Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008206.1 Hibiscus syriacus cultivar Beakdansim tig00110828_pilon, whole genome shotgun sequence
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: 1504526
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1205743 original size:102 final size:101
Alignment explanation
Indices: 1205620--1206043 Score: 414
Period size: 100 Copynumber: 4.2 Consensus size: 101
1205610 AAAAAAATAT
* * * * * * *
1205620 GTTACCTATTATGTTATCATGAAAAACCTGTTTTATCTTACTTTTACATAATATAAACAATTTCA
1 GTTACCTACTACGTTATCATGAAAAACATATTTTGTCTTACTTTTGCATAATATAAACAGTTTCA
* * *
1205685 TACTTATAATTTAAACGATT-ATCATTTAAAAAAATGT
66 TACTTATAACTTAAACGATTGA-CA-TTAAAAAAAGGC
* * * * ** *
1205722 GTTACCTAGTACATTATCATGAACAATATATTTTGTCTTACTTTTGGC-TAATATAAATGGTTTT
1 GTTACCTACTACGTTATCATGAAAAACATATTTTGTCTTACTTTT-GCATAATATAAACAGTTTC
* *
1205786 ATACTTATAATTTAAACGATTGACATTAAAAAAA-AC
65 ATACTTATAACTTAAACGATTGACATTAAAAAAAGGC
* * ** * * * *
1205822 GCTACCTAATACGTTATCATGAGCAACATGTTTTGTC-TAGCTTTTGCATAATATCAACATTTTT
1 GTTACCTACTACGTTATCATGAAAAACATATTTTGTCTTA-CTTTTGCATAATATAAACAGTTTC
*
1205886 ATACTTATAACTTAAACAATTGACA-T-AAAAAAGGC
65 ATACTTATAACTTAAACGATTGACATTAAAAAAAGGC
* * * * *
1205921 GCTACCTACTACATTATCATGAGAAACATATTTTGTCTTACATTTG-ATCATATAAA-AGGTTTC
1 GTTACCTACTACGTTATCATGAAAAACATATTTTGTCTTACTTTTGCATAATATAAACA-GTTTC
* *
1205984 ATACTTATAACTTAAACGATGGACATTAAAAAAAAGGA
65 ATACTTATAACTTAAACGATTGACATT-AAAAAAAGGC
*
1206022 GTTTCCTACTACGTTATCATGA
1 GTTACCTACTACGTTATCATGA
1206044 GCATAACAAA
Statistics
Matches: 269, Mismatches: 43, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
97 1 0.00
98 40 0.15
99 45 0.17
100 73 0.27
101 36 0.13
102 72 0.27
103 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (101 bp):
GTTACCTACTACGTTATCATGAAAAACATATTTTGTCTTACTTTTGCATAATATAAACAGTTTCA
TACTTATAACTTAAACGATTGACATTAAAAAAAGGC
Found at i:1205874 original size:100 final size:100
Alignment explanation
Indices: 1205622--1206046 Score: 396
Period size: 102 Copynumber: 4.2 Consensus size: 100
1205612 AAAAATATGT
* * ** * * * * ***
1205622 TACCTATTATGTTATCATGAAAAACCTGTTTTATCTTACTTTTACATAATATAAACAATTTCATA
1 TACCTACTACGTTATCATGAGCAACATATTTTGTCTTACTTTTGCATAATATAAATGGTTTCATA
* ** *
1205687 CTTATAATTTAAACGATT-ATCATTTAAAAAAATGTGT
66 CTTATAACTTAAACGATTGA-CA-TTAAAAAAA-ACGC
* * * * *
1205724 TACCTAGTACATTATCATGAACAATATATTTTGTCTTACTTTTGGC-TAATATAAATGGTTTTAT
1 TACCTACTACGTTATCATGAGCAACATATTTTGTCTTACTTTT-GCATAATATAAATGGTTTCAT
*
1205788 ACTTATAATTTAAACGATTGACATTAAAAAAAACGC
65 ACTTATAACTTAAACGATTGACATTAAAAAAAACGC
* * *
1205824 TACCTAATACGTTATCATGAGCAACATGTTTTGTC-TAGCTTTTGCATAATATCAACAT--TTTT
1 TACCTACTACGTTATCATGAGCAACATATTTTGTCTTA-CTTTTGCATAATAT-AA-ATGGTTTC
* **
1205886 ATACTTATAACTTAAACAATTGACA-TAAAAAAGGCGC
63 ATACTTATAACTTAAACGATTGACATTAAAAAAAACGC
* * * * *
1205923 TACCTACTACATTATCATGAGAAACATATTTTGTCTTACATTTG-ATCATATAAAAGGTTTCATA
1 TACCTACTACGTTATCATGAGCAACATATTTTGTCTTACTTTTGCATAATATAAATGGTTTCATA
* * *
1205987 CTTATAACTTAAACGATGGACATTAAAAAAAAGGAGT
66 CTTATAACTTAAACGATTGACATTAAAAAAAA--CGC
*
1206024 TTCCTACTACGTTATCATGAGCA
1 TACCTACTACGTTATCATGAGCA
1206047 TAACAAAATA
Statistics
Matches: 269, Mismatches: 42, Indels: 25
0.80 0.12 0.07
Matches are distributed among these distances:
96 1 0.00
97 2 0.01
98 32 0.12
99 57 0.21
100 71 0.26
101 32 0.12
102 72 0.27
103 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (100 bp):
TACCTACTACGTTATCATGAGCAACATATTTTGTCTTACTTTTGCATAATATAAATGGTTTCATA
CTTATAACTTAAACGATTGACATTAAAAAAAACGC
Found at i:1206474 original size:39 final size:39
Alignment explanation
Indices: 1206410--1206484 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
1206400 TCATTTCAAT
* * *
1206410 CCAATATTTAGTCTTGTCAAAACTCCTTTGGAAGACAAC
1 CCAATATCTAGTCTTATCAAAACTCCTTGGGAAGACAAC
*
1206449 CCAATATCTAGTCTTATCAATACTCCTTGGGAAGAC
1 CCAATATCTAGTCTTATCAAAACTCCTTGGGAAGAC
1206485 CACATGATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (39 bp):
CCAATATCTAGTCTTATCAAAACTCCTTGGGAAGACAAC
Found at i:1208551 original size:22 final size:23
Alignment explanation
Indices: 1208521--1208566 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1208511 AAGCTCCAGT
* *
1208521 TTGTAAAAGT-ATTTTATGAATA
1 TTGTAAAAGTCATTTCATAAATA
*
1208543 TTGTTAAAGTCATTTCATAAATA
1 TTGTAAAAGTCATTTCATAAATA
1208566 T
1 T
1208567 ATAGTGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (23 bp):
TTGTAAAAGTCATTTCATAAATA
Found at i:1208946 original size:77 final size:77
Alignment explanation
Indices: 1208822--1209120 Score: 309
Period size: 77 Copynumber: 3.9 Consensus size: 77
1208812 CTTTCGAGTT
* * * * *
1208822 TTTTA-TAATAGAAAA-ATTAACATTCCATATCATAAC-TCATTTTCTTAGTGAACCATAATATT
1 TTTTATTAATA-AAAATATTAACATTTCAGATCACAACAT-A-TTTCTTAGTGAACCATGACATT
*
1208884 CTTAGGCGAAACTCA
63 CTTAGGTGAAACTCA
** * *
1208899 TTTTATTAATAAAAATATTAACATTTCAGATTGCAACCTATTTCTTAGTGAACCGTGACATTCTT
1 TTTTATTAATAAAAATATTAACATTTCAGATCACAACATATTTCTTAGTGAACCATGACATTCTT
* * *
1208964 GGGTGCAACCCA
66 AGGTGAAACTCA
* * * * * *
1208976 TTTTATTAAAAAAAATATTAATATTTCATATCACAACATATTTCTTAGTAAACCGTGACATTTTT
1 TTTTATTAATAAAAATATTAACATTTCAGATCACAACATATTTCTTAGTGAACCATGACATTCTT
* *
1209041 TGGTGTAACTCA
66 AGGTGAAACTCA
* * * *
1209053 TTTTATTAATAAAAATATTAACA-TTCTAGATCACAACTTGTTTCTTAGTGAACCATGTCATTTT
1 TTTTATTAATAAAAATATTAACATTTC-AGATCACAACATATTTCTTAGTGAACCATGACATTCT
1209117 TAGG
65 TAGG
1209121 CGCACCCATA
Statistics
Matches: 186, Mismatches: 32, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
76 3 0.02
77 160 0.86
78 22 0.12
79 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (77 bp):
TTTTATTAATAAAAATATTAACATTTCAGATCACAACATATTTCTTAGTGAACCATGACATTCTT
AGGTGAAACTCA
Found at i:1209970 original size:37 final size:36
Alignment explanation
Indices: 1209895--1209970 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1209885 TTTTTATATT
*
1209895 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1209931 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1209968 TTT
1 TTT
1209971 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1210490 original size:102 final size:102
Alignment explanation
Indices: 1210369--1210582 Score: 403
Period size: 102 Copynumber: 2.1 Consensus size: 102
1210359 AGATCAGATA
*
1210369 CATATGGTTATCCCTAAAAAAATTGATTTAAAATTTAAATGTTATTATTAAAATGTATTTAAAAA
1 CATATGGTTATCCCTAAAAAAATTGATTTAAAATTTAAATGTTATTATTAAAATGAATTTAAAAA
1210434 ATAAATTATAAAATAACCTTACCATAAAATAATAAAT
66 ATAAATTATAAAATAACCTTACCATAAAATAATAAAT
1210471 CATATGGTTATCCCTAAAAAAATTGATTTAAAATTTAAATGTTATTATTAAAATGAATTTAAAAA
1 CATATGGTTATCCCTAAAAAAATTGATTTAAAATTTAAATGTTATTATTAAAATGAATTTAAAAA
1210536 ATAAATTATAAAATAACCTTACCATAAAATAATAAAT
66 ATAAATTATAAAATAACCTTACCATAAAATAATAAAT
*
1210573 CAGAT-GTTAT
1 CATATGGTTAT
1210583 TGTAGGTTTA
Statistics
Matches: 110, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
101 5 0.05
102 105 0.95
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (102 bp):
CATATGGTTATCCCTAAAAAAATTGATTTAAAATTTAAATGTTATTATTAAAATGAATTTAAAAA
ATAAATTATAAAATAACCTTACCATAAAATAATAAAT
Found at i:1210882 original size:2 final size:2
Alignment explanation
Indices: 1210875--1210909 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1210865 TGGTAAGAGC
1210875 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 A
1210910 AACCATTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1216944 original size:51 final size:52
Alignment explanation
Indices: 1216868--1216969 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 52
1216858 ACCCCTTGAC
* *
1216868 TCACTTGATTTTGTTACTTTCCCCCTTGTAGAATGAGTGGCCTG-AAGAGAT
1 TCACTTGATTTTGTTAATTTCCCCCTTGTAGAATGAGTGACCTGAAAGAGAT
*
1216919 TCACTTGATTTTGTTAATTTTCCCCTTGTAGAATGAGTGACCTGAAAGAGA
1 TCACTTGATTTTGTTAATTTCCCCCTTGTAGAATGAGTGACCTGAAAGAGA
1216970 ATTAATATTC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 41 0.87
52 6 0.13
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.37
Consensus pattern (52 bp):
TCACTTGATTTTGTTAATTTCCCCCTTGTAGAATGAGTGACCTGAAAGAGAT
Found at i:1219078 original size:2 final size:2
Alignment explanation
Indices: 1219071--1219111 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1219061 CTCAGTAAAC
1219071 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1219112 GAGCTTAAGG
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1219661 original size:26 final size:27
Alignment explanation
Indices: 1219632--1219686 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1219622 AGTTTTAAAC
* **
1219632 TTTGAT-TTTAAATTTTAATTGTATGA
1 TTTGATCTATAAATTTTAACGGTATGA
1219658 TTTGATCTATAAATTTTAACGGTATGA
1 TTTGATCTATAAATTTTAACGGTATGA
1219685 TT
1 TT
1219687 ATGTAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.53
Consensus pattern (27 bp):
TTTGATCTATAAATTTTAACGGTATGA
Found at i:1219696 original size:27 final size:27
Alignment explanation
Indices: 1219640--1219702 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
1219630 ACTTTGATTT
** **
1219640 TAAATTTTAATTGTATGATTTGATCTA
1 TAAATTTTAACGGTATGATTTGATAAA
1219667 TAAATTTTAACGGTATGATTATG-TAAA
1 TAAATTTTAACGGTATGATT-TGATAAA
1219694 TAAAATTTT
1 T-AAATTTT
1219703 TCATCGTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (27 bp):
TAAATTTTAACGGTATGATTTGATAAA
Found at i:1221590 original size:29 final size:29
Alignment explanation
Indices: 1221548--1221603 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
1221538 CAGTGGCAAC
1221548 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1221577 ATAGGTCGCCATGCACGCCCGGCGTCC
1 ATAGGTCGCCATGCACGCCCGGCGTCC
1221604 ATCATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.39, G:0.29, T:0.18
Consensus pattern (29 bp):
ATAGGTCGCCATGCACGCCCGGCGTCCTT
Found at i:1221650 original size:10 final size:10
Alignment explanation
Indices: 1221632--1221718 Score: 52
Period size: 10 Copynumber: 8.5 Consensus size: 10
1221622 CTTTGGTTCT
*
1221632 TTGCCCGCTG
1 TTGCTCGCTG
1221642 TTGCTCGCTG
1 TTGCTCGCTG
*
1221652 ATGCT-GCTTTG
1 TTGCTCGC--TG
* *
1221663 GTGCCCGCTG
1 TTGCTCGCTG
1221673 TTGCTCGCTG
1 TTGCTCGCTG
*
1221683 ATGCT-GCTTTG
1 TTGCTCGC--TG
* *
1221694 GTGCCCGCTG
1 TTGCTCGCTG
1221704 TTGCTCGCTG
1 TTGCTCGCTG
*
1221714 ATGCT
1 TTGCT
1221719 GCTTTGGTGC
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
9 4 0.07
10 41 0.69
11 10 0.17
12 4 0.07
ACGTcount: A:0.03, C:0.30, G:0.31, T:0.36
Consensus pattern (10 bp):
TTGCTCGCTG
Found at i:1221668 original size:31 final size:31
Alignment explanation
Indices: 1221633--1221728 Score: 192
Period size: 31 Copynumber: 3.1 Consensus size: 31
1221623 TTTGGTTCTT
1221633 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1221664 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1221695 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1221726 TGC
1 TGC
1221729 TATGCATGGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.03, C:0.29, G:0.32, T:0.35
Consensus pattern (31 bp):
TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
Found at i:1221927 original size:29 final size:29
Alignment explanation
Indices: 1221891--1221961 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
1221881 AGGTTGCCGG
*
1221891 CGACATGGTAGGTTGCCATGGAGTCCCGA
1 CGACATGGTAGGTCGCCATGGAGTCCCGA
1221920 CGACATGGTAGGTCGCCATGGAGTCCCGA
1 CGACATGGTAGGTCGCCATGGAGTCCCGA
1221949 CGACATGGTAGGT
1 CGACATGGTAGGT
1221962 GGTAGGGTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.24, G:0.35, T:0.20
Consensus pattern (29 bp):
CGACATGGTAGGTCGCCATGGAGTCCCGA
Found at i:1221972 original size:12 final size:12
Alignment explanation
Indices: 1221955--1221979 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1221945 CCGACGACAT
1221955 GGTAGGTGGTAG
1 GGTAGGTGGTAG
1221967 GGTAGGTGGTAG
1 GGTAGGTGGTAG
1221979 G
1 G
1221980 TCGCCATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.60, T:0.24
Consensus pattern (12 bp):
GGTAGGTGGTAG
Found at i:1222058 original size:35 final size:35
Alignment explanation
Indices: 1222019--1222086 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
1222009 TCCTGCATCG
1222019 CGACCAAGCTTTAACTGTATCACTCATGCATGCAA
1 CGACCAAGCTTTAACTGTATCACTCATGCATGCAA
1222054 CGACCAAGCTTTAACTGTATCACTCATGCATGC
1 CGACCAAGCTTTAACTGTATCACTCATGCATGC
1222087 GTTGCATCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (35 bp):
CGACCAAGCTTTAACTGTATCACTCATGCATGCAA
Found at i:1222537 original size:21 final size:21
Alignment explanation
Indices: 1222512--1222555 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1222502 AATCTAGTTA
*
1222512 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTGGTTAGTATAAATT
* *
1222533 ATTAGTTGGTTAGTTTAAGTT
1 ATTAGTTGGTTAGTATAAATT
1222554 AT
1 AT
1222556 ATATTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (21 bp):
ATTAGTTGGTTAGTATAAATT
Found at i:1223362 original size:26 final size:25
Alignment explanation
Indices: 1223333--1223397 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
1223323 AAATCATATT
*
1223333 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AATAAATATCAAATC
* *
1223359 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATCAAATC
1223385 ATTATT-AATAATA
1 ATTATTAAATAATA
1223398 TTAGTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.29
26 18 0.53
27 3 0.09
28 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAATAAATATCAAATC
Found at i:1226195 original size:19 final size:18
Alignment explanation
Indices: 1226173--1226226 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
1226163 ATCATTATAA
1226173 AAATGATTAATAATGATTT
1 AAATGATT-ATAATGATTT
1226192 AAAT-ATT-TAATGATTT
1 AAATGATTATAATGATTT
*
1226208 -GATGATTTAGTAATGATTT
1 AAATGA-TTA-TAATGATTT
1226227 GATAATAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 2 0.07
16 10 0.33
17 2 0.07
18 3 0.10
19 13 0.43
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (18 bp):
AAATGATTATAATGATTT
Found at i:1226244 original size:26 final size:26
Alignment explanation
Indices: 1226215--1226668 Score: 333
Period size: 26 Copynumber: 18.7 Consensus size: 26
1226205 TTTGATGATT
1226215 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1226241 TAGTAATGATTTG---ATAATCATT-
1 TAGTAATGATTTGATAATAATCATTA
*
1226263 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
1226289 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1226311 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
1226335 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1226361 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1226387 -A-TAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
1226411 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1226433 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
1226457 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1226483 TAGTAATGATTTGATAATAATCA-T-
1 TAGTAATGATTTGATAATAATCATTA
1226507 TA-TAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
**
1226532 TAAAAATGATTT-ATAATTAA--A-TA
1 TAGTAATGATTTGATAA-TAATCATTA
* *
1226555 T-TTAATGATTTG------ATGATT-
1 TAGTAATGATTTGATAATAATCATTA
1226573 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1226599 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
1226625 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
1226651 TAAAAATGATTTAATAAT
1 TAGTAATGATTTGATAAT
1226669 GATTTAAATA
Statistics
Matches: 359, Mismatches: 24, Indels: 90
0.76 0.05 0.19
Matches are distributed among these distances:
16 1 0.00
18 2 0.01
19 13 0.04
20 10 0.03
22 26 0.07
23 53 0.15
24 43 0.12
25 39 0.11
26 159 0.44
27 13 0.04
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:1226671 original size:11 final size:11
Alignment explanation
Indices: 1226209--1226800 Score: 132
Period size: 11 Copynumber: 49.2 Consensus size: 11
1226199 TAATGATTTG
*
1226209 ATGATTTAGTA
1 ATGATTTAATA
1226220 ATGATTTGATAATA
1 ATGA-TT--TAATA
* *
1226234 ATCATTATAGTA
1 ATGATT-TAATA
*
1226246 ATGATTTGATA
1 ATGATTTAATA
*
1226257 ATCATTTAATA
1 ATGATTTAATA
1226268 ATGATTTAGTAATA
1 ATGA-TT--TAATA
* *
1226282 ATCATTATAAAA
1 ATGATT-TAATA
1226294 ATGATTTAATA
1 ATGATTTAATA
1226305 ATGATTT-A-A
1 ATGATTTAATA
1226314 AT-ATTTAATGA
1 ATGATTTAAT-A
*
1226325 TTTGATGATTTAGTA
1 ----ATGATTTAATA
1226340 ATGATTTGATAATA
1 ATGA-TT--TAATA
* *
1226354 ATCATTATAGTA
1 ATGATT-TAATA
*
1226366 ATGATTTGATA
1 ATGATTTAATA
*
1226377 ATAATCATTAATA
1 ATGAT--TTAATA
1226390 ATGATTTAGTAATA
1 ATGA-TT--TAATA
* *
1226404 ATCATTATAAAA
1 ATGATT-TAATA
1226416 ATGATTTAATA
1 ATGATTTAATA
1226427 ATGATTT-A-A
1 ATGATTTAATA
1226436 AT-ATTTAATGA
1 ATGATTTAAT-A
*
1226447 TTTGATGATTTAGTA
1 ----ATGATTTAATA
1226462 ATGATTTGATAATA
1 ATGA-TT--TAATA
* *
1226476 ATCATTATAGTA
1 ATGATT-TAATA
*
1226488 ATGATTTGATA
1 ATGATTTAATA
*
1226499 ATAATCATT-ATA
1 ATGAT--TTAATA
1226511 ATGATTTAGTAATA
1 ATGA-TT--TAATA
* *
1226525 ATCATTATAAAA
1 ATGATT-TAATA
1226537 ATGATTT-ATA
1 ATGATTTAATA
* ** *
1226547 ATTAAATATTTA
1 ATGATTTA-ATA
*
1226559 ATGA-TT--TG
1 ATGATTTAATA
*
1226567 ATGATTTAGTA
1 ATGATTTAATA
1226578 ATGATTTGATAATA
1 ATGA-TT--TAATA
* *
1226592 ATCATTATAGTA
1 ATGATT-TAATA
1226604 ATGATTTGATAATA
1 ATGA-TT--TAATA
*
1226618 ATCATTATAATA
1 ATGATT-TAATA
1226630 ATGATTTAGTAATA
1 ATGA-TT--TAATA
* *
1226644 ATCATTATAAAA
1 ATGATT-TAATA
1226656 ATGATTTAATA
1 ATGATTTAATA
1226667 ATGATTT-A-A
1 ATGATTTAATA
1226676 AT-ATTTAATGA
1 ATGATTTAAT-A
*
1226687 TTTGATGATTTAGTA
1 ----ATGATTTAATA
*
1226702 ATGATTTGATA
1 ATGATTTAATA
*
1226713 ATCATTATAATA
1 ATGATT-TAATA
1226725 ATGATTTTATAATA
1 ATGA--TT-TAATA
* * *
1226739 ATTATTTAGTT
1 ATGATTTAATA
* *
1226750 ATTATTTAGTA
1 ATGATTTAATA
*
1226761 ATTATTTATAATA
1 ATGA-TT-TAATA
1226774 ATGATTTAATACTA
1 ATGATTT-A-A-TA
1226788 ATGATTTAATA
1 ATGATTTAATA
1226799 AT
1 AT
1226801 TATTACTAAT
Statistics
Matches: 438, Mismatches: 76, Indels: 134
0.68 0.12 0.21
Matches are distributed among these distances:
8 17 0.04
9 14 0.03
10 9 0.02
11 121 0.28
12 120 0.27
13 43 0.10
14 87 0.20
15 9 0.02
16 18 0.04
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (11 bp):
ATGATTTAATA
Found at i:1226674 original size:116 final size:114
Alignment explanation
Indices: 1226426--1226784 Score: 457
Period size: 116 Copynumber: 3.1 Consensus size: 114
1226416 ATGATTTAAT
1226426 AATGATTT-A-AATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
1 AATGATTTAATAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
1226489 TGATTTGATAATAATCA-TT-ATAATGATTTAGTAATAATCATTATAAA
66 TGATTTGATAATAATCATTTAATAATGATTTAGTAATAATCATTATAAA
1226536 AATGATTTATAATTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATA
1 AATGA-TT-TAA-T-AATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATA
1226601 GTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAA
62 GTAATGATTTGATAATAATCATT-TAATAATGATTTAGTAATAATCATTATAAA
1226655 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTG---ATAATCA
1 AATGA-TT--T-A--A--T-AATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
* * * * * * * *
1226717 TTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTAT--TTATAAT
57 TTATAGTAATGATTTGATAATAATCATTTAATAATGATTTAGTAATAATCATTATAAA
1226773 AATGATTTAATA
1 AATGATTTAATA
1226785 CTAATGATTT
Statistics
Matches: 227, Mismatches: 8, Indels: 29
0.86 0.03 0.11
Matches are distributed among these distances:
109 1 0.00
110 6 0.03
111 2 0.01
112 2 0.01
113 1 0.00
114 1 0.00
115 1 0.00
116 71 0.31
117 3 0.01
118 12 0.05
119 36 0.16
120 19 0.08
121 33 0.15
123 1 0.00
124 38 0.17
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (114 bp):
AATGATTTAATAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
TGATTTGATAATAATCATTTAATAATGATTTAGTAATAATCATTATAAA
Found at i:1226683 original size:19 final size:20
Alignment explanation
Indices: 1226654--1226731 Score: 67
Period size: 23 Copynumber: 4.0 Consensus size: 20
1226644 ATCATTATAA
1226654 AAATGATTTAATAATGATTT
1 AAATGATTTAATAATGATTT
1226674 AAAT-A-TT--TAATGATTT
1 AAATGATTTAATAATGATTT
* *
1226690 -GATGATTTAGTAATGATTT
1 AAATGATTTAATAATGATTT
*
1226709 GATAATCATTATAATAATGATTT
1 -A-AATGATT-TAATAATGATTT
1226732 TATAATAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
15 2 0.04
16 10 0.22
17 2 0.04
18 2 0.04
19 10 0.22
20 4 0.09
22 5 0.11
23 11 0.24
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (20 bp):
AAATGATTTAATAATGATTT
Found at i:1226791 original size:14 final size:14
Alignment explanation
Indices: 1226719--1226800 Score: 61
Period size: 14 Copynumber: 6.4 Consensus size: 14
1226709 GATAATCATT
*
1226719 ATAATAATGATTTT
1 ATAATAATGATTTA
*
1226733 ATAATAATTATTTA
1 ATAATAATGATTTA
* *
1226747 GT--T-ATTATTTA
1 ATAATAATGATTTA
*
1226758 GTAAT--T-ATTT-
1 ATAATAATGATTTA
1226768 ATAATAATGATTTA
1 ATAATAATGATTTA
*
1226782 ATACTAATGATTTA
1 ATAATAATGATTTA
1226796 ATAAT
1 ATAAT
1226801 TATTACTAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
10 4 0.07
11 14 0.25
12 3 0.05
13 5 0.09
14 30 0.54
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (14 bp):
ATAATAATGATTTA
Found at i:1226823 original size:38 final size:38
Alignment explanation
Indices: 1226753--1226826 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1226743 TTTAGTTATT
* **
1226753 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
1226791 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
1226827 CAAATGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:1227031 original size:17 final size:17
Alignment explanation
Indices: 1227006--1227038 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1226996 ACTAAATATT
*
1227006 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
1227023 TAATGATTTGATACTA
1 TAATGATTTGATACTA
1227039 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:1227031 original size:25 final size:24
Alignment explanation
Indices: 1226958--1227031 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
1226948 ATTGTTAATA
1226958 TTAATTATTTGATAC--TAATGAT
1 TTAATTATTTGATACTATAATGAT
* *
1226980 TTAAAATAGTTGATTTACTA-AAT-AT
1 TT-AATTATTTGA--TACTATAATGAT
1227005 TTAATTATTTGATACTAGTAATGAT
1 TTAATTATTTGATACTA-TAATGAT
1227030 TT
1 TT
1227032 GATACTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
22 7 0.17
23 8 0.20
24 11 0.28
25 11 0.28
26 3 0.08
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (24 bp):
TTAATTATTTGATACTATAATGAT
Found at i:1229185 original size:12 final size:13
Alignment explanation
Indices: 1229168--1229197 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1229158 CACTAAACTT
1229168 TAATATAAT-AAC
1 TAATATAATAAAC
1229180 TAATATAATAAAC
1 TAATATAATAAAC
1229193 TAATA
1 TAATA
1229198 AACTAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (13 bp):
TAATATAATAAAC
Found at i:1229533 original size:21 final size:22
Alignment explanation
Indices: 1229507--1229547 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1229497 TTTTTTATGT
*
1229507 ATATAA-CTTAAACTAACAATC
1 ATATAACCCTAAACTAACAATC
1229528 ATATAACCCTAAACTAACAA
1 ATATAACCCTAAACTAACAA
1229548 ACTAATTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (22 bp):
ATATAACCCTAAACTAACAATC
Found at i:1229701 original size:19 final size:20
Alignment explanation
Indices: 1229654--1229703 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1229644 CTCCCTTTCT
*
1229654 TTCTTACTTTCCTTTCTCCC
1 TTCTTTCTTTCCTTTCTCCC
1229674 TTCTTTCTTTCCTTTCTCCC
1 TTCTTTCTTTCCTTTCTCCC
1229694 TT-TTTCTTTC
1 TTCTTTCTTTC
1229704 TCGGCTGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (20 bp):
TTCTTTCTTTCCTTTCTCCC
Found at i:1229736 original size:23 final size:23
Alignment explanation
Indices: 1229708--1229753 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1229698 TCTTTCTCGG
1229708 CTGCAATCTCTTCTAACTTTCTT
1 CTGCAATCTCTTCTAACTTTCTT
**
1229731 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTAACTTTCTT
1229754 TCTTTCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.35, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTAACTTTCTT
Found at i:1229794 original size:25 final size:26
Alignment explanation
Indices: 1229766--1229818 Score: 99
Period size: 25 Copynumber: 2.1 Consensus size: 26
1229756 TTTCTTTTAT
1229766 AACCGGCTGCCTCAATTA-TTTCACC
1 AACCGGCTGCCTCAATTATTTTCACC
1229791 AACCGGCTGCCTCAATTATTTTCACC
1 AACCGGCTGCCTCAATTATTTTCACC
1229817 AA
1 AA
1229819 TAATTGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.26, C:0.34, G:0.11, T:0.28
Consensus pattern (26 bp):
AACCGGCTGCCTCAATTATTTTCACC
Found at i:1230031 original size:29 final size:29
Alignment explanation
Indices: 1229999--1230105 Score: 171
Period size: 29 Copynumber: 3.7 Consensus size: 29
1229989 GGGAATGGCA
*
1229999 CCGGGACTACATGGCAACCTACAAGGTCG
1 CCGGGACTACATGGCGACCTACAAGGTCG
1230028 CCGGGACTACATGGCGACCTACAAGGTCG
1 CCGGGACTACATGGCGACCTACAAGGTCG
1230057 CCGGGACTACATGGCGACCTACAAGGTCG
1 CCGGGACTACATGGCGACCTACAAGGTCG
* *
1230086 CCTAGG-CTGCATGGCGACCT
1 CC-GGGACTACATGGCGACCT
1230106 CTCTATTCCT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
29 72 0.97
30 2 0.03
ACGTcount: A:0.23, C:0.32, G:0.30, T:0.15
Consensus pattern (29 bp):
CCGGGACTACATGGCGACCTACAAGGTCG
Found at i:1230145 original size:13 final size:13
Alignment explanation
Indices: 1230127--1230152 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1230117 GTATAGGACT
1230127 GCATGGCGACCTC
1 GCATGGCGACCTC
1230140 GCATGGCGACCTC
1 GCATGGCGACCTC
1230153 TCCCCATTGG
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:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GCATGGCGACCTC
Found at i:1230208 original size:11 final size:12
Alignment explanation
Indices: 1230174--1230216 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
1230164 TCGTATGGCT
1230174 CGTATGTCACCC
1 CGTATGTCACCC
1230186 CGTATGTCACCC
1 CGTATGTCACCC
1230198 CGTAT-TCACCC
1 CGTATGTCACCC
1230209 CGTATGTC
1 CGTATGTC
1230217 GCCTGGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.16, C:0.40, G:0.16, T:0.28
Consensus pattern (12 bp):
CGTATGTCACCC
Found at i:1230923 original size:13 final size:14
Alignment explanation
Indices: 1230903--1230943 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
1230893 CACCAAAACC
1230903 ACGAGCAAGCAACG
1 ACGAGCAAGCAACG
1230917 A-GAGCAAGCAACG
1 ACGAGCAAGCAACG
*
1230930 ACGACCAA-CAACG
1 ACGAGCAAGCAACG
1230943 A
1 A
1230944 AAAGAAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.46, C:0.29, G:0.24, T:0.00
Consensus pattern (14 bp):
ACGAGCAAGCAACG
Found at i:1232219 original size:114 final size:113
Alignment explanation
Indices: 1232032--1232250 Score: 305
Period size: 114 Copynumber: 1.9 Consensus size: 113
1232022 TTATTTTAAG
* * * *
1232032 AAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAAA
1 AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACATAAA
* * * *
1232097 AGCTCTTTTCTGATATTTTTGAATAAATAAATATCTTATTATATTAAAAT
66 AGCCCTTTTATGATATTTCTAAATAAATAAAT-T-TTATTATATTAAAAT
* *
1232147 AAAATGTTTTTGATATTTATTTATTTTT-AATATCAAAGAAAAGAGCTGTCTTAAAGCACATAGA
1 AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACATAAA
* *
1232211 CGCCCTTTTATGATATTTCTAAATAAGTAAATTTTATTAT
66 AGCCCTTTTATGATATTTCTAAATAAATAAATTTTATTAT
1232251 GTTATTAATA
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
112 7 0.08
113 1 0.01
114 58 0.63
115 26 0.28
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (113 bp):
AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACATAAA
AGCCCTTTTATGATATTTCTAAATAAATAAATTTTATTATATTAAAAT
Found at i:1236068 original size:22 final size:22
Alignment explanation
Indices: 1236043--1236093 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1236033 CTACGGCGAC
*
1236043 ATCCGTCCCCATTTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
1236065 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
1236087 ATCCGTC
1 ATCCGTC
1236094 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1236234 original size:24 final size:24
Alignment explanation
Indices: 1236207--1236252 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1236197 AAATTTTTGC
1236207 ATTATTAGGTTTTTCATATTGATT
1 ATTATTAGGTTTTTCATATTGATT
1236231 ATTATTAGGTTTTTCATATTGA
1 ATTATTAGGTTTTTCATATTGA
1236253 AATTGATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (24 bp):
ATTATTAGGTTTTTCATATTGATT
Found at i:1236586 original size:20 final size:20
Alignment explanation
Indices: 1236538--1236588 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1236528 CGATTATCTC
**
1236538 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
1236558 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
1236578 GTTGCGATTTT
1 GTTGCGATTTT
1236589 AAGTTTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.14, G:0.24, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:1236595 original size:20 final size:20
Alignment explanation
Indices: 1236552--1236595 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1236542 CGATAGTCAT
* *
1236552 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1236572 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1236592 TTTC
1 TTTC
1236596 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1238608 original size:19 final size:20
Alignment explanation
Indices: 1238570--1238608 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1238560 ACAACGCGAA
* *
1238570 TTTAGTTTCGCGTTGTGATT
1 TTTAGTTTCGCATTGCGATT
1238590 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
1238609 ATCCCGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.54
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:1238661 original size:20 final size:19
Alignment explanation
Indices: 1238615--1238681 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
1238605 GATTATCCCG
*
1238615 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTC-ATTTCGCA
* *
1238635 TTACGATAGTCATTTCCGCT
1 TTGCGATAGTCATTT-CGCA
*
1238655 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCA-TTTCGCA
1238675 TTGCGAT
1 TTGCGAT
1238682 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.08
20 34 0.85
21 3 0.08
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
TTGCGATAGTCATTTCGCA
Found at i:1238691 original size:20 final size:20
Alignment explanation
Indices: 1238668--1238712 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1238658 CGATAGTCAT
*
1238668 TTTCGCGTTGCGATTTTAAG
1 TTTCACGTTGCGATTTTAAG
*
1238688 TTTCATGTTGCGATTTTAAG
1 TTTCACGTTGCGATTTTAAG
1238708 TTTCA
1 TTTCA
1238713 GAAACTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.13, G:0.20, T:0.49
Consensus pattern (20 bp):
TTTCACGTTGCGATTTTAAG
Found at i:1239197 original size:21 final size:22
Alignment explanation
Indices: 1239165--1239283 Score: 86
Period size: 21 Copynumber: 5.6 Consensus size: 22
1239155 GACTCACCTG
*
1239165 TCATCATTCAAGAGGCCTCTCC
1 TCATCGTTCAAGAGGCCTCTCC
* *
1239187 T-ATCGTTCAAGAGGCCCCT-A
1 TCATCGTTCAAGAGGCCTCTCC
** *
1239207 TCATCCCTCAAGAGTCCTCTCC
1 TCATCGTTCAAGAGGCCTCTCC
* * *
1239229 -CACCGTTCAAGAGGCCCCT-G
1 TCATCGTTCAAGAGGCCTCTCC
* *
1239249 TCATCGTTGAAGAGGTCTCTCC
1 TCATCGTTCAAGAGGCCTCTCC
* *
1239271 -CACCATTCAAGAG
1 TCATCGTTCAAGAG
1239284 CCCGATTCAC
Statistics
Matches: 71, Mismatches: 22, Indels: 9
0.70 0.22 0.09
Matches are distributed among these distances:
20 1 0.01
21 69 0.97
22 1 0.01
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (22 bp):
TCATCGTTCAAGAGGCCTCTCC
Found at i:1239226 original size:42 final size:42
Alignment explanation
Indices: 1239172--1239283 Score: 143
Period size: 42 Copynumber: 2.7 Consensus size: 42
1239162 CTGTCATCAT
* *
1239172 TCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGGCCTCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* * **
1239214 TCAAGAGTCCTCTCCCACCGTTCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGCCTCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* * *
1239256 TGAAGAGGTCTCTCCCACCATTCAAGAG
1 TCAAGAGGCCTCTCCCACCGTTCAAGAG
1239284 CCCGATTCAC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
TCAAGAGGCCTCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:1240850 original size:20 final size:20
Alignment explanation
Indices: 1240823--1240886 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
1240813 AACGCTAAAC
1240823 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
*
1240843 TTAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
* *
1240863 CCAAAATCGCAACGCGAAAG
1 TCAAAATCGCAATGCGAAAG
1240883 TCAA
1 TCAA
1240887 TTCGCGTTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (20 bp):
TCAAAATCGCAATGCGAAAG
Found at i:1240950 original size:20 final size:20
Alignment explanation
Indices: 1240925--1241035 Score: 126
Period size: 20 Copynumber: 5.8 Consensus size: 20
1240915 GTGATTTTCT
1240925 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1240945 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1240965 CGTAGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
1240979 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
**
1240999 TATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1241019 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1241036 GAATGTGTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
14 11 0.15
16 1 0.01
18 1 0.01
20 61 0.82
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1240975 original size:54 final size:54
Alignment explanation
Indices: 1240876--1241027 Score: 191
Period size: 54 Copynumber: 2.8 Consensus size: 54
1240866 AAATCGCAAC
* * * * * *
1240876 GCGAAAGTC-AATTCGCGTTGTGATAGTCTAATACGCTTTGTGATTTTCT-CGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGCGTT
*
1240929 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTAGCGATTTTTGCGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
***
1240983 GCGATAGTCAAATTCATATTGCGATAGTCAAATTCGCGTTGCGAT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1241028 ATTCAAATGA
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 9 0.10
54 77 0.90
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (54 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
Found at i:1241032 original size:34 final size:34
Alignment explanation
Indices: 1240927--1241035 Score: 87
Period size: 34 Copynumber: 3.0 Consensus size: 34
1240917 GATTTTCTCG
*
1240927 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAA
1 TTGCGATAGTCAAATTCGCGTTGCGATATTCAAA
** * *
1240961 TTCGCG-TAG-CGATTTTTGCGTTGCGATAGTCAAATTCATA
1 TT-GCGATAGTC-AAATTCGCGTTGCG--A-T---ATTCAAA
1241001 TTGCGATAGTCAAATTCGCGTTGCGATATTCAAA
1 TTGCGATAGTCAAATTCGCGTTGCGATATTCAAA
1241035 T
1 T
1241036 GAATGTGTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 20
0.66 0.11 0.24
Matches are distributed among these distances:
33 1 0.02
34 23 0.41
35 3 0.05
36 1 0.02
37 2 0.04
38 1 0.02
39 3 0.05
40 21 0.38
41 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (34 bp):
TTGCGATAGTCAAATTCGCGTTGCGATATTCAAA
Found at i:1241229 original size:18 final size:18
Alignment explanation
Indices: 1241206--1241240 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1241196 AAGCCGGTTG
1241206 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
1241224 TGATTGCGATTTTGATT
1 TGATTGAGATTTTGATT
1241241 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:1243107 original size:31 final size:31
Alignment explanation
Indices: 1243069--1243193 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
1243059 CCCGAAGGAC
* * *
1243069 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1243100 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1243131 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1243162 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1243193 C
1 C
1243194 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1244019 original size:21 final size:21
Alignment explanation
Indices: 1243995--1244038 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1243985 TGTTGTTCGT
*
1243995 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
1244016 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
1244037 TT
1 TT
1244039 TCCCAGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:1247215 original size:31 final size:31
Alignment explanation
Indices: 1247177--1247301 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
1247167 CCCGAAGGAC
* * *
1247177 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1247208 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1247239 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1247270 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1247301 C
1 C
1247302 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1248138 original size:21 final size:21
Alignment explanation
Indices: 1248108--1248152 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1248098 TGTTGTTTGT
* *
1248108 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1248129 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1248150 TTG
1 TTG
1248153 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1249267 original size:21 final size:21
Alignment explanation
Indices: 1249241--1249285 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1249231 GATTTCTGGG
* *
1249241 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1249262 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1249283 CAA
1 CAA
1249286 ACGATAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1249889 original size:18 final size:18
Alignment explanation
Indices: 1249866--1249900 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1249856 CTAGGAGATT
1249866 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1249884 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1249901 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1249986 original size:21 final size:22
Alignment explanation
Indices: 1249957--1250000 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1249947 GTTGTATGAT
1249957 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
1249978 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
1250000 A
1 A
1250001 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:1251039 original size:149 final size:149
Alignment explanation
Indices: 1250769--1251072 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
1250759 GAGTCGAGGG
1250769 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* * *
1250834 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTTTGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCATTATGGACATCATTA
1250899 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1250918 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1250983 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCATTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCATTATGGACATCATTA
1251048 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1251067 TCTACG
1 TCTACG
1251073 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCATTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1251095 original size:23 final size:23
Alignment explanation
Indices: 1251051--1251095 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1251041 ATCATTATAT
*
1251051 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1251074 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1251096 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1254388 original size:21 final size:21
Alignment explanation
Indices: 1254362--1254406 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1254352 GATTTCTGGG
* *
1254362 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1254383 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1254404 CAA
1 CAA
1254407 ACGACAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1255009 original size:18 final size:18
Alignment explanation
Indices: 1254986--1255020 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1254976 CTAGGAGATT
1254986 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1255004 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1255021 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1255106 original size:21 final size:22
Alignment explanation
Indices: 1255077--1255120 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1255067 GTTGTATGAT
1255077 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
1255098 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
1255120 A
1 A
1255121 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:1256089 original size:149 final size:149
Alignment explanation
Indices: 1255908--1256211 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
1255898 GAGTCGAGGG
1255908 TCTACGCAGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCAGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
1255973 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
1256038 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
1256057 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCAGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1256122 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
1256187 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1256206 TCTACG
1 TCTACG
1256212 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCAGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1256234 original size:23 final size:23
Alignment explanation
Indices: 1256190--1256234 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1256180 ATCATTATAT
*
1256190 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1256213 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1256235 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1258179 original size:14 final size:14
Alignment explanation
Indices: 1258160--1258186 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1258150 TCCCGTGGCA
1258160 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
1258174 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
1258187 TTTCTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1259080 original size:17 final size:17
Alignment explanation
Indices: 1259054--1259091 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1259044 CGGATGGGGA
1259054 AGGATATCGTTGGATAT
1 AGGATATCGTTGGATAT
*
1259071 AGGATGTCGTTGGATAT
1 AGGATATCGTTGGATAT
1259088 AGGA
1 AGGA
1259092 ACGGATGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (17 bp):
AGGATATCGTTGGATAT
Found at i:1259279 original size:21 final size:21
Alignment explanation
Indices: 1259253--1259344 Score: 116
Period size: 21 Copynumber: 4.4 Consensus size: 21
1259243 GATAGTCAGA
1259253 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
1259274 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* * **
1259295 ATCACGTTGCGA--TAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
*
1259315 ATCGCATTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
1259336 ATCGCGTTG
1 ATCGCGTTG
1259345 TGATAGTCAG
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.05
20 11 0.19
21 41 0.71
22 3 0.05
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.41
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:1259319 original size:41 final size:41
Alignment explanation
Indices: 1259274--1259371 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
1259264 ATTTTGTATT
1259274 ATCGCGTTGCGATTTTGTATTATCACGTTGCGATAGTCAGA
1 ATCGCGTTGCGATTTTGTATTATCACGTTGCGATAGTCAGA
* * *
1259315 ATCGCATTGCGATTTTGTATTATCGCGTTGTGATAGTCAGA
1 ATCGCGTTGCGATTTTGTATTATCACGTTGCGATAGTCAGA
1259356 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
1259372 CTAAAATTGC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.39
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCACGTTGCGATAGTCAGA
Found at i:1259467 original size:20 final size:19
Alignment explanation
Indices: 1259444--1259489 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1259434 GGAAACTGAT
* *
1259444 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
1259464 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
1259483 TTGCGAT
1 TTGCGAT
1259490 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:1259479 original size:19 final size:19
Alignment explanation
Indices: 1259455--1259491 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1259445 TGCGATACTG
*
1259455 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1259474 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1259492 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1266582 original size:38 final size:38
Alignment explanation
Indices: 1266531--1266618 Score: 158
Period size: 38 Copynumber: 2.3 Consensus size: 38
1266521 TTCGCACCTC
* *
1266531 TGAATGATTCAGTGCTGATCGATTTAGCAAAACAGTGT
1 TGAATGATTCAGTGCTGATCGATTCAACAAAACAGTGT
1266569 TGAATGATTCAGTGCTGATCGATTCAACAAAACAGTGT
1 TGAATGATTCAGTGCTGATCGATTCAACAAAACAGTGT
1266607 TGAATGATTCAG
1 TGAATGATTCAG
1266619 CATAGAAGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.31
Consensus pattern (38 bp):
TGAATGATTCAGTGCTGATCGATTCAACAAAACAGTGT
Found at i:1276280 original size:21 final size:20
Alignment explanation
Indices: 1276243--1276298 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
1276233 GACATGTGAA
** *
1276243 ATCTATGTCCCTTAGGACCT
1 ATCTATGTCCCGAAGGACAT
1276263 CATCTATGTCCCGAAGGACAT
1 -ATCTATGTCCCGAAGGACAT
*
1276284 ATCACATGTCCCGAA
1 ATC-TATGTCCCGAA
1276299 TGACTTATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 3 0.10
21 27 0.90
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (20 bp):
ATCTATGTCCCGAAGGACAT
Found at i:1281427 original size:21 final size:20
Alignment explanation
Indices: 1281401--1281464 Score: 92
Period size: 21 Copynumber: 3.1 Consensus size: 20
1281391 GGCATGTGAA
*
1281401 ATCTATGTCCCGAATGACCT
1 ATCTATGTCCCGAAAGACCT
1281421 CATCTATGTCCCGAAAGACCT
1 -ATCTATGTCCCGAAAGACCT
*
1281442 ATCATATGTCCCGAAGGACCT
1 ATC-TATGTCCCGAAAGACCT
1281463 AT
1 AT
1281465 GTAACCCTCG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 3 0.08
21 37 0.93
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.27
Consensus pattern (20 bp):
ATCTATGTCCCGAAAGACCT
Found at i:1285091 original size:27 final size:27
Alignment explanation
Indices: 1285061--1285116 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1285051 TCTTAAGGGT
1285061 AATGGTAGAATTTGATTGCTTTGGAGA
1 AATGGTAGAATTTGATTGCTTTGGAGA
1285088 AATGGTAGAATTTGATTGCTTTGGAGA
1 AATGGTAGAATTTGATTGCTTTGGAGA
1285115 AA
1 AA
1285117 GGGGTTGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.36
Consensus pattern (27 bp):
AATGGTAGAATTTGATTGCTTTGGAGA
Found at i:1285440 original size:32 final size:33
Alignment explanation
Indices: 1285376--1285442 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 33
1285366 GGAGGATCTC
** *
1285376 CAGAACTGTATGACTGGAGTCGGATTGATTGAT
1 CAGAACTGTATGACTGGAGTAAGAGTGATTGAT
* *
1285409 CAGAACT-TATGACTGGATTAAGAGTGGTTGAT
1 CAGAACTGTATGACTGGAGTAAGAGTGATTGAT
1285441 CA
1 CA
1285443 TTCATATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 22 0.76
33 7 0.24
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (33 bp):
CAGAACTGTATGACTGGAGTAAGAGTGATTGAT
Found at i:1285491 original size:77 final size:78
Alignment explanation
Indices: 1285397--1285549 Score: 254
Period size: 78 Copynumber: 2.0 Consensus size: 78
1285387 GACTGGAGTC
*
1285397 GGATTGATTGATCAGAACT-TATGACTGGATTAAGAGTGGTTGATCATTCATATATTGAACCTGT
1 GGATTGATTGATCAGAACTGTATGACTGGACTAAGAGTGGTTGATCATTCATATATTGAACCTGT
1285461 GTTTACTTGGTTT
66 GTTTACTTGGTTT
* * * *
1285474 GGATTGGTTGATCAGAACTGTATGATTTGACTAAGATTGGTTGATCATTCATATATTGAACCTGT
1 GGATTGATTGATCAGAACTGTATGACTGGACTAAGAGTGGTTGATCATTCATATATTGAACCTGT
1285539 GTTTACTTGGT
66 GTTTACTTGGT
1285550 CTAATAAGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
77 18 0.26
78 52 0.74
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (78 bp):
GGATTGATTGATCAGAACTGTATGACTGGACTAAGAGTGGTTGATCATTCATATATTGAACCTGT
GTTTACTTGGTTT
Found at i:1285670 original size:137 final size:137
Alignment explanation
Indices: 1285424--1285700 Score: 464
Period size: 137 Copynumber: 2.0 Consensus size: 137
1285414 CTTATGACTG
*
1285424 GATTAAGAGTGGTTGATCATTCATATATTGAACCTGTGTTTACTTGGTTTGGATTGGTTGATCAG
1 GATTAAGAGTGGTTGATCATTCATATACTGAACCTGTGTTTACTTGGTTTGGATTGGTTGATCAG
*
1285489 AACTGTATGATTTGACTAAGATTGGTTGATCATTCATATATTGAACCTGTGTTTACTTGGTCTAA
66 AACTGTATGATTGGACTAAGATTGGTTGATCATTCATATATTGAACCTGTGTTTACTTGGTCTAA
1285554 TAAGCAA
131 TAAGCAA
* *
1285561 GATTAAGATTGGTTGATCATTCATATACTGAACTTGTGTTTACTTGGTTTGGATTGGTTGATCAG
1 GATTAAGAGTGGTTGATCATTCATATACTGAACCTGTGTTTACTTGGTTTGGATTGGTTGATCAG
** * * *
1285626 AACTGTATGATTGGGTTAATATTGGTTTATTATTCATATATTGAACCTGTGTTTACTTGGTCTAA
66 AACTGTATGATTGGACTAAGATTGGTTGATCATTCATATATTGAACCTGTGTTTACTTGGTCTAA
*
1285691 TAAGTAA
131 TAAGCAA
1285698 GAT
1 GAT
1285701 GGTTGTTTCT
Statistics
Matches: 130, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
137 130 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.42
Consensus pattern (137 bp):
GATTAAGAGTGGTTGATCATTCATATACTGAACCTGTGTTTACTTGGTTTGGATTGGTTGATCAG
AACTGTATGATTGGACTAAGATTGGTTGATCATTCATATATTGAACCTGTGTTTACTTGGTCTAA
TAAGCAA
Found at i:1285768 original size:17 final size:16
Alignment explanation
Indices: 1285746--1285780 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1285736 GGATGGATGG
1285746 TTCCTTGCTAGGAACGT
1 TTCCTTGCTAGGAA-GT
*
1285763 TTCCTTGCTGGGAAGT
1 TTCCTTGCTAGGAAGT
1285779 TT
1 TT
1285781 GGACCTAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.14, C:0.20, G:0.26, T:0.40
Consensus pattern (16 bp):
TTCCTTGCTAGGAAGT
Found at i:1289311 original size:18 final size:19
Alignment explanation
Indices: 1289288--1289325 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1289278 TGAGGGCAGA
1289288 AATTTTATAG-GTT-ATTGT
1 AATTTT-TAGAGTTAATTGT
1289306 AATTTTTAGAGTTAATTGT
1 AATTTTTAGAGTTAATTGT
1289325 A
1 A
1289326 CTATATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.17
18 9 0.50
19 6 0.33
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (19 bp):
AATTTTTAGAGTTAATTGT
Found at i:1289774 original size:59 final size:60
Alignment explanation
Indices: 1289678--1289807 Score: 185
Period size: 59 Copynumber: 2.2 Consensus size: 60
1289668 TAGAATGAAG
* * *
1289678 GTTATATTTTGGGGGTGAATTTGAAAATGTTCAATAGTTTAAGGATTAATGT-AAAATAAGA
1 GTTATAGTTT-GGGGTGAAATTGAAAATGTTCAATAGTTTAAGGAATAAT-TCAAAATAAGA
1289739 -TTCATAGTTTGGGGTGAAATTG-AAATGTTCAATAGTTTAAGGAATAATTCAAAATAAGA
1 GTT-ATAGTTTGGGGTGAAATTGAAAATGTTCAATAGTTTAAGGAATAATTCAAAATAAGA
1289798 GTTATAGTTT
1 GTTATAGTTT
1289808 AGGAACATAT
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
58 1 0.02
59 41 0.65
60 15 0.24
61 6 0.10
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (60 bp):
GTTATAGTTTGGGGTGAAATTGAAAATGTTCAATAGTTTAAGGAATAATTCAAAATAAGA
Found at i:1289787 original size:28 final size:28
Alignment explanation
Indices: 1289701--1289793 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 28
1289691 GGTGAATTTG
*
1289701 AAAATGTTCAATAGTTTAAGGATTAATGT
1 AAAATGTTCAATAGTTTAAGGAATAAT-T
** *
1289730 AAAATAAGATTC-ATAGTTTGGGGTGA-AATT
1 AAAAT--G-TTCAATAGTTTAAGG-AATAATT
*
1289760 GAAATGTTCAATAGTTTAAGGAATAATT
1 AAAATGTTCAATAGTTTAAGGAATAATT
1289788 CAAAAT
1 -AAAAT
1289794 AAGAGTTATA
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
27 4 0.08
28 14 0.29
29 9 0.19
30 5 0.10
31 13 0.27
32 3 0.06
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.34
Consensus pattern (28 bp):
AAAATGTTCAATAGTTTAAGGAATAATT
Found at i:1292057 original size:30 final size:30
Alignment explanation
Indices: 1292021--1292087 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
1292011 TGATAGGAGA
1292021 CCTGTGGGGCCTGAAGAGTGTGTTGCGGAT
1 CCTGTGGGGCCTGAAGAGTGTGTTGCGGAT
1292051 CCTGTGGGGCCTGAAGAGTGTGTTGCGGAT
1 CCTGTGGGGCCTGAAGAGTGTGTTGCGGAT
1292081 CCTGTGG
1 CCTGTGG
1292088 ATTTTGAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.12, C:0.18, G:0.43, T:0.27
Consensus pattern (30 bp):
CCTGTGGGGCCTGAAGAGTGTGTTGCGGAT
Found at i:1292932 original size:19 final size:19
Alignment explanation
Indices: 1292891--1292952 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
1292881 GAAAATAATG
**
1292891 TAACAAAAAAAAAGAAAATAA
1 TAACAAAAACTAA-AAAA-AA
*
1292912 TAA-AAGAAAGTAAAAAAAA
1 TAACAA-AAACTAAAAAAAA
1292931 TAACAAAAACTAAAAATAAA
1 TAACAAAAACTAAAAA-AAA
1292951 TA
1 TA
1292953 TTGAAAGTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 14 0.40
20 13 0.37
21 8 0.23
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (19 bp):
TAACAAAAACTAAAAAAAA
Found at i:1298459 original size:13 final size:13
Alignment explanation
Indices: 1298441--1298470 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1298431 TGACTTTTTG
1298441 TCAAAGTCAACGA
1 TCAAAGTCAACGA
*
1298454 TCAAAGTCAACGG
1 TCAAAGTCAACGA
1298467 TCAA
1 TCAA
1298471 CAGGAAAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (13 bp):
TCAAAGTCAACGA
Found at i:1298520 original size:18 final size:18
Alignment explanation
Indices: 1298475--1298520 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1298465 GGTCAACAGG
* *
1298475 AAAGTCAACAATTAGGTC
1 AAAGTCAACGATTAAGTC
1298493 AAAGTCAACGATTAAGTC
1 AAAGTCAACGATTAAGTC
1298511 AAAGTCAACG
1 AAAGTCAACG
1298521 GGTCAGACCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (18 bp):
AAAGTCAACGATTAAGTC
Found at i:1306171 original size:21 final size:21
Alignment explanation
Indices: 1306145--1306196 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1306135 ACGTCACACT
1306145 TCAACACCGTGGATCGCCACG
1 TCAACACCGTGGATCGCCACG
* *
1306166 TCAACACCGTGGATCGCTATG
1 TCAACACCGTGGATCGCCACG
*
1306187 TTAACACCGT
1 TCAACACCGT
1306197 AACGATCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.21
Consensus pattern (21 bp):
TCAACACCGTGGATCGCCACG
Found at i:1307090 original size:18 final size:19
Alignment explanation
Indices: 1307053--1307090 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1307043 AGTAATTATT
*
1307053 TTATTATTTTATTTAGAAA
1 TTATTATTTTATTTACAAA
*
1307072 TTATT-TTTTATTTCCAAA
1 TTATTATTTTATTTACAAA
1307090 T
1 T
1307091 AAAGTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (19 bp):
TTATTATTTTATTTACAAA
Found at i:1307514 original size:13 final size:14
Alignment explanation
Indices: 1307498--1307529 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1307488 TTATCCTTTT
1307498 AATATTTAA-TAAA
1 AATATTTAATTAAA
1307511 AATATTTAATTAAA
1 AATATTTAATTAAA
1307525 AATAT
1 AATAT
1307530 ATTTTGTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATTTAATTAAA
Found at i:1315958 original size:24 final size:25
Alignment explanation
Indices: 1315931--1315977 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1315921 TTCATGTGAC
1315931 TAAATACAAAAA-T-AAATTTATTAT
1 TAAATA-AAAAATTAAAATTTATTAT
1315955 TAAATAAAAAATTAAAATTTATT
1 TAAATAAAAAATTAAAATTTATT
1315978 CTATTTTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 7 0.33
25 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAATAAAAAATTAAAATTTATTAT
Found at i:1321776 original size:16 final size:16
Alignment explanation
Indices: 1321755--1321804 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
1321745 TGGGGTTAGA
1321755 TTGGGCTTCCCATGAG
1 TTGGGCTTCCCATGAG
1321771 TTGGGC-T---A-GA-
1 TTGGGCTTCCCATGAG
1321781 TTGGGCTTCCCATGAG
1 TTGGGCTTCCCATGAG
1321797 TTGGGCTT
1 TTGGGCTT
1321805 GAGCCCAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
10 6 0.21
11 3 0.11
12 1 0.04
14 1 0.04
15 3 0.11
16 14 0.50
ACGTcount: A:0.12, C:0.20, G:0.34, T:0.34
Consensus pattern (16 bp):
TTGGGCTTCCCATGAG
Found at i:1321781 original size:26 final size:26
Alignment explanation
Indices: 1321751--1321803 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1321741 TGTTTGGGGT
1321751 TAGATTGGGCTTCCCATGAGTTGGGC
1 TAGATTGGGCTTCCCATGAGTTGGGC
1321777 TAGATTGGGCTTCCCATGAGTTGGGC
1 TAGATTGGGCTTCCCATGAGTTGGGC
1321803 T
1 T
1321804 TGAGCCCAAC
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:0.15, C:0.19, G:0.34, T:0.32
Consensus pattern (26 bp):
TAGATTGGGCTTCCCATGAGTTGGGC
Found at i:1324453 original size:19 final size:19
Alignment explanation
Indices: 1324429--1324478 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1324419 ATGCAATTAG
1324429 TGCATCGATGCATAAGGAA
1 TGCATCGATGCATAAGGAA
* *
1324448 TGCATCGATGCATATGGAG
1 TGCATCGATGCATAAGGAA
1324467 TGCATCGATGCA
1 TGCATCGATGCA
1324479 CCCCCTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAA
Found at i:1331579 original size:23 final size:23
Alignment explanation
Indices: 1331530--1331580 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1331520 GTGTTATATT
**
1331530 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
1331553 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
1331576 ATATT
1 ATATT
1331581 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1331592 original size:19 final size:19
Alignment explanation
Indices: 1331568--1331638 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
1331558 TTAAATATCT
*
1331568 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTAAA
* * *
1331587 TTATTAGATTAATATTAAA
1 TTATTAAAATATTATTAAA
* *
1331606 TATATAAATAATATTATT-CA
1 T-TATTAA-AATATTATTAAA
1331626 TTATTAAATATAT
1 TTATTAAA-ATAT
1331639 AAAAAATTTA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 1 0.03
19 25 0.64
20 6 0.15
21 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (19 bp):
TTATTAAAATATTATTAAA
Found at i:1331692 original size:8 final size:8
Alignment explanation
Indices: 1331681--1331746 Score: 50
Period size: 8 Copynumber: 8.6 Consensus size: 8
1331671 ATATAATATC
1331681 TTATATTA
1 TTATATTA
*
1331689 TTATAATA
1 TTATATTA
1331697 -TA-ATTGA
1 TTATATT-A
*
1331704 TTATTTTA
1 TTATATTA
*
1331712 TTATAATA
1 TTATATTA
*
1331720 TTA-A-AA
1 TTATATTA
*
1331726 ATATATTA
1 TTATATTA
1331734 TTATATTA
1 TTATATTA
1331742 TTATA
1 TTATA
1331747 AATATTAATA
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
6 5 0.11
7 5 0.11
8 32 0.73
9 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (8 bp):
TTATATTA
Found at i:1331722 original size:31 final size:31
Alignment explanation
Indices: 1331681--1331764 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
1331671 ATATAATATC
* *
1331681 TTATATTATTATAATATA-ATTGATTATTTTA
1 TTATAATATTATAATATATATT-ATTATATTA
*
1331712 TTATAATATTA-AAAATATATTATTATATTA
1 TTATAATATTATAATATATATTATTATATTA
1331742 TTATAAATATTAATAA-ATATATT
1 TTAT-AATATT-ATAATATATATT
1331765 TTAAATATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
30 17 0.37
31 19 0.41
32 8 0.17
33 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (31 bp):
TTATAATATTATAATATATATTATTATATTA
Found at i:1331743 original size:30 final size:33
Alignment explanation
Indices: 1331683--1331764 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 33
1331673 ATAATATCTT
* *
1331683 ATATTATTATAATATAATTGATTATTTTATTAT-A
1 ATATTAATA-AATAT-ATTGATTATATTATTATAA
1331717 ATATTAA-AAATATATT-ATTATATTATTATAA
1 ATATTAATAAATATATTGATTATATTATTATAA
1331748 ATATTAATAAATATATT
1 ATATTAATAAATATATT
1331765 TTAAATATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
30 12 0.27
31 11 0.25
32 14 0.32
33 1 0.02
34 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (33 bp):
ATATTAATAAATATATTGATTATATTATTATAA
Found at i:1331761 original size:22 final size:22
Alignment explanation
Indices: 1331717--1331779 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
1331707 TTTTATTATA
* * *
1331717 ATATTAAAAATATATTATTATAT
1 ATATTATAAATAT-TTAATAAAT
1331740 -TATTATAAATA-TTAATAAAT
1 ATATTATAAATATTTAATAAAT
*
1331760 ATATTTTAAATATTTAATAA
1 ATATTATAAATATTTAATAA
1331780 TTAATATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 7 0.21
21 10 0.29
22 17 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATTATAAATATTTAATAAAT
Found at i:1331769 original size:21 final size:23
Alignment explanation
Indices: 1331740--1331789 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
1331730 ATTATTATAT
*
1331740 TATTATAAATA-TTAATAAAT-A
1 TATTTTAAATATTTAATAAATAA
*
1331761 TATTTTAAATATTTAATAATTAA
1 TATTTTAAATATTTAATAAATAA
1331784 TATTTT
1 TATTTT
1331790 GAAGAAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 8 0.32
23 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTTTAAATATTTAATAAATAA
Found at i:1332027 original size:42 final size:42
Alignment explanation
Indices: 1331971--1332065 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
1331961 TTCCTCCAAC
*
1331971 CAAACACTG-GAAAACATTTTCCGAAAAACGAATTACGTGAAA
1 CAAACAC-GAGAAAACATTTTCCAAAAAACGAATTACGTGAAA
**
1332013 CAAACACGAGAAAACATTTTTTAAAAAACGAATTACGTGAAA
1 CAAACACGAGAAAACATTTTCCAAAAAACGAATTACGTGAAA
1332055 CAAACACGAGA
1 CAAACACGAGA
1332066 TTTCGGAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
41 1 0.02
42 48 0.98
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.18
Consensus pattern (42 bp):
CAAACACGAGAAAACATTTTCCAAAAAACGAATTACGTGAAA
Found at i:1332078 original size:37 final size:38
Alignment explanation
Indices: 1331994--1332089 Score: 95
Period size: 42 Copynumber: 2.4 Consensus size: 38
1331984 ACATTTTCCG
***
1331994 AAAAACGAATTACGTGAAACAAACACGAGAAAACATTTTTTA
1 AAAAACGAATTACGTGAAACAAACACGAG---A-ATTTCGGA
1332036 AAAAACGAATTACGTGAAACAAACACGAG-ATTTCGGA
1 AAAAACGAATTACGTGAAACAAACACGAGAATTTCGGA
* * *
1332073 GAAAACCAATTCCGTGA
1 AAAAACGAATTACGTGA
1332090 TTCATTTTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
37 19 0.40
42 29 0.60
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.19
Consensus pattern (38 bp):
AAAAACGAATTACGTGAAACAAACACGAGAATTTCGGA
Found at i:1333700 original size:18 final size:18
Alignment explanation
Indices: 1333677--1333713 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1333667 AGAGAAAGGA
1333677 CTAGGGATGGCAAACGGG
1 CTAGGGATGGCAAACGGG
1333695 CTAGGGATGGCAAACGGG
1 CTAGGGATGGCAAACGGG
1333713 C
1 C
1333714 GGGTCGGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.19, G:0.43, T:0.11
Consensus pattern (18 bp):
CTAGGGATGGCAAACGGG
Found at i:1334882 original size:18 final size:19
Alignment explanation
Indices: 1334832--1334882 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
1334822 TTAAATTGGT
*
1334832 TCGAAATTGATT-AATTAA
1 TCGAAATTAATTAAATTAA
* *
1334850 CCG-AATTAATCAAATTAA
1 TCGAAATTAATTAAATTAA
1334868 TCGAAATT-ATTAAAT
1 TCGAAATTAATTAAAT
1334883 ATTTAATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 6 0.23
18 16 0.62
19 4 0.15
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (19 bp):
TCGAAATTAATTAAATTAA
Found at i:1334895 original size:2 final size:2
Alignment explanation
Indices: 1334888--1334922 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1334878 TAAATATTTA
1334888 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 A
1334923 GCTTTAGGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1336596 original size:25 final size:25
Alignment explanation
Indices: 1336562--1336620 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
1336552 TATTGATACT
1336562 TCCTAAATCCAACT-TTGGAAAAAGA
1 TCCTAAATCCAA-TGTTGGAAAAAGA
*
1336587 TCCTAAATCCAATGTTGGAAAAAGT
1 TCCTAAATCCAATGTTGGAAAAAGA
1336612 TCCTAAATC
1 TCCTAAATC
1336621 TGAAATCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 1 0.03
25 31 0.97
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (25 bp):
TCCTAAATCCAATGTTGGAAAAAGA
Found at i:1338102 original size:10 final size:10
Alignment explanation
Indices: 1338089--1338137 Score: 55
Period size: 10 Copynumber: 4.7 Consensus size: 10
1338079 TCCATTTTTT
*
1338089 ACCAAATCAA
1 ACCAAATAAA
1338099 ACCATTAAATAAA
1 ACCA--AA-TAAA
1338112 ACCAAATAAA
1 ACCAAATAAA
1338122 ACCAAAT-AA
1 ACCAAATAAA
1338131 ACCAAAT
1 ACCAAAT
1338138 GTTGAAATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
9 9 0.26
10 15 0.43
11 2 0.06
12 2 0.06
13 7 0.20
ACGTcount: A:0.63, C:0.22, G:0.00, T:0.14
Consensus pattern (10 bp):
ACCAAATAAA
Found at i:1338134 original size:9 final size:10
Alignment explanation
Indices: 1338105--1338137 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
1338095 TCAAACCATT
1338105 AAATAAAACC
1 AAATAAAACC
1338115 AAATAAAACC
1 AAATAAAACC
1338125 AAAT-AAACC
1 AAATAAAACC
1338134 AAAT
1 AAAT
1338138 GTTGAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.70, C:0.18, G:0.00, T:0.12
Consensus pattern (10 bp):
AAATAAAACC
Found at i:1339905 original size:60 final size:60
Alignment explanation
Indices: 1339841--1339957 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
1339831 GACTATAACA
* * * * *
1339841 TGTTGCTTAGTTGAGCCCATCGGTTGTTAAAAGTTATAAAATGATCCCTTGACTATTGGG
1 TGTTGCTTAGTTGAGCCCATCGATTATTAAAAGTTACAAAATGATCACTCGACTATTGGG
* * * *
1339901 TGTTGCTTTGTTGAGTCCATTGATTATTAAAAGTTACAAAATGTTCACTCGACTATT
1 TGTTGCTTAGTTGAGCCCATCGATTATTAAAAGTTACAAAATGATCACTCGACTATT
1339958 CTTATGTTCC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (60 bp):
TGTTGCTTAGTTGAGCCCATCGATTATTAAAAGTTACAAAATGATCACTCGACTATTGGG
Found at i:1340230 original size:60 final size:59
Alignment explanation
Indices: 1340152--1340288 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 59
1340142 GAACATATAA
* * * * **
1340152 ATAGTCGGGTGGCTATTTTATAACTTTTAATAGTCA-AGGGACTCAACAAAGTAATGCCCT
1 ATAGTCGGG-GACCATTTTATAACTTTTAATAATCAGA-GAACTCAACAAAGTAACACCCT
* * *
1340212 ATAGTCGGAGGATCATTTTGTAACTTTTAATAATCAGAGAACTCAACAAAGTAACATCCT
1 ATAGTCGG-GGACCATTTTATAACTTTTAATAATCAGAGAACTCAACAAAGTAACACCCT
1340272 ATAGTCGGGGACCATTT
1 ATAGTCGGGGACCATTT
1340289 GTACAATTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
59 8 0.12
60 55 0.85
61 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (59 bp):
ATAGTCGGGGACCATTTTATAACTTTTAATAATCAGAGAACTCAACAAAGTAACACCCT
Found at i:1342567 original size:2 final size:2
Alignment explanation
Indices: 1342555--1342623 Score: 129
Period size: 2 Copynumber: 34.0 Consensus size: 2
1342545 TCTACTTTTG
1342555 AT AT CAT 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
1342598 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
1342624 GAGTTTTACA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 64 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1350667 original size:23 final size:23
Alignment explanation
Indices: 1350636--1350693 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
1350626 CATGGACCTG
*
1350636 TAAAAATAAAAAAA-TATTAATAA
1 TAAAAATAAAAAAATTA-TAACAA
* *
1350659 TAATAATAAATAAATTATAACAA
1 TAAAAATAAAAAAATTATAACAA
1350682 TAAAAATAAAAA
1 TAAAAATAAAAA
1350694 CATAAAACCC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 27 0.93
24 2 0.07
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
TAAAAATAAAAAAATTATAACAA
Found at i:1351097 original size:16 final size:16
Alignment explanation
Indices: 1351056--1351111 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
1351046 CAAAAATATT
*
1351056 TCTGAGGGAATTGGAA
1 TCTGAAGGAATTGGAA
1351072 TCTGTGAAGGAATTGGAA
1 TC--TGAAGGAATTGGAA
1351090 TCTGAAGGAATTGGAA
1 TCTGAAGGAATTGGAA
*
1351106 TATGAA
1 TCTGAA
1351112 TCTGAAACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
16 21 0.58
18 15 0.42
ACGTcount: A:0.36, C:0.05, G:0.32, T:0.27
Consensus pattern (16 bp):
TCTGAAGGAATTGGAA
Found at i:1355772 original size:16 final size:16
Alignment explanation
Indices: 1355751--1355802 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 16
1355741 TCCTTAAAAA
1355751 AATAATTTATTATTTT
1 AATAATTTATTATTTT
1355767 AATAA--T-TTATTTT
1 AATAATTTATTATTTT
* *
1355780 AATTATTTATTA-CTT
1 AATAATTTATTATTTT
1355795 AATAATTT
1 AATAATTT
1355803 TTTTATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
13 11 0.37
14 1 0.03
15 10 0.33
16 8 0.27
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
AATAATTTATTATTTT
Found at i:1355776 original size:13 final size:13
Alignment explanation
Indices: 1355760--1355807 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
1355750 AAATAATTTA
1355760 TTATTTTAATAAT
1 TTATTTTAATAAT
*
1355773 TTATTTTAATTAT
1 TTATTTTAATAAT
1355786 TTATTACTTAATAAT
1 TTATT--TTAATAAT
1355801 TT-TTTTA
1 TTATTTTA
1355808 TATATCATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 3 0.10
13 17 0.55
14 2 0.06
15 9 0.29
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATTTTAATAAT
Found at i:1355950 original size:13 final size:13
Alignment explanation
Indices: 1355932--1355962 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1355922 AACAGTTAAA
*
1355932 TTTTAAATCATAC
1 TTTTAAATAATAC
1355945 TTTTAAATAATAC
1 TTTTAAATAATAC
1355958 TTTTA
1 TTTTA
1355963 CAAGTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTAAATAATAC
Found at i:1362004 original size:374 final size:374
Alignment explanation
Indices: 1361315--1362063 Score: 1464
Period size: 374 Copynumber: 2.0 Consensus size: 374
1361305 CTCTTTTAAA
1361315 ATAGAAACATCGAATGCAATTATTGCATCGATGCATAAGGCATGCATCGATGCATCCCAGTGATA
1 ATAGAAACATCGAATGCAATTATTGCATCGATGCATAAGGCATGCATCGATGCATCCCAGTGATA
1361380 ATACAACATCGAATGCATTTTATGCACCGATGCATCAGTAGTGCATCGATGCATACTTTCATTGA
66 ATACAACATCGAATGCATTTTATGCACCGATGCATCAGTAGTGCATCGATGCATACTTTCATTGA
1361445 AAGATGAAATTGGCATTTTTCTTAATCTAAAGAGTGAACCATTAGAGTATATTAGTTATAATACT
131 AAGATGAAATTGGCATTTTTCTTAATCTAAAGAGTGAACCATTAGAGTATATTAGTTATAATACT
1361510 AATATAGATCTATGTATGATTATGTAGATATAGAAAGTGATCCCGTTCTGAATCAATTGAATGAT
196 AATATAGATCTATGTATGATTATGTAGATATAGAAAGTGATCCCGTTCTGAATCAATTGAATGAT
1361575 TAGAATCGAATCAAAGCAAAGCTAAGGTGAGTGCACATTATTTAGTATATGATGTTAAATGGAAA
261 TAGAATCGAATCAAAGCAAAGCTAAGGTGAGTGCACATTATTTAGTATATGATGTTAAATGGAAA
1361640 ATAAGACTTATGATAAGTCTATTTCCAATAGTAAAATGCATGAATTCAT
326 ATAAGACTTATGATAAGTCTATTTCCAATAGTAAAATGCATGAATTCAT
1361689 ATAGAAACATCGAATGCAATTATTGCATCGATGCATAAGGCATGCATCGATGCATCCCAGTGATA
1 ATAGAAACATCGAATGCAATTATTGCATCGATGCATAAGGCATGCATCGATGCATCCCAGTGATA
1361754 ATACAACATCGAATGCATTTTATGCACCGATGCATCAGTAGTGCATCGATGCATACTTTCATTGA
66 ATACAACATCGAATGCATTTTATGCACCGATGCATCAGTAGTGCATCGATGCATACTTTCATTGA
1361819 AAGATGAAATTGGCATTTTTCTTAATCTAAAGAGTGAACCATTAGAGTATATTAGTTATAATACT
131 AAGATGAAATTGGCATTTTTCTTAATCTAAAGAGTGAACCATTAGAGTATATTAGTTATAATACT
* *
1361884 AATATAGATCTATGTATGATTATGTAGATATAGAACA-TGATCTCGTTCTGAATTAATTGAATGA
196 AATATAGATCTATGTATGATTATGTAGATATAGAA-AGTGATCCCGTTCTGAATCAATTGAATGA
1361948 TTAGAATCGAATCAAAGCAAAGCTAAGGTGAGTGCACATTATTTAGTATATGATGTTAAATGGAA
260 TTAGAATCGAATCAAAGCAAAGCTAAGGTGAGTGCACATTATTTAGTATATGATGTTAAATGGAA
1362013 AATAAGACTTATGATAAGTCTATTTCCAATAGTAAAATGCATGAATTCAT
325 AATAAGACTTATGATAAGTCTATTTCCAATAGTAAAATGCATGAATTCAT
1362063 A
1 A
1362064 GAGGTATGTG
Statistics
Matches: 372, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
374 371 1.00
375 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (374 bp):
ATAGAAACATCGAATGCAATTATTGCATCGATGCATAAGGCATGCATCGATGCATCCCAGTGATA
ATACAACATCGAATGCATTTTATGCACCGATGCATCAGTAGTGCATCGATGCATACTTTCATTGA
AAGATGAAATTGGCATTTTTCTTAATCTAAAGAGTGAACCATTAGAGTATATTAGTTATAATACT
AATATAGATCTATGTATGATTATGTAGATATAGAAAGTGATCCCGTTCTGAATCAATTGAATGAT
TAGAATCGAATCAAAGCAAAGCTAAGGTGAGTGCACATTATTTAGTATATGATGTTAAATGGAAA
ATAAGACTTATGATAAGTCTATTTCCAATAGTAAAATGCATGAATTCAT
Found at i:1363019 original size:31 final size:32
Alignment explanation
Indices: 1362966--1363083 Score: 145
Period size: 32 Copynumber: 3.8 Consensus size: 32
1362956 GTTCTACGGA
1362966 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAATTACCTATGTCTTTCGAG
* * *
1362998 ACATATGTACAGTA-TACCTATGT-TCTACG-G
1 ACATATGGACAGAATTACCTATGTCT-TTCGAG
*
1363028 AACATATGGAAAGAATTACCTATGTCTTTCGAG
1 -ACATATGGACAGAATTACCTATGTCTTTCGAG
*
1363061 ACATATGGACAGTA-TACCTATGT
1 ACATATGGACAGAATTACCTATGT
1363084 TCTAAGGAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
30 2 0.03
31 32 0.44
32 36 0.50
33 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (32 bp):
ACATATGGACAGAATTACCTATGTCTTTCGAG
Done.