Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002218.1 Hibiscus syriacus cultivar Beakdansim tig00004515_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: 60987
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:5466 original size:21 final size:21
Alignment explanation
Indices: 5442--5496 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
5432 CAAGGTAATT
*
5442 TGTTGTAAAGCCAAGCTACAC
1 TGTTGCAAAGCCAAGCTACAC
5463 TGTTGCAAAGCCAAGCTACAC
1 TGTTGCAAAGCCAAGCTACAC
5484 TGTTGCAAAGCCA
1 TGTTGCAAAGCCA
5497 TAGTTCATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (21 bp):
TGTTGCAAAGCCAAGCTACAC
Found at i:17973 original size:61 final size:60
Alignment explanation
Indices: 17878--17999 Score: 194
Period size: 61 Copynumber: 2.0 Consensus size: 60
17868 GTCTGTTTTA
*
17878 TTTTACCGTTTATATTATTAGTAACCTTTAAACAAA-CTGGTAGGT-ATTTTAACGTAATAGG
1 TTTTACCGTTTACATTATTAGTAACCTTTAAACAAATC-GGTAGGTGA--TTAACGTAATAGG
17939 TTTTACCGTTTACATTATTAGTAACCTTTAAACAAATCGGTAGGTGATTAACGTAATAGG
1 TTTTACCGTTTACATTATTAGTAACCTTTAAACAAATCGGTAGGTGATTAACGTAATAGG
17999 T
1 T
18000 AACACCTATT
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
60 14 0.24
61 42 0.72
62 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (60 bp):
TTTTACCGTTTACATTATTAGTAACCTTTAAACAAATCGGTAGGTGATTAACGTAATAGG
Found at i:18257 original size:6 final size:6
Alignment explanation
Indices: 18246--18283 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
18236 AGTGGAGCTC
18246 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AA
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AA
18284 CATGTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
AAATTG
Found at i:20259 original size:57 final size:56
Alignment explanation
Indices: 20189--20309 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 56
20179 AATTATGCCC
* * * *
20189 AATATATGAGTATATGTTTTATGTGA-ATAAATAATAATTTGAATAATTTTATGTGA
1 AATATATAAGTATATGTTATATGTGAGA-AAATAATAAATTGAATAATGTTATGTGA
* *
20245 AATACTATAAGTATATGTTATATGTGAGAAAATGATAAATTGCATAATGTTATGTGA
1 AATA-TATAAGTATATGTTATATGTGAGAAAATAATAAATTGAATAATGTTATGTGA
*
20302 ACTATATA
1 AATATATA
20310 TATGGTTAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
56 8 0.14
57 47 0.84
58 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.40
Consensus pattern (56 bp):
AATATATAAGTATATGTTATATGTGAGAAAATAATAAATTGAATAATGTTATGTGA
Found at i:20496 original size:24 final size:24
Alignment explanation
Indices: 20443--20499 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
20433 TCTTTCGGGA
* *
20443 CAAA-TCTATGTGACACTTCGGTG
1 CAAATTCTACGTGACACTTCGGAG
* * *
20466 TATATTCTACGTGGCACTTCGGAG
1 CAAATTCTACGTGACACTTCGGAG
20490 CAAATTCTAC
1 CAAATTCTAC
20500 TCGACAGTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (24 bp):
CAAATTCTACGTGACACTTCGGAG
Found at i:22620 original size:47 final size:45
Alignment explanation
Indices: 22550--22674 Score: 175
Period size: 47 Copynumber: 2.8 Consensus size: 45
22540 TATAAAATCT
*
22550 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAA-ACTA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATA-TA
*
22595 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
22642 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
22675 GCATACTTAC
Statistics
Matches: 74, Mismatches: 3, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
43 21 0.28
44 3 0.04
45 10 0.14
46 2 0.03
47 37 0.50
48 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:22682 original size:38 final size:41
Alignment explanation
Indices: 22550--22688 Score: 131
Period size: 47 Copynumber: 3.2 Consensus size: 41
22540 TATAAAATCT
* *
22550 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAACTA
1 CTTACCA-TTAT-TCATAAGCTCGTAAGCTTATTTTAGC-AA-TA
*
22595 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCA-TT--ATT-CATAAGCTCGTAAGCTTATTTTAGC-A-ATA
*
22642 CTTGCCATTATTCATAAGCTCGTAAGCTTA-TTT-GC-ATA
1 CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
22680 CTTACCATT
1 CTTACCATT
22689 TATTAACCAT
Statistics
Matches: 85, Mismatches: 5, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
38 11 0.13
41 1 0.01
42 3 0.04
43 18 0.21
44 3 0.04
45 10 0.12
46 2 0.02
47 36 0.42
48 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (41 bp):
CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
Found at i:26595 original size:17 final size:17
Alignment explanation
Indices: 26573--26642 Score: 51
Period size: 17 Copynumber: 4.3 Consensus size: 17
26563 CAAGTGAAAT
26573 ATTTTTTTTCATCTCTC
1 ATTTTTTTTCATCTCTC
* *
26590 ATTTTTTCTC-TTTCTC
1 ATTTTTTTTCATCTCTC
*
26606 -TTTTCTTTCTCAT-TTTC
1 ATTTT-TTT-TCATCTCTC
*
26623 A-TTTTTTTCTTCT-TC
1 ATTTTTTTTCATCTCTC
26638 ATTTT
1 ATTTT
26643 CATTTTCTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
15 10 0.24
16 14 0.33
17 17 0.40
18 1 0.02
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTTTTCATCTCTC
Found at i:26628 original size:33 final size:33
Alignment explanation
Indices: 26578--26670 Score: 95
Period size: 33 Copynumber: 2.8 Consensus size: 33
26568 GAAATATTTT
*
26578 TTTTCATCTCTCATTTTTTCTCTT-TCTC-TTTTC-
1 TTTTCAT-TTTCATTTTTT-TCTTCT-TCATTTTCA
26611 TTTCTCATTTTCATTTTTTTCTTCTTCATTTTCA
1 TTT-TCATTTTCATTTTTTTCTTCTTCATTTTCA
*
26645 TTTTCTTTTTCTATTTTTTT-TTCTTC
1 TTTTCATTTTC-ATTTTTTTCTTCTTC
26671 TTCTGTTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
32 6 0.11
33 32 0.60
34 15 0.28
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.71
Consensus pattern (33 bp):
TTTTCATTTTCATTTTTTTCTTCTTCATTTTCA
Found at i:26632 original size:21 final size:21
Alignment explanation
Indices: 26606--26661 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
26596 TCTCTTTCTC
26606 TTTTCTTTCTCATTTTCATTT
1 TTTTCTTTCTCATTTTCATTT
26627 TTTTC-TTCTTCATTTTCATTT
1 TTTTCTTTC-TCATTTTCATTT
*
26648 TCTT-TTTCT-ATTTT
1 TTTTCTTTCTCATTTT
26662 TTTTTCTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.16
20 4 0.12
21 23 0.72
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTCTTTCTCATTTTCATTT
Found at i:26650 original size:18 final size:18
Alignment explanation
Indices: 26627--26690 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
26617 ATTTTCATTT
26627 TTTTCTTCTTC-ATTTTCA
1 TTTTCTTCTTCTATTTT-A
* *
26645 TTTTCTTTTTCTATTTTT
1 TTTTCTTCTTCTATTTTA
* *
26663 TTTTCTTCTTCTGTTTTT
1 TTTTCTTCTTCTATTTTA
26681 TTTTCTTCTT
1 TTTTCTTCTT
26691 ATAATATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 36 0.88
19 5 0.12
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTCTTCTTCTATTTTA
Found at i:26668 original size:12 final size:13
Alignment explanation
Indices: 26593--26668 Score: 59
Period size: 12 Copynumber: 5.9 Consensus size: 13
26583 ATCTCTCATT
* *
26593 TTTTCTCTTTCTC
1 TTTTCTTTTTCTA
*
26606 TTTTCTTTCTC-A
1 TTTTCTTTTTCTA
* *
26618 TTTTCATTTTTTTC
1 TTTTC-TTTTTCTA
*
26632 TTCTTCATTTTC-A
1 TT-TTCTTTTTCTA
26645 TTTTCTTTTTCTA
1 TTTTCTTTTTCTA
26658 TTTT-TTTTTCT
1 TTTTCTTTTTCT
26669 TCTTCTGTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
12 20 0.41
13 20 0.41
14 6 0.12
15 3 0.06
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTCTTTTTCTA
Found at i:27922 original size:37 final size:35
Alignment explanation
Indices: 27833--27932 Score: 148
Period size: 34 Copynumber: 2.8 Consensus size: 35
27823 TTTCGTCATA
* *
27833 CTAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
*
27868 -TAGAATTCAAACTCCTAAAAATAGGATAAAATTTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAA--TTT
27904 CTAGGATTCAAACTCCTAAAAATAGGATA
1 CTAGGATTCAAACTCCTAAAAATAGGATA
27933 GAGTTCTACT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.48
36 3 0.05
37 27 0.47
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
Found at i:27958 original size:37 final size:37
Alignment explanation
Indices: 27831--27968 Score: 147
Period size: 37 Copynumber: 3.8 Consensus size: 37
27821 TTTTTCGTCA
* *
27831 TACTAGGATTCAAACTCCTAAAAATATGATAGAATT-
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* *
27867 T--TAGAATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * *
27902 TTCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
** * * *
27939 TACTATTATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
27969 CCACACTATA
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
34 30 0.35
35 1 0.01
36 1 0.01
37 54 0.63
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.33
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
Found at i:32593 original size:9 final size:10
Alignment explanation
Indices: 32575--32604 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
32565 AGAAAAGAAG
*
32575 CAAAAAAAAA
1 CAAAGAAAAA
32585 CAAAGAAAAA
1 CAAAGAAAAA
32595 CAAAGAAAAA
1 CAAAGAAAAA
32605 AGAGAAACAC
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:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (10 bp):
CAAAGAAAAA
Found at i:32610 original size:19 final size:21
Alignment explanation
Indices: 32557--32611 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
32547 TCCAATCAAG
32557 AAGAAAAAAGA-AAAGAAGCA
1 AAGAAAAAAGAGAAAGAAGCA
* *
32577 AAAAAAAACAAAGAAA-AA-CA
1 AAGAAAAA-AGAGAAAGAAGCA
32597 AAGAAAAAAGAGAAA
1 AAGAAAAAAGAGAAA
32612 CACGAACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 6 0.21
20 16 0.55
21 4 0.14
22 3 0.10
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (21 bp):
AAGAAAAAAGAGAAAGAAGCA
Found at i:32612 original size:17 final size:16
Alignment explanation
Indices: 32558--32630 Score: 53
Period size: 17 Copynumber: 4.5 Consensus size: 16
32548 CCAATCAAGA
32558 AGAAAAAAGAAAAGAAG
1 AGAAAAAAGAAAA-AAG
*
32575 CA-AAAAAA-AACAAAG
1 -AGAAAAAAGAAAAAAG
*
32590 AAAAACAAAGAAAAAAG
1 AGAAA-AAAGAAAAAAG
* *
32607 AGAAACACGAACAAAAG
1 AGAAAAAAGAA-AAAAG
32624 -GAAAAAA
1 AGAAAAAA
32631 AACAAGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
14 1 0.02
15 6 0.14
16 15 0.34
17 21 0.48
18 1 0.02
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (16 bp):
AGAAAAAAGAAAAAAG
Found at i:33309 original size:22 final size:22
Alignment explanation
Indices: 33281--33335 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
33271 GCTATCCCAT
33281 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
33303 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
33325 CAAACCTTTGA
1 CAAACCTTTGA
33336 CCAAACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:34375 original size:36 final size:36
Alignment explanation
Indices: 34292--34390 Score: 135
Period size: 36 Copynumber: 2.7 Consensus size: 36
34282 TTTCGTCCCC
* * * * *
34292 CTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCT
1 CTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTAT
34329 CTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTAT
1 CTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTAT
*
34365 CTTGAGACAGTTTCCCTTGAAACAAA
1 CTTGAGACAGTTTCTCTTGAAACAAA
34391 ATCTTTGAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
36 35 0.62
37 21 0.38
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (36 bp):
CTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTAT
Found at i:34452 original size:65 final size:65
Alignment explanation
Indices: 34348--34522 Score: 224
Period size: 65 Copynumber: 2.6 Consensus size: 65
34338 GTTTCTCTTG
* ** * **
34348 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
* *
34413 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
34478 TA
64 TA
* * *
34480 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
34523 CAGATATCTT
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
65 31 0.33
66 6 0.06
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:35357 original size:105 final size:105
Alignment explanation
Indices: 35126--35786 Score: 940
Period size: 105 Copynumber: 6.3 Consensus size: 105
35116 GCCATCTGCG
* * * * * *
35126 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
35191 GGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
35235 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
35300 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
35340 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
35405 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
35445 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
35510 ACCGCTGCTTGTCAACAACAACTTCCCAATCTT-AGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TTCAGAGCCA
*
35550 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGTG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
35615 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * * *
35650 ATTTCAACTTCACAACGGAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * ** *
35715 ACGGATGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
35756 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
35787 TGGAACAATG
Statistics
Matches: 509, Mismatches: 34, Indels: 21
0.90 0.06 0.04
Matches are distributed among these distances:
99 2 0.00
100 78 0.15
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 305 0.60
106 84 0.17
107 5 0.01
109 22 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:36377 original size:34 final size:36
Alignment explanation
Indices: 36333--36434 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
36323 TTTCGTCATA
*
36333 CTAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
36368 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
36403 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
36435 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:36458 original size:37 final size:37
Alignment explanation
Indices: 36331--36468 Score: 156
Period size: 37 Copynumber: 3.8 Consensus size: 37
36321 TTTTTCGTCA
* *
36331 TACTAGGATTCAAACTCCTAAAAATATGATAGAATT-
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
*
36367 T--TAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * *
36402 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
** * * *
36439 TACTATTATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
36469 CCACACTATA
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
34 31 0.35
35 1 0.01
36 1 0.01
37 55 0.62
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
Found at i:37118 original size:17 final size:17
Alignment explanation
Indices: 37096--37129 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
37086 TGTTTATGTA
37096 ATATATCTTATA-ATTTT
1 ATATAT-TTATATATTTT
37113 ATATATTTATATATTTT
1 ATATATTTATATATTTT
37130 TTATTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATATTTATATATTTT
Found at i:37367 original size:2 final size:2
Alignment explanation
Indices: 37360--37389 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
37350 TAATACTTTG
*
37360 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37390 TTTTCCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:38369 original size:17 final size:17
Alignment explanation
Indices: 38347--38431 Score: 97
Period size: 17 Copynumber: 5.1 Consensus size: 17
38337 CTGGAGAACA
38347 ATTTGATTCACATAATC
1 ATTTGATTCACATAATC
*
38364 ATTTGATTCAC--AAGC
1 ATTTGATTCACATAATC
*
38379 AAGGTTTGA-ACACATAATC
1 -A--TTTGATTCACATAATC
38398 ATTTGATTCACATAATC
1 ATTTGATTCACATAATC
38415 ATTTGATTCAC-TAATC
1 ATTTGATTCACATAATC
38431 A
1 A
38432 ACAATGATTC
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
15 3 0.05
16 12 0.21
17 34 0.59
18 6 0.10
19 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (17 bp):
ATTTGATTCACATAATC
Found at i:39717 original size:47 final size:45
Alignment explanation
Indices: 39647--39771 Score: 166
Period size: 47 Copynumber: 2.8 Consensus size: 45
39637 ATATAAATCC
*
39647 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAA-ACTA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATA-TA
*
39692 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
**
39739 CTTGTCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
39772 GCATACTTAC
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
43 21 0.29
44 3 0.04
45 10 0.14
46 2 0.03
47 36 0.49
48 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:45999 original size:57 final size:57
Alignment explanation
Indices: 45937--46046 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
45927 ACGCCCATTA
* *
45937 TATGAGTATATGTTTTATGTGA-ATAAATGATAATTTGAATAATGCTATGTGAAATAC
1 TATGAGTATATGTTTTATGTGAGA-AAATGATAAATTGAATAATCCTATGTGAAATAC
*
45994 TATGAGTATATGTTTTATGTGAGAAAATGATAAATTGCATAATCCTATGTGAA
1 TATGAGTATATGTTTTATGTGAGAAAATGATAAATTGAATAATCCTATGTGAA
46047 CTATTTATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
57 48 0.98
58 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (57 bp):
TATGAGTATATGTTTTATGTGAGAAAATGATAAATTGAATAATCCTATGTGAAATAC
Found at i:46177 original size:24 final size:24
Alignment explanation
Indices: 46143--46222 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
46133 CTTCAGGAAA
* * *
46143 ATTCTATGTGGAACTTTGGTGCAT
1 ATTCTACGTGGTACTTCGGTGCAT
*
46167 ATTCTACGTGGTACTTCAGTGCAT
1 ATTCTACGTGGTACTTCGGTGCAT
* *
46191 ATTCTATGTGGTACTTCGGTGCAA
1 ATTCTACGTGGTACTTCGGTGCAT
46215 ATTCTACG
1 ATTCTACG
46223 CGATAGTTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (24 bp):
ATTCTACGTGGTACTTCGGTGCAT
Found at i:49203 original size:31 final size:32
Alignment explanation
Indices: 49168--49237 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
49158 ATAAATTACT
*
49168 AATTTGACCTCT-AAACTTTAGATAAAATATC
1 AATTTGACCTCTGAAACTTTAAATAAAATATC
* *
49199 AATTTGA-TTTTGAAACTTTAAATAAAATATC
1 AATTTGACCTCTGAAACTTTAAATAAAATATC
*
49230 AAATTGAC
1 AATTTGAC
49238 TCGTGAATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (32 bp):
AATTTGACCTCTGAAACTTTAAATAAAATATC
Found at i:49542 original size:2 final size:2
Alignment explanation
Indices: 49535--49561 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49525 CAAAATTTAA
49535 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
49562 CAATACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51082 original size:2 final size:2
Alignment explanation
Indices: 51075--51107 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
51065 TTTATTTATT
51075 TA TA TA TA 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 TA TA TA TA T
51108 CTCCAAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54323 original size:23 final size:23
Alignment explanation
Indices: 54297--54341 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
54287 AGGGAAAGGG
54297 AAAAATA-ATAAATA-AAGAAATA
1 AAAAATATATAAATAGAA-AAATA
54319 AAAAATATATAAATAGAAAAATA
1 AAAAATATATAAATAGAAAAATA
54342 TAACTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 12 0.57
24 2 0.10
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAAATATATAAATAGAAAAATA
Found at i:54351 original size:18 final size:15
Alignment explanation
Indices: 54299--54343 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
54289 GGAAAGGGAA
* * *
54299 AAATAATAAATAAAG
1 AAATAAAAAATATAT
54314 AAATAAAAAATATAT
1 AAATAAAAAATATAT
54329 AAATAGAAAAATATA
1 AAATA-AAAAATATA
54344 ACTAAATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (15 bp):
AAATAAAAAATATAT
Found at i:54468 original size:21 final size:21
Alignment explanation
Indices: 54395--54488 Score: 84
Period size: 21 Copynumber: 4.2 Consensus size: 21
54385 GAAAAAAAAC
* *
54395 TAAAAAAATAGTAACAAATAA
1 TAAAATAATAATAACAAATAA
*
54416 TAAAATAGTAAGAATAACAAGA-AA
1 T-AAA-A-TAATAATAACAA-ATAA
54440 TGGAAAATAATAATAA-AAGATAA
1 T--AAAATAATAATAACAA-ATAA
54463 TAAAATAATAATAACAAATAA
1 TAAAATAATAATAACAAATAA
54484 TAAAA
1 TAAAA
54489 GGTATAATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
21 23 0.38
22 9 0.15
23 12 0.20
24 13 0.21
25 4 0.07
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.20
Consensus pattern (21 bp):
TAAAATAATAATAACAAATAA
Found at i:56197 original size:34 final size:35
Alignment explanation
Indices: 56125--56225 Score: 125
Period size: 34 Copynumber: 2.9 Consensus size: 35
56115 GAACTCGGAG
*
56125 GTGTTTCAAGAGAAACAATCTCGAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATCTCAAAGG-TTTTTTTT
* * *
56161 GTGTTTCAAGGGAAATAATTTCAAAGG-TTTTTTT
1 GTGTTTCAAGAGAAACAATCTCAAAGGTTTTTTTT
*
56195 GTGTTTCAAGAGAAACAGAT-TCAAAGATTTT
1 GTGTTTCAAGAGAAACA-ATCTCAAAGGTTTT
56226 GTTTCAAGGG
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
34 28 0.50
35 5 0.09
36 23 0.41
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (35 bp):
GTGTTTCAAGAGAAACAATCTCAAAGGTTTTTTTT
Found at i:56300 original size:33 final size:35
Alignment explanation
Indices: 56224--56334 Score: 120
Period size: 36 Copynumber: 3.2 Consensus size: 35
56214 TTCAAAGATT
* *
56224 TTGTTTCAAGGGAAACT-AACTCAAGAGAGACAGAAC
1 TTGTTTTAAGAGAAACTGAA-TCAAGAGAGACA-AAC
56260 TTGTTTTAAGAGAAA-TGAATCAAGAGAGACAAA-
1 TTGTTTTAAGAGAAACTGAATCAAGAGAGACAAAC
* * **
56293 TTTTTTTAAGATAAACTGTCTCAAGAGAGACAAAC
1 TTGTTTTAAGAGAAACTGAATCAAGAGAGACAAAC
56328 TTTGTTT
1 -TTGTTT
56335 CAAGTTGGGT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
33 13 0.20
34 18 0.28
35 13 0.20
36 20 0.31
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.29
Consensus pattern (35 bp):
TTGTTTTAAGAGAAACTGAATCAAGAGAGACAAAC
Found at i:56322 original size:34 final size:34
Alignment explanation
Indices: 56224--56334 Score: 116
Period size: 34 Copynumber: 3.2 Consensus size: 34
56214 TTCAAAGATT
* * *
56224 TTGTTTCAAGGGAAACTAACTCAAGAGAGACAGAAC
1 TTGTTTTAAGAGAAA-TGACTCAAGAGAGACA-AAC
*
56260 TTGTTTTAAGAGAAATGAATCAAGAGAGACAAA-
1 TTGTTTTAAGAGAAATGACTCAAGAGAGACAAAC
* * *
56293 TTTTTTTAAGATAAACTGTCTCAAGAGAGACAAAC
1 TTGTTTTAAGAGAAA-TGACTCAAGAGAGACAAAC
56328 TTTGTTT
1 -TTGTTT
56335 CAAGTTGGGT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
33 13 0.21
34 18 0.29
35 14 0.22
36 18 0.29
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.29
Consensus pattern (34 bp):
TTGTTTTAAGAGAAATGACTCAAGAGAGACAAAC
Found at i:56882 original size:99 final size:99
Alignment explanation
Indices: 56700--56936 Score: 323
Period size: 99 Copynumber: 2.3 Consensus size: 99
56690 ATTGCTCTGA
* *
56700 GTCCAATATCCTTCG-TCGTGAAGTTGAAATTGGTTCTGGAACTGGAAAATTGTTTGTTGACAGT
1 GTCCAATATCCTTCGAT-GTGAAGTTGAAATT-G-ACT----CT-GAAAATTGTTTGTTGACAAT
*
56764 CAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTTGG
58 CAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTATTGG
* * * *
56806 GTCCAATATTCTTTGCTGTGAAGTTGAAATTGACTCTGAAAGTTGTTTGTTGACAATCAGCCGCC
1 GTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAAATTGTTTGTTGACAATCAGCCGCC
*
56871 CCTTCGTCGTGAAGTTGAGCTTGTGTTGTATTGG
66 CCTTCGCCGTGAAGTTGAGCTTGTGTTGTATTGG
56905 GTCCAATATCCTTCGATGTGAAGTTGAAATTG
1 GTCCAATATCCTTCGATGTGAAGTTGAAATTG
56937 GTTATGAAAT
Statistics
Matches: 120, Mismatches: 10, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
99 87 0.73
100 2 0.02
104 2 0.02
105 1 0.01
106 27 0.22
107 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (99 bp):
GTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAAATTGTTTGTTGACAATCAGCCGCC
CCTTCGCCGTGAAGTTGAGCTTGTGTTGTATTGG
Found at i:58367 original size:18 final size:19
Alignment explanation
Indices: 58323--58369 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
58313 TAAAATTTTA
*
58323 ATAATATATAAATAATTTAT
1 ATAATATA-AAATAATATAT
* *
58343 ATGATATAAAA-AATATCT
1 ATAATATAAAATAATATAT
58361 ATAATATAA
1 ATAATATAA
58370 TATTAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 13 0.57
19 3 0.13
20 7 0.30
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAATATAAAATAATATAT
Found at i:59010 original size:46 final size:43
Alignment explanation
Indices: 58872--59152 Score: 238
Period size: 42 Copynumber: 6.5 Consensus size: 43
58862 AATTAGAGAA
* * *
58872 CTCAATTATAAATGTACAAA--TGAGATTGAAAAAATTGGGGGA
1 CTCAATTATAAATGTA-AAAGTTGAGATTGAAAAAATTAGGAGC
* * * *
58914 ATCGATTATAAATATAAAAGTAG-GATTG-AAAAATTAGGAGC
1 CTCAATTATAAATGTAAAAGTTGAGATTGAAAAAATTAGGAGC
*
58955 CTCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAAACTAGG-GC
1 CTC-AATTATAAATGTAAAAGTTGAGATTG----AAAAAATTAGGAGC
* * * *
59002 CTCGATTATAAATGTACAAA-ATGAGATTGAAAAAATT-GGGGA
1 CTCAATTATAAATGTA-AAAGTTGAGATTGAAAAAATTAGGAGC
* * * *
59044 ATCGATTATAAATATAAAAAG-T-ATGATTGAAAAAATTAGGAGT
1 CTCAATTATAAATGT-AAAAGTTGA-GATTGAAAAAATTAGGAGC
*
59087 ATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAATATAGGAGC
1 CTC-AATTATAAATGTAAAAGTTGAGATTG-AAAAAAT-TAGGAGC
59133 CTCAATTATAAATGTAAAAG
1 CTCAATTATAAATGTAAAAG
59153 GCATGATTAA
Statistics
Matches: 195, Mismatches: 24, Indels: 37
0.76 0.09 0.14
Matches are distributed among these distances:
41 18 0.09
42 73 0.37
43 18 0.09
44 16 0.08
45 25 0.13
46 28 0.14
47 8 0.04
48 9 0.05
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (43 bp):
CTCAATTATAAATGTAAAAGTTGAGATTGAAAAAATTAGGAGC
Found at i:59040 original size:131 final size:130
Alignment explanation
Indices: 58872--59148 Score: 452
Period size: 131 Copynumber: 2.1 Consensus size: 130
58862 AATTAGAGAA
58872 CTCAATTATAAATGTACAAATGAGATTGAAAAAATTGGGGGAATCGATTATAAATAT-AAAAGTA
1 CTCAATTATAAATGTACAAATGAGATTGAAAAAATT-GGGGAATCGATTATAAATATAAAAAGTA
*
58936 GGATTG-AAAAATTAGGAGCCTCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAAACTAGG
65 GGATTGAAAAAATTAGGAGCATCAAATTATAAATGTAAAAGTTGAGATTG-AAAAAAAAA-TAGG
59000 -GC
128 AGC
*
59002 CTCGATTATAAATGTACAAAATGAGATTGAAAAAATTGGGGAATCGATTATAAATATAAAAAGTA
1 CTCAATTATAAATGTAC-AAATGAGATTGAAAAAATTGGGGAATCGATTATAAATATAAAAAGTA
* * *
59067 TGATTGAAAAAATTAGGAGTATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAATATAGGAG
65 GGATTGAAAAAATTAGGAGCATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAATAGGAG
59132 C
130 C
59133 CTCAATTATAAATGTA
1 CTCAATTATAAATGTA
59149 AAAGGCATGA
Statistics
Matches: 137, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
130 40 0.29
131 56 0.41
132 41 0.30
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (130 bp):
CTCAATTATAAATGTACAAATGAGATTGAAAAAATTGGGGAATCGATTATAAATATAAAAAGTAG
GATTGAAAAAATTAGGAGCATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAATAGGAGC
Found at i:59181 original size:89 final size:85
Alignment explanation
Indices: 58918--59186 Score: 226
Period size: 89 Copynumber: 3.1 Consensus size: 85
58908 GGGGGAATCG
* * *
58918 ATTATAAATATAAAAGTAG-GATTG-AAAAATTAGGAGCCTCAAATTATAAATGTAAAAGTTGAG
1 ATTATAAATGTAAAAGTTGAGATTGAAAAAATTAGGAGCCTC-AATTATAAATGTAAAAG--G-C
** * *
58981 ATTGAAAAAAAAAACTAGGGCCTC-G
62 A-TG-ATTAAAAAATTAGGGCCTCAA
* * ** * * * *
59006 ATTATAAATGTACAAA-ATGAGATTGAAAAAATT-GGGGAATCGATTATAAATATAAAAAGTATG
1 ATTATAAATGTA-AAAGTTGAGATTGAAAAAATTAGGAGCCTCAATTATAAATGTAAAAGGCATG
**
59069 ATTGAAAAAATTAGGAGTATCAA
65 ATT-AAAAAATTAGG-GCCTCAA
59092 ATTATAAATGTAAAAGTTGAGATTGAAAAAAATATAGGAGCCTCAATTATAAATGTAAAAGGCAT
1 ATTATAAATGTAAAAGTTGAGATTG-AAAAAAT-TAGGAGCCTCAATTATAAATGTAAAAGGCAT
59157 GATTAAAAAATTTAGGGCCGTCAA
64 GATTAAAAAA-TTAGGGCC-TCAA
59181 A-TATAA
1 ATTATAA
59187 TAAAATAAAA
Statistics
Matches: 143, Mismatches: 26, Indels: 24
0.74 0.13 0.12
Matches are distributed among these distances:
83 1 0.01
84 12 0.08
85 7 0.05
86 21 0.15
87 7 0.05
88 39 0.27
89 49 0.34
90 7 0.05
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.27
Consensus pattern (85 bp):
ATTATAAATGTAAAAGTTGAGATTGAAAAAATTAGGAGCCTCAATTATAAATGTAAAAGGCATGA
TTAAAAAATTAGGGCCTCAA
Found at i:59186 original size:43 final size:43
Alignment explanation
Indices: 58872--59186 Score: 161
Period size: 42 Copynumber: 7.3 Consensus size: 43
58862 AATTAGAGAA
* * * * *
58872 CTCAATTATAAATGTACAAA-TGAGATTGAAAAAAT-TGGGGGA
1 CTCAAATATAAATGTA-AAAGTGAGATTAAAAAAATATAGGAGC
* * * * *
58914 ATCGATTATAAATATAAAAGT-AGGATT-GAAAAAT-TAGGAGC
1 CTCAAATATAAATGTAAAAGTGA-GATTAAAAAAATATAGGAGC
*
58955 CTCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAAACTAGG-GC
1 CTCAAA-TATAAATGTAAAAG-TGAGATT--AAAAAAATA-TAGGAGC
* * * * * *
59002 CTCGATTATAAATGTACAAAATGAGATTGAAAAAAT-T-GGGGA
1 CTCAAATATAAATGTA-AAAGTGAGATTAAAAAAATATAGGAGC
* * * * * *
59044 ATCGATTATAAATATAAAAAGT-ATGATTGAAAAAAT-TAGGAGT
1 CTCAAATATAAATGT-AAAAGTGA-GATTAAAAAAATATAGGAGC
*
59087 ATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAATATAGGAGC
1 CTCAAA-TATAAATGTAAAAG-TGAGATT-AAAAAAATATAGGAGC
* *
59133 CTCAATTATAAATGTAAAAG-GCATGATT-AAAAAATTTAGG-GC
1 CTCAAATATAAATGTAAAAGTG-A-GATTAAAAAAATATAGGAGC
59175 CGTCAAATATAA
1 C-TCAAATATAA
59187 TAAAATAAAA
Statistics
Matches: 217, Mismatches: 33, Indels: 45
0.74 0.11 0.15
Matches are distributed among these distances:
41 20 0.09
42 66 0.30
43 39 0.18
44 21 0.10
45 26 0.12
46 32 0.15
47 9 0.04
48 4 0.02
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.27
Consensus pattern (43 bp):
CTCAAATATAAATGTAAAAGTGAGATTAAAAAAATATAGGAGC
Found at i:59186 original size:132 final size:129
Alignment explanation
Indices: 58872--59186 Score: 377
Period size: 131 Copynumber: 2.4 Consensus size: 129
58862 AATTAGAGAA
* * * * *
58872 CTCAATTATAAATGTACAAATGAGATTGAAAAAATTGGGGGAATCGATTATAAATATAAAAGTAG
1 CTCAATTATAAATGTAAAAAGGAGATTGAAAAAATT-GGGCAATCAAATATAAATATAAAAGTAG
*
58937 GATTGAAAAATTAGGAGCCTCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAAACTAGGGC
65 GATTGAAAAATTAGGAGCATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAAACTAGGGC
* * * * *
59002 CTCGATTATAAATGTACAAAATGAGATTGAAAAAATTGGGGAATCGATTATAAATATAAAAAGTA
1 CTCAATTATAAATGTA-AAAAGGAGATTGAAAAAATTGGGCAATCAAATATAAATAT-AAAAGTA
* * *
59067 TGATTGAAAAAATTAGGAGTATCAAATTATAAATGTAAAAGTTGAGATTG-AAAAAAATA-TAGG
64 GGATTG-AAAAATTAGGAGCATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAAACTAGG
59130 AGC
128 -GC
**
59133 CTCAATTATAAATGT-AAAAGGCATGATT-AAAAAATTTAGGGCCGTCAAATATAA
1 CTCAATTATAAATGTAAAAAGG-A-GATTGAAAAAA-TT-GGGCAATCAAATATAA
59187 TAAAATAAAA
Statistics
Matches: 164, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
129 5 0.03
130 46 0.28
131 61 0.37
132 52 0.32
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.27
Consensus pattern (129 bp):
CTCAATTATAAATGTAAAAAGGAGATTGAAAAAATTGGGCAATCAAATATAAATATAAAAGTAGG
ATTGAAAAATTAGGAGCATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAAACTAGGGC
Done.