Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 137 of 204
Found at i:41603055 original size:44 final size:42
Alignment explanation
Indices: 41602995--41603266 Score: 237
Period size: 44 Copynumber: 6.3 Consensus size: 42
41602985 ATCTTTCATC
*
41602995 TTCAATCTTCTCCACTGCAACTTCAGGGAGATAAGATTGGTAT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGT-T
* *
41603038 CTTCAACCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTT
1 -TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-TGGTT
*
41603084 TT-AAT-TCGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTT
1 TTCAATCT-GCTCCACTGCAACTTCAGGGAGATAAGATTGG-TT
** * *
41603126 CTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGG-A
1 -TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTT
* * * * * *
41603168 TGCGATATGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-TGGTT
* * *
41603213 TT-AATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGCTT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-TT
*
41603255 CTTAAATCTGCT
1 -TTCAATCTGCT
41603267 TCCCTACTAC
Statistics
Matches: 185, Mismatches: 28, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
41 35 0.19
42 6 0.03
43 5 0.03
44 129 0.70
45 4 0.02
46 2 0.01
47 4 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (42 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTT
Found at i:41603265 original size:129 final size:131
Alignment explanation
Indices: 41602993--41603266 Score: 408
Period size: 129 Copynumber: 2.1 Consensus size: 131
41602983 TCATCTTTCA
* * * *
41602993 TCTTCAATCTTCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGCTCCACTGCA
1 TCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTA-CTGCAACATGCTCCACTGCA
*
41603058 ACTTCAGAGAGATAAGATCTGTGGTTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTGG
65 ACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGG
41603123 CT
130 CT
** * * *
41603125 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGG-A-TGCGATATGCTCTACTGCAA
1 TCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTACTGCAACATGCTCCACTGCAA
* *
41603188 CTTTAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGC
66 CTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGC
41603253 T
131 T
*
41603254 TCTTAAATCTGCT
1 TCTTCAATCTGCT
41603267 TCCCTACTAC
Statistics
Matches: 127, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
129 88 0.69
131 1 0.01
132 38 0.30
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (131 bp):
TCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTACTGCAACATGCTCCACTGCAA
CTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGC
T
Found at i:41603288 original size:129 final size:128
Alignment explanation
Indices: 41603046--41603291 Score: 361
Period size: 129 Copynumber: 1.9 Consensus size: 128
41603036 ATCTTCAACC
*
41603046 TGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATTCGCTCCACTGCAACTTCAGGG
1 TGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGG
*** *
41603111 AGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATA
66 AGATAGGATTGGCTTCTTAAATCTGCTCCACTACAACTT-AGGGAGATAAGACTGGATGCGATA
* * *
41603175 TGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTTAGGG
1 TGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGG
*
41603240 AGATAGGATTGGCTTCTTAAATCTGCTTCC-CTACTACCTT-GGGAAGATAAGA
66 AGATAGGATTGGCTTCTTAAATCTGC-TCCACTAC-AACTTAGGG-AGATAAGA
41603292 TTTCGTCTTT
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
128 3 0.03
129 95 0.90
130 7 0.07
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (128 bp):
TGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGG
AGATAGGATTGGCTTCTTAAATCTGCTCCACTACAACTTAGGGAGATAAGACTGGATGCGATA
Found at i:41603358 original size:44 final size:43
Alignment explanation
Indices: 41603303--41603638 Score: 154
Period size: 44 Copynumber: 7.7 Consensus size: 43
41603293 TTCGTCTTTG
* *
41603303 ATCTGCTCCACTACTGCTTAGGGAGACAGGATCTGCAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAGGATCT-CAATCTTCA
* * * * *
41603347 ACCTACTCCACTGCTGCTCAAGGAGATAGGA-CT-AATGGCTTAA
1 ATCTACTCCACTACTGCTTAGGGAGATAGGATCTCAAT--CTTCA
* * * **
41603390 ATCTGCTTCCGCACTA-T-CTTAGGAAGATAAGAT-TCACCATCTTTG
1 ATCTAC-T-C-CACTACTGCTTAGGGAGATAGGATCTCA--ATCTTCA
* * * **
41603435 ATCTGCACCACTACTGCTTAGGGAGACAAAATCTACAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAGGATCT-CAATCTTCA
* * ** ** *
41603479 ACCTACTCCACTGCTGCTCGGGGAGATAGGA-C-CGGT-TTAA
1 ATCTACTCCACTACTGCTTAGGGAGATAGGATCTCAATCTTCA
* * * * *
41603519 ATCTGCTTCCTTACTAC--CTT-GGGAAGATAAGATTTACCATCTTCG
1 ATCTAC-TCC--ACTACTGCTTAGGG-AGATAGGATCT-CAATCTTCA
* * * *
41603564 ATATACTCCACTACTGCTTAGGGAGACAGGACCTACAATCTTCG
1 ATCTACTCCACTACTGCTTAGGGAGATAGGATCT-CAATCTTCA
*
41603608 ACCTACTCCACTACTGCTTAGGGAGATAGGA
1 ATCTACTCCACTACTGCTTAGGGAGATAGGA
41603639 CTGGTGTCTT
Statistics
Matches: 214, Mismatches: 54, Indels: 48
0.68 0.17 0.15
Matches are distributed among these distances:
40 10 0.05
41 17 0.08
42 10 0.05
43 17 0.08
44 130 0.61
45 22 0.10
46 6 0.03
47 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (43 bp):
ATCTACTCCACTACTGCTTAGGGAGATAGGATCTCAATCTTCA
Found at i:41603590 original size:129 final size:130
Alignment explanation
Indices: 41603255--41603639 Score: 535
Period size: 129 Copynumber: 3.0 Consensus size: 130
41603245 GGATTGGCTT
*
41603255 CTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTT--CGTCTTTGATCTGCTCCACTACT
1 CTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTTACCATCTTTGATCTGCTCCACTACT
* * *
41603318 GCTTAGGGAGACAGGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAGGACTAAT
66 GCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGAC--AC
41603383 GG
129 GG
* * * *
41603385 CTTAAATCTGCTTCCGC-ACTATCTTAGGAAGATAAGATTCACCATCTTTGATCTGCACCACTAC
1 CTTAAATCTGCTTCC-CTACTACCTTGGGAAGATAAGATTTACCATCTTTGATCTGCTCCACTAC
** *
41603449 TGCTTAGGGAGACAAAATCTACAATCTTCAACCTACTCCACTGCTGCTCGGGGAGATAGGAC-CG
65 TGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACACG
41603513 G
130 G
* * * * *
41603514 TTTAAATCTGCTTCCTTACTACCTTGGGAAGATAAGATTTACCATCTTCGATATACTCCACTACT
1 CTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTTACCATCTTTGATCTGCTCCACTACT
* * * *
41603579 GCTTAGGGAGACAGGACCTACAATCTTCGACCTACTCCACTACTGCTTAGGGAGATAGGAC
66 GCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGAC
41603640 TGGTGTCTTC
Statistics
Matches: 224, Mismatches: 27, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
129 111 0.50
130 35 0.16
131 1 0.00
132 77 0.34
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (130 bp):
CTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTTACCATCTTTGATCTGCTCCACTACT
GCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACACGG
Found at i:41604940 original size:25 final size:25
Alignment explanation
Indices: 41604907--41604972 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 25
41604897 GCCTCTCCTT
41604907 TTTCCTTTTTCTTTTCTTCTTCTTC
1 TTTCCTTTTTCTTTTCTTCTTCTTC
*
41604932 TTTCC--TTT-TTTTCTTCTTTTTC
1 TTTCCTTTTTCTTTTCTTCTTCTTC
* *
41604954 CTTCTTTTTTCTTTT-TTCT
1 TTTCCTTTTTCTTTTCTTCT
41604973 CTTTTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
22 16 0.46
23 3 0.09
24 7 0.20
25 9 0.26
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTCCTTTTTCTTTTCTTCTTCTTC
Found at i:41604945 original size:19 final size:18
Alignment explanation
Indices: 41604911--41604980 Score: 81
Period size: 18 Copynumber: 3.8 Consensus size: 18
41604901 CTCCTTTTTC
*
41604911 CTTTTT-CTTTTCTTCTT
1 CTTTTTCCTTTTTTTCTT
41604928 CTTCTTTCCTTTTTTTCTT
1 CTT-TTTCCTTTTTTTCTT
*
41604947 CTTTTTCCTTCTTTT-TT
1 CTTTTTCCTTTTTTTCTT
41604964 CTTTTTTCTCTTTTTTT
1 C-TTTTTC-CTTTTTTT
41604981 TAAGAATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
17 6 0.13
18 20 0.43
19 20 0.43
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
CTTTTTCCTTTTTTTCTT
Found at i:41604969 original size:29 final size:28
Alignment explanation
Indices: 41604907--41604981 Score: 75
Period size: 29 Copynumber: 2.8 Consensus size: 28
41604897 GCCTCTCCTT
*
41604907 TTTCC-TTTT-TC-TTTTCTTCTTCTTC
1 TTTCCTTTTTCTCTTTTTTTTCTTCTTC
* * *
41604932 TTTCCTTTTTTTCTTCTTTTTCCTTCTTT
1 TTTCCTTTTTCTCTT-TTTTTTCTTCTTC
*
41604961 TTTCTTTTTTCTCTTTTTTTT
1 TTTCCTTTTTCTCTTTTTTTT
41604982 AAGAATTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 5 0.12
26 4 0.10
27 2 0.05
28 6 0.15
29 23 0.57
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTCCTTTTTCTCTTTTTTTTCTTCTTC
Found at i:41606059 original size:106 final size:106
Alignment explanation
Indices: 41605928--41606165 Score: 379
Period size: 106 Copynumber: 2.2 Consensus size: 106
41605918 GGCTAATTGG
*
41605928 TCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAATTTTTAAAAGGATATTTGGCTAATTGGT
1 TCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAAAGGATATTTGGCTAATTGGT
** * ** *
41605993 CGAACG-TGAAATCGAAACCCAGCACGTTAGGGCATGTTTTC
66 CGAACGAAAAAATCGAAACCCAGAAAATTA-GGCACGTTTTC
*
41606034 TCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGT
1 TCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAAAGGATATTTGGCTAATTGGT
41606099 CGAACGAAAAAATCGAAACCCAGAAAATTAGGCACGTTTTC
66 CGAACGAAAAAATCGAAACCCAGAAAATTAGGCACGTTTTC
*
41606140 TCGAATTTCTAAACGCAAAATATTGC
1 TCGAATTTCCAAACGCAAAATATTGC
41606166 TTTATTTAGA
Statistics
Matches: 122, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
106 104 0.85
107 18 0.15
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (106 bp):
TCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAAAGGATATTTGGCTAATTGGT
CGAACGAAAAAATCGAAACCCAGAAAATTAGGCACGTTTTC
Found at i:41606228 original size:21 final size:21
Alignment explanation
Indices: 41606204--41606243 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
41606194 GTATGGTGTT
41606204 AATATGTATAATG-GAATAACA
1 AATATG-ATAATGTGAATAACA
41606225 AATATGATAATGTGAATAA
1 AATATGATAATGTGAATAA
41606244 AATTAATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.30
Consensus pattern (21 bp):
AATATGATAATGTGAATAACA
Found at i:41606563 original size:3 final size:3
Alignment explanation
Indices: 41606555--41606619 Score: 112
Period size: 3 Copynumber: 21.3 Consensus size: 3
41606545 AAATAGAAGT
*
41606555 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41606603 ATA ATA ATA ATCA ATA A
1 ATA ATA ATA AT-A ATA A
41606620 GATAACAAGA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:41607655 original size:25 final size:25
Alignment explanation
Indices: 41607624--41607673 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
41607614 ACCGTAGTTT
*
41607624 GGCTATTGTTTT-TTTGGGCCTGTTG
1 GGCTATT-TTTTATTCGGGCCTGTTG
41607649 GGCTATTTTTTAATTCGGGCCTGTT
1 GGCTATTTTTT-ATTCGGGCCTGTT
41607674 TGGGTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 7 0.32
26 11 0.50
ACGTcount: A:0.08, C:0.14, G:0.28, T:0.50
Consensus pattern (25 bp):
GGCTATTTTTTATTCGGGCCTGTTG
Found at i:41616583 original size:31 final size:31
Alignment explanation
Indices: 41616531--41616600 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
41616521 ATATATATAT
** **
41616531 ATATATATATTATATGACTATA-ATCTCATGC
1 ATATATATATTATAAAACTATAGA-CTCACCC
41616562 ATATATATATT-TAAAACCTATAGACTCACCC
1 ATATATATATTATAAAA-CTATAGACTCACCC
41616593 ATATATAT
1 ATATATAT
41616601 TGTATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 3 0.09
31 29 0.88
32 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.39
Consensus pattern (31 bp):
ATATATATATTATAAAACTATAGACTCACCC
Found at i:41617960 original size:19 final size:19
Alignment explanation
Indices: 41617936--41617974 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
41617926 ACTACTAGCC
41617936 TTAATTTACACAATTAACA
1 TTAATTTACACAATTAACA
41617955 TTAATTTACACAATTAACA
1 TTAATTTACACAATTAACA
41617974 T
1 T
41617975 CAACTTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAATTTACACAATTAACA
Found at i:41618942 original size:35 final size:35
Alignment explanation
Indices: 41618857--41618945 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 35
41618847 GTTATCTACT
* * *
41618857 GGTCTTTCAGGGAGACACCGTGTTAACGGTATATA
1 GGTCTTTCAGGGTGACACCATGTAAACGGTATATA
* * *
41618892 TGTCCTTC-GGAGTGACATCATGTAAACGGTATATA
1 GGTCTTTCAGG-GTGACACCATGTAAACGGTATATA
41618927 GGTCTTTCAGGGTGACACC
1 GGTCTTTCAGGGTGACACC
41618946 GTGCAAATAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
34 2 0.05
35 39 0.91
36 2 0.05
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (35 bp):
GGTCTTTCAGGGTGACACCATGTAAACGGTATATA
Found at i:41622482 original size:28 final size:28
Alignment explanation
Indices: 41622450--41622536 Score: 113
Period size: 28 Copynumber: 3.1 Consensus size: 28
41622440 GTCACCAGAA
*
41622450 AAGAGGGAAGCCCA-CAAGGGACTCTCTT
1 AAGAGGGAAGACCACCAA-GGACTCTCTT
* *
41622478 AAGAGGGGAGTCCACCAAGGACTCTCTT
1 AAGAGGGAAGACCACCAAGGACTCTCTT
* *
41622506 AAGAGAGAAGACCACCAAGGACTATCTT
1 AAGAGGGAAGACCACCAAGGACTCTCTT
41622534 AAG
1 AAG
41622537 TGGATTGACC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 49 0.94
29 3 0.06
ACGTcount: A:0.36, C:0.23, G:0.26, T:0.15
Consensus pattern (28 bp):
AAGAGGGAAGACCACCAAGGACTCTCTT
Found at i:41622612 original size:30 final size:31
Alignment explanation
Indices: 41622534--41622614 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
41622524 GGACTATCTT
*
41622534 AAGTGGATTGACCGTTAGGAATTAACAAAGG
1 AAGTGGATTGACCGTTAGGAATTAACAAAAG
41622565 AAGTGGATTGACCGTTAGGAATTAACAAAAG
1 AAGTGGATTGACCGTTAGGAATTAACAAAAG
*
41622596 AAGTGGA-TGTCCGTTAGGA
1 AAGTGGATTGACCGTTAGGA
41622615 CTATCTAGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 11 0.23
31 37 0.77
ACGTcount: A:0.37, C:0.10, G:0.30, T:0.23
Consensus pattern (31 bp):
AAGTGGATTGACCGTTAGGAATTAACAAAAG
Found at i:41632561 original size:13 final size:13
Alignment explanation
Indices: 41632543--41632567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41632533 GGTAGGATTT
41632543 TGTATATCTGATC
1 TGTATATCTGATC
41632556 TGTATATCTGAT
1 TGTATATCTGAT
41632568 TCTATCATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (13 bp):
TGTATATCTGATC
Found at i:41634028 original size:16 final size:17
Alignment explanation
Indices: 41634004--41634036 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41633994 TTCAATTAAT
*
41634004 TTAATTAATTTT-TCAA
1 TTAAATAATTTTCTCAA
41634020 TTAAATAATTTTCTCAA
1 TTAAATAATTTTCTCAA
41634037 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATAATTTTCTCAA
Found at i:41635349 original size:24 final size:25
Alignment explanation
Indices: 41635296--41635358 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
41635286 TACATAGATA
* *
41635296 TTTTCCTAGTTAAA--TTGAGTTTC
1 TTTTCCTAGTTAAACTTTGACTATC
*
41635319 TTCTCCTAGTTAAACTTTG-CTATC
1 TTTTCCTAGTTAAACTTTGACTATC
*
41635343 TTTTCCTAGTTGAACT
1 TTTTCCTAGTTAAACT
41635359 CCGATTATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 13 0.39
24 17 0.52
25 3 0.09
ACGTcount: A:0.21, C:0.19, G:0.11, T:0.49
Consensus pattern (25 bp):
TTTTCCTAGTTAAACTTTGACTATC
Found at i:41647328 original size:135 final size:137
Alignment explanation
Indices: 41647173--41647451 Score: 413
Period size: 135 Copynumber: 2.0 Consensus size: 137
41647163 CATAAAATAA
* * *
41647173 AAATTACAAATGTATTTAGAAGAGGAGGAATTGAACTTGGGATTCAAGGATAAAATCA-TA-A-T
1 AAATTACAAATATATTTAGAAGAGGAGGAATTGAAATTGGGACTCAAGGATAAAATCATTACATT
* * *
41647235 -TATTTAACTAAGGGAGTTAATATGTTAAAAATATTAATTAAAAATAATAAAAAAGCTTAAAACA
66 ATATTTAACCAAAGGAGCTAATATGTTAAAAA-ATTAATTAAAAATAAT-AAAAAGCTTAAAACA
41647299 ACATGAAAT
129 ACATGAAAT
41647308 AAATTACAAATATATTTAGAAGAGGAGGAATTGAAATTGGGACTCAAGGATAAAATCATTATCAT
1 AAATTACAAATATATTTAGAAGAGGAGGAATTGAAATTGGGACTCAAGGATAAAATCATTA-CA-
*
41647373 TTAACTATTTAACCAAAGGAGCTAATATGTTAAAAAATTAATTAAAATTAATAAAAAGCTTAAAA
64 TT-A-TATTTAACCAAAGGAGCTAATATGTTAAAAAATTAATTAAAAATAATAAAAAGCTTAAAA
41647438 CAACATGAAAT
127 CAACATGAAAT
41647449 AAA
1 AAA
41647452 AAATACAAAT
Statistics
Matches: 129, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
135 55 0.43
136 2 0.02
138 1 0.01
140 1 0.01
141 27 0.21
142 15 0.12
143 28 0.22
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.28
Consensus pattern (137 bp):
AAATTACAAATATATTTAGAAGAGGAGGAATTGAAATTGGGACTCAAGGATAAAATCATTACATT
ATATTTAACCAAAGGAGCTAATATGTTAAAAAATTAATTAAAAATAATAAAAAGCTTAAAACAAC
ATGAAAT
Found at i:41647526 original size:140 final size:143
Alignment explanation
Indices: 41647247--41647529 Score: 328
Period size: 140 Copynumber: 2.0 Consensus size: 143
41647237 TTTAACTAAG
* *
41647247 GGAGTTAATATGTTAAAAATATTAATTAAAAATAATAAAAAAGCTTAAAACAACATGAAATAAAT
1 GGAGCTAATATGTTAAAAATATTAATTAAAAATAATAAAAAAGCTTAAAACAACATGAAATAAAA
* * * * ** * *
41647312 TACAAATATATTTAGAAGAGGAGGAATTGAAATTGGGACTCAAGGATAAAATCATTATCATTTAA
66 TACAAATATATATAGAAGAGAAGGAATCGAAACTACGACTCAAGAATAAAATCATTAACATTTAA
* *
41647377 CTATTTAACCAAA
131 CCATCTAACCAAA
*
41647390 GGAGCTAATATGTTAAAAA-ATTAATTAAAATTAAT-AAAAAGCTTAAAACAACATGAAATAAAA
1 GGAGCTAATATGTTAAAAATATTAATTAAAAATAATAAAAAAGCTTAAAACAACATGAAAT--AA
* **
41647453 AATACAAATGTGA-AT-G-AGA-AAGGAATCGAGCCTACGACTCAA-AACTAAAATCATTAACAT
64 AATACAAATAT-ATATAGAAGAGAAGGAATCGAAACTACGACTCAAGAA-TAAAATCATTAACAT
*
41647513 TTATCCATCTAACCAAA
127 TTAACCATCTAACCAAA
41647530 AAACATAATT
Statistics
Matches: 119, Mismatches: 17, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
139 1 0.01
140 44 0.37
141 27 0.23
142 16 0.13
143 30 0.25
144 1 0.01
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.26
Consensus pattern (143 bp):
GGAGCTAATATGTTAAAAATATTAATTAAAAATAATAAAAAAGCTTAAAACAACATGAAATAAAA
TACAAATATATATAGAAGAGAAGGAATCGAAACTACGACTCAAGAATAAAATCATTAACATTTAA
CCATCTAACCAAA
Found at i:41647866 original size:17 final size:17
Alignment explanation
Indices: 41647844--41647881 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
41647834 TAAAAAACTT
41647844 AATAAA-TAATATAGATA
1 AATAAATTAATATA-ATA
*
41647861 AATAAATTTATATAATA
1 AATAAATTAATATAATA
41647878 AATA
1 AATA
41647882 TACTAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AATAAATTAATATAATA
Found at i:41648443 original size:22 final size:23
Alignment explanation
Indices: 41648387--41648444 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
41648377 CAGCCCGTTT
* * *
41648387 TTAATTAAAATTAAAATTATTTTT
1 TTAA-TAAAATTAAAACTATATTG
41648411 TTAATAAAATTAAAACTA-ATTG
1 TTAATAAAATTAAAACTATATTG
*
41648433 TTAGTAAAATTA
1 TTAATAAAATTA
41648445 TCAAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 13 0.43
23 13 0.43
24 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (23 bp):
TTAATAAAATTAAAACTATATTG
Found at i:41648524 original size:59 final size:61
Alignment explanation
Indices: 41648454--41648633 Score: 256
Period size: 68 Copynumber: 2.9 Consensus size: 61
41648444 ATCAAATTTT
*
41648454 TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A
*
41648519 TTAATTATATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTAATTAGTAAATTTATC-A
1 -TAA-T-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
*
41648582 -AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
41648634 ACAAACTTGA
Statistics
Matches: 108, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
59 47 0.44
60 1 0.01
61 2 0.02
63 1 0.01
66 3 0.03
67 1 0.01
68 53 0.49
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (61 bp):
TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
Found at i:41648551 original size:68 final size:67
Alignment explanation
Indices: 41648433--41648603 Score: 281
Period size: 68 Copynumber: 2.5 Consensus size: 67
41648423 AAACTAATTG
* * *
41648433 TTAGTAAAATTATCAAATTTTTAA-TTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAATTTATCAAATTATTAATTTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
*
41648497 GA
66 AA
41648499 TTAGTAAATTTATCAAATTATTAATTATATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATT-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
41648564 TAA
65 TAA
41648567 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATT-TATTAATTGT
41648604 TGTAACAAAA
Statistics
Matches: 98, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
66 22 0.22
67 1 0.01
68 75 0.77
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (67 bp):
TTAGTAAATTTATCAAATTATTAATTTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
AA
Found at i:41659946 original size:29 final size:28
Alignment explanation
Indices: 41659909--41659966 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
41659899 ATATACATAT
* * *
41659909 TTTGTGGATGTAATTAGAATATTTTGAAG
1 TTTGAGGATGTAACTAGAAT-TTTTAAAG
41659938 TTTGAGGATGTAACTAGAATTTTTAAAG
1 TTTGAGGATGTAACTAGAATTTTTAAAG
41659966 T
1 T
41659967 CTGAAAATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (28 bp):
TTTGAGGATGTAACTAGAATTTTTAAAG
Found at i:41663539 original size:15 final size:15
Alignment explanation
Indices: 41663515--41663550 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
41663505 TTGGTTCTAG
41663515 AAAA-AAAAAAAAGA
1 AAAAGAAAAAAAAGA
41663529 AAAAGAAAAAAAAGA
1 AAAAGAAAAAAAAGA
41663544 ATAAAGA
1 A-AAAGA
41663551 CTCAAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 11 0.55
16 5 0.25
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (15 bp):
AAAAGAAAAAAAAGA
Found at i:41666446 original size:17 final size:17
Alignment explanation
Indices: 41666425--41666458 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41666415 AAAAGTACAA
*
41666425 AAAAAAAAAAGCAAAAGC
1 AAAAAGAAAAG-AAAAGC
41666443 AAAAAGAAAAGAAAAG
1 AAAAAGAAAAGAAAAG
41666459 AAGAATTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAGC
Found at i:41669852 original size:2 final size:2
Alignment explanation
Indices: 41669845--41669874 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
41669835 TCTTCACATT
41669845 AG AG AG AG AG AG AG AG AG A- AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
41669875 TTATAGACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41678804 original size:3 final size:3
Alignment explanation
Indices: 41678762--41678790 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41678752 TTACTTTATT
41678762 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
41678791 TAAACCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:41682284 original size:43 final size:42
Alignment explanation
Indices: 41682121--41682291 Score: 161
Period size: 43 Copynumber: 4.0 Consensus size: 42
41682111 GACTTGTACA
* * *
41682121 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACA-ATCG
* * *
41682164 ATGCC-ACTGTCCCAGACAG-GGTCATACA-CAAATCA-AATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAAACACAAT-CG
* * * **
41682205 ATGCCAATGTCCCAGACATGGTCTTACACGTCAACACAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACAA-TCG
41682248 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACA-ATCG
41682291 A
1 A
41682292 AATCCTATGT
Statistics
Matches: 103, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
40 2 0.02
41 25 0.24
42 10 0.10
43 63 0.61
44 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACAATCG
Found at i:41684919 original size:41 final size:40
Alignment explanation
Indices: 41684802--41684937 Score: 143
Period size: 41 Copynumber: 3.5 Consensus size: 40
41684792 ATCAGTTTGG
* *
41684802 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAATAATTCGAAGTAGTAAATTGA
* * * ** * *
41684842 CACGCAGTGTCTCATTGGCTAA-ACCAA--AGTAAATTGA
1 CACCCAGTGCCTCATCGAATAATTCGAAGTAGTAAATTGA
*
41684879 CACTCAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATTCGAAGTAGTAAATTGA
*
41684920 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
41684938 CTCGAAGTCG
Statistics
Matches: 76, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 23 0.30
38 3 0.04
39 6 0.08
40 18 0.24
41 26 0.34
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAATTCGAAGTAGTAAATTGA
Found at i:41685789 original size:10 final size:10
Alignment explanation
Indices: 41685776--41685839 Score: 56
Period size: 10 Copynumber: 5.7 Consensus size: 10
41685766 TCATTTCCTT
41685776 TTTCTTTTTC
1 TTTCTTTTTC
41685786 TTTCTTTCTTC
1 TTTCTTT-TTC
*
41685797 TTTTTTGTTTC
1 TTTCTT-TTTC
41685808 GTTTCTATCTTTC
1 -TTTCT-T-TTTC
41685821 TATTTCTTTTTC
1 --TTTCTTTTTC
41685833 TTTCTTT
1 TTTCTTT
41685840 ATTTTGTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
10 14 0.31
11 11 0.24
12 9 0.20
13 6 0.13
14 5 0.11
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:41685789 original size:17 final size:18
Alignment explanation
Indices: 41685764--41685835 Score: 62
Period size: 17 Copynumber: 4.1 Consensus size: 18
41685754 TCCTTCCTTC
41685764 TTTCATTTCCTTT-TTCTT
1 TTTCATTT-CTTTCTTCTT
41685782 TTTC-TTTCTTTCTTCTT
1 TTTCATTTCTTTCTTCTT
**
41685799 TTTTGTTTCGTTTCTATCTT
1 TTTCATTTC-TTTCT-TCTT
*
41685819 TCT-ATTTCTTT-TTCTT
1 TTTCATTTCTTTCTTCTT
41685835 T
1 T
41685836 CTTTATTTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
16 9 0.19
17 12 0.26
18 11 0.23
19 9 0.19
20 6 0.13
ACGTcount: A:0.04, C:0.19, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTCATTTCTTTCTTCTT
Found at i:41689405 original size:76 final size:76
Alignment explanation
Indices: 41689279--41689425 Score: 231
Period size: 76 Copynumber: 1.9 Consensus size: 76
41689269 CATCCTGTGT
* * * *
41689279 TTCGTAAGCCAATCTATGCCCAAAATCACATCAAAATCACCAAATGGCATTATCAACAAATCAAC
1 TTCGTAAGCCAATCCATACCCAAAAGCACATCAAAATCACCAAACGGCATTATCAACAAATCAAC
41689344 AGGGAACATGC
66 AGGGAACATGC
* * *
41689355 TTCGTAAGCCAATCCATACCTAAAAGCATATCAAAATCACCAAACGGCATTATCAACAAATCAAT
1 TTCGTAAGCCAATCCATACCCAAAAGCACATCAAAATCACCAAACGGCATTATCAACAAATCAAC
41689420 AGGGAA
66 AGGGAA
41689426 GGTCATATTC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.20
Consensus pattern (76 bp):
TTCGTAAGCCAATCCATACCCAAAAGCACATCAAAATCACCAAACGGCATTATCAACAAATCAAC
AGGGAACATGC
Found at i:41696601 original size:22 final size:22
Alignment explanation
Indices: 41696575--41696620 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
41696565 CAAAAGTTAT
*
41696575 AAAATGGTCATTTAATTAATTA
1 AAAATGGTCATTTAAGTAATTA
** *
41696597 AAAATTTTCATTTAAGTCATTA
1 AAAATGGTCATTTAAGTAATTA
41696619 AA
1 AA
41696621 CTGTTAGTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (22 bp):
AAAATGGTCATTTAAGTAATTA
Found at i:41699969 original size:6 final size:6
Alignment explanation
Indices: 41699958--41699987 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
41699948 TTGATGATTC
41699958 TATTTT TATTTT TATTTT TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT
41699988 AAGAAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:41703137 original size:21 final size:21
Alignment explanation
Indices: 41703097--41703137 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41703087 AATCGAGTTA
*
41703097 TTCGAATCAACTCGATTTTTT
1 TTCGAATCAACTCGAGTTTTT
* *
41703118 TTCGAATCAAGTTGAGTTTT
1 TTCGAATCAACTCGAGTTTT
41703138 CGAATTCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (21 bp):
TTCGAATCAACTCGAGTTTTT
Found at i:41703158 original size:9 final size:9
Alignment explanation
Indices: 41703140--41703175 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
41703130 TGAGTTTTCG
*
41703140 AATTCAAAT
1 AATTCGAAT
41703149 AATTCGAAT
1 AATTCGAAT
41703158 AATTCGAAT
1 AATTCGAAT
41703167 AATTCGAAT
1 AATTCGAAT
41703176 CTCAAACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:41705072 original size:2 final size:2
Alignment explanation
Indices: 41705065--41705094 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41705055 AACATTCTGA
41705065 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41705095 TAATTTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41706118 original size:18 final size:20
Alignment explanation
Indices: 41706092--41706138 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
41706082 ACACGTTGGG
*
41706092 TTATTTATTGAA-GACAAAA
1 TTATTTATTGAAGGAAAAAA
*
41706111 TT-TTTATTTAAGGAAAAAA
1 TTATTTATTGAAGGAAAAAA
41706130 TTATTTATT
1 TTATTTATT
41706139 TATTTTAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.33
19 10 0.42
20 6 0.25
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (20 bp):
TTATTTATTGAAGGAAAAAA
Found at i:41718961 original size:112 final size:109
Alignment explanation
Indices: 41718744--41718964 Score: 259
Period size: 112 Copynumber: 2.0 Consensus size: 109
41718734 AAATAATTTT
* * * *
41718744 TGTATCATTAATTTTACAAATAATTTATATTAATTAATTAAAATTTATATTTCATGTATCATTAT
1 TGTATCATTAATTTTAAAAATAATTTATATAAAGTAATTAAAATTTACATTTCATGTATCATTAT
* * *
41718809 ATTAAATTATTAAATATCATTTATCATTATATTTCAATTTTTAAA
66 ATTAAATTATTAAATATCATCTA-CATCATATTTAAATTTTTAAA
* * * *
41718854 TGTATCATTAATTTTAAAAATAA-TTATACTCAAACGTATTTAAATTTTACATTTCATTTCTCAT
1 TGTATCATTAATTTTAAAAATAATTTATA-T-AAA-GTAATTAAAATTTACATTTCATGTATCAT
41718918 TATATTAAATTATTTAAATATCATCTA-AGTCA-ATTTAATATTTTTAA
63 TATATTAAATTA-TTAAATATCATCTACA-TCATATTTAA-ATTTTTAA
41718965 TTTCCAGCAT
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
109 5 0.05
110 23 0.24
111 8 0.09
112 45 0.48
113 13 0.14
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.49
Consensus pattern (109 bp):
TGTATCATTAATTTTAAAAATAATTTATATAAAGTAATTAAAATTTACATTTCATGTATCATTAT
ATTAAATTATTAAATATCATCTACATCATATTTAAATTTTTAAA
Found at i:41730645 original size:16 final size:16
Alignment explanation
Indices: 41730620--41730669 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
41730610 CACACTATGT
41730620 CATAAGTGAATAAATC
1 CATAAGTGAATAAATC
*
41730636 CATAAATGAATAAATC
1 CATAAGTGAATAAATC
41730652 CATAAGTGAATAAATC
1 CATAAGTGAATAAATC
41730668 CA
1 CA
41730670 CTATTATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.24
Consensus pattern (16 bp):
CATAAGTGAATAAATC
Found at i:41730818 original size:210 final size:210
Alignment explanation
Indices: 41730456--41730853 Score: 769
Period size: 210 Copynumber: 1.9 Consensus size: 210
41730446 GGCTATGAAT
41730456 TCCACTATTATGAATGATGTTACATACTACAGAAGTCATATACCCAACGCACCAACTTTCGGTTC
1 TCCACTATTATGAATGATGTTACATACTACAGAAGTCATATACCCAACGCACCAACTTTCGGTTC
*
41730521 CTTATCTATTCAAATTTAGACTTTTACTTACATCAAAGTATACAAGTCACGCATACATAGTTCAT
66 CTTATCTATTCAAACTTAGACTTTTACTTACATCAAAGTATACAAGTCACGCATACATAGTTCAT
41730586 CATACACTCAAGATTAAGGTATGTCACACTATGTCATAAGTGAATAAATCCATAAATGAATAAAT
131 CATACACTCAAGATTAAGGTATGTCACACTATGTCATAAGTGAATAAATCCATAAATGAATAAAT
41730651 CCATAAGTGAATAAA
196 CCATAAGTGAATAAA
*
41730666 TCCACTATTATGAATGATGTTACATACTACAGAAGTCATATACCCAACGCACCAACTTTCGGTTT
1 TCCACTATTATGAATGATGTTACATACTACAGAAGTCATATACCCAACGCACCAACTTTCGGTTC
41730731 CTTATCTATTCAAACTTAGACTTTTACTTACATCAAAGTATACAAGTCACGCATACATAGTTCAT
66 CTTATCTATTCAAACTTAGACTTTTACTTACATCAAAGTATACAAGTCACGCATACATAGTTCAT
*
41730796 CATACACTCAAGATTAAGGTATGTCACACTATGTCATAAGTGAATAAATTCATAAATG
131 CATACACTCAAGATTAAGGTATGTCACACTATGTCATAAGTGAATAAATCCATAAATG
41730854 GATTCAAGAT
Statistics
Matches: 185, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
210 185 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (210 bp):
TCCACTATTATGAATGATGTTACATACTACAGAAGTCATATACCCAACGCACCAACTTTCGGTTC
CTTATCTATTCAAACTTAGACTTTTACTTACATCAAAGTATACAAGTCACGCATACATAGTTCAT
CATACACTCAAGATTAAGGTATGTCACACTATGTCATAAGTGAATAAATCCATAAATGAATAAAT
CCATAAGTGAATAAA
Found at i:41739239 original size:13 final size:13
Alignment explanation
Indices: 41739221--41739262 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
41739211 AGATTTTTCT
41739221 TAAATATTATCAC
1 TAAATATTATCAC
*
41739234 TAAATA--AT-TC
1 TAAATATTATCAC
41739244 TAAATATTATCAC
1 TAAATATTATCAC
41739257 TAAATA
1 TAAATA
41739263 ATTCAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 2 0.08
13 13 0.54
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATTATCAC
Found at i:41739248 original size:23 final size:23
Alignment explanation
Indices: 41739221--41739271 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
41739211 AGATTTTTCT
41739221 TAAATATTATCACTAAATAATTC
1 TAAATATTATCACTAAATAATTC
41739244 TAAATATTATCACTAAATAATTC
1 TAAATATTATCACTAAATAATTC
*
41739267 AAAAT
1 TAAAT
41739272 TTAAAAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAATATTATCACTAAATAATTC
Found at i:41742327 original size:40 final size:41
Alignment explanation
Indices: 41742270--41742359 Score: 94
Period size: 42 Copynumber: 2.2 Consensus size: 41
41742260 TCCTCGTAGG
* *
41742270 CGCGATTTGTGTCCACGTAAGC-AAAGCGCGCTGACGTGGA
1 CGCGATTTGTGTACACGTAACCGAAAGCGCGCTGACGTGGA
** * *
41742310 CGCGATTTGCTG-ACACGTCTCCTGACATCGCGCTGACGTGGA
1 CGCGATTTG-TGTACACGTAACC-GAAAGCGCGCTGACGTGGA
41742352 CGCGATTT
1 CGCGATTT
41742360 TGGGGAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
40 15 0.37
41 2 0.05
42 24 0.59
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.23
Consensus pattern (41 bp):
CGCGATTTGTGTACACGTAACCGAAAGCGCGCTGACGTGGA
Found at i:41746199 original size:77 final size:77
Alignment explanation
Indices: 41746085--41746836 Score: 694
Period size: 77 Copynumber: 9.8 Consensus size: 77
41746075 TTTAGTTTGA
** * * * *
41746085 CTGTCATTTTTACGAATCGC-TGATTTAATATCGCGACCTTCGATTTTCTAGCAGTTTGCTTGAT
1 CTGTCATTTTTACGGTTCGCTTGATTTAAGATCGCGACCTTCGATATTCTAACAGTTCGCTTGAT
* *
41746149 TTAATATCACAG
66 TTAATATCGCGG
* * * * * *
41746161 CTGTCATTTTTATGGTTTGCTCGATTTAATATCACGACCTTCGATATTCTAACAATTCGCTTGAT
1 CTGTCATTTTTACGGTTCGCTTGATTTAAGATCGCGACCTTCGATATTCTAACAGTTCGCTTGAT
*
41746226 TTAATATTGCGG
66 TTAATATCGCGG
* * * *
41746238 CTGTCATTTTTACGGTTCGCTTGATTTAAGATCGCGACATTTGATATTCTAACTGTTCACTTGAT
1 CTGTCATTTTTACGGTTCGCTTGATTTAAGATCGCGACCTTCGATATTCTAACAGTTCGCTTGAT
*
41746303 TTAATATCGCGA
66 TTAATATCGCGG
* * * * * *
41746315 CTGTCATTTTTACGGTTCGCTCGATATAAGATCGCGACATCCAATATTCTAACAGTTCGCTCGAT
1 CTGTCATTTTTACGGTTCGCTTGATTTAAGATCGCGACCTTCGATATTCTAACAGTTCGCTTGAT
41746380 TTAATATCGCGAG
66 TTAATATCGCG-G
* * * ** *
41746393 -TGTCATTTTCACGGTTTGCTCGATTTAAGATCATGACCTTCGATATTCTAACAGTTCGTTTGAT
1 CTGTCATTTTTACGGTTCGCTTGATTTAAGATCGCGACCTTCGATATTCTAACAGTTCGCTTGAT
* *
41746457 TTAAGATCGCGAC
66 TTAATATCGCG-G
* * * * * * * ** *
41746470 CTTTGATATTCTAACAGTTTGCTTGATTTAATATCGCGA-CTATC-AT-TT-TTATGGTTTGCTT
1 CTGTCAT-TT-TTACGGTTCGCTTGATTTAAGATCGCGACCT-TCGATATTCTAACAGTTCGCTT
*
41746531 GATTTAATATTGCGG
63 GATTTAATATCGCGG
* * * * * * *
41746546 TTATCATTTTTACGGTTCACTTGATTTAAGATTGCAACTTTCGATATTCTAACAGTTCACTTGAT
1 CTGTCATTTTTACGGTTCGCTTGATTTAAGATCGCGACCTTCGATATTCTAACAGTTCGCTTGAT
*
41746611 TTAATATTGCGG
66 TTAATATCGCGG
* * * * * *
41746623 TTTTCATTTTTACGATTCGCTTGATTTAAGATCCCGACCTTCGATATTCTAATAGTTCGCTCGAT
1 CTGTCATTTTTACGGTTCGCTTGATTTAAGATCGCGACCTTCGATATTCTAACAGTTCGCTTGAT
*
41746688 TTAATATTGCGG
66 TTAATATCGCGG
* * * * * * *
41746700 CTGTCATTTTTACGGTTCACTTGATTTAAGATTGCAACCATC-AGTTTTCTAATAGTTCACTTGA
1 CTGTCATTTTTACGGTTCGCTTGATTTAAGATCGCGACCTTCGA-TATTCTAACAGTTCGCTTGA
* *
41746764 TTTAATATCGTGA
65 TTTAATATCGCGG
* * * * * * *
41746777 CTGTCATTTTTACAGTCCG-TTGATTTAATATCACGACTTTC-AGTTTTCTAATAGTTCGCT
1 CTGTCATTTTTACGGTTCGCTTGATTTAAGATCGCGACCTTCGA-TATTCTAACAGTTCGCT
41746837 AATTCACAAT
Statistics
Matches: 553, Mismatches: 112, Indels: 22
0.80 0.16 0.03
Matches are distributed among these distances:
74 23 0.04
75 5 0.01
76 57 0.10
77 432 0.78
78 6 0.01
79 6 0.01
80 24 0.04
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (77 bp):
CTGTCATTTTTACGGTTCGCTTGATTTAAGATCGCGACCTTCGATATTCTAACAGTTCGCTTGAT
TTAATATCGCGG
Found at i:41746766 original size:308 final size:307
Alignment explanation
Indices: 41746219--41746773 Score: 767
Period size: 308 Copynumber: 1.8 Consensus size: 307
41746209 CTAACAATTC
* * *
41746219 GCTTGATTTAATATTGCGGCTGTCATTTTTACGGTTCGCTTGATTTAAGATCGCGACATTTGATA
1 GCTTGATTTAATATTGCGGCTATCATTTTTACGGTTCACTTGATTTAAGATCGCAACATTTGATA
* * *
41746284 TTCTAACTGTTCACTTGATTTAATATCGCGACTGTCATTTTTACGGTTCGCTCGATATAAGATCG
66 TTCTAACAGTTCACTTGATTTAATATCGCGACTGTCATTTTTACGATTCGCTCGATATAAGATCC
**
41746349 CGACATCCAATATTCTAACAGTTCGCTCGATTTAATATCGCGAGTGTCATTTTCACGGTTTGCTC
131 CGACATCCAATATTCTAACAGTTCGCTCGATTTAATATCGCGAGTGTCATTTTCACGGTTCACTC
* **
41746414 GATTTAAGATCATGACCTTCGATATTCTAACAGTTCGTTTGATTTAAGATCGCGACCTTTGATAT
196 GATTTAAGATCA-GACCATCGATATTCTAACAGTTCACTTGATTTAAGATCGCGACCTTTGATAT
41746479 TCTAACAGTTTGCTTGATTTAATATCGCGACTATCATTTTTATGGTTT
260 TCTAACAGTTTGCTTGATTTAATATCGCGACTATCATTTTTATGGTTT
* *
41746527 GCTTGATTTAATATTGCGGTTATCATTTTTACGGTTCACTTGATTTAAGATTGCAAC-TTTCGAT
1 GCTTGATTTAATATTGCGGCTATCATTTTTACGGTTCACTTGATTTAAGATCGCAACATTT-GAT
* ** * * *
41746591 ATTCTAACAGTTCACTTGATTTAATATTGCGGTTTTCATTTTTACGATTCGCTTGATTTAAGATC
65 ATTCTAACAGTTCACTTGATTTAATATCGCGACTGTCATTTTTACGATTCGCTCGATATAAGATC
* * * * * *
41746656 CCGACCTTCGATATTCTAATAGTTCGCTCGATTTAATATTGCG-GCTGTCATTTTTACGGTTCAC
130 CCGACATCCAATATTCTAACAGTTCGCTCGATTTAATATCGCGAG-TGTCATTTTCACGGTTCAC
* * * *
41746720 TTGATTTAAGATTGCA-ACCATC-AGTTTTCTAATAGTTCACTTGATTTAATATCG
194 TCGATTTAAGA-T-CAGACCATCGA-TATTCTAACAGTTCACTTGATTTAAGATCG
41746774 TGACTGTCAT
Statistics
Matches: 213, Mismatches: 29, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
307 5 0.02
308 205 0.96
309 1 0.00
310 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.42
Consensus pattern (307 bp):
GCTTGATTTAATATTGCGGCTATCATTTTTACGGTTCACTTGATTTAAGATCGCAACATTTGATA
TTCTAACAGTTCACTTGATTTAATATCGCGACTGTCATTTTTACGATTCGCTCGATATAAGATCC
CGACATCCAATATTCTAACAGTTCGCTCGATTTAATATCGCGAGTGTCATTTTCACGGTTCACTC
GATTTAAGATCAGACCATCGATATTCTAACAGTTCACTTGATTTAAGATCGCGACCTTTGATATT
CTAACAGTTTGCTTGATTTAATATCGCGACTATCATTTTTATGGTTT
Found at i:41747205 original size:2 final size:2
Alignment explanation
Indices: 41747198--41747264 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
41747188 TTAACCTCCC
41747198 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
41747240 TA TA TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
41747265 TGAGGGGGCG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:41748098 original size:12 final size:12
Alignment explanation
Indices: 41748081--41748107 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41748071 CAAACCATAC
41748081 ATTTCATTGTTT
1 ATTTCATTGTTT
41748093 ATTTCATTGTTT
1 ATTTCATTGTTT
41748105 ATT
1 ATT
41748108 GTATGTTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (12 bp):
ATTTCATTGTTT
Found at i:41752458 original size:17 final size:18
Alignment explanation
Indices: 41752432--41752466 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
41752422 ATAAAAATGG
41752432 TAATAAACAGA-AACAAT
1 TAATAAACAGATAACAAT
*
41752449 TAATAGACAGATAACAAT
1 TAATAAACAGATAACAAT
41752467 CAAAGTTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.20
Consensus pattern (18 bp):
TAATAAACAGATAACAAT
Found at i:41758668 original size:60 final size:60
Alignment explanation
Indices: 41758581--41758719 Score: 233
Period size: 60 Copynumber: 2.3 Consensus size: 60
41758571 AACCTCATCC
* *
41758581 TTACTAGTCTAGGCTAAATCCCCTGCAACGACAATTTACTCTAATGAGCTTGGATCTGAA
1 TTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTTACTCTAATGAGCTTGGATCTGAA
* *
41758641 TTACCAGTCCAGGCTAAATCTCTTGCAACGACAATTTACTCTAATGAGCTTGGATCTGAA
1 TTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTTACTCTAATGAGCTTGGATCTGAA
*
41758701 TTACCAGTCCAAGCTAAAT
1 TTACCAGTCCAGGCTAAAT
41758720 TCAGACCCTA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 74 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (60 bp):
TTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTTACTCTAATGAGCTTGGATCTGAA
Found at i:41761268 original size:65 final size:67
Alignment explanation
Indices: 41761187--41761313 Score: 159
Period size: 65 Copynumber: 1.9 Consensus size: 67
41761177 GACAAAAAAC
* * * * *
41761187 ATATAATTTCTGAAGAAACTAAAACTTAGGCTATA-A-ATATATATGTGAAAAATATTTAAATGT
1 ATATAATTTATCAAGAAACTAAAAATTAGACTATATATATATATATGCGAAAAATATTTAAATGT
41761250 AT
66 AT
* * * *
41761252 ATATAATTTATCAAGAAATTAAAAATTAGATTATATATATGTATATGCGAACAATATTTAAA
1 ATATAATTTATCAAGAAACTAAAAATTAGACTATATATATATATATGCGAAAAATATTTAAA
41761314 AGTTTCAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 29 0.57
66 1 0.02
67 21 0.41
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (67 bp):
ATATAATTTATCAAGAAACTAAAAATTAGACTATATATATATATATGCGAAAAATATTTAAATGT
AT
Found at i:41762070 original size:14 final size:14
Alignment explanation
Indices: 41762051--41762098 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
41762041 TTAAGATAGT
41762051 CAAATATATGAAAG
1 CAAATATATGAAAG
* *
41762065 CAAATAATTAAGATAG
1 CAAAT-A-TATGAAAG
41762081 TCAAATATATGAAAG
1 -CAAATATATGAAAG
41762096 CAA
1 CAA
41762099 TCAACTGCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 8 0.30
15 7 0.26
16 7 0.26
17 5 0.19
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.23
Consensus pattern (14 bp):
CAAATATATGAAAG
Found at i:41762073 original size:31 final size:31
Alignment explanation
Indices: 41762035--41762098 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
41762025 TCTGGTGTAT
41762035 AAATAATTAAGATAGTCAAATATATGAAAGC
1 AAATAATTAAGATAGTCAAATATATGAAAGC
41762066 AAATAATTAAGATAGTCAAATATATGAAAGC
1 AAATAATTAAGATAGTCAAATATATGAAAGC
41762097 AA
1 AA
41762099 TCAACTGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (31 bp):
AAATAATTAAGATAGTCAAATATATGAAAGC
Found at i:41762087 original size:17 final size:17
Alignment explanation
Indices: 41762035--41762087 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
41762025 TCTGGTGTAT
41762035 AAATAATTAAGATAGTC
1 AAATAATTAAGATAGTC
* *
41762052 AAAT-A-TATGAAAG-C
1 AAATAATTAAGATAGTC
41762066 AAATAATTAAGATAGTC
1 AAATAATTAAGATAGTC
41762083 AAATA
1 AAATA
41762088 TATGAAAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 5 0.17
15 7 0.24
16 7 0.24
17 10 0.34
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (17 bp):
AAATAATTAAGATAGTC
Found at i:41775935 original size:75 final size:75
Alignment explanation
Indices: 41775844--41775993 Score: 230
Period size: 75 Copynumber: 2.0 Consensus size: 75
41775834 TAATACAAAG
*
41775844 AACCCCTAAAATTAATAACTAAAAT-GACAAAAAAGTCATTACATAAATACAAACTTAACTATTT
1 AACCCCTAAAATTAATAACTAAAATGGA-AAAAAAGTCATTACATAAATACAAACTTAACTATTC
41775908 AAATTGAAAAA
65 AAATTGAAAAA
* * * *
41775919 AACCCCTAAAATTAATAATTGAAATGGAAAAAAAGTCATTACATAAATACAAACTTGATTATTCA
1 AACCCCTAAAATTAATAACTAAAATGGAAAAAAAGTCATTACATAAATACAAACTTAACTATTCA
*
41775984 AATTGCAAAA
66 AATTGAAAAA
41775994 CCCCCTTAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 66 0.97
76 2 0.03
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (75 bp):
AACCCCTAAAATTAATAACTAAAATGGAAAAAAAGTCATTACATAAATACAAACTTAACTATTCA
AATTGAAAAA
Found at i:41776269 original size:33 final size:33
Alignment explanation
Indices: 41776168--41776285 Score: 114
Period size: 33 Copynumber: 3.6 Consensus size: 33
41776158 CTTGAGCTGG
* ** **
41776168 GGAGTGAAGTACTGCGGTGGATACAAGCC-GAGA
1 GGAGTGGAGTACTAAGGTGGATACGGGCCGGA-A
* * * *
41776201 GGAGTGG-GTACTAAAGTGGATATGGGCTGGGA
1 GGAGTGGAGTACTAAGGTGGATACGGGCCGGAA
* *
41776233 GGAGTGGAGTATTGAGGTGGATACGGGCCGGAA
1 GGAGTGGAGTACTAAGGTGGATACGGGCCGGAA
41776266 GGAGTGGAGTACTAAGGTGG
1 GGAGTGGAGTACTAAGGTGG
41776286 TAGTGGGCTG
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
32 22 0.33
33 44 0.67
ACGTcount: A:0.26, C:0.09, G:0.46, T:0.19
Consensus pattern (33 bp):
GGAGTGGAGTACTAAGGTGGATACGGGCCGGAA
Found at i:41776272 original size:65 final size:66
Alignment explanation
Indices: 41776168--41776295 Score: 163
Period size: 65 Copynumber: 2.0 Consensus size: 66
41776158 CTTGAGCTGG
*
41776168 GGAGTGAAGTACTGCGGTGGATACAAGCCGAGAGGAGTGG-GTACTAAAGTGGATA-TGGGCTGG
1 GGAGTGAAGTACTGAGGTGGATACAAGCCGAGAGGAGTGGAGTACTAAAGTGG-TAGTGGGCTGG
41776231 GA
65 GA
* * ** *
41776233 GGAGTGGAGTATTGAGGTGGATACGGGCCG-GAAGGAGTGGAGTACTAAGGTGGTAGTGGGCTG
1 GGAGTGAAGTACTGAGGTGGATACAAGCCGAG-AGGAGTGGAGTACTAAAGTGGTAGTGGGCTG
41776296 AAGATATCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
64 1 0.02
65 35 0.65
66 18 0.33
ACGTcount: A:0.25, C:0.09, G:0.46, T:0.20
Consensus pattern (66 bp):
GGAGTGAAGTACTGAGGTGGATACAAGCCGAGAGGAGTGGAGTACTAAAGTGGTAGTGGGCTGGG
A
Found at i:41778362 original size:104 final size:100
Alignment explanation
Indices: 41778282--41778767 Score: 541
Period size: 104 Copynumber: 4.8 Consensus size: 100
41778272 AAAATCAAAT
* *
41778282 AAATTTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTAATCAT
1 AAATCTACATTACTAAAAAATCACAAAACACTAAACTTAACACTAACAATTTATAACCTAATCAT
41778347 AAATTACTAACAAAATAACTATAAATTTTAAAAAAAAA
66 AAATTACTAACAAAAT-A-TATAAA-TTTAAAAAAAAA
*
41778385 AAATCTACATTACTAAAAAAATCACAAAACACAAAACTTAACACTAACAATTTATAACCTAATCA
1 AAATCTACATTACT-AAAAAATCACAAAACACTAAACTTAACACTAACAATTTATAACCTAATCA
***
41778450 TAAATTACTAACAAAATAACTATAAATTTTTTTAAAAAA
65 TAAATTACTAACAAAAT-A-TATAAA-TTTAAAAAAAAA
41778489 AAATCTACATTACTTAAAAAATCACAAAACACTAAACTTAACACTAACAATTTATAACCTAATCA
1 AAATCTACATTAC-TAAAAAATCACAAAACACTAAACTTAACACTAACAATTTATAACCTAATCA
* ***
41778554 TAAATTACTAACAAAATAACTATAATTTTTTTTAAAAAA
65 TAAATTACTAACAAAAT-A-TATAA-ATTTAAAAAAAAA
* ** *
41778593 AAATCTACATTACTTAAAAAATCACAAAACACTAACAATTTATA-ACCTAATC-ATAAATTA-CT
1 AAATCTACATTAC-TAAAAAATCACAAAACACT-A-AACTTA-ACA-CTAA-CAATTTATAACCT
* * ***
41778655 AA-CA-AAATAACT-ATAAAAT-T-T---TTT-TTTAAAA-
60 AATCATAAATTACTAACAAAATATATAAATTTAAAAAAAAA
41778686 -AATCTACATTACTAAAAAAATCACAAAACACTAAACTTAACACTAACAATTTATAACCTAATCA
1 AAATCTACATTACT-AAAAAATCACAAAACACTAAACTTAACACTAACAATTTATAACCTAATCA
41778750 TAAATTACTAACAAAATA
65 TAAATTACTAACAAAATA
41778768 ATTTTACATT
Statistics
Matches: 346, Mismatches: 21, Indels: 41
0.85 0.05 0.10
Matches are distributed among these distances:
88 1 0.00
89 10 0.03
90 10 0.03
91 4 0.01
92 37 0.11
93 6 0.02
94 6 0.02
95 3 0.01
99 1 0.00
100 1 0.00
103 19 0.05
104 223 0.64
105 4 0.01
106 10 0.03
107 10 0.03
108 1 0.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (100 bp):
AAATCTACATTACTAAAAAATCACAAAACACTAAACTTAACACTAACAATTTATAACCTAATCAT
AAATTACTAACAAAATATATAAATTTAAAAAAAAA
Found at i:41778686 original size:92 final size:91
Alignment explanation
Indices: 41778424--41778719 Score: 405
Period size: 92 Copynumber: 3.1 Consensus size: 91
41778414 CACAAAACTT
*
41778424 AACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTATAAATTTTTTTAAAAAA
1 AACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTAT-AATTTTTTTTAAAAA
*
41778489 AAATCTACATTACTTAAAAAATCACAAAACACTAAA
65 AAATCTACATTAC-T---AAA--A-AAATCAC--AA
41778525 CTTAACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTATAATTTTTTTTAAA
1 ---AACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTATAATTTTTTTT-AA
*
41778590 AAAAAATCTACATTACTTAAAAAATCACAA
62 AAAAAATCTACATTACTAAAAAAATCACAA
*
41778620 AACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTATAAAATTTTTTTT-TAA
1 AACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTAT--AATTTTTTTTAAAA
41778684 AAAATCTACATTACTAAAAAAATCACAA
64 AAAATCTACATTACTAAAAAAATCACAA
41778712 AACACTAA
1 AACACTAA
41778720 ACTTAACACT
Statistics
Matches: 184, Mismatches: 5, Indels: 18
0.89 0.02 0.09
Matches are distributed among these distances:
92 86 0.47
94 10 0.05
95 2 0.01
97 6 0.03
98 1 0.01
100 2 0.01
103 10 0.05
104 67 0.36
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (91 bp):
AACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTATAATTTTTTTTAAAAAA
AATCTACATTACTAAAAAAATCACAA
Found at i:41778835 original size:80 final size:82
Alignment explanation
Indices: 41778690--41778853 Score: 224
Period size: 80 Copynumber: 2.0 Consensus size: 82
41778680 TTAAAAAATC
* ** * *
41778690 TACATTACTAAAAAAATCACAAAACACTAAACTTAACACTAACAATTTATAACCTAATCATAAAT
1 TACATTAATAAAAAAATCACAAAACAAAAAACTAAACACTAACAATTTATAACATAATCATAAAT
41778755 TACTAACAAAATAATTT
66 TACTAACAAAATAATTT
* *
41778772 TACATTAAT-AAAAAATCACAAAATAAAAAACTAAACAC-AACAATTTATAACATAATCCTAAAT
1 TACATTAATAAAAAAATCACAAAACAAAAAACTAAACACTAACAATTTATAACATAATCATAAAT
* * *
41778835 TATTTACAAAATGATTT
66 TACTAACAAAATAATTT
41778852 TA
1 TA
41778854 AAATAATTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
80 39 0.54
81 25 0.35
82 8 0.11
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.29
Consensus pattern (82 bp):
TACATTAATAAAAAAATCACAAAACAAAAAACTAAACACTAACAATTTATAACATAATCATAAAT
TACTAACAAAATAATTT
Found at i:41778891 original size:15 final size:16
Alignment explanation
Indices: 41778853--41778892 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
41778843 AAATGATTTT
41778853 AAAATA-ATT-ATAAA
1 AAAATACATTCATAAA
41778867 AAAATTACATTCATAAA
1 AAAA-TACATTCATAAA
41778884 AAAA-ACATT
1 AAAATACATT
41778893 AAACCATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.17
15 7 0.30
16 3 0.13
17 9 0.39
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATACATTCATAAA
Found at i:41779061 original size:24 final size:27
Alignment explanation
Indices: 41779016--41779079 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 27
41779006 CTTACATTTT
* *
41779016 TTCTTTCTTTCTT-TCTTCTTC-TTC-
1 TTCTTTTTTTCTTCTCCTCTTCTTTCA
41779040 TTCTTTTTTTCTTCTCCT-TTCTTTCA
1 TTCTTTTTTTCTTCTCCTCTTCTTTCA
*
41779066 CTCTTTTTTTCTTC
1 TTCTTTTTTTCTTC
41779080 ACTCCTGCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 15 0.44
25 6 0.18
26 13 0.38
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (27 bp):
TTCTTTTTTTCTTCTCCTCTTCTTTCA
Found at i:41779352 original size:24 final size:24
Alignment explanation
Indices: 41779320--41779367 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
41779310 GTCCAGATAT
* *
41779320 ATATATTTTTAAATAATAAAAAAA
1 ATATATTTTTAAAAAACAAAAAAA
41779344 ATATATTTTTAAAAAACAAAAAAA
1 ATATATTTTTAAAAAACAAAAAAA
41779368 TTATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
ATATATTTTTAAAAAACAAAAAAA
Found at i:41780282 original size:18 final size:18
Alignment explanation
Indices: 41780261--41780313 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
41780251 GACAAAAAGG
41780261 ACAAGAAAGACAAAGATC
1 ACAAGAAAGACAAAGATC
**
41780279 ACAAGAAAGGTAAAGATC
1 ACAAGAAAGACAAAGATC
*
41780297 ATAA-AGAAGACAAAGAT
1 ACAAGA-AAGACAAAGAT
41780314 GAAGGGATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 1 0.03
18 28 0.97
ACGTcount: A:0.60, C:0.11, G:0.19, T:0.09
Consensus pattern (18 bp):
ACAAGAAAGACAAAGATC
Found at i:41780382 original size:105 final size:105
Alignment explanation
Indices: 41780306--41780562 Score: 334
Period size: 105 Copynumber: 2.4 Consensus size: 105
41780296 CATAAAGAAG
41780306 ACAAAGATGAAGGGATGATGGATAAAATCAAGGACATGATCACGGGTGATAAAGATGACGATAAG
1 ACAAAGATGAAGGGATGATGGATAAAATCAAGGACATGATCACGGGTGATAAAGATGACGATAAG
* * * * *
41780371 CATAAGAAAGATGACCATAAGCACAAGGACCGCAAAGAGC
66 CACAAGAAAGATCACAAAAAGCACAAGGACCACAAAGAGC
* *
41780411 ACAAGGATGAAGGGATGATGGATAAAATCAAGGACATGATCACTGGTGATAAAGATGACGATAAG
1 ACAAAGATGAAGGGATGATGGATAAAATCAAGGACATGATCACGGGTGATAAAGATGACGATAAG
* * * * * *
41780476 CACAAGAAAGATGACCATAAGCACAAGGAACGCAAAGAAC
66 CACAAGAAAGATCACAAAAAGCACAAGGACCACAAAGAGC
* * * * * *
41780516 ACAAGGATGAAGGGATGCTAGATAAGATCAAAGACAAGATCCACGGG
1 ACAAAGATGAAGGGATGATGGATAAAATCAAGGACATGAT-CACGGG
41780563 GATGACGATC
Statistics
Matches: 140, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
105 135 0.96
106 5 0.04
ACGTcount: A:0.46, C:0.14, G:0.27, T:0.13
Consensus pattern (105 bp):
ACAAAGATGAAGGGATGATGGATAAAATCAAGGACATGATCACGGGTGATAAAGATGACGATAAG
CACAAGAAAGATCACAAAAAGCACAAGGACCACAAAGAGC
Found at i:41780485 original size:21 final size:21
Alignment explanation
Indices: 41780461--41780502 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
41780451 CACTGGTGAT
*
41780461 AAAGATGACGATAAGCACAAG
1 AAAGATGACCATAAGCACAAG
41780482 AAAGATGACCATAAGCACAAG
1 AAAGATGACCATAAGCACAAG
41780503 GAACGCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.17, G:0.21, T:0.10
Consensus pattern (21 bp):
AAAGATGACCATAAGCACAAG
Found at i:41780623 original size:18 final size:18
Alignment explanation
Indices: 41780583--41780623 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
41780573 GTGGCCGCGA
* *
41780583 CCGTCGTCGCGATAGTAG
1 CCGTGGTCGCGATAGCAG
41780601 CCGTGGTCGCGATAGCAG
1 CCGTGGTCGCGATAGCAG
*
41780619 TCGTG
1 CCGTG
41780624 ATCGTGACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.27, G:0.37, T:0.22
Consensus pattern (18 bp):
CCGTGGTCGCGATAGCAG
Found at i:41780763 original size:15 final size:16
Alignment explanation
Indices: 41780726--41780765 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
41780716 AGTGATGACG
41780726 AGAAG-AAGAAAAAGA
1 AGAAGAAAGAAAAAGA
*
41780741 AGAAGAAAGGAAAA-A
1 AGAAGAAAGAAAAAGA
41780756 AGAAGAAAGA
1 AGAAGAAAGA
41780766 CGATGGTAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (16 bp):
AGAAGAAAGAAAAAGA
Found at i:41784160 original size:9 final size:9
Alignment explanation
Indices: 41784146--41784182 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41784136 TATAGTTTGA
41784146 TATTCGAAT
1 TATTCGAAT
41784155 TATTCGAAT
1 TATTCGAAT
*
41784164 TATTCGAGT
1 TATTCGAAT
41784173 TATTCGAAT
1 TATTCGAAT
41784182 T
1 T
41784183 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41784377 original size:6 final size:6
Alignment explanation
Indices: 41784366--41784399 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
41784356 ATAATTATCA
41784366 AATAGT AATAGT AATAGT AATAGT AATAGT AATA
1 AATAGT AATAGT AATAGT AATAGT AATAGT AATA
41784400 TAAGGTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (6 bp):
AATAGT
Found at i:41792608 original size:13 final size:13
Alignment explanation
Indices: 41792590--41792614 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41792580 ACAATTACAG
41792590 ATTTAACCCAGAA
1 ATTTAACCCAGAA
41792603 ATTTAACCCAGA
1 ATTTAACCCAGA
41792615 TTTCAGGGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (13 bp):
ATTTAACCCAGAA
Found at i:41793344 original size:21 final size:22
Alignment explanation
Indices: 41793318--41793386 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 22
41793308 CTATATGAGT
41793318 GGTGTCGCTTCAAACAATAGAA
1 GGTGTCGCTTCAAACAATAGAA
*
41793340 -GTGTCGCTTCAAGCAACATAAGAAA
1 GGTGTCGCTTCAAAC-A-AT-AG-AA
41793365 TGGTGTCGCTTCAAACAATAGA
1 -GGTGTCGCTTCAAACAATAGA
41793387 TGTGGGGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
21 13 0.33
22 1 0.03
23 3 0.08
24 4 0.10
25 4 0.10
26 1 0.03
27 13 0.33
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (22 bp):
GGTGTCGCTTCAAACAATAGAA
Found at i:41813897 original size:18 final size:19
Alignment explanation
Indices: 41813857--41813898 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
41813847 TCTTGTTGAC
*
41813857 ATAAAATTCTTAAATAACT
1 ATAAAATCCTTAAATAACT
*
41813876 -TAAAATCCTT-AATAATT
1 ATAAAATCCTTAAATAACT
41813893 ATAAAA
1 ATAAAA
41813899 AATTCGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAAATCCTTAAATAACT
Found at i:41819230 original size:3 final size:3
Alignment explanation
Indices: 41819222--41819258 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
41819212 TTAAAAGGAA
41819222 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41819259 AAGTGATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:41823588 original size:38 final size:38
Alignment explanation
Indices: 41823537--41823612 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
41823527 CAAAATCCTC
41823537 CCTATCTACAAGTAAGACTTGGTTTTCTTTTTATCCAA
1 CCTATCTACAAGTAAGACTTGGTTTTCTTTTTATCCAA
41823575 CCTATCTACAAGTAAGACTTGGTTTTCTTTTTATCCAA
1 CCTATCTACAAGTAAGACTTGGTTTTCTTTTTATCCAA
41823613 GTTTTCATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (38 bp):
CCTATCTACAAGTAAGACTTGGTTTTCTTTTTATCCAA
Found at i:41829795 original size:43 final size:43
Alignment explanation
Indices: 41829747--41830166 Score: 515
Period size: 43 Copynumber: 9.8 Consensus size: 43
41829737 GCGCTGCAAA
* *
41829747 AAACGCCGCTAAAGACCATGAGCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
41829790 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
41829833 AAATGCCGCTAAAGACCAAGATCATTAGCGGCGCTTTTCCAAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
41829876 AAACGCCGCTAAAGACCAAGACCATTAGCGGTGCTTTACCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
41829919 AAACGCCGCAAAAGACAAAGACCATTAGCGACGCTTTTCCTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
41829962 AAACGCCGCTAAAGACAAAGACCTTTAGTGACACTTTCCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
41830005 AAACGCCGCTATAGATCAA-ACCTTTAGCGACGCTTCTCACGA-
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTC-CCAC
*
41830047 AAACGCCGCTAAAGACCAAGACCATTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
41830090 AAACGCCGCTAAAAACAAAGACCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
41830133 AAACGCCGCTATAGATCAA-A-CTTTAGCGGCGCTT
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT
41830167 CTGGCGAAAA
Statistics
Matches: 327, Mismatches: 47, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
41 14 0.04
42 35 0.11
43 278 0.85
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:41830082 original size:128 final size:127
Alignment explanation
Indices: 41829769--41830186 Score: 525
Period size: 128 Copynumber: 3.3 Consensus size: 127
41829759 AGACCATGAG
* * * * * *
41829769 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTCCCACA
1 CTTTAGCGGCGCTTCTACGA-AAACGCCGCTAAAGACCAAGACCATTAGCGGCGCTTTTCCCACA
* * * * * * * *
41829834 AATGCCGCTAAAGACCAAGATCATTAGCGGCGCTTTTCCAACAAACGCCGCTAAAGACCAAGAC
65 AACGCCGCTAAAGACAAAGACCTTTAGCGGCGCTTTCCCCACAAACGCCGCTATAGATCAA-AC
* * * * * * *
41829898 CATTAGCGGTGCTT-TACCCACAAACGCCGCAAAAGACAAAGACCATTAGCGACGCTTTTCCTAC
1 CTTTAGCGGCGCTTCTA-CGA-AAACGCCGCTAAAGACCAAGACCATTAGCGGCGCTTTTCCCAC
* * *
41829962 AAACGCCGCTAAAGACAAAGACCTTTAGTGACACTTTCCCCACAAACGCCGCTATAGATCAAAC
64 AAACGCCGCTAAAGACAAAGACCTTTAGCGGCGCTTTCCCCACAAACGCCGCTATAGATCAAAC
*
41830026 CTTTAGCGACGCTTCTCACGAAAACGCCGCTAAAGACCAAGACCATTAGCGGCGCTTTTCCCACA
1 CTTTAGCGGCGCTTCT-ACGAAAACGCCGCTAAAGACCAAGACCATTAGCGGCGCTTTTCCCACA
*
41830091 AACGCCGCTAAAAACAAAGACCTTTAGCGGCGCTTTCCCCACAAACGCCGCTATAGATCAAA-
65 AACGCCGCTAAAGACAAAGACCTTTAGCGGCGCTTTCCCCACAAACGCCGCTATAGATCAAAC
*
41830153 CTTTAGCGGCGCTTCTGGCGAAAACGCCGCTAAA
1 CTTTAGCGGCGCTTCT-ACGAAAACGCCGCTAAA
41830187 AACATAACCT
Statistics
Matches: 250, Mismatches: 36, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
127 31 0.12
128 112 0.45
129 106 0.42
130 1 0.00
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.19
Consensus pattern (127 bp):
CTTTAGCGGCGCTTCTACGAAAACGCCGCTAAAGACCAAGACCATTAGCGGCGCTTTTCCCACAA
ACGCCGCTAAAGACAAAGACCTTTAGCGGCGCTTTCCCCACAAACGCCGCTATAGATCAAAC
Found at i:41830552 original size:43 final size:43
Alignment explanation
Indices: 41830486--41830572 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
41830476 ACATATGCAA
* *
41830486 GGTAATAAAACATACAATGCATTT-TCTTAATCAAGTAAATCTT
1 GGTAATAAAACATACAATACATTTAT-TTAATCAAGGAAATCTT
* *
41830529 GGTAATAAAAGATATAATACATTTATTTAATCAAGGAAATCTT
1 GGTAATAAAACATACAATACATTTATTTAATCAAGGAAATCTT
41830572 G
1 G
41830573 CAATGAACTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 38 0.97
44 1 0.03
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (43 bp):
GGTAATAAAACATACAATACATTTATTTAATCAAGGAAATCTT
Found at i:41836497 original size:33 final size:33
Alignment explanation
Indices: 41836455--41836526 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
41836445 AATCTAAATT
* *
41836455 CTAAACCCTAACCCGACCCTAAATCCCTAATCC
1 CTAAACCCTAACCCGACCCAAAATCCCTAACCC
*
41836488 CTAAACCCTAACTCGACCCAAAATCCCTAACCC
1 CTAAACCCTAACCCGACCCAAAATCCCTAACCC
41836521 CTAAAC
1 CTAAAC
41836527 ATTATTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.36, C:0.44, G:0.03, T:0.17
Consensus pattern (33 bp):
CTAAACCCTAACCCGACCCAAAATCCCTAACCC
Found at i:41837439 original size:41 final size:41
Alignment explanation
Indices: 41837379--41837619 Score: 308
Period size: 41 Copynumber: 5.9 Consensus size: 41
41837369 TTTTATTATT
* *
41837379 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGTCCAGAGC
1 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGGCCAGAGC
41837420 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGGTCC-GAGC
1 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGG-CCAGAGC
* * *
41837461 ATTAGCGGCGCTTCATCAAAAACGCCGTTAAAAGCCAGAGC
1 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGGCCAGAGC
* *
41837502 ATTAGTGGCGCTTCTA-CAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTT-TATCAAAAACGCCGCTAAAGGCCAGAGC
* * * ** *
41837543 ATTAGCGGCGCTTTTTTAGAAATACCGTTAAAGGCCAGAGC
1 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGGCCAGAGC
*
41837584 ATTAGCGGCGCTTCT-TCAAAAACGCCGTTAAAGGCC
1 ATTAGCGGCGCTT-TATCAAAAACGCCGCTAAAGGCC
41837620 CCAAAAACTC
Statistics
Matches: 173, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
40 3 0.02
41 166 0.96
42 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (41 bp):
ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGGCCAGAGC
Found at i:41837522 original size:82 final size:82
Alignment explanation
Indices: 41837379--41837620 Score: 344
Period size: 82 Copynumber: 3.0 Consensus size: 82
41837369 TTTTATTATT
*
41837379 ATTAGCGGCGCTTTTTCAAAAACGCCGCT-AAAGTCCAGAGCATTAGCGGCGCTT-TATCAAAAA
1 ATTAGCGGCGCTTTTTCAAAAACGCCGTTAAAAG-CCAGAGCATTAGCGGCGCTTCTA-CAAAAA
*
41837442 CGCCGCTAAAGGTCCGAGC
64 CGCCGCTAAAGGCCCGAGC
** *
41837461 ATTAGCGGCGCTTCATCAAAAACGCCGTTAAAAGCCAGAGCATTAGTGGCGCTTCTACAAAAACG
1 ATTAGCGGCGCTTTTTCAAAAACGCCGTTAAAAGCCAGAGCATTAGCGGCGCTTCTACAAAAACG
41837526 CCGCTAAAGGCCCGAGC
66 CCGCTAAAGGCCCGAGC
* * ** * *
41837543 ATTAGCGGCGCTTTTTTAGAAATACCGTTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACG
1 ATTAGCGGCGCTTTTTCAAAAACGCCGTTAAAAGCCAGAGCATTAGCGGCGCTTCTACAAAAACG
*
41837608 CCGTTAAAGGCCC
66 CCGCTAAAGGCCC
41837621 CAAAAACTCA
Statistics
Matches: 143, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
82 137 0.96
83 6 0.04
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (82 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGTTAAAAGCCAGAGCATTAGCGGCGCTTCTACAAAAACG
CCGCTAAAGGCCCGAGC
Found at i:41837603 original size:123 final size:123
Alignment explanation
Indices: 41837379--41837615 Score: 350
Period size: 123 Copynumber: 1.9 Consensus size: 123
41837369 TTTTATTATT
* * * *
41837379 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGTCCAGAGCATTAGCGGCGCTTTATCAAAAACG
1 ATTAGCGGCGCTTCTACAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTTATCAAAAACA
41837444 CCGCTAAAGGTCCGAGCATTAGCGGCGCTTCATCAAAAACGCCGTTAAAAGCCAGAGC
66 CCGCTAAAGGTCCGAGCATTAGCGGCGCTTCATCAAAAACGCCGTTAAAAGCCAGAGC
* * * * * *
41837502 ATTAGTGGCGCTTCTACAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTTTTTAGAAATA
1 ATTAGCGGCGCTTCTACAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTTATCAAAAACA
* *
41837567 CCGTTAAAGG-CCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGTTAAA
66 CCGCTAAAGGTCC-GAGCATTAGCGGCGCTTCATCAAAAACGCCGTTAAA
41837616 GGCCCCAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
122 2 0.02
123 99 0.98
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (123 bp):
ATTAGCGGCGCTTCTACAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTTATCAAAAACA
CCGCTAAAGGTCCGAGCATTAGCGGCGCTTCATCAAAAACGCCGTTAAAAGCCAGAGC
Found at i:41837780 original size:40 final size:38
Alignment explanation
Indices: 41837681--41837790 Score: 112
Period size: 40 Copynumber: 2.8 Consensus size: 38
41837671 TCAGAAAACG
* *
41837681 CCGCTAATGCTTATTTTTAGAGGCGTTTTCCAAAAAGCG
1 CCGCTAATGCTTATTTTTAGAGGCGTTTT-TAAAAAGCA
* ** *
41837720 CTGCTAATGCTATACCTTTAGAGGCGTTTTTATAAAAGTA
1 CCGCTAATGCT-TATTTTTAGAGGCGTTTTTA-AAAAGCA
* *
41837760 CCGCTAATGCTCGATTTTTAGTGGCGTTTTT
1 CCGCTAATGCT-TATTTTTAGAGGCGTTTTT
41837791 TGTCCAAACG
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
39 11 0.19
40 46 0.81
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (38 bp):
CCGCTAATGCTTATTTTTAGAGGCGTTTTTAAAAAGCA
Found at i:41837813 original size:12 final size:12
Alignment explanation
Indices: 41837796--41837821 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41837786 TTTTTTGTCC
41837796 AAACGCTGCTAA
1 AAACGCTGCTAA
41837808 AAACGCTGCTAA
1 AAACGCTGCTAA
41837820 AA
1 AA
41837822 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (12 bp):
AAACGCTGCTAA
Found at i:41837982 original size:18 final size:18
Alignment explanation
Indices: 41837959--41837993 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41837949 AAATATGTAG
41837959 ATAAATATATAA-ACTAAT
1 ATAAATA-ATAATACTAAT
41837977 ATAAATAATAATACTAA
1 ATAAATAATAATACTAA
41837994 CAATAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAATAATAATACTAAT
Found at i:41838813 original size:13 final size:13
Alignment explanation
Indices: 41838797--41838821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41838787 AAAGAAAAAG
41838797 AAAAATAAAAATA
1 AAAAATAAAAATA
41838810 AAAAATAAAAAT
1 AAAAATAAAAAT
41838822 CAAATCCCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:41839566 original size:100 final size:100
Alignment explanation
Indices: 41839412--41840129 Score: 1114
Period size: 100 Copynumber: 7.2 Consensus size: 100
41839402 TACTGTTGTA
* * *
41839412 GCTTCAATCTG-TCCACTGCACCGCCAGGGAAGTAAGATTTGCCGCTGTGGCTTTAATCTTTTTA
1 GCTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTA
41839476 ACTGCAATGTCGGGGAAGCGAGATTCACCGATGTG
66 ACTGCAATGTCGGGGAAGCGAGATTCACCGATGTG
* *
41839511 GCTTTAATCTGCTCCACTGCACCGCTAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTGA
1 GCTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTA
*
41839576 ACTGCAATGTCGGAGAAGCGAGATTCACCGATGTG
66 ACTGCAATGTCGGGGAAGCGAGATTCACCGATGTG
* * * *
41839611 GCTTTAATCTGCTCCACTGCACCGCCAGAGAAGCAGGATTTGCCGCTGTGGCTTTAACCTTTTTA
1 GCTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTA
*
41839676 ACTGCAATATCGGGGAAGCGAGATTCACCGATGTG
66 ACTGCAATGTCGGGGAAGCGAGATTCACCGATGTG
* * *
41839711 GCTTTAATCTGCTCAACTACACCGCCAAGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTA
1 GCTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTA
* *
41839776 ACTGCAATGTCGGGGAAGCGAGATTCACTGATATG
66 ACTGCAATGTCGGGGAAGCGAGATTCACCGATGTG
* ** * *
41839811 GCTTTAATCTGCTCCATTGCACCGATAGGGAAGTATGATTCACCGCTGTGGCTTTAATCTTTTTA
1 GCTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTA
* * * *
41839876 ACTACAATGTCAGAGAAGCGAGATTCACCGATATG
66 ACTGCAATGTCGGGGAAGCGAGATTCACCGATGTG
* * * *
41839911 GCTTTAATCTGCTCTACTGCACCGCCAGAGAAGTAGGATTCGCCACTGTGGCTTTAACCTTTTTA
1 GCTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTA
41839976 ACTGCAATGTCGGGGAAGCGAGATTCACCGATGTG
66 ACTGCAATGTCGGGGAAGCGAGATTCACCGATGTG
* *
41840011 GCTTTAATCTGCTCCACTGCACCGCCAAGGAAGTAGGATTCGCCACTGTGGCTTTAATCTTTTTA
1 GCTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTA
* *
41840076 ACTGCAACGTCAGGGAAGCGAGATTCACCGATGTG
66 ACTGCAATGTCGGGGAAGCGAGATTCACCGATGTG
* *
41840111 ACTTTAATCTGTTCCACTG
1 GCTTTAATCTGCTCCACTG
41840130 TAATCTCAGG
Statistics
Matches: 561, Mismatches: 57, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
99 10 0.02
100 551 0.98
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (100 bp):
GCTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTA
ACTGCAATGTCGGGGAAGCGAGATTCACCGATGTG
Found at i:41840139 original size:50 final size:50
Alignment explanation
Indices: 41839457--41840141 Score: 403
Period size: 50 Copynumber: 13.7 Consensus size: 50
41839447 GATTTGCCGC
* * ** *
41839457 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACCGA
1 TGTGGCTTTAATCTGTTCAACTGCAACCTCAGGGAAGCGAGATTCACCGA
* * * * * *
41839507 TGTGGCTTTAATCTGCTCCACTGC-ACCGCTAGGGAAG-TAGGATTCGCCGC
1 TGTGGCTTTAATCTGTTCAACTGCAACCTC-AGGGAAGCGA-GATTCACCGA
* * **
41839557 TGTGGCTTTAATCTTTTGAACTGCAATGTC-GGAGAAGCGAGATTCACCGA
1 TGTGGCTTTAATCTGTTCAACTGCAACCTCAGG-GAAGCGAGATTCACCGA
* * * * ** *
41839607 TGTGGCTTTAATCTGCTCCACTGC-ACCGCCAGAGAAGC-AGGATTTGCCGC
1 TGTGGCTTTAATCTGTTCAACTGCAACC-TCAGGGAAGCGA-GATTCACCGA
* * * ** *
41839657 TGTGGCTTTAACCTTTTTAACTGCAATATCGGGGAAGCGAGATTCACCGA
1 TGTGGCTTTAATCTGTTCAACTGCAACCTCAGGGAAGCGAGATTCACCGA
* * * * * * *
41839707 TGTGGCTTTAATCTGCTCAACTAC-ACCGCCAAGGAAG-TAGGATTCGCCGC
1 TGTGGCTTTAATCTGTTCAACTGCAACC-TCAGGGAAGCGA-GATTCACCGA
* * ** * *
41839757 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACTGA
1 TGTGGCTTTAATCTGTTCAACTGCAACCTCAGGGAAGCGAGATTCACCGA
* * * * * *
41839807 TATGGCTTTAATCTGCTCCATTGC-ACCGAT-AGGGAAG-TATGATTCACCGC
1 TGTGGCTTTAATCTGTTCAACTGCAACC--TCAGGGAAGCGA-GATTCACCGA
* * * ** *
41839857 TGTGGCTTTAATCTTTTTAACTACAATGTCAGAGAAGCGAGATTCACCGA
1 TGTGGCTTTAATCTGTTCAACTGCAACCTCAGGGAAGCGAGATTCACCGA
* * * * * * *
41839907 TATGGCTTTAATCTGCTCTACTGC-ACCGCCAGAGAAG-TAGGATTCGCC-A
1 TGTGGCTTTAATCTGTTCAACTGCAACC-TCAGGGAAGCGA-GATTCACCGA
* * * ** *
41839956 CTGTGGCTTTAACCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACCGA
1 -TGTGGCTTTAATCTGTTCAACTGCAACCTCAGGGAAGCGAGATTCACCGA
* * * * * *
41840007 TGTGGCTTTAATCTGCTCCACTGC-ACCGCCAAGGAAG-TAGGATTCGCC-A
1 TGTGGCTTTAATCTGTTCAACTGCAACC-TCAGGGAAGCGA-GATTCACCGA
* * *
41840056 CTGTGGCTTTAATCTTTTTAACTGCAACGTCAGGGAAGCGAGATTCACCGA
1 -TGTGGCTTTAATCTGTTCAACTGCAACCTCAGGGAAGCGAGATTCACCGA
* * * *
41840107 TGTGACTTTAATCTGTTCCACTGTAATCTCAGGGA
1 TGTGGCTTTAATCTGTTCAACTGCAACCTCAGGGA
41840142 GATAAGATCT
Statistics
Matches: 456, Mismatches: 147, Indels: 64
0.68 0.22 0.10
Matches are distributed among these distances:
49 18 0.04
50 420 0.92
51 18 0.04
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (50 bp):
TGTGGCTTTAATCTGTTCAACTGCAACCTCAGGGAAGCGAGATTCACCGA
Found at i:41840174 original size:46 final size:46
Alignment explanation
Indices: 41840116--41840369 Score: 176
Period size: 46 Copynumber: 5.7 Consensus size: 46
41840106 ATGTGACTTT
*
41840116 AATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGTAATTCTTC
1 AATCTATTCCACTGTAATCTCAGGGAGATAAGATCTGTAATTCTTC
* * * *
41840162 AGTCTATTCCACTGTAATATCAGGGAGATAAGACCTG--A---TAC
1 AATCTATTCCACTGTAATCTCAGGGAGATAAGATCTGTAATTCTTC
* * * * *
41840203 GATCTACTCTACTGTAA-CTTC-GGAGAGATAATATTCT-TTATT-TT-
1 AATCTATTCCACTGTAATC-TCAGG-GAGATAAGA-TCTGTAATTCTTC
** * * * * *
41840247 AATCCGTTCTACTGTAATCTCAGGGAAATAGGA--T-TACTGGCTTC
1 AATCTATTCCACTGTAATCTCAGGGAGATAAGATCTGTAAT-TCTTC
*
41840291 AATCTACTT-CGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTC
1 AATCTA-TTCCACTGTAATCTCAGGGAGATAAGATCTGTAATTCTTC
** *
41840337 GGTCTATTCCACTGTAATCTCAGGAAGATAAGA
1 AATCTATTCCACTGTAATCTCAGGGAGATAAGA
41840370 CCTGATGCGA
Statistics
Matches: 156, Mismatches: 35, Indels: 34
0.69 0.16 0.15
Matches are distributed among these distances:
40 2 0.01
41 28 0.18
42 2 0.01
43 3 0.02
44 46 0.29
45 8 0.05
46 64 0.41
47 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (46 bp):
AATCTATTCCACTGTAATCTCAGGGAGATAAGATCTGTAATTCTTC
Found at i:41840271 original size:85 final size:85
Alignment explanation
Indices: 41840168--41840447 Score: 271
Period size: 85 Copynumber: 3.2 Consensus size: 85
41840158 CTTCAGTCTA
*
41840168 TTCCACTGTAATATCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCGGAGAGATA
1 TTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCGGAGAGATA
*
41840233 ATATTCTTTATTTTAATCCG
66 AGATTCTTTATTTTAATCCG
* * * * * * * *
41840253 TTCTACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTACT-TCGCTGTAA-TCTCAGG-
1 TTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATACGATCTACTCT-ACTGTAACT-TC-GGA
* ** **
41840315 GAGATAAGA-TCTGTAATTCTTCGGTCTA
60 GAGATAAGATTCT-TTATT-TT-AATCCG
* * *
41840343 TTCCACTGTAATCTCAGGAAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATA
1 TTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCGGAGAGATA
* *
41840408 AGATCCTTTATTTTAATTCG
66 AGATTCTTTATTTTAATCCG
41840428 TTCCACTGTAATCTCAGGGA
1 TTCCACTGTAATCTCAGGGA
41840448 AATAGGATTA
Statistics
Matches: 149, Mismatches: 33, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
85 43 0.29
86 3 0.02
87 38 0.26
88 36 0.24
89 4 0.03
90 25 0.17
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (85 bp):
TTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCGGAGAGATA
AGATTCTTTATTTTAATCCG
Found at i:41840419 original size:175 final size:175
Alignment explanation
Indices: 41840127--41840499 Score: 647
Period size: 175 Copynumber: 2.1 Consensus size: 175
41840117 ATCTGTTCCA
*
41840127 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATATCAGGGAGATA
1 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATATCAGGAAGATA
* * * *
41840192 AGACCTGATACGATCTACTCTACTGTAACTTCGGAGAGATAATATTCTTTATTTTAATCCGTTCT
66 AGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCC
*
41840257 ACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTACTTCG
131 ACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTACTCCG
* *
41840302 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGAAGATA
1 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATATCAGGAAGATA
* *
41840367 AGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATTCGTTCC
66 AGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCC
*
41840432 ACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTCCG
131 ACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTACTCCG
41840477 CTGTAATCTCAGGGAGATAAGAT
1 CTGTAATCTCAGGGAGATAAGAT
41840500 TCATCATTTT
Statistics
Matches: 187, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 187 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (175 bp):
CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATATCAGGAAGATA
AGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCC
ACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTACTCCG
Found at i:41841703 original size:7 final size:7
Alignment explanation
Indices: 41841684--41841730 Score: 60
Period size: 7 Copynumber: 6.4 Consensus size: 7
41841674 TTAGCCTCTC
41841684 CATTTTT
1 CATTTTT
41841691 -ACTTTTT
1 CA-TTTTT
41841698 CATTTTTT
1 CA-TTTTT
41841706 CATTTTT
1 CATTTTT
41841713 CATGTTTT
1 CAT-TTTT
41841721 CATTTTT
1 CATTTTT
41841728 CAT
1 CAT
41841731 CATTTTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 1 0.03
7 20 0.56
8 15 0.42
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:41841704 original size:8 final size:8
Alignment explanation
Indices: 41841693--41841738 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
41841683 CCATTTTTAC
41841693 TTTTTCAT
1 TTTTTCAT
41841701 TTTTTCA-
1 TTTTTCAT
41841708 TTTTTCAT
1 TTTTTCAT
*
41841716 GTTTTCAT
1 TTTTTCAT
41841724 TTTTCATCAT
1 TTTT--TCAT
41841734 TTTTT
1 TTTTT
41841739 TTGACTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 7 0.21
8 18 0.55
10 8 0.24
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (8 bp):
TTTTTCAT
Found at i:41841711 original size:15 final size:15
Alignment explanation
Indices: 41841684--41841730 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
41841674 TTAGCCTCTC
*
41841684 CATTTTTAC-TTTTT
1 CATTTTTTCATTTTT
41841698 CATTTTTTCATTTTT
1 CATTTTTTCATTTTT
*
41841713 CATGTTTTCATTTTT
1 CATTTTTTCATTTTT
41841728 CAT
1 CAT
41841731 CATTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.68
Consensus pattern (15 bp):
CATTTTTTCATTTTT
Found at i:41842633 original size:14 final size:14
Alignment explanation
Indices: 41842605--41842636 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
41842595 TTTTTTTATA
41842605 TTTTGATTTTAATT
1 TTTTGATTTTAATT
*
41842619 TTTTGATTTTGATT
1 TTTTGATTTTAATT
41842633 TTTT
1 TTTT
41842637 TATTGAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.75
Consensus pattern (14 bp):
TTTTGATTTTAATT
Found at i:41847518 original size:18 final size:18
Alignment explanation
Indices: 41847495--41847531 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41847485 AAATATGTAG
41847495 ATAAATATATAA-ACTAAT
1 ATAAATA-ATAATACTAAT
41847513 ATAAATAATAATACTAAT
1 ATAAATAATAATACTAAT
41847531 A
1 A
41847532 ATAATGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAATAATACTAAT
Found at i:41848345 original size:13 final size:13
Alignment explanation
Indices: 41848327--41848351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41848317 CCGAACAAAG
41848327 AAAAATAAAAATA
1 AAAAATAAAAATA
41848340 AAAAATAAAAAT
1 AAAAATAAAAAT
41848352 CAAATCCCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:41854467 original size:28 final size:27
Alignment explanation
Indices: 41854427--41854480 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
41854417 GGCTGCTATT
*
41854427 TCCTTTTTCATTTCCCCTTTTTTTCTC
1 TCCTTTTTCATTTCCCCTCTTTTTCTC
* *
41854454 TCCTTTTTATATTTTCCCTCTTTTTCT
1 TCCTTTTT-CATTTCCCCTCTTTTTCT
41854481 TCCCTACTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.06, C:0.30, G:0.00, T:0.65
Consensus pattern (27 bp):
TCCTTTTTCATTTCCCCTCTTTTTCTC
Found at i:41854841 original size:22 final size:22
Alignment explanation
Indices: 41854811--41854853 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41854801 ACACCAAAAC
*
41854811 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
*
41854833 AGGCCTTTAGCGGTGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
41854854 AGCGCCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:41855144 original size:86 final size:86
Alignment explanation
Indices: 41855012--41855198 Score: 288
Period size: 86 Copynumber: 2.2 Consensus size: 86
41855002 AGACTAAGAC
* * * *
41855012 CTTTAGCGGCGCTTTAGTGGA-AG-CGCCGCTAAAGATCAGGGTCTTTAGCGACGTTTTTGCTAG
1 CTTTAGCGGCGCTTT-TTCGAGAGTCGCCGCTAAAGATCAGGGTCTTTAGCGACGTTTTTGCAAC
41855075 AAGCGCCGCTAAAGATTAGGGT
65 AAGCGCCGCTAAAGATTAGGGT
* * *
41855097 CTTTAGCGGCGTTTTTTCGAGAGTCGCCGCTGAAGATCAGGGTCTTTAGCGGCGTTTTTGCAACA
1 CTTTAGCGGCGCTTTTTCGAGAGTCGCCGCTAAAGATCAGGGTCTTTAGCGACGTTTTTGCAACA
41855162 AGCGCCGCTAAAGATTAGGGT
66 AGCGCCGCTAAAGATTAGGGT
41855183 CTTTAGCGGCGCTTTT
1 CTTTAGCGGCGCTTTT
41855199 CCCACAAACG
Statistics
Matches: 92, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
84 3 0.03
85 16 0.17
86 73 0.79
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (86 bp):
CTTTAGCGGCGCTTTTTCGAGAGTCGCCGCTAAAGATCAGGGTCTTTAGCGACGTTTTTGCAACA
AGCGCCGCTAAAGATTAGGGT
Found at i:41855211 original size:43 final size:43
Alignment explanation
Indices: 41855035--41855348 Score: 250
Period size: 43 Copynumber: 7.3 Consensus size: 43
41855025 TTAGTGGAAG
* * * * * *
41855035 CGCCGCTAAAGATCAGGGTCTTTAGCGACGTTTTTGCTAGAAG
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAA
* * * * * **
41855078 CGCCGCTAAAGATTAGGGTCTTTAGCGGCGTTTTTTCGAGAGT
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAA
* * * * *
41855121 CGCCGCTGAAGATCAGGGTCTTTAGCGGCGTTTTTGCAACAAG
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAA
*
41855164 CGCCGCTAAAGATTAGGGTCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAA
* * ** * * * ***
41855207 CGCCGCAAAAGACCCTGATCTATAGCGGCGCCTAGACCACAAA
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAA
* **** * *
41855250 CGCCACTAAAGATCCTAATTTTTAGCGGCGCTTTCCCCACAAA
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAA
* * * * *
41855293 CGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTTCCACAAA
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGC-TTTTCCCACAAA
41855337 CGCCGCTAAAGA
1 CGCCGCTAAAGA
41855349 CCCTTATCTT
Statistics
Matches: 222, Mismatches: 48, Indels: 1
0.82 0.18 0.00
Matches are distributed among these distances:
43 200 0.90
44 22 0.10
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (43 bp):
CGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAA
Found at i:41855233 original size:86 final size:86
Alignment explanation
Indices: 41855035--41855348 Score: 292
Period size: 86 Copynumber: 3.6 Consensus size: 86
41855025 TTAGTGGAAG
* * * * * * *
41855035 CGCCGCTAAAGATCAGGGTCTTTAGCGACGTTTTTGCTAGAAGCGCCGCTAAAGATTAGGGTCTT
1 CGCCGCTAAAGACCATGATCTTTAGCGGCGTTTTTGCCACAAACGCCGCTAAAGATTAGGGTCTT
* * * * **
41855100 TAGCGGCGTTTTTTCGAGAGT
66 TAGCGGCGCTTTTCCCACAAA
* * * * * *
41855121 CGCCGCTGAAGATCAGGGTCTTTAGCGGCGTTTTTGCAACAAGCGCCGCTAAAGATTAGGGTCTT
1 CGCCGCTAAAGACCATGATCTTTAGCGGCGTTTTTGCCACAAACGCCGCTAAAGATTAGGGTCTT
41855186 TAGCGGCGCTTTTCCCACAAA
66 TAGCGGCGCTTTTCCCACAAA
* * * ** * * *
41855207 CGCCGCAAAAGACCCTGATCTATAGCGGCG-CCTAGACCACAAACGCCACTAAAGATCCTA--AT
1 CGCCGCTAAAGACCATGATCTTTAGCGGCGTTTTTG-CCACAAACGCCGCTAAAGAT--TAGGGT
* *
41855269 TTTTAGCGGCGCTTTCCCCACAAA
63 CTTTAGCGGCGCTTTTCCCACAAA
* *
41855293 CGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTTCCACAAACGCCGCTAAAGA
1 CGCCGCTAAAGACCATGATCTTTAGCGGCG-TTTTTGCCACAAACGCCGCTAAAGA
41855349 CCCTTATCTT
Statistics
Matches: 188, Mismatches: 35, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
85 2 0.01
86 165 0.88
87 18 0.10
88 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (86 bp):
CGCCGCTAAAGACCATGATCTTTAGCGGCGTTTTTGCCACAAACGCCGCTAAAGATTAGGGTCTT
TAGCGGCGCTTTTCCCACAAA
Found at i:41855262 original size:129 final size:130
Alignment explanation
Indices: 41855129--41855364 Score: 294
Period size: 129 Copynumber: 1.8 Consensus size: 130
41855119 GTCGCCGCTG
** * ** * ** *
41855129 AAGATCAGGGTCTTTAGCGGCGTTTTTGCAACAAGCGCCGCTAAAGATTAGGGTCTTTAGCGGCG
1 AAGATCAGAATCTTTAGCGGCGCTTTCCCAACAAACGCCGCTAAAGACCAGGATCTTTAGCGGCG
41855194 C-TTTTCCCACAAACGCCGCAAAAGACCCTGATCTATAGCGGCGCCTAGACCACAAACGCCACTA
66 CTTTTTCCCACAAACGCCGCAAAAGACCCTGATCTATAGCGGCGCCTAGACCACAAACGCCACTA
** * * * *
41855258 AAGATCCTAATTTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCATGATCTTTAGTGGCG
1 AAGATCAGAATCTTTAGCGGCGCTTTCCCAACAAACGCCGCTAAAGACCAGGATCTTTAGCGGCG
* * * *
41855323 CTTTTTTCCACAAACGCCGCTAAAGACCCTTATCTTTAGCGG
66 CTTTTTCCCACAAACGCCGCAAAAGACCCTGATCTATAGCGG
41855365 TGCTTTTACC
Statistics
Matches: 87, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
129 51 0.59
130 36 0.41
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (130 bp):
AAGATCAGAATCTTTAGCGGCGCTTTCCCAACAAACGCCGCTAAAGACCAGGATCTTTAGCGGCG
CTTTTTCCCACAAACGCCGCAAAAGACCCTGATCTATAGCGGCGCCTAGACCACAAACGCCACTA
Found at i:41855382 original size:44 final size:43
Alignment explanation
Indices: 41855139--41855390 Score: 234
Period size: 43 Copynumber: 5.8 Consensus size: 43
41855129 AAGATCAGGG
* * * * **** *
41855139 TCTTTAGCGGCGTTTTTGCAACAAGCGCCGCTAAAGATTAGGG
1 TCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGA
* *
41855182 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGA
1 TCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGA
* * ** * * *
41855225 TCTATAGCGGCGCCTAGACCACAAACGCCACTAAAGATCCTAA
1 TCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGA
* ** *
41855268 TTTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCATGA
1 TCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGA
* * *
41855311 TCTTTAGTGGCGCTTTTTTCCACAAACGCCGCTAAAGACCCTTA
1 TCTTTAGCGGCGC-TTTTACCACAAACGCCGCTAAAGACCCTGA
* * *
41855355 TCTTTAGCGGTGCTTTTACCAAAAAACGCCACTAAA
1 TCTTTAGCGGCGCTTTTACC-ACAAACGCCGCTAAA
41855391 TTTGGCAGAT
Statistics
Matches: 167, Mismatches: 40, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
43 117 0.70
44 50 0.30
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGA
Found at i:41855736 original size:21 final size:21
Alignment explanation
Indices: 41855707--41855794 Score: 104
Period size: 21 Copynumber: 4.2 Consensus size: 21
41855697 TTTGACGCTG
*
41855707 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
**
41855728 CTCTACTTCCCTCGCTATAGC
1 CTCTACTTCCCTCGCTGCAGC
*
41855749 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
* * * *
41855770 CTGTACTTCTCTCGTTGCCGC
1 CTCTACTTCCCTCGCTGCAGC
41855791 CTCT
1 CTCT
41855795 GTTTCTCTTG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.07, C:0.44, G:0.16, T:0.33
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCAGC
Found at i:41855800 original size:21 final size:21
Alignment explanation
Indices: 41855776--41855816 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41855766 CAGCCTGTAC
* *
41855776 TTCTCTCGTTGCCGCCTCTGT
1 TTCTCTCGCTGCCGCATCTGT
*
41855797 TTCTCTTGCTGCCGCATCTG
1 TTCTCTCGCTGCCGCATCTG
41855817 CTTTAAGCTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.37, G:0.20, T:0.41
Consensus pattern (21 bp):
TTCTCTCGCTGCCGCATCTGT
Found at i:41855874 original size:66 final size:66
Alignment explanation
Indices: 41855797--41855936 Score: 194
Period size: 66 Copynumber: 2.1 Consensus size: 66
41855787 CCGCCTCTGT
* *
41855797 TTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTAGAGTTTTTCATA-CTTTCGTTGAACCTC
1 TTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTAGAGTTCTTCATATCTTT-GTTGAACCTC
41855860 AGC
64 AGC
* * * *
41855863 TTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTCAG
1 TTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTAGAGTTCTTCATATCTTTGTTGAACCTCAG
41855928 C
66 C
41855929 TTCTCTCG
1 TTCTCTCG
41855937 ATGTTTCCTC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 1 0.02
66 61 0.92
67 4 0.06
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.41
Consensus pattern (66 bp):
TTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTAGAGTTCTTCATATCTTTGTTGAACCTCAG
C
Found at i:41855952 original size:66 final size:65
Alignment explanation
Indices: 41855810--41855960 Score: 178
Period size: 66 Copynumber: 2.3 Consensus size: 65
41855800 TCTTGCTGCC
* * * *
41855810 GCATCTGCTTTAAGCTGCTGCTAGAGTTTTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGC
1 GCATCCGCTTTAAGTTG-TGCTAGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGC
41855875 T
65 T
* * *
41855876 GCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATG
1 GCATCCGCTTTAAGTTGT-GCTAGAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGATG
*
41855940 TT
64 CT
* *
41855942 TCCTCCGCTTTAAGTTGTG
1 GCATCCGCTTTAAGTTGTG
41855961 TAATTTGCTC
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
65 2 0.03
66 68 0.92
67 4 0.05
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.42
Consensus pattern (65 bp):
GCATCCGCTTTAAGTTGTGCTAGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGCT
Found at i:41861400 original size:16 final size:16
Alignment explanation
Indices: 41861379--41861412 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
41861369 ATAGTTAAGC
41861379 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
41861395 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
41861411 TA
1 TA
41861413 CCCAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:41861444 original size:25 final size:25
Alignment explanation
Indices: 41861393--41861448 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
41861383 TAAGTTATGT
* *
41861393 ATTATGTAAGTTATTTATTACCCAA
1 ATTATGTAAGTTATGTATTACCAAA
* **
41861418 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATGTATTACCAAA
41861443 ATTATG
1 ATTATG
41861449 CTATGTAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATGTATTACCAAA
Found at i:41861462 original size:9 final size:9
Alignment explanation
Indices: 41861450--41861778 Score: 168
Period size: 9 Copynumber: 38.7 Consensus size: 9
41861440 AAAATTATGC
41861450 TATGTAAGT
1 TATGTAAGT
41861459 TATGTAAGT
1 TATGTAAGT
* *
41861468 CATATAAGT
1 TATGTAAGT
41861477 TATGTAAG-
1 TATGTAAGT
41861485 T-TGTAAGT
1 TATGTAAGT
41861493 TATGTAAGT
1 TATGTAAGT
*
41861502 TAT-TTA-T
1 TATGTAAGT
* *
41861509 TATGAAAAT
1 TATGTAAGT
*
41861518 TAAGTAAGT
1 TATGTAAGT
*
41861527 TATGTAATT
1 TATGTAAGT
*
41861536 TACG-AA-T
1 TATGTAAGT
* **
41861543 AAT-TAAAA
1 TATGTAAGT
*
41861551 AATGTAAGT
1 TATGTAAGT
41861560 TATGTAAG-
1 TATGTAAGT
41861568 T-TGTAAGT
1 TATGTAAGT
41861576 TATGTAAG-
1 TATGTAAGT
41861584 T-TGTAAGT
1 TATGTAAGT
41861592 TATGTAAGT
1 TATGTAAGT
*
41861601 TATGTATA-A
1 TATGTA-AGT
41861610 TAT-TAA-T
1 TATGTAAGT
** *
41861617 TAACTAACT
1 TATGTAAGT
*
41861626 TATGTAATT
1 TATGTAAGT
* *
41861635 TAAGTATAATAT
1 T-A-TGTAA-GT
41861647 TAATGTAAGT
1 T-ATGTAAGT
41861657 TATGTAAG-
1 TATGTAAGT
41861665 T-TGTAAGT
1 TATGTAAGT
41861673 TATGTAAGT
1 TATGTAAGT
*
41861682 TAT-TTA-T
1 TATGTAAGT
* *
41861689 TATGAAAAT
1 TATGTAAGT
*
41861698 TAAGTAAGT
1 TATGTAAGT
*
41861707 TATGTAATT
1 TATGTAAGT
*
41861716 TACG-AA-T
1 TATGTAAGT
* **
41861723 AAT-TAAAAA
1 TATGT-AAGT
*
41861732 AATGTAAGT
1 TATGTAAGT
41861741 TATGTAAG-
1 TATGTAAGT
41861749 T-TGTAAGT
1 TATGTAAGT
41861757 TATGTAAG-
1 TATGTAAGT
41861765 T-TGTAAGT
1 TATGTAAGT
41861773 TATGTA
1 TATGTA
41861779 TAATATTAAT
Statistics
Matches: 247, Mismatches: 44, Indels: 58
0.71 0.13 0.17
Matches are distributed among these distances:
7 53 0.21
8 32 0.13
9 145 0.59
10 5 0.02
11 8 0.03
12 4 0.02
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.42
Consensus pattern (9 bp):
TATGTAAGT
Found at i:41861493 original size:16 final size:16
Alignment explanation
Indices: 41861452--41861778 Score: 142
Period size: 16 Copynumber: 19.8 Consensus size: 16
41861442 AATTATGCTA
41861452 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
*
41861468 CATATAAGTTATGTAAGT
1 --TGTAAGTTATGTAAGT
41861486 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
* * * *
41861502 TATTTA-TTATGAAAAT
1 T-GTAAGTTATGTAAGT
*
41861518 TAAGTAAGTTATGTAATT
1 T--GTAAGTTATGTAAGT
* **
41861536 TACGAATAA-TTA--AAAAA
1 T--G--TAAGTTATGTAAGT
41861553 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
41861569 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
41861585 TGTAAGTTATGTAAGTT
1 TGTAAGTTATGTAAG-T
*
41861602 ATGTATA-ATAT-TAA-T
1 -TGTA-AGTTATGTAAGT
* *
41861617 TAACTAACTTATGTAA-T
1 T--GTAAGTTATGTAAGT
*
41861634 T-TAAGTATAATATTAA--
1 TGTAAGT-T-AT-GTAAGT
41861650 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
41861666 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
* * * *
41861682 TATTTA-TTATGAAAAT
1 T-GTAAGTTATGTAAGT
*
41861698 TAAGTAAGTTATGTAATT
1 T--GTAAGTTATGTAAGT
** **
41861716 TACGAATAA-TTA-AAAAAA
1 T--G--TAAGTTATGTAAGT
41861734 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
41861750 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
41861766 TGTAAGTTATGTA
1 TGTAAGTTATGTA
41861779 TAATATTAAT
Statistics
Matches: 241, Mismatches: 40, Indels: 58
0.71 0.12 0.17
Matches are distributed among these distances:
13 3 0.01
14 14 0.06
15 9 0.04
16 125 0.52
17 30 0.12
18 47 0.20
19 7 0.03
20 6 0.02
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.42
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:41861663 original size:31 final size:31
Alignment explanation
Indices: 41861516--41862230 Score: 387
Period size: 31 Copynumber: 23.2 Consensus size: 31
41861506 TATTATGAAA
* *
41861516 ATTAA-GTAAGTTATGTAATTTACGAATAATT
1 ATTAATGTAAGTTATGTAATTTAAGTATAA-T
**
41861547 AAAAAATGTAAGTTATGTAAGTTGTAAGT-T-AT
1 -ATTAATGTAAGTTATGTAA-TT-TAAGTATAAT
* * *
41861579 -GTAAGTTGTAAGTTATGTAAGTTATGTATAAT
1 ATTAA--TGTAAGTTATGTAATTTAAGTATAAT
* *
41861611 ATTAATTAACTAACTTATGTAATTTAAGTATAAT
1 ATTAA-T--GTAAGTTATGTAATTTAAGTATAAT
41861645 ATTAATGTAAGTTATGTAAGTTGTAAGTTATGTAA-
1 ATTAATGTAAGTTATGTAA-TT-TAAG-TA--TAAT
* * * *
41861680 GTT-AT-TTA-TTATGAAAATTAAG--TAA-
1 ATTAATGTAAGTTATGTAATTTAAGTATAAT
* * *
41861705 GTT-ATGTAATTTACG-AA--TAA-T-TAA-
1 ATTAATGTAAGTTATGTAATTTAAGTATAAT
**
41861729 AAAAATGTAAGTTATGTAAGTTGTAAGT-T-AT
1 ATTAATGTAAGTTATGTAA-TT-TAAGTATAAT
* *
41861760 -GTAAGTTGTAAGTTATGT-A--TAA-TATTA-
1 ATTAA--TGTAAGTTATGTAATTTAAGTATAAT
* *
41861787 ATTAA-CTAACTTATGTAATTTAAGTATAAT
1 ATTAATGTAAGTTATGTAATTTAAGTATAAT
*
41861817 ATTAATGTAAGTTATGT-A--TAA-TATTA-
1 ATTAATGTAAGTTATGTAATTTAAGTATAAT
** *
41861843 ATTAA-CAAAGTTATGTAATTTATGTATAAT
1 ATTAATGTAAGTTATGTAATTTAAGTATAAT
* *
41861873 ATTAATGTAATTAGTTATGTAATTTATGTATATT
1 ATTAATGT-A--AGTTATGTAATTTAAGTATAAT
*
41861907 AATTAAT-TAAGTTATGTAATTTATGTATAAT
1 -ATTAATGTAAGTTATGTAATTTAAGTATAAT
* *
41861938 ATTAATGTAAGTTATGTAATTTATGAATAATT
1 ATTAATGTAAGTTATGTAATTTAAGTATAA-T
*
41861970 ATAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTATAAT
1 AT--TAATGTAAGTTATGTAA-TT-T-A---A-GTATAAT
* *
41862010 ATTAATTAATTAAGTTATGTAATTTATGTATAAT
1 ATTAA-T--GTAAGTTATGTAATTTAAGTATAAT
** * *
41862044 ATTAATGTAAGCAATGTAATTTATGTGTAAT
1 ATTAATGTAAGTTATGTAATTTAAGTATAAT
*
41862075 ACTTAAT-TAAGTTATGTAATTTATGTATAAT
1 A-TTAATGTAAGTTATGTAATTTAAGTATAAT
* *
41862106 ACTAATGTAAGTTATGTAATTTATGTATAAT
1 ATTAATGTAAGTTATGTAATTTAAGTATAAT
* *
41862137 ATTAATGCAAGTTATGT-A--TAA-TATTA-
1 ATTAATGTAAGTTATGTAATTTAAGTATAAT
*
41862163 ATTAAT-TAAGTTATGTAATTTATGTATAAT
1 ATTAATGTAAGTTATGTAATTTAAGTATAAT
* * *
41862193 ATTAATGTAACTTATGTAATTTATGTATATT
1 ATTAATGTAAGTTATGTAATTTAAGTATAAT
41862224 AATTAAT
1 -ATTAAT
41862231 TAAATGATAT
Statistics
Matches: 546, Mismatches: 67, Indels: 140
0.73 0.09 0.19
Matches are distributed among these distances:
24 6 0.01
25 45 0.08
26 21 0.04
27 16 0.03
28 16 0.03
29 12 0.02
30 44 0.08
31 174 0.32
32 58 0.11
33 26 0.05
34 83 0.15
35 13 0.02
36 4 0.01
37 1 0.00
38 3 0.01
39 2 0.00
40 5 0.01
41 17 0.03
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.45
Consensus pattern (31 bp):
ATTAATGTAAGTTATGTAATTTAAGTATAAT
Found at i:41861824 original size:22 final size:22
Alignment explanation
Indices: 41861799--41861844 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
41861789 TAACTAACTT
*
41861799 ATGTAATTTAAGTATAATATTA
1 ATGTAAGTTAAGTATAATATTA
*
41861821 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTAAGTATAATATTA
41861843 AT
1 AT
41861845 TAACAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (22 bp):
ATGTAAGTTAAGTATAATATTA
Found at i:41861856 original size:172 final size:177
Alignment explanation
Indices: 41861472--41861856 Score: 588
Period size: 172 Copynumber: 2.2 Consensus size: 177
41861462 GTAAGTCATA
* ***
41861472 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT
1 TAAGTTATGTAAATTGTAAGTTAACAAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT
41861537 ACGAATAATTAAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTGTAAGTTATGTAAGTT
66 ACGAATAATTAAAAAATGTAAGTTATGTAAGTTGTAAG-T-TGTAAG-TGTAAGTTATGTAAGTT
41861602 ATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAATG
128 ATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAATG
* ***
41861652 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT
1 TAAGTTATGTAAATTGTAAGTTAACAAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT
41861717 ACGAATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAG-T-T-A-TGTAAG-T-TGTAAGTTAT
66 ACGAATAATT-AAAAAATGTAAGTTATGTAAGTTGTAAGTTGTAAGTGTAAGTTATGTAAGTTAT
41861776 GTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAATG
130 GTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAATG
41861824 TAAGTTATGTATAATAT-TAA-TTAACAAAGTTAT
1 TAAGTTATGTA-AAT-TGTAAGTTAACAAAGTTAT
41861857 GTAATTTATG
Statistics
Matches: 198, Mismatches: 4, Indels: 14
0.92 0.02 0.06
Matches are distributed among these distances:
172 79 0.40
173 6 0.03
174 7 0.04
176 1 0.01
177 1 0.01
178 1 0.01
180 75 0.38
181 28 0.14
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.43
Consensus pattern (177 bp):
TAAGTTATGTAAATTGTAAGTTAACAAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT
ACGAATAATTAAAAAATGTAAGTTATGTAAGTTGTAAGTTGTAAGTGTAAGTTATGTAAGTTATG
TATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAATG
Found at i:41861867 original size:9 final size:9
Alignment explanation
Indices: 41861853--41862219 Score: 78
Period size: 9 Copynumber: 37.8 Consensus size: 9
41861843 ATTAACAAAG
41861853 TTATGTAAT
1 TTATGTAAT
41861862 TTATGTATAAT
1 TTATG--TAAT
41861873 ATTAATGTAATT
1 -TT-ATGTAA-T
41861885 AGTTATGTAAT
1 --TTATGTAAT
41861896 TTATGT-A-
1 TTATGTAAT
41861903 -TAT-TAAT
1 TTATGTAAT
* *
41861910 TAAT-TAAG
1 TTATGTAAT
41861918 TTATGTAAT
1 TTATGTAAT
41861927 TTATGTATAAT
1 TTATG--TAAT
*
41861938 ATTAATGTAAG
1 -TT-ATGTAAT
41861949 TTATGTAAT
1 TTATGTAAT
41861958 TTATGAATAAT
1 TTATG--TAAT
*
41861969 TATAAAAATGTAAG
1 T-T----ATGTAAT
41861983 TTATGTAA-
1 TTATGTAAT
* *
41861991 GT-TGTAAG
1 TTATGTAAT
41861999 TTATGT-AT
1 TTATGTAAT
*
41862007 AATAT-TAAT
1 -TTATGTAAT
* *
41862016 TAAT-TAAG
1 TTATGTAAT
41862024 TTATGTAAT
1 TTATGTAAT
41862033 TTATGTATAAT
1 TTATG--TAAT
*
41862044 ATTAATGTAAG
1 -TT-ATGTAAT
**
41862055 CAATGTAAT
1 TTATGTAAT
41862064 TTATGTGTAAT
1 TTA--TGTAAT
*
41862075 ACTTAAT-TAAG
1 --TT-ATGTAAT
41862086 TTATGTAAT
1 TTATGTAAT
41862095 TTATGTATAAT
1 TTATG--TAAT
* *
41862106 ACTAATGTAAG
1 --TTATGTAAT
41862117 TTATGTAAT
1 TTATGTAAT
41862126 TTATGTATAAT
1 TTATG--TAAT
* *
41862137 ATTAATGCAAG
1 -TT-ATGTAAT
41862148 TTATGT-AT
1 TTATGTAAT
*
41862156 AATAT-TAAT
1 -TTATGTAAT
* *
41862165 TAAT-TAAG
1 TTATGTAAT
41862173 TTATGTAAT
1 TTATGTAAT
41862182 TTATGTATAAT
1 TTATG--TAAT
*
41862193 ATTAATGTAAC
1 -TT-ATGTAAT
41862204 TTATGTAAT
1 TTATGTAAT
41862213 TTATGTA
1 TTATGTA
41862220 TATTAATTAA
Statistics
Matches: 266, Mismatches: 41, Indels: 102
0.65 0.10 0.25
Matches are distributed among these distances:
5 1 0.00
6 4 0.02
7 5 0.02
8 33 0.12
9 110 0.41
10 6 0.02
11 56 0.21
12 19 0.07
13 24 0.09
14 5 0.02
16 3 0.01
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (9 bp):
TTATGTAAT
Done.