Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 62 of 150
Found at i:18462623 original size:20 final size:20
Alignment explanation
Indices: 18462600--18462650 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
18462590 CAACTCATAT
18462600 TATCGATACTTACCTTTGGG
1 TATCGATACTTACCTTTGGG
18462620 TATCGATACTTACCTTTGGG
1 TATCGATACTTACCTTTGGG
18462640 TATCGATACTT
1 TATCGATACTT
18462651 TCTTTTGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (20 bp):
TATCGATACTTACCTTTGGG
Found at i:18462657 original size:20 final size:19
Alignment explanation
Indices: 18462554--18462667 Score: 93
Period size: 20 Copynumber: 5.8 Consensus size: 19
18462544 CTAATCTGAG
* *
18462554 CTTTGGGTATCGATACTTT
1 CTTTTGGTATCGATACTTA
* *
18462573 CTTTTGGTATTGATACTCAA
1 CTTTTGGTATCGATACT-TA
** **
18462593 CTCATATTATCGATACTTA
1 CTTTTGGTATCGATACTTA
*
18462612 CCTTTGGGTATCGATACTTA
1 -CTTTTGGTATCGATACTTA
* *
18462632 CCTTTGGGTATCGATACTTT
1 -CTTTTGGTATCGATACTTA
*
18462652 CTTTTGGTACCGATAC
1 CTTTTGGTATCGATAC
18462668 CATTTTAACA
Statistics
Matches: 75, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
19 30 0.40
20 45 0.60
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (19 bp):
CTTTTGGTATCGATACTTA
Found at i:18468458 original size:40 final size:40
Alignment explanation
Indices: 18468392--18468490 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 40
18468382 TAGGGTAACA
* *
18468392 ACCTTTTTTAACCTTTTAATTGGATATCCATTTCAGATAT
1 ACCTTTTTCAACCTTTTCATTGGATATCCATTTCAGATAT
* * * * *
18468432 ATCTTTTTCAACATTTTCATTTGATATCTATTTCGGATAT
1 ACCTTTTTCAACCTTTTCATTGGATATCCATTTCAGATAT
*
18468472 ACCCTTTTCAACCTTTTCA
1 ACCTTTTTCAACCTTTTCA
18468491 AGAATTCAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.48
Consensus pattern (40 bp):
ACCTTTTTCAACCTTTTCATTGGATATCCATTTCAGATAT
Found at i:18472392 original size:18 final size:18
Alignment explanation
Indices: 18472371--18472409 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
18472361 TAGCCATTTA
* *
18472371 TTTGTATTTATTTTTATT
1 TTTGTATTTAGTTTAATT
*
18472389 TTTGTTTTTAGTTTAATT
1 TTTGTATTTAGTTTAATT
18472407 TTT
1 TTT
18472410 ACATTCTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (18 bp):
TTTGTATTTAGTTTAATT
Found at i:18478311 original size:26 final size:24
Alignment explanation
Indices: 18478250--18478327 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 24
18478240 TTATCTATTA
*
18478250 TTATTAGTTATATTA-TATTATTTAT
1 TTATTAGTTATATTATTATT-TTT-C
18478275 TTATT-GTTTATCATCTATTATTTTTC
1 TTATTAG-TTAT-AT-TATTATTTTTC
18478301 TTATTAGTTATATTATTTTATTTTTC
1 TTATTAGTTATATTA--TTATTTTTC
18478327 T
1 T
18478328 AATTCTACTT
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
24 3 0.07
25 11 0.24
26 21 0.47
27 6 0.13
28 4 0.09
ACGTcount: A:0.24, C:0.05, G:0.04, T:0.67
Consensus pattern (24 bp):
TTATTAGTTATATTATTATTTTTC
Found at i:18478312 original size:46 final size:46
Alignment explanation
Indices: 18478221--18478323 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 46
18478211 TTGCCCTATT
* * *
18478221 TTATTTATTTATTTGTTTCTTATCTATTATTATTAGTTATATTATA
1 TTATTTATTTATTTGTTTATCATCTATTATTATTACTTATATTATA
*
18478267 TTATTTATTTA-TTGTTTATCATCTATTATT-TTTCTTATTAGTTATA
1 TTATTTATTTATTTGTTTATCATCTATTATTATTACTTA-TA-TTATA
18478313 TTATTTTATTT
1 TTA-TTTATTT
18478324 TTCTAATTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
44 5 0.10
45 19 0.38
46 19 0.38
47 7 0.14
ACGTcount: A:0.24, C:0.05, G:0.04, T:0.67
Consensus pattern (46 bp):
TTATTTATTTATTTGTTTATCATCTATTATTATTACTTATATTATA
Found at i:18480026 original size:5 final size:5
Alignment explanation
Indices: 18480016--18480075 Score: 68
Period size: 5 Copynumber: 11.6 Consensus size: 5
18480006 ATGAGGATCA
* *
18480016 TTTAT TTTAT TTTCT TTCT-T TTTAT TTTAT TTTAT TTTAT TTTAT GTTTTT
1 TTTAT TTTAT TTTAT TT-TAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT
18480067 TTCTAT TTT
1 TT-TAT TTT
18480076 TAGTCGTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
4 1 0.02
5 38 0.79
6 9 0.19
ACGTcount: A:0.13, C:0.05, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:18494747 original size:20 final size:20
Alignment explanation
Indices: 18494719--18494764 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18494709 ATAAACGTAT
*
18494719 ATATATTATATTTTCTATAC
1 ATATATTATAATTTCTATAC
* *
18494739 ATATTTTATAATTTCTATAT
1 ATATATTATAATTTCTATAC
18494759 ATATAT
1 ATATAT
18494765 ATTTCTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATTATAATTTCTATAC
Found at i:18494815 original size:22 final size:22
Alignment explanation
Indices: 18494787--18494863 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
18494777 TCGTGAATGC
18494787 AAGCTCTCATGTTTAACGTACT
1 AAGCTCTCATGTTTAACGTACT
*
18494809 AAGCTCTCATGTTTAACGAACT
1 AAGCTCTCATGTTTAACGTACT
* * **
18494831 AAACCCTCATGGCTAACGTACT
1 AAGCTCTCATGTTTAACGTACT
18494853 AAGCTCTCATG
1 AAGCTCTCATG
18494864 GCGCCTTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (22 bp):
AAGCTCTCATGTTTAACGTACT
Found at i:18495031 original size:26 final size:25
Alignment explanation
Indices: 18495002--18495052 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
18494992 GCATGTCATT
*
18495002 GTTTTTTTATTATTTATATTAATTTC
1 GTTTATTTATTATTTATATT-ATTTC
18495028 GTTTATTTATTATTTATATTATTTC
1 GTTTATTTATTATTTATATTATTTC
18495053 TATATCATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (25 bp):
GTTTATTTATTATTTATATTATTTC
Found at i:18507452 original size:44 final size:44
Alignment explanation
Indices: 18507355--18507463 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
18507345 GAATAGGGTA
* *
18507355 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTAAAACCAAT
* **
18507399 AATCCTATCTCCCTGAAGTTGAAGTGGAGTGGATTAAAACCACA-
1 AATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTAAAACCA-AT
* * *
18507443 GATCTTATCTCTCTAAAGTTG
1 AATCTTATCTCCCTGAAGTTG
18507464 CTGAGAGCAG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 54 0.98
45 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTAAAACCAAT
Found at i:18507546 original size:44 final size:46
Alignment explanation
Indices: 18507482--18507594 Score: 142
Period size: 44 Copynumber: 2.5 Consensus size: 46
18507472 AGTCGCATCT
* * * *
18507482 AGTCTTATCTCCCTAAAGTTGCAGA-GGAGTAGACT-GAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGATGGAGCAGACTCAAGAAAGCA
*
18507526 GGTCTTATCTCCCTGAAGTTGCA-ATGGAGCAGACTCAAGAAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGATGGAGCAGACTCAAGAAAGCA
* *
18507571 AGTCTTATCCCCCTGAAATTGCAG
1 AGTCTTATCTCCCTGAAGTTGCAG
18507595 TGGGGTAGGC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.02
44 30 0.52
45 27 0.47
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (46 bp):
AGTCTTATCTCCCTGAAGTTGCAGATGGAGCAGACTCAAGAAAGCA
Found at i:18509240 original size:20 final size:20
Alignment explanation
Indices: 18509212--18509258 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18509202 ATATACGTAT
*
18509212 ATATATTATATTTTCTATAC
1 ATATATTATAATTTCTATAC
* *
18509232 ATATTTTATAATTTCTATAT
1 ATATATTATAATTTCTATAC
18509252 ATATATT
1 ATATATT
18509259 TTTCTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATTATAATTTCTATAC
Found at i:18509319 original size:16 final size:17
Alignment explanation
Indices: 18509286--18509318 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
18509276 ATTCATTATA
18509286 TATATATTTATAAATTT
1 TATATATTTATAAATTT
18509303 TATA-ATTTAT-AATTT
1 TATATATTTATAAATTT
18509318 T
1 T
18509319 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATATTTATAAATTT
Found at i:18514973 original size:25 final size:25
Alignment explanation
Indices: 18514945--18515010 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
18514935 CCTATACATT
18514945 TATGCTCAAACGAGCTATGAATCGG
1 TATGCTCAAACGAGCTATGAATCGG
** * *
18514970 TATGCTCTCACGACCTGTGAATCGG
1 TATGCTCAAACGAGCTATGAATCGG
*
18514995 TAAGCTCATAA-GAGCT
1 TATGCTCA-AACGAGCT
18515011 GTGGTGTGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (25 bp):
TATGCTCAAACGAGCTATGAATCGG
Found at i:18518291 original size:50 final size:50
Alignment explanation
Indices: 18518223--18518412 Score: 175
Period size: 50 Copynumber: 3.7 Consensus size: 50
18518213 TTTTTTGTAC
* * **
18518223 TGCCAATGCCATATCCCAGATATGGTCTTACATGCGAGTTCTCATA-TCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGCGACCTCTCA-ACTCGG
* ** * *
18518273 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCAACTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGCGACCTCTCAACTCGG
* * *
18518323 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGCGACCTCTC--AA-CTC---GG
* * *
18518379 TGCCAATGCCAAGTTCCAAACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
18518413 GGATCTCATC
Statistics
Matches: 114, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.01
50 78 0.68
52 2 0.02
53 2 0.02
56 31 0.27
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGCGACCTCTCAACTCGG
Found at i:18521643 original size:18 final size:18
Alignment explanation
Indices: 18521616--18521653 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
18521606 CAAATTAGAG
18521616 CAACAGCCTCAACAACCA
1 CAACAGCCTCAACAACCA
* *
18521634 CAACATCCTCCACAACCA
1 CAACAGCCTCAACAACCA
18521652 CA
1 CA
18521654 CCGAGAGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.47, G:0.03, T:0.08
Consensus pattern (18 bp):
CAACAGCCTCAACAACCA
Found at i:18527929 original size:23 final size:21
Alignment explanation
Indices: 18527897--18527969 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 21
18527887 GATTCAATCC
*
18527897 AAAAAAAAAAAAGAAGAGAGAA
1 AAAAAAAAAAAAGAA-AAAGAA
18527919 AACAAAAAAAAAAGAAAAAGAA
1 AA-AAAAAAAAAAGAAAAAGAA
*
18527941 AAAAAAGGGAAAAAGAAAAA-AA
1 AAAAAA--AAAAAAGAAAAAGAA
*
18527963 AAGAAAA
1 AAAAAAA
18527970 GAACCCCGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.09
22 16 0.36
23 24 0.55
ACGTcount: A:0.84, C:0.01, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAAGAAAAAGAA
Found at i:18527934 original size:16 final size:16
Alignment explanation
Indices: 18527923--18527969 Score: 76
Period size: 17 Copynumber: 2.9 Consensus size: 16
18527913 AGAGAAAACA
18527923 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
*
18527939 AAAAAAAAGGGAAAAAG
1 AAAAAAAA-AGAAAAAG
18527956 AAAAAAAAAGAAAA
1 AAAAAAAAAGAAAA
18527970 GAACCCCGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:18530219 original size:44 final size:44
Alignment explanation
Indices: 18530170--18530862 Score: 208
Period size: 44 Copynumber: 15.8 Consensus size: 44
18530160 CCCTGGGCAG
* *
18530170 CAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAGGCATT
1 CAGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCTAGG-ATT
* * * * * *
18530215 -AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCTCGT-GG-TT
1 CAGTGGAGTAGATTGAAGATGTCAGATCTTATCTCC-C-TAGGATT
* **
18530258 ACAGTGGAGTACATTGAAGCCGT-A-AT-TCTATCTCCCT-GG-TT
1 -CAGTGGAGTAGATTGAAGATGTCAGATCT-TATCTCCCTAGGATT
* * *
18530299 GGCAATGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAGGCATT
1 --CAGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCTAGG-ATT
* * * * * * *
18530346 -AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCTCT-GTGGTT
1 CAGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCTAG-GATT
* *
18530389 ACAGTGGAGTACATTGAAG-TCGT-A-AT-TCTAACTCCCT-GG-TT
1 -CAGTGGAGTAGATTGAAGAT-GTCAGATCT-TATCTCCCTAGGATT
* * *
18530430 GGCAGTGGAATAGATTGAAGAT-TACATATCTTATCTCCCTAGGCAGT
1 --CAGTGGAGTAGATTGAAGATGT-CAGATCTTATCTCCCTAGG-ATT
** * * *
18530477 -AGTGGAGTAGATCAAAGATGGCAGATTTTACCTCCCTGAGG-TT
1 CAGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCT-AGGATT
* * *
18530520 ACAGTGGAGTACATTGAAGCCA-GT-A-AT-TCTATCTCCCTGGGCA-G
1 -CAGTGGAGTAGATTGAAG--ATGTCAGATCT-TATCTCCCTAGG-ATT
* * * *
18530564 CAGTGGAATTGATTGAAGAT-TACATATCTTATCTCCCTAGGCAGT
1 CAGTGGAGTAGATTGAAGATGT-CAGATCTTATCTCCCTAGG-ATT
** * * *
18530609 -AGTGGAGTAGATCAAAGATGGCAGATTTTACCTCCCTGAGG-TT
1 CAGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCT-AGGATT
*
18530652 ACAGTGGAGTACATTGAAGCCA-GT-A-ATGC-TATCTCCCT-GG-TT
1 -CAGTGGAGTAGATTGAAG--ATGTCAGAT-CTTATCTCCCTAGGATT
* * * *
18530694 GGCAGTGGAATAGATTGAAGATTTCAGATCTTAGCTCCCTAAGCG-GT
1 --CAGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCT-AG-GATT
* * * * * * *
18530741 -AGTGGAGCAGATCGAAAATGGCAGATTTTACCTCCCT-GTGGTT
1 CAGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCTAG-GATT
* ** *
18530784 ACAGTGGAGTACATTGAAGCCGT-A-AT-TCTATCT-CCTTGG-TT
1 -CAGTGGAGTAGATTGAAGATGTCAGATCT-TATCTCCCTAGGATT
* *
18530825 GGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCC
1 --CAGTGGAGTAGATTGAAGATGTCAGATCTTATCTCC
18530863 TTAAGCGGCA
Statistics
Matches: 473, Mismatches: 109, Indels: 132
0.66 0.15 0.18
Matches are distributed among these distances:
41 13 0.03
42 65 0.14
43 74 0.16
44 218 0.46
45 92 0.19
46 4 0.01
47 7 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (44 bp):
CAGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCTAGGATT
Found at i:18530323 original size:263 final size:264
Alignment explanation
Indices: 18529916--18530882 Score: 1448
Period size: 263 Copynumber: 3.7 Consensus size: 264
18529906 ACAGAGAAGC
* *
18529916 AGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGCAGATTTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
* *
18529981 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGGGAAGCAGCGG
66 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGTAGCAGTGG
* *
18530045 AATAGATTG-AGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAAATGGCAGAT
130 AATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGAT
***
18530109 TTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGT
195 TTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGTTGGCAGT
18530174 GGAAT
260 GGAAT
* * * *
18530179 AGATTGAAGATTTCAGATCTTATCTCCCTAGGCATTAGTGGAGCAGATCGAAGATGGCGGATTTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
* * *
18530244 ACCT-CCTCGTGGTTACAGTGGAGTACATTGAAGCC-GTAATTCTATCTCCCTGGTTGGCAATGG
66 ACCTCCCT-GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGTAGCAGTGG
* * *
18530307 AATAGATTGAAGATTTCAGATCTTATCTCCCTAGGCATTAGTGGAGCAGATCGAAGATGGCAGAT
130 AATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGAT
* *
18530372 TTTACCTCTCTGTGGTTACAGTGGAGTACATTGAAGTC-GTAATTCTAAC-TCCCTGGTTGGCAG
195 TTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT-ACTTCCCTGGTTGGCAG
18530435 TGGAAT
259 TGGAAT
* * * *
18530441 AGATTGAAGATTACATATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCAAAGATGGCAGATTTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
* *
18530506 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGA
66 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGTAGCAGTGGA
* * * * *
18530571 ATTGATTGAAGATTACATATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCAAAGATGGCAGATT
131 ATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATT
* *
18530636 TTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATGCTA-TCTCCCTGGTTGGCAGT
196 TTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGTTGGCAGT
18530700 GGAAT
260 GGAAT
* *
18530705 AGATTGAAGATTTCAGATCTTAGCTCCCTAAGCGGTAGTGGAGCAGATCGAAA-ATGGCAGATTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AAAGATGGCAGATTT
* * *
18530769 TACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC-GTAATTCTATCTCCTTGGTTGGCAGTGG
65 TACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGTAGCAGTGG
* * *
18530833 AATAGATTGAAGATTTCAGATCTTATCTCCTTAAGCGGCAGTGGAGCAGA
130 AATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
18530883 CTAATGATAG
Statistics
Matches: 633, Mismatches: 61, Indels: 20
0.89 0.09 0.03
Matches are distributed among these distances:
262 147 0.23
263 367 0.58
264 116 0.18
265 3 0.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (264 bp):
AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGTAGCAGTGGA
ATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATT
TTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGTTGGCAGTG
GAAT
Found at i:18530605 original size:132 final size:132
Alignment explanation
Indices: 18529916--18530882 Score: 1455
Period size: 131 Copynumber: 7.4 Consensus size: 132
18529906 ACAGAGAAGC
* * *
18529916 AGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGCAGATTTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAGGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
*** *
18529981 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGGGAAGCAGCGG
66 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGTTGGCAGTGG
18530045 AAT
130 AAT
* * *
18530048 AGATTG-AGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAAATGGCAGATTTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAGGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
***
18530112 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGGGCAGCAGTGG
66 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGTTGGCAGTGG
18530176 AAT
130 AAT
* * *
18530179 AGATTGAAGATTTCAGATCTTATCTCCCTAGGCATTAGTGGAGCAGATCGAAGATGGCGGATTTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAGGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
*
18530244 ACCT-CCTCGTGGTTACAGTGGAGTACATTGAAGCC-GTAATTCTATCTCCCTGGTTGGCAATGG
66 ACCTCCCT-GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGCAGTGG
18530307 AAT
130 AAT
* *
18530310 AGATTGAAGATTTCAGATCTTATCTCCCTAGGCATTAGTGGAGCAGATCGAAGATGGCAGATTTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAGGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
* * *
18530375 ACCTCTCTGTGGTTACAGTGGAGTACATTGAAGTC-GTAATTCTAACTCCCTGGTTGGCAGTGGA
66 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGCAGTGGA
18530439 AT
131 AT
* * *
18530441 AGATTGAAGATTACATATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCAAAGATGGCAGATTTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAGGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
* ***
18530506 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGA
66 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGCAGTGGA
18530571 AT
131 AT
* * * *
18530573 TGATTGAAGATTACATATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCAAAGATGGCAGATTTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAGGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
* *
18530638 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATGCTATCTCCCTGGTTGGCAGTGGA
66 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGCAGTGGA
18530703 AT
131 AT
* * *
18530705 AGATTGAAGATTTCAGATCTTAGCTCCCTAAGCGGTAGTGGAGCAGATCGAAA-ATGGCAGATTT
1 AGATTGAAGATTTCAGATCTTATCTCCCTAGGCAGTAGTGGAGCAGATC-AAAGATGGCAGATTT
*
18530769 TACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC-GTAATTCTATCTCCTTGGTTGGCAGTGG
65 TACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGCAGTGG
18530833 AAT
130 AAT
* * * *
18530836 AGATTGAAGATTTCAGATCTTATCTCCTTAAGCGGCAGTGGAGCAGA
1 AGATTGAAGATTTCAGATCTTATCTCCCTAGGCAGTAGTGGAGCAGA
18530883 CTAATGATAG
Statistics
Matches: 780, Mismatches: 49, Indels: 13
0.93 0.06 0.02
Matches are distributed among these distances:
131 443 0.57
132 334 0.43
133 3 0.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (132 bp):
AGATTGAAGATTTCAGATCTTATCTCCCTAGGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGCAGTGGA
AT
Found at i:18540881 original size:16 final size:17
Alignment explanation
Indices: 18540854--18540887 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
18540844 AGATATAGTA
18540854 AAATATTTTAAAAAAAT
1 AAATATTTTAAAAAAAT
18540871 AAATA-TTTAAAAAAAT
1 AAATATTTTAAAAAAAT
18540887 A
1 A
18540888 CATGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATATTTTAAAAAAAT
Found at i:18543535 original size:16 final size:17
Alignment explanation
Indices: 18543508--18543539 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
18543498 GCTTAGAAAT
18543508 TATTTTTATCATACTAC
1 TATTTTTATCATACTAC
18543525 TATTTTT-TCATACTA
1 TATTTTTATCATACTA
18543540 ATTAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTTTATCATACTAC
Found at i:18545184 original size:28 final size:28
Alignment explanation
Indices: 18545152--18545223 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
18545142 TAATGGGATT
* *
18545152 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGATTAATTATAA
* *
18545180 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTAATTATAA
18545208 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
18545224 ACTTATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTAATTATAA
Found at i:18545229 original size:24 final size:24
Alignment explanation
Indices: 18545152--18545232 Score: 63
Period size: 28 Copynumber: 3.0 Consensus size: 24
18545142 TAATGGGATT
* *
18545152 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGA----AATTATTA
18545180 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGA-A---ATTATTA
*
18545208 AGCACTAAGTGTGCGAACTTATTA
1 AGCACTAAGTGTGCGAAATTATTA
18545232 A
1 A
18545233 ATATTTTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
24 7 0.15
25 1 0.02
27 1 0.02
28 37 0.80
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (24 bp):
AGCACTAAGTGTGCGAAATTATTA
Found at i:18546028 original size:70 final size:70
Alignment explanation
Indices: 18545944--18546186 Score: 369
Period size: 70 Copynumber: 3.4 Consensus size: 70
18545934 TTTGATGCTT
* * * * *
18545944 AAATGCTGCCCAATTCGTTGTATTTATGCTACCTAAATTGTTGTATATATGCTGTCCAATTTTGA
1 AAATGTTGCTCAATTCGTTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGA
18546009 TGTAA
66 TGTAA
* * *
18546014 AAATGTTGCTCAATTTGGTATATATATGCTGCCTAAATTGTTCTATATATGCTGTCCAATTTTGA
1 AAATGTTGCTCAATTCGTTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGA
18546079 TGTAA
66 TGTAA
*
18546084 AAATGTTGCTCAATTTGGTATATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTT
1 AAATGTTGCTCAA-TTCGT-TATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTT
18546149 GATGTAA
64 GATGTAA
* *
18546156 AAATGTTGCTCAATTTGGTATATATATGCTG
1 AAATGTTGCTCAATTCGTTATATATATGCTG
18546187 TCCAATTTTG
Statistics
Matches: 158, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
70 88 0.56
71 6 0.04
72 64 0.41
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.42
Consensus pattern (70 bp):
AAATGTTGCTCAATTCGTTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGA
TGTAA
Found at i:18546043 original size:47 final size:47
Alignment explanation
Indices: 18545987--18546241 Score: 223
Period size: 47 Copynumber: 5.4 Consensus size: 47
18545977 TAAATTGTTG
18545987 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTA
1 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTA
* * * * * * * *
18546034 TATATATGCTG-CCTAA-ATTGTTCTATATATGCTG-TCCAATTTTGATG
1 TATATATGCTGTCC-AATTTTGATGTAAAAATGTTGCT-CAA-TTTGGTA
* * * * * * * * * * *
18546081 TAAAAATGTTG-CTCAATTTGGTATATATATATGCTGC-CTAAATTGTTG
1 TATATATGCTGTC-CAATTTTG-ATGTAAAAATGTTGCTC-AATTTGGTA
18546129 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTA
1 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTA
*
18546176 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTTAATTTGGTA
1 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTA
* *
18546223 TATATATCCTGCCCAATTT
1 TATATATGCTGTCCAATTT
18546242 GTTGTATATA
Statistics
Matches: 167, Mismatches: 31, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
45 1 0.01
46 17 0.10
47 109 0.65
48 25 0.15
49 15 0.09
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (47 bp):
TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTA
Found at i:18546060 original size:23 final size:23
Alignment explanation
Indices: 18545946--18546336 Score: 104
Period size: 23 Copynumber: 16.6 Consensus size: 23
18545936 TGATGCTTAA
* *
18545946 ATGCTGCC-CAATTCGTTGTATTT
1 ATGCTGCCTAAATT-GTTGTATAT
*
18545969 ATGCTACCTAAATTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
* * * *
18545992 ATGCTGTCC-AATTTTGATGTAAAA
1 ATGCTG-CCTAA-ATTGTTGTATAT
* * * *
18546016 ATGTTG-CTCAATTTGGTATATAT
1 ATGCTGCCT-AAATTGTTGTATAT
*
18546039 ATGCTGCCTAAATTGTTCTATAT
1 ATGCTGCCTAAATTGTTGTATAT
* * * *
18546062 ATGCTGTCC-AATTTTGATGTAAAA
1 ATGCTG-CCTAA-ATTGTTGTATAT
* * *
18546086 ATGTTG-CTCAATTTGGTATATATAT
1 ATGCTGCCT-AAATT-GT-TGTATAT
18546111 ATGCTGCCTAAATTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
* * * *
18546134 ATGCTGTCC-AATTTTGATGTAAAA
1 ATGCTG-CCTAA-ATTGTTGTATAT
* * * *
18546158 ATGTTG-CTCAATTTGGTATATAT
1 ATGCTGCCT-AAATTGTTGTATAT
* * * *
18546181 ATGCTGTCC-AATTTTGATGTAAAA
1 ATGCTG-CCTAA-ATTGTTGTATAT
* * * * *
18546205 ATGTTGCTTAATTTGGTATATAT
1 ATGCTGCCTAAATTGTTGTATAT
* * *
18546228 ATCCTGCCCAATTTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
* * * *
18546251 ATGCTGTCC-AATTTTTGGTGTAAAA
1 ATGCTG-CCTAA--ATTGTTGTATAT
* *
18546276 ATGCTG-CTCAATTTTGTTGTGTAT
1 ATGCTGCCT-AA-ATTGTTGTATAT
18546300 ATGCTGACC-AAATTGTTGTATAT
1 ATGCTG-CCTAAATTGTTGTATAT
18546323 ATGCTGTCC-AAATT
1 ATGCTG-CCTAAATT
18546337 TTAGTGTGAA
Statistics
Matches: 273, Mismatches: 67, Indels: 56
0.69 0.17 0.14
Matches are distributed among these distances:
22 3 0.01
23 143 0.52
24 93 0.34
25 31 0.11
26 3 0.01
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (23 bp):
ATGCTGCCTAAATTGTTGTATAT
Found at i:18546123 original size:72 final size:72
Alignment explanation
Indices: 18545968--18546182 Score: 398
Period size: 72 Copynumber: 3.0 Consensus size: 72
18545958 TCGTTGTATT
*
18545968 TATGCTACCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGG-
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
18546032 -TATATA
66 ATATATA
*
18546038 TATGCTGCCTAAATTGTTCTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
18546103 ATATATA
66 ATATATA
18546110 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
18546175 ATATATA
66 ATATATA
18546182 T
1 T
18546183 GCTGTCCAAT
Statistics
Matches: 140, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
70 62 0.44
72 78 0.56
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (72 bp):
TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
ATATATA
Found at i:18546249 original size:72 final size:70
Alignment explanation
Indices: 18546176--18546392 Score: 240
Period size: 72 Copynumber: 3.1 Consensus size: 70
18546166 CAATTTGGTA
* * *
18546176 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTTAATTTGGTATATATATCCTGCCCAATT
1 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTTAATTTGGTATATATATGCTGACCAAAT
18546241 TGTTG
66 TGTTG
* * * * * *
18546246 TATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTTGTTGTGTATATGCTGACCAA
1 TATATATGCTGTCCAA-TTTTGATGTAAAAATGTTGCTTAA-TTTGGTATATATATGCTGACCAA
18546311 ATTGTTG
64 ATTGTTG
* * * * *
18546318 TATATATGCTGTCCAAATTTT-AGTGTGAAAATGTCG-TCTAGTTTGGTATATAAATGCTGTCCA
1 TATATATGCTGTCC-AATTTTGA-TGTAAAAATGTTGCT-TAATTTGGTATATATATGCTGACCA
*
18546381 AATTGATG
63 AATTGTTG
18546389 TATA
1 TATA
18546393 AGGGCTGTCC
Statistics
Matches: 121, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
70 16 0.13
71 50 0.41
72 53 0.44
73 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (70 bp):
TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTTAATTTGGTATATATATGCTGACCAAAT
TGTTG
Found at i:18546280 original size:142 final size:141
Alignment explanation
Indices: 18545943--18546392 Score: 396
Period size: 142 Copynumber: 3.2 Consensus size: 141
18545933 TTTTGATGCT
* * * * * *
18545943 TAAATGCTGCCCAATTCGTTGTATTTATGCTACCTAAATTGTTGTATATATGCTGTCCAATTTTG
1 TAAATGCTGCCCAATTTGTTGTATATATGCTGCCTAAATTGGTGTAAAAATGCTGTCCAATTTTG
* * * * *
18546008 ATGTAAAAATGTTGCTCAATTTGGTATATATATGCTG-CCTAAA--TTGTTCTATATATGCTGTC
66 ATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGTCC-AAATTTTGATGTAAAAATGTTGTC
* * *
18546070 CAATTTTGATGTA
130 TAA-TTTGGTATA
* * * * * * *
18546083 AAAATGTTGCTCAATTTGGTATATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTT
1 TAAATGCTGCCCAATTT-GT-TGTATATATGCTGCCTAAATTGGTGTAAAAATGCTGTCCAATTT
18546148 TGATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGTCC-AATTTTGATGTAAAAATGTTG-
64 TGATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGTCCAAATTTTGATGTAAAAATGTTGT
18546211 CTTAATTTGGTATA
129 C-TAATTTGGTATA
* * *
18546225 TATATCCTGCCCAATTTGTTGTATATATGCTGTCC-AATTTTTGGTGTAAAAATGCTG-CTCAAT
1 TAAATGCTGCCCAATTTGTTGTATATATGCTG-CCTAA--ATTGGTGTAAAAATGCTGTC-CAAT
* ** * * * * * *
18546288 TTTGTTGTGTATATGCTGAC-CAAATTGTTGTATATATGCTGTCCAAATTTT-AGTGTGAAAATG
62 TTTGATGTAAAAATGTTG-CTCAATTTGGTATATATATGCTGTCCAAATTTTGA-TGTAAAAATG
* *
18546351 TCGTCTAGTTTGGTATA
125 TTGTCTAATTTGGTATA
* * *
18546368 TAAATGCTGTCCAAATTGATGTATA
1 TAAATGCTGCCCAATTTGTTGTATA
18546393 AGGGCTGTCC
Statistics
Matches: 255, Mismatches: 41, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
140 27 0.11
141 9 0.04
142 153 0.60
143 65 0.25
144 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (141 bp):
TAAATGCTGCCCAATTTGTTGTATATATGCTGCCTAAATTGGTGTAAAAATGCTGTCCAATTTTG
ATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGTCCAAATTTTGATGTAAAAATGTTGTCT
AATTTGGTATA
Found at i:18546305 original size:119 final size:118
Alignment explanation
Indices: 18546057--18546289 Score: 387
Period size: 119 Copynumber: 2.0 Consensus size: 118
18546047 TAAATTGTTC
* *
18546057 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATATGCTGCCTAA
1 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGG-ATATATATATCCTGCCCAA
*
18546122 ATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTA
65 ATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTA
* *
18546176 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTTAATTTGG-TATATATATCCTGCCCAAT
1 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGATATATATATCCTGCCCAAA
*
18546240 TTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTT
66 TTGTTGTATATATGCTGTCCAA-TTTTGATGTAAAAATGCTGCTCAATTT
18546290 TGTTGTGTAT
Statistics
Matches: 107, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
117 38 0.36
118 25 0.23
119 44 0.41
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.43
Consensus pattern (118 bp):
TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGATATATATATCCTGCCCAAA
TTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTA
Found at i:18546315 original size:189 final size:190
Alignment explanation
Indices: 18545987--18546390 Score: 595
Period size: 189 Copynumber: 2.1 Consensus size: 190
18545977 TAAATTGTTG
* *
18545987 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGCCTAAAT
1 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATCCTGCCCAAAT
*
18546052 TGTTCTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATATGCTG
66 TGTTCTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTATATATATATGCTG
*
18546117 CCTAAATTGTTGTATATATGCTGTCC-AATTTT-GATGTAAAAATGTTG-CTCAATTTGGTA
131 CCTAAATTGTTGTATATATGCTGTCCAAATTTTAG-TGTAAAAATGTCGTCT-AATTTGGTA
* *
18546176 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTTAATTTGGTATATATATCCTGCCCAATT
1 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATCCTGCCCAAAT
* * * * *
18546241 TGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTTGT-TGTGTATATGCT
66 TGTTCTATATATGCTGTCCAA-TTTTGATGTAAAAATGCTGCTCAATTTGGTATATATATATGCT
* *
18546305 GACC-AAATTGTTGTATATATGCTGTCCAAATTTTAGTGTGAAAATGTCGTCTAGTTTGGTA
130 G-CCTAAATTGTTGTATATATGCTGTCCAAATTTTAGTGTAAAAATGTCGTCTAATTTGGTA
* *
18546366 TATAAATGCTGTCCAA-ATTGATGTA
1 TATATATGCTGTCCAATTTTGATGTA
18546391 TAAGGGCTGT
Statistics
Matches: 195, Mismatches: 15, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
189 123 0.63
190 69 0.35
191 3 0.02
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (190 bp):
TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATCCTGCCCAAAT
TGTTCTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTATATATATATGCTG
CCTAAATTGTTGTATATATGCTGTCCAAATTTTAGTGTAAAAATGTCGTCTAATTTGGTA
Found at i:18552726 original size:23 final size:23
Alignment explanation
Indices: 18552696--18552742 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
18552686 TGCTTAATTA
18552696 TGTTGTATATATGCTGCCCAAAT
1 TGTTGTATATATGCTGCCCAAAT
*
18552719 TGTTGTATATATGCTGTCCAAAT
1 TGTTGTATATATGCTGCCCAAAT
18552742 T
1 T
18552743 TTGGTGTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.43
Consensus pattern (23 bp):
TGTTGTATATATGCTGCCCAAAT
Found at i:18552760 original size:25 final size:25
Alignment explanation
Indices: 18552701--18552790 Score: 75
Period size: 23 Copynumber: 3.8 Consensus size: 25
18552691 AATTATGTTG
* *
18552701 TATATATGCTGCCCAAATTGTT-GTA
1 TATAAATGCTGTCCAAATT-TTGGTA
*
18552726 TAT--ATGCTGTCCAAATTTTGGTG
1 TATAAATGCTGTCCAAATTTTGGTA
* *
18552749 TGA-AAATGCTGT-C-TAGTTTGGTA
1 T-ATAAATGCTGTCCAAATTTTGGTA
18552772 TATAAATGCTGTCCAAATT
1 TATAAATGCTGTCCAAATT
18552791 GATATATAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
22 3 0.06
23 33 0.65
24 3 0.06
25 12 0.24
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (25 bp):
TATAAATGCTGTCCAAATTTTGGTA
Found at i:18552811 original size:71 final size:72
Alignment explanation
Indices: 18552663--18552811 Score: 160
Period size: 71 Copynumber: 2.1 Consensus size: 72
18552653 TTTGGTACTA
* * * * * *
18552663 TCCAATTTTTGGTGTAAAAATGCTGCTTAATTATGTTGTATATATGCTGCCCAAATTGTTGTATA
1 TCCAAATTTTGGTGTAAAAATGCTGCTTAATTATGGTATATAAATGCTGCCCAAATTGATATATA
*
18552728 TATGCTG
66 TAGGCTG
* * *
18552735 TCCAAATTTTGGTGTGAAAATGCTG-TCTAGTT-TGGTATATAAATGCTGTCCAAATTGATATAT
1 TCCAAATTTTGGTGTAAAAATGCTGCT-TAATTATGGTATATAAATGCTGCCCAAATTGATATAT
*
18552798 A-AGGGTTG
65 ATA-GGCTG
18552806 TCCAAA
1 TCCAAA
18552812 CAGGGTAGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
70 1 0.02
71 36 0.56
72 27 0.42
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (72 bp):
TCCAAATTTTGGTGTAAAAATGCTGCTTAATTATGGTATATAAATGCTGCCCAAATTGATATATA
TAGGCTG
Found at i:18559205 original size:28 final size:28
Alignment explanation
Indices: 18559173--18559244 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
18559163 TAATGAGATT
* *
18559173 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGATTAATTATAA
* *
18559201 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTAATTATAA
18559229 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
18559245 ACTTATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTAATTATAA
Found at i:18559250 original size:24 final size:24
Alignment explanation
Indices: 18559173--18559253 Score: 63
Period size: 28 Copynumber: 3.0 Consensus size: 24
18559163 TAATGAGATT
* *
18559173 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGA----AATTATTA
18559201 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGA-A---ATTATTA
*
18559229 AGCACTAAGTGTGCGAACTTATTA
1 AGCACTAAGTGTGCGAAATTATTA
18559253 A
1 A
18559254 ATATTTTCGA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
24 7 0.15
25 1 0.02
27 1 0.02
28 37 0.80
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (24 bp):
AGCACTAAGTGTGCGAAATTATTA
Found at i:18559994 original size:23 final size:23
Alignment explanation
Indices: 18559967--18560158 Score: 71
Period size: 23 Copynumber: 8.3 Consensus size: 23
18559957 TGATGTTTAA
* *
18559967 ATGCTGCCC-AAGTCGTTGTATTT
1 ATGCTGCCCAAACT-GTTGTATAT
*
18559990 ATGCTGCCTAAACTGTTGTATAT
1 ATGCTGCCCAAACTGTTGTATAT
* ** * * *
18560013 ATGCTGTCCAATTTTGATGTAAAA
1 ATGCTGCCCAA-ACTGTTGTATAT
* * ** * *
18560037 ATGTTGCTCAATTTGGTATATAT
1 ATGCTGCCCAAACTGTTGTATAT
* *
18560060 ATGCTGCCTAAATTGTTGTATAT
1 ATGCTGCCCAAACTGTTGTATAT
* ** * * *
18560083 ATGCTGTCCAATTTTGATGTAAAA
1 ATGCTGCCCAA-ACTGTTGTATAT
* * ** * *
18560107 ATGTTGCTCAATTTGGTATATAT
1 ATGCTGCCCAAACTGTTGTATAT
* *
18560130 ATGCTGCCTAAATTGTTGTATAT
1 ATGCTGCCCAAACTGTTGTATAT
18560153 ATGCTG
1 ATGCTG
18560159 TTCAATTTTG
Statistics
Matches: 124, Mismatches: 42, Indels: 6
0.72 0.24 0.03
Matches are distributed among these distances:
23 90 0.73
24 34 0.27
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.42
Consensus pattern (23 bp):
ATGCTGCCCAAACTGTTGTATAT
Found at i:18560039 original size:70 final size:70
Alignment explanation
Indices: 18559989--18560201 Score: 381
Period size: 70 Copynumber: 3.0 Consensus size: 70
18559979 TCGTTGTATT
*
18559989 TATGCTGCCTAAACTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
18560054 ATATA
66 ATATA
18560059 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
18560124 ATATA
66 ATATA
* * * *
18560129 TATGCTGCCTAAATTGTTGTATATATGCTGTTCAATTTTGATGTAAAAATATTGCTCTATTTGAT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
18560194 ATATA
66 ATATA
18560199 TAT
1 TAT
18560202 ATATATATAT
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 138 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (70 bp):
TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
ATATA
Found at i:18560048 original size:24 final size:24
Alignment explanation
Indices: 18560013--18560178 Score: 69
Period size: 23 Copynumber: 7.1 Consensus size: 24
18560003 TGTTGTATAT
18560013 ATGCTG-TCCAATTTTGATGTAAAA
1 ATGCTGCT-CAATTTTGATGTAAAA
* * * * *
18560037 ATGTTGCTCAA-TTTGGTATATAT
1 ATGCTGCTCAATTTTGATGTAAAA
* * * *
18560060 ATGCTGC-CTAA-ATTGTTGTATAT
1 ATGCTGCTC-AATTTTGATGTAAAA
18560083 ATGCTG-TCCAATTTTGATGTAAAA
1 ATGCTGCT-CAATTTTGATGTAAAA
* * * * *
18560107 ATGTTGCTCAA-TTTGGTATATAT
1 ATGCTGCTCAATTTTGATGTAAAA
* * * *
18560130 ATGCTGC-CTAA-ATTGTTGTATAT
1 ATGCTGCTC-AATTTTGATGTAAAA
*
18560153 ATGCTGTTCAATTTTGATGTAAAA
1 ATGCTGCTCAATTTTGATGTAAAA
18560177 AT
1 AT
18560179 ATTGCTCTAT
Statistics
Matches: 106, Mismatches: 27, Indels: 18
0.70 0.18 0.12
Matches are distributed among these distances:
22 2 0.02
23 66 0.62
24 36 0.34
25 2 0.02
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (24 bp):
ATGCTGCTCAATTTTGATGTAAAA
Found at i:18560199 original size:2 final size:2
Alignment explanation
Indices: 18560192--18560221 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18560182 GCTCTATTTG
*
18560192 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18560222 GCTGCCCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18560248 original size:23 final size:24
Alignment explanation
Indices: 18560218--18560319 Score: 100
Period size: 23 Copynumber: 4.3 Consensus size: 24
18560208 ATATATATAC
18560218 ATATGCTGCCCAA-TTTGTTGTAT
1 ATATGCTGCCCAATTTTGTTGTAT
* * * *
18560241 ATACGCTGTCCAATTTTTGGTGTAA
1 ATATGCTGCCCAA-TTTTGTTGTAT
* * *
18560266 AAATACTGCTCAATTTTGTTGTAT
1 ATATGCTGCCCAATTTTGTTGTAT
**
18560290 ATATGCTGCCCAA-ACTGTTGTAT
1 ATATGCTGCCCAATTTTGTTGTAT
18560313 ATATGCT
1 ATATGCT
18560320 ATTCAAATTT
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
23 26 0.43
24 19 0.31
25 16 0.26
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (24 bp):
ATATGCTGCCCAATTTTGTTGTAT
Found at i:18562752 original size:41 final size:41
Alignment explanation
Indices: 18562698--18562911 Score: 252
Period size: 41 Copynumber: 5.2 Consensus size: 41
18562688 TACCAATCAT
* * *
18562698 ATAGCTGAAGCTATTACAATTCTGCACACTAAGTGCCTTAC
1 ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
* * * *
18562739 CTAGCCGAAGCTATTATAATTCCACAAACTAAGTGCCTTCC
1 ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
*
18562780 ATAGCCAAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
1 ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
** * *
18562821 ATAGCCGAAGCTATTATAATTATGCACACTAAGTGCCATAT
1 ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
* ** *
18562862 ATAGCCAAAGCTATTCCAAAT-CGCACACTAAGTGCCATTA-
1 ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGCC-TTAC
*
18562902 ATAACCGAAG
1 ATAGCCGAAG
18562912 ATATCTCGAA
Statistics
Matches: 147, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
40 22 0.15
41 125 0.85
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (41 bp):
ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
Found at i:18570069 original size:41 final size:41
Alignment explanation
Indices: 18570003--18570198 Score: 218
Period size: 41 Copynumber: 4.8 Consensus size: 41
18569993 CAATGTTTCA
* *
18570003 CACACTAATTGCCAATCATATAGCCGAAGCTATTATAATTCTG
1 CACACTAAGTGCC-TTC-TATAGCCGAAGCTATTATAATTCTG
*
18570046 CACACTAAGTGCCTTCTATAGCCGAAGCTATTATAATTCAG
1 CACACTAAGTGCCTTCTATAGCCGAAGCTATTATAATTCTG
*
18570087 CACACTAAGTGCCTTAC-ATAGCCGAAGCTATTATAATTCTA
1 CACACTAAGTGCCTT-CTATAGCCGAAGCTATTATAATTCTG
* * * * ** *
18570128 TACACTAAGTGCCATATATAGCCAAAGCTATTCCAAATC-G
1 CACACTAAGTGCCTTCTATAGCCGAAGCTATTATAATTCTG
* *
18570168 CACACTAAGTGCCATT-AATAACCGAAGCTAT
1 CACACTAAGTGCC-TTCTATAGCCGAAGCTAT
18570199 CTCGAATTTC
Statistics
Matches: 132, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
40 24 0.18
41 93 0.70
42 3 0.02
43 12 0.09
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (41 bp):
CACACTAAGTGCCTTCTATAGCCGAAGCTATTATAATTCTG
Found at i:18570159 original size:82 final size:81
Alignment explanation
Indices: 18570003--18570198 Score: 250
Period size: 82 Copynumber: 2.4 Consensus size: 81
18569993 CAATGTTTCA
* * * * *
18570003 CACACTAATTGCCAATCATATAGCCGAAGCTATTATAATTCTGCACACTAAGTGCCTTCTATAGC
1 CACACTAAGTGCC-ATTA-ATAGCCGAAGCTATTATAATTCTACACACTAAGTGCCATATATAGC
* * *
18570068 CGAAGCTATTATAATTCAG
64 CAAAGCTATTACAAATC-G
*
18570087 CACACTAAGTGCC-TTACATAGCCGAAGCTATTATAATTCTATACACTAAGTGCCATATATAGCC
1 CACACTAAGTGCCATTA-ATAGCCGAAGCTATTATAATTCTACACACTAAGTGCCATATATAGCC
*
18570151 AAAGCTATTCCAAATCG
65 AAAGCTATTACAAATCG
*
18570168 CACACTAAGTGCCATTAATAACCGAAGCTAT
1 CACACTAAGTGCCATTAATAGCCGAAGCTAT
18570199 CTCGAATTTC
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
81 27 0.27
82 60 0.61
84 12 0.12
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (81 bp):
CACACTAAGTGCCATTAATAGCCGAAGCTATTATAATTCTACACACTAAGTGCCATATATAGCCA
AAGCTATTACAAATCG
Found at i:18575110 original size:25 final size:25
Alignment explanation
Indices: 18575064--18575111 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
18575054 CGTTATATGG
*
18575064 CTCTTTGTGAACTTCTCAATTAAAT
1 CTCTTTGTGAACTTCCCAATTAAAT
*
18575089 CTCTTTGTGAGA-TTCCCGATTAA
1 CTCTTTGTGA-ACTTCCCAATTAA
18575112 TGGCTCTCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (25 bp):
CTCTTTGTGAACTTCCCAATTAAAT
Found at i:18586495 original size:103 final size:105
Alignment explanation
Indices: 18586293--18586495 Score: 311
Period size: 103 Copynumber: 2.0 Consensus size: 105
18586283 CACATGACCT
* * * * *
18586293 TGTGTCATTTTTATTTTAGGTGTAGGTTTCACACGGTCTGAGACACGGCCGTGTGTACCAAGTTA
1 TGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGGACGTGTGTACCAAGTCA
* *
18586358 GTGACTTACACGGTCTGGCACACGGCTTGTGACACAGTCG
66 ATGACTTACACGGTCTGGCACACGGCTTGCGACACAGTCG
18586398 TGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACAC-GAC-TGTGTACCAAGTCA
1 TGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGGACGTGTGTACCAAGTCA
* *
18586461 ATGAGTTACACGGTCTGGCACATGGCTTGCGACAC
66 ATGACTTACACGGTCTGGCACACGGCTTGCGACAC
18586496 GACCGTGTGA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
103 44 0.49
104 2 0.02
105 43 0.48
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (105 bp):
TGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGGACGTGTGTACCAAGTCA
ATGACTTACACGGTCTGGCACACGGCTTGCGACACAGTCG
Found at i:18597563 original size:42 final size:41
Alignment explanation
Indices: 18597497--18597581 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 41
18597487 TTAGAAAGTA
*
18597497 ATTGATAGATCTTCCCAAAAAAAAAAGAAGAATAAATTTGTT
1 ATTGATAGATCTTCCCAAAAAAAAAAGAAAAAT-AATTTGTT
** * *
18597539 ATTGATAGATCTTCCCCCAGAAAAAAGAAAAATAATTTTTT
1 ATTGATAGATCTTCCCAAAAAAAAAAGAAAAATAATTTGTT
18597580 AT
1 AT
18597582 ATACTATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
41 9 0.24
42 29 0.76
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.31
Consensus pattern (41 bp):
ATTGATAGATCTTCCCAAAAAAAAAAGAAAAATAATTTGTT
Found at i:18605215 original size:25 final size:24
Alignment explanation
Indices: 18605186--18605266 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 24
18605176 AAGCTCTTTC
*
18605186 GAGCTGAATAATGGGAAGATCATG
1 GAGCTGAATAATGGGAAGCTCATG
*
18605210 TGAGCTGAATAATGGGAAGCTCATAC
1 -GAGCTGAATAATGGGAAGCTCAT-G
* *
18605236 GAGCTAAATAACGGGAAGCTCATAG
1 GAGCTGAATAATGGGAAGCTCAT-G
18605261 GAGCTG
1 GAGCTG
18605267 TGGTGTGTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.20
Consensus pattern (24 bp):
GAGCTGAATAATGGGAAGCTCATG
Found at i:18621235 original size:45 final size:45
Alignment explanation
Indices: 18621166--18621251 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
18621156 AGATACTTGG
* *
18621166 TGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCCGA
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGA
18621211 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
18621252 TCGGTTCACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (45 bp):
TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGA
Found at i:18621430 original size:50 final size:50
Alignment explanation
Indices: 18621253--18621439 Score: 171
Period size: 51 Copynumber: 3.7 Consensus size: 50
18621243 CAATGATGTT
* * * * *
18621253 CGGTTCACATAGTAGCCTGTACATAGTACTACACATGTAACAATTACCA-TC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGAC--TTAACATTC
* * * * **
18621304 CGATATACGTAGTAGCCTGCATATAGTACTACACACGTGATCGAAAC-TATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CTTAACAT-TC
* * * * *
18621355 CAGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACTTATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACTTAACATTC
*
18621405 CGGTACACGTAGCAGCCTGCACATAGTACTACACA
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACA
18621440 CATGACCATC
Statistics
Matches: 106, Mismatches: 26, Indels: 9
0.75 0.18 0.06
Matches are distributed among these distances:
50 38 0.36
51 67 0.63
52 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACTTAACATTC
Found at i:18621468 original size:101 final size:99
Alignment explanation
Indices: 18621259--18621444 Score: 239
Period size: 101 Copynumber: 1.8 Consensus size: 99
18621249 TGTTCGGTTC
* * * *
18621259 ACATAGTAGCCTGTACATAGTACTACACATGTAACAATTACCATCCGATATACGTAGTAGCCTGC
1 ACATAGTAGCCTGCACATAGTACTACACATGCAAC-ATTACCATCCGATACACGTAGCAGCCTGC
* * *
18621324 ATATAGTACTACACACGTGATCGAAACTATCCAGT
65 ACATAGTACTACACACATGATCCAAACTATCCAGT
* * *
18621359 ACGCATAGTAGCCTGCACATAGTACTACACATGCGAC-TTATCATTCCGGTACACGTAGCAGCCT
1 A--CATAGTAGCCTGCACATAGTACTACACATGCAACATTACCA-TCCGATACACGTAGCAGCCT
18621423 GCACATAGTACTACACACATGA
63 GCACATAGTACTACACACATGA
18621445 CCATCACTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
100 6 0.08
101 37 0.50
102 31 0.42
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.24
Consensus pattern (99 bp):
ACATAGTAGCCTGCACATAGTACTACACATGCAACATTACCATCCGATACACGTAGCAGCCTGCA
CATAGTACTACACACATGATCCAAACTATCCAGT
Found at i:18622806 original size:36 final size:36
Alignment explanation
Indices: 18622759--18622832 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
18622749 AGCAAGCTCT
*
18622759 ATTCAATTCAGTAGCCTCTT-GGATCTATTCTGACTG
1 ATTCAATTCAGTAGCCT-TTCGGATCTATTCTAACTG
18622795 ATTCAATTCAGTAGCCTTTCGGATCTATTCTAACTG
1 ATTCAATTCAGTAGCCTTTCGGATCTATTCTAACTG
18622831 AT
1 AT
18622833 ATGCTCATCC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 2 0.06
36 34 0.94
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (36 bp):
ATTCAATTCAGTAGCCTTTCGGATCTATTCTAACTG
Found at i:18625275 original size:69 final size:69
Alignment explanation
Indices: 18625175--18625657 Score: 426
Period size: 69 Copynumber: 7.1 Consensus size: 69
18625165 GTTCTGGTTT
* * ** * **
18625175 TTCATCTGCAAACCTTAATATGACAACTGGGAGTTTTGCTCTTACTAACTGTTTTGGAGGTTGC-
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
*
18625239 GATTC
66 G-CTC
** * * * * *
18625244 TTCACCTGTAAACCTTATTATGATAGTTGGGAGCTTTGCTCTCGTTAA-TTTTTATGGAGGTTGT
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTT-TGGAGGTTGC
*
18625308 GGCTC
65 AGCTC
* * * ** * *
18625313 TTCACCTGTGAACCTTAATATTACAATTGGGAGCTTTATTGTCGCTAACTATTTTGGAGGTTGCA
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
18625378 GCTC
66 GCTC
* * * * * * * *
18625382 TTCACTTGCGAACTTTAATATGACAGCTGAGAGCTTTACTCTCGCTAATTTTTTTGGAGGTTACA
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
18625447 GCTC
66 GCTC
* * * * *
18625451 TTCGCCTGCGAACATTAATATGACAGTTGGGAGCTTTGCTCTCACTAACAGTTTTGGAGGTTGTA
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
*
18625516 GTTC
66 GCTC
** * * * ** * *
18625520 TTTGCCTACGAACTTTAACATGACAACTGGGAGCTTTGCTTTCGCTAACTGTTTTAGAGGTT--A
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
18625583 ---C
66 GCTC
* * * *
18625584 -T-GCCTGCGAGCCTTAATATGACAGTTGTGAGCTTTGCTCTCGCTAACTGCTTTGGAGGTTGCA
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
18625647 GCTC
66 GCTC
*
18625651 TTTACCT
1 TTCACCT
18625658 TTAAACCTTA
Statistics
Matches: 333, Mismatches: 71, Indels: 20
0.79 0.17 0.05
Matches are distributed among these distances:
62 49 0.15
63 1 0.00
64 2 0.01
67 2 0.01
68 5 0.02
69 269 0.81
70 5 0.02
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (69 bp):
TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
GCTC
Found at i:18641805 original size:262 final size:262
Alignment explanation
Indices: 18641346--18641817 Score: 600
Period size: 262 Copynumber: 1.8 Consensus size: 262
18641336 AAATAAGAAC
* * * * * *
18641346 ATATCCCCAAAACTAAGATGGGAATTTTAAAGTCAAATTGTACAATTCTGAAACTTTAAATTTAG
1 ATATCCACAAAACTAAGATGGGAACTTTAAAGTCAAATTGCACAATTCTAAAAATTCAAATTTAG
* * *
18641411 GAGAAAATGAAAAAGTATGACATTAGCTTTCTCATAGATTTTATGATTACAAAGAGCTAAAGTTA
66 GAGAAAATGAAAAAGTATAACATTAGCTTTCTCATAGAATTTATGATTACAAAGAGCAAAAGTTA
*
18641476 TGCCACAAAATTTTCATCAGCCAATAATCATGCAACCCATATAACCAGAAACCGAGACTACATCT
131 TGCCACAAAATTTTCATCAACCAATAATCATGCAACCCATATAACCAGAAACCGAGACTACATCT
*
18641541 AGTCAGTAAAACTCTGATGTCCAAGAAACACACTGCTCAAAACCTGGACATTTTAAAATAACAAA
196 AGTCAGGAAAACTCTGATGTCCAAGAAACACACTGCTCAAAACCTGGACATTTTAAAATAACAAA
18641606 AT
261 AT
*
18641608 ATATCCACAAAACTAAGATGGGAACTTTAAAGTCAATTTGCACAATTCTAAAAATTCAAATTTTC
1 ATATCCACAAAACTAAGATGGGAACTTTAAAGTCAAATTGCACAATTCTAAAAATTCAAA-TTT-
* *
18641673 A-GAGAAAATGAAGAAGTATAACGTTAGCTTTCTGGCA-A-AATTTATG-TTAGCAGAA-AGTCA
64 AGGAGAAAATGAAAAAGTATAACATTAGCTTTCT--CATAGAATTTATGATTA-CA-AAGAG-CA
* ** * * * * * *
18641733 AAATTTATGCTGCAAATTTTTCATCAACCGATAATTATGCCACCTATATAACCAGAAA-C-TGAC
124 AAAGTTATGCCACAAAATTTTCATCAACCAATAATCATGCAACCCATATAACCAGAAACCGAGAC
*
18641796 T-CTATCTAGTTAGGAAAACTCT
189 TAC-ATCTAGTCAGGAAAACTCT
18641818 CTAGTCCCAA
Statistics
Matches: 178, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
261 1 0.01
262 77 0.43
263 44 0.25
264 54 0.30
265 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (262 bp):
ATATCCACAAAACTAAGATGGGAACTTTAAAGTCAAATTGCACAATTCTAAAAATTCAAATTTAG
GAGAAAATGAAAAAGTATAACATTAGCTTTCTCATAGAATTTATGATTACAAAGAGCAAAAGTTA
TGCCACAAAATTTTCATCAACCAATAATCATGCAACCCATATAACCAGAAACCGAGACTACATCT
AGTCAGGAAAACTCTGATGTCCAAGAAACACACTGCTCAAAACCTGGACATTTTAAAATAACAAA
AT
Found at i:18647925 original size:9 final size:9
Alignment explanation
Indices: 18647911--18647951 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
18647901 ACAAATTAAG
18647911 AAAGAAAAA
1 AAAGAAAAA
18647920 AAAGAAAAA
1 AAAGAAAAA
18647929 AAAGAAAGAA
1 AAAGAAA-AA
*
18647939 AAAGAAAAG
1 AAAGAAAAA
18647948 AAAG
1 AAAG
18647952 GGAGAAAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 21 0.70
10 9 0.30
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:18647958 original size:19 final size:19
Alignment explanation
Indices: 18647911--18647951 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
18647901 ACAAATTAAG
18647911 AAAGAAA-AAAAAGAAAAA
1 AAAGAAAGAAAAAGAAAAA
*
18647929 AAAGAAAGAAAAAGAAAAG
1 AAAGAAAGAAAAAGAAAAA
18647948 AAAG
1 AAAG
18647952 GGAGAAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAAAAAGAAAAA
Found at i:18648636 original size:16 final size:16
Alignment explanation
Indices: 18648617--18648649 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18648607 TTTGGCACTT
18648617 TTATA-TTGAATTGAAA
1 TTATAGTTG-ATTGAAA
18648633 TTATAGTTGATTGAAA
1 TTATAGTTGATTGAAA
18648649 T
1 T
18648650 GGATTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (16 bp):
TTATAGTTGATTGAAA
Found at i:18649902 original size:21 final size:22
Alignment explanation
Indices: 18649878--18649924 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
18649868 TAGAATGATA
18649878 GTTTTG-GCATGTTTTGAGTGT
1 GTTTTGAGCATGTTTTGAGTGT
* *
18649899 G-TTTGATCGTGTTTTGAGTGT
1 GTTTTGAGCATGTTTTGAGTGT
18649920 GTTTT
1 GTTTT
18649925 TGAGTTGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 4 0.18
21 15 0.68
22 3 0.14
ACGTcount: A:0.09, C:0.04, G:0.32, T:0.55
Consensus pattern (22 bp):
GTTTTGAGCATGTTTTGAGTGT
Found at i:18649925 original size:12 final size:11
Alignment explanation
Indices: 18649887--18649929 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
18649877 AGTTTTGGCA
18649887 TGTTTTGAGTG
1 TGTTTTGAGTG
18649898 TG-TTTGA-TCG
1 TGTTTTGAGT-G
18649908 TGTTTTGAGTG
1 TGTTTTGAGTG
18649919 TGTTTTTGAGT
1 TG-TTTTGAGT
18649930 TGCTTAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 1 0.04
10 8 0.29
11 10 0.36
12 9 0.32
ACGTcount: A:0.09, C:0.02, G:0.33, T:0.56
Consensus pattern (11 bp):
TGTTTTGAGTG
Found at i:18654799 original size:14 final size:14
Alignment explanation
Indices: 18654780--18654818 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
18654770 TCTCTTCACG
18654780 TAATTTTCTCTCTA
1 TAATTTTCTCTCTA
18654794 TAATTTTCTCTCTA
1 TAATTTTCTCTCTA
*
18654808 TAACTTTCTCT
1 TAATTTTCTCT
18654819 TGAATTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTTTCTCTCTA
Found at i:18655070 original size:37 final size:37
Alignment explanation
Indices: 18655008--18655078 Score: 85
Period size: 37 Copynumber: 1.9 Consensus size: 37
18654998 GATAATCACT
18655008 TTAATATTAAATTAATAAAATATTA-TAAAGATAAGTA
1 TTAATATTAAATTAATAAAATATTATTAAA-ATAAGTA
*
18655045 TTAA-ATTAAATTTAATATTAA-ATTATTAAAATAA
1 TTAATATTAAA-TTAATA-AAATATTATTAAAATAA
18655079 TATGATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
36 6 0.20
37 18 0.60
38 6 0.20
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (37 bp):
TTAATATTAAATTAATAAAATATTATTAAAATAAGTA
Found at i:18657036 original size:30 final size:31
Alignment explanation
Indices: 18657000--18657059 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
18656990 AAACCTTTTA
*
18657000 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
18657030 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
18657060 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:18657714 original size:5 final size:5
Alignment explanation
Indices: 18657704--18657734 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
18657694 GAACAAATAT
18657704 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
18657735 ATTTCATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:18658057 original size:101 final size:102
Alignment explanation
Indices: 18657942--18658126 Score: 266
Period size: 101 Copynumber: 1.8 Consensus size: 102
18657932 AAAGTGATGG
* ** *
18657942 TCACATGTGTAGTACTATGTGCAAGCTACTACGTGTATCAGAATGAT-A-GGTTGCATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAAGCTACTACGAGTATC-GAATGATAATGGTCACATGTATAGT
18658005 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
* * * *
18658043 TCACGTGTGTAGTACTATGTGCAGGCTATTACGAGTATCGGATGATAATGGTCACATGTATAGTA
1 TCACATGTGTAGTACTATGTGCAAGCTACTACGAGTATCGAATGATAATGGTCACATGTATAGTA
*
18658108 CTATGTGCAGGTTACTATG
66 CTATGTGCAGGCTACTATG
18658127 TGAACCGAAC
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
100 6 0.08
101 36 0.49
102 31 0.42
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (102 bp):
TCACATGTGTAGTACTATGTGCAAGCTACTACGAGTATCGAATGATAATGGTCACATGTATAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:18658107 original size:51 final size:50
Alignment explanation
Indices: 18657938--18658124 Score: 198
Period size: 51 Copynumber: 3.7 Consensus size: 50
18657928 AGTGAAAGTG
* * *
18657938 ATGGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTATCAGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGAGTATC-GGATGAT
** * * *
18657989 A-GGTTGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT-AGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGAGTATCGGATGA-T
* * * *
18658038 TTCGATCACGTGTGTAGTACTATGTGCAGGCTATTACGAGTATCGGATGAT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGAGTATCGGATGAT
* *
18658089 AATGGTCACATGTATAGTACTATGTGCAGGTTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
18658125 TGTGAACCGA
Statistics
Matches: 109, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
48 1 0.01
49 4 0.04
50 35 0.32
51 67 0.61
52 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGAGTATCGGATGAT
Found at i:18658199 original size:45 final size:45
Alignment explanation
Indices: 18658135--18658220 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
18658125 TGTGAACCGA
* *
18658135 ACATCATTAATTAGGAAGGTGGTTGCTATGTGCTGATTCCAGCAG
1 ACATCATTAATTAAGAAGGTGGTTGCTATGTGCTGAATCCAGCAG
* *
18658180 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCA
1 ACATCATTAATTAAGAAGGTGGTTGCTATGTGCTGAATCCA
18658221 CCAAGTATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (45 bp):
ACATCATTAATTAAGAAGGTGGTTGCTATGTGCTGAATCCAGCAG
Found at i:18662674 original size:34 final size:34
Alignment explanation
Indices: 18662631--18662700 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
18662621 TTAAAGATTG
18662631 TAAATGTTGCCATTGATGAATCTTGTGATTTTTT
1 TAAATGTTGCCATTGATGAATCTTGTGATTTTTT
18662665 TAAATGTTGCCATTGATGAATCTTGTGATTTTTT
1 TAAATGTTGCCATTGATGAATCTTGTGATTTTTT
18662699 TA
1 TA
18662701 TGTTAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (34 bp):
TAAATGTTGCCATTGATGAATCTTGTGATTTTTT
Found at i:18669945 original size:66 final size:65
Alignment explanation
Indices: 18669866--18670001 Score: 236
Period size: 66 Copynumber: 2.1 Consensus size: 65
18669856 TGAGATAGGT
* *
18669866 AATTAAAATAAAATTGCTAACCGAGGTTTCCATGGTTCTATTTCTAGAAAATAAATAAAAAAATA
1 AATTAAAATAAAATTGCTAACCAAGGTTTCCATGGTTCTATTTATAGAAAATAAAT-AAAAAATA
18669931 A
65 A
*
18669932 AATTAAAATAAAATTTCTAACCAAGGTTTCCATGGTTCTATTTATAGAAAATAAATAAAAAATAA
1 AATTAAAATAAAATTGCTAACCAAGGTTTCCATGGTTCTATTTATAGAAAATAAATAAAAAATAA
18669997 AATTA
1 AATTA
18670002 CATAGTTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 14 0.21
66 53 0.79
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.32
Consensus pattern (65 bp):
AATTAAAATAAAATTGCTAACCAAGGTTTCCATGGTTCTATTTATAGAAAATAAATAAAAAATAA
Found at i:18670032 original size:25 final size:25
Alignment explanation
Indices: 18670004--18670051 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
18669994 TAAAATTACA
18670004 TAGTTTTTCACCACAAGGCATTCCT
1 TAGTTTTTCACCACAAGGCATTCCT
*
18670029 TAGTTTTTCACCACAAGTCATTC
1 TAGTTTTTCACCACAAGGCATTC
18670052 ATTGGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (25 bp):
TAGTTTTTCACCACAAGGCATTCCT
Found at i:18670060 original size:26 final size:25
Alignment explanation
Indices: 18670004--18670063 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
18669994 TAAAATTACA
*
18670004 TAGTTTTTCACCACAAGGCATTCCT
1 TAGTTTTTCACCACAAGGCATTCAT
*
18670029 TAGTTTTTCACCACAAGTCATTCAT
1 TAGTTTTTCACCACAAGGCATTCAT
* *
18670054 TGGGTTTTCA
1 TAGTTTTTCA
18670064 GCCGCCATCA
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:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (25 bp):
TAGTTTTTCACCACAAGGCATTCAT
Found at i:18670895 original size:37 final size:36
Alignment explanation
Indices: 18670835--18670910 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 36
18670825 CTTAATCACT
*
18670835 TTAATATTAAATTAATAAAAAACTATTAAGATAAGTA
1 TTAATATTAAATTAATAAAAAACTATTAAAATAA-TA
**
18670872 TTAA-ATTAAATTTAATATTAAACTATTAAAATAATA
1 TTAATATTAAA-TTAATAAAAAACTATTAAAATAATA
18670908 TTA
1 TTA
18670911 TTTTGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 11 0.31
37 24 0.69
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAAAACTATTAAAATAATA
Found at i:18671949 original size:91 final size:90
Alignment explanation
Indices: 18671787--18671978 Score: 226
Period size: 91 Copynumber: 2.1 Consensus size: 90
18671777 CACTAGTGAG
* * * * *
18671787 TTATCCACAAAATTATTGGCAGCTTTTATATGCAAACATGTTGTGTATTCACAGCCTAATGACAG
1 TTATCCACAAAATTATTGGCAACTTTTATATGCAAACATATTGTGCATTCACAACCTAATGACAA
* *
18671852 CGTATTAACATGCAATCACTGGTGGT
66 CATATTAACATACAAT-ACTGGTGGT
* * * *
18671878 TTATCCACAAATTTATTGGCAACTTTTATCTGCAAACCTATTGTGCATTCACAATCTACCA-G-C
1 TTATCCACAAAATTATTGGCAACTTTTATATGCAAACATATTGTGCATTCACAACCTA--ATGAC
*
18671941 AACATATTAACCTACAATACTGGTGGT
64 AACATATTAACATACAATACTGGTGGT
*
18671968 TCATCCACAAA
1 TTATCCACAAA
18671979 CTAGAGTGTC
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
90 19 0.22
91 65 0.76
92 1 0.01
93 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (90 bp):
TTATCCACAAAATTATTGGCAACTTTTATATGCAAACATATTGTGCATTCACAACCTAATGACAA
CATATTAACATACAATACTGGTGGT
Found at i:18699925 original size:38 final size:39
Alignment explanation
Indices: 18699857--18699942 Score: 147
Period size: 40 Copynumber: 2.2 Consensus size: 39
18699847 CTTATTCTTT
*
18699857 AAAAAAATAAAAAGCAAAAAGCGCAAAAAAAAAACCGCAA
1 AAAAAAAGAAAAAGCAAAAAGCGC-AAAAAAAAACCGCAA
18699897 AAAAAAAGAAAAAGCAAAAAGCGC-AAAAAAAACCGCAA
1 AAAAAAAGAAAAAGCAAAAAGCGCAAAAAAAAACCGCAA
18699935 AAAAAAAG
1 AAAAAAAG
18699943 TTGCCTACCT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 22 0.49
40 23 0.51
ACGTcount: A:0.73, C:0.14, G:0.12, T:0.01
Consensus pattern (39 bp):
AAAAAAAGAAAAAGCAAAAAGCGCAAAAAAAAACCGCAA
Found at i:18711534 original size:31 final size:32
Alignment explanation
Indices: 18711471--18711534 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
18711461 TAATAAGGTA
18711471 AGATTTCTATCCTTAATTATAGGGATTCCAAC
1 AGATTTCTATCCTTAATTATAGGGATTCCAAC
*
18711503 AGATTTCTATCCTTAATTATA-GGATTTCAAC
1 AGATTTCTATCCTTAATTATAGGGATTCCAAC
18711534 A
1 A
18711535 CTCCCTCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (32 bp):
AGATTTCTATCCTTAATTATAGGGATTCCAAC
Found at i:18719151 original size:20 final size:20
Alignment explanation
Indices: 18719123--18719165 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
18719113 CAAATGTTAC
*
18719123 AATAATTTATATAATTGAAT
1 AATAATTTATAAAATTGAAT
* *
18719143 AATATTTTATAAAATTGTAT
1 AATAATTTATAAAATTGAAT
18719163 AAT
1 AAT
18719166 TATATAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
AATAATTTATAAAATTGAAT
Found at i:18726052 original size:21 final size:22
Alignment explanation
Indices: 18726011--18726056 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
18726001 CATACTTGAT
18726011 TTCTTTCAAATTGATTTAATTC
1 TTCTTTCAAATTGATTTAATTC
18726033 TTCTTTCAAATTGA-TTAATTC
1 TTCTTTCAAATTGATTTAATTC
18726054 TTC
1 TTC
18726057 ATGCATAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.54
Consensus pattern (22 bp):
TTCTTTCAAATTGATTTAATTC
Found at i:18733696 original size:42 final size:42
Alignment explanation
Indices: 18733583--18733746 Score: 204
Period size: 43 Copynumber: 3.8 Consensus size: 42
18733573 CAAAAAGCTC
* *
18733583 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAA
1 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAATCAA
* * *
18733625 ATAACGATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAT
1 AT-ACGATGCCAATGTCCCAGACATGGTCTTACACGTAATCAA
*
18733668 ATACGATGCCAATGTCCCAAACATGGTCTTACACGTAAATCGCAA
1 ATACGATGCCAATGTCCCAGACATGGTCTTACACGT-AAT--CAA
* * *
18733713 AT-CGATGCCAATTTCCCAGACGTTGTCTTACACG
1 ATACGATGCCAATGTCCCAGACATGGTCTTACACG
18733747 ATATCACATA
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.31
43 40 0.38
44 28 0.27
45 4 0.04
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAATCAA
Found at i:18734854 original size:13 final size:13
Alignment explanation
Indices: 18734836--18734860 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18734826 ACAAACGATA
18734836 AAATTTTCACACG
1 AAATTTTCACACG
18734849 AAATTTTCACAC
1 AAATTTTCACAC
18734861 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:18737113 original size:16 final size:16
Alignment explanation
Indices: 18737089--18737120 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18737079 TGAACATGAC
*
18737089 AATTGATTCAATTAAA
1 AATTCATTCAATTAAA
18737105 AATTCATTCAATTAAA
1 AATTCATTCAATTAAA
18737121 GTCTATTTAA
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:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (16 bp):
AATTCATTCAATTAAA
Found at i:18746927 original size:2 final size:2
Alignment explanation
Indices: 18746920--18746956 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
18746910 AGAGAATCGA
18746920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18746957 TGCTAAATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18750917 original size:187 final size:187
Alignment explanation
Indices: 18750585--18750967 Score: 579
Period size: 187 Copynumber: 2.0 Consensus size: 187
18750575 TGTATTCAAG
*
18750585 TCAGTGAGTTACAAGGCCTAGCACACGGGCGTATAGGGCAACTCAGAGAGTTATACGGCCCAGCA
1 TCAGT-AGTTACAAGGCCTAGCACACGGGCGTATAGGGCAACTCAGAGAGTTACACGGCCCAGCA
* * *
18750650 CACGAGCGTGTGACACGACCGTGTGACCCTACTTAGAGAGTTACACAGGTAAGAACACAGGCTGA
65 CACGAGCATGTGACACGACCGTGTGACCCTACTTAAAGAGTTACACAGGTAAGAACACAGGCCGA
** * * *
18750715 GACACAGTAGTGTGTCCCTAGTTCGAAGGCTACACAGCCTGAGACACGGGCGTGTGTC
130 GACACAACAGTGTGTCCCGAGTTCAAAGGCTACACAGCCTGAGACACGGACGTGTGTC
* * **
18750773 TCAGTAGTTACAAGGCCTAGCACACGGGCGTATGGGGCAACTTAGAGAGTTACACGGCCTGGCAC
1 TCAGTAGTTACAAGGCCTAGCACACGGGCGTATAGGGCAACTCAGAGAGTTACACGGCCCAGCAC
* *
18750838 ACGAGCATGTGACACTG-TCGTGTGACCCTACTTAAAGAGTTACACAGGTAAGAACACAGGCCGG
66 ACGAGCATGTGACAC-GACCGTGTGACCCTACTTAAAGAGTTACACAGGTAAGAACACAGGCCGA
* * *
18750902 GACACAACCGTGTGTCTCGAGTTCAAAGGCTACATAGCCTGAGACACGGACGTGTGTC
130 GACACAACAGTGTGTCCCGAGTTCAAAGGCTACACAGCCTGAGACACGGACGTGTGTC
18750960 TCAGTAGT
1 TCAGTAGT
18750968 GTGAGGTACA
Statistics
Matches: 176, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
187 170 0.97
188 6 0.03
ACGTcount: A:0.28, C:0.25, G:0.29, T:0.19
Consensus pattern (187 bp):
TCAGTAGTTACAAGGCCTAGCACACGGGCGTATAGGGCAACTCAGAGAGTTACACGGCCCAGCAC
ACGAGCATGTGACACGACCGTGTGACCCTACTTAAAGAGTTACACAGGTAAGAACACAGGCCGAG
ACACAACAGTGTGTCCCGAGTTCAAAGGCTACACAGCCTGAGACACGGACGTGTGTC
Found at i:18756659 original size:20 final size:20
Alignment explanation
Indices: 18756634--18756672 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18756624 AACTACTTTT
*
18756634 AGAATGCTCCTTTTGTACAC
1 AGAATGCTCCTTTTATACAC
*
18756654 AGAATGCTCTTTTTATACA
1 AGAATGCTCCTTTTATACA
18756673 TAAACCTCGA
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:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (20 bp):
AGAATGCTCCTTTTATACAC
Found at i:18759261 original size:54 final size:53
Alignment explanation
Indices: 18759083--18759249 Score: 208
Period size: 54 Copynumber: 3.1 Consensus size: 53
18759073 CATGGTAAGC
* * * * * *
18759083 GAATACCATATAGTGTAAGGCCTAGCCATTTGCAATGACTTTATATTGAGAAAT
1 GAATACCATATAGTGTAAGGCCTAG-CGTTTGCTATGACATCATATGGGGAAAT
* * * *
18759137 AAATACCATATAGTGTAAGCCCTAGACGTTTGTTATGGCATCATATGGGGAAAT
1 GAATACCATATAGTGTAAGGCCTAG-CGTTTGCTATGACATCATATGGGGAAAT
*
18759191 GAAGACCATATAGTGTAAGGCCTAGCTGTTTGCTATGACATCATATGGGGAAAT
1 GAATACCATATAGTGTAAGGCCTAGC-GTTTGCTATGACATCATATGGGGAAAT
18759245 GAATA
1 GAATA
18759250 ATACATAGTG
Statistics
Matches: 95, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
53 1 0.01
54 94 0.99
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (53 bp):
GAATACCATATAGTGTAAGGCCTAGCGTTTGCTATGACATCATATGGGGAAAT
Found at i:18759269 original size:54 final size:54
Alignment explanation
Indices: 18759092--18759269 Score: 144
Period size: 54 Copynumber: 3.3 Consensus size: 54
18759082 CGAATACCAT
* ** * * * * * * * * *
18759092 ATAGTGTAAGGCCTAGCCATTTGCAATGACTTTATATTGAGAAATAAATACCAT
1 ATAGTGTAAGACCTAGCTGTTTGCTATGACATCATATGGGGAAATGAAGAACAC
* * * * *
18759146 ATAGTGTAAGCCCTAGAC-GTTTGTTATGGCATCATATGGGGAAATGAAGACCAT
1 ATAGTGTAAGACCTAG-CTGTTTGCTATGACATCATATGGGGAAATGAAGAACAC
* * *
18759200 ATAGTGTAAGGCCTAGCTGTTTGCTATGACATCATATGGGGAAATGAATAATAC
1 ATAGTGTAAGACCTAGCTGTTTGCTATGACATCATATGGGGAAATGAAGAACAC
18759254 ATAGTGTATA-ACCTAG
1 ATAGTGTA-AGACCTAG
18759270 TCTAGGACTA
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
53 1 0.01
54 99 0.97
55 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (54 bp):
ATAGTGTAAGACCTAGCTGTTTGCTATGACATCATATGGGGAAATGAAGAACAC
Found at i:18759650 original size:29 final size:31
Alignment explanation
Indices: 18759602--18759661 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
18759592 TAATGATATA
*
18759602 TGGACGCCTCTATGGCTATCTA-AG-TCAAG
1 TGGACGCCTCTATGGATATCTATAGATCAAG
* *
18759631 TGGACGCCTTTGTGGATATCTATAGATCAAG
1 TGGACGCCTCTATGGATATCTATAGATCAAG
18759662 CAAGTGTCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 19 0.73
30 2 0.08
31 5 0.19
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (31 bp):
TGGACGCCTCTATGGATATCTATAGATCAAG
Found at i:18759959 original size:6 final size:6
Alignment explanation
Indices: 18759923--18759957 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
18759913 CTCTACCCCA
* *
18759923 CCCTTT CCCTCT CCCTCT CCCTCT CCCTCC CCCTC
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTC
18759958 CCAACATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (6 bp):
CCCTCT
Found at i:18762560 original size:66 final size:62
Alignment explanation
Indices: 18762474--18762686 Score: 174
Period size: 66 Copynumber: 3.4 Consensus size: 62
18762464 AAATATATTT
*
18762474 AATATTAATTATTTCAAATTTTCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTA-TT-AAAATTT-TTTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
18762539 G
62 G
* * * * **
18762540 AATATTAATTATTAAGAATTTTATTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTAA-AATTTTTTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* * *
18762594 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TAAAATT-T-TTTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
18762659 G
62 G
*
18762660 AATATTAATTATTAAGAATTTTATTAA
1 AATATTAATTATTAA-AATTTTTTTAA
18762687 ATTATATATT
Statistics
Matches: 112, Mismatches: 20, Indels: 33
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.12
55 7 0.06
56 5 0.04
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 4 0.04
64 11 0.10
65 13 0.12
66 25 0.22
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (62 bp):
AATATTAATTATTAAAATTTTTTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:18762574 original size:120 final size:120
Alignment explanation
Indices: 18762436--18762728 Score: 509
Period size: 120 Copynumber: 2.4 Consensus size: 120
18762426 AATTATTTTA
* * * *
18762436 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTATATT
*
18762499 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
18762556 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
18762621 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
18762676 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
18762729 TAAATATGAT
Statistics
Matches: 166, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
119 5 0.03
120 159 0.96
121 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:18762596 original size:15 final size:15
Alignment explanation
Indices: 18762561--18762612 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
18762551 TTAAGAATTT
*
18762561 TATTAAATTAT-ATA
1 TATTTAATTATAATA
18762575 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
18762589 TATTTAATAATAAT-
1 TATTTAATTATAATA
18762603 TATGTTAATT
1 TAT-TTAATT
18762613 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:18762711 original size:16 final size:16
Alignment explanation
Indices: 18762690--18762731 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
18762680 TTATTAAATT
*
18762690 ATATATTTTAATTATA
1 ATATATTTTAATAATA
18762706 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
18762721 AT-TATGTTTAA
1 ATATAT-TTTAA
18762732 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:18762716 original size:15 final size:15
Alignment explanation
Indices: 18762681--18762722 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
18762671 TTAAGAATTT
*
18762681 TATTAAATTAT-ATA
1 TATTTAATTATAATA
18762695 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
18762709 TATTTAATAATAAT
1 TATTTAATTATAAT
18762723 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:18762841 original size:156 final size:157
Alignment explanation
Indices: 18762665--18762980 Score: 580
Period size: 156 Copynumber: 2.0 Consensus size: 157
18762655 ATAAGAATAT
*
18762665 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
18762730 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
18762795 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
18762822 TAATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
18762886 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
18762951 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
18762978 TAA
1 TAA
18762981 GGGTATTCTA
Statistics
Matches: 154, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
156 148 0.96
157 6 0.04
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:18762861 original size:18 final size:17
Alignment explanation
Indices: 18762833--18762867 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18762823 AATTATAAGA
*
18762833 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
18762850 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
18762868 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:18763096 original size:44 final size:45
Alignment explanation
Indices: 18763032--18763122 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
18763022 ACCTCTATTC
* * *
18763032 CATTCAACCAAACACAAGA-TTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTTACTATTACACCTCTAATCCAATA
** *
18763076 CATTCAACCAAACAGTAGATTTGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTTACTATTACACCTCTAATCCAATA
18763121 CA
1 CA
18763123 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 17 0.43
45 23 0.57
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTTACTATTACACCTCTAATCCAATA
Found at i:18763124 original size:16 final size:16
Alignment explanation
Indices: 18763103--18763138 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
18763093 GATTTGCTAT
18763103 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
18763119 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
18763135 TACA
1 TACA
18763139 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:18765591 original size:12 final size:13
Alignment explanation
Indices: 18765561--18765590 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18765551 ATAAGGGCTT
*
18765561 TTTTTATTTAATA
1 TTTTTATATAATA
18765574 TTTTTATATAATA
1 TTTTTATATAATA
18765587 TTTT
1 TTTT
18765591 AAATAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTATATAATA
Found at i:18765775 original size:20 final size:20
Alignment explanation
Indices: 18765747--18765790 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
18765737 CCAAATTTAT
*
18765747 AATACTTTAAA-TACATTAAA
1 AATACTTTAAACT-CAGTAAA
*
18765767 AATAGTTTAAACTCAGTAAA
1 AATACTTTAAACTCAGTAAA
18765787 AATA
1 AATA
18765791 TTTCTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.32
Consensus pattern (20 bp):
AATACTTTAAACTCAGTAAA
Found at i:18772310 original size:9 final size:9
Alignment explanation
Indices: 18772293--18772485 Score: 149
Period size: 9 Copynumber: 22.3 Consensus size: 9
18772283 TATGTATTAA
*
18772293 GTAAATTAT
1 GTAAGTTAT
18772302 GTAAGTTAT
1 GTAAGTTAT
18772311 GTACA-TGTA-
1 GTA-AGT-TAT
18772320 -TAAGTTAT
1 GTAAGTTAT
18772328 GTAAGTTAT
1 GTAAGTTAT
*
18772337 GT-A-TTAA
1 GTAAGTTAT
*
18772344 GTAAGCTAT
1 GTAAGTTAT
*
18772353 GTAAGTTGT
1 GTAAGTTAT
18772362 GT-A-TTAT
1 GTAAGTTAT
18772369 GTAAGTTAT
1 GTAAGTTAT
18772378 GTAAGTTAT
1 GTAAGTTAT
** *
18772387 CAAAGTAAT
1 GTAAGTTAT
*
18772396 GTATGTTAT
1 GTAAGTTAT
*
18772405 TTAAG-T-T
1 GTAAGTTAT
18772412 GTAAGTTAT
1 GTAAGTTAT
*
18772421 -TATGTATTAT
1 GTAAG--TTAT
18772431 GTAAGTTAT
1 GTAAGTTAT
18772440 GTAAGTTAT
1 GTAAGTTAT
18772449 GTAAGTT-T
1 GTAAGTTAT
* *
18772457 TTCA-TTAT
1 GTAAGTTAT
*
18772465 GTAAGTTCT
1 GTAAGTTAT
18772474 GTAAGTTAT
1 GTAAGTTAT
18772483 GTA
1 GTA
18772486 TGCTATATTT
Statistics
Matches: 143, Mismatches: 25, Indels: 32
0.71 0.12 0.16
Matches are distributed among these distances:
7 20 0.14
8 18 0.13
9 95 0.66
10 7 0.05
11 3 0.02
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:18772313 original size:25 final size:25
Alignment explanation
Indices: 18772282--18772386 Score: 122
Period size: 25 Copynumber: 4.2 Consensus size: 25
18772272 TGATATATAT
18772282 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* *
18772307 TTATGTA-CATGTATAAGTTATGTAAG
1 TTATGTATTAAGTA-AA-TTATGTAAG
**
18772333 TTATGTATTAAGTAAGCTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* * *
18772358 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
18772383 TTAT
1 TTAT
18772387 CAAAGTAATG
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
24 4 0.06
25 42 0.63
26 17 0.25
27 4 0.06
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (25 bp):
TTATGTATTAAGTAAATTATGTAAG
Found at i:18772369 original size:16 final size:16
Alignment explanation
Indices: 18772350--18772528 Score: 75
Period size: 18 Copynumber: 10.8 Consensus size: 16
18772340 TTAAGTAAGC
*
18772350 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
18772366 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
** *
18772384 TATCAAAGTAATGTATGT
1 TATGTAAGTTATGTA--T
*
18772402 TATTTAAG-T-TGTA-
1 TATGTAAGTTATGTAT
*
18772415 -A-GTTA-TTATGTAT
1 TATGTAAGTTATGTAT
18772428 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
*
18772446 TATGTAAGTT-TTTCAT
1 TATGTAAGTTATGT-AT
*
18772462 TATGTAAGTTCTGTAAGT
1 TATGTAAGTTATGT-A-T
* * * *
18772480 TATGTATGCTATATTT
1 TATGTAAGTTATGTAT
18772496 TATGTAAGTTGTTATGTTAT
1 TATGTAA---GTTATG-TAT
*
18772516 TACGTAAGTTATG
1 TATGTAAGTTATG
18772529 CAAGTTTATA
Statistics
Matches: 122, Mismatches: 24, Indels: 33
0.68 0.13 0.18
Matches are distributed among these distances:
11 3 0.02
12 5 0.04
14 1 0.01
15 3 0.02
16 41 0.34
17 15 0.12
18 42 0.34
19 4 0.03
20 8 0.07
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.49
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:18772382 original size:34 final size:34
Alignment explanation
Indices: 18772297--18772505 Score: 140
Period size: 34 Copynumber: 6.4 Consensus size: 34
18772287 TATTAAGTAA
18772297 ATTATGTAAGTTATGTACA-TGTA--TAAGTTATGT
1 ATTATGTAAGTTATGTA-AGT-TATGTAAGTTATGT
* * *
18772330 AAGTTATGT-A-TTAAGTAAGCTATGTAAGTTGTGT
1 -A-TTATGTAAGTTATGTAAGTTATGTAAGTTATGT
** *
18772364 ATTATGTAAGTTATGTAAGTTATCAAAGTAATGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTATGT
*
18772398 ATGTTATTTAAG-T-TGTAAG---T-T-A-TTATGT
1 A--TTATGTAAGTTATGTAAGTTATGTAAGTTATGT
*
18772426 ATTATGTAAGTTATGTAAGTTATGTAAGTT-TTT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTATGT
* * * *
18772459 CATTATGTAAGTTCTGTAAGTTATGTATGCTATAT
1 -ATTATGTAAGTTATGTAAGTTATGTAAGTTATGT
*
18772494 TTTATGTAAGTT
1 ATTATGTAAGTT
18772506 GTTATGTTAT
Statistics
Matches: 138, Mismatches: 19, Indels: 36
0.72 0.10 0.19
Matches are distributed among these distances:
26 8 0.06
27 1 0.01
28 12 0.09
29 1 0.01
31 2 0.01
32 10 0.07
33 11 0.08
34 76 0.55
35 9 0.07
36 8 0.06
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.47
Consensus pattern (34 bp):
ATTATGTAAGTTATGTAAGTTATGTAAGTTATGT
Found at i:18772392 original size:18 final size:17
Alignment explanation
Indices: 18772293--18772485 Score: 116
Period size: 16 Copynumber: 11.2 Consensus size: 17
18772283 TATGTATTAA
*
18772293 GTAAATTATGTAAGTTAT
1 GTAAGTTAT-TAAGTTAT
18772311 GTACA-TGTA-TAAGTTAT
1 GTA-AGT-TATTAAGTTAT
*
18772328 GTAAGTTATGT-A-TTAA
1 GTAAGTTAT-TAAGTTAT
* *
18772344 GTAAGCTATGTAAGTTGT
1 GTAAGTTAT-TAAGTTAT
18772362 GT-A-TTATGTAAGTTAT
1 GTAAGTTAT-TAAGTTAT
* *
18772378 GTAAGTTATCAAAGTAAT
1 GTAAGTTAT-TAAGTTAT
*
18772396 GTATGTTATTTAAG-T-T
1 GTAAGTTA-TTAAGTTAT
*
18772412 GTAAGTTATTATGTATTAT
1 GTAAGTTATTAAG--TTAT
18772431 GTAAGTTATGTAAGTTAT
1 GTAAGTTAT-TAAGTTAT
* *
18772449 GTAAGTTTTTCA-TTAT
1 GTAAGTTATTAAGTTAT
*
18772465 GTAAGTTCTGTAAGTTAT
1 GTAAGTTAT-TAAGTTAT
18772483 GTA
1 GTA
18772486 TGCTATATTT
Statistics
Matches: 139, Mismatches: 19, Indels: 34
0.72 0.10 0.18
Matches are distributed among these distances:
15 4 0.03
16 49 0.35
17 20 0.14
18 49 0.35
19 14 0.10
20 3 0.02
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.46
Consensus pattern (17 bp):
GTAAGTTATTAAGTTAT
Found at i:18772465 original size:87 final size:87
Alignment explanation
Indices: 18772333--18772534 Score: 214
Period size: 87 Copynumber: 2.3 Consensus size: 87
18772323 GTTATGTAAG
* *
18772333 TTATGTATTAAGTAAGCTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGT
1 TTATGTATTAAGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGT
18772398 ATG-T-TATTTAAGTTGTAAGTTA
66 ATGCTATATTTAA--TGTAAGTTA
* * * * ** *
18772420 TTATGTATTATGTAAGTTATGTAAGTTATGTAAGTT-TTTCA-TTATGTAAGTTCTGTAAGTTAT
1 TTATGTATTAAGTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTATGTAAGTTATCAAAGTAAT
* *
18772483 GTATGCTATATTTTATGTAAGTTG
64 GTATGCTATATTTAATGTAAGTTA
* *
18772507 TTATGTTATTACGTAAGTTATGCAAGTT
1 TTATG-TATTAAGTAAGTTATGTAAGTT
18772535 TATATATAAG
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
87 64 0.66
88 25 0.26
89 8 0.08
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (87 bp):
TTATGTATTAAGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGT
ATGCTATATTTAATGTAAGTTA
Found at i:18772471 original size:53 final size:55
Alignment explanation
Indices: 18772320--18772455 Score: 142
Period size: 53 Copynumber: 2.6 Consensus size: 55
18772310 TGTACATGTA
** * * *
18772320 TAAGTTATGTAAGTTAT-GTATTAA-GTAAGCTATGTAAGTTGT--G-TATTATG
1 TAAGTTATGTAAGTTATCAAAGTAATGTAAGTTATTTAAGTTGTAAGTTATTATG
*
18772370 TAAGTTATGTAAGTTATCAAAGTAATGTATGTTATTTAAGTTGTAAGTTATTATG
1 TAAGTTATGTAAGTTATCAAAGTAATGTAAGTTATTTAAGTTGTAAGTTATTATG
** *
18772425 T-A-TTATGTAAGTTATGTAAGTTATGTAAGTT
1 TAAGTTATGTAAGTTATCAAAGTAATGTAAGTT
18772456 TTTCATTATG
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
50 17 0.24
51 4 0.06
52 15 0.21
53 25 0.35
54 2 0.03
55 8 0.11
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (55 bp):
TAAGTTATGTAAGTTATCAAAGTAATGTAAGTTATTTAAGTTGTAAGTTATTATG
Found at i:18774104 original size:15 final size:15
Alignment explanation
Indices: 18774084--18774112 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18774074 TGATAACAGT
18774084 AAATTAGTACCAAAG
1 AAATTAGTACCAAAG
18774099 AAATTAGTACCAAA
1 AAATTAGTACCAAA
18774113 TACTTCAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (15 bp):
AAATTAGTACCAAAG
Found at i:18776183 original size:13 final size:14
Alignment explanation
Indices: 18776158--18776201 Score: 63
Period size: 13 Copynumber: 3.1 Consensus size: 14
18776148 CATAAATTCT
18776158 AAACCTTAAACCCCA
1 AAACC-TAAACCCCA
18776173 AAACC-AAACCCCA
1 AAACCTAAACCCCA
*
18776186 AACCCTAAACCCCA
1 AAACCTAAACCCCA
18776200 AA
1 AA
18776202 TCCCAAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 12 0.44
14 10 0.37
15 5 0.19
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (14 bp):
AAACCTAAACCCCA
Found at i:18776186 original size:7 final size:7
Alignment explanation
Indices: 18776165--18776209 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
18776155 TCTAAACCTT
18776165 AAACCCC
1 AAACCCC
*
18776172 AAA-ACC
1 AAACCCC
18776178 AAACCCC
1 AAACCCC
*
18776185 AAACCCT
1 AAACCCC
18776192 AAACCCC
1 AAACCCC
*
18776199 AAATCCC
1 AAACCCC
18776206 AAAC
1 AAAC
18776210 TGAAATATTC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.49, C:0.47, G:0.00, T:0.04
Consensus pattern (7 bp):
AAACCCC
Found at i:18776197 original size:14 final size:14
Alignment explanation
Indices: 18776158--18776201 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
18776148 CATAAATTCT
*
18776158 AAACCTTAAACCCC
1 AAACCCTAAACCCC
*
18776172 AAAACC-AAACCCC
1 AAACCCTAAACCCC
18776185 AAACCCTAAACCCC
1 AAACCCTAAACCCC
18776199 AAA
1 AAA
18776202 TCCCAAACTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (14 bp):
AAACCCTAAACCCC
Found at i:18776209 original size:14 final size:13
Alignment explanation
Indices: 18776165--18776209 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 13
18776155 TCTAAACCTT
*
18776165 AAACCCCAAAACC
1 AAACCCCAAACCC
18776178 AAACCCCAAACCC
1 AAACCCCAAACCC
18776191 TAAACCCCAAATCCC
1 -AAACCCCAAA-CCC
18776206 AAAC
1 AAAC
18776210 TGAAATATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 12 0.41
14 14 0.48
15 3 0.10
ACGTcount: A:0.49, C:0.47, G:0.00, T:0.04
Consensus pattern (13 bp):
AAACCCCAAACCC
Found at i:18776735 original size:81 final size:80
Alignment explanation
Indices: 18776583--18776738 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 80
18776573 AACCATTAAC
* * *
18776583 CCCTAACTACTAACCCTAACCTTATTTAATATACAAATTAAAAATATTAATTAATCAAAACCCTA
1 CCCTAACCACTAACCCTAACCTTATTTAATATACAAATTAAAAACACTAATTAATCAAAACCCTA
18776648 AATCCTAACCCGAAT
66 AATCCTAACCCGAAT
* * *
18776663 CCCTAACCCCTAACCCTTAAACCTTATTTCATA-A-AAATTAAAACACACTAATTAATCTAAACC
1 CCCTAACCACTAACCC-T-AACCTTATTTAATATACAAATTAAAA-ACACTAATTAATCAAAACC
18776726 CTAAATCCTAACC
63 CTAAATCCTAACC
18776739 TGACACCGAA
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
80 23 0.34
81 31 0.46
82 13 0.19
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.28
Consensus pattern (80 bp):
CCCTAACCACTAACCCTAACCTTATTTAATATACAAATTAAAAACACTAATTAATCAAAACCCTA
AATCCTAACCCGAAT
Found at i:18777754 original size:115 final size:114
Alignment explanation
Indices: 18777254--18777834 Score: 628
Period size: 114 Copynumber: 5.1 Consensus size: 114
18777244 CGCTTCAACA
* * * *
18777254 AAAATGCCGCTAAAGCCCTAAGCATTAGCGGCGCATT-CTT-AAAACGCCGCTAAAGCCCACGAA
1 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC-TTACTTAAAAACGCCACTAAATCCC-CGAA
* * ** * * * *
18777317 TTG-TCAGAAAATAGTGTAGTTCGG-TTTAGTTTTTGTTGTGGCGCTTTCTCA
64 -AGCTCAAAAAACGGCGTCGTTGGGCTTTAGTTTTT-TTGTGGCGCTTTCTCG
*
18777368 AAAACGCCGCTAAAGCCCTGAACATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAG
1 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAG
* *
18777433 CTCAAAAAACAGCATCGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTC-
66 CTCAAAAAACGGCGTCGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCG
*
18777481 AAAA-GCACTGCTAAAG-CCTGAGCATTAGCGGCGCTTACCTAAAAACGCCACTAAATCCCCGAA
1 AAAACGC-C-GCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAA
* * * * * *
18777544 TGCTCAGAAAACGGCGTCATTGGGC-TTAGGTATTTTT-TCGCTGCTTTCCCG
64 AGCTCAAAAAACGGCGTCGTTGGGCTTTA-GTTTTTTTGTGGC-GCTTTCTCG
* * * * *
18777595 AAAACGCTGCTAAAGCCCTGAGCATTAGCGGTG-TCTACTAAAAAATGCCATTAAATCCCCGAAA
1 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCT-TACTTAAAAACGCCACTAAATCCCCGAAA
*
18777659 GCTCAAAAAACGGCGTCGTTGGGCTTTGGTTTTTTTTGTGGCGCTTTCTCG
65 GCTCAAAAAACGGCGTCGTTGGGCTTTAG-TTTTTTTGTGGCGCTTTCTCG
* * * *
18777710 AAAACGCCGCTAAAGCCCAGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGAAAG
1 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAG
* ** * * * *
18777775 CTCGAAAAACGGCGTCGTTATGC-TTAGGTATTTTGCGGCGCTTTAT-G
66 CTCAAAAAACGGCGTCGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCG
*
18777822 GAAACGCCGCTAA
1 AAAACGCCGCTAA
18777835 TGCTTATTTT
Statistics
Matches: 398, Mismatches: 53, Indels: 34
0.82 0.11 0.07
Matches are distributed among these distances:
112 21 0.05
113 110 0.28
114 145 0.36
115 118 0.30
116 4 0.01
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (114 bp):
AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAG
CTCAAAAAACGGCGTCGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCG
Found at i:18779447 original size:21 final size:22
Alignment explanation
Indices: 18779422--18779462 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
18779412 TTTAATTATT
18779422 TTTA-TAACATCTTTGGAAAGA
1 TTTATTAACATCTTTGGAAAGA
* *
18779443 TTTATTAATATCTTTTGAAA
1 TTTATTAACATCTTTGGAAA
18779463 TTTAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (22 bp):
TTTATTAACATCTTTGGAAAGA
Found at i:18779837 original size:15 final size:16
Alignment explanation
Indices: 18779816--18779851 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
18779806 GCTATGGATT
18779816 ATTAAAGTAAAGACCC
1 ATTAAAGTAAAGACCC
18779832 -TTAAAGTAAAGACCC
1 ATTAAAGTAAAGACCC
18779847 ATTAA
1 ATTAA
18779852 TAAGATAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (16 bp):
ATTAAAGTAAAGACCC
Found at i:18780899 original size:43 final size:42
Alignment explanation
Indices: 18780806--18780968 Score: 211
Period size: 43 Copynumber: 3.8 Consensus size: 42
18780796 AGGGTTTCCA
* *
18780806 AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATCTA
1 AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATATG
*
18780848 AGACTT-CGTGTAAGACCATATCTGGGACATTGGCATCGATATG
1 AGA-TTACGTGTAAGACCATATCTGGGATA-TGGCATCGATATG
* * ** *
18780891 TGATTTCGTGTAAGACCATGGCTGGGATATTGGCATCGATACG
1 AGATTACGTGTAAGACCATATCTGGGATA-TGGCATCGATATG
*
18780934 AGATTACATGTAAGACCATATCTGGGATATGGCAT
1 AGATTACGTGTAAGACCATATCTGGGATATGGCAT
18780969 TGTTACGGTA
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.31
43 72 0.69
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (42 bp):
AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATATG
Found at i:18782539 original size:12 final size:12
Alignment explanation
Indices: 18782519--18782551 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
18782509 GGCAATAATA
18782519 AGTTAAAAA-CG
1 AGTTAAAAATCG
18782530 AGTGTAAAAATCG
1 AGT-TAAAAATCG
18782543 AGTTAAAAA
1 AGTTAAAAA
18782552 GGCATAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.15
12 12 0.60
13 5 0.25
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.21
Consensus pattern (12 bp):
AGTTAAAAATCG
Found at i:18783213 original size:25 final size:23
Alignment explanation
Indices: 18783159--18783201 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
18783149 AATGCTTGGG
18783159 TTATATA-GTTTTGGTCATGATA
1 TTATATATGTTTTGGTCATGATA
18783181 TATATATATGTTTTGG-CATGA
1 T-TATATATGTTTTGGTCATGA
18783202 AGTAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 1 0.05
23 11 0.58
24 7 0.37
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.49
Consensus pattern (23 bp):
TTATATATGTTTTGGTCATGATA
Found at i:18790868 original size:43 final size:42
Alignment explanation
Indices: 18790773--18790937 Score: 163
Period size: 43 Copynumber: 3.9 Consensus size: 42
18790763 TTAGGGTTAT
* *
18790773 TGAGATTACGTGTAAGACCATATCTAGGATATGACATCGATA
1 TGAGATTACGTGTAAGACCATATCTAGGACATGGCATCGATA
* * *
18790815 TGAGACTT-CGTGTAACACCATGTCTGGGACATTGGCATCGATA
1 TGAGA-TTACGTGTAAGACCATATCTAGGACA-TGGCATCGATA
* * **
18790858 TGTGATTTCGTGTAAGACCATGGCTAGG-CTATTGGCATCGATA
1 TGAGATTACGTGTAAGACCATATCTAGGAC-A-TGGCATCGATA
* * * *
18790901 CGAGATTACTTGTAAGACCATATCTGGGATATGGCAT
1 TGAGATTACGTGTAAGACCATATCTAGGACATGGCAT
18790938 TGTTACGGTA
Statistics
Matches: 101, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 33 0.33
43 68 0.67
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (42 bp):
TGAGATTACGTGTAAGACCATATCTAGGACATGGCATCGATA
Done.