Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 142 of 199
Found at i:41470313 original size:12 final size:12
Alignment explanation
Indices: 41470298--41470357 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 12
41470288 TTTTGCTCGA
*
41470298 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
41470310 TTTTTTTTGAATT
1 TTTTTTTTCAA-T
41470323 TTTTTTTCAATCAAT
1 TTTTTTT---TCAAT
41470338 TTTTTTTTCGAAT
1 TTTTTTTTC-AAT
41470351 TTTTTTT
1 TTTTTTT
41470358 GATTTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 11 0.28
13 18 0.45
15 8 0.20
16 3 0.08
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:41472009 original size:20 final size:19
Alignment explanation
Indices: 41471986--41472050 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
41471976 AAGCTCAAAC
41471986 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
41472006 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
41472026 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
41472046 GAGCT
1 GAGCT
41472051 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:41476461 original size:13 final size:13
Alignment explanation
Indices: 41476445--41476504 Score: 66
Period size: 13 Copynumber: 4.4 Consensus size: 13
41476435 TTTTGCTCGA
*
41476445 TTTTTTTTCACTT
1 TTTTTTTTCAATT
*
41476458 TTTTTTTTGAATT
1 TTTTTTTTCAATT
*
41476471 TTTTTTTTCAATCAA
1 TTTTTTTTCAAT--T
41476486 TTTTTTTTCGAATT
1 TTTTTTTTC-AATT
41476500 TTTTT
1 TTTTT
41476505 GATTTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
13 22 0.56
14 5 0.13
15 9 0.23
16 3 0.08
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.73
Consensus pattern (13 bp):
TTTTTTTTCAATT
Found at i:41481697 original size:14 final size:14
Alignment explanation
Indices: 41481674--41481738 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 14
41481664 GTAACAAAAA
41481674 AAAAAGAAAATTTCG
1 AAAAA-AAAATTTCG
*
41481689 AAAAAAAAATTGATTG
1 AAAAAAAAATT--TCG
*
41481705 AAAAAAAAAATTC-
1 AAAAAAAAATTTCG
*
41481718 AAAAAAAAA-GT-G
1 AAAAAAAAATTTCG
41481730 AAAAAAAAA
1 AAAAAAAAA
41481739 ATCGAGCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
12 10 0.23
13 9 0.21
14 7 0.16
15 5 0.12
16 12 0.28
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.15
Consensus pattern (14 bp):
AAAAAAAAATTTCG
Found at i:41481764 original size:16 final size:14
Alignment explanation
Indices: 41481717--41481770 Score: 58
Period size: 16 Copynumber: 3.7 Consensus size: 14
41481707 AAAAAAAATT
41481717 CAAAAAAAAAGTGA
1 CAAAAAAAAAGTGA
41481731 -AAAAAAAAA-TCGA
1 CAAAAAAAAAGT-GA
41481744 GCAAAAAAAAAGGTGA
1 -CAAAAAAAAA-GTGA
41481760 CCAAAAAAAAA
1 -CAAAAAAAAA
41481771 TCAAGTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 1 0.03
13 11 0.32
15 9 0.26
16 12 0.35
17 1 0.03
ACGTcount: A:0.72, C:0.09, G:0.13, T:0.06
Consensus pattern (14 bp):
CAAAAAAAAAGTGA
Found at i:41481766 original size:31 final size:29
Alignment explanation
Indices: 41481717--41481792 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 29
41481707 AAAAAAAATT
*
41481717 CAAAAAAAAA-GTGAAAAAAAAAATCGAG
1 CAAAAAAAAAGGTGAAAAAAAAAATCAAG
41481745 CAAAAAAAAAGGTGACCAAAAAAAAATCAAG
1 CAAAAAAAAAGGTGA--AAAAAAAAATCAAG
**
41481776 TTAAAAAAAA-GTGAAAA
1 CAAAAAAAAAGGTGAAAA
41481793 GTCTTGCGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.31
29 4 0.10
30 4 0.10
31 21 0.50
ACGTcount: A:0.70, C:0.08, G:0.13, T:0.09
Consensus pattern (29 bp):
CAAAAAAAAAGGTGAAAAAAAAAATCAAG
Found at i:41482760 original size:18 final size:18
Alignment explanation
Indices: 41482722--41482763 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41482712 AAATCGAAAG
* **
41482722 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
41482740 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
41482758 AAAAGA
1 AAAAGA
41482764 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:41486632 original size:14 final size:16
Alignment explanation
Indices: 41486613--41486708 Score: 58
Period size: 15 Copynumber: 5.9 Consensus size: 16
41486603 TATTGATCGA
41486613 GAAAAAGAAAAAG-G-
1 GAAAAAGAAAAAGAGT
*
41486627 GAAAAACAAAAAGAGT
1 GAAAAAGAAAAAGAGT
**
41486643 G-AAAAGAAAAAGAAA
1 GAAAAAGAAAAAGAGT
*
41486658 G-AAAAGAATGAGGAGAGT
1 GAAAAAGAA--A-AAGAGT
*
41486676 GAGATAAA-AACAAGAGT
1 GA-A-AAAGAAAAAGAGT
41486693 GACAAAAGAAAAAGAG
1 GA-AAAAGAAAAAGAG
41486709 CAAGAGTGTG
Statistics
Matches: 62, Mismatches: 11, Indels: 15
0.70 0.12 0.17
Matches are distributed among these distances:
14 12 0.19
15 20 0.32
16 4 0.06
17 16 0.26
18 4 0.06
20 3 0.05
21 3 0.05
ACGTcount: A:0.66, C:0.03, G:0.26, T:0.05
Consensus pattern (16 bp):
GAAAAAGAAAAAGAGT
Found at i:41486661 original size:15 final size:15
Alignment explanation
Indices: 41486611--41486665 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
41486601 TCTATTGATC
41486611 GAGA-AAAAGAAAAA
1 GAGAGAAAAGAAAAA
* *
41486625 GGGA-AAAACAAAAA
1 GAGAGAAAAGAAAAA
*
41486639 GAGTGAAAAGAAAAA
1 GAGAGAAAAGAAAAA
*
41486654 GAAAGAAAAGAA
1 GAGAGAAAAGAA
41486666 TGAGGAGAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
14 14 0.42
15 19 0.58
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (15 bp):
GAGAGAAAAGAAAAA
Found at i:41493269 original size:14 final size:16
Alignment explanation
Indices: 41493250--41493345 Score: 58
Period size: 15 Copynumber: 5.9 Consensus size: 16
41493240 TATTGATCGA
41493250 GAAAAAGAAAAAG-G-
1 GAAAAAGAAAAAGAGT
*
41493264 GAAAAACAAAAAGAGT
1 GAAAAAGAAAAAGAGT
**
41493280 G-AAAAGAAAAAGAAA
1 GAAAAAGAAAAAGAGT
*
41493295 G-AAAAGAATGAGGAGAGT
1 GAAAAAGAA--A-AAGAGT
*
41493313 GAGATAAA-AACAAGAGT
1 GA-A-AAAGAAAAAGAGT
41493330 GACAAAAGAAAAAGAG
1 GA-AAAAGAAAAAGAG
41493346 CAAGAGTGTG
Statistics
Matches: 62, Mismatches: 11, Indels: 15
0.70 0.12 0.17
Matches are distributed among these distances:
14 12 0.19
15 20 0.32
16 4 0.06
17 16 0.26
18 4 0.06
20 3 0.05
21 3 0.05
ACGTcount: A:0.66, C:0.03, G:0.26, T:0.05
Consensus pattern (16 bp):
GAAAAAGAAAAAGAGT
Found at i:41493298 original size:15 final size:15
Alignment explanation
Indices: 41493248--41493302 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
41493238 TCTATTGATC
41493248 GAGA-AAAAGAAAAA
1 GAGAGAAAAGAAAAA
* *
41493262 GGGA-AAAACAAAAA
1 GAGAGAAAAGAAAAA
*
41493276 GAGTGAAAAGAAAAA
1 GAGAGAAAAGAAAAA
*
41493291 GAAAGAAAAGAA
1 GAGAGAAAAGAA
41493303 TGAGGAGAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
14 14 0.42
15 19 0.58
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (15 bp):
GAGAGAAAAGAAAAA
Found at i:41499904 original size:14 final size:16
Alignment explanation
Indices: 41499885--41499980 Score: 58
Period size: 15 Copynumber: 5.9 Consensus size: 16
41499875 TATTGATCGA
41499885 GAAAAAGAAAAAG-G-
1 GAAAAAGAAAAAGAGT
*
41499899 GAAAAACAAAAAGAGT
1 GAAAAAGAAAAAGAGT
**
41499915 G-AAAAGAAAAAGAAA
1 GAAAAAGAAAAAGAGT
*
41499930 G-AAAAGAATGAGGAGAGT
1 GAAAAAGAA--A-AAGAGT
*
41499948 GAGATAAA-AACAAGAGT
1 GA-A-AAAGAAAAAGAGT
41499965 GACAAAAGAAAAAGAG
1 GA-AAAAGAAAAAGAG
41499981 CAAGAGTGTG
Statistics
Matches: 62, Mismatches: 11, Indels: 15
0.70 0.12 0.17
Matches are distributed among these distances:
14 12 0.19
15 20 0.32
16 4 0.06
17 16 0.26
18 4 0.06
20 3 0.05
21 3 0.05
ACGTcount: A:0.66, C:0.03, G:0.26, T:0.05
Consensus pattern (16 bp):
GAAAAAGAAAAAGAGT
Found at i:41499933 original size:15 final size:15
Alignment explanation
Indices: 41499883--41499937 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
41499873 TCTATTGATC
41499883 GAGA-AAAAGAAAAA
1 GAGAGAAAAGAAAAA
* *
41499897 GGGA-AAAACAAAAA
1 GAGAGAAAAGAAAAA
*
41499911 GAGTGAAAAGAAAAA
1 GAGAGAAAAGAAAAA
*
41499926 GAAAGAAAAGAA
1 GAGAGAAAAGAA
41499938 TGAGGAGAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
14 14 0.42
15 19 0.58
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (15 bp):
GAGAGAAAAGAAAAA
Found at i:41506973 original size:17 final size:18
Alignment explanation
Indices: 41506951--41506984 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41506941 ACAACACTCC
*
41506951 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
41506968 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
41506985 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:41507092 original size:15 final size:16
Alignment explanation
Indices: 41507067--41507098 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
41507057 TATCTCACAC
41507067 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
41507083 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
41507098 T
1 T
41507099 TTCATTTTCT
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:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:41508075 original size:14 final size:13
Alignment explanation
Indices: 41508058--41508136 Score: 52
Period size: 13 Copynumber: 5.6 Consensus size: 13
41508048 GGTCACCTTT
41508058 TTTTTTTTGCTCAA
1 TTTTTTTT-CTCAA
* *
41508072 TTTTTTTTTTCAC
1 TTTTTTTTCTCAA
* *
41508085 TTTTTTTTTTGAATA
1 TTTTTTTTCT-CA-A
41508100 TTTTTTTTTCAATCAA
1 -TTTTTTTTC--TCAA
41508116 TTTTTTTT-TCGAA
1 TTTTTTTTCTC-AA
41508129 TTTTTTTT
1 TTTTTTTT
41508137 GATTTTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
12 2 0.04
13 23 0.43
14 9 0.17
15 8 0.15
16 9 0.17
17 1 0.02
18 1 0.02
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTTTTTCTCAA
Found at i:41508075 original size:16 final size:14
Alignment explanation
Indices: 41508056--41508136 Score: 67
Period size: 15 Copynumber: 5.6 Consensus size: 14
41508046 TTGGTCACCT
41508056 TTTTTTTTTTGCTCAA
1 TTTTTTTTTT--TCAA
41508072 -TTTTTTTTTTC-A
1 TTTTTTTTTTTCAA
* *
41508084 CTTTTTTTTTTGAA
1 TTTTTTTTTTTCAA
*
41508098 TATTTTTTTTTCAA
1 TTTTTTTTTTTCAA
*
41508112 TCAATTTTTTTTTCGAA
1 T--TTTTTTTTTTC-AA
41508129 TTTTTTTT
1 TTTTTTTT
41508137 GATTTTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
12 1 0.02
13 12 0.22
14 13 0.24
15 15 0.27
16 11 0.20
17 3 0.05
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTTTCAA
Found at i:41508075 original size:17 final size:18
Alignment explanation
Indices: 41508041--41508081 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41508031 TTTAACTTGA
* *
41508041 TTTTTTTGGTCACCTTTT
1 TTTTTTTGCTCACATTTT
41508059 TTTTTTTGCTCA-ATTTT
1 TTTTTTTGCTCACATTTT
41508076 TTTTTT
1 TTTTTT
41508082 CACTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.73
Consensus pattern (18 bp):
TTTTTTTGCTCACATTTT
Found at i:41508088 original size:13 final size:13
Alignment explanation
Indices: 41508017--41508110 Score: 62
Period size: 13 Copynumber: 6.5 Consensus size: 13
41508007 CTCGCAAGAC
41508017 TTTTCACTTTTTT
1 TTTTCACTTTTTT
*
41508030 TTTTAACTTGATTTT
1 TTTTCACTT--TTTT
41508045 TTTGGTCACCTTTTTTTT
1 TTT--TCA-C--TTTTTT
*
41508063 TTTGCTCAATTTTTT
1 TTT--TCACTTTTTT
41508078 TTTTCACTTTTTT
1 TTTTCACTTTTTT
* *
41508091 TTTTGAATATTTTT
1 TTTTCACT-TTTTT
41508105 TTTTCA
1 TTTTCA
41508111 ATCAATTTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
13 23 0.35
14 10 0.15
15 16 0.25
17 2 0.03
18 12 0.18
20 2 0.03
ACGTcount: A:0.13, C:0.12, G:0.05, T:0.70
Consensus pattern (13 bp):
TTTTCACTTTTTT
Found at i:41508130 original size:13 final size:13
Alignment explanation
Indices: 41508073--41508147 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 13
41508063 TTTGCTCAAT
*
41508073 TTTTTTTTTC-AC
1 TTTTTTTTTCGAA
*
41508085 TTTTTTTTTTGAATA
1 TTTTTTTTTCG-A-A
*
41508100 TTTTTTTTTCAATCAA
1 TTTTTTTTTC---GAA
41508116 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
41508129 -TTTTTTTT-G-A
1 TTTTTTTTTCGAA
41508139 TTTTTTTTT
1 TTTTTTTTT
41508148 GTTACTCCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
10 1 0.02
11 9 0.18
12 17 0.33
13 2 0.04
14 1 0.02
15 9 0.18
16 11 0.22
17 1 0.02
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.75
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:41508146 original size:11 final size:11
Alignment explanation
Indices: 41508115--41508148 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
41508105 TTTTCAATCA
41508115 ATTTTTTTTTCG
1 ATTTTTTTTT-G
*
41508127 AATTTTTTTTG
1 ATTTTTTTTTG
41508138 ATTTTTTTTTG
1 ATTTTTTTTTG
41508149 TTACTCCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (11 bp):
ATTTTTTTTTG
Found at i:41514284 original size:12 final size:12
Alignment explanation
Indices: 41514268--41514330 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 12
41514258 TTTTTGCTCG
41514268 ATTTTTTTTTCA
1 ATTTTTTTTTCA
* *
41514280 CTTTTTTTTTGA
1 ATTTTTTTTTCA
41514292 ATTTTTTTTTTCAATCA
1 A--TTTTTTTT---TCA
41514309 ATTTTTTTTTCGA
1 ATTTTTTTTTC-A
41514322 ATTTTTTTT
1 ATTTTTTTT
41514331 GATTTTTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
12 12 0.29
13 10 0.24
14 8 0.20
15 8 0.20
17 3 0.07
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:41514324 original size:13 final size:13
Alignment explanation
Indices: 41514255--41514330 Score: 59
Period size: 13 Copynumber: 5.6 Consensus size: 13
41514245 GCTCACCTAT
41514255 TTTTTTTTGCTCG-A
1 TTTTTTTT--TCGAA
*
41514269 TTTTTTTTTC-AC
1 TTTTTTTTTCGAA
41514281 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
*
41514293 TTTTTTTTTTCAATCAA
1 -TTTTTTTTTC---GAA
41514310 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
41514323 TTTTTTTT
1 TTTTTTTT
41514331 GATTTTTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
12 12 0.24
13 19 0.37
14 8 0.16
16 10 0.20
17 2 0.04
ACGTcount: A:0.13, C:0.09, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:41515046 original size:20 final size:20
Alignment explanation
Indices: 41515000--41515046 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
41514990 AGCTTGTTTC
*
41515000 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
41515020 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
41515040 CAGCTCA
1 CAGCTCA
41515047 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:41515771 original size:20 final size:20
Alignment explanation
Indices: 41515725--41515771 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
41515715 AGCTTGTTTC
*
41515725 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
41515745 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
41515765 CAGCTCA
1 CAGCTCA
41515772 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:41516334 original size:725 final size:725
Alignment explanation
Indices: 41514885--41516335 Score: 2850
Period size: 725 Copynumber: 2.0 Consensus size: 725
41514875 TGACCACGCC
41514885 TGATACGGCCACGCCTTGGGCACACTTTTGGACCAGCTCCCTAAGCATTGTTTGCAAATCCATGC
1 TGATACGGCCACGCCTTGGGCACACTTTTGGACCAGCTCCCTAAGCATTGTTTGCAAATCCATGC
41514950 AAGCTGAATTAGTTCAATTCCTTCTCATTGAGCTCTGTTTAGCTTGTTTCCAGCTCACTCGAGCT
66 AAGCTGAATTAGTTCAATTCCTTCTCATTGAGCTCTGTTTAGCTTGTTTCCAGCTCACTCGAGCT
41515015 CAAGTCAACTCATTCAAGCTCAATTCAGCTCAATCTTAACCTAATGAGCTTATTTTTAGCTTTCT
131 CAAGTCAACTCATTCAAGCTCAATTCAGCTCAATCTTAACCTAATGAGCTTATTTTTAGCTTTCT
41515080 TTAGCTTGCATTTATTTTCCTGAAATAAATCATTTAATTTGTCTTTAGTTGAATTAGTTGTTTAT
196 TTAGCTTGCATTTATTTTCCTGAAATAAATCATTTAATTTGTCTTTAGTTGAATTAGTTGTTTAT
41515145 TTTAAGTTAATTAATTTGTTAAATCTGGACAAATAATTAATTAAGTGTTTTAATTATATCTAAAT
261 TTTAAGTTAATTAATTTGTTAAATCTGGACAAATAATTAATTAAGTGTTTTAATTATATCTAAAT
41515210 TAAATACTTAATTAATTATGATGTTTTAAATATGTATGAAATTGTTAATATGTATGGCCAAATTT
326 TAAATACTTAATTAATTATGATGTTTTAAATATGTATGAAATTGTTAATATGTATGGCCAAATTT
41515275 AATGTGCAAATTATTGAGTTCATATGCTGCTAATTTAATGTGTTTGAAATGCATTTAACTTGCTG
391 AATGTGCAAATTATTGAGTTCATATGCTGCTAATTTAATGTGTTTGAAATGCATTTAACTTGCTG
*
41515340 ATTTAATTTGCTGCAGGTTCATGAACGGATTGGTGCAATGTATGGGAGTGTGCATGCACAATTGA
456 ATTTAATTTACTGCAGGTTCATGAACGGATTGGTGCAATGTATGGGAGTGTGCATGCACAATTGA
*
41515405 GGTTCAATGGATGGCATTTGAAGGAGCACATGCATTTGGGACGTTCATGCAAGAGGGAGTTGCTG
521 GGTTCAATGGATGGCATTTAAAGGAGCACATGCATTTGGGACGTTCATGCAAGAGGGAGTTGCTG
*
41515470 AAAGTTCATGTATTTGAAGATTCATGGATCATATTTATGGGGGAAAATACATGGGACGTTTCATG
586 AAAGTTCATGTATTTGAAGATTCATGGATCATATTTATGGGGGAAAATACATGGGACATTTCATG
41515535 CATGATTCATGCATTTTCAAGATGACCATTCAAGTATTTTAGGCACATTAATGCCTCATTCAGCC
651 CATGATTCATGCATTTTCAAGATGACCATTCAAGTATTTTAGGCACATTAATGCCTCATTCAGCC
41515600 AAGGGAGATG
716 AAGGGAGATG
41515610 TGATACGGCCACGCCTTGGGCACACTTTTGGACCAGCTCCCTAAGCATTGTTTGCAAATCCATGC
1 TGATACGGCCACGCCTTGGGCACACTTTTGGACCAGCTCCCTAAGCATTGTTTGCAAATCCATGC
*
41515675 AAGCTGAATTAGTTCAATTCCTTCTCGTTGAGCTCTGTTTAGCTTGTTTCCAGCTCACTCGAGCT
66 AAGCTGAATTAGTTCAATTCCTTCTCATTGAGCTCTGTTTAGCTTGTTTCCAGCTCACTCGAGCT
41515740 CAAGTCAACTCATTCAAGCTCAATTCAGCTCAATCTTAACCTAATGAGCTTATTTTTAGCTTTCT
131 CAAGTCAACTCATTCAAGCTCAATTCAGCTCAATCTTAACCTAATGAGCTTATTTTTAGCTTTCT
41515805 TTAGCTTGCATTTATTTTCCTGAAATAAATCATTTAATTTGTCTTTAGTTGAATTAGTTGTTTAT
196 TTAGCTTGCATTTATTTTCCTGAAATAAATCATTTAATTTGTCTTTAGTTGAATTAGTTGTTTAT
41515870 TTTAAGTTAATTAATTTGTTAAATCTGGACAAATAATTAATTAAGTGTTTTAATTATATCTAAAT
261 TTTAAGTTAATTAATTTGTTAAATCTGGACAAATAATTAATTAAGTGTTTTAATTATATCTAAAT
41515935 TAAATACTTAATTAATTATGATGTTTTAAATATGTATGAAATTGTTAATATGTATGGCCAAATTT
326 TAAATACTTAATTAATTATGATGTTTTAAATATGTATGAAATTGTTAATATGTATGGCCAAATTT
41516000 AATGTGCAAATTATTGAGTTCATATGCTGCTAATTTAATGTGTTTGAAATGCATTTAACTTGCTG
391 AATGTGCAAATTATTGAGTTCATATGCTGCTAATTTAATGTGTTTGAAATGCATTTAACTTGCTG
41516065 ATTTAATTTACTGCAGGTTCATGAACGGATTGGTGCAATGTATGGGAGTGTGCATGCACAATTGA
456 ATTTAATTTACTGCAGGTTCATGAACGGATTGGTGCAATGTATGGGAGTGTGCATGCACAATTGA
41516130 GGTTCAATGGATGGCATTTAAAGGAGCACATGCATTTGGGACGTTCATGCAAGAGGGAGTTGCTG
521 GGTTCAATGGATGGCATTTAAAGGAGCACATGCATTTGGGACGTTCATGCAAGAGGGAGTTGCTG
41516195 AAAGTTCATGTATTTGAAGATTCATGGATCATATTTATGGGGGAAAATTACATGGGACATTTCAT
586 AAAGTTCATGTATTTGAAGATTCATGGATCATATTTATGGGGGAAAA-TACATGGGACATTTCAT
41516260 GCATGATTCATGCATTTTCAAGATGACCATTCAAGTATTTTAGGCACATTAATGCCTCATTCAGC
650 GCATGATTCATGCATTTTCAAGATGACCATTCAAGTATTTTAGGCACATTAATGCCTCATTCAGC
41516325 CAA-GGAGATG
715 CAAGGGAGATG
41516335 T
1 T
41516336 AGGATCATTA
Statistics
Matches: 721, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
725 637 0.88
726 84 0.12
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (725 bp):
TGATACGGCCACGCCTTGGGCACACTTTTGGACCAGCTCCCTAAGCATTGTTTGCAAATCCATGC
AAGCTGAATTAGTTCAATTCCTTCTCATTGAGCTCTGTTTAGCTTGTTTCCAGCTCACTCGAGCT
CAAGTCAACTCATTCAAGCTCAATTCAGCTCAATCTTAACCTAATGAGCTTATTTTTAGCTTTCT
TTAGCTTGCATTTATTTTCCTGAAATAAATCATTTAATTTGTCTTTAGTTGAATTAGTTGTTTAT
TTTAAGTTAATTAATTTGTTAAATCTGGACAAATAATTAATTAAGTGTTTTAATTATATCTAAAT
TAAATACTTAATTAATTATGATGTTTTAAATATGTATGAAATTGTTAATATGTATGGCCAAATTT
AATGTGCAAATTATTGAGTTCATATGCTGCTAATTTAATGTGTTTGAAATGCATTTAACTTGCTG
ATTTAATTTACTGCAGGTTCATGAACGGATTGGTGCAATGTATGGGAGTGTGCATGCACAATTGA
GGTTCAATGGATGGCATTTAAAGGAGCACATGCATTTGGGACGTTCATGCAAGAGGGAGTTGCTG
AAAGTTCATGTATTTGAAGATTCATGGATCATATTTATGGGGGAAAATACATGGGACATTTCATG
CATGATTCATGCATTTTCAAGATGACCATTCAAGTATTTTAGGCACATTAATGCCTCATTCAGCC
AAGGGAGATG
Found at i:41517326 original size:29 final size:28
Alignment explanation
Indices: 41517276--41517330 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
41517266 AACGAAATTC
** *
41517276 AAAAAAAAAAGAAGTGAGCAAAAAAAGA
1 AAAAAAAAAAGAAAAGAACAAAAAAAGA
41517304 AAAAAATAAAAGAAAAGAACAAAAAAA
1 AAAAAA-AAAAGAAAAGAACAAAAAAA
41517331 AGTGAAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.04
Consensus pattern (28 bp):
AAAAAAAAAAGAAAAGAACAAAAAAAGA
Found at i:41517339 original size:19 final size:18
Alignment explanation
Indices: 41517298--41517332 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41517288 AGTGAGCAAA
41517298 AAAAGAAAAAAATAAAAG
1 AAAAGAAAAAAATAAAAG
*
41517316 AAAAGAACAAAA-AAAAG
1 AAAAGAAAAAAATAAAAG
41517333 TGAAAAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.83, C:0.03, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAAAATAAAAG
Found at i:41518436 original size:48 final size:47
Alignment explanation
Indices: 41518357--41518462 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
41518347 GAGTGTCATG
*
41518357 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
41518405 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
41518453 GAAAAAGAAA
1 GAAAAAGAAA
41518463 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:41520177 original size:20 final size:20
Alignment explanation
Indices: 41520131--41520177 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
41520121 AGCTTGTTTC
*
41520131 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
41520151 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
41520171 CAGCTCA
1 CAGCTCA
41520178 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:41522538 original size:10 final size:10
Alignment explanation
Indices: 41522522--41522579 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
41522512 CAACTCCGAC
41522522 CAGCTCAATT
1 CAGCTCAATT
* *
41522532 GAGCTCATTT
1 CAGCTCAATT
41522542 CAGCTCAA-T
1 CAGCTCAATT
41522551 CGAGCTCAATT
1 C-AGCTCAATT
*
41522562 TAGCTACAATT
1 CAGCT-CAATT
41522573 CAGCTCA
1 CAGCTCA
41522580 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:41522545 original size:20 final size:20
Alignment explanation
Indices: 41522522--41522582 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
41522512 CAACTCCGAC
41522522 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
41522542 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
41522563 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
41522583 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:41523966 original size:11 final size:12
Alignment explanation
Indices: 41523943--41523967 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41523933 AAAAGAGAAG
41523943 AAATTCAAAAAA
1 AAATTCAAAAAA
41523955 AAATTCAAAAAA
1 AAATTCAAAAAA
41523967 A
1 A
41523968 TCGAAAAAAA
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:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:41523985 original size:21 final size:21
Alignment explanation
Indices: 41523929--41523988 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
41523919 TATTGGATTT
* * *
41523929 AAAAAAAAGAGAAGAAATTCA
1 AAAAAAAAGAAAAAAAAATCA
*** *
41523950 AAAAAAAATTCAAAAAAATCG
1 AAAAAAAAGAAAAAAAAATCA
41523971 AAAAAAAAGAAAAAAAAA
1 AAAAAAAAGAAAAAAAAA
41523989 GAAGTGACAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.78, C:0.05, G:0.08, T:0.08
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAAAATCA
Found at i:41525075 original size:18 final size:18
Alignment explanation
Indices: 41525049--41525098 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
41525039 AAATTGAAAG
*
41525049 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
41525067 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
41525085 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
41525099 TCAAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:41525077 original size:6 final size:6
Alignment explanation
Indices: 41525045--41525098 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
41525035 AAAGAAATTG
* * ** *
41525045 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
41525092 AAAGAA A
1 AAAGAA A
41525099 TCAAAATAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:41525158 original size:18 final size:18
Alignment explanation
Indices: 41525137--41525171 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41525127 AGAAAAGAAA
41525137 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
41525155 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
41525172 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:41527255 original size:10 final size:10
Alignment explanation
Indices: 41527239--41527296 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
41527229 CAACTCCGAC
41527239 CAGCTCAATT
1 CAGCTCAATT
* *
41527249 GAGCTCATTT
1 CAGCTCAATT
41527259 CAGCTCAA-T
1 CAGCTCAATT
41527268 CGAGCTCAATT
1 C-AGCTCAATT
*
41527279 TAGCTACAATT
1 CAGCT-CAATT
41527290 CAGCTCA
1 CAGCTCA
41527297 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:41527262 original size:20 final size:20
Alignment explanation
Indices: 41527239--41527299 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
41527229 CAACTCCGAC
41527239 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
41527259 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
41527280 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
41527300 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:41529461 original size:20 final size:20
Alignment explanation
Indices: 41529438--41529484 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
41529428 GGGTTAAGAT
*
41529438 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
41529458 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
41529478 TGAGCTG
1 TGAGCTG
41529485 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:41530257 original size:21 final size:21
Alignment explanation
Indices: 41530212--41530274 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
41530202 TTTGAACCAT
* *
41530212 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
41530234 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
41530255 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
41530275 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:41531360 original size:14 final size:14
Alignment explanation
Indices: 41531311--41531360 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
41531301 ACTCTCCTCA
41531311 TTCTTTTCTT-TCTT
1 TTCTTTT-TTCTCTT
**
41531325 TTCTTTTCACTCTT
1 TTCTTTTTTCTCTT
41531339 TT-TGTTTTTCTCTT
1 TTCT-TTTTTCTCTT
41531353 TTCTTTTT
1 TTCTTTTT
41531361 CTCGCTCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (14 bp):
TTCTTTTTTCTCTT
Found at i:41533464 original size:13 final size:13
Alignment explanation
Indices: 41533446--41533489 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
41533436 GAATACAAAC
41533446 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
41533458 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
41533471 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
41533484 TTTTTT
1 TTTTTT
41533490 ACAATCTCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 8 0.26
13 23 0.74
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.75
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:41539864 original size:12 final size:11
Alignment explanation
Indices: 41539833--41539863 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
41539823 AAAAGAGTTC
41539833 GAAAAAAAATT
1 GAAAAAAAATT
41539844 GAAAAAAAATT
1 GAAAAAAAATT
41539855 GAAAAAAAA
1 GAAAAAAAA
41539864 AAATTGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (11 bp):
GAAAAAAAATT
Found at i:41540961 original size:18 final size:18
Alignment explanation
Indices: 41540923--41540964 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41540913 AAATCGAAAG
* **
41540923 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
41540941 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
41540959 AAAAGA
1 AAAAGA
41540965 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:41544137 original size:10 final size:11
Alignment explanation
Indices: 41544121--41544151 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
41544111 AAGAGTTCGA
41544121 AAAAAAAATTG
1 AAAAAAAATTG
41544132 AAAAAAAATTG
1 AAAAAAAATTG
41544143 AAAAGAAAA
1 AAAA-AAAA
41544152 AAAATTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:41545249 original size:18 final size:18
Alignment explanation
Indices: 41545211--41545252 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41545201 AAATCGAAAG
* **
41545211 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
41545229 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
41545247 AAAAGA
1 AAAAGA
41545253 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:41549743 original size:13 final size:13
Alignment explanation
Indices: 41549725--41549750 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41549715 TGTGTCCTAA
41549725 TATGAATTAAATT
1 TATGAATTAAATT
41549738 TATGAATTAAATT
1 TATGAATTAAATT
41549751 GCTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:41552059 original size:22 final size:22
Alignment explanation
Indices: 41552016--41552058 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
41552006 AAGGGCATAA
*
41552016 AATGCTCTTTAAAACTCCTTTT
1 AATGATCTTTAAAACTCCTTTT
*
41552038 AATGATCTTT-AAGCTCCTTTT
1 AATGATCTTTAAAACTCCTTTT
41552059 TTTAACAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.47
Consensus pattern (22 bp):
AATGATCTTTAAAACTCCTTTT
Found at i:41552209 original size:21 final size:23
Alignment explanation
Indices: 41552164--41552210 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
41552154 TCACCTGCAA
* *
41552164 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
41552187 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
41552208 TAA
1 TAA
41552211 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:41555015 original size:20 final size:20
Alignment explanation
Indices: 41554992--41555038 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
41554982 GGGTTAAGAT
*
41554992 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
41555012 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
41555032 TGAGCTG
1 TGAGCTG
41555039 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:41557877 original size:11 final size:11
Alignment explanation
Indices: 41557863--41557887 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41557853 TTTTTTTTCT
41557863 TTTTTTTCGAA
1 TTTTTTTCGAA
41557874 TTTTTTTCGAA
1 TTTTTTTCGAA
41557885 TTT
1 TTT
41557888 CTTCTCTTTT
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:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:41557877 original size:36 final size:35
Alignment explanation
Indices: 41557809--41557878 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
41557799 TCGCAAGACT
**
41557809 TTTCACTTTTTTTTTTCTCTTTTTTCTCATTTTTA
1 TTTCACTTTTTTTTTTCTCTTTTTTCGAATTTTTA
*
41557844 TTTCACTTCTTTTTTTTCTTTTTTTTCGAATTTTT
1 TTTCACTT-TTTTTTTTCTCTTTTTTCGAATTTTT
41557879 TTCGAATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 8 0.26
36 23 0.74
ACGTcount: A:0.09, C:0.16, G:0.01, T:0.74
Consensus pattern (35 bp):
TTTCACTTTTTTTTTTCTCTTTTTTCGAATTTTTA
Found at i:41557890 original size:36 final size:36
Alignment explanation
Indices: 41557809--41557881 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
41557799 TCGCAAGACT
*
41557809 TTTCACTT-TTTTTTTTCTCTTTTTTCTCATTTTTA
1 TTTCACTTCTTTTTTTTCTCTTTTTTCTCAATTTTA
41557844 TTTCACTTCTTTTTTTTCT-TTTTTT-TCGAATTTT-
1 TTTCACTTCTTTTTTTTCTCTTTTTTCTC-AATTTTA
41557878 TTTC
1 TTTC
41557882 GAATTTCTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
34 6 0.17
35 19 0.54
36 10 0.29
ACGTcount: A:0.08, C:0.16, G:0.01, T:0.74
Consensus pattern (36 bp):
TTTCACTTCTTTTTTTTCTCTTTTTTCTCAATTTTA
Found at i:41559405 original size:20 final size:20
Alignment explanation
Indices: 41559382--41559428 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
41559372 GGGTTAAGAT
*
41559382 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
41559402 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
41559422 TGAGCTG
1 TGAGCTG
41559429 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:41561526 original size:23 final size:22
Alignment explanation
Indices: 41561474--41561526 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
41561464 TCCACGTCTT
*
41561474 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
41561496 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
41561519 TTTCTTTT
1 TTTCTTTT
41561527 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:41565528 original size:19 final size:18
Alignment explanation
Indices: 41565492--41565531 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41565482 TTTCCACTCG
*
41565492 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
41565510 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
41565529 TTT
1 TTT
41565532 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:41566621 original size:17 final size:16
Alignment explanation
Indices: 41566599--41566652 Score: 76
Period size: 15 Copynumber: 3.4 Consensus size: 16
41566589 CTTCTTCTTC
41566599 TTTTTTTTCACGAAATT
1 TTTTTTTTCACG-AATT
*
41566616 TTTTTTTTCATGAA-T
1 TTTTTTTTCACGAATT
41566631 TTTTTTTTCACG-ATT
1 TTTTTTTTCACGAATT
41566646 TTTTTTT
1 TTTTTTT
41566653 CAACTTGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 1 0.03
15 20 0.59
16 2 0.06
17 11 0.32
ACGTcount: A:0.17, C:0.09, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTTTTTCACGAATT
Found at i:41566633 original size:14 final size:15
Alignment explanation
Indices: 41566599--41566654 Score: 78
Period size: 14 Copynumber: 3.7 Consensus size: 15
41566589 CTTCTTCTTC
41566599 TTTTTTTTCACGAAATT
1 TTTTTTTTCACG-AA-T
*
41566616 TTTTTTTTCATGAAT
1 TTTTTTTTCACGAAT
41566631 TTTTTTTTCACG-AT
1 TTTTTTTTCACGAAT
41566645 TTTTTTTTCA
1 TTTTTTTTCA
41566655 ACTTGATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 12 0.32
15 12 0.32
16 2 0.05
17 11 0.30
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.66
Consensus pattern (15 bp):
TTTTTTTTCACGAAT
Found at i:41566708 original size:12 final size:12
Alignment explanation
Indices: 41566691--41566725 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
41566681 AATATAAACC
41566691 AATTTTTTTTTG
1 AATTTTTTTTTG
*
41566703 AATTTTTTTTCG
1 AATTTTTTTTTG
*
41566715 AGTTTTTTTTT
1 AATTTTTTTTT
41566726 CAAGAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:41567607 original size:22 final size:22
Alignment explanation
Indices: 41567564--41567606 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
41567554 AAGGGCATAA
*
41567564 AATGCTCTTTAAAACTCCTTTT
1 AATGATCTTTAAAACTCCTTTT
*
41567586 AATGATCTTT-AAGCTCCTTTT
1 AATGATCTTTAAAACTCCTTTT
41567607 TTTAACAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.47
Consensus pattern (22 bp):
AATGATCTTTAAAACTCCTTTT
Found at i:41567757 original size:21 final size:23
Alignment explanation
Indices: 41567712--41567758 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
41567702 TCACCTGCAA
* *
41567712 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
41567735 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
41567756 TAA
1 TAA
41567759 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:41574798 original size:17 final size:18
Alignment explanation
Indices: 41574776--41574809 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41574766 ACAACACTCC
*
41574776 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
41574793 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
41574810 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:41575850 original size:12 final size:12
Alignment explanation
Indices: 41575835--41575899 Score: 53
Period size: 13 Copynumber: 5.4 Consensus size: 12
41575825 CTCACAATAC
41575835 TTTTCACTTTTT
1 TTTTCACTTTTT
** *
41575847 TTTTGTTCTTTTC
1 TTTT-CACTTTTT
41575860 TTTT-ACTTTTT
1 TTTTCACTTTTT
*
41575871 TTTTCGATTTTTT
1 TTTTC-ACTTTTT
*
41575884 TTTTGA-TTTTT
1 TTTTCACTTTTT
41575895 TTTTC
1 TTTTC
41575900 TGAATCAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
11 18 0.43
12 5 0.12
13 19 0.45
ACGTcount: A:0.06, C:0.11, G:0.05, T:0.78
Consensus pattern (12 bp):
TTTTCACTTTTT
Found at i:41575868 original size:24 final size:26
Alignment explanation
Indices: 41575834--41575899 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 26
41575824 ACTCACAATA
41575834 CTTTTCACTTTTTTTTT-G-TTCTTTT
1 CTTTTCACTTTTTTTTTCGATT-TTTT
41575859 CTTTT-ACTTTTTTTTTCGATTTTTT
1 CTTTTCACTTTTTTTTTCGATTTTTT
*
41575884 -TTTTGA-TTTTTTTTTC
1 CTTTTCACTTTTTTTTTC
41575900 TGAATCAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
24 25 0.66
25 11 0.29
26 2 0.05
ACGTcount: A:0.06, C:0.12, G:0.05, T:0.77
Consensus pattern (26 bp):
CTTTTCACTTTTTTTTTCGATTTTTT
Found at i:41575882 original size:13 final size:13
Alignment explanation
Indices: 41575866--41575939 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
41575856 TTTCTTTTAC
41575866 TTTTTTTTTCGAT
1 TTTTTTTTTCGAT
41575879 TTTTTTTTT-GATT
1 TTTTTTTTTCGA-T
*
41575892 TTTTTTTCTGAATCAAT
1 TTTTTTT-T---TCGAT
*
41575909 TTTTTTTTTCGAA
1 TTTTTTTTTCGAT
41575922 TTTTTTTTT-GAT
1 TTTTTTTTTCGAT
41575934 TTTTTT
1 TTTTTT
41575940 GTTACTCCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
12 10 0.20
13 29 0.57
14 1 0.02
16 1 0.02
17 9 0.18
18 1 0.02
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCGAT
Found at i:41575935 original size:11 final size:13
Alignment explanation
Indices: 41575866--41575939 Score: 57
Period size: 12 Copynumber: 5.5 Consensus size: 13
41575856 TTTCTTTTAC
41575866 TTTTTTTTTCG-A
1 TTTTTTTTTCGAA
*
41575878 TTTTTTTTTTG-A
1 TTTTTTTTTCGAA
41575890 TTTTTTTTTCTGAATCAA
1 TTTTTTTTTC-G----AA
41575908 TTTTTTTTTTCGAA
1 -TTTTTTTTTCGAA
41575922 TTTTTTTTT-G-A
1 TTTTTTTTTCGAA
41575933 TTTTTTT
1 TTTTTTT
41575940 GTTACTCCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
11 8 0.15
12 21 0.40
13 10 0.19
14 2 0.04
18 2 0.04
19 10 0.19
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:41583078 original size:6 final size:6
Alignment explanation
Indices: 41583058--41583118 Score: 54
Period size: 6 Copynumber: 9.8 Consensus size: 6
41583048 AAGAGAAAAC
*
41583058 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
*
41583107 ATAAAAA AAAGA
1 A-AAGAA AAAGA
41583119 GAGGCAAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
5 9 0.19
6 25 0.53
7 7 0.15
8 3 0.06
9 3 0.06
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:41583198 original size:11 final size:12
Alignment explanation
Indices: 41583166--41583196 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
41583156 TTGAGAGAAC
41583166 TTGAAAAAGCCT
1 TTGAAAAAGCCT
41583178 TTGAAAAAGCCT
1 TTGAAAAAGCCT
41583190 TTGAAAA
1 TTGAAAA
41583197 GCAAAAAGAA
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:41583214 original size:12 final size:12
Alignment explanation
Indices: 41583199--41583232 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
41583189 TTTGAAAAGC
41583199 AAAAAGAAAATG
1 AAAAAGAAAATG
*
41583211 AAAAAGGAAATG
1 AAAAAGAAAATG
41583223 AAAAA-AAAAT
1 AAAAAGAAAAT
41583233 TGAGAGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:41583243 original size:30 final size:30
Alignment explanation
Indices: 41583209--41583265 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
41583199 AAAAAGAAAA
41583209 TGAAAAAGGAA-ATGAAAAAAAAATTGAGAG
1 TGAAAAA-GAAGATGAAAAAAAAATTGAGAG
*
41583239 TGAAAAAGAAGATGAAAAAGAAATTGA
1 TGAAAAAGAAGATGAAAAAAAAATTGA
41583266 AACAAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.14
Consensus pattern (30 bp):
TGAAAAAGAAGATGAAAAAAAAATTGAGAG
Found at i:41592043 original size:22 final size:21
Alignment explanation
Indices: 41592015--41592070 Score: 80
Period size: 19 Copynumber: 2.7 Consensus size: 21
41592005 ATAAAACTTG
41592015 ACATATTAAAAACAAGCAACAA
1 ACATATT-AAAACAAGCAACAA
41592037 ACATATT--AACAAGCAACAA
1 ACATATTAAAACAAGCAACAA
*
41592056 ACATATTAATACAAG
1 ACATATTAAAACAAG
41592071 TGCATGAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 19 0.61
21 5 0.16
22 7 0.23
ACGTcount: A:0.59, C:0.18, G:0.05, T:0.18
Consensus pattern (21 bp):
ACATATTAAAACAAGCAACAA
Found at i:41601552 original size:11 final size:11
Alignment explanation
Indices: 41601536--41601569 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
41601526 ATTGGAGTAA
41601536 CAAAAAAAAAT
1 CAAAAAAAAAT
41601547 CAAAAAAAAATT
1 CAAAAAAAAA-T
*
41601559 CGAAAAAAAAT
1 CAAAAAAAAAT
41601570 TGATTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (11 bp):
CAAAAAAAAAT
Found at i:41601555 original size:13 final size:13
Alignment explanation
Indices: 41601537--41601609 Score: 69
Period size: 13 Copynumber: 5.5 Consensus size: 13
41601527 TTGGAGTAAC
41601537 AAAAAAAAA-TC-
1 AAAAAAAAATTCA
41601548 AAAAAAAAATTCGA
1 AAAAAAAAATTC-A
* *
41601562 AAAAAAATTGATTGA
1 AAAAAAA--AATTCA
41601577 AAAAAAAAATTCA
1 AAAAAAAAATTCA
* *
41601590 AAAAAAAAAGTGA
1 AAAAAAAAATTCA
41601603 AAAAAAA
1 AAAAAAA
41601610 TCGAGCAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
11 9 0.18
12 2 0.04
13 22 0.43
14 7 0.14
15 8 0.16
16 3 0.06
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:41601608 original size:29 final size:29
Alignment explanation
Indices: 41601548--41601609 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
41601538 AAAAAAAATC
* * **
41601548 AAAAAAAAATTCGAAAAAAAATTGATTGA
1 AAAAAAAAATTCAAAAAAAAAGTGATAAA
41601577 AAAAAAAAATTCAAAAAAAAAAGTGA-AAA
1 AAAAAAAAATTC-AAAAAAAAAGTGATAAA
41601606 AAAA
1 AAAA
41601610 TCGAGCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (29 bp):
AAAAAAAAATTCAAAAAAAAAGTGATAAA
Found at i:41601621 original size:16 final size:16
Alignment explanation
Indices: 41601602--41601639 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41601592 AAAAAAAGTG
41601602 AAAAAAA-ATCGAGCAA
1 AAAAAAAGAT-GAGCAA
*
41601618 AAAAAAAGGTGAGCAA
1 AAAAAAAGATGAGCAA
41601634 AAAAAA
1 AAAAAA
41601640 TCAAGTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.71, C:0.08, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAAAAGATGAGCAA
Found at i:41601621 original size:41 final size:40
Alignment explanation
Indices: 41601537--41601624 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 40
41601527 TTGGAGTAAC
* *
41601537 AAAAAAAAATCAAAAAAAAATTCGAAAAAAAATTGATTG-AA
1 AAAAAAAAATCAAAAAAAAAGTCGAAAAAAAATCGA--GCAA
*
41601578 AAAAAAAATTCAAAAAAAAAAGT-GAAAAAAAATCGAGCAA
1 AAAAAAAAATC-AAAAAAAAAGTCGAAAAAAAATCGAGCAA
41601618 AAAAAAA
1 AAAAAAA
41601625 GGTGAGCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 1 0.02
40 9 0.21
41 22 0.52
42 10 0.24
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (40 bp):
AAAAAAAAATCAAAAAAAAAGTCGAAAAAAAATCGAGCAA
Found at i:41602553 original size:18 final size:18
Alignment explanation
Indices: 41602532--41602566 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41602522 AGAAAAGAAA
41602532 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
41602550 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
41602567 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:41607701 original size:23 final size:22
Alignment explanation
Indices: 41607650--41607701 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
41607640 CCTCGTCTTT
*
41607650 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
41607672 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
41607695 TTCTTTT
1 TTCTTTT
41607702 TCAGCTCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:41607759 original size:10 final size:10
Alignment explanation
Indices: 41607743--41607800 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
41607733 CAACTCCGAC
41607743 CAGCTCAATT
1 CAGCTCAATT
* *
41607753 GAGCTCATTT
1 CAGCTCAATT
41607763 CAGCTCAA-T
1 CAGCTCAATT
41607772 CGAGCTCAATT
1 C-AGCTCAATT
*
41607783 TAGCTACAATT
1 CAGCT-CAATT
41607794 CAGCTCA
1 CAGCTCA
41607801 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:41607766 original size:20 final size:20
Alignment explanation
Indices: 41607743--41607803 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
41607733 CAACTCCGAC
41607743 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
41607763 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
41607784 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
41607804 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:41609164 original size:12 final size:12
Alignment explanation
Indices: 41609147--41609219 Score: 56
Period size: 12 Copynumber: 5.7 Consensus size: 12
41609137 TTGGAGTAAC
41609147 AAAAAAAAATCA
1 AAAAAAAAATCA
*
41609159 AAAAAAAATTCGA
1 AAAAAAAAATC-A
*
41609172 AAAAAAAATTGATTGA
1 AAAAAAAA---A-TCA
*
41609188 AAAAAAAATTCA
1 AAAAAAAAATCA
* *
41609200 AAAAAAAAGTGA
1 AAAAAAAAATCA
41609212 AAAAAAAA
1 AAAAAAAA
41609220 TCGAGCAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
12 30 0.61
13 9 0.18
16 9 0.18
17 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATCA
Found at i:41609231 original size:40 final size:40
Alignment explanation
Indices: 41609147--41609235 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 40
41609137 TTGGAGTAAC
* *
41609147 AAAAAAAAATCAAAAAAAAATTCGAAAAAAAAATTGATTG-A
1 AAAAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGA--GCA
*
41609188 AAAAAAAATTCAAAAAAAAAGT-GAAAAAAAAATCGAGCA
1 AAAAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGAGCA
41609227 AAAAAAAAA
1 AAAAAAAAA
41609236 GGTGACCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.02
39 9 0.21
40 13 0.30
41 20 0.47
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (40 bp):
AAAAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGAGCA
Found at i:41609261 original size:30 final size:28
Alignment explanation
Indices: 41609199--41609270 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
41609189 AAAAAAATTC
*
41609199 AAAAAAAAAGTGAAAAAAAAATCGAGCA
1 AAAAAAAAAGTGAAAAAAAAATCAAGCA
*
41609227 AAAAAAAAAGGTGACCAAAAAAATCAAG--
1 AAAAAAAAA-GTGA-AAAAAAAATCAAGCA
**
41609255 TTAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
41609271 GTCTTGCGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
26 2 0.05
27 4 0.11
28 16 0.43
29 4 0.11
30 11 0.30
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.10
Consensus pattern (28 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGCA
Found at i:41610161 original size:18 final size:18
Alignment explanation
Indices: 41610140--41610174 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41610130 AGAAAAGAAA
41610140 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
41610158 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
41610175 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:41612262 original size:10 final size:10
Alignment explanation
Indices: 41612246--41612303 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
41612236 CAACTCCGAC
41612246 CAGCTCAATT
1 CAGCTCAATT
* *
41612256 GAGCTCATTT
1 CAGCTCAATT
41612266 CAGCTCAA-T
1 CAGCTCAATT
41612275 CGAGCTCAATT
1 C-AGCTCAATT
*
41612286 TAGCTACAATT
1 CAGCT-CAATT
41612297 CAGCTCA
1 CAGCTCA
41612304 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:41612269 original size:20 final size:20
Alignment explanation
Indices: 41612246--41612306 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
41612236 CAACTCCGAC
41612246 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
41612266 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
41612287 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
41612307 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:41615430 original size:13 final size:13
Alignment explanation
Indices: 41615412--41615437 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41615402 GTAGCTTCGA
41615412 AAAAAAAAAAGTT
1 AAAAAAAAAAGTT
41615425 AAAAAAAAAAGTT
1 AAAAAAAAAAGTT
41615438 TCGAAAAAAA
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAAAAAAAAGTT
Found at i:41615459 original size:30 final size:30
Alignment explanation
Indices: 41615407--41615464 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
41615397 AAATCGTAGC
***
41615407 TTCGAAAAAAAAAAAGTTAAAAAAAAAAGT
1 TTCGAAAAAAAAAAACCGAAAAAAAAAAGT
*
41615437 TTCGAAAAAAAAAATCCGAAAAAAAAAA
1 TTCGAAAAAAAAAAACCGAAAAAAAAAA
41615465 AGAGAAGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.71, C:0.07, G:0.09, T:0.14
Consensus pattern (30 bp):
TTCGAAAAAAAAAAACCGAAAAAAAAAAGT
Found at i:41615463 original size:14 final size:15
Alignment explanation
Indices: 41615412--41615464 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
41615402 GTAGCTTCGA
*
41615412 AAAAAAAAAAGT--T
1 AAAAAAAAAAGTCCG
*
41615425 AAAAAAAAAAGTTTCG
1 AAAAAAAAAAG-TCCG
41615441 AAAAAAAAAA-TCCG
1 AAAAAAAAAAGTCCG
41615455 AAAAAAAAAA
1 AAAAAAAAAA
41615465 AGAGAAGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 11 0.31
14 14 0.40
16 10 0.29
ACGTcount: A:0.75, C:0.06, G:0.08, T:0.11
Consensus pattern (15 bp):
AAAAAAAAAAGTCCG
Found at i:41615490 original size:14 final size:13
Alignment explanation
Indices: 41615412--41615494 Score: 51
Period size: 15 Copynumber: 5.8 Consensus size: 13
41615402 GTAGCTTCGA
41615412 AAAAAAAAAAGTT-
1 AAAAAAAAAA-TTG
41615425 AAAAAAAAAAGTTTCG
1 AAAAAAAAAA--TT-G
*
41615441 AAAAAAAAAATCCG
1 AAAAAAAAAAT-TG
**
41615455 AAAAAAAAAAAGAG
1 -AAAAAAAAAATTG
41615469 AAGGAAAAAAAATTG
1 AA--AAAAAAAATTG
41615484 CAAAAAAAAAA
1 -AAAAAAAAAA
41615495 AATTGCATAC
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
13 12 0.21
14 13 0.23
15 19 0.34
16 12 0.21
ACGTcount: A:0.75, C:0.05, G:0.11, T:0.10
Consensus pattern (13 bp):
AAAAAAAAAATTG
Found at i:41615548 original size:1 final size:1
Alignment explanation
Indices: 41615542--41615571 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
41615532 AAATATCCGT
41615542 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
41615572 GAAGAGTCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:41617803 original size:24 final size:25
Alignment explanation
Indices: 41617776--41617832 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
41617766 ATGAGTGATA
*
41617776 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
41617800 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
41617824 AAAAAAGAA
1 AAAAAAGAA
41617833 TTTGTTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 13 0.46
24 7 0.25
25 8 0.29
ACGTcount: A:0.63, C:0.04, G:0.23, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:41623133 original size:40 final size:40
Alignment explanation
Indices: 41623089--41623275 Score: 295
Period size: 40 Copynumber: 4.7 Consensus size: 40
41623079 GCAAACACAT
* ** *
41623089 TTGCCTTCGGGTCTTAACCCGGACGTATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
41623129 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
41623169 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
41623209 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
41623249 TTGCCTT-GGGGCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
41623276 TCCAATGCTC
Statistics
Matches: 139, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 18 0.13
40 121 0.87
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:41631708 original size:40 final size:40
Alignment explanation
Indices: 41631660--41631847 Score: 340
Period size: 40 Copynumber: 4.7 Consensus size: 40
41631650 GCAAACACAT
* * *
41631660 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
41631700 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
41631740 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
41631780 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
41631820 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
41631848 TCCAATGCTC
Statistics
Matches: 143, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 143 1.00
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:41635592 original size:13 final size:13
Alignment explanation
Indices: 41635574--41635598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41635564 TGATTGCAGA
41635574 TTTTTCTTCTTTC
1 TTTTTCTTCTTTC
41635587 TTTTTCTTCTTT
1 TTTTTCTTCTTT
41635599 GGATTCTTTT
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:41636329 original size:24 final size:23
Alignment explanation
Indices: 41636299--41636368 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 23
41636289 CATATTTTTG
41636299 AAGTTATCGTGTATTATTATTCTAA
1 AAGTTAT-GTGTATTATTATT-TAA
* *
41636324 AA-TTATTATGTATTATTACTTAA
1 AAGTTA-TGTGTATTATTATTTAA
41636347 AAGTTATGTTGTATTATTATTT
1 AAGTTATG-TGTATTATTATTT
41636369 TATTATTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 6 0.16
24 29 0.76
25 3 0.08
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (23 bp):
AAGTTATGTGTATTATTATTTAA
Found at i:41638857 original size:44 final size:44
Alignment explanation
Indices: 41638792--41639960 Score: 1510
Period size: 44 Copynumber: 26.7 Consensus size: 44
41638782 GAAACTATAT
* * * * * *
41638792 GTCCTATCTCCATGAACAGTAGTGGAATAGGTAGAAGATTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* *
41638836 GTCCTAGCTCCCTGACCAGTAGTGGAATAGGTGGAAGACTGAAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * ** *
41638880 GTCCTAGCTCCCTGAACAGTAGTGGAATAGGCAGAAGATTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * * *
41638924 ATCCTAGCTTCCTGACTAGCAGTGGAATAGGTGGAAGACTGAAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
** *
41638968 GTCCTAGCTCCCTGTA-CAGCAGTGGAATAGGCAGAAGATTGTAA
1 GTCCTAGCTCCCTG-ACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * *
41639012 ATCCTAGCTCTCTGACCAGCAGTGGAATAGGTGGAAGACTGAAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * * *
41639056 GTCCTAGCTCCCTGAACAACAGTGGAATAGGCGGAAGATTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * * *
41639100 ATCCTAGCTCCCTGACCAACAATGGAATAGGTGGAAGACTGAAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* *
41639144 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGACTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
*
41639188 ATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * * *
41639232 GTCCTAGCTCCCTGACAAGCAGTGTAATAGGTAGAAGATTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
*
41639276 GTCC-AGCTCCCTGACCAGTAGTGG-A-AGGTGGAAGACTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * *
41639317 GTCCTAGCTCCCTGACCAGCAGTGTAATAGGTAGAAGATTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
*
41639361 GTCCTAGCTCCCTGACCAGTAGTGG-A-AGGTGGAAGACTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
*
41639403 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * * ** *
41639447 GTCCTAACTCCCTGAACAGTAGTGGAATAGGCAGAAGATTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * *
41639491 ATCCTAGCTTCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* *
41639535 GTCCTAGCTCCCTGTA-CAGCAGTGGAATAGGCGGAAGATTGTAA
1 GTCCTAGCTCCCTG-ACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * *
41639579 ATCCTAGCTCTCTGACCAGCAGTGGAATAGGTGGAAGACTGAAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * * *
41639623 GTCCTAGCTCCCTGAACAACAGTGGAATAGGCGGAAGATTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * * *
41639667 ATCCTAGCTCCCTGACCAACAGTGGAATAGGTGGAAGGCTGAAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * *
41639711 GTCCTAGCTCCCTGAACAGTAGTGGAATAGGCGGAAGACTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
*
41639755 ATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * * * *
41639799 GTCCTAACTCCCTGACAAGCAGTGTAATAGGTAGAAGATTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
**
41639843 GTCCTAGCTCCCTGACCAATAGTGG-A-AGGTGGAAGACTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * *
41639885 GTCCTAGCTCCCTGACCAGCAGTGGAAGAGGTAGAAGATTGTAA
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
* * *
41639929 GTCCTAGCTCCCTGAGCAGCTGTGGAGTAGGT
1 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGT
41639961 TGAAAATTAC
Statistics
Matches: 968, Mismatches: 146, Indels: 22
0.85 0.13 0.02
Matches are distributed among these distances:
41 18 0.02
42 94 0.10
43 24 0.02
44 830 0.86
45 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (44 bp):
GTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAA
Found at i:41640109 original size:44 final size:43
Alignment explanation
Indices: 41639980--41640113 Score: 112
Period size: 44 Copynumber: 3.0 Consensus size: 43
41639970 CAAATCTTAT
* * *
41639980 CTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGC
1 CTCCCTCAGTTGTAGTGGAACA-GTTGAAGATAGCAGGTCTTGC
* * * * * *
41640024 CTTCCTACA-TCGACAGT-GAAGCAGATCGAAGACA-CAAGTCTTGC
1 CTCCCT-CAGTTG-TAGTGGAA-CAG-TTGAAGATAGCAGGTCTTGC
41640068 CTCCCTCAGTTGTAGTGGAACATGTTGAAGATAGCAGGTCTTGC
1 CTCCCTCAGTTGTAGTGGAACA-GTTGAAGATAGCAGGTCTTGC
41640112 CT
1 CT
41640114 TCTTGCATCG
Statistics
Matches: 67, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
43 14 0.21
44 40 0.60
45 13 0.19
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (43 bp):
CTCCCTCAGTTGTAGTGGAACAGTTGAAGATAGCAGGTCTTGC
Found at i:41640134 original size:88 final size:88
Alignment explanation
Indices: 41639980--41640142 Score: 254
Period size: 88 Copynumber: 1.9 Consensus size: 88
41639970 CAAATCTTAT
* *
41639980 CTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAGTGAAG
1 CTCCCTCAGTTGTAGTGGAACAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAGTGAAG
41640045 CAGATCGAAGACACAAGTCTTGC
66 CAGATCGAAGACACAAGTCTTGC
* * * * * *
41640068 CTCCCTCAGTTGTAGTGGAACATGTTGAAGATAGCAGGTCTTGCCTTCTTGCATCGATAGTTAAG
1 CTCCCTCAGTTGTAGTGGAACAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAGTGAAG
41640133 CAGATCGAAG
66 CAGATCGAAG
41640143 CCAATGGTCC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 67 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (88 bp):
CTCCCTCAGTTGTAGTGGAACAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAGTGAAG
CAGATCGAAGACACAAGTCTTGC
Found at i:41640872 original size:13 final size:13
Alignment explanation
Indices: 41640854--41640878 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41640844 TGATTGCAGA
41640854 TTTTTCTTCTTTC
1 TTTTTCTTCTTTC
41640867 TTTTTCTTCTTT
1 TTTTTCTTCTTT
41640879 GGATTCTTTT
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:41642015 original size:40 final size:40
Alignment explanation
Indices: 41641886--41642147 Score: 307
Period size: 40 Copynumber: 6.6 Consensus size: 40
41641876 TTGAATGCTG
* * * * * *
41641886 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
41641926 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAG-AACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
41641965 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
41642005 TCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
41642045 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41642085 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41642124 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41642148 TGAACGAGGA
Statistics
Matches: 198, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
38 1 0.01
39 65 0.33
40 124 0.63
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:41642022 original size:79 final size:80
Alignment explanation
Indices: 41641886--41642147 Score: 305
Period size: 79 Copynumber: 3.3 Consensus size: 80
41641876 TTGAATGCTG
* * * * * * *
41641886 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAGACCCGAAGGCCTT
*
41641950 TGTGCGAG-AACTAAA
65 TGTGCGAGTTACTAAA
* * * *
41641965 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGCCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGACCCGAAGGCCTTT
*
41642030 GTGCGAGTTATTAAA
66 GTGCGAGTTACTAAA
* * * * *
41642045 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGG-CATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGACCCGAAGGCCTTT
*
41642109 GTGTGAGTTACTAAA
66 GTGCGAGTTACTAAA
* *
41642124 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
41642148 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
79 89 0.57
80 68 0.43
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGACCCGAAGGCCTTT
GTGCGAGTTACTAAA
Found at i:41642167 original size:79 final size:80
Alignment explanation
Indices: 41641925--41642182 Score: 238
Period size: 79 Copynumber: 3.3 Consensus size: 80
41641915 AAGTGAATAT
* * * * * *
41641925 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAG-AACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
41641988 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * * *
41642004 ATCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
41642069 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
41642084 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
41642148 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
41642163 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
41642183 TACGTGATTT
Statistics
Matches: 153, Mismatches: 23, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
78 14 0.09
79 75 0.49
80 64 0.42
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:41653984 original size:12 final size:12
Alignment explanation
Indices: 41653978--41654006 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
41653968 AAAAAAACTC
41653978 AAAAAAATTCAA
1 AAAAAAATTCAA
41653990 AAAAAAATTCAA
1 AAAAAAATTCAA
41654002 AAAAA
1 AAAAA
41654007 CATTTTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:41654003 original size:10 final size:10
Alignment explanation
Indices: 41653968--41654006 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
41653958 AGTTTCTCGA
*
41653968 AAAAAAACTC
1 AAAAAAATTC
41653978 AAAAAAATTC
1 AAAAAAATTC
41653988 AAAAAAAAATTC
1 --AAAAAAATTC
41654000 AAAAAAA
1 AAAAAAA
41654007 CATTTTTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 16 0.62
12 10 0.38
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:41654068 original size:13 final size:13
Alignment explanation
Indices: 41654047--41654097 Score: 93
Period size: 13 Copynumber: 3.9 Consensus size: 13
41654037 GGATATCAAG
41654047 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
*
41654060 TTTTGAAAAAAAA
1 TTGTGAAAAAAAA
41654073 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
41654086 TTGTGAAAAAAA
1 TTGTGAAAAAAA
41654098 GAGAGCTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:41658274 original size:12 final size:13
Alignment explanation
Indices: 41658241--41658272 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
41658231 AAAAAAACTC
41658241 AAAAAAATTCAAA
1 AAAAAAATTCAAA
41658254 AAAAAAATTCAAA
1 AAAAAAATTCAAA
41658267 AAAAAA
1 AAAAAA
41658273 TTTTTGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:41658335 original size:14 final size:14
Alignment explanation
Indices: 41658313--41658366 Score: 92
Period size: 14 Copynumber: 3.9 Consensus size: 14
41658303 GGATATCAAG
41658313 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
*
41658327 TTTTG-AAAAAAAA
1 TTGTGAAAAAAAAA
41658340 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
41658354 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
41658367 GAGAGCTAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.32
14 25 0.68
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:41658337 original size:13 final size:13
Alignment explanation
Indices: 41658313--41658366 Score: 81
Period size: 13 Copynumber: 4.0 Consensus size: 13
41658303 GGATATCAAG
41658313 TTGTGAAAAAAAAA
1 TTGTG-AAAAAAAA
*
41658327 TTTTGAAAAAAAA
1 TTGTGAAAAAAAA
41658340 TTGTGAAAAAAAAA
1 TTGTG-AAAAAAAA
41658354 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
41658367 GAGAGCTAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 20 0.54
14 17 0.46
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:41658351 original size:27 final size:27
Alignment explanation
Indices: 41658313--41658366 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
41658303 GGATATCAAG
*
41658313 TTGTGAAAAAAAAATTTTGAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAA
41658340 TTGTGAAAAAAAAATTGTGAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAA
41658367 GAGAGCTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (27 bp):
TTGTGAAAAAAAAATTGTGAAAAAAAA
Found at i:41668489 original size:30 final size:33
Alignment explanation
Indices: 41668453--41668515 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
41668443 CACCCAAGTA
41668453 TGAAAAC-AAATTC-AAAAAGCCTTGT-ATGTG
1 TGAAAACAAAATTCTAAAAAGCCTTGTAATGTG
* *
41668483 TGAAAACAAAATTCTAGACAGCCTTGTAATGTG
1 TGAAAACAAAATTCTAAAAAGCCTTGTAATGTG
41668516 AACGGAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 7 0.25
31 6 0.21
32 10 0.36
33 5 0.18
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (33 bp):
TGAAAACAAAATTCTAAAAAGCCTTGTAATGTG
Found at i:41668516 original size:31 final size:30
Alignment explanation
Indices: 41668453--41668517 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
41668443 CACCCAAGTA
*
41668453 TGAAAACAAATTCAAAAAGCCTTGTATGTG
1 TGAAAACAAATTCAAAAAGCCTTGTATATG
* *
41668483 TGAAAACAAAATTCTAGACAGCCTTGTA-ATG
1 TGAAAAC-AAATTC-AAAAAGCCTTGTATATG
41668514 TGAA
1 TGAA
41668518 CGGAATGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 12 0.40
32 11 0.37
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (30 bp):
TGAAAACAAATTCAAAAAGCCTTGTATATG
Found at i:41668975 original size:21 final size:22
Alignment explanation
Indices: 41668946--41668989 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
41668936 AAAAACAAAG
41668946 TAAACACTT-AACTAAATTTAT
1 TAAACACTTAAACTAAATTTAT
* *
41668967 TAAATACTTAAACTAATTTTAT
1 TAAACACTTAAACTAAATTTAT
41668989 T
1 T
41668990 CCAGCAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAACACTTAAACTAAATTTAT
Found at i:41678078 original size:52 final size:52
Alignment explanation
Indices: 41677995--41678095 Score: 168
Period size: 52 Copynumber: 1.9 Consensus size: 52
41677985 TAAGGCAACG
*
41677995 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
*
41678047 TAATAGACAGTAGCTTAAGA-CTTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGATC-TCATTTCTAGCTCGGTTGAAGCTCAAA
41678096 TATGTGCATG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 1 0.02
52 45 0.98
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:41683145 original size:37 final size:37
Alignment explanation
Indices: 41683095--41683173 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
41683085 TTATTACGAA
* * *
41683095 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
* *
41683132 GTCTTACCTGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
41683169 GTCTT
1 GTCTT
41683174 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:41683354 original size:47 final size:47
Alignment explanation
Indices: 41683292--41683565 Score: 467
Period size: 47 Copynumber: 5.8 Consensus size: 47
41683282 CCCTTCGGGA
* * * * *
41683292 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCCTTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41683339 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41683386 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41683433 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41683480 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41683527 CTTATCACATATATATACACTTTCACATTCATCACATCG
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCG
41683566 AATCCTAAAT
Statistics
Matches: 216, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
47 187 0.87
49 29 0.13
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41690184 original size:11 final size:11
Alignment explanation
Indices: 41690168--41690230 Score: 85
Period size: 12 Copynumber: 5.7 Consensus size: 11
41690158 AATACAAACT
41690168 TTTTTTTTGAA
1 TTTTTTTTGAA
41690179 TTTTTTTTCGAA
1 TTTTTTTT-GAA
41690191 TTTTTTTTCGAA
1 TTTTTTTT-GAA
*
41690203 TTTTTTTTCAA
1 TTTTTTTTGAA
41690214 -TTTTTTTG-A
1 TTTTTTTTGAA
41690223 TTTTTTTT
1 TTTTTTTT
41690231 ACAATACCGT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
9 1 0.02
10 14 0.29
11 10 0.21
12 23 0.48
ACGTcount: A:0.14, C:0.05, G:0.06, T:0.75
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:41690230 original size:12 final size:12
Alignment explanation
Indices: 41690167--41690220 Score: 92
Period size: 12 Copynumber: 4.6 Consensus size: 12
41690157 GAATACAAAC
*
41690167 TTTTTTTTTGAA
1 TTTTTTTTCGAA
41690179 TTTTTTTTCGAA
1 TTTTTTTTCGAA
41690191 TTTTTTTTCGAA
1 TTTTTTTTCGAA
41690203 TTTTTTTTC-AA
1 TTTTTTTTCGAA
41690214 TTTTTTT
1 TTTTTTT
41690221 GATTTTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
11 9 0.22
12 32 0.78
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:41707777 original size:24 final size:24
Alignment explanation
Indices: 41707753--41707799 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
41707743 AAACTACTTC
41707753 TAAAAAAAACTCAAGAGAGAATTCT
1 TAAAAAAAACTCAA-AGAGAATTCT
** *
41707778 TGGAGAAAACTCAAAGAGAATT
1 TAAAAAAAACTCAAAGAGAATT
41707800 TTCACTCAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (24 bp):
TAAAAAAAACTCAAAGAGAATTCT
Done.