
Found at i:1257204 original size:23 final size:24
Alignment explanation
Indices: 1257141--1257207 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 24
1257131 TTTTCAATTT
*
1257141 ATAAATAAAAATTTTAATTTTATTA
1 ATAAATAAAAAATTT-ATTTTATTA
1257166 A-AAATTTAAAATAAATTTATTTTA-TA
1 ATAAA--T-AAA-AAATTTATTTTATTA
1257192 ATAAATAAAAAATTTA
1 ATAAATAAAAAATTTA
1257208 AGGTTTGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
23 7 0.19
24 6 0.17
25 2 0.06
26 4 0.11
27 12 0.33
28 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAAATAAAAAATTTATTTTATTA
Found at i:1259989 original size:32 final size:32
Alignment explanation
Indices: 1259940--1260030 Score: 96
Period size: 36 Copynumber: 2.8 Consensus size: 32
1259930 CAACACTATC
*
1259940 TTTC-AAGGCTAAAATAGAAACCTCCCTATC-T
1 TTTCAAAGGCTAAGATAG-AACCTCCCTATCTT
**
1259971 TTTCACGGGCTAAGATAGAACTTTTCTCCCTATCTT
1 TTTCAAAGGCTAAGATAGAAC----CTCCCTATCTT
1260007 TTTCAAAGGCTAAGATAGAACCTC
1 TTTCAAAGGCTAAGATAGAACCTC
1260031 ACAATCACTT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
31 7 0.14
32 13 0.27
35 9 0.18
36 20 0.41
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (32 bp):
TTTCAAAGGCTAAGATAGAACCTCCCTATCTT
Found at i:1260421 original size:20 final size:20
Alignment explanation
Indices: 1260396--1260447 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1260386 TACACGCTAC
1260396 AATGTATCGATATAATTCAT
1 AATGTATCGATATAATTCAT
1260416 AATGTATCGATATAATTCAT
1 AATGTATCGATATAATTCAT
1260436 AATGTATCGATA
1 AATGTATCGATA
1260448 CATACACTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (20 bp):
AATGTATCGATATAATTCAT
Found at i:1260538 original size:24 final size:24
Alignment explanation
Indices: 1260506--1260551 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1260496 ACACTGTATC
1260506 GATACATGAACAGTGATGAATAGT
1 GATACATGAACAGTGATGAATAGT
*
1260530 GATACATGAATAGTGATGAATA
1 GATACATGAACAGTGATGAATA
1260552 ATAATGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (24 bp):
GATACATGAACAGTGATGAATAGT
Found at i:1263978 original size:20 final size:20
Alignment explanation
Indices: 1263953--1264010 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
1263943 CTGCTAGTTT
*
1263953 CATGTATCGATATAATTGTC
1 CATGTATCGATATAATTGTA
* *
1263973 CATGTATCGATACAA-TGAA
1 CATGTATCGATATAATTGTA
1263992 CATGTATCGATAT-ATTGTA
1 CATGTATCGATATAATTGTA
1264011 TCGATACAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.03
19 17 0.53
20 14 0.44
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (20 bp):
CATGTATCGATATAATTGTA
Found at i:1264016 original size:32 final size:33
Alignment explanation
Indices: 1263975--1264036 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
1263965 TAATTGTCCA
*
1263975 TGTATCGATACAATG-A-ACATGTATCGATATAT
1 TGTATCGATACAAAGCATA-ATGTATCGATATAT
1264007 TGTATCGATACAAAGCATAATGTATCGATA
1 TGTATCGATACAAAGCATAATGTATCGATA
1264037 CATCTGGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 14 0.52
33 12 0.44
34 1 0.04
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAAGCATAATGTATCGATATAT
Found at i:1265025 original size:21 final size:20
Alignment explanation
Indices: 1265001--1265057 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
1264991 TCTTAGTTAG
1265001 CTCATTATTTTCATCTTGCAA
1 CTCATTATTTTC-TCTTGCAA
* * *
1265022 CTCATTTCTTTTCTTTTGTAA
1 CTCA-TTATTTTCTCTTGCAA
1265043 CTCATTCATTTTCTC
1 CTCATT-ATTTTCTC
1265058 CTCTAGTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.54
Consensus pattern (20 bp):
CTCATTATTTTCTCTTGCAA
Found at i:1267209 original size:10 final size:10
Alignment explanation
Indices: 1267190--1267221 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1267180 GTATTGATAC
*
1267190 ATGAACAGTG
1 ATGAATAGTG
1267200 ATGAATAGTG
1 ATGAATAGTG
1267210 ATGAATAGTG
1 ATGAATAGTG
1267220 AT
1 AT
1267222 ACATGAACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.41, C:0.03, G:0.28, T:0.28
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:1267227 original size:24 final size:24
Alignment explanation
Indices: 1267200--1267266 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
1267190 ATGAACAGTG
1267200 ATGAATAGTGATGAATAGTGATAC
1 ATGAATAGTGATGAATAGTGATAC
* * *
1267224 ATGAACAGTTATGAACAGTGATAC
1 ATGAATAGTGATGAATAGTGATAC
*
1267248 ATGAATAGTGATAAATAGT
1 ATGAATAGTGATGAATAGT
1267267 AATGTATCAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.28
Consensus pattern (24 bp):
ATGAATAGTGATGAATAGTGATAC
Found at i:1267257 original size:14 final size:14
Alignment explanation
Indices: 1267210--1267260 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1267200 ATGAATAGTG
*
1267210 ATGAATAGTGATAC
1 ATGAACAGTGATAC
1267224 ATGAACAGT--T--
1 ATGAACAGTGATAC
1267234 ATGAACAGTGATAC
1 ATGAACAGTGATAC
*
1267248 ATGAATAGTGATA
1 ATGAACAGTGATA
1267261 AATAGTAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 9 0.29
12 2 0.06
14 20 0.65
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (14 bp):
ATGAACAGTGATAC
Found at i:1267841 original size:14 final size:14
Alignment explanation
Indices: 1267822--1267855 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1267812 TATTGTTTTG
1267822 GGATTAGATT-TTAA
1 GGATTAG-TTATTAA
1267836 GGATTAGTTATTAA
1 GGATTAGTTATTAA
1267850 GGATTA
1 GGATTA
1267856 CTGTTTGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 17 0.89
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (14 bp):
GGATTAGTTATTAA
Found at i:1269369 original size:20 final size:20
Alignment explanation
Indices: 1269344--1269395 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1269334 GTCGAAAAAT
*
1269344 TGTATCGATACATGAGTAAA
1 TGTATCGATACATGACTAAA
* **
1269364 TGTATCAATACATTCCTAAA
1 TGTATCGATACATGACTAAA
1269384 TGTATCGATACA
1 TGTATCGATACA
1269396 ATTTGCTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATGACTAAA
Found at i:1269804 original size:20 final size:20
Alignment explanation
Indices: 1269781--1269825 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1269771 CAGATTACCA
1269781 ATACAAATTGCAATGTATCG
1 ATACAAATTGCAATGTATCG
*
1269801 ATACAAGTTGCAATGTATCG
1 ATACAAATTGCAATGTATCG
1269821 ATACA
1 ATACA
1269826 TTACGTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (20 bp):
ATACAAATTGCAATGTATCG
Found at i:1269900 original size:22 final size:22
Alignment explanation
Indices: 1269872--1269929 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
1269862 CTACCCTTTA
1269872 AATGTATCGATACACATATAGG
1 AATGTATCGATACACATATAGG
*
1269894 AATGTATTGATACACATATAGG
1 AATGTATCGATACACATATAGG
1269916 AATGTATCGATACA
1 AATGTATCGATACA
1269930 ATTCCAGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (22 bp):
AATGTATCGATACACATATAGG
Found at i:1270433 original size:54 final size:54
Alignment explanation
Indices: 1270350--1270459 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
1270340 GTGTTCAACC
*
1270350 TTGAATGCAATCACTAGAGAATTTTGGATATAATTCTCGAAGTGATTGAGAGGT
1 TTGAATGCAATCACTAGAGAATTTGGGATATAATTCTCGAAGTGATTGAGAGGT
1270404 TTGAATGCAATCACTAGAGAATTTGGGATATAATTCTCGAAGTGATTGAGAGGT
1 TTGAATGCAATCACTAGAGAATTTGGGATATAATTCTCGAAGTGATTGAGAGGT
1270458 TT
1 TT
1270460 TATCTTAGCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.34
Consensus pattern (54 bp):
TTGAATGCAATCACTAGAGAATTTGGGATATAATTCTCGAAGTGATTGAGAGGT
Found at i:1270552 original size:34 final size:34
Alignment explanation
Indices: 1270460--1270553 Score: 152
Period size: 34 Copynumber: 2.8 Consensus size: 34
1270450 TGAGAGGTTT
*
1270460 TATCTTAGCCTTCGAAAAGACAGTGTAGGTGTTC
1 TATCTTAGCCTTCGAAAAGATAGTGTAGGTGTTC
*
1270494 TATCTTAGCCTTCGAAAAGTTAGTGTAGGTGTTC
1 TATCTTAGCCTTCGAAAAGATAGTGTAGGTGTTC
* *
1270528 TATCTTAGCCTTCAAAAAAATAGTGT
1 TATCTTAGCCTTCGAAAAGATAGTGT
1270554 TGTAAGGTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (34 bp):
TATCTTAGCCTTCGAAAAGATAGTGTAGGTGTTC
Found at i:1274298 original size:30 final size:30
Alignment explanation
Indices: 1274264--1274322 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
1274254 CCCCACTCCA
**
1274264 AGGAACATTTGTACTAAAAACGATAAAGCT
1 AGGAACATTCATACTAAAAACGATAAAGCT
*
1274294 AGGAACATTCATACTCAAAACGATAAAGC
1 AGGAACATTCATACTAAAAACGATAAAGC
1274323 CACACTCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (30 bp):
AGGAACATTCATACTAAAAACGATAAAGCT
Found at i:1276419 original size:34 final size:34
Alignment explanation
Indices: 1276380--1276447 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
1276370 GAAACGATTG
1276380 AGAGGTTCTATCTTAGCCTTCGAAAAGATAGTGT
1 AGAGGTTCTATCTTAGCCTTCGAAAAGATAGTGT
* *
1276414 AGAGGTTCTATCTTAGCCTTTGAAAATATAGTGT
1 AGAGGTTCTATCTTAGCCTTCGAAAAGATAGTGT
1276448 TGTAAGGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.35
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCCTTCGAAAAGATAGTGT
Found at i:1276487 original size:29 final size:32
Alignment explanation
Indices: 1276426--1276494 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 32
1276416 AGGTTCTATC
* *
1276426 TTAGCCTTTGAAAATATAGTGTTGTAAGGTTA
1 TTAGCCTTTGAAAATAGAGTGTTGTAAGATTA
1276458 TTAGCCTTTG-AAA-AGA-TGTTGTAAGATTA
1 TTAGCCTTTGAAAATAGAGTGTTGTAAGATTA
1276487 -TA-CCTTTG
1 TTAGCCTTTG
1276495 CCTTAAAGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 6 0.17
28 2 0.06
29 12 0.34
30 2 0.06
31 3 0.09
32 10 0.29
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (32 bp):
TTAGCCTTTGAAAATAGAGTGTTGTAAGATTA
Found at i:1290856 original size:22 final size:21
Alignment explanation
Indices: 1290821--1290871 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
1290811 GTTTACTAGA
1290821 TAAATATAAATG-TTTTCAAAGCT
1 TAAA-ATAAATGTTTTTC-AAG-T
*
1290844 TAAAATAAGTGTTTTTCAAGT
1 TAAAATAAATGTTTTTCAAGT
1290865 TAAAATA
1 TAAAATA
1290872 TATCAAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.31
22 9 0.35
23 9 0.35
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (21 bp):
TAAAATAAATGTTTTTCAAGT
Found at i:1291008 original size:13 final size:13
Alignment explanation
Indices: 1290990--1291014 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1290980 AGATTGCACA
1290990 GTATCGATACATT
1 GTATCGATACATT
1291003 GTATCGATACAT
1 GTATCGATACAT
1291015 GACCAAATGT
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):
GTATCGATACATT
Found at i:1291027 original size:20 final size:21
Alignment explanation
Indices: 1291002--1291054 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1290992 ATCGATACAT
*
1291002 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
1291022 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
1291043 TGTATCGATACA
1 TGTATCGATACA
1291055 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:1291128 original size:20 final size:20
Alignment explanation
Indices: 1291085--1291136 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1291075 CTTAATTGTT
* *
1291085 TGTATCAATACA-CACAATA
1 TGTATCGATACATCACAAAA
*
1291104 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
1291124 TGTATCGATACAT
1 TGTATCGATACAT
1291137 TGGCTTGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:1297265 original size:47 final size:50
Alignment explanation
Indices: 1297176--1297273 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 50
1297166 AGGGTCAAAT
*
1297176 TCTGGAAAAATTCCAGAATGTATCGATACAGGTTCAAATGTATCGATACA
1 TCTGGAAAAATTCCAGAATGTATCGATACAGATTCAAATGTATCGATACA
**
1297226 TCTGG-AAAATT-CAGAA-GTATCGATACAGCATTC-TCTGTATCGATACA
1 TCTGGAAAAATTCCAGAATGTATCGATACAG-ATTCAAATGTATCGATACA
1297273 T
1 T
1297274 TGTATCGATA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
47 25 0.57
48 8 0.18
49 6 0.14
50 5 0.11
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (50 bp):
TCTGGAAAAATTCCAGAATGTATCGATACAGATTCAAATGTATCGATACA
Found at i:1297279 original size:13 final size:13
Alignment explanation
Indices: 1297260--1297298 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1297250 ACAGCATTCT
1297260 CTGTATCGATACA
1 CTGTATCGATACA
*
1297273 TTGTATCGATACA
1 CTGTATCGATACA
*
1297286 CAGTATCGATACA
1 CTGTATCGATACA
1297299 AAGGGTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:1299602 original size:22 final size:21
Alignment explanation
Indices: 1299572--1299617 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
1299562 CTAGATAAGT
1299572 ATAAATG-TTTTCAAAGCTTAAA
1 ATAAATGTTTTTC-AAG-TTAAA
*
1299594 ATAAGTGTTTTTCAAGTTAAA
1 ATAAATGTTTTTCAAGTTAAA
1299615 ATA
1 ATA
1299618 TATCAAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 9 0.41
23 5 0.23
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (21 bp):
ATAAATGTTTTTCAAGTTAAA
Found at i:1299848 original size:13 final size:13
Alignment explanation
Indices: 1299830--1299855 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1299820 ACACACAATA
1299830 TGTATCGATACAT
1 TGTATCGATACAT
1299843 TGTATCGATACAT
1 TGTATCGATACAT
1299856 CCCAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1299871 original size:33 final size:32
Alignment explanation
Indices: 1299810--1299877 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1299800 CCTTAACTGT
*
1299810 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
1299842 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
1299875 TTG
1 TTG
1299878 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:1300911 original size:13 final size:14
Alignment explanation
Indices: 1300887--1300917 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1300877 CACTAAATGT
1300887 TATTATTATTATTA
1 TATTATTATTATTA
1300901 TATTA-TATTATTA
1 TATTATTATTATTA
1300914 TATT
1 TATT
1300918 TGTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:1300983 original size:26 final size:26
Alignment explanation
Indices: 1300950--1301023 Score: 139
Period size: 26 Copynumber: 2.8 Consensus size: 26
1300940 AGATTATATT
1300950 ATTAATAAAAGTTTATATTATTTTAA
1 ATTAATAAAAGTTTATATTATTTTAA
1300976 ATTAATAAAAGTTTATATTATTTTAA
1 ATTAATAAAAGTTTATATTATTTTAA
*
1301002 ATTAATAAAAGATTATATTATT
1 ATTAATAAAAGTTTATATTATT
1301024 AAGAGGCTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (26 bp):
ATTAATAAAAGTTTATATTATTTTAA
Found at i:1301125 original size:19 final size:19
Alignment explanation
Indices: 1301103--1301177 Score: 82
Period size: 19 Copynumber: 4.0 Consensus size: 19
1301093 CAAATTCAAA
1301103 AATATAATCTTATACTAAT
1 AATATAATCTTATACTAAT
*
1301122 AATATAATTTTATACTAACT
1 AATATAATCTTATACTAA-T
* * * *
1301142 -A-ATAATATGAGATTAAT
1 AATATAATCTTATACTAAT
1301159 AATATAATCTTATACTAAT
1 AATATAATCTTATACTAAT
1301178 TATTTTTTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
17 1 0.02
18 12 0.27
19 30 0.68
20 1 0.02
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (19 bp):
AATATAATCTTATACTAAT
Found at i:1301324 original size:19 final size:19
Alignment explanation
Indices: 1301287--1301327 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1301277 ATTAATTTAA
*
1301287 AATAATATAAATTTTTATT
1 AATAATATAAATTTATATT
1301306 AATAATAT-AATCTTATATT
1 AATAATATAAAT-TTATATT
1301325 AAT
1 AAT
1301328 TTAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
AATAATATAAATTTATATT
Found at i:1301351 original size:8 final size:8
Alignment explanation
Indices: 1301305--1301367 Score: 58
Period size: 8 Copynumber: 8.0 Consensus size: 8
1301295 AAATTTTTAT
1301305 TAATAATA
1 TAATAATA
**
1301313 TAATCTTA
1 TAATAATA
* *
1301321 TATTAATT
1 TAATAATA
1301329 TAA-AATA
1 TAATAATA
1301336 TACA-AATA
1 TA-ATAATA
1301344 TAATAATA
1 TAATAATA
*
1301352 TAATATTA
1 TAATAATA
1301360 TAATAATA
1 TAATAATA
1301368 ACATATTGGC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
7 6 0.14
8 37 0.86
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (8 bp):
TAATAATA
Found at i:1301590 original size:30 final size:29
Alignment explanation
Indices: 1301545--1301602 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
1301535 TATTCTGATG
* *
1301545 ATTTATTTTAAATTAATAATATTTTAATA
1 ATTTATTTAAAATTAATAATAGTTTAATA
*
1301574 ATTTATTTAAAAATTAATAGTAGTTTAAT
1 ATTTATTT-AAAATTAATAATAGTTTAAT
1301603 TAATATACCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
ATTTATTTAAAATTAATAATAGTTTAATA
Found at i:1304989 original size:13 final size:13
Alignment explanation
Indices: 1304971--1304997 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1304961 ACATGCTGCT
1304971 TTGTATCGATACA
1 TTGTATCGATACA
1304984 TTGTATCGATACA
1 TTGTATCGATACA
1304997 T
1 T
1304998 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1305012 original size:32 final size:33
Alignment explanation
Indices: 1304952--1305016 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1304942 CACACCCAGA
* *
1304952 TGTATTGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATGCTGCATTGTATCGATACAT
*
1304985 TGTATCGATACATG-TTCATTGTATCGATACAT
1 TGTATCGATACATGCTGCATTGTATCGATACAT
1305017 GGACAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATGCTGCATTGTATCGATACAT
Found at i:1305028 original size:21 final size:19
Alignment explanation
Indices: 1304981--1305037 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1304971 TTGTATCGAT
*
1304981 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
1305000 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
1305019 ACAAATTGTATCGATACAT
1 AC--ATTGTATCGATACAT
1305038 AAAACTGGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
21 15 0.45
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1305240 original size:11 final size:11
Alignment explanation
Indices: 1305224--1305253 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1305214 GAAAGCATGA
1305224 AAACAAGCACC
1 AAACAAGCACC
1305235 AAACAAGCACC
1 AAACAAGCACC
1305246 AAACAAGC
1 AAACAAGC
1305254 TTATAACGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.33, G:0.10, T:0.00
Consensus pattern (11 bp):
AAACAAGCACC
Found at i:1316424 original size:64 final size:63
Alignment explanation
Indices: 1316355--1316481 Score: 173
Period size: 64 Copynumber: 2.0 Consensus size: 63
1316345 TCAAAGCTTT
* * *
1316355 TTCCAAAAGCCCACGACTCTGTGGCACCCTTCCTAAAGTCTACGACTCAGTGGCATCTTTTTTC
1 TTCCAAAAGCCCACGACTCTGTGGCACCCTTCCT-AAGTCCACAACTCAGTGGCATCTCTTTTC
* * * * *
1316419 TTCCAAAAGCCCATGACTTTGTGGCATCTTTCCTAAGTCCACAACTTAGTGGCATCTCTTTTC
1 TTCCAAAAGCCCACGACTCTGTGGCACCCTTCCTAAGTCCACAACTCAGTGGCATCTCTTTTC
1316482 CAGGTCCACG
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 25 0.45
64 30 0.55
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (63 bp):
TTCCAAAAGCCCACGACTCTGTGGCACCCTTCCTAAGTCCACAACTCAGTGGCATCTCTTTTC
Found at i:1316522 original size:30 final size:30
Alignment explanation
Indices: 1316390--1316539 Score: 117
Period size: 30 Copynumber: 4.9 Consensus size: 30
1316380 ACCCTTCCTA
* *
1316390 AAGTCTACGACTCAGTGGCATCTTTTTTCTTCC
1 AAGTCCACGACTTAGTGGCATC--TTTT-TTCC
* * *
1316423 AAAAGCCCATGACTTTGTGGCATC---TTTCC
1 --AAGTCCACGACTTAGTGGCATCTTTTTTCC
* *
1316452 TAAGTCCACAACTTAGTGGCATCTCTTTTCC
1 -AAGTCCACGACTTAGTGGCATCTTTTTTCC
*
1316483 AGGTCCACGACTTAGTGGCATCTTTTTTCC
1 AAGTCCACGACTTAGTGGCATCTTTTTTCC
* * * *
1316513 AAGTTCACGACTCAATGGTATCTTTTT
1 AAGTCCACGACTTAGTGGCATCTTTTT
1316540 CCTTTACAAA
Statistics
Matches: 94, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
28 18 0.19
29 4 0.04
30 50 0.53
31 5 0.05
35 17 0.18
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (30 bp):
AAGTCCACGACTTAGTGGCATCTTTTTTCC
Found at i:1316677 original size:34 final size:34
Alignment explanation
Indices: 1316639--1317117 Score: 213
Period size: 34 Copynumber: 15.3 Consensus size: 34
1316629 CCTTTTAAGT
** *
1316639 CCACAACTCTGTGGCACTTTTTTCTTTTCAAAGC
1 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
*
1316673 CCACAACTCCATGGCACC-----CTTTT--AAGT
1 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
* *
1316700 CCATAACT-CAGTGGCATCCTTATTCTTTTCAAAGC
1 CCACAACTCCA-TGGCA-CCTTTTTCTTTTCAAAGC
*
1316735 CCACAACTCCATGGCATCCTTTTTCCTTTT--AAGT
1 CCACAACTCCATGGCA-CCTTTTT-CTTTTCAAAGC
* * *
1316769 CCATAACTCCGTGGCACATTTTTCTTTTCAAAGC
1 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
* *
1316803 CCACAACTCCATGGCACCTTTTTC----C--TGT
1 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
* * * *
1316831 CCACAACTCCGTAGC-CC----TCTTTTA--AGT
1 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
* *
1316858 CCACAACTCCATGGAACCTTTTTCTTTTCAAAGT
1 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
* * * *
1316892 CCACAACTTCGTGACACCATTTTTCCTTTT--AAGT
1 CCACAACTCCATGGCACC-TTTTT-CTTTTCAAAGC
* *
1316926 CCACAACTCCATGGCAAC----T-TTTT--AAGT
1 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
* *
1316953 CCACAACTCCGTGGCACTTTTTTCTTTTCAAAGC
1 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
** * * *
1316987 CCACAACTCTGTTGCACC-----CGTTT--AAGT
1 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
* *
1317014 CCACAACTCCGTGGCACCTTTTTCTTTTCAAAGT
1 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
* * *
1317048 CCATAACTCTATGGCACC-----CTTTT--AAGT
1 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
* * * *
1317075 CCACAATTTCGTGGCACCTTTTTCTTTGCAAAGC
1 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
*
1317109 CCATAACTC
1 CCACAACTC
1317118 TGTGGCTCCT
Statistics
Matches: 339, Mismatches: 59, Indels: 94
0.69 0.12 0.19
Matches are distributed among these distances:
23 2 0.01
26 2 0.01
27 90 0.27
28 18 0.05
29 15 0.04
30 1 0.00
31 1 0.00
32 23 0.07
33 11 0.03
34 137 0.40
35 27 0.08
36 12 0.04
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (34 bp):
CCACAACTCCATGGCACCTTTTTCTTTTCAAAGC
Found at i:1316698 original size:61 final size:61
Alignment explanation
Indices: 1316563--1317159 Score: 505
Period size: 61 Copynumber: 9.6 Consensus size: 61
1316553 TATAATTTCG
* * * * * * *
1316563 TGGCACCGTTTTAAGTTCACAACTCAGTGGCACCTTTTTCCTTTT--AAGTCCACAACTTCG
1 TGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CTTTTTTCTTTTCAAAGCCCACAACTCCA
*
1316623 TGGCACCCTTTTAAGTCCACAACTCTGTGGCACTTTTTTCTTTTCAAAGCCCACAACTCCA
1 TGGCACCCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTCAAAGCCCACAACTCCA
* * * *
1316684 TGGCACCCTTTTAAGTCCATAACTCAGTGGCATCCTTATTCTTTTCAAAGCCCACAACTCCA
1 TGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CTTTTTTCTTTTCAAAGCCCACAACTCCA
* *
1316746 TGGCATCCTTTTTCCTTTTAAGTCCATAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACT
1 TGGCA--C-----CCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTCAAAGCCCACAACT
1316811 CCA
59 CCA
* ** * * *
1316814 TGGCACCTTTTTCCTGTCCACAACTCCGTAGC-C----CTCTTTT--AAGTCCACAACTCCA
1 TGGCACCCTTTT-AAGTCCACAACTCCGTGGCACTTTTTTCTTTTCAAAGCCCACAACTCCA
* * * * *
1316869 TGGAACCTTTTTCTTTTCAAAGTCCACAACTTCGTGACACCATTTTTCCTTTT--AAGTCCACAA
1 TGGCACC-----CTTTT--AAGTCCACAACTCCGTGGCA-C-TTTTTTCTTTTCAAAGCCCACAA
1316932 CTCCA
57 CTCCA
* * **
1316937 TGGCAACTTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTCAAAGCCCACAACTCTG
1 TGGCACCCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTCAAAGCCCACAACTCCA
* * * * * *
1316998 TTGCACCCGTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGTCCATAACTCTA
1 TGGCACCCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTCAAAGCCCACAACTCCA
* * * * * **
1317059 TGGCACCCTTTTAAGTCCACAATTTCGTGGCACCTTTTTCTTTGCAAAGCCCATAACTCTG
1 TGGCACCCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTCAAAGCCCACAACTCCA
* * *
1317120 TGGCTCCTTCCTTTTAAAGTCTATAACTCCGTGGCACTTT
1 TGGC-AC--CCTTTT-AAGTCCACAACTCCGTGGCACTTT
1317160 ATCCCTTCAA
Statistics
Matches: 446, Mismatches: 61, Indels: 55
0.79 0.11 0.10
Matches are distributed among these distances:
55 20 0.04
57 6 0.01
59 21 0.05
60 34 0.08
61 203 0.46
62 48 0.11
63 5 0.01
64 7 0.02
65 19 0.04
66 1 0.00
68 57 0.13
69 25 0.06
ACGTcount: A:0.22, C:0.31, G:0.12, T:0.35
Consensus pattern (61 bp):
TGGCACCCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTCAAAGCCCACAACTCCA
Found at i:1316708 original size:27 final size:27
Alignment explanation
Indices: 1316561--1317097 Score: 140
Period size: 27 Copynumber: 17.5 Consensus size: 27
1316551 CCTATAATTT
* *
1316561 CGTGGCACCGTTTTAAGTTCACAACTC
1 CGTGGCACCCTTTTAAGTCCACAACTC
* *
1316588 AGTGGCACCTTTTTCCTTTTAAGTCCACAACTT
1 CGTGGCA-C-----CCTTTTAAGTCCACAACTC
1316621 CGTGGCACCCTTTTAAGTCCACAACTC
1 CGTGGCACCCTTTTAAGTCCACAACTC
* * *
1316648 TGTGGCACTTTTTTCTTTTCAAAGCCCACAACTC
1 CGTGGCAC-----CCTTTT--AAGTCCACAACTC
* *
1316682 CATGGCACCCTTTTAAGTCCATAACTC
1 CGTGGCACCCTTTTAAGTCCACAACTC
* *
1316709 AGTGGCATCCTTATTCTTTTCAAAGCCCACAACTC
1 CGTGGCA-CC-----CTTTT--AAGTCCACAACTC
* *
1316744 CATGGCATCCTTTTTCCTTTTAAGTCCATAACTC
1 CGTGGCA--C-----CCTTTTAAGTCCACAACTC
* *
1316778 CGTGGCACATTTTTCTTTTCAAAGCCCACAACTC
1 CGTGGCAC-----CCTTTT--AAGTCCACAACTC
* * **
1316812 CATGGCACCTTTTTCCTGTCCACAACTC
1 CGTGGCACCCTTTT-AAGTCCACAACTC
*
1316840 CGTAGC-CCTCTTTTAAGTCCACAACTC
1 CGTGGCACC-CTTTTAAGTCCACAACTC
* * *
1316867 CATGGAACCTTTTTCTTTTCAAAGTCCACAACTT
1 CGTGGCACC-----CTTTT--AAGTCCACAACTC
*
1316901 CGTGACACCATTTTTCCTTTTAAGTCCACAACTC
1 CGTGGCA-C------CCTTTTAAGTCCACAACTC
* * *
1316935 CATGGCAACTTTTTAAGTCCACAACTC
1 CGTGGCACCCTTTTAAGTCCACAACTC
* *
1316962 CGTGGCACTTTTTTCTTTTCAAAGCCCACAACTC
1 CGTGGCAC-----CCTTTT--AAGTCCACAACTC
* * *
1316996 TGTTGCACCCGTTTAAGTCCACAACTC
1 CGTGGCACCCTTTTAAGTCCACAACTC
*
1317023 CGTGGCACCTTTTTCTTTTCAAAGTCCATAACTC
1 CGTGGCACC-----CTTTT--AAGTCCACAACTC
** * *
1317057 TATGGCACCCTTTTAAGTCCACAATTT
1 CGTGGCACCCTTTTAAGTCCACAACTC
*
1317084 CGTGGCACCTTTTT
1 CGTGGCACCCTTTT
1317098 CTTTGCAAAG
Statistics
Matches: 378, Mismatches: 74, Indels: 116
0.67 0.13 0.20
Matches are distributed among these distances:
27 127 0.34
28 23 0.06
29 18 0.05
32 30 0.08
33 27 0.07
34 123 0.33
35 17 0.04
36 11 0.03
41 2 0.01
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.34
Consensus pattern (27 bp):
CGTGGCACCCTTTTAAGTCCACAACTC
Found at i:1316834 original size:28 final size:28
Alignment explanation
Indices: 1316563--1317098 Score: 129
Period size: 34 Copynumber: 17.5 Consensus size: 28
1316553 TATAATTTCG
* *
1316563 TGGCACCGTTTT-AAGTTCACAACT-CA
1 TGGCACCTTTTTCAAGTCCACAACTCCA
* *
1316589 GTGGCACCTTTTTCCTTTTAAGTCCACAACTTCG
1 -TGGCACCTTTTT-C----AAGTCCACAACTCCA
* **
1316623 TGGCACCCTTTT-AAGTCCACAACTCTG
1 TGGCACCTTTTTCAAGTCCACAACTCCA
* *
1316650 TGGCACTTTTTTCTTTTCAAAGCCCACAACTCCA
1 TGGCAC----CT-TTTTC-AAGTCCACAACTCCA
* *
1316684 TGGCACCCTTTT-AAGTCCATAACT-CA
1 TGGCACCTTTTTCAAGTCCACAACTCCA
*
1316710 GTGGCATCCTTATTCTTTTCAAAGCCCACAACTCCA
1 -TGGCA-CC----T-TTTTC-AAGTCCACAACTCCA
* *
1316746 TGGCATCCTTTTTCCTTTTAAGTCCATAACTCCG
1 TGGCA-CCTTTTT-C----AAGTCCACAACTCCA
* *
1316780 TGGCACATTTTTCTTTTCAAAGCCCACAACTCCA
1 TGGCAC----CT-TTTTC-AAGTCCACAACTCCA
** *
1316814 TGGCACCTTTTTCCTGTCCACAACTCCG
1 TGGCACCTTTTTCAAGTCCACAACTCCA
*
1316842 TAGC-CCTCTTTT-AAGTCCACAACTCCA
1 TGGCACCT-TTTTCAAGTCCACAACTCCA
* * *
1316869 TGGAACCTTTTTCTTTTCAAAGTCCACAACTTCG
1 TGGCACC----T-TTTTC-AAGTCCACAACTCCA
*
1316903 TGACACCATTTTTCCTTTTAAGTCCACAACTCCA
1 TGGCACC-TTTTT-C----AAGTCCACAACTCCA
* *
1316937 TGGCAACTTTTT-AAGTCCACAACTCCG
1 TGGCACCTTTTTCAAGTCCACAACTCCA
* * **
1316964 TGGCACTTTTTTCTTTTCAAAGCCCACAACTCTG
1 TGGCAC----CT-TTTTC-AAGTCCACAACTCCA
* ** *
1316998 TTGCACCCGTTT-AAGTCCACAACTCCG
1 TGGCACCTTTTTCAAGTCCACAACTCCA
* *
1317025 TGGCACCTTTTTCTTTTCAAAGTCCATAACTCTA
1 TGGCACC----T-TTTTC-AAGTCCACAACTCCA
* * * *
1317059 TGGCACCCTTTT-AAGTCCACAATTTCG
1 TGGCACCTTTTTCAAGTCCACAACTCCA
1317086 TGGCACCTTTTTC
1 TGGCACCTTTTTC
1317099 TTTGCAAAGC
Statistics
Matches: 377, Mismatches: 72, Indels: 119
0.66 0.13 0.21
Matches are distributed among these distances:
26 2 0.01
27 121 0.32
28 22 0.06
29 16 0.04
30 9 0.02
31 5 0.01
32 17 0.05
33 32 0.08
34 127 0.34
35 18 0.05
36 2 0.01
37 2 0.01
38 4 0.01
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.34
Consensus pattern (28 bp):
TGGCACCTTTTTCAAGTCCACAACTCCA
Found at i:1316938 original size:123 final size:121
Alignment explanation
Indices: 1316629--1316964 Score: 363
Period size: 130 Copynumber: 2.7 Consensus size: 121
1316619 TTCGTGGCAC
* * * * *
1316629 CCTTTTAAGTCCACAACTCTGTGGCACTTTTTTCTTTTCAAAGCCCACAACTCCATGGCACCCTT
1 CCTTTTAAGTCCACAACTCCGTGACACATTTTTCTTTT-AAAGCCCACAACTCCATGGCAACTTT
* * * * *
1316694 TTAAGTCCATAACTCAGTGGCATCCTTATTCTTTTCAAAGCCCACAACTCCATGGCATCCTTTTT
65 TTAAGTCCACAACTCCGTAGC--CC----TCTTTT--AAGTCCACAACTCCATGGCAACCTTTTT
* * *
1316759 CCTTTTAAGTCCATAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACTCCATGGCACCTTT
1 CCTTTTAAGTCCACAACTCCGTGACACATTTTTCTTTT-AAAGCCCACAACTCCATGGCAACTTT
**
1316824 TTCCTGTCCACAACTCCGTAGCCCTCTTTTAAGTCCACAACTCCATGG-AACCTTTTT
65 TT-AAGTCCACAACTCCGTAGCCCTCTTTTAAGTCCACAACTCCATGGCAACCTTTTT
* *
1316881 -CTTTTCAAAGTCCACAACTTCGTGACACCATTTTTCCTTTT-AAGTCCACAACTCCATGGCAAC
1 CCTTTT--AAGTCCACAACTCCGTGACA-CATTTTT-CTTTTAAAGCCCACAACTCCATGGCAAC
1316944 TTTTTAAGTCCACAACTCCGT
62 TTTTTAAGTCCACAACTCCGT
1316965 GGCACTTTTT
Statistics
Matches: 183, Mismatches: 18, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
121 5 0.03
122 22 0.12
123 59 0.32
124 7 0.04
125 11 0.06
129 2 0.01
130 63 0.34
131 14 0.08
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34
Consensus pattern (121 bp):
CCTTTTAAGTCCACAACTCCGTGACACATTTTTCTTTTAAAGCCCACAACTCCATGGCAACTTTT
TAAGTCCACAACTCCGTAGCCCTCTTTTAAGTCCACAACTCCATGGCAACCTTTTT
Found at i:1316956 original size:95 final size:89
Alignment explanation
Indices: 1316760--1316995 Score: 294
Period size: 95 Copynumber: 2.6 Consensus size: 89
1316750 ATCCTTTTTC
* *
1316760 CTTTTAAGTCCATAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACTCCATGGCACCTTTT
1 CTTTTAAGTCCACAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACTCCATGACACCTTTT
* *
1316825 TCCTGTCCACAACTCCGTAGCCCT
66 TCCTGTCCACAACTCCATAGCACT
* * * * * *
1316849 CTTTTAAGTCCACAACTCCATGGAACCTTTTTCTTTTCAAAGTCCACAACTTCGTGACACCATTT
1 CTTTTAAGTCCACAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACTCCATGACACC-TTT
*
1316914 TTCCTTTTAAGTCCACAACTCCATGGCAACT
65 TTCC---T--GTCCACAACTCCATAGC-ACT
*
1316945 -TTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTCAAAGCCCACAACTC
1 CTTTTAAGTCCACAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACTC
1316996 TGTTGCACCC
Statistics
Matches: 124, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
89 53 0.43
90 7 0.06
93 1 0.01
95 61 0.49
96 2 0.02
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34
Consensus pattern (89 bp):
CTTTTAAGTCCACAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACTCCATGACACCTTTT
TCCTGTCCACAACTCCATAGCACT
Found at i:1317056 original size:95 final size:89
Alignment explanation
Indices: 1316760--1317036 Score: 276
Period size: 95 Copynumber: 3.1 Consensus size: 89
1316750 ATCCTTTTTC
* ** * *
1316760 CTTTTAAGTCCATAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACTCCATGGCACCTTTT
1 CTTTTAAGTCCACAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACTCTGTTGCACCCTTT
** * *
1316825 TCCTGTCCACAACTCCGTAGC-CCT
66 T-AAGTCCACAACTCCATGGCACCT
* * * *
1316849 CTTTTAAGTCCACAACTCCATGGAACCTTTTTCTTTTCAAAGTCCACAACT-TCG-TGACACCAT
1 CTTTTAAGTCCACAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACTCT-GTTG-CA-C--
*
1316912 TTTTCCTTTTAAGTCCACAACTCCATGGCAACT
61 ----CCTTTTAAGTCCACAACTCCATGGCACCT
* *
1316945 -TTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTCAAAGCCCACAACTCTGTTGCACCCGTT
1 CTTTTAAGTCCACAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACTCTGTTGCACCCTTT
*
1317009 TAAGTCCACAACTCCGTGGCACCT
66 TAAGTCCACAACTCCATGGCACCT
1317033 -TTTT
1 CTTTT
1317037 CTTTTCAAAG
Statistics
Matches: 155, Mismatches: 21, Indels: 25
0.77 0.10 0.12
Matches are distributed among these distances:
88 31 0.20
89 48 0.31
90 1 0.01
94 1 0.01
95 64 0.41
96 10 0.06
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (89 bp):
CTTTTAAGTCCACAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACTCTGTTGCACCCTTT
TAAGTCCACAACTCCATGGCACCT
Found at i:1317242 original size:32 final size:32
Alignment explanation
Indices: 1317197--1317265 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
1317187 TGGCACCCCC
*
1317197 TTAAAGCCTACACAAG-CTGGTGGCAACCATT-T
1 TTAAAGCCTACACAAGTC-GGTGACAACC-TTCT
1317229 TTAAAG-CTCACACAAGTCGGTGACAACCTTCT
1 TTAAAGCCT-ACACAAGTCGGTGACAACCTTCT
1317261 TTAAA
1 TTAAA
1317266 AGCTTGCACA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
31 4 0.12
32 28 0.85
33 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (32 bp):
TTAAAGCCTACACAAGTCGGTGACAACCTTCT
Found at i:1317420 original size:50 final size:50
Alignment explanation
Indices: 1317335--1317768 Score: 271
Period size: 52 Copynumber: 8.7 Consensus size: 50
1317325 TCTAAGCCCC
* * * * *
1317335 ATGTCACTGGCCTTGAATCAACACCTTGGCGCCTTTTTTTCTTAAATCCA
1 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTTTTCTTAAGTCCA
* * *
1317385 ATATCGCTGGCCTTGAATCAACACATTGGCACCTTTTTTTCTTAAATCCA
1 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTTTTCTTAAGTCCA
* * ** * **
1317435 ATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTGGTCATCTTCAAGTCCA
1 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT-TTTTTCTT-AAGTCCA
*
1317487 ATGTCGCTAGCCTTGAATCAGCACATTGGCA-C----TTTCTTAAGTCCA
1 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTTTTCTTAAGTCCA
* * *
1317532 ATGTCACTAGCCTTGAATCAGTACATTGGCA-C----TTTCTTAAGTCCA
1 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTTTTCTTAAGTCCA
* * * * * * * ** * * *
1317577 ATTTCACTGGCCTTGAATTAACATATTGACGCCTTTGTCATCTTTAAATTCG
1 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTT-TTTTC-TTAAGTCCA
* * * * * * * * *
1317629 ATATCGCTAGCCTTGACTCAGCATATTAGCATCTTTATCATTCCTAAGCCCA
1 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTT-T-TTTCTTAAGTCCA
* * * *
1317681 ATGTCGCTGGCCTTGAATTAGCACATTGGCA--TTTTTCCCATGTTCAAGTCTA
1 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTT---TTCTT-AAGTCCA
* * *
1317733 ATGTCGTTGGCCTTGCATCAACACATTGGCACCTTT
1 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTT
1317769 GTCATCTTTA
Statistics
Matches: 300, Mismatches: 68, Indels: 28
0.76 0.17 0.07
Matches are distributed among these distances:
45 73 0.24
46 5 0.02
49 1 0.00
50 80 0.27
51 10 0.03
52 126 0.42
53 2 0.01
54 3 0.01
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.35
Consensus pattern (50 bp):
ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTTTTCTTAAGTCCA
Found at i:1317544 original size:45 final size:46
Alignment explanation
Indices: 1317371--1317594 Score: 220
Period size: 45 Copynumber: 4.7 Consensus size: 46
1317361 TGGCGCCTTT
* *
1317371 TTTTCTTAAATCCAATATCGCTGGCCTTGAATCAACACATTGGCACC
1 TTTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-C
* *
1317418 TTTTTTTCTTAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGTGC-C
1 ---TTTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-G-GCAC
* *
1317468 TTGGTCATCTTCAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCAC
1 TT--T--TCTT-AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
1317519 -TTTCTTAAGTCCAATGTCACTAGCCTTGAATCAGTACATTGGCAC
1 TTTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* *
1317564 -TTTCTTAAGTCCAATTTCACTGGCCTTGAAT
1 TTTTCTTAAGTCCAATATCGCTGGCCTTGAAT
1317595 TAACATATTG
Statistics
Matches: 156, Mismatches: 10, Indels: 21
0.83 0.05 0.11
Matches are distributed among these distances:
45 66 0.42
46 4 0.03
47 2 0.01
48 1 0.01
49 1 0.01
50 43 0.28
51 7 0.04
52 32 0.21
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (46 bp):
TTTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1317636 original size:142 final size:144
Alignment explanation
Indices: 1317372--1317651 Score: 339
Period size: 142 Copynumber: 1.9 Consensus size: 144
1317362 GGCGCCTTTT
* *
1317372 TTTCTTAAATCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTTTTTTCTTAAATCCAAT
1 TTTCTTAAATCCAATATCACTAGCCTTGAATCAACACATTGGCACC---TTTTCTTAAATCCAAT
* * ** * *
1317437 ATCGCTGGCCTTGAATCAGCATATTGGTGCCTTGGTCATCTTCAAGTCCAATGTCGCTAGCCTTG
63 ATCACTGGCCTTGAATCAACATATTGACGCCTTGGTCATCTTCAAATCCAATATCGCTAGCCTTG
1317502 AATCAGCACATTGGCAC
128 AATCAGCACATTGGCAC
* * ** * *
1317519 TTTCTTAAGTCCAATGTCACTAGCCTTGAATCAGTACATTGGCA-C-TTTCTTAAGTCCAATTTC
1 TTTCTTAAATCCAATATCACTAGCCTTGAATCAACACATTGGCACCTTTTCTTAAATCCAATATC
* * * * * *
1317582 ACTGGCCTTGAATTAACATATTGACGCCTTTGTCATCTTTAAATTCGATATCGCTAGCCTTGACT
66 ACTGGCCTTGAATCAACATATTGACGCCTTGGTCATCTTCAAATCCAATATCGCTAGCCTTGAAT
1317647 CAGCA
131 CAGCA
1317652 TATTAGCATC
Statistics
Matches: 113, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
142 74 0.65
146 1 0.01
147 38 0.34
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (144 bp):
TTTCTTAAATCCAATATCACTAGCCTTGAATCAACACATTGGCACCTTTTCTTAAATCCAATATC
ACTGGCCTTGAATCAACATATTGACGCCTTGGTCATCTTCAAATCCAATATCGCTAGCCTTGAAT
CAGCACATTGGCAC
Found at i:1317812 original size:26 final size:26
Alignment explanation
Indices: 1317776--1317828 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1317766 TTTGTCATCT
1317776 TTAAGCCCAATATCACTAGCCTTGAA
1 TTAAGCCCAATATCACTAGCCTTGAA
1317802 TTAAGCCCAATATCACTAGCCTTGAA
1 TTAAGCCCAATATCACTAGCCTTGAA
1317828 T
1 T
1317829 CAGCATATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.28
Consensus pattern (26 bp):
TTAAGCCCAATATCACTAGCCTTGAA
Found at i:1317989 original size:187 final size:182
Alignment explanation
Indices: 1317629--1317973 Score: 426
Period size: 187 Copynumber: 1.9 Consensus size: 182
1317619 TTTAAATTCG
* * * *
1317629 ATATCGCTAGCCTTGACTCAGCATATTAGCATCTTTATCATTCCTAAGCCCAATGTCGCTGGCCT
1 ATATCACTAGCCTTGAATCAGCATATTAGCACCTTTATCATTCCTAAGCCCAATGTCACTGGCCT
* * * * * * *
1317694 TGAATTAGCACATTGGCATTTTTCCCATGTTCAAGTCTAATGTCGTTGGCCTTGCATCAACACAT
66 CGAATCAGCACATTGCCATTTTTCCCATGTTCAAGTCCAATATCATTGGCCTTGAATCAACACAT
1317759 TGGCACCTTTGTCATCTTTAAGCCCAATATCACTAGCCTTGAATTAAGCCCA
131 TGGCACCTTTGTCATCTTTAAGCCCAATATCACTAGCCTTGAATTAAGCCCA
* * * *
1317811 ATATCACTAGCCTTGAATCAGCATATTGGCACCTTTCTCATTCCTCTCATAAGTCCAATGTCATT
1 ATATCACTAGCCTTGAATCAGCATATTAGCACCTTTATCA-T--TC-C-TAAGCCCAATGTCACT
*
1317876 GGCCTCGAATCAGCACATTGCCACTTTTT-TC-T-TTCATAAGTCCAATATCATTGGCCTTGAAT
61 GGCCTCGAATCAGCACATTGCCA-TTTTTCCCATGTTC--AAGTCCAATATCATTGGCCTTGAAT
* * *
1317938 CAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
123 CAACACATTGGCACCTTTGTCATCTTTAAGCCCAAT
1317974 GTCGTTGGCC
Statistics
Matches: 136, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
182 35 0.26
183 1 0.01
185 5 0.04
186 2 0.01
187 88 0.65
188 5 0.04
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (182 bp):
ATATCACTAGCCTTGAATCAGCATATTAGCACCTTTATCATTCCTAAGCCCAATGTCACTGGCCT
CGAATCAGCACATTGCCATTTTTCCCATGTTCAAGTCCAATATCATTGGCCTTGAATCAACACAT
TGGCACCTTTGTCATCTTTAAGCCCAATATCACTAGCCTTGAATTAAGCCCA
Found at i:1318004 original size:52 final size:53
Alignment explanation
Indices: 1317803--1318064 Score: 246
Period size: 52 Copynumber: 4.9 Consensus size: 53
1317793 AGCCTTGAAT
* * * *
1317803 TAAGCCCAATATCACTAGCCTTGAATCAGCATATTGGCACCTTTCTCATTCCTCTCA
1 TAAGTCCAATATCATTGGCCTTGAATCAGCATATTGGCACCTTTGTCA-T-CT-T-A
* * * * * *
1317860 TAAGTCCAATGTCATTGGCCTCGAATCAGCACATTGCCACTTTTTTC-T-TTCA
1 TAAGTCCAATATCATTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT-A
1317912 TAAGTCCAATATCATTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT-
1 TAAGTCCAATATCATTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTA
* * **
1317964 TAAGTCCAATGTCGTTGGCCTTGAATCAGCACCTTGGCACCTTTGTCATCTT-
1 TAAGTCCAATATCATTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTA
* ** * * * *
1318016 CAAG-CCTAATATCGCTAGCCTTGAATTAGCTTATTGGCACCTTTATCAT
1 TAAGTCC-AATATCATTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
1318065 TTTTCTCATG
Statistics
Matches: 174, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
51 2 0.01
52 129 0.74
53 2 0.01
54 2 0.01
55 1 0.01
57 38 0.22
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.35
Consensus pattern (53 bp):
TAAGTCCAATATCATTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTA
Found at i:1318028 original size:104 final size:105
Alignment explanation
Indices: 1317808--1318064 Score: 306
Period size: 104 Copynumber: 2.4 Consensus size: 105
1317798 TGAATTAAGC
*
1317808 CCAATATCACTAGCCTTGAATCAGCATATTGGCACCTTTCTCATTCCTCTCATAAGTCCAATGTC
1 CCAATATCACTAGCCTTGAATCAGCATATTGGCACCTTTATCA-TCCTCT-ATAAGTCCAATGTC
* *
1317873 ATTGGCCTCGAATCAGCACATTGCCACTTTTTTCTTTCATAAG
64 ATTGGCCTCGAATCAGCACATTGCCACCTTTGTCTTTCA-AAG
* * * *
1317916 TCCAATATCATTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT-CT-T-TAAGTCCAATGTCG
1 -CCAATATCACTAGCCTTGAATCAGCATATTGGCACCTTTATCATCCTCTATAAGTCCAATGTCA
* * *
1317978 TTGGCCTTGAATCAGCACCTTGGCACCTTTGTCATCTTC-AAG
65 TTGGCCTCGAATCAGCACATTGCCACCTTTGTC-T-TTCAAAG
* * *
1318020 CCTAATATCGCTAGCCTTGAATTAGCTTATTGGCACCTTTATCAT
1 CC-AATATCACTAGCCTTGAATCAGCATATTGGCACCTTTATCAT
1318065 TTTTCTCATG
Statistics
Matches: 130, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
103 2 0.02
104 80 0.62
105 1 0.01
106 4 0.03
107 2 0.02
108 1 0.01
109 40 0.31
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (105 bp):
CCAATATCACTAGCCTTGAATCAGCATATTGGCACCTTTATCATCCTCTATAAGTCCAATGTCAT
TGGCCTCGAATCAGCACATTGCCACCTTTGTCTTTCAAAG
Found at i:1318675 original size:13 final size:13
Alignment explanation
Indices: 1318657--1318682 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1318647 ACATAAGTTT
1318657 TGTATCGATACAA
1 TGTATCGATACAA
1318670 TGTATCGATACAA
1 TGTATCGATACAA
1318683 AACTACCCTA
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1324100 original size:18 final size:18
Alignment explanation
Indices: 1324061--1324106 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1324051 TCATCATGAA
*
1324061 TTTAATATTTTTTATTTC
1 TTTAATATTTTTTATGTC
1324079 TTTAATATTTTTTGATGT-
1 TTTAATATTTTTT-ATGTC
1324097 TTTAA-ATTTT
1 TTTAATATTTT
1324107 AATGGCACGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 18 0.69
19 3 0.12
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTAATATTTTTTATGTC
Found at i:1329475 original size:6 final size:6
Alignment explanation
Indices: 1329466--1329499 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1329456 TCAAATAAGA
*
1329466 ATAATG ATAATG ATAATG ATAGTG ATAATG ATAA
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAA
1329500 CACTAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (6 bp):
ATAATG
Found at i:1332130 original size:31 final size:29
Alignment explanation
Indices: 1332064--1332142 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 29
1332054 TATTTAGATT
* * *
1332064 TTATTTATTTTTAGTTGTTTTTAAATTAATT
1 TTATTTATTTTT--TTATATTTAAATTAATA
1332095 TTATTTATTTTTTTATATTTAAATTATATAA
1 TTATTTATTTTTTTATATTTAAATTA-AT-A
*
1332126 TTATTTAATATTTTTAT
1 TTATTT-ATTTTTTTAT
1332143 GTTTTTGTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 12 0.29
30 2 0.05
31 18 0.44
32 9 0.22
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (29 bp):
TTATTTATTTTTTTATATTTAAATTAATA
Found at i:1332467 original size:18 final size:20
Alignment explanation
Indices: 1332444--1332483 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1332434 CATCTTAGTT
*
1332444 TTCTTTTT-TTTTTCTT-TA
1 TTCTTTTTAATTTTCTTGTA
1332462 TTCTTTTTAATTTTCTTGTA
1 TTCTTTTTAATTTTCTTGTA
1332482 TT
1 TT
1332484 ATTTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.78
Consensus pattern (20 bp):
TTCTTTTTAATTTTCTTGTA
Found at i:1332492 original size:20 final size:19
Alignment explanation
Indices: 1332453--1332492 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1332443 TTTCTTTTTT
* *
1332453 TTTTCTTTATTCTTTTTAA
1 TTTTCTTTATTATTTATAA
1332472 TTTTCTTGTATTATTTATAA
1 TTTTCTT-TATTATTTATAA
1332492 T
1 T
1332493 AGTAAAACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTTCTTTATTATTTATAA
Found at i:1333389 original size:28 final size:30
Alignment explanation
Indices: 1333337--1333392 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
1333327 CAACCTTTAC
*
1333337 TCACTATTTTTTGAAGGCTAAAATAGAATT
1 TCACTATTTTTTCAAGGCTAAAATAGAATT
1333367 TCACTA-TTTTTCAAGGCT-AAATAGAA
1 TCACTATTTTTTCAAGGCTAAAATAGAA
1333393 ACCTCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 8 0.32
29 11 0.44
30 6 0.24
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (30 bp):
TCACTATTTTTTCAAGGCTAAAATAGAATT
Found at i:1333634 original size:28 final size:30
Alignment explanation
Indices: 1333581--1333637 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1333571 GCAACATTCA
* *
1333581 CTCACTATCTTTTGAAGGTTAAAATAGAAT
1 CTCACTATCTTTTCAAGGCTAAAATAGAAT
1333611 CTCACTAT-TTTTCAAGGCT-AAATAGAA
1 CTCACTATCTTTTCAAGGCTAAAATAGAA
1333638 ACCTCCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.32
29 9 0.36
30 8 0.32
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (30 bp):
CTCACTATCTTTTCAAGGCTAAAATAGAAT
Found at i:1336375 original size:41 final size:41
Alignment explanation
Indices: 1336308--1336409 Score: 141
Period size: 41 Copynumber: 2.4 Consensus size: 41
1336298 AAATGTGTCT
* * *
1336308 TGCTATTTGAGGACACAAGAGAAAAGGAAATAAAGTGCGTCC
1 TGCTCTTTGAGGATA-AAAAGAAAAGGAAATAAAGTGCGTCC
1336350 TGCTCTTTGAGGATAAAAAGAAAAGGAAATAAAGTGCGTCC
1 TGCTCTTTGAGGATAAAAAGAAAAGGAAATAAAGTGCGTCC
* *
1336391 TGCTCCTTGGGGACTAAAA
1 TGCTCTTTGAGGA-TAAAA
1336410 GGTGCCACCA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 36 0.67
42 18 0.33
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (41 bp):
TGCTCTTTGAGGATAAAAAGAAAAGGAAATAAAGTGCGTCC
Found at i:1336619 original size:123 final size:121
Alignment explanation
Indices: 1336380--1336830 Score: 638
Period size: 123 Copynumber: 3.7 Consensus size: 121
1336370 AAAAGGAAAT
* * *
1336380 AAAGTGCGTCCTGCTCCTTGGGGACTAAAAGGTGCCACCAAC-T-TGTGGGTTTTGAAAAGAAAA
1 AAAG-GCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAA
* * * * *
1336443 GGCGTCATGCTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGGCCTTAAAAGGA
64 GGTGACCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * *
1336501 AAAAGCATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA-GAAAA
* * *
1336566 GGTGACCTGTTCTTCGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
64 GGTGACCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
*
1336624 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAACAGAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAG-
* *
1336689 AGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAGAAGGA
65 -GTGACCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
*
1336747 AAAGGCGTCCTGCTCTTTGAGGACAAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAG
*
1336812 G-CATCCTGCTCTTTGAGGA
65 GTGA-CCTGCTCTTTGAGGA
1336831 TTGAAAGGAT
Statistics
Matches: 296, Mismatches: 27, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
120 33 0.11
121 10 0.03
122 33 0.11
123 214 0.72
124 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (121 bp):
AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
TGACCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
Found at i:1336748 original size:184 final size:184
Alignment explanation
Indices: 1336401--1336830 Score: 661
Period size: 184 Copynumber: 2.3 Consensus size: 184
1336391 TGCTCCTTGG
* * *
1336401 GGACTAAAAGGTGCCACCAAC-T-TGTGGGTTTTGAAAA-GAAAAGGCGTCATGCTCTTTGAAGA
1 GGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCGTCCTGCTCTTTGAGGA
*
1336463 CTAAAAGGTGCCACCAACTTGTGTGGGCCTTAAAAGGAAAAAGCATCCTGCTCTTTGAGGACTAA
65 CTAAAAGGTGCCACCAACTTGTGTGGGCCTTAAAAGAAAAAAGCATCCTGCTCTTTGAGGACTAA
* * *
1336528 AGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGTGACCTGTTCTTCGA
130 AAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCGACCTGCTCTTCGA
*
1336583 GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGAC
1 GGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGAC
* * **
1336648 TAAAAGGTGCCACCAACTTGTGTGGGCTTTAACAGAAAAGAAGTGTCCTGCTCTTTGAGGACTAA
66 TAAAAGGTGCCACCAACTTGTGTGGGCCTTAAAAGAAAA-AAGCATCCTGCTCTTTGAGGACTAA
* * *
1336713 AAGGTGCCACCAACTTGTGTGGGCTTT-AGAAGGAAAAGGCGTCCTGCTCTTTGA
130 AAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCGACCTGCTCTTCGA
* *
1336767 GGACAAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGA
1 GGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGA
1336831 TTGAAAGGAT
Statistics
Matches: 226, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
182 20 0.09
183 5 0.02
184 152 0.67
185 49 0.22
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (184 bp):
GGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGAC
TAAAAGGTGCCACCAACTTGTGTGGGCCTTAAAAGAAAAAAGCATCCTGCTCTTTGAGGACTAAA
AGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCGACCTGCTCTTCGA
Found at i:1336838 original size:61 final size:61
Alignment explanation
Indices: 1336380--1336830 Score: 658
Period size: 61 Copynumber: 7.4 Consensus size: 61
1336370 AAAAGGAAAT
* * *
1336380 AAAGTGCGTCCTGCTCCTTGGGGACTAAAAGGTGCCACCAAC-T-TGTGGGTTTTGAAAA-GA
1 AAAG-GCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* * *
1336440 AAAGGCGTCATGCTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGGCCTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * *
1336501 AAAAGCATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* * * * *
1336563 AAAGGTGACCTGTTCTTCGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
*
1336624 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAACA-GA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* *
1336684 AAAGAAGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAGAAGGA
1 AAAG--GCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
*
1336747 AAAGGCGTCCTGCTCTTTGAGGACAAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
*
1336808 AAAGGCATCCTGCTCTTTGAGGA
1 AAAGGCGTCCTGCTCTTTGAGGA
1336831 TTGAAAGGAT
Statistics
Matches: 351, Mismatches: 33, Indels: 13
0.88 0.08 0.03
Matches are distributed among these distances:
59 33 0.09
60 15 0.04
61 193 0.55
62 104 0.30
63 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (61 bp):
AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
Found at i:1350173 original size:74 final size:74
Alignment explanation
Indices: 1350076--1350411 Score: 345
Period size: 74 Copynumber: 4.6 Consensus size: 74
1350066 GGACGCCTTT
** * *
1350076 TTTTTCTTCAAAGCCCATGCAAGCTGGTGGCATCATTTATCTTTTTCAATCCTCAAAGAGCAGGA
1 TTTTTCTTCAAAGCCCACACAAGCTAGTGGCATCATTTATCCTTTTCAATCCTCAAAGAGCAGGA
* *
1350141 GGACTTTTC
66 TGACTTGTC
* * * ** * * *
1350150 TTTTTCTTCAAAACTCAAACAAGCTAGTGGCATCACATATCCTTGTCAGTCCTCAAAGAGTAGGA
1 TTTTTCTTCAAAGCCCACACAAGCTAGTGGCATCATTTATCCTTTTCAATCCTCAAAGAGCAGGA
* *
1350215 -CACCTTTTC
66 TGA-CTTGTC
* * * * * * **
1350224 -TTTTCTTCAAAGCCCACATACGCTGGTGGCATTATTTATCCTTTTTAACCCTCAAAGAGCTTGA
1 TTTTTCTTCAAAGCCCACACAAGCTAGTGGCATCATTTATCCTTTTCAATCCTCAAAGAGCAGGA
*
1350288 TGCCTTGTC
66 TGACTTGTC
* * *
1350297 TTTTTCTTCAAAGCCGACACAAGCTAGTGGCATTATTTATCCTTTTCAATCCTCAAAGAGTAGGA
1 TTTTTCTTCAAAGCCCACACAAGCTAGTGGCATCATTTATCCTTTTCAATCCTCAAAGAGCAGGA
*
1350362 TGCCTTGTC
66 TGACTTGTC
* * *
1350371 TTTTTCTTCAAATCCCACATAAGCTATTGGCA-CTATTTATC
1 TTTTTCTTCAAAGCCCACACAAGCTAGTGGCATC-ATTTATC
1350412 TACTCTAGTC
Statistics
Matches: 213, Mismatches: 45, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
73 54 0.25
74 159 0.75
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (74 bp):
TTTTTCTTCAAAGCCCACACAAGCTAGTGGCATCATTTATCCTTTTCAATCCTCAAAGAGCAGGA
TGACTTGTC
Found at i:1350350 original size:147 final size:147
Alignment explanation
Indices: 1350054--1350411 Score: 422
Period size: 147 Copynumber: 2.4 Consensus size: 147
1350044 CTTGCACAAG
* *
1350054 TCCTCAAA-ATTAGGACGCCTTTT-TTTTCTTCAAAGCCCATGCA-AGCTGGTGGCATCATTTAT
1 TCCTCAAAGAGTAGGACGCCTTTTCTTTTCTTCAAAGCCCA--CATAGCTGGTGGCATTATTTAT
* *
1350116 -CTTTTTCAATCCTCAAAGAGCAGGAGGACTTTTCTTTTTCTTCAAAACTCAAACAAGCTAGTGG
64 CCTTTTTCAACCCTCAAAGAGCAGGAGGACTTGTCTTTTTCTTCAAAACTCAAACAAGCTAGTGG
*
1350180 CATCACATATCCTTGTCAG
129 CATCACATATCCTTGTCAA
*
1350199 TCCTCAAAGAGTAGGACACCTTTTCTTTTCTTCAAAGCCCACATACGCTGGTGGCATTATTTATC
1 TCCTCAAAGAGTAGGACGCCTTTTCTTTTCTTCAAAGCCCACATA-GCTGGTGGCATTATTTATC
** * * * *
1350264 CTTTTT-AACCCTCAAAGAGCTTGATGCCTTGTCTTTTTCTTCAAAGC-CGACACAAGCTAGTGG
65 CTTTTTCAACCCTCAAAGAGCAGGAGGACTTGTCTTTTTCTTCAAAACTC-AAACAAGCTAGTGG
* ** *
1350327 CATTATTTATCCTTTTCAA
129 CATCACATATCCTTGTCAA
* * * ** *
1350346 TCCTCAAAGAGTAGGATGCCTTGTCTTTTTCTTCAAATCCCACATAAGCTATTGGCACTATTTAT
1 TCCTCAAAGAGTAGGACGCCTTTTC-TTTTCTTCAAAGCCCACAT-AGCTGGTGGCATTATTTAT
1350411 C
64 C
1350412 TACTCTAGTC
Statistics
Matches: 182, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
145 10 0.05
146 15 0.08
147 116 0.64
148 40 0.22
149 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.35
Consensus pattern (147 bp):
TCCTCAAAGAGTAGGACGCCTTTTCTTTTCTTCAAAGCCCACATAGCTGGTGGCATTATTTATCC
TTTTTCAACCCTCAAAGAGCAGGAGGACTTGTCTTTTTCTTCAAAACTCAAACAAGCTAGTGGCA
TCACATATCCTTGTCAA
Found at i:1355296 original size:21 final size:20
Alignment explanation
Indices: 1355248--1355305 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1355238 TCATTGGGTC
* *
1355248 AAATATATCGATATAATTGA
1 AAATGTATCGATACAATTGA
* *
1355268 TAATGTATCGATACAATTTA
1 AAATGTATCGATACAATTGA
*
1355288 AACATGTATTGATACAAT
1 AA-ATGTATCGATACAAT
1355306 CACAGGGTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (20 bp):
AAATGTATCGATACAATTGA
Found at i:1356110 original size:14 final size:13
Alignment explanation
Indices: 1356091--1356120 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1356081 TTGGTGTTCT
1356091 TTTGTTTATGATTA
1 TTTGTTTATGA-TA
1356105 TTTGTTTATGATA
1 TTTGTTTATGATA
1356118 TTT
1 TTT
1356121 CATATTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (13 bp):
TTTGTTTATGATA
Found at i:1365139 original size:21 final size:21
Alignment explanation
Indices: 1365106--1365150 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1365096 TTGCAAGTTG
*
1365106 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1365128 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1365148 AAA
1 AAA
1365151 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1370936 original size:11 final size:11
Alignment explanation
Indices: 1370920--1370944 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1370910 GGGGGAGCAA
1370920 ATAAATTTTTG
1 ATAAATTTTTG
1370931 ATAAATTTTTG
1 ATAAATTTTTG
1370942 ATA
1 ATA
1370945 TGAATTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (11 bp):
ATAAATTTTTG
Found at i:1371706 original size:13 final size:13
Alignment explanation
Indices: 1371688--1371713 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1371678 TACAGCAAGT
1371688 ATGTATCGATACA
1 ATGTATCGATACA
1371701 ATGTATCGATACA
1 ATGTATCGATACA
1371714 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1373838 original size:33 final size:32
Alignment explanation
Indices: 1373796--1373860 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1373786 CATACCCAGA
1373796 TGTATCGATACATATTGCTTAGTATCAATACAT
1 TGTATCGATACATATT-CTTAGTATCAATACAT
* * *
1373829 TGTATCGATACATGTTCTTGGTATCGATACAT
1 TGTATCGATACATATTCTTAGTATCAATACAT
1373861 CATCAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATATTCTTAGTATCAATACAT
Found at i:1373874 original size:20 final size:19
Alignment explanation
Indices: 1373826--1373877 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1373816 AGTATCAATA
**
1373826 CATTGTATCGATACATGTT
1 CATTGTATCGATACATCAT
1373845 C-TTGGTATCGATACATCAT
1 CATT-GTATCGATACATCAT
1373864 CAATTGTATCGATA
1 C-ATTGTATCGATA
1373878 TATAAAACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.07
19 15 0.54
20 9 0.32
21 2 0.07
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATCAT
Found at i:1373972 original size:13 final size:13
Alignment explanation
Indices: 1373954--1373980 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1373944 TCACTATTCA
1373954 TGTATCGATACAT
1 TGTATCGATACAT
1373967 TGTATCGATACAT
1 TGTATCGATACAT
1373980 T
1 T
1373981 ATGAATAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1374491 original size:30 final size:31
Alignment explanation
Indices: 1374433--1374491 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
1374423 GGTAAGGACA
1374433 AAGGTTCTATCTTAGCCCGTGAAAAGATATG
1 AAGGTTCTATCTTAGCCCGTGAAAAGATATG
1374464 AAGGTTTCTATCTTAGCCC-TG-AAAGATA
1 AAGG-TTCTATCTTAGCCCGTGAAAAGATA
1374492 GTATTGTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 7 0.26
31 6 0.22
32 14 0.52
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (31 bp):
AAGGTTCTATCTTAGCCCGTGAAAAGATATG
Found at i:1376097 original size:21 final size:21
Alignment explanation
Indices: 1376073--1376130 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1376063 GAACTAGAGG
*
1376073 AGAAAATGAATGAGTTGGAAA
1 AGAAAATGAATGAGTTGCAAA
1376094 AGAAAA-GAAATGAGTTGCAAA
1 AGAAAATG-AATGAGTTGCAAA
1376115 ATGAAAATG-ATGAGTT
1 A-GAAAATGAATGAGTT
1376131 AACTAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.03
21 26 0.79
22 5 0.15
23 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.26, T:0.21
Consensus pattern (21 bp):
AGAAAATGAATGAGTTGCAAA
Found at i:1376734 original size:19 final size:19
Alignment explanation
Indices: 1376710--1376765 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1376700 TGTATCAACA
1376710 CATTGTATCGATACATGCT
1 CATTGTATCGATACATGCT
* *
1376729 CATTGTAACGATACATACT
1 CATTGTATCGATACATGCT
1376748 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
1376766 AAATTGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:1378897 original size:15 final size:14
Alignment explanation
Indices: 1378872--1378904 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1378862 ATGAAAAGGA
1378872 ATTTTTTATTATTT
1 ATTTTTTATTATTT
1378886 ATTTTGTTATTATTT
1 ATTTT-TTATTATTT
1378901 -TTTT
1 ATTTT
1378905 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (14 bp):
ATTTTTTATTATTT
Found at i:1380068 original size:22 final size:23
Alignment explanation
Indices: 1380031--1380073 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
1380021 TTGGTCACGT
1380031 TGCTTTCTCTTTTACGTTGCTCG
1 TGCTTTCTCTTTTACGTTGCTCG
1380054 TGCTTTCT-TTTTACGTTGCT
1 TGCTTTCTCTTTTACGTTGCT
1380074 GCTGTTTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.05, C:0.23, G:0.16, T:0.56
Consensus pattern (23 bp):
TGCTTTCTCTTTTACGTTGCTCG
Found at i:1381038 original size:18 final size:18
Alignment explanation
Indices: 1380999--1381054 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
1380989 GGCTCCCCTC
*
1380999 TTTTTAATT-TGATTAT-
1 TTTTTAATTATTATTATA
* *
1381015 TTTTTAATTATTTTTTTA
1 TTTTTAATTATTATTATA
*
1381033 TTTTTATTTATTATTATA
1 TTTTTAATTATTATTATA
1381051 TTTT
1 TTTT
1381055 ATATTGAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 9 0.28
17 4 0.12
18 19 0.59
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTTAATTATTATTATA
Found at i:1381039 original size:25 final size:25
Alignment explanation
Indices: 1381011--1381059 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1381001 TTTAATTTGA
* *
1381011 TTATTTTTTAATTAT-TTTTTTATTT
1 TTATTTATT-ATTATATTTTATATTT
1381036 TTATTTATTATTATATTTTATATT
1 TTATTTATTATTATATTTTATATT
1381060 GAACAAATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (25 bp):
TTATTTATTATTATATTTTATATTT
Found at i:1381619 original size:43 final size:43
Alignment explanation
Indices: 1381571--1381895 Score: 331
Period size: 42 Copynumber: 7.7 Consensus size: 43
1381561 AAATCCCCAA
* * * *
1381571 GGTCAAAGCCGACAGGCAGGCTGAAGGTAGGACAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAAAGTCTCCAG
* * *
1381614 GGTCAAAGCTGACAGGCAGACTGAGGGTCGG-AAAGTCTTCAG
1 GGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAAAGTCTCCAG
* * * *** *
1381656 GGTCAAAGCTGACAGGTAGACTTAAAATGAGG--TAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTGAGGGT-AGGAAAAGTCTCCAG
* *
1381698 GGTCAAAGCCGATAGGCAGGCTGAGGGTAGGAAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAAAGTCTCCAG
1381741 GGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAAAGTCTCCAG
* * * *
1381784 GGTCAAAGCCGACAGGCAGACTTTA-GATGAGG--CAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGAC-TGAGGGT-AGGAAAAGTCTCCAG
* ** *
1381826 GGTTAAAGTGGATAGGCAGACTGAGGGTA-GAAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAAAGTCTCCAG
* * *
1381868 GGTCAAAGCTGATAGGCAGACTAAGGGT
1 GGTCAAAGCCGACAGGCAGACTGAGGGT
1381896 CCAAAAGTCC
Statistics
Matches: 232, Mismatches: 42, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
40 1 0.00
41 6 0.03
42 118 0.51
43 102 0.44
44 5 0.02
ACGTcount: A:0.32, C:0.19, G:0.34, T:0.16
Consensus pattern (43 bp):
GGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAAAGTCTCCAG
Found at i:1381865 original size:127 final size:127
Alignment explanation
Indices: 1381567--1381957 Score: 520
Period size: 127 Copynumber: 3.1 Consensus size: 127
1381557 AAAAAAATCC
* * * *
1381567 CCAAGGTCAAAGCCGACAGGCAGGCTGAAGGTAGGACAAGTCTCCAAGGTCAAAGCTGACAGGCA
1 CCAAGGTCAAAGCCGATAGGCAGGCTGAGGGTAGGAAAAGTCTCCAGGGTCAAAGCTGACAGGCA
* * * * *
1381632 GACTGAGGGTCGG-AAAGTCTTCAGGGTCAAAGCTGACAGGTAGACTTAAAATGAGGTAGTCT
66 GACTGAGGGT-GGAAAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCT
* *
1381694 CCAGGGTCAAAGCCGATAGGCAGGCTGAGGGTAGGAAAAGTCTCCAGGGTCAAAGCCGACAGGCA
1 CCAAGGTCAAAGCCGATAGGCAGGCTGAGGGTAGGAAAAGTCTCCAGGGTCAAAGCTGACAGGCA
*
1381759 GACTGAGGGTAGGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCT
66 GACTGAGGGT-GGAAAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCT
* ** * *
1381822 CCAAGGTTAAAGTGGATAGGCAGACTGAGGGTA-GAAAAGTCTCCAGGGTCAAAGCTGATAGGCA
1 CCAAGGTCAAAGCCGATAGGCAGGCTGAGGGTAGGAAAAGTCTCCAGGGTCAAAGCTGACAGGCA
* ** * * *
1381886 GACTAAGGGTCCAAAAGTC-CCTAGGATCAAAGTTGACAGGCAAACTTTAGATGAGGCAGTCT
66 GACTGAGGGTGGAAAAGTCTCC-AGGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCT
1381948 CC-AGGTCAAA
1 CCAAGGTCAAA
1381958 ATGAAGGATC
Statistics
Matches: 234, Mismatches: 28, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
125 9 0.04
126 45 0.19
127 109 0.47
128 71 0.30
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.16
Consensus pattern (127 bp):
CCAAGGTCAAAGCCGATAGGCAGGCTGAGGGTAGGAAAAGTCTCCAGGGTCAAAGCTGACAGGCA
GACTGAGGGTGGAAAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCT
Found at i:1390282 original size:20 final size:19
Alignment explanation
Indices: 1390259--1390312 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1390249 CGCTTTCAGA
*
1390259 TGTATCGATACATTATGCTT
1 TGTATCGATACATTAT-CAT
1390279 TGTATCGATACATGT-TCAT
1 TGTATCGATACAT-TATCAT
*
1390298 TATATCGATACATTA
1 TGTATCGATACATTA
1390313 ACAAATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 14 0.47
21 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTATCAT
Found at i:1390397 original size:13 final size:13
Alignment explanation
Indices: 1390379--1390405 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1390369 TACATGGCAT
1390379 AATGTATCGATAC
1 AATGTATCGATAC
1390392 AATGTATCGATAC
1 AATGTATCGATAC
1390405 A
1 A
1390406 TGAAGAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1390418 original size:33 final size:33
Alignment explanation
Indices: 1390362--1390425 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1390352 ACCACTATTC
* * *
1390362 GTATCGATACATGGCATAATGTATCGATACAAT
1 GTATCGATACATGGAAGAATGTATCAATACAAT
1390395 GTATCGATACAT-GAAGAATTGTATCAATACA
1 GTATCGATACATGGAAGAA-TGTATCAATACA
1390426 TTGCCTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (33 bp):
GTATCGATACATGGAAGAATGTATCAATACAAT
Found at i:1397066 original size:38 final size:37
Alignment explanation
Indices: 1397020--1397091 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
1397010 TCATGCATGA
* *
1397020 ATGCATGCATTGCCACCTAA-TTAATTTAGGTGGCAGC
1 ATGCATGCAATGCCACCTAAGTCAA-TTAGGTGGCAGC
1397057 ATGCAATGCAATGCCACCTAAGTCAATTAGGTGGC
1 ATGC-ATGCAATGCCACCTAAGTCAATTAGGTGGC
1397092 TACAAATCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 4 0.13
38 24 0.77
39 3 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (37 bp):
ATGCATGCAATGCCACCTAAGTCAATTAGGTGGCAGC
Found at i:1397165 original size:15 final size:14
Alignment explanation
Indices: 1397122--1397154 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1397112 AGCTCCCCTC
*
1397122 TTTTTAATT-TGAT
1 TTTTTAATTATTAT
1397135 TTTTTAATTATTAT
1 TTTTTAATTATTAT
1397149 TTTTTA
1 TTTTTA
1397155 TATATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTTTAATTATTAT
Found at i:1410815 original size:16 final size:16
Alignment explanation
Indices: 1410796--1410840 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 16
1410786 CCTCAAAAGT
1410796 ACAAACACAAAAAAAA
1 ACAAACACAAAAAAAA
1410812 AC-AAC-C-AAAAAAA
1 ACAAACACAAAAAAAA
*
1410825 ACAAAAACAAAAAAAA
1 ACAAACACAAAAAAAA
1410841 GAGTGGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 9 0.36
14 3 0.12
15 4 0.16
16 9 0.36
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (16 bp):
ACAAACACAAAAAAAA
Found at i:1410822 original size:15 final size:15
Alignment explanation
Indices: 1410796--1410840 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1410786 CCTCAAAAGT
*
1410796 ACAAACACAAAAAAA
1 ACAAAAACAAAAAAA
* *
1410811 A-ACAACCAAAAAAA
1 ACAAAAACAAAAAAA
1410825 ACAAAAACAAAAAAA
1 ACAAAAACAAAAAAA
1410840 A
1 A
1410841 GAGTGGAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (15 bp):
ACAAAAACAAAAAAA
Found at i:1412276 original size:126 final size:125
Alignment explanation
Indices: 1412054--1412927 Score: 866
Period size: 126 Copynumber: 7.1 Consensus size: 125
1412044 TCTTTAAATC
* * * * * ** *
1412054 TCTCTTCTCAAAGTCCATGACTCAGTGGCAT-CTTGTC--CCAAAGTCCACAACTCAGTGGTAT-
1 TCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCC-AAGTCCATGACTCAGTGGAATC
* *
1412115 TTTTCTC-CAAAGTCCACGACTCAGTGGCAACCTCTTTTCAAAGTCCACAACTCAGTGGCA
65 TTTTTTCTCAAAGTCCACGACTCAGTGGCAATCTCTTTTCAAAGTCCACAACTCAGTGGCA
1412175 TCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCATGACTCAGTGGAATCT
1 TCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCATGACTCAGTGGAATCT
* *
1412240 TTTTTCATCAAAGTCCACGTCTGAGTGGCAATCTCTTTTCAAAGTCCACAACTCAGTGGCA
66 TTTTTC-TCAAAGTCCACGACTCAGTGGCAATCTCTTTTCAAAGTCCACAACTCAGTGGCA
* *
1412301 TCTCTTTTCTAAGTCCACAACTTAGTGGCATCCTTTTCTT-CAAGTCCATGACTTAGTGGAATCT
1 TCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCATGACTCAGTGGAATCT
* *
1412365 TTTTTCATCAAAGTCCACGCCTGAGTGGCAATCTCTTTTCAAAGTCCACAACTCAGTGGCA
66 TTTTTC-TCAAAGTCCACGACTCAGTGGCAATCTCTTTTCAAAGTCCACAACTCAGTGGCA
* ** * ** *
1412426 TCTCTTTTCTAAGTCCATGACTTAAAGGCATCCTTTTCTGCCAAGTCCACAACTTAGTGGAATCT
1 TCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCATGACTCAGTGGAATCT
* * * * * *
1412491 TTTTTCTTCAAAGTCCATGAGTCAGTGGCAATCTCTTCTCAAAGCCCACGACTTAGTGGCA
66 TTTTTC-TCAAAGTCCACGACTCAGTGGCAATCTCTTTTCAAAGTCCACAACTCAGTGGCA
** * *
1412552 TCT-TGTCCCAAAGTCCACGACTTAGTGGCAT-TTTTTC-TCCAAAGTCCATGACTCAGTGGCAA
1 TCTCT-TTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCC-AAGTCCATGACTCAGTGG-AA
* * * *
1412614 TC-TCTTT-TCAAAGTCCGCAACTCAGTGGCAATCTCTTTTCTAAA-TCCACAACTTAGTGGCA
63 TCTTTTTTCTCAAAGTCCACGACTCAGTGGCAATCTCTTTTC-AAAGTCCACAACTCAGTGGCA
* * *
1412675 TC-CTTTTCTTCCAAGTCCACGACTTAGTGGAATCTTTTTTCTTCAAAGTCCATGACTCAGTGGC
1 TCTCTTTTC-T--AAGTCCACGACTTAGTGGCATC-CTTTTCTTCCAAGTCCATGACTCAGTGG-
* * * ** * *
1412739 AATC--TCTTCTCAAAGCCCACGACTCAATGGC-ATCT-TGTCCCAAAGTTCACGACTCAGTGGC
61 AATCTTTTTTCTCAAAGTCCACGACTCAGTGGCAATCTCT-TTTCAAAGTCCACAACTCAGTGGC
1412800 A
125 A
* * * ** *
1412801 T-T-TTTTCTCAA---CACGACTCAGTGGCAAT-CTCTT-TTCAAAGTCCACAACTCAGTGGCAT
1 TCTCTTTTCT-AAGTCCACGACTTAGTGGC-ATCCTTTTCTTCCAAGTCCATGACTCAGTGGAAT
* * * * *
1412859 CTCTTTTCT--AAGTCCACGACTTAGTGGC-ATCTTTTTTTTCCAAGTCCACGACTCAGTGGCA
64 CTTTTTTCTCAAAGTCCACGACTCAGTGGCAATC--TCTTTTCAAAGTCCACAACTCAGTGGCA
*
1412920 TCTTTTTT
1 TCTCTTTT
1412928 TTTCTTCAAT
Statistics
Matches: 642, Mismatches: 81, Indels: 60
0.82 0.10 0.08
Matches are distributed among these distances:
117 22 0.03
118 20 0.03
119 31 0.05
120 14 0.02
121 33 0.05
122 7 0.01
123 67 0.10
124 14 0.02
125 172 0.27
126 213 0.33
127 47 0.07
128 2 0.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (125 bp):
TCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCATGACTCAGTGGAATCT
TTTTTCTCAAAGTCCACGACTCAGTGGCAATCTCTTTTCAAAGTCCACAACTCAGTGGCA
Found at i:1412568 original size:251 final size:250
Alignment explanation
Indices: 1412054--1412927 Score: 835
Period size: 251 Copynumber: 3.5 Consensus size: 250
1412044 TCTTTAAATC
* ** * * ** *
1412054 TCTCTTCTCAAAGTCCATGACTCAGTGGCATCTTGTC-CCAAAGTCCACAACTCAGTGG---TAT
1 TCTCTTCCCAAAGTCCACAACTTAGTGGCATCTTTTCTCCAAAGTCCATGACTCAGTGGCAATCT
*
1412115 TTTTCTCCAAAGTCCACGACTCAGTGGCAACCTCTTTTCAAAGTCCACAACTCAGTGGCATCTCT
66 TTTTCT-CAAAGTCCACGACTCAGTGGCAATCTCTTTTCAAAGTCCACAACTCAGTGGCATCTCT
** * **
1412180 TTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCATGACTCAGTGGAATCTTTTTT
130 TTTCTAAGTCCACGACTTAAAGGCATCCTTTTCTGCCAAGTCCACAACTCAGTGGAATCTTTTTT
* * * *
1412245 CATCAAAGTCCACGTCTGAGTGGCAATCTCTTTTCAAAGTCCACAACTCAGTGGCA
195 CATCAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCACAACTCAGTGGCA
** * * *
1412301 TCTCTTTTCTAAGTCCACAACTTAGTGGCATCCTTTTCTTC-AAGTCCATGACTTAGTGG-AATC
1 TCTCTTCCCAAAGTCCACAACTTAGTGGCAT-CTTTTCTCCAAAGTCCATGACTCAGTGGCAATC
* *
1412364 TTTTTTCATCAAAGTCCACGCCTGAGTGGCAATCTCTTTTCAAAGTCCACAACTCAGTGGCATCT
65 -TTTTTC-TCAAAGTCCACGACTCAGTGGCAATCTCTTTTCAAAGTCCACAACTCAGTGGCATCT
* *
1412429 CTTTTCTAAGTCCATGACTTAAAGGCATCCTTTTCTGCCAAGTCCACAACTTAGTGGAATCTTTT
128 CTTTTCTAAGTCCACGACTTAAAGGCATCCTTTTCTGCCAAGTCCACAACTCAGTGGAATCTTTT
* * * * *
1412494 TTCTTCAAAGTCCATGAGTCAGTGGCAATCTCTTCTCAAAGCCCACGACTTAGTGGCA
193 TTCATCAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCACAACTCAGTGGCA
* *
1412552 TCT-TGTCCCAAAGTCCACGACTTAGTGGCATTTTTTCTCCAAAGTCCATGACTCAGTGGCAATC
1 TCTCT-TCCCAAAGTCCACAACTTAGTGGCATCTTTTCTCCAAAGTCCATGACTCAGTGGCAATC
* * * *
1412616 TCTTT-TCAAAGTCCGCAACTCAGTGGCAATCTCTTTTCTAAA-TCCACAACTTAGTGGCATC-C
65 TTTTTCTCAAAGTCCACGACTCAGTGGCAATCTCTTTTC-AAAGTCCACAACTCAGTGGCATCTC
** * * * * **
1412678 TTTTCTTCCAAGTCCACGACTTAGTGGAATCTTTTTTCTTCAAAGTCCATGACTCAGTGGCAATC
129 TTTTC-T--AAGTCCACGACTTAAAGGCATC-CTTTTCTGCCAAGTCCACAACTCAGTGG-AATC
* * * * ** *
1412743 --TCTTC-TCAAAGCCCACGACTCAATGGC-ATCT-TGTCCCAAAGTTCACGACTCAGTGGCA
189 TTTTTTCATCAAAGTCCACGACTCAGTGGCAATCTCT-TCTCAAAGCCCACAACTCAGTGGCA
* * * * * **
1412801 TTTTTTCTC-AA---CACGACTCAGTGGCAATCTCTTT-T-CAAAGTCCACAACTCAGTGGC-AT
1 TCTCTTCCCAAAGTCCACAACTTAGTGGC-ATCT-TTTCTCCAAAGTCCATGACTCAGTGGCAAT
* * * *
1412859 CTCTTTTCT--AAGTCCACGACTTAGTGGC-ATCTTTTTTTTCCAAGTCCACGACTCAGTGGCAT
64 CT-TTTTCTCAAAGTCCACGACTCAGTGGCAATC--TCTTTTCAAAGTCCACAACTCAGTGGCAT
*
1412921 CTTTTTT
126 CTCTTTT
1412928 TTTCTTCAAT
Statistics
Matches: 525, Mismatches: 77, Indels: 51
0.80 0.12 0.08
Matches are distributed among these distances:
243 3 0.01
244 22 0.04
245 58 0.11
246 9 0.02
247 29 0.06
248 29 0.06
249 79 0.15
250 31 0.06
251 234 0.45
252 27 0.05
253 4 0.01
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (250 bp):
TCTCTTCCCAAAGTCCACAACTTAGTGGCATCTTTTCTCCAAAGTCCATGACTCAGTGGCAATCT
TTTTCTCAAAGTCCACGACTCAGTGGCAATCTCTTTTCAAAGTCCACAACTCAGTGGCATCTCTT
TTCTAAGTCCACGACTTAAAGGCATCCTTTTCTGCCAAGTCCACAACTCAGTGGAATCTTTTTTC
ATCAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCACAACTCAGTGGCA
Found at i:1412861 original size:30 final size:30
Alignment explanation
Indices: 1412054--1412986 Score: 643
Period size: 31 Copynumber: 30.0 Consensus size: 30
1412044 TCTTTAAATC
* *
1412054 TCTCTTCTCAAAGTCCATGACTCAGTGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
** * *
1412084 TCT-TGTCCCAAAGTCCACAACTCAGTGGTA
1 TCTCT-TTTCAAAGTCCACGACTCAGTGGCA
1412114 T-T-TTTCTCCAAAGTCCACGACTCAGTGGCAA
1 TCTCTTT-T-CAAAGTCCACGACTCAGTGGC-A
* *
1412145 CCTCTTTTCAAAGTCCACAACTCAGTGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
* *
1412175 TCTCTTTTCTAAGTCCACGACTTAGTGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
* * * *
1412205 TCCTTTTCTTCCAAGTCCATGACTCAGTGGAA
1 T-CTCTT-TTCAAAGTCCACGACTCAGTGGCA
* * *
1412237 TCTTTTTTCATCAAAGTCCACGTCTGAGTGGCAA
1 TC-TCTTT--TCAAAGTCCACGACTCAGTGGC-A
*
1412271 TCTCTTTTCAAAGTCCACAACTCAGTGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
* * *
1412301 TCTCTTTTCTAAGTCCACAACTTAGTGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
* * * *
1412331 TC-CTTTTCTTCAAGTCCATGACTTAGTGGAA
1 TCTCTTTTC--AAAGTCCACGACTCAGTGGCA
* * *
1412362 TCTTTTTTCATCAAAGTCCACGCCTGAGTGGCAA
1 TC-TCTTT--TCAAAGTCCACGACTCAGTGGC-A
*
1412396 TCTCTTTTCAAAGTCCACAACTCAGTGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
* * * **
1412426 TCTCTTTTCTAAGTCCATGACTTAAAGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
* * * *
1412456 TC-CTTTTCTGCCAAGTCCACAACTTAGTGGAA
1 TCTC-TTT-T-CAAAGTCCACGACTCAGTGGCA
* * *
1412488 TCTTTTTTCTTCAAAGTCCATGAGTCAGTGGCAA
1 TC--TCTT-TTCAAAGTCCACGACTCAGTGGC-A
* * *
1412522 TCTCTTCTCAAAGCCCACGACTTAGTGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
** *
1412552 TCT-TGTCCCAAAGTCCACGACTTAGTGGCA
1 TCTCT-TTTCAAAGTCCACGACTCAGTGGCA
* *
1412582 T-TTTTTCTCCAAAGTCCATGACTCAGTGGCAA
1 TCTCTTT-T-CAAAGTCCACGACTCAGTGGC-A
* *
1412614 TCTCTTTTCAAAGTCCGCAACTCAGTGGCAA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGC-A
* *
1412645 TCTCTTTTCTAAA-TCCACAACTTAGTGGCA
1 TCTCTTTTC-AAAGTCCACGACTCAGTGGCA
* * * *
1412675 TCCTTTTCTTCCAAGTCCACGACTTAGTGGAA
1 T-CTCTT-TTCAAAGTCCACGACTCAGTGGCA
* *
1412707 TCTTTTTTCTTCAAAGTCCATGACTCAGTGGCAA
1 TC--TCTT-TTCAAAGTCCACGACTCAGTGGC-A
* * *
1412741 TCTCTTCTCAAAGCCCACGACTCAATGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
** *
1412771 TCT-TGTCCCAAAGTTCACGACTCAGTGGCA
1 TCTCT-TTTCAAAGTCCACGACTCAGTGGCA
*
1412801 T-T-TTTTCTCAA---CACGACTCAGTGGCAA
1 TCTCTTTTC-AAAGTCCACGACTCAGTGGC-A
*
1412828 TCTCTTTTCAAAGTCCACAACTCAGTGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
* *
1412858 TCTCTTTTCTAAGTCCACGACTTAGTGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
* *
1412888 TCTTTTTTTTCCAAGTCCACGACTCAGTGGCA
1 TC--TCTTTTCAAAGTCCACGACTCAGTGGCA
* * * *
1412920 TCTTTTTTTTTCTTCAATGTACACGACTCAATGGCAA
1 TC-----TCTT-TTCAAAGTCCACGACTCAGTGGC-A
* * *
1412957 TCTCCTCTCAAAGTCCACGACTCCGTGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
1412987 CACATTTAAG
Statistics
Matches: 728, Mismatches: 120, Indels: 110
0.76 0.13 0.11
Matches are distributed among these distances:
26 14 0.02
27 2 0.00
28 6 0.01
29 23 0.03
30 221 0.30
31 222 0.30
32 105 0.14
33 89 0.12
34 15 0.02
35 9 0.01
36 19 0.03
37 3 0.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (30 bp):
TCTCTTTTCAAAGTCCACGACTCAGTGGCA
Done.