Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012095.1 Corchorus olitorius cultivar O-4 contig12128, 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: 39637
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3596 original size:16 final size:17
Alignment explanation
Indices: 3575--3613 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3565 CTGAAACAGA
*
3575 AAAAAAAAAT-TAAAAT
1 AAAAAAAAATAAAAAAT
*
3591 AAAAAAATATAAAAAAT
1 AAAAAAAAATAAAAAAT
3608 AAAAAA
1 AAAAAA
3614 TCTATGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAAAAAATAAAAAAT
Found at i:3614 original size:16 final size:14
Alignment explanation
Indices: 3574--3614 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
3564 TCTGAAACAG
3574 AAAAAAAAAATTAA
1 AAAAAAAAAATTAA
*
3588 AATAAAAAAATATAA
1 AAAAAAAAAAT-TAA
3603 AAAATAAAAAAT
1 AAAA-AAAAAAT
3615 CTATGATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.43
15 6 0.26
16 7 0.30
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAAAAAATTAA
Found at i:8590 original size:67 final size:67
Alignment explanation
Indices: 8482--8617 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
8472 TTAAGGATAC
8482 TACCCTGCAAAGCTCTAAATGATTCTACAGACAAACAAAGCTAGGTGTATAACCATATAGCAATA
1 TACCCTGCAAAGCTCTAAATGATTCTACAGACAAACAAAGCTAGGTGTATAACCATATAGCAATA
8547 AG
66 AG
8549 TACCCTGCAAAGCTCTAAATGATTCTACAGACAAACAAAGCTAGGTGTATAACCATATAGCAATA
1 TACCCTGCAAAGCTCTAAATGATTCTACAGACAAACAAAGCTAGGTGTATAACCATATAGCAATA
8614 AG
66 AG
8616 TA
1 TA
8618 TGAAGGAAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (67 bp):
TACCCTGCAAAGCTCTAAATGATTCTACAGACAAACAAAGCTAGGTGTATAACCATATAGCAATA
AG
Found at i:16625 original size:106 final size:104
Alignment explanation
Indices: 16461--16657 Score: 342
Period size: 106 Copynumber: 1.9 Consensus size: 104
16451 TCTTAATTTA
*
16461 ACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTAATAATT
1 ACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAA--
16526 TATTGTTATAGGGTTTTAGAAATAAAATACAAAACTAGTTTC
64 TATTGTTA-AGGGTTTTAGAAATAAAATACAAAACTAGTTTC
*
16568 ACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAATA
1 ACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAATA
16632 TTGTTAAGGGTTTTAGAAATAAAATA
66 TTGTTAAGGGTTTTAGAAATAAAATA
16658 TATAACTAAT
Statistics
Matches: 88, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
103 20 0.23
104 8 0.09
106 49 0.56
107 11 0.12
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (104 bp):
ACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAATA
TTGTTAAGGGTTTTAGAAATAAAATACAAAACTAGTTTC
Found at i:24856 original size:21 final size:22
Alignment explanation
Indices: 24832--24952 Score: 69
Period size: 22 Copynumber: 5.6 Consensus size: 22
24822 TTTATTAGGA
24832 GGTTATCAAAATTCT-TAGTGT
1 GGTTATCAAAATTCTATAGTGT
*
24853 GGTTA-CTAGAATTTCTA-A--GT
1 GGTTATC-A-AAATTCTATAGTGT
* *
24873 GGTTATTAAAATTTTATAGTGT
1 GGTTATCAAAATTCTATAGTGT
24895 GGTTA-CAAAAATT-TCATAG-GTT
1 GGTTATC-AAAATTCT-ATAGTG-T
* *
24917 AGGTTATCAAAATTTTATAATGT
1 -GGTTATCAAAATTCTATAGTGT
* *
24940 AGTTATCACAATT
1 GGTTATCAAAATT
24953 TCATGGGATG
Statistics
Matches: 78, Mismatches: 8, Indels: 27
0.69 0.07 0.24
Matches are distributed among these distances:
19 6 0.08
20 10 0.13
21 8 0.10
22 36 0.46
23 15 0.19
24 3 0.04
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (22 bp):
GGTTATCAAAATTCTATAGTGT
Found at i:24900 original size:42 final size:45
Alignment explanation
Indices: 24831--24944 Score: 137
Period size: 45 Copynumber: 2.6 Consensus size: 45
24821 TTTTATTAGG
* * *
24831 AGGTTATCAAAATTCT-TAGTGTGGTTACTAGAATTTC-TAAG-T
1 AGGTTATCAAAATTTTATAGTGTGGTTACAAAAATTTCATAAGTT
* *
24873 -GGTTATTAAAATTTTATAGTGTGGTTACAAAAATTTCATAGGTT
1 AGGTTATCAAAATTTTATAGTGTGGTTACAAAAATTTCATAAGTT
* *
24917 AGGTTATCAAAATTTTATAATGTAGTTA
1 AGGTTATCAAAATTTTATAGTGTGGTTA
24945 TCACAATTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
41 13 0.22
42 19 0.32
43 3 0.05
44 1 0.02
45 24 0.40
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (45 bp):
AGGTTATCAAAATTTTATAGTGTGGTTACAAAAATTTCATAAGTT
Found at i:24913 original size:22 final size:22
Alignment explanation
Indices: 24839--24913 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
24829 GGAGGTTATC
*
24839 AAAA-TTCTTAGTGTGGTTACT
1 AAAATTTCATAGTGTGGTTACT
* * *
24860 AGAATTTC-TA-AGTGGTTATT
1 AAAATTTCATAGTGTGGTTACT
* *
24880 AAAATTTTATAGTGTGGTTACA
1 AAAATTTCATAGTGTGGTTACT
24902 AAAATTTCATAG
1 AAAATTTCATAG
24914 GTTAGGTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 14 0.33
21 7 0.17
22 21 0.50
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (22 bp):
AAAATTTCATAGTGTGGTTACT
Found at i:24953 original size:45 final size:43
Alignment explanation
Indices: 24829--24974 Score: 118
Period size: 45 Copynumber: 3.4 Consensus size: 43
24819 AATTTTATTA
* * * * * *
24829 GGAGGTTATCAAAATTCT-TAGTGTGGTTACTAGAATTTC-TA
1 GGAGGTTATCAAAATTTTATAATGTAGTTACAAAAATTTCATG
* * * * *
24870 AGTGGTTATTAAAATTTTATAGTGTGGTTACAAAAATTTCATAG
1 GGAGGTTATCAAAATTTTATAATGTAGTTACAAAAATTTCAT-G
* *
24914 GTTAGGTTATCAAAATTTTATAATGTAGTTATC-ACAATTTCATG
1 G-GAGGTTATCAAAATTTTATAATGTAGTTA-CAAAAATTTCATG
*
24958 GGATGTTATCAAAATTT
1 GGAGGTTATCAAAATTT
24975 CGTAGGCAAG
Statistics
Matches: 84, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
41 14 0.17
42 19 0.23
43 15 0.18
44 2 0.02
45 33 0.39
46 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.41
Consensus pattern (43 bp):
GGAGGTTATCAAAATTTTATAATGTAGTTACAAAAATTTCATG
Found at i:25037 original size:49 final size:48
Alignment explanation
Indices: 24949--25044 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 48
24939 TAGTTATCAC
* * * *
24949 AATTTCATGGGATGTTATCAAAATTTCGTAGGCAAGTTATTAAAATTA
1 AATTTCAAGGGATGCTATCAAAATTTCATAGGCAAGTTATCAAAATTA
* *
24997 AATTTCACAGGGATGCTATCAAAATTTTATATGG-AGGTTATCAAAATT
1 AATTTCA-AGGGATGCTATCAAAATTTCATA-GGCAAGTTATCAAAATT
25045 TCATAAGGAG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
48 7 0.17
49 31 0.77
50 2 0.05
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (48 bp):
AATTTCAAGGGATGCTATCAAAATTTCATAGGCAAGTTATCAAAATTA
Found at i:25038 original size:22 final size:22
Alignment explanation
Indices: 25013--25137 Score: 130
Period size: 22 Copynumber: 5.7 Consensus size: 22
25003 ACAGGGATGC
*
25013 TATCAAAATTTTATATGGAGGT
1 TATCAAAATTTCATATGGAGGT
*
25035 TATCAAAATTTCATAAGGAGGT
1 TATCAAAATTTCATATGGAGGT
* *
25057 TATCAGAATTCCAT-TGGAAGGT
1 TATCAAAATTTCATATGG-AGGT
* *
25079 TATCAAAATTTCACAGGGAGGT
1 TATCAAAATTTCATATGGAGGT
**
25101 TA-CTAAAATTTCATACT-CTGGT
1 TATC-AAAATTTCATA-TGGAGGT
25123 TATCAAAATTTCATA
1 TATCAAAATTTCATA
25138 GTGTGCTAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.04
22 79 0.93
23 3 0.04
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATATGGAGGT
Found at i:25100 original size:44 final size:44
Alignment explanation
Indices: 24996--25135 Score: 142
Period size: 44 Copynumber: 3.2 Consensus size: 44
24986 TATTAAAATT
* * **
24996 AAATTTCACAGGGATGCTATCAAAATTTTATATGGAGGTTATCA
1 AAATTTCACAGGGAGGTTATCAAAATTCCATATGGAGGTTATCA
* * *
25040 AAATTTCATAAGGAGGTTATCAGAATTCCAT-TGGAAGGTTATCA
1 AAATTTCACAGGGAGGTTATCAAAATTCCATATGG-AGGTTATCA
* **
25084 AAATTTCACAGGGAGGTTA-CTAAAATTTCATACT-CTGGTTATCA
1 AAATTTCACAGGGAGGTTATC-AAAATTCCATA-TGGAGGTTATCA
25128 AAATTTCA
1 AAATTTCA
25136 TAGTGTGCTA
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
43 4 0.05
44 74 0.94
46 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (44 bp):
AAATTTCACAGGGAGGTTATCAAAATTCCATATGGAGGTTATCA
Found at i:25152 original size:22 final size:22
Alignment explanation
Indices: 25104--25162 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
25094 GGGAGGTTAC
* * * *
25104 TAAAATTTCATACTCTGGTTAT
1 TAAAATTTCATAGTGTGCTAAT
*
25126 CAAAATTTCATAGTGTGCTAAT
1 TAAAATTTCATAGTGTGCTAAT
*
25148 TAAAATTACATAGTG
1 TAAAATTTCATAGTG
25163 AGATAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (22 bp):
TAAAATTTCATAGTGTGCTAAT
Found at i:25152 original size:44 final size:44
Alignment explanation
Indices: 25076--25159 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
25066 TCCATTGGAA
* * *
25076 GGTTATCAAAATTTCACAGGGAGGTTACTAAAATTTCATACTCT
1 GGTTATCAAAATTTCACAGGGAGCTAACTAAAATTACATACTCT
* * * *
25120 GGTTATCAAAATTTCATAGTGTGCTAATTAAAATTACATA
1 GGTTATCAAAATTTCACAGGGAGCTAACTAAAATTACATA
25160 GTGAGATAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (44 bp):
GGTTATCAAAATTTCACAGGGAGCTAACTAAAATTACATACTCT
Found at i:25307 original size:22 final size:22
Alignment explanation
Indices: 25176--25326 Score: 87
Period size: 22 Copynumber: 7.0 Consensus size: 22
25166 TAGAGTGAGC
*
25176 TTATCAAAATTTCA-AGTGTCG
1 TTATCAAAATTTCATAGTGTGG
* **
25197 TTACCAAAATTTCATAGTGTAA
1 TTATCAAAATTTCATAGTGTGG
* * *
25219 TTATCACAATTTCACA--G-AG
1 TTATCAAAATTTCATAGTGTGG
* * *
25238 TTAACAAAATTTCAT-GGGAAGG
1 TTATCAAAATTTCATAGTG-TGG
* * * * * *
25260 TTATCGAAATTTTAGAGGGAGA
1 TTATCAAAATTTCATAGTGTGG
25282 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* * *
25304 TTATAAAAATTTTATAATGTGG
1 TTATCAAAATTTCATAGTGTGG
25326 T
1 T
25327 ACATCAGAGG
Statistics
Matches: 99, Mismatches: 25, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
19 13 0.13
20 2 0.02
21 13 0.13
22 68 0.69
23 3 0.03
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:25397 original size:43 final size:43
Alignment explanation
Indices: 25349--25446 Score: 117
Period size: 44 Copynumber: 2.3 Consensus size: 43
25339 GATGTTATAA
* **
25349 AAAATTTATAGCGTGGTTACTAAAATTTCATTA-GAAGGTTATC
1 AAAATTTATAGCGTGGTTAATAAAATTTCACAATG-AGGTTATC
* * *
25392 AAAATTTTATTGTGTGGTTAATAAAATTTCACAATGAGTTTATC
1 AAAA-TTTATAGCGTGGTTAATAAAATTTCACAATGAGGTTATC
25436 AAAATTTATAG
1 AAAATTTATAG
25447 TGAGATTAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
43 10 0.22
44 35 0.76
45 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (43 bp):
AAAATTTATAGCGTGGTTAATAAAATTTCACAATGAGGTTATC
Found at i:25595 original size:22 final size:21
Alignment explanation
Indices: 25509--25761 Score: 208
Period size: 22 Copynumber: 11.7 Consensus size: 21
25499 ATGTAGTTAA
* *
25509 TTATCAAGATTTCAATGGGA-G
1 TTATCAAAATTTC-ATAGGAGG
* * *
25530 TGATCAAAATTTAATA-GAGTTC
1 TTATCAAAATTTCATAGGAG--G
*
25552 TTATCAAAATTTCGTAGGAGG
1 TTATCAAAATTTCATAGGAGG
*
25573 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
25595 TTATCAAAAATTCATAGGAAGG
1 TTATCAAAATTTCATAGG-AGG
* *
25617 TTATCAAAATCTCATAAGGTGG
1 TTATCAAAATTTCAT-AGGAGG
* *
25639 TTATCAAAATTTCATGGGGTGG
1 TTATCAAAATTTCAT-AGGAGG
*
25661 TTTTCAAAATTTCAT--GAGG
1 TTATCAAAATTTCATAGGAGG
* *
25680 TTATTAAAATTTCAAATGGAGG
1 TTATCAAAATTTCATA-GGAGG
*
25702 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
* *
25724 TTTATAAAAATTTTATAGTGAGG
1 -TTATCAAAATTTCATAG-GAGG
*
25747 TTATCACAATTTCAT
1 TTATCAAAATTTCAT
25762 GGTATGTTTA
Statistics
Matches: 188, Mismatches: 32, Indels: 23
0.77 0.13 0.09
Matches are distributed among these distances:
19 17 0.09
20 2 0.01
21 26 0.14
22 118 0.63
23 25 0.13
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:25701 original size:107 final size:109
Alignment explanation
Indices: 25555--25763 Score: 264
Period size: 107 Copynumber: 1.9 Consensus size: 109
25545 AGAGTTCTTA
25555 TCAAAATTTCGTAGGAGGTTAACAAAATTTCATAAGGAGGTTATCAAAAATTCATAGGAAGG-TT
1 TCAAAATTTCG-AGGAGGTTAACAAAATTTCATAAGGAGGTTATCAAAAATTCATAGGAAGGTTT
* *
25619 ATCAAAATCTCATAAG-GTGGTTATCAAAATTTCATGGGGTGGTTT
65 ATAAAAATCTCAT-AGTGAGGTTATCAAAATTTCATGGGGTGGTTT
* ** * * *
25664 TCAAAATTTC-ATGAGGTTATTAAAATTTCA-AATGGAGGTTATCAAAATTTTATAGGGAGGTTT
1 TCAAAATTTCGAGGAGGTTAACAAAATTTCATAA-GGAGGTTATCAAAAATTCATAGGAAGGTTT
* * *
25727 ATAAAAATTTTATAGTGAGGTTATCACAATTTCATGG
65 ATAAAAATCTCATAGTGAGGTTATCAAAATTTCATGG
25764 TATGTTTATG
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
106 2 0.02
107 43 0.50
108 31 0.36
109 10 0.12
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.35
Consensus pattern (109 bp):
TCAAAATTTCGAGGAGGTTAACAAAATTTCATAAGGAGGTTATCAAAAATTCATAGGAAGGTTTA
TAAAAATCTCATAGTGAGGTTATCAAAATTTCATGGGGTGGTTT
Found at i:25822 original size:44 final size:46
Alignment explanation
Indices: 25769--25874 Score: 119
Period size: 46 Copynumber: 2.3 Consensus size: 46
25759 CATGGTATGT
* * * *
25769 TTATGAAAATTTTATAATGTG-A-TTACCAATATTTTA-TCGTAATG
1 TTATCAAAATTTTATAATGTGCACTTACCAACATTTCATTCGGAA-G
* * *
25813 TTATCAAAATTTCATAATGTGCACTTACCCACATTTCATTGGGAAG
1 TTATCAAAATTTTATAATGTGCACTTACCAACATTTCATTCGGAAG
25859 TTATCAAAATTTTATA
1 TTATCAAAATTTTATA
25875 GGCTGATTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 19 0.37
45 1 0.02
46 27 0.53
47 4 0.08
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (46 bp):
TTATCAAAATTTTATAATGTGCACTTACCAACATTTCATTCGGAAG
Found at i:25824 original size:22 final size:22
Alignment explanation
Indices: 25702--25824 Score: 79
Period size: 22 Copynumber: 5.5 Consensus size: 22
25692 CAAATGGAGG
* *
25702 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATA-GTATGT
* *
25725 TTATAAAAATTTTATAGTGA-GG
1 TTATCAAAATTTTATAGT-ATGT
* * *
25747 TTATCACAATTTCATGGTATGT
1 TTATCAAAATTTTATAGTATGT
* * * *
25769 TTATGAAAATTTTATAATGTGA
1 TTATCAAAATTTTATAGTATGT
* * *
25791 TTACCAATATTTTATCGTAATG-
1 TTATCAAAATTTTATAGT-ATGT
25813 TTATCAAAATTT
1 TTATCAAAATTT
25825 CATAATGTGC
Statistics
Matches: 74, Mismatches: 23, Indels: 7
0.71 0.22 0.07
Matches are distributed among these distances:
21 1 0.01
22 55 0.74
23 18 0.24
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (22 bp):
TTATCAAAATTTTATAGTATGT
Found at i:25906 original size:22 final size:22
Alignment explanation
Indices: 25845--25911 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
25835 ACTTACCCAC
* *
25845 ATTTCATTGGGAAGTTATCAAA
1 ATTTCATTAGGAGGTTATCAAA
* * *
25867 ATTTTA-TAGGCTGATTATCAAA
1 ATTTCATTAGG-AGGTTATCAAA
* *
25889 ATTTCATTAGGTGGTTATTAAA
1 ATTTCATTAGGAGGTTATCAAA
25911 A
1 A
25912 AATTTATAGG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 3 0.09
22 28 0.80
23 4 0.11
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.40
Consensus pattern (22 bp):
ATTTCATTAGGAGGTTATCAAA
Found at i:25906 original size:44 final size:43
Alignment explanation
Indices: 25552--25911 Score: 162
Period size: 44 Copynumber: 8.2 Consensus size: 43
25542 AATAGAGTTC
* * * * *
25552 TTATCAAAATTTCGTAGGAGGTTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATAGGTGATTATCAAAATTTCATTAGGAGG
* * * * * *
25595 TTATCAAAAATTCATAGGAAGGTTATCAAAATCTCATAAGGTGG
1 TTATCAAAATTTCATAGG-TGATTATCAAAATTTCATTAGGAGG
* * *
25639 TTATCAAAATTTCATGGGGTGGTTTTCAAAATTTCA-T--GAGG
1 TTATCAAAATTTCAT-AGGTGATTATCAAAATTTCATTAGGAGG
* * * * *
25680 TTATTAAAATTTCAAATGGAGGTTATCAAAATTTTA-TAGGGAGG
1 TTATCAAAATTTCATA-GGTGATTATCAAAATTTCATTA-GGAGG
* * * *
25724 TTTATAAAAATTTTATA-GTGAGGTTATCACAATTTCA-T-GGTATGT
1 -TTATCAAAATTTCATAGGTGA--TTATCAAAATTTCATTAGG-A-GG
* * * * * * *
25769 TTATGAAAATTTTATAATGTGATTACCAATATTTTATCGTA--ATG
1 TTATCAAAATTTCAT-AGGTGATTATCAAAATTTCAT--TAGGAGG
* * * * * *
25813 TTATCAAAATTTCATAATGTGCACTTACCCACATTTCATTGGGAAG
1 TTATCAAAATTTCAT-AGGTG-A-TTATCAAAATTTCATTAGGAGG
* *
25859 TTATCAAAATTTTATAGGCTGATTATCAAAATTTCATTAGGTGG
1 TTATCAAAATTTCATAGG-TGATTATCAAAATTTCATTAGGAGG
*
25903 TTATTAAAA
1 TTATCAAAA
25912 AATTTATAGG
Statistics
Matches: 246, Mismatches: 49, Indels: 43
0.73 0.14 0.13
Matches are distributed among these distances:
41 33 0.13
43 20 0.08
44 123 0.50
45 35 0.14
46 34 0.14
47 1 0.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (43 bp):
TTATCAAAATTTCATAGGTGATTATCAAAATTTCATTAGGAGG
Found at i:25943 original size:25 final size:21
Alignment explanation
Indices: 25906--25962 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
25896 TAGGTGGTTA
25906 TTAA-AAAATTTATAGGGAGTAG
1 TTAACAAAATTTATAGGGA--AG
*
25928 TGTAACAAAATCTTATATGGAAG
1 T-TAACAAAAT-TTATAGGGAAG
25951 TTAACAAAATTT
1 TTAACAAAATTT
25963 CATATGGAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 2 0.06
22 10 0.32
23 6 0.19
24 5 0.16
25 8 0.26
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.33
Consensus pattern (21 bp):
TTAACAAAATTTATAGGGAAG
Found at i:26062 original size:20 final size:20
Alignment explanation
Indices: 26012--26070 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
26002 AACTTCAAAG
26012 TATA-ATTATCAAAATTTTA
1 TATAGATTATCAAAATTTTA
26031 TATAGAGGTTATCAAAATTTTA
1 TATAGA--TTATCAAAATTTTA
*
26053 TAGT-GATTATTAAAATTT
1 TA-TAGATTATCAAAATTT
26071 CATAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
19 4 0.11
20 12 0.34
22 18 0.51
23 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (20 bp):
TATAGATTATCAAAATTTTA
Found at i:26139 original size:2 final size:2
Alignment explanation
Indices: 26132--26157 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26122 ACTAAAACTA
26132 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
26158 GTAGACACAC
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:26315 original size:15 final size:15
Alignment explanation
Indices: 26295--26325 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
26285 TAATACATTG
26295 ATTTTCCTGTTTACA
1 ATTTTCCTGTTTACA
26310 ATTTTCCTGTTTACA
1 ATTTTCCTGTTTACA
26325 A
1 A
26326 ATTGAAACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (15 bp):
ATTTTCCTGTTTACA
Found at i:26432 original size:30 final size:30
Alignment explanation
Indices: 26397--26459 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
26387 TACACTAAAT
26397 ACACAAACAAATAAATTACAAAGAAAACTC
1 ACACAAACAAATAAATTACAAAGAAAACTC
26427 ACACAAACAAATAAATTACAAAGAAAACTC
1 ACACAAACAAATAAATTACAAAGAAAACTC
26457 ACA
1 ACA
26460 TTCTGTGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.63, C:0.21, G:0.03, T:0.13
Consensus pattern (30 bp):
ACACAAACAAATAAATTACAAAGAAAACTC
Found at i:26881 original size:32 final size:32
Alignment explanation
Indices: 26819--26881 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
26809 CAAATATATT
**
26819 AAACATATTTCAACGCATTGATTCCAAAAAAA
1 AAACATATTTCAACGCATAAATTCCAAAAAAA
*
26851 AAACATATTTCAACGCATAAAGTTTCAAAAA
1 AAACATATTTCAACGCATAAA-TTCCAAAAA
26882 TTTATGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.51, C:0.17, G:0.06, T:0.25
Consensus pattern (32 bp):
AAACATATTTCAACGCATAAATTCCAAAAAAA
Found at i:28887 original size:28 final size:28
Alignment explanation
Indices: 28855--29537 Score: 398
Period size: 28 Copynumber: 24.4 Consensus size: 28
28845 TTGTCTTCGA
*
28855 GAGCGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * * *
28883 GAGCGTACTACCGCTTCGCGGTCGTTAG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * *
28911 GAGCGTACCACCGCTTCGCGGTCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * *
28939 GAGCGTACTACCGCTTCGCGCTCTCTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * * *
28967 GAGCGTACTACCTCTTTGCGATCCTTGA
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * * * *
28995 GAGCGTACTATCACCTCGAGAGCTTGGAGG
1 GAGCGTACTACCACTTCGCGATCTT--TGG
* * * * *
29025 GGGCGTTCTATCAATTCGCGAGCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* *
29053 GAGCGTACTACCGCTTCGCGCTCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* *** * *
29081 GAGCATACTACGCA-TTTTTG-TCTTCGA
1 GAGCGTACTAC-CACTTCGCGATCTTTGG
* *
29108 GAGTGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* *
29136 GAGCGTACTACCGCTTCGCTG-TCGTTGG
1 GAGCGTACTACCACTTCGC-GATCTTTGG
* * * *
29164 GAGCGTACTACCTCTTTGCGATCCTTGA
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * * *
29192 GAGCGTACTACCACCTCGAGAGCTTGGAGG
1 GAGCGTACTACCACTTCGCGATCTT--TGG
* * * *
29222 GGGCGTTCTACCAATTCGCGAGCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* *
29250 GAGCGTACTACCACTTCGGGCTCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * *
29278 GAGCGTACTACCACCTCGAGAGC-TTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * * *
29305 AGGGCGTAGTACCAATTCGCGAGC-TT-G
1 -GAGCGTACTACCACTTCGCGATCTTTGG
* * *
29332 GAGGCATACTACCACTTCGAGAGC-TTGG
1 GA-GCGTACTACCACTTCGCGATCTTTGG
* * * * * *
29360 AGGGAGTACTACCATTTTGCGAACTTTGA
1 -GAGCGTACTACCACTTCGCGATCTTTGG
* *
29389 G-GCGTACTACCACTTCGAGAGC-TTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * * * * * *
29415 AGGGTGTACTACCATTTCGAGAACTCTGA
1 -GAGCGTACTACCACTTCGCGATCTTTGG
* * *
29444 G-GCGTACTACCACTTTGCGATCCTTGA
1 GAGCGTACTACCACTTCGCGATCTTTGG
* *
29471 GAGCGTACTACCACCTCGGGATC-TTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * * * * *
29498 AGGGAGTACTACCATTTCGTGAACTTTAG
1 -GAGCGTACTACCACTTCGCGATCTTTGG
*
29527 GAGCGTTCTAC
1 GAGCGTACTAC
29538 GCCTTAGGAT
Statistics
Matches: 501, Mismatches: 134, Indels: 40
0.74 0.20 0.06
Matches are distributed among these distances:
26 5 0.01
27 82 0.16
28 361 0.72
29 11 0.02
30 42 0.08
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.27
Consensus pattern (28 bp):
GAGCGTACTACCACTTCGCGATCTTTGG
Found at i:29288 original size:86 final size:83
Alignment explanation
Indices: 29160--29456 Score: 262
Period size: 83 Copynumber: 3.6 Consensus size: 83
29150 TTCGCTGTCG
* *
29160 TTGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGG
1 TTGGGAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGA--GGG
*
29225 CGTTCTACCAATTCGCGAGC
64 CGTACTACCAATTCGCGAGC
* * * *
29245 TTTGGGAGCGTACTACCACTTCGGGCTCTTTGGGAGCGTACTACCACCTCGAGAGCTTGGAGGGC
1 -TTGGGAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGC
*
29310 GTAGTACCAATTCGCGAGC
65 GTACTACCAATTCGCGAGC
* * * * * ** * * * *
29329 TT-GGAGGCATACTACCACTTCGAGA-GCTTGGAGGGAGTACTACCATTTTGCGAACTTTGA-GG
1 TTGGGA-GCGTACTACCACTTCGCGATCCTT-GAGAGCGTACTACCACCTCGAGAGCTTGGAGGG
* *
29391 CGTACTACCACTTCGAGAGC
64 CGTACTACCAATTCGCGAGC
* * * * *
29411 TTGGAGGGTGTACTACCATTTCGAGA-ACTCTGAG-GCGTACTACCAC
1 TTGG-GAGCGTACTACCACTTCGCGATCCT-TGAGAGCGTACTACCAC
29457 TTTGCGATCC
Statistics
Matches: 174, Mismatches: 32, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
82 36 0.21
83 61 0.35
84 23 0.13
86 54 0.31
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (83 bp):
TTGGGAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGCG
TACTACCAATTCGCGAGC
Found at i:29344 original size:197 final size:197
Alignment explanation
Indices: 28855--29530 Score: 669
Period size: 197 Copynumber: 3.4 Consensus size: 197
28845 TTGTCTTCGA
* * * * * * *
28855 GAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACCGCTTCGCGGTCGTT--AGGAGCGTA
1 GAGCGTACTACCACTTCGCGCTCTTTGGGAGCGTACTACCACCTCGAGATC-TTGGAGG-GAGTA
* ** *
28918 CCACCGCTTCGCG-GTCTTTGGGAGCGTACTACCGCTTCGCGCTC-TCTGGGAGCGTACTACCTC
64 CTACCAATTCGCGAG-CTTTGGGAGCATACTACCGCTTCGCG-TCGT-TGGGAGCGTACTACCTC
* *
28981 TTTGCGATCCTTGAGAGCGTACTATCACCTCGAGAGCTTGGAGGGGGCGTTCTATCAATTCGCGA
126 TTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGGCGTTCTACCAATTCGCGA
29046 GCTTTGG
191 GCTTTGG
* * * *** * * *
29053 GAGCGTACTACCGCTTCGCGCTCTTTGGGAGCATACTACGCA-TTTTTG-TCTTCGAGAGTGTAC
1 GAGCGTACTACCACTTCGCGCTCTTTGGGAGCGTACTAC-CACCTCGAGATCTTGGAGGGAGTAC
** * *
29116 TACCTCTTCGCGATCTTTGGGAGCGTACTACCGCTTCGCTGTCGTTGGGAGCGTACTACCTCTTT
65 TACCAATTCGCGAGCTTTGGGAGCATACTACCGCTTCGC-GTCGTTGGGAGCGTACTACCTCTTT
29181 GCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGGCGTTCTACCAATTCGCGAGCT
129 GCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGGCGTTCTACCAATTCGCGAGCT
29246 TTGG
194 TTGG
* * * *
29250 GAGCGTACTACCACTTCGGGCTCTTTGGGAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTAGT
1 GAGCGTACTACCACTTCGCGCTCTTTGGGAGCGTACTACCACCTCGAGATCTTGGAGGGAGTACT
* * * * *
29315 ACCAATTCGCGAGC-TT-GGAGGCATACTACCACTTCGAG-AGCTTGGAGGGAGTACTACCAT-T
66 ACCAATTCGCGAGCTTTGGGA-GCATACTACCGCTTCGCGTCG-TTGG-GAGCGTACTACC-TCT
* * * * * * * *
29376 TTGCGAACTTTGAG-GCGTACTACCACTTCGAGAGCTTGGA--GGGTGTACTACCATTTCGAGAA
127 TTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGGCGTTCTACCAATTCGCGAG
* *
29438 CTCTGA
192 CTTTGG
* * * * *
29444 G-GCGTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGGGATCTTGGAGGGAGTACT
1 GAGCGTACTACCACTTCGCGCTCTTTGGGAGCGTACTACCACCTCGAGATCTTGGAGGGAGTACT
* * * *
29508 ACCATTTCGTGAACTTTAGGAGC
66 ACCAATTCGCGAGCTTTGGGAGC
29531 GTTCTACGCC
Statistics
Matches: 407, Mismatches: 57, Indels: 32
0.82 0.11 0.06
Matches are distributed among these distances:
193 65 0.16
194 26 0.06
195 4 0.01
196 37 0.09
197 208 0.51
198 66 0.16
199 1 0.00
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.27
Consensus pattern (197 bp):
GAGCGTACTACCACTTCGCGCTCTTTGGGAGCGTACTACCACCTCGAGATCTTGGAGGGAGTACT
ACCAATTCGCGAGCTTTGGGAGCATACTACCGCTTCGCGTCGTTGGGAGCGTACTACCTCTTTGC
GATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGGCGTTCTACCAATTCGCGAGCTTT
GG
Found at i:29354 original size:55 final size:54
Alignment explanation
Indices: 29280--29458 Score: 250
Period size: 55 Copynumber: 3.3 Consensus size: 54
29270 CTCTTTGGGA
* * * * *
29280 GCGTACTACCACCTCGAGAGCTTGGAGGGCGTAGTACCAATTCGCGAGCTTGGAG
1 GCGTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGCGAACTT-GAG
* *
29335 GCATACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTTGCGAACTTTGAG
1 GCGTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGCGAAC-TTGAG
* *
29390 GCGTACTACCACTTCGAGAGCTTGGAGGGTGTACTACCATTTCGAGAACTCTGAG
1 GCGTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGCGAACT-TGAG
29445 GCGTACTACCACTT
1 GCGTACTACCACTT
29459 TGCGATCCTT
Statistics
Matches: 111, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
54 1 0.01
55 108 0.97
56 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (54 bp):
GCGTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGCGAACTTGAG
Found at i:29425 original size:83 final size:82
Alignment explanation
Indices: 29307--29522 Score: 256
Period size: 83 Copynumber: 2.6 Consensus size: 82
29297 GAGCTTGGAG
* * * * * *
29307 GGCGTAGTACCAATTCGCGAGCTTGGAGGCA-TACTACCACTTCGAGAGCT-TGGAGGGAGTACT
1 GGCGTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGAGAACTCT-GA-GGAGTACT
* *
29370 ACCATTTTGCGAACTTTGA
64 ACCACTTTGCGAACCTTGA
* *
29389 GGCGTACTACCACTTCGAGAGCTTGGAGGGTGTACTACCATTTCGAGAACTCTGAGGCGTACTAC
1 GGCGTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGAGAACTCTGAGGAGTACTAC
*
29454 CACTTTGCGATCCTTGA
66 CACTTTGCGAACCTTGA
* * * *
29471 GAGCGTACTACCACCTCGGGATCTTGGAGGGAGTACTACCATTTCGTGAACT
1 G-GCGTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGAGAACT
29523 TTAGGAGCGT
Statistics
Matches: 115, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
82 50 0.43
83 64 0.56
84 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (82 bp):
GGCGTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGAGAACTCTGAGGAGTACTAC
CACTTTGCGAACCTTGA
Found at i:29479 original size:55 final size:54
Alignment explanation
Indices: 29166--29516 Score: 213
Period size: 55 Copynumber: 6.3 Consensus size: 54
29156 GTCGTTGGGA
* * * * *
29166 GCGTACTACCTCTTTGCGATCCTT-GAGAGCGTACTACCACCTCGAGAGCTTGGAGGGG
1 GCGTACTACCACTTCGAGA-CCTTGGAGAGCGTACTACCACTTCGAGAACTT-GA---G
* * * * * ** *
29224 GCGTTCTACCAATTCGCGAGCTTTGG-GAGCGTACTACCACTTCGGGCTCTTTGGG
1 GCGTACTACCACTTCGAGA-CCTTGGAGAGCGTACTACCACTTCGAGAAC-TTGAG
* * * * * * *
29279 AGCGTACTACCACCTCGAGAGCTTGGAGGGCGTAGTACCAATTCGCGAGCTTGGAG
1 -GCGTACTACCACTTCGAGACCTTGGAGAGCGTACTACCACTTCGAGAACTT-GAG
* * * * * * *
29335 GCATACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTTGCGAACTTTGAG
1 GCGTACTACCACTTCGAGACCTTGGAGAGCGTACTACCACTTCGAGAAC-TTGAG
* * * *
29390 GCGTACTACCACTTCGAGAGCTTGGAGGGTGTACTACCATTTCGAGAACTCTGAG
1 GCGTACTACCACTTCGAGACCTTGGAGAGCGTACTACCACTTCGAGAACT-TGAG
* * * * *
29445 GCGTACTACCACTTTGCGATCCTT-GAGAGCGTACTACCACCTCGGGATCTTGGAGG
1 GCGTACTACCACTTCGAGA-CCTTGGAGAGCGTACTACCACTTCGAGAACTT-GA-G
* *
29501 GAGTACTACCATTTCG
1 GCGTACTACCACTTCG
29517 TGAACTTTAG
Statistics
Matches: 236, Mismatches: 47, Indels: 22
0.77 0.15 0.07
Matches are distributed among these distances:
54 2 0.01
55 140 0.59
56 53 0.22
58 38 0.16
59 3 0.01
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (54 bp):
GCGTACTACCACTTCGAGACCTTGGAGAGCGTACTACCACTTCGAGAACTTGAG
Found at i:29479 original size:110 final size:110
Alignment explanation
Indices: 29280--29483 Score: 268
Period size: 110 Copynumber: 1.9 Consensus size: 110
29270 CTCTTTGGGA
* * *
29280 GCGTACTACCACCTCGAGAGCTTGGAGGGCGTAGTACCAATTCGCGAGCTTGGAGGCATACTACC
1 GCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACCAATTCGAGAACTTGGAGGCATACTACC
* *
29345 ACTTCGAGAGCTTGGAGGGAGTACTACCATTTTGCGAACTTTGAG
66 ACTTCGAGACCTTGGAGAGAGTACTACCATTTTGCGAACTTTGAG
* * * *
29390 GCGTACTACCACTTCGAGAGCTTGGAGGGTGTACTACCATTTCGAGAACTCT-GAGGCGTACTAC
1 GCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACCAATTCGAGAACT-TGGAGGCATACTAC
* * *
29454 CACTTTGCGATCCTT-GAGAGCGTACTACCA
65 CACTTCGAGA-CCTTGGAGAGAGTACTACCA
29484 CCTCGGGATC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
110 76 0.95
111 4 0.05
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.25
Consensus pattern (110 bp):
GCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACCAATTCGAGAACTTGGAGGCATACTACC
ACTTCGAGACCTTGGAGAGAGTACTACCATTTTGCGAACTTTGAG
Found at i:30503 original size:58 final size:58
Alignment explanation
Indices: 30314--30503 Score: 247
Period size: 58 Copynumber: 3.3 Consensus size: 58
30304 TAGGTTGTAC
* * * *
30314 GACCGTGGGATGCTCGTTTTTCTTTTTGCGCAAGTGGGGGTTGCTCATTGGGTCGTGT
1 GACCGAGGGATGCTCGATTTTCTTTTTGCGCAAGTGGGGGATGCACATTGGGTCGTGT
30372 GACCGAGGGATGCTC-ATTTTTCTTTTTGCGCAAGTGGGGGATGCACATTGGGTCGTGT
1 GACCGAGGGATGCTCGA-TTTTCTTTTTGCGCAAGTGGGGGATGCACATTGGGTCGTGT
* *** * * ** *
30430 GACCGAGGGATGCTCGATTTTCTTATTGCATGAGTGGGGGATGCCCACTAAGTCATGT
1 GACCGAGGGATGCTCGATTTTCTTTTTGCGCAAGTGGGGGATGCACATTGGGTCGTGT
30488 GACCGAGGGATGCTCG
1 GACCGAGGGATGCTCG
30504 GTCGTTCTTG
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
58 116 0.99
59 1 0.01
ACGTcount: A:0.15, C:0.18, G:0.35, T:0.32
Consensus pattern (58 bp):
GACCGAGGGATGCTCGATTTTCTTTTTGCGCAAGTGGGGGATGCACATTGGGTCGTGT
Found at i:38199 original size:34 final size:35
Alignment explanation
Indices: 38161--38229 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
38151 ATCAATATAT
*
38161 CAATTTACAATATATCAAA-CAACTAATCAAATCC
1 CAATTTACAATATATCAAATCAACTAATAAAATCC
38195 CAATTTACAATATATCAAATCAACTAATAAAATCC
1 CAATTTACAATATATCAAATCAACTAATAAAATCC
38230 TTAGATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 19 0.58
35 14 0.42
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.28
Consensus pattern (35 bp):
CAATTTACAATATATCAAATCAACTAATAAAATCC
Found at i:38274 original size:42 final size:43
Alignment explanation
Indices: 38196--38297 Score: 188
Period size: 42 Copynumber: 2.4 Consensus size: 43
38186 ATCAAATCCC
38196 AATTTACAATATATCAAATCAACTAATAAAATCCTTAGATAAT
1 AATTTACAATATATCAAATCAACTAATAAAATCCTTAGATAAT
*
38239 AATTTACAATATATCAAA-CAACTAATAAGATCCTTAGATAAT
1 AATTTACAATATATCAAATCAACTAATAAAATCCTTAGATAAT
38281 AATTTACAATATATCAA
1 AATTTACAATATATCAA
38298 TTTTGCCTAT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 40 0.69
43 18 0.31
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (43 bp):
AATTTACAATATATCAAATCAACTAATAAAATCCTTAGATAAT
Done.