Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008914.1 Hibiscus syriacus cultivar Beakdansim tig00112217_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: 1601432
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1365898 original size:32 final size:32
Alignment explanation
Indices: 1365792--1365899 Score: 101
Period size: 32 Copynumber: 3.4 Consensus size: 32
1365782 GCATCTTTGA
* * ***
1365792 AGATTCAACATCAAATGTTGGGGCATTTTTTT
1 AGATTAAACATCAAATATTGGGGCATTTTGGG
* * **
1365824 AGATTTAACATCAAATGTTGGGGCATTTTTTG
1 AGATTAAACATCAAATATTGGGGCATTTTGGG
* *
1365856 AGATTCAACATCGAATATTGGGGCATCTTTGGG
1 AGATTAAACATCAAATATTGGGGCAT-TTTGGG
1365889 A-ATTAAACATC
1 AGATTAAACATC
1365900 CTGATGCAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 62 0.93
33 5 0.07
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (32 bp):
AGATTAAACATCAAATATTGGGGCATTTTGGG
Found at i:1366596 original size:106 final size:106
Alignment explanation
Indices: 1366475--1366689 Score: 331
Period size: 106 Copynumber: 2.0 Consensus size: 106
1366465 ATATCGTGCC
1366475 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGTTGTCAACAAAAAAATTCCC
1 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGTTGTCAACAAAAAAATTCCC
*
1366540 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1366581 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAATAATTTCCT
1 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGTTGTCAACAAAAAAATTCCC
* * * * *
1366646 AGTTCCAGAGCCAATTTTAACTTCACGGCGGATGATATTGG
66 AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1366687 ACT
1 ACT
1366690 TGGAACAATA
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGTTGTCAACAAAAAAATTCCC
AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1367091 original size:101 final size:101
Alignment explanation
Indices: 1366920--1367286 Score: 567
Period size: 101 Copynumber: 3.6 Consensus size: 101
1366910 TTATGGAACT
1366920 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* * *
1366985 GAATTTTATATCGATCGAGATAGTTTCCCTTGAAAC
66 GAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
1367021 GAAATTTTGTCTCCCTTGAGACAGTTTCTCTT-AAACATAAACATTGAAAACATTTCCCTTGAAA
1 -AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
* * *
1367085 TAAATTTTATCTCGCTTGGGGTAGTTTCCCTTGAAAC
65 TGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* *
1367122 AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTTCTTTGAAA
1 -AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
* *
1367187 TGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
65 TGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* * * **
1367224 AAA-ATTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACCTTGAAAATGTTTCCCTTGAAA
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
1367287 CACAAAATAT
Statistics
Matches: 243, Mismatches: 21, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
100 53 0.22
101 97 0.40
102 93 0.38
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (101 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
GAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
Found at i:1367148 original size:37 final size:37
Alignment explanation
Indices: 1367073--1367259 Score: 114
Period size: 37 Copynumber: 5.4 Consensus size: 37
1367063 ATTGAAAACA
* * * * *
1367073 TTTCCCTTGAAA-TAAATTTTATCTCGCTTGGGGTAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
1367109 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
* * * *
1367146 TTTCTCTTGAAACATAAA---------CATTGA-AAACA
1 TTTCCCTTGAAACA-AAATTTTGTCTCCCTTGAGATA-G
* * ** *
1367175 TTTTCTTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
1367211 TTTCCCTTGAAACAAAA--TTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
1367246 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1367260 TAAACCTTGA
Statistics
Matches: 112, Mismatches: 25, Indels: 29
0.67 0.15 0.17
Matches are distributed among these distances:
27 2 0.02
28 2 0.02
29 14 0.12
35 30 0.27
36 26 0.23
37 35 0.31
38 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
Found at i:1367173 original size:203 final size:202
Alignment explanation
Indices: 1366920--1367286 Score: 601
Period size: 203 Copynumber: 1.8 Consensus size: 202
1366910 TTATGGAACT
1366920 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
*
1366985 GAATTTTATATCGATCGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCCCTTGAGACAGTTTCT
66 GAATTTTATATCGATCGAGATAGTTTCCCTTGAAAC-AAA-ATTGTCTCCCTTGAGACAGTTTCT
1367050 CTT-AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
129 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1367114 CTTGAAACA
194 CTTGAAACA
* *
1367123 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTTCTTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* * ** * *
1367188 GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTGTCTCCCTTGAGATAGTTTCTCT
66 GAATTTTATATCGATCGAGATAGTTTCCCTTGAAACAAAATTGTCTCCCTTGAGACAGTTTCTCT
* **
1367253 TGAAACATAAACCTTGAAAATGTTTCCCTTGAAA
131 TGAAACATAAACATTGAAAACATTTCCCTTGAAA
1367287 CACAAAATAT
Statistics
Matches: 151, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
201 25 0.17
202 32 0.21
203 94 0.62
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (202 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
GAATTTTATATCGATCGAGATAGTTTCCCTTGAAACAAAATTGTCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCCCT
TGAAACA
Found at i:1367233 original size:35 final size:35
Alignment explanation
Indices: 1367193--1367259 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
1367183 GAAATGAATT
*
1367193 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAAA
*
1367228 TTGTCTCCCTTGAGATAGTTTCTCTTGAAACA
1 TTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
1367260 TAAACCTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (35 bp):
TTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAAA
Found at i:1367374 original size:37 final size:37
Alignment explanation
Indices: 1367324--1367426 Score: 172
Period size: 36 Copynumber: 2.8 Consensus size: 37
1367314 AAAATGAGTT
*
1367324 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTTTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
*
1367361 TTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
*
1367397 TTGAGAAAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTT
1367427 TGAATATCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 33 0.54
37 28 0.46
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
Found at i:1367546 original size:36 final size:35
Alignment explanation
Indices: 1367324--1367556 Score: 119
Period size: 36 Copynumber: 6.6 Consensus size: 35
1367314 AAAATGAGTT
** * **
1367324 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTTTC
1 TTGAGACAGTTTCTTTTGAAAC-AAAT-TTTTCCCTC
** *
1367361 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTC
1 TTGAGACAGTTTCTTTTGAAACAAATTTT-TCCCTC
* ** *
1367397 TTGAGAAAGTTTCCCTTGAAACAAA---AT--CT-
1 TTGAGACAGTTTCTTTTGAAACAAATTTTTCCCTC
* *
1367426 TTGA-ATA-TCTT-TTCCTTGAAACAAATTTCATCTCC-C
1 TTGAGACAGT-TTCTT--TTGAAACAAATTT-TTC-CCTC
* *
1367462 TTGAGACAGTTTCTTTT-AGAACTAAGTTTTACCTCTC
1 TTGAGACAGTTTCTTTTGA-AAC-AAATTTTTCC-CTC
1367499 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
1 TTGAGACAGTTTCTTTTGAAACAAATTTT-TCCCTC
* *
1367535 TTGAGATAGTTTCTCTTGAAAC
1 TTGAGACAGTTTCTTTTGAAAC
1367557 GCAAAAAAAA
Statistics
Matches: 160, Mismatches: 15, Indels: 43
0.73 0.07 0.20
Matches are distributed among these distances:
27 1 0.01
28 4 0.03
29 14 0.09
30 2 0.01
32 1 0.01
33 2 0.01
35 4 0.03
36 74 0.46
37 54 0.34
38 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (35 bp):
TTGAGACAGTTTCTTTTGAAACAAATTTTTCCCTC
Found at i:1368883 original size:33 final size:33
Alignment explanation
Indices: 1368823--1368906 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
1368813 TTTATTATCA
* * * *
1368823 ATTTTATTAATTTATATATATATATATATTTACT
1 ATTTT-TTATTTTTTATTTATATATATATATACT
*
1368857 ATTTTTTATTTTTTATTTATATATATATATATT
1 ATTTTTTATTTTTTATTTATATATATATATACT
1368890 A-TTTTTACTTTTTTATT
1 ATTTTTTA-TTTTTTATT
1368907 ATTATTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
32 6 0.14
33 33 0.75
34 5 0.11
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (33 bp):
ATTTTTTATTTTTTATTTATATATATATATACT
Found at i:1368956 original size:51 final size:50
Alignment explanation
Indices: 1368851--1368969 Score: 131
Period size: 48 Copynumber: 2.4 Consensus size: 50
1368841 TATATATATA
*
1368851 TTTACTATTTTTTATTTTTTATTTATATATATATATATTATTTTTACTTT
1 TTTATTATTTTTTATTTTTTATTTATATATATATATATTATTTTTACTTT
* *
1368901 TTTATTATTATTTTATTTGTTTGTTT-TAT-T-TATATATT-TTTTTTCTTT
1 TTTATTATT-TTTTATTT-TTTATTTATATATATATATATTATTTTTACTTT
*
1368949 TTCT-TTATTTCGTTATTTTTT
1 TT-TATTATTT-TTTATTTTTT
1368970 TATATTTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
47 4 0.07
48 22 0.36
49 9 0.15
50 9 0.15
51 11 0.18
52 6 0.10
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.74
Consensus pattern (50 bp):
TTTATTATTTTTTATTTTTTATTTATATATATATATATTATTTTTACTTT
Found at i:1369004 original size:23 final size:20
Alignment explanation
Indices: 1368967--1369024 Score: 53
Period size: 23 Copynumber: 2.7 Consensus size: 20
1368957 TTCGTTATTT
*
1368967 TTTTATATTTATTTTACTTACTA
1 TTTTATCTTTATTTT-CTT--TA
*
1368990 TTTTATCTTTGTTTTCTTTA
1 TTTTATCTTTATTTTCTTTA
*
1369010 TCTTATCTTTTATTT
1 TTTTATC-TTTATTT
1369025 AATTTGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 8 0.27
21 6 0.20
22 3 0.10
23 13 0.43
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTATCTTTATTTTCTTTA
Found at i:1369058 original size:4 final size:4
Alignment explanation
Indices: 1369049--1369079 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1369039 TCATTTTAAT
1369049 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1369080 CTTATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1372559 original size:19 final size:19
Alignment explanation
Indices: 1372535--1372572 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1372525 CATAACACCA
1372535 AACCCCCAGATTATAACCC
1 AACCCCCAGATTATAACCC
*
1372554 AACCCCCAGATTGTAACCC
1 AACCCCCAGATTATAACCC
1372573 TTAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.42, G:0.08, T:0.16
Consensus pattern (19 bp):
AACCCCCAGATTATAACCC
Found at i:1372652 original size:37 final size:37
Alignment explanation
Indices: 1372605--1372713 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 37
1372595 CTTTGAGATT
*
1372605 GTTTCGCTTGAAACAAAGTTTCATCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTCATCTCGCTTGAGACA
* **
1372642 GTTTCTCTTGAAACATAA-----A-CT--TTTGAGATT
1 GTTTCTCTTGAAACA-AAGTTTCATCTCGCTTGAGACA
* *
1372672 GTTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTCATCTCGCTTGAGACA
1372709 GTTTC
1 GTTTC
1372714 CATTAAAGCC
Statistics
Matches: 54, Mismatches: 9, Indels: 18
0.67 0.11 0.22
Matches are distributed among these distances:
29 2 0.04
30 20 0.37
32 2 0.04
33 1 0.02
35 2 0.04
37 25 0.46
38 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (37 bp):
GTTTCTCTTGAAACAAAGTTTCATCTCGCTTGAGACA
Found at i:1372699 original size:67 final size:67
Alignment explanation
Indices: 1372587--1372713 Score: 211
Period size: 67 Copynumber: 1.9 Consensus size: 67
1372577 ATTTAAAATC
*
1372587 ACATAAATCTTTGAGATTGTTTCGCTTGAAACAAAGTTTCATCTCGCTTGAGACAGTTTCTCTTG
1 ACATAAATCTTTGAGATTGTTTCGCTCGAAACAAAGTTTCATCTCGCTTGAGACAGTTTCTCTTG
1372652 AA
66 AA
* *
1372654 ACATAAA-CTTTTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGACAGTTTC
1 ACATAAATC-TTTGAGATTGTTTCGCTCGAAACAAAGTTTCATCTCGCTTGAGACAGTTTC
1372714 CATTAAAGCC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 1 0.02
67 55 0.98
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (67 bp):
ACATAAATCTTTGAGATTGTTTCGCTCGAAACAAAGTTTCATCTCGCTTGAGACAGTTTCTCTTG
AA
Found at i:1384070 original size:26 final size:27
Alignment explanation
Indices: 1384004--1384072 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1383994 ATCACTATCA
1384004 TCAAAATATTACAAACAAATAAAATTC
1 TCAAAATATTACAAACAAATAAAATTC
1384031 TCAAAATATTACAAACAAATAAAATTC
1 TCAAAATATTACAAACAAATAAAATTC
*
1384058 TC-AAATGTTACAAAC
1 TCAAAATATTACAAAC
1384073 GGAAGAAGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 12 0.29
27 29 0.71
ACGTcount: A:0.57, C:0.16, G:0.01, T:0.26
Consensus pattern (27 bp):
TCAAAATATTACAAACAAATAAAATTC
Found at i:1389318 original size:19 final size:15
Alignment explanation
Indices: 1389279--1389331 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
1389269 TGTATTTAGT
1389279 GGGCGGGTGGATGTG
1 GGGCGGGTGGATGTG
1389294 GGGCGGGTGGATGTG
1 GGGCGGGTGGATGTG
* * *
1389309 AGGCGGGCGGATGCG
1 GGGCGGGTGGATGTG
1389324 GGGCGGGT
1 GGGCGGGT
1389332 AAGGTCTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.08, C:0.11, G:0.66, T:0.15
Consensus pattern (15 bp):
GGGCGGGTGGATGTG
Found at i:1390710 original size:12 final size:12
Alignment explanation
Indices: 1390693--1390718 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1390683 TTTAAACCCA
1390693 AAGAATAAATAG
1 AAGAATAAATAG
1390705 AAGAATAAATAG
1 AAGAATAAATAG
1390717 AA
1 AA
1390719 TAGGTCGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (12 bp):
AAGAATAAATAG
Found at i:1390764 original size:60 final size:60
Alignment explanation
Indices: 1390693--1390814 Score: 208
Period size: 60 Copynumber: 2.0 Consensus size: 60
1390683 TTTAAACCCA
* * *
1390693 AAGAATAAATAGAAGAATAAATAGAATAGGTCGATGTCTTTTCAACTAGAGAAAATCATT
1 AAGAAAAAATAGAAGAAGAAATAGAATAGGTCGATGTCTTTTCAACTACAGAAAATCATT
*
1390753 AAGAAAAAATAGAAGAAGAAATAGAATAGGTCGGTGTCTTTTCAACTACAGAAAATCATT
1 AAGAAAAAATAGAAGAAGAAATAGAATAGGTCGATGTCTTTTCAACTACAGAAAATCATT
1390813 AA
1 AA
1390815 ACAATGACAG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.25
Consensus pattern (60 bp):
AAGAAAAAATAGAAGAAGAAATAGAATAGGTCGATGTCTTTTCAACTACAGAAAATCATT
Found at i:1392228 original size:21 final size:20
Alignment explanation
Indices: 1392164--1392264 Score: 107
Period size: 20 Copynumber: 5.0 Consensus size: 20
1392154 AAATGACTAA
* *
1392164 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGAATTT
*
1392184 CAATTTCGCAACGC-AATTT
1 CAAATTCGCAACGCGAATTT
*
1392203 CCAAATTCGCAACACTGAATTT
1 -CAAATTCGCAACGC-GAATTT
*
1392225 CAAATTCGCAACTCG-ATTT
1 CAAATTCGCAACGCGAATTT
*
1392244 CTGAATTCGCAACGCGAATTT
1 C-AAATTCGCAACGCGAATTT
1392265 TGTTTTCGCA
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
19 8 0.12
20 38 0.56
21 17 0.25
22 5 0.07
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:1392252 original size:20 final size:19
Alignment explanation
Indices: 1392227--1392292 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
1392217 CTGAATTTCA
1392227 AATTCGCAACTCGATTTCTG
1 AATTCGCAACTCGATTT-TG
*
1392247 AATTCGCAACGCGAATTTTG
1 AATTCGCAACTCG-ATTTTG
**
1392267 TTTTCGCAACTCGATTTTCG
1 AATTCGCAACTCGATTTT-G
1392287 AATTCG
1 AATTCG
1392293 GAACATGAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 5 0.13
20 29 0.76
21 4 0.11
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (19 bp):
AATTCGCAACTCGATTTTG
Found at i:1392303 original size:40 final size:40
Alignment explanation
Indices: 1392166--1392314 Score: 138
Period size: 40 Copynumber: 3.7 Consensus size: 40
1392156 ATGACTAACA
* * ** * * **
1392166 AATTCGCAACGCGAACTCCAATTTCGCAACGCAATTTCCA
1 AATTCGCAACACGAATTTTAATTTCGCAACTCGATTTCTG
* *
1392206 AATTCGCAACACTGAATTTCAAATTCGCAACTCGATTTCTG
1 AATTCGCAACAC-GAATTTTAATTTCGCAACTCGATTTCTG
* **
1392247 AATTCGCAACGCGAATTTTGTTTTCGCAACTCGATTT-TCG
1 AATTCGCAACACGAATTTTAATTTCGCAACTCGATTTCT-G
* *
1392287 AATTCGGAACATGAATTTTAATTTCGCA
1 AATTCGCAACACGAATTTTAATTTCGCA
1392315 CCAGGTTTTA
Statistics
Matches: 89, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 1 0.01
40 56 0.63
41 32 0.36
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (40 bp):
AATTCGCAACACGAATTTTAATTTCGCAACTCGATTTCTG
Found at i:1392492 original size:14 final size:15
Alignment explanation
Indices: 1392473--1392510 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1392463 TCCTCATCTC
1392473 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1392487 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1392503 TAATTTTT
1 TAATTTTT
1392511 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1393126 original size:12 final size:12
Alignment explanation
Indices: 1393105--1393138 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1393095 ACCACATTTC
*
1393105 CAATACCAAACA
1 CAATATCAAACA
1393117 CAATATCAAACA
1 CAATATCAAACA
*
1393129 CAATCTCAAA
1 CAATATCAAA
1393139 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1393292 original size:24 final size:24
Alignment explanation
Indices: 1393265--1393318 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1393255 GTATTCGAAA
1393265 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1393289 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1393313 TTTGAT
1 TTTGAT
1393319 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1395901 original size:29 final size:29
Alignment explanation
Indices: 1395856--1395912 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1395846 GCGATTTTTT
*
1395856 GTTGCGATTGTTGCGAAAGTCAAATTCGC
1 GTTGCGATTGTTACGAAAGTCAAATTCGC
1395885 GTTGCGATTGTTACGAAAGTCAAATTCG
1 GTTGCGATTGTTACGAAAGTCAAATTCG
1395913 AAACGCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (29 bp):
GTTGCGATTGTTACGAAAGTCAAATTCGC
Found at i:1395929 original size:20 final size:20
Alignment explanation
Indices: 1395900--1395942 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1395890 GATTGTTACG
*
1395900 AAAGTCAAATTCGAAACGCA
1 AAAGTAAAATTCGAAACGCA
*
1395920 AAAGTAAAATTCGCAACGCA
1 AAAGTAAAATTCGAAACGCA
1395940 AAA
1 AAA
1395943 ATCGCAACGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAGTAAAATTCGAAACGCA
Found at i:1397506 original size:21 final size:21
Alignment explanation
Indices: 1397480--1397593 Score: 149
Period size: 21 Copynumber: 5.4 Consensus size: 21
1397470 GTGAATCGGG
* *
1397480 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGGGC
** *
1397501 CTCTTGAACGATGACATGGGC
1 CTCTTGAACGATGGGAGGGGC
1397522 CTCTTGAAC-AGTGGGAGGGGC
1 CTCTTGAACGA-TGGGAGGGGC
*
1397543 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
1397564 CTCTTGAACGATAGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
1397585 CTCTTGAAC
1 CTCTTGAAC
1397594 AATGAAAGTT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
20 1 0.01
21 78 0.98
22 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.36, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:1397539 original size:42 final size:41
Alignment explanation
Indices: 1397480--1397598 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 41
1397470 GTGAATCGGG
* *
1397480 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACATGGGC
1 CTCTTGAAC-GTGGGAGGGGCCTCTTGAACGATGACAGGGGC
*
1397522 CTCTTGAACAGTGGGAGGGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAAC-GTGGGAGGGGCCTCTTGAACGATGACAGGGGC
* *
1397564 CTCTTGAACGATAGGAGGGGCCTCTTGAACAATGA
1 CTCTTGAACG-TGGGAGGGGCCTCTTGAACGATGA
1397599 AAGTTGAATC
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
41 1 0.01
42 69 0.99
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.21
Consensus pattern (41 bp):
CTCTTGAACGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
Found at i:1397904 original size:21 final size:21
Alignment explanation
Indices: 1397878--1397929 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
1397868 TAAAACAATG
* * *
1397878 TCACGTAGAGTGGCTACCTCA
1 TCACGTAAAGTAGATACCTCA
1397899 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGTAGATACCTCA
* *
1397920 CCACATAAAG
1 TCACGTAAAG
1397930 CACCATTGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (21 bp):
TCACGTAAAGTAGATACCTCA
Found at i:1397968 original size:21 final size:21
Alignment explanation
Indices: 1397948--1397987 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1397938 TCATCGCGTA
1397948 AAACATC-TACCTCACCACGT
1 AAACATCGTACCTCACCACGT
* *
1397968 AAAGATCGTACCTCATCACG
1 AAACATCGTACCTCACCACG
1397988 CCATGCACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.35, G:0.10, T:0.20
Consensus pattern (21 bp):
AAACATCGTACCTCACCACGT
Found at i:1398243 original size:42 final size:42
Alignment explanation
Indices: 1398168--1398266 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
1398158 GTGATGGAAT
* * * * *
1398168 AGGTGATGGCTCTCGTTGTGGAGGTGTATAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTATAGAATCGGCTCGATC
*
1398210 AGGTGATGGCTCTGGGTGTCGAGCTATAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTATAGAATCGGCTCGATC
1398252 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
1398267 AAGTGAGGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.17, C:0.18, G:0.36, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTATAGAATCGGCTCGATC
Found at i:1399996 original size:22 final size:22
Alignment explanation
Indices: 1399969--1400038 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
1399959 GGAGATAGAA
*
1399969 GGATTTCGTCGGAGATGGGGAT
1 GGATTTCGTCGGAGATGGGGAC
1399991 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCGTCGGAGATGGGGAC
* *
1400013 GGATTTCGCCGAAGATGGGGAC
1 GGATTTCGTCGGAGATGGGGAC
1400035 GGAT
1 GGAT
1400039 GTCGCCGTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.20, C:0.13, G:0.44, T:0.23
Consensus pattern (22 bp):
GGATTTCGTCGGAGATGGGGAC
Found at i:1401321 original size:3 final size:3
Alignment explanation
Indices: 1401307--1401369 Score: 90
Period size: 3 Copynumber: 20.0 Consensus size: 3
1401297 AAATTTAAAT
*
1401307 TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
1401353 TTA TATA TTA TTTA TTA
1 TTA T-TA TTA -TTA TTA
1401370 AATATTACAA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
3 46 0.84
4 9 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1401375 original size:7 final size:7
Alignment explanation
Indices: 1401308--1401376 Score: 69
Period size: 6 Copynumber: 10.7 Consensus size: 7
1401298 AATTTAAATT
1401308 TATTATA
1 TATTATA
1401315 -ATTAT-
1 TATTATA
1401320 TATTAT-
1 TATTATA
1401326 TATTAT-
1 TATTATA
1401332 TATTAT-
1 TATTATA
1401338 TATTAT-
1 TATTATA
*
1401344 TATTATT
1 TATTATA
1401351 TATTATA
1 TATTATA
*
1401358 TATTATT
1 TATTATA
*
1401365 TATTAAA
1 TATTATA
1401372 TATTA
1 TATTA
1401377 CAAAGCCCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
6 34 0.61
7 22 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TATTATA
Found at i:1401375 original size:11 final size:14
Alignment explanation
Indices: 1401315--1401376 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 14
1401305 ATTTATTATA
1401315 ATTAT-TATTA-TT
1 ATTATATATTATTT
1401327 ATTAT-TATTA-TT
1 ATTATATATTATTT
1401339 ATTAT-TATTATTT
1 ATTATATATTATTT
1401352 ATTATATATTATTT
1 ATTATATATTATTT
*
1401366 ATTAAATATTA
1 ATTATATATTA
1401377 CAAAGCCCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
12 22 0.47
13 7 0.15
14 18 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATATATTATTT
Found at i:1403154 original size:111 final size:111
Alignment explanation
Indices: 1402921--1403154 Score: 258
Period size: 111 Copynumber: 2.1 Consensus size: 111
1402911 TGATATTTAT
* * * * * *
1402921 TTATTTT-TAATATAAAAGAAAAGAGATGTCTTAAGGTACCTAGAAGCTCTTTTCTGATATTTTT
1 TTATTTTGAAATATAAAAGAAAAGAGATGTCTTAAAGCACCTAGAAGCCCTTTTCTAATATTTCT
* * * *
1402985 GAATAAATAAATATCTTACTATATTAAAATAAAATGTTTTTGATAT
66 AAATAAATAAATATCTTACTATATTAAAATAAAATATTTTTGAAAA
* * *
1403031 TTATTTTTAAATATCAAAGAAAAGAGTTGTCTTAAAGCACCTAGAAGCCCTTTTCTAATATTTCT
1 TTATTTTGAAATATAAAAGAAAAGAGATGTCTTAAAGCACCTAGAAGCCCTTTTCTAATATTTCT
* * * * * *
1403096 AAATAAGTAAATATCTTA-TTTATGTATATTAATATATTTTCTTAAAA
66 AAATAAATAAATATCTTACTATAT-TAAAATAAAATATTTT-TGAAAA
1403143 TTA-TTTGAAATA
1 TTATTTTGAAATA
1403155 GTAGAATTAT
Statistics
Matches: 102, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
110 11 0.11
111 85 0.83
112 6 0.06
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (111 bp):
TTATTTTGAAATATAAAAGAAAAGAGATGTCTTAAAGCACCTAGAAGCCCTTTTCTAATATTTCT
AAATAAATAAATATCTTACTATATTAAAATAAAATATTTTTGAAAA
Found at i:1405299 original size:27 final size:27
Alignment explanation
Indices: 1405269--1405336 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
1405259 TTCACATTTT
*
1405269 TTTTTTTTGCATTTTTTCATATTTGCA
1 TTTTTTTTGCATTTATTCATATTTGCA
* * *
1405296 --TTTTTTACGTTCGTATTCATATTTTCA
1 TTTTTTTTGCATT--TATTCATATTTGCA
1405323 TTTTTTTTGCATTT
1 TTTTTTTTGCATTT
1405337 GCATCTTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
25 9 0.29
27 13 0.42
29 9 0.29
ACGTcount: A:0.15, C:0.12, G:0.07, T:0.66
Consensus pattern (27 bp):
TTTTTTTTGCATTTATTCATATTTGCA
Found at i:1411769 original size:50 final size:49
Alignment explanation
Indices: 1411636--1411790 Score: 168
Period size: 54 Copynumber: 3.0 Consensus size: 49
1411626 TAATTGAGAA
1411636 ATCTGAACAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGCTTTATGAAC
1 ATCTG-ACAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATG-TTT-T--AC
* *
1411690 ATCTGAGCAGAAGCTACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
1 ATCTGA-CAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTAC
* * ***
1411740 ATCTCGACAGAAACCACAGGAAAA-AATGAATGCACTGTCAAATGTTTTAC
1 ATCT-GACAGAAGCCACA-GAAAAGGATGAATGTGTTGTCAAATGTTTTAC
1411790 A
1 A
1411791 AACCTACTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
50 37 0.42
51 7 0.08
52 1 0.01
53 4 0.04
54 40 0.45
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (49 bp):
ATCTGACAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTAC
Found at i:1412188 original size:22 final size:22
Alignment explanation
Indices: 1412160--1412214 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1412150 ATCTACACTC
1412160 TTCAAAGATGATAGATTATCTT
1 TTCAAAGATGATAGATTATCTT
* *
1412182 TTTAAAGATGATAGATTTTCTT
1 TTCAAAGATGATAGATTATCTT
1412204 TTCAAAGATGA
1 TTCAAAGATGA
1412215 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTATCTT
Found at i:1413000 original size:164 final size:166
Alignment explanation
Indices: 1412728--1413052 Score: 600
Period size: 164 Copynumber: 2.0 Consensus size: 166
1412718 AAGAATGAAA
1412728 ATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACG
1 ATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACG
1412793 ATTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
66 ATTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
1412858 CTTAG-TTTTTTACTTAGTAAACTATTTCCAACAGT
131 CTTAGTTTTTTTACTTAGTAAACTATTTCCAACAGT
**
1412893 ATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-TGAAAAATAATGAGAAAACG
1 ATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACG
1412957 ATTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
66 ATTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
*
1413022 CTTAGTTTTTTTTACTTAGTAAACTTTTTCC
131 CTTAG-TTTTTTTACTTAGTAAACTATTTCC
1413053 CACATCTGTA
Statistics
Matches: 155, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
164 88 0.57
165 44 0.28
166 23 0.15
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (166 bp):
ATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACG
ATTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
CTTAGTTTTTTTACTTAGTAAACTATTTCCAACAGT
Found at i:1413292 original size:77 final size:76
Alignment explanation
Indices: 1413055--1413550 Score: 821
Period size: 77 Copynumber: 6.5 Consensus size: 76
1413045 CTTTTTCCCA
* *
1413055 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1413120 AACCTTCGGGT
66 AGCCTTCGGGT
* *
1413131 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTCAAAAAAGCCTTTGGGAGCTTTTCGATGTTTTC
1 CATCTGTAAGCCCTTCAGTGCATGATG-TTTTC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
*
1413196 AAAACCTTCGGGT
64 AAAGCCTTCGGGT
1413209 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATG-TTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1413274 AAGCCTTCGGGT
65 AAGCCTTCGGGT
1413286 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATG-TTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
1413351 AAGCCTTTGGGT
65 AAGCCTTCGGGT
1413363 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1413428 AAGCCTTCGGGT
65 AAGCCTTCGGGT
* * * *
1413440 CATCTGTAAGCCTTTCAGTACAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1413505 AGCCTTCGGGT
66 AGCCTTCGGGT
* * *
1413516 CGTCTGTAAGTCCTGCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1413551 CATTTTCATC
Statistics
Matches: 399, Mismatches: 18, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
76 103 0.26
77 220 0.55
78 76 0.19
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:1413700 original size:3 final size:3
Alignment explanation
Indices: 1413686--1413760 Score: 114
Period size: 3 Copynumber: 24.0 Consensus size: 3
1413676 AAATTTAAAT
*
1413686 TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1413734 TTA TTA TTA TTTA TATA TTA TTTA TTA
1 TTA TTA TTA -TTA T-TA TTA -TTA TTA
1413761 AATATTACAA
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
3 58 0.87
4 9 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1415545 original size:111 final size:111
Alignment explanation
Indices: 1415312--1415545 Score: 258
Period size: 111 Copynumber: 2.1 Consensus size: 111
1415302 TGATATTTAT
* * * * *
1415312 TTATTTT-TAATATAAAAGAAAAGAGATGTCTTAAGGTACCTAGAAGCTCTTTTCTGATATTTTT
1 TTATTTTGAAATATAAAAGAAAAGAGATGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTTCT
* * * *
1415376 GAATAAATAAATATCTTACTATATTAAAATAAAATGTTTTTGATAT
66 AAATAAATAAATATCTTACTATATTAAAATAAAATATTTTTGAAAA
* * * *
1415422 TTATTTTTAAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATGTTTCT
1 TTATTTTGAAATATAAAAGAAAAGAGATGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTTCT
* * * * * *
1415487 AAATAAGTAAATATCTTA-TTTATGTATATTAATATATTTTCTTAAAA
66 AAATAAATAAATATCTTACTATAT-TAAAATAAAATATTTT-TGAAAA
1415534 TTA-TTTGAAATA
1 TTATTTTGAAATA
1415546 GTAGAATTAT
Statistics
Matches: 102, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
110 11 0.11
111 85 0.83
112 6 0.06
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (111 bp):
TTATTTTGAAATATAAAAGAAAAGAGATGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTTCT
AAATAAATAAATATCTTACTATATTAAAATAAAATATTTTTGAAAA
Found at i:1425116 original size:135 final size:136
Alignment explanation
Indices: 1424851--1425129 Score: 515
Period size: 135 Copynumber: 2.1 Consensus size: 136
1424841 AAAGTAACAA
1424851 TTAATATTGAATATTTCCCAAGAGAATGTTTCAAACGTCCTTGATAAGTCTGGCCAGTACCGGGT
1 TTAATATTGAATATTTCCCAAGAGAATGTTTCAAACGTCCTTGATAAGTCTGGCCAGTACCGGGT
1424916 TTATTAACACTTCTCCAAGCATTACCAATAATTTTACACATACTTCCACAATAAAAAGCTGTGAA
66 TTATTAACACTTCTCCAAGCATTACCAATAATTTTACACATACTTCCACAATAAAAAGCTGTGAA
1424981 ACTTGT
131 ACTTGT
* * *
1424987 TTAATATTGAATATTT-TCAAGAGATTGTTTCAAACGTCCTTGATAAGTCTGGCCAGTACTGGGT
1 TTAATATTGAATATTTCCCAAGAGAATGTTTCAAACGTCCTTGATAAGTCTGGCCAGTACCGGGT
*
1425051 TTATTAACACTTCTCCAAGCATTACCAATAATTTTACACATACTTCCACAATAAAAAGCTTTGAA
66 TTATTAACACTTCTCCAAGCATTACCAATAATTTTACACATACTTCCACAATAAAAAGCTGTGAA
1425116 ACTTGT
131 ACTTGT
1425122 TTAATATT
1 TTAATATT
1425130 TACTTAGCTG
Statistics
Matches: 139, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
135 123 0.88
136 16 0.12
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (136 bp):
TTAATATTGAATATTTCCCAAGAGAATGTTTCAAACGTCCTTGATAAGTCTGGCCAGTACCGGGT
TTATTAACACTTCTCCAAGCATTACCAATAATTTTACACATACTTCCACAATAAAAAGCTGTGAA
ACTTGT
Found at i:1429411 original size:23 final size:24
Alignment explanation
Indices: 1429358--1429414 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
1429348 GTAAACAACT
*
1429358 AAATAAAAATAAAATGATAATACAA
1 AAATATAAATAAAATGATAATA-AA
*
1429383 ATATATAAATAAAAT-A-AATAAA
1 AAATATAAATAAAATGATAATAAA
1429405 AGAATATAAA
1 A-AATATAAA
1429415 ACATAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 3 0.11
23 11 0.39
24 1 0.04
25 13 0.46
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (24 bp):
AAATATAAATAAAATGATAATAAA
Found at i:1429495 original size:22 final size:22
Alignment explanation
Indices: 1429467--1429537 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
1429457 AATGAGTAAA
1429467 ATATATAAAAAAGTAAAA-ACAT
1 ATATATAAAAAAGTAAAATA-AT
* *
1429489 ATATATATATAAGTAAAATAAT
1 ATATATAAAAAAGTAAAATAAT
*
1429511 A-ATAATAAAAAAATCAAAAGTAAT
1 ATAT-ATAAAAAAGT-AAAA-TAAT
1429535 ATA
1 ATA
1429538 CGTATTTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.05
22 26 0.67
23 5 0.13
24 5 0.13
25 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (22 bp):
ATATATAAAAAAGTAAAATAAT
Found at i:1429576 original size:2 final size:2
Alignment explanation
Indices: 1429563--1429628 Score: 55
Period size: 2 Copynumber: 33.5 Consensus size: 2
1429553 AAAATAGGAA
* * * * * *
1429563 AT AT AT AA AT AT AT AT AT AT AT A- AT A- AC ACT AA AA AA AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
1429604 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 A
1429629 ATAAAATTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.04
2 52 0.95
3 1 0.02
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (2 bp):
AT
Found at i:1431329 original size:23 final size:23
Alignment explanation
Indices: 1431272--1431340 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
1431262 AAATATAAAA
*
1431272 TATAATAAA-TAATATTATTTAT
1 TATAAAAAATTAATATTATTTAT
*
1431294 TATAAAAACTTAATATTA-TTAT
1 TATAAAAAATTAATATTATTTAT
* * *
1431316 TTTAAAAATATTAAAATAATTTAT
1 TATAAAAA-ATTAATATTATTTAT
1431340 T
1 T
1431341 TAATACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 18 0.47
23 15 0.39
24 5 0.13
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
TATAAAAAATTAATATTATTTAT
Found at i:1435884 original size:21 final size:22
Alignment explanation
Indices: 1435839--1435886 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1435829 CTAAGGTGAG
*
1435839 GGGTTGGAATTGGGAAATAAAA
1 GGGTTGAAATTGGGAAATAAAA
*
1435861 GGGTTGAAATTGGGAAATAAAG
1 GGGTTGAAATTGGGAAATAAAA
1435883 GGGT
1 GGGT
1435887 GAGTCTCCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.23
Consensus pattern (22 bp):
GGGTTGAAATTGGGAAATAAAA
Found at i:1436967 original size:43 final size:43
Alignment explanation
Indices: 1436901--1437000 Score: 164
Period size: 43 Copynumber: 2.3 Consensus size: 43
1436891 GATACTAGAA
*
1436901 GAACAGTATCGATACTATAGGTTTAACTTTGAAGAATTACGAT
1 GAACAGTATCGATACTATAGGTTTAAATTTGAAGAATTACGAT
* *
1436944 GAACGGTATCGATACTATAGGTTTAAATTTGAAGAATTATGAT
1 GAACAGTATCGATACTATAGGTTTAAATTTGAAGAATTACGAT
*
1436987 GAACAGTATTGATA
1 GAACAGTATCGATA
1437001 TTGATGCAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (43 bp):
GAACAGTATCGATACTATAGGTTTAAATTTGAAGAATTACGAT
Found at i:1443440 original size:24 final size:24
Alignment explanation
Indices: 1443397--1443452 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1443387 CACAAACAAT
* **
1443397 TTTATTTATTAATTTGTTTATAAA
1 TTTATTTATTAACTAATTTATAAA
*
1443421 TTTATTTATTAACTAATTTATAAG
1 TTTATTTATTAACTAATTTATAAA
*
1443445 TTTGTTTA
1 TTTATTTA
1443453 CCTTATTATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (24 bp):
TTTATTTATTAACTAATTTATAAA
Found at i:1443735 original size:31 final size:31
Alignment explanation
Indices: 1443691--1443788 Score: 142
Period size: 31 Copynumber: 3.2 Consensus size: 31
1443681 CTTATCCAGA
* * *
1443691 TGTCTAATGTTACAAACGTTACCATTTTAGG
1 TGTCTAATATTACAAACGTTATCACTTTAGG
*
1443722 AGTCTAATATTACAAACGTTATCACTTTAGG
1 TGTCTAATATTACAAACGTTATCACTTTAGG
* *
1443753 TGTCTCATATTACAAATGTTATCACTTTAGG
1 TGTCTAATATTACAAACGTTATCACTTTAGG
1443784 TGTCT
1 TGTCT
1443789 TTGTCATAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (31 bp):
TGTCTAATATTACAAACGTTATCACTTTAGG
Found at i:1447291 original size:20 final size:20
Alignment explanation
Indices: 1447255--1447292 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1447245 ATCCTATTCC
**
1447255 CTGGTAATCTTTTATTCCCG
1 CTGGTAATCTTACATTCCCG
1447275 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1447293 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.26, G:0.13, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCG
Found at i:1447920 original size:659 final size:656
Alignment explanation
Indices: 1446734--1447950 Score: 1962
Period size: 659 Copynumber: 1.8 Consensus size: 656
1446724 TCGGAATGTT
* * * * * *
1446734 ATTCCCGGTAATCTTATATTACTAATAGTGAATTTTTTGGGTATATTATCGATAATGTCATTATC
1 ATTCCCGGTAATATTATATTACCAATAGTGAATTTTTTAGGTATATTACCGAGAATGTCATTACC
1446799 TCCATTTCCTTAGGTATTGTTAGATTACCGTCGTTTTGGACTAAAATGCCCTTAAATTTTTTTCT
66 TCCATTTCCTTAGGTATTGTTAGATTACCGTCGTTTTGGACTAAAATGCCCTTAAATTTTTTTCT
* * *
1446864 ATAAAAAATATCCTTATTCTGTCATTGAATAATAAAAATTCAACGAAGGTTGAATTACAAATTTA
131 ATAAAAAATATCATTATTCTGTCATTAAATAATAAAAATTCAACGAAGGTTAAATTACAAATTTA
* *
1446929 TACTTAAACTATTTTAGATTTACAAAAAAAAATCTATAATCAAAATTTTATATGAAGTTCGGAGG
196 TACTTAAACTATTTTAGATTTAC-AAAAAAAATCTAAAATCAAAATTTTATATGAAGTTCAGAGG
*
1446994 TTAAAATAAAATTTTACCCTTTTATTAAACCTTTTTATATTTTCAATTTTGTAAAAAATTATATA
260 TTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAAATTATATA
*
1447059 AATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAACAAACCAA
325 AATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAACAAAACAA
*
1447124 ATATATAATAAGAACAATTTGGTTAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACA
390 ATATATAATAAGAACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACA
* *
1447189 CGGCAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCTAGTAATCCTATTC
455 CGACAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCCTATTC
* ** *
1447254 CCTGGTAATCTTTTATTCCCGCTGGTAATCTTACATTCCGTGAACCAAACGCACCCTAAGGGGTG
520 ACTGGTAATCTTACATTCCCCCTGGTAATCTTACATTCCGTGAACCAAACGCACCCTAAGGGGTG
1447319 TTTGGATCAATGAATGTGGGATTCCCAAGAGAATCGAATCCACATTCTCATGTTTGGTTGGCCAG
585 TTTGGATCAATGAATGTGGGATTCCCAAGAGAATCGAATCCACATTCTCATGTTTGGTTGGCCAG
1447384 GAATCTC
650 GAATCTC
* * *
1447391 ATTCCTGGTAATATTTTATTACCAATAGT-AGTTTTTTTAGGTATATTACCGAGAATGTCATTAC
1 ATTCCCGGTAATATTATATTACCAATAGTGA-ATTTTTTAGGTATATTACCGAGAATGTCATTAC
* * * * *
1447455 CTCCCTTTCCTTATGTATTGTTGGATTACTGGT-GTTTTGGACTAAAATGCCCTTAATTTTTTTT
65 CTCCATTTCCTTAGGTATTGTTAGATTAC-CGTCGTTTTGGACTAAAATGCCCTTAAATTTTTTT
* *
1447519 CT-TCAAAAATATCA-TATTTCTGTCATTAAATAATAAAAATTCTACGAAGGTTAAATTACAAAT
129 CTATAAAAAATATCATTA-TTCTGTCATTAAATAATAAAAATTCAACGAAGGTTAAATTACAAAT
* * *
1447582 TTATCCTTAAACTATTTTAGATTTAC-AAAAAAAT-TAAAATTAAAATTTTATATGAATTTCAGA
193 TTATACTTAAACTATTTTAGATTTACAAAAAAAATCTAAAATCAAAATTTTATATGAAGTTCAGA
*
1447645 GGTTAAAATAAAATTTTACCCTTTCATTAAATCTTTTTATATTTTCAATTTTGTAAAAAATATAT
258 GGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTGT---AAA-A-A-
1447710 ATATATATAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTA
317 AT-TATATAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTA
*
1447775 A-AAAACAAATATATAATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTT
381 ACAAAACAAATATATAATAAGAACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTT
*
1447839 AACCAAACACGATAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTA
446 AACCAAACACGACAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTA
1447904 ATCCTATTCACTGGTAATCTTACATTCCCCCTGGTAATCTTACATTC
511 ATCCTATTCACTGGTAATCTTACATTCCCCCTGGTAATCTTACATTC
1447951 TCACTGGTAA
Statistics
Matches: 514, Mismatches: 36, Indels: 18
0.90 0.06 0.03
Matches are distributed among these distances:
653 77 0.15
654 8 0.02
655 2 0.00
656 82 0.16
657 112 0.22
658 3 0.01
659 167 0.32
660 63 0.12
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (656 bp):
ATTCCCGGTAATATTATATTACCAATAGTGAATTTTTTAGGTATATTACCGAGAATGTCATTACC
TCCATTTCCTTAGGTATTGTTAGATTACCGTCGTTTTGGACTAAAATGCCCTTAAATTTTTTTCT
ATAAAAAATATCATTATTCTGTCATTAAATAATAAAAATTCAACGAAGGTTAAATTACAAATTTA
TACTTAAACTATTTTAGATTTACAAAAAAAATCTAAAATCAAAATTTTATATGAAGTTCAGAGGT
TAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAAATTATATAA
ATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAACAAAACAAA
TATATAATAAGAACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACAC
GACAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCCTATTCA
CTGGTAATCTTACATTCCCCCTGGTAATCTTACATTCCGTGAACCAAACGCACCCTAAGGGGTGT
TTGGATCAATGAATGTGGGATTCCCAAGAGAATCGAATCCACATTCTCATGTTTGGTTGGCCAGG
AATCTC
Found at i:1447939 original size:20 final size:20
Alignment explanation
Indices: 1447914--1447975 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
1447904 ATCCTATTCA
1447914 CTGGTAATCTTACATTCCCC
1 CTGGTAATCTTACATTCCCC
* *
1447934 CTGGTAATCTTACATTCTCA
1 CTGGTAATCTTACATTCCCC
1447954 CTGGTAATCTTACATTCCCC
1 CTGGTAATCTTACATTCCCC
1447974 CT
1 CT
1447976 AAAAGTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.21, C:0.32, G:0.10, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCC
Found at i:1449290 original size:20 final size:20
Alignment explanation
Indices: 1449265--1449303 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1449255 ATGTGAAATT
*
1449265 TGTCCCGAAGGACCTCTATA
1 TGTCCCGAAGGACCACTATA
1449285 TGTCCCGAAGGACCACTAT
1 TGTCCCGAAGGACCACTAT
1449304 CCATATGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.23
Consensus pattern (20 bp):
TGTCCCGAAGGACCACTATA
Found at i:1449405 original size:31 final size:31
Alignment explanation
Indices: 1449299--1449424 Score: 105
Period size: 32 Copynumber: 4.0 Consensus size: 31
1449289 CCGAAGGACC
1449299 ACTATCCATATGTTCC--AAGGAACATAGGTAA
1 ACTATCCATATG-TCCTGAAGG-ACATAGGTAA
* ** * *
1449330 CACTGTATATATATCCCGAAGGACATAGGTAA
1 -ACTATCCATATGTCCTGAAGGACATAGGTAA
* *
1449362 TCATGTCCATATGTCCTGAAGGACATAGGTAA
1 AC-TATCCATATGTCCTGAAGGACATAGGTAA
* *
1449394 ACTATCCATATGT-CTCGAAAGACATATGTAA
1 ACTATCCATATGTCCT-GAAGGACATAGGTAA
1449425 CCCTCGACTC
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
30 2 0.03
31 27 0.35
32 44 0.57
33 4 0.05
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (31 bp):
ACTATCCATATGTCCTGAAGGACATAGGTAA
Found at i:1450410 original size:20 final size:19
Alignment explanation
Indices: 1450387--1450439 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 19
1450377 CCTTTAGGGA
1450387 GTATCGATACCCTTATTAGG
1 GTATCG-TACCCTTATTAGG
*
1450407 GTATTGTAACCCTTATTAGG
1 GTATCGT-ACCCTTATTAGG
1450427 GTATCGGTACCCT
1 GTATC-GTACCCT
1450440 CATTGCATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 26 0.90
21 2 0.07
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (19 bp):
GTATCGTACCCTTATTAGG
Found at i:1451748 original size:21 final size:21
Alignment explanation
Indices: 1451722--1451761 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1451712 ATCGTTGACT
1451722 TTAACC-TTGACTGTTGACCCG
1 TTAACCGTTGACTG-TGACCCG
1451743 TTAACCGTTGACTGTGACC
1 TTAACCGTTGACTGTGACC
1451762 AAAAAGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (21 bp):
TTAACCGTTGACTGTGACCCG
Found at i:1452271 original size:27 final size:27
Alignment explanation
Indices: 1452187--1452256 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
1452177 TACTTGGAAA
*
1452187 AAAAATATGAAAATACTCATATTAGGT
1 AAAATTATGAAAATACTCATATTAGGT
1452214 AAAATTATGAAAATACTCATATTAGGT
1 AAAATTATGAAAATACTCATATTAGGT
1452241 AAAATTATGAAAATAC
1 AAAATTATGAAAATAC
1452257 CCTTATGATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (27 bp):
AAAATTATGAAAATACTCATATTAGGT
Found at i:1458155 original size:37 final size:37
Alignment explanation
Indices: 1458113--1458187 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 37
1458103 CATTAAACCT
*
1458113 TTTTAT-AATTTTAATTTTGTAAAAAAAATTATATAAA
1 TTTTATGAATTTAAATTTTGTAAAAAAAA-TATATAAA
* *
1458150 TTTTATGAATTTAAATTTTTTAAAGAAAATATATAAA
1 TTTTATGAATTTAAATTTTGTAAAAAAAATATATAAA
1458187 T
1 T
1458188 ATTTTCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 15 0.44
38 19 0.56
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTTATGAATTTAAATTTTGTAAAAAAAATATATAAA
Found at i:1477771 original size:22 final size:23
Alignment explanation
Indices: 1477739--1477784 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1477729 AACAAGATTG
* *
1477739 AGACATAAAACAAAAGAGAACAA
1 AGACATAAAACAAAACAAAACAA
1477762 AGACA-AAAACAAAACAAAACAA
1 AGACATAAAACAAAACAAAACAA
1477784 A
1 A
1477785 CAAAGCTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.74, C:0.15, G:0.09, T:0.02
Consensus pattern (23 bp):
AGACATAAAACAAAACAAAACAA
Found at i:1478339 original size:27 final size:27
Alignment explanation
Indices: 1478309--1478360 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1478299 AATTTTGGGT
*
1478309 AAAAAT-TTATTTTGATTTAATAAAAAC
1 AAAAATATT-TTTTAATTTAATAAAAAC
*
1478336 AAAAATATTTTTTAATTTGATAAAA
1 AAAAATATTTTTTAATTTAATAAAA
1478361 TAAAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (27 bp):
AAAAATATTTTTTAATTTAATAAAAAC
Found at i:1480553 original size:23 final size:24
Alignment explanation
Indices: 1480511--1480572 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
1480501 ATGTATTTAT
*
1480511 AAAATTTATATTA-AATTATTCT-A
1 AAAATTTAT-TTATAATTATTATGA
1480534 AAAAGTTTATTTATAA-TATTATGA
1 AAAA-TTTATTTATAATTATTATGA
1480558 AAATATTTATTTATA
1 AAA-ATTTATTTATA
1480573 TTTTAAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
23 12 0.35
24 21 0.62
25 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (24 bp):
AAAATTTATTTATAATTATTATGA
Found at i:1480580 original size:20 final size:20
Alignment explanation
Indices: 1480557--1480638 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 20
1480547 TAATATTATG
1480557 AAAATATTTATTTATATTTT
1 AAAATATTTATTTATATTTT
*
1480577 AAAATCATATTATTTATTTATTT
1 AAAAT-AT-TTATTTATAT-TTT
* *
1480600 GAAATA-ATA-TTAT-TTTT
1 AAAATATTTATTTATATTTT
* *
1480617 AAATTATCTATTTA-ATTTT
1 AAAATATTTATTTATATTTT
1480636 AAA
1 AAA
1480639 TAATATTGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
17 7 0.14
18 3 0.06
19 14 0.28
20 7 0.14
21 2 0.04
22 10 0.20
23 7 0.14
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (20 bp):
AAAATATTTATTTATATTTT
Found at i:1480604 original size:23 final size:22
Alignment explanation
Indices: 1480559--1480614 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
1480549 ATATTATGAA
1480559 AATATTTATTTATATTTTAAAAT
1 AATA-TTATTTATATTTTAAAAT
* * *
1480582 CATATTATTTATTTATTTGAAAT
1 AATATTATTTATAT-TTTAAAAT
1480605 AATATTATTT
1 AATATTATTT
1480615 TTAAATTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
AATATTATTTATATTTTAAAAT
Found at i:1482041 original size:35 final size:34
Alignment explanation
Indices: 1481995--1482063 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 34
1481985 AAAACAGTCA
* * *
1481995 TCAATTTCATTCTAAATCCCAAATTCTAAAATAAT
1 TCAATTACATTCTAAACCCCAAA-TCCAAAATAAT
1482030 TCAATTACATTCTAAACCCCAAATCCAAAATAAT
1 TCAATTACATTCTAAACCCCAAATCCAAAATAAT
1482064 CAAAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 10 0.32
35 21 0.68
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (34 bp):
TCAATTACATTCTAAACCCCAAATCCAAAATAAT
Found at i:1482891 original size:35 final size:35
Alignment explanation
Indices: 1482845--1482918 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
1482835 CGATATTATT
*
1482845 TTGAAGTATTTTAGAATTTGGGGTTTAGAATGTAA
1 TTGAAGTATTTTAGAATTTGGGGTTTAGAATGAAA
* *
1482880 TTGAATTATTTTGGAATTTGGGGTTTAGAATGAAA
1 TTGAAGTATTTTAGAATTTGGGGTTTAGAATGAAA
1482915 TTGA
1 TTGA
1482919 GGATTGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (35 bp):
TTGAAGTATTTTAGAATTTGGGGTTTAGAATGAAA
Found at i:1486764 original size:2 final size:2
Alignment explanation
Indices: 1486757--1486795 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1486747 ATCCGTGATT
1486757 TA 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 TA T
1486796 TGGTGTAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1487164 original size:27 final size:27
Alignment explanation
Indices: 1487126--1487191 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
1487116 TCCTCTTAAG
1487126 GACATTTTAGTCACTTAAAGCATATTA
1 GACATTTTAGTCACTTAAAGCATATTA
1487153 GACATTTTAGTCACTTAAAGCATATTA
1 GACATTTTAGTCACTTAAAGCATATTA
1487180 GACATTTTAGTC
1 GACATTTTAGTC
1487192 TTCAAGGCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (27 bp):
GACATTTTAGTCACTTAAAGCATATTA
Found at i:1487608 original size:21 final size:21
Alignment explanation
Indices: 1487583--1487631 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1487573 TCATCATAAT
1487583 TCATAATTTATCACATCAATA
1 TCATAATTTATCACATCAATA
* *
1487604 TCATAAATTATCACATTAATA
1 TCATAATTTATCACATCAATA
*
1487625 TCCTAAT
1 TCATAAT
1487632 AGTTAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (21 bp):
TCATAATTTATCACATCAATA
Found at i:1489912 original size:33 final size:33
Alignment explanation
Indices: 1489874--1489981 Score: 164
Period size: 33 Copynumber: 3.3 Consensus size: 33
1489864 AAAGAAGGAA
*
1489874 GGAAGAAGAGAGGTTG-ACGCGTGAGAAGCAGCG
1 GGAAGAAGAGAGATTGCA-GCGTGAGAAGCAGCG
* *
1489907 TGAAGAAGAGAGATTGCAGCGTGAGAAGCAGAG
1 GGAAGAAGAGAGATTGCAGCGTGAGAAGCAGCG
*
1489940 GGAAGAAGAGAGATTGCAGCGCGAGAAGCAGCG
1 GGAAGAAGAGAGATTGCAGCGTGAGAAGCAGCG
1489973 GGAAGAAGA
1 GGAAGAAGA
1489982 AAGAAGACAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 67 0.99
34 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.43, T:0.08
Consensus pattern (33 bp):
GGAAGAAGAGAGATTGCAGCGTGAGAAGCAGCG
Found at i:1497104 original size:2 final size:2
Alignment explanation
Indices: 1497097--1497121 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1497087 AAAACAATCC
1497097 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
1497122 CTGGAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1500005 original size:20 final size:20
Alignment explanation
Indices: 1499976--1500029 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1499966 CGTTGGACCC
*
1499976 AAAGTATCGAAACT-TTAATG
1 AAAGTTTCGAAACTCTTAA-G
*
1499996 AAAGTTTCGAAACTCTTGAG
1 AAAGTTTCGAAACTCTTAAG
*
1500016 ATAGTTTCGAAACT
1 AAAGTTTCGAAACT
1500030 ATTGGAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 27 0.90
21 3 0.10
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
AAAGTTTCGAAACTCTTAAG
Found at i:1500133 original size:21 final size:21
Alignment explanation
Indices: 1500107--1500147 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1500097 CATTTTAAGG
1500107 TTTTGATTG-GACTTTGAATTA
1 TTTTGA-TGAGACTTTGAATTA
1500128 TTTTGATGAAGACTTTGAAT
1 TTTTGATG-AGACTTTGAAT
1500148 AAATTCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 6 0.33
22 10 0.56
ACGTcount: A:0.27, C:0.05, G:0.20, T:0.49
Consensus pattern (21 bp):
TTTTGATGAGACTTTGAATTA
Found at i:1500262 original size:88 final size:88
Alignment explanation
Indices: 1500109--1500279 Score: 270
Period size: 88 Copynumber: 1.9 Consensus size: 88
1500099 TTTTAAGGTT
* * * *
1500109 TTGATTGGACTTTGAATTATTTTGATGAAGACTTTGAATAAATTCAATTTAGTCCAAAAATATTT
1 TTGATTAGACTTTGAATTATTTTGATGAAAACTTTAAATAAATTCAATTTAGTCCAAAAACATTT
*
1500174 TGCCCTTATTTGTTATATTAACA
66 TGCCATTATTTGTTATATTAACA
* *
1500197 TTGATTAGACTTTGAATTATTTTTATGAAAATTTTAAATAAATTCAATTTAGTCCAAAAACATTT
1 TTGATTAGACTTTGAATTATTTTGATGAAAACTTTAAATAAATTCAATTTAGTCCAAAAACATTT
*
1500262 TGTCATTATTTGTTATAT
66 TGCCATTATTTGTTATAT
1500280 CAAAATATTA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 75 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (88 bp):
TTGATTAGACTTTGAATTATTTTGATGAAAACTTTAAATAAATTCAATTTAGTCCAAAAACATTT
TGCCATTATTTGTTATATTAACA
Found at i:1500691 original size:16 final size:16
Alignment explanation
Indices: 1500670--1500703 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1500660 TATTCAATCA
1500670 AGTGAAAACATAAACT
1 AGTGAAAACATAAACT
1500686 AGTGAAAACATAAACT
1 AGTGAAAACATAAACT
1500702 AG
1 AG
1500704 AAAGAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.18
Consensus pattern (16 bp):
AGTGAAAACATAAACT
Found at i:1505157 original size:9 final size:9
Alignment explanation
Indices: 1505130--1505160 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1505120 CTGTGGCGAT
1505130 GCCGACGAC
1 GCCGACGAC
*
1505139 ACCGACGAC
1 GCCGACGAC
1505148 GCCGACGAC
1 GCCGACGAC
1505157 GCCG
1 GCCG
1505161 GTGTCGGCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.32, T:0.00
Consensus pattern (9 bp):
GCCGACGAC
Found at i:1508896 original size:20 final size:21
Alignment explanation
Indices: 1508873--1508919 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1508863 AAATTATTTA
1508873 AATATATAA-ACAATTAAAAC
1 AATATATAATACAATTAAAAC
* *
1508893 AATA-AAAATACAATTAGAAC
1 AATATATAATACAATTAAAAC
1508913 AATATAT
1 AATATAT
1508920 TTAAAAGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
AATATATAATACAATTAAAAC
Found at i:1510198 original size:3 final size:3
Alignment explanation
Indices: 1510190--1510365 Score: 244
Period size: 3 Copynumber: 57.7 Consensus size: 3
1510180 TTATTTATTA
*
1510190 AAT AAT AAT AAT ATAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
* **
1510238 ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
1510286 AAT AAT AAT ACT AAT AAT AAT AAT ATT AAT AAT AAT AAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1510334 GAT AAT AAT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1510366 AATGGATAAA
Statistics
Matches: 152, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
3 143 0.94
4 9 0.06
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1510910 original size:113 final size:113
Alignment explanation
Indices: 1510663--1511335 Score: 1132
Period size: 113 Copynumber: 5.9 Consensus size: 113
1510653 GATATCAAAC
* *
1510663 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * *
1510728 CATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACA
66 -ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
*
1510777 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
1510842 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
1510890 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTCTTCTCAT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG-TTCTTCTCAT
* * *
1510955 TATGAACTTTCTCTGGAAA-GATGATCCACCAAATGATGGATTCAGGCA
65 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
1511003 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
1511068 ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
1511116 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
1511181 ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
1511229 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
1511294 ATGAACTTTCTCTGGTAATGATGATCCATCAAATGATGAATT
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATT
1511336 TGAATCTTTG
Statistics
Matches: 535, Mismatches: 22, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
112 29 0.05
113 415 0.78
114 91 0.17
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
Found at i:1511971 original size:52 final size:52
Alignment explanation
Indices: 1511893--1512866 Score: 1679
Period size: 52 Copynumber: 18.7 Consensus size: 52
1511883 CACTTCTTCG
* * *
1511893 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCCATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1511945 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1511997 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1512049 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1512101 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1512153 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1512205 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1512257 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1512309 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
* *
1512361 GATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
1512413 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1512465 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
1512517 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1512569 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
1512621 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1512673 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
1512725 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1512777 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1512829 GATCAGATAACTCAAACAACACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1512867 TGAGCACATA
Statistics
Matches: 885, Mismatches: 29, Indels: 16
0.95 0.03 0.02
Matches are distributed among these distances:
51 4 0.00
52 877 0.99
53 4 0.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (52 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:1526563 original size:3 final size:3
Alignment explanation
Indices: 1526549--1526715 Score: 234
Period size: 3 Copynumber: 55.0 Consensus size: 3
1526539 GGTCCAGTTG
1526549 TAA TATA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TATA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
*
1526595 T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
*
1526643 TAA TATA TAA TAA TAA TAA TTA TAA -AA TAA TATA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
1526689 TAA TAA -AA TTAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA
1526716 AATGGATAAA
Statistics
Matches: 150, Mismatches: 4, Indels: 20
0.86 0.02 0.11
Matches are distributed among these distances:
2 8 0.05
3 125 0.83
4 17 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1527392 original size:22 final size:23
Alignment explanation
Indices: 1527359--1527401 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1527349 ATGGATGCAT
1527359 TGCATGATGCATCGATGCATTAG
1 TGCATGATGCATCGATGCATTAG
*
1527382 TGCA-GATGCATGGATGCATT
1 TGCATGATGCATCGATGCATT
1527402 GCAGGGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (23 bp):
TGCATGATGCATCGATGCATTAG
Found at i:1527412 original size:21 final size:21
Alignment explanation
Indices: 1527343--1527441 Score: 114
Period size: 21 Copynumber: 4.7 Consensus size: 21
1527333 TTAGATGTTT
*
1527343 GGATGTATGGATGCATTGCA-
1 GGATGCATGGATGCATTGCAG
* *
1527363 TGATGCATCGATGCATT--AG
1 GGATGCATGGATGCATTGCAG
1527382 TGCAGATGCATGGATGCATTGCAG
1 -G--GATGCATGGATGCATTGCAG
*
1527406 GGATGCATGGATGCACTGCAG
1 GGATGCATGGATGCATTGCAG
1527427 GGATGCATGGATGCA
1 GGATGCATGGATGCA
1527442 CTTTGACACC
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.01
20 14 0.21
21 34 0.51
22 15 0.22
23 1 0.01
24 2 0.03
ACGTcount: A:0.25, C:0.15, G:0.34, T:0.25
Consensus pattern (21 bp):
GGATGCATGGATGCATTGCAG
Found at i:1527582 original size:30 final size:30
Alignment explanation
Indices: 1527525--1527584 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1527515 AACTTTGAAT
1527525 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
1527555 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
1527585 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:1528930 original size:15 final size:14
Alignment explanation
Indices: 1528907--1528948 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1528897 ACATAACAAG
*
1528907 AAATTAATAAATAGA
1 AAATAAATAAATA-A
1528922 AAATAAATAAATAA
1 AAATAAATAAATAA
1528936 AAATAATATAAAT
1 AAATAA-ATAAAT
1528949 TATATAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:1529031 original size:69 final size:69
Alignment explanation
Indices: 1528949--1529184 Score: 241
Period size: 69 Copynumber: 3.3 Consensus size: 69
1528939 TAATATAAAT
* *
1528949 TATATAATATATATATTTCAAAAATATTTTGTTTAAACTATATATTAT-ATTTTTAAAAAAGTTT
1 TATATATTATATAT-TTTCAAAAATA-TTT-TTTAAACTATATATTATAATTTTTAAAAATGTTT
1529013 TTAAAAC
63 TTAAAAC
* * * *
1529020 TATATATTATATAGTTTTCGAAAA-ATGTTTTAAA-AATAT-TATATAAGTTTTCAAAAATGTTT
1 TATATATTATATA-TTTTCAAAAATATTTTTTAAACTATATAT-TATAA-TTTTTAAAAATGTTT
1529082 TTAAAAC
63 TTAAAAC
1529089 TATATATTATATAATTTTTCAAAAATA-TTTTTAAACTATATTATTATAATTTTTCAAAAATGTT
1 TATATATTATAT-A-TTTTCAAAAATATTTTTTAAACTATA-TATTATAATTTTT-AAAAATGTT
*
1529153 TTAAAAAAAC
62 TT--TAAAAC
*
1529163 TATATACTATA-AGTTTTCAAAA
1 TATATATTATATA-TTTTCAAAA
1529185 TGTTTTAAAA
Statistics
Matches: 139, Mismatches: 14, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
66 1 0.01
67 7 0.05
68 7 0.05
69 34 0.24
70 18 0.13
71 28 0.20
72 28 0.20
73 1 0.01
74 15 0.11
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (69 bp):
TATATATTATATATTTTCAAAAATATTTTTTAAACTATATATTATAATTTTTAAAAATGTTTTTA
AAAC
Found at i:1529063 original size:37 final size:35
Alignment explanation
Indices: 1528987--1529217 Score: 205
Period size: 36 Copynumber: 6.7 Consensus size: 35
1528977 TTGTTTAAAC
* *
1528987 TATATATTATAT--TTTT-AAAAAAGTTTTTAAAAC
1 TATATATTATATAGTTTTCAAAAATG-TTTTAAAAA
1529020 TATATATTATATAGTTTTCGAAAAATGTTTTAAAAA
1 TATATATTATATAGTTTTC-AAAAATGTTTTAAAAA
*
1529056 TAT-TA-TATA-AGTTTTCAAAAATGTTTTTAAAAC
1 TATATATTATATAGTTTTCAAAAATG-TTTTAAAAA
* * * *
1529089 TATATATTATATAATTTTTCAAAAATATTTTTAAAC
1 TATATATTATAT-AGTTTTCAAAAATGTTTTAAAAA
*
1529125 TATATTATTATA-ATTTTTCAAAAATGTTTTAAAAA
1 TATA-TATTATATAGTTTTCAAAAATGTTTTAAAAA
*
1529160 AACTATA-TACTATAAGTTTTC-AAAATGTTTTAAAAA
1 TA-TATATTA-TAT-AGTTTTCAAAAATGTTTTAAAAA
* *
1529196 -ATATA-AATAAATGTTTTCAAAA
1 TATATATTATATA-GTTTTCAAAA
1529218 CTATATATAT
Statistics
Matches: 169, Mismatches: 13, Indels: 31
0.79 0.06 0.15
Matches are distributed among these distances:
32 8 0.05
33 38 0.22
34 16 0.09
35 36 0.21
36 40 0.24
37 31 0.18
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (35 bp):
TATATATTATATAGTTTTCAAAAATGTTTTAAAAA
Found at i:1529207 original size:22 final size:22
Alignment explanation
Indices: 1529182--1529237 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1529172 TAAGTTTTCA
1529182 AAATGTTTTAAAAAATATAAAT
1 AAATGTTTTAAAAAATATAAAT
* * *
1529204 AAATGTTTTCAAAACTATATAT
1 AAATGTTTTAAAAAATATAAAT
* *
1529226 ATATCTTTTAAA
1 AAATGTTTTAAA
1529238 CTACTTTCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (22 bp):
AAATGTTTTAAAAAATATAAAT
Found at i:1530049 original size:13 final size:14
Alignment explanation
Indices: 1530031--1530059 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1530021 GATAACTCAT
1530031 ATATCAT-TATAAA
1 ATATCATATATAAA
1530044 ATATCATATATAAA
1 ATATCATATATAAA
1530058 AT
1 AT
1530060 TAAGTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATCATATATAAA
Found at i:1534568 original size:13 final size:14
Alignment explanation
Indices: 1534534--1534571 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1534524 ATATAATTAT
*
1534534 AATTTATAATAACA
1 AATTTAAAATAACA
*
1534548 AATATAAAATAA-A
1 AATTTAAAATAACA
1534561 AATTTAAAATA
1 AATTTAAAATA
1534572 CAATTATACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
AATTTAAAATAACA
Found at i:1538783 original size:17 final size:18
Alignment explanation
Indices: 1538761--1538799 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1538751 ATTGTTGAAC
1538761 ACCGCCA-TTAACCATTG
1 ACCGCCACTTAACCATTG
1538778 ACCGCCACCGTTAACCATTG
1 ACCGCCA-C-TTAACCATTG
1538798 AC
1 AC
1538800 TTTGTAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
20 12 0.63
ACGTcount: A:0.28, C:0.38, G:0.13, T:0.21
Consensus pattern (18 bp):
ACCGCCACTTAACCATTG
Found at i:1544473 original size:23 final size:23
Alignment explanation
Indices: 1544447--1544522 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
1544437 TTAGGTTTTA
1544447 TCTATTCAGCCTAAATTTTGTGT
1 TCTATTCAGCCTAAATTTTGTGT
* * * ** *
1544470 TCTAATTTA-CTTAGTATTAGGTTTT
1 TCT-ATTCAGCCTA-AATTTTG-TGT
1544495 ATCTATTCAGCCTAAATTTTGTGT
1 -TCTATTCAGCCTAAATTTTGTGT
1544519 TCTA
1 TCTA
1544523 ATTTACTTAG
Statistics
Matches: 36, Mismatches: 12, Indels: 10
0.62 0.21 0.17
Matches are distributed among these distances:
23 10 0.28
24 10 0.28
25 10 0.28
26 6 0.17
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (23 bp):
TCTATTCAGCCTAAATTTTGTGT
Found at i:1544486 original size:49 final size:49
Alignment explanation
Indices: 1544374--1544546 Score: 258
Period size: 49 Copynumber: 3.5 Consensus size: 49
1544364 ATAATAAAAA
* * * * *
1544374 AATTTACTTACG-ATTAGGTTTTATTTGTTCATCCTAAATTCTAGTGTTGT
1 AATTTACTTA-GTATTAGGTTTTATCTATTCAGCCTAAATT-TTGTGTTCT
1544424 AATTTACTTAGTATTAGGTTTTATCTATTCAGCCTAAATTTTGTGTTCT
1 AATTTACTTAGTATTAGGTTTTATCTATTCAGCCTAAATTTTGTGTTCT
1544473 AATTTACTTAGTATTAGGTTTTATCTATTCAGCCTAAATTTTGTGTTCT
1 AATTTACTTAGTATTAGGTTTTATCTATTCAGCCTAAATTTTGTGTTCT
* *
1544522 AATTTACTTAGGATTAGATTTTATC
1 AATTTACTTAGTATTAGGTTTTATC
1544547 CTTTTAAAAG
Statistics
Matches: 115, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
49 80 0.70
50 35 0.30
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.50
Consensus pattern (49 bp):
AATTTACTTAGTATTAGGTTTTATCTATTCAGCCTAAATTTTGTGTTCT
Found at i:1544841 original size:24 final size:23
Alignment explanation
Indices: 1544814--1544878 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
1544804 CTCGATAATC
1544814 TGTTCGTTTATGTTCATTCATAT
1 TGTTCGTTTATGTTCATTCATAT
* * * *
1544837 ATGTTTGTTTATGTTCGTTTATGT
1 -TGTTCGTTTATGTTCATTCATAT
*
1544861 TCGTTCGTTTATTTTCAT
1 T-GTTCGTTTATGTTCAT
1544879 CCCAATCTCC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.14, C:0.11, G:0.15, T:0.60
Consensus pattern (23 bp):
TGTTCGTTTATGTTCATTCATAT
Found at i:1544851 original size:10 final size:10
Alignment explanation
Indices: 1544836--1544865 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1544826 TTCATTCATA
*
1544836 TATGTTTGTT
1 TATGTTCGTT
1544846 TATGTTCGTT
1 TATGTTCGTT
1544856 TATGTTCGTT
1 TATGTTCGTT
1544866 CGTTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.07, G:0.20, T:0.63
Consensus pattern (10 bp):
TATGTTCGTT
Found at i:1548190 original size:2 final size:2
Alignment explanation
Indices: 1548183--1548231 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1548173 TATGGCAGCA
1548183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1548225 AT AT AT A
1 AT AT AT A
1548232 ATGGTGATAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1548842 original size:20 final size:20
Alignment explanation
Indices: 1548792--1548835 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1548782 TGCTGGTTAT
*
1548792 ATGGAGCTTCTTGGACGTGC
1 ATGGAGCTTCTTGGACGTGA
1548812 ATGGAGCTTCTTGGACGTGA
1 ATGGAGCTTCTTGGACGTGA
1548832 ATGG
1 ATGG
1548836 GTCTTCTCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (20 bp):
ATGGAGCTTCTTGGACGTGA
Found at i:1551884 original size:2 final size:2
Alignment explanation
Indices: 1551877--1551925 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1551867 TGTCAGCGGA
1551877 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1551919 AT AT AT A
1 AT AT AT A
1551926 ATGGTGATAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1555380 original size:79 final size:79
Alignment explanation
Indices: 1555256--1555417 Score: 315
Period size: 79 Copynumber: 2.1 Consensus size: 79
1555246 TATTAAATAA
1555256 ATATTGTTCGTGCGAGCAAGTTACTTTTATAAATCATTATTAAGATAGATTAAATCATAAATGAA
1 ATATTGTTCGTGCGAGCAAGTTACTTTTATAAATCATTATTAAGATAGATTAAATCATAAATGAA
1555321 AAGATTTAATAAAT
66 AAGATTTAATAAAT
1555335 ATATTGTTCGTGCGAGCAAGTTACTTTTATAAATCATTATTAAGATAGATTAAATCATAAATGAA
1 ATATTGTTCGTGCGAGCAAGTTACTTTTATAAATCATTATTAAGATAGATTAAATCATAAATGAA
*
1555400 AAGCTTTAATAAAT
66 AAGATTTAATAAAT
1555414 ATAT
1 ATAT
1555418 AAATATAACT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 82 1.00
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (79 bp):
ATATTGTTCGTGCGAGCAAGTTACTTTTATAAATCATTATTAAGATAGATTAAATCATAAATGAA
AAGATTTAATAAAT
Found at i:1556225 original size:39 final size:38
Alignment explanation
Indices: 1556182--1556314 Score: 160
Period size: 39 Copynumber: 3.4 Consensus size: 38
1556172 GGTTTTCTCC
* * * *
1556182 ATTTGTCTGAAGACGCTATGTAGTCGTGGGGTCTTCTTT
1 ATTTGCCTGAAGACGCTATGCAGTCATGGAGTCTTC-TT
1556221 ATTTGCCTGAAGACG-TCATGCAGTCATGGAGTCTTCATT
1 ATTTGCCTGAAGACGCT-ATGCAGTCATGGAGTCTTC-TT
* *
1556260 ATTTGCCTGAAGACGCCATGCAGTCATGGAGTCTTCAT
1 ATTTGCCTGAAGACGCTATGCAGTCATGGAGTCTTCTT
*
1556298 ATTTGACTTGAAGACGC
1 ATTTG-CCTGAAGACGC
1556315 GTGAAACACC
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
38 7 0.08
39 76 0.92
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (38 bp):
ATTTGCCTGAAGACGCTATGCAGTCATGGAGTCTTCTT
Found at i:1560161 original size:3 final size:3
Alignment explanation
Indices: 1560141--1560328 Score: 77
Period size: 3 Copynumber: 60.7 Consensus size: 3
1560131 CATTGGTCAA
* * **
1560141 ATT ACT ATT ATT ACTT ATT ATT ATT ATT ATCT ATTT ATT A-C ATT AGA
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT AT-T A-TT ATT ATT ATT ATT
* * *
1560188 ATT ATCT -TT TTT A-T GTT ATT ACT ATT ATTT ATT ATT ATT ATCT ATTT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT AT-T A-TT
* ** * *
1560235 ATT -TT A-C ATT AGA ATT ATCT -TT ATAT ATT ATT ATT ATT ACT CTT
1 ATT ATT ATT ATT ATT ATT AT-T ATT AT-T ATT ATT ATT ATT ATT ATT
*
1560279 ATT AGT ATTT ATT ATT ATAT ATT ATT -TGT ATAT ATT ATAT ATT ATT
1 ATT ATT A-TT ATT ATT AT-T ATT ATT AT-T AT-T ATT AT-T ATT ATT
1560325 -TT AT
1 ATT AT
1560329 ATACTCTCTT
Statistics
Matches: 138, Mismatches: 26, Indels: 42
0.67 0.13 0.20
Matches are distributed among these distances:
2 10 0.07
3 95 0.69
4 31 0.22
5 2 0.01
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1560164 original size:13 final size:14
Alignment explanation
Indices: 1560145--1560181 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1560135 GGTCAAATTA
1560145 CTATTATTACTTAT
1 CTATTATTACTTAT
1560159 -TATTATTA-TTAT
1 CTATTATTACTTAT
1560171 CTATTTATTAC
1 CTA-TTATTAC
1560182 ATTAGAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.20
13 10 0.50
14 6 0.30
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (14 bp):
CTATTATTACTTAT
Found at i:1560220 original size:58 final size:60
Alignment explanation
Indices: 1560149--1560287 Score: 185
Period size: 58 Copynumber: 2.3 Consensus size: 60
1560139 AAATTACTAT
* * *
1560149 TATTACTTATTATTATTATTATCTATTTA-TTACATTAGAATTATCTTTTTTATGTTATTAC
1 TATTAC-TCTTATTATTATTATCTATTTATTTACATTAGAATTATC-TTTATATATTATTAC
*
1560210 TATTA-T-TTATTATTATTATCTATTTATTTTACATTAGAATTATCTTTATATATTATTAT
1 TATTACTCTTATTATTATTATCTATTTA-TTTACATTAGAATTATCTTTATATATTATTAC
*
1560269 TATTACTCTTATTAGTATT
1 TATTACTCTTATTATTATT
1560288 TATTATTATA
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
58 20 0.29
59 18 0.26
60 17 0.24
61 15 0.21
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (60 bp):
TATTACTCTTATTATTATTATCTATTTATTTACATTAGAATTATCTTTATATATTATTAC
Found at i:1560225 original size:10 final size:10
Alignment explanation
Indices: 1560203--1560324 Score: 56
Period size: 10 Copynumber: 11.8 Consensus size: 10
1560193 CTTTTTTATG
*
1560203 TTATTACTA-
1 TTATTATTAT
1560212 TTATTTATTA-
1 TTA-TTATTAT
1560222 TTATTATCTAT
1 TTATTAT-TAT
*
1560233 TTATT-TTACA
1 TTATTATTA-T
**
1560243 TTAGAATTAT
1 TTATTATTAT
1560253 CTTTATATATTA-
1 --TTAT-TATTAT
1560265 TTATTATTACT
1 TTATTATTA-T
*
1560276 CTTATTAGTAT
1 -TTATTATTAT
1560287 TTATTATTAT
1 TTATTATTAT
*
1560297 ATATTATT-T
1 TTATTATTAT
*
1560306 GTATATATTAT
1 TTAT-TATTAT
*
1560317 ATATTATT
1 TTATTATT
1560325 TTATATACTC
Statistics
Matches: 88, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
9 18 0.20
10 42 0.48
11 13 0.15
12 11 0.12
13 4 0.05
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (10 bp):
TTATTATTAT
Found at i:1560290 original size:25 final size:24
Alignment explanation
Indices: 1560262--1560328 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
1560252 TCTTTATATA
*
1560262 TTATTATTATTACTCTTATTAGTAT
1 TTATTATTATTA-TATTATTAGTAT
*
1560287 TTATTATTA-TATATTATTTGTAT
1 TTATTATTATTATATTATTAGTAT
* *
1560310 ATATTATATATTATTTTAT
1 TTATTAT-TATTATATTAT
1560329 ATACTCTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.44
24 4 0.11
25 16 0.44
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (24 bp):
TTATTATTATTATATTATTAGTAT
Found at i:1560314 original size:20 final size:19
Alignment explanation
Indices: 1560255--1560331 Score: 79
Period size: 19 Copynumber: 4.0 Consensus size: 19
1560245 AGAATTATCT
1560255 TTATATATTATTATTAT-TA
1 TTATATATTATT-TTATATA
* *
1560274 CTCT-TATTAGTATTTAT-TA
1 TTATATATTA-T-TTTATATA
1560293 TTATATATTATTTGTATATA
1 TTATATATTATTT-TATATA
1560313 TTATATATTATTTTATATA
1 TTATATATTATTTTATATA
1560332 CTCTCTTCGT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.14
19 21 0.43
20 21 0.43
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (19 bp):
TTATATATTATTTTATATA
Found at i:1560329 original size:10 final size:10
Alignment explanation
Indices: 1560255--1560330 Score: 68
Period size: 10 Copynumber: 7.8 Consensus size: 10
1560245 AGAATTATCT
1560255 TTATATATTA
1 TTATATATTA
1560265 TTAT-TATTA
1 TTATATATTA
* *
1560274 CTCT-TATTA
1 TTATATATTA
* *
1560283 GTATTTATTA
1 TTATATATTA
1560293 TTATATATTA
1 TTATATATTA
*
1560303 TT-TGTATATA
1 TTATATAT-TA
1560313 TTATATATTA
1 TTATATATTA
*
1560323 TTTTATAT
1 TTATATAT
1560331 ACTCTCTTCG
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
9 18 0.33
10 32 0.59
11 4 0.07
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (10 bp):
TTATATATTA
Found at i:1561634 original size:24 final size:24
Alignment explanation
Indices: 1561607--1561676 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
1561597 AAACGAAGAT
1561607 ATCATAAATCAAAACAGAATTCAG
1 ATCATAAATCAAAACAGAATTCAG
* * *
1561631 ATCAT--ATCAGAACAGAATCCAT
1 ATCATAAATCAAAACAGAATTCAG
* *
1561653 ATCAGAAATCATAACAGAATTCAG
1 ATCATAAATCAAAACAGAATTCAG
1561677 GTATGTATCA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 18 0.49
24 19 0.51
ACGTcount: A:0.50, C:0.19, G:0.10, T:0.21
Consensus pattern (24 bp):
ATCATAAATCAAAACAGAATTCAG
Found at i:1561672 original size:46 final size:46
Alignment explanation
Indices: 1561605--1561709 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 46
1561595 GTAAACGAAG
*
1561605 ATATCATAAATCAAAACAGAATTCA-G-ATCATATCAGAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTCAGGTAT-ATATCAGAACA-AATCC
* * *
1561651 ATATCAGAAATCATAACAGAATTCAGGTATGTATCAGAACAAATTC
1 ATATCAGAAATCAAAACAGAATTCAGGTATATATCAGAACAAATCC
1561697 A-AGTCAGAAATCA
1 ATA-TCAGAAATCA
1561710 GATAAATATT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
45 1 0.02
46 38 0.73
47 11 0.21
48 2 0.04
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (46 bp):
ATATCAGAAATCAAAACAGAATTCAGGTATATATCAGAACAAATCC
Found at i:1561709 original size:23 final size:24
Alignment explanation
Indices: 1561612--1561711 Score: 70
Period size: 22 Copynumber: 4.3 Consensus size: 24
1561602 AAGATATCAT
*
1561612 AAATCAAAACAGAATTC-AGATC--
1 AAATCAGAACAGAATTCAAG-TCAG
* *
1561634 ATATCAGAACAGAATCCATA-TCAG
1 AAATCAGAACAGAATTCA-AGTCAG
* *
1561658 AAATCATAACAGAATTCAGGT-ATG
1 AAATCAGAACAGAATTCAAGTCA-G
*
1561682 -TATCAGAACA-AATTCAAGTCAG
1 AAATCAGAACAGAATTCAAGTCAG
1561704 AAATCAGA
1 AAATCAGA
1561712 TAAATATTTA
Statistics
Matches: 59, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
22 25 0.42
23 16 0.27
24 18 0.31
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAAGTCAG
Found at i:1563566 original size:18 final size:18
Alignment explanation
Indices: 1563545--1563587 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1563535 TAAAAGTCAT
1563545 CTGAACCATAATCAATTA
1 CTGAACCATAATCAATTA
1563563 CTGAACCATAATCAATTA
1 CTGAACCATAATCAATTA
1563581 CTGAACC
1 CTGAACC
1563588 TTTTTACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.26
Consensus pattern (18 bp):
CTGAACCATAATCAATTA
Found at i:1564405 original size:13 final size:13
Alignment explanation
Indices: 1564401--1564437 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
1564391 GTAAACGGGT
1564401 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
1564414 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
1564427 CGGGTCGGGTC
1 CGGGTCGGGTC
1564438 GGGTTGTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.11, C:0.24, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1564410 original size:31 final size:31
Alignment explanation
Indices: 1564375--1564441 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
1564365 CAATGGTCAA
*
1564375 CGGGTCAACAGGTTGGGTAAACGGGTCGGGT
1 CGGGTCAACAGGTCGGGTAAACGGGTCGGGT
* *
1564406 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACAGGTCGGGTAAACGGGTCGGGT
1564437 CGGGT
1 CGGGT
1564442 TGTGACCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.15, C:0.19, G:0.48, T:0.18
Consensus pattern (31 bp):
CGGGTCAACAGGTCGGGTAAACGGGTCGGGT
Found at i:1564441 original size:18 final size:18
Alignment explanation
Indices: 1564389--1564424 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1564379 TCAACAGGTT
1564389 GGGTAAACGGGTCGGGTC
1 GGGTAAACGGGTCGGGTC
*
1564407 GGGTCAACGGGTCGGGTC
1 GGGTAAACGGGTCGGGTC
1564425 AACGGGTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.19, G:0.50, T:0.17
Consensus pattern (18 bp):
GGGTAAACGGGTCGGGTC
Found at i:1568198 original size:22 final size:22
Alignment explanation
Indices: 1568151--1568250 Score: 85
Period size: 23 Copynumber: 4.5 Consensus size: 22
1568141 ATAATTTGCA
* * *
1568151 CCGAAGTACCACATA-ATTATC
1 CCGAAGGACCACATATTTTGTC
* * *
1568172 TCGAATGACCAAATATTTTGTC
1 CCGAAGGACCACATATTTTGTC
*
1568194 CCGAAGGACCACATAGGTTTGTC
1 CCGAAGGACCACATA-TTTTGTC
*
1568217 CCAAAGGACCACATAATTTTGTC
1 CCGAAGGACCACAT-ATTTTGTC
* *
1568240 TCGAATGACCA
1 CCGAAGGACCA
1568251 TATAGAACCC
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
21 11 0.18
22 16 0.26
23 33 0.54
24 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (22 bp):
CCGAAGGACCACATATTTTGTC
Found at i:1575022 original size:23 final size:22
Alignment explanation
Indices: 1574951--1575023 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
1574941 CACCGAAGTG
*
1574951 CCACATA-ATTGTCTCT-AAGGA
1 CCACATAGTTTGTC-CTGAAGGA
* * *
1574972 CCACATATTTTAT-CTCGAATGA
1 CCACATAGTTTGTCCT-GAAGGA
1574994 CCACATAGGTTTGTCCTGAAGGA
1 CCACATA-GTTTGTCCTGAAGGA
1575017 CCACATA
1 CCACATA
1575024 ATTTTATCCC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 2 0.05
21 7 0.17
22 14 0.34
23 16 0.39
24 2 0.05
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (22 bp):
CCACATAGTTTGTCCTGAAGGA
Found at i:1575037 original size:23 final size:23
Alignment explanation
Indices: 1574967--1575040 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
1574957 AATTGTCTCT
*
1574967 AAGGACCACAT-ATTTTATCTCG
1 AAGGACCACATAATTTTATCCCG
* ** * *
1574989 AATGACCACATAGGTTTGTCCTG
1 AAGGACCACATAATTTTATCCCG
1575012 AAGGACCACATAATTTTATCCCG
1 AAGGACCACATAATTTTATCCCG
1575035 AAGGAC
1 AAGGAC
1575041 TATATAGAAC
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
22 10 0.25
23 30 0.75
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (23 bp):
AAGGACCACATAATTTTATCCCG
Done.