Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000478.1 Hibiscus syriacus cultivar Beakdansim tig00000891_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: 132084
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:8739 original size:26 final size:26
Alignment explanation
Indices: 8704--8763 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
8694 AAAACACCGT
8704 CGTTTTGGACCTAAACGAAGTGACGC
1 CGTTTTGGACCTAAACGAAGTGACGC
* *
8730 CGTTTTGGACCTAAACGAAGTGGCGT
1 CGTTTTGGACCTAAACGAAGTGACGC
8756 CGTTTTGG
1 CGTTTTGG
8764 CGTGGCAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (26 bp):
CGTTTTGGACCTAAACGAAGTGACGC
Found at i:10712 original size:54 final size:54
Alignment explanation
Indices: 10308--10957 Score: 469
Period size: 55 Copynumber: 11.9 Consensus size: 54
10298 AATGTCCTAG
* * * * * * * * *
10308 AAACAGGTTCGCTCCCTCTTCCTTCAGGAAGTATAAAACTTGAACAATCATCAAT
1 AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAAC-ATCTTCTAC
* * *
10363 AATCGTG-TCTGCTCCCTA-TTTCTTCA-GGAGTATAAGAA-TCGAACAATCTTCAAC
1 AAACGGGTTC-GCTCCC-ACTTTCTTCAGGGAGTAT-AGAACTCGAAC-ATCTTCTAC
* * * * *
10417 AATCGTG-TCTACTCCCTA-TTTCTTCAGAGAGTATA-AGACTCGAACACTCTTCAAC
1 AAACGGGTTC-GCTCCC-ACTTTCTTCAGGGAGTATAGA-ACTCGAACA-TCTTCTAC
* * * * *
10472 AATCGTG-TCAACTCCCTA-TTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAAC
1 AAACGGGTTC-GCTCCC-ACTTTCTTCAGGGAGTATAGA-ACTCGAAC-ATCTTCTAC
* * * *
10527 AATCGTGTAT-GCTCCCTA-TTTCTTCAGAGAGTATA-AGACTCAAACAATCTTCTGA-
1 AAACGGGT-TCGCTCCC-ACTTTCTTCAGGGAGTATAGA-ACTCGAAC-ATCTTCT-AC
* * *
10582 AAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAT-GAAACTCAAACAATCTTCTAT
1 AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAG-AACTCGAAC-ATCTTCTAC
10637 AAACGGGTTCGCT-CCATCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTAC
1 AAACGGGTTCGCTCCCA-CTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTAC
* *
10691 AAACGGGTTCGCTCTCACTTTCTTCAGGGAGTATAGAACTCGAACAATC-TCTAT
1 AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAAC-ATCTTCTAC
* * * * *
10745 AAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTTTTC
1 AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTAC
* * *
10799 AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATTCTTCT--
1 AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAACA-TCTTCTAC
* * * * * * *
10852 -TACGGGTTCGCTCTCTA-TTCCTTTCAGAGAGTATAAAACTCGAATAATCTTCTGC
1 AAACGGGTTCGCTC-CCACTTTC-TTCAGGGAGTATAGAACTCGAA-CATCTTCTAC
* * * *
10907 AAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAAAATTCAAACATCTTC
1 AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAACATCTTC
10958 ATTTGCTTCA
Statistics
Matches: 514, Mismatches: 52, Indels: 59
0.82 0.08 0.09
Matches are distributed among these distances:
52 15 0.03
53 29 0.06
54 200 0.39
55 250 0.49
56 19 0.04
57 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (54 bp):
AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTAC
Found at i:10793 original size:108 final size:109
Alignment explanation
Indices: 10373--10941 Score: 590
Period size: 110 Copynumber: 5.2 Consensus size: 109
10363 AATCGTGTCT
* * * * * *
10373 GCTCCCTATTTCTTCA-GGAGTATAAGAA-TCGAACAATCTTCAACAATCGTG-TCTACTCCCTA
1 GCTCCCTCTTTCTTCAGGGAGTAT-AGAACTCGAACAATCTTCTATAAACGGGTTC-GCTCCCTA
* * *
10435 TTTCTTCAGAGAGTATA-AGACTCGAACACTCTTCAACAATCGTG-TC
64 TTTCTTCAGAGAGTATAGA-ACTCGAACA-TCTTCTACAAACGGGTTC
* * * * * * *
10481 AACTCCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAATCGTGTAT-GCTCCCT
1 -GCTCCCTCTTTCTTCAGGGAGTATAGA-ACTCGAACAATCTTCTATAAACGGGT-TCGCTCCCT
*
10544 ATTTCTTCAGAGAGTATA-AGACTCAAACAATCTTCTGA-AAACGGGTTC
63 ATTTCTTCAGAGAGTATAGA-ACTCGAAC-ATCTTCT-ACAAACGGGTTC
* * *
10592 GCTCCCTCTTTCTTCAGGGAGTAT-GAAACTCAAACAATCTTCTATAAACGGGTTCGCTCCATCT
1 GCTCCCTCTTTCTTCAGGGAGTATAG-AACTCGAACAATCTTCTATAAACGGGTTCGCTCCCTAT
*
10656 TTCTTCAGGGAGTATAGAACTCGAACATCTTCTACAAACGGGTTC
65 TTCTTCAGAGAGTATAGAACTCGAACATCTTCTACAAACGGGTTC
* * * *
10701 GCTCTCACTTTCTTCAGGGAGTATAGAACTCGAACAATC-TCTATAAATGGGTTCGCTCCCTCTT
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTATAAACGGGTTCGCTCCCTATT
* * * *
10765 TCTTTAGGGAGTATAGAACTCGAACATCTTTTTCAAACGGGTTC
66 TCTTCAGAGAGTATAGAACTCGAACATCTTCTACAAACGGGTTC
* * * *
10809 GCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATTCTTCT-T--ACGGGTTCGCTCTCTATT
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTATAAACGGGTTCGCTCCCTATT
* * * *
10871 CCTTTCAGAGAGTATAAAACTCGAATAATCTTCTGCAAACGGGTTC
66 TC-TTCAGAGAGTATAGAACTCGAA-CATCTTCTACAAACGGGTTC
10917 GCTCCCTCTTTCTTCAGGGAGTATA
1 GCTCCCTCTTTCTTCAGGGAGTATA
10942 AAATTCAAAC
Statistics
Matches: 399, Mismatches: 44, Indels: 35
0.83 0.09 0.07
Matches are distributed among these distances:
106 16 0.04
107 19 0.05
108 141 0.35
109 72 0.18
110 144 0.36
111 6 0.02
112 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (109 bp):
GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTATAAACGGGTTCGCTCCCTATT
TCTTCAGAGAGTATAGAACTCGAACATCTTCTACAAACGGGTTC
Found at i:11394 original size:37 final size:37
Alignment explanation
Indices: 11300--11396 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
11290 TTGCTCCAAC
* * * *
11300 ACTCTTCCGAGAAGGCTTAAAATGGATTTGCTTCACT
1 ACTCTTCAGTGAAGGCTTAAGATGGATTTACTTCACT
*
11337 ACTCTTTAGTGAAGGCTTAAGATGGATTTACTTCACT
1 ACTCTTCAGTGAAGGCTTAAGATGGATTTACTTCACT
*
11374 ACTCTTCGGTGAAGGCTTAAGAT
1 ACTCTTCAGTGAAGGCTTAAGAT
11397 TGACTTTGCC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (37 bp):
ACTCTTCAGTGAAGGCTTAAGATGGATTTACTTCACT
Found at i:20089 original size:25 final size:25
Alignment explanation
Indices: 20055--20108 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
20045 AGTCCAGTGG
20055 CCCTACAAAATCACGGCCACCGTGA
1 CCCTACAAAATCACGGCCACCGTGA
20080 CCCTACAAAATCACGGCCACCGTGA
1 CCCTACAAAATCACGGCCACCGTGA
20105 CCCT
1 CCCT
20109 TTCCCTTCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.43, G:0.15, T:0.13
Consensus pattern (25 bp):
CCCTACAAAATCACGGCCACCGTGA
Found at i:21363 original size:23 final size:23
Alignment explanation
Indices: 21337--21423 Score: 111
Period size: 23 Copynumber: 3.8 Consensus size: 23
21327 TAGCTCATAT
21337 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
** * *
21360 AAATGCACTAAAGTGTCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
21383 AAATGCACCGAAGTGTCGCGTAA
1 AAATGCACCGAAGTGCCACGTAG
21406 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
21424 TATAAAATGT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:22761 original size:17 final size:17
Alignment explanation
Indices: 22739--22784 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
22729 AATTTCCATA
*
22739 TAATAATATGCACGTTC
1 TAATAATATGCACATTC
22756 TAATAATATGCACATTC
1 TAATAATATGCACATTC
22773 TAATAATATGCA
1 TAATAATATGCA
22785 TTCACCTGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (17 bp):
TAATAATATGCACATTC
Found at i:33416 original size:85 final size:85
Alignment explanation
Indices: 33262--33426 Score: 201
Period size: 85 Copynumber: 1.9 Consensus size: 85
33252 TCTATGACGC
* * *
33262 AAATTTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCCCCAGTCATAAATGAAGAC
1 AAATTTATGACACACATTTATGACGCTCATTGCGCGTCATTGAAGCCACAGTCATAAATAAAGAC
*
33327 GACACACATTTGTGTATAAT
66 GACACACATTCGTGTATAAT
* * * *
33347 AAATTTATGACACACATTTATGAC-TTACATTGCGTGTCATTGAAG-CATACGTTATTAAA-AAA
1 AAATTTATGACACACATTTATGACGCT-CATTGCGCGTCATTGAAGCCACA-GTCA-TAAATAAA
*
33409 GATGACACACATTCGTGT
63 GACGACACACATTCGTGT
33427 GTCGTGATTA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 3 0.04
85 61 0.90
86 4 0.06
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (85 bp):
AAATTTATGACACACATTTATGACGCTCATTGCGCGTCATTGAAGCCACAGTCATAAATAAAGAC
GACACACATTCGTGTATAAT
Found at i:33456 original size:2 final size:2
Alignment explanation
Indices: 33449--33475 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33439 TGTCATAAAT
33449 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 T
33476 TGCATATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35461 original size:13 final size:13
Alignment explanation
Indices: 35443--35470 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35433 AAAGTATTAC
35443 TTGTCACAATTTT
1 TTGTCACAATTTT
35456 TTGTCACAATTTT
1 TTGTCACAATTTT
35469 TT
1 TT
35471 ATATTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (13 bp):
TTGTCACAATTTT
Found at i:37927 original size:23 final size:23
Alignment explanation
Indices: 37858--37949 Score: 112
Period size: 23 Copynumber: 4.0 Consensus size: 23
37848 GGACATTATA
37858 TGGCACTACGGTGCATTTCTACG
1 TGGCACTACGGTGCATTTCTACG
* * * *
37881 CGACACTTCGGTGCAATTCTACG
1 TGGCACTACGGTGCATTTCTACG
37904 TGGCACTACGGTGCATTTCTACG
1 TGGCACTACGGTGCATTTCTACG
* * * *
37927 TGGTACTTCGGTACATTTATACG
1 TGGCACTACGGTGCATTTCTACG
37950 AGCTGTGGTG
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.32
Consensus pattern (23 bp):
TGGCACTACGGTGCATTTCTACG
Found at i:41189 original size:411 final size:409
Alignment explanation
Indices: 40409--41240 Score: 1163
Period size: 411 Copynumber: 2.0 Consensus size: 409
40399 ATTATAAAAC
* * * * *
40409 TTTTACTATATAATATTTTTGACACTAAAAAATAAGGAGAATTGTTTCTGATAATATACTTTTTC
1 TTTTACTATATAACATTTTTGACACTAAAAAATAAGAAGAAATGATTCTGATAATATAATTTTTC
*
40474 ATAATGATTAAAATATATAACTACAAATATAATTGATTACAAAAAACTTAAATTTTATTATTTAT
66 ATAATGATTAAAATATATAACTACAAAAATAATTGATTACAAAAAACTTAAATTTTATTATTTAT
* *
40539 TGTGATAATTTTTCTATAACAATAACTATAAATTATAATTACAAAACTTATCAACATAACTTTTG
131 TATGATAATTTTTCTATAACAATAACTATAAATTATAATTACAAAACTTACCAACATAACTTTTG
*
40604 GAAACAAAAAAATGGAGAAAAATATTTATCACAATATATGTTAACACTAAAATTAAAATTTATAA
196 GAAAC-AAAAAATGGAGAAAAATAATTATCACAATATATGTTAACACTAAAATTAAAATTTATAA
* * * * * *
40669 GTATAAGTATAATCTGTCACAAAAATATGAATACCATTATTTTTGTGACAATTTTTTTGTAATAA
260 CTACAAATATAATCTGTCACAAAAACATGAATAACATTATTTTTGTGACAATATTTTTGTAATAA
* * * *
40734 TTATAAACACTATAGTAACAAAAATTGTTACTATATGATTTTTTGGC-ACAAAAAATATGG-AGG
325 GTATAAACACTATAGTAACAAAAATTGTCACTATATGATTTTTTGACGA-AAAAAATATGGAAAG
40797 AAAATCTTTATGACAATATATT
389 -AAATCTTTATGACAATATATT
* *
40819 TTGTTACTATATAACATTTTTGACACTAAAAAATATGAAGAAATGATTCTGATAGTATAATTTTT
1 TT-TTACTATATAACATTTTTGACACTAAAAAATAAGAAGAAATGATTCTGATAATATAATTTTT
* * * * *
40884 CATAATGATTAAAATATATAAGTACAAAAATATTTTATTACAAAAACCTTGAATTTTATTATTTG
65 CATAATGATTAAAATATATAACTACAAAAATAATTGATTACAAAAAACTTAAATTTTATTATTT-
* * *
40949 A-TATGATAATTTTTCTATAACAATAACTATAAATTATAATTATAAAA-TTGCCAATATAACTTT
129 ATTATGATAATTTTTCTATAACAATAACTATAAATTATAATTACAAAACTTACCAACATAACTTT
* * * * *
41012 T-GAAAC-AAAAGTGGAGAAAAAATAATTATGACAATATATGTTATCACTATAGTTAAAATTTAT
194 TGGAAACAAAAAATGGAG-AAAAATAATTATCACAATATATGTTAACACTAAAATTAAAATTTAT
* * *
41075 AACTACAAATATAATTTGTCACGAAAACGTGAATAACATTATTTTTTGTGACAATATTTTTGTAA
258 AACTACAAATATAATCTGTCACAAAAACATGAATAACATTA-TTTTTGTGACAATATTTTTGTAA
* * *
41140 TAAGTATTAACACTTATAGTTACAAAATTTGTCACTATATGATTTTTTTGACGAAAAAAATATGG
322 TAAGTATAAACAC-TATAGTAACAAAAATTGTCACTATATGA-TTTTTTGACGAAAAAAATATGG
*
41205 AAAGAAATCTTTGTGACAATATATT
385 AAAGAAATCTTTATGACAATATATT
41230 TTTTCACTATA
1 TTTT-ACTATA
41241 ATTAAAACAT
Statistics
Matches: 372, Mismatches: 41, Indels: 17
0.87 0.10 0.04
Matches are distributed among these distances:
407 9 0.02
408 74 0.20
409 38 0.10
410 43 0.12
411 204 0.55
412 4 0.01
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (409 bp):
TTTTACTATATAACATTTTTGACACTAAAAAATAAGAAGAAATGATTCTGATAATATAATTTTTC
ATAATGATTAAAATATATAACTACAAAAATAATTGATTACAAAAAACTTAAATTTTATTATTTAT
TATGATAATTTTTCTATAACAATAACTATAAATTATAATTACAAAACTTACCAACATAACTTTTG
GAAACAAAAAATGGAGAAAAATAATTATCACAATATATGTTAACACTAAAATTAAAATTTATAAC
TACAAATATAATCTGTCACAAAAACATGAATAACATTATTTTTGTGACAATATTTTTGTAATAAG
TATAAACACTATAGTAACAAAAATTGTCACTATATGATTTTTTGACGAAAAAAATATGGAAAGAA
ATCTTTATGACAATATATT
Found at i:53168 original size:27 final size:27
Alignment explanation
Indices: 53116--53172 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
53106 AATCTCGAGC
*
53116 ATATATTTTAATTATACATATAATTAA
1 ATATATTTTAATTAGACATATAATTAA
* *
53143 ATATA-TTTAATTAGACCTATTTATTAA
1 ATATATTTTAATTAGACATA-TAATTAA
53170 ATA
1 ATA
53173 AACTATTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (27 bp):
ATATATTTTAATTAGACATATAATTAA
Found at i:60078 original size:21 final size:21
Alignment explanation
Indices: 60048--60102 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
60038 TGTAACCTGG
60048 AAAT-CTTTTTTTCCAATCAA
1 AAATCCTTTTTTTCCAATCAA
60068 AAATCCTTTTTTTCCAATCAA
1 AAATCCTTTTTTTCCAATCAA
60089 AAATCCTTTTTTTC
1 AAATCCTTTTTTTC
60103 TTCCAATTGT
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:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATCCTTTTTTTCCAATCAA
Found at i:64345 original size:15 final size:14
Alignment explanation
Indices: 64325--64363 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
64315 CAGTGAATAA
64325 AATGAATAAAATGAC
1 AATGAATAAAATG-C
*
64340 AATGAAGAAAATGC
1 AATGAATAAAATGC
64354 AAT-AATAAAA
1 AATGAATAAAA
64364 AAATAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 6 0.27
14 4 0.18
15 12 0.55
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (14 bp):
AATGAATAAAATGC
Found at i:64426 original size:14 final size:13
Alignment explanation
Indices: 64394--64418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64384 TAAACTAAAT
64394 AGAAAAAAAAGAA
1 AGAAAAAAAAGAA
64407 AGAAAAAAAAGA
1 AGAAAAAAAAGA
64419 CGAGAAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAGAA
Found at i:64686 original size:17 final size:17
Alignment explanation
Indices: 64652--64686 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
64642 AATAAATAAT
*
64652 AATGTATATATTTAAAA
1 AATGTATATATGTAAAA
64669 AATGTATATATAGTAAAA
1 AATGTATATAT-GTAAAA
64687 TAAAATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (17 bp):
AATGTATATATGTAAAA
Found at i:65789 original size:2 final size:2
Alignment explanation
Indices: 65769--65834 Score: 82
Period size: 2 Copynumber: 32.5 Consensus size: 2
65759 ATGTATAAGG
*
65769 TA TA -A TA TA GTA CA TA TA TA T- TA TA TA GTA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
65811 TA TA TA TA TA TA TA TA TA CTA TA T
1 TA TA TA TA TA TA TA TA TA -TA TA T
65835 GTTATAAATG
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
1 2 0.04
2 49 0.86
3 6 0.11
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:65796 original size:18 final size:17
Alignment explanation
Indices: 65769--65834 Score: 91
Period size: 16 Copynumber: 3.9 Consensus size: 17
65759 ATGTATAAGG
*
65769 TATA-ATATAGTACATA
1 TATATATATAGTATATA
65785 TATATTATATAGTATATA
1 TATA-TATATAGTATATA
65803 TATATATATA-TATATA
1 TATATATATAGTATATA
*
65819 TATATATATACTATAT
1 TATATATATAGTATAT
65835 GTTATAAATG
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
16 20 0.43
17 11 0.24
18 15 0.33
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TATATATATAGTATATA
Found at i:69287 original size:36 final size:37
Alignment explanation
Indices: 69240--69316 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
69230 TTCTACAAAC
*
69240 TATATAATATATA-TTTTCAAAA-GTATTTTAAAATTA
1 TATATAATATATATTTTTCAAAACGT-TTTCAAAATTA
* *
69276 TATATTATATATATTTTTTAAAACGTTTTCAAAATTA
1 TATATAATATATATTTTTCAAAACGTTTTCAAAATTA
69313 TATA
1 TATA
69317 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 12 0.33
37 22 0.61
38 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (37 bp):
TATATAATATATATTTTTCAAAACGTTTTCAAAATTA
Found at i:69335 original size:66 final size:61
Alignment explanation
Indices: 69247--69379 Score: 160
Period size: 63 Copynumber: 2.1 Consensus size: 61
69237 AACTATATAA
* * * *
69247 TATATATTTTCAAAAGTATTTTAAAATTATATATTATATATATTTTTTAAAACGTTTTCAAAAT
1 TATATATTTTCAAAAGTATTTTAAAACTATATA-T-TATA-AGTTTTTAAAACGATTTCAAAAC
*
69311 TATATAGTTTTCAAAAATGT-TTTTAAAACTATATATTATAAGTTTTTAAAATGATTTCAAAAC
1 TATATA-TTTTC-AAAA-GTATTTTAAAACTATATATTATAAGTTTTTAAAACGATTTCAAAAC
69374 TATATA
1 TATATA
69380 ATATATATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
63 25 0.41
64 10 0.16
65 6 0.10
66 18 0.30
67 2 0.03
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (61 bp):
TATATATTTTCAAAAGTATTTTAAAACTATATATTATAAGTTTTTAAAACGATTTCAAAAC
Found at i:69363 original size:34 final size:34
Alignment explanation
Indices: 69309--69521 Score: 103
Period size: 36 Copynumber: 6.0 Consensus size: 34
69299 CGTTTTCAAA
*
69309 ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
1 ATTATA-AGTTTT-TAAAATGTTTTTAAAACTATAT
* *
69345 ATTATAAGTTTTTAAAATGATTTCAAAACTATAT
1 ATTATAAGTTTTTAAAATGTTTTTAAAACTATAT
* *
69379 AATATATATATGTTTTCAAAATGTTTCTTTTTAAAAAT-TAT
1 -AT-TATA-A-GTTTTTAAAATG----TTTTTAAAACTATAT
** * **
69420 ATT-T-A--TTTTAATTTTTTTTTAAAACCGTAT
1 ATTATAAGTTTTTAAAATGTTTTTAAAACTATAT
* ** * *
69450 AATATATTTTTTTAAAAACGTTTTGAAAACTATAT
1 ATTATAAGTTTTT-AAAATGTTTTTAAAACTATAT
** * *
69485 ATTATATTTATTTTCAAAGTGTTTTAAAAACTATAT
1 ATTATAAGT-TTTT-AAAATGTTTTTAAAACTATAT
69521 A
1 A
69522 ATAGATAAAT
Statistics
Matches: 135, Mismatches: 27, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
29 9 0.07
30 5 0.04
31 1 0.01
33 6 0.04
34 23 0.17
35 30 0.22
36 34 0.25
37 1 0.01
38 12 0.09
39 1 0.01
40 2 0.01
41 3 0.02
42 8 0.06
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (34 bp):
ATTATAAGTTTTTAAAATGTTTTTAAAACTATAT
Found at i:69378 original size:100 final size:103
Alignment explanation
Indices: 69222--69404 Score: 241
Period size: 100 Copynumber: 1.8 Consensus size: 103
69212 ATAATAATAT
* * *
69222 AAAATATTTTCTACAAACTATATAATATATATTTTCAAAAGTATTTTAAAATTATATATTATATA
1 AAAATATTTTCTACAAACTATATAATATATATTTTCAAAAGTATTTCAAAACTATATAATATATA
*
69287 TAT-TTTTTAAAACGTTTTCAAAATTATATAGTTTTCA
66 TATGTTTTCAAAACGTTTTCAAAATTATATAGTTTTCA
* * *
69324 AAAATGTTTT-TA-AAACTATATATTATA-AGTTTTTAAAA-TGATTTCAAAACTATATAATATA
1 AAAATATTTTCTACAAACTATATAATATATA-TTTTCAAAAGT-ATTTCAAAACTATATAATATA
*
69385 TATATGTTTTCAAAATGTTT
64 TATATGTTTTCAAAACGTTT
69405 CTTTTTAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
99 2 0.03
100 45 0.64
101 14 0.20
102 9 0.13
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (103 bp):
AAAATATTTTCTACAAACTATATAATATATATTTTCAAAAGTATTTCAAAACTATATAATATATA
TATGTTTTCAAAACGTTTTCAAAATTATATAGTTTTCA
Found at i:69515 original size:36 final size:35
Alignment explanation
Indices: 69324--69521 Score: 109
Period size: 35 Copynumber: 5.6 Consensus size: 35
69314 ATAGTTTTCA
* **
69324 AAAATGTTTTTAAAACTATATATTATAAGT-TTTT
1 AAAATGTTTTAAAAACTATATATTATATTTATTTT
* * * *
69358 AAAATGATTTCAAAACTATATAATATATATATGTTTT
1 AAAATGTTTTAAAAACTATAT-AT-TATATTTATTTT
***
69395 CAAAATGTTTCTTTTTAA--A-A-ATTATATTTATTTT
1 -AAAATG-TT-TTAAAAACTATATATTATATTTATTTT
** * * ** * * *
69429 AATTTTTTTTTAAAACCGTATAATATATTTTTTTA
1 AAAATGTTTTAAAAACTATATATTATATTTATTTT
* *
69464 AAAACGTTTTGAAAACTATATATTATATTTATTTT
1 AAAATGTTTTAAAAACTATATATTATATTTATTTT
*
69499 CAAAGTGTTTTAAAAACTATATA
1 -AAAATGTTTTAAAAACTATATA
69522 ATAGATAAAT
Statistics
Matches: 121, Mismatches: 32, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
31 5 0.04
32 2 0.02
33 3 0.02
34 30 0.25
35 40 0.33
36 24 0.20
37 5 0.04
38 7 0.06
39 1 0.01
40 4 0.03
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (35 bp):
AAAATGTTTTAAAAACTATATATTATATTTATTTT
Found at i:70489 original size:84 final size:83
Alignment explanation
Indices: 70209--71077 Score: 888
Period size: 84 Copynumber: 10.5 Consensus size: 83
70199 GAGTCTTTGG
* * * *
70209 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCAAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
*
70274 CTC-AAGGTCTTTTGGT-C
65 CTCGAAGGTCTTTTGTTGC
* * * ** * *
70291 ACAGATAACCCTTCTAG-CATTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATC
1 -CAGATAACCCTTCTCGAC-TTAAGTTATGCTGCAAATGATGTG-CCT-TGAGCTGAGCGTAGTC
* **
70355 AAACTCGGGGGTC-TTTG--G-
62 GAACTCGAAGGTCTTTTGTTGC
* * *
70373 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAA
*
70438 CTCAAAGGTCTTTTGTTGC
65 CTCGAAGGTCTTTTGTTGC
* * * * *
70457 CAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTTGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
* *
70522 CTCGAAGGTCTTTGGTTGA
65 CTCGAAGGTCTTTTGTTGC
* * *
70541 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGTCGA
**
70606 ACTCGGGGGTC-TTTG--G-
64 ACTCGAAGGTCTTTTGTTGC
* * *
70622 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
* *
70687 CTCAAAGGTCTTTTGGT-C
65 CTCGAAGGTCTTTTGTTGC
* * * * * * * *
70705 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCA
1 -CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGTCG
**
70770 AACTCGGGGGTC-TTTG--G-
63 AACTCGAAGGTCTTTTGTTGC
* * *
70787 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAA
*
70852 CTCAAAGGTCTTTTGTTGC
65 CTCGAAGGTCTTTTGTTGC
* * * * *
70871 CAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTGGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
* * *
70936 CTCGTAGGTCTTTGGTTGG
65 CTCGAAGGTCTTTTGTTGC
*
70955 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAA
* *
71020 CTCAAAGGTCTTTTGTTGG
65 CTCGAAGGTCTTTTGTTGC
* * * * *
71039 TAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGAT
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
71078 TTGTTTTTTT
Statistics
Matches: 644, Mismatches: 112, Indels: 59
0.79 0.14 0.07
Matches are distributed among these distances:
80 71 0.11
81 124 0.19
82 3 0.00
83 40 0.06
84 351 0.55
85 55 0.09
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (83 bp):
CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCGAAC
TCGAAGGTCTTTTGTTGC
Found at i:70671 original size:165 final size:165
Alignment explanation
Indices: 70209--71077 Score: 907
Period size: 165 Copynumber: 5.2 Consensus size: 165
70199 GAGTCTTTGG
* * * * * *
70209 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTG-CCTTGGAGCTGAGCGTAGTCAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
* * *
70273 ACTC-AAGGTCTTTTGGTCACAGATAACCCTTCTAG-CATTGAGTTATGCTGTAAATGATGTGCC
66 ACTCGAAGGTCTTTTGG---CAGATAACCCTTCTCGAC-TTAAGTTATGCTGCAAATGATGTG-C
** * * * ***
70336 CTCAAAGCTGAGTGTAATCAAACTCGGGGGTCTTT-G--G-
126 CT-TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGA
* * * * *
70373 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
* * * * *
70437 ACTCAAAGGTCTTTTGTTGCCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCT
66 ACTCGAAGGTCTTTTG--G-CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
* *
70502 TGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTTGA
128 T-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGA
* * * *
70541 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
** * * *
70606 ACTCGGGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGG
66 ACTCGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-G
*
70670 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG-TCA
130 AGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTTGA
* * * * * * *
70706 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
** * * *
70771 ACTCGGGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTG
66 ACTCGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTG
* *
70835 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGC
130 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGA
* * * * *
70871 CAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTGGTCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
* *
70935 ACTCGTAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAATGTGCCG
66 ACTCGAAGGTC-TT--TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-
* *
71000 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGG
127 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGA
* * * *
71039 TAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGAT
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
71078 TTGTTTTTTT
Statistics
Matches: 618, Mismatches: 69, Indels: 32
0.86 0.10 0.04
Matches are distributed among these distances:
164 115 0.19
165 302 0.49
166 10 0.02
167 2 0.00
168 167 0.27
169 22 0.04
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
ACTCGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGA
GCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGA
Found at i:70780 original size:414 final size:413
Alignment explanation
Indices: 70160--71022 Score: 1566
Period size: 414 Copynumber: 2.1 Consensus size: 413
70150 GCTATGTTGT
* * *
70160 AAATGATATGACCTCGAAGTTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCG
70225 ACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAGGTCTTTTGGT
66 ACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAGGTCTTTTGGT
70290 CACAGATAACCCTTCTAGCATTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATC
131 CACAGATAACCCTTCTAGCATTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATC
70355 AAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT
196 AAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT
70420 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGCCAGACAACCCTTCTAGACTTAAGTTGTG
261 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGCCAGACAACCCTTCTAGACTTAAGTTGTG
*
70485 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTTGACAGATAACC
326 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACC
70550 CTTCTCGACTTAAGTTATGCTGC
391 CTTCTCGACTTAAGTTATGCTGC
*
70573 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCG
*
70638 ACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG
66 ACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTC-AAGGTCTTTTGG
* *
70703 TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
130 TCACAGATAACCCTTCTAGCATTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAAT
70768 CAAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGT
195 CAAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGT
70833 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGCCAGACAACCCTTCTAGACTTAAGTTGT
260 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGCCAGACAACCCTTCTAGACTTAAGTTGT
* * *
70898 GCTGCAAATGATATGCCTTGGAGCTGAGCGTGGTCGAACTCGTAGGTCTTTGGTTGGCAGATAAC
325 GCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAAC
70963 CCTTCTCGACTTAAGTTATGCTGC
390 CCTTCTCGACTTAAGTTATGCTGC
* * * * *
70987 AAATAATGTGCCGTTG-AGCTGAGCGTAGTCGAACTC
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
71023 AAAGGTCTTT
Statistics
Matches: 433, Mismatches: 16, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
413 130 0.30
414 303 0.70
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (413 bp):
AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAGGTCTTTTGGT
CACAGATAACCCTTCTAGCATTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATC
AAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT
GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGCCAGACAACCCTTCTAGACTTAAGTTGTG
CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACC
CTTCTCGACTTAAGTTATGCTGC
Found at i:74498 original size:19 final size:18
Alignment explanation
Indices: 74474--74520 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
74464 AGTTAATGTG
74474 AATGCAAAGAAAATAACAA
1 AATGCAAA-AAAATAACAA
*
74493 AATGCAACACAAATAACAA
1 AATGCAA-AAAAATAACAA
74512 AATGCAAAA
1 AATGCAAAA
74521 TGTCTAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 23 0.92
20 1 0.04
ACGTcount: A:0.66, C:0.15, G:0.09, T:0.11
Consensus pattern (18 bp):
AATGCAAAAAAATAACAA
Found at i:75279 original size:16 final size:17
Alignment explanation
Indices: 75253--75285 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
75243 AAAAATGAAC
75253 ATATCCTACCCCACATG
1 ATATCCTACCCCACATG
75270 ATAT-CTACCCCACATG
1 ATATCCTACCCCACATG
75286 CTTTAATTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.30, C:0.39, G:0.06, T:0.24
Consensus pattern (17 bp):
ATATCCTACCCCACATG
Found at i:77796 original size:29 final size:29
Alignment explanation
Indices: 77763--77829 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
77753 AAAATTATAT
*
77763 ATTATATATTTTTTTAAAACGTTTTCAAA
1 ATTATATATTTTTTCAAAACGTTTTCAAA
* * *
77792 ATTATATA-CTTTTCAAAATGTTTTTAAA
1 ATTATATATTTTTTCAAAACGTTTTCAAA
*
77820 ACTATATATT
1 ATTATATATT
77830 ATAAGTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 23 0.74
29 8 0.26
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (29 bp):
ATTATATATTTTTTCAAAACGTTTTCAAA
Found at i:77798 original size:34 final size:36
Alignment explanation
Indices: 77724--77799 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
77714 TTATACAAAC
*
77724 TATATAATATATATTTTCAAAAGTATTTTAAAATTA
1 TATATAATATATATTTTCAAAAGTATTTCAAAATTA
* * *
77760 TATATTATATATTTTTTTAAAACGT-TTTCAAAATTA
1 TATATAATATATATTTTCAAAA-GTATTTCAAAATTA
77796 TATA
1 TATA
77800 CTTTTCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 33 0.94
37 2 0.06
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (36 bp):
TATATAATATATATTTTCAAAAGTATTTCAAAATTA
Found at i:77805 original size:64 final size:61
Alignment explanation
Indices: 77731--77861 Score: 174
Period size: 64 Copynumber: 2.1 Consensus size: 61
77721 AACTATATAA
* * * *
77731 TATATATTTTCAAAA-GTATTTTAAAATTATATATTATATATTTTTTTAAAACGTTTTCAAAAT
1 TATATATTTTCAAAATGT-TTTTAAAACTATATATTATA-A-GTTTTTAAAACGATTTCAAAAC
*
77794 TATATACTTTTCAAAATGTTTTTAAAACTATATATTATAAGTTTTTAAAATGATTTCAAAAC
1 TATATA-TTTTCAAAATGTTTTTAAAACTATATATTATAAGTTTTTAAAACGATTTCAAAAC
77856 TATATA
1 TATATA
77862 ATATATATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
62 24 0.39
63 7 0.11
64 28 0.46
65 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (61 bp):
TATATATTTTCAAAATGTTTTTAAAACTATATATTATAAGTTTTTAAAACGATTTCAAAAC
Found at i:77845 original size:34 final size:33
Alignment explanation
Indices: 77705--78047 Score: 136
Period size: 34 Copynumber: 9.8 Consensus size: 33
77695 AATAATAATA
* *
77705 TAAAATATTTTATACAAACTATATAATATATATTTT
1 TAAAATGTTTT-TA-AAACTATATATTATA-ATTTT
* *
77741 CAAAA-GTATTTTAAAATTATATATTATATATTTTTT
1 TAAAATGT-TTTTAAAACTATATATTATA-A--TTTT
* * *
77777 TAAAACG-TTTTCAAA--AT-TA-TATACTTTT
1 TAAAATGTTTTTAAAACTATATATTATAATTTT
*
77805 CAAAATGTTTTTAAAACTATATATTATAAGTTTT
1 TAAAATGTTTTTAAAACTATATATTATAA-TTTT
* *
77839 TAAAATGATTTCAAAACTATATAATATATATATGTTT
1 TAAAATGTTTTTAAAACTATAT-AT-TATA-AT-TTT
*
77876 TCAAAATGTTTCTTTTTAAAAAT-TATATT-T-A-TTT
1 T-AAAATG----TTTTTAAAACTATATATTATAATTTT
**
77910 TAAAATGTTTTTTAAAACCGTATA--AT-ATTTT
1 TAAAATG-TTTTTAAAACTATATATTATAATTTT
* *
77941 TAAAAAAAAGTTTTAAAAACTATATATTATATTTATTTT
1 T---AAAATGTTTTTAAAACTATATATTATA---ATTTT
* * *
77980 CAAAGTGTTTTAAAAACTATATAATATATAAATGTTT
1 TAAAATGTTTTTAAAACTATAT-AT-TAT-AAT-TTT
* *
78017 CAAATATGTTTTCAAAACTATTATATATATA
1 TAAA-ATGTTTTTAAAACTA-TATAT-TATA
78048 TATATATATA
Statistics
Matches: 241, Mismatches: 29, Indels: 73
0.70 0.08 0.21
Matches are distributed among these distances:
28 9 0.04
29 7 0.03
30 11 0.05
31 14 0.06
32 4 0.02
33 25 0.10
34 47 0.20
35 14 0.06
36 42 0.17
37 16 0.07
38 29 0.12
39 10 0.04
40 2 0.01
41 3 0.01
42 8 0.03
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (33 bp):
TAAAATGTTTTTAAAACTATATATTATAATTTT
Found at i:77991 original size:36 final size:38
Alignment explanation
Indices: 77950--78049 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 38
77940 TTAAAAAAAA
** *
77950 GTTTTAAAAACTATATATTATATTTAT-TTTCAAA-GT
1 GTTTTAAAAACTATATATTATATAAATGTTTCAAATAT
*
77986 GTTTTAAAAACTATATAATATATAAATGTTTCAAATAT
1 GTTTTAAAAACTATATATTATATAAATGTTTCAAATAT
*
78024 GTTTTCAAAACTATTATATATATATA
1 GTTTTAAAAACTA-TATAT-TATATA
78050 TATATATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
36 24 0.44
37 7 0.13
38 13 0.24
39 4 0.07
40 6 0.11
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (38 bp):
GTTTTAAAAACTATATATTATATAAATGTTTCAAATAT
Found at i:78045 original size:2 final size:2
Alignment explanation
Indices: 78038--78073 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
78028 TCAAAACTAT
78038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
78074 AAAAAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:78538 original size:45 final size:45
Alignment explanation
Indices: 78474--78591 Score: 193
Period size: 45 Copynumber: 2.6 Consensus size: 45
78464 ATATCCAAAT
*
78474 CGCCCTTT-CGGGTTTTCAACTTGGACCCATCCTTGGTTGCAAGA
1 CGCCCTTTGCGGGTTTTCAACTTGGACCCATCCTTAGTTGCAAGA
*
78518 CGCCCTTTGCGGGTTGTCAACTTGGACCCATCCTTAGTTGCAAGA
1 CGCCCTTTGCGGGTTTTCAACTTGGACCCATCCTTAGTTGCAAGA
* *
78563 CGCCCTTTGCGGGTTTTCATCTTGAACCC
1 CGCCCTTTGCGGGTTTTCAACTTGGACCC
78592 GCCTTATTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
44 8 0.12
45 60 0.88
ACGTcount: A:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (45 bp):
CGCCCTTTGCGGGTTTTCAACTTGGACCCATCCTTAGTTGCAAGA
Found at i:78703 original size:17 final size:17
Alignment explanation
Indices: 78683--78718 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
78673 CTAAACATTT
78683 TTTTCTCTTTTTTATTC
1 TTTTCTCTTTTTTATTC
* *
78700 TTTTTTCTTTTTTTTTC
1 TTTTCTCTTTTTTATTC
78717 TT
1 TT
78719 CAACTTAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTCTCTTTTTTATTC
Found at i:78705 original size:19 final size:17
Alignment explanation
Indices: 78681--78718 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
78671 CCCTAAACAT
78681 TTTTTTCTCTTTTTTATTC
1 TTTTTTCT-TTTTTT-TTC
78700 TTTTTTCTTTTTTTTTC
1 TTTTTTCTTTTTTTTTC
78717 TT
1 TT
78719 CAACTTAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 8 0.42
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTCTTTTTTTTTC
Found at i:78718 original size:10 final size:10
Alignment explanation
Indices: 78681--78719 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
78671 CCCTAAACAT
78681 TTTTTTC-TC
1 TTTTTTCTTC
*
78690 TTTTTTATTC
1 TTTTTTCTTC
*
78700 TTTTTTCTTT
1 TTTTTTCTTC
78710 TTTTTTCTTC
1 TTTTTTCTTC
78720 AACTTAGGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
9 6 0.24
10 19 0.76
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:89060 original size:27 final size:24
Alignment explanation
Indices: 89016--89088 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
89006 AAAAATGTAG
*
89016 AAAT-AAT-AAAAAAGAAAAATAAT
1 AAATAAATAAAAAAAGGAAAA-AAT
* *
89039 CATTAAATAAAAAAAGGAAAAAAT
1 AAATAAATAAAAAAAGGAAAAAAT
89063 AAATAAATAAAATAGAGAGGAAAAAA
1 AAATAAATAAAA-A-A-AGGAAAAAA
89089 AATAAACCGA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 2 0.05
24 16 0.40
25 12 0.30
26 1 0.03
27 9 0.22
ACGTcount: A:0.74, C:0.01, G:0.10, T:0.15
Consensus pattern (24 bp):
AAATAAATAAAAAAAGGAAAAAAT
Found at i:90649 original size:39 final size:38
Alignment explanation
Indices: 90586--90863 Score: 227
Period size: 37 Copynumber: 7.2 Consensus size: 38
90576 AAAACTATAT
*
90586 TATATGTTTTCAAAATG-TTTAAAAAAACCATATATTA
1 TATATATTTTCAAAATGTTTTAAAAAAACCATATATTA
90623 TATATATTTTCAAAATGTTTTAAAAAAA-CATATATTA
1 TATATATTTTCAAAATGTTTTAAAAAAACCATATATTA
* *
90660 TGTATATATTTTCAAAATGATTT--AAAAACTATATATTA
1 --TATATATTTTCAAAATGTTTTAAAAAAACCATATATTA
*
90698 TATATAATTTTTCAAAATGTTTT--AGAAACCATATTATATA
1 TATAT-A-TTTTCAAAATGTTTTAAAAAAACCATA-TAT-TA
* *
90738 TATATATATATTCAAAACGCTTTTAAAAAAACTATATATTA
1 TATATAT-T-TTCAAAATG-TTTTAAAAAAACCATATATTA
* *
90779 TATA-AGTTTTCCAAAAT-TATTTAAAAAAAAACTATATATTC
1 TATATA-TTTT-CAAAATGT-TTT--AAAAAAACCATATATTA
* * * *
90820 TACA-AGTTGTCAAAAT-TATTT-AAAAAACTATATAATA
1 TATATA-TTTTCAAAATGT-TTTAAAAAAACCATATATTA
90857 TATATAT
1 TATATAT
90864 GTATATGTAT
Statistics
Matches: 206, Mismatches: 16, Indels: 38
0.79 0.06 0.15
Matches are distributed among these distances:
36 5 0.02
37 49 0.24
38 43 0.21
39 30 0.15
40 33 0.16
41 35 0.17
42 3 0.01
43 8 0.04
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (38 bp):
TATATATTTTCAAAATGTTTTAAAAAAACCATATATTA
Found at i:90834 original size:40 final size:41
Alignment explanation
Indices: 90762--90846 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
90752 AAACGCTTTT
* *
90762 AAAAAAACTATATATTATATAAGTTTTCCAAAATTATTTAA
1 AAAAAAACTATATATTATACAAGTTGTCCAAAATTATTTAA
*
90803 AAAAAAACTATATATTCTACAAGTTGT-CAAAATTATTTAA
1 AAAAAAACTATATATTATACAAGTTGTCCAAAATTATTTAA
90843 AAAA
1 AAAA
90847 CTATATAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 17 0.41
41 24 0.59
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (41 bp):
AAAAAAACTATATATTATACAAGTTGTCCAAAATTATTTAA
Found at i:91291 original size:18 final size:19
Alignment explanation
Indices: 91270--91309 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
91260 ATCAAATTAT
91270 TTTTA-AAAAATTAT-ATGA
1 TTTTATAAAAA-TATCATGA
91288 TTTTATAAAAATATCATGA
1 TTTTATAAAAATATCATGA
91307 TTT
1 TTT
91310 AATTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (19 bp):
TTTTATAAAAATATCATGA
Found at i:105150 original size:23 final size:23
Alignment explanation
Indices: 105124--105171 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
105114 ATAAAGTACA
*
105124 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
105147 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
105170 AT
1 AT
105172 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:108879 original size:184 final size:184
Alignment explanation
Indices: 108570--109280 Score: 1359
Period size: 184 Copynumber: 3.9 Consensus size: 184
108560 TTTTAAATGG
* *
108570 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
108635 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
108700 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
108754 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
108819 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
108884 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
108938 TATGGATATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
109003 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
109068 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
109122 TATGGATATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
* *
109187 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGTGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
109252 GATGTGTAAAATGTCGACACTTTTGTAAA
131 GATGTGTAAAATGTCGACACTTTTTTAAA
109281 AAGTGTCCAT
Statistics
Matches: 521, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 521 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:109302 original size:22 final size:22
Alignment explanation
Indices: 109272--109324 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
109262 ATGTCGACAC
*
109272 TTTTGTAAAAAGTG-TCCATACT
1 TTTTATAAAAAG-GATCCATACT
*
109294 TTTTATAAAAAGGATCGATACT
1 TTTTATAAAAAGGATCCATACT
*
109316 TTTTTTAAA
1 TTTTATAAA
109325 GATATGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (22 bp):
TTTTATAAAAAGGATCCATACT
Found at i:110750 original size:3 final size:3
Alignment explanation
Indices: 110742--110815 Score: 76
Period size: 3 Copynumber: 24.7 Consensus size: 3
110732 ACTTGTTTGG
* * * **
110742 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
110790 AGC TTC ATC GTC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
110816 TGTCATCTTC
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.26, C:0.34, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:110809 original size:42 final size:42
Alignment explanation
Indices: 110750--110840 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
110740 GGATCATCAT
*
110750 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* ** * *
110792 CTTCATCGTCATCATCATCATCATTGTCATCTTCATTGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
110834 CTTCATC
1 CTTCATC
110841 TTCTGCGACC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.37
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:110821 original size:9 final size:9
Alignment explanation
Indices: 110755--110822 Score: 57
Period size: 9 Copynumber: 7.6 Consensus size: 9
110745 ATCATCTTCA
*
110755 TCATCATCA
1 TCATCATCG
110764 TCATCATCG
1 TCATCATCG
*
110773 TCATCATCT
1 TCATCATCG
**
110782 TCATCGCCAG
1 TCATCATC-G
*
110792 -CTTCATCG
1 TCATCATCG
*
110800 TCATCATCA
1 TCATCATCG
*
110809 TCATCATTG
1 TCATCATCG
110818 TCATC
1 TCATC
110823 TTCATTGTCA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
8 1 0.02
9 44 0.98
ACGTcount: A:0.24, C:0.34, G:0.07, T:0.35
Consensus pattern (9 bp):
TCATCATCG
Found at i:110843 original size:6 final size:6
Alignment explanation
Indices: 110746--110843 Score: 56
Period size: 6 Copynumber: 16.3 Consensus size: 6
110736 GTTTGGATCA
* * * * * * * *
110746 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
110794 TCATCG TCATCA TCATCA TCAT-T GTCATCT TCAT-T GTCAGCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT -TCATCT TCATCT -TCATCT TCATCT
110842 TC
1 TC
110844 TGCGACCGAT
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
5 1 0.01
6 70 0.96
7 2 0.03
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:111824 original size:199 final size:199
Alignment explanation
Indices: 111076--111971 Score: 1697
Period size: 198 Copynumber: 4.5 Consensus size: 199
111066 ACACTTTATT
**
111076 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTA
1 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG
111141 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
66 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
* *
111206 CGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
131 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGATGATT
111271 TTGG
196 TTGG
* *
111275 GATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG
1 GATCGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG
111340 GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
65 GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
111405 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGATGAT
130 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGATGAT
111470 TTTGG
195 TTTGG
111475 GATCGACAC-TTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG
1 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG
111539 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
66 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
111604 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGATGATT
131 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGATGATT
111669 TTGG
196 TTGG
111673 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG
1 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG
111738 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
66 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
111803 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGATGATT
131 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGATGATT
111868 TTGG
196 TTGG
*
111872 GATCGACAC-TTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGA
1 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG
*
111936 AAAAAAATATCGACACAAACTATATTAGTATCGACA
66 AAAAAAATATCGACACAAACTATATTAGTGTCGACA
111972 TGACCCTTAA
Statistics
Matches: 685, Mismatches: 10, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
198 285 0.42
199 207 0.30
200 193 0.28
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG
AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGATGATT
TTGG
Found at i:111883 original size:397 final size:398
Alignment explanation
Indices: 111076--111971 Score: 1713
Period size: 397 Copynumber: 2.3 Consensus size: 398
111066 ACACTTTATT
*
111076 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTA
1 GATCGACAC-TTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGA
111141 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
65 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
111206 CGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
130 CGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
*
111271 TTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATT
195 TTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATT
111336 CTGGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT
260 CTGGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT
111401 AAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGA
325 AAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGA
111466 TGATTTTGG
390 TGATTTTGG
*
111475 GATCGACACTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGA
1 GATCGACACTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAA
111540 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
66 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
* *
111605 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGATGATTT
131 GGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
*
111670 TGGGATCGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTC
196 TGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTC
111734 TGGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATA
261 TGGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATA
111799 AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGAT
326 AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGAT
111864 GATTTTGG
391 GATTTTGG
111872 GATCGACACTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAA
1 GATCGACACTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAA
*
111937 AAAAAATATCGACACAAACTATATTAGTATCGACA
66 AAAAAATATCGACACAAACTATATTAGTGTCGACA
111972 TGACCCTTAA
Statistics
Matches: 489, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
397 286 0.58
398 194 0.40
399 9 0.02
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (398 bp):
GATCGACACTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAA
AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
GGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
TGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTC
TGGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATA
AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGAT
GATTTTGG
Found at i:112080 original size:19 final size:19
Alignment explanation
Indices: 112053--112097 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
112043 ATTCACATAA
*
112053 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
112072 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
112091 AAAATTA
1 AAAATTA
112098 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:113921 original size:33 final size:33
Alignment explanation
Indices: 113884--113949 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
113874 CATCTTAATA
*
113884 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
113917 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
113950 CCTTCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:116304 original size:19 final size:19
Alignment explanation
Indices: 116249--116295 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
116239 ATCCGGTATC
116249 ATTTTACCGGTTTTATCAT
1 ATTTTACCGGTTTTATCAT
*
116268 TTTATTACCGGTTTTATCAT
1 ATT-TTACCGGTTTTATCAT
116288 ATTTTACC
1 ATTTTACC
116296 TGTTATATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
ATTTTACCGGTTTTATCAT
Found at i:116442 original size:20 final size:20
Alignment explanation
Indices: 116416--116461 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
116406 CACTTTTAAA
116416 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
116435 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
116456 TTTACC
1 TTTACC
116462 TGGTATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:126432 original size:2 final size:2
Alignment explanation
Indices: 126425--126473 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
126415 ATGTAGCTTC
126425 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
126467 AT AT AT A
1 AT AT AT A
126474 GGATGGTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:127404 original size:15 final size:15
Alignment explanation
Indices: 127383--127421 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
127373 TGGTATAAAA
*
127383 TATTAATAT-ATTAT
1 TATTAATATAATAAT
127397 TCATTAATATAATAAT
1 T-ATTAATATAATAAT
127413 TATTAATAT
1 TATTAATAT
127422 GTATAGCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 16 0.73
16 5 0.23
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTAATATAATAAT
Found at i:129914 original size:130 final size:131
Alignment explanation
Indices: 129640--129996 Score: 477
Period size: 130 Copynumber: 2.7 Consensus size: 131
129630 GAGAAAAAAA
* * *
129640 ATAATATATAATTATTTCCAATCGAAAATAAATGACCTCTTATACTTTAAAACAGTCATTTATTA
1 ATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTTATACCTTAAAGCAGTCATTTATTA
* * * * **
129705 CTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATTCAATATCAATTCGAGTGAAATT
66 CTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATCAATTCGAGAGAAAAC
129770 G
131 G
* * *
129771 ATAATATCTAATTATTTCTAATTGAGAATAAATGACCTCTTATACCTTAAAGC-GTTCATTTATT
1 ATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTTATACCTTAAAGCAG-TCATTTATT
* * *
129835 GCTCCAATC-AAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTAGTTCGAGAGAAAA
65 ACTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATCAATTCGAGAGAAAA
129899 CG
130 CG
* * * *
129901 ATAATAT-TGAATTAATTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTAATTTATT
1 ATAATATAT-AATTATTTCCAATCGAGAATAAATGACCTCTTATACCTTAAAGCAGTCATTTATT
* * *
129965 ACTCCAACCAAAATGAAAAGATATTACTATTC
65 ACTCCAATCAAAATGAAGAGATATCACTATTC
129997 TCAATATCGA
Statistics
Matches: 198, Mismatches: 24, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
129 1 0.01
130 112 0.57
131 85 0.43
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (131 bp):
ATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTTATACCTTAAAGCAGTCATTTATTA
CTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATCAATTCGAGAGAAAAC
G
Done.