Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015372.1 Kokia drynarioides strain JFW-HI SEQ_130419, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 487716
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 308 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2094 original size:17 final size:18
Alignment explanation
Indices: 2061--2095 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2051 TAGAAGCTAT
2061 AATAATTACACATTTAAA
1 AATAATTACACATTTAAA
*
2079 AATAATTAGA-ATTTAAA
1 AATAATTACACATTTAAA
2096 TTACAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (18 bp):
AATAATTACACATTTAAA
Found at i:6164 original size:25 final size:23
Alignment explanation
Indices: 6135--6180 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
6125 GTTGGATTCA
6135 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
6160 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
6181 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:10799 original size:2 final size:2
Alignment explanation
Indices: 10794--10819 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10784 CCCGAATTAC
10794 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
10820 GTTGAATTTA
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:11096 original size:28 final size:27
Alignment explanation
Indices: 11065--11119 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
11055 CATACTCATC
11065 ATATGGATGAAAAACTTATGTAATAAAT
1 ATATGGATGAAAAACTTATGTAA-AAAT
** * *
11093 ATATTTATTAAAAATTTATGTAAAAAT
1 ATATGGATGAAAAACTTATGTAAAAAT
11120 TAAATGAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (27 bp):
ATATGGATGAAAAACTTATGTAAAAAT
Found at i:18803 original size:13 final size:13
Alignment explanation
Indices: 18785--18810 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18775 ATAAAAAAAA
18785 ACTCATATTATTT
1 ACTCATATTATTT
18798 ACTCATATTATTT
1 ACTCATATTATTT
18811 CAATAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
ACTCATATTATTT
Found at i:27025 original size:14 final size:17
Alignment explanation
Indices: 27008--27043 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
26998 AACTTTTGGC
27008 TTTTAA-AAAA-TA-TT
1 TTTTAATAAAATTACTT
27022 TTTTAATAAAATTACTT
1 TTTTAATAAAATTACTT
27039 TTTTA
1 TTTTA
27044 TCTCCTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.32
15 4 0.21
16 2 0.11
17 7 0.37
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAATAAAATTACTT
Found at i:27584 original size:18 final size:20
Alignment explanation
Indices: 27539--27592 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 20
27529 AAAAAGTTTG
27539 AATAAAATTATAATATCAAAA
1 AATAAAATT-TAATATCAAAA
27560 AAT-AAATTTAA-A-CAAAA
1 AATAAAATTTAATATCAAAA
*
27577 AATAAAATTTATTATC
1 AATAAAATTTAATATC
27593 TAAACAGACT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 8 0.28
18 8 0.28
19 4 0.14
20 6 0.21
21 3 0.10
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAAAATTTAATATCAAAA
Found at i:39771 original size:31 final size:31
Alignment explanation
Indices: 39704--39793 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
39694 TAACATGAAT
**
39704 ACAGGTACA-AAGTACCTGAT--AATATAGTC
1 ACAGGTACACAA-TACCTGATAAAATATAAAC
*
39733 ACTGGTACACAATACCTGATAAAATATAAAC
1 ACAGGTACACAATACCTGATAAAATATAAAC
* *
39764 ACAGGTACACAGTAACTGATAAAATATAAA
1 ACAGGTACACAATACCTGATAAAATATAAA
39794 GACATGTCAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.31
30 2 0.04
31 34 0.65
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (31 bp):
ACAGGTACACAATACCTGATAAAATATAAAC
Found at i:41858 original size:18 final size:19
Alignment explanation
Indices: 41835--41872 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41825 AATAAGAAAC
*
41835 AAATCTTT-TAATTTTTTA
1 AAATCTTTAGAATTTTTTA
41853 AAATCTTTAGAATTTTTTA
1 AAATCTTTAGAATTTTTTA
41872 A
1 A
41873 TGCACATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (19 bp):
AAATCTTTAGAATTTTTTA
Found at i:46498 original size:9 final size:9
Alignment explanation
Indices: 46484--46516 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
46474 CATTCCATTT
46484 TTTTTATTA
1 TTTTTATTA
46493 TTTTTATT-
1 TTTTTATTA
*
46501 TATTTATTA
1 TTTTTATTA
46510 TTTTTAT
1 TTTTTAT
46517 AAATATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTATTA
Found at i:46592 original size:63 final size:62
Alignment explanation
Indices: 46477--46665 Score: 220
Period size: 63 Copynumber: 3.0 Consensus size: 62
46467 GAAATTCCAT
46477 TCCATTTT-TTTTATTATTTTTATTTATTTATTATTTTTATAAATATAAATAAATATAAAATAAA
1 TCCATTTTATTTTATTA--TTTATTTATTTATTA-TTTTATAAATATAAATAAATA-AAAATAAA
46541 A
62 A
* * **
46542 TCCATTTTATTTTATTATTTATTTATTTATTATTGTATTAATATAAATAAATAAATGTAAAA
1 TCCATTTTATTTTATTATTTATTTATTTATTATTTTATAAATATAAATAAATAAAAATAAAA
* * * * *
46604 T-AATATTAATTTTATTTTATTGTTTATTTATTATTTTATGAATATAAATAAATAAATAATAA
1 TCCAT-TTTATTTTATTAT-TTATTTATTTATTATTTTATAAATATAAATAAATAAA-AATAA
46666 CAAACCAAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
61 2 0.02
62 19 0.18
63 53 0.49
64 18 0.17
65 8 0.07
66 8 0.07
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (62 bp):
TCCATTTTATTTTATTATTTATTTATTTATTATTTTATAAATATAAATAAATAAAAATAAAA
Found at i:46603 original size:67 final size:66
Alignment explanation
Indices: 46477--46661 Score: 231
Period size: 67 Copynumber: 2.8 Consensus size: 66
46467 GAAATTCCAT
46477 TCCATTTT-TTTTATTATTTTTATTTATTTATTATTT-TT-ATA-AATATAAATAAATATAAAAT
1 TCCATTTTATTTTATTA--TTTATTTATTTATTATTTATTAATATAA-ATAAATAAATATAAAAT
46538 AAAA
63 AAAA
*
46542 TCCATTTTATTTTATTATTTATTTATTTATTATTGTATTAATATAAATAAATAAATGTAAAATAA
1 TCCATTTTATTTTATTATTTATTTATTTATTATT-TATTAATATAAATAAATAAATATAAAATAA
*
46607 TA
65 AA
** * *
46609 TTAATTTTATTTTATTGTTTATTTA-TTA-T-TTTATGAATATAAATAAATAAATA
1 TCCATTTTATTTTATTATTTATTTATTTATTATTTATTAATATAAATAAATAAATA
46662 ATAACAAACC
Statistics
Matches: 108, Mismatches: 7, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
63 20 0.19
64 19 0.18
65 10 0.09
66 13 0.12
67 44 0.41
68 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (66 bp):
TCCATTTTATTTTATTATTTATTTATTTATTATTTATTAATATAAATAAATAAATATAAAATAAA
A
Found at i:50371 original size:475 final size:475
Alignment explanation
Indices: 49481--50431 Score: 1758
Period size: 475 Copynumber: 2.0 Consensus size: 475
49471 CTGATGCAAG
* *
49481 TCCTCCAACAATTTCAAAAGCCAAGTGCTCTCTTGAGCTGCCATTGTTGCTGCACGATACTCTAC
1 TCCTCCAACAATTTCAAAAGCCAAGTGCTCTCTTGAGCTGCCATTGTCGCTACACGATACTCTAC
*
49546 TTCGGTGGTTGACAAAGACACTGTGAGTTGTCTTTTGCTGCACTAGGAAATTGCTCCGAATCTAA
66 TTCGGTGGTTGACAAAGACACTGTGAGTTGTCTTTTGCTGCACCAGGAAATTGCTCCGAATCTAA
49611 GTATAAACACATACCCTATAGTTGAGCATCGGGTATCATGGTCACCTGAATAGTCAATATCACAA
131 GTATAAACACATACCCTATAGTTGAGCATCGGGTATCATGGTCACCTGAATAGTCAATATCACAA
49676 TAGCCAACTAGCTTGTAATCTCCACCTTTTCTGTACAGAATATCATGATCAATCGTACTCTTCAC
196 TAGCCAACTAGCTTGTAATCTCCACCTTTTCTGTACAGAATATCATGATCAATCGTACTCTTCAC
** *
49741 GTACCTCAAAATTCGTCGAATTGGTTCCAAGTGAAGTTTCTTTGGATTTTGCATGTAACGGCTCA
261 GTACCTCAAAATTCACCGAATTGGTTCCAAGTGAAGTTTCTTTGGATTTTGCATGTAACGACTCA
* * *
49806 CAGTGCCAACTGCAAAAAAAATATTTGGCCTTGTTAAAGTTAAGTAGATAAGACTACGTACTACT
326 CAATGCCAACTGCAAAAAAAATATTTGGCCTTGTTAAAGTTAAGTAGATAAGACTACCTACTAAT
49871 TGTTGATACATCGTTGTATCTTCTAAATCTTTCCCTTCGTTGGCATAGATTTTGGCATTTGGTTC
391 TGTTGATACATCGTTGTATCTTCTAAATCTTTCCCTTCGTTGGCATAGATTTTGGCATTTGGTTC
*
49936 TATCGGCGTAGAAATTGGCT
456 TATCAGCGTAGAAATTGGCT
49956 TCCTCCAACAATTTCAAAAGCCAAGTGCTCTCTTGAGCTGCCATTGTCGCTACACGATACTCTAC
1 TCCTCCAACAATTTCAAAAGCCAAGTGCTCTCTTGAGCTGCCATTGTCGCTACACGATACTCTAC
*
50021 TTCGGTGGTTGACAAAGACACTGTGAGTTGTCTTTTGCTGCACCAGGAAATTGCTCTGAATCTAA
66 TTCGGTGGTTGACAAAGACACTGTGAGTTGTCTTTTGCTGCACCAGGAAATTGCTCCGAATCTAA
* * * *
50086 GTATAAACATATACCCTGTAGTTGAGCGTCGGGTATCATGGTCACCTGCATAGTCAATATCACAA
131 GTATAAACACATACCCTATAGTTGAGCATCGGGTATCATGGTCACCTGAATAGTCAATATCACAA
50151 TAGCCAACTAGCTTGTAATCTCCACCTTTTCTGTACAGAATATCATGATCAATCGTACTCTTCAC
196 TAGCCAACTAGCTTGTAATCTCCACCTTTTCTGTACAGAATATCATGATCAATCGTACTCTTCAC
50216 GTACCTCAAAATTCACCGAATTGGTTCCAAGTGAAGTTTCTTTGGATTTTGCATGTAACGACTCA
261 GTACCTCAAAATTCACCGAATTGGTTCCAAGTGAAGTTTCTTTGGATTTTGCATGTAACGACTCA
*
50281 CAATGCCAACTGCAAAAGAAATATTTGGCCTTGTTAAAGTTAAGTAGATAAGACTACCTACTAAT
326 CAATGCCAACTGCAAAAAAAATATTTGGCCTTGTTAAAGTTAAGTAGATAAGACTACCTACTAAT
50346 TGTTGATACATCGTTGTATCTTCTAAATCTTTCCCTTCGTTGGCATAGATTTTGGCATTTGGTTC
391 TGTTGATACATCGTTGTATCTTCTAAATCTTTCCCTTCGTTGGCATAGATTTTGGCATTTGGTTC
50411 TATCAGCGTAGAAATTGGCT
456 TATCAGCGTAGAAATTGGCT
50431 T
1 T
50432 GCATTTTAGC
Statistics
Matches: 460, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
475 460 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (475 bp):
TCCTCCAACAATTTCAAAAGCCAAGTGCTCTCTTGAGCTGCCATTGTCGCTACACGATACTCTAC
TTCGGTGGTTGACAAAGACACTGTGAGTTGTCTTTTGCTGCACCAGGAAATTGCTCCGAATCTAA
GTATAAACACATACCCTATAGTTGAGCATCGGGTATCATGGTCACCTGAATAGTCAATATCACAA
TAGCCAACTAGCTTGTAATCTCCACCTTTTCTGTACAGAATATCATGATCAATCGTACTCTTCAC
GTACCTCAAAATTCACCGAATTGGTTCCAAGTGAAGTTTCTTTGGATTTTGCATGTAACGACTCA
CAATGCCAACTGCAAAAAAAATATTTGGCCTTGTTAAAGTTAAGTAGATAAGACTACCTACTAAT
TGTTGATACATCGTTGTATCTTCTAAATCTTTCCCTTCGTTGGCATAGATTTTGGCATTTGGTTC
TATCAGCGTAGAAATTGGCT
Found at i:56047 original size:16 final size:16
Alignment explanation
Indices: 56028--56079 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
56018 TCTTATCAAG
56028 TTGAATTTTTTTAGAT
1 TTGAATTTTTTTAGAT
**
56044 TTG-ACCTTTTTAGAGT
1 TTGAATTTTTTTAGA-T
* *
56060 TTGGATTTTTTTATAT
1 TTGAATTTTTTTAGAT
56076 TTGA
1 TTGA
56080 TGTAATTACA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 9 0.32
16 11 0.39
17 8 0.29
ACGTcount: A:0.21, C:0.04, G:0.15, T:0.60
Consensus pattern (16 bp):
TTGAATTTTTTTAGAT
Found at i:60006 original size:21 final size:23
Alignment explanation
Indices: 59965--60008 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
59955 TTCCCTCATT
*
59965 TTTTTCTTTCTTGCCAAACACCA
1 TTTTTCTTTCTTGCAAAACACCA
59988 TTTTTC-TTCTT-CAAAACACCA
1 TTTTTCTTTCTTGCAAAACACCA
60009 GGCCAGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 5 0.25
23 6 0.30
ACGTcount: A:0.25, C:0.30, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTTTCTTTCTTGCAAAACACCA
Found at i:85513 original size:31 final size:28
Alignment explanation
Indices: 85445--85520 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
85435 AAACGAATAT
*
85445 TTTATTTTTATAATTAATTGGTTTTCAC
1 TTTATTTTTATAATTAATTGGTTTTCAA
* * *
85473 TCTATTTTTATAATTAATTAATGTTTTTAA
1 TTTATTTTTATAATTAATT--GGTTTTCAA
85503 TATTATTTTTATAATTAA
1 T-TTATTTTTATAATTAA
85521 CTTTTTTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 18 0.45
30 7 0.17
31 15 0.38
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (28 bp):
TTTATTTTTATAATTAATTGGTTTTCAA
Found at i:91337 original size:17 final size:17
Alignment explanation
Indices: 91315--91353 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
91305 AGGTGAATAA
* * *
91315 CTTGTTCGTTGAGAGTT
1 CTTGTTCATAGAGAATT
91332 CTTGTTCATAGAGAATT
1 CTTGTTCATAGAGAATT
91349 CTTGT
1 CTTGT
91354 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCATAGAGAATT
Found at i:91919 original size:25 final size:25
Alignment explanation
Indices: 91882--91977 Score: 106
Period size: 25 Copynumber: 3.8 Consensus size: 25
91872 TTCGATATTC
* *
91882 CAAAATTTAGCTCATACGAGCCTAGA
1 CAAAA-TTAGCTCTTACGAGCCTAAA
91908 CAAAATTAGCTCTTACGAG-CTAAA
1 CAAAATTAGCTCTTACGAGCCTAAA
* *
91932 AAAGAATTAGCTCTTACGAGCCCAAA
1 CAA-AATTAGCTCTTACGAGCCTAAA
*
91958 -AAGAATTAACTCTTACGAGC
1 CAA-AATTAGCTCTTACGAGC
91978 TAGAAAGGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.10
25 48 0.76
26 9 0.14
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.23
Consensus pattern (25 bp):
CAAAATTAGCTCTTACGAGCCTAAA
Found at i:105773 original size:16 final size:18
Alignment explanation
Indices: 105741--105775 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
105731 CAACCTTGAA
105741 AAAATTCTTTAAAATATT
1 AAAATTCTTTAAAATATT
105759 AAAATT-TTT-AAATATT
1 AAAATTCTTTAAAATATT
105775 A
1 A
105776 TGTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTCTTTAAAATATT
Found at i:106663 original size:23 final size:22
Alignment explanation
Indices: 106622--106667 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
106612 AGATTTAAAA
*
106622 TTTTAAATTAAATTGTTAATATT
1 TTTTAAATTAAATTATTAA-ATT
**
106645 TTTTAAATTATTTTATTAAATT
1 TTTTAAATTAAATTATTAAATT
106667 T
1 T
106668 GTTAGTGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTAAATTAAATTATTAAATT
Found at i:108614 original size:47 final size:47
Alignment explanation
Indices: 108560--108653 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
108550 CACCCCAATA
*
108560 TAATAACCTCACTTTTGTACTCAAAGGCTAGTTCTCACCACTAAATT
1 TAATAACCTCACTTTTGTACTCAAAGGCTAGATCTCACCACTAAATT
*
108607 TAATAACCTCACTTTTGTACTCAAAGGCTAGATCTCACCAGTAAATT
1 TAATAACCTCACTTTTGTACTCAAAGGCTAGATCTCACCACTAAATT
108654 CTCCCCATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (47 bp):
TAATAACCTCACTTTTGTACTCAAAGGCTAGATCTCACCACTAAATT
Found at i:109826 original size:6 final size:6
Alignment explanation
Indices: 109805--109870 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
109795 TTTATATTGG
** ** **
109805 TTTAAA TTTATT TTTAAA TTTAAA TTTATCTT TTTAAA TTTAAA TTT-GC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
109854 TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
109871 TCAAATTTGA
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
5 3 0.07
6 38 0.84
8 4 0.09
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:110654 original size:21 final size:22
Alignment explanation
Indices: 110624--110673 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
110614 TAATAACTAT
110624 TAATAATAACAACAGTAAT-AA
1 TAATAATAACAACAGTAATAAA
* *
110645 TAATAGTAACAGCAGTAATAAA
1 TAATAATAACAACAGTAATAAA
110667 TAATAAT
1 TAATAAT
110674 TAATATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (22 bp):
TAATAATAACAACAGTAATAAA
Found at i:111883 original size:29 final size:29
Alignment explanation
Indices: 111850--111952 Score: 145
Period size: 29 Copynumber: 3.6 Consensus size: 29
111840 CTAAACTGTT
* *
111850 CAAAAATTACATTTTTACCCCCAAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* *
111879 CAAAAGTT-CATTTTCGACCCCAAAACTTC
1 CAAAAATTCCATTTT-TACCCCAAAACTTC
*
111908 CAAAAATTCCATTTTTACCCCTAAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
111937 CAAAAATTCCATTTTT
1 CAAAAATTCCATTTTT
111953 NNNNNNNNNN
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
28 6 0.09
29 54 0.82
30 6 0.09
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCAAAACTTC
Found at i:113181 original size:16 final size:18
Alignment explanation
Indices: 113149--113183 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
113139 CAACCTTGAA
113149 AAAATTCTTTAAAATATT
1 AAAATTCTTTAAAATATT
113167 AAAATT-TTT-AAATATT
1 AAAATTCTTTAAAATATT
113183 A
1 A
113184 TGTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTCTTTAAAATATT
Found at i:114071 original size:23 final size:22
Alignment explanation
Indices: 114030--114075 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
114020 AGATTTAAAA
*
114030 TTTTAAATTAAATTGTTAATATT
1 TTTTAAATTAAATTATTAA-ATT
**
114053 TTTTAAATTATTTTATTAAATT
1 TTTTAAATTAAATTATTAAATT
114075 T
1 T
114076 GTTAGTGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTAAATTAAATTATTAAATT
Found at i:116022 original size:47 final size:47
Alignment explanation
Indices: 115968--116061 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
115958 CACCCCAATA
*
115968 TAATAACCTCACTTTTGTACTCAAAGGCTAGTTCTCACCACTAAATT
1 TAATAACCTCACTTTTGTACTCAAAGGCTAGATCTCACCACTAAATT
*
116015 TAATAACCTCACTTTTGTACTCAAAGGCTAGATCTCACCAGTAAATT
1 TAATAACCTCACTTTTGTACTCAAAGGCTAGATCTCACCACTAAATT
116062 CTCCCCATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (47 bp):
TAATAACCTCACTTTTGTACTCAAAGGCTAGATCTCACCACTAAATT
Found at i:117234 original size:6 final size:6
Alignment explanation
Indices: 117213--117278 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
117203 TTTATATTGG
** ** **
117213 TTTAAA TTTATT TTTAAA TTTAAA TTTATCTT TTTAAA TTTAAA TTT-GC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
117262 TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
117279 TCAAATTTGA
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
5 3 0.07
6 38 0.84
8 4 0.09
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:118062 original size:21 final size:22
Alignment explanation
Indices: 118032--118081 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
118022 TAATAACTAT
118032 TAATAATAACAACAGTAAT-AA
1 TAATAATAACAACAGTAATAAA
* *
118053 TAATAGTAACAGCAGTAATAAA
1 TAATAATAACAACAGTAATAAA
118075 TAATAAT
1 TAATAAT
118082 TAATATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (22 bp):
TAATAATAACAACAGTAATAAA
Found at i:119291 original size:29 final size:29
Alignment explanation
Indices: 119258--119631 Score: 407
Period size: 29 Copynumber: 12.8 Consensus size: 29
119248 CTAAACTGTT
*
119258 CAAAAATTACATTTTTACCCCCAAACTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
* * *
119287 CAAAAGTT-CATTTTCGACCCCAAAACTTC
1 CAAAAATTCCATTTT-TACCCCCAAACTTC
*
119316 CAAAAATTCCATTTTTACCCCTAAACTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
*
119345 CAAAAATTCCATTTTTACCCCTAAACTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
*
119374 CAAAAATTCCATTTTTACCCCTAAACTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
*
119403 CAAAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
* *
119433 CAAAAATTCCATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
*
119462 CAAAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
* *** *
119492 CAAAGATTCCATTTTTACCCTTGAACCTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
* * *
119521 CAAAATTTCCATTTTTGACCCCGAAACTTT
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
* *
119551 CAAAAATTACCA-TTTTGCCCCCGAA-TGTC
1 CAAAAATT-CCATTTTTACCCCCAAACT-TC
* * *
119580 CAAAAACTCCATTTTTTACCTCGAAAC-TC
1 CAAAAATTCCA-TTTTTACCCCCAAACTTC
*
119609 TC-AAAATTACCTTTTTTACCCCC
1 -CAAAAATT-CCATTTTTACCCCC
119632 CGAATGTCTA
Statistics
Matches: 294, Mismatches: 39, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
28 10 0.03
29 191 0.65
30 90 0.31
31 3 0.01
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCCAAACTTC
Found at i:119447 original size:88 final size:87
Alignment explanation
Indices: 119246--119630 Score: 431
Period size: 88 Copynumber: 4.4 Consensus size: 87
119236 CCCTTGAGAT
* * * * *
119246 CCCTAAACTGTTCAAAAATTACATTTTTACCCCCAAACTTCCAAAAGTT-CATTTTCGACCCCAA
1 CCCTAAACT-TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTT-TACCCCAA
119310 AACTTCCAAAAATTCCATTTTTAC
64 AACTTCCAAAAATTCCATTTTTAC
*
119334 CCCTAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTACCCCTAAA
1 CCCTAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTACCCCAAAA
119399 CTTCCAAAAATTCCATTTTTGAC
66 CTTCCAAAAATTCCATTTTT-AC
* *
119422 CCCAAAACTTCCAAAAATTCCATTTTTA-CCCTCGAACTTCCAAAAATTCCATTTTTGACCCCAA
1 CCCTAAACTTCCAAAAATTCCATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTT-ACCCCAA
*
119486 AACTTCCAAAGATTCCATTTTTAC
64 AACTTCCAAAAATTCCATTTTTAC
* * * * * * * **
119510 CCTTGAACCTCCAAAATTTCCATTTTTGACCCCGAAACTTTCAAAAATTACCA-TTTTGCCCCCG
1 CCCTAAACTTCCAAAAATTCCATTTTT-ACCCCTAAACTTCCAAAAATT-CCATTTTTACCCCAA
*
119574 AA-TGTCCAAAAACTCCATTTTTTAC
64 AACT-TCCAAAAATTCCA-TTTTTAC
* * *
119599 CTCGAAAC-TCTC-AAAATTACCTTTTTTACCCC
1 CCCTAAACTTC-CAAAAATT-CCATTTTTACCCC
119631 CCGAATGTCT
Statistics
Matches: 257, Mismatches: 29, Indels: 22
0.83 0.09 0.07
Matches are distributed among these distances:
87 68 0.26
88 119 0.46
89 64 0.25
90 6 0.02
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.33
Consensus pattern (87 bp):
CCCTAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTACCCCAAAA
CTTCCAAAAATTCCATTTTTAC
Found at i:119460 original size:59 final size:59
Alignment explanation
Indices: 119258--119655 Score: 468
Period size: 59 Copynumber: 6.8 Consensus size: 59
119248 CTAAACTGTT
* * * *
119258 CAAAAATTACATTTTTACCCCCAAACTTCCAAAAGTT-CATTTTCGACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
** *
119316 CAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTT-ACCCCTAAACTTC
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
**
119374 CAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
*
119433 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* ** * * * *
119492 CAAAGATTCCATTTTTACCCTTGAACCTCCAAAATTTCCATTTTTGACCCCGAAACTTT
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* * * * *
119551 CAAAAATTACCA-TTTTGCCCCCGAA-TGTCCAAAAACTCCATTTTTTACCTCGAAAC-TC
1 CAAAAATT-CCATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTTGACCCCAAAACTTC
* * *
119609 TC-AAAATTACCTTTTTTACCCCCCGAA-TGTCTAAAAATTCTATTTTT
1 -CAAAAATT-CCATTTTTA-CCCCCGAACT-TCCAAAAATTCCATTTTT
119656 AACCTCGAAT
Statistics
Matches: 303, Mismatches: 30, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
58 101 0.33
59 174 0.57
60 28 0.09
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (59 bp):
CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
Found at i:119665 original size:29 final size:29
Alignment explanation
Indices: 119572--119665 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
119562 ATTTTGCCCC
* * * *
119572 CGAATGTCCAAAAACTCCATTTTTTACCT
1 CGAATGTCTAAAAATTCTATTTTTAACCT
** * * *
119601 CGAAACTCTCAAAATTACCT-TTTTTACCCCC
1 CGAATGTCTAAAAATT--CTATTTTTA-ACCT
119632 CGAATGTCTAAAAATTCTATTTTTAACCT
1 CGAATGTCTAAAAATTCTATTTTTAACCT
119661 CGAAT
1 CGAAT
119666 TGTCCCAAAA
Statistics
Matches: 47, Mismatches: 14, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
29 20 0.43
30 11 0.23
31 16 0.34
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (29 bp):
CGAATGTCTAAAAATTCTATTTTTAACCT
Found at i:129725 original size:2 final size:2
Alignment explanation
Indices: 129718--129751 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
129708 GAGTTAATTA
* *
129718 AT AT AT AT AT AT AT AT AT AT AT AA AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
129752 TTAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:134196 original size:19 final size:20
Alignment explanation
Indices: 134164--134201 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
134154 ACTCAAACTA
134164 TTTATTCAAA-TTTTGAATT
1 TTTATTCAAATTTTTGAATT
134183 TTTATT-AAATTTTTTGAAT
1 TTTATTCAAA-TTTTTGAAT
134202 CGAATCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 6 0.35
20 8 0.47
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTATTCAAATTTTTGAATT
Found at i:136606 original size:20 final size:18
Alignment explanation
Indices: 136578--136624 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
136568 TCACGTCAGC
*
136578 AAATAATTTTTAAATTATTA
1 AAATTATTTTTAAA-TA-TA
136598 AAATTATTTTTTAAATATA
1 AAATTA-TTTTTAAATATA
136617 AAATTATT
1 AAATTATT
136625 AAAACTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 8 0.32
20 7 0.28
21 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATTATTTTTAAATATA
Found at i:136618 original size:19 final size:21
Alignment explanation
Indices: 136584--136624 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
136574 CAGCAAATAA
136584 TTTTTAAATTATTAAAATTAT
1 TTTTTAAATTATTAAAATTAT
136605 TTTTTAAA-TA-TAAAATTAT
1 TTTTTAAATTATTAAAATTAT
136624 T
1 T
136625 AAAACTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 2 0.10
21 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTTAAATTATTAAAATTAT
Found at i:137450 original size:12 final size:11
Alignment explanation
Indices: 137432--137472 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
137422 ATAATTTTAT
*
137432 ATTTAAAAATA
1 ATTTTAAAATA
*
137443 ATTTTAAATTA
1 ATTTTAAAATA
137454 ATTTTAAAATA
1 ATTTTAAAATA
*
137465 TTTTTAAA
1 ATTTTAAA
137473 TAAAAAAATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:137457 original size:22 final size:22
Alignment explanation
Indices: 137432--137473 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
137422 ATAATTTTAT
137432 ATTTAAAAATAATTTTAAATTA
1 ATTTAAAAATAATTTTAAATTA
* *
137454 ATTTTAAAATATTTTTAAAT
1 ATTTAAAAATAATTTTAAAT
137474 AAAAAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTAAAAATAATTTTAAATTA
Found at i:144313 original size:12 final size:12
Alignment explanation
Indices: 144296--144321 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
144286 TTATTATTTC
144296 TTTTCTTTCTTT
1 TTTTCTTTCTTT
144308 TTTTCTTTCTTT
1 TTTTCTTTCTTT
144320 TT
1 TT
144322 AATTATTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:145881 original size:39 final size:39
Alignment explanation
Indices: 145766--145939 Score: 147
Period size: 39 Copynumber: 4.5 Consensus size: 39
145756 ATAACCTGGT
* * * * *
145766 AGTGTTTATC-GTGTCACTACCACTTCATTATAACATTGC
1 AGTGTTTA-CAGTGTCACTGCCAGTTCAGTGTAGCATTGC
* * *
145805 -GATGTTTACAGTGTCACTACCAGTTCAATATTA-CATTGC
1 AG-TGTTTACAGTGTCACTGCCAGTTCAGT-GTAGCATTGC
* * * * *
145844 AGTGTGTACAGTGTCATTGCTAGTTTAGTGTAGCATTGT
1 AGTGTTTACAGTGTCACTGCCAGTTCAGTGTAGCATTGC
* *
145883 AGTGTTTACAGTGTTACTGCCAGTTCAGTGTAGCATTAC
1 AGTGTTTACAGTGTCACTGCCAGTTCAGTGTAGCATTGC
* *
145922 AATGTTTACAATGTCACT
1 AGTGTTTACAGTGTCACT
145940 ACCGATTCAG
Statistics
Matches: 109, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
38 4 0.04
39 102 0.94
40 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTGCCAGTTCAGTGTAGCATTGC
Found at i:150875 original size:12 final size:12
Alignment explanation
Indices: 150860--150899 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
150850 TTTAGACTTC
150860 TTTTTTTTTAAT
1 TTTTTTTTTAAT
150872 TTTTTTTTTAAT
1 TTTTTTTTTAAT
150884 TTTTTTTTTAAT
1 TTTTTTTTTAAT
150896 TTTT
1 TTTT
150900 AGGTAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTAAT
Found at i:150908 original size:24 final size:24
Alignment explanation
Indices: 150860--150908 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
150850 TTTAGACTTC
*** *
150860 TTTTTTTTTAATTTTTTTTTTAAT
1 TTTTTTTTTAATTTTTAGGTAAAT
150884 TTTTTTTTTAATTTTTAGGTAAAT
1 TTTTTTTTTAATTTTTAGGTAAAT
150908 T
1 T
150909 ACGTGATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTTTTTTTAATTTTTAGGTAAAT
Found at i:151478 original size:15 final size:15
Alignment explanation
Indices: 151451--151484 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
151441 GAAATTTATG
151451 ATTTATAAATTTTTT
1 ATTTATAAATTTTTT
*
151466 ATTTTTAAATTTTTT
1 ATTTATAAATTTTTT
151481 ATTT
1 ATTT
151485 GAGAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTATAAATTTTTT
Found at i:151491 original size:15 final size:15
Alignment explanation
Indices: 151438--151484 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
151428 AAATTTTAGC
* *
151438 TTTGAAATTTATGAT
1 TTTGAAATTTTTTAT
151453 TTAT-AAATTTTTTAT
1 TT-TGAAATTTTTTAT
*
151468 TTTTAAATTTTTTAT
1 TTTGAAATTTTTTAT
151483 TT
1 TT
151485 GAGAATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (15 bp):
TTTGAAATTTTTTAT
Found at i:151916 original size:16 final size:15
Alignment explanation
Indices: 151899--151953 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
151889 TATAAAATAT
151899 ATTATATTAATTAT-
1 ATTATATTAATTATA
* *
151913 A-TATGTTAAATGATA
1 ATTATATT-AATTATA
*
151928 ATTATATATATTTATA
1 ATTATAT-TAATTATA
151944 ATTATATTAA
1 ATTATATTAA
151954 ATCACTAACT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
13 5 0.16
14 6 0.19
15 3 0.10
16 16 0.52
17 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTATATTAATTATA
Found at i:152099 original size:15 final size:16
Alignment explanation
Indices: 152079--152110 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
152069 CATTTAGTGT
152079 ATTATTTTTAAA-AAA
1 ATTATTTTTAAATAAA
152094 ATTATTTTTAAATAAA
1 ATTATTTTTAAATAAA
152110 A
1 A
152111 ACTAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATTTTTAAATAAA
Found at i:179396 original size:17 final size:19
Alignment explanation
Indices: 179374--179416 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
179364 CATTTTTTTC
179374 TTCTTTTC-TTTTCTC-TT
1 TTCTTTTCTTTTTCTCATT
179391 TTC-TTTCTTTTTCTCATT
1 TTCTTTTCTTTTTCTCATT
179409 TTCCTTTT
1 TT-CTTTT
179417 TCAAATGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 10 0.45
18 4 0.18
19 1 0.05
20 3 0.14
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (19 bp):
TTCTTTTCTTTTTCTCATT
Found at i:179397 original size:24 final size:23
Alignment explanation
Indices: 179366--179417 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
179356 ATAGCAAACA
179366 TTTTTTTCTTCTTT-TC-TTTTCTC
1 TTTTTTTCTT-TTTCTCATTTTC-C
179389 TTTTCTTTCTTTTTCTCATTTTCC
1 TTTT-TTTCTTTTTCTCATTTTCC
179413 TTTTT
1 TTTTT
179418 CAAATGACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
23 8 0.31
24 13 0.50
25 5 0.19
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTTTCTTTTTCTCATTTTCC
Found at i:180032 original size:16 final size:17
Alignment explanation
Indices: 180013--180047 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
180003 CTAAAAAAAA
180013 CAATG-CAATAAAAATG
1 CAATGACAATAAAAATG
*
180029 CAATGACAATAAATATG
1 CAATGACAATAAAAATG
180046 CA
1 CA
180048 TGCGAACTAT
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:0.54, C:0.14, G:0.11, T:0.20
Consensus pattern (17 bp):
CAATGACAATAAAAATG
Found at i:186054 original size:53 final size:52
Alignment explanation
Indices: 185927--186063 Score: 147
Period size: 51 Copynumber: 2.7 Consensus size: 52
185917 AGCTATAAAC
* * * *
185927 CAAAGGTCCGATGACTA-AGTATCATTGTGAGTAAATGAATCCATGATGGAT
1 CAAAGGTCCGATGACTATAGTGTCATCGTGAGTAAATGAATCCATGACGGAA
* * * *
185978 TAAAGGTCTGCTGACT-TAGTGTCATCGTGAGTATATGAATTCCTAT-ACGGAA
1 CAAAGGTCCGATGACTATAGTGTCATCGTGAGTAAATGAA-TCC-ATGACGGAA
186030 CAAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 CAA-AGGTCCGATGACTATAGTGTCATCGTGAGTA
186064 CTAAATAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
51 32 0.46
52 9 0.13
53 27 0.39
54 2 0.03
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29
Consensus pattern (52 bp):
CAAAGGTCCGATGACTATAGTGTCATCGTGAGTAAATGAATCCATGACGGAA
Found at i:186107 original size:122 final size:122
Alignment explanation
Indices: 185955--186199 Score: 400
Period size: 122 Copynumber: 2.0 Consensus size: 122
185945 GTATCATTGT
* * * *
185955 GAGTAAATGAATCCATGATGGATTAAAGGTCTGCTGACTTAGTGTCATCGTGAGTATATGAATTC
1 GAGTAAATAAATCCATGATGGATTAAAGGTCTGATGACTCAGTGTCATCATGAGTATATGAATTC
* * *
186020 CTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTACTAAATAAAATGA
66 CTATACGAAACAAAAGGTCCGATGACTATATGTCATCGTAAGTACTAAATAAAATGA
186077 GAGTAAATAAATCCATGATGGATTAAAGGTCTGATGACTCAGTGTCATCATGAGTATATGAATTC
1 GAGTAAATAAATCCATGATGGATTAAAGGTCTGATGACTCAGTGTCATCATGAGTATATGAATTC
* * *
186142 CTATACGAAACAAAATGTCCGATGACTATATGTCATCGTAAGTATTAAATGAAATGA
66 CTATACGAAACAAAAGGTCCGATGACTATATGTCATCGTAAGTACTAAATAAAATGA
186199 G
1 G
186200 TTCTTATACG
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
122 113 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.29
Consensus pattern (122 bp):
GAGTAAATAAATCCATGATGGATTAAAGGTCTGATGACTCAGTGTCATCATGAGTATATGAATTC
CTATACGAAACAAAAGGTCCGATGACTATATGTCATCGTAAGTACTAAATAAAATGA
Found at i:186269 original size:60 final size:60
Alignment explanation
Indices: 186134--186311 Score: 225
Period size: 61 Copynumber: 3.0 Consensus size: 60
186124 TCATGAGTAT
* * *
186134 ATGAATTCCTATACGAAACAAAATGTCCGATGACTATATGTCATCGTAAGTATTAAATGAA
1 ATGAGTTCCTATACGGAACAAAAGGTCCGATGACTATATGTC-TCGTAAGTATTAAATGAA
*
186195 ATGAGTTCTTATACGGAACAAAAGGTCCGATGACTATATGTCTCGTAAGTATTAAATGAA
1 ATGAGTTCCTATACGGAACAAAAGGTCCGATGACTATATGTCTCGTAAGTATTAAATGAA
* * ** * * *
186255 ATGAGTTCCAATAC-GAAC-AAGGGTCAAATGACTTTATGTCCTCGTGAGTAATAAATG
1 ATGAGTTCCTATACGGAACAAAAGGTCCGATGACTATATGT-CTCGTAAGTATTAAATG
186312 TGAGTGACAC
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
58 17 0.16
59 19 0.18
60 30 0.29
61 38 0.37
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (60 bp):
ATGAGTTCCTATACGGAACAAAAGGTCCGATGACTATATGTCTCGTAAGTATTAAATGAA
Found at i:188766 original size:51 final size:51
Alignment explanation
Indices: 188660--188942 Score: 338
Period size: 51 Copynumber: 5.5 Consensus size: 51
188650 TTTCATTTAA
* * ** *
188660 TACTCATGATGACA-TATAGTCATCGGACCTCTTGTTCCGTATAGGAATTCA--
1 TACTCACGATGACACT-TAGTCATCGGA-CTTTTAATCCGTAAAGG-ATTCATT
* ** * * * *
188711 TACTCACGATAACACGGAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCATT
*
188762 TACTCACGATGACACTTAGTTATCGGACTTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCATT
* * *
188813 TACTCATGATGACACTTCGTCATCGGATTTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCATT
* *
188864 TACTCACGATGACACTTAGTCATTGGACTTTTAATCCGTAAAGGGTTCATT
1 TACTCACGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCATT
**
188915 TACTCTTGATGACACTTAGTCATCGGAC
1 TACTCACGATGACACTTAGTCATCGGAC
188943 CCTTTCGTTT
Statistics
Matches: 197, Mismatches: 32, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
49 5 0.03
50 9 0.05
51 183 0.93
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCATT
Found at i:200153 original size:51 final size:51
Alignment explanation
Indices: 200077--200217 Score: 246
Period size: 51 Copynumber: 2.8 Consensus size: 51
200067 GCTATAAACG
* *
200077 AAAGGTCCGATGACTAAGTGACATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTCAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
*
200128 AAAGGTTCGATGACTCAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTCAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
*
200179 AAAGGTCCGATGACTCAGTGTCATCGTGAGTATATGAAT
1 AAAGGTCCGATGACTCAGTGTCATCGTGAGTAAATGAAT
200218 TCCTATACGG
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 85 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTCAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
Found at i:200262 original size:53 final size:57
Alignment explanation
Indices: 200181--200383 Score: 197
Period size: 61 Copynumber: 3.5 Consensus size: 57
200171 GATGGATTAA
*
200181 AGGTCCGATGACTCA-GTGTCATCGTGAGTAT-ATG-A-A-TTCCTATACGGAACAAG
1 AGGTCCGATGACT-ATATGTCATCGTGAGTATAATGAAGAGTTCCTATACGGAACAAG
* *
200234 AGGTCCGATGACTATATGTCATCATGAGTATTAAATGAAATGAGTTCTTATACGGAACAAG
1 AGGTCCGATGACTATATGTCATCGTGAGTA-T-AATG-AA-GAGTTCCTATACGGAACAAG
* *
200295 AGGTCCAATGACTATATGTCATCGTGAGTATTAAATGAAATGAGTTCC-A-ATGTGAACAAG
1 AGGTCCGATGACTATATGTCATCGTGAGTA-T-AATG-AA-GAGTTCCTATACG-GAACAAG
* *
200355 -GGTCCGATGACTTTGTGTCATCGTGAGTA
1 AGGTCCGATGACTATATGTCATCGTGAGTA
200384 ATAAATGCGA
Statistics
Matches: 130, Mismatches: 10, Indels: 14
0.84 0.06 0.09
Matches are distributed among these distances:
52 1 0.01
53 26 0.20
54 1 0.01
56 3 0.02
58 1 0.01
59 28 0.22
60 9 0.07
61 61 0.47
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (57 bp):
AGGTCCGATGACTATATGTCATCGTGAGTATAATGAAGAGTTCCTATACGGAACAAG
Found at i:200316 original size:61 final size:60
Alignment explanation
Indices: 200220--200390 Score: 247
Period size: 61 Copynumber: 2.9 Consensus size: 60
200210 ATATGAATTC
*
200220 CTATACGGAACAAGAGGTCCGATGACTATATGTCATCATGAGTATTAAATGAAATGAGTT
1 CTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAAATGAGTT
*
200280 CTTATACGGAACAAGAGGTCCAATGACTATATGTCATCGTGAGTATTAAATGAAATGAGTT
1 C-TATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAAATGAGTT
* * * * *
200341 CCA-ATGTGAACAAG-GGTCCGATGACTTTGTGTCATCGTGAGTAATAAATG
1 CTATACG-GAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATG
200391 CGAGTGAAAC
Statistics
Matches: 101, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
59 34 0.34
60 9 0.09
61 58 0.57
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (60 bp):
CTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAAATGAGTT
Found at i:201049 original size:21 final size:21
Alignment explanation
Indices: 201025--201100 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
201015 ATGCATGACA
*
201025 TGTATCGGTAGAACTTATACT
1 TGTATCGGTAGAACTAATACT
*
201046 TGTATCGGTAAAACTAATACT
1 TGTATCGGTAGAACTAATACT
** * *
201067 TGTATCATTAGAACTAGTACA
1 TGTATCGGTAGAACTAATACT
* *
201088 GGTACCGGTAGAA
1 TGTATCGGTAGAA
201101 ATCTACACCA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (21 bp):
TGTATCGGTAGAACTAATACT
Found at i:207401 original size:11 final size:11
Alignment explanation
Indices: 207387--207411 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
207377 AATTTTCGAA
207387 AAATCTTCTAT
1 AAATCTTCTAT
207398 AAATCTTCTAT
1 AAATCTTCTAT
207409 AAA
1 AAA
207412 AACCAGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATCTTCTAT
Found at i:213942 original size:5 final size:5
Alignment explanation
Indices: 213932--213978 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
213922 TTAATGTGAA
213932 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
213979 TTTTCAATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:221225 original size:2 final size:2
Alignment explanation
Indices: 221214--221248 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
221204 AACATTTAAA
221214 AT AT -T 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
221249 CATAATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:224105 original size:24 final size:24
Alignment explanation
Indices: 224077--224139 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
224067 AGAAATAATC
224077 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* * *
224101 TTTCAATTAAATTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
224125 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
224140 TATTAGTCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:227926 original size:24 final size:24
Alignment explanation
Indices: 227890--227963 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 24
227880 GCAAGTTTAT
* *
227890 TACGTTTATGCTCGTCAACATAAA
1 TACGTTTACGCTCGTCAGCATAAA
* ** *
227914 TACGTCTACGCTCACCAGCATGAA
1 TACGTTTACGCTCGTCAGCATAAA
227938 TACGTTTACGCTCGTCAGCATAAA
1 TACGTTTACGCTCGTCAGCATAAA
227962 TA
1 TA
227964 TAAGAAACAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (24 bp):
TACGTTTACGCTCGTCAGCATAAA
Found at i:228067 original size:14 final size:15
Alignment explanation
Indices: 228041--228070 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
228031 TGCAATATAC
228041 ATATTTCACATTTAT
1 ATATTTCACATTTAT
228056 ATATTT-ACATTTAT
1 ATATTTCACATTTAT
228070 A
1 A
228071 ACTTTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTCACATTTAT
Found at i:230473 original size:18 final size:18
Alignment explanation
Indices: 230443--230492 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
230433 TACTCAACAG
230443 AAGAGTC-CACAAAACCAC
1 AAGAGTCGC-CAAAACCAC
230461 AAGAGTCGCC-AAACCAC
1 AAGAGTCGCCAAAACCAC
*
230478 -AGATCTCGCCAAAAC
1 AAGA-GTCGCCAAAAC
230493 AAAGAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 3 0.11
17 12 0.43
18 12 0.43
19 1 0.04
ACGTcount: A:0.44, C:0.34, G:0.14, T:0.08
Consensus pattern (18 bp):
AAGAGTCGCCAAAACCAC
Found at i:231058 original size:23 final size:23
Alignment explanation
Indices: 231009--231060 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
230999 ATATGTTTAT
* *
231009 ATTTTTTAAAATGATTTTTAGTT
1 ATTTTTTAAAATGATTTTTACTC
*
231032 ATTTTTTAATA-GATTTTCTACTC
1 ATTTTTTAAAATGATTTT-TACTC
231055 ATTTTT
1 ATTTTT
231061 AGTCATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.62
Consensus pattern (23 bp):
ATTTTTTAAAATGATTTTTACTC
Found at i:231114 original size:20 final size:21
Alignment explanation
Indices: 231086--231124 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
231076 TTTTTTTTAC
231086 AATTATTAAGAA-AATTTTAAA
1 AATTATTAA-AATAATTTTAAA
231107 AATT-TTAAAATAATTTTA
1 AATTATTAAAATAATTTTA
231125 TAACTATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 11 0.65
21 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
AATTATTAAAATAATTTTAAA
Found at i:231805 original size:25 final size:25
Alignment explanation
Indices: 231777--231827 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
231767 AAAAGAAAAA
*
231777 TTGA-ACTAAAATTCTCCTAATTTTT
1 TTGATACT-AAATTCTCCTAAATTTT
* *
231802 TTGATAGTTAATTCTCCTAAATTTT
1 TTGATACTAAATTCTCCTAAATTTT
231827 T
1 T
231828 ATCAAACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (25 bp):
TTGATACTAAATTCTCCTAAATTTT
Found at i:232727 original size:18 final size:18
Alignment explanation
Indices: 232693--232731 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
232683 CTAATTTCAT
232693 TTGAAAATTCAAGTTGGCA
1 TTGAAAATTCAAGTTGG-A
*
232712 TTGAAAA-TCTAGTTGGA
1 TTGAAAATTCAAGTTGGA
232729 TTG
1 TTG
232732 CCACGTAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 8 0.42
19 7 0.37
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (18 bp):
TTGAAAATTCAAGTTGGA
Found at i:233353 original size:15 final size:15
Alignment explanation
Indices: 233333--233363 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
233323 CGCAAAAAAT
*
233333 ACCGCTAAAGATAAC
1 ACCGCTAAAAATAAC
233348 ACCGCTAAAAATAAC
1 ACCGCTAAAAATAAC
233363 A
1 A
233364 GTGTTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.10, T:0.13
Consensus pattern (15 bp):
ACCGCTAAAAATAAC
Found at i:235556 original size:12 final size:12
Alignment explanation
Indices: 235539--235563 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
235529 TCTATAAAAG
235539 AAGATTAAGAAA
1 AAGATTAAGAAA
235551 AAGATTAAGAAA
1 AAGATTAAGAAA
235563 A
1 A
235564 CCATCTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AAGATTAAGAAA
Found at i:237891 original size:41 final size:41
Alignment explanation
Indices: 237829--237954 Score: 148
Period size: 41 Copynumber: 3.1 Consensus size: 41
237819 AAACTCAACT
* * *
237829 TTTAGTGGTGCTTTTTCATAAGCGTCGTTATTGCTTTGACC
1 TTTAGCGGTGCTTTTTCATAAGCGCCGCTATTGCTTTGACC
* *
237870 TTTAGCGGTGTTTTTTTATAAGCGCCGCTATTGCTTTGACC
1 TTTAGCGGTGCTTTTTCATAAGCGCCGCTATTGCTTTGACC
* * * *
237911 TTTAAC--TGCGTTTGTCATAAGTGCTGCTATTGCTTTGACC
1 TTTAGCGGTGC-TTTTTCATAAGCGCCGCTATTGCTTTGACC
237951 TTTA
1 TTTA
237955 CTAAGCGTCG
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.03
40 30 0.41
41 41 0.56
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (41 bp):
TTTAGCGGTGCTTTTTCATAAGCGCCGCTATTGCTTTGACC
Found at i:237942 original size:40 final size:41
Alignment explanation
Indices: 237840--237954 Score: 135
Period size: 40 Copynumber: 2.9 Consensus size: 41
237830 TTAGTGGTGC
* * * *
237840 TTTT-TCATAAGCGTCGTTATTGCTTTGACCTTTAGCGGTG
1 TTTTGTCATAAGCGCCGCTATTGCTTTGACCTTTAACGGCG
* * *
237880 TTTTTTTATAAGCGCCGCTATTGCTTTGACCTTTAACTGCG
1 TTTTGTCATAAGCGCCGCTATTGCTTTGACCTTTAACGGCG
* *
237921 -TTTGTCATAAGTGCTGCTATTGCTTTGACCTTTA
1 TTTTGTCATAAGCGCCGCTATTGCTTTGACCTTTA
237955 CTAAGCGTCG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 34 0.53
41 30 0.47
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (41 bp):
TTTTGTCATAAGCGCCGCTATTGCTTTGACCTTTAACGGCG
Found at i:238216 original size:41 final size:42
Alignment explanation
Indices: 237956--238227 Score: 148
Period size: 41 Copynumber: 6.6 Consensus size: 42
237946 TGACCTTTAC
* * *
237956 TAAGCGTCGTTATTGCTCTAACCTTTAGCGA-GC--TTGCCTA
1 TAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTTTGCC-A
* * * * * ****
237996 TCAGCGTCGCTATTGCTCTAACTTTTAGC-AGTGCTTTTTTTTT
1 TAAGCGCCGCTATTGCTCTGACCTTTAGCGA-CGC-TTTTGCCA
* * * * *
238039 TAAGCGCCGCTATTGCTCTAACTTTTAGCGGCGCTTATG-GA
1 TAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTTTGCCA
* * * * * * *
238080 AAAGTGTCGCTGTTGCTCTGACCTTTATCTACGCTTGT-CCA
1 TAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTTTGCCA
* * * * *
238121 TAAGCGGCTCTATTGCTTTGACCTTTAGCGGCGC-TTTCCCA
1 TAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTTTGCCA
* * **
238162 TAAGCGACACTATTGCTCTGACCTTTAGCGACGCTTTTGGGA
1 TAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTTTGCCA
*
238204 -AAGTGCCGCTATTGCTCT-ACCTTT
1 TAAGCGCCGCTATTGCTCTGACCTTT
238228 TGCGGCATTT
Statistics
Matches: 177, Mismatches: 46, Indels: 18
0.73 0.19 0.07
Matches are distributed among these distances:
39 1 0.01
40 34 0.19
41 104 0.59
42 7 0.04
43 29 0.16
44 2 0.01
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (42 bp):
TAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTTTGCCA
Found at i:238799 original size:28 final size:28
Alignment explanation
Indices: 238753--238812 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
238743 CTTTCGTTGT
238753 TTTTCTTTTTCTTTGTTCTTTATTCTCTC
1 TTTTCTTTTTCTTTGTTCTTTATTCT-TC
* *
238782 TTTTC-TTTTCTTTTTTCTTTTTTCTTC
1 TTTTCTTTTTCTTTGTTCTTTATTCTTC
238809 TTTT
1 TTTT
238813 GGTCAACCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 6 0.21
28 18 0.62
29 5 0.17
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (28 bp):
TTTTCTTTTTCTTTGTTCTTTATTCTTC
Found at i:238802 original size:17 final size:17
Alignment explanation
Indices: 238758--238812 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
238748 GTTGTTTTTC
*
238758 TTTTTCTTTGTTCTT-T
1 TTTTTCTTTTTTCTTCT
*
238774 ATTCTCTCTTTTCTT-TTCT
1 -TT-TTTCTTTT-TTCTTCT
238793 TTTTTCTTTTTTCTTCT
1 TTTTTCTTTTTTCTTCT
238810 TTT
1 TTT
238813 GGTCAACCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.06
17 16 0.52
18 10 0.32
19 3 0.10
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTTTCTTCT
Found at i:238804 original size:7 final size:7
Alignment explanation
Indices: 238752--238812 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
238742 ACTTTCGTTG
238752 TTTTTC-
1 TTTTTCT
238758 TTTTTCT
1 TTTTTCT
*
238765 TTGTTCT
1 TTTTTCT
238772 TTATTCTCT
1 TT-TT-TCT
*
238781 CTTTTC-
1 TTTTTCT
238787 -TTTTCT
1 TTTTTCT
238793 TTTTTCT
1 TTTTTCT
238800 TTTTTCT
1 TTTTTCT
238807 TCTTTT
1 T-TTTT
238813 GGTCAACCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
5 5 0.11
6 6 0.13
7 24 0.52
8 7 0.15
9 4 0.09
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (7 bp):
TTTTTCT
Found at i:240771 original size:52 final size:51
Alignment explanation
Indices: 240683--240927 Score: 238
Period size: 52 Copynumber: 4.7 Consensus size: 51
240673 ATTTCACTTC
* * * * * * *
240683 ATTCATATACCCGCGATGACACATAGCCACCAGACCTTATAATCCGCAAGGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTT-TAATCCGTAAAGG
* * * *
240735 ATTCGTATACTCATGATGACACAGAGTCATCGGACCTCTTAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCT-TTAATCCGTAAAGG
* * * * *
240787 ATCCATATACTCACGATAACACTTTGTCATCGAACCTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACC-TTTAATCCGTAAAGG
* * * * *
240839 ATTCATATACTCAAGATAACACTTAGTCATCAGACCGTTTAATCCGTAAAAG
1 ATTCATATACTCACGATGACACATAGTCATCGGACC-TTTAATCCGTAAAGG
* * *
240891 ATTCATATACTCACAATGACACATAATCATCGAACCT
1 ATTCATATACTCACGATGACACATAGTCATCGGACCT
240928 CTTCGTTTAT
Statistics
Matches: 157, Mismatches: 34, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
51 1 0.01
52 154 0.98
53 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAAAGG
Found at i:242624 original size:3 final size:3
Alignment explanation
Indices: 242618--242658 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
242608 CATCATCATC
242618 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
242659 TAAAACATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:271821 original size:22 final size:21
Alignment explanation
Indices: 271794--271836 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
271784 CCTCCTTGGC
*
271794 TTTTCTTCTGCTTTTTTTTTCT
1 TTTTC-TCTGCTTCTTTTTTCT
271816 TTTTCTCTGCTTCTTTTTTCT
1 TTTTCTCTGCTTCTTTTTTCT
271837 CGGCTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTTCTCTGCTTCTTTTTTCT
Found at i:271835 original size:15 final size:15
Alignment explanation
Indices: 271815--271846 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
271805 TTTTTTTTTC
*
271815 TTTTTCTCTGCTTCT
1 TTTTTCTCGGCTTCT
271830 TTTTTCTCGGCTTCT
1 TTTTTCTCGGCTTCT
271845 TT
1 TT
271847 CTGTTTCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.25, G:0.09, T:0.66
Consensus pattern (15 bp):
TTTTTCTCGGCTTCT
Found at i:272775 original size:15 final size:15
Alignment explanation
Indices: 272755--272784 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
272745 TGTGAAGAAT
*
272755 TTTTCTTTTTTCTTG
1 TTTTCTTTTTCCTTG
272770 TTTTCTTTTTCCTTG
1 TTTTCTTTTTCCTTG
272785 GATCTAACGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTTCTTTTTCCTTG
Found at i:279071 original size:22 final size:23
Alignment explanation
Indices: 279030--279072 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
279020 AATGCAAATT
*
279030 TACCACAAAGGTAGACGAAAACG
1 TACCACAAAGATAGACGAAAACG
*
279053 TACCAC-AAGATAGAGGAAAA
1 TACCACAAAGATAGACGAAAA
279073 ACGTGCCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.51, C:0.19, G:0.21, T:0.09
Consensus pattern (23 bp):
TACCACAAAGATAGACGAAAACG
Found at i:279073 original size:23 final size:23
Alignment explanation
Indices: 279030--279099 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
279020 AATGCAAATT
* *
279030 TACCACAAAGGTAGACG-AAAACG
1 TACCAC-AAGATAGAAGAAAAACG
*
279053 TACCACAAGATAGAGGAAAAACG
1 TACCACAAGATAGAAGAAAAACG
* * * *
279076 TGCCATAAGACAAAAGAAAAACG
1 TACCACAAGATAGAAGAAAAACG
279099 T
1 T
279100 GTCACAAAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 8 0.21
23 31 0.79
ACGTcount: A:0.51, C:0.19, G:0.20, T:0.10
Consensus pattern (23 bp):
TACCACAAGATAGAAGAAAAACG
Found at i:282848 original size:12 final size:12
Alignment explanation
Indices: 282833--282863 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
282823 TATATGTTCA
282833 TGAACATGTGCG
1 TGAACATGTGCG
*
282845 TGAACATGTTCG
1 TGAACATGTGCG
282857 TGAACAT
1 TGAACAT
282864 TAAACAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (12 bp):
TGAACATGTGCG
Found at i:283547 original size:6 final size:6
Alignment explanation
Indices: 283536--283599 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
283526 AATGGAACTT
* * * ** *
283536 TTTAAA TTTAAA -ATAAT TTTAAT TTTAAA AGTAAA TTTAAA CTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
283582 TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
283600 ACAAATTTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
5 7 0.15
6 39 0.85
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:283555 original size:17 final size:17
Alignment explanation
Indices: 283536--283610 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
283526 AATGGAACTT
*
283536 TTTAAATTTAAAATAAT
1 TTTAAATTTAAAATAAA
*
283553 TTTAATTTTAAAAGTAAA
1 TTTAAATTTAAAA-TAAA
* **
283571 TTTAAACTTAATTTAAA
1 TTTAAATTTAAAATAAA
*
283588 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
283605 TTTAAA
1 TTTAAA
283611 AAGAAATTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
17 35 0.74
18 12 0.26
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:283585 original size:11 final size:12
Alignment explanation
Indices: 283567--283599 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
283557 ATTTTAAAAG
283567 TAAATTTAAACT
1 TAAATTTAAACT
*
283579 T-AATTTAAATT
1 TAAATTTAAACT
283590 TAAATTTAAA
1 TAAATTTAAA
283600 ACAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAATTTAAACT
Found at i:283585 original size:23 final size:23
Alignment explanation
Indices: 283554--283620 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
283544 TAAAATAATT
283554 TTAATTTTAAAAGTAAATTTAAAC
1 TTAA-TTTAAAAGTAAATTTAAAC
**
283578 TTAATTTAAATTTAAATTTAAAAC
1 TTAATTTAAAAGTAAATTT-AAAC
*
283602 -AAATTTAAAAAG-AAATTTA
1 TTAATTT-AAAAGTAAATTTA
283621 GTTTAAGCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
22 1 0.03
23 24 0.67
24 11 0.31
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (23 bp):
TTAATTTAAAAGTAAATTTAAAC
Found at i:283585 original size:29 final size:29
Alignment explanation
Indices: 283538--283593 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
283528 TGGAACTTTT
*
283538 TAAATTTAAAATAATTTTAATTTTAAAAG
1 TAAATTTAAAATAATTTTAAATTTAAAAG
*
283567 TAAATTTAAACTTAA-TTTAAATTTAAA
1 TAAATTTAAA-ATAATTTTAAATTTAAA
283594 TTTAAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAATTTAAAATAATTTTAAATTTAAAAG
Found at i:283599 original size:29 final size:29
Alignment explanation
Indices: 283536--283599 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
283526 AATGGAACTT
*
283536 TTTAAATTTAAAATAATTTTAATTTTAAA
1 TTTAAATTTAAAATAATTTTAAATTTAAA
** *
283565 AGTAAATTTAAACTTAA-TTTAAATTTAAA
1 TTTAAATTTAAA-ATAATTTTAAATTTAAA
283594 TTTAAA
1 TTTAAA
283600 ACAAATTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTAAATTTAAAATAATTTTAAATTTAAA
Found at i:293431 original size:19 final size:20
Alignment explanation
Indices: 293394--293438 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
293384 AATTTTTAAA
* *
293394 TTTTTATGTTATTTGATTTT
1 TTTTTATGTTAATTGATTTG
*
293414 TTTTTATTTTAATT-ATTTG
1 TTTTTATGTTAATTGATTTG
293433 TTTTTA
1 TTTTTA
293439 AATATGGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.76
Consensus pattern (20 bp):
TTTTTATGTTAATTGATTTG
Found at i:295550 original size:4 final size:4
Alignment explanation
Indices: 295541--295573 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
295531 GTCCTCTTCC
295541 CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA C
295574 TCAGCAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:299772 original size:3 final size:3
Alignment explanation
Indices: 299764--299819 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
299754 AATTGCCTGA
* * *
299764 TGC TGC TGC TGC AGC TG- TAGC TGT TGC TGC TGC TGC TG- TAGC TGT
1 TGC TGC TGC TGC TGC TGC T-GC TGC TGC TGC TGC TGC TGC T-GC TGC
299809 TGC TGC TGC TG
1 TGC TGC TGC TG
299820 TCGTTGATGG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.05, C:0.25, G:0.34, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:299818 original size:21 final size:21
Alignment explanation
Indices: 299767--299819 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
299757 TGCCTGATGC
*
299767 TGCTGCTGCAGCTGTAGCTGT
1 TGCTGCTGCTGCTGTAGCTGT
299788 TGCTGCTGCTGCTGTAGCTGT
1 TGCTGCTGCTGCTGTAGCTGT
299809 TGCTGCTGCTG
1 TGCTGCTGCTG
299820 TCGTTGATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.06, C:0.25, G:0.34, T:0.36
Consensus pattern (21 bp):
TGCTGCTGCTGCTGTAGCTGT
Found at i:302294 original size:3 final size:3
Alignment explanation
Indices: 302281--302317 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
302271 TTCATTGTGG
*
302281 GCT GCT GGCT GCT GCT GCT GCT GCT GCT GCT GTT GCT
1 GCT GCT -GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
302318 CCTCTATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.30, G:0.35, T:0.35
Consensus pattern (3 bp):
GCT
Found at i:306332 original size:19 final size:19
Alignment explanation
Indices: 306297--306333 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
306287 TAGGTGGTTA
*
306297 GTATTAGTTAAGTCAGTTG
1 GTATTAGTTAAGGCAGTTG
*
306316 GTATTAGTTGAGGCAGTT
1 GTATTAGTTAAGGCAGTT
306334 AGTCATTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.05, G:0.30, T:0.41
Consensus pattern (19 bp):
GTATTAGTTAAGGCAGTTG
Found at i:316292 original size:5 final size:5
Alignment explanation
Indices: 316282--316323 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
316272 TTTACACATC
* *
316282 CCTAT CCTAT CGTAT CCTAT CCTAT CCTAT CCGAT CCTAT CC
1 CCTAT CCTAT CCTAT CCTAT CCTAT CCTAT CCTAT CCTAT CC
316324 AGCTTACGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.19, C:0.40, G:0.05, T:0.36
Consensus pattern (5 bp):
CCTAT
Found at i:318228 original size:24 final size:24
Alignment explanation
Indices: 318201--318246 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
318191 AAAAATTCAA
318201 TAAAAAATATA-AAATTATTAAATT
1 TAAAAAATATATAAA-TATTAAATT
318225 TAAAAAATATATAAATATTAAA
1 TAAAAAATATATAAATATTAAA
318247 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TAAAAAATATATAAATATTAAATT
Found at i:318254 original size:27 final size:26
Alignment explanation
Indices: 318188--318265 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 26
318178 ACCCACTATA
*
318188 TAAAAAAATTCAATAAAAAATATAAAAT
1 TAAAAAAATT-AA-AAAATATATAAAAT
** *
318216 TATTAAATTTAAAAAATATATAAATAT
1 TAAAAAAATTAAAAAATATATAAA-AT
318243 TAAAAAAATTAAAAAATAATATA
1 TAAAAAAATTAAAAAAT-ATATA
318266 GACAGGCCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
26 11 0.27
27 18 0.44
28 12 0.29
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAAAAAATTAAAAAATATATAAAAT
Found at i:339058 original size:21 final size:20
Alignment explanation
Indices: 339025--339063 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
339015 ATTTTTTAAA
339025 AATTTAACTTTCAATTTTATC
1 AATTTAACTTTC-ATTTTATC
339046 AATTTAA-TCTTCATTTTA
1 AATTTAACT-TTCATTTTA
339064 AAAATTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTTAACTTTCATTTTATC
Found at i:346138 original size:17 final size:18
Alignment explanation
Indices: 346116--346153 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
346106 TATTTAAATG
*
346116 ATTATTTCTATTTAGT-T
1 ATTATTTATATTTAGTCT
346133 ATTATTTATATTTAGTCT
1 ATTATTTATATTTAGTCT
346151 ATT
1 ATT
346154 TAGAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.63
Consensus pattern (18 bp):
ATTATTTATATTTAGTCT
Found at i:346273 original size:22 final size:22
Alignment explanation
Indices: 346248--346303 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
346238 TTTCGCTTTC
346248 ATGTCTCGAGACATATAGTCAT
1 ATGTCTCGAGACATATAGTCAT
346270 ATGTCTCGAGACATATAGTCAT
1 ATGTCTCGAGACATATAGTCAT
*
346292 ATGTCTCAAGAC
1 ATGTCTCGAGAC
346304 TTGACTACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (22 bp):
ATGTCTCGAGACATATAGTCAT
Found at i:371092 original size:88 final size:89
Alignment explanation
Indices: 370874--371093 Score: 263
Period size: 88 Copynumber: 2.5 Consensus size: 89
370864 TGCACTTATT
* * * * *
370874 AATTGAGTACTTGAACTTTGAAATGCA-TAAAAAGGTCCTCATACTTTTCAAAAAAAAGCAATTA
1 AATTGAGTACTTGAACTTTCAAATGCACAAAAAAGCTCTTCAAACTTTTCAAAAAAAAGCAATTA
*
370938 AGCCCTTGTTTTTTTTTTTCACTC
66 AGCCCTTGTTTTTTTTTTGCACTC
*
370962 AATTGGGTACTTGAACTTTCAAAATGCATCCAAAAAA-C-CTTCAAACTTTT-AAAAAAAAGCAA
1 AATTGAGTACTTGAACTTTC-AAATGCA--CAAAAAAGCTCTTCAAACTTTTCAAAAAAAAGCAA
*
371024 TTAAGATCC-T-TTTTTTTTTTGCACTC
63 TTAAG-CCCTTGTTTTTTTTTTGCACTC
* *
371050 AATTGAGTACTTGAACTGTCAAAGTACACAAAAAAGCTCTTCAA
1 AATTGAGTACTTGAACTTTCAAA-TGCACAAAAAAGCTCTTCAA
371094 TCATTAACTT
Statistics
Matches: 113, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
86 7 0.06
87 4 0.04
88 60 0.53
89 25 0.22
90 12 0.11
92 5 0.04
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (89 bp):
AATTGAGTACTTGAACTTTCAAATGCACAAAAAAGCTCTTCAAACTTTTCAAAAAAAAGCAATTA
AGCCCTTGTTTTTTTTTTGCACTC
Found at i:371230 original size:20 final size:19
Alignment explanation
Indices: 371200--371268 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 19
371190 AATATAAAAA
371200 ATAAAAA-TAATTAAAAGTT
1 ATAAAAATTAATTAAAA-TT
371219 ATAAAAATTAA-T-AAATT
1 ATAAAAATTAATTAAAATT
* *
371236 ATAATAAAAATATTTAAAATTT
1 AT-A-AAAATTAATTAAAA-TT
371258 ATTAAAAATTA
1 A-TAAAAATTA
371269 GGAAAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
17 4 0.10
18 4 0.10
19 14 0.35
20 4 0.10
21 9 0.22
22 4 0.10
23 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (19 bp):
ATAAAAATTAATTAAAATT
Found at i:371286 original size:9 final size:9
Alignment explanation
Indices: 371187--371327 Score: 63
Period size: 10 Copynumber: 14.6 Consensus size: 9
371177 GACATGTGGC
371187 AAAAA-TAT
1 AAAAATTAT
371195 AAAAA--AT
1 AAAAATTAT
*
371202 AAAAATAATT
1 AAAAATTA-T
*
371212 AAAAGTTAT
1 AAAAATTAT
371221 AAAAATTAAT
1 AAAAATT-AT
* *
371231 AAATTATAAT
1 AAA-AATTAT
*
371241 AAAAATATTT
1 AAAAAT-TAT
*
371251 AAAATTTATT
1 AAAAATTA-T
*
371261 AAAAATTAGGAAA
1 AAAAATT----AT
371274 AAAAATTAT
1 AAAAATTAT
*
371283 AAAAATTGT
1 AAAAATTAT
371292 AAAAATTTAT
1 AAAAA-TTAT
371302 AAAAAATTTAT
1 -AAAAA-TTAT
*
371313 AAAATTTTAT
1 AAAA-ATTAT
371323 AAAAA
1 AAAAA
371328 AACATAAAAA
Statistics
Matches: 102, Mismatches: 17, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
7 7 0.07
8 5 0.05
9 25 0.25
10 45 0.44
11 12 0.12
13 7 0.07
14 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:371286 original size:62 final size:62
Alignment explanation
Indices: 371212--371348 Score: 149
Period size: 62 Copynumber: 2.2 Consensus size: 62
371202 AAAAATAATT
* * **
371212 AAAAGTTATAAAAA-T-TAATAAA-TTATAATAAAAATATT-TAAAA-TTTATTAAAAATTAGGA
1 AAAAATTATAAAAATTGTAA-AAATTTAT-A-AAAAAT-TTATAAAATTTTATAAAAAAACA-GA
371272 AA
61 AA
*
371274 AAAAATTATAAAAATTGTAAAAATTTATAAAAAATTTATAAAATTTTATAAAAAAACATAAA
1 AAAAATTATAAAAATTGTAAAAATTTATAAAAAATTTATAAAATTTTATAAAAAAACAGAAA
371336 AAAAATTATAAAA
1 AAAAATTATAAAA
371349 TATATAGAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
61 2 0.03
62 40 0.62
63 16 0.25
64 7 0.11
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (62 bp):
AAAAATTATAAAAATTGTAAAAATTTATAAAAAATTTATAAAATTTTATAAAAAAACAGAAA
Found at i:371315 original size:21 final size:20
Alignment explanation
Indices: 371202--371328 Score: 75
Period size: 21 Copynumber: 6.2 Consensus size: 20
371192 TATAAAAAAT
* * *
371202 AAAAATAATTAAAAGTTAT-
1 AAAAATTATAAAAATTTATA
*
371221 AAAAATTA-ATAAATTATAATA
1 AAAAATTATAAAAATT-T-ATA
*
371242 AAAATATT-T-AAAATTTATT
1 AAAA-ATTATAAAAATTTATA
* *
371261 AAAAATTAGGAAAAAAAATTAT-
1 AAAAATT---ATAAAAATTTATA
*
371283 AAAAATTGTAAAAATTTATA
1 AAAAATTATAAAAATTTATA
*
371303 AAAAATTTATAAAATTTTATA
1 AAAAA-TTATAAAAATTTATA
371324 AAAAA
1 AAAAA
371329 ACATAAAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
18 7 0.08
19 23 0.28
20 8 0.10
21 27 0.33
22 10 0.12
23 8 0.10
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAAATTATAAAAATTTATA
Found at i:371348 original size:10 final size:10
Alignment explanation
Indices: 371273--371373 Score: 75
Period size: 10 Copynumber: 10.2 Consensus size: 10
371263 AAATTAGGAA
371273 AAAAAATTAT
1 AAAAAATTAT
*
371283 -AAAAATTGT
1 AAAAAATTAT
*
371292 AAAAATTTAT
1 AAAAAATTAT
371302 AAAAAATTTAT
1 AAAAAA-TTAT
**
371313 AAAATTTTAT
1 AAAAAATTAT
* *
371323 AAAAAAACATAA
1 -AAAAAA-TTAT
371335 AAAAAATTAT
1 AAAAAATTAT
*
371345 AAAATA-TAT
1 AAAAAATTAT
*
371354 AGAAAA--AT
1 AAAAAATTAT
371362 AAAAAATTAT
1 AAAAAATTAT
371372 AA
1 AA
371374 TTTTTTTAAA
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
8 7 0.10
9 15 0.22
10 27 0.39
11 18 0.26
12 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:371348 original size:11 final size:11
Alignment explanation
Indices: 371272--371348 Score: 56
Period size: 11 Copynumber: 7.4 Consensus size: 11
371262 AAAATTAGGA
371272 AAAAAAATTAT
1 AAAAAAATTAT
*
371283 --AAAAATTGT
1 AAAAAAATTAT
*
371292 -AAAAATTTAT
1 AAAAAAATTAT
*
371302 AAAAAATTTAT
1 AAAAAAATTAT
**
371313 -AAAATTTTAT
1 AAAAAAATTAT
*
371323 AAAAAAA-CAT
1 AAAAAAATTAT
371333 AAAAAAAATTAT
1 -AAAAAAATTAT
371345 AAAA
1 AAAA
371349 TATATAGAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
9 8 0.15
10 18 0.34
11 25 0.47
12 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:371737 original size:16 final size:16
Alignment explanation
Indices: 371701--371738 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
371691 TTTATTTCTA
* *
371701 ATTTTTAAATATATAT
1 ATTTTTAAATTTAAAT
371717 ATTTTTAAATTTAAAT
1 ATTTTTAAATTTAAAT
371733 -TTTTTA
1 ATTTTTA
371739 TAAACTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTAAATTTAAAT
Found at i:380235 original size:21 final size:21
Alignment explanation
Indices: 380211--380251 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
380201 CCCTCGATTG
*
380211 CCTCGCTGCTGCCTCTGCTTC
1 CCTCGCTGCTGCCTCCGCTTC
380232 CCTCGCTGCTGCCTCCGCTT
1 CCTCGCTGCTGCCTCCGCTT
380252 TAAGTTGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.49, G:0.20, T:0.32
Consensus pattern (21 bp):
CCTCGCTGCTGCCTCCGCTTC
Found at i:380390 original size:30 final size:30
Alignment explanation
Indices: 380356--380413 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
380346 CGCTTGTATT
380356 TGAGCCAATTGATCTCTTAACCTCTGAATC
1 TGAGCCAATTGATCTCTTAACCTCTGAATC
380386 TGAGCCAATTGATCTCTTAACCTCTGAA
1 TGAGCCAATTGATCTCTTAACCTCTGAA
380414 CTTCAGCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
TGAGCCAATTGATCTCTTAACCTCTGAATC
Found at i:384608 original size:41 final size:41
Alignment explanation
Indices: 384548--384838 Score: 303
Period size: 41 Copynumber: 7.0 Consensus size: 41
384538 TTAAATAAAA
* * * *
384548 TAGCGGCGTTTTTGAGAAAGCACCGCTAATGCTTTGACCTT
1 TAGCGGCGTTTGTGGGAAAGCGCCGCTAATGCTCTGACCTT
** *
384589 TAGCGGCGTTTGTGGGAAAGCGCTACTAACGCTCTGACCTT
1 TAGCGGCGTTTGTGGGAAAGCGCCGCTAATGCTCTGACCTT
* * * *
384630 TAGCGGCGTTTGTGGAAAAGCGTCGTTAATGCTCTAACCTT
1 TAGCGGCGTTTGTGGGAAAGCGCCGCTAATGCTCTGACCTT
* * * *
384671 TAGCAGCGTTTATGAGAAAGCGTCGCTAATGCTCTGACCTT
1 TAGCGGCGTTTGTGGGAAAGCGCCGCTAATGCTCTGACCTT
* * * * *
384712 TAGCGACATTTGAGGGAAAGTGCCGCTAATGATCTGACCTT
1 TAGCGGCGTTTGTGGGAAAGCGCCGCTAATGCTCTGACCTT
*
384753 TAGCGGCGTTCTTTTTAGGGAAAGCGCCGCTAATGCTCTGACCTT
1 TAGCGGCG---TTTGT-GGGAAAGCGCCGCTAATGCTCTGACCTT
* * * ** *
384798 TAGCGGCATTTATGAGAAAGCATCGCTAATACTCTGACCTT
1 TAGCGGCGTTTGTGGGAAAGCGCCGCTAATGCTCTGACCTT
384839 CTGACCTTTA
Statistics
Matches: 205, Mismatches: 41, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
41 165 0.80
42 4 0.02
44 3 0.01
45 33 0.16
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (41 bp):
TAGCGGCGTTTGTGGGAAAGCGCCGCTAATGCTCTGACCTT
Found at i:384690 original size:82 final size:83
Alignment explanation
Indices: 384548--384898 Score: 307
Period size: 82 Copynumber: 4.1 Consensus size: 83
384538 TTAAATAAAA
* * * *
384548 TAGCGGCGTTT-TTGAGAAAGCACCGCTAATGCTTTGACCTTTAGCGGCGTTTGTGGGAAAGCGC
1 TAGCGGCGTTTGTGGAGAAAGCACCGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCGC
* *
384612 TACTAACGCTCTGACCTT
66 TGCTAATGCTCTGACCTT
** * * *
384630 TAGCGGCGTTTGTGGA-AAAGCGTCGTTAATGCTCTAACCTTTAGCAGCGTTTATGAGAAAGCG-
1 TAGCGGCGTTTGTGGAGAAAGCACCGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCGC
384693 TCGCTAATGCTCTGACCTT
66 T-GCTAATGCTCTGACCTT
* * * ** * * *
384712 TAGCGACATTTGAGG-GAAAGTGCCGCTAATGATCTGACCTTTAGCGGCGTTCTTTTTAGGGAAA
1 TAGCGGCGTTTGTGGAGAAAGCACCGCTAATGCTCTGACCTTTAGCGGCG---TTTAT-GAGAAA
*
384776 GCGCCGCTAATGCTCTGACCTT
62 GCGCTGCTAATGCTCTGACCTT
* * * * *
384798 TAGCGGCATTTAT-GAGAAAGCATCGCTAATACTCTGACCTTCTGACCTTTAGCTGCATTTATGA
1 TAGCGGCGTTTGTGGAGAAAGCACCGCT-A-A---TG--C-TCTGACCTTTAGCGGCGTTTATGA
* *
384862 GAATGCGCTGCTAATGCTCTGATCTT
58 GAAAGCGCTGCTAATGCTCTGACCTT
384888 TAGCGGCGTTT
1 TAGCGGCGTTT
384899 TAGCGGCGTT
Statistics
Matches: 214, Mismatches: 38, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
81 1 0.00
82 104 0.49
83 3 0.01
85 5 0.02
86 44 0.21
87 1 0.00
88 1 0.00
90 34 0.16
91 6 0.03
94 15 0.07
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (83 bp):
TAGCGGCGTTTGTGGAGAAAGCACCGCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCGC
TGCTAATGCTCTGACCTT
Found at i:384861 original size:49 final size:48
Alignment explanation
Indices: 384789--384939 Score: 162
Period size: 49 Copynumber: 3.0 Consensus size: 48
384779 CCGCTAATGC
*
384789 TCTGACCTTTAGCGGCATTTATGAGAAAGCATCGCTAATACTCTGACCT
1 TCTGACCTTTAGCGGCATTTATGAGAAAGC-TCGCTAATGCTCTGACCT
* * * *
384838 TCTGACCTTTAGCTGCATTTATGAGAATGCGCTGCTAATGCTCTGATCT
1 TCTGACCTTTAGCGGCATTTATGAGAAAGCTC-GCTAATGCTCTGACCT
*
384887 T-T-AGCGGCGTTTTAGCGGCGTTTATGAGAAAGCGTCGCTAATGCTCTGACCT
1 TCTGA-C--C--TTTAGCGGCATTTATGAGAAAGC-TCGCTAATGCTCTGACCT
384939 T
1 T
384940 TAATGGTGTT
Statistics
Matches: 85, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
47 1 0.01
48 3 0.04
49 43 0.51
50 1 0.01
52 36 0.42
53 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (48 bp):
TCTGACCTTTAGCGGCATTTATGAGAAAGCTCGCTAATGCTCTGACCT
Found at i:384951 original size:52 final size:52
Alignment explanation
Indices: 384796--384951 Score: 158
Period size: 52 Copynumber: 3.1 Consensus size: 52
384786 TGCTCTGACC
* * * **
384796 TTTAGCGGCATTTATGAGAAAGCATCGCTAATACTCTGACC-TT-CT-GACC
1 TTTAGCGGCATTTATGAGAAAGCGTCGCTAATGCTCTGACCTTTAATGGAGT
* * * ** *
384845 TTTAGCTGCATTTATGAGAATGCG-CTGCTAATGCTCTGATCTTTAGCGGCGT
1 TTTAGCGGCATTTATGAGAAAGCGTC-GCTAATGCTCTGACCTTTAATGGAGT
* *
384897 TTTAGCGGCGTTTATGAGAAAGCGTCGCTAATGCTCTGACCTTTAATGGTGT
1 TTTAGCGGCATTTATGAGAAAGCGTCGCTAATGCTCTGACCTTTAATGGAGT
384949 TTT
1 TTT
384952 CCCATAAGCG
Statistics
Matches: 85, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
48 1 0.01
49 34 0.40
50 2 0.02
52 47 0.55
53 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (52 bp):
TTTAGCGGCATTTATGAGAAAGCGTCGCTAATGCTCTGACCTTTAATGGAGT
Found at i:385666 original size:20 final size:18
Alignment explanation
Indices: 385641--385688 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
385631 ACTTGTTTAG
*
385641 ATTTTTTTATTATACTAAT
1 ATTTTTTTAGTA-ACTAAT
*
385660 AATTTTTTATAGTAATTAAT
1 -ATTTTTT-TAGTAACTAAT
385680 ATTTTTTTA
1 ATTTTTTTA
385689 AAATATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 2 0.08
19 7 0.28
20 12 0.48
21 4 0.16
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTTTTTAGTAACTAAT
Found at i:390527 original size:57 final size:57
Alignment explanation
Indices: 390439--390555 Score: 216
Period size: 57 Copynumber: 2.1 Consensus size: 57
390429 TATCATATTG
* *
390439 CTTATACTAATAACTATTTTACATACAGGAGTCATGCACGTTTTACATGTAATTATA
1 CTTATACTAACAACTATTTTACATACAGGAGTCATGCACATTTTACATGTAATTATA
390496 CTTATACTAACAACTATTTTACATACAGGAGTCATGCACATTTTACATGTAATTATA
1 CTTATACTAACAACTATTTTACATACAGGAGTCATGCACATTTTACATGTAATTATA
390553 CTT
1 CTT
390556 CTAGAGTTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.38
Consensus pattern (57 bp):
CTTATACTAACAACTATTTTACATACAGGAGTCATGCACATTTTACATGTAATTATA
Found at i:397075 original size:6 final size:6
Alignment explanation
Indices: 397058--397089 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
397048 GAAAACAAAT
397058 GGGAGAA GGGAGA GGGAGA GGGAGA GGGAGA G
1 GGGAG-A GGGAGA GGGAGA GGGAGA GGGAGA G
397090 TGGAACGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GGGAGA
Done.