Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 18 of 19
Found at i:3776491 original size:28 final size:28
Alignment explanation
Indices: 3776451--3776506 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3776441 AAGATGGGGT
3776451 TTCTGATGCTTTGTCGTGTCATACATTG
1 TTCTGATGCTTTGTCGTGTCATACATTG
3776479 TTCTGATGCTTTGTCGTGTCATACATTG
1 TTCTGATGCTTTGTCGTGTCATACATTG
3776507 AAAGTTCTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.18, G:0.21, T:0.46
Consensus pattern (28 bp):
TTCTGATGCTTTGTCGTGTCATACATTG
Found at i:3776907 original size:26 final size:26
Alignment explanation
Indices: 3776878--3776929 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3776868 TAGCCAAAAA
3776878 GAAAGAATTTATTTCTCTTTTTCACT
1 GAAAGAATTTATTTCTCTTTTTCACT
3776904 GAAAGAATTTATTTCTCTTTTTCACT
1 GAAAGAATTTATTTCTCTTTTTCACT
3776930 TTCAACAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (26 bp):
GAAAGAATTTATTTCTCTTTTTCACT
Found at i:3778061 original size:16 final size:16
Alignment explanation
Indices: 3778042--3778075 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3778032 TTCATAAATT
*
3778042 TATAATATTTTAAAAA
1 TATAAAATTTTAAAAA
3778058 TATAAAATTTTAAAAA
1 TATAAAATTTTAAAAA
3778074 TA
1 TA
3778076 AATTATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAAAATTTTAAAAA
Found at i:3778695 original size:35 final size:31
Alignment explanation
Indices: 3778625--3778694 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 31
3778615 CGAATTTATC
*
3778625 AAAATTTATATAAAATCATAATTAACATAAA
1 AAAATTTATATAAAATAATAATTAACATAAA
3778656 AAAATTTATATAAATTTATAATATATTAAACATAAA
1 AAAATTTATATAAA---ATAATA-ATT-AACATAAA
3778692 AAA
1 AAA
3778695 TAACCTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
31 14 0.42
34 5 0.15
35 3 0.09
36 11 0.33
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATTTATATAAAATAATAATTAACATAAA
Found at i:3778861 original size:18 final size:19
Alignment explanation
Indices: 3778838--3778889 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
3778828 AATACATTGA
3778838 ATAAAACTAAAATAAA-AT-
1 ATAAAA-TAAAATAAACATG
*
3778856 ATAAAAATAATATAAACATG
1 AT-AAAATAAAATAAACATG
3778876 ATAAAA-AAAATAAA
1 ATAAAATAAAATAAA
3778890 TGTATCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 17 0.59
19 10 0.34
20 2 0.07
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
ATAAAATAAAATAAACATG
Found at i:3778974 original size:11 final size:11
Alignment explanation
Indices: 3778958--3778998 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
3778948 AACTTTGATC
3778958 ATATAAAAATA
1 ATATAAAAATA
*
3778969 ATATAAATATA
1 ATATAAAAATA
*
3778980 ACATAAAAATA
1 ATATAAAAATA
3778991 ATATAAAA
1 ATATAAAA
3778999 CGAGTACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:3779083 original size:26 final size:25
Alignment explanation
Indices: 3779044--3779135 Score: 91
Period size: 26 Copynumber: 3.5 Consensus size: 25
3779034 TATTAACTAC
3779044 TAAATATAT-AAATTTATAATATTT
1 TAAATATATAAAATTTATAATATTT
*
3779068 TAAATATATTAAAATTTAAAAATAAATTAT
1 TAAATATA-TAAAATTT-ATAAT--ATT-T
3779098 T-AATATATAAAATTTTTATAATATTT
1 TAAATATATAAAA--TTTATAATATTT
3779124 TAAA-ATATAAAA
1 TAAATATATAAAA
3779136 AAATAATATA
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
24 8 0.14
25 1 0.02
26 16 0.28
27 9 0.16
28 5 0.09
29 13 0.23
30 5 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TAAATATATAAAATTTATAATATTT
Found at i:3779100 original size:21 final size:22
Alignment explanation
Indices: 3779068--3779145 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 22
3779058 TATAATATTT
*
3779068 TAAATATATTAAAATTTAAAAA
1 TAAATATATTAAAATATAAAAA
* *
3779090 TAAAT-TATTAATATATAAAATTTT
1 TAAATATATTAAAATATAAAA---A
*
3779114 TATAATATTTTAAAATATAAAAA
1 TA-AATATATTAAAATATAAAAA
*
3779137 AATAATATA
1 TA-AATATA
3779146 ATCACAAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
21 13 0.30
22 5 0.12
23 7 0.16
24 2 0.05
25 3 0.07
26 13 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATATATTAAAATATAAAAA
Found at i:3779451 original size:13 final size:13
Alignment explanation
Indices: 3779403--3779459 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
3779393 TTTAGTTTTT
3779403 ATATTATAATTTA
1 ATATTATAATTTA
* *
3779416 AT-GTATAATTTG
1 ATATTATAATTTA
3779428 ATATTATAATTTA
1 ATATTATAATTTA
3779441 ATATT-TAAATTTA
1 ATATTAT-AATTTA
*
3779454 AAATTA
1 ATATTA
3779460 ATAAAATACG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
12 11 0.31
13 25 0.69
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (13 bp):
ATATTATAATTTA
Found at i:3780120 original size:28 final size:29
Alignment explanation
Indices: 3780054--3780121 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
3780044 TAATTAAAAT
*
3780054 TTTTAATATT-TATATCATATTTTAATTA
1 TTTTAATATTATATATCATATTATAATTA
*
3780082 TTTTTATATTATATA-CATA-TATAATTA
1 TTTTAATATTATATATCATATTATAATTA
3780109 TATTTAATATTAT
1 T-TTTAATATTAT
3780122 CAAATTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.23
28 23 0.66
29 4 0.11
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTAATATTATATATCATATTATAATTA
Found at i:3781525 original size:2 final size:2
Alignment explanation
Indices: 3781518--3781559 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3781508 ATCAAGAAGC
3781518 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3781560 AATGTGTGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3783769 original size:17 final size:18
Alignment explanation
Indices: 3783747--3783787 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
3783737 TTACAACCAC
3783747 AATATAAAATAAT-TAAA
1 AATATAAAATAATATAAA
*
3783764 AATATAATATAATATAAA
1 AATATAAAATAATATAAA
*
3783782 TATATA
1 AATATA
3783788 TTCTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATATAAAATAATATAAA
Found at i:3783819 original size:14 final size:13
Alignment explanation
Indices: 3783791--3783824 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
3783781 ATATATATTC
*
3783791 TAATATTAAATAT
1 TAATATTAAAAAT
3783804 TAATATATAAAAAT
1 TAATAT-TAAAAAT
3783818 TAATATT
1 TAATATT
3783825 TATAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATATTAAAAAT
Found at i:3785957 original size:20 final size:18
Alignment explanation
Indices: 3785905--3785954 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
3785895 TATTTTTTAA
3785905 TATTTTTATAAAAATATT
1 TATTTTTATAAAAATATT
3785923 TATTTTTATAAAAATATT
1 TATTTTTATAAAAATATT
*
3785941 TATTTTTTTAAAAA
1 TATTTTTATAAAAA
3785955 AATTACTCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTTATAAAAATATT
Found at i:3786225 original size:2 final size:2
Alignment explanation
Indices: 3786220--3786267 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3786210 ACCATGTGTG
3786220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3786262 TA TA TA
1 TA TA TA
3786268 ATAAAGGTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3786445 original size:27 final size:24
Alignment explanation
Indices: 3786393--3786446 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 24
3786383 AAAAAAAACA
* *
3786393 TAATTAATTTTAATAATATTATTT
1 TAATTAATTTTAATAAAATTAATT
3786417 TAATTATATTTTTAAGTAAAATTAATT
1 TAATTA-A-TTTTAA-TAAAATTAATT
3786444 TAA
1 TAA
3786447 CATCATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 1 0.04
26 6 0.24
27 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TAATTAATTTTAATAAAATTAATT
Found at i:3787428 original size:7 final size:7
Alignment explanation
Indices: 3787417--3787450 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
3787407 TCAAAAGTAA
3787417 AAAAATT
1 AAAAATT
*
3787424 TAAAATT
1 AAAAATT
*
3787431 AAAAAGT
1 AAAAATT
3787438 AAAAATT
1 AAAAATT
3787445 AAAAAT
1 AAAAAT
3787451 ATATGCATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:3787752 original size:22 final size:23
Alignment explanation
Indices: 3787725--3787775 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
3787715 AATTGTCCCA
3787725 TTTTTACAGAAAAAAA-ATCTAT
1 TTTTTACAGAAAAAAATATCTAT
**
3787747 TTTTTACTTAAAAAAATTATCTAT
1 TTTTTACAGAAAAAAA-TATCTAT
3787771 TTTTT
1 TTTTT
3787776 TACTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 14 0.56
24 11 0.44
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTTTACAGAAAAAAATATCTAT
Found at i:3787774 original size:25 final size:25
Alignment explanation
Indices: 3787725--3787803 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
3787715 AATTGTCCCA
**
3787725 TTTTTACAGAAAAAAA--ATCTA-T
1 TTTTTACTTAAAAAAATTATCTATT
3787747 TTTTTACTTAAAAAAATTATCTATT
1 TTTTTACTTAAAAAAATTATCTATT
* *
3787772 TTTTTACTTAAAAATATT-TATATT
1 TTTTTACTTAAAAAAATTATCTATT
3787796 TTTATTAC
1 TTT-TTAC
3787804 ATTATTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 14 0.29
24 13 0.27
25 22 0.45
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.51
Consensus pattern (25 bp):
TTTTTACTTAAAAAAATTATCTATT
Found at i:3788134 original size:2 final size:2
Alignment explanation
Indices: 3788127--3788152 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3788117 TCTGAACCAT
3788127 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3788153 AAAGTCAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3788483 original size:25 final size:24
Alignment explanation
Indices: 3788447--3788538 Score: 81
Period size: 23 Copynumber: 4.0 Consensus size: 24
3788437 CAGTACCATC
3788447 TAAATATA--AAATAATATAAAATT
1 TAAATATATTAAAT-ATATAAAATT
* *
3788470 TAAATATATTAAATTATATATAATA
1 TAAATATATTAAA-TATATAAAATT
3788495 TAAAT-TATT-AATATATTAAAATT
1 TAAATATATTAAATATA-TAAAATT
*
3788518 TATA-ATA-TAAATATA-AAAATT
1 TAAATATATTAAATATATAAAATT
3788539 AATATAAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
21 6 0.10
22 5 0.09
23 26 0.45
24 4 0.07
25 16 0.28
26 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TAAATATATTAAATATATAAAATT
Found at i:3788493 original size:32 final size:34
Alignment explanation
Indices: 3788451--3788544 Score: 113
Period size: 32 Copynumber: 2.8 Consensus size: 34
3788441 ACCATCTAAA
*
3788451 TATAAAATAATATAAAATTTAAATATATT-AAA-T
1 TATAATATAATATAAAATTT-AATATATTAAAATT
*
3788484 TAT-ATATAATATAAATTATTAATATATTAAAATT
1 TATAATATAATATAAAAT-TTAATATATTAAAATT
*
3788518 TATAATATAAATATAAAAATTAATATA
1 TATAATAT-AATATAAAATTTAATATA
3788545 AATACGATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
32 20 0.38
33 8 0.15
34 4 0.08
35 12 0.23
36 8 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
TATAATATAATATAAAATTTAATATATTAAAATT
Found at i:3788909 original size:3 final size:3
Alignment explanation
Indices: 3788901--3788952 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
3788891 TTTGAAGTAA
3788901 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3788949 AAT A
1 AAT A
3788953 GCAGTAAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3792695 original size:25 final size:25
Alignment explanation
Indices: 3792659--3792709 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
3792649 CGAGACACTA
3792659 TTACATGCCATGTATAACTGGTGAT
1 TTACATGCCATGTATAACTGGTGAT
* *
3792684 TTACATGTCATGTATAACTGTTGAT
1 TTACATGCCATGTATAACTGGTGAT
3792709 T
1 T
3792710 ACAATCTTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (25 bp):
TTACATGCCATGTATAACTGGTGAT
Found at i:3797455 original size:15 final size:14
Alignment explanation
Indices: 3797438--3797486 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
3797428 TAATAAAGTT
3797438 TTATATAATTTATA
1 TTATATAATTTATA
3797452 TTTATATAATTTA-A
1 -TTATATAATTTATA
*
3797466 TTATTATATTTTATA
1 TTA-TATAATTTATA
3797481 TTATAT
1 TTATAT
3797487 TTAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 3 0.10
14 12 0.39
15 16 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATATAATTTATA
Found at i:3797502 original size:29 final size:28
Alignment explanation
Indices: 3797438--3797512 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
3797428 TAATAAAGTT
* * *
3797438 TTATATAATTTATATTTATATAATTTAA
1 TTATATATTTTATATTTATATAAATAAA
*
3797466 TTATTATATTTTATATTATATTTAAATAAA
1 TTA-TATATTTTATATT-TATATAAATAAA
* *
3797496 TTATATATGTTAAATTT
1 TTATATATTTTATATTT
3797513 TAAATAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 4 0.10
29 23 0.59
30 12 0.31
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
TTATATATTTTATATTTATATAAATAAA
Found at i:3800568 original size:27 final size:28
Alignment explanation
Indices: 3800509--3800577 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 28
3800499 ATATTTTTTT
* *
3800509 ATTTATTATAAATATTAATTATATAAAAT
1 ATTTATTAT-TATATTAATTATATAAAAA
*
3800538 ATTTATTATTATA-TATTTATATAAAAA
1 ATTTATTATTATATTAATTATATAAAAA
3800565 ATTTATATATTAT
1 ATTTAT-TATTAT
3800578 TATACATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.50
28 9 0.25
29 9 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATTTATTATTATATTAATTATATAAAAA
Found at i:3800570 original size:13 final size:13
Alignment explanation
Indices: 3800508--3800573 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
3800498 AATATTTTTT
3800508 TATTTATTATAAATA
1 TATTTA-TATAAA-A
*
3800523 TTAATTATATAAAA
1 -TATTTATATAAAA
* *
3800537 TATTTATTATTATA
1 TATTTA-TATAAAA
3800551 TATTTATATAAAA
1 TATTTATATAAAA
*
3800564 AATTTATATA
1 TATTTATATA
3800574 TTATTATACA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
13 19 0.45
14 12 0.29
15 6 0.14
16 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTTATATAAAA
Found at i:3800586 original size:27 final size:27
Alignment explanation
Indices: 3800529--3800586 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
3800519 AATATTAATT
* **
3800529 ATATAAAATATTTATTATTATATATTT
1 ATATAAAAAATTTATTATTATATATAC
3800556 ATATAAAAAATTTATATATTAT-TATAC
1 ATATAAAAAATTTAT-TATTATATATAC
3800583 ATAT
1 ATAT
3800587 TTTTTCTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
ATATAAAAAATTTATTATTATATATAC
Found at i:3801241 original size:22 final size:24
Alignment explanation
Indices: 3801210--3801262 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
3801200 CTATAGGTTT
3801210 AATTAAATGAT-AA-TTATTTTATA
1 AATT-AATGATAAATTTATTTTATA
* *
3801233 TATTAATGATAAATTTTTTTTATA
1 AATTAATGATAAATTTATTTTATA
3801257 AATTAA
1 AATTAA
3801263 ATTAATAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 6 0.24
23 5 0.20
24 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
AATTAATGATAAATTTATTTTATA
Found at i:3802851 original size:14 final size:14
Alignment explanation
Indices: 3802834--3802881 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3802824 TAAAATTAAC
3802834 ATAATTAATTAATA
1 ATAATTAATTAATA
3802848 ATAA-TAATT-A-A
1 ATAATTAATTAATA
3802859 ATAATATAATTTAATA
1 ATAAT-TAA-TTAATA
3802875 A-AATTAA
1 ATAATTAA
3802882 AAATTTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 8 0.28
14 9 0.31
15 4 0.14
16 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATTAATTAATA
Found at i:3802856 original size:17 final size:16
Alignment explanation
Indices: 3802834--3802868 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3802824 TAAAATTAAC
*
3802834 ATAATTAATTAATAATA
1 ATAATTAAATAAT-ATA
3802851 ATAATTAAATAATATA
1 ATAATTAAATAATATA
3802867 AT
1 AT
3802869 TTAATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAATTAAATAATATA
Found at i:3803642 original size:3 final size:3
Alignment explanation
Indices: 3803634--3803672 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
3803624 CTAAACGTGC
*
3803634 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CAT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3803673 TGTCTCATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:3810830 original size:13 final size:13
Alignment explanation
Indices: 3810810--3810847 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3810800 ATATAATTAC
3810810 ATAA-TATAAAAA
1 ATAATTATAAAAA
*
3810822 ATAATTATATAAA
1 ATAATTATAAAAA
*
3810835 ATAATAATAAAAA
1 ATAATTATAAAAA
3810848 TACGACATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAATTATAAAAA
Found at i:3810842 original size:16 final size:15
Alignment explanation
Indices: 3810813--3810842 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
3810803 TAATTACATA
3810813 ATATAAAAAATAATT
1 ATATAAAAAATAATT
3810828 ATATAAAATAATAAT
1 ATATAAAA-AATAAT
3810843 AAAAATACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATATAAAAAATAATT
Found at i:3812109 original size:18 final size:18
Alignment explanation
Indices: 3812078--3812128 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
3812068 AATTTTAAAT
*
3812078 ATAAA-ATAATTATAAGAA
1 ATAAATATAA-TATAAAAA
3812096 ATAAATATAATATAAAAA
1 ATAAATATAATATAAAAA
* *
3812114 ATAATTAAAATATAA
1 ATAAATATAATATAA
3812129 TATAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
ATAAATATAATATAAAAA
Found at i:3812135 original size:16 final size:16
Alignment explanation
Indices: 3812074--3812145 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
3812064 TAATAATTTT
3812074 AAATATAAAATAATTA
1 AAATATAAAATAATTA
*
3812090 TAAGAAAT-AAAT-A-TA
1 -AA-ATATAAAATAATTA
* *
3812105 ATATAAAAAATAATTA
1 AAATATAAAATAATTA
*
3812121 AAATATAATATAATTA
1 AAATATAAAATAATTA
*
3812137 AAAAATAAA
1 AAATATAAA
3812146 CTGAAAAGGA
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
13 2 0.05
14 5 0.12
15 3 0.07
16 23 0.55
17 6 0.14
18 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (16 bp):
AAATATAAAATAATTA
Found at i:3815059 original size:2 final size:2
Alignment explanation
Indices: 3815052--3815093 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3815042 AATCTATAAA
3815052 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3815094 CATAATTTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3816048 original size:20 final size:20
Alignment explanation
Indices: 3816023--3816064 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3816013 ACTTACAATA
*
3816023 TATTTTAAATATTTTATGTT
1 TATTTTAAATATTTGATGTT
*
3816043 TATTTTAATTATTTGATGTT
1 TATTTTAAATATTTGATGTT
3816063 TA
1 TA
3816065 AAATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (20 bp):
TATTTTAAATATTTGATGTT
Found at i:3816581 original size:2 final size:2
Alignment explanation
Indices: 3816574--3816621 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
3816564 TTCCTACGCG
* *
3816574 TA TA TA TA AA TA TA T- TA TA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3816615 TG TA TA T
1 TA TA TA T
3816622 GTGTGTGCAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3828572 original size:30 final size:29
Alignment explanation
Indices: 3828538--3828594 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
3828528 GCTTATTTAG
*
3828538 ATACACATCAAAGGATAGGGACTTACTTGA
1 ATACA-ATAAAAGGATAGGGACTTACTTGA
* *
3828568 ATACAATAAAATGATAGGGGCTTACTT
1 ATACAATAAAAGGATAGGGACTTACTT
3828595 AGGTAAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (29 bp):
ATACAATAAAAGGATAGGGACTTACTTGA
Found at i:3829633 original size:39 final size:38
Alignment explanation
Indices: 3829590--3829684 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 38
3829580 ACAATGGTTG
* *
3829590 TAGTGAGTCAGAAGATGGTTCT-GATTGCAACAATGCTCA
1 TAGTG-GTCAGAAGATGGTTCTAG-TGGCAACAATGCACA
* * *
3829629 TAGTGGACAAGAAGATGGTTCTAGTGGCAGCAGTGCACA
1 TAGTGGTC-AGAAGATGGTTCTAGTGGCAACAATGCACA
3829668 TAGTGGCTCAGAAGATG
1 TAGTGG-TCAGAAGATG
3829685 TTTCAAATGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
38 2 0.04
39 43 0.91
40 2 0.04
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.24
Consensus pattern (38 bp):
TAGTGGTCAGAAGATGGTTCTAGTGGCAACAATGCACA
Found at i:3836686 original size:23 final size:22
Alignment explanation
Indices: 3836627--3836686 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
3836617 CTACTTTTAT
*
3836627 TAAAATATATTTATAAAAAATAA
1 TAAAATA-ATTTATAAAAAAAAA
**
3836650 TAAGTTAATATTATAAATAAAAAA
1 TAAAATAAT-TTATAAA-AAAAAA
3836674 TAAAATAATTTAT
1 TAAAATAATTTAT
3836687 TCAAAAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 2 0.07
23 16 0.53
24 12 0.40
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TAAAATAATTTATAAAAAAAAA
Found at i:3838519 original size:32 final size:32
Alignment explanation
Indices: 3838466--3838526 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
3838456 TGAATTGAAA
*
3838466 TTGCTTCGGTTGTGTGGATTCTGGAGTCTAAG
1 TTGCTTCGGTTGTGTGAATTCTGGAGTCTAAG
* * *
3838498 TTGCTTTGGTTTTGTGAATTCTGTAGTCT
1 TTGCTTCGGTTGTGTGAATTCTGGAGTCT
3838527 GTAGAGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.11, C:0.11, G:0.30, T:0.48
Consensus pattern (32 bp):
TTGCTTCGGTTGTGTGAATTCTGGAGTCTAAG
Found at i:3841533 original size:4 final size:4
Alignment explanation
Indices: 3841524--3841549 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3841514 CTTCTTCAGC
3841524 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
3841550 TACAGTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:3842714 original size:20 final size:20
Alignment explanation
Indices: 3842691--3842734 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3842681 TTTAATATTC
*
3842691 TATATTTAT-ATAAATTTTAA
1 TATATTAATAATAAATTTT-A
*
3842711 TATATTAATAATTAATTTTA
1 TATATTAATAATAAATTTTA
3842731 TATA
1 TATA
3842735 AATTTTGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATTAATAATAAATTTTA
Found at i:3842791 original size:11 final size:11
Alignment explanation
Indices: 3842754--3842795 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
3842744 ATATGTTTAG
3842754 ATTTTTATTTT
1 ATTTTTATTTT
* **
3842765 ATTTATATCAT
1 ATTTTTATTTT
3842776 A-TTTTATTTT
1 ATTTTTATTTT
3842786 ATTTTTATTT
1 ATTTTTATTT
3842796 CCTGTGCTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:3845271 original size:2 final size:2
Alignment explanation
Indices: 3845264--3845301 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3845254 AACTATTTAT
3845264 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3845302 TGGCCTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3847375 original size:2 final size:2
Alignment explanation
Indices: 3847362--3847401 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3847352 GAAAAGATCC
*
3847362 CA CA CA CG CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3847402 TATATATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3851012 original size:23 final size:23
Alignment explanation
Indices: 3850985--3851028 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3850975 AATAAATATC
3850985 AAATATAAATATTTATTTATTAT
1 AAATATAAATATTTATTTATTAT
** *
3851008 AAATATATTTATTTTTTTATT
1 AAATATAAATATTTATTTATT
3851029 TTTTATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AAATATAAATATTTATTTATTAT
Found at i:3851018 original size:15 final size:16
Alignment explanation
Indices: 3850988--3851020 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3850978 AAATATCAAA
3850988 TATAAATATTTATTTAT
1 TATAAATA-TTATTTAT
3851005 TATAAATA-TATTTAT
1 TATAAATATTATTTAT
3851020 T
1 T
3851021 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATAAATATTATTTAT
Found at i:3857370 original size:23 final size:23
Alignment explanation
Indices: 3857353--3857416 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 23
3857343 ATATTTGAAT
3857353 TTAAATTTTAAATTTATTAAATA
1 TTAAATTTTAAATTTATTAAATA
* *
3857376 TTAAGTTTTAAAAAATTATATAAATTAA
1 TTAAATTTT--AAATTTAT-TAAA-T-A
3857404 TTAAATTTTAAAT
1 TTAAATTTTAAAT
3857417 ACTTTTAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
23 8 0.25
25 7 0.22
26 7 0.22
27 1 0.03
28 9 0.28
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAAATTTTAAATTTATTAAATA
Found at i:3859530 original size:22 final size:22
Alignment explanation
Indices: 3859485--3859534 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
3859475 ATTAAAAGTA
*
3859485 ATTTAATATAAGTTAAATTATT
1 ATTTAATATAAATTAAATTATT
** *
3859507 ATTTAATATAAATTTTATTTTT
1 ATTTAATATAAATTAAATTATT
3859529 ATTTAA
1 ATTTAA
3859535 ATTTAATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTAATATAAATTAAATTATT
Found at i:3860950 original size:2 final size:2
Alignment explanation
Indices: 3860943--3860983 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3860933 ATCATATTAC
3860943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3860984 CAAAGACATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3862360 original size:23 final size:22
Alignment explanation
Indices: 3862334--3862402 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
3862324 TAAATTTTTT
3862334 ATATAAAAATAAATAATATTAA
1 ATATAAAAATAAATAATATTAA
* *
3862356 GATATTAAAATATATTAA-ATTATA
1 -ATATAAAAATA-AATAATATTA-A
*
3862380 ATATAAATAATTAAT-ATATTAA
1 ATATAAA-AATAAATAATATTAA
3862402 A
1 A
3862403 ATTTTTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
22 3 0.08
23 26 0.70
24 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (22 bp):
ATATAAAAATAAATAATATTAA
Found at i:3862399 original size:38 final size:42
Alignment explanation
Indices: 3862333--3862423 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 42
3862323 ATAAATTTTT
*
3862333 TATATAAAAATAAATAATATTAAGATATTAAAATATAT-TAAA
1 TATAT-AATATAAATAATATTAAGATATTAAAATATATATAAA
* * *
3862375 T-TATAATATAAAT-A-ATTAATATATTAAAATTTTTATAAA
1 TATATAATATAAATAATATTAAGATATTAAAATATATATAAA
3862414 TATATAATAT
1 TATATAATAT
3862424 TTTAAATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
38 17 0.40
39 6 0.14
40 16 0.37
41 3 0.07
42 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (42 bp):
TATATAATATAAATAATATTAAGATATTAAAATATATATAAA
Found at i:3862421 original size:27 final size:29
Alignment explanation
Indices: 3862364--3862429 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 29
3862354 AAGATATTAA
3862364 AATATATT-AAATTATAATATAAATAATT
1 AATATATTAAAATTATAATATAAATAATT
*
3862392 AATATATTAAAATT-T-TTATAAAT-ATAT
1 AATATATTAAAATTATAATATAAATAAT-T
*
3862419 AATATTTTAAA
1 AATATATTAAA
3862430 TATAATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 2 0.06
27 18 0.53
28 9 0.26
29 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AATATATTAAAATTATAATATAAATAATT
Found at i:3863021 original size:14 final size:14
Alignment explanation
Indices: 3863002--3863034 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3862992 AAATAGGTTC
*
3863002 TATTTTTTTATTAT
1 TATTTTTTAATTAT
3863016 TATTTTTTAATTAT
1 TATTTTTTAATTAT
3863030 TATTT
1 TATTT
3863035 ATAAATGTGA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTTTAATTAT
Found at i:3863315 original size:2 final size:2
Alignment explanation
Indices: 3863308--3863335 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3863298 AAATAATCAT
3863308 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3863336 ACTTTTCGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3868402 original size:21 final size:22
Alignment explanation
Indices: 3868371--3868412 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3868361 TTATATTTAT
3868371 ATTATTTAATATAATAAAAATA
1 ATTATTTAATATAATAAAAATA
* *
3868393 ATTA-TTAATATTATATAAAT
1 ATTATTTAATATAATAAAAAT
3868413 TTAAATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTATTTAATATAATAAAAATA
Found at i:3868427 original size:6 final size:6
Alignment explanation
Indices: 3868418--3868485 Score: 81
Period size: 6 Copynumber: 12.0 Consensus size: 6
3868408 TAAATTTAAA
*
3868418 TATATT TATA-T TATATT TATATT TATATT TATACT TATA-T TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
* *
3868464 T-TAAT TATTTT TATATT T-TATT
1 TATATT TATATT TATATT TATATT
3868486 AATGTTCGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
5 18 0.33
6 36 0.67
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:3868438 original size:17 final size:17
Alignment explanation
Indices: 3868418--3868485 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
3868408 TAAATTTAAA
3868418 TATATTTATATTATATT
1 TATATTTATATTATATT
*
3868435 TATATTTATATTTATACT
1 TATATTTATA-TTATATT
* *
3868453 TATA-TTATATTTTAAT
1 TATATTTATATTATATT
* *
3868469 TATTTTTATATTTTATT
1 TATATTTATATTATATT
3868486 AATGTTCGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
16 8 0.18
17 26 0.59
18 10 0.23
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (17 bp):
TATATTTATATTATATT
Found at i:3869378 original size:3 final size:3
Alignment explanation
Indices: 3869372--3869408 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3869362 CTTCTTCTTC
3869372 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3869409 CGGACAGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3873070 original size:16 final size:17
Alignment explanation
Indices: 3873025--3873062 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3873015 AAAAAATAAT
*
3873025 TAAAATAT-GATATTAA
1 TAAAATATAAATATTAA
3873041 TAAAATATAAATATT-A
1 TAAAATATAAATATTAA
3873057 TAAAAT
1 TAAAAT
3873063 TTATATATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
TAAAATATAAATATTAA
Found at i:3873153 original size:19 final size:19
Alignment explanation
Indices: 3873129--3873168 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
3873119 TATGATTATG
3873129 ATATAAAA-AAATAATATAA
1 ATATAAAATAAAT-ATATAA
3873148 ATATAAAATAAATATATAA
1 ATATAAAATAAATATATAA
3873167 AT
1 AT
3873169 TATTAGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATATAAAATAAATATATAA
Found at i:3875246 original size:2 final size:2
Alignment explanation
Indices: 3875239--3875274 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3875229 AAATTTGATA
* *
3875239 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3875275 TCATTAGGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3875418 original size:2 final size:2
Alignment explanation
Indices: 3875413--3875447 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3875403 AATATATGTG
3875413 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3875448 TTGATGAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3875622 original size:2 final size:2
Alignment explanation
Indices: 3875615--3875653 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3875605 TTAAGTAGGC
3875615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3875654 ATTAAAGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3877198 original size:23 final size:22
Alignment explanation
Indices: 3877171--3877220 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
3877161 AAAAAATCAA
3877171 AAATAA-AATAAAATTG-TAAT
1 AAATAATAATAAAATTGATAAT
*
3877191 AAATAATATTAAAATTGACTAAT
1 AAATAATAATAAAATTGA-TAAT
3877214 AAATAAT
1 AAATAAT
3877221 TATTGACTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
23 11 0.42
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (22 bp):
AAATAATAATAAAATTGATAAT
Found at i:3877488 original size:21 final size:22
Alignment explanation
Indices: 3877451--3877498 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
3877441 TAAAATATTT
*
3877451 TATATTTATTATAAATTT-TAA
1 TATATGTATTATAAATTTATAA
*
3877472 TATATGTATTA-ATAATTTATAT
1 TATATGTATTATA-AATTTATAA
3877494 TATAT
1 TATAT
3877499 AAAATAACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 15 0.65
22 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATATGTATTATAAATTTATAA
Found at i:3878806 original size:18 final size:17
Alignment explanation
Indices: 3878780--3878815 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3878770 ATTAAATAAC
3878780 ATATAATTATAAAATTA
1 ATATAATTATAAAATTA
*
3878797 ATATATATTATATAATTA
1 ATATA-ATTATAAAATTA
3878815 A
1 A
3878816 AAAATAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTATAAAATTA
Found at i:3878892 original size:15 final size:16
Alignment explanation
Indices: 3878869--3878899 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3878859 AAATTTAATT
3878869 AATT-TTTTTTAAAAA
1 AATTATTTTTTAAAAA
3878884 AATTATTTTTTAAAAA
1 AATTATTTTTTAAAAA
3878900 TAATAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTATTTTTTAAAAA
Found at i:3878908 original size:17 final size:16
Alignment explanation
Indices: 3878873--3878908 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3878863 TTAATTAATT
*
3878873 TTTTTTAAAAAAATTA
1 TTTTTTAAAAAAATAA
3878889 TTTTTTAAAAATAATAA
1 TTTTTTAAAAA-AATAA
3878906 TTT
1 TTT
3878909 AACTCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTTTAAAAAAATAA
Found at i:3885495 original size:2 final size:2
Alignment explanation
Indices: 3885488--3885513 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3885478 GGCTTAAATA
3885488 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3885514 TTTGTACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3886045 original size:2 final size:2
Alignment explanation
Indices: 3886038--3886066 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3886028 GGCGAAAGAA
3886038 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3886067 AATTTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3886101 original size:14 final size:15
Alignment explanation
Indices: 3886084--3886114 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3886074 AATATTTATC
3886084 TTTATTT-TTTTGAA
1 TTTATTTCTTTTGAA
3886098 TTTATTTCTTTTGAA
1 TTTATTTCTTTTGAA
3886113 TT
1 TT
3886115 GTAATCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTATTTCTTTTGAA
Found at i:3886637 original size:2 final size:2
Alignment explanation
Indices: 3886630--3886660 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3886620 CAACTTCATC
3886630 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3886661 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3886665 original size:2 final size:2
Alignment explanation
Indices: 3886660--3886692 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3886650 TATATATATA
3886660 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3886693 ATGAAAAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3887164 original size:108 final size:108
Alignment explanation
Indices: 3886975--3887192 Score: 436
Period size: 108 Copynumber: 2.0 Consensus size: 108
3886965 TAGAGTTGAG
3886975 TCCATTTCCATTATTGTTTTGGTTTTCTCTTCGTTATTGTGTCATCTCATTTTCACCATAATTCC
1 TCCATTTCCATTATTGTTTTGGTTTTCTCTTCGTTATTGTGTCATCTCATTTTCACCATAATTCC
3887040 CAAAGAAAAACAGATTTAGTGCACCACAAGATCTATGCTTTAA
66 CAAAGAAAAACAGATTTAGTGCACCACAAGATCTATGCTTTAA
3887083 TCCATTTCCATTATTGTTTTGGTTTTCTCTTCGTTATTGTGTCATCTCATTTTCACCATAATTCC
1 TCCATTTCCATTATTGTTTTGGTTTTCTCTTCGTTATTGTGTCATCTCATTTTCACCATAATTCC
3887148 CAAAGAAAAACAGATTTAGTGCACCACAAGATCTATGCTTTAA
66 CAAAGAAAAACAGATTTAGTGCACCACAAGATCTATGCTTTAA
3887191 TC
1 TC
3887193 AGTTAAACAA
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 110 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (108 bp):
TCCATTTCCATTATTGTTTTGGTTTTCTCTTCGTTATTGTGTCATCTCATTTTCACCATAATTCC
CAAAGAAAAACAGATTTAGTGCACCACAAGATCTATGCTTTAA
Found at i:3887255 original size:2 final size:2
Alignment explanation
Indices: 3887250--3887291 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3887240 TTTTCTCTCG
3887250 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3887292 GACACACACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3887606 original size:20 final size:20
Alignment explanation
Indices: 3887560--3887607 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
3887550 ATGATTTATT
3887560 TATTAAAT-TTAAAAACATA
1 TATTAAATATTAAAAACATA
*
3887579 TATTAAATATTATAAA-ATA
1 TATTAAATATTAAAAACATA
3887598 TATTTAAATA
1 TA-TTAAATA
3887608 AAATTAATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TATTAAATATTAAAAACATA
Found at i:3887729 original size:13 final size:13
Alignment explanation
Indices: 3887711--3887743 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3887701 AAAATATAAC
3887711 ATAATATACATAT
1 ATAATATACATAT
*
3887724 ATAATATATATAT
1 ATAATATACATAT
3887737 AT-ATATA
1 ATAATATA
3887744 TTTTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAATATACATAT
Found at i:3887750 original size:17 final size:17
Alignment explanation
Indices: 3887704--3887743 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3887694 AATATACAAA
*
3887704 ATATAACATAATATACAT
1 ATATAATAT-ATATACAT
*
3887722 ATATAATATATATATAT
1 ATATAATATATATACAT
3887739 ATATA
1 ATATA
3887744 TTTTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATATATACAT
Found at i:3887750 original size:19 final size:19
Alignment explanation
Indices: 3887704--3887744 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3887694 AATATACAAA
*
3887704 ATATAACATA-ATATACAT
1 ATATAATATATATATACAT
*
3887722 ATATAATATATATATATAT
1 ATATAATATATATATACAT
3887741 ATAT
1 ATAT
3887745 TTTATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATAATATATATATACAT
Found at i:3888070 original size:32 final size:32
Alignment explanation
Indices: 3888033--3888148 Score: 112
Period size: 32 Copynumber: 3.5 Consensus size: 32
3888023 TAGACCATTC
3888033 TTATATAAATTTTAATATATTAATAATTTATA
1 TTATATAAATTTTAATATATTAATAATTTATA
*
3888065 TTATATAAATTTTAAAATATTTACATATATTTATA
1 TTATATAAATTTTAATATA-TTA-ATA-ATTTATA
* * *
3888100 TTTATATTTAATTTT--TATATT-ATAAATATATT
1 -TTATA-TAAATTTTAATATATTAAT-AATTTATA
3888132 TTATATAATATTTTAAT
1 TTATATAA-ATTTTAAT
3888149 TTTTTTTAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
30 2 0.03
31 10 0.14
32 25 0.36
33 5 0.07
34 5 0.07
35 10 0.14
36 5 0.07
37 7 0.10
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (32 bp):
TTATATAAATTTTAATATATTAATAATTTATA
Found at i:3888128 original size:22 final size:24
Alignment explanation
Indices: 3888079--3888128 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 24
3888069 ATAAATTTTA
3888079 AAATATTTACATATATTTATATTT
1 AAATATTTACATATATTTATATTT
3888103 --ATATTTA-AT-T-TTTATATTAT
1 AAATATTTACATATATTTATATT-T
3888123 AAATAT
1 AAATAT
3888129 ATTTTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
19 8 0.35
20 2 0.09
21 2 0.09
22 11 0.48
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
AAATATTTACATATATTTATATTT
Found at i:3888129 original size:36 final size:36
Alignment explanation
Indices: 3888040--3888151 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 36
3888030 TTCTTATATA
* *
3888040 AATTTTAATA-TATTAATA-ATTTATA-TTATA-TA
1 AATTTTAATATTATAAATATATTTATATTTATATTT
*
3888072 AATTTTAAAATATT-TACATATATTTATATTTATATTT
1 AATTTT--AATATTATAAATATATTTATATTTATATTT
* *
3888109 AATTTTTATATTATAAATATATTT-TATATAATATTTT
1 AATTTTAATATTATAAATATATTTATAT-TTATA-TTT
3888146 AATTTT
1 AATTTT
3888152 TTTTAATTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
32 6 0.09
34 8 0.12
35 16 0.25
36 19 0.29
37 16 0.25
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (36 bp):
AATTTTAATATTATAAATATATTTATATTTATATTT
Found at i:3888135 original size:37 final size:35
Alignment explanation
Indices: 3888081--3888152 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 35
3888071 AAATTTTAAA
* *
3888081 ATATTTACATATATTTATAT-TTATATTTAATTTTT
1 ATATTTAAATATATTTATATAATAT-TTTAATTTTT
3888116 ATATTATAAATATATTTTATATAATATTTTAATTTTT
1 ATATT-TAAATATA-TTTATATAATATTTTAATTTTT
3888153 TTTAATTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 5 0.16
36 7 0.22
37 17 0.53
38 3 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (35 bp):
ATATTTAAATATATTTATATAATATTTTAATTTTT
Found at i:3888636 original size:18 final size:20
Alignment explanation
Indices: 3888613--3888652 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
3888603 ATATTTATTA
*
3888613 AATAATTATAAT-T-ATTTT
1 AATAATTAAAATATGATTTT
3888631 AATAATTAAAATATGATTTT
1 AATAATTAAAATATGATTTT
3888651 AA
1 AA
3888653 GGTATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 1 0.05
20 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AATAATTAAAATATGATTTT
Found at i:3889971 original size:18 final size:18
Alignment explanation
Indices: 3889948--3889982 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3889938 TTTTAGATTT
3889948 TAAAAAATAAAATAAATC
1 TAAAAAATAAAATAAATC
3889966 TAAAAAATAAAATAAAT
1 TAAAAAATAAAATAAAT
3889983 TTTCTTTGAT
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:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAAAAATAAAATAAATC
Found at i:3890657 original size:23 final size:25
Alignment explanation
Indices: 3890615--3890672 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 25
3890605 ATTATATATT
3890615 TATAA-TATATTTTGATAAA-TTAA
1 TATAATTATATTTTGATAAATTTAA
*
3890638 TA-ATTTATATTTT-ATAAAATTTAA
1 TATAATTATATTTTGAT-AAATTTAA
3890662 TATAATTATAT
1 TATAATTATAT
3890673 ACATATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 3 0.10
23 13 0.45
24 6 0.21
25 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TATAATTATATTTTGATAAATTTAA
Found at i:3891298 original size:20 final size:19
Alignment explanation
Indices: 3891259--3891303 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3891249 CTTATTTAAA
* *
3891259 AATAAATAAATATGATAAT
1 AATAAATAAATATAAAAAT
*
3891278 ATTAAATATAATATAAAAAT
1 AATAAATA-AATATAAAAAT
3891298 AATAAA
1 AATAAA
3891304 AATATATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AATAAATAAATATAAAAAT
Found at i:3891318 original size:35 final size:34
Alignment explanation
Indices: 3891250--3891326 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 34
3891240 CGATGATCAC
* *
3891250 TTATTTAAAAATAAATAAATATGATAATATTAAA
1 TTATATAAAAATAAAAAAATATGATAATATTAAA
*
3891284 TATAATATAAAAATAATAAAAATAT-AT-ATTTTAAA
1 T-T-ATATAAAAATAA-AAAAATATGATAATATTAAA
3891319 TTATATAA
1 TTATATAA
3891327 TATAAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 6 0.16
34 2 0.05
35 9 0.24
36 13 0.35
37 7 0.19
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (34 bp):
TTATATAAAAATAAAAAAATATGATAATATTAAA
Found at i:3891325 original size:14 final size:14
Alignment explanation
Indices: 3891283--3891340 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
3891273 ATAATATTAA
3891283 ATATAATATAAA--
1 ATATAATATAAATT
*
3891295 A-ATAATA-AAAAT
1 ATATAATATAAATT
* *
3891307 ATATATTTTAAATT
1 ATATAATATAAATT
3891321 ATATAATATAAATT
1 ATATAATATAAATT
3891335 AT-TAAT
1 ATATAAT
3891341 TTATTAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 3 0.08
11 6 0.16
12 2 0.05
13 8 0.22
14 18 0.49
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATAATATAAATT
Found at i:3891328 original size:21 final size:23
Alignment explanation
Indices: 3891302--3891355 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
3891292 AAAAATAATA
3891302 AAAATATATATT-TTAAATTA-T
1 AAAATATATATTATTAAATTATT
* * *
3891323 ATAATATAAATTATTAATTTATT
1 AAAATATATATTATTAAATTATT
3891346 AAAATATATA
1 AAAATATATA
3891356 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.38
22 7 0.27
23 9 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAATATATATTATTAAATTATT
Found at i:3891382 original size:27 final size:27
Alignment explanation
Indices: 3891369--3891428 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
3891359 TTTTAAAATT
*
3891369 TAAATATAATTATAATATAATAAAATTA
1 TAAATATAA-TATAAAATAATAAAATTA
3891397 TAAATATAATAT-AAAT-ATATAAATTA
1 TAAATATAATATAAAATAATA-AAATTA
3891423 TTAAAT
1 -TAAAT
3891429 CTATCCGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.10
26 9 0.31
27 8 0.28
28 9 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAATATAATATAAAATAATAAAATTA
Found at i:3891385 original size:11 final size:11
Alignment explanation
Indices: 3891371--3891415 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
3891361 TTAAAATTTA
*
3891371 AATATAATTAT
1 AATATAAATAT
*
3891382 AATAT-AATAA
1 AATATAAATAT
3891392 AATTATAAATAT
1 AA-TATAAATAT
3891404 AATATAAATAT
1 AATATAAATAT
3891415 A
1 A
3891416 TAAATTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 5 0.17
11 18 0.62
12 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATAAATAT
Found at i:3891399 original size:8 final size:8
Alignment explanation
Indices: 3891316--3891428 Score: 53
Period size: 8 Copynumber: 14.5 Consensus size: 8
3891306 TATATATTTT
3891316 AAATTATA
1 AAATTATA
*
3891324 TAA-TAT-
1 AAATTATA
*
3891330 AAATTATT
1 AAATTATA
*
3891338 AATTTATTA
1 AAATTA-TA
3891347 AAATATATA
1 AAAT-TATA
*
3891356 AAATTTTA
1 AAATTATA
3891364 AAATT-T-
1 AAATTATA
3891370 AAA-TAT-
1 AAATTATA
3891376 -AATTATA
1 AAATTATA
* *
3891383 ATATAATA
1 AAATTATA
3891391 AAATTATA
1 AAATTATA
*
3891399 AATATAATA
1 AA-ATTATA
3891408 TAAA-TATA
1 -AAATTATA
*
3891416 TAAATTATT
1 -AAATTATA
3891425 AAAT
1 AAAT
3891429 CTATCCGTAT
Statistics
Matches: 81, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
5 3 0.04
6 9 0.11
7 7 0.09
8 39 0.48
9 19 0.23
10 4 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
AAATTATA
Found at i:3892682 original size:21 final size:20
Alignment explanation
Indices: 3892618--3892682 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 20
3892608 GTCATTGTTT
* *
3892618 TAAATAATATTAGATTTTTTAA
1 TAAAAAATATTA-A-TTTTAAA
*
3892640 TAAAAAAT-TATAATTTAAAAA
1 TAAAAAATAT-TAATTT-TAAA
3892661 TAAAAAATATTAATATTTAAA
1 TAAAAAATATTAAT-TTTAAA
3892682 T
1 T
3892683 TTAAAATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
20 3 0.09
21 20 0.57
22 12 0.34
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TAAAAAATATTAATTTTAAA
Found at i:3892687 original size:23 final size:23
Alignment explanation
Indices: 3892635--3892715 Score: 58
Period size: 23 Copynumber: 3.5 Consensus size: 23
3892625 TATTAGATTT
*
3892635 TTTAATAAAAAATT-ATAATTTAAA
1 TTTAA-AAAATATTAAT-ATTTAAA
**
3892659 AATAAAAAATATTAATATTTAAA
1 TTTAAAAAATATTAATATTTAAA
** *
3892682 TTTAAAATTTATTAA-ATATTAAT
1 TTTAAAAAATATTAATAT-TTAAA
*
3892705 TTTTAAAAATA
1 TTTAAAAAATA
3892716 ATTATATAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
22 2 0.05
23 37 0.84
24 5 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAAAAAATATTAATATTTAAA
Found at i:3892934 original size:24 final size:23
Alignment explanation
Indices: 3892894--3892939 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
3892884 CATTATTTAA
*
3892894 ATTTAATTATAAATATATTAAAT
1 ATTTAATAATAAATATATTAAAT
*
3892917 ATTTAATAAATAATTATATTAAA
1 ATTTAAT-AATAAATATATTAAA
3892940 GTAAACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATAATAAATATATTAAAT
Found at i:3893274 original size:58 final size:58
Alignment explanation
Indices: 3893205--3893322 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
3893195 TGTGTGTGTG
*
3893205 TTTTTTTTAAATATTTGAAAGAGTTTGAGTGAATTACAAGGTAAAAATTTTCATTTGT
1 TTTTTTTTAAATATTTGAAAGAGTTTGAGTGAATTACAAGATAAAAATTTTCATTTGT
3893263 TTTTTTTTAAATATTTGAAAGAGTTTGAGTGAATTACAAGATAAAAATTTTCATTTGT
1 TTTTTTTTAAATATTTGAAAGAGTTTGAGTGAATTACAAGATAAAAATTTTCATTTGT
3893321 TT
1 TT
3893323 ACTTTGGTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.47
Consensus pattern (58 bp):
TTTTTTTTAAATATTTGAAAGAGTTTGAGTGAATTACAAGATAAAAATTTTCATTTGT
Found at i:3893463 original size:6 final size:6
Alignment explanation
Indices: 3893449--3893485 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
3893439 AAAATGTGAA
*
3893449 ATATAT ATATGT ATATGT ATATGT ATATGT ATATGT A
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT A
3893486 ATGAAAGGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.49
Consensus pattern (6 bp):
ATATGT
Found at i:3894815 original size:2 final size:2
Alignment explanation
Indices: 3894808--3894850 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
3894798 CCATCCCTCA
* *
3894808 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT TT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
3894851 TTATGAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3895363 original size:44 final size:46
Alignment explanation
Indices: 3895272--3895372 Score: 129
Period size: 47 Copynumber: 2.2 Consensus size: 46
3895262 ATTATAAAAA
*
3895272 ATTTTATATA-TTAATATTTATAATTTTTTTACATTTAAAATATTAT
1 ATTTTATATATTTAATATATATAATTTTTTTACATTT-AAATATTAT
* *
3895318 ATTTTATATATTTAATATATATAATTTTATTT-TATTT-TATA-TAT
1 ATTTTATATATTTAATATATATAATTTT-TTTACATTTAAATATTAT
3895362 ATTTTATATAT
1 ATTTTATATAT
3895373 GACGAGAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
44 14 0.28
45 3 0.06
46 10 0.20
47 20 0.40
48 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (46 bp):
ATTTTATATATTTAATATATATAATTTTTTTACATTTAAATATTAT
Found at i:3895646 original size:21 final size:22
Alignment explanation
Indices: 3895621--3895670 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
3895611 TATTTATATC
3895621 ATGTTCAT-ATTATTTTTTA-TT
1 ATGTT-ATAATTATTTTTTATTT
*
3895642 ATGTTTTAATTATTTTTTATTT
1 ATGTTATAATTATTTTTTATTT
3895664 ATGTTAT
1 ATGTTAT
3895671 GTTCATATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.64
22 8 0.32
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (22 bp):
ATGTTATAATTATTTTTTATTT
Found at i:3895665 original size:11 final size:10
Alignment explanation
Indices: 3895628--3895662 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
3895618 ATCATGTTCA
3895628 TATTATTTTT
1 TATTATTTTT
3895638 TATTATGTTTT
1 TATTAT-TTTT
*
3895649 AATTATTTTT
1 TATTATTTTT
3895659 TATT
1 TATT
3895663 TATGTTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (10 bp):
TATTATTTTT
Found at i:3896633 original size:28 final size:29
Alignment explanation
Indices: 3896590--3896674 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 29
3896580 TCAACACTAC
**
3896590 TACTTAAATTAATTTAAATTTTATATT-T
1 TACTTAAAAAAATTTAAATTTTATATTAT
* * *
3896618 TATTTAAAAAAATTTAAA-TATAAATTAT
1 TACTTAAAAAAATTTAAATTTTATATTAT
* *
3896646 TACTTAATAAAATTT-AATTTTATAATAT
1 TACTTAAAAAAATTTAAATTTTATATTAT
3896674 T
1 T
3896675 TTTATTAATA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
27 8 0.18
28 37 0.82
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
TACTTAAAAAAATTTAAATTTTATATTAT
Found at i:3897786 original size:19 final size:18
Alignment explanation
Indices: 3897756--3897801 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
3897746 TTGGTTGGTT
3897756 GAAAAGAAAAAGAAA-AAA
1 GAAAA-AAAAAGAAAGAAA
3897774 TGAGAAAAAAAAGAAAGAAA
1 -GA-AAAAAAAAGAAAGAAA
3897794 GAAAAAAA
1 GAAAAAAA
3897802 TTATATATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.24
19 13 0.52
20 6 0.24
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (18 bp):
GAAAAAAAAAGAAAGAAA
Found at i:3897851 original size:18 final size:19
Alignment explanation
Indices: 3897821--3897859 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3897811 CGTATTTATA
3897821 TTATTTTTATATAA-AATT
1 TTATTTTTATATAATAATT
3897839 TTATATTTT-TATAATAATT
1 TTAT-TTTTATATAATAATT
3897858 TT
1 TT
3897860 TTACATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTTTATATAATAATT
Found at i:3898212 original size:15 final size:16
Alignment explanation
Indices: 3898186--3898215 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3898176 ATAAATTTTT
3898186 TAATTAAATAAAATTA
1 TAATTAAATAAAATTA
3898202 TAATT-AATAAAATT
1 TAATTAAATAAAATT
3898216 TATTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATTAAATAAAATTA
Found at i:3898218 original size:16 final size:17
Alignment explanation
Indices: 3898176--3898218 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3898166 TTTAATATTC
* *
3898176 ATAAATTTTTTAATTAA
1 ATAAAATTTATAATTAA
3898193 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
3898208 ATAAAATTTAT
1 ATAAAATTTAT
3898219 TTAAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 11 0.48
17 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:3899427 original size:20 final size:20
Alignment explanation
Indices: 3899399--3899439 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3899389 TAATTTTTTT
* *
3899399 ATAAATAAATTTTATTAATA
1 ATAAATAAAATTTATAAATA
*
3899419 ATAATTAAAATTTATAAATA
1 ATAAATAAAATTTATAAATA
3899439 A
1 A
3899440 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAATAAAATTTATAAATA
Found at i:3910377 original size:2 final size:2
Alignment explanation
Indices: 3910370--3910408 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3910360 TGTTTTTGAT
*
3910370 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3910409 TCAAGTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3912237 original size:38 final size:35
Alignment explanation
Indices: 3912195--3912291 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 35
3912185 TTTTCGTACA
3912195 TAATAATTATATTTAAAATATTATATTATATAAAATTT
1 TAATAATT-TATTT--AATATTATATTATATAAAATTT
* * *
3912233 TAATATTTTAATT-A-ATTATATTTTATAAAATTT
1 TAATAATTTATTTAATATTATATTATATAAAATTT
*
3912266 AAATAATTTATTT-AT-TTATATTATAT
1 TAATAATTTATTTAATATTATATTATAT
3912292 TTATATTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
33 39 0.76
34 1 0.02
37 4 0.08
38 7 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (35 bp):
TAATAATTTATTTAATATTATATTATATAAAATTT
Found at i:3912251 original size:33 final size:33
Alignment explanation
Indices: 3912214--3912291 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
3912204 TATTTAAAAT
* *
3912214 ATTATATTATATAAAATTTTAATATTTTAATTA
1 ATTATATTATATAAAATTTAAATAATTTAATTA
* *
3912247 ATTATATTTTATAAAATTTAAATAATTTATTTA
1 ATTATATTATATAAAATTTAAATAATTTAATTA
*
3912280 TTTATATTATAT
1 ATTATATTATAT
3912292 TTATATTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
ATTATATTATATAAAATTTAAATAATTTAATTA
Found at i:3912255 original size:23 final size:24
Alignment explanation
Indices: 3912198--3912257 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
3912188 TCGTACATAA
3912198 TAATTATA-TTTAAAATATTATAT
1 TAATTATATTTTAAAATATTATAT
* * * *
3912221 TATATAAAATTTTAATATTTTA-AT
1 TA-ATTATATTTTAAAATATTATAT
3912245 TAATTATATTTTA
1 TAATTATATTTTA
3912258 TAAAATTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
23 11 0.38
24 8 0.28
25 10 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TAATTATATTTTAAAATATTATAT
Found at i:3912294 original size:11 final size:11
Alignment explanation
Indices: 3912274--3912326 Score: 72
Period size: 11 Copynumber: 4.9 Consensus size: 11
3912264 TTAAATAATT
3912274 TATT-TATTTA
1 TATTATATTTA
3912284 TATTATATTTA
1 TATTATATTTA
*
3912295 TATTATTTTTA
1 TATTATATTTA
*
3912306 TATCATATTTA
1 TATTATATTTA
*
3912317 TTTTATATTT
1 TATTATATTT
3912327 TAATTAAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
10 4 0.11
11 33 0.89
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTATATTTA
Found at i:3912307 original size:22 final size:23
Alignment explanation
Indices: 3912280--3912332 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
3912270 AATTTATTTA
3912280 TTTATATTATATTTATATTAT-T
1 TTTATATTATATTTATATTATAT
* *
3912302 TTTATATCATATTTATTTTATAT
1 TTTATATTATATTTATATTATAT
3912325 TTTA-ATTA
1 TTTATATTA
3912333 AAACTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATATTATATTTATATTATAT
Found at i:3912313 original size:16 final size:16
Alignment explanation
Indices: 3912278--3912324 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3912268 ATAATTTATT
* *
3912278 TATTTATATTATAT-T
1 TATTTATTTTATATCA
3912293 TATATTATTTTTATATCA
1 TAT-TTA-TTTTATATCA
3912311 TATTTATTTTATAT
1 TATTTATTTTATAT
3912325 TTTAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 10 0.37
18 3 0.11
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTATTTTATATCA
Done.