Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 94 of 126
Found at i:29022817 original size:12 final size:12
Alignment explanation
Indices: 29022738--29022841 Score: 63
Period size: 12 Copynumber: 8.3 Consensus size: 12
29022728 AATCCGAGTG
*
29022738 TTTTTATTTTTA
1 TTTTTATATTTA
29022750 TTTATT-TATTTA
1 TTT-TTATATTTA
*
29022762 TTTTACTTTCATGTTA
1 TTTT--TAT-AT-TTA
29022778 TTTTT-TATTTA
1 TTTTTATATTTA
*
29022789 GTTTTATATTT-
1 TTTTTATATTTA
*
29022800 TATTTATATTTA
1 TTTTTATATTTA
29022812 TTTTTATAATTCTA
1 TTTTTAT-ATT-TA
*
29022826 TTTCTAT-TTCTA
1 TTTTTATATT-TA
29022838 TTTT
1 TTTT
29022842 ATTATGCACA
Statistics
Matches: 75, Mismatches: 7, Indels: 20
0.74 0.07 0.20
Matches are distributed among these distances:
11 17 0.23
12 32 0.43
13 7 0.09
14 10 0.13
15 2 0.03
16 7 0.09
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (12 bp):
TTTTTATATTTA
Found at i:29027326 original size:41 final size:40
Alignment explanation
Indices: 29027278--29027378 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
29027268 TCGACCTTGA
** *
29027278 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
29027318 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
29027356 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
29027379 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:29029268 original size:18 final size:17
Alignment explanation
Indices: 29029245--29029295 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
29029235 TTTAGCTTTC
29029245 AAAATTATT-ATTTTAGAA
1 AAAATT-TTAATTTTA-AA
29029263 AAAATTTTAATTTTAAA
1 AAAATTTTAATTTTAAA
*
29029280 AATTATTTTAAATTTT
1 AA-AATTTT-AATTTT
29029296 GTTGTAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.21
18 17 0.59
19 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AAAATTTTAATTTTAAA
Found at i:29033779 original size:50 final size:50
Alignment explanation
Indices: 29033711--29033808 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
29033701 TCAAATATGA
** * *
29033711 TGTTTTAAATAAGTATAAATATTTATTTGAT-TTGTTTTGTTTAGATCTAG
1 TGTTTTAAATAAACATAAATATTTATTT-ATATTATTTTGTTCAGATCTAG
*
29033761 TGTTTTACATAAACATAAATATTTATTTATATTATTTTGTTCAGATCT
1 TGTTTTAAATAAACATAAATATTTATTTATATTATTTTGTTCAGATCT
29033809 TATATTTGCG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 2 0.05
50 40 0.95
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.53
Consensus pattern (50 bp):
TGTTTTAAATAAACATAAATATTTATTTATATTATTTTGTTCAGATCTAG
Found at i:29040722 original size:8 final size:9
Alignment explanation
Indices: 29040701--29040740 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
29040691 TTTTTATGAT
29040701 TTTTTAATA
1 TTTTTAATA
*
29040710 CTTTTAATA
1 TTTTTAATA
*
29040719 TTTTTTATA
1 TTTTTAATA
*
29040728 TTTTTATTA
1 TTTTTAATA
29040737 TTTT
1 TTTT
29040741 ATAGAATTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTAATA
Found at i:29040732 original size:18 final size:19
Alignment explanation
Indices: 29040699--29040740 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
29040689 AGTTTTTATG
29040699 ATTTTTTAATACTTTTAAT
1 ATTTTTTAATACTTTTAAT
* *
29040718 ATTTTTT-ATATTTTTATT
1 ATTTTTTAATACTTTTAAT
29040736 ATTTT
1 ATTTT
29040741 ATAGAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTTAATACTTTTAAT
Found at i:29040856 original size:37 final size:36
Alignment explanation
Indices: 29040815--29040904 Score: 94
Period size: 37 Copynumber: 2.5 Consensus size: 36
29040805 ATTTATTAGA
29040815 ATTTTTATAAATTTTTTAAT-TTTATATCAAATTTCAT
1 ATTTTTATAAATTTTTTAATATTTA-AT-AAATTTCAT
* * * *
29040852 ATTTTTA-ATATTGTTTAATATTTAATAATTTTTAT
1 ATTTTTATAAATTTTTTAATATTTAATAAATTTCAT
*
29040887 ATTTTTTTAGAATTTTTT
1 ATTTTTATA-AATTTTTT
29040905 CTTATTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
35 13 0.30
36 13 0.30
37 17 0.40
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (36 bp):
ATTTTTATAAATTTTTTAATATTTAATAAATTTCAT
Found at i:29040893 original size:10 final size:10
Alignment explanation
Indices: 29040880--29040927 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
29040870 TATTTAATAA
29040880 TTTTTATATT
1 TTTTTATATT
*
29040890 TTTTTAGAATT
1 TTTTTA-TATT
29040901 TTTTCT-TATT
1 TTTT-TATATT
29040911 TTTTTAT-TT
1 TTTTTATATT
29040920 TTTTTATA
1 TTTTTATA
29040928 AAATTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
9 10 0.31
10 14 0.44
11 7 0.22
12 1 0.03
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (10 bp):
TTTTTATATT
Found at i:29043176 original size:44 final size:45
Alignment explanation
Indices: 29043101--29043186 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
29043091 AAAAGTAAAA
* *
29043101 TTATATTTTTATTTTTTAAAAATGATAAAATTTTAATTTAATCTT
1 TTATATTTATATTTTTTAAAAATGATAAAATTATAATTTAATCTT
* *
29043146 TTATATTTATATTTTTATTATAAT-A-AAAATTATAATTTAAT
1 TTATATTTATATTTTT-TAAAAATGATAAAATTATAATTTAAT
29043187 TTCGATTCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 15 0.42
45 16 0.44
46 5 0.14
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (45 bp):
TTATATTTATATTTTTTAAAAATGATAAAATTATAATTTAATCTT
Found at i:29045760 original size:93 final size:93
Alignment explanation
Indices: 29045601--29045776 Score: 298
Period size: 93 Copynumber: 1.9 Consensus size: 93
29045591 ACTTAGAACA
* *
29045601 ATTCAATGGCATAGGAAAAGAGTGTCATGGCCAAATTTGAATCATTTTAGTAAATAGTACATTAA
1 ATTCAATGGCATAGGAAAAGAGTGTCATGACCAAATTTGAATCATTTTAGCAAATAGTACATTAA
29045666 CACCAATAGTAGTGAAAATTGCACTCAT
66 CACCAATAGTAGTGAAAATTGCACTCAT
* * * *
29045694 ATTCAATGGCATAGGAAAAGAGTGTGATGATCAAATTTGAATTATTTTAGCAAATAGTCCATTAA
1 ATTCAATGGCATAGGAAAAGAGTGTCATGACCAAATTTGAATCATTTTAGCAAATAGTACATTAA
29045759 CACCAATAGTAGTGAAAA
66 CACCAATAGTAGTGAAAA
29045777 GATAGGCAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (93 bp):
ATTCAATGGCATAGGAAAAGAGTGTCATGACCAAATTTGAATCATTTTAGCAAATAGTACATTAA
CACCAATAGTAGTGAAAATTGCACTCAT
Found at i:29050423 original size:14 final size:15
Alignment explanation
Indices: 29050400--29050428 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29050390 TAAATTTAAA
29050400 AAAAATTAAAAAAAT
1 AAAAATTAAAAAAAT
29050415 AAAAA-TAAAAAAAT
1 AAAAATTAAAAAAAT
29050429 TAATTACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATTAAAAAAAT
Found at i:29054277 original size:29 final size:28
Alignment explanation
Indices: 29054245--29054345 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 28
29054235 ACCCGGGGGC
29054245 AAAAA-GGTAATTTTGGTGTAATCGGGGTT
1 AAAAATGG-AATTTTGGTG-AATCGGGGTT
*** * *
29054274 AAAAATGGAATTTTAAAGATTCGGGGGT
1 AAAAATGGAATTTTGGTGAATCGGGGTT
29054302 -AAAATGGCAATTTTCGGTGAAATCGGGGTT
1 AAAAATGG-AATTTT-GGTG-AATCGGGGTT
29054332 AAAAATGGAATTTT
1 AAAAATGGAATTTT
29054346 AGAGGCTTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
27 7 0.12
28 14 0.25
29 13 0.23
30 16 0.28
31 7 0.12
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (28 bp):
AAAAATGGAATTTTGGTGAATCGGGGTT
Found at i:29054326 original size:58 final size:57
Alignment explanation
Indices: 29054238--29054346 Score: 173
Period size: 58 Copynumber: 1.9 Consensus size: 57
29054228 TATGGATACC
* *
29054238 CGGGGGCAAAAAGGTAATTTTGGTGTAATCGGGGTTAAAAATGGAATTTTAAAGATT
1 CGGGGGCAAAAAGGCAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGATT
* *
29054295 CGGGGGTAAAATGGCAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTA
1 CGGGGGCAAAAAGGCAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTA
29054347 GAGGCTTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 18 0.38
58 29 0.62
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.29
Consensus pattern (57 bp):
CGGGGGCAAAAAGGCAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGATT
Found at i:29054403 original size:30 final size:30
Alignment explanation
Indices: 29054369--29054590 Score: 255
Period size: 30 Copynumber: 7.3 Consensus size: 30
29054359 GATAAAATGG
* *
29054369 TAATTTTTGAAAAGTTTTAGGGTCGAAATA
1 TAATTTTGGAAAAGTTTTAGGGTCAAAATA
* * *
29054399 TAATTTTAGAAAATTTTTAGGGTTAAAATA
1 TAATTTTGGAAAAGTTTTAGGGTCAAAATA
* *
29054429 TAATTTTGGAAAAGTTTTGGGGTTAAAATA
1 TAATTTTGGAAAAGTTTTAGGGTCAAAATA
*
29054459 TAATTTTGGAAAAGTTTTAGGGTCAAAATG
1 TAATTTTGGAAAAGTTTTAGGGTCAAAATA
* * *
29054489 TAATTCTGGAAAAGTTTTGGGGTCAAAATG
1 TAATTTTGGAAAAGTTTTAGGGTCAAAATA
* * *
29054519 TAATTTTGGAAAAGTTTTTGGGGTTAAAATG
1 TAATTTTGGAAAAG-TTTTAGGGTCAAAATA
** * *
29054550 TAATTTCAGAAAAGTTCTGGGGTCAAAATA
1 TAATTTTGGAAAAGTTTTAGGGTCAAAATA
*
29054580 TGATTTCTGGA
1 TAATTT-TGGA
29054591 CAATTTAAGG
Statistics
Matches: 168, Mismatches: 22, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
30 139 0.83
31 29 0.17
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTTAGGGTCAAAATA
Found at i:29054404 original size:60 final size:57
Alignment explanation
Indices: 29054340--29054585 Score: 222
Period size: 60 Copynumber: 4.1 Consensus size: 57
29054330 TTAAAAATGG
* * * * *
29054340 AATTTTAGAGGCTTTAGGGGATAAAATGGTAATTTTTGAAAAGTTTTAGGGTCGAAATAT
1 AATTTTAGAAGTTTTA-GGG-TAAAAT-GTAATTTTGGAAAAGTTTTGGGGTCAAAATAT
* * *
29054400 AATTTTAGAAAATTTTTAGGGTTAAAATATAATTTTGGAAAAGTTTTGGGGTTAAAATAT
1 AATTTTAG--AAGTTTTAGGG-TAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATAT
* * *
29054460 AATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTCTGGAAAAGTTTTGGGGTCAAAATGT
1 AATTTT--AGAAGTTTTAGGGT-AAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATAT
* * ** *
29054520 AATTTTGGAAAAGTTTTTGGGGTTAAAATGTAATTTCAGAAAAGTTCTGGGGTCAAAATAT
1 AATTTT--AGAAG-TTTTAGGG-TAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATAT
*
29054581 GATTT
1 AATTT
29054586 CTGGACAATT
Statistics
Matches: 157, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.01
60 97 0.62
61 52 0.33
62 7 0.04
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (57 bp):
AATTTTAGAAGTTTTAGGGTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATAT
Found at i:29055050 original size:13 final size:13
Alignment explanation
Indices: 29055032--29055059 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29055022 TATTTTAGTT
29055032 TTTTTTAATTTCA
1 TTTTTTAATTTCA
29055045 TTTTTTAATTTCA
1 TTTTTTAATTTCA
29055058 TT
1 TT
29055060 AAAAATCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTAATTTCA
Found at i:29055811 original size:3 final size:3
Alignment explanation
Indices: 29055803--29055863 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
29055793 TATTACTAGC
* * *
29055803 ATT ATT ATT ACTA ATT ATT GTT ATT ATT ATT AAT ATT ATT A-T ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
29055848 AAT AGTT ATT AAT ATT
1 ATT A-TT ATT ATT ATT
29055864 TTAGCTACTA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.87
4 4 0.09
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:29056427 original size:18 final size:15
Alignment explanation
Indices: 29056394--29056424 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29056384 TCAGCAGATG
29056394 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
29056409 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
29056424 G
1 G
29056425 CAGCACGTGG
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:0.13, C:0.13, G:0.55, T:0.19
Consensus pattern (15 bp):
GAGCTGGTGGTGGCA
Found at i:29056638 original size:6 final size:6
Alignment explanation
Indices: 29056614--29056722 Score: 73
Period size: 6 Copynumber: 18.0 Consensus size: 6
29056604 GACATTGGGC
* * ** *
29056614 TTTAAA TTTTTAA TGTTAAA TTTAATA TTTTAA TTTTTA TTTAGA TTTAAA
1 TTTAAA -TTTAAA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
* * *
29056665 TTCAAA -TTAAA TTTAAATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
29056713 --TAAA TTTAAA
1 TTTAAA TTTAAA
29056723 ATCAATTTAA
Statistics
Matches: 82, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 47 0.57
7 19 0.23
8 4 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:29056686 original size:25 final size:25
Alignment explanation
Indices: 29056658--29056707 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
29056648 TTTTATTTAG
* *
29056658 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
29056683 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
29056708 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:29056686 original size:31 final size:31
Alignment explanation
Indices: 29056651--29056714 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
29056641 TTTTAATTTT
* *
29056651 TATTTAGATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
29056682 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
29056713 TA
1 TA
29056715 AATTTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:29056724 original size:17 final size:16
Alignment explanation
Indices: 29056652--29056722 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 16
29056642 TTTAATTTTT
*
29056652 ATTTAGATTTAAATTCAA
1 ATTTAAATTTAAA-T-AA
29056670 A-TTAAATTTAAAT--
1 ATTTAAATTTAAATAA
29056683 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
*
29056700 ATCTAAATTTAAATAA
1 ATTTAAATTTAAATAA
29056716 ATTTAAA
1 ATTTAAA
29056723 ATCAATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 4 0.09
16 13 0.28
17 19 0.41
18 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:29057114 original size:38 final size:38
Alignment explanation
Indices: 29057049--29057606 Score: 589
Period size: 38 Copynumber: 15.6 Consensus size: 38
29057039 ACGTTGTTCT
*
29057049 TACTTCAATTTC-AGAGATGAAGACGTGTTATCCACTC
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
29057086 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
* *
29057124 TACTTCAATTTCAAGGGATG-A-AC--G-T-TGCTCT-
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
*
29057155 TACTTCAATTTC--GGAGATGAAGACGTATTATCCACTC
1 TACTTCAATTTCAAGG-GATGAAGACGTGTTATCCACTC
**
29057192 TACTTCAATTTCAAGGGATGAAGGTGTGTTATCCACTC
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
* * *
29057230 TACTTCAATTTCAAGGG--GATGAC--G-T-TGCTCT-
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
*
29057261 TACTTCAATTTC--GGAGATGAAGACGTATTATCCACTC
1 TACTTCAATTTCAAGG-GATGAAGACGTGTTATCCACTC
29057298 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
* * *
29057336 TACTTCAATTTCAAGGGAT---GAC---AT-TGCTCT-
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
*
29057366 TACTTCAATTTC--GGAGATGAAGACGTATTATCCACTC
1 TACTTCAATTTCAAGG-GATGAAGACGTGTTATCCACTC
29057403 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
* **
29057441 TACTTCAATTTCAAGGGCTGAAGGTGTGTTATCCACTC
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
* * *
29057479 TACTTCAATTTCAAGGG--GATGAC--G-T-TGCTCT-
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
*
29057510 TACTTCAATTTC--GGAGATGAAGACGTATTATCCACTC
1 TACTTCAATTTCAAGG-GATGAAGACGTGTTATCCACTC
* **
29057547 TACTTCAATTTCAAGGGCTGAAGGTGTGTTATCCACTC
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
29057585 TACTTCAATTTCAAGGGGATGA
1 TACTTCAATTTCAA-GGGATGA
29057607 CATTGAGACC
Statistics
Matches: 435, Mismatches: 43, Indels: 84
0.77 0.08 0.15
Matches are distributed among these distances:
28 2 0.00
29 9 0.02
30 18 0.04
31 41 0.09
32 28 0.06
33 3 0.01
34 3 0.01
35 7 0.02
36 24 0.06
37 61 0.14
38 225 0.52
39 14 0.03
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (38 bp):
TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
Found at i:29057203 original size:106 final size:105
Alignment explanation
Indices: 29057008--29057457 Score: 801
Period size: 106 Copynumber: 4.2 Consensus size: 105
29056998 AAGACTTTGC
* * *
29057008 TATCCAACTTTACTTCAATTTCAAGAGGATGACGTTGTTCTTACTTCAATTTCAGAGATGAAGAC
1 TATCC-ACTCTACTTCAATTTCAAG-GGATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGAC
*
29057073 GTGTTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGT
64 GTATTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGT
29057115 TATCCACTCTACTTCAATTTCAAGGGATGAACGTTGCTCTTACTTCAATTTCGGAGATGAAGACG
1 TATCCACTCTACTTCAATTTCAAGGGATG-ACGTTGCTCTTACTTCAATTTCGGAGATGAAGACG
**
29057180 TATTATCCACTCTACTTCAATTTCAAGGGATGAAGGTGTGT
65 TATTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGT
29057221 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACG
1 TATCCACTCTACTTCAATTTCAA-GGGATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACG
29057286 TATTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGT
65 TATTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGT
*
29057327 TATCCACTCTACTTCAATTTCAAGGGATGACATTGCTCTTACTTCAATTTCGGAGATGAAGACGT
1 TATCCACTCTACTTCAATTTCAAGGGATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACGT
29057392 ATTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGT
66 ATTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGT
29057432 TATCCACTCTACTTCAATTTCAAGGG
1 TATCCACTCTACTTCAATTTCAAGGG
29057458 CTGAAGGTGT
Statistics
Matches: 332, Mismatches: 9, Indels: 6
0.96 0.03 0.02
Matches are distributed among these distances:
105 112 0.34
106 209 0.63
107 11 0.03
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (105 bp):
TATCCACTCTACTTCAATTTCAAGGGATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACGT
ATTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGT
Found at i:29057487 original size:249 final size:242
Alignment explanation
Indices: 29057049--29057611 Score: 828
Period size: 249 Copynumber: 2.3 Consensus size: 242
29057039 ACGTTGTTCT
*
29057049 TACTTCAATTTC-AGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGATGAAGACGT
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGAT---GAC--
* * * *
29057113 GTTATCCACTCTACTTCAATTTCAAGGGATGAACGTTGCTCTTACTTCAATTTCGGAGATGAAGA
61 -AT-TGCACTCTACTTCAATTTC-AGGGATGAACGTTCCACTTACTTCAATTTCGGAGATGAAGA
29057178 CGTATTATCCACTCTACTTCAATTTCAAGGGATGAAGGTGTGTTATCCACTCTACTTCAATTTCA
123 CGTATTATCCACTCTACTTCAATTTCAAGGGATGAAGGTGTGTTATCCACTCTACTTCAATTTCA
29057243 AGGGGATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACGTATTATCCACTC
188 AGGGGATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACGTATTATCCACTC
29057298 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGATGACATTGC
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGATGACATTGC
*
29057363 TCT-TACTTCAATTTC-GGAGATGAAGACGTATTATCCACTCTACTTCAATTTCAAGG-GATGAA
66 ACTCTACTTCAATTTCAGG-GATG-A-ACG---T-TCCACT-TACTTCAATTTC--GGAGATGAA
* *
29057425 GACGTGTTATCCACTCTACTTCAATTTCAAGGGCTGAAGGTGTGTTATCCACTCTACTTCAATTT
121 GACGTATTATCCACTCTACTTCAATTTCAAGGGATGAAGGTGTGTTATCCACTCTACTTCAATTT
29057490 CAAGGGGATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACGTATTATCCACTC
186 CAAGGGGATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACGTATTATCCACTC
* **
29057547 TACTTCAATTTCAAGGGCTGAAGGTGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTG
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAA-GGGATGACATTG
29057612 AGACCTGCAG
Statistics
Matches: 291, Mismatches: 11, Indels: 23
0.90 0.03 0.07
Matches are distributed among these distances:
240 2 0.01
241 4 0.01
242 13 0.04
243 7 0.02
244 1 0.00
246 1 0.00
247 7 0.02
248 12 0.04
249 187 0.64
250 57 0.20
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (242 bp):
TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGATGACATTGC
ACTCTACTTCAATTTCAGGGATGAACGTTCCACTTACTTCAATTTCGGAGATGAAGACGTATTAT
CCACTCTACTTCAATTTCAAGGGATGAAGGTGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
ACGTTGCTCTTACTTCAATTTCGGAGATGAAGACGTATTATCCACTC
Found at i:29057562 original size:106 final size:106
Alignment explanation
Indices: 29057403--29057607 Score: 376
Period size: 106 Copynumber: 1.9 Consensus size: 106
29057393 TTATCCACTC
*
29057403 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGCTGAAGGTGT
1 TACTTCAATTTC-AGGGATGAAGACGTATTATCCACTCTACTTCAATTTCAAGGGCTGAAGGTGT
29057468 GTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCT
65 GTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCT
29057510 TACTTCAATTTC-GGAGATGAAGACGTATTATCCACTCTACTTCAATTTCAAGGGCTGAAGGTGT
1 TACTTCAATTTCAGG-GATGAAGACGTATTATCCACTCTACTTCAATTTCAAGGGCTGAAGGTGT
29057574 GTTATCCACTCTACTTCAATTTCAAGGGGATGAC
65 GTTATCCACTCTACTTCAATTTCAAGGGGATGAC
29057608 ATTGAGACCT
Statistics
Matches: 96, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
105 2 0.02
106 82 0.85
107 12 0.12
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (106 bp):
TACTTCAATTTCAGGGATGAAGACGTATTATCCACTCTACTTCAATTTCAAGGGCTGAAGGTGTG
TTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCT
Found at i:29057569 original size:144 final size:143
Alignment explanation
Indices: 29057086--29057606 Score: 603
Period size: 144 Copynumber: 3.7 Consensus size: 143
29057076 TTATCCACTC
*
29057086 TACTTCAATTTCAAGG-GATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGATG-A-AC-
1 TACTTCAATTTC--GGAGATGAAGACGTATTATCCACTCTACTTCAATTTCAAGGGATGAAGACG
* * *
29057147 -G-T-TGCTCT-TACTTCAATTTC--GGAGATGAAGACGTATTATCCACTCTACTTCAATTTCAA
64 TGTTATCCACTCTACTTCAATTTCAAGG-GATGAAGACGTGTTATCCACTCTACTTCAATTTCAA
*
29057206 GGGATGA-AGGTGTGTTATCCACT
128 GGGATGACA--T-TG-----CTCT
* ** * * *
29057229 CTACTTCAATTTC-AAGGGGATGACG---T-TGCTCT-TACTTCAATTTC--GGAGATGAAGACG
1 -TACTTCAATTTCGGAGATGAAGACGTATTATCCACTCTACTTCAATTTCAAGG-GATGAAGACG
*
29057286 TATTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAG
64 TGTTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAG
29057351 GGATGACATTGCTCT
129 GGATGACATTGCTCT
29057366 TACTTCAATTTCGGAGATGAAGACGTATTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTG
1 TACTTCAATTTCGGAGATGAAGACGTATTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTG
* **
29057431 TTATCCACTCTACTTCAATTTCAAGGGCTGAAGGTGTGTTATCCACTCTACTTCAATTTCAAGGG
66 TTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAA-GG
*
29057496 GATGACGTTGCTCT
130 GATGACATTGCTCT
* **
29057510 TACTTCAATTTCGGAGATGAAGACGTATTATCCACTCTACTTCAATTTCAAGGGCTGAAGGTGTG
1 TACTTCAATTTCGGAGATGAAGACGTATTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTG
29057575 TTATCCACTCTACTTCAATTTCAAGGGGATGA
66 TTATCCACTCTACTTCAATTTCAA-GGGATGA
29057607 CATTGAGACC
Statistics
Matches: 329, Mismatches: 26, Indels: 43
0.83 0.07 0.11
Matches are distributed among these distances:
135 2 0.01
136 16 0.05
137 24 0.07
138 6 0.02
139 1 0.00
140 1 0.00
141 5 0.02
142 25 0.08
143 83 0.25
144 157 0.48
145 9 0.03
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (143 bp):
TACTTCAATTTCGGAGATGAAGACGTATTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTG
TTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
ATGACATTGCTCT
Found at i:29069662 original size:65 final size:65
Alignment explanation
Indices: 29069559--29069691 Score: 205
Period size: 65 Copynumber: 2.0 Consensus size: 65
29069549 CCGGGGGCAA
* *
29069559 AATGGTAATTTTGGTGTAATCGGGGTTAAAAATGGAATTTTAAAAGATTCAGGGG-TAAAATGGT
1 AATGGTAATTTTGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCAGGGGATAAAATGGT
* * *
29069623 AATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAAAGGCTTCGGGGGATAAAATGG
1 AATGGTAATTTT-GATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCAGGGGATAAAATGG
29069688 T
65 T
29069689 AAT
1 AAT
29069692 TTTTGAAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
64 12 0.19
65 38 0.61
66 12 0.19
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (65 bp):
AATGGTAATTTTGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCAGGGGATAAAATGGT
Found at i:29069722 original size:30 final size:30
Alignment explanation
Indices: 29069688--29069997 Score: 415
Period size: 30 Copynumber: 10.3 Consensus size: 30
29069678 GATAAAATGG
* *
29069688 TAATTTTTGAAAAGTTTTGGGGTCGAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
* * *
29069718 TAATTTTGGAAAAGTTATGGGGTCAACATG
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
*
29069748 T-ATTTTGGAAAAGTTTTAGGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
* *
29069777 TAATTTTGGAAAAGTTTCGGGGTTAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
*
29069807 TAATTTTGGAAAAGTTTTGGGGTTAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
* *
29069837 TAATTTTGGAAAAGTTTTAGGGTCGAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
* *
29069867 TAATTTTGGAAAAGTTTTGGGGTCGAAATG
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
* * *
29069897 TAATTTTGGAAAAGTTTTAGGGTTAAAATC
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
*
29069927 TAATTTTGGAAAAGTTTTGGGGTCAAAATG
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
** *
29069957 TAATTTCAGAAAAGTTCTGGGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
*
29069987 TGATTTCTGGA
1 TAATTT-TGGA
29069998 CAATTTAAGG
Statistics
Matches: 246, Mismatches: 32, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
29 25 0.10
30 219 0.89
31 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTTGGGGTCAAAATA
Found at i:29071215 original size:3 final size:3
Alignment explanation
Indices: 29071207--29071267 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
29071197 TATTACTAGC
* * *
29071207 ATT ATT ATT ACTA ATT ATT GTT ATT ATT ATT AAT ATT ATT A-T ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
29071252 AAT AGTT ATT AAT ATT
1 ATT A-TT ATT ATT ATT
29071268 TTAGCTACTA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.87
4 4 0.09
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:29071830 original size:18 final size:15
Alignment explanation
Indices: 29071797--29071827 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29071787 TCAGCAGATG
29071797 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
29071812 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
29071827 G
1 G
29071828 CAGCACGTGG
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:0.13, C:0.13, G:0.55, T:0.19
Consensus pattern (15 bp):
GAGCTGGTGGTGGCA
Found at i:29072040 original size:20 final size:19
Alignment explanation
Indices: 29072017--29072098 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 19
29072007 GACATTGGGC
29072017 TTTAAATTTTTAATGTTAAA
1 TTTAAATTTTTAAT-TTAAA
**
29072037 TTT-AATATTTTAATTTTTA
1 TTTAAAT-TTTTAATTTAAA
* *
29072056 TTTAAA-TTTAAATTCAAA
1 TTTAAATTTTTAATTTAAA
**
29072074 -TTAAATTTAAATATTTAAA
1 TTTAAATTTTTA-ATTTAAA
29072093 TTTAAA
1 TTTAAA
29072099 ATAAATCTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
17 5 0.10
18 12 0.24
19 15 0.31
20 17 0.35
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (19 bp):
TTTAAATTTTTAATTTAAA
Found at i:29072041 original size:6 final size:6
Alignment explanation
Indices: 29072017--29072125 Score: 82
Period size: 6 Copynumber: 18.0 Consensus size: 6
29072007 GACATTGGGC
* * **
29072017 TTTAAA TTTTTAA TGTTAAA TTTAATA TTTTAA TTTTTA TTTAAA TTTAAA
1 TTTAAA -TTTAAA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
* * *
29072068 TTCAAA -TTAAA TTTAAATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
29072116 --TAAA TTTAAA
1 TTTAAA TTTAAA
29072126 ATCAATTTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 48 0.58
7 19 0.23
8 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:29072089 original size:25 final size:25
Alignment explanation
Indices: 29072061--29072110 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
29072051 TTTTATTTAA
* *
29072061 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
29072086 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
29072111 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:29072089 original size:31 final size:31
Alignment explanation
Indices: 29072054--29072117 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
29072044 TTTTAATTTT
*
29072054 TATTTAAATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
29072085 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
29072116 TA
1 TA
29072118 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:29072104 original size:42 final size:43
Alignment explanation
Indices: 29072032--29072125 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
29072022 ATTTTTAATG
* * ** *
29072032 TTAAATTT-AATATTTTAATTTTTATTTAAATTTAAATTCAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
*
29072074 TTAAATTTAAATA-TTTAAATTTAAAATAAATCTAAATTTAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
29072116 -TAAATTTAAA
1 TTAAATTTAAA
29072126 ATCAATTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 10 0.22
42 31 0.69
43 4 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (43 bp):
TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
Found at i:29072127 original size:17 final size:16
Alignment explanation
Indices: 29072055--29072125 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
29072045 TTTAATTTTT
29072055 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAA-T-AA
29072073 A-TTAAATTTAAAT--
1 ATTTAAATTTAAATAA
29072086 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
*
29072103 ATCTAAATTTAAATAA
1 ATTTAAATTTAAATAA
29072119 ATTTAAA
1 ATTTAAA
29072126 ATCAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 4 0.09
16 13 0.28
17 20 0.43
18 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:29084950 original size:29 final size:29
Alignment explanation
Indices: 29084918--29085014 Score: 122
Period size: 30 Copynumber: 3.3 Consensus size: 29
29084908 CATTAAAATC
*
29084918 GGGTCAAATTTGAATTTTGGAAAGTTTAA
1 GGGTCAAATTTGAATTTTGAAAAGTTTAA
* * *
29084947 GGGTCAAATTTGAATTTTCAAAAAGTTCAG
1 GGGTCAAATTTGAATTTT-GAAAAGTTTAA
* *
29084977 GGGTAAAATTAGAATTTTTGAAAAGTTTAA
1 GGGTCAAATTTGAA-TTTTGAAAAGTTTAA
29085007 GGGTCAAA
1 GGGTCAAA
29085015 ACATAATTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
29 18 0.32
30 34 0.61
31 4 0.07
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (29 bp):
GGGTCAAATTTGAATTTTGAAAAGTTTAA
Found at i:29085023 original size:30 final size:30
Alignment explanation
Indices: 29084932--29085025 Score: 84
Period size: 30 Copynumber: 3.1 Consensus size: 30
29084922 CAAATTTGAA
* *
29084932 TTTTGGAAAGTTTAAGGGTC-AAATTTGAAT
1 TTTTGAAAAGTTTAAGGGTCAAAATAT-AAT
** * * *
29084962 TTTCAAAAAGTTCAGGGGT-AAAATTAGAAT
1 TTTTGAAAAGTTTAAGGGTCAAAA-TATAAT
*
29084992 TTTTGAAAAGTTTAAGGGTCAAAACATAAT
1 TTTTGAAAAGTTTAAGGGTCAAAATATAAT
29085022 TTTT
1 TTTT
29085026 AAATAAAGCA
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
30 43 0.90
31 5 0.10
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.37
Consensus pattern (30 bp):
TTTTGAAAAGTTTAAGGGTCAAAATATAAT
Found at i:29087039 original size:21 final size:21
Alignment explanation
Indices: 29087015--29087060 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
29087005 TAATCATGAT
29087015 TTATTTACTTAGTTAA-GATAA
1 TTATTTACTTA-TTAATGATAA
*
29087036 TTATTTACTTATTAATTATAA
1 TTATTTACTTATTAATGATAA
29087057 TTAT
1 TTAT
29087061 AAAACTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (21 bp):
TTATTTACTTATTAATGATAA
Found at i:29087908 original size:21 final size:20
Alignment explanation
Indices: 29087871--29087910 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
29087861 CTAGATGGCA
* *
29087871 AAATAATGAAACTAATAAAT
1 AAATAATAAAACAAATAAAT
29087891 AAATAAATAAAACAAATAAA
1 AAAT-AATAAAACAAATAAA
29087911 ATAGAGTGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (20 bp):
AAATAATAAAACAAATAAAT
Found at i:29091840 original size:14 final size:14
Alignment explanation
Indices: 29091821--29091848 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29091811 GATAATATAA
29091821 TACCAAATGTTGCT
1 TACCAAATGTTGCT
29091835 TACCAAATGTTGCT
1 TACCAAATGTTGCT
29091849 GTGCGAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (14 bp):
TACCAAATGTTGCT
Found at i:29096457 original size:24 final size:24
Alignment explanation
Indices: 29096439--29096501 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
29096429 GCAAATGAAT
29096439 AGAGTTTAATTGAAACAAAGAAAC
1 AGAGTTTAATTGAAACAAAGAAAC
**
29096463 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAATTGAAACAAAGAAAC
* *
29096487 AGAATTTAACTGAAA
1 AGAGTTTAATTGAAA
29096502 GATTATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAAGAAAC
Found at i:29098622 original size:4 final size:4
Alignment explanation
Indices: 29098613--29098638 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
29098603 GTATTAACAT
29098613 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
29098639 ACTGTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:29098845 original size:23 final size:22
Alignment explanation
Indices: 29098803--29098847 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
29098793 AATTACAAAC
*
29098803 ATAATTATTAATTATTAATATT
1 ATAATTATAAATTATTAATATT
29098825 ATAATATATAAATT-TTAAATATT
1 ATAAT-TATAAATTATT-AATATT
29098848 TTTTAAGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATTATAAATTATTAATATT
Found at i:29101027 original size:2 final size:2
Alignment explanation
Indices: 29100986--29101010 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29100976 AAACCATTTA
29100986 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29101011 AAAAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29101921 original size:23 final size:22
Alignment explanation
Indices: 29101886--29101930 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
29101876 TTGCTTAAAA
*
29101886 AATATTTAAAATTTATATATTAT
1 AATATTTAAAATTAATA-ATTAT
29101909 AATA-TTAATAATTAATAATTAT
1 AATATTTAA-AATTAATAATTAT
29101931 GTTTGTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATATTTAAAATTAATAATTAT
Found at i:29102104 original size:4 final size:4
Alignment explanation
Indices: 29102095--29102120 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
29102085 TTATAACAGT
29102095 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
29102121 ATGTTAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:29104260 original size:24 final size:24
Alignment explanation
Indices: 29104232--29104294 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
29104222 AGAAATAATC
* *
29104232 TTTCAGTTAAATTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
**
29104256 TTTCAATTAAACTCTGTTTCTTTG
1 TTTCAATTAAACTCTGTTTAATTG
29104280 TTTCAATTAAACTCT
1 TTTCAATTAAACTCT
29104295 ATTCATTTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.52
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:29104303 original size:24 final size:24
Alignment explanation
Indices: 29104253--29104303 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
29104243 TTCTGTTTAA
*
29104253 TTGTTTCAATTAAACTCTGTTTCT
1 TTGTTTCAATTAAACTCTGATTCT
29104277 TTGTTTCAATTAAACTCT-ATTCAT
1 TTGTTTCAATTAAACTCTGATTC-T
29104301 TTG
1 TTG
29104304 CTTGAGTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.53
Consensus pattern (24 bp):
TTGTTTCAATTAAACTCTGATTCT
Found at i:29106611 original size:59 final size:59
Alignment explanation
Indices: 29106505--29107107 Score: 644
Period size: 59 Copynumber: 10.3 Consensus size: 59
29106495 TGACTTCCAA
* ** *
29106505 GGGTAAAAAT-GTATTTTTTGGTGAAATTAGGGTT-AAAATGGAATTTTGGAAAGTTTAG
1 GGGT-AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTCG
* * *
29106563 GGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGG-AAGGTTCG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTCG
* * * *
29106621 AAGGT-AAATAGTAGTTTTTGGTGAAATCGAGGG-TAAAAATGGGATTTTGGAAAG-TTCG
1 -GGGTAAAATGGTAATTTTTGGTGAAATCG-GGGTTAAAAATGGAATTTTGGAAAGTTTCG
* * * * **
29106679 GAGGTAAAATGGTAATTTTTGGTTAAAATTGAGGTTAAAAATGGAATTTTAG-AAGGCTCG
1 G-GGTAAAATGGTAATTTTTGG-TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTCG
* * * *
29106739 AGGGTAAAATGGTAATTTTGGGTGAAATTGGGGTT-AAAATGGAATTTTGGAAGGCTT-G
1 -GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTCG
* *
29106797 GGGATAAAATGGTAATTTTTGGTGAAATCGGGGCTAAAAATGGAATTTTGGAAGGTTT-G
1 GGG-TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTCG
* * * *
29106856 GGGATAAAATTGTAATTTTTGGTGAACTTGGGGTTAAAAATGGAATTTTGG-AAGGTTCGG
1 GGG-TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTC-G
* * * * *
29106916 GGGTAAAATGGTAATTTTAGATGAAATCGAGGTT-AAAATGGAATTTTGGAAGGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTCG
* * *
29106974 GGGTAAAATGGT-ATTTTTTGTGAAATCGAGGTT-AAAATGGAATTTTGG-AAGGTTCG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTCG
* * *
29107030 AGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAT-GAATATTTGGAAAATTTAG
1 -GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAAT-TTTGGAAAGTTTCG
*
29107090 GGGTAAAATGGTAGTTTT
1 GGGTAAAATGGTAATTTT
29107108 ATAAAAGTTT
Statistics
Matches: 466, Mismatches: 57, Indels: 43
0.82 0.10 0.08
Matches are distributed among these distances:
56 5 0.01
57 53 0.11
58 174 0.37
59 181 0.39
60 52 0.11
61 1 0.00
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.34
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTCG
Found at i:29106639 original size:117 final size:117
Alignment explanation
Indices: 29106504--29107082 Score: 685
Period size: 117 Copynumber: 4.9 Consensus size: 117
29106494 TTGACTTCCA
* *
29106504 AGGGTAAAAAT-GTATTTTTTGGTGAAATTAGGGTTAAAATGGAATTTTGGAAAGTTTAGGGGTA
1 AGGGT-AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAATGGAATTTTGGAAAGTTTCGGGGTA
* * *
29106568 AAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAGGTTCG
65 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAGGTTCG
* * * * * *
29106621 AAGGT-AAATAGTAGTTTTTGGTGAAATCGAGGGTAAAAATGGGATTTTGGAAAG-TTCGGAGGT
1 AGGGTAAAATGGTAATTTTTGGTGAAAT-TAGGGTTAAAATGGAATTTTGGAAAGTTTCGG-GGT
* * * *
29106684 AAAATGGTAATTTTTGGTTAAAATTGAGGTTAAAAATGGAATTTTAGAAGGCTCG
64 AAAATGGTAATTTTTGG-TGAAATCGAGGTTAAAAATGGAATTTTGGAAGGTTCG
* * * *
29106739 AGGGTAAAATGGTAATTTTGGGTGAAATTGGGGTTAAAATGGAATTTTGGAAGGCTT-GGGGATA
1 AGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAATGGAATTTTGGAAAGTTTCGGGG-TA
* * *
29106803 AAATGGTAATTTTTGGTGAAATCGGGGCTAAAAATGGAATTTTGGAAGGTTTG
65 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAGGTTCG
* * * *
29106856 -GGGATAAAATTGTAATTTTTGGTGAACTTGGGGTTAAAAATGGAATTTTGG-AAGGTTCGGGGG
1 AGGG-TAAAATGGTAATTTTTGGTGAAATTAGGGTT-AAAATGGAATTTTGGAAAGTTTC-GGGG
* * *
29106919 TAAAATGGTAATTTTAGATGAAATCGAGGTT-AAAATGGAATTTTGGAAGGTTTG
63 TAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAGGTTCG
* * * *
29106973 GGGGTAAAATGGT-ATTTTTTGTGAAA-TCGAGGTTAAAATGGAATTTTGG-AAGGTTCGAGGGT
1 AGGGTAAAATGGTAATTTTTGGTGAAATTAG-GGTTAAAATGGAATTTTGGAAAGTTTCG-GGGT
29107035 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAT-GAATATTTGGAA
64 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAAT-TTTGGAA
29107083 AATTTAGGGG
Statistics
Matches: 404, Mismatches: 42, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
114 1 0.00
115 64 0.16
116 50 0.12
117 142 0.35
118 122 0.30
119 25 0.06
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (117 bp):
AGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAATGGAATTTTGGAAAGTTTCGGGGTAA
AATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAGGTTCG
Found at i:29107727 original size:21 final size:21
Alignment explanation
Indices: 29107693--29107739 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
29107683 CTATTTCTCC
29107693 TTCTTT-TCTTTTGTTCTTTA
1 TTCTTTATCTTTTGTTCTTTA
*
29107713 TTCTTTATTTTTTGTTCTTTA
1 TTCTTTATCTTTTGTTCTTTA
29107734 TT-TTTA
1 TTCTTTA
29107740 AAACCTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.77
Consensus pattern (21 bp):
TTCTTTATCTTTTGTTCTTTA
Found at i:29108904 original size:11 final size:11
Alignment explanation
Indices: 29108880--29108921 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
29108870 AATGTATTTA
*
29108880 AATTT-AAATA
1 AATTTAAAATT
29108890 AATTTAAAATT
1 AATTTAAAATT
* *
29108901 AATTCAAACTT
1 AATTTAAAATT
29108912 AATTTAAAAT
1 AATTTAAAAT
29108922 CCAAGTTGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:29109771 original size:200 final size:200
Alignment explanation
Indices: 29109300--29110069 Score: 1251
Period size: 200 Copynumber: 3.9 Consensus size: 200
29109290 CAATCATCTG
29109300 TTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCA
1 TTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCA
* ** **
29109365 GGAAGCTAA-CATTTTATTGCTTCGACTTGCTTCTCAGTACCTCATCAGGAAGATGGGTTCGAAG
66 GGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCCGGGTTCGAAG
* * *
29109429 ATTTGCTCGCGTTGAGCGTTGAGTTGGTATTCTTCTC--TATATCATCAGGAAGATGA-TCGTCT
131 ATTTGCTCGCGTTGAGCGCTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACT-GCCT
29109491 CGCTTA
195 CGCTTA
* * *
29109497 TTTCAATTCGCTTCTCTGGATCTCCTCAGGAAGACAAATTTGGTCCACTTCTCTGTATCTCATCA
1 TTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCA
* *
29109562 GGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAG
66 GGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCCGGGTTCGAAG
* * *
29109627 ATTTGCTCGCATTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCCTCAGGAAGATGACTGCCTC
131 ATTTGCTCGCGTTGAGCGCTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTC
*
29109692 GCTTG
196 GCTTA
*
29109697 TTTTAATTCGCTTCTCTGGATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCA
1 TTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCA
* *
29109762 GGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAATGTCTCATCAGGAAGCCGGGTTCGAAG
66 GGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCCGGGTTCGAAG
* * **
29109827 ATTTGCTCGCGTTGAGCGCTGAGTTGGTATTCTTCTTTGTATCTCATCAAGAAGATGACCACCTC
131 ATTTGCTCGCGTTGAGCGCTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTC
29109892 GCTTA
196 GCTTA
29109897 TTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCA
1 TTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCA
*
29109962 GGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCCGGGTTCGAAT
66 GGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCCGGGTTCGAAG
* * *
29110027 ATTTGCTCACGTTGAGTGCTGAGTTGGTATTCTTCTCTATATC
131 ATTTGCTCGCGTTGAGCGCTGAGTTGGTATTCTTCTCTGTATC
29110070 AAGAAGATGA
Statistics
Matches: 532, Mismatches: 37, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
197 71 0.13
198 86 0.16
200 374 0.70
201 1 0.00
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36
Consensus pattern (200 bp):
TTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCA
GGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCCGGGTTCGAAG
ATTTGCTCGCGTTGAGCGCTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTC
GCTTA
Found at i:29122130 original size:59 final size:59
Alignment explanation
Indices: 29122064--29122498 Score: 486
Period size: 59 Copynumber: 7.4 Consensus size: 59
29122054 TTGACTTTCG
** * * * *
29122064 GGGGTAAAAAAGTAATTTTTGGTCAAATTGGGGTCAAAAATAGAATTTTAGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTA
* * * *
29122123 GGGGTAAAATGGTAATTTTTGGTGAAAT--GGGTCAAAAATGGGATTTTGGTAGGTTCGA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTT-TA
* * * *
29122181 GTGG-AAAATAGTAATTTTTGGTGAAATCCAGGGT-AAAAAT-GAGATTTTGGAAAGTTCGA
1 GGGGTAAAATGGTAATTTTTGGTGAAAT-CGGGGTCAAAAATGGA-ATTTTGGAAAGTT-TA
* * * * **
29122240 GGGGTAAAATGGTAATTTTTGGGTGAAATCGAGGTTAAAAATAGAATTTTGGAAGGTTCC
1 GGGGTAAAATGGTAATTTTT-GGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTA
* * * * *
29122300 GGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAAATTTGGAAGGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTA
* * *
29122359 GGGGTAAAATAGTAATTTTTGGTGAAATCGGGGTCAAAAATGAAATTTT-GAAAGGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAA-GTTTA
* *
29122418 GGGGTAAAATGGTATTTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTA
* *
29122477 GTGGTAAAATGGTAAGTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
29122499 GGTCAAAATG
Statistics
Matches: 323, Mismatches: 42, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
57 44 0.14
58 8 0.02
59 198 0.61
60 45 0.14
61 26 0.08
62 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTA
Found at i:29122258 original size:30 final size:30
Alignment explanation
Indices: 29122224--29122498 Score: 90
Period size: 30 Copynumber: 9.2 Consensus size: 30
29122214 TAAAAATGAG
29122224 ATTTTGGAAAGTTCGAGGGGTAAAATGGTA
1 ATTTTGGAAAGTTCGAGGGGTAAAATGGTA
* *
29122254 ATTTTTGGGTGAAA--TCGA-GGTTAAAAATAG-A
1 A-TTTT--G-GAAAGTTCGAGGGGT-AAAATGGTA
* *
29122285 ATTTTGGAAGGTTC-CGGGGTAAAATGGTA
1 ATTTTGGAAAGTTCGAGGGGTAAAATGGTA
*
29122314 ATTTTGGGTGAAA--TCGA-GGTTAAAAATGG-A
1 ATTTT--G-GAAAGTTCGAGGGGT-AAAATGGTA
* * * *
29122344 AATTTGGAAGGTT-TAGGGGTAAAATAGTA
1 ATTTTGGAAAGTTCGAGGGGTAAAATGGTA
*
29122373 ATTTTTGGTGAAA--TC--GGGGTCAAAAAT-GAA
1 A-TTTT-G-GAAAGTTCGAGGGGT--AAAATGGTA
29122403 ATTTT-GAAAGGTTC-AGGGGTAAAATGGTA
1 ATTTTGGAAA-GTTCGAGGGGTAAAATGGTA
* *
29122432 TTTTTTGGTGAAA--TCG-GGGTTAAAAATGG-A
1 -ATTTT-G-GAAAGTTCGAGGGGT-AAAATGGTA
* *
29122462 ATTTTGGAAAGTT-TAGTGGTAAAATGGTA
1 ATTTTGGAAAGTTCGAGGGGTAAAATGGTA
29122491 AGTTTTGG
1 A-TTTTGG
29122499 GGTCAAAATG
Statistics
Matches: 181, Mismatches: 24, Indels: 80
0.64 0.08 0.28
Matches are distributed among these distances:
26 4 0.02
27 10 0.06
28 28 0.15
29 40 0.22
30 44 0.24
31 30 0.17
32 16 0.09
33 5 0.03
34 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (30 bp):
ATTTTGGAAAGTTCGAGGGGTAAAATGGTA
Found at i:29122424 original size:118 final size:118
Alignment explanation
Indices: 29122064--29122498 Score: 538
Period size: 118 Copynumber: 3.7 Consensus size: 118
29122054 TTGACTTTCG
* * * * * * *
29122064 GGGGTAAAAAAGTAATTTTTGGTCAAATTGGGGTCAAAAATAGAATTTTAGAAAGTTTAGGGGTA
1 GGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
** *
29122129 AAATGGTAATTTTTGGTGAAAT--GGGTCAAAAATGGGATTTTGGTAGGTTCGA
66 AAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGAAATTTTGGAAGGTTC-A
* * * *
29122181 GTGG-AAAATAGTAATTTTTGGTGAAATCCAGGGTAAAAAT-GAGATTTTGGAAAGTTCGAGGGG
1 GGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTTAAAAATGGA-ATTTTGGAAAGTT-TAGGGG
* * *
29122244 TAAAATGGTAATTTTTGGGTGAAATCGAGGTTAAAAAT-AGAATTTTGGAAGGTTCC
64 TAAAATGGTAATTTTT-GGTGAAATCGGGGTCAAAAATGA-AATTTTGGAAGGTTCA
* * * *
29122300 GGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAAATTTGGAAGGTTTAGGGGTA
1 GGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
* *
29122365 AAATAGTAATTTTTGGTGAAATCGGGGTCAAAAATGAAATTTTGAAAGGTTCA
66 AAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGAAATTTTGGAAGGTTCA
* * * *
29122418 GGGGTAAAATGGTATTTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGTGGTA
1 GGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
*
29122483 AAATGGTAAGTTTTGG
66 AAATGGTAATTTTTGG
29122499 GGTCAAAATG
Statistics
Matches: 272, Mismatches: 37, Indels: 17
0.83 0.11 0.05
Matches are distributed among these distances:
115 2 0.01
116 41 0.15
117 24 0.09
118 114 0.42
119 24 0.09
120 65 0.24
121 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (118 bp):
GGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
AAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGAAATTTTGGAAGGTTCA
Found at i:29122444 original size:177 final size:176
Alignment explanation
Indices: 29122060--29122499 Score: 575
Period size: 177 Copynumber: 2.5 Consensus size: 176
29122050 ATTTTTGACT
** * * * * *
29122060 TTCG-GGGGTAAAAAAGTAATTTTTGGTCAAATTGGGGTCAAAAATAGAATTTTAGAAAGTTTAG
1 TTCGAGGGGTAAAATGGTATTTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTAG
* * * * *
29122124 GGGTAAAATGGTAATTTTTGGTGAAATGGGTCAAAAATGGGATTTTGGTAGGTTCGAGTGGAAAA
66 GGGTAAAATGGTAATTTTGGGTGAAATGGGTCAAAAATGGAAATTTGGAAGGTTCGAGGGGAAAA
*
29122189 TAGTAATTTTTGGTGAAATCCAGGGTAAAAATGAGATTTTGGAAAG
131 TAGTAATTTTTGGTGAAATCCAGGGTAAAAATGAAATTTTGGAAAG
* * * **
29122235 TTCGAGGGGTAAAATGGTAATTTTTGGGTGAAATCGAGGTTAAAAATAGAATTTTGGAAGGTTCC
1 TTCGAGGGGTAAAATGGT-ATTTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTA
* *
29122300 GGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAAATTTGGAAGGTT-TAGGGGT
65 GGGGTAAAATGGTAATTTTGGGTGAAAT-G-GGTCAAAAATGGAAATTTGGAAGGTTCGAGGGG-
*
29122364 AAAATAGTAATTTTTGGTGAAAT-CGGGGTCAAAAATGAAATTTT-GAAAGG
127 AAAATAGTAATTTTTGGTGAAATCCAGGGT-AAAAATGAAATTTTGGAAA-G
*
29122414 TTC-AGGGGTAAAATGGTATTTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
1 TTCGAGGGGTAAAATGGTATTTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTAG
*
29122478 TGGTAAAATGGTAAGTTTTGGG
66 GGGTAAAATGGTAA-TTTTGGG
29122500 GTCAAAATGT
Statistics
Matches: 229, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
175 4 0.02
176 11 0.05
177 117 0.51
178 35 0.15
179 62 0.27
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (176 bp):
TTCGAGGGGTAAAATGGTATTTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTAG
GGGTAAAATGGTAATTTTGGGTGAAATGGGTCAAAAATGGAAATTTGGAAGGTTCGAGGGGAAAA
TAGTAATTTTTGGTGAAATCCAGGGTAAAAATGAAATTTTGGAAAG
Found at i:29122466 original size:29 final size:28
Alignment explanation
Indices: 29122196--29122468 Score: 93
Period size: 29 Copynumber: 9.2 Consensus size: 28
29122186 AAATAGTAAT
*
29122196 TTTTGGTGAAATCCAGGGTAAAAAT-GAGA
1 TTTTGGTGAAAT-CGGGGTAAAAATGGA-A
29122225 TTTT-G-GAAAGTTCGAGGGGT-AAAATGGTAA
1 TTTTGGTGAAA--TC--GGGGTAAAAATGG-AA
* *
29122255 TTTTTGGGTGAAATCGAGGTTAAAAATAGAA
1 -TTTT-GGTGAAATCG-GGGTAAAAATGGAA
*
29122286 TTTT-G-GAAGGTTCCGGGGT-AAAATGGTAA
1 TTTTGGTGAA--AT-CGGGGTAAAAATGG-AA
*
29122315 TTTTGGGTGAAATCGAGGTTAAAAATGGAA
1 TTTT-GGTGAAATCG-GGGTAAAAATGGAA
* * *** * *
29122345 ATTTGGAAGGTTTAGGGGT-AAAATAGTAA
1 TTTTGG-TGAAATCGGGGTAAAAAT-GGAA
29122374 TTTTTGGTGAAATCGGGGTCAAAAAT-GAA
1 -TTTTGGTGAAATCGGGGT-AAAAATGGAA
* *
29122403 ATTT--TGAAAGGTTCAGGGGT-AAAATGGTATT
1 TTTTGGTGAAA---TC-GGGGTAAAAATGG-A-A
29122434 TTTTGGTGAAATCGGGGTTAAAAATGGAA
1 TTTTGGTGAAATCGGGG-TAAAAATGGAA
29122463 TTTTGG
1 TTTTGG
29122469 AAAGTTTAGT
Statistics
Matches: 180, Mismatches: 27, Indels: 74
0.64 0.10 0.26
Matches are distributed among these distances:
26 5 0.03
27 7 0.04
28 22 0.12
29 52 0.29
30 40 0.22
31 33 0.18
32 11 0.06
33 6 0.03
34 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (28 bp):
TTTTGGTGAAATCGGGGTAAAAATGGAA
Found at i:29123128 original size:21 final size:21
Alignment explanation
Indices: 29123094--29123140 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
29123084 CTATTTCTCC
29123094 TTCTTT-TCTTTTGTTCTTTA
1 TTCTTTATCTTTTGTTCTTTA
*
29123114 TTCTTTATTTTTTGTTCTTTA
1 TTCTTTATCTTTTGTTCTTTA
29123135 TT-TTTA
1 TTCTTTA
29123141 AAACCTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.77
Consensus pattern (21 bp):
TTCTTTATCTTTTGTTCTTTA
Found at i:29123556 original size:120 final size:120
Alignment explanation
Indices: 29123343--29123584 Score: 457
Period size: 120 Copynumber: 2.0 Consensus size: 120
29123333 ACAACGAGGC
* *
29123343 TTCCGCGACTGTGGATGGCGGCTCTGGGGAACTCCGGCGTGCTTCGGCGATGGCGACTAGGGAAG
1 TTCCGCGACTATGGATGGCGGCTCTGGGAAACTCCGGCGTGCTTCGGCGATGGCGACTAGGGAAG
29123408 GGTCTTTTTTTGTCCCTTCGACTTTCTTTTTTCTTTTTTTTATATTTAATAATTA
66 GGTCTTTTTTTGTCCCTTCGACTTTCTTTTTTCTTTTTTTTATATTTAATAATTA
*
29123463 TTCCGCGACTATGGATGGCGGCTCTGGGAAACTCCGGCGTGCTTCGGCTATGGCGACTAGGGAAG
1 TTCCGCGACTATGGATGGCGGCTCTGGGAAACTCCGGCGTGCTTCGGCGATGGCGACTAGGGAAG
29123528 GGTCTTTTTTTGTCCCTTCGACTTTCTTTTTTCTTTTTTTTATATTTAATAATTA
66 GGTCTTTTTTTGTCCCTTCGACTTTCTTTTTTCTTTTTTTTATATTTAATAATTA
29123583 TT
1 TT
29123585 ATTATAATAT
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (120 bp):
TTCCGCGACTATGGATGGCGGCTCTGGGAAACTCCGGCGTGCTTCGGCGATGGCGACTAGGGAAG
GGTCTTTTTTTGTCCCTTCGACTTTCTTTTTTCTTTTTTTTATATTTAATAATTA
Found at i:29124415 original size:17 final size:17
Alignment explanation
Indices: 29124395--29124457 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 17
29124385 TTTTAAATGT
29124395 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
29124412 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
* **
29124428 ATTTAAAATTAATTCAA
1 ATTTAAATTTAAAACAA
*
29124445 ACTT-AATTTAAAA
1 ATTTAAATTTAAAA
29124458 TCCAAGTTGG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:29124441 original size:27 final size:27
Alignment explanation
Indices: 29124379--29124450 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
29124369 TTTAAGTTTC
* * **
29124379 AAATTATTTTAAATGTATTTAAATTTA
1 AAATTAATTTAAATTTAAATAAATTTA
**
29124406 AAACAAATTTAAATTTAAATAAATTTA
1 AAATTAATTTAAATTTAAATAAATTTA
* *
29124433 AAATTAATTCAAACTTAA
1 AAATTAATTTAAATTTAA
29124451 TTTAAAATCC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (27 bp):
AAATTAATTTAAATTTAAATAAATTTA
Found at i:29127465 original size:14 final size:14
Alignment explanation
Indices: 29127446--29127473 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29127436 CTTTTCGCAC
29127446 AGCAACATTTGGTA
1 AGCAACATTTGGTA
29127460 AGCAACATTTGGTA
1 AGCAACATTTGGTA
29127474 TTATATTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
AGCAACATTTGGTA
Found at i:29129554 original size:24 final size:22
Alignment explanation
Indices: 29129501--29129554 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
29129491 CCCATCAATT
*
29129501 TAACTAAATAAATTATTAAAAA
1 TAACTAAATAAAATATTAAAAA
*
29129523 T-TCATAAATATAGAATATTAAAAA
1 TAAC-TAAATA-A-AATATTAAAAA
29129547 TAACTAAA
1 TAACTAAA
29129555 AACTATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
21 1 0.04
22 7 0.28
23 1 0.04
24 15 0.60
25 1 0.04
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (22 bp):
TAACTAAATAAAATATTAAAAA
Found at i:29130524 original size:21 final size:23
Alignment explanation
Indices: 29130500--29130542 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
29130490 AATGTTTTTT
29130500 AATAATTTT-AT-ATTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
29130521 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
29130543 TTATTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Found at i:29131062 original size:27 final size:27
Alignment explanation
Indices: 29131015--29131083 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
29131005 GCAATTTATA
* *
29131015 ATTTGAATATTTATTATTATTATTATTT
1 ATTT-AATGTTTACTATTATTATTATTT
29131043 ATTT-ATGTTTACTATGTATTATTATTT
1 ATTTAATGTTTACTAT-TATTATTATTT
* *
29131070 TTTTAATTTTTACT
1 ATTTAATGTTTACT
29131084 TTTAAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 9 0.26
27 14 0.40
28 12 0.34
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (27 bp):
ATTTAATGTTTACTATTATTATTATTT
Found at i:29136137 original size:239 final size:239
Alignment explanation
Indices: 29135711--29136191 Score: 890
Period size: 239 Copynumber: 2.0 Consensus size: 239
29135701 TGACTTTAAC
* * *
29135711 ATCTCATCATGGTTGGATTCTACGACAAATTGACATCAATAATGCTTTCCTAAAGGGAGAATTAT
1 ATCTCACCATGGTTGGATTCTACGACAAATTGACATCAACAATGCTCTCCTAAAGGGAGAATTAT
*
29135776 CCGAAGACATCTACATGGATCAACCTCCGGGTTTCGAACAATATTGTTATGATGGCAATGTCCTT
66 CCGAAGACATCTACATGGATCAACCTCCGGGTTTCGAACAATATTGTTATGATGGCAAGGTCCTT
*
29135841 GTTTGCAAGCTTCACAAAGTCCTATATGGCTTGCGTCAAGCACCAAGGAATTGGTTTTACAAGCT
131 GTTTGCAAGCTTCACAAAGCCCTATATGGCTTGCGTCAAGCACCAAGGAATTGGTTTTACAAGCT
*
29135906 TCAGCAGTTCCTTCATACCATTGGCTTCAGCTCCTTTAAGGCAA
196 TCAGCAGTTCCTTCATACCATTGGCTTCAGCTCCTCTAAGGCAA
*
29135950 ATCTCACCATGGTTGGATTCTACGATAAATTGACATCAACAATGCTCTCCTAAAGGGAGAATTAT
1 ATCTCACCATGGTTGGATTCTACGACAAATTGACATCAACAATGCTCTCCTAAAGGGAGAATTAT
29136015 CCGAAGACATCTACATGGATCAACCTCCGGGTTTCGAACAATATTGTTATGATGGCAAGGTCCTT
66 CCGAAGACATCTACATGGATCAACCTCCGGGTTTCGAACAATATTGTTATGATGGCAAGGTCCTT
29136080 GTTTGCAAGCTTCACAAAGCCCTATATGGCTTGCGTCAAGCACCAAGGAATTGGTTTTACAAGCT
131 GTTTGCAAGCTTCACAAAGCCCTATATGGCTTGCGTCAAGCACCAAGGAATTGGTTTTACAAGCT
*
29136145 TCAGCAGTTCCTTCATACCATTGGTTTCAGCTCCTCTAAGGCAA
196 TCAGCAGTTCCTTCATACCATTGGCTTCAGCTCCTCTAAGGCAA
29136189 ATC
1 ATC
29136192 CCTCATTGTT
Statistics
Matches: 234, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
239 234 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (239 bp):
ATCTCACCATGGTTGGATTCTACGACAAATTGACATCAACAATGCTCTCCTAAAGGGAGAATTAT
CCGAAGACATCTACATGGATCAACCTCCGGGTTTCGAACAATATTGTTATGATGGCAAGGTCCTT
GTTTGCAAGCTTCACAAAGCCCTATATGGCTTGCGTCAAGCACCAAGGAATTGGTTTTACAAGCT
TCAGCAGTTCCTTCATACCATTGGCTTCAGCTCCTCTAAGGCAA
Found at i:29165072 original size:6 final size:6
Alignment explanation
Indices: 29165063--29165088 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29165053 ATTATTATTA
29165063 TTATGT TTATGT TTATGT TTATGT TT
1 TTATGT TTATGT TTATGT TTATGT TT
29165089 TACTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTATGT
Found at i:29166161 original size:31 final size:31
Alignment explanation
Indices: 29166126--29166188 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
29166116 AACAAATCGA
* *
29166126 TGACTTAAAT-AAAATTTTTTGAATAATTCAG
1 TGACTTAAATGAAAA-CTTTAGAATAATTCAG
*
29166157 TGACTTAAATGAAAACTTTAGAGTAATTCAG
1 TGACTTAAATGAAAACTTTAGAATAATTCAG
29166188 T
1 T
29166189 AACCGTTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTAGAATAATTCAG
Found at i:29166803 original size:3 final size:3
Alignment explanation
Indices: 29166795--29166830 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
29166785 AGGGATTTTT
29166795 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
29166831 TGAATGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29168249 original size:17 final size:17
Alignment explanation
Indices: 29168200--29168247 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
29168190 GAGATTATTT
* *
29168200 TATTTAATTCATTTGATA
1 TATTTAAAT-ATTTTATA
29168218 TATTTAAATATTTTATA
1 TATTTAAATATTTTATA
29168235 TA-TTAAATATTTT
1 TATTTAAATATTTT
29168248 TAAAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.39
17 9 0.32
18 8 0.29
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTAAATATTTTATA
Found at i:29170228 original size:6 final size:6
Alignment explanation
Indices: 29170217--29170253 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
29170207 TTTCAGCCGG
29170217 CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC C
1 CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC C
29170254 GCAGCCGCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.16
Consensus pattern (6 bp):
CTGAGC
Found at i:29170697 original size:6 final size:6
Alignment explanation
Indices: 29170686--29170732 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
29170676 GGCCATTAAA
*
29170686 TATGTT TATGTT TATGTT TATGTT TATGTT CT-TATT TATGTT TATGT
1 TATGTT TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT TATGT
29170733 ATGCAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 1 0.03
6 35 0.95
7 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:29170861 original size:26 final size:26
Alignment explanation
Indices: 29170805--29170881 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
29170795 TGCTAAACCT
*
29170805 AATTAAATAAATTCAAACATAAAAAT
1 AATTAAATAAATTCAAACATAAAAAG
* ** *
29170831 TATTAAATAAATTCAAATTTAAATAG
1 AATTAAATAAATTCAAACATAAAAAG
* *
29170857 AATTAATTCCAAATTCAATCATAAA
1 AATTAAAT--AAATTCAAACATAAA
29170882 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.32
Consensus pattern (26 bp):
AATTAAATAAATTCAAACATAAAAAG
Found at i:29173724 original size:25 final size:25
Alignment explanation
Indices: 29173690--29173739 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
29173680 TTTGCTTCCT
29173690 TTCCTTCTTCAAAAATTTACTGTTA
1 TTCCTTCTTCAAAAATTTACTGTTA
29173715 TTCCTTCTTCAAAAATTTACTGTTA
1 TTCCTTCTTCAAAAATTTACTGTTA
29173740 AACAGATCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.04, T:0.48
Consensus pattern (25 bp):
TTCCTTCTTCAAAAATTTACTGTTA
Found at i:29174013 original size:58 final size:60
Alignment explanation
Indices: 29173881--29174024 Score: 142
Period size: 58 Copynumber: 2.5 Consensus size: 60
29173871 TGTATTATTT
*
29173881 TTTATATTTAAATTTTTCTTATATTATTATTGTAAAAATTTGGAGATTATTATTATTGTGATA
1 TTTA-ATTT-AATTTTT-TTATATTATTATTGTAAAAATTTGGAGATTATTATTATTGTAATA
** * *
29173944 AATAA-AT-ATTTTTTTATATTATTTATT-TAAAAATATT-GAG-TTATTCTTATT-TAATA
1 TTTAATTTAATTTTTTTATATTA-TTATTGTAAAAAT-TTGGAGATTATTATTATTGTAATA
29174000 TTTAATTTAATTTTTTTA-ATT-TTAT
1 TTTAATTTAATTTTTTTATATTATTAT
29174025 AATATTTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
55 4 0.06
56 7 0.10
57 14 0.20
58 27 0.39
59 13 0.19
61 1 0.01
62 1 0.01
63 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (60 bp):
TTTAATTTAATTTTTTTATATTATTATTGTAAAAATTTGGAGATTATTATTATTGTAATA
Found at i:29174209 original size:27 final size:27
Alignment explanation
Indices: 29174179--29174241 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
29174169 CTTGATAGAA
* *
29174179 AGGCACCATTGGTGCCTCCTGACAGGT
1 AGGCACCACTGGTGCCGCCTGACAGGT
*
29174206 AGGCACCACTGGTGCCGCCTGTCAGGT
1 AGGCACCACTGGTGCCGCCTGACAGGT
29174233 AGGCACCAC
1 AGGCACCAC
29174242 CCATTTATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.19, C:0.33, G:0.30, T:0.17
Consensus pattern (27 bp):
AGGCACCACTGGTGCCGCCTGACAGGT
Found at i:29180348 original size:23 final size:23
Alignment explanation
Indices: 29180322--29180398 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
29180312 TCTGTTTGAT
29180322 CTTTGTGGCGAATTTTAATTAGC
1 CTTTGTGGCGAATTTTAATTAGC
* *
29180345 CTTTGTGGC-ACATTCTATTTAGC
1 CTTTGTGGCGA-ATTTTAATTAGC
* * *
29180368 CTTTGTGACGAATTTTGATTAGT
1 CTTTGTGGCGAATTTTAATTAGC
29180391 CTTTGTGG
1 CTTTGTGG
29180399 TGCATTTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.02
23 42 0.95
24 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.45
Consensus pattern (23 bp):
CTTTGTGGCGAATTTTAATTAGC
Found at i:29180395 original size:46 final size:46
Alignment explanation
Indices: 29180286--29180398 Score: 138
Period size: 46 Copynumber: 2.5 Consensus size: 46
29180276 CAGTTGTAGA
* * * * * *
29180286 AATTCTAATTAACCTTTATGGCACATTCTGTTTGATCTTTGTGGCG
1 AATTTTAATTAGCCTTTGTGGCACATTCTATTTGACCTTTGTGACG
29180332 AATTTTAATTAGCCTTTGTGGCACATTCTATTT-AGCCTTTGTGACG
1 AATTTTAATTAGCCTTTGTGGCACATTCTATTTGA-CCTTTGTGACG
* *
29180378 AATTTTGATTAGTCTTTGTGG
1 AATTTTAATTAGCCTTTGTGG
29180399 TGCATTTTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 1 0.02
46 57 0.98
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (46 bp):
AATTTTAATTAGCCTTTGTGGCACATTCTATTTGACCTTTGTGACG
Found at i:29180405 original size:23 final size:23
Alignment explanation
Indices: 29180322--29180424 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 23
29180312 TCTGTTTGAT
*
29180322 CTTTGTGGCGAATTTTAATTAGC
1 CTTTGTGGCGAATTTTGATTAGC
*
29180345 CTTTGTGGC-ACATTCT-ATTTAGC
1 CTTTGTGGCGA-ATTTTGA-TTAGC
* *
29180368 CTTTGTGACGAATTTTGATTAGT
1 CTTTGTGGCGAATTTTGATTAGC
* *
29180391 CTTTGTGGTGCATTTTGTATGCT-GC
1 CTTTGTGGCGAATTTTG-AT--TAGC
29180416 CTTTGTGGC
1 CTTTGTGGC
29180425 ATATTCTATT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
22 2 0.03
23 48 0.75
24 4 0.06
25 9 0.14
26 1 0.02
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.46
Consensus pattern (23 bp):
CTTTGTGGCGAATTTTGATTAGC
Found at i:29181074 original size:19 final size:19
Alignment explanation
Indices: 29181048--29181096 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
29181038 TATTTTATAT
29181048 TATG-ATTTAATATTTAAGA
1 TATGTATTTAATATTTAA-A
*
29181067 TAT-TATTTATTATTTAAA
1 TATGTATTTAATATTTAAA
*
29181085 TTTGTATTTAAT
1 TATGTATTTAAT
29181097 TTATGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (19 bp):
TATGTATTTAATATTTAAA
Found at i:29181447 original size:11 final size:11
Alignment explanation
Indices: 29181427--29181501 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
29181417 AAGCCTCTCA
*
29181427 TCTTTCCTTTC
1 TCTTTTCTTTC
*
29181438 TCTTTTCTTTT
1 TCTTTTCTTTC
*
29181449 TCTCATTCATTTC
1 TCT-TTTC-TTTC
29181462 T-TATTTCTTTC
1 TCT-TTTCTTTC
*
29181473 TCTTTTCTTTTT
1 TCTTTTC-TTTC
* *
29181485 TATTTTCTTCC
1 TCTTTTCTTTC
29181496 TCTTTT
1 TCTTTT
29181502 AATCACACTT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
11 28 0.57
12 17 0.35
13 4 0.08
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:29181906 original size:21 final size:21
Alignment explanation
Indices: 29181882--29181940 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
29181872 CCCAAATCCT
29181882 ATTTAAACCAAACCCATATTC
1 ATTTAAACCAAACCCATATTC
*
29181903 ATTTAAACCAAACCCAAATTC
1 ATTTAAACCAAACCCATATTC
29181924 ATTTAAACCAAACCCAT
1 ATTTAAACCAAACCCAT
29181941 TTGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (21 bp):
ATTTAAACCAAACCCATATTC
Found at i:29181941 original size:15 final size:15
Alignment explanation
Indices: 29181923--29181952 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29181913 AACCCAAATT
29181923 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
29181938 CATTTGAACCAAACC
1 CATTTAAACCAAACC
29181953 AAATGAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:29182032 original size:21 final size:21
Alignment explanation
Indices: 29181989--29182066 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 21
29181979 TGTCAAACCA
** *
29181989 TTGACCGA-CGTTGACTAGCG
1 TTGACCGACCGTTGACCGGTG
29182009 TTGACCGACCGTTGACCGGTG
1 TTGACCGACCGTTGACCGGTG
**
29182030 TTGATTGACCGTTGACCGGTG
1 TTGACCGACCGTTGACCGGTG
**
29182051 TTGATTGACCGTTGAC
1 TTGACCGACCGTTGAC
29182067 TTTGATTGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
20 8 0.15
21 44 0.85
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (21 bp):
TTGACCGACCGTTGACCGGTG
Found at i:29182080 original size:20 final size:20
Alignment explanation
Indices: 29182055--29182109 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
29182045 CCGGTGTTGA
*
29182055 TTGACCGTTGACTTTGATTG
1 TTGACCGTTGACTTTGATCG
29182075 TTGACCGTTGACTTTGATCG
1 TTGACCGTTGACTTTGATCG
29182095 TTGACCGTTGACTTT
1 TTGACCGTTGACTTT
29182110 TTCGAAAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.44
Consensus pattern (20 bp):
TTGACCGTTGACTTTGATCG
Found at i:29184022 original size:21 final size:21
Alignment explanation
Indices: 29183996--29184045 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
29183986 CCCTTCTAGC
29183996 CAAAGGTTATCAAATATTCCT
1 CAAAGGTTATCAAATATTCCT
29184017 CAAAGGTTATCAAATATTCCT
1 CAAAGGTTATCAAATATTCCT
*
29184038 CCAAGGTT
1 CAAAGGTT
29184046 CATGAGGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (21 bp):
CAAAGGTTATCAAATATTCCT
Found at i:29187378 original size:4 final size:4
Alignment explanation
Indices: 29187351--29187395 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
29187341 TTTTATTATT
29187351 TTTA TTT- TTCTA TCTTA TTTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TT-TA T-TTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT
29187396 TTGCCCAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 2 0.05
4 27 0.73
5 6 0.16
6 2 0.05
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:29187674 original size:4 final size:4
Alignment explanation
Indices: 29187647--29187691 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
29187637 TTATTTTATT
29187647 TTTA TTT- TTCTA TCTTA TTTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TT-TA T-TTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT
29187692 TTGTCCAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 2 0.05
4 27 0.73
5 6 0.16
6 2 0.05
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:29187880 original size:296 final size:296
Alignment explanation
Indices: 29187346--29187951 Score: 1149
Period size: 296 Copynumber: 2.0 Consensus size: 296
29187336 ATTATTTTTA
29187346 TTATTTTTATTTTTCTATCTTATTTTATTTATTTATTTATTTATTTATTTTTGCCCAGGAAACTC
1 TTATTTTTATTTTTCTATCTTATTTTATTTATTTATTTATTTATTTATTTTTGCCCAGGAAACTC
*
29187411 GAGGAATTTATTTCAAAAAAAAATTAATGATGGAAACTGCAACACTACGAGAGCAACGATAACAT
66 GAGGAATTTATTTAAAAAAAAAATTAATGATGGAAACTGCAACACTACGAGAGCAACGATAACAT
*
29187476 GGAGAGTATTCTAAACCCTTTTCTTTTCGTATTTATCTTCACATTGAGGGCAATGCATTTTAAGA
131 GGAGAGTATTCTAAACCCTTTTCTTTTCGTATTTATCTTCACATTGAGAGCAATGCATTTTAAGA
*
29187541 AGGGGGAGACGTTTCTCATTGTTTTTGCTATTTTTATCTGCTGTTTGTGCTGCTATGGGTTTATT
196 AGGGGGAGACGTTCCTCATTGTTTTTGCTATTTTTATCTGCTGTTTGTGCTGCTATGGGTTTATT
29187606 GTTGCTGCTACCTTACTATTTTCTGCCTGTTTTATT
261 GTTGCTGCTACCTTACTATTTTCTGCCTGTTTTATT
*
29187642 TTATTTTTATTTTTCTATCTTATTTTATTTATTTATTTATTTATTTATTTTTGTCCAGGAAACTC
1 TTATTTTTATTTTTCTATCTTATTTTATTTATTTATTTATTTATTTATTTTTGCCCAGGAAACTC
29187707 GAGGAATTTATTTAAAAAAAAAATTAATGATGGAAACTGCAACACTACGAGAGCAACGATAACAT
66 GAGGAATTTATTTAAAAAAAAAATTAATGATGGAAACTGCAACACTACGAGAGCAACGATAACAT
** *
29187772 GGAGAGTATTCTAAACCCTTTTCTTTTCGTATTTATCTTCACATTGAGAGCAATGGTTTTTAAGT
131 GGAGAGTATTCTAAACCCTTTTCTTTTCGTATTTATCTTCACATTGAGAGCAATGCATTTTAAGA
29187837 AGGGGGAGACGTTCCTCATTGTTTTTGCTATTTTTATCTGCTGTTTGTGCTGCTATGGGTTTATT
196 AGGGGGAGACGTTCCTCATTGTTTTTGCTATTTTTATCTGCTGTTTGTGCTGCTATGGGTTTATT
29187902 GTTGCTGCTACCTTACTATTTTCTGCCTGTTTTATT
261 GTTGCTGCTACCTTACTATTTTCTGCCTGTTTTATT
29187938 TTATTTTTATTTTT
1 TTATTTTTATTTTT
29187952 TAAGTATATT
Statistics
Matches: 303, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
296 303 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.46
Consensus pattern (296 bp):
TTATTTTTATTTTTCTATCTTATTTTATTTATTTATTTATTTATTTATTTTTGCCCAGGAAACTC
GAGGAATTTATTTAAAAAAAAAATTAATGATGGAAACTGCAACACTACGAGAGCAACGATAACAT
GGAGAGTATTCTAAACCCTTTTCTTTTCGTATTTATCTTCACATTGAGAGCAATGCATTTTAAGA
AGGGGGAGACGTTCCTCATTGTTTTTGCTATTTTTATCTGCTGTTTGTGCTGCTATGGGTTTATT
GTTGCTGCTACCTTACTATTTTCTGCCTGTTTTATT
Found at i:29188646 original size:99 final size:102
Alignment explanation
Indices: 29188483--29188667 Score: 263
Period size: 99 Copynumber: 1.8 Consensus size: 102
29188473 ATGTGTTAGA
* * *
29188483 CTGAGTAATCGAGGTGGAGTGCTTGGTTGTCATTTCATTTCGCGTCAAAAGGGTTAACGCATTC-
1 CTGAGTAACCGAGGTGGAGTGCTTGGGTGTCATTTCATTTCGCATCAAAAGGGTTAACGCATTCT
*
29188547 TACA-AAAAAAAAAA-AAAAATTGAGAGCATGTTGGG
66 TAAAGAAAAAAAAAAGAAAAATTGAGAGCATGTTGGG
* *
29188582 CTGAGTAACCG-GGATGGAGTGCTTGGGTGTCATTTCATTTCGCATCAAAA-GGTCTAATGTATT
1 CTGAGTAACCGAGG-TGGAGTGCTTGGGTGTCATTTCATTTCGCATCAAAAGGGT-TAACGCATT
29188645 CTTAAAGAAAAAAAAAAGAAAAA
64 CTTAAAGAAAAAAAAAAGAAAAA
29188668 AATTGACAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
98 5 0.07
99 52 0.69
100 3 0.04
101 10 0.13
102 5 0.07
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (102 bp):
CTGAGTAACCGAGGTGGAGTGCTTGGGTGTCATTTCATTTCGCATCAAAAGGGTTAACGCATTCT
TAAAGAAAAAAAAAAGAAAAATTGAGAGCATGTTGGG
Found at i:29189259 original size:19 final size:19
Alignment explanation
Indices: 29189237--29189281 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29189227 TTATATTAGG
29189237 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATAT
* *
29189256 ATTTATTATTTAAATTTAT
1 ATTTAATATTTAAATATAT
29189275 ATTTAAT
1 ATTTAAT
29189282 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATAT
Found at i:29202323 original size:24 final size:24
Alignment explanation
Indices: 29202270--29202324 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
29202260 CATTTAAGTA
* *
29202270 TGTTTAAATAAAATTATCTGTATT
1 TGTTTAAAAAAAATTATATGTATT
* *
29202294 TATTTAAAAAAAATTCATAT-TTTT
1 TGTTTAAAAAAAATT-ATATGTATT
29202318 TGTTTAA
1 TGTTTAA
29202325 TTTAATTATG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (24 bp):
TGTTTAAAAAAAATTATATGTATT
Found at i:29203399 original size:22 final size:21
Alignment explanation
Indices: 29203366--29203413 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
29203356 AAATTCCTTT
* *
29203366 AAATTTT-TTTTATAATTTATA
1 AAATTTTATTTAATAA-TAATA
29203387 AAATTTTAATTTAATAATAATA
1 AAATTTT-ATTTAATAATAATA
29203409 AAATT
1 AAATT
29203414 ACATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 9 0.39
23 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATTTTATTTAATAATAATA
Found at i:29203433 original size:83 final size:83
Alignment explanation
Indices: 29203345--29203503 Score: 187
Period size: 83 Copynumber: 1.9 Consensus size: 83
29203335 GCTCTCCAAA
* * * * * * *
29203345 AAAAAAAAAAAAAATTCCTTTAAATTTTTTTTATAATTTATAAAATTTTAA-T-TTAATAATAAT
1 AAAAATAAAAAAAATTCATTT-AATTTTTTTAAAAATATA-AAAATATAAACTATTAA-AATAAT
29203408 AAAATTACATTTTAATCTCTT
63 AAAATTACATTTTAATCTCTT
* * *
29203429 AAAAATATAAAAATTTGATTTAATTTTTTTAAAAATATAAAAATATAAACTATTAAAATAATAAA
1 AAAAATAAAAAAAATTCATTTAATTTTTTTAAAAATATAAAAATATAAACTATTAAAATAATAAA
29203494 ATTACATTTT
66 ATTACATTTT
29203504 TACTATCGTA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
82 8 0.13
83 35 0.56
84 20 0.32
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (83 bp):
AAAAATAAAAAAAATTCATTTAATTTTTTTAAAAATATAAAAATATAAACTATTAAAATAATAAA
ATTACATTTTAATCTCTT
Found at i:29208073 original size:31 final size:30
Alignment explanation
Indices: 29208002--29208073 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 30
29207992 TTAAATAACC
29208002 TTAAAAGTTATGTAATTTCATTAAATATATAA
1 TTAAAA-TTAT-TAATTTCATTAAATATATAA
*
29208034 --AAAA-TATTAATTTTATATAAATA-ATAA
1 TTAAAATTATTAATTTCAT-TAAATATATAA
29208061 TTAAAATTTATTA
1 TTAAAA-TTATTA
29208074 TCATATATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
27 12 0.35
28 9 0.26
29 4 0.12
30 4 0.12
31 5 0.15
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (30 bp):
TTAAAATTATTAATTTCATTAAATATATAA
Found at i:29208085 original size:20 final size:21
Alignment explanation
Indices: 29208060--29208112 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
29208050 ATAAATAATA
29208060 ATTAAAATTTATTATCATA-T
1 ATTAAAATTTATTATCATATT
* *
29208080 ATTAAAATTTATTGTTATATT
1 ATTAAAATTTATTATCATATT
*
29208101 ATTTAAATTTAT
1 ATTAAAATTTAT
29208113 AGTTATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTAAAATTTATTATCATATT
Found at i:29208108 original size:21 final size:20
Alignment explanation
Indices: 29208060--29208123 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
29208050 ATAAATAATA
* *
29208060 ATTAAAATTTATTATCATAT
1 ATTAAAATTTATTGTTATAT
29208080 ATTAAAATTTATTGTTATATT
1 ATTAAAATTTATTGTTATA-T
* *
29208101 ATTTAAATTTATAGTTATTAT
1 ATTAAAATTTATTGTTA-TAT
29208122 AT
1 AT
29208124 AATATGTGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 17 0.45
21 19 0.50
22 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTAAAATTTATTGTTATAT
Found at i:29225426 original size:52 final size:52
Alignment explanation
Indices: 29225354--29225574 Score: 343
Period size: 52 Copynumber: 4.2 Consensus size: 52
29225344 ATGATTATGC
*
29225354 GTCATCGTGAGTATACGAATCCTTTACGGATTATGAGGTCTGATGACTACGT
1 GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCTGATGACTACGT
* * *
29225406 GTCATCATGAGTATATGAATCCTTTACGAATTATGAGGTCTGATGACTATGT
1 GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCTGATGACTACGT
* *
29225458 GTCATTGTGAGTATATGAATCCTTTACGGATTATGAGGTCTGATGGCTACGT
1 GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCTGATGACTACGT
* * * * *
29225510 GTCATTGTGAGTATGTGAATCCTTTACGGATTGTGAGGTCCGATGACTATGT
1 GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCTGATGACTACGT
29225562 GTCATCGTGAGTA
1 GTCATCGTGAGTA
29225575 CTAAAGGAAT
Statistics
Matches: 154, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 154 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.35
Consensus pattern (52 bp):
GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCTGATGACTACGT
Found at i:29232626 original size:52 final size:52
Alignment explanation
Indices: 29232548--29232784 Score: 366
Period size: 52 Copynumber: 4.6 Consensus size: 52
29232538 AATGTAAAAG
* *
29232548 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGCATTATAA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
*
29232600 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
*
29232652 GGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * * * * *
29232704 GGTCCGGTGACTACGAGTCATCATGAGTATGTGAATCCTTTACGGATTGTGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
29232756 GGTCTGATGACTATGTGTCATCATGAGTA
1 GGTCCGATGACTATGTGTCATCGTGAGTA
29232785 CTAAAGGAAA
Statistics
Matches: 169, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 169 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Found at i:29233560 original size:21 final size:21
Alignment explanation
Indices: 29233534--29233583 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
29233524 AAGACTTGTT
*
29233534 TCGGTAGAAGAGTCACCTGTA
1 TCGGTAGAACAGTCACCTGTA
* *
29233555 TTGGTAGAACAGTCACTTGTA
1 TCGGTAGAACAGTCACCTGTA
29233576 TCGGTAGA
1 TCGGTAGA
29233584 GATCTGCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (21 bp):
TCGGTAGAACAGTCACCTGTA
Found at i:29241143 original size:29 final size:29
Alignment explanation
Indices: 29241059--29241254 Score: 209
Period size: 29 Copynumber: 6.8 Consensus size: 29
29241049 GGCGTCCTTT
29241059 TAACAAAGAT-AGCCACAAAGGCTC-CAT-
1 TAACAAA-ATCAGCCACAAAGGCTCTCATA
* * * * *
29241086 TATCAGATTCGGCCACAAAGGCTCACATA
1 TAACAAAATCAGCCACAAAGGCTCTCATA
*
29241115 TAACAAAATCAGTCACAAAGGCTCTCATA
1 TAACAAAATCAGCCACAAAGGCTCTCATA
* *
29241144 TAACAAAATCAACCACAAAGGGTCTCATA
1 TAACAAAATCAGCCACAAAGGCTCTCATA
* * * *
29241173 TAGCAAAATCAACCATAAAGGCTCTTATA
1 TAACAAAATCAGCCACAAAGGCTCTCATA
* * ***
29241202 TAATAGAATCAGCCACAAACATTCTCATA
1 TAACAAAATCAGCCACAAAGGCTCTCATA
29241231 TAACAAAATCAGCCACAAAGGCTC
1 TAACAAAATCAGCCACAAAGGCTC
29241255 CTTCTGTAAC
Statistics
Matches: 135, Mismatches: 31, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
26 1 0.01
27 18 0.13
28 3 0.02
29 113 0.84
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (29 bp):
TAACAAAATCAGCCACAAAGGCTCTCATA
Found at i:29242476 original size:16 final size:16
Alignment explanation
Indices: 29242455--29242486 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29242445 GATGATTTTT
*
29242455 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
29242471 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
29242487 TTTGTAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:29244199 original size:21 final size:21
Alignment explanation
Indices: 29244156--29244209 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
29244146 AGAGTTTTTA
* *
29244156 GTATCGGTAGAAGCATGATTT
1 GTATAGGTAGAAGCATGACTT
* * *
29244177 GTTTAGGTAGAAGCTTTACTT
1 GTATAGGTAGAAGCATGACTT
*
29244198 GTATCGGTAGAA
1 GTATAGGTAGAA
29244210 CTGTCATAAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (21 bp):
GTATAGGTAGAAGCATGACTT
Found at i:29248021 original size:41 final size:41
Alignment explanation
Indices: 29247975--29248064 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 41
29247965 TTTGCTTTTT
29247975 TGTTTTGCA-CATTGTTTGTCATTATGCTTATGACATATATA
1 TGTTTTGCATC-TTGTTTGTCATTATGCTTATGACATATATA
**
29248016 TGTTTTTTTATTCTTGTTTGTCATTATGCTTATGACATATATA
1 TG-TTTTGCA-TCTTGTTTGTCATTATGCTTATGACATATATA
29248059 TGTTTT
1 TGTTTT
29248065 TTTATTCTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
41 2 0.05
42 9 0.20
43 32 0.73
44 1 0.02
ACGTcount: A:0.21, C:0.10, G:0.13, T:0.56
Consensus pattern (41 bp):
TGTTTTGCATCTTGTTTGTCATTATGCTTATGACATATATA
Found at i:29248034 original size:43 final size:43
Alignment explanation
Indices: 29247986--29248073 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
29247976 GTTTTGCACA
29247986 TTGTTTGTCATTATGCTTATGACATATATATGTTTTTTTATTC
1 TTGTTTGTCATTATGCTTATGACATATATATGTTTTTTTATTC
29248029 TTGTTTGTCATTATGCTTATGACATATATATGTTTTTTTATTC
1 TTGTTTGTCATTATGCTTATGACATATATATGTTTTTTTATTC
29248072 TT
1 TT
29248074 TAAATTGCAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.59
Consensus pattern (43 bp):
TTGTTTGTCATTATGCTTATGACATATATATGTTTTTTTATTC
Found at i:29248554 original size:18 final size:18
Alignment explanation
Indices: 29248531--29248571 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
29248521 AAGGGTCGTA
*
29248531 AGGGTTTGGG-AGGTGGTG
1 AGGGTTTGGGTAAG-GGTG
29248549 AGGGTTTGGGTAAGGGTG
1 AGGGTTTGGGTAAGGGTG
29248567 AGGGT
1 AGGGT
29248572 GTTGAGGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.15, C:0.00, G:0.59, T:0.27
Consensus pattern (18 bp):
AGGGTTTGGGTAAGGGTG
Found at i:29248649 original size:36 final size:36
Alignment explanation
Indices: 29248602--29248692 Score: 155
Period size: 36 Copynumber: 2.5 Consensus size: 36
29248592 TGAGGGTGAG
* *
29248602 ATGTTTTTTAATTTAAATTTGATAGCAGACTTCCTT
1 ATGTTTTTTAATTTAAATTTGACAGCAGACTTACTT
*
29248638 ATGTTTTTTAATTTAAATTTGACAGTAGACTTACTT
1 ATGTTTTTTAATTTAAATTTGACAGCAGACTTACTT
29248674 ATGTTTTTTAATTTAAATT
1 ATGTTTTTTAATTTAAATT
29248693 GCAGGGTCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.53
Consensus pattern (36 bp):
ATGTTTTTTAATTTAAATTTGACAGCAGACTTACTT
Found at i:29249887 original size:161 final size:161
Alignment explanation
Indices: 29249614--29250062 Score: 602
Period size: 161 Copynumber: 2.8 Consensus size: 161
29249604 CAAACAATAT
* * *
29249614 CCTAACACAACGGGAACACAAGTATATTGTAAACAC-TTCTCATTGTCAATTCCAAATTATAATA
1 CCTAACACAACTGGATCACAAGTATATCGTAAACACTTTCTCATTGTCAATTCCAAATTATAATA
* * *
29249678 ATTTAATTTCGGTTTTGATTTTTTGTGTCTTAGTCTGGTATGAGTACGAGAACTATAACCTAAAA
66 ATCTAATTTCGGTTTTGATTTTTTGTGTCTTAGTCTGGTACGAGTACGAGAACTATAACCCAAAA
* * *
29249743 AATGAACGATAGAACATCA-TCATGCATTCAG
131 AAAGAACGACAGAACACCACT-ATGCATTCAG
* *
29249774 CCTAACACAACTAGATCACAAGTATATCGTAAACACTTTCTTATTGTCAATTCCAAATTATAATA
1 CCTAACACAACTGGATCACAAGTATATCGTAAACACTTTCTCATTGTCAATTCCAAATTATAATA
* * * *
29249839 ATCTAATTTCAGTTTTGATTTTTTGTGTCTTAGTTTGGTACAAGTACGAGAGCTATAACCCAAAA
66 ATCTAATTTCGGTTTTGATTTTTTGTGTCTTAGTCTGGTACGAGTACGAGAACTATAACCCAAAA
*
29249904 AAAGAATGACAGAACACCACTATGCATTCAG
131 AAAGAACGACAGAACACCACTATGCATTCAG
* * * *
29249935 CCTAACACAACTGGATCATAGGTATATCATAAACACTTTCTCATTGTCAATTCCAAATTAT-TTA
1 CCTAACACAACTGGATCACAAGTATATCGTAAACACTTTCTCATTGTCAATTCCAAATTATAAT-
* ** * * * *
29249999 AATCTAATTTGGGTACTGA-TTGTTGT-TCTTAGTCTGGTACGAGTATGAGAACTAGAAGCCAAA
65 AATCTAATTTCGGTTTTGATTTTTTGTGTCTTAGTCTGGTACGAGTACGAGAACTATAACCCAAA
29250062 A
130 A
29250063 TAGGATGGCA
Statistics
Matches: 253, Mismatches: 33, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
159 32 0.13
160 39 0.15
161 181 0.72
162 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (161 bp):
CCTAACACAACTGGATCACAAGTATATCGTAAACACTTTCTCATTGTCAATTCCAAATTATAATA
ATCTAATTTCGGTTTTGATTTTTTGTGTCTTAGTCTGGTACGAGTACGAGAACTATAACCCAAAA
AAAGAACGACAGAACACCACTATGCATTCAG
Found at i:29251875 original size:22 final size:22
Alignment explanation
Indices: 29251845--29251894 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
29251835 GTAGAAGGAA
* *
29251845 TAAAAAAAACAACAATATCGAT
1 TAAACAAAACAACAACATCGAT
*
29251867 TAAACAAAACAATAACATCGAT
1 TAAACAAAACAACAACATCGAT
29251889 TAAACA
1 TAAACA
29251895 TGATTAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.62, C:0.16, G:0.04, T:0.18
Consensus pattern (22 bp):
TAAACAAAACAACAACATCGAT
Found at i:29260503 original size:435 final size:435
Alignment explanation
Indices: 29259693--29260562 Score: 1740
Period size: 435 Copynumber: 2.0 Consensus size: 435
29259683 TATCAACATA
29259693 TATTAGCGAAATATTAAATCGAATAAATCATTCCAAATCAAAAGAAAAACTTAATCAATCCCTAA
1 TATTAGCGAAATATTAAATCGAATAAATCATTCCAAATCAAAAGAAAAACTTAATCAATCCCTAA
29259758 TAATTTGACATGACTAGGCTCAGATGTCACATATTATAATCGAAAAACTAATAAAAAATTTAATT
66 TAATTTGACATGACTAGGCTCAGATGTCACATATTATAATCGAAAAACTAATAAAAAATTTAATT
29259823 AACTAGAATCTGTTATACCATATCATCAAGAACAAAACTAGATGCAAAAACATATCTGAATCCAT
131 AACTAGAATCTGTTATACCATATCATCAAGAACAAAACTAGATGCAAAAACATATCTGAATCCAT
29259888 TGATATCTTGAAATATTCAAATCTTGTGATTTTGATCTTTCAAATTTACACATATATAATTTAGA
196 TGATATCTTGAAATATTCAAATCTTGTGATTTTGATCTTTCAAATTTACACATATATAATTTAGA
29259953 GTATCTATACATAAGTAATTTGGGGACCATAACCCTAATATATAACTTTTGCACATTAATATTAA
261 GTATCTATACATAAGTAATTTGGGGACCATAACCCTAATATATAACTTTTGCACATTAATATTAA
29260018 TTTCTAATCAATCCATCATCAATTAGAAATTAGTTACTAGAGTATCTACACATATTTGGCTCATA
326 TTTCTAATCAATCCATCATCAATTAGAAATTAGTTACTAGAGTATCTACACATATTTGGCTCATA
29260083 CTTTATTTAATAATTGAATCCCAGTAAGCCCTAACCAAATTAGAT
391 CTTTATTTAATAATTGAATCCCAGTAAGCCCTAACCAAATTAGAT
29260128 TATTAGCGAAATATTAAATCGAATAAATCATTCCAAATCAAAAGAAAAACTTAATCAATCCCTAA
1 TATTAGCGAAATATTAAATCGAATAAATCATTCCAAATCAAAAGAAAAACTTAATCAATCCCTAA
29260193 TAATTTGACATGACTAGGCTCAGATGTCACATATTATAATCGAAAAACTAATAAAAAATTTAATT
66 TAATTTGACATGACTAGGCTCAGATGTCACATATTATAATCGAAAAACTAATAAAAAATTTAATT
29260258 AACTAGAATCTGTTATACCATATCATCAAGAACAAAACTAGATGCAAAAACATATCTGAATCCAT
131 AACTAGAATCTGTTATACCATATCATCAAGAACAAAACTAGATGCAAAAACATATCTGAATCCAT
29260323 TGATATCTTGAAATATTCAAATCTTGTGATTTTGATCTTTCAAATTTACACATATATAATTTAGA
196 TGATATCTTGAAATATTCAAATCTTGTGATTTTGATCTTTCAAATTTACACATATATAATTTAGA
29260388 GTATCTATACATAAGTAATTTGGGGACCATAACCCTAATATATAACTTTTGCACATTAATATTAA
261 GTATCTATACATAAGTAATTTGGGGACCATAACCCTAATATATAACTTTTGCACATTAATATTAA
29260453 TTTCTAATCAATCCATCATCAATTAGAAATTAGTTACTAGAGTATCTACACATATTTGGCTCATA
326 TTTCTAATCAATCCATCATCAATTAGAAATTAGTTACTAGAGTATCTACACATATTTGGCTCATA
29260518 CTTTATTTAATAATTGAATCCCAGTAAGCCCTAACCAAATTAGAT
391 CTTTATTTAATAATTGAATCCCAGTAAGCCCTAACCAAATTAGAT
29260563 CATTTTTAAA
Statistics
Matches: 435, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
435 435 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.33
Consensus pattern (435 bp):
TATTAGCGAAATATTAAATCGAATAAATCATTCCAAATCAAAAGAAAAACTTAATCAATCCCTAA
TAATTTGACATGACTAGGCTCAGATGTCACATATTATAATCGAAAAACTAATAAAAAATTTAATT
AACTAGAATCTGTTATACCATATCATCAAGAACAAAACTAGATGCAAAAACATATCTGAATCCAT
TGATATCTTGAAATATTCAAATCTTGTGATTTTGATCTTTCAAATTTACACATATATAATTTAGA
GTATCTATACATAAGTAATTTGGGGACCATAACCCTAATATATAACTTTTGCACATTAATATTAA
TTTCTAATCAATCCATCATCAATTAGAAATTAGTTACTAGAGTATCTACACATATTTGGCTCATA
CTTTATTTAATAATTGAATCCCAGTAAGCCCTAACCAAATTAGAT
Found at i:29261242 original size:17 final size:19
Alignment explanation
Indices: 29261216--29261252 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
29261206 TAATCACATG
29261216 AACAAAACAA-AAA-TAAA
1 AACAAAACAAGAAATTAAA
*
29261233 AACAACACAAGAAATTAAA
1 AACAAAACAAGAAATTAAA
29261252 A
1 A
29261253 TTATGATACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.76, C:0.14, G:0.03, T:0.08
Consensus pattern (19 bp):
AACAAAACAAGAAATTAAA
Found at i:29277377 original size:16 final size:16
Alignment explanation
Indices: 29277332--29277370 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
29277322 GTTTTATAGT
* *
29277332 TTTTGTTGGAGCCTAA
1 TTTTGATGGAGCCCAA
29277348 TTTTGATGGAGCCCAA
1 TTTTGATGGAGCCCAA
29277364 TTTTGAT
1 TTTTGAT
29277371 CGGGCCCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.44
Consensus pattern (16 bp):
TTTTGATGGAGCCCAA
Found at i:29277402 original size:17 final size:17
Alignment explanation
Indices: 29277380--29277490 Score: 132
Period size: 17 Copynumber: 6.4 Consensus size: 17
29277370 TCGGGCCCCT
*
29277380 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
*
29277397 TTTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
*
29277414 TTTAAATTTATTCTAAAA
1 TTTAAATTTATT-TTAAA
* *
29277432 TTTAAATTTAATTTCAA
1 TTTAAATTTATTTTAAA
*
29277449 TTTAAATTTATATTTATA
1 TTTAAATTTAT-TTTAAA
* *
29277467 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
29277484 TTTAAAT
1 TTTAAAT
29277491 AATAAAATAT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
17 49 0.63
18 29 0.37
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:29277419 original size:6 final size:6
Alignment explanation
Indices: 29277380--29277490 Score: 74
Period size: 6 Copynumber: 19.2 Consensus size: 6
29277370 TCGGGCCCCT
* * * *
29277380 TTTAAA TTT-AT TTTGAA TTTAAA ATT-AT TTTAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
29277424 TTCTAAAA TTTAAA TTT-AA TTTCAA TTTAAA TTTATA TTTATA TTTAAA
1 TT-T-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
29277473 ATT--A TTATAAA TTTAAA T
1 TTTAAA TT-TAAA TTTAAA T
29277491 AATAAAATAT
Statistics
Matches: 83, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
4 5 0.06
5 14 0.17
6 57 0.69
7 4 0.05
8 3 0.04
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:29277451 original size:35 final size:34
Alignment explanation
Indices: 29277380--29277490 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 34
29277370 TCGGGCCCCT
** *
29277380 TTTAAATTTATTTTGAATTTAAAATTATTTTAAA
1 TTTAAATTTATTTAAAATTTAAAATTAATTTAAA
* *
29277414 TTTAAATTTATTCTAAAATTTAAATTTAATTTCAA
1 TTTAAATTTATT-TAAAATTTAAAATTAATTTAAA
* *
29277449 TTTAAATTTATATTTATATTTAAAATT-ATTATAAA
1 TTTAAATTTAT-TTAAAATTTAAAATTAATT-TAAA
29277484 TTTAAAT
1 TTTAAAT
29277491 AATAAAATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
34 15 0.23
35 49 0.75
36 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTAAAATTTAAAATTAATTTAAA
Found at i:29278243 original size:10 final size:10
Alignment explanation
Indices: 29278230--29278254 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29278220 ATAATAATAA
29278230 TAAATATTAT
1 TAAATATTAT
29278240 TAAATATTAT
1 TAAATATTAT
29278250 TAAAT
1 TAAAT
29278255 TTTTAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TAAATATTAT
Found at i:29279582 original size:28 final size:28
Alignment explanation
Indices: 29279551--29279613 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
29279541 ATCCTGAACT
29279551 TCCAAAATTACCATATTGCCCCCAA-TA
1 TCCAAAATTACCATATTGCCCCCAAGTA
* * *
29279578 GTCCAAAATTATCATTTTGCCTCCAAGTA
1 -TCCAAAATTACCATATTGCCCCCAAGTA
29279607 TCCAAAA
1 TCCAAAA
29279614 AGACTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.29
Consensus pattern (28 bp):
TCCAAAATTACCATATTGCCCCCAAGTA
Done.