Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005546.1 Hibiscus syriacus cultivar Beakdansim tig00012840_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: 1755203
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:499132 original size:58 final size:59
Alignment explanation
Indices: 499053--499171 Score: 231
Period size: 58 Copynumber: 2.0 Consensus size: 59
499043 GGAGGTGAAT
499053 GAAGAAAAAGTAACACCAACATGGTTGGGAAAAGAAAAAATGAATGGGAGGAAAAAATG
1 GAAGAAAAAGTAACACCAACATGGTTGGGAAAAGAAAAAATGAATGGGAGGAAAAAATG
499112 GAAG-AAAAGTAACACCAACATGGTTGGGAAAAGAAAAAATGAATGGGAGGAAAAAATG
1 GAAGAAAAAGTAACACCAACATGGTTGGGAAAAGAAAAAATGAATGGGAGGAAAAAATG
499170 GA
1 GA
499172 GGTATTGAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 56 0.93
59 4 0.07
ACGTcount: A:0.54, C:0.07, G:0.28, T:0.12
Consensus pattern (59 bp):
GAAGAAAAAGTAACACCAACATGGTTGGGAAAAGAAAAAATGAATGGGAGGAAAAAATG
Found at i:501832 original size:14 final size:14
Alignment explanation
Indices: 501808--501852 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
501798 GCTTTCTGTC
*
501808 TATATGCAGAGATT
1 TATACGCAGAGATT
*
501822 TTTACGCAGAGATT
1 TATACGCAGAGATT
501836 TATACGCAGAGATT
1 TATACGCAGAGATT
501850 TAT
1 TAT
501853 TTATTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (14 bp):
TATACGCAGAGATT
Found at i:506951 original size:17 final size:16
Alignment explanation
Indices: 506925--506963 Score: 69
Period size: 17 Copynumber: 2.4 Consensus size: 16
506915 AACCATGATT
506925 ATGTCACATTTATAAA
1 ATGTCACATTTATAAA
506941 ATGTGCACATTTATAAA
1 ATGT-CACATTTATAAA
506958 ATGTCA
1 ATGTCA
506964 TGACAAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (16 bp):
ATGTCACATTTATAAA
Found at i:507031 original size:3 final size:3
Alignment explanation
Indices: 507023--507092 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
507013 ACAAGTTGTG
507023 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
507071 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
507093 GGGGCACATG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:508992 original size:21 final size:21
Alignment explanation
Indices: 508968--509007 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
508958 TTTTACTAGG
*
508968 CATGTTGCTTGTTGATTTAAA
1 CATGTTGATTGTTGATTTAAA
*
508989 CATGTTGATTGTTTATTTA
1 CATGTTGATTGTTGATTTA
509008 TTCTTGTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (21 bp):
CATGTTGATTGTTGATTTAAA
Found at i:511416 original size:77 final size:80
Alignment explanation
Indices: 511313--511466 Score: 201
Period size: 77 Copynumber: 2.0 Consensus size: 80
511303 CGAATTAATA
**
511313 AAACATCTTATTTAATTAATTCAAATTAAATAT-TCATT-AAAGACTTATAATCTGAATTACAAT
1 AAACATCTTATTTAATTAATTCAAATTAAATATCT-ATTAAAAGACTTATAATCAAAATTACAAT
*
511376 C-TTTAACGTTTATTT
65 CTTTTAACATTTATTT
* * *
511391 AAAC-TCTTATTTAATT-ATTCCAAATTAAATATCTATTAAAAGAGTTGTAATCAAAATTACATT
1 AAACATCTTATTTAATTAATT-CAAATTAAATATCTATTAAAAGACTTATAATCAAAATTACAAT
511454 CTTTTAACATTTA
65 CTTTTAACATTTA
511467 CTTACTATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
76 3 0.05
77 27 0.41
78 26 0.39
79 10 0.15
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.43
Consensus pattern (80 bp):
AAACATCTTATTTAATTAATTCAAATTAAATATCTATTAAAAGACTTATAATCAAAATTACAATC
TTTTAACATTTATTT
Found at i:518380 original size:77 final size:79
Alignment explanation
Indices: 518285--518431 Score: 201
Period size: 77 Copynumber: 1.9 Consensus size: 79
518275 ATAAAAAATA
**
518285 TTATTTAATTAATTCAAATTAAATATCCATT-AAAGACTTATAATCTGAATTACAATC-TTTAAC
1 TTATTTAATTAATTCAAATTAAATATCCATTAAAAGACTTATAATCAAAATTACAATCTTTTAAC
518348 GTTTATTTAAACTC
66 GTTTATTTAAACTC
* * * *
518362 TTATTTAATT-ATTCCAAATTAAATATCTATTAAAAGAGTTGTAATCAAAATTACATTCTTTTAA
1 TTATTTAATTAATT-CAAATTAAATATCCATTAAAAGACTTATAATCAAAATTACAATCTTTTAA
*
518426 TGTTTA
65 CGTTTA
518432 CTTACTATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
76 3 0.05
77 26 0.43
78 21 0.35
79 10 0.17
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (79 bp):
TTATTTAATTAATTCAAATTAAATATCCATTAAAAGACTTATAATCAAAATTACAATCTTTTAAC
GTTTATTTAAACTC
Found at i:522571 original size:38 final size:39
Alignment explanation
Indices: 522526--522599 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
522516 ACTAACGTTA
522526 TTTTTCACTTTTGAA-TTTTAATTTGAATTTATTATTAT
1 TTTTTCACTTTTGAAGTTTTAATTTGAATTTATTATTAT
*
522564 TTTTTCACTTTTGAAGTTTTAATTTGAATTTTTTAT
1 TTTTTCACTTTTGAAGTTTTAATTTGAATTTATTAT
522600 AATAAAAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 15 0.44
39 19 0.56
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.64
Consensus pattern (39 bp):
TTTTTCACTTTTGAAGTTTTAATTTGAATTTATTATTAT
Found at i:530658 original size:18 final size:18
Alignment explanation
Indices: 530632--530666 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
530622 ACCAAATTGC
*
530632 AGTGTTGGACAAAGGGAA
1 AGTGGTGGACAAAGGGAA
*
530650 AGTGGTGGAGAAAGGGA
1 AGTGGTGGACAAAGGGA
530667 CCCATCAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.46, T:0.14
Consensus pattern (18 bp):
AGTGGTGGACAAAGGGAA
Found at i:530937 original size:2 final size:2
Alignment explanation
Indices: 530930--530958 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
530920 TCACGTTAAT
530930 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
530959 TCAATCAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:534884 original size:22 final size:22
Alignment explanation
Indices: 534830--534884 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
534820 TAACTTTACT
534830 TGTAAATCAAGTACTTGTTCAAGA
1 TGTAAATC-A-TACTTGTTCAAGA
*
534854 T-CAAATCATACTT-TTCAAGA
1 TGTAAATCATACTTGTTCAAGA
534874 CTGTAAATCAT
1 -TGTAAATCAT
534885 GAATTTTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 7 0.26
21 6 0.22
22 8 0.30
23 5 0.19
24 1 0.04
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (22 bp):
TGTAAATCATACTTGTTCAAGA
Found at i:535053 original size:164 final size:168
Alignment explanation
Indices: 534777--535114 Score: 623
Period size: 164 Copynumber: 2.0 Consensus size: 168
534767 TTACTTAGGA
*
534777 ACATCAACATGTATGCTTGTACAAATAACTTTAGTTTCTCACGTAACTTTACTTGTAAATCAAGT
1 ACATTAACATGTATGCTTGTACAAATAACTTTAGTTTCTCACGTAACTTTACTTGTAAATCAAGT
534842 ACTTGTTCAAGATCAAATCATACTTTTCAAGACTGTAAATCATGAATTTTAGGTCCATAAAT-AA
66 ACTTGTTCAAGATCAAATCATACTTTTCAAGACTGTAAATCATGAATTTTAGGTCCATAAATAAA
534906 AACATTAA-TCA-GCAGATCATATCTTC-AAACAAGAC
131 AACATTAATTCATGCAGATCATATCTTCAAAACAAGAC
534941 ACATTAACATGTATGCTTGTACAAATAACTTTAGTTTCTCACGTAAC-TTACTTGTAAATCAAGT
1 ACATTAACATGTATGCTTGTACAAATAACTTTAGTTTCTCACGTAACTTTACTTGTAAATCAAGT
535005 AACTTGTTCAAGATCAAATCATACTTTTCAAGACTGTAAATCATGAATTTTAGGTCCATAAATAA
66 -ACTTGTTCAAGATCAAATCATACTTTTCAAGACTGTAAATCATGAATTTTAGGTCCATAAATAA
535070 AAACATTAATTCATGCAGATCATATCTTCAAAACAAGAC
130 AAACATTAATTCATGCAGATCATATCTTCAAAACAAGAC
535109 ACATTA
1 ACATTA
535115 TGCATTAGCA
Statistics
Matches: 168, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
163 17 0.10
164 108 0.64
165 10 0.06
166 3 0.02
167 15 0.09
168 15 0.09
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (168 bp):
ACATTAACATGTATGCTTGTACAAATAACTTTAGTTTCTCACGTAACTTTACTTGTAAATCAAGT
ACTTGTTCAAGATCAAATCATACTTTTCAAGACTGTAAATCATGAATTTTAGGTCCATAAATAAA
AACATTAATTCATGCAGATCATATCTTCAAAACAAGAC
Found at i:537167 original size:24 final size:24
Alignment explanation
Indices: 537135--537182 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
537125 CCTCTGTGGC
537135 CGTACATAGTTTATATAATTAGGT
1 CGTACATAGTTTATATAATTAGGT
*
537159 CGTACATAGTTTATGTAATTAGGT
1 CGTACATAGTTTATATAATTAGGT
537183 TGTCCCTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (24 bp):
CGTACATAGTTTATATAATTAGGT
Found at i:540072 original size:41 final size:40
Alignment explanation
Indices: 540013--540095 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 40
540003 CCCCAAAATC
*
540013 CCGTGTTGTTTCATGTAATTCATTTTCCGGAAAATATTTT
1 CCGTGTTGTTTCACGTAATTCATTTTCCGGAAAATATTTT
*
540053 CCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTT
1 CCGTG-TTGTTTCACGTAATTCATTTTCCGGAAAATATTTT
540094 CC
1 CC
540096 AGGGTTTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 5 0.12
41 35 0.88
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (40 bp):
CCGTGTTGTTTCACGTAATTCATTTTCCGGAAAATATTTT
Found at i:540390 original size:22 final size:23
Alignment explanation
Indices: 540365--540432 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 23
540355 TATATTTTTA
540365 ATATTATAATAAATAATCA-ATT
1 ATATTATAATAAATAATCATATT
* *
540387 ATATTATAATATAT-ATTATATT
1 ATATTATAATAAATAATCATATT
* *
540409 ATATTTTAATAAATATATAATATT
1 ATATTATAATAAATA-ATCATATT
540433 TTTTTTATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
21 3 0.08
22 28 0.74
24 7 0.18
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTATAATAAATAATCATATT
Found at i:540391 original size:31 final size:28
Alignment explanation
Indices: 540328--540381 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
540318 TATTTAAAAA
540328 ATATTTATTAATATTTAAATAATATAAT
1 ATATTTATTAATATTTAAATAATATAAT
540356 ATATTT-TTAATA-TTATAATAA-ATAAT
1 ATATTTATTAATATTTA-AATAATATAAT
540382 CAATTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 8 0.32
27 11 0.44
28 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
ATATTTATTAATATTTAAATAATATAAT
Found at i:540431 original size:19 final size:19
Alignment explanation
Indices: 540363--540434 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 19
540353 AATATATTTT
*
540363 TAATATTATAATAAATA-A
1 TAATATTTTAATAAATATA
540381 TCAATTATATTATAATATATATTATA
1 T-AA-TAT-TT-TAATA-A-A-TATA
*
540407 TTATATTTTAATAAATATA
1 TAATATTTTAATAAATATA
540426 TAATATTTT
1 TAATATTTT
540435 TTTTATATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
18 1 0.02
19 14 0.33
20 4 0.09
21 2 0.05
22 10 0.23
23 3 0.07
24 4 0.09
25 3 0.07
26 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATATTTTAATAAATATA
Found at i:540457 original size:13 final size:13
Alignment explanation
Indices: 540441--540511 Score: 53
Period size: 13 Copynumber: 5.6 Consensus size: 13
540431 TTTTTTTTAT
540441 ATATTTAATAATA
1 ATATTTAATAATA
*
540454 ATATTTATATATTTA
1 ATATTTA-ATA-ATA
540469 ATA-TTAAT-ATA
1 ATATTTAATAATA
* *
540480 ATA-AT-CTAATA
1 ATATTTAATAATA
540491 ATATTTAATAA-A
1 ATATTTAATAATA
540503 TATATTTAA
1 -ATATTTAA
540512 ATACTAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
10 1 0.02
11 12 0.26
12 2 0.04
13 20 0.43
14 6 0.13
15 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTTAATAATA
Found at i:540462 original size:21 final size:21
Alignment explanation
Indices: 540436--540478 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
540426 TAATATTTTT
540436 TTTATATATTTAATAATAATA
1 TTTATATATTTAATAATAATA
*
540457 TTTATATATTTAATATTAATA
1 TTTATATATTTAATAATAATA
540478 T
1 T
540479 AATAATCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTATATATTTAATAATAATA
Found at i:540493 original size:74 final size:75
Alignment explanation
Indices: 540343--540509 Score: 168
Period size: 74 Copynumber: 2.3 Consensus size: 75
540333 TATTAATATT
* *
540343 TAAATAATATAATATATTTTTAATATTATAATAAATAATCAATTATATTATAATATATATTATAT
1 TAAATAATATAATATATTTTTAATATTATAATAAATAATCAATTATATTATAATATATAATATAA
*
540408 TATATTTTAA
66 TATATTATAA
* * *
540418 TAAAT-ATATAATATTTTTTTTATATATT-TAAT-AATAAT-ATTTATATATTTAATAT-TAATA
1 TAAATAATATAATA-TATTTTTA-ATATTATAATAAATAATCAATTATAT-TATAATATATAATA
540478 TAATA-ATCTAATAA
63 TAATATAT-T-ATAA
**
540492 TATTTAATA-AATATATTT
1 TAAATAATATAATATATTT
540510 AAATACTAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
72 2 0.03
73 20 0.26
74 31 0.40
75 19 0.25
76 5 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (75 bp):
TAAATAATATAATATATTTTTAATATTATAATAAATAATCAATTATATTATAATATATAATATAA
TATATTATAA
Found at i:540507 original size:29 final size:31
Alignment explanation
Indices: 540441--540546 Score: 80
Period size: 29 Copynumber: 3.5 Consensus size: 31
540431 TTTTTTTTAT
* * *
540441 ATATTTAATAATAATATTTATATATTTAAT-A
1 ATATATAATAATACTAATTA-ATATTTAATAA
*
540472 TTAATATAATAAT-CTAA-TAATATTTAATAA
1 AT-ATATAATAATACTAATTAATATTTAATAA
* *
540502 ATATAT-TTAAATACTAATTAATATTT-TTAA
1 ATATATAAT-AATACTAATTAATATTTAATAA
*
540532 A-ATATAATAACACTA
1 ATATATAATAATACTA
540547 TCACTTTAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
28 1 0.02
29 26 0.43
30 13 0.22
31 11 0.18
32 9 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (31 bp):
ATATATAATAATACTAATTAATATTTAATAA
Found at i:540539 original size:20 final size:20
Alignment explanation
Indices: 540496--540541 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
540486 TAATAATATT
540496 TAATAAATATATTTAAATAC
1 TAATAAATATATTTAAATAC
* *
540516 TAATTAATATTTTTAAAATA-
1 TAATAAATATATTT-AAATAC
540536 TAATAA
1 TAATAA
540542 CACTATCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TAATAAATATATTTAAATAC
Found at i:540887 original size:15 final size:15
Alignment explanation
Indices: 540862--540926 Score: 96
Period size: 15 Copynumber: 4.4 Consensus size: 15
540852 ATATATCCAT
540862 TTCCA-TAATTCAAA
1 TTCCAGTAATTCAAA
**
540876 TTCCAGTAATTCATT
1 TTCCAGTAATTCAAA
*
540891 TTCCAGTAATTTAAA
1 TTCCAGTAATTCAAA
540906 TTCCAGTAATTCAAA
1 TTCCAGTAATTCAAA
540921 TTCCAG
1 TTCCAG
540927 AAAACCAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 5 0.11
15 39 0.89
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.38
Consensus pattern (15 bp):
TTCCAGTAATTCAAA
Found at i:543849 original size:21 final size:21
Alignment explanation
Indices: 543819--543861 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
543809 GATGTTATCT
*
543819 TGGTGGAGAAATGGATGAAAA
1 TGGTGAAGAAATGGATGAAAA
*
543840 TGGTGAAGAAATTGATGAAAA
1 TGGTGAAGAAATGGATGAAAA
543861 T
1 T
543862 TTGAGAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (21 bp):
TGGTGAAGAAATGGATGAAAA
Found at i:544829 original size:64 final size:64
Alignment explanation
Indices: 544757--544904 Score: 219
Period size: 64 Copynumber: 2.3 Consensus size: 64
544747 ACACACCATT
* * * *
544757 TCGAATGCATTTTATGCATCGATGCACTG-TCATACATGGATGCACTCAGG-TTTTTATGAAAAC
1 TCGAATGCATTTTATGCATCGATGCACAGACCATACATCGATGCACTCAGGCTTGTT-TG-AAAC
544820 A
64 A
*
544821 TCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTTTGAAACA
1 TCGAATGCATTTTATGCATCGATGCACAGACCATACATCGATGCACTCAGGCTTGTTTGAAACA
544885 TCGAATGCATTTTATGCATC
1 TCGAATGCATTTTATGCATC
544905 AATTCACCCT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
64 53 0.69
65 20 0.26
66 4 0.05
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTATGCATCGATGCACAGACCATACATCGATGCACTCAGGCTTGTTTGAAACA
Found at i:546582 original size:41 final size:42
Alignment explanation
Indices: 546525--546607 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 42
546515 ATGAAGGCTT
546525 CAAAACTGAACCAAAGGAGAAGGACCCATCATTTGC-ACGAA
1 CAAAACTGAACCAAAGGAGAAGGACCCATCATTTGCTACGAA
546566 CAAAACTGAACCAAAGGAGAAGGACCCATCATTTGCTACGAA
1 CAAAACTGAACCAAAGGAGAAGGACCCATCATTTGCTACGAA
546608 TACAAAAAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 36 0.88
42 5 0.12
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.13
Consensus pattern (42 bp):
CAAAACTGAACCAAAGGAGAAGGACCCATCATTTGCTACGAA
Found at i:546894 original size:21 final size:21
Alignment explanation
Indices: 546869--546908 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
546859 AAGACTCTAT
546869 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
546890 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
546909 AAACAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:554120 original size:2 final size:2
Alignment explanation
Indices: 554113--554142 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
554103 ACAATTTTTA
554113 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
554143 GTGTGTGTGT
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:556727 original size:22 final size:22
Alignment explanation
Indices: 556695--556739 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
556685 TGTTGTGGAA
*
556695 ACAAGACCAAAGAAAAGGAGGT
1 ACAAGAACAAAGAAAAGGAGGT
556717 ACAAGAACAAAGAAAAGGAGGT
1 ACAAGAACAAAGAAAAGGAGGT
556739 A
1 A
556740 GGTCAGTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.11, G:0.27, T:0.04
Consensus pattern (22 bp):
ACAAGAACAAAGAAAAGGAGGT
Found at i:557562 original size:16 final size:15
Alignment explanation
Indices: 557531--557570 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
557521 ATATTTTAGT
*
557531 TTTAAATACTAGTCCA
1 TTTAAATA-GAGTCCA
557547 TATTAAATAGAGTCCA
1 T-TTAAATAGAGTCCA
557563 TTTAAATA
1 TTTAAATA
557571 TTACCTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 8 0.36
17 7 0.32
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (15 bp):
TTTAAATAGAGTCCA
Found at i:558848 original size:3 final size:3
Alignment explanation
Indices: 558840--558880 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
558830 AAGTCTAAAA
* *
558840 CTT CTT CTT CTT CTT CTT CTT ATT -TT CTT CTT CTT TTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
558881 TCCGTGAGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (3 bp):
CTT
Found at i:558938 original size:24 final size:27
Alignment explanation
Indices: 558910--558958 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
558900 GGTGAGTTGA
558910 TTTTAAGTT-G-T-TTGTTCTTTGAAT
1 TTTTAAGTTGGTTCTTGTTCTTTGAAT
558934 TTTTAAGTTGGTTCTTGTTCTTTGA
1 TTTTAAGTTGGTTCTTGTTCTTTGA
558959 GTGATTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 1 0.05
26 1 0.05
27 11 0.50
ACGTcount: A:0.14, C:0.06, G:0.18, T:0.61
Consensus pattern (27 bp):
TTTTAAGTTGGTTCTTGTTCTTTGAAT
Found at i:559465 original size:20 final size:20
Alignment explanation
Indices: 559420--559472 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
559410 TTGATTGATT
559420 GAGGTATCGATACTAAAATA
1 GAGGTATCGATACTAAAATA
*
559440 GGGGTATCGATAC-AAAGAGTA
1 GAGGTATCGATACTAAA-A-TA
559461 -AGGTATCGATAC
1 GAGGTATCGATAC
559473 CATTATCAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.10
20 24 0.83
21 2 0.07
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (20 bp):
GAGGTATCGATACTAAAATA
Found at i:568562 original size:20 final size:21
Alignment explanation
Indices: 568533--568573 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
568523 GTCGATCAGA
*
568533 GGATATCTTT-ACATTATCCT
1 GGATAACTTTCACATTATCCT
*
568553 GGATAACTTTCACTTTATCCT
1 GGATAACTTTCACATTATCCT
568574 CCATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (21 bp):
GGATAACTTTCACATTATCCT
Found at i:573282 original size:48 final size:48
Alignment explanation
Indices: 573230--573460 Score: 268
Period size: 48 Copynumber: 5.0 Consensus size: 48
573220 AATTGAACCG
*
573230 TTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCTAAAATACACCT
1 TTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCCAAAATACACCT
*
573278 TTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCCAAAATGCACCT
1 TTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCCAAAATACACCT
* ** *
573326 TTATGCATTTAAGTTTCATTTGTGGCACCTTTCTTCCAAAATGTA-TT
1 TTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCCAAAATACACCT
* *
573373 GTTATGCA--T---TTTGATTTATGGCACCTTTCTGCCAATAATACACCT
1 -TTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCCAA-AATACACCT
* *
573418 TTATGCA-TT---TTT-ATTTATGGCACCTTTCTGCCAATAATGCACC
1 TTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCCAA-AATACACC
573461 ATTACACATT
Statistics
Matches: 167, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
43 23 0.14
44 41 0.25
45 5 0.03
46 1 0.01
47 1 0.01
48 96 0.57
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (48 bp):
TTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCCAAAATACACCT
Found at i:573378 original size:96 final size:91
Alignment explanation
Indices: 573207--573515 Score: 306
Period size: 96 Copynumber: 3.4 Consensus size: 91
573197 CCAGGAATGT
* * * * * *
573207 CACCTTTCTACCGAATTGAACCGTTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCTAAAAT
1 CACCTTTCTGCCAAAATGCACCTTTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCCAAAAT
*
573272 ACACCTTTATGCATTTAAGTTTCATTTGTGG
66 ACACCTTTATGCA--T---TTTCATTTATGG
*
573303 CACCTTTCTGCCAAAATGCACCTTTATGCATTTAAGTTTCATTTGTGGCACCTTTCTTCCAAAAT
1 CACCTTTCTGCCAAAATGCACCTTTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCCAAAAT
** * *
573368 GTA-TTGTTATGCATTTTGATTTATGG
66 ACACCT-TTATGCATTTTCATTTATGG
* *
573394 CACCTTTCTGCCAATAATACACCTTTATGCA-TT---TTT-ATTTATGGCACCTTTCTGCCAATA
1 CACCTTTCTGCCAA-AATGCACCTTTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCCAA-A
* * **
573454 ATGCACCATTACACATTTTCATTTATGG
64 ATACACCTTTATGCATTTTCATTTATGG
* * *
573482 CAACTTTATGCCAATAATGCACCGTTATGCATTT
1 CACCTTTCTGCCAA-AATGCACCTTTATGCATTT
573516 TCATTTATTC
Statistics
Matches: 183, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
87 20 0.11
88 52 0.28
89 2 0.01
91 26 0.14
92 15 0.08
94 1 0.01
95 1 0.01
96 66 0.36
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (91 bp):
CACCTTTCTGCCAAAATGCACCTTTATGCATTTAAGTTTCATTTGTGGCACCTTTCTGCCAAAAT
ACACCTTTATGCATTTTCATTTATGG
Found at i:573434 original size:44 final size:43
Alignment explanation
Indices: 573247--573523 Score: 259
Period size: 44 Copynumber: 6.1 Consensus size: 43
573237 TTTAAGTTTC
* * *
573247 ATTTGTGGCACCTTTCTGCTAAAATACACCTTTATGCATTTAAGTTT
1 ATTTATGGCACCTTTCTGCCAAAATGCACCTTTATGCA-TT---TTT
*
573294 CATTTGTGGCACCTTTCTGCCAAAATGCACCTTTATGCATTTAAGTTT
1 -ATTTATGGCACCTTTCTGCCAAAATGCACCTTTATGCA-TT---TTT
* * * * *
573342 CATTTGTGGCACCTTTCTTCCAAAATGTA-TTGTTATGCATTTTG
1 -ATTTATGGCACCTTTCTGCCAAAATGCACCT-TTATGCATTTTT
*
573386 ATTTATGGCACCTTTCTGCCAATAATACACCTTTATGCATTTTT
1 ATTTATGGCACCTTTCTGCCAA-AATGCACCTTTATGCATTTTT
* ** *
573430 ATTTATGGCACCTTTCTGCCAATAATGCACCATTACACATTTTC
1 ATTTATGGCACCTTTCTGCCAA-AATGCACCTTTATGCATTTTT
* * * *
573474 ATTTATGGCAACTTTATGCCAATAATGCACCGTTATGCATTTTC
1 ATTTATGGCACCTTTCTGCCAA-AATGCACCTTTATGCATTTTT
573518 ATTTAT
1 ATTTAT
573524 TCATTCATTT
Statistics
Matches: 204, Mismatches: 22, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
43 20 0.10
44 101 0.50
45 1 0.00
47 3 0.01
48 79 0.39
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (43 bp):
ATTTATGGCACCTTTCTGCCAAAATGCACCTTTATGCATTTTT
Found at i:575174 original size:23 final size:24
Alignment explanation
Indices: 575144--575204 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
575134 TCGAGGGTTT
575144 TATGTGGTCCTTCAGGAC-AAACC
1 TATGTGGTCCTTCAGGACAAAACC
* **
575167 TATGTGGTCATTTGGGACAAAACC
1 TATGTGGTCCTTCAGGACAAAACC
575191 TATGTGGTCCTTCA
1 TATGTGGTCCTTCA
575205 AGAGAAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (24 bp):
TATGTGGTCCTTCAGGACAAAACC
Found at i:576681 original size:20 final size:20
Alignment explanation
Indices: 576656--576697 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
576646 CTAATATTAA
576656 AATT-AAACCTTAGACTTTTT
1 AATTAAAACCTTAGA-TTTTT
*
576676 AATTAAAACTTTAGATTTTT
1 AATTAAAACCTTAGATTTTT
576696 AA
1 AA
576698 AGTTATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (20 bp):
AATTAAAACCTTAGATTTTT
Found at i:577411 original size:27 final size:27
Alignment explanation
Indices: 577374--577496 Score: 158
Period size: 27 Copynumber: 4.6 Consensus size: 27
577364 TATTTATTTT
*
577374 TTTATT-CTTTTAATTTACTTTTAATC
1 TTTATTCCTTTTAATTTCCTTTTAATC
* *
577400 TTTATTCTTTTTAATTTCCTTTTAATA
1 TTTATTCCTTTTAATTTCCTTTTAATC
* * *
577427 TTTTTTCCTTTTGATTTCTTTTTAATC
1 TTTATTCCTTTTAATTTCCTTTTAATC
* *
577454 TTTATTCCTTTTAATTCCCTTTAAATC
1 TTTATTCCTTTTAATTTCCTTTTAATC
*
577481 TTTATTTCTTTTAATT
1 TTTATTCCTTTTAATT
577497 CTTATAAATA
Statistics
Matches: 82, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
26 6 0.07
27 76 0.93
ACGTcount: A:0.20, C:0.14, G:0.01, T:0.66
Consensus pattern (27 bp):
TTTATTCCTTTTAATTTCCTTTTAATC
Found at i:580650 original size:60 final size:60
Alignment explanation
Indices: 580545--580876 Score: 169
Period size: 52 Copynumber: 5.9 Consensus size: 60
580535 AATGAAGAAA
** * *
580545 AGTTAAATGCCTAACTGTGTATATTGGTAGAAAGGTGCTATTAATGCAAGTTAGATTATC
1 AGTTAAATGCCTAACTGTACATATTGGCAGAAAGGTGCTAATAATGCAAGTTAGATTATC
* *
580605 AGTTAAATGCCTAACTGTACATATTGGCATAAAGTTG-TCAATAATGCAAGTTAG---AT-
1 AGTTAAATGCCTAACTGTACATATTGGCAGAAAGGTGCT-AATAATGCAAGTTAGATTATC
* * * * * *
580661 -G--AAAGGCCTAACTGTGCATTTTTGTAGAAAGGTG-TCAATAAT----GTAAGA-TAT-
1 AGTTAAATGCCTAACTGTACATATTGGCAGAAAGGTGCT-AATAATGCAAGTTAGATTATC
* * * * * * *
580712 A-TGAAAGGTCTAACTGTGCA-ATTGGTAGAAAGCTGCCAATAATGCAAGTTAG---AT-
1 AGTTAAATGCCTAACTGTACATATTGGCAGAAAGGTGCTAATAATGCAAGTTAGATTATC
* * * * * * *
580766 A---AAAGGCCTAACTATGCAT-TTGGCAGAAAGGTGCAAATAATACAAGTTAGATGA-A
1 AGTTAAATGCCTAACTGTACATATTGGCAGAAAGGTGCTAATAATGCAAGTTAGATTATC
* * * * *
580821 ATGTTAAATGTCTAACTGTGCAT-TTGGCAGAAAGGTGCCACTAATGCAATTTAGAT
1 A-GTTAAATGCCTAACTGTACATATTGGCAGAAAGGTGCTAATAATGCAAGTTAGAT
580877 GAAAAATCGT
Statistics
Matches: 219, Mismatches: 33, Indels: 41
0.75 0.11 0.14
Matches are distributed among these distances:
49 4 0.02
51 2 0.01
52 60 0.27
53 50 0.23
54 3 0.01
55 3 0.01
56 4 0.02
57 2 0.01
59 45 0.21
60 46 0.21
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (60 bp):
AGTTAAATGCCTAACTGTACATATTGGCAGAAAGGTGCTAATAATGCAAGTTAGATTATC
Found at i:580697 original size:53 final size:52
Alignment explanation
Indices: 580613--580880 Score: 250
Period size: 52 Copynumber: 5.0 Consensus size: 52
580603 TCAGTTAAAT
* * * *
580613 GCCTAACTGTACATATTGGCATAAAGTTGTCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCAT-TTGGTAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * * *
580666 GCCTAACTGTGCATTTTTGTAGAAAGGTGTCAATAATGTAAGATATATGAAAG
1 GCCTAACTGTGCA-TTTGGTAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * * * *
580719 GTCTAACTGTGCAATTGGTAGAAAGCTGCCAATAATGCAAGTTAGATAAAAG
1 GCCTAACTGTGCATTTGGTAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * *
580771 GCCTAACTATGCATTTGGCAGAAAGGTG-CAAATAATACAAGTTAGATGAAATG
1 GCCTAACTGTGCATTTGGTAGAAAGGTGTC-AATAATGCAAGTTAGATGAAA-G
* * * * *
580824 TTAAATGTCTAACTGTGCATTTGGCAGAAAGGTGCCACTAATGCAATTTAGATGAAA
1 ------GCCTAACTGTGCATTTGGTAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
580881 AATCGTGTAT
Statistics
Matches: 176, Mismatches: 29, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
51 1 0.01
52 73 0.41
53 56 0.32
54 1 0.01
59 44 0.25
60 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (52 bp):
GCCTAACTGTGCATTTGGTAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
Found at i:589839 original size:2 final size:2
Alignment explanation
Indices: 589832--589863 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
589822 TTCTGAATTT
589832 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
589864 ATTCACCCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:595400 original size:20 final size:18
Alignment explanation
Indices: 595357--595404 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
595347 GATGCAATTA
*
595357 GTATCGATACTAAGGTAG
1 GTATCGATACTAAGGAAG
*
595375 GTATCGATACTAAGAGAAAT
1 GTATCGATACTAAG-G-AAG
595395 GTATCGATAC
1 GTATCGATAC
595405 AGTGGATTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 14 0.54
19 1 0.04
20 11 0.42
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (18 bp):
GTATCGATACTAAGGAAG
Found at i:596016 original size:60 final size:60
Alignment explanation
Indices: 595913--596028 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
595903 TGAAGAAAAG
* *
595913 TTAAATGCCTAACTATGCATATTGACAGAAAGGTGCCATTAATGCAAGTTAGATGATCAA
1 TTAAATGCCTAACTATGCATATTGACAGAAAGGAGCCAATAATGCAAGTTAGATGATCAA
* * * * * * * *
595973 TTAAATGTCTAACTGTGCATATTGGCATAATGGAGTCAATAATGTAATTTAGATGA
1 TTAAATGCCTAACTATGCATATTGACAGAAAGGAGCCAATAATGCAAGTTAGATGA
596029 AAGGCCCAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (60 bp):
TTAAATGCCTAACTATGCATATTGACAGAAAGGAGCCAATAATGCAAGTTAGATGATCAA
Found at i:596048 original size:53 final size:53
Alignment explanation
Indices: 595981--596245 Score: 288
Period size: 52 Copynumber: 4.9 Consensus size: 53
595971 AATTAAATGT
* * * * *
595981 CTAACTGTGCATATTGGCATAATGGAGTCAATAATGTAATTTAGATGAAAGGC
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
* * * *
596034 CCAACTGTGTATATTGGCA-AGAGTGTGTCAATAATGTAAGTTAGATG-AAGGC
1 CTAACTGTGCATATTGGCAGAAAG-GTGTCAATAATGCAAGTTAGATGAAAGGC
* *
596086 CTAACTGTGCA-ATTGGTAGAAAGGTGTCAATAATGCAAGTTATATGAAAGGC
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
*
596138 CTAACTGTGCAT-TTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAATGTTAAATGC
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA-G------GC
* * *
596197 CTAACTCTGCAT-TTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAA
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
596246 AATAATGTAT
Statistics
Matches: 184, Mismatches: 17, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
51 27 0.15
52 69 0.38
53 39 0.21
59 49 0.27
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (53 bp):
CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
Found at i:597534 original size:18 final size:18
Alignment explanation
Indices: 597513--597549 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
597503 AAGCCTCCAC
597513 TATAATTTGGATTTCAAT
1 TATAATTTGGATTTCAAT
597531 TATAATTTGGATTTCAAT
1 TATAATTTGGATTTCAAT
597549 T
1 T
597550 TAGTCCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TATAATTTGGATTTCAAT
Found at i:599486 original size:13 final size:14
Alignment explanation
Indices: 599468--599517 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
599458 AATTCCTTTG
599468 TTGCATTTA-CATT
1 TTGCATTTAGCATT
599481 TTGCATTTAGCATT
1 TTGCATTTAGCATT
* *
599495 CT-CATTTTTGCATTT
1 TTGCA-TTTAGCA-TT
599510 TTGCATTT
1 TTGCATTT
599518 TTGTATTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 11 0.37
14 11 0.37
15 6 0.20
16 2 0.07
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.56
Consensus pattern (14 bp):
TTGCATTTAGCATT
Found at i:599540 original size:20 final size:20
Alignment explanation
Indices: 599511--599549 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
599501 TTTGCATTTT
* *
599511 TGCATTTTTGTATTTGCATG
1 TGCATCTTTGTATTAGCATG
599531 TGCATCTTTGTATTAGCAT
1 TGCATCTTTGTATTAGCAT
599550 CTATACATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (20 bp):
TGCATCTTTGTATTAGCATG
Found at i:601003 original size:16 final size:15
Alignment explanation
Indices: 600934--601018 Score: 50
Period size: 16 Copynumber: 5.3 Consensus size: 15
600924 AAAAATATAC
*
600934 GAAAGAAAGAAAGAAGG
1 GAAA-AAAGAAAGAA-A
*
600951 GAAATAAG-AA-AAA
1 GAAAAAAGAAAGAAA
600964 GTAAAAAAGAGAGAGAGAA
1 G-AAAAAAGA-A-AGA-AA
*
600983 AAAAAAAGCAAA-AAA
1 GAAAAAAG-AAAGAAA
600998 GGAAAAAAGAAAGAAA
1 -GAAAAAAGAAAGAAA
601014 GAAAA
1 GAAAA
601019 CAGATCAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 20
0.68 0.06 0.25
Matches are distributed among these distances:
13 1 0.02
14 8 0.15
15 12 0.22
16 15 0.28
17 6 0.11
18 9 0.17
19 3 0.06
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.02
Consensus pattern (15 bp):
GAAAAAAGAAAGAAA
Found at i:601342 original size:2 final size:2
Alignment explanation
Indices: 601335--601359 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
601325 TTTATTTGCA
601335 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
601360 AAATCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:601638 original size:28 final size:29
Alignment explanation
Indices: 601592--601669 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 29
601582 CAAAGACACG
*
601592 AACCTTAAACACATTACCTTCC-TAAATT
1 AACCTGAAACACATTACCTTCCTTAAATT
* * *
601620 AACTTGAAACACTTTACC-TCCTTGAATT
1 AACCTGAAACACATTACCTTCCTTAAATT
601648 AACCTGAAACACATTACCTTCC
1 AACCTGAAACACATTACCTTCC
601670 CAAGTTAGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 3 0.07
28 36 0.86
29 3 0.07
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (29 bp):
AACCTGAAACACATTACCTTCCTTAAATT
Found at i:604600 original size:54 final size:54
Alignment explanation
Indices: 604432--604751 Score: 333
Period size: 54 Copynumber: 5.9 Consensus size: 54
604422 ATATGCTATT
* * * * * *
604432 TTCAAATGAATATTCTTAAAGTAGCTCAGCCTAATTTTCAAGGGTTTCTTGATGTT
1 TTCAAATGAAT-TT-TGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
* * * * ** ** *
604488 TTCAAAT-AATTTTTAAA-AGAGCTAAG-TTCGATTTTCAGAAGTCTTGATGATTTC
1 TTCAAATGAATTTTGAAAGA-AGCTAAGCCT-AATTTTTAGGGGT-TTCTTGATGTC
* * * * *
604542 TTCAAAT-AATTTTTGAAAGAAGTTAAGCCTAATTTTTATGGTTTTCTTGATCTT
1 TTCAAATGAA-TTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
*
604596 TTCAAATGAATTTTGAAAAAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
1 TTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
* *
604650 TTCAAATGAATTTTGAAAGAAACTAAGCCTAATTTTTATGGGTTTCTTGATGTC
1 TTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
* *
604704 TTCAAATGAATTTTGAAAGAAGTTAAGCCTAAATTTTAGGGGTTTCTT
1 TTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
604752 AATGATAACT
Statistics
Matches: 220, Mismatches: 37, Indels: 16
0.81 0.14 0.06
Matches are distributed among these distances:
52 1 0.00
53 20 0.09
54 165 0.75
55 25 0.11
56 9 0.04
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (54 bp):
TTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
Found at i:607271 original size:315 final size:318
Alignment explanation
Indices: 606675--607309 Score: 836
Period size: 315 Copynumber: 2.0 Consensus size: 318
606665 GGATAAACCA
* *
606675 ATCAACATTTACAATAGAAGGGTTTATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCA
1 ATCAACATTTACAATAGAAGAGTTTATAATAAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCA
* * ** *
606740 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCCATCGTAGAAGGAGGTGGATCAAAATTTCT
66 TAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTAGATCAAAATTTCT
* * * * * * *
606805 AGTAGAGGGTTCATATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATATTGAGAATAACT
131 AGTAGAGAGATCATATGAGAAGAAATCATCCAATGAGGGAGAAGAAGTTCATAATAAGAAAAAAT
*
606870 TATTCAACCTTAGCTTGATTCCATCACATAATGAGTTGGAACAACACCAATACCGGCTCATCCAT
196 TATTCAACCTTAGCTTGATTCCATCACATAAGGAGTTGGAACAACACCAATACCGGCTCATCCAT
* *
606935 CATATATGAAGTTTGATCAGCATCATCACTTTGTTCT-ATTCCATCATAGAAGGAGGTGG
261 CACATATGAAGTTGGATCAGCATCATCACTTTGTT-TGATTCCATCATA-AAGGAGGTGG
* * *
606994 ATCAACATTTACAGT-GGAGAGTTTATAATAAGGAGAACTCATCCAATGAGGGAG-AG-AGTTCA
1 ATCAACATTTACAATAGAAGAGTTTATAATAAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCA
* * * * *
607056 TAATGAGAA-AACTTGTTCAACCTTAGCTCAATTCTATCACATAATGAGGTATATCAATATTTCT
66 TAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTAGATCAAAATTTCT
* *
607120 AG-AGGAGAGATCTTAATGAGAAGAAATCATCTGAA-GAGGGAGAAGAAGTTCATAATAAGAAAA
131 AGTA-GAGAGATCAT-ATGAGAAGAAATCATC-CAATGAGGGAGAAGAAGTTCATAATAAGAAAA
* * **
607183 AATTGTTCAACCTTAGC-TGATTCCATCACATAAGGAGTTGGAACAACACTAATACTTGCTCATC
193 AATTATTCAACCTTAGCTTGATTCCATCACATAAGGAGTTGGAACAACACCAATACCGGCTCATC
* * ** * *
607247 TATCACATATGGAGTTGGATCAGCATCATCTTTTTGTTTGATTCCATTATAAAGGATGTGG
258 CATCACATATGAAGTTGGATCAGCATCATCACTTTGTTTGATTCCATCATAAAGGAGGTGG
607308 AT
1 AT
607310 AGTTCATAAT
Statistics
Matches: 275, Mismatches: 37, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
314 13 0.05
315 139 0.51
316 70 0.25
317 4 0.01
318 35 0.13
319 14 0.05
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (318 bp):
ATCAACATTTACAATAGAAGAGTTTATAATAAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTAGATCAAAATTTCT
AGTAGAGAGATCATATGAGAAGAAATCATCCAATGAGGGAGAAGAAGTTCATAATAAGAAAAAAT
TATTCAACCTTAGCTTGATTCCATCACATAAGGAGTTGGAACAACACCAATACCGGCTCATCCAT
CACATATGAAGTTGGATCAGCATCATCACTTTGTTTGATTCCATCATAAAGGAGGTGG
Found at i:611836 original size:42 final size:42
Alignment explanation
Indices: 611784--611896 Score: 165
Period size: 42 Copynumber: 2.7 Consensus size: 42
611774 CTTGGCTCAT
*
611784 CCATCGCATAAGAAGTTGGATCAGCATCATCATTTTGT-TCCA
1 CCATCGCATAAGGAGTTGGATCAGCATCATCATTTT-TCTCCA
* **
611826 CCATCGCATAAGGAGTTGGATCAACATCATCATTTTTCTCGT
1 CCATCGCATAAGGAGTTGGATCAGCATCATCATTTTTCTCCA
*
611868 CCATCACATAAGGAGTTGGATCAGCATCA
1 CCATCGCATAAGGAGTTGGATCAGCATCA
611897 CCTTGGGTCA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 1 0.02
42 63 0.98
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (42 bp):
CCATCGCATAAGGAGTTGGATCAGCATCATCATTTTTCTCCA
Found at i:612189 original size:3 final size:3
Alignment explanation
Indices: 612181--612212 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
612171 TTTTATCCCA
*
612181 AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
612213 AGAAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:621996 original size:20 final size:20
Alignment explanation
Indices: 621959--621997 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
621949 AGATTGAGTG
* * *
621959 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
621979 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
621998 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:632649 original size:24 final size:24
Alignment explanation
Indices: 632620--632669 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
632610 TTGTTATAAA
632620 TATGTTTTA-TTACTATTTTTATTT
1 TATG-TTTAGTTACTATTTTTATTT
*
632644 TATGTTTAGTTATTATTTTTATTT
1 TATGTTTAGTTACTATTTTTATTT
632668 TA
1 TA
632670 ATGATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (24 bp):
TATGTTTAGTTACTATTTTTATTT
Found at i:632664 original size:13 final size:12
Alignment explanation
Indices: 632624--632666 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
632614 TATAAATATG
*
632624 TTTTATTACTAT
1 TTTTATTATTAT
632636 TTTTATT-TTAT
1 TTTTATTATTAT
*
632647 GTTTAGTTATTAT
1 TTTTA-TTATTAT
632660 TTTTATT
1 TTTTATT
632667 TTAATGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 7 0.27
12 11 0.42
13 8 0.31
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:650982 original size:43 final size:43
Alignment explanation
Indices: 650927--651009 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
650917 AGCATCTGTA
* *
650927 TTGTATTGAGCACGAGTTTGACGTATGTGTTACGCTGGTGTGT
1 TTGTATTGAGCACAAGTTTGACGTATGTGTGACGCTGGTGTGT
* * *
650970 TTGTACTT-AGCACAAGTTTGATGTTTGTGTGACGGTGGTG
1 TTGTA-TTGAGCACAAGTTTGACGTATGTGTGACGCTGGTG
651010 CTAAAGCACC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 32 0.94
44 2 0.06
ACGTcount: A:0.17, C:0.11, G:0.33, T:0.40
Consensus pattern (43 bp):
TTGTATTGAGCACAAGTTTGACGTATGTGTGACGCTGGTGTGT
Found at i:651259 original size:27 final size:28
Alignment explanation
Indices: 651200--651267 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 28
651190 TTTACATTGG
* *
651200 GCTATGAAATGAAAAGTGAAAGGTATAT
1 GCTATGAAATGAAAAGTCAAAGGTACAT
* *
651228 GCTATGAGATGAAAA-TCAATGGTACAT
1 GCTATGAAATGAAAAGTCAAAGGTACAT
651255 GCTATGAAATGAA
1 GCTATGAAATGAA
651268 TTAAATGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 21 0.60
28 14 0.40
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.25
Consensus pattern (28 bp):
GCTATGAAATGAAAAGTCAAAGGTACAT
Found at i:651318 original size:30 final size:30
Alignment explanation
Indices: 651200--651319 Score: 83
Period size: 30 Copynumber: 4.2 Consensus size: 30
651190 TTTACATTGG
* * * *
651200 GCTATGAAATG-AA-AAGTGAAAGGTATAT
1 GCTATGAAATGAAATAAATGAATGGAACAT
* * *
651228 GCTATGAGATG--A-AAATCAATGGTACAT
1 GCTATGAAATGAAATAAATGAATGGAACAT
* **
651255 GCTATGAAATGAATTAAATGAAT-GATATGT
1 GCTATGAAATGAAATAAATGAATGGA-ACAT
651285 GCTATGAAAT-AAATAAAGTGAATGGAACAT
1 GCTATGAAATGAAATAAA-TGAATGGAACAT
651315 GCTAT
1 GCTAT
651320 AATATGATAT
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
27 22 0.31
28 10 0.14
29 7 0.10
30 31 0.43
31 2 0.03
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.28
Consensus pattern (30 bp):
GCTATGAAATGAAATAAATGAATGGAACAT
Found at i:651554 original size:24 final size:24
Alignment explanation
Indices: 651525--651574 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
651515 TTGTTATAAA
651525 TATGTTTTATTACTATTTTTATTT
1 TATGTTTTATTACTATTTTTATTT
*
651549 TATGTTTTATTTCTATTTTTATTT
1 TATGTTTTATTACTATTTTTATTT
651573 TA
1 TA
651575 ATGATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (24 bp):
TATGTTTTATTACTATTTTTATTT
Found at i:651572 original size:12 final size:12
Alignment explanation
Indices: 651529--651572 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
651519 TATAAATATG
*
651529 TTTTATTACTAT
1 TTTTATTTCTAT
651541 TTTTATTT-TAT
1 TTTTATTTCTAT
651552 GTTTTATTTCTAT
1 -TTTTATTTCTAT
651565 TTTTATTT
1 TTTTATTT
651573 TAATGATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 3 0.10
12 23 0.79
13 3 0.10
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTATTTCTAT
Found at i:654409 original size:17 final size:17
Alignment explanation
Indices: 654383--654416 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
654373 CTTAAAATTA
654383 ATTAACACTTTATTTGT
1 ATTAACACTTTATTTGT
*
654400 ATTAATACTTTATTTGT
1 ATTAACACTTTATTTGT
654417 TATATCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (17 bp):
ATTAACACTTTATTTGT
Found at i:662607 original size:21 final size:23
Alignment explanation
Indices: 662579--662634 Score: 80
Period size: 21 Copynumber: 2.5 Consensus size: 23
662569 ATCATCATCA
*
662579 AGGGTATCGGTACCT-TTGGGAT
1 AGGGTATCGGTACCTCTTGGCAT
*
662601 A-GGTATCGGTACCTCTTTGCAT
1 AGGGTATCGGTACCTCTTGGCAT
662623 AGGGTATCGGTA
1 AGGGTATCGGTA
662635 TCCTATAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 13 0.43
22 7 0.23
23 10 0.33
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (23 bp):
AGGGTATCGGTACCTCTTGGCAT
Found at i:663749 original size:2 final size:2
Alignment explanation
Indices: 663737--663775 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
663727 GTTGAGACCC
663737 AT AT CAT 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
663776 TACATAAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:667690 original size:7 final size:7
Alignment explanation
Indices: 667670--667757 Score: 94
Period size: 7 Copynumber: 12.7 Consensus size: 7
667660 CCCCTTTTAT
667670 TTTTTTC
1 TTTTTTC
*
667677 -TTCTTC
1 TTTTTTC
667683 TTTTTTC
1 TTTTTTC
667690 TCTTTTTC
1 T-TTTTTC
667698 -TTTTTC
1 TTTTTTC
667704 -TTTTTC
1 TTTTTTC
*
667710 ATTTTTC
1 TTTTTTC
*
667717 -TTTTCC
1 TTTTTTC
667723 TTTTTATC
1 TTTTT-TC
667731 TTTTTTCC
1 TTTTTT-C
667739 TTTTTTC
1 TTTTTTC
667746 TTTTTTC
1 TTTTTTC
667753 TTTTT
1 TTTTT
667758 CTATCTTCAG
Statistics
Matches: 71, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
6 22 0.31
7 30 0.42
8 19 0.27
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:667706 original size:6 final size:6
Alignment explanation
Indices: 667664--667759 Score: 70
Period size: 6 Copynumber: 15.0 Consensus size: 6
667654 CTTGAACCCC
* * *
667664 TTTTAT TTTT-T TCTTCT TCTTT-T TTCTCT TTTTCT TTTTCT TTTTCAT
1 TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT TTTTCT TTTTC-T
*
667712 TTTTCT TTTCCTT TTTATCTT TTTTCCTT TTTTCTT TTTTCT TTTTCT
1 TTTTCT TTTTC-T TTT-TC-T TTTT-C-T TTTTC-T TTTTCT TTTTCT
667760 ATCTTCAGGA
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
5 6 0.08
6 37 0.48
7 21 0.27
8 13 0.17
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:680516 original size:47 final size:45
Alignment explanation
Indices: 680440--680564 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
680430 TATAAAATCT
*
680440 CTTACCATTTATTCGATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
680485 CTTACCATTTAAATTCCATAAGCTTGAAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
680532 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
680565 GCATACTTCC
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 19 0.27
44 3 0.04
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:680581 original size:24 final size:25
Alignment explanation
Indices: 680554--680604 Score: 95
Period size: 24 Copynumber: 2.1 Consensus size: 25
680544 CATAAGCTCG
680554 TAAGCTTATTTGCATACTT-CCATT
1 TAAGCTTATTTGCATACTTACCATT
680578 TAAGCTTATTTGCATACTTACCATT
1 TAAGCTTATTTGCATACTTACCATT
680603 TA
1 TA
680605 TTAACCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (25 bp):
TAAGCTTATTTGCATACTTACCATT
Found at i:682867 original size:21 final size:21
Alignment explanation
Indices: 682841--682884 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
682831 ATTTTAGTTT
682841 TAAATACTAATCAATATTAAA
1 TAAATACTAATCAATATTAAA
* *
682862 TAAATACTAGTCCATATTAAA
1 TAAATACTAATCAATATTAAA
682883 TA
1 TA
682885 GAGTCCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAATACTAATCAATATTAAA
Found at i:682898 original size:15 final size:16
Alignment explanation
Indices: 682870--682899 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
682860 AATAAATACT
682870 AGTCCATATTAAATAG
1 AGTCCATATTAAATAG
682886 AGTCCAT-TTAAATA
1 AGTCCATATTAAATA
682900 CTATCCCGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (16 bp):
AGTCCATATTAAATAG
Found at i:684415 original size:31 final size:31
Alignment explanation
Indices: 684380--684439 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
684370 ATTAAAATAG
*
684380 AATGTATGTTTATTTTCTGTATTGAAAGGGA
1 AATGTATGTTTATTTTCTGTATTCAAAGGGA
684411 AATGTATGTTTATTTTCTGTATTCAAAGG
1 AATGTATGTTTATTTTCTGTATTCAAAGG
684440 CATGGCCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (31 bp):
AATGTATGTTTATTTTCTGTATTCAAAGGGA
Found at i:685544 original size:41 final size:42
Alignment explanation
Indices: 685498--685584 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
685488 GATGGGTCGG
**
685498 AGGATTT-ATCATCTTGCTCGAAAGACTTACAGATGACCCGA
1 AGGATTTAATCATCAGGCTCGAAAGACTTACAGATGACCCGA
* * *
685539 AGGATTTAATCATCAGGCTTGGAAGACTTACTGATGACCCGA
1 AGGATTTAATCATCAGGCTCGAAAGACTTACAGATGACCCGA
685581 AGGA
1 AGGA
685585 CTTACTAGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 7 0.17
42 33 0.82
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (42 bp):
AGGATTTAATCATCAGGCTCGAAAGACTTACAGATGACCCGA
Found at i:685846 original size:260 final size:259
Alignment explanation
Indices: 685331--686550 Score: 1391
Period size: 260 Copynumber: 4.7 Consensus size: 259
685321 AGGACATGAG
* * * *
685331 TTTTGGAAATAATCTAGTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTTAAAATTTTCAT
1 TTTTGGAAATAGTCTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAA-TTTCAT
*
685396 TTTC-GAAAAAGATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTTTCACAAATATCATA
65 TTTCTG-AAAAGATTAAATGAGAAACTTTGAAAATC-GTTTCTCATTTTTTTCACAAATATCATA
* * * * ** * *
685460 TGAAAACATTATACCCGGAGGTCTTATAGATGGGTCGGAGGATTTATCATCTTGCTCGAAAGACT
128 TGAAAACATCATGCCCAGAGGTCTTATAGAT-GGCCCAAAGACTTATCATCTTGCTCGAAAGACT
* * * * *
685525 TACAGATGACCCGAAGGATTTAATCATCAGGCTTGGAAGACTTACTGATGACCCGAAGGACTTAC
192 TACAGATGACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
*
685590 TAG
257 TAA
* * *
685593 TTTTAGAAATAGTCTACTAGTTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTAATT
1 TTTTGGAAATAGTCTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTCATT
** *
685658 TTCAAAAAAGATTAAATGAGAAACTTTTAAAATCGTTTACTCATTTTTTTCACAAATATCATATG
66 TTCTGAAAAGATTAAATGAGAAACTTTGAAAATCGTTT-CTCATTTTTTTCACAAATATCATATG
*
685723 AAAACATCATGCCCAGAGGTCTTATAGATGACCCAAAGACTTATCATCTTGCTCGAAAGACTTAC
130 AAAACATCATGCCCAGAGGTCTTATAGATGGCCCAAAGACTTATCATCTTGCTCGAAAGACTTAC
* * * * * * *
685788 AGATGACC-CAGAGGATTTAATTATTA-GTCTTGGAAGACTTACTGATGGTCTGAAGGACTTACT
195 AGATGACCTGA-AGGATTTAATCATCATG-CTCGAAAGACTTACTGATGGCCCGAAGGACTTACT
685851 AA
258 AA
*
685853 TTTTGGAAATAGTCTACTTGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTTCA-
1 TTTTGGAAATAGTCTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAA-TTTCAT
* ** * * * *
685917 -TTATGAAAAGATTAAATGAGAAAAATTGAAAAATTGCATTCTCATTTTTTGCA-AAAAATCATA
65 TTTCTGAAAAGATTAAATGAGAAACTTTG-AAAATCG-TTTCTCATTTTTTTCACAAATATCATA
* * *
685980 TGAAAGCATCTTGCCC-GAAGGTCTTATAGATGGCCCAAAGAACTTATCATCTTGCTCAAAAGA-
128 TGAAAACATCATGCCCAG-AGGTCTTATAGATGGCCCAAAG-ACTTATCATCTTGCTCGAAAGAC
* * **
686043 TTGACAGATGATCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAAAACTT
191 TT-ACAGATGACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
686108 ACTAA
255 ACTAA
* * * * *
686113 TTTTGGAAATATTTTACTGGGTAAGAAACTTTGGAAATTGCTTTCTTACTTTTCAAAAATTCCAT
1 TTTTGGAAATAGTCTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTC-AAAATTTCAT
** **
686178 TTTCTGAAAATCTTAAATGAGAAACTTTGAAAATCGTTTTCTCATTTTTTTTTTTCAAATATCAT
65 TTTCTGAAAAGATTAAATGAGAAACTTTGAAAATCG-TTTCTCA--TTTTTTTCACAAATATCAT
* * * * * *
686243 ATGGAAACATCATGCTCAAAGGTCTTATAGATGGCCTGAAGGACTTATCATCTTGCTCGAGAGAC
127 ATGAAAACATCATGCCCAGAGGTCTTATAGATGGCC-CAAAGACTTATCATCTTGCTCGAAAGAC
* * * *
686308 TGATAGATGACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTCATGGCTCGAAGGACTTA
191 TTACAGATGACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
*
686373 CCAA
256 CTAA
* * * * * * * *
686377 TTTCGGAAAATGGTCTATTGGGTTAGATACTTTGGACATCGCTTTCTTATTTTTCAAAAATTTCA
1 TTTTGG-AAATAGTCTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTC-AAAATTTCA
* * * *
686442 TTTTCTGAAAATATTAAATGAGAAATTTTGAAAATCTTTTTCTCA--TTTTTCAAAAACT-TCAT
64 TTTTCTGAAAAGATTAAATGAGAAACTTTGAAAATC-GTTTCTCATTTTTTTCACAAA-TATCAT
** * * *
686504 ATGAAAGGATCTTGCCGAAAGGTCTTATAGATGGCCCAAAGGACTTA
127 ATGAAAACATCATGCCCAGAGGTCTTATAGATGGCCCAAA-GACTTA
686551 CTCAAACAAG
Statistics
Matches: 818, Mismatches: 115, Indels: 51
0.83 0.12 0.05
Matches are distributed among these distances:
258 1 0.00
259 70 0.09
260 289 0.35
261 161 0.20
262 76 0.09
263 6 0.01
264 122 0.15
265 93 0.11
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (259 bp):
TTTTGGAAATAGTCTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTCATT
TTCTGAAAAGATTAAATGAGAAACTTTGAAAATCGTTTCTCATTTTTTTCACAAATATCATATGA
AAACATCATGCCCAGAGGTCTTATAGATGGCCCAAAGACTTATCATCTTGCTCGAAAGACTTACA
GATGACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAA
Found at i:686314 original size:41 final size:42
Alignment explanation
Indices: 686250--686350 Score: 125
Period size: 41 Copynumber: 2.4 Consensus size: 42
686240 CATATGGAAA
* * *
686250 CATCATGCTC-AAAGGTCTTATAGATGGCCTGAAGGACTT-AT
1 CATCATGCTCGAAA-GACTGATAGATGACCTGAAGGACTTAAT
* * *
686291 CATCTTGCTCGAGAGACTGATAGATGACCTGAAGGATTTAAT
1 CATCATGCTCGAAAGACTGATAGATGACCTGAAGGACTTAAT
686333 CATCATGCTCGAAAGACT
1 CATCATGCTCGAAAGACT
686351 TACTCATGGC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 30 0.60
42 20 0.40
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTGATAGATGACCTGAAGGACTTAAT
Found at i:686364 original size:20 final size:19
Alignment explanation
Indices: 686335--686373 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
686325 GATTTAATCA
686335 TCATGCTCGAAAGACTTAC
1 TCATGCTCGAAAGACTTAC
*
686354 TCATGGCTCGAAGGACTTAC
1 TCAT-GCTCGAAAGACTTAC
686374 CAATTTCGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (19 bp):
TCATGCTCGAAAGACTTAC
Found at i:690126 original size:28 final size:27
Alignment explanation
Indices: 690086--690145 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
690076 CTTGTATTGA
* * * *
690086 AAAAGGACCAAAATGCCCCTAAAGTGT
1 AAAATGACCAAAATACCCCTAAAATCT
*
690113 AAAATGACCTAAAATACCTCTAAAATCT
1 AAAATGACC-AAAATACCCCTAAAATCT
690141 AAAAT
1 AAAAT
690146 AACTAATACA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.50, C:0.20, G:0.10, T:0.20
Consensus pattern (27 bp):
AAAATGACCAAAATACCCCTAAAATCT
Found at i:692836 original size:21 final size:21
Alignment explanation
Indices: 692810--692855 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
692800 GTTGTTCGGG
*
692810 CACCTCA-CCCTAAGTCATGAC
1 CACCTCAGCCC-AACTCATGAC
692831 CACCTCAGCCCAACTCATGAC
1 CACCTCAGCCCAACTCATGAC
692852 CACC
1 CACC
692856 GACATACTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.28, C:0.48, G:0.09, T:0.15
Consensus pattern (21 bp):
CACCTCAGCCCAACTCATGAC
Found at i:695761 original size:73 final size:72
Alignment explanation
Indices: 695684--695828 Score: 281
Period size: 73 Copynumber: 2.0 Consensus size: 72
695674 AGGTTTTAAT
695684 AAAAAAATTAAATTTTTCTGAGATTTTTACTGTAGGTCACTCCGCTGGCCCTAATGTGACACCTC
1 AAAAAAATTAAATTTTTCTGAGATTTTTACTGTAGGTCACTCCGCTGGCCCTAATGTGACACC-C
695749 GAATCAGA
65 GAATCAGA
695757 AAAAAAATTAAATTTTTCTGAGATTTTTACTGTAGGTCACTCCGCTGGCCCTAATGTGACACCCG
1 AAAAAAATTAAATTTTTCTGAGATTTTTACTGTAGGTCACTCCGCTGGCCCTAATGTGACACCCG
695822 AATCAGA
66 AATCAGA
695829 TCTAGCCACC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 9 0.12
73 63 0.88
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (72 bp):
AAAAAAATTAAATTTTTCTGAGATTTTTACTGTAGGTCACTCCGCTGGCCCTAATGTGACACCCG
AATCAGA
Found at i:700737 original size:13 final size:15
Alignment explanation
Indices: 700703--700734 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
700693 AGTATCTTTT
700703 AAAATAATTTTAAGA
1 AAAATAATTTTAAGA
700718 AAAATAATTTTAA-A
1 AAAATAATTTTAAGA
700732 AAA
1 AAA
700735 TAAAACTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAATAATTTTAAGA
Found at i:703314 original size:27 final size:27
Alignment explanation
Indices: 703283--703342 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
703273 GATAATGGTT
*
703283 CTGAATAATTCATAATATATTTTGATG
1 CTGAATAATTCAGAATATATTTTGATG
* *
703310 CTGAATCATTTAGAATATATTTTGATG
1 CTGAATAATTCAGAATATATTTTGATG
*
703337 TTGAAT
1 CTGAAT
703343 CATTAAGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (27 bp):
CTGAATAATTCAGAATATATTTTGATG
Found at i:705838 original size:20 final size:20
Alignment explanation
Indices: 705813--705869 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
705803 ACCACCCAAA
705813 ACAGGTAGTATTGATACCCT
1 ACAGGTAGTATTGATACCCT
**
705833 ACAGGTAGTATCAATACCCT
1 ACAGGTAGTATTGATACCCT
*
705853 ACATGTAGTATTGATAC
1 ACAGGTAGTATTGATAC
705870 TGCCTAGTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (20 bp):
ACAGGTAGTATTGATACCCT
Found at i:707801 original size:38 final size:42
Alignment explanation
Indices: 707759--707847 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 42
707749 ATATTAAGTA
707759 GTCACTATTATTA-TTCAT-AATTGTGACGA-AAACATT-TT
1 GTCACTATTATTAGTTCATGAATTGTGACGACAAACATTATT
* ** * *
707797 GTCACTAGTATTAGTTGGTGATTTGTGACGACAAATATTATT
1 GTCACTATTATTAGTTCATGAATTGTGACGACAAACATTATT
707839 GTCACTATT
1 GTCACTATT
707848 GAAGTGAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
38 12 0.29
39 3 0.07
40 10 0.24
41 6 0.15
42 10 0.24
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (42 bp):
GTCACTATTATTAGTTCATGAATTGTGACGACAAACATTATT
Found at i:708195 original size:16 final size:16
Alignment explanation
Indices: 708174--708208 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
708164 CTAATAAAAA
708174 TTGAAGATTTAAGAAT
1 TTGAAGATTTAAGAAT
*
708190 TTGAAGATTTAAGAGT
1 TTGAAGATTTAAGAAT
708206 TTG
1 TTG
708209 TCTAGACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (16 bp):
TTGAAGATTTAAGAAT
Found at i:709283 original size:4 final size:4
Alignment explanation
Indices: 709274--709298 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
709264 ACCAGTTCAT
709274 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
709299 GGGATATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:709545 original size:14 final size:14
Alignment explanation
Indices: 709515--709553 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
709505 ATAAACATTA
709515 AATAAAT-AAATGC
1 AATAAATAAAATGC
*
709528 AATAAATAAAATGG
1 AATAAATAAAATGC
*
709542 AATAAAGAAAAT
1 AATAAATAAAAT
709554 AAATGACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.67, C:0.03, G:0.10, T:0.21
Consensus pattern (14 bp):
AATAAATAAAATGC
Found at i:721230 original size:216 final size:216
Alignment explanation
Indices: 720856--721293 Score: 786
Period size: 216 Copynumber: 2.0 Consensus size: 216
720846 TTCATCGTTT
*
720856 AAACAAAACATAAAGTTTACAATATGGAGAGCTCACAAGTTAACACATCAAAATATATTAAGTCT
1 AAACAAAACATAAAGTTTACAATATGAAGAGCTCACAAGTTAACACATCAAAATATATTAAGTCT
*
720921 ATCAAAAGAGTTACGACTCAATTATACATAAATGATTTATGAAATGCATGCCCACTAAAAATAAT
66 ATCAAAAGAGTTACGACTCAATTATACATAAAGGATTTATGAAATGCATGCCCACTAAAAATAAT
* * *
720986 CGAGACGTACTCTGAACTTGACTAAATCTAGAATCTGCACGCTGACGACAAGGTCCTTCGAGTGG
131 CGAGACGTACTCTGAACTTGACTAAATCTAGAATCTGCACGCTGACGACAAGCTCCTCCGAGTGA
*
721051 AACCTAAAGACTTGTGAATAG
196 AACCTAAAGACCTGTGAATAG
* *
721072 AAACAAAACATAAAGTTTACAATATGAATAGCTTACAAGTTAACACATCAAAATATATTAAGTCT
1 AAACAAAACATAAAGTTTACAATATGAAGAGCTCACAAGTTAACACATCAAAATATATTAAGTCT
*
721137 ATCAAAAGAGTTACGACTCAATTATACATAAAGGGTTTATGAAATGCATGCCCACTAAAAATAAT
66 ATCAAAAGAGTTACGACTCAATTATACATAAAGGATTTATGAAATGCATGCCCACTAAAAATAAT
*
721202 CGAGACGTACTCTGAACTTGACTAAATCTGGAATCTGCACGCTGACGACAAGCTCCTCCGAGTGA
131 CGAGACGTACTCTGAACTTGACTAAATCTAGAATCTGCACGCTGACGACAAGCTCCTCCGAGTGA
721267 AACCTAAAGACCTGTGAATAG
196 AACCTAAAGACCTGTGAATAG
721288 AAACAA
1 AAACAA
721294 CTCTGAACAC
Statistics
Matches: 212, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
216 212 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (216 bp):
AAACAAAACATAAAGTTTACAATATGAAGAGCTCACAAGTTAACACATCAAAATATATTAAGTCT
ATCAAAAGAGTTACGACTCAATTATACATAAAGGATTTATGAAATGCATGCCCACTAAAAATAAT
CGAGACGTACTCTGAACTTGACTAAATCTAGAATCTGCACGCTGACGACAAGCTCCTCCGAGTGA
AACCTAAAGACCTGTGAATAG
Found at i:721509 original size:22 final size:22
Alignment explanation
Indices: 721469--721529 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
721459 TTGAATAACT
*
721469 AAAGTG-CTTCAGCAGTAGTACA
1 AAAGTGTCTT-AGCACTAGTACA
* *
721491 AAATTG-CATTAGCACTAGTACT
1 AAAGTGTC-TTAGCACTAGTACA
721513 AAAGTGTCTTAGCACTA
1 AAAGTGTCTTAGCACTA
721530 TTGAATCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 30 0.91
23 3 0.09
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (22 bp):
AAAGTGTCTTAGCACTAGTACA
Found at i:722654 original size:139 final size:138
Alignment explanation
Indices: 722494--722958 Score: 583
Period size: 139 Copynumber: 3.3 Consensus size: 138
722484 TAAAGAACCT
* * * * ** * *
722494 ATTAAACCTAAAAATGTAGGCTCTGA-TATTAACCCAAATCAATTTTTGCCATTTATTTGATTCA
1 ATTAAACCTAAAATTG-AGGCTCTAATTATTAA-CCTAGTCAATTTTAACCAATTATTTGATTAA
* * *
722558 AATAATTAAAATGGAACCTC-AGGTAAAAACGAGGACCAAATTAAAAGTTCCTCTAAATTTAAGG
64 AATAATTAAAATGGAACCTCGA-G-AAAAACGAGGACCAAATTAAAAATTCCCCTAAATTTAAAG
*
722622 ACTAAGTTTCAA
127 ACTAAGTTTGAA
* *
722634 ATTAAGCCTAAAATTGAGGCTCTAATTATTAACCTAGTCAATTTTAACCAATTATTTGACTAAAA
1 ATTAAACCTAAAATTGAGGCTCTAATTATTAACCTAGTCAATTTTAACCAATTATTTGATTAAAA
* *
722699 TAATTAAAATCGAACCTCGAGAAAAAGCGAGGACCAAATTAAAAATTCCCCTAAATTTAAATACT
66 TAATTAAAATGGAACCTCGAGAAAAA-CGAGGACCAAATTAAAAATTCCCCTAAATTTAAAGACT
722764 AAGTTTGAA
130 AAGTTTGAA
* * * * * **
722773 ATTAAACCTAAAATGGAAGATCTAATTATTAACCTAGTCAATTTTAATCAATTATTTAATTTGAA
1 ATTAAACCTAAAATTGAGGCTCTAATTATTAACCTAGTCAATTTTAACCAATTATTTGATTAAAA
* * *
722838 TAATTAAAAAGGAACCTCGAGCAAACACGAGGACCAAATTAAAAATTCCCCTAATTTTAAAGACT
66 TAATTAAAATGGAACCTCGAG-AAAAACGAGGACCAAATTAAAAATTCCCCTAAATTTAAAGACT
*
722903 AAGTTAGAA
130 AAGTTTGAA
* * * *
722912 ATTAAGCCTAAAATAGAGGCACTAATTATTAACATAGTCAATTTTAA
1 ATTAAACCTAAAATTGAGGCTCTAATTATTAACCTAGTCAATTTTAA
722959 TAAATTATGG
Statistics
Matches: 284, Mismatches: 37, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
138 5 0.02
139 254 0.89
140 25 0.09
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (138 bp):
ATTAAACCTAAAATTGAGGCTCTAATTATTAACCTAGTCAATTTTAACCAATTATTTGATTAAAA
TAATTAAAATGGAACCTCGAGAAAAACGAGGACCAAATTAAAAATTCCCCTAAATTTAAAGACTA
AGTTTGAA
Found at i:723464 original size:16 final size:16
Alignment explanation
Indices: 723443--723477 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
723433 TACCCATACT
723443 ATAAATAACTA-GAATC
1 ATAAATAA-TATGAATC
723459 ATAAATAATATGAATC
1 ATAAATAATATGAATC
723475 ATA
1 ATA
723478 GCTCAGGGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.29
Consensus pattern (16 bp):
ATAAATAATATGAATC
Found at i:725714 original size:26 final size:25
Alignment explanation
Indices: 725680--725739 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
725670 TTATTATTTC
725680 TTTCTTTTTTTCCAT-TTTCATTCAT
1 TTTCTTTTTTT-CATGTTTCATTCAT
* *
725705 TTTCTCTTTTTTCATGTTTTATTTAT
1 TTTCT-TTTTTTCATGTTTCATTCAT
725731 TTTCTTTTT
1 TTTCTTTTT
725740 CGTATCAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 12 0.39
26 19 0.61
ACGTcount: A:0.10, C:0.15, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTCTTTTTTTCATGTTTCATTCAT
Found at i:726301 original size:118 final size:115
Alignment explanation
Indices: 726167--726388 Score: 329
Period size: 118 Copynumber: 1.9 Consensus size: 115
726157 AGAAAAATGG
* *
726167 TGAACAAGTTCTTCTCATTATGAAATTTTTCTCCCTCTCTGTATGAGTTTTTCTCATTATG-ACC
1 TGAACAAGTTCTTCTCATTATGAAATTCTTCTCCCTCTCTGAATGAGTTTTTCTCATTATGAACC
* *
726231 CATTCAATTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTTGAACAAAGGT
66 C-TTCAATTGAAAATGTCGATCCA---CCTTCTGTGATGGATTTGAACAAAGGT
* *
726285 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTGAATGAGTTTTTCTCATTATGAACC
1 TGAACAAGTTCTTCTCATTATGAAATTCTTCTCCCTCTCTGAATGAGTTTTTCTCATTATGAACC
**
726350 CTTCCTTTGAAAATGTCGATCCACCTTCTGTGATGGATT
66 CTTCAATTGAAAATGTCGATCCACCTTCTGTGATGGATT
726389 CCAATCTATA
Statistics
Matches: 95, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
115 16 0.17
118 75 0.79
119 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (115 bp):
TGAACAAGTTCTTCTCATTATGAAATTCTTCTCCCTCTCTGAATGAGTTTTTCTCATTATGAACC
CTTCAATTGAAAATGTCGATCCACCTTCTGTGATGGATTTGAACAAAGGT
Found at i:726772 original size:102 final size:101
Alignment explanation
Indices: 726629--726831 Score: 289
Period size: 102 Copynumber: 2.0 Consensus size: 101
726619 AAGAGAAGCT
* * * *
726629 ATCTCAGGTGAGATAAATTTTGTTTCGAGTTAAATAATTTCAAAATTTGTGTTTCAAGGGAAACT
1 ATCTCAAGTGAGATAAATTTTGTTTCGAATGAAATAATTTCAAAAATTGTGTTTCAAGGGAAACT
* *
726694 GTCTCAAGAGAGACGAAATTGGTTTTAAGAAAAAAA
66 ATATCAAGAGAGACGAAATTGGTTTTAAGAAAAAAA
* * *
726730 ATCTCAAGTTAGATAAGTCTTTGTTTCGAATGAAATAGTTTCAAAAATTGTGTTTCAAGGGAAAC
1 ATCTCAAGTGAGATAAAT-TTTGTTTCGAATGAAATAATTTCAAAAATTGTGTTTCAAGGGAAAC
** *
726795 TATATCAAGCTAGACGGAATTGGTTTTAAGAAAAAAA
65 TATATCAAGAGAGACGAAATTGGTTTTAAGAAAAAAA
726832 CAATCCCAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
101 15 0.17
102 74 0.83
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (101 bp):
ATCTCAAGTGAGATAAATTTTGTTTCGAATGAAATAATTTCAAAAATTGTGTTTCAAGGGAAACT
ATATCAAGAGAGACGAAATTGGTTTTAAGAAAAAAA
Found at i:734592 original size:138 final size:139
Alignment explanation
Indices: 734231--734707 Score: 627
Period size: 139 Copynumber: 3.4 Consensus size: 139
734221 CTAAAAACGT
* * * * *
734231 AGGCTCTAA-TATTAACCCAAATCAATTTTAACCAATAATTTGATTCGAATAATTGAAATGGAAC
1 AGGCTCTAATTATTAA-CCTAATCAATTTTAACCAATTATTTGATTCAAATAATTAAAATGGAAT
* *
734295 CTCGGGTAAAAGCGAGGACCAAATTAAAAGTTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAG
65 CTCGAGTAAAAGCGAGGACCAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAG
734360 CCTAAAATGG
130 CCTAAAATGG
* * * *
734370 AGGCTCTAATTATTAACCTAGTCAATTTTAACCAATTACTTGACTCGAATAATTAAAATGGAATC
1 AGGCTCTAATTATTAACCTAATCAATTTTAACCAATTATTTGATTCAAATAATTAAAATGGAATC
* * ** **
734435 TCGAGCAAAAGCGACGACCAAATTAAAAATTCCTTTAAATTTAAGGACTAAGTTTGAAATTACCC
66 TCGAGTAAAAGCGAGGACCAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAGC
*
734500 CTAAAAT-A
131 CTAAAATGG
* * * *
734508 AGACTCTAATTATTAACCTAATCAAATTTAATCAATTATTTGATTCAAATAATTAAAATGAAATC
1 AGGCTCTAATTATTAACCTAATCAATTTTAACCAATTATTTGATTCAAATAATTAAAATGGAATC
* * * * *
734573 TCGAGTAAAATCGAGGACCAAATTAATAATTCCCCTAAATTTAAAGACTAATTTTAAAATTAAGC
66 TCGAGTAAAAGCGAGGACCAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAGC
734638 CTAAAATGG
131 CTAAAATGG
* * *
734647 AGGCTCTAATTATTAACCTAGTCAATTTTAATCAATTA-TGGAATATTCAAATAATTAAAAT
1 AGGCTCTAATTATTAACCTAATCAATTTTAACCAATTATTTG---ATTCAAATAATTAAAAT
734708 TTTTAGGGAT
Statistics
Matches: 293, Mismatches: 40, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
138 120 0.41
139 150 0.51
140 6 0.02
141 17 0.06
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (139 bp):
AGGCTCTAATTATTAACCTAATCAATTTTAACCAATTATTTGATTCAAATAATTAAAATGGAATC
TCGAGTAAAAGCGAGGACCAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAGC
CTAAAATGG
Found at i:734856 original size:33 final size:34
Alignment explanation
Indices: 734819--734887 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
734809 TTAATCAAAA
734819 AACCTAAATAGGCTATCAAGGA-TAAATTAAACT
1 AACCTAAATAGGCTATCAAGGACTAAATTAAACT
734852 AACCTAAATAGGCTATCAAGGACTAAATTAAACT
1 AACCTAAATAGGCTATCAAGGACTAAATTAAACT
734886 AA
1 AA
734888 GTTAAAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 22 0.63
34 13 0.37
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (34 bp):
AACCTAAATAGGCTATCAAGGACTAAATTAAACT
Found at i:739481 original size:29 final size:29
Alignment explanation
Indices: 739426--739481 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
739416 TTAAATTTTC
* * * *
739426 TTTCTTAAATTTCCTATTTTTCGTTTTAA
1 TTTCTTAAATTACCTAGTTTCCCTTTTAA
*
739455 TTTCTTAAATTACGTAGTTTCCCTTTT
1 TTTCTTAAATTACCTAGTTTCCCTTTT
739482 TCTTAAATTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.20, C:0.16, G:0.05, T:0.59
Consensus pattern (29 bp):
TTTCTTAAATTACCTAGTTTCCCTTTTAA
Found at i:740172 original size:20 final size:20
Alignment explanation
Indices: 740147--740218 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
740137 TCGCAATGCG
*
740147 CGCAACGAGATACTTACTTT
1 CGCAACGCGATACTTACTTT
*
740167 CGCAACGCGATACTGACTTT
1 CGCAACGCGATACTTACTTT
*
740187 CGCAACGCGATTCTGT-CTTT
1 CGCAACGCGATACT-TACTTT
740207 CGCAACGCGATA
1 CGCAACGCGATA
740219 ATACATAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (20 bp):
CGCAACGCGATACTTACTTT
Found at i:740177 original size:49 final size:47
Alignment explanation
Indices: 740100--740191 Score: 139
Period size: 49 Copynumber: 1.9 Consensus size: 47
740090 ATCGCAAAAT
*
740100 CGCAACGAGTATAACTTTCGCAATGCGATACTGACTATCGCAATGCG
1 CGCAACGAGTATAACTTTCGCAACGCGATACTGACTATCGCAATGCG
* *
740147 CGCAACGAGATACTTACTTTCGCAACGCGATACTGACTTTCGCAA
1 CGCAACGAG-TA-TAACTTTCGCAACGCGATACTGACTATCGCAA
740192 CGCGATTCTG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 9 0.22
48 2 0.05
49 29 0.73
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (47 bp):
CGCAACGAGTATAACTTTCGCAACGCGATACTGACTATCGCAATGCG
Found at i:740434 original size:22 final size:22
Alignment explanation
Indices: 740406--740449 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
740396 CACTCTCTCA
740406 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
740428 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
740450 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:740751 original size:20 final size:20
Alignment explanation
Indices: 740728--740770 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
740718 GATAGTCGAA
740728 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
740748 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
740768 TTC
1 TTC
740771 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:742108 original size:18 final size:18
Alignment explanation
Indices: 742087--742131 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
742077 TCCACTTCGG
*
742087 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
742105 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
742123 GATCCATCA
1 GAGCCATCA
742132 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.44, G:0.13, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:742666 original size:19 final size:20
Alignment explanation
Indices: 742612--742678 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
742602 TAGTTTACTT
* *
742612 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
742632 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
742652 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
742671 TCGCAACG
1 TCGCAACG
742679 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:742686 original size:14 final size:14
Alignment explanation
Indices: 742667--742724 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
742657 ATGCGAAATG
742667 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
742681 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
742697 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
742713 AAAATCGCAACG
1 AAAATCGCAACG
742725 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:742709 original size:32 final size:33
Alignment explanation
Indices: 742651--742741 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
742641 GGAAATGGCT
*
742651 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
742684 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
742716 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
742742 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:742735 original size:19 final size:19
Alignment explanation
Indices: 742612--742746 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
742602 TAGTTTACTT
* **
742612 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
742632 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
742652 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
742671 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
742685 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
742703 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
742717 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
742736 TCGCAATGCGA
1 TCGCAACGCGA
742747 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:742792 original size:32 final size:32
Alignment explanation
Indices: 742753--742830 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 32
742743 GCGATTTGTG
742753 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTT-TCGTTGCGATTTTCA
742785 TTTCGCGTTGCGATTTTTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTTCGTTGCGATTTTCA
**
742817 TTTCGTATTGCGAT
1 TTTCGCGTTGCGAT
742831 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 9 0.21
32 34 0.79
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.49
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTTCGTTGCGATTTTCA
Found at i:742806 original size:13 final size:13
Alignment explanation
Indices: 742758--742814 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
742748 TTGTGTTTCG
742758 CGTTGCGATTTTGT
1 CGTTGCGATTTT-T
742772 CGTTGCGATTTCATTT
1 CGTTGCGA-TT--TTT
742788 CGCGTTGCGATTTTT
1 --CGTTGCGATTTTT
742803 CGTTGCGATTTT
1 CGTTGCGATTTT
742815 CATTTCGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
13 12 0.32
14 8 0.21
15 5 0.13
16 1 0.03
17 4 0.11
18 8 0.21
ACGTcount: A:0.09, C:0.18, G:0.25, T:0.49
Consensus pattern (13 bp):
CGTTGCGATTTTT
Found at i:742865 original size:19 final size:20
Alignment explanation
Indices: 742824--742869 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
742814 TCATTTCGTA
742824 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* *
742844 TTGCGATAGTCATTT-TGCG
1 TTGCGATAGCCATTTCCGCG
742863 TTGCGAT
1 TTGCGAT
742870 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:745211 original size:19 final size:20
Alignment explanation
Indices: 745166--745213 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
745156 TTTGAGAATG
*
745166 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGCGGAAACA
**
745186 ACTATCGCAACGC-GAAACA
1 AAAATCGCAACGCGGAAACA
745205 AAAATCGCA
1 AAAATCGCA
745214 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.48, C:0.25, G:0.17, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGCGGAAACA
Found at i:745231 original size:19 final size:19
Alignment explanation
Indices: 745209--745392 Score: 138
Period size: 19 Copynumber: 10.1 Consensus size: 19
745199 GAAACAAAAA
* *
745209 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
745228 TCGCGTTGCGGTTTTCATT
1 TCGCGTTGCGATTTTCATT
*
745247 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
745266 TCGCGGTTGTGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
745286 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
745302 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
745319 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
745333 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
745352 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
745372 ATCTCGTTGCGA-TTTCATT
1 -TCGCGTTGCGATTTTCATT
745391 TC
1 TC
745393 AACCAAAAGA
Statistics
Matches: 132, Mismatches: 20, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 3 0.02
19 60 0.45
20 41 0.31
21 1 0.01
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:745265 original size:38 final size:39
Alignment explanation
Indices: 745209--745298 Score: 146
Period size: 39 Copynumber: 2.3 Consensus size: 39
745199 GAAACAAAAA
* *
745209 TCGCATTGCGATTTTTATTTCGC-GTTGCGGTTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
*
745247 TCGCGTTGCGATTTTTATTTCGCGGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
745286 TCGCGTTGCGATT
1 TCGCGTTGCGATT
745299 GTCTGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 22 0.46
39 26 0.54
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.49
Consensus pattern (39 bp):
TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
Found at i:745363 original size:34 final size:33
Alignment explanation
Indices: 745281--745368 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
745271 GTTGTGATTT
* *
745281 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
745314 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
745347 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
745369 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:745370 original size:20 final size:19
Alignment explanation
Indices: 745336--745392 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
745326 GCGATTCTCT
*
745336 CGTTGCGATAGTCATTTCCG
1 CGTTGCGAT-TTCATTTCCG
*
745356 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATT-TCATT-TCCG
745376 CGTTGCGATTTCATTTC
1 CGTTGCGATTTCATTTC
745393 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 1 0.03
19 5 0.16
20 25 0.78
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTCATTTCCG
Found at i:747444 original size:41 final size:42
Alignment explanation
Indices: 747385--747476 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 42
747375 GCCCGACTCG
* *
747385 CCTATCATCCCTCAAGAGTCCACTCCTA-CGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
747426 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
747468 ACTGTCATC
1 CCTATCATC
747477 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 24 0.57
42 18 0.43
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:748864 original size:13 final size:14
Alignment explanation
Indices: 748833--748867 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
748823 ATTGTTTAAT
748833 TGATTTGTAAAATG
1 TGATTTGTAAAATG
748847 TGATTTGTAAAA-G
1 TGATTTGTAAAATG
748860 TGATTTGT
1 TGATTTGT
748868 TTAATTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAATG
Found at i:749050 original size:19 final size:20
Alignment explanation
Indices: 749006--749045 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
748996 GCAACGAGAG
749006 AATCGCAACGCGAAAATAAA
1 AATCGCAACGCGAAAATAAA
*
749026 AATCGCAACGCGAAATTAAA
1 AATCGCAACGCGAAAATAAA
749046 TTCGCGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.15, T:0.12
Consensus pattern (20 bp):
AATCGCAACGCGAAAATAAA
Found at i:749092 original size:33 final size:32
Alignment explanation
Indices: 749050--749176 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
749040 ATTAAATTCG
749050 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
749083 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
749116 CGTTGCGATTTTCATTTCGCATTGCGATTCGCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
749149 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
749177 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:749139 original size:66 final size:66
Alignment explanation
Indices: 749043--749175 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
749033 ACGCGAAATT
*
749043 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
749108 G
66 G
*
749109 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCGCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
749174 G
66 G
749175 A
1 A
749176 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Done.