Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001596.1 Hibiscus syriacus cultivar Beakdansim tig00003178_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: 93557
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:181 original size:18 final size:18
Alignment explanation
Indices: 151--195 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
141 ACTTAGGGTA
*
151 TAGGTTT-ATGATTAGGT
1 TAGGTTTGATGATTAGGG
*
168 TAGGTTTGATGATTTGGG
1 TAGGTTTGATGATTAGGG
186 TAGGTTTGAT
1 TAGGTTTGAT
196 TCACTGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (18 bp):
TAGGTTTGATGATTAGGG
Found at i:2115 original size:20 final size:20
Alignment explanation
Indices: 2090--2129 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2080 ACTTGTTCTA
2090 AATCTGGGTGAGACCAAACT
1 AATCTGGGTGAGACCAAACT
2110 AATCTGGGTGAGACCAAACT
1 AATCTGGGTGAGACCAAACT
2130 GCTGTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (20 bp):
AATCTGGGTGAGACCAAACT
Found at i:4387 original size:59 final size:59
Alignment explanation
Indices: 4321--4457 Score: 197
Period size: 59 Copynumber: 2.3 Consensus size: 59
4311 GAGTCTATTG
*
4321 ACTATTAAAAGTTACAAAACAGTCCCCCAATTATAGGGTGTTACTTTATT-ATGTCCTTA
1 ACTATTAAAAGTTACAAAACAATCCCCCAATTATAGGGTGTTACTTTATTGA-GTCCTTA
* * * *
4380 ACTATTAAAAATTACAAAACAATTCTCCAATTATAGGGTGTTACTTTGTTGAGTCCTTA
1 ACTATTAAAAGTTACAAAACAATCCCCCAATTATAGGGTGTTACTTTATTGAGTCCTTA
4439 ACT-TCTAAAAGTTACAAAA
1 ACTAT-TAAAAGTTACAAAA
4458 TGATTACTCA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
58 1 0.01
59 68 0.97
60 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (59 bp):
ACTATTAAAAGTTACAAAACAATCCCCCAATTATAGGGTGTTACTTTATTGAGTCCTTA
Found at i:6296 original size:16 final size:15
Alignment explanation
Indices: 6277--6311 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
6267 AGACCCTGTT
6277 TCAAAAGATGGAACAC
1 TCAAAAGATGGAAC-C
6293 TCAAAAGATGGAACC
1 TCAAAAGATGGAACC
6308 TCAA
1 TCAA
6312 CATAAGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (15 bp):
TCAAAAGATGGAACC
Found at i:6845 original size:17 final size:18
Alignment explanation
Indices: 6825--6865 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
6815 AAGATATATA
*
6825 AAAATAA-AATAAATAAT
1 AAAATAAGAAAAAATAAT
6842 AAAA-AAGAAAAAATAAT
1 AAAATAAGAAAAAATAAT
*
6859 ATAATAA
1 AAAATAA
6866 CAAATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 16 0.80
18 2 0.10
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAATAAGAAAAAATAAT
Found at i:7565 original size:20 final size:18
Alignment explanation
Indices: 7542--7585 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
7532 AAAAACAAGC
*
7542 TAAACATCTTAAATCCTATT
1 TAAACA-CTTAAA-ACTATT
7562 TAAAACACTTAAAACTATT
1 T-AAACACTTAAAACTATT
7581 TAAAC
1 TAAAC
7586 TAAGATACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 7 0.32
21 5 0.23
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAACACTTAAAACTATT
Found at i:7581 original size:19 final size:21
Alignment explanation
Indices: 7543--7584 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
7533 AAAACAAGCT
*
7543 AAACATCTTAAATCCTATTTA
1 AAACATCTTAAATACTATTTA
7564 AAACA-CTTAAA-ACTATTTA
1 AAACATCTTAAATACTATTTA
7583 AA
1 AA
7585 CTAAGATACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 6 0.30
21 5 0.25
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (21 bp):
AAACATCTTAAATACTATTTA
Found at i:7676 original size:64 final size:64
Alignment explanation
Indices: 7554--7676 Score: 162
Period size: 64 Copynumber: 1.9 Consensus size: 64
7544 AACATCTTAA
* * *
7554 ATCCTATTTAAAACACTTAAAACTATTTAAACTAAGATACCTAAAAAATAATATAATATTCTAG
1 ATCCTAATTAAAACACTTAAAACTATTCAAACTAAGATACCTAAAAAATAATAAAATATTCTAG
*
7618 ATCCTAATTAAAATAC-TAAAACCTATTCAAACTAA-ATACCTAAAACAA-AGATAAAATAT
1 ATCCTAATTAAAACACTTAAAA-CTATTCAAACTAAGATACCTAAAA-AATA-ATAAAATAT
7677 AAAATAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
63 16 0.31
64 36 0.69
ACGTcount: A:0.53, C:0.15, G:0.02, T:0.29
Consensus pattern (64 bp):
ATCCTAATTAAAACACTTAAAACTATTCAAACTAAGATACCTAAAAAATAATAAAATATTCTAG
Found at i:7767 original size:75 final size:72
Alignment explanation
Indices: 7595--7743 Score: 174
Period size: 74 Copynumber: 2.0 Consensus size: 72
7585 CTAAGATACC
* * * * * *
7595 TAAAAAATAATATAATATTCTAGATCCTAATTAAAATACTAAAACCTATTCAAACTAAATACCTA
1 TAAAATATAAAATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTCAAACTAAATA-C-A
*
7660 AAACAAAGA
64 AAACAAAAA
*
7669 TAAAATATAAAATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATA-A
1 TAAAATATAAAATAATATCCTAAAACTTAATTAAAATACT-AAAACCTATTCAAACT-AAATACA
*
7733 AAATAAAAA
64 AAACAAAAA
7742 TA
1 TA
7744 TAATGTTTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
73 10 0.16
74 34 0.53
75 15 0.23
76 5 0.08
ACGTcount: A:0.59, C:0.12, G:0.01, T:0.28
Consensus pattern (72 bp):
TAAAATATAAAATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTCAAACTAAATACAAA
ACAAAAA
Found at i:9376 original size:14 final size:15
Alignment explanation
Indices: 9357--9388 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
9347 GCATCTGATA
9357 AAATAAAAT-AAAAT
1 AAATAAAATGAAAAT
9371 AAATAAAATGAAAAT
1 AAATAAAATGAAAAT
9386 AAA
1 AAA
9389 ATGAAATGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AAATAAAATGAAAAT
Found at i:9396 original size:5 final size:5
Alignment explanation
Indices: 9329--9395 Score: 64
Period size: 5 Copynumber: 13.0 Consensus size: 5
9319 TGTTCAGAGA
***
9329 AAAAT AAAAT AAAAT AAAGCAT CTGAT AAAAT AAAAT AAAAT -AAAT AAAAT
1 AAAAT AAAAT AAAAT AAA--AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
9380 GAAAAT AAAAT GAAAT
1 -AAAAT AAAAT AAAAT
9396 GGGTTACCTC
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
4 4 0.08
5 40 0.78
6 5 0.10
7 2 0.04
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:14899 original size:19 final size:18
Alignment explanation
Indices: 14861--14904 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
14851 GTTGTTTTAA
*
14861 AAATAAAAAATAAGAATT
1 AAATAAAAAAAAAGAATT
*
14879 AAATAAAAGAAAAATAATT
1 AAATAAAA-AAAAAGAATT
14898 AAATAAA
1 AAATAAA
14905 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (18 bp):
AAATAAAAAAAAAGAATT
Found at i:20011 original size:124 final size:124
Alignment explanation
Indices: 19781--20013 Score: 387
Period size: 124 Copynumber: 1.9 Consensus size: 124
19771 ATTGCAAGTC
*
19781 TCTTTCTTTCTTTGCATTTGCCTCAGCACCCAAATATTGTTACCTTGAAGGCTACTTATGAGGAT
1 TCTTTCTTTCTTTGCATTTGCCTCAGCACCCAAATATTGATACCTTGAAGGCTACTTATGAGGAT
* *
19846 GACAATGCGGTCCATTTGGTTATGGACTTGTGTGAATGTGGTGAGTCACTTTCTTTCTT
66 GACAATGCGGTCCATTTGGTTATGGACTTGTATGAAGGTGGTGAGTCACTTTCTTTCTT
* *
19905 TCTTTCTTTCTTTGCATTTGCCTCATCACGCAAATATTGATACCTTGAAGGCTACCTT-TGAGGA
1 TCTTTCTTTCTTTGCATTTGCCTCAGCACCCAAATATTGATACCTTGAAGGCTA-CTTATGAGGA
* *
19969 TGACAATGCGGTCCATTTTGTTATGGAGTTGTATGAAGGTGGTGA
65 TGACAATGCGGTCCATTTGGTTATGGACTTGTATGAAGGTGGTGA
20014 CTTATTTGAC
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
124 98 0.97
125 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (124 bp):
TCTTTCTTTCTTTGCATTTGCCTCAGCACCCAAATATTGATACCTTGAAGGCTACTTATGAGGAT
GACAATGCGGTCCATTTGGTTATGGACTTGTATGAAGGTGGTGAGTCACTTTCTTTCTT
Found at i:21640 original size:17 final size:17
Alignment explanation
Indices: 21618--21660 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
21608 CAACTTGAGC
21618 TGCTGCCCAAGTTTTGT
1 TGCTGCCCAAGTTTTGT
21635 TGCTGCCCAAGTTTTGT
1 TGCTGCCCAAGTTTTGT
21652 TGCTGCCCA
1 TGCTGCCCA
21661 CTCATATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.12, C:0.28, G:0.23, T:0.37
Consensus pattern (17 bp):
TGCTGCCCAAGTTTTGT
Found at i:29559 original size:57 final size:58
Alignment explanation
Indices: 29480--29588 Score: 184
Period size: 57 Copynumber: 1.9 Consensus size: 58
29470 GGTGCCATTT
*
29480 TTTCAGACAATGATGGGGGAAGGAGGAAGGGG-AGGCAAAAGGCCAGAACCATTTTTG
1 TTTCAGACAATGATGGGGGAAGGAGGAAGGGGAAGACAAAAGGCCAGAACCATTTTTG
* *
29537 TTTCAGACAATGATGGGGGAAGGAGGAAGGGGAAGACAGAAGGCCATAACCA
1 TTTCAGACAATGATGGGGGAAGGAGGAAGGGGAAGACAAAAGGCCAGAACCA
29589 GAAAGGTTGG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
57 32 0.67
58 16 0.33
ACGTcount: A:0.36, C:0.13, G:0.37, T:0.15
Consensus pattern (58 bp):
TTTCAGACAATGATGGGGGAAGGAGGAAGGGGAAGACAAAAGGCCAGAACCATTTTTG
Found at i:34626 original size:12 final size:12
Alignment explanation
Indices: 34594--34639 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
34584 GGGTCTGAAA
*
34594 AATAAAAATATT
1 AATAATAATATT
*
34606 AATTAATAATTTT
1 AA-TAATAATATT
34619 AATAATAATATT
1 AATAATAATATT
*
34631 AATATTAAT
1 AATAATAAT
34640 TTCGGATGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AATAATAATATT
Found at i:35181 original size:233 final size:230
Alignment explanation
Indices: 34774--35619 Score: 1090
Period size: 233 Copynumber: 3.6 Consensus size: 230
34764 GAGAGGGACC
* * * * * * *
34774 TGTGAAAACATCTTGCCTAAAGGTCTTATTAATGGCTCGAAAGACTTATCACCTTGTTCGAAAGA
1 TGTGAAAACATCATGCCCAAAGGTCTTA-TAATAGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* *
34839 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAATGACTTACTGATGGCCTGAAGGACTT
65 CTTACAGATAACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCC-GAAGGACTT
34904 ATAAATTTTGGAAATAGTTTACTAAGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCA
129 ATAAATTTTGGAAATAGTTTACT-AGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCA
*
34969 AATTTGAACGAGAAACCTTTCTCATTTTTCGAGAGACA
193 AATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
* *
35007 TGTGAAAACATCATGCCCAAAGGTCTTATGGATAGCCCGAAGGACTTACCATCTTGCTCGAAAGA
1 TGTGAAAACATCATGCCCAAAGGTCTTAT-AATAGCCCGAAGGACTTATCATCTTGCTCGAAAGA
*
35072 CTTACAGATAACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCTCGAAGGACTT
65 CTTACAGATAACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGC-CGAAGGACTT
**
35137 ATAAATTTTGGAAATAGTTTTTTATGTAAGAAACCTTTCTTACTTTTCAAAAATTT-ATATTTTC
129 ATAAATTTTGGAAATAGTTTACTA-GTAAGAAACCTTTCTTACTTTTCAAAAATTTCA-ATTTTC
* *
35201 AAATCTGAATGAGAAATCTTTCTCATTTTTCGAGAGACA
192 AAATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
* * * * * * *
35240 TGTGAAAACATCTTACCCGAAGGACTTATAGATGGCCAGAATGACTTATCATCTTGCTCGAAAGA
1 TGTGAAAACATCATGCCCAAAGGTCTTATA-ATAGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * * * *
35305 CTTA-AAAGTGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTGCTGATGGACCGAATGACT
65 CTTACAGA-TAACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGG-CCGAAGGACT
*
35369 TATAAATTTTGGAAATAGTTTACTAGATAAGAAACCTTTCTCACTTTTCAAAAATTTCAAATTTT
128 TATAAATTTTGGAAATAGTTTACTAG-TAAGAAACCTTTCTTACTTTTCAAAAATTTC-AATTTT
* * * *
35434 CAGATTTAAATGAGAAACCTTTCTCATATTTCGATAGACA
191 CAAATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
* * * * * * * *
35474 TGTGAAAACAT-ACTGCCGAAAGTTCTTATAAAAGGCTCGAAGGATTTATGATCTTGCTCAAAAT
1 TGTGAAAACATCA-TGCCCAAAGGTCTTATAATA-GCCCGAAGGACTTATCATCTTGCTCGAAAG
* * * *
35538 ACTTACAGATAACCCGAATGATTTAAGAATCA-GACTCGAAAGACTTACTGATGACCCGAAGGAT
64 ACTTACAGATAACCCGAAGGATTTAAGCATCATG-CTCAAAAGACTTACTGATG-GCCGAAGGA-
35602 CTTAT-AATTTTGGAAATA
126 CTTATAAATTTTGGAAATA
35620 TTTTTCGAGA
Statistics
Matches: 534, Mismatches: 63, Indels: 31
0.85 0.10 0.05
Matches are distributed among these distances:
232 6 0.01
233 370 0.69
234 150 0.28
235 8 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (230 bp):
TGTGAAAACATCATGCCCAAAGGTCTTATAATAGCCCGAAGGACTTATCATCTTGCTCGAAAGAC
TTACAGATAACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCGAAGGACTTAT
AAATTTTGGAAATAGTTTACTAGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAAT
TTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
Found at i:39891 original size:22 final size:22
Alignment explanation
Indices: 39866--39907 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
39856 CAATTCATTT
39866 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
39888 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
39908 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:40265 original size:25 final size:24
Alignment explanation
Indices: 40227--40275 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
40217 ATTTTTTTTT
**
40227 AAAAACAAAAAAAAGGCAAAAAAA
1 AAAAACAAAAAAAACACAAAAAAA
40251 AAAACACAAAAAAAACACAAAAAAA
1 AAAA-ACAAAAAAAACACAAAAAAA
40276 GCCAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (24 bp):
AAAAACAAAAAAAACACAAAAAAA
Found at i:40282 original size:10 final size:11
Alignment explanation
Indices: 40247--40275 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
40237 AAAAGGCAAA
40247 AAAAAAAACAC
1 AAAAAAAACAC
40258 AAAAAAAACAC
1 AAAAAAAACAC
40269 AAAAAAA
1 AAAAAAA
40276 GCCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAC
Found at i:44604 original size:22 final size:22
Alignment explanation
Indices: 44579--44620 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
44569 CAATTCATTT
44579 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
44601 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
44621 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:48707 original size:234 final size:229
Alignment explanation
Indices: 48298--49611 Score: 1545
Period size: 234 Copynumber: 5.7 Consensus size: 229
48288 AAGAGGGACC
*
48298 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGTCCGAAAGAATTATCATCTTGCTC-AACAG
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGG-CCGAAAGACTTATCATCTTGCTCGAA-AG
* * * * *
48362 ACTTACAAATGACCCAAAGGATTTAAGCATCATGCTCAAAAGAGTTACTGATTGCCTGAAGGACT
64 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACT
* * *
48427 TATAAATTTTGTAAATAGTTTACTAAGTAAGAAACCTTTCTTACTTTTTGAAAAAAAATTATTTT
129 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTAC-TTTT--AAAAAATTTATTTT
*
48492 CAAATTTGAATAAGAAACCTTTCTCATTTTTCGAGAGACA
191 CAAATTTGAATGAGAAACCTTTCTCATTTTT-GAGAGACA
* * * *
48532 TGTGAAAACATCATGCCCAAAGGTCTTATGGATGGGTCGAAGGACTTACCATCTTGCTCGAAAGA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGAT-GGCCGAAAGACTTATCATCTTGCTCGAAAGA
* * * * * * * *
48597 CTTAGAGATGACCCAAAGGATTTAATCATCATGCTCCAAAGACTTATTGAAGGCTCGAAGGAATT
65 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTT
* * *
48662 ATAAATTTTGGAAATAGTTTTCTATGTAAGAAACCATTT-TTACTTTTCAAAAATTTATATTTGC
130 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACC-TTTCTTACTTTTAAAAAATTTAT-TTT-C
* *
48726 AAATATGAATGAGAAACCTTTCTCATTGTTTGAGAGATA
192 AAATTTGAATGAGAAACCTTTCTCATT-TTTGAGAGACA
* * * * *
48765 TGTGAAAACATCTTACCCTGAAGGACTTATGGATGGCCAGAAAGACTTATCATCTTTCTCGAAAG
1 TGTGAAAACATCCTGCCC-AAAGGTCTTATGGATGGCC-GAAAGACTTATCATCTTGCTCGAAAG
* * * * *
48830 AATTACAGATGACCCGAAGGATTTAAGAATCATGTTCAAAAGACTTGCTGATGGACCGAAGGACT
64 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACT
* * * *
48895 TATAAATTTTGGAAATAGATTACTAGGTAAGAAATCTTTCTTAGTTTTCAAAAATTTCAAATTTT
129 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTAAAAAATTT---ATTTT
* * * * *
48960 TAGATTTAAATGAGAAACCTTTCTCATATTTCGATAGACA
191 CAAATTTGAATGAGAAACCTTTCTCAT-TTTTGAGAGACA
* * * * * * *
49000 TATGAAAACATACTGCCGAAAGGTCTTATGGATTGCCCGAATGATTTATCATCTTGCTCAAAAGA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGA-TGGCCGAAAGACTTATCATCTTGCTCGAAAGA
* *
49065 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTT
65 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTT
* * *
49130 AT-AATTTTGG-AA-A---TACTAGGTAAGAAAACTTTCTTACTTTTCAAAAATTTCAATTTTTA
130 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTAAAAAATTT--ATTTTCA
*
49189 AATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACG
193 AATTTGAATGAGAAACCTTTCTCA-TTTTTGAGAGACA
* * * *
49227 TGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCTAAAGAACTTATCATCTTGCTTGAAAGG
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCGAAAG-ACTTATCATCTTGCTCGAAAGA
* * * * *
49292 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAATACTTACTAATGGCCCGTAGAACTT
65 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTT
* * * *
49357 ATAAATTTTTGAAATAGTTTACTAGGTTAGAAACCTTTCTTACTTTTGAAAATTTTCAATTTTCA
130 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTAAAAAATTT--ATTTTCA
* *
49422 AATTTAAATGAGAAACCTTTCTCATATTTTGATAGAC-
193 AATTTGAATGAGAAACCTTTCTCAT-TTTTGAGAGACA
** * * * *
49459 T-CAAAAACATCCTTCCCAAAGGTCTTAAGGATGGCCCGAATGACTTATCATCTAGCTCTG-AAG
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGG-CCGAAAGACTTATCATCTTGCTC-GAAAG
** *
49522 TTTTATAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACT
64 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACT
*
49587 TATAAA-TTTGAAAATAGTTTACTAG
129 TATAAATTTTGGAAATAGTTTACTAG
49612 CTCTGAAGTC
Statistics
Matches: 928, Mismatches: 127, Indels: 54
0.84 0.11 0.05
Matches are distributed among these distances:
226 7 0.01
227 147 0.16
228 43 0.05
229 2 0.00
230 18 0.02
231 118 0.13
232 13 0.01
233 141 0.15
234 378 0.41
235 55 0.06
236 4 0.00
237 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (229 bp):
TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCGAAAGACTTATCATCTTGCTCGAAAGAC
TTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTA
TAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTAAAAAATTTATTTTCAAAT
TTGAATGAGAAACCTTTCTCATTTTTGAGAGACA
Found at i:49108 original size:42 final size:41
Alignment explanation
Indices: 49035--49126 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 41
49025 TTATGGATTG
* * *
49035 CCCGAATGATTTATCATCTTGCTCAAAAGACTTACAGATGA
1 CCCGAAGGATTTAGCATCATGCTCAAAAGACTTACAGATGA
* *
49076 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGA
1 CCCGAAGGATTT-AGCATCATGCTCAAAAGACTTACAGATGA
49118 CCCGAAGGA
1 CCCGAAGGA
49127 CTTATAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 11 0.24
42 34 0.76
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (41 bp):
CCCGAAGGATTTAGCATCATGCTCAAAAGACTTACAGATGA
Found at i:49128 original size:20 final size:20
Alignment explanation
Indices: 49063--49130 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
49053 TTGCTCAAAA
*
49063 GACTTACAGATGACCCGAAG
1 GACTTACTGATGACCCGAAG
* * * *
49083 GATTTAAGCATCATG-CTCGAAA
1 GACTT-A-C-TGATGACCCGAAG
49105 GACTTACTGATGACCCGAAG
1 GACTTACTGATGACCCGAAG
49125 GACTTA
1 GACTTA
49131 TAATTTTGGA
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
19 4 0.11
20 16 0.46
21 2 0.06
22 10 0.29
23 3 0.09
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (20 bp):
GACTTACTGATGACCCGAAG
Found at i:55603 original size:9 final size:9
Alignment explanation
Indices: 55589--55613 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55579 TAATATTAAT
55589 TAATAATTA
1 TAATAATTA
55598 TAATAATTA
1 TAATAATTA
55607 TAATAAT
1 TAATAAT
55614 ATTAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAATAATTA
Found at i:56142 original size:233 final size:233
Alignment explanation
Indices: 55728--58464 Score: 3491
Period size: 233 Copynumber: 11.9 Consensus size: 233
55718 AAGAGGGACT
* * *
55728 TGTGAAAACATCCTTCCCAAAGGTCTTATGGATGGCCCAAATGACTTATCATCTTGCTCGAAAGA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * * *
55793 CTTATAGATTACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCTGAAGGACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* * * * *
55858 ATAAATTTTGAAAATAGTTTACTAAGTAAAAAACCTATCTTACTATTCAAAAATTTCAATTTTCA
131 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCA
* * *
55923 AATTTGAACGAGAAACCTTTATCATTTTTCAAGAGACA
196 AATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
* * *
55961 TGTGAAAACATCATGCCCAAAGGTCTTATGAATGGCCCGAAAGACTTATCATCTTGCTCGAAAGA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * *
56026 GTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAAGAACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* ** * *
56091 ATAAATTTTGGAAATAGTTTTCTACATAAGAAACCTTTCTTATTTTTCAAAAATTTTCTATTTTC
131 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAA-TTTCAATTTTC
*
56156 AAATTTGAATGAGAAACCTTTCTCATTTTTCGAGATACA
195 AAATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
* * *
56195 TGTGAAAACATCCTACCCGAAGGACTTATGGAT--------GG---------C---CT-GAAAGA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
*
56239 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG-CCGAAGGACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* *
56303 ATAAATTTTGGAAATAGTTTACTAGATAAGAAACATTTCTTACTTTTCAAAAATTTCAAATTTTC
131 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTC-AATTTTC
* * ** * * *
56368 AGATTTAAATGAGAAATATTTCTTATATTTCGATAGACA
195 AAATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
* * * * * * *
56407 TGTGAAAATATTCTGTCGAAAGGTATTATGGATGGCTCGAAGGACTTATCATCTTGCTAGAAAGA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * * *
56472 CTTACAGATGACCCGAAGGATTTAAGCATCATGTTTGAAAGACTTACTGATGACTCGAAGGACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* *
56537 CT-AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTTA
131 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCA
*
56601 AATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACG
196 AATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
* * * * *
56639 TGTGAAAATATCTTGCTCGAAGGTCTTATGGATGG-CCGAAGGACTTATCATCTTGGTCGAAAGA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * *
56703 CTTACAAATGACTCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGGCTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* *
56768 ATAAATTTTGGAAATAGTTTACTAGGTTAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTACA
131 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCA
* * * **
56833 AATTTAAATGATAAACGTTTCTCATATTTT-GATTGACA
196 AATTTGAATGAGAAACCTTTCTCAT-TTTTCGAGAGACA
* *
56871 --TGAAAACATCCTGCCCAAAGGTCTTAAGGATGGCCCGAAGGACTTATCATCTT-CATTGAAAG
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC-TCGAAAG
* *
56933 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATAGCCCGAAGGACT
65 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACT
* *
56998 TATAAA-TTTGAAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT-AAACAATTTTCTATTT
130 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAA-AA-TTTCAATTT
*
57061 TCAAATTTGAATGAGAAACCTTTCTCATTTTTCGAGATACA
193 TCAAATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
* * * *
57102 TGTGAAAACATCATACCCGAAGGACTTATGGATGGCCCGAAGGACTTATCATCTT-CATCGAAAG
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC-TCGAAAG
* *
57166 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATAGCCCGAAGGACT
65 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACT
* * *
57231 TATAAA-TTTGGAAATACTTTACTAGGTAAGAAACCTTTCTTAATTTTCAAAATTTTCAAATTTT
130 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTC-AATTTT
* * * *
57295 CAGATTTAAATGAGAAACCTTTCTCATATTTCGATAGACA
194 CAAATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
* * * * * * * * *
57335 TGTGAAAACATCCCGTCGAAAGGTATTATGGATGGCCCAAATGACTTATTATCTTGTTAGAAAGA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * * *
57400 CTTACTTG-TGACCCGAAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGACCCGAAGGAAT
66 CTTAC-AGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACT
* *
57464 TAT-AATTTTGGAAATAGTTTATTAGGTAAGAAAACTTTCTTACTTTTCAAAAATTT--A-----
130 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTC
* *
57521 AAATTTGAATAAGAAACCTTTCTCATTTTTCGAGAGACG
195 AAATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
** * * *
57560 TGTTTAAACATCTTGCCCGAAGGTCTTATGCATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* ** * *
57625 CTTATAGATGACTTGAAGGATTTAAGGATCATGCTCGAAAGACTTACTGATGGCCAGAAGGACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* * * *
57690 ATAAATTTTGGAAATACTTTACTATGTAAGAAACCTTTCTTAATTTTCAAAATTTTCAAATTTTC
131 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTC-AATTTTC
* * * * *
57755 AGATTTAAATGAGAAACCTTTCTCATATTTCTATAGACA
195 AAATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
* * * * * *
57794 TGTGAAAACATCCTGTCGAAAGGTATTATGGATGGCCCGAATGACTTATTATCTTGCTAGAAAGA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * * * *
57859 CTTACTTG-TGACCTGAAGGATTTAAGCATCATGTTTGAAAGACTTACTGATGACCCGAAGGACT
66 CTTAC-AGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACT
* * * * *
57923 TAT-AATTTTGGAAATAGTTTATTAGGTAAGAAAACTTTCTTACTTTTCAAAAATTTAAAATTTA
130 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTC
* *
57987 AAATTTGAATAAGAAACCTTTCTCATTTTTCGAGAGACG
195 AAATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
** * *
58026 TGTTTAAACATCTTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * * **
58091 CTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCAAAAGGACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* * *
58156 ATAAATTTTGGAAACAATTTACTAGGTAA-AAACCTTTCTTAATTTTCAAAAATTTCAATTTTCA
131 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCA
* * **
58220 AATTTAAATGAGAAGCCTTTCTCATATTTT-GATTGACA
196 AATTTGAATGAGAAACCTTTCTCAT-TTTTCGAGAGACA
* * * * * *
58258 --TGAAAATATCCTACCCAAAGGTCTTATGGATGTCCCGAAGGACTTATCATCTTTCTCGGAAGG
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* *
58321 CTTACAGATGACCCGAAGGATTTAAGTATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* * * *
58386 ATAAA-TTTGAAAATAGTTTACTAGGTAAGAATCCTTTCTCACTTTTCAAAATTTTCAATTTTCA
131 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCA
58450 AATTTGAATGAGAAA
196 AATTTGAATGAGAAA
58465 TTATTCTCAT
Statistics
Matches: 2152, Mismatches: 299, Indels: 109
0.84 0.12 0.04
Matches are distributed among these distances:
211 4 0.00
212 120 0.06
213 57 0.03
214 2 0.00
217 1 0.00
220 2 0.00
224 1 0.00
225 140 0.07
226 48 0.02
229 25 0.01
230 234 0.11
231 214 0.10
232 363 0.17
233 709 0.33
234 231 0.11
235 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (233 bp):
TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCA
AATTTGAATGAGAAACCTTTCTCATTTTTCGAGAGACA
Found at i:56442 original size:212 final size:213
Alignment explanation
Indices: 56020--56414 Score: 623
Period size: 212 Copynumber: 1.9 Consensus size: 213
56010 CATCTTGCTC
*
56020 GAAAGAGTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAA
1 GAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAA
* * * *
56085 GAACTTATAAATTTTGGAAATAGTTTTCTACATAAGAAACCTTTCTTATTTTTCAAAAATTTTCT
66 GAACTTATAAATTTTGGAAATAGTTTACTACATAAGAAACATTTCTTACTTTTCAAAAATTTTCA
* * * *
56150 ATTTTCAAATTTGAATGAGAAACCTTTCTCATTTTTCGAGATACATGTGAAAACATCCTACCCGA
131 ATTTTCAAATTTAAATGAGAAACATTTCTCATATTTCGAGAGACATGTGAAAACATCCTACCCGA
56215 AGGACTTATGGATGGCCT
196 AGGACTTATGGATGGCCT
*
56233 GAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGC-CGAA
1 GAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAA
* *
56297 GGACTTATAAATTTTGGAAATAGTTTACTAGATAAGAAACATTTCTTACTTTTCAAAAA-TTTCA
66 GAACTTATAAATTTTGGAAATAGTTTACTACATAAGAAACATTTCTTACTTTTCAAAAATTTTC-
* * * *
56361 AATTTTCAGATTTAAATGAGAAATATTTCTTATATTTCGATAGACATGTGAAAA
130 AATTTTCAAATTTAAATGAGAAACATTTCTCATATTTCGAGAGACATGTGAAAA
56415 TATTCTGTCG
Statistics
Matches: 165, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
211 4 0.02
212 103 0.62
213 58 0.35
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (213 bp):
GAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAA
GAACTTATAAATTTTGGAAATAGTTTACTACATAAGAAACATTTCTTACTTTTCAAAAATTTTCA
ATTTTCAAATTTAAATGAGAAACATTTCTCATATTTCGAGAGACATGTGAAAACATCCTACCCGA
AGGACTTATGGATGGCCT
Found at i:56762 original size:42 final size:41
Alignment explanation
Indices: 56652--56768 Score: 103
Period size: 42 Copynumber: 2.9 Consensus size: 41
56642 GAAAATATCT
* * * *
56652 TGCTCGAAGGTCTTA-TGGATGG-CCGAAGGACTTATCATCT
1 TGCTCGAAAGACTTACT-GATGGCCCGAAGGACTTAGCATCA
* ** * * *
56692 TGGTCGAAAGACTTACAAATGACTCGAAGGATTTAAGCATCA
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTT-AGCATCA
*
56734 TGCTCGAAAGACTTACTGATGGCCCGAAGGGCTTA
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
56769 TAAATTTTGG
Statistics
Matches: 57, Mismatches: 17, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
40 15 0.26
41 10 0.18
42 32 0.56
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (41 bp):
TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAGCATCA
Found at i:58095 original size:41 final size:42
Alignment explanation
Indices: 58029--58136 Score: 119
Period size: 41 Copynumber: 2.6 Consensus size: 42
58019 AGAGACGTGT
* * * * * *
58029 TTAAACATCTTGCCCGAAGGTCTTATGGATGGCCCGAAGGAC
1 TTAAGCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGAC
* * *
58071 TT-ATCATCTTGCTCGAAAGACTTATAGATGACTCGAAGGAT
1 TTAAGCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGAC
*
58112 TTAAGCATCATGCTCGAAAGACTTA
1 TTAAGCATCTTGCTCGAAAGACTTA
58137 CTGATAGCCA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 33 0.60
42 22 0.40
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (42 bp):
TTAAGCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGAC
Found at i:84765 original size:13 final size:13
Alignment explanation
Indices: 84747--84771 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84737 AATCCTGACC
84747 CTAAGCAAAGTTT
1 CTAAGCAAAGTTT
84760 CTAAGCAAAGTT
1 CTAAGCAAAGTT
84772 GTGTTTCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
CTAAGCAAAGTTT
Found at i:85686 original size:120 final size:120
Alignment explanation
Indices: 85467--85690 Score: 340
Period size: 120 Copynumber: 1.9 Consensus size: 120
85457 TGTTAAATAA
* * *
85467 CTCACCACCTTCATACGACTCCATAACAAAATGGACCGCATTGTCATCCTCATAATTAGCCTTCA
1 CTCACCACCTTCACACAACTCCATAACAAAATGGACCGCATTGTCATCCTCATAAGTAGCCTTCA
** * *
85532 AGGTATGAATATTTGAGTGCTTAGGCAAGCGCAAAGAAATAAAGAAAGAAAGTGG
66 AGGTAACAATATTTGAGTGCTGAGGCAAACGCAAAGAAATAAAGAAAGAAAGTGG
* * *
85587 CTCACCACCTTCACACAATTCCATAACCAAATGGACTGCATTGTCATCCTCATAAGTAGCCTTCA
1 CTCACCACCTTCACACAACTCCATAACAAAATGGACCGCATTGTCATCCTCATAAGTAGCCTTCA
* *
85652 AGGTAACAATATTTGGGTGCTGAGGCAAATGCAAAGAAA
66 AGGTAACAATATTTGAGTGCTGAGGCAAACGCAAAGAAA
85691 GAATGTGACT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
120 92 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (120 bp):
CTCACCACCTTCACACAACTCCATAACAAAATGGACCGCATTGTCATCCTCATAAGTAGCCTTCA
AGGTAACAATATTTGAGTGCTGAGGCAAACGCAAAGAAATAAAGAAAGAAAGTGG
Found at i:87868 original size:32 final size:31
Alignment explanation
Indices: 87832--87906 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
87822 GGGCCACGGT
* *
87832 GCCTACCTAAGAATTCATCTTAGGGTCGTAGA
1 GCCTACCTAAGAA-TCATCTCAGGGTCGCAGA
** *
87864 GCCTACCCGAGAATGATCTCAGGGTCGCAGA
1 GCCTACCTAAGAATCATCTCAGGGTCGCAGA
87895 GCCTACCTAAGA
1 GCCTACCTAAGA
87907 GTCACATTAG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 25 0.69
32 11 0.31
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (31 bp):
GCCTACCTAAGAATCATCTCAGGGTCGCAGA
Found at i:92615 original size:20 final size:20
Alignment explanation
Indices: 92590--92660 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
92580 AATGCACTTA
92590 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
* *
92610 GTGCATCGATACATCTTGCT
1 GTGCATCGATGCATCCTGCT
92630 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
92650 GTGCATCGATG
1 GTGCATCGATG
92661 TTGTGCATCG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:92667 original size:13 final size:13
Alignment explanation
Indices: 92649--92673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
92639 TGCATCCTGC
92649 TGTGCATCGATGT
1 TGTGCATCGATGT
92662 TGTGCATCGATG
1 TGTGCATCGATG
92674 CATCCTGTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (13 bp):
TGTGCATCGATGT
Done.