Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007889.1 Hibiscus syriacus cultivar Beakdansim tig00110271_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: 1663484
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1057694 original size:12 final size:12
Alignment explanation
Indices: 1057677--1057704 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1057667 AGCAAGTAGG
1057677 ACAACGTGGAGA
1 ACAACGTGGAGA
1057689 ACAACGTGGAGA
1 ACAACGTGGAGA
1057701 ACAA
1 ACAA
1057705 TCCCTTAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.18, G:0.29, T:0.07
Consensus pattern (12 bp):
ACAACGTGGAGA
Found at i:1062450 original size:19 final size:20
Alignment explanation
Indices: 1062426--1062467 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1062416 TTGAAGAGTT
1062426 CATTTA-GACCATATAGATG
1 CATTTAGGACCATATAGATG
* *
1062445 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
1062465 CAT
1 CAT
1062468 GTAGTGGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:1063946 original size:23 final size:23
Alignment explanation
Indices: 1063919--1063962 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1063909 AATACAATTT
*
1063919 AATTTGCCAAGACATTTCCATCC
1 AATTTGCCAAGACATATCCATCC
* *
1063942 AATTTTCCACGACATATCCAT
1 AATTTGCCAAGACATATCCAT
1063963 TTGCTACCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.32
Consensus pattern (23 bp):
AATTTGCCAAGACATATCCATCC
Found at i:1072907 original size:257 final size:255
Alignment explanation
Indices: 1072455--1073019 Score: 760
Period size: 257 Copynumber: 2.2 Consensus size: 255
1072445 AATAAAGATA
1072455 TTTTTTATTATTTCGGGTCAGGTCAGGTTTCTAATTC--ATA-T--GTCGGGTCGGGTGAAACTT
1 TTTTTTATTATTTCGGGTC-GGTC-GGTTTCTAATTCATATATTGGGTCGGGTCGGGTGAAACTT
* * * * * * *
1072515 TAATTTGGTTGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCAGGTCGAGTTCGGGTTTA
64 TAATTTGGTCGAGTCAGGTC-GATTTTTTAAGTGTGATATTCGGGCCAAGTAGAGTTCGGGTTTA
*
1072580 GGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATAAATTTAGGAATAATTACAA
128 GGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATAAATTTAGGAATAATTACAA
* *
1072645 TAATACC-C-CTCTCTAT-A-TTTTTTCCAATTAAGTCACTGTTTTTATTGAATAAAAATAAT
193 TAATACCTCACTATATATAATTTTTTTCCAATTAAGTCACTGTTTTTATTGAATAAAAATAAT
*
1072704 TTTTTTATTATTTCGGGTCTGGTCGGGTTTTTAATTCATATATTCGGGTCGGGTCGGGTGAAACT
1 TTTTTTATTATTTCGGGTC-GGTC-GGTTTCTAATTCATATATT-GGGTCGGGTCGGGTGAAACT
* **
1072769 TTATTTTGGTCGAGTCAGGTC-ATTTTTTAAGTGTGATATTCGGGCCAAGTAGAGTTTTGGTTTA
63 TTAATTTGGTCGAGTCAGGTCGATTTTTTAAGTGTGATATTCGGGCCAAGTAGAGTTCGGGTTTA
* *
1072833 GGGTGAAAAATACCCGGCCCGATCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATT
128 GGGTGAAAAATACCCGACCCG----AAAAAATATATAATTTTACCTTATAAATTTAGGAATAATT
* *
1072898 ACAATAATACCTCACTATATATAATTTTTTTTCAATTAAGTCATTGTTTTTATTGAATAAAAATA
189 ACAATAATACCTCACTATATATAATTTTTTTCCAATTAAGTCACTGTTTTTATTGAATAAAAATA
1072963 AT
254 AT
*
1072965 TTTTTTATTATTTCGGGTC-AT--GTTTCTAATTCATATATTTGGGGTCGGGTCGGGT
1 TTTTTTATTATTTCGGGTCGGTCGGTTTCTAATTCATATA-TT-GGGTCGGGTCGGGT
1073020 AGACCAAAAA
Statistics
Matches: 278, Mismatches: 23, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
249 34 0.12
251 3 0.01
252 1 0.00
253 57 0.21
255 35 0.13
256 15 0.05
257 65 0.23
258 1 0.00
259 7 0.03
260 1 0.00
261 59 0.21
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (255 bp):
TTTTTTATTATTTCGGGTCGGTCGGTTTCTAATTCATATATTGGGTCGGGTCGGGTGAAACTTTA
ATTTGGTCGAGTCAGGTCGATTTTTTAAGTGTGATATTCGGGCCAAGTAGAGTTCGGGTTTAGGG
TGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATAAATTTAGGAATAATTACAATAA
TACCTCACTATATATAATTTTTTTCCAATTAAGTCACTGTTTTTATTGAATAAAAATAAT
Found at i:1073366 original size:17 final size:18
Alignment explanation
Indices: 1073344--1073390 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1073334 TATGGAATTG
*
1073344 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
1073361 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1073379 GATTCCAATTCC
1 GATTCCAATTCC
1073391 CTCATAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1074095 original size:20 final size:20
Alignment explanation
Indices: 1074070--1074112 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1074060 TATAAGAGTT
*
1074070 CATTTAGGACCATGTAGATG
1 CATTTAGGACCATATAGATG
* *
1074090 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
1074110 CAT
1 CAT
1074113 GTAGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:1075577 original size:23 final size:23
Alignment explanation
Indices: 1075549--1075592 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1075539 AATACAATTT
*
1075549 AATTTGCCAAGACATTTCCATCC
1 AATTTGCCAAGACATATCCATCC
*
1075572 AATTTGCCACGACATATCCAT
1 AATTTGCCAAGACATATCCAT
1075593 TTGCTGCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.30
Consensus pattern (23 bp):
AATTTGCCAAGACATATCCATCC
Found at i:1080001 original size:25 final size:25
Alignment explanation
Indices: 1079940--1079991 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1079930 ATCCATTTTT
* *
1079940 GAAAATTCAATGGGATGTGTCTTGG
1 GAAAATTCGATAGGATGTGTCTTGG
1079965 GAAAATTCGATAGGATGTGTCTTGG
1 GAAAATTCGATAGGATGTGTCTTGG
1079990 GA
1 GA
1079992 TAACATGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.31
Consensus pattern (25 bp):
GAAAATTCGATAGGATGTGTCTTGG
Found at i:1083995 original size:2 final size:2
Alignment explanation
Indices: 1083938--1083979 Score: 66
Period size: 2 Copynumber: 20.0 Consensus size: 2
1083928 TTTATTACAT
1083938 TA TA TA GTA TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
1083980 ATTTCAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 34 0.89
3 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1084075 original size:36 final size:38
Alignment explanation
Indices: 1083985--1084088 Score: 151
Period size: 36 Copynumber: 2.8 Consensus size: 38
1083975 ATATAATTTC
1083985 AAAA-ATATATAATATAGTTTTTGAAAACACATTTTTG
1 AAAACATATATAATATAGTTTTTGAAAACACATTTTTG
**
1084022 AAAAACATATATAATATAGTTTTT-AAAACAGTTTTTTG
1 -AAAACATATATAATATAGTTTTTGAAAACACATTTTTG
*
1084060 -AAACATATATCATATAGTTTTTGAAAACA
1 AAAACATATATAATATAGTTTTTGAAAACA
1084089 TATTATATAG
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
36 21 0.34
37 6 0.10
38 16 0.26
39 18 0.30
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (38 bp):
AAAACATATATAATATAGTTTTTGAAAACACATTTTTG
Found at i:1084091 original size:22 final size:23
Alignment explanation
Indices: 1084054--1084102 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
1084044 TTAAAACAGT
*
1084054 TTTTTGAAACATATATCATATAG
1 TTTTTGAAACACATATCATATAG
*
1084077 TTTTTGAAA-ACATATTATATAG
1 TTTTTGAAACACATATCATATAG
1084099 TTTT
1 TTTT
1084103 CAAAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (23 bp):
TTTTTGAAACACATATCATATAG
Found at i:1084108 original size:22 final size:24
Alignment explanation
Indices: 1084060--1084108 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
1084050 CAGTTTTTTG
**
1084060 AAACATATATCATATAGTTTTTGA
1 AAACATATATCATATAGTTTTCAA
1084084 AAACATAT-T-ATATAGTTTTCAA
1 AAACATATATCATATAGTTTTCAA
1084106 AAA
1 AAA
1084109 TATAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 1 0.04
24 8 0.35
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (24 bp):
AAACATATATCATATAGTTTTCAA
Found at i:1084142 original size:27 final size:29
Alignment explanation
Indices: 1084091--1084144 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1084081 TGAAAACATA
1084091 TTATATAGTTTTCAAAAATATAATTTATG
1 TTATATAGTTTTCAAAAATATAATTTATG
*
1084120 TTATATAGTTTT-TAAAATA-AATTTA
1 TTATATAGTTTTCAAAAATATAATTTA
1084145 GTGTACATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.25
28 6 0.25
29 12 0.50
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.50
Consensus pattern (29 bp):
TTATATAGTTTTCAAAAATATAATTTATG
Found at i:1084154 original size:29 final size:29
Alignment explanation
Indices: 1084093--1084154 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
1084083 AAAACATATT
*
1084093 ATATAGTTTTCAAAAATATAATTTATGTT
1 ATATAGTTTTCAAAAATATAATTTATGTC
*
1084122 ATATAGTTTT-TAAAATA-AATTTAGTGTAC
1 ATATAGTTTTCAAAAATATAATTTA-TGT-C
1084151 ATAT
1 ATAT
1084155 TATTTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.21
28 9 0.31
29 14 0.48
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (29 bp):
ATATAGTTTTCAAAAATATAATTTATGTC
Found at i:1084160 original size:27 final size:28
Alignment explanation
Indices: 1084095--1084153 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
1084085 AACATATTAT
* *
1084095 ATAGTTTTCAAAAATATAATTTATGTTAT
1 ATAGTTTT-TAAAATATAATTTATGTTAC
1084124 ATAGTTTTTAAAATA-AATTTA-GTGTAC
1 ATAGTTTTTAAAATATAATTTATGT-TAC
1084151 ATA
1 ATA
1084154 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.07
27 11 0.41
28 6 0.22
29 8 0.30
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (28 bp):
ATAGTTTTTAAAATATAATTTATGTTAC
Found at i:1085709 original size:6 final size:6
Alignment explanation
Indices: 1085698--1085727 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1085688 CGGATCGAAT
1085698 ATTTTA ATTTTA ATTTTA ACTTTTA ATTTT
1 ATTTTA ATTTTA ATTTTA A-TTTTA ATTTT
1085728 CGTAATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:1085723 original size:13 final size:12
Alignment explanation
Indices: 1085698--1085727 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1085688 CGGATCGAAT
1085698 ATTTTAATTTTA
1 ATTTTAATTTTA
1085710 ATTTTAACTTTTA
1 ATTTTAA-TTTTA
1085723 ATTTT
1 ATTTT
1085728 CGTAATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTTAATTTTA
Found at i:1086588 original size:59 final size:59
Alignment explanation
Indices: 1086449--1086589 Score: 160
Period size: 59 Copynumber: 2.4 Consensus size: 59
1086439 GTATATGTAT
* * * * *
1086449 ATAGTTTGGGATGAAATTGGAATGTTCAGAGAGTTTAGGGATTAATTTATAATGAAGGTC
1 ATAGTTTGGGATGAAATT-GAATGTTCAGAAAGTTTAAGGACTAATTTAGAATGAAAGTC
*
1086509 ATAGTTTGGGGATGACATTGAATGTTCA-AAAGTTTAAGGACTAATTTAGAAT-AATAGTC
1 ATAGTTT-GGGATGAAATTGAATGTTCAGAAAGTTTAAGGACTAATTTAGAATGAA-AGTC
* *
1086568 ATAGTTTATGGATAAAATTGAA
1 ATAGTTT-GGGATGAAATTGAA
1086590 ACGTTTAATA
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
58 2 0.03
59 41 0.59
60 16 0.23
61 10 0.14
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGAATGTTCAGAAAGTTTAAGGACTAATTTAGAATGAAAGTC
Found at i:1086602 original size:29 final size:29
Alignment explanation
Indices: 1086568--1086660 Score: 150
Period size: 29 Copynumber: 3.2 Consensus size: 29
1086558 AATAATAGTC
* *
1086568 ATAGTTTATGGATAAAATTGAAACGTTTA
1 ATAGTTTATGAATGAAATTGAAACGTTTA
1086597 ATAGTTTATGAATGAAATTGAAACGTTTA
1 ATAGTTTATGAATGAAATTGAAACGTTTA
*
1086626 ATAGTTTATGAATGAAATTGAAACATTTA
1 ATAGTTTATGAATGAAATTGAAACGTTTA
*
1086655 AAAGTT
1 ATAGTT
1086661 AAGAGATTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (29 bp):
ATAGTTTATGAATGAAATTGAAACGTTTA
Found at i:1086815 original size:16 final size:16
Alignment explanation
Indices: 1086794--1086827 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1086784 TAAACATTTT
1086794 TCAATCAATCTAGGTA
1 TCAATCAATCTAGGTA
*
1086810 TCAATCAATCTTGGTA
1 TCAATCAATCTAGGTA
1086826 TC
1 TC
1086828 TAACATCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (16 bp):
TCAATCAATCTAGGTA
Found at i:1090019 original size:13 final size:13
Alignment explanation
Indices: 1090003--1090065 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
1089993 CCTAAAACTC
1090003 AAAATAAAAAAAT
1 AAAATAAAAAAAT
1090016 AAAATAAAATAAAT
1 AAAATAAAA-AAAT
* *
1090030 -AAGTGAAATAAAT
1 AAAAT-AAAAAAAT
1090043 -AAATAAATAAAAT
1 AAAATAAA-AAAAT
*
1090056 AATATAAAAA
1 AAAATAAAAA
1090066 CTAACTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 3 0.07
13 25 0.61
14 13 0.32
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:1090031 original size:4 final size:4
Alignment explanation
Indices: 1090004--1090063 Score: 57
Period size: 4 Copynumber: 13.8 Consensus size: 4
1089994 CTAAAACTCA
* *
1090004 AAAT AAAA AAAT AAAAT AAAAT AAAT AAGT GAAAT AAAT AAAT AAAT AAAAT
1 AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT -AAAT AAAT AAAT AAAT -AAAT
1090056 AATAT AAA
1 AA-AT AAA
1090064 AACTAACTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
4 28 0.58
5 20 0.42
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1090044 original size:17 final size:17
Alignment explanation
Indices: 1090004--1090063 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 17
1089994 CTAAAACTCA
*
1090004 AAATAAAAAAATAAAAT
1 AAATAAATAAATAAAAT
* *
1090021 AAAATAAATAAGTGAAAT
1 -AAATAAATAAATAAAAT
1090039 AAATAAATAAATAAAAT
1 AAATAAATAAATAAAAT
1090056 AATATAAA
1 AA-ATAAA
1090064 AACTAACTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
17 17 0.47
18 19 0.53
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AAATAAATAAATAAAAT
Found at i:1090077 original size:20 final size:18
Alignment explanation
Indices: 1090054--1090141 Score: 59
Period size: 20 Copynumber: 4.4 Consensus size: 18
1090044 AATAAATAAA
1090054 ATAATATAAAAACTAACTAT
1 ATAATATAAAAA-TAA-TAT
*
1090074 ATAATACTAAACATAATAT
1 ATAATA-TAAAAATAATAT
* *
1090093 ATATATATATATATATATAT
1 ATA-ATATAAAAATA-ATAT
* *
1090113 ATATATATATATATATATAT
1 ATA-ATATAAAAATA-ATAT
1090133 ATATATATA
1 ATA-ATATA
1090142 TATATACGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
19 12 0.19
20 45 0.73
21 5 0.08
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATATAAAAATAATAT
Found at i:1090094 original size:2 final size:2
Alignment explanation
Indices: 1090089--1090147 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1090079 ACTAAACATA
1090089 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
1090131 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1090148 CGTTTTCAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1090210 original size:35 final size:35
Alignment explanation
Indices: 1090162--1090328 Score: 237
Period size: 36 Copynumber: 4.7 Consensus size: 35
1090152 TTCAAAACCG
*
1090162 TTTCAAAATTATTTTAAAAACTATATATTATATAT
1 TTTCAAAATTATTTTAAAAACTATATATTATATGT
*
1090197 TTTCAAAACTATTTTTAAAAACTATATATTATATGT
1 TTTCAAAATTA-TTTTAAAAACTATATATTATATGT
1090233 TTTCAAAATTATTTTAAAAACTATATATTA-ATGT
1 TTTCAAAATTATTTTAAAAACTATATATTATATGT
* ***
1090267 TTTCAAAATTGTTTTTTTAACTATATATTATATGT
1 TTTCAAAATTATTTTAAAAACTATATATTATATGT
* *
1090302 TTTCAAAAATTGTTTTCAAAACTATAT
1 TTTC-AAAATTATTTTAAAAACTATAT
1090329 CAAAAATTGT
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
34 30 0.25
35 37 0.31
36 52 0.44
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (35 bp):
TTTCAAAATTATTTTAAAAACTATATATTATATGT
Found at i:1090317 original size:13 final size:13
Alignment explanation
Indices: 1090299--1090346 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1090289 ATATATTATA
1090299 TGTTTTCAAAAAT
1 TGTTTTCAAAAAT
*
1090312 TGTTTTC-AAAAC
1 TGTTTTCAAAAAT
* *
1090324 T-ATATCAAAAAT
1 TGTTTTCAAAAAT
1090336 TGTTTTCAAAA
1 TGTTTTCAAAA
1090347 CTATATAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
11 3 0.11
12 10 0.37
13 14 0.52
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (13 bp):
TGTTTTCAAAAAT
Found at i:1090336 original size:24 final size:24
Alignment explanation
Indices: 1090304--1090352 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1090294 TTATATGTTT
1090304 TCAAAAATTGTTTTCAAAACTATA
1 TCAAAAATTGTTTTCAAAACTATA
1090328 TCAAAAATTGTTTTCAAAACTATA
1 TCAAAAATTGTTTTCAAAACTATA
1090352 T
1 T
1090353 AATATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (24 bp):
TCAAAAATTGTTTTCAAAACTATA
Found at i:1090336 original size:60 final size:61
Alignment explanation
Indices: 1090271--1090406 Score: 188
Period size: 60 Copynumber: 2.3 Consensus size: 61
1090261 TAATGTTTTC
*** * *
1090271 AAAATTGTTTTTTTAACTATATATTATATGTTTTCAAAAAT-TGTTTTCAAAACTATATCA
1 AAAATTGTTTTCAAAACTATATAATATATATTTTCAAAAATGTGTTTTCAAAACTATATCA
1090331 AAAATTGTTTTCAAAACTATATAATATATATTTTCAAAAATGTGTTTTCAAAACTATAT--
1 AAAATTGTTTTCAAAACTATATAATATATATTTTCAAAAATGTGTTTTCAAAACTATATCA
*
1090390 AATATATGTTTTCAAAA
1 AAAAT-TGTTTTCAAAA
1090407 ATTGTTTTTC
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
59 4 0.06
60 47 0.69
61 17 0.25
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (61 bp):
AAAATTGTTTTCAAAACTATATAATATATATTTTCAAAAATGTGTTTTCAAAACTATATCA
Found at i:1090368 original size:23 final size:24
Alignment explanation
Indices: 1090304--1090369 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
1090294 TTATATGTTT
*
1090304 TCAAAAATTGTTTTCAAAACTATA
1 TCAAAAATTATTTTCAAAACTATA
*
1090328 TCAAAAATTGTTTTCAAAACTATA
1 TCAAAAATTATTTTCAAAACTATA
*
1090352 T--AATATATATTTTCAAAA
1 TCAAAAAT-TATTTTCAAAA
1090370 ATGTGTTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
22 4 0.10
23 10 0.26
24 25 0.64
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (24 bp):
TCAAAAATTATTTTCAAAACTATA
Found at i:1090377 original size:37 final size:36
Alignment explanation
Indices: 1090328--1090453 Score: 198
Period size: 37 Copynumber: 3.4 Consensus size: 36
1090318 CAAAACTATA
1090328 TCAAAAATTGTTTTCAAAACTATATAATATATATTT
1 TCAAAAATTGTTTTCAAAACTATATAATATATATTT
*
1090364 TCAAAAATGTGTTTTCAAAACTATATAATATATGTTT
1 TCAAAAAT-TGTTTTCAAAACTATATAATATATATTT
*
1090401 TCAAAAATTGTTTTTCAAAACTATATAATATATTTTT
1 TCAAAAATTG-TTTTCAAAACTATATAATATATATTT
*
1090438 TCGAAAATGTGTTTTC
1 TCAAAAAT-TGTTTTC
1090454 GAAATCATAT
Statistics
Matches: 84, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
36 10 0.12
37 72 0.86
38 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (36 bp):
TCAAAAATTGTTTTCAAAACTATATAATATATATTT
Found at i:1090527 original size:39 final size:38
Alignment explanation
Indices: 1090474--1090588 Score: 121
Period size: 38 Copynumber: 3.0 Consensus size: 38
1090464 TTTCAGAACC
* *
1090474 ATATTATATATTTTCAAAAATTGATTTTTTAAAAACTAT
1 ATATTATATGTTTTC-AAAATTGATTTTCTAAAAACTAT
* *
1090513 ATATTATATGTTTTCAAAATCCG-TTTTCTAAAAATTAT
1 ATATTATATGTTTTCAAAAT-TGATTTTCTAAAAACTAT
*
1090551 ATGTTATATGTTTTTCGAAAA-T-ATTTTCT-AAAACTAT
1 ATATTATATG-TTTTC-AAAATTGATTTTCTAAAAACTAT
1090588 A
1 A
1090589 CTATATTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
37 8 0.12
38 33 0.51
39 20 0.31
40 4 0.06
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (38 bp):
ATATTATATGTTTTCAAAATTGATTTTCTAAAAACTAT
Found at i:1090868 original size:20 final size:19
Alignment explanation
Indices: 1090843--1090904 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
1090833 TAATTAGTTT
1090843 TGAAATGATATCCTTCGTCA
1 TGAAATGATATCCTTC-TCA
*
1090863 TGAAATTGAT-TCAGTT-T--
1 TGAAA-TGATATC-CTTCTCA
1090880 TGAAATGATATCCTTCATCA
1 TGAAATGATATCCTTC-TCA
1090900 TGAAA
1 TGAAA
1090905 ATGAGTCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
16 6 0.18
17 7 0.21
18 1 0.03
19 1 0.03
20 12 0.36
21 6 0.18
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (19 bp):
TGAAATGATATCCTTCTCA
Found at i:1102506 original size:21 final size:22
Alignment explanation
Indices: 1102481--1102524 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1102471 TTAATGTCAA
**
1102481 ATTCAGCTTCAAATTG-TCTAG
1 ATTCAGCCCCAAATTGATCTAG
*
1102502 ATTCATCCCCAAATTGATCTAG
1 ATTCAGCCCCAAATTGATCTAG
1102524 A
1 A
1102525 ATTTTTAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (22 bp):
ATTCAGCCCCAAATTGATCTAG
Found at i:1105215 original size:20 final size:20
Alignment explanation
Indices: 1105187--1105357 Score: 108
Period size: 20 Copynumber: 7.7 Consensus size: 20
1105177 TCATTTATGA
*
1105187 CATCTTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
1105207 CATCCTTTCGTGCATTTCATTTATGG
1 CATCCTTTCATGC----C-TTAAT-G
*
1105233 CATCCTTTCATGCTTTAATG
1 CATCCTTTCATGCCTTAATG
*
1105253 CATCCTTTCATGCATTTCATTTATG
1 CATCCTTTCATGC----C-TTAATG
*
1105278 ACATCCTTTCATGCCTTATTG
1 -CATCCTTTCATGCCTTAATG
*
1105299 CATCCTTTCATGCATTTCATTTATGG
1 CATCCTTTCATGC----C-TTAAT-G
1105325 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
1105345 TATCCTTTCATGC
1 CATCCTTTCATGC
1105358 ATTTCATTTA
Statistics
Matches: 119, Mismatches: 14, Indels: 36
0.70 0.08 0.21
Matches are distributed among these distances:
20 51 0.43
21 12 0.10
22 2 0.02
24 2 0.02
25 12 0.10
26 40 0.34
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.45
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:1105237 original size:26 final size:26
Alignment explanation
Indices: 1105206--1105370 Score: 159
Period size: 26 Copynumber: 7.0 Consensus size: 26
1105196 ATGCCTTAAT
*
1105206 GCATCCTTTCGTGCATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
1105232 GCATCCTTTCATGC-TTT-A---AT-
1 GCATCCTTTCATGCATTTCATTTATG
1105252 GCATCCTTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
* *
1105278 ACATCCTTTCATGC----C--TTATT
1 GCATCCTTTCATGCATTTCATTTATG
1105298 GCATCCTTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
*
1105324 GCATCCTTTCATGC----C-TTAAT-
1 GCATCCTTTCATGCATTTCATTTATG
*
1105344 GTATCCTTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
1105370 G
1 G
1105371 ATTCATTTTA
Statistics
Matches: 113, Mismatches: 8, Indels: 36
0.72 0.05 0.23
Matches are distributed among these distances:
20 44 0.39
21 9 0.08
22 3 0.03
24 3 0.03
25 9 0.08
26 45 0.40
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.45
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTCATTTATG
Found at i:1105370 original size:46 final size:46
Alignment explanation
Indices: 1105174--1105370 Score: 331
Period size: 46 Copynumber: 4.3 Consensus size: 46
1105164 TTATTCGTTA
* * *
1105174 ATTTCATTTATGACATCTTTTCATGCCTTAATGCATCCTTTCGTGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
1105220 ATTTCATTTATGGCATCCTTTCATGCTTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
1105266 ATTTCATTTATGACATCCTTTCATGCCTTATTGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
1105312 ATTTCATTTATGGCATCCTTTCATGCCTTAATGTATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1105358 ATTTCATTTATGG
1 ATTTCATTTATGG
1105371 ATTCATTTTA
Statistics
Matches: 141, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 141 1.00
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.46
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:1110797 original size:22 final size:22
Alignment explanation
Indices: 1110746--1110800 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
1110736 TTGATGTTCA
1110746 ATGGTATCGATACCCTCTACAT
1 ATGGTATCGATACCCTCTACAT
*
1110768 A-GGTATCGATA-CCTCTTCCAT
1 ATGGTATCGATACCCTC-TACAT
1110789 ATGGTATCGATA
1 ATGGTATCGATA
1110801 TTGTTCATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 4 0.13
21 15 0.50
22 11 0.37
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (22 bp):
ATGGTATCGATACCCTCTACAT
Found at i:1114273 original size:8 final size:8
Alignment explanation
Indices: 1114260--1114290 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
1114250 CTCATAGTAA
1114260 TATATATT
1 TATATATT
1114268 TATATATT
1 TATATATT
1114276 TATATATT
1 TATATATT
1114284 TATATAT
1 TATATAT
1114291 ATGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATATATT
Found at i:1114297 original size:2 final size:2
Alignment explanation
Indices: 1114292--1114383 Score: 177
Period size: 2 Copynumber: 46.5 Consensus size: 2
1114282 TTTATATATA
1114292 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1114333 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1114375 TG TG TG TG T
1 TG TG TG TG T
1114384 ATAATAACTT
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 88 0.99
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1115471 original size:20 final size:20
Alignment explanation
Indices: 1115442--1115493 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1115432 CATATGCTAG
1115442 GGTACCGATACCCCTAACCT
1 GGTACCGATACCCCTAACCT
* *
1115462 GGTACTGATACCCCTACCCT
1 GGTACCGATACCCCTAACCT
1115482 GGTACCGATACC
1 GGTACCGATACC
1115494 AAAATTAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (20 bp):
GGTACCGATACCCCTAACCT
Found at i:1115542 original size:21 final size:21
Alignment explanation
Indices: 1115516--1115591 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
1115506 AATGTTCCCT
1115516 GGTATCGATACCCTTCATATA
1 GGTATCGATACCCTTCATATA
1115537 GGTATCGATACCTCTTCA-ATA
1 GGTATCGATACC-CTTCATATA
*** *
1115558 TGGTATCGATATTGTTCATACA
1 -GGTATCGATACCCTTCATATA
*
1115580 GGTATTGATACC
1 GGTATCGATACC
1115592 TGATGAATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
21 28 0.62
22 17 0.38
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.36
Consensus pattern (21 bp):
GGTATCGATACCCTTCATATA
Found at i:1115562 original size:22 final size:20
Alignment explanation
Indices: 1115515--1115568 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 20
1115505 TAATGTTCCC
1115515 TGGTATCGATACCCTTCATA
1 TGGTATCGATACCCTTCATA
1115535 TAGGTATCGATACCTCTTCAATA
1 T-GGTATCGATACC-CTTC-ATA
1115558 TGGTATCGATA
1 TGGTATCGATA
1115569 TTGTTCATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 1 0.03
21 12 0.39
22 14 0.45
23 4 0.13
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (20 bp):
TGGTATCGATACCCTTCATA
Found at i:1122888 original size:9 final size:9
Alignment explanation
Indices: 1122873--1122929 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
1122863 CCTAAAAACC
1122873 AAAATAAA-
1 AAAATAAAT
*
1122881 ATAAATAAGT
1 A-AAATAAAT
*
1122891 GAAATAAAT
1 AAAATAAAT
1122900 AAAA-AAAT
1 AAAATAAAT
*
1122908 AATATAAAT
1 AAAATAAAT
1122917 AAAATAATAT
1 AAAATAA-AT
1122927 AAA
1 AAA
1122930 TTACTAACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 8 0.21
9 26 0.67
10 5 0.13
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (9 bp):
AAAATAAAT
Found at i:1123025 original size:35 final size:36
Alignment explanation
Indices: 1122986--1123135 Score: 200
Period size: 36 Copynumber: 4.2 Consensus size: 36
1122976 TTCAAAATCG
1122986 TTTCAAAA-TTATTTTAAAAACTATATATTATATGT
1 TTTCAAAACTTATTTTAAAAACTATATATTATATGT
*
1123021 TTTCAAAACCGT-TTTTAAAAACTATATATTATATGT
1 TTTCAAAA-CTTATTTTAAAAACTATATATTATATGT
1123057 TTTCAAAA-TTATTTTAAAAACTATATATTA-ATGT
1 TTTCAAAACTTATTTTAAAAACTATATATTATATGT
* * ** *
1123091 TTTCAAAATTGTTTTTTTTAAATTATATATTATATGT
1 TTTCAAAACT-TATTTTAAAAACTATATATTATATGT
1123128 TTTCAAAA
1 TTTCAAAA
1123136 AAAAATTCAA
Statistics
Matches: 103, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
34 13 0.13
35 28 0.27
36 49 0.48
37 13 0.13
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTCAAAACTTATTTTAAAAACTATATATTATATGT
Found at i:1123061 original size:71 final size:71
Alignment explanation
Indices: 1122986--1123135 Score: 239
Period size: 71 Copynumber: 2.1 Consensus size: 71
1122976 TTCAAAATCG
1122986 TTTCAAAATTATTTTAAAAACTATATATTATATGTTTTCAAAACCG-TTTTTAAAAACTATATAT
1 TTTCAAAATTATTTTAAAAACTATATATTA-ATGTTTTCAAAACCGTTTTTTAAAAACTATATAT
1123050 TATATGT
65 TATATGT
** ** *
1123057 TTTCAAAATTATTTTAAAAACTATATATTAATGTTTTCAAAATTGTTTTTTTTAAATTATATATT
1 TTTCAAAATTATTTTAAAAACTATATATTAATGTTTTCAAAACCGTTTTTTAAAAACTATATATT
1123122 ATATGT
66 ATATGT
1123128 TTTCAAAA
1 TTTCAAAA
1123136 AAAAATTCAA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
70 13 0.18
71 60 0.82
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (71 bp):
TTTCAAAATTATTTTAAAAACTATATATTAATGTTTTCAAAACCGTTTTTTAAAAACTATATATT
ATATGT
Found at i:1123148 original size:71 final size:71
Alignment explanation
Indices: 1122999--1123153 Score: 204
Period size: 71 Copynumber: 2.2 Consensus size: 71
1122989 CAAAATTATT
1122999 TTAAAAACTATATATTATATGTTTTCAAAACCGTTTTTAAAAACTATATATTATATGTTTTCAAA
1 TTAAAAACTATATATTATATGTTTTCAAAACCGTTTTTAAAAACTATATATTATATGTTTTCAAA
** **
1123064 ATTATT
66 AAAAAA
** ** *
1123070 TTAAAAACTATATATTA-ATGTTTTCAAAATTGTTTTTTTTAAATTATATATTATATGTTTTCAA
1 TTAAAAACTATATATTATATGTTTTCAAAACCG-TTTTTAAAAACTATATATTATATGTTTTCAA
1123134 AAAAAAA
65 AAAAAAA
*
1123141 TTCAAAACTATAT
1 TTAAAAACTATAT
1123154 CAAAAAATGT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
70 13 0.18
71 60 0.82
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (71 bp):
TTAAAAACTATATATTATATGTTTTCAAAACCGTTTTTAAAAACTATATATTATATGTTTTCAAA
AAAAAA
Found at i:1123194 original size:37 final size:37
Alignment explanation
Indices: 1123153--1123281 Score: 140
Period size: 37 Copynumber: 3.5 Consensus size: 37
1123143 CAAAACTATA
* *
1123153 TCAAAAAATGTTTTTCAAAATTATATAATATACATTT
1 TCAAAAAATGTTTTTCAAAACTATATAATATACGTTT
*
1123190 TCAAAAATATGTTTTT-AAAACTATATAATATATGTTT
1 TCAAAAA-ATGTTTTTCAAAACTATATAATATACGTTT
***
1123227 TCAAAAAA--AAATTCAAAACTATATAATATACGTTT
1 TCAAAAAATGTTTTTCAAAACTATATAATATACGTTT
**
1123262 T-TGAAAATGTGTTTTCAAAA
1 TCAAAAAATGT-TTTTCAAAA
1123282 TCAAATTTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
34 6 0.08
35 21 0.28
36 1 0.01
37 39 0.52
38 8 0.11
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (37 bp):
TCAAAAAATGTTTTTCAAAACTATATAATATACGTTT
Found at i:1123355 original size:24 final size:24
Alignment explanation
Indices: 1123323--1123368 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1123313 AAAATTTGAT
*
1123323 TTTTTAAAAACTATATATTATATG
1 TTTTCAAAAACTATATATTATATG
* *
1123347 TTTTCAAAAATTATATGTTATA
1 TTTTCAAAAACTATATATTATA
1123369 CATTTTTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (24 bp):
TTTTCAAAAACTATATATTATATG
Found at i:1123375 original size:25 final size:23
Alignment explanation
Indices: 1123321--1123382 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
1123311 TAAAAATTTG
* *
1123321 ATTTTTTAAAAACTATATATTAT
1 ATTTTTCAAAAATTATATATTAT
*
1123344 ATGTTTTCAAAAATTATATGTTAT
1 AT-TTTTCAAAAATTATATATTAT
*
1123368 ACATTTTTCGAAAAT
1 --ATTTTTCAAAAAT
1123383 ATTTTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 18 0.56
25 10 0.31
26 2 0.06
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.48
Consensus pattern (23 bp):
ATTTTTCAAAAATTATATATTAT
Found at i:1123712 original size:2 final size:2
Alignment explanation
Indices: 1123705--1123736 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1123695 TAGACCAGTC
1123705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1123737 CTTATAGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1140504 original size:14 final size:13
Alignment explanation
Indices: 1140472--1140503 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1140462 TAATCAACTC
1140472 TTTTTTCTGTTTT
1 TTTTTTCTGTTTT
1140485 TTTTTTCTGTTTT
1 TTTTTTCTGTTTT
1140498 TTTTTT
1 TTTTTT
1140504 TTTTTTTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (13 bp):
TTTTTTCTGTTTT
Found at i:1144289 original size:20 final size:21
Alignment explanation
Indices: 1144264--1144310 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1144254 GTTTGTGGTC
*
1144264 ATTTCTAGCCG-TTGGGGATG
1 ATTTCTAGACGTTTGGGGATG
*
1144284 ATTTCTAGATGTTTGGGGATG
1 ATTTCTAGACGTTTGGGGATG
*
1144305 TTTTCT
1 ATTTCT
1144311 CTTCAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.15, C:0.11, G:0.30, T:0.45
Consensus pattern (21 bp):
ATTTCTAGACGTTTGGGGATG
Found at i:1146104 original size:21 final size:20
Alignment explanation
Indices: 1146064--1146105 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
1146054 TCACGTGATA
*
1146064 ATTTTTTTATAAAAGAAAAT
1 ATTTTTTTATAAAAAAAAAT
1146084 ATTTTTTTA-AAATAAATAAAT
1 ATTTTTTTATAAA-AAA-AAAT
1146105 A
1 A
1146106 AATAGTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 3 0.16
20 11 0.58
21 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATTTTTTTATAAAAAAAAAT
Found at i:1146794 original size:182 final size:182
Alignment explanation
Indices: 1146536--1146898 Score: 532
Period size: 182 Copynumber: 2.0 Consensus size: 182
1146526 GATATATTGA
*
1146536 AAGTGTCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAATGTCGATACTTT
1 AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAATGTCGATACTTT
* *
1146601 ATAACAATGTATCGATCCACAACGATATAGCACATAAAAATATGACAAAATC-GGTCTCTAAAG-
66 ATAAAAATGTATCGATCCACAACGATATAACACATAAAAATATGACAAAA-CGGGTCTC-AAAGT
* * *
1146664 GACAAAATCGGTATAGAGAGATCAGATATATTGAAAGTGTCGATACTTTAATAT
129 GACAAAACCGGTAAAGAGAGACCAGATATATTGAAAGTGTCGATACTTTAATAT
* *
1146718 AAGTATCGACACTTTGTGAATTTAAAAGAGAATCAGTTTTAGCGCCTATAAAGTGTCGATACTTT
1 AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAATGTCGATACTTT
* **** *
1146783 ATAAAAATGTATCGATCCATAACGATATAATGGGTAAAAATATGACAAAACGGGTTTCAAAGTGA
66 ATAAAAATGTATCGATCCACAACGATATAACACATAAAAATATGACAAAACGGGTCTCAAAGTGA
* ** *
1146848 CAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
131 CAAAACCGGTAAAGAGAGACCAGATATATTGAAAGTGTCGATACTTTAATA
1146899 CGTACGCGTA
Statistics
Matches: 161, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
181 5 0.03
182 156 0.97
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (182 bp):
AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAATGTCGATACTTT
ATAAAAATGTATCGATCCACAACGATATAACACATAAAAATATGACAAAACGGGTCTCAAAGTGA
CAAAACCGGTAAAGAGAGACCAGATATATTGAAAGTGTCGATACTTTAATAT
Found at i:1148903 original size:22 final size:23
Alignment explanation
Indices: 1148851--1148907 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
1148841 GTTGAAGAAC
* *
1148851 ATTTTTTTATATAAAATGATAGT
1 ATTTTATTATATAAAATGATAGA
* *
1148874 ATAGTTATTATATAAAATTATA-A
1 AT-TTTATTATATAAAATGATAGA
1148897 ATTTTATTATA
1 ATTTTATTATA
1148908 AATACAGGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 8 0.29
23 4 0.14
24 16 0.57
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (23 bp):
ATTTTATTATATAAAATGATAGA
Found at i:1149204 original size:14 final size:14
Alignment explanation
Indices: 1149185--1149215 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1149175 GGTTATATCG
*
1149185 GGGGATGACGGTGA
1 GGGGATGACAGTGA
1149199 GGGGATGACAGTGA
1 GGGGATGACAGTGA
1149213 GGG
1 GGG
1149216 AAACAGAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.58, T:0.13
Consensus pattern (14 bp):
GGGGATGACAGTGA
Found at i:1149330 original size:21 final size:21
Alignment explanation
Indices: 1149297--1149337 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1149287 AGACAATCAA
1149297 GAGTCGAAAAGACACTTGAGG
1 GAGTCGAAAAGACACTTGAGG
1149318 GAGTC-AAAGAGACACTTGAG
1 GAGTCGAAA-AGACACTTGAG
1149338 AGGAATAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.39, C:0.15, G:0.32, T:0.15
Consensus pattern (21 bp):
GAGTCGAAAAGACACTTGAGG
Found at i:1149470 original size:33 final size:33
Alignment explanation
Indices: 1149375--1149472 Score: 178
Period size: 33 Copynumber: 3.0 Consensus size: 33
1149365 ATAGATGGAC
*
1149375 TGGTGAAAGAAGTTGAGGTGTTGAGGGGTAAAG
1 TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAAG
1149408 TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAAG
1 TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAAG
*
1149441 TGGTGAAAGAAGTTAAGGTGTTGAGGGGTGAA
1 TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAA
1149473 CTTAAGATGG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.30, C:0.00, G:0.46, T:0.24
Consensus pattern (33 bp):
TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAAG
Found at i:1151255 original size:19 final size:19
Alignment explanation
Indices: 1151231--1151279 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1151221 AATATAGGGT
1151231 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1151250 TAATTTTGTATATGATTTA
1 TAATTTTGTATAAGATTTA
1151269 TAATTTTGTAT
1 TAATTTTGTAT
1151280 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1152278 original size:202 final size:197
Alignment explanation
Indices: 1151883--1152293 Score: 551
Period size: 202 Copynumber: 2.1 Consensus size: 197
1151873 CCCATAATTA
* * *
1151883 TAATGTAACCGGTATAACTATATCGATTTTATGAGAGAATAGGTCTACATAATGTATCGACACTT
1 TAATGTAACCGGTATAAATAAACCGATTTTATGAGAGAATAGGTCTACATAATGTATCGACACTT
*
1151948 CTGGAATTTGTCAATACTGTTTGTCTAGAAGGAATTCCCAAAAGGGTGCACACATAAAATGTCGA
66 CTGGAATTTGTCAATACTGTTTGTCTAGAAGGAATGCCCAAAAGGGTGCACACATAAAATGTCGA
* * * *
1152013 TACATTTTTAAAATGTGTCGATCTCTGAGACATCGAAACCCATAATTATAATGTAATAGGTAATT
131 TACATTTATAAAAAGTATCGATCTCTGAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
1152078 TT
196 TT
* *
1152080 GTAATGTAACCGGTATAAATAAACCGGTTTTATGTGAGAATAGGTCTACATAATGTATCGACACT
1 -TAATGTAACCGGTATAAATAAACCGATTTTATGAGAGAATAGGTCTACATAATGTATCGACACT
** * * * *
1152145 T-TTTAATTTTGTGTCGATACAT-TTTGT-TCAGAATGAATGCCCAAAAAATGGTGCACGCATAA
65 TCTGGAA--TT-TGTCAATAC-TGTTTGTCT-AGAAGGAATGCCC--AAAAGGGTGCACACATAA
*
1152207 AGTGTCGATACATTTATAAAAAGTATCGATC-CTAGAAACATCGAAACCCATAATTATAATGTAA
123 AATGTCGATACATTTATAAAAAGTATCGATCTCT-GAAACATCGAAACCCATAATTATAATGTAA
1152271 TAGGTAATTTT
187 TAGGTAATTTT
1152282 TCAATGTAACCG
1 T-AATGTAACCG
1152294 ATATGATTTT
Statistics
Matches: 187, Mismatches: 17, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
197 3 0.02
198 60 0.32
199 3 0.02
200 24 0.13
201 4 0.02
202 93 0.50
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (197 bp):
TAATGTAACCGGTATAAATAAACCGATTTTATGAGAGAATAGGTCTACATAATGTATCGACACTT
CTGGAATTTGTCAATACTGTTTGTCTAGAAGGAATGCCCAAAAGGGTGCACACATAAAATGTCGA
TACATTTATAAAAAGTATCGATCTCTGAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
TT
Found at i:1152708 original size:18 final size:18
Alignment explanation
Indices: 1152685--1152730 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1152675 CAATAGGTCA
1152685 ATGAAGATGAAGATGACG
1 ATGAAGATGAAGATGACG
* *
1152703 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
*
1152721 ATGATGATGA
1 ATGAAGATGA
1152731 TCCAAACAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.22
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:1152731 original size:6 final size:6
Alignment explanation
Indices: 1152685--1152730 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
1152675 CAATAGGTCA
* * * *
1152685 ATGAAG ATGAAG ATGACG ATGAAG ATGACG ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
1152731 TCCAAACAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.22
Consensus pattern (6 bp):
ATGAAG
Found at i:1152731 original size:12 final size:12
Alignment explanation
Indices: 1152685--1152730 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1152675 CAATAGGTCA
*
1152685 ATGAAGATGAAG
1 ATGACGATGAAG
1152697 ATGACGATGAAG
1 ATGACGATGAAG
*
1152709 ATGACGATGATG
1 ATGACGATGAAG
*
1152721 ATGATGATGA
1 ATGACGATGA
1152731 TCCAAACAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:1154801 original size:200 final size:198
Alignment explanation
Indices: 1154291--1155057 Score: 992
Period size: 200 Copynumber: 3.9 Consensus size: 198
1154281 TAAAGTTTCC
* *
1154291 CATAAAATGTTGATACATTTTTAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
* * * *
1154356 GTAATAGGTAAATTTACAATGTGA-TCGGTATAAATATACTGA-TTTATGAGCAAATAGGTCAGC
66 GTAATAGGTAAATTTACAATGTAACT-GGTATAAATATACCGATTTTATGAGAAAATAGGTCAAC
* * * * **
1154419 ATAAAGTATCAATACCTTTTAAATTTGTGTCGATAC-TTTTAGTCCAAGCT-TTTGCTC-AACGA
130 ATAATGTATCGACA-CTTTTAAATTTGTGTCGATACATTTT-GTCCAA-ATGAATGC-CAAACGA
* * *
1154481 GCTTCACA
191 GATGCACG
* * *
1154489 TATAAAAGTGTCGATACA--TTTAAAATTGTATCGATCCAAAAAATATCGAAACCGAAAATTATA
1 CAT-AAAGTGTCGATACATTTTTAAAA-AGTATCGATCCAAAAAACATCGAAACCGAAAATTATA
* * *
1154552 ATGTAATAGGTAAATTTACAATGTGACCGGTATAAATATACCAATTTTATGAGAAAATAGGT-AT
64 ATGTAATAGGTAAATTTACAATGTAACTGGTATAAATATACCGATTTTATGAGAAAATAGGTCA-
* *
1154616 ACATAATGTATCGACACTGTTTAAATTTGTGTCGATACAATTTGTCCATAATGAATGCCAAACAA
128 ACATAATGTATCGACACT-TTTAAATTTGTGTCGATACATTTTGTCCA-AATGAATGCCAAACGA
1154681 GATGCACG
191 GATGCACG
* * * *
1154689 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCTAAAAAACATTGAAACTGATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
* *
1154754 GTAATAGGTAAATTTACAATGTAACTGGTATAAGTATACCGATTTTATGAGAAAATAGGTGAACA
66 GTAATAGGTAAATTTACAATGTAACTGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACA
* * * *
1154819 TAATGTATCGACACTTTTTAGATTTGTGTCGATACATTTTGTCCAGAATGAATGCAAAACGGGGT
131 TAATGTATCGACAC-TTTTAAATTTGTGTCGATACATTTTGTCCA-AATGAATGCCAAACGAGAT
*
1154884 GTACG
194 GCACG
* * *
1154889 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCAAAACTGAAAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
* *
1154954 GTAATAGGTAAATTTACAATGTAACTGATATAAATATACCGATTTTATGAGAAAATAGGTTAACA
66 GTAATAGGTAAATTTACAATGTAACTGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACA
* * *
1155019 TTATGTATCGACACTTTTAAATTTGTGTGGATACGTTTT
131 TAATGTATCGACACTTTTAAATTTGTGTCGATACATTTT
1155058 TAAATTACAC
Statistics
Matches: 503, Mismatches: 52, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
197 7 0.01
198 80 0.16
199 102 0.20
200 305 0.61
201 9 0.02
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (198 bp):
CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
GTAATAGGTAAATTTACAATGTAACTGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACA
TAATGTATCGACACTTTTAAATTTGTGTCGATACATTTTGTCCAAATGAATGCCAAACGAGATGC
ACG
Found at i:1156414 original size:19 final size:19
Alignment explanation
Indices: 1156387--1156433 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
1156377 AATGTAGGGT
1156387 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
* *
1156406 TAATGTTG--TACGATTTA
1 TAATTTTGTATAAGATTTA
1156423 TAATTTTGTAT
1 TAATTTTGTAT
1156434 GTGAATGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 15 0.65
19 8 0.35
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1158177 original size:20 final size:22
Alignment explanation
Indices: 1158152--1158201 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1158142 TATATTCTTA
1158152 AAAGATGATAGA-T-TCTATTC
1 AAAGATGATAGATTCTCTATTC
*
1158172 AAAGATGATAGATTCTCTTTTC
1 AAAGATGATAGATTCTCTATTC
1158194 AAAGATGA
1 AAAGATGA
1158202 AAGCTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 12 0.44
21 1 0.04
22 14 0.52
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTATTC
Found at i:1159185 original size:45 final size:45
Alignment explanation
Indices: 1159063--1159375 Score: 540
Period size: 45 Copynumber: 7.0 Consensus size: 45
1159053 ATCCTCCGAA
**
1159063 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTTC-GG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGG
*
1159107 TCATCTGTAAGCCC-TCAGTGCATGATGTTTTCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGG
*
1159151 TCATCTGTAAGCCCTTCGGTGCATGATGTTTTCAAAGCCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGG
*
1159196 TCATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAGCCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGG
*
1159241 TTATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGG
1159286 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGG
* *
1159331 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTAAAAGCGTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGG
1159376 AGCTTTTTGA
Statistics
Matches: 257, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
43 26 0.10
44 30 0.12
45 201 0.78
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (45 bp):
TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGG
Found at i:1159278 original size:26 final size:26
Alignment explanation
Indices: 1159249--1159324 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 26
1159239 GGTTATCTGT
1159249 AAGCCCTTCAGTGCATGATGTTTTCA
1 AAGCCCTTCAGTGCATGATGTTTTCA
* *
1159275 AAG-CCTTC-GGGTCAT-CTG---T--
1 AAGCCCTTCAGTG-CATGATGTTTTCA
1159294 AAGCCCTTCAGTGCATGATGTTTTCA
1 AAGCCCTTCAGTGCATGATGTTTTCA
1159320 AAGCC
1 AAGCC
1159325 TTCGGGTCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 18
0.63 0.07 0.31
Matches are distributed among these distances:
19 3 0.08
20 8 0.22
21 5 0.14
24 5 0.14
25 8 0.22
26 8 0.22
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (26 bp):
AAGCCCTTCAGTGCATGATGTTTTCA
Found at i:1159522 original size:116 final size:114
Alignment explanation
Indices: 1159338--1159555 Score: 337
Period size: 116 Copynumber: 1.9 Consensus size: 114
1159328 GGGTCATCTG
* * * * * *
1159338 TAAGCCCTTCAGTGCATGATGTTTTAAAAGCGTTCGGGAGCTTTTTGATATTTAAAGCCTTCGGG
1 TAAGACCTACAGTGCAGGATGTTTTAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCAGG
*
1159403 TCATCTGTAAGACCTACAGTGCAAGATAATAAGACCTCAGGGCCATCCA
66 TCATCTGTAAGACCTACAGTACAAGATAATAAGACCTCAGGGCCATCCA
*
1159452 TAAGACCTACAGTGCAGGATGTTTTCAAATAGCCTTCGGGAGCTTTTTGATATTTAAATCCTCCA
1 TAAGACCTACAGTGCAGGATGTTTT-AAA-AGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCA
*
1159517 GGTCATCTGTAAGACCTACAGTACAAGATGATAAGACCT
64 GGTCATCTGTAAGACCTACAGTACAAGATAATAAGACCT
1159556 ACAATGCAGG
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 22 0.24
115 3 0.03
116 68 0.73
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (114 bp):
TAAGACCTACAGTGCAGGATGTTTTAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCAGG
TCATCTGTAAGACCTACAGTACAAGATAATAAGACCTCAGGGCCATCCA
Found at i:1159849 original size:3 final size:3
Alignment explanation
Indices: 1159841--1159920 Score: 97
Period size: 3 Copynumber: 26.3 Consensus size: 3
1159831 TATTTTTAAA
** * *
1159841 ATT ATT ATT ATT ATT ACA ATT ATT ATT ATT ATT ATT AAT ATA ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
* *
1159887 ATT ATT ATT ATT ATT ATT ATC ATC ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1159921 AATTACAGGC
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
3 64 0.97
4 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:1159851 original size:18 final size:18
Alignment explanation
Indices: 1159830--1159906 Score: 75
Period size: 18 Copynumber: 4.2 Consensus size: 18
1159820 ATTTTTCATT
*
1159830 TTATTTTTAAAATTATTA
1 TTATTATTAAAATTATTA
*
1159848 TTATTATTACAATTATTA
1 TTATTATTAAAATTATTA
* *
1159866 TTATTATTATTAA-TATAA
1 TTATTATTA-AAATTATTA
**
1159884 TATATTATTATTATTATTA
1 T-TATTATTAAAATTATTA
1159903 TTAT
1 TTAT
1159907 CATCATTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
18 35 0.70
19 15 0.30
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATTAAAATTATTA
Found at i:1161124 original size:2 final size:2
Alignment explanation
Indices: 1161105--1161146 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1161095 TTTCTTAGTC
* *
1161105 AT AT AA AT AT AT AA 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
1161147 TTGTTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1162573 original size:38 final size:38
Alignment explanation
Indices: 1162518--1162603 Score: 127
Period size: 38 Copynumber: 2.3 Consensus size: 38
1162508 TTCTGTGCTG
*
1162518 AATCATTCAGCACTGTTTTGCTGAATCAGTCATCACTA
1 AATCATTCAGCACTGTTTTGCTGAATCAGTCACCACTA
* * * *
1162556 AATCATTCAGCATTGTTTTGTTGAATTAGTCACCACTG
1 AATCATTCAGCACTGTTTTGCTGAATCAGTCACCACTA
1162594 AATCATTCAG
1 AATCATTCAG
1162604 AGGTGCGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (38 bp):
AATCATTCAGCACTGTTTTGCTGAATCAGTCACCACTA
Found at i:1164154 original size:59 final size:60
Alignment explanation
Indices: 1164087--1164214 Score: 165
Period size: 62 Copynumber: 2.1 Consensus size: 60
1164077 AATTGTCCCC
* *
1164087 CGATTATAA-AGTATTAT-TTTGTTGAG-TATTCGACTATTAAAAGTTACAAAAT-GATCATT
1 CGATTATAAGA-TATTATATTTGTTGAGTTA-TCGACTATTAAAAATTACAAAATAG-TCACT
1164146 CGATTATAAGATATTATACTTTGTTGAGTTCATCGACTATTAAAAATTACAAAATAGTCACT
1 CGATTATAAGATATTATA-TTTGTTGAGTT-ATCGACTATTAAAAATTACAAAATAGTCACT
1164208 CGATTAT
1 CGATTAT
1164215 TCATATGTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
59 15 0.25
60 1 0.02
61 9 0.15
62 34 0.56
63 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (60 bp):
CGATTATAAGATATTATATTTGTTGAGTTATCGACTATTAAAAATTACAAAATAGTCACT
Found at i:1167441 original size:60 final size:60
Alignment explanation
Indices: 1167319--1167448 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 60
1167309 ATATCTCTCC
* * * * *
1167319 AAACTATAACTTTCATTTTAAATTGATCGTTAAACTTTTGAGGATTCTAATTTGATCTCT
1 AAACTATAACTATCATTCTAAATTGATCCTTAAACTTTTGAGGATTCAAATTTGATCCCT
* *
1167379 AAACTATGACTATCATTCTAAATT-AGTCCTTAAACTTTTGCA-TATTCAAA-TTGTATCCCT
1 AAACTATAACTATCATTCTAAATTGA-TCCTTAAACTTTTG-AGGATTCAAATTTG-ATCCCT
*
1167439 AAATTATAAC
1 AAACTATAAC
1167449 CCTTTATCTA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
59 4 0.07
60 53 0.91
61 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.42
Consensus pattern (60 bp):
AAACTATAACTATCATTCTAAATTGATCCTTAAACTTTTGAGGATTCAAATTTGATCCCT
Found at i:1167726 original size:60 final size:58
Alignment explanation
Indices: 1167618--1167811 Score: 158
Period size: 60 Copynumber: 3.2 Consensus size: 58
1167608 AATATATGCA
* ** *
1167618 TATAGTTTGGGATGAAATTAGAATGTTCAGAAAATTTGGGGA-TCAATTTAGACTGAAAGT
1 TATAGTTTGGGATGAAATTA-AATGTTCA-AAAGTTTAAGGACT-AATTTAGAATGAAAGT
* *
1167678 TATAGTTTGGGGATGAAATTGAAATGTCCAAAAGTTTAAGGACTAATTTAGAATGATAGT
1 TATAGTTT-GGGATGAAATT-AAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAAAGT
* * * * * * * *
1167738 CATAGTATAGGGATAAAATTAAAATATTTAAAAGTTTAAGAACCAATTTAAAAT-AAGAGT
1 TATAGT-TTGGGATGAAATT-AAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAA-AGT
*
1167798 TATACTTTGAGGAT
1 TATAGTTTG-GGAT
1167812 ATGTAATGCA
Statistics
Matches: 108, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
59 3 0.03
60 84 0.78
61 20 0.19
62 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (58 bp):
TATAGTTTGGGATGAAATTAAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAAAGT
Found at i:1176044 original size:7 final size:7
Alignment explanation
Indices: 1176022--1176054 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1176012 CTTGATTTTT
1176022 TTATTTA
1 TTATTTA
*
1176029 TCATTTA
1 TTATTTA
1176036 TTATTTA
1 TTATTTA
1176043 TTA-TTA
1 TTATTTA
1176049 TTATTT
1 TTATTT
1176055 TTCTTTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (7 bp):
TTATTTA
Found at i:1176195 original size:6 final size:6
Alignment explanation
Indices: 1176179--1176221 Score: 59
Period size: 6 Copynumber: 6.7 Consensus size: 6
1176169 TCGAATCGAG
1176179 TTTTAAA TTTTAA TTTTAA TTTTTAA TTTTAA TTTTTAA TTTT
1 TTTT-AA TTTTAA TTTTAA -TTTTAA TTTTAA -TTTTAA TTTT
1176222 CACAATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 18 0.53
7 16 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:1176197 original size:13 final size:13
Alignment explanation
Indices: 1176179--1176221 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
1176169 TCGAATCGAG
*
1176179 TTTTAAATTTTAA
1 TTTTAATTTTTAA
1176192 TTTTAATTTTTAA
1 TTTTAATTTTTAA
1176205 TTTTAATTTTTAA
1 TTTTAATTTTTAA
1176218 TTTT
1 TTTT
1176222 CACAATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:1176550 original size:6 final size:6
Alignment explanation
Indices: 1176539--1176564 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1176529 GTGAAAATGG
1176539 TAAATT TAAATT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
1176565 TTTATTCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:1181692 original size:165 final size:164
Alignment explanation
Indices: 1181381--1181936 Score: 724
Period size: 165 Copynumber: 3.4 Consensus size: 164
1181371 CATTTGCAGT
* * * * * *
1181381 ATAAATCAAGACTAGAAGGGTTATTTGCCAACAAAGACCTTCGAGTTCGATTACGCTCAGCTCCA
1 ATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCA
** * * *
1181446 AGGTGTATCATTTGTAGCATAGCTTAAGTTGAGAAGGGCTATCTACCAAAGACCCTCAAGTTCGA
66 AGGCATATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGA
*
1181511 TTACACTCAGCTTCGAGGGCACATCATTTACAAT
131 TTACACTCAGCTTCGAGGGCACATCATTTACAAC
*
1181545 ATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACTTTCGAGTTCGACTACGCTCAGCTCC
1 ATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCC
* *
1181610 AAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCGAGTTCG
65 AAGGCATATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCG
*
1181675 ATTACACTCGGCTTCGAGGGCACATCATTTACAAC
130 ATTACACTCAGCTTCGAGGGCACATCATTTACAAC
* *
1181710 ATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCAAGTTCTACTACGCTCAGCTCCA
1 ATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCA
* * * *
1181775 AGGCATATCATTTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCTAACCAAAGACCTTCGAG
66 AGGCATATCA-TTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAG
* * * * * *
1181840 TTCGACTACGCTCAGC-TCCAAGGCACATAATTTACAGC
126 TTCGATTACACTCAGCTTCGAGGGCACATCATTTACAAC
* * * * * *
1181878 ATAGCTTAAGTCGAGAAGGGTTATCTG---CCAAAGACCCTCGAGTTCGACTGCGCTCAGCT
1 ATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
1181937 TCGAGGGTAC
Statistics
Matches: 346, Mismatches: 40, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
164 66 0.19
165 212 0.61
168 41 0.12
169 27 0.08
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (164 bp):
ATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCA
AGGCATATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGA
TTACACTCAGCTTCGAGGGCACATCATTTACAAC
Found at i:1181846 original size:249 final size:247
Alignment explanation
Indices: 1181490--1182126 Score: 778
Period size: 249 Copynumber: 2.6 Consensus size: 247
1181480 AGGGCTATCT
* * * * * * * *
1181490 ACCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAATATAACTCAAG
1 ACCAAAGACCTTCAAGTTCTACTAC-CTCAGC-TCCAAGGCACATCATTTGCAGTATAACTTAAG
* * * *
1181555 GCTAGAAGGGTTATCTG-TCACCAAAAGACTTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
64 TCGAGAAGGGTTATCTGCTAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* ** *
1181619 CATTTGTAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTC
128 AATTTACAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTC
*
1181684 GGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC
193 AGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC
* *
1181739 ACCAAAGACCTTCAAGTTCTACTACGCTCAGCTCCAAGGCATATCATTTTGCAGCATAACTTAAG
1 ACCAAAGACCTTCAAGTTCTACTAC-CTCAGCTCCAAGGCACATCA-TTTGCAGTATAACTTAAG
1181804 TCGAGAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATA
64 TCGAGAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATA
* * * *
1181869 ATTTACAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGACTGCGCTCA
129 ATTTACAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCA
* *
1181934 GCTTCGAGGGTACATTATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC
194 GCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC
* * * * * * *
1181988 ACCAAAGAACTTCGA-TTTTGACTA--ACATCTCTAAGGCACATCATTTGCAGTATAGCTTAAGT
1 ACCAAAGACCTTCAAGTTCT-ACTACCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGT
* * * * * * * * ** **
1182050 CGAGAAGTGCTATCTGCCAACCGAAGACCTCCGGGTTTGATTACATTCAGCTAAAAGGCACATCA
65 CGAGAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT--
1182115 AATTTACAGCAT
128 AATTTACAGCAT
1182127 GGCTCAAGGC
Statistics
Matches: 336, Mismatches: 47, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
245 68 0.20
246 15 0.04
247 12 0.04
248 14 0.04
249 223 0.66
250 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (247 bp):
ACCAAAGACCTTCAAGTTCTACTACCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTC
GAGAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATAAT
TTACAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCAGC
TTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC
Found at i:1183781 original size:19 final size:19
Alignment explanation
Indices: 1183753--1183805 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
1183743 ATTTTTTTAT
*
1183753 TTATCGTTTTTTTATTTATTA
1 TTAT-GTTTTTTT-TTCATTA
*
1183774 TTAT-TTTTTCTTTTCATTC
1 TTATGTTTTT-TTTTCATTA
1183793 TTATGTTTTTTTT
1 TTATGTTTTTTTT
1183806 GTTTGATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 17 0.61
20 7 0.25
21 4 0.14
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.75
Consensus pattern (19 bp):
TTATGTTTTTTTTTCATTA
Found at i:1183924 original size:13 final size:13
Alignment explanation
Indices: 1183906--1183935 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1183896 TCGAATCGAG
1183906 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
1183919 TTTTAATTTTTAA
1 TTTTAAATTTTAA
1183932 TTTT
1 TTTT
1183936 CGAAATTAAA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:1185190 original size:3 final size:3
Alignment explanation
Indices: 1185177--1185213 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1185167 TTAATCCAAG
*
1185177 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1185214 ATATTATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1185573 original size:13 final size:13
Alignment explanation
Indices: 1185555--1185590 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1185545 CAACTTTGTG
1185555 AGTTGTGTCTCAA
1 AGTTGTGTCTCAA
*
1185568 AGTTGTCTCTCAA
1 AGTTGTGTCTCAA
1185581 AGTTGTGTCT
1 AGTTGTGTCT
1185591 AAGATTGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (13 bp):
AGTTGTGTCTCAA
Found at i:1192982 original size:13 final size:13
Alignment explanation
Indices: 1192961--1192990 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1192951 ACTTTGTGAA
*
1192961 TTGTGTCTCAAAG
1 TTGTCTCTCAAAG
1192974 TTGTCTCTCAAAG
1 TTGTCTCTCAAAG
1192987 TTGT
1 TTGT
1192991 GTATAAGATT
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:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (13 bp):
TTGTCTCTCAAAG
Found at i:1193949 original size:21 final size:21
Alignment explanation
Indices: 1193921--1194035 Score: 137
Period size: 21 Copynumber: 5.5 Consensus size: 21
1193911 GTTTCCAGAT
*
1193921 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
1193942 TTGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1193963 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
1193984 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
1194004 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
1194025 TCGCAATGCGA
1 TCGCAATGCGA
1194036 TTATGTAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
20 15 0.18
21 67 0.82
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1194008 original size:20 final size:20
Alignment explanation
Indices: 1193983--1194052 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1193973 AACTTGGACT
1193983 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
1194003 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
*
1194024 ATCGCAATGCGATTATGTAA
1 ATCGCAATGCGAATATGTAA
1194044 ATCGCAATG
1 ATCGCAATG
1194053 GGATAGTCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
18 2 0.05
19 3 0.07
20 21 0.50
21 12 0.29
22 2 0.05
23 2 0.05
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:1194024 original size:41 final size:41
Alignment explanation
Indices: 1193921--1194052 Score: 160
Period size: 41 Copynumber: 3.2 Consensus size: 41
1193911 GTTTCCAGAT
* * * *
1193921 TCGCAATGCGAACTTCGACTATTGCAATGCGAACT-TGGACTA
1 TCGCAATGCGAACGTCGACTATCGCAATGCGAA-TATGTA-AA
* *
1193963 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAACGTCGACTATCGCAATGCGAATATGTAAA
*
1194004 TCGCAATGCGATA-GTCGACTATCGCAATGCGATTATGTAAA
1 TCGCAATGCGA-ACGTCGACTATCGCAATGCGAATATGTAAA
1194045 TCGCAATG
1 TCGCAATG
1194053 GGATAGTCCA
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
41 46 0.57
42 35 0.43
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (41 bp):
TCGCAATGCGAACGTCGACTATCGCAATGCGAATATGTAAA
Found at i:1194036 original size:21 final size:21
Alignment explanation
Indices: 1193921--1194098 Score: 97
Period size: 21 Copynumber: 8.6 Consensus size: 21
1193911 GTTTCCAGAT
*
1193921 TCGCAATGCGA-ACTTCGACTA
1 TCGCAATGCGATA-GTCGACTA
* * *
1193942 TTGCAATGCGA-ACTTGGACTA
1 TCGCAATGCGATA-GTCGACTA
* *
1193963 TCGCAATGCGA-ACTTGGACTA
1 TCGCAATGCGATA-GTCGACTA
*
1193984 TCGCAATGCGAATA-T-GTA-AA
1 TCGCAATGCG-ATAGTCG-ACTA
1194004 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGATAGTCGACTA
*
1194025 TCGCAATGCGATTA-T-GTA-AA
1 TCGCAATGCGA-TAGTCG-ACTA
* * *
1194045 TCGCAATGGGATAGTCCAAGT-
1 TCGCAATGCGATAGT-CGACTA
*
1194066 TCGCATTGCGATAGTCGACTA
1 TCGCAATGCGATAGTCGACTA
*
1194087 TCGCATTGCGAT
1 TCGCAATGCGAT
1194099 TTACATATTC
Statistics
Matches: 131, Mismatches: 13, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.04
20 30 0.23
21 92 0.70
22 3 0.02
23 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGATAGTCGACTA
Found at i:1194070 original size:41 final size:41
Alignment explanation
Indices: 1193980--1194077 Score: 135
Period size: 41 Copynumber: 2.4 Consensus size: 41
1193970 GCGAACTTGG
* *
1193980 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCG
1 ACTATCGCAATGCGATTATGTAAATCGCAATGCGATAGTCA
*
1194021 ACTATCGCAATGCGATTATGTAAATCGCAATGGGATAGTCCA
1 ACTATCGCAATGCGATTATGTAAATCGCAATGCGATAGT-CA
* *
1194063 AGT-TCGCATTGCGAT
1 ACTATCGCAATGCGAT
1194078 AGTCGACTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 48 0.94
42 3 0.06
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (41 bp):
ACTATCGCAATGCGATTATGTAAATCGCAATGCGATAGTCA
Found at i:1194111 original size:62 final size:62
Alignment explanation
Indices: 1193983--1194143 Score: 181
Period size: 62 Copynumber: 2.6 Consensus size: 62
1193973 AACTTGGACT
* **
1193983 ATCGCAATGCGAATATGT--AAA-TCGCAATGCGATAGTCGACTATCGCAATGCGATTATGTAA
1 ATCGCAATGCG-ATA-GTCCAAATTCGCATTGCGATAGTCGACTATCGCAATGCGATTACATAA
* * *
1194044 ATCGCAATGGGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACAT-A
1 ATCGCAATGCGATAGTCCAAATTCGCATTGCGATAGTCGACTATCGCAATGCGA-TTACATAA
* *
1194106 TTCGCATTGCGATAGTCCAAATTCG--TTGCGATAGTCGA
1 ATCGCAATGCGATAGTCCAAATTCGCATTGCGATAGTCGA
1194144 AGTTCGCGTT
Statistics
Matches: 86, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
59 2 0.02
60 16 0.19
61 12 0.14
62 52 0.60
63 4 0.05
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (62 bp):
ATCGCAATGCGATAGTCCAAATTCGCATTGCGATAGTCGACTATCGCAATGCGATTACATAA
Found at i:1194280 original size:5 final size:5
Alignment explanation
Indices: 1194252--1194299 Score: 69
Period size: 5 Copynumber: 9.0 Consensus size: 5
1194242 CGTATTACCA
1194252 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGACC CGACC
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGACC
1194300 TGAAACGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 25 0.60
6 17 0.40
ACGTcount: A:0.25, C:0.56, G:0.19, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:1194367 original size:19 final size:19
Alignment explanation
Indices: 1194343--1194381 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1194333 GAGAGTCCTC
1194343 CTTGTTCTCTATCACTCAA
1 CTTGTTCTCTATCACTCAA
1194362 CTTGTTCTCTATCACTCAA
1 CTTGTTCTCTATCACTCAA
1194381 C
1 C
1194382 AAGGAAGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.41
Consensus pattern (19 bp):
CTTGTTCTCTATCACTCAA
Found at i:1194905 original size:6 final size:6
Alignment explanation
Indices: 1194849--1194901 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
1194839 ATCTCGTCTC
*
1194849 GGGTCG TGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTC- GGGTCG
1 GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG
*
1194896 TGGTCG
1 GGGTCG
1194902 TGGTAATACG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
5 5 0.12
6 38 0.88
ACGTcount: A:0.00, C:0.17, G:0.62, T:0.21
Consensus pattern (6 bp):
GGGTCG
Found at i:1195004 original size:21 final size:20
Alignment explanation
Indices: 1194978--1195023 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1194968 ATGCAGTCGT
* *
1194978 TGCGAATTTGGACTATCGCAA
1 TGCGAATATGGA-AATCGCAA
*
1194999 TGCGAATATGTAAATCGCAA
1 TGCGAATATGGAAATCGCAA
1195019 TGCGA
1 TGCGA
1195024 TAGTCGACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCGAATATGGAAATCGCAA
Found at i:1195078 original size:21 final size:21
Alignment explanation
Indices: 1195034--1195145 Score: 90
Period size: 21 Copynumber: 5.4 Consensus size: 21
1195024 TAGTCGACTA
* *
1195034 TCGCATTGCGAT-TTACATGT
1 TCGCATTGCGATAGTACAAGT
*
1195054 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTACAAGT
* * *
1195075 TCGCATTACGATAGT-CGACT
1 TCGCATTGCGATAGTACAAGT
*
1195095 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTACA-AGT
1195116 TCGCATTGCGATAGT-CGAAGT
1 TCGCATTGCGATAGTAC-AAGT
*
1195137 TCGCGTTGC
1 TCGCATTGC
1195146 AAATCTGGAA
Statistics
Matches: 74, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
20 30 0.41
21 43 0.58
22 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATAGTACAAGT
Found at i:1195079 original size:62 final size:62
Alignment explanation
Indices: 1195013--1195140 Score: 220
Period size: 62 Copynumber: 2.1 Consensus size: 62
1195003 AATATGTAAA
* *
1195013 TCGCAATGCGATAGTCGACTATCGCATTGCGATTTACATGTTCGCATTGCGATAGTCCAAGT
1 TCGCAATACGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
* *
1195075 TCGCATTACGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
1 TCGCAATACGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1195137 TCGC
1 TCGC
1195141 GTTGCAAATC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (62 bp):
TCGCAATACGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
Found at i:1197420 original size:184 final size:184
Alignment explanation
Indices: 1197046--1197988 Score: 1216
Period size: 184 Copynumber: 5.0 Consensus size: 184
1197036 CCCTGTCAAA
* * * *
1197046 TGATTCACAACATATTAGAACCGCATGATTAGGATGTAGGTGAAAGAACACCAACATCATCGACA
1 TGATTCACAACATATTAGAACCGCACGATTAGGATGCAGGTGAAAGCATACCAACATCATCGACA
* * *
1197111 AAGATTACCCTGTCTCGGATCTATCACTATTCACTAGGGGGTAATAGACATGCTTTTGTCATGAC
66 AAGATTACCCTGCCTCGG----AT--CTA-TCACTAGGGGGAAATAGACATGCTTTTATCATGAC
* * * *
1197176 ATGTTCGCCATATCAACGAAGG-TAAACAAGAAACTGAAAAACAACGGGTATATCAAATCTG
124 ATGTTGGCCATATCAATG-AGGATAAACAAGAAACTGAAAAACAATGAGTATATCAAATCTG
* *
1197237 TGATTCCCAACGTATTAGAACCGCACGATTAGGATGCAGGTGAAAGCATACCAACATCATCGACA
1 TGATTCACAACATATTAGAACCGCACGATTAGGATGCAGGTGAAAGCATACCAACATCATCGACA
* * * *
1197302 AAGATTACCCTGTCTCGGATCTATCACTAGGGGGTAATAGACATGCTTTTGTCATGACATGTTCG
66 AAGATTACCCTGCCTCGGATCTATCACTAGGGGGAAATAGACATGCTTTTATCATGACATGTTGG
*
1197367 CCATATCAATGAGGATAAACAAGAAACTGAAAAACAATGAGTATATAAAATCTG
131 CCATATCAATGAGGATAAACAAGAAACTGAAAAACAATGAGTATATCAAATCTG
* * *
1197421 TGATTCCCAACGTATTAGAACCGCACGATTAGGATGCAGGTGAAAGCATACCAACATCATTGACA
1 TGATTCACAACATATTAGAACCGCACGATTAGGATGCAGGTGAAAGCATACCAACATCATCGACA
* * *
1197486 AAGATTACCCTGCCTTGGATCTATCACTAGGGGGAAATTGACCTGCTTTTATCATGACATGTTGG
66 AAGATTACCCTGCCTCGGATCTATCACTAGGGGGAAATAGACATGCTTTTATCATGACATGTTGG
* *
1197551 CCATATCAATGAGGGTAAAGTAAACAAGAAACCGAAAAACAATGGGTATATCAAATCTTG
131 CCATATCAATGA-GG---A-TAAACAAGAAACTGAAAAACAATGAGTATATCAAATC-TG
* *
1197611 TGATTCACAACATATTAGAACCGCACGATTAGGATGCAGATGAAAGCATACCAACATCATTGACA
1 TGATTCACAACATATTAGAACCGCACGATTAGGATGCAGGTGAAAGCATACCAACATCATCGACA
* **
1197676 AAGATTACCCTGCCTCGGATCCTATCAATAGGGGGAAATTTACATGCTTTTATCATGACGTGTAT
66 AAGATTACCCTGCCTCGGAT-CTATCACTAGGGGGAAATAGACATGCTTTTATCATGAC----A-
* * * *
1197741 TGTTGGCCATATCAACGAAGG-TAAACAAGAAACTGAAAAACAA-CAG-GTAT--AATCTA
125 TGTTGGCCATATCAATG-AGGATAAACAAGAAACTGAAAAACAATGAGTATATCAAATCTG
** ** * *
1197797 TGATTCACAACATATTAGAACCATACGATTAGGACACAGGTGCAAGCATATCAACATCATCGACA
1 TGATTCACAACATATTAGAACCGCACGATTAGGATGCAGGTGAAAGCATACCAACATCATCGACA
* * * * *
1197862 AAGATTAACCTGCCTCGGATCTATCACTAAGGGGAAATCGATATGCTTTTATCATGACAT-TAGG
66 AAGATTACCCTGCCTCGGATCTATCACTAGGGGGAAATAGACATGCTTTTATCATGACATGTTGG
*
1197926 CCATATCAATGAGGATAAACAAGAAACTGAAAAACAATGTGTATATCAAATCTG
131 CCATATCAATGAGGATAAACAAGAAACTGAAAAACAATGAGTATATCAAATCTG
*
1197980 TGAATCACA
1 TGATTCACA
1197989 TTTGCAAGTC
Statistics
Matches: 678, Mismatches: 55, Indels: 46
0.87 0.07 0.06
Matches are distributed among these distances:
178 3 0.00
179 35 0.05
180 2 0.00
181 4 0.01
183 16 0.02
184 222 0.33
185 38 0.06
186 77 0.11
187 6 0.01
188 1 0.00
189 37 0.05
190 84 0.12
191 133 0.20
195 1 0.00
196 18 0.03
197 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (184 bp):
TGATTCACAACATATTAGAACCGCACGATTAGGATGCAGGTGAAAGCATACCAACATCATCGACA
AAGATTACCCTGCCTCGGATCTATCACTAGGGGGAAATAGACATGCTTTTATCATGACATGTTGG
CCATATCAATGAGGATAAACAAGAAACTGAAAAACAATGAGTATATCAAATCTG
Found at i:1202219 original size:15 final size:15
Alignment explanation
Indices: 1202199--1202237 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1202189 GATCAAATAT
*
1202199 ATCAACATGATTAAC
1 ATCAACATGAGTAAC
* *
1202214 ATCAACATTAGTATC
1 ATCAACATGAGTAAC
1202229 ATCAACATG
1 ATCAACATG
1202238 GTCATTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.28
Consensus pattern (15 bp):
ATCAACATGAGTAAC
Found at i:1203046 original size:22 final size:24
Alignment explanation
Indices: 1203021--1203073 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
1203011 ATATTTTTAT
1203021 TAATAATC-T-AAAAATAAAA-AA
1 TAATAATCTTAAAAAATAAAATAA
1203042 CTAATAATCTTGAAAAAATAAAATAA
1 -TAATAATCTT-AAAAAATAAAATAA
1203068 TAATAA
1 TAATAA
1203074 AAACATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 8 0.30
23 1 0.04
25 16 0.59
26 2 0.07
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (24 bp):
TAATAATCTTAAAAAATAAAATAA
Found at i:1203611 original size:60 final size:59
Alignment explanation
Indices: 1203471--1203617 Score: 147
Period size: 59 Copynumber: 2.5 Consensus size: 59
1203461 AATGGTCTCC
* * * * *
1203471 CGACTATAGGACGTTATTTTATTGAGTCCATCGACTTCTAAATATTATAAAAGGTCCTT
1 CGACTATAAGAAGTTATTTTGTTGAGTCCATCAACTTCTAAATATTACAAAAGGTCCTT
* * **
1203530 CGATTAT-AGAGTGTTGCTTTGTTGAGTCCATCAACTGT-TAAA-AGTTACAAAACGGTCCTT
1 CGACTATAAGA-AGTTATTTTGTTGAGTCCATCAACT-TCTAAATA-TTACAAAA-GGTCCTT
*
1203590 CTACTATAAGAAGTTATTTTGTTGAGTC
1 CGACTATAAGAAGTTATTTTGTTGAGTC
1203618 TCTCGATTAT
Statistics
Matches: 70, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
58 3 0.04
59 37 0.53
60 27 0.39
61 3 0.04
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (59 bp):
CGACTATAAGAAGTTATTTTGTTGAGTCCATCAACTTCTAAATATTACAAAAGGTCCTT
Found at i:1204133 original size:26 final size:26
Alignment explanation
Indices: 1204084--1204136 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
1204074 AAAATGCATT
*
1204084 TTATATGTCATTATATGTGCTTTGAA
1 TTATATGTCATTATATGTGATTTGAA
1204110 TTATATGTCATTATATGCT-ATTTGAA
1 TTATATGTCATTATATG-TGATTTGAA
1204136 T
1 T
1204137 GAGTGATGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.51
Consensus pattern (26 bp):
TTATATGTCATTATATGTGATTTGAA
Found at i:1205201 original size:16 final size:16
Alignment explanation
Indices: 1205180--1205214 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1205170 TTAACGTTAT
1205180 TTTAAAATTAAATTAA
1 TTTAAAATTAAATTAA
* *
1205196 TTTAAATTTAAATTGA
1 TTTAAAATTAAATTAA
1205212 TTT
1 TTT
1205215 TTCTTACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTAAAATTAAATTAA
Found at i:1207171 original size:3 final size:3
Alignment explanation
Indices: 1207151--1207211 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
1207141 TTTTTTCATT
* * * * * *
1207151 TTA TT- TTA TTG TTG TTA TTA TTA TTA TTA TTA TTA TTG TTG TTG TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1207198 TTA CTA TTA TTA TT
1 TTA TTA TTA TTA TT
1207212 TACCTTTTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1207843 original size:18 final size:17
Alignment explanation
Indices: 1207801--1207843 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
1207791 AAGAGAGAAA
1207801 ATAGAAAGAAAAAAAACC
1 ATAGAAA-AAAAAAAACC
*
1207819 -TAG-AAAAGAAAAACC
1 ATAGAAAAAAAAAAACC
1207834 ATAGAAAAAA
1 ATAGAAAAAA
1207844 TTAAAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.72, C:0.09, G:0.12, T:0.07
Consensus pattern (17 bp):
ATAGAAAAAAAAAAACC
Found at i:1208844 original size:2 final size:2
Alignment explanation
Indices: 1208837--1208888 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1208827 TAATATTATG
1208837 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
1208879 AT AT AT AT AT
1 AT AT AT AT AT
1208889 TACTTAATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1210622 original size:4 final size:5
Alignment explanation
Indices: 1210611--1210639 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1210601 TTTTGACTAA
1210611 TTGTT TTG-T TTGTT TTGTT TTGTT TTGTT
1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT
1210640 ATTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (5 bp):
TTGTT
Found at i:1210645 original size:19 final size:18
Alignment explanation
Indices: 1210611--1210649 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
1210601 TTTTGACTAA
1210611 TTGTTTTGTTTGTTTTGTT
1 TTGTTTTGTTTGTTTT-TT
1210630 TTGTTTTGTTAT-TTTTTT
1 TTGTTTTGTT-TGTTTTTT
1210648 TT
1 TT
1210650 CTTCATATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 14 0.74
20 1 0.05
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (18 bp):
TTGTTTTGTTTGTTTTTT
Found at i:1213364 original size:30 final size:28
Alignment explanation
Indices: 1213301--1213391 Score: 87
Period size: 30 Copynumber: 3.2 Consensus size: 28
1213291 TTTTTGCACT
* *
1213301 TGCATCATTCATTATGCATA-AAT-AAA
1 TGCATCATTTATAATGCATACAATAAAA
*
1213327 TTCATCATTTATAATGCATCACCAATAAAA
1 TGCATCATTTATAATGCAT-A-CAATAAAA
* *
1213357 TGCATCATTTATAACGCATTAGCAATAACA
1 TGCATCATTTATAATGCA-TA-CAATAAAA
1213387 TGCAT
1 TGCAT
1213392 TCAAATTTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
26 16 0.30
27 1 0.02
29 3 0.06
30 32 0.60
31 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.33
Consensus pattern (28 bp):
TGCATCATTTATAATGCATACAATAAAA
Found at i:1220319 original size:7 final size:7
Alignment explanation
Indices: 1220307--1220380 Score: 82
Period size: 7 Copynumber: 10.6 Consensus size: 7
1220297 CACATGAAGA
1220307 AAAAAAG
1 AAAAAAG
1220314 AAAAAA-
1 AAAAAAG
1220320 AAAGGAAATG
1 AAA--AAA-G
1220330 AAAAAAG
1 AAAAAAG
*
1220337 AAAACAG
1 AAAAAAG
1220344 AAAAAAG
1 AAAAAAG
*
1220351 -GAAAAG
1 AAAAAAG
1220357 AAAAAAG
1 AAAAAAG
1220364 AAAAAAG
1 AAAAAAG
1220371 -AAAAAG
1 AAAAAAG
1220377 AAAA
1 AAAA
1220381 TTAAATAAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
6 14 0.25
7 34 0.60
8 6 0.11
10 3 0.05
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:1220347 original size:27 final size:27
Alignment explanation
Indices: 1220317--1220375 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
1220307 AAAAAAGAAA
* *
1220317 AAAAAAGGAAATGAAAAAAGAAAACAG
1 AAAAAAGGAAAAGAAAAAAGAAAAAAG
1220344 AAAAAAGGAAAAGAAAAAAGAAAAAAG
1 AAAAAAGGAAAAGAAAAAAGAAAAAAG
1220371 AAAAA
1 AAAAA
1220376 GAAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (27 bp):
AAAAAAGGAAAAGAAAAAAGAAAAAAG
Found at i:1220355 original size:20 final size:20
Alignment explanation
Indices: 1220308--1220380 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
1220298 ACATGAAGAA
1220308 AAAAAGAAAAAA-AAAGGAAATG
1 AAAAAGAAAAAAGAAA--AAA-G
*
1220330 AAAAAAGAAAACAGAAAAAAG
1 -AAAAAGAAAAAAGAAAAAAG
*
1220351 GAAAAGAAAAAAGAAAAAAG
1 AAAAAGAAAAAAGAAAAAAG
1220371 AAAAAGAAAA
1 AAAAAGAAAA
1220381 TTAAATAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
20 27 0.60
21 1 0.02
22 3 0.07
23 11 0.24
24 3 0.07
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAAGAAAAAAG
Found at i:1220368 original size:13 final size:13
Alignment explanation
Indices: 1220303--1220380 Score: 81
Period size: 13 Copynumber: 6.1 Consensus size: 13
1220293 ATTACACATG
*
1220303 AAGAAAAAA-AGA
1 AAGAAAAAAGAAA
*
1220315 AA-AAAAAAGGAA
1 AAGAAAAAAGAAA
*
1220327 ATGAAAAAAGAAA
1 AAGAAAAAAGAAA
*
1220340 ACAGAAAAAAGGAA
1 A-AGAAAAAAGAAA
1220354 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
1220367 AA-AGAAAAAGAAA
1 AAGA-AAAAAGAAA
1220380 A
1 A
1220381 TTAAATAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
11 6 0.11
12 5 0.09
13 33 0.60
14 11 0.20
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:1220390 original size:27 final size:26
Alignment explanation
Indices: 1220305--1220390 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 26
1220295 TACACATGAA
* *
1220305 GAAAAAA-AGAAAA-AAAAAGGAAAT
1 GAAAAAAGAAAAAAGAAAAAGAAAAT
*
1220329 GAAAAAAGAAAACAGAAAAAAGGAAAA-
1 GAAAAAAGAAAAAAG-AAAAA-GAAAAT
1220356 GAAAAAAGAAAAAAGAAAAAGAAAAT
1 GAAAAAAGAAAAAAGAAAAAGAAAAT
*
1220382 TAAATAAAG
1 GAAA-AAAG
1220391 GAGGGATCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
24 7 0.14
25 9 0.18
26 8 0.16
27 23 0.45
28 4 0.08
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.05
Consensus pattern (26 bp):
GAAAAAAGAAAAAAGAAAAAGAAAAT
Found at i:1221571 original size:20 final size:20
Alignment explanation
Indices: 1221546--1221588 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1221536 TCTAAGAGCT
*
1221546 CATTTAGGACCATGTAGATG
1 CATTTAGGACCATATAGATG
* *
1221566 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
1221586 CAT
1 CAT
1221589 GTGGTAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:1223416 original size:12 final size:12
Alignment explanation
Indices: 1223372--1223422 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
1223362 CATAGCATCT
1223372 TTATTTTACTTG
1 TTATTTTACTTG
*
1223384 TTAATTTT-TTTG
1 TT-ATTTTACTTG
1223396 TATAGTTTTACTTG
1 T-TA-TTTTACTTG
*
1223410 TTATTTTCCTTG
1 TTATTTTACTTG
1223422 T
1 T
1223423 CTTTTTCAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 16 0.50
13 12 0.38
14 4 0.12
ACGTcount: A:0.16, C:0.08, G:0.10, T:0.67
Consensus pattern (12 bp):
TTATTTTACTTG
Found at i:1226217 original size:11 final size:11
Alignment explanation
Indices: 1226197--1226227 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1226187 GTGCACACGT
*
1226197 CGCACGACCGC
1 CGCACCACCGC
1226208 CGCACCACCGC
1 CGCACCACCGC
1226219 CGCACCACC
1 CGCACCACC
1226228 ATAAGTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.61, G:0.19, T:0.00
Consensus pattern (11 bp):
CGCACCACCGC
Done.