Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002308.1 Hibiscus syriacus cultivar Beakdansim tig00004701_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: 60713
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Found at i:3758 original size:19 final size:19
Alignment explanation
Indices: 3730--3772 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3720 TTAGTATGTT
3730 TAAAAAGAAAACTT-AAAA
1 TAAAAAGAAAACTTGAAAA
3748 TAAAAATGAAAACTTGAAAA
1 TAAAAA-GAAAACTTGAAAA
*
3768 GAAAA
1 TAAAA
3773 GATAGAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 8 0.36
20 8 0.36
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (19 bp):
TAAAAAGAAAACTTGAAAA
Found at i:4271 original size:18 final size:18
Alignment explanation
Indices: 4250--4287 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4240 AGGGAAGTTT
* *
4250 TAGTAAAAATATATTAAA
1 TAGTAAAAAGAAATTAAA
4268 TAGTAAAAAGAAATTAAA
1 TAGTAAAAAGAAATTAAA
4286 TA
1 TA
4288 AAAGGCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (18 bp):
TAGTAAAAAGAAATTAAA
Found at i:12933 original size:27 final size:26
Alignment explanation
Indices: 12893--12945 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
12883 CCAGAAGGCG
*
12893 CTGACTAGATCTTCTAGAAAACTGCCA
1 CTGACTAGACCTTCTAG-AAACTGCCA
*
12920 CTGACTGGACCTTCTAGAAACTGCCA
1 CTGACTAGACCTTCTAGAAACTGCCA
12946 TGTCAGACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (26 bp):
CTGACTAGACCTTCTAGAAACTGCCA
Found at i:15716 original size:2 final size:2
Alignment explanation
Indices: 15709--15734 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15699 TCTAACCATA
15709 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
15735 CATTCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16183 original size:157 final size:156
Alignment explanation
Indices: 16010--16390 Score: 469
Period size: 157 Copynumber: 2.4 Consensus size: 156
16000 TGTGGTATAT
* ***
16010 GAGCATGTGGTTCAAATTTGATAAATAAAAGACTTAAAATAAATC-ACAAATTGAAGGTGTAAAG
1 GAGCATGTGGTTCAAATTTGGTAAA-AAAAGACTTAAAATAAA-CGAC-AATTGAAGAAATAAAG
* *
16074 AGATTATGAAAAATAGAAGGACTAAATTGAAAAATA-AAAACTTTATATCAAAAAGAGGAATTGA
63 AAATTATGAAAAATAGAAAGACTAAATTGAAAAATATAAAACTTTATATCAAAAAGAGGAATTGA
*
16138 AAGTAAATATGTATTCTACTATGGTTTAG
128 AAGTAAACATGTATTCTACTATGGTTTAG
* ** * * * *
16167 GAGCATGTGGCTCAAATTTGGTGAAAACCACACTTAAAATAAACGACGATTGACGAAATAAGGAA
1 GAGCATGTGGTTCAAATTTGGT-AAAAAAAGACTTAAAATAAACGACAATTGAAGAAATAAAGAA
* ** *
16232 ATTATGAAAAATTGAAAGACTAAATTGAAAAATATAAATTTTTTTATCAAAAAGAGGAATTGAAA
65 ATTATGAAAAATAGAAAGACTAAATTGAAAAATATAAAACTTTATATCAAAAAGAGGAATTGAAA
*
16297 GTACACATGTATTCTACTATGGTTTAG
130 GTAAACATGTATTCTACTATGGTTTAG
** ** * * *
16324 GAGCATGTGGTTCAAATTTGGTAAAAATGGACTTAAAATGGAGGAGAAATTGAAGAAATAATGAA
1 GAGCATGTGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAACGA-CAATTGAAGAAATAAAGAA
16389 AT
65 AT
16391 CAGGGACTAA
Statistics
Matches: 189, Mismatches: 31, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
156 60 0.32
157 126 0.67
158 3 0.02
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.28
Consensus pattern (156 bp):
GAGCATGTGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAACGACAATTGAAGAAATAAAGAAA
TTATGAAAAATAGAAAGACTAAATTGAAAAATATAAAACTTTATATCAAAAAGAGGAATTGAAAG
TAAACATGTATTCTACTATGGTTTAG
Found at i:20910 original size:46 final size:46
Alignment explanation
Indices: 20857--20947 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
20847 CCTAATCGAC
*
20857 CTCCACTGGTTAACAACTCGTAACTTCTACCATTGAGATTTGGGAG
1 CTCCACTGGTTAACAACTCGTAACTTCAACCATTGAGATTTGGGAG
20903 CTCCACTGGTTAACAACTCGTAACTTCAACCATTGAGATTTGGGA
1 CTCCACTGGTTAACAACTCGTAACTTCAACCATTGAGATTTGGGA
20948 CATACATATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (46 bp):
CTCCACTGGTTAACAACTCGTAACTTCAACCATTGAGATTTGGGAG
Found at i:21837 original size:18 final size:18
Alignment explanation
Indices: 21814--21849 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21804 AAGATAAATC
21814 TTATATCATAGACGAATA
1 TTATATCATAGACGAATA
21832 TTATATCATAGACGAATA
1 TTATATCATAGACGAATA
21850 GATCCGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
TTATATCATAGACGAATA
Found at i:22408 original size:3 final size:3
Alignment explanation
Indices: 22400--22433 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
22390 CATCCCGAAG
22400 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
22434 GTAGCCCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25923 original size:131 final size:131
Alignment explanation
Indices: 25710--26039 Score: 376
Period size: 131 Copynumber: 2.5 Consensus size: 131
25700 TTGAAGTAAA
* * * *
25710 AAATGAATGCTTCAAGGCATGAGAGGTCATTTATTTTCGATTGGAAATAATT-CGATAGTACCGT
1 AAATGAATGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAC-ATATTATCGT
* * * * *
25774 TCTCTCTCGAATCAATATT-GATTTTTAAGACAAAATAGTGATATCTCTTCATTTCAATTGGAGC
65 TTTCACTCGAATCAATATTAGA-TCTTAAGACAAAATAGTAATATCTCCTCATTTCAATTGGAGC
25838 AAT
129 AAT
* * * * *
25841 AAATGATTGCTTTAAGGTATGAGAGGTAATTTATTCTCGAATGGAAATTATTACATATTATCGTT
1 AAATGAATGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTACATATTATCGTT
* * * * * *
25906 TTCACTTGAATCGATATTAGATCTTACGACAAAATAGTAATATCTCCTCATTTTAATTGGGGTAA
66 TTCACTCGAATCAATATTAGATCTTAAGACAAAATAGTAATATCTCCTCATTTCAATTGGAGCAA
25971 T
131 T
* * * * * * * *
25972 AAATTACTGTTTTAAGGCATGAAAAGTCTTTTATTCTCGATTGGAAATAATTAGATATTATCATT
1 AAATGAATGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTACATATTATCGTT
26037 TTC
66 TTC
26040 TCTCTTAAAA
Statistics
Matches: 165, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
131 162 0.98
132 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.38
Consensus pattern (131 bp):
AAATGAATGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTACATATTATCGTT
TTCACTCGAATCAATATTAGATCTTAAGACAAAATAGTAATATCTCCTCATTTCAATTGGAGCAA
T
Found at i:28030 original size:29 final size:27
Alignment explanation
Indices: 27998--28068 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 27
27988 AGAATATATC
*
27998 TTTTTATTTATTTTAATTTGGTCATACA
1 TTTTTATTTATTTTAATTTAGTCAT-CA
* *
28026 ATTTTAGTTTATTTTAATTTAGTCCTCA
1 TTTTTA-TTTATTTTAATTTAGTCATCA
28054 TGTTTTATTTATTTT
1 T-TTTTATTTATTTT
28069 GTTCTATGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.41
29 22 0.59
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (27 bp):
TTTTTATTTATTTTAATTTAGTCATCA
Found at i:28915 original size:131 final size:131
Alignment explanation
Indices: 28684--29014 Score: 409
Period size: 131 Copynumber: 2.5 Consensus size: 131
28674 TTTATTTCGG
* * * *
28684 TTGGAGTAATAAATGGCTGCTTCAAGGCATGAGAGGTCATTTATTCCCGATTGGAAATAATTCGA
1 TTGGAGTAATAAATGACTGCTTCAAGGCATGAGAGGTCATTTATTCTCGATTAGAAATAATTAGA
* *
28749 TATTACCATTTTCTATCGAATCAATATTGATTTTTAAGACAAAATAGTGATATGCCTTCATTTCA
66 TATTACCATTTTCTATCGAATCAATATTGATTTTTAAGACAAAATAGTAATATACCTTCATTTCA
28814 A
131 A
* * * * *
28815 TTGGAGCAATAAATGATTGCTTCAAGGTATGAGAGGTCATTTATTCTCAATT-GACAATCATTAG
1 TTGGAGTAATAAATGACTGCTTCAAGGCATGAGAGGTCATTTATTCTCGATTAGA-AATAATTAG
* * ** *
28879 ATATTAGCATTTT-TACTCGAATCGATATTAGA-TTTTAAGATGAAATAGTAATATATCTTCATT
65 ATATTACCATTTTCTA-TCGAATCAATATT-GATTTTTAAGACAAAATAGTAATATACCTTCATT
*
28942 TTAA
128 TCAA
* * * * *
28946 TTGGGGTAATAATTGACTGTTTTAAGGCATGAAAGGTCA-TTATTCTCGATTAGAAATAATTAGA
1 TTGGAGTAATAAATGACTGCTTCAAGGCATGAGAGGTCATTTATTCTCGATTAGAAATAATTAGA
29010 TATTA
66 TATTA
29015 TAGTTTTCTC
Statistics
Matches: 170, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
130 29 0.17
131 139 0.82
132 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (131 bp):
TTGGAGTAATAAATGACTGCTTCAAGGCATGAGAGGTCATTTATTCTCGATTAGAAATAATTAGA
TATTACCATTTTCTATCGAATCAATATTGATTTTTAAGACAAAATAGTAATATACCTTCATTTCA
A
Found at i:35244 original size:19 final size:19
Alignment explanation
Indices: 35220--35264 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
35210 ACCCACATTG
35220 GATCATGACCAAAAACCCA
1 GATCATGACCAAAAACCCA
35239 GATCATGACCAAAAACCCA
1 GATCATGACCAAAAACCCA
35258 GATCATG
1 GATCATG
35265 TTGAGATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.44, C:0.29, G:0.13, T:0.13
Consensus pattern (19 bp):
GATCATGACCAAAAACCCA
Found at i:35966 original size:30 final size:30
Alignment explanation
Indices: 35931--35999 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
35921 AAAAAAATGA
35931 GAAATTTTTTCTCATTTAAATCTGAAAATT
1 GAAATTTTTTCTCATTTAAATCTGAAAATT
35961 GAAATTTTTTCTCATTTAAATCTGAAAATT
1 GAAATTTTTTCTCATTTAAATCTGAAAATT
35991 GAAATTTTT
1 GAAATTTTT
36000 GAAAAGTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (30 bp):
GAAATTTTTTCTCATTTAAATCTGAAAATT
Found at i:37441 original size:136 final size:136
Alignment explanation
Indices: 37192--37648 Score: 603
Period size: 136 Copynumber: 3.4 Consensus size: 136
37182 CCGAAAGTAT
* * * * * *
37192 ACTTGTTCGACCTATTGCTCGATTCATGACATTTCGAATCAGCAATACCACTCTTGAGGGATTGA
1 ACTTGTTCGACCTATTGCTCGATTCACGATATTTCGAATCAGTAATACCTCACTTGAGGGATTAA
* * * *
37257 CATTTCGAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTTATAATG
66 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATG
*
37322 AAAAGA
131 AGAAGA
* * * *
37328 AATTGTTGGACCTATTGCTCGATTCACGGTATTTCGAATCAGTAATACCTCACTTGAGGGATCAA
1 ACTTGTTCGACCTATTGCTCGATTCACGATATTTCGAATCAGTAATACCTCACTTGAGGGATTAA
*
37393 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGATAAGAAGTTCATAATG
66 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATG
37458 AGAAGA
131 AGAAGA
* * * * ** * *
37464 ACTTGTTCAACCTATTGCTCGATTCACAATATTTCAAATCAGTAACACCTTGCTTAAAGGATTAA
1 ACTTGTTCGACCTATTGCTCGATTCACGATATTTCGAATCAGTAATACCTCACTTGAGGGATTAA
* * * *
37529 CATTTCCAATGGAGAGTTCATATTGAGAAGTACTCATCCG-TCGAAGGGAGAATAAGTTCATAAT
66 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAT-AAAGGGAGAAGAAGTTCATAAT
37593 GAGAAGA
130 GAGAAGA
* * *
37600 ACTTGTTCGACCTATTGCTTGATTCACGACATTTCAAATCTA-TAATACC
1 ACTTGTTCGACCTATTGCTCGATTCACGATATTTCGAATC-AGTAATACC
37649 CCAAACATCA
Statistics
Matches: 281, Mismatches: 38, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
135 1 0.00
136 279 0.99
137 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (136 bp):
ACTTGTTCGACCTATTGCTCGATTCACGATATTTCGAATCAGTAATACCTCACTTGAGGGATTAA
CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATG
AGAAGA
Found at i:39373 original size:54 final size:54
Alignment explanation
Indices: 39309--39426 Score: 128
Period size: 54 Copynumber: 2.2 Consensus size: 54
39299 AACGGTGCAT
* * * **
39309 TTTCGACACTAAATGTGCAACCCATTGTATTCATAATGTGTTTATGAATAACCA
1 TTTCGGCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAACCA
** * * **
39363 TTTCGGCACTATGTGTGCAATCCATGGAATTCATAATAAGTTTGTGAATTTCCA
1 TTTCGGCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAACCA
*
39417 TTTTGGCACT
1 TTTCGGCACT
39427 TTGGTGCAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (54 bp):
TTTCGGCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAACCA
Found at i:44575 original size:90 final size:89
Alignment explanation
Indices: 44423--44595 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
44413 ACACACCCTT
44423 TTATAGCCAAGTTAACCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTAACCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
*
44488 ATTAATTAAAATTTAATAATCCTC
66 ATTAATTAAAATTAAATAATCCTC
* *
44512 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTAACCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
*
44577 AATTAATTGAAATTAAATA
65 AATTAATTAAAATTAAATA
44596 TTCAGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 29 0.37
90 50 0.63
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (89 bp):
TTATAGCCAAGTTAACCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTAAAATTAAATAATCCTC
Found at i:47634 original size:54 final size:54
Alignment explanation
Indices: 47573--47690 Score: 146
Period size: 54 Copynumber: 2.2 Consensus size: 54
47563 AACGGTGCAT
* * **
47573 TTTCGGCACTAAATGTGCAACCCATGGTATTCATAATGTGTTTATGAATAACCA
1 TTTCGGCACTAAATGTGCAACCCATAGAATTCATAATAAGTTTATGAATAACCA
** * * **
47627 TTTCGGCACTATGTGTGCAATCCATAGAATTCATAATAAGTTTGTGAATTTCCA
1 TTTCGGCACTAAATGTGCAACCCATAGAATTCATAATAAGTTTATGAATAACCA
47681 TTTCGGCACT
1 TTTCGGCACT
47691 TCGGTGCAGT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (54 bp):
TTTCGGCACTAAATGTGCAACCCATAGAATTCATAATAAGTTTATGAATAACCA
Found at i:48585 original size:136 final size:135
Alignment explanation
Indices: 48325--48612 Score: 335
Period size: 136 Copynumber: 2.1 Consensus size: 135
48315 GGGATTAACA
* *
48325 TTCATAATTAGAAGAACTCATCAGACAGAGGGAGAAGAATTCATAATGAGAAGAACTTGTTCGAC
1 TTCATAATGAGAAGAACTCATCAGACAAAGGGAGAAGAATTCATAATGAGAAGAACTTGTTCGAC
* ** * ** * * *
48390 CTATTGCTCGATTCACGGCATTTCGAATCAGCAACACCTCGCTTGAGTGATTAATATTTCCAATT
66 CTATTGCTCAATTCACGAAATTTCGAATCAGCAACACCTCACTCAAGTGATCAACATTTCCAATA
*
48455 GAGAG
131 GAAAG
* * *
48460 TTCATTATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGA
1 TTCATAATGAGAAGAACTCATCAGACAAAGGGAGAAGAA-TTCATAATGAGAAGAACTTGTTCGA
* * * * * * *
48525 CTTATTGCTTAATTCATGAAATTTTGAATCAGTAACGCCTCACTCAAG-GAATCAACATTTCCAG
65 CCTATTGCTCAATTCACGAAATTTCGAATCAGCAACACCTCACTCAAGTG-ATCAACATTTCCAA
48589 TAGAAAG
129 TAGAAAG
* *
48596 ATCATGATGAGAAGAAC
1 TTCATAATGAGAAGAAC
48613 CTATAGCATG
Statistics
Matches: 127, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
135 35 0.28
136 92 0.72
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (135 bp):
TTCATAATGAGAAGAACTCATCAGACAAAGGGAGAAGAATTCATAATGAGAAGAACTTGTTCGAC
CTATTGCTCAATTCACGAAATTTCGAATCAGCAACACCTCACTCAAGTGATCAACATTTCCAATA
GAAAG
Found at i:50593 original size:10 final size:10
Alignment explanation
Indices: 50578--50607 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
50568 ATGAATCTAA
*
50578 AAATTAATTT
1 AAATTAATAT
50588 AAATTAATAT
1 AAATTAATAT
50598 AAATTAATAT
1 AAATTAATAT
50608 TAGAGTCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AAATTAATAT
Found at i:51987 original size:48 final size:45
Alignment explanation
Indices: 51918--52099 Score: 221
Period size: 48 Copynumber: 4.1 Consensus size: 45
51908 ATCCAAGGCT
* * * *
51918 TTTG-ATTATTGGGTTGTCAAAAGTAAAATCAAAGGATTTGTTCAT
1 TTTGAATTATTGTGTTGCCAAAAGTAAAATCAAAGGATTAGTTC-C
*
51963 TTTGATTATTATTGTGTTGCCAAAAGTAAAATCAATGGATTAGTTCC
1 TTTGA--ATTATTGTGTTGCCAAAAGTAAAATCAAAGGATTAGTTCC
52010 TTTG-ATTATTGT-TT-CCAAAAGTAAAATCAAAGGATTAGTTCC
1 TTTGAATTATTGTGTTGCCAAAAGTAAAATCAAAGGATTAGTTCC
* * *
52052 TTTCAATTATTG-GATTGCAAAAATTAAAATCAAAGGATTAGTTCC
1 TTTGAATTATTGTG-TTGCCAAAAGTAAAATCAAAGGATTAGTTCC
52097 TTT
1 TTT
52100 TGATTTTTGG
Statistics
Matches: 121, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
42 30 0.25
43 9 0.07
44 10 0.08
45 33 0.27
47 4 0.03
48 35 0.29
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.40
Consensus pattern (45 bp):
TTTGAATTATTGTGTTGCCAAAAGTAAAATCAAAGGATTAGTTCC
Found at i:52124 original size:45 final size:45
Alignment explanation
Indices: 51916--52113 Score: 240
Period size: 45 Copynumber: 4.4 Consensus size: 45
51906 TAATCCAAGG
* *
51916 CTTTTGATTATTGGGTTGTCAAAAGTAAAATCAAAGGATTTGTTC
1 CTTTTGATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAGTTC
* * *
51961 ATTTTGATTATTATTGTGTTGCCAAAAGTAAAATCAATGGATTAGTTC
1 CTTTTG---ATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAGTTC
*
52009 C-TTTGATTATT--GTTTCCAAAAGTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAGTTC
** * * *
52051 CTTTCAATTATTGGATTGCAAAAATTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAGTTC
*
52096 CTTTTGATTTTTGGGTTG
1 CTTTTGATTATTGGGTTG
52114 GTAAAATTAA
Statistics
Matches: 129, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
42 30 0.23
43 8 0.06
44 6 0.05
45 46 0.36
47 4 0.03
48 35 0.27
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (45 bp):
CTTTTGATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAGTTC
Found at i:52344 original size:58 final size:58
Alignment explanation
Indices: 52273--52463 Score: 292
Period size: 58 Copynumber: 3.3 Consensus size: 58
52263 AATCTTGCAT
* *
52273 TGATTCTAACTTTGTAAGGAAAATAGATTTTTGAATTTATTTACTTGGGAATCTTAAA
1 TGATTCTAACTTTGTAAGGAAAATAGATTTTTGAATTTATTTCCTTGAGAATCTTAAA
* * * * * *
52331 TGATTCTAGCTTTGTAAGGAAAATATATCTTTAAATATATTTCCTTGAGAATCTTTAA
1 TGATTCTAACTTTGTAAGGAAAATAGATTTTTGAATTTATTTCCTTGAGAATCTTAAA
* *
52389 TGATTCTAAATTTGTAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGGAAAATAGATTTTTGAATTTATTTCCTTGAGAATCTTAAA
52447 TGATTCTAACTTTGTAA
1 TGATTCTAACTTTGTAA
52464 TTGTTGAATT
Statistics
Matches: 116, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 116 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (58 bp):
TGATTCTAACTTTGTAAGGAAAATAGATTTTTGAATTTATTTCCTTGAGAATCTTAAA
Found at i:52471 original size:48 final size:48
Alignment explanation
Indices: 52415--52507 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 48
52405 AGGAAAATAG
*
52415 ATTGTTGAATTTATTTCCTT-GAGAATCTTAAATGATTCTAACTTTGTA
1 ATTGTTGAATTTATTTCCTTGGA-AATATTAAATGATTCTAACTTTGTA
* *
52463 ATTGTTGAATTTATTTCCTTGGAAATATTGAATGATTTTAACTTT
1 ATTGTTGAATTTATTTCCTTGGAAATATTAAATGATTCTAACTTT
52508 ATAAGAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 39 0.95
49 2 0.05
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (48 bp):
ATTGTTGAATTTATTTCCTTGGAAATATTAAATGATTCTAACTTTGTA
Found at i:52556 original size:106 final size:106
Alignment explanation
Indices: 52368--52560 Score: 262
Period size: 106 Copynumber: 1.8 Consensus size: 106
52358 TCTTTAAATA
* * * * * **
52368 TATTTCCTTGAGAATCTTTAATGATTCTAAATTTGTAAGGAAAATAGATTGTTGAATTTATTTCC
1 TATTTCCTTGAGAATATTGAATGATTCTAAATTTATAAGAAAAATAAATTGTCAAATTTATTTCC
*
52433 TTGAGAATCTTAAATGATTCTAACTTTGTAATTGTTGAATT
66 TTGAGAATCGTAAATGATTCTAACTTTGTAATTGTTGAATT
* * *
52474 TATTTCCTTG-GAAATATTGAATGATTTTAACTTTATAAGAAAAATAAATTGTCAAATTTATTTT
1 TATTTCCTTGAG-AATATTGAATGATTCTAAATTTATAAGAAAAATAAATTGTCAAATTTATTTC
*
52538 CTTGAGAATCGTAGATGATTCTA
65 CTTGAGAATCGTAAATGATTCTA
52561 TCATTTAAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
105 1 0.01
106 73 0.99
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.44
Consensus pattern (106 bp):
TATTTCCTTGAGAATATTGAATGATTCTAAATTTATAAGAAAAATAAATTGTCAAATTTATTTCC
TTGAGAATCGTAAATGATTCTAACTTTGTAATTGTTGAATT
Found at i:52657 original size:55 final size:55
Alignment explanation
Indices: 52566--52715 Score: 194
Period size: 55 Copynumber: 2.7 Consensus size: 55
52556 TTCTATCATT
* * * * * *
52566 TAAAAAGAAATAACTTGTTAAAATTATTTTCTTGTTTTGTTATTTTCCT-ATTGTG
1 TAAAAGGAAATAAATCGTTGAATTTATTTTCATGTTTTGTTATTTT-CTGATTGTG
* * *
52621 TAAAAGGAAATAAATCGTTGAATTTAGTTTCCTGTTTTGTTATTTTTTGATTGTG
1 TAAAAGGAAATAAATCGTTGAATTTATTTTCATGTTTTGTTATTTTCTGATTGTG
*
52676 TAAAAGGAAATAAATCGTAGAATTTATTTTCATGTTTTGT
1 TAAAAGGAAATAAATCGTTGAATTTATTTTCATGTTTTGT
52716 AGAATAAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
54 1 0.01
55 82 0.99
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (55 bp):
TAAAAGGAAATAAATCGTTGAATTTATTTTCATGTTTTGTTATTTTCTGATTGTG
Found at i:52814 original size:39 final size:39
Alignment explanation
Indices: 52771--52884 Score: 147
Period size: 39 Copynumber: 2.9 Consensus size: 39
52761 GATTATGATA
* **
52771 TGTAAAAGGAAATAAATCGTTCGATTTATTTTCCTATCT
1 TGTAAAAGGAAATAAATCATTAAATTTATTTTCCTATCT
* * * *
52810 TGTAAAAGGAAATAAATCATAAAATTTATTTTCGTGTTT
1 TGTAAAAGGAAATAAATCATTAAATTTATTTTCCTATCT
* *
52849 TGAAAAAGGAAATAAATCAATAAATTTATTTTCCTA
1 TGTAAAAGGAAATAAATCATTAAATTTATTTTCCTA
52885 AGAACCTTGT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (39 bp):
TGTAAAAGGAAATAAATCATTAAATTTATTTTCCTATCT
Found at i:52838 original size:136 final size:136
Alignment explanation
Indices: 52674--52924 Score: 376
Period size: 136 Copynumber: 1.8 Consensus size: 136
52664 TTTTTGATTG
* * * * * **
52674 TGTAAAAGGAAATAAATCGTAGAATTTATTTTCATGTTTTGTAGAATAAAATAAATCGTTAAATT
1 TGTAAAAGGAAATAAATCATAAAATTTATTTTCATGTTTTGAAAAAGAAAATAAATCAATAAATT
* **
52739 TATTTTCCTATGAATTTTATATGATTATGATATGTAAAAGGAAATAAATCGTTCGATTTATTTTC
66 TATTTTCCTAAGAACCTTATATGATTATGATATGTAAAAGGAAATAAATCGTTCGATTTATTTTC
52804 CTATCT
131 CTATCT
* *
52810 TGTAAAAGGAAATAAATCATAAAATTTATTTTCGTGTTTTGAAAAAGGAAATAAATCAATAAATT
1 TGTAAAAGGAAATAAATCATAAAATTTATTTTCATGTTTTGAAAAAGAAAATAAATCAATAAATT
* *
52875 TATTTTCCTAAGAACCTTGTATGATTCTGATATGTAAAAGGAAATAAATC
66 TATTTTCCTAAGAACCTTATATGATTATGATATGTAAAAGGAAATAAATC
52925 ATAGAATTTA
Statistics
Matches: 101, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
136 101 1.00
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.39
Consensus pattern (136 bp):
TGTAAAAGGAAATAAATCATAAAATTTATTTTCATGTTTTGAAAAAGAAAATAAATCAATAAATT
TATTTTCCTAAGAACCTTATATGATTATGATATGTAAAAGGAAATAAATCGTTCGATTTATTTTC
CTATCT
Found at i:52978 original size:98 final size:97
Alignment explanation
Indices: 52810--53077 Score: 369
Period size: 98 Copynumber: 2.7 Consensus size: 97
52800 TTTCCTATCT
*
52810 TGTAAAAGGAAATAAATCATAAAATTTATTTTCGTGTTTTGAAAAAGGAAATAAATCAATAAATT
1 TGTAAAAGGAAATAAATCATAGAATTTATTTTCGTGTTTTGAAAAAGGAAATAAATCAATAAATT
52875 TATTTTCCTAAGAACCTTGTATGATTCTGATA
66 TATTTTCCTAAGAACCTTGTATGATTCTGATA
* * ***
52907 TGTAAAAGGAAATAAATCATAGAATTTACTTTTTGTGTTTTGAAAAATGAAATAAATTGGTAAAT
1 TGTAAAAGGAAATAAATCATAGAATTTA-TTTTCGTGTTTTGAAAAAGGAAATAAATCAATAAAT
* * *
52972 TTATTTTCCTATGAATCTTGTATGATTTTGATA
65 TTATTTTCCTAAGAACCTTGTATGATTCTGATA
* * * *
53005 TGTAAAAGGAAATAAATCGATAG-ATTTATATTCCTATATTGAAAAAGGAAATAAATC-ATAGAA
1 TGTAAAAGGAAATAAATC-ATAGAATTTATTTTCGTGTTTTGAAAAAGGAAATAAATCAATA-AA
53068 TTTAGTTTTC
64 TTTA-TTTTC
53078 TAGTTTGTAA
Statistics
Matches: 150, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
96 2 0.01
97 55 0.37
98 89 0.59
99 4 0.03
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.38
Consensus pattern (97 bp):
TGTAAAAGGAAATAAATCATAGAATTTATTTTCGTGTTTTGAAAAAGGAAATAAATCAATAAATT
TATTTTCCTAAGAACCTTGTATGATTCTGATA
Found at i:53010 original size:234 final size:233
Alignment explanation
Indices: 52674--53099 Score: 649
Period size: 234 Copynumber: 1.8 Consensus size: 233
52664 TTTTTGATTG
* * * *
52674 TGTAAAAGGAAATAAATCGTAGAATTTATTTTCATGTTTTGTAGAATAAAATAAATCGTTAAATT
1 TGTAAAAGGAAATAAATCATAGAATTTATTTTCATGTTTTGAAAAATAAAATAAATCGGTAAATT
* * * *
52739 TATTTTCCTATGAATTTTATATGATTATGATATGTAAAAGGAAATAAATCGTTCGATTTATTTTC
66 TATTTTCCTATGAATCTTATATGATTATGATATGTAAAAGGAAATAAATCGATAGATTTATATTC
* *
52804 CTATCTTGTAAAAGGAAATAAATCATAAAATTTA-TTTTCGT-GTTTTGAAAAAGGAAATAAATC
131 CTATATTGAAAAAGGAAATAAATCATAAAATTTAGTTTTC-TAG-TTTGAAAAAGGAAATAAATC
52867 AATAAATTTATTTTCCTAAGAACCTTGTATGATTCTGATA
194 AATAAATTTATTTTCCTAAGAACCTTGTATGATTCTGATA
** * *
52907 TGTAAAAGGAAATAAATCATAGAATTTACTTTTTGTGTTTTGAAAAATGAAATAAATTGGTAAAT
1 TGTAAAAGGAAATAAATCATAGAATTTA-TTTTCATGTTTTGAAAAATAAAATAAATCGGTAAAT
* *
52972 TTATTTTCCTATGAATCTTGTATGATTTTGATATGTAAAAGGAAATAAATCGATAGATTTATATT
65 TTATTTTCCTATGAATCTTATATGATTATGATATGTAAAAGGAAATAAATCGATAGATTTATATT
* *
53037 CCTATATTGAAAAAGGAAATAAATCATAGAATTTAGTTTTCTAGTTTGTAAAAGGAAATAAAT
130 CCTATATTGAAAAAGGAAATAAATCATAAAATTTAGTTTTCTAGTTTGAAAAAGGAAATAAAT
53100 TGTTATATTT
Statistics
Matches: 172, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
233 27 0.16
234 139 0.81
235 6 0.03
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (233 bp):
TGTAAAAGGAAATAAATCATAGAATTTATTTTCATGTTTTGAAAAATAAAATAAATCGGTAAATT
TATTTTCCTATGAATCTTATATGATTATGATATGTAAAAGGAAATAAATCGATAGATTTATATTC
CTATATTGAAAAAGGAAATAAATCATAAAATTTAGTTTTCTAGTTTGAAAAAGGAAATAAATCAA
TAAATTTATTTTCCTAAGAACCTTGTATGATTCTGATA
Found at i:53071 original size:39 final size:39
Alignment explanation
Indices: 53008--53307 Score: 211
Period size: 39 Copynumber: 7.4 Consensus size: 39
52998 TTTGATATGT
* *
53008 AAAAGGAAATAAATCGATAG-ATTTATATTCCTATATTGA
1 AAAAGGAAATAAATC-ATAGAATTTATTTTCCTATTTTGA
* *
53047 AAAAGGAAATAAATCATAGAATTTAGTTTT-CTAGTTTGT
1 AAAAGGAAATAAATCATAGAATTTA-TTTTCCTATTTTGA
** * * *
53086 AAAAGGAAATAAATTGTTA-TATTTAATTTCCTATTTTGT
1 AAAAGGAAATAAA-TCATAGAATTTATTTTCCTATTTTGA
* * *
53125 AACAGGAAATAAATTGAAACAAATCGTACGATTTATTTTCCTGTTTTGTA
1 AAAAGGAAATAAA-T----C--ATAG-A--ATTTATTTTCCTATTTTG-A
** * *
53175 AAATTG-AATAAATCGTAGGATTTATTTTCCTATTTTGTA
1 AAAAGGAAATAAATCATAGAATTTATTTTCCTATTTTG-A
*
53214 AAAA-GAAATAAATCATTAG-ATTTATTTTCCTATTTTGC
1 AAAAGGAAATAAATCA-TAGAATTTATTTTCCTATTTTGA
*
53252 AAAAGGAAATAAA-CAGTTA-AATTTATTTTCCTATTTTGT
1 AAAAGGAAATAAATCA--TAGAATTTATTTTCCTATTTTGA
*
53291 AAAAGAAAATAAATCAT
1 AAAAGGAAATAAATCAT
53308 TGGATTTTTT
Statistics
Matches: 211, Mismatches: 29, Indels: 43
0.75 0.10 0.15
Matches are distributed among these distances:
38 15 0.07
39 155 0.73
40 11 0.05
42 2 0.01
44 1 0.00
45 1 0.00
48 1 0.00
49 22 0.10
50 3 0.01
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (39 bp):
AAAAGGAAATAAATCATAGAATTTATTTTCCTATTTTGA
Found at i:53134 original size:78 final size:78
Alignment explanation
Indices: 53005--53307 Score: 269
Period size: 78 Copynumber: 3.8 Consensus size: 78
52995 GATTTTGATA
* * *
53005 TGTAAAAGGAAATAAATCGATAGATTT-ATATTCCTATATTGAAAAAGGAAATAAATCATAGAAT
1 TGTAAAAGGAAATAAATCGTTAGATTTAAT-TTCCTATTTTGTAAAAGGAAATAAATCATAGAAT
53069 TTAGTTTT-CTAGTT
65 TTA-TTTTCCTAGTT
* * *
53083 TGTAAAAGGAAATAAATTGTTATATTTAATTTCCTATTTTGTAACAGGAAATAAATTGAAACAAA
1 TGTAAAAGGAAATAAATCGTTAGATTTAATTTCCTATTTTGTAAAAGGAAATAAA-T----C--A
*
53148 TCGTACGATTTATTTTCCT-GTTT
59 TAG-A--ATTTATTTTCCTAG-TT
* * *
53171 TGTAAAATTG-AATAAATCG-TAGGATTTATTTTCCTATTTTGTAAAAAGAAATAAATCATTAG-
1 TGTAAAA-GGAAATAAATCGTTA-GATTTAATTTCCTATTTTGTAAAAGGAAATAAATCA-TAGA
*
53233 ATTTATTTTCCTATTT
63 ATTTATTTTCCTAGTT
* * * *
53249 TGCAAAAGGAAATAAA-CAGTTAAATTTATTTTCCTATTTTGTAAAAGAAAATAAATCAT
1 TGTAAAAGGAAATAAATC-GTTAGATTTAATTTCCTATTTTGTAAAAGGAAATAAATCAT
53308 TGGATTTTTT
Statistics
Matches: 185, Mismatches: 20, Indels: 41
0.75 0.08 0.17
Matches are distributed among these distances:
77 3 0.02
78 106 0.57
79 5 0.03
81 1 0.01
82 2 0.01
83 2 0.01
85 3 0.02
86 1 0.01
87 8 0.04
88 53 0.29
89 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (78 bp):
TGTAAAAGGAAATAAATCGTTAGATTTAATTTCCTATTTTGTAAAAGGAAATAAATCATAGAATT
TATTTTCCTAGTT
Found at i:55328 original size:108 final size:108
Alignment explanation
Indices: 55119--55370 Score: 303
Period size: 108 Copynumber: 2.3 Consensus size: 108
55109 TCACTAAACA
* * *
55119 TGACCAAAATGCAAAAACACGCCTAAATAAGGGGGACTAAATAGAAAATATTCCAAAAAATACAT
1 TGACCAACATGCAAAAACACG-CTAAATAAGGGGGACTAAACAGAAAATATCCCAAAAAATACAT
* *
55184 AACATTCATGAAAATGGGTAAATAACAACTTCGGTCC-CTACAGG
65 AACATGCATGAAAATGGGTAAATAACAACTTAGGTCCTC-ACAGG
* * * *
55228 TGACCAACATGTAAAAACACGCTAAACTATGGGGGACTAAACA-ACAAATA-CCCTAAAAATATA
1 TGACCAACATGCAAAAACACGCTAAA-TAAGGGGGACTAAACAGA-AAATATCCCAAAAAATACA
* *
55291 TAGCATGCATGAAAATGGGTAAATAATAACTTAGGTCCTCACAGG
64 TAACATGCATGAAAATGGGTAAATAACAACTTAGGTCCTCACAGG
* * *
55336 TGACTAACATGGAAAAACACTGCTAACTTAAGGGG
1 TGACCAACATGCAAAAACAC-GCTAA-ATAAGGGG
55371 ACCTATGTGT
Statistics
Matches: 123, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
108 73 0.59
109 50 0.41
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (108 bp):
TGACCAACATGCAAAAACACGCTAAATAAGGGGGACTAAACAGAAAATATCCCAAAAAATACATA
ACATGCATGAAAATGGGTAAATAACAACTTAGGTCCTCACAGG
Found at i:56348 original size:6 final size:6
Alignment explanation
Indices: 56337--56403 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
56327 TGGGCCTGAG
*
56337 AAATAA AAATAA AGATAA TATAA-ATA AAATAA AAAT-A AAAT-A AAATAA
1 AAATAA AAATAA AAATAA -A-AATA-A AAATAA AAATAA AAATAA AAATAA
* *
56385 ATAATAG AAATAA TAATAA
1 A-AATAA AAATAA AAATAA
56404 TTAATAACAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
5 10 0.20
6 29 0.58
7 9 0.18
8 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (6 bp):
AAATAA
Found at i:56363 original size:9 final size:9
Alignment explanation
Indices: 56339--56409 Score: 60
Period size: 9 Copynumber: 8.1 Consensus size: 9
56329 GGCCTGAGAA
56339 ATAAA-AAT
1 ATAAATAAT
56347 A-AAGATAAT
1 ATAA-ATAAT
*
56356 ATAAATAAA
1 ATAAATAAT
56365 ATAAA-AAT
1 ATAAATAAT
*
56373 A-AAATAAA
1 ATAAATAAT
56381 ATAAATAAT
1 ATAAATAAT
*
56390 AGAAATAAT
1 ATAAATAAT
*
56399 AATAATTAAT
1 -ATAAATAAT
56409 A
1 A
56410 ACATTAATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
7 5 0.10
8 8 0.16
9 28 0.56
10 9 0.18
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (9 bp):
ATAAATAAT
Found at i:56366 original size:5 final size:5
Alignment explanation
Indices: 56337--56385 Score: 55
Period size: 5 Copynumber: 9.4 Consensus size: 5
56327 TGGGCCTGAG
*
56337 AAATAA AAATA AAGATA ATAT- AAATA AAATAA AAATA AAATA AAATA
1 AAAT-A AAATA AA-ATA AAATA AAATA AAAT-A AAATA AAATA AAATA
56384 AA
1 AA
56386 TAATAGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
4 3 0.08
5 22 0.58
6 13 0.34
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:56367 original size:11 final size:11
Alignment explanation
Indices: 56337--56385 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
56327 TGGGCCTGAG
56337 AAATAAAA-AT
1 AAATAAAATAT
* *
56347 AAAGATAATAT
1 AAATAAAATAT
*
56358 AAATAAAATAA
1 AAATAAAATAT
56369 AAATAAAATA-
1 AAATAAAATAT
56379 AAATAAA
1 AAATAAA
56386 TAATAGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
10 13 0.39
11 20 0.61
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (11 bp):
AAATAAAATAT
Found at i:56939 original size:134 final size:133
Alignment explanation
Indices: 56630--56952 Score: 429
Period size: 133 Copynumber: 2.4 Consensus size: 133
56620 TTAAGGGTAG
* * * * * *
56630 ATCAGATCTGGAAACATTTATTAATTCGACTGTTCTTCAGTGAATATTGAATCGAGGCAGACTTG
1 ATCAGATCTGGAAACGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCGAGACAGACTTG
*
56695 TTCCACTGCTTCCTCGGGAAAGATCAAATCTGGAAAAAGGGATTTGTTTCGCTACTTCTTTAGGG
66 TTCCACTGCTTCCTCGGGAAAGATCAAATCTGGAAAAAGGGATTTGTTTCGCTACTTCTTCAGGG
56760 AAA
131 AAA
* * *
56763 ATCAGATCTGGAGACGTTGATTCATTCCACTATTCTTCAGGGAATATTGAATCGAGATAGACTTG
1 ATCAGATCTGGAAACGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCGAGACAGACTTG
* *
56828 TTCCACTG-TTCCTTGGGGAAA-ATCAAATCTGGAAAAACAAGGGATTTGCTTT-GCTGCTTCTT
66 TTCCACTGCTTCC-TCGGGAAAGATCAAATCTGG--AAA-AAGGGATTTG-TTTCGCTACTTCTT
56890 CA-GGAAA
126 CAGGGAAA
* * * *
56897 ATCATATCTAGAAACGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAATCGAG
1 ATCAGATCTGGAAACGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCGAG
56953 TTCAATTTGC
Statistics
Matches: 167, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
132 15 0.09
133 71 0.43
134 58 0.35
135 20 0.12
136 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (133 bp):
ATCAGATCTGGAAACGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCGAGACAGACTTG
TTCCACTGCTTCCTCGGGAAAGATCAAATCTGGAAAAAGGGATTTGTTTCGCTACTTCTTCAGGG
AAA
Found at i:59412 original size:18 final size:19
Alignment explanation
Indices: 59384--59419 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
59374 TTCCTTTAGG
59384 GGGGAAATCGATACCCCCA
1 GGGGAAATCGATACCCCCA
59403 GGGG-AATCGATACCCCC
1 GGGGAAATCGATACCCCC
59420 TAGACATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.28, C:0.33, G:0.28, T:0.11
Consensus pattern (19 bp):
GGGGAAATCGATACCCCCA
Done.