Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 199 of 335
Found at i:59653830 original size:21 final size:20
Alignment explanation
Indices: 59653794--59653842 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
59653784 ATCAGCTCAC
*
59653794 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
59653814 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
59653835 TTCAGCTC
1 TTGAGCTC
59653843 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:59654085 original size:13 final size:13
Alignment explanation
Indices: 59654067--59654091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59654057 AATAGTTGTG
59654067 TGTTATTTAATTA
1 TGTTATTTAATTA
59654080 TGTTATTTAATT
1 TGTTATTTAATT
59654092 TTGTAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:59656283 original size:19 final size:20
Alignment explanation
Indices: 59656251--59656291 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
59656241 GAATGAAATC
59656251 GAGAGAAGAAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
59656271 GAGAGAA-AAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
59656290 GA
1 GA
59656292 AAATGAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (20 bp):
GAGAGAAGAAACAAAGAAAA
Found at i:59658665 original size:21 final size:22
Alignment explanation
Indices: 59658621--59658665 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
59658611 TTGTGTTCAA
*
59658621 ATTTAGTTAATGATATTAAGTT
1 ATTTAGTTAATGATATTAAATT
* *
59658643 ATTTAGTT-ATTATTTTAAATT
1 ATTTAGTTAATGATATTAAATT
59658664 AT
1 AT
59658666 AATTATATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (22 bp):
ATTTAGTTAATGATATTAAATT
Found at i:59658703 original size:13 final size:13
Alignment explanation
Indices: 59658685--59658709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59658675 AATAGTTGTG
59658685 TGTTATTTAATTA
1 TGTTATTTAATTA
59658698 TGTTATTTAATT
1 TGTTATTTAATT
59658710 TTGTAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:59661467 original size:11 final size:11
Alignment explanation
Indices: 59661451--59661476 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
59661441 ATTGCATGTA
59661451 TGATATTATTG
1 TGATATTATTG
59661462 TGATATTATTG
1 TGATATTATTG
59661473 TGAT
1 TGAT
59661477 GTGGGCTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (11 bp):
TGATATTATTG
Found at i:59662961 original size:14 final size:14
Alignment explanation
Indices: 59662938--59662981 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
59662928 ATTCGGCTAC
*
59662938 CAAAAGAAAAATAG
1 CAAAACAAAAATAG
59662952 CAAAACAAAAGAT-G
1 CAAAACAAAA-ATAG
59662966 -AAAACAAAAATAG
1 CAAAACAAAAATAG
59662979 CAA
1 CAA
59662982 GGAAGAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 2 0.08
13 10 0.38
14 12 0.46
15 2 0.08
ACGTcount: A:0.70, C:0.11, G:0.11, T:0.07
Consensus pattern (14 bp):
CAAAACAAAAATAG
Found at i:59665180 original size:40 final size:40
Alignment explanation
Indices: 59665123--59665246 Score: 140
Period size: 40 Copynumber: 3.1 Consensus size: 40
59665113 TGAATGATAC
* * * *
59665123 CCGGGCTAAGTCTCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * ** *
59665163 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * *
59665203 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
59665243 CCGG
1 CCGG
59665247 TTGAATCCCG
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
Found at i:59673349 original size:39 final size:40
Alignment explanation
Indices: 59673186--59673347 Score: 170
Period size: 40 Copynumber: 4.1 Consensus size: 40
59673176 TGAATGATAC
* * *
59673186 CCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
*
59673225 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTATAT
* * ** *
59673265 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * *
59673305 CC-GGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
59673344 CCGG
1 CCGG
59673348 TTGAATCCCG
Statistics
Matches: 100, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
39 44 0.44
40 51 0.51
41 5 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
Found at i:59677586 original size:71 final size:71
Alignment explanation
Indices: 59677502--59677665 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
59677492 CGATTTGTCT
59677502 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
59677567 CTTTCA
66 CTTTCA
59677573 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
59677638 CTTTCA
66 CTTTCA
59677644 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
59677666 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:59677703 original size:71 final size:70
Alignment explanation
Indices: 59677502--59677699 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
59677492 CGATTTGTCT
* * * *
59677502 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
59677567 CTTTCA
65 CTTTCA
* * * *
59677573 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
59677638 CTTTCA
65 CTTTCA
* *
59677644 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
59677700 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:59682174 original size:30 final size:31
Alignment explanation
Indices: 59682140--59682236 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
59682130 AGCTCACTCC
*
59682140 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
59682170 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
59682200 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
59682230 TAGCTCA
1 TAGCTCA
59682237 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:59684887 original size:5 final size:5
Alignment explanation
Indices: 59684873--59684932 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
59684863 AAAGAGAAAC
*
59684873 AAAG- AAAGA AAAGA AAAGCA AAAGA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAGA AAAG-A AAAGA AAAGA AAAGA AAAGA AAA-GA AA-AGA
59684923 AAAGA AAAGA
1 AAAGA AAAGA
59684933 GAGGCAAGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
4 8 0.17
5 30 0.62
6 9 0.19
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:59684897 original size:11 final size:10
Alignment explanation
Indices: 59684873--59684932 Score: 63
Period size: 11 Copynumber: 6.0 Consensus size: 10
59684863 AAAGAGAAAC
59684873 AAAG-AAAGA
1 AAAGAAAAGA
59684882 AAAGAAAAGCA
1 AAAGAAAAG-A
59684893 AAAGAAAAGA
1 AAAGAAAAGA
*
59684903 AGA-AAAAGA
1 AAAGAAAAGA
59684912 AAATGAAATA-A
1 AAA-GAAA-AGA
59684923 AAAGAAAAGA
1 AAAGAAAAGA
59684933 GAGGCAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
9 13 0.30
10 12 0.28
11 17 0.40
12 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:59684898 original size:16 final size:15
Alignment explanation
Indices: 59684873--59684932 Score: 63
Period size: 16 Copynumber: 4.0 Consensus size: 15
59684863 AAAGAGAAAC
59684873 AAAG-AAAGAAAAGA
1 AAAGAAAAGAAAAGA
59684887 AAAGCAAAAGAAAAGA
1 AAAG-AAAAGAAAAGA
*
59684903 AGA-AAAAGAAAATGA
1 AAAGAAAAGAAAA-GA
59684918 AATA-AAAAGAAAAGA
1 AA-AGAAAAGAAAAGA
59684933 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
14 13 0.32
15 5 0.12
16 22 0.55
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (15 bp):
AAAGAAAAGAAAAGA
Found at i:59685012 original size:11 final size:12
Alignment explanation
Indices: 59684980--59685010 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
59684970 TTGAGAGAAC
59684980 TTGAAAAAGCCT
1 TTGAAAAAGCCT
59684992 TTGAAAAAGCCT
1 TTGAAAAAGCCT
59685004 TTGAAAA
1 TTGAAAA
59685011 GCAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:59685086 original size:30 final size:31
Alignment explanation
Indices: 59685022--59685093 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
59685012 CAAAAAAAAT
* *
59685022 GAAAAAGAAA-ATGAGATTGAAAAAGAGAAC
1 GAAAAAGAAATTTGAGAGTGAAAAAGAGAAC
*
59685052 G-AAAAGAAATTTGAGAGTGAAAAAGA-AGAT
1 GAAAAAGAAATTTGAGAGTGAAAAAGAGA-AC
59685082 GAAAAAGAAATT
1 GAAAAAGAAATT
59685094 GAAACAAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 9 0.25
30 17 0.47
31 10 0.28
ACGTcount: A:0.61, C:0.01, G:0.24, T:0.14
Consensus pattern (31 bp):
GAAAAAGAAATTTGAGAGTGAAAAAGAGAAC
Found at i:59687229 original size:30 final size:31
Alignment explanation
Indices: 59687195--59687289 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 31
59687185 AGCTCACTCC
*
59687195 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
59687225 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
59687255 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
59687285 TAGCT
1 TAGCT
59687290 ATTTTAGTTT
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
30 45 0.92
31 4 0.08
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:59689863 original size:30 final size:30
Alignment explanation
Indices: 59689769--59689864 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
59689759 AGCTCACTCC
*
59689769 TAGCTC-ACTTTCAACTCACGAGCTAAA-CT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
59689798 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
59689828 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
59689858 TAGCTCA
1 TAGCTCA
59689865 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
28 2 0.04
29 13 0.26
30 32 0.64
31 3 0.06
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:59692484 original size:30 final size:30
Alignment explanation
Indices: 59692389--59692485 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
59692379 AGCTCACTCC
*
59692389 TAGCTC-ACTTTCAACTCACGAGCTAAA-CTT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGC-T
* * * **
59692419 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
59692449 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
59692479 TAGCTCA
1 TAGCTCA
59692486 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
29 2 0.04
30 40 0.80
31 8 0.16
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:59694945 original size:21 final size:21
Alignment explanation
Indices: 59694921--59694964 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
59694911 ACGACCTAAT
*
59694921 TAAATAGAAAGGATA-ATTAAA
1 TAAATA-AAAGGATACAATAAA
*
59694942 TAAATAAAATGATACAATAAA
1 TAAATAAAAGGATACAATAAA
59694963 TA
1 TA
59694965 CTAAAGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (21 bp):
TAAATAAAAGGATACAATAAA
Found at i:59697763 original size:15 final size:15
Alignment explanation
Indices: 59697743--59697790 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
59697733 TCAAAGATGG
59697743 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
59697758 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
59697773 -TTTATGGATATAAA
1 GTTTATGGATATGAA
59697787 GTTT
1 GTTT
59697791 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:59697770 original size:29 final size:29
Alignment explanation
Indices: 59697737--59697796 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
59697727 AAGGATTCAA
* *
59697737 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
59697766 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
59697795 AG
1 AG
59697797 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:59705817 original size:42 final size:42
Alignment explanation
Indices: 59705749--59705854 Score: 185
Period size: 42 Copynumber: 2.5 Consensus size: 42
59705739 CATTTAAGCC
* *
59705749 TCTTAGTTTAATAAATAAGTTTCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
59705791 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
59705833 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
59705855 TATTTAATGA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
42 51 0.84
43 10 0.16
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:59705856 original size:14 final size:14
Alignment explanation
Indices: 59705837--59705881 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
59705827 AACTCATCTT
*
59705837 AGTTTAATTAAATG
1 AGTTTAATTTAATG
59705851 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
59705864 AATTTAATTTAATG
1 AGTTTAATTTAATG
59705878 AGTT
1 AGTT
59705882 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:59707093 original size:21 final size:21
Alignment explanation
Indices: 59707049--59707094 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
59707039 TAAGTTTCAA
**
59707049 AAAAAAATCGAAAAAAAATTC
1 AAAAAAATCGAAAAAAAAAAC
*
59707070 AAAAAAATTGAAAAAAAAAAC
1 AAAAAAATCGAAAAAAAAAAC
59707091 AAAA
1 AAAA
59707095 TCTGAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (21 bp):
AAAAAAATCGAAAAAAAAAAC
Found at i:59710469 original size:21 final size:20
Alignment explanation
Indices: 59710435--59710502 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
59710425 ACATTCTTGT
59710435 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
59710456 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
59710477 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
59710498 AAAGA
1 AAAGA
59710503 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:59710470 original size:6 final size:5
Alignment explanation
Indices: 59710446--59710502 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
59710436 AAGAGAAAAC
*
59710446 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
59710493 AAAGA AAAGA
1 AAAGA AAAGA
59710503 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:59710477 original size:15 final size:14
Alignment explanation
Indices: 59710446--59710502 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
59710436 AAGAGAAAAC
59710446 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
59710462 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
59710477 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
59710493 AAAGAAAAGA
1 AAAGAAAAGA
59710503 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:59710581 original size:11 final size:12
Alignment explanation
Indices: 59710550--59710580 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
59710540 TTGAGAGAAC
59710550 TTGAAAAAGCCT
1 TTGAAAAAGCCT
*
59710562 TTGAAAAAGTCT
1 TTGAAAAAGCCT
59710574 TTGAAAA
1 TTGAAAA
59710581 GCAAAAAGAA
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:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:59710591 original size:12 final size:12
Alignment explanation
Indices: 59710583--59710607 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59710573 TTTGAAAAGC
59710583 AAAAAGAAAATG
1 AAAAAGAAAATG
59710595 AAAAAGAAAATG
1 AAAAAGAAAATG
59710607 A
1 A
59710608 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:59710604 original size:18 final size:18
Alignment explanation
Indices: 59710577--59710632 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
59710567 AAAGTCTTTG
59710577 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
59710596 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
59710614 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
59710631 AA
1 AA
59710633 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:59710617 original size:30 final size:31
Alignment explanation
Indices: 59710583--59710664 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
59710573 TTTGAAAAGC
*
59710583 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
59710613 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
59710643 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
59710665 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:59712893 original size:30 final size:30
Alignment explanation
Indices: 59712859--59712956 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
59712849 AGCTCACTCC
59712859 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
59712889 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
59712919 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
59712949 TAGCTCAT
1 TAGCTCAT
59712957 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:59718459 original size:14 final size:14
Alignment explanation
Indices: 59718437--59718484 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
59718427 ACCTAAACCG
* *
59718437 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
59718451 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
59718465 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
59718479 ACCATT
1 ACCATT
59718485 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:59718878 original size:12 final size:11
Alignment explanation
Indices: 59718855--59718904 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 11
59718845 TATACAAGTT
59718855 AAAAAAAAA--
1 AAAAAAAAATC
*
59718864 AAAAAAAATTC
1 AAAAAAAAATC
59718875 AAAAAAAAAT-
1 AAAAAAAAATC
59718885 -AAAAAAAATC
1 AAAAAAAAATC
59718895 GAAAAAAAAA
1 -AAAAAAAAA
59718905 GTGATTTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 17 0.50
11 9 0.26
12 8 0.24
ACGTcount: A:0.86, C:0.04, G:0.02, T:0.08
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:59718878 original size:20 final size:21
Alignment explanation
Indices: 59718855--59718904 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
59718845 TATACAAGTT
59718855 AAAAAAAAA-AAAAAAAATTC-
1 AAAAAAAAATAAAAAAAA-TCG
59718875 AAAAAAAAATAAAAAAAATCG
1 AAAAAAAAATAAAAAAAATCG
59718896 AAAAAAAAA
1 AAAAAAAAA
59718905 GTGATTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.86, C:0.04, G:0.02, T:0.08
Consensus pattern (21 bp):
AAAAAAAAATAAAAAAAATCG
Found at i:59718879 original size:21 final size:20
Alignment explanation
Indices: 59718855--59718904 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
59718845 TATACAAGTT
*
59718855 AAAAAAAAAAAAAAAAATTC
1 AAAAAAAAAAAAAAAAAATC
*
59718875 AAAAAAAAATAAAAAAAATC
1 AAAAAAAAAAAAAAAAAATC
59718895 GAAAAAAAAA
1 -AAAAAAAAA
59718905 GTGATTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.86, C:0.04, G:0.02, T:0.08
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAAATC
Found at i:59725380 original size:21 final size:21
Alignment explanation
Indices: 59725356--59725399 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
59725346 GAATCTTTAG
*
59725356 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
59725377 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
59725398 TA
1 TA
59725400 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:59727776 original size:30 final size:30
Alignment explanation
Indices: 59727742--59727829 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
59727732 CTAGCTTATA
*
59727742 TTCAGCTCACGAGCTAAACCTTAGCTCAGC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * *
59727772 TTCAGCTTAGGAGTTTAATCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* *
59727802 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
59727830 TTTTAGTTTA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:59729066 original size:14 final size:14
Alignment explanation
Indices: 59729044--59729091 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
59729034 ACCTAAACCG
* *
59729044 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
59729058 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
59729072 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
59729086 ACCATT
1 ACCATT
59729092 CCATTCATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:59729525 original size:30 final size:31
Alignment explanation
Indices: 59729491--59729587 Score: 103
Period size: 30 Copynumber: 3.2 Consensus size: 31
59729481 TAAACTAAAA
59729491 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
59729521 TGAGCTGAGGC-TAAGCTCCTAAGCTAAAGT
1 TGAGCTAAAGCTTTAGCTCGTGAGCTAAAGT
*
59729551 TGAGCTAAAG-TTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAAGCTTTAGCTCGTGAGCT-AAAGT
59729581 TGAGCTA
1 TGAGCTA
59729588 GGAGTGAGCT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
30 47 0.87
31 7 0.13
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (31 bp):
TGAGCTAAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:59733068 original size:30 final size:30
Alignment explanation
Indices: 59732997--59733079 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
59732987 CTTTTCTTTC
* *
59732997 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
59733028 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
59733057 ATTTTCTTTTTCTTTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
59733080 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.12, C:0.22, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:59733097 original size:12 final size:12
Alignment explanation
Indices: 59733082--59733112 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
59733072 TTCTTTTTGC
59733082 TTTTCAAAGACT
1 TTTTCAAAGACT
*
59733094 TTTTCAAAGGCT
1 TTTTCAAAGACT
59733106 TTTTCAA
1 TTTTCAA
59733113 GTTCTCTCAA
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:0.10, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGACT
Found at i:59733170 original size:5 final size:5
Alignment explanation
Indices: 59733160--59733222 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
59733150 CTCTTGCCTC
*
59733160 TCTTT TCTTT T-TATT TCGTTT TCTTTT TCTTT T-TCT TCTTT TGCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTTT TCTTT T-C-TTT
59733208 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
59733223 GTTTTCTCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
4 4 0.08
5 29 0.59
6 11 0.22
7 5 0.10
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:59733182 original size:6 final size:6
Alignment explanation
Indices: 59733173--59733222 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
59733163 TTTCTTTTTA
*
59733173 TTTCGT TTTCTT TTTCTT TTTCTTCT TTTGCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTC-T-T TTT-CTT TTTCTT TTTCTT TTTCTT
59733222 T
1 T
59733223 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 18 0.46
7 5 0.13
8 5 0.13
9 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:59733206 original size:21 final size:20
Alignment explanation
Indices: 59733162--59733222 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 20
59733152 CTTGCCTCTC
59733162 TTTTCTTTTTATTTCGTTTTCT
1 TTTTCTTTTT-TTTC-TTTTCT
*
59733184 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTTTTCTTTT-CT
59733205 TTTTCTTTTCTTTTCTTT
1 TTTTCTTTT-TTTTCTTT
59733223 GTTTTCTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.11
21 14 0.40
22 17 0.49
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTCTTTTTTTTCTTTTCT
Found at i:59733223 original size:21 final size:21
Alignment explanation
Indices: 59733162--59733233 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
59733152 CTTGCCTCTC
*
59733162 TTTTCTTTTTATTTCGTTTTCT
1 TTTTCTTTTT-TTTCGTTTGCT
* *
59733184 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTTTTCGTTTGCT
59733205 TTTTCTTTTCTTTTC-TTTG-T
1 TTTTCTTTT-TTTTCGTTTGCT
59733225 TTTCTCTTT
1 TTT-TCTTT
59733234 ACAAGAATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
20 4 0.09
21 26 0.59
22 14 0.32
ACGTcount: A:0.01, C:0.17, G:0.04, T:0.78
Consensus pattern (21 bp):
TTTTCTTTTTTTTCGTTTGCT
Found at i:59734157 original size:11 final size:11
Alignment explanation
Indices: 59734143--59734171 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
59734133 TCTTTTTCTT
59734143 TTTTTTTCGAA
1 TTTTTTTCGAA
59734154 TTTTTTTCGAA
1 TTTTTTTCGAA
59734165 TTTTTTT
1 TTTTTTT
59734172 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:59735913 original size:30 final size:30
Alignment explanation
Indices: 59735827--59735924 Score: 106
Period size: 30 Copynumber: 3.3 Consensus size: 30
59735817 TTAAACTAAA
* *
59735827 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * *
59735857 TTGAGCTAAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
59735887 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
59735917 ATGAGCTA
1 ATGAGCTA
59735925 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:59737776 original size:17 final size:18
Alignment explanation
Indices: 59737746--59737779 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
59737736 AGCAACTCAT
59737746 TTATTAATCTAAGATGAG
1 TTATTAATCTAAGATGAG
59737764 TTATTAA-CTAAGATGA
1 TTATTAATCTAAGATGA
59737780 ACTCAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (18 bp):
TTATTAATCTAAGATGAG
Found at i:59737790 original size:19 final size:19
Alignment explanation
Indices: 59737766--59737817 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
59737756 AAGATGAGTT
59737766 ATTAACTAAGATGAACTCA
1 ATTAACTAAGATGAACTCA
*
59737785 ATTAACTAAAATGAACTCA
1 ATTAACTAAGATGAACTCA
59737804 ATTAACTAAGATGA
1 ATTAACTAAGATGA
59737818 GTAATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (19 bp):
ATTAACTAAGATGAACTCA
Found at i:59740021 original size:21 final size:20
Alignment explanation
Indices: 59739992--59740030 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
59739982 TCTTTTCAAA
59739992 CTCAATCTCATTTTGCTTTCT
1 CTCAATCTC-TTTTGCTTTCT
* *
59740013 CTCATTCTCTTTTTCTTT
1 CTCAATCTCTTTTGCTTT
59740031 ATCATTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.10, C:0.28, G:0.03, T:0.59
Consensus pattern (20 bp):
CTCAATCTCTTTTGCTTTCT
Found at i:59742242 original size:30 final size:30
Alignment explanation
Indices: 59742157--59742253 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
59742147 TAAACTAAAA
* *
59742157 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
59742187 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
59742217 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
59742246 ATGAGCTA
1 -TGAGCTA
59742254 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:59744557 original size:30 final size:30
Alignment explanation
Indices: 59744486--59744568 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
59744476 CTTTTGTTTC
* *
59744486 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
59744517 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
59744546 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
59744569 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:59744568 original size:18 final size:18
Alignment explanation
Indices: 59744519--59744574 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
59744509 CACTCTCAAA
* *
59744519 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
59744536 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
59744554 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
59744573 TT
1 TT
59744575 CAAAGACTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:59744575 original size:12 final size:12
Alignment explanation
Indices: 59744544--59744568 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59744534 TTTTTCAATC
59744544 TCATTTTCTTTT
1 TCATTTTCTTTT
59744556 TCATTTTCTTTT
1 TCATTTTCTTTT
59744568 T
1 T
59744569 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:59744659 original size:5 final size:5
Alignment explanation
Indices: 59744649--59744711 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
59744639 CTCTTGCCTC
*
59744649 TCTTT TCTTT T-TATT TCGTTT TCGTTT TCTTT T-TCT TCTTT TGCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTTT TCTTT T-C-TTT
59744697 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
59744712 GTTTTCTCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 4 0.08
5 29 0.58
6 12 0.24
7 5 0.10
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:59744682 original size:12 final size:11
Alignment explanation
Indices: 59744649--59744711 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
59744639 CTCTTGCCTC
59744649 TCTTTTCTTTT
1 TCTTTTCTTTT
* *
59744660 T-ATTTCGTTT
1 TCTTTTCTTTT
59744670 TCGTTTTCTTTT
1 TC-TTTTCTTTT
59744682 TC--TTCTTTT
1 TCTTTTCTTTT
*
59744691 GCTTTT-TCTTT
1 TCTTTTCT-TTT
59744702 TCTTTTCTTT
1 TCTTTTCTTT
59744712 GTTTTCTCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
9 8 0.20
10 9 0.22
11 13 0.32
12 10 0.25
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:59744690 original size:31 final size:30
Alignment explanation
Indices: 59744653--59744711 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
59744643 TGCCTCTCTT
59744653 TTCTTTT-TATTTCGTTTTCGTTTTCTTTTTC
1 TTCTTTTCTATTTC-TTTTC-TTTTCTTTTTC
*
59744684 TTCTTTTGCTTTTTCTTTTCTTTTCTTT
1 TTCTTTT-CTATTTCTTTTCTTTTCTTT
59744712 GTTTTCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 15 0.60
32 5 0.20
33 5 0.20
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (30 bp):
TTCTTTTCTATTTCTTTTCTTTTCTTTTTC
Found at i:59744712 original size:21 final size:21
Alignment explanation
Indices: 59744651--59744722 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
59744641 CTTGCCTCTC
* *
59744651 TTTTCTTTTTATTTCGTTTTCG
1 TTTTCTTTTT-TTTCGTTTGCT
* *
59744673 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTTTTCGTTTGCT
59744694 TTTTCTTTTCTTTTC-TTTG-T
1 TTTTCTTTT-TTTTCGTTTGCT
59744714 TTTCTCTTT
1 TTT-TCTTT
59744723 ACAAGAATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.09
21 25 0.58
22 14 0.33
ACGTcount: A:0.01, C:0.17, G:0.06, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTTTTTCGTTTGCT
Found at i:59745659 original size:13 final size:13
Alignment explanation
Indices: 59745633--59745699 Score: 97
Period size: 13 Copynumber: 5.5 Consensus size: 13
59745623 ACTCTTTTTC
59745633 TTTTTTTCG-A-T
1 TTTTTTTCGAATT
59745644 TTTTTTTCGAATT
1 TTTTTTTCGAATT
59745657 TTTTTTTCGAATT
1 TTTTTTTCGAATT
*
59745670 TTTTTTTCAAATT
1 TTTTTTTCGAATT
59745683 TTTTTTT-G-ATT
1 TTTTTTTCGAATT
59745694 TTTTTT
1 TTTTTT
59745700 AACTTGTATA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
11 18 0.35
12 1 0.02
13 33 0.63
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.75
Consensus pattern (13 bp):
TTTTTTTCGAATT
Found at i:59749241 original size:19 final size:19
Alignment explanation
Indices: 59749196--59749241 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
59749186 ATTAACACAC
*
59749196 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
59749215 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
59749233 AATTAATAA
1 AATTAATAA
59749242 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:59749497 original size:20 final size:20
Alignment explanation
Indices: 59749452--59749499 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
59749442 AGTAAGCTCG
59749452 GTTGAGCTCAAACAAGCTGA
1 GTTGAGCTCAAACAAGCTGA
** **
59749472 AATGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACAAGCTGA
59749492 GTTGAGCT
1 GTTGAGCT
59749500 GGACGGAGCT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (20 bp):
GTTGAGCTCAAACAAGCTGA
Found at i:59749934 original size:30 final size:31
Alignment explanation
Indices: 59749900--59749996 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
59749890 AGCTCACTCC
*
59749900 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
59749930 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
59749960 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
59749990 TAGCTCA
1 TAGCTCA
59749997 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:59752212 original size:18 final size:18
Alignment explanation
Indices: 59752189--59752233 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
59752179 CTTTTCGTTC
59752189 TCTTTTTCAATCTCATTT
1 TCTTTTTCAATCTCATTT
* *
59752207 TCTTTTTC-ATTTCTTTT
1 TCTTTTTCAATCTCATTT
*
59752224 TGTTTTTCAA
1 TCTTTTTCAA
59752234 AGGTTTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.13, C:0.18, G:0.02, T:0.67
Consensus pattern (18 bp):
TCTTTTTCAATCTCATTT
Found at i:59752214 original size:30 final size:30
Alignment explanation
Indices: 59752143--59752224 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
59752133 CTTTTGTTTC
* *
59752143 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
59752174 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
*
59752203 ATTTTCTTTTTCATT-TCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
59752225 GTTTTTCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 12 0.27
30 25 0.56
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.63
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:59752303 original size:5 final size:5
Alignment explanation
Indices: 59752293--59752349 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
59752283 CTCTTGCCTC
** *
59752293 TCTTT TCTTT TAATT TCTTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCTTT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
59752340 TCTTT TCTTT
1 TCTTT TCTTT
59752350 ATTTTCTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
4 3 0.07
5 29 0.69
6 6 0.14
7 4 0.10
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:59752313 original size:15 final size:13
Alignment explanation
Indices: 59752293--59752356 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 13
59752283 CTCTTGCCTC
59752293 TCTTTTCTTTTAATT
1 TCTTTTCTTTT--TT
59752308 TCTTTTTCTTTTTCT
1 TC-TTTTCTTTTT-T
59752323 TCTTTTGC--TTTT
1 TCTTTT-CTTTTTT
59752335 TCTTTTCTTTTCTT
1 TCTTTTCTTTT-TT
*
59752349 TATTTTCT
1 TCTTTTCT
59752357 CTTTACTAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
11 1 0.02
12 7 0.17
13 5 0.12
14 14 0.33
15 6 0.14
16 9 0.21
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTTT
Found at i:59752359 original size:21 final size:20
Alignment explanation
Indices: 59752291--59752360 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 20
59752281 GCCTCTTGCC
*
59752291 TCTCTTTTCTTTTAATTTCTTT
1 TCTCTTTTCTTTT-CTTT-TTT
*
59752313 T-TCTTTT-TCTTCTTTTGCTT
1 TCTCTTTTCTTTTCTTTT--TT
*
59752333 TTTCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTTCTTT-TTT
59752354 TCTCTTT
1 TCTCTTT
59752361 ACTAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
18 1 0.03
19 3 0.08
20 6 0.15
21 20 0.51
22 8 0.21
23 1 0.03
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTCTTTTTT
Found at i:59753291 original size:21 final size:21
Alignment explanation
Indices: 59753264--59753313 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
59753254 ATTAAACACT
59753264 TTTTTTTCAGATTTTTTTTCG-A
1 TTTTTTTCA-ATTTTTTTT-GAA
*
59753286 TTTTTTTTAATTTTTTTTGAA
1 TTTTTTTCAATTTTTTTTGAA
59753307 TTTTTTT
1 TTTTTTT
59753314 GACTTGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.65
22 8 0.31
ACGTcount: A:0.14, C:0.04, G:0.06, T:0.76
Consensus pattern (21 bp):
TTTTTTTCAATTTTTTTTGAA
Found at i:59753303 original size:11 final size:11
Alignment explanation
Indices: 59753263--59753313 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
59753253 CATTAAACAC
59753263 TTTTTTTTCAGA
1 TTTTTTTTCA-A
*
59753275 TTTTTTTTCGA
1 TTTTTTTTCAA
59753286 TTTTTTTT-AA
1 TTTTTTTTCAA
*
59753296 TTTTTTTTGAA
1 TTTTTTTTCAA
59753307 TTTTTTT
1 TTTTTTT
59753314 GACTTGTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
10 9 0.25
11 18 0.50
12 9 0.25
ACGTcount: A:0.14, C:0.04, G:0.06, T:0.76
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:59755043 original size:19 final size:19
Alignment explanation
Indices: 59755019--59755058 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
59755009 AGCTCCCATG
59755019 TAGCTC-CACACCAGCTCAT
1 TAGCTCGCA-ACCAGCTCAT
*
59755038 TAGCTCGGAACCAGCTCAT
1 TAGCTCGCAACCAGCTCAT
59755057 TA
1 TA
59755059 TCAGCTTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGCAACCAGCTCAT
Found at i:59756728 original size:12 final size:11
Alignment explanation
Indices: 59756711--59756762 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
59756701 TATACAAGTT
59756711 AAAAAAAATCA
1 AAAAAAAATCA
* *
59756722 AAAAAAATTCG
1 AAAAAAAATCA
59756733 AAAAAAAATCGA
1 AAAAAAAATC-A
*
59756745 AAAAAAAATCG
1 AAAAAAAATCA
59756756 AAAAAAA
1 AAAAAAA
59756763 GAAAAAGAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.77, C:0.08, G:0.06, T:0.10
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:59756737 original size:23 final size:23
Alignment explanation
Indices: 59756711--59756762 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
59756701 TATACAAGTT
*
59756711 AAAAAAAATC-AAAAAAAATTCG
1 AAAAAAAATCGAAAAAAAAATCG
59756733 AAAAAAAATCGAAAAAAAAATCG
1 AAAAAAAATCGAAAAAAAAATCG
59756756 AAAAAAA
1 AAAAAAA
59756763 GAAAAAGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.77, C:0.08, G:0.06, T:0.10
Consensus pattern (23 bp):
AAAAAAAATCGAAAAAAAAATCG
Found at i:59763271 original size:14 final size:14
Alignment explanation
Indices: 59763249--59763296 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
59763239 ACCTAAACCG
* *
59763249 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
59763263 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
*
59763277 ACCCTTTTGTTCCT
1 ACCATTTTGTTCCT
59763291 ACCATT
1 ACCATT
59763297 CCATTCGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:59763655 original size:30 final size:30
Alignment explanation
Indices: 59763621--59763687 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
59763611 TAAACTAAAA
59763621 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAG
1 TGAGCTAAGCTTTAGCTCGTGAGCTGAAAG
* *
59763650 TTGAGCTAAGGTTTAGCTCGTGAGTTGAAAG
1 -TGAGCTAAGCTTTAGCTCGTGAGCTGAAAG
59763681 TGAGCTA
1 TGAGCTA
59763688 GGAGTGAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTGAAAG
Found at i:59763698 original size:30 final size:30
Alignment explanation
Indices: 59763634--59763699 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
59763624 GCTAAGCTTT
* *
59763634 AGCTCGTGAGCTAAAGTTGAGCTAAGGTTT
1 AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
*
59763664 AGCTCGTGAGTTGAAAG-TGAGCT-AGGAGTG
1 AGCTCGTGAGCT-AAAGTTGAGCTAAGG-GTG
59763694 AGCTCG
1 AGCTCG
59763700 GTTTAGCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 3 0.10
30 24 0.77
31 4 0.13
ACGTcount: A:0.26, C:0.14, G:0.35, T:0.26
Consensus pattern (30 bp):
AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
Found at i:59769967 original size:19 final size:19
Alignment explanation
Indices: 59769943--59769981 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
59769933 AATAAATTAC
*
59769943 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
59769962 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
59769981 T
1 T
59769982 GATGGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:59770064 original size:9 final size:10
Alignment explanation
Indices: 59770041--59770087 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
59770031 TAAGTCTAAT
59770041 ATGTGTTTAA
1 ATGTGTTTAA
59770051 ATGTGTTT-A
1 ATGTGTTTAA
59770060 ATGTGTTTAA
1 ATGTGTTTAA
*
59770070 TATGT-TTTTA
1 -ATGTGTTTAA
59770080 ATGTGTTT
1 ATGTGTTT
59770088 GTTTGTAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 13 0.39
10 16 0.48
11 4 0.12
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.57
Consensus pattern (10 bp):
ATGTGTTTAA
Found at i:59770079 original size:11 final size:11
Alignment explanation
Indices: 59770037--59770081 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
59770027 AAGTTAAGTC
59770037 TAATATGTGTT
1 TAATATGTGTT
59770048 TAA-ATGTGTT
1 TAATATGTGTT
59770058 T-A-ATGTGTT
1 TAATATGTGTT
*
59770067 TAATATGTTTT
1 TAATATGTGTT
59770078 TAAT
1 TAAT
59770082 GTGTTTGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.29
10 9 0.29
11 13 0.42
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.56
Consensus pattern (11 bp):
TAATATGTGTT
Found at i:59770079 original size:20 final size:19
Alignment explanation
Indices: 59770041--59770087 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
59770031 TAAGTCTAAT
59770041 ATGTGTTTAAATGTGTTTA
1 ATGTGTTTAAATGTGTTTA
*
59770060 ATGTGTTTAATATGTTTTTA
1 ATGTGTTTAA-ATGTGTTTA
59770080 ATGTGTTT
1 ATGTGTTT
59770088 GTTTGTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.57
Consensus pattern (19 bp):
ATGTGTTTAAATGTGTTTA
Found at i:59777299 original size:18 final size:17
Alignment explanation
Indices: 59777276--59777329 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 17
59777266 AACAACTCAT
59777276 TTATTAATCTAAGATGAG
1 TTATTAA-CTAAGATGAG
* *
59777294 TTATTAACTAATATGAAC
1 TTATTAACTAAGATG-AG
*
59777312 TCAATTAACTAAGATGAG
1 T-TATTAACTAAGATGAG
59777330 CAATTTATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 7 0.24
18 10 0.34
19 12 0.41
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (17 bp):
TTATTAACTAAGATGAG
Found at i:59777309 original size:17 final size:18
Alignment explanation
Indices: 59777276--59777309 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
59777266 AACAACTCAT
59777276 TTATTAATCTAAGATGAG
1 TTATTAATCTAAGATGAG
*
59777294 TTATTAA-CTAATATGA
1 TTATTAATCTAAGATGA
59777310 ACTCAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (18 bp):
TTATTAATCTAAGATGAG
Found at i:59780457 original size:26 final size:26
Alignment explanation
Indices: 59780418--59780527 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
59780408 TGATACAAAT
* *
59780418 TGATAAAAGTTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
59780444 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
59780470 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
59780496 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
59780522 TGATAA
1 TGATAA
59780528 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:59782187 original size:27 final size:27
Alignment explanation
Indices: 59782146--59782284 Score: 165
Period size: 27 Copynumber: 5.2 Consensus size: 27
59782136 GAGGAAGCGT
*
59782146 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
59782173 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
59782200 TCTGGTGGCTTTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
59782227 TC-GGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
59782254 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
59782280 TCTGG
1 TCTGG
59782285 CAGCCATGCT
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
26 24 0.24
27 62 0.63
28 12 0.12
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:59782257 original size:54 final size:54
Alignment explanation
Indices: 59782146--59782284 Score: 183
Period size: 54 Copynumber: 2.6 Consensus size: 54
59782136 GAGGAAGCGT
* *
59782146 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTATGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGA
* * *
59782200 TCTGGTGGCTTTGCCACATATATCTGTTC-GGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTATGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTG-A
* * *
59782254 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 TCTGGTGGCTATGCCACATATATCTGTTCTGG
59782285 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
53 30 0.40
54 45 0.60
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (54 bp):
TCTGGTGGCTATGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGA
Found at i:59785079 original size:30 final size:30
Alignment explanation
Indices: 59785045--59785126 Score: 76
Period size: 30 Copynumber: 2.8 Consensus size: 30
59785035 TAAACTAAAA
* *
59785045 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
* * * * * *
59785075 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
*
59785105 T-AGCTAAGGTTTAGCTCGTGAG
1 TGAGCTAAGATTTAGCTCGTGAG
59785127 TGAATATGAG
Statistics
Matches: 38, Mismatches: 14, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
29 15 0.39
30 23 0.61
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
Found at i:59787420 original size:30 final size:30
Alignment explanation
Indices: 59787349--59787431 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
59787339 CTTTTGTTTC
* *
59787349 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
*
59787380 AATTTC-TTTTCGTTCTCTTTTTTAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
59787409 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
59787432 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 5 0.11
30 31 0.70
31 8 0.18
ACGTcount: A:0.13, C:0.20, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:59787438 original size:12 final size:12
Alignment explanation
Indices: 59787407--59787431 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59787397 TTTTTTAATC
59787407 TCATTTTCTTTT
1 TCATTTTCTTTT
59787419 TCATTTTCTTTT
1 TCATTTTCTTTT
59787431 T
1 T
59787432 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:59787449 original size:12 final size:12
Alignment explanation
Indices: 59787434--59787464 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
59787424 TTCTTTTTGC
59787434 TTTTCAAAGACT
1 TTTTCAAAGACT
*
59787446 TTTTCAAAGGCT
1 TTTTCAAAGACT
59787458 TTTTCAA
1 TTTTCAA
59787465 GTTCTCTCAA
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:0.10, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGACT
Found at i:59787522 original size:5 final size:5
Alignment explanation
Indices: 59787512--59787568 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
59787502 CTCTTGCCTC
*
59787512 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
59787559 TCTTT TCTTT
1 TCTTT TCTTT
59787569 GATTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:59787552 original size:15 final size:14
Alignment explanation
Indices: 59787512--59787568 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
59787502 CTCTTGCCTC
*
59787512 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
59787527 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
59787542 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
59787559 TCTTTTCTTT
1 TCTTTTCTTT
59787569 GATTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:59787569 original size:21 final size:21
Alignment explanation
Indices: 59787512--59787579 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
59787502 CTCTTGCCTC
* *
59787512 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
59787533 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
* *
59787554 TCTTTTCTTTTCTTTGATTTC
1 TCTTTTCTTTTCTTTGCTTTT
59787575 TCTTT
1 TCTTT
59787580 ACAAGAATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.08
21 30 0.79
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.04, T:0.75
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:59788514 original size:12 final size:12
Alignment explanation
Indices: 59788490--59788551 Score: 96
Period size: 12 Copynumber: 5.5 Consensus size: 12
59788480 ACTCTTTTTC
59788490 TTTTTTCG-ATT
1 TTTTTTCGAATT
59788501 TTTTTT-GAATT
1 TTTTTTCGAATT
59788512 TTTTTTCGAATT
1 TTTTTTCGAATT
59788524 TTTTTTCGAATT
1 TTTTTTCGAATT
59788536 TTTTTT-G-ATT
1 TTTTTTCGAATT
59788546 TTTTTT
1 TTTTTT
59788552 AACTTGTATA
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.20
11 16 0.33
12 23 0.47
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (12 bp):
TTTTTTCGAATT
Found at i:59788518 original size:22 final size:23
Alignment explanation
Indices: 59788490--59788551 Score: 101
Period size: 22 Copynumber: 2.7 Consensus size: 23
59788480 ACTCTTTTTC
59788490 TTTTTTCGATTTTTTTT-GAATT
1 TTTTTTCGATTTTTTTTCGAATT
59788512 TTTTTTCGAATTTTTTTTCGAATT
1 TTTTTTCG-ATTTTTTTTCGAATT
59788536 TTTTTT-GATTTTTTTT
1 TTTTTTCGATTTTTTTT
59788552 AACTTGTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.45
23 10 0.26
24 11 0.29
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (23 bp):
TTTTTTCGATTTTTTTTCGAATT
Found at i:59790229 original size:30 final size:30
Alignment explanation
Indices: 59790195--59790277 Score: 76
Period size: 30 Copynumber: 2.8 Consensus size: 30
59790185 TAAACTAAAA
* * *
59790195 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCATGAGCTAAAGC
* * * * * *
59790225 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAGATTTAGCTCATGAGCTAAAGC
*
59790255 TGAGCTAAGGTTTAGCTCATGAG
1 TGAGCTAAGATTTAGCTCATGAG
59790278 TTGAATATGA
Statistics
Matches: 39, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCATGAGCTAAAGC
Found at i:59794844 original size:14 final size:14
Alignment explanation
Indices: 59794825--59794858 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
59794815 CAATCCATTG
59794825 AAAGAGAAAAAGAA
1 AAAGAGAAAAAGAA
* *
59794839 AAAGAGCAAAATAA
1 AAAGAGAAAAAGAA
59794853 AAAGAG
1 AAAGAG
59794859 TGGAAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (14 bp):
AAAGAGAAAAAGAA
Found at i:59795724 original size:30 final size:30
Alignment explanation
Indices: 59795690--59795787 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
59795680 AGCTCACTCC
59795690 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
59795720 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
59795750 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
59795780 TAGCTCAT
1 TAGCTCAT
59795788 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:59795787 original size:324 final size:319
Alignment explanation
Indices: 59795198--59795840 Score: 1090
Period size: 324 Copynumber: 2.0 Consensus size: 319
59795188 TGGAGTAACC
* * * * *
59795198 CTGATACGAGCACGCCCTGCGAACTTTATCGAGCAAGTCTGTCAAGCCGAGCAATGACATGTTGG
1 CTGATACAAGCACGCCCCGCGAACTTCATCGAACAAGCCTGTCAAGCCGAGCAATGACATGTTGG
*
59795263 CAAGCTGATCCAAGCTCGTTTCCAGTTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCGAG
66 CAAGCTGATCCAAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCGAG
* *
59795328 CTCAATCCATCTTGCCTGAGCTAAACCGAGCTTACTCCTAGCTCACTTTCAACTCACGAGCTAAA
131 CTCAATCCAACTTGCCTGAGCTAAACCGAGCTCACTCCTAGCTCACTTTCAACTCACGAGCTAAA
* *
59795393 CCTTAGCTCAACTTCAGCTTAGGAGTTTAGCCTCAGCTTAACTTTAGCTCACGAGCTAAAGCTTA
196 CCTTAGCTCAACTTCAGCTTAGGAGTTTAACCTCAGCTCAACTTTAGCTCACGAGCTAAAGCTTA
59795458 GCTCATTTTAGTTTAAACTCAGTTTTGTCTTTATTAATACATTAAATAAAAATTTGCACATATT
261 GCTCATTTTAGTTT-AACTCAGTTTTGTC--T-TTAATACATTAAAT-AAAATTTGCACATATT
*
59795522 CTGATACAAGCACGCCCCGCGAACTTCATCGAACAAGCCTGTCAAGCCGAGCATTGACATGTTGG
1 CTGATACAAGCACGCCCCGCGAACTTCATCGAACAAGCCTGTCAAGCCGAGCAATGACATGTTGG
59795587 CAAGCTGATCCAAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCGAG
66 CAAGCTGATCCAAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCGAG
*
59795652 CTCAATCCAACTTGCCTGAGCTAAACCGAGCTCACTCCTAGCTCA-TATTCAGCTCACGAGCTAA
131 CTCAATCCAACTTGCCTGAGCTAAACCGAGCTCACTCCTAGCTCACT-TTCAACTCACGAGCTAA
* *
59795716 ACCTTAGCTCAGCTTCAGCTTAGGAGTTTAATCTCAGCTCAACTTTAGCTCACGAGCTAAAGCTT
195 ACCTTAGCTCAACTTCAGCTTAGGAGTTTAACCTCAGCTCAACTTTAGCTCACGAGCTAAAGCTT
*
59795781 AGCTCATTTTAGTTTAACTCAGTTTTGTCTTTAATGCATTAAATAAAATTTGCACATATT
260 AGCTCATTTTAGTTTAACTCAGTTTTGTCTTTAATACATTAAATAAAATTTGCACATATT
59795841 TATTTAAGCA
Statistics
Matches: 303, Mismatches: 15, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
319 16 0.05
320 13 0.04
321 1 0.00
323 15 0.05
324 258 0.85
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (319 bp):
CTGATACAAGCACGCCCCGCGAACTTCATCGAACAAGCCTGTCAAGCCGAGCAATGACATGTTGG
CAAGCTGATCCAAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCGAG
CTCAATCCAACTTGCCTGAGCTAAACCGAGCTCACTCCTAGCTCACTTTCAACTCACGAGCTAAA
CCTTAGCTCAACTTCAGCTTAGGAGTTTAACCTCAGCTCAACTTTAGCTCACGAGCTAAAGCTTA
GCTCATTTTAGTTTAACTCAGTTTTGTCTTTAATACATTAAATAAAATTTGCACATATT
Found at i:59801494 original size:15 final size:15
Alignment explanation
Indices: 59801474--59801521 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
59801464 TCAAAGATGG
59801474 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
59801489 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
59801503 GTTTATGGATATAAA
1 GTTTATGGATATGAA
59801518 GTTT
1 GTTT
59801522 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:59801508 original size:14 final size:14
Alignment explanation
Indices: 59801468--59801511 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
59801458 AAGGATTCAA
59801468 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
59801482 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
59801497 AGATGGGTTTATGG
1 AGATGGGTTTATGG
59801511 A
1 A
59801512 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:59801537 original size:29 final size:29
Alignment explanation
Indices: 59801468--59801527 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
59801458 AAGGATTCAA
*
59801468 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
59801497 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
59801526 AG
1 AG
59801528 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:59802547 original size:14 final size:14
Alignment explanation
Indices: 59802505--59802549 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
59802495 TTAAAGAAGC
59802505 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
59802519 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
59802532 AACTCATTTAATTA
1 AACTCATTAAATTA
59802546 AACT
1 AACT
59802550 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:59803660 original size:17 final size:17
Alignment explanation
Indices: 59803630--59803684 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
59803620 AGCAACTCAT
59803630 TTATTAATCTAAGATGAG
1 TTATTAA-CTAAGATGAG
*
59803648 TTATTAACTAAGATGAAC
1 TTATTAACTAAGATG-AG
*
59803666 TCAATTAACTAAGATGAG
1 T-TATTAACTAAGATGAG
59803684 T
1 T
59803685 AATTTATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 8 0.25
18 11 0.34
19 13 0.41
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (17 bp):
TTATTAACTAAGATGAG
Found at i:59805522 original size:15 final size:15
Alignment explanation
Indices: 59805502--59805549 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
59805492 TCAAAGATGG
59805502 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
59805517 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
59805531 GTTTATGGATATAAA
1 GTTTATGGATATGAA
59805546 GTTT
1 GTTT
59805550 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:59805536 original size:14 final size:14
Alignment explanation
Indices: 59805496--59805539 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
59805486 AAGGATTCAA
59805496 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
59805510 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
59805525 AGATGGGTTTATGG
1 AGATGGGTTTATGG
59805539 A
1 A
59805540 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:59805565 original size:29 final size:29
Alignment explanation
Indices: 59805496--59805555 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
59805486 AAGGATTCAA
*
59805496 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
59805525 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
59805554 AG
1 AG
59805556 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:59808845 original size:30 final size:28
Alignment explanation
Indices: 59808791--59808847 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
59808781 TTTCTTCCAC
* *
59808791 ACTTTCTTTTTGCTCACTCTCTTTTTCA
1 ACTTTCTTTTTGCACACACTCTTTTTCA
59808819 ACTTTACTTTCTTGCACACACTCTTTTTC
1 ACTTT-CTTT-TTGCACACACTCTTTTTC
59808848 TTTTTCGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 4 0.16
30 16 0.64
ACGTcount: A:0.14, C:0.30, G:0.04, T:0.53
Consensus pattern (28 bp):
ACTTTCTTTTTGCACACACTCTTTTTCA
Found at i:59812908 original size:20 final size:20
Alignment explanation
Indices: 59812885--59812932 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
59812875 AGCTCCGTCC
59812885 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
59812905 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
59812925 AGCTCAAC
1 AGCTCAAC
59812933 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:59814404 original size:12 final size:12
Alignment explanation
Indices: 59814387--59814457 Score: 88
Period size: 12 Copynumber: 5.6 Consensus size: 12
59814377 ATACAAGTAT
59814387 AAAAAAAATTCA
1 AAAAAAAATTCA
*
59814399 AAAAAAAATTTGGA
1 AAAAAAAA-TT-CA
*
59814413 AAAAAAAATTCG
1 AAAAAAAATTCA
59814425 AAAAAAAATTCA
1 AAAAAAAATTCA
59814437 AAAAAAAAGTTTCA
1 AAAAAAAA--TTCA
59814451 AAAAAAA
1 AAAAAAA
59814458 TGATTTATGC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
12 27 0.53
13 4 0.08
14 20 0.39
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:59814405 original size:13 final size:13
Alignment explanation
Indices: 59814387--59814457 Score: 81
Period size: 13 Copynumber: 5.5 Consensus size: 13
59814377 ATACAAGTAT
59814387 AAAAAAAATTCAA
1 AAAAAAAATTCAA
* **
59814400 AAAAAAATTTGGA
1 AAAAAAAATTCAA
*
59814413 AAAAAAAATTC-G
1 AAAAAAAATTCAA
59814425 AAAAAAAATTCAA
1 AAAAAAAATTCAA
*
59814438 AAAAAAAGTTTCAA
1 AAAAAAA-ATTCAA
59814452 AAAAAA
1 AAAAAA
59814458 TGATTTATGC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
12 11 0.23
13 26 0.54
14 11 0.23
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:59815377 original size:9 final size:10
Alignment explanation
Indices: 59815370--59815426 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
59815360 AAGAGAAAAT
59815370 AAAGAAAAGA
1 AAAGAAAAGA
59815380 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
59815392 AAAGAAGA-A
1 AAAGAAAAGA
59815401 AAAGAAAATGA
1 AAAGAAAA-GA
59815412 AATA-AAAAGA
1 AA-AGAAAAGA
59815422 AAAGA
1 AAAGA
59815427 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:59815394 original size:6 final size:5
Alignment explanation
Indices: 59815370--59815426 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
59815360 AAGAGAAAAT
*
59815370 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
59815417 AAAGA AAAGA
1 AAAGA AAAGA
59815427 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:59815401 original size:15 final size:14
Alignment explanation
Indices: 59815370--59815426 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
59815360 AAGAGAAAAT
59815370 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
59815386 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
59815401 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
59815417 AAAGAAAAGA
1 AAAGAAAAGA
59815427 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:59815503 original size:12 final size:12
Alignment explanation
Indices: 59815495--59815519 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59815485 TTTGAAAAGC
59815495 AAAAAGAAAATG
1 AAAAAGAAAATG
59815507 AAAAAGAAAATG
1 AAAAAGAAAATG
59815519 A
1 A
59815520 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:59815516 original size:18 final size:18
Alignment explanation
Indices: 59815489--59815544 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
59815479 AAATCCTTTG
59815489 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
59815508 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
59815526 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
59815543 AA
1 AA
59815545 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:59815529 original size:30 final size:31
Alignment explanation
Indices: 59815495--59815576 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
59815485 TTTGAAAAGC
*
59815495 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
59815525 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
**
59815555 AAAAAGAAGTTGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
59815577 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 25 0.60
31 9 0.21
ACGTcount: A:0.63, C:0.01, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:59817855 original size:30 final size:30
Alignment explanation
Indices: 59817821--59817905 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
59817811 CTAGCTCATA
*
59817821 TTCAGCTCACGAGCTAAACCTTAGCACAGC
1 TTCAGCTCACGAGCTAAACCTTAGCACAAC
* * * * * * *
59817851 TTCAGCTTAGGAGTTTAATCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCACAAC
* *
59817881 TTTAGCTCACGAGCTAAAGCTTAGC
1 TTCAGCTCACGAGCTAAACCTTAGC
59817906 TCATTTTAGT
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCACAAC
Found at i:59819934 original size:27 final size:27
Alignment explanation
Indices: 59819903--59819959 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
59819893 AGCAATTGGA
*
59819903 ATGAATGGGAGCTGATTTGCTATGTCT
1 ATGAATAGGAGCTGATTTGCTATGTCT
59819930 ATGAATAGGAGCTGATTTGCTATGTCT
1 ATGAATAGGAGCTGATTTGCTATGTCT
59819957 ATG
1 ATG
59819960 TTCGGCCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.37
Consensus pattern (27 bp):
ATGAATAGGAGCTGATTTGCTATGTCT
Done.