Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000830.1 Hibiscus syriacus cultivar Beakdansim tig00001606_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: 151632
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2897 original size:19 final size:19
Alignment explanation
Indices: 2873--2938 Score: 123
Period size: 19 Copynumber: 3.5 Consensus size: 19
2863 TGATTCGTGT
*
2873 ATCGATGCATGAGTAGTGC
1 ATCGATGCATGGGTAGTGC
2892 ATCGATGCATGGGTAGTGC
1 ATCGATGCATGGGTAGTGC
2911 ATCGATGCATGGGTAGTGC
1 ATCGATGCATGGGTAGTGC
2930 ATCGATGCA
1 ATCGATGCA
2939 CATGTTAAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (19 bp):
ATCGATGCATGGGTAGTGC
Found at i:2972 original size:20 final size:20
Alignment explanation
Indices: 2947--2984 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2937 CACATGTTAA
2947 AGAATGCATCGATACACTAT
1 AGAATGCATCGATACACTAT
* *
2967 AGAATGTATCGATGCACT
1 AGAATGCATCGATACACT
2985 TCAAGGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTAT
Found at i:3624 original size:2 final size:2
Alignment explanation
Indices: 3617--3670 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3607 AGAGATAACA
3617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3659 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3671 TACATGTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6688 original size:19 final size:19
Alignment explanation
Indices: 6664--6715 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
6654 GAATGCAATT
6664 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
6683 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
6702 AGTGCATCGATGCA
1 AGTGCATCGATGCA
6716 CCCCCTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:6783 original size:19 final size:19
Alignment explanation
Indices: 6759--6795 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6749 TGTATCAATG
*
6759 CATGGGTAGTGCATCGATA
1 CATGGGCAGTGCATCGATA
6778 CATGGGCAGTGCATCGAT
1 CATGGGCAGTGCATCGAT
6796 GCACATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (19 bp):
CATGGGCAGTGCATCGATA
Found at i:6815 original size:24 final size:20
Alignment explanation
Indices: 6787--6844 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
6777 ACATGGGCAG
6787 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
6811 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
6831 TGTATCGATGCACT
1 TGCATCGATGCACT
6845 TCAAGGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:9518 original size:63 final size:65
Alignment explanation
Indices: 9415--9544 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 65
9405 CTCCAATATT
* * *
9415 ATCAAGACCAGCAGCATCAACTACATTTTCAGCAACCCTCTCAGCAGCATAATCACCAGCACCCT
1 ATCAAGACCAGCA-CATCAACTACATTTTCAGCAACCCTCTCAGCAGCACAATCAACAACACCCT
9480 C
65 C
*
9481 ATCAAGACCAGCA-A-CAACTACATTTTCAGCAAGCCTCTCAGCAGCACAATCAACAACACCCTC
1 ATCAAGACCAGCACATCAACTACATTTTCAGCAACCCTCTCAGCAGCACAATCAACAACACCCTC
9544 A
1 A
9545 CCAACACCCT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
63 46 0.77
64 1 0.02
66 13 0.22
ACGTcount: A:0.36, C:0.37, G:0.10, T:0.17
Consensus pattern (65 bp):
ATCAAGACCAGCACATCAACTACATTTTCAGCAACCCTCTCAGCAGCACAATCAACAACACCCTC
Found at i:9559 original size:36 final size:36
Alignment explanation
Indices: 9517--9594 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
9507 CAGCAAGCCT
9517 CTCAGCAGCACAATCAACAACACCCTCACCAACACC
1 CTCAGCAGCACAATCAACAACACCCTCACCAACACC
* * **
9553 CTCAGCAGCACAATCAGCAGCACCCTCACCAGTACC
1 CTCAGCAGCACAATCAACAACACCCTCACCAACACC
9589 CTCAGC
1 CTCAGC
9595 GACATTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.33, C:0.46, G:0.10, T:0.10
Consensus pattern (36 bp):
CTCAGCAGCACAATCAACAACACCCTCACCAACACC
Found at i:9593 original size:24 final size:24
Alignment explanation
Indices: 9537--9594 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
9527 CAATCAACAA
* *
9537 CACCCTCACCAACACCCTCAGCAG
1 CACCCTCAGCAACACCCTCACCAG
** *
9561 CACAATCAGCAGCACCCTCACCAG
1 CACCCTCAGCAACACCCTCACCAG
*
9585 TACCCTCAGC
1 CACCCTCAGC
9595 GACATTTATT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.50, G:0.10, T:0.10
Consensus pattern (24 bp):
CACCCTCAGCAACACCCTCACCAG
Found at i:17819 original size:60 final size:59
Alignment explanation
Indices: 17726--17855 Score: 197
Period size: 60 Copynumber: 2.2 Consensus size: 59
17716 ATGGCAAGAA
* * *
17726 AGTTGAGAGGCCAAATTGATAGCATAAATTCTTAAATGGCCGCATTGTTTGATAGGGTAT
1 AGTTGAGTGGCCAAATTGATAGCAAAAATTCTTAAATGGCCACA-TGTTTGATAGGGTAT
* * *
17786 AGTTGAGTGGCCAAATTGATAGTAAAAATTCTTAGATGGCCACATGTTTGATAGGGTTT
1 AGTTGAGTGGCCAAATTGATAGCAAAAATTCTTAAATGGCCACATGTTTGATAGGGTAT
17845 AGTTGAGTGGC
1 AGTTGAGTGGC
17856 TATAGTGGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
59 25 0.39
60 39 0.61
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (59 bp):
AGTTGAGTGGCCAAATTGATAGCAAAAATTCTTAAATGGCCACATGTTTGATAGGGTAT
Found at i:24455 original size:33 final size:33
Alignment explanation
Indices: 24418--24500 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
24408 ATGGTTTGGG
* *
24418 CATATGGATTAGCATTTGGCTACGCAAGTTGAC
1 CATATGGATTAGTATTTGGCTACACAAGTTGAC
* *
24451 CATATGGATTAGTATTTGGCTGCACAGGTTGAC
1 CATATGGATTAGTATTTGGCTACACAAGTTGAC
24484 CATATGGATTAGTATTT
1 CATATGGATTAGTATTT
24501 AGCTGTGAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (33 bp):
CATATGGATTAGTATTTGGCTACACAAGTTGAC
Found at i:24514 original size:33 final size:33
Alignment explanation
Indices: 24418--24528 Score: 125
Period size: 33 Copynumber: 3.4 Consensus size: 33
24408 ATGGTTTGGG
* * * * *
24418 CATATGGATTAGCATTTGGCTACGCAAGTTGAC
1 CATATGGATTAGTATTTAGCTGCACAGGTTGAC
*
24451 CATATGGATTAGTATTTGGCTGCACAGGTTGAC
1 CATATGGATTAGTATTTAGCTGCACAGGTTGAC
* * *
24484 CATATGGATTAGTATTTAGCTGTGA-GGGTTGGC
1 CATATGGATTAGTATTTAGCTG-CACAGGTTGAC
24517 CATATGGATTAG
1 CATATGGATTAG
24529 CACCTGGTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 68 0.99
34 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (33 bp):
CATATGGATTAGTATTTAGCTGCACAGGTTGAC
Found at i:29660 original size:2 final size:2
Alignment explanation
Indices: 29653--29678 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29643 TAAATTACTT
29653 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
29679 GAACTCTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38248 original size:3 final size:3
Alignment explanation
Indices: 38242--38294 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
38232 ATATATTAAA
** *
38242 ATT ATT ATT A-T ATT AAA ATT ATT ATT ATC A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
38288 ATT ATT A
1 ATT ATT A
38295 CAAATATTAC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 3 0.07
3 39 0.93
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:38255 original size:17 final size:17
Alignment explanation
Indices: 38233--38291 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
38223 CGTCCAATAA
38233 TATATTAAAATTATTAT
1 TATATTAAAATTATTAT
38250 TATATTAAAATTATTAT
1 TATATTAAAATTATTAT
**
38267 TATCA-TATTATTATTAT
1 TAT-ATTAAAATTATTAT
38284 TATTATTA
1 TA-TATTA
38292 TTACAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 33 0.89
18 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTAAAATTATTAT
Found at i:38267 original size:20 final size:20
Alignment explanation
Indices: 38242--38292 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
38232 ATATATTAAA
38242 ATTATTATTATATTAAAATT
1 ATTATTATTATATTAAAATT
* **
38262 ATTATTATCATATTATTATT
1 ATTATTATTATATTAAAATT
38282 ATTATTATTAT
1 ATTATTATTAT
38293 TACAAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATTATTATATTAAAATT
Found at i:39804 original size:9 final size:9
Alignment explanation
Indices: 39790--39822 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
39780 TATCTTATGC
39790 TAATTAATT
1 TAATTAATT
39799 TAATTAATT
1 TAATTAATT
*
39808 TTA-TAATT
1 TAATTAATT
39816 TAATTAA
1 TAATTAA
39823 AGAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:43302 original size:45 final size:46
Alignment explanation
Indices: 43213--43303 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
43203 TTGAAAAAGC
* *
43213 CTGAGTGCATCGATGCATGGTCTTATGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATATGCATCGATGCATAAAATGCA
* *
43259 CTGAGTGTATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATATGCATCGATGCATAAAATGCA
43304 TTCGATGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATATGCATCGATGCATAAAATGCA
Found at i:48320 original size:15 final size:15
Alignment explanation
Indices: 48300--48336 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
48290 TCGGAGAAAA
*
48300 AGAATAAGAAATGTC
1 AGAATAAGAAATGCC
48315 AGAATAAGAAATGCC
1 AGAATAAGAAATGCC
48330 AGAATAA
1 AGAATAA
48337 TGAAGCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.57, C:0.08, G:0.19, T:0.16
Consensus pattern (15 bp):
AGAATAAGAAATGCC
Found at i:50204 original size:99 final size:99
Alignment explanation
Indices: 50033--50264 Score: 401
Period size: 99 Copynumber: 2.3 Consensus size: 99
50023 CACAAATTTG
*
50033 TAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGTGA
1 TAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATAAAAATGAGAAAGTGA
50098 TTACCAAAGTTTCTCATTTAATGTTCAAGAAAAT
66 TTACCAAAGTTTCTCATTTAATGTTCAAGAAAAT
*
50132 TAAATCCTCCGAGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATAAAAATGAGAAAGTGA
1 TAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATAAAAATGAGAAAGTGA
*
50197 TTACCAAAGTTTCTCATTTAATGTTCTAGAAAAT
66 TTACCAAAGTTTCTCATTTAATGTTCAAGAAAAT
* * * *
50231 TAAAACCTCCGGGTAATTTGTAAAACCTCTGGGT
1 TAAATCCTCCGGGTCATCTGTAAAACCTCAGGGT
50265 CTTCTGTAAA
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 125 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (99 bp):
TAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATAAAAATGAGAAAGTGA
TTACCAAAGTTTCTCATTTAATGTTCAAGAAAAT
Found at i:50256 original size:20 final size:20
Alignment explanation
Indices: 50231--50278 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
50221 TCTAGAAAAT
50231 TAAAACCTCCGGGTAATT-TG
1 TAAAACCTCCGGGT-ATTCTG
* *
50251 TAAAACCTCTGGGTCTTCTG
1 TAAAACCTCCGGGTATTCTG
50271 TAAAACCT
1 TAAAACCT
50279 TAGGGTAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (20 bp):
TAAAACCTCCGGGTATTCTG
Found at i:50359 original size:119 final size:119
Alignment explanation
Indices: 50148--50383 Score: 409
Period size: 119 Copynumber: 2.0 Consensus size: 119
50138 CTCCGAGTCA
50148 TCTGTAAAACCTCAGGGTAGGATGTTTTCGCATAAAAATGAGAAAGTGATTACCAAAGTTTCTCA
1 TCTGTAAAACCTCAGGGTAGGATGTTTTCGCATAAAAATGAGAAAGTGATTACCAAAGTTTCTCA
* * *
50213 TTTAATGTTCTAGAAAATTAAAACCTCCGGGTAATTTGTAAAACCTCTGGGTCT
66 TTTAATGTTCAAGAAAATTAAAACCTCCGGGTAATCTGTAAAACCTCAGGGTCT
* *
50267 TCTGTAAAACCTTAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGTGATTACCAAAGTTTCTCA
1 TCTGTAAAACCTCAGGGTAGGATGTTTTCGCATAAAAATGAGAAAGTGATTACCAAAGTTTCTCA
* *
50332 TTTAATGTTCAAGAAAATTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGT
66 TTTAATGTTCAAGAAAATTAAAACCTCCGGGTAATCTGTAAAACCTCAGGGT
50384 AGGATGTTTT
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 110 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (119 bp):
TCTGTAAAACCTCAGGGTAGGATGTTTTCGCATAAAAATGAGAAAGTGATTACCAAAGTTTCTCA
TTTAATGTTCAAGAAAATTAAAACCTCCGGGTAATCTGTAAAACCTCAGGGTCT
Found at i:50406 original size:218 final size:218
Alignment explanation
Indices: 50027--50579 Score: 980
Period size: 218 Copynumber: 2.5 Consensus size: 218
50017 ATTTCCCACA
50027 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
*
50092 AAGTGATTACCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCCGAGTCATCTGTAAAA
66 AAGTGATTACCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCCGGGTCATCTGTAAAA
**
50157 CCTCAGGGTAGGATGTTTTCGCATAAAAATGAGAAAGTGATTACCAAAGTTTCTCATTTAATGTT
131 CCTCAGGGTAGGATGTTTTCGCATAAAAATGAGAAAACGATTACCAAAGTTTCTCATTTAATGTT
*
50222 CTAGAAAATTAAAACCTCCGGGT
196 CTAGAAAATTAAAACCTCCAGGT
* * * *
50245 AATTTGTAAAACCTCTGGGTCTTCTGTAAAACCTTAGGGTAGGATGTTTTCGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
50310 AAGTGATTACCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCCGGGTCATCTGTAAAA
66 AAGTGATTACCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCCGGGTCATCTGTAAAA
*
50375 CCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAACGATTACCAAAGTTTCTCATTTAATGTT
131 CCTCAGGGTAGGATGTTTTCGCATAAAAATGAGAAAACGATTACCAAAGTTTCTCATTTAATGTT
50440 CTAGAAAATTAAAACCTCCAGGT
196 CTAGAAAATTAAAACCTCCAGGT
* *
50463 AATTTGTAAATCCTCCGGATCATCTGTAAAACCTCAGGGTAGGATGTTTTCACATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
** *
50528 AAACGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGG
66 AAGTGATTACCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCCGG
50580 TTGGTTTATA
Statistics
Matches: 317, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
218 317 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (218 bp):
AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
AAGTGATTACCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCCGGGTCATCTGTAAAA
CCTCAGGGTAGGATGTTTTCGCATAAAAATGAGAAAACGATTACCAAAGTTTCTCATTTAATGTT
CTAGAAAATTAAAACCTCCAGGT
Found at i:50432 original size:99 final size:99
Alignment explanation
Indices: 50251--50477 Score: 355
Period size: 99 Copynumber: 2.3 Consensus size: 99
50241 GGGTAATTTG
* * * **
50251 TAAAACCTCTGGGTCTTCTGTAAAACCTTAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGTGA
1 TAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAACGA
50316 TTACCAAAGTTTCTCATTTAATGTTCAAGAAAAT
66 TTACCAAAGTTTCTCATTTAATGTTCAAGAAAAT
*
50350 TAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAACGA
1 TAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAACGA
*
50415 TTACCAAAGTTTCTCATTTAATGTTCTAGAAAAT
66 TTACCAAAGTTTCTCATTTAATGTTCAAGAAAAT
* * * *
50449 TAAAACCTCCAGGTAATTTGTAAATCCTC
1 TAAAACCTCCGGGTCATCTGTAAAACCTC
50478 CGGATCATCT
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 116 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (99 bp):
TAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAACGA
TTACCAAAGTTTCTCATTTAATGTTCAAGAAAAT
Found at i:50561 original size:119 final size:119
Alignment explanation
Indices: 50350--50631 Score: 449
Period size: 119 Copynumber: 2.4 Consensus size: 119
50340 TCAAGAAAAT
*
50350 TAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAACGA
1 TAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCACATGAAAATGAGAAAACGA
*
50415 TTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCAGG-TAATTTG
66 TTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCC-GGTTAATTTA
*
50469 TAAATCCTCCGGATCATCTGTAAAACCTCAGGGTAGGATGTTTTCACATGAAAATGAGAAAACGA
1 TAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCACATGAAAATGAGAAAACGA
* **
50534 TTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGTTGGTTTA
66 TTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGTTAATTTA
* * * * *
50588 TAAAACCTCTGGGTCATTTGTAAAACCTCCGGGTATGATGTTTT
1 TAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTT
50632 TACTTTAATT
Statistics
Matches: 150, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
118 2 0.01
119 148 0.99
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (119 bp):
TAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCACATGAAAATGAGAAAACGA
TTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGTTAATTTA
Found at i:50596 original size:20 final size:20
Alignment explanation
Indices: 50584--50621 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
50574 CTCCGGTTGG
*
50584 TTTATAAAACCTCTGGGTCA
1 TTTATAAAACCTCCGGGTCA
*
50604 TTTGTAAAACCTCCGGGT
1 TTTATAAAACCTCCGGGT
50622 ATGATGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (20 bp):
TTTATAAAACCTCCGGGTCA
Found at i:50769 original size:3 final size:3
Alignment explanation
Indices: 50763--50859 Score: 135
Period size: 3 Copynumber: 33.0 Consensus size: 3
50753 TCCAATAATA
* * * *
50763 TAT TAT TAT TAT TAT TAT TAT TAT TTT TA- TAT TAC AAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
50810 CA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
50857 TAT
1 TAT
50860 AAATATTACA
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 3 0.04
3 81 0.96
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:52791 original size:9 final size:9
Alignment explanation
Indices: 52777--52809 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
52767 TATCTTATGC
52777 TAATTAATT
1 TAATTAATT
52786 TAATTAATT
1 TAATTAATT
*
52795 TTA-TAATT
1 TAATTAATT
52803 TAATTAA
1 TAATTAA
52810 AGAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:55677 original size:65 final size:63
Alignment explanation
Indices: 55558--55767 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
55548 TTTTTCAGAG
* * *
55558 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATT-CAACATTGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATTGAATGC
55620 ATT
61 ATT
* *
55623 TCATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATTGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATTGAATGCAT
55687 T
63 T
* * * * *
55688 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATTGAATGCATT
55752 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
55768 TCTTAGTGCA
Statistics
Matches: 125, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 47 0.38
65 70 0.56
66 5 0.04
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATTGAATGCATT
Found at i:63152 original size:21 final size:21
Alignment explanation
Indices: 63111--63153 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
63101 CCCTGGGAGT
*
63111 TAGCTCTTCACGAGCTGCTCC
1 TAGCTCTTCACGAGCTCCTCC
* *
63132 TAGCTCTTCTCGTGCTCCTCC
1 TAGCTCTTCACGAGCTCCTCC
63153 T
1 T
63154 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.40, G:0.16, T:0.35
Consensus pattern (21 bp):
TAGCTCTTCACGAGCTCCTCC
Found at i:64290 original size:45 final size:46
Alignment explanation
Indices: 64234--64341 Score: 125
Period size: 46 Copynumber: 2.4 Consensus size: 46
64224 TGCACCAATC
64234 CATGCATCGATGCATCATGA-ATTAAATTG-AACATCGAATGCATTT
1 CATGCATCGATGCATCATGAGATTAAA-TGAAACATCGAATGCATTT
**
64279 CATGCATCGATGCA-C-TGAGGATTTTATGAAAACATCGAATGCATTT
1 CATGCATCGATGCATCATGA-GATTAAATG-AAACATCGAATGCATTT
* *
64325 GATGCATCAATGCATCA
1 CATGCATCGATGCATCA
64342 GCCATGCATC
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
43 3 0.06
44 3 0.06
45 18 0.34
46 28 0.53
47 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (46 bp):
CATGCATCGATGCATCATGAGATTAAATGAAACATCGAATGCATTT
Found at i:64421 original size:19 final size:19
Alignment explanation
Indices: 64399--64442 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
64389 GATGCATCGG
64399 TGCACTCTTAGTGCACCGA
1 TGCACTCTTAGTGCACCGA
64418 TGCACTCTTAGTGCACCGA
1 TGCACTCTTAGTGCACCGA
64437 TGCACT
1 TGCACT
64443 AAGGGTCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.27
Consensus pattern (19 bp):
TGCACTCTTAGTGCACCGA
Found at i:73459 original size:21 final size:21
Alignment explanation
Indices: 73435--73474 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
73425 TGCAATTAGC
73435 TTTTCCTAGGACGTAACCAAT
1 TTTTCCTAGGACGTAACCAAT
* * *
73456 TTTTCTTGGGATGTAACCA
1 TTTTCCTAGGACGTAACCA
73475 GCTTTCTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (21 bp):
TTTTCCTAGGACGTAACCAAT
Found at i:75064 original size:27 final size:26
Alignment explanation
Indices: 75015--75065 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
75005 TTATTTAAAG
*
75015 AAATAAAAAGATAAAGATTAAAAATA
1 AAATAAAAAGATAAAGATAAAAAATA
**
75041 AAATAAAAGAGATATGGATAAAAAA
1 AAATAAAA-AGATAAAGATAAAAAA
75066 ACTTATTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (26 bp):
AAATAAAAAGATAAAGATAAAAAATA
Found at i:75778 original size:85 final size:82
Alignment explanation
Indices: 75688--75858 Score: 245
Period size: 85 Copynumber: 2.0 Consensus size: 82
75678 AACAACATCT
75688 TAAATCCTAATTAAAACACTTAA-AACTATTTAAACTAAAATACCTAAAACAAAGATAAAATAAA
1 TAAATCCTAATTAAAACAC-TAACAACTATTTAAACTAAAATACCTAAAACAAAGATAAAAT---
*
75752 ATACTATTTAAAATAATATCC
62 ATAATATTTAAAATAATATCC
* * *
75773 TAAATCCTAATTGAAATACTAACATCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAACACTAACAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
* *
75838 TGTTTAAAATATTATCC
66 TATTTAAAATAATATCC
75855 TAAA
1 TAAA
75859 ACTTGAGTTT
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
82 22 0.28
84 3 0.04
85 54 0.68
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (82 bp):
TAAATCCTAATTAAAACACTAACAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
TATTTAAAATAATATCC
Found at i:79176 original size:38 final size:38
Alignment explanation
Indices: 79125--79200 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
79115 TTTGATCTTC
79125 CCACGCGGACGACATCAACAGTCTGCAATCATTATTGT
1 CCACGCGGACGACATCAACAGTCTGCAATCATTATTGT
79163 CCACGCGGACGACATCAACAGTCTGCAATCATTATTGT
1 CCACGCGGACGACATCAACAGTCTGCAATCATTATTGT
79201 GATTCTGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (38 bp):
CCACGCGGACGACATCAACAGTCTGCAATCATTATTGT
Found at i:89289 original size:2 final size:2
Alignment explanation
Indices: 89282--89333 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
89272 ATAACAAGTC
89282 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
89324 GA GA GA GA GA
1 GA GA GA GA GA
89334 AGTGGGGACC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:92342 original size:62 final size:62
Alignment explanation
Indices: 92248--92435 Score: 349
Period size: 62 Copynumber: 3.0 Consensus size: 62
92238 GCAACCATGT
92248 ATACATAGTGTGTGTGCAGTGTGCGCTAACAATAAAGTAAGAAAATTCTAAACATATACTAC
1 ATACATAGTGTGTGTGCAGTGTGCGCTAACAATAAAGTAAGAAAATTCTAAACATATACTAC
* *
92310 ATGCATAGTGTGTGTGCAGTGTGCGCTAACAATAAAGTAAAAAAATTCTAAACATATACTAC
1 ATACATAGTGTGTGTGCAGTGTGCGCTAACAATAAAGTAAGAAAATTCTAAACATATACTAC
*
92372 ATACATAGTGTGTGTGCAGTGTGCGCTAACAATGAAGTAAGAAAATTCTAAACATATACTAC
1 ATACATAGTGTGTGTGCAGTGTGCGCTAACAATAAAGTAAGAAAATTCTAAACATATACTAC
92434 AT
1 AT
92436 TATAATCATC
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 121 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (62 bp):
ATACATAGTGTGTGTGCAGTGTGCGCTAACAATAAAGTAAGAAAATTCTAAACATATACTAC
Found at i:100183 original size:2 final size:2
Alignment explanation
Indices: 100176--100207 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
100166 ACCCATAAAT
100176 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
100208 AAAGAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:100340 original size:20 final size:20
Alignment explanation
Indices: 100294--100343 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
100284 ATGACCAACA
*
100294 AAATCGCAACGCGAATTTGT
1 AAATCGCAACGCGAATTCGT
100314 AAATCGCAACGCGAATCTCG-
1 AAATCGCAACGCGAAT-TCGT
*
100334 AATTCGCAAC
1 AAATCGCAAC
100344 ACAAAAGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATTCGT
Found at i:100543 original size:22 final size:22
Alignment explanation
Indices: 100518--100567 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
100508 CTACGGCGAC
100518 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* * *
100540 ATCCAT-CCCATCTTCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
100561 ATCCGTC
1 ATCCGTC
100568 TATCTCCATC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.22, C:0.42, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:100931 original size:20 final size:20
Alignment explanation
Indices: 100906--100944 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
100896 TTTTAAACTT
100906 AAATTCGCAACACGAAAATA
1 AAATTCGCAACACGAAAATA
100926 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
100945 CGCAATGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.21, G:0.10, T:0.15
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATA
Found at i:101004 original size:20 final size:20
Alignment explanation
Indices: 100950--101004 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
100940 AAAATCGCAA
* *
100950 TGCG-ATTTTAGTTTCGCTT
1 TGCGAATTTAAGTTTCGCGT
* *
100969 TGC-AATTTTCATTTTCGCGT
1 TGCGAA-TTTAAGTTTCGCGT
100989 TGCGAATTTAAGTTTC
1 TGCGAATTTAAGTTTC
101005 AGAAACTACT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 4 0.14
20 22 0.79
21 2 0.07
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.49
Consensus pattern (20 bp):
TGCGAATTTAAGTTTCGCGT
Found at i:102385 original size:42 final size:42
Alignment explanation
Indices: 102326--102422 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
102316 CCTCACTTCG
* * * *
102326 AGAGCCATCACCTGATCGAG-TCGATTCTACAGCTCGACACCC
1 AGAGCCATCACCTGATCGAGCT-GATTATACACCTCCACAACC
*
102368 AGAGCCATCACCTGATCGAGCTGATTATACACCTCCACAACG
1 AGAGCCATCACCTGATCGAGCTGATTATACACCTCCACAACC
102410 AGAGCCATCACCT
1 AGAGCCATCACCT
102423 ATTCCATCAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
42 48 0.98
43 1 0.02
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.19
Consensus pattern (42 bp):
AGAGCCATCACCTGATCGAGCTGATTATACACCTCCACAACC
Found at i:102580 original size:21 final size:21
Alignment explanation
Indices: 102540--102580 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
102530 AGGGGAGTTA
*
102540 CGTGATGAGGTCAGTGCTTTG
1 CGTGATGAGGTCAGTACTTTG
102561 CGTGATGAGGTC-GATACTTT
1 CGTGATGAGGTCAG-TACTTT
102581 ACATCACGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.17, C:0.15, G:0.34, T:0.34
Consensus pattern (21 bp):
CGTGATGAGGTCAGTACTTTG
Found at i:102736 original size:42 final size:42
Alignment explanation
Indices: 102619--102719 Score: 193
Period size: 42 Copynumber: 2.4 Consensus size: 42
102609 AAGGTACGGT
102619 CTTTACGTGGTGAGGTAGATGTTTTATGCGATGACAATGGTG
1 CTTTACGTGGTGAGGTAGATGTTTTATGCGATGACAATGGTG
*
102661 CTTTACGTGGTGAGATAGATGTTTTATGCGATGACAATGGTG
1 CTTTACGTGGTGAGGTAGATGTTTTATGCGATGACAATGGTG
102703 CTTTACGTGGTGAGGTA
1 CTTTACGTGGTGAGGTA
102720 TCTACTTTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.22, C:0.10, G:0.33, T:0.36
Consensus pattern (42 bp):
CTTTACGTGGTGAGGTAGATGTTTTATGCGATGACAATGGTG
Found at i:102872 original size:12 final size:12
Alignment explanation
Indices: 102846--102887 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
102836 ATTTTTGACA
102846 TTATTTATTTG-T
1 TTATTTA-TTGAT
102858 TTATTTATTGAT
1 TTATTTATTGAT
* *
102870 TTATGTATTAAT
1 TTATTTATTGAT
102882 TTATTT
1 TTATTT
102888 TTAGCGGCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
TTATTTATTGAT
Found at i:103059 original size:21 final size:21
Alignment explanation
Indices: 103037--103128 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
103027 TTTGTCATCG
*
103037 TTCAAGAGGCCCCTCCTATCG
1 TTCAAGAGGCCCCTCCTATCA
* **
103058 TTCAAGAGGCCCCTCCCAAAA
1 TTCAAGAGGCCCCTCCTATCA
*
103079 TTCAAGAGGCCCCT-ATCATCA
1 TTCAAGAGGCCCCTCCT-ATCA
* * *
103100 TTCAAGAGGTCCCTCCCACCA
1 TTCAAGAGGCCCCTCCTATCA
103121 TTCAAGAG
1 TTCAAGAG
103129 CCCGATTTAC
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.27, C:0.36, G:0.16, T:0.21
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCTATCA
Found at i:103104 original size:42 final size:42
Alignment explanation
Indices: 103037--103128 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
103027 TTTGTCATCG
*
103037 TTCAAGAGGCCCCTCCTATCGTTCAAGAGGCCCCTCCCAAAA
1 TTCAAGAGGCCCCTCCTATCATTCAAGAGGCCCCTCCCAAAA
* * **
103079 TTCAAGAGGCCCCT-ATCATCATTCAAGAGGTCCCTCCCACCA
1 TTCAAGAGGCCCCTCCT-ATCATTCAAGAGGCCCCTCCCAAAA
103121 TTCAAGAG
1 TTCAAGAG
103129 CCCGATTTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.02
42 43 0.98
ACGTcount: A:0.27, C:0.36, G:0.16, T:0.21
Consensus pattern (42 bp):
TTCAAGAGGCCCCTCCTATCATTCAAGAGGCCCCTCCCAAAA
Found at i:108189 original size:20 final size:19
Alignment explanation
Indices: 108143--108270 Score: 64
Period size: 20 Copynumber: 6.5 Consensus size: 19
108133 AAAACATTTT
* *
108143 TGTTGCGAAAATAAAA-CC
1 TGTTGCGAAATTAAAATCG
*
108161 TGGTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAA-TCG
108181 TGTTGCG-AATTCGAAAATCG
1 TGTTGCGAAATT--AAAATCG
* **
108201 AGTTGCGAAAACAAAATTCG
1 TGTTGCGAAATTAAAA-TCG
**
108221 CATTGCG-AATTCAGAAATCG
1 TGTTGCGAAATT-A-AAATCG
* * *
108241 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATT-AAAATC-G
108262 TGTTGCGAA
1 TGTTGCGAA
108271 TTTGGAAACT
Statistics
Matches: 83, Mismatches: 17, Indels: 17
0.71 0.15 0.15
Matches are distributed among these distances:
18 14 0.17
19 10 0.12
20 37 0.45
21 22 0.27
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (19 bp):
TGTTGCGAAATTAAAATCG
Found at i:108217 original size:40 final size:40
Alignment explanation
Indices: 108164--108272 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 40
108154 TAAAACCTGG
108164 TGCGAAATTAAAATTCGTGTTGCGAATTC-GAAAATCGAGT
1 TGCGAAATTAAAATTCGTGTTGCGAATTCAG-AAATCGAGT
** **
108204 TGCGAAAACAAAATTCGCATTGCGAATTCAGAAATCGAGT
1 TGCGAAATTAAAATTCGTGTTGCGAATTCAGAAATCGAGT
* *
108244 TGCGAATTTGAAATTCAGTGTTGCGAATT
1 TGCGAAATTAAAATTC-GTGTTGCGAATT
108273 TGGAAACTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
40 46 0.81
41 11 0.19
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (40 bp):
TGCGAAATTAAAATTCGTGTTGCGAATTCAGAAATCGAGT
Found at i:109763 original size:58 final size:57
Alignment explanation
Indices: 109598--109788 Score: 197
Period size: 58 Copynumber: 3.3 Consensus size: 57
109588 CCAAATAATC
** * * * *
109598 ATTTTGTAACTTTTAATTGTT-AGAAAAGTAAACAAGTAATGCCCTATAATTAGGTGAA
1 ATTTTGTAACTTTTAACAGTTGA-AAAACTCAACAA-CAATGCCCTATAATTAGATGAA
* *
109656 GATTTTGTAACTTTTAACAGTTGAAAAACTCAACAACAACGCACTATAATTAGATGACA
1 -ATTTTGTAACTTTTAACAGTTGAAAAACTCAACAACAATGCCCTATAATTAGATGA-A
* * * *
109715 ATTTTGTAACTTTTAAGAGTTGAAAAACTCAACAACAGTGCCCAATAATTA-ATAGATT
1 ATTTTGTAACTTTTAACAGTTGAAAAACTCAACAACAATGCCCTATAATTAGAT-GA-A
*
109773 ATTTCGTAACTTTTAA
1 ATTTTGTAACTTTTAA
109789 TAATCAGTGG
Statistics
Matches: 113, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
57 2 0.02
58 80 0.71
59 30 0.27
60 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (57 bp):
ATTTTGTAACTTTTAACAGTTGAAAAACTCAACAACAATGCCCTATAATTAGATGAA
Found at i:115830 original size:22 final size:23
Alignment explanation
Indices: 115796--115838 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
115786 ATATAATAAA
115796 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
115819 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
115839 TATTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:116189 original size:13 final size:13
Alignment explanation
Indices: 116171--116204 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
116161 TTAAAATAAG
116171 AATATAATAGTAT
1 AATATAATAGTAT
* *
116184 AATATATTATTAT
1 AATATAATAGTAT
116197 AATATAAT
1 AATATAAT
116205 TGAGTATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
AATATAATAGTAT
Found at i:116217 original size:26 final size:26
Alignment explanation
Indices: 116166--116248 Score: 71
Period size: 26 Copynumber: 3.1 Consensus size: 26
116156 TATTATTAAA
*
116166 ATAAGAATATAATAGTATAATATATT
1 ATAATAATATAATAGTATAATATATT
*
116192 ATTATAATATAATTGAGTAT-AT-TATT
1 ATAATAATATAA-T-AGTATAATATATT
* * *
116218 GTAATAATAATATATATTATATTATATT
1 ATAATAAT-ATA-ATAGTATAATATATT
116246 ATA
1 ATA
116249 TTATTAAAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
26 24 0.55
27 8 0.18
28 12 0.27
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (26 bp):
ATAATAATATAATAGTATAATATATT
Found at i:117312 original size:67 final size:69
Alignment explanation
Indices: 117218--117373 Score: 163
Period size: 73 Copynumber: 2.2 Consensus size: 69
117208 AGCAAGAAGC
* *
117218 TTAATGAGCTTAACCAGCAAAGGGTCGA-T-CAACAAATTTTCTTAACAAGCACGAGTCAAGAAA
1 TTAATGAGCTTAACAAGCAAAGAGTCGAGTGCAACAAATTTTCTTAACAAGCACGAGTCAAGAAA
117281 ACTT
66 ACTT
* * * * * *
117285 TTAACGAGCTTAACAATCAATGAGTCGAGGTCGAGCAACAATTTTTTTTAACGAGCACGAGTCAA
1 TTAATGAGCTTAACAAGCAAAGAGTCGA-GT---GCAACAAATTTTCTTAACAAGCACGAGTCAA
* *
117350 GCAAATTT
62 GAAAACTT
*
117358 TTAATGAGTTTAACAA
1 TTAATGAGCTTAACAA
117374 ACAACGAATA
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
67 23 0.32
69 1 0.01
73 47 0.66
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (69 bp):
TTAATGAGCTTAACAAGCAAAGAGTCGAGTGCAACAAATTTTCTTAACAAGCACGAGTCAAGAAA
ACTT
Found at i:117904 original size:21 final size:20
Alignment explanation
Indices: 117869--117924 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
117859 TTCAGAAGGG
*
117869 AAAAA-AATAAAAATAAATA
1 AAAAATAATAATAATAAATA
117888 AATAAATAATAATAAT-AATA
1 AA-AAATAATAATAATAAATA
117908 AAAAAT-ATAATAA-AAAT
1 AAAAATAATAATAATAAAT
117925 GTTAAAAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 10 0.30
19 6 0.18
20 9 0.27
21 8 0.24
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAATAATAATAATAAATA
Found at i:117953 original size:22 final size:22
Alignment explanation
Indices: 117927--117975 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
117917 ATAAAAATGT
*
117927 TAAAAGAGAAAAAAAACAG-AAA
1 TAAAAGA-AAAAAAAAAAGTAAA
*
117949 TAAAATAAAAAAAAAAAGTAAA
1 TAAAAGAAAAAAAAAAAGTAAA
117971 TAAAA
1 TAAAA
117976 TAAAGATTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10
Consensus pattern (22 bp):
TAAAAGAAAAAAAAAAAGTAAA
Found at i:117976 original size:22 final size:21
Alignment explanation
Indices: 117935--117979 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
117925 GTTAAAAGAG
*
117935 AAAAAAAACAGAAATAAAATA
1 AAAAAAAAAAGAAATAAAATA
117956 AAAAAAAAAAGTAAATAAAATA
1 AAAAAAAAAAG-AAATAAAATA
117978 AA
1 AA
117980 GATTGGGGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.82, C:0.02, G:0.04, T:0.11
Consensus pattern (21 bp):
AAAAAAAAAAGAAATAAAATA
Found at i:119188 original size:24 final size:24
Alignment explanation
Indices: 119151--119211 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
119141 AAAATAAGTA
119151 AATAAATAAAATTAAT-TGAATA-AT
1 AATAAA-AAAATTAATAT-AATATAT
119175 AATAAAAAATATTAATATAATATAT
1 AATAAAAAA-ATTAATATAATATAT
119200 AATAATAAAAAT
1 AATAA-AAAAAT
119212 AAATTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
23 3 0.09
24 16 0.48
25 10 0.30
26 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
AATAAAAAAATTAATATAATATAT
Found at i:119228 original size:28 final size:28
Alignment explanation
Indices: 119170--119230 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
119160 AATTAATTGA
* *
119170 ATAATAATAAAAAATATTAATATAATAT
1 ATAATAATAAAAAAAATTAATAAAATAT
**
119198 ATAATAATAAAAATAAATTTTTAAAATTAT
1 ATAATAATAAAAA-AAATTAATAAAA-TAT
119228 ATA
1 ATA
119231 TCATATATGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 13 0.48
29 8 0.30
30 6 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
ATAATAATAAAAAAAATTAATAAAATAT
Found at i:119327 original size:36 final size:37
Alignment explanation
Indices: 119278--119638 Score: 369
Period size: 38 Copynumber: 9.4 Consensus size: 37
119268 ATATAATCTA
* * *
119278 ATATA-TTTTCAAAAT-ATTTAAAAATTGTATATTAT
1 ATATATTTTTCAAAATGTTTTAAAAACTATATATTAT
119313 ATATATTTTTCAAAATGTTTTAAAAACTATATATTAT
1 ATATATTTTTCAAAATGTTTTAAAAACTATATATTAT
* *
119350 ATATATATATATAT-ATATATATTTTCAAAATGTTTTTAAAACTATATTATATAT
1 ATATAT-T-T-T-TCA-A-A-A-TGT--------TTTAAAAACTATA-TAT-TAT
*
119404 ATATATATTT-AAAATGTTTTAAAAACTATATATTAT
1 ATATATTTTTCAAAATGTTTTAAAAACTATATATTAT
* *
119440 ATATATTTTTTAAAAATGTTTTAAAAACAATATATTAT
1 ATATA-TTTTTCAAAATGTTTTAAAAACTATATATTAT
*
119478 ATA-AGTTTTCAAAATGTTTTAAAAACTATATATTAT
1 ATATATTTTTCAAAATGTTTTAAAAACTATATATTAT
*
119514 ATATATATTTTCAAAATGTTTTATAAACTATATATTAT
1 ATATAT-TTTTCAAAATGTTTTAAAAACTATATATTAT
* *
119552 ATA-AGTTTTCAAAATGTTTT-AAAACTATGTATTAT
1 ATATATTTTTCAAAATGTTTTAAAAACTATATATTAT
119587 ATATATATTTTCAAAATGTTTTAAAAACTATATATTAT
1 ATATAT-TTTTCAAAATGTTTTAAAAACTATATATTAT
119625 ATATA-TTTTCAAAA
1 ATATATTTTTCAAAA
119639 ACCGATTTTT
Statistics
Matches: 279, Mismatches: 20, Indels: 53
0.79 0.06 0.15
Matches are distributed among these distances:
35 21 0.08
36 75 0.27
37 48 0.17
38 93 0.33
39 1 0.00
40 2 0.01
41 2 0.01
42 1 0.00
43 1 0.00
44 2 0.01
46 2 0.01
47 1 0.00
48 1 0.00
49 1 0.00
50 2 0.01
51 1 0.00
52 13 0.05
53 3 0.01
54 9 0.03
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (37 bp):
ATATATTTTTCAAAATGTTTTAAAAACTATATATTAT
Found at i:119352 original size:2 final size:2
Alignment explanation
Indices: 119340--119371 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
119330 TTTTAAAAAC
119340 TA TA TA T- 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
119372 TTTCAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:119361 original size:52 final size:51
Alignment explanation
Indices: 119305--119412 Score: 175
Period size: 52 Copynumber: 2.1 Consensus size: 51
119295 TTAAAAATTG
119305 TATATTATATATAT-TTTTCAAAATGTTTTAAAAACTATA-TATTATATATA
1 TATATTATATATATATTTTCAAAATGTTTTAAAAACTATATTA-TATATATA
*
119355 TATATATATATATATATTTTCAAAATGTTTTTAAAACTATATTATATATATA
1 TATAT-TATATATATATTTTCAAAATGTTTTAAAAACTATATTATATATATA
119407 TATATT
1 TATATT
119413 TAAAATGTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
50 5 0.09
51 10 0.19
52 37 0.69
53 2 0.04
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (51 bp):
TATATTATATATATATTTTCAAAATGTTTTAAAAACTATATTATATATATA
Found at i:119401 original size:50 final size:50
Alignment explanation
Indices: 119305--119411 Score: 173
Period size: 50 Copynumber: 2.1 Consensus size: 50
119295 TTAAAAATTG
119305 TATAT-TATATATATTTTTCAAAATGTTTTAAAAACTATATATTATATATA
1 TATATATATATATATTTTTCAAAATGTTTTAAAAAC-ATATATTATATATA
*
119355 TATATATATATATATATTTTCAAAATGTTTTTAAAAC-TATATTATATATA
1 TATATATATATATAT-TTTTCAAAATGTTTTAAAAACATATATTATATATA
119405 TATATAT
1 TATATAT
119412 TTAAAATGTT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
50 25 0.46
51 9 0.17
52 20 0.37
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (50 bp):
TATATATATATATATTTTTCAAAATGTTTTAAAAACATATATTATATATA
Found at i:119405 original size:38 final size:37
Alignment explanation
Indices: 119355--119638 Score: 402
Period size: 38 Copynumber: 7.7 Consensus size: 37
119345 ATTATATATA
*
119355 TATATATATATATATATTTTCAAAATGTTTTTAAAAC
1 TATATATATATATATATTTTCAAAATGTTTTAAAAAC
119392 TATATTATATATATATATATTT-AAAATGTTTTAAAAAC
1 TATA-TATATATATATAT-TTTCAAAATGTTTTAAAAAC
* *
119430 TATATATTATATATATTTTTTAAAAATGTTTTAAAAAC
1 TATATA-TATATATATATTTTCAAAATGTTTTAAAAAC
*
119468 AATATAT-TATATA-AGTTTTCAAAATGTTTTAAAAAC
1 TATATATATATATATA-TTTTCAAAATGTTTTAAAAAC
*
119504 TATATATTATATATATATTTTCAAAATGTTTTATAAAC
1 TATATA-TATATATATATTTTCAAAATGTTTTAAAAAC
119542 TATATAT-TATATA-AGTTTTCAAAATGTTTT-AAAAC
1 TATATATATATATATA-TTTTCAAAATGTTTTAAAAAC
*
119577 TATGTATTATATATATATTTTCAAAATGTTTTAAAAAC
1 TATATA-TATATATATATTTTCAAAATGTTTTAAAAAC
119615 TATATAT-TATATATATTTTCAAAA
1 TATATATATATATATATTTTCAAAA
119639 ACCGATTTTT
Statistics
Matches: 224, Mismatches: 10, Indels: 27
0.86 0.04 0.10
Matches are distributed among these distances:
35 10 0.04
36 70 0.31
37 34 0.15
38 106 0.47
39 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (37 bp):
TATATATATATATATATTTTCAAAATGTTTTAAAAAC
Found at i:119421 original size:90 final size:88
Alignment explanation
Indices: 119278--119445 Score: 257
Period size: 90 Copynumber: 1.9 Consensus size: 88
119268 ATATAATCTA
* * *
119278 ATATATTTTCAAAATATTTAAAAATTGTATATTATATATATTTTTCAAAATGTTTTAAAAACTAT
1 ATATATTTTCAAAATATTTAAAAACTATATATTATATATATATTTCAAAATGTTTTAAAAACTAT
119343 ATATTATATATATATATATATAT
66 ATATTATATATATATATATATAT
* *
119366 ATATATTTTCAAAATGTTTTTAAAACTATATTATATATATATATATTT-AAAATGTTTTAAAAAC
1 ATATATTTTCAAAAT-ATTTAAAAACTATA-TAT-TATATATATATTTCAAAATGTTTTAAAAAC
119430 TATATATTATATATAT
63 TATATATTATATATAT
119446 TTTTTAAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
88 15 0.21
89 10 0.14
90 35 0.49
91 12 0.17
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (88 bp):
ATATATTTTCAAAATATTTAAAAACTATATATTATATATATATTTCAAAATGTTTTAAAAACTAT
ATATTATATATATATATATATAT
Found at i:119495 original size:74 final size:74
Alignment explanation
Indices: 119353--119638 Score: 436
Period size: 74 Copynumber: 3.8 Consensus size: 74
119343 ATATTATATA
*
119353 TATATATATATATATATATTTTCAAAATGTTTTTAAAACTATATTATATATATATATATTT-AAA
1 TATATAT-TATATATATATTTTCAAAATGTTTTAAAAACTATA-TAT-TATATATAT-TTTCAAA
119417 ATGTTTTAAAAAC
62 ATGTTTTAAAAAC
* * *
119430 TATATATTATATATATTTTTTAAAAATGTTTTAAAAACAATATATTATATA-AGTTTTCAAAATG
1 TATATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATA-TTTTCAAAATG
119494 TTTTAAAAAC
65 TTTTAAAAAC
*
119504 TATATATTATATATATATTTTCAAAATGTTTTATAAACTATATATTATATA-AGTTTTCAAAATG
1 TATATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATA-TTTTCAAAATG
119568 TTTT-AAAAC
65 TTTTAAAAAC
*
119577 TATGTATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAA
1 TATATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAA
119639 ACCGATTTTT
Statistics
Matches: 196, Mismatches: 10, Indels: 10
0.91 0.05 0.05
Matches are distributed among these distances:
73 67 0.34
74 88 0.45
75 3 0.02
76 31 0.16
77 7 0.04
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (74 bp):
TATATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGT
TTTAAAAAC
Found at i:121894 original size:18 final size:18
Alignment explanation
Indices: 121871--121995 Score: 169
Period size: 18 Copynumber: 6.9 Consensus size: 18
121861 TTACATGGAC
121871 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
121889 AGTGGTCCTTTGAGACAT
1 AGTGGTCCTTCGGGACAT
121907 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
121925 AATGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
*
121943 AATGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
121961 AGTGGTCATTCGGGATAT
1 AGTGGTCCTTCGGGACAT
* *
121979 AATGGTCCTCCGGGACA
1 AGTGGTCCTTCGGGACA
121996 AATATTCAGT
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 93 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:122766 original size:85 final size:85
Alignment explanation
Indices: 122622--123030 Score: 507
Period size: 85 Copynumber: 4.9 Consensus size: 85
122612 GGTGTGACAC
* * * *
122622 CCTTGAGCTGAATGGAATCGAACTTGAAGGTATTTGTTGACAGATAACCCTTCTCGCCTTGAGTT
1 CCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCT
122687 ATGCTGTAAATTTGATATGT
66 ATGCTGTAAATTTGATATGT
* * * * * * *
122707 CCTTGAGCTGAATGTAATCGTACTCGAATGTCTTTGTTAACAAATATCCCTTCTTGCCTTGAGAT
1 CCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCT
*
122772 ATGCTGTAAATTTGACATG-
66 ATGCTGTAAATTTGATATGT
* *
122791 CCTTTGAGCTGAATGTAATCAAACTC-AGAGGTCTTTATTGACAGATAA--------GACCTTGA
1 CC-TTGAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTCG-CCTTGA
* *
122847 GTTATGCTATAAATTTGATATGT
63 GCTATGCTGTAAATTTGATATGT
* * *
122870 CTTTGAGCTGAATGTAATCGAACTCGAAGGT-TTAGGTTGACAGATAGCCCTTCTCGCCTTGAGC
1 CCTTGAGCTGAATGTAATCGAACTCGAAGGTCTT-TGTTGACAGATAACCCTTCTCGCCTTGAGC
* *
122934 TATGCTATAAATTTAATATGT
65 TATGCTGTAAATTTGATATGT
122955 CCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCT
1 CCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCT
*
123020 ATGCTGCAAAT
66 ATGCTGTAAAT
123031 AGTTCCTTTA
Statistics
Matches: 276, Mismatches: 33, Indels: 30
0.81 0.10 0.09
Matches are distributed among these distances:
77 3 0.01
78 61 0.22
79 2 0.01
84 3 0.01
85 204 0.74
86 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (85 bp):
CCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCT
ATGCTGTAAATTTGATATGT
Found at i:122923 original size:163 final size:163
Alignment explanation
Indices: 122678--123001 Score: 465
Period size: 163 Copynumber: 2.0 Consensus size: 163
122668 ACCCTTCTCG
* * * *
122678 CCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGTACTCGAATGTCTTTG
1 CCTTGAGTTATGCTATAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTGG
* * * *
122743 TTAACAAATATCCCTTCTTGCCTTGAGATATGCTGTAAATTTGACATG-CCTTTGAGCTGAATGT
66 TTAACAAATAGCCCTTCTCGCCTTGAGATATGCTATAAATTTAACATGTCC-TTGAGCTGAATGT
122807 AATCAAACTC-AGAGGTCTTTATTGACAGATAAGA
130 AATCAAACTCGA-AGGTCTTTATTGACAGATAAGA
*
122841 CCTTGAGTTATGCTATAAATTTGATATGTCTTTGAGCTGAATGTAATCGAACTCGAAGGT-TTAG
1 CCTTGAGTTATGCTATAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTT-G
* * * *
122905 GTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTTAATATGTCCTTGAGCTGAATGT
65 GTTAACAAATAGCCCTTCTCGCCTTGAGATATGCTATAAATTTAACATGTCCTTGAGCTGAATGT
* *
122970 AATCGAACTCGAAGGTCTTTGTTGACAGATAA
130 AATCAAACTCGAAGGTCTTTATTGACAGATAA
123002 CCCTTCTCGC
Statistics
Matches: 143, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
162 2 0.01
163 138 0.97
164 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (163 bp):
CCTTGAGTTATGCTATAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTGG
TTAACAAATAGCCCTTCTCGCCTTGAGATATGCTATAAATTTAACATGTCCTTGAGCTGAATGTA
ATCAAACTCGAAGGTCTTTATTGACAGATAAGA
Found at i:123238 original size:86 final size:86
Alignment explanation
Indices: 123091--123279 Score: 270
Period size: 86 Copynumber: 2.2 Consensus size: 86
123081 AATTCTTTAA
* * *
123091 ATGAATCCCCTTCATGGGAAAGCCAAGTGGTATATTCTTCAGGTGGTTCCCCTTAGCGGGTCTGA
1 ATGAATCCCCTTCATGGGAAAGCCAAGTGGTATATTCTTCAAGTAGTTCCACTTAGCGGGTCTGA
123156 ACCAGGTGAGACGATCTTTGG
66 ACCAGGTGAGACGATCTTTGG
* * * *
123177 ATGACTCCCCTTCATGGGAAAGTCAAGTGGTATATTCTTCAAGTAGTTCCACTTCGTGGGTCTGA
1 ATGAATCCCCTTCATGGGAAAGCCAAGTGGTATATTCTTCAAGTAGTTCCACTTAGCGGGTCTGA
* *
123242 ACTAGGTGAGATGATCTTTGG
66 ACCAGGTGAGACGATCTTTGG
** *
123263 ATGGTTCTCCTTCATGG
1 ATGAATCCCCTTCATGG
123280 TTAGAGAGAC
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 91 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (86 bp):
ATGAATCCCCTTCATGGGAAAGCCAAGTGGTATATTCTTCAAGTAGTTCCACTTAGCGGGTCTGA
ACCAGGTGAGACGATCTTTGG
Found at i:123928 original size:25 final size:25
Alignment explanation
Indices: 123893--123948 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
123883 AAAAGAATAA
*
123893 ATAGCTCTTTAATACTTTTAGAGTT
1 ATAGCTATTTAATACTTTTAGAGTT
*
123918 ATAGCTATTTAATGCTTTTAGAGTT
1 ATAGCTATTTAATACTTTTAGAGTT
123943 ATAGCT
1 ATAGCT
123949 CTTTGACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (25 bp):
ATAGCTATTTAATACTTTTAGAGTT
Found at i:128151 original size:16 final size:16
Alignment explanation
Indices: 128130--128163 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
128120 TCGGACACCA
* *
128130 TCTTACCTGATATGTG
1 TCTTACCAGAAATGTG
128146 TCTTACCAGAAATGTG
1 TCTTACCAGAAATGTG
128162 TC
1 TC
128164 GGGTTTGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.38
Consensus pattern (16 bp):
TCTTACCAGAAATGTG
Found at i:128600 original size:6 final size:5
Alignment explanation
Indices: 128571--128614 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
128561 AACAAAATTG
* *
128571 AAATG AAATG AAATA AAATAA AAAGTA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAAT-A AAA-TA AAATA AAATA AAATA AA
128615 GGTTGGGGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
5 27 0.75
6 8 0.22
7 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:130007 original size:38 final size:38
Alignment explanation
Indices: 129901--130266 Score: 424
Period size: 38 Copynumber: 9.5 Consensus size: 38
129891 ATTATTTTCT
* * *
129901 AAACCATATAATATA-ATATATTTTCAAAAT-ATTTAA
1 AAACTATATATTATATATATATTTTCAAAATGTTTTAA
*
129937 AAATTATATATTATATATAT-TTTTCAAAATGTTTTAA
1 AAACTATATATTATATATATATTTTCAAAATGTTTTAA
*
129974 AAACTATATATTATATATATTTTTTCAAAATGTTTTAA
1 AAACTATATATTATATATATATTTTCAAAATGTTTTAA
*
130012 AAACTATATATTATATATATATATTCAAAATGTTTTAA
1 AAACTATATATTATATATATATTTTCAAAATGTTTTAA
*
130050 AAACTATAT-TATATATATATATTTTCAAAATGTTTTAG
1 AAACTATATAT-TATATATATATTTTCAAAATGTTTTAA
** * * *
130088 AAGTTATACATTATACA-A-GTTTTCAAAATGTTTTAA
1 AAACTATATATTATATATATATTTTCAAAATGTTTTAA
* * *
130124 AAATTATATTATATATATATATATATTCAAAATGTTTTAG
1 AAACTATA-TAT-TATATATATATTTTCAAAATGTTTTAA
*
130164 AAACTATATATTATATA-A-GTTTTCAAAATGTTTTAA
1 AAACTATATATTATATATATATTTTCAAAATGTTTTAA
130200 AAACTATATATTATATATATATATATATATATTTCAAAATGTTTTAA
1 AAAC-------TATATAT-TATATATATAT-TTTCAAAATGTTTTAA
130247 AAACTATATATTATATATAT
1 AAACTATATATTATATATAT
130267 GTTCAAAAAC
Statistics
Matches: 284, Mismatches: 26, Indels: 37
0.82 0.07 0.11
Matches are distributed among these distances:
36 64 0.23
37 33 0.12
38 109 0.38
39 14 0.05
40 29 0.10
43 7 0.02
44 6 0.02
45 1 0.00
46 1 0.00
47 20 0.07
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (38 bp):
AAACTATATATTATATATATATTTTCAAAATGTTTTAA
Found at i:130220 original size:47 final size:47
Alignment explanation
Indices: 130168--130266 Score: 168
Period size: 47 Copynumber: 2.1 Consensus size: 47
130158 TTTTAGAAAC
130168 TATATAT-TATATA-AGT-TTTCAAAATGTTTTAAAAACTATATATTA
1 TATATATATATATATA-TATTTCAAAATGTTTTAAAAACTATATATTA
130213 TATATATATATATATATATTTCAAAATGTTTTAAAAACTATATATTA
1 TATATATATATATATATATTTCAAAATGTTTTAAAAACTATATATTA
130260 TATATAT
1 TATATAT
130267 GTTCAAAAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
45 7 0.14
46 7 0.14
47 37 0.73
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (47 bp):
TATATATATATATATATATTTCAAAATGTTTTAAAAACTATATATTA
Found at i:130530 original size:32 final size:32
Alignment explanation
Indices: 130504--130565 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
130494 GTCGGGTTGG
130504 GTCATTTCGGGTTTCGGTTTTAGTCGGGTCAA
1 GTCATTTCGGGTTTCGGTTTTAGTCGGGTCAA
* * * *
130536 GTCATTTTGTGTTTTGGTTTTATTCGGGTC
1 GTCATTTCGGGTTTCGGTTTTAGTCGGGTC
130566 TATAGTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.10, C:0.13, G:0.29, T:0.48
Consensus pattern (32 bp):
GTCATTTCGGGTTTCGGTTTTAGTCGGGTCAA
Found at i:131422 original size:28 final size:28
Alignment explanation
Indices: 131369--131422 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
131359 TGACTCTCAT
* *
131369 TTCAAATTATTCCTTAAACTTTTGAACA
1 TTCAAATTATTCCCTAAACTTATGAACA
*
131397 TTCAAATTTCTTCCCTAAAC-TATGAA
1 TTCAAA-TTATTCCCTAAACTTATGAA
131423 TTTCATACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 11 0.50
29 11 0.50
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (28 bp):
TTCAAATTATTCCCTAAACTTATGAACA
Found at i:131465 original size:60 final size:61
Alignment explanation
Indices: 131348--131475 Score: 138
Period size: 60 Copynumber: 2.1 Consensus size: 61
131338 GCATCATATC
* * * *
131348 TCCCTAAACTATGACTCTCATTTCAAATTATTCCTTAAACTTTTGAACATTCAAATTTC-T
1 TCCCTAAACTATGAATCTCATCTCAAATTAGTCCCTAAACTTTTGAACATTCAAATTTCAT
* * * *
131408 TCCCTAAACTATGAATTTCATACT-AAATTGGTCCCTAAACTTTTAGATCTTTC-AATTTCAT
1 TCCCTAAACTATGAATCTCAT-CTCAAATTAGTCCCTAAACTTTT-GAACATTCAAATTTCAT
131469 T-CCTAAA
1 TCCCTAAA
131476 TTCATCCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
60 48 0.84
61 9 0.16
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (61 bp):
TCCCTAAACTATGAATCTCATCTCAAATTAGTCCCTAAACTTTTGAACATTCAAATTTCAT
Found at i:134068 original size:19 final size:19
Alignment explanation
Indices: 134044--134090 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
134034 GCATAAAGGG
*
134044 GTTAAATAATTGATGAGGA
1 GTTAAAGAATTGATGAGGA
134063 GTTAAAGAATTGATGAGGA
1 GTTAAAGAATTGATGAGGA
134082 G--AAAGAATT
1 GTTAAAGAATT
134091 TGCAGACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 8 0.30
19 19 0.70
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (19 bp):
GTTAAAGAATTGATGAGGA
Found at i:138041 original size:21 final size:21
Alignment explanation
Indices: 138013--138067 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
138003 CCAGAACAGA
138013 GGAA-ATCGGTACTCATATGG
1 GGAATATCGGTACTCATATGG
138033 GGAATATCGGTACTCATATGG
1 GGAATATCGGTACTCATATGG
138054 GGAATATCGGTACT
1 GGAATATCGGTACT
138068 TCCTTTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.12
21 30 0.88
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (21 bp):
GGAATATCGGTACTCATATGG
Found at i:146000 original size:29 final size:28
Alignment explanation
Indices: 145950--146010 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
145940 TTTAAATAGG
145950 TTTTTATATTTTAATTAAGTTTTAGGATA
1 TTTTTATATTTTAATTAAGTTTTAGG-TA
**
145979 TTTTTATATTTT-ATCTTTGTTTTAGGTA
1 TTTTTATATTTTAAT-TAAGTTTTAGGTA
146007 TTTT
1 TTTT
146011 AGTTGAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.23, C:0.02, G:0.10, T:0.66
Consensus pattern (28 bp):
TTTTTATATTTTAATTAAGTTTTAGGTA
Done.