Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 103 of 230
Found at i:29438524 original size:22 final size:21
Alignment explanation
Indices: 29438478--29438531 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
29438468 GGGTGAGAAG
29438478 TAAAAG-TTT-AGGGGGAAAA
1 TAAAAGTTTTGAGGGGGAAAA
*
29438497 TAAAAAGTTTTGAGGGAGTAAAA
1 T-AAAAGTTTTGAGGG-GGAAAA
29438520 TAAAAGTTTTGA
1 TAAAAGTTTTGA
29438532 CGGTTTTGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.03
20 5 0.17
21 3 0.10
22 15 0.50
23 6 0.20
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (21 bp):
TAAAAGTTTTGAGGGGGAAAA
Found at i:29450666 original size:22 final size:22
Alignment explanation
Indices: 29450640--29450684 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29450630 AACAAATAAC
29450640 TTAGGTATATGCTCATAACCAA
1 TTAGGTATATGCTCATAACCAA
29450662 TTAGGTATATGCTCATAACCAA
1 TTAGGTATATGCTCATAACCAA
29450684 T
1 T
29450685 CACTTGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (22 bp):
TTAGGTATATGCTCATAACCAA
Found at i:29454717 original size:20 final size:20
Alignment explanation
Indices: 29454692--29454729 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29454682 CCTATGATTG
*
29454692 ATTAAATCACTAATTATCTA
1 ATTAAATAACTAATTATCTA
*
29454712 ATTAAATAATTAATTATC
1 ATTAAATAACTAATTATC
29454730 CTAAATTGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTAAATAACTAATTATCTA
Found at i:29455104 original size:21 final size:21
Alignment explanation
Indices: 29455070--29455110 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29455060 AATGCTAATT
*
29455070 AATAAAGTTAATGAAAATATA
1 AATAAAGCTAATGAAAATATA
* *
29455091 AATAAAGCTCATGAACATAT
1 AATAAAGCTAATGAAAATAT
29455111 TGAATTGTGG
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:0.56, C:0.07, G:0.10, T:0.27
Consensus pattern (21 bp):
AATAAAGCTAATGAAAATATA
Found at i:29456293 original size:17 final size:16
Alignment explanation
Indices: 29456259--29456297 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
29456249 AACATCAATT
*
29456259 AATCTAATTAACCTAAA
1 AATC-AATTAAACTAAA
29456276 AATCAATTAAACTAAA
1 AATCAATTAAACTAAA
29456292 AATCAA
1 AATCAA
29456298 CCAATTACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (16 bp):
AATCAATTAAACTAAA
Found at i:29456612 original size:43 final size:43
Alignment explanation
Indices: 29456564--29456729 Score: 260
Period size: 43 Copynumber: 3.9 Consensus size: 43
29456554 TTATGAGGCA
* * * *
29456564 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTAACCAC
* *
29456607 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTAAACAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTAACCAC
*
29456650 AAATGCCGCTAAAGAACATGATCTTTAGCGACGCTTTAACCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTAACCAC
*
29456693 AAACGCCGCTAAAAAACATGATCTTTAGCGACGCTTT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTT
29456730 TGATAAAAGC
Statistics
Matches: 114, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 114 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTAACCAC
Found at i:29458974 original size:20 final size:20
Alignment explanation
Indices: 29458924--29459002 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
29458914 GTAACAGAGT
29458924 AAGCAAGCAAAATAAGAAAA
1 AAGCAAGCAAAATAAGAAAA
* *
29458944 AAACAAACAAACA-AA-AATAA
1 AAGCAAGCAAA-ATAAGAA-AA
** *
29458964 AAGCAAGCAAAATGGGGAAA
1 AAGCAAGCAAAATAAGAAAA
29458984 AAG-AA-CAAAATAAGCAAAA
1 AAGCAAGCAAAATAAG-AAAA
29459003 CATTGCCGGA
Statistics
Matches: 44, Mismatches: 10, Indels: 11
0.68 0.15 0.17
Matches are distributed among these distances:
18 7 0.16
19 8 0.18
20 27 0.61
21 2 0.05
ACGTcount: A:0.70, C:0.11, G:0.14, T:0.05
Consensus pattern (20 bp):
AAGCAAGCAAAATAAGAAAA
Found at i:29461133 original size:16 final size:16
Alignment explanation
Indices: 29461100--29461139 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
29461090 TTTCGGGTAT
29461100 GGGAA-AAA-TTGAAG
1 GGGAATAAATTTGAAG
*
29461114 GGGAATAAATTTGGAG
1 GGGAATAAATTTGAAG
29461130 GGGAATAAAT
1 GGGAATAAAT
29461140 ATTTCAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 3 0.13
16 15 0.65
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (16 bp):
GGGAATAAATTTGAAG
Found at i:29461517 original size:47 final size:48
Alignment explanation
Indices: 29461459--29461557 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 48
29461449 CATAGTTTTG
*
29461459 TTTAAGTAATATTTATAAAAATTAGATAAAATTATAAATTTTAGT-TT
1 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
29461506 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
1 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
29461554 TTTA
1 TTTA
29461558 TTTCATTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 44 0.88
48 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (48 bp):
TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
Found at i:29461571 original size:25 final size:26
Alignment explanation
Indices: 29461543--29461595 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
29461533 AAAATTAAAA
* *
29461543 ATTTTAGTGTTTTTATTTCATTT-TT
1 ATTTTAGTATTTTAATTTCATTTCTT
* *
29461568 ATTTTTGTATTTTAATTTTATTTCTT
1 ATTTTAGTATTTTAATTTCATTTCTT
29461594 AT
1 AT
29461596 AATTTGGTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.72
Consensus pattern (26 bp):
ATTTTAGTATTTTAATTTCATTTCTT
Found at i:29461578 original size:19 final size:18
Alignment explanation
Indices: 29461542--29461595 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
29461532 TAAAATTAAA
29461542 AATTTTAGTGTTTTTATTTC
1 AATTTTA-T-TTTTTATTTC
* *
29461562 ATTTTTATTTTTGTATTTT
1 AATTTTATTTTT-TATTTC
*
29461581 AATTTTATTTCTTAT
1 AATTTTATTTTTTAT
29461596 AATTTGGTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (18 bp):
AATTTTATTTTTTATTTC
Found at i:29461945 original size:14 final size:14
Alignment explanation
Indices: 29461912--29461962 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
29461902 ATCCTTAAGT
* *
29461912 CCTAACCCCTAAATC
1 CCTAA-CCCTTAACC
*
29461927 CCTAACTCTTAACC
1 CCTAACCCTTAACC
29461941 CCTAACCCTTAACC
1 CCTAACCCTTAACC
*
29461955 ACTAACCC
1 CCTAACCC
29461963 CTAAACCTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
14 26 0.84
15 5 0.16
ACGTcount: A:0.31, C:0.47, G:0.00, T:0.22
Consensus pattern (14 bp):
CCTAACCCTTAACC
Found at i:29461980 original size:21 final size:21
Alignment explanation
Indices: 29461904--29461982 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
29461894 ACCCTTGAAT
*
29461904 CCTTAAGTCCTAACCCCTAAA
1 CCTTAAATCCTAACCCCTAAA
* * * *
29461925 TCCCTAACTCTTAACCCCTAAC
1 -CCTTAAATCCTAACCCCTAAA
*
29461947 CCTT-AACCACTAACCCCTAAA
1 CCTTAAATC-CTAACCCCTAAA
29461968 CCTTAAATCCTAACC
1 CCTTAAATCCTAACC
29461983 TTTAAACCCA
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.04
21 23 0.51
22 20 0.44
ACGTcount: A:0.33, C:0.42, G:0.01, T:0.24
Consensus pattern (21 bp):
CCTTAAATCCTAACCCCTAAA
Found at i:29462280 original size:26 final size:26
Alignment explanation
Indices: 29462244--29462297 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
29462234 GCCCTAAATC
* *
29462244 CCTAACTCTTAACATCTAACCCCTAA
1 CCTAACCCTTAACACCTAACCCCTAA
* *
29462270 CCTAACCCTTAACCCCTAACCCTTAA
1 CCTAACCCTTAACACCTAACCCCTAA
29462296 CC
1 CC
29462298 CATAAACCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.44, G:0.00, T:0.24
Consensus pattern (26 bp):
CCTAACCCTTAACACCTAACCCCTAA
Found at i:29462298 original size:14 final size:14
Alignment explanation
Indices: 29462243--29462309 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
29462233 AGCCCTAAAT
*
29462243 CCCTAACTCTTAAC
1 CCCTAACCCTTAAC
** *
29462257 ATCTAACCCCTAA-
1 CCCTAACCCTTAAC
29462270 -CCTAACCCTTAAC
1 CCCTAACCCTTAAC
29462283 CCCTAACCCTTAAC
1 CCCTAACCCTTAAC
* *
29462297 CCATAAACCTTAA
1 CCCTAACCCTTAA
29462310 ATCACATTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 10 0.23
14 33 0.77
ACGTcount: A:0.34, C:0.42, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAACCCTTAAC
Found at i:29462326 original size:7 final size:7
Alignment explanation
Indices: 29462260--29462309 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
29462250 TCTTAACATC
*
29462260 TAACCCC
1 TAACCCT
29462267 TAA-CC-
1 TAACCCT
29462272 TAACCCT
1 TAACCCT
*
29462279 TAACCCC
1 TAACCCT
29462286 TAACCCT
1 TAACCCT
*
29462293 TAACCCA
1 TAACCCT
*
29462300 TAAACCT
1 TAACCCT
29462307 TAA
1 TAA
29462310 ATCACATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 3 0.08
6 4 0.11
7 29 0.81
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (7 bp):
TAACCCT
Found at i:29462351 original size:14 final size:15
Alignment explanation
Indices: 29462332--29462364 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
29462322 CTTAAATCAG
29462332 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
29462346 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
29462361 AATC
1 AATC
29462365 TATAAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:29463292 original size:146 final size:145
Alignment explanation
Indices: 29462930--29463735 Score: 1389
Period size: 146 Copynumber: 5.5 Consensus size: 145
29462920 ATTTGGGAAA
* *
29462930 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACACCGCTATTGCTTACCTTTA
1 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTA
29462995 GCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCA-TTTGAACAAAACGACGCCGTTTTGCTAT
66 GCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTAT
*
29463059 TCTAAATTTTTTTTTTATT
131 TCTAAA---ATTTTTTA-T
*
29463078 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGGAAACGCCGCTATTGCTTACCTTTA
1 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTA
* * *
29463143 GCGGCGCTTCTTATAAAGCACCGTAAAATTTTTTCATTTTGAAAAAAACGACGCCGTTTTGCTAT
66 GCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTAT
29463208 TCTAACAATTTTTTAT
131 TCTAA-AATTTTTTAT
* * *
29463224 TTTTTTATAAGTTGATTTATTTTTTGCAGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
1 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTA
*
29463289 GCGGCGCTTCTTATAAAGCGTCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTAT
66 GCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTAT
29463354 TCTAAAATTTTTTTAT
131 TCTAAAA-TTTTTTAT
29463370 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTA
1 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTA
*
29463435 GCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCTTTTTGCTAT
66 GCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTAT
*
29463500 TCTAAATTTTTTTTAT
131 TCTAAA-ATTTTTTAT
29463516 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTA
1 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTA
* *
29463581 GCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGCTTTGCTAT
66 GCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTAT
29463646 TCTAAAATTTTTTTAT
131 TCTAAAA-TTTTTTAT
29463662 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTA
1 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTA
*
29463727 GCGACGCTT
66 GCGGCGCTT
29463736 TACGAAAAAC
Statistics
Matches: 627, Mismatches: 26, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
145 2 0.00
146 489 0.78
147 7 0.01
148 96 0.15
149 32 0.05
150 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.44
Consensus pattern (145 bp):
TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTA
GCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTAT
TCTAAAATTTTTTAT
Found at i:29463850 original size:73 final size:72
Alignment explanation
Indices: 29463731--29463899 Score: 223
Period size: 73 Copynumber: 2.3 Consensus size: 72
29463721 CCTTTAGCGA
* * * * *
29463731 CGCTTTA-CGAAAAACACCGCTAAATCTCTGAAAGTTCAGAAAACGGCATCGTTGGGCTTGGGTT
1 CGCTTTATC-AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGG-T
*
29463795 TTTTTGCGG
64 TATTTGCGG
* *
29463804 CGCTTTATCAAAAACGTCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTA
1 CGCTTTATCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTA
29463869 TTTGCGG
66 TTTGCGG
*
29463876 CGCTTTGCTCAAAAACGCCGCTAA
1 CGCTTT-ATCAAAAACGCCGCTAA
29463900 TGCTTTTTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
72 15 0.18
73 68 0.81
74 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (72 bp):
CGCTTTATCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTA
TTTGCGG
Found at i:29463984 original size:12 final size:12
Alignment explanation
Indices: 29463967--29463992 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29463957 TTTTTTATCC
29463967 AAACGCCGCTAA
1 AAACGCCGCTAA
29463979 AAACGCCGCTAA
1 AAACGCCGCTAA
29463991 AA
1 AA
29463993 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:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:29473594 original size:22 final size:21
Alignment explanation
Indices: 29473569--29473882 Score: 304
Period size: 22 Copynumber: 14.2 Consensus size: 21
29473559 AGCAATTATC
*
29473569 CAACATTCAGACAGCATTTAAT
1 CAACATT-GGACAGCATTTAAT
* *
29473591 CAACAATTGGATAGCATTAAAT
1 CAAC-ATTGGACAGCATTTAAT
*
29473613 CAACATTTGGACAACATTTAAT
1 CAACA-TTGGACAGCATTTAAT
*
29473635 CAACAATTGGACAGCATTCAAT
1 CAAC-ATTGGACAGCATTTAAT
* * *
29473657 CAATATTTGGACAACTTTTAAT
1 CAACA-TTGGACAGCATTTAAT
*
29473679 CAACAACTGGACAGCATTTAAT
1 CAAC-ATTGGACAGCATTTAAT
* * *
29473701 CAACAATTGGGCATCATTCAAT
1 CAAC-ATTGGACAGCATTTAAT
*
29473723 CAATATTTGGACAGCATTTAAT
1 CAACA-TTGGACAGCATTTAAT
* *
29473745 CAACAATTGGACAACATTCAAT
1 CAAC-ATTGGACAGCATTTAAT
* *
29473767 CAATATTTGGACAACATTTAAT
1 CAACA-TTGGACAGCATTTAAT
*
29473789 CAACAATTGGACAGCATTAAAT
1 CAAC-ATTGGACAGCATTTAAT
*
29473811 CAACATTTGGACAACATTTTAAT
1 CAACA-TTGGACAGCA-TTTAAT
*
29473834 CAACAATTGGACAGCATTCAAT
1 CAAC-ATTGGACAGCATTTAAT
*
29473856 CAATATTTGGACAGCATTTAAT
1 CAACA-TTGGACAGCATTTAAT
29473878 CAACA
1 CAACA
29473883 ATTTTTACTT
Statistics
Matches: 240, Mismatches: 39, Indels: 26
0.79 0.13 0.09
Matches are distributed among these distances:
21 6 0.03
22 208 0.87
23 25 0.10
24 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (21 bp):
CAACATTGGACAGCATTTAAT
Found at i:29473649 original size:66 final size:66
Alignment explanation
Indices: 29473578--29473885 Score: 418
Period size: 66 Copynumber: 4.7 Consensus size: 66
29473568 CCAACATTCA
* * * * * *
29473578 GACAGCATTTAATCAACAATTGGATAGCATTAAATCAACATTTGGACAACATTTAATCAACAATT
1 GACAGCATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAACATTTAATCAACAATT
29473643 G
66 G
* * * *
29473644 GACAGCATTCAATCAATATTTGGACAACTTTTAATCAACAACTGGACAGCATTTAATCAACAATT
1 GACAGCATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAACATTTAATCAACAATT
29473709 G
66 G
* * * * *
29473710 GGCATCATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAACATTCAATCAATATTT
1 GACAGCATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAACATTTAATCAACAATT
29473775 G
66 G
* * * * * *
29473776 GACAACATTTAATCAACAATTGGACAGCATTAAATCAACATTTGGACAACATTTTAATCAACAAT
1 GACAGCATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAACA-TTTAATCAACAAT
29473841 TG
65 TG
29473843 GACAGCATTCAATCAATATTTGGACAGCATTTAATCAACAATT
1 GACAGCATTCAATCAATATTTGGACAGCATTTAATCAACAATT
29473886 TTTACTTCAA
Statistics
Matches: 206, Mismatches: 35, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
66 157 0.76
67 49 0.24
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.30
Consensus pattern (66 bp):
GACAGCATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAACATTTAATCAACAATT
G
Found at i:29474769 original size:42 final size:44
Alignment explanation
Indices: 29474711--29474819 Score: 143
Period size: 44 Copynumber: 2.5 Consensus size: 44
29474701 ACGATGCCAC
*
29474711 TGTCCCAGACAGGGTCTTACACGT-AATCAT-AAAT-GACACCAA
1 TGTCCCAGACATGGTCTTACACGTAAAT-ATCAAATCGACACCAA
* **
29474753 TGTCCCAGACATGGTCTTACACGTAAATTTCAAATCGAGGCCAA
1 TGTCCCAGACATGGTCTTACACGTAAATATCAAATCGACACCAA
*
29474797 TGTCCCAGACGTGGTCTTACACG
1 TGTCCCAGACATGGTCTTACACG
29474820 ACGTCACATT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
42 24 0.41
43 7 0.12
44 28 0.47
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (44 bp):
TGTCCCAGACATGGTCTTACACGTAAATATCAAATCGACACCAA
Found at i:29474806 original size:44 final size:42
Alignment explanation
Indices: 29474679--29474819 Score: 140
Period size: 42 Copynumber: 3.3 Consensus size: 42
29474669 GTTCCAAACG
* * * * * *
29474679 TGGTCTTTCATGTAATCAAACAACGATGCCACTGTCCCAGACA
1 TGGTCTTACACGTAATCATA-AATGACGCCAATGTCCCAGACA
* *
29474722 GGGTCTTACACGTAATCATAAATGACACCAATGTCCCAGACA
1 TGGTCTTACACGTAATCATAAATGACGCCAATGTCCCAGACA
* * *
29474764 TGGTCTTACACGTAAAT-TTCAAATCGAGGCCAATGTCCCAGACG
1 TGGTCTTACACGT-AATCAT-AAAT-GACGCCAATGTCCCAGACA
29474808 TGGTCTTACACG
1 TGGTCTTACACG
29474820 ACGTCACATT
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
42 31 0.38
43 23 0.28
44 28 0.34
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
TGGTCTTACACGTAATCATAAATGACGCCAATGTCCCAGACA
Found at i:29477753 original size:115 final size:113
Alignment explanation
Indices: 29477466--29478107 Score: 552
Period size: 115 Copynumber: 5.6 Consensus size: 113
29477456 AACACATAGT
* * * * **
29477466 AGCGCCGCAAAAGATCTTAACCAAAACACAGAG-TTCGGTCTTGA-GCTATGTTAGAATTAGTGG
1 AGCGCCGCAAAATATCCTAACCAAAACGCAGAGTTTTGGTCTTGATG-TATACTAGAATTAGTGG
* * ** *
29477529 CGCTTATAGGAAAACGCCGC-AAACGGATAGTATTAGCGGAAC-TTTTGAAA
65 CGCTTA-CGGAAAACGCCGCTAAA-GCATAGTATTAGCGGCGCTTTTTG-CA
** * ** * *
29477579 AGCGCCGCAAAAT-TTTTGAACCAAAATGCATTGTTTTGGTATTGATGTATATTAGAATTAGTGG
1 AGCGCCGCAAAATATCCT-AACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGG
* * * *
29477643 CGTTTACGGTAAAACGCCGCTAAAGCATAGTATTAGCAGCGATTCTTTGCT
65 CGCTTACGG-AAAACGCCGCTAAAGCATAGTATTAGCGGCGCTT-TTTGCA
* * *
29477694 AGCGCCGCAAAATATCCTAACTAAAACGCAGCGTTTTGGTCTTGATGTATACTAAAATTAGTGGC
1 AGCGCCGCAAAATATCCTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
* * * * *
29477759 ACTTACGGGAAACCACCGCTAAAGAATAGTATTAGCGGCGCTTTTTGAAA
66 GCTTAC-GGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTG-CA
* * * **
29477809 AGTGCCGCAAAATATCTTAACCAAAACGCATAGTTTTAATCTTGATGTATACTAGAATTAGTGGC
1 AGCGCCGCAAAATATCCTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
* *
29477874 GCTTACTAGAAAACGCCGTTAAAGCATAGTATTAGCGGCGC--TTTGCAAAA
66 GCTTAC-GGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGC---A
* * * * * ** *
29477924 AGTGCCGCAACATATCTTAA-CAAAACACAGAG-TTTGGTCTTGAGGTATGTTAGAATTAGTGGT
1 AGCGCCGCAAAATATCCTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
* * * ** *
29477987 GCTTATAGGAAAACGCCGC-AACTGGATAGTATTAGCGGCGCTTTACGGA
66 GCTTA-CGGAAAACGCCGCTAA-AGCATAGTATTAGCGGCGCTTTTTGCA
* * **
29478036 AGCGCCGCAAAATAT-CTGAACCAAAACGCATCA-TTTTGGTCTCGATGTATACTTCAATTAGTG
1 AGCGCCGCAAAATATCCT-AACCAAAACGCA-GAGTTTTGGTCTTGATGTATACTAGAATTAGTG
29478099 GCGCTTACG
64 GCGCTTACG
29478108 TTGAAACGCC
Statistics
Matches: 426, Mismatches: 82, Indels: 42
0.77 0.15 0.08
Matches are distributed among these distances:
111 1 0.00
112 21 0.05
113 95 0.22
114 97 0.23
115 204 0.48
116 8 0.02
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (113 bp):
AGCGCCGCAAAATATCCTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
GCTTACGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGCA
Found at i:29477904 original size:230 final size:224
Alignment explanation
Indices: 29477465--29478119 Score: 730
Period size: 230 Copynumber: 2.9 Consensus size: 224
29477455 TAACACATAG
* *
29477465 TAGCGCCGCAAAAGATCTTAACCAAAACACAGAGTTCGGTCTTGAGCTATGTTAGAATTAGTGGC
1 TAGCGCCGCAAAATATCTTAA-CAAAACACAGAGTTTGGTCTTGAG-TATGTTAGAATTAGTGGC
**
29477530 GCTTATAGGAAAACGCCGCAAACGGATAGTATTAGCGGAAC-TTTTGAAAAGCGCCGCAAAAT-T
64 GCTTATAGGAAAACGCCGCAAA-GGATAGTATTAGCGGCGCTTTTTGAAAAGCGCCGCAAAATAT
* * * * * * *
29477593 TTTGAACCAAAATGCATTGTTTTGGTATTGATGTATATTAGAATTAGTGGCGTTTACGGTAAAAC
128 CTT-AACCAAAACGCATAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACAGTAAAAC
29477658 GCCGCTAAAGCATAGTATTAGCAGCGATTCTTTGC-
192 GCCGCTAAAGCATAGTATTAGCAGCG---CTTTGCA
* * * ** *
29477693 TAGCGCCGCAAAATATCCTAACTAAAACGCAGCGTTTTGGTCTTGATGTATACTAAAATTAGTGG
1 TAGCGCCGCAAAATATCTTAAC-AAAACACAGAG-TTTGGTCTTGA-GTATGTTAGAATTAGTGG
* ** * * * *
29477758 CACTTACGGGAAACCACCGCTAAAGAATAGTATTAGCGGCGCTTTTTGAAAAGTGCCGCAAAATA
63 CGCTTATAGGAAAACGCCGC-AAAGGATAGTATTAGCGGCGCTTTTTGAAAAGCGCCGCAAAATA
**
29477823 TCTTAACCAAAACGCATAGTTTTAATCTTGATGTATACTAGAATTAGTGGCGCTTACTAG-AAAA
127 TCTTAACCAAAACGCATAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTAC-AGTAAAA
* *
29477887 CGCCGTTAAAGCATAGTATTAGCGGCGCTTTGCAAA
191 CGCCGCTAAAGCATAGTATTAGCAGCGCTTTGC--A
* * * *
29477923 AAGTGCCGCAACATATCTTAACAAAACACAGAGTTTGGTCTTGAGGTATGTTAGAATTAGTGGTG
1 TAGCGCCGCAAAATATCTTAACAAAACACAGAGTTTGGTCTTGA-GTATGTTAGAATTAGTGGCG
* ** *
29477988 CTTATAGGAAAACGCCGCAACTGGATAGTATTAGCGGCGCTTTACG-GAAGCGCCGCAAAATATC
65 CTTATAGGAAAACGCCGCAA-AGGATAGTATTAGCGGCGCTTTTTGAAAAGCGCCGCAAAATATC
* * ** *
29478052 TGAACCAAAACGCATCA-TTTTGGTCTCGATGTATACTTCAATTAGTGGCGCTTAC-GTTGAAAC
129 TTAACCAAAACGCAT-AGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACAG-TAAAAC
29478115 GCCGC
192 GCCGC
29478120 CAAAACACAA
Statistics
Matches: 355, Mismatches: 58, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
225 1 0.00
227 80 0.23
228 90 0.25
229 63 0.18
230 117 0.33
231 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (224 bp):
TAGCGCCGCAAAATATCTTAACAAAACACAGAGTTTGGTCTTGAGTATGTTAGAATTAGTGGCGC
TTATAGGAAAACGCCGCAAAGGATAGTATTAGCGGCGCTTTTTGAAAAGCGCCGCAAAATATCTT
AACCAAAACGCATAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACAGTAAAACGCCG
CTAAAGCATAGTATTAGCAGCGCTTTGCA
Found at i:29478671 original size:20 final size:21
Alignment explanation
Indices: 29478646--29478684 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29478636 TACAATGCAT
29478646 GGTTTT-GAGTGTAAGGTTAC
1 GGTTTTAGAGTGTAAGGTTAC
29478666 GGTTTTAGAGTGTAAGGTT
1 GGTTTTAGAGTGTAAGGTT
29478685 TGTAGTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.21, C:0.03, G:0.36, T:0.41
Consensus pattern (21 bp):
GGTTTTAGAGTGTAAGGTTAC
Found at i:29479531 original size:22 final size:23
Alignment explanation
Indices: 29479490--29479556 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 23
29479480 CCCCACTCTG
29479490 ATTTCCCCAATTTCATTTCCCTA
1 ATTTCCCCAATTTCATTTCCCTA
*
29479513 ATTT-CCC-ATTTCATATTCCCCCA
1 ATTTCCCCAATTTCAT-TT-CCCTA
* *
29479536 ACTTCCCCGATTTCATTTCCC
1 ATTTCCCCAATTTCATTTCCC
29479557 GCCAATTCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 7 0.18
22 5 0.13
23 14 0.37
24 5 0.13
25 7 0.18
ACGTcount: A:0.19, C:0.39, G:0.01, T:0.40
Consensus pattern (23 bp):
ATTTCCCCAATTTCATTTCCCTA
Found at i:29481095 original size:15 final size:15
Alignment explanation
Indices: 29481075--29481107 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
29481065 AAGTTTTCTA
29481075 TATTAGTATTAAATT
1 TATTAGTATTAAATT
29481090 TATTAGTATTAAATT
1 TATTAGTATTAAATT
29481105 TAT
1 TAT
29481108 AAGCTTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
TATTAGTATTAAATT
Found at i:29481146 original size:45 final size:43
Alignment explanation
Indices: 29481056--29481167 Score: 152
Period size: 45 Copynumber: 2.6 Consensus size: 43
29481046 ATAAGTTTTC
* *
29481056 TAAATTTATAAGTTTTCTATATTAGTATTAAATTTATTAGTAT
1 TAAATTTATAAGTTTTCTAAATAAGTATTAAATTTATTAGTAT
* *
29481099 TAAATTTATAAGCTTTCTAAATAAGTGTTCTAAATTTATTAGTAT
1 TAAATTTATAAGTTTTCTAAATAAGT-AT-TAAATTTATTAGTAT
* *
29481144 TAATTTTTTAAGTTTTCTAAATAA
1 TAAATTTATAAGTTTTCTAAATAA
29481168 TTATATCACC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 23 0.38
44 1 0.02
45 36 0.60
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (43 bp):
TAAATTTATAAGTTTTCTAAATAAGTATTAAATTTATTAGTAT
Found at i:29481295 original size:17 final size:17
Alignment explanation
Indices: 29481275--29481341 Score: 88
Period size: 17 Copynumber: 4.2 Consensus size: 17
29481265 TTAATATCTA
*
29481275 TATAAGTTTTCTAAATT
1 TATAAGTGTTCTAAATT
29481292 TATAAGTGTTCTAAATT
1 TATAAGTGTTCTAAATT
*
29481309 TATAAGTTTTCT--A--
1 TATAAGTGTTCTAAATT
29481322 TATAAGTGTTCTAAATT
1 TATAAGTGTTCTAAATT
29481339 TAT
1 TAT
29481342 TAGTAATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 30 0.70
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (17 bp):
TATAAGTGTTCTAAATT
Found at i:29481428 original size:24 final size:24
Alignment explanation
Indices: 29481401--29481449 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
29481391 TATATAAGCT
* * *
29481401 TATATATCTTACATAATACATAAC
1 TATATAACATACATAATACAGAAC
29481425 TATATAACATACATAATACAGAAC
1 TATATAACATACATAATACAGAAC
29481449 T
1 T
29481450 TACATAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (24 bp):
TATATAACATACATAATACAGAAC
Found at i:29481492 original size:9 final size:9
Alignment explanation
Indices: 29481468--29481678 Score: 79
Period size: 9 Copynumber: 24.8 Consensus size: 9
29481458 AAGCATACCG
29481468 TACATAAAT
1 TACATAAAT
* *
29481477 TAAATAAGT
1 TACATAAAT
29481486 TACAT-AA-
1 TACATAAAT
*
29481493 TACACAAA-
1 TACATAAAT
* *
29481501 AACAAAAACT
1 TACATAAA-T
*
29481511 TACATAACT
1 TACATAAAT
29481520 TACAT-AA-
1 TACATAAAT
* *
29481527 TACACAACT
1 TACATAAAT
* *
29481536 GACATAACT
1 TACATAAAT
29481545 TACAT-AA-
1 TACATAAAT
* *
29481552 TACACAACT
1 TACATAAAT
*
29481561 TACATAACT
1 TACATAAAT
29481570 TACAT-AA-
1 TACATAAAT
*
29481577 TACATAATT
1 TACATAAAT
*
29481586 TACATAACT
1 TACATAAAT
29481595 TACAT-AA-
1 TACATAAAT
* *
29481602 GACATAAGT
1 TACATAAAT
*
29481611 TTCAT-AA-
1 TACATAAAT
* *
29481618 TACACAACT
1 TACATAAAT
* *
29481627 TACACAACT
1 TACATAAAT
*
29481636 TACATAACT
1 TACATAAAT
* *
29481645 TACACAACT
1 TACATAAAT
*
29481654 TACATAACT
1 TACATAAAT
*
29481663 TACATAACT
1 TACATAAAT
29481672 TACATAA
1 TACATAA
29481679 TAAATAACTT
Statistics
Matches: 154, Mismatches: 35, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
7 24 0.16
8 19 0.12
9 106 0.69
10 5 0.03
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.28
Consensus pattern (9 bp):
TACATAAAT
Found at i:29481535 original size:16 final size:17
Alignment explanation
Indices: 29481507--29481678 Score: 151
Period size: 16 Copynumber: 10.1 Consensus size: 17
29481497 CAAAAACAAA
29481507 AACTTACATAACTTACAT
1 AACTTACATAAC-TACAT
*
29481525 AA--TACACAACTGACAT
1 AACTTACATAACT-ACAT
*
29481541 AACTTACATAA-TACAC
1 AACTTACATAACTACAT
29481557 AACTTACATAACTTACAT
1 AACTTACATAAC-TACAT
*
29481575 AA--TACATAATTTACAT
1 AACTTACATAA-CTACAT
*
29481591 AACTTACATAA-GACAT
1 AACTTACATAACTACAT
* * *
29481607 AAGTTTCATAA-TACAC
1 AACTTACATAACTACAT
*
29481623 AACTTACACAACTTACAT
1 AACTTACATAAC-TACAT
*
29481641 AACTTACACAACTTACAT
1 AACTTACATAAC-TACAT
29481659 AACTTACATAACTTACAT
1 AACTTACATAAC-TACAT
29481677 AA
1 AA
29481679 TAAATAACTT
Statistics
Matches: 129, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.01
16 65 0.50
17 1 0.01
18 62 0.48
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (17 bp):
AACTTACATAACTACAT
Found at i:29481535 original size:25 final size:25
Alignment explanation
Indices: 29481507--29481689 Score: 217
Period size: 25 Copynumber: 7.2 Consensus size: 25
29481497 CAAAAACAAA
*
29481507 AACTTACATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAT
* *
29481532 AACTGACATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAT
29481557 AACTTACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
29481582 AATTTACATAACTTACATAAGACAT
1 AACTTACATAACTTACATAATACAT
* * * *
29481607 AAGTTTCATAA--TACACAACTTACAC
1 AACTTACATAACTTACATAA--TACAT
*
29481632 AACTTACATAACTTACACAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
*
29481659 AACTTACATAACTTACATAATAAAT
1 AACTTACATAACTTACATAATACAT
29481684 AACTTA
1 AACTTA
29481690 TTCCTAAATC
Statistics
Matches: 139, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.04
25 101 0.73
27 32 0.23
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.30
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:29487177 original size:21 final size:21
Alignment explanation
Indices: 29487152--29487215 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
29487142 AACTTAAAAC
*
29487152 AGAGGCAGCAGCGAGGGAAGT
1 AGAGGCTGCAGCGAGGGAAGT
*
29487173 AGAGGCTGCAGTGAGGGAAGT
1 AGAGGCTGCAGCGAGGGAAGT
29487194 AGAGGCTGCAGCGAGGGAAGT
1 AGAGGCTGCAGCGAGGGAAGT
29487215 A
1 A
29487216 AAGGTTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.31, C:0.12, G:0.47, T:0.09
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGGGAAGT
Found at i:29487765 original size:85 final size:84
Alignment explanation
Indices: 29487652--29487946 Score: 326
Period size: 85 Copynumber: 3.5 Consensus size: 84
29487642 GTTTGTGAAA
* * *
29487652 TAAGCGCCGCAAAAGAACACT-A-CTTTTAGCGGCGTTTTTTACCAAGCGCCGCTATAGAACATT
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAACATG
* *
29487715 A-CTTTTAGCGGCTTTTTTTTC
64 ATC-ATTAGCGGCTTTTTTTCC
* * * * * * * *
29487736 TAAACGCCACTAAAGATCATGTTTCTTTAGCGGCGTTTTCTCCCAAGTGCTGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATG-ATCTTTAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAACATGA
*
29487801 TCATTAGCGGCGTTTTTTCC
65 TCATTAGCGGCTTTTTTTCC
** * *
29487821 TAAGCGCCGCTAAAGAACATGATAATTAGCGGCGTTTTTTTCCTGAGCGCCGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACC-AAGCGCCGCTAAAGAACATGA
29487886 TCATTAGCGGCGTTTTTTTCC
65 TCATTAGCGGC-TTTTTTTCC
* * *
29487907 TAAGCACCGCTAAAGAACATGACCTTTAGCAGCGTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
29487947 TCTGTAAGCG
Statistics
Matches: 174, Mismatches: 31, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
83 1 0.01
84 32 0.18
85 96 0.55
86 45 0.26
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (84 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAACATGAT
CATTAGCGGCTTTTTTTCC
Found at i:29487945 original size:43 final size:43
Alignment explanation
Indices: 29487652--29487965 Score: 327
Period size: 43 Copynumber: 7.3 Consensus size: 43
29487642 GTTTGTGAAA
* *
29487652 TAAGCGCCGCAAAAGAACACT-A-CTTTTAGCGGCGTTTTTTACC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTTTCC
* * *
29487695 -AAGCGCCGCTATAGAACATTA-CTTTTAGCGGC-TTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTTTCC
* * * * *
29487736 TAAACGCCACTAAAGATCATGTTTCTTTAGCGGCG-TTTTCTCC
1 TAAGCGCCGCTAAAGAACATG-ATCTTTAGCGGCGTTTTTTTCC
* * * *
29487779 CAAGTGCTGCTAAAGAACATGATCATTAGCGGCG-TTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCC
**
29487821 TAAGCGCCGCTAAAGAACATGATAATTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCC
* *
29487864 TGAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCC
* * * *
29487907 TAAGCACCGCTAAAGAACATGACCTTTAGCAGCGTTTTTTTCTG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC-C
*
29487951 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
29487966 TTAGCGACGT
Statistics
Matches: 229, Mismatches: 35, Indels: 13
0.83 0.13 0.05
Matches are distributed among these distances:
41 8 0.03
42 91 0.40
43 116 0.51
44 14 0.06
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (43 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCC
Found at i:29488712 original size:15 final size:15
Alignment explanation
Indices: 29488692--29488720 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29488682 ATTTAAGATC
29488692 CTTTAATAGAAATTG
1 CTTTAATAGAAATTG
29488707 CTTTAATAGAAATT
1 CTTTAATAGAAATT
29488721 ATGAACAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (15 bp):
CTTTAATAGAAATTG
Found at i:29491868 original size:13 final size:12
Alignment explanation
Indices: 29491846--29491875 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
29491836 AAATCAATTT
29491846 TAAATTTTTATA
1 TAAATTTTTATA
29491858 TAAATTTTT-TA
1 TAAATTTTTATA
29491869 TAAATTT
1 TAAATTT
29491876 ATTACATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAATTTTTATA
Found at i:29492035 original size:44 final size:44
Alignment explanation
Indices: 29491972--29492059 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
29491962 TTTAATTAGG
29491972 GAAATAGGCCATTTCTAGGAGAGAGAAACAAAAAGCACGTCCAA
1 GAAATAGGCCATTTCTAGGAGAGAGAAACAAAAAGCACGTCCAA
* *
29492016 GAAATAGGCCATTTTTAGGAGAGAGGAACAAAAAGCACGTCCAA
1 GAAATAGGCCATTTCTAGGAGAGAGAAACAAAAAGCACGTCCAA
29492060 CAAGACTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (44 bp):
GAAATAGGCCATTTCTAGGAGAGAGAAACAAAAAGCACGTCCAA
Found at i:29496950 original size:10 final size:9
Alignment explanation
Indices: 29496918--29496980 Score: 81
Period size: 9 Copynumber: 6.8 Consensus size: 9
29496908 ACAATCAAAA
29496918 TGAGAGAGT
1 TGAGAGAGT
*
29496927 TGAGAGACT
1 TGAGAGAGT
*
29496936 TGAGAGGGTT
1 TGAGAGAG-T
*
29496946 TGAGAAAGT
1 TGAGAGAGT
29496955 TGAGAGAGTT
1 TGAGAGAG-T
29496965 TGAGAGAGT
1 TGAGAGAGT
29496974 TGAGAGA
1 TGAGAGA
29496981 ATGATGTGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
9 30 0.65
10 16 0.35
ACGTcount: A:0.33, C:0.02, G:0.41, T:0.24
Consensus pattern (9 bp):
TGAGAGAGT
Found at i:29496950 original size:19 final size:19
Alignment explanation
Indices: 29496918--29496980 Score: 92
Period size: 19 Copynumber: 3.4 Consensus size: 19
29496908 ACAATCAAAA
*
29496918 TGAGAGAG-TTGAGAGACT
1 TGAGAGAGTTTGAGAGAGT
* *
29496936 TGAGAGGGTTTGAGAAAGT
1 TGAGAGAGTTTGAGAGAGT
29496955 TGAGAGAGTTTGAGAGAGT
1 TGAGAGAGTTTGAGAGAGT
29496974 TGAGAGA
1 TGAGAGA
29496981 ATGATGTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
18 7 0.18
19 32 0.82
ACGTcount: A:0.33, C:0.02, G:0.41, T:0.24
Consensus pattern (19 bp):
TGAGAGAGTTTGAGAGAGT
Found at i:29497290 original size:28 final size:29
Alignment explanation
Indices: 29497234--29497292 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
29497224 ACCTATTTCT
** *
29497234 CTAATTAATTTTAAAATCGGCCTAAAGGC
1 CTAATTAATTAAAAAATCAGCCTAAAGGC
*
29497263 CTAATTAATTAAAAAAT-AGCCTATAGGC
1 CTAATTAATTAAAAAATCAGCCTAAAGGC
29497291 CT
1 CT
29497293 TATTTTGCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.31
Consensus pattern (29 bp):
CTAATTAATTAAAAAATCAGCCTAAAGGC
Found at i:29499581 original size:56 final size:56
Alignment explanation
Indices: 29499495--29499606 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
29499485 ACCTATCATC
29499495 AGAGGATGGGTTAGAGTTTGCAAAACTACTACACAGAAGGTCGGGCCACGCGAGTT
1 AGAGGATGGGTTAGAGTTTGCAAAACTACTACACAGAAGGTCGGGCCACGCGAGTT
*
29499551 AGAGGATGGGTTGGAGTTTGCAAAACTACTACACAGAAGGTCGGGCCACGCGAGTT
1 AGAGGATGGGTTAGAGTTTGCAAAACTACTACACAGAAGGTCGGGCCACGCGAGTT
29499607 CTTCGTTGTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.29, C:0.18, G:0.33, T:0.20
Consensus pattern (56 bp):
AGAGGATGGGTTAGAGTTTGCAAAACTACTACACAGAAGGTCGGGCCACGCGAGTT
Found at i:29502088 original size:21 final size:25
Alignment explanation
Indices: 29502064--29502118 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 25
29502054 AAAATATATA
29502064 TAAAATAATACAT-TAT-G-AAA-T
1 TAAAATAATACATATATGGAAAACT
29502085 T-AAATAATA-ATATATGGAAAACT
1 TAAAATAATACATATATGGAAAACT
29502108 TAAAATAATAC
1 TAAAATAATAC
29502119 TACATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.07
20 11 0.39
21 2 0.07
22 3 0.11
23 2 0.07
24 8 0.29
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (25 bp):
TAAAATAATACATATATGGAAAACT
Found at i:29502859 original size:14 final size:14
Alignment explanation
Indices: 29502821--29502851 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29502811 TTAATAATAT
*
29502821 AAAAACAGAAATGA
1 AAAAAAAGAAATGA
29502835 AAAAAAAGAAATGA
1 AAAAAAAGAAATGA
29502849 AAA
1 AAA
29502852 GAGAGAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.06
Consensus pattern (14 bp):
AAAAAAAGAAATGA
Found at i:29507053 original size:27 final size:26
Alignment explanation
Indices: 29507011--29507062 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
29507001 ATCTTTTAAA
29507011 ATTTTAAATAAAAATAAAATAAATTTT
1 ATTTTAAATAAAAAT-AAATAAATTTT
** *
29507038 ATTTTAAATATTAATAATTAAATTT
1 ATTTTAAATAAAAATAAATAAATTT
29507063 ATTATTATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTTAAATAAAAATAAATAAATTTT
Found at i:29507919 original size:41 final size:41
Alignment explanation
Indices: 29507866--29508000 Score: 175
Period size: 40 Copynumber: 3.3 Consensus size: 41
29507856 ATTTATTTTT
* *
29507866 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAA
* * * *
29507907 ATTTTTTAAATTTTTAATTTTTTTTAAAATAC-TTTTTAAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAA
*
29507947 ATTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTAAT
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAA
*
29507987 TTTTGTTTTAATTT
1 ATTT-TTTTAATTT
29508001 CGGGCCCATA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 45 0.56
41 36 0.44
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (41 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAA
Found at i:29507922 original size:17 final size:17
Alignment explanation
Indices: 29507900--29507974 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 17
29507890 TAAAATACTT
29507900 TTTTTAAATTTTTTAAA
1 TTTTTAAATTTTTTAAA
*
29507917 TTTTTAATTTTTTTTAAAATA
1 TTTTTAA-ATTTTTT--AA-A
*
29507938 CTTTTTAAAATTTTTTTAA
1 -TTTTT-AAATTTTTTAAA
*
29507957 TTTTAAAATATTTTTAAA
1 TTTTTAAAT-TTTTTAAA
29507975 ATACTTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
17 11 0.24
18 17 0.37
19 1 0.02
20 3 0.07
21 1 0.02
22 11 0.24
23 2 0.04
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTAAATTTTTTAAA
Found at i:29507971 original size:11 final size:11
Alignment explanation
Indices: 29507876--29507985 Score: 69
Period size: 11 Copynumber: 10.5 Consensus size: 11
29507866 ATTTTTTTAA
*
29507876 TTTTAAAATAC
1 TTTTAAAATAT
29507887 TTTTAAAATACTT
1 TTTTAAAATA--T
*
29507900 TTTTTAAAT-T
1 TTTTAAAATAT
29507910 TTTT--AA-AT
1 TTTTAAAATAT
* *
29507918 TTTT-AATTTT
1 TTTTAAAATAT
29507928 TTTTAAAATACT
1 TTTTAAAATA-T
29507940 TTTTAAAAT-T
1 TTTTAAAATAT
*
29507950 TTTT----TAA
1 TTTTAAAATAT
29507957 TTTTAAAATAT
1 TTTTAAAATAT
29507968 TTTTAAAATACT
1 TTTTAAAATA-T
29507980 TTTTAA
1 TTTTAA
29507986 TTTTTGTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
8 7 0.09
9 1 0.01
10 15 0.19
11 25 0.32
12 17 0.22
13 8 0.10
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:29508388 original size:18 final size:16
Alignment explanation
Indices: 29508356--29508399 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
29508346 ATAAGATGAG
29508356 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
29508372 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
29508386 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
29508400 ACCCTAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:29509020 original size:24 final size:24
Alignment explanation
Indices: 29508993--29509044 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
29508983 TTAGTAAGTC
*
29508993 AAATAAATTATACTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
29509017 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
29509041 AAAT
1 AAAT
29509045 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:29510982 original size:24 final size:24
Alignment explanation
Indices: 29510955--29511006 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
29510945 TTAGTAAGTC
*
29510955 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
29510979 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
29511003 AAAT
1 AAAT
29511007 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:29512848 original size:43 final size:43
Alignment explanation
Indices: 29512738--29512978 Score: 270
Period size: 43 Copynumber: 5.6 Consensus size: 43
29512728 CGCAAAAAAC
* * *
29512738 GCCGCTAAAGAACATGACCTTTAGTGGCGC-TTTACCCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTA-TCACAAAT
* *
29512781 GCCGCTAAAGAGCATGACCTTTAGCGGCGCTATTATCACAAAT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAT
* *** * * *
29512824 GCCGCTAAAGAACATGGCCTTTAGCAATGCTTTTATCATAGAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAT
***
29512867 GTTACTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAT
** *
29512910 GCTACTAAAGAACATGACCTTTAGCGACGCTTTTATCACAAAT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAT
* *
29512953 GTCGCTATAGAGA-ATGACCTTTAGCG
1 GCCGCTAAAGA-ACATGACCTTTAGCG
29512979 ACACTTTTTT
Statistics
Matches: 166, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
43 162 0.98
44 4 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAT
Found at i:29512946 original size:129 final size:129
Alignment explanation
Indices: 29512742--29512977 Score: 341
Period size: 129 Copynumber: 1.8 Consensus size: 129
29512732 AAAAACGCCG
* * *
29512742 CTAAAGAACATGACCTTTAGTGGCGCTTTACCCACAAACGCCGCTAAAGAGCATGACCTTTAGCG
1 CTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAACGCCACTAAAGAACATGACCTTTAGCG
* *
29512807 GCGCTATTATCACAAATGCCGCTAAAGA-ACATGGCCTTTAGCAATGCTTTTATCATAGACGTTA
66 ACGCTATTATCACAAATGCCGCTAAAGAGA-ATGACCTTTAGCAATGCTTTTATCATAGACGTTA
* * *
29512871 CTAAAGAACATGACCTTTAGCGGCGCTTTTA-TCACAAATGCTACTAAAGAACATGACCTTTAGC
1 CTAAAGAACATGACCTTTAGCGGCGC-TTTACCCACAAACGCCACTAAAGAACATGACCTTTAGC
* * *
29512935 GACGCTTTTATCACAAATGTCGCTATAGAGAATGACCTTTAGC
65 GACGCTATTATCACAAATGCCGCTAAAGAGAATGACCTTTAGC
29512978 GACACTTTTT
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
129 89 0.95
130 5 0.05
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (129 bp):
CTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAACGCCACTAAAGAACATGACCTTTAGCG
ACGCTATTATCACAAATGCCGCTAAAGAGAATGACCTTTAGCAATGCTTTTATCATAGACGTTA
Found at i:29515795 original size:31 final size:32
Alignment explanation
Indices: 29515748--29515819 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
29515738 CAATAATGTA
*
29515748 ATTA-TTATTATTTATATATATGTA-AT-TATT
1 ATTATTTATAATTTATATATATGTATATAT-TT
29515778 ATTATTTATAATTTATATATATGTATATATTT
1 ATTATTTATAATTTATATATATGTATATATTT
*
29515810 ATTTTTTATA
1 ATTATTTATA
29515820 TATGTACATG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 4 0.11
31 19 0.51
32 13 0.35
33 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (32 bp):
ATTATTTATAATTTATATATATGTATATATTT
Found at i:29521775 original size:25 final size:25
Alignment explanation
Indices: 29521740--29521804 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
29521730 ATAAAATACA
* *
29521740 TCTTTGCATTCATTTTTGAGCAA-TAT
1 TCTTT-CATTC-TTTTCGAACAATTAT
*
29521766 TCTTTCATTCTTTTCGAATAATTAT
1 TCTTTCATTCTTTTCGAACAATTAT
*
29521791 TCTTTCATTGTTTT
1 TCTTTCATTCTTTT
29521805 GGATTTTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.24
25 21 0.62
26 5 0.15
ACGTcount: A:0.20, C:0.15, G:0.08, T:0.57
Consensus pattern (25 bp):
TCTTTCATTCTTTTCGAACAATTAT
Found at i:29522764 original size:3 final size:3
Alignment explanation
Indices: 29522756--29522838 Score: 148
Period size: 3 Copynumber: 27.7 Consensus size: 3
29522746 TGAGTCGCAA
29522756 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
29522804 AAG AAG AAA AAT AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
29522839 AAAAGAAACA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:29524065 original size:50 final size:50
Alignment explanation
Indices: 29523997--29524111 Score: 122
Period size: 50 Copynumber: 2.3 Consensus size: 50
29523987 AAGACATTAG
* * * * *
29523997 TCTTATCGCCTTGACGTTGTAATGGAAAAGATTGAAGCCACAACGGCGAA
1 TCTTATCTCCCTGGCGTTGTAACGGAAAAGATTGAAGCCACAACGGCAAA
* * ** **
29524047 TCTTATTTCCCTGGCGTTGTAGCGGAGTAGATTGAAGCCATGACGGCAAA
1 TCTTATCTCCCTGGCGTTGTAACGGAAAAGATTGAAGCCACAACGGCAAA
*
29524097 TCTTATCTCCTTGGC
1 TCTTATCTCCCTGGC
29524112 ATTAAGGCTT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (50 bp):
TCTTATCTCCCTGGCGTTGTAACGGAAAAGATTGAAGCCACAACGGCAAA
Found at i:29524245 original size:50 final size:50
Alignment explanation
Indices: 29524184--29524450 Score: 152
Period size: 50 Copynumber: 5.3 Consensus size: 50
29524174 TTGGCATTAC
* *
29524184 AGTAGAGCAGATTGAAGTAGCAACGGTGAATCTTACTCCCCTGGCGGTGT
1 AGTAGAACAGATTGAAGTAGCAACGGTGAATCTTACTCCCCTGGCGTTGT
* ** ** * *
29524234 AGTAGAACAGATTGAAGCTAG-GACGGTGAATCTTGTTTCCCC-AACATTGCA
1 AGTAGAACAGATTGAAG-TAGCAACGGTGAATCTT-ACTCCCCTGGCGTTG-T
* * * ** * *
29524285 ATTA-AAAAGATTGAGGCCGCAACGGCGAATCTTACTTCCCTGGCGTTGT
1 AGTAGAACAGATTGAAGTAGCAACGGTGAATCTTACTCCCCTGGCGTTGT
* * * ** * * *
29524334 AGTAGAATAGATTGAAGCTA-CGATGGTGAATCTTGTTTCCCC-AGCATTGCA
1 AGTAGAACAGATTGAAG-TAGCAACGGTGAATCTT-ACTCCCCTGGCGTTG-T
* * ** *
29524385 ATTA-AAAAGATTGAAGCCGCAAC-GTCGAATCTTACTCCCCTGGCGGTGT
1 AGTAGAACAGATTGAAGTAGCAACGGT-GAATCTTACTCCCCTGGCGTTGT
*
29524434 AGTGGAACAGATTGAAG
1 AGTAGAACAGATTGAAG
29524451 CTACGACGAC
Statistics
Matches: 152, Mismatches: 52, Indels: 26
0.66 0.23 0.11
Matches are distributed among these distances:
49 17 0.11
50 117 0.77
51 18 0.12
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (50 bp):
AGTAGAACAGATTGAAGTAGCAACGGTGAATCTTACTCCCCTGGCGTTGT
Found at i:29524335 original size:100 final size:100
Alignment explanation
Indices: 29524192--29524700 Score: 705
Period size: 100 Copynumber: 5.1 Consensus size: 100
29524182 ACAGTAGAGC
** * * * *
29524192 AGATTGAAGTAGCAACGGTGAATCTTACTCCCCTGGCGGTGTAGTAGAACAGATTGAAGCTAGGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
29524257 CGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
66 CGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * * *
29524292 AGATTGAGGCCGCAACGGCGAATCTTACTTCCCTGGCGTTGTAGTAGAATAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* *
29524357 TGGTGAATCTTGTTTCCCCAGCATTGCAATTAAAA
66 CGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
* *
29524392 AGATTGAAGCCGCAACGTCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
***
29524457 CGACAAATCTTGTTTCCCCAACATTGCAATTAAAA
66 CGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * * * *
29524492 AGATTGAAGCCGCAATGGCAAATCTTACTTCCTTGGTGGTATAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
*
29524557 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
66 CGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * * * * * *
29524592 AGATTGAAGCCACAATGTCGAATCTTACTTCCTTGGTGGTATAGTGGAACAGATTGATGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* * *
29524657 CGGTGAATCTTGTTTCCCCGACATT-CTAGTTAAAC
66 CGGTGAATCTTGTTTCCCCAACATTGC-AATTAAAA
29524692 AGATTGAAG
1 AGATTGAAG
29524701 ATGGCGAATC
Statistics
Matches: 370, Mismatches: 38, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
99 1 0.00
100 369 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (100 bp):
AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
CGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
Found at i:29524496 original size:50 final size:50
Alignment explanation
Indices: 29524242--29524601 Score: 197
Period size: 50 Copynumber: 7.2 Consensus size: 50
29524232 GTAGTAGAAC
* *
29524242 AGATTGAAGCTAGGACGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* ** * ** *** * * * *
29524292 AGATTGAGGCCGCAACGGCGAATCTTACTTCCCTGGCGTTG-TAGTAGAAT
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTA-AAA
* * *
29524342 AGATTGAAGCTACGATGGTGAATCTTGTTTCCCCAGCATTGCAATTAAAA
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
** * * ** ** ** * * ** *
29524392 AGATTGAAGCCGCAACGTCGAATCTT-ACTCCCCTGGCGGTGTAGTGGAAC
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCC-AACATTGCAATTAAAA
* *
29524442 AGATTGAAGCTACGACGACAAATCTTGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
** * * * ** **** * * ** *
29524492 AGATTGAAGCCGCAATGGCAAATCTTACTT--CCTTGGTGGTATAGTGGAAC
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCA-A-TTAAAA
29524542 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
29524592 AGATTGAAGC
1 AGATTGAAGC
29524602 CACAATGTCG
Statistics
Matches: 209, Mismatches: 93, Indels: 16
0.66 0.29 0.05
Matches are distributed among these distances:
48 5 0.02
49 9 0.04
50 181 0.87
51 9 0.04
52 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
Found at i:29524646 original size:50 final size:50
Alignment explanation
Indices: 29524492--29524648 Score: 129
Period size: 50 Copynumber: 3.1 Consensus size: 50
29524482 GCAATTAAAA
* *
29524492 AGATTGAAGCCGCAATGGCAAATCTTACTTCCTTGGTGGTATAGTGGAAC
1 AGATTGAAGCCACAATGGCGAATCTTACTTCCTTGGTGGTATAGTGGAAC
* * * ** **** * * ** *
29524542 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCA-A-TTAAAA
1 AGATTGAAGCCACAATGGCGAATCTTACTT--CCTTGGTGGTATAGTGGAAC
*
29524592 AGATTGAAGCCACAATGTCGAATCTTACTTCCTTGGTGGTATAGTGGAAC
1 AGATTGAAGCCACAATGGCGAATCTTACTTCCTTGGTGGTATAGTGGAAC
29524642 AGATTGA
1 AGATTGA
29524649 TGCTACGACG
Statistics
Matches: 72, Mismatches: 31, Indels: 8
0.65 0.28 0.07
Matches are distributed among these distances:
48 5 0.07
49 1 0.01
50 60 0.83
51 1 0.01
52 5 0.07
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (50 bp):
AGATTGAAGCCACAATGGCGAATCTTACTTCCTTGGTGGTATAGTGGAAC
Found at i:29524761 original size:44 final size:44
Alignment explanation
Indices: 29524707--29525005 Score: 231
Period size: 44 Copynumber: 6.9 Consensus size: 44
29524697 GAAGATGGCG
29524707 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAT
* ** *
29524751 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAG-TGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAT
* * * * *
29524794 AGATCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-T--CGC-ATCT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-AT
* * * * * **
29524835 AGTCTTATCTCCTTGAAGTTGCAGGGGAGCAGACT-GAG-TACGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-AT
* * * * *
29524878 AAGTCTTATC-CTCCTTAAGTTGCAGTGGGGCAGACTGAAGATGGAA-
1 AA-TCTTATCTC-CCTGAAGTTGCAGTGGAGCAGATTAAAGCT--AAT
* * *
29524924 AATCTTATCTCCTTGAAGCTGCAGTGGACCAGATTAAAGCTAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAT
* *
29524968 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
29525006 ACAGATCTTA
Statistics
Matches: 198, Mismatches: 42, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
40 20 0.10
41 9 0.05
42 2 0.01
43 15 0.08
44 116 0.59
45 31 0.16
46 4 0.02
48 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAT
Found at i:29526579 original size:33 final size:32
Alignment explanation
Indices: 29526518--29526587 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 32
29526508 AATGTAATTA
* *
29526518 TTATTATTTTATATATATATGTAATTATTTTT
1 TTATAATTTTATATATATATATAATTATTTTT
* *
29526550 TTATAATTTATATATATGTATATATTTATTTTT
1 TTATAATTT-TATATATATATATAATTATTTTT
*
29526583 ATATA
1 TTATA
29526588 TGTACATGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 8 0.25
33 24 0.75
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (32 bp):
TTATAATTTTATATATATATATAATTATTTTT
Found at i:29526612 original size:8 final size:8
Alignment explanation
Indices: 29526525--29526654 Score: 52
Period size: 8 Copynumber: 16.1 Consensus size: 8
29526515 TTATTATTAT
29526525 TTTATATA
1 TTTATATA
* *
29526533 TATATGTA
1 TTTATATA
* * *
29526541 ATTATTTT
1 TTTATATA
29526549 TTTATA-A
1 TTTATATA
29526556 TTTATATA
1 TTTATATA
29526564 TATGTATATA
1 T-T-TATATA
29526574 TTTAT-T-
1 TTTATATA
29526580 TTTATATA
1 TTTATATA
* * *
29526588 TGTACATG
1 TTTATATA
**
29526596 TAAATATA
1 TTTATATA
29526604 TTTATATA
1 TTTATATA
* *
29526612 TTTTTTCTA
1 -TTTATATA
* *
29526621 ATGA-ATA
1 TTTATATA
*
29526628 TTTTTATA
1 TTTATATA
29526636 TTTATATA
1 TTTATATA
29526644 TATGTATATA
1 T-T-TATATA
29526654 T
1 T
29526655 CTATGTTTTT
Statistics
Matches: 85, Mismatches: 28, Indels: 16
0.66 0.22 0.12
Matches are distributed among these distances:
6 5 0.06
7 11 0.13
8 46 0.54
9 9 0.11
10 14 0.16
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (8 bp):
TTTATATA
Found at i:29528401 original size:9 final size:9
Alignment explanation
Indices: 29528387--29528748 Score: 210
Period size: 9 Copynumber: 38.6 Consensus size: 9
29528377 TATTTATGTA
29528387 TTATGTAAG
1 TTATGTAAG
29528396 TTATGTAAG
1 TTATGTAAG
*
29528405 TTATGTGAG
1 TTATGTAAG
29528414 TTATGTAAG
1 TTATGTAAG
29528423 TTATGTAAG
1 TTATGTAAG
*
29528432 TTATGTGAG
1 TTATGTAAG
*
29528441 TTATGTGAG
1 TTATGTAAG
29528450 TTATGTAAG
1 TTATGTAAG
*
29528459 TTATGATATG
1 TTATG-TAAG
*
29528469 ATATATATAAG
1 -T-TATGTAAG
29528480 TTATGTAAG
1 TTATGTAAG
* *
29528489 TTATGTGAC
1 TTATGTAAG
*
29528498 TTATGTGAG
1 TTATGTAAG
*
29528507 TTATGTGAG
1 TTATGTAAG
29528516 TTATGTAAG
1 TTATGTAAG
* *
29528525 TTACGATATG
1 TTATG-TAAG
*
29528535 ATATATATAAG
1 -T-TATGTAAG
29528546 TTAT-TAAG
1 TTATGTAAG
*
29528554 TTATGTATG
1 TTATGTAAG
*
29528563 TTATGTGAG
1 TTATGTAAG
29528572 TTATGTAAG
1 TTATGTAAG
29528581 TTAT-TATATG
1 TTATGTA-A-G
* *
29528591 AATATATAAG
1 -TTATGTAAG
29528601 TTAT-TAAG
1 TTATGTAAG
*
29528609 TTAAGATCCAAAG
1 TTATG-T---AAG
* *
29528622 TTTTTTTTTAA-
1 ---TTATGTAAG
* *
29528633 TTCTTTAAAG
1 TTATGT-AAG
*
29528643 TTATGTAAA
1 TTATGTAAG
*
29528652 TTTTGTAAG
1 TTATGTAAG
29528661 TTATGTAAG
1 TTATGTAAG
* *
29528670 TTTTGATATG
1 TTATG-TAAG
* * *
29528680 ATATATATAT
1 TTATGTA-AG
29528690 TTATGTAAG
1 TTATGTAAG
* *
29528699 TTAGGTAAA
1 TTATGTAAG
*
29528708 TTATGCAAG
1 TTATGTAAG
* *
29528717 TAATGCAAG
1 TTATGTAAG
*
29528726 TAATGTAAG
1 TTATGTAAG
*
29528735 TTGTGTAAG
1 TTATGTAAG
29528744 TTATG
1 TTATG
29528749 ATATATATTT
Statistics
Matches: 276, Mismatches: 54, Indels: 46
0.73 0.14 0.12
Matches are distributed among these distances:
8 22 0.08
9 202 0.73
10 25 0.09
11 12 0.04
12 9 0.03
13 3 0.01
15 1 0.00
16 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:29531559 original size:7 final size:7
Alignment explanation
Indices: 29531547--29531609 Score: 54
Period size: 7 Copynumber: 8.6 Consensus size: 7
29531537 TATATGGAAA
29531547 TAAACCC
1 TAAACCC
29531554 TAAACCC
1 TAAACCC
*
29531561 TAAAACTC
1 T-AAACCC
*
29531569 TAAACCT
1 TAAACCC
29531576 TAAACCC
1 TAAACCC
29531583 TAAAACTCC
1 T-AAAC-CC
* *
29531592 AAAACTC
1 TAAACCC
*
29531599 TAAACCT
1 TAAACCC
29531606 TAAA
1 TAAA
29531610 TACTAAAACC
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
7 28 0.64
8 14 0.32
9 2 0.05
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:29531571 original size:8 final size:8
Alignment explanation
Indices: 29531555--29531641 Score: 53
Period size: 8 Copynumber: 11.5 Consensus size: 8
29531545 AATAAACCCT
*
29531555 AAACCCTA
1 AAACTCTA
29531563 AAACTCT-
1 AAACTCTA
*
29531570 AAAC-CTT
1 AAACTCTA
*
29531577 AAACCCTA
1 AAACTCTA
*
29531585 AAACTCCA
1 AAACTCTA
29531593 AAACTCT-
1 AAACTCTA
*
29531600 AAAC-CTT
1 AAACTCTA
29531607 AAA-TACTA
1 AAACT-CTA
29531615 AAAC-CTTA
1 AAACTC-TA
29531623 AAACTCT-
1 AAACTCTA
*
29531630 AAATTCTA
1 AAACTCTA
29531638 AAAC
1 AAAC
29531642 CCAAAATAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
6 4 0.06
7 22 0.35
8 35 0.56
9 1 0.02
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (8 bp):
AAACTCTA
Found at i:29531579 original size:22 final size:22
Alignment explanation
Indices: 29531547--29531624 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
29531537 TATATGGAAA
*
29531547 TAAACCCTAAACCCTAAAACTC
1 TAAACCTTAAACCCTAAAACTC
29531569 TAAACCTTAAACCCTAAAACTC
1 TAAACCTTAAACCCTAAAACTC
* * *
29531591 CAAAACTCTAAACCTTAAATACT-
1 TAAACCT-TAAACCCTAAA-ACTC
*
29531614 AAAACCTTAAA
1 TAAACCTTAAA
29531625 ACTCTAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
22 30 0.62
23 15 0.31
24 3 0.06
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAACCTTAAACCCTAAAACTC
Found at i:29531598 original size:30 final size:29
Alignment explanation
Indices: 29531547--29531632 Score: 111
Period size: 30 Copynumber: 2.9 Consensus size: 29
29531537 TATATGGAAA
29531547 TAAACCCT-AAACCCTAAAACTCTAAACCT
1 TAAACCCTAAAACCC-AAAACTCTAAACCT
29531576 TAAACCCTAAAACTCCAAAACTCTAAACCT
1 TAAACCCTAAAAC-CCAAAACTCTAAACCT
** *
29531606 TAAATACTAAAACCTTAAAACTCTAAA
1 TAAACCCTAAAACC-CAAAACTCTAAA
29531633 TTCTAAAACC
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
29 9 0.18
30 40 0.78
31 2 0.04
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (29 bp):
TAAACCCTAAAACCCAAAACTCTAAACCT
Found at i:29532005 original size:40 final size:40
Alignment explanation
Indices: 29531950--29532084 Score: 175
Period size: 40 Copynumber: 3.4 Consensus size: 40
29531940 GAAAAGTGCC
29531950 GCTAATG-TTGATCTATAGCGGCATTTTTCAAATAGCACT
1 GCTAATGCTTGATCTATAGCGGCATTTTTCAAATAGCACT
* ** * *
29531989 GCTAATGCTCGATCTATTA-CGGGGTTTTGCAAAAAGCACT
1 GCTAATGCTTGATCTA-TAGCGGCATTTTTCAAATAGCACT
* * *
29532029 GCTAATGCTTGATCTATAGTGGCATTTTTCAAATAGCGCC
1 GCTAATGCTTGATCTATAGCGGCATTTTTCAAATAGCACT
29532069 GCTAATGCTTGATCTA
1 GCTAATGCTTGATCTA
29532085 CTGCGACGTT
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 9 0.11
40 69 0.86
41 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (40 bp):
GCTAATGCTTGATCTATAGCGGCATTTTTCAAATAGCACT
Found at i:29532103 original size:80 final size:80
Alignment explanation
Indices: 29531932--29532116 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 80
29531922 TTTTTTGCAG
* ** *
29531932 CGTTTTGCGAAAAGTGCCGCTAATG-TTGATCTATAGCGGCATTTTTCAAATAGCACTGCTAATG
1 CGTTTTGCAAAAAGCACCGCTAATGCTTGATCTATAGCGGCATTTTTCAAATAGCACCGCTAATG
* *
29531996 CTCGATCTATTACGG
66 CTCGATCTACTACGA
* * * *
29532011 GGTTTTGCAAAAAGCACTGCTAATGCTTGATCTATAGTGGCATTTTTCAAATAGCGCCGCTAATG
1 CGTTTTGCAAAAAGCACCGCTAATGCTTGATCTATAGCGGCATTTTTCAAATAGCACCGCTAATG
* *
29532076 CTTGATCTACTGCGA
66 CTCGATCTACTACGA
* *
29532091 CG-TTTGTTAAAAAGCGCCGCTAATGC
1 CGTTTTG-CAAAAAGCACCGCTAATGC
29532117 CACTAAAGCT
Statistics
Matches: 88, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
79 24 0.27
80 64 0.73
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (80 bp):
CGTTTTGCAAAAAGCACCGCTAATGCTTGATCTATAGCGGCATTTTTCAAATAGCACCGCTAATG
CTCGATCTACTACGA
Found at i:29532107 original size:40 final size:40
Alignment explanation
Indices: 29531941--29532116 Score: 153
Period size: 40 Copynumber: 4.4 Consensus size: 40
29531931 GCGTTTTGCG
* *
29531941 AAAAGTGCCGCTAATG-TTGATCTATAGCGGCATTTTTCA
1 AAAAGCGCCGCTAATGCTTGATCTATAGCGACATTTTTCA
* * * * *** *
29531980 AATAGCACTGCTAATGCTCGATCTATTA-CGGGGTTTTGCA
1 AAAAGCGCCGCTAATGCTTGATCTA-TAGCGACATTTTTCA
* * * *
29532020 AAAAGCACTGCTAATGCTTGATCTATAGTGGCATTTTTCA
1 AAAAGCGCCGCTAATGCTTGATCTATAGCGACATTTTTCA
* *
29532060 AATAGCGCCGCTAATGCTTGATCTACT-GCGACGTTTGTT-A
1 AAAAGCGCCGCTAATGCTTGATCTA-TAGCGACATTT-TTCA
29532100 AAAAGCGCCGCTAATGC
1 AAAAGCGCCGCTAATGC
29532117 CACTAAAGCT
Statistics
Matches: 111, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
39 14 0.13
40 92 0.83
41 5 0.05
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTTGATCTATAGCGACATTTTTCA
Found at i:29532228 original size:40 final size:40
Alignment explanation
Indices: 29532166--29532272 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 40
29532156 TTTATTGTGG
* ** *
29532166 CGTTTTCCAAAAAGTGCCGCTAATGCTCGATCTATAGCAA
1 CGTTTTTCAAAAAACGCCGCTAATGCTCAATCTATAGCAA
* *
29532206 CGTTTTTCAAAAAACGCTGCTAATGCTCAATCTATAGCAG
1 CGTTTTTCAAAAAACGCCGCTAATGCTCAATCTATAGCAA
* * **
29532246 CGTTTTTTAAAAAGCATCGCTAATGCT
1 CGTTTTTCAAAAAACGCCGCTAATGCT
29532273 TGACCTTTTG
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (40 bp):
CGTTTTTCAAAAAACGCCGCTAATGCTCAATCTATAGCAA
Found at i:29532396 original size:40 final size:40
Alignment explanation
Indices: 29532352--29532516 Score: 134
Period size: 40 Copynumber: 4.1 Consensus size: 40
29532342 TTATGTCGTG
* * *
29532352 TTTTTCGAAAAGCGCCACTAATGCTCGATCTATAGTGGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGTGGCA
* ** * * ** * *
29532392 TTTTTCTAGGAGTGCTGCTAATGCTTAACCTATAGCGGTA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGTGGCA
* * * *
29532432 CTTTTCAAAAAGCGTCGCTAATGCTCGACCTATAGCT-ACG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAG-TGGCA
* * * *
29532472 TTTTTCAAAAAGCGCCGCTAATGCTTGACCTTTTGCGGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGTGGCA
29532512 TTTTT
1 TTTTT
29532517 GTCATAAACA
Statistics
Matches: 91, Mismatches: 32, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
40 91 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (40 bp):
TTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGTGGCA
Found at i:29533621 original size:23 final size:25
Alignment explanation
Indices: 29533567--29533622 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
29533557 TTTTTTTGCT
*
29533567 GTTTTTCTTTTAAAAAAATATTTTTT
1 GTTTTTCTTTT-AAAAAATATTTTTA
*
29533593 GTTTTTTCTTTT-AACAAT-TTTTTA
1 G-TTTTTCTTTTAAAAAATATTTTTA
29533617 GTTTTT
1 GTTTTT
29533623 AAGCTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 6 0.22
25 5 0.19
26 1 0.04
27 10 0.37
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.66
Consensus pattern (25 bp):
GTTTTTCTTTTAAAAAATATTTTTA
Found at i:29534433 original size:29 final size:30
Alignment explanation
Indices: 29534368--29534442 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
29534358 AACTACCAAA
**
29534368 ATAGTCACTTTTGTTTGTCTCAGGTTACATT
1 ATAGTCACTTTTGTTTG-CAAAGGTTACATT
* * *
29534399 TTAGTCACTTTTGTTTG-AAATGTTACGTT
1 ATAGTCACTTTTGTTTGCAAAGGTTACATT
*
29534428 ATAGTCACTTATGTT
1 ATAGTCACTTTTGTT
29534443 ATCGTATTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 21 0.57
31 16 0.43
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.49
Consensus pattern (30 bp):
ATAGTCACTTTTGTTTGCAAAGGTTACATT
Found at i:29535503 original size:75 final size:75
Alignment explanation
Indices: 29535416--29535565 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
29535406 TATTGAGTAA
29535416 GAGGGAACTCAACATCTTTCTCTTATACGCAATCGAAGAGTTTAATAGTTGAATTTTTAATTAAT
1 GAGGGAACTCAACATCTTTCTCTTATACGCAATCGAAGAGTTTAATAGTTGAATTTTTAATTAAT
29535481 ATATTTAATT
66 ATATTTAATT
29535491 GAGGGAACTCAACATCTTTCTCTTATACGCAATCGAAGAGTTTAATAGTTGAATTTTTAATTAAT
1 GAGGGAACTCAACATCTTTCTCTTATACGCAATCGAAGAGTTTAATAGTTGAATTTTTAATTAAT
29535556 ATATTTAATT
66 ATATTTAATT
29535566 CTATTTTTAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (75 bp):
GAGGGAACTCAACATCTTTCTCTTATACGCAATCGAAGAGTTTAATAGTTGAATTTTTAATTAAT
ATATTTAATT
Found at i:29535898 original size:16 final size:16
Alignment explanation
Indices: 29535879--29535909 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29535869 ATAACGAAAT
29535879 GTTGTTATAGAGAGTG
1 GTTGTTATAGAGAGTG
*
29535895 GTTGTTATAGGGAGT
1 GTTGTTATAGAGAGT
29535910 CTTGACTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.39
Consensus pattern (16 bp):
GTTGTTATAGAGAGTG
Found at i:29536953 original size:21 final size:21
Alignment explanation
Indices: 29536929--29536995 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
29536919 AATTAATAAT
*
29536929 AAATACTATGTAATTTAGTTA
1 AAATACTATTTAATTTAGTTA
* *
29536950 AAATTAGTATAATTAATTTA-TAAA
1 AAA-TACTAT--TTAATTTAGT-TA
29536974 AAATACTATTTAATTTAGTTA
1 AAATACTATTTAATTTAGTTA
29536995 A
1 A
29536996 TTATTTGGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
21 13 0.36
22 6 0.17
23 6 0.17
24 11 0.31
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (21 bp):
AAATACTATTTAATTTAGTTA
Found at i:29536978 original size:45 final size:45
Alignment explanation
Indices: 29536910--29536995 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
29536900 TTATTGGCTA
*
29536910 AGTATACATAATTAATAATAAATACTATGTAATTTAGTTAAAATT
1 AGTATACATAATTAATAAAAAATACTATGTAATTTAGTTAAAATT
* *
29536955 AGTATA-ATTAATTTATAAAAAATACTATTTAATTTAGTTAA
1 AGTATACA-TAATTAATAAAAAATACTATGTAATTTAGTTAA
29536996 TTATTTGGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.03
45 36 0.97
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (45 bp):
AGTATACATAATTAATAAAAAATACTATGTAATTTAGTTAAAATT
Found at i:29540497 original size:27 final size:28
Alignment explanation
Indices: 29540421--29540502 Score: 130
Period size: 28 Copynumber: 3.0 Consensus size: 28
29540411 TCATAAACAC
*
29540421 ATATGAAAAGGAATGCCTTTGTGGCAAT
1 ATATGAAAAGAAATGCCTTTGTGGCAAT
29540449 ATATGAAAAGAAATGCCTTTGTGGCAAT
1 ATATGAAAAGAAATGCCTTTGTGGCAAT
* *
29540477 ATGTGGAAA-AAATGCCTTTGTGGCAA
1 ATATGAAAAGAAATGCCTTTGTGGCAA
29540503 ACTCTAAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 17 0.33
28 34 0.67
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (28 bp):
ATATGAAAAGAAATGCCTTTGTGGCAAT
Found at i:29540517 original size:27 final size:27
Alignment explanation
Indices: 29540426--29540575 Score: 128
Period size: 27 Copynumber: 5.5 Consensus size: 27
29540416 AACACATATG
*
29540426 AAAAGGAATGCCTTTGTGGCAATA-TAT
1 AAAAGGAATGCCTTTGTGGCAA-ACTCT
* *
29540453 GAAAAGAAATGCCTTTGTGGCAATA-TGT
1 -AAAAGGAATGCCTTTGTGGCAA-ACTCT
29540481 GGAAAA--AATGCCTTTGTGGCAAACTCT
1 --AAAAGGAATGCCTTTGTGGCAAACTCT
** ** *
29540508 AAAAGGAATGAGTTTGTCACAGACTCT
1 AAAAGGAATGCCTTTGTGGCAAACTCT
* *
29540535 GAAAGGAATGCCTTTGTGGAAAACTCT
1 AAAAGGAATGCCTTTGTGGCAAACTCT
*
29540562 AAAAGGAATTCCTT
1 AAAAGGAATGCCTT
29540576 GACGGTATAC
Statistics
Matches: 101, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
25 4 0.04
26 1 0.01
27 66 0.65
28 25 0.25
29 5 0.05
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (27 bp):
AAAAGGAATGCCTTTGTGGCAAACTCT
Found at i:29541705 original size:46 final size:46
Alignment explanation
Indices: 29541647--29541740 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
29541637 CTTTTTATGG
* * *
29541647 AAAGAATTTATATCTAAATTCATAGGTTGAACTATTTTAAGGTATT
1 AAAGAATTTATATCTAAATTCATAGGGTAAACTATTGTAAGGTATT
*
29541693 AAAGGATTTATATCTAAATTCATAGGGTAAACTATTGTAAGGTATT
1 AAAGAATTTATATCTAAATTCATAGGGTAAACTATTGTAAGGTATT
29541739 AA
1 AA
29541741 TCTTCATTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (46 bp):
AAAGAATTTATATCTAAATTCATAGGGTAAACTATTGTAAGGTATT
Found at i:29542058 original size:27 final size:27
Alignment explanation
Indices: 29541948--29542064 Score: 126
Period size: 28 Copynumber: 4.2 Consensus size: 27
29541938 CGACAGTGTG
* *
29541948 TCCCTTATTTTTCAAATTTTACAATTT
1 TCCCCTATTTTTCAAATTTTATAATTT
*
29541975 TGCCCCTATTTTTCAAATTTTATAGTTT
1 T-CCCCTATTTTTCAAATTTTATAATTT
* * * * *
29542003 ACCTCTATTTTTTAGATTTTATAGTTTT
1 TCCCCTATTTTTCAAATTTTATA-ATTT
*
29542031 TCCCCTATTTTTCAGATTTTATAATTT
1 TCCCCTATTTTTCAAATTTTATAATTT
29542058 TCTCCCT
1 TC-CCCT
29542065 TGCTTCACAA
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
27 25 0.33
28 50 0.67
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.56
Consensus pattern (27 bp):
TCCCCTATTTTTCAAATTTTATAATTT
Found at i:29545066 original size:154 final size:154
Alignment explanation
Indices: 29544825--29545131 Score: 551
Period size: 154 Copynumber: 2.0 Consensus size: 154
29544815 GAGATTCTGG
29544825 TTCTACTGACTCAAATTCTCATCCTATAAAACAAACTACAAAGGGTAGACCACAACAAGAGGTTG
1 TTCTACTGACTCAAATTCTCATCCTATAAAACAAACTACAAAGGGTAGACCACAACAAGAGGTTG
* * *
29544890 TTGTAACTAATTCGAGGGGTTAGACTCCTAGTTATGCGTATTGTGAAAAATACCACATAAGTAAG
66 TTGTAACTAATTCAAGGCGTTAGACTCCTAGTTATGCGTATTGAGAAAAATACCACATAAGTAAG
29544955 TGTTGGAAGAAATTGAGTGCTTGT
131 TGTTGGAAGAAATTGAGTGCTTGT
* * *
29544979 TTCTACTGACTCAAATTCTCATCCTATAAAACAAACTAGAAAGGGTAGACCGCAATAAGAGGTTG
1 TTCTACTGACTCAAATTCTCATCCTATAAAACAAACTACAAAGGGTAGACCACAACAAGAGGTTG
*
29545044 TTGTAACTAATTCAAGGCGTTAGACTCCTAGTTATGCGTATTGAGAAAAATACCACATAGGTAAG
66 TTGTAACTAATTCAAGGCGTTAGACTCCTAGTTATGCGTATTGAGAAAAATACCACATAAGTAAG
29545109 TGTTGGAAGAAATTGAGTGCTTG
131 TGTTGGAAGAAATTGAGTGCTTG
29545132 CTTAAAGTGT
Statistics
Matches: 146, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
154 146 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (154 bp):
TTCTACTGACTCAAATTCTCATCCTATAAAACAAACTACAAAGGGTAGACCACAACAAGAGGTTG
TTGTAACTAATTCAAGGCGTTAGACTCCTAGTTATGCGTATTGAGAAAAATACCACATAAGTAAG
TGTTGGAAGAAATTGAGTGCTTGT
Found at i:29546080 original size:19 final size:19
Alignment explanation
Indices: 29546044--29546085 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
29546034 TAAATAGGGT
*
29546044 TTTTCCTCTCTTCTCTTTA
1 TTTTCCTCTCTTCCCTTTA
* *
29546063 TTTTCTTCTTTTCCCTTTA
1 TTTTCCTCTCTTCCCTTTA
29546082 TTTT
1 TTTT
29546086 TTTGTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTCCTCTCTTCCCTTTA
Found at i:29550051 original size:13 final size:13
Alignment explanation
Indices: 29550035--29550059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29550025 TTTTCTACAA
29550035 CACTTTTTAAAAT
1 CACTTTTTAAAAT
29550048 CACTTTTTAAAA
1 CACTTTTTAAAA
29550060 GCATTGCTAA
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:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
CACTTTTTAAAAT
Found at i:29551720 original size:18 final size:18
Alignment explanation
Indices: 29551697--29551731 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29551687 TCTAAGAAAA
*
29551697 CCAAAAAATAGAAATCAT
1 CCAAAAAATAAAAATCAT
29551715 CCAAAAAATAAAAATCA
1 CCAAAAAATAAAAATCA
29551732 CAAGTTTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.17, G:0.03, T:0.14
Consensus pattern (18 bp):
CCAAAAAATAAAAATCAT
Found at i:29551769 original size:6 final size:7
Alignment explanation
Indices: 29551743--29551768 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29551733 AAGTTTGGAG
29551743 TAAAAAT
1 TAAAAAT
29551750 TAAAAAT
1 TAAAAAT
29551757 TAAAAAT
1 TAAAAAT
29551764 TAAAA
1 TAAAA
29551769 TGGTCCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAAAT
Found at i:29555007 original size:16 final size:17
Alignment explanation
Indices: 29554977--29555008 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29554967 TATTTTTCAA
29554977 AATTAAATAAATTTTCC
1 AATTAAATAAATTTTCC
29554994 AATTAAAT-AATTTTC
1 AATTAAATAAATTTTC
29555009 TCATTCCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTAAATAAATTTTCC
Found at i:29557568 original size:39 final size:39
Alignment explanation
Indices: 29557505--29557594 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
29557495 CATGGCACAA
* ** *
29557505 AAGTACGATCAGGGGTACTGAAGTACAACAAGGACATGT
1 AAGTGCGATCAGGGGTACCAAAGTACAACAAGGACACGT
* * * *
29557544 AAGTGTGATCAGGGGTACCAAAGTACAATAGGGGCACGT
1 AAGTGCGATCAGGGGTACCAAAGTACAACAAGGACACGT
29557583 AAGTGCGATCAG
1 AAGTGCGATCAG
29557595 AGGTGTAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.18
Consensus pattern (39 bp):
AAGTGCGATCAGGGGTACCAAAGTACAACAAGGACACGT
Found at i:29560191 original size:27 final size:27
Alignment explanation
Indices: 29560145--29560202 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
29560135 GGTGTATACT
*
29560145 AGCTCGCCAAGCATTTTGGTAAACACC
1 AGCTCGCCAAGCATTCTGGTAAACACC
*
29560172 AGCTCGCCAAGTC-TTCTGGTGAACACC
1 AGCTCGCCAAG-CATTCTGGTAAACACC
29560199 AGCT
1 AGCT
29560203 TGATAATCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.22
Consensus pattern (27 bp):
AGCTCGCCAAGCATTCTGGTAAACACC
Found at i:29560229 original size:27 final size:27
Alignment explanation
Indices: 29560161--29560246 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
29560151 CCAAGCATTT
* * **
29560161 TGGTAAACACCAGCTCGCCAAGT-CTTC
1 TGGTGAACACCAGCTCACCAA-TCCTAG
* *
29560188 TGGTGAACACCAGCTTGA-TAATCCTAG
1 TGGTGAACACCAGC-TCACCAATCCTAG
* *
29560215 TGGTGAACTCTAGCTCACCAATCCTAG
1 TGGTGAACACCAGCTCACCAATCCTAG
29560242 TGGTG
1 TGGTG
29560247 TTCTCCTGCT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
26 3 0.07
27 42 0.91
28 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (27 bp):
TGGTGAACACCAGCTCACCAATCCTAG
Found at i:29568342 original size:8 final size:8
Alignment explanation
Indices: 29568329--29568410 Score: 85
Period size: 8 Copynumber: 10.0 Consensus size: 8
29568319 TGCGATTTAA
29568329 AAAATTTT
1 AAAATTTT
29568337 AAAATTTT
1 AAAATTTT
*
29568345 AAAAATTT
1 AAAATTTT
29568353 AAAA-TTT
1 AAAATTTT
29568360 AAAATTTT
1 AAAATTTT
**
29568368 TTAATTTT
1 AAAATTTT
29568376 ATAAATTTT
1 A-AAATTTT
**
29568385 CTAATTTT
1 AAAATTTT
29568393 AATAATTTT
1 AA-AATTTT
29568402 AATAATTTT
1 AA-AATTTT
29568411 TTGTATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
7 7 0.11
8 34 0.55
9 21 0.34
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (8 bp):
AAAATTTT
Found at i:29568348 original size:17 final size:17
Alignment explanation
Indices: 29568323--29568410 Score: 83
Period size: 17 Copynumber: 5.3 Consensus size: 17
29568313 AGTAAATGCG
*
29568323 ATTTAAAAAATTTTAAA
1 ATTTTAAAAATTTTAAA
29568340 ATTTTAAAAA-TTTAAA
1 ATTTTAAAAATTTTAAA
**
29568356 A-TTT-AAAATTTTTTA
1 ATTTTAAAAATTTTAAA
* **
29568371 ATTTTATAAATTTTCTA
1 ATTTTAAAAATTTTAAA
*
29568388 ATTTTAATAATTTTAATA
1 ATTTTAAAAATTTTAA-A
29568406 ATTTT
1 ATTTT
29568411 TTGTATTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
14 4 0.07
15 8 0.14
16 10 0.17
17 30 0.52
18 6 0.10
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTAAAAATTTTAAA
Found at i:29568885 original size:130 final size:130
Alignment explanation
Indices: 29568652--29568975 Score: 479
Period size: 130 Copynumber: 2.5 Consensus size: 130
29568642 ATGCTTGAAG
* * *
29568652 GTAGTTGTTTGTTGATGTATTAGATTGGGTTGATCGTACTTGATTTAAAGTGATTGATTGAATCT
1 GTAGTTGTTTGTTGATGTATTAGATTGGGTTGATCGTATTTGATTTAAAGTGATTGATTGAGTCA
* * **
29568717 ATATTTTCACAACTAAATTTGATGACATTAAAATATAATATTAAAATAACATATCATTTATAAAT
66 ATATTTCCACAACTAAATGTGACAACATTAAAATATAATATTAAAATAACATATCATTTATAAAT
* *
29568782 GTAGTTGGTTGTTGATGTATTAGATTGGGTTGATGGTATTTGATTTAAAGTGATTGATTGAGTCA
1 GTAGTTGTTTGTTGATGTATTAGATTGGGTTGATCGTATTTGATTTAAAGTGATTGATTGAGTCA
* *
29568847 ATATTTCCACAACTAAATGTGACAACATTAAAATATAATATTGAAATAACATATCATTTATACAT
66 ATATTTCCACAACTAAATGTGACAACATTAAAATATAATATTAAAATAACATATCATTTATAAAT
* * ** * *
29568912 GTAGTTGTTTGTTGATGTCTTAGATTAGGTTGA-CCAACTTTAATTTAAAATGATTGATTGAGTC
1 GTAGTTGTTTGTTGATGTATTAGATTGGGTTGATCGTA-TTTGATTTAAAGTGATTGATTGAGTC
29568976 CAGGCTTCTA
Statistics
Matches: 174, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
129 1 0.01
130 173 0.99
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (130 bp):
GTAGTTGTTTGTTGATGTATTAGATTGGGTTGATCGTATTTGATTTAAAGTGATTGATTGAGTCA
ATATTTCCACAACTAAATGTGACAACATTAAAATATAATATTAAAATAACATATCATTTATAAAT
Found at i:29572188 original size:50 final size:52
Alignment explanation
Indices: 29572049--29572203 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
29572039 GAACAAATGA
*
29572049 GATGCAGACTTAAACTAACATGGGAGTTACATAATGCAAGACTTAATTTAAT
1 GATGCAGACTTAAACTAACATGGGAGTTACATAATGCATGACTTAATTTAAT
*
29572101 GATGCAGACTTAAACTAACATGGGAGTTACATAATGCATGTCATT-ATTT-AT
1 GATGCAGACTTAAACTAACATGGGAGTTACATAATGCATGAC-TTAATTTAAT
* * * * * *
29572152 GATGCATACTT-AACTAGCATGGAAGTTACATAATGCATAACTTTATTAAAT
1 GATGCAGACTTAAACTAACATGGGAGTTACATAATGCATGACTTAATTTAAT
29572203 G
1 G
29572204 CAGAACACAC
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
49 2 0.02
50 29 0.32
51 15 0.16
52 44 0.48
53 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (52 bp):
GATGCAGACTTAAACTAACATGGGAGTTACATAATGCATGACTTAATTTAAT
Found at i:29572284 original size:20 final size:19
Alignment explanation
Indices: 29572243--29572284 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
29572233 AAAAATATGC
*
29572243 AAACTTATTAATTTAAATA
1 AAACTTATTAATTTAAAAA
29572262 AAACTATATTGAA-TTAAAAA
1 AAACT-TATT-AATTTAAAAA
29572282 AAA
1 AAA
29572285 ATTCCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 13 0.65
21 2 0.10
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (19 bp):
AAACTTATTAATTTAAAAA
Found at i:29572285 original size:21 final size:19
Alignment explanation
Indices: 29572243--29572285 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
29572233 AAAAATATGC
* *
29572243 AAACTTATTAATTTAAATA
1 AAACTTATTAATTAAAAAA
29572262 AAACTATATTGAATTAAAAAA
1 AAACT-TATT-AATTAAAAAA
29572283 AAA
1 AAA
29572286 TTCCTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
21 11 0.55
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (19 bp):
AAACTTATTAATTAAAAAA
Found at i:29572536 original size:57 final size:56
Alignment explanation
Indices: 29572432--29572581 Score: 171
Period size: 57 Copynumber: 2.7 Consensus size: 56
29572422 GTTTCATGTA
* * * * * *
29572432 TTTATTTA-TTATTCTTTTACCTTTTAAATATTTAAATTCGATTTTATTTTTATTTG
1 TTTATTTATTTATTCTTTTACTTTTTAAATACTTAAATTCAATATTATTTGT-TTTC
* *
29572488 TTTATCTATTTATTCTTTTACTTTTTAAATACTTAAATTTAATATTATTTGTTTTC
1 TTTATTTATTTATTCTTTTACTTTTTAAATACTTAAATTCAATATTATTTGTTTTC
* *
29572544 TCTATTTATTTATTATTTT--TTTTTGAAATACTTAAATT
1 TTTATTTATTTATTCTTTTACTTTTT-AAATACTTAAATT
29572582 GGATACTACT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
54 5 0.06
55 13 0.16
56 26 0.32
57 37 0.46
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (56 bp):
TTTATTTATTTATTCTTTTACTTTTTAAATACTTAAATTCAATATTATTTGTTTTC
Found at i:29574302 original size:7 final size:7
Alignment explanation
Indices: 29574291--29574327 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
29574281 TGTTAAGCTT
*
29574291 AATGGAT
1 AATGGAG
29574298 AATGGAG
1 AATGGAG
29574305 AATGGAG
1 AATGGAG
*
29574312 AATGTAG
1 AATGGAG
29574319 AATGGAG
1 AATGGAG
29574326 AA
1 AA
29574328 AGATATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (7 bp):
AATGGAG
Found at i:29586496 original size:16 final size:18
Alignment explanation
Indices: 29586455--29586496 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
29586445 CAACACTGTA
29586455 TGTGAAAAAGGAAGGGTG
1 TGTGAAAAAGGAAGGGTG
29586473 TTGTGAAAAAGGAA-GGTG
1 -TGTGAAAAAGGAAGGGTG
29586491 -GTGAAA
1 TGTGAAA
29586497 CACTACTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.26
18 4 0.17
19 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.19
Consensus pattern (18 bp):
TGTGAAAAAGGAAGGGTG
Found at i:29591812 original size:23 final size:22
Alignment explanation
Indices: 29591760--29591812 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
29591750 TCCACGTCTT
*
29591760 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
29591782 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
29591805 TTTCTTTT
1 TTTCTTTT
29591813 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:29595918 original size:34 final size:35
Alignment explanation
Indices: 29595853--29595920 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
29595843 TACGAAACAT
*
29595853 AAGGATACTAATCTTAATAAAATAAACATTAAATA
1 AAGGATACTAATATTAATAAAATAAACATTAAATA
* *
29595888 AAGGATACTAATATT-ATAAAATACAGATTAAAT
1 AAGGATACTAATATTAATAAAATAAACATTAAAT
29595921 TAGGGATGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.29
Consensus pattern (35 bp):
AAGGATACTAATATTAATAAAATAAACATTAAATA
Found at i:29596391 original size:43 final size:43
Alignment explanation
Indices: 29596330--29596524 Score: 205
Period size: 43 Copynumber: 4.5 Consensus size: 43
29596320 AAATAAACGC
* * *
29596330 CGCTTATCCCACAAACGCCGCAATAGATCATGATTTTTAGCGG
1 CGCTTTTCCCACAAACGCCGCTATAGATCATGACTTTTAGCGG
* **
29596373 CGCTTTTCCCACAAACGCCGCTATAGGTCATGACTTTTAGTAG
1 CGCTTTTCCCACAAACGCCGCTATAGATCATGACTTTTAGCGG
* * * *
29596416 CGTTTTTCCCACTAACGCCGCTATAGATCATCACTTTTAGCGA
1 CGCTTTTCCCACAAACGCCGCTATAGATCATGACTTTTAGCGG
*** * * *
29596459 CGCTTTTTTGTACAAACACCGCTATAGAACA-GACCTTTAGCGAG
1 CGC-TTTTCCCACAAACGCCGCTATAGATCATGACTTTTAGCG-G
*
29596503 -GCTTTTCACACAAACGCCGCTA
1 CGCTTTTCCCACAAACGCCGCTA
29596525 AAAACATATC
Statistics
Matches: 123, Mismatches: 27, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
42 16 0.13
43 86 0.70
44 21 0.17
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (43 bp):
CGCTTTTCCCACAAACGCCGCTATAGATCATGACTTTTAGCGG
Found at i:29596856 original size:43 final size:42
Alignment explanation
Indices: 29596784--29596874 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 42
29596774 ACATATGCAA
* ** *
29596784 TGTAATAAAACATACAATGCATTTTCTTAATCAAGTAAATCT
1 TGTAATAAAACATACAATACATTGACTTAATCAAGGAAATCT
* *
29596826 TGGTAATAAAAGATATAATACATTGACTTAATCAAGGAAATCT
1 T-GTAATAAAACATACAATACATTGACTTAATCAAGGAAATCT
29596869 TGTAAT
1 TGTAAT
29596875 GAACTCAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 6 0.14
43 36 0.86
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (42 bp):
TGTAATAAAACATACAATACATTGACTTAATCAAGGAAATCT
Found at i:29603747 original size:20 final size:21
Alignment explanation
Indices: 29603714--29603759 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
29603704 CTGTGACTAA
29603714 ATGTGATTAAATGTAATT-AT
1 ATGTGATTAAATGTAATTCAT
* * *
29603734 ATGTGCTTATATGTGATTCAT
1 ATGTGATTAAATGTAATTCAT
29603755 ATGTG
1 ATGTG
29603760 TTGAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (21 bp):
ATGTGATTAAATGTAATTCAT
Found at i:29619006 original size:68 final size:67
Alignment explanation
Indices: 29618907--29619042 Score: 175
Period size: 68 Copynumber: 2.0 Consensus size: 67
29618897 AATTCAGGAT
* ** *
29618907 TACCAAAGTACAAACAGGGCACGTATATGCATTC-AGGGATACTTAAGTACAAATAAGGGCATGT
1 TACCAAAGTACAAACAGAGCACGTATATGCATTCAAGGG-TACCAAAGTACAAATAAGGGCACGT
29618971 ATG
65 ATG
* * * *
29618974 TACCAAAGTACAATCAAGAGCACGTATGTGCATTCAAGGGTACCAAAGTACAATTAGGGGCACGT
1 TACCAAAGTACAAAC-AGAGCACGTATATGCATTCAAGGGTACCAAAGTACAAATAAGGGCACGT
29619039 ATG
65 ATG
29619042 T
1 T
29619043 GCATTCAGGG
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
67 14 0.24
68 41 0.69
69 4 0.07
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.22
Consensus pattern (67 bp):
TACCAAAGTACAAACAGAGCACGTATATGCATTCAAGGGTACCAAAGTACAAATAAGGGCACGTA
TG
Found at i:29619037 original size:40 final size:40
Alignment explanation
Indices: 29618973--29619289 Score: 341
Period size: 40 Copynumber: 7.9 Consensus size: 40
29618963 GGGCATGTAT
* * *
29618973 GTACCAAAGTACAATCAAGAGCACGTATGTGCATTCAAGG
1 GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
* * *
29619013 GTACCAAAGTACAATTAGGGGCACGTATGTGCATTCAGGG
1 GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
** * * *
29619053 GTATGGAAGTATAAACAGGGGCATGTATGTGCATTCAAGG
1 GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
* * *
29619093 ATACCGAAGTACAATCAGGAGCACGTGTGTGCATTCAAGG
1 GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
* * * *
29619133 GTACTGAAGTACAATCAGAGGCACGTATGTGCATTTAGGG
1 GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
* * * *
29619173 GTATCGAAGTACAATCAGAGGCATGTATGTGCATCCAAGG
1 GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
* * *
29619213 GTACCGAAGTACAAACAAGGGCACGTATGTGCATT-TAGG
1 GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
* * * *
29619252 TGTATCGAAGTACAAAT-ATGGGAATGTATGTGCATTCA
1 -GTACCGAAGTAC-AATCAGGGGCACGTATGTGCATTCA
29619290 TTCAATAATT
Statistics
Matches: 228, Mismatches: 46, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
39 3 0.01
40 223 0.98
41 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (40 bp):
GTACCGAAGTACAATCAGGGGCACGTATGTGCATTCAAGG
Found at i:29619196 original size:120 final size:120
Alignment explanation
Indices: 29618974--29619247 Score: 397
Period size: 120 Copynumber: 2.3 Consensus size: 120
29618964 GGCATGTATG
* * * *
29618974 TACCAAAGTACAATCAAGAGCACGTATGTGCATTCAAGGGTACCAAAGTACAATTAGGGGCACGT
1 TACCGAAGTACAATCAGGAGCACGTATGTGCATTCAAGGGTACCAAAGTACAATCAGAGGCACGT
* * * *
29619039 ATGTGCATTCAGGGGTATGGAAGTATAAACAGGGGCATGTATGTGCATTCAAGGA
66 ATGTGCATTCAGGGGTATCGAAGTACAAACAGAGGCATGTATGTGCATCCAAGGA
* **
29619094 TACCGAAGTACAATCAGGAGCACGTGTGTGCATTCAAGGGTACTGAAGTACAATCAGAGGCACGT
1 TACCGAAGTACAATCAGGAGCACGTATGTGCATTCAAGGGTACCAAAGTACAATCAGAGGCACGT
* * *
29619159 ATGTGCATTTAGGGGTATCGAAGTACAATCAGAGGCATGTATGTGCATCCAAGGG
66 ATGTGCATTCAGGGGTATCGAAGTACAAACAGAGGCATGTATGTGCATCCAAGGA
*
29619214 TACCGAAGTACAAACAAGG-GCACGTATGTGCATT
1 TACCGAAGTACAATC-AGGAGCACGTATGTGCATT
29619248 TAGGTGTATC
Statistics
Matches: 137, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
120 134 0.98
121 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (120 bp):
TACCGAAGTACAATCAGGAGCACGTATGTGCATTCAAGGGTACCAAAGTACAATCAGAGGCACGT
ATGTGCATTCAGGGGTATCGAAGTACAAACAGAGGCATGTATGTGCATCCAAGGA
Found at i:29622459 original size:95 final size:95
Alignment explanation
Indices: 29622293--29622469 Score: 257
Period size: 95 Copynumber: 1.9 Consensus size: 95
29622283 TATTCTCTAG
* *
29622293 TTGGATATTTAATTGGACATTGGAAACCCATATGATCTTTTGAACTACACCAATAACATTGCACA
1 TTGGATATTTAATTGGACATTAGAAACCCATATGATCTTTTGAACTACACCAATAAAATTGCACA
* *
29622358 AAAGGTGATAGCTCAATCGTATTCACTCAA
66 AAAGGTGAAAGATCAATCGTATTCACTCAA
* **
29622388 TTGGATATTTAATTGGACATTAGAAACCC-TCCTGATCTTTTGAACTACACCAATAAAATTTTAC
1 TTGGATATTTAATTGGACATTAGAAACCCAT-ATGATCTTTTGAACTACACCAATAAAATTGCAC
* *
29622452 GATAGGTGAAAGATCAAT
65 AAAAGGTGAAAGATCAAT
29622470 TGTACTCCTC
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
94 1 0.01
95 71 0.99
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (95 bp):
TTGGATATTTAATTGGACATTAGAAACCCATATGATCTTTTGAACTACACCAATAAAATTGCACA
AAAGGTGAAAGATCAATCGTATTCACTCAA
Found at i:29623808 original size:22 final size:21
Alignment explanation
Indices: 29623754--29623809 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
29623744 TTCAAGTCAG
* *
29623754 ATAAAACAATTAAAATAAATA
1 ATAAATCAAATAAAATAAATA
29623775 ACTAAGAT-AAATAAAATAAAATA
1 A-TAA-ATCAAATAAAAT-AAATA
29623798 ATAAATCAAATA
1 ATAAATCAAATA
29623810 TTAGAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 3 0.10
22 19 0.66
23 7 0.24
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (21 bp):
ATAAATCAAATAAAATAAATA
Found at i:29629231 original size:19 final size:19
Alignment explanation
Indices: 29629207--29629249 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
29629197 AGACTGAGAG
29629207 AAAAGAGACCTTTAGTGAT
1 AAAAGAGACCTTTAGTGAT
*
29629226 AAAAGAGACGTTTAGTGAT
1 AAAAGAGACCTTTAGTGAT
29629245 AAAAG
1 AAAAG
29629250 TTCACTTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (19 bp):
AAAAGAGACCTTTAGTGAT
Found at i:29631022 original size:191 final size:192
Alignment explanation
Indices: 29630698--29631084 Score: 749
Period size: 191 Copynumber: 2.0 Consensus size: 192
29630688 TGTTTTACTA
29630698 AAAACCTTATTTAATAAATATACAACTATTTTAAGTGCATGCATCCACAATGATATAGGTAAGAA
1 AAAACCTTATTTAATAAATATACAACTATTTTAAGTGCATGCATCCACAATGATATAGGTAAGAA
29630763 GGAGCTAGTTATCATCCTCCTAACCATATCCAATAAAGTCTGATTACGCCTTTCTACAATATCA-
66 GGAGCTAGTTATCATCCTCCTAACCATATCCAATAAAGTCTGATTACGCCTTTCTACAATATCAT
29630827 TTTTTGAGGTATGTCTGGTATGGTATACTGTGCACATATGCCACAACTTTTGAGGAATTTAG
131 TTTTTGAGGTATGTCTGGTATGGTATACTGTGCACATATGCCACAACTTTTGAGGAATTTAG
*
29630889 AAAACCTTATTTAATAAATATACAACTATTTTAAGTGCATGCATCCACAATGATATAGGTAATAA
1 AAAACCTTATTTAATAAATATACAACTATTTTAAGTGCATGCATCCACAATGATATAGGTAAGAA
*
29630954 GGAGCTAGTTATCATCCTCCTAACCATATCCAATAAAGTCTGATTACGCCTTTCTGCAATATCAT
66 GGAGCTAGTTATCATCCTCCTAACCATATCCAATAAAGTCTGATTACGCCTTTCTACAATATCAT
29631019 TTTTTGAGGTATGTCTGGTATGGTATACTGTGCACATATGCCACAACTTTTGAGGAATTTAG
131 TTTTTGAGGTATGTCTGGTATGGTATACTGTGCACATATGCCACAACTTTTGAGGAATTTAG
29631081 AAAA
1 AAAA
29631085 TGGACCTGGA
Statistics
Matches: 193, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
191 127 0.66
192 66 0.34
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (192 bp):
AAAACCTTATTTAATAAATATACAACTATTTTAAGTGCATGCATCCACAATGATATAGGTAAGAA
GGAGCTAGTTATCATCCTCCTAACCATATCCAATAAAGTCTGATTACGCCTTTCTACAATATCAT
TTTTTGAGGTATGTCTGGTATGGTATACTGTGCACATATGCCACAACTTTTGAGGAATTTAG
Found at i:29631383 original size:38 final size:38
Alignment explanation
Indices: 29631332--29631410 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
29631322 CACATATATC
29631332 AGTGTGTATTATCTTAAAGGGTTGGGTACTTCTTGTGG
1 AGTGTGTATTATCTTAAAGGGTTGGGTACTTCTTGTGG
29631370 AGTGTGTATTATCTTAAAGGGTTGGGTACTTCTTGTGG
1 AGTGTGTATTATCTTAAAGGGTTGGGTACTTCTTGTGG
29631408 AGT
1 AGT
29631411 TTGTCTTAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.19, C:0.08, G:0.32, T:0.42
Consensus pattern (38 bp):
AGTGTGTATTATCTTAAAGGGTTGGGTACTTCTTGTGG
Found at i:29631403 original size:19 final size:19
Alignment explanation
Indices: 29631343--29631403 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
29631333 GTGTGTATTA
29631343 TCTTAAAGGGTTGGGTACT
1 TCTTAAAGGGTTGGGTACT
** * *
29631362 TCTT-GTGGAG-TGTGTATT
1 TCTTAAAGG-GTTGGGTACT
29631380 ATCTTAAAGGGTTGGGTACT
1 -TCTTAAAGGGTTGGGTACT
29631400 TCTT
1 TCTT
29631404 GTGGAGTTTG
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
18 8 0.27
19 14 0.47
20 8 0.27
ACGTcount: A:0.18, C:0.10, G:0.30, T:0.43
Consensus pattern (19 bp):
TCTTAAAGGGTTGGGTACT
Found at i:29635725 original size:195 final size:194
Alignment explanation
Indices: 29635195--29635772 Score: 858
Period size: 190 Copynumber: 3.0 Consensus size: 194
29635185 TAAAGGTGAA
* * *
29635195 AAAAAATGCCTCTATAAATAGAATTTCTTATAGTGGCAAGCAACAACATGGTACCAGAAGTGCAA
1 AAAAAATGCCACTATAAACAGAATTTCTTGTAGTGGCAAGCAACAACATGGTACCAGAAGTGCAA
*
29635260 CTGATCCTGACAACATTAATCAAAGCTAGCAGTTGAATGAGGATATGTTCATGGAGAAAATGCAA
66 CTGATCCTGACAACATTAATCAAAGCTAGCAGTTGAATGAGGATATATTCATGGAGAAAATGCAA
* *
29635325 CAATTAAGGAAAGAAATGTATAAGTATAAGAAATCAAAATCATTTGGCTAACTAAGAAAATA-T
131 CAATTAAGGAAAGAAATGTAAAAGTATAAGAAATCAAAATCATTTGGCTAACTAATAAAATATT
29635388 AAAAAATGCCACTATAAACAGAATTTCTTGTAGTGGCAAG---CAACATGGTACCAGAAGTGCAA
1 AAAAAATGCCACTATAAACAGAATTTCTTGTAGTGGCAAGCAACAACATGGTACCAGAAGTGCAA
* ** * ** *
29635450 CTGATCTTGACAACATTAATCAAAGCTAGTTGTTGAATAAGGATATATTCATAAAGAAAATGAAA
66 CTGATCCTGACAACATTAATCAAAGCTAGCAGTTGAATGAGGATATATTCATGGAGAAAATGCAA
* * * *
29635515 TAGTTAAGGAAAGAAATATAAAAGTATAAGAAACCAAAATCATTTGGCTAACTAATAAAATATTT
131 CAATTAAGGAAAGAAATGTAAAAGTATAAGAAATCAAAATCATTTGGCTAACTAATAAAATA-TT
* * * *
29635580 AAAAAATGCCACTATAAACAAAATTTCTTGTAGTGGCAAGCAACAACATAGTACCAAAACTGCAA
1 AAAAAATGCCACTATAAACAGAATTTCTTGTAGTGGCAAGCAACAACATGGTACCAGAAGTGCAA
* * * *
29635645 TTGATCCTGACAACATTAATCAAAGCTAACAATTGAATGAGGATATATCCATGGAGAAAATGCAA
66 CTGATCCTGACAACATTAATCAAAGCTAGCAGTTGAATGAGGATATATTCATGGAGAAAATGCAA
* * * *
29635710 CAATTAAGTAAAGAAATGTAAAAGTATAAGAAATCAACATCATTCGACTAACTAATAAAATAT
131 CAATTAAGGAAAGAAATGTAAAAGTATAAGAAATCAAAATCATTTGGCTAACTAATAAAATAT
29635773 ACCAAGAAGC
Statistics
Matches: 340, Mismatches: 40, Indels: 9
0.87 0.10 0.02
Matches are distributed among these distances:
190 135 0.40
192 40 0.12
193 37 0.11
194 1 0.00
195 127 0.37
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (194 bp):
AAAAAATGCCACTATAAACAGAATTTCTTGTAGTGGCAAGCAACAACATGGTACCAGAAGTGCAA
CTGATCCTGACAACATTAATCAAAGCTAGCAGTTGAATGAGGATATATTCATGGAGAAAATGCAA
CAATTAAGGAAAGAAATGTAAAAGTATAAGAAATCAAAATCATTTGGCTAACTAATAAAATATT
Done.