Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004961.1 Hibiscus syriacus cultivar Beakdansim tig00011152_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: 87036
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:874 original size:9 final size:9
Alignment explanation
Indices: 852--928 Score: 57
Period size: 9 Copynumber: 8.2 Consensus size: 9
842 TCTTGAACCC
852 TTCTTTTTCT
1 TTCTTTTT-T
*
862 TTCTTTTTG
1 TTCTTTTTT
871 TTCTTTTTT
1 TTCTTTTTT
880 TTCCTTTTTT
1 TT-CTTTTTT
* * *
890 TTCATATAT
1 TTCTTTTTT
*
899 TT-TTTTTA
1 TTCTTTTTT
*
907 TTATTTTTT
1 TTCTTTTTT
916 TATCATTTTTT
1 T-TC-TTTTTT
927 TT
1 TT
929 GTTCATATTC
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
8 4 0.08
9 22 0.42
10 19 0.37
11 7 0.13
ACGTcount: A:0.09, C:0.10, G:0.01, T:0.79
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:874 original size:19 final size:19
Alignment explanation
Indices: 852--888 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
842 TCTTGAACCC
852 TTCTTTTTCTTT-CTTTTTG
1 TTCTTTTT-TTTCCTTTTTG
871 TTCTTTTTTTTCCTTTTT
1 TTCTTTTTTTTCCTTTTT
889 TTTCATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (19 bp):
TTCTTTTTTTTCCTTTTTG
Found at i:913 original size:11 final size:11
Alignment explanation
Indices: 885--927 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
875 TTTTTTTCCT
885 TTTTTTTCATATA
1 TTTTTTT-AT-TA
898 TTTTTTTTATTA
1 -TTTTTTTATTA
*
910 TTTTTTTATCA
1 TTTTTTTATTA
921 TTTTTTT
1 TTTTTTT
928 TGTTCATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 17 0.61
12 2 0.07
13 2 0.07
14 7 0.25
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTATTA
Found at i:934 original size:13 final size:13
Alignment explanation
Indices: 884--934 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
874 TTTTTTTTCC
884 TTTTTTTTCATATA
1 TTTTTTTTCAT-TA
898 TTTTTTTT-ATTA
1 TTTTTTTTCATTA
910 TTTTTTTATCATT-
1 TTTTTTT-TCATTA
923 TTTTTTGTTCAT
1 TTTTTT-TTCAT
935 ATTCAAGCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
12 9 0.26
13 13 0.38
14 12 0.35
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTTTTCATTA
Found at i:12188 original size:3 final size:3
Alignment explanation
Indices: 12182--12217 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
12172 ACATTATTAT
12182 TAA TAA TAA -AA TAA TAA TAA T-A TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12218 TCCCGGATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12198 original size:11 final size:11
Alignment explanation
Indices: 12182--12217 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
12172 ACATTATTAT
12182 TAATAATAAAA
1 TAATAATAAAA
*
12193 TAATAATAATA
1 TAATAATAAAA
12204 TAATAATAATAA
1 TAATAATAA-AA
12216 TA
1 TA
12218 TCCCGGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 19 0.86
12 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:12218 original size:14 final size:14
Alignment explanation
Indices: 12182--12218 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12172 ACATTATTAT
*
12182 TAATAATAAAATAA
1 TAATAATATAATAA
12196 TAATAATATAATAA
1 TAATAATATAATAA
12210 TAATAATAT
1 TAATAATAT
12219 CCCGGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATAATATAATAA
Found at i:13477 original size:103 final size:105
Alignment explanation
Indices: 13260--13477 Score: 287
Period size: 103 Copynumber: 2.1 Consensus size: 105
13250 GTTAAAAAGT
* * * * *
13260 TATTGTTAATAGTGTCAAACATTTGGTCACTAAAAAACACTTATTGTGACAACATTGGTGGTCAC
1 TATTGATAATAGTATCAAACATTTGGTCAATAAAAAACACTTAGTGTGACAACATTGATGGTCAC
* ** * *
13325 AAAATATACTTTTAGTGTCAAATAAATTTTTCACGATTTC
66 AAAATATACTTTTAGTGTCAAAAAAATTCATCACAATTTA
* * * *
13365 TATTAATAATAGTATCAAACATTTGGTCAAT-AAAAATA-TTAGTGTGACAATATTGATTGTCAC
1 TATTGATAATAGTATCAAACATTTGGTCAATAAAAAACACTTAGTGTGACAACATTGATGGTCAC
*
13428 AAAATATATTTTTAGTGTCAAAAAAATTCATCACAATTTA
66 AAAATATACTTTTAGTGTCAAAAAAATTCATCACAATTTA
13468 TATTGATAAT
1 TATTGATAAT
13478 TGTGTCGAAT
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
103 64 0.66
104 6 0.06
105 27 0.28
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.38
Consensus pattern (105 bp):
TATTGATAATAGTATCAAACATTTGGTCAATAAAAAACACTTAGTGTGACAACATTGATGGTCAC
AAAATATACTTTTAGTGTCAAAAAAATTCATCACAATTTA
Found at i:13496 original size:103 final size:102
Alignment explanation
Indices: 13304--13502 Score: 236
Period size: 103 Copynumber: 1.9 Consensus size: 102
13294 AAACACTTAT
* * ** * *
13304 TGTGACAACATTGGTGGTCACAAAATATACTTTTAGTGTCAAATAAATTTTTCACGATTTCTATT
1 TGTGACAACATTGATGGTCACAAAATATACTTTTAGTGTCAAAAAAATTCATCACAATTTATATT
***
13369 AATAATAGTATCAAACATTTGGTCAATAAAAATATTAG
66 AATAATAGTATCAAACAAAAGGTCAA-AAAAATATTAG
* * *
13407 TGTGACAATATTGATTGTCACAAAATATATTTTTAGTGTCAAAAAAATTCATCACAATTTATATT
1 TGTGACAACATTGATGGTCACAAAATATACTTTTAGTGTCAAAAAAATTCATCACAATTTATATT
* * * * *
13472 GATAATTGTGTCGAATAAAAGGTCAAAAAAA
66 AATAATAGTATCAAACAAAAGGTCAAAAAAA
13503 GAACAATTGT
Statistics
Matches: 79, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
102 5 0.06
103 74 0.94
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.36
Consensus pattern (102 bp):
TGTGACAACATTGATGGTCACAAAATATACTTTTAGTGTCAAAAAAATTCATCACAATTTATATT
AATAATAGTATCAAACAAAAGGTCAAAAAAATATTAG
Found at i:13514 original size:103 final size:103
Alignment explanation
Indices: 13266--13514 Score: 221
Period size: 103 Copynumber: 2.4 Consensus size: 103
13256 AAGTTATTGT
* *** * * *
13266 TAATAGTGTCAAACATTTGGTCACTAAAAAACACTTATTGTGACAACATTGGTGGTCACAAAATA
1 TAATAGTATCAAACAAAAGGTCAATAAAAAA-AC-AATTGTGACAACATTGATGGTCACAAAATA
* ** * *
13331 TACTTTTAGTGTCAAATAAATTTTTCACGATTTCTATTAA
64 TACTTTTAGTGTCAAAAAAATTCATCACAATTTATATTAA
*** * ** * * *
13371 TAATAGTATCAAACATTTGGTCAATAAAAATATTAGTGTGACAATATTGATTGTCACAAAATATA
1 TAATAGTATCAAACAAAAGGTCAATAAAAAAACAATTGTGACAACATTGATGGTCACAAAATATA
* *
13436 TTTTTAGTGTCAAAAAAATTCATCACAATTTATATTGA
66 CTTTTAGTGTCAAAAAAATTCATCACAATTTATATTAA
* * * *
13474 TAATTGTGTCGAATAAAAGGTCAA-AAAAAGAACAATTGTGA
1 TAATAGTATCAAACAAAAGGTCAATAAAAA-AACAATTGTGA
13515 AAAATTTTAG
Statistics
Matches: 117, Mismatches: 26, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
102 5 0.04
103 83 0.71
104 1 0.01
105 28 0.24
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (103 bp):
TAATAGTATCAAACAAAAGGTCAATAAAAAAACAATTGTGACAACATTGATGGTCACAAAATATA
CTTTTAGTGTCAAAAAAATTCATCACAATTTATATTAA
Found at i:13549 original size:16 final size:16
Alignment explanation
Indices: 13528--13560 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
13518 ATTTTAGAAT
13528 AATTGTCACTAATATA
1 AATTGTCACTAATATA
13544 AATTGTCACTAATATA
1 AATTGTCACTAATATA
13560 A
1 A
13561 TAGTGACGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (16 bp):
AATTGTCACTAATATA
Found at i:14644 original size:2 final size:2
Alignment explanation
Indices: 14637--14726 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
14627 AAATTTACCC
14637 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
14679 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
14721 AT AT AT
1 AT AT AT
14727 CTTTGGATTA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15552 original size:19 final size:16
Alignment explanation
Indices: 15530--15573 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
15520 AATGTAAGTC
15530 TTTTTATTCTCTTCATTCA
1 TTTTTATT-TCTT-ATT-A
15549 TTTTTATTTCTTATTA
1 TTTTTATTTCTTATTA
*
15565 CTTTTATTT
1 TTTTTATTT
15574 AAAAACCCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 9 0.38
17 3 0.12
18 4 0.17
19 8 0.33
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTATTTCTTATTA
Found at i:16412 original size:13 final size:13
Alignment explanation
Indices: 16363--16412 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
16353 GCATTTGAAT
*
16363 ATTTGCATTATGA
1 ATTTGCATTATGC
* *
16376 ATTTTCATCACTGC
1 ATTTGCATTA-TGC
16390 ATTATGCATTATGC
1 ATT-TGCATTATGC
16404 ATTTGCATT
1 ATTTGCATT
16413 TATATTTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 14 0.47
14 11 0.37
15 5 0.17
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (13 bp):
ATTTGCATTATGC
Found at i:26816 original size:15 final size:15
Alignment explanation
Indices: 26796--26825 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26786 CTTTCTCATA
26796 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
26811 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
26826 CCAGCCTCGT
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:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:35795 original size:3 final size:3
Alignment explanation
Indices: 35787--35841 Score: 62
Period size: 3 Copynumber: 18.3 Consensus size: 3
35777 TAGTATATAT
35787 ATA ATA ATA AT- ATA TATA ATA ATA AT- ATAA ATA ATA ATA AT- ATAA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA AT-A
35832 ATA ATA ATA A
1 ATA ATA ATA A
35842 AGAGAAGAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
2 6 0.13
3 33 0.72
4 7 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:35801 original size:15 final size:15
Alignment explanation
Indices: 35781--35841 Score: 104
Period size: 15 Copynumber: 4.1 Consensus size: 15
35771 TTTGGTTAGT
*
35781 ATATATATAATAATA
1 ATATAAATAATAATA
*
35796 ATATATATAATAATA
1 ATATAAATAATAATA
35811 ATATAAATAATAATA
1 ATATAAATAATAATA
35826 ATATAAATAATAATA
1 ATATAAATAATAATA
35841 A
1 A
35842 AGAGAAGAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATAAATAATAATA
Found at i:38013 original size:105 final size:105
Alignment explanation
Indices: 37691--38888 Score: 2081
Period size: 105 Copynumber: 11.4 Consensus size: 105
37681 GTATTGCTCC
* * * * * *
37691 GAGTCCAATATCCTCCGCTGTGAAGTTGAAAATGGTTCTGGAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
* * * *
37756 CTAACGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCCG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * ** *
37797 GAGTCCAGTATCATTCGTTGTGAAGTTGAAATTGGCTCTTGAAATTGAGAAGTTGTCGGTTGGCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAA-ATGTTTGTTGACA
** *** * *
37862 GTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTATCTT
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
37904 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
37969 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
38009 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGACATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
38074 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
38114 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
38179 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
38219 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
38284 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
38324 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
38389 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
38429 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
38494 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
38534 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
38599 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
38639 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
38704 TAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
38744 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
38809 TAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
38849 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
38889 GGTAAAACCT
Statistics
Matches: 1043, Mismatches: 47, Indels: 5
0.95 0.04 0.00
Matches are distributed among these distances:
105 911 0.87
106 44 0.04
107 88 0.08
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:49050 original size:18 final size:19
Alignment explanation
Indices: 49029--49067 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
49019 AAAGGTTAGT
49029 AAAATAGAAA-AAAAAATA
1 AAAATAGAAATAAAAAATA
* *
49047 AAAATATAAATAATAAATA
1 AAAATAGAAATAAAAAATA
49066 AA
1 AA
49068 TGGTAAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (19 bp):
AAAATAGAAATAAAAAATA
Found at i:50523 original size:3 final size:3
Alignment explanation
Indices: 50515--50572 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
50505 AGTAATATAT
50515 ATA ATA ATA ATA AT- ATA TATA ATA ATA AT- ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA
*
50560 TTA ATA ATA ATA A
1 ATA ATA ATA ATA A
50573 AGAGAAGAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 4 0.08
3 40 0.82
4 5 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:50536 original size:15 final size:16
Alignment explanation
Indices: 50507--50572 Score: 104
Period size: 15 Copynumber: 4.4 Consensus size: 16
50497 GTTTGGTTAG
50507 TAAT-ATATATAATAA
1 TAATAATATATAATAA
50522 TAATAATATAT-ATAA
1 TAATAATATATAATAA
50537 TAATAATATA-AATAA
1 TAATAATATATAATAA
50552 TAATAATAT-TAATAA
1 TAATAATATATAATAA
50567 TAATAA
1 TAATAA
50573 AGAGAAGAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
15 42 0.88
16 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAATATATAATAA
Found at i:51917 original size:15 final size:15
Alignment explanation
Indices: 51897--51929 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
51887 TGGAAACATG
51897 AAATAA-AAAATAAAT
1 AAATAATAAAAT-AAT
51912 AAATAATAAAATAAT
1 AAATAATAAAATAAT
51927 AAA
1 AAA
51930 ATATGTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATAATAAAATAAT
Found at i:53200 original size:2 final size:2
Alignment explanation
Indices: 53193--53262 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
53183 CTTTAAGTTT
53193 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53235 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
53263 ATTTTACCTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55255 original size:41 final size:41
Alignment explanation
Indices: 55207--55295 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
55197 CAATGAATTA
55207 AAAAATAAAAAATATTAAGTTATTTGTATACAAAATTTATT
1 AAAAATAAAAAATATTAAGTTATTTGTATACAAAATTTATT
** *
55248 AAAAATAAAATTTATTAAGTTATTTGTATACAAATTTTATT
1 AAAAATAAAAAATATTAAGTTATTTGTATACAAAATTTATT
*
55289 ACAAATA
1 AAAAATA
55296 TATATAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (41 bp):
AAAAATAAAAAATATTAAGTTATTTGTATACAAAATTTATT
Found at i:58606 original size:34 final size:34
Alignment explanation
Indices: 58551--58633 Score: 130
Period size: 34 Copynumber: 2.4 Consensus size: 34
58541 AGATTGTATT
*
58551 CAATCAATATTGTGTGTGTGTATATATATATATATC
1 CAATCAATA-T-TGTGTGTGTATACATATATATATC
*
58587 CAATCAATATTGTGTGTGTATACATATATATGTC
1 CAATCAATATTGTGTGTGTATACATATATATATC
58621 CAATCAATATTGT
1 CAATCAATATTGT
58634 ATGTATAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 35 0.78
35 1 0.02
36 9 0.20
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (34 bp):
CAATCAATATTGTGTGTGTATACATATATATATC
Found at i:62175 original size:58 final size:59
Alignment explanation
Indices: 62080--62228 Score: 171
Period size: 59 Copynumber: 2.5 Consensus size: 59
62070 TTAGATTGAT
* * *
62080 CCTTAAACTTTTTAATATTCCAATTTCATCCCAAAACTATGA-CT-TATTCTAAATTAG-C
1 CCTTAAACTTTTGAATATTCTAATTTCATCCCAAAACTA-AACCTCT-TTCTAAATTAGTC
* * *
62138 CCTTAAACTTTTGAATATTCTAATTTTATTCCTAAACTAAACCCTCTTTCTAAATTAGTC
1 CCTTAAACTTTTGAATATTCTAATTTCATCCCAAAACTAAA-CCTCTTTCTAAATTAGTC
* *
62198 CC-CAAAATTTTGAATATTCTAATTTCATCCC
1 CCTTAAACTTTTGAATATTCTAATTTCATCCC
62229 CAATTCATCC
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 34 0.44
59 38 0.49
60 4 0.05
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (59 bp):
CCTTAAACTTTTGAATATTCTAATTTCATCCCAAAACTAAACCTCTTTCTAAATTAGTC
Found at i:65974 original size:27 final size:28
Alignment explanation
Indices: 65900--65977 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 28
65890 GTGTGCAATA
* *
65900 CGCACTCGCAAGTGCCTCATATATTAAT
1 CGCACTCGAAAGTGCCTCATATAGTAAT
* **
65928 CACACTCGAAAGTGTTTCAT-TAGTAAT
1 CGCACTCGAAAGTGCCTCATATAGTAAT
* *
65955 CGCACTTGGAAGTGCCTCATATA
1 CGCACTCGAAAGTGCCTCATATA
65978 ACTTGCACCA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (28 bp):
CGCACTCGAAAGTGCCTCATATAGTAAT
Found at i:66255 original size:22 final size:22
Alignment explanation
Indices: 66227--66274 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
66217 AAAATCATCC
66227 ATAACCATATATTATATATCAT
1 ATAACCATATATTATATATCAT
66249 ATAACCATATATTATATATCAT
1 ATAACCATATATTATATATCAT
66271 ATAA
1 ATAA
66275 AATATCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAACCATATATTATATATCAT
Found at i:66279 original size:12 final size:12
Alignment explanation
Indices: 66264--66288 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66254 CATATATTAT
66264 ATATCATATAAA
1 ATATCATATAAA
66276 ATATCATATAAA
1 ATATCATATAAA
66288 A
1 A
66289 ATGTATTAGG
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATCATATAAA
Found at i:74706 original size:153 final size:148
Alignment explanation
Indices: 74423--74724 Score: 446
Period size: 153 Copynumber: 2.0 Consensus size: 148
74413 GTTAAAAAAT
* *
74423 TGCATGATTTAATTTTCATGGAACTTTACATCAAAGTTCATTGAACCAAAAAAAAAGTAAACATG
1 TGCATGATTTAATTTTCACGAAACTTTACATCAAAGTTCATTGAACCAAAAAAAAAGTAAACATG
*
74488 AAACTCAGAAACGTCGTTGAATGTCATCTAGATTTTAGATTTTGAAGAAAAACCCTATTCCTCTA
66 -AACTCAGAAACGTCGTTGAATGTCAACTAGATTTTAGATTTTGAAGAAAAACCCTATTCCTCTA
74553 TAATAAAACTTTCATCATTC
130 TAAT-AAACTTTCATCATTC
*
74573 TGCATTGATTTGATTTTCACGAAACTTTACATCAAAGTTCATTGAACCAAAAAAAAATTAAGTAA
1 TGCA-TGATTTAATTTTCACGAAACTTTACATCAAAGTTCATTGAACC--AAAAAAA--AAGTAA
* *
74638 ACATG-ACTTAGAAACGTCGTTGAATGTCAACTATG-TTTTAGATTTTGAAGAAAAACCTTATTC
61 ACATGAACTCAGAAACGTCGTTGAATGTCAACTA-GATTTTAGATTTTGAAGAAAAACCCTATTC
* *
74701 TTCTATAATACACTTTCATCATTC
125 CTCTATAATAAACTTTCATCATTC
74725 CTTCAATGGT
Statistics
Matches: 138, Mismatches: 8, Indels: 10
0.88 0.05 0.06
Matches are distributed among these distances:
150 4 0.03
151 40 0.29
152 14 0.10
153 68 0.49
154 1 0.01
155 11 0.08
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (148 bp):
TGCATGATTTAATTTTCACGAAACTTTACATCAAAGTTCATTGAACCAAAAAAAAAGTAAACATG
AACTCAGAAACGTCGTTGAATGTCAACTAGATTTTAGATTTTGAAGAAAAACCCTATTCCTCTAT
AATAAACTTTCATCATTC
Found at i:76671 original size:543 final size:544
Alignment explanation
Indices: 74573--77490 Score: 3011
Period size: 540 Copynumber: 5.4 Consensus size: 544
74563 TTCATCATTC
* *
74573 TGCATTGATTTGATTTTCACGAAACTTTACATCAAAGTTCATTGAACCAAAAAAAAATTAAGTAA
1 TGCATTGATTTGCTTTTCATGAAACTTTACATCAAAGTTCATTGAACC--AAAAAAA--AA--AA
* * *
74638 ACATG--ACTTAGAAACGTCGTTGAATGTCA-ACTATG-TTTTAGATTTTGAAGAAAAACCTTAT
60 ACATGAAACTCAGAAACGTCGTTGATTGTCATA-TA-GATTTTAGATTTTGAAG---AACCCTAT
* * * * *
74699 TCTTCTATAATAC-ACTTTCATCATTCCTTCAATGGTGCACCAACTGAGAATCGAA-CTCGGGTC
120 TCTTCTATAATACAACTTTCATCATTGCTTCAAAGGTGCACCAGCCGAGAATCGAACCT-GAGTC
* *** * *
74762 TATACCAT-GAAGGGTACTA-T-TATTGCTCGACCACTAGTGCTTGTTGTCATCCTAGAAATAAA
184 TTTACCATGGAAGGGTACTATTCTACCACTAGACCACTGGTGCTTGTTGTCATCCTAGAAATAAA
*
74824 TTATTAT-AGTTGTTTTTTCTAATATAAATAAAATTAAAGC-AAAAAGAAAATCTAGGAAATGCC
249 TTATTATAAG-T-TTTTTCCTAATATAAATAAAATTAAAGCAAAAAAGAAAATCTAGGAAATGCC
* **
74887 CTTGCATTGGATTTTTCGAATAAATAGAAGGAAATAACTTAATATCCATATGACTTAAA-TTTAA
312 CTTGCATTGGATTTTTCGAATTAATAGAAGGAAATAACTTAATATTTATATGACTTAAATTTTAA
* *
74951 AGTGAGTGTTAAATATAAGTACATATTT--T-CGATTATAGTTAT-AATTTTTATTTTAAATT-A
377 AGTGAGTGTTAAATATAAGTTCATATTTAATAAGATTATAGTTATAAATTTTTATTTT-AATTCA
* *
75011 TTGTGAAATATATTTATCAATAATATTAAAATTTTTGGTGGTCCAAAGTCACACTAAATTATTAT
441 -TGTGAAATAT-TTT-TCAATAATATTAAAAATTTTGATGGTCCAAAGTCACACTAAATTATTAT
*
75076 TTATACTAAAATCTTGATGGTTTTTGAAA-CTAGGTTGAAAAAT
503 TTATACTAAACTCTTGATGGTTTTTGAAATC-AGGTTG-AAAAT
* *
75119 TGCATTGATTTGCTTTTCATGAAACTTTACATCAAAGTTCATT-AA--AAAAAATTAAGTAAACT
1 TGCATTGATTTGCTTTTCATGAAACTTTACATCAAAGTTCATTGAACCAAAAAA--AA-AAAACA
* *
75181 TGAAACTCAG---CGTCATTGATTGTCATCA-AGATTTTAGATTTTGAGGAAGAACCAC-ATTTT
63 TGAAACTCAGAAACGTCGTTGATTGTCAT-ATAGATTTTAGATTTT---GAAGAACC-CTATTCT
* * * * * *
75241 TCTATAAAACAACTTTCATCATTACTCCAAAGGTGCACCAGCCAATAATCGAACCCGAGT-TTGT
123 TCTATAATACAACTTTCATCATTGCTTCAAAGGTGCACCAGCCGAGAATCGAACCTGAGTCTT-T
* * * *
75305 ACCATGGTAGGGTACTCTTCTACCACTAAACCAC-GATGCTTGTTGTCATCCTAGAAATAAATTA
187 ACCATGGAAGGGTACTATTCTACCACTAGACCACTGGTGCTTGTTGTCATCCTAGAAATAAATTA
* * * *
75369 TAATAGGTTTTTTCCTAATATAAAT-AAATTAAAGCAAAAAAGAAAAAT-TAGG-AATACCCTTA
252 TTATAAGTTTTTTCCTAATATAAATAAAATTAAAGCAAAAAAG-AAAATCTAGGAAATGCCCTTG
* * * * * *
75431 CGTTGGA-TATT-GAATTAATAAAAGGAAATAATTTAATA-TTAGATGACTTAAATTTAAAAGTG
316 CATTGGATTTTTCGAATTAATAGAAGGAAATAACTTAATATTTATATGACTTAAATTTTAAAGTG
* * **
75493 AGTGCTAAATATAAGTTGATATTTAATATTATTATAGTTATAAA-TTTTATTTTAATTTCATGTA
381 AGTGTTAAATATAAGTTCATATTTAATAAGATTATAGTTATAAATTTTTATTTTAA-TTCATGT-
* * ** * *
75557 AAAATATTTTTCAATAATAGTAAAAACATTGATGGTCCAAATTCACATTAAATTATTATTTATAC
444 GAAATATTTTTCAATAATATTAAAAATTTTGATGGTCCAAAGTCACACTAAATTATTATTTATAC
* * * * *
75622 TAAAATCCTCATGGTTTTTTTAAA-CTAGGATGGAAAAT
509 TAAACTCTTGATGG-TTTTTGAAATC-AGG-TTGAAAAT
*
75660 TGCATTGATTTGCTTTTCATGAAACGTTACATCAAAGTTCATTGAACCAAAAAGATTAAATAAAC
1 TGCATTGATTTGCTTTTCATGAAACTTTACATCAAAGTTCATTGAACCAAAAA-A--AAA-AAAC
* * * * * * *
75725 TTG--AGTCAGAAACGTTGTTGACTATCATCTAGATTTTAGATTTTGAAGAAGAACCCCATTCTT
62 ATGAAACTCAGAAACGTCGTTGATTGTCATATAGATTTTAGATTTT---GAAGAACCCTATTCTT
* * * * * * * * * * *
75788 ATATTATACAACTTCCATCTTTTCTTCAAAGGTTCACCAGTCAAAAATCGAACCCGGGT-TTGTA
124 CTATAATACAACTTTCATCATTGCTTCAAAGGTGCACCAGCCGAGAATCGAACCTGAGTCTT-TA
* * * *
75852 CCATGGCAGGGTATTA-T-TACCACTAGACTACTGATGCTTGTTGTCATCCTAGAAATAAATTAT
188 CCATGGAAGGGTACTATTCTACCACTAGACCACTGGTGCTTGTTGTCATCCTAGAAATAAATTAT
* *
75915 TAT-AG-GTTTTCCTAATATAAATAAAATTAAAGC--AAAA-AAAA---A--AAATACCCTTGCA
253 TATAAGTTTTTTCCTAATATAAATAAAATTAAAGCAAAAAAGAAAATCTAGGAAATGCCCTTGCA
* * * *
75970 TTGGATTTTTCGAAATAATAAAAGGAAATAATTTAATATTTATATGATTTAAATTTTAAAGTGAG
318 TTGGATTTTTCGAATTAATAGAAGGAAATAACTTAATATTTATATGACTTAAATTTTAAAGTGAG
* *
76035 TGATAAATATAAGTTCATATTTAATACA-ATTATAGTTATAAATTTTTATTTTAAGATCATGTGA
383 TGTTAAATATAAGTTCATATTTAATA-AGATTATAGTTATAAATTTTTATTTTAA-TTCATGTGA
* * * *
76099 AATATGTTTCAATAATATTAGAAATTTTGATGGTCCATAGTCACACTAAAGTATTA-TTATACTA
446 AATATTTTTCAATAATATTAAAAATTTTGATGGTCCAAAGTCACACTAAATTATTATTTATACTA
*
76163 AACTCTTGATGGTTTTTGAAATCAGG-TCAAAAT
511 AACTCTTGATGGTTTTTGAAATCAGGTTGAAAAT
*** *
76196 TGCATTGATCTAATTTTTCATAAAACTTTACATCAAAGTTCATTGAACCAAAAAAAAAAAACATG
1 TGCATTGAT-TTGCTTTTCATGAAACTTTACATCAAAGTTCATTGAACCAAAAAAAAAAAACATG
* *
76261 AAGCTCAGAAA-GTCATTGATTGTCATATCA-ATTTTAGATTTTGAAGAACCCTATTCTTCTATA
65 AAACTCAGAAACGTCGTTGATTGTCATAT-AGATTTTAGATTTTGAAGAACCCTATTCTTCTATA
* * * * **
76324 AAACAACTTTCATCATTTCTTCAAAGGTGCACCAGCCGGGAATCAAACCTGTCTCTTTACCATGG
129 ATACAACTTTCATCATTGCTTCAAAGGTGCACCAGCCGAGAATCGAACCTGAGTCTTTACCATGG
* * * *
76389 AAAGGTATTATTCTATCACTAGACAACTGGTGCTTGTTGTCATCCTAGAAATAAATTATTATAAG
194 AAGGGTACTATTCTACCACTAGACCACTGGTGCTTGTTGTCATCCTAGAAATAAATTATTATAAG
* * * *
76454 TTCTTTTGCTAATGTAAATAAAATTTAAGCAAAAAAGAAAATCTAGGAAATGCCCTTGCGTTGGA
259 TT-TTTTCCTAATATAAATAAAATTAAAGCAAAAAAGAAAATCTAGGAAATGCCCTTGCATTGGA
* * * * **
76519 TTTTTCGAATTATTAGACGGAAATAACTTAATATTTTTATGACATAAATTTTAAAGTCCGTGTTA
323 TTTTTCGAATTAATAGAAGGAAATAACTTAATATTTATATGACTTAAATTTTAAAGTGAGTGTTA
*
76584 AATACAAGTTCATATTTAATAAGA-TATAGTTATAAATTTTTATTTTAGATTCATGTGAAATATT
388 AATATAAGTTCATATTTAATAAGATTATAGTTATAAATTTTTATTTTA-ATTCATGTGAAATATT
* * *
76648 TTTCAATAATATTAAAAATTTTGATGGTCCATAGTCACAGTAAATTATTATTTATACTAAACTCA
452 TTTCAATAATATTAAAAATTTTGATGGTCCAAAGTCACACTAAATTATTATTTATACTAAACTCT
* * *
76713 TGAAGGTTTTTGAAATTAGGTTGAAAAA
517 TGATGGTTTTTGAAATCAGGTTGAAAAT
* *
76741 TGCATTGATTTGCTTTTCACGAAAATTTACATCAAAGTTCATTGAACCAAAAAAAAATTAAGTAC
1 TGCATTGATTTGCTTTTCATGAAACTTTACATCAAAGTTCATTGAACC-AAAAAAAA--AA--A-
* *
76806 ACAT-AAACTCAGAAACGTCGTTGATTGTAATATAGATTTTAGATTTTGAAGGAGAACCCCATTC
60 ACATGAAACTCAGAAACGTCGTTGATTGTCATATAGATTTTAGATTTTG-A--AGAACCCTATTC
** * ** *
76870 TTCTATAATACAACTCCCATCATTGCTTCAAAGGTGCACCAGCCGGGAATTAAACCTGACTCTTT
122 TTCTATAATACAACTTTCATCATTGCTTCAAAGGTGCACCAGCCGAGAATCGAACCTGAGTCTTT
*
76935 ACCATGGGAA-GGTACTATTCTACCACTAGACCACTAGTGCTTGTTGTCATCCTAGAAATAAATT
187 ACCAT-GGAAGGGTACTATTCTACCACTAGACCACTGGTGCTTGTTGTCATCCTAGAAATAAATT
* * * *
76999 ATTATATGTTATTTTGCTAATGTAAATAAAATTAAAG---AAAA-AATATCTAGGAAATGCCCTT
251 ATTATAAGTT-TTTTCCTAATATAAATAAAATTAAAGCAAAAAAGAAAATCTAGGAAATGCCCTT
* ** * *
77060 GCATTGGATTTTTCAAAAAAAAAAGAAGAAAAGAAGGAAGTAACTTAATATTCATATGACTTAAA
315 GCATTGGATTTTTC-GAATTAATAGAAG----G-A--AA-TAACTTAATATTTATATGACTTAAA
* * *
77125 TTTTAAAGTGAGTGTTAAATATAAGTACGTATTTAATACGATTATAGTTAT-AA-TTTTATTTTT
371 TTTTAAAGTGAGTGTTAAATATAAGTTCATATTTAATAAGATTATAGTTATAAATTTTTA-TTTT
* **
77188 AATTTCATGTGAAATATCTTTTTCAATAATATT-AAAATTTTGATGGTCTAAAGTTGCACTAAAT
435 AA-TTCATGTGAAATA--TTTTTCAATAATATTAAAAATTTTGATGGTCCAAAGTCACACTAAAT
* *
77252 TATTATTTATACTAAACTCTTGATGATTTTT--AATTAGGTT-AAAAT
497 TATTATTTATACTAAACTCTTGATGGTTTTTGAAATCAGGTTGAAAAT
* * * * *
77297 TGCATTGAATTGC-TTTCATGAAACTTTACATAAAAGTTCATTGAAACAAAAAAAGTAAAA-TTG
1 TGCATTGATTTGCTTTTCATGAAACTTTACATCAAAGTTCATTGAACCAAAAAAA-AAAAACATG
* * * * *
77360 AAACTCAGTAAA-ATCGTTGATTGCCATCTAGATTTT-GA---AGAAGAACCTTATTCTTCTATA
65 AAACTCAG-AAACGTCGTTGATTGTCATATAGATTTTAGATTTTGAAGAACCCTATTCTTCTATA
* * * * * *
77420 ATACAACTTTCGTCATTGCTTCAAAGGTGCACCAGTCAAGAATC-AAACTCGAGTCTATACCGTG
129 ATACAACTTTCATCATTGCTTCAAAGGTGCACCAGCCGAGAATCGAACCT-GAGTCTTTACCATG
*
77484 GTAGGGT
193 GAAGGGT
77491 TGTAACCCCT
Statistics
Matches: 2016, Mismatches: 253, Indels: 209
0.81 0.10 0.08
Matches are distributed among these distances:
531 76 0.04
532 3 0.00
533 52 0.03
534 29 0.01
535 8 0.00
536 39 0.02
537 65 0.03
538 73 0.04
539 94 0.05
540 250 0.12
541 149 0.07
542 72 0.04
543 183 0.09
544 184 0.09
545 72 0.04
546 149 0.07
547 2 0.00
549 47 0.02
550 72 0.04
551 5 0.00
553 161 0.08
554 12 0.01
555 31 0.02
556 16 0.01
557 17 0.01
558 77 0.04
559 63 0.03
560 15 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (544 bp):
TGCATTGATTTGCTTTTCATGAAACTTTACATCAAAGTTCATTGAACCAAAAAAAAAAAACATGA
AACTCAGAAACGTCGTTGATTGTCATATAGATTTTAGATTTTGAAGAACCCTATTCTTCTATAAT
ACAACTTTCATCATTGCTTCAAAGGTGCACCAGCCGAGAATCGAACCTGAGTCTTTACCATGGAA
GGGTACTATTCTACCACTAGACCACTGGTGCTTGTTGTCATCCTAGAAATAAATTATTATAAGTT
TTTTCCTAATATAAATAAAATTAAAGCAAAAAAGAAAATCTAGGAAATGCCCTTGCATTGGATTT
TTCGAATTAATAGAAGGAAATAACTTAATATTTATATGACTTAAATTTTAAAGTGAGTGTTAAAT
ATAAGTTCATATTTAATAAGATTATAGTTATAAATTTTTATTTTAATTCATGTGAAATATTTTTC
AATAATATTAAAAATTTTGATGGTCCAAAGTCACACTAAATTATTATTTATACTAAACTCTTGAT
GGTTTTTGAAATCAGGTTGAAAAT
Found at i:80645 original size:342 final size:342
Alignment explanation
Indices: 80020--80687 Score: 904
Period size: 342 Copynumber: 2.0 Consensus size: 342
80010 CCCATTATTC
*
80020 TATAATACAACTTCTATCATTGCTTCAAAGGTGCACCAGACAAAAATCAAACCCGGGTCTGTATC
1 TATAATACAACTTCTATCATTGCTTCAAAGGTGCACCAGACAAAAATCAAACCCGGGTCTATATC
*
80085 ATGGCAGGGTACTATTCTACCACTAGACCACTGGTGCTTGTTGTCATCCTAGAAATAATTATTAT
66 ATGGCAGGGTACTATTCTACCACTAGACCACTAGTGCTTGTTGTCATCCTAGAAATAATTATTAT
* * *
80150 AGGTTCTTTTTGCTAATGTAAATAAAATTAAAAAAAGGAAAATCTAGGAAATGCCCTTGTATTGG
131 AGGGTCTTTTTGCTAATGTAAATAAAATTAAAAAAAAGAAAATCTAGGAAATGCCCATGTATTGG
**
80215 ATTTATTTTAATAAATAGAAGGAAATAACTAAATATTCATATGACATAAAATTTAAAGAGAGTGT
196 ATTTATTCGAATAAATAGAAGGAAATAACTAAATATTCATATGACATAAAATTTAAAGAGAGTGT
** * *
80280 TAAATATAAGTTTAGATTTAATACGGTTATAGTTATAAATT-TTTATTTTAAATTTATGTGAAAT
261 TAAATATAAGTACAGATTTAATACGATTATAGTTAT-AATTCTTTATTTTAAATTCATGTGAAAT
80344 ATCATAACCCTATTCTTG
325 ATCATAACCCTATTCTTG
* * *** **
80362 TATAATACAACTT-TCATCATTGCTTGAAAGGTGCATCA-ATCGGGAATCAAACTTGGGTCTATA
1 TATAATACAACTTCT-ATCATTGCTTCAAAGGTGCACCAGA-CAAAAATCAAACCCGGGTCTATA
* *
80425 TCATGGCAGGGTACTATTCTACCACTAGACCACTAGTTCTTGTTGTCCTCCTAGAAATAAATTAT
64 TCATGGCAGGGTACTATTCTACCACTAGACCACTAGTGCTTGTTGTCATCCTAGAAAT-AATTAT
**
80490 TATAGGAGT-TTTTTGCTAATGTAAATAAAATTAAAGAAAAAAAGAAAATCTAGG-TTTGCCCAT
128 TATAGG-GTCTTTTTGCTAATGTAAATAAAATT--A-AAAAAAAGAAAATCTAGGAAATGCCCAT
** * * * * *
80553 GCT-TTGGATTT-TTCGCTTAAATAGAA-GAAATAACTTAATATTCTTATGGCTTAAATTTTAAA
189 G-TATTGGATTTATTCGAATAAATAGAAGGAAATAACTAAATATTCATATGACATAAAATTTAAA
* * *
80615 G-GGGTGTTAAATATAAGTACATATTTAATACTATTATAGTTATAATTCTTTATTTTAAATTCAT
253 GAGAGTGTTAAATATAAGTACAGATTTAATACGATTATAGTTATAATTCTTTATTTTAAATTCAT
80679 GTGAAATAT
318 GTGAAATAT
80688 TTTTCAATAA
Statistics
Matches: 285, Mismatches: 32, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
341 6 0.02
342 166 0.58
343 67 0.24
344 12 0.04
345 16 0.06
346 18 0.06
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (342 bp):
TATAATACAACTTCTATCATTGCTTCAAAGGTGCACCAGACAAAAATCAAACCCGGGTCTATATC
ATGGCAGGGTACTATTCTACCACTAGACCACTAGTGCTTGTTGTCATCCTAGAAATAATTATTAT
AGGGTCTTTTTGCTAATGTAAATAAAATTAAAAAAAAGAAAATCTAGGAAATGCCCATGTATTGG
ATTTATTCGAATAAATAGAAGGAAATAACTAAATATTCATATGACATAAAATTTAAAGAGAGTGT
TAAATATAAGTACAGATTTAATACGATTATAGTTATAATTCTTTATTTTAAATTCATGTGAAATA
TCATAACCCTATTCTTG
Found at i:84759 original size:70 final size:70
Alignment explanation
Indices: 84646--84785 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 70
84636 GCTAAAGTGG
*
84646 ATGGCTTCTACTGGAGTTTTGTGTGACAAGAAGGTGCCTCTAAAACTTAAGGGAAAATTTTATAT
1 ATGGCTTCTACTGGAGTTTTGTGTGACAAGAAGGTGCCTCTAAAACTTAAGGGAAAATTTTATAG
84711 AATGA
66 AATGA
*
84716 ATGGCTTTTACTGGAGTTTTGTGTGACAAGAAGGTGCCTCTAAAACTTAAGGGAAAATTTTATAG
1 ATGGCTTCTACTGGAGTTTTGTGTGACAAGAAGGTGCCTCTAAAACTTAAGGGAAAATTTTATAG
84781 AATGA
66 AATGA
84786 CAATAAGACC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (70 bp):
ATGGCTTCTACTGGAGTTTTGTGTGACAAGAAGGTGCCTCTAAAACTTAAGGGAAAATTTTATAG
AATGA
Done.