Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009588.1 Hibiscus syriacus cultivar Beakdansim tig00116967_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: 190935
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2440 original size:22 final size:20
Alignment explanation
Indices: 2393--2440 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
2383 TTCTTGCATT
**
2393 TTATATTTCATGTTTTTTTA
1 TTATATTTCATGTTTTTACA
2413 TTATATTTCCATGTTTTTACA
1 TTATATTT-CATGTTTTTACA
2434 TTCATAT
1 TT-ATAT
2441 AACTAACAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 12 0.50
22 4 0.17
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.62
Consensus pattern (20 bp):
TTATATTTCATGTTTTTACA
Found at i:10497 original size:105 final size:105
Alignment explanation
Indices: 10315--11073 Score: 1222
Period size: 105 Copynumber: 7.2 Consensus size: 105
10305 AGGTTTTACC
10315 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
10380 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
10420 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
10485 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
10525 CAGAGCCAATTTCAACTTCACAACGAAGGGTATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
10590 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
10630 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
10695 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
10735 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCCGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* ** *
10800 ACGAAGGGACCGCTGGTTGTCAATAAACACCTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
**
10840 CAGAGCCAATTTCAACTTTGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
10905 ACGAAGGGACCGCTGGTTGTCAACAAACATCTCTC-AATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT-T
* * * * * * * *
10945 CAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCAAGACAGCACAAGCTCGACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
**
11010 ACGAAGGGA-CGACTGACTGTCAACGAATA-ATTTCTC-AATT
66 ACGAAGGGACCG-CTGGTTGTCAAC-AA-ACATTTCTCAAATT
*
11050 CCATAGCC-ATTTCCAACTTCACAA
1 -CAGAGCCAATTT-CAACTTCACAA
11074 ACAGGTTGAC
Statistics
Matches: 614, Mismatches: 34, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
104 4 0.01
105 582 0.95
106 27 0.04
107 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:11425 original size:2 final size:2
Alignment explanation
Indices: 11418--11482 Score: 89
Period size: 2 Copynumber: 33.5 Consensus size: 2
11408 CCTTTAACAT
* * *
11418 TA TA TA TA TA TT TA CA T- TA TA -A TT TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11458 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
11483 TTTACATATG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12525 original size:63 final size:63
Alignment explanation
Indices: 12426--12551 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
12416 TTGTTAAAAG
*
12426 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTGAAAAACATTCAATTTGGTCCCCAAACCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTCAATTTGGTCCCCAAACCGGTT
* * *
12489 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACGTTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTCAATTTGGTCCCCAAACCGGTT
12552 TAATTCCCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (63 bp):
GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTCAATTTGGTCCCCAAACCGGTT
Found at i:13063 original size:12 final size:12
Alignment explanation
Indices: 13048--13086 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
13038 TTATATTTTA
13048 ATATATATGTAT
1 ATATATATGTAT
13060 ATATATATGTAT
1 ATATATATGTAT
*
13072 ATATCTATGTAT
1 ATATATATGTAT
13084 ATA
1 ATA
13087 CTTGTAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:13092 original size:10 final size:12
Alignment explanation
Indices: 13048--13124 Score: 67
Period size: 12 Copynumber: 6.8 Consensus size: 12
13038 TTATATTTTA
*
13048 ATATATATGTAT
1 ATATCTATGTAT
*
13060 ATATATATGTAT
1 ATATCTATGTAT
13072 ATATCTATGTAT
1 ATATCTATGTAT
13084 ATA-CT-TGTA-
1 ATATCTATGTAT
* *
13093 ATAGTTTATTTAT
1 ATA-TCTATGTAT
13106 ATATCTAT-TAT
1 ATATCTATGTAT
13117 -TAT-TATGT
1 ATATCTATGT
13125 GTACATTTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
9 6 0.11
10 8 0.14
11 6 0.11
12 33 0.59
13 3 0.05
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (12 bp):
ATATCTATGTAT
Found at i:14918 original size:400 final size:410
Alignment explanation
Indices: 14110--14925 Score: 1183
Period size: 417 Copynumber: 2.0 Consensus size: 410
14100 ATGTTTTATG
14110 TTATCCATTAATTTTCTTTTATTTATTAATTATAAATAATTAACAATATTTTAGATATGACTATG
1 TTATCCATTAATTTTCTTTTATTTATTAATTATAAATAATTAACAATATTTTAGATATGACTATG
* * *
14175 TTGCACTTACCCGCTTAATATTTAGAATTATACTTCAAAGGCAGGATAAAATACATTTGAATATT
66 TTGCACTTACCAGCTTAAAATTTAGAATTATACTTCAAAAGCAGGATAAAATACATTTGAATATT
* *
14240 GTAATTTTAAAAAACCATTAAATTTATTATTACAAAGTAATAATTGTACGTTATAAAAATAATAT
131 GTAATTTTAAAAAACAATTAAATTTATTATTACAAAGTAATAATTGGACGTTATAAAAATAATAT
* *
14305 AAATCAACCCTAAAAAATATTTTATAACGGCAATATTTTTAATAATTTAATTTTTTAATTGTTGA
196 AAATCAACCCTAAAAAATATTTTATAACGGCAATA--TATAATAA--TAA-TATTTAATTGTTGA
* *
14370 AATTTTTAAAACTACAATTTGATTTTTAAATTTATTAAAATATTATAAAGTAATAATTGAGTATT
256 AATTTTAAAAACTACAAATTGATTTTTAAATTTATTAAAATATTATAAAGTAATAATTGAG-ATT
* * * *
14435 TATAAAAAAATATAATGATAAATGAACTCCAAAAATTATTTTATAACAGTAATTAAATTTAAATA
320 TATAAAAAAATATAATGATAAATGAACTCCAAAAATTATTTTATAAAAGTAAATAAAATTAAAGA
14500 TTATTTTATAAATTTTTAAATTTAAT
385 TTATTTTATAAATTTTTAAATTTAAT
* * *
14526 TTATCCATTTAATTTTCTTTTATTTATTAATTATGAATAATTAATAATATTTTAGGTATGACTAT
1 TTATCCA-TTAATTTTCTTTTATTTATTAATTATAAATAATTAACAATATTTTAGATATGACTAT
* *
14591 GTTGCACTTACCAGCTTAAAATTTAGAATTATGCTTCAAAAG-TGGATAAAATACATTTGAATAT
65 GTTGCACTTACCAGCTTAAAATTTAGAATTATACTTCAAAAGCAGGATAAAATACATTTGAATAT
* * * * *
14655 TGTAATTTT-AAAAACAATTTAATTTATTATTATAATGTAATAATTGGATGTTATAAAAATAGTG
130 TGTAATTTTAAAAAACAATTAAATTTATTATTACAAAGTAATAATTGGACGTTATAAAAATAAT-
* * *
14719 ATAAATCAACTCT-AAAAAT-TTATTTTAA-TGC-ATCA-ATAA-AA-AA-ATTTAATTGTTGAA
194 ATAAATCAACCCTAAAAAATATT-TTATAACGGCAAT-ATATAATAATAATATTTAATTGTTGAA
*
14776 ATTTTAAAAACTACAAATTG-TTTTTAAATTTATTAAACTATTATAAAGTAATAATTGA-ATTT-
257 ATTTTAAAAACTACAAATTGATTTTTAAATTTATTAAAATATTATAAAGTAATAATTGAGATTTA
* *
14838 TTATAAAA-ATAATGATAAATGAACTCCAAAAATTATTTTATAAAAGTAAATAAAATTAAAGATT
322 TAAAAAAATATAATGATAAATGAACTCCAAAAATTATTTTATAAAAGTAAATAAAATTAAAGATT
14902 ATTTTATAAATTTTTAAATTTAAT
387 ATTTTATAAATTTTTAAATTTAAT
14926 AAAAAATAAA
Statistics
Matches: 367, Mismatches: 29, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
400 76 0.21
401 6 0.02
402 4 0.01
404 37 0.10
405 31 0.08
407 2 0.01
410 2 0.01
411 3 0.01
413 2 0.01
414 5 0.01
415 58 0.16
416 49 0.13
417 92 0.25
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (410 bp):
TTATCCATTAATTTTCTTTTATTTATTAATTATAAATAATTAACAATATTTTAGATATGACTATG
TTGCACTTACCAGCTTAAAATTTAGAATTATACTTCAAAAGCAGGATAAAATACATTTGAATATT
GTAATTTTAAAAAACAATTAAATTTATTATTACAAAGTAATAATTGGACGTTATAAAAATAATAT
AAATCAACCCTAAAAAATATTTTATAACGGCAATATATAATAATAATATTTAATTGTTGAAATTT
TAAAAACTACAAATTGATTTTTAAATTTATTAAAATATTATAAAGTAATAATTGAGATTTATAAA
AAAATATAATGATAAATGAACTCCAAAAATTATTTTATAAAAGTAAATAAAATTAAAGATTATTT
TATAAATTTTTAAATTTAAT
Found at i:15495 original size:3 final size:3
Alignment explanation
Indices: 15487--15511 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
15477 AGAACCGGAC
15487 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
15512 AAAAACCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:26149 original size:3 final size:3
Alignment explanation
Indices: 26143--26208 Score: 96
Period size: 3 Copynumber: 21.0 Consensus size: 3
26133 ATTTATTTAT
*
26143 TAA TAA TAA TAAA TAA TAAA TAA TAA TAA TAA TGTA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA T-AA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
26191 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
26209 AAACAAACTA
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
3 50 0.86
4 8 0.14
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:26549 original size:75 final size:73
Alignment explanation
Indices: 26391--26561 Score: 254
Period size: 75 Copynumber: 2.3 Consensus size: 73
26381 ATCATTTTGC
* * * *
26391 ACTGTAGGTCTTATAGATGACCCGGAGGCTTTAAAATCAAAAAGCTCTCTAAGGCTTTTTGAAAA
1 ACTGTAGGTCTTACAGATGACCCGAAGGCTTTAAAATCAAAAAACTCTCCAAGGCTTTTTGAAAA
*
26456 CATCATGC
66 CATCATGA
*
26464 ACTGTAGGTCTTACAGATGACCCTAAGGCTTTAAAATCAAAAAAAACTC-CCAAGGGCTTTTTGA
1 ACTGTAGGTCTTACAGATGACCCGAAGGCTTTAAAATC--AAAAAACTCTCCAA-GGCTTTTTGA
26528 AAACATCATGA
63 AAACATCATGA
26539 ACTGTAGGTCTTACAGATGACCC
1 ACTGTAGGTCTTACAGATGACCC
26562 CGAAACCCCA
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
73 35 0.39
74 3 0.03
75 51 0.57
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (73 bp):
ACTGTAGGTCTTACAGATGACCCGAAGGCTTTAAAATCAAAAAACTCTCCAAGGCTTTTTGAAAA
CATCATGA
Found at i:30039 original size:7 final size:7
Alignment explanation
Indices: 30027--30057 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
30017 TGATATTATT
30027 ATTTTTA
1 ATTTTTA
30034 ATTTTTA
1 ATTTTTA
30041 ATTTTTA
1 ATTTTTA
30048 ATTTTTA
1 ATTTTTA
30055 ATT
1 ATT
30058 AAGGATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTTA
Found at i:30455 original size:32 final size:34
Alignment explanation
Indices: 30419--30481 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
30409 AAAAAAGAAA
*
30419 AATAAT-AA-ATAATAAATAATGA-TTTTAAAAAT
1 AATAATAAAGATAA-AAAAAATGAGTTTTAAAAAT
30451 AATAATAAAGATAAAAAAAATGAGTTTTAAA
1 AATAATAAAGATAAAAAAAATGAGTTTTAAA
30482 TTATTTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 6 0.22
33 10 0.37
34 11 0.41
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.30
Consensus pattern (34 bp):
AATAATAAAGATAAAAAAAATGAGTTTTAAAAAT
Found at i:30458 original size:35 final size:34
Alignment explanation
Indices: 30410--30481 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
30400 AAGAAAAGAA
*
30410 AAAAAGAAAAATAATAAATAATAAATAATGA-TTTT
1 AAAAAGAAAAATAA-AAATAA-AAAAAATGAGTTTT
* * *
30445 AAAAATAATAATAAAGATAAAAAAAATGAGTTTT
1 AAAAAGAAAAATAAAAATAAAAAAAATGAGTTTT
30479 AAA
1 AAA
30482 TTATTTAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 8 0.25
34 12 0.38
35 12 0.38
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (34 bp):
AAAAAGAAAAATAAAAATAAAAAAAATGAGTTTT
Found at i:30533 original size:17 final size:17
Alignment explanation
Indices: 30508--30541 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30498 AATGAGATAA
*
30508 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
30525 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
30542 TGAGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:32107 original size:17 final size:17
Alignment explanation
Indices: 32087--32124 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
32077 GTCAAAGGAG
32087 GTCAACGGTCGGGTCGA
1 GTCAACGGTCGGGTCGA
32104 GTCAACGGTCGGGTCGA
1 GTCAACGGTCGGGTCGA
32121 GTCA
1 GTCA
32125 GACCGGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.39, T:0.18
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGA
Found at i:36073 original size:21 final size:22
Alignment explanation
Indices: 36031--36075 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
36021 GTCAAGGGGG
*
36031 AACCGATACCCCCATAGGAGGA
1 AACCGATACCCCCATAGAAGGA
* *
36053 AACCGATTCCCCCCTA-AAGGA
1 AACCGATACCCCCATAGAAGGA
36074 AA
1 AA
36076 ATTATAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.38, C:0.33, G:0.18, T:0.11
Consensus pattern (22 bp):
AACCGATACCCCCATAGAAGGA
Found at i:36950 original size:103 final size:103
Alignment explanation
Indices: 36766--36983 Score: 355
Period size: 103 Copynumber: 2.1 Consensus size: 103
36756 GTCGAGGGTC
* * * *
36766 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGCGAGACACAGAC
* *
36831 TTGATCCTTGGAATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGAATATGTATATGATTCTTAAGGAATGA
36869 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGCGAGACACAGAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGCGAGACACAGAC
*
36934 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGAATATGTATATGATTCTTAAGGAATGA
* *
36972 TACGTAGTCCTT
1 TATGTGGTCCTT
36984 ATGGACATTA
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGCGAGACACAGAC
TTGATCCCTAGAATATGTATATGATTCTTAAGGAATGA
Found at i:41859 original size:23 final size:22
Alignment explanation
Indices: 41811--41859 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
41801 CCAGAATGTC
41811 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
41832 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
41855 AAGGA
1 AAGGA
41860 AAATTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:42736 original size:103 final size:103
Alignment explanation
Indices: 42552--42769 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
42542 GTCGAGGGTC
*
42552 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGATACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
42617 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
42655 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
42720 TTGATCCCTT-GTATATGTATATGATTCTTAAGGAATGA
66 TTGAT-CCTTGGCATATGTATATGATTCTTAAGGAATGA
*
42758 TACGTGGTCCTT
1 TATGTGGTCCTT
42770 ATAGATATTA
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 107 0.96
104 4 0.04
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:42834 original size:47 final size:47
Alignment explanation
Indices: 42776--42895 Score: 179
Period size: 47 Copynumber: 2.6 Consensus size: 47
42766 CCTTATAGAT
*
42776 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGTA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
* *
42823 ATTATTATATGGCACTCCAGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
* * *
42870 ATTA-TATGTGGCACTTCGGTGAAATT
1 ATTATTATATGGCACTACGGTGCAATT
42896 ATATGAGCTG
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
46 18 0.27
47 48 0.73
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
Found at i:42896 original size:23 final size:23
Alignment explanation
Indices: 42776--42900 Score: 115
Period size: 23 Copynumber: 5.3 Consensus size: 23
42766 CCTTATAGAT
* *
42776 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTCCGGTGCA
* * * *
42800 ATTCTACGCGGCACTCCGGTGTA
1 ATTATATGTGGCACTCCGGTGCA
* *
42823 ATTATTATATGGCACTCCAGTGCA
1 ATTA-TATGTGGCACTCCGGTGCA
* * *
42847 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTCCGGTGCA
* *
42870 ATTATATGTGGCACTTCGGTGAA
1 ATTATATGTGGCACTCCGGTGCA
42893 ATTATATG
1 ATTATATG
42901 AGCTGTGGTG
Statistics
Matches: 78, Mismatches: 22, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
23 58 0.74
24 20 0.26
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTCCGGTGCA
Found at i:47751 original size:5 final size:5
Alignment explanation
Indices: 47741--47790 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
47731 AACGTTTAAT
* *
47741 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC- TGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
47791 AGATCAATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
4 3 0.08
5 31 0.82
7 4 0.11
ACGTcount: A:0.04, C:0.22, G:0.52, T:0.22
Consensus pattern (5 bp):
GGTCG
Found at i:47778 original size:14 final size:14
Alignment explanation
Indices: 47759--47785 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47749 CGGGTCAACG
47759 GTCGGGTCGGGTCT
1 GTCGGGTCGGGTCT
47773 GTCGGGTCGGGTC
1 GTCGGGTCGGGTC
47786 GGGTCAGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.22, G:0.52, T:0.26
Consensus pattern (14 bp):
GTCGGGTCGGGTCT
Found at i:48830 original size:73 final size:71
Alignment explanation
Indices: 48615--48840 Score: 246
Period size: 73 Copynumber: 3.2 Consensus size: 71
48605 AACAAGCAAA
* ***
48615 AATATCTTAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCCAAAAAA-ATAT-
1 AATATCCTAAATCCTAATTAAAACAC-TAAAACCTATTTAAACTAAAATATAAAAAAAATATATA
*
48677 TTAAACT
65 TTAAAAT
* * *
48684 AATATTCTAAATCCTAATTAAAACACTAAAACATATTTAAACTAAAATACCTAAAACAAAGATAA
1 AATATCCTAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATA--TAAAA-AAA-ATAT
48749 ATA-T-AAAT
62 ATATTAAAAT
* * *
48757 AATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATATAAAGAAAAATATATG
1 AATATCCTAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATATAAA-AAAAATATAT-
48822 ATTAAAAT
64 ATTAAAAT
*
48830 ATTATCCTAAA
1 AATATCCTAAA
48841 CTTGAGTTTA
Statistics
Matches: 131, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
68 5 0.04
69 40 0.31
70 5 0.04
71 10 0.08
72 5 0.04
73 62 0.47
74 4 0.03
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (71 bp):
AATATCCTAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATATAAAAAAAATATATAT
TAAAAT
Found at i:66465 original size:18 final size:18
Alignment explanation
Indices: 66438--66472 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
66428 GCTCACTTCT
* *
66438 TTTCTTTTGTTGACTAAC
1 TTTCTCTTGTCGACTAAC
66456 TTTCTCTTGTCGACTAA
1 TTTCTCTTGTCGACTAA
66473 GGGATTGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.20, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTCTCTTGTCGACTAAC
Found at i:69167 original size:65 final size:65
Alignment explanation
Indices: 69034--69193 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
69024 TGCACTAAGA
* * * *
69034 GTGCATTGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGATG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCAATGCATGGATG
* * *
69098 GTGCATGGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCAATGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCAATGCATGG-A
69162 T-
64 TG
* * *
69163 GTGCATCGATGCATGAAATACAGTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
69194 CAATTTAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 27 0.33
65 51 0.61
66 5 0.06
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCAATGCATGGATG
Found at i:69232 original size:65 final size:64
Alignment explanation
Indices: 69034--69243 Score: 166
Period size: 65 Copynumber: 3.2 Consensus size: 64
69024 TGCACTAAGA
* * * * * *
69034 GTGCATTGATGCATCAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGA-
1 GTGCATCGATGCATCAAATACAGTCGATGTTTCATAAA-ATCTC--AGTGCATCAATGCATGGAT
69096 TG
63 TG
* * *
69098 GTGCATGGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCAATGCATGG-TA
1 GTGCATCGATGCATCAAATACAGTCGATG-TTTCATAAAAT-CTCAGTGCATCAATGCATGGAT-
69162 T-
63 TG
* **
69163 GTGCATCGATGCATGAAATACAGTCGATG-TTCAATTTAAT-TCATGGTGCATCAATGCATGGAT
1 GTGCATCGATGCATCAAATACAGTCGATGTTTC-ATAAAATCTCA--GTGCATCAATGCATGGAT
69226 TG
63 TG
69228 GTGCATCGGA-GCATCA
1 GTGCATC-GATGCATCA
69244 CTCTGAAAAA
Statistics
Matches: 123, Mismatches: 11, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 49 0.40
65 60 0.49
66 7 0.06
67 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATACAGTCGATGTTTCATAAAATCTCAGTGCATCAATGCATGGATTG
Found at i:70383 original size:21 final size:21
Alignment explanation
Indices: 70359--70402 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
70349 CCAGAGGAGG
*
70359 AGGAGGAGCACAAGAAGAGCT
1 AGGAGCAGCACAAGAAGAGCT
* **
70380 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACAAGAAGAGCT
70401 AG
1 AG
70403 CTCCCGGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACAAGAAGAGCT
Found at i:77912 original size:64 final size:64
Alignment explanation
Indices: 77826--78035 Score: 194
Period size: 65 Copynumber: 3.2 Consensus size: 64
77816 TGCACTAAGA
* *
77826 GTGCATCGATGCATCAAGTGCATTCGATGTTT-A-AAAATAGCCAGAGTGCATCAATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAT--CCACAGTGCATCAATGCATGG-T
77889 -G
63 AG
* * * * *
77890 GTGCATCGATGCATTAAATGCATTTGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCACAGTGCATCAATGCATGGTAG
* * ** * ** *
77955 GTGCATCAATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCAATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCCACAGTGCATCAATGCATGG-TA
78019 G
64 G
*
78020 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
78036 CTCTGAAAAT
Statistics
Matches: 118, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
63 3 0.03
64 48 0.41
65 61 0.52
66 1 0.01
67 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCACAGTGCATCAATGCATGGTAG
Found at i:79922 original size:57 final size:57
Alignment explanation
Indices: 79832--80060 Score: 332
Period size: 57 Copynumber: 4.0 Consensus size: 57
79822 GTTGGAGGAA
* *
79832 GAATACTTGCAAGTTCCTCGGCTTTGTGTTGAGGGCCTTACTATTCGTGACGGGGTT
1 GAATACTTGCAAGTTCCTCGGCTTTGTGCTGAGGGCCTTACTGTTCGTGACGGGGTT
* * *
79889 GAATACTTGCAGGTTCCTCGACTTTGTGCTGAGGGCCTTATTGTTCGTGACGGGGTT
1 GAATACTTGCAAGTTCCTCGGCTTTGTGCTGAGGGCCTTACTGTTCGTGACGGGGTT
* * *
79946 GAATACTTGCAGGTTCCTCGGCTTTGTGCCGAGGGTCTTACTGTTCGTGACGGGGTT
1 GAATACTTGCAAGTTCCTCGGCTTTGTGCTGAGGGCCTTACTGTTCGTGACGGGGTT
* * * * * *
80003 GAATACTTGCAAGTTCCTCGGTTTTGTACTTAGGGTCTTATTGTTCATGACGGGGTT
1 GAATACTTGCAAGTTCCTCGGCTTTGTGCTGAGGGCCTTACTGTTCGTGACGGGGTT
80060 G
1 G
80061 TATGGTTCTG
Statistics
Matches: 156, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 156 1.00
ACGTcount: A:0.15, C:0.19, G:0.31, T:0.36
Consensus pattern (57 bp):
GAATACTTGCAAGTTCCTCGGCTTTGTGCTGAGGGCCTTACTGTTCGTGACGGGGTT
Found at i:81266 original size:24 final size:24
Alignment explanation
Indices: 81213--81259 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
81203 TCTTCAACAA
* *
81213 CGGTGAGTAGCTTAGGCAATTTCT
1 CGGTTAGTAGCTCAGGCAATTTCT
81237 CGGTTAGTAGCTCAGGCAATTTC
1 CGGTTAGTAGCTCAGGCAATTTC
81260 CTGGTTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (24 bp):
CGGTTAGTAGCTCAGGCAATTTCT
Found at i:83556 original size:2 final size:2
Alignment explanation
Indices: 83551--83626 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
83541 TATATATGTA
83551 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
83593 TG TG TG TG TG TG TG TG TG -G TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
83627 ATTAGTAACA
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:84274 original size:16 final size:16
Alignment explanation
Indices: 84253--84286 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
84243 TTACTATTCA
*
84253 TGTGAATAGTGAATTT
1 TGTGAATAGTGAAATT
84269 TGTGAATAGTGAAATT
1 TGTGAATAGTGAAATT
84285 TG
1 TG
84287 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (16 bp):
TGTGAATAGTGAAATT
Found at i:90061 original size:38 final size:38
Alignment explanation
Indices: 90019--90097 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
90009 CCTCTTCCAC
90019 TATCTCGAATAAACATTGATTCCGTTATCTAGAGTGAA
1 TATCTCGAATAAACATTGATTCCGTTATCTAGAGTGAA
*
90057 TATCTCGAATAAACTTTGATTCCGTTATCTAGAGTGAA
1 TATCTCGAATAAACATTGATTCCGTTATCTAGAGTGAA
90095 TAT
1 TAT
90098 AAGACGGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (38 bp):
TATCTCGAATAAACATTGATTCCGTTATCTAGAGTGAA
Found at i:101883 original size:19 final size:20
Alignment explanation
Indices: 101827--101889 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 20
101817 CTATTTAAAC
* **
101827 TAAAATACCTAAAAAATAA-
1 TAAAATATCTAAAACCTAAT
*
101846 TAAAATATTCTAAATCCTAAT
1 TAAAATA-TCTAAAACCTAAT
*
101867 TAAAATA-CTAAAACCTATT
1 TAAAATATCTAAAACCTAAT
101886 TAAA
1 TAAA
101890 CTAAAATACA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 21 0.58
20 8 0.22
21 7 0.19
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAATATCTAAAACCTAAT
Found at i:101942 original size:75 final size:75
Alignment explanation
Indices: 101836--102010 Score: 228
Period size: 76 Copynumber: 2.3 Consensus size: 75
101826 CTAAAATACC
* * * *
101836 TAAAAAATAATAA-AATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATAC
1 TAAAATATAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
101899 AAAGATAAAGA
66 AAAGATAAA-A
* *
101910 TAAAATATAAAAATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAATTAAAATAC
1 TAAAATATAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
101975 AAAGATAAAA
66 AAAGATAAAA
* * * *
101985 TATAATGTTTAAAATATTATCCTAAA
1 TAAAAT-ATAAAAATAATATCCTAAA
102011 TTTGAGTTTA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
74 11 0.12
75 30 0.34
76 47 0.53
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (75 bp):
TAAAATATAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
AAAGATAAAA
Found at i:103713 original size:19 final size:20
Alignment explanation
Indices: 103676--103721 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
103666 AAGTTCGCTA
103676 AAAAATAAAAAAAATAAAAC
1 AAAAATAAAAAAAATAAAAC
* **
103696 GAAAATAAAAATTA-AAAAC
1 AAAAATAAAAAAAATAAAAC
103715 AAAAATA
1 AAAAATA
103722 TAACGAAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.13
Consensus pattern (20 bp):
AAAAATAAAAAAAATAAAAC
Found at i:107636 original size:15 final size:15
Alignment explanation
Indices: 107616--107649 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
107606 TTCCTCTTGT
*
107616 TCTTCCTGATGTGTG
1 TCTTCCTGATGTGCG
*
107631 TCTTCCTTATGTGCG
1 TCTTCCTGATGTGCG
107646 TCTT
1 TCTT
107650 TTTCTGCTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.21, T:0.50
Consensus pattern (15 bp):
TCTTCCTGATGTGCG
Found at i:112274 original size:149 final size:149
Alignment explanation
Indices: 112000--112280 Score: 508
Period size: 149 Copynumber: 1.9 Consensus size: 149
111990 CCACAGCTCG
*
112000 TATAATAATGTTCATAAGGACCACATATTATTCCTTAAGAATCATATACATATACTAGGGATCAA
1 TATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCATATACATATACTAGGGATCAA
* *
112065 GTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATATATATATATCCCGAAAGACCGCGTA
66 GTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACATATATCCCGAAAGACCGCGTA
112130 GAATTGCACCGTAGTGCCA
131 GAATTGCACCGTAGTGCCA
112149 TATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCATATACATATACTAGGGATCAA
1 TATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCATATACATATACTAGGGATCAA
* * *
112214 GTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACATATGTCCCGAAGGACCGCGTA
66 GTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACATATATCCCGAAAGACCGCGTA
112279 GA
131 GA
112281 CCCTCGACTC
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 126 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (149 bp):
TATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCATATACATATACTAGGGATCAA
GTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACATATATCCCGAAAGACCGCGTA
GAATTGCACCGTAGTGCCA
Found at i:114003 original size:21 final size:22
Alignment explanation
Indices: 113959--114001 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
113949 TTTTGTTCGT
* *
113959 TTGAAGGGGTATCGGTTCCCCC
1 TTGAAGGGGTACCGATTCCCCC
*
113981 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
114002 TTACCTAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (22 bp):
TTGAAGGGGTACCGATTCCCCC
Found at i:115864 original size:75 final size:76
Alignment explanation
Indices: 115797--115960 Score: 242
Period size: 76 Copynumber: 2.2 Consensus size: 76
115787 AAAAAATAAT
* *
115797 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
115861 AAAATATAAAA
66 AAAATATAAAA
*
115872 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
* * *
115936 ATAATGTTTAAA
66 AAAAT-ATAAAA
*
115948 ATATTATCCTAAA
1 ATAATATCCTAAA
115961 TTTTAGTTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
75 32 0.40
76 48 0.60
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
AAAATATAAAA
Found at i:120098 original size:31 final size:31
Alignment explanation
Indices: 120057--120117 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
120047 GTTAAGGGAC
**
120057 TAAAACCGAATGAATCAATAATGTTAGAGAT
1 TAAAACCGAATGAATCAATAACATTAGAGAT
*
120088 TAAAATCGAATGAATCAATAACATTAGAGA
1 TAAAACCGAATGAATCAATAACATTAGAGA
120118 CAATTCCCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.25
Consensus pattern (31 bp):
TAAAACCGAATGAATCAATAACATTAGAGAT
Found at i:120388 original size:12 final size:12
Alignment explanation
Indices: 120371--120395 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
120361 TTTAAAAATT
120371 ATAAAATTATTA
1 ATAAAATTATTA
120383 ATAAAATTATTA
1 ATAAAATTATTA
120395 A
1 A
120396 ATTATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAAAATTATTA
Found at i:120416 original size:17 final size:18
Alignment explanation
Indices: 120366--120421 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 18
120356 TTAATTTTAA
*
120366 AAATTATAAAATTATTAAT
1 AAATTATTAAATTA-TAAT
120385 AAAATTATTAAATTATAAT
1 -AAATTATTAAATTATAAT
*
120404 AAATTATT-CATTATAAT
1 AAATTATTAAATTATAAT
120421 A
1 A
120422 TTATAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 9 0.26
18 8 0.24
19 4 0.12
20 13 0.38
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTATTAAATTATAAT
Found at i:127397 original size:94 final size:95
Alignment explanation
Indices: 127235--127425 Score: 375
Period size: 94 Copynumber: 2.0 Consensus size: 95
127225 TAGTTGGGTA
127235 TTGTGATCAGACTATGCATGTGATTTGGACAAGCGTCGATCAACTACTAGTTATGTGTTTACATT
1 TTGTGATCAGACTATGCATGTGATTTGGACAAGCGTCGATCAACTACTAGTTATGTGTTTACATT
127300 TGCAAATGCACCAGTCAGTGGAAGTCCACC
66 TGCAAATGCACCAGTCAGTGGAAGTCCACC
127330 TTGTGATCAGACTATGCATGTGATTT-GACAAGCGTCGATCAACTACTAGTTATGTGTTTACATT
1 TTGTGATCAGACTATGCATGTGATTTGGACAAGCGTCGATCAACTACTAGTTATGTGTTTACATT
127394 TGCAAATGCACCAGTCAGTGGAAGTCCACC
66 TGCAAATGCACCAGTCAGTGGAAGTCCACC
127424 TT
1 TT
127426 AAGGGAATAC
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 70 0.73
95 26 0.27
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (95 bp):
TTGTGATCAGACTATGCATGTGATTTGGACAAGCGTCGATCAACTACTAGTTATGTGTTTACATT
TGCAAATGCACCAGTCAGTGGAAGTCCACC
Found at i:130267 original size:8 final size:8
Alignment explanation
Indices: 130254--130288 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
130244 GTATTTTATC
130254 TTTATTTT
1 TTTATTTT
130262 TTTATTTT
1 TTTATTTT
130270 TTTATTTT
1 TTTATTTT
130278 TTTATTTT
1 TTTATTTT
130286 TTT
1 TTT
130289 TTTACTGCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTATTTT
Found at i:130767 original size:59 final size:58
Alignment explanation
Indices: 130700--130839 Score: 149
Period size: 59 Copynumber: 2.3 Consensus size: 58
130690 ATTGGTCTCT
* *
130700 AAACTTTTAAATATTTTAATTCCATCC-CTAAACTA-AACTATCATTCTAAATAAGTCCTC
1 AAACTTTT-AACATTTCAATTCCATCCTC-AAACTAGAACT-TCATTCTAAATAAGTCCTC
* * * **
130759 AAACTTTTAACATTTCATTTTCATCCTCAAACTATGATCTTCATTCTAAATTGGTCCTC
1 AAACTTTTAACATTTCAATTCCATCCTCAAACTA-GAACTTCATTCTAAATAAGTCCTC
130818 AAACTTTATGAACATTTCAATT
1 AAACTTT-T-AACATTTCAATT
130840 TAATCATAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
58 20 0.29
59 33 0.49
60 4 0.06
61 11 0.16
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (58 bp):
AAACTTTTAACATTTCAATTCCATCCTCAAACTAGAACTTCATTCTAAATAAGTCCTC
Found at i:131113 original size:60 final size:60
Alignment explanation
Indices: 131013--131160 Score: 172
Period size: 60 Copynumber: 2.5 Consensus size: 60
131003 TTTATGTACC
* * * * *
131013 AATTTAGAATGATATTCAT-GTTTGGGGATGAAATTGGAATGTTCAAAGGTTTAATGACT
1 AATTTAGAATGAAAGTCATAGTTTGGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACT
* ** * * *
131072 AATTTAGAATGAGAGTCATAGTTTTTGGATGAAATTAGAATGTTTAAAATTTTGAGGACT
1 AATTTAGAATGAAAGTCATAGTTTGGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACT
* *
131132 AATTTACAATGAAAGTCATAGTTAGGGGA
1 AATTTAGAATGAAAGTCATAGTTTGGGGA
131161 CATATGATCC
Statistics
Matches: 73, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
59 17 0.23
60 56 0.77
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (60 bp):
AATTTAGAATGAAAGTCATAGTTTGGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACT
Found at i:135761 original size:21 final size:21
Alignment explanation
Indices: 135732--135777 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
135722 ACGGGCGTGT
*
135732 CGGTTCACGGTGCTAATGTGA
1 CGGTCCACGGTGCTAATGTGA
* *
135753 CGGTCCACGGTGCTGATGTGG
1 CGGTCCACGGTGCTAATGTGA
135774 CGGT
1 CGGT
135778 TCATCTTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.22, G:0.39, T:0.26
Consensus pattern (21 bp):
CGGTCCACGGTGCTAATGTGA
Found at i:136720 original size:13 final size:13
Alignment explanation
Indices: 136702--136728 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
136692 CATTTAACCC
136702 ATGAGTTACCTTA
1 ATGAGTTACCTTA
136715 ATGAGTTACCTTA
1 ATGAGTTACCTTA
136728 A
1 A
136729 ACCCTAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ATGAGTTACCTTA
Found at i:136747 original size:14 final size:14
Alignment explanation
Indices: 136724--136823 Score: 50
Period size: 14 Copynumber: 7.4 Consensus size: 14
136714 AATGAGTTAC
136724 CTTAAACCCTAAAT
1 CTTAAACCCTAAAT
*
136738 CTTAACCCCTAAAT
1 CTTAAACCCTAAAT
* * *
136752 C--ATA-CATACACT
1 CTTAAACCCTA-AAT
*
136764 CTT-AACCCTAGACT
1 CTTAAACCCTA-AAT
*
136778 CTT-AACCTTAAAT
1 CTTAAACCCTAAAT
* *
136791 CTTAAATCTTAAAT
1 CTTAAACCCTAAAT
* *
136805 C-TAAACCTTAAAC
1 CTTAAACCCTAAAT
136818 CTTAAA
1 CTTAAA
136824 TACAAAATAA
Statistics
Matches: 67, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
11 3 0.04
12 4 0.06
13 17 0.25
14 43 0.64
ACGTcount: A:0.40, C:0.28, G:0.01, T:0.31
Consensus pattern (14 bp):
CTTAAACCCTAAAT
Found at i:136796 original size:7 final size:7
Alignment explanation
Indices: 136784--136824 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
136774 GACTCTTAAC
136784 CTTAAAT
1 CTTAAAT
136791 CTTAAAT
1 CTTAAAT
136798 CTTAAAT
1 CTTAAAT
*
136805 C-TAAAC
1 CTTAAAT
*
136811 CTTAAAC
1 CTTAAAT
136818 CTTAAAT
1 CTTAAAT
136825 ACAAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (7 bp):
CTTAAAT
Found at i:136809 original size:13 final size:14
Alignment explanation
Indices: 136777--136823 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 14
136767 AACCCTAGAC
136777 TCTT-AACCTTAAA
1 TCTTAAACCTTAAA
*
136790 TCTTAAATCTTAAA
1 TCTTAAACCTTAAA
136804 TC-TAAACCTTAAA
1 TCTTAAACCTTAAA
*
136817 CCTTAAA
1 TCTTAAA
136824 TACAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 15 0.52
14 14 0.48
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (14 bp):
TCTTAAACCTTAAA
Found at i:136809 original size:20 final size:20
Alignment explanation
Indices: 136786--136824 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
136776 CTCTTAACCT
* *
136786 TAAATCTTAAATCTTAAATC
1 TAAACCTTAAACCTTAAATC
136806 TAAACCTTAAACCTTAAAT
1 TAAACCTTAAACCTTAAAT
136825 ACAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAACCTTAAACCTTAAATC
Found at i:137252 original size:20 final size:20
Alignment explanation
Indices: 137227--137275 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
137217 GATTTATCTT
137227 CATGTTTATAACAGCACTAG
1 CATGTTTATAACAGCACTAG
137247 CATGTTTATAACAGCACTAG
1 CATGTTTATAACAGCACTAG
137267 CATGTTTAT
1 CATGTTTAT
137276 TAAGTTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTTTATAACAGCACTAG
Found at i:138207 original size:16 final size:15
Alignment explanation
Indices: 138183--138218 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
138173 ATTATATAAA
*
138183 ATATAATGAATTATTT
1 ATATTATGAATTA-TT
138199 ATATTATGAATTATT
1 ATATTATGAATTATT
138214 ATATT
1 ATATT
138219 TTGTATTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
ATATTATGAATTATT
Found at i:138388 original size:17 final size:17
Alignment explanation
Indices: 138363--138423 Score: 104
Period size: 17 Copynumber: 3.6 Consensus size: 17
138353 ACCCGATTAC
138363 CGGGTACCCGCAAAATT
1 CGGGTACCCGCAAAATT
*
138380 CGAGTACCCGCAAAATT
1 CGGGTACCCGCAAAATT
*
138397 CGGGTACTCGCAAAATT
1 CGGGTACCCGCAAAATT
138414 CGGGTACCCG
1 CGGGTACCCG
138424 ATTACCGGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.18
Consensus pattern (17 bp):
CGGGTACCCGCAAAATT
Found at i:138704 original size:32 final size:31
Alignment explanation
Indices: 138663--138724 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
138653 AGACGCAAGT
* *
138663 GATGAATGACATACATTATA-GATATATAAAA
1 GATGAATGACACACATCATATG-TATATAAAA
138694 GATGATATGACACACATCATATGTATATAAA
1 GATGA-ATGACACACATCATATGTATATAAA
138725 TGATAGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 5 0.19
32 21 0.78
33 1 0.04
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (31 bp):
GATGAATGACACACATCATATGTATATAAAA
Found at i:153583 original size:73 final size:73
Alignment explanation
Indices: 153457--153592 Score: 218
Period size: 73 Copynumber: 1.9 Consensus size: 73
153447 ATTATTTCAC
* * *
153457 TTGTTAATATTTTTGTTTATCAGACTATCACTAAACGATTATTGTTATGTTTTATTTATGATAGT
1 TTGTTAATATTTTTATTTATCAGACTATCACTAAACGATTATTATTATATTTTATTTATGATAGT
153522 TGATTTAA
66 TGATTTAA
* **
153530 TTGTTAATATTTTTATTTATCATACTATCACTAAGTGATTATTATTATATTTTATTTATGATA
1 TTGTTAATATTTTTATTTATCAGACTATCACTAAACGATTATTATTATATTTTATTTATGATA
153593 ATATGTAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 57 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.54
Consensus pattern (73 bp):
TTGTTAATATTTTTATTTATCAGACTATCACTAAACGATTATTATTATATTTTATTTATGATAGT
TGATTTAA
Found at i:153973 original size:2 final size:2
Alignment explanation
Indices: 153966--154015 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
153956 TAATTTAATT
153966 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
154008 TA TA TA TA
1 TA TA TA TA
154016 ATTATTTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:162020 original size:24 final size:24
Alignment explanation
Indices: 161993--162040 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
161983 TTACTCTCTC
*
161993 GAATCCCTAACCCTTCTTTCTCCA
1 GAATCCCTAACCCTGCTTTCTCCA
*
162017 GAATCCCTAACCCTGCTTTTTCCA
1 GAATCCCTAACCCTGCTTTCTCCA
162041 TTCCCAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.40, G:0.06, T:0.33
Consensus pattern (24 bp):
GAATCCCTAACCCTGCTTTCTCCA
Done.