Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003200.1 Hibiscus syriacus cultivar Beakdansim tig00006734_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: 159614
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1296 original size:19 final size:19
Alignment explanation
Indices: 1269--1307 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1259 GTTTACTGTA
*
1269 TATGTATGTATGTGTCATG
1 TATGCATGTATGTGTCATG
1288 TATGCATGTATGTGTCATG
1 TATGCATGTATGTGTCATG
1307 T
1 T
1308 TTACTTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.46
Consensus pattern (19 bp):
TATGCATGTATGTGTCATG
Found at i:9745 original size:13 final size:13
Alignment explanation
Indices: 9727--9753 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9717 AGAAAGATGG
9727 TAATTACTACTAA
1 TAATTACTACTAA
9740 TAATTACTACTAA
1 TAATTACTACTAA
9753 T
1 T
9754 TTAGTAACCT
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:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATTACTACTAA
Found at i:15110 original size:15 final size:15
Alignment explanation
Indices: 15090--15126 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
15080 GGATCCACGT
15090 TAGGTTTAGGGTGGA
1 TAGGTTTAGGGTGGA
15105 TAGGTTTAGGGTGGA
1 TAGGTTTAGGGTGGA
*
15120 TACGTTT
1 TAGGTTT
15127 CTACCATGCA
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:0.19, C:0.03, G:0.41, T:0.38
Consensus pattern (15 bp):
TAGGTTTAGGGTGGA
Found at i:21048 original size:22 final size:22
Alignment explanation
Indices: 21023--21073 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
21013 TATATTTATA
*
21023 AAAAATATTAATT-TTATTCAAT
1 AAAAATATT-ATTATTATTAAAT
*
21045 AAAAATATTATTATTTTTAAAT
1 AAAAATATTATTATTATTAAAT
21067 AAAAATA
1 AAAAATA
21074 ATATATAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAATATTATTATTATTAAAT
Found at i:21892 original size:2 final size:2
Alignment explanation
Indices: 21885--21912 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21875 ATAATTTTAA
21885 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
21913 GAGATGATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23481 original size:16 final size:16
Alignment explanation
Indices: 23462--23496 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
23452 TGTGTGTGTG
*
23462 TGCGCGCGCGCGCGCA
1 TGCGCGCACGCGCGCA
*
23478 TGCGCGCATGCGCGCA
1 TGCGCGCACGCGCGCA
23494 TGC
1 TGC
23497 ATGTATGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.40, G:0.40, T:0.11
Consensus pattern (16 bp):
TGCGCGCACGCGCGCA
Found at i:23482 original size:8 final size:8
Alignment explanation
Indices: 23471--23496 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
23461 GTGCGCGCGC
23471 GCGCGCAT
1 GCGCGCAT
23479 GCGCGCAT
1 GCGCGCAT
23487 GCGCGCAT
1 GCGCGCAT
23495 GC
1 GC
23497 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.38, G:0.38, T:0.12
Consensus pattern (8 bp):
GCGCGCAT
Found at i:23504 original size:4 final size:4
Alignment explanation
Indices: 23497--25574 Score: 2702
Period size: 4 Copynumber: 522.2 Consensus size: 4
23487 GCGCGCATGC
* * *
23497 ATGT ATGT ATGT ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * *
23545 ATGC ATGC ATGA ATGT ATGC ATGC ATGC ATGT ATGT ATGT ATGC ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
23593 ATGT ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGT ATGC ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
23641 ATGT ATGC ATGT ATGT ATGC ATGC ATGT ATGT ATGC ATGT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
23689 ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGG ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
23737 ATGT ATGT ATGT ATGT ATAT ATTT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * *
23785 ATGC ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGC ATGC ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * *
23833 ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
23881 ATGT ATGC ATGT ATGC ATGT ATGT ATGC ATGT ATGC ATGT ATGT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
23929 ATGT ATGC ATGT ATGT ATGT ATGC ATGC ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * *
23977 ATGC ATGC ATGC ATGC ATGC ATGT ATGT ATGT ATGT ATAT ATGC ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
24025 ATGC ATGC ATGC ATGT ATGT ATGT ATGC ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
24073 ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24121 ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT A--T
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
24165 ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * * *
24211 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT ATGT ATG- -TGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * * * *
24257 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT ATGT ATGT GTGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * * * *
24305 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT CTGT ATGT ATGT GTGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * * *
24353 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * * * *
24401 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT CTGT ATGT ATGT GTGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
24449 GTGT ATGT ATGT ATGT GTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24497 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24545 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24593 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24639 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24687 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
24735 ATTT ATGT ATGT ATGT ATGT ATGT AT-T ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
24782 ATGT ATGT ATGT ATTT ATGT ATGT ATGC ATGT ATGT ATGC ATGT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * *
24830 ATGC ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGT ATGC ATGT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
24878 ATGT ATGC ATGT ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * *
24926 ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGC ATGC ATGC ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * * *
24974 ATGT ATTT ATGT ATGT ATGG ATGC ATGC ATGC ATGC ATGC ATGC ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
25022 ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
25070 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
25118 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
25166 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
25214 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
25262 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
25310 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
25358 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
25406 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
25454 ATGC ATGT ATGT ATGT ATGT ATGC ATGT ATGT ATGC ATGC ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * *
25502 ATGC ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
25550 ATGC ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
25575 CATACATACA
Statistics
Matches: 1900, Mismatches: 163, Indels: 22
0.91 0.08 0.01
Matches are distributed among these distances:
2 10 0.01
3 3 0.00
4 1887 0.99
ACGTcount: A:0.23, C:0.04, G:0.27, T:0.46
Consensus pattern (4 bp):
ATGT
Found at i:27361 original size:60 final size:59
Alignment explanation
Indices: 27271--27428 Score: 147
Period size: 60 Copynumber: 2.6 Consensus size: 59
27261 TTTCAATTTG
* * * * * * * * *
27271 GTCCCTAAACTTTTAAACAATTCAATTTCATCCTCGAATTATGACTCCCATTCTGAATTA
1 GTCCCTAAAATTTTGAGC-ATTCAATTTCATCCCCAAACTATGAATCCCATTCTAAATCA
* *
27331 GTCCTTAAAATTTTGAGCATTCAAATTTCATCCCCAAACTATGAATCTCATTCTAAATCA
1 GTCCCTAAAATTTTGAGCATTC-AATTTCATCCCCAAACTATGAATCCCATTCTAAATCA
* * *
27391 GTCCCTAAACTTTT-AGAACTTCCAATCTCATCCCCAAA
1 GTCCCTAAAATTTTGAGCA-TT-CAATTTCATCCCCAAA
27429 TTCATCCAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
59 7 0.09
60 72 0.90
61 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (59 bp):
GTCCCTAAAATTTTGAGCATTCAATTTCATCCCCAAACTATGAATCCCATTCTAAATCA
Found at i:27681 original size:60 final size:59
Alignment explanation
Indices: 27557--27694 Score: 145
Period size: 60 Copynumber: 2.3 Consensus size: 59
27547 TGAATAATTT
* * *
27557 AGGAT-AAAATAGAAATATTTAAAAGTTTGGGACCAATTTAGAATGAATATCACAACTTG
1 AGGATGAAAAT-GAAATGTTCAAAAGTTTGGGACCAATTTAGAATGAATATCACAACTTA
* * * * **
27616 GGGATGAAAATGAAATGTTCAAAAGTTTGAGGACTAATTTATAAT-AATAGTCATAGTTTA
1 AGGATGAAAATGAAATGTTCAAAAGTTTG-GGACCAATTTAGAATGAATA-TCACAACTTA
*
27676 AGGATGAAATTGAAATGTT
1 AGGATGAAAATGAAATGTT
27695 TACTATTTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
59 24 0.37
60 41 0.63
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (59 bp):
AGGATGAAAATGAAATGTTCAAAAGTTTGGGACCAATTTAGAATGAATATCACAACTTA
Found at i:29790 original size:3 final size:3
Alignment explanation
Indices: 29782--29806 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29772 TGGTGGGTCC
29782 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
29807 ATTTGATGCT
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:30545 original size:166 final size:166
Alignment explanation
Indices: 30263--30773 Score: 787
Period size: 166 Copynumber: 3.1 Consensus size: 166
30253 AGCTTAAATG
* * *
30263 CCACATGAACACGGTTCTTTGGTGCATAGGAACTCCAGTCATTTGCTGTATAGTTCATTTTCCGT
1 CCACATGAACATGGTTCTTTGGTGCATAGGAACTCCAGTCATTTGTTGTATAGTTCGTTTTCCGT
* * *
30328 TCGGCATTTCCGATTTCTTCGATTTGTGCTAGTCGGAGAAGTGTTTTAGGTAAGGCAATTGAAAG
66 TCGACATTTCCGATTTCTTCGATTTGTGCTAGTCGGAGAAGTGTATTAGGTAAGGCAATCGAAAG
30393 GGATATGAAACATCAGTGTTTTCTAGAGCATAACCA
131 GGATATGAAACATCAGTGTTTTCTAGAGCATAACCA
*
30429 CCGCATGAACATGGTTCTTTGGTGCATAGGAACTCCAGTCATTTGTTGTATAGTTCGTTTTCCGT
1 CCACATGAACATGGTTCTTTGGTGCATAGGAACTCCAGTCATTTGTTGTATAGTTCGTTTTCCGT
30494 TCGACATTTCCGATTTCTTCGATTTGTGCTAGTCGGAGAAGTGTATTAGGTAAGGCAATCGAAAG
66 TCGACATTTCCGATTTCTTCGATTTGTGCTAGTCGGAGAAGTGTATTAGGTAAGGCAATCGAAAG
30559 GGATATGAAACATCAGTGTTTTCTAGAGCATAACCA
131 GGATATGAAACATCAGTGTTTTCTAGAGCATAACCA
* ** ** * * * *
30595 CCACATGAACATGGTTCATCAGT---TAAAAACTCCAGTCTTTTATTGGGA-AGTTCGTTTTCCT
1 CCACATGAACATGGTTCTTTGGTGCATAGGAACTCCAGTCATTTGTT-GTATAGTTCGTTTTCCG
30656 TTCGACATTTCCGATTTCTTCGATTTGTGCTAGTCGGAGAAGTGTATTAGGTAAGGCAATCGAAA
65 TTCGACATTTCCGATTTCTTCGATTTGTGCTAGTCGGAGAAGTGTATTAGGTAAGGCAATCGAAA
* * * *
30721 GGGGTATGTAACGATCAGTGTTTTCTAGAGCTTAACTA
130 GGGATATGAAAC-ATCAGTGTTTTCTAGAGCATAACCA
*
30759 CCACATGGACATGGT
1 CCACATGAACATGGT
30774 ACATAAAGAC
Statistics
Matches: 321, Mismatches: 22, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
163 104 0.32
164 39 0.12
166 178 0.55
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (166 bp):
CCACATGAACATGGTTCTTTGGTGCATAGGAACTCCAGTCATTTGTTGTATAGTTCGTTTTCCGT
TCGACATTTCCGATTTCTTCGATTTGTGCTAGTCGGAGAAGTGTATTAGGTAAGGCAATCGAAAG
GGATATGAAACATCAGTGTTTTCTAGAGCATAACCA
Found at i:30704 original size:163 final size:163
Alignment explanation
Indices: 30293--30857 Score: 746
Period size: 166 Copynumber: 3.5 Consensus size: 163
30283 GGTGCATAGG
* * * *
30293 AACTCCAGTCATTTGCTGTATAGTTCATTTTCCGTTCGGCATTTCCGATTTCTTCGATTTGTGCT
1 AACTCCAGTCATTTGTTGGAAAGTTCATTTTCCGTTCGACATTTCCGATTTCTTCGATTTGTGCT
* *
30358 AGTCGGAGAAGTGTTTTAGGTAAGGCAATTGAAAGGGATATGAAACATCAGTGTTTTCTAGAGCA
66 AGTCGGAGAAGTGTATTAGGTAAGGCAATCGAAAGGGATATGAAACATCAGTGTTTTCTAGAGCA
* * ** **
30423 TAACCACCGCATGAACATGGTTCTTTGGTGCATAGG
131 TAACCACCACATGAACATGGTTCATCAGT---TAAA
* * *
30459 AACTCCAGTCATTTGTTGTATAGTTCGTTTTCCGTTCGACATTTCCGATTTCTTCGATTTGTGCT
1 AACTCCAGTCATTTGTTGGAAAGTTCATTTTCCGTTCGACATTTCCGATTTCTTCGATTTGTGCT
30524 AGTCGGAGAAGTGTATTAGGTAAGGCAATCGAAAGGGATATGAAACATCAGTGTTTTCTAGAGCA
66 AGTCGGAGAAGTGTATTAGGTAAGGCAATCGAAAGGGATATGAAACATCAGTGTTTTCTAGAGCA
30589 TAACCACCACATGAACATGGTTCATCAGTTAAA
131 TAACCACCACATGAACATGGTTCATCAGTTAAA
* * * * *
30622 AACTCCAGTCTTTTATTGGGAAGTTCGTTTTCCTTTCGACATTTCCGATTTCTTCGATTTGTGCT
1 AACTCCAGTCATTTGTTGGAAAGTTCATTTTCCGTTCGACATTTCCGATTTCTTCGATTTGTGCT
* *
30687 AGTCGGAGAAGTGTATTAGGTAAGGCAATCGAAAGGGGTATGTAACGATCAGTGTTTTCTAGAGC
66 AGTCGGAGAAGTGTATTAGGTAAGGCAATCGAAAGGGATATGAAAC-ATCAGTGTTTTCTAGAGC
* * *
30752 TTAACTACCACATGGACATGG-T-A-CA--TAAA
130 ATAACCACCACATGAACATGGTTCATCAGTTAAA
* * * * * * * * *
30781 GACTCCAGTCATTTGTTGTAAATTTCATTTTCCTTTCGGCATTTTCGA-TTCTTCAATTTGTACC
1 AACTCCAGTCATTTGTTGGAAAGTTCATTTTCCGTTCGACATTTCCGATTTCTTCGATTTGTGCT
30845 AGTCGGAGAAGTG
66 AGTCGGAGAAGTG
30858 GCAATCGAAA
Statistics
Matches: 364, Mismatches: 34, Indels: 10
0.89 0.08 0.02
Matches are distributed among these distances:
158 26 0.07
159 43 0.12
161 2 0.01
162 1 0.00
163 106 0.29
164 36 0.10
166 150 0.41
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (163 bp):
AACTCCAGTCATTTGTTGGAAAGTTCATTTTCCGTTCGACATTTCCGATTTCTTCGATTTGTGCT
AGTCGGAGAAGTGTATTAGGTAAGGCAATCGAAAGGGATATGAAACATCAGTGTTTTCTAGAGCA
TAACCACCACATGAACATGGTTCATCAGTTAAA
Found at i:33734 original size:29 final size:28
Alignment explanation
Indices: 33626--33734 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 28
33616 TGATCCTCAT
*
33626 TTTAAATTAGTCCTTAAACTTTTAAATA
1 TTTAAATTAGTCCTTAAACTTTTGAATA
* * * *
33654 TTTCAATTTTA-TCCTTAAACTATGGTTATCA
1 TTT-AA-ATTAGTCCTTAAACTTTTG-AAT-A
*
33685 TTATAAATTAGTCTTTAAACTTTTGAATA
1 TT-TAAATTAGTCCTTAAACTTTTGAATA
*
33714 TTTAAATTACTTCCTTAAACT
1 TTTAAATTA-GTCCTTAAACT
33735 ATGACCTTCA
Statistics
Matches: 62, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
28 10 0.16
29 25 0.40
30 10 0.16
31 16 0.26
32 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.48
Consensus pattern (28 bp):
TTTAAATTAGTCCTTAAACTTTTGAATA
Found at i:33796 original size:60 final size:60
Alignment explanation
Indices: 33606--33787 Score: 201
Period size: 60 Copynumber: 3.0 Consensus size: 60
33596 TTATCACATG
* *
33606 TCCTT-AACTATGATCC-TCATTTTAAATTAGTCCTTAAACTTTTAAATATTTCAATTTTA
1 TCCTTAAACTATGA-CCTTCATTTTAAATTAGTCCTTAAACTTTTAAATATTTAAATTTCA
** * * * * *
33665 TCCTTAAACTATG-GTTATCATTATAAATTAGTCTTTAAACTTTTGAATATTTAAATTACT
1 TCCTTAAACTATGACCT-TCATTTTAAATTAGTCCTTAAACTTTTAAATATTTAAATTTCA
* *
33725 TCCTTAAACTATGACCTTCATTTTAAATTAGTCCCTAAACTTTTTAAACATTCT-AATTTCA
1 TCCTTAAACTATGACCTTCATTTTAAATTAGTCCTTAAAC-TTTTAAATATT-TAAATTTCA
33786 TC
1 TC
33788 TCGAACTATA
Statistics
Matches: 99, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
59 5 0.05
60 76 0.77
61 17 0.17
62 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (60 bp):
TCCTTAAACTATGACCTTCATTTTAAATTAGTCCTTAAACTTTTAAATATTTAAATTTCA
Found at i:37075 original size:42 final size:42
Alignment explanation
Indices: 37028--37143 Score: 162
Period size: 42 Copynumber: 2.8 Consensus size: 42
37018 TCATAAATTT
* *
37028 CGTGTTTGTTTCATGTAATTCGTTTT-TCGGAAAATCTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCT-GGAAAATATTTTCC
37070 CGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAATATTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAATATTTTCC
* * * *
37112 GGTGTTTGTTTTACGTAATTCATTCTCTGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCTGGAA
37144 TGTAATTCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 66 0.99
43 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAATATTTTCC
Found at i:37358 original size:21 final size:23
Alignment explanation
Indices: 37315--37365 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
37305 CATTTTCATC
37315 AAAATATTATTTATTAAAATATTT
1 AAAATATTATTTATT-AAATATTT
37339 AAAATA-TATTTATT-AATATTT
1 AAAATATTATTTATTAAATATTT
*
37360 ATAATA
1 AAAATA
37366 ATATAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
23 8 0.31
24 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATTATTTATTAAATATTT
Found at i:37368 original size:24 final size:23
Alignment explanation
Indices: 37317--37393 Score: 70
Period size: 23 Copynumber: 3.3 Consensus size: 23
37307 TTTTCATCAA
*
37317 AATATTATTTATTAAAATATTTAA-
1 AATA-TATTTATTAATAT-TTTAAT
37341 AATATATTTATTAATATTTATAAT
1 AATATATTTATTAATATTT-TAAT
*
37365 AATATAATT-TT-ATATTTTTAAT
1 AATATATTTATTAATA-TTTTAAT
*
37387 ATTATAT
1 AATATAT
37394 AAAATAATCA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 14 0.30
23 20 0.43
24 12 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATATATTTATTAATATTTTAAT
Found at i:37409 original size:31 final size:31
Alignment explanation
Indices: 37343--37477 Score: 88
Period size: 31 Copynumber: 4.4 Consensus size: 31
37333 ATATTTAAAA
37343 TATATTTATTAATATTTATAATAATATAATTT
1 TATATTTATTAATATTTATAATAATATAA-TT
37375 TATATTT-TTAATATTATATAA-AATAATCAA-T
1 TATATTTATTAATATT-TATAATAAT-AT-AATT
* * * *
37406 TATATTATAATAATATAATATAA-GATATTATT
1 TATATT-TATTAATAT-TTATAATAATATAATT
* **
37438 TAT-TTTAATAATA--TATAATAAT-TTTTT
1 TATATTTATTAATATTTATAATAATATAATT
*
37465 TATATTTAATAAT
1 TATATTTATTAAT
37478 GAATAATATT
Statistics
Matches: 88, Mismatches: 6, Indels: 22
0.76 0.05 0.19
Matches are distributed among these distances:
27 12 0.14
28 11 0.12
30 8 0.09
31 21 0.24
32 21 0.24
33 15 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.53
Consensus pattern (31 bp):
TATATTTATTAATATTTATAATAATATAATT
Found at i:37427 original size:33 final size:30
Alignment explanation
Indices: 37383--37452 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
37373 TTTATATTTT
*
37383 TAATATTATATAAAATAATCAATTATATTATAA
1 TAATATAATATAAAAT-AT-AATT-TATTATAA
* * *
37416 TAATATAATATAAGATATTATTTATTTTAA
1 TAATATAATATAAAATATAATTTATTATAA
37446 TAATATA
1 TAATATA
37453 TAATAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 14 0.42
31 3 0.09
32 2 0.06
33 14 0.42
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (30 bp):
TAATATAATATAAAATATAATTTATTATAA
Found at i:37483 original size:28 final size:28
Alignment explanation
Indices: 37363--37508 Score: 93
Period size: 28 Copynumber: 5.0 Consensus size: 28
37353 AATATTTATA
* * *
37363 ATAATATAATTTTATATTTTTAATATTAT
1 ATAATATTATTTT-TATATTTAATAATAT
* * **
37392 ATAAAATAATCAATTATATTATAATAATAT
1 ATAATATTAT-TTTTATATT-TAATAATAT
*
37422 A-ATATAAGATATTATTTAT-TTTAATAATAT
1 ATA-AT-A-TTATT-TTTATATTTAATAATAT
37452 ATAATAATT-TTTTTATATTTAATAATGA-
1 ATAAT-ATTATTTTTATATTTAATAAT-AT
*
37480 ATAATATTATTTATATATTTAAATAATAT
1 ATAATATTATTTTTATATTT-AATAATAT
37509 TTTAGTAAAG
Statistics
Matches: 93, Mismatches: 12, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
27 8 0.09
28 27 0.29
29 23 0.25
30 25 0.27
31 4 0.04
32 6 0.06
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
ATAATATTATTTTTATATTTAATAATAT
Found at i:37507 original size:25 final size:24
Alignment explanation
Indices: 37446--37507 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 24
37436 TTTATTTTAA
37446 TAATATATAATAATTTTTTTATATT
1 TAATA-ATAATAATTTTTTTATATT
37471 TAATAATGAATAATATTATTTATATATT
1 TAATAAT-AATAAT-TT-TTT-TATATT
37499 TAAATAATA
1 T-AATAATA
37508 TTTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
24 2 0.06
25 11 0.34
26 2 0.06
27 3 0.09
28 8 0.25
29 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TAATAATAATAATTTTTTTATATT
Found at i:37637 original size:90 final size:86
Alignment explanation
Indices: 37524--37693 Score: 200
Period size: 90 Copynumber: 1.9 Consensus size: 86
37514 TAAAGATATT
* * * * * *
37524 TAAAATATACTAATTAATATTTTTA-AAATATAA-TATAACACTATTACTTTAATAAATAATTAA
1 TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATA-TTTAAT-AATAAATAA
37587 TATAATTTATAATATTTTATTTCAC
64 -ATAATTT-TAATATTTTATTTCAC
*
37612 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA
1 TAAAATATA-CAA-ATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAA
*
37677 ATTATTTTAATATTTTA
64 ATAATTTTAATATTTTA
37694 AAATAATAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 19 0.27
89 8 0.11
90 21 0.30
91 12 0.17
92 10 0.14
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (86 bp):
TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAAAT
AATTTTAATATTTTATTTCAC
Found at i:37687 original size:27 final size:28
Alignment explanation
Indices: 37657--37712 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
37647 ATTATAAAAA
37657 TAATA-TTTAATAATAAATAA-ATT-ATTT
1 TAATATTTTAA-AAT-AATAATATTAATTT
37684 TAATATTTTAAAATAATAATATTAATTT
1 TAATATTTTAAAATAATAATATTAATTT
37712 T
1 T
37713 TATGATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 5 0.19
27 11 0.42
28 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TAATATTTTAAAATAATAATATTAATTT
Found at i:37708 original size:22 final size:22
Alignment explanation
Indices: 37671--37729 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
37661 ATTTAATAAT
* *
37671 AAATAAATTATTTTAATATTTTA
1 AAATAAATAATATTAAT-TTTTA
37694 AAAT-AATAATATTAATTTTTA
1 AAATAAATAATATTAATTTTTA
**
37715 TGATAAATAATATTA
1 AAATAAATAATATTA
37730 TTTATTACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 20 0.65
23 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATAAATAATATTAATTTTTA
Found at i:37862 original size:20 final size:20
Alignment explanation
Indices: 37837--37883 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
37827 TTTCCAGATG
37837 TTTTCCAAAAATGTAATTCA
1 TTTTCCAAAAATGTAATTCA
*
37857 TTTTCCATAAATGTAATTCA
1 TTTTCCAAAAATGTAATTCA
37877 TTTTCCA
1 TTTTCCA
37884 GAATTCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (20 bp):
TTTTCCAAAAATGTAATTCA
Found at i:37890 original size:14 final size:15
Alignment explanation
Indices: 37869--37920 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
37859 TTCCATAAAT
37869 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
** *
37884 G-AATTCAAATTCTA
1 GTAATTCATTTTCCA
37898 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
37913 GTAATTCA
1 GTAATTCA
37921 AATTGCAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:37894 original size:20 final size:20
Alignment explanation
Indices: 37837--37895 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
37827 TTTCCAGATG
* **
37837 TTTTCCAAAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
* **
37857 TTTTCCATAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
37877 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
37896 TAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:38153 original size:23 final size:23
Alignment explanation
Indices: 38127--38182 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
38117 AATAAGTTTA
*
38127 TCTTTATGACACATTTTTATTTG
1 TCTTTATGACACATTTTTATCTG
* * *
38150 TCTTTATGATATATTTTTCTCTG
1 TCTTTATGACACATTTTTATCTG
38173 TCTTT-TGACA
1 TCTTTATGACA
38183 TGTTTTCAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.20, C:0.14, G:0.09, T:0.57
Consensus pattern (23 bp):
TCTTTATGACACATTTTTATCTG
Found at i:49840 original size:28 final size:28
Alignment explanation
Indices: 49808--49867 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
49798 GGCTCAACGT
*
49808 GATAGTATTTTAGACACTAGCTCGATGA
1 GATAGTATTTCAGACACTAGCTCGATGA
49836 GATAGTATTTCAGACACTAGCTCGATGA
1 GATAGTATTTCAGACACTAGCTCGATGA
49864 GATA
1 GATA
49868 ATATAAATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (28 bp):
GATAGTATTTCAGACACTAGCTCGATGA
Found at i:51417 original size:23 final size:21
Alignment explanation
Indices: 51387--51433 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 21
51377 TTTTAATTTC
51387 AAAGAATTTTTTTAAAAG-CATG
1 AAAGAA-TTTTTT-AAAGTCATG
51409 AAAGTAATTTTTTAAAGTCATG
1 AAAG-AATTTTTTAAAGTCATG
51431 AAA
1 AAA
51434 CTCAACAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.17
22 17 0.74
23 2 0.09
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (21 bp):
AAAGAATTTTTTAAAGTCATG
Found at i:53277 original size:30 final size:32
Alignment explanation
Indices: 53202--53312 Score: 83
Period size: 30 Copynumber: 3.6 Consensus size: 32
53192 CTTATATAAT
*
53202 AAATAAGTACCTAAAGTA-TGCTCTATTT-TTC-
1 AAATAAGTACCTAAAGTATTG-TCT-TTTAATCA
** * *
53233 ATTTAAGTATCTAAAGTATT-T-TTTTGATCA
1 AAATAAGTACCTAAAGTATTGTCTTTTAATCA
*
53263 AAATAAGTACCTAAA--ATTGTCTTTTAATTA
1 AAATAAGTACCTAAAGTATTGTCTTTTAATCA
* *
53293 AAATATGTACTTAAAGTATT
1 AAATAAGTACCTAAAGTATT
53313 CCAATTTTTC
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
28 6 0.10
29 4 0.06
30 33 0.53
31 15 0.24
32 4 0.06
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (32 bp):
AAATAAGTACCTAAAGTATTGTCTTTTAATCA
Found at i:53453 original size:28 final size:28
Alignment explanation
Indices: 53393--53498 Score: 79
Period size: 28 Copynumber: 3.6 Consensus size: 28
53383 GAAAAAGTTT
* * *
53393 GAATAGTTTAGGTACATATTTTGACATAA
1 GAATACTTTAAGTACTTATTTTGACA-AA
*
53422 -AATACTTTAAGTACTTACTTTGACAAA
1 GAATACTTTAAGTACTTATTTTGACAAA
* *
53449 GAATATAACTTTAAATATTTATTTTGATCAAA
1 G-A-AT-ACTTTAAGTACTTATTTTGA-CAAA
* * *
53481 AAATATTTTAGGTACTTA
1 GAATACTTTAAGTACTTA
53499 AATGAAAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
27 2 0.03
28 21 0.35
29 11 0.18
30 4 0.07
31 18 0.30
32 4 0.07
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (28 bp):
GAATACTTTAAGTACTTATTTTGACAAA
Found at i:53475 original size:31 final size:29
Alignment explanation
Indices: 53409--53490 Score: 78
Period size: 31 Copynumber: 2.8 Consensus size: 29
53399 TTTAGGTACA
* *
53409 TATTTTGACATAAA-ATACTTTAAGTACT
1 TATTTTGACAAAAATATACTTTAAATACT
* *
53437 TACTTTGACAAAGAATATAACTTTAAATATT
1 TATTTTGACAAA-AATAT-ACTTTAAATACT
*
53468 TATTTTGATCAAAAA-ATATTTTA
1 TATTTTGA-CAAAAATATACTTTA
53491 GGTACTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 10 0.23
29 7 0.16
30 4 0.09
31 19 0.43
32 4 0.09
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (29 bp):
TATTTTGACAAAAATATACTTTAAATACT
Found at i:59769 original size:32 final size:32
Alignment explanation
Indices: 59733--59801 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
59723 AAATTCAGGA
* * *
59733 TCGGGTC-AGATTTTTTAAGTTTGATGTTTGGG
1 TCGGGTCGAGA-TTTTTAAGTGTGATATTCGGG
*
59765 TCGGGTCGGGATTTTTAAGTGTGATATTCGGG
1 TCGGGTCGAGATTTTTAAGTGTGATATTCGGG
59797 TCGGG
1 TCGGG
59802 GTCGGGTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.14, C:0.09, G:0.36, T:0.41
Consensus pattern (32 bp):
TCGGGTCGAGATTTTTAAGTGTGATATTCGGG
Found at i:59804 original size:33 final size:32
Alignment explanation
Indices: 59744--59807 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
59734 CGGGTCAGAT
* * *
59744 TTTTTAAGTTTGATGTTTGGGTCGGGTCGGGA
1 TTTTTAAGTGTGATATTCGGGTCGGGTCGGGA
59776 TTTTTAAGTGTGATATTCGGGTCGGGGTCGGG
1 TTTTTAAGTGTGATATTCGGGTC-GGGTCGGG
59808 TTTAGGGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.12, C:0.08, G:0.39, T:0.41
Consensus pattern (32 bp):
TTTTTAAGTGTGATATTCGGGTCGGGTCGGGA
Found at i:68598 original size:29 final size:29
Alignment explanation
Indices: 68556--68611 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
68546 AAAAAATACT
68556 ATAGTCAAAGGACTA-TTTTGTAACTTTTA
1 ATAGTCAAAGGACTATTTTTGT-ACTTTTA
* *
68585 ATAGTCGAATGACTATTTTTGTACTTT
1 ATAGTCAAAGGACTATTTTTGTACTTT
68612 ACCCTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (29 bp):
ATAGTCAAAGGACTATTTTTGTACTTTTA
Found at i:69897 original size:2 final size:2
Alignment explanation
Indices: 69890--69944 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
69880 TCATTTACCC
69890 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
69932 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
69945 GTACAATATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:73026 original size:29 final size:29
Alignment explanation
Indices: 72950--73026 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
72940 CTTCCCAGCA
*
72950 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
72979 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
73008 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
73027 CCTGCTCCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:75111 original size:47 final size:47
Alignment explanation
Indices: 75041--75130 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 47
75031 ATCTTTCAAA
* * *
75041 AGTTTGGGGATGAAATTGAAACATTCAAGAGTTTAGAGACCAACCGT
1 AGTTTGGGAATGAAATTGAAACATTCAAAAGTTCAGAGACCAACCGT
* * *
75088 AGTTTGGGAATGAATTTGGAACATTCAAAAGTTCGGAGACCAA
1 AGTTTGGGAATGAAATTGAAACATTCAAAAGTTCAGAGACCAA
75131 ATTAGAATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.26
Consensus pattern (47 bp):
AGTTTGGGAATGAAATTGAAACATTCAAAAGTTCAGAGACCAACCGT
Found at i:81491 original size:3 final size:3
Alignment explanation
Indices: 81483--81524 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
81473 ATTTCCCAGA
81483 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
81525 GATATTCGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:86905 original size:74 final size:74
Alignment explanation
Indices: 86770--86917 Score: 217
Period size: 74 Copynumber: 2.0 Consensus size: 74
86760 GTCGATCATA
*
86770 CTATTATTACTATGTCAAGTATTTTTCACATTAAACCTAAACCCGATATGACTTGAACTTATCTT
1 CTATTATTACTATGTCAAGTATTTTTCACATTAAACCTAAACCCGACATGACTTGAACTTATCTT
*
86835 TTGAAAAAT
66 TCGAAAAAT
* * * * *
86844 CTATTATTACTA-GATCATGTATTTTTCACATTAAACCTAAACCTGACGTGATTTGATCTTATCT
1 CTATTATTACTATG-TCAAGTATTTTTCACATTAAACCTAAACCCGACATGACTTGAACTTATCT
86908 TTCGAAAAAT
65 TTCGAAAAAT
86918 TCAATTTGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 1 0.02
74 65 0.98
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.40
Consensus pattern (74 bp):
CTATTATTACTATGTCAAGTATTTTTCACATTAAACCTAAACCCGACATGACTTGAACTTATCTT
TCGAAAAAT
Found at i:100014 original size:2 final size:2
Alignment explanation
Indices: 100007--100040 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
99997 TGAGTTCTAA
100007 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
100041 TAGAACTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:100504 original size:2 final size:2
Alignment explanation
Indices: 100497--100526 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
100487 TAATTTATTC
100497 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
100527 TCTTATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101945 original size:60 final size:59
Alignment explanation
Indices: 101867--101995 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 59
101857 AAAGGTAAAA
* *
101867 TACACAAATGGTTCCCTGACTATAAGACGA-TGTTTTATTGAGTCTCTTGACTATTAAAAGT
1 TACA-AAATGGTTCCCTGACTATAAGA-GATTGTTTTATTGAGTCCCTTAACTATT-AAAGT
* * * * *
101928 TATAAAATGG-TCTCCTGACTATAGGATATTGTTTTTTTGTGTCCCTTAACTATTAAAGT
1 TACAAAATGGTTC-CCTGACTATAAGAGATTGTTTTATTGAGTCCCTTAACTATTAAAGT
101987 TACAAAATG
1 TACAAAATG
101996 ACCATTCAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 16 0.28
60 39 0.67
61 3 0.05
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39
Consensus pattern (59 bp):
TACAAAATGGTTCCCTGACTATAAGAGATTGTTTTATTGAGTCCCTTAACTATTAAAGT
Found at i:102591 original size:5 final size:5
Alignment explanation
Indices: 102581--102608 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
102571 ATAGACGAAG
102581 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
102609 GAAGAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:107674 original size:21 final size:22
Alignment explanation
Indices: 107649--107697 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
107639 CATTTTTGAA
107649 TTTAGTAAT-TAAACTATCAAT
1 TTTAGTAATCTAAACTATCAAT
*
107670 TTTAGT-ATCTAAACTATCAGT
1 TTTAGTAATCTAAACTATCAAT
107691 TTTAGTA
1 TTTAGTA
107698 CGTATTTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (22 bp):
TTTAGTAATCTAAACTATCAAT
Found at i:107720 original size:32 final size:32
Alignment explanation
Indices: 107670--107730 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
107660 AACTATCAAT
* *
107670 TTTAGTATCTAAACTATCAGTTTTAGTACGTA
1 TTTAGTATATAAACTATCAATTTTAGTACGTA
*
107702 TTTAGTATATAAATTATCAATTTTAGTAC
1 TTTAGTATATAAACTATCAATTTTAGTAC
107731 TTAAAGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (32 bp):
TTTAGTATATAAACTATCAATTTTAGTACGTA
Found at i:108509 original size:29 final size:30
Alignment explanation
Indices: 108477--108584 Score: 119
Period size: 31 Copynumber: 3.6 Consensus size: 30
108467 ATTTTTCATT
* *
108477 TAAGTACCTAAAGTA-ATTTTTGGTCGAAA
1 TAAGTACCTAAAGTATTTTTTTGGTCAAAA
* *
108506 TAAGTATCTAAACTTATTTTTTTGGTCAAAA
1 TAAGTACCTAAA-GTATTTTTTTGGTCAAAA
* * *
108537 TATGTAACTAAAGTATTTTTTTTTGTCAAAA
1 TAAGTACCTAAAGTA-TTTTTTTGGTCAAAA
*
108568 TAGGTACCTAAAGTATT
1 TAAGTACCTAAAGTATT
108585 CAATTTTTCT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
29 11 0.17
30 6 0.09
31 49 0.74
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (30 bp):
TAAGTACCTAAAGTATTTTTTTGGTCAAAA
Found at i:108707 original size:27 final size:28
Alignment explanation
Indices: 108672--108724 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
108662 AAACAAATTG
* *
108672 AATAATTTAGGTACCTA-TTTGACAAAA
1 AATAATTTAGGCAACTATTTTGACAAAA
*
108699 AATACTTTAGGCAACTATTTTGACAA
1 AATAATTTAGGCAACTATTTTGACAA
108725 CAGCAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (28 bp):
AATAATTTAGGCAACTATTTTGACAAAA
Found at i:112324 original size:28 final size:28
Alignment explanation
Indices: 112280--112485 Score: 240
Period size: 28 Copynumber: 7.5 Consensus size: 28
112270 ACACACACAC
* * * *
112280 ATATATATATGTATGTACATATATATAT
1 ATATATGTATATATGTATATATATATGT
* *
112308 ATGTATGTATATATGTATGTATATATG-
1 ATATATGTATATATGTATATATATATGT
*
112335 ---TATGTATATATGTATGTATATATGT
1 ATATATGTATATATGTATATATATATGT
* * *
112360 ATGTATATATATATGTATATATGTATGT
1 ATATATGTATATATGTATATATATATGT
* *
112388 ATATATGTATGTATGTATATATGTATGT
1 ATATATGTATATATGTATATATATATGT
*
112416 ATATATGTATATATGTATGTATATATGT
1 ATATATGTATATATGTATATATATATGT
* *
112444 ATATATGTATATATGTATGTATATATAT
1 ATATATGTATATATGTATATATATATGT
*
112472 ATATATATATATAT
1 ATATATGTATATAT
112486 ATTACAAAAA
Statistics
Matches: 157, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
24 24 0.15
28 133 0.85
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (28 bp):
ATATATGTATATATGTATATATATATGT
Found at i:112487 original size:12 final size:12
Alignment explanation
Indices: 112283--112481 Score: 262
Period size: 12 Copynumber: 16.6 Consensus size: 12
112273 CACACACATA
112283 TATATATGTATG
1 TATATATGTATG
*
112295 TACATA--TA--
1 TATATATGTATG
112303 TATATATGTATG
1 TATATATGTATG
112315 TATATATGTATG
1 TATATATGTATG
112327 TATATATGTATG
1 TATATATGTATG
112339 TATATATGTATG
1 TATATATGTATG
112351 TATATATGTATG
1 TATATATGTATG
*
112363 TATATATATATG
1 TATATATGTATG
112375 TATATATGTATG
1 TATATATGTATG
112387 TATATATGTATG
1 TATATATGTATG
* *
112399 TATGTATATATG
1 TATATATGTATG
* *
112411 TATGTATATATG
1 TATATATGTATG
112423 TATATATGTATG
1 TATATATGTATG
112435 TATATATGTATATATG
1 TATATATG----TATG
112451 TATATATGTATG
1 TATATATGTATG
* *
112463 TATATATATATA
1 TATATATGTATG
112475 TATATAT
1 TATATAT
112482 ATATATTACA
Statistics
Matches: 169, Mismatches: 10, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
8 5 0.03
10 4 0.02
12 148 0.88
16 12 0.07
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.50
Consensus pattern (12 bp):
TATATATGTATG
Found at i:113220 original size:42 final size:40
Alignment explanation
Indices: 113043--113308 Score: 220
Period size: 42 Copynumber: 6.8 Consensus size: 40
113033 TATATTTTCG
113043 AAAACATTTTG---AAAATATATA-ATATATAG--TTTTT
1 AAAACATTTTGAAAAAAATATATATATATATAGTTTTTTT
* * * *
113077 AAAACATTTTG-AAAACATTTATATATTATATAATTTGTTT
1 AAAACATTTTGAAAAAAATATATATA-TATATAGTTTTTTT
* * *
113117 AAAACGTTTTTACAAAAAA-ATATA-ATATATAG--TTTTC
1 AAAACATTTTGA-AAAAAATATATATATATATAGTTTTTTT
113154 AAAACATTTTTGAAAAAATATATATATATTATATAGTTTTTTT
1 AAAACA-TTTTGAAAAAA-ATATATATA-TATATAGTTTTTTT
*
113197 TAAACATTTTGAAAATAAATATATA-ATATATAGTTTTTTT
1 AAAACATTTTGAAAA-AAATATATATATATATAGTTTTTTT
* **
113237 AAAAAACATTTTGAAAATAAATATATA-ATATATAATTTTTCGAA
1 --AAAACATTTTGAAAA-AAATATATATATATATAGTTTTT--TT
*
113281 AAAACATTTTG-AAAATATATA-ATATATA
1 AAAACATTTTGAAAAAAATATATATATATA
113309 ATTTTTAAAA
Statistics
Matches: 191, Mismatches: 20, Indels: 36
0.77 0.08 0.15
Matches are distributed among these distances:
34 11 0.06
36 8 0.04
37 14 0.07
38 12 0.06
39 12 0.06
40 40 0.21
41 15 0.08
42 68 0.36
43 11 0.06
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (40 bp):
AAAACATTTTGAAAAAAATATATATATATATAGTTTTTTT
Found at i:113348 original size:18 final size:16
Alignment explanation
Indices: 113321--113381 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 16
113311 TTTTAAAATA
*
113321 TTTTTGAAAATTATAT
1 TTTTTAAAAATTATAT
113337 GGTTTTTAAAAA--ATAT
1 --TTTTTAAAAATTATAT
*
113353 TTTTTGAAAATTATACAT
1 TTTTTAAAAATTAT--AT
113371 TTTTTAAAAAT
1 TTTTTAAAAAT
113382 ATTTTTGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 9 0.25
16 6 0.17
18 21 0.58
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (16 bp):
TTTTTAAAAATTATAT
Found at i:113362 original size:32 final size:32
Alignment explanation
Indices: 113303--113399 Score: 112
Period size: 31 Copynumber: 3.2 Consensus size: 32
113293 AAATATATAA
*
113303 TATATAATTTTT--AAAATA-TTTTTGAAAAT
1 TATATCATTTTTAAAAAATATTTTTTGAAAAT
**
113332 TATATGGTTTTTAAAAAATATTTTTTGAAAAT
1 TATATCATTTTTAAAAAATATTTTTTGAAAAT
* * *
113364 TATA-CATTTTTTAAAAATATTTTTGGAAATT
1 TATATCATTTTTAAAAAATATTTTTTGAAAAT
113395 TATAT
1 TATAT
113400 ATAATTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.18
31 32 0.56
32 15 0.26
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (32 bp):
TATATCATTTTTAAAAAATATTTTTTGAAAAT
Found at i:113457 original size:3 final size:3
Alignment explanation
Indices: 113451--113518 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
113441 GTTTTTTTAT
* *
113451 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TCA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
113497 ATA TT- TTA TTA CTTA TT- TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TT
113519 TTAATTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
2 4 0.07
3 45 0.82
4 6 0.11
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:113477 original size:25 final size:25
Alignment explanation
Indices: 113447--113518 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 25
113437 TATAGTTTTT
113447 TTATTTATTATTATTATTATTATTA
1 TTATTTATTATTATTATTATTATTA
* *
113472 TTATTTATTATCACTATTATTATTA
1 TTATTTATTATTATTATTATTATTA
*
113497 ATATTTTATTACTTATT-TTATT
1 TTA-TTTATTA-TTATTATTATT
113519 TTAATTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
25 25 0.62
26 12 0.30
27 3 0.08
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATTTATTATTATTATTATTATTA
Found at i:114009 original size:15 final size:15
Alignment explanation
Indices: 113989--114026 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
113979 AAACACGAGA
113989 AAGAACCAC-AAACGC
1 AAGAACCACAAAAC-C
*
114004 AAGAACAACAAAACC
1 AAGAACCACAAAACC
114019 AAGAACCA
1 AAGAACCA
114027 TTTTTCTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.61, C:0.29, G:0.11, T:0.00
Consensus pattern (15 bp):
AAGAACCACAAAACC
Found at i:120163 original size:84 final size:82
Alignment explanation
Indices: 119923--120576 Score: 635
Period size: 84 Copynumber: 7.9 Consensus size: 82
119913 TCTGCCCACC
* * *
119923 AAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTC-AAGGCACATCATTTACAGCATAGCTTAAGTCGAG
*
119988 AAGAGCTATC--T-GCCA
65 AAGGGCTATCTGTAGCCA
* * * * * * * * * *
120003 AAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTA
1 AAGACCTTTGAGTTCGACTACGCTCAGC-TCAA-GGCACATCATTTACAGCATAGCTTAAGTCGA
* *
120068 GAAGGGTTATCTGTTAGCAA
64 GAAGGGCTATCTG-TAGCCA
* * *
120088 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTACGTTGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTACAGCATAGCTTAAGTCGAG
120153 AAGGGCTATC--T-GCCA
65 AAGGGCTATCTGTAGCCA
* * ** * *
120168 AAGACCTTTGAGTTCGATTTCATTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTACAGCATAGCTTAAGTCGAG
*
120233 AAGAGCTATC--T-GCCA
65 AAGGGCTATCTGTAGCCA
* * * * * * * * * *
120248 AAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTA
1 AAGACCTTTGAGTTCGACTACGCTCAGC-TCAA-GGCACATCATTTACAGCATAGCTTAAGTCGA
* *
120313 GAAGGGTTATCTGTTAGCAA
64 GAAGGGCTATCTG-TAGCCA
* *
120333 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAACTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTACAGCATAGCTTAAGTCGAG
* * *
120398 AAGGGTTATCTGCCAACCA
65 AAGGGCTATCTG-TAGCCA
** * ** * *
120417 AAGACCTACGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACCCAAGGCTAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTACAGCATAGCTTAAGTCGAG
* *
120482 AAGGGTTATCTGT-GATCA
65 AAGGGCTATCTGTAG-CCA
*
120500 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTACAGCATAGCTTAAGTCGAG
120565 AAGGGCTATCTG
65 AAGGGCTATCTG
120577 CTAAAGACAT
Statistics
Matches: 472, Mismatches: 87, Indels: 27
0.81 0.15 0.05
Matches are distributed among these distances:
80 123 0.26
81 71 0.15
83 72 0.15
84 149 0.32
85 57 0.12
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (82 bp):
AAGACCTTTGAGTTCGACTACGCTCAGCTCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGA
AGGGCTATCTGTAGCCA
Found at i:120165 original size:165 final size:162
Alignment explanation
Indices: 119923--120596 Score: 630
Period size: 165 Copynumber: 4.1 Consensus size: 162
119913 TCTGCCCACC
* * *
119923 AAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTC-AAGGCACATCATTTACAGCATAGCTTAAGTTGAG
* * * * * *
119988 AAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
65 AAGGGCTATCTGCCAAAGACCTTTGAGTTCGATTACACTCAGCTTCAA-GGCACATCATTTGCAG
* * * *
120053 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAA
129 CATAACTTAAGTCGAGAAGGGTTATCTG-TAGCCA
* * *
120088 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTACGTTGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTACAGCATAGCTTAAGTTGAG
* * * *
120153 AAGGGCTATCTGCCAAAGACCTTTGAGTTCGATTTCATTCAGCTCCAAGGCACATCATTTGCAGT
65 AAGGGCTATCTGCCAAAGACCTTTGAGTTCGATTACACTCAGCTTCAAGGCACATCATTTGCAGC
* * *
120218 ATAGCTTAAGTCGAGAAGAGCTATC--T-GCCA
130 ATAACTTAAGTCGAGAAGGGTTATCTGTAGCCA
* * * * * * * *
120248 AAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCT
1 AAGA-CCTTCGAGTTCGACTACGCTCAGC-TCAA-GGCACATCATTTACAGCATAGCTTAA-GTT
* * * *
120312 -AGAAGGGTTATCTGTTAGCAAAAGACCTTTGAGTTCGACTACGCTCAGC-TCAACGGCACATCA
62 GAGAAGGGCTATC---T-GCCAAAGACCTTTGAGTTCGATTACACTCAGCTTCAA-GGCACATCA
* *
120375 TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCA
122 TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-TAGCCA
* * ** *
120417 AAGACCTACGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACCCAAGGCT-A
1 AAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTACAGCATAGCTTAA-GTTGA
* * * * * * *
120481 GAAGGGTTATCTGTGATCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
64 GAAGGGCTATC--TG-CCAAAGACCTTTGAGTTCGATTACACTCAGCTTCAAGGCACATCATTTG
* * *
120546 CAGCATAGCTTAAGTCGAGAAGGGCTATC--T-GCTA
126 CAGCATAACTTAAGTCGAGAAGGGTTATCTGTAGCCA
*
120580 AAGACATTCGAGTTCGA
1 AAGACCTTCGAGTTCGA
120597 TTATATTCAA
Statistics
Matches: 426, Mismatches: 66, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
160 23 0.05
161 40 0.09
162 2 0.00
163 17 0.04
164 38 0.09
165 165 0.39
166 1 0.00
167 68 0.16
168 46 0.11
169 26 0.06
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (162 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACATCATTTACAGCATAGCTTAAGTTGAGA
AGGGCTATCTGCCAAAGACCTTTGAGTTCGATTACACTCAGCTTCAAGGCACATCATTTGCAGCA
TAACTTAAGTCGAGAAGGGTTATCTGTAGCCA
Found at i:120353 original size:245 final size:246
Alignment explanation
Indices: 119903--120461 Score: 967
Period size: 245 Copynumber: 2.3 Consensus size: 246
119893 GCTCAAGGCC
*
119903 AGAAGGGCTATCTGCCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTT
1 AGAAGGGCTATCTGCCCA--AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
119968 GCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTT
64 GCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTT
120033 CAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAAGACCTTTG
129 CAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAAGACCTTTG
* * *
120098 AGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTACGTTG
194 AGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAACTTAAGTCG
* * * **
120151 AGAAGGGCTATCTG-CCAAAGACCTTTGAGTTCGATTTCATTCAGCTCCAAGGCACATCATTTGC
1 AGAAGGGCTATCTGCCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGC
120215 AGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCA
66 AGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCA
120280 AGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAAGACCTTTGAG
131 AGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAAGACCTTTGAG
120345 TTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAACTTAAGTCG
196 TTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAACTTAAGTCG
* *
120396 AGAAGGGTTATCTGCCAACCAAAGACCTACGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTG-C--CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
120461 T
63 T
120462 ACAGCATAAC
Statistics
Matches: 291, Mismatches: 16, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
245 232 0.80
247 3 0.01
248 14 0.05
249 42 0.14
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (246 bp):
AGAAGGGCTATCTGCCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGC
AGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCA
AGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAAGACCTTTGAG
TTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAACTTAAGTCG
Found at i:121390 original size:40 final size:39
Alignment explanation
Indices: 121211--121493 Score: 220
Period size: 42 Copynumber: 7.4 Consensus size: 39
121201 TATATTTTCG
121211 AAAACATTTTG---AAAATATAT-ATATATAG--TTTTT
1 AAAACATTTTGAAAAAAATATATAATATATAGTTTTTTT
* * * * *
121244 AAAACATTTTG-AAAACATTTATATTATATAATTTGTTT
1 AAAACATTTTGAAAAAAATATATAATATATAGTTTTTTT
* * * *
121282 AAAACGTTTTTACAAAAA-A-ATAATATATAG--TTTTC
1 AAAACATTTTGAAAAAAATATATAATATATAGTTTTTTT
121317 AAAACATTTTTGAAAAAATATATATATATTATATAGTTTTTTT
1 AAAACA-TTTTGAAAAAA-ATATATA-A-TATATAGTTTTTTT
*
121360 TAAACATTTTGAAAATAAATATATAATATATAGTTTTTTT
1 AAAACATTTTGAAAA-AAATATATAATATATAGTTTTTTT
* **
121400 AAAAAACATTTTGAAAATAAATATATAATATATAATTTTTCGAA
1 --AAAACATTTTGAAAA-AAATATATAATATATAGTTTTT--TT
*
121444 AAAACATTTTG---AAAATATATAATATATA--ATTTTT
1 AAAACATTTTGAAAAAAATATATAATATATAGTTTTTTT
*
121478 AAAATATTTTTGAAAA
1 AAAACA-TTTTGAAAA
121494 TTATATGGTT
Statistics
Matches: 200, Mismatches: 27, Indels: 41
0.75 0.10 0.15
Matches are distributed among these distances:
33 11 0.05
34 5 0.03
35 20 0.10
36 18 0.09
37 10 0.05
38 31 0.16
39 8 0.04
40 15 0.08
41 8 0.04
42 63 0.31
43 11 0.05
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (39 bp):
AAAACATTTTGAAAAAAATATATAATATATAGTTTTTTT
Found at i:121516 original size:31 final size:31
Alignment explanation
Indices: 121466--121572 Score: 132
Period size: 32 Copynumber: 3.5 Consensus size: 31
121456 AAATATATAA
121466 TATATAATTTTT--AAAATATTTTTGAAAAT
1 TATATAATTTTTAAAAAATATTTTTGAAAAT
**
121495 TATATGGTTTTTAAAAAATATTTTTTGAAAAT
1 TATATAATTTTTAAAAAATA-TTTTTGAAAAT
* *
121527 TATA-CATTTTT-AAAAATATTTTTGGAAATT
1 TATATAATTTTTAAAAAATATTTTT-GAAAAT
121557 TATATAATTTTTAAAA
1 TATATAATTTTTAAAA
121573 GAAACGGTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
29 15 0.23
30 16 0.24
31 17 0.26
32 18 0.27
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (31 bp):
TATATAATTTTTAAAAAATATTTTTGAAAAT
Found at i:121525 original size:32 final size:32
Alignment explanation
Indices: 121466--121572 Score: 134
Period size: 30 Copynumber: 3.5 Consensus size: 32
121456 AAATATATAA
121466 TATATAATTTTT--AAAATA-TTTTTGAAAAT
1 TATATAATTTTTAAAAAATATTTTTTGAAAAT
**
121495 TATATGGTTTTTAAAAAATATTTTTTGAAAAT
1 TATATAATTTTTAAAAAATATTTTTTGAAAAT
* * *
121527 TATA-CATTTTT-AAAAATATTTTTGGAAATT
1 TATATAATTTTTAAAAAATATTTTTTGAAAAT
121557 TATATAATTTTTAAAA
1 TATATAATTTTTAAAA
121573 GAAACGGTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.15
30 21 0.32
31 17 0.26
32 18 0.27
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (32 bp):
TATATAATTTTTAAAAAATATTTTTTGAAAAT
Found at i:121615 original size:3 final size:3
Alignment explanation
Indices: 121609--121673 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
121599 GTTTTTTTAT
* * *
121609 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TCA CTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
121655 TT- TTA TTA CTTA TT- TTA TT
1 TTA TTA TTA -TTA TTA TTA TT
121674 TTAATTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 4 0.08
3 42 0.81
4 6 0.12
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:122804 original size:18 final size:18
Alignment explanation
Indices: 122781--122824 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
122771 ACCGGTCACA
122781 ACCCGACCCAACCCGTTT
1 ACCCGACCCAACCCGTTT
*
122799 ACCCGACCCGACCCGTTT
1 ACCCGACCCAACCCGTTT
122817 ACCCGACC
1 ACCCGACC
122825 GTTGACCCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.52, G:0.14, T:0.14
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTT
Found at i:122807 original size:13 final size:13
Alignment explanation
Indices: 122803--122864 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
122793 CCGTTTACCC
122803 GACCCGACCCGTT
1 GACCCGACCCGTT
*
122816 TACCCGA-CCGTT
1 GACCCGACCCGTT
122828 GACCCGACTCGACTCGTT
1 GACCCGA--C--C-CGTT
122846 GACCCGACCCGTT
1 GACCCGACCCGTT
122859 GACCCG
1 GACCCG
122865 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
12 11 0.27
13 16 0.39
14 1 0.02
16 1 0.02
17 1 0.02
18 11 0.27
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:122827 original size:30 final size:31
Alignment explanation
Indices: 122785--122864 Score: 108
Period size: 30 Copynumber: 2.6 Consensus size: 31
122775 GTCACAACCC
* *
122785 GACCCAACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
122816 TACCCGA-CCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
122846 GACCCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
122865 TTGACCGTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 26 0.62
31 16 0.38
ACGTcount: A:0.17, C:0.45, G:0.20, T:0.17
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:122847 original size:18 final size:17
Alignment explanation
Indices: 122820--122853 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
122810 CCCGTTTACC
122820 CGACCGTTGACCCGACT
1 CGACCGTTGACCCGACT
122837 CGACTCGTTGACCCGAC
1 CGAC-CGTTGACCCGAC
122854 CCGTTGACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.18, C:0.41, G:0.24, T:0.18
Consensus pattern (17 bp):
CGACCGTTGACCCGACT
Found at i:122874 original size:7 final size:7
Alignment explanation
Indices: 122854--122890 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
122844 TTGACCCGAC
122854 CCGTTGA
1 CCGTTGA
122861 CCCGTTGA
1 -CCGTTGA
122869 CCGTTGA
1 CCGTTGA
122876 CCGTTGA
1 CCGTTGA
122883 CCGTTGA
1 CCGTTGA
122890 C
1 C
122891 TACTGTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (7 bp):
CCGTTGA
Found at i:125359 original size:24 final size:24
Alignment explanation
Indices: 125332--125446 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
125322 TCGATTTGAT
125332 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
125356 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
125380 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
125404 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
125427 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
125447 TTGATTTATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:126400 original size:15 final size:15
Alignment explanation
Indices: 126380--126417 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
126370 AAACACGAGA
126380 AAGAACCAC-AAACGC
1 AAGAACCACAAAAC-C
*
126395 AAGAACAACAAAACC
1 AAGAACCACAAAACC
126410 AAGAACCA
1 AAGAACCA
126418 TTTTTCTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.61, C:0.29, G:0.11, T:0.00
Consensus pattern (15 bp):
AAGAACCACAAAACC
Found at i:130108 original size:16 final size:16
Alignment explanation
Indices: 130087--130118 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
130077 ACTATTCACA
*
130087 TGAATAGTGAATTTCG
1 TGAATAGTGAAATTCG
130103 TGAATAGTGAAATTCG
1 TGAATAGTGAAATTCG
130119 GTCGACGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
TGAATAGTGAAATTCG
Found at i:134193 original size:22 final size:22
Alignment explanation
Indices: 134162--134205 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
134152 GGCAACCAAC
134162 TTTGGAAAATATTTTTTCAAAA
1 TTTGGAAAATATTTTTTCAAAA
* * *
134184 TTTGGTAAATGTTTTTTTAAAA
1 TTTGGAAAATATTTTTTCAAAA
134206 AATATTTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (22 bp):
TTTGGAAAATATTTTTTCAAAA
Found at i:136443 original size:22 final size:22
Alignment explanation
Indices: 136417--136462 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
136407 ACAATTAATT
*
136417 AAAAATAATATATAAATATTGA
1 AAAAATAATATATAAACATTGA
136439 AAAAATAATATATAAACATTGA
1 AAAAATAATATATAAACATTGA
136461 AA
1 AA
136463 TTAATAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (22 bp):
AAAAATAATATATAAACATTGA
Found at i:137436 original size:21 final size:22
Alignment explanation
Indices: 137400--137458 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
137390 GATTATACCA
* *
137400 AAATAATAATAATAATAATTAT-
1 AAATAA-AAAAATAATAATCATC
*
137422 AAATAAATAAATAATAATCATC
1 AAATAAAAAAATAATAATCATC
*
137444 TAATAAAAAAATAAT
1 AAATAAAAAAATAAT
137459 TTCTTTGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 12 0.39
22 19 0.61
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATAAAAAAATAATAATCATC
Found at i:138964 original size:19 final size:20
Alignment explanation
Indices: 138921--138973 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
138911 GAAACCCCTT
*
138921 TGAAAATACATGATTTTTTTTA
1 TGAAAATACATGA--TTTTTAA
138943 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
138962 TGAAGATACATG
1 TGAAAATACATG
138974 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
22 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:139909 original size:30 final size:31
Alignment explanation
Indices: 139870--139929 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
139860 ACATATTGCC
**
139870 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
139901 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
139930 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:148082 original size:2 final size:2
Alignment explanation
Indices: 148075--148115 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
148065 GAGTTTAGCC
148075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
148116 TAAATCCCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:148483 original size:12 final size:11
Alignment explanation
Indices: 148453--148480 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
148443 ATAGATAATT
148453 TATTTTAAAAA
1 TATTTTAAAAA
148464 TATTTTAAAAA
1 TATTTTAAAAA
148475 TATTTT
1 TATTTT
148481 TAATTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:155474 original size:19 final size:19
Alignment explanation
Indices: 155432--155467 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
155422 ATAAATTAGA
155432 TAGT-AAAATTAATATTTC
1 TAGTAAAAATTAATATTTC
*
155450 TTGTAAAAATTAATATTT
1 TAGTAAAAATTAATATTT
155468 TAAGTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 3 0.19
19 13 0.81
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (19 bp):
TAGTAAAAATTAATATTTC
Found at i:157055 original size:15 final size:15
Alignment explanation
Indices: 157006--157066 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
156996 CATAGATCTA
* *
157006 TATAAAATTTTATGT
1 TATAAAATATTATAT
*
157021 TA-ATAATATTATA-
1 TATAAAATATTATAT
157034 TACTAAAATATTATAT
1 TA-TAAAATATTATAT
157050 TATAAATAATATTATAT
1 TAT-AA-AATATTATAT
157067 GGAATTATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 2 0.05
14 8 0.22
15 13 0.35
16 4 0.11
17 10 0.27
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
TATAAAATATTATAT
Found at i:159542 original size:31 final size:30
Alignment explanation
Indices: 159481--159543 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
159471 TAGGATATGA
* * * *
159481 TCCCTACGTTATCGATATGTTCGATTTTAG
1 TCCCTACATTATCGATACGTTCAATGTTAG
*
159511 TCCCTAACATTATCGATCCGTTCAATGTTAG
1 TCCCT-ACATTATCGATACGTTCAATGTTAG
159542 TC
1 TC
159544 TCTTAGCCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (30 bp):
TCCCTACATTATCGATACGTTCAATGTTAG
Done.