Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004574.1 Hibiscus syriacus cultivar Beakdansim tig00010185_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: 97716
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:4817 original size:60 final size:60
Alignment explanation
Indices: 4739--4852 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
4729 AACATAATGA
*
4739 ATAGTCAGATGACAATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACATCTT
1 ATAGTCAGAAGACAATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACATCTT
* * * * * * *
4799 ATAGTCGGAAGACCATTTTTTAACTTTTAATAGTTGAGGGACTTAATAAAGCAA
1 ATAGTCAGAAGACAATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAA
4853 TACCCTATAG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (60 bp):
ATAGTCAGAAGACAATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACATCTT
Found at i:4885 original size:60 final size:60
Alignment explanation
Indices: 4749--4885 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 60
4739 ATAGTCAGAT
* * *
4749 GACAATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACATCTTATAGTCGGAA
1 GACAATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACCCTATAGCCGGAA
* * * * * * * **
4809 GACCATTTTTTAACTTTTAATAGTTGAGGGACTTAATAAAGCAATACCCTATAGCCGGGG
1 GACAATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACCCTATAGCCGGAA
4869 GACAATTTATGT-ACTTT
1 GACAATTT-TGTAACTTT
4886 ATCCTAAAAT
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
60 60 0.97
61 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (60 bp):
GACAATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACCCTATAGCCGGAA
Found at i:6131 original size:329 final size:332
Alignment explanation
Indices: 5697--6342 Score: 1050
Period size: 327 Copynumber: 1.9 Consensus size: 332
5687 TATACTAAAT
*
5697 TTAGAGATATTTTTCATATATTTTTTTTCTTGCTTATGTTGCCCCCACGAGAAAATTTAGTCTTT
1 TTAGAGATATTTTTCATATA-TTTTTTTCTTGCTTATGTTGCCACCACGAGAAAATTTAGTCTTT
*
5762 GCATTCACTCATTTTTCTCTTTAATGGCCCATATACTTGGCCTAATTTGAAGGCTATAAAGCAAT
65 ACATTCACTCATTTTTCTC-----T-GCCCATATACTTGGCCTAATTTGAAGGCTATAAAGCAAT
*
5827 CTCACTTAATGCAGTTGGACTTATTTGGATATGAGGTTTAACAATTTCATTTTCCCATCATTATA
124 CTCACTTAATGCAGTTGGACTTATTTGG--ATGAGGTCTAACAATTTCATTTTCCCATCATTATA
* * * *
5892 GCTTAGATGTTGATTGTTTTGACTAAAGGTGTGAATGAATCGGGCTTGAATGAATAAGGTTATGT
187 GCTTAGATGTTGATTGTTTTGACTAAAGGTGTAAATGAACCGAGCTTGAACGAATAAGGTTATGT
* * *
5957 TCGTGTTCATTTGTTTA-TTTTTAAGGCGTTCGTTTACATTTTTAATATTGTGTTCATGCTAGTT
252 TCGTGTTCATTTATTTATTTTTTAAGGCGTTCGTTTAAATTTTTAATATCGTGTTCATGCTAGTT
6021 TAATTTTTTTAAGGTG
317 TAATTTTTTTAAGGTG
*
6037 TTAGATATATTTTTCATATA-TTTTTTCTTGCTTATGTTG-CACCACGAGAAAATTTAGT-TTTA
1 TTAGAGATATTTTTCATATATTTTTTTCTTGCTTATGTTGCCACCACGAGAAAATTTAGTCTTTA
6099 CATTCACTCATTTTTCTC-GCCCATATACTTGGCCTAATTTGAAGGCTATAAAGCAATCTCACTT
66 CATTCACTCATTTTTCTCTGCCCATATACTTGGCCTAATTTGAAGGCTATAAAGCAATCTCACTT
6163 AATGCAGTTGGACTTATTTGGATGAGGTCTAACAATTTCATTTTCCCATCATTATAGCTTAGATG
131 AATGCAGTTGGACTTATTTGGATGAGGTCTAACAATTTCATTTTCCCATCATTATAGCTTAGATG
* *
6228 TTGATTGTTTTGACTAAAGGTGTAAATGAACCGAGCTTGAACGAATAAGGTTATGTTTGTGTTCG
196 TTGATTGTTTTGACTAAAGGTGTAAATGAACCGAGCTTGAACGAATAAGGTTATGTTCGTGTTCA
*
6293 TTTATTTATTTTTTAAGGTGTTCGTTTAAATTTTTAATATCGTGTTCATG
261 TTTATTTATTTTTTAAGGCGTTCGTTTAAATTTTTAATATCGTGTTCATG
6343 TTCGTTTATT
Statistics
Matches: 291, Mismatches: 14, Indels: 14
0.91 0.04 0.04
Matches are distributed among these distances:
327 109 0.37
328 38 0.13
329 67 0.23
336 21 0.07
337 18 0.06
338 19 0.07
340 19 0.07
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.44
Consensus pattern (332 bp):
TTAGAGATATTTTTCATATATTTTTTTCTTGCTTATGTTGCCACCACGAGAAAATTTAGTCTTTA
CATTCACTCATTTTTCTCTGCCCATATACTTGGCCTAATTTGAAGGCTATAAAGCAATCTCACTT
AATGCAGTTGGACTTATTTGGATGAGGTCTAACAATTTCATTTTCCCATCATTATAGCTTAGATG
TTGATTGTTTTGACTAAAGGTGTAAATGAACCGAGCTTGAACGAATAAGGTTATGTTCGTGTTCA
TTTATTTATTTTTTAAGGCGTTCGTTTAAATTTTTAATATCGTGTTCATGCTAGTTTAATTTTTT
TAAGGTG
Found at i:6391 original size:12 final size:12
Alignment explanation
Indices: 6376--6444 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 12
6366 CTGTTCGTGA
6376 ATATGTTCATTT
1 ATATGTTCATTT
***
6388 ATATGTTCACGA
1 ATATGTTCATTT
*
6400 ATGTGTTCATTT
1 ATATGTTCATTT
***
6412 ATATGTTCACAA
1 ATATGTTCATTT
**
6424 ACGTGTTCATTT
1 ATATGTTCATTT
6436 ATATGTTCA
1 ATATGTTCA
6445 CGAACGTGTT
Statistics
Matches: 39, Mismatches: 18, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (12 bp):
ATATGTTCATTT
Found at i:6467 original size:24 final size:24
Alignment explanation
Indices: 6379--6457 Score: 140
Period size: 24 Copynumber: 3.3 Consensus size: 24
6369 TTCGTGAATA
*
6379 TGTTCATTTATATGTTCACGAATG
1 TGTTCATTTATATGTTCACGAACG
*
6403 TGTTCATTTATATGTTCACAAACG
1 TGTTCATTTATATGTTCACGAACG
6427 TGTTCATTTATATGTTCACGAACG
1 TGTTCATTTATATGTTCACGAACG
6451 TGTTCAT
1 TGTTCAT
6458 GAACATGTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.44
Consensus pattern (24 bp):
TGTTCATTTATATGTTCACGAACG
Found at i:6886 original size:20 final size:20
Alignment explanation
Indices: 6861--6900 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6851 CACCAAACCT
*
6861 TCTATTTATTTACACCCCTA
1 TCTATTCATTTACACCCCTA
6881 TCTATTCATTTACACCCCTA
1 TCTATTCATTTACACCCCTA
6901 GTTTTGACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.42
Consensus pattern (20 bp):
TCTATTCATTTACACCCCTA
Found at i:9036 original size:19 final size:19
Alignment explanation
Indices: 9012--9048 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
9002 AGATTTATTG
*
9012 GTGTTAGTTTGCTTTGTTA
1 GTGTTAGTTTACTTTGTTA
9031 GTGTTAGTTTACTTTGTT
1 GTGTTAGTTTACTTTGTT
9049 TCTATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.05, G:0.24, T:0.59
Consensus pattern (19 bp):
GTGTTAGTTTACTTTGTTA
Found at i:9185 original size:90 final size:86
Alignment explanation
Indices: 8978--9187 Score: 202
Period size: 90 Copynumber: 2.4 Consensus size: 86
8968 AATTTTGACA
* **
8978 TGTAATTGATGTTTGTTTGTAAGTAGATTTATTG-GTGTTAGTTTGCTTTGTTAGTGTTAGTTTA
1 TGTAATTGATGTTTGTTTGTAAGTAGATTTATTGAGTATTAGTTTGAGTTGTTAGTGTTAGTTTA
9042 CTTTGTTTCTATTTTGAAAGT
66 CTTTGTTTCTATTTTGAAAGT
* * *
9063 TCAAGTACATT-A--TTTGAATTT-T--G-ATATGTTATTGACATGTAATTATTTTGAGTTGTTG
1 T---GTA-ATTGATGTTTG--TTTGTAAGTAGAT-TTATTG--A-GT-ATTAGTTTGAGTTGTTA
*
9121 GTGTTAGTTTACTTTGTTTCTATTTTGAATGT
55 GTGTTAGTTTACTTTGTTTCTATTTTGAAAGT
9153 TGTAATTGATGTTTGTTTGTAAGTAGATTTATTGA
1 TGTAATTGATGTTTGTTTGTAAGTAGATTTATTGA
9188 TGTGTGTATC
Statistics
Matches: 98, Mismatches: 8, Indels: 35
0.70 0.06 0.25
Matches are distributed among these distances:
84 3 0.03
85 8 0.08
86 7 0.07
87 8 0.08
88 9 0.09
89 9 0.09
90 51 0.52
91 3 0.03
ACGTcount: A:0.22, C:0.04, G:0.20, T:0.54
Consensus pattern (86 bp):
TGTAATTGATGTTTGTTTGTAAGTAGATTTATTGAGTATTAGTTTGAGTTGTTAGTGTTAGTTTA
CTTTGTTTCTATTTTGAAAGT
Found at i:10073 original size:23 final size:23
Alignment explanation
Indices: 10047--10092 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
10037 CCAATTAACG
*
10047 CATTGATTAATATCATTCAAATC
1 CATTGACTAATATCATTCAAATC
*
10070 CATTGACTCATATCATTCAAATC
1 CATTGACTAATATCATTCAAATC
10093 AGCCATAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (23 bp):
CATTGACTAATATCATTCAAATC
Found at i:13732 original size:20 final size:20
Alignment explanation
Indices: 13709--13802 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
13699 AGATGATCTA
* *
13709 AAGGATTCACAAATTACCCG
1 AAGGATTTACAAATGACCCG
13729 AAGGATTTACAAATGACCCG
1 AAGGATTTACAAATGACCCG
*
13749 AAGGATTTACAAATGACCCT
1 AAGGATTTACAAATGACCCG
*
13769 AAGGATTTACAAATGACCCT
1 AAGGATTTACAAATGACCCG
*
13789 AAGGTTTTACAAAT
1 AAGGATTTACAAAT
13803 TCATGGAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.24
Consensus pattern (20 bp):
AAGGATTTACAAATGACCCG
Found at i:22134 original size:17 final size:17
Alignment explanation
Indices: 22097--22141 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
22087 AAATCTTCAG
* **
22097 TGCATCGGTGCATGGTT
1 TGCATCGATGCATGGAA
22114 TGCATCGATGCATGGAA
1 TGCATCGATGCATGGAA
22131 TGCATTCGATG
1 TGCA-TCGATG
22142 TTCAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (17 bp):
TGCATCGATGCATGGAA
Found at i:22580 original size:19 final size:19
Alignment explanation
Indices: 22558--22595 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
22548 TTTAAAAAAC
22558 ATTTCAACACTTAACATTT
1 ATTTCAACACTTAACATTT
22577 ATTTCAACACTTAACATTT
1 ATTTCAACACTTAACATTT
22596 CTCCCCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTCAACACTTAACATTT
Found at i:23347 original size:21 final size:18
Alignment explanation
Indices: 23289--23331 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
23279 GAGGAGGAAG
23289 AGGAGCACGAGAGGAGCT
1 AGGAGCACGAGAGGAGCT
23307 AGGAGCACGAGAGGAGCT
1 AGGAGCACGAGAGGAGCT
23325 AGGAGCA
1 AGGAGCA
23332 GCTCGAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.44, T:0.05
Consensus pattern (18 bp):
AGGAGCACGAGAGGAGCT
Found at i:30792 original size:64 final size:63
Alignment explanation
Indices: 30706--30864 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
30696 TGCACTAAGA
*
30706 GTGCATCGATGCATCAAGTGCATTCGATGTT-TTA-AAATAGC-CCGAGTGCATCGATGCATGGC
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTTATAAA-AGCTCC-AGTGCATCGATGCATGG-
30768 T
63 T
* * *
30769 GGTGCATCGATGCATCAAATGCATTCGATGTTCTTATAAAATCTTCAGTGCATCGGTGCATGGT
1 -GTGCATCGATGCATCAAATGCATTCGATGTTCTTATAAAAGCTCCAGTGCATCGATGCATGGT
**
30833 GTGCATCGATGCATGGAATGCATTCGATGTTC
1 GTGCATCGATGCATCAAATGCATTCGATGTTC
30865 AATTTAATTC
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
63 30 0.35
64 31 0.36
65 21 0.24
66 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCTTATAAAAGCTCCAGTGCATCGATGCATGGT
Found at i:30838 original size:17 final size:17
Alignment explanation
Indices: 30816--30848 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30806 AAAATCTTCA
*
30816 GTGCATCGGTGCATGGT
1 GTGCATCGATGCATGGT
30833 GTGCATCGATGCATGG
1 GTGCATCGATGCATGG
30849 AATGCATTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.18, G:0.39, T:0.27
Consensus pattern (17 bp):
GTGCATCGATGCATGGT
Found at i:30854 original size:17 final size:17
Alignment explanation
Indices: 30817--30861 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
30807 AAATCTTCAG
* **
30817 TGCATCGGTGCATGGTG
1 TGCATCGATGCATGGAA
30834 TGCATCGATGCATGGAA
1 TGCATCGATGCATGGAA
30851 TGCATTCGATG
1 TGCA-TCGATG
30862 TTCAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (17 bp):
TGCATCGATGCATGGAA
Found at i:33007 original size:16 final size:16
Alignment explanation
Indices: 32986--33048 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
32976 GCCTTCAGGC
32986 TTTATAAATAATAATA
1 TTTATAAATAATAATA
*
33002 TTTATAATATAATATTA
1 TTTATAA-ATAATAATA
* *
33019 -TTATATATAATAACA
1 TTTATAAATAATAATA
* *
33034 TATATATATAATAAT
1 TTTATAAATAATAAT
33049 CGTCACTCGG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.18
16 24 0.62
17 8 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTATAAATAATAATA
Found at i:33036 original size:20 final size:18
Alignment explanation
Indices: 32988--33048 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 18
32978 CTTCAGGCTT
*
32988 TATAA-ATAATA-ATATT
1 TATAATATAATATATATA
33004 TATAATATAATATTATTATA
1 TATAATATAATA-TA-TATA
33024 TATAATA-ACATATATATA
1 TATAATATA-ATATATATA
33042 TAATAAT
1 T-ATAAT
33049 CGTCACTCGG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
16 5 0.13
17 6 0.16
18 5 0.13
19 9 0.24
20 13 0.34
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAATATAATATATATA
Found at i:33996 original size:37 final size:39
Alignment explanation
Indices: 33908--34000 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 39
33898 CCATTCAATC
*
33908 AAAAAACAATTTGAATTAGTGATTATTGATAATAATAAT
1 AAAAAACAATTTGAATTAGTGAATATTGATAATAATAAT
33947 AAGAAAACAATTTGAATTAGTGAATATTGATAATAATAAT
1 AA-AAAACAATTTGAATTAGTGAATATTGATAATAATAAT
33987 -AAAAA-AATTTGAAT
1 AAAAAACAATTTGAAT
34001 GAAAGTGATT
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
37 9 0.17
38 4 0.08
39 3 0.06
40 36 0.69
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (39 bp):
AAAAAACAATTTGAATTAGTGAATATTGATAATAATAAT
Found at i:34435 original size:36 final size:36
Alignment explanation
Indices: 34383--34455 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
34373 ATGCAAATAC
* *
34383 ATAATCAAACAGCCTATTGAACTCCTCTACAACACT
1 ATAATCAAACAACCTATTCAACTCCTCTACAACACT
34419 ATAATCAAACAACCTATTCAACTCCTCTACAACACT
1 ATAATCAAACAACCTATTCAACTCCTCTACAACACT
34455 A
1 A
34456 CCCCTTATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.41, C:0.32, G:0.03, T:0.25
Consensus pattern (36 bp):
ATAATCAAACAACCTATTCAACTCCTCTACAACACT
Found at i:35170 original size:18 final size:18
Alignment explanation
Indices: 35144--35210 Score: 116
Period size: 18 Copynumber: 3.7 Consensus size: 18
35134 ATCATCCCCT
*
35144 TCATAAGGCCCACTTTCA
1 TCATTAGGCCCACTTTCA
35162 TCATTAGGCCCACTTTCA
1 TCATTAGGCCCACTTTCA
35180 TCATTAGGCCCACTTTCA
1 TCATTAGGCCCACTTTCA
*
35198 GCATTAGGCCCAC
1 TCATTAGGCCCAC
35211 AACTAATAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.24, C:0.34, G:0.13, T:0.28
Consensus pattern (18 bp):
TCATTAGGCCCACTTTCA
Found at i:35386 original size:19 final size:19
Alignment explanation
Indices: 35334--35386 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 19
35324 CAATACCCCC
*
35334 AAACTAATAGTGAAATAGT
1 AAACTTATAGTGAAATAGT
**
35353 TTACTTA-A-T--AATAGT
1 AAACTTATAGTGAAATAGT
35368 AAACTTATAGTGAAATAGT
1 AAACTTATAGTGAAATAGT
35387 TTACCATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 8
0.66 0.13 0.21
Matches are distributed among these distances:
15 11 0.44
16 1 0.04
17 2 0.08
18 1 0.04
19 10 0.40
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (19 bp):
AAACTTATAGTGAAATAGT
Found at i:36050 original size:238 final size:236
Alignment explanation
Indices: 35634--36088 Score: 653
Period size: 238 Copynumber: 1.9 Consensus size: 236
35624 TTTACCTTAA
* *
35634 TTTGGTACCTCTGAATCTTAATGAATTACTGAATAAATAAATGCTATATTATGCATTACATGTTT
1 TTTGGTACCTCTGAATCTTAATGAATTACTGAATAAATAAAGGCTATATTATGCAATACATGTTT
*
35699 TTTTTCTTAAATATTTTCACGTGCTTCTGTTGTTATCTTCATGGAAACATATATTTCAAGTACCA
66 TTTTTCTTAAATATTTTCACGTGCTTCTGTTGTTATCTTCATGGAAACATATATTTCAAGCACCA
*
35764 AGCATTATGTGTGAAAATTTTCTATTACAAGACTTGTGTGGTTTACCAACAATATTGGTGCTGCA
131 AGCATTATGTGTGAAAATTTTATATTACAAGACTTGTGTGGTTTACCAACAATATTGGTGCTGCA
*
35829 AAGTGACATAAAAATTCCTCTATTTTTACTCTATACTACAC
196 AAGTGACATAAAAATACCTCTATTTTTACTCTATACTACAC
* * * * *
35870 TTTGGTA-CTCCTGAATCTTAATGAGTTGCTGAATAAATAAAGGTTATCTTCTGCAATACATGTC
1 TTTGGTACCT-CTGAATCTTAATGAATTACTGAATAAATAAAGGCTATATTATGCAATACATGT-
*** * *
35934 TTTCTTTTCTTAAATATTTTTTTGTGCTTCTGTTGTTATCTTCTTGGAAACATATATTTCGAGCA
64 TTT-TTTTCTTAAATATTTTCACGTGCTTCTGTTGTTATCTTCATGGAAACATATATTTCAAGCA
** * * * * *
35999 GTAAGCATTTTCGT-TGAAAATTTTATGTTTCAAGACTTGTGTTGTTTACCAACAATATTGTTGC
128 CCAAGCATTAT-GTGTGAAAATTTTATATTACAAGACTTGTGTGGTTTACCAACAATATTGGTGC
*
36063 TGCAAAGTGACATGAAAATACCTCTA
192 TGCAAAGTGACATAAAAATACCTCTA
36089 CTCATTTTAG
Statistics
Matches: 192, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
235 2 0.01
236 53 0.28
237 3 0.02
238 132 0.69
239 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (236 bp):
TTTGGTACCTCTGAATCTTAATGAATTACTGAATAAATAAAGGCTATATTATGCAATACATGTTT
TTTTTCTTAAATATTTTCACGTGCTTCTGTTGTTATCTTCATGGAAACATATATTTCAAGCACCA
AGCATTATGTGTGAAAATTTTATATTACAAGACTTGTGTGGTTTACCAACAATATTGGTGCTGCA
AAGTGACATAAAAATACCTCTATTTTTACTCTATACTACAC
Found at i:36574 original size:30 final size:30
Alignment explanation
Indices: 36533--36590 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
36523 TTTGTAACAC
*
36533 AACTTATATATAAAAAAGTCATAAAAAAAG
1 AACTTAAATATAAAAAAGTCATAAAAAAAG
36563 AACTTAAATATAAAAAAGTCATAAAAAA
1 AACTTAAATATAAAAAAGTCATAAAAAA
36591 GTAGTTTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (30 bp):
AACTTAAATATAAAAAAGTCATAAAAAAAG
Found at i:45207 original size:3 final size:3
Alignment explanation
Indices: 45193--45251 Score: 55
Period size: 3 Copynumber: 18.7 Consensus size: 3
45183 TAATTTTTTC
* * * *
45193 TAT TAT TTT TAT TAT TAT TAAA TAA AAT ATAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT -TAT TAT TAT TAT TAT TAT
45240 ATAT TAT TAT TA
1 -TAT TAT TAT TA
45252 AAAAAAAACA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 40 0.85
4 7 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:46844 original size:145 final size:146
Alignment explanation
Indices: 46561--46838 Score: 311
Period size: 145 Copynumber: 1.9 Consensus size: 146
46551 TTCATAATAG
* * *
46561 TATTTATTTATTTATTTATATCAAAGAAAGAGGCAGTCTTAAAACAACTAGATGTCTGTTTTCTG
1 TATTTATTTATTTATTAATATCAAAGAAAGAGGCAGTCTTAAAACAACTAGAAGTCTATTTTCTG
* * * *** * *
46626 ATATTTTTAATAAATAAATATTTTACTTTTATAAAATTGTATATATTAATCTATTTTTTTATTAT
66 ATATTTTTAATAAATAAATATCTTACTTTTATAAAATTATAAATATTAATCTAAAATTATATAAT
*
46691 GAGATAAATATTTTAA
131 GAAATAAATATTTTAA
* * *
46707 TATTTATTTATTT-TTAATATCAAAGAAA-AGAGCTGTCTTAAAGCACCTAGAAGTC-ATTTTCT
1 TATTTATTTATTTATTAATATCAAAGAAAGAG-GCAGTCTTAAAACAACTAGAAGTCTATTTTCT
*
46769 GATATTTTTAAATAAATAAATATCTTA--TTTATATAAATTAATAAAT-TTACT-TAAAATTATA
65 GATATTTTT-AATAAATAAATATCTTACTTTTATA-AAATT-ATAAATATTAATCTAAAATTATA
46830 GTAAT-AAAT
127 -TAATGAAAT
46839 TTAAATTAAA
Statistics
Matches: 111, Mismatches: 16, Indels: 13
0.79 0.11 0.09
Matches are distributed among these distances:
143 15 0.14
144 29 0.26
145 54 0.49
146 13 0.12
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (146 bp):
TATTTATTTATTTATTAATATCAAAGAAAGAGGCAGTCTTAAAACAACTAGAAGTCTATTTTCTG
ATATTTTTAATAAATAAATATCTTACTTTTATAAAATTATAAATATTAATCTAAAATTATATAAT
GAAATAAATATTTTAA
Found at i:54121 original size:114 final size:114
Alignment explanation
Indices: 53921--54142 Score: 390
Period size: 114 Copynumber: 1.9 Consensus size: 114
53911 AATGTTCTCG
*
53921 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
53986 GGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
*
54035 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
54100 GGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAATT
66 GGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
54143 GCATGATCAT
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
Found at i:55349 original size:76 final size:77
Alignment explanation
Indices: 55193--55371 Score: 204
Period size: 76 Copynumber: 2.4 Consensus size: 77
55183 TTTTAGCATC
** * *
55193 TATCAGC-AAATGTTGGGGCATGCTGAAAACCTTTTTTCAATCAGAATCAGGAATGTTGATGTAT
1 TATCAGCAAAATACTGGGGCATGCTGAAAACCTTTTTTCAATCAGAATCAAGAAGGTTGATGTAT
*
55257 CCTGAATGTTTA
66 CCTGAACGTTTA
* * *
55269 TATCAGCAAAATACTGGGGCATGTTGAAAGCC-TTTTTCAATCAGAATGAAGAAGGTTGATGTAT
1 TATCAGCAAAATACTGGGGCATGCTGAAAACCTTTTTTCAATCAGAATCAAGAAGGTTGATGTAT
**
55333 TTTGAACG-TTA
66 CCTGAACGTTTA
* **
55344 GTATCAGC-AATTGTTGGGGCATGCTGAA
1 -TATCAGCAAAATACTGGGGCATGCTGAA
55372 GGCCCACATC
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
75 19 0.22
76 48 0.55
77 20 0.23
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (77 bp):
TATCAGCAAAATACTGGGGCATGCTGAAAACCTTTTTTCAATCAGAATCAAGAAGGTTGATGTAT
CCTGAACGTTTA
Found at i:56736 original size:22 final size:22
Alignment explanation
Indices: 56704--56762 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
56694 ACATTTACAC
56704 TCTTTTCAAAGATGATAGATTA
1 TCTTTTCAAAGATGATAGATTA
* *
56726 TCTTTTTAAAGATGATAGATTC
1 TCTTTTCAAAGATGATAGATTA
56748 TCTTTTCAAAGATGA
1 TCTTTTCAAAGATGA
56763 AAGCTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (22 bp):
TCTTTTCAAAGATGATAGATTA
Found at i:57538 original size:76 final size:76
Alignment explanation
Indices: 57439--59003 Score: 2733
Period size: 76 Copynumber: 20.6 Consensus size: 76
57429 CTATTTCCAA
* *
57439 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
57504 AGCCTTAGGGT
66 AGCCTTAGGGT
*
57515 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
57580 AACCTTAGGGT
66 AGCCTTAGGGT
* *
57591 CATCTGTAAGTCCTACAGTGCATGATGTTCCCAAAAAGCCTTCTGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
57656 AGCCTTAGGGT
66 AGCCTTAGGGT
** *
57667 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAAGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
57732 AGCCTTAGGGT
66 AGCCTTAGGGT
*
57743 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
57808 AGCCTTAGGGT
66 AGCCTTAGGGT
*
57819 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
57884 AGCCTTAGGGT
66 AGCCTTAGGGT
57895 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT-ATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
57959 AGCCTTAGGGG
66 AGCCTTAGGGT
57970 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
58035 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
58046 TATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
58111 AGCCTTAGGGT
66 AGCCTTAGGGT
*
58122 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAGAAAGCCTTCGGGAG-TTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
58186 AGCCTTAGGGT
66 AGCCTTAGGGT
*
58197 CATCTGTAAGTCCTACAGTGCATGATGTTCCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
58262 AGCCTTAGGGT
66 AGCCTTAGGGT
*
58273 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
58338 AGCCTTAGGGT
66 AGCCTTAGGGT
58349 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
58414 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
58425 CATCTGTAAGTCCTATAGTGCGTGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
58490 AGCCTTAGGGT
66 AGCCTTAGGGT
*
58501 CATCTGTAAGTCGTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
58566 AGCCTTAGGGT
66 AGCCTTAGGGT
58577 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
58642 AACCTTAGGGT
66 AGCCTTAGGGT
*
58653 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
58718 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
58729 CATCTGTAAGTCCTATAGTGCATGATGTTACAAAAAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTTC---CAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
58794 CAAAGCCTTAGGGT
63 CAAAGCCTTAGGGT
* * *
58808 CATCTGTAAGTCCTATAGTGCGTGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
58873 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
58884 CATCTGTAAGTCTTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
58949 AGCCTTCGGGT
66 AGCCTTAGGGT
* * * * *
58960 CATCTATAAGCCCTTCAGTGCATGATATTTTC-AAAA-CCTTCGGG
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
59004 TCATATATAA
Statistics
Matches: 1424, Mismatches: 60, Indels: 12
0.95 0.04 0.01
Matches are distributed among these distances:
74 7 0.00
75 151 0.11
76 1193 0.84
79 73 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:59061 original size:46 final size:45
Alignment explanation
Indices: 58936--59084 Score: 226
Period size: 45 Copynumber: 3.3 Consensus size: 45
58926 TGGGAGCTTT
*
58936 TTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGC
1 TTGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGC
* * *
58981 ATGATATTTTCAAAACCTTCGGGTCATATATAAGCCCTTCAGTGC
1 TTGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGC
* * *
59026 TTGATGTTTTCAAAAACCTTAGGGTCATCTGTAAGCTCTTCAGTGC
1 TTGATGTTTTC-AAAACCTTCGGGTCATCTATAAGCCCTTCAGTGC
59072 TTGATGTTTTCAA
1 TTGATGTTTTCAA
59085 CATTTCAAGA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
45 52 0.56
46 41 0.44
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (45 bp):
TTGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGC
Found at i:59205 original size:3 final size:3
Alignment explanation
Indices: 59191--59260 Score: 70
Period size: 3 Copynumber: 22.7 Consensus size: 3
59181 TAATTTTTTC
* * * *
59191 TAT TAT TTT TAT TAT TAT TAAA TAA AAT ATAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT -TAT TAT TAT TAT TAT TAT
59238 TAT TA- TAT ATAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TA
59261 AATAAAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
2 2 0.04
3 48 0.84
4 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:64041 original size:17 final size:17
Alignment explanation
Indices: 64009--64055 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 17
63999 TTATTAAAAA
64009 TAACATTTCATTTTATCAC
1 TAACATTT--TTTTATCAC
64028 TAACATTTTTTTATCAC
1 TAACATTTTTTTATCAC
64045 TAACACTTTTT
1 TAACA-TTTTT
64056 GATTTGTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.52
18 5 0.19
19 8 0.30
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (17 bp):
TAACATTTTTTTATCAC
Found at i:65355 original size:25 final size:25
Alignment explanation
Indices: 65303--65355 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
65293 ACATGTACTC
** *
65303 AATGCTATTTATTGTTTTTTTTATA
1 AATGCTATTTATTGTTTTTTAGAAA
65328 AATGCTATTTATTG-TTTTTAGAGAA
1 AATGCTATTTATTGTTTTTTAGA-AA
65353 AAT
1 AAT
65356 ATTGGGGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (25 bp):
AATGCTATTTATTGTTTTTTAGAAA
Found at i:75143 original size:19 final size:18
Alignment explanation
Indices: 75113--75148 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
75103 GGGGTTTTGT
75113 AATTTTGGATTTTTTAGG
1 AATTTTGGATTTTTTAGG
75131 AATTTTAGGATTTTTTAG
1 AATTTT-GGATTTTTTAG
75149 AAAATTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (18 bp):
AATTTTGGATTTTTTAGG
Found at i:75874 original size:12 final size:13
Alignment explanation
Indices: 75857--75890 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
75847 CTAGTTTTAA
75857 TTAATTTAAT-AT
1 TTAATTTAATGAT
*
75869 TTAATTTAATGTT
1 TTAATTTAATGAT
75882 TTAATTTAA
1 TTAATTTAA
75891 AATGACTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTAATTTAATGAT
Found at i:77882 original size:19 final size:20
Alignment explanation
Indices: 77850--77889 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
77840 TTAAAATTAA
* *
77850 ATTTTAAATTTAAAGTTTTT
1 ATTTTAAATATAAAATTTTT
77870 ATTTTAAA-ATAAAATTTTT
1 ATTTTAAATATAAAATTTTT
77889 A
1 A
77890 AAATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTTAAATATAAAATTTTT
Found at i:77888 original size:20 final size:20
Alignment explanation
Indices: 77850--77889 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
77840 TTAAAATTAA
* *
77850 ATTTTAAATTTAAAGTTTTT
1 ATTTTAAAATAAAAGTTTTT
77870 ATTTTAAAATAAAA-TTTTT
1 ATTTTAAAATAAAAGTTTTT
77889 A
1 A
77890 AAATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTTAAAATAAAAGTTTTT
Found at i:82536 original size:20 final size:19
Alignment explanation
Indices: 82502--82548 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
82492 TTTGAGTTAA
82502 TTAAAATATTTTAAAG-TGT
1 TTAAAATATTTTAAAGCT-T
*
82521 TTAAAATGTGTTTAAAGCTT
1 TTAAAATAT-TTTAAAGCTT
82541 TTAAAATA
1 TTAAAATA
82549 ATAAGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.33
20 15 0.62
21 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (19 bp):
TTAAAATATTTTAAAGCTT
Found at i:87540 original size:54 final size:54
Alignment explanation
Indices: 87254--87846 Score: 645
Period size: 54 Copynumber: 11.1 Consensus size: 54
87244 CTTGAAAAAC
* * * * *
87254 CTTCTGTC-AACGGGTTCGTTCCCTCTTTCT-TCATGGAGTATATAACTTGAGCAAT
1 CTTCT-TCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAAC-AT
* * * *
87309 CATT-TGCAAACGAGTTTGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAACAT
1 C-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
** * *
87363 CTTCTTCTTACGGGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAACA-
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACAT
* * * *
87417 --TCTTCAAACGGGTTCGCCCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAA-CAT
* * *
87471 CTTCTGCAAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
* * * * *
87525 CTTCTTCAAACAGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAATAAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAA-CAT
* *
87580 CTTCTGCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAACAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
** * * *
87634 CTTCTTCTTACGGGTTCG-TTCCTCTTTATCTAGGGAGTATGGAACTCGAACA-
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
*
87686 --TCTTCAAACGGGTTCGCTCCCTCTTTCTGTAGGGAGTATAGAACTCGAACAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
*** * * *
87738 CTTCTTCTTGCGGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAACAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
* * *
87792 CTTC-T--AACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAAAAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
87843 CTTC
1 CTTC
87847 AAACGTGTCT
Statistics
Matches: 457, Mismatches: 67, Indels: 32
0.82 0.12 0.06
Matches are distributed among these distances:
50 14 0.03
51 72 0.16
52 47 0.10
53 34 0.07
54 141 0.31
55 120 0.26
56 29 0.06
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (54 bp):
CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
Found at i:87817 original size:105 final size:105
Alignment explanation
Indices: 87262--87846 Score: 651
Period size: 109 Copynumber: 5.5 Consensus size: 105
87252 ACCTTCTGTC
* * * * * * *
87262 AACGGGTTCGTTCCCTCTTTCT-TCATGGAGTATATAACTTGAGCAATCATT-TGCAAACGAGTT
1 AACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAAC-ATC-TTCTTCAAACGGGTT
* * * * *
87325 TGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAACATCTTCTTCT
63 CGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAACA---TCTTCT
* * *
87371 TACGGGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAACA---TCTTCAAACGGGTTCG
1 AACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCG
** * * * * *
87433 CCCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCT
65 TTCCCTCTTTATCT-AGGGAGTATGGAACTCGAA-CATCTTCT
* * *
87476 GCAAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATATCTTCTTCAAACAGGTT
1 ---AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTT
*
87541 CGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAATAATCTTCT
63 CGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAA-CATCTTCT
* **
87585 GCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAACATCTTCTTCTTACGGGTT
1 ---AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTT
*
87650 CGTT-CCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCA
63 CGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCT
* ***
87692 AACGGGTTCGCTCCCTCTTTCTGTAGGGAGTATAGAACTCGAACATCTTCTTCTTGCGGGTTCGT
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGT
87757 TCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCT
66 TCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCT
* * *
87797 AACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAAAATCTTC
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTC
87847 AAACGTGTCT
Statistics
Matches: 423, Mismatches: 42, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
104 63 0.15
105 91 0.22
106 23 0.05
107 42 0.10
108 52 0.12
109 110 0.26
110 42 0.10
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (105 bp):
AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGT
TCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCT
Found at i:87970 original size:53 final size:53
Alignment explanation
Indices: 87850--88012 Score: 240
Period size: 53 Copynumber: 3.1 Consensus size: 53
87840 AATCTTCAAA
* *
87850 CGTGTCTGCTCCCTATTTCTTTAGAGAGTATAAGA-CCACAATCTTCAACGAT
1 CGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAAT
*
87902 CGCGTCTGC-CTCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAAT
1 CGTGTCTGCTC-CCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAAT
* *
87955 CGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAAT
1 CGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAAT
88010 CGT
1 CGT
88013 TGGGAAACCT
Statistics
Matches: 100, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
51 1 0.01
52 31 0.31
53 48 0.48
54 2 0.02
55 18 0.18
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (53 bp):
CGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAAT
Found at i:89002 original size:8 final size:8
Alignment explanation
Indices: 88989--89042 Score: 83
Period size: 8 Copynumber: 6.9 Consensus size: 8
88979 TGAAACCTCA
88989 TTTTTCAT
1 TTTTTCAT
88997 TTTTTCAT
1 TTTTTCAT
*
89005 TTTTTTAT
1 TTTTTCAT
*
89013 TTTTTTAT
1 TTTTTCAT
89021 TTTTT-AT
1 TTTTTCAT
89028 TTTTTCAT
1 TTTTTCAT
89036 TTTTTCA
1 TTTTTCA
89043 CTCATTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
7 7 0.16
8 37 0.84
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTCAT
Found at i:89006 original size:15 final size:15
Alignment explanation
Indices: 88986--89040 Score: 83
Period size: 15 Copynumber: 3.6 Consensus size: 15
88976 TCTTGAAACC
*
88986 TCATTTTTCATTTTT
1 TCATTTTTTATTTTT
89001 TCATTTTTTTATTTTT
1 TCA-TTTTTTATTTTT
*
89017 TTATTTTTTATTTTT
1 TCATTTTTTATTTTT
89032 TCATTTTTT
1 TCATTTTTT
89041 CACTCATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 23 0.64
16 13 0.36
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
TCATTTTTTATTTTT
Found at i:89015 original size:6 final size:7
Alignment explanation
Indices: 88988--89040 Score: 61
Period size: 7 Copynumber: 7.0 Consensus size: 7
88978 TTGAAACCTC
*
88988 ATTTTTC
1 ATTTTTT
88995 ATTTTTT
1 ATTTTTT
89002 CATTTTTTT
1 -A-TTTTTT
89011 ATTTTTTT
1 A-TTTTTT
89019 ATTTTTT
1 ATTTTTT
89026 ATTTTTT
1 ATTTTTT
89033 CATTTTTT
1 -ATTTTTT
89041 CACTCATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
7 19 0.45
8 17 0.40
9 6 0.14
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (7 bp):
ATTTTTT
Done.