Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007130.1 Hibiscus syriacus cultivar Beakdansim tig00018633_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: 102725
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5495 original size:114 final size:114
Alignment explanation
Indices: 5236--5573 Score: 559
Period size: 114 Copynumber: 3.0 Consensus size: 114
5226 TACCACGTTA
*
5236 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
5301 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTTGGTATGAACCCC-AAAACCAATCATTGGATTTGAAAGATGAATTTGC
*
5351 TCATAGTATAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
*
5416 TTTGGTATGAACCCCAAAACTAATCATTGGATTTGAAAGATGAATTTGC
66 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
* * *
5465 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * * * * *
5530 TTCGGTAGGAACCACAGAACCAATCATTAGAATTGAAAGATGAA
66 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAA
5574 CTGCATGATC
Statistics
Matches: 209, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
114 131 0.63
115 78 0.37
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
Found at i:6485 original size:113 final size:113
Alignment explanation
Indices: 6287--7184 Score: 1476
Period size: 113 Copynumber: 7.9 Consensus size: 113
6277 GATTTAAATC
* * *
6287 CATCATTCAATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATTTGAAGAAGAA
1 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
6352 AGAAGAAGTTTATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATT
* * * *
6400 CATCATTCAATGGATCATCATTACCTGGTCGAGTTCATAATGAGAAGAACTTATCTGAAAAAGGA
1 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
6465 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACTCTTTGCTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATT
*
6513 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGA
1 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
6578 AGAAGAAATTCATAATGAGAAGAATTTGTTCAAATTTTTGCTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATT
*
6626 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGA
1 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
6691 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATT
*
6739 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAAAACTCATCTGAAGAAGGA
1 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
6804 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTTGCTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAAC-TTTTTGCTTGAATT
6853 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
6918 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTTTGCTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAAC--TTTTTGCTTGAATT
* *
6968 CATCATTCATTGGATCAGCATTACCAAGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
7033 AGAAGAAATTCATAATAAGAAGAATTTGTTCAACTGTTTT-CTTAAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACT-TTTTGCTTGAATT
* ** ** * *
7081 CATCACTCGGTGGAAAAGCAGTT-CCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAAAAGG
1 CATCATTCAATGGATCAGCA-TTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
7145 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT
65 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-CTTTT
7185 GCATGATTCT
Statistics
Matches: 746, Mismatches: 34, Indels: 10
0.94 0.04 0.01
Matches are distributed among these distances:
113 515 0.69
114 120 0.16
115 111 0.15
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATT
Found at i:7477 original size:3 final size:3
Alignment explanation
Indices: 7471--7517 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
7461 ATTTATTATT
* * * *
7471 ATA ATA ATA ATA ATA ATA ATA ATA ATT ATT ATT ATT ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7518 TATTATTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
ATA
Found at i:7519 original size:18 final size:18
Alignment explanation
Indices: 7463--7553 Score: 105
Period size: 18 Copynumber: 5.2 Consensus size: 18
7453 ATTTATTTAT
7463 TTATTATTATAATAATAA
1 TTATTATTATAATAATAA
* * * *
7481 TAATAATAATAATAATTA
1 TTATTATTATAATAATAA
7499 TTATTATTATAATAATAA
1 TTATTATTATAATAATAA
*
7517 TTATTATTAT-AT-ATTA
1 TTATTATTATAATAATAA
* *
7533 TTATTATTAAAAAAATAA
1 TTATTATTATAATAATAA
7551 TTA
1 TTA
7554 CAGGCCCAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
16 12 0.20
17 3 0.05
18 44 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATTATTATAATAATAA
Found at i:7522 original size:3 final size:3
Alignment explanation
Indices: 7495--7541 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
7485 AATAATAATA
* * *
7495 ATT ATT ATT ATT ATA ATA ATA ATT ATT ATT ATAT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
7541 A
1 A
7542 AAAAAATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:14990 original size:40 final size:40
Alignment explanation
Indices: 14935--15014 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
14925 GGGAAGTTCG
* * *
14935 TGAATAAGGTTTTTTGTTCGTTTAATTAAATGAATGAACA
1 TGAATAAAGTTTTTTGCTCATTTAATTAAATGAATGAACA
*
14975 TGAATAAATTTTTTTGCTCATTTAATTAAATGAATGAACA
1 TGAATAAAGTTTTTTGCTCATTTAATTAAATGAATGAACA
15015 CAAACAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (40 bp):
TGAATAAAGTTTTTTGCTCATTTAATTAAATGAATGAACA
Found at i:15080 original size:32 final size:31
Alignment explanation
Indices: 15044--15110 Score: 73
Period size: 32 Copynumber: 2.1 Consensus size: 31
15034 TTCATTTGCA
*
15044 TTAA-TGAAAGTTTAATAATTCGTTCATTTATG
1 TTAATTGAAA-TTTAATAATCCGTTCATTTA-G
* * *
15076 TTAATTTATATTTAATAATCCGTTCGTTTAG
1 TTAATTGAAATTTAATAATCCGTTCATTTAG
15107 TTAA
1 TTAA
15111 ATTTATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
31 5 0.17
32 22 0.73
33 3 0.10
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.49
Consensus pattern (31 bp):
TTAATTGAAATTTAATAATCCGTTCATTTAG
Found at i:15114 original size:32 final size:32
Alignment explanation
Indices: 15054--15121 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
15044 TTAATGAAAG
*
15054 TTTAATAATTCGTTCATTTATGTTAATTTATA
1 TTTAATAATCCGTTCATTTATGTTAATTTATA
*
15086 TTTAATAATCCGTTCGTTTA-GTTAAATTTATA
1 TTTAATAATCCGTTCATTTATGTT-AATTTATA
15118 TTTA
1 TTTA
15122 TCTTTATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 3 0.09
32 30 0.91
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.54
Consensus pattern (32 bp):
TTTAATAATCCGTTCATTTATGTTAATTTATA
Found at i:38212 original size:2 final size:2
Alignment explanation
Indices: 38201--38249 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
38191 TTTGTCAATC
38201 TA TA -A 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
38242 TA TA TA TA
1 TA TA TA TA
38250 ATTTAAGACA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:38426 original size:13 final size:13
Alignment explanation
Indices: 38408--38459 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
38398 ACACGCAATA
38408 TGCGTCATAAATG
1 TGCGTCATAAATG
38421 TGCGTCATAAATG
1 TGCGTCATAAATG
* *
38434 CGTGTCATAAATG
1 TGCGTCATAAATG
*
38447 TGTGTCATAAATG
1 TGCGTCATAAATG
38460 CGCATCATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (13 bp):
TGCGTCATAAATG
Found at i:38442 original size:26 final size:26
Alignment explanation
Indices: 38411--38461 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
38401 CGCAATATGC
38411 GTCATAAATGTGCGTCATAAATGCGT
1 GTCATAAATGTGCGTCATAAATGCGT
*
38437 GTCATAAATGTGTGTCATAAATGCG
1 GTCATAAATGTGCGTCATAAATGCG
38462 CATCATAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (26 bp):
GTCATAAATGTGCGTCATAAATGCGT
Found at i:38467 original size:13 final size:13
Alignment explanation
Indices: 38409--38468 Score: 75
Period size: 13 Copynumber: 4.6 Consensus size: 13
38399 CACGCAATAT
*
38409 GCGTCATAAATGT
1 GCGTCATAAATGC
38422 GCGTCATAAATGC
1 GCGTCATAAATGC
* *
38435 GTGTCATAAATGT
1 GCGTCATAAATGC
*
38448 GTGTCATAAATGC
1 GCGTCATAAATGC
*
38461 GCATCATA
1 GCGTCATA
38469 GATTTATGAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (13 bp):
GCGTCATAAATGC
Found at i:38467 original size:26 final size:26
Alignment explanation
Indices: 38412--38468 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
38402 GCAATATGCG
**
38412 TCATAAATGTGCGTCATAAATGCGTG
1 TCATAAATGTGCGTCATAAATGCGCA
*
38438 TCATAAATGTGTGTCATAAATGCGCA
1 TCATAAATGTGCGTCATAAATGCGCA
38464 TCATA
1 TCATA
38469 GATTTATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (26 bp):
TCATAAATGTGCGTCATAAATGCGCA
Found at i:41493 original size:2 final size:2
Alignment explanation
Indices: 41486--41511 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41476 TATTTTTGAA
41486 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
41512 TCAATATTAA
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:41982 original size:49 final size:48
Alignment explanation
Indices: 41909--42048 Score: 176
Period size: 49 Copynumber: 2.9 Consensus size: 48
41899 AAATAAATTT
* *
41909 ACATAAATACTAAAAAAGAGTTTGTTATAACAATAAGCACATGACAAA-A
1 ACATAAAGAC-AAAAAAGA-TTTGTTACAACAATAAGCACATGACAAATA
* *
41958 ACATAAAGGCAAAAAAGGAATTTGTTGCAACAATAAGCACATGACAAATA
1 ACATAAAGACAAAAAA-G-ATTTGTTACAACAATAAGCACATGACAAATA
* *
42008 ACATAAAGACAAAAAAG-TTAGTTACAACAATAAGCAAATGA
1 ACATAAAGACAAAAAAGATTTGTTACAACAATAAGCACATGA
42049 GGAATAAATA
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
47 21 0.26
48 6 0.08
49 36 0.45
50 17 0.21
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (48 bp):
ACATAAAGACAAAAAAGATTTGTTACAACAATAAGCACATGACAAATA
Found at i:42055 original size:47 final size:46
Alignment explanation
Indices: 41921--42048 Score: 150
Period size: 47 Copynumber: 2.7 Consensus size: 46
41911 ATAAATACTA
* *
41921 AAAAAGAGTTTGTTATAACAATAAGCACATGACAAA-AACATAAAGGC
1 AAAAA-AGTTTGTTACAACAATAAGCACATGA-AAATAACATAAAGAC
*
41968 AAAAAAGGAATTTGTTGCAACAATAAGCACATGACAAATAACATAAAGAC
1 AAAAAA-G--TTTGTTACAACAATAAGCACATGA-AAATAACATAAAGAC
* *
42018 AAAAAAGTTAGTTACAACAATAAGCAAATGA
1 AAAAAAGTTTGTTACAACAATAAGCACATGA
42049 GGAATAAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
46 1 0.01
47 27 0.38
49 27 0.38
50 16 0.23
ACGTcount: A:0.55, C:0.12, G:0.14, T:0.19
Consensus pattern (46 bp):
AAAAAAGTTTGTTACAACAATAAGCACATGAAAATAACATAAAGAC
Found at i:45990 original size:29 final size:29
Alignment explanation
Indices: 45949--46947 Score: 781
Period size: 29 Copynumber: 34.4 Consensus size: 29
45939 GCACCCTAAC
* *
45949 AAAAATTAATTACAAAACTAACACCCTTTT
1 AAAAA-TATTTACGAAACTAACACCCTTTT
* * **
45979 AAAAATATTTACTAAATTAACACTATTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
* * *
46008 AAAAATATTTACTAAACTAAAACCTTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
*
46037 AAAAATATTTACGAAACTAACATCCTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
* *
46066 AAAAATATTTACGAAACTAACAACTTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
*
46095 AAAAATATTTACGAAACTAACAACCTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
*
46124 AAAAATATTTACGAAACTAACAGCCTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
46153 -AAAATATTTACGAAACTAACACCC-TTT
1 AAAAATATTTACGAAACTAACACCCTTTT
* * *
46180 AAAAATATTTAGGAAAATAACACCTTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
*
46209 AAAAATATTTATGAAACTAACA-CCTTTCT
1 AAAAATATTTACGAAACTAACACCCTTT-T
* *
46238 AAAAATATTTACAAAACTAACACTCTTTCT
1 AAAAATATTTACGAAACTAACACCCTTT-T
* *
46268 AAAAATATTTAAGAAAGTAACACCCTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
46297 ---AATATTTACGAAACTAACACCCTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
* * * * **
46323 TAAAA-ATGT-CAGAATA-TGTATA--CTTGG
1 AAAAATATTTAC-GAA-ACT-AACACCCTTTT
* ** **** * ** **
46350 AAAAA-GTCAACGGCTGTTTACTAGTC-GGT
1 AAAAATATTTAC-GAAACTAAC-ACCCTTTT
* ****** ** ** * *
46379 CAACGCCGGT-C-AAAGTTCTGGTCAACGGTGCTC
1 AAAAATATTTACGAAA---CT-AAC-ACCCT-TTT
* * * ***
46412 AACAGTCAACT-TTTACAAAAATAGCACCCTAAC
1 AA-A---AA-TATTTACGAAACTAACACCCTTTT
* * *
46445 AGAAATTAATTACAAAACTAACACCCTTTT
1 A-AAAATATTTACGAAACTAACACCCTTTT
* * **
46475 AAAAATATTTACTAAATTAACACTATTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
* * *
46504 AAAAATATTTACTAAACTAAAACCTTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
* *
46533 AAAAATATTTACGAAACTAACATCTTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
*
46562 AAAAATATTTACGAAACTAACACCTTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
* *
46591 AAAAATATTTATGAAACTAACAACCTTTTT
1 AAAAATATTTACGAAACTAAC-ACCCTTTT
*
46621 AAAAATATTTACGAAACTAACAGCCTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
*
46650 -AAAATATTTACGAAACTAACACCC-TTA
1 AAAAATATTTACGAAACTAACACCCTTTT
* * *
46677 AAAAATATTTAGGAAAATAACACCTTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
46706 AAAAATATTTACGAAACTAACA-CCTTTCT
1 AAAAATATTTACGAAACTAACACCCTTT-T
* *
46735 AAAAATATTTACAAAACTAACACTCTTTCT
1 AAAAATATTTACGAAACTAACACCCTTT-T
*
46765 AAAAATATTTAAGAAACTAACACCCTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
46794 ---AATATTTACGAAACTAACACCCTTTTT
1 AAAAATATTTACGAAACTAACACCC-TTTT
* *
46821 AGAAATATTTACAAAACT-A-ACCCTTTCT
1 AAAAATATTTACGAAACTAACACCCTTT-T
* *
46849 AAAAATATTTATGAAACTAACAACCTTTTT
1 AAAAATATTTACGAAACTAAC-ACCCTTTT
*
46879 AAAAATATTTACAAAACT-A-ACCCTTTCT
1 AAAAATATTTACGAAACTAACACCCTTT-T
*
46907 AAAAATATTTACGAAACTAATACCCTTTT
1 AAAAATATTTACGAAACTAACACCCTTTT
46936 AAAAATATTTAC
1 AAAAATATTTAC
46948 AAAAATAGCA
Statistics
Matches: 791, Mismatches: 131, Indels: 95
0.78 0.13 0.09
Matches are distributed among these distances:
26 45 0.06
27 29 0.04
28 145 0.18
29 396 0.50
30 152 0.19
31 8 0.01
33 4 0.01
34 5 0.01
35 1 0.00
36 1 0.00
37 1 0.00
38 1 0.00
39 3 0.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAAATATTTACGAAACTAACACCCTTTT
Found at i:54250 original size:29 final size:29
Alignment explanation
Indices: 54218--54568 Score: 446
Period size: 30 Copynumber: 12.1 Consensus size: 29
54208 CATAAATTAA
*
54218 TTACAAAACTAACACTCTTTTAAAAATAT
1 TTACGAAACTAACACTCTTTTAAAAATAT
*
54247 TTACGAAATTAACACT-TTTTAAAAATAT
1 TTACGAAACTAACACTCTTTTAAAAATAT
54275 TTACGAAACTAACACAT-TTTTAAAAATAT
1 TTACGAAACTAACAC-TCTTTTAAAAATAT
54304 TTACGAAACTAACAC-CTTTTAAAAATAT
1 TTACGAAACTAACACTCTTTTAAAAATAT
*
54332 TTACGAAACTAACA--ATTTTAAAAATAT
1 TTACGAAACTAACACTCTTTTAAAAATAT
* *
54359 TTACGAAACTAACGCCCTTTTTAAAAATAT
1 TTACGAAACTAACACTC-TTTTAAAAATAT
* * *
54389 TTATGAAACTAACCCACTTTTAAAAATAT
1 TTACGAAACTAACACTCTTTTAAAAATAT
* *
54418 CTAC-ATAACTAACACCCTTTCTAAAAATAT
1 TTACGA-AACTAACACTCTTT-TAAAAATAT
* * *
54448 TTGCAAAACTAACACACTTTCTAAAAATAT
1 TTACGAAACTAACACTCTTT-TAAAAATAT
*
54478 TTACGAAACTAACAGT-TTTTAAAAATAT
1 TTACGAAACTAACACTCTTTTAAAAATAT
* *
54506 TTACGAAACTGACACCCTTTCTAAAAATAT
1 TTACGAAACTAACACTCTTT-TAAAAATAT
*
54536 TTACGAAACTAACACGCTTTTAAAAATAT
1 TTACGAAACTAACACTCTTTTAAAAATAT
54565 TTAC
1 TTAC
54569 AAAAATAGCA
Statistics
Matches: 287, Mismatches: 25, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
27 25 0.09
28 75 0.26
29 87 0.30
30 99 0.34
31 1 0.00
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.33
Consensus pattern (29 bp):
TTACGAAACTAACACTCTTTTAAAAATAT
Found at i:54311 original size:57 final size:57
Alignment explanation
Indices: 54218--54568 Score: 440
Period size: 57 Copynumber: 6.1 Consensus size: 57
54208 CATAAATTAA
* *
54218 TTACAAAACTAACAC-TCTTTTAAAAATATTTACGAAATTAACACTTTTTAAAAATAT
1 TTACGAAACTAACACAT-TTTTAAAAATATTTACGAAACTAACACTTTTTAAAAATAT
*
54275 TTACGAAACTAACACATTTTTAAAAATATTTACGAAACTAACACCTTTTAAAAATAT
1 TTACGAAACTAACACATTTTTAAAAATATTTACGAAACTAACACTTTTTAAAAATAT
*
54332 TTACGAAACTAACA-A-TTTTAAAAATATTTACGAAACTAACGCCCTTTTTAAAAATAT
1 TTACGAAACTAACACATTTTTAAAAATATTTACGAAACTAA--CACTTTTTAAAAATAT
* * * * *
54389 TTATGAAACTAACCCACTTTTAAAAATATCTAC-ATAACTAACACCCTTTCTAAAAATAT
1 TTACGAAACTAACACATTTTTAAAAATATTTACGA-AACTAACA--CTTTTTAAAAATAT
* * * *
54448 TTGCAAAACTAACACACTTTCTAAAAATATTTACGAAACTAACAGTTTTTAAAAATAT
1 TTACGAAACTAACACA-TTTTTAAAAATATTTACGAAACTAACACTTTTTAAAAATAT
* * * *
54506 TTACGAAACTGACACCCTTTCTAAAAATATTTACGAAACTAACACGCTTTTAAAAATAT
1 TTACGAAACTAACA-CATTTTTAAAAATATTTACGAAACTAACAC-TTTTTAAAAATAT
54565 TTAC
1 TTAC
54569 AAAAATAGCA
Statistics
Matches: 257, Mismatches: 25, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
55 24 0.09
56 1 0.00
57 93 0.36
58 53 0.21
59 63 0.25
60 22 0.09
61 1 0.00
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.33
Consensus pattern (57 bp):
TTACGAAACTAACACATTTTTAAAAATATTTACGAAACTAACACTTTTTAAAAATAT
Found at i:60889 original size:20 final size:21
Alignment explanation
Indices: 60852--60890 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60842 AAAATCTTTT
*
60852 CTTTATTTTTACTTTAAATCA
1 CTTTATTATTACTTTAAATCA
60873 CTTTATTATTA-TTTAAAT
1 CTTTATTATTACTTTAAAT
60891 ATCTTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (21 bp):
CTTTATTATTACTTTAAATCA
Found at i:60896 original size:20 final size:22
Alignment explanation
Indices: 60851--60896 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
60841 CAAAATCTTT
*
60851 TCTTTATTTTTACTTTAAATCA
1 TCTTTATTATTACTTTAAATCA
60873 -CTTTATTATTA-TTTAAAT-A
1 TCTTTATTATTACTTTAAATCA
60892 TCTTT
1 TCTTT
60897 TTACCAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 1 0.05
20 11 0.50
21 10 0.45
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (22 bp):
TCTTTATTATTACTTTAAATCA
Found at i:61306 original size:39 final size:40
Alignment explanation
Indices: 61230--61307 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
61220 TTAGAGCATC
*
61230 ATACGATGCACGTAATACATATTTAAATTTATAAACCTTG
1 ATACGATGCACATAATACATATTTAAATTTATAAACCTTG
61270 ATACGATGCACATAATACATA-TTAAATTTATAAACCTT
1 ATACGATGCACATAATACATATTTAAATTTATAAACCTT
61308 CAGTAAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 17 0.46
40 20 0.54
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (40 bp):
ATACGATGCACATAATACATATTTAAATTTATAAACCTTG
Found at i:63800 original size:16 final size:16
Alignment explanation
Indices: 63779--63809 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63769 TGAATTAGAG
*
63779 TTTTTTAAGTTTTGAT
1 TTTTTTAAGATTTGAT
63795 TTTTTTAAGATTTGA
1 TTTTTTAAGATTTGA
63810 GAAAAAAATT
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:0.23, C:0.00, G:0.13, T:0.65
Consensus pattern (16 bp):
TTTTTTAAGATTTGAT
Found at i:64305 original size:19 final size:20
Alignment explanation
Indices: 64262--64313 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
64252 ATAGTTGGTA
64262 TTCTTTATTTTT-TATATTG
1 TTCTTTATTTTTCTATATTG
64281 TATCTTTATTTTTCTGATA-T-
1 T-TCTTTATTTTTCT-ATATTG
64301 TTCTTTATTTTTC
1 TTCTTTATTTTTC
64314 AATAATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 13 0.43
20 12 0.40
21 2 0.07
22 3 0.10
ACGTcount: A:0.15, C:0.10, G:0.04, T:0.71
Consensus pattern (20 bp):
TTCTTTATTTTTCTATATTG
Found at i:68298 original size:13 final size:13
Alignment explanation
Indices: 68282--68347 Score: 62
Period size: 13 Copynumber: 4.9 Consensus size: 13
68272 AACTATATAT
*
68282 TTTATGTATAAAC
1 TTTATATATAAAC
*
68295 TTTATAAGTATATA-
1 TTTAT-A-TATAAAC
68309 TATTATATATAAAC
1 T-TTATATATAAAC
*
68323 TATATATATAAAC
1 TTTATATATAAAC
*
68336 TATATATATAAA
1 TTTATATATAAA
68348 TTATATAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
13 33 0.73
14 3 0.07
15 9 0.20
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (13 bp):
TTTATATATAAAC
Found at i:68309 original size:28 final size:28
Alignment explanation
Indices: 68252--68368 Score: 95
Period size: 26 Copynumber: 4.4 Consensus size: 28
68242 AACAATTATA
* * *
68252 ATATA-TATATATACACTGTA-AACTAT
1 ATATATTATATATAAACTATATAAGTAT
* * *
68278 ATATTTTATGTATAAACTTTATAAGTAT
1 ATATATTATATATAAACTATATAAGTAT
68306 ATATATTATATATAAACTATAT-A-TAT
1 ATATATTATATATAAACTATATAAGTAT
* * *
68332 AAACTA-TATATATAAATTATAT-AGTTT
1 ATA-TATTATATATAAACTATATAAGTAT
68359 ATAT-TTATAT
1 ATATATTATAT
68369 TATTATATAC
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
26 31 0.42
27 19 0.26
28 24 0.32
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (28 bp):
ATATATTATATATAAACTATATAAGTAT
Found at i:68352 original size:13 final size:13
Alignment explanation
Indices: 68312--68354 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
68302 GTATATATAT
68312 TATATATAAACTA
1 TATATATAAACTA
68325 TATATATAAACTA
1 TATATATAAACTA
*
68338 TATATATAAATTA
1 TATATATAAACTA
68351 TATA
1 TATA
68355 GTTTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:68397 original size:2 final size:2
Alignment explanation
Indices: 68303--68377 Score: 50
Period size: 2 Copynumber: 38.0 Consensus size: 2
68293 ACTTTATAAG
* *
68303 TA TA TA TA T- TA TA TA TA AA CTA TA TA TA TA AA CTA 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
* * *
68346 AA T- TA TA TA GTT TA TA TT TA TA T- TA T- TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
68378 CCATGTATAA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
1 4 0.07
2 49 0.88
3 3 0.05
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:68522 original size:20 final size:17
Alignment explanation
Indices: 68479--68527 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 17
68469 AAACTTGTAT
*
68479 TTATATATTATATATAA
1 TTATAAATTATATATAA
68496 TTATAAATTATATATACTA
1 TTATAAATTATATATA--A
68515 TGTATAAATTATA
1 T-TATAAATTATA
68528 GTCTATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 15 0.54
19 2 0.07
20 11 0.39
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TTATAAATTATATATAA
Found at i:68602 original size:34 final size:34
Alignment explanation
Indices: 68558--68739 Score: 90
Period size: 34 Copynumber: 5.1 Consensus size: 34
68548 AATTACGTAT
*
68558 ATATATAGTATAATTATAAAGATTAAAG-TATAT-A
1 ATATAAAGTATAA-TATAAAGA-TAAAGATATATAA
* *
68592 ATATAAAGTAT-ACATAAATATAAAGTATATATAA
1 ATATAAAGTATAATATAAAGATAAAG-ATATATAA
*
68626 ATATAAAGTATAAGTATATATATATATATATG-TATATAA
1 ATATAAAGTATAA-TATA-A-AGATA-A-A-GATATATAA
* * * *
68665 ACTATAAAGTAAAAGTATATATATAAA-CTATA-AA
1 A-TATAAAGTATAA-TATAAAGATAAAGATATATAA
* * *
68699 GTA-AAAGTATATATATAAACTATAAAGTATATATAT
1 ATATAAAGTATA-ATATAAA-GATAAAG-ATATATAA
68735 ATATA
1 ATATA
68740 TACACACATA
Statistics
Matches: 118, Mismatches: 12, Indels: 33
0.72 0.07 0.20
Matches are distributed among these distances:
31 5 0.04
32 18 0.15
33 15 0.13
34 24 0.20
35 9 0.08
36 7 0.06
37 3 0.03
38 10 0.08
39 9 0.08
40 17 0.14
41 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (34 bp):
ATATAAAGTATAATATAAAGATAAAGATATATAA
Found at i:68629 original size:6 final size:6
Alignment explanation
Indices: 68566--68741 Score: 67
Period size: 6 Copynumber: 27.7 Consensus size: 6
68556 ATATATATAG
* * *
68566 TATAAT TATAAA GATTAAA GTATATAA TATAAA GTAT--A CATAAA TATAAA
1 TATAAA TATAAA TA-TAAA -TATA-AA TATAAA -TATAAA TATAAA TATAAA
* * **
68616 GTAT--A TATAAA TATAAA GTATAAGTA TATATA TATATA TATGTA TATAAA
1 -TATAAA TATAAA TATAAA -TATAA--A TATAAA TATAAA TATAAA TATAAA
* *
68666 CTATAAA GTA-AAA GTATATA TATAAA CTATAAA GTA-AAA GTATATA
1 -TATAAA -TATAAA -TATAAA TATAAA -TATAAA -TATAAA -TATAAA
* *
68712 TATAAA CTATAAA GTATATA TATATA TATA
1 TATAAA -TATAAA -TATAAA TATAAA TATA
68742 CACACATACT
Statistics
Matches: 136, Mismatches: 17, Indels: 34
0.73 0.09 0.18
Matches are distributed among these distances:
4 5 0.04
5 2 0.01
6 69 0.51
7 52 0.38
8 7 0.05
9 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (6 bp):
TATAAA
Found at i:68647 original size:17 final size:17
Alignment explanation
Indices: 68591--68637 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
68581 TAAAGTATAT
68591 AATATAAAGTATACATA
1 AATATAAAGTATACATA
*
68608 AATATAAAGTATATATA
1 AATATAAAGTATACATA
68625 AATATAAAGTATA
1 AATATAAAGTATA
68638 AGTATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (17 bp):
AATATAAAGTATACATA
Found at i:68687 original size:26 final size:26
Alignment explanation
Indices: 68658--68741 Score: 143
Period size: 26 Copynumber: 3.2 Consensus size: 26
68648 TATATATATG
68658 TATATAAACTATAAAGTAAAAGTATA
1 TATATAAACTATAAAGTAAAAGTATA
68684 TATATAAACTATAAAGTAAAAGTATA
1 TATATAAACTATAAAGTAAAAGTATA
*
68710 TATATAAACTATAAAGTATATA-TATA
1 TATATAAACTATAAAGTA-AAAGTATA
68736 TATATA
1 TATATA
68742 CACACATACT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
26 54 0.96
27 2 0.04
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (26 bp):
TATATAAACTATAAAGTAAAAGTATA
Found at i:72744 original size:17 final size:19
Alignment explanation
Indices: 72719--72757 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
72709 ATATCTGTAT
72719 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
72737 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
72756 TA
1 TA
72758 AGTTGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:78504 original size:19 final size:19
Alignment explanation
Indices: 78479--78545 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
78469 GCTTAAAAAT
*
78479 CGGTTTGACCAGTCCGAAC
1 CGGTTTGACCGGTCCGAAC
*
78498 TGGTTTGACCGGTCCGAAC
1 CGGTTTGACCGGTCCGAAC
* *
78517 CGGGTTGATCGGTCCGAAC
1 CGGTTTGACCGGTCCGAAC
*
78536 CAGTTTGACC
1 CGGTTTGACC
78546 CAACCCGACC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.18, C:0.28, G:0.30, T:0.24
Consensus pattern (19 bp):
CGGTTTGACCGGTCCGAAC
Found at i:80139 original size:34 final size:34
Alignment explanation
Indices: 80082--80152 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
80072 GGCTACATGG
*
80082 TATGTGTTATCTGATTATGGTTTTCACTAAAAAA
1 TATGTGTTATCTGATTATAGTTTTCACTAAAAAA
* * *
80116 TATGTGTTCTCTGATT-TCAGTTTTCATTGAAAAA
1 TATGTGTTATCTGATTAT-AGTTTTCACTAAAAAA
80150 TAT
1 TAT
80153 AATTTTTCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 1 0.03
34 31 0.97
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (34 bp):
TATGTGTTATCTGATTATAGTTTTCACTAAAAAA
Found at i:80680 original size:31 final size:29
Alignment explanation
Indices: 80612--80682 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
80602 TAGGCTCCAA
* *
80612 GGCCTCGAGATCTTTCTTGGGTAGGCCCT
1 GGCCCCGAGATCTTTCATGGGTAGGCCCT
*
80641 GCTACCCCGAGATCTTTCATGGGTAGGTCCCAT
1 G--GCCCCGAGATCTTTCATGGGTAGG-CCC-T
80674 GGCCCCGAG
1 GGCCCCGAG
80683 TAACTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 1 0.03
31 28 0.82
32 3 0.09
33 2 0.06
ACGTcount: A:0.14, C:0.31, G:0.30, T:0.25
Consensus pattern (29 bp):
GGCCCCGAGATCTTTCATGGGTAGGCCCT
Found at i:81352 original size:25 final size:25
Alignment explanation
Indices: 81304--81386 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 25
81294 TTTACTTTTG
*
81304 TATATAAGTAT-TAAATATAAAGTATA
1 TATA-AAGTATATAAGTATAAAGTA-A
* * *
81330 TATACA-TATATACGTATATAGTAA
1 TATAAAGTATATAAGTATAAAGTAA
*
81354 TATAAAGTATATAAGTAT-TA--AA
1 TATAAAGTATATAAGTATAAAGTAA
81376 TATAAAGTATA
1 TATAAAGTATA
81387 AGTATATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
22 13 0.27
24 11 0.22
25 21 0.43
26 4 0.08
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
TATAAAGTATATAAGTATAAAGTAA
Found at i:81380 original size:22 final size:22
Alignment explanation
Indices: 81352--81431 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 22
81342 CGTATATAGT
81352 AATATAAAGTATATAAGTATTA
1 AATATAAAGTATATAAGTATTA
81374 AATATAAAG--TATAAGTA-TA
1 AATATAAAGTATATAAGTATTA
* * *
81393 TATATAAAATATA-AATTATATA
1 AATATAAAGTATATAAGTAT-TA
81415 TATATATAAAGTATATA
1 -A-ATATAAAGTATATA
81432 TACATATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
19 9 0.20
20 12 0.26
21 2 0.04
22 11 0.24
24 11 0.24
25 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (22 bp):
AATATAAAGTATATAAGTATTA
Found at i:81396 original size:2 final size:2
Alignment explanation
Indices: 81389--81479 Score: 61
Period size: 2 Copynumber: 48.0 Consensus size: 2
81379 AAAGTATAAG
* * *
81389 TA TA TA TA TA -A AA TA TA AA T- TA TA TA TA TA TA TA AA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
81430 TA TA CA TA TA TA -A TA -A TA TA AA T- TG TA -A GTA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
81468 TA TA TA TA TA TA
1 TA TA TA TA TA TA
81480 GGGTCGGGTA
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
1 7 0.10
2 61 0.87
3 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (2 bp):
TA
Found at i:81414 original size:57 final size:57
Alignment explanation
Indices: 81303--81428 Score: 150
Period size: 57 Copynumber: 2.2 Consensus size: 57
81293 TTTTACTTTT
** *
81303 GTATATAAGTATTAAATATAAAGTATATATACATATATACGTATATAGTAATATAAA
1 GTATATAAGTATTAAATATAAAGTATATATACATATATAAATATATAATAATATAAA
* * *
81360 GTATATAAGTATTAAATATAAAGTATA-AGTATATATATAAA-ATATAAATTATATATA
1 GTATATAAGTATTAAATATAAAGTATATA-TACATATATAAATATAT-AATAATATAAA
81417 -TATATAAAGTAT
1 GTATAT-AAGTAT
81429 ATATACATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
56 10 0.17
57 50 0.83
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (57 bp):
GTATATAAGTATTAAATATAAAGTATATATACATATATAAATATATAATAATATAAA
Found at i:81429 original size:7 final size:7
Alignment explanation
Indices: 81354--81412 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
81344 TATATAGTAA
81354 TATAAAG
1 TATAAAG
81361 TATATAAG
1 TATA-AAG
81369 TATTAAA-
1 TA-TAAAG
81376 TATAAAG
1 TATAAAG
81383 TAT-AAG
1 TATAAAG
*
81389 TATATA-
1 TATAAAG
*
81395 TATAAAA
1 TATAAAG
*
81402 TATAAAT
1 TATAAAG
81409 TATA
1 TATA
81413 TATATATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 15 0.34
7 20 0.45
8 7 0.16
9 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (7 bp):
TATAAAG
Found at i:83476 original size:2 final size:2
Alignment explanation
Indices: 83469--83642 Score: 109
Period size: 2 Copynumber: 89.0 Consensus size: 2
83459 AAATATAAAG
* * *
83469 TA TA TA TA CA TA TA TA CA TA TA TA GTA -A TA TA AA GTA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA
* * * *
83511 GTA T- TA AA TA TA AA GTA TA -A GTA TA TA TA TA -A AA TA TA AA
1 -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
83551 T- TA TA TA TA TA TA TA AA GTA TA TA TA CA TA TA TA -A TA -A TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* *
83591 TA AA T- TC TA -A GTA TA T- 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
83631 TA TA TA TA TA TA
1 TA TA TA TA TA TA
83643 GAGTCGGGTA
Statistics
Matches: 134, Mismatches: 20, Indels: 36
0.71 0.11 0.19
Matches are distributed among these distances:
1 11 0.08
2 115 0.86
3 8 0.06
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (2 bp):
TA
Found at i:83557 original size:57 final size:56
Alignment explanation
Indices: 83446--83571 Score: 157
Period size: 57 Copynumber: 2.2 Consensus size: 56
83436 TTTTACTTTT
* *
83446 ATATATAAGTATTAAATATAAAGTATATATACATATATACATATATAGTAATATAA
1 ATATATAAGTATTAAATATAAAGTATATATACATATATAAATATATAATAATATAA
* * *
83502 AGTATATAAGTATTAAATATAAAGTATA-AGTATATATATAAA-ATATAAATTATATAT
1 A-TATATAAGTATTAAATATAAAGTATATA-TACATATATAAATATAT-AATAATATAA
83559 ATATATAAAGTAT
1 ATATAT-AAGTAT
83572 ATATACATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
56 11 0.18
57 50 0.82
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (56 bp):
ATATATAAGTATTAAATATAAAGTATATATACATATATAAATATATAATAATATAA
Found at i:83572 original size:7 final size:7
Alignment explanation
Indices: 83497--83555 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
83487 TATATAGTAA
83497 TATAAAG
1 TATAAAG
83504 TATATAAG
1 TATA-AAG
83512 TATTAAA-
1 TA-TAAAG
83519 TATAAAG
1 TATAAAG
83526 TAT-AAG
1 TATAAAG
*
83532 TATATA-
1 TATAAAG
*
83538 TATAAAA
1 TATAAAG
*
83545 TATAAAT
1 TATAAAG
83552 TATA
1 TATA
83556 TATATATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 15 0.34
7 20 0.45
8 7 0.16
9 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (7 bp):
TATAAAG
Found at i:84304 original size:50 final size:42
Alignment explanation
Indices: 84184--84357 Score: 314
Period size: 42 Copynumber: 4.2 Consensus size: 42
84174 TGATGTTGAT
**
84184 TTTA-TTTAGACTTATTGAGACTTGTTGGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
*
84225 TTTATTTTAGATTTATTGAGACTTAATGGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
84267 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
84309 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
84351 TTTATTT
1 TTTATTT
84358 ACTTGTTTAT
Statistics
Matches: 128, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
41 4 0.03
42 124 0.97
ACGTcount: A:0.22, C:0.04, G:0.21, T:0.52
Consensus pattern (42 bp):
TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
Found at i:84754 original size:22 final size:22
Alignment explanation
Indices: 84729--84874 Score: 77
Period size: 21 Copynumber: 6.4 Consensus size: 22
84719 TTATAAAGAC
*
84729 TAAAGTATATAAACATATAATA
1 TAAAGTATATAAACATAAAATA
*
84751 TAAAGTATAT-AATATAAAATA
1 TAAAGTATATAAACATAAAATA
*
84772 TATAAGTA-ATAAATATAAAAAATA
1 TA-AAGTATATAAACAT--AAAATA
* *
84796 TATATATGTATATAATACA-CACATA
1 TA-A-A-GTATATAA-ACATAAAATA
* * *
84821 TATA-TATGTACATATATAATAATA
1 TAAAGTATATA-A-ACATAA-AATA
* *
84845 TAAAGTATAT-AAGATTAAATA
1 TAAAGTATATAAACATAAAATA
84866 TAAAGTATA
1 TAAAGTATA
84875 ATTATAAAGA
Statistics
Matches: 98, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
21 31 0.32
22 28 0.29
23 3 0.03
24 16 0.16
25 11 0.11
26 3 0.03
27 4 0.04
28 2 0.02
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (22 bp):
TAAAGTATATAAACATAAAATA
Found at i:84760 original size:9 final size:8
Alignment explanation
Indices: 84729--84856 Score: 56
Period size: 7 Copynumber: 16.4 Consensus size: 8
84719 TTATAAAGAC
84729 TAAAGTATA
1 TAAA-TATA
*
84738 TAAACATA
1 TAAATATA
84746 T-AATATA
1 TAAATATA
*
84753 -AAGTATA
1 TAAATATA
84760 T-AATATA
1 TAAATATA
84767 -AAATATA
1 TAAATATA
*
84774 TAAGTA-A
1 TAAATATA
84781 TAAATATA
1 TAAATATA
*
84789 -AAAAATA
1 TAAATATA
* *
84796 TATATATG
1 TAAATATA
*
84804 TATATA-A
1 TAAATATA
*
84811 TACACACATA
1 TA-A-ATATA
* *
84821 TATATATG
1 TAAATATA
*
84829 TACATATA
1 TAAATATA
84837 T-AATAATA
1 TAAAT-ATA
84845 TAAAGTATA
1 TAAA-TATA
84854 TAA
1 TAA
84857 GATTAAATAT
Statistics
Matches: 88, Mismatches: 19, Indels: 24
0.67 0.15 0.18
Matches are distributed among these distances:
7 37 0.42
8 33 0.38
9 14 0.16
10 4 0.05
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (8 bp):
TAAATATA
Found at i:84766 original size:29 final size:28
Alignment explanation
Indices: 84704--84773 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
84694 TACATATTAC
*
84704 ATATATAAAGTATAATTATAAAGACTAA
1 ATATATAAAATATAATTATAAAGACTAA
*
84732 AGTATATAAACATATAA-TATAAAG--TAT
1 A-TATATAAA-ATATAATTATAAAGACTAA
84759 ATAATATAAAATATA
1 AT-ATATAAAATATA
84774 TAAGTAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 6 0.16
27 10 0.27
28 1 0.03
29 15 0.41
30 5 0.14
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.33
Consensus pattern (28 bp):
ATATATAAAATATAATTATAAAGACTAA
Found at i:84938 original size:17 final size:15
Alignment explanation
Indices: 84893--85133 Score: 81
Period size: 15 Copynumber: 16.3 Consensus size: 15
84883 GATTGAACTA
84893 TATAAGTATATAAAG
1 TATAAGTATATAAAG
84908 TATACA-TACATATAAAG
1 TATA-AGT--ATATAAAG
*
84925 TATAAGTATGT--A-
1 TATAAGTATATAAAG
84937 TATACA-TATATAAAG
1 TATA-AGTATATAAAG
* *
84952 TAAAAGTATATATA-
1 TATAAGTATATAAAG
84966 TATAA--ACTATAAAG
1 TATAAGTA-TATAAAG
* ** *
84980 TGTGTGTATAT-ATG
1 TATAAGTATATAAAG
84994 TATAA-TAATATAAAG
1 TATAAGT-ATATAAAG
*
85009 TATAAGTATACTATA-
1 TATAAGTATA-TAAAG
*
85024 TAT-A-TGTATAAAG
1 TATAAGTATATAAAG
*
85037 TATAATTATAAAACTAAAG
1 TATAAGTAT---A-TAAAG
*
85056 TAGATAAGCATATAACA-
1 T--ATAAGTATATAA-AG
*
85073 TA-AAGTATATAAACA
1 TATAAGTATATAAA-G
85088 TATAAGTAT-TAAA-
1 TATAAGTATATAAAG
85101 TATAAAGTATAT-AAG
1 TAT-AAGTATATAAAG
85116 TAT-A-TAATATAAAG
1 TATAAGT-ATATAAAG
85130 TATA
1 TATA
85134 TAAGTGTTAA
Statistics
Matches: 169, Mismatches: 21, Indels: 72
0.65 0.08 0.27
Matches are distributed among these distances:
12 13 0.08
13 23 0.14
14 41 0.24
15 47 0.28
16 13 0.08
17 17 0.10
18 3 0.02
19 6 0.04
21 6 0.04
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (15 bp):
TATAAGTATATAAAG
Found at i:84941 original size:25 final size:26
Alignment explanation
Indices: 84908--84967 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
84898 GTATATAAAG
* *
84908 TATACATAC-ATATAAAGTATAAGTA
1 TATATATACAATATAAAGTAAAAGTA
*
84933 TGTATATACATATATAAAGTAAAAGTA
1 TATATATACA-ATATAAAGTAAAAGTA
84960 TATATATA
1 TATATATA
84968 TAAACTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 7 0.24
27 22 0.76
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (26 bp):
TATATATACAATATAAAGTAAAAGTA
Found at i:85077 original size:22 final size:22
Alignment explanation
Indices: 85051--85092 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
85041 ATTATAAAAC
*
85051 TAAAGTAGATAAGCATATAACA
1 TAAAGTAGATAAACATATAACA
*
85073 TAAAGTATATAAACATATAA
1 TAAAGTAGATAAACATATAA
85093 GTATTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.26
Consensus pattern (22 bp):
TAAAGTAGATAAACATATAACA
Found at i:85105 original size:13 final size:14
Alignment explanation
Indices: 85087--85149 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
85077 GTATATAAAC
85087 ATATAAGTATTAA-
1 ATATAAGTATTAAG
85100 ATATAAAGTATATAAG
1 ATAT-AAGTAT-TAAG
*
85116 TATATAA-TATAAAG
1 -ATATAAGTATTAAG
*
85130 TATATAAGTGTTAA-
1 -ATATAAGTATTAAG
85144 ATATAA
1 ATATAA
85150 ATTATGTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
13 10 0.24
14 16 0.38
15 10 0.24
16 2 0.05
17 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (14 bp):
ATATAAGTATTAAG
Found at i:85112 original size:22 final size:20
Alignment explanation
Indices: 85079--85230 Score: 121
Period size: 22 Copynumber: 7.2 Consensus size: 20
85069 AACATAAAGT
*
85079 ATATAAACATATAAGTATTAA
1 ATATAAATATATAAGTA-TAA
85100 ATATAAAGTATATAAGTATATA
1 ATATAAA-TATATAAGTATA-A
*
85122 ATATAAAGTATATAAGTGTTAA
1 ATATAAA-TATATAAGT-ATAA
* *
85144 ATATAAATTATGTAAGTATAT
1 ATATAAA-TATATAAGTATAA
85165 ATATAAACTATA-AAGTATATA
1 ATATAAA-TATATAAGTATA-A
* *
85186 TATGTAAAT-TATAAGTATAT
1 -ATATAAATATATAAGTATAA
* *
85206 ATATAAACTATA-AATTATAT
1 ATATAAA-TATATAAGTATAA
85226 ATATA
1 ATATA
85231 CTTTATATTA
Statistics
Matches: 110, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
19 6 0.05
20 22 0.20
21 31 0.28
22 49 0.45
23 2 0.02
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (20 bp):
ATATAAATATATAAGTATAA
Found at i:85161 original size:52 final size:52
Alignment explanation
Indices: 85051--85185 Score: 136
Period size: 52 Copynumber: 2.6 Consensus size: 52
85041 ATTATAAAAC
* * * *
85051 TAAAGTAGATAAGCATATAACATAAAGTATATAAACATATAAGTATTAAATA
1 TAAAGTATATAAGTATATAATATAAAGTATATAAACATATAAATATTAAATA
***
85103 TAAAGTATATAAGTATATAATATAAAGTATATAAGTGT-TAAATA-TAAATTA
1 TAAAGTATATAAGTATATAATATAAAGTATATAAACATATAAATATTAAA-TA
*
85154 TGTAAGTATAT-A-TATA-AACTATAAAGTATATA
1 T-AAAGTATATAAGTATATAA-TATAAAGTATATA
85186 TATGTAAATT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
49 2 0.03
50 21 0.29
51 9 0.12
52 40 0.56
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.34
Consensus pattern (52 bp):
TAAAGTATATAAGTATATAATATAAAGTATATAAACATATAAATATTAAATA
Found at i:85219 original size:41 final size:41
Alignment explanation
Indices: 85078--85217 Score: 176
Period size: 43 Copynumber: 3.3 Consensus size: 41
85068 TAACATAAAG
85078 TATATAAAC-ATATAAGTATTAAATATAAAGTATATAAGTATA
1 TATATAAACTATATAAGTATTAAATATAAA-T-TATAAGTATA
* *
85120 TAATATAAAGTATATAAGTGTTAAATATAAATTATGTAAGTATA
1 T-ATATAAACTATATAAGTATTAAATATAAATTA--TAAGTATA
* *
85164 TATATAAACTATA-AAGTATATATATGTAAATTATAAGTATA
1 TATATAAACTATATAAGTAT-TAAATATAAATTATAAGTATA
85205 TATATAAACTATA
1 TATATAAACTATA
85218 AATTATATAT
Statistics
Matches: 87, Mismatches: 6, Indels: 11
0.84 0.06 0.11
Matches are distributed among these distances:
41 21 0.24
42 8 0.09
43 30 0.34
44 28 0.32
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (41 bp):
TATATAAACTATATAAGTATTAAATATAAATTATAAGTATA
Found at i:85225 original size:41 final size:41
Alignment explanation
Indices: 85078--85230 Score: 168
Period size: 41 Copynumber: 3.6 Consensus size: 41
85068 TAACATAAAG
*
85078 TATATAAAC-ATATAAGTAT-TAAATATAAAGTATATAAGTATA
1 TATATAAACTATA-AAGTATATATATATAAA-T-TATAAGTATA
* * *
85120 TAATATAAAGTATATAAGTGT-TAAATATAAATTATGTAAGTATA
1 T-ATATAAACTATA-AAGTATATATATATAAATTA--TAAGTATA
*
85164 TATATAAACTATAAAGTATATATATGTAAATTATAAGTATA
1 TATATAAACTATAAAGTATATATATATAAATTATAAGTATA
*
85205 TATATAAACTATAAATTATATATATA
1 TATATAAACTATAAAGTATATATATA
85231 CTTTATATTA
Statistics
Matches: 98, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
41 32 0.33
42 8 0.08
43 30 0.31
44 28 0.29
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (41 bp):
TATATAAACTATAAAGTATATATATATAAATTATAAGTATA
Found at i:85283 original size:2 final size:2
Alignment explanation
Indices: 85276--85331 Score: 55
Period size: 2 Copynumber: 28.5 Consensus size: 2
85266 AATTTTAGTC
* *
85276 TA TA TA TA TA TA TA TA TA TA TA TA TA -A AA TA TA CT- TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
85317 TA TA GTA T- TA TA TA T
1 TA TA -TA TA TA TA TA T
85332 GTTTATTACT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
1 3 0.07
2 40 0.87
3 3 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:85579 original size:2 final size:2
Alignment explanation
Indices: 85421--85564 Score: 114
Period size: 2 Copynumber: 70.0 Consensus size: 2
85411 CATGTGTGCG
85421 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
* * *
85463 TA TA TA TA TA TA TA CTT TA TA CTA -A AA CTT 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
* * * * * *
85505 TT TA CA CTT TA TA GTT TA TA TA TA TA CT- TA TG TA CTT TA TA T-
1 TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA
*
85547 TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
85565 CCTTATATTT
Statistics
Matches: 113, Mismatches: 19, Indels: 20
0.74 0.12 0.13
Matches are distributed among these distances:
1 3 0.03
2 104 0.92
3 6 0.05
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:85712 original size:2 final size:2
Alignment explanation
Indices: 85705--85760 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
85695 GATTCATACG
85705 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
85747 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
85761 CAGAAGACCG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91343 original size:17 final size:18
Alignment explanation
Indices: 91321--91362 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
91311 CGTGCACCCT
91321 AAATAAAAAAT-AAACAA
1 AAATAAAAAATAAAACAA
* *
91338 AAATAAATAATAAAATAA
1 AAATAAAAAATAAAACAA
91356 AAATAAA
1 AAATAAA
91363 CAACTCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATAAAAAATAAAACAA
Found at i:98064 original size:45 final size:44
Alignment explanation
Indices: 98015--98103 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
98005 GCACAAACCT
* * *
98015 GAGGAGCCTGCGGAAAGCGGTAAGGTCTTACCCTTGCACATAGCA
1 GAGGAGCCTGC-AAAAACAGTAAGGTCTTACCCTTGCACATAGCA
* * *
98060 GAGGAGCCTTCAAAAATAGTAAGGTCTTACCCTTGCACTTAGCA
1 GAGGAGCCTGCAAAAACAGTAAGGTCTTACCCTTGCACATAGCA
98104 AATAAGCCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
44 28 0.74
45 10 0.26
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (44 bp):
GAGGAGCCTGCAAAAACAGTAAGGTCTTACCCTTGCACATAGCA
Found at i:98112 original size:44 final size:44
Alignment explanation
Indices: 98034--98119 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
98024 GCGGAAAGCG
* * *
98034 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAAAAATA
1 GTAAGGTCTTACCCTTGCACATAGCAAAGAAGCCTTAAAAAATA
* *
98078 GTAAGGTCTTACCCTTGCACTTAGCAAATAAGCCTTAAAAAA
1 GTAAGGTCTTACCCTTGCACATAGCAAAGAAGCCTTAAAAAA
98120 CTTCCTCCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (44 bp):
GTAAGGTCTTACCCTTGCACATAGCAAAGAAGCCTTAAAAAATA
Found at i:98211 original size:29 final size:29
Alignment explanation
Indices: 98149--98211 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
98139 CAATGACAGT
* **
98149 AATAAACATGTATGTATTTGAGTGACAGT
1 AATAAACATGTATGTATTTGAGTGAAAAC
98178 AATAAACATGTATGTATTCT-AGTGAAAAC
1 AATAAACATGTATGTATT-TGAGTGAAAAC
*
98207 GATAA
1 AATAA
98212 TGAATCCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (29 bp):
AATAAACATGTATGTATTTGAGTGAAAAC
Done.