Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 132 of 172
Found at i:43825875 original size:3 final size:3
Alignment explanation
Indices: 43825867--43825918 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
43825857 ATACACTAAC
* * ** *
43825867 ATA ATA ATA ATT ATA ATA ATA CTA GCA ATA ATA ATA ATTA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
43825913 ATA ATA
1 ATA ATA
43825919 TATACACAAC
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:43825914 original size:16 final size:16
Alignment explanation
Indices: 43825879--43825918 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
43825869 AATAATAATT
43825879 ATAATAAT-ACTAGCA
1 ATAATAATAACTAGCA
* *
43825894 ATAATAATAATTAGTA
1 ATAATAATAACTAGCA
43825910 ATAATAATA
1 ATAATAATA
43825919 TATACACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
ATAATAATAACTAGCA
Found at i:43826072 original size:23 final size:23
Alignment explanation
Indices: 43825953--43826090 Score: 92
Period size: 23 Copynumber: 6.0 Consensus size: 23
43825943 AAATAAAAAT
* *
43825953 AAAATATATATATAATAGTATTTA
1 AAAATATATACATAATA-TATATA
* *
43825977 AGAATATATACATAAGATGATAT-
1 AAAATATATACATAATAT-ATATA
*
43826000 AAAATACATACATGGAATA-ATATA
1 AAAATATATACAT--AATATATATA
**
43826024 AGAAATATATA-ACTAATGGCAT-TA
1 A-AAATATATACA-TAAT-ATATATA
43826048 AAAATATATACATAATATATAT-
1 AAAATATATACATAATATATATA
*
43826070 AAAATACAT--ATAATATATATA
1 AAAATATATACATAATATATATA
43826091 CATATTAGAA
Statistics
Matches: 91, Mismatches: 12, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
20 11 0.12
22 10 0.11
23 33 0.36
24 23 0.25
25 14 0.15
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (23 bp):
AAAATATATACATAATATATATA
Found at i:43828062 original size:18 final size:18
Alignment explanation
Indices: 43828036--43828075 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 18
43828026 ATAATTTAAA
43828036 AAATAATAATAAAAAT---
1 AAATAAT-ATAAAAATAAG
43828052 AAATAATATAAAAATAAG
1 AAATAATATAAAAATAAG
43828070 AAATAA
1 AAATAA
43828076 GAATATCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
18 6 0.29
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
AAATAATATAAAAATAAG
Found at i:43828074 original size:15 final size:15
Alignment explanation
Indices: 43828036--43828068 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
43828026 ATAATTTAAA
43828036 AAATAATAATAAAAAT
1 AAATAAT-ATAAAAAT
43828052 AAATAATATAAAAAT
1 AAATAATATAAAAAT
43828067 AA
1 AA
43828069 GAAATAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAATATAAAAAT
Found at i:43828080 original size:21 final size:21
Alignment explanation
Indices: 43828038--43828081 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
43828028 AATTTAAAAA
* *
43828038 ATAATAATAAAAATAAATAAT
1 ATAAAAATAAAAATAAAGAAT
43828059 ATAAAAATAAGAAAT-AAGAAT
1 ATAAAAATAA-AAATAAAGAAT
43828080 AT
1 AT
43828082 CATTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (21 bp):
ATAAAAATAAAAATAAAGAAT
Found at i:43832910 original size:10 final size:9
Alignment explanation
Indices: 43832895--43833068 Score: 52
Period size: 10 Copynumber: 18.6 Consensus size: 9
43832885 TCCTAAAATA
43832895 AAAAATTAT
1 AAAAATTAT
43832904 CAAAAA-TAT
1 -AAAAATTAT
*
43832913 AAAAATGATT
1 AAAAATTA-T
*
43832923 AAATATT-T
1 AAAAATTAT
*
43832931 AAAAA-GAT
1 AAAAATTAT
*
43832939 GAAAATTGAT
1 AAAAATT-AT
* *
43832949 ATCAACTTAT
1 A-AAAATTAT
**
43832959 AAATTTTAT
1 AAAAATTAT
*
43832968 AAAAAATAT
1 AAAAATTAT
* *
43832977 AAAAGAATCT
1 AAAA-ATTAT
43832987 AATAAATTAT
1 AA-AAATTAT
*
43832997 AAAAA-AAT
1 AAAAATTAT
*
43833005 ATAAATTAAT
1 AAAAATT-AT
43833015 AAAACATATAT
1 AAAA-AT-TAT
43833026 AAAATATT-T
1 AAAA-ATTAT
*
43833035 AAAATTTTAT
1 AAAA-ATTAT
*
43833045 AAAAACATAT
1 AAAAA-TTAT
* *
43833055 TAAAATTCT
1 AAAAATTAT
43833064 AAAAA
1 AAAAA
43833069 AATCATAAAA
Statistics
Matches: 119, Mismatches: 31, Indels: 29
0.66 0.17 0.16
Matches are distributed among these distances:
8 21 0.18
9 36 0.30
10 45 0.38
11 16 0.13
12 1 0.01
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:43833010 original size:17 final size:19
Alignment explanation
Indices: 43832988--43833028 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
43832978 AAAGAATCTA
43832988 ATAAATT-ATAAAA-AAAT
1 ATAAATTAATAAAACAAAT
*
43833005 ATAAATTAATAAAACATAT
1 ATAAATTAATAAAACAAAT
43833024 ATAAA
1 ATAAA
43833029 ATATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 6 0.29
19 8 0.38
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAAATTAATAAAACAAAT
Found at i:43833057 original size:21 final size:22
Alignment explanation
Indices: 43833026--43833075 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
43833016 AAACATATAT
* *
43833026 AAAAT-AT-TTAAAATTTTATA
1 AAAATCATATTAAAATTCTAAA
43833046 AAAA-CATATTAAAATTCTAAA
1 AAAATCATATTAAAATTCTAAA
43833067 AAAATCATA
1 AAAATCATA
43833076 AAACATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.24
21 15 0.60
22 4 0.16
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATCATATTAAAATTCTAAA
Found at i:43833576 original size:15 final size:15
Alignment explanation
Indices: 43833556--43833585 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43833546 TCAACTTTAA
43833556 TATTTTTTAAGAATT
1 TATTTTTTAAGAATT
43833571 TATTTTTTAAGAATT
1 TATTTTTTAAGAATT
43833586 CTAACACATT
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:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TATTTTTTAAGAATT
Found at i:43833638 original size:10 final size:10
Alignment explanation
Indices: 43833623--43833664 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
43833613 GTTTTATTAA
43833623 TTTTATATTT
1 TTTTATATTT
*
43833633 TTTTATAATT
1 TTTTATATTT
* *
43833643 TATTAGATTT
1 TTTTATATTT
43833653 TTTTAT-TTT
1 TTTTATATTT
43833662 TTT
1 TTT
43833665 ATAATATTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
9 6 0.23
10 20 0.77
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (10 bp):
TTTTATATTT
Found at i:43833657 original size:30 final size:28
Alignment explanation
Indices: 43833623--43833714 Score: 96
Period size: 33 Copynumber: 3.0 Consensus size: 28
43833613 GTTTTATTAA
*
43833623 TTTTATATTTTTTTATAATTTATTAGATT
1 TTTTATATTTTTTTATAATTTATAAG-TT
43833652 TTTT-TATTTTTTTATAATATTTATAAGTT
1 TTTTATATTTTTTTAT-A-ATTTATAAGTT
43833681 TTTATATAATATTTTTTATAATTTTAATAAGTT
1 TTT-TAT-AT-TTTTTTATAA-TTT-ATAAGTT
43833714 T
1 T
43833715 ATATTAATTT
Statistics
Matches: 54, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
28 11 0.20
29 10 0.19
30 9 0.17
31 2 0.04
32 6 0.11
33 16 0.30
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTTATATTTTTTTATAATTTATAAGTT
Found at i:43833673 original size:21 final size:21
Alignment explanation
Indices: 43833627--43833697 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
43833617 TATTAATTTT
** *
43833627 ATATTTTTTTA-TAATTTATT
1 ATATTTTTTTATTTTTTTATA
*
43833647 AGATTTTTTTATTTTTTTATA
1 ATATTTTTTTATTTTTTTATA
* * *
43833668 ATA-TTTATAAGTTTTTATATA
1 ATATTTTTTTA-TTTTTTTATA
43833689 ATATTTTTT
1 ATATTTTTT
43833698 ATAATTTTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 15 0.38
21 20 0.51
22 4 0.10
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
ATATTTTTTTATTTTTTTATA
Found at i:43833698 original size:33 final size:32
Alignment explanation
Indices: 43833659--43833722 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
43833649 ATTTTTTTAT
*
43833659 TTTTTTATAATATTT-ATAAGTTTTTATATAATA
1 TTTTTTATAAT-TTTAATAAGTTTATAT-TAATA
43833692 TTTTTTATAATTTTAATAAGTTTATATTAAT
1 TTTTTTATAATTTTAATAAGTTTATATTAAT
43833723 TTTAATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 7 0.24
33 22 0.76
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (32 bp):
TTTTTTATAATTTTAATAAGTTTATATTAATA
Found at i:43833710 original size:21 final size:21
Alignment explanation
Indices: 43833593--43833710 Score: 62
Period size: 20 Copynumber: 6.0 Consensus size: 21
43833583 ATTCTAACAC
43833593 ATTTTTT-TAATTTT-A-AAT
1 ATTTTTTATAATTTTAATAAT
**
43833611 AAGTTTTATTAATTTT-AT-AT
1 ATTTTTTA-TAATTTTAATAAT
*
43833631 -TTTTTTATAA-TTTATTAGAT
1 ATTTTTTATAATTTTAATA-AT
* *
43833651 -TTTTTTAT-TTTTTTATAAT
1 ATTTTTTATAATTTTAATAAT
43833670 A---TTTATAAGTTTTTATATAAT
1 ATTTTTTATAA--TTTTA-ATAAT
43833691 ATTTTTTATAATTTTAATAA
1 ATTTTTTATAATTTTAATAA
43833711 GTTTATATTA
Statistics
Matches: 75, Mismatches: 10, Indels: 27
0.67 0.09 0.24
Matches are distributed among these distances:
17 8 0.11
18 9 0.12
19 7 0.09
20 29 0.39
21 10 0.13
22 5 0.07
24 7 0.09
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (21 bp):
ATTTTTTATAATTTTAATAAT
Found at i:43833732 original size:28 final size:27
Alignment explanation
Indices: 43833701--43833761 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
43833691 ATTTTTTATA
43833701 ATTTTAATAAGTTT-ATATTA-ATTTTAAT
1 ATTTTAAT-A-TTTAATATTATA-TTTAAT
43833729 ATTTTTAATATTTAATATTATATTTAAT
1 A-TTTTAATATTTAATATTATATTTAAT
43833757 ATTTT
1 ATTTT
43833762 TTTATTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
27 7 0.23
28 15 0.50
29 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
ATTTTAATATTTAATATTATATTTAAT
Found at i:43833762 original size:28 final size:28
Alignment explanation
Indices: 43833666--43833762 Score: 81
Period size: 29 Copynumber: 3.4 Consensus size: 28
43833656 TATTTTTTTA
* * * *
43833666 TAATATTTATAAGTTTTTATATAATATTTT
1 TAATATTTTTAA-TATTTA-ATATTATATT
* *
43833696 TTATAATTTTAATAAGTTT-ATATTA-ATTT
1 TAATATTTTTAAT-A-TTTAATATTATA-TT
43833725 TAATATTTTTAATATTTAATATTATATT
1 TAATATTTTTAATATTTAATATTATATT
43833753 TAATATTTTT
1 TAATATTTTT
43833763 TTATTTCTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
27 3 0.06
28 19 0.35
29 20 0.37
30 9 0.17
31 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TAATATTTTTAATATTTAATATTATATT
Found at i:43833790 original size:9 final size:9
Alignment explanation
Indices: 43833623--43833790 Score: 54
Period size: 9 Copynumber: 17.6 Consensus size: 9
43833613 GTTTTATTAA
43833623 TTTTATATTT
1 TTTTATA-TT
43833633 TTTTATAATT
1 TTTTAT-ATT
* *
43833643 TATTAGATT
1 TTTTATATT
43833652 TTTT-TATTT
1 TTTTATA-TT
*
43833661 TTTTATAAT
1 TTTTATATT
*
43833670 ATTTATAAGTTT
1 TTTTAT-A--TT
43833682 TTATATAATATT
1 TT-T-T-ATATT
*
43833694 TTTTATAAT
1 TTTTATATT
* *
43833703 TTTAATA-A
1 TTTTATATT
*
43833711 GTTTATATT
1 TTTTATATT
43833720 AATTTTAATATT
1 --TTTT-ATATT
*
43833732 TTTAATATT
1 TTTTATATT
** *
43833741 TAATATTATA
1 TTTTA-TATT
*
43833751 TTTAATATT
1 TTTTATATT
43833760 TTTT-TATT
1 TTTTATATT
* * *
43833768 TCTTCTAAT
1 TTTTATATT
43833777 TTTTATATT
1 TTTTATATT
43833786 TTTTA
1 TTTTA
43833791 ATCGAAAAAT
Statistics
Matches: 113, Mismatches: 30, Indels: 31
0.65 0.17 0.18
Matches are distributed among these distances:
8 13 0.12
9 55 0.49
10 24 0.21
11 5 0.04
12 11 0.10
13 1 0.01
14 2 0.02
15 2 0.02
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTATATT
Found at i:43836852 original size:17 final size:17
Alignment explanation
Indices: 43836830--43836862 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43836820 ACATTAATAT
43836830 ATAAAATAATAATAATG
1 ATAAAATAATAATAATG
*
43836847 ATAAAATAATACTAAT
1 ATAAAATAATAATAAT
43836863 ATTTAATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (17 bp):
ATAAAATAATAATAATG
Found at i:43838389 original size:45 final size:44
Alignment explanation
Indices: 43838337--43838469 Score: 142
Period size: 44 Copynumber: 3.0 Consensus size: 44
43838327 ATCTTCTCTT
* * *
43838337 CTGTAAC-TCTAGCAAAGCAAGATCTGATATCCTCGATCAGCTCCA
1 CTGTAACTTC-AGCAAA-CAAAATCTGACATCCTCAATCAGCTCCA
* * * *
43838382 CTGTAACTTCAGGAGACAAAATCTGACATCTTCAATTAGCTCCA
1 CTGTAACTTCAGCAAACAAAATCTGACATCCTCAATCAGCTCCA
* * * *
43838426 CTGTAACTTCAGGAGACAAAATCTGACATCTTCAATTAGCTCCA
1 CTGTAACTTCAGCAAACAAAATCTGACATCCTCAATCAGCTCCA
43838470 ATCTTTATTC
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
44 67 0.84
45 11 0.14
46 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (44 bp):
CTGTAACTTCAGCAAACAAAATCTGACATCCTCAATCAGCTCCA
Found at i:43838423 original size:44 final size:44
Alignment explanation
Indices: 43838375--43838469 Score: 190
Period size: 44 Copynumber: 2.2 Consensus size: 44
43838365 ATCCTCGATC
43838375 AGCTCCACTGTAACTTCAGGAGACAAAATCTGACATCTTCAATT
1 AGCTCCACTGTAACTTCAGGAGACAAAATCTGACATCTTCAATT
43838419 AGCTCCACTGTAACTTCAGGAGACAAAATCTGACATCTTCAATT
1 AGCTCCACTGTAACTTCAGGAGACAAAATCTGACATCTTCAATT
43838463 AGCTCCA
1 AGCTCCA
43838470 ATCTTTATTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (44 bp):
AGCTCCACTGTAACTTCAGGAGACAAAATCTGACATCTTCAATT
Found at i:43838627 original size:54 final size:54
Alignment explanation
Indices: 43838504--43838710 Score: 244
Period size: 56 Copynumber: 3.9 Consensus size: 54
43838494 GATCTTGAGT
** * *
43838504 TCAACTCGTCTCTCGCAATATGAATTGATTTTTGAAAAA-A-ACA--AAAAGG-
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTAAAAGGC
* * * * *
43838553 TATAACTCAACTCTCACAATATGAGTTGCTTTTTGAAAAACAGAAATTAAAAGGC
1 T-CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTAAAAGGC
* *
43838608 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATATAAATTGAAAGGC
1 TCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACATAAATTAAAAGGC
*
43838664 TCAACTCACCTCTCGCAACATGAGTTGATTTTTGAAAAACATAAATT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT
43838711 GAGCAGAAAT
Statistics
Matches: 134, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
49 1 0.01
50 32 0.24
51 1 0.01
52 2 0.01
54 47 0.35
55 1 0.01
56 50 0.37
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (54 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTAAAAGGC
Found at i:43838785 original size:58 final size:58
Alignment explanation
Indices: 43838715--43838828 Score: 174
Period size: 58 Copynumber: 2.0 Consensus size: 58
43838705 TAAATTGAGC
* * *
43838715 AGAAATTGAAAATACCTCAACGGGTCTTGAGGTTCAACTCACCTCTCGCAATATGAAT
1 AGAAATTGAAAATACCTCAACGGGACCTGAGGCTCAACTCACCTCTCGCAATATGAAT
** *
43838773 AGAAATTGAAAATACCTCGGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
1 AGAAATTGAAAATACCTCAACGGGACCTGAGGCTCAACTCACCTCTCGCAATATGA
43838829 GCTGATTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (58 bp):
AGAAATTGAAAATACCTCAACGGGACCTGAGGCTCAACTCACCTCTCGCAATATGAAT
Found at i:43838889 original size:54 final size:54
Alignment explanation
Indices: 43838802--43838941 Score: 201
Period size: 54 Copynumber: 2.6 Consensus size: 54
43838792 GCGTGACCTG
*
43838802 AGGCTCAACTCACCTCTCGCAATATGAGCTGA-TTTTGAAAAAGTAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA-TAGAAATTAAA
* * ** * *
43838856 AGGTTCAACCCACCTCTCGCAATATGAGTTGATTTTTGATTAATATAAATTGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAA
43838910 AGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA
43838942 AATTAAAACA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
54 68 0.89
55 8 0.11
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (54 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAA
Found at i:43839129 original size:122 final size:124
Alignment explanation
Indices: 43838860--43839156 Score: 420
Period size: 122 Copynumber: 2.4 Consensus size: 124
43838850 ATTAAAAGGT
* * * * *
43838860 TCAACCCACCTCTCGCAATATGAGTTGATTTTTGATTAATATAAATTGAAAGGCTCAACTCACCT
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTGA-AAAAAAAAATTAAAAGGCTCAACTCACCT
* *
43838925 CTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGC
64 CTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCGTGCCCCGAGGC
* *
43838986 TCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAA-AAAAATTAAAAGGCTCAACTCACCTC
* * * *
43839051 TCGCAATATGAG-T-CAATTTAAA-ACATAAACTAAAAATACCTCGGCGTGCCCCGAGGC
65 TCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCGTGCCCCGAGGC
*
43839108 TCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAAA
43839157 ATACCTCAAC
Statistics
Matches: 155, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
121 11 0.07
122 67 0.43
123 7 0.05
124 3 0.02
125 41 0.26
126 26 0.17
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (124 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAAAGGCTCAACTCACCTCT
CGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCGTGCCCCGAGGC
Found at i:43839183 original size:71 final size:70
Alignment explanation
Indices: 43839035--43839210 Score: 212
Period size: 71 Copynumber: 2.5 Consensus size: 70
43839025 AAAAATTAAA
* * * * * * **
43839035 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGTG
43839099 CCCCG
66 CCCCG
*
43839104 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAAAAAAAACTAAAAATACCTCAACGT
* **
43839169 GTCTTG
65 GCCCCG
43839175 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
43839211 CCTTGGAAAG
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
69 26 0.28
70 6 0.07
71 60 0.65
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:43847273 original size:45 final size:44
Alignment explanation
Indices: 43847216--43847353 Score: 143
Period size: 44 Copynumber: 3.1 Consensus size: 44
43847206 TTGCGATCTT
* * * *
43847216 CTCCTCTGTAAC-TCTAGCAAAGCAAGATCTGATATCCTCGATCAG
1 CTCCACTGTAACTTC-AGCAAA-CAAAATCTGACATCCTCAATCAG
* * * *
43847261 CTCCACTGTAACTTCAGGAGACAAAATCTGACATCTTCAATTAG
1 CTCCACTGTAACTTCAGCAAACAAAATCTGACATCCTCAATCAG
* * * *
43847305 CTCCACTGTAACTTCAGGAGACAAAATCTGACATCTTCAATTAG
1 CTCCACTGTAACTTCAGCAAACAAAATCTGACATCCTCAATCAG
43847349 CTCCA
1 CTCCA
43847354 ATCTTTATTC
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
44 67 0.80
45 15 0.18
46 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.27
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGCAAACAAAATCTGACATCCTCAATCAG
Found at i:43847307 original size:44 final size:44
Alignment explanation
Indices: 43847259--43847353 Score: 190
Period size: 44 Copynumber: 2.2 Consensus size: 44
43847249 ATCCTCGATC
43847259 AGCTCCACTGTAACTTCAGGAGACAAAATCTGACATCTTCAATT
1 AGCTCCACTGTAACTTCAGGAGACAAAATCTGACATCTTCAATT
43847303 AGCTCCACTGTAACTTCAGGAGACAAAATCTGACATCTTCAATT
1 AGCTCCACTGTAACTTCAGGAGACAAAATCTGACATCTTCAATT
43847347 AGCTCCA
1 AGCTCCA
43847354 ATCTTTATTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (44 bp):
AGCTCCACTGTAACTTCAGGAGACAAAATCTGACATCTTCAATT
Found at i:43847511 original size:54 final size:54
Alignment explanation
Indices: 43847388--43847594 Score: 226
Period size: 56 Copynumber: 3.9 Consensus size: 54
43847378 GATCTTGAGT
** * *
43847388 TCAACTCGTCTCTCGCAATATGAATTGATTTTTGAAAAA-A-ACA--AAAAGG-
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGC
* * * *
43847437 TATAACTCAACTCTCACAATATGAGTTGCTTTTTGAAAAACAGAAATTAAAAGGC
1 T-CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGC
* * *
43847492 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATATAAATTGAAAGGC
1 TCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTAAAAGGC
* * *
43847548 TCAACTCACCTCTCGCAACATGAGTTGATTCTTGAAAAACAGGAATT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
43847595 GGAAAATAGA
Statistics
Matches: 131, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
49 1 0.01
50 32 0.24
51 1 0.01
52 2 0.02
54 44 0.34
55 1 0.01
56 50 0.38
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (54 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGC
Found at i:43847722 original size:88 final size:87
Alignment explanation
Indices: 43847544--43847760 Score: 305
Period size: 88 Copynumber: 2.5 Consensus size: 87
43847534 ATAAATTGAA
* *
43847544 AGGCTCAACTCACCTCTCGCAACATGAGTTGATTCTTGAAAAACAGGAATTGGAAAATAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTCAAAAACAGGAATTGGAAAATAGAAATT
*
43847609 GAAAATACCTCAGCATGCCCCG
66 GAAAATACCTCAGCATGACCCG
*
43847631 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTCAAAAACA-TAATAAT-GAAAATAGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTC-TTCAAAAACAGGAAT--TGGAAAATAGAA
* * *
43847694 ATTGAAAATACCTCGGCGTGACCTG
63 ATTGAAAATACCTCAGCATGACCCG
* *
43847719 AGGCTCAACTCACCTCTCGCAATATGAGCTGATT-TTGAAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTCAAAAA
43847761 GTAGAAATTA
Statistics
Matches: 118, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
86 7 0.06
87 37 0.31
88 73 0.62
89 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (87 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTCAAAAACAGGAATTGGAAAATAGAAATT
GAAAATACCTCAGCATGACCCG
Found at i:43847855 original size:54 final size:54
Alignment explanation
Indices: 43847719--43847858 Score: 219
Period size: 54 Copynumber: 2.6 Consensus size: 54
43847709 GCGTGACCTG
*
43847719 AGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAGTAGAAATTAAA
* * * *
43847773 AGGTTCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAAA-TATAAATTGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAAAGTAGAAATTAAA
43847827 AGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA
43847859 AATTAAAACA
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 68 0.87
55 10 0.13
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (54 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAGTAGAAATTAAA
Found at i:43848051 original size:122 final size:125
Alignment explanation
Indices: 43847777--43848073 Score: 424
Period size: 122 Copynumber: 2.4 Consensus size: 125
43847767 ATTAAAAGGT
* * * * *
43847777 TCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAGGCTCAACTCACCT
1 TCAACTCACCTCTCACAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTCAACTCACCT
* *
43847842 CTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGC
65 CTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCGTGCCCCGAGGC
*
43847903 TCAACTCACCTCT-AGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCT
1 TCAACTCACCTCTCA-CAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTCAACTCACCT
* * * *
43847967 CTCGCAATATGAG-T-CAATTTAAA-ACATAAACTAAAAATACCTCGGCGTGCCCCGAGGC
65 CTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCGTGCCCCGAGGC
*
43848025 TCAACTCACTTCTCACAATATGAGTTGATTTTG-AAAACAAAAATTAAAA
1 TCAACTCACCTCTCACAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
43848074 ATACCTCAAC
Statistics
Matches: 156, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
121 16 0.10
122 61 0.39
123 8 0.05
124 1 0.01
125 45 0.29
126 25 0.16
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (125 bp):
TCAACTCACCTCTCACAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTCAACTCACCTC
TCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCGTGCCCCGAGGC
Found at i:43848095 original size:71 final size:70
Alignment explanation
Indices: 43847952--43848127 Score: 212
Period size: 71 Copynumber: 2.5 Consensus size: 70
43847942 AAAAATTAAA
* * * * * **
43847952 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
43848016 CCCCG
66 CCCCG
* *
43848021 AGGCTCAACTCACTTCTCACAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTCAACGT
* **
43848086 GTCTTG
65 GCCCCG
43848092 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
43848128 CCTTGGAAAG
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
69 25 0.27
70 6 0.07
71 60 0.66
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:43864057 original size:27 final size:28
Alignment explanation
Indices: 43863973--43864070 Score: 126
Period size: 27 Copynumber: 3.5 Consensus size: 28
43863963 CATGAGATTG
* * * * *
43863973 GCACTAAGTGTACGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
43864002 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
43864030 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
43864057 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
43864071 GACTTAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.35
29 17 0.27
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:43864084 original size:29 final size:27
Alignment explanation
Indices: 43864001--43864084 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
43863991 TAAATTGTAC
* *
43864001 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
43864029 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
43864056 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
43864085 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.46
28 22 0.44
29 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:43867942 original size:22 final size:21
Alignment explanation
Indices: 43867913--43867954 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
43867903 TGAGTTTGCA
*
43867913 TTTAAAAATATTTAAATTATT
1 TTTAAAAATAATTAAATTATT
43867934 TTTATAAAATAATTAAATTAT
1 TTTA-AAAATAATTAAATTAT
43867955 ATCTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAAAAATAATTAAATTATT
Found at i:43875890 original size:22 final size:23
Alignment explanation
Indices: 43875839--43875892 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 23
43875829 TTTTCATTAT
43875839 TTTCTTTACTTTTTTAATTATAAATA
1 TTTC-TTA-TTTTTTAA-TATAAATA
43875865 --TCTTATTTTTTAA-ATAAATA
1 TTTCTTATTTTTTAATATAAATA
43875885 TTTCTTAT
1 TTTCTTAT
43875893 AATCATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
20 7 0.27
22 14 0.54
23 3 0.12
24 2 0.08
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTCTTATTTTTTAATATAAATA
Found at i:43878224 original size:30 final size:30
Alignment explanation
Indices: 43878132--43878225 Score: 161
Period size: 30 Copynumber: 3.1 Consensus size: 30
43878122 NNNNNNNNNN
*
43878132 GTGGAGCAAGTGTGGCTAGTAGAGTAGGTG
1 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTG
*
43878162 GTAGAGCAAGTGTGGCTAGTGGAGTAGGTG
1 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTG
*
43878192 GTGGAGCAAGTGTGGCTAGTGGAGTTGGTG
1 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTG
43878222 GTGG
1 GTGG
43878226 CAAAGGCTAG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.20, C:0.06, G:0.49, T:0.24
Consensus pattern (30 bp):
GTGGAGCAAGTGTGGCTAGTGGAGTAGGTG
Found at i:43878785 original size:21 final size:21
Alignment explanation
Indices: 43878756--43878795 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43878746 ATCATCGATC
43878756 AGCTCCACTGCAACTTCAATT
1 AGCTCCACTGCAACTTCAATT
* *
43878777 AGCTTCACTGTAACTTCAA
1 AGCTCCACTGCAACTTCAA
43878796 GGATATAAAA
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:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (21 bp):
AGCTCCACTGCAACTTCAATT
Found at i:43879013 original size:87 final size:88
Alignment explanation
Indices: 43878875--43879426 Score: 398
Period size: 87 Copynumber: 6.2 Consensus size: 88
43878865 ACTCATTTCA
* * * * * * *
43878875 CGCAATATGAATTGACTCTTTAAAACTAGATATT-AAAAACAGAAATTGAAAATAGCTCAGCACG
1 CGCAATATGAGTTGATTTTTTAAAACAAAAT-TTGAAAAACAGAAATTGAAAATACCTCAGCATG
* * *
43878939 TGAGCCAAGGCTTAACTCACTTCT
65 TGAGCCGAGGCTCAACTCACCTCT
* * ** * *
43878963 CACAATATGAGTTGA-TTTTTAAAACAAAATTTGTAAAACAGATTTTGAAAATACCTCGGTATGT
1 CGCAATATGAGTTGATTTTTTAAAACAAAATTTGAAAAACAGAAATTGAAAATACCTCAGCATGT
* *
43879027 GACCCGAGGCTCAACTCACCTAT
66 GAGCCGAGGCTCAACTCACCTCT
* ** * * * *
43879050 CGTAATATGAGTTGATTGTTGCAAAGCATAAA-TTGAAAAAAAAAATCAATTGAAAATACCTCGG
1 CGCAATATGAGTTGATT-TTTTAAAACA-AAATTTG-AAAAACAGA--AATTGAAAATACCTCAG
* * *
43879114 CGTGTGATCTGAGGCTCAACTCACCTCT
61 CATGTGAGCCGAGGCTCAACTCACCTCT
*
43879142 CGCAATATGAGTTGATTTTTTTGACAAACATAAA-TTG--AAA-AGAAATTGAAAATATCTCAGC
1 CGCAATATGAGTTGA-TTTTTT-A-AAACA-AAATTTGAAAAACAGAAATTGAAAATACCTCAGC
* *
43879203 --GTG-TCCTGAGGCTGAACTCACCTCT
62 ATGTGAGCC-GAGGCTCAACTCACCTCT
* *
43879228 CGCAATATGAGTTGATTTTTTGGAAAAACAAAATTTGAAAAACAGAATTTGAAAATACCTCAGCG
1 CGCAATATGAGTTGATTTTTT---AAAACAAAATTTGAAAAACAGAAATTGAAAATACCTCAGCA
* * *
43879293 TGTGAGTCAAGGCTCAACTCACCACT
63 TGTGAGCCGAGGCTCAACTCACCTCT
* * * ** * *
43879319 TGCAATATGGGCTGATTTTTTTGAAACACAGAAA-TTGACGAACAGAAATGGAAAACACCTCAGC
1 CGCAATATGAGTTGA-TTTTTT-AAA-ACA-AAATTTGAAAAACAGAAATTGAAAATACCTCAGC
* *
43879383 --GT---CTTGAGGTTCAACTCACCTCT
62 ATGTGAGC-CGAGGCTCAACTCACCTCT
* *
43879406 CGCAATATGCGCTGATTTTTT
1 CGCAATATGAGTTGATTTTTT
43879427 TTTGAAAGAC
Statistics
Matches: 375, Mismatches: 65, Indels: 50
0.77 0.13 0.10
Matches are distributed among these distances:
85 11 0.03
86 51 0.14
87 96 0.26
88 33 0.09
89 31 0.08
90 14 0.04
91 61 0.16
92 64 0.17
93 3 0.01
94 11 0.03
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (88 bp):
CGCAATATGAGTTGATTTTTTAAAACAAAATTTGAAAAACAGAAATTGAAAATACCTCAGCATGT
GAGCCGAGGCTCAACTCACCTCT
Found at i:43879282 original size:13 final size:14
Alignment explanation
Indices: 43879250--43879282 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
43879240 TGATTTTTTG
43879250 GAAAAACAAAATTT
1 GAAAAACAAAATTT
*
43879264 GAAAAACAGAATTT
1 GAAAAACAAAATTT
43879278 GAAAA
1 GAAAA
43879283 TACCTCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18
Consensus pattern (14 bp):
GAAAAACAAAATTT
Found at i:43879429 original size:91 final size:84
Alignment explanation
Indices: 43879123--43879742 Score: 407
Period size: 75 Copynumber: 7.7 Consensus size: 84
43879113 GCGTGTGATC
* *
43879123 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACATAAATTGAAA-AGAAA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGA-AAACAGAAATTGAAACAGAAA
* *
43879187 TTGAAAATATCTCAGCGTGTCC
65 TTGAAAATACCTCAGC--GTCT
* * *
43879209 TGAGGCTGAACTCACCTCTCGCAATATGAGTTGATTTTTTGGAAAAACA-AAATTTGAAAAACAG
1 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTG-AAAACAGAAA-TTG--AAACAG
* *
43879273 AATTTGAAAATACCTCAGCGTGT
62 AAATTGAAAATACCTCAGCGTCT
* * * *
43879296 GAGTCAAGGCTCAACTCACCACTTGCAATATGGGCTGATTTTTTTGAAACACAGAAATTGACGAA
1 ---T-GAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAA-ACAGAAATTGA--AA
* *
43879361 CAGAAATGGAAAACACCTCAGCGTCT
59 CAGAAATTGAAAATACCTCAGCGTCT
* * **
43879387 TGAGGTTCAACTCACCTCTCGCAATATGCGCTGATTTTTTT-----TTGAAA--G--ACAGAAAT
1 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAACAGAAATTGAAACAGAAAT
* *
43879443 TGAAAATATCTCAACGTGTCT
66 TGAAAATACCTC-A-GCGTCT
* * *
43879464 TGAGGCTCAACTCACCTCTCACAATATGAGTTGA--TTTTTG---AC---AA---ACA-A-AAAT
1 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAACAGAAATTGAAACAGAAAT
* *
43879516 TGAAATTACCTCAGCATCT
66 TGAAAATACCTCAGCGTCT
* *
43879535 TGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTT-------G-AA---AAACAGAAAT
1 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAACAGAAATTGAAACAGAAAT
*
43879589 TGAAAATACCTCAACGTGTCT
66 TGAAAATACCTC-A-GCGTCT
* **
43879610 TGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTTTAAAC----------ACAGAAAT
1 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAACAGAAATTGAAACAGAAAT
*
43879665 TGAAAATACCTCAACGTGTCT
66 TGAAAATACCTC-A-GCGTCT
* *
43879686 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGACAAACAAAAATTGAAA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGA-AAACAGAAATTGAAA
43879743 TTACCTCAGC
Statistics
Matches: 441, Mismatches: 50, Indels: 87
0.76 0.09 0.15
Matches are distributed among these distances:
71 40 0.09
72 2 0.00
73 34 0.08
74 9 0.02
75 69 0.16
76 62 0.14
77 35 0.08
79 1 0.00
81 4 0.01
85 4 0.01
86 48 0.11
87 38 0.09
88 4 0.01
89 20 0.05
90 4 0.01
91 64 0.15
92 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (84 bp):
TGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAACAGAAATTGAAACAGAAAT
TGAAAATACCTCAGCGTCT
Found at i:43879689 original size:76 final size:75
Alignment explanation
Indices: 43879360--43879803 Score: 508
Period size: 75 Copynumber: 5.9 Consensus size: 75
43879350 AAATTGACGA
* * * * * *
43879360 ACAGAAATGGAAAACACCTC-A-GCGTCTTGAGGTTCAACTCACCTCTCGCAATATGCGCTGATT
1 ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--
* *
43879423 TTTTTTTGAAAG
64 TTTTTTTCAAAC
* *
43879435 ACAGAAATTGAAAATATCTCAACGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAGTTGATT
1 ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
**
43879500 TTTGACAAAC
66 TTTTTCAAAC
* ** *
43879510 A-A-AAATTGAAATTACCTC-A-GCATCTTGAGGCTCAACTCACCTATCGCAATATGAGTTGATT
1 ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* *
43879571 TTTTTGAAAA
66 TTTTTCAAAC
* *
43879581 ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATT
1 ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T
*
43879646 TTTTTTTAAAC
65 TTTTTTCAAAC
43879657 ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
**
43879722 TTTGACAAAC
66 TTTTTCAAAC
* * * *
43879732 A-A-AAATTGAAATTACCTCAGCGTGTCCATGCCCCGAGGCTCAGCTCACCTCTCGCAATATGAG
1 ACAGAAATTGAAAATACCTCAACGTGT-C-T----TGAGGCTCAACTCACCTCTCGCAATATGAG
43879795 TTGATTTTT
60 TTGATTTTT
43879804 GAAAAATAGA
Statistics
Matches: 317, Mismatches: 39, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
71 45 0.14
72 2 0.01
73 50 0.16
74 4 0.01
75 72 0.23
76 72 0.23
77 35 0.11
79 37 0.12
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (75 bp):
ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTTTTCAAAC
Found at i:43879817 original size:79 final size:74
Alignment explanation
Indices: 43879359--43879822 Score: 528
Period size: 73 Copynumber: 6.2 Consensus size: 74
43879349 GAAATTGACG
* * * * * *
43879359 AACAGAAATGGAAAACACCTC-A-GCGTCTTGAGGTTCAACTCACCTCTCGCAATATGCGCTGAT
1 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
43879422 TTTTTTTTGAAA
65 --TTTTTTGAAA
* * *
43879434 GACAGAAATTGAAAATATCTCAACGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAGTTGA-
1 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
43879498 TTTTTGACA
66 TTTTTGAAA
* * ** *
43879507 AACAAAAATTGAAATTACCTC-A-GCATCTTGAGGCTCAACTCACCTATCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
43879570 TTTTTTGAAA
65 TTTTTTGAAA
* *
43879580 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGAT
1 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
*
43879645 TTTTTTTTAAA
65 -TTTTTTGAAA
*
43879656 CACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
1 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
43879720 TTTTTGACA
66 TTTTTGAAA
* * * * *
43879729 AACAAAAATTGAAATTACCTCAGCGTGTCCATGCCCCGAGGCTCAGCTCACCTCTCGCAATATGA
1 AACAGAAATTGAAAATACCTCAACGTGT-C-T----TGAGGCTCAACTCACCTCTCGCAATATGA
43879794 GTTGA-TTTTTGAAA
60 GTTGATTTTTTGAAA
* *
43879808 AATAGAAATTAAAAA
1 AACAGAAATTGAAAA
43879823 CAAAAATTGA
Statistics
Matches: 333, Mismatches: 43, Indels: 22
0.84 0.11 0.06
Matches are distributed among these distances:
71 36 0.11
72 1 0.00
73 83 0.25
74 2 0.01
75 53 0.16
76 72 0.22
77 35 0.11
79 51 0.15
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (74 bp):
AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTGAAA
Found at i:43879829 original size:13 final size:13
Alignment explanation
Indices: 43879813--43879849 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
43879803 TGAAAAATAG
43879813 AAATTAAAAACAA
1 AAATTAAAAACAA
*
43879826 AAATTGAAAAACAG
1 AAATT-AAAAACAA
43879840 AAATTAAAAA
1 AAATTAAAAA
43879850 TACCTCGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.16
Consensus pattern (13 bp):
AAATTAAAAACAA
Found at i:43879835 original size:14 final size:13
Alignment explanation
Indices: 43879805--43879849 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
43879795 TTGATTTTTG
*
43879805 AAAAATAGAAATT
1 AAAAACAGAAATT
*
43879818 AAAAACAAAAATT
1 AAAAACAGAAATT
43879831 GAAAAACAGAAATT
1 -AAAAACAGAAATT
43879845 AAAAA
1 AAAAA
43879850 TACCTCGGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:43880042 original size:146 final size:143
Alignment explanation
Indices: 43879829--43880138 Score: 417
Period size: 146 Copynumber: 2.1 Consensus size: 143
43879819 AAAACAAAAA
** *
43879829 TTGAAAAACAGAAATTAAAAATACCTCGGCATGCCCCGAGGCTCAGCTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAACATGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
* *
43879894 GTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGC-ATCTTGAGGCTCAACTCACCTATCGC
66 GTTGAGTTTTG----ACAAAAATTGAAATTACCTCAGCGATCCTGAGGCTCAACTCACCTATCGC
43879958 AATATGAGTTGATTTTT
127 AATATGAGTTGATTTTT
* * * ** *
43879975 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTTGCAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAACATGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
* * *
43880040 GTTGAGTTTTGACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAAT
66 GTTGAGTTTTGACAAAAATTGAAATTACCTCAGCG-ATCCTGAGGCTCAACTCACCTATCGCAAT
43880105 ATGAGTTGATTTTT
130 ATGAGTTGATTTTT
* *
43880119 TT-AGAAACATAAATTAAAAA
1 TTGAAAAACAGAAATTAAAAA
43880139 AATGAAAATT
Statistics
Matches: 145, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
142 23 0.16
143 15 0.10
144 41 0.28
146 66 0.46
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (143 bp):
TTGAAAAACAGAAATTAAAAATACCTCAACATGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGAGTTTTGACAAAAATTGAAATTACCTCAGCGATCCTGAGGCTCAACTCACCTATCGCAATA
TGAGTTGATTTTT
Found at i:43880104 original size:69 final size:70
Alignment explanation
Indices: 43879866--43880118 Score: 323
Period size: 69 Copynumber: 3.5 Consensus size: 70
43879856 GGCATGCCCC
*
43879866 GAGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG---AACAAAAATTGAAATTACCTCAG
*
43879931 C--ATCTT
63 CGTGTCTT
* * *
43879937 GAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG---AACAAAAATTGAAATTACCTC
*
43880002 AACGTGTCTT
61 AGCGTGTCTT
* *
43880012 GAGGCTCAACTCACCTCTTGCAATATGAGTTGAGTTTTG-ACAAAAATTGAAATTACCTCAGCGT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAACAAAAATTGAAATTACCTCAGCGT
*
43880076 GTCCT
66 GTCTT
*
43880081 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
43880119 TTAGAAACAT
Statistics
Matches: 161, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
69 61 0.38
71 31 0.19
73 34 0.21
75 35 0.22
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (70 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAACAAAAATTGAAATTACCTCAGCGT
GTCTT
Found at i:43880159 original size:89 final size:89
Alignment explanation
Indices: 43880054--43880591 Score: 434
Period size: 89 Copynumber: 5.8 Consensus size: 89
43880044 AGTTTTGACA
*
43880054 AAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
1 AAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
43880119 TTAGAAACATAAATTAAAAAAATG
66 TTAGAAACATAAATTAAAAAAATG
* * *
43880143 AAAATTGAAAATACCTCAGCGTGACTTGAGGCTTAACTCACTTCTCGCAATATGAGTTGATTTTT
1 AAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
43880208 TTAGAAACATAAATTAAAAAAATG
66 TTAGAAACATAAATTAAAAAAATG
* *
43880232 AAAATTGAAAATACCTCAGCGTGTCTTGAGGCTTAACTCACTTCTCGCAATATGAGTTGATTTGA
1 AAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTT--
** * *
43880297 AAAGCAGAATTTGTA-AGGCAAAAATTGAAAAACA--
64 ---------TTT-TAGAAACATAAATT-AAAAAAATG
*
43880331 AAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCAAC-TCTCGCAATATGAGTTGA-TTT
1 AAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTC-ACTTCTCGCAATATGAGTTGATTTT
* * * * *
43880394 TTGAAAAATAGAAATTAAAAACA--
65 TTTAGAAACATAAATTAAAAAAATG
* * *** * * * *
43880417 AAAATTGAAAA-ACAGAAATTAAAAAT-ACCTCGGCATGCCCCGAGGCTCAGCTCACCTCTCGCA
1 AAAATTGAAAATAC-----CTCAGCGTGTCCT--G-A-GGCTC-A-ACTCA-CT----TCTCGCA
*
43880480 ATATGAGTTGA-TTTTTGA-AAAGCATAAATTAAAAAAATG
50 ATATGAGTTGATTTTTTTAGAAA-CATAAATTAAAAAAATG
* * *
43880519 GAAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTT
1 AAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTT
43880584 TTTT-GAAA
64 TTTTAGAAA
43880592 GATAGAAATA
Statistics
Matches: 368, Mismatches: 40, Indels: 80
0.75 0.08 0.16
Matches are distributed among these distances:
85 2 0.01
86 19 0.05
87 10 0.03
89 150 0.41
90 21 0.06
91 9 0.02
92 1 0.00
93 3 0.01
94 3 0.01
95 8 0.02
96 1 0.00
97 4 0.01
98 6 0.02
99 58 0.16
100 50 0.14
101 11 0.03
102 10 0.03
103 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Consensus pattern (89 bp):
AAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
TTAGAAACATAAATTAAAAAAATG
Found at i:43880334 original size:14 final size:14
Alignment explanation
Indices: 43880315--43880341 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43880305 ATTTGTAAGG
43880315 CAAAAATTGAAAAA
1 CAAAAATTGAAAAA
43880329 CAAAAATTGAAAA
1 CAAAAATTGAAAA
43880342 TACCTCAGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (14 bp):
CAAAAATTGAAAAA
Found at i:43880421 original size:13 final size:13
Alignment explanation
Indices: 43880405--43880441 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
43880395 TGAAAAATAG
43880405 AAATTAAAAACAA
1 AAATTAAAAACAA
*
43880418 AAATTGAAAAACAG
1 AAATT-AAAAACAA
43880432 AAATTAAAAA
1 AAATTAAAAA
43880442 TACCTCGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.16
Consensus pattern (13 bp):
AAATTAAAAACAA
Found at i:43880427 original size:14 final size:13
Alignment explanation
Indices: 43880397--43880441 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
43880387 TTGATTTTTG
*
43880397 AAAAATAGAAATT
1 AAAAACAGAAATT
*
43880410 AAAAACAAAAATT
1 AAAAACAGAAATT
43880423 GAAAAACAGAAATT
1 -AAAAACAGAAATT
43880437 AAAAA
1 AAAAA
43880442 TACCTCGGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:43880456 original size:100 final size:100
Alignment explanation
Indices: 43880232--43880585 Score: 378
Period size: 100 Copynumber: 3.6 Consensus size: 100
43880222 TAAAAAAATG
* * *
43880232 AAAATTGAAAATACCTCAGCGTGTCTTGAGGCTTAACTC-ACTTCTCGCAATATGAGTTGA--TT
1 AAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCAAC-TCTCGCAATATGAGTTGATTTT
* * **
43880294 TGAAAAGCAGAATTTGTAAGGCAAAAATTGAAAAACA
65 TGAAAAGCAGAAATT-AAAAACAAAAATTGAAAAACA
43880331 AAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTT
1 AAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTT
**
43880396 GAAAAATAGAAATTAAAAACAAAAATTGAAAAACA
66 GAAAAGCAGAAATTAAAAACAAAAATTGAAAAACA
* * * * * * *
43880431 GAAATTAAAAATACCTCGGCATGCCCCGAGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTT
1 AAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTT
*
43880496 GAAAAGCATAAATT---AA-AAAAA-TG-------
66 GAAAAGCAGAAATTAAAAACAAAAATTGAAAAACA
* * * *
43880519 GAAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTT
1 AAAATTGAAAATACCTCAGC--GTGCCCTGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTT
43880584 TT
64 TT
43880586 TTGAAAGATA
Statistics
Matches: 224, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
88 18 0.08
90 40 0.18
95 2 0.01
96 5 0.02
97 2 0.01
99 54 0.24
100 89 0.40
101 14 0.06
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (100 bp):
AAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTT
GAAAAGCAGAAATTAAAAACAAAAATTGAAAAACA
Found at i:43884873 original size:15 final size:15
Alignment explanation
Indices: 43884851--43884919 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
43884841 ATATATTGGG
43884851 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
43884866 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
43884881 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
43884896 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
43884911 TTTCTTTAT
1 TTTCTTTAT
43884920 TCGATTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:43900264 original size:25 final size:23
Alignment explanation
Indices: 43900212--43900266 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
43900202 TATAAATAGT
43900212 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
43900235 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
43900260 AATAGTG
1 AATAGTG
43900267 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:43900325 original size:32 final size:31
Alignment explanation
Indices: 43900287--43900384 Score: 109
Period size: 32 Copynumber: 3.3 Consensus size: 31
43900277 TAGTAATGTT
43900287 AAGATATATATAATATATACATATGTATGAA
1 AAGATATATATAATATATACATATGTATGAA
**
43900318 ATAGATATA-A-AA-A-A-A-ATATGTAATGTT
1 A-AGATATATATAATATATACATATGT-ATGAA
43900345 AAGATATATATAATATATACATATGTATGAAA
1 AAGATATATATAATATATACATATGTATG-AA
43900377 AAGATATA
1 AAGATATA
43900385 AAAAAATATG
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
26 13 0.24
27 6 0.11
28 3 0.06
29 2 0.04
30 3 0.06
31 6 0.11
32 21 0.39
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (31 bp):
AAGATATATATAATATATACATATGTATGAA
Found at i:43900341 original size:58 final size:57
Alignment explanation
Indices: 43900279--43900396 Score: 218
Period size: 58 Copynumber: 2.1 Consensus size: 57
43900269 AATATAACTA
*
43900279 GTAATGTTAAGATATATATAATATATACATATGTATGAAATAGATATAAAAAAAATAT
1 GTAATGTTAAGATATATATAATATATACATATGTATGAAAAAGATAT-AAAAAAATAT
43900337 GTAATGTTAAGATATATATAATATATACATATGTATGAAAAAGATATAAAAAAATAT
1 GTAATGTTAAGATATATATAATATATACATATGTATGAAAAAGATATAAAAAAATAT
43900394 GTA
1 GTA
43900397 CATAATATAG
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
57 13 0.22
58 46 0.78
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.34
Consensus pattern (57 bp):
GTAATGTTAAGATATATATAATATATACATATGTATGAAAAAGATATAAAAAAATAT
Found at i:43900413 original size:25 final size:25
Alignment explanation
Indices: 43900385--43900534 Score: 124
Period size: 25 Copynumber: 5.9 Consensus size: 25
43900375 AAAAGATATA
**
43900385 AAAAAATATGTACATAATATAGTGT
1 AAAAAATACATACATAATATAGTGT
43900410 AAAAAATACATACATAATATAGTGT
1 AAAAAATACATACATAATATAGTGT
*
43900435 AAAAAATACATACATAATATAAT-T
1 AAAAAATACATACATAATATAGTGT
* * *
43900459 AAAATATATACATAAGATAACAT-GTAGA
1 AAAA-A-ATACAT-ACATAATATAGT-GT
* * * *
43900487 AAAAAATATATAAATAATATAATAT
1 AAAAAATACATACATAATATAGTGT
* * * *
43900512 TAAAGATATATACATAAAATAGT
1 AAAAAATACATACATAATATAGT
43900535 ATAATATATA
Statistics
Matches: 101, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
24 5 0.05
25 71 0.70
26 13 0.13
27 8 0.08
28 4 0.04
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (25 bp):
AAAAAATACATACATAATATAGTGT
Found at i:43900423 original size:58 final size:58
Alignment explanation
Indices: 43900286--43900425 Score: 167
Period size: 58 Copynumber: 2.4 Consensus size: 58
43900276 CTAGTAATGT
* * * **
43900286 TAAGATATATATAATATATACATATGTATGAAATAGATATAAAAAAAATATGTAATGT
1 TAAGATATAAAAAATATATACATATGTATGAAAAAGATATAAAAAAAATATGTAATAA
* *
43900344 TAAGATATATATAATATATACATATGTATGAAAAAGATAT-AAAAAAATATGTACATAA
1 TAAGATATAAAAAATATATACATATGTATGAAAAAGATATAAAAAAAATATGTA-ATAA
* *
43900402 TATAG-TGTAAAAAATACATACATA
1 TA-AGATATAAAAAATATATACATA
43900426 ATATAGTGTA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
57 13 0.18
58 58 0.79
59 2 0.03
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (58 bp):
TAAGATATAAAAAATATATACATATGTATGAAAAAGATATAAAAAAAATATGTAATAA
Found at i:43900601 original size:26 final size:24
Alignment explanation
Indices: 43900572--43900626 Score: 58
Period size: 29 Copynumber: 2.1 Consensus size: 24
43900562 AGAATATACC
43900572 TAAT-ATATTAAAAGAATATATATATA
1 TAATAATATTAAAA-AATATA-ATA-A
43900598 TAATACAATATTAAAAAATATAATAA
1 TAAT--AATATTAAAAAATATAATAA
43900624 TAA
1 TAA
43900627 CAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
26 8 0.31
27 3 0.12
28 6 0.23
29 9 0.35
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
TAATAATATTAAAAAATATAATAA
Found at i:43901140 original size:30 final size:30
Alignment explanation
Indices: 43901104--43901170 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
43901094 AGGAAGAAGT
*
43901104 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
1 GGTGGTGGAACAAGTGTGGCTAGTGGAGTA
*
43901134 GGTGGTGGAACAAGTGTGGCTAGTGGAGTT
1 GGTGGTGGAACAAGTGTGGCTAGTGGAGTA
43901164 GGTGGTG
1 GGTGGTG
43901171 ACAAAGGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.18, C:0.06, G:0.51, T:0.25
Consensus pattern (30 bp):
GGTGGTGGAACAAGTGTGGCTAGTGGAGTA
Found at i:43901934 original size:6 final size:6
Alignment explanation
Indices: 43901923--43901959 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
43901913 CTTTCTTCCC
43901923 TCTCTT TCTCTT TCTCTT TC-CTT TCT-TT TCTTCTT TC
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TC-TCTT TC
43901960 CTCGGTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 9 0.32
6 15 0.54
7 4 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTCTT
Found at i:43901946 original size:17 final size:17
Alignment explanation
Indices: 43901926--43901961 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
43901916 TCTTCCCTCT
43901926 CTTTCTCTTTC-TCTTTC
1 CTTTCT-TTTCTTCTTTC
43901943 CTTTCTTTTCTTCTTTC
1 CTTTCTTTTCTTCTTTC
43901960 CT
1 CT
43901962 CGGTTCTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
CTTTCTTTTCTTCTTTC
Found at i:43901949 original size:21 final size:20
Alignment explanation
Indices: 43901916--43901954 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
43901906 ACCAATTCTT
43901916 TCTTCCCTCTCTTTCTCTTTC
1 TCTTCCCTCTCTTT-TCTTTC
* *
43901937 TCTTTCCTTTCTTTTCTT
1 TCTTCCCTCTCTTTTCTT
43901955 CTTTCCTCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (20 bp):
TCTTCCCTCTCTTTTCTTTC
Found at i:43903716 original size:6 final size:6
Alignment explanation
Indices: 43903689--43903717 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
43903679 ATTTTTATAC
43903689 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
43903718 AATATTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:43909238 original size:3 final size:3
Alignment explanation
Indices: 43909230--43909257 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
43909220 AACACACGTT
43909230 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
43909258 TTAGGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:43913316 original size:18 final size:18
Alignment explanation
Indices: 43913293--43913327 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43913283 TTCCCAAACT
43913293 TTTTCTCTATCTTCTTCA
1 TTTTCTCTATCTTCTTCA
43913311 TTTTCTCTATCTTCTTC
1 TTTTCTCTATCTTCTTC
43913328 TTCAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.09, C:0.29, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTCTCTATCTTCTTCA
Found at i:43914117 original size:12 final size:12
Alignment explanation
Indices: 43914100--43914133 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
43914090 CGGCTCGCCC
43914100 ATATTAATTTTT
1 ATATTAATTTTT
*
43914112 ATATTATTTTTT
1 ATATTAATTTTT
43914124 ATA-TAATTTT
1 ATATTAATTTT
43914134 AAAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:43914293 original size:30 final size:30
Alignment explanation
Indices: 43914258--43914321 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
43914248 ACTTAACAAG
*
43914258 CAAATGCT-TCTAAAATAATAACAAAATTAA
1 CAAATG-TGTCTAAAATAATAAAAAAATTAA
* *
43914288 CAAATGTGTTTAAAATGATAAAAAAATTAA
1 CAAATGTGTCTAAAATAATAAAAAAATTAA
43914318 -AAAT
1 CAAAT
43914322 AAAATAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (30 bp):
CAAATGTGTCTAAAATAATAAAAAAATTAA
Found at i:43914375 original size:22 final size:22
Alignment explanation
Indices: 43914350--43914392 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43914340 TATCCAAACA
43914350 ATAACAACAAAATAGTAGCAAT
1 ATAACAACAAAATAGTAGCAAT
* **
43914372 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
43914393 AATAGAGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAT
Found at i:43914396 original size:11 final size:11
Alignment explanation
Indices: 43914357--43914397 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
43914347 ACAATAACAA
43914357 CAAAATAGTAG
1 CAAAATAGTAG
* *
43914368 CAATATAATAG
1 CAAAATAGTAG
*
43914379 TAAAATAGTAG
1 CAAAATAGTAG
43914390 CAAAATAG
1 CAAAATAG
43914398 AGAGAAAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:43914405 original size:22 final size:22
Alignment explanation
Indices: 43914358--43914406 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
43914348 CAATAACAAC
* *
43914358 AAAATAGTAGCAATATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
*
43914380 AAAATAGTAGCAAAATAGAGAGA
1 AAAATAGTAGCAAAATA-AGAGT
43914403 AAAA
1 AAAA
43914407 AATAAGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.61, C:0.04, G:0.16, T:0.18
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:43917211 original size:5 final size:5
Alignment explanation
Indices: 43917201--43917230 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
43917191 TAGGAAGATA
43917201 TTATT TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT
43917231 AAATTAGTTA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:43929110 original size:18 final size:17
Alignment explanation
Indices: 43929082--43929116 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43929072 ATTATTAAGA
*
43929082 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43929099 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43929117 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43929330 original size:44 final size:45
Alignment explanation
Indices: 43929281--43929371 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
43929271 ACCTCTATTC
* * *
43929281 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
43929325 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
43929370 CA
1 CA
43929372 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:43929373 original size:16 final size:16
Alignment explanation
Indices: 43929352--43929403 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
43929342 GATTAGCTAT
43929352 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
43929368 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
43929384 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
43929400 TACA
1 TACA
43929404 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:43929458 original size:7 final size:7
Alignment explanation
Indices: 43929446--43929470 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43929436 TTGCATATAA
43929446 TTTTAAT
1 TTTTAAT
43929453 TTTTAAT
1 TTTTAAT
43929460 TTTTAAT
1 TTTTAAT
43929467 TTTT
1 TTTT
43929471 TTAAATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:43929502 original size:23 final size:24
Alignment explanation
Indices: 43929458--43929505 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
43929448 TTAATTTTTA
* *
43929458 ATTTTTAATTTTTTTAAATAATGT
1 ATTTTTAATTATTGTAAATAATGT
*
43929482 ATTTTTAATTATTGT-ATTAATGT
1 ATTTTTAATTATTGTAAATAATGT
43929505 A
1 A
43929506 AAGTGATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (24 bp):
ATTTTTAATTATTGTAAATAATGT
Found at i:43931561 original size:26 final size:26
Alignment explanation
Indices: 43931519--43931570 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
43931509 AATTTAATTC
*
43931519 TTTTTTTATGTTATTTTAATTTTCTT
1 TTTTTTTATGTTATTTTAATTCTCTT
* *
43931545 TTTTTTTCT-TTATTTTTCATTCTCTT
1 TTTTTTTATGTTA-TTTTAATTCTCTT
43931571 CTACTCCTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTTTTTATGTTATTTTAATTCTCTT
Found at i:43932062 original size:26 final size:26
Alignment explanation
Indices: 43932033--43932116 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 26
43932023 TGATACAAAT
*
43932033 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
43932059 TGATAATAGATTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
43932085 CGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
43932111 TGATAA
1 TGATAA
43932117 GAATTTCATG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:43933619 original size:26 final size:26
Alignment explanation
Indices: 43933590--43933642 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
43933580 TTTACAGTTT
43933590 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
43933616 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
43933642 T
1 T
43933643 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:43943653 original size:26 final size:26
Alignment explanation
Indices: 43943623--43943704 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
43943613 TGAAATGCCC
43943623 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
43943649 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
43943675 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
43943701 ATCA
1 ATCA
43943705 ATTTGTACCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:43944059 original size:21 final size:21
Alignment explanation
Indices: 43944033--43944073 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
43944023 ACAACATTAG
43944033 TCTTTCAATAATTATTTAAAA
1 TCTTTCAATAATTATTTAAAA
43944054 TCTTTCAATAATTATTTAAA
1 TCTTTCAATAATTATTTAAA
43944074 CCAACATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (21 bp):
TCTTTCAATAATTATTTAAAA
Found at i:43945510 original size:16 final size:17
Alignment explanation
Indices: 43945479--43945511 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
43945469 AAGTTCTATC
43945479 CAATTTATACCCTAATT
1 CAATTTATACCCTAATT
*
43945496 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
43945512 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
CAATTTATACCCTAATT
Found at i:43949672 original size:23 final size:23
Alignment explanation
Indices: 43949642--43949728 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
43949632 GCTTTACTGA
* *
43949642 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
43949665 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
43949686 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
43949708 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
43949729 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:43951257 original size:15 final size:14
Alignment explanation
Indices: 43951225--43951263 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
43951215 CAAATATATG
43951225 TTTTAAAATAGCTT
1 TTTTAAAATAGCTT
*
43951239 TTTTAAAAGTAGTTT
1 TTTTAAAA-TAGCTT
*
43951254 TTTTGAAATA
1 TTTTAAAATA
43951264 TTTTCAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (14 bp):
TTTTAAAATAGCTT
Found at i:43951441 original size:14 final size:14
Alignment explanation
Indices: 43951419--43951456 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
43951409 CCAGAAAAGT
* *
43951419 AAATCATTTTCTAG
1 AAATTATTTTCCAG
43951433 AAATTATTTTCCAG
1 AAATTATTTTCCAG
43951447 AAATTATTTT
1 AAATTATTTT
43951457 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (14 bp):
AAATTATTTTCCAG
Found at i:43953059 original size:61 final size:61
Alignment explanation
Indices: 43952983--43953104 Score: 145
Period size: 61 Copynumber: 2.0 Consensus size: 61
43952973 AATGTAATTA
* ** * *
43952983 AAAATTATAAATATATGGTTGTTAATAAATTTTAAGATATTAAGTAAGATTATATTTTTAC
1 AAAATTATAAATATATAGTCATTAATAAATTTAAAGATATGAAGTAAGATTATATTTTTAC
* ** * **
43953044 AAAATTATAAGTATATAGTCATTAATTCATTTAAAGATATGATGTACTATTATATTTTTAC
1 AAAATTATAAATATATAGTCATTAATAAATTTAAAGATATGAAGTAAGATTATATTTTTAC
43953105 CTTCGAATAA
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (61 bp):
AAAATTATAAATATATAGTCATTAATAAATTTAAAGATATGAAGTAAGATTATATTTTTAC
Found at i:43954391 original size:23 final size:23
Alignment explanation
Indices: 43954361--43954408 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
43954351 TCATGATGAT
*
43954361 AATTGAAATTGACAAAATCAACG
1 AATTGAAATAGACAAAATCAACG
* *
43954384 AATTGAAATAGAGAAATTCAACG
1 AATTGAAATAGACAAAATCAACG
43954407 AA
1 AA
43954409 GAATCTTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.21
Consensus pattern (23 bp):
AATTGAAATAGACAAAATCAACG
Found at i:43956310 original size:24 final size:23
Alignment explanation
Indices: 43956276--43956321 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
43956266 CCACATAAAA
43956276 TTAATTTGAATTAAATTAACTTT
1 TTAATTTGAATTAAATTAACTTT
**
43956299 TTAATTTTGAATTATTTTAACTT
1 TTAA-TTTGAATTAAATTAACTT
43956322 GAATTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
TTAATTTGAATTAAATTAACTTT
Found at i:43958826 original size:29 final size:30
Alignment explanation
Indices: 43958795--43958866 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
43958785 TAATTTTATT
43958795 AAAAATTAGAAAAAGATTATAAAAATCATA
1 AAAAATTAGAAAAAGATTATAAAAATCATA
* ** *
43958825 AAAAATT-GTAAAATTTTATAAAAATCGTA
1 AAAAATTAGAAAAAGATTATAAAAATCATA
*
43958854 AAAAATTATAAAA
1 AAAAATTAGAAAA
43958867 TATATAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 25 0.71
30 10 0.29
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.28
Consensus pattern (30 bp):
AAAAATTAGAAAAAGATTATAAAAATCATA
Found at i:43958828 original size:10 final size:10
Alignment explanation
Indices: 43958790--43958889 Score: 69
Period size: 10 Copynumber: 9.7 Consensus size: 10
43958780 ATATTTAATT
*
43958790 TTATTAAAAA
1 TTATAAAAAA
*
43958800 TTAGAAAAAGA
1 TTATAAAAA-A
43958811 TTAT-AAAAA
1 TTATAAAAAA
*
43958820 TCATAAAAAA
1 TTATAAAAAA
* **
43958830 TTGTAAAATT
1 TTATAAAAAA
43958840 TTAT-AAAAA
1 TTATAAAAAA
**
43958849 TCGTAAAAAA
1 TTATAAAAAA
43958859 TTATAAAATATA
1 TTATAAAA-A-A
43958871 TAATATAAAAAA
1 T--TATAAAAAA
43958883 TTATAAA
1 TTATAAA
43958890 TTTTATAAAG
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
9 9 0.13
10 42 0.62
11 5 0.07
12 4 0.06
13 1 0.01
14 7 0.10
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:43958847 original size:19 final size:19
Alignment explanation
Indices: 43958815--43958866 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
43958805 AAAAGATTAT
* *
43958815 AAAAATCATAAAAAATTGTA
1 AAAAATTAT-AAAAATCGTA
**
43958835 AAATTTTATAAAAATCGTA
1 AAAAATTATAAAAATCGTA
43958854 AAAAATTATAAAA
1 AAAAATTATAAAA
43958867 TATATAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
AAAAATTATAAAAATCGTA
Found at i:43958866 original size:9 final size:9
Alignment explanation
Indices: 43958711--43958963 Score: 51
Period size: 10 Copynumber: 27.0 Consensus size: 9
43958701 ACATGTGGCA
*
43958711 AAAAATGAT
1 AAAAATTAT
43958720 AAAAA--AT
1 AAAAATTAT
*
43958727 AAAAATCAAT
1 AAAAAT-TAT
*
43958737 AAAAGTTAT
1 AAAAATTAT
*
43958746 AAAAGTTATT
1 AAAAATTA-T
**
43958756 AAATTTTAAT
1 AAAAATT-AT
*
43958766 AAAAAATAT
1 AAAAATTAT
43958775 AAGAAA-TATT
1 AA-AAATTA-T
* **
43958785 TAATTTTATT
1 AAAAATTA-T
*
43958795 AAAAATTAGA
1 AAAAATTA-T
43958805 AAAAGATTAT
1 AAAA-ATTAT
*
43958815 AAAAATCAT
1 AAAAATTAT
*
43958824 AAAAAATTGT
1 -AAAAATTAT
*
43958834 AAAATTTTAT
1 AAAA-ATTAT
43958844 AAAAATCGTA-
1 AAAAAT--TAT
43958854 AAAAATTAT
1 AAAAATTAT
43958863 -AAAA-TAT
1 AAAAATTAT
*
43958870 -ATAA-TAT
1 AAAAATTAT
43958877 AAAAAATTAT
1 -AAAAATTAT
**
43958887 AAATTTTAT
1 AAAAATTAT
* *
43958896 -AAAGTCAT
1 AAAAATTAT
43958904 AAGAAAATTAT
1 -A-AAAATTAT
43958915 ACAAAATGTA-
1 A-AAAAT-TAT
43958925 AAGAAA-TAT
1 AA-AAATTAT
* *
43958934 AAAATTTGTCAA
1 AAAA-AT-T-AT
43958946 AAAAATTAT
1 AAAAATTAT
43958955 AAAAATTAT
1 AAAAATTAT
43958964 CGCACCAAAA
Statistics
Matches: 181, Mismatches: 36, Indels: 54
0.67 0.13 0.20
Matches are distributed among these distances:
7 16 0.09
8 15 0.08
9 54 0.30
10 74 0.41
11 17 0.09
12 5 0.03
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:43958896 original size:24 final size:27
Alignment explanation
Indices: 43958812--43958915 Score: 90
Period size: 29 Copynumber: 3.9 Consensus size: 27
43958802 AGAAAAAGAT
* *
43958812 TATA-AAAATCATAAAAAATTGTAAAA
1 TATATAAAGTCATAAAAAATTATAAAA
* * *
43958838 TTTTATAAAAATCGTAAAAAATTATAAAA
1 -TATAT-AAAGTCATAAAAAATTATAAAA
*
43958867 TATAT-AA-T-ATAAAAAATTATAAAT
1 TATATAAAGTCATAAAAAATTATAAAA
*
43958891 TTTATAAAGTCATAAGAAAATTATA
1 TATATAAAGTCATAA-AAAATTATA
43958916 CAAAATGTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
24 18 0.28
25 3 0.05
26 3 0.05
27 7 0.11
28 13 0.20
29 20 0.31
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.34
Consensus pattern (27 bp):
TATATAAAGTCATAAAAAATTATAAAA
Found at i:43959175 original size:10 final size:10
Alignment explanation
Indices: 43959160--43959205 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
43959150 AAAAAAATTC
43959160 TAATTTTTAA
1 TAATTTTTAA
43959170 TAATTTTT-A
1 TAATTTTTAA
*
43959179 -AATTTTTAT
1 TAATTTTTAA
**
43959188 TAAAGTTTAA
1 TAATTTTTAA
43959198 TAATTTTT
1 TAATTTTT
43959206 CTAAAAGTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
8 7 0.25
9 1 0.04
10 20 0.71
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:43959204 original size:20 final size:19
Alignment explanation
Indices: 43959179--43959227 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
43959169 ATAATTTTTA
43959179 AATTTTTATTAAAGTTTAAT
1 AATTTTTATTAAAG-TTAAT
* * *
43959199 AATTTTTCTAAAAGTTATT
1 AATTTTTATTAAAGTTAAT
*
43959218 ATTTTTTATT
1 AATTTTTATT
43959228 TTTCTATATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (19 bp):
AATTTTTATTAAAGTTAAT
Found at i:43962096 original size:18 final size:18
Alignment explanation
Indices: 43962073--43962109 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
43962063 TTGAGCAAAA
43962073 TAGTTTGATGGGTTTCTT
1 TAGTTTGATGGGTTTCTT
43962091 TAGTTTGATGGGTTTCTT
1 TAGTTTGATGGGTTTCTT
43962109 T
1 T
43962110 GTTATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.05, G:0.27, T:0.57
Consensus pattern (18 bp):
TAGTTTGATGGGTTTCTT
Found at i:43964529 original size:23 final size:23
Alignment explanation
Indices: 43964503--43964570 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
43964493 TATTTTTTAA
43964503 AAATAAAAAAAAAACATTTTGAT
1 AAATAAAAAAAAAACATTTTGAT
* *
43964526 AAATAGAAATAAAAACATGTT-AT
1 AAATA-AAAAAAAAACATTTTGAT
*
43964549 TAATAAAATAAAATAA-ATTTTG
1 AAATAAAA-AAAA-AACATTTTG
43964571 TATTGATATG
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
22 3 0.08
23 18 0.50
24 15 0.42
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (23 bp):
AAATAAAAAAAAAACATTTTGAT
Found at i:43971569 original size:27 final size:27
Alignment explanation
Indices: 43971546--43971614 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
43971536 GCGGAGCTAC
*
43971546 AGCCATTTGAGGAGGTGGCTGAGCCGG
1 AGCCATCTGAGGAGGTGGCTGAGCCGG
* *
43971573 AGCCGTCTGAGGAGGTTGCTGAGCCGG
1 AGCCATCTGAGGAGGTGGCTGAGCCGG
43971600 AGCCATCTGAGGAGG
1 AGCCATCTGAGGAGG
43971615 AAGGGGGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.19, C:0.20, G:0.43, T:0.17
Consensus pattern (27 bp):
AGCCATCTGAGGAGGTGGCTGAGCCGG
Found at i:43971766 original size:12 final size:12
Alignment explanation
Indices: 43971745--43971787 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
43971735 CCGGCCACGT
43971745 CCACCACGACCA
1 CCACCACGACCA
*
43971757 CCACCCCGACCA
1 CCACCACGACCA
** *
43971769 CTGCCACGTCCA
1 CCACCACGACCA
43971781 CCACCAC
1 CCACCAC
43971788 CTCGACCAGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.26, C:0.60, G:0.09, T:0.05
Consensus pattern (12 bp):
CCACCACGACCA
Found at i:43972318 original size:19 final size:19
Alignment explanation
Indices: 43972290--43972334 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
43972280 TATAATTAAA
43972290 ATAA-AATTTGTGATAATC
1 ATAATAATTTGTGATAATC
43972308 ATAATAATTTGTGATAATC
1 ATAATAATTTGTGATAATC
43972327 ATAATAAT
1 ATAATAAT
43972335 CTTAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (19 bp):
ATAATAATTTGTGATAATC
Found at i:43972827 original size:21 final size:22
Alignment explanation
Indices: 43972801--43972846 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
43972791 ATATATAAGC
*
43972801 ATGATA-ATTTTATT-TATTTTT
1 ATGATATATTTT-TTGTATATTT
43972822 ATGATATATTTTTTGTATATTT
1 ATGATATATTTTTTGTATATTT
43972844 ATG
1 ATG
43972847 CAAAATACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (22 bp):
ATGATATATTTTTTGTATATTT
Found at i:43973499 original size:17 final size:19
Alignment explanation
Indices: 43973477--43973519 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
43973467 ATGGAAATAT
43973477 AATCTT-CA-ATGATATGC
1 AATCTTACATATGATATGC
*
43973494 AATCTTAGATATGATATGC
1 AATCTTACATATGATATGC
43973513 AATCTTA
1 AATCTTA
43973520 GAAGATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 1 0.04
19 16 0.70
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
AATCTTACATATGATATGC
Found at i:43973509 original size:19 final size:19
Alignment explanation
Indices: 43973485--43973521 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
43973475 ATAATCTTCA
43973485 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
43973504 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
43973522 AGATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:43973547 original size:22 final size:22
Alignment explanation
Indices: 43973485--43973544 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 22
43973475 ATAATCTTCA
43973485 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
43973504 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
43973526 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
43973545 GATTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.43
22 8 0.23
23 12 0.34
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:43984903 original size:27 final size:27
Alignment explanation
Indices: 43984873--43984924 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
43984863 CCTGCCCCCG
43984873 GCCACG-TCGACCACCACCCCGACCACT
1 GCCACGTTC-ACCACCACCCCGACCACT
* *
43984900 GCCACGTTCACCACCGCCTCGACCA
1 GCCACGTTCACCACCACCCCGACCA
43984925 GACATTGCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.21, C:0.54, G:0.15, T:0.10
Consensus pattern (27 bp):
GCCACGTTCACCACCACCCCGACCACT
Found at i:43985245 original size:23 final size:21
Alignment explanation
Indices: 43985194--43985250 Score: 53
Period size: 23 Copynumber: 2.6 Consensus size: 21
43985184 AAATACCCGA
43985194 TTTGTTTTCATTTTTATCCTC
1 TTTGTTTTCATTTTTATCCTC
* *
43985215 TCTT-TTTTCTATTCTTTATTCTG
1 T-TTGTTTTC-ATT-TTTATCCTC
*
43985238 TTTGTTTTAATTT
1 TTTGTTTTCATTT
43985251 GTAAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
21 7 0.24
22 10 0.34
23 12 0.41
ACGTcount: A:0.11, C:0.14, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTGTTTTCATTTTTATCCTC
Found at i:43985911 original size:24 final size:22
Alignment explanation
Indices: 43985863--43985907 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
43985853 ATATCTAAGC
*
43985863 ATGATAATTTTATTTATTTATT
1 ATGATAATTTTATTTATATATT
43985885 ATGATATATTTT-TTGTATATATT
1 ATGATA-ATTTTATT-TATATATT
43985908 TATGCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (22 bp):
ATGATAATTTTATTTATATATT
Found at i:43992708 original size:12 final size:12
Alignment explanation
Indices: 43992691--43992716 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43992681 ATATTCATAT
43992691 TTTAAAATTTTA
1 TTTAAAATTTTA
43992703 TTTAAAATTTTA
1 TTTAAAATTTTA
43992715 TT
1 TT
43992717 CTAATCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTAAAATTTTA
Found at i:43993063 original size:22 final size:21
Alignment explanation
Indices: 43993033--43993078 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
43993023 AATCTATCTA
43993033 CTAAGCCTAATA-CCCAACAGC
1 CTAAGCCTAATAGCCC-ACAGC
43993054 CTAAGGCCTAATAGCCCACAGC
1 CTAA-GCCTAATAGCCCACAGC
43993076 CTA
1 CTA
43993079 TACTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.17
22 16 0.70
23 3 0.13
ACGTcount: A:0.35, C:0.37, G:0.13, T:0.15
Consensus pattern (21 bp):
CTAAGCCTAATAGCCCACAGC
Found at i:43993588 original size:14 final size:14
Alignment explanation
Indices: 43993569--43993595 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43993559 AAATTGGAAA
43993569 GATGATAAAATAAT
1 GATGATAAAATAAT
43993583 GATGATAAAATAA
1 GATGATAAAATAA
43993596 AGAAAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (14 bp):
GATGATAAAATAAT
Found at i:43997788 original size:18 final size:18
Alignment explanation
Indices: 43997765--43997800 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
43997755 ATATTAAGAA
43997765 TTTTATTAAATTATATTT
1 TTTTATTAAATTATATTT
43997783 TTTTATTAAATTATATTT
1 TTTTATTAAATTATATTT
43997801 AATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATTAAATTATATTT
Found at i:43998068 original size:16 final size:16
Alignment explanation
Indices: 43998047--43998101 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
43998037 TGAATTACTG
43998047 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
43998063 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
43998079 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
43998095 ATTACAG
1 ATTACAG
43998102 TGAACCAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:43998693 original size:25 final size:24
Alignment explanation
Indices: 43998612--43998694 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 24
43998602 TTTCACGAGC
* *
43998612 TTCTCAATTAATGGCTTTCTTGAGT
1 TTCTCGATTAATGGCTCTC-TGAGT
* * * *
43998637 TTCCCGTTTTATGGCTCGTATGAGCT
1 TTCTCGATTAATGGCTC-TCTGAG-T
43998663 TT-TCGATTAATGGCTCTCTGAAGT
1 TTCTCGATTAATGGCTCTCTG-AGT
43998687 TTCTCGAT
1 TTCTCGAT
43998695 ATTAGCTCAT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
24 6 0.14
25 34 0.77
26 4 0.09
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (24 bp):
TTCTCGATTAATGGCTCTCTGAGT
Found at i:44002385 original size:26 final size:26
Alignment explanation
Indices: 44002356--44002408 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
44002346 ATCTAAAATG
*
44002356 AAAATTTTTAATGTTTTTACTTATAT
1 AAAATTTTTAATGTCTTTACTTATAT
44002382 AAAATTTTTAATGTCTTTACTTATAT
1 AAAATTTTTAATGTCTTTACTTATAT
44002408 A
1 A
44002409 GGCGCCACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.55
Consensus pattern (26 bp):
AAAATTTTTAATGTCTTTACTTATAT
Found at i:44004493 original size:26 final size:26
Alignment explanation
Indices: 44004464--44004571 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
44004454 TGGTACAAAT
44004464 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
44004490 TGATAATGGATTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
44004516 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
44004542 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
44004568 TGAT
1 TGAT
44004572 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:44006994 original size:115 final size:115
Alignment explanation
Indices: 44006792--44007028 Score: 411
Period size: 115 Copynumber: 2.1 Consensus size: 115
44006782 GGTAATATTT
*
44006792 ATATTTAACTGTTGAAATTGGATAGCTTTAGGGCGCGTTTTCAAAAACATTAATTGATTTCAAAA
1 ATATTTAACTGTTGAAATTGGATAGCTTTAGGGCGCGTTTTCAAAAACAGTAATTGATTTCAAAA
*
44006857 TAACACGAAAACAAGCAAAGCTTCCGCAATGAAGATATTTTCCAAAATTA
66 TAACACAAAAACAAGCAAAGCTTCCGCAATGAAGATATTTTCCAAAATTA
44006907 ATATTTAACTGTTGAAATTGGATAGCTTTAGGGCGCGTTTTCAAAAACAGTAATTGATTTCAAAA
1 ATATTTAACTGTTGAAATTGGATAGCTTTAGGGCGCGTTTTCAAAAACAGTAATTGATTTCAAAA
* * * *
44006972 TAACACAAAAATAGGCCAAGCTTCCGCAATGAAGATATTTTTCAAAATTA
66 TAACACAAAAACAAGCAAAGCTTCCGCAATGAAGATATTTTCCAAAATTA
44007022 ATCATTT
1 AT-ATTT
44007029 TTCCTAAAAA
Statistics
Matches: 115, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
115 111 0.97
116 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (115 bp):
ATATTTAACTGTTGAAATTGGATAGCTTTAGGGCGCGTTTTCAAAAACAGTAATTGATTTCAAAA
TAACACAAAAACAAGCAAAGCTTCCGCAATGAAGATATTTTCCAAAATTA
Found at i:44007397 original size:71 final size:69
Alignment explanation
Indices: 44007269--44007410 Score: 230
Period size: 71 Copynumber: 2.0 Consensus size: 69
44007259 GGAAATGTTT
* **
44007269 TGAATGCTTCGATGTGGCATGTCGGATCCGGCCATAACGTCTGGGCCGGGTTTGGGGTGCTACAG
1 TGAATGCTTCGATGTGGCATGTCGGATCCGGCCATAACGTCTGGACCGGGTAAGGGGTGCTACA-
44007334 TTTTAG
65 -TTTAG
*
44007340 TGAATGCTTCGATGTGGCATGTCGGATCCGGCCATAACGTCTGGACCGGGTAAGGGGTGTTACAT
1 TGAATGCTTCGATGTGGCATGTCGGATCCGGCCATAACGTCTGGACCGGGTAAGGGGTGCTACAT
44007405 TTAG
66 TTAG
44007409 TG
1 TG
44007411 GTATCAGAGC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 7 0.10
71 60 0.90
ACGTcount: A:0.18, C:0.19, G:0.35, T:0.29
Consensus pattern (69 bp):
TGAATGCTTCGATGTGGCATGTCGGATCCGGCCATAACGTCTGGACCGGGTAAGGGGTGCTACAT
TTAG
Found at i:44014045 original size:50 final size:50
Alignment explanation
Indices: 44014010--44014175 Score: 137
Period size: 45 Copynumber: 3.4 Consensus size: 50
44014000 ATAATAGCGA
* *
44014010 ATCTTATTTTCCTGAAGTTGCAATGGAACAAATTGAAGCTATAATTACAG
1 ATCTTATCTCCCTGAAGTTGCAATGGAACAAATTGAAGCTATAATTACAG
* * * * * *
44014060 ATCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAAG--AT-A--GCAA
1 ATCTTATCTCCCTGAAGTTGCAATGGAACAAATTGAAGCTATAATTACAG
* * * *
44014105 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AGAGCTACAAATTACAG
1 ATCTTATCTCCCTGAAGTTGCAATGGAACAAATTGA-AGCTA-TAATTACAG
* * *
44014156 ACCTTGTTTCCCTGAAGTTG
1 ATCTTATCTCCCTGAAGTTG
44014176 TAGTGGAGCA
Statistics
Matches: 93, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
44 1 0.01
45 36 0.39
47 2 0.02
48 2 0.02
49 1 0.01
50 32 0.34
51 19 0.20
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (50 bp):
ATCTTATCTCCCTGAAGTTGCAATGGAACAAATTGAAGCTATAATTACAG
Done.