Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 117 of 128
Found at i:38922372 original size:20 final size:20
Alignment explanation
Indices: 38922333--38922374 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
38922323 ATGTTAGAGT
*
38922333 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
38922353 TAATATAGTCAAAACTGTTG
1 TAATATAGTCAAAACAGTTG
38922373 TA
1 TA
38922375 CCGTTGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:38922403 original size:15 final size:15
Alignment explanation
Indices: 38922383--38922413 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38922373 TACCGTTGTA
38922383 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
38922398 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
38922413 A
1 A
38922414 AAGATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:38924976 original size:20 final size:20
Alignment explanation
Indices: 38924937--38924978 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
38924927 ATGTTAGAGT
*
38924937 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
38924957 TAATATAGTCAAAACTGTTG
1 TAATATAGTCAAAACAGTTG
38924977 TA
1 TA
38924979 CCGTTGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:38925007 original size:15 final size:15
Alignment explanation
Indices: 38924987--38925017 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38924977 TACCGTTGTA
38924987 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
38925002 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
38925017 A
1 A
38925018 AAGATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:38926003 original size:9 final size:10
Alignment explanation
Indices: 38925989--38926062 Score: 64
Period size: 10 Copynumber: 7.3 Consensus size: 10
38925979 AAAATATTTT
38925989 AAAA-TTAAA
1 AAAATTTAAA
38925998 AAAATTTAAA
1 AAAATTTAAA
38926008 AAAATTTAAAA
1 AAAATTT-AAA
38926019 AAAGTATTTTAAA
1 AAA--A-TTTAAA
* *
38926032 AATATTT--T
1 AAAATTTAAA
38926040 AAAATTTAAA
1 AAAATTTAAA
*
38926050 AAAAATTAAA
1 AAAATTTAAA
38926060 AAA
1 AAA
38926063 GTATGTAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
8 6 0.11
9 4 0.08
10 27 0.51
11 7 0.13
13 6 0.11
14 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:38926032 original size:12 final size:11
Alignment explanation
Indices: 38925930--38926043 Score: 66
Period size: 11 Copynumber: 10.9 Consensus size: 11
38925920 GGCCCATTTT
38925930 TATTTT-AAAA
1 TATTTTAAAAA
38925940 -ATTTTAAAAA
1 TATTTTAAAAA
***
38925950 -ATAAAAAAAA
1 TATTTTAAAAA
*
38925960 GTATTTTGAAAA
1 -TATTTTAAAAA
*
38925972 TATTTTGAAAA
1 TATTTTAAAAA
38925983 TATTTT--AAA
1 TATTTTAAAAA
38925992 -A--TTAAAAA
1 TATTTTAAAAA
*
38926000 -AATTTAAAAA
1 TATTTTAAAAA
* *
38926010 AATTTAAAAAAA
1 TATTT-TAAAAA
38926022 GTATTTTAAAAA
1 -TATTTTAAAAA
38926034 TATTTTAAAA
1 TATTTTAAAA
38926044 TTTAAAAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
6 2 0.02
8 5 0.06
9 8 0.10
10 18 0.22
11 30 0.36
12 16 0.19
13 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:38926059 original size:42 final size:41
Alignment explanation
Indices: 38925998--38926093 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
38925988 TAAAATTAAA
* * *
38925998 AAAATTTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTT
1 AAAATTTAAAAAAAATT-AAAAAAGTATGTAAAAAATATTTT
*
38926040 AAAATTTAAAAAAAATTAAAAAAGTATGTAAAAAATGTTTT
1 AAAATTTAAAAAAAATTAAAAAAGTATGTAAAAAATATTTT
38926081 AAAATTTAAAAAA
1 AAAATTTAAAAAA
38926094 TATATATTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 34 0.68
42 16 0.32
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (41 bp):
AAAATTTAAAAAAAATTAAAAAAGTATGTAAAAAATATTTT
Found at i:38926073 original size:62 final size:62
Alignment explanation
Indices: 38925936--38926075 Score: 153
Period size: 62 Copynumber: 2.3 Consensus size: 62
38925926 TTTTTATTTT
* * **
38925936 AAAAAT-TTTAAAAAATAAAAAAAAGTATTTTGAAAATATTTTGAAAATATTTTAAAATTAA
1 AAAAATATATAAAAAATAAAAAAAAGTATTTTAAAAATATTTTGAAAATATTAAAAAATTAA
* *
38925997 AAAAATTTA-AAAAAATTTAAAAAAAGTATTTTAAAAATATTTT-AAAAT-TTAAAAAAAATTAA
1 AAAAATATATAAAAAA-TAAAAAAAAGTATTTTAAAAATATTTTGAAAATATT--AAAAAATTAA
* *
38926059 AAAAGTATGTAAAAAAT
1 AAAAATATATAAAAAAT
38926076 GTTTTAAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
60 2 0.03
61 17 0.26
62 41 0.62
63 6 0.09
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (62 bp):
AAAAATATATAAAAAATAAAAAAAAGTATTTTAAAAATATTTTGAAAATATTAAAAAATTAA
Found at i:38926085 original size:51 final size:52
Alignment explanation
Indices: 38925930--38926084 Score: 176
Period size: 52 Copynumber: 3.0 Consensus size: 52
38925920 GGCCCATTTT
** *
38925930 TATTTTAAAAATTTTAAAAAATAA--AAAAAAGTATTTTGAAAATATTTTGAAAA
1 TATTTT-AAAA-TTTAAAAAA-AATTAAAAAAGTATTTAAAAAATATTTTAAAAA
*
38925983 TATTTTAAAA-TTAAAAAAATTTAAAAAA--ATTTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAAAATTAAAAAAGTATTT-AAAAAA-TATTTTAAAAA
* *
38926034 TATTTTAAAATTTAAAAAAAATTAAAAAAGTATGTAAAAAATGTTTTAAAA
1 TATTTTAAAATTTAAAAAAAATTAAAAAAGTATTTAAAAAATATTTTAAAA
38926085 TTTAAAAAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
49 5 0.06
50 12 0.14
51 26 0.30
52 30 0.34
53 12 0.14
54 3 0.03
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (52 bp):
TATTTTAAAATTTAAAAAAAATTAAAAAAGTATTTAAAAAATATTTTAAAAA
Found at i:38926090 original size:19 final size:19
Alignment explanation
Indices: 38926024--38926096 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
38926014 TAAAAAAAGT
*
38926024 ATTTTAAAAATATTTTAAA
1 ATTTAAAAAATATTTTAAA
* **
38926043 ATTTAAAAAAAATTAAAAA
1 ATTTAAAAAATATTTTAAA
*
38926062 AGTATGTAAAAAATGTTTTAAA
1 A-T-T-TAAAAAATATTTTAAA
38926084 ATTTAAAAAATAT
1 ATTTAAAAAATAT
38926097 ATATTTATTA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
19 25 0.60
20 2 0.05
21 2 0.05
22 13 0.31
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (19 bp):
ATTTAAAAAATATTTTAAA
Found at i:38927997 original size:27 final size:25
Alignment explanation
Indices: 38927937--38928016 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
38927927 TAAAAATTCA
*
38927937 AAAAATATAAAAA-A-AATATTTTT
1 AAAAATATAAAAATATAAAATTTTT
*
38927960 TAAAAT-T-AAAATCATAAAATTATTT
1 AAAAATATAAAAAT-ATAAAATT-TTT
* *
38927985 AAAAATATAAAAATTTTAAATTTTTT
1 AAAAATATAAAAA-TATAAAATTTTT
38928011 AAAAAT
1 AAAAAT
38928017 TAATTAAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
21 4 0.09
22 1 0.02
23 6 0.13
24 5 0.11
25 8 0.18
26 10 0.22
27 10 0.22
28 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAAATATAAAAATATAAAATTTTT
Found at i:38928258 original size:27 final size:27
Alignment explanation
Indices: 38928204--38928259 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
38928194 TCTTGAATGG
38928204 AATATAAAAAATCATAAATTATTTAAA
1 AATATAAAAAATCATAAATTATTTAAA
** *
38928231 AATAT-AAAAATTTTAAATTTTTTAAA
1 AATATAAAAAATCATAAATTATTTAAA
38928257 AAT
1 AAT
38928260 TAATTAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
AATATAAAAAATCATAAATTATTTAAA
Found at i:38928404 original size:243 final size:244
Alignment explanation
Indices: 38927967--38928453 Score: 967
Period size: 243 Copynumber: 2.0 Consensus size: 244
38927957 TTTTAAAATT
38927967 AAAATCATAAAATTATTTAAAAATATAAAAATTTTAAATTTTTTAAAAATTAATTAAATGTTTAT
1 AAAATCATAAAATTATTTAAAAATATAAAAATTTTAAATTTTTTAAAAATTAATTAAATGTTTAT
38928032 ATGTGAATATTCCATACATAAATTTGGAGGAAGAAAAGGTCAATTATACATAAAAAAGATAGAGC
66 ATGTGAATATTCCATACATAAATTTGGAGGAAGAAAAGGTCAATTATACATAAAAAAGATAGAGC
38928097 ATGGAATATTTCTTGTGGTGACTGCAGTTGATAGTGGAGGAAAAGGTCATAAGTCATATTCCAGG
131 ATGGAATATTTCTTGTGGTGACTGCAGTTGATAGTGGAGGAAAAGGTCATAAGTCATATTCCAGG
38928162 CTTCTAGATCTTGCATAGATTTGGGTAAAAGTTCTTGAATGGAATATAA
196 CTTCTAGATCTTGCATAGATTTGGGTAAAAGTTCTTGAATGGAATATAA
38928211 AAAATCAT-AAATTATTTAAAAATATAAAAATTTTAAATTTTTTAAAAATTAATTAAATGTTTAT
1 AAAATCATAAAATTATTTAAAAATATAAAAATTTTAAATTTTTTAAAAATTAATTAAATGTTTAT
38928275 ATGTGAATATTCCATACATAAATTTGGAGGAAGAAAAGGTCAATTATACATAAAAAAGATAGAGC
66 ATGTGAATATTCCATACATAAATTTGGAGGAAGAAAAGGTCAATTATACATAAAAAAGATAGAGC
38928340 ATGGAATATTTCTTGTGGTGACTGCAGTTGATAGTGGAGGAAAAGGTCATAAGTCATATTCCAGG
131 ATGGAATATTTCTTGTGGTGACTGCAGTTGATAGTGGAGGAAAAGGTCATAAGTCATATTCCAGG
38928405 CTTCTAGATCTTGCATAGATTTGGGTAAAAGTTCTTGAATGGAATATAA
196 CTTCTAGATCTTGCATAGATTTGGGTAAAAGTTCTTGAATGGAATATAA
38928454 TATTGACTTA
Statistics
Matches: 243, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
243 235 0.97
244 8 0.03
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (244 bp):
AAAATCATAAAATTATTTAAAAATATAAAAATTTTAAATTTTTTAAAAATTAATTAAATGTTTAT
ATGTGAATATTCCATACATAAATTTGGAGGAAGAAAAGGTCAATTATACATAAAAAAGATAGAGC
ATGGAATATTTCTTGTGGTGACTGCAGTTGATAGTGGAGGAAAAGGTCATAAGTCATATTCCAGG
CTTCTAGATCTTGCATAGATTTGGGTAAAAGTTCTTGAATGGAATATAA
Found at i:38937677 original size:19 final size:18
Alignment explanation
Indices: 38937650--38937685 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
38937640 ATGAATAACA
*
38937650 AGAATTATAAAATCATTAG
1 AGAAATATAAAAT-ATTAG
38937669 AGAAATATAAAATATTA
1 AGAAATATAAAATATTA
38937686 TTATATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (18 bp):
AGAAATATAAAATATTAG
Found at i:38948086 original size:37 final size:37
Alignment explanation
Indices: 38948036--38948109 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
38948026 TGCATGGAAT
38948036 ATGTGTTAAAAACTAGTGTAGTGAAGAATTTGGGTAA
1 ATGTGTTAAAAACTAGTGTAGTGAAGAATTTGGGTAA
38948073 ATGTGTTAAAAACTAGTGTAGTGAAGAATTTGGGTAA
1 ATGTGTTAAAAACTAGTGTAGTGAAGAATTTGGGTAA
38948110 CACAGCATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (37 bp):
ATGTGTTAAAAACTAGTGTAGTGAAGAATTTGGGTAA
Found at i:38949607 original size:110 final size:110
Alignment explanation
Indices: 38949493--38949713 Score: 433
Period size: 110 Copynumber: 2.0 Consensus size: 110
38949483 TATATATATA
38949493 TTTTTTAATTTTTATTTTCAATTTGTTCAGAAATATTTATTTTAATGTTTTTAGTATTTCTGATG
1 TTTTTTAA-TTTTATTTTCAATTTGTTCAGAAATATTTATTTTAATGTTTTTAGTATTTCTGATG
38949558 TATTATATATATTTAAAAAAATTGAAAAAATTAATATAAAAAATTT
65 TATTATATATATTTAAAAAAATTGAAAAAATTAATATAAAAAATTT
38949604 TTTTTTAATTTTATTTTCAATTTGTTCAGAAATATTTATTTTAATGTTTTTAGTATTTCTGATGT
1 TTTTTTAATTTTATTTTCAATTTGTTCAGAAATATTTATTTTAATGTTTTTAGTATTTCTGATGT
38949669 ATTATATATATTTAAAAAAATTGAAAAAATTAATATAAAAAATTT
66 ATTATATATATTTAAAAAAATTGAAAAAATTAATATAAAAAATTT
38949714 AATATGGGGG
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
110 102 0.93
111 8 0.07
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (110 bp):
TTTTTTAATTTTATTTTCAATTTGTTCAGAAATATTTATTTTAATGTTTTTAGTATTTCTGATGT
ATTATATATATTTAAAAAAATTGAAAAAATTAATATAAAAAATTT
Found at i:38950721 original size:27 final size:28
Alignment explanation
Indices: 38950690--38950742 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
38950680 ACCAAAAATT
38950690 TATTTTAAAAAT-AAAAAATAAAAAAAG
1 TATTTTAAAAATAAAAAAATAAAAAAAG
*
38950717 TATTTTACAAATAAAAAAATAAAAAA
1 TATTTTAAAAATAAAAAAATAAAAAA
38950743 TATATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (28 bp):
TATTTTAAAAATAAAAAAATAAAAAAAG
Found at i:38962019 original size:24 final size:25
Alignment explanation
Indices: 38961982--38962032 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
38961972 CATTTTTCCC
* *
38961982 TTCTGTTTCATTTTCTTTCTTTCTT
1 TTCTATTTCATTTTATTTCTTTCTT
*
38962007 TTCTATTTC-TTTTATTTCTTTGTT
1 TTCTATTTCATTTTATTTCTTTCTT
38962031 TT
1 TT
38962033 ATAATATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.75
Consensus pattern (25 bp):
TTCTATTTCATTTTATTTCTTTCTT
Found at i:38962138 original size:20 final size:20
Alignment explanation
Indices: 38962113--38962152 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38962103 CGTAAAATGA
*
38962113 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
38962133 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
38962153 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:38962142 original size:34 final size:35
Alignment explanation
Indices: 38962098--38962164 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
38962088 CAGTAAAATA
*
38962098 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
38962132 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
38962165 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:38962168 original size:14 final size:15
Alignment explanation
Indices: 38962092--38962168 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
38962082 GATTGCCAGT
* *
38962092 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
38962106 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
38962120 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
38962140 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
38962155 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
38962169 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:38971523 original size:5 final size:5
Alignment explanation
Indices: 38971508--38971545 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
38971498 TTCTATATGA
38971508 ATTTT ATTTTT ATTTT ATTTT A--TT ATTTT ATTTT ATTT
1 ATTTT A-TTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
38971546 AAATAAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.10
5 22 0.73
6 5 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:38971535 original size:13 final size:13
Alignment explanation
Indices: 38971508--38971544 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
38971498 TTCTATATGA
38971508 ATTTTA-TTT-TT
1 ATTTTATTTTATT
38971519 ATTTTATTTTATT
1 ATTTTATTTTATT
38971532 ATTTTATTTTATT
1 ATTTTATTTTATT
38971545 TAAATAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 6 0.25
12 3 0.12
13 15 0.62
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
ATTTTATTTTATT
Found at i:38973308 original size:249 final size:250
Alignment explanation
Indices: 38972870--38973368 Score: 991
Period size: 249 Copynumber: 2.0 Consensus size: 250
38972860 ATTTTATAAT
38972870 AAAAAAAATGATTATTTTAATTATATAAATACGAGTATTTGTTTAAATCATGCCCTTCCAATCTC
1 AAAAAAAATGATTATTTTAATTATATAAATACGAGTATTTGTTTAAATCATGCCCTTCCAATCTC
38972935 TTAAATGTCATTTTACACTGTTACATGTAAATTAAACGATTTGTGATTCAAACGACTGTTGATAT
66 TTAAATGTCATTTTACACTGTTACATGTAAATTAAACGATTTGTGATTCAAACGACTGTTGATAT
38973000 TCTATTTTATTTTATTTTATTCAAATAACGACTTCAAAATTATGAAATGTATTTAAAACTATAAA
131 TCTATTTTATTTTATTTTATTCAAATAACGACTTCAAAATTATGAAATGTATTTAAAACTATAAA
38973065 AGGCAGACAACTTCCTATAAATTCCTAACATTTATATTATGGGAACGAAAGTTGA
196 AGGCAGACAACTTCCTATAAATTCCTAACATTTATATTATGGGAACGAAAGTTGA
38973120 AAAAAAAATG-TTATTTTAATTATATAAATACGAGTATTTGTTTAAATCATGCCCTTCCAATCTC
1 AAAAAAAATGATTATTTTAATTATATAAATACGAGTATTTGTTTAAATCATGCCCTTCCAATCTC
38973184 TTAAATGTCATTTTACACTGTTACATGTAAATTAAACGATTTGTGATTCAAACGACTGTTGATAT
66 TTAAATGTCATTTTACACTGTTACATGTAAATTAAACGATTTGTGATTCAAACGACTGTTGATAT
38973249 TCTATTTTATTTTATTTTATTCAAATAACGACTTCAAAATTATGAAATGTATTTAAAACTATAAA
131 TCTATTTTATTTTATTTTATTCAAATAACGACTTCAAAATTATGAAATGTATTTAAAACTATAAA
38973314 AGGCAGACAACTTCCTATAAATTCCTAACATTTATATTATGGGAACGAAAGTTGA
196 AGGCAGACAACTTCCTATAAATTCCTAACATTTATATTATGGGAACGAAAGTTGA
38973369 TGTGTTTGAT
Statistics
Matches: 249, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
249 239 0.96
250 10 0.04
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (250 bp):
AAAAAAAATGATTATTTTAATTATATAAATACGAGTATTTGTTTAAATCATGCCCTTCCAATCTC
TTAAATGTCATTTTACACTGTTACATGTAAATTAAACGATTTGTGATTCAAACGACTGTTGATAT
TCTATTTTATTTTATTTTATTCAAATAACGACTTCAAAATTATGAAATGTATTTAAAACTATAAA
AGGCAGACAACTTCCTATAAATTCCTAACATTTATATTATGGGAACGAAAGTTGA
Found at i:38982614 original size:3 final size:3
Alignment explanation
Indices: 38982608--38982668 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
38982598 TTGGATGTTC
38982608 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38982656 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
38982669 TTGTTATTGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38985107 original size:3 final size:3
Alignment explanation
Indices: 38985101--38985190 Score: 173
Period size: 3 Copynumber: 30.3 Consensus size: 3
38985091 TTGGATGTTC
38985101 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38985149 TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
38985191 TAGTTATTGT
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 84 0.98
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38987606 original size:46 final size:46
Alignment explanation
Indices: 38987529--38987859 Score: 330
Period size: 46 Copynumber: 7.6 Consensus size: 46
38987519 AACGTATGAT
* * * *
38987529 CACTTATCAC-TTGTC-CCTGGTTAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
38987573 CCCTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
38987619 TACTTAACACTTATCATTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC---T--TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
38987670 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-AA--T--
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
38987707 -ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAACTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
38987752 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
38987788 CACTTATCACTTTGTCACTTGATCAAATAAATGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
38987834 CACTTATCACTTTATC-CTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
38987860 AGTACTCAAA
Statistics
Matches: 243, Mismatches: 17, Indels: 53
0.78 0.05 0.17
Matches are distributed among these distances:
36 57 0.23
38 4 0.02
39 2 0.01
40 4 0.02
41 4 0.02
42 4 0.02
43 2 0.01
44 13 0.05
45 14 0.06
46 94 0.39
48 1 0.00
49 1 0.00
51 43 0.18
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:38987658 original size:51 final size:51
Alignment explanation
Indices: 38987575--38987704 Score: 180
Period size: 51 Copynumber: 2.6 Consensus size: 51
38987565 AAGGCTACCC
*
38987575 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACTACTTAACA
1 CTTATCA--TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAACA
*
38987628 CTTATCATTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCA
1 CTTATCATTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAACA
*
38987679 C---T--TTGTCTCTTGATCAGATAAGTGTA
1 CTTATCATTGTCACTTGATCAGATAAGTGTA
38987705 ATACTTATCA
Statistics
Matches: 74, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
46 23 0.31
48 1 0.01
51 43 0.58
53 7 0.09
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (51 bp):
CTTATCATTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAACA
Found at i:38987691 original size:97 final size:97
Alignment explanation
Indices: 38987529--38987704 Score: 282
Period size: 97 Copynumber: 1.8 Consensus size: 97
38987519 AACGTATGAT
* * * *
38987529 CACTTATCACTTGTCCCTGGTTAGATAAGTGTAGCTAAGGCTACCCCTTATCACTTTGTCACTTG
1 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
38987594 ATCAGATAAGTGTAGCTAAAGCTACTACTTAA
66 ATCAGATAAGTGTAGCTAAAGCTACTACTTAA
* *
38987626 CACTTATCA-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTT
1 CACTTATCACTTGTC-CCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
38987690 GATCAGATAAGTGTA
65 GATCAGATAAGTGTA
38987705 ATACTTATCA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
96 5 0.07
97 67 0.93
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (97 bp):
CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
ATCAGATAAGTGTAGCTAAAGCTACTACTTAA
Found at i:38987712 original size:36 final size:36
Alignment explanation
Indices: 38987671--38987822 Score: 169
Period size: 36 Copynumber: 3.9 Consensus size: 36
38987661 TAAAGCTACC
38987671 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAAT
1 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAAT
38987707 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAACTAAAGCT
1 ACTTATCACTTTGTCTCTTGATCAGATAAGTG----T-AA--T
**
38987750 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 ---ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAAT
* * *
38987789 ACTTATCACTTTGTCACTTGATCAAATAAATGTA
1 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
38987823 GCTAAAGCTA
Statistics
Matches: 101, Mismatches: 5, Indels: 20
0.80 0.04 0.16
Matches are distributed among these distances:
36 63 0.62
40 1 0.01
41 3 0.03
42 1 0.01
43 1 0.01
46 32 0.32
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (36 bp):
ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAAT
Found at i:38987731 original size:82 final size:82
Alignment explanation
Indices: 38987623--38987859 Score: 390
Period size: 82 Copynumber: 2.9 Consensus size: 82
38987613 AGCTACTACT
38987623 TAACACTTATCA--TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
1 TAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
38987686 TCTTGATCAGATAAGTG
66 TCTTGATCAGATAAGTG
* * *
38987703 TAATACTTATCACTTTGTCTCTTGATCAGATAAGTGTAACTAAAGCTACCACTTATCACTTTGTC
1 TAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
38987768 TCTTGATCAGATAAGTG
66 TCTTGATCAGATAAGTG
* * * *
38987785 TAGCACTTATCACTTTGTCACTTGATCAAATAAATGTAGCTAAAGCTACCACTTATCACTTTATC
1 TAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
38987850 -CTTGATCAGA
66 TCTTGATCAGA
38987860 AGTACTCAAA
Statistics
Matches: 145, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
80 11 0.08
81 10 0.07
82 124 0.86
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (82 bp):
TAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
TCTTGATCAGATAAGTG
Found at i:38989606 original size:21 final size:21
Alignment explanation
Indices: 38989582--38989623 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38989572 CTTTTTGTTC
*
38989582 AATTAATTATCGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
**
38989603 AATTTCTTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
38989624 TACTAACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:38995900 original size:17 final size:18
Alignment explanation
Indices: 38995868--38995901 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38995858 AAATTAATAA
*
38995868 AAATATAATCATTTTAAC
1 AAATATAATAATTTTAAC
38995886 AAATATAA-AATTTTAA
1 AAATATAATAATTTTAA
38995902 ATTGAAATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATAATAATTTTAAC
Found at i:38996016 original size:21 final size:20
Alignment explanation
Indices: 38995992--38996042 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
38995982 ATTGATATTT
*
38995992 TTAAAAATAAATTTTACAAAA
1 TTAAAAATAAATTGT-CAAAA
*
38996013 TT-AAAATAAAATTGTGAAAA
1 TTAAAAAT-AAATTGTCAAAA
38996033 TTAAAAATAA
1 TTAAAAATAA
38996043 TAATAACAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (20 bp):
TTAAAAATAAATTGTCAAAA
Found at i:38996811 original size:3 final size:3
Alignment explanation
Indices: 38996803--38996861 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
38996793 TAATTAAACA
38996803 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38996851 AAT AAT AAT AA
1 AAT AAT AAT AA
38996862 AGGACCGCAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:39001123 original size:48 final size:48
Alignment explanation
Indices: 39001059--39001156 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
39001049 TATACCCACT
39001059 AACACTCTAGCCTTTCCTACTATCCAATCATCTCCTTTACCCCCAACA
1 AACACTCTAGCCTTTCCTACTATCCAATCATCTCCTTTACCCCCAACA
* * * *
39001107 AACACTCTAGCTTTTCCTACTATTCAGTCCTCTCCTTTACCCCCAACA
1 AACACTCTAGCCTTTCCTACTATCCAATCATCTCCTTTACCCCCAACA
39001155 AA
1 AA
39001157 TACAAATCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.27, C:0.40, G:0.03, T:0.31
Consensus pattern (48 bp):
AACACTCTAGCCTTTCCTACTATCCAATCATCTCCTTTACCCCCAACA
Found at i:39002054 original size:25 final size:25
Alignment explanation
Indices: 39002007--39002054 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
39001997 TTTTTATAAC
* *
39002007 CAATTCACATATCATAGCTTTATTT
1 CAATTCACATAACATAGCATTATTT
39002032 CAATTCACATAACAT-GCCATTAT
1 CAATTCACATAACATAG-CATTAT
39002055 CAAGTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (25 bp):
CAATTCACATAACATAGCATTATTT
Found at i:39008430 original size:50 final size:50
Alignment explanation
Indices: 39008355--39008455 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
39008345 TCTACCATTT
39008355 TTTTATGGGGGGCAAGAACACTGCATGTCTCCCTTTGTCTTAGTCCCTAC
1 TTTTATGGGGGGCAAGAACACTGCATGTCTCCCTTTGTCTTAGTCCCTAC
*
39008405 TTTTATGGGGGGCAAGAACATTGCATGTCTCCCTTTGTCTTAGTCCCTAC
1 TTTTATGGGGGGCAAGAACACTGCATGTCTCCCTTTGTCTTAGTCCCTAC
39008455 T
1 T
39008456 CCCTAACTGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.36
Consensus pattern (50 bp):
TTTTATGGGGGGCAAGAACACTGCATGTCTCCCTTTGTCTTAGTCCCTAC
Found at i:39008899 original size:13 final size:13
Alignment explanation
Indices: 39008881--39008905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39008871 AGTTTTTTTA
39008881 TTTTTAATTAATC
1 TTTTTAATTAATC
39008894 TTTTTAATTAAT
1 TTTTTAATTAAT
39008906 AACTCTTTTA
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:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATC
Found at i:39009129 original size:25 final size:27
Alignment explanation
Indices: 39009091--39009142 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
39009081 CATATAAAAA
*
39009091 TTATATTTACTAAA-AATAATAGTTATT
1 TTATATTTACTAAATAA-AAGAGTTATT
39009118 TTAT-TTTA-TAAATAAAAGAGTTATT
1 TTATATTTACTAAATAAAAGAGTTATT
39009143 GATTAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 13 0.57
26 6 0.26
27 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (27 bp):
TTATATTTACTAAATAAAAGAGTTATT
Found at i:39011480 original size:22 final size:21
Alignment explanation
Indices: 39011440--39011488 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
39011430 AATTTTAAAA
**
39011440 TATTTTTAAAATACTTTTTTT
1 TATTTTTAAAATAAATTTTTT
*
39011461 TATTTTTAAAATAAA-ATTTT
1 TATTTTTAAAATAAATTTTTT
*
39011481 GATTTTTA
1 TATTTTTA
39011489 TTAAAAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTT
Found at i:39013226 original size:14 final size:15
Alignment explanation
Indices: 39013200--39013229 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39013190 AAGATCTAAT
39013200 AAAAGAAACAAACAA
1 AAAAGAAACAAACAA
39013215 AAAAGAAA-AAACAA
1 AAAAGAAACAAACAA
39013229 A
1 A
39013230 GTATCCCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAGAAACAAACAA
Found at i:39016230 original size:13 final size:13
Alignment explanation
Indices: 39016214--39016243 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39016204 TAATCATTCA
39016214 TCATCAAATAAAT
1 TCATCAAATAAAT
*
39016227 TCATGAAATAAAT
1 TCATCAAATAAAT
39016240 TCAT
1 TCAT
39016244 AGTTGCTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:39018842 original size:122 final size:123
Alignment explanation
Indices: 39018699--39018949 Score: 495
Period size: 122 Copynumber: 2.0 Consensus size: 123
39018689 CAATCGGTCA
39018699 AAACTTTGTTGGCATTTATCTGTCCATTCAAATTTAACATCTTTCTGTAATAAACGGGTTATAGG
1 AAACTTTGTTGGCATTTATCTGTCCATTCAAATTTAACATCTTTCTGTAATAAACGGGTTATAGG
39018764 AGAAGCTATCATAGAAAACCCCTGTACAGATCTCCGATAATAACCAGCTAAACCCAAG
66 AGAAGCTATCATAGAAAACCCCTGTACAGATCTCCGATAATAACCAGCTAAACCCAAG
39018822 AAACTTTGTT-GCATTTATCTGTCCATTCAAATTTAACATCTTTCTGTAATAAACGGGTTATAGG
1 AAACTTTGTTGGCATTTATCTGTCCATTCAAATTTAACATCTTTCTGTAATAAACGGGTTATAGG
39018886 AGAAGCTATCATAGAAAACCCCTGTACAGATCTCCGATAATAACCAGCTAAACCCAAG
66 AGAAGCTATCATAGAAAACCCCTGTACAGATCTCCGATAATAACCAGCTAAACCCAAG
39018944 AAACTT
1 AAACTT
39018950 CTAACTTCAG
Statistics
Matches: 128, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 118 0.92
123 10 0.08
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (123 bp):
AAACTTTGTTGGCATTTATCTGTCCATTCAAATTTAACATCTTTCTGTAATAAACGGGTTATAGG
AGAAGCTATCATAGAAAACCCCTGTACAGATCTCCGATAATAACCAGCTAAACCCAAG
Found at i:39022470 original size:13 final size:13
Alignment explanation
Indices: 39022454--39022483 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39022444 TAATCATTCA
39022454 TCATCAAATAAAT
1 TCATCAAATAAAT
*
39022467 TCATGAAATAAAT
1 TCATCAAATAAAT
39022480 TCAT
1 TCAT
39022484 AGTTGCTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:39024963 original size:25 final size:25
Alignment explanation
Indices: 39024923--39024983 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
39024913 AAGTCCAAGC
* * *
39024923 GAGCCA-TATCGGGAAGTTC-CGGA
1 GAGCCATTATCGAGAAGCTCACGAA
39024946 GAGCCATTAATCGAGAAGCTCACGAA
1 GAGCCATT-ATCGAGAAGCTCACGAA
39024972 GAGCCATATATC
1 GAGCCAT-TATC
39024984 AGGACGCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 6 0.19
24 1 0.03
25 10 0.32
26 13 0.42
27 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (25 bp):
GAGCCATTATCGAGAAGCTCACGAA
Found at i:39027165 original size:2 final size:2
Alignment explanation
Indices: 39027158--39027202 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
39027148 TTTGTATGTA
39027158 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
39027200 TG T
1 TG T
39027203 TTGAGTTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:39027340 original size:18 final size:18
Alignment explanation
Indices: 39027317--39027356 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
39027307 AACTCTTTTT
39027317 ATTCTCTCTAA-ACTCTCA
1 ATTCTCTC-AACACTCTCA
*
39027335 ATTCTCTCAACTCTCTCA
1 ATTCTCTCAACACTCTCA
39027353 ATTC
1 ATTC
39027357 CTTAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTCTCTCAACACTCTCA
Found at i:39030666 original size:41 final size:41
Alignment explanation
Indices: 39030604--39030725 Score: 174
Period size: 41 Copynumber: 3.0 Consensus size: 41
39030594 GGTGTTTCAT
* *
39030604 TTATAACCTGATTCAGTTCACCGATACTTAGCCTACTAGGC
1 TTATAACCTGATTCAGTTCACCGACACTTAGCCTGCTAGGC
* *
39030645 TTATGACCTGATTCAGATCACC-AGCACTTAGCCTGCTAGGC
1 TTATAACCTGATTCAGTTCACCGA-CACTTAGCCTGCTAGGC
* *
39030686 TTATAACCTGATTTAGTTCACCGGCACTTAGCCTGCTAGG
1 TTATAACCTGATTCAGTTCACCGACACTTAGCCTGCTAGG
39030726 TGCTAAGCCT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
40 1 0.01
41 70 0.99
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (41 bp):
TTATAACCTGATTCAGTTCACCGACACTTAGCCTGCTAGGC
Found at i:39031396 original size:17 final size:17
Alignment explanation
Indices: 39031374--39031426 Score: 67
Period size: 15 Copynumber: 3.3 Consensus size: 17
39031364 TCAAGAATTT
39031374 ATATATATATTACACAC
1 ATATATATATTACACAC
*
39031391 ATATATATATT-CATAC
1 ATATATATATTACACAC
*
39031407 AT-TATATA-TACACAA
1 ATATATATATTACACAC
39031422 ATATA
1 ATATA
39031427 ACATCCAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 1 0.03
15 11 0.35
16 8 0.26
17 11 0.35
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATATATATTACACAC
Found at i:39031518 original size:203 final size:206
Alignment explanation
Indices: 39031253--39031687 Score: 698
Period size: 203 Copynumber: 2.1 Consensus size: 206
39031243 TATATACAAA
* * * * *
39031253 TATATTATATATAGATATACATTTGATTAAAAGCCAAAAATTATACATGTATATACCTTAATGTA
1 TATACTAT-TATATATATACCTTTGATTAAAAACAAAAAATTATACATGTATATACCTTAATGTA
39031318 TTCAAACCTTTTATGAACTTATATAACATTCATACTTCAATTAAGTTCAAGAATTTATATATATA
65 TTCAAACCTTTTATGAACTTATATAACATTCATACTTCAATTAAGTTCAAGAATTTATATATATA
39031383 TT-ACACAC-ATATATATATTCATACATTATATATACACAAATATAACATCCAAACTTTTAATTA
130 TTAACACACAATATATATATTCATACATTATATATACACAAATATAACATCCAAACTTTTAATTA
39031446 AATCCAAAAATT
195 AATCCAAAAATT
39031458 TA-A-TATTATATATATACCTTTGATTAAAAACAAAAAAATTATACATGTATATACCTTAATGTA
1 TATACTATTATATATATACCTTTGATTAAAAAC-AAAAAATTATACATGTATATACCTTAATGTA
**
39031521 TTTGAACCTTTTATGAACTTATATAACATTCATACTTCAATTAAGTTCAAGAATTTATATATATA
65 TTCAAACCTTTTATGAACTTATATAACATTCATACTTCAATTAAGTTCAAGAATTTATATATATA
*
39031586 TTACACACACACATATATATATATTCGTACATTATATATACACAAATATAACATCCAAACTTTTA
130 TT--A-ACACACA-ATATATATATTCATACATTATATATACACAAATATAACATCCAAACTTTTA
*
39031651 ATTAAATCCAAGAATT
191 ATTAAATCCAAAAATT
*
39031667 TATACTTTTATATATATACCT
1 TATACTATTATATATATACCT
39031688 ATTCGAACAT
Statistics
Matches: 212, Mismatches: 9, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
202 22 0.10
203 98 0.46
204 1 0.00
205 2 0.01
207 6 0.03
209 67 0.32
210 1 0.00
211 15 0.07
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.39
Consensus pattern (206 bp):
TATACTATTATATATATACCTTTGATTAAAAACAAAAAATTATACATGTATATACCTTAATGTAT
TCAAACCTTTTATGAACTTATATAACATTCATACTTCAATTAAGTTCAAGAATTTATATATATAT
TAACACACAATATATATATTCATACATTATATATACACAAATATAACATCCAAACTTTTAATTAA
ATCCAAAAATT
Found at i:39037511 original size:12 final size:12
Alignment explanation
Indices: 39037494--39037524 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
39037484 AAAAAAATAG
39037494 ATATATACATAT
1 ATATATACATAT
39037506 ATATATACATAT
1 ATATATACATAT
*
39037518 AAATATA
1 ATATATA
39037525 AAAGAATATT
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:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATATACATAT
Found at i:39041691 original size:173 final size:174
Alignment explanation
Indices: 39041466--39041802 Score: 423
Period size: 173 Copynumber: 1.9 Consensus size: 174
39041456 TGATGCAATC
* *
39041466 TGCTCTACTGTAATTTCAGAGAAATAAGATCCATCATTCTAAGCCACTCCACTACAACTTTAGGG
1 TGCTCTACTGCAACTTCAGAGAAATAAGATCCATCATTCTAAGCCACTCCACTACAACTTTAGGG
* * * * * * **
39041531 AGATAGGATTTGTT-TATTCAATCTGCCCCACTGCAATTTCAGGGGGATAAGACTT-GCTTTCTT
66 AGATAGGA-TTGTTGGACTAAATCTACCCCACTGCAACTTCAGGGAGATAAGA-TTCGCCATCTT
* *
39041594 GGGTCTGCTCCACTGCAACTTCAGG-GAGATAAGACTAAATGTGATA
129 GAGTCTGCCCCACTGCAACTTCAGGAG-GATAAGACTAAATGTGATA
* * * * *
39041640 TGCTCT-CTGCAACTTCAGAGAGATAAGATCTATTACTT-TAATCCACTCCACTGCAACTTTAGG
1 TGCTCTACTGCAACTTCAGAGAAATAAGATCCATCA-TTCTAAGCCACTCCACTACAACTTTAGG
* * *
39041703 GAGATAGGATTGTTGGCCTAAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTT
65 GAGATAGGATTGTTGGACTAAATCTACCCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTG
39041768 AGTCTGCCCCACTGCAACTTCAGGAGGATAAGACT
130 AGTCTGCCCCACTGCAACTTCAGGAGGATAAGACT
39041803 TGCTTATTTG
Statistics
Matches: 139, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
172 7 0.05
173 123 0.88
174 9 0.06
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (174 bp):
TGCTCTACTGCAACTTCAGAGAAATAAGATCCATCATTCTAAGCCACTCCACTACAACTTTAGGG
AGATAGGATTGTTGGACTAAATCTACCCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTGA
GTCTGCCCCACTGCAACTTCAGGAGGATAAGACTAAATGTGATA
Found at i:39041698 original size:44 final size:44
Alignment explanation
Indices: 39041646--39041975 Score: 166
Period size: 44 Copynumber: 7.5 Consensus size: 44
39041636 GATATGCTCT
*
39041646 CTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCACTCCA
1 CTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCTACTCCA
* * * * * * *
39041690 CTGCAACTTTAGGGAGATAGGAT-TGTTGGCCTAAATCTACTCCA
1 CTGCAACTTCAGAGAGATAAGATCTATT-ACTTTAATCTACTCCA
* * * * *
39041734 CTGCAACTTCAGGGAGATAAGATTCGCCA-T-CTTTAGTCTGCCCCA
1 CTGCAACTTCAGAGAGATAAGA-T--CTATTACTTTAATCTACTCCA
* * *
39041779 CTGCAACTTCAG-GAGGATAAGA-CTTGCTTA-TTTGAGTCTGCTCCA
1 CTGCAACTTCAGAGA-GATAAGATC-T-ATTACTTT-AATCTACTCCA
* * * * *
39041824 CTGCAACTTCAG-GAAGATAAGACCCGA-TGC---GATCT-CTTCTA
1 CTGCAACTTCAGAG-AGATAAGA-TCTATTACTTTAATCTAC-TCCA
* * * *
39041865 CTGCAACTTCAAAGAGATAAGATCTATCACTTTAATCCACTCCT
1 CTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCTACTCCA
* * *
39041909 CTGCAACTTCA-AGGAGATAGGAT-TATTGGCTTTAATCTGCTCCA
1 CTGCAACTTCAGA-GAGATAAGATCTATT-ACTTTAATCTACTCCA
* * *
39041953 TTGCAACTTTAGGGAGATAAGAT
1 CTGCAACTTCAGAGAGATAAGAT
39041976 TCGCCATCTT
Statistics
Matches: 216, Mismatches: 45, Indels: 50
0.69 0.14 0.16
Matches are distributed among these distances:
40 3 0.01
41 27 0.12
42 1 0.00
43 7 0.03
44 114 0.53
45 61 0.28
46 1 0.00
47 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (44 bp):
CTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCTACTCCA
Found at i:39041786 original size:45 final size:45
Alignment explanation
Indices: 39041731--39041846 Score: 148
Period size: 45 Copynumber: 2.6 Consensus size: 45
39041721 TAAATCTACT
*
39041731 CCACTGCAACTTCAGGGAGATAAGA-TTCGC-CATCTTTAGTCTGCC
1 CCACTGCAACTTCAGGGAGATAAGACTT-GCTCAT-TTGAGTCTGCC
* *
39041776 CCACTGCAACTTCA-GGAGGATAAGACTTGCTTATTTGAGTCTGCT
1 CCACTGCAACTTCAGGGA-GATAAGACTTGCTCATTTGAGTCTGCC
*
39041821 CCACTGCAACTTCAGGAAGATAAGAC
1 CCACTGCAACTTCAGGGAGATAAGAC
39041847 CCGATGCGAT
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
44 3 0.05
45 54 0.86
46 6 0.10
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAGATAAGACTTGCTCATTTGAGTCTGCC
Found at i:39041932 original size:219 final size:218
Alignment explanation
Indices: 39041552--39041985 Score: 647
Period size: 219 Copynumber: 2.0 Consensus size: 218
39041542 GTTTATTCAA
* * *
39041552 TCTGCCCCACTGCAATTTCAGGGGGATAAGACTTGCTTTCTTGGGTCTGCTCCACTGCAACTTCA
1 TCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTTCTTGAGTCTGCTCCACTGCAACTTCA
* * * * *
39041617 GGGAGATAAGACTAAATGTGATATGCTCTCTGCAACTTCAGAGAGATAAGATCTATTACTTTAAT
66 GGAAGATAAGACCAAATGCGATATGCTCTCTGCAACTTCAAAGAGATAAGATCTATCACTTTAAT
* * *
39041682 CCACTCCACTGCAACTTTAGGGAGATAGGATTGTTGGCCTAAATCTACTCCACTGCAACTTCAGG
131 CCACTCCACTGCAACTTCAAGGAGATAGGATTATTGGCCTAAATCTACTCCACTGCAACTTCAGG
39041747 GAGATAAGATTCGCCATCTTTAG
196 GAGATAAGATTCGCCATCTTTAG
39041770 TCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTAT-TTGAGTCTGCTCCACTGCAACTTC
1 TCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTT-TCTTGAGTCTGCTCCACTGCAACTTC
** *
39041834 AGGAAGATAAGACCCGATGCGATCT-CTTCTACTGCAACTTCAAAGAGATAAGATCTATCACTTT
65 AGGAAGATAAGACCAAATGCGATATGC-TCT-CTGCAACTTCAAAGAGATAAGATCTATCACTTT
* * * * * *
39041898 AATCCACTCCTCTGCAACTTCAAGGAGATAGGATTATTGGCTTTAATCTGCTCCATTGCAACTTT
128 AATCCACTCCACTGCAACTTCAAGGAGATAGGATTATTGGCCTAAATCTACTCCACTGCAACTTC
39041963 AGGGAGATAAGATTCGCCATCTT
193 AGGGAGATAAGATTCGCCATCTT
39041986 CAATCTTTTT
Statistics
Matches: 193, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
217 1 0.01
218 81 0.42
219 111 0.58
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (218 bp):
TCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTTCTTGAGTCTGCTCCACTGCAACTTCA
GGAAGATAAGACCAAATGCGATATGCTCTCTGCAACTTCAAAGAGATAAGATCTATCACTTTAAT
CCACTCCACTGCAACTTCAAGGAGATAGGATTATTGGCCTAAATCTACTCCACTGCAACTTCAGG
GAGATAAGATTCGCCATCTTTAG
Found at i:39042251 original size:117 final size:117
Alignment explanation
Indices: 39042107--39042338 Score: 349
Period size: 117 Copynumber: 2.0 Consensus size: 117
39042097 GCTGTATTGC
* *
39042107 CTGTAAGGCCAAAAAGATAGGATTCGCTGCCCATAGCTACAATCCGCTCCACTTCAGCTAATTCC
1 CTGTAAGGCCAAAAAGATAGGATTCGCTGCCCATAGCTACAATCCACTCCACTTCAGCCAA-TCC
*
39042172 -AGCCTTAACACCAGAGAGATAAGATTCGCCGTCGTGGCTTCAATCTGCTCTA
65 AAGCCTTAACACCAGAGAGATAAGATTCGACGTCGTGGCTTCAATCTGCTCTA
* * * *
39042224 CTGTAATGCCAAAGAGATAGGATTCGCTGCCCGTAGCTTCAATCCACTCCACTTCAGCCAATCCA
1 CTGTAAGGCCAAAAAGATAGGATTCGCTGCCCATAGCTACAATCCACTCCACTTCAGCCAATCCA
* ** *
39042289 AGCTTTAATGCCAGGGAGATAAGATTCGACGTCGTGGCTTCAATCTGCTC
66 AGCCTTAACACCAGAGAGATAAGATTCGACGTCGTGGCTTCAATCTGCTC
39042339 GCTACATCGC
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
116 3 0.03
117 100 0.97
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (117 bp):
CTGTAAGGCCAAAAAGATAGGATTCGCTGCCCATAGCTACAATCCACTCCACTTCAGCCAATCCA
AGCCTTAACACCAGAGAGATAAGATTCGACGTCGTGGCTTCAATCTGCTCTA
Found at i:39057883 original size:23 final size:23
Alignment explanation
Indices: 39057850--39057925 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
39057840 ATAAGTGTCA
*
39057850 CACTGATATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
39057873 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
39057896 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
39057919 CACTGAT
1 CACTGAT
39057926 CAATAANNNN
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:39059427 original size:267 final size:268
Alignment explanation
Indices: 39058944--39059474 Score: 780
Period size: 267 Copynumber: 2.0 Consensus size: 268
39058934 GGCTATCATA
*
39058944 GGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTACACCGCCAGAGGAGTAAGATTC
1 GGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGAGGAGTAAGATTC
* *
39059009 GCCGTTGCGGCTTCAATCTACTCCTACTGTAATGCCAAAGAGATAAGATTCGCTGTCCACAGGTT
66 GCCGTTGCGGCTTCAATCTACTCCTACTGTAATGCCAAAGAGATAAGATTCGCTGCCCACAGCTT
* * * * *
39059074 CAATCCACTCTACTTTAGCTAATACAGGCCTTAACACTAGGGAGATAAGATTCACCGTCGTGGCT
131 CAATCCACTCCACTTCAGCTAATACAAGCCTTAACACCAGGGAGATAAGATTCACCATCGTGGCT
* *
39059139 TCAATCTGCTCCGCTACAACGCCACG-GAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTAAAT
196 TCAATCTGCCCCGCTACAACGCCA-GAGAAATAAGATTCGTCGTTGTGGCTTCAATCTTTTAAAT
39059203 TGCAATGTT
260 TGCAATGTT
* * * * *
39059212 GGGGAATCAAGATTCACCGTCGTAGCTTTAATCTGTTTCACTACACCGCTAGGGGAGTAAGATTC
1 GGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGAGGAGTAAGATTC
* * *
39059277 GCCGTTGCGGCTTTAATCTGCTCC-ACTGTAATGCCAAAGAGATAGGATTTC-CTGCCCACAGCT
66 GCCGTTGCGGCTTCAATCTACTCCTACTGTAATGCCAAAGAGATAAGA-TTCGCTGCCCACAGCT
* * * * **
39059340 TCAATCCGCTCCACTTCAGCTAATCCAAGCCTTAACGCCAGGGAGATAGGATTTGCCATCGTGGC
130 TCAATCCACTCCACTTCAGCTAATACAAGCCTTAACACCAGGGAGATAAGATTCACCATCGTGGC
* **
39059405 TTCAATCTGCCCCGCTACAACGCCAGAGAAATAAGATTCGTCGTTGTGGCTTCAATTTTTTCCAT
195 TTCAATCTGCCCCGCTACAACGCCAGAGAAATAAGATTCGTCGTTGTGGCTTCAATCTTTTAAAT
39059470 TGCAA
260 TGCAA
39059475 CGTCGAGGCG
Statistics
Matches: 234, Mismatches: 27, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
266 1 0.00
267 149 0.64
268 84 0.36
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (268 bp):
GGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGAGGAGTAAGATTC
GCCGTTGCGGCTTCAATCTACTCCTACTGTAATGCCAAAGAGATAAGATTCGCTGCCCACAGCTT
CAATCCACTCCACTTCAGCTAATACAAGCCTTAACACCAGGGAGATAAGATTCACCATCGTGGCT
TCAATCTGCCCCGCTACAACGCCAGAGAAATAAGATTCGTCGTTGTGGCTTCAATCTTTTAAATT
GCAATGTT
Found at i:39060701 original size:19 final size:18
Alignment explanation
Indices: 39060679--39060733 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 18
39060669 TGGCCTCTCC
39060679 TTTTCCTTTTCTTCTTTCT
1 TTTTCCTTTTCTTCTTT-T
* *
39060698 TTTTCTTTTTTTTCTTTT
1 TTTTCCTTTTCTTCTTTT
39060716 TTTT-CTTTTC--CTTTT
1 TTTTCCTTTTCTTCTTTT
39060731 TTT
1 TTT
39060734 CATCATCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 8 0.25
17 4 0.12
18 5 0.16
19 15 0.47
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCCTTTTCTTCTTTT
Found at i:39060713 original size:15 final size:15
Alignment explanation
Indices: 39060685--39060733 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
39060675 CTCCTTTTCC
39060685 TTTTCTTCTTTCTTTT
1 TTTTCTT-TTTCTTTT
39060701 TCTTT-TTTTTCTTTT
1 T-TTTCTTTTTCTTTT
*
39060716 TTTTCTTTTCCTTTT
1 TTTTCTTTTTCTTTT
39060731 TTT
1 TTT
39060734 CATCATCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 3 0.10
15 21 0.70
16 3 0.10
17 3 0.10
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTCTTTTTCTTTT
Found at i:39060733 original size:18 final size:17
Alignment explanation
Indices: 39060679--39060733 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
39060669 TGGCCTCTCC
* *
39060679 TTTTCCTTTTCTTCTTTC
1 TTTTTCTTTTCTT-TTTT
*
39060697 TTTTTCTTTTTTTTCTTT
1 TTTTTCTTTTCTTT-TTT
*
39060715 TTTTTCTTTTCCTTTTT
1 TTTTTCTTTTCTTTTTT
39060732 TT
1 TT
39060734 CATCATCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 6 0.19
18 25 0.81
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTTT
Found at i:39060734 original size:9 final size:9
Alignment explanation
Indices: 39060679--39060724 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
39060669 TGGCCTCTCC
*
39060679 TTTTCCTTT
1 TTTTCTTTT
*
39060688 TCTTCTTTCT
1 TTTTCTTT-T
39060698 TTTTCTTTT
1 TTTTCTTTT
39060707 TTTTCTTTT
1 TTTTCTTTT
39060716 TTTTCTTTT
1 TTTTCTTTT
39060725 CCTTTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
9 25 0.76
10 8 0.24
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:39063484 original size:9 final size:9
Alignment explanation
Indices: 39063465--39063497 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
39063455 ATGCAAAGCT
39063465 AATGC-ATG
1 AATGCAATG
39063473 AATGCAATG
1 AATGCAATG
*
39063482 AATGCCATG
1 AATGCAATG
39063491 AATGCAA
1 AATGCAA
39063498 AAGAAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (9 bp):
AATGCAATG
Found at i:39066205 original size:17 final size:18
Alignment explanation
Indices: 39066174--39066210 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
39066164 ACCGAGTTAT
39066174 AAAATTTCATTAATTATTA
1 AAAATTTCA-TAATTATTA
39066193 AAAATTTCA-AATTATTA
1 AAAATTTCATAATTATTA
39066210 A
1 A
39066211 CATGCTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTTCATAATTATTA
Found at i:39069151 original size:10 final size:10
Alignment explanation
Indices: 39069136--39069161 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
39069126 TGCCCTTCCT
39069136 CTCTCTCTCC
1 CTCTCTCTCC
39069146 CTCTCTCTCC
1 CTCTCTCTCC
39069156 CTCTCT
1 CTCTCT
39069162 TTAGTAGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (10 bp):
CTCTCTCTCC
Found at i:39069605 original size:30 final size:31
Alignment explanation
Indices: 39069557--39069616 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
39069547 AAACCTTTTA
*
39069557 TTTTCTCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCTCCCAAAACTTTTACTCCCTTCCCAC
*
39069587 TTTT-TCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCTCCC-AAAACTTTTACTCCCTTCCCA
39069617 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 17 0.65
31 5 0.19
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCTCCCAAAACTTTTACTCCCTTCCCAC
Found at i:39070549 original size:26 final size:25
Alignment explanation
Indices: 39070488--39070572 Score: 161
Period size: 25 Copynumber: 3.4 Consensus size: 25
39070478 AATATGGGTT
39070488 CCTTTTAAATATGAGAATCTGCCAA
1 CCTTTTAAATATGAGAATCTGCCAA
39070513 CCTTTTAAATATGAGAATCTGCCAA
1 CCTTTTAAATATGAGAATCTGCCAA
39070538 TCCTTTTAAATATGAGAATCTGCCAA
1 -CCTTTTAAATATGAGAATCTGCCAA
39070564 CCTTTTAAA
1 CCTTTTAAA
39070573 GATTGTACTC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
25 34 0.58
26 25 0.42
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (25 bp):
CCTTTTAAATATGAGAATCTGCCAA
Found at i:39082561 original size:18 final size:18
Alignment explanation
Indices: 39082534--39082568 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39082524 GATTAAATAC
39082534 ATGTTACAAATA-GGTAT
1 ATGTTACAAATATGGTAT
39082551 ATGTATACAAATATGGTA
1 ATGT-TACAAATATGGTA
39082569 CGAAACGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (18 bp):
ATGTTACAAATATGGTAT
Found at i:39086354 original size:73 final size:74
Alignment explanation
Indices: 39086225--39086372 Score: 235
Period size: 73 Copynumber: 2.0 Consensus size: 74
39086215 AAAGAATGGA
*
39086225 AAAGGAAGGTGAGTGCAGGCCACATAAAAATGGGTGTTACAAAGAAGCAAACGCAGAGCAGAGGA
1 AAAGGAAGGTGAGTGAAGGCCACATAAAAATGGGTGTTACAAAGAAGCAAACGCAGAGCAGAGGA
39086290 GAGAAACAT
66 GAGAAACAT
* * * * *
39086299 AAAGGAAGGTGCGTGAAGGCCACGTAGAAAT-GGTGTTACAATGAAGCAAACGCAGAGCAGATGA
1 AAAGGAAGGTGAGTGAAGGCCACATAAAAATGGGTGTTACAAAGAAGCAAACGCAGAGCAGAGGA
39086363 GAGAAACAT
66 GAGAAACAT
39086372 A
1 A
39086373 TACGCTACGT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
73 41 0.60
74 27 0.40
ACGTcount: A:0.43, C:0.14, G:0.31, T:0.12
Consensus pattern (74 bp):
AAAGGAAGGTGAGTGAAGGCCACATAAAAATGGGTGTTACAAAGAAGCAAACGCAGAGCAGAGGA
GAGAAACAT
Found at i:39090011 original size:26 final size:26
Alignment explanation
Indices: 39089982--39090044 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
39089972 AACGAATTTC
39089982 TCAAAATTTTATTAG-GGGTAAAATCA
1 TCAAAATTTTA-TAGAGGGTAAAATCA
**
39090008 TCAAAATTTTATAGAGGGTAAAATTG
1 TCAAAATTTTATAGAGGGTAAAATCA
39090034 TCAAAATTTTA
1 TCAAAATTTTA
39090045 CTCAAGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 3 0.09
26 31 0.91
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (26 bp):
TCAAAATTTTATAGAGGGTAAAATCA
Found at i:39093350 original size:18 final size:18
Alignment explanation
Indices: 39093307--39093350 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
39093297 ACTCAATCCA
* *
39093307 AACCCAAGTATCCAACCC
1 AACCCAATTACCCAACCC
39093325 AACCCAATTACCCAACCC
1 AACCCAATTACCCAACCC
39093343 AACCCAAT
1 AACCCAAT
39093351 CATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.41, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
AACCCAATTACCCAACCC
Found at i:39099564 original size:23 final size:22
Alignment explanation
Indices: 39099537--39099622 Score: 97
Period size: 21 Copynumber: 4.0 Consensus size: 22
39099527 GCTTTGCCGA
39099537 TCAGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
*
39099559 CTCAGGCACTTTATTTGTCGTA-
1 -TCAGGCACTTTATGTGTCGTAT
* * **
39099581 TCAGACACCTCGTGTGTCGT-T
1 TCAGGCACTTTATGTGTCGTAT
39099602 TCAGGCAC-TTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
39099623 ACTGATCAGG
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
20 9 0.17
21 23 0.44
23 20 0.38
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (22 bp):
TCAGGCACTTTATGTGTCGTAT
Found at i:39104025 original size:32 final size:31
Alignment explanation
Indices: 39103969--39104028 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
39103959 TAACAGTACC
**
39103969 TAAATTTATTGTAAAAAATTTACTATTTTCT
1 TAAATTTATTGTAAAAAACATACTATTTTCT
*
39104000 TAAATTTTATTGTAAAAGACATACTATTT
1 TAAA-TTTATTGTAAAAAACATACTATTT
39104029 AAATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 4 0.16
32 21 0.84
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (31 bp):
TAAATTTATTGTAAAAAACATACTATTTTCT
Found at i:39107253 original size:37 final size:37
Alignment explanation
Indices: 39107212--39107286 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
39107202 ACCATAACAT
*
39107212 ACCTCTTAGTTGTACCTTTTTATAATTAATAAAATCC
1 ACCTCTTAGTTGTACCTTTCTATAATTAATAAAATCC
39107249 ACCTCTTAGTTGTACCTTTCTATAATTAATAAAATCC
1 ACCTCTTAGTTGTACCTTTCTATAATTAATAAAATCC
39107286 A
1 A
39107287 TTTGCTGAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.41
Consensus pattern (37 bp):
ACCTCTTAGTTGTACCTTTCTATAATTAATAAAATCC
Found at i:39110517 original size:23 final size:23
Alignment explanation
Indices: 39110473--39110524 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
39110463 AGAATAAATT
39110473 ATAAAAAATAATTATAAAATTAA
1 ATAAAAAATAATTATAAAATTAA
* * *
39110496 GTAAAAAATTA-TATTAATATTAA
1 ATAAAAAATAATTA-TAAAATTAA
39110519 ATAAAA
1 ATAAAA
39110525 TAAAACCCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
ATAAAAAATAATTATAAAATTAA
Found at i:39111060 original size:24 final size:23
Alignment explanation
Indices: 39111030--39111094 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
39111020 GGGGGGTTAT
39111030 TTTATATTAATATAATTATTTTA
1 TTTATATTAATATAATTATTTTA
*
39111053 TTTAATATTAATATACAGT-TTTTA
1 TTT-ATATTAATATA-ATTATTTTA
39111077 TTTA-ATTAA-ATAATTATT
1 TTTATATTAATATAATTATT
39111095 AAGAAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 2 0.05
21 5 0.14
22 5 0.14
23 4 0.11
24 19 0.51
25 2 0.05
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTATATTAATATAATTATTTTA
Found at i:39113171 original size:14 final size:14
Alignment explanation
Indices: 39113152--39113197 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
39113142 TTTCAGATCA
39113152 TTTGAATAAATATT
1 TTTGAATAAATATT
39113166 TTTGAACTAGAATTATT
1 TTTGAA-TA-AA-TATT
39113183 TTT--ATAAATATT
1 TTTGAATAAATATT
39113195 TTT
1 TTT
39113198 TTTAGGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 7 0.24
13 2 0.07
14 8 0.28
15 3 0.10
16 2 0.07
17 7 0.24
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (14 bp):
TTTGAATAAATATT
Found at i:39113846 original size:24 final size:25
Alignment explanation
Indices: 39113819--39113865 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
39113809 AATTATCAAG
39113819 TTTAAGACC-TAATT-TAAAAAAAAA
1 TTTAA-ACCATAATTGTAAAAAAAAA
39113843 TTTAAACCATAATTGTAAAAAAA
1 TTTAAACCATAATTGTAAAAAAA
39113866 TTTGCGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 10 0.48
25 8 0.38
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (25 bp):
TTTAAACCATAATTGTAAAAAAAAA
Found at i:39125187 original size:20 final size:20
Alignment explanation
Indices: 39125162--39125224 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
39125152 CAAACAAAAT
*
39125162 AAAAACAAGATTAAACATAA
1 AAAAACAAGATTAAAAATAA
* *
39125182 AAAAACACGATGAAATAATAA
1 AAAAACAAGATTAAA-AATAA
*
39125203 AAATAA-AAGAGTAAAAATAA
1 AAA-AACAAGATTAAAAATAA
39125223 AA
1 AA
39125225 TAAAACAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 20 0.57
21 13 0.37
22 2 0.06
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.14
Consensus pattern (20 bp):
AAAAACAAGATTAAAAATAA
Found at i:39127247 original size:23 final size:21
Alignment explanation
Indices: 39127202--39127247 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
39127192 ATTTAAGTTA
* *
39127202 TAAAATTATTTGATATATTAT
1 TAAAATTATTTGAAATATAAT
39127223 TAAAATTAATTATGAAATATAAT
1 TAAAATT-ATT-TGAAATATAAT
39127246 TA
1 TA
39127248 GCTTGTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (21 bp):
TAAAATTATTTGAAATATAAT
Found at i:39130353 original size:24 final size:24
Alignment explanation
Indices: 39130325--39130388 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
39130315 TTTTTTCTTT
39130325 AATTTTTTAATATGTTTAAATT-TA
1 AATTTTTTAATAT-TTTAAATTCTA
*
39130349 AATTTTTCT-ATATTTTAATTTCTA
1 AATTTTT-TAATATTTTAAATTCTA
*
39130373 AGTTTTTTAATATTTT
1 AATTTTTTAATATTTT
39130389 TATAGCCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 8 0.23
24 26 0.74
25 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (24 bp):
AATTTTTTAATATTTTAAATTCTA
Found at i:39136244 original size:16 final size:16
Alignment explanation
Indices: 39136223--39136254 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39136213 ATTACAGAAA
39136223 AAAATAAAAAGAAAAT
1 AAAATAAAAAGAAAAT
39136239 AAAATAAAAAGAAAAT
1 AAAATAAAAAGAAAAT
39136255 CTCCCAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAATAAAAAGAAAAT
Found at i:39145946 original size:132 final size:132
Alignment explanation
Indices: 39145784--39146032 Score: 392
Period size: 132 Copynumber: 1.9 Consensus size: 132
39145774 TTTATTTTTT
* * *
39145784 AAATATTTATATTATTTTAATTTAATATTTAATAATTTTATATATTTTTTATTTATTGAAAATTT
1 AAATATTTATATTATATTAATTTAATATTTAATAATTTTATACATTTTTTATTTATGGAAAATTT
* *
39145849 TTATA-GTCATCTTAACATTATTTTACTGTTTACATTAGAGTAGTATTATATTAAAATCTTTGAA
66 TTATATGTCATCTTAACATTATTTTAC-ATTTACATTAGAATAGTATTATATTAAAATCTTTGAA
39145913 AAA
130 AAA
* * *
39145916 AAATCTTTATGTTATATTATTTTAATATTTAATAATTTTATACATTTTTTATTTATGGAAAATTT
1 AAATATTTATATTATATTAATTTAATATTTAATAATTTTATACATTTTTTATTTATGGAAAATTT
*
39145981 TTATATTGTCATCTTAACATTATTTTACATTTATATTAGAATAGTATTATAT
66 TTATA-TGTCATCTTAACATTATTTTACATTTACATTAGAATAGTATTATAT
39146033 ATTTAGTATA
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
132 64 0.60
133 21 0.20
134 21 0.20
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (132 bp):
AAATATTTATATTATATTAATTTAATATTTAATAATTTTATACATTTTTTATTTATGGAAAATTT
TTATATGTCATCTTAACATTATTTTACATTTACATTAGAATAGTATTATATTAAAATCTTTGAAA
AA
Found at i:39146950 original size:21 final size:19
Alignment explanation
Indices: 39146896--39146963 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 19
39146886 TTGTCTATTT
*
39146896 ATTATAGATTGATATAATAA
1 ATTATAGATTGATATTA-AA
39146916 ATATATTAGATTGAT-TTGAAA
1 AT-TA-TAGATTGATATT-AAA
39146937 ATGTATAGACTTGATATTAAA
1 AT-TATAGA-TTGATATTAAA
39146958 ATTATA
1 ATTATA
39146964 TAGATAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
20 10 0.24
21 19 0.46
22 12 0.29
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.41
Consensus pattern (19 bp):
ATTATAGATTGATATTAAA
Found at i:39147342 original size:232 final size:233
Alignment explanation
Indices: 39146936--39147401 Score: 925
Period size: 232 Copynumber: 2.0 Consensus size: 233
39146926 TTGATTTGAA
39146936 AATGTATAGACTTGATATTAAAATTATATAGATAAATTCAACTTATTTATTGTTAAAATATTAAT
1 AATGTATAGACTTGATATTAAAATTATATAGATAAATTCAACTTATTTATTGTTAAAATATTAAT
39147001 TATACAAAAAGGTTAAAAAAGTGTATAAAACTAATTTTAAAAAATAATAGTGCATATAGATCATT
66 TATACAAAAAGGTTAAAAAAGTGTATAAAACTAATTTTAAAAAATAATAGTGCATATAGATCATT
39147066 TCCCTATTCATACATACACATGGACGAAATCAAAAGTATAAATAAGAGGTATATATAAAAATTTT
131 TCCCTATTCATACATACACATGGACGAAATCAAAAGTATAAATAAGAGGTATATATAAAAATTTT
39147131 AAGTAAATAAATTGTTGCGAAAAAAAC-TATAAAGTTT
196 AAGTAAATAAATTGTTGCGAAAAAAACTTATAAAGTTT
39147168 AATGTATAGACTTGATATTAAAATTATATAGATAAATTCAACTTATTTATTGTTAAAATATTAAT
1 AATGTATAGACTTGATATTAAAATTATATAGATAAATTCAACTTATTTATTGTTAAAATATTAAT
39147233 TATACAAAAAGGTTAAAAAAGTGTATAAAACTAATTTTAAAAAATAATAGTGCATATAGATCATT
66 TATACAAAAAGGTTAAAAAAGTGTATAAAACTAATTTTAAAAAATAATAGTGCATATAGATCATT
39147298 TCCCTATTCATACATACACATGGACGAAATCAAAAGTATAAATAAGAGGTATATATAAAAATTTT
131 TCCCTATTCATACATACACATGGACGAAATCAAAAGTATAAATAAGAGGTATATATAAAAATTTT
39147363 AAGTAAATAAATTGTTGCGAAAAAAACTTATAAAGTTT
196 AAGTAAATAAATTGTTGCGAAAAAAACTTATAAAGTTT
39147401 A
1 A
39147402 TTTTATTTAA
Statistics
Matches: 233, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
232 222 0.95
233 11 0.05
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (233 bp):
AATGTATAGACTTGATATTAAAATTATATAGATAAATTCAACTTATTTATTGTTAAAATATTAAT
TATACAAAAAGGTTAAAAAAGTGTATAAAACTAATTTTAAAAAATAATAGTGCATATAGATCATT
TCCCTATTCATACATACACATGGACGAAATCAAAAGTATAAATAAGAGGTATATATAAAAATTTT
AAGTAAATAAATTGTTGCGAAAAAAACTTATAAAGTTT
Found at i:39152562 original size:69 final size:67
Alignment explanation
Indices: 39152489--39152624 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 67
39152479 TATAGATTAA
*
39152489 TTCAAAATCTTAAATTTTAAATATTTTAATTTCCAAAAAG-AATTT-AAAAATAATAAATTATCC
1 TTCAAAATCTTAAAATTTAAATATTTTAATTT-CAAAAAGAAATTTGAAAAA-AATAAATTA--C
39152552 AAAATT
62 AAAATT
*
39152558 TTCAAAATCTTAAAATTTAAATATTTTAATTTCTAAAAGAAATTTGAAAAAAATAAATTACAAAA
1 TTCAAAATCTTAAAATTTAAATATTTTAATTTCAAAAAGAAATTTGAAAAAAATAAATTACAAAA
39152623 TT
66 TT
39152625 AAAATATAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
67 7 0.11
68 6 0.10
69 45 0.71
70 5 0.08
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (67 bp):
TTCAAAATCTTAAAATTTAAATATTTTAATTTCAAAAAGAAATTTGAAAAAAATAAATTACAAAA
TT
Found at i:39156849 original size:27 final size:27
Alignment explanation
Indices: 39156814--39156895 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
39156804 TACATAGTAT
*
39156814 TGGTGCCTATCTCAGAGGCGCCAATGG
1 TGGTGCCTATCTGAGAGGCGCCAATGG
* * *
39156841 TGGTGCCTATCTGAGAGGTGCCATTAG
1 TGGTGCCTATCTGAGAGGCGCCAATGG
*
39156868 TGGTGCC-ATGTTGAGAGGCGCCAATGG
1 TGGTGCCTAT-CTGAGAGGCGCCAATGG
39156895 T
1 T
39156896 ATTATTTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 2 0.04
27 44 0.96
ACGTcount: A:0.18, C:0.21, G:0.35, T:0.26
Consensus pattern (27 bp):
TGGTGCCTATCTGAGAGGCGCCAATGG
Found at i:39156980 original size:15 final size:16
Alignment explanation
Indices: 39156960--39156996 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
39156950 ACAAAATCAA
39156960 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
39156975 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
39156991 ATAAAA
1 ATAAAA
39156997 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:39157756 original size:19 final size:19
Alignment explanation
Indices: 39157728--39157861 Score: 106
Period size: 19 Copynumber: 6.3 Consensus size: 19
39157718 ATTATAAAAT
39157728 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
*
39157747 AATTATAATATTCATATAAAATTACAA
1 AATTACAATATTC-------A-TACAA
39157774 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* *
39157793 AATTACAATATTAATTATAAAA
1 AATTACAATA-T--TCATACAA
39157815 TAATTACAATATTCATACAAA
1 -AATTACAATATTCATAC-AA
*
39157836 AAGTTACAATATACATACAA
1 AA-TTACAATATTCATACAA
39157856 AATTAC
1 AATTAC
39157862 CCATTGGCCC
Statistics
Matches: 94, Mismatches: 7, Indels: 28
0.73 0.05 0.22
Matches are distributed among these distances:
19 31 0.33
20 12 0.13
21 16 0.17
22 7 0.07
23 10 0.11
26 1 0.01
27 17 0.18
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:39157756 original size:28 final size:28
Alignment explanation
Indices: 39157664--39157756 Score: 64
Period size: 32 Copynumber: 3.1 Consensus size: 28
39157654 TTAATTATAA
39157664 AATAATTACAATATTCATACAAAA-TACT
1 AATAATTACAATATTCATACAAAATTA-T
** * * *
39157692 AATAAAAAACTATAAAT-ATAAAACTAATTAT
1 AAT-AATTACAAT-ATTCATACAA--AATTAT
39157723 AAAATAATTACAATATTCATACAAAATTAT
1 --AATAATTACAATATTCATACAAAATTAT
39157753 AATA
1 AATA
39157757 TTCATATAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 16
0.64 0.14 0.22
Matches are distributed among these distances:
28 7 0.15
29 11 0.23
30 8 0.17
31 5 0.11
32 13 0.28
33 3 0.06
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (28 bp):
AATAATTACAATATTCATACAAAATTAT
Found at i:39157756 original size:61 final size:61
Alignment explanation
Indices: 39157606--39157749 Score: 261
Period size: 61 Copynumber: 2.4 Consensus size: 61
39157596 NNNNNTACAA
* *
39157606 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACAAAACTAATTATAAAAT
*
39157667 AATTACAATATTCATACAAAATACTAATAAAAAACTATAAATATAAAACTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACAAAACTAATTATAAAAT
39157728 AATTACAATATTCATACAAAAT
1 AATTACAATATTCATACAAAAT
39157750 TATAATATTC
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 80 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (61 bp):
AATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACAAAACTAATTATAAAAT
Found at i:39157777 original size:27 final size:27
Alignment explanation
Indices: 39157742--39157805 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
39157732 ACAATATTCA
* *
39157742 TACAAAATTATAATATTCATATAAAAT
1 TACAAAATTACAATATTCATACAAAAT
39157769 TACAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
*
39157796 TACAATATTA
1 TACAAAATTA
39157806 ATTATAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (27 bp):
TACAAAATTACAATATTCATACAAAAT
Found at i:39157783 original size:46 final size:44
Alignment explanation
Indices: 39157728--39157861 Score: 166
Period size: 46 Copynumber: 3.0 Consensus size: 44
39157718 ATTATAAAAT
*
39157728 AATTACAATATTCATACAAAATTATAATATTCATATAAAATTAC
1 AATTACAATATTCATACAAAATTACAATATTCATATAAAATTAC
*
39157772 AAAATTACAATATTCATACAAAATTACAATATTAATTATAAAA-T--
1 --AATTACAATATTCATACAAAATTACAATATTCA-TATAAAATTAC
* *
39157816 AATTACAATATTCATACAAAAAGTTACAATATACATACAAAATTAC
1 AATTACAATATTCATAC-AAAA-TTACAATATTCATATAAAATTAC
39157862 CCATTGGCCC
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
42 17 0.22
43 10 0.13
44 11 0.14
46 32 0.42
47 7 0.09
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (44 bp):
AATTACAATATTCATACAAAATTACAATATTCATATAAAATTAC
Found at i:39175767 original size:29 final size:28
Alignment explanation
Indices: 39175735--39175814 Score: 65
Period size: 28 Copynumber: 2.8 Consensus size: 28
39175725 TGGAGGGGGA
39175735 TGGAAGAGATTTGTCAGGCGGCACCCAAG
1 TGGAAGAGATTTGTCAGGCGGCA-CCAAG
* * * **
39175764 TGG-AGGGACATTGTCAGGCGACACCATT
1 TGGAAGAGA-TTTGTCAGGCGGCACCAAG
*
39175792 TGGAGGA-ATGTTGTCAGGCGGCA
1 TGGAAGAGAT-TTGTCAGGCGGCA
39175815 TCGGACCCCT
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
28 23 0.59
29 16 0.41
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.20
Consensus pattern (28 bp):
TGGAAGAGATTTGTCAGGCGGCACCAAG
Found at i:39181435 original size:12 final size:12
Alignment explanation
Indices: 39181418--39181442 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39181408 CGGGATGCCC
39181418 TCTCTCGAGCCA
1 TCTCTCGAGCCA
39181430 TCTCTCGAGCCA
1 TCTCTCGAGCCA
39181442 T
1 T
39181443 ATAACAGGAA
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:0.16, C:0.40, G:0.16, T:0.28
Consensus pattern (12 bp):
TCTCTCGAGCCA
Found at i:39181472 original size:25 final size:25
Alignment explanation
Indices: 39181436--39181483 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
39181426 GCCATCTCTC
*
39181436 GAGCCATATAACAGGAAGCTTATGT
1 GAGCCATATAACAAGAAGCTTATGT
*
39181461 GAGCCATGTAACAAGAAGCTTAT
1 GAGCCATATAACAAGAAGCTTAT
39181484 TCGGGCTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (25 bp):
GAGCCATATAACAAGAAGCTTATGT
Found at i:39181497 original size:25 final size:25
Alignment explanation
Indices: 39181469--39181522 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
39181459 GTGAGCCATG
*
39181469 TAACAAGAAGCTTATTCGGGCTGTA
1 TAACAAGAAGCTTATCCGGGCTGTA
**
39181494 TAACGGGAAGCTTATCCGGGCTGTA
1 TAACAAGAAGCTTATCCGGGCTGTA
39181519 TAAC
1 TAAC
39181523 GGGAAGCTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (25 bp):
TAACAAGAAGCTTATCCGGGCTGTA
Found at i:39181523 original size:25 final size:25
Alignment explanation
Indices: 39181475--39181530 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
39181465 CATGTAACAA
*
39181475 GAAGCTTATTCGGGCTGTATAACGG
1 GAAGCTTATCCGGGCTGTATAACGG
39181500 GAAGCTTATCCGGGCTGTATAACGG
1 GAAGCTTATCCGGGCTGTATAACGG
39181525 GAAGCT
1 GAAGCT
39181531 CATAAGAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (25 bp):
GAAGCTTATCCGGGCTGTATAACGG
Found at i:39181594 original size:24 final size:24
Alignment explanation
Indices: 39181567--39181625 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
39181557 TACGAGGTAA
*
39181567 TAACGGGTAGCTCCAAAGAGCCAT
1 TAACGGGAAGCTCCAAAGAGCCAT
* *
39181591 TAACGGGAAGCTTCAAATAGCCAT
1 TAACGGGAAGCTCCAAAGAGCCAT
*
39181615 ATATCGGGAAG
1 -TAACGGGAAG
39181626 TTCTGGAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 21 0.70
25 9 0.30
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (24 bp):
TAACGGGAAGCTCCAAAGAGCCAT
Found at i:39190421 original size:27 final size:27
Alignment explanation
Indices: 39190391--39190443 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
39190381 GAGATAGATG
39190391 TTCACCAACCAA-TTGCTGATCTGAATT
1 TTCACCAA-CAATTTGCTGATCTGAATT
*
39190418 TTCATCAACAATTTGCTGATCTGAAT
1 TTCACCAACAATTTGCTGATCTGAAT
39190444 GTATAGCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 3 0.12
27 21 0.88
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (27 bp):
TTCACCAACAATTTGCTGATCTGAATT
Found at i:39193698 original size:26 final size:26
Alignment explanation
Indices: 39193645--39193698 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
39193635 TTCTAAATTG
* * *
39193645 GTGCTTAATCCATTTTTTGGTGAAAA
1 GTGCTTAATCCATATTTTGATCAAAA
39193671 GTGCTTAATCCA-ATTTTGATCAATAA
1 GTGCTTAATCCATATTTTGATCAA-AA
39193697 GT
1 GT
39193699 CATTAACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (26 bp):
GTGCTTAATCCATATTTTGATCAAAA
Found at i:39195164 original size:20 final size:21
Alignment explanation
Indices: 39195132--39195170 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
39195122 AACCTCTCAT
39195132 TCTTTAGCAAACT-TTTTGGC
1 TCTTTAGCAAACTATTTTGGC
39195152 TCTTTAAGC-AACTATTTTG
1 TCTTT-AGCAAACTATTTTG
39195171 ACCATCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (21 bp):
TCTTTAGCAAACTATTTTGGC
Found at i:39197613 original size:20 final size:20
Alignment explanation
Indices: 39197568--39197614 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39197558 CCAAGGTATC
*
39197568 AGTATCAGTACTTAAAGGTA
1 AGTATCAGTACTTAAACGTA
*
39197588 AGTATCAGTACTTTAAACTTA
1 AGTATCAGTAC-TTAAACGTA
39197609 A-TATCA
1 AGTATCA
39197615 ATACCTTCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (20 bp):
AGTATCAGTACTTAAACGTA
Found at i:39198391 original size:22 final size:22
Alignment explanation
Indices: 39198366--39198409 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
39198356 GAAAACCCGA
39198366 AAACA-AAGAACTCTCAAAATGT
1 AAACACAA-AACTCTCAAAATGT
* *
39198388 AAACACAAAATTCTCTAAATGT
1 AAACACAAAACTCTCAAAATGT
39198410 GTTATGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.52, C:0.18, G:0.07, T:0.23
Consensus pattern (22 bp):
AAACACAAAACTCTCAAAATGT
Found at i:39198458 original size:57 final size:57
Alignment explanation
Indices: 39198386--39198496 Score: 206
Period size: 57 Copynumber: 1.9 Consensus size: 57
39198376 CTCTCAAAAT
39198386 GTAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATCTCTAATGGGTGTATAAC
1 GTAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATCTCTAATGGGTGTATAAC
39198443 GTAAACA-AAATATTCTCTAAATGTGTTATGAGTTCTAATCTCTAATGGGTGTAT
1 GTAAACACAAA-ATTCTCTAAATGTGTTATGAGTTCTAATCTCTAATGGGTGTAT
39198497 TTTCTAATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
56 3 0.06
57 50 0.94
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (57 bp):
GTAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATCTCTAATGGGTGTATAAC
Found at i:39203998 original size:1 final size:1
Alignment explanation
Indices: 39203992--39204057 Score: 132
Period size: 1 Copynumber: 66.0 Consensus size: 1
39203982 CTTAAAATGC
39203992 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39204057 A
1 A
39204058 TCCCGTGGCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39205061 original size:31 final size:31
Alignment explanation
Indices: 39204995--39205062 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
39204985 TAAAATGGGG
* ****
39204995 TTTTAAGTTCCTTAAAAGTTGGAGAAATTTT
1 TTTTAAGTCCCTTAAAAGTTGGAGAAAAAAA
39205026 TTTTAAGTCCCTTAAAAGTTGGTA-AAAAAAA
1 TTTTAAGTCCCTTAAAAGTTGG-AGAAAAAAA
39205057 TTTTAA
1 TTTTAA
39205063 CTTTTAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.41
Consensus pattern (31 bp):
TTTTAAGTCCCTTAAAAGTTGGAGAAAAAAA
Found at i:39210679 original size:11 final size:11
Alignment explanation
Indices: 39210660--39210770 Score: 90
Period size: 11 Copynumber: 10.4 Consensus size: 11
39210650 TATTTTTTAA
39210660 TTTTAAAATAT
1 TTTTAAAATAT
* *
39210671 TTTTTAAATAC
1 TTTTAAAATAT
39210682 TTTTAAAATACT
1 TTTTAAAATA-T
* *
39210694 TTTT---TTAA
1 TTTTAAAATAT
39210702 TTTTAAAATAT
1 TTTTAAAATAT
*
39210713 TTTTAAAATAC
1 TTTTAAAATAT
39210724 TTTTAAAATACT
1 TTTTAAAATA-T
* *
39210736 TTTT---TTAA
1 TTTTAAAATAT
39210744 TTTTAAAATAT
1 TTTTAAAATAT
39210755 TTTTAAAATACT
1 TTTTAAAATA-T
39210767 TTTT
1 TTTT
39210771 TTAATTTTTA
Statistics
Matches: 77, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
8 8 0.10
9 4 0.05
11 52 0.68
12 13 0.17
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:39210704 original size:42 final size:42
Alignment explanation
Indices: 39210652--39210769 Score: 227
Period size: 42 Copynumber: 2.8 Consensus size: 42
39210642 AATATATTTA
*
39210652 TTTTTTAATTTTAAAATATTTTTTAAATACTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTAAAATACT
39210694 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTAAAATACT
39210736 TTTTTTAATTTTAAAATATTTTTAAAATACTTTT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTT
39210770 TTTAATTTTT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (42 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTAAAATACT
Found at i:39210748 original size:31 final size:32
Alignment explanation
Indices: 39210711--39210785 Score: 134
Period size: 31 Copynumber: 2.4 Consensus size: 32
39210701 ATTTTAAAAT
39210711 ATTTTTAAAATACTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATACTTTTAAAATACTTTTTTTA
*
39210743 A-TTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATACTTTTAAAATACTTTTTTTA
39210774 ATTTTTAAAATA
1 ATTTTTAAAATA
39210786 AATTTTTGGG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 30 0.73
32 11 0.27
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (32 bp):
ATTTTTAAAATACTTTTAAAATACTTTTTTTA
Found at i:39210791 original size:21 final size:21
Alignment explanation
Indices: 39210753--39210792 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39210743 ATTTTAAAAT
**
39210753 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
39210774 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
39210793 GGGATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:39211486 original size:26 final size:26
Alignment explanation
Indices: 39211457--39211506 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
39211447 TTTAAGAAAA
*
39211457 ATTTTGATAGGGTTAGGGTTTTTTTT
1 ATTTTGATAGGGTTAAGGTTTTTTTT
*
39211483 ATTTTGTTAGGGTTAAGGTTTTTT
1 ATTTTGATAGGGTTAAGGTTTTTT
39211507 AGGAATTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (26 bp):
ATTTTGATAGGGTTAAGGTTTTTTTT
Found at i:39216870 original size:23 final size:22
Alignment explanation
Indices: 39216844--39216910 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 22
39216834 TCCTATGTGC
39216844 ACAAATGAAAGTAGCACTTC-GAT
1 ACAAATGAAAGT-GCACTTCTG-T
*
39216867 ACAATTGAAATGTGGCACTTCTGT
1 ACAAATGAAA-GT-GCACTTCTGT
*
39216891 GCAAATGAAAGTGACACTTC
1 ACAAATGAAAGTG-CACTTC
39216911 AATGCAATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
22 1 0.03
23 17 0.46
24 18 0.49
25 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (22 bp):
ACAAATGAAAGTGCACTTCTGT
Found at i:39216899 original size:24 final size:23
Alignment explanation
Indices: 39216844--39216910 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
39216834 TCCTATGTGC
*
39216844 ACAAATGAAAGTAGCACTTCGAT
1 ACAAATGAAAGTGGCACTTCGAT
*
39216867 ACAATTGAAATGTGGCACTTCTG-T
1 ACAAATGAAA-GTGGCACTTC-GAT
* *
39216891 GCAAATGAAAGTGACACTTC
1 ACAAATGAAAGTGGCACTTC
39216911 AATGCAATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 18 0.49
24 18 0.49
25 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (23 bp):
ACAAATGAAAGTGGCACTTCGAT
Found at i:39221099 original size:2 final size:2
Alignment explanation
Indices: 39221092--39221121 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39221082 AAAGCCAAAG
39221092 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39221122 ACACACGCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:39221213 original size:2 final size:2
Alignment explanation
Indices: 39221206--39221236 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39221196 CCTCTCAGCG
39221206 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
39221237 ACACACACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:39239523 original size:18 final size:18
Alignment explanation
Indices: 39239463--39239523 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
39239453 ACTATTATTT
*
39239463 TATTGTTAATTTTGTTAC
1 TATTGTTAATTTTGCTAC
**
39239481 TATT-TTATCAGTATTTGCTTT
1 TATTGTTA--A-T-TTTGCTAC
39239502 TATTGTTAATTTTGCTAC
1 TATTGTTAATTTTGCTAC
39239520 TATT
1 TATT
39239524 TTATGTGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 3 0.09
18 14 0.42
19 2 0.06
20 2 0.06
21 9 0.27
22 3 0.09
ACGTcount: A:0.21, C:0.08, G:0.10, T:0.61
Consensus pattern (18 bp):
TATTGTTAATTTTGCTAC
Found at i:39239669 original size:13 final size:14
Alignment explanation
Indices: 39239653--39239682 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
39239643 TAAATTTTTT
39239653 ATATAAAAAAA-TA
1 ATATAAAAAAATTA
39239666 ATATAAAAAAATTA
1 ATATAAAAAAATTA
39239680 ATA
1 ATA
39239683 CGGGCTGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATATAAAAAAATTA
Found at i:39244262 original size:23 final size:23
Alignment explanation
Indices: 39244236--39244280 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
39244226 AAGCAAAAAC
*
39244236 GAAACAGAAAAGAAAGAAAGAAA
1 GAAACAAAAAAGAAAGAAAGAAA
* **
39244259 GAAAGAAAAAAGGGAGAAAGAA
1 GAAACAAAAAAGAAAGAAAGAA
39244281 GGAGACGAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (23 bp):
GAAACAAAAAAGAAAGAAAGAAA
Done.