Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 29
Found at i:1140709 original size:60 final size:59
Alignment explanation
Indices: 1140601--1140756 Score: 156
Period size: 61 Copynumber: 2.6 Consensus size: 59
1140591 ACTAAAACCT
* ** *
1140601 GTTGCGAAATTAAATTCGTGTTGCGAA-TTCAAAAATCGAGTTGTGAATTTGAAATTC-A
1 GTTGCGAATTTAAATTCGTGTTGCGAATTTGGAAAATCGAGTTGGGAATTTG-AATTCTA
* * *
1140659 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGGAAAA-CGCGTTGGGAATTTGACTTCTTT
1 GTTGCGAATTT-AAATTC-GTGTTGCGAATTTGGAAAATCGAGTTGGGAATTTGAATTC-TA
* *
1140720 GTTGTGATTTTCTAAATTCGTGTTGCGAATTTGGAAA
1 GTTGCGA-ATT-TAAATTCGTGTTGCGAATTTGGAAA
1140757 CTGGGTATTG
Statistics
Matches: 82, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
58 10 0.12
59 10 0.12
60 23 0.28
61 30 0.37
62 8 0.10
63 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (59 bp):
GTTGCGAATTTAAATTCGTGTTGCGAATTTGGAAAATCGAGTTGGGAATTTGAATTCTA
Found at i:1144386 original size:30 final size:31
Alignment explanation
Indices: 1144332--1144399 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
1144322 TGTATATATT
* * *
1144332 TTAACTTGATCCCAAGATTTTAGATAAGATA
1 TTAATTTGATCCCAAGACTTTAGATAAAATA
*
1144363 TTAATTTGATCCTAA-ACTTTAGATAAAATA
1 TTAATTTGATCCCAAGACTTTAGATAAAATA
*
1144393 CTAATTT
1 TTAATTT
1144400 AACCTCTGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (31 bp):
TTAATTTGATCCCAAGACTTTAGATAAAATA
Found at i:1145043 original size:16 final size:16
Alignment explanation
Indices: 1144995--1145043 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1144985 TTTGATTTAG
*
1144995 TAAAATATTTGAATAAT
1 TAAAATATTT-AATATT
*
1145012 TAAAATTATTTTATATT
1 TAAAA-TATTTAATATT
*
1145029 TTAAATATTTAATAT
1 TAAAATATTTAATAT
1145044 AGTAACTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 9 0.33
17 13 0.48
18 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TAAAATATTTAATATT
Found at i:1145298 original size:11 final size:9
Alignment explanation
Indices: 1145262--1145293 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1145252 ATAAGTTTGA
*
1145262 TATACTAAT
1 TATATTAAT
1145271 TATATTAAT
1 TATATTAAT
1145280 TATATTAAT
1 TATATTAAT
1145289 TATAT
1 TATAT
1145294 ATTAAATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (9 bp):
TATATTAAT
Found at i:1146444 original size:2 final size:2
Alignment explanation
Indices: 1146437--1146505 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1146427 TTTGCATACA
1146437 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
1146479 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 A
1146506 CGAGTCTAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1147411 original size:2 final size:2
Alignment explanation
Indices: 1147404--1147623 Score: 128
Period size: 2 Copynumber: 116.0 Consensus size: 2
1147394 TTTTGTAAGC
* *
1147404 AT AT AT AT AT AT AT -T AT AT -T AT TT A- AGT GT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * * *
1147443 AT AT AT AT AT AGT AT GT AG A- AT GT AT AT TT AT -T TT AT -T AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
** *
1147483 CC AT AT -T AT GT A- 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
* ** * * *
1147523 AT AT AT AT AT AT AT AT AT AT AC AT GC GT A- AC ACT -T AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
1147564 AT AT AT A- AT -T AT TT TT AT -T A- AT TT AC 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
1147602 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1147624 TTATGCATAT
Statistics
Matches: 167, Mismatches: 33, Indels: 36
0.71 0.14 0.15
Matches are distributed among these distances:
1 15 0.09
2 150 0.90
3 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1155892 original size:2 final size:2
Alignment explanation
Indices: 1155885--1155909 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1155875 CCTGTATTTG
1155885 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 T
1155910 CTTTTCATTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1159412 original size:12 final size:12
Alignment explanation
Indices: 1159397--1159446 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1159387 GAAAAAAATG
1159397 AAAAAGAAAAGA
1 AAAAAGAAAAGA
*
1159409 AAAAAGGAAAGA
1 AAAAAGAAAAGA
* *
1159421 AAAATG--AGGA
1 AAAAAGAAAAGA
1159431 AAAAAGAAAAAGA
1 AAAAAG-AAAAGA
1159444 AAA
1 AAA
1159447 TAAAAGGAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
10 8 0.27
12 16 0.53
13 6 0.20
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:1159451 original size:27 final size:29
Alignment explanation
Indices: 1159403--1159456 Score: 69
Period size: 27 Copynumber: 1.9 Consensus size: 29
1159393 AATGAAAAAG
*
1159403 AAAAGAAAAAAGGAAAGAAAAATGAGGAA
1 AAAAGAAAAAAGGAAAGAAAAAGGAGGAA
1159432 AAAAG-AAAAA-GAAA-ATAAAAGGAGG
1 AAAAGAAAAAAGGAAAGA-AAAAGGAGG
1159457 GTTCAAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.04
27 12 0.52
28 5 0.22
29 5 0.22
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (29 bp):
AAAAGAAAAAAGGAAAGAAAAAGGAGGAA
Found at i:1160459 original size:47 final size:45
Alignment explanation
Indices: 1160347--1160460 Score: 104
Period size: 47 Copynumber: 2.5 Consensus size: 45
1160337 CGATCCAATC
* * * *
1160347 TTCCCTGAGTGACAGCGAAATGGATCAACTCCTCCAGATCTGATA
1 TTCCCTGAGTAACAGCGGAATAGATCAACTACTCCAGATCTGATA
* * * * * *
1160392 TTCCCTTAG-AAGAAGTGGAATAGATCACCATATTCCAAGATTTGATA
1 TTCCCTGAGTAA-CAGCGGAATAGATCAAC-TACTCC-AGATCTGATA
1160439 TTCCCTGAGTAACAGCGGAATA
1 TTCCCTGAGTAACAGCGGAATA
1160461 AGTCTACCTC
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
44 1 0.02
45 20 0.38
46 4 0.08
47 25 0.48
48 2 0.04
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (45 bp):
TTCCCTGAGTAACAGCGGAATAGATCAACTACTCCAGATCTGATA
Found at i:1160682 original size:109 final size:111
Alignment explanation
Indices: 1160365--1160791 Score: 639
Period size: 111 Copynumber: 3.9 Consensus size: 111
1160355 GTGACAGCGA
* *
1160365 AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAATAGATCACCATATTCCAA
1 AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACCCTATTCCAA
* * *
1160430 GATTTGATATTCCCTGAGTAACAGCGGAATAAGTCTACCTCGATTC
66 GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTC
* * *
1160476 AATGGATTAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACATATCACTCTATTCCAA
1 AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACCCTATTCCAA
*
1160541 GATTTGATATTCCATGAGTGACAGCGGAACAAGTCTACCCCGATTC
66 GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTC
1160587 AATGGATCAACTCCTCCAGATCTGATATT-CCTTAGAAGAAGTGGAACA-ATCACCCTATTCCAA
1 AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACCCTATTCCAA
* *
1160650 GATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCCCAATTC
66 GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTC
* *
1160696 AATGGATCAACTCC-CCAGATCTGATATTCCCTTTAGAAGAAGTGGAATAGATC-CCTCTCATCC
1 AATGGATCAACTCCTCCAGATCTGATATTCCC-TTAGAAGAAGTGGAACAGATCACC-CT-ATTC
* * *
1160759 CCAGATTTGATA-TCCCTTGAGTGATAGTGGAAC
63 CAAGATTTGATATTCCC-TGAGTGACAGCGGAAC
1160792 TGATCATTTA
Statistics
Matches: 292, Mismatches: 18, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
108 14 0.05
109 73 0.25
110 37 0.13
111 139 0.48
112 29 0.10
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (111 bp):
AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACCCTATTCCAA
GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTC
Found at i:1162425 original size:2 final size:2
Alignment explanation
Indices: 1162418--1162487 Score: 85
Period size: 2 Copynumber: 36.5 Consensus size: 2
1162408 TTTTGTAAGC
* *
1162418 AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT A- AGT GT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
1162458 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1162488 GTATGTAGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
1 4 0.07
2 55 0.93
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1164222 original size:69 final size:69
Alignment explanation
Indices: 1164092--1164223 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 69
1164082 GGTTACGACA
* * **
1164092 GAAACATTATTAGGCGCTACCGGTTTTGTTATTATTGGGCGTTTTACCGGATTTTGATAAAAATG
1 GAAACATTATTAGGCGCTACCAGTTTTATTATTATTGGGCGTTTTACCGGATAATGATAAAAATG
1164157 ACCG
66 ACCG
* * * *
1164161 GAAACATTATTAGGCGCTACTAGTTTTATTATTGTTGGGCATTTTTACCGGA-AATGTTAAAAA
1 GAAACATTATTAGGCGCTACCAGTTTTATTATTATTGGGC-GTTTTACCGGATAATGATAAAAA
1164224 ATGATGTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
69 44 0.81
70 10 0.19
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (69 bp):
GAAACATTATTAGGCGCTACCAGTTTTATTATTATTGGGCGTTTTACCGGATAATGATAAAAATG
ACCG
Found at i:1164932 original size:21 final size:21
Alignment explanation
Indices: 1164906--1164947 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1164896 TGGGTCAGTG
1164906 ACTTAAATGC-AAATTTTGAAA
1 ACTT-AATGCTAAATTTTGAAA
*
1164927 ACTTAATGCTCAATTTTGAAA
1 ACTTAATGCTAAATTTTGAAA
1164948 TAAGTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (21 bp):
ACTTAATGCTAAATTTTGAAA
Found at i:1165124 original size:33 final size:33
Alignment explanation
Indices: 1165077--1165144 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
1165067 AGGAATTAAC
*
1165077 TCACGTGGAAGAGGAAAGAAAGGCCAAGTTGAT
1 TCACATGGAAGAGGAAAGAAAGGCCAAGTTGAT
1165110 TCACATGGAAGAGGAAAGAAAGGCCAAGTTGAT
1 TCACATGGAAGAGGAAAGAAAGGCCAAGTTGAT
1165143 TC
1 TC
1165145 CAGAGTTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.13, G:0.31, T:0.16
Consensus pattern (33 bp):
TCACATGGAAGAGGAAAGAAAGGCCAAGTTGAT
Found at i:1166586 original size:18 final size:17
Alignment explanation
Indices: 1166559--1166592 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1166549 TAAGTGTAGT
*
1166559 GATTATATGATCATAAGA
1 GATTAAATGAT-ATAAGA
1166577 GATTAAATGATATAAG
1 GATTAAATGATATAAG
1166593 TTATATGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (17 bp):
GATTAAATGATATAAGA
Found at i:1166830 original size:18 final size:18
Alignment explanation
Indices: 1166807--1166913 Score: 169
Period size: 18 Copynumber: 5.9 Consensus size: 18
1166797 AGGGATTTAC
*
1166807 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
*
1166825 AGTGGTCCTTAGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1166843 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAT
1166861 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1166879 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAT
*
1166897 AGTGGTTCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1166914 AACATTCAGT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 82 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1168868 original size:19 final size:19
Alignment explanation
Indices: 1168846--1168890 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1168836 GGATTATTTC
1168846 TGAATGGGAAGAATATATA
1 TGAATGGGAAGAATATATA
*
1168865 TGAATGGGAAGAATGTATA
1 TGAATGGGAAGAATATATA
1168884 TGAATGG
1 TGAATGG
1168891 TTCGATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (19 bp):
TGAATGGGAAGAATATATA
Found at i:1170478 original size:21 final size:21
Alignment explanation
Indices: 1170452--1170493 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1170442 TGGGTCAGTG
1170452 ACTTAAATGC-AAATTTTGAAA
1 ACTT-AATGCTAAATTTTGAAA
*
1170473 ACTTAATGCTCAATTTTGAAA
1 ACTTAATGCTAAATTTTGAAA
1170494 TAAGTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (21 bp):
ACTTAATGCTAAATTTTGAAA
Found at i:1170663 original size:33 final size:33
Alignment explanation
Indices: 1170621--1170687 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1170611 TAAGGAATTA
1170621 ACTCACGTGGAAGAGGAAAGAAAGGCCAAGTTG
1 ACTCACGTGGAAGAGGAAAGAAAGGCCAAGTTG
*
1170654 ACTCACGTGGAAGAGGAAATAAAGGCCAAGTTG
1 ACTCACGTGGAAGAGGAAAGAAAGGCCAAGTTG
1170687 A
1 A
1170688 TTCCAGAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.31, T:0.13
Consensus pattern (33 bp):
ACTCACGTGGAAGAGGAAAGAAAGGCCAAGTTG
Found at i:1172357 original size:18 final size:18
Alignment explanation
Indices: 1172334--1172380 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
1172324 AGGGATTTAC
*
1172334 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAA
1172352 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAA
1172370 AGTGGTCCTTC
1 AGTGGTCCTTC
1172381 AAGAAAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.23, G:0.32, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAA
Found at i:1186080 original size:173 final size:172
Alignment explanation
Indices: 1185867--1186215 Score: 441
Period size: 173 Copynumber: 2.0 Consensus size: 172
1185857 TTTGTCAAAA
* * *
1185867 CGCCGCTAAAGTACTAATTTGTTACGGCGTTTATTAAAAAACGTCCCTATATGTCTACAGTTAAT
1 CGCCGCTAAAGTACTAATCTGTTACGACGTTTATTAAAAAACGTCCCTATATGTCTAAAGTTAAT
* * * * * ***
1185932 GACGTTTAAACAAAAAACATCTGC-GTCGTTTTTTGTCAAAACGCCACTAATGATTTTAATAATT
66 GACGTTCAAACAAAAAACATCTGCGGT-ATTTTTTGACAAAACACCACTAAAG-TACAAATAATT
**
1185996 TACTG-CGTTTGTTACCAAAACGCCGCTATATGTTAACCCTCTTG
129 T-CTGTCGTTTGTTACCAAAACAACGCTATATGTTAACCCTCTTG
* * * *
1186040 CGCCGCTATAGTACTAATCTGTTGCGACGTTTATTAAAAAATGTCGCTATATGTCTAAAGTTAAT
1 CGCCGCTAAAGTACTAATCTGTTACGACGTTTATTAAAAAACGTCCCTATATGTCTAAAGTTAAT
* * * * * *
1186105 GGCGTTCAAATACAAAACATTTGCGGTATTTTTTGACAAAACACCACTAAAGTACAAATTATTTG
66 GACGTTCAAACAAAAAACATCTGCGGTATTTTTTGACAAAACACCACTAAAGTACAAATAATTTC
*
1186170 TGTCGTTTGTTACCAAAACAATGCTATATGTTAACCCTCTTG
131 TGTCGTTTGTTACCAAAACAACGCTATATGTTAACCCTCTTG
1186212 CGCC
1 CGCC
1186216 ATTTTCGTCA
Statistics
Matches: 150, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
171 2 0.01
172 48 0.32
173 98 0.65
174 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (172 bp):
CGCCGCTAAAGTACTAATCTGTTACGACGTTTATTAAAAAACGTCCCTATATGTCTAAAGTTAAT
GACGTTCAAACAAAAAACATCTGCGGTATTTTTTGACAAAACACCACTAAAGTACAAATAATTTC
TGTCGTTTGTTACCAAAACAACGCTATATGTTAACCCTCTTG
Found at i:1186388 original size:190 final size:189
Alignment explanation
Indices: 1186048--1186402 Score: 496
Period size: 190 Copynumber: 1.9 Consensus size: 189
1186038 TGCGCCGCTA
* *
1186048 TAGTACTAATCTGTTGCGACGTTTATTAAAAAATGTCGCTATATGTCTAAAGTTAATGGCGTTCA
1 TAGTACTAATCTGTTGCGACGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGGCGTTCA
* ** * * * *
1186113 AATACAAAACATTTGCGGTATTTTTTGACAAAACACCACTAAAGTACAAATTATTTGTGTCGTTT
66 AATAAAAAACATTCACAGCATTTTTTGACAAAACACCACTAAACTACAAATTATTTGTGGCGTTT
* * * *
1186178 GTTACCAAAACAATGCTATATGTTAACCCTCTTGCGCCATTTTCGTCAAAACGCTGCTG
131 GTTACCAAAACAACGCTATATATAAACCCTATTGCGCCATTTTCGTCAAAACGCTGCTG
* * * *
1186237 TAGTACTAATCTGTTGCGGCGTTTATTAAAACACGCCGTTATATGTCTAAAGTTAATGGCGTTTA
1 TAGTACTAATCTGTTGCGACGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGGCGTTCA
* *
1186302 AATAAAAAAACATTCACAGCGTTTTTTGACAAAACGA-CACTAAACTACGAATTATTTGTGGCGT
66 AAT-AAAAAACATTCACAGCATTTTTTGACAAAAC-ACCACTAAACTACAAATTATTTGTGGCGT
**
1186366 TTGTTACCAAAACGCCGCTATATATAAACCCTATTGC
129 TTGTTACCAAAACAACGCTATATATAAACCCTATTGC
1186403 AGTATTTTTT
Statistics
Matches: 143, Mismatches: 21, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
189 62 0.43
190 80 0.56
191 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (189 bp):
TAGTACTAATCTGTTGCGACGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGGCGTTCA
AATAAAAAACATTCACAGCATTTTTTGACAAAACACCACTAAACTACAAATTATTTGTGGCGTTT
GTTACCAAAACAACGCTATATATAAACCCTATTGCGCCATTTTCGTCAAAACGCTGCTG
Found at i:1188690 original size:14 final size:14
Alignment explanation
Indices: 1188671--1188700 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1188661 TTTAGATTTT
*
1188671 TTAAAATTACATTA
1 TTAAAAATACATTA
1188685 TTAAAAATACATTA
1 TTAAAAATACATTA
1188699 TT
1 TT
1188701 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:1191982 original size:200 final size:203
Alignment explanation
Indices: 1191637--1192040 Score: 771
Period size: 200 Copynumber: 2.0 Consensus size: 203
1191627 TGGATCTAGA
1191637 AATAATTTTGAGATGGATACTTATATATTAACAACACAAAATCTTTAGTCAATATTTAGTAATAA
1 AATAATTTTGAGATGGATACTTATATATTAACAACACAAAATCTTTAGTCAATATTTAGTAATAA
1191702 TTTATATATGGATGAGCACAAATAAAATCTTAGTATGTGTATAATCAGTAAAATATATAACTAAC
66 TTTATATATGGATGAGCACAAATAAAATCTTAGTATGTGTATAATCAGTAAAATATATAACTAAC
1191767 AGGAAAAAAAATTAAATTTCGTTAGACACCTATTTACCCTTAATAATATGTGAATCGG-CACCAC
131 AGGAAAAAAAATTAAATTTCGTTAGACACCTATTTACCCTTAATAATATGTGAATCGGCCACCAC
1191831 ACATGAGT
196 ACATGAGT
1191839 AATAATTTTGAGATGGGATACTTATATATTAACAACAC-AAATCTTTAG-CAATA-TTAGTAATA
1 AATAATTTTGAGAT-GGATACTTATATATTAACAACACAAAATCTTTAGTCAATATTTAGTAATA
1191901 ATTTATATATGGATGAGCACAAATAAAATCTTAGTATGTGTATAATCAGTAAAATATATAACTAA
65 ATTTATATATGGATGAGCACAAATAAAATCTTAGTATGTGTATAATCAGTAAAATATATAACTAA
1191966 CAGGAAAAAAAATTAAATTTCGTTAGACACCTATTTACCCTTAATAATATGTGAATCGGCCACCA
130 CAGGAAAAAAAATTAAATTTCGTTAGACACCTATTTACCCTTAATAATATGTGAATCGGCCACCA
1192031 CACATGAGT
195 CACATGAGT
1192040 A
1 A
1192041 TGCTCTTTTG
Statistics
Matches: 200, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
200 133 0.67
201 20 0.10
202 24 0.12
203 23 0.12
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (203 bp):
AATAATTTTGAGATGGATACTTATATATTAACAACACAAAATCTTTAGTCAATATTTAGTAATAA
TTTATATATGGATGAGCACAAATAAAATCTTAGTATGTGTATAATCAGTAAAATATATAACTAAC
AGGAAAAAAAATTAAATTTCGTTAGACACCTATTTACCCTTAATAATATGTGAATCGGCCACCAC
ACATGAGT
Found at i:1192963 original size:30 final size:30
Alignment explanation
Indices: 1192927--1193006 Score: 160
Period size: 30 Copynumber: 2.7 Consensus size: 30
1192917 ATATTACTAC
1192927 ATAGGAGAAGCTTAATTAGTACTAGTATAT
1 ATAGGAGAAGCTTAATTAGTACTAGTATAT
1192957 ATAGGAGAAGCTTAATTAGTACTAGTATAT
1 ATAGGAGAAGCTTAATTAGTACTAGTATAT
1192987 ATAGGAGAAGCTTAATTAGT
1 ATAGGAGAAGCTTAATTAGT
1193007 GCTTCGGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (30 bp):
ATAGGAGAAGCTTAATTAGTACTAGTATAT
Found at i:1194681 original size:118 final size:119
Alignment explanation
Indices: 1194472--1194709 Score: 460
Period size: 118 Copynumber: 2.0 Consensus size: 119
1194462 TCTCTAAATA
*
1194472 TGATTTAGGATTAGGAAATAAATGGAGTTTATATTGATGATCCAAGTTACTTGACCCCCATAAAT
1 TGATTTAGGATTAGGAAAAAAATGGAGTTTATATTGATGATCCAAGTTACTTGACCCCCATAAAT
1194537 CTACTTCCTCCAATAATTTTAAGATTCTTAATTGTATGTTCAAACAATATTATT
66 CTACTTCCTCCAATAATTTTAAGATTCTTAATTGTATGTTCAAACAATATTATT
1194591 TGATTTAGGATTAGGAAAAAAATGG-GTTTATATTGATGATCCAAGTTACTTGACCCCCATAAAT
1 TGATTTAGGATTAGGAAAAAAATGGAGTTTATATTGATGATCCAAGTTACTTGACCCCCATAAAT
1194655 CTACTTCCTCCAATAATTTTAAGATTCTTAATTGTATGTTCAAACAATATTATT
66 CTACTTCCTCCAATAATTTTAAGATTCTTAATTGTATGTTCAAACAATATTATT
1194709 T
1 T
1194710 TGAGTCCACT
Statistics
Matches: 118, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
118 94 0.80
119 24 0.20
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (119 bp):
TGATTTAGGATTAGGAAAAAAATGGAGTTTATATTGATGATCCAAGTTACTTGACCCCCATAAAT
CTACTTCCTCCAATAATTTTAAGATTCTTAATTGTATGTTCAAACAATATTATT
Found at i:1201625 original size:13 final size:13
Alignment explanation
Indices: 1201607--1201636 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1201597 ACCGGTCAAC
*
1201607 GGTCAACGGGTCG
1 GGTCAACGGGTCA
1201620 GGTCAACGGGTCA
1 GGTCAACGGGTCA
1201633 GGTC
1 GGTC
1201637 GGGTTGTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:1203619 original size:43 final size:43
Alignment explanation
Indices: 1203556--1203841 Score: 374
Period size: 43 Copynumber: 6.6 Consensus size: 43
1203546 GCAAAAATGA
* * * *
1203556 TAAGGTCTTATCCTTACACATAGCAAAAGAGCCTGGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTG
* * * *
1203600 TAAGGCTTATCCTTGCACATAGCAAAGGAACTTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTG
1203643 TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTG
* * *
1203686 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTG
* * * * * *
1203729 TAAGGCTTATCCTTGCACACAACAAAGGGACATGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTG
* *
1203772 TAAGGCTTACCCTTGTACACAGCAAAAGGAACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAA-GAACCTGGGGAAACTG
*
1203816 TAAGGCTTACCCTTGCACACAACAAA
1 TAAGGCTTACCCTTGCACACAGCAAA
1203842 GGGACTTGCT
Statistics
Matches: 219, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
43 176 0.80
44 43 0.20
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTG
Found at i:1203771 original size:129 final size:130
Alignment explanation
Indices: 1203587--1203846 Score: 450
Period size: 129 Copynumber: 2.0 Consensus size: 130
1203577 AGCAAAAGAG
* * *
1203587 CCTGGGGAAACTGTAAGGCTTATCCTTGCACATAGCAAAGGAACTTGGGGAAACTGTAAGGCTTA
1 CCTGGGGAAACTGTAAGGCTTATCCTTGCACACAACAAAGGAACATGGGGAAACTGTAAGGCTTA
1203652 CCCTTGCACACAGCAAAA-GAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
66 CCCTTGCACACAGCAAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
* *
1203716 CCTGGGGAAACTGTAAGGCTTATCCTTGCACACAACAAAGGGACATGGGGGAACTGTAAGGCTTA
1 CCTGGGGAAACTGTAAGGCTTATCCTTGCACACAACAAAGGAACATGGGGAAACTGTAAGGCTTA
* *
1203781 CCCTTGTACACAGCAAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
66 CCCTTGCACACAGCAAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
1203846 C
1 C
1203847 TTGCTGTAAC
Statistics
Matches: 123, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
129 77 0.63
130 46 0.37
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (130 bp):
CCTGGGGAAACTGTAAGGCTTATCCTTGCACACAACAAAGGAACATGGGGAAACTGTAAGGCTTA
CCCTTGCACACAGCAAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
Found at i:1205840 original size:17 final size:18
Alignment explanation
Indices: 1205808--1205846 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1205798 AACTAACATT
*
1205808 TTTTATGCACATCAATAG
1 TTTTATGCACATCAATAA
*
1205826 TTTTAT-CATATCAATAA
1 TTTTATGCACATCAATAA
1205843 TTTT
1 TTTT
1205847 TTTCAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (18 bp):
TTTTATGCACATCAATAA
Found at i:1208741 original size:43 final size:43
Alignment explanation
Indices: 1208679--1208965 Score: 367
Period size: 43 Copynumber: 6.6 Consensus size: 43
1208669 GCAAAAACGA
* * * * *
1208679 TAAGGTCTTATCCTTGCACATAGTAAAAGAGCTTGGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTG
* * *
1208723 TAAGGCTTATCCTTGCACACAGCAAAGGAACTTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTG
*
1208766 TAAGGCTTACCCTTGCACACAGCAAATGAACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTG
* * * *
1208809 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAAAATG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAACCT-GGGGAAACTG
* * * * * *
1208853 TAAGTCATATCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTG
*
1208896 TAAGGCTTACCCTTGCACACAGCAAAAAGAACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGC-AAAAGAACCTGGGGAAACTG
1208940 TAAGGCTTACCCTTGCACACAGCAAA
1 TAAGGCTTACCCTTGCACACAGCAAA
1208966 GGGACCTGCT
Statistics
Matches: 219, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
43 135 0.62
44 84 0.38
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTG
Found at i:1208867 original size:44 final size:44
Alignment explanation
Indices: 1208713--1208973 Score: 377
Period size: 43 Copynumber: 6.0 Consensus size: 44
1208703 AAAAGAGCTT
* * *
1208713 GGGGAAACTGTAAGGCTTATCCTTGCACACAGCAAA-GGAACTT
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTG
* *
1208756 GGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAATGAACCT-
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTG
*
1208799 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTG
* * * *
1208843 GGGGAAAATGTAAGTCATATCCTTGCACACAGCAAAGGGACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTG
* *
1208887 GGGG-AACTGTAAGGCTTACCCTTGCACACAGCAAAAAGAACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAGC-AAAGGGACCTG
1208931 GGGG-AACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTG
1208974 CTGTAATGGT
Statistics
Matches: 196, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
43 108 0.55
44 88 0.45
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (44 bp):
GGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTG
Found at i:1208895 original size:87 final size:86
Alignment explanation
Indices: 1208712--1208973 Score: 382
Period size: 87 Copynumber: 3.0 Consensus size: 86
1208702 TAAAAGAGCT
* * *
1208712 TGGGGAAACTGTAAGGCTTATCCTTGCACACAGCAAAGGAACTTGGGGAAACTGTAAGGCTTACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGACCTGGGGGAAACTGTAAGGCTTACC
* *
1208777 CTTGCACACAGCAAATGAACC
66 CTTGCACACAGCAAAGGGACC
* * * * *
1208798 TGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAAAATGTAAGTCATAT
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAA-GGACCTGGGGGAAACTGTAAGGCTTAC
1208863 CCTTGCACACAGCAAAGGGACC
65 CCTTGCACACAGCAAAGGGACC
* *
1208885 TGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAAAGAACCTGGGGG-AACTGTAAGGCTTA
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGC--AAAGGACCTGGGGGAAACTGTAAGGCTTA
1208949 CCCTTGCACACAGCAAAGGGACC
64 CCCTTGCACACAGCAAAGGGACC
1208972 TG
1 TG
1208974 CTGTAATGGT
Statistics
Matches: 156, Mismatches: 17, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
86 35 0.22
87 108 0.69
88 10 0.06
89 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (86 bp):
TGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGACCTGGGGGAAACTGTAAGGCTTACC
CTTGCACACAGCAAAGGGACC
Found at i:1213037 original size:14 final size:14
Alignment explanation
Indices: 1213018--1213048 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1213008 GATAAACTTG
1213018 TAATTTTTCATTTA
1 TAATTTTTCATTTA
1213032 TAATTTTTCATTTA
1 TAATTTTTCATTTA
1213046 TAA
1 TAA
1213049 ATACAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (14 bp):
TAATTTTTCATTTA
Found at i:1214758 original size:36 final size:36
Alignment explanation
Indices: 1214713--1214966 Score: 128
Period size: 36 Copynumber: 7.1 Consensus size: 36
1214703 GAAGGTGAAT
* *
1214713 AAGAAGAACGAAATGAAGCATCATCACTTTCAATTC
1 AAGATGAACGAAAGGAAGCATCATCACTTTCAATTC
* *** **
1214749 AA-AGTGAACGGAAGGAAGCATTGGCACTTTTGATTC
1 AAGA-TGAACGAAAGGAAGCATCATCACTTTCAATTC
* * *
1214785 AAGAAGAACGGAAA-GAAGCAACGA-CACTTCCAATTC
1 AAGATGAAC-GAAAGGAAGCATC-ATCACTTTCAATTC
* * * * *
1214821 AAGTTGAACGGAAGGAAGCAACGTCACTTTCGATTC
1 AAGATGAACGAAAGGAAGCATCATCACTTTCAATTC
* ** * *
1214857 AAG-TCGAACGAAATGAAGCATCGGCACTTCCGATTC
1 AAGAT-GAACGAAAGGAAGCATCATCACTTTCAATTC
* * * *
1214893 AAG-TCGAGCGGAAGGAAGCATCGA-AACTTTCGATTC
1 AAGAT-GAACGAAAGGAAGCATC-ATCACTTTCAATTC
* * * *
1214929 AAGACGAACGGAA-GAAGGCGTC-GCACTTTCAATTC
1 AAGATGAACGAAAGGAA-GCATCATCACTTTCAATTC
1214964 AAG
1 AAG
1214967 TGTTCATCTT
Statistics
Matches: 169, Mismatches: 38, Indels: 23
0.73 0.17 0.10
Matches are distributed among these distances:
35 21 0.12
36 144 0.85
37 4 0.02
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.19
Consensus pattern (36 bp):
AAGATGAACGAAAGGAAGCATCATCACTTTCAATTC
Found at i:1214803 original size:72 final size:71
Alignment explanation
Indices: 1214713--1214968 Score: 268
Period size: 72 Copynumber: 3.6 Consensus size: 71
1214703 GAAGGTGAAT
* * * *
1214713 AAGAAGAACGAAATGAAGCATCATCACTTTCAATTCAAAGTGAACGGAAGGAAGCATTGGCACTT
1 AAGAAGAACGAAATGAAGCATCAGCACTTCCAATTC-AAGTGAACGGAAGGAAGCATCGACACTT
*
1214778 TTGATTC
65 TCGATTC
* * *
1214785 AAGAAGAACGGAAA-GAAGCAAC-GACACTTCCAATTCAAGTTGAACGGAAGGAAGCAACGTCAC
1 AAGAAGAAC-GAAATGAAGCATCAG-CACTTCCAATTCAAG-TGAACGGAAGGAAGCATCGACAC
1214848 TTTCGATTC
63 TTTCGATTC
** * * * *
1214857 AAGTCGAACGAAATGAAGCATCGGCACTTCCGATTCAAGTCGAGCGGAAGGAAGCATCGAAACTT
1 AAGAAGAACGAAATGAAGCATCAGCACTTCCAATTCAAGT-GAACGGAAGGAAGCATCGACACTT
1214922 TCGATTC
65 TCGATTC
* * * *
1214929 AAGACGAACGGAA-GAAGGCGTC-GCACTTTCAATTCAAGTG
1 AAGAAGAACGAAATGAA-GCATCAGCACTTCCAATTCAAGTG
1214969 TTCATCTTTT
Statistics
Matches: 157, Mismatches: 20, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
70 1 0.01
71 26 0.17
72 125 0.80
73 5 0.03
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (71 bp):
AAGAAGAACGAAATGAAGCATCAGCACTTCCAATTCAAGTGAACGGAAGGAAGCATCGACACTTT
CGATTC
Found at i:1214883 original size:108 final size:106
Alignment explanation
Indices: 1214713--1214968 Score: 271
Period size: 108 Copynumber: 2.4 Consensus size: 106
1214703 GAAGGTGAAT
* * * * *
1214713 AAGAAGAACGAAATGAAGCATCATCACTTTCAATTCAAAGTGAACGGAAGGAAGCATTGGCACTT
1 AAGACGAACGGAA-GAAGCATCGTCACTTTCAATTC-AAGTGAACGAAAGGAAGCATCGGCACTT
** *
1214778 TTGATTCAAGAAGAACGGAAAGAAGCAACGACACTTCCAATTC
64 CCGATTCAAGAAGAACGGAAAGAAGCAACGAAACTTCCAATTC
** * * *
1214821 AAGTTGAACGGAAGGAAGCAACGTCACTTTCGATTCAAGTCGAACGAAATGAAGCATCGGCACTT
1 AAGACGAACGGAA-GAAGCATCGTCACTTTCAATTCAAGT-GAACGAAAGGAAGCATCGGCACTT
** * * * * *
1214886 CCGATTCAAGTCGAGCGGAAGGAAGCATCGAAACTTTCGATTC
64 CCGATTCAAGAAGAACGGAAAGAAGCAACGAAACTTCCAATTC
*
1214929 AAGACGAACGGAAGAAGGCGTCG-CACTTTCAATTCAAGTG
1 AAGACGAACGGAAGAA-GCATCGTCACTTTCAATTCAAGTG
1214969 TTCATCTTTT
Statistics
Matches: 121, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
106 1 0.01
107 22 0.18
108 98 0.81
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (106 bp):
AAGACGAACGGAAGAAGCATCGTCACTTTCAATTCAAGTGAACGAAAGGAAGCATCGGCACTTCC
GATTCAAGAAGAACGGAAAGAAGCAACGAAACTTCCAATTC
Found at i:1216416 original size:36 final size:36
Alignment explanation
Indices: 1216367--1216600 Score: 267
Period size: 36 Copynumber: 6.5 Consensus size: 36
1216357 GTGATTTCAT
* *
1216367 CGACACTTCCGATTCAAGTCGAACGGAAGGAAGTAA
1 CGACACTTTCGATTCAAGTCGAACGGAAGGAAGCAA
* *
1216403 CGACACTTTCGATTCAAGTCGAACAGAAAGAAGCAA
1 CGACACTTTCGATTCAAGTCGAACGGAAGGAAGCAA
* *
1216439 TGACACTTCCGATTCAAGTCGAACGGAAGGAAGCAA
1 CGACACTTTCGATTCAAGTCGAACGGAAGGAAGCAA
* * * *
1216475 CGTCACTTTCGATTCAAGTCGAACGAAATGAAGCAT
1 CGACACTTTCGATTCAAGTCGAACGGAAGGAAGCAA
* * * *
1216511 TGGCAC-TTCTGATTCAAGTCGAACGGAAGGAAACAT
1 CGACACTTTC-GATTCAAGTCGAACGGAAGGAAGCAA
* * **
1216547 CGGCACTTTCGATTCAAGACGAACGGAA-GAAGGCGT
1 CGACACTTTCGATTCAAGTCGAACGGAAGGAA-GCAA
1216583 CG-CACTTTCGATTCAAGT
1 CGACACTTTCGATTCAAGT
1216601 GTTCATATTT
Statistics
Matches: 171, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
35 21 0.12
36 147 0.86
37 3 0.02
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (36 bp):
CGACACTTTCGATTCAAGTCGAACGGAAGGAAGCAA
Found at i:1216485 original size:72 final size:71
Alignment explanation
Indices: 1216368--1216578 Score: 314
Period size: 72 Copynumber: 2.9 Consensus size: 71
1216358 TGATTTCATC
*
1216368 GACACTTCCGATTCAAGTCGAACGGAAGGAAGTAACGACACTTTCGATTCAAGTCGAACAGAAAG
1 GACACTTCCGATTCAAGTCGAACGGAAGGAAGCAACGACACTTTCGATTCAAGTCGAAC-GAAAG
1216433 AAGCAAT
65 AAGCAAT
*
1216440 GACACTTCCGATTCAAGTCGAACGGAAGGAAGCAACGTCACTTTCGATTCAAGTCGAACGAAATG
1 GACACTTCCGATTCAAGTCGAACGGAAGGAAGCAACGACACTTTCGATTCAAGTCGAACGAAA-G
*
1216505 AAGCATT
65 AAGCAAT
* * * * * * *
1216512 GGCACTTCTGATTCAAGTCGAACGGAAGGAAACATCGGCACTTTCGATTCAAGACGAACGGAAGA
1 GACACTTCCGATTCAAGTCGAACGGAAGGAAGCAACGACACTTTCGATTCAAGTCGAACGAAAGA
1216577 AG
66 AG
1216579 GCGTCGCACT
Statistics
Matches: 128, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
71 8 0.06
72 120 0.94
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (71 bp):
GACACTTCCGATTCAAGTCGAACGGAAGGAAGCAACGACACTTTCGATTCAAGTCGAACGAAAGA
AGCAAT
Found at i:1246052 original size:20 final size:21
Alignment explanation
Indices: 1246029--1246088 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
1246019 TTAAAATTTA
1246029 TATAATAATACATTTAGTCC-
1 TATAATAATACATTTAGTCCT
1246049 TATAATAATACATTTAGTCCTT
1 TATAATAATACATTTAGTCC-T
* *
1246071 TATATTTATACATTTAGT
1 TATAATAATACATTTAGT
1246089 TAATTTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 20 0.56
22 16 0.44
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (21 bp):
TATAATAATACATTTAGTCCT
Found at i:1246099 original size:22 final size:22
Alignment explanation
Indices: 1246056--1246104 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1246046 TCCTATAATA
**
1246056 ATACATTTAGTCCTTTATATTT
1 ATACATTTAGTAATTTATATTT
1246078 ATACATTTAGTTAATTTA-ATTT
1 ATACATTTAG-TAATTTATATTT
1246100 -TACAT
1 ATACAT
1246105 AATTGGTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.21
22 14 0.58
23 5 0.21
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.53
Consensus pattern (22 bp):
ATACATTTAGTAATTTATATTT
Found at i:1254717 original size:2 final size:2
Alignment explanation
Indices: 1254705--1254740 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1254695 TAAGAGGGAT
*
1254705 TA TA AA 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
1254741 GTTTAATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1255348 original size:15 final size:16
Alignment explanation
Indices: 1255328--1255362 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1255318 TTCTAAATCA
1255328 TTAATAA-TGCTTAAG
1 TTAATAACTGCTTAAG
*
1255343 TTAATAACTGCTTACG
1 TTAATAACTGCTTAAG
1255359 TTAA
1 TTAA
1255363 AATAATTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (16 bp):
TTAATAACTGCTTAAG
Found at i:1266598 original size:46 final size:44
Alignment explanation
Indices: 1266440--1266592 Score: 225
Period size: 44 Copynumber: 3.4 Consensus size: 44
1266430 ATAACCATGC
*
1266440 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTACGGAATAATGGCAAGTATATTAGTA
1266484 AAATAAGCTTACGAGCTTACGGAATAATGGCAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTACGGAATAATGGCAAGTATATTAGTA
* * * * *
1266528 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTGTATTGGTA
1 AAATAAGCTTACGAGCTTA-CGGAAT-AATGGCAAGTATATTAGTA
*
1266574 AAATAAGCCTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
1266593 TGGGATAAAT
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
44 62 0.62
45 4 0.04
46 34 0.34
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTACGGAATAATGGCAAGTATATTAGTA
Found at i:1267079 original size:22 final size:21
Alignment explanation
Indices: 1267026--1267078 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1267016 GATTGCGGGT
*
1267026 ACCAATTCCCTTGCTACAGGA
1 ACCAATTCCCCTGCTACAGGA
1267047 ACCAATTCCCCTGCTACAGGA
1 ACCAATTCCCCTGCTACAGGA
1267068 ACCAATTCCCC
1 ACCAATTCCCC
1267079 CACTATACAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.40, G:0.11, T:0.21
Consensus pattern (21 bp):
ACCAATTCCCCTGCTACAGGA
Found at i:1275860 original size:36 final size:37
Alignment explanation
Indices: 1275807--1275886 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 37
1275797 AATTTACTCA
* *
1275807 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1275844 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1275880 AAACAAA
1 AAACAAA
1275887 ATCTTTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 34 0.83
37 7 0.17
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (37 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:1276005 original size:36 final size:36
Alignment explanation
Indices: 1275899--1276120 Score: 284
Period size: 36 Copynumber: 6.1 Consensus size: 36
1275889 CTTTGAATCT
* * *
1275899 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
** * *
1275935 GTTTCTTTTGGAACAAAGTTTTATCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* *
1275972 GTTTCTCTTTAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
1276008 ATTTCCCTTAAAATAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1276044 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
1276080 GTTTCCCTTGGAAATAAGTTTTG-CTTCTCTTGAGACA
1 GTTTCCCTT-GAAACAAATTTTGTC-TCTCTTGAGACA
1276117 GTTT
1 GTTT
1276121 TGAATATGTT
Statistics
Matches: 163, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
36 106 0.65
37 57 0.35
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:1276008 original size:21 final size:21
Alignment explanation
Indices: 1275975--1276075 Score: 64
Period size: 21 Copynumber: 5.4 Consensus size: 21
1275965 TGAGACAGTT
*
1275975 TCTCTTTAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
*
1275996 TCTCTTGAGAC-AA--TT-TC
1 TCTCTTGAAACAAATTTTGTC
* *
1276013 -C-CTTAAAATAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
1276032 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
1276049 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
1276068 TCTCTTGA
1 TCTCTTGA
1276076 GACAGTTTCC
Statistics
Matches: 57, Mismatches: 11, Indels: 24
0.62 0.12 0.26
Matches are distributed among these distances:
15 12 0.21
16 4 0.07
17 5 0.09
18 8 0.14
19 5 0.09
20 4 0.07
21 19 0.33
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.43
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:1276058 original size:72 final size:72
Alignment explanation
Indices: 1275899--1276120 Score: 293
Period size: 73 Copynumber: 3.1 Consensus size: 72
1275889 CTTTGAATCT
* * * ** * * *
1275899 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACAAAGTTTTATCTCTC
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA-TTTTGTCTCTC
1275964 TTGAGACA
65 TTGAGACA
* * * *
1275972 GTTTCTCTTTAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAATAAATTTTGTCTCTCT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCT
1276037 TGAGACA
66 TGAGACA
*
1276044 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGGAAATAAGTTTTG-CTTCT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTC-TCT
1276108 CTTGAGACA
64 CTTGAGACA
1276117 GTTT
1 GTTT
1276121 TGAATATGTT
Statistics
Matches: 130, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
72 61 0.47
73 69 0.53
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (72 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCT
TGAGACA
Found at i:1276257 original size:34 final size:33
Alignment explanation
Indices: 1276165--1276279 Score: 187
Period size: 33 Copynumber: 3.5 Consensus size: 33
1276155 CCTGGAGACA
*
1276165 GTTTCTCTTGAAACAATAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACAAAAAAAACCTTTGAAATC
*
1276198 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACAAAAAAAACCTTTGAAATC
1276231 GTTTCTCTTGAAACAAAAAAAAACCTTTGAAAAT-
1 GTTTCTCTTGAAAC-AAAAAAAACCTTTG-AAATC
1276265 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
1276280 CAAAGACCTT
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
33 46 0.60
34 27 0.35
35 4 0.05
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (33 bp):
GTTTCTCTTGAAACAAAAAAAACCTTTGAAATC
Found at i:1280383 original size:45 final size:45
Alignment explanation
Indices: 1280334--1280435 Score: 134
Period size: 45 Copynumber: 2.2 Consensus size: 45
1280324 ATATTTAACA
* *
1280334 TATTTATTTTATTATTTCATATGGTATGAATACATAACA-TGATTT
1 TATTTATTTTATTATTTCATATGGGACGAATACATAA-ATTGATTT
* *
1280379 TATTTATTTTGTTATTTCATATGGGGCGAATACATAAATTGATTT
1 TATTTATTTTATTATTTCATATGGGACGAATACATAAATTGATTT
*
1280424 TATGTTGTTTTA
1 TAT-TTATTTTA
1280436 ATTTATCTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
44 1 0.02
45 42 0.86
46 6 0.12
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (45 bp):
TATTTATTTTATTATTTCATATGGGACGAATACATAAATTGATTT
Found at i:1281317 original size:23 final size:24
Alignment explanation
Indices: 1281276--1281324 Score: 82
Period size: 23 Copynumber: 2.0 Consensus size: 24
1281266 AGTCATAATC
1281276 TCATTGTTCGAAAGGATTGTTCTTT
1 TCATTGTTC-AAAGGATTGTTCTTT
1281301 TCATTGTTC-AAGGATTGTTCTTT
1 TCATTGTTCAAAGGATTGTTCTTT
1281324 T
1 T
1281325 TGGCAGGGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 15 0.62
25 9 0.38
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.51
Consensus pattern (24 bp):
TCATTGTTCAAAGGATTGTTCTTT
Found at i:1282994 original size:27 final size:26
Alignment explanation
Indices: 1282944--1282998 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
1282934 AATATTTGTG
*
1282944 TATTTTAACCATTTAATTAATATAATA
1 TATTTTAACCATTTAATCAATAT-ATA
* *
1282971 TATTTTAACCATTTGATCACTATATA
1 TATTTTAACCATTTAATCAATATATA
1282997 TA
1 TA
1282999 CAGCCTCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (26 bp):
TATTTTAACCATTTAATCAATATATA
Found at i:1287658 original size:22 final size:23
Alignment explanation
Indices: 1287630--1287672 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1287620 CTTTCCACTG
1287630 TTTATTTA-TTTAAAATTAAAGA
1 TTTATTTATTTTAAAATTAAAGA
*
1287652 TTTATTTATTTTAAAGTTAAA
1 TTTATTTATTTTAAAATTAAA
1287673 CCACTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (23 bp):
TTTATTTATTTTAAAATTAAAGA
Found at i:1292393 original size:16 final size:17
Alignment explanation
Indices: 1292374--1292410 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1292364 TAAAATATTA
1292374 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
1292390 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
1292407 TTTT
1 TTTT
1292411 TCCTTCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:1302028 original size:22 final size:23
Alignment explanation
Indices: 1302000--1302043 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1301990 TCCAATGTTT
*
1302000 ATTTATTTA-TTTAAATTTAAAG
1 ATTTATTTATTTTAAAGTTAAAG
1302022 ATTTATTTATTTTAAAGTTAAA
1 ATTTATTTATTTTAAAGTTAAA
1302044 CCACTTGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
ATTTATTTATTTTAAAGTTAAAG
Found at i:1306689 original size:12 final size:11
Alignment explanation
Indices: 1306669--1306712 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
1306659 TTTGGTGCTG
*
1306669 AAAACAAGATT
1 AAAAAAAGATT
1306680 AAAAATAAGATT
1 AAAAA-AAGATT
1306692 AAAAAAAGA-T
1 AAAAAAAGATT
1306702 AAAGAAAAGAT
1 AAA-AAAAGAT
1306713 AAAGGAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 4 0.14
11 14 0.48
12 11 0.38
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.16
Consensus pattern (11 bp):
AAAAAAAGATT
Found at i:1309033 original size:19 final size:19
Alignment explanation
Indices: 1309011--1309060 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1309001 AGGTGAGAAC
1309011 AAATAAATAAAGTATA-AAA
1 AAATAAATAAA-TATATAAA
* *
1309030 AAATATATAAATTTATAAA
1 AAATAAATAAATATATAAA
1309049 AAATAAAATAAA
1 AAAT-AAATAAA
1309061 CAAACTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 3 0.12
19 17 0.65
20 6 0.23
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAATAAATAAATATATAAA
Found at i:1309059 original size:20 final size:19
Alignment explanation
Indices: 1309011--1309060 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
1309001 AGGTGAGAAC
1309011 AAAT-AAATAAAGTATAAA
1 AAATAAAATAAAGTATAAA
* *
1309029 AAA-ATATATAAATTTATAAA
1 AAATA-AAATAAA-GTATAAA
1309049 AAATAAAATAAA
1 AAATAAAATAAA
1309061 CAAACTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
18 3 0.12
19 6 0.24
20 15 0.60
21 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAATAAAATAAAGTATAAA
Found at i:1309388 original size:14 final size:15
Alignment explanation
Indices: 1309369--1309399 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1309359 ATGTGTGAAT
1309369 AAATGGTTTT-TTAA
1 AAATGGTTTTCTTAA
1309383 AAATGGTTTTCTTAA
1 AAATGGTTTTCTTAA
1309398 AA
1 AA
1309400 TGTTTTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (15 bp):
AAATGGTTTTCTTAA
Found at i:1310683 original size:22 final size:22
Alignment explanation
Indices: 1310616--1310684 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
1310606 GCCATCTGTC
* *
1310616 GGCCACCGCCGATCAATATTCT
1 GGCCACCGTCGATCACTATTCT
*
1310638 GACCACCGTCGATCACTATTCT
1 GGCCACCGTCGATCACTATTCT
*
1310660 GGTCACCGTCGATCACTATTCT
1 GGCCACCGTCGATCACTATTCT
1310682 GGC
1 GGC
1310685 TGTCGGTCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.26
Consensus pattern (22 bp):
GGCCACCGTCGATCACTATTCT
Found at i:1311121 original size:23 final size:23
Alignment explanation
Indices: 1311095--1311140 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1311085 GGGGAACATA
*
1311095 ACGGCAGAGCAGTTGGAGTAGAG
1 ACGGCAGAGCAGTTGAAGTAGAG
**
1311118 ACGGTGGAGCAGTTGAAGTAGAG
1 ACGGCAGAGCAGTTGAAGTAGAG
1311141 GAACGGCTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.43, T:0.15
Consensus pattern (23 bp):
ACGGCAGAGCAGTTGAAGTAGAG
Found at i:1312128 original size:119 final size:119
Alignment explanation
Indices: 1311889--1312130 Score: 263
Period size: 119 Copynumber: 2.0 Consensus size: 119
1311879 TACTATAATA
* ** *
1311889 GTAAATAATTCTAAAAATAATATTTAAAATTATTATTTTAAAACTAAATGATTAAAATTGTAAAA
1 GTAAATAATCCTAAAAATAATATTTAAAATTAAAATATTAAAACTAAATGATTAAAATTGTAAAA
* * * * * * **
1311954 TATCAAAATTAAAAATCCTAATTCTAAATATCATGAAATCTAGGTATTATTAGT
66 TATAAAAATTAAAAATCCTAATTCAAAATATCATAAAATATAAGTACTAACAGT
* * *
1312008 GTAAATAATCCT-AAAATATTATTTAAAATTAAAATATTAAACCTCAATGATT-AAATTGTAAAA
1 GTAAATAATCCTAAAAATAATATTTAAAATTAAAATATTAAAACTAAATGATTAAAATTGT-AAA
*** * * *
1312071 ATATAAAAAATTAATGGTCTTAATTCAAAATATTATAAAATATAATTACTAACAGT
65 ATAT-AAAAATTAAAAATCCTAATTCAAAATATCATAAAATATAAGTACTAACAGT
1312127 GTAA
1 GTAA
1312131 TTTAACCCTA
Statistics
Matches: 100, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
117 7 0.07
118 41 0.41
119 52 0.52
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (119 bp):
GTAAATAATCCTAAAAATAATATTTAAAATTAAAATATTAAAACTAAATGATTAAAATTGTAAAA
TATAAAAATTAAAAATCCTAATTCAAAATATCATAAAATATAAGTACTAACAGT
Found at i:1313608 original size:138 final size:138
Alignment explanation
Indices: 1313297--1313739 Score: 570
Period size: 137 Copynumber: 3.2 Consensus size: 138
1313287 AGATCCAACT
* ** * *
1313297 GGTGTATGACATTGTTCCTTAATGATGAGGACGTCTGACCATCTTTGAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * * * * * ** * *
1313362 AGGTTCCTTTATGATGAGGACGTCTGGTTATCTGAGAATGA-CTCGGCTCCTACATGATGAGGAG
66 TGGTTTCTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTTGCTCCTTCGTGATGAGGAG
*
1313426 TTCTAATC
131 TTCTGATC
* * * *
1313434 GGTGGATGACATTATTCCTTCGTGATGAGGATGTCTGGCCATCTTTAAATATATTTAAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* *
1313499 TGGTTTCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATATTTGCTCCTTCGTGATGAGGAG
66 TGGTTTCTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTTGCTCCTTCGTGATGAGGAG
*
1313564 TTATGATC
131 TTCTGATC
*
1313572 GGTGGATGACATTGTTCCTTCGTGATGAGAACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * * *
1313637 CT-G-TTCTTTCATGATGAGGATATATGGTTATCTAAGAATGATGTTT-CTCTTTCGTGATGAGG
66 -TGGTTTC-TTCATGATGAGGACATCTGGTTATCTAAGAATGATATTTGCTCCTTCGTGATGAGG
1313699 AGTTCTGATC
129 AGTTCTGATC
* *
1313709 GATGGATGACATTGCTCCTTCGTGATGAGGA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGA
1313740 GTTCTGATCG
Statistics
Matches: 265, Mismatches: 38, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
137 145 0.55
138 119 0.45
139 1 0.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (138 bp):
GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
TGGTTTCTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTTGCTCCTTCGTGATGAGGAG
TTCTGATC
Found at i:1313735 original size:40 final size:40
Alignment explanation
Indices: 1313687--1313779 Score: 168
Period size: 40 Copynumber: 2.3 Consensus size: 40
1313677 ATGTTTCTCT
1313687 TTCGTGATGAGGAGTTCTGATCGATGGATGACATTGCTCC
1 TTCGTGATGAGGAGTTCTGATCGATGGATGACATTGCTCC
* *
1313727 TTCGTGATGAGGAGTTCTGATCGATGTATGACATTGTTCC
1 TTCGTGATGAGGAGTTCTGATCGATGGATGACATTGCTCC
1313767 TTCGTGATGAGGA
1 TTCGTGATGAGGA
1313780 CGTCTTGCCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.34
Consensus pattern (40 bp):
TTCGTGATGAGGAGTTCTGATCGATGGATGACATTGCTCC
Found at i:1323069 original size:3 final size:3
Alignment explanation
Indices: 1323063--1323097 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1323053 TATTATTTAT
*
1323063 TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1323098 TAAAAAGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1329839 original size:30 final size:29
Alignment explanation
Indices: 1329797--1329873 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
1329787 TAAAATATAT
* * *
1329797 AACTTTTAAAAATTATAATTTCGGTCC-CTA
1 AACTTTCAAAACTTATAATTT-AG-CCACTA
* *
1329827 AACTTCTCAAAATTTATACTTTAGCCACTA
1 AACTT-TCAAAACTTATAATTTAGCCACTA
1329857 AACTTTCAAAACTTATA
1 AACTTTCAAAACTTATA
1329874 TTTTTGTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 13 0.32
30 14 0.35
31 13 0.32
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (29 bp):
AACTTTCAAAACTTATAATTTAGCCACTA
Found at i:1329884 original size:29 final size:29
Alignment explanation
Indices: 1329797--1329884 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 29
1329787 TAAAATATAT
* ** *
1329797 AACTTTTAAAAATTATAATTTCGGTCCCTA
1 AACTTTCAAAAATTAT-ATTTTAGTCACTA
* * *
1329827 AACTTCTCAAAATTTATACTTTAGCCACTA
1 AACTT-TCAAAAATTATATTTTAGTCACTA
* *
1329857 AACTTTCAAAACTTATATTTTTGTCACT
1 AACTTTCAAAAATTATATTTTAGTCACT
1329885 GGTCAAAATT
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
29 19 0.41
30 18 0.39
31 9 0.20
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (29 bp):
AACTTTCAAAAATTATATTTTAGTCACTA
Found at i:1330097 original size:146 final size:146
Alignment explanation
Indices: 1329919--1330209 Score: 582
Period size: 146 Copynumber: 2.0 Consensus size: 146
1329909 TTAAGTATGG
1329919 TTTTGCACTAAATGTGAACCACATGTTCCTATATCACTATATAATATATACTTAACTTTAATTCA
1 TTTTGCACTAAATGTGAACCACATGTTCCTATATCACTATATAATATATACTTAACTTTAATTCA
1329984 TACTTTTTACTAAAAATATATTCTCTTTTTTAATTTAAAAAAAATAGTTGACCATATTCTCATAT
66 TACTTTTTACTAAAAATATATTCTCTTTTTTAATTTAAAAAAAATAGTTGACCATATTCTCATAT
1330049 ATAATGGGGTAAGGGT
131 ATAATGGGGTAAGGGT
1330065 TTTTGCACTAAATGTGAACCACATGTTCCTATATCACTATATAATATATACTTAACTTTAATTCA
1 TTTTGCACTAAATGTGAACCACATGTTCCTATATCACTATATAATATATACTTAACTTTAATTCA
1330130 TACTTTTTACTAAAAATATATTCTCTTTTTTAATTTAAAAAAAATAGTTGACCATATTCTCATAT
66 TACTTTTTACTAAAAATATATTCTCTTTTTTAATTTAAAAAAAATAGTTGACCATATTCTCATAT
1330195 ATAATGGGGTAAGGG
131 ATAATGGGGTAAGGG
1330210 AAGGAAGGAT
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 145 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (146 bp):
TTTTGCACTAAATGTGAACCACATGTTCCTATATCACTATATAATATATACTTAACTTTAATTCA
TACTTTTTACTAAAAATATATTCTCTTTTTTAATTTAAAAAAAATAGTTGACCATATTCTCATAT
ATAATGGGGTAAGGGT
Found at i:1339262 original size:17 final size:17
Alignment explanation
Indices: 1339240--1339280 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1339230 TCCGTATCCG
1339240 ATCCGAAAAAATCGGAT
1 ATCCGAAAAAATCGGAT
* *
1339257 ATCCG-AACATTCGGAT
1 ATCCGAAAAAATCGGAT
1339273 ATCCGAAA
1 ATCCGAAA
1339281 TTTCGGATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (17 bp):
ATCCGAAAAAATCGGAT
Found at i:1339272 original size:16 final size:16
Alignment explanation
Indices: 1339251--1339288 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1339241 TCCGAAAAAA
1339251 TCGGATATCCGAACA-T
1 TCGGATATCCGAA-ATT
1339267 TCGGATATCCGAAATT
1 TCGGATATCCGAAATT
1339283 TCGGAT
1 TCGGAT
1339289 CGGATATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (16 bp):
TCGGATATCCGAAATT
Found at i:1339293 original size:21 final size:22
Alignment explanation
Indices: 1339267--1339319 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
1339257 ATCCGAACAT
1339267 TCGGATATCCGAAAT-TTCGGA
1 TCGGATATCCGAAATATTCGGA
1339288 TCGGATATCC-AAATATTCGGA
1 TCGGATATCCGAAATATTCGGA
*
1339309 TCCGA-ATCCGA
1 TCGGATATCCGA
1339320 TTTTTGTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (22 bp):
TCGGATATCCGAAATATTCGGA
Found at i:1346168 original size:26 final size:24
Alignment explanation
Indices: 1346134--1346226 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 24
1346124 GTGTCCTTAC
1346134 TAATAATGATTTAATAATTATTAT
1 TAATAATGATTTAATAATTATTAT
* *
1346158 TAATTTAATGATTTGATATTTAATTATT
1 TAA--TAATGATTTAATAATT-ATTA-T
1346186 TAATAATGATTACTAATAATTATTTAT
1 TAATAATGATT--TAATAATTA-TTAT
1346213 T-ATAAAT-ATTTAAT
1 TAAT-AATGATTTAAT
1346227 GATTTAGATT
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
24 7 0.12
26 27 0.47
27 10 0.18
28 13 0.23
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (24 bp):
TAATAATGATTTAATAATTATTAT
Found at i:1347186 original size:441 final size:440
Alignment explanation
Indices: 1346362--1347215 Score: 1289
Period size: 441 Copynumber: 1.9 Consensus size: 440
1346352 GTCGATGCCG
* * * *
1346362 GTTGCATCACGCATTTGATGACTCTACTCTCCTGGCATACGTACTAGAGTTTGTGCAGCCTCAGG
1 GTTGCATCACGCATCTGATGACTCTACTCTCCTGGCATACGTACCAGAGTTTATACAGCCTCAGG
* * * * * * *
1346427 CACCTATCTATTTTCCAATGTTTGAGTTGAAGTATGACTTTGATCAAATGACATATATGATGTCA
66 CACCCATCTACTCTCCAATATTTGAGTCGAAGTATGACTTTGACCAAATGACATATATGATGCCA
* * **
1346492 AATACTACTATTTGTCAGCCATCGTTTTCAAGTGGGATGGAAGAGCAAACTGGTGGAATGGTAGA
131 AATACCACTATTTGTCAGCCATCGTTTCCAAGTGGGATGGAAGAGCAAACTGGTGGAATGACAGA
* * *
1346557 GCATAGTGGTTGAAAATATTTACAACACCAGTTGAAATGCTCCCAATGAATGAGGAGGATGGGTA
196 ACATAATGGTTGAAAATATTTACAACACCAGTTGAAATGCCCCCAATGAATGAGGAGGATGGGTA
* *
1346622 CCATACTCATGAGCAACCGCAACCACCACAACGCATCAGATGTCTGCTCCAACATTATCATTCAA
261 CCATACTCATGAGCAACCGCAACCACCACAACGCATCAGATGTCCGCTCCAACATTATAATTCAA
*
1346687 CAACACCCCGACATCGACAACAATTATAAACTAATTTTTTATATGTTTAAAATTAGTAGTAATCA
326 CAACACCCCGACATCGACAACAATTATAAACTAATTTGTTATATGTTTAAAATTAGTAGTAATCA
*
1346752 TTATTAAAACATTCTTATCAAATCATTCACTGGTAACCTGAAGCAGGATC
391 TTATTAAAACATTATTATCAAATCATTCACTGGTAACCTGAAGCAGGATC
** * * *
1346802 GTTGCATCGTGCATCTGATGACTCTATTGTCCTGGCATACGTACCAGAGTTTATATAGCCTCAGG
1 GTTGCATCACGCATCTGATGACTCTACTCTCCTGGCATACGTACCAGAGTTTATACAGCCTCAGG
* * *
1346867 CACCCATCTACTCTCCCATATTTGAGTCGACGTATGACTTTGACCAAATGACATCTATGATGCCA
66 CACCCATCTACTCTCCAATATTTGAGTCGAAGTATGACTTTGACCAAATGACATATATGATGCCA
* **
1346932 AATACCAGTATTTGTCATTCATCGTTTCCAAGTGGGATGGAAGAGCAAACTGGTGGAATGACAGA
131 AATACCACTATTTGTCAGCCATCGTTTCCAAGTGGGATGGAAGAGCAAACTGGTGGAATGACAGA
* *
1346997 ATATAATGGTTGGAATATATTTACAACACCAGTTGAAATGCCCCCAATGAATGAGGAGGATGGGT
196 ACATAATGGTT-GAAAATATTTACAACACCAGTTGAAATGCCCCCAATGAATGAGGAGGATGGGT
* ** *
1347062 ACCATACTCCTGAGCAACCGCAATGACCACAACGCATCAGACT-TCCG-TCCCGACATTATAATT
260 ACCATACTCATGAGCAACCGCAACCACCACAACGCATCAGA-TGTCCGCT-CCAACATTATAATT
* * *
1347125 CAACAACACCCCGTCATCGACAACAATTATAAACTCATTTGTTATTTGTTTAAAATTAGTAGTAA
323 CAACAACACCCCGACATCGACAACAATTATAAACTAATTTGTTATATGTTTAAAATTAGTAGTAA
1347190 TCATTATTAAAACATTATTATCAAAT
388 TCATTATTAAAACATTATTATCAAAT
1347216 TATTATCAAA
Statistics
Matches: 369, Mismatches: 42, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
440 178 0.48
441 190 0.51
442 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (440 bp):
GTTGCATCACGCATCTGATGACTCTACTCTCCTGGCATACGTACCAGAGTTTATACAGCCTCAGG
CACCCATCTACTCTCCAATATTTGAGTCGAAGTATGACTTTGACCAAATGACATATATGATGCCA
AATACCACTATTTGTCAGCCATCGTTTCCAAGTGGGATGGAAGAGCAAACTGGTGGAATGACAGA
ACATAATGGTTGAAAATATTTACAACACCAGTTGAAATGCCCCCAATGAATGAGGAGGATGGGTA
CCATACTCATGAGCAACCGCAACCACCACAACGCATCAGATGTCCGCTCCAACATTATAATTCAA
CAACACCCCGACATCGACAACAATTATAAACTAATTTGTTATATGTTTAAAATTAGTAGTAATCA
TTATTAAAACATTATTATCAAATCATTCACTGGTAACCTGAAGCAGGATC
Found at i:1347339 original size:16 final size:16
Alignment explanation
Indices: 1347314--1347345 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1347304 TTATTAGTAA
*
1347314 TCATTGCTAAATCATT
1 TCATTACTAAATCATT
1347330 TCATTACTAAATCATT
1 TCATTACTAAATCATT
1347346 AAATATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.03, T:0.44
Consensus pattern (16 bp):
TCATTACTAAATCATT
Found at i:1356048 original size:18 final size:19
Alignment explanation
Indices: 1356013--1356050 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1356003 TTTTTTCCGT
1356013 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
1356033 AAGATTATCA-GGGAATAA
1 AAGATTATCAGGGGAATAA
1356051 GATTACTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Found at i:1360618 original size:24 final size:24
Alignment explanation
Indices: 1360586--1360645 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
1360576 GGCACTTTTT
1360586 AAGCACAATGCTAAATTAGCCCAA
1 AAGCACAATGCTAAATTAGCCCAA
*
1360610 AAGCACAATGCTAAATTAGCTCAA
1 AAGCACAATGCTAAATTAGCCCAA
1360634 AAGCACAATGCT
1 AAGCACAATGCT
1360646 GAACTGATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.18
Consensus pattern (24 bp):
AAGCACAATGCTAAATTAGCCCAA
Found at i:1363599 original size:2 final size:2
Alignment explanation
Indices: 1363592--1363617 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1363582 CTAAAAAGTA
1363592 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
1363618 GTAACGCCCC
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):
AT
Found at i:1364524 original size:63 final size:63
Alignment explanation
Indices: 1364457--1364600 Score: 168
Period size: 63 Copynumber: 2.3 Consensus size: 63
1364447 GTTGGACCCT
* *
1364457 TAGTGCATCGGTGCACTACG-AGTGCATCGATGCATCAAGTGCATTCGA-TTTTCA-AAATAGCC
1 TAGTGCATCGATGCA-T-CGTAGTGCATCGATGCATCAAATGCATTCGAGTTTTCATAAA-AGCC
1364519 A
63 A
* * * *
1364520 TAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCT
1 TAGTGCATCGATGCATCG-TAGTGCATCGATGCATCAAATGCATTCGA-GTTTTCATAAAAGCCA
1364585 TAGTGCATCGATGCAT
1 TAGTGCATCGATGCAT
1364601 GAAATGCATT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 40 0.57
65 25 0.36
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (63 bp):
TAGTGCATCGATGCATCGTAGTGCATCGATGCATCAAATGCATTCGAGTTTTCATAAAAGCCA
Found at i:1364609 original size:63 final size:63
Alignment explanation
Indices: 1364479--1364615 Score: 163
Period size: 63 Copynumber: 2.2 Consensus size: 63
1364469 GCACTACGAG
* ***
1364479 TGCATCGATGCATCAAGTGCATTCGATTTTCAAAATAGCCATAGTGCATCGATGCATGGTTTG
1 TGCATCGATGCATCAAATGCATTCGATTTTCAAAATAGCCATAGTGCATCGATGCATGGTAAA
* *
1364542 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTTAGTGCATCGATGCAT-G-AA
1 TGCATCGATGCATCAAATGCATTCGA--TTTTCA-AAATAGCCATAGTGCATCGATGCATGGTAA
1364604 A
63 A
1364605 TGCATTCGATG
1 TGCA-TCGATG
1364616 TTCAATTTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
63 29 0.45
64 7 0.11
65 25 0.39
66 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (63 bp):
TGCATCGATGCATCAAATGCATTCGATTTTCAAAATAGCCATAGTGCATCGATGCATGGTAAA
Found at i:1372816 original size:64 final size:65
Alignment explanation
Indices: 1372736--1372860 Score: 191
Period size: 64 Copynumber: 1.9 Consensus size: 65
1372726 TGCACTAAGA
*
1372736 GTGCATAGATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCATAGTGCATCGATGCATGGTT
1 GTGCATAGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCCATAGTGCATCGATGCATGGTT
1372799 T
65 T
* * *
1372800 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGATGCATG
1 GTGCATAGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCATAGTGCATCGATGCATG
1372861 AAATGCATTC
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
64 27 0.49
65 25 0.45
66 3 0.05
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (65 bp):
GTGCATAGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCATAGTGCATCGATGCATGGTTT
Found at i:1372873 original size:64 final size:64
Alignment explanation
Indices: 1372737--1372874 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 64
1372727 GCACTAAGAG
* * ***
1372737 TGCATAGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCATAGTGCATCGATGCATGGTTTG
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCATAGTGCATCGATGCATGGTAAA
* *
1372801 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTTAGTGCATCGATGCAT-G-AA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCATAGTGCATCGATGCATGGTAA
1372863 A
64 A
1372864 TGCATTCGATG
1 TGCA-TCGATG
1372875 TTCAATTTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
63 4 0.06
64 33 0.52
65 24 0.38
66 3 0.05
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCATAGTGCATCGATGCATGGTAAA
Found at i:1373751 original size:20 final size:21
Alignment explanation
Indices: 1373717--1373778 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
1373707 GAACTAAAAT
1373717 TTGTCCCGAAAGACCACTGTA
1 TTGTCCCGAAAGACCACTGTA
* *
1373738 TTGT-CCGAAGGACCATTGTA
1 TTGTCCCGAAAGACCACTGTA
* *
1373758 TTGTCCCGTATGACCACTGTA
1 TTGTCCCGAAAGACCACTGTA
1373779 ACCCTCGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 18 0.51
21 17 0.49
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (21 bp):
TTGTCCCGAAAGACCACTGTA
Found at i:1375534 original size:17 final size:16
Alignment explanation
Indices: 1375512--1375545 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1375502 TAAAAACAGT
1375512 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1375529 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1375545 A
1 A
1375546 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1377511 original size:12 final size:12
Alignment explanation
Indices: 1377494--1377518 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1377484 AATGCCAAGA
1377494 CTAACTAAAGTT
1 CTAACTAAAGTT
1377506 CTAACTAAAGTT
1 CTAACTAAAGTT
1377518 C
1 C
1377519 CTTCATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (12 bp):
CTAACTAAAGTT
Found at i:1389071 original size:24 final size:23
Alignment explanation
Indices: 1389044--1389089 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1389034 ATTTAATTTT
*
1389044 ATAAGATTGAACTACTATTAAAAA
1 ATAAGATTGAACTA-TACTAAAAA
* *
1389068 ATAATATTTAACTATACTAAAA
1 ATAAGATTGAACTATACTAAAA
1389090 TTTAAATAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (23 bp):
ATAAGATTGAACTATACTAAAAA
Found at i:1389379 original size:15 final size:16
Alignment explanation
Indices: 1389341--1389380 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1389331 ACAGAATCTC
1389341 TAAATCATTCAATATT
1 TAAATCATTCAATATT
1389357 TAAATCATTCAACT-TT
1 TAAATCATTCAA-TATT
1389373 T-AATCATT
1 TAAATCATT
1389381 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.30
16 15 0.65
17 1 0.04
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATCATTCAATATT
Found at i:1398859 original size:2 final size:2
Alignment explanation
Indices: 1398852--1398882 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1398842 CCAATAAGAC
1398852 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 T
1398883 GTGTGTGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1399357 original size:234 final size:232
Alignment explanation
Indices: 1398902--1399355 Score: 621
Period size: 234 Copynumber: 1.9 Consensus size: 232
1398892 AGCTACGATT
* *
1398902 CTGTTAGACAATGTAAAATTCTTTTAGTTTTACACATATTTAAGACTGTTGGATAAGTGAAAATA
1 CTGTTACACAATGTAAAACTCTTTTAGTTTTACACATATTTAAGACTGTTGGATAAGTGAAAATA
* * *
1398967 GATGACTAAGATTAACAGTAGAAAATGAGAAGATATTTACTGGGGAAAAAAACAAGGAGTTAATC
66 GATGACTAAGATTAAAAGTAGAAAATGAGAAGATATTCACT--GGAAAAAAACAAGGAGTCAATC
* * *
1399032 TTAGCAATTTATTTTCACTTATCCAACGATCCTAAACTTGTGTAAAACTAAAGAGTTTTACATTG
129 TTAACAATCTATTTTCACTCATCCAACGATCCTAAACTTGTGTAAAACTAAAGAGTTTTACATTG
*
1399097 TGTAAGTGGATCCTAACCATATATATACGAGATAGGATC
194 TGTAAGTAGATCCTAACCATATATATACGAGATAGGATC
* *
1399136 CTGTTACACAATGTAAAACTCTTTTAGTTTTACACA-AGTTTAGGA-TAGTTGGATGAGTGAAAA
1 CTGTTACACAATGTAAAACTCTTTTAGTTTTACACATA-TTTAAGACT-GTTGGATAAGTGAAAA
* * * * *
1399199 TAGATGACTGATATTAAAAGTAGGAAATGAGAAGATATTCCCT-GAAAAACAGATAAGGAGTCAA
64 TAGATGACTAAGATTAAAAGTAGAAAATGAGAAGATATTCACTGGAAAAA-A-ACAAGGAGTCAA
** *
1399263 TCTTAATTATCTATTTTCACTCATCCAACGATCTTAAA-TATGTGT-AAACTAAAGAGTTTTACA
127 TCTTAACAATCTATTTTCACTCATCCAACGATCCTAAACT-TGTGTAAAACTAAAGAGTTTTACA
* *
1399326 TTGTGTAAGTAGATTCTAACCCTATATATA
191 TTGTGTAAGTAGATCCTAACCATATATATA
1399356 TATAATTTTT
Statistics
Matches: 194, Mismatches: 21, Indels: 12
0.85 0.09 0.05
Matches are distributed among these distances:
231 6 0.03
232 47 0.24
233 49 0.25
234 92 0.47
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (232 bp):
CTGTTACACAATGTAAAACTCTTTTAGTTTTACACATATTTAAGACTGTTGGATAAGTGAAAATA
GATGACTAAGATTAAAAGTAGAAAATGAGAAGATATTCACTGGAAAAAAACAAGGAGTCAATCTT
AACAATCTATTTTCACTCATCCAACGATCCTAAACTTGTGTAAAACTAAAGAGTTTTACATTGTG
TAAGTAGATCCTAACCATATATATACGAGATAGGATC
Found at i:1403664 original size:106 final size:106
Alignment explanation
Indices: 1402620--1403664 Score: 1856
Period size: 106 Copynumber: 9.9 Consensus size: 106
1402610 TGAAATTTTG
1402620 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* * ** *
1402685 TTGTGAAGTTGAAATTGGCCCTGAGATTGAGAAACTGTTTA
66 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
* *
1402726 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* * * * ** *
1402791 TTGTGAAGTTGAAATCGGCCCTGACATTGGGAAACTGTTTA
66 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
*
1402832 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1402897 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
66 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
1402938 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1403003 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
66 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
* *
1403044 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGCCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
1403109 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGGTTA
66 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
* *
1403150 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGAAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
1403215 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGGTTA
66 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
*
1403256 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCA
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
1403321 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGGTTA
66 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
* *
1403362 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGAAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
1403427 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGGTTA
66 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
1403468 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1403533 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
66 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
1403574 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1403639 TTGTGAAGTTGAAATTGGCTCTGAAA
66 TTGTGAAGTTGAAATTGGCTCTGAAA
1403665 GTGTTAACTG
Statistics
Matches: 911, Mismatches: 28, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 911 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTA
Found at i:1409105 original size:21 final size:21
Alignment explanation
Indices: 1409079--1409130 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1409069 TTACTTGGTG
1409079 TATCAATATTTATATGTTTAA
1 TATCAATATTTATATGTTTAA
1409100 TATCAATATTTATATGTTTAA
1 TATCAATATTTATATGTTTAA
1409121 TATCAATATT
1 TATCAATATT
1409131 AACATTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (21 bp):
TATCAATATTTATATGTTTAA
Found at i:1409439 original size:55 final size:55
Alignment explanation
Indices: 1409378--1409491 Score: 228
Period size: 55 Copynumber: 2.1 Consensus size: 55
1409368 AAAATTTTGG
1409378 GTGTTGAATTTAGAAATTGTGTGATATTTTTTAAGTGTCTGAAAATAAATAATAA
1 GTGTTGAATTTAGAAATTGTGTGATATTTTTTAAGTGTCTGAAAATAAATAATAA
1409433 GTGTTGAATTTAGAAATTGTGTGATATTTTTTAAGTGTCTGAAAATAAATAATAA
1 GTGTTGAATTTAGAAATTGTGTGATATTTTTTAAGTGTCTGAAAATAAATAATAA
1409488 GTGT
1 GTGT
1409492 CAATTTATAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (55 bp):
GTGTTGAATTTAGAAATTGTGTGATATTTTTTAAGTGTCTGAAAATAAATAATAA
Found at i:1409659 original size:16 final size:16
Alignment explanation
Indices: 1409638--1409668 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1409628 TTGAAATCTG
*
1409638 TGAAGGAATTGAAATA
1 TGAAGGAAATGAAATA
1409654 TGAAGGAAATGAAAT
1 TGAAGGAAATGAAAT
1409669 CTAAATCTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.26, T:0.23
Consensus pattern (16 bp):
TGAAGGAAATGAAATA
Found at i:1410230 original size:26 final size:27
Alignment explanation
Indices: 1410198--1410280 Score: 132
Period size: 26 Copynumber: 3.1 Consensus size: 27
1410188 CCTAAACCCG
1410198 AACCCGACCCAAATATCACACTTAAAA
1 AACCCGACCCAAATATCACACTTAAAA
*
1410225 AA-CCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCAAATATCACACTT-AAAA
*
1410252 AACCCGACCCAAATATCAAACTTAAAA
1 AACCCGACCCAAATATCACACTTAAAA
1410279 AA
1 AA
1410281 ACTAGACCCG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
26 19 0.37
27 14 0.27
28 18 0.35
ACGTcount: A:0.51, C:0.30, G:0.05, T:0.14
Consensus pattern (27 bp):
AACCCGACCCAAATATCACACTTAAAA
Found at i:1410261 original size:28 final size:28
Alignment explanation
Indices: 1410198--1410282 Score: 138
Period size: 28 Copynumber: 3.1 Consensus size: 28
1410188 CCTAAACCCG
1410198 AACCCGACCCAAATATCACACTT-AAAA
1 AACCCGACCCAAATATCACACTTAAAAA
*
1410225 AA-CCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCAAATATCACACTTAAAAA
*
1410252 AACCCGACCCAAATATCAAACTTAAAAA
1 AACCCGACCCAAATATCACACTTAAAAA
1410280 AAC
1 AAC
1410283 TAGACCCGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 19 0.36
27 8 0.15
28 26 0.49
ACGTcount: A:0.51, C:0.31, G:0.05, T:0.14
Consensus pattern (28 bp):
AACCCGACCCAAATATCACACTTAAAAA
Found at i:1410321 original size:32 final size:32
Alignment explanation
Indices: 1410285--1410423 Score: 122
Period size: 32 Copynumber: 4.2 Consensus size: 32
1410275 AAAAAAACTA
* *
1410285 GACCCGAACCCGATTTTTTTGAAAAAAAATCC
1 GACCCGAACCCAATTTTTTTAAAAAAAAATCC
* * * *
1410317 GACCCGATCCCAAAATGTTTTAAAAAAAACCCAACCC
1 GACCCGAACCC--AATTTTTTTAAAAAAA---AATCC
1410354 GACCCGAACCCAATTTTTTTAAAAAAAAATCC
1 GACCCGAACCCAATTTTTTTAAAAAAAAATCC
* * *
1410386 GACCCGATCCCGAA--ATTTT-AAAAAAAATCT
1 GACCCGAACCC-AATTTTTTTAAAAAAAAATCC
1410416 GACCCGAA
1 GACCCGAA
1410424 TACCAAAATA
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
30 17 0.20
31 4 0.05
32 24 0.28
33 2 0.02
34 12 0.14
35 14 0.16
37 14 0.16
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (32 bp):
GACCCGAACCCAATTTTTTTAAAAAAAAATCC
Found at i:1410370 original size:69 final size:67
Alignment explanation
Indices: 1410285--1410412 Score: 211
Period size: 69 Copynumber: 1.9 Consensus size: 67
1410275 AAAAAAACTA
* *
1410285 GACCCGAACCCGATTTTTTTGAAAAAAAATCCGACCCGATCCCAAAATGTTTTAAAAAAAACCCA
1 GACCCGAACCCAATTTTTTTAAAAAAAAATCCGACCCGATCCCAAAA--TTTTAAAAAAAACCCA
1410350 ACCC
64 ACCC
*
1410354 GACCCGAACCCAATTTTTTTAAAAAAAAATCCGACCCGATCCCGAAATTTTAAAAAAAA
1 GACCCGAACCCAATTTTTTTAAAAAAAAATCCGACCCGATCCCAAAATTTTAAAAAAAA
1410413 TCTGACCCGA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
67 12 0.21
69 44 0.79
ACGTcount: A:0.43, C:0.27, G:0.09, T:0.21
Consensus pattern (67 bp):
GACCCGAACCCAATTTTTTTAAAAAAAAATCCGACCCGATCCCAAAATTTTAAAAAAAACCCAAC
CC
Found at i:1413261 original size:27 final size:26
Alignment explanation
Indices: 1413215--1413266 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
1413205 ATTACTATGA
1413215 TCATATCATACATAACCATATCACATC
1 TCATATCATACATAACCATAT-ACATC
1413242 TCATATCACTA-AT-ACACATATACAT
1 TCATATCA-TACATAAC-CATATACAT
1413267 TTGTTACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
26 6 0.26
27 15 0.65
28 2 0.09
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (26 bp):
TCATATCATACATAACCATATACATC
Found at i:1413509 original size:18 final size:18
Alignment explanation
Indices: 1413486--1413535 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1413476 GCGTAGAATT
*
1413486 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1413504 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
1413522 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
1413536 GCGTAGACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.22, C:0.34, G:0.26, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1417709 original size:18 final size:18
Alignment explanation
Indices: 1417686--1417735 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
1417676 GCGTAGAATT
* *
1417686 TGTCCCGAATGACCACTG
1 TGTCCCGAAGGACCACTA
*
1417704 TGTCCCGAAGGATCACTA
1 TGTCCCGAAGGACCACTA
1417722 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
1417736 GCGTAGACCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1421824 original size:106 final size:106
Alignment explanation
Indices: 1421696--1421889 Score: 325
Period size: 106 Copynumber: 1.8 Consensus size: 106
1421686 AAAACAAGAA
* * *
1421696 TTTTAAATAATTTTTATCGATTACTTTGATTCTAAAATTTTACATAATTTTAAAATAATTCTAAA
1 TTTTAAAGAATTTTGATAGATTACTTTGATTCTAAAATTTTACATAATTTTAAAATAATTCTAAA
*
1421761 ATCAATCCATTCGTAGAATAATAGGTCAGTTTAAATTTTCT
66 ATCAATCCATTCGTAAAATAATAGGTCAGTTTAAATTTTCT
*
1421802 TTTTAAAGAATTTTGATAGATTACTTTGATTCTAAAATTTTACATACTTTTAAAATAATTCTAAA
1 TTTTAAAGAATTTTGATAGATTACTTTGATTCTAAAATTTTACATAATTTTAAAATAATTCTAAA
* *
1421867 ATCAATTCATTCTTAAAATAATA
66 ATCAATCCATTCGTAAAATAATA
1421890 TGCCAGTTGA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 81 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.45
Consensus pattern (106 bp):
TTTTAAAGAATTTTGATAGATTACTTTGATTCTAAAATTTTACATAATTTTAAAATAATTCTAAA
ATCAATCCATTCGTAAAATAATAGGTCAGTTTAAATTTTCT
Found at i:1422234 original size:20 final size:21
Alignment explanation
Indices: 1422209--1422249 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1422199 TTATTTTATA
*
1422209 AAAGA-GTGGGAAACAGGAAC
1 AAAGAGGTGGAAAACAGGAAC
*
1422229 AAAGAGGTGGAAAACATGAAC
1 AAAGAGGTGGAAAACAGGAAC
1422250 TCATGTTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.10, G:0.32, T:0.07
Consensus pattern (21 bp):
AAAGAGGTGGAAAACAGGAAC
Found at i:1429403 original size:231 final size:230
Alignment explanation
Indices: 1429000--1429460 Score: 886
Period size: 231 Copynumber: 2.0 Consensus size: 230
1428990 TTTGCATAGT
1429000 TCTATTTTGGTAACTTAATTATTATTATTTTTTATTAATTTAAGGTGATTATAAGGTATTACACG
1 TCTATTTTGGTAACTTAATTATTATTATTTTTTATTAATTTAAGGTGATTATAAGGTATTACACG
*
1429065 TTCTAAAATTTTTTAACTATTTGACAATGAAAACTTAAATATTCTTACAATCTCTGGTGCTTAAA
66 TTCTAAAATTTTTTAACTATTTGACAATGAAAACTTAAATATTCTTACAATATCTGGTGCTTAAA
1429130 CCTGGATCTCTAGAGATAACAATCATCTTTTTAACTACTAATGTAACTTGATTGGTGCAATTTAA
131 CCTGGATCTCTAGAGATAACAATCATCTTTTTAACTACTAATGTAACTTGATTGGTGCAATTTAA
1429195 TTATTTTTTTAAAATTATAGTTTCATTTTAATAAAA
196 TTA-TTTTTTAAAATTATAGTTTCATTTTAATAAAA
*
1429231 TCTATTTTGGTAACTTAATTATTATTATTTTTTATTAATTTAAGGTGATTATAAGGTATTATACG
1 TCTATTTTGGTAACTTAATTATTATTATTTTTTATTAATTTAAGGTGATTATAAGGTATTACACG
1429296 TTCTAAAATTTTTTAACTATTTGACAATGAAAACTTAAATATTCTTACAATATCTGGTGCTTAAA
66 TTCTAAAATTTTTTAACTATTTGACAATGAAAACTTAAATATTCTTACAATATCTGGTGCTTAAA
*
1429361 CCTGGATCTCTAGATATAACAATCATCTTTTTAACTACTAATGTAACTTGATTGGTGCAATTTAA
131 CCTGGATCTCTAGAGATAACAATCATCTTTTTAACTACTAATGTAACTTGATTGGTGCAATTTAA
1429426 TTATTTTTTAAAATTATAGTTTCATTTTAATAAAA
196 TTATTTTTTAAAATTATAGTTTCATTTTAATAAAA
1429461 AAATCCACAT
Statistics
Matches: 227, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
230 32 0.14
231 195 0.86
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (230 bp):
TCTATTTTGGTAACTTAATTATTATTATTTTTTATTAATTTAAGGTGATTATAAGGTATTACACG
TTCTAAAATTTTTTAACTATTTGACAATGAAAACTTAAATATTCTTACAATATCTGGTGCTTAAA
CCTGGATCTCTAGAGATAACAATCATCTTTTTAACTACTAATGTAACTTGATTGGTGCAATTTAA
TTATTTTTTAAAATTATAGTTTCATTTTAATAAAA
Found at i:1439798 original size:51 final size:51
Alignment explanation
Indices: 1439697--1439801 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 51
1439687 ATTTTGTAAC
* *
1439697 TTTTAATAGTCAATGAACTCAACAAAATAACATCTTATAGTCAGAAGACCA
1 TTTTAATAATCAATGAACTCAACAAAATAACATCTTATAATCAGAAGACCA
* * *
1439748 TTTTAATAATC-ATGAAACTCAACAAAATAAC-TTTCTATAATTAGAGGACCA
1 TTTTAATAATCAATG-AACTCAACAAAATAACATCT-TATAATCAGAAGACCA
1439799 TTT
1 TTT
1439802 GGGTACGTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
50 5 0.11
51 42 0.89
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (51 bp):
TTTTAATAATCAATGAACTCAACAAAATAACATCTTATAATCAGAAGACCA
Found at i:1444358 original size:22 final size:21
Alignment explanation
Indices: 1444310--1444358 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1444300 TAATTTAAAA
* * *
1444310 AATTAAAAAATTAAATATTTT
1 AATTTAAAAATCAAATAATTT
1444331 ATATTTAAAAATCAAATCAATTT
1 A-ATTTAAAAATCAAAT-AATTT
1444354 AATTT
1 AATTT
1444359 TTATAATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 17 0.74
23 5 0.22
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTAAAAATCAAATAATTT
Found at i:1444361 original size:30 final size:31
Alignment explanation
Indices: 1444296--1444363 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
1444286 TATTAATTTA
*
1444296 TTTATAATTTAAAAAATTAAAAAATTAAATAT
1 TTTAT-ATTTAAAAAATCAAAAAATTAAATAT
* *
1444328 TTTATATTT-AAAAATCAAATCAATTTAAT-T
1 TTTATATTTAAAAAATCAAA-AAATTAAATAT
1444358 TTTATA
1 TTTATA
1444364 ATACTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 16 0.50
31 11 0.34
32 5 0.16
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTATATTTAAAAAATCAAAAAATTAAATAT
Found at i:1445867 original size:16 final size:17
Alignment explanation
Indices: 1445827--1445870 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1445817 CCCTACTTAA
1445827 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** *
1445844 TTTTATATTT-TTAAAT
1 TTAAATATTTAATAAAT
1445860 TTAAATATTTA
1 TTAAATATTTA
1445871 TTTTTACATG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:1446716 original size:15 final size:15
Alignment explanation
Indices: 1446698--1446727 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1446688 AGCAGCATTT
*
1446698 TCAACAGCAGCAGCA
1 TCAACAGCAACAGCA
1446713 TCAACAGCAACAGCA
1 TCAACAGCAACAGCA
1446728 GTGGCTCAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.17, T:0.07
Consensus pattern (15 bp):
TCAACAGCAACAGCA
Found at i:1449045 original size:107 final size:106
Alignment explanation
Indices: 1448859--1449072 Score: 419
Period size: 107 Copynumber: 2.0 Consensus size: 106
1448849 CTCCAGTTCC
1448859 TCGTATTCCCTTTCATTTTTTATATTTTTAAAAATTTCTTATATTTACATAAATTCTAGTTTTGG
1 TCGTATTCCCTTTCATTTTTTATATTTTTAAAAATTTCTTATATTTACATAAATTCTAGTTTTGG
1448924 AAGTAGAATTCTGAAGTGTTATTTCATTGGTATAACAATTCT
66 AAGTAGAATTCTGAAGTGTTA-TTCATTGGTATAACAATTCT
1448966 TCGTATTCCCTTTCATTTTTTATATTTTTAAAAATTTCTTATATTTACATAAATTCTAGTTTTGG
1 TCGTATTCCCTTTCATTTTTTATATTTTTAAAAATTTCTTATATTTACATAAATTCTAGTTTTGG
1449031 AAGTAGAATTCTGAAGTGTTATTCATTGGTATAACAATTCT
66 AAGTAGAATTCTGAAGTGTTATTCATTGGTATAACAATTCT
1449072 T
1 T
1449073 AAAAAGGAAG
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 21 0.20
107 86 0.80
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.50
Consensus pattern (106 bp):
TCGTATTCCCTTTCATTTTTTATATTTTTAAAAATTTCTTATATTTACATAAATTCTAGTTTTGG
AAGTAGAATTCTGAAGTGTTATTCATTGGTATAACAATTCT
Found at i:1450495 original size:19 final size:20
Alignment explanation
Indices: 1450464--1450508 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1450454 GGGGTACATA
1450464 ATGCGGTCTGATGCGATCCG
1 ATGCGGTCTGATGCGATCCG
* *
1450484 ATGCGG-CTGATGCGGTCTG
1 ATGCGGTCTGATGCGATCCG
1450503 ATGCGG
1 ATGCGG
1450509 GCCGATGCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.13, C:0.22, G:0.40, T:0.24
Consensus pattern (20 bp):
ATGCGGTCTGATGCGATCCG
Found at i:1450503 original size:10 final size:10
Alignment explanation
Indices: 1450464--1450508 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
1450454 GGGGTACATA
1450464 ATGCGGTCTG
1 ATGCGGTCTG
* *
1450474 ATGCGATCCG
1 ATGCGGTCTG
1450484 ATGCGG-CTG
1 ATGCGGTCTG
1450493 ATGCGGTCTG
1 ATGCGGTCTG
1450503 ATGCGG
1 ATGCGG
1450509 GCCGATGCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.13, C:0.22, G:0.40, T:0.24
Consensus pattern (10 bp):
ATGCGGTCTG
Found at i:1450928 original size:16 final size:16
Alignment explanation
Indices: 1450903--1450941 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1450893 TAGATAAGTT
* *
1450903 CTTTTTGTTGCAATAG
1 CTTTTAGTTGCAAAAG
1450919 CTTTTAGTTGCAAAAG
1 CTTTTAGTTGCAAAAG
1450935 CTTTTAG
1 CTTTTAG
1450942 CTTTTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (16 bp):
CTTTTAGTTGCAAAAG
Found at i:1450982 original size:112 final size:112
Alignment explanation
Indices: 1450843--1451118 Score: 534
Period size: 112 Copynumber: 2.5 Consensus size: 112
1450833 ATGTGTACTA
1450843 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
1 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
*
1450908 TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
66 TGTTGCAATAGCTTTTACTTGCAAAAGCTTTTAGCTTTTAGAAACAT
1450955 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
1 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
1451020 TGTTGCAATAGCTTTTACTTGCAAAAGCTTTTAGCTTTTAGAAACAT
66 TGTTGCAATAGCTTTTACTTGCAAAAGCTTTTAGCTTTTAGAAACAT
1451067 AAACAAGTTGTTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTAT
1 AAACAAGTTG-TTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTAT
1451119 GATTTTACTG
Statistics
Matches: 162, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
112 121 0.75
113 41 0.25
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (112 bp):
AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
TGTTGCAATAGCTTTTACTTGCAAAAGCTTTTAGCTTTTAGAAACAT
Found at i:1451041 original size:16 final size:16
Alignment explanation
Indices: 1451022--1451052 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1451012 GTTCTTTTTG
*
1451022 TTGCAATAGCTTTTAC
1 TTGCAAAAGCTTTTAC
1451038 TTGCAAAAGCTTTTA
1 TTGCAAAAGCTTTTA
1451053 GCTTTTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (16 bp):
TTGCAAAAGCTTTTAC
Found at i:1456511 original size:46 final size:47
Alignment explanation
Indices: 1456455--1456578 Score: 178
Period size: 46 Copynumber: 2.7 Consensus size: 47
1456445 TTTTGAATAA
* *
1456455 ATGTATGCGAATTAGAAATCATGCGGTTAGGTTTATTTTT-TTGAGC
1 ATGTATGCGAATTAGAAATCATGCGGTTAGGTTTATTTTTCTCGAAC
* *
1456501 ATGTATGCGAACTAGAAATCATGCGGCTAGGTTTATTTTTCTCGAAC
1 ATGTATGCGAATTAGAAATCATGCGGTTAGGTTTATTTTTCTCGAAC
* * *
1456548 AAGCATGCGAATTAGATATCATGCGGTTAGG
1 ATGTATGCGAATTAGAAATCATGCGGTTAGG
1456579 ATTTTTTGTG
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 38 0.56
47 30 0.44
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (47 bp):
ATGTATGCGAATTAGAAATCATGCGGTTAGGTTTATTTTTCTCGAAC
Found at i:1456957 original size:55 final size:55
Alignment explanation
Indices: 1456891--1456998 Score: 189
Period size: 55 Copynumber: 2.0 Consensus size: 55
1456881 GCGTTCAGAT
* *
1456891 GATTCATGAAGAATGACATCCGATGAATGAAGAAATTTGAACCTGACTGAAGAAC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGACTGAAGAAC
*
1456946 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGA
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGACTGAAGA
1456999 CTGATCCACA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (55 bp):
GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGACTGAAGAAC
Found at i:1457013 original size:55 final size:55
Alignment explanation
Indices: 1456899--1457021 Score: 167
Period size: 55 Copynumber: 2.2 Consensus size: 55
1456889 ATGATTCATG
* * * **
1456899 AAGAATGACATCCGATGAATGAAGAAATTTGAACCTGACTGAAGAACGATTCATG
1 AAGAAAGACATCCGATGAATGAAGAAATTTGAAACTGACTGAAGAACGATCCACA
* *
1456954 AAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAG-ACTGATCCACA
1 AAGAAAGACATCCGATGAATGAAGAAATTTGAAACTGACTGAAGAAC-GATCCACA
1457009 AAGAAAGACATCC
1 AAGAAAGACATCC
1457022 TGAAGATGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 2 0.03
55 58 0.97
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (55 bp):
AAGAAAGACATCCGATGAATGAAGAAATTTGAAACTGACTGAAGAACGATCCACA
Found at i:1457798 original size:72 final size:72
Alignment explanation
Indices: 1457681--1457830 Score: 264
Period size: 72 Copynumber: 2.1 Consensus size: 72
1457671 CCCTATTACA
1457681 CAAGAAAATATAAAGACTTCAGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGTGATGATAGC
1 CAAGAAAATATAAAGACTTCAGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGTGATGATAGC
1457746 AAATGAT
66 AAATGAT
* * *
1457753 CAAGAAAATATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
1 CAAGAAAATATAAAGACTTCAGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGTGATGATAGC
*
1457818 AACTGAT
66 AAATGAT
1457825 CAAGAA
1 CAAGAA
1457831 CCTGTTAGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (72 bp):
CAAGAAAATATAAAGACTTCAGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGTGATGATAGC
AAATGAT
Found at i:1461416 original size:125 final size:125
Alignment explanation
Indices: 1461184--1461419 Score: 303
Period size: 125 Copynumber: 1.9 Consensus size: 125
1461174 GGCATGACTA
** * * *
1461184 AACCCACATCATGTTGAGATGACAAGATTTGGACCAAGGAGTCATGAAGAATGAGCCTTACAAAT
1 AACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGGCATGAAAAATGAGCCTTACAAAT
* * *
1461249 TGAGATGATGGGGCATTTTGAAGGCCCGTACCAGTATGAGATAATGTCGGGGCACAACTG
66 TGAGATGATGGAGCATTTTGAAGGCCCGTACCAGAATAAGATAATGTCGGGGCACAACTG
* * * * *
1461309 AACCCACATCATGTTGAGATGATAAGGTTCAGACCAAGAAGGCATTAAAAATGAGCCTTATAATT
1 AACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGGCATGAAAAATGAGCCTTACAAAT
* * * *
1461374 TGAGGTGTTGGAGTATTTTGAAGGCTCGTACCTA-AATAAGATAATG
66 TGAGATGATGGAGCATTTTGAAGGCCCGTACC-AGAATAAGATAATG
1461420 GGTCGACATT
Statistics
Matches: 93, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
125 92 0.99
126 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (125 bp):
AACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGGCATGAAAAATGAGCCTTACAAAT
TGAGATGATGGAGCATTTTGAAGGCCCGTACCAGAATAAGATAATGTCGGGGCACAACTG
Done.