Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005544.1 Hibiscus syriacus cultivar Beakdansim tig00012838_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: 98024
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:810 original size:4 final size:4
Alignment explanation
Indices: 801--830 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
791 ATTTTTTCAT
801 ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
831 ATCTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.47, G:0.00, T:0.27
Consensus pattern (4 bp):
ATCC
Found at i:1616 original size:10 final size:10
Alignment explanation
Indices: 1601--1625 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1591 GCCTCCAAAG
1601 GGAAGCTGAA
1 GGAAGCTGAA
1611 GGAAGCTGAA
1 GGAAGCTGAA
1621 GGAAG
1 GGAAG
1626 GAAGTTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.08, G:0.44, T:0.08
Consensus pattern (10 bp):
GGAAGCTGAA
Found at i:19273 original size:2 final size:2
Alignment explanation
Indices: 19266--19290 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19256 CATTTTTCCC
19266 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19291 TTTGGAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22322 original size:23 final size:23
Alignment explanation
Indices: 22296--22339 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
22286 ATAAAAATCA
*
22296 TAATTATTTTTTAAAATAATATT
1 TAATTATTTTTTAAAAGAATATT
22319 TAATTATTTTTTAAAAGAATA
1 TAATTATTTTTTAAAAGAATA
22340 GTTATGACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TAATTATTTTTTAAAAGAATATT
Found at i:24264 original size:2 final size:2
Alignment explanation
Indices: 24257--24282 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24247 AATTTCTAGT
24257 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
24283 AGGGTAAAAG
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):
TA
Found at i:28962 original size:4 final size:4
Alignment explanation
Indices: 28942--28976 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
28932 CAGAAGTAGA
28942 AATT ATATT AA-T AATT AATT AATT AATT AATT AAT
1 AATT A-ATT AATT AATT AATT AATT AATT AATT AAT
28977 GAGAATAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
4 22 0.76
5 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
AATT
Found at i:29053 original size:3 final size:3
Alignment explanation
Indices: 29045--29132 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
29035 TGGACTCCTT
29045 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29093 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29133 CATCATCATC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29137 original size:3 final size:3
Alignment explanation
Indices: 29131--29161 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
29121 TATTATTATT
29131 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
29162 ATTTCATGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:31438 original size:32 final size:32
Alignment explanation
Indices: 31402--31502 Score: 89
Period size: 32 Copynumber: 3.2 Consensus size: 32
31392 TATTTAAATA
31402 AAAATAATGAGGATATTACTAATCTTGCCATC
1 AAAATAATGAGGATATTACTAATCTTGCCATC
* * * * *** *
31434 AAAATTGATGA-GAT-CTAATAAGTATTTAAATA
1 AAAA-TAATGAGGATATTACTAA-TCTTGCCATC
*
31466 AAAATAATGAGGATATTTCTAATCTTGCCATC
1 AAAATAATGAGGATATTACTAATCTTGCCATC
31498 AAAAT
1 AAAAT
31503 TGATGAGATC
Statistics
Matches: 48, Mismatches: 17, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
31 10 0.21
32 29 0.60
33 9 0.19
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (32 bp):
AAAATAATGAGGATATTACTAATCTTGCCATC
Found at i:31445 original size:33 final size:33
Alignment explanation
Indices: 31408--31509 Score: 93
Period size: 33 Copynumber: 3.2 Consensus size: 33
31398 AATAAAAATA
31408 ATGAGGATATTACTAATCTTGCCATCAAAATTG
1 ATGAGGATATTACTAATCTTGCCATCAAAATTG
* * * *** * *
31441 ATGA-GAT-CTAATAAGTATTTAAAT-AAAAATA
1 ATGAGGATATTACTAA-TCTTGCCATCAAAATTG
*
31472 ATGAGGATATTTCTAATCTTGCCATCAAAATTG
1 ATGAGGATATTACTAATCTTGCCATCAAAATTG
31505 ATGAG
1 ATGAG
31510 ATCTAATAAG
Statistics
Matches: 48, Mismatches: 17, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
31 14 0.29
32 16 0.33
33 18 0.38
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (33 bp):
ATGAGGATATTACTAATCTTGCCATCAAAATTG
Found at i:31457 original size:64 final size:64
Alignment explanation
Indices: 31389--31537 Score: 282
Period size: 64 Copynumber: 2.3 Consensus size: 64
31379 TGGATTGAAG
31389 AAGTATTTAAATAAAAATAATGAGGATATTACTAATCTTGCCATCAAAATTGATGAGATCTAAT
1 AAGTATTTAAATAAAAATAATGAGGATATTACTAATCTTGCCATCAAAATTGATGAGATCTAAT
*
31453 AAGTATTTAAATAAAAATAATGAGGATATTTCTAATCTTGCCATCAAAATTGATGAGATCTAAT
1 AAGTATTTAAATAAAAATAATGAGGATATTACTAATCTTGCCATCAAAATTGATGAGATCTAAT
31517 AAGTATTTAAATAAAAA-AATG
1 AAGTATTTAAATAAAAATAATG
31538 GAAGTCAAAA
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
63 4 0.05
64 80 0.95
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (64 bp):
AAGTATTTAAATAAAAATAATGAGGATATTACTAATCTTGCCATCAAAATTGATGAGATCTAAT
Found at i:33644 original size:64 final size:64
Alignment explanation
Indices: 33559--33782 Score: 227
Period size: 64 Copynumber: 3.5 Consensus size: 64
33549 TGTTTGAATG
* ** ** *
33559 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGTAATTC
1 TGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
33622 A
64 A
* **
33623 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
* ** * ** * ** *
33687 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATATTACTACATCGAATACCTTTTA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
* *
33751 TGCACCGATGCATCAGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAGTAGTGCATCGATGCAT
33783 ACCTTCATTA
Statistics
Matches: 134, Mismatches: 24, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
64 128 0.96
65 6 0.04
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:36925 original size:64 final size:64
Alignment explanation
Indices: 36857--36997 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 64
36847 TGTTTGAATG
** * **
36857 TGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTC
1 TGCATCGATGCATAAGTAGTGCATCAATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
36920 A
64 A
* * **
36921 TGCATCAATGCATAAGTAGTGCATCAATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAAGTAGTGCATCAATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
36985 TGCATCGATGCAT
1 TGCATCGATGCAT
36998 CCCAGCAATA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
64 59 0.91
65 6 0.09
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATAAGTAGTGCATCAATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:43339 original size:36 final size:36
Alignment explanation
Indices: 43289--43386 Score: 160
Period size: 36 Copynumber: 2.7 Consensus size: 36
43279 GAAACAGAAT
43289 GAAGCATCGACACTTTCGATTCAAGTCGAACGGAAA
1 GAAGCATCGACACTTTCGATTCAAGTCGAACGGAAA
* * *
43325 GAAGCATCGGCACTTTCGATTCAAATCGAACGGAAT
1 GAAGCATCGACACTTTCGATTCAAGTCGAACGGAAA
*
43361 GAGGCATCGACACTTTCGATTCAAGT
1 GAAGCATCGACACTTTCGATTCAAGT
43387 GTTAATATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (36 bp):
GAAGCATCGACACTTTCGATTCAAGTCGAACGGAAA
Found at i:48946 original size:21 final size:21
Alignment explanation
Indices: 48830--48972 Score: 145
Period size: 21 Copynumber: 6.8 Consensus size: 21
48820 TTGTACCAAG
*
48830 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
48851 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
48872 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
*
48893 GACGAGAAGGCCATTCATCAA
1 GACGAGAAGACCATTCATCAA
* *
48914 GACGAGAGGACCTTTCAT-AA
1 GACGAGAAGACCATTCATCAA
48934 CGACGAGAAGACC-TTCAT-AA
1 -GACGAGAAGACCATTCATCAA
48954 CGAC-ATGAAGACCACTTCA
1 -GACGA-GAAGACCA-TTCA
48973 CATTGGAGGT
Statistics
Matches: 110, Mismatches: 6, Indels: 11
0.87 0.05 0.09
Matches are distributed among these distances:
19 1 0.01
20 21 0.19
21 83 0.75
22 5 0.05
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:53868 original size:36 final size:36
Alignment explanation
Indices: 53712--53899 Score: 238
Period size: 36 Copynumber: 5.2 Consensus size: 36
53702 AAGTCAATCC
53712 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * *
53748 GAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* *
53784 GAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCA
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * *
53820 TAAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * *
53856 TAAGTCTTCACC--AAAAGTAGTGAAGCAGATCCAT-T
1 TAAGCCTTCACCGGAGAA-TAGTGAAGCA-AACCATCT
53891 TAAGCCTTC
1 TAAGCCTTC
53900 TCAGAAGAGT
Statistics
Matches: 135, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
34 2 0.01
35 19 0.14
36 114 0.84
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (36 bp):
TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
Found at i:54342 original size:51 final size:51
Alignment explanation
Indices: 54277--54727 Score: 591
Period size: 51 Copynumber: 8.7 Consensus size: 51
54267 AAGATTATTT
* *
54277 GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTTGAAGATGTCC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
* * * *
54328 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
* * * *
54379 GAGTTCTATACT-CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
* * *
54429 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGA-GATGTC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATG-T-TC
* * *
54481 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCC
1 -GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
* *
54533 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
* *
54584 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAAATTGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGA-TGTTC
* * * *
54636 GAGTTCTATACTCCCTAGAGAAAGAGAGAGCGAACTCGTTTGCAGAAGATATTC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT---GAAGATGTTC
* *
54690 GAGTTCCATAATCCCTAGAGAAAGAGGGAACGAACCCG
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG
54728 ATTGTTGAAG
Statistics
Matches: 357, Mismatches: 34, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
50 45 0.13
51 181 0.51
52 47 0.13
53 43 0.12
54 37 0.10
55 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (51 bp):
GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
Found at i:54640 original size:154 final size:156
Alignment explanation
Indices: 54277--55001 Score: 642
Period size: 154 Copynumber: 4.6 Consensus size: 156
54267 AAGATTATTT
* * * *
54277 GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTTGAAGA-TGTCCGAGTTCCATACTC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAAATTGTTCGAGTTCCATACTC
* * * *
54341 CCTAGAGAAAGAAGGAGCGAACCCGTG-TGAAGATATGCGAGTTCTATACT-CTTAAAGAAAGAA
66 CCTAGAGAAAGAGGGAGCGAACCCGTGCTGAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAG
54404 GGAGCGAACCCG-TTTGAAGATGTTC
131 GGAGCGAACCCGTTTTGAAGATGTTC
* * * *
54429 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGA-TG-TCTGAGTTCCATA
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA-A-ATTGTTC-GAGTTCCATA
*
54492 CTCCCTAGAGAAAGAGGGAGCGAACCCGTG-TGAAGATATCCGAGTTCTATACTCCCTAAAGAAA
63 CTCCCTAGAGAAAGAGGGAGCGAACCCGTGCTGAAGATATTCGAGTTCTATACTCCCTAAAGAAA
54556 GAGGGAGCGAACCCG-TTTGAAGATGTTC
128 GAGGGAGCGAACCCGTTTTGAAGATGTTC
*
54584 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAAATTGTTCGAGTTCTATACTC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAAATTGTTCGAGTTCCATACTC
* * * * * *
54649 CCTAGAGAAAGAGAGAGCGAACTCGTTTGCAGAAGATATTCGAGTTCCATAATCCCTAGAGAAAG
66 CCTAGAGAAAGAGGGAGCGAACCCG--TGCTGAAGATATTCGAGTTCTATACTCCCTAAAGAAAG
* *
54714 AGGGAACGAACCCGATTGTTGAAGTTTGTTC
129 AGGGAGCGAACCCG-TT-TTGAAG-ATGTTC
* * * * * *
54745 GAG-TCTTATACTCTCT-GAAAGAATAGGGAGC-AGACACGATTGTTGAAGATTATTCGAG-TCT
1 GAGTTC-TATACTCCCTAGAGA-AAGAGGGAGCGA-ACCCG--T-TTGAAAATTGTTCGAGTTC-
* * * * * * *
54806 CATACTCTCT-GAAAGAATAGGGAG-TAGACACGATTGTTGAAGATTGTTCGAG-TCTCATACTC
59 CATACTCCCTAGAGA-AAGAGGGAGCGA-ACCCG--TGCTGAAGA-TATTCGAGTTCT-ATACTC
* * * * * * *
54868 TCTGAAGGAATAGGGAGC-ATACACGTTTTCAAAAGATTTTC
118 CCTAAAGAAAGAGGGAGCGA-ACCCGTTTT--GAAGATGTTC
* * * *
54909 GAGTTCTATGCTCCCT-GAAGAAAGTGGGAGCGAACCCGTTTGCAGAAGATT-TTCAAGTTCTAT
1 GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTG-A-AA-ATTGTTCGAGTTCCAT
54972 ACTCCCT-GAAGAAAGAGGGAGCGAACCCGT
62 ACTCCCTAG-AGAAAGAGGGAGCGAACCCGT
55002 AGACAAAAGA
Statistics
Matches: 470, Mismatches: 67, Indels: 63
0.78 0.11 0.10
Matches are distributed among these distances:
152 40 0.09
153 2 0.00
154 102 0.22
155 78 0.17
156 2 0.00
157 43 0.09
159 1 0.00
160 12 0.03
161 34 0.07
162 2 0.00
163 36 0.08
164 82 0.17
165 36 0.08
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (156 bp):
GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAAATTGTTCGAGTTCCATACTC
CCTAGAGAAAGAGGGAGCGAACCCGTGCTGAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAG
GGAGCGAACCCGTTTTGAAGATGTTC
Found at i:54884 original size:55 final size:55
Alignment explanation
Indices: 54726--54892 Score: 280
Period size: 55 Copynumber: 3.0 Consensus size: 55
54716 GGAACGAACC
* *
54726 CGATTGTTGAAGTTTGTTCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
* *
54781 CGATTGTTGAAGATTATTCGAGTCTCATACTCTCTGAAAGAATAGGGAGTAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
* *
54836 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCATACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
54891 CG
1 CG
54893 TTTTCAAAAG
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 104 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (55 bp):
CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
Found at i:54938 original size:54 final size:54
Alignment explanation
Indices: 54267--55036 Score: 333
Period size: 51 Copynumber: 14.5 Consensus size: 54
54257 GAAGCAAATG
* * * * *
54267 AAGATTATTTGAGTTCCATACTCCCT-AGAGAGAGAGGGAGCGAACCCGTTTG---
1 AAGATT-TTCGAGTTCTATACTCCCTGA-AGAAAGTGGGAGCGAACACGTTTGCAA
* * * ** * *
54319 AAGATGTCCGAGTTCCATACTCCCT-AGAGAAAGAAGGAGCGAACCCGTGTG---
1 AAGATTTTCGAGTTCTATACTCCCTGA-AGAAAGTGGGAGCGAACACGTTTGCAA
* * * * ** *
54370 AAGATATGCGAGTTCTATACT-CTTAAAGAAAGAAGGAGCGAACCCGTTTG---
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGTGGGAGCGAACACGTTTGCAA
* * * * ** *
54420 AAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-AA
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGTGGGAGCGAACACGTTTGCAA
* * * * * *
54473 GAGA-TGTCTGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTGTG---
1 AAGATTTTC-GAGTTCTATACTCCCTGA-AGAAAGTGGGAGCGAACACGTTTGCAA
* * * * *
54524 AAGATATCCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG---
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGTGGGAGCGAACACGTTTGCAA
* * *
54575 AAGATGTTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTG--A
1 AAGATTTTCGAGTTCTATACTCCCTGA-AGAAAGTGGGAGCGAACACGTTTGCAA
* * * *
54627 AA-ATTGTTCGAGTTCTATACTCCCT-AGAGAAAGAGAGAGCGAACTCGTTTGCAG
1 AAGATT-TTCGAGTTCTATACTCCCTGA-AGAAAGTGGGAGCGAACACGTTTGCAA
* * * * * * * ***
54681 AAGATATTCGAGTTCCATAATCCCT-AGAGAAAGAGGGAACGAACCCGATTGTTG
1 AAGATTTTCGAGTTCTATACTCCCTGA-AGAAAGTGGGAGCGAACACGTTTGCAA
* * * ***
54735 AAGTTTGTTCGAG-TCTTATACTCTCTGAA-AGAA-TAGGGAGC-AGACACGATTGTTG
1 AAGATT-TTCGAGTTC-TATACTCCCTGAAGA-AAGT-GGGAGCGA-ACACGTTTGCAA
* * * ***
54790 AAGATTATTCGAG-TCTCATACTCTCTGAA-AGAA-TAGGGAG-TAGACACGATTGTTG
1 AAGATT-TTCGAGTTCT-ATACTCCCTGAAGA-AAGT-GGGAGCGA-ACACGTTTGCAA
* * *
54845 AAGATTGTTCGAG-TCTCATACTCTCTGAAGGAA-TAGGGAGC-ATACACGTTTTCAA
1 AAGATT-TTCGAGTTCT-ATACTCCCTGAAGAAAGT-GGGAGCGA-ACACGTTTGCAA
* * *
54900 AAGATTTTCGAGTTCTATGCTCCCTGAAGAAAGTGGGAGCGAACCCGTTTGCAG
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGTGGGAGCGAACACGTTTGCAA
* * * *
54954 AAGATTTTCAAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TAGACAA
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGTGGGAGCGAACACGTTTG-CAA
* *
55008 AAGATTGTACGAGTT-TCTACTCCCTGAAG
1 AAGATT-TTCGAGTTCTATACTCCCTGAAG
55037 GAATAGGGAG
Statistics
Matches: 616, Mismatches: 73, Indels: 56
0.83 0.10 0.08
Matches are distributed among these distances:
50 44 0.07
51 178 0.29
52 55 0.09
53 42 0.07
54 150 0.24
55 146 0.24
56 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (54 bp):
AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGTGGGAGCGAACACGTTTGCAA
Found at i:55045 original size:54 final size:52
Alignment explanation
Indices: 54395--55051 Score: 239
Period size: 54 Copynumber: 12.3 Consensus size: 52
54385 TATACTCTTA
* * * * * *
54395 AAGAAAGAAGGAGCGAACCCGTTTG---AAGATGTTCGAGTTCCATACTCCTTA
1 AAGAAATAGGGAGCGAACCCG-TTGCAAAAGATTTTCGAGTTTC-TACTCCCTG
* * * * *
54446 AAGAAAGAAGGAGCGAACCCGTTTG-AAGAGA-TGTCTGAGTTCCATACTCCCT-
1 AAGAAATAGGGAGCGAACCCG-TTGCAAAAGATTTTC-GAGTTTC-TACTCCCTG
* * * * *
54498 AGAGAAAGAGGGAGCGAACCCGTGTG---AAGATATCCGAGTTCTATACTCCCTA
1 A-AGAAATAGGGAGCGAACCCGT-TGCAAAAGATTTTCGAGTT-TCTACTCCCTG
* * *
54550 AAGAAAGAGGGAGCGAACCCGTTTG---AAGATGTTCGAGTTCTATACTCCCT-
1 AAGAAATAGGGAGCGAACCCG-TTGCAAAAGATTTTCGAGTT-TCTACTCCCTG
* *
54600 AGAGAAAGAGGGAGCGAACCCGTTTG--AAA-ATTGTTCGAGTTCTATACTCCCT-
1 A-AGAAATAGGGAGCGAACCCG-TTGCAAAAGATT-TTCGAGTT-TCTACTCCCTG
* * * * * * *
54652 AGAGAAAGAGAGAGCGAACTCGTTTGCAGAAGATATTCGAGTTCCATAATCCCT-
1 A-AGAAATAGGGAGCGAACCCG-TTGCAAAAGATTTTCGAGTTTC-TACTCCCTG
* * *** * * *
54706 AGAGAAAGAGGGAACGAACCCGATTGTTGAAGTTTGTTCGAGTCTTATACTCTCTG
1 A-AGAAATAGGGAGCGAACCCG-TTGCAAAAGATT-TTCGAGT-TTCTACTCCCTG
* *** * *
54762 AA-AGAATAGGGAGC-AGACACGATTGTTGAAGATTATTCGAGTCTCATACTCTCTG
1 AAGA-AATAGGGAGCGA-ACCCG-TTGCAAAAGATT-TTCGAGTTTC-TACTCCCTG
* * *** * *
54817 AA-AGAATAGGGAG-TAGACACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTG
1 AAGA-AATAGGGAGCGA-ACCCG-TTGCAAAAGATT-TTCGAGTTTC-TACTCCCTG
* * *
54872 AAGGAATAGGGAGC-ATACACGTTTTCAAAAGATTTTCGAG-TTCTATGCTCCCTG
1 AAGAAATAGGGAGCGA-ACCCG-TTGCAAAAGATTTTCGAGTTTCTA--CTCCCTG
* * *
54926 AAGAAAGT-GGGAGCGAACCCGTTTGCAGAAGATTTTCAAGTTCTATACTCCCTG
1 AAGAAA-TAGGGAGCGAACCCG-TTGCAAAAGATTTTCGAGTT-TCTACTCCCTG
* * *
54980 AAGAAAGAGGGAGCGAACCCGTAGACAAAAGATTGTACGAGTTTCTACTCCCTG
1 AAGAAATAGGGAGCGAACCCGTTG-CAAAAGATT-TTCGAGTTTCTACTCCCTG
* *
55034 AAGGAATAGGGAGTGAAC
1 AAGAAATAGGGAGCGAAC
55052 ATGTTTTCCA
Statistics
Matches: 507, Mismatches: 65, Indels: 65
0.80 0.10 0.10
Matches are distributed among these distances:
50 1 0.00
51 112 0.22
52 54 0.11
53 43 0.08
54 149 0.29
55 143 0.28
56 5 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (52 bp):
AAGAAATAGGGAGCGAACCCGTTGCAAAAGATTTTCGAGTTTCTACTCCCTG
Found at i:55238 original size:14 final size:14
Alignment explanation
Indices: 55219--55245 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55209 GCAAACCACC
55219 AGATAAAAAAAAAG
1 AGATAAAAAAAAAG
55233 AGATAAAAAAAAA
1 AGATAAAAAAAAA
55246 AAGTCGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.07
Consensus pattern (14 bp):
AGATAAAAAAAAAG
Found at i:61613 original size:36 final size:36
Alignment explanation
Indices: 61563--61660 Score: 160
Period size: 36 Copynumber: 2.7 Consensus size: 36
61553 GAAACAGAAT
61563 GAAGCATCGACACTTTCGATTCAAGTCGAACGGAAA
1 GAAGCATCGACACTTTCGATTCAAGTCGAACGGAAA
* * *
61599 GAAGCATCGGCACTTTCGATTCAAATCGAACGGAAT
1 GAAGCATCGACACTTTCGATTCAAGTCGAACGGAAA
*
61635 GAGGCATCGACACTTTCGATTCAAGT
1 GAAGCATCGACACTTTCGATTCAAGT
61661 GTTAATATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (36 bp):
GAAGCATCGACACTTTCGATTCAAGTCGAACGGAAA
Found at i:66279 original size:31 final size:30
Alignment explanation
Indices: 66244--66337 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 30
66234 GCCAATATGG
* *
66244 AAATCGGATATAGTTCAAGCACTAATACGAA
1 AAATCGGATATAGTT-AAGAACTAATATGAA
*
66275 AAATCGGATATAGTATAAGTACTAATATG-A
1 AAATCGGATATAGT-TAAGAACTAATATGAA
* *
66305 AAATCTGATGTAGTTTAAGAACTAATATGAA
1 AAATCGGATATAG-TTAAGAACTAATATGAA
66336 AA
1 AA
66338 TTAGGATGGT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
30 25 0.45
31 29 0.53
32 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.28
Consensus pattern (30 bp):
AAATCGGATATAGTTAAGAACTAATATGAA
Found at i:66329 original size:30 final size:30
Alignment explanation
Indices: 66237--66338 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 30
66227 CACACATGCC
* * *
66237 AATATGGAAATCGGATATAGTTCAAGCACT
1 AATATGAAAATCGGATATAGTTTAAGAACT
* * *
66267 AATACGAAAAATCGGATATAGTATAAGTACT
1 AATATG-AAAATCGGATATAGTTTAAGAACT
* *
66298 AATATGAAAATCTGATGTAGTTTAAGAACT
1 AATATGAAAATCGGATATAGTTTAAGAACT
66328 AATATGAAAAT
1 AATATGAAAAT
66339 TAGGATGGTT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
30 36 0.59
31 25 0.41
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (30 bp):
AATATGAAAATCGGATATAGTTTAAGAACT
Found at i:70456 original size:2 final size:2
Alignment explanation
Indices: 70449--70494 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
70439 CTATGTTGTT
* *
70449 TA TA TA TA TA TCA TA T- TA TT TA TA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70491 TA TA
1 TA TA
70495 AATTAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:70574 original size:18 final size:19
Alignment explanation
Indices: 70538--70575 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
70528 TAACGTCTAT
*
70538 TTTATTTTATTTGACTTTA
1 TTTATTTTATTTCACTTTA
*
70557 TTTA-TTTATTTCATTTTA
1 TTTATTTTATTTCACTTTA
70575 T
1 T
70576 AAGATGATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (19 bp):
TTTATTTTATTTCACTTTA
Found at i:82075 original size:27 final size:26
Alignment explanation
Indices: 82045--82136 Score: 89
Period size: 27 Copynumber: 3.4 Consensus size: 26
82035 GGGAACAAAT
82045 AAAAAGATAAAAAAATGAAAAAGAA-AA
1 AAAAAGA-AAAAAAATGAAAAA-AATAA
*
82072 AAAAATGAAAAAAAATGAAAAAAATGA
1 AAAAA-GAAAAAAAATGAAAAAAATAA
* *
82099 AAAATGAAAAAAGAAATG-AAAAAATGA
1 AAAAAG-AAAAA-AAATGAAAAAAATAA
*
82126 AAAGAGAAAAA
1 AAAAAGAAAAA
82137 GGAGGGTTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
26 8 0.14
27 42 0.74
28 7 0.12
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (26 bp):
AAAAAGAAAAAAAATGAAAAAAATAA
Found at i:82084 original size:19 final size:18
Alignment explanation
Indices: 82045--82128 Score: 100
Period size: 19 Copynumber: 4.6 Consensus size: 18
82035 GGGAACAAAT
*
82045 AAAAAGATAAAAAAATG-
1 AAAAAGAAAAAAAAATGA
82062 AAAAAGAAAAAAAAATGA
1 AAAAAGAAAAAAAAATGA
82080 AAAAA-AATGAAAAAAATGA
1 AAAAAGAA--AAAAAAATGA
*
82099 AAAATGAAAAAAGAAATGA
1 AAAAAGAAAAAA-AAATGA
82118 AAAAATGAAAA
1 AAAAA-GAAAA
82129 GAGAAAAAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
17 18 0.31
18 9 0.16
19 24 0.41
20 7 0.12
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAAAGAAAAAAAAATGA
Found at i:82085 original size:36 final size:38
Alignment explanation
Indices: 82045--82122 Score: 126
Period size: 36 Copynumber: 2.1 Consensus size: 38
82035 GGGAACAAAT
*
82045 AAAAAGAT-AAAAAAATGAAAAA-GAAAAAA-AAATGA
1 AAAAAAATGAAAAAAATGAAAAATGAAAAAAGAAATGA
82080 AAAAAAATGAAAAAAATGAAAAATGAAAAAAGAAATGA
1 AAAAAAATGAAAAAAATGAAAAATGAAAAAAGAAATGA
82118 AAAAA
1 AAAAA
82123 TGAAAAGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 7 0.18
36 14 0.36
37 7 0.18
38 11 0.28
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (38 bp):
AAAAAAATGAAAAAAATGAAAAATGAAAAAAGAAATGA
Found at i:82123 original size:8 final size:8
Alignment explanation
Indices: 82041--82128 Score: 62
Period size: 8 Copynumber: 11.1 Consensus size: 8
82031 AAAAGGGAAC
82041 AAAT-AAA
1 AAATGAAA
*
82048 AAGATAAAA
1 AA-ATGAAA
82057 AAATGAAA
1 AAATGAAA
**
82065 AAGAAAAAA
1 AA-ATGAAA
82074 AAATGAAAAA
1 AAATG--AAA
82084 AAATGAAAA
1 AAATG-AAA
82093 AAATG-AA
1 AAATGAAA
82100 AAATGAAA
1 AAATGAAA
82108 AAA-G---
1 AAATGAAA
82112 AAATGAAA
1 AAATGAAA
82120 AAATGAAA
1 AAATGAAA
82128 A
1 A
82129 GAGAAAAAGG
Statistics
Matches: 66, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
4 3 0.05
5 1 0.02
7 10 0.15
8 24 0.36
9 20 0.30
10 8 0.12
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.10
Consensus pattern (8 bp):
AAATGAAA
Found at i:82123 original size:36 final size:34
Alignment explanation
Indices: 82041--82128 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 34
82031 AAAAGGGAAC
82041 AAAT-AAAAAGAT-AAAAAAATGAAAAAGAAAAAA
1 AAATGAAAAA-ATGAAAAAAATGAAAAAGAAAAAA
82074 AAATGAAAAAAAATGAAAAAAATGAAAAATGAAAAAA
1 AAATG--AAAAAATGAAAAAAATGAAAAA-GAAAAAA
82111 GAAATGAAAAAATGAAAA
1 -AAATGAAAAAATGAAAA
82129 GAGAAAAAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
33 4 0.08
35 2 0.04
36 31 0.63
37 7 0.14
38 5 0.10
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.10
Consensus pattern (34 bp):
AAATGAAAAAATGAAAAAAATGAAAAAGAAAAAA
Found at i:86014 original size:2 final size:2
Alignment explanation
Indices: 86007--86057 Score: 61
Period size: 2 Copynumber: 26.0 Consensus size: 2
85997 CTATGTTGTT
* *
86007 TA TA TA TA T- TA TA TCA TA T- TA TT TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
86048 TA TA TA TA TA
1 TA TA TA TA TA
86058 AATTAATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:86138 original size:18 final size:19
Alignment explanation
Indices: 86102--86139 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
86092 TAACGTCTAT
*
86102 TTTATTTTATTTGACTTTA
1 TTTATTTTATTTCACTTTA
*
86121 TTTA-TTTATTTCATTTTA
1 TTTATTTTATTTCACTTTA
86139 T
1 T
86140 AAGATGATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (19 bp):
TTTATTTTATTTCACTTTA
Found at i:87716 original size:29 final size:30
Alignment explanation
Indices: 87690--87759 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 30
87680 ATTTGTTTCG
87690 TTTTGATC-ACTAGTTTTGACAAAGTTTAA
1 TTTTGATCAACTAGTTTTGACAAAGTTTAA
*
87719 TTTTTATCAAAACTAGTTTTGACAAAGTTTAA
1 TTTTGATC--AACTAGTTTTGACAAAGTTTAA
*
87751 TTTTTATCA
1 TTTTGATCA
87760 GTTATGTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 7 0.19
30 1 0.03
32 29 0.78
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (30 bp):
TTTTGATCAACTAGTTTTGACAAAGTTTAA
Found at i:87739 original size:32 final size:32
Alignment explanation
Indices: 87698--87759 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
87688 CGTTTTGATC
87698 ACTAGTTTTGACAAAGTTTAATTTTTATCAAA
1 ACTAGTTTTGACAAAGTTTAATTTTTATCAAA
87730 ACTAGTTTTGACAAAGTTTAATTTTTATCA
1 ACTAGTTTTGACAAAGTTTAATTTTTATCA
87760 GTTATGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (32 bp):
ACTAGTTTTGACAAAGTTTAATTTTTATCAAA
Found at i:87754 original size:16 final size:16
Alignment explanation
Indices: 87703--87754 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
87693 TGATCACTAG
87703 TTTTGACAAAGTTTAA
1 TTTTGACAAAGTTTAA
* ** *
87719 TTTTTATCAAA-ACTAG
1 TTTTGA-CAAAGTTTAA
87735 TTTTGACAAAGTTTAA
1 TTTTGACAAAGTTTAA
87751 TTTT
1 TTTT
87755 TATCAGTTAT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 4 0.15
16 18 0.69
17 4 0.15
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTTGACAAAGTTTAA
Found at i:93025 original size:57 final size:59
Alignment explanation
Indices: 92962--93071 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 59
92952 TGAATGATCC
* * *
92962 CTCAACTATAAAATATTATTTT-TT-AGTACTCTGACTATTAAAAGTTACAAATGCTCT
1 CTCAACTATAAAATACTATTTTGTTGAGTACCCCGACTATTAAAAGTTACAAATGCTCT
** * *
93019 CTCAACTATATGATACTGTTTTGTTGAGTCCCCCGACTATTAAAAGTTACAAA
1 CTCAACTATAAAATACTATTTTGTTGAGTACCCCGACTATTAAAAGTTACAAA
93072 ATGGTAACCC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
57 18 0.41
58 2 0.05
59 24 0.55
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (59 bp):
CTCAACTATAAAATACTATTTTGTTGAGTACCCCGACTATTAAAAGTTACAAATGCTCT
Found at i:95299 original size:60 final size:60
Alignment explanation
Indices: 95217--95350 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
95207 GTTTAAAACA
* * * * *
95217 TATAAAA-TAATTTATAACTTTTAGTAA-CAGATAGACTTAATAAAATAACACCTTATAGT
1 TATAAAATTATTTTATAACTTTTAATAATC-GAAAGACTCAATAAAATAACACCTTATAAT
* * * *
95276 TATAAAATTATTTTATAATTTTTAATAATCGAAATACTCAATAAATTAACATCTTATAAT
1 TATAAAATTATTTTATAACTTTTAATAATCGAAAGACTCAATAAAATAACACCTTATAAT
*
95336 TAAAAATATTATTTT
1 TATAAA-ATTATTTT
95351 TGTAGTAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 7 0.11
60 46 0.74
61 9 0.15
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (60 bp):
TATAAAATTATTTTATAACTTTTAATAATCGAAAGACTCAATAAAATAACACCTTATAAT
Found at i:95384 original size:65 final size:60
Alignment explanation
Indices: 95251--95389 Score: 154
Period size: 65 Copynumber: 2.2 Consensus size: 60
95241 TAACAGATAG
* *
95251 ACTTAATAAAATAACACCTTATAGTTATAAAATTATTTTATAATTTTTAATAATCGAAAT
1 ACTTAATAAAATAACACCTTATAATTAAAAAATTATTTTATAATTTTTAATAATCGAAAT
* * * *
95311 ACTCAATAAATTAACATCTTATAATTAAAAATATTATTTTTGTAGTAATTTTTAATAATTGATAA
1 ACTTAATAAAATAACACCTTATAATTAAAAA-ATTA--TTT-TA-TAATTTTTAATAATCGA-AA
95376 -
60 T
*
95376 ATTTAATAAAATAA
1 ACTTAATAAAATAA
95390 TGTAATGTGC
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
60 26 0.41
61 4 0.06
63 3 0.05
64 2 0.03
65 27 0.42
66 2 0.03
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.42
Consensus pattern (60 bp):
ACTTAATAAAATAACACCTTATAATTAAAAAATTATTTTATAATTTTTAATAATCGAAAT
Found at i:96206 original size:37 final size:39
Alignment explanation
Indices: 96157--96238 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 39
96147 GTTGTCGTAC
*
96157 TTGAACTG-TT-T-GTCTTTAGTAATAAATGAATGGGTG
1 TTGAACTGTTTGTCGTCTTTAGTAATAAATGAATGGATG
96193 TTGAACATGTTTGTCCGTCTTTAGTAATAAATGAATGGATG
1 TTGAAC-TGTTTGT-CGTCTTTAGTAATAAATGAATGGATG
96234 TTGAA
1 TTGAA
96239 ATCATACATG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
36 6 0.15
37 2 0.05
38 2 0.05
39 1 0.03
41 29 0.73
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.40
Consensus pattern (39 bp):
TTGAACTGTTTGTCGTCTTTAGTAATAAATGAATGGATG
Done.