Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008031.1 Hibiscus syriacus cultivar Beakdansim tig00110511_pilon, whole genome shotgun sequence
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: 1788856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1154855 original size:21 final size:21
Alignment explanation
Indices: 1154837--1154954 Score: 202
Period size: 21 Copynumber: 5.6 Consensus size: 21
1154827 TGATCTTCAT
*
1154837 GTCTTTATGAAGGGTCTTCAT-
1 GTCTTTATGAATGGTCTTC-TC
1154858 GTCTTTATGAATGGTCTTCTC
1 GTCTTTATGAATGGTCTTCTC
1154879 GTCTTTATGAATGGTCTTCTC
1 GTCTTTATGAATGGTCTTCTC
1154900 GTCTTTATGAATGGTCTTCTC
1 GTCTTTATGAATGGTCTTCTC
1154921 GTCTTTATGAATGGTCTTCTC
1 GTCTTTATGAATGGTCTTCTC
*
1154942 GTCCTTATGAATG
1 GTCTTTATGAATG
1154955 ACTATATATA
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
20 1 0.01
21 93 0.99
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.46
Consensus pattern (21 bp):
GTCTTTATGAATGGTCTTCTC
Found at i:1158397 original size:3 final size:3
Alignment explanation
Indices: 1158391--1158426 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1158381 ACATTATTAT
1158391 TAA TAA TAA -AA TAA T-A TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1158427 TCCCGGATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1159671 original size:39 final size:39
Alignment explanation
Indices: 1159628--1159953 Score: 231
Period size: 39 Copynumber: 8.5 Consensus size: 39
1159618 ATTTTTTGAA
*
1159628 ATATATAATATATAGTTTTTGAAAACATTTTGAAAACAT
1 ATATATAATATATAGTTTTTGAAATCATTTTGAAAACAT
* *
1159667 ATATAT--TATATAGTTTTTTGAAATCATTTTTAAAAAACT
1 ATATATAATATATAG-TTTTTGAAATCATTTTGAAAACA-T
** *
1159706 -TATATAATATATA-TAGTTTTGAAATCATTTAAAAAACTT
1 ATATATAATATATAGT--TTTTGAAATCATTTTGAAAACAT
* * * * * *
1159745 ATATAT-ATATATA-TATAT-ATAT-A-TAT-ATATATAT
1 ATATATAATATATAGTTTTTGAAATCATTTTGA-AAACAT
*
1159779 ATATATATATATATAG-TTTTGAAATCATTTTGAAAAACTT
1 ATATATA-ATATATAGTTTTTGAAATCATTTTG-AAAACAT
* *
1159819 ATATA-ATATATATAG-TTTTGAAATTATTTTGAAAAACTT
1 ATATATA-ATATATAGTTTTTGAAATCATTTTG-AAAACAT
* *
1159858 ATATA-ATATATATAG-TTTTGAAATCATTTTTAAAAAACT
1 ATATATA-ATATATAGTTTTTGAAATCATTTTGAAAACA-T
1159897 -TATATAATATATATAGTTTTT-AAATCATTTTGAAAA-ACT
1 ATATAT-A-ATATATAGTTTTTGAAATCATTTTGAAAACA-T
*
1159936 -TATATAATACATAGTTTT
1 ATATATAATATATAGTTTT
1159954 AAAATGTTTT
Statistics
Matches: 238, Mismatches: 29, Indels: 42
0.77 0.09 0.14
Matches are distributed among these distances:
33 1 0.00
34 10 0.04
35 1 0.00
36 12 0.05
37 23 0.10
38 36 0.15
39 89 0.37
40 61 0.26
41 5 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (39 bp):
ATATATAATATATAGTTTTTGAAATCATTTTGAAAACAT
Found at i:1159749 original size:2 final size:2
Alignment explanation
Indices: 1159744--1159793 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1159734 TTAAAAAACT
1159744 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1159786 TA TA TA TA
1 TA TA TA TA
1159794 GTTTTGAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1160029 original size:37 final size:39
Alignment explanation
Indices: 1159971--1160046 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 39
1159961 TTTTTAAAAC
1159971 TATATAAATTTGAAAACA-TTTT-AA-AAATATATATATA
1 TATATAAATTTGAAAACATTTTTGAACAAATAT-TATATA
* * *
1160008 TATATAAGTTTTAAAATATTTTTGAACAAATATTATATA
1 TATATAAATTTGAAAACATTTTTGAACAAATATTATATA
1160047 GGTTTTGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 15 0.45
38 4 0.12
39 8 0.24
40 6 0.18
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (39 bp):
TATATAAATTTGAAAACATTTTTGAACAAATATTATATA
Found at i:1160089 original size:19 final size:17
Alignment explanation
Indices: 1160065--1160106 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
1160055 AGAAATGTTT
1160065 TTATAATATATTATTATAA
1 TTATAATATATT-TT-TAA
*
1160084 TTATAATTTATTTTTAA
1 TTATAATATATTTTTAA
1160101 TT-TAAT
1 TTATAAT
1160107 TTAATTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 5 0.23
18 2 0.09
19 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATAATATATTTTTAA
Found at i:1160681 original size:22 final size:24
Alignment explanation
Indices: 1160638--1160686 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
1160628 CCACAGATCG
*
1160638 AACAACAATACCATCACAAAACCAC
1 AACAACAATACCA-CACAAAACAAC
*
1160663 AACAACAA-ACC-CACGAAACAAC
1 AACAACAATACCACACAAAACAAC
1160685 AA
1 AA
1160687 ACAAAACCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.50
24 3 0.14
25 8 0.36
ACGTcount: A:0.59, C:0.35, G:0.02, T:0.04
Consensus pattern (24 bp):
AACAACAATACCACACAAAACAAC
Found at i:1161506 original size:20 final size:19
Alignment explanation
Indices: 1161483--1161544 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
1161473 TTCCTTTGAC
1161483 TTTTTATTTTTATTTATTTA
1 TTTTT-TTTTTATTTATTTA
* * *
1161503 TTTTTGCTTTGATTTA-ATA
1 TTTTT-TTTTTATTTATTTA
*
1161522 TTTTTTTCTTATTTGATTTA
1 TTTTTTTTTTATTT-ATTTA
1161542 TTT
1 TTT
1161545 AACATTTATT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 6 0.19
19 8 0.25
20 18 0.56
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTTTTTTATTTATTTA
Found at i:1161513 original size:33 final size:33
Alignment explanation
Indices: 1161457--1161540 Score: 84
Period size: 33 Copynumber: 2.5 Consensus size: 33
1161447 GCTCCCTTTA
* *
1161457 ATTTTTATTTA-CT-TTTTTCCTTTGACTTT-TT
1 ATTTTTATTTATTTATTTTTCCTTTGA-TTTAAT
*
1161488 ATTTTTATTTATTTATTTTTGCTTTGATTTAAT
1 ATTTTTATTTATTTATTTTTCCTTTGATTTAAT
*
1161521 ATTTTTTTCTTATTTGATTT
1 ATTTTTAT-TTATTT-ATTT
1161541 ATTTAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
31 11 0.25
32 4 0.09
33 19 0.43
34 6 0.14
35 4 0.09
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (33 bp):
ATTTTTATTTATTTATTTTTCCTTTGATTTAAT
Found at i:1161523 original size:27 final size:27
Alignment explanation
Indices: 1161485--1161561 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
1161475 CCTTTGACTT
* *
1161485 TTTATTT-TTATTTATTTATT-TTTGC
1 TTTATTTAATATTTATTTATTATTTGA
* *
1161510 TTTGATTTAATATTTTTTTCTTATTTGA
1 TTT-ATTTAATATTTATTTATTATTTGA
*
1161538 TTTATTTAACATTTATTTATTATT
1 TTTATTTAATATTTATTTATTATT
1161562 ATTATTATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 3 0.07
26 4 0.10
27 28 0.67
28 7 0.17
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (27 bp):
TTTATTTAATATTTATTTATTATTTGA
Found at i:1164849 original size:26 final size:26
Alignment explanation
Indices: 1164813--1164866 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1164803 GAATAGTCGA
1164813 GTAAGCAAGTCTAGTTTAGGTCAGTT
1 GTAAGCAAGTCTAGTTTAGGTCAGTT
1164839 GTAAGCAAGTCTAGTTTAGGTCAGTT
1 GTAAGCAAGTCTAGTTTAGGTCAGTT
1164865 GT
1 GT
1164867 TTAGAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (26 bp):
GTAAGCAAGTCTAGTTTAGGTCAGTT
Found at i:1165141 original size:95 final size:95
Alignment explanation
Indices: 1164978--1165232 Score: 351
Period size: 95 Copynumber: 2.7 Consensus size: 95
1164968 CGAATATAAT
* * *
1164978 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCCAGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTAT
* *
1165043 GGATACGATTCAACTAGCCTGATAAAGGTG
66 GGATAAGATTCAACTAGCCTGATAAAGGTC
1165073 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTAT
* * *
1165138 GGATAATATTCAGCTAGCTTGATAAAGGTC
66 GGATAAGATTCAACTAGCCTGATAAAGGTC
* * *
1165168 A-T-T-ATATACAATGATA--TTAAGTTGTCCCTCTAGAGCAATTGGTTAAA-AGCCTCGGCTTT
1 ATTATAATATACAAT-AAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACA-CCCCGGCTTT
1165227 ATGGAT
64 ATGGAT
1165233 TCAGCTAGCC
Statistics
Matches: 147, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
90 1 0.01
91 45 0.31
92 9 0.06
93 3 0.02
94 1 0.01
95 88 0.60
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTAT
GGATAAGATTCAACTAGCCTGATAAAGGTC
Found at i:1166822 original size:84 final size:84
Alignment explanation
Indices: 1166316--1167513 Score: 1306
Period size: 84 Copynumber: 14.3 Consensus size: 84
1166306 AGCATAATTT
** * * * *
1166316 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTTAAGTTTGACTACGTTGAGCT-CAACGACA
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCA
*
1166380 CATCATTTGCAGCATAGCTT
65 CATCATTTGCAGCATAGCTC
* * * * * * * **
1166400 AAGGCAAGAAGGGCTATCTG-C--C-AAAGACCCTCGAGTTTGATTACACTCAACTTTGAAGGCA
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCA
* * *
1166461 CATCAATTGCAGAATAACTC
65 CATCATTTGCAGCATAGCTC
** * *
1166481 AAGGCTAGAAGGGTTATCTTTCAAC-AAAGACCTTTGAGTTAGACTACGCTCAGCT-CAACGGCA
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCA
*
1166544 CATCATTTGCAGCATAGCTT
65 CATCATTTGCAGCATAGCTC
** * * * * * *
1166564 AAGGAAAGAAGGGTTATCT-TC--C-AAAGACCATCGAGTTCGATTACACTCAGCTTCGAGGGCA
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCA
* *
1166625 CATCATTTGTAGCATAACTC
65 CATCATTTGCAGCATAGCTC
* * * *
1166645 AAGGCTAGAAGGGTTATCTGTCAAC-AACGATCTTCGAGTTCGACTATGCTCAGCTCCAAGGCAC
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
* *
1166709 ATCATTTGCAACATAACTC
66 ATCATTTGCAGCATAGCTC
* *
1166728 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGACAC
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
*
1166793 ATCATTTGCAACATAGCTC
66 ATCATTTGCAGCATAGCTC
* * * * ** *
1166812 AAGGCAAGAAGGGCTATTTTCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTAAAAGGCAT
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
*
1166877 ATCATTTGCAGCATAACTC
66 ATCATTTGCAGCATAGCTC
* *
1166896 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGAAC
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
*
1166961 ATCATTTGCATCATAGCTC
66 ATCATTTGCAGCATAGCTC
* ** * * * * * * *
1166980 AAGGCAAGAAGGACTATTTTCCAATAAAAGACCTTCGAGTTCCACTACGCTCAACTCAAAGGAAC
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
*
1167045 ATCATTTGCAGCATATCTC
66 ATCATTTGCAGCATAGCTC
* * * * * *
1167064 AAGACTAGAAGGGTTATTTGCCACCAAAAGACGTTTGAGTTCGACTACGCTCAGCTCCAAGGCAT
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
* *
1167129 ATCATTTGTAGCATAACTC
66 ATCATTTGCAGCATAGCTC
* * * * * *
1167148 AAGGCTAGAAGGGTTATCTGTCGACCATAGACCTTCGAGTTCAACTACGCTCAGCTCAAAGGCAC
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
1167213 ATCATTTGCAGCATAGCTC
66 ATCATTTGCAGCATAGCTC
* * * *
1167232 AAGGCAAGAAGGGCTATCTACC-ACTAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCA
1 AAGGCTAGAAGGGTTATCTGCCAAC-AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
* *
1167296 TATCATTTGCAGCATAACTC
65 CATCATTTGCAGCATAGCTC
* * * * * *
1167316 AAGGCTTGAAGGGTTATCTACCGACCAAAGACCTTTGAGTTCGACTATGCTCAGCTCCAAGGCAC
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
* *
1167381 ATCATTTGCATCATAGCTT
66 ATCATTTGCAGCATAGCTC
* * * * * * *
1167400 AAAGCAAGAAGGGCTATTTGCCAACAAAGGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCGC
1 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC-A
1167465 CATCATTTGCAGCATAGCTC
65 CATCATTTGCAGCATAGCTC
* * * * *
1167485 AAGACAAGAGGGGCTATCTGTCAACAAAA
1 AAGGCTAGAAGGGTTATCTGCCAACAAAA
1167514 TTGTTGAGTT
Statistics
Matches: 931, Mismatches: 168, Indels: 29
0.83 0.15 0.03
Matches are distributed among these distances:
80 46 0.05
81 77 0.08
82 10 0.01
83 90 0.10
84 665 0.71
85 43 0.05
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (84 bp):
AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
ATCATTTGCAGCATAGCTC
Found at i:1168047 original size:2 final size:2
Alignment explanation
Indices: 1168040--1168084 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1168030 TTTTGTTATT
*
1168040 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1168081 TA TA
1 TA TA
1168085 GTTTGCACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1168173 original size:38 final size:38
Alignment explanation
Indices: 1168108--1168220 Score: 131
Period size: 40 Copynumber: 2.9 Consensus size: 38
1168098 TTTTTGAAAA
* * **
1168108 ATATAATATATAGTTTTTGAAAACATTT-CGAAAACAT
1 ATATATTATATAGTTTTTGAAATCATTTAAAAAAACAT
*
1168145 ATATATTATATAGTTTTTTGAAATCATTTTAAAAAAACTT
1 ATATATTATATAG-TTTTTGAAATCA-TTTAAAAAAACAT
1168185 ATATAATATATATAG-TTTTGAAATCATTTAAAAAAA
1 ATAT-AT-TATATAGTTTTTGAAATCATTTAAAAAAA
1168221 AAATTATACA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
37 12 0.18
38 11 0.17
39 13 0.20
40 21 0.32
41 2 0.03
42 7 0.11
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (38 bp):
ATATATTATATAGTTTTTGAAATCATTTAAAAAAACAT
Found at i:1168330 original size:39 final size:39
Alignment explanation
Indices: 1168250--1168429 Score: 250
Period size: 39 Copynumber: 4.8 Consensus size: 39
1168240 ATATATATAT
1168250 ATATATATAGTTTTGAAATCATTTTG-AAAACTTATTTA
1 ATATATATAGTTTTGAAATCATTTTGAAAAACTTATTTA
1168288 ATATATATAGTTTTGAAATCATTTTGAAAAACTTATTTA
1 ATATATATAGTTTTGAAATCATTTTGAAAAACTTATTTA
*
1168327 ATATATATAGTTTTGAAATCATTTTTAAAAAAC--A--TA
1 ATATATATAGTTTTGAAATCA-TTTTGAAAAACTTATTTA
* *
1168363 ATATATATAGTTTTTAAATCATTTTGAAAAACTTATAT-
1 ATATATATAGTTTTGAAATCATTTTGAAAAACTTATTTA
*
1168401 A-ATATATAGTTTTAAAAT-ATTTTTGAAAA
1 ATATATATAGTTTTGAAATCA-TTTTGAAAA
1168430 CTATATAATT
Statistics
Matches: 131, Mismatches: 4, Indels: 15
0.87 0.03 0.10
Matches are distributed among these distances:
35 10 0.08
36 23 0.18
37 26 0.20
38 28 0.21
39 34 0.26
40 10 0.08
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (39 bp):
ATATATATAGTTTTGAAATCATTTTGAAAAACTTATTTA
Found at i:1168382 original size:75 final size:74
Alignment explanation
Indices: 1168245--1168429 Score: 257
Period size: 75 Copynumber: 2.5 Consensus size: 74
1168235 TACATATATA
* * **
1168245 TATATATATATATAGTTTTGAAATCATTTTGAAAACTTATTTAATATATATAGTTTTGAAATCAT
1 TATATATATATATAGTTTTGAAATCATTTTTAAAA--AACATAATATATATAGTTTTGAAATCAT
1168310 TTTGAAAAACT
64 TTTGAAAAACT
* *
1168321 TATTTAATATATATAGTTTTGAAATCATTTTTAAAAAACATAATATATATAGTTTTTAAATCATT
1 TATAT-ATATATATAGTTTTGAAATCATTTTTAAAAAACATAATATATATAGTTTTGAAATCATT
1168386 TTGAAAAACT
65 TTGAAAAACT
* *
1168396 TATATA-ATATATAGTTTTAAAAT-ATTTTTGAAAA
1 TATATATATATATAGTTTTGAAATCATTTTTAAAAA
1168430 CTATATAATT
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
72 10 0.10
73 16 0.16
74 1 0.01
75 39 0.39
76 4 0.04
77 29 0.29
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (74 bp):
TATATATATATATAGTTTTGAAATCATTTTTAAAAAACATAATATATATAGTTTTGAAATCATTT
TGAAAAACT
Found at i:1168441 original size:28 final size:27
Alignment explanation
Indices: 1168383--1168463 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 27
1168373 TTTTTAAATC
* * *
1168383 ATTTTGAAAA-ACTTATATAATATATA
1 ATTTTGAAAATATTTTTAAAATATATA
*
1168409 GTTTT-AAAATATTTTTGAAAACTATATA
1 ATTTTGAAAATATTTTT-AAAA-TATATA
1168437 ATTTTGAAAATATTTTTAAAATATATA
1 ATTTTGAAAATATTTTTAAAATATATA
1168464 TATATATAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
25 4 0.09
26 8 0.17
27 9 0.20
28 14 0.30
29 11 0.24
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (27 bp):
ATTTTGAAAATATTTTTAAAATATATA
Found at i:1168463 original size:29 final size:28
Alignment explanation
Indices: 1168401--1168465 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
1168391 AAACTTATAT
*
1168401 AATATATAGTTTTAAAATATTTTTGAAA
1 AATATATAATTTTAAAATATTTTTGAAA
*
1168429 ACTATATAATTTTGAAAATATTTTT-AAA
1 AATATATAATTTT-AAAATATTTTTGAAA
1168457 ATATATATA
1 A-ATATATA
1168466 TATATAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (28 bp):
AATATATAATTTTAAAATATTTTTGAAA
Found at i:1170874 original size:3 final size:3
Alignment explanation
Indices: 1170868--1170893 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1170858 TATTAGTGAA
1170868 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1170894 CGATAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1171295 original size:21 final size:21
Alignment explanation
Indices: 1171271--1171413 Score: 123
Period size: 21 Copynumber: 7.4 Consensus size: 21
1171261 GGAAACTATC
1171271 TCAAGGGAGACGAAATTTGTT
1 TCAAGGGAGACGAAATTTGTT
* *
1171292 TCAA--G-G--GAAA-CTGTC
1 TCAAGGGAGACGAAATTTGTT
1171307 TCAAGGGAGACGAAATTTGTT
1 TCAAGGGAGACGAAATTTGTT
* *
1171328 TCAA--G-G--GAAA-CTGTC
1 TCAAGGGAGACGAAATTTGTT
*
1171343 TCAAGGGAGA-AAAATTTTGTT
1 TCAAGGGAGACGAAA-TTTGTT
*
1171364 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACGAAATTTGTT
*
1171385 TCGAGGGAGACGAAATTTGTT
1 TCAAGGGAGACGAAATTTGTT
1171406 TCAAGGGA
1 TCAAGGGA
1171414 AACTGTCTCA
Statistics
Matches: 97, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
15 14 0.14
16 8 0.08
17 2 0.02
18 4 0.04
19 5 0.05
20 4 0.04
21 56 0.58
22 4 0.04
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (21 bp):
TCAAGGGAGACGAAATTTGTT
Found at i:1171297 original size:36 final size:36
Alignment explanation
Indices: 1171108--1171855 Score: 494
Period size: 36 Copynumber: 21.4 Consensus size: 36
1171098 GGGTATAATG
* ** * **
1171108 GTTTCAAGAGAAACCATCTCAAGAGAGACAACACAT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
1171144 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAATT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
1171180 -TTTCAAAGGAAAGTGTATCAAGAGAGACAAAATTTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTT
* * *
1171216 GTTTCAAGGGAAACTGTCACAAGGGAGACGAAATTTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATTT
* * *
1171253 GTTTCAAGGGAAACTATCTCAAGGGAGACGAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
1171289 GTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
1171325 GTTTCAAGGGAAACTGTCTCAAGGGAGA-AAAATTTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTT
* * * * *
1171361 GTTTCAAGGGAGACAAAATTTGTTTCGAGGGAGACGAAATTT
1 GTTTCAA-GG-G---AAA-CTGTCTCAAGAGAGACAAAATTT
*
1171403 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
1171439 ATTTCAAGGGAAACAT-TCTC-A-A-AG-----TTTAT
1 GTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATT-T
*
1171468 GTTTCAAGAGAAACTGTCTCAATG-GAGACAAAATTT
1 GTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
* * * *
1171504 GGTTTAAAGGGAAA-TAGACT-TA-A-AGAC---TTTT
1 -GTTTCAAGGGAAACT-GTCTCAAGAGAGACAAAATTT
* * * *
1171535 GTTTCAAGAGAAACTGTCTCTAGAGAGACAACA-TA
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** **
1171570 GTTTCAAGGGAAACAAAT-TC-A-A-AG---ATTTTGT
1 GTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATT-T
* * *
1171601 GTTTCAAGAGAAACTTTCTCAAGGGAGAC--AATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
1171635 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
1171671 ATTTCTAGGGAAAC-GTTTTC-A-A-AG-----TTTAT
1 GTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT-T
* * *
1171700 GTTTCAAGAGAAACTGTCTAAATAGAGACAAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
1171736 GTTTCAAGGGAAAGTATCTCAAGAGAGACAAAACTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
1171772 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
1171808 GTTTCAAGGGAAAAT-TCTCAAGAGAGAAAAAAATC
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
1171843 GTTTCATGGGAAA
1 GTTTCAAGGGAAA
1171856 TGTTTTCAAA
Statistics
Matches: 565, Mismatches: 92, Indels: 111
0.74 0.12 0.14
Matches are distributed among these distances:
28 5 0.01
29 30 0.05
30 19 0.03
31 22 0.04
32 8 0.01
33 9 0.02
34 36 0.06
35 80 0.14
36 244 0.43
37 77 0.14
38 4 0.01
40 1 0.00
41 5 0.01
42 22 0.04
43 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (36 bp):
GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:1171371 original size:145 final size:147
Alignment explanation
Indices: 1171108--1171460 Score: 421
Period size: 145 Copynumber: 2.4 Consensus size: 147
1171098 GGGTATAATG
* * ** *
1171108 GTTTCAAGAGAAACCATCTCAAGAGAGACAACACATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
1 GTTTCAAGGGAAACTATCTCAAGAGAGACAA-ATTTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
*
1171173 AAAAATTTTTCAAAGGAAAGTGTATCAAGAGAGACAAAATTTTGTTTCAA-GG-G-AAA-CTGTC
65 AAAAATTTTTCAAAGGAAACTGTATCAAGAGAGACAAAATTTTGTTTCAAGGGAGAAAATCTGTC
1171234 ACAAGGGAGACGAAATTTT
130 ACAAGGGAGACGAAA-TTT
*
1171253 GTTTCAAGGGAAACTATCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
1 GTTTCAAGGGAAACTATCTCAAGAGAGAC-AAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
* * * * * *
1171318 GAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGA-AAAATTTTGTTTCAAGGGAGACAAAATTT
65 AAAAATT-TTTCAAAGGAAACTGTATCAAGAGAGACAAAATTTTGTTTCAAGGGAG--AAAATCT
** *
1171382 GTTTCGAGGGAGACGAAATTT
127 GTCACAAGGGAGACGAAATTT
* **
1171403 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAT-TCTCAA
1 GTTTCAAGGGAAACTATCTCAAGAGAGAC-AAATTTGTTTCAAGGGAAAC-TGTCTCAA
1171461 AGTTTATGTT
Statistics
Matches: 178, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
145 76 0.43
146 27 0.15
147 1 0.01
150 57 0.32
151 17 0.10
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (147 bp):
GTTTCAAGGGAAACTATCTCAAGAGAGACAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACA
AAAATTTTTCAAAGGAAACTGTATCAAGAGAGACAAAATTTTGTTTCAAGGGAGAAAATCTGTCA
CAAGGGAGACGAAATTT
Found at i:1171417 original size:114 final size:109
Alignment explanation
Indices: 1171108--1171855 Score: 466
Period size: 101 Copynumber: 7.1 Consensus size: 109
1171098 GGGTATAATG
* ** * * ** * *
1171108 GTTTCAAGAGAAACCATCTCAAGAGAGACAACA-CATGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGGGAGA
* * * * *
1171172 CAAAAATT-TTTCAAAGGAAAGTGTATCAAGAGAGACAAAATTTT
66 CGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTT
* *
1171216 GTTTCAAGGGAAACTGTCACAAGGGAGACGAAATTTTGTTTCAAGGGAAACTATCTCAAGGGAGA
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGGGAGA
* *
1171281 CGAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTT
66 CGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
1171325 GTTTCAAGGGAAACTGTCTCAAGGGAGA-AAAATTTTGTTTCAAGGGAGACAAAATTTGTTTCGA
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAA-GG-G---AAA-CTATCTCAA
*
1171389 GGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
60 GGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
1171439 ATTTCAAGGGAAACAT-TCTCAA---AG------TTTATGTTTCAAGAGAAACTGTCTCAATGGA
1 GTTTCAAGGGAAAC-TGTCTCAAGGGAGACAAAATTT-TGTTTCAAGGGAAACTATCTCAAGGGA
* * * * *
1171494 GACAAAATTTGGTTTAAAGGGAAA-TAGACT-TA-A-AGAC---TTTT
64 GACGAAATTT-GTTTCAAGGGAAACT-GTCTCAAGAGAGACAAAATTT
* * * * * *
1171535 GTTTCAAGAGAAACTGTCTCTAGAGAGACAACA--TAGTTTCAAGGGAAACAAAT-TC-A---A-
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAC-TATCTCAAGGGAG
** * * *
1171592 A-GATTTTGTGTTTCAAGAGAAACTTTCTCAAGGGAGAC--AATTT
65 ACGAAATT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * ** * *
1171635 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTCATTTCTAGGGAAACGT-TTTC-A---A-
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAC-TATCTCAAGGGAG
* * * *
1171693 A-G--TTTATGTTTCAAGAGAAACTGTCTAAATAGAGACAAAATTT
65 ACGAAATT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * * * * *
1171736 GTTTCAAGGGAAAGTATCTCAAGAGAGACAAAA-CTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGGGAGA
* * * * * *
1171800 CAAAATTCGTTTCAAGGGAAAAT-TCTCAAGAGAGAAAAAAATC
66 CGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
1171843 GTTTCATGGGAAA
1 GTTTCAAGGGAAA
1171856 TGTTTTCAAA
Statistics
Matches: 511, Mismatches: 87, Indels: 85
0.75 0.13 0.12
Matches are distributed among these distances:
95 1 0.00
96 35 0.07
97 4 0.01
98 1 0.00
99 39 0.08
100 35 0.07
101 93 0.18
102 34 0.07
103 2 0.00
105 2 0.00
106 5 0.01
107 35 0.07
108 53 0.10
109 67 0.13
110 28 0.05
111 2 0.00
113 3 0.01
114 71 0.14
115 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (109 bp):
GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGGGAGA
CGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:1171629 original size:66 final size:65
Alignment explanation
Indices: 1171400--1171648 Score: 262
Period size: 65 Copynumber: 3.8 Consensus size: 65
1171390 GGAGACGAAA
* *
1171400 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCA-TTTCAAGGGAAAC-ATTCTCAAAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-AGTTTCAAGGGAAACAAAT-TCAAAG
1171463 -T
64 AT
* * * *
1171464 TTATGTTTCAAGAGAAACTGTCTCAATG-GAGACAAAATTTGGTTTAAAGGGAAATAGACTT-AA
1 TT-TGTTTCAAGAGAAACTGTCTCAA-GAGAGACAAAA-TTAGTTTCAAGGGAAACA-AATTCAA
1171527 AGACT
62 AGA-T
* *
1171532 TTTGTTTCAAGAGAAACTGTCTCTAGAGAGACAACA-TAGTTTCAAGGGAAACAAATTCAAAGAT
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAGGGAAACAAATTCAAAGA-
1171596 T
65 T
* * *
1171597 TTGTGTTTCAAGAGAAACTTTCTCAAGGGAGAC--AATTTGTTTCAAGGGAAAC
1 TT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAGGGAAAC
1171649 TATCTCAAGA
Statistics
Matches: 156, Mismatches: 17, Indels: 23
0.80 0.09 0.12
Matches are distributed among these distances:
64 6 0.04
65 68 0.44
66 46 0.29
67 31 0.20
68 5 0.03
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (65 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAGGGAAACAAATTCAAAGAT
Found at i:1171878 original size:172 final size:171
Alignment explanation
Indices: 1171600--1171911 Score: 459
Period size: 172 Copynumber: 1.8 Consensus size: 171
1171590 AAAGATTTTG
* * * * *
1171600 TGTTTCAAGAGAAACTTTCTCAAGGGAGACAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAATTCGTTTCAAGGGAAAATATCTCAAGAGAGAAA
* *
1171665 AAATTCATTTCTAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCT-AAATAGAGAC
66 AAAATCATTTCTAGGGAAACGTTTTCAAAGTTTACGTTTCAAGAGAAACTGTCTCAAA-AGAGAC
*
1171729 AAAATTTGTTTCAAGGGAAAGTATCTCAAGAGAGACAAAACT
130 AAAACTTGTTTCAAGGGAAAGTATCTCAAGAGAGACAAAACT
*
1171771 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAAAT-TCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC--AATTCGTTTCAAGGGAAAATATCTCAAGAGAGA
* * *
1171835 AAAAAATCGTTTC-ATGGGAAATGTTTTCAAAGTTTACGTTTCAAGAGAAACTGTCTCAAAGGAG
64 AAAAAATCATTTCTA-GGGAAACGTTTTCAAAGTTTACGTTTCAAGAGAAACTGTCTCAAAAGAG
1171899 ACAAAACTTGTTT
128 ACAAAACTTGTTT
1171912 GAGTAAAAAT
Statistics
Matches: 125, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
171 28 0.22
172 76 0.61
173 21 0.17
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (171 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAATTCGTTTCAAGGGAAAATATCTCAAGAGAGAAA
AAAATCATTTCTAGGGAAACGTTTTCAAAGTTTACGTTTCAAGAGAAACTGTCTCAAAAGAGACA
AAACTTGTTTCAAGGGAAAGTATCTCAAGAGAGACAAAACT
Found at i:1172085 original size:36 final size:36
Alignment explanation
Indices: 1172037--1172139 Score: 93
Period size: 37 Copynumber: 2.9 Consensus size: 36
1172027 GAGATGAAAC
*
1172037 TTGTTTTGAGAGAAATTGTCTCAAGCAAGACAAAAT
1 TTGTTTTCAGAGAAATTGTCTCAAGCAAGACAAAAT
* * * * * *
1172073 TTGTTTTTAGAGAAAACTGCCTCTAGTGAA-ACAAATT
1 TTGTTTTCAGAG-AAATTGTCTCAAG-CAAGACAAAAT
* *
1172110 TTGTTTTCAGA-AAATTTTCTCAAGCGAGAC
1 TTGTTTTCAGAGAAATTGTCTCAAGCAAGAC
1172140 GACCCCTTGT
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 11 0.22
36 11 0.22
37 26 0.51
38 2 0.04
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (36 bp):
TTGTTTTCAGAGAAATTGTCTCAAGCAAGACAAAAT
Found at i:1173293 original size:12 final size:12
Alignment explanation
Indices: 1173278--1173349 Score: 71
Period size: 12 Copynumber: 5.9 Consensus size: 12
1173268 TTCTTCTTGT
1173278 CTTTTTTCTTTG
1 CTTTTTTCTTTG
1173290 C-TTTTTCTTTTG
1 CTTTTTTC-TTTG
1173302 -TTTTTTCTTTG
1 CTTTTTTCTTTG
1173313 CTTTTTTTTTCTTTG
1 C---TTTTTTCTTTG
1173328 CTTTTTCTCTTT-
1 CTTTTT-TCTTTG
1173340 -TTTTTTCTTT
1 CTTTTTTCTTT
1173350 TTCTTTCATT
Statistics
Matches: 53, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
10 5 0.09
11 15 0.28
12 16 0.30
13 5 0.09
15 12 0.23
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (12 bp):
CTTTTTTCTTTG
Found at i:1173296 original size:11 final size:11
Alignment explanation
Indices: 1173280--1173355 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
1173270 CTTCTTGTCT
1173280 TTTTTCTTTGC
1 TTTTTCTTTGC
*
1173291 TTTTTCTTTTGT
1 TTTTTC-TTTGC
1173303 TTTTTCTTTGC
1 TTTTTCTTTGC
1173314 TTTTTTTTTCTTTGC
1 ----TTTTTCTTTGC
1173329 TTTTTC--T-C
1 TTTTTCTTTGC
*
1173337 TTTTT-TTTTC
1 TTTTTCTTTGC
1173347 TTTTTCTTT
1 TTTTTCTTT
1173356 CATTTAATCT
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
8 6 0.11
9 2 0.04
10 6 0.11
11 19 0.35
12 10 0.19
15 11 0.20
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.80
Consensus pattern (11 bp):
TTTTTCTTTGC
Found at i:1173305 original size:23 final size:22
Alignment explanation
Indices: 1173279--1173355 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
1173269 TCTTCTTGTC
1173279 TTTTTTCTTTGCTTTTTCTTTTG
1 TTTTTTCTTTGCTTTTT-TTTTG
*
1173302 TTTTTTCTTTGCTTTTTTTTTC
1 TTTTTTCTTTGCTTTTTTTTTG
1173324 TTTGCTTT-TTCT-CTTTTTTTTT-
1 TTT--TTTCTT-TGCTTTTTTTTTG
*
1173346 CTTTTTCTTT
1 TTTTTTCTTT
1173356 CATTTAATCT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.08
21 2 0.04
22 9 0.19
23 29 0.60
24 4 0.08
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (22 bp):
TTTTTTCTTTGCTTTTTTTTTG
Found at i:1173322 original size:15 final size:15
Alignment explanation
Indices: 1173302--1173333 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1173292 TTTTCTTTTG
1173302 TTTTTTCTTTGCTTT
1 TTTTTTCTTTGCTTT
1173317 TTTTTTCTTTGCTTT
1 TTTTTTCTTTGCTTT
1173332 TT
1 TT
1173334 CTCTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTTTTCTTTGCTTT
Found at i:1175054 original size:149 final size:146
Alignment explanation
Indices: 1174763--1175044 Score: 334
Period size: 149 Copynumber: 1.9 Consensus size: 146
1174753 TTATACCTTG
* * * * * *
1174763 TCTCTTACTTTTAGAAGTCTTTTGAGTTGGTTTATGATCTTCCATTATTTTTGGTGTCGAATCAT
1 TCTCTTACTTTTAGAAATCTTTCGAGTTGGTTTATGATCTTCAACTATTTTTAGTATCGAATCAT
* * * * * * *
1174828 CTCGAGTCTAACTTGTTACCTCTGCAGGCAAATGTCTGTATTGTCTCCTTGGCAGATAGACTTCC
66 CACGAGTCCAACTTGTTACCTCAGCAGGCAAATGTCTGGATCGTCTCCTTAGCAGATAGACTCCC
1174893 TCTAGCTGCTACTTCA
131 TCTAGCTGCTACTTCA
* *
1174909 TCTCTTA-TTTTCAGAAATCTTTCGAGTTGGTTTGTGATCTTCAACTGTTGTCTTCAGTATCGAA
1 TCTCTTACTTTT-AGAAATCTTTCGAGTTGGTTTATGATCTTCAACTATT-T-TT-AGTATCGAA
* * * *
1174973 TCGTCACGAGTCCAACTTGTTACCTCAGTAGGTAAATGTCTGGATCGTCTCCTTAGTATG-TAGA
62 TCATCACGAGTCCAACTTGTTACCTCAGCAGGCAAATGTCTGGATCGTCTCCTTAGCA-GATAGA
1175037 CTCCCTCT
126 CTCCCTCT
1175045 TGACTCTACT
Statistics
Matches: 112, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
145 4 0.04
146 38 0.34
147 1 0.01
148 2 0.02
149 66 0.59
150 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (146 bp):
TCTCTTACTTTTAGAAATCTTTCGAGTTGGTTTATGATCTTCAACTATTTTTAGTATCGAATCAT
CACGAGTCCAACTTGTTACCTCAGCAGGCAAATGTCTGGATCGTCTCCTTAGCAGATAGACTCCC
TCTAGCTGCTACTTCA
Found at i:1177663 original size:15 final size:15
Alignment explanation
Indices: 1177640--1177670 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1177630 TGTAAATTAT
*
1177640 TAGTGATAATAATAA
1 TAGTAATAATAATAA
1177655 TAGTAATAATAATAA
1 TAGTAATAATAATAA
1177670 T
1 T
1177671 TATTATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (15 bp):
TAGTAATAATAATAA
Found at i:1183647 original size:20 final size:20
Alignment explanation
Indices: 1183611--1183648 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1183601 CTGGGTTAGG
*
1183611 GTATCGATATCGGATGAATA
1 GTATCGATATCGAATGAATA
1183631 GTATCGATA-CTGAATGAA
1 GTATCGATATC-GAATGAA
1183649 CTAGGATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (20 bp):
GTATCGATATCGAATGAATA
Found at i:1183699 original size:18 final size:18
Alignment explanation
Indices: 1183676--1183722 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 18
1183666 TATTTTATGC
1183676 AAGGAGTATCGATACTCT
1 AAGGAGTATCGATACTCT
*
1183694 AAGGAGTAATATGGATACTCT
1 AAGGAG---TATCGATACTCT
1183715 AAGGAGTA
1 AAGGAGTA
1183723 ATATAGATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 8 0.32
21 17 0.68
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.26
Consensus pattern (18 bp):
AAGGAGTATCGATACTCT
Found at i:1183712 original size:21 final size:21
Alignment explanation
Indices: 1183686--1183733 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1183676 AAGGAGTATC
*
1183686 GATACTCTAAGGAGTAATATG
1 GATACTCTAAGGAGTAATATA
1183707 GATACTCTAAGGAGTAATATA
1 GATACTCTAAGGAGTAATATA
1183728 GATACT
1 GATACT
1183734 ACAACCATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (21 bp):
GATACTCTAAGGAGTAATATA
Found at i:1191263 original size:20 final size:21
Alignment explanation
Indices: 1191226--1191265 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1191216 AAATTAAGTT
1191226 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1191247 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1191266 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1191520 original size:19 final size:19
Alignment explanation
Indices: 1191496--1191534 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1191486 TCGAATGCAT
1191496 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1191515 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1191534 T
1 T
1191535 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1191639 original size:64 final size:65
Alignment explanation
Indices: 1191482--1191642 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
1191472 GAATTAATTG
* * *** *
1191482 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
1191547 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
1191610 A
65 A
*
1191611 AACATCGAATGTATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1191643 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 36 0.43
65 48 0.57
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1191657 original size:64 final size:64
Alignment explanation
Indices: 1191482--1191662 Score: 211
Period size: 64 Copynumber: 2.8 Consensus size: 64
1191472 GAATTAATTG
* * * *
1191482 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
1191547 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
* *** *
1191611 AACATCGAATGTATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
1191663 AGTGTTCCAA
Statistics
Matches: 98, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 50 0.51
65 48 0.49
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:1197459 original size:20 final size:21
Alignment explanation
Indices: 1197430--1197485 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1197420 TTTGCGCTTC
*
1197430 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
1197450 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
1197472 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1197486 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:1199045 original size:21 final size:21
Alignment explanation
Indices: 1199003--1199046 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1198993 ACCCCGGGAG
*
1199003 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1199024 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1199045 CT
1 CT
1199047 CCTCCTCCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1199573 original size:20 final size:21
Alignment explanation
Indices: 1199536--1199575 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1199526 AAATTAAGTT
1199536 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1199557 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1199576 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1199830 original size:19 final size:19
Alignment explanation
Indices: 1199806--1199844 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1199796 TCGAATGCAT
1199806 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1199825 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1199844 T
1 T
1199845 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1199945 original size:64 final size:65
Alignment explanation
Indices: 1199792--1199952 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
1199782 GAATTAATTG
* * *** *
1199792 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
1199857 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
1199920 A
65 A
1199921 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1199953 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1199967 original size:64 final size:64
Alignment explanation
Indices: 1199792--1199972 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
1199782 GAATTAATTG
* * * *
1199792 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
1199857 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
1199921 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
1199973 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
64 51 0.52
65 48 0.48
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:1206550 original size:53 final size:52
Alignment explanation
Indices: 1206425--1206584 Score: 225
Period size: 53 Copynumber: 3.1 Consensus size: 52
1206415 TTCATACTAC
*
1206425 AAAAAAGTGTAGCACTAAACACATACTTACACCGTGTAAGTGAATAAAAT--
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGTGTAAGTGAATAAAATAA
* * *
1206475 ATAAAAGTGTAGTACTTAACACATATTTACACCTGTGTAAGTGAATAAAATAA
1 AAAAAAGTGTAGCACTTAACACATACTTACACC-GTGTAAGTGAATAAAATAA
* * *
1206528 AAAAAAGTGTAGCATTTAACACATACTTACACCGGTGTGAGTGAATAAAACAA
1 AAAAAAGTGTAGCACTTAACACATACTTACACC-GTGTAAGTGAATAAAATAA
1206581 AAAA
1 AAAA
1206585 GTATGGTACT
Statistics
Matches: 96, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
50 29 0.30
51 17 0.18
53 50 0.52
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (52 bp):
AAAAAAGTGTAGCACTTAACACATACTTACACCGTGTAAGTGAATAAAATAA
Found at i:1206619 original size:104 final size:103
Alignment explanation
Indices: 1206425--1206620 Score: 284
Period size: 104 Copynumber: 1.9 Consensus size: 103
1206415 TTCATACTAC
* * *
1206425 AAAAAAGTGTAGCACTAAACACATACTTACACCGTGTAAGTGAATAAAATATAAAAGTGTAGTAC
1 AAAAAAGTGTAGCACTAAACACATACTTACACCGTGTAAGTGAATAAAACAAAAAAGTATAGTAC
* *
1206490 TTAACACATATTTACACCTGTGTAAGTGAATAAAATAA
66 TTAACACATATTTACACCGGCGTAAGTGAATAAAATAA
* * * *
1206528 AAAAAAGTGTAGCATTTAACACATACTTACACCGGTGTGAGTGAATAAAACAAAAAAGTATGGTA
1 AAAAAAGTGTAGCACTAAACACATACTTACACC-GTGTAAGTGAATAAAACAAAAAAGTATAGTA
* *
1206593 CTTAACACATATTTATATCGGCGTAAGT
65 CTTAACACATATTTACACCGGCGTAAGT
1206621 ATGTACATCT
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
103 31 0.38
104 50 0.62
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (103 bp):
AAAAAAGTGTAGCACTAAACACATACTTACACCGTGTAAGTGAATAAAACAAAAAAGTATAGTAC
TTAACACATATTTACACCGGCGTAAGTGAATAAAATAA
Found at i:1209258 original size:832 final size:834
Alignment explanation
Indices: 1207644--1209296 Score: 3229
Period size: 832 Copynumber: 2.0 Consensus size: 834
1207634 CGGGTATCTT
*
1207644 CACATCTAAAACTCAAGAAAACATCATACTTCTTTCTAGAAATAGATGGGGAGATAAAGGTAACA
1 CACATATAAAACTCAAGAAAACATCATACTTCTTTCTAGAAATAGATGGGGAGATAAAGGTAACA
1207709 ATCGGAAGTATATAAGCATCAGTAAAGAGAAAAATATATAGAATTTGCCAGAAAACAAAACAAAG
66 ATCGGAAGTATATAAGCATCAGTAAAGAGAAAAATATATAGAATTTGCCAGAAAACAAAACAAAG
1207774 GTTTCTATGCAATTTCTGAAGAAAAAAAAAGTGTAATAGCAGAAGTAATGGGTTTTCCAAGAAGA
131 GTTTCTATGCAATTTCT--AG-AAAAAAAAGTGTAATAGCAGAAGTAATGGGTTTTCCAAGAAGA
*
1207839 ACCCTGATGTGATCCAATTCAGCATCATGGATATTCCACCCTTACAAGGGAAGAGACTTTCTAAC
193 ACCCTAATGTGATCCAATTCAGCATCATGGATATTCCACCCTTACAAGGGAAGAGACTTTCTAAC
1207904 TTTACACATATATATGATTATTTTATAGTTATTTTCATCTACATATATTATATCTATAGTTATTA
258 TTTACACATATATATGATTATTTTATAGTTATTTTCATCTACATATATTATATCTATAGTTATTA
1207969 TGATGATAACCTATCCATTAATATGTGAAATATAAGTTATCATAATATACTATAGTTCACATTCT
323 TGATGATAACCTATCCATTAATATGTGAAATATAAGTTATCATAATATACTATAGTTCACATTCT
1208034 TATATAATACATTATATAAGTTCATTTACTTAGTTTATTTCTTTATGTTATGCATGTAGGCACAT
388 TATATAATACATTATATAAGTTCATTTACTTAGTTTATTTCTTTATGTTATGCATGTAGGCACAT
1208099 TCGGCCAGTACTTGGGAGCTACATTGGAGCTAAATAGAGCATGCAAAAGCAAGGATACTTACATG
453 TCGGCCAGTACTTGGGAGCTACATTGGAGCTAAATAGAGCATGCAAAAGCAAGGATACTTACATG
1208164 GGAACGATTAGGAGAGCATAAGGAGCAAATTCGTGAAAAGTTGTTTTGAGGCCGTAAGCTCATAG
518 GGAACGATTAGGAGAGCATAAGGAGCAAATTCGTGAAAAGTTGTTTTGAGGCCGTAAGCTCATAG
1208229 CTGGATTGAGCTGAAGATTTGAGCTACAAGATGACCTCATTTCAGCTAGGGAGTTGTACCATCAT
583 CTGGATTGAGCTGAAGATTTGAGCTACAAGATGACCTCATTTCAGCTAGGGAGTTGTACCATCAT
1208294 CATCACCACTTAGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGCG
648 CATCACCACTTAGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGCG
1208359 AATAGTTGCCAACTCAAGAGGTACCTTTTCACAAGGAGCTGCCATAATGTTCACCATGCTACAAG
713 AATAGTTGCCAACTCAAGAGGTACCTTTTCACAAGGAGCTGCCATAATGTTCACCATGCTACAAG
1208424 TCACCTATGGTCAGCTCACCTTTAGCTCATTCACACCATAAATATATAGAATTTGCC
778 TCACCTATGGTCAGCTCACCTTTAGCTCATTCACACCATAAATATATAGAATTTGCC
1208481 CACATATAAAACTCAAGAAAACATCATACTTCTTTCTAGAAATAGATGGGGAGATAAAGGTAACA
1 CACATATAAAACTCAAGAAAACATCATACTTCTTTCTAGAAATAGATGGGGAGATAAAGGTAACA
1208546 ATCGGAAGTATATAAGCATCAGTAAAGAGAAAAATATATAGAATTTGCCAGAAAACAAAACAAAG
66 ATCGGAAGTATATAAGCATCAGTAAAGAGAAAAATATATAGAATTTGCCAGAAAACAAAACAAAG
1208611 GTTTCTATGCAATTTCT-G-AAAAAAAGTGTAATAGCAGAAGTAATGGGTTTTCCAAGAAGAACC
131 GTTTCTATGCAATTTCTAGAAAAAAAAGTGTAATAGCAGAAGTAATGGGTTTTCCAAGAAGAACC
1208674 CTAATGTGATCCAATTCAGCATCATGGATATTCCACCCTTACAAGGGAAGAGACTTTCTAACTTT
196 CTAATGTGATCCAATTCAGCATCATGGATATTCCACCCTTACAAGGGAAGAGACTTTCTAACTTT
1208739 ACACATATATATGATTATTTTATAGTTATTTTCATCTACATATATTATATCTATAGTTATTATGA
261 ACACATATATATGATTATTTTATAGTTATTTTCATCTACATATATTATATCTATAGTTATTATGA
1208804 TGATAACCTATCCATTAATATGTGAAATATAAGTTATCATAATATACTATAGTTCACATTCTTAT
326 TGATAACCTATCCATTAATATGTGAAATATAAGTTATCATAATATACTATAGTTCACATTCTTAT
1208869 ATAATACATTATATAAGTTCATTTACTTAGTTTATTTCTTTATGTTATGCATGTAGGCACATTCG
391 ATAATACATTATATAAGTTCATTTACTTAGTTTATTTCTTTATGTTATGCATGTAGGCACATTCG
*
1208934 GCCAGTACTTGGGAGCTACATTGGAGCTAAATGGAGCATGCAAAAGCAAGGATACTTACATGGGA
456 GCCAGTACTTGGGAGCTACATTGGAGCTAAATAGAGCATGCAAAAGCAAGGATACTTACATGGGA
*
1208999 ACGATTAGGAGAGCATAAGGAGTAAATTCGTGAAAAGTTGTTTTGAGGCCGTAAGCTCATAGCTG
521 ACGATTAGGAGAGCATAAGGAGCAAATTCGTGAAAAGTTGTTTTGAGGCCGTAAGCTCATAGCTG
1209064 GATTGAGCTGAAGATTTGAGCTACAAGATGACCTCATTTCAGCTAGGGAGTTGTACCATCATCAT
586 GATTGAGCTGAAGATTTGAGCTACAAGATGACCTCATTTCAGCTAGGGAGTTGTACCATCATCAT
1209129 CACCACTTAGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGCGAAT
651 CACCACTTAGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGCGAAT
1209194 AGTTGCCAACTCAAGAGGTACCTTTTCACAAGGAGCTGCCATAATGTTCACCATGCTACAAGTCA
716 AGTTGCCAACTCAAGAGGTACCTTTTCACAAGGAGCTGCCATAATGTTCACCATGCTACAAGTCA
1209259 CCTATGGTCAGCTCACCTTTAGCTCATTCACACCATAA
781 CCTATGGTCAGCTCACCTTTAGCTCATTCACACCATAA
1209297 GTAGCTCAAA
Statistics
Matches: 812, Mismatches: 4, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
832 665 0.82
834 1 0.00
837 146 0.18
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (834 bp):
CACATATAAAACTCAAGAAAACATCATACTTCTTTCTAGAAATAGATGGGGAGATAAAGGTAACA
ATCGGAAGTATATAAGCATCAGTAAAGAGAAAAATATATAGAATTTGCCAGAAAACAAAACAAAG
GTTTCTATGCAATTTCTAGAAAAAAAAGTGTAATAGCAGAAGTAATGGGTTTTCCAAGAAGAACC
CTAATGTGATCCAATTCAGCATCATGGATATTCCACCCTTACAAGGGAAGAGACTTTCTAACTTT
ACACATATATATGATTATTTTATAGTTATTTTCATCTACATATATTATATCTATAGTTATTATGA
TGATAACCTATCCATTAATATGTGAAATATAAGTTATCATAATATACTATAGTTCACATTCTTAT
ATAATACATTATATAAGTTCATTTACTTAGTTTATTTCTTTATGTTATGCATGTAGGCACATTCG
GCCAGTACTTGGGAGCTACATTGGAGCTAAATAGAGCATGCAAAAGCAAGGATACTTACATGGGA
ACGATTAGGAGAGCATAAGGAGCAAATTCGTGAAAAGTTGTTTTGAGGCCGTAAGCTCATAGCTG
GATTGAGCTGAAGATTTGAGCTACAAGATGACCTCATTTCAGCTAGGGAGTTGTACCATCATCAT
CACCACTTAGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGCGAAT
AGTTGCCAACTCAAGAGGTACCTTTTCACAAGGAGCTGCCATAATGTTCACCATGCTACAAGTCA
CCTATGGTCAGCTCACCTTTAGCTCATTCACACCATAAATATATAGAATTTGCC
Found at i:1210141 original size:13 final size:13
Alignment explanation
Indices: 1210105--1210133 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1210095 TTATTCTTTC
1210105 ATTTCATCATT-T
1 ATTTCATCATTCT
1210117 ATTTCATCATTCT
1 ATTTCATCATTCT
1210130 ATTT
1 ATTT
1210134 ATCCATTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTCATCATTCT
Found at i:1213201 original size:2 final size:2
Alignment explanation
Indices: 1213194--1213226 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1213184 ATCCTAACTA
1213194 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1213227 ACCTTTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1213565 original size:4 final size:4
Alignment explanation
Indices: 1213558--1213587 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1213548 ACAAATCAAT
1213558 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
1213588 GGATAGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:1216668 original size:12 final size:12
Alignment explanation
Indices: 1216646--1216681 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1216636 TTCATATCTC
1216646 TATACCATATATA
1 TATA-CATATATA
1216659 TATACATATATA
1 TATACATATATA
*
1216671 TATACTTATAT
1 TATACATATAT
1216682 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (12 bp):
TATACATATATA
Found at i:1219044 original size:2 final size:2
Alignment explanation
Indices: 1219037--1219062 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1219027 ATAAGTGAAT
1219037 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1219063 ATTAATATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1222694 original size:2 final size:2
Alignment explanation
Indices: 1222687--1222723 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1222677 ATCACAAAAT
1222687 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1222724 TGCAATAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1225970 original size:20 final size:20
Alignment explanation
Indices: 1225923--1225971 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
1225913 TATTTTTAGG
*
1225923 TATCGATACTACATAAACAT
1 TATCGATACTACATAAACAA
* * * *
1225943 TATGGATATTGCATGAACAA
1 TATCGATACTACATAAACAA
1225963 TATCGATAC
1 TATCGATAC
1225972 CATAAGGCAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (20 bp):
TATCGATACTACATAAACAA
Found at i:1226045 original size:35 final size:35
Alignment explanation
Indices: 1226002--1226071 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
1225992 ATTCTTCATG
* *
1226002 GGGTATCGATACCGAA-GTGGTAGCATCGGTACCAT
1 GGGTATCGATACC-AAGGTGGAAGCATCAGTACCAT
*
1226037 GGGTATCGATACCAAGGTGGAAGTATCAGTACCAT
1 GGGTATCGATACCAAGGTGGAAGCATCAGTACCAT
1226072 TCTTACAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.23
Consensus pattern (35 bp):
GGGTATCGATACCAAGGTGGAAGCATCAGTACCAT
Found at i:1227226 original size:23 final size:23
Alignment explanation
Indices: 1227171--1227226 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1227161 CAGGTAAGAG
* *
1227171 ATGAAAGTAGGTGATTGTATGAT
1 ATGAAAGTATGTGATTATATGAT
*
1227194 ATGAAAGTATGT-ATATATATGTT
1 ATGAAAGTATGTGAT-TATATGAT
1227217 ATGAAAGTAT
1 ATGAAAGTAT
1227227 ATCACTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 2 0.07
23 27 0.93
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.38
Consensus pattern (23 bp):
ATGAAAGTATGTGATTATATGAT
Found at i:1227237 original size:23 final size:22
Alignment explanation
Indices: 1227171--1227239 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
1227161 CAGGTAAGAG
*
1227171 ATGAAAGTAGGTGAT-TGTATGAT
1 ATGAAAGTA-GT-ATATGTATGTT
*
1227194 ATGAAAGTATGTATATATATGTT
1 ATGAAAGTA-GTATATGTATGTT
1227217 ATGAAAGTA-TATCACTGTATGTT
1 ATGAAAGTAGTAT-A-TGTATGTT
1227240 TCATTGGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 3 0.08
22 3 0.08
23 33 0.85
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (22 bp):
ATGAAAGTAGTATATGTATGTT
Found at i:1230610 original size:3 final size:3
Alignment explanation
Indices: 1230602--1230627 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1230592 ATGTTAGCAA
1230602 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1230628 ATAAATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1230666 original size:23 final size:23
Alignment explanation
Indices: 1230638--1230751 Score: 77
Period size: 23 Copynumber: 5.2 Consensus size: 23
1230628 ATAAATGTTA
1230638 AATAAATCAAAGAAGAAAAAAAT
1 AATAAATCAAAGAAGAAAAAAAT
*
1230661 AATAAATCAAAG--CAAAAAAAT
1 AATAAATCAAAGAAGAAAAAAAT
* *
1230682 -ATAAAT-AAATAA-ATAAAAAT
1 AATAAATCAAAGAAGAAAAAAAT
1230702 AA-AAATTCAAAG--GAAAAATATAT
1 AATAAA-TCAAAGAAGAAAAA-A-AT
* *
1230725 AA-AAATTAAA-AAGAACAAAAAA
1 AATAAATCAAAGAAGAA-AAAAAT
1230747 AATAA
1 AATAA
1230752 GAAAAGTTAG
Statistics
Matches: 72, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
19 3 0.04
20 16 0.22
21 14 0.19
22 11 0.15
23 25 0.35
24 3 0.04
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.17
Consensus pattern (23 bp):
AATAAATCAAAGAAGAAAAAAAT
Found at i:1230685 original size:20 final size:20
Alignment explanation
Indices: 1230639--1230727 Score: 81
Period size: 21 Copynumber: 4.2 Consensus size: 20
1230629 TAAATGTTAA
1230639 ATAAATCAAAGAAGAAAAAAAT
1 ATAAATCAAAG--GAAAAAAAT
*
1230661 AATAAATCAAAGCAAAAAAAT
1 -ATAAATCAAAGGAAAAAAAT
**
1230682 ATAAAT-AAATAAATAAAAAT
1 ATAAATCAAAGGAA-AAAAAT
* *
1230702 AAAAATTCAAAGGAAAAATAT
1 ATAAA-TCAAAGGAAAAAAAT
1230723 ATAAA
1 ATAAA
1230728 AATTAAAAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
19 5 0.09
20 16 0.29
21 18 0.33
22 5 0.09
23 11 0.20
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (20 bp):
ATAAATCAAAGGAAAAAAAT
Found at i:1230745 original size:39 final size:41
Alignment explanation
Indices: 1230667--1230745 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
1230657 AAATAATAAA
*
1230667 TCAAAGCAAAAAAATATAAATAAATAAATAAAAATAAAAAT
1 TCAAAGCAAAAAAATATAAATAAATAAATAAAAACAAAAAT
* * * *
1230708 TCAAAGGAAAAATATATAAA-AATTAAA-AAGAACAAAAA
1 TCAAAGCAAAAAAATATAAATAAATAAATAAAAACAAAAA
1230746 AAATAAGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 9 0.27
40 6 0.18
41 18 0.55
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (41 bp):
TCAAAGCAAAAAAATATAAATAAATAAATAAAAACAAAAAT
Found at i:1230747 original size:41 final size:41
Alignment explanation
Indices: 1230653--1230749 Score: 97
Period size: 41 Copynumber: 2.3 Consensus size: 41
1230643 ATCAAAGAAG
*
1230653 AAAAAAATAATAAATCAAAGCAAAAAAATATAAATAAATAAAT
1 AAAAAAA-AA-AATTCAAAGCAAAAAAATATAAATAAATAAAT
* * * * *
1230696 AAAAATAAAAATTCAAAGGAAAAATATATAAA-AATTAAAA
1 AAAAAAAAAAATTCAAAGCAAAAAAATATAAATAAATAAAT
1230736 AGAACAAAAAAAAT
1 A-AA-AAAAAAAAT
1230750 AAGAAAAGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
40 7 0.16
41 22 0.49
42 10 0.22
43 6 0.13
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (41 bp):
AAAAAAAAAAATTCAAAGCAAAAAAATATAAATAAATAAAT
Found at i:1230885 original size:5 final size:5
Alignment explanation
Indices: 1230875--1230913 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
1230865 AGATAATAAG
1230875 AAATA AAATAA AAATA ATAA-A AAATA AAATA AAATA AAA
1 AAATA AAAT-A AAATA A-AATA AAATA AAATA AAATA AAA
1230914 AAGGATCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 2 0.06
5 22 0.71
6 7 0.23
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:1230893 original size:21 final size:21
Alignment explanation
Indices: 1230867--1230915 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1230857 AAATAGTAAG
*
1230867 ATAATAAGAAATAAAATAAAA
1 ATAATAAAAAATAAAATAAAA
1230888 ATAATAAAAAATAAAAT-AAA
1 ATAATAAAAAATAAAATAAAA
1230908 ATAA-AAAA
1 ATAATAAAA
1230916 GGATCAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 4 0.15
20 7 0.26
21 16 0.59
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (21 bp):
ATAATAAAAAATAAAATAAAA
Found at i:1237703 original size:20 final size:19
Alignment explanation
Indices: 1237690--1237743 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 19
1237680 ATACTGACAT
1237690 GGAGGTATCGATACCAAGA
1 GGAGGTATCGATACCAAGA
1237709 GGGAGGTATCGATACCAAGA
1 -GGAGGTATCGATACCAAGA
1237729 GGAAGGTATCGATAC
1 GG-AGGTATCGATAC
1237744 TGTAATGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.35, C:0.15, G:0.33, T:0.17
Consensus pattern (19 bp):
GGAGGTATCGATACCAAGA
Found at i:1238723 original size:53 final size:53
Alignment explanation
Indices: 1238660--1238764 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
1238650 GTACTTTCGA
*
1238660 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTTTAAATTACCATTTTGG
1 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTAAATTACCATTTTGG
* *
1238713 CACTATGTGTGCATCCATGGTATTCGTAATGAGTTTGTGAATTACCATTTTG
1 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTAAATTACCATTTTG
1238765 TTACCTTAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (53 bp):
CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTAAATTACCATTTTGG
Found at i:1240154 original size:18 final size:18
Alignment explanation
Indices: 1240123--1240157 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1240113 TCATTCAGGA
*
1240123 TGATGACGAGGATGATGT
1 TGATGACGACGATGATGT
*
1240141 TGATGGCGACGATGATG
1 TGATGACGACGATGATG
1240158 CATCGGAGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.40, T:0.26
Consensus pattern (18 bp):
TGATGACGACGATGATGT
Found at i:1243940 original size:22 final size:23
Alignment explanation
Indices: 1243897--1243940 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
1243887 GTGATTCATT
**
1243897 TAAAATTATAATTACATTTTAAC
1 TAAAATTATAATTACACATTAAC
*
1243920 TAAAA-TATAATTATACATTAA
1 TAAAATTATAATTACACATTAA
1243941 ATACCTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAAATTATAATTACACATTAAC
Found at i:1245140 original size:49 final size:49
Alignment explanation
Indices: 1245068--1245165 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
1245058 AAAGCCATAG
1245068 CCTCTAATAGTTAGGAAACAATAGAGATAATGAGCAAATACTTGATTTA
1 CCTCTAATAGTTAGGAAACAATAGAGATAATGAGCAAATACTTGATTTA
1245117 CCTCTAATAGTTAGGAAACAATAGAGATAATGAGCAAATACTTGATTTA
1 CCTCTAATAGTTAGGAAACAATAGAGATAATGAGCAAATACTTGATTTA
1245166 TTTTATGTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (49 bp):
CCTCTAATAGTTAGGAAACAATAGAGATAATGAGCAAATACTTGATTTA
Found at i:1245689 original size:56 final size:56
Alignment explanation
Indices: 1245617--1245786 Score: 313
Period size: 56 Copynumber: 3.0 Consensus size: 56
1245607 ATACATACAA
1245617 GCAAGATGTGTCACAACTTATTTTTCCTGCAGAGTAATTACCACATATCATTCTAG
1 GCAAGATGTGTCACAACTTATTTTTCCTGCAGAGTAATTACCACATATCATTCTAG
1245673 GCAAGATGTGTCACAACTTATTTTTCCTGCAGAGTAATTACCACATATCATTCTAG
1 GCAAGATGTGTCACAACTTATTTTTCCTGCAGAGTAATTACCACATATCATTCTAG
* * *
1245729 GCAAGATGTGTCACAACTTATTTTTCTTACAGAGTAATTACCACATATCATTGTAG
1 GCAAGATGTGTCACAACTTATTTTTCCTGCAGAGTAATTACCACATATCATTCTAG
1245785 GC
1 GC
1245787 CAATTTGATA
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 111 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34
Consensus pattern (56 bp):
GCAAGATGTGTCACAACTTATTTTTCCTGCAGAGTAATTACCACATATCATTCTAG
Found at i:1251499 original size:18 final size:18
Alignment explanation
Indices: 1251473--1251515 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1251463 GTCTAACTAT
*
1251473 AAATAAGTAACTCCCTAA
1 AAATTAGTAACTCCCTAA
1251491 AAATTAGTAACTCCCTAA
1 AAATTAGTAACTCCCTAA
*
1251509 GAATTAG
1 AAATTAG
1251516 AGACTAAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.26
Consensus pattern (18 bp):
AAATTAGTAACTCCCTAA
Found at i:1253150 original size:90 final size:90
Alignment explanation
Indices: 1252995--1253171 Score: 286
Period size: 90 Copynumber: 2.0 Consensus size: 90
1252985 TTAACACACC
* *
1252995 CTTTTATAGTCAAGTTACCCTAATCATATTAGGGTTTCTATTATTTCAAATTAATTAAATCTATA
1 CTTTTATAGTCAAGTTACCCTAATCATATTAGGATTTCTATTATTTCAAATTAATTAAATATATA
* *
1253060 TTTAATTAATTGGAATTTAATAATT
66 TTTAATTAATTGAAATTAAATAATT
1253085 CTTTTATA-TCCAAGTTACCCTAATCATATTATGGATTT-TATTATTTCAAATTAATTAAATATA
1 CTTTTATAGT-CAAGTTACCCTAATCATATTA-GGATTTCTATTATTTCAAATTAATTAAATATA
1253148 TATTTAATTAATTGAAATTAAATA
64 TATTTAATTAATTGAAATTAAATA
1253172 TTCAGGATTA
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
89 1 0.01
90 75 0.93
91 5 0.06
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (90 bp):
CTTTTATAGTCAAGTTACCCTAATCATATTAGGATTTCTATTATTTCAAATTAATTAAATATATA
TTTAATTAATTGAAATTAAATAATT
Found at i:1253158 original size:20 final size:21
Alignment explanation
Indices: 1253133--1253202 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
1253123 TATTATTTCA
1253133 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* * *
1253153 AATTAATTGAAATTAAATATTC
1 AATTAATT-AAAATATATATTT
*
1253175 AGGATT-ATTAAAATATATACTT
1 A--ATTAATTAAAATATATATTT
1253197 AATTAA
1 AATTAA
1253203 ATATAGATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 11 0.29
21 1 0.03
22 20 0.53
23 3 0.08
24 3 0.08
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:1262804 original size:15 final size:15
Alignment explanation
Indices: 1262769--1262805 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
1262759 TTAACTGTAT
*
1262769 TCATTTATGTTTTTA
1 TCATTTATGTTTTCA
1262784 TACATTTATGTTTTCA
1 T-CATTTATGTTTTCA
1262800 TCATTT
1 TCATTT
1262806 GAGTTAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (15 bp):
TCATTTATGTTTTCA
Found at i:1264826 original size:13 final size:13
Alignment explanation
Indices: 1264777--1264824 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
1264767 TGCGTCATAA
*
1264777 ATTTATTACACGC
1 ATTTATGACACGC
1264790 ATTTATGACACGC
1 ATTTATGACACGC
*
1264803 ATTTATGACGCGC
1 ATTTATGACACGC
1264816 ATTTATGAC
1 ATTTATGAC
1264825 GCTCATTGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:1264831 original size:13 final size:13
Alignment explanation
Indices: 1264777--1264831 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
1264767 TGCGTCATAA
* *
1264777 ATTTATTACACGC
1 ATTTATGACGCGC
*
1264790 ATTTATGACACGC
1 ATTTATGACGCGC
1264803 ATTTATGACGCGC
1 ATTTATGACGCGC
*
1264816 ATTTATGACGCTC
1 ATTTATGACGCGC
1264829 ATT
1 ATT
1264832 GCGCGTCATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:1264939 original size:85 final size:85
Alignment explanation
Indices: 1264803--1264968 Score: 203
Period size: 85 Copynumber: 2.0 Consensus size: 85
1264793 TATGACACGC
* * * * *
1264803 ATTTATGACGCGCATTTATGACGCTCATTGCGCGTCATTGAAGCCCCCGTCA-TAAATGAAGATG
1 ATTTATGACACGCATGTATGACGCTCATTGCGCGTCATTGAAGCACACGTCATTAAA-AAAGATG
1264867 ACACACATT-TGTGTGTCATAA
65 ACACACATTCT-TGTGTCATAA
* * * *
1264888 ATTTATGACACGCATGTATGAC-TTACATTGCGTGTCATTGAAGTATACGTCATTAAAAAAGATG
1 ATTTATGACACGCATGTATGACGCT-CATTGCGCGTCATTGAAGCACACGTCATTAAAAAAGATG
1264952 ACACACATTCTTGTGTC
65 ACACACATTCTTGTGTC
1264969 GTGAATGTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 63 0.91
86 5 0.07
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACGCTCATTGCGCGTCATTGAAGCACACGTCATTAAAAAAGATGA
CACACATTCTTGTGTCATAA
Found at i:1264995 original size:2 final size:2
Alignment explanation
Indices: 1264988--1265020 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1264978 TTTCGTAAAT
1264988 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1265021 TGTAGATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1269694 original size:59 final size:59
Alignment explanation
Indices: 1269623--1269969 Score: 536
Period size: 59 Copynumber: 5.9 Consensus size: 59
1269613 TTCCCATAAA
* * *
1269623 GAAATTCATACACCTAATATGAATTTCTTAACATGTTT-GCACACAAAGTGCCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACAT-TTTAGCACACATAGTGCCCAATACG
*
1269682 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTG-CTAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACG
* * * * * *
1269740 AAAATTCGTACACTTAATATGAGTTTCTTAATATTTTAGCACACATAGTGCCCAATATG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACG
* *
1269799 GAAATTCATATACTTAGTATGAAATTCTTAACATTTTAGCACACATAGTGCCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACG
*
1269858 GAAATTCATACACTCAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACG
*
1269917 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGTGCC
1 GAAATTCATACACTTAGTATGAATTTCTTAACA-TTTTAGCACACATAGTGCC
1269970 ATTCAGTAAT
Statistics
Matches: 261, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
58 55 0.21
59 188 0.72
60 18 0.07
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (59 bp):
GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACG
Found at i:1269761 original size:117 final size:117
Alignment explanation
Indices: 1269624--1269970 Score: 543
Period size: 117 Copynumber: 2.9 Consensus size: 117
1269614 TCCCATAAAG
* *
1269624 AAATTCATACACCTAATATGAATTTCTTAACATGTTT-GCACACAAAGTGCCCAATACGGAAATT
1 AAATTCATACACTTAATATGAATTTCTTAACAT-TTTAGCACACATAGTGCCCAATACGGAAATT
*
1269688 CATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCTAATACGA
65 CATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCAATACGA
* * * *
1269741 AAATTCGTACACTTAATATGAGTTTCTTAATATTTTAGCACACATAGTGCCCAATATGGAAATTC
1 AAATTCATACACTTAATATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGGAAATTC
* * *
1269806 ATATACTTAGTATGAAATTCTTAACATTTTAGCACACATAGTGCCCAATACGG
66 ATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTG-CCAATACGA
* *
1269859 AAATTCATACACTCAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGGAAATTC
1 AAATTCATACACTTAATATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGGAAATTC
*
1269924 ATACACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGTGCCA
66 ATACACTTAGTATGAATTTCTTAACA-TTTTAGCACACATAGTGCCA
1269971 TTCAGTAATC
Statistics
Matches: 208, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
116 3 0.01
117 96 0.46
118 93 0.45
119 16 0.08
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (117 bp):
AAATTCATACACTTAATATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGGAAATTC
ATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCAATACGA
Found at i:1271965 original size:29 final size:28
Alignment explanation
Indices: 1271921--1272054 Score: 169
Period size: 29 Copynumber: 4.6 Consensus size: 28
1271911 GGAAAATTAT
** * *
1271921 TTTATAAATTTTAATAAAGGACAAAATT
1 TTTATAAATTACAATAAAGTACAAAATA
* *
1271949 TGTTATAAATTACAATAACGTACACAACTA
1 T-TTATAAATTACAATAAAGTACA-AAATA
1271979 TTTATAAATTACAATAAAGTACAAAATAA
1 TTTATAAATTACAATAAAGTACAAAAT-A
*
1272008 TTTATAAATTACAATAAAATACAAAACTA
1 TTTATAAATTACAATAAAGTACAAAA-TA
1272037 TTTATAAATTACAATAAA
1 TTTATAAATTACAATAAA
1272055 AGATAAAACC
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
28 4 0.04
29 84 0.90
30 5 0.05
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.34
Consensus pattern (28 bp):
TTTATAAATTACAATAAAGTACAAAATA
Found at i:1271984 original size:58 final size:58
Alignment explanation
Indices: 1271921--1272054 Score: 189
Period size: 58 Copynumber: 2.3 Consensus size: 58
1271911 GGAAAATTAT
** * ** *
1271921 TTTATAAATTTTAATAAAGGACAAAAT-TTGTTATAAATTACAATAACGTACACAACTA
1 TTTATAAATTACAATAAAGGACAAAATAAT-TTATAAATTACAATAAAATACAAAACTA
*
1271979 TTTATAAATTACAATAAAGTACAAAATAATTTATAAATTACAATAAAATACAAAACTA
1 TTTATAAATTACAATAAAGGACAAAATAATTTATAAATTACAATAAAATACAAAACTA
1272037 TTTATAAATTACAATAAA
1 TTTATAAATTACAATAAA
1272055 AGATAAAACC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 67 0.99
59 1 0.01
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.34
Consensus pattern (58 bp):
TTTATAAATTACAATAAAGGACAAAATAATTTATAAATTACAATAAAATACAAAACTA
Found at i:1272055 original size:29 final size:29
Alignment explanation
Indices: 1271951--1272084 Score: 164
Period size: 29 Copynumber: 4.6 Consensus size: 29
1271941 ACAAAATTTG
** *
1271951 TTATAAATTACAATAACGTACACAACTAT
1 TTATAAATTACAATAAAATACAAAACTAT
*
1271980 TTATAAATTACAATAAAGTACAAAA-TAAT
1 TTATAAATTACAATAAAATACAAAACT-AT
1272009 TTATAAATTACAATAAAATACAAAACTAT
1 TTATAAATTACAATAAAATACAAAACTAT
* *
1272038 TTATAAATTACAATAAAAGATAAAACCT-T
1 TTATAAATTACAATAAAATACAAAA-CTAT
* *
1272067 TTATAAATCATAATAAAA
1 TTATAAATTACAATAAAA
1272085 GGAGACAATT
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
28 1 0.01
29 91 0.96
30 3 0.03
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (29 bp):
TTATAAATTACAATAAAATACAAAACTAT
Found at i:1272070 original size:87 final size:84
Alignment explanation
Indices: 1271840--1272083 Score: 206
Period size: 87 Copynumber: 2.8 Consensus size: 84
1271830 AAAAATCATC
* ** * * * *
1271840 AAATTACAATAAAAGACAAAATGTTT-TAAAATTTGTAATAAAAGTTTAAACTTTTTAGAATTTA
1 AAATTACAATAAAAGACAAAATATTTAT-AAA-TTACAATAAAAG-TAAAACCTTTTATAAATTA
* * *
1271904 CAGTAAAGGAAAATTATTTTAT
63 CAATAAAGGAAAAATAATTTAT
** * * *
1271926 AAATTTTAATAAAGGACAAAATTTGTTATAAATTACAAT-AACGTACACAA-CTATTTATAAATT
1 AAATTACAATAAAAGACAAAATAT-TTATAAATTACAATAAAAGTA-A-AACCT-TTTATAAATT
*
1271989 ACAATAAAGTACAAAATAATTTAT
62 ACAATAAAGGA-AAAATAATTTAT
* * *
1272013 AAATTACAATAAAATACAAAACTATTTATAAATTACAATAAAAGATAAAACCTTTTATAAATCAT
1 AAATTACAATAAAAGACAAAA-TATTTATAAATTACAATAAAAG-TAAAACCTTTTATAAATTAC
1272078 AATAAA
64 AATAAA
1272084 AGGAGACAAT
Statistics
Matches: 125, Mismatches: 23, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
84 1 0.01
85 5 0.04
86 44 0.35
87 64 0.51
88 9 0.07
89 2 0.02
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.34
Consensus pattern (84 bp):
AAATTACAATAAAAGACAAAATATTTATAAATTACAATAAAAGTAAAACCTTTTATAAATTACAA
TAAAGGAAAAATAATTTAT
Found at i:1272085 original size:29 final size:29
Alignment explanation
Indices: 1271921--1272085 Score: 160
Period size: 29 Copynumber: 5.7 Consensus size: 29
1271911 GGAAAATTAT
** * *
1271921 TTTATAAATTTTAATAAAGGACAAAA-TT
1 TTTATAAATTACAATAAAAGACAAAACTA
* *
1271949 TGTTATAAATTACAAT-AACGTACACAACTA
1 T-TTATAAATTACAATAAAAG-ACAAAACTA
1271979 TTTATAAATTACAAT-AAAGTACAAAA-TAA
1 TTTATAAATTACAATAAAAG-ACAAAACT-A
*
1272008 TTTATAAATTACAATAAAATACAAAACTA
1 TTTATAAATTACAATAAAAGACAAAACTA
*
1272037 TTTATAAATTACAATAAAAGATAAAACCT-
1 TTTATAAATTACAATAAAAGACAAAA-CTA
* *
1272066 TTTATAAATCATAATAAAAG
1 TTTATAAATTACAATAAAAG
1272086 GAGACAATTT
Statistics
Matches: 118, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
28 5 0.04
29 105 0.89
30 8 0.07
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (29 bp):
TTTATAAATTACAATAAAAGACAAAACTA
Found at i:1282467 original size:52 final size:50
Alignment explanation
Indices: 1282340--1282566 Score: 260
Period size: 50 Copynumber: 4.7 Consensus size: 50
1282330 TATAAAATCC
* * * *
1282340 CTTACCATTT--ATCCCATAAGCTCGTAAGC-T-TA-TTTTACTAAAATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTCCAATATA
* *
1282385 CTTACCGTTTAAAATTCCATAAGCTCGTAAGCTTATATTTTTTTTCCATTATA
1 CTTACCATTT-AAATTCCATAAGCTCGTAAGCTTATA--TTTTTTCCAATATA
1282438 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTCCAATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTCCAATATA
* *
1282488 CTTACCATTTAAATTCCATAAGCTCGTAAGC-T-TA-TTTTACCCATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTCCAATATA
* *
1282535 CTTGCCA-TT--ATTCCAAAAGCTCGTAAGCTTAT
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTAT
1282567 TTGTATGCTT
Statistics
Matches: 160, Mismatches: 12, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
44 18 0.11
45 10 0.06
46 3 0.02
47 17 0.11
48 20 0.12
49 2 0.01
50 46 0.29
52 26 0.16
53 18 0.11
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (50 bp):
CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTCCAATATA
Found at i:1282512 original size:102 final size:98
Alignment explanation
Indices: 1282340--1282568 Score: 274
Period size: 102 Copynumber: 2.4 Consensus size: 98
1282330 TATAAAATCC
* *
1282340 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACTAAAATACTTACCGTTTAAAATTCCAT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAAATTCCAT
1282405 AAGCTCGTAAGCTTATATTTTTTTTCCATTATA
66 AAGCTCGTAAGCTTATATTTTTTTTCCATTATA
* * *
1282438 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTCCAATATACTTACCATTT-AAAT
1 CTTACCATTT--ATCCCATAAGCTCGTAAGC-T-TA-TTTTACCAAAATACTTACCATTTAAAAT
**
1282502 TCCATAAGCTCGTAAGC-T-TA--TTTTACCCA-TATA
61 TCCATAAGCTCGTAAGCTTATATTTTTTTTCCATTATA
* * *
1282535 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
1282569 GTATGCTTAC
Statistics
Matches: 117, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
91 3 0.03
92 2 0.02
93 1 0.01
94 18 0.15
96 2 0.02
97 10 0.09
98 17 0.15
100 20 0.17
101 2 0.02
102 23 0.20
103 19 0.16
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (98 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAAATTCCAT
AAGCTCGTAAGCTTATATTTTTTTTCCATTATA
Found at i:1282717 original size:40 final size:40
Alignment explanation
Indices: 1282673--1282794 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
1282663 ACCGTAGTGC
1282673 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1282713 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1282753 TACACATAAGGTCTTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1282793 TA
1 TA
1282795 TAAACCTGCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1286454 original size:6 final size:6
Alignment explanation
Indices: 1286438--1286564 Score: 75
Period size: 6 Copynumber: 21.3 Consensus size: 6
1286428 TATCTCATTT
* * * *
1286438 TTTTCTC TTTTTC -TTTTC TTTCTC GTTTTC ATTTT- TTTCTC TTTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * * *
1286485 -TTTTC TTTCTC GTTTTCATT TTTTTC TTCTTC GTTTTC ATTTTC TTTTTC
1 TTTTTC TTTTTC -TTTT--TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * *
1286535 TATTT- TTTTTC TTCTTC TGTTT- TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
1286565 CTTATAATAT
Statistics
Matches: 90, Mismatches: 22, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
5 21 0.23
6 57 0.63
7 7 0.08
8 4 0.04
9 1 0.01
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:1286459 original size:17 final size:16
Alignment explanation
Indices: 1286435--1286564 Score: 111
Period size: 17 Copynumber: 7.8 Consensus size: 16
1286425 TCATATCTCA
1286435 TTTTTTTCTCTTTTTC
1 TTTTTTTCTCTTTTTC
*
1286451 TTTTCTTTCTCGTTTTC
1 TTTT-TTTCTCTTTTTC
1286468 ATTTTTTTCTCTTTTTC
1 -TTTTTTTCTCTTTTTC
*
1286485 TTTTCTTTCTCGTTTTC
1 TTTT-TTTCTCTTTTTC
* *
1286502 ATTTTTT-TCTTCTTC
1 TTTTTTTCTCTTTTTC
1286517 GTTTTCATTT-TCTTTTTC
1 -TTTT--TTTCTCTTTTTC
* *
1286535 TATTTTTTTTCTTCTTC
1 T-TTTTTTCTCTTTTTC
*
1286552 TGTTTTTTTTCTT
1 T-TTTTTTCTCTT
1286565 CTTATAATAT
Statistics
Matches: 96, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
15 6 0.06
16 17 0.18
17 56 0.58
18 17 0.18
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTTTTCTCTTTTTC
Found at i:1286474 original size:51 final size:53
Alignment explanation
Indices: 1286418--1286547 Score: 124
Period size: 51 Copynumber: 2.4 Consensus size: 53
1286408 GTGAAATATT
*
1286418 TTTTTTTTCATATCTCATTTT-TTTCTCTTTTTC-TTTTCT-TTC-TCGTTTTCA
1 TTTTTTTTC-TATCTC-TTTTCTTTCTCGTTTTCATTTTCTCTTCTTCGTTTTCA
* * *
1286469 TTTTTTTCTCTTTTTCTTTTCTTTCTCGTTTTCATTTTTTTCTTCTTCGTTTTCA
1 TTTTTTT-TCTATCTCTTTTCTTTCTCGTTTTCA-TTTTCTCTTCTTCGTTTTCA
* *
1286524 TTTTCTTTTTCTATTTTTTTTCTT
1 -TTT-TTTTTCTATCTCTTTTCTT
1286548 CTTCTGTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
50 4 0.06
51 22 0.34
52 2 0.03
53 5 0.08
54 3 0.05
55 9 0.14
56 16 0.25
57 4 0.06
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.74
Consensus pattern (53 bp):
TTTTTTTTCTATCTCTTTTCTTTCTCGTTTTCATTTTCTCTTCTTCGTTTTCA
Found at i:1286542 original size:21 final size:21
Alignment explanation
Indices: 1286485--1286535 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
1286475 TCTCTTTTTC
1286485 TTTTCTT-TCTCGTTTTCATTT
1 TTTTCTTCT-TCGTTTTCATTT
1286506 TTTTCTTCTTCGTTTTCATTT
1 TTTTCTTCTTCGTTTTCATTT
1286527 TCTTT-TTCT
1 T-TTTCTTCT
1286536 ATTTTTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.04, C:0.20, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTTCTTCTTCGTTTTCATTT
Found at i:1286564 original size:34 final size:34
Alignment explanation
Indices: 1286432--1286552 Score: 160
Period size: 34 Copynumber: 3.6 Consensus size: 34
1286422 TTTTCATATC
*
1286432 TCATTTTTTTCTCTTTTTCTTTTCTTTCTCGTTT
1 TCATTTTTTTCTCTTCTTCTTTTCTTTCTCGTTT
*
1286466 TCATTTTTTTCTCTTTTTCTTTTCTTTCTCGTTT
1 TCATTTTTTTCTCTTCTTCTTTTCTTTCTCGTTT
*
1286500 TCA-TTTTTT-TCTTCTTCGTTTTCATTT-TCTTTT
1 TCATTTTTTTCTCTTCTTC-TTTTC-TTTCTCGTTT
1286533 TCTATTTTTTT-TCTTCTTCT
1 TC-ATTTTTTTCTCTTCTTCT
1286553 GTTTTTTTTC
Statistics
Matches: 81, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
32 7 0.09
33 18 0.22
34 42 0.52
35 14 0.17
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (34 bp):
TCATTTTTTTCTCTTCTTCTTTTCTTTCTCGTTT
Found at i:1286567 original size:55 final size:54
Alignment explanation
Indices: 1286435--1286567 Score: 136
Period size: 55 Copynumber: 2.5 Consensus size: 54
1286425 TCATATCTCA
* *
1286435 TTTT-TTTCTCTTTTTCTTTTC-T-TTC-TCGTTTTCATTTTTTTCTCTTTTTC
1 TTTTCTTTCTCGTTTTATTTTCTTCTTCTTCGTTTTCATTTTTTTCTCTTTTTC
* *
1286485 TTTTCTTTCTCGTTTTCATTTTTTTCTTCTTCGTTTTCATTTTCTTTTTCTATTTT-
1 TTTTCTTTCTCGTTTT-ATTTTCTTCTTCTTCGTTTTCATTTT-TTTCTCT-TTTTC
1286541 TTTTC-TTCTTCTGTTTT-TTTTCTTCTT
1 TTTTCTTTC-TC-GTTTTATTTTCTTCTT
1286568 ATAATATATA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
50 4 0.06
51 10 0.14
52 4 0.06
53 1 0.01
54 3 0.04
55 25 0.36
56 13 0.19
57 9 0.13
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (54 bp):
TTTTCTTTCTCGTTTTATTTTCTTCTTCTTCGTTTTCATTTTTTTCTCTTTTTC
Found at i:1289540 original size:50 final size:50
Alignment explanation
Indices: 1289422--1289607 Score: 240
Period size: 50 Copynumber: 3.8 Consensus size: 50
1289412 TTTTACTAAA
*
1289422 ATACTTACCGTTTAAAATTCCATAAGCTCGTAAGCTTATATTTTTTTTCCCAAT
1 ATACTTACCATTT-AAATTCCATAAGCTCGTAAGCTTATA--TTTTTT-CCAAT
*
1289476 ATACTTACCATTTAAATTTCATAAGCTCGTAAGCTTATATTTTTTCCAAT
1 ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTCCAAT
* *
1289526 ATACTTACCATTTAAATTCCATAAGCTCGTAAGC-T-TA-TTTTACCCAT
1 ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTCCAAT
* *
1289573 ATACTTGCCA-TT--ATTCCAAAAGCTCGTAAGCTTAT
1 ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTAT
1289608 TTGTATGCAT
Statistics
Matches: 123, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
44 18 0.15
45 1 0.01
46 3 0.02
47 17 0.14
48 2 0.02
49 1 0.01
50 38 0.31
51 6 0.05
53 25 0.20
54 12 0.10
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (50 bp):
ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTCCAAT
Found at i:1289598 original size:44 final size:46
Alignment explanation
Indices: 1289380--1289609 Score: 187
Period size: 50 Copynumber: 4.8 Consensus size: 46
1289370 TATAAAATCC
* * * * * *
1289380 CTTACCATTT-ATCCCATAAGTTCATAAGCTTATTTTACTAAAATA
1 CTTACCATTTAATTCCAAAAGCTCGTAAGCTTATTTTACCAATATA
* * *
1289425 CTTACCGTTTAAAATTCCATAAGCTCGTAAGCTTATATTTTTTTTCCCAATATA
1 CTTACCATTT--AATTCCAAAAGCTCGTAAGC-T-TA----TTTTACCAATATA
* * *
1289479 CTTACCATTTAAATTTCATAAGCTCGTAAGCTTATATTTTTTCCAATATA
1 CTTACCATTT-AATTCCAAAAGCTCGTAAGC-T-TA-TTTTACCAATATA
* *
1289529 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT-AATTCCAAAAGCTCGTAAGCTTATTTTACCAATATA
*
1289576 CTTGCCA-TT-ATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATTCCAAAAGCTCGTAAGCTTATTT
1289610 GTATGCATAC
Statistics
Matches: 161, Mismatches: 15, Indels: 19
0.83 0.08 0.10
Matches are distributed among these distances:
44 24 0.15
45 9 0.06
46 2 0.01
47 17 0.11
48 18 0.11
49 2 0.01
50 45 0.28
53 25 0.16
54 19 0.12
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (46 bp):
CTTACCATTTAATTCCAAAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:1289785 original size:39 final size:40
Alignment explanation
Indices: 1289714--1289834 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
1289704 ACCGTAGTGC
1289714 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1289754 TACACATAAGGTCGTG-CCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1289793 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1289833 TA
1 TA
1289835 TAAACCTGCA
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
39 39 0.49
40 41 0.51
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1293964 original size:13 final size:13
Alignment explanation
Indices: 1293946--1293970 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1293936 AATGAATTTT
1293946 AAGATTTTCTAAA
1 AAGATTTTCTAAA
1293959 AAGATTTTCTAA
1 AAGATTTTCTAA
1293971 GTATATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Found at i:1297124 original size:34 final size:33
Alignment explanation
Indices: 1297055--1297125 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
1297045 CATTTACAAC
* *
1297055 TCCCTAGTTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACACGGGATAAACTAGAACATT
* * * *
1297088 TCCCTAGCTTTTACACGGGCTTAGCTAGAATATT
1 TCCCTAG-TTTTACACGGGATAAACTAGAACATT
1297122 TCCC
1 TCCC
1297126 CTTTACAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
33 7 0.23
34 24 0.77
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGATAAACTAGAACATT
Found at i:1297661 original size:36 final size:37
Alignment explanation
Indices: 1297592--1297661 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
1297582 CAATCATAGA
* *
1297592 TGTATGGATACACCTGCTAGGGGTATCGGTACACCAG
1 TGTATGGATACACCTGATAGGGGTATCGATACACCAG
* *
1297629 TGTATGGATACA-CTTATATGGGTATCGATACAC
1 TGTATGGATACACCTGATAGGGGTATCGATACAC
1297662 ATTTGCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 17 0.59
37 12 0.41
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (37 bp):
TGTATGGATACACCTGATAGGGGTATCGATACACCAG
Found at i:1302166 original size:59 final size:59
Alignment explanation
Indices: 1302096--1302566 Score: 671
Period size: 59 Copynumber: 8.0 Consensus size: 59
1302086 TATATTTCCC
* * * * *
1302096 ATACGGAAATTCATACACCTAGTAGGAATTTCTTAACATGTTT-GCAAACAAAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACAT-TTTAGCACACATAGTGCCCA
* * * *
1302155 ATACGAAAATTCATGCACTTAATATGAATTTCTTAACATTTTTAGCACACTTACTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACA-TTTTAGCACACATAGTGCCCA
* *
1302215 ATAC-AGAAATTCATACACTTAGTATGAATTTCTTAACATTTTATCACACATAGTTCCCA
1 ATACGA-AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* *
1302274 ATACGAAAATTCATATATTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* *
1302333 ATACGGAAATTCATATACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* * * * *
1302392 ATACGAAAATTCATACCCTTAGTATGAATTTCTTTACATTTTTGCATATATAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
1302451 ATAC-AGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
1 ATACGA-AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* *
1302510 ATACTG-AAATCCATACACTTAGTATGAATTTCTTAACATTTTAGCACACTTAGTGCC
1 ATAC-GAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCC
1302567 ATTTGGTAAT
Statistics
Matches: 370, Mismatches: 35, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
58 1 0.00
59 321 0.87
60 48 0.13
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (59 bp):
ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
Found at i:1302559 original size:31 final size:31
Alignment explanation
Indices: 1302465--1302563 Score: 80
Period size: 31 Copynumber: 3.3 Consensus size: 31
1302455 AGAAATTCAT
1302465 ACACTTAGTATGAATTTCTTAACATTTTAGC
1 ACACTTAGTATGAATTTCTTAACATTTTAGC
* *** * * ** *
1302496 ACACATAGTGCCCAA-TACTGAA-A-TCCA-T
1 ACACTTAGT-ATGAATTTCTTAACATTTTAGC
1302524 ACACTTAGTATGAATTTCTTAACATTTTAGC
1 ACACTTAGTATGAATTTCTTAACATTTTAGC
1302555 ACACTTAGT
1 ACACTTAGT
1302564 GCCATTTGGT
Statistics
Matches: 45, Mismatches: 18, Indels: 10
0.62 0.25 0.14
Matches are distributed among these distances:
27 2 0.04
28 13 0.29
29 3 0.07
30 3 0.07
31 22 0.49
32 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.35
Consensus pattern (31 bp):
ACACTTAGTATGAATTTCTTAACATTTTAGC
Found at i:1306400 original size:3 final size:3
Alignment explanation
Indices: 1306392--1306551 Score: 313
Period size: 3 Copynumber: 53.7 Consensus size: 3
1306382 GTGTGTGTAT
1306392 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1306440 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1306487 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1306535 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
1306552 GATTACATAT
Statistics
Matches: 156, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.01
3 154 0.99
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1307784 original size:2 final size:2
Alignment explanation
Indices: 1307779--1307807 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1307769 TGTGAGTAAT
1307779 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1307808 GTAGAAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1314660 original size:81 final size:81
Alignment explanation
Indices: 1314540--1314702 Score: 272
Period size: 81 Copynumber: 2.0 Consensus size: 81
1314530 AGTCTCTTGC
* * *
1314540 ACAACTGGATCGGTAGCTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCATGT
1 ACAACTGGATCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCAGCCATTTCATGT
1314605 GCGAACCATTCTCTAT
66 GCGAACCATTCTCTAT
* * *
1314621 ACAACTGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTTGCTCAGCCATTTCATGT
1 ACAACTGGATCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCAGCCATTTCATGT
1314686 GCGAACCATTCTCTAT
66 GCGAACCATTCTCTAT
1314702 A
1 A
1314703 ACTCGCTGGC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.31
Consensus pattern (81 bp):
ACAACTGGATCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCAGCCATTTCATGT
GCGAACCATTCTCTAT
Found at i:1314912 original size:27 final size:27
Alignment explanation
Indices: 1314821--1314913 Score: 91
Period size: 27 Copynumber: 3.4 Consensus size: 27
1314811 AACGATTGAG
*
1314821 CACCTCTGTGCTTCAATCGAGAGCTGA
1 CACCTCTGTGCTTCAATCGAGAACTGA
* ** * *
1314848 CACCTCTGTG-TAGCCAAAAGTG-ATTGA
1 CACCTCTGTGCT--TCAATCGAGAACTGA
1314875 GCACCTCTGTGCTTCAATCGAGAACTGA
1 -CACCTCTGTGCTTCAATCGAGAACTGA
1314903 CACCTCTGTGC
1 CACCTCTGTGC
1314914 AGTTAAAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
26 1 0.02
27 29 0.58
28 19 0.38
29 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26
Consensus pattern (27 bp):
CACCTCTGTGCTTCAATCGAGAACTGA
Found at i:1315017 original size:54 final size:55
Alignment explanation
Indices: 1314814--1315115 Score: 317
Period size: 54 Copynumber: 5.5 Consensus size: 55
1314804 TAGAATTAAC
* *
1314814 GATTGAGCACCTCTGTGCTTCAATCGA-GAGCTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGGAGCTGACACCTCTGTGCAGCTAAAA-T
* *
1314869 GATTGAGCACCTCTGTGCTTCAATCGA-GAACTGACACCTCTGTGCAGTTAAAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGGAGCTGACACCTCTGTGCAGCT------AAAAT
* * ** * *
1314929 GACTGAGCACCTCTGTGATTCAGCCG-GGAGCTGACACCTCTGTGTAGCTAAGAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGGAGCTGACACCTCTGTGCAGCTAAAAT
*
1314983 GATTGAGCACCTCTGTGCTTCAATCGAGGA-CTGACACCTCTGTGCAGCCAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGGAGCTGACACCTCTGTGCAGCTAAAAT
* * ** * * * * *
1315037 GACTGAGCACCTCTGTGCTTCAATCTAAAATCTGGCACCTCTGTGCA-TTAGAAG
1 GATTGAGCACCTCTGTGCTTCAATCGAGGAGCTGACACCTCTGTGCAGCTAAAAT
*
1315091 GATTGAGCACCTCTGTGCTACAATC
1 GATTGAGCACCTCTGTGCTTCAATC
1315116 TAAAATCAAG
Statistics
Matches: 208, Mismatches: 30, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
54 99 0.48
55 63 0.30
60 42 0.20
61 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (55 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGGAGCTGACACCTCTGTGCAGCTAAAAT
Found at i:1315018 original size:114 final size:115
Alignment explanation
Indices: 1314817--1315029 Score: 356
Period size: 114 Copynumber: 1.9 Consensus size: 115
1314807 AATTAACGAT
* *
1314817 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGATTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1314882 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAATGAC
66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAATGAC
* * * *
1314932 TGAGCACCTCTGTGATTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGA-TGATTGAGCACCTC
1 TGAGCACCTCTGTGATTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
*
1314996 TGTGCTTCAATCGAGGACTGACACCTCTGTGCAG
66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAG
1315030 CCAAAATGAC
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
114 47 0.52
115 44 0.48
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.25
Consensus pattern (115 bp):
TGAGCACCTCTGTGATTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAATGAC
Found at i:1315020 original size:27 final size:28
Alignment explanation
Indices: 1314986--1315115 Score: 96
Period size: 27 Copynumber: 4.8 Consensus size: 28
1314976 CTAAGATGAT
*
1314986 TGAGCACCTCTGTGCTTCAATCGAGGAC
1 TGAGCACCTCTGTGCTTCAATCAAGGAC
** *
1315014 TGA-CACCTCTGTGCAGCCAA--AATGAC
1 TGAGCACCTCTGTGC-TTCAATCAAGGAC
*
1315040 TGAGCACCTCTGTGCTTCAATCTAA-AATC
1 TGAGCACCTCTGTGCTTCAATC-AAGGA-C
* *
1315069 TG-GCACCTCTGTGCATT--A-GAAGGAT
1 TGAGCACCTCTGTGC-TTCAATCAAGGAC
*
1315094 TGAGCACCTCTGTGCTACAATC
1 TGAGCACCTCTGTGCTTCAATC
1315116 TAAAATCAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
25 5 0.06
26 23 0.29
27 24 0.31
28 19 0.24
29 7 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (28 bp):
TGAGCACCTCTGTGCTTCAATCAAGGAC
Found at i:1317679 original size:18 final size:18
Alignment explanation
Indices: 1317656--1317698 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1317646 CTTTAGATTA
*
1317656 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
1317674 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
1317692 TTTATTT
1 TTTATTT
1317699 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1317786 original size:15 final size:16
Alignment explanation
Indices: 1317768--1317797 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1317758 TATTTCCCTT
1317768 TTTTATCTTT-TTTTG
1 TTTTATCTTTATTTTG
1317783 TTTTATCTTTATTTT
1 TTTTATCTTTATTTT
1317798 CTCACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTATCTTTATTTTG
Found at i:1317815 original size:36 final size:37
Alignment explanation
Indices: 1317765--1317836 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 37
1317755 TTATATTTCC
* *
1317765 CTTTTTTATCTTTTTTTGTTTTATCTTTATTTTCTCA
1 CTTTTTTATCTTTTTTTATTTTATCTTTATGTTCTCA
*
1317802 CTTTTTTAT-TTTTTTTATTTTATTTTTATGTTCTC
1 CTTTTTTATCTTTTTTTATTTTATCTTTATGTTCTC
1317837 TTTTAACATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 23 0.72
37 9 0.28
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.75
Consensus pattern (37 bp):
CTTTTTTATCTTTTTTTATTTTATCTTTATGTTCTCA
Found at i:1317971 original size:24 final size:27
Alignment explanation
Indices: 1317921--1317971 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1317911 ATTTTTAACA
*
1317921 TTTTTTTAATATTTCATTCTTTGATTT
1 TTTTTTTAATATTTAATTCTTTGATTT
1317948 TTTTTTTAA-ATTTAATT-TTT-ATTT
1 TTTTTTTAATATTTAATTCTTTGATTT
1317972 GATATTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 3 0.13
26 7 0.30
27 9 0.39
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (27 bp):
TTTTTTTAATATTTAATTCTTTGATTT
Found at i:1323684 original size:123 final size:123
Alignment explanation
Indices: 1323475--1323698 Score: 324
Period size: 123 Copynumber: 1.8 Consensus size: 123
1323465 CGAGCCAATG
* * *
1323475 CAATTTTCAAGATTGGATTTCAACTTCACAACGAATGACATCCAATTCAAAGCTCAAATTCACAG
1 CAATTTACAAGATTGGATTTCAACTTCACAACGAAGGACATCCAATTCAAAGCTCAAATTCACAA
* * *
1323540 GGAAGGAGCCATCCACAATTTCAACTTGACAGCGAAAGATATTAATCTCAAAGCGATT
66 CGAAGGAGCCATCCACAATTTCAACTTCACAACGAAAGATATTAATCTCAAAGCGATT
* * * *
1323598 CAATTTACAAGATTGGATTTTAACTTCAGAACGAAGGATATCCAATTCAAAGCTCAACTTCACAA
1 CAATTTACAAGATTGGATTTCAACTTCACAACGAAGGACATCCAATTCAAAGCTCAAATTCACAA
* *
1323663 CGAAGGAGCCA-CCTACGATTTCGACTTCACAACGAA
66 CGAAGGAGCCATCC-ACAATTTCAACTTCACAACGAA
1323699 TAATATCGTA
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
122 2 0.02
123 86 0.98
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (123 bp):
CAATTTACAAGATTGGATTTCAACTTCACAACGAAGGACATCCAATTCAAAGCTCAAATTCACAA
CGAAGGAGCCATCCACAATTTCAACTTCACAACGAAAGATATTAATCTCAAAGCGATT
Found at i:1324523 original size:12 final size:13
Alignment explanation
Indices: 1324496--1324524 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1324486 TCAATTAGGA
1324496 TTTAACATATTAT
1 TTTAACATATTAT
1324509 TTTAA-ATATTAT
1 TTTAACATATTAT
1324521 TTTA
1 TTTA
1324525 TTTTATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTAACATATTAT
Found at i:1325141 original size:18 final size:19
Alignment explanation
Indices: 1325118--1325161 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
1325108 CTTTAGATTA
*
1325118 TTTATTTAATTATTTTC-T
1 TTTATTTAATTATTATCTT
1325136 TTTATTTAATTATTATCTT
1 TTTATTTAATTATTATCTT
1325155 TTTATTT
1 TTTATTT
1325162 TAAAAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTAATTATTATCTT
Found at i:1325251 original size:15 final size:16
Alignment explanation
Indices: 1325231--1325260 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1325221 ATTTCCCTTT
1325231 TTTTATC-TTATTTTG
1 TTTTATCTTTATTTTG
1325246 TTTTATCTTTATTTT
1 TTTTATCTTTATTTT
1325261 CCCACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATCTTTATTTTG
Found at i:1325278 original size:5 final size:5
Alignment explanation
Indices: 1325268--1325301 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1325258 TTTCCCACTT
* *
1325268 TTTTA TTTTA TTTTG TTTTG TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1325302 CTCTTTTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (5 bp):
TTTTA
Done.