Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 179 of 186
Found at i:59401548 original size:20 final size:20
Alignment explanation
Indices: 59401523--59401574 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
59401513 ATAAAGGACT
59401523 AAAAATGAAA-TTTTTTTATA
1 AAAAAT-AAATTTTTTTTATA
59401543 AAAAATAAATTTTTTTTATA
1 AAAAATAAATTTTTTTTATA
*
59401563 AAAAATATATTT
1 AAAAATAAATTT
59401575 AAAATTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AAAAATAAATTTTTTTTATA
Found at i:59403137 original size:28 final size:28
Alignment explanation
Indices: 59403105--59403160 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
59403095 ATATATACTT
59403105 AACCAAAAGGCATATACAAGTATAACCC
1 AACCAAAAGGCATATACAAGTATAACCC
59403133 AACCAAAAGGCATATACAAGTATAACCC
1 AACCAAAAGGCATATACAAGTATAACCC
59403161 TTACAGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.11, T:0.14
Consensus pattern (28 bp):
AACCAAAAGGCATATACAAGTATAACCC
Found at i:59425140 original size:20 final size:21
Alignment explanation
Indices: 59425117--59425158 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
59425107 CCCTTAAAAC
59425117 AGGGC-ACACACCCGTGTGGA
1 AGGGCAACACACCCGTGTGGA
*
59425137 AGGGCAACACGCCCGTGTGGA
1 AGGGCAACACACCCGTGTGGA
59425158 A
1 A
59425159 CTTGTACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.26, C:0.29, G:0.36, T:0.10
Consensus pattern (21 bp):
AGGGCAACACACCCGTGTGGA
Found at i:59426609 original size:94 final size:94
Alignment explanation
Indices: 59426448--59426619 Score: 229
Period size: 94 Copynumber: 1.8 Consensus size: 94
59426438 AAGCTGACGC
* ** * * *
59426448 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATCGCGAGGCTGATGCCTGTTCCAAACATGTC
1 CATGTCCCAGACAGGTCTAACACTAGCTTAAATATCGCAAGGCTGATGCATGTCCCAAACATGTC
59426513 TTACACTAGCTCTCTTCTCAACGCCGATG
66 TTACACTAGCTCTCTTCTCAACGCCGATG
* * * * *
59426542 CATGTCCTAGACATGTCTAACACTGGCTTAAATATCTCAAGGCTG-TAGCATGTCCCAGACATGT
1 CATGTCCCAGACAGGTCTAACACTAGCTTAAATATCGCAAGGCTGAT-GCATGTCCCAAACATGT
59426606 CTTACACTAGCTCT
65 CTTACACTAGCTCT
59426620 TATATTGTGG
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
93 1 0.02
94 65 0.98
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (94 bp):
CATGTCCCAGACAGGTCTAACACTAGCTTAAATATCGCAAGGCTGATGCATGTCCCAAACATGTC
TTACACTAGCTCTCTTCTCAACGCCGATG
Found at i:59428187 original size:11 final size:11
Alignment explanation
Indices: 59428160--59428194 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
59428150 CTCCAATTTT
59428160 CACACGGCCTAG
1 CACACGGCCT-G
59428172 CACACGGCCTG
1 CACACGGCCTG
59428183 CACACGGGCCTG
1 CACAC-GGCCTG
59428195 TGAGGCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.20, C:0.43, G:0.29, T:0.09
Consensus pattern (11 bp):
CACACGGCCTG
Found at i:59431208 original size:15 final size:16
Alignment explanation
Indices: 59431177--59431208 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
59431167 AGTTTAGGGG
59431177 TAAAATTGTGAATTTT
1 TAAAATTGTGAATTTT
59431193 TAAAATTGTG-ATTTT
1 TAAAATTGTGAATTTT
59431208 T
1 T
59431209 GGGTCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (16 bp):
TAAAATTGTGAATTTT
Found at i:59432224 original size:6 final size:6
Alignment explanation
Indices: 59432213--59432246 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
59432203 ATGAATGAAC
*
59432213 TTATGT TTATGT TTATGT TTATGA TTATGT TTAT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTAT
59432247 TATGTCATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (6 bp):
TTATGT
Found at i:59433665 original size:18 final size:18
Alignment explanation
Indices: 59433641--59433683 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
59433631 CAGTTATGAA
*
59433641 TTCACTTTCATATAACAC
1 TTCACTTTCATAAAACAC
*
59433659 TTTACTTTCATAAAACAC
1 TTCACTTTCATAAAACAC
59433677 TTCACTT
1 TTCACTT
59433684 AATATTTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.42
Consensus pattern (18 bp):
TTCACTTTCATAAAACAC
Found at i:59434306 original size:14 final size:14
Alignment explanation
Indices: 59434287--59434316 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59434277 ACGTTTCTGT
59434287 TTTTCTTACTTTTC
1 TTTTCTTACTTTTC
*
59434301 TTTTCTTTCTTTTC
1 TTTTCTTACTTTTC
59434315 TT
1 TT
59434317 CTTTCCTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCTTACTTTTC
Found at i:59437765 original size:46 final size:46
Alignment explanation
Indices: 59437713--59437976 Score: 218
Period size: 46 Copynumber: 5.7 Consensus size: 46
59437703 TGTGTACGCT
*
59437713 AGTGTAAGACATGTCTGGGACATTCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
* *
59437759 AGTGTAAGACCATATCTGGGACATGGCATCGG---CATTGATACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATT-AT--GAGAGCC
* * **
59437807 AGTGTAAGACATGTCTGGAACATGCATCGGCCTCAAAATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATG-AGAGCC
* * * * * * * * *
59437853 AGTGTAAGATATATTTGGGACACGCATCGACTAC--GA-GATGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGA-GAGCC
* *
59437897 AGTGTAAGACATGTCTGGGACATGCATCGGCACAGATATGTGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC-CACAT-TATGAGAGCC
59437945 AGTGTAAGACCATGTCTGGGACATGGCATCGG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG
59437977 TATTATACCC
Statistics
Matches: 170, Mismatches: 30, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 29 0.17
45 5 0.03
46 48 0.28
47 26 0.15
48 35 0.21
49 18 0.11
50 7 0.04
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
Found at i:59441324 original size:31 final size:31
Alignment explanation
Indices: 59441289--59441350 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
59441279 ATAACAAAAG
59441289 GATGCCCAACTATTTGGTCCAACGAAAAATC
1 GATGCCCAACTATTTGGTCCAACGAAAAATC
59441320 GATGCCCAACTATTTGGTCCAACGAAAAATC
1 GATGCCCAACTATTTGGTCCAACGAAAAATC
59441351 CTCAGTAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (31 bp):
GATGCCCAACTATTTGGTCCAACGAAAAATC
Found at i:59442031 original size:19 final size:19
Alignment explanation
Indices: 59442007--59442044 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
59441997 GAAATGAATA
*
59442007 ATTTCAGGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
59442026 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
59442045 GCAATCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ATTTCAAGCAAATAGGTTG
Found at i:59442333 original size:17 final size:17
Alignment explanation
Indices: 59442311--59442357 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
59442301 AAGTAGGTAA
*
59442311 ATTATATATAAATATAT
1 ATTATAAATAAATATAT
*
59442328 ATTATAAAAAAATATAT
1 ATTATAAATAAATATAT
*
59442345 ATATATACATAAA
1 AT-TATAAATAAA
59442358 CAGATAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTATAAATAAATATAT
Found at i:59442985 original size:19 final size:20
Alignment explanation
Indices: 59442952--59442991 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
59442942 ATGTATATAT
59442952 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
59442971 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
59442991 A
1 A
59442992 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:59443624 original size:44 final size:44
Alignment explanation
Indices: 59443561--59444093 Score: 423
Period size: 44 Copynumber: 12.3 Consensus size: 44
59443551 CGTCTAATAT
*
59443561 AGAGACGCCAAATCCGTTATCTTCGATCTGCTCTCCGCCGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
***
59443605 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGTCTAATAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCG-CCGCTAC
* * * * ***
59443650 AGAGACGCCAAATCTGCT-TCTTCAATCTACTCACCGTCTAATAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCG-CCGCTAC
* * * * * * ***
59443694 AGATATGCCAAATCTATTATCTCCGATTTGCTCCCCGTCTAATAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCG-CCGCTAC
* * * * **
59443739 AGAGATGCCAAATCTGTCATCTTGGATCTACT-T-CGATG-TAAAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCT--AC
* * ** * * * * * *
59443782 ACATGAAGGTTAGATCTGCTAT-GTC--TTTGATCT-----GCTAT
1 AGA-G-ACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
* * *
59443820 AGAGACGCCAAATCTATTATCTTCGATTTGCTCTTCGCCGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
*
59443864 AGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
* * * *
59443908 AGAGATGCTAAATC----ATCTTCGATCTGCTCTTCGCCGCTAT
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
* *
59443948 AGAGATGCCAAATCTATTATCTTCGATCTGCTCTCCGCCGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
* * * * *
59443992 AAAGACTCTAAATCTGTTATCTTTGACCTGCTCTCCGCCGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
*
59444036 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
59444080 AGAGACGCCAAATC
1 AGAGACGCCAAATC
59444094 ATCTTGGATT
Statistics
Matches: 396, Mismatches: 73, Indels: 40
0.78 0.14 0.08
Matches are distributed among these distances:
36 10 0.03
37 3 0.01
38 3 0.01
39 8 0.02
40 38 0.10
41 1 0.00
42 4 0.01
43 7 0.02
44 245 0.62
45 77 0.19
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.30
Consensus pattern (44 bp):
AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
Found at i:59443936 original size:84 final size:84
Alignment explanation
Indices: 59443838--59444098 Score: 371
Period size: 84 Copynumber: 3.1 Consensus size: 84
59443828 CAAATCTATT
*
59443838 ATCTTCGATTTGCTCTTCGCCGCTACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
1 ATCTTCGATCTGCTCTTCGCCGCTACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
59443903 GCTACAGAGATGCTAAATC
66 GCTACAGAGATGCTAAATC
* *
59443922 ATCTTCGATCTGCTCTTCGCCGCTATAGAGATGCCAAATCTATTATCTTCGATCTGCTCTCCGCC
1 ATCTTCGATCTGCTCTTCGCCGCTACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
*
59443987 GCTACAAAGACT-CTAAATC
66 GCTACAGAGA-TGCTAAATC
* * * *
59444006 TGTTATCTTTGACCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTC
1 ----ATCTTCGATCTGCTCTTCGCCGCTACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTC
* * *
59444071 TGCCGCTACAGAGACGCCAAATC
62 CGCCGCTACAGAGATGCTAAATC
59444094 ATCTT
1 ATCTT
59444099 GGATTTGATT
Statistics
Matches: 157, Mismatches: 14, Indels: 12
0.86 0.08 0.07
Matches are distributed among these distances:
84 83 0.53
85 1 0.01
88 73 0.46
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (84 bp):
ATCTTCGATCTGCTCTTCGCCGCTACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
GCTACAGAGATGCTAAATC
Found at i:59443973 original size:128 final size:129
Alignment explanation
Indices: 59443815--59444093 Score: 402
Period size: 128 Copynumber: 2.1 Consensus size: 129
59443805 TCTTTGATCT
* * *
59443815 GCTATAGAGACGCCAAATCTATTATCTTCGATTTGCTCTTCGCCGCTACAGAGA-TGCCAAATCT
1 GCTATAGAGACGCCAAATCTATTATCTTCGATCTGCTCTCCGCCGCTACAAAGACT-CCAAATCT
* * *
59443879 GTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCTAAATC-ATCTTCGATCTGCTCT-TCGC
65 GTTATCTTCGACCTGCTCTCCGCCGCTACAGAGACGCCAAATCTATCTTCGATCTGCTCTCT-GC
59443942 C
129 C
* *
59443943 GCTATAGAGATGCCAAATCTATTATCTTCGATCTGCTCTCCGCCGCTACAAAGACTCTAAATCTG
1 GCTATAGAGACGCCAAATCTATTATCTTCGATCTGCTCTCCGCCGCTACAAAGACTCCAAATCTG
*
59444008 TTATCTTTGACCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTG
66 TTATCTTCGACCTGCTCTCCGCCGCTACAGAGACGCCAAATC---TATCTTCGATCTGCTCTCTG
59444073 CC
128 CC
*
59444075 GCTACAGAGACGCCAAATC
1 GCTATAGAGACGCCAAATC
59444094 ATCTTGGATT
Statistics
Matches: 134, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
128 96 0.72
129 1 0.01
132 36 0.27
133 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (129 bp):
GCTATAGAGACGCCAAATCTATTATCTTCGATCTGCTCTCCGCCGCTACAAAGACTCCAAATCTG
TTATCTTCGACCTGCTCTCCGCCGCTACAGAGACGCCAAATCTATCTTCGATCTGCTCTCTGCC
Found at i:59444178 original size:88 final size:88
Alignment explanation
Indices: 59444055--59444278 Score: 344
Period size: 88 Copynumber: 2.6 Consensus size: 88
59444045 AAATCTGTTA
* * * * * *
59444055 TCTTCGATCTGCTCTCTGCC-GCTACAGAGACGCCAAATCATCTTGGATTTGA-TTCAATGTAAA
1 TCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATCT-ACTTCAACGTAAA
59444118 CACGTGAAAGCCAAATCAGCTATG
65 CACGTGAAAGCCAAATCAGCTATG
*
59444142 TCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATTATCTTGGATCTACTTCAACGTAAAC
1 TCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATCTACTTCAACGTAAAC
59444207 ACGTGAAAGCCAAATCAGCTATG
66 ACGTGAAAGCCAAATCAGCTATG
* *
59444230 TCTTCGATCTGCTCCCCGCTTGATACAGAAATGCCAAATCATCTTGGAT
1 TCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGAT
59444279 ATCTTCAGCT
Statistics
Matches: 125, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
87 19 0.15
88 106 0.85
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (88 bp):
TCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATCTACTTCAACGTAAAC
ACGTGAAAGCCAAATCAGCTATG
Found at i:59444269 original size:47 final size:46
Alignment explanation
Indices: 59444123--59444270 Score: 121
Period size: 47 Copynumber: 3.3 Consensus size: 46
59444113 GTAAACACGT
*
59444123 GAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCCGCCTGATACA
1 GAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCCGCTTGATACA
* * * ** ** * *
59444169 GAGATGCCAAAT----TA--TCTTGGATCTACTTCAACG-TAAACACGT
1 GA-AAGCCAAATCAGCTATGTCTTCGATCTGC-TCCCCGCTTGATAC-A
59444211 GAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCCGCTTGATACA
1 GAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCCGCTTGATACA
59444257 GAAATGCCAAATCA
1 GAAA-GCCAAATCA
59444271 TCTTGGATAT
Statistics
Matches: 72, Mismatches: 19, Indels: 21
0.64 0.17 0.19
Matches are distributed among these distances:
41 21 0.29
42 6 0.08
43 2 0.03
45 2 0.03
46 10 0.14
47 31 0.43
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (46 bp):
GAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCCGCTTGATACA
Found at i:59444506 original size:61 final size:65
Alignment explanation
Indices: 59444392--59444510 Score: 192
Period size: 61 Copynumber: 1.9 Consensus size: 65
59444382 GTATCCATGC
59444392 TTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATGTGATGTT
1 TTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATGTGATGTT
* *
59444457 TTATGTCAAATAATTAGGATG-T-T-A-TGAAATGAATCAAATGTTCCTAACTAAATG
1 TTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATG
59444511 AATGGTTATG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
61 29 0.56
62 1 0.02
63 1 0.02
64 1 0.02
65 20 0.38
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (65 bp):
TTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATGTGATGTT
Found at i:59446176 original size:25 final size:24
Alignment explanation
Indices: 59446148--59446196 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
59446138 CCTCTAATGT
59446148 TATTT-TTCTTCTTCTTCTTTCTTTC
1 TATTTATT-TTCTT-TTCTTTCTTTC
59446173 TATTTCATTTTCTTTTCTTTCTTT
1 TATTT-ATTTTCTTTTCTTTCTTT
59446197 TACATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 15 0.68
26 5 0.23
27 2 0.09
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.73
Consensus pattern (24 bp):
TATTTATTTTCTTTTCTTTCTTTC
Found at i:59446552 original size:21 final size:22
Alignment explanation
Indices: 59446528--59446570 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
59446518 TTTTTTCTAC
59446528 TTCTTTC-TTTCTGTTT-CATTT
1 TTCTTTCGTTTCT-TTTACATTT
59446549 TTCTTTCGTTTCTTTTACATTT
1 TTCTTTCGTTTCTTTTACATTT
59446571 ATTGCCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.07, C:0.19, G:0.05, T:0.70
Consensus pattern (22 bp):
TTCTTTCGTTTCTTTTACATTT
Found at i:59446553 original size:17 final size:15
Alignment explanation
Indices: 59446531--59446564 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
59446521 TTTCTACTTC
59446531 TTTCTTTCTGTTTCATT
1 TTTCTTTC-GTTTC-TT
59446548 TTTCTTTCGTTTCTT
1 TTTCTTTCGTTTCTT
59446563 TT
1 TT
59446565 ACATTTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 5 0.29
17 8 0.47
ACGTcount: A:0.03, C:0.18, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTCTTTCGTTTCTT
Found at i:59446854 original size:366 final size:369
Alignment explanation
Indices: 59446044--59449021 Score: 2634
Period size: 372 Copynumber: 8.1 Consensus size: 369
59446034 GGGTGTTACA
* *
59446044 TACTCTTCTGGCGAGTGAAAATTTTAGCAATTTCCCTAAATTTTTTATGTTCCTCTCTTTCCACT
1 TACTCTTCTGGCGAGTGAGAATTTTAGCAATTTCCCCAAATTTTTTATGTTCCTCTCTTTCCACT
* * * *
59446109 ATTTCCATTTCTTTTTTCCATTTTCTGTTCCTCTAATGTTATTTTTCTTCTTCTTCTTTCTTTCT
66 ACTTCCATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTTCTTCTTCTTCTTTCTTTCT
*
59446174 ATTTCATTTTCTTTTC-TTTCTTTTACATTTGTTGCCATATTCCCTTG-TGTCGTCTCTTACTAC
131 ATTTCATTTTC-TTTCGTTTCTTTTACATTTGTTGCCATATTCCCTTGTTGTCGTCTCTTGCTA-
* * * **
59446237 TAT-TTTGTT-ATTGTTGACCTATCTTCTGTTATGCTGCCATTTAAACTGTATTGGTGTTATTAA
194 T-TGTTTCTTCATTGTTGACCTATCTTCTGTTGTGCTGCCATTTAGACTGCGTTGGTGTTATTAA
* * *
59446300 AATCTTCAGGTAAG---AA-TAATTCGTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAAGC
258 AATCTTCAGGTAAGTATAATTAGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAAGG
* * *
59446361 TATTTTGGTTTCATTAGTTGTAATTTTGCTAAGGGTGGTTTGTGAGGCATT
323 TCTTTTGGTTTCATTA--TGT-ATTTTGCT-AGGGTGGTTCGTGAGGCGTT
* * * *
59446412 TACTCTCCTAGCGAGTGAGAATTTTAGCAATTTCCCCAAATTTTTTATGTTCCTCTTTTTTCACT
1 TACTCTTCTGGCGAGTGAGAATTTTAGCAATTTCCCCAAATTTTTTATGTTCCTCTCTTTCCACT
* *
59446477 ACTTCTATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTA-TTTT-TTCTACTTCTTTCTTTCT
66 ACTTCCATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTTCTTCTTCTTCTTTCTTTCT
* * * *
59446540 GTTTCATTTTTCTTTCGTTTCTTTTACATTTATTGCCATATTCCCTTGTTATCGTCTCTTGTTAT
131 ATTTCA-TTTTCTTTCGTTTCTTTTACATTTGTTGCCATATTCCCTTGTTGTCGTCTCTTGCTAT
* * * *
59446605 TGTTTCTTCATTGTTAACCTATCTTATGTTGTGCTGCCATTTAGACTGCGTTGTTCTTATTAAAA
195 TGTTTCTTCATTGTTGACCTATCTTCTGTTGTGCTGCCATTTAGACTGCGTTGGTGTTATTAAAA
* *
59446670 TCTTCAGATAAGTATAATTAGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATTTTTGGAAGGTC
260 TCTTCAGGTAAGTATAATTAGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAAGGTC
* *
59446735 TTTTGGTTTCATTA-GT-TTTTGCTAGGATGGTACGTGAGAG-GTT
325 TTTTGGTTTCATTATGTATTTTGCTAGGGTGGTTCGTGAG-GCGTT
* *
59446778 TACTCTTCTGGTGAGTGAGAATTTTAGTC-ATTTCCCCTAATTTTTTATGTTCCTCTCTTTCCAC
1 TACTCTTCTGGCGAGTGAGAATTTTAG-CAATTTCCCCAAATTTTTTATGTTCCTCTCTTTCCAC
** * *
59446842 TACTTTTATTTCTTTTTCCCATTTTTTGTTCCTCTGACGCTA-TTTTCTTCTTCTTCTTTCTTTC
65 TACTTCCATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTTCTTCTTCTTCTTTCTTTC
* * * *
59446906 TATTTCATTTTCTTTTGTTTCTTTTACATTTGTTGCCATATTCCCCTGTTGTCATCTCTTGCTAC
130 TATTTCATTTTCTTTCGTTTCTTTTACATTTGTTGCCATATTCCCTTGTTGTCGTCTCTTGCTAT
* * * *
59446971 TGTTTCTTCATTGTCGACCTATCTTCTGTTGTACCGCCATTTAAACTGCGTTGGTGTTATTAAAA
195 TGTTTCTTCATTGTTGACCTATCTTCTGTTGTGCTGCCATTTAGACTGCGTTGGTGTTATTAAAA
* * * *
59447036 TCTTCAAGTAAGTATAATTAGTTAGTTTTC-TTTTAGGTTGGTTGTCTTGATATCTTTAGAAAGT
260 TCTTCAGGTAAGTATAATTAGTTAG-TTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAAGGT
* *
59447100 ATTTTGGTTTCATTAGTTGTGATTTTGCTAGAGGTCGTTCGTGAGGCGTT
324 CTTTTGGTTTCATTA--TGT-ATTTTGCTAG-GGTGGTTCGTGAGGCGTT
* * * * * * *
59447150 TACTCTTC-AGTGAGTAAGGATATTAGCAATTTCCCTAAATTTTTTATGTTCTTCTCTTTCCACT
1 TACTCTTCTGGCGAGTGAGAATTTTAGCAATTTCCCCAAATTTTTTATGTTCCTCTCTTTCCACT
59447214 ACTTCCATTTCTTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTCTTCTTCTTCTTCTTTCTT
66 ACTTCCATTTC-TTTTTCCCATTTTTTGTTCCTCTAACGTTA-TTT-TTCTTCTTCTTCTTTCTT
* * * * * *
59447279 TTTGTTTCATTTTTCTTTCATTTCTTTTACATTTTTTGCTATATTCCCCTGTTGTCGTCTCTTGC
128 TCTATTTCA-TTTTCTTTCGTTTCTTTTACATTTGTTGCCATATTCCCTTGTTGTCGTCTCTTGC
* * * * *
59447344 TATTATTTTTTCATTG-TGACCTATCTTCTGTTGTG-TGGCCATTTAGCCTACATTGGTGTTATT
192 TATTGTTTCTTCATTGTTGACCTATCTTCTGTTGTGCT-GCCATTTAGACTGCGTTGGTGTTATT
* * * *
59447407 AAAATCTTTAGGTAAGTATAATTCGTTAGTTTCGTTTTAGGGTGGTTGTCTTGATATCTTTGTAA
256 AAAATCTTCAGGTAAGTATAATTAGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAA
* * * *
59447472 GGTCGTTTAGTTTCATTAGCTGTGATTTTGCTAGGGTGGTTCGTGAAGTGTT
321 GGTCTTTTGGTTTCATTA--TGT-ATTTTGCTAGGGTGGTTCGTGAGGCGTT
* * * * *
59447524 TACTCTTCTGGCGAGTAAGGATTTTAGCAATTTCACCAAATTTTTTATGTTTCTCTCTTACCACT
1 TACTCTTCTGGCGAGTGAGAATTTTAGCAATTTCCCCAAATTTTTTATGTTCCTCTCTTTCCACT
* * * *
59447589 ACTTCCATTTCTTTTTCCCATTTTCTATTCCTCTAACATTATTTTT-TTCTTCTTTATTTCTTTC
66 ACTTCCATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTTCTTCTTC-TTCTTTCTTTC
* * * * *
59447653 TATTTTATTTTCTTTTGTTTCTTTTACATTTGTTACTATATTCTCC-TGTTGTCGGT-TCTTGTT
130 TATTTCATTTTCTTTCGTTTCTTTTACATTTGTTGCCATATTC-CCTTGTTGTC-GTCTCTTGCT
** ** *
59447716 ATTGTTTCTTCATTGCCGACCTATCTTCTGTTGTGCTGCCATTTAGACTATGTCGGTGTTATTAA
193 ATTGTTTCTTCATTGTTGACCTATCTTCTGTTGTGCTGCCATTTAGACTGCGTTGGTGTTATTAA
* * *
59447781 AATCTTTAGGTAAGTATAATTCGTTAGTTTCATTTTAGAGTGGTTGTCTTGATATCTTTGGAAGG
258 AATCTTCAGGTAAGTATAATTAGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAAGG
* * *
59447846 TCTTTTGGTTTCATTAGTTGTGATTTTGCTAGGGGTGGTTCCTGATGTGTT
323 TCTTTTGGTTTCATTA--TGT-ATTTTGCTA-GGGTGGTTCGTGAGGCGTT
* *
59447897 TACTCTTCTGGCGAGTGAGAATTTTAGCAACTTCCGCAAATTTTTTATGTTCCTCTCTTTCCACT
1 TACTCTTCTGGCGAGTGAGAATTTTAGCAATTTCCCCAAATTTTTTATGTTCCTCTCTTTCCACT
* * * *
59447962 ACTTCTATTTCTTTTTCCCATTTTTTGTTCTTTTAACATTA-TTTTCTTCTTCTTCTTTCTTTCT
66 ACTTCCATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTTCTTCTTCTTCTTTCTTTCT
* * * * *
59448026 GTTTCATTTTCTTTTGTTTCTTTTACATTTGTTGCCATATT-CCTCTGTTTTCGTCTTTTTCTAT
131 ATTTCATTTTCTTTCGTTTCTTTTACATTTGTTGCCATATTCCCT-TGTTGTCGTCTCTTGCTAT
* * * * * * ** * *
59448090 AGTTTTTTCATTGCTAACCTATCTTCTATTATGCTGTAATTTAG-TTTCGTTTTAGGGTGGTTGT
195 TGTTTCTTCATTGTTGACCTATCTTCTGTTGTGCTGCCATTTAGACTGCG--TT--GGT-G-T-T
* * * * * * * * *
59448154 CTTGATATCTT-TGG-AAGGTCT-TTTGGTTTAAGTAGTTGTGATTTTGCTAGAGGTGG-T-TCG
253 ATTAAAATCTTCAGGTAA-GTATAATTAG--T---TAGTT-TCA-TTT--TAG-GGTGGTTGTCT
** *** ** ** * **** * ** *
59448214 TGA-GGCGTTTACTAGG---GGTGG-TTC-TTGA-GGCTTTTCCTCTTCTAGTGAGTGAGG-ATT
307 TGATATC-TTTGGAAGGTCTTTTGGTTTCATT-ATGTATTTTGCTAGGGTGGTTCGTGAGGCGTT
** ** * * * ** *
59448271 TCAGCAATT-TCCCCA---A-ATTTTTTACGTTC-CTTCTTTCC--ATTACTTTAATG-T-CT-T
1 T-A-CTCTTCTGGCGAGTGAGA-ATTTTA-G--CAATT-TCCCCAAATT--TTTTATGTTCCTCT
*** * * ** * * * * *
59448325 -TTTCCA--A-TTTTGTGTTC-CTCTAACGTTATTTTTTTCTTCT-TC-TT-TCTTTCTGT-TTC
57 CTTTCCACTACTTCCAT-TTCTTTTTCCCATT-TTTTGTTCCTCTAACGTTATTTTTCT-TCTTC
* * * * *
59448381 AT-TTTCTTTC-GTTT-A--TT-TTAC--AT-TTT--------TTGCCATATTCCCCTGTTGTCG
119 TTCTTTCTTTCTATTTCATTTTCTTTCGTTTCTTTTACATTTGTTGCCATATTCCCTTGTTGTCG
* *** * *
59448429 TTTCTTGCTATTGTTTCTTCATTGCAAACCTATCTTCTGTTGTG-TCGCCATTTAGATTGTGTTG
184 TCTCTTGCTATTGTTTCTTCATTGTTGACCTATCTTCTGTTGTGCT-GCCATTTAGACTGCGTTG
*
59448493 GTGTTATTAAAATCTTCAGGTAAGTATAATTCGTTAGTTTCATTTTAGGGTGGTTGTCTTGATAT
248 GTGTTATTAAAATCTTCAGGTAAGTATAATTAGTTAGTTTCATTTTAGGGTGGTTGTCTTGATAT
* * *
59448558 CTTTGAAAGGTCTTTTGGTTTCATTAGTTGTGATTTTGCTAGGGTGGTTCATAAGGCGTT
313 CTTTGGAAGGTCTTTTGGTTTCATTA--TGT-ATTTTGCTAGGGTGGTTCGTGAGGCGTT
* * * * *
59448618 TACTCTTCTAGCAAGTAAGGATTTTAACAATTTCCCCAAATTTTTT-TGTATTCCTCTCTTTCCA
1 TACTCTTCTGGCGAGTGAGAATTTTAGCAATTTCCCCAAATTTTTTATG--TTCCTCTCTTTCCA
* * * *
59448682 CTACTTCCATTTCTTTTTTCCAATTTTCTGTTCCTTTGACGTTATTTTT-TTCTTCTTCTTTCTT
64 CTACTTCCATTTC-TTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTTCTTCTTCTTCTTTCTT
* * * * * **
59448746 TCTATTTCATTTTTATTTTGTTTCTTTTAAATTTGTTACCATTTTCCCTTGTTGTTATCTCTTGC
128 TCTATTTCA-TTTTCTTTCGTTTCTTTTACATTTGTTGCCATATTCCCTTGTTGTCGTCTCTTGC
* * *** ** *
59448811 TATTATTTCTTCGTTGCCAACCTATCTTCAT-TTGTGCCACCATTTAGAATGCGTTGGTGTT-TT
192 TATTGTTTCTTCATTGTTGACCTATCTTC-TGTTGTGCTGCCATTTAGACTGCGTTGGTGTTATT
* * *
59448874 CAAAATCTTCA-G--A-TATAATTCGTTAGTTTCATTTTAGGGTGGTTGTTTTGATATCTTTGTA
256 -AAAATCTTCAGGTAAGTATAATTAGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGA
* **
59448935 GGGTCTTTTGGTTTCATTAGTTGTGATTTTGCTAAGGGTGGTTCGTGAGATGTT
320 AGGTCTTTTGGTTTCATTA--TGT-ATTTTGCT-AGGGTGGTTCGTGAGGCGTT
* * * *
59448989 TACTC-TATGGCAAGTAAGGATTTTAGCAATTTC
1 TACTCTTCTGGCGAGTGAGAATTTTAGCAATTTC
59449022 TTTTCACTTC
Statistics
Matches: 2137, Mismatches: 337, Indels: 270
0.78 0.12 0.10
Matches are distributed among these distances:
336 5 0.00
337 4 0.00
338 11 0.01
339 4 0.00
340 2 0.00
341 8 0.00
342 4 0.00
343 2 0.00
344 10 0.00
345 12 0.01
346 30 0.01
347 8 0.00
348 4 0.00
349 11 0.01
350 61 0.03
351 11 0.01
353 4 0.00
354 11 0.01
355 6 0.00
356 7 0.00
357 12 0.01
358 6 0.00
359 2 0.00
361 2 0.00
362 4 0.00
363 2 0.00
364 1 0.00
365 5 0.00
366 326 0.15
367 91 0.04
368 177 0.08
369 18 0.01
370 106 0.05
371 165 0.08
372 364 0.17
373 131 0.06
374 146 0.07
375 230 0.11
376 78 0.04
377 7 0.00
378 10 0.00
379 2 0.00
380 4 0.00
381 8 0.00
382 2 0.00
383 4 0.00
384 11 0.01
385 4 0.00
386 4 0.00
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.51
Consensus pattern (369 bp):
TACTCTTCTGGCGAGTGAGAATTTTAGCAATTTCCCCAAATTTTTTATGTTCCTCTCTTTCCACT
ACTTCCATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTTCTTCTTCTTCTTTCTTTCT
ATTTCATTTTCTTTCGTTTCTTTTACATTTGTTGCCATATTCCCTTGTTGTCGTCTCTTGCTATT
GTTTCTTCATTGTTGACCTATCTTCTGTTGTGCTGCCATTTAGACTGCGTTGGTGTTATTAAAAT
CTTCAGGTAAGTATAATTAGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAAGGTCT
TTTGGTTTCATTATGTATTTTGCTAGGGTGGTTCGTGAGGCGTT
Found at i:59447297 original size:21 final size:22
Alignment explanation
Indices: 59447270--59447314 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
59447260 CTTCTTCTTC
*
59447270 TTCTTTC-TTT-TTGTTTCATTT
1 TTCTTTCATTTCTT-TTACATTT
59447291 TTCTTTCATTTCTTTTACATTT
1 TTCTTTCATTTCTTTTACATTT
59447313 TT
1 TT
59447315 TGCTATATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 12 0.57
23 2 0.10
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.73
Consensus pattern (22 bp):
TTCTTTCATTTCTTTTACATTT
Found at i:59447859 original size:372 final size:369
Alignment explanation
Indices: 59446044--59448125 Score: 2649
Period size: 372 Copynumber: 5.6 Consensus size: 369
59446034 GGGTGTTACA
59446044 TACTCTTCTGGCGAGTGAA-AATTTTAGCAATTTCCCTAAATTTTTTATGTTCCTCTCTTTCCAC
1 TACTCTTCTGGCGAGT-AAGAATTTTAGCAATTTCCC-AAATTTTTTATGTTCCTCTCTTTCCAC
* * * *
59446108 TATTTCCATTTCTTTTTTCCATTTTCTGTTCCTCTAATGTTATTTTTCTTCTTCTTCTTTCTTTC
64 TACTTCCATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTA-TTTTCTTCTTCTTCTTTCTTTC
* *
59446173 TATTTCATTTTCTTTTCTTTCTTTTACATTTGTTGCCATATTCCCT-TGTGTCGTCTCTTACTAC
128 TATTTCATTTTCTTTTGTTTCTTTTACATTTGTTGCCATATTCCCTGT-TGTCGTCTCTTGCTA-
* * * **
59446237 TAT-TTTGTT-ATTGTTGACCTATCTTCTGTTATGCTGCCATTTAAACTGTATTGGTGTTATTAA
191 T-TGTTTCTTCATTGTTGACCTATCTTCTGTTGTGCTGCCATTTAGACTGCGTTGGTGTTATTAA
* *
59446300 AATCTTCAGGTAAGAATAATTC----GTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAAGC
255 AATCTTCAGGTAAGTATAATTCGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAAGG
* * * * *
59446361 TATTTTGGTTTCATTAGTTGTAATTTTGCTAAGGGTGGTTTGTGAGGCATT
320 TCTTTTGGTTTCATTAGTTGTGATTTTGCT-AGGGTGGTTCGTGAAGCGTT
* * * * *
59446412 TACTCTCCTAGCGAGTGAGAATTTTAGCAATTTCCCCAAATTTTTTATGTTCCTCTTTTTTCACT
1 TACTCTTCTGGCGAGTAAGAATTTTAGCAATTT-CCCAAATTTTTTATGTTCCTCTCTTTCCACT
* * *
59446477 ACTTCTATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTT-TTCTACTTCTTTCTTTCTG
65 ACTTCCATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTCTTCTTCTTCTTTCTTTCTA
* * * *
59446541 TTTCATTTTTCTTTCGTTTCTTTTACATTTATTGCCATATTCCCTTGTTATCGTCTCTTGTTATT
130 TTTCA-TTTTCTTTTGTTTCTTTTACATTTGTTGCCATATTCCC-TGTTGTCGTCTCTTGCTATT
* * * *
59446606 GTTTCTTCATTGTTAACCTATCTTATGTTGTGCTGCCATTTAGACTGCGTTGTTCTTATTAAAAT
193 GTTTCTTCATTGTTGACCTATCTTCTGTTGTGCTGCCATTTAGACTGCGTTGGTGTTATTAAAAT
* * *
59446671 CTTCAGATAAGTATAATTAGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATTTTTGGAAGGTCT
258 CTTCAGGTAAGTATAATTCGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAAGGTCT
* *
59446736 TTTGGTTTCATTA---GT--TTTTGCTAGGATGGTACGTGAGAG-GTT
323 TTTGGTTTCATTAGTTGTGATTTTGCTAGGGTGGTTCGTGA-AGCGTT
* * *
59446778 TACTCTTCTGGTGAGTGAGAATTTTAGTC-ATTTCCCCTAATTTTTTATGTTCCTCTCTTTCCAC
1 TACTCTTCTGGCGAGTAAGAATTTTAG-CAATTT-CCCAAATTTTTTATGTTCCTCTCTTTCCAC
** * *
59446842 TACTTTTATTTCTTTTTCCCATTTTTTGTTCCTCTGACGCTATTTTCTTCTTCTTCTTTCTTTCT
64 TACTTCCATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTCTTCTTCTTCTTTCTTTCT
* *
59446907 ATTTCATTTTCTTTTGTTTCTTTTACATTTGTTGCCATATTCCCCTGTTGTCATCTCTTGCTACT
129 ATTTCATTTTCTTTTGTTTCTTTTACATTTGTTGCCATATT-CCCTGTTGTCGTCTCTTGCTATT
* * * *
59446972 GTTTCTTCATTGTCGACCTATCTTCTGTTGTACCGCCATTTAAACTGCGTTGGTGTTATTAAAAT
193 GTTTCTTCATTGTTGACCTATCTTCTGTTGTGCTGCCATTTAGACTGCGTTGGTGTTATTAAAAT
* * * * * *
59447037 CTTCAAGTAAGTATAATTAGTTAGTTTTC-TTTTAGGTTGGTTGTCTTGATATCTTTAGAAAGTA
258 CTTCAGGTAAGTATAATTCGTTAG-TTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAAGGTC
* *
59447101 TTTTGGTTTCATTAGTTGTGATTTTGCTAGAGGTCGTTCGTGAGGCGTT
322 TTTTGGTTTCATTAGTTGTGATTTTGCTAG-GGTGGTTCGTGAAGCGTT
* * * * *
59447150 TACTCTTC-AGTGAGTAAGGATATTAGCAATTTCCCTAAATTTTTTATGTTCTTCTCTTTCCACT
1 TACTCTTCTGGCGAGTAAGAATTTTAGCAATTTCCC-AAATTTTTTATGTTCCTCTCTTTCCACT
59447214 ACTTCCATTTCTTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTCTTCTTCTTCTTCTTTCTT
65 ACTTCCATTTC-TTTTTCCCATTTTTTGTTCCTCTAACGTTA--TT-TTCTTCTTCTTCTTTCTT
* * ** * *
59447279 TTTGTTTCATTTTTCTTTCATTTCTTTTACATTTTTTGCTATATTCCCCTGTTGTCGTCTCTTGC
126 TCTATTTCA-TTTTCTTTTGTTTCTTTTACATTTGTTGCCATATT-CCCTGTTGTCGTCTCTTGC
* * * * *
59447344 TATTATTTTTTCATTG-TGACCTATCTTCTGTTGTG-TGGCCATTTAGCCTACATTGGTGTTATT
189 TATTGTTTCTTCATTGTTGACCTATCTTCTGTTGTGCT-GCCATTTAGACTGCGTTGGTGTTATT
* * *
59447407 AAAATCTTTAGGTAAGTATAATTCGTTAGTTTCGTTTTAGGGTGGTTGTCTTGATATCTTTGTAA
253 AAAATCTTCAGGTAAGTATAATTCGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAA
* * * *
59447472 GGTCGTTTAGTTTCATTAGCTGTGATTTTGCTAGGGTGGTTCGTGAAGTGTT
318 GGTCTTTTGGTTTCATTAGTTGTGATTTTGCTAGGGTGGTTCGTGAAGCGTT
* * *
59447524 TACTCTTCTGGCGAGTAAGGATTTTAGCAATTTCACCAAATTTTTTATGTTTCTCTCTTACCACT
1 TACTCTTCTGGCGAGTAAGAATTTTAGCAATTTC-CCAAATTTTTTATGTTCCTCTCTTTCCACT
* * * * *
59447589 ACTTCCATTTCTTTTTCCCATTTTCTATTCCTCTAACATTATTTTTTTCTTCTTTATTTCTTTCT
65 ACTTCCATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTCTTCTTC-TTCTTTCTTTCT
* * * *
59447654 ATTTTATTTTCTTTTGTTTCTTTTACATTTGTTACTATATTCTCCTGTTGTCGGT-TCTTGTTAT
129 ATTTCATTTTCTTTTGTTTCTTTTACATTTGTTGCCATATTC-CCTGTTGTC-GTCTCTTGCTAT
** ** *
59447718 TGTTTCTTCATTGCCGACCTATCTTCTGTTGTGCTGCCATTTAGACTATGTCGGTGTTATTAAAA
192 TGTTTCTTCATTGTTGACCTATCTTCTGTTGTGCTGCCATTTAGACTGCGTTGGTGTTATTAAAA
* *
59447783 TCTTTAGGTAAGTATAATTCGTTAGTTTCATTTTAGAGTGGTTGTCTTGATATCTTTGGAAGGTC
257 TCTTCAGGTAAGTATAATTCGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAAGGTC
* * *
59447848 TTTTGGTTTCATTAGTTGTGATTTTGCTAGGGGTGGTTCCTGATGTGTT
322 TTTTGGTTTCATTAGTTGTGATTTTGCTA-GGGTGGTTCGTGAAGCGTT
* *
59447897 TACTCTTCTGGCGAGTGAGAATTTTAGCAACTTCCGCAAATTTTTTATGTTCCTCTCTTTCCACT
1 TACTCTTCTGGCGAGTAAGAATTTTAGCAATTTCC-CAAATTTTTTATGTTCCTCTCTTTCCACT
* * * * *
59447962 ACTTCTATTTCTTTTTCCCATTTTTTGTTCTTTTAACATTATTTTCTTCTTCTTCTTTCTTTCTG
65 ACTTCCATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTCTTCTTCTTCTTTCTTTCTA
* * * *
59448027 TTTCATTTTCTTTTGTTTCTTTTACATTTGTTGCCATATTCCTCTGTTTTCGTCTTTTTCTATAG
130 TTTCATTTTCTTTTGTTTCTTTTACATTTGTTGCCATATTCC-CTGTTGTCGTCTCTTGCTATTG
* * * * *
59448092 TTTTTTCATTGCTAACCTATCTTCTATTATGCTG
194 TTTCTTCATTGTTGACCTATCTTCTGTTGTGCTG
59448126 TAATTTAGTT
Statistics
Matches: 1496, Mismatches: 175, Indels: 82
0.85 0.10 0.05
Matches are distributed among these distances:
366 307 0.21
367 84 0.06
368 168 0.11
369 8 0.01
370 5 0.00
371 133 0.09
372 343 0.23
373 122 0.08
374 56 0.04
375 205 0.14
376 65 0.04
ACGTcount: A:0.17, C:0.18, G:0.14, T:0.52
Consensus pattern (369 bp):
TACTCTTCTGGCGAGTAAGAATTTTAGCAATTTCCCAAATTTTTTATGTTCCTCTCTTTCCACTA
CTTCCATTTCTTTTTCCCATTTTTTGTTCCTCTAACGTTATTTTCTTCTTCTTCTTTCTTTCTAT
TTCATTTTCTTTTGTTTCTTTTACATTTGTTGCCATATTCCCTGTTGTCGTCTCTTGCTATTGTT
TCTTCATTGTTGACCTATCTTCTGTTGTGCTGCCATTTAGACTGCGTTGGTGTTATTAAAATCTT
CAGGTAAGTATAATTCGTTAGTTTCATTTTAGGGTGGTTGTCTTGATATCTTTGGAAGGTCTTTT
GGTTTCATTAGTTGTGATTTTGCTAGGGTGGTTCGTGAAGCGTT
Found at i:59448045 original size:15 final size:15
Alignment explanation
Indices: 59448017--59448049 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
59448007 CTTCTTCTTC
59448017 TTTCTTTCTGTTTCAT
1 TTTCTTTCTGTTTC-T
59448033 TTTCTTT-TGTTTCT
1 TTTCTTTCTGTTTCT
59448047 TTT
1 TTT
59448050 ACATTTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTCTTTCTGTTTCT
Found at i:59453101 original size:22 final size:22
Alignment explanation
Indices: 59453058--59453102 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
59453048 AGGTAAGCTA
*
59453058 TGAGAATATTCTTTGGTCAATG
1 TGAGAATATTCTTTGATCAATG
*
59453080 TGAGAATATTTTTTAGAT-AATG
1 TGAGAATATTCTTT-GATCAATG
59453102 T
1 T
59453103 TGGATTGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.44
Consensus pattern (22 bp):
TGAGAATATTCTTTGATCAATG
Found at i:59458557 original size:13 final size:13
Alignment explanation
Indices: 59458537--59458587 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
59458527 AGTTTGGCAA
*
59458537 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
*
59458550 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
*
59458563 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
59458576 TGCTTTTGAAAA
1 TGCTTTTGAAAA
59458588 TTTTAGTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:59459409 original size:6 final size:6
Alignment explanation
Indices: 59459398--59459422 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
59459388 ATGTGAGCAT
59459398 TTACAG TTACAG TTACAG TTACAG T
1 TTACAG TTACAG TTACAG TTACAG T
59459423 CACACTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (6 bp):
TTACAG
Found at i:59459711 original size:14 final size:14
Alignment explanation
Indices: 59459671--59459715 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
59459661 TACGAAAGAA
*
59459671 TTATATA-AATGAG
1 TTATATAGAATAAG
59459684 -TATAT-GAATAAG
1 TTATATAGAATAAG
*
59459696 TTATATAGAATTAG
1 TTATATAGAATAAG
59459710 TTATAT
1 TTATAT
59459716 GAAGTGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 10 0.37
13 5 0.19
14 12 0.44
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (14 bp):
TTATATAGAATAAG
Found at i:59459726 original size:27 final size:24
Alignment explanation
Indices: 59459669--59459734 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 24
59459659 TATACGAAAG
59459669 AATTATATAAATGAGTATATGAAT
1 AATTATATAAATGAGTATATGAAT
*
59459693 AAGTTATATAGAATTAGTTATATGAAGT
1 AA-TTATATA-AATGAG-TATATGAA-T
*
59459721 GATTATATGAAATG
1 AATTATAT-AAATG
59459735 TTTTCACTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 2 0.06
25 7 0.21
26 5 0.15
27 17 0.50
28 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (24 bp):
AATTATATAAATGAGTATATGAAT
Found at i:59466999 original size:19 final size:19
Alignment explanation
Indices: 59466977--59467037 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
59466967 ATTTATTTAT
59466977 AAATAAATCATTTTCCAGA
1 AAATAAATCATTTTCCAGA
* * *
59466996 AAATATTAGC-TATTCCAGA
1 AAATA-AATCATTTTCCAGA
*
59467015 AAAGTAATTCATTTTTCCAGA
1 AAA-TAAATCA-TTTTCCAGA
59467036 AA
1 AA
59467038 TAATTTTTCA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
19 17 0.55
20 4 0.13
21 10 0.32
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (19 bp):
AAATAAATCATTTTCCAGA
Found at i:59470574 original size:7 final size:7
Alignment explanation
Indices: 59470564--59470600 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
59470554 TTTATTTTTT
59470564 ATTTTAA
1 ATTTTAA
59470571 ATTTTTAA
1 A-TTTTAA
59470579 ATTTTAA
1 ATTTTAA
59470586 ATTTTAA
1 ATTTTAA
59470593 ATTTTAA
1 ATTTTAA
59470600 A
1 A
59470601 AAATAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTTAA
Found at i:59470574 original size:14 final size:14
Alignment explanation
Indices: 59470557--59470600 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
59470547 TTTATGTTTT
*
59470557 ATTTTTTATTTTAA
1 ATTTTTAATTTTAA
59470571 ATTTTTAAATTTTAA
1 ATTTTT-AATTTTAA
*
59470586 ATTTTAAATTTTAA
1 ATTTTTAATTTTAA
59470600 A
1 A
59470601 AAATAAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTTTAATTTTAA
Found at i:59470896 original size:15 final size:15
Alignment explanation
Indices: 59470876--59470905 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59470866 AACTATAAAT
*
59470876 CATAATCCCTAAACC
1 CATAATCCATAAACC
59470891 CATAATCCATAAACC
1 CATAATCCATAAACC
59470906 TTAAAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (15 bp):
CATAATCCATAAACC
Found at i:59470941 original size:7 final size:7
Alignment explanation
Indices: 59470929--59470954 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
59470919 TTATACACTT
59470929 TAAACCC
1 TAAACCC
59470936 TAAACCC
1 TAAACCC
59470943 TAAACCC
1 TAAACCC
59470950 TAAAC
1 TAAAC
59470955 TACAATGATA
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:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:59471137 original size:14 final size:14
Alignment explanation
Indices: 59471120--59471169 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
59471110 TGAACCCATC
59471120 ACCCTTAACCCCTA
1 ACCCTTAACCCCTA
* *
59471134 ACCCCTAACACCTA
1 ACCCTTAACCCCTA
*
59471148 AACCTTAAACCCC-A
1 ACCCTT-AACCCCTA
59471162 ACCCTTAA
1 ACCCTTAA
59471170 ACCACCTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
13 2 0.07
14 22 0.76
15 5 0.17
ACGTcount: A:0.36, C:0.46, G:0.00, T:0.18
Consensus pattern (14 bp):
ACCCTTAACCCCTA
Found at i:59471172 original size:21 final size:21
Alignment explanation
Indices: 59471120--59471172 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
59471110 TGAACCCATC
*
59471120 ACCCTTAACCCCTAACCCCTA
1 ACCCTTAAACCCTAACCCCTA
*
59471141 ACACC-TAAACCTTAAACCCC-A
1 AC-CCTTAAACCCT-AACCCCTA
59471162 ACCCTTAAACC
1 ACCCTTAAACC
59471173 ACCTTTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 2 0.07
21 17 0.63
22 8 0.30
ACGTcount: A:0.36, C:0.47, G:0.00, T:0.17
Consensus pattern (21 bp):
ACCCTTAAACCCTAACCCCTA
Found at i:59471293 original size:21 final size:21
Alignment explanation
Indices: 59471267--59471308 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
59471257 AGTGATAATT
59471267 AATTCAATAATTTAAAATTAA
1 AATTCAATAATTTAAAATTAA
*
59471288 AATTCAATATTTTAAAATTAA
1 AATTCAATAATTTAAAATTAA
59471309 TACTATCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTCAATAATTTAAAATTAA
Found at i:59471823 original size:154 final size:154
Alignment explanation
Indices: 59471506--59471838 Score: 551
Period size: 155 Copynumber: 2.2 Consensus size: 154
59471496 TACTTATAGT
* * *
59471506 GGCGTTTCTTAAAAAACACCGCTTATACTCGATCTTTAGCGGCGTTTTTGAAAAGCGCCGCTAAA
1 GGCGTTTTTTAAAAAGCACCGC-TATACTCGATCTTTAGCGGCGTTTTTGAAAAGCACCGCTAAA
* * *
59471571 GCCACTAAACGCTCAATACAAAGCGCCCTCATTTTGAAAAATTCTTTTGCGGCGTTTTTTGAAAA
65 GCCACTAAAAGCTCAATACAAAACGACCTCATTTTGAAAAATTCTTTTGCGGCGTTTTTTGAAAA
59471636 ACGCCACTAAAGATCAAGCATTAGC
130 ACGCCACTAAAGATCAAGCATTAGC
*
59471661 GGCGTTTTTTAAAAAGCACCGCTAGTACTCGATCTTTAGCGGTGTTTTTGAAAAGCACCGCTAAA
1 GGCGTTTTTTAAAAAGCACCGCTA-TACTCGATCTTTAGCGGCGTTTTTGAAAAGCACCGCTAAA
* *
59471726 GCCACTAAAAGCTCAATACAAAACGACGTCATTTTG-CAAATTCTTTTGCGGCGTTTTTTGAAAA
65 GCCACTAAAAGCTCAATACAAAACGACCTCATTTTGAAAAATTCTTTTGCGGCGTTTTTTGAAAA
59471790 ACGCCACTAAAGATCAAGCATTAGC
130 ACGCCACTAAAGATCAAGCATTAGC
*
59471815 GGCGTTTTTTAAAAAGCGCCGCTA
1 GGCGTTTTTTAAAAAGCACCGCTA
59471839 AAGGAGGACT
Statistics
Matches: 167, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
154 77 0.46
155 90 0.54
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (154 bp):
GGCGTTTTTTAAAAAGCACCGCTATACTCGATCTTTAGCGGCGTTTTTGAAAAGCACCGCTAAAG
CCACTAAAAGCTCAATACAAAACGACCTCATTTTGAAAAATTCTTTTGCGGCGTTTTTTGAAAAA
CGCCACTAAAGATCAAGCATTAGC
Found at i:59471855 original size:154 final size:154
Alignment explanation
Indices: 59471506--59471880 Score: 524
Period size: 155 Copynumber: 2.4 Consensus size: 154
59471496 TACTTATAGT
* * *
59471506 GGCGTTTCTTAAAAAACACCGCTTA-TACTCGATCTTTAGCGGCGTTTTTGAAAAGCGCCGCTAA
1 GGCGTTTTTTAAAAAGCACCGC-TAGGAC-CGATCTTTAGCGGCGTTTTTGAAAAGCGCCGCTAA
* * *
59471570 AGCCACTAAACGCTCAATACAAAGCGCCCTCATTTTGAAAAATTCTTTTGCGGCGTTTTTTGAAA
64 AGCCACTAAAAGCTCAATACAAAACGACCTCATTTTGAAAAATTCTTTTGCGGCGTTTTTTGAAA
59471635 AACGCCACTAAAGATCAAGCATTAGC
129 AACGCCACTAAAGATCAAGCATTAGC
* * *
59471661 GGCGTTTTTTAAAAAGCACCGCTAGTACTCGATCTTTAGCGGTGTTTTTGAAAAGCACCGCTAAA
1 GGCGTTTTTTAAAAAGCACCGCTAGGAC-CGATCTTTAGCGGCGTTTTTGAAAAGCGCCGCTAAA
* *
59471726 GCCACTAAAAGCTCAATACAAAACGACGTCATTTTG-CAAATTCTTTTGCGGCGTTTTTTGAAAA
65 GCCACTAAAAGCTCAATACAAAACGACCTCATTTTGAAAAATTCTTTTGCGGCGTTTTTTGAAAA
59471790 ACGCCACTAAAGATCAAGCATTAGC
130 ACGCCACTAAAGATCAAGCATTAGC
* * *
59471815 GGCGTTTTTTAAAAAGCGCCGCTAAAGGA-GGA-CTTATAGCGGCGTTTCTTAAAAAAGCGCCGC
1 GGCGTTTTTTAAAAAGCACCGCT--AGGACCGATCTT-TAGCGGCGTTT-TT-GAAAAGCGCCGC
59471878 TAA
61 TAA
59471881 TACTCAATCT
Statistics
Matches: 199, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
153 3 0.02
154 88 0.44
155 92 0.46
156 16 0.08
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (154 bp):
GGCGTTTTTTAAAAAGCACCGCTAGGACCGATCTTTAGCGGCGTTTTTGAAAAGCGCCGCTAAAG
CCACTAAAAGCTCAATACAAAACGACCTCATTTTGAAAAATTCTTTTGCGGCGTTTTTTGAAAAA
CGCCACTAAAGATCAAGCATTAGC
Found at i:59471921 original size:39 final size:38
Alignment explanation
Indices: 59471767--59471943 Score: 144
Period size: 39 Copynumber: 4.4 Consensus size: 38
59471757 TTTTGCAAAT
* * *
59471767 TCTTTTGCGGCGTTTTTTGAAAAA-CGCCACTAAAGATCAA
1 TCTTTAGCGGCG-TTTTT-AAAAAGCGCCGCTAAA-CTCAA
* * **
59471807 GCATTAGCGGCGTTTTTTAAAAAGCGCCGCTAAA-GGAGGA
1 TCTTTAGCGGCG-TTTTTAAAAAGCGCCGCTAAACTCA--A
59471847 -CTTATAGCGGCGTTTCTTAAAAAAGCGCCGCTAATACTCAA
1 TCTT-TAGCGGCGTTT-TT-AAAAAGCGCCGCTAA-ACTCAA
* *
59471888 TCTTTAGCGGCGTTTTTGAAAAGCGCCGCTAATACTCAT
1 TCTTTAGCGGCGTTTTTAAAAAGCGCCGCTAA-ACTCAA
*
59471927 TCTTTAGTGGCGTTTTT
1 TCTTTAGCGGCGTTTTT
59471944 CATTCAAACG
Statistics
Matches: 116, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
38 1 0.01
39 46 0.40
40 37 0.32
41 27 0.23
42 4 0.03
43 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (38 bp):
TCTTTAGCGGCGTTTTTAAAAAGCGCCGCTAAACTCAA
Found at i:59474406 original size:11 final size:12
Alignment explanation
Indices: 59474390--59474422 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
59474380 AAAACAAATA
59474390 AAAATAATAC-T
1 AAAATAATACTT
59474401 AAAATAATACTT
1 AAAATAATACTT
*
59474413 AAAACAATAC
1 AAAATAATAC
59474423 ACAAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAATACTT
Found at i:59474501 original size:21 final size:21
Alignment explanation
Indices: 59474451--59474501 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
59474441 AAAAAATGGT
*
59474451 TATATTAA-AAAATTAAAATA
1 TATATTAATAAAATAAAAATA
**
59474471 -ATTAAAAATAAAATAAAAATA
1 TA-TATTAATAAAATAAAAATA
59474492 TATATTAATA
1 TATATTAATA
59474502 TATAATTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 5
0.70 0.15 0.15
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 17 0.74
22 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TATATTAATAAAATAAAAATA
Found at i:59480234 original size:20 final size:19
Alignment explanation
Indices: 59480197--59480235 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
59480187 ATAATTTTTT
*
59480197 AAATTCAAAATATTTATAA
1 AAATTCAAAATATGTATAA
*
59480216 AAATTCTAAAATCTGTATAA
1 AAATTC-AAAATATGTATAA
59480236 TTTTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (19 bp):
AAATTCAAAATATGTATAA
Found at i:59480404 original size:16 final size:17
Alignment explanation
Indices: 59480374--59480406 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
59480364 GCTTTAAACA
59480374 GTTTACAAATATATATG
1 GTTTACAAATATATATG
*
59480391 GTTT-CAAATTTATATG
1 GTTTACAAATATATATG
59480407 CTCTAACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
GTTTACAAATATATATG
Found at i:59480683 original size:65 final size:67
Alignment explanation
Indices: 59480542--59480711 Score: 245
Period size: 65 Copynumber: 2.5 Consensus size: 67
59480532 TCTAAATAAG
* * * *
59480542 AAAAGATAAAATTACGTCATTTTAATAAATGTTTACCTTATTTAAAATTAAAAGTCAAAACTATA
1 AAAAG-TAAAATTACGTTATTTTGATAAATATTTACCTTA--TAAAATTAAAACTCAAAACTATA
59480607 AAGTT
63 AAGTT
*
59480612 AAAAGTAAAATTACGTTATTTTGATAAATATTTACC-TA-AAAGTTAAAACTCAAAACTATAAAG
1 AAAAGTAAAATTACGTTATTTTGATAAATATTTACCTTATAAAATTAAAACTCAAAACTATAAAG
59480675 TT
66 TT
*
59480677 AAAAGTAAAATTACGTTGTTTTGATAAATATTTAC
1 AAAAGTAAAATTACGTTATTTTGATAAATATTTAC
59480712 TTAATAATTT
Statistics
Matches: 94, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
65 59 0.63
68 2 0.02
69 28 0.30
70 5 0.05
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (67 bp):
AAAAGTAAAATTACGTTATTTTGATAAATATTTACCTTATAAAATTAAAACTCAAAACTATAAAG
TT
Found at i:59485500 original size:15 final size:15
Alignment explanation
Indices: 59485480--59485518 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
59485470 TATAGGGCAT
59485480 AATAAAATATTAAAA
1 AATAAAATATTAAAA
59485495 AAT-AAATATTTAAAA
1 AATAAAATA-TTAAAA
59485510 AA-AAAATAT
1 AATAAAATAT
59485519 GCATGCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAAAATATTAAAA
Found at i:59495604 original size:52 final size:48
Alignment explanation
Indices: 59495542--59495734 Score: 196
Period size: 47 Copynumber: 4.0 Consensus size: 48
59495532 GAAATGTGAT
* *
59495542 TTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATC-GAG---TGTGATATGTGC
* *
59495594 TTCCGTATAAGACCATATCCGGGATATGGCATCG-GTGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * *
59495641 TACTGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTG-
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * * * *
59495687 ATCCGTGTAAGACCATGGCTGGGCTATGGCCTCG-GTATGTGATATGTG
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAG--TGTGATATGTG
59495735 ACTATGTGCA
Statistics
Matches: 122, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
46 26 0.21
47 54 0.44
48 11 0.09
50 1 0.01
51 1 0.01
52 29 0.24
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (48 bp):
TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
Found at i:59495722 original size:93 final size:97
Alignment explanation
Indices: 59495546--59495752 Score: 226
Period size: 93 Copynumber: 2.1 Consensus size: 97
59495536 TGTGATTTCC
* * *
59495546 GTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGCTTCCGTATAAGACCATA
1 GTATAAGACCATAGCTGGGATATGGCATC-GAG--ATGTGATATGTGCATCCGTATAAGACCATA
*
59495611 TCCGGGATATGGCATCGG-TGTGATATGTG-CTACT
63 GCCGGGATATGGCATCGGATGTGATATGTGACTA-T
* * * *
59495645 GTATAAGACCATATCTGGGATATGGCATC-AG-TGTGATATGTG-ATCCGTGTAAGACCATGGCT
1 GTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATATGTGCATCCGTATAAGACCATAGCC
* *
59495707 GGGCTATGGCCTCGGTATGTGATATGTGACTAT
66 GGGATATGGCATCGG-ATGTGATATGTGACTAT
**
59495740 GTGCAAGACCATA
1 GTATAAGACCATA
59495753 ATTTTACTAT
Statistics
Matches: 93, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
93 28 0.30
94 11 0.12
95 23 0.25
96 3 0.03
97 2 0.02
99 26 0.28
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (97 bp):
GTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATATGTGCATCCGTATAAGACCATAGCC
GGGATATGGCATCGGATGTGATATGTGACTAT
Found at i:59505152 original size:46 final size:46
Alignment explanation
Indices: 59505100--59505419 Score: 570
Period size: 46 Copynumber: 7.0 Consensus size: 46
59505090 AGTGTGCTCT
59505100 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
59505146 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
59505192 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
59505238 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
59505284 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
59505330 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
59505376 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
59505420 TCATGTCAAA
Statistics
Matches: 267, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
45 1 0.00
46 266 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:59506345 original size:6 final size:6
Alignment explanation
Indices: 59506334--59506409 Score: 73
Period size: 6 Copynumber: 12.5 Consensus size: 6
59506324 AGTCAATTTG
* * * *
59506334 TTTTAT TTTTAT TTTTCT TTTTAT CTTTAT TTTTAT TTGTAT TTGTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* *
59506382 ATTTAT GTTTAT TTTGT-T TTTCTAT TTT
1 TTTTAT TTTTAT TTT-TAT TTT-TAT TTT
59506410 AAACTTTATT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
6 53 0.91
7 5 0.09
ACGTcount: A:0.14, C:0.04, G:0.05, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:59512354 original size:18 final size:17
Alignment explanation
Indices: 59512317--59512355 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
59512307 TGGCCGAAAA
*
59512317 CCTACACGCCCGTGTGG
1 CCTACACGCCCATGTGG
*
59512334 CCTACACGCCCAATTTGG
1 CCTACACGCCC-ATGTGG
59512352 CCTA
1 CCTA
59512356 GCCCGTGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.18, C:0.41, G:0.21, T:0.21
Consensus pattern (17 bp):
CCTACACGCCCATGTGG
Found at i:59513596 original size:19 final size:19
Alignment explanation
Indices: 59513561--59513628 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
59513551 GAAATATATT
59513561 TATACAAATAATGTATATAAG
1 TATA-AAATAAT-TATATAAG
*
59513582 TATAAAATAATTATAAAAG
1 TATAAAATAATTATATAAG
* *
59513601 TA-AATACTTAA-TATTTAAG
1 TATAA-A-ATAATTATATAAG
59513620 TATAAAATA
1 TATAAAATA
59513629 TAATAATTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
18 4 0.10
19 19 0.49
20 12 0.31
21 4 0.10
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (19 bp):
TATAAAATAATTATATAAG
Found at i:59513771 original size:11 final size:12
Alignment explanation
Indices: 59513755--59513798 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
59513745 TTAAGTAAAT
59513755 ATATTA-TATTA
1 ATATTATTATTA
59513766 ATATTA-TATTA
1 ATATTATTATTA
*
59513777 TTA-TATTATT-
1 ATATTATTATTA
59513787 ATATTATTATTA
1 ATATTATTATTA
59513799 GAATTAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 4 0.14
11 24 0.86
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATATTATTATTA
Found at i:59513780 original size:8 final size:8
Alignment explanation
Indices: 59513754--59513796 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
59513744 TTTAAGTAAA
59513754 TATATTA-
1 TATATTAT
*
59513761 TATTAATAT
1 TA-TATTAT
59513770 TATATTAT
1 TATATTAT
59513778 TATATTAT
1 TATATTAT
59513786 TATATTAT
1 TATATTAT
59513794 TAT
1 TAT
59513797 TAGAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
7 2 0.06
8 28 0.88
9 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATATTAT
Found at i:59513826 original size:17 final size:18
Alignment explanation
Indices: 59513804--59513842 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
59513794 TATTAGAATT
*
59513804 AAACAAAAAAAT-AAAGG
1 AAACAAAAAAATGAAAAG
*
59513821 AAACAAAAGAATGAAAAG
1 AAACAAAAAAATGAAAAG
59513839 AAAC
1 AAAC
59513843 TGAATAGCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.74, C:0.08, G:0.13, T:0.05
Consensus pattern (18 bp):
AAACAAAAAAATGAAAAG
Found at i:59515173 original size:22 final size:21
Alignment explanation
Indices: 59515142--59515219 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 21
59515132 GAATAGAAAT
59515142 TATGAAATTGAAACAGTATGA
1 TATGAAATTGAAACAGTATGA
**
59515163 TATGAGAATTGAAAGTGTTAT-A
1 TATGA-AATTGAAACAG-TATGA
* *
59515185 AATGATATTGAAACAGTATGA
1 TATGAAATTGAAACAGTATGA
59515206 TATGAGAATTGAAA
1 TATGA-AATTGAAA
59515220 GTGTTATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
20 3 0.07
21 18 0.40
22 21 0.47
23 3 0.07
ACGTcount: A:0.46, C:0.03, G:0.21, T:0.31
Consensus pattern (21 bp):
TATGAAATTGAAACAGTATGA
Found at i:59515196 original size:21 final size:21
Alignment explanation
Indices: 59515170--59515233 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
59515160 TGATATGAGA
59515170 ATTGAAAGTGTTATAAATGAT
1 ATTGAAAGTGTTATAAATGAT
** * *
59515191 ATTGAAACAG-TATGATATGAGA
1 ATTGAAAGTGTTAT-AAATGA-T
59515213 ATTGAAAGTGTTATAAATGAT
1 ATTGAAAGTGTTATAAATGAT
59515234 GCATTTATGA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.09
21 13 0.41
22 13 0.41
23 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (21 bp):
ATTGAAAGTGTTATAAATGAT
Found at i:59515196 original size:43 final size:43
Alignment explanation
Indices: 59515143--59515233 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
59515133 AATAGAAATT
*
59515143 ATGAAATTGAAACAGTATGATATGAGAATTGAAAGTGTTATAA
1 ATGATATTGAAACAGTATGATATGAGAATTGAAAGTGTTATAA
59515186 ATGATATTGAAACAGTATGATATGAGAATTGAAAGTGTTATAA
1 ATGATATTGAAACAGTATGATATGAGAATTGAAAGTGTTATAA
59515229 ATGAT
1 ATGAT
59515234 GCATTTATGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.45, C:0.02, G:0.21, T:0.32
Consensus pattern (43 bp):
ATGATATTGAAACAGTATGATATGAGAATTGAAAGTGTTATAA
Found at i:59515232 original size:22 final size:22
Alignment explanation
Indices: 59515164--59515232 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
59515154 ACAGTATGAT
59515164 ATGAGAATTGAAAGTGTTATAA
1 ATGAGAATTGAAAGTGTTATAA
* ** *
59515186 ATGA-TATTGAAACAG-TATGAT
1 ATGAGAATTGAAAGTGTTAT-AA
59515207 ATGAGAATTGAAAGTGTTATAA
1 ATGAGAATTGAAAGTGTTATAA
59515229 ATGA
1 ATGA
59515233 TGCATTTATG
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
20 3 0.08
21 13 0.36
22 17 0.47
23 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGAGAATTGAAAGTGTTATAA
Found at i:59528209 original size:47 final size:47
Alignment explanation
Indices: 59528143--59528236 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
59528133 ACATTAATCG
*
59528143 ATTAATTAGTAATTAGTATTTTATTTCTCAAGGATGATATATACTTA
1 ATTAATTAGTAATTAGTATTTTATTTCTCAAGGATAATATATACTTA
59528190 ATTAATTAGTAATTAGTATTTTATTTCTCAAGGATAATATATACTTA
1 ATTAATTAGTAATTAGTATTTTATTTCTCAAGGATAATATATACTTA
59528237 CTCTTTTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (47 bp):
ATTAATTAGTAATTAGTATTTTATTTCTCAAGGATAATATATACTTA
Found at i:59533318 original size:20 final size:20
Alignment explanation
Indices: 59533290--59533329 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
59533280 CTCTAATTAG
*
59533290 AATCTCTAAAAATCAACTAT
1 AATCCCTAAAAATCAACTAT
* *
59533310 AATCCCTAAAGATTAACTAT
1 AATCCCTAAAAATCAACTAT
59533330 TCAATGTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (20 bp):
AATCCCTAAAAATCAACTAT
Found at i:59534347 original size:26 final size:26
Alignment explanation
Indices: 59534318--59534371 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
59534308 TATGTCATCA
59534318 ACATAAACTATAAGGAGAGTAATCTT
1 ACATAAACTATAAGGAGAGTAATCTT
59534344 ACATAAACTATAAGGAGAGTAATCTT
1 ACATAAACTATAAGGAGAGTAATCTT
59534370 AC
1 AC
59534372 TCTTGTGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (26 bp):
ACATAAACTATAAGGAGAGTAATCTT
Found at i:59536722 original size:21 final size:22
Alignment explanation
Indices: 59536698--59536744 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
59536688 CTATACGAGT
59536698 AAATTTAACATT-AATTTAATA
1 AAATTTAACATTCAATTTAATA
* *
59536719 AAA-TTCACATTCAATTTAATC
1 AAATTTAACATTCAATTTAATA
59536740 AAATT
1 AAATT
59536745 CAAATTCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 7 0.32
21 14 0.64
22 1 0.05
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATTTAACATTCAATTTAATA
Found at i:59536745 original size:21 final size:21
Alignment explanation
Indices: 59536705--59536751 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
59536695 AGTAAATTTA
59536705 ACATT-AATTTAATAAAATTC
1 ACATTCAATTTAATAAAATTC
*
59536725 ACATTCAATTTAATCAAATTC
1 ACATTCAATTTAATAAAATTC
*
59536746 AAATTC
1 ACATTC
59536752 TAGGAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (21 bp):
ACATTCAATTTAATAAAATTC
Found at i:59542015 original size:40 final size:39
Alignment explanation
Indices: 59541978--59542069 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
59541968 GCTACTCGTT
*
59541978 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
59542018 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
59542057 CAAATGCCTTCGG
1 CAAATGCCTTCGG
59542070 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:59542049 original size:39 final size:40
Alignment explanation
Indices: 59541959--59542122 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
59541949 CGGAATTTAA
** *
59541959 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
59541999 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
59542038 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
59542078 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
59542118 CCGGA
1 CCGGA
59542123 CATCATTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:59546249 original size:17 final size:17
Alignment explanation
Indices: 59546216--59546250 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
59546206 GTATAAACAT
**
59546216 TGTTAAATTTATTATTA
1 TGTTAAATTTAAAATTA
59546233 TGTTAAATTTAAAATTA
1 TGTTAAATTTAAAATTA
59546250 T
1 T
59546251 CATGTTAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TGTTAAATTTAAAATTA
Found at i:59547806 original size:20 final size:19
Alignment explanation
Indices: 59547781--59547820 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
59547771 TTTTATTAAT
*
59547781 TTAAAATTTTTAAAAAAAA
1 TTAAAAATTTTAAAAAAAA
*
59547800 TTAAAAATTTTAAAAATAA
1 TTAAAAATTTTAAAAAAAA
59547819 TT
1 TT
59547821 TTACATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAAAATTTTAAAAAAAA
Found at i:59549242 original size:20 final size:20
Alignment explanation
Indices: 59549192--59549230 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
59549182 TGGAGTAGGA
*
59549192 ATATCGATACATTAAGAAAT
1 ATATCGATACCTTAAGAAAT
59549212 ATATCGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
59549231 AGTATTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:59564926 original size:35 final size:35
Alignment explanation
Indices: 59564868--59564962 Score: 86
Period size: 35 Copynumber: 2.7 Consensus size: 35
59564858 ATAAATTTAG
* **
59564868 TATAAATACAATTTAATTTATATTTT-ATTATTTGAT
1 TATAAATATAATTTAA-AAATATTTTGA-TATTTGAT
* *
59564904 T-TAAATATAATTTGTAAAATATTTTGATATTTTAT
1 TATAAATATAATTT-AAAAATATTTTGATATTTGAT
**
59564939 TATGGATATAATTTAAAAATATTT
1 TATAAATATAATTTAAAAATATTT
59564963 AAATTTTATT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
35 35 0.73
36 13 0.27
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (35 bp):
TATAAATATAATTTAAAAATATTTTGATATTTGAT
Found at i:59566290 original size:28 final size:28
Alignment explanation
Indices: 59566237--59566302 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
59566227 CAAATAATTT
* * **
59566237 TTTAAATAATTATAAAATATACAAAATCA
1 TTTAAA-ATTTATAAAAGATACAAAAGAA
*
59566266 TTTAAAATTTATAAAAGATATAAAAGAA
1 TTTAAAATTTATAAAAGATACAAAAGAA
59566294 TTTAAAATT
1 TTTAAAATT
59566303 ATTAAAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 26 0.81
29 6 0.19
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (28 bp):
TTTAAAATTTATAAAAGATACAAAAGAA
Found at i:59568030 original size:31 final size:31
Alignment explanation
Indices: 59567995--59568053 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
59567985 GCCAAGTGAC
59567995 TTAAATAAAAACTCTTT-AATAGTTTAGTTAT
1 TTAAATAAAAACT-TTTGAATAGTTTAGTTAT
**
59568026 TTAAATGGAAACTTTTGAATAGTTTAGT
1 TTAAATAAAAACTTTTGAATAGTTTAGT
59568054 GATCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (31 bp):
TTAAATAAAAACTTTTGAATAGTTTAGTTAT
Found at i:59568070 original size:31 final size:30
Alignment explanation
Indices: 59568003--59568062 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
59567993 ACTTAAATAA
* **
59568003 AAACTCTTTAATAGTTTAGTTATTTAAATGG
1 AAACT-TTTAATAGTTTAGTGATCAAAATGG
59568034 AAACTTTTGAATAGTTTAGTGATCAAAAT
1 AAACTTTT-AATAGTTTAGTGATCAAAAT
59568063 TGTAACTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (30 bp):
AAACTTTTAATAGTTTAGTGATCAAAATGG
Found at i:59568722 original size:114 final size:114
Alignment explanation
Indices: 59568553--59568768 Score: 353
Period size: 114 Copynumber: 1.9 Consensus size: 114
59568543 AAGATGGCAG
* *
59568553 CAACAAAACCATCTCTAAAACCACTTGCAAAAGCAAGACTACATGCAGAAGTAAGACTAAAAAAC
1 CAACAAAACCATCTCTAAAACCACTTGCAAAAACAAGACTACATGCAGAAATAAGACTAAAAAAC
*
59568618 ATGTCACAAGAGCAGA-ACAAAACTTCTAAAAGTGAAGTCTTATGGACAA
66 ATATCACAAGAGCAGACA-AAAACTTCTAAAAGTGAAGTCTTATGGACAA
* * *
59568667 CAACAAAGCCATCTCTAAAACCACTTGCAAAAATAAGACTACATGCATAAATAAGACTAAAAAAC
1 CAACAAAACCATCTCTAAAACCACTTGCAAAAACAAGACTACATGCAGAAATAAGACTAAAAAAC
*
59568732 ATATCACAAGAGCAGACAAAAACTTCTAAAATTGAAG
66 ATATCACAAGAGCAGACAAAAACTTCTAAAAGTGAAG
59568769 GCTTGTTAAA
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
114 93 0.99
115 1 0.01
ACGTcount: A:0.50, C:0.21, G:0.12, T:0.17
Consensus pattern (114 bp):
CAACAAAACCATCTCTAAAACCACTTGCAAAAACAAGACTACATGCAGAAATAAGACTAAAAAAC
ATATCACAAGAGCAGACAAAAACTTCTAAAAGTGAAGTCTTATGGACAA
Found at i:59569330 original size:24 final size:24
Alignment explanation
Indices: 59569303--59569354 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
59569293 TTCAATCTTT
59569303 ATATTAAAAA-AATTACAATTA-AAA
1 ATATTAAAAATAATT--AATTATAAA
59569327 ATA-TAAAAATAATTAATTATAAA
1 ATATTAAAAATAATTAATTATAAA
59569350 ATATT
1 ATATT
59569355 TCAATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 5 0.20
23 12 0.48
24 8 0.32
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
ATATTAAAAATAATTAATTATAAA
Found at i:59578280 original size:93 final size:93
Alignment explanation
Indices: 59578172--59578342 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
59578162 GCCCCTAAGT
* * *
59578172 GAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59578237 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
59578265 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59578330 CGAGTTCGGATGC
66 CGAGTTCGGATGC
59578343 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:59578339 original size:46 final size:46
Alignment explanation
Indices: 59578167--59578339 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
59578157 AAACCGCCCC
* * * *
59578167 TAAGTGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
59578213 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
59578261 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
59578306 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
59578340 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 60 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:59579208 original size:25 final size:25
Alignment explanation
Indices: 59579180--59579227 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
59579170 GAGCTTCCCG
59579180 ATTCACAGCTCGTGA-GAGCATACTA
1 ATTCACAGCTCGT-ATGAGCATACTA
*
59579205 ATTCATAGCTCGTATGAGCATAC
1 ATTCACAGCTCGTATGAGCATAC
59579228 ATGAATATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (25 bp):
ATTCACAGCTCGTATGAGCATACTA
Found at i:59589828 original size:16 final size:16
Alignment explanation
Indices: 59589807--59589838 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
59589797 GCCCAATAAC
*
59589807 CTAAACTACCAGCCCA
1 CTAAACTAACAGCCCA
59589823 CTAAACTAACAGCCCA
1 CTAAACTAACAGCCCA
59589839 TTACGCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.41, G:0.06, T:0.12
Consensus pattern (16 bp):
CTAAACTAACAGCCCA
Found at i:59590398 original size:22 final size:23
Alignment explanation
Indices: 59590354--59590401 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
59590344 AAAATACGAC
* * *
59590354 AAATATACGAAAATATAATATAA
1 AAATATAAGAAAATAAAAAATAA
59590377 AAATATAAG-AAATAAAAAATAA
1 AAATATAAGAAAATAAAAAATAA
59590399 AAA
1 AAA
59590402 AATTAGAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (23 bp):
AAATATAAGAAAATAAAAAATAA
Found at i:59601389 original size:72 final size:72
Alignment explanation
Indices: 59601177--59601656 Score: 586
Period size: 72 Copynumber: 6.5 Consensus size: 72
59601167 TAAGCCTTTT
* * **
59601177 AATTTTTGTTTTTC-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
*
59601241 GTAATTTT
65 GTAATTTC
*
59601249 AATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCT
1 AATTTCTGTT-TT---CAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCT
59601314 GAGGTAATTTC
62 GAGGTAATTTC
* * * *
59601325 AATTTCTGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
*
59601390 TATTTTC
66 TAATTTC
* * * *
59601397 AATTTCTGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
*
59601462 TATTTTC
66 TAATTTC
* ** *
59601469 AATTTCTGTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGC
1 AATTTCTGTTTTC--AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG---ACACGC
*
59601533 TGAGGTATTTTC
61 TGAGGTAATTTC
* ** *
59601545 AATTTCTGTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATG
1 AATTTCTG-TTTT--CAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTG
59601610 AGGTAATTTC
63 AGGTAATTTC
*
59601620 AATTTCTGTTTGTCAAGAATCAACTCATATTGCGAGA
1 AATTTCTGTTT-TCAAAAATCAACTCATATTGCGAGA
59601657 GGTGGGTTGA
Statistics
Matches: 368, Mismatches: 25, Indels: 29
0.87 0.06 0.07
Matches are distributed among these distances:
71 2 0.01
72 148 0.40
73 23 0.06
74 38 0.10
75 26 0.07
76 88 0.24
77 41 0.11
78 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (72 bp):
AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
TAATTTC
Found at i:59602059 original size:72 final size:73
Alignment explanation
Indices: 59601942--59602267 Score: 505
Period size: 73 Copynumber: 4.5 Consensus size: 73
59601932 TTTGAAAGAA
* * *
59601942 TCAACTCATATTGCGAGAAATAAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTG-TT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGCTT
59602006 TTCAAAAT
66 TTCAAAAT
*
59602014 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTATGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGCTT
59602079 TTCAAAAT
66 TTCAAAAT
*
59602087 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTATGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGCTT
59602152 TTCAAAAT
66 TTCAAAAT
** * *
59602160 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTG-TT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGCTT
* *
59602224 GTCAAAAAAA
66 TTC--AAAAT
59602234 TCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCA
1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA
59602268 GTTCACATGT
Statistics
Matches: 238, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
72 62 0.26
73 143 0.60
74 33 0.14
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (73 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGCTT
TTCAAAAT
Found at i:59603006 original size:16 final size:16
Alignment explanation
Indices: 59602985--59603016 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
59602975 GCCCAATAAC
59602985 CTAAACTACCAGCCCA
1 CTAAACTACCAGCCCA
*
59603001 CTAAACTATCAGCCCA
1 CTAAACTACCAGCCCA
59603017 TTACACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.41, G:0.06, T:0.16
Consensus pattern (16 bp):
CTAAACTACCAGCCCA
Found at i:59603576 original size:22 final size:23
Alignment explanation
Indices: 59603532--59603579 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
59603522 AAAATACGAC
* * *
59603532 AAATATACGAAAATATAATATAA
1 AAATATAAGAAAATAAAAAATAA
59603555 AAATATAAG-AAATAAAAAATAA
1 AAATATAAGAAAATAAAAAATAA
59603577 AAA
1 AAA
59603580 AAATTAGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (23 bp):
AAATATAAGAAAATAAAAAATAA
Found at i:59604237 original size:16 final size:15
Alignment explanation
Indices: 59604204--59604246 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
59604194 GTTACTATTA
59604204 TATTTATTATTATAT
1 TATTTATTATTATAT
59604219 TATTTATT-TTCACTAT
1 TATTTATTATT-A-TAT
59604235 TA-TTATTATTAT
1 TATTTATTATTAT
59604247 TTTCATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.12
15 15 0.60
16 7 0.28
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTATTATTATAT
Found at i:59604246 original size:21 final size:21
Alignment explanation
Indices: 59604211--59604261 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
59604201 TTATATTTAT
59604211 TATTA-TATTATTTATTTTCA
1 TATTATTATTATTTATTTTCA
59604231 CTATTATTATTA-TTATTTTCA
1 -TATTATTATTATTTATTTTCA
59604252 TCATTATTAT
1 T-ATTATTAT
59604262 ACATATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 1 0.04
21 22 0.79
22 5 0.18
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTATTATTATTTATTTTCA
Found at i:59614079 original size:30 final size:30
Alignment explanation
Indices: 59614043--59614103 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
59614033 AACAATTATC
*
59614043 ATAATTACTCCATATCTATTGTCCAAAAAA
1 ATAATTACTCCATATATATTGTCCAAAAAA
59614073 ATAATTACTCCATATATATTGTCCAAAAAA
1 ATAATTACTCCATATATATTGTCCAAAAAA
59614103 A
1 A
59614104 CCACCCCACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (30 bp):
ATAATTACTCCATATATATTGTCCAAAAAA
Found at i:59621695 original size:18 final size:18
Alignment explanation
Indices: 59621672--59621759 Score: 131
Period size: 18 Copynumber: 4.9 Consensus size: 18
59621662 CCGTTTATGG
59621672 TACTATTCACGTATACGA
1 TACTATTCACGTATACGA
*
59621690 TACTATTCACGTATACAA
1 TACTATTCACGTATACGA
*
59621708 TACTATTCACATATACGA
1 TACTATTCACGTATACGA
* *
59621726 CACTATTCACGTATACGG
1 TACTATTCACGTATACGA
*
59621744 TACTGTTCACGTATAC
1 TACTATTCACGTATAC
59621760 AGTAGTTGGG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (18 bp):
TACTATTCACGTATACGA
Found at i:59626636 original size:21 final size:21
Alignment explanation
Indices: 59626612--59626651 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
59626602 TGATAGGAAG
59626612 GTAGATGAGTTGAACAAAACA
1 GTAGATGAGTTGAACAAAACA
59626633 GTAGATGAGTTGAACAAAA
1 GTAGATGAGTTGAACAAAA
59626652 AGGCATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.25, T:0.20
Consensus pattern (21 bp):
GTAGATGAGTTGAACAAAACA
Found at i:59628209 original size:19 final size:20
Alignment explanation
Indices: 59628185--59628226 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
59628175 TCCAAACATC
59628185 AAAAGTAAATCA-TTTCCAG
1 AAAAGTAAATCATTTTCCAG
59628204 AAAAGTAAATCATTTTCCAG
1 AAAAGTAAATCATTTTCCAG
59628224 AAA
1 AAA
59628227 TCATTTTCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAAGTAAATCATTTTCCAG
Found at i:59628229 original size:14 final size:14
Alignment explanation
Indices: 59628210--59628247 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
59628200 CCAGAAAAGT
59628210 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
59628224 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
59628238 AAAACATTTT
1 AAATCATTTT
59628248 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:59628737 original size:31 final size:31
Alignment explanation
Indices: 59628702--59628784 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
59628692 AAAATTTAAA
*
59628702 AATTTAAAAAGTA-CAGTGATTAAAATTGATC
1 AATTTAAAAAGTATAAG-GATTAAAATTGATC
*
59628733 AATTTCAAAAGTATAAGGATTAAAATTGATC
1 AATTTAAAAAGTATAAGGATTAAAATTGATC
* *
59628764 AAATT-AAAA-TATAAAGATTAA
1 AATTTAAAAAGTATAAGGATTAA
59628785 TTCCACAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 11 0.23
30 4 0.09
31 30 0.64
32 2 0.04
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.31
Consensus pattern (31 bp):
AATTTAAAAAGTATAAGGATTAAAATTGATC
Found at i:59629075 original size:23 final size:22
Alignment explanation
Indices: 59629049--59629094 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
59629039 TTTGATATTA
*
59629049 TGTTTTGATATAACAAATTAAAG
1 TGTTTTGAAATAA-AAATTAAAG
* *
59629072 TGTTTTTAAATAAAAGTTAAAG
1 TGTTTTGAAATAAAAATTAAAG
59629094 T
1 T
59629095 TAAAAACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.41
Consensus pattern (22 bp):
TGTTTTGAAATAAAAATTAAAG
Found at i:59635297 original size:12 final size:12
Alignment explanation
Indices: 59635280--59635309 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
59635270 ACGAGATGAA
59635280 AATAATGATAAT
1 AATAATGATAAT
59635292 AATAATGATAAT
1 AATAATGATAAT
59635304 AATAAT
1 AATAAT
59635310 AATATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (12 bp):
AATAATGATAAT
Found at i:59635341 original size:3 final size:3
Alignment explanation
Indices: 59635280--59635321 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
59635270 ACGAGATGAA
* *
59635280 AAT AAT GAT AAT AAT AAT GAT AAT AAT AAT AAT -AT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
59635322 ATGTATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:59635405 original size:3 final size:3
Alignment explanation
Indices: 59635397--59635507 Score: 84
Period size: 3 Copynumber: 37.7 Consensus size: 3
59635387 GGAAAACAAT
* * * * *
59635397 ATA ATA ATA ATA GTA GTA GTA AT- ACA ATA GTA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
59635443 ATA AAA ATA ATA ATA GTG ATGA A-A ATA ATA ATA ATA GTA ATA AAA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* *
59635488 ATA ATA ATA GTT ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
59635508 GACACATATG
Statistics
Matches: 84, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
2 5 0.06
3 78 0.93
4 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:59635469 original size:18 final size:19
Alignment explanation
Indices: 59635428--59635503 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 19
59635418 ATACAATAGT
* *
59635428 AATAATAATAATAAAATAAA
1 AATAATAATAGTAATA-AAA
*
59635448 AATAATAATAGTGATGAAAA
1 AATAATAATAGTAAT-AAAA
59635468 TAATAATAATAGTAAT-AAA
1 -AATAATAATAGTAATAAAA
*
59635487 AATAATAATAGTTATAA
1 AATAATAATAGTAATAA
59635504 TAATGACACA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
18 14 0.29
19 4 0.08
20 15 0.31
21 15 0.31
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (19 bp):
AATAATAATAGTAATAAAA
Found at i:59635474 original size:21 final size:21
Alignment explanation
Indices: 59635399--59635496 Score: 97
Period size: 23 Copynumber: 4.5 Consensus size: 21
59635389 AAAACAATAT
* *
59635399 AATAATAATAGTAGTAGTAATA
1 AATAATAATAATAGTAATAA-A
* *
59635421 CAATAGTAATAATAATAATAAAA
1 -AATAATAATAATAGTAAT-AAA
* * *
59635444 TAAAAATAATAATAGTGATGAA
1 -AATAATAATAATAGTAATAAA
59635466 AATAATAATAATAGTAATAAA
1 AATAATAATAATAGTAATAAA
59635487 AATAATAATA
1 AATAATAATA
59635497 GTTATAATAA
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
21 28 0.46
22 2 0.03
23 29 0.48
24 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (21 bp):
AATAATAATAATAGTAATAAA
Found at i:59637314 original size:44 final size:44
Alignment explanation
Indices: 59637266--59637415 Score: 144
Period size: 44 Copynumber: 3.4 Consensus size: 44
59637256 CGATTCACAT
* *
59637266 CTTCAATCTGCCCCACTGCAACTTTAGAGAGATACGATTTGTAA
1 CTTCAATCTGCTCCACTGCAACTTTAGAGAGATAAGATTTGTAA
* * * * *
59637310 CTTCAA-CTTGCTCCACTGGAACATCA-AGGAGATAAGATTCGCTAT
1 CTTCAATC-TGCTCCACTGCAACTTTAGA-GAGATAAGATTTG-TAA
* * *
59637355 CTTCAATGTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAA
1 CTTCAATCTGCTCCACTGCAACTTTAGAGAGATAAGATTTGTAA
*
59637399 TTTCAA-CTTGCTCCACT
1 CTTCAATC-TGCTCCACT
59637416 ACTGCTTAGG
Statistics
Matches: 83, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
43 2 0.02
44 47 0.57
45 34 0.41
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTTAGAGAGATAAGATTTGTAA
Found at i:59637368 original size:45 final size:44
Alignment explanation
Indices: 59637232--59637415 Score: 137
Period size: 44 Copynumber: 4.2 Consensus size: 44
59637222 CTTCGATCTA
* * ** *
59637232 CTCCACTGTAACTTCAGGGAGATTCGATTCAC-ATCTTCAATCTG
1 CTCCACTGCAACTTCAAGGAGATAAGATTCGCTATCTTCAAT-TG
* * * * *
59637276 CCCCACTGCAACTT-TAGAGAGATACGATTTG-TAACTTCAACTTG
1 CTCCACTGCAACTTCAAG-GAGATAAGATTCGCTATCTTCAA-TTG
* *
59637320 CTCCACTGGAACATCAAGGAGATAAGATTCGCTATCTTCAATGTG
1 CTCCACTGCAACTTCAAGGAGATAAGATTCGCTATCTTCAAT-TG
* *
59637365 CTCCACTGCAACTTTAGGGAGATAAGACTT-G-TAAT-TTCAACTTG
1 CTCCACTGCAACTTCAAGGAGATAAGA-TTCGCT-ATCTTCAA-TTG
59637409 CTCCACT
1 CTCCACT
59637416 ACTGCTTAGG
Statistics
Matches: 112, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
43 1 0.01
44 69 0.62
45 40 0.36
46 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
CTCCACTGCAACTTCAAGGAGATAAGATTCGCTATCTTCAATTG
Found at i:59637387 original size:89 final size:88
Alignment explanation
Indices: 59637232--59637415 Score: 251
Period size: 89 Copynumber: 2.1 Consensus size: 88
59637222 CTTCGATCTA
* * * **
59637232 CTCCACTGTAACTTCAGGGAGATTCGATTCACATCTTCAATCTGCCCCACTGCAACTTTAGAGAG
1 CTCCACTGGAACATCAAGGAGATAAGATTCACATCTTCAATCTGCCCCACTGCAACTTTAGAGAG
* *
59637297 ATACGATTTGTAACTTCAACTTG
66 ATAAGACTTGTAACTTCAACTTG
* * * *
59637320 CTCCACTGGAACATCAAGGAGATAAGATTCGCTATCTTCAATGTGCTCCACTGCAACTTTAGGGA
1 CTCCACTGGAACATCAAGGAGATAAGATTCAC-ATCTTCAATCTGCCCCACTGCAACTTTAGAGA
*
59637385 GATAAGACTTGTAATTTCAACTTG
65 GATAAGACTTGTAACTTCAACTTG
59637409 CTCCACT
1 CTCCACT
59637416 ACTGCTTAGG
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
88 26 0.31
89 57 0.69
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (88 bp):
CTCCACTGGAACATCAAGGAGATAAGATTCACATCTTCAATCTGCCCCACTGCAACTTTAGAGAG
ATAAGACTTGTAACTTCAACTTG
Found at i:59637521 original size:45 final size:44
Alignment explanation
Indices: 59637457--59637789 Score: 216
Period size: 45 Copynumber: 7.5 Consensus size: 44
59637447 TTTGCTTCAT
* * * *
59637457 TGCAATTTCAGAGAGACAAGATTTGCCGTCTTCGATCTGTTCCAC
1 TGCAACTTCAGGGAGACAAGATCTG-CGTCTTCGATCTGCTCCAC
* * *
59637502 TGCAACTTCAGGGAGACAAGATCTGCAATCTTC-AGCCTACTCCAC
1 TGCAACTTCAGGGAGACAAGATCTGC-GTCTTCGA-TCTGCTCCAC
* ** * * * **
59637547 TACTGCTT-AGGGAGATAGGATGTTG-G-CTTAAATCTGCTCCAC
1 TGCAACTTCAGGGAGACAAGAT-CTGCGTCTTCGATCTGCTCCAC
* **
59637589 TGCAACTTCAGAGAGACAAGAT-TCGCCGTCTTCGATCTATTCCAC
1 TGCAACTTCAGGGAGACAAGATCT-G-CGTCTTCGATCTGCTCCAC
* * * *
59637634 TGTAACTTCAGGGAGACAAGATCTGCAATCTTC-AGCCTACTCCAC
1 TGCAACTTCAGGGAGACAAGATCTGC-GTCTTCGA-TCTGCTCCAC
* * * ** *
59637679 TACAACTT-AGGGAGATAAGATGGTG-G-CTTAAATCTGCTTCAC
1 TGCAACTTCAGGGAGACAAGAT-CTGCGTCTTCGATCTGCTCCAC
* ** *
59637721 TGCAACTTCAGGAAGACAAGATCCACTGTCTTCGATCTGCTCCAT
1 TGCAACTTCAGGGAGACAAGATCTGC-GTCTTCGATCTGCTCCAC
*
59637766 TGCAACTTTAGGGAGACAAGATCT
1 TGCAACTTCAGGGAGACAAGATCT
59637790 ACAATCTTCA
Statistics
Matches: 216, Mismatches: 54, Indels: 36
0.71 0.18 0.12
Matches are distributed among these distances:
41 1 0.00
42 34 0.16
43 23 0.11
44 29 0.13
45 128 0.59
46 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (44 bp):
TGCAACTTCAGGGAGACAAGATCTGCGTCTTCGATCTGCTCCAC
Found at i:59637577 original size:132 final size:132
Alignment explanation
Indices: 59637354--59637959 Score: 788
Period size: 132 Copynumber: 4.6 Consensus size: 132
59637344 AGATTCGCTA
* * * * * * * *
59637354 TCTTCAATGTGCTCCACTGCAACTTTAGGGAGATAAGA-CTTGTAAT-TTCAACTTGCTCCACTA
1 TCTTCGATCTGCTCCACTGCAACTTCAGGGAGACAAGATC-TGCAATCTTCAGCCTACTCCACTA
* * * *
59637417 CTGCTTAGGGAGATAGGATGGTGGCTTAAATTTGCTTCATTGCAATTTCA-GAGAGACAAGATTT
65 CTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGA-AGACAAGATTC
*
59637481 GCCG
129 ACCG
*
59637485 TCTTCGATCTGTTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTACTCCACTAC
1 TCTTCGATCTGCTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTACTCCACTAC
* * *
59637550 TGCTTAGGGAGATAGGATGTTGGCTTAAATCTGCTCCACTGCAACTTCA-GAGAGACAAGATTCG
66 TGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGA-AGACAAGATTCA
59637614 CCG
130 CCG
** *
59637617 TCTTCGATCTATTCCACTGTAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTACTCCACTAC
1 TCTTCGATCTGCTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTACTCCACTAC
** * *
59637682 AACTTAGGGAGATAAGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGACAAGATCCAC
66 TGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGACAAGATTCAC
*
59637747 TG
131 CG
* * * *
59637749 TCTTCGATCTGCTCCATTGCAACTTTAGGGAGACAAGATCTACAATCTTCAGCCTACTCTACTAC
1 TCTTCGATCTGCTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTACTCCACTAC
** * * * *
59637814 AACTTAGGAAGATAGGATGGTTGCTTAAATCTTCTTCACTGCAACTTTAGGAAGACAAGATTCAC
66 TGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGACAAGATTCAC
*
59637879 CA
131 CG
* * * * *
59637881 TCTTTGATCTGCTCCACTGTAACTTCAGGGAGACAATACCTACAATCTTCAGCCTACTCCACTAC
1 TCTTCGATCTGCTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTACTCCACTAC
59637946 TGCTTAGGGAGATA
66 TGCTTAGGGAGATA
59637960 AGGCTTGTGA
Statistics
Matches: 422, Mismatches: 50, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
131 38 0.09
132 382 0.91
133 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
TCTTCGATCTGCTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTACTCCACTAC
TGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGACAAGATTCAC
CG
Found at i:59637798 original size:45 final size:45
Alignment explanation
Indices: 59637578--59637930 Score: 143
Period size: 45 Copynumber: 8.0 Consensus size: 45
59637568 GTTGGCTTAA
* * **
59637578 ATCTGCTCCACTGCAACTTCA-GAGAGACAAGATTCGCCGTCTTCG
1 ATCTGCTCCACTGCAACTTCAGGA-AGACAAGATCCACAATCTTCG
** * * **
59637623 ATCTATTCCACTGTAACTTCAGGGAGACAAGATCTGCAATCTTC-
1 ATCTGCTCCACTGCAACTTCAGGAAGACAAGATCCACAATCTTCG
* * * * * ***** **
59637667 AGCCTACTCCACTACAACTT-AGGGAGATAAGAT--GGTGGCTTAA
1 A-TCTGCTCCACTGCAACTTCAGGAAGACAAGATCCACAATCTTCG
* **
59637710 ATCTGCTTCACTGCAACTTCAGGAAGACAAGATCCACTGTCTTCG
1 ATCTGCTCCACTGCAACTTCAGGAAGACAAGATCCACAATCTTCG
* * * *
59637755 ATCTGCTCCATTGCAACTTTAGGGAGACAAGATCTACAATCTTC-
1 ATCTGCTCCACTGCAACTTCAGGAAGACAAGATCCACAATCTTCG
* * * * * * *** **
59637799 AGCCTACTCTACTACAACTT-AGGAAGATAGGAT---GGTTGCTTAA
1 A-TCTGCTCCACTGCAACTTCAGGAAGACAAGATCCACAAT-CTTCG
* * * * * *
59637842 ATCTTCTTCACTGCAACTTTAGGAAGACAAGATTCACCATCTTTG
1 ATCTGCTCCACTGCAACTTCAGGAAGACAAGATCCACAATCTTCG
* * *
59637887 ATCTGCTCCACTGTAACTTCAGGGAGACAATA-CCTACAATCTTC
1 ATCTGCTCCACTGCAACTTCAGGAAGACAAGATCC-ACAATCTTC
59637931 AGCCTACTCC
Statistics
Matches: 225, Mismatches: 69, Indels: 28
0.70 0.21 0.09
Matches are distributed among these distances:
41 1 0.00
42 34 0.15
43 24 0.11
44 25 0.11
45 139 0.62
46 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (45 bp):
ATCTGCTCCACTGCAACTTCAGGAAGACAAGATCCACAATCTTCG
Found at i:59638135 original size:64 final size:64
Alignment explanation
Indices: 59638034--59638158 Score: 223
Period size: 64 Copynumber: 2.0 Consensus size: 64
59638024 TCATGTATCT
*
59638034 ATGCTTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAGATATG
1 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATATG
* *
59638098 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTTCTAACTAGAT
1 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGAT
59638159 GTATTATTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATATG
Found at i:59642065 original size:19 final size:19
Alignment explanation
Indices: 59642041--59642086 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
59642031 ATGAAAGTTT
59642041 AATGCAAAT-AATGCAATG
1 AATGCAAATGAATGCAATG
* *
59642059 CAATGCAAATGCATGGAATG
1 -AATGCAAATGAATGCAATG
59642079 AATGCAAA
1 AATGCAAA
59642087 AGAAAGGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.48, C:0.13, G:0.20, T:0.20
Consensus pattern (19 bp):
AATGCAAATGAATGCAATG
Found at i:59645354 original size:12 final size:12
Alignment explanation
Indices: 59645337--59645366 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
59645327 ACGAGATGAA
59645337 AATAATGATAAT
1 AATAATGATAAT
59645349 AATAATGATAAT
1 AATAATGATAAT
59645361 AATAAT
1 AATAAT
59645367 AATATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (12 bp):
AATAATGATAAT
Found at i:59645398 original size:3 final size:3
Alignment explanation
Indices: 59645337--59645378 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
59645327 ACGAGATGAA
* *
59645337 AAT AAT GAT AAT AAT AAT GAT AAT AAT AAT AAT -AT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
59645379 ATGTATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:59645409 original size:23 final size:23
Alignment explanation
Indices: 59645383--59645427 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
59645373 AAATAAATGT
*
59645383 ATTTAAAATAATAATATTAACTC
1 ATTTAAAATAATAATAATAACTC
* *
59645406 ATTTGATATAATAATAATAACT
1 ATTTAAAATAATAATAATAACT
59645428 TATGTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTTAAAATAATAATAATAACTC
Found at i:59645465 original size:3 final size:3
Alignment explanation
Indices: 59645457--59645567 Score: 84
Period size: 3 Copynumber: 37.7 Consensus size: 3
59645447 GGAAAACAAT
* * * * *
59645457 ATA ATA ATA ATA GTA GTA GTA AT- ACA ATA GTA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
59645503 ATA AAA ATA ATA ATA GTG ATGA A-A ATA ATA ATA ATA GTA ATA AAA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* *
59645548 ATA ATA ATA GTT ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
59645568 GACACATATG
Statistics
Matches: 84, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
2 5 0.06
3 78 0.93
4 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:59645529 original size:18 final size:19
Alignment explanation
Indices: 59645488--59645563 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 19
59645478 ATACAATAGT
* *
59645488 AATAATAATAATAAAATAAA
1 AATAATAATAGTAATA-AAA
*
59645508 AATAATAATAGTGATGAAAA
1 AATAATAATAGTAAT-AAAA
59645528 TAATAATAATAGTAAT-AAA
1 -AATAATAATAGTAATAAAA
*
59645547 AATAATAATAGTTATAA
1 AATAATAATAGTAATAA
59645564 TAATGACACA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
18 14 0.29
19 4 0.08
20 15 0.31
21 15 0.31
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (19 bp):
AATAATAATAGTAATAAAA
Found at i:59645534 original size:21 final size:21
Alignment explanation
Indices: 59645459--59645556 Score: 97
Period size: 23 Copynumber: 4.5 Consensus size: 21
59645449 AAAACAATAT
* *
59645459 AATAATAATAGTAGTAGTAATA
1 AATAATAATAATAGTAATAA-A
* *
59645481 CAATAGTAATAATAATAATAAAA
1 -AATAATAATAATAGTAAT-AAA
* * *
59645504 TAAAAATAATAATAGTGATGAA
1 -AATAATAATAATAGTAATAAA
59645526 AATAATAATAATAGTAATAAA
1 AATAATAATAATAGTAATAAA
59645547 AATAATAATA
1 AATAATAATA
59645557 GTTATAATAA
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
21 28 0.46
22 2 0.03
23 29 0.48
24 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (21 bp):
AATAATAATAATAGTAATAAA
Found at i:59647244 original size:61 final size:61
Alignment explanation
Indices: 59647169--59647289 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 61
59647159 TAAAATTTGT
*
59647169 GTGCTATTGCAATTTAGCCCGCGCCTAAACTCTGCTTTTTAGGATCTGGAATATTTCCAAG
1 GTGCTATTGCAATTTAGCCCGCGCCTAAACTCTGCGTTTTAGGATCTGGAATATTTCCAAG
59647230 GTGCTATTGCAATTTAGCCCGCGCCTAAACTCTGCGTTTTAGGATCTGGAATATTTCCAA
1 GTGCTATTGCAATTTAGCCCGCGCCTAAACTCTGCGTTTTAGGATCTGGAATATTTCCAA
59647290 TTCTGATCCC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (61 bp):
GTGCTATTGCAATTTAGCCCGCGCCTAAACTCTGCGTTTTAGGATCTGGAATATTTCCAAG
Found at i:59649307 original size:23 final size:23
Alignment explanation
Indices: 59649277--59649322 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
59649267 AGTGGGAGTA
*
59649277 AGAAACTATGCTTTCGTGAGGTT
1 AGAAACTATGCTTTCATGAGGTT
59649300 AGAAACTATGCTTTCATGAGGTT
1 AGAAACTATGCTTTCATGAGGTT
59649323 TTCACCTCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (23 bp):
AGAAACTATGCTTTCATGAGGTT
Found at i:59654233 original size:25 final size:25
Alignment explanation
Indices: 59654205--59654264 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
59654195 CAATGAAATG
*
59654205 CATTCTTTTTTAGTAAATATTCTTT
1 CATTCTTTTTGAGTAAATATTCTTT
*
59654230 CATTCCTTTTGAGTAAATATTCTTT
1 CATTCTTTTTGAGTAAATATTCTTT
*
59654255 CGTTCTTTTT
1 CATTCTTTTT
59654265 ATATTCTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.58
Consensus pattern (25 bp):
CATTCTTTTTGAGTAAATATTCTTT
Found at i:59655744 original size:14 final size:14
Alignment explanation
Indices: 59655721--59655759 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
59655711 AGAGAGATTG
59655721 AAAT-AAAAAAGAA
1 AAATAAAAAAAGAA
59655734 AAATAAAAAAAGAA
1 AAATAAAAAAAGAA
59655748 AAATTAAAAAAA
1 AAA-TAAAAAAA
59655760 TAATTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 4 0.17
14 12 0.50
15 8 0.33
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (14 bp):
AAATAAAAAAAGAA
Found at i:59655756 original size:12 final size:12
Alignment explanation
Indices: 59655727--59655792 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
59655717 ATTGAAATAA
*
59655727 AAAAGAAAAATAAA
1 AAAAGAAAAAT--T
59655741 AAAAGAAAAATT
1 AAAAGAAAAATT
59655753 AAAA-AAATAATT
1 AAAAGAAA-AATT
**
59655765 AAAATTAAAATT
1 AAAAGAAAAATT
**
59655777 AAAATTAAAATT
1 AAAAGAAAAATT
59655789 AAAA
1 AAAA
59655793 TTAAAATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
11 3 0.06
12 32 0.67
13 2 0.04
14 11 0.23
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (12 bp):
AAAAGAAAAATT
Done.