Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 19 of 332
Found at i:5514464 original size:27 final size:26
Alignment explanation
Indices: 5514434--5514485 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
5514424 ATGTATACAT
*
5514434 TTTTAAATACTATATTATATACATATA
1 TTTTAAATACCATA-TATATACATATA
* *
5514461 TTTTTAATACCATATATGTACATAT
1 TTTTAAATACCATATATATACATAT
5514486 CATTATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTAAATACCATATATATACATATA
Found at i:5514591 original size:18 final size:18
Alignment explanation
Indices: 5514564--5514621 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
5514554 ATATATATAC
*
5514564 TTTTTA-ATATAGTATTA
1 TTTTTATATATATTATTA
5514581 TTTTTATATATCATTA-TA
1 TTTTTATATAT-ATTATTA
5514599 TTTATTAT-TATACTTATTA
1 TTT-TTATATATA-TTATTA
5514618 TTTT
1 TTTT
5514622 CGCTATTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 7 0.20
18 16 0.46
19 12 0.34
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATATATATTATTA
Found at i:5523320 original size:16 final size:16
Alignment explanation
Indices: 5523299--5523329 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5523289 TATGTTAGAG
5523299 CACATAAATTTGAAAT
1 CACATAAATTTGAAAT
*
5523315 CACATATATTTGAAA
1 CACATAAATTTGAAA
5523330 ACTTTTTCAA
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:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (16 bp):
CACATAAATTTGAAAT
Found at i:5523516 original size:18 final size:19
Alignment explanation
Indices: 5523479--5523515 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5523469 TTTAAAAAAA
5523479 TATAAA-ATTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
5523497 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
5523516 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:5523522 original size:28 final size:28
Alignment explanation
Indices: 5523491--5523544 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5523481 TAAAATTTGG
* *
5523491 AATTTTTAT-AAATATTTTGAATTTTAAA
1 AATTATTATGAAA-ATTTTGAAATTTAAA
5523519 AATTATTATGAAAATTTTGAAATTTA
1 AATTATTATGAAAATTTTGAAATTTA
5523545 TTTTGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (28 bp):
AATTATTATGAAAATTTTGAAATTTAAA
Found at i:5524296 original size:21 final size:21
Alignment explanation
Indices: 5524272--5524314 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5524262 TCAACAATAC
5524272 TAAAAACATTAAAATAAATGT
1 TAAAAACATTAAAATAAATGT
5524293 TAAAAACATTAAAATAAATGT
1 TAAAAACATTAAAATAAATGT
5524314 T
1 T
5524315 CCCCAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAAAACATTAAAATAAATGT
Found at i:5524344 original size:19 final size:20
Alignment explanation
Indices: 5524320--5524358 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5524310 ATGTTCCCCA
5524320 ACAAATTGA-AAATAAATTT
1 ACAAATTGATAAATAAATTT
*
5524339 ACAAATTGATTAATAAATTT
1 ACAAATTGATAAATAAATTT
5524359 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
ACAAATTGATAAATAAATTT
Found at i:5527991 original size:3 final size:3
Alignment explanation
Indices: 5527983--5528017 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5527973 TGAAGGCAGA
5527983 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5528018 AATTTAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5530047 original size:22 final size:23
Alignment explanation
Indices: 5530022--5530064 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5530012 TATATCACAA
5530022 TCTCATA-TATTA-TGTATGTACT
1 TCTCATATTATTAGT-TATGTACT
5530044 TCTCATATTATTAGTTATGTA
1 TCTCATATTATTAGTTATGTA
5530065 TATATTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 11 0.58
24 1 0.05
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (23 bp):
TCTCATATTATTAGTTATGTACT
Found at i:5539671 original size:111 final size:111
Alignment explanation
Indices: 5539471--5539682 Score: 293
Period size: 111 Copynumber: 1.9 Consensus size: 111
5539461 CAGCTCCAGG
* * *
5539471 AAGCCTCTCATTTGCTCTCAAACTTTGCCTGCTTGAACTGCTTACACCATCTGCATTTAATCCAT
1 AAGCCTCTCACTTGATCTCAAACTTTGCCTGCTTGAACTGCTTACACCATCTGCATTTAACCCAT
*
5539536 AGCTCGAACTGAGCTCACCAGTACCTTCATCAAACCCTTCTCTAGC
66 AGCTCGAACTAAGCTCACCAGTACCTTCATCAAACCCTTCTCTAGC
* * *
5539582 AAGCCTCTCACTTGATCTCAAACTTTGCCTTCTTGCATTGCTTACACCGA-CTGCATTTAACCCA
1 AAGCCTCTCACTTGATCTCAAACTTTGCCTGCTTGAACTGCTTACACC-ATCTGCATTTAACCCA
* * **
5539646 TTGCTCGATAC-AAGCTCGCTGGTACCTTCATCAAACC
65 TAGCTCGA-ACTAAGCTCACCAGTACCTTCATCAAACC
5539683 GCACTGATGA
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
111 85 0.97
112 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.12, T:0.31
Consensus pattern (111 bp):
AAGCCTCTCACTTGATCTCAAACTTTGCCTGCTTGAACTGCTTACACCATCTGCATTTAACCCAT
AGCTCGAACTAAGCTCACCAGTACCTTCATCAAACCCTTCTCTAGC
Found at i:5541416 original size:87 final size:90
Alignment explanation
Indices: 5541287--5541504 Score: 234
Period size: 89 Copynumber: 2.5 Consensus size: 90
5541277 GCTCTTCAAT
* * ** * * *
5541287 TTTTTCAAAAAAGCAATTAAGTCTTTAC--TTTTTTCACTCAA-TTGAGTACTTTAACTTT-TAA
1 TTTTTCAAAAAAACAATTAAGCCCATACTTTTTTTTCACTCAATTTG-GCACTTGAACTTTCAAA
* **
5541348 A-ATGCATAAAAAAGGACCTTCAAAC
65 ATATACATAAAAAAAAACCTTCAAAC
*
5541373 TTTTTC-AAAAAA-AATTAAGCCCCTACTTTTTTTTACACTCAATTTGGCACTTGAACTTTCAAA
1 TTTTTCAAAAAAACAATTAAGCCCATACTTTTTTTT-CACTCAATTTGGCACTTGAACTTTCAAA
* *
5541436 ATATATATAAAAAAAAACCTTCAAGC
65 ATATACATAAAAAAAAACCTTCAAAC
*
5541462 TTTTTCAAAAAAAGCAATTAAGCCCATACTTTTTTTTTACTCA
1 TTTTTCAAAAAAA-CAATTAAGCCCATACTTTTTTTTCACTCA
5541505 GTTGATTGGG
Statistics
Matches: 109, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
84 11 0.10
85 5 0.05
86 12 0.11
87 18 0.17
88 6 0.06
89 25 0.23
90 6 0.06
91 5 0.05
92 21 0.19
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (90 bp):
TTTTTCAAAAAAACAATTAAGCCCATACTTTTTTTTCACTCAATTTGGCACTTGAACTTTCAAAA
TATACATAAAAAAAAACCTTCAAAC
Found at i:5541719 original size:18 final size:18
Alignment explanation
Indices: 5541682--5541751 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
5541672 AATACAAGTT
*
5541682 ATAAAAAGTATTAAACTTTA
1 ATAAAAA-TA-TAAAATTTA
5541702 ATAAAAATATAAAATTTA
1 ATAAAAATATAAAATTTA
* * * *
5541720 TTAAAATTGTAAAATTTT
1 ATAAAAATATAAAATTTA
5541738 ATAAAAATCATAAA
1 ATAAAAAT-ATAAA
5541752 TAATTATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 28 0.68
19 6 0.15
20 7 0.17
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAAAAATATAAAATTTA
Found at i:5541752 original size:18 final size:17
Alignment explanation
Indices: 5541680--5541762 Score: 58
Period size: 18 Copynumber: 4.5 Consensus size: 17
5541670 TCAATACAAG
5541680 TTATAAAAAGTATTAAACTT
1 TTATAAAAA-TA-TAAA-TT
* *
5541700 TAATAAAAATATAAAAT
1 TTATAAAAATATAAATT
* *
5541717 TTATTAAAATTGTAAAATT
1 TTA-TAAAAATAT-AAATT
*
5541736 TTATAAAAATCATAAATAA
1 TTATAAAAAT-ATAAAT-T
5541755 TTATAAAA
1 TTATAAAA
5541763 TGTATCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
17 3 0.06
18 21 0.42
19 18 0.36
20 8 0.16
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
TTATAAAAATATAAATT
Found at i:5541996 original size:19 final size:19
Alignment explanation
Indices: 5541969--5542095 Score: 105
Period size: 19 Copynumber: 6.6 Consensus size: 19
5541959 TTTTGGTACG
5541969 ATAATTTTTATATTTTTTT
1 ATAATTTTTATATTTTTTT
* *
5541988 ATAAATTTTATATTTCTTT
1 ATAATTTTTATATTTTTTT
* * *
5542007 ACATTTTTTTATAATTTTCTT
1 ATA-ATTTTTAT-ATTTTTTT
* * *
5542028 ACAATTTTTATAATTGTTT
1 ATAATTTTTATATTTTTTT
*
5542047 ATGATTTTTATAATTTTTTTT
1 ATAATTTTTAT-A-TTTTTTT
* *
5542068 CTAATTTTTA-ATATTTTT
1 ATAATTTTTATATTTTTTT
5542086 AT-ATTTTTAT
1 ATAATTTTTAT
5542096 TAAAATTTAA
Statistics
Matches: 84, Mismatches: 19, Indels: 11
0.74 0.17 0.10
Matches are distributed among these distances:
17 7 0.08
18 7 0.08
19 34 0.40
20 14 0.17
21 22 0.26
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (19 bp):
ATAATTTTTATATTTTTTT
Found at i:5542018 original size:39 final size:40
Alignment explanation
Indices: 5541973--5542093 Score: 106
Period size: 39 Copynumber: 3.1 Consensus size: 40
5541963 GGTACGATAA
* *
5541973 TTTTTATATTTTTTTATAAATTTTATATTTCTTTA-CATT
1 TTTTTATATTTTTTTACAAATTTTATAATTCTTTATCATT
* * * *
5542012 TTTTTATAATTTTCTTACAATTTTTATAATTGTTTATGATT
1 TTTTTAT-ATTTTTTTACAAATTTTATAATTCTTTATCATT
* * * *
5542053 TTTATA-ATTTTTTTTCTAATTTT-TAATATTTTTAT-ATT
1 TTTTTATATTTTTTTACAAATTTTATAAT-TCTTTATCATT
5542091 TTT
1 TTT
5542094 ATTAAAATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
38 10 0.15
39 26 0.39
40 23 0.34
41 8 0.12
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.69
Consensus pattern (40 bp):
TTTTTATATTTTTTTACAAATTTTATAATTCTTTATCATT
Found at i:5542037 original size:40 final size:39
Alignment explanation
Indices: 5541972--5542095 Score: 114
Period size: 40 Copynumber: 3.2 Consensus size: 39
5541962 TGGTACGATA
* *
5541972 ATTTTTAT-ATTTTTTTATAAATTTTATATTTCTTTACAT-
1 ATTTTTATAATTTTTTTACAATTTTTATATTTCTTT--ATG
* * * *
5542011 TTTTTTATAATTTTCTTACAATTTTTATAATTGTTTATG
1 ATTTTTATAATTTTTTTACAATTTTTATATTTCTTTATG
*
5542050 ATTTTTATAATTTTTTTTCTAATTTTTA-ATATT-TTTAT-
1 ATTTTTATAATTTTTTTAC-AATTTTTATAT-TTCTTTATG
5542088 ATTTTTAT
1 ATTTTTAT
5542096 TAAAATTTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
38 10 0.14
39 29 0.41
40 32 0.45
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (39 bp):
ATTTTTATAATTTTTTTACAATTTTTATATTTCTTTATG
Found at i:5542042 original size:9 final size:9
Alignment explanation
Indices: 5541969--5542095 Score: 78
Period size: 9 Copynumber: 13.2 Consensus size: 9
5541959 TTTTGGTACG
5541969 ATAATTTTT
1 ATAATTTTT
*
5541978 ATATTTTTTT
1 ATA-ATTTTT
*
5541988 ATAAATTTT
1 ATAATTTTT
*
5541997 ATATTTCTTT
1 ATAATT-TTT
* *
5542007 ACATTTTTTT
1 ATA-ATTTTT
5542017 ATAATTTTCTT
1 ATAA-TTT-TT
*
5542028 ACAATTTTT
1 ATAATTTTT
5542037 ATAATTGTTT
1 ATAATT-TTT
*
5542047 ATGATTTTT
1 ATAATTTTT
5542056 ATAATTTTTTTT
1 ATAA---TTTTT
*
5542068 CTAATTTTT
1 ATAATTTTT
5542077 A-ATATTTTT
1 ATA-ATTTTT
5542086 AT-ATTTTT
1 ATAATTTTT
5542094 AT
1 AT
5542096 TAAAATTTAA
Statistics
Matches: 93, Mismatches: 14, Indels: 23
0.72 0.11 0.18
Matches are distributed among these distances:
8 9 0.10
9 36 0.39
10 32 0.34
11 8 0.09
12 8 0.09
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (9 bp):
ATAATTTTT
Found at i:5542066 original size:30 final size:29
Alignment explanation
Indices: 5542032--5542129 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 29
5542022 TTTCTTACAA
5542032 TTTTTATAATTGTTTATGATTTTTATAATTT
1 TTTTTATAATT-TTTATGATTTTTATAA-TT
*
5542063 TTTTTCTAATTTTTAAT-ATTTTTAT-ATT
1 TTTTTATAATTTTT-ATGATTTTTATAATT
* *
5542091 TTTATTA-AAATTTAATGATTTTTTATAAATT
1 TTT-TTATAATTTTTATGA-TTTTTAT-AATT
5542122 TTATTTAT
1 TT-TTTAT
5542130 TTTTAATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
27 2 0.04
28 11 0.20
29 10 0.18
30 11 0.20
31 20 0.36
32 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (29 bp):
TTTTTATAATTTTTATGATTTTTATAATT
Found at i:5542131 original size:20 final size:21
Alignment explanation
Indices: 5542083--5542133 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
5542073 TTTTAATATT
5542083 TTTATATTTTTATTAAAATTTA
1 TTTAT-TTTTTATTAAAATTTA
* * *
5542105 ATGATTTTTTA-TAAATTTTA
1 TTTATTTTTTATTAAAATTTA
5542125 TTTATTTTT
1 TTTATTTTT
5542134 AATTTTTATC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 15 0.62
21 6 0.25
22 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTATTTTTTATTAAAATTTA
Found at i:5542132 original size:19 final size:19
Alignment explanation
Indices: 5542031--5542134 Score: 61
Period size: 19 Copynumber: 5.4 Consensus size: 19
5542021 TTTTCTTACA
* *
5542031 ATTTTTATAATTGTTTA-TG
1 ATTTTTATAAAT-TTTATTT
* *
5542050 ATTTTTATAATTTTTTTTCT
1 ATTTTTATAAATTTTATT-T
* *
5542070 AATTTTTA-ATATTTT-TAT
1 -ATTTTTATAAATTTTATTT
* * *
5542088 ATTTTTATTAAAATTTAATG
1 ATTTTTA-TAAATTTTATTT
5542108 ATTTTTTATAAATTTTATTT
1 A-TTTTTATAAATTTTATTT
5542128 ATTTTTA
1 ATTTTTA
5542135 ATTTTTATCA
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
17 7 0.11
18 4 0.06
19 25 0.38
20 16 0.25
21 13 0.20
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (19 bp):
ATTTTTATAAATTTTATTT
Found at i:5545609 original size:11 final size:12
Alignment explanation
Indices: 5545588--5545629 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
5545578 CAAAAAAAAA
5545588 TCAAAATAATTT
1 TCAAAATAATTT
5545600 TCAAAA-AATTT
1 TCAAAATAATTT
5545611 T-AAATATAATTT
1 TCAAA-ATAATTT
*
5545623 TTAAAAT
1 TCAAAAT
5545630 TCAGAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.11
11 7 0.26
12 14 0.52
13 3 0.11
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (12 bp):
TCAAAATAATTT
Found at i:5548754 original size:29 final size:29
Alignment explanation
Indices: 5548712--5548778 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
5548702 ACAACACATT
* *
5548712 AACATAAGTGACTGAAATGTAACAATTGA
1 AACATAAGTAACTGAAATATAACAATTGA
*
5548741 AACATAAGTAACTGAAATATAATAATTGA
1 AACATAAGTAACTGAAATATAACAATTGA
5548770 AACATAAGT
1 AACATAAGT
5548779 GACTATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.25
Consensus pattern (29 bp):
AACATAAGTAACTGAAATATAACAATTGA
Found at i:5548776 original size:14 final size:15
Alignment explanation
Indices: 5548735--5548778 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
5548725 GAAATGTAAC
5548735 AATTGAAACATAAGT
1 AATTGAAACATAAGT
* *
5548750 AACTGAAATATAA-T
1 AATTGAAACATAAGT
5548764 AATTGAAACATAAGT
1 AATTGAAACATAAGT
5548779 GACTATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (15 bp):
AATTGAAACATAAGT
Found at i:5551822 original size:6 final size:6
Alignment explanation
Indices: 5551811--5551839 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5551801 AGGATTGCAA
5551811 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
5551840 CATTGAAACC
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:5554984 original size:40 final size:40
Alignment explanation
Indices: 5554923--5555060 Score: 177
Period size: 40 Copynumber: 3.5 Consensus size: 40
5554913 CTCGAGAATA
* * *
5554923 TAAAGTGGATAGGATTCGTTCCTGATTCACTATAATACCT
1 TAAAGTGGATAGGATTTGTTCCTGATTCACTATGATAACT
* *
5554963 CAAAGTGGATAGGATTTGTTCCTGATTCACTATGATAATT
1 TAAAGTGGATAGGATTTGTTCCTGATTCACTATGATAACT
** * * *
5555003 TAAAGTAAATAGGATTTATTCTTGATTCACTATGGTAACT
1 TAAAGTGGATAGGATTTGTTCCTGATTCACTATGATAACT
*
5555043 TAAGGTGGATAGGATTTG
1 TAAAGTGGATAGGATTTG
5555061 ACCTGAAAAG
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (40 bp):
TAAAGTGGATAGGATTTGTTCCTGATTCACTATGATAACT
Found at i:5555352 original size:76 final size:76
Alignment explanation
Indices: 5555226--5555378 Score: 270
Period size: 76 Copynumber: 2.0 Consensus size: 76
5555216 AAGGGTTATT
* *
5555226 TCTGAATATGAATTTATGGAATATGGAAATGTACGCTTTGAATGTACTGTTGAAAAATCCATCCG
1 TCTGAATATGAATTGATGGAATATGAAAATGTACGCTTTGAATGTACTGTTGAAAAATCCATCCG
5555291 AACTCCAATGA
66 AACTCCAATGA
* *
5555302 TCTGAATATGAATTGATGGAATATGAAAATGTACGCTTTGAGTGTACTGTTGAAAAATCCATCGG
1 TCTGAATATGAATTGATGGAATATGAAAATGTACGCTTTGAATGTACTGTTGAAAAATCCATCCG
5555367 AACTCCAATGA
66 AACTCCAATGA
5555378 T
1 T
5555379 TCAACGGATA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (76 bp):
TCTGAATATGAATTGATGGAATATGAAAATGTACGCTTTGAATGTACTGTTGAAAAATCCATCCG
AACTCCAATGA
Found at i:5556292 original size:17 final size:17
Alignment explanation
Indices: 5556270--5556330 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
5556260 TTAATTACTT
5556270 TAATATTAAATTTAATA
1 TAATATTAAATTTAATA
* *
5556287 TAATATT-TA-TTAAGA
1 TAATATTAAATTTAATA
* * *
5556302 TAAATATTAGATTAAATT
1 T-AATATTAAATTTAATA
5556320 TAATATTAAAT
1 TAATATTAAAT
5556331 CTTATTAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 6 0.18
16 7 0.21
17 17 0.50
18 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TAATATTAAATTTAATA
Found at i:5556416 original size:20 final size:18
Alignment explanation
Indices: 5556369--5556475 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 18
5556359 TAGGATAAAC
5556369 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
5556386 ATTAAGA-TAATTACTTTAAT
1 ATTAA-ATTAA-TA-TTTAAT
**
5556406 ATTAAATTAATA-AAACACT
1 ATTAAATTAATATTTA-A-T
*
5556425 ATTAAGATTAGTA-TTAA-
1 ATTAA-ATTAATATTTAAT
*
5556442 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
5556462 ATTAAAATAATATT
1 ATTAAATTAATATT
5556476 ATTTTTTGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
16 1 0.01
17 19 0.27
18 5 0.07
19 18 0.26
20 27 0.39
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:5567757 original size:24 final size:24
Alignment explanation
Indices: 5567704--5567757 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
5567694 TTCTAATTAA
*
5567704 ATTTTATAAATAATTAATATTTAT
1 ATTTTAAAAATAATTAATATTTAT
*
5567728 -TATTTAAAAATATTTAA-ATTTTAT
1 AT-TTTAAAAATAATTAATA-TTTAT
5567752 ATTTTA
1 ATTTTA
5567758 TTTATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 2 0.08
24 22 0.88
25 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTTAAAAATAATTAATATTTAT
Found at i:5577296 original size:72 final size:72
Alignment explanation
Indices: 5577179--5577323 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
5577169 CTGAACAAAC
5577179 ACATATTCGCTTGAGGAGGAGGTAGAGGTGGCCTATAGTTCGTGCTTTTGTAGGTGGTGTCAAAA
1 ACATATTCGCTTGAGGAGGAGGTAGAGGTGGCCTATAGTTCGTGCTTTTGTAGGTGGTGTCAAAA
5577244 CGATAGT
66 CGATAGT
5577251 ACATATTCGCTTGAGGAGGAGGTAGAGGTGGCCTATAGTTCGTGCTTTTGTAGGTGGTGTCAAAA
1 ACATATTCGCTTGAGGAGGAGGTAGAGGTGGCCTATAGTTCGTGCTTTTGTAGGTGGTGTCAAAA
5577316 CGATAGT
66 CGATAGT
5577323 A
1 A
5577324 GCTGTAGTAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.30
Consensus pattern (72 bp):
ACATATTCGCTTGAGGAGGAGGTAGAGGTGGCCTATAGTTCGTGCTTTTGTAGGTGGTGTCAAAA
CGATAGT
Found at i:5579219 original size:27 final size:25
Alignment explanation
Indices: 5579169--5579218 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
5579159 TATCTCATGT
5579169 ATATATTTCAAACACTATATATATA
1 ATATATTTCAAACACTATATATATA
*
5579194 ATATATTTCTAACACTATATATATA
1 ATATATTTCAAACACTATATATATA
5579219 TTTTACATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATATTTCAAACACTATATATATA
Found at i:5581079 original size:16 final size:16
Alignment explanation
Indices: 5581058--5581090 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5581048 ATAATCTTTG
5581058 CTATAATTGATTTAGT
1 CTATAATTGATTTAGT
5581074 CTATAATTGATTTAGT
1 CTATAATTGATTTAGT
5581090 C
1 C
5581091 ATAGACTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.48
Consensus pattern (16 bp):
CTATAATTGATTTAGT
Found at i:5584533 original size:26 final size:28
Alignment explanation
Indices: 5584479--5584539 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
5584469 TATTATCAAG
* *
5584479 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
5584507 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
5584533 AATTATA
1 AATTATA
5584540 CAAATTCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:5584735 original size:16 final size:16
Alignment explanation
Indices: 5584714--5584755 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5584704 TTATTAAATT
*
5584714 ATATATTTTAATTATA
1 ATATATTTTAATAATA
5584730 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
5584745 AT-TATGTTTAA
1 ATATAT-TTTAA
5584756 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:5584740 original size:15 final size:15
Alignment explanation
Indices: 5584705--5584746 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5584695 TTAAGAATTT
*
5584705 TATTAAATTAT-ATA
1 TATTTAATTATAATA
5584719 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
5584733 TATTTAATAATAAT
1 TATTTAATTATAAT
5584747 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:5584992 original size:16 final size:16
Alignment explanation
Indices: 5584971--5585038 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
5584961 GATTTGCTAT
5584971 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5584987 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
5585003 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
5585019 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5585035 TACA
1 TACA
5585039 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:5585417 original size:19 final size:20
Alignment explanation
Indices: 5585381--5585418 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5585371 TTTTTTAGTA
*
5585381 AATTATATAAATAATTATTC
1 AATTATATAAAAAATTATTC
5585401 AATTATA-AAAAAATTATT
1 AATTATATAAAAAATTATT
5585419 TTAGATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTATATAAAAAATTATTC
Found at i:5589263 original size:30 final size:30
Alignment explanation
Indices: 5589227--5589287 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
5589217 TCCTAAACTT
5589227 TATTTTATATTATTATTAATAATTTTTATA
1 TATTTTATATTATTATTAATAATTTTTATA
5589257 TATTTTATATTATTATTAATAATTTTTATA
1 TATTTTATATTATTATTAATAATTTTTATA
5589287 T
1 T
5589288 GAATAACAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TATTTTATATTATTATTAATAATTTTTATA
Found at i:5592168 original size:35 final size:35
Alignment explanation
Indices: 5592122--5592189 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
5592112 TCCGGAGCTC
*
5592122 GGCAAATATGGAAAGTAATATTCAAAGATATGCTT
1 GGCAAATATGGAAAGGAATATTCAAAGATATGCTT
* * *
5592157 GGCAAATATGGAAGGGGATCTTCAAAGATATGC
1 GGCAAATATGGAAAGGAATATTCAAAGATATGC
5592190 GATCCTAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (35 bp):
GGCAAATATGGAAAGGAATATTCAAAGATATGCTT
Found at i:5594941 original size:21 final size:21
Alignment explanation
Indices: 5594915--5594965 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
5594905 ATGTGGAACA
5594915 TTTGAGGGAGGTGTTCCAAAC
1 TTTGAGGGAGGTGTTCCAAAC
5594936 TTTGAGGGAGGTGTTCCAAAC
1 TTTGAGGGAGGTGTTCCAAAC
5594957 TTTGAGGGA
1 TTTGAGGGA
5594966 AAATGAGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.12, G:0.35, T:0.29
Consensus pattern (21 bp):
TTTGAGGGAGGTGTTCCAAAC
Found at i:5597337 original size:35 final size:35
Alignment explanation
Indices: 5597298--5597369 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
5597288 CATCTCCGGA
*
5597298 GCTTGGCAAATATGGAAAGTAATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
* *
5597333 GCTTGGCAAATATGGAAGGGGATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
5597368 GC
1 GC
5597370 GATCCTAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.26
Consensus pattern (35 bp):
GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
Found at i:5600813 original size:51 final size:53
Alignment explanation
Indices: 5600729--5600846 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 53
5600719 ATATGTCGAC
* *
5600729 TACTGTGACTGTTCCGGATTCGTTCTGAAGAGGTAC-TT-TGTACCTG-ACTGT
1 TACTGTTACTGTTCCGGATTCGTTCCGAAGAGGTACTTTGTGTA-CTGCACTGT
* * *
5600780 TACTGTTACTGTTCTGGATTTGTTCCGATGAGGTACTTTGTGTACTGCTACTGT
1 TACTGTTACTGTTCCGGATTCGTTCCGAAGAGGTACTTTGTGTACTGC-ACTGT
*
5600834 TATTGTTACTGTT
1 TACTGTTACTGTT
5600847 ACCCTTACGG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 31 0.54
52 5 0.09
53 4 0.07
54 17 0.30
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (53 bp):
TACTGTTACTGTTCCGGATTCGTTCCGAAGAGGTACTTTGTGTACTGCACTGT
Found at i:5601013 original size:18 final size:18
Alignment explanation
Indices: 5600992--5601026 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5600982 CTGAATAATT
*
5600992 GACTGTTACAGAATAAAC
1 GACTGATACAGAATAAAC
*
5601010 GACTGATACTGAATAAA
1 GACTGATACAGAATAAA
5601027 TAAATATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (18 bp):
GACTGATACAGAATAAAC
Found at i:5609311 original size:26 final size:26
Alignment explanation
Indices: 5609282--5609333 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5609272 AACAACTGGG
*
5609282 TTCATTCTGGTACTTGAACTTAGAAA
1 TTCATTCTGATACTTGAACTTAGAAA
* *
5609308 TTCATTTTGATCCTTGAACTTAGAAA
1 TTCATTCTGATACTTGAACTTAGAAA
5609334 AATATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (26 bp):
TTCATTCTGATACTTGAACTTAGAAA
Found at i:5616479 original size:9 final size:9
Alignment explanation
Indices: 5616467--5616491 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5616457 CCTTCATCGT
5616467 CTTCTTCCA
1 CTTCTTCCA
5616476 CTTCTTCCA
1 CTTCTTCCA
5616485 CTTCTTC
1 CTTCTTC
5616492 GGCGGCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (9 bp):
CTTCTTCCA
Found at i:5625389 original size:12 final size:12
Alignment explanation
Indices: 5625368--5625430 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
5625358 CAATTTAATC
5625368 TTTTCTTTTATTT
1 TTTTC-TTTATTT
5625381 TTTTCTTTATTT
1 TTTTCTTTATTT
* * *
5625393 TTCAT-TTTAATC
1 TT-TTCTTTATTT
5625405 TTTTCATTTA-TT
1 TTTTC-TTTATTT
5625417 TTTTCTTTATTT
1 TTTTCTTTATTT
5625429 TT
1 TT
5625431 CATTCTCTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
11 5 0.12
12 26 0.63
13 10 0.24
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTTATTT
Found at i:5625426 original size:36 final size:37
Alignment explanation
Indices: 5625361--5625434 Score: 132
Period size: 36 Copynumber: 2.0 Consensus size: 37
5625351 TGTTGAGCAA
*
5625361 TTTAATCTTTTCTTTTATTTTTTTCTTTATTTTTCAT
1 TTTAATCTTTTCATTTATTTTTTTCTTTATTTTTCAT
5625398 TTTAATCTTTTCATTTA-TTTTTTCTTTATTTTTCAT
1 TTTAATCTTTTCATTTATTTTTTTCTTTATTTTTCAT
5625434 T
1 T
5625435 CTCTTCTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 20 0.56
37 16 0.44
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (37 bp):
TTTAATCTTTTCATTTATTTTTTTCTTTATTTTTCAT
Found at i:5635805 original size:125 final size:125
Alignment explanation
Indices: 5635583--5635822 Score: 426
Period size: 125 Copynumber: 1.9 Consensus size: 125
5635573 ACTCATTCAT
* *
5635583 ACAACTGTTTTCAACTATCTGATTATGGTTTTAGCTTTGTATTTATCAATTCATAGCCATGCTTT
1 ACAACTGTTTTCAACTATCTGATTATGGTTTTAGCTTCGTATTTATCAAATCATAGCCATGCTTT
*
5635648 CATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAATCATCAAACTCGTTCATAG
66 CATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAACCATCAAACTCGTTCATAG
* *
5635708 ACAACTGTTTTCAACTATCTGATTATGGTTTTAGCTTCGTATTTATTAAATCATATCCATGCTTT
1 ACAACTGTTTTCAACTATCTGATTATGGTTTTAGCTTCGTATTTATCAAATCATAGCCATGCTTT
*
5635773 CATAGACAACATTGTTAGGAATTAGTATGATGAGAATGAAACCATCAAAC
66 CATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAACCATCAAAC
5635823 CAGGACCTGG
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 109 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (125 bp):
ACAACTGTTTTCAACTATCTGATTATGGTTTTAGCTTCGTATTTATCAAATCATAGCCATGCTTT
CATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAACCATCAAACTCGTTCATAG
Found at i:5636862 original size:43 final size:42
Alignment explanation
Indices: 5636800--5636881 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 42
5636790 AAGACTTCGT
*
5636800 AATAACTCTATAGCGAGCTTTTCATTGACATCAGATAAAAAA
1 AATAACTCTATAGCAAGCTTTTCATTGACATCAGATAAAAAA
*
5636842 AATAAGCTCTATAGCAAGCTTTTCATTGACATTAGATAAA
1 AATAA-CTCTATAGCAAGCTTTTCATTGACATCAGATAAA
5636882 CTGATTATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
42 5 0.14
43 32 0.86
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30
Consensus pattern (42 bp):
AATAACTCTATAGCAAGCTTTTCATTGACATCAGATAAAAAA
Found at i:5643079 original size:12 final size:12
Alignment explanation
Indices: 5643046--5643079 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5643036 AAATATCTAT
* *
5643046 ATCCATCCACCC
1 ATCCATACATCC
5643058 ATCCATACATCC
1 ATCCATACATCC
5643070 ATCCATACAT
1 ATCCATACAT
5643080 ACATGTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (12 bp):
ATCCATACATCC
Found at i:5644509 original size:23 final size:22
Alignment explanation
Indices: 5644479--5644530 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
5644469 AAATTTTAAA
5644479 AATATATTTATTTTTTAATATTT
1 AATATATTTATTTTTTAAT-TTT
5644502 AATATATTTATTTATTATAATTTT
1 AATATATTTATTT-TT-TAATTTT
5644526 -ATATA
1 AATATA
5644531 GTCATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 18 0.67
24 5 0.19
25 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AATATATTTATTTTTTAATTTT
Found at i:5645708 original size:33 final size:31
Alignment explanation
Indices: 5645663--5645730 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 31
5645653 TCTTTAAATC
5645663 TATACAATTAAATCAAAATTAAAATTTTATA
1 TATACAATTAAATCAAAATTAAAATTTTATA
* * * *
5645694 TATACATATTTAAATCATATTTTAAATTTTTTA
1 TATACA-A-TTAAATCAAAATTAAAATTTTATA
5645727 TATA
1 TATA
5645731 ATTGCATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 6 0.19
32 1 0.03
33 24 0.77
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (31 bp):
TATACAATTAAATCAAAATTAAAATTTTATA
Found at i:5647461 original size:28 final size:26
Alignment explanation
Indices: 5647421--5647472 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 26
5647411 CTTTTTTTAA
5647421 AAATGTTATAATTAAATTATAAAATTTT
1 AAATGTTATAATT-AATT-TAAAATTTT
5647449 AAATGGTTA-AATTAATTTAAAATT
1 AAAT-GTTATAATTAATTTAAAATT
5647473 ATACAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 7 0.30
27 4 0.17
28 8 0.35
29 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (26 bp):
AAATGTTATAATTAATTTAAAATTTT
Found at i:5653305 original size:18 final size:18
Alignment explanation
Indices: 5653282--5653333 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
5653272 GTTAATATAC
*
5653282 GAGTAAATCCCTGATTGG
1 GAGTAAATCCTTGATTGG
5653300 GAGTAAATCCTTGATTGG
1 GAGTAAATCCTTGATTGG
5653318 GAGTAAATCCTTGATT
1 GAGTAAATCCTTGATT
5653334 AGGATTTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (18 bp):
GAGTAAATCCTTGATTGG
Found at i:5656265 original size:18 final size:18
Alignment explanation
Indices: 5656242--5656294 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
5656232 GATAAATCCT
5656242 AATCAAGGATTTACTCCC
1 AATCAAGGATTTACTCCC
*
5656260 AATCAAGGATTGACTCCC
1 AATCAAGGATTTACTCCC
*
5656278 AATCAGGGATTTACTCC
1 AATCAAGGATTTACTCC
5656295 TATATTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (18 bp):
AATCAAGGATTTACTCCC
Found at i:5657666 original size:100 final size:100
Alignment explanation
Indices: 5657490--5657690 Score: 375
Period size: 100 Copynumber: 2.0 Consensus size: 100
5657480 TGTCAAAGGT
* *
5657490 ACTAATAATATTATTGTTGATTATCTTAGCAGGCCTTATGGATAGAGGTAAAAAACCTCTAGAAC
1 ACTAATAATATTATTGCTGATTATCTTAGCAGGCCTTATGGATAGAGGTAAAAAAACTCTAGAAC
5657555 AAGTCGGGGAATGGACTACTGTCCATAAAAAACCC
66 AAGTCGGGGAATGGACTACTGTCCATAAAAAACCC
5657590 ACTAATAATATTATTGCTGATTATCTTAGCAGGCCTTATGGATAGAGGTAAAAAAACTCTAGAAC
1 ACTAATAATATTATTGCTGATTATCTTAGCAGGCCTTATGGATAGAGGTAAAAAAACTCTAGAAC
*
5657655 AAGTCGTGGAATGGACTACTGTCCATAAAAAACCC
66 AAGTCGGGGAATGGACTACTGTCCATAAAAAACCC
5657690 A
1 A
5657691 ACAAAGGAAA
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (100 bp):
ACTAATAATATTATTGCTGATTATCTTAGCAGGCCTTATGGATAGAGGTAAAAAAACTCTAGAAC
AAGTCGGGGAATGGACTACTGTCCATAAAAAACCC
Found at i:5657737 original size:18 final size:18
Alignment explanation
Indices: 5657714--5657766 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
5657704 GATAAATCCT
5657714 AATCAAGGATTTACTCCC
1 AATCAAGGATTTACTCCC
*
5657732 AATCAAGGATTGACTCCC
1 AATCAAGGATTTACTCCC
*
5657750 AATCAGGGATTTACTCC
1 AATCAAGGATTTACTCC
5657767 TATATTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (18 bp):
AATCAAGGATTTACTCCC
Found at i:5658936 original size:18 final size:18
Alignment explanation
Indices: 5658910--5658961 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
5658900 GTTAATATAC
*
5658910 GAGTAAATCCCTGATTGG
1 GAGTAAATCCTTGATTGG
*
5658928 GAGTCAATCCTTGATTGG
1 GAGTAAATCCTTGATTGG
5658946 GAGTAAATCCTTGATT
1 GAGTAAATCCTTGATT
5658962 AGGATTTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (18 bp):
GAGTAAATCCTTGATTGG
Found at i:5663275 original size:30 final size:30
Alignment explanation
Indices: 5663239--5663300 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
5663229 GTAAATTAAA
5663239 GATAAGAACTTACAATGAGTATTATGATAT
1 GATAAGAACTTACAATGAGTATTATGATAT
5663269 GATAAGAACTTACAATGAGTATTATGATAT
1 GATAAGAACTTACAATGAGTATTATGATAT
5663299 GA
1 GA
5663301 ATTTCCAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (30 bp):
GATAAGAACTTACAATGAGTATTATGATAT
Found at i:5666165 original size:18 final size:18
Alignment explanation
Indices: 5666107--5666190 Score: 89
Period size: 18 Copynumber: 4.6 Consensus size: 18
5666097 GGAACATAAT
*
5666107 ATCCTTGATTAGGA-TAA
1 ATCCTTGATTGGGAGTAA
* *
5666124 ATCCTGTTAATATAGGAGTAA
1 ATCC--TTGAT-TGGGAGTAA
* *
5666145 ATCCCTGATTGGGAGTCA
1 ATCCTTGATTGGGAGTAA
5666163 ATCCTTGATTGGGAGTAA
1 ATCCTTGATTGGGAGTAA
5666181 ATCCTTGATT
1 ATCCTTGATT
5666191 AGGATTTATC
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
17 4 0.07
18 33 0.59
19 7 0.12
20 5 0.09
21 7 0.12
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (18 bp):
ATCCTTGATTGGGAGTAA
Found at i:5666387 original size:100 final size:100
Alignment explanation
Indices: 5666214--5666414 Score: 357
Period size: 100 Copynumber: 2.0 Consensus size: 100
5666204 TTTCCTTTGT
* * * *
5666214 TGGGTTTTTTATGGATAGTAGTTCATTCCTCGACTTGTTTTAGAGGTTTTTTACCTCTATCCACA
1 TGGGTTTTTTATGGACAGTAGTCCATTCCCCGACTTGTTCTAGAGGTTTTTTACCTCTATCCACA
5666279 AGGCCTGCTAAGATAATCAGCAATAATATTATTAG
66 AGGCCTGCTAAGATAATCAGCAATAATATTATTAG
*
5666314 TGGGTTTTTTATGGACAGTAGTCCATTCCCCGACTTGTTCTAGAGGTTTTTTACCTCTATCCATA
1 TGGGTTTTTTATGGACAGTAGTCCATTCCCCGACTTGTTCTAGAGGTTTTTTACCTCTATCCACA
5666379 AGGCCTGCTAAGATAATCAGCAATAATATTATTAG
66 AGGCCTGCTAAGATAATCAGCAATAATATTATTAG
5666414 T
1 T
5666415 ACCTTTGACA
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (100 bp):
TGGGTTTTTTATGGACAGTAGTCCATTCCCCGACTTGTTCTAGAGGTTTTTTACCTCTATCCACA
AGGCCTGCTAAGATAATCAGCAATAATATTATTAG
Found at i:5667658 original size:18 final size:18
Alignment explanation
Indices: 5667631--5667683 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
5667621 TGTTAATATA
*
5667631 GGAGTAAATCCCTGATTG
1 GGAGTAAATCCTTGATTG
*
5667649 GGAGTCAATCCTTGATTG
1 GGAGTAAATCCTTGATTG
5667667 GGAGTAAATCCTTGATT
1 GGAGTAAATCCTTGATT
5667684 AGGATTTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (18 bp):
GGAGTAAATCCTTGATTG
Found at i:5668207 original size:18 final size:18
Alignment explanation
Indices: 5668184--5668236 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
5668174 GATAAATCCT
5668184 AATCAAGGATTTACTCCC
1 AATCAAGGATTTACTCCC
* *
5668202 AATCAAGGATTGACTCTC
1 AATCAAGGATTTACTCCC
*
5668220 AATCAGGGATTTACTCC
1 AATCAAGGATTTACTCC
5668237 TATATTAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (18 bp):
AATCAAGGATTTACTCCC
Found at i:5675767 original size:25 final size:25
Alignment explanation
Indices: 5675739--5675788 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5675729 GTCTAAGACT
5675739 AAAATTTTGAAATATGAAAAGTACA
1 AAAATTTTGAAATATGAAAAGTACA
5675764 AAAATTTTGAAATATGAAAAGTACA
1 AAAATTTTGAAATATGAAAAGTACA
5675789 GGAACTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.12, T:0.28
Consensus pattern (25 bp):
AAAATTTTGAAATATGAAAAGTACA
Found at i:5676856 original size:21 final size:22
Alignment explanation
Indices: 5676830--5676888 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
5676820 GTTTTAAGAA
*
5676830 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
5676851 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
5676873 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
5676889 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:5677270 original size:38 final size:39
Alignment explanation
Indices: 5677218--5677308 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 39
5677208 TATATTTTTC
* *
5677218 TCGAGTTTCAAGTTTATGATTTAGGGTTTATATC-AGATT
1 TCGAGTTT-GAGTTTAGGATTTAGGGTTTATATCGAGATT
* *
5677257 TCGAGTTTGAGTTTAGGATTTATGGTTTATATCGAGTTT
1 TCGAGTTTGAGTTTAGGATTTAGGGTTTATATCGAGATT
*
5677296 TAG-GTTTGAGTTT
1 TCGAGTTTGAGTTT
5677309 CATATTTTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 32 0.70
39 14 0.30
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.48
Consensus pattern (39 bp):
TCGAGTTTGAGTTTAGGATTTAGGGTTTATATCGAGATT
Found at i:5679373 original size:36 final size:36
Alignment explanation
Indices: 5679322--5679437 Score: 112
Period size: 36 Copynumber: 3.3 Consensus size: 36
5679312 AGATCATTCG
*
5679322 TGTGCCTAGCACTAGTCGAACAAATCGACAAATTAT
1 TGTGCCCAGCACTAGTCGAACAAATCGACAAATTAT
* * * * *
5679358 TGTGCCCAGCGCTAGTCGGA-TAACCAAC-AA-TAGT
1 TGTGCCCAGCACTAGTCGAACAAATCGACAAATTA-T
* * *
5679392 TGTGCCCAGCACTAGTCGAACGAATTGAGAAATTAT
1 TGTGCCCAGCACTAGTCGAACAAATCGACAAATTAT
*
5679428 TGCGCCCAGC
1 TGTGCCCAGC
5679438 TTTGGTCGAT
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
33 2 0.03
34 21 0.34
35 8 0.13
36 29 0.47
37 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (36 bp):
TGTGCCCAGCACTAGTCGAACAAATCGACAAATTAT
Found at i:5679477 original size:69 final size:70
Alignment explanation
Indices: 5679322--5679477 Score: 215
Period size: 70 Copynumber: 2.2 Consensus size: 70
5679312 AGATCATTCG
* *
5679322 TGTGCCTAGCACTAGTCGAACAAATCGACAAATTATTGTGCCCAGCGCTAGTCGGATAACCAACA
1 TGTGCCCAGCACTAGTCGAACAAATCGACAAATTATTGCGCCCAGCGCTAGTCGGATAACCAACA
5679387 ATAGT
66 ATAGT
* * * ** * * *
5679392 TGTGCCCAGCACTAGTCGAACGAATTGAGAAATTATTGCGCCCAGCTTTGGTC-GATAACCAGCG
1 TGTGCCCAGCACTAGTCGAACAAATCGACAAATTATTGCGCCCAGCGCTAGTCGGATAACCAACA
5679456 ATAGT
66 ATAGT
5679461 TGTGCCCAGCACTAGTC
1 TGTGCCCAGCACTAGTC
5679478 AAATAAACTG
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
69 31 0.41
70 45 0.59
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (70 bp):
TGTGCCCAGCACTAGTCGAACAAATCGACAAATTATTGCGCCCAGCGCTAGTCGGATAACCAACA
ATAGT
Found at i:5694143 original size:59 final size:60
Alignment explanation
Indices: 5694029--5694166 Score: 147
Period size: 59 Copynumber: 2.3 Consensus size: 60
5694019 TTTTTATTCG
* * * *
5694029 AATTTGATACCTAAATTTTGTTGGACCCAATTTGGTATCTAAAATTTACACTTTTT-CTT
1 AATTTGGTACCTAAATTTTGTTGGACCCAATTTGGTACCTAAAATTGACACTTTTTCCCT
* * * *
5694088 AATTTGGTACCTAAACTTTTTTTGG-CTCAATTTGGTACCT-GAATGTGACATTTTTTCCCCT
1 AATTTGGTACCTAAA-TTTTGTTGGACCCAATTTGGTACCTAAAAT-TGACACTTTTT-CCCT
*
5694149 AATTTGGTACGTAAATTT
1 AATTTGGTACCTAAATTT
5694167 ATTAAATGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
58 3 0.05
59 36 0.55
60 11 0.17
61 16 0.24
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (60 bp):
AATTTGGTACCTAAATTTTGTTGGACCCAATTTGGTACCTAAAATTGACACTTTTTCCCT
Found at i:5694644 original size:31 final size:31
Alignment explanation
Indices: 5694609--5694769 Score: 125
Period size: 31 Copynumber: 5.3 Consensus size: 31
5694599 AAGGATTAAA
* *
5694609 TACCAACTTAAGAAAAAATGACAAGTTTAGG
1 TACCAAATTAAGAAAAAATGTCAAGTTTAGG
* *
5694640 TACCAAATT-AGCAAAAAGTGTCAAGTTTAAG
1 TACCAAATTAAG-AAAAAATGTCAAGTTTAGG
* * *
5694671 TATCAAATTAGGAAAAAAGTGTCAAGTTTAGA
1 TACCAAATTAAGAAAAAA-TGTCAAGTTTAGG
* ***
5694703 TACCAAATT-GGGCCAAA---CAAAGTTTAGG
1 TACCAAATTAAGAAAAAATGTC-AAGTTTAGG
* * *
5694731 TACCAAATTATGAAAAAGTGTCAAATTTAGG
1 TACCAAATTAAGAAAAAATGTCAAGTTTAGG
*
5694762 CACCAAAT
1 TACCAAAT
5694770 GTTATATTAA
Statistics
Matches: 101, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
27 1 0.01
28 17 0.17
29 3 0.03
30 2 0.02
31 57 0.56
32 21 0.21
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (31 bp):
TACCAAATTAAGAAAAAATGTCAAGTTTAGG
Found at i:5700801 original size:20 final size:21
Alignment explanation
Indices: 5700755--5700807 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
5700745 TACTAATTAC
5700755 AAATATTTAATAATTATATTT
1 AAATATTTAATAATTATATTT
5700776 AAATATTTAA-AA-TATAGTTT
1 AAATATTTAATAATTATA-TTT
*
5700796 ATATATTCTAAT
1 AAATATT-TAAT
5700808 TAAATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.14
20 11 0.39
21 13 0.46
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATATTTAATAATTATATTT
Found at i:5701092 original size:13 final size:13
Alignment explanation
Indices: 5701053--5701101 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
5701043 AAAACCAAAT
5701053 TTTTTAAAAGCAC
1 TTTTTAAAAGCAC
* *
5701066 TTTTTCACAGCAC
1 TTTTTAAAAGCAC
*
5701079 TTTTTAAAAACAC
1 TTTTTAAAAGCAC
*
5701092 TTTTCAAAAG
1 TTTTTAAAAG
5701102 TATTGCCAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (13 bp):
TTTTTAAAAGCAC
Found at i:5706912 original size:3 final size:3
Alignment explanation
Indices: 5706904--5706931 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5706894 GCTAAAATTT
5706904 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5706932 AAGCAGATTG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5709271 original size:47 final size:47
Alignment explanation
Indices: 5709202--5709295 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
5709192 ACTCTTTAAT
5709202 GAGTTTGAATCATGATTTCTAGTAAAATTTTTAGTTTAATTTGGTAA
1 GAGTTTGAATCATGATTTCTAGTAAAATTTTTAGTTTAATTTGGTAA
5709249 GAGTTTGAATCATGATTTCTAGTAAAATTTTTAGTTTAATTTGGTAA
1 GAGTTTGAATCATGATTTCTAGTAAAATTTTTAGTTTAATTTGGTAA
5709296 ACTAATATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (47 bp):
GAGTTTGAATCATGATTTCTAGTAAAATTTTTAGTTTAATTTGGTAA
Found at i:5709444 original size:64 final size:64
Alignment explanation
Indices: 5709315--5709445 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 64
5709305 AATTTGTGTC
* * * * ** *
5709315 TAAATATTAATTTGGTAAAAAAAATAAAGTTTAATAATTGTAATATCTAAGTATGAATGATATT
1 TAAATATTAATTAGGTAAAAAAAATAAACTTAAATAATTATAATATCTAAGTACAAATGACATT
5709379 TAAATATTAATTAGGT-AAAAAAATAAACTTAAATAATTATAATATCTAA-TACAAATTGAACAT
1 TAAATATTAATTAGGTAAAAAAAATAAACTTAAATAATTATAATATCTAAGTACAAA-TG-ACAT
5709442 T
64 T
5709443 TAA
1 TAA
5709446 CTTATTTTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 4 0.07
63 32 0.55
64 22 0.38
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.37
Consensus pattern (64 bp):
TAAATATTAATTAGGTAAAAAAAATAAACTTAAATAATTATAATATCTAAGTACAAATGACATT
Found at i:5713277 original size:22 final size:19
Alignment explanation
Indices: 5713235--5713278 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
5713225 TTTTTATCAT
*
5713235 ATTATTTATAATTTTTTTA
1 ATTATTTATAATTTTTGTA
5713254 ATTATTTAATAATATTTTAGTA
1 ATTATTT-ATAAT-TTTT-GTA
5713276 ATT
1 ATT
5713279 TTTTCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 4 0.19
22 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTATTTATAATTTTTGTA
Found at i:5715247 original size:21 final size:22
Alignment explanation
Indices: 5715206--5715248 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5715196 ATACATTTAT
* *
5715206 AATAATATTTTTATTTATTAAA
1 AATAATATTTTAAATTATTAAA
5715228 AATAATATTTTAAATT-TTAAA
1 AATAATATTTTAAATTATTAAA
5715249 TTAAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATAATATTTTAAATTATTAAA
Found at i:5720071 original size:24 final size:25
Alignment explanation
Indices: 5720024--5720071 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5720014 ATAGCCCTCT
* *
5720024 CGAGCTTCCCGTTATATAGTTCTTG
1 CGAGCTTCCCATTATATAGCTCTTG
*
5720049 CGAGCTTCCTATTA-ATAGCTCTT
1 CGAGCTTCCCATTATATAGCTCTT
5720072 CGGAGCATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.40
Consensus pattern (25 bp):
CGAGCTTCCCATTATATAGCTCTTG
Found at i:5730672 original size:13 final size:13
Alignment explanation
Indices: 5730654--5730679 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5730644 AGAATGAAAG
5730654 AATAAAGAAAAAA
1 AATAAAGAAAAAA
5730667 AATAAAGAAAAAA
1 AATAAAGAAAAAA
5730680 TAACTAGTGA
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:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
AATAAAGAAAAAA
Found at i:5734498 original size:136 final size:129
Alignment explanation
Indices: 5734314--5734666 Score: 454
Period size: 122 Copynumber: 2.7 Consensus size: 129
5734304 CTTAAGAATT
* *
5734314 TTTTTTTTTCCTTTTTGCCAAAGGTA-TTAAGTGTTCTAATATATATCTATCACTACAAATAACC
1 TTTTTTTTTCCTTTTTGCCAAAGGTATTTAAGAGTTCTAATAAATATCTATCACTACAAATAACC
*
5734378 ATTCAATTAAAAAAAATCAGTTTTTTAATCAGTTTTTAGTTTTAATTTATTTATAAAATCTTTTT
66 ATTCAATTAAAAAAAATCA--TTTTT-A-C--TTTTTAGTTTTAATTTATTTATAAAATCTTTTA
5734443 TAAGA
125 TAAGA
* * *
5734448 TTTTTTTTTCCCTTTTTGCCAAAAGTATTTAAGACTTTTAATAAATATCTATCACTACAAATAAC
1 TTTTTTTTT-CCTTTTTGCCAAAGGTATTTAAGAGTTCTAATAAATATCTATCACTACAAATAAC
**
5734513 CATTCAATGCAAAAAAATC------ACTTTTTAGTTTTAATTTATTTATAAAATCTTTTATAAGA
65 CATTCAATTAAAAAAAATCATTTTTACTTTTTAGTTTTAATTTATTTATAAAATCTTTTATAAGA
* * *
5734572 -TTCTTTTTCCTTTTTGCCAAAGGTATTTAAGAG-TCGCAATAAATATCTATCACCACAAATAAC
1 TTTTTTTTTCCTTTTTGCCAAAGGTATTTAAGAGTTC-TAATAAATATCTATCACTACAAATAAC
*
5734635 CATTCAATTAAAAAAAATCACTTTTTAGTTTT
65 CATTCAATTAAAAAAAATCA-TTTTTACTTTT
5734667 AATTTCTTTA
Statistics
Matches: 192, Mismatches: 17, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
121 1 0.01
122 65 0.34
123 7 0.04
124 37 0.19
126 1 0.01
127 1 0.01
129 5 0.03
134 9 0.05
135 16 0.08
136 50 0.26
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (129 bp):
TTTTTTTTTCCTTTTTGCCAAAGGTATTTAAGAGTTCTAATAAATATCTATCACTACAAATAACC
ATTCAATTAAAAAAAATCATTTTTACTTTTTAGTTTTAATTTATTTATAAAATCTTTTATAAGA
Found at i:5735698 original size:27 final size:27
Alignment explanation
Indices: 5735668--5735743 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
5735658 AGGGGGTGTG
*
5735668 GTGCCTATTTAATAGGCGGCATTGGTT
1 GTGCCTATTTGATAGGCGGCATTGGTT
*
5735695 GTGCCTATCTGATAGGCGGCATTGGTT
1 GTGCCTATTTGATAGGCGGCATTGGTT
* * *
5735722 ATGCTTATTTGATAGGCAGCAT
1 GTGCCTATTTGATAGGCGGCAT
5735744 ACCTAGTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.36
Consensus pattern (27 bp):
GTGCCTATTTGATAGGCGGCATTGGTT
Found at i:5735858 original size:17 final size:18
Alignment explanation
Indices: 5735824--5735860 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5735814 AGAGAAGGAG
*
5735824 AAGAGAAGAAAGAAAGAA
1 AAGAGAAGAAAAAAAGAA
5735842 AAGAGAA-AAAAAAAGAA
1 AAGAGAAGAAAAAAAGAA
5735859 AA
1 AA
5735861 TGTATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AAGAGAAGAAAAAAAGAA
Found at i:5735957 original size:25 final size:23
Alignment explanation
Indices: 5735923--5735968 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
5735913 AAAATTATTT
5735923 TGTTAGTTTTATGTAGTTTGTTTAG
1 TGTTAGTTTTATGT--TTTGTTTAG
*
5735948 TGTTATTTTTATGTTTTGTTT
1 TGTTAGTTTTATGTTTTGTTT
5735969 TAAAGTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
25 13 0.65
ACGTcount: A:0.13, C:0.00, G:0.20, T:0.67
Consensus pattern (23 bp):
TGTTAGTTTTATGTTTTGTTTAG
Found at i:5735970 original size:24 final size:24
Alignment explanation
Indices: 5735923--5735980 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
5735913 AAAATTATTT
* *
5735923 TGTTAGTTTTATGTAGTTTGTTTAG
1 TGTTATTTTTATGTA-TTTGTTTAA
5735948 TGTTATTTTTATGT-TTTGTTTTAA
1 TGTTATTTTTATGTATTTG-TTTAA
*
5735972 AGTTATTTT
1 TGTTATTTT
5735981 ATTTATTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.14
24 12 0.41
25 13 0.45
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (24 bp):
TGTTATTTTTATGTATTTGTTTAA
Found at i:5737879 original size:18 final size:18
Alignment explanation
Indices: 5737856--5737904 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
5737846 TAACAGTCAG
*
5737856 TTATTCAGAAACGATAAA
1 TTATTCAGAAACAATAAA
* *
5737874 TTATTCAGAAATAATCAA
1 TTATTCAGAAACAATAAA
*
5737892 TTATTCAGTAACA
1 TTATTCAGAAACA
5737905 TTTTTTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (18 bp):
TTATTCAGAAACAATAAA
Found at i:5737968 original size:18 final size:18
Alignment explanation
Indices: 5737916--5737974 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
5737906 TTTTTTTAAG
*
5737916 CAGTAGCAGTCAGTTATC
1 CAGTAGCAGTCAGTTATT
*
5737934 CAGTAACAGTCAGTTATT
1 CAGTAGCAGTCAGTTATT
* *
5737952 CAGTAGCAGTTAATTATT
1 CAGTAGCAGTCAGTTATT
5737970 CAGTA
1 CAGTA
5737975 CCTTTATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (18 bp):
CAGTAGCAGTCAGTTATT
Found at i:5738109 original size:18 final size:18
Alignment explanation
Indices: 5738082--5738120 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5738072 GGAATATACC
*
5738082 GTAATGGTAACAATAACA
1 GTAATAGTAACAATAACA
*
5738100 GTAATAGTAACAGTAACA
1 GTAATAGTAACAATAACA
5738118 GTA
1 GTA
5738121 GTGGTACACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (18 bp):
GTAATAGTAACAATAACA
Found at i:5742666 original size:10 final size:10
Alignment explanation
Indices: 5742641--5742669 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
5742631 AAAATATAAA
5742641 AATTTTCAAT
1 AATTTTCAAT
5742651 AA-TTTCAAT
1 AATTTTCAAT
5742660 AATTTTCAAT
1 AATTTTCAAT
5742670 TTAATCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (10 bp):
AATTTTCAAT
Found at i:5744294 original size:45 final size:45
Alignment explanation
Indices: 5744220--5744504 Score: 349
Period size: 45 Copynumber: 6.3 Consensus size: 45
5744210 ATCAGTAATA
* * * *
5744220 GTAATAGTAACGGTAACAGTATTCAACACACAAAGTGCTGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCTGAATCG
* *
5744265 GTAACGGTAACAGTAACAATATTCGACACACAAAGTG-TCGCATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCT-GAATCG
* * * *
5744310 GTAACGGTAACAGTAACAATATTTGACACACAAAGCGCCGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCTGAATCG
* * * * * * *
5744355 GTAACAATATCAGTAACAATATTCGAGACATAAAGTGCAGACTTG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCTGAATCG
* *
5744400 GTAACGGTAATAGTAACAATATTCGACACACAAAGTG-TCGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCT-GAATCG
*
5744445 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCTGAATCG
*
5744490 GTAACAGTAGCAGTA
1 GTAACAGTAACAGTA
5744505 GTGGTAACAG
Statistics
Matches: 203, Mismatches: 33, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
44 1 0.00
45 202 1.00
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCTGAATCG
Found at i:5744403 original size:135 final size:135
Alignment explanation
Indices: 5744232--5744504 Score: 420
Period size: 135 Copynumber: 2.0 Consensus size: 135
5744222 AATAGTAACG
* *
5744232 GTAACAGTATTCAACACACAAAGTGCTGAATCGGTAACGGTAACAGTAACAATATTCGACACACA
1 GTAACAATATTCAACACACAAAGTGCAGAATCGGTAACGGTAACAGTAACAATATTCGACACACA
* * *
5744297 AAGTGTCGCATCGGTAACGGTAACAGTAACAATATTTGACACACAAAGCGCCGAATCGGTAACAA
66 AAGTGTCGAATCGGTAACAGTAACAGTAACAATATTCGACACACAAAGCGCCGAATCGGTAACAA
*
5744362 TATCA
131 TAGCA
* * * * * *
5744367 GTAACAATATTCGAGACATAAAGTGCAGACTTGGTAACGGTAATAGTAACAATATTCGACACACA
1 GTAACAATATTCAACACACAAAGTGCAGAATCGGTAACGGTAACAGTAACAATATTCGACACACA
* *
5744432 AAGTGTCGAATCGGTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACAG
66 AAGTGTCGAATCGGTAACAGTAACAGTAACAATATTCGACACACAAAGCGCCGAATCGGTAACAA
5744497 TAGCA
131 TAGCA
5744502 GTA
1 GTA
5744505 GTGGTAACAG
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
135 124 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (135 bp):
GTAACAATATTCAACACACAAAGTGCAGAATCGGTAACGGTAACAGTAACAATATTCGACACACA
AAGTGTCGAATCGGTAACAGTAACAGTAACAATATTCGACACACAAAGCGCCGAATCGGTAACAA
TAGCA
Found at i:5745780 original size:20 final size:19
Alignment explanation
Indices: 5745744--5745782 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5745734 CTTTAGGATT
*
5745744 TATTTTTTTTTCCTTCTTC
1 TATTTTTTATTCCTTCTTC
5745763 TATTTTTTATT-CTT-TTC
1 TATTTTTTATTCCTTCTTC
5745780 TAT
1 TAT
5745783 CCTTCTCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 10 0.53
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTTATTCCTTCTTC
Found at i:5748380 original size:21 final size:21
Alignment explanation
Indices: 5748356--5748398 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5748346 AATTAATCAT
* * *
5748356 AATTCCATTCCATTCAATTTC
1 AATTCAATTCAATTCAAATTC
5748377 AATTCAATTCAATTCAAATTC
1 AATTCAATTCAATTCAAATTC
5748398 A
1 A
5748399 CTTTTCCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTCAATTCAATTCAAATTC
Found at i:5748382 original size:5 final size:5
Alignment explanation
Indices: 5748356--5748398 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
5748346 AATTAATCAT
* *
5748356 AATTC CATTC CATTC AATTTC AATTC AATTC AATTC AAATTC A
1 AATTC AATTC AATTC AA-TTC AATTC AATTC AATTC -AATTC A
5748399 CTTTTCCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 24 0.71
6 10 0.29
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTC
Found at i:5748383 original size:11 final size:10
Alignment explanation
Indices: 5748356--5748398 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
5748346 AATTAATCAT
*
5748356 AATTCCATTC
1 AATTCAATTC
*
5748366 CATTCAATTTC
1 AATTCAA-TTC
5748377 AATTCAATTC
1 AATTCAATTC
5748387 AATTCAAATTC
1 AATTC-AATTC
5748398 A
1 A
5748399 CTTTTCCACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 13 0.46
11 15 0.54
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTCAATTC
Found at i:5748398 original size:16 final size:16
Alignment explanation
Indices: 5748341--5748390 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
5748331 ACCAATACAC
5748341 ATTTCAATT-AA-TCA
1 ATTTCAATTCAATTCA
* * *
5748355 TAATTCCATTCCATTCA
1 -ATTTCAATTCAATTCA
5748372 ATTTCAATTCAATTCA
1 ATTTCAATTCAATTCA
5748388 ATT
1 ATT
5748391 CAAATTCACT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 7 0.26
16 17 0.63
17 3 0.11
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTCAATTCAATTCA
Found at i:5748800 original size:17 final size:18
Alignment explanation
Indices: 5748764--5748801 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5748754 ATCAATTGAC
**
5748764 ATTTTAATTTCAATTTCA
1 ATTTTAATTTCAATAACA
5748782 ATTTTAA-TTCAATAACA
1 ATTTTAATTTCAATAACA
5748799 ATT
1 ATT
5748802 CACTTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTAATTTCAATAACA
Found at i:5753532 original size:42 final size:40
Alignment explanation
Indices: 5753462--5753656 Score: 160
Period size: 42 Copynumber: 4.7 Consensus size: 40
5753452 GCAAAATGAA
* * * *
5753462 TAAAAATACCCAATAAAAGAAAATAATAAGAGAATAGTTT
1 TAAAAAAACCTAAAAAAATAAAATAATAAGAGAATAGTTT
5753502 TAAATATAAACCTAAAAAAATAAAATAATAAGAGAATAGTTT
1 TAAA-A-AAACCTAAAAAAATAAAATAATAAGAGAATAGTTT
* * * * * * **
5753544 TAAAAAGGA-GTAATAAAAGTAAAAACAATAA-AGAAAAATGAA
1 TAAAAA-AACCTAA-AAAAAT-AAAATAATAAGAGAATAGT-TT
* * *
5753586 TAAAAATACCCAAAAAAAGAAAATAATAAGAGAATAGTTT
1 TAAAAAAACCTAAAAAAATAAAATAATAAGAGAATAGTTT
5753626 TAAATATAAACCTAAAAAAAATAAAATAATA
1 TAAA-A-AAACCT-AAAAAAATAAAATAATA
5753657 CAAAATAAGC
Statistics
Matches: 119, Mismatches: 25, Indels: 19
0.73 0.15 0.12
Matches are distributed among these distances:
40 21 0.18
41 26 0.22
42 56 0.47
43 16 0.13
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.21
Consensus pattern (40 bp):
TAAAAAAACCTAAAAAAATAAAATAATAAGAGAATAGTTT
Found at i:5753555 original size:124 final size:125
Alignment explanation
Indices: 5753420--5753656 Score: 440
Period size: 124 Copynumber: 1.9 Consensus size: 125
5753410 TAAGCACATA
* * *
5753420 TAAAAAGGAGTAATAAAAGTAAAAATAATAAAGCAAAATGAATAAAAATACCCAATAAAAGAAAA
1 TAAAAAGGAGTAATAAAAGTAAAAACAATAAAGAAAAATGAATAAAAATACCCAAAAAAAGAAAA
5753485 TAATAAGAGAATAGTTTTAAATATAAACCT-AAAAAAATAAAATAATAAGAGAATAGTTT
66 TAATAAGAGAATAGTTTTAAATATAAACCTAAAAAAAATAAAATAATAAGAGAATAGTTT
5753544 TAAAAAGGAGTAATAAAAGTAAAAACAATAAAGAAAAATGAATAAAAATACCCAAAAAAAGAAAA
1 TAAAAAGGAGTAATAAAAGTAAAAACAATAAAGAAAAATGAATAAAAATACCCAAAAAAAGAAAA
5753609 TAATAAGAGAATAGTTTTAAATATAAACCTAAAAAAAATAAAATAATA
66 TAATAAGAGAATAGTTTTAAATATAAACCTAAAAAAAATAAAATAATA
5753657 CAAAATAAGC
Statistics
Matches: 109, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
124 92 0.84
125 17 0.16
ACGTcount: A:0.65, C:0.05, G:0.10, T:0.20
Consensus pattern (125 bp):
TAAAAAGGAGTAATAAAAGTAAAAACAATAAAGAAAAATGAATAAAAATACCCAAAAAAAGAAAA
TAATAAGAGAATAGTTTTAAATATAAACCTAAAAAAAATAAAATAATAAGAGAATAGTTT
Found at i:5756586 original size:23 final size:23
Alignment explanation
Indices: 5756558--5756602 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
5756548 TAGTGGAAAG
5756558 AAAGTGTCCTTAATTAAATTGGA
1 AAAGTGTCCTTAATTAAATTGGA
5756581 AAAGTGTCCTTAATTAAATTGG
1 AAAGTGTCCTTAATTAAATTGG
5756603 TCTATTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (23 bp):
AAAGTGTCCTTAATTAAATTGGA
Found at i:5758538 original size:24 final size:23
Alignment explanation
Indices: 5758417--5758565 Score: 68
Period size: 22 Copynumber: 6.6 Consensus size: 23
5758407 ATAGTATTTG
5758417 AAATATATACATAAA-ATA-GTAA
1 AAATATATACATAAATATATG-AA
* *
5758439 AAATATATA-ACT-AGTA-ATGTTA
1 AAATATATACA-TAAATATATG-AA
*
5758461 AAATATATACAT-AATA-AT-AT
1 AAATATATACATAAATATATGAA
* * *
5758481 ATATA-AAAAATAAATAT-TGAA
1 AAATATATACATAAATATATGAA
*
5758502 AAATGTATGTACATAACATATATGAA
1 AAA--TATATACATAA-ATATATGAA
*
5758528 AAATATATACAT-AATATAGTAGTA
1 AAATATATACATAAATATA-T-GAA
*
5758552 AAATATTTACATAA
1 AAATATATACATAA
5758566 TGTGTACATA
Statistics
Matches: 96, Mismatches: 16, Indels: 27
0.69 0.12 0.19
Matches are distributed among these distances:
19 4 0.04
20 9 0.09
21 6 0.06
22 34 0.35
23 5 0.05
24 26 0.27
25 5 0.05
26 7 0.07
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.32
Consensus pattern (23 bp):
AAATATATACATAAATATATGAA
Found at i:5758740 original size:12 final size:11
Alignment explanation
Indices: 5758725--5758835 Score: 55
Period size: 12 Copynumber: 9.4 Consensus size: 11
5758715 CAATAGTGAA
5758725 AATAATAAGTAT
1 AATAATAA-TAT
*
5758737 AATAATAAACAT
1 AATAAT-AATAT
* *
5758749 AATGATATATAA
1 AATAATA-ATAT
*
5758761 AATAATACTAT
1 AATAATAATAT
*
5758772 ATATAAAAAGTAT
1 A-ATAATAA-TAT
*
5758785 ATATATACAAGTAT
1 A-ATA-ATAA-TAT
5758799 AATAA-AATAT
1 AATAATAATAT
*
5758809 -ATACTAATATT
1 AATAATAATA-T
5758820 AATAATAAATAT
1 AATAAT-AATAT
5758832 AATA
1 AATA
5758836 GGGTAAAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
9 3 0.04
10 7 0.09
11 7 0.09
12 36 0.46
13 17 0.22
14 8 0.10
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (11 bp):
AATAATAATAT
Found at i:5758787 original size:15 final size:17
Alignment explanation
Indices: 5758753--5758791 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5758743 AAACATAATG
5758753 ATATATAAAATAATACT
1 ATATATAAAATAATACT
*
5758770 ATATATAAAA-AGTA-T
1 ATATATAAAATAATACT
5758785 ATATATA
1 ATATATA
5758792 CAAGTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 3 0.14
17 10 0.48
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
ATATATAAAATAATACT
Found at i:5758824 original size:21 final size:21
Alignment explanation
Indices: 5758785--5758832 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5758775 TAAAAAGTAT
5758785 ATATATACAAGTATAATAA-A
1 ATATATACAAGTATAATAATA
5758805 ATATATACTAA-TATTAATAATA
1 ATATATAC-AAGTA-TAATAATA
5758827 A-ATATA
1 ATATATA
5758833 ATAGGGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 10 0.40
21 13 0.52
22 2 0.08
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
ATATATACAAGTATAATAATA
Found at i:5758995 original size:14 final size:14
Alignment explanation
Indices: 5758972--5759009 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
5758962 TTAATAATGC
5758972 TACATAAATAGATATA
1 TACAT-AATAG-TATA
5758988 TA-ATAATAGTATA
1 TACATAATAGTATA
5759001 TACATAATA
1 TACATAATA
5759010 TAGTTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 11 0.52
15 2 0.10
16 2 0.10
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (14 bp):
TACATAATAGTATA
Found at i:5759005 original size:29 final size:28
Alignment explanation
Indices: 5758972--5759078 Score: 76
Period size: 31 Copynumber: 3.7 Consensus size: 28
5758962 TTAATAATGC
*
5758972 TACATAA-ATAGATATATAATAATAGTATA
1 TACATAATATAGATAT-TAAAAATA-TATA
*
5759001 TACATAATATAGTTATTAAAAATATATA
1 TACATAATATAGATATTAAAAATATATA
* * * *
5759029 TGTAAGATAATAT-GAAAAATAAAAAAATATA
1 --T-ACATAATATAG-ATATTAAAAATATATA
*
5759060 TAAATAATATAG-TATTAAA
1 TACATAATATAGATATTAAA
5759079 GATGTATACA
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
27 5 0.08
28 12 0.19
29 16 0.26
30 9 0.15
31 20 0.32
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.34
Consensus pattern (28 bp):
TACATAATATAGATATTAAAAATATATA
Found at i:5759122 original size:25 final size:24
Alignment explanation
Indices: 5759093--5759164 Score: 67
Period size: 28 Copynumber: 2.9 Consensus size: 24
5759083 TATACATAAC
*
5759093 ATATAAAAATATAATATTAAATGAT
1 ATATAATAATATAATATTAAATG-T
*
5759118 ATATATATGTAATAT-ATATAAAAATGT
1 ATATA-A--TAATATAATAT-TAAATGT
5759145 ATAT-ATAATATAATATTAAA
1 ATATAATAATATAATATTAAA
5759165 AATATTTACA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
23 9 0.23
24 4 0.10
25 6 0.15
26 1 0.03
27 9 0.23
28 10 0.26
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (24 bp):
ATATAATAATATAATATTAAATGT
Found at i:5759135 original size:38 final size:35
Alignment explanation
Indices: 5759054--5759140 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 35
5759044 AAAATAAAAA
* *
5759054 AATATATAAATAATATAGTATTAAAGATGTATACAT
1 AATATATAAA-AATATAATATTAAAGATATATACAT
* *
5759090 AACATATAAAAATATAATATTAAATGATATATATATGT
1 AATATATAAAAATATAATATTAAA-GATATATACA--T
5759128 AATATATATAAAA
1 AATATATA-AAAA
5759141 ATGTATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
35 13 0.31
36 17 0.40
38 8 0.19
39 4 0.10
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (35 bp):
AATATATAAAAATATAATATTAAAGATATATACAT
Found at i:5759165 original size:25 final size:25
Alignment explanation
Indices: 5759100--5759169 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 25
5759090 AACATATAAA
*
5759100 AATATAATATTAAATGATATATATATGT
1 AATATAATATTAAA--A-ATATATATAT
*
5759128 AATAT-ATA-TAAAAATGTATATAT
1 AATATAATATTAAAAATATATATAT
5759151 AATATAATATTAAAAATAT
1 AATATAATATTAAAAATAT
5759170 TTACATAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 13 0.35
24 4 0.11
25 8 0.22
26 4 0.11
27 3 0.08
28 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (25 bp):
AATATAATATTAAAAATATATATAT
Found at i:5759516 original size:23 final size:24
Alignment explanation
Indices: 5759446--5759526 Score: 80
Period size: 23 Copynumber: 3.4 Consensus size: 24
5759436 AAACAATTAT
*
5759446 TAATA-ATATTACATAAATATATACA
1 TAATATATATTA-A-AAGTATATACA
*
5759471 T-ATATATATT-AAAGATAAATACA
1 TAATATATATTAAAAG-TATATACA
*
5759494 TAATA-ATATTAAAAGTATGTACA
1 TAATATATATTAAAAGTATATACA
5759517 TAATATATAT
1 TAATATATAT
5759527 ACATAATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
22 2 0.04
23 25 0.53
24 14 0.30
25 6 0.13
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (24 bp):
TAATATATATTAAAAGTATATACA
Found at i:5759517 original size:58 final size:57
Alignment explanation
Indices: 5759443--5759556 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 57
5759433 AAAAAACAAT
5759443 TATTAATAATATTACATAA-ATATATACATATATATATTAAAGATAAATACATAATAA
1 TATTAATAATATTACATAATATATATACATA-ATATATTAAAGATAAATACATAATAA
**
5759500 TATTAA-AAGTATGTACATAATATATATACATAATATATTAAAGATATGTACATAATA
1 TATTAATAA-TAT-TACATAATATATATACATAATATATTAAAGATAAATACATAATA
5759557 TAATAAATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
56 2 0.04
57 9 0.17
58 30 0.58
59 11 0.21
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (57 bp):
TATTAATAATATTACATAATATATATACATAATATATTAAAGATAAATACATAATAA
Found at i:5759531 original size:13 final size:13
Alignment explanation
Indices: 5759446--5759537 Score: 58
Period size: 13 Copynumber: 7.6 Consensus size: 13
5759436 AAACAATTAT
5759446 TAATA-ATATTACA
1 TAATATATA-TACA
5759459 TAA-ATATATACA
1 TAATATATATACA
*
5759471 T-ATATATAT-TA
1 TAATATATATACA
* *
5759482 -AAGATAAATACA
1 TAATATATATACA
5759494 TAATA-ATATTA-A
1 TAATATATA-TACA
* *
5759506 -AA-GTATGTACA
1 TAATATATATACA
5759517 TAATATATATACA
1 TAATATATATACA
5759530 TAATATAT
1 TAATATAT
5759538 TAAAGATATG
Statistics
Matches: 59, Mismatches: 10, Indels: 20
0.66 0.11 0.22
Matches are distributed among these distances:
10 2 0.03
11 13 0.22
12 18 0.31
13 26 0.44
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.37
Consensus pattern (13 bp):
TAATATATATACA
Found at i:5759546 original size:22 final size:22
Alignment explanation
Indices: 5759521--5759612 Score: 89
Period size: 22 Copynumber: 4.2 Consensus size: 22
5759511 TGTACATAAT
*
5759521 ATATATACATAATATATTAAAG
1 ATATATACATAATATATTAAAA
* * *
5759543 ATATGTACATAATATAATAAAT
1 ATATATACATAATATATTAAAA
* ** *
5759565 ATATGA-ATATAGGATATAAAAA
1 ATAT-ATACATAATATATTAAAA
5759587 ATATATACATAATATA-TAAAA
1 ATATATACATAATATATTAAAA
5759608 ATATA
1 ATATA
5759613 ATATTTAAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
21 10 0.19
22 44 0.81
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (22 bp):
ATATATACATAATATATTAAAA
Found at i:5759548 original size:35 final size:36
Alignment explanation
Indices: 5759489--5759558 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
5759479 TTAAAGATAA
5759489 ATACATAATAATATTAAAAGTATGTACATAATATAT
1 ATACATAATAATATTAAAAGTATGTACATAATATAT
5759525 ATACATAAT-ATATT-AAAGATATGTACATAATATA
1 ATACATAATAATATTAAAAG-TATGTACATAATATA
5759559 ATAAATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 4 0.12
35 20 0.61
36 9 0.27
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (36 bp):
ATACATAATAATATTAAAAGTATGTACATAATATAT
Found at i:5759581 original size:35 final size:35
Alignment explanation
Indices: 5759495--5759573 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
5759485 ATAAATACAT
*
5759495 AATAATATTA-AAAG-TATGTACATAATATATATA
1 AATAATATAATAAAGATATGTACATAATATATATA
* *
5759528 CATAATATATTAAAGATATGTACATAATATA-ATA
1 AATAATATAATAAAGATATGTACATAATATATATA
5759562 AAT-ATATGAATA
1 AATAATAT-AATA
5759574 TAGGATATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
33 11 0.29
34 12 0.32
35 15 0.39
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35
Consensus pattern (35 bp):
AATAATATAATAAAGATATGTACATAATATATATA
Found at i:5759599 original size:39 final size:40
Alignment explanation
Indices: 5759556--5759639 Score: 93
Period size: 39 Copynumber: 2.1 Consensus size: 40
5759546 TGTACATAAT
** *
5759556 ATAATAAATATATGAATATAGGATAT-AAAAAAT-ATATAC
1 ATAAT-AATATAAAAATATAAGATATAAAAAAATAATATAC
* *
5759595 ATAAT-ATATAAAAATATAATATTTAAAAAAATAATATAC
1 ATAATAATATAAAAATATAAGATATAAAAAAATAATATAC
5759634 ATAATA
1 ATAATA
5759640 TAAGATTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
37 14 0.38
38 7 0.19
39 16 0.43
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (40 bp):
ATAATAATATAAAAATATAAGATATAAAAAAATAATATAC
Found at i:5759613 original size:15 final size:15
Alignment explanation
Indices: 5759595--5759632 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5759585 AAATATATAC
*
5759595 ATAATATATAAAAAT
1 ATAATATATAAAAAA
*
5759610 ATAATATTTAAAAAA
1 ATAATATATAAAAAA
5759625 ATAATATA
1 ATAATATA
5759633 CATAATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAATATATAAAAAA
Found at i:5759825 original size:24 final size:24
Alignment explanation
Indices: 5759774--5759827 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
5759764 GTATAATAAT
5759774 GATAA-AAAAATAATAATAGTGAAA
1 GATAATAAAAATAATAATAG-GAAA
*
5759798 -ATAATAAATATAATAATA-GAAA
1 GATAATAAAAATAATAATAGGAAA
5759820 CGATAATA
1 -GATAATA
5759828 CTATATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 18 0.69
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (24 bp):
GATAATAAAAATAATAATAGGAAA
Found at i:5759850 original size:22 final size:24
Alignment explanation
Indices: 5759825--5759869 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5759815 AGAAACGATA
*
5759825 ATAC-TATATAA-AAAGTATATAT
1 ATACATATATAATAAAATATATAT
5759847 ATACATATATAATAAAATATATA
1 ATACATATATAATAAAATATATA
5759870 CTAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 9 0.45
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (24 bp):
ATACATATATAATAAAATATATAT
Found at i:5759869 original size:26 final size:25
Alignment explanation
Indices: 5759832--5759917 Score: 65
Period size: 28 Copynumber: 3.4 Consensus size: 25
5759822 ATAATACTAT
5759832 ATAAAA-AGTATATATATACATATATA
1 ATAAAATA-TATATATATACATA-ATA
5759858 ATAAAATATATACTAATATTA-ATAATGA
1 ATAAAATATATA-T-ATA-TACATAAT-A
*
5759886 ATATAATAT-TATA-ATAC-TAATA
1 ATAAAATATATATATATACATAATA
5759908 ATAACAATAT
1 ATAA-AATAT
5759918 GAAATTAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
22 4 0.08
23 11 0.22
24 1 0.02
25 1 0.02
26 11 0.22
27 6 0.12
28 15 0.29
29 2 0.04
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (25 bp):
ATAAAATATATATATATACATAATA
Found at i:5759876 original size:20 final size:21
Alignment explanation
Indices: 5759843--5759882 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5759833 TAAAAAGTAT
5759843 ATATATACATATA-TAATAAA
1 ATATATACATATATTAATAAA
5759863 ATATATAC-TAATATTAATAA
1 ATATATACAT-ATATTAATAA
5759883 TGAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 11 0.61
21 6 0.33
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATATACATATATTAATAAA
Done.