Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 68 of 206
Found at i:19171624 original size:16 final size:16
Alignment explanation
Indices: 19171586--19171627 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
19171576 TTTATAACAT
19171586 TTTTATAAAAATTTAAA
1 TTTT-TAAAAATTTAAA
**
19171603 AATTTAAAAATTTAAA
1 TTTTTAAAAATTTAAA
19171619 TTTTTAAAA
1 TTTTTAAAA
19171628 GAAATTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 19 0.90
17 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTTTAAAAATTTAAA
Found at i:19178510 original size:14 final size:14
Alignment explanation
Indices: 19178468--19178503 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
19178458 ATTGCTTTCG
19178468 TAAAGAGTATACAA
1 TAAAGAGTATACAA
19178482 TAAAGAGTATACAA
1 TAAAGAGTATACAA
19178496 TAAAGAGT
1 TAAAGAGT
19178504 TTTCAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (14 bp):
TAAAGAGTATACAA
Found at i:19180615 original size:37 final size:35
Alignment explanation
Indices: 19180572--19180669 Score: 91
Period size: 37 Copynumber: 2.9 Consensus size: 35
19180562 TAATATTATT
*
19180572 TTAATAGTTTAATATTAAATTTAATTTAATACTTA
1 TTAATAGTTTAATATTAAATTTAATTTAATACTGA
* *
19180607 TCTCAATAGTATT-TTATT-AATTTAATATTAA-AGTGA
1 T-T-AATAGT-TTAATATTAAATTTAAT-TTAATACTGA
19180643 TT-AT-G-TTAATATTAAATTTAATTTAAT
1 TTAATAGTTTAATATTAAATTTAATTTAAT
19180670 GTATTCTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
30 2 0.04
31 8 0.15
32 9 0.17
33 2 0.04
35 2 0.04
36 13 0.25
37 14 0.27
38 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (35 bp):
TTAATAGTTTAATATTAAATTTAATTTAATACTGA
Found at i:19183925 original size:20 final size:19
Alignment explanation
Indices: 19183892--19183959 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
19183882 GCATCATAGA
19183892 TGCATAACAGAGGCACTGAAG
1 TGCA-AACAGAGGCAC-GAAG
*
19183913 TGCAAACAAAGGCACGAATG
1 TGCAAACAGAGGCACGAA-G
* *
19183933 TGCGATCAGAGGCACCGAAG
1 TGCAAACAGAGGCA-CGAAG
*
19183953 CGCAAAC
1 TGCAAAC
19183960 CAAGACACCA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.08
20 27 0.71
21 8 0.21
ACGTcount: A:0.38, C:0.24, G:0.28, T:0.10
Consensus pattern (19 bp):
TGCAAACAGAGGCACGAAG
Found at i:19199952 original size:50 final size:49
Alignment explanation
Indices: 19199898--19200069 Score: 141
Period size: 50 Copynumber: 3.4 Consensus size: 49
19199888 CAAAGCCATG
* * *
19199898 TCCCAGACATGGTCTTACATGAGATGTTTTCTTGTAC-TGCCAATGTCATA
1 TCCCAGACATGGTCTTACATG-GATGTTCTCATAT-CGTGCCAATGTCATA
* * * *
19199948 TCCCAGATATGGTCTTACATGGGTGTTCTCATATCGGTGCCCATGTCATG
1 TCCCAGACATGGTCTTACATGGATGTTCTCATATC-GTGCCAATGTCATA
** ** ** * * *
19199998 TCCCAGACATGGTCTTACGGGGGA-CCTCTCATCCCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTAC-ATGGATGTTCTCATATC-GTGCCAATGTCATA
19200048 TCCCAGACATGGTCTTACATGG
1 TCCCAGACATGGTCTTACATGG
19200070 GACCTCTCAT
Statistics
Matches: 99, Mismatches: 20, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
48 1 0.01
49 11 0.11
50 85 0.86
51 2 0.02
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (49 bp):
TCCCAGACATGGTCTTACATGGATGTTCTCATATCGTGCCAATGTCATA
Found at i:19200072 original size:50 final size:50
Alignment explanation
Indices: 19199935--19200132 Score: 207
Period size: 50 Copynumber: 3.8 Consensus size: 50
19199925 TTTCTTGTAC
* * *** **
19199935 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGTGTTCTCATATCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCCCGG
* **
19199985 TGCCCATGTCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCCCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCCCGG
* * *
19200035 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT--CC-C---GG
* *
19200091 TGCCAATTTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCT
19200133 TTACCCAAAT
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 80 0.66
52 2 0.02
53 1 0.01
56 39 0.32
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCCCGG
Found at i:19207552 original size:14 final size:14
Alignment explanation
Indices: 19207533--19207561 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19207523 AAATTATGGT
19207533 TTCATATTCTACTC
1 TTCATATTCTACTC
19207547 TTCATATTCTACTC
1 TTCATATTCTACTC
19207561 T
1 T
19207562 ATGAGACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.52
Consensus pattern (14 bp):
TTCATATTCTACTC
Found at i:19208115 original size:47 final size:47
Alignment explanation
Indices: 19208059--19208153 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
19208049 ATTAAATATA
19208059 AATGGTTCTATTTATATTTCATTATATATATAAATATTTATTTATTT
1 AATGGTTCTATTTATATTTCATTATATATATAAATATTTATTTATTT
19208106 AATGGTTCTATTTATATTTCATTATATATATAAATATTTATTTATTT
1 AATGGTTCTATTTATATTTCATTATATATATAAATATTTATTTATTT
19208153 A
1 A
19208154 TATTTATCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (47 bp):
AATGGTTCTATTTATATTTCATTATATATATAAATATTTATTTATTT
Found at i:19214010 original size:14 final size:14
Alignment explanation
Indices: 19213991--19214030 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
19213981 TTGATAGTGT
*
19213991 CTTCAAATTTTAGC
1 CTTCAAATTTTACC
19214005 CTTCAAATTTTACC
1 CTTCAAATTTTACC
*
19214019 CTTAAAATTTTA
1 CTTCAAATTTTA
19214031 ACATTGATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (14 bp):
CTTCAAATTTTACC
Found at i:19220078 original size:27 final size:27
Alignment explanation
Indices: 19220027--19220078 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
19220017 AAGCATACTC
*
19220027 CAAACAAAAAGAGTAAAAAACAAGAGT
1 CAAACAAAAAGAGTAAAAAAAAAGAGT
*
19220054 CAAACAAATAGAG-AAACAAAAAAGA
1 CAAACAAAAAGAGTAAA-AAAAAAGA
19220079 AAATAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.69, C:0.12, G:0.13, T:0.06
Consensus pattern (27 bp):
CAAACAAAAAGAGTAAAAAAAAAGAGT
Found at i:19222143 original size:2 final size:2
Alignment explanation
Indices: 19222138--19222175 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
19222128 TGAGTGGGGC
19222138 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA T- TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19222176 GTGTGGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:19222162 original size:19 final size:17
Alignment explanation
Indices: 19222140--19222175 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
19222130 AGTGGGGCTA
19222140 TATATATATATATATATAT
1 TATATATAT-TAT-TATAT
19222159 TATATATATTATTATAT
1 TATATATATTATTATAT
19222176 GTGTGGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATATATTATTATAT
Found at i:19224947 original size:14 final size:14
Alignment explanation
Indices: 19224930--19224966 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
19224920 TCACTAGATT
19224930 CGATTCAACCAATG
1 CGATTCAACCAATG
19224944 CGATTCAACCAATG
1 CGATTCAACCAATG
*
19224958 CGGTTCAAC
1 CGATTCAAC
19224967 TGGACCCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (14 bp):
CGATTCAACCAATG
Found at i:19225684 original size:18 final size:18
Alignment explanation
Indices: 19225663--19225702 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
19225653 AAGAAAGTTA
19225663 TTTTAGCTCTTAATTAAT
1 TTTTAGCTCTTAATTAAT
* *
19225681 TTTTCGTTCTTAATTAAT
1 TTTTAGCTCTTAATTAAT
19225699 TTTT
1 TTTT
19225703 CGTTCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTTAGCTCTTAATTAAT
Found at i:19225719 original size:18 final size:18
Alignment explanation
Indices: 19225670--19225709 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
19225660 TTATTTTAGC
19225670 TCTTAATTAATTTTTCGT
1 TCTTAATTAATTTTTCGT
19225688 TCTTAATTAATTTTTCGT
1 TCTTAATTAATTTTTCGT
19225706 TCTT
1 TCTT
19225710 TTTTACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.62
Consensus pattern (18 bp):
TCTTAATTAATTTTTCGT
Found at i:19226205 original size:28 final size:29
Alignment explanation
Indices: 19226173--19226234 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 29
19226163 AATTCTTTTT
19226173 AAAATA-ATACAAATTTTGTAAAAA-ATTA
1 AAAATATATA-AAATTTTGTAAAAATATTA
*
19226201 AAAATATTTAAAATTTTGTAAAAATTATTA
1 AAAATATATAAAATTTTGTAAAAA-TATTA
19226231 AAAA
1 AAAA
19226235 CTCTAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 20 0.67
29 2 0.07
30 8 0.27
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATATATAAAATTTTGTAAAAATATTA
Found at i:19234593 original size:13 final size:13
Alignment explanation
Indices: 19234575--19234608 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
19234565 ATATTAATTT
19234575 TAAAAAAGAATAA
1 TAAAAAAGAATAA
*
19234588 TAAAAAATAATAA
1 TAAAAAAGAATAA
19234601 TAAAAAAG
1 TAAAAAAG
19234609 GAAAATCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (13 bp):
TAAAAAAGAATAA
Found at i:19235385 original size:17 final size:17
Alignment explanation
Indices: 19235344--19235385 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
19235334 AAGGCTAGAG
19235344 AAAAAAAAGAAAGAAAA
1 AAAAAAAAGAAAGAAAA
* *
19235361 AAGAAAAAGCAAGAAAA
1 AAAAAAAAGAAAGAAAA
19235378 AAAAAAAA
1 AAAAAAAA
19235386 ACTAGAACAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAGAAAA
Found at i:19235392 original size:17 final size:17
Alignment explanation
Indices: 19235338--19235392 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
19235328 AAGGCTAAGG
* *
19235338 CTAGAGAAAAAAAAGAA
1 CTAGAAAAAAAAAAAAA
* *
19235355 --AGAAAAAAGAAAAAG
1 CTAGAAAAAAAAAAAAA
*
19235370 CAAGAAAAAAAAAAAAA
1 CTAGAAAAAAAAAAAAA
19235387 CTAGAA
1 CTAGAA
19235393 CAGCTGGGTC
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 11 0.38
17 18 0.62
ACGTcount: A:0.76, C:0.05, G:0.15, T:0.04
Consensus pattern (17 bp):
CTAGAAAAAAAAAAAAA
Found at i:19236142 original size:13 final size:13
Alignment explanation
Indices: 19236120--19236156 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
19236110 GACTCTTTGT
19236120 AAAA-GAATTTTA
1 AAAATGAATTTTA
19236132 AAAATGAATTTTA
1 AAAATGAATTTTA
19236145 AAAATGAATTTT
1 AAAATGAATTTT
19236157 CTTTTCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAATGAATTTTA
Found at i:19236793 original size:24 final size:24
Alignment explanation
Indices: 19236758--19236803 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
19236748 GTGATGACCA
19236758 AGGCTCCATACTAGCCTTAGTACG
1 AGGCTCCATACTAGCCTTAGTACG
*
19236782 AGGCTCCGTACTAGCCTTAGTA
1 AGGCTCCATACTAGCCTTAGTA
19236804 TGTGACAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (24 bp):
AGGCTCCATACTAGCCTTAGTACG
Found at i:19242461 original size:292 final size:292
Alignment explanation
Indices: 19241914--19242497 Score: 1015
Period size: 292 Copynumber: 2.0 Consensus size: 292
19241904 AAGTTTATTA
* *
19241914 AGCACAATAAATATAACGTTGTTGAGTAATTAAACAAGCAGTCGGCGCAAATCTCGATATTATCT
1 AGCACAATAAATATAACATTGTGGAGTAATTAAACAAGCAGTCGGCGCAAATCTCGATATTATCT
*
19241979 CTATTGCTGAACTTAGAGCCACATCAAAACGTATTGCTAAAAGTGTTAAATCAAGCTTATGTGGT
66 CTATTGCTGAACTTAGAGCCACATCAAAACGTATTGCTAAAAGTGTTAAATCAAGCTTATGTGGC
*
19242044 GAGCAATGTATCTGTAGAAAAGCTCGATAGGTGGATAAATAACCTGAATGCGGATAATTTCATCT
131 GAGCAATGTATCTGTAGAAAAGCTCGATAGGTGGATAAATAACCTGAATGCAGATAATTTCATCT
*
19242109 GTTTTAGTGATGAGGAAATACCACCGAATGGTAGGGGCTCTGTAAAAACATTACACATCACAACC
196 GTTTTAGTGATGACGAAATACCACCGAATGGTAGGGGCTCTGTAAAAACATTACACATCACAACC
*
19242174 AGTTGCAAGGGTTACATAGTACCGAATGTGCT
261 AGTTACAAGGGTTACATAGTACCGAATGTGCT
* * * * *
19242206 AGCACAGTGAATATAGCATTGTGGAGTAATTAAACAAGCAGTCGGCGCGAATCTCGGTATTATCT
1 AGCACAATAAATATAACATTGTGGAGTAATTAAACAAGCAGTCGGCGCAAATCTCGATATTATCT
* * *
19242271 CTATTGTTGAACTTAGCGCTACATCAAAACGTATTGCTAAAAGTGTTAAATCAAGCTTATGTGGC
66 CTATTGCTGAACTTAGAGCCACATCAAAACGTATTGCTAAAAGTGTTAAATCAAGCTTATGTGGC
*
19242336 GAGCAATGTATCTGTAGAAAAGCTCGATAGGTGGGTAAATAACCTGAATGCAGATAATTTCATCT
131 GAGCAATGTATCTGTAGAAAAGCTCGATAGGTGGATAAATAACCTGAATGCAGATAATTTCATCT
* *
19242401 TTTTTAGTGATGACGAAATGCCACCGAATGGTAGGGGCTCTGTAAAAACATTACACATCACAACC
196 GTTTTAGTGATGACGAAATACCACCGAATGGTAGGGGCTCTGTAAAAACATTACACATCACAACC
19242466 AGTTACAAGGGTTACATAGTACCGAATGTGCT
261 AGTTACAAGGGTTACATAGTACCGAATGTGCT
19242498 CATCGATAAC
Statistics
Matches: 275, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
292 275 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (292 bp):
AGCACAATAAATATAACATTGTGGAGTAATTAAACAAGCAGTCGGCGCAAATCTCGATATTATCT
CTATTGCTGAACTTAGAGCCACATCAAAACGTATTGCTAAAAGTGTTAAATCAAGCTTATGTGGC
GAGCAATGTATCTGTAGAAAAGCTCGATAGGTGGATAAATAACCTGAATGCAGATAATTTCATCT
GTTTTAGTGATGACGAAATACCACCGAATGGTAGGGGCTCTGTAAAAACATTACACATCACAACC
AGTTACAAGGGTTACATAGTACCGAATGTGCT
Found at i:19249233 original size:13 final size:13
Alignment explanation
Indices: 19249215--19249239 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19249205 TAACTAAAAC
19249215 AACACATAAATAA
1 AACACATAAATAA
19249228 AACACATAAATA
1 AACACATAAATA
19249240 TCATATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (13 bp):
AACACATAAATAA
Found at i:19250107 original size:41 final size:41
Alignment explanation
Indices: 19249911--19250098 Score: 313
Period size: 41 Copynumber: 4.6 Consensus size: 41
19249901 ACCGGCAGTT
* *
19249911 AGCCTGCTAGACATAAAGTCTGATATGTTTCACCGGCATCA
1 AGCCTGCTAGACATAATGTCTGGTATGTTTCACCGGCATCA
*
19249952 AGCCTGCTAGACATAAAGTCTGGTATGTTTCACCGGCATCA
1 AGCCTGCTAGACATAATGTCTGGTATGTTTCACCGGCATCA
* * *
19249993 AGCCTGCTAGACGTAATGTCTGGTATGTTTCAACAGCATCA
1 AGCCTGCTAGACATAATGTCTGGTATGTTTCACCGGCATCA
19250034 AGCCTGCTAGACATAATGTCTGGTATGTTTCACCGGCATCA
1 AGCCTGCTAGACATAATGTCTGGTATGTTTCACCGGCATCA
*
19250075 AGCCTGCTAGACGTAATGTCTGGT
1 AGCCTGCTAGACATAATGTCTGGT
19250099 TTACTTCACT
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 138 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACATAATGTCTGGTATGTTTCACCGGCATCA
Found at i:19250744 original size:2 final size:2
Alignment explanation
Indices: 19250739--19250774 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
19250729 ATTCGAATCT
*
19250739 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19250775 CTTTGATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:19252811 original size:76 final size:75
Alignment explanation
Indices: 19252651--19253153 Score: 693
Period size: 76 Copynumber: 6.6 Consensus size: 75
19252641 ATCATTTCTT
* * * *
19252651 TTTCTGTTTTTTAAAAAATCAACTCATAATCCGATAGGTGAGTGGAGCCTCGGGTCGCACGCCGA
1 TTTCTG-TTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGA
19252716 GGTA-TTTTCAA
65 -GTATTTTTCAA
* * * *
19252727 TTTCTGTTTTTCAAAGATCACCTCATAATCCGAGAGGCGAGTTGAGCCTCGAGTCGCACGCTGAT
1 TTTCTGTTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGA-
*
19252792 GTGTTTTTCAA
65 GTATTTTTCAA
* * *
19252803 TTTCTGTTTTTAAAAGATCAAATCATAATCCGAGAGGTGAGTGGAGCCTCGGGTCGCACGCCGAT
1 TTTCTGTTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGA-
19252868 GTATTTTTCAA
65 GTATTTTTCAA
*
19252879 TTTCTGTTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGTCGAG
1 TTTCTGTTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGA-
19252944 GTATTTTTCAA
65 GTATTTTTCAA
* * * * * *
19252955 TTTCTATTTTTTAAAGATCAACTCATAATCCGAAAGGTGAGTTGAGCCTCGGCTCGCACACTGAG
1 TTTCTGTTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGA-
19253020 GTATTTTTCAA
65 GTATTTTTCAA
* * * *
19253031 TTTTTGTTTTTCAAAGATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGAGTGGCACGCCGAG
1 TTTCTGTTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAG
19253096 ATATTTTTCAA
66 -TATTTTTCAA
* * * *
19253107 TTTCTATTTTTCAAAGATTAACTCATAATCTGAGAGGTGATTTGAGC
1 TTTCTGTTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGC
19253154 TTTAGGCCGC
Statistics
Matches: 379, Mismatches: 46, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
75 53 0.14
76 326 0.86
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (75 bp):
TTTCTGTTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAG
TATTTTTCAA
Found at i:19253843 original size:30 final size:28
Alignment explanation
Indices: 19253745--19253851 Score: 135
Period size: 28 Copynumber: 3.8 Consensus size: 28
19253735 TACAAAAATA
* * *
19253745 TACTAATTATATTTTGGCCCCTATTTTT
1 TACTAATTACATTTTAGCCCCTACTTTT
*
19253773 TACTAATTACATTTTGGCCCCTACTTTT
1 TACTAATTACATTTTAGCCCCTACTTTT
*
19253801 TACTATTTACATTTTAGCCCCTAACTTTT
1 TACTAATTACATTTTAGCCCCT-ACTTTT
19253830 T-CTAAAATTACATTTTAGCCCC
1 TACT--AATTACATTTTAGCCCC
19253852 GAGATTTTTG
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
28 48 0.68
29 7 0.10
30 16 0.23
ACGTcount: A:0.24, C:0.23, G:0.06, T:0.47
Consensus pattern (28 bp):
TACTAATTACATTTTAGCCCCTACTTTT
Found at i:19254528 original size:3 final size:3
Alignment explanation
Indices: 19254522--19254568 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
19254512 AGAAAAAAAG
19254522 AGA AGA AGA AGA AGA AGAA AGA AGA AGA AGAA AGA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AG-A AGA AGA AGA AG-A AGA AGA AGA AGA AGA
19254568 A
1 A
19254569 AACAAAGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 33 0.80
4 6 0.15
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19254543 original size:13 final size:13
Alignment explanation
Indices: 19254522--19254563 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
19254512 AGAAAAAAAG
19254522 AGAAG-AAGAAGA
1 AGAAGAAAGAAGA
19254534 AGAAGAAAGAAGA
1 AGAAGAAAGAAGA
19254547 AGAAGAAAGAAGA
1 AGAAGAAAGAAGA
19254560 AGAA
1 AGAA
19254564 AAGAAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 5 0.17
13 24 0.83
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AGAAGAAAGAAGA
Found at i:19254581 original size:6 final size:6
Alignment explanation
Indices: 19254516--19254599 Score: 60
Period size: 6 Copynumber: 12.8 Consensus size: 6
19254506 GGCTAGAGAA
* * * *
19254516 AAAAAG AGAAGAAG AAGAAG AAGAAAG AAGAAG AAGAAAG AAGAAG AAAAGAA
1 AAAAAG A-AA-AAG AAAAAG AA-AAAG AAAAAG AA-AAAG AAAAAG AAAA-AG
*
19254569 AACAAAG AAAAAG AAAAAAG AAAAAT AAAAA
1 AA-AAAG AAAAAG -AAAAAG AAAAAG AAAAA
19254600 AGAACAGTCG
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
6 31 0.50
7 25 0.40
8 6 0.10
ACGTcount: A:0.76, C:0.01, G:0.21, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:19254590 original size:13 final size:13
Alignment explanation
Indices: 19254530--19254603 Score: 67
Period size: 13 Copynumber: 5.4 Consensus size: 13
19254520 AGAGAAGAAG
* *
19254530 AAGAAGAAGAAAG
1 AAGAAAAAGAAAA
* *
19254543 AAGAAGAAGAAAG
1 AAGAAAAAGAAAA
19254556 AAGAAGAAAAGAAAACA
1 AAG-A-AAAAG-AAA-A
19254573 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
*
19254586 AAGAAAAATAAAA
1 AAGAAAAAGAAAA
19254599 AAGAA
1 AAGAA
19254604 CAGTCGGGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
13 34 0.63
14 4 0.07
15 9 0.17
16 4 0.07
17 3 0.06
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.01
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:19254599 original size:20 final size:20
Alignment explanation
Indices: 19254536--19254603 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
19254526 GAAGAAGAAG
* * * *
19254536 AAGAAAGAAGAAGAAGAAAG
1 AAGAAAAAAGAAAAAAAAAA
19254556 AAGAAGAAAAGAAAACAAAGAAA
1 AAGAA-AAAAGAAAA-AAA-AAA
*
19254579 AAGAAAAAAGAAAAATAAAA
1 AAGAAAAAAGAAAAAAAAAA
19254599 AAGAA
1 AAGAA
19254604 CAGTCGGGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 13 0.32
21 9 0.22
22 11 0.28
23 7 0.17
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (20 bp):
AAGAAAAAAGAAAAAAAAAA
Found at i:19258675 original size:12 final size:13
Alignment explanation
Indices: 19258642--19258678 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
19258632 TTATTTTTAT
19258642 TTATT-TGAAAAA
1 TTATTATGAAAAA
19258654 TTAGTTATGAAAAA
1 TTA-TTATGAAAAA
19258668 -TATTATGAAAA
1 TTATTATGAAAA
19258679 TTTTCATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 12 0.52
13 4 0.17
14 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (13 bp):
TTATTATGAAAAA
Found at i:19262682 original size:21 final size:22
Alignment explanation
Indices: 19262656--19262707 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
19262646 TTGCATTTTA
*
19262656 TTTTTGTTTT-TAGTTTAATTT
1 TTTTTGTTTTCTAATTTAATTT
*
19262677 TTTTTGTTTTCTAATTTTATTT
1 TTTTTGTTTTCTAATTTAATTT
*
19262699 TATTTGTTT
1 TTTTTGTTT
19262708 CTGGTAGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.13, C:0.02, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTTGTTTTCTAATTTAATTT
Found at i:19268059 original size:4 final size:4
Alignment explanation
Indices: 19268050--19268120 Score: 52
Period size: 4 Copynumber: 16.2 Consensus size: 4
19268040 TATTAGATTA
* * *
19268050 TTAT TTAT TTAT TTAT TCTAA TTATT TTAT TTTT ATTAGTT TTAC TTATT
1 TTAT TTAT TTAT TTAT T-TAT TTA-T TTAT TTAT -TTA--T TTAT TTA-T
*
19268100 TTAT TTAT TTCT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT T
19268121 ATTGTTTATT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
4 38 0.72
5 11 0.21
6 3 0.06
7 1 0.02
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:19268084 original size:24 final size:24
Alignment explanation
Indices: 19268049--19268105 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
19268039 TTATTAGATT
*
19268049 ATTA-TTTATTTAT-TTA-TTCTA
1 ATTATTTTATTTTTATTAGTTCTA
*
19268070 ATTATTTTATTTTTATTAGTTTTA
1 ATTATTTTATTTTTATTAGTTCTA
*
19268094 CTTATTTTATTT
1 ATTATTTTATTT
19268106 ATTTCTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.13
22 8 0.27
23 3 0.10
24 15 0.50
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (24 bp):
ATTATTTTATTTTTATTAGTTCTA
Found at i:19268092 original size:9 final size:8
Alignment explanation
Indices: 19268028--19268123 Score: 51
Period size: 8 Copynumber: 12.0 Consensus size: 8
19268018 TCTTTTCTTA
19268028 TTATTATT
1 TTATTATT
*
19268036 CTATTATT
1 TTATTATT
**
19268044 AGATTATT
1 TTATTATT
*
19268052 AT-TTA-T
1 TTATTATT
19268058 TTATTTATT
1 TTA-TTATT
*
19268067 CTAATTATT
1 -TTATTATT
19268076 TTA-T-TT
1 TTATTATT
19268082 TTATTAGTT
1 TTATTA-TT
19268091 TTACTTATT
1 TTA-TTATT
19268100 TTATTTATT
1 TTA-TTATT
19268109 TCT-TTA-T
1 T-TATTATT
19268116 TTATTATT
1 TTATTATT
19268124 GTTTATTCAA
Statistics
Matches: 69, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
6 8 0.12
7 10 0.14
8 23 0.33
9 22 0.32
10 6 0.09
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (8 bp):
TTATTATT
Found at i:19268223 original size:7 final size:8
Alignment explanation
Indices: 19268206--19268230 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19268196 TTTGATTTGA
19268206 TTTATTTT
1 TTTATTTT
19268214 TTTATTTT
1 TTTATTTT
19268222 TTTATTTT
1 TTTATTTT
19268230 T
1 T
19268231 CATTAAGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:19269766 original size:6 final size:6
Alignment explanation
Indices: 19269750--19269811 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
19269740 AGTCCATTTG
* *
19269750 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT GTTTAT GTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
19269797 TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTT
19269812 CTTAGACTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
5 5 0.09
6 49 0.91
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:19272540 original size:14 final size:14
Alignment explanation
Indices: 19272517--19272548 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
19272507 TGTCGCGTTC
*
19272517 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
19272531 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
19272545 TTAG
1 TTAG
19272549 AACAATCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:19277762 original size:45 final size:44
Alignment explanation
Indices: 19277696--19277865 Score: 250
Period size: 45 Copynumber: 3.8 Consensus size: 44
19277686 AGTATACAGT
* * * *
19277696 AATCAGTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTG
1 AATC-GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
*
19277741 AATCTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCG
1 AATC-GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
19277786 AATCGATAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AATCG-TAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
*
19277831 AGTCGGTAACAGTAACAGTAACAGTATTCGACACA
1 AATC-GTAACAGTAACAGTAACAGTATTCGACACA
19277866 NNNNNNNNNN
Statistics
Matches: 115, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
44 1 0.01
45 113 0.98
46 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (44 bp):
AATCGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
Found at i:19281409 original size:49 final size:49
Alignment explanation
Indices: 19281354--19281500 Score: 188
Period size: 49 Copynumber: 3.0 Consensus size: 49
19281344 TTCATTTTCT
*
19281354 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACATATCACATAC
1 CGATGCCATAGTCCAACTATGGTCTTACACGAAATCACATATCACATAC
* * * * *
19281403 CGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACTTAC
1 CGATGCCATAGTCCAACTATGGTCTTACACGAAATCACATATCACATAC
* *
19281452 CGATGACATA-TCCCAAATATGGTCTTACACGGAAATCACATAATCACAT
1 CGATGCCATAGT-CCAACTATGGTCTTACAC-GAAATCACAT-ATCACAT
19281501 TTTCACATGT
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 68 0.82
50 9 0.11
51 6 0.07
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (49 bp):
CGATGCCATAGTCCAACTATGGTCTTACACGAAATCACATATCACATAC
Found at i:19282669 original size:45 final size:44
Alignment explanation
Indices: 19282603--19282802 Score: 301
Period size: 45 Copynumber: 4.4 Consensus size: 44
19282593 AGTATACAGT
* * * *
19282603 AATCAGTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTG
1 AATC-GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
*
19282648 AATCTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCG
1 AATC-GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
19282693 AATCGATAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AATCG-TAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
*
19282738 AGTCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AATC-GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
19282783 AATCAGTAACAGTAACAGTA
1 AATC-GTAACAGTAACAGTA
19282803 GTCGGCACAT
Statistics
Matches: 143, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
44 1 0.01
45 141 0.99
46 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.19
Consensus pattern (44 bp):
AATCGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
Found at i:19282708 original size:39 final size:42
Alignment explanation
Indices: 19282618--19282824 Score: 215
Period size: 45 Copynumber: 4.8 Consensus size: 42
19282608 GTAACGGTAG
* * *
19282618 CAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATC-G-GA-AGTAA
* *
19282663 CGGTAACAGTATTCGACACACAAAGTGCCGAATCGATAACAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATCG--GA-AGTAA
*
19282708 CAGTAACAGTATTCGACACACAAAGTGCCGAGTCGGTAACAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATCGG--A-AGTAA
19282753 CAGTAACAGTATTCGACACACAAAGTGCCGAATC---AGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATCGGAAGTAA
* * * *
19282792 CAGTAACAGTAGTCGGCACA-TAAGTGCCTAATC
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATC
19282825 AGTAAGCCGG
Statistics
Matches: 148, Mismatches: 11, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
38 11 0.07
39 23 0.16
44 1 0.01
45 113 0.76
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (42 bp):
CAGTAACAGTATTCGACACACAAAGTGCCGAATCGGAAGTAA
Found at i:19300541 original size:22 final size:21
Alignment explanation
Indices: 19300505--19300545 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
19300495 AAAGAGGGAG
*
19300505 AAAACAACAAGAAAATAGCATT
1 AAAACAACAA-AAAAAAGCATT
*
19300527 AAAACAATAAAAAAAAGCA
1 AAAACAACAAAAAAAAGCA
19300546 GTTTTTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.71, C:0.12, G:0.07, T:0.10
Consensus pattern (21 bp):
AAAACAACAAAAAAAAGCATT
Found at i:19305476 original size:13 final size:14
Alignment explanation
Indices: 19305448--19305476 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19305438 ATTTAATTAC
19305448 TTTAAAATTAATTT
1 TTTAAAATTAATTT
19305462 TTTAAAATT-ATTT
1 TTTAAAATTAATTT
19305475 TT
1 TT
19305477 ATTTTTTCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTAAAATTAATTT
Found at i:19313873 original size:28 final size:28
Alignment explanation
Indices: 19313833--19313921 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 28
19313823 GGCCAAGCAA
*
19313833 AATGTCTCTACAGGGACCACTGTTACTG
1 AATGTCTCTACAGAGACCACTGTTACTG
* *
19313861 AATGCCTCTACAGAGACCACCGTTA-TCG
1 AATGTCTCTACAGAGACCACTGTTACT-G
* * *
19313889 AATGTCTATTCAAAGACCACTGTTACTG
1 AATGTCTCTACAGAGACCACTGTTACTG
*
19313917 TATGT
1 AATGT
19313922 GTCATATCCT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
27 1 0.02
28 48 0.96
29 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (28 bp):
AATGTCTCTACAGAGACCACTGTTACTG
Found at i:19315899 original size:4 final size:4
Alignment explanation
Indices: 19315890--19315930 Score: 57
Period size: 4 Copynumber: 10.0 Consensus size: 4
19315880 TATCATCGTT
19315890 TTTC TTTC TTTC TTTC TTTC TTTC TTT- TGTTC TTTCC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTT-C TTTC
19315931 CTTCCTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 1 0.03
4 28 0.82
5 5 0.15
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:19315939 original size:21 final size:20
Alignment explanation
Indices: 19315899--19315941 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
19315889 TTTTCTTTCT
* *
19315899 TTCTTTCTTTCTTTCTTTTG
1 TTCTTTCTTTCCTTCCTTTG
19315919 TTCTTTCCTTTCCTTCCTTTG
1 TTCTTT-CTTTCCTTCCTTTG
19315940 TT
1 TT
19315942 AATCTGGCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.00, C:0.26, G:0.05, T:0.70
Consensus pattern (20 bp):
TTCTTTCTTTCCTTCCTTTG
Found at i:19318694 original size:21 final size:21
Alignment explanation
Indices: 19318668--19318727 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
19318658 TTGGGTGGAT
19318668 CAACTCTTACGAGCTTCTGTG
1 CAACTCTTACGAGCTTCTGTG
* *
19318689 CAACTCTTACGAGCTTCTATT
1 CAACTCTTACGAGCTTCTGTG
*
19318710 CAGCT-TT-CGAGCTTCTGT
1 CAACTCTTACGAGCTTCTGT
19318728 TCGTGTATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.29
20 2 0.06
21 23 0.66
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.37
Consensus pattern (21 bp):
CAACTCTTACGAGCTTCTGTG
Found at i:19319689 original size:67 final size:67
Alignment explanation
Indices: 19319576--19319702 Score: 200
Period size: 67 Copynumber: 1.9 Consensus size: 67
19319566 CGTGTGTAGC
* * * *
19319576 ACACGGCCTGGCACATGGCCGTGTGGCTTGGTTGTGTGACCTAAGTCAGTGAGTTACACAGGCAC
1 ACACGGCCTGGCACATGACCGTGTGGCTTGGCTGTATGACCCAAGTCAGTGAGTTACACAGGCAC
19319641 GG
66 GG
* *
19319643 ACACGGGCTGGGACATGACCGTGTGGCTTGGCTGTATGACCCAAGTCAGTGAGTTACACA
1 ACACGGCCTGGCACATGACCGTGTGGCTTGGCTGTATGACCCAAGTCAGTGAGTTACACA
19319703 TACACGGGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.21, C:0.24, G:0.33, T:0.22
Consensus pattern (67 bp):
ACACGGCCTGGCACATGACCGTGTGGCTTGGCTGTATGACCCAAGTCAGTGAGTTACACAGGCAC
GG
Found at i:19320239 original size:17 final size:18
Alignment explanation
Indices: 19320217--19320250 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19320207 GTCATGTTTT
*
19320217 GGTTTA-ACTATTTAAAG
1 GGTTTAGACTAATTAAAG
19320234 GGTTTAGACTAATTAAA
1 GGTTTAGACTAATTAAA
19320251 TTTTCAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (18 bp):
GGTTTAGACTAATTAAAG
Found at i:19340671 original size:2 final size:2
Alignment explanation
Indices: 19340664--19340754 Score: 73
Period size: 2 Copynumber: 47.5 Consensus size: 2
19340654 TGTAAAAGAG
* *
19340664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AG AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
19340705 AT AA AT AT AT A- AT A- AG AT AT AA AG AT AT AT AG AT AT A- AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
19340744 GT AT AT AT AT A
1 AT AT AT AT AT A
19340755 CGTATACGAA
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
1 4 0.06
2 68 0.94
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (2 bp):
AT
Found at i:19340819 original size:2 final size:2
Alignment explanation
Indices: 19340812--19340848 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19340802 TAAAATCTTA
19340812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19340849 GAAATAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19341665 original size:22 final size:23
Alignment explanation
Indices: 19341611--19341653 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19341601 TGGTATCTAC
19341611 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
19341633 AAATCATATCTTCTAAGATTA
1 AAATCAAATCTTCTAAGATTA
19341654 TATATCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:19348519 original size:49 final size:49
Alignment explanation
Indices: 19348466--19348567 Score: 186
Period size: 49 Copynumber: 2.1 Consensus size: 49
19348456 ATCAGGCGTG
19348466 ATTCCAAAAAAAAAAAAATTTAGACTCAAACCCAACTTTCCCTATCTAA
1 ATTCCAAAAAAAAAAAAATTTAGACTCAAACCCAACTTTCCCTATCTAA
* *
19348515 ATTCCAAAAAAAATAAATTTTAGACTCAAACCCAACTTTCCCTATCTAA
1 ATTCCAAAAAAAAAAAAATTTAGACTCAAACCCAACTTTCCCTATCTAA
19348564 ATTC
1 ATTC
19348568 TCCATTTTAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (49 bp):
ATTCCAAAAAAAAAAAAATTTAGACTCAAACCCAACTTTCCCTATCTAA
Found at i:19348630 original size:22 final size:24
Alignment explanation
Indices: 19348605--19348659 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
19348595 AAATATTTTT
19348605 TATTTAAACT-AAATTA-TATAAA
1 TATTTAAACTAAAATTATTATAAA
*
19348627 TATTTAAA-TAAAATTATTTATATA
1 TATTTAAACTAAAATTA-TTATAAA
19348651 TATTTAAAC
1 TATTTAAAC
19348660 AATAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.04
22 14 0.50
24 13 0.46
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
TATTTAAACTAAAATTATTATAAA
Found at i:19355718 original size:20 final size:21
Alignment explanation
Indices: 19355695--19355738 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
19355685 CTAAAAAATT
19355695 TAAAAATTTATAAAAATA-AA
1 TAAAAATTTATAAAAATATAA
* * *
19355715 TAAATATTTTTTAAAATATAA
1 TAAAAATTTATAAAAATATAA
19355736 TAA
1 TAA
19355739 CTTATTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAAATTTATAAAAATATAA
Found at i:19355767 original size:29 final size:29
Alignment explanation
Indices: 19355728--19355792 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
19355718 ATATTTTTTA
* *
19355728 AAATATAATAACTTAT-TTAA-ATTTATATT
1 AAATAAAATAA-TTATATTAATA-TTAAATT
19355757 AAATAAAATAATTATATTAATATTAAATT
1 AAATAAAATAATTATATTAATATTAAATT
19355786 AAA-AAAA
1 AAATAAAA
19355793 CAACCCTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 8 0.25
29 23 0.72
30 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
AAATAAAATAATTATATTAATATTAAATT
Found at i:19356751 original size:29 final size:29
Alignment explanation
Indices: 19356709--19356807 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 29
19356699 CAATCACGAT
* *
19356709 TAGTTTGGTGACCAGTTTAAAAAAAATCA
1 TAGTTAGGTGACCAATTTAAAAAAAATCA
***
19356738 TAGTTAGGTGACCAAAAAAAAAACAAATCTA
1 TAGTTAGGTGACCAATTTAAAAA-AAATC-A
* *
19356769 TAGTT-GGATGACTAATTT-AAAAAATTCA
1 TAGTTAGG-TGACCAATTTAAAAAAAATCA
19356797 TAGTTAGGTGA
1 TAGTTAGGTGA
19356808 TAAAAAAATG
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
28 9 0.16
29 24 0.43
30 11 0.20
31 12 0.21
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.29
Consensus pattern (29 bp):
TAGTTAGGTGACCAATTTAAAAAAAATCA
Found at i:19364379 original size:34 final size:34
Alignment explanation
Indices: 19364327--19364394 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
19364317 GCATTTTTGA
* *
19364327 CACTATATTGAGATGGGCTAAGGCCCAA-ACTGT
1 CACTATATTGAAAAGGGCTAAGGCCCAAGACTGT
*
19364360 CACTGATATTGAAAAGGGCTTAGGCCCAAGACTGT
1 CACT-ATATTGAAAAGGGCTAAGGCCCAAGACTGT
19364395 TCAACTGTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 4 0.13
34 21 0.70
35 5 0.17
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (34 bp):
CACTATATTGAAAAGGGCTAAGGCCCAAGACTGT
Found at i:19365151 original size:26 final size:26
Alignment explanation
Indices: 19365104--19365165 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
19365094 CTGTAAGTGT
* * *
19365104 TCTGAAATTGATACATGCTATGATAA
1 TCTGAAACTAATAAATGCTATGATAA
* *
19365130 TCTGAAACTAATAAATGTTATGATAT
1 TCTGAAACTAATAAATGCTATGATAA
19365156 TCTGAAACTA
1 TCTGAAACTA
19365166 TTGTAGGTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (26 bp):
TCTGAAACTAATAAATGCTATGATAA
Found at i:19368505 original size:77 final size:77
Alignment explanation
Indices: 19368378--19368526 Score: 280
Period size: 77 Copynumber: 1.9 Consensus size: 77
19368368 GTTGTTGTGG
* *
19368378 GAGGTTAGGGAGAGAATTAAGGAGATGAGTTGCCAGATTTTTATGCATTATCTTTTTGTTTAGTT
1 GAGGTTAGGGAGAGAATTAAGGAGATAAGTTGCCAAATTTTTATGCATTATCTTTTTGTTTAGTT
19368443 TTTTTTTTCCAA
66 TTTTTTTTCCAA
19368455 GAGGTTAGGGAGAGAATTAAGGAGATAAGTTGCCAAATTTTTATGCATTATCTTTTTGTTTAGTT
1 GAGGTTAGGGAGAGAATTAAGGAGATAAGTTGCCAAATTTTTATGCATTATCTTTTTGTTTAGTT
19368520 TTTTTTT
66 TTTTTTT
19368527 CAAATTTCAG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.45
Consensus pattern (77 bp):
GAGGTTAGGGAGAGAATTAAGGAGATAAGTTGCCAAATTTTTATGCATTATCTTTTTGTTTAGTT
TTTTTTTTCCAA
Found at i:19370260 original size:23 final size:24
Alignment explanation
Indices: 19370234--19370278 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
19370224 ATATCCCCAA
*
19370234 ATGGAGTGTAG-GGTTGGATGGAG
1 ATGGAGTGTAGAGGCTGGATGGAG
*
19370257 ATGGTGTGTAGAGGCTGGATGG
1 ATGGAGTGTAGAGGCTGGATGG
19370279 GTAGAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.02, G:0.51, T:0.27
Consensus pattern (24 bp):
ATGGAGTGTAGAGGCTGGATGGAG
Found at i:19372902 original size:45 final size:46
Alignment explanation
Indices: 19372815--19372902 Score: 108
Period size: 45 Copynumber: 1.9 Consensus size: 46
19372805 CATTTAATTT
* * * *
19372815 GAAAACCATAATTCATTTCCAAGTCATTTTGATTTTTCATTTTGGA
1 GAAAACCATAATTCAATTCCAAATCATTTTCATTTTTAATTTTGGA
*
19372861 GAAAACCA-CATTCAATTCCAAAT-ATTTTCATTTCTTAATTTT
1 GAAAACCATAATTCAATTCCAAATCATTTTCATTT-TTAATTTT
19372903 TATTTTCATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 9 0.25
45 19 0.53
46 8 0.22
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (46 bp):
GAAAACCATAATTCAATTCCAAATCATTTTCATTTTTAATTTTGGA
Found at i:19372908 original size:58 final size:58
Alignment explanation
Indices: 19372840--19372953 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 58
19372830 TTTCCAAGTC
19372840 ATTTTGATTTTTCATTTTGGAGAAAACCACATTCAATTCCAAATATTT-TCATTTCTTA
1 ATTTTGA-TTTTCATTTTGGAGAAAACCACATTCAATTCCAAATATTTCTCATTTCTTA
* * * * *
19372898 ATTTTTATTTTCATTTTGGAGAAAATCATATTCATTTCCAAATGTTTCTCATTTCT
1 ATTTTGATTTTCATTTTGGAGAAAACCACATTCAATTCCAAATATTTCTCATTTCT
19372954 CCATTTTCAC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
57 36 0.72
58 14 0.28
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (58 bp):
ATTTTGATTTTCATTTTGGAGAAAACCACATTCAATTCCAAATATTTCTCATTTCTTA
Found at i:19374938 original size:35 final size:35
Alignment explanation
Indices: 19374899--19374980 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
19374889 TTAGTAGACC
* * *
19374899 ATTTTCATGGTGACGCTCCATAGAGCCAGTAGATT
1 ATTTTCATGATGACACTACATAGAGCCAGTAGATT
* * * *
19374934 ATTTTCATGATGCCATTATATAGAGCTAGTAGATT
1 ATTTTCATGATGACACTACATAGAGCCAGTAGATT
*
19374969 ATTTTCACGATG
1 ATTTTCATGATG
19374981 TTGCCCCGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (35 bp):
ATTTTCATGATGACACTACATAGAGCCAGTAGATT
Found at i:19379055 original size:35 final size:35
Alignment explanation
Indices: 19379016--19379088 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
19379006 ATTGTAACTA
19379016 TTGGGCATATTTGTTGGGGTTACAATTGCTTCTTG
1 TTGGGCATATTTGTTGGGGTTACAATTGCTTCTTG
*
19379051 TTGGGCATATTTGTTGGGGTTACAATTGCTTGTTG
1 TTGGGCATATTTGTTGGGGTTACAATTGCTTCTTG
19379086 TTG
1 TTG
19379089 TAGTGATAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.14, C:0.10, G:0.30, T:0.47
Consensus pattern (35 bp):
TTGGGCATATTTGTTGGGGTTACAATTGCTTCTTG
Found at i:19383573 original size:46 final size:46
Alignment explanation
Indices: 19383502--19383597 Score: 149
Period size: 46 Copynumber: 2.1 Consensus size: 46
19383492 GTGATTTGGC
19383502 ATTGTAGGCAATGTCTGAACGTGGCCAAGATACCGTTCCAATACAT
1 ATTGTAGGCAATGTCTGAACGTGGCCAAGATACCGTTCCAATACAT
* * *
19383548 ATTGTGGGCACTGTCTG-ACGCTGGCCAAGATATCGTTCCAATACAT
1 ATTGTAGGCAATGTCTGAACG-TGGCCAAGATACCGTTCCAATACAT
19383594 ATTG
1 ATTG
19383598 AGAAATGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 3 0.07
46 43 0.93
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (46 bp):
ATTGTAGGCAATGTCTGAACGTGGCCAAGATACCGTTCCAATACAT
Found at i:19383977 original size:22 final size:23
Alignment explanation
Indices: 19383943--19383985 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
19383933 ATGATTTGAC
* *
19383943 AAAAAATATAAATTCAATAAATA
1 AAAAAACATAAATTAAATAAATA
19383966 AAAAAACA-AAATTAAATAAA
1 AAAAAACATAAATTAAATAAA
19383986 AGACTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (23 bp):
AAAAAACATAAATTAAATAAATA
Found at i:19391768 original size:48 final size:48
Alignment explanation
Indices: 19391697--19391791 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
19391687 TTCTTTGCTC
* *
19391697 AAAAACGCCTAAGTCAGCCTAACTTGCAGTAATAAAGGATTCAACAGT
1 AAAAACGCCTAAGTCAGCCTAACTCGCAATAATAAAGGATTCAACAGT
*
19391745 AAAAACGCCTAAGTCAGCTTAACTCGCAATAATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGCAATAATAAAGGATTCAACAG
19391792 AATTCCTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGCAATAATAAAGGATTCAACAGT
Found at i:19392129 original size:35 final size:36
Alignment explanation
Indices: 19392089--19392160 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
19392079 TCTAGGATCA
19392089 CATATC-TCAAAAGATCACCTTCCATATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
* *
19392124 CATATCTTCAAAAGATCACTTTCCTTATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
19392160 C
1 C
19392161 TTCGGAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 6 0.18
36 28 0.82
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (36 bp):
CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
Found at i:19396957 original size:48 final size:48
Alignment explanation
Indices: 19396886--19396980 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
19396876 TTCTTTGCTC
* * **
19396886 AAAAACGCCTAAGTCAGCCTAACTTGCAGTAATAAAGGATTCAACAGT
1 AAAAACGCCTAAGTCAGCCTAACTCGAAACAATAAAGGATTCAACAGT
*
19396934 AAAAACGCCTAAGTCAGCTTAACTCGAAACAATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGAAACAATAAAGGATTCAACAG
19396981 AATTCCCTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGAAACAATAAAGGATTCAACAGT
Found at i:19397318 original size:35 final size:36
Alignment explanation
Indices: 19397278--19397349 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
19397268 TCTAGGATCA
19397278 CATATC-TCAAAAGATCACCTTCCATATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
* *
19397313 CATATCTTCAAAAGATCACTTTCCTTATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
19397349 C
1 C
19397350 TTCGGAGACG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 6 0.18
36 28 0.82
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (36 bp):
CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
Found at i:19402777 original size:22 final size:22
Alignment explanation
Indices: 19402730--19402779 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
19402720 CTCCGATTAT
*
19402730 TAGCACATTAGTGCTCTTCGTT
1 TAGCACATTAGTGCTCTTCGTA
*
19402752 TAGCACATTCGTGCTC-TCTGTA
1 TAGCACATTAGTGCTCTTC-GTA
19402774 TAGCAC
1 TAGCAC
19402780 TTGTAACAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTTCGTA
Found at i:19403194 original size:4 final size:4
Alignment explanation
Indices: 19403185--19403211 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
19403175 ATCCACCAAA
19403185 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
19403212 CCTAATCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:19404150 original size:25 final size:25
Alignment explanation
Indices: 19404024--19404147 Score: 160
Period size: 25 Copynumber: 5.0 Consensus size: 25
19404014 CACACCACAG
* * *
19404024 CTCGTATGAGCTTTCCGATT-TACAA
1 CTCGCATGAGCTTCCCG-TTATTCAA
*
19404049 CTCGCATGAGCTTCCCGATATTCAA
1 CTCGCATGAGCTTCCCGTTATTCAA
*
19404074 CTCGCATGAGTTTCCCGTTATTCAA
1 CTCGCATGAGCTTCCCGTTATTCAA
* *
19404099 CTCGCATGAACTTCCCGTTATTCAG
1 CTCGCATGAGCTTCCCGTTATTCAA
*
19404124 CTCGCATGAGCTTCTCGTTATTCA
1 CTCGCATGAGCTTCCCGTTATTCA
19404148 GCTTGGAAGA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
24 1 0.01
25 86 0.99
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (25 bp):
CTCGCATGAGCTTCCCGTTATTCAA
Found at i:19404159 original size:25 final size:25
Alignment explanation
Indices: 19404049--19404161 Score: 118
Period size: 25 Copynumber: 4.5 Consensus size: 25
19404039 CGATTTACAA
* * *
19404049 CTCGCATGAGCTTCCCGATATTCAA
1 CTCGCAAGAGCTTCCCGTTATTCAG
* * *
19404074 CTCGCATGAGTTTCCCGTTATTCAA
1 CTCGCAAGAGCTTCCCGTTATTCAG
* *
19404099 CTCGCATGAACTTCCCGTTATTCAG
1 CTCGCAAGAGCTTCCCGTTATTCAG
* *
19404124 CTCGCATGAGCTTCTCGTTATTCAG
1 CTCGCAAGAGCTTCCCGTTATTCAG
* *
19404149 CTTGGAAGAGCTT
1 CTCGCAAGAGCTT
19404162 ACTGTTTACA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 78 1.00
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (25 bp):
CTCGCAAGAGCTTCCCGTTATTCAG
Found at i:19406120 original size:20 final size:20
Alignment explanation
Indices: 19406082--19406120 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19406072 AAACTCTATC
* *
19406082 TATTTTGGTTTTATGTGAAG
1 TATTTTGGTTCTATATGAAG
19406102 TATTTTGGTTCTATATGAA
1 TATTTTGGTTCTATATGAA
19406121 ATGAATTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.21, T:0.54
Consensus pattern (20 bp):
TATTTTGGTTCTATATGAAG
Found at i:19408746 original size:30 final size:31
Alignment explanation
Indices: 19408703--19408763 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
19408693 GGGTTGGGAG
*
19408703 GGGAAGAGAGTAAAAGTTTTGGGGGAAAAGT
1 GGGAAGAGAGTAAAAGTTTTGAGGGAAAAGT
19408734 GGGAAG-GAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAAGAGAGTAAAAGTTTTGAGGGAAAAGT
19408764 AAAAAGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (31 bp):
GGGAAGAGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:19408910 original size:9 final size:9
Alignment explanation
Indices: 19408893--19408923 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19408883 TCGAGTTGAT
19408893 TCGAATAAC
1 TCGAATAAC
*
19408902 TCGATTAAC
1 TCGAATAAC
19408911 TCGAATAAC
1 TCGAATAAC
19408920 TCGA
1 TCGA
19408924 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:19413543 original size:15 final size:15
Alignment explanation
Indices: 19413506--19413556 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
19413496 AAATTACAAT
19413506 AATATTTAATAA-CA
1 AATATTTAATAATCA
19413520 AGA-ATTTAATAATCA
1 A-ATATTTAATAATCA
19413535 AATATTTAA-ACATCTA
1 AATATTTAATA-ATC-A
19413551 AATATT
1 AATATT
19413557 ATGCATACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 12 0.38
15 13 0.41
16 7 0.22
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (15 bp):
AATATTTAATAATCA
Found at i:19415059 original size:5 final size:5
Alignment explanation
Indices: 19415049--19415084 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
19415039 TGAGCATTCG
19415049 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
19415085 AAATTTCGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:19421176 original size:2 final size:2
Alignment explanation
Indices: 19421169--19421202 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
19421159 CCAGTACATC
* *
19421169 AT AT AT AT AC AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19421203 GAGTATTGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19436098 original size:36 final size:36
Alignment explanation
Indices: 19436058--19436127 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
19436048 TTTTTATTAA
*
19436058 GAAACATTTATTTCAATATTTTTAATGTATTTTAGG
1 GAAACATCTATTTCAATATTTTTAATGTATTTTAGG
* * * *
19436094 GAAACATCTGTTTTAATGTTTTTACTGTATTTTA
1 GAAACATCTATTTCAATATTTTTAATGTATTTTA
19436128 TATATTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.51
Consensus pattern (36 bp):
GAAACATCTATTTCAATATTTTTAATGTATTTTAGG
Found at i:19437721 original size:15 final size:15
Alignment explanation
Indices: 19437712--19437744 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19437702 CAAATGCTAT
19437712 AATAATAAATACAAC
1 AATAATAAATACAAC
*
19437727 AATAATAAATACATC
1 AATAATAAATACAAC
19437742 AAT
1 AAT
19437745 GGCATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:19437770 original size:13 final size:12
Alignment explanation
Indices: 19437752--19437790 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
19437742 AATGGCATAA
19437752 AAATAATATAAAC
1 AAATAA-ATAAAC
19437765 AAATAAATAAAC
1 AAATAAATAAAC
19437777 GAAATAAA-AAAC
1 -AAATAAATAAAC
19437789 AA
1 AA
19437791 TAATCCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 10 0.40
13 13 0.52
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (12 bp):
AAATAAATAAAC
Found at i:19439869 original size:44 final size:45
Alignment explanation
Indices: 19439793--19440116 Score: 166
Period size: 44 Copynumber: 7.4 Consensus size: 45
19439783 AATCTGCTTC
*
19439793 ACTTCAGGA-GATAAGATTTGCCATCTTCAGTCTGC-CTCACTGCA
1 ACTTCAGGAGGATAAGACTTGCCATCTTCAGTCTGCTC-CACTGCA
**
19439837 ACTTCAGGAGGATAAGACTTGCTTTCTT-AGTCTGCTCCACTGCA
1 ACTTCAGGAGGATAAGACTTGCCATCTTCAGTCTGCTCCACTGCA
* * *
19439881 ACTTCAGG-GAGATAAGACTAG--A--TGC-GATCTGCT-CTCTGCA
1 ACTTCAGGAG-GATAAGACTTGCCATCTTCAG-TCTGCTCCACTGCA
* * **
19439921 ACTTCA-GAGAGATAAGA--T-CCAAGGT-TTTAATCCACTCCACTGCA
1 ACTTCAGGAG-GATAAGACTTGCC-A--TCTTCAGTCTGCTCCACTGCA
* * * * ** * * ** *
19439965 ACTTTAGAAAGATAGGA-TTATCAGCTTTAACCTGCTTCACTGCA
1 ACTTCAGGAGGATAAGACTTGCCATCTTCAGTCTGCTCCACTGCA
* *
19440009 ACTTCA-GAGAGATAAGATTTGCCATCTTCAGTCT-ATCTCACTGCA
1 ACTTCAGGAG-GATAAGACTTGCCATCTTCAGTCTGCTC-CACTGCA
**** *
19440054 ACTTCAGGAGGATAAGACTTAATTTCTT-AGTTTGCTCCACTGCA
1 ACTTCAGGAGGATAAGACTTGCCATCTTCAGTCTGCTCCACTGCA
19440098 ACTTCAGG-GAGATAAGACT
1 ACTTCAGGAG-GATAAGACT
19440117 AGATGCGATC
Statistics
Matches: 213, Mismatches: 43, Indels: 48
0.70 0.14 0.16
Matches are distributed among these distances:
39 1 0.00
40 24 0.11
41 6 0.03
43 8 0.04
44 113 0.53
45 57 0.27
46 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (45 bp):
ACTTCAGGAGGATAAGACTTGCCATCTTCAGTCTGCTCCACTGCA
Found at i:19440034 original size:217 final size:210
Alignment explanation
Indices: 19439654--19440201 Score: 747
Period size: 217 Copynumber: 2.5 Consensus size: 210
19439644 CTTCAATCTA
* * * **
19439654 CTCCTCTGCAACTTCAAGGAGATAAGACTAGATGTGATCTGCTCTCTGCGGCTTCAGAGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
* * ** *
19439719 GATCCAAGATTTGTGGTTCTAATCCGCTCCATTGCAACTTCA-AGGAGACAGGATTATTGGTTTT
66 GATCCAAG----GT--TT-TAATCCACTCCATTGCAACTTCAGA-GAGATAGGATTATCAGCTTT
* *
19439783 AATCTGCTTCACTTCAGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGG
123 AACCTGCTTCACTTCAGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGCAACTTCAGGAGG
**
19439848 ATAAGACTTGCTTTCTTAGTCTG
188 ATAAGACTTAATTTCTTAGTCTG
19439871 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
* * *
19439936 GATCCAAGGTTTTAATCCACTCCACTGCAACTTTAGAAAGATAGGATTATCAGCTTTAACCTGCT
66 GATCCAAGGTTTTAATCCACTCCATTGCAACTTCAGAGAGATAGGATTATCAGCTTTAACCTGC-
*
19440001 TCACTGCAACTTCAGAGAGATAAGATTTGCCATCTTCAGTCTATCTCACTGCAACTTCAGGAGGA
130 T---T-C-ACTTCAG-GAGATAAGATTTGCCATCTTCAGTCTACCTCACTGCAACTTCAGGAGGA
*
19440066 TAAGACTTAATTTCTTAGTTTG
189 TAAGACTTAATTTCTTAGTCTG
*
19440088 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGACAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
* * *
19440153 GATCCAAGGTTTTAATCCACCCCATTGTAACTTCAGGGAGATAGGATTA
66 GATCCAAGGTTTTAATCCACTCCATTGCAACTTCAGAGAGATAGGATTA
19440202 CTAGCTACTG
Statistics
Matches: 297, Mismatches: 26, Indels: 16
0.88 0.08 0.05
Matches are distributed among these distances:
210 41 0.14
211 4 0.01
213 2 0.01
214 1 0.00
215 1 0.00
216 7 0.02
217 241 0.81
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (210 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
GATCCAAGGTTTTAATCCACTCCATTGCAACTTCAGAGAGATAGGATTATCAGCTTTAACCTGCT
TCACTTCAGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGCAACTTCAGGAGGATAAGACT
TAATTTCTTAGTCTG
Found at i:19441299 original size:98 final size:99
Alignment explanation
Indices: 19441130--19441327 Score: 353
Period size: 98 Copynumber: 2.0 Consensus size: 99
19441120 CAAACCAAGA
*
19441130 ACCATCCTGAATTTAACATGTGTTTAAGGAATTTACAGCACTTTGTCGATGCCCCTAAAACGTCG
1 ACCATCCTGAATTTAACATGTGTTTAAGGAATTTACAGCACTTTGTCGATGCCCCCAAAACGTCG
* *
19441195 TCTATCCTTTTCTTGTTGACTT-AGTGTAGCAGG
66 TCTATCCTTTCCTTGTTGACTTAAGTATAGCAGG
*
19441228 ACCATCCTGAATTTAACATGTGTTTAGGGAATTTACAGCACTTTGTCGATGCCCCCAAAACGTCG
1 ACCATCCTGAATTTAACATGTGTTTAAGGAATTTACAGCACTTTGTCGATGCCCCCAAAACGTCG
19441293 TCTATCCTTTCCTTGTTGACTTAAGTATAGCAGG
66 TCTATCCTTTCCTTGTTGACTTAAGTATAGCAGG
19441327 A
1 A
19441328 TCACCATATA
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
98 84 0.88
99 11 0.12
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (99 bp):
ACCATCCTGAATTTAACATGTGTTTAAGGAATTTACAGCACTTTGTCGATGCCCCCAAAACGTCG
TCTATCCTTTCCTTGTTGACTTAAGTATAGCAGG
Found at i:19448367 original size:24 final size:24
Alignment explanation
Indices: 19448340--19448385 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
19448330 TCATTTTTTT
* *
19448340 CTGCTCATTCATTTTCTTTTGAAG
1 CTGCTCATGCATTTCCTTTTGAAG
*
19448364 CTGCTCCTGCATTTCCTTTTGA
1 CTGCTCATGCATTTCCTTTTGA
19448386 GACTGTTCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.26, G:0.13, T:0.48
Consensus pattern (24 bp):
CTGCTCATGCATTTCCTTTTGAAG
Found at i:19451770 original size:13 final size:12
Alignment explanation
Indices: 19451752--19451790 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
19451742 AATGGCATAA
19451752 AAATAATATAAAC
1 AAATAA-ATAAAC
19451765 AAATAAATAAAC
1 AAATAAATAAAC
19451777 GAAATAAA-AAAC
1 -AAATAAATAAAC
19451789 AA
1 AA
19451791 TAATCCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 10 0.40
13 13 0.52
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (12 bp):
AAATAAATAAAC
Found at i:19452276 original size:21 final size:20
Alignment explanation
Indices: 19452242--19452280 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
19452232 ATTATACTAC
19452242 AAAAATAAATATGCATATGT
1 AAAAATAAATATGCATATGT
*
19452262 AAAATATATATATGCATAT
1 AAAA-ATAAATATGCATAT
19452281 ATTTTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAAATAAATATGCATATGT
Found at i:19470945 original size:24 final size:25
Alignment explanation
Indices: 19470828--19470958 Score: 83
Period size: 25 Copynumber: 5.3 Consensus size: 25
19470818 AATTCATTTT
19470828 CGGGAATGCTCATACA-AGCACATA-AA
1 CGGGAA-GCTCATA-AGAGC-CATATAA
* * **
19470854 CGAGAAGCTCTTCTGAGCCATATAA
1 CGGGAAGCTCATAAGAGCCATATAA
* ** *
19470879 CGGGAGGCTCATGTGAGCCATGTAA
1 CGGGAAGCTCATAAGAGCCATATAA
*
19470904 CGGGAAGCT-TTAGAGAGCCAT-TAA
1 CGGGAAGCTCATA-AGAGCCATATAA
* * *
19470928 CAGGAAGCTCATACGAGCCA-ATAT
1 CGGGAAGCTCATAAGAGCCATATAA
19470952 CGGGAAG
1 CGGGAAG
19470959 GTTCAAGCAA
Statistics
Matches: 82, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
24 30 0.37
25 47 0.57
26 5 0.06
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.18
Consensus pattern (25 bp):
CGGGAAGCTCATAAGAGCCATATAA
Found at i:19471456 original size:67 final size:68
Alignment explanation
Indices: 19471379--19471514 Score: 238
Period size: 67 Copynumber: 2.0 Consensus size: 68
19471369 TTCAAACATA
*
19471379 TAAATATACATAATTTAGTTACACGAACTTACCTCGACAATT-TACGTTGATTTGTTGTATACTA
1 TAAATATACATAATTTAGTGACACGAACTTACCTCGACAATTGTACGTTGATTTGTTGTATACTA
19471443 ATC
66 ATC
* *
19471446 TAAATATACATAATTTAGTGAGAGGAACTTACCTCGACAATTGTACGTTGATTTGTTGTATACTA
1 TAAATATACATAATTTAGTGACACGAACTTACCTCGACAATTGTACGTTGATTTGTTGTATACTA
19471511 ATC
66 ATC
19471514 T
1 T
19471515 GACACTTTCT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
67 39 0.60
68 26 0.40
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (68 bp):
TAAATATACATAATTTAGTGACACGAACTTACCTCGACAATTGTACGTTGATTTGTTGTATACTA
ATC
Found at i:19479907 original size:13 final size:13
Alignment explanation
Indices: 19479891--19479916 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19479881 AATGTGGTTT
19479891 GCTCATGTTTTAA
1 GCTCATGTTTTAA
19479904 GCTCATGTTTTAA
1 GCTCATGTTTTAA
19479917 ATATTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
GCTCATGTTTTAA
Found at i:19480064 original size:16 final size:16
Alignment explanation
Indices: 19480020--19480067 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
19480010 CATGTTTACG
19480020 TATGCTTTAATAT-TA
1 TATGCTTTAATATATA
*
19480035 -A-GCTTGT-ATGTATA
1 TATGCTT-TAATATATA
19480049 TATGCTTTAATATATA
1 TATGCTTTAATATATA
19480065 TAT
1 TAT
19480068 ATAGTCACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
13 7 0.27
14 4 0.15
15 2 0.08
16 13 0.50
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.50
Consensus pattern (16 bp):
TATGCTTTAATATATA
Found at i:19486957 original size:30 final size:30
Alignment explanation
Indices: 19486918--19486978 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
19486908 AGGAGGAGTA
19486918 AGTACATATTCCTGGTTCTATATGTCAATG
1 AGTACATATTCCTGGTTCTATATGTCAATG
* *
19486948 AGTATATATTCCTTGTTCTATATGTCAATG
1 AGTACATATTCCTGGTTCTATATGTCAATG
19486978 A
1 A
19486979 CATTTTGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (30 bp):
AGTACATATTCCTGGTTCTATATGTCAATG
Found at i:19497077 original size:53 final size:53
Alignment explanation
Indices: 19496997--19497101 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
19496987 ATATTTGACT
*
19496997 TGTTACAAACATGTTCTATGATATGTTAAGATTAATTATTTCATTGTTGAACA
1 TGTTACAAACATGTTCCATGATATGTTAAGATTAATTATTTCATTGTTGAACA
19497050 TGTTACAAACATGTTCCATGATATGTTAAGATTAATTATTTCATTGTTGAAC
1 TGTTACAAACATGTTCCATGATATGTTAAGATTAATTATTTCATTGTTGAAC
19497102 TCACTAACTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (53 bp):
TGTTACAAACATGTTCCATGATATGTTAAGATTAATTATTTCATTGTTGAACA
Found at i:19500150 original size:11 final size:11
Alignment explanation
Indices: 19500134--19500161 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
19500124 CATCAAATCA
19500134 AAATTTAATAT
1 AAATTTAATAT
19500145 AAATTTAATAT
1 AAATTTAATAT
19500156 AAATTT
1 AAATTT
19500162 CATCAAATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAATTTAATAT
Found at i:19503237 original size:17 final size:16
Alignment explanation
Indices: 19503214--19503259 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
19503204 TATTAAATAT
19503214 TATTAAAATAATAGAA
1 TATTAAAATAATAGAA
**
19503230 TGATTAAAATAAATTTAA
1 T-ATTAAAAT-AATAGAA
19503248 TATTAAAATAAT
1 TATTAAAATAAT
19503260 TAATTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 4 0.15
17 16 0.62
18 6 0.23
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (16 bp):
TATTAAAATAATAGAA
Found at i:19503266 original size:20 final size:20
Alignment explanation
Indices: 19503241--19503279 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19503231 GATTAAAATA
19503241 AATTTAATATTAAAATAATT
1 AATTTAATATTAAAATAATT
*
19503261 AATTTAATATTAAATTAAT
1 AATTTAATATTAAAATAAT
19503280 AAAATACTAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTTAATATTAAAATAATT
Found at i:19503317 original size:37 final size:36
Alignment explanation
Indices: 19503248--19503339 Score: 96
Period size: 37 Copynumber: 2.4 Consensus size: 36
19503238 ATAAATTTAA
*
19503248 TATTAAAATAATTAATTTAATATTAAATTAATA-AAATAC
1 TATTAAAATAA-T-ATTAAAT-TTAAATTAATATAAA-AC
* * *
19503287 TATTAAGATAAGTATTAAATTTAATTTAATATTAAAC
1 TATTAAAATAA-TATTAAATTTAAATTAATATAAAAC
19503324 TATTAAAATAATATTA
1 TATTAAAATAATATTA
19503340 TTTTTAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
36 5 0.11
37 22 0.48
38 8 0.17
39 11 0.24
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (36 bp):
TATTAAAATAATATTAAATTTAAATTAATATAAAAC
Found at i:19512633 original size:31 final size:31
Alignment explanation
Indices: 19512597--19512691 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
19512587 CTTAGATAAT
19512597 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
19512628 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
*
19512659 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
19512690 TT
1 TT
19512692 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:19513043 original size:29 final size:27
Alignment explanation
Indices: 19512994--19513052 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
19512984 AATCTATCCT
*
19512994 TTTTATTTATTTATTTATTATTTAACTAA
1 TTTTATTTATTTAGTTATTATTT--CTAA
*
19513023 TTTTATTTATTCTCGTT-TTATTTCTAA
1 TTTTATTTATT-TAGTTATTATTTCTAA
19513050 TTT
1 TTT
19513053 GTGTTTCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.26
29 17 0.63
30 3 0.11
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTATTTATTTAGTTATTATTTCTAA
Found at i:19517128 original size:36 final size:36
Alignment explanation
Indices: 19517061--19517134 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
19517051 GGAGGAGTGC
* *
19517061 ATCAGTCAGAATAGATCCAAAAGTCTATTGAACTGA
1 ATCAGTCAAAATAGATCCAAAAATCTATTGAACTGA
*
19517097 ATCAGTCAAAATAGATCCAAAAAAT-TGTTGAACTGA
1 ATCAGTCAAAATAGATCC-AAAAATCTATTGAACTGA
19517133 AT
1 AT
19517135 AGAGTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 29 0.85
37 5 0.15
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.26
Consensus pattern (36 bp):
ATCAGTCAAAATAGATCCAAAAATCTATTGAACTGA
Found at i:19520539 original size:21 final size:19
Alignment explanation
Indices: 19520513--19520555 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
19520503 GTGTTTACTA
*
19520513 TCTGTTTAGCTCTCATGAGCT
1 TCTGTTCAGC-CT-ATGAGCT
*
19520534 TCTGTTCAGCCTTTGAGCT
1 TCTGTTCAGCCTATGAGCT
19520553 TCT
1 TCT
19520556 AAGTATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (19 bp):
TCTGTTCAGCCTATGAGCT
Found at i:19521970 original size:17 final size:17
Alignment explanation
Indices: 19521948--19521987 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
19521938 AATAATAACA
**
19521948 AAATTTAAATTAATGCT
1 AAATTTAAATTAACACT
19521965 AAATTTAAATTAACACT
1 AAATTTAAATTAACACT
19521982 AAATTT
1 AAATTT
19521988 GAACCAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (17 bp):
AAATTTAAATTAACACT
Found at i:19531479 original size:44 final size:41
Alignment explanation
Indices: 19531401--19531562 Score: 114
Period size: 44 Copynumber: 3.8 Consensus size: 41
19531391 TTATGGTAGA
* * *
19531401 TTTAATCCGAC-CTACTGCCACTTCAGAGG-TATAGGATTCATC
1 TTTAATCCG-CTCCACTGCAACTTCAG-GGAGATAGGATT-ATC
* *
19531443 ATTTTAATCCGCTCCACTGCAACTTGAGGGAGATAGGATTAGC
1 --TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATC
* * * * *
19531486 TTCAATCTGCTCCACTACAACTTCAGTGAGATAAGATTGGGATC
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT---ATC
* *
19531530 TTTAA-CCTGCTCCACTGCAAATTTAGGGAGATA
1 TTTAATCC-GCTCCACTGCAACTTCAGGGAGATA
19531563 AGGTTTGATA
Statistics
Matches: 94, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
41 32 0.34
43 6 0.06
44 56 0.60
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (41 bp):
TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATC
Found at i:19531688 original size:45 final size:44
Alignment explanation
Indices: 19531453--19531831 Score: 234
Period size: 44 Copynumber: 8.5 Consensus size: 44
19531443 ATTTTAATCC
* * * *
19531453 GCTCCACTGCAACTTGAGGGAGATAGGA-T--TAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGCTATCTTCAGTCT
* * ** * **
19531494 GCTCCACTACAACTTCAGTGAGATAAGATTGGGATCTTTAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGCTATCTTCAGTCT
* * * * *
19531538 GCTCCACTGCAAATTTAGGGAGATAAGGTT--TGAT-ATGA-TCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGCT-ATCTTCAGTCT
* * * *
19531579 GCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-TGC----TAT--CTTCAGTCT
* * *
19531630 GTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT-GCTATCTTCAGTCT
** * ** *
19531675 GCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGCTATCTTCAGTCT
* * * *
19531719 GCTCCGCTGCAACTTCAGGGAGATAGGGTTTGCGATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATA-AGATTGCTATCTTCAGTCT
* * **
19531764 GCTCCACTGCAACTTTAGGGATATAAGACTTG-TATCTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTGCTATCTTCAGTCT
* * * *
19531808 GTTACACTGTAACTTCAGAGAGAT
1 GCTCCACTGCAACTTCAGGGAGAT
19531832 GCTCCACTGC
Statistics
Matches: 256, Mismatches: 64, Indels: 33
0.73 0.18 0.09
Matches are distributed among these distances:
41 50 0.20
42 4 0.02
43 2 0.01
44 95 0.37
45 68 0.27
47 5 0.02
48 1 0.00
50 3 0.01
51 28 0.11
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTGCTATCTTCAGTCT
Found at i:19531803 original size:89 final size:89
Alignment explanation
Indices: 19531455--19531831 Score: 275
Period size: 89 Copynumber: 4.2 Consensus size: 89
19531445 TTTAATCCGC
* * * * * *
19531455 TCCACTGCAACTTGAGGGAGATAGGATT----AGCTTCAATCTGCTCCACTACAACTTCAGTGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTCGCGATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
* * * * * *
19531516 ATAAGATTGGGATCTTTAACCTGC
66 ATAAGACTGGTAGCTTCAATCTGT
* * * * * * * *
19531540 TCCACTGCAAATTTAGGGAGATAAGGTT--TGAT-ATGA-TCTGCTCTACTGCAACTTCAGAGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTCGCGATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
* *
19531601 ATAAGATCTGCAATTTATAGCTTCAATTTGT
66 ATAAGA-CTG------GTAGCTTCAATCTGT
* * *
19531632 TCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTCGCGATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
* * *
19531697 ATAAGGCTGGTGGCTTCAATCTGC
66 ATAAGACTGGTAGCTTCAATCTGT
* * * * * *
19531721 TCCGCTGCAACTTCAGGGAGATAGGGTTTGCGATCTTCAGTCTGCTCCACTGCAACTTTAGGGAT
1 TCCACTGCAACTTCAGGGAGATAAGATTCGCGATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
* * *
19531786 ATAAGACTTGTATCTTCAACCTGT
66 ATAAGACTGGTAGCTTCAATCTGT
* * *
19531810 TACACTGTAACTTCAGAGAGAT
1 TCCACTGCAACTTCAGGGAGAT
19531832 GCTCCACTGC
Statistics
Matches: 226, Mismatches: 53, Indels: 22
0.75 0.18 0.07
Matches are distributed among these distances:
85 52 0.23
86 4 0.02
87 1 0.00
89 103 0.46
92 31 0.14
94 2 0.01
95 5 0.02
96 28 0.12
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (89 bp):
TCCACTGCAACTTCAGGGAGATAAGATTCGCGATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
ATAAGACTGGTAGCTTCAATCTGT
Found at i:19531892 original size:44 final size:43
Alignment explanation
Indices: 19531831--19532080 Score: 250
Period size: 44 Copynumber: 5.7 Consensus size: 43
19531821 TTCAGAGAGA
* *
19531831 TGCTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTTAAC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCAAC
* * * ** * *
19531874 ATGTTCCACTACAGCTTCAGGGAGATAAGGTTTTCTATCTTCAGTC
1 -TGCTCCACTGCAACTTCAGGGAGATAA-GACTTGTATCTTCA-AC
* *
19531920 TACTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTCAACC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCAA-C
* *
19531964 TGCTCCACTGCAACTTCAGGGAGATAA-AGTTTGTTATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CTTG-TATCTTCA-AC
* * **
19532009 TGCTCCACTGTAACTTTAGGGAGATAAGACTTGTGGCTTCAAC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCAAC
* *
19532052 TTGCCCCACTGCAACTTCAGAGAGATAAG
1 -TGCTCCACTGCAACTTCAGGGAGATAAG
19532081 GTTCACCATG
Statistics
Matches: 166, Mismatches: 32, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
43 2 0.01
44 93 0.56
45 69 0.42
46 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCAAC
Found at i:19531892 original size:68 final size:68
Alignment explanation
Indices: 19531763--19531899 Score: 202
Period size: 68 Copynumber: 2.0 Consensus size: 68
19531753 ATCTTCAGTC
* * **
19531763 TGCTCCACTGCAACTTTAGGGATATAAGACTTGTATCTTCAACCTGTTACACTGTAACTTCAGAG
1 TGCTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTCAACATGTTACACTACAACTTCAGAG
19531828 AGA
66 AGA
* * * *
19531831 TGCTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTTAACATGTTCCACTACAGCTTCAGGG
1 TGCTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTCAACATGTTACACTACAACTTCAGAG
19531896 AGA
66 AGA
19531899 T
1 T
19531900 AAGGTTTTCT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (68 bp):
TGCTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTCAACATGTTACACTACAACTTCAGAG
AGA
Found at i:19531928 original size:157 final size:157
Alignment explanation
Indices: 19531674--19531988 Score: 443
Period size: 157 Copynumber: 2.0 Consensus size: 157
19531664 ATCTTCAGTC
* * * *
19531674 TGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCGCTGCAACTTCAGGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGTAGCTTCAATCTGCTCCACTACAACTTCAGGG
* * *
19531739 AGATAGGGTTTGCGATCTTCAGTCTGCTCCACTGCAACTTTAGGGATATAAGACTTGTATCTTCA
66 AGATAAGGTTTGCGATCTTCAGTCTACTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTCA
* *
19531804 ACCTGTTACACTGTAACTTCAGAGAGA
131 ACCTGCTACACTGCAACTTCAGAGAGA
* * * * * *
19531831 TGCTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTTAA-CATGTTCCACTACAGCTTCAGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGTAGCTTCAATC-TGCTCCACTACAACTTCAGG
* *
19531895 GAGATAAGGTTTTCTATCTTCAGTCTACTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTC
65 GAGATAAGGTTTGCGATCTTCAGTCTACTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTC
* *
19531960 AACCTGCTCCACTGCAACTTCAGGGAGA
130 AACCTGCTACACTGCAACTTCAGAGAGA
19531988 T
1 T
19531989 AAAGTTTGTT
Statistics
Matches: 138, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
156 1 0.01
157 137 0.99
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (157 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTGGTAGCTTCAATCTGCTCCACTACAACTTCAGGG
AGATAAGGTTTGCGATCTTCAGTCTACTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTCA
ACCTGCTACACTGCAACTTCAGAGAGA
Found at i:19531932 original size:89 final size:89
Alignment explanation
Indices: 19531833--19532083 Score: 351
Period size: 89 Copynumber: 2.8 Consensus size: 89
19531823 CAGAGAGATG
* * * *
19531833 CTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTTAACATGTTCCACTACAGCTTCAGGGAG
1 CTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTCAACATGCTCCACTGCAACTTCAGGGAG
19531898 ATAAGGTTT-TCTATCTTCAGTCTA
66 ATAAGGTTTGT-TATCTTCAGTCTA
*
19531922 CTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTCAACCTGCTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTCAACATGCTCCACTGCAACTTCAGGGAG
* *
19531987 ATAAAGTTTGTTATCTTCAGTCTG
66 ATAAGGTTTGTTATCTTCAGTCTA
* * * ** * * *
19532011 CTCCACTGTAACTTTAGGGAGATAAGACTTGTGGCTTCAACTTGCCCCACTGCAACTTCAGAGAG
1 CTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTCAACATGCTCCACTGCAACTTCAGGGAG
19532076 ATAAGGTT
66 ATAAGGTT
19532084 CACCATGATG
Statistics
Matches: 145, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
89 144 0.99
90 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (89 bp):
CTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTCAACATGCTCCACTGCAACTTCAGGGAG
ATAAGGTTTGTTATCTTCAGTCTA
Found at i:19532070 original size:246 final size:246
Alignment explanation
Indices: 19531629--19532077 Score: 664
Period size: 246 Copynumber: 1.8 Consensus size: 246
19531619 AGCTTCAATT
*
19531629 TGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGG
1 TGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTACTCCACTGCAACTTCAGG
* * * * **
19531694 GAGATAAGGCTGGTGGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAGGGTTTGCGATCTTC
66 GAGATAAGACTGGTAGCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAAGTTTGCGATCTTC
* * ** *
19531759 AGTCTGCTCCACTGCAACTTTAGGGATATAAGACTTGTATCTTCAACCTGTTACACTGTAACTTC
131 AGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAGCTTCAACCTGCCACACTGCAACTTC
19531824 AGAGAGATGCTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTTAACA
196 AGAGAGATGCTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTTAACA
* * * **
19531875 TGTTCCACTACAGCTTCAGGGAGATAAGGTTTTCTATCTTCAGTCTACTCCACTGCAACTTCAGG
1 TGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTACTCCACTGCAACTTCAGG
* * * **
19531940 GATATAAGACTTGTATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAAGTTTGTTATCTTC
66 GAGATAAGACTGGTAGCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAAGTTTGCGATCTTC
* * * *
19532005 AGTCTGCTCCACTGTAACTTTAGGGAGATAAGACTTGTGGCTTCAACTTGCCCCACTGCAACTTC
131 AGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAGCTTCAACCTGCCACACTGCAACTTC
19532070 AGAGAGAT
196 AGAGAGAT
19532078 AAGGTTCACC
Statistics
Matches: 177, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
246 177 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (246 bp):
TGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTACTCCACTGCAACTTCAGG
GAGATAAGACTGGTAGCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAAGTTTGCGATCTTC
AGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAGCTTCAACCTGCCACACTGCAACTTC
AGAGAGATGCTCCACTGCAACTTCAGGGATATAAGACTTGTATCTTTAACA
Found at i:19540974 original size:40 final size:40
Alignment explanation
Indices: 19540919--19540998 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
19540909 ATTCGATAAA
19540919 CCTTCCCTCTCCCGCTCTTCAACACGAGCTCAAGGATCTG
1 CCTTCCCTCTCCCGCTCTTCAACACGAGCTCAAGGATCTG
*
19540959 CCTTCCCTCTCCCGCTCTTTAACACGAGCTCAAGGATCTG
1 CCTTCCCTCTCCCGCTCTTCAACACGAGCTCAAGGATCTG
19540999 AATGTTTCTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.17, C:0.41, G:0.15, T:0.26
Consensus pattern (40 bp):
CCTTCCCTCTCCCGCTCTTCAACACGAGCTCAAGGATCTG
Found at i:19554617 original size:89 final size:89
Alignment explanation
Indices: 19554466--19554842 Score: 567
Period size: 89 Copynumber: 4.2 Consensus size: 89
19554456 TCGGTGAAAC
* *
19554466 CACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCTTGT
1 CACCAGCCTTGCCTCCCTGGGTTTACAGCGAAGCAGACTGAAGATAGCAGATCTTGCCTTCTTGT
19554531 ACTGACAACGAAGCAGATCAAAGA
66 ACTGACAACGAAGCAGATCAAAGA
* * * *
19554555 CACCAGCCTTGCCTCCCTGGGTTTGCAGCGAAGCAGACGGAATAAAGCAGATCTTGCCTTCTTGT
1 CACCAGCCTTGCCTCCCTGGGTTTACAGCGAAGCAGACTGAAGATAGCAGATCTTGCCTTCTTGT
* *
19554620 ACTGACAATGAAGCAGATCGAAGA
66 ACTGACAACGAAGCAGATCAAAGA
*
19554644 CACCAGCCTTGCCTCCCTGGGTTTACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCTTGT
1 CACCAGCCTTGCCTCCCTGGGTTTACAGCGAAGCAGACTGAAGATAGCAGATCTTGCCTTCTTGT
19554709 ACTGACAACGAAGCAGATCAAAGA
66 ACTGACAACGAAGCAGATCAAAGA
* * * * *
19554733 CACCAGCCTTGCCTCCCTGAGTTTACAGC-AGAGCACACTGAAGATAGCGGACCTTGCCTTCCTG
1 CACCAGCCTTGCCTCCCTGGGTTTACAGCGA-AGCAGACTGAAGATAGCAGATCTTGCCTTCTTG
* * *
19554797 TATTGACAGCGAAGCAGATCGAAGA
65 TACTGACAACGAAGCAGATCAAAGA
* *
19554822 TACCAGCCTTGTCTCCCTGGG
1 CACCAGCCTTGCCTCCCTGGG
19554843 CAGCAGCTGA
Statistics
Matches: 262, Mismatches: 25, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
89 262 1.00
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (89 bp):
CACCAGCCTTGCCTCCCTGGGTTTACAGCGAAGCAGACTGAAGATAGCAGATCTTGCCTTCTTGT
ACTGACAACGAAGCAGATCAAAGA
Found at i:19554821 original size:45 final size:45
Alignment explanation
Indices: 19554491--19554832 Score: 204
Period size: 45 Copynumber: 7.7 Consensus size: 45
19554481 CCTGGGTTTG
* * * *
19554491 CAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCTTGTACTGA
1 CAGCGAAGCAGACTGAAGATAGCAGACCTTGCCTTCCTGTATTGA
* * * * *
19554536 CAACGAAGCAGA-TCAAAGACACCAG-CCTTGCCTCCCTGGGT-TTG-
1 CAGCGAAGCAGACT-GAAGATAGCAGACCTTGCCTTCCT--GTATTGA
* * * * * *
19554580 CAGCGAAGCAGACGGAATAAAGCAGATCTTGCCTTCTTGTACTGA
1 CAGCGAAGCAGACTGAAGATAGCAGACCTTGCCTTCCTGTATTGA
** * * * ** *
19554625 CAATGAAGCAGA-TCGAAGACACCAG-CCTTGCCTCCCTGGGTTTA
1 CAGCGAAGCAGACT-GAAGATAGCAGACCTTGCCTTCCTGTATTGA
* * * *
19554669 CAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCTTGTACTGA
1 CAGCGAAGCAGACTGAAGATAGCAGACCTTGCCTTCCTGTATTGA
* * * * * *
19554714 CAACGAAGCAGA-TCAAAGACACCAG-CCTTGCCTCCCTG-AGTTTA
1 CAGCGAAGCAGACT-GAAGATAGCAGACCTTGCCTTCCTGTA-TTGA
* *
19554758 CAGC-AGAGCACACTGAAGATAGCGGACCTTGCCTTCCTGTATTGA
1 CAGCGA-AGCAGACTGAAGATAGCAGACCTTGCCTTCCTGTATTGA
*
19554803 CAGCGAAGCAGA-TCGAAGATACCAG-CCTTG
1 CAGCGAAGCAGACT-GAAGATAGCAGACCTTG
19554833 TCTCCCTGGG
Statistics
Matches: 214, Mismatches: 65, Indels: 37
0.68 0.21 0.12
Matches are distributed among these distances:
43 4 0.02
44 94 0.44
45 112 0.52
46 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.21
Consensus pattern (45 bp):
CAGCGAAGCAGACTGAAGATAGCAGACCTTGCCTTCCTGTATTGA
Found at i:19559378 original size:12 final size:12
Alignment explanation
Indices: 19559358--19559388 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19559348 TCGCTTCTTC
*
19559358 ACCATCATCGGA
1 ACCAGCATCGGA
19559370 ACCAGCATCGGA
1 ACCAGCATCGGA
19559382 ACCAGCA
1 ACCAGCA
19559389 CCAACACCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.35, G:0.19, T:0.10
Consensus pattern (12 bp):
ACCAGCATCGGA
Done.