Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 145 of 199
Found at i:43526447 original size:32 final size:33
Alignment explanation
Indices: 43526409--43526495 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 33
43526399 ACTTTTCCGA
* *
43526409 AAAATATTTT-CAGGAAATC-TGCCAAACAGCAG
1 AAAATATTTTACAGCAAATCAT-CCAAACACCAG
*
43526441 AAAATATTTTACA-CAGATTCATCCAAACACCAG
1 AAAATATTTTACAGCA-AATCATCCAAACACCAG
* *
43526474 AAAATATTTTCCAGTAAATCAT
1 AAAATATTTTACAGCAAATCAT
43526496 TTTACAGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
32 11 0.24
33 32 0.71
34 2 0.04
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.26
Consensus pattern (33 bp):
AAAATATTTTACAGCAAATCATCCAAACACCAG
Found at i:43526528 original size:34 final size:35
Alignment explanation
Indices: 43526474--43526540 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
43526464 CAAACACCAG
*
43526474 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
43526509 AAAACATTTTCTAG-AAATCATTTTACCGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
43526541 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:43527706 original size:17 final size:18
Alignment explanation
Indices: 43527676--43527721 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
43527666 ATTTAAATTG
43527676 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
43527694 CGGTCGC-GTCGCG-TTT
1 CGGTCGCGGTCGCGTTTT
43527710 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
43527722 GACATAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 3 0.11
17 6 0.22
18 7 0.26
ACGTcount: A:0.00, C:0.30, G:0.41, T:0.28
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:43528547 original size:29 final size:30
Alignment explanation
Indices: 43528502--43528571 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
43528492 TTCATATTTC
*
43528502 TTTTTCTATTGCTTTTGAGTT-TTGATTACT
1 TTTTTCTATTGCTTTTGACTTCTT-ATTACT
* *
43528532 TTTTTCTATTTC-TTTGACTTCTTTTTACT
1 TTTTTCTATTGCTTTTGACTTCTTATTACT
*
43528561 TTTTTTTATTG
1 TTTTTCTATTG
43528572 AAAGCTCTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.69
Consensus pattern (30 bp):
TTTTTCTATTGCTTTTGACTTCTTATTACT
Found at i:43529528 original size:5 final size:5
Alignment explanation
Indices: 43529518--43529547 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
43529508 AACCTTATTC
43529518 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
43529548 GAAGTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:43532007 original size:23 final size:23
Alignment explanation
Indices: 43531977--43532022 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
43531967 TCTTCCGACT
43531977 TGCACAGTTTATTAAACTCATCA
1 TGCACAGTTTATTAAACTCATCA
43532000 TGCACAGTTTATTAAACTCATCA
1 TGCACAGTTTATTAAACTCATCA
43532023 GAACAGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (23 bp):
TGCACAGTTTATTAAACTCATCA
Found at i:43533257 original size:18 final size:18
Alignment explanation
Indices: 43533234--43533270 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
43533224 TATAGTTTGA
*
43533234 TATTCGAATTATTCTAAT
1 TATTCGAATTATTCAAAT
*
43533252 TATTCGAGTTATTCAAAT
1 TATTCGAATTATTCAAAT
43533270 T
1 T
43533271 CGAAAACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (18 bp):
TATTCGAATTATTCAAAT
Found at i:43551387 original size:19 final size:21
Alignment explanation
Indices: 43551365--43551414 Score: 77
Period size: 19 Copynumber: 2.4 Consensus size: 21
43551355 TTTAAAAATA
43551365 TTTTAAAATAC-TTTTTT-AT
1 TTTTAAAATACTTTTTTTAAT
43551384 TTTTAAAATACTTTTTTTAAT
1 TTTTAAAATACTTTTTTTAAT
43551405 TTTCTAAAAT
1 TTT-TAAAAT
43551415 TTTTTGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.39
20 6 0.21
21 5 0.18
22 6 0.21
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAAAATACTTTTTTTAAT
Found at i:43551418 original size:20 final size:19
Alignment explanation
Indices: 43551365--43551425 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
43551355 TTTAAAAATA
*
43551365 TTTTAAAATACTTTTTTAT
1 TTTTAAAATATTTTTTTAT
43551384 TTTTAAAATACTTTTTTTAAT
1 TTTTAAAATA-TTTTTTT-AT
*
43551405 TTTCTAAAAT-TTTTTGTAT
1 TTT-TAAAATATTTTTTTAT
43551424 TT
1 TT
43551426 ATTTAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 14 0.38
20 12 0.32
21 5 0.14
22 6 0.16
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTAAAATATTTTTTTAT
Found at i:43551657 original size:13 final size:13
Alignment explanation
Indices: 43551639--43551708 Score: 52
Period size: 13 Copynumber: 5.4 Consensus size: 13
43551629 AAATGGTTCA
43551639 CACATTGAGCTCG
1 CACATTGAGCTCG
*
43551652 CACATT-AGGCTTG
1 CACATTGA-GCTCG
*** *
43551665 TGTATTGAGCTCA
1 CACATTGAGCTCG
*
43551678 CACATTGGGCTCG
1 CACATTGAGCTCG
* *
43551691 CATATTGAGCTCA
1 CACATTGAGCTCG
43551704 CACAT
1 CACAT
43551709 AGGGCTCGCG
Statistics
Matches: 40, Mismatches: 15, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
12 1 0.03
13 38 0.95
14 1 0.03
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (13 bp):
CACATTGAGCTCG
Found at i:43551681 original size:26 final size:26
Alignment explanation
Indices: 43551642--43551731 Score: 92
Period size: 26 Copynumber: 3.5 Consensus size: 26
43551632 TGGTTCACAC
* * **
43551642 ATTGAGCTCGCACATTAGGCTTGTGT
1 ATTGAGCTCACACATTAGGCTCGCAT
*
43551668 ATTGAGCTCACACATTGGGCTCGCAT
1 ATTGAGCTCACACATTAGGCTCGCAT
*
43551694 ATTGAGCTCACACA-TAGGGCTCGCGT
1 ATTGAGCTCACACATTA-GGCTCGCAT
**
43551720 AGAGAGCTCACA
1 ATTGAGCTCACA
43551732 TGACGCTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
25 1 0.02
26 53 0.98
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (26 bp):
ATTGAGCTCACACATTAGGCTCGCAT
Found at i:43551715 original size:13 final size:13
Alignment explanation
Indices: 43551668--43551715 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
43551658 AGGCTTGTGT
*
43551668 ATTGAGCTCACAC
1 ATTGGGCTCACAC
* *
43551681 ATTGGGCTCGCAT
1 ATTGGGCTCACAC
*
43551694 ATTGAGCTCACAC
1 ATTGGGCTCACAC
*
43551707 ATAGGGCTC
1 ATTGGGCTC
43551716 GCGTAGAGAG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (13 bp):
ATTGGGCTCACAC
Found at i:43562237 original size:16 final size:17
Alignment explanation
Indices: 43562212--43562244 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
43562202 TTCCATGTTA
43562212 GATTAAATTG-AATGAG
1 GATTAAATTGAAATGAG
*
43562228 GATTATATTGAAATGAG
1 GATTAAATTGAAATGAG
43562245 TTAAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.33
Consensus pattern (17 bp):
GATTAAATTGAAATGAG
Found at i:43567851 original size:22 final size:22
Alignment explanation
Indices: 43567826--43567874 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
43567816 GTTTTGTTTG
**
43567826 TTATTTTGATGTTATTTTATTA
1 TTATTTTGATACTATTTTATTA
* * *
43567848 TTATATTGTTACTATTTTATTG
1 TTATTTTGATACTATTTTATTA
43567870 TTATT
1 TTATT
43567875 ATTTGGATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.67
Consensus pattern (22 bp):
TTATTTTGATACTATTTTATTA
Found at i:43567868 original size:14 final size:14
Alignment explanation
Indices: 43567837--43567878 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
43567827 TATTTTGATG
43567837 TTATT-TTATTATT
1 TTATTGTTATTATT
* *
43567850 ATATTGTTACTATT
1 TTATTGTTATTATT
43567864 TTATTGTTATTATT
1 TTATTGTTATTATT
43567878 T
1 T
43567879 GGATATTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (14 bp):
TTATTGTTATTATT
Found at i:43568450 original size:13 final size:13
Alignment explanation
Indices: 43568432--43568466 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
43568422 ATTATTTTCT
43568432 ATATTCTTTTAAA
1 ATATTCTTTTAAA
*
43568445 ATATTCTTATAAA
1 ATATTCTTTTAAA
43568458 ATATT-TTTT
1 ATATTCTTTT
43568467 TCCTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 3 0.15
13 17 0.85
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATTCTTTTAAA
Found at i:43568608 original size:14 final size:16
Alignment explanation
Indices: 43568576--43568605 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43568566 ATTTATTCAT
43568576 TTTTCATTATTAAAAA
1 TTTTCATTATTAAAAA
43568592 TTTTC-TTATTAAAA
1 TTTTCATTATTAAAA
43568606 TTTAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTCATTATTAAAAA
Found at i:43569847 original size:19 final size:21
Alignment explanation
Indices: 43569806--43569848 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43569796 TTTAACTAGT
43569806 TCAAAACACGATCAAATACAA
1 TCAAAACACGATCAAATACAA
*
43569827 TCAAAACATG-TCAAA-ACAA
1 TCAAAACACGATCAAATACAA
43569846 TCA
1 TCA
43569849 TCCTAGGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.56, C:0.23, G:0.05, T:0.16
Consensus pattern (21 bp):
TCAAAACACGATCAAATACAA
Found at i:43571219 original size:22 final size:22
Alignment explanation
Indices: 43571193--43571235 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43571183 TATATGTATT
43571193 AATTTATAATATAA-TTAATTTC
1 AATTTAT-ATATAATTTAATTTC
*
43571215 AATTTATATCTAATTTAATTT
1 AATTTATATATAATTTAATTT
43571236 GGGTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTTATATATAATTTAATTTC
Found at i:43572930 original size:16 final size:16
Alignment explanation
Indices: 43572909--43572939 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43572899 CCAATATCCA
*
43572909 ATTATCATATTTACAC
1 ATTATCACATTTACAC
43572925 ATTATCACATTTACA
1 ATTATCACATTTACA
43572940 AAAATATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:43578232 original size:130 final size:130
Alignment explanation
Indices: 43577999--43578356 Score: 445
Period size: 130 Copynumber: 2.8 Consensus size: 130
43577989 CAACTTGGGA
* *
43577999 AAGATTGTTCATGATAGTAAATCAATAAACTTAGGATGTGATCGTAAATCAAC-AATCCTTAATA
1 AAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAACGAA-CCTTAATA
* * * * * * *
43578063 ACATCAATTGTGATATTAAATCAGTGAGTTGTTTGAAGTAGCAATAGTAGATCAGCTAACTCAGA
65 ATATCAGTTGTGACATTAAATCAGTGAGTTGTTTAAAGTAACAATAGTAAATCAACTAACTCAGA
43578128 G
130 G
* * *
43578129 AAGATTGTTCATGATAGTAAATTAATGAATTTAGGTTGTGATCATAAATCAACGAACCTTAATAA
1 AAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAACGAACCTTAATAA
* * * *
43578194 TGTCAGCTGTGACCTTAAATCAGCT-A-TCTGTTTAAAGTAACAATAGTAAATCAACTAACTTAG
66 TATCAGTTGTGACATTAAATCAG-TGAGT-TGTTTAAAGTAACAATAGTAAATCAACTAACTCAG
43578257 AG
129 AG
* * * * *
43578259 AAGATTTTTCATGATAGTAAATCAATGAACTTAGTTTGTGATCGTAAATTAGA-GAGCATTAATA
1 AAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCGTAAATCA-ACGAACCTTAATA
* *
43578323 ATATCAGTTGTGACTTTAAATCAGTGATTTGTTT
65 ATATCAGTTGTGACATTAAATCAGTGAGTTGTTT
43578357 TACATATTTC
Statistics
Matches: 195, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
129 2 0.01
130 188 0.96
131 5 0.03
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (130 bp):
AAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAACGAACCTTAATAA
TATCAGTTGTGACATTAAATCAGTGAGTTGTTTAAAGTAACAATAGTAAATCAACTAACTCAGAG
Found at i:43580866 original size:29 final size:29
Alignment explanation
Indices: 43580828--43580883 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
43580818 ACTTTGGTGC
43580828 CCTCTATTCTAACATAGCACTCTGGTGTT
1 CCTCTATTCTAACATAGCACTCTGGTGTT
* ** *
43580857 CCTCTGTTCTATTATTGCACTCTGGTG
1 CCTCTATTCTAACATAGCACTCTGGTG
43580884 CATTACTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.41
Consensus pattern (29 bp):
CCTCTATTCTAACATAGCACTCTGGTGTT
Found at i:43586449 original size:22 final size:23
Alignment explanation
Indices: 43586421--43586463 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
43586411 AAAAGCTATA
43586421 AAAATTTTAAAAATAA-AAAATG
1 AAAATTTTAAAAATAATAAAATG
*
43586443 AAAATTTTGAAAATAATAAAA
1 AAAATTTTAAAAATAATAAAA
43586464 GATTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (23 bp):
AAAATTTTAAAAATAATAAAATG
Found at i:43597900 original size:27 final size:27
Alignment explanation
Indices: 43597862--43597924 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
43597852 TTTTAGTCTT
* * *
43597862 GTGCCGCCAATGGGAATGGCATCACCG
1 GTGCCGCCAATGAGAAAGGCACCACCG
43597889 GTGCCGCCAATGAGAAAGGCACCACCG
1 GTGCCGCCAATGAGAAAGGCACCACCG
43597916 GTGCCGCCA
1 GTGCCGCCA
43597925 TTCCATTACC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.24, C:0.33, G:0.32, T:0.11
Consensus pattern (27 bp):
GTGCCGCCAATGAGAAAGGCACCACCG
Found at i:43598019 original size:19 final size:21
Alignment explanation
Indices: 43597978--43598026 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
43597968 ATAAATAATT
43597978 TTTTTTGTATATTATTTTAGTA
1 TTTTTT-TATATTATTTTAGTA
*
43598000 TTTTTTTAT-TTCTTTT-GTA
1 TTTTTTTATATTATTTTAGTA
*
43598019 TTATTTTA
1 TTTTTTTA
43598027 GTAAAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 6 0.24
21 3 0.12
22 6 0.24
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTTTTTATATTATTTTAGTA
Found at i:43598827 original size:23 final size:22
Alignment explanation
Indices: 43598773--43598816 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
43598763 AAAATATATT
43598773 AAATATATATA-TTTTATTTTTA
1 AAATATA-ATAGTTTTATTTTTA
*
43598795 AAATATAATAGTTTTAGTTTTA
1 AAATATAATAGTTTTATTTTTA
43598817 TACAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
AAATATAATAGTTTTATTTTTA
Found at i:43599281 original size:16 final size:16
Alignment explanation
Indices: 43599260--43599299 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
43599250 TAATTTGATG
*
43599260 ATTTTACTAACAATTA
1 ATTTTAATAACAATTA
*
43599276 ATTTTAATAATAATTA
1 ATTTTAATAACAATTA
*
43599292 GTTTTAAT
1 ATTTTAAT
43599300 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTTAATAACAATTA
Found at i:43599300 original size:22 final size:23
Alignment explanation
Indices: 43599273--43599334 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
43599263 TTACTAACAA
* *
43599273 TTAATTTTAATAATAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
*
43599295 TTAATTTTATTAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
43599318 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
43599335 CGGACAGGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 15 0.44
23 13 0.38
24 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:43611959 original size:23 final size:23
Alignment explanation
Indices: 43611930--43612021 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
43611920 ATAAGTGCCA
*
43611930 CACTGATATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
43611953 CACTGATACGTAGCCAAAGCTAT
1 CACTGATATGTAGCCGAAGCTAC
* *
43611976 CACTGATATGTAACCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
43611999 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
43612022 TAATAATCAA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:43612272 original size:18 final size:17
Alignment explanation
Indices: 43612246--43612284 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
43612236 ATTTTCCTTC
43612246 CACATTC-AATAGTAATT
1 CACATTCAAATA-TAATT
43612263 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
43612281 CACA
1 CACA
43612285 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.31
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:43615714 original size:26 final size:26
Alignment explanation
Indices: 43615678--43615729 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
43615668 ACTTGATGTG
*
43615678 TGTACGCTAAAGAGTGGTTAATAGTA
1 TGTACGCTAAAGAGCGGTTAATAGTA
43615704 TGTACGCTAAAGAGCGGTTAATAGTA
1 TGTACGCTAAAGAGCGGTTAATAGTA
43615730 CTTGTACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.29
Consensus pattern (26 bp):
TGTACGCTAAAGAGCGGTTAATAGTA
Found at i:43631455 original size:35 final size:35
Alignment explanation
Indices: 43631401--43631471 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
43631391 GACAAATGAG
* *
43631401 AAAGTTTGTGTAATTTTTACCTCTTCTAAACTCCT
1 AAAGTTTGTGCAATATTTACCTCTTCTAAACTCCT
43631436 AAAGTTTGTGCAATATTTACCTCTTCTAAACTCCT
1 AAAGTTTGTGCAATATTTACCTCTTCTAAACTCCT
43631471 A
1 A
43631472 TAAAATGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.42
Consensus pattern (35 bp):
AAAGTTTGTGCAATATTTACCTCTTCTAAACTCCT
Found at i:43633932 original size:15 final size:18
Alignment explanation
Indices: 43633896--43633931 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
43633886 ACTTTCTTTT
43633896 TAAAAAATATATATATAA
1 TAAAAAATATATATATAA
43633914 TAAAAAATA-ATATTATAA
1 TAAAAAATATATA-TATAA
43633932 ACGTAACAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAAATATATATATAA
Found at i:43633989 original size:128 final size:127
Alignment explanation
Indices: 43633809--43634056 Score: 322
Period size: 128 Copynumber: 1.9 Consensus size: 127
43633799 CACCAGCCTG
* * * * * *
43633809 ACAGCCTGCCACCGATGTGACCTGTCAGCCACGGGTCTGGGTTCCAATACCCAATTATTTTATTT
1 ACAGCCTGCCACCGATGTGACCCGTCAGCCACAGGTCCGAGTTCCAACACCCAATTATTTTATAT
*
43633874 ATCAA-CTT-TTTTACTTTCTTTTTAAAAAATATATATATAATAAAAAATAATATTATAAACGTA
66 AT-AAGCTTCTTTTACTTTCTGTTT-AAAAATATATATATAAT-AAAAATAATATTATAAACGTA
* * *
43633937 ACAGCCTGCCACTGATGTGACCCGTC-GATCACAGGTCCGAGTTCTAACACCCAATTATTTTATA
1 ACAGCCTGCCACCGATGTGACCCGTCAG-CCACAGGTCCGAGTTCCAACACCCAATTATTTTATA
* **
43634001 TATAAGTTTCTTTTACTTTCTGTTTAAATGTATATATATAATAAAAATAATATTAT
65 TATAAGCTTCTTTTACTTTCTGTTTAAAAATATATATATAATAAAAATAATATTAT
43634057 GAATATTATA
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
127 17 0.16
128 73 0.70
129 14 0.13
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (127 bp):
ACAGCCTGCCACCGATGTGACCCGTCAGCCACAGGTCCGAGTTCCAACACCCAATTATTTTATAT
ATAAGCTTCTTTTACTTTCTGTTTAAAAATATATATATAATAAAAATAATATTATAAACGTA
Found at i:43639318 original size:2 final size:2
Alignment explanation
Indices: 43639311--43639374 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
43639301 AGGAGGAGGA
43639311 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
43639353 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
43639375 GAATGAATAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43640045 original size:57 final size:57
Alignment explanation
Indices: 43639931--43640073 Score: 171
Period size: 57 Copynumber: 2.4 Consensus size: 57
43639921 AATTGACGGT
43639931 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCTTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTG---C-ATCTTGATATAGCCCTCCCGAAGAATATGTG-G
* *
43639994 AAAAAGATCTAGCCCGGACGGGTG-ATCTTGATATAGCTCTCCTGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGCATCTTGATATAGCCCTCCCGAAGAATATGTGG
* * *
43640050 AAAATGGATTTAGCCCGGATGGGT
1 AAAA-AGATCTAGCCCGGACGGGT
43640074 AATCCGAATT
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
56 5 0.07
57 45 0.61
62 19 0.26
63 5 0.07
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (57 bp):
AAAAAGATCTAGCCCGGACGGGTGCATCTTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:43644478 original size:23 final size:23
Alignment explanation
Indices: 43644448--43644504 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
43644438 AACCTATCTT
43644448 AATAAACATACACTACAAAATAA
1 AATAAACATACACTACAAAATAA
*
43644471 AATAAACATATACTACAAAATAA
1 AATAAACATACACTACAAAATAA
*
43644494 TATAAACATAC
1 AATAAACATAC
43644505 TTACACTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.63, C:0.16, G:0.00, T:0.21
Consensus pattern (23 bp):
AATAAACATACACTACAAAATAA
Found at i:43645839 original size:18 final size:18
Alignment explanation
Indices: 43645818--43645862 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
43645808 ATATAATTGT
* *
43645818 AAATTTATAAATTTATAG
1 AAATATATAAATATATAG
43645836 AAATATATAAATATAT--
1 AAATATATAAATATATAG
43645852 AAATATATAAA
1 AAATATATAAA
43645863 ATTAGTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.44
18 14 0.56
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATATATAAATATATAG
Found at i:43645844 original size:10 final size:8
Alignment explanation
Indices: 43645798--43645862 Score: 69
Period size: 8 Copynumber: 7.9 Consensus size: 8
43645788 TAAAAAAACC
43645798 ATATAAAT
1 ATATAAAT
43645806 ATATATAAT
1 ATATA-AAT
*
43645815 -TGTAAAT
1 ATATAAAT
*
43645822 TTATAAATTT
1 ATATAAA--T
*
43645832 ATAGAAAT
1 ATATAAAT
43645840 ATATAAAT
1 ATATAAAT
43645848 ATATAAAT
1 ATATAAAT
43645856 ATATAAA
1 ATATAAA
43645863 ATTAGTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
7 3 0.06
8 36 0.75
9 3 0.06
10 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:43646089 original size:18 final size:19
Alignment explanation
Indices: 43646060--43646100 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
43646050 CCAGGTTCAT
43646060 TTTTTATGTAAAAAATATA
1 TTTTTATGTAAAAAATATA
**
43646079 TTTTTAT-TAAATTATATA
1 TTTTTATGTAAAAAATATA
43646097 TTTT
1 TTTT
43646101 AAAGATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTTATGTAAAAAATATA
Found at i:43647814 original size:26 final size:25
Alignment explanation
Indices: 43647775--43647824 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
43647765 TGTATATAAC
*
43647775 TTATTATAAATATCTTTATATCTTA
1 TTATTATAAATATCTATATATCTTA
* *
43647800 TTATGTATATATATCTATATCTCTT
1 TTAT-TATAAATATCTATATATCTT
43647825 TTTAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTATAAATATCTATATATCTTA
Found at i:43650570 original size:17 final size:17
Alignment explanation
Indices: 43650544--43650592 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
43650534 TTCCTTCGTC
*
43650544 TTTTCATTTTTCTTTCT
1 TTTTCCTTTTTCTTTCT
*
43650561 TTTTCCTTTTTC-CTCT
1 TTTTCCTTTTTCTTTCT
43650577 TTTTCGCTTTATTCTT
1 TTTTC-CTTT-TTCTT
43650593 CTTCTATTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 8 0.31
17 15 0.58
18 3 0.12
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTCCTTTTTCTTTCT
Found at i:43653449 original size:43 final size:42
Alignment explanation
Indices: 43653266--43653469 Score: 245
Period size: 42 Copynumber: 4.8 Consensus size: 42
43653256 GCGTCGCTAA
*
43653266 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGA-CAAGAC
* *
43653309 CTCTAGCGGCGC--TTCCCTACAAACGCCACTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCC-ACAAACGCCGCTAAAGA-CAAGAC
*
43653351 CTTTAGCGGCGC-TTCCCCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGA-CAAGAC
* *
43653393 CTTTAGCGGCGCTTTTTCCCACAAACGTCGCTATAGA-ATAGAC
1 CTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAAAGACA-AGAC
* **
43653436 CTTTAGCGACGCTTTTAACACAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
43653470 AATATATCTT
Statistics
Matches: 142, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
41 5 0.04
42 87 0.61
43 30 0.21
44 20 0.14
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.20
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACAAGAC
Found at i:43653810 original size:43 final size:43
Alignment explanation
Indices: 43653744--43653834 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
43653734 ACATATGCAA
* * * *
43653744 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
43653787 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
43653830 -GTAAT
1 GGTAAT
43653835 GAACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:43657725 original size:13 final size:13
Alignment explanation
Indices: 43657707--43657732 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43657697 ATTGTCAATC
43657707 TGTTACATTAATT
1 TGTTACATTAATT
43657720 TGTTACATTAATT
1 TGTTACATTAATT
43657733 AATTTATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
TGTTACATTAATT
Found at i:43659021 original size:41 final size:41
Alignment explanation
Indices: 43658946--43659147 Score: 289
Period size: 41 Copynumber: 5.0 Consensus size: 41
43658936 TCAAAAGCGG
*
43658946 GCATTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGGCCCAA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
* *
43658986 TCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
* ** *
43659027 GCATTAGCTGCGCTGATTCAAAAACGCCACTAAAGGCCCGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
* * *
43659068 GCATTAGCTGCGCTTCTTCACAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
* *
43659109 GAATTAGCGGCGCTTTTTCAAAAACACCGCTAAAGGCCC
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC
43659148 CAAAAACTCA
Statistics
Matches: 143, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 12 0.08
41 131 0.92
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (41 bp):
GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
Found at i:43659249 original size:39 final size:39
Alignment explanation
Indices: 43659202--43659316 Score: 126
Period size: 40 Copynumber: 2.9 Consensus size: 39
43659192 CGCTTTTTGG
* * *
43659202 AAAA-CGCCGGTAATGCTTATTTTTAGCGGCATTTTCCA-
1 AAAAGCGCCGCTAATGCTTATTTTTAGTGGCGTTTT-CAT
* ** *
43659240 AAAAGCGCCGCTAATGCTCGACCTTTAGTGGCGTTTTTAT
1 AAAAGCGCCGCTAATGCT-TATTTTTAGTGGCGTTTTCAT
43659280 AAAAGCGCCGCTAATGCTTGATTTTTAGTGGCGTTTT
1 AAAAGCGCCGCTAATGCTT-ATTTTTAGTGGCGTTTT
43659317 TTATCCAAAC
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
38 4 0.06
39 13 0.21
40 46 0.73
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (39 bp):
AAAAGCGCCGCTAATGCTTATTTTTAGTGGCGTTTTCAT
Found at i:43659284 original size:40 final size:40
Alignment explanation
Indices: 43659240--43659317 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
43659230 GCATTTTCCA
43659240 AAAAGCGCCGCTAATGCTCGACCTTTAGTGGCGTTTTTAT
1 AAAAGCGCCGCTAATGCTCGACCTTTAGTGGCGTTTTTAT
* **
43659280 AAAAGCGCCGCTAATGCTTGATTTTTAGTGGCGTTTTT
1 AAAAGCGCCGCTAATGCTCGACCTTTAGTGGCGTTTTT
43659318 TATCCAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTCGACCTTTAGTGGCGTTTTTAT
Found at i:43663652 original size:3 final size:3
Alignment explanation
Indices: 43663644--43663702 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
43663634 TATTTTTCAC
* * *
43663644 TAT TAT TA- TAT TAT TAAT TAT TGT TAT TAT AAT TAT AAT TA- TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43663688 TAT ATAT TAT TAT TA
1 TAT -TAT TAT TAT TA
43663703 CACCTATAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.09
3 36 0.78
4 6 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:43663670 original size:21 final size:20
Alignment explanation
Indices: 43663644--43663699 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
43663634 TATTTTTCAC
43663644 TATTATTATATTATTAATTA
1 TATTATTATATTATTAATTA
*
43663664 TTGTTATTATAATTA-TAATTA
1 -TATTATTAT-ATTATTAATTA
43663685 TATTA-TATATTATTA
1 TATTATTATATTATTA
43663700 TTACACCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 4 0.13
19 5 0.16
20 4 0.13
21 14 0.45
22 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTATTATATTATTAATTA
Found at i:43663869 original size:18 final size:19
Alignment explanation
Indices: 43663848--43663887 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
43663838 GTACACGTAC
43663848 ATATATTTATA-TTTTATA
1 ATATATTTATAGTTTTATA
*
43663866 ATATTTTTATAGTTTTTATA
1 ATATATTTATAG-TTTTATA
43663886 AT
1 AT
43663888 CCAAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
20 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
ATATATTTATAGTTTTATA
Found at i:43665019 original size:18 final size:18
Alignment explanation
Indices: 43664996--43665030 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43664986 TTTTTCAAAT
*
43664996 ATATTTTTGAGTAAAAAA
1 ATATTTTTGAGCAAAAAA
43665014 ATATTTTTGAGCAAAAA
1 ATATTTTTGAGCAAAAA
43665031 TTAAAAGTTT
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:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (18 bp):
ATATTTTTGAGCAAAAAA
Found at i:43667066 original size:21 final size:21
Alignment explanation
Indices: 43667008--43667099 Score: 107
Period size: 21 Copynumber: 4.4 Consensus size: 21
43666998 TCTAATCAGT
43667008 ATACGACACAT-AAGTGCCTG
1 ATACGACACATAAAGTGCCTG
* ** *
43667028 AAACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTG
*
43667049 ATACGACACATAAAGTGCTTGAG
1 ATACGACACATAAAGTGCCT--G
43667072 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
43667093 AT-CGACA
1 ATACGACA
43667100 AAGCCGATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
20 14 0.23
21 26 0.43
23 20 0.33
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:43667419 original size:16 final size:17
Alignment explanation
Indices: 43667398--43667429 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
43667388 TAATAATAAT
43667398 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
43667414 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
43667430 GCTTACCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:43668112 original size:8 final size:8
Alignment explanation
Indices: 43668101--43668148 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
43668091 TGGTCTTTGT
*
43668101 TTCTTTTC
1 TTCTTTTA
43668109 TTCTTTTA
1 TTCTTTTA
43668117 TTTCTTTTA
1 -TTCTTTTA
43668126 TTCTTTTA
1 TTCTTTTA
*
43668134 TT-TTAT-
1 TTCTTTTA
43668140 TTCTTTTA
1 TTCTTTTA
43668148 T
1 T
43668149 GTATTAGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
6 2 0.06
7 6 0.18
8 18 0.53
9 8 0.24
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTTTTA
Found at i:43668122 original size:17 final size:17
Alignment explanation
Indices: 43668100--43668136 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
43668090 ATGGTCTTTG
*
43668100 TTTCTTTTCTTCTTTTA
1 TTTCTTTTATTCTTTTA
43668117 TTTCTTTTATTCTTTTA
1 TTTCTTTTATTCTTTTA
43668134 TTT
1 TTT
43668137 TATTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTTTATTCTTTTA
Found at i:43668165 original size:3 final size:3
Alignment explanation
Indices: 43668157--43668227 Score: 108
Period size: 3 Copynumber: 23.7 Consensus size: 3
43668147 ATGTATTAGT
* *
43668157 TAA TAA TAA TAG CAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
43668203 TAA TAA TAA T-A TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
43668228 TTTAATTCAC
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 57 0.92
4 3 0.05
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:43668396 original size:30 final size:26
Alignment explanation
Indices: 43668360--43668423 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 26
43668350 TTTCCTATAA
*
43668360 TATAATATCTTAATTTTAATTAATATAATT
1 TATAATATCTTAA--TTAAATAATAT--TT
*
43668390 TATAATATTTTAATTAAATAATATTT
1 TATAATATCTTAATTAAATAATATTT
43668416 TATAATAT
1 TATAATAT
43668424 AAATCAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.31
28 10 0.31
30 12 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
TATAATATCTTAATTAAATAATATTT
Found at i:43668404 original size:24 final size:26
Alignment explanation
Indices: 43668372--43668423 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
43668362 TAATATCTTA
43668372 ATTTTAATT-AAT-ATAATTTATAAT
1 ATTTTAATTAAATAATAATTTATAAT
*
43668396 ATTTTAATTAAATAATATTTTATAAT
1 ATTTTAATTAAATAATAATTTATAAT
43668422 AT
1 AT
43668424 AAATCAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 9 0.36
25 3 0.12
26 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTTAATTAAATAATAATTTATAAT
Found at i:43669659 original size:21 final size:21
Alignment explanation
Indices: 43669634--43669699 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
43669624 TTTTACATAA
43669634 TTATAATTTTAAAAAATATTT
1 TTATAATTTTAAAAAATATTT
* * * *
43669655 TTATAA-ATTCAAAAATAAATA
1 TTATAATTTTAAAAAAT-ATTT
43669676 TTA-AATTTTCAAAAAATTATTT
1 TTATAATTTT-AAAAAA-TATTT
43669698 TT
1 TT
43669700 TATATTCTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
20 10 0.30
21 13 0.39
22 9 0.27
23 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATAATTTTAAAAAATATTT
Found at i:43672669 original size:25 final size:26
Alignment explanation
Indices: 43672641--43672696 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
43672631 ATGATTTGAA
43672641 ATTAATTGATA-AAATAAA-AAATTAG
1 ATTAATTGA-ACAAATAAATAAATTAG
* *
43672666 ATTAATTGAACACATAAATACATTAG
1 ATTAATTGAACAAATAAATAAATTAG
43672692 ATTAA
1 ATTAA
43672697 AAATATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 1 0.04
25 15 0.56
26 11 0.41
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (26 bp):
ATTAATTGAACAAATAAATAAATTAG
Found at i:43676672 original size:38 final size:38
Alignment explanation
Indices: 43676620--43676692 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
43676610 CCTATTGCGC
* *
43676620 ACATGATAAACATGTCTACTACTAGTGTTCAATTGAAT
1 ACATGATAAACATGTCCACTACTAGTGTTAAATTGAAT
* * *
43676658 ACATGTTAAGCATGTCCACTGCTAGTGTTAAATTG
1 ACATGATAAACATGTCCACTACTAGTGTTAAATTG
43676693 TTCTATTACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (38 bp):
ACATGATAAACATGTCCACTACTAGTGTTAAATTGAAT
Found at i:43676840 original size:43 final size:43
Alignment explanation
Indices: 43676760--43677040 Score: 332
Period size: 43 Copynumber: 6.6 Consensus size: 43
43676750 AGAGTGGCAG
* * *
43676760 TTTATCTGCAAATATGCTGTGCATCCATAGCCCAGTGACAATT
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGACAATT
* * * *
43676803 TTTAGCTGCAAATATGTTGTGCAACCACAACCTAGTGAAAATT
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGACAATT
* * * *
43676846 TTTATTTGCAAATATGTTGTGCAACCACAACCTAATGACAATTT
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGACAA-TT
* * * * *
43676890 TTTTTTTGAAAATATGTTGTGCATCCACAACCCAGTGGC-A-G
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGACAATT
* *
43676931 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTTACAGTT
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGACAATT
* * * *
43676974 TTTATCTGCAAATATGTTGTACATCCACAACCTAATGGCAATT
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGACAATT
*
43677017 TTTATTTGCAAATATGTTGTGCAT
1 TTTATCTGCAAATATGTTGTGCAT
43677041 TTGATTTGCC
Statistics
Matches: 202, Mismatches: 33, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
41 34 0.17
43 133 0.66
44 35 0.17
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (43 bp):
TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGACAATT
Found at i:43677002 original size:128 final size:129
Alignment explanation
Indices: 43676760--43677040 Score: 368
Period size: 128 Copynumber: 2.2 Consensus size: 129
43676750 AGAGTGGCAG
* * * * * *
43676760 TTTATCTGCAAATATGCTGTGCATCCATAGCCCAGTGACAATTTTTAGCTGCAAATATGTTGTGC
1 TTTATTTGAAAATATGTTGTGCATCCACAACCCAGTGACAATGTTTAGCTGCAAATATGTTGTGC
* * *
43676825 AACCACAACCTAGTGAAAATTTTTATTTGCAAATATGTTGTGCAACCACAACCTAATGACAATTT
66 AACCACAACCCAGTGAAAATTTTTATCTGCAAATATGTTGTACAACCACAACCTAATGACAA-TT
* * *
43676890 TTTTTTTGAAAATATGTTGTGCATCCACAACCCAGTGGC-A-GTTTATCTGCAAATATGTTGTGC
1 TTTATTTGAAAATATGTTGTGCATCCACAACCCAGTGACAATGTTTAGCTGCAAATATGTTGTGC
* * * * * *
43676953 ATCCACAACCCAGTTACAGTTTTTATCTGCAAATATGTTGTACATCCACAACCTAATGGCAATT
66 AACCACAACCCAGTGAAAATTTTTATCTGCAAATATGTTGTACAACCACAACCTAATGACAATT
*
43677017 TTTATTTGCAAATATGTTGTGCAT
1 TTTATTTGAAAATATGTTGTGCAT
43677041 TTGATTTGCC
Statistics
Matches: 131, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
127 24 0.18
128 74 0.56
129 1 0.01
130 32 0.24
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (129 bp):
TTTATTTGAAAATATGTTGTGCATCCACAACCCAGTGACAATGTTTAGCTGCAAATATGTTGTGC
AACCACAACCCAGTGAAAATTTTTATCTGCAAATATGTTGTACAACCACAACCTAATGACAATT
Found at i:43686073 original size:21 final size:21
Alignment explanation
Indices: 43686044--43686083 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43686034 TATTTTAGGG
**
43686044 CCCAGGTATTGATACCTTACC
1 CCCAGGTATCAATACCTTACC
*
43686065 CCCATGTATCAATACCTTA
1 CCCAGGTATCAATACCTTA
43686084 GGTTAAATTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.33, G:0.10, T:0.30
Consensus pattern (21 bp):
CCCAGGTATCAATACCTTACC
Found at i:43687591 original size:23 final size:23
Alignment explanation
Indices: 43687562--43687686 Score: 169
Period size: 23 Copynumber: 5.4 Consensus size: 23
43687552 ATCCAAATAG
* * *
43687562 AGCCTTTATGGTGTATTATGATT
1 AGCCTTTGTGGCGTATTCTGATT
*
43687585 AGACTTTGTGGCGTATTCTGATT
1 AGCCTTTGTGGCGTATTCTGATT
*
43687608 AGCCTTTCTGGCGTATTCTGATT
1 AGCCTTTGTGGCGTATTCTGATT
* *
43687631 AGCCTTTGTGGCGTATTTTAATT
1 AGCCTTTGTGGCGTATTCTGATT
* *
43687654 AGTCTTTGTGGCATATTCTGATT
1 AGCCTTTGTGGCGTATTCTGATT
43687677 AGCCTTTGTG
1 AGCCTTTGTG
43687687 TTAGCCTTTG
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 88 1.00
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (23 bp):
AGCCTTTGTGGCGTATTCTGATT
Found at i:43687705 original size:58 final size:58
Alignment explanation
Indices: 43687629--43687744 Score: 151
Period size: 58 Copynumber: 2.0 Consensus size: 58
43687619 CGTATTCTGA
* * *
43687629 TTAGCCTTTGTGGCGTATTTTAATTAGTCTTTGTGGCATATTCTGATTAGCCTTTGTG
1 TTAGCCTTTGTAGCGTATTATAATTAGCCTTTGTGGCATATTCTGATTAGCCTTTGTG
* * ** * *
43687687 TTAGCCTTTGTAGTGTATTATGATTAGCCTTTGTGGTGTATTTTGATTGGCCTTTGTG
1 TTAGCCTTTGTAGCGTATTATAATTAGCCTTTGTGGCATATTCTGATTAGCCTTTGTG
43687745 ACGTATTCGA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.15, C:0.12, G:0.24, T:0.49
Consensus pattern (58 bp):
TTAGCCTTTGTAGCGTATTATAATTAGCCTTTGTGGCATATTCTGATTAGCCTTTGTG
Found at i:43687744 original size:23 final size:23
Alignment explanation
Indices: 43687687--43687744 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
43687677 AGCCTTTGTG
*
43687687 TTAGCCTTTGTAGTGTATTATGA
1 TTAGCCTTTGTGGTGTATTATGA
*
43687710 TTAGCCTTTGTGGTGTATTTTGA
1 TTAGCCTTTGTGGTGTATTATGA
*
43687733 TTGGCCTTTGTG
1 TTAGCCTTTGTG
43687745 ACGTATTCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.14, C:0.10, G:0.26, T:0.50
Consensus pattern (23 bp):
TTAGCCTTTGTGGTGTATTATGA
Found at i:43687750 original size:23 final size:23
Alignment explanation
Indices: 43687687--43687751 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
43687677 AGCCTTTGTG
*
43687687 TTAGCCTTTGT-AGTGTATTATGA
1 TTAGCCTTTGTGA-CGTATTATGA
** *
43687710 TTAGCCTTTGTGGTGTATTTTGA
1 TTAGCCTTTGTGACGTATTATGA
*
43687733 TTGGCCTTTGTGACGTATT
1 TTAGCCTTTGTGACGTATT
43687752 CGACAAAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.15, C:0.11, G:0.25, T:0.49
Consensus pattern (23 bp):
TTAGCCTTTGTGACGTATTATGA
Found at i:43691371 original size:17 final size:17
Alignment explanation
Indices: 43691344--43691385 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
43691334 ATATAAATCA
**
43691344 TATAAAA-ATATTGAAT
1 TATAAAATATATAAAAT
43691360 TATAAAATATATAAAAT
1 TATAAAATATATAAAAT
*
43691377 GATAAAATA
1 TATAAAATA
43691386 ATTAGTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
TATAAAATATATAAAAT
Found at i:43701420 original size:2 final size:2
Alignment explanation
Indices: 43701413--43701443 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43701403 GGTTTAGATT
43701413 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43701444 TGTTTAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43701694 original size:63 final size:63
Alignment explanation
Indices: 43701595--43701720 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
43701585 ATGCTTACCA
43701595 TTCTTTAAACTCATAAGCGGTGCTATAAAATTTAAAAGGACTAGTCAGTGCTAAAAAAAAGTT
1 TTCTTTAAACTCATAAGCGGTGCTATAAAATTTAAAAGGACTAGTCAGTGCTAAAAAAAAGTT
*
43701658 TTCTTTAAACTCATAAGCGGTGCTATAAAATTTAAAAGGACTAGTCAGTGCTAAAAAGAAGTT
1 TTCTTTAAACTCATAAGCGGTGCTATAAAATTTAAAAGGACTAGTCAGTGCTAAAAAAAAGTT
43701721 GAAAACATCA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (63 bp):
TTCTTTAAACTCATAAGCGGTGCTATAAAATTTAAAAGGACTAGTCAGTGCTAAAAAAAAGTT
Found at i:43709091 original size:42 final size:43
Alignment explanation
Indices: 43709045--43709200 Score: 168
Period size: 42 Copynumber: 3.8 Consensus size: 43
43709035 GGCCCATATT
***
43709045 TATTTTAAAAAT-TTTTAAAAATTAAAAAAAGTATT-TTTAAAA-
1 TATTTTAAAAATATTTTAAAAATTAAAAAAA--ATTAAAAAAAAG
*
43709087 TATTTTTAAAATATTTT-AAAATTAAAAAAAATTAAAAAAAAG
1 TATTTTAAAAATATTTTAAAAATTAAAAAAAATTAAAAAAAAG
*
43709129 TATTTTAAAAATATTTTAAAATTTAAAAAAAAATT---AAAAAG
1 TATTTTAAAAATATTTTAAAAATT-AAAAAAAATTAAAAAAAAG
*
43709170 TA-TGTAAAAATATTTT-AAAATTAAAAAAAAT
1 TATTTTAAAAATATTTTAAAAATTAAAAAAAAT
43709201 AAATATATTT
Statistics
Matches: 101, Mismatches: 8, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
38 9 0.09
39 5 0.05
40 16 0.16
41 12 0.12
42 40 0.40
43 9 0.09
44 10 0.10
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (43 bp):
TATTTTAAAAATATTTTAAAAATTAAAAAAAATTAAAAAAAAG
Found at i:43709108 original size:10 final size:11
Alignment explanation
Indices: 43709047--43709108 Score: 67
Period size: 10 Copynumber: 5.8 Consensus size: 11
43709037 CCCATATTTA
43709047 TTTTAAAA-AT
1 TTTTAAAATAT
43709057 TTTTAAAA-AT
1 TTTTAAAATAT
***
43709067 TAAAAAAAGTAT
1 TTTTAAAA-TAT
43709079 TTTTAAAATAT
1 TTTTAAAATAT
43709090 TTTTAAAATA-
1 TTTTAAAATAT
43709100 TTTTAAAAT
1 TTTTAAAAT
43709109 TAAAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
10 24 0.55
11 13 0.30
12 7 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:43709189 original size:11 final size:11
Alignment explanation
Indices: 43709045--43709149 Score: 62
Period size: 11 Copynumber: 9.9 Consensus size: 11
43709035 GGCCCATATT
43709045 TATTTTAAAAA
1 TATTTTAAAAA
43709056 T-TTTT-AAAA
1 TATTTTAAAAA
**
43709065 -ATTAAAAAAA
1 TATTTTAAAAA
*
43709075 GTATTTTTAAAA
1 -TATTTTAAAAA
*
43709087 TATTTTTAAAA
1 TATTTTAAAAA
43709098 TATTTT--AAA
1 TATTTTAAAAA
*
43709107 -A-TTAAAAAA
1 TATTTTAAAAA
* **
43709116 AATTAAAAAAAA
1 TATT-TTAAAAA
43709128 GTATTTTAAAAA
1 -TATTTTAAAAA
43709140 TATTTTAAAA
1 TATTTTAAAA
43709150 TTTAAAAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
7 2 0.03
8 1 0.01
9 12 0.16
10 9 0.12
11 29 0.39
12 18 0.24
13 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:43709964 original size:20 final size:21
Alignment explanation
Indices: 43709939--43709977 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43709929 GTATACCATG
43709939 CAATAC-TTTACATTTCAATC
1 CAATACTTTTACATTTCAATC
*
43709959 CAATACTTTTCCATTTCAA
1 CAATACTTTTACATTTCAA
43709978 ACTTACTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (21 bp):
CAATACTTTTACATTTCAATC
Found at i:43711257 original size:31 final size:31
Alignment explanation
Indices: 43711218--43711285 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
43711208 GGTTTATCTA
*
43711218 CTAA-TACAAATTGTCTTTGCATGTTGTGAT
1 CTAACTACAAACTGTCTTTGCATGTTGTGAT
43711248 CTAACTACAAACTGTCTTTGCATGTTGTGAT
1 CTAACTACAAACTGTCTTTGCATGTTGTGAT
43711279 CTAACTA
1 CTAACTA
43711286 TGTAACATCG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 4 0.11
31 32 0.89
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (31 bp):
CTAACTACAAACTGTCTTTGCATGTTGTGAT
Found at i:43727471 original size:3 final size:3
Alignment explanation
Indices: 43727463--43727503 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
43727453 GCTTCCTTTG
* * *
43727463 CTT CTT CTT CTT CTC CTT CTT CTT CTT CTT GTT ATT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
43727504 CCTCTTTCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:43728180 original size:7 final size:7
Alignment explanation
Indices: 43728168--43728218 Score: 93
Period size: 7 Copynumber: 7.1 Consensus size: 7
43728158 CACGGACTTG
43728168 GGGAAAT
1 GGGAAAT
43728175 GGGAAAT
1 GGGAAAT
43728182 GGGAAAT
1 GGGAAAT
43728189 GGGAAAT
1 GGGAAAT
43728196 GGGAAAT
1 GGGAAAT
43728203 GGAGAAAT
1 GG-GAAAT
43728211 GGGAAAT
1 GGGAAAT
43728218 G
1 G
43728219 CATTTTAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
7 36 0.84
8 7 0.16
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (7 bp):
GGGAAAT
Found at i:43729856 original size:16 final size:17
Alignment explanation
Indices: 43729830--43729866 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
43729820 TTATTTTCCA
*
43729830 ATTTAATTTAATTTTTT
1 ATTTAATTTAAATTTTT
43729847 ATTT-ATTTAAATTTTT
1 ATTTAATTTAAATTTTT
43729863 ATTT
1 ATTT
43729867 CTGCTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTAATTTAAATTTTT
Found at i:43732291 original size:15 final size:15
Alignment explanation
Indices: 43732273--43732302 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43732263 TGGACTTAGT
43732273 GGTCATGGTTATAGA
1 GGTCATGGTTATAGA
43732288 GGTCATGGTTATAGA
1 GGTCATGGTTATAGA
43732303 AAGGACCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.33, T:0.33
Consensus pattern (15 bp):
GGTCATGGTTATAGA
Found at i:43741046 original size:26 final size:26
Alignment explanation
Indices: 43740995--43741046 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
43740985 AGTTGTAGAG
* *
43740995 AGAAAATTCTCTAAAGAGATTATTTT
1 AGAAAATTCTCTAAAAAAATTATTTT
*
43741021 AGAAAATT-TCTAAAAATAATTTTTTT
1 AGAAAATTCTCTAAAAA-AATTATTTT
43741047 GATTTACAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (26 bp):
AGAAAATTCTCTAAAAAAATTATTTT
Found at i:43743589 original size:135 final size:136
Alignment explanation
Indices: 43743283--43743593 Score: 322
Period size: 135 Copynumber: 2.3 Consensus size: 136
43743273 TGTCCTAGCG
* * *
43743283 GACTTCATATACTACCATAGCCCAGCTATGGTCTTACACAATATAATCTCATGTTTACTATCATG
1 GACTTCATATGCTACCATAACCCAGCTATGATCTTACACAATATAATCTCATGTTTACTATCATG
* * * *
43743348 GCAGACTTCATATGTTGCCATAGCCCAACCATGATCTTACGCAATATAATTCCATGTTTACTGTC
66 GCAGACTTCATATGCTGCCATAACCCAACCACGATCTTACACAATATAATTCCATGTTTACTGTC
*
43743413 CTGGCA
131 CTGACA
* * * * ** ** * *
43743419 GACTTCTTATGATGCCATATCCCAAATAT-AGTCTTATGCAATATAATCTCATG-TTACTGTCTT
1 GACTTCATATGCTACCATAACCCAGCTATGA-TCTTACACAATATAATCTCATGTTTACTATCAT
** * * * * *
43743482 GGTGGACTTCATATGCTGCCATAATCCAGCTACGGTCTTACACAATGTAATAT-CATGTTTACTG
65 GGCAGACTTCATATGCTGCCATAACCCAACCACGATCTTACACAATATAAT-TCCATGTTTACTG
** *
43743546 TTTTGATA
129 TCCTGACA
*
43743554 GACTTCATATGCTACCCTAACCCAGCTATGATCTTACACA
1 GACTTCATATGCTACCATAACCCAGCTATGATCTTACACA
43743594 TTAAACATCT
Statistics
Matches: 136, Mismatches: 36, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
135 92 0.68
136 44 0.32
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (136 bp):
GACTTCATATGCTACCATAACCCAGCTATGATCTTACACAATATAATCTCATGTTTACTATCATG
GCAGACTTCATATGCTGCCATAACCCAACCACGATCTTACACAATATAATTCCATGTTTACTGTC
CTGACA
Found at i:43743591 original size:68 final size:68
Alignment explanation
Indices: 43743283--43743593 Score: 304
Period size: 68 Copynumber: 4.6 Consensus size: 68
43743273 TGTCCTAGCG
* * * * * *
43743283 GACTTCATATACTACCATAGCCCAGCTATGGTCTTACACAATATAATCTCATGTTTACTATCATG
1 GACTTCATATGCTGCCATAACCCAGCTATGATCTTACACAATATAATCTCATGTTTACTGTCTTG
43743348 GCA
66 GCA
* * * * * *
43743351 GACTTCATATGTTGCCATAGCCCAACCATGATCTTACGCAATATAAT-TCCATGTTTACTGTCCT
1 GACTTCATATGCTGCCATAACCCAGCTATGATCTTACACAATATAATCT-CATGTTTACTGTCTT
43743415 GGCA
65 GGCA
* * * ** **
43743419 GACTTCTTATGATGCCATATCCCAAATAT-AGTCTTATGCAATATAATCTCATG-TTACTGTCTT
1 GACTTCATATGCTGCCATAACCCAGCTATGA-TCTTACACAATATAATCTCATGTTTACTGTCTT
**
43743482 GGTG
65 GGCA
* * * * * *
43743486 GACTTCATATGCTGCCATAATCCAGCTACGGTCTTACACAATGTAATATCATGTTTACTGTTTTG
1 GACTTCATATGCTGCCATAACCCAGCTATGATCTTACACAATATAATCTCATGTTTACTGTCTTG
**
43743551 ATA
66 GCA
* *
43743554 GACTTCATATGCTACCCTAACCCAGCTATGATCTTACACA
1 GACTTCATATGCTGCCATAACCCAGCTATGATCTTACACA
43743594 TTAAACATCT
Statistics
Matches: 200, Mismatches: 38, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
67 53 0.26
68 146 0.73
69 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (68 bp):
GACTTCATATGCTGCCATAACCCAGCTATGATCTTACACAATATAATCTCATGTTTACTGTCTTG
GCA
Found at i:43748723 original size:22 final size:21
Alignment explanation
Indices: 43748706--43748745 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43748696 ATGTGGCAGT
*
43748706 TTAACTGCAATTATGTGGTCG
1 TTAACGGCAATTATGTGGTCG
*
43748727 TTATCGGCAATTATGTGGT
1 TTAACGGCAATTATGTGGT
43748746 GGTTTATCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.40
Consensus pattern (21 bp):
TTAACGGCAATTATGTGGTCG
Found at i:43748790 original size:48 final size:48
Alignment explanation
Indices: 43748738--43748854 Score: 180
Period size: 48 Copynumber: 2.4 Consensus size: 48
43748728 TATCGGCAAT
* *
43748738 TATGTGGTGGTTTATCCACGATGTGCTATGTGACCGTTCATCGGTATC
1 TATGTGGTGGTTTATCCACAATGTGCTATGTGACCGTTCATCAGTATC
* *
43748786 TATGTGGTGGTTTATCCACAATGTGTTATGTGACCGTTCATCAGTATT
1 TATGTGGTGGTTTATCCACAATGTGCTATGTGACCGTTCATCAGTATC
* *
43748834 TATGTGGTGGCTTGTCCACAA
1 TATGTGGTGGTTTATCCACAA
43748855 ACTTATGTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 63 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (48 bp):
TATGTGGTGGTTTATCCACAATGTGCTATGTGACCGTTCATCAGTATC
Found at i:43750423 original size:19 final size:19
Alignment explanation
Indices: 43750367--43750424 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
43750357 AAAAGAATAA
*
43750367 TTTTTTTAATTTA-A-ACTT
1 TTTTTTTAATTTATAGA-AT
43750385 TTTTTTGTAA-TTAT-GTAAT
1 TTTTTT-TAATTTATAG-AAT
43750404 TTTTTTTAATTTATAGAAT
1 TTTTTTTAATTTATAGAAT
43750423 TT
1 TT
43750425 ATATGTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
18 12 0.36
19 19 0.58
20 2 0.06
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTTTTAATTTATAGAAT
Found at i:43761425 original size:26 final size:27
Alignment explanation
Indices: 43761396--43761446 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
43761386 CGACCCAACA
*
43761396 TAGTGATTA-CAACTCGCCAAGCCCAC
1 TAGTGAATACCAACTCGCCAAGCCCAC
* *
43761422 TAGTGAATACCAGCTCGCCTAGCCC
1 TAGTGAATACCAACTCGCCAAGCCC
43761447 TATGACGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20
Consensus pattern (27 bp):
TAGTGAATACCAACTCGCCAAGCCCAC
Found at i:43771884 original size:41 final size:42
Alignment explanation
Indices: 43771826--43771914 Score: 171
Period size: 41 Copynumber: 2.1 Consensus size: 42
43771816 TGAAGAAAAG
43771826 AAAGTACATGGTCTGACACCAGTCATGTCCAAAATATGTATC
1 AAAGTACATGGTCTGACACCAGTCATGTCCAAAATATGTATC
43771868 AAAGT-CATGGTCTGACACCAGTCATGTCCAAAATATGTATC
1 AAAGTACATGGTCTGACACCAGTCATGTCCAAAATATGTATC
43771909 AAAGTA
1 AAAGTA
43771915 ATATACATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 41 0.89
42 5 0.11
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (42 bp):
AAAGTACATGGTCTGACACCAGTCATGTCCAAAATATGTATC
Found at i:43794062 original size:24 final size:24
Alignment explanation
Indices: 43794035--43794097 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
43794025 CAGCTCGAAA
*
43794035 GAGCGTCCCGTTATTAGCTCTCAT
1 GAGCATCCCGTTATTAGCTCTCAT
* * *
43794059 GAGCATCCTGATATTTGGCTCTCAT
1 GAGCATCCCGTTA-TTAGCTCTCAT
* *
43794084 GAGCTTCCCATTAT
1 GAGCATCCCGTTAT
43794098 ATGGTTCTTG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 11 0.37
25 19 0.63
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (24 bp):
GAGCATCCCGTTATTAGCTCTCAT
Found at i:43794248 original size:27 final size:27
Alignment explanation
Indices: 43794204--43794263 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
43794194 TCCCGATATA
*
43794204 TGGCTC-TTCAGAGCTTCCTAATT-AC
1 TGGCTCTTTCAGAGCTTCCCAATTAAC
*
43794229 TGGCTCTTTCATGAGCTTCCCAATTAAT
1 TGGCTCTTTCA-GAGCTTCCCAATTAAC
43794257 TGGCTCT
1 TGGCTCT
43794264 CCGGAGCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 6 0.20
26 4 0.13
27 12 0.40
28 8 0.27
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (27 bp):
TGGCTCTTTCAGAGCTTCCCAATTAAC
Found at i:43794303 original size:25 final size:25
Alignment explanation
Indices: 43794270--43794334 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
43794260 CTCTCCGGAG
43794270 CTTCCCGATATTGGCTCGCTTGAAC
1 CTTCCCGATATTGGCTCGCTTGAAC
* *
43794295 CTTCTCGATATTGGTTCGCTTGAAC
1 CTTCCCGATATTGGCTCGCTTGAAC
*
43794320 CTTCCCAATATTGGC
1 CTTCCCGATATTGGC
43794335 CCGTATGAGC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.35
Consensus pattern (25 bp):
CTTCCCGATATTGGCTCGCTTGAAC
Found at i:43809829 original size:43 final size:43
Alignment explanation
Indices: 43809785--43810030 Score: 307
Period size: 43 Copynumber: 5.7 Consensus size: 43
43809775 GTGAAGAAAT
** * *
43809785 GCCGCTAAAGGCCATGACTTTTAGCGGCGCTTTTGTCACAAAT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTCACAAAC
* * *
43809828 GCTGCTAAAGAACATGACCTTTAGCGGCGCTTCTGTCATAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTCACAAAC
* *
43809871 GCCACTAAAGAACATGACCTTTAGCGGCGCTTCTGTCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTCACAAAC
*
43809914 GCCGCTAAAGAACATGACCTTTAGCGGCG-TTTCTATCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTT-TGTCACAAAC
*** * *
43809957 GCCGCTAAAGAACATGACCTTTAGCAATGCTTTTATCATAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTCACAAAC
* * *
43810000 GCCGCTAAAAAACA-AACCTTTAGCGACGCTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTT
43810031 CTCGCAAAAA
Statistics
Matches: 180, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
42 16 0.09
43 161 0.89
44 3 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTCACAAAC
Found at i:43814357 original size:38 final size:38
Alignment explanation
Indices: 43814314--43814395 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 38
43814304 TAAAACAATT
* * * *
43814314 GATAAACCAAACTTTGTGAGATAAACATGTAAAAAGCA
1 GATAAAACAAAATTTGTGAGATAAACATATAAAAAACA
*
43814352 GATAAAAGAAAATTTGTGAGATAAACATATAAAAAACA
1 GATAAAACAAAATTTGTGAGATAAACATATAAAAAACA
43814390 GATAAA
1 GATAAA
43814396 GTTTGTAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.21
Consensus pattern (38 bp):
GATAAAACAAAATTTGTGAGATAAACATATAAAAAACA
Found at i:43815845 original size:7 final size:7
Alignment explanation
Indices: 43815819--43815903 Score: 73
Period size: 7 Copynumber: 12.1 Consensus size: 7
43815809 CACTAACTCT
*
43815819 TAACCTC
1 TAACCCC
*
43815826 TAACCTC
1 TAACCCC
43815833 TAACCCC
1 TAACCCC
43815840 TAACCCC
1 TAACCCC
*
43815847 -AAACCC
1 TAACCCC
*
43815853 TAAACCC
1 TAACCCC
43815860 TAAACCCC
1 T-AACCCC
**
43815868 TAACTAC
1 TAACCCC
*
43815875 TATCCCC
1 TAACCCC
*
43815882 TATCCCC
1 TAACCCC
*
43815889 TAACCCT
1 TAACCCC
43815896 TAACCCC
1 TAACCCC
43815903 T
1 T
43815904 CTTTTACAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
6 5 0.08
7 54 0.83
8 6 0.09
ACGTcount: A:0.31, C:0.48, G:0.00, T:0.21
Consensus pattern (7 bp):
TAACCCC
Found at i:43815884 original size:196 final size:197
Alignment explanation
Indices: 43815682--43816036 Score: 640
Period size: 197 Copynumber: 1.8 Consensus size: 197
43815672 AAACCCTAAA
* *
43815682 CCCCTATCCCTTATCCCCTAACCCCTCTTTTACAATTATATAAGAACTTAATTAATATATAAATT
1 CCCCTATCCCCTAACCCCTAACCCCTCTTTTACAATTATATAAGAACTTAATTAATATATAAATT
*
43815747 -AAAAATACTAATTAATTTAAACCTTAAACCCTTACCCGACCCCGAATCTCTAAACCTTAAATCA
66 AAAAAATACTAATTAATTTAAACCTTAAACCCTAACCCGACCCCGAATCTCTAAACCTTAAATCA
43815811 CTAACTCTTAACCTCTAACCTCTAACCCCTAACCCCAAACCCTAAACCCTAAACCCCTAACTACT
131 CTAACTCTTAACCTCTAACCTCTAACCCCTAACCCCAAACCCTAAACCCTAAACCCCTAACTACT
43815876 AT
196 AT
*
43815878 CCCCTATCCCCTAACCCTTAACCCCTCTTTTACAATTATATAAGAACTTAATTAATATATAAATT
1 CCCCTATCCCCTAACCCCTAACCCCTCTTTTACAATTATATAAGAACTTAATTAATATATAAATT
* *
43815943 AAAAAATACTAATTAATTTAAACCTTAAACCCTAACCTGACCCCGAATCTTTAAACCTTAAATCA
66 AAAAAATACTAATTAATTTAAACCTTAAACCCTAACCCGACCCCGAATCTCTAAACCTTAAATCA
*
43816008 CTAACTCTTAACCTCTAACCTTTAACCCC
131 CTAACTCTTAACCTCTAACCTCTAACCCC
43816037 AAATCCCTAA
Statistics
Matches: 151, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
196 62 0.41
197 89 0.59
ACGTcount: A:0.37, C:0.31, G:0.02, T:0.30
Consensus pattern (197 bp):
CCCCTATCCCCTAACCCCTAACCCCTCTTTTACAATTATATAAGAACTTAATTAATATATAAATT
AAAAAATACTAATTAATTTAAACCTTAAACCCTAACCCGACCCCGAATCTCTAAACCTTAAATCA
CTAACTCTTAACCTCTAACCTCTAACCCCTAACCCCAAACCCTAAACCCTAAACCCCTAACTACT
AT
Found at i:43816517 original size:41 final size:41
Alignment explanation
Indices: 43816470--43816701 Score: 376
Period size: 41 Copynumber: 5.7 Consensus size: 41
43816460 AATGTTTTTT
*
43816470 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCAGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
* * *
43816511 GCGGCGCTTCTTT-AAAAACGCTGCTAAAAGCATGAGCAATA
1 GCGGCGCTT-TTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
43816552 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
* *
43816593 GCGGCGCTTTTTTAAAAACACCGCTAAAAGCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
* *
43816634 GCGGCGCTTTTTCACAAACGCCGCTAAAAGCTTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
43816675 GCGGCGCTTTTTCAAAAACGCCGCTAA
1 GCGGCGCTTTTTCAAAAACGCCGCTAA
43816702 TGCCCCAAAA
Statistics
Matches: 175, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 3 0.02
41 169 0.97
42 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
Found at i:43817762 original size:50 final size:50
Alignment explanation
Indices: 43817703--43818094 Score: 378
Period size: 50 Copynumber: 7.7 Consensus size: 50
43817693 CAAGTTAAAA
* * *
43817703 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCAGTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCATTGCAGTGGAAC
* * * * ** *
43817753 AGATTGAAGCTACAACAGCAGATCTTGCTTTCCCGACATTGCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCATTGCAGTGGAAC
** *
43817803 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCGGTGTAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCATTGCAGTGGAAC
* * * ** *
43817853 AGATTGAAGCTACAACAGCGGATCTTACTTCCCCGACATTGCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCATTGCAGTGGAAC
*
43817903 AGATTGAAGCTACAACAGTGGATCTTAC-TTCCTTGGCATTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCC-TGGCATTGCAGTGGAAC
* * *
43817953 AGATTGAAGCTACAACAG-TGAGTCTTAC-TTCCTTGACGAACCTTACTTCCA-TGGCAC
1 AGATTGAAGCTACAACAGCGGA-TCTTACTTTCC-TG--G---C--A-TTGCAGTGGAAC
* * ** *
43818010 AGATTGAAGCTACAACAGTGAATCTTACTGCCCTGGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCATTGCAGTGGAAC
* * *
43818060 AGATTGAAGGTACAACAGCGAATCTTACTTCCCTG
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTG
43818095 ACGAACCTTA
Statistics
Matches: 280, Mismatches: 49, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
49 9 0.03
50 228 0.81
52 2 0.01
55 2 0.01
57 32 0.11
58 7 0.03
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCATTGCAGTGGAAC
Found at i:43817868 original size:100 final size:100
Alignment explanation
Indices: 43817690--43818092 Score: 465
Period size: 100 Copynumber: 4.0 Consensus size: 100
43817680 ACCCCTGAGG
* *
43817690 TTGCAAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCAGTGCAGTGGAACAG
1 TTGC-AGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCAGTGCAGTGGAACAG
* *
43817755 ATTGAAGCTACAACAGCAGATCTTGCTTTCCCGACA
65 ATTGAAGCTACAACAGCAGATCTTACTTCCCCGACA
* *
43817791 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCGGTGTAGTGGAACAGA
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCAGTGCAGTGGAACAGA
*
43817856 TTGAAGCTACAACAGCGGATCTTACTTCCCCGACA
66 TTGAAGCTACAACAGCAGATCTTACTTCCCCGACA
* *
43817891 TTGCAGTTAAAAAGATTGAAGCTACAACAGTGGATCTTAC-TTCCTTGGCATTGCAGTGGAACAG
1 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCC-TGGCAGTGCAGTGGAACAG
* *
43817955 ATTGAAGCTACAACAG-TGAGTCTTACTTCCTTGACGAACCTTA
65 ATTGAAGCTACAACAGCAGA-TCTTACTTCC---CCG-A-C--A
* *** * * * **
43817998 CTTCCA-TGGCACAGATTGAAGCTACAACAGTGAATCTTACTGCCCTGGC-GTTGCAGTGGAACA
1 -TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCAG-TGCAGTGGAACA
*
43818061 GATTGAAGGTACAACAGC-GAATCTTACTTCCC
64 GATTGAAGCTACAACAGCAG-ATCTTACTTCCC
43818093 TGACGAACCT
Statistics
Matches: 264, Mismatches: 24, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
99 6 0.02
100 170 0.64
101 4 0.02
103 2 0.01
104 1 0.00
105 1 0.00
107 73 0.28
108 7 0.03
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (100 bp):
TTGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCAGTGCAGTGGAACAGA
TTGAAGCTACAACAGCAGATCTTACTTCCCCGACA
Found at i:43819287 original size:518 final size:519
Alignment explanation
Indices: 43818287--43819330 Score: 1887
Period size: 519 Copynumber: 2.0 Consensus size: 519
43818277 GAAGTCAAGA
*
43818287 ATCGACAAGATCGGGCAAATTTGGTCTTTCTTGGTCTTTGCTCTGTTCTCGTTACATGACAACGA
1 ATCGACAAGATCGGGCAAATTTGGTCTTTCTTGGTCTTTGCTCTGTTCTCGTTACACGACAACGA
*
43818352 GCAAAGAGGGGCAGCTGTACAGCCCAAATTTTGCCCGGGCCTAAAAACCCACCTAAACCTACCCA
66 GCAAAGAGGGGCAGCTGTACAGCCCAAATTTTGCCCAGGCCTAAAAACCCACCTAAACCTACCCA
43818417 AACCCAATTACAATGCTGACCCAATAACCCTAAAGGCCCAATAACCTAACTACCCAAATAACCCA
131 AACCCAATTACAATGCTGACCCAATAACCCTAAAGGCCCAATAACCTAACTACCCAAATAACCCA
*
43818482 AATCAGAAAACAAAAAAGTAACCCTAACCCTAGGTGCGCCGTACCTAGGGTCGTCCACTTGCTCT
196 AATCAGAAAACAAAAAAGTAACCCTAACCCTAGGTGCGCCGCACCTAGGGTCGTCCACTTGCTCT
*
43818547 GCCGCCGCCCTAGCCTATAACCACTGTCCCATCGCACGTCCACCGCCATGCCCACTTGCCGCGTT
261 GCCGCCGCCCTAGCCTACAACCACTGTCCCATCGCACGTCCACCGCCATGCCCACTTGCCGCGTT
* *
43818612 AATCACCTACAAAGAGAGAAACCAACACGCAACAACAAGCAGTAGAAATAGATAAAAATAATATG
326 AATCACCTACAAAGAGAGAAACCAAAACGCAACAACAAGCAGTAGAAATAGATAAAAATAATATA
* *
43818677 TAAAATCGGCTATAAAAGCCGGATTAAAAATGTATTAGGGCCAGCTTTTTCTTCAGAAATAAAGA
391 TAAAATCGGCTATAAAAGCCGGATTAAAAATATATTAGGGCCAGCTTTTTCTTCAGAAAAAAAGA
43818742 AATAAAAAAAGAACAGATTCAAAAAAAAAA-TTTGCAACAAAGTAGAAAAAAAGAACAAGGCAG
456 AATAAAAAAAGAACAGATTCAAAAAAAAAATTTTGCAACAAAGTAGAAAAAAAGAACAAGGCAG
* *
43818805 ATCGACAAGATCGGGCAAATTTGGTCTTTCTTGGTGTTTGCTTTGTTCTCGTTACACGACAACGA
1 ATCGACAAGATCGGGCAAATTTGGTCTTTCTTGGTCTTTGCTCTGTTCTCGTTACACGACAACGA
*
43818870 GTAAAGAGGGGCAGCTGTACAGCCCAAATTTTGCCCAGGCCTAAAAACCCACCTAAACCTACCCA
66 GCAAAGAGGGGCAGCTGTACAGCCCAAATTTTGCCCAGGCCTAAAAACCCACCTAAACCTACCCA
43818935 AACCCAATTACAATGCTGACCCAATAACCCTAAAGGCCCAATAACCTAACTACCCAAATAACCCA
131 AACCCAATTACAATGCTGACCCAATAACCCTAAAGGCCCAATAACCTAACTACCCAAATAACCCA
*
43819000 AATTAGAAAACAAAAAAAGTAACCCTAACCCTAGGTGCGCCGCACCTAGGGTCGTCCACTTGCTC
196 AATCAGAAAAC-AAAAAAGTAACCCTAACCCTAGGTGCGCCGCACCTAGGGTCGTCCACTTGCTC
43819065 TGCCGCCGCCCTAGCCTACAACCA-TCGTCCCATCGCACGTCCACCGCCATGCCCACTTGCCGCG
260 TGCCGCCGCCCTAGCCTACAACCACT-GTCCCATCGCACGTCCACCGCCATGCCCACTTGCCGCG
* *
43819129 TTAATCACCTGCAAAGAGAGAAACCAAAACGCAACAACAAGCAGTAGAAATAGATAAAAATAATG
324 TTAATCACCTACAAAGAGAGAAACCAAAACGCAACAACAAGCAGTAGAAATAGATAAAAATAATA
*
43819194 TATAAAATCGGCTATAAAAGCCGGATTAAAAATATATTAGGGCC-GACTTTTTTTTCAGAAAAAA
389 TATAAAATCGGCTATAAAAGCCGGATTAAAAATATATTAGGGCCAG-CTTTTTCTTCAGAAAAAA
*
43819258 AGAAATAAAAAAAGAACAGATTCAAAAAAAAATTTTTTGCAACAAAGTAGAAAAAAAGAACAAGG
453 AGAAATAAAAAAAGAACAGATTCAAAAAAAAA-ATTTTGCAACAAAGTAGAAAAAAAGAACAAGG
43819323 CAG
517 CAG
43819326 ATCGA
1 ATCGA
43819331 GCAAAAGGTT
Statistics
Matches: 505, Mismatches: 16, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
518 202 0.40
519 265 0.52
521 38 0.08
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (519 bp):
ATCGACAAGATCGGGCAAATTTGGTCTTTCTTGGTCTTTGCTCTGTTCTCGTTACACGACAACGA
GCAAAGAGGGGCAGCTGTACAGCCCAAATTTTGCCCAGGCCTAAAAACCCACCTAAACCTACCCA
AACCCAATTACAATGCTGACCCAATAACCCTAAAGGCCCAATAACCTAACTACCCAAATAACCCA
AATCAGAAAACAAAAAAGTAACCCTAACCCTAGGTGCGCCGCACCTAGGGTCGTCCACTTGCTCT
GCCGCCGCCCTAGCCTACAACCACTGTCCCATCGCACGTCCACCGCCATGCCCACTTGCCGCGTT
AATCACCTACAAAGAGAGAAACCAAAACGCAACAACAAGCAGTAGAAATAGATAAAAATAATATA
TAAAATCGGCTATAAAAGCCGGATTAAAAATATATTAGGGCCAGCTTTTTCTTCAGAAAAAAAGA
AATAAAAAAAGAACAGATTCAAAAAAAAAATTTTGCAACAAAGTAGAAAAAAAGAACAAGGCAG
Found at i:43820070 original size:12 final size:12
Alignment explanation
Indices: 43820053--43820077 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43820043 TTCTACCTTT
43820053 TTAATTTTGTTA
1 TTAATTTTGTTA
43820065 TTAATTTTGTTA
1 TTAATTTTGTTA
43820077 T
1 T
43820078 ATACATTAAA
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTAATTTTGTTA
Found at i:43821529 original size:13 final size:13
Alignment explanation
Indices: 43821513--43821538 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43821503 ATTGATTTAA
43821513 TAATTTATGTAAT
1 TAATTTATGTAAT
43821526 TAATTTATGTAAT
1 TAATTTATGTAAT
43821539 GTGAAATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TAATTTATGTAAT
Found at i:43821594 original size:26 final size:27
Alignment explanation
Indices: 43821552--43821603 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
43821542 AAATCAAAAA
*
43821552 AATTAAAGGGACATTTTTAA-AGAAAG
1 AATTAAACGGACATTTTTAATAGAAAG
43821578 AATTATAACGGAC-TTTTTAATAGAAA
1 AATTA-AACGGACATTTTTAATAGAAA
43821604 TAAAAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (27 bp):
AATTAAACGGACATTTTTAATAGAAAG
Found at i:43821967 original size:19 final size:21
Alignment explanation
Indices: 43821929--43821968 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43821919 GTTTTTTTGT
*
43821929 AAAGAATAAGAGGAAGAAAAA
1 AAAGAAAAAGAGGAAGAAAAA
43821950 AAAGAAAAAGA-G-AGAAAAA
1 AAAGAAAAAGAGGAAGAAAAA
43821969 TTATATTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03
Consensus pattern (21 bp):
AAAGAAAAAGAGGAAGAAAAA
Found at i:43828304 original size:13 final size:13
Alignment explanation
Indices: 43828286--43828315 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
43828276 AGCCCAAACT
43828286 CAATTACCCAACC
1 CAATTACCCAACC
43828299 CAATTACCCAACC
1 CAATTACCCAACC
43828312 CAAT
1 CAAT
43828316 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:43828464 original size:8 final size:7
Alignment explanation
Indices: 43828437--43828462 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43828427 TTTAAATTTT
43828437 AAAAATA
1 AAAAATA
43828444 AAAAATA
1 AAAAATA
43828451 AAAAATA
1 AAAAATA
43828458 AAAAA
1 AAAAA
43828463 ATTCGGGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:43828507 original size:9 final size:9
Alignment explanation
Indices: 43828493--43828522 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
43828483 TATTTTTTGG
43828493 TAATTCGGT
1 TAATTCGGT
43828502 TAATTCGGT
1 TAATTCGGT
43828511 TAATTCGGT
1 TAATTCGGT
43828520 TAA
1 TAA
43828523 NNNNNNNNNN
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (9 bp):
TAATTCGGT
Found at i:43844951 original size:23 final size:23
Alignment explanation
Indices: 43844901--43844952 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
43844891 GTTAGGTGTC
* *
43844901 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
43844924 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
43844947 AGTATG
1 AGTATG
43844953 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:43847705 original size:16 final size:17
Alignment explanation
Indices: 43847671--43847706 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
43847661 AAATAATTTA
43847671 AAATTTATAAAATATTC
1 AAATTTATAAAATATTC
43847688 AAATTTATAAAA-ATTC
1 AAATTTATAAAATATTC
43847704 AAA
1 AAA
43847707 AAAAAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTTATAAAATATTC
Found at i:43850013 original size:23 final size:24
Alignment explanation
Indices: 43849987--43850045 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
43849977 AAAAACCTAC
43849987 AAAATATA-ATCTAAATTAAAAA-T
1 AAAATATATAT-TAAATTAAAAATT
* **
43850010 AAAAAATATATTTGATTAAAAATT
1 AAAATATATATTAAATTAAAAATT
43850034 AAAATATATATT
1 AAAATATATATT
43850046 TAATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAATATATATTAAATTAAAAATT
Found at i:43854940 original size:5 final size:5
Alignment explanation
Indices: 43854930--43854978 Score: 98
Period size: 5 Copynumber: 9.8 Consensus size: 5
43854920 AGATTTACAC
43854930 AATCA AATCA AATCA AATCA AATCA AATCA AATCA AATCA AATCA AATC
1 AATCA AATCA AATCA AATCA AATCA AATCA AATCA AATCA AATCA AATC
43854979 TTTTTAGATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.59, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AATCA
Found at i:43857751 original size:20 final size:20
Alignment explanation
Indices: 43857726--43857766 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
43857716 CTTGTATATA
43857726 AATTAGTCATATGCCCGATT
1 AATTAGTCATATGCCCGATT
43857746 AATTAGTCATATGCCCGATT
1 AATTAGTCATATGCCCGATT
43857766 A
1 A
43857767 TAATGGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (20 bp):
AATTAGTCATATGCCCGATT
Found at i:43861657 original size:20 final size:21
Alignment explanation
Indices: 43861621--43861665 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
43861611 AAGGAGGAAG
*
43861621 TATTGGCAGCCTTGTCTGCAT
1 TATTGGCAGCCTTGTCTGCAC
*
43861642 TATTGGCAG-TTTGTCTGCAC
1 TATTGGCAGCCTTGTCTGCAC
43861662 TATT
1 TATT
43861666 AGTGGCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (21 bp):
TATTGGCAGCCTTGTCTGCAC
Found at i:43861794 original size:21 final size:21
Alignment explanation
Indices: 43861733--43861795 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
43861723 AATGGCAGTT
* *
43861733 TATCTGCATTACTGGTGGCTC
1 TATCAGCATTACTGGTGGCAC
* * * **
43861754 AACCA-TATTACTGGCAGCAC
1 TATCAGCATTACTGGTGGCAC
43861774 TATCAGCATTACTGGTGGCAC
1 TATCAGCATTACTGGTGGCAC
43861795 T
1 T
43861796 GTCTATAAAT
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (21 bp):
TATCAGCATTACTGGTGGCAC
Found at i:43863160 original size:5 final size:5
Alignment explanation
Indices: 43863150--43863178 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
43863140 AGATTTACAC
43863150 AATCA AATCA AATCA AATCA AATCA AATC
1 AATCA AATCA AATCA AATCA AATCA AATC
43863179 TTTCCAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (5 bp):
AATCA
Found at i:43865157 original size:18 final size:18
Alignment explanation
Indices: 43865111--43865157 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
43865101 AACACAATCC
*
43865111 TATGAAAGGGTAT-TTCA
1 TATGAAAAGGTATATTCA
*
43865128 T-T-AAAAGATATATTCA
1 TATGAAAAGGTATATTCA
43865144 TATGAAAAGGTATA
1 TATGAAAAGGTATA
43865158 GCATGGAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 2 0.08
18 9 0.38
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (18 bp):
TATGAAAAGGTATATTCA
Found at i:43866080 original size:16 final size:16
Alignment explanation
Indices: 43866054--43866095 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
43866044 TCTTCAATAC
*
43866054 TTAATTTTTTCCCACAT
1 TTAA-TTTTTCCAACAT
43866071 TTAATTTTT-CAACAT
1 TTAATTTTTCCAACAT
*
43866086 TTAACTTTTC
1 TTAATTTTTC
43866096 AAATTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 13 0.59
16 5 0.23
17 4 0.18
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATTTTTCCAACAT
Found at i:43866085 original size:15 final size:15
Alignment explanation
Indices: 43866067--43866097 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43866057 ATTTTTTCCC
*
43866067 ACATTTAATTTTTCA
1 ACATTTAACTTTTCA
43866082 ACATTTAACTTTTCA
1 ACATTTAACTTTTCA
43866097 A
1 A
43866098 ATTATCAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (15 bp):
ACATTTAACTTTTCA
Found at i:43866182 original size:2 final size:2
Alignment explanation
Indices: 43866175--43866204 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43866165 TTCAAAATTA
43866175 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
43866205 TCACTTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43866755 original size:23 final size:23
Alignment explanation
Indices: 43866701--43866756 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
43866691 TGATCAAATT
* * *
43866701 ATAATATAAATTTAAATTTAAAT
1 ATAATAAAAATTAAAATTTAAAC
43866724 ATTAA-AAAAATTAAAATTTAAAC
1 A-TAATAAAAATTAAAATTTAAAC
43866747 ATAATAAAAA
1 ATAATAAAAA
43866757 AACAAAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 3 0.11
23 22 0.79
24 3 0.11
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
ATAATAAAAATTAAAATTTAAAC
Done.