Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016219.1 Corchorus olitorius cultivar O-4 contig16252, 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: 83377
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2969 original size:21 final size:24
Alignment explanation
Indices: 2940--2990 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
2930 TTTTGAATTC
2940 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
2963 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
2986 ATTAT
1 ATTAT
2991 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:2985 original size:25 final size:25
Alignment explanation
Indices: 2940--2988 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2930 TTTTGAATTC
*
2940 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
2965 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
2989 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:3377 original size:16 final size:17
Alignment explanation
Indices: 3352--3385 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3342 TGCTGGTGGG
3352 TTTTTCCTTTTTCTTTC
1 TTTTTCCTTTTTCTTTC
*
3369 TTTTT-CTTTTTTTTTC
1 TTTTTCCTTTTTCTTTC
3385 T
1 T
3386 CCTATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCCTTTTTCTTTC
Found at i:4236 original size:31 final size:31
Alignment explanation
Indices: 4103--4247 Score: 130
Period size: 31 Copynumber: 4.5 Consensus size: 31
4093 TCCTTTTGTG
*
4103 CACGTGGCATGCCACGTGTCACTTTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGATA
* * *
4134 CACATGGCATGCCATGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGATA
* * *
4165 CACATGGTGTG-ATACGTACGTGTCACTTTTTGGTA
1 CAC---GTG-GCATGC-CACGTGTCACTTTTTGATA
* * * *
4200 TACGTGGCGTGCCACATGTCGCTTTTTGATA
1 CACGTGGCATGCCACGTGTCACTTTTTGATA
*
4231 CACGTGGCATGTCACGT
1 CACGTGGCATGCCACGT
4248 CAGACACCGT
Statistics
Matches: 89, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
31 59 0.66
32 5 0.06
34 5 0.06
35 20 0.22
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGATA
Found at i:12336 original size:11 final size:11
Alignment explanation
Indices: 12315--12356 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
12305 GTTTTTCTGT
12315 TTTTTGTTTTTG
1 TTTTTG-TTTTG
12327 TTTTTGTTTTG
1 TTTTTGTTTTG
*
12338 TTTTCGTTTTG
1 TTTTTGTTTTG
12349 TTTTTGTT
1 TTTTTGTT
12357 GCGCTGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 22 0.79
12 6 0.21
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (11 bp):
TTTTTGTTTTG
Found at i:12338 original size:17 final size:16
Alignment explanation
Indices: 12314--12356 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
12304 CGTTTTTCTG
*
12314 TTTTTTGTTTTTGTTT
1 TTTTTTGTTTTCGTTT
12330 TTGTTTTGTTTTCGTTT
1 TT-TTTTGTTTTCGTTT
12347 TGTTTTTGTT
1 T-TTTTTGTT
12357 GCGCTGTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 2 0.08
17 21 0.88
18 1 0.04
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.81
Consensus pattern (16 bp):
TTTTTTGTTTTCGTTT
Found at i:12353 original size:6 final size:6
Alignment explanation
Indices: 12315--12356 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
12305 GTTTTTCTGT
*
12315 TTTTTG TTTTTG TTTTTG -TTTTG TTTTCG -TTTTG TTTTTG TT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT
12357 GCGCTGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (6 bp):
TTTTTG
Found at i:20683 original size:46 final size:46
Alignment explanation
Indices: 20616--20709 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
20606 AGATAAGGGG
20616 AATGCAGATACATCAAAAATCACTTCATGGTAATGACAAATATGTT
1 AATGCAGATACATCAAAAATCACTTCATGGTAATGACAAATATGTT
20662 AATGCAGATACATCAAAAATCACTTCATGGTAATGACAAATATGTT
1 AATGCAGATACATCAAAAATCACTTCATGGTAATGACAAATATGTT
20708 AA
1 AA
20710 AGAATTCTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.28
Consensus pattern (46 bp):
AATGCAGATACATCAAAAATCACTTCATGGTAATGACAAATATGTT
Found at i:20701 original size:23 final size:23
Alignment explanation
Indices: 20629--20701 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
20619 GCAGATACAT
20629 CAAAAATCACTTCATGGTAATGA
1 CAAAAATCACTTCATGGTAATGA
* * *
20652 CAAATAT--GTTAATGCAGATACAT--
1 CAAAAATCACTTCATG--G-TA-ATGA
20675 CAAAAATCACTTCATGGTAATGA
1 CAAAAATCACTTCATGGTAATGA
20698 CAAA
1 CAAA
20702 TATGTTAAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
21 7 0.19
22 2 0.06
23 18 0.50
24 2 0.06
25 7 0.19
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.26
Consensus pattern (23 bp):
CAAAAATCACTTCATGGTAATGA
Found at i:24228 original size:2 final size:2
Alignment explanation
Indices: 24189--24216 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24179 AACTCGACGG
24189 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
24217 TACTACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25979 original size:2 final size:2
Alignment explanation
Indices: 25974--26001 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25964 GGTGTGTGTC
25974 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
26002 ATTTACCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26512 original size:22 final size:22
Alignment explanation
Indices: 26460--26609 Score: 115
Period size: 22 Copynumber: 6.8 Consensus size: 22
26450 TCATAGTGTA
* * **
26460 GTTATCAAAATTCCATACCAAG
1 GTTAACAAAATTTCATAAGAAG
* * *
26482 ATTACCAAAATTTCATAAAAAG
1 GTTAACAAAATTTCATAAGAAG
* *
26504 GTTAACAAAATTTC-TTAGCGAG
1 GTTAACAAAATTTCATAAG-AAG
* *
26526 GTTAATAAAATTTCATATGAAG
1 GTTAACAAAATTTCATAAGAAG
*** * *
26548 GTTATTGAAATTTTATAATGTA-
1 GTTAACAAAATTTCATAA-GAAG
*
26570 GTTATCAAAATTTCATAAGAAG
1 GTTAACAAAATTTCATAAGAAG
26592 GTTAACAAAATTTCATAA
1 GTTAACAAAATTTCATAA
26610 TGAGGGACGT
Statistics
Matches: 100, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
21 4 0.04
22 92 0.92
23 4 0.04
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (22 bp):
GTTAACAAAATTTCATAAGAAG
Found at i:26610 original size:44 final size:45
Alignment explanation
Indices: 26487--26614 Score: 145
Period size: 44 Copynumber: 2.9 Consensus size: 45
26477 CCAAGATTAC
* * **
26487 CAAAATTTCATAAAAAGGTTAACAAAATTTCTTAGCGAGGTTAAT
1 CAAAATTTCATAAGAAGGTTAACAAAATTTCATAATGAGGTTAAT
* *** *
26532 -AAAATTTCATATGAAGGTTATTGAAATTTTATAATGTA-GTT-AT
1 CAAAATTTCATAAGAAGGTTAACAAAATTTCATAATG-AGGTTAAT
26575 CAAAATTTCATAAGAAGGTTAACAAAATTTCATAATGAGG
1 CAAAATTTCATAAGAAGGTTAACAAAATTTCATAATGAGG
26615 GACGTTATCA
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
43 3 0.05
44 62 0.94
45 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (45 bp):
CAAAATTTCATAAGAAGGTTAACAAAATTTCATAATGAGGTTAAT
Found at i:26628 original size:26 final size:22
Alignment explanation
Indices: 26460--26630 Score: 80
Period size: 22 Copynumber: 7.6 Consensus size: 22
26450 TCATAGTGTA
* **
26460 GTTATCAAAATTCCATACCAA-
1 GTTATCAAAATTTCATAAGAAC
* * *
26481 GATTACCAAAATTTCATAAAAAG
1 G-TTATCAAAATTTCATAAGAAC
* * * *
26504 GTTAACAAAATTTC-TTAGCGAG
1 GTTATCAAAATTTCATAAG-AAC
* *
26526 GTTAAT-AAAATTTCATATGAAG
1 GTT-ATCAAAATTTCATAAGAAC
** * *
26548 GTTATTGAAATTTTATAATGTA-
1 GTTATCAAAATTTCATAA-GAAC
*
26570 GTTATCAAAATTTCATAAGAAG
1 GTTATCAAAATTTCATAAGAAC
*
26592 GTTAACAAAATTTCATAATGAGGGAC
1 GTTATCAAAATTTCATAA-GA---AC
26618 GTTATCAAAATTT
1 GTTATCAAAATTT
26631 GTGCTTATCA
Statistics
Matches: 115, Mismatches: 23, Indels: 19
0.73 0.15 0.12
Matches are distributed among these distances:
21 7 0.06
22 87 0.76
23 8 0.07
26 13 0.11
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGAAC
Found at i:26764 original size:22 final size:22
Alignment explanation
Indices: 26734--26977 Score: 147
Period size: 22 Copynumber: 11.0 Consensus size: 22
26724 ATCACAGTTT
**
26734 AATTCTCATAGGGAGGTTATTGA
1 AATT-TCATAGGGAGGTTATCAA
* *
26757 AATTTCATAGTGTGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
*
26779 AATTTTAT-GAGGAGGTTATCAA
1 AATTTCATAG-GGAGGTTATCAA
* * * **
26801 AATTTTCATAGCGCGATTA-CCC
1 AA-TTTCATAGGGAGGTTATCAA
* * ** * *
26823 ATTTTTATACTGTGGTTTTCAA
1 AATTTCATAGGGAGGTTATCAA
*
26845 AATTTTATAGGG-GGATTATCAA
1 AATTTCATAGGGAGG-TTATCAA
*
26867 AATTTCATA-GTATGGTTATCAA
1 AATTTCATAGGGA-GGTTATCAA
* *
26889 AATTTCACA-GTATGGTTATCAA
1 AATTTCATAGGGA-GGTTATCAA
* ** *
26911 AATTTCACAATGTGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
* * *
26933 ATTTTTATAGGGAGGTTATCGA
1 AATTTCATAGGGAGGTTATCAA
*
26955 AATTTCATAGTGAGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
26977 A
1 A
26978 TTTTTCAGTG
Statistics
Matches: 170, Mismatches: 43, Indels: 17
0.74 0.19 0.07
Matches are distributed among these distances:
21 14 0.08
22 139 0.82
23 16 0.09
24 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (22 bp):
AATTTCATAGGGAGGTTATCAA
Found at i:26883 original size:44 final size:43
Alignment explanation
Indices: 26756--27003 Score: 155
Period size: 44 Copynumber: 5.7 Consensus size: 43
26746 GAGGTTATTG
* * * *
26756 AAATTTCATAGTGTGGTTATCAAAATTTTATGAGGA-GGTTATCA
1 AAATTTTATAG-GGGGTTATCAAAATTTCAT-AGTATGGTTATCA
* * ** * * * * *
26800 AAATTTTCATAGCGCGATTA-CCCATTTTTATACTGTGGTTTTCA
1 AAATTTT-ATAG-GGGGTTATCAAAATTTCATAGTATGGTTATCA
26844 AAATTTTATAGGGGGATTATCAAAATTTCATAGTATGGTTATCA
1 AAATTTTATAGGGGG-TTATCAAAATTTCATAGTATGGTTATCA
* * ** * * *
26888 AAATTTCACAGTATGGTTATCAAAATTTCACAATGTGGTTATCA
1 AAATTTTATAG-GGGGTTATCAAAATTTCATAGTATGGTTATCA
* *
26932 AATTTTTATAGGGAGGTTATCGAAATTTCATAGTGA-GGTTATC-
1 AAATTTTATAGGG-GGTTATCAAAATTTCATAGT-ATGGTTATCA
* *
26975 AAATTTT-TCAGTGTGGTTATCAATATTTC
1 AAATTTTAT-AG-GGGGTTATCAAAATTTC
27004 TACGTTGGTT
Statistics
Matches: 155, Mismatches: 40, Indels: 19
0.72 0.19 0.09
Matches are distributed among these distances:
42 3 0.02
43 29 0.19
44 112 0.72
45 11 0.07
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.40
Consensus pattern (43 bp):
AAATTTTATAGGGGGTTATCAAAATTTCATAGTATGGTTATCA
Found at i:26930 original size:66 final size:65
Alignment explanation
Indices: 26860--27003 Score: 166
Period size: 66 Copynumber: 2.2 Consensus size: 65
26850 TATAGGGGGA
*
26860 TTATCAAAATTTCATA-GTATGGTTATCAAAATTTCACAGT-ATGGTTATCAAAATTTCACAATG
1 TTATCAAAATTTCATAGGGA-GGTTATCAAAATTTCACAGTGA-GGTTATC-AAATTTCACAATG
26923 TGG
63 TGG
* * * * ** *
26926 TTATCAAATTTTTATAGGGAGGTTATCGAAATTTCATAGTGAGGTTATCAAATTTTTCAGTGTGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAGTGAGGTTATCAAATTTCACAATGTGG
*
26991 TTATCAATATTTC
1 TTATCAAAATTTC
27004 TACGTTGGTT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
65 23 0.35
66 39 0.60
67 3 0.05
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (65 bp):
TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAGTGAGGTTATCAAATTTCACAATGTGG
Found at i:32361 original size:16 final size:15
Alignment explanation
Indices: 32342--32378 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
32332 ATTTTCCTTT
32342 TTTAATATAAATCATA
1 TTTAATATAAAT-ATA
32358 TTTAATATAAATATA
1 TTTAATATAAATATA
*
32373 TATAAT
1 TTTAAT
32379 TATTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAATATAAATATA
Found at i:32372 original size:22 final size:23
Alignment explanation
Indices: 32345--32390 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
32335 TTCCTTTTTT
* *
32345 AATATAAATCA-TATTTAATATA
1 AATATAAATAATTATTTAAAATA
*
32367 AATATATATAATTATTTAAAATA
1 AATATAAATAATTATTTAAAATA
32390 A
1 A
32391 TTTCTGATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATAAATAATTATTTAAAATA
Found at i:34973 original size:25 final size:27
Alignment explanation
Indices: 34931--34987 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
34921 ATTTCCTTTA
*
34931 TTTTAATAATAGATAA-TTA-AAATAAT
1 TTTTAATAATAGACAATTTAGAAAT-AT
34957 TTTTAATAAT-GACAATTTAGAAATAT
1 TTTTAATAATAGACAATTTAGAAATAT
34983 TTTTA
1 TTTTA
34988 TAAAAAAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 4 0.14
26 20 0.71
27 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (27 bp):
TTTTAATAATAGACAATTTAGAAATAT
Found at i:43666 original size:2 final size:2
Alignment explanation
Indices: 43659--43690 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
43649 TATCTGCCAT
*
43659 TA TA TA TA TA AA 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
43691 CTAAATAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:44076 original size:43 final size:43
Alignment explanation
Indices: 44014--44096 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
44004 ACTAAGGATC
*
44014 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTTCT
1 ATGATTTGAGTTGACTATTTCTTAATTTACAAAGAATTTTTCT
*
44057 ATGATTTGAGTTGACTATTTCTTAATTTACAGAGAATTTT
1 ATGATTTGAGTTGACTATTTCTTAATTTACAAAGAATTTT
44097 CAAGACTTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.48
Consensus pattern (43 bp):
ATGATTTGAGTTGACTATTTCTTAATTTACAAAGAATTTTTCT
Found at i:49837 original size:13 final size:12
Alignment explanation
Indices: 49823--49872 Score: 64
Period size: 13 Copynumber: 4.0 Consensus size: 12
49813 TTCCTATTTC
*
49823 CCTTTTTTTTTT
1 CCTTTTCTTTTT
49835 CCCTTTTCTTTTT
1 -CCTTTTCTTTTT
*
49848 CCTTTTCCTTTT
1 CCTTTTCTTTTT
49860 CCTTTTTCTTTTT
1 CC-TTTTCTTTTT
49873 TTTTTCCTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 13 0.39
13 20 0.61
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
CCTTTTCTTTTT
Found at i:49846 original size:12 final size:12
Alignment explanation
Indices: 49819--49871 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
49809 TATTTTCCTA
*
49819 TTTCCCTTTTTTT
1 TTTCCC-TTTTCT
49832 TTTCCCTTTTCT
1 TTTCCCTTTTCT
*
49844 TTTTCCTTTTCCT
1 TTTCCCTTTT-CT
*
49857 TTTCCTTTTTCT
1 TTTCCCTTTTCT
49869 TTT
1 TTT
49872 TTTTTTCCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 19 0.54
13 16 0.46
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTCCCTTTTCT
Found at i:49847 original size:6 final size:6
Alignment explanation
Indices: 49824--49878 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
49814 TCCTATTTCC
* * *
49824 CTTTTT -TTTTT CCCTTTT CTTTTT CCTTTTC CTTTTC CTTTTT CTTTTT
1 CTTTTT CTTTTT -CTTTTT CTTTTT -CTTTTT CTTTTT CTTTTT CTTTTT
49873 -TTTTT C
1 CTTTTT C
49879 CTGCTTGGGC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 10 0.24
6 22 0.54
7 9 0.22
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (6 bp):
CTTTTT
Found at i:50867 original size:20 final size:20
Alignment explanation
Indices: 50839--50880 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
50829 ATGTTCAATC
* *
50839 AATTGATTTTTTTATGGTAA
1 AATTCATTTATTTATGGTAA
50859 AATTCATTTATTTATGGTAA
1 AATTCATTTATTTATGGTAA
50879 AA
1 AA
50881 GTTAATAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (20 bp):
AATTCATTTATTTATGGTAA
Found at i:50953 original size:65 final size:65
Alignment explanation
Indices: 50869--50993 Score: 189
Period size: 65 Copynumber: 1.9 Consensus size: 65
50859 AATTCATTTA
* * * *
50869 TTTATGGTAAAAGTTAATAATCATCAGTCAGTTATAAATTTGATTGGCAAAGTTAACTAACGACT
1 TTTATGGTAAAAGTTAATAATCACCAATCAGTTACAAATTTGATTGGCAAAATTAACTAACGACT
*
50934 TTTATGGTAAAA-TTAAATAATCACCAATCAGTTACAACTTTGATTGGCAAAATTAACTAA
1 TTTATGGTAAAAGTT-AATAATCACCAATCAGTTACAAATTTGATTGGCAAAATTAACTAA
50994 TGACATGTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 2 0.04
65 52 0.96
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (65 bp):
TTTATGGTAAAAGTTAATAATCACCAATCAGTTACAAATTTGATTGGCAAAATTAACTAACGACT
Found at i:51331 original size:105 final size:108
Alignment explanation
Indices: 51147--51410 Score: 394
Period size: 107 Copynumber: 2.5 Consensus size: 108
51137 AATTTTTCTA
* **
51147 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATATTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATATTT
* *
51210 TATTTCTAAAATCCTATAACAAT-ATTATTAATTATGGAATTT
66 TATTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* *
51252 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAATTTAGTGAAATTAGTT-T-TGTATTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATATTT
* *
51315 TCTTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TATTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
*
51359 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
51411 AGCCTAAACT
Statistics
Matches: 144, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
105 54 0.38
106 15 0.10
107 75 0.52
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.41
Consensus pattern (108 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATATTT
TATTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:51868 original size:140 final size:141
Alignment explanation
Indices: 51542--52073 Score: 878
Period size: 141 Copynumber: 3.8 Consensus size: 141
51532 TTATTATTAC
* **
51542 TTTTTTGGTATCATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTCCGTAGCGATTTTA
1 TTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCGATTTTA
*
51607 TGGTAAAGTTAAATAATCATCAATCAATTACAAC-TTGATTGGCAAAATTAACTAACGACATGTT
66 TGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATGTT
51671 TAATAA-TT-T
131 TAATAATTTAT
*
51680 TCTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCGA-TTTA
1 TTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCGATTTTA
51744 TGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATGTT
66 TGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATGTT
51809 TAATAATTTAT
131 TAATAATTTAT
*
51820 TTTTTTGGTAACAAAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTTGGTAGCGATTTT
1 TTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAA-TTTTTTTGGTAGCGATTTT
* * *
51885 ATAGTAAAATTAAATAATCTTCAATCAATTAC-ATTTTGATTGGCAAAATTAACTAACGACATGT
65 ATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATGT
*
51949 TCAATAATTTAT
130 TTAATAATTTAT
* *
51961 TTTTTTGGTAACATAATTACTAATTGATCTATTTATTTATGATAATTTTTTTGGCTAGCGA-TTT
1 TTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTGG-TAGCGATTTT
* *
52025 ATGGTAAAATTAAATAATTATCAATCAATTACAACTTTGATTGGAAAAA
65 ATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGGCAAAA
52074 AATCAATTAC
Statistics
Matches: 368, Mismatches: 19, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
137 37 0.10
138 92 0.25
139 2 0.01
140 85 0.23
141 119 0.32
142 33 0.09
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.44
Consensus pattern (141 bp):
TTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCGATTTTA
TGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATGTT
TAATAATTTAT
Found at i:52085 original size:27 final size:27
Alignment explanation
Indices: 52047--52100 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
52037 AATAATTATC
*
52047 AATCAATTACAACTTTGATTGGAAAAA
1 AATCAATTACAACTTTGATCGGAAAAA
52074 AATCAATTACAACTTTGATCGGAAAAA
1 AATCAATTACAACTTTGATCGGAAAAA
52101 TTTACTAACG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (27 bp):
AATCAATTACAACTTTGATCGGAAAAA
Found at i:52194 original size:167 final size:166
Alignment explanation
Indices: 51907--52392 Score: 708
Period size: 167 Copynumber: 3.0 Consensus size: 166
51897 AATAATCTTC
* * *
51907 AATCAATTAC-ATTTTGATTGGCAAAATTAACTAACGACATGTTCAATAATTTATTTTTTTGGTA
1 AATCAATTACAACTTTGATTGGAAAAATTTACTAACGACATGTTCAATAATTTATTTTTTTGGTA
* *
51971 ACATAATTACTAATTGATCTATTTATTTATGAT-AATTTTTTTGGCTAGCGATTTATGGTAAAAT
66 ACATAATTACT-ATTTAT-TATTTATTTATGGTAAATTTTTTTGG-TAGCGATTTATGGTAAAAT
*
52035 TAAATAATTATCAATCAATTACAACTTTGATTGGAAAAA
128 TAAATAATCATCAATCAATTACAACTTTGATTGGAAAAA
* *
52074 AATCAATTACAACTTTGATCGGAAAAATTTACTAACGACATGTTCAATAA-AT-TTTTTTTGGTA
1 AATCAATTACAACTTTGATTGGAAAAATTTACTAACGACATGTTCAATAATTTATTTTTTTGGTA
*
52137 ACATAATTACTAGTTTATTTATTTATTTATGGTAAATTTTTTTGGTAGCAAATTTATGGTAAAAT
66 ACATAATTACTA-TTTA-TTATTTATTTATGGTAAATTTTTTTGGTAGC-GATTTATGGTAAAAT
*
52202 TAAATAATCATCAACCAATTACAACTTTGATTGGAAAAA
128 TAAATAATCATCAATCAATTACAACTTTGATTGGAAAAA
*
52241 AATCAATTATAACTTTGATTGGAAAAATTTACTAACGACATGTTCAATAATTTATTTTTTTGGTA
1 AATCAATTACAACTTTGATTGGAAAAATTTACTAACGACATGTTCAATAATTTATTTTTTTGGTA
* * *
52306 ACATAATTAC----TA--ATTTATTTATGGTAATTTTTTTTTGTATCGATTTATGGTAAAATTAA
66 ACATAATTACTATTTATTATTTATTTATGGTAAATTTTTTTGGTAGCGATTTATGGTAAAATTAA
52365 ATAATCATCAATCAA--ACAACTTTGATTG
131 ATAATCATCAATCAATTACAACTTTGATTG
52393 ACAAAATTAA
Statistics
Matches: 294, Mismatches: 18, Indels: 23
0.88 0.05 0.07
Matches are distributed among these distances:
158 13 0.04
160 31 0.11
161 26 0.09
164 2 0.01
165 1 0.00
166 42 0.14
167 122 0.41
168 36 0.12
169 21 0.07
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (166 bp):
AATCAATTACAACTTTGATTGGAAAAATTTACTAACGACATGTTCAATAATTTATTTTTTTGGTA
ACATAATTACTATTTATTATTTATTTATGGTAAATTTTTTTGGTAGCGATTTATGGTAAAATTAA
ATAATCATCAATCAATTACAACTTTGATTGGAAAAA
Found at i:52476 original size:161 final size:160
Alignment explanation
Indices: 51919--52479 Score: 541
Period size: 167 Copynumber: 3.4 Consensus size: 160
51909 TCAATTACAT
* *
51919 TTTGATTGGC-AAAATTAACTAACGACATGTTCAATAATTTATTTTTTTGGTAACATAATTACTA
1 TTTGATT-GCAAAAATTTACTAACGACATGTTCAATAATTTATTTTTTTGCTAACATAATTACTA
** * *
51983 ATTGATCTATTTATTTATGATAATTTTTTTGGCTAGC-GATTTATGGTAAAATTAAATAATTATC
65 A-T--T-TATTTA-TGGT-A-AATTTTTTTGG-TAGCAAATTTATGGTAAAATTAAATAATCATC
* * * *
52047 AATCAATTACAACTTTGATTGGAAAAAAATCAATTACAAC
122 AACCAA-TACAACTTTGATTGGAAAAAAATAAATCATAAC
* * * *
52087 TTTGATCGGAAAAATTTACTAACGACATGTTCAATAA-AT-TTTTTTTGGTAACATAATTACTAG
1 TTTGATTGCAAAAATTTACTAACGACATGTTCAATAATTTATTTTTTTGCTAACATAATTAC---
52150 TTTATTTATTTATTTATGGTAAATTTTTTTGGTAGCAAATTTATGGTAAAATTAAATAATCATCA
63 --TA---ATTTATTTATGGTAAATTTTTTTGGTAGCAAATTTATGGTAAAATTAAATAATCATCA
* *
52215 ACCAATTACAACTTTGATTGGAAAAAAATCAATTATAAC
123 ACCAA-TACAACTTTGATTGGAAAAAAATAAATCATAAC
* *
52254 TTTGATTGGAAAAATTTACTAACGACATGTTCAATAATTTATTTTTTTGGTAACATAATTACTAA
1 TTTGATTGCAAAAATTTACTAACGACATGTTCAATAATTTATTTTTTTGCTAACATAATTACTAA
* * * * *
52319 TTTATTTATGGTAATTTTTTTTTGTATC-GATTTATGGTAAAATTAAATAATCATCAATCAA-AC
66 TTTATTTATGGTAAATTTTTTTGGTAGCAAATTTATGGTAAAATTAAATAATCATCAACCAATAC
52382 AACTTTGATT-GACAAAATTAACTAAAGATCACTAAC
131 AACTTTGATTGGA-AAAA--AA-T-AA-ATCA-TAAC
*** * * *
52418 -TTGATT-CATTTATTTATTTA-G-CATGTTCAATCAATTTATTTTTTTGCTAACGTAATTACTA
1 TTTGATTGCAAAAATTTACTAACGACATGTTCAAT-AATTTATTTTTTTGCTAACATAATTACTA
52479 A
65 A
52480 ATGATTCATT
Statistics
Matches: 346, Mismatches: 27, Indels: 47
0.82 0.06 0.11
Matches are distributed among these distances:
157 2 0.01
158 16 0.05
160 43 0.12
161 56 0.16
162 9 0.03
163 9 0.03
164 6 0.02
166 25 0.07
167 112 0.32
168 34 0.10
169 23 0.07
170 6 0.02
171 3 0.01
173 1 0.00
174 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (160 bp):
TTTGATTGCAAAAATTTACTAACGACATGTTCAATAATTTATTTTTTTGCTAACATAATTACTAA
TTTATTTATGGTAAATTTTTTTGGTAGCAAATTTATGGTAAAATTAAATAATCATCAACCAATAC
AACTTTGATTGGAAAAAAATAAATCATAAC
Found at i:52705 original size:27 final size:29
Alignment explanation
Indices: 52663--52716 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
52653 ATAACTTTGA
52663 TTGGCAAAGTTAATTAACGACTAATTTTT
1 TTGGCAAAGTTAATTAACGACTAATTTTT
*
52692 TTGGC-AA-TTAATTAATGACTAATTT
1 TTGGCAAAGTTAATTAACGACTAATTT
52717 GATTCACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 17 0.71
28 2 0.08
29 5 0.21
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (29 bp):
TTGGCAAAGTTAATTAACGACTAATTTTT
Found at i:55881 original size:400 final size:398
Alignment explanation
Indices: 55111--56119 Score: 1504
Period size: 400 Copynumber: 2.5 Consensus size: 398
55101 TTGAAGACAT
*
55111 AAAATTCATTGCAAAATTTGGTGATTGATGAAGAGGTGTAAGTGGGCTTCTCTGATTATGCAG-A
1 AAAATTCATTGCAAAATTTGGTGATTGATGAAGAGGTGTAAGTGGGCTTGT-TGATTATGC-GTA
55175 CCTATATTGATATCAAGGTTTTTGAATTCAATAATGGTATATGAATAATAAGATATTATTTAGTA
64 CCTATATTGATATCAAGGTTTTTGAATTCAATAATGGTATATGAATAATAAGATATTATTTA-TA
55240 AATGTAATAATCTTGATGAATTACCTTGAAATAGATTGCTAGACATATATAGGTGTATAACCAAA
128 AATGTAATAATCTTGATGAATTACCTTGAAATAGATTGCTAGAC----ATAGGTGTAT-A--AAA
* *
55305 CACATTATTCTAATTTATTTGTGGACATAAAAGTGGTGAATGTGATTGACTGGAACCGGCATTCT
186 CACATTATTATAATTTATTTGTGGACATAAAAGTGGTGAATGTGATTGACTGGAACCGACATTCT
55370 CGGTTCGTCCTTGGCTAGGTGTTTGCAAGCTTTCTTGATTTGGGCTGCCTAAATTGATAATGTTG
251 CGGTTCGTCCTTGGCTAGGTGTTTGCAAGCTTTCTTGATTTGGGCTGCCTAAATTGATAATGTTG
*
55435 CTCTGTGTAGATGCAACATTACTTGGATGAATGTTCTCACCAATTGCGGGCCGTACATTCCTTGT
316 CTCTGTATAGATGCAACATTACTTGGATGAATGTTCTCACCAATTGCGGGCCGTACATTCCTTGT
55500 ATTTTGTCTTTGTGAGAAA
381 ATTTTGTCTTTGTGA-AAA
* *
55519 AAAATTCATTTCAAAATTTGGTAATTGATGAAGAGGTGTAAGTGGGCTTAGTTGATTATGCGTAC
1 AAAATTCATTGCAAAATTTGGTGATTGATGAAGAGGTGTAAGTGGGCTT-GTTGATTATGCGTAC
*
55584 CTATATTGATATCAAGGTTTTTGCATTCAATAATGGTATATGAATAATAAGATATTATTTAATAA
65 CTATATTGATATCAAGGTTTTTGAATTCAATAATGGTATATGAATAATAAGATATTATTT-ATAA
* *
55649 ATGTAATAATCTTGATGACTTACCTTGAAATAGATTGCTAGACATAGGTGTAT-TAACACATTAT
129 ATGTAATAATCTTGATGAATTACCTTGAAATAGATTGCTAGACATAGGTGTATAAAACACATTAT
* *
55713 TATAATTTATTTGTGTATATAAAAGTGGTGAACT-TGATTGACTGGAACCGACATTCTCGGTTCG
194 TATAATTTATTTGTGGACATAAAAGTGGTGAA-TGTGATTGACTGGAACCGACATTCTCGGTTCG
* * * *
55777 TCCTTTGCTAGGTGTTTGCAAGTTTTCTTGATTTGGGCTGCTTGAATTGATAATGTTGCTCTGTA
258 TCCTTGGCTAGGTGTTTGCAAGCTTTCTTGATTTGGGCTGCCTAAATTGATAATGTTGCTCTGTA
55842 TAGATGCAACATTACTTGGATGAATGTTCTCACCAATTGCGGGCCGTACATTCCTTGTATTTTGT
323 TAGATGCAACATTACTTGGATGAATGTTCTCACCAATTGCGGGCCGTACATTCCTTGTATTTTGT
*
55907 CTTTGTGACAA
388 CTTTGTGAAAA
* * * *
55918 AAAATTCATTGCAAAATTTGGTGATTAATGAAGAGGTGTAAGTAGGTTTCGTTGATTATGCATAC
1 AAAATTCATTGCAAAATTTGGTGATTGATGAAGAGGTGTAAGTGGGCTT-GTTGATTATGCGTAC
* * * * **
55983 CTATATTAATATCAAGGTTATTGAATTGAATAATAATGGTATAGGAATAATAAGATCGTAGGTTT
65 CTATATTGATATCAAGGTTTTTGAATT---CAATAATGGTATATGAATAATAAGATATTA--TTT
* * * * *
56048 -TGAATGTAATAATCTTAATGAATTACCTTGAAATAAATTGCTAGACATAAGTGTTTGACCAAAC
125 ATAAATGTAATAATCTTGATGAATTACCTTGAAATAGATTGCTAGACATAGGTGTAT-A--AAAC
56112 ACATTATT
187 ACATTATT
56120 CTCGGTTCGT
Statistics
Matches: 551, Mismatches: 37, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
399 84 0.15
400 201 0.36
401 1 0.00
402 76 0.14
404 13 0.02
406 11 0.02
407 1 0.00
408 162 0.29
409 2 0.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (398 bp):
AAAATTCATTGCAAAATTTGGTGATTGATGAAGAGGTGTAAGTGGGCTTGTTGATTATGCGTACC
TATATTGATATCAAGGTTTTTGAATTCAATAATGGTATATGAATAATAAGATATTATTTATAAAT
GTAATAATCTTGATGAATTACCTTGAAATAGATTGCTAGACATAGGTGTATAAAACACATTATTA
TAATTTATTTGTGGACATAAAAGTGGTGAATGTGATTGACTGGAACCGACATTCTCGGTTCGTCC
TTGGCTAGGTGTTTGCAAGCTTTCTTGATTTGGGCTGCCTAAATTGATAATGTTGCTCTGTATAG
ATGCAACATTACTTGGATGAATGTTCTCACCAATTGCGGGCCGTACATTCCTTGTATTTTGTCTT
TGTGAAAA
Found at i:60396 original size:20 final size:20
Alignment explanation
Indices: 60301--60412 Score: 67
Period size: 20 Copynumber: 6.0 Consensus size: 20
60291 GAGCTAAATT
* *
60301 AATCAATTAATTGATTGATC
1 AATCAATCAATTAATTGATC
* *
60321 AATTAATCAGTTAATT--TC
1 AATCAATCAATTAATTGATC
* *
60339 --GCAATCAATTGATTGATC
1 AATCAATCAATTAATTGATC
* * **
60357 AATTACT-AA-TAA-AAATC
1 AATCAATCAATTAATTGATC
*
60374 AATCAATCATTTAATTGATC
1 AATCAATCAATTAATTGATC
*
60394 AATTAATCAATTAATTGAT
1 AATCAATCAATTAATTGAT
60413 TGATGACCCA
Statistics
Matches: 64, Mismatches: 21, Indels: 14
0.65 0.21 0.14
Matches are distributed among these distances:
16 10 0.16
17 8 0.12
18 7 0.11
19 5 0.08
20 34 0.53
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (20 bp):
AATCAATCAATTAATTGATC
Found at i:61615 original size:15 final size:15
Alignment explanation
Indices: 61595--61625 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
61585 TATGTTAACA
61595 ATTGAAAAACTCCCC
1 ATTGAAAAACTCCCC
61610 ATTGAAAAACTCCCC
1 ATTGAAAAACTCCCC
61625 A
1 A
61626 ACTTATTGTG
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:0.42, C:0.32, G:0.06, T:0.19
Consensus pattern (15 bp):
ATTGAAAAACTCCCC
Found at i:67105 original size:16 final size:16
Alignment explanation
Indices: 67084--67172 Score: 71
Period size: 16 Copynumber: 5.9 Consensus size: 16
67074 GCTAAATTAC
*
67084 TCAATTAATTGATTGA
1 TCAATTAATTAATTGA
67100 TCAATTAATTAA--G-
1 TCAATTAATTAATTGA
* *
67113 -CAATAAATTGATTGA
1 TCAATTAATTAATTGA
* **
67128 TCAATT-ACTAATCAA
1 TCAATTAATTAATTGA
*
67143 TCAATCAATTAATTGA
1 TCAATTAATTAATTGA
*
67159 TCAATTAATCAATT
1 TCAATTAATTAATT
67173 ATTTGATTGA
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
12 9 0.17
14 2 0.04
15 10 0.19
16 33 0.61
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (16 bp):
TCAATTAATTAATTGA
Found at i:67163 original size:20 final size:20
Alignment explanation
Indices: 67138--67179 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
67128 TCAATTACTA
67138 ATCAATCAATCAATTAATTG
1 ATCAATCAATCAATTAATTG
* *
67158 ATCAATTAATCAATTATTTG
1 ATCAATCAATCAATTAATTG
67178 AT
1 AT
67180 TGATGACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (20 bp):
ATCAATCAATCAATTAATTG
Found at i:68862 original size:41 final size:41
Alignment explanation
Indices: 68805--68882 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
68795 CCAAGACTTG
68805 GTGCCTAATTATTCGTTGGTAGTTCATCTAGAATTTTCTTA
1 GTGCCTAATTATTCGTTGGTAGTTCATCTAGAATTTTCTTA
*
68846 GTGCCTAATTATTCGTTGGTAGTTCCTCTAGAATTTT
1 GTGCCTAATTATTCGTTGGTAGTTCATCTAGAATTTT
68883 ATTGTGATCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (41 bp):
GTGCCTAATTATTCGTTGGTAGTTCATCTAGAATTTTCTTA
Found at i:69705 original size:2 final size:2
Alignment explanation
Indices: 69698--69725 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
69688 TACAGTTTTA
69698 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
69726 GATTTCCTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75827 original size:26 final size:29
Alignment explanation
Indices: 75791--75845 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
75781 TTTTTATTTG
*
75791 AGTTTG-TTTTT-GAGTCGATTT-GAGTC
1 AGTTTGTTTTTTCGAGTCAATTTCGAGTC
75817 AGTTTGTTTTTTCGAGTCAATTTCGAGTC
1 AGTTTGTTTTTTCGAGTCAATTTCGAGTC
75846 CAGTCTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 9 0.36
29 5 0.20
ACGTcount: A:0.16, C:0.11, G:0.24, T:0.49
Consensus pattern (29 bp):
AGTTTGTTTTTTCGAGTCAATTTCGAGTC
Found at i:81441 original size:19 final size:19
Alignment explanation
Indices: 81417--81454 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
81407 GTGAGGTAAT
*
81417 GGTGATGTAGTTGATGATA
1 GGTGATCTAGTTGATGATA
81436 GGTGATCTAGTTGATGATA
1 GGTGATCTAGTTGATGATA
81455 ACACTGGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.34, T:0.37
Consensus pattern (19 bp):
GGTGATCTAGTTGATGATA
Found at i:82483 original size:47 final size:47
Alignment explanation
Indices: 82417--83252 Score: 1221
Period size: 47 Copynumber: 18.1 Consensus size: 47
82407 TTGACTACTC
* * *
82417 TTTACTACTTAGTTCAATTACCTGGACTTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
82464 TTTACTACTTAGTTTAATTACC-----TTAAACTAA--T-TTCTTC-
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* *
82502 --T--T-CTTAGTATAATTACCTAGAATTAAACTAATTTCTTTTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* *
82544 TTTACTACTTAGTTTAATTA-CTAGAATTAAGCTAATTTCTCCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
82590 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* * *
82637 TTTACTACTTAGTTTAATTACCTATAACTAAACTAATTTTTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* *
82684 TTTACTACTTTGTTTAATTACCTAGAATTAAACTAATTTCTTTTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
82731 TTTACTACTTAATTTAATTACCTAGAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAT-TTCTTCTTCT
* *
82778 TTTACTACTTAGTTTAATTACCTAGAACTAAACTAATTTCTACTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* * *
82825 TTTACTGCTTTGTTTAATTACCTAGAATTAAACTAATTTCTTTTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
82872 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAT-TTCTTCTTCT
82919 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAT-TTCTTCTTCT
82966 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTT-TCTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAT-TTCT-TCTTCT
* *
83014 TTTACTACTTTGTTTAATTACTTAGAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAT-TTCTTCTTCT
83061 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAT-TTCTTCTTCT
* * *
83108 TTTACTACTTAGTTTAATTAGCTAGAATTAAATTAATTTCCTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
83155 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTTTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
83202 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAT-TTCTTCTTCT
83249 TTTA
1 TTTA
83253 GTTTAAAATT
Statistics
Matches: 722, Mismatches: 44, Indels: 46
0.89 0.05 0.06
Matches are distributed among these distances:
33 14 0.02
34 1 0.00
36 1 0.00
38 9 0.01
39 6 0.01
40 2 0.00
41 5 0.01
42 9 0.01
44 1 0.00
46 50 0.07
47 571 0.79
48 53 0.07
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (47 bp):
TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
Done.