Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 2 of 292
Found at i:360418 original size:101 final size:98
Alignment explanation
Indices: 360234--360468 Score: 278
Period size: 101 Copynumber: 2.4 Consensus size: 98
360224 GTGAGGTCAC
* *
360234 GTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATTATTGGTCACATGTATAGTACTAAGT
1 GTGT-TAGTACTAAGTGCAGGCTACTACGTGTACCAGATGATTGGTCACATGTATAGTACTAAGT
* *
360299 GCAGGCTACTATGCGTACCCA-ATAACTTCGAT-CAT
65 GCAAGCTACTACGCGTA-CCAGATAA-TT-GATCCAT
* * * *
360334 GTGTTTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAG
1 GTG-TTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGATT-GGTCACATGTATAGTACTAAG
* *
360399 TGCAAGCTACTACGTGTACCAGATAATTGGTCGCAT
64 TGCAAGCTACTACGCGTACCAGATAATTGATC-CAT
* *
360435 GTG-TAGTACTAAGTGCAGGCTACTATGCGTACCA
1 GTGTTAGTACTAAGTGCAGGCTACTACGTGTACCA
360469 AATAGCTTTG
Statistics
Matches: 117, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
99 30 0.26
100 42 0.36
101 45 0.38
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (98 bp):
GTGTTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGATTGGTCACATGTATAGTACTAAGTG
CAAGCTACTACGCGTACCAGATAATTGATCCAT
Found at i:378088 original size:7 final size:7
Alignment explanation
Indices: 378076--378121 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
378066 CATACGAACC
378076 AGAAAGA
1 AGAAAGA
378083 AGAAAGA
1 AGAAAGA
378090 A-AAAGA
1 AGAAAGA
378096 A-AAAG-
1 AGAAAGA
378101 AGAAAGA
1 AGAAAGA
*
378108 AGAAAGG
1 AGAAAGA
378115 AGAAAGA
1 AGAAAGA
378122 CGCACAGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 1 0.03
6 14 0.40
7 20 0.57
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
AGAAAGA
Found at i:380819 original size:43 final size:43
Alignment explanation
Indices: 380758--380849 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 43
380748 GGAAAGTGAG
380758 TAAGTAAGTTGATCTAAATGACTTCTATATTTGGCCACATAGA
1 TAAGTAAGTTGATCTAAATGACTTCTATATTTGGCCACATAGA
*
380801 TAAGTAAGTTGATCTAAATGACTTCTATATTTGGCCACATAGG
1 TAAGTAAGTTGATCTAAATGACTTCTATATTTGGCCACATAGA
380844 TAAGTA
1 TAAGTA
380850 TAAGTGAGGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (43 bp):
TAAGTAAGTTGATCTAAATGACTTCTATATTTGGCCACATAGA
Found at i:380892 original size:34 final size:34
Alignment explanation
Indices: 380853--381051 Score: 186
Period size: 34 Copynumber: 5.8 Consensus size: 34
380843 GTAAGTATAA
* *
380853 GTGAGGTTATATTGAACTTGTATGTTCGCTACAT
1 GTGAGGTTATATTGAACTTGTATATTCGTTACAT
* *
380887 ATGAGGTTATATTGAACTTGTGTATTCGATTACAT
1 GTGAGGTTATATTGAACTTGTATATTCG-TTACAT
* *
380922 GTGAGCTTATATTGAACTTGTATATTGGTTACAT
1 GTGAGGTTATATTGAACTTGTATATTCGTTACAT
* * **
380956 GTGAGATTATATTGAATTTGTATATTCG-GCCAT
1 GTGAGGTTATATTGAACTTGTATATTCGTTACAT
* * * *
380989 ATGAGATGTT-TATTTGAACTTGAACATTAGGTTACAT
1 GTGAG--GTTATA-TTGAACTTGTATATT-CGTTACAT
* * *
381026 GTGATGATATATTGAACTTATATATT
1 GTGAGGTTATATTGAACTTGTATATT
381052 TGGCCATATG
Statistics
Matches: 131, Mismatches: 27, Indels: 13
0.77 0.16 0.08
Matches are distributed among these distances:
33 7 0.05
34 58 0.44
35 57 0.44
36 3 0.02
37 6 0.05
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (34 bp):
GTGAGGTTATATTGAACTTGTATATTCGTTACAT
Found at i:381006 original size:69 final size:69
Alignment explanation
Indices: 380859--381062 Score: 214
Period size: 69 Copynumber: 2.9 Consensus size: 69
380849 ATAAGTGAGG
* * * * * * *** * *
380859 TTATATTGAACTTGTATGTTCGCTACATATGAGGTTATATTGAACTTGTGTATTCGATTACATGT
1 TTATATTGAACTTGTATATTGGTTACATGTGAGATTATATTGAACTTGTATATTCGGCCATATGA
380924 GAGC
66 GAGC
*
380928 TTATATTGAACTTGTATATTGGTTACATGTGAGATTATATTGAATTTGTATATTCGGCCATATGA
1 TTATATTGAACTTGTATATTGGTTACATGTGAGATTATATTGAACTTGTATATTCGGCCATATGA
*
380993 GATGT
66 GA-GC
* * * *
380998 TTAT-TTGAACTTGAACATTAGGTTACATGTGATGA-TATATTGAACTTATATATTTGGCCATAT
1 TTATATTGAACTTGTATATT-GGTTACATGTGA-GATTATATTGAACTTGTATATTCGGCCATAT
381061 GA
64 GA
381063 AATAATATAA
Statistics
Matches: 114, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
69 68 0.60
70 44 0.39
71 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (69 bp):
TTATATTGAACTTGTATATTGGTTACATGTGAGATTATATTGAACTTGTATATTCGGCCATATGA
GAGC
Found at i:381040 original size:70 final size:70
Alignment explanation
Indices: 380928--381062 Score: 193
Period size: 70 Copynumber: 1.9 Consensus size: 70
380918 ACATGTGAGC
* * * *
380928 TTATATTGAACTTGTATATTGGTTACATGTGAGATTATATTGAATTTGTATATTCGGCCATATGA
1 TTATATTGAACTTGAACATTGGTTACATGTGAGATTATATTGAACTTATATATTCGGCCATATGA
380993 GATGT
66 GATGT
*
380998 TTAT-TTGAACTTGAACATTAGGTTACATGTGATGA-TATATTGAACTTATATATTTGGCCATAT
1 TTATATTGAACTTGAACATT-GGTTACATGTGA-GATTATATTGAACTTATATATTCGGCCATAT
381061 GA
64 GA
381063 AATAATATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
69 13 0.22
70 43 0.74
71 2 0.03
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (70 bp):
TTATATTGAACTTGAACATTGGTTACATGTGAGATTATATTGAACTTATATATTCGGCCATATGA
GATGT
Found at i:381077 original size:70 final size:68
Alignment explanation
Indices: 380929--381077 Score: 174
Period size: 70 Copynumber: 2.1 Consensus size: 68
380919 CATGTGAGCT
* * * * *
380929 TATATTGAACTTGTATATTGGTTACATGTGAGATTATATTGAATTTGTATATTCGGCCATATGAG
1 TATATTGAACTTGAACATTGGTTACATGTGAGATTATATTGAACTTATATATTCGGCCATATGAA
*
380994 ATG
66 ATA
* *
380997 TTTATTTGAACTTGAACATTAGGTTACATGTGATGA-TATATTGAACTTATATATTTGGCCATAT
1 TATA-TTGAACTTGAACATT-GGTTACATGTGA-GATTATATTGAACTTATATATTCGGCCATAT
381061 GAAATAA
63 GAAAT-A
*
381068 TATAATGAAC
1 TATATTGAAC
381078 CTTGTGTATT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
68 3 0.04
69 13 0.19
70 46 0.69
71 5 0.07
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (68 bp):
TATATTGAACTTGAACATTGGTTACATGTGAGATTATATTGAACTTATATATTCGGCCATATGAA
ATA
Found at i:386283 original size:35 final size:35
Alignment explanation
Indices: 386244--386315 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
386234 ATTTTTAAAG
*
386244 AAAACTTTAAGAAAAAGAATGAAGAGAATCATGTT
1 AAAACTTCAAGAAAAAGAATGAAGAGAATCATGTT
386279 AAAACTTCAAGAAAAAGAATGAAGAGAATCATGTT
1 AAAACTTCAAGAAAAAGAATGAAGAGAATCATGTT
386314 AA
1 AA
386316 TAATGTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.56, C:0.07, G:0.17, T:0.21
Consensus pattern (35 bp):
AAAACTTCAAGAAAAAGAATGAAGAGAATCATGTT
Found at i:400782 original size:27 final size:27
Alignment explanation
Indices: 400744--400797 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
400734 GTAACAATGG
400744 GATGAAGTTATGCACTAAAATAATTAA
1 GATGAAGTTATGCACTAAAATAATTAA
400771 GATGAAGTTATGCACTAAAATAATTAA
1 GATGAAGTTATGCACTAAAATAATTAA
400798 CTCATCCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (27 bp):
GATGAAGTTATGCACTAAAATAATTAA
Found at i:407600 original size:16 final size:17
Alignment explanation
Indices: 407574--407614 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
407564 ATAATATGTT
*
407574 TTATAAGTATTAATATA
1 TTATAAATATTAATATA
*
407591 -TATAAATATTATTATA
1 TTATAAATATTAATATA
407607 TTATAAAT
1 TTATAAAT
407615 TATAGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TTATAAATATTAATATA
Found at i:409729 original size:24 final size:22
Alignment explanation
Indices: 409686--409729 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
409676 ATTTAAAACC
*
409686 TTAAAATATTTTTATAAAATAA
1 TTAAAATATTTTTAGAAAATAA
409708 TTAAAATATGTTTTAGACAAAT
1 TTAAAATAT-TTTTAGA-AAAT
409730 TGAAAGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 6 0.32
24 4 0.21
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (22 bp):
TTAAAATATTTTTAGAAAATAA
Found at i:412183 original size:49 final size:47
Alignment explanation
Indices: 412124--412233 Score: 139
Period size: 49 Copynumber: 2.3 Consensus size: 47
412114 ATCAACATGC
*
412124 ATAATTGATTTCCCCGAGAAAATTATGGAGCCAGACATCATCCCAAAAA
1 ATAATTGATTTCCCCGAGAAAATTATGGAGACAGACATCATCCC--AAA
** * * *
412173 ATAATTGATTTCATCGAGGAAATTATGGGGATAGACATCATCCCAAA
1 ATAATTGATTTCCCCGAGAAAATTATGGAGACAGACATCATCCCAAA
*
412220 ATAATTTATTTCCC
1 ATAATTGATTTCCC
412234 TAAGGAAGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 14 0.27
49 38 0.73
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (47 bp):
ATAATTGATTTCCCCGAGAAAATTATGGAGACAGACATCATCCCAAA
Found at i:417786 original size:66 final size:66
Alignment explanation
Indices: 417644--417770 Score: 200
Period size: 66 Copynumber: 1.9 Consensus size: 66
417634 TTACACTCAA
* * *
417644 ACACTCGTGTGCTAGGTCGTGTGAAAACTAGAGGGTATACTGACTTGTGCCACAAGGCCAAGCCA
1 ACACTCGTGTGCCAGGCCGTGTAAAAACTAGAGGGTATACTGACTTGTGCCACAAGGCCAAGCCA
417709 T
66 T
* * *
417710 ACACTCGTGTGCCAGGCCGTGTAAAAACTGGAGGGTATACTGGCTTGTGCCACAGGGCCAA
1 ACACTCGTGTGCCAGGCCGTGTAAAAACTAGAGGGTATACTGACTTGTGCCACAAGGCCAA
417771 TGTGCTAGGC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (66 bp):
ACACTCGTGTGCCAGGCCGTGTAAAAACTAGAGGGTATACTGACTTGTGCCACAAGGCCAAGCCA
T
Found at i:419845 original size:93 final size:93
Alignment explanation
Indices: 419733--419903 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
419723 GCCCATAAGT
* *
419733 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
419798 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
419826 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
419891 CGAGTTCGGATGC
66 CGAGTTCGGATGC
419904 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:419900 original size:46 final size:46
Alignment explanation
Indices: 419725--419900 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
419715 TGTAACCCGC
* * *
419725 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
419771 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
419821 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
419864 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
419901 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:422312 original size:29 final size:29
Alignment explanation
Indices: 422273--422360 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
422263 CAAAGATAAC
*
422273 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
422302 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
422331 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
422361 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:422331 original size:15 final size:15
Alignment explanation
Indices: 422273--422351 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
422263 CAAAGATAAC
*
422273 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
422287 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
422302 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
422316 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
422331 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
422346 AAGAAA
1 AAGAAA
422352 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:422360 original size:15 final size:15
Alignment explanation
Indices: 422284--422360 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
422274 AGAAAACCGA
422284 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
422299 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
422313 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
422327 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
422343 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
422358 ATA
1 ATA
422361 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:425429 original size:93 final size:93
Alignment explanation
Indices: 425317--425487 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
425307 GCCCATAAGT
* *
425317 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
425382 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
425410 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
425475 CGAGTTCGGATGC
66 CGAGTTCGGATGC
425488 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:425484 original size:46 final size:46
Alignment explanation
Indices: 425309--425484 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
425299 TGTAACCCGC
* * *
425309 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
425355 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
425405 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
425448 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
425485 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:437509 original size:22 final size:22
Alignment explanation
Indices: 437482--437523 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
437472 ACAAAATGAT
437482 CTGTTGATTATCAAAATATACC
1 CTGTTGATTATCAAAATATACC
* *
437504 CTGTTGATTATTAAGATATA
1 CTGTTGATTATCAAAATATA
437524 TTCAGGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
CTGTTGATTATCAAAATATACC
Found at i:441133 original size:54 final size:54
Alignment explanation
Indices: 441073--441188 Score: 137
Period size: 54 Copynumber: 2.1 Consensus size: 54
441063 GTCTCCTCAC
**
441073 CCATGTAACTCATTGAGATGCCCCACACAC-CT-GTGTGCCAGGTTGTGTGCTAGG
1 CCATGTAACTCATTGAGATG--CCACACACGCTCGTGTGCCAGGCCGTGTGCTAGG
* * * * *
441127 CTATGTAACTCTTTGAGTTGCCACACACGTTCGTGTGTCAGGCCGTGTGCTAGG
1 CCATGTAACTCATTGAGATGCCACACACGCTCGTGTGCCAGGCCGTGTGCTAGG
441181 CCATGTAA
1 CCATGTAA
441189 TTCACTAACT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
52 8 0.15
53 1 0.02
54 43 0.83
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (54 bp):
CCATGTAACTCATTGAGATGCCACACACGCTCGTGTGCCAGGCCGTGTGCTAGG
Found at i:441596 original size:18 final size:18
Alignment explanation
Indices: 441575--441614 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
441565 TAAAAGTAGT
441575 CAAGATGACCTTACTTAA
1 CAAGATGACCTTACTTAA
441593 CAAGATGACCTTACTTAA
1 CAAGATGACCTTACTTAA
441611 CAAG
1 CAAG
441615 CTTTACAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (18 bp):
CAAGATGACCTTACTTAA
Found at i:443892 original size:2 final size:2
Alignment explanation
Indices: 443885--443909 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
443875 CTAACATGCT
443885 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
443910 TCACCATTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:444394 original size:4 final size:4
Alignment explanation
Indices: 444364--444421 Score: 57
Period size: 4 Copynumber: 14.0 Consensus size: 4
444354 TTTTCCCTTC
*
444364 TTCT CTTCT TT-T TTCTT TTCTT TTCT TTCT TTCT TTCT TTCA TTC- TTCT
1 TTCT -TTCT TTCT TTC-T TTC-T TTCT TTCT TTCT TTCT TTCT TTCT TTCT
444413 TCTCT TTCT
1 T-TCT TTCT
444422 CCTTAGCTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
3 6 0.12
4 25 0.52
5 17 0.35
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:449549 original size:54 final size:54
Alignment explanation
Indices: 449485--449616 Score: 212
Period size: 54 Copynumber: 2.4 Consensus size: 54
449475 ATCCTTACAG
449485 CGGGATTACCAGTTCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTTCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
*
449539 CGGGATTACCAG-TCCGTGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTTCAG-GCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
* * *
449593 CGGAATTATCAGTCCAGGCTAAAT
1 CGGGATTACCAGTTCAGGCTAAAT
449617 TTAGACCCTG
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
53 3 0.04
54 66 0.93
55 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (54 bp):
CGGGATTACCAGTTCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
Found at i:452282 original size:47 final size:48
Alignment explanation
Indices: 452176--452303 Score: 167
Period size: 47 Copynumber: 2.7 Consensus size: 48
452166 TGTAACCCGC
452176 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTTACAT
* * *
452226 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-C-ATTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTT-ACAT
452270 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
452304 AGATGTTCAA
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
43 3 0.04
44 5 0.07
45 1 0.01
46 2 0.03
47 55 0.80
48 2 0.03
49 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (48 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
Found at i:458705 original size:24 final size:24
Alignment explanation
Indices: 458673--458724 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
458663 TATAATGCCA
458673 TATCCCATTTATGGTCTTACATGT
1 TATCCCATTTATGGTCTTACATGT
458697 TATCCCATTTATGGTCTTACATGT
1 TATCCCATTTATGGTCTTACATGT
458721 TATC
1 TATC
458725 ACATATCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (24 bp):
TATCCCATTTATGGTCTTACATGT
Found at i:459451 original size:36 final size:36
Alignment explanation
Indices: 459404--459480 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
459394 TTTCACTAAA
*
459404 AATCACTTTATAAAACAAGATAATCTATCAACAAAT
1 AATCACTTTATAAAAAAAGATAATCTATCAACAAAT
459440 AATCACTTTATAAAAAAAGATAATCTATCAACAAAT
1 AATCACTTTATAAAAAAAGATAATCTATCAACAAAT
459476 AATCA
1 AATCA
459481 TTTTCCATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.55, C:0.16, G:0.03, T:0.27
Consensus pattern (36 bp):
AATCACTTTATAAAAAAAGATAATCTATCAACAAAT
Found at i:460039 original size:33 final size:33
Alignment explanation
Indices: 460002--460067 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
459992 TGCTGTAAAC
460002 ACCAAAAATAATATTAAAATAATTTTATGACAT
1 ACCAAAAATAATATTAAAATAATTTTATGACAT
460035 ACCAAAAATAATATTAAAATAATTTTATGACAT
1 ACCAAAAATAATATTAAAATAATTTTATGACAT
460068 CGGATTTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (33 bp):
ACCAAAAATAATATTAAAATAATTTTATGACAT
Found at i:462566 original size:27 final size:27
Alignment explanation
Indices: 462489--462565 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 27
462479 CCCCAAGACA
**
462489 GGTAAAATGACACAAAATACCCCTAAAG
1 GGTAAAATGAC-CATTATACCCCTAAAG
* *
462517 GGTAAAATGACTATTTTACCCCTAATAG
1 GGTAAAATGACCATTATACCCCTAA-AG
* *
462545 GTTAAAATGACCGTTATACCC
1 GGTAAAATGACCATTATACCC
462566 TTCGAGGTAG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 10 0.25
28 30 0.75
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (27 bp):
GGTAAAATGACCATTATACCCCTAAAG
Found at i:462723 original size:21 final size:21
Alignment explanation
Indices: 462698--462752 Score: 56
Period size: 27 Copynumber: 2.3 Consensus size: 21
462688 AAGTGTACTG
462698 TACTGATGGCTTTGCCATATA
1 TACTGATGGCTTTGCCATATA
462719 TACTGTTAATGGTGGCTTTGCCATATA
1 TACTG---A---TGGCTTTGCCATATA
462746 TACTGAT
1 TACTGAT
462753 ACTGGTAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
21 6 0.21
24 2 0.07
27 20 0.71
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (21 bp):
TACTGATGGCTTTGCCATATA
Found at i:462736 original size:27 final size:27
Alignment explanation
Indices: 462704--462765 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
462694 ACTGTACTGA
*
462704 TGGCTTTGCCATATATACTGTTAATGG
1 TGGCTTTGCCATATATACTGATAATGG
*
462731 TGGCTTTGCCATATATACTGATACTGG
1 TGGCTTTGCCATATATACTGATAATGG
*
462758 TAGCTTTG
1 TGGCTTTG
462766 TTGTGTTACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (27 bp):
TGGCTTTGCCATATATACTGATAATGG
Found at i:466989 original size:1 final size:1
Alignment explanation
Indices: 466983--467009 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
466973 ATGCAAAACC
466983 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
467010 GCTGATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:467813 original size:3 final size:3
Alignment explanation
Indices: 467805--467843 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
467795 CTCCGTCTTA
467805 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
467844 CTCAAGTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:474704 original size:13 final size:12
Alignment explanation
Indices: 474673--474706 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
474663 ATTTTTTTAT
474673 AAAATTATAAAA
1 AAAATTATAAAA
*
474685 AGAATTATAAAA
1 AAAATTATAAAA
474697 AAAGATTATA
1 AAA-ATTATA
474707 TAAATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (12 bp):
AAAATTATAAAA
Found at i:483325 original size:3 final size:3
Alignment explanation
Indices: 483317--483349 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
483307 AGAGAATTGC
483317 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
483350 AAGCAAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:485023 original size:2 final size:2
Alignment explanation
Indices: 485016--485050 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
485006 CTAGGTACCT
485016 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
485051 TAACTCTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:485473 original size:21 final size:19
Alignment explanation
Indices: 485441--485488 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
485431 TTAATTAAGA
*
485441 TAAAATTGTAGTGATAATAT
1 TAAAATTATAGTGATAA-AT
*
485461 TAAATATTATAGTGATTAAT
1 TAAA-ATTATAGTGATAAAT
485481 TAAAATTA
1 TAAAATTA
485489 GTTGTGAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 10 0.40
21 11 0.44
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (19 bp):
TAAAATTATAGTGATAAAT
Found at i:485495 original size:20 final size:21
Alignment explanation
Indices: 485441--485495 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
485431 TTAATTAAGA
485441 TAAAATT-GTAGTGATAATAT
1 TAAAATTAGTAGTGATAATAT
*
485461 TAAATATTA-TAGTGATTA-AT
1 TAAA-ATTAGTAGTGATAATAT
*
485481 TAAAATTAGTTGTGA
1 TAAAATTAGTAGTGA
485496 GATATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 4 0.13
20 15 0.50
21 11 0.37
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.42
Consensus pattern (21 bp):
TAAAATTAGTAGTGATAATAT
Found at i:488140 original size:22 final size:22
Alignment explanation
Indices: 488115--488164 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
488105 ACATGTATTG
*
488115 AGACATTGG-CTCTTATGTCTCA
1 AGACATTGGTC-CTTATGTCACA
* *
488137 AGACTTTGGTCCTTATGTCACG
1 AGACATTGGTCCTTATGTCACA
488159 AGACAT
1 AGACAT
488165 GACCTTAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (22 bp):
AGACATTGGTCCTTATGTCACA
Found at i:491628 original size:64 final size:64
Alignment explanation
Indices: 491550--491723 Score: 267
Period size: 64 Copynumber: 2.7 Consensus size: 64
491540 TAAAAATGAT
*
491550 AGTGAGTCATACGGCCTAGGCGCACGCCTATGTCCCTGGGCTGTGTAGTCCCTATATGGTGAAC
1 AGTGAGTCACACGGCCTAGGCGCACGCCTATGTCCCTGGGCTGTGTAGTCCCTATATGGTGAAC
* *
491614 AGTGAGTCACACGGCCTAGGCGCACGCCTATGTCCCTGGGCCGTGTAGTCCTTATATGGTGAAC
1 AGTGAGTCACACGGCCTAGGCGCACGCCTATGTCCCTGGGCTGTGTAGTCCCTATATGGTGAAC
* * * * * *
491678 AGTGAGTTACACGGCCTAGACACACGCCCATGTCCTTGGCCTGTGT
1 AGTGAGTCACACGGCCTAGGCGCACGCCTATGTCCCTGGGCTGTGT
491724 GAACAATACA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 100 1.00
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.24
Consensus pattern (64 bp):
AGTGAGTCACACGGCCTAGGCGCACGCCTATGTCCCTGGGCTGTGTAGTCCCTATATGGTGAAC
Found at i:494842 original size:27 final size:25
Alignment explanation
Indices: 494785--494849 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 25
494775 CTTTTGTATT
*
494785 TTTTTTATATTTGTCTAGTTACAAA
1 TTTTTTATATTTGTCTACTTACAAA
**
494810 TATTTTTAATATTTGTCTAACTTTTAAA
1 T-TTTTT-ATATTTGTCT-ACTTACAAA
494838 TTTTTTATATTT
1 TTTTTTATATTT
494850 ACTATCGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 1 0.03
26 11 0.32
27 15 0.44
28 7 0.21
ACGTcount: A:0.28, C:0.06, G:0.05, T:0.62
Consensus pattern (25 bp):
TTTTTTATATTTGTCTACTTACAAA
Found at i:502115 original size:28 final size:28
Alignment explanation
Indices: 502031--502127 Score: 106
Period size: 28 Copynumber: 3.4 Consensus size: 28
502021 AATTATTGCA
*
502031 CTTATCG-TATTATTTTACACTTTGGTG
1 CTTATCGTTATTATTTTGCACTTTGGTG
** *
502058 CTTATCGTTGCAAAAATTTGCACTTTGGTG
1 CTTATCGTT--ATTATTTTGCACTTTGGTG
* *
502088 CTTATCGTTATTATTTTGCACCTAGGTG
1 CTTATCGTTATTATTTTGCACTTTGGTG
*
502116 CTTTTCGTTATT
1 CTTATCGTTATT
502128 TTCACTTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
27 7 0.12
28 26 0.46
30 24 0.42
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.48
Consensus pattern (28 bp):
CTTATCGTTATTATTTTGCACTTTGGTG
Found at i:506708 original size:10 final size:10
Alignment explanation
Indices: 506693--506752 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
506683 TAATTTTAGG
506693 ATTTAT-TTT
1 ATTTATCTTT
506702 CATTTATCTTT
1 -ATTTATCTTT
506713 ATTTATCTTT
1 ATTTATCTTT
*
506723 AATTATCTTT
1 ATTTATCTTT
506733 ATTTAT-TTGT
1 ATTTATCTT-T
506743 ATTTATCTTT
1 ATTTATCTTT
506753 TAGAATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:507509 original size:18 final size:18
Alignment explanation
Indices: 507474--507507 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
507464 TATTCCTCAT
*
507474 TTTAATTTTTGCAATTTA
1 TTTAATTTTCGCAATTTA
507492 TTTAA-TTTCGCAATTT
1 TTTAATTTTCGCAATTT
507508 TAATTCACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTAATTTTCGCAATTTA
Found at i:510466 original size:15 final size:15
Alignment explanation
Indices: 510448--510501 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
510438 AATTTTTATT
510448 TTTATTTTTTTTTAG
1 TTTATTTTTTTTTAG
* **
510463 TTTAGTTTAGTTTAG
1 TTTATTTTTTTTTAG
*
510478 TTTATTTTTATTTA-
1 TTTATTTTTTTTTAG
510492 -TTATTTTTTT
1 TTTATTTTTTT
510502 ACTTATTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
13 9 0.28
15 23 0.72
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (15 bp):
TTTATTTTTTTTTAG
Found at i:510502 original size:15 final size:16
Alignment explanation
Indices: 510482--510514 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
510472 GTTTAGTTTA
*
510482 TTTTTATTTATT-ATT
1 TTTTTACTTATTAATT
510497 TTTTTACTTATTAATT
1 TTTTTACTTATTAATT
510513 TT
1 TT
510515 AGATATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTACTTATTAATT
Found at i:511423 original size:96 final size:97
Alignment explanation
Indices: 511259--511440 Score: 303
Period size: 96 Copynumber: 1.9 Consensus size: 97
511249 TTTAAGAATG
* * *
511259 TGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTATCTTCGCGTCAAAAGGTTCGAT
1 TGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTATCATCTATCTTCGCATCAAAAGGTTCAAT
*
511324 ATATTCTTAAG-AAAAATAAAAATTAGGAGTA
66 ATATTCCTAAGTAAAAATAAAAATTAGGAGTA
* *
511355 TGTTGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTATCATCTCTCTTCGCATCAAAAGGTTCAAT
1 TGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTATCATCTATCTTCGCATCAAAAGGTTCAAT
511420 ATATTCCTAAGTAAAAATAAA
66 ATATTCCTAAGTAAAAATAAA
511441 TAAATAAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
96 70 0.89
97 9 0.11
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (97 bp):
TGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTATCATCTATCTTCGCATCAAAAGGTTCAAT
ATATTCCTAAGTAAAAATAAAAATTAGGAGTA
Found at i:511476 original size:11 final size:11
Alignment explanation
Indices: 511462--511487 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
511452 AAAATTCTAT
511462 AAAAAAAGAAA
1 AAAAAAAGAAA
511473 AAAAAAAGAAA
1 AAAAAAAGAAA
511484 AAAA
1 AAAA
511488 GAGACATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:513542 original size:10 final size:10
Alignment explanation
Indices: 513527--513586 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
513517 TAATTTTAGG
513527 ATTTAT-TTT
1 ATTTATCTTT
513536 CATTTATCTTT
1 -ATTTATCTTT
513547 ATTTATCTTT
1 ATTTATCTTT
*
513557 AATTATCTTT
1 ATTTATCTTT
513567 ATTTAT-TTGT
1 ATTTATCTT-T
513577 ATTTATCTTT
1 ATTTATCTTT
513587 TAGAATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:518447 original size:25 final size:24
Alignment explanation
Indices: 518375--518458 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 24
518365 AGCTGTAAAC
* *
518375 GGTAAGCTCCTCTGAGCTAAACAAT
1 GGTAAGCTCCTCCGAGCTAAA-TAT
* *
518400 GGTAAGCTCCTCCAAAC-AGAATAT
1 GGTAAGCTCCTCCGAGCTA-AATAT
*
518424 CGGTAAGCTCTTCCGAGCTAAATAAT
1 -GGTAAGCTCCTCCGAGCTAAAT-AT
518450 GGTAAGCTC
1 GGTAAGCTC
518459 GTATGAGCTG
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
24 3 0.06
25 42 0.88
26 3 0.06
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (24 bp):
GGTAAGCTCCTCCGAGCTAAATAT
Found at i:533132 original size:56 final size:55
Alignment explanation
Indices: 533034--533195 Score: 184
Period size: 56 Copynumber: 2.9 Consensus size: 55
533024 CGAAGCCAAC
* * *
533034 TCGCACATACTTTTCAGGAAAC-TCAAA-AAGGTCCGCCTTAGGTCACAAGACTGGT
1 TCGCACATACTTATCAGAAAACAT-AAACAAGGTCTGCCTTAGGTCA-AAGACTGGT
* * *
533089 TGGCACATACTTATCAGAAAACATGAACAAGGTCTGCCTTAGGTCGAGAGACTGGT
1 TCGCACATACTTATCAGAAAACATAAACAAGGTCTGCCTTAGGTC-AAAGACTGGT
* * * *
533145 TCGTACATACTTATTAAAAAACATAAACAAGGTTTGCCTTAGGTCATAAGA
1 TCGCACATACTTATCAGAAAACATAAACAAGGTCTGCCTTAGGTCA-AAGA
533196 TCTGTTCACT
Statistics
Matches: 90, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
55 22 0.24
56 67 0.74
57 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (55 bp):
TCGCACATACTTATCAGAAAACATAAACAAGGTCTGCCTTAGGTCAAAGACTGGT
Found at i:551409 original size:40 final size:40
Alignment explanation
Indices: 551351--551427 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 40
551341 ACACACCATG
** *
551351 TGGGGATAGAATTGACCCACCCAACCCTTCAAACCAAGTA
1 TGGGGATAGAATCAACCCACCCAACCCTACAAACCAAGTA
* * * *
551391 TGGGGATATAATCAACCCATCCAGCCCTACACACCAA
1 TGGGGATAGAATCAACCCACCCAACCCTACAAACCAA
551428 AAGGTACCGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.35, C:0.32, G:0.16, T:0.17
Consensus pattern (40 bp):
TGGGGATAGAATCAACCCACCCAACCCTACAAACCAAGTA
Found at i:556386 original size:40 final size:41
Alignment explanation
Indices: 556297--556401 Score: 151
Period size: 41 Copynumber: 2.6 Consensus size: 41
556287 TATTCGAATG
* * *
556297 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGTTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAAGTGACT
556338 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCT-AGTGA-T
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAAGTGACT
*
556377 CATATCCGGGCTAAGACCCGAAGGC
1 -ATATCCGGGCTAAGTCCCGAAGGC
556402 CTTGTGCGAG
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
39 1 0.02
40 28 0.47
41 30 0.51
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (41 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAAGTGACT
Found at i:564446 original size:40 final size:41
Alignment explanation
Indices: 564355--564459 Score: 142
Period size: 41 Copynumber: 2.6 Consensus size: 41
564345 TATTCGAATG
* * *
564355 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGTTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAAGTGACT
564396 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCT-AGTGA-T
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAAGTGACT
* *
564435 CATATCTGGGCTAAGACCCGAAGGC
1 -ATATCCGGGCTAAGTCCCGAAGGC
564460 CTTGTGCGAG
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
39 1 0.02
40 27 0.47
41 30 0.52
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (41 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAAGTGACT
Found at i:566597 original size:3 final size:3
Alignment explanation
Indices: 566591--566664 Score: 58
Period size: 3 Copynumber: 24.7 Consensus size: 3
566581 TTTTTTATAC
* * * * * * * *
566591 ATT ATT ATT AAT ATC ATA ATC ATT ATT ATT ATT ATC GTT ATT AAT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
566639 ATT ATT ATC ATT ACT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
566665 GCTTACCCCT
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:566661 original size:21 final size:21
Alignment explanation
Indices: 566591--566664 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
566581 TTTTTTATAC
*
566591 ATTATTATTAATATCA-TAAT
1 ATTATTATTATTATCATTAAT
* *
566611 CATTATTATTATTATCGTTATT
1 -ATTATTATTATTATCATTAAT
* * *
566633 AATGTTATTATTATCATTACT
1 ATTATTATTATTATCATTAAT
566654 ATTATTATTAT
1 ATTATTATTAT
566665 GCTTACCCCT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
21 40 0.93
22 3 0.07
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTATTATTATTATCATTAAT
Found at i:578973 original size:18 final size:20
Alignment explanation
Indices: 578952--578994 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
578942 CTATTTTCTG
578952 TTATTGAAA-GTTTTGAAA-
1 TTATTGAAACGTTTTGAAAT
*
578970 TTATT-AAACTTTTTGAAAT
1 TTATTGAAACGTTTTGAAAT
578989 TTATTG
1 TTATTG
578995 GTGAAAGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.14
18 13 0.62
19 5 0.24
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (20 bp):
TTATTGAAACGTTTTGAAAT
Found at i:581048 original size:65 final size:66
Alignment explanation
Indices: 580941--581087 Score: 215
Period size: 66 Copynumber: 2.2 Consensus size: 66
580931 GATACACGGA
* * * * *
580941 TCTCCATCACACCAAATAGACTCATAGAGTCAGACATGTCCC-ATAAGTGAAGCATAAAACTAAC
1 TCTCCAACACACC-AATAGACTCATACAGTCAAACATATCCCAAAAAGTGAAGCATAAAACTAAC
581005 AC
65 AC
* *
581007 TCTCCAACACACCAATTGACTCATACAGTCAAACATATCCCAAAAAGTGAAGCATAAAGCTAACA
1 TCTCCAACACACCAATAGACTCATACAGTCAAACATATCCCAAAAAGTGAAGCATAAAACTAACA
581072 C
66 C
581073 TCTCCAACACACCAA
1 TCTCCAACACACCAA
581088 ACATGTCCCG
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
65 24 0.33
66 49 0.67
ACGTcount: A:0.42, C:0.30, G:0.10, T:0.18
Consensus pattern (66 bp):
TCTCCAACACACCAATAGACTCATACAGTCAAACATATCCCAAAAAGTGAAGCATAAAACTAACA
C
Found at i:583500 original size:30 final size:28
Alignment explanation
Indices: 583460--583517 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
583450 TGGAGAACTC
583460 ACAGTAAGTGGCGAGCGCTACCTCAAATGA
1 ACAGTAAGTGGCGA--GCTACCTCAAATGA
* * *
583490 ACAGTGAGTGGTGAGCTACCTCGAATGA
1 ACAGTAAGTGGCGAGCTACCTCAAATGA
583518 GTATAAGCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 13 0.52
30 12 0.48
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (28 bp):
ACAGTAAGTGGCGAGCTACCTCAAATGA
Found at i:585810 original size:25 final size:25
Alignment explanation
Indices: 585776--585826 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
585766 ATAGTTTGAC
585776 TTCACAAAGAAAGGATGTAGGGGTA
1 TTCACAAAGAAAGGATGTAGGGGTA
585801 TTCACAAAGAAAGGATGTAGGGGTA
1 TTCACAAAGAAAGGATGTAGGGGTA
585826 T
1 T
585827 ATGAAAGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.31, T:0.22
Consensus pattern (25 bp):
TTCACAAAGAAAGGATGTAGGGGTA
Found at i:586608 original size:32 final size:32
Alignment explanation
Indices: 586567--586664 Score: 187
Period size: 32 Copynumber: 3.1 Consensus size: 32
586557 TTTTTATGAC
586567 TTAACTAAAACCCTTTATAAATTAATTAAGGT
1 TTAACTAAAACCCTTTATAAATTAATTAAGGT
586599 TTAACTAAAACCCTTTATAAATTAATTAAGGT
1 TTAACTAAAACCCTTTATAAATTAATTAAGGT
*
586631 TTAACTAAAACCCTTTACAAATTAATTAAGGT
1 TTAACTAAAACCCTTTATAAATTAATTAAGGT
586663 TT
1 TT
586665 TATATCTCAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (32 bp):
TTAACTAAAACCCTTTATAAATTAATTAAGGT
Found at i:596133 original size:13 final size:13
Alignment explanation
Indices: 596115--596141 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
596105 GGAAATTATT
596115 TTTGCACCTTCTA
1 TTTGCACCTTCTA
596128 TTTGCACCTTCTA
1 TTTGCACCTTCTA
596141 T
1 T
596142 ATCGTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTGCACCTTCTA
Found at i:597228 original size:18 final size:18
Alignment explanation
Indices: 597205--597241 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
597195 GCAGAAATCA
597205 CCCTTTTTCCAATTCTAT
1 CCCTTTTTCCAATTCTAT
597223 CCCTTTTTCCAATTCTAT
1 CCCTTTTTCCAATTCTAT
597241 C
1 C
597242 TTTATCTAAC
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:0.16, C:0.35, G:0.00, T:0.49
Consensus pattern (18 bp):
CCCTTTTTCCAATTCTAT
Found at i:601430 original size:6 final size:6
Alignment explanation
Indices: 601421--601466 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
601411 TCTTCATCTT
601421 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATC
601467 GTCGTATGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
CATCAC
Found at i:605663 original size:74 final size:74
Alignment explanation
Indices: 605570--605715 Score: 220
Period size: 74 Copynumber: 2.0 Consensus size: 74
605560 CGACTACCTG
* * * *
605570 TGGGTGCAAATATCGTTGGTAAATCCAACTAGAGCTAGGCTCACTATTTATTCGTTGGCTTATCC
1 TGGGTGCAAATACCGTTGGTAAATCCAACTAGAGCTAAGCTCACTAATTATTCGTCGGCTTATCC
605635 AACTAGCAT
66 AACTAGCAT
* * *
605644 TGGGTGCAAATACCTTTGGTATATCCAACTAGAGCTAAGCTCACTAATTATTCGTCGGTTTATCC
1 TGGGTGCAAATACCGTTGGTAAATCCAACTAGAGCTAAGCTCACTAATTATTCGTCGGCTTATCC
*
605709 GACTAGC
66 AACTAGC
605716 GCTGGGCACA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 64 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (74 bp):
TGGGTGCAAATACCGTTGGTAAATCCAACTAGAGCTAAGCTCACTAATTATTCGTCGGCTTATCC
AACTAGCAT
Found at i:605740 original size:35 final size:35
Alignment explanation
Indices: 605694--605795 Score: 100
Period size: 35 Copynumber: 2.9 Consensus size: 35
605684 TCACTAATTA
* *
605694 TTCGTCGGTTTATCCGACTAGCGCTGGGCACAACT
1 TTCGTCAGTTTATCCGACTAGCGCTAGGCACAACT
* *
605729 TTCGTCAGTTTATCTGACTAGTGCTAGGCAC-ACAT
1 TTCGTCAGTTTATCCGACTAGCGCTAGGCACAAC-T
* ** * *
605764 TT-TTTGGTTTATCTGACTAGCGCTAGGTACAA
1 TTCGTCAGTTTATCCGACTAGCGCTAGGCACAA
605796 ACTCTTTCAC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
34 25 0.45
35 31 0.55
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.34
Consensus pattern (35 bp):
TTCGTCAGTTTATCCGACTAGCGCTAGGCACAACT
Found at i:608408 original size:16 final size:16
Alignment explanation
Indices: 608359--608412 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
608349 TAATTAGTTA
608359 TTAATTATAA-TTAA-C
1 TTAATTA-AACTTAAGC
* * *
608374 TTAACT-AACCTAAGT
1 TTAATTAAACTTAAGC
608389 TTAATTAAACTTAAGC
1 TTAATTAAACTTAAGC
608405 TTAATTAA
1 TTAATTAA
608413 CAATTTTGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 2 0.07
14 3 0.10
15 10 0.33
16 15 0.50
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (16 bp):
TTAATTAAACTTAAGC
Found at i:613793 original size:17 final size:17
Alignment explanation
Indices: 613770--613811 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
613760 TATCGAAATA
*
613770 AATATTAGATTAAATTT
1 AATATTAAATTAAATTT
*
613787 CATATTAAATTAAATTT
1 AATATTAAATTAAATTT
613804 AATATTAA
1 AATATTAA
613812 GATACTCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
AATATTAAATTAAATTT
Found at i:615670 original size:15 final size:14
Alignment explanation
Indices: 615646--615676 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
615636 CAACGTATTT
615646 GTTAAAAAGTCCTA
1 GTTAAAAAGTCCTA
615660 GTTACAAAAGTCCTA
1 GTTA-AAAAGTCCTA
615675 GT
1 GT
615677 AAACGGACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (14 bp):
GTTAAAAAGTCCTA
Found at i:616096 original size:39 final size:39
Alignment explanation
Indices: 616042--616120 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
616032 ATTTCCTTAA
616042 ATCTTTACAGGTTTGGAAGGCTGAGTCTGTAGATCCAAT
1 ATCTTTACAGGTTTGGAAGGCTGAGTCTGTAGATCCAAT
* *
616081 ATCTTTACAGGTTTGGAAGTCTGAGTCTGTAGATCTAAT
1 ATCTTTACAGGTTTGGAAGGCTGAGTCTGTAGATCCAAT
616120 A
1 A
616121 GGAGTAAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (39 bp):
ATCTTTACAGGTTTGGAAGGCTGAGTCTGTAGATCCAAT
Found at i:617456 original size:60 final size:62
Alignment explanation
Indices: 617348--617481 Score: 150
Period size: 61 Copynumber: 2.2 Consensus size: 62
617338 ATTTTTAAAC
* * * * *
617348 TTTTACAATTAGAATTAAATTGAAAATTTTTGTAAATTTTAAGAGTT-AAATCTATT-AAATT
1 TTTTAGAATTAGAATAAAAATGAAAATTTTTGTAAAATTAAAGAGTTAAAATCTATTGAAA-T
* *
617409 TTTTAGAATTAGAA-AAAAATGAAAGTTTTTGTAAACATTAAAG-GTTAAAATTTATTGAAAT
1 TTTTAGAATTAGAATAAAAATGAAAATTTTTGTAAA-ATTAAAGAGTTAAAATCTATTGAAAT
*
617470 TTTTAGATTTAG
1 TTTTAGAATTAG
617482 TATCAAATTG
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
60 21 0.34
61 38 0.61
62 3 0.05
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (62 bp):
TTTTAGAATTAGAATAAAAATGAAAATTTTTGTAAAATTAAAGAGTTAAAATCTATTGAAAT
Found at i:617812 original size:6 final size:6
Alignment explanation
Indices: 617803--617830 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
617793 GAGAGAGCCA
617803 TTTCTG TTTCTG TTTCTG TTTCTG TTTC
1 TTTCTG TTTCTG TTTCTG TTTCTG TTTC
617831 AGTGAGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.14, T:0.68
Consensus pattern (6 bp):
TTTCTG
Found at i:630109 original size:7 final size:7
Alignment explanation
Indices: 630097--630124 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
630087 AATAATTTAA
630097 AAAATTT
1 AAAATTT
630104 AAAATTT
1 AAAATTT
630111 AAAATTT
1 AAAATTT
630118 AAAATTT
1 AAAATTT
630125 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAAATTT
Found at i:635234 original size:26 final size:26
Alignment explanation
Indices: 635209--635258 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
635199 TTAAATATTA
635209 AAATAA-ATA-ATATTTTATGATAATT
1 AAATAATATATATA-TTTATGATAATT
*
635234 AAATAATATTTATATTTATGATAAT
1 AAATAATATATATATTTATGATAAT
635259 ATTATTTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 13 0.59
27 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
AAATAATATATATATTTATGATAATT
Found at i:636956 original size:22 final size:22
Alignment explanation
Indices: 636906--636989 Score: 82
Period size: 22 Copynumber: 3.8 Consensus size: 22
636896 AGACTTAAAA
* *
636906 AATATAAAAATAAA-ATATTTT
1 AATAAAAAAATAAATATAATTT
* *
636927 AATGTAAAATATTAAATATAATTT
1 AA--TAAAAAAATAAATATAATTT
636951 AATAAAAAAATAAATATAATTT
1 AATAAAAAAATAAATATAATTT
* *
636973 AAT-ATAAAATAATTATA
1 AATAAAAAAATAAATATA
636990 TTAAGAATGT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
21 14 0.27
22 21 0.40
23 9 0.17
24 8 0.15
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (22 bp):
AATAAAAAAATAAATATAATTT
Found at i:637060 original size:26 final size:25
Alignment explanation
Indices: 637023--637074 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
637013 ATTATTTTTT
* *
637023 TATTAAATTATATTTAATAATAATTA
1 TATTAAAATATAATTAA-AATAATTA
*
637049 TATTAAAATATAATTAAAATATTTA
1 TATTAAAATATAATTAAAATAATTA
637074 T
1 T
637075 TTTTTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTAAAATATAATTAAAATAATTA
Found at i:637084 original size:57 final size:60
Alignment explanation
Indices: 636980--637105 Score: 179
Period size: 57 Copynumber: 2.1 Consensus size: 60
636970 TTTAATATAA
* *
636980 AATAATTATATTAAGAATGTTATCAAATTATATATTATTTTTTTATTAAATTATATTTAAT
1 AATAATTATATTAAGAATATAATCAAA-TATATATTATTTTTTTATTAAATTATATTTAAT
* *
637041 AATAATTATATTAA-AATATAATTAAA-ATAT-TTATTTTTTTATTAAATTATATTTACT
1 AATAATTATATTAAGAATATAATCAAATATATATTATTTTTTTATTAAATTATATTTAAT
637098 AAT-ATTAT
1 AATAATTAT
637106 TAAAATTTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
56 5 0.08
57 29 0.48
58 4 0.07
60 9 0.15
61 14 0.23
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (60 bp):
AATAATTATATTAAGAATATAATCAAATATATATTATTTTTTTATTAAATTATATTTAAT
Found at i:637137 original size:57 final size:57
Alignment explanation
Indices: 637019--637137 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 57
637009 ATATATTATT
* * * *
637019 TTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAATATTTATT
1 TTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAACAATAATC
* *
637076 TTTTTATTAAATTATATTTACTAAT-A-T-TATTAAAATTTAATAATAATAACAATAATC
1 TTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAAT--TAA-AACAATAATC
637133 TTTTT
1 TTTTT
637138 TATCTAAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
54 13 0.25
55 1 0.02
56 4 0.08
57 35 0.66
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (57 bp):
TTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAACAATAATC
Found at i:643000 original size:138 final size:138
Alignment explanation
Indices: 642833--643116 Score: 453
Period size: 138 Copynumber: 2.1 Consensus size: 138
642823 ATATATATAT
*
642833 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATAATAATTGTATATATTTTACTGAATTTATT
* * * *
642898 AATATAAAAAATTATATTAATTAATTTCAGTCAAAATATTAAAGACAT-GAAAGTTAATATTCTT
66 AATATAAAAAATTATATTAATTAATTGCAGGCAAAATATAAAAGACATGGAAA-TTAATATTATT
*
642962 TTGGAAAGA
130 TTAGAAAGA
* * *
642971 TTATAATTAATATATGAATTTGATTCATACAAAGTAATAATTGTATATATTTTATTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATAATAATTGTATATATTTTACTGAATTTATT
* *
643036 AATATAAACAATTATATTAATTAATTGCAGGCAAAATATAAAAGACATGGAAATTTATATTATTT
66 AATATAAAAAATTATATTAATTAATTGCAGGCAAAATATAAAAGACATGGAAATTAATATTATTT
643101 TAGAAAGA
131 TAGAAAGA
643109 ATATAATT
1 ATATAATT
643117 CTTTTTTCTA
Statistics
Matches: 133, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
138 129 0.97
139 4 0.03
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATAATAATTGTATATATTTTACTGAATTTATT
AATATAAAAAATTATATTAATTAATTGCAGGCAAAATATAAAAGACATGGAAATTAATATTATTT
TAGAAAGA
Found at i:643217 original size:76 final size:75
Alignment explanation
Indices: 643091--643239 Score: 262
Period size: 76 Copynumber: 2.0 Consensus size: 75
643081 CATGGAAATT
643091 TATATTATTTTAGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTGCCTTTCTCTATTAATAA
1 TATATTATTTTAGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTGCCTTT-TCTATTAATAA
643156 GGGAATAATCC
65 GGGAATAATCC
* * *
643167 TATATTCTTTTGGAAAGAATATGATTCTTTTTTCTAACTTTCCATTTGCCTTTTCTATTAATAAG
1 TATATTATTTTAGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTGCCTTTTCTATTAATAAG
643232 GGAATAAT
66 GGAATAAT
643240 TCTGGTTTTC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 20 0.29
76 50 0.71
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.47
Consensus pattern (75 bp):
TATATTATTTTAGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTGCCTTTTCTATTAATAAG
GGAATAATCC
Found at i:643983 original size:24 final size:24
Alignment explanation
Indices: 643956--644015 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
643946 GAATGTTTTG
* *
643956 TATTTTATATAATATTGATATAAA
1 TATTTTATTTAATATTAATATAAA
643980 TATTTTTATTTAA-ATTAATATAAA
1 TA-TTTTATTTAATATTAATATAAA
644004 T-TTTTATTTAAT
1 TATTTTATTTAAT
644016 TAAATTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 10 0.31
24 13 0.41
25 9 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TATTTTATTTAATATTAATATAAA
Found at i:644009 original size:22 final size:24
Alignment explanation
Indices: 643958--644018 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 24
643948 ATGTTTTGTA
* *
643958 TTTTATATAATATTGATATAAATAT
1 TTTTATTTAA-ATTAATATAAATAT
643983 TTTTATTTAAATTAATAT-AA-AT
1 TTTTATTTAAATTAATATAAATAT
644005 TTTTATTT-AATTAA
1 TTTTATTTAAATTAA
644019 ATTTTAGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 6 0.18
22 10 0.29
23 2 0.06
24 7 0.21
25 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTATTTAAATTAATATAAATAT
Found at i:644204 original size:16 final size:16
Alignment explanation
Indices: 644185--644221 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
644175 GGAAAGTGAT
644185 TAAAATAGAAACGATC
1 TAAAATAGAAACGATC
**
644201 TAAAATAGAAATTATC
1 TAAAATAGAAACGATC
644217 TAAAA
1 TAAAA
644222 CATTAGCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24
Consensus pattern (16 bp):
TAAAATAGAAACGATC
Found at i:644835 original size:12 final size:12
Alignment explanation
Indices: 644820--644844 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
644810 TTCAATTTAC
644820 ATTCTTCCTTCA
1 ATTCTTCCTTCA
644832 ATTCTTCCTTCA
1 ATTCTTCCTTCA
644844 A
1 A
644845 GGGAAGCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTCTTCCTTCA
Found at i:647699 original size:19 final size:19
Alignment explanation
Indices: 647660--647699 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
647650 AAAAAAATCA
*
647660 TTTTGGTCCTTTATATAAT
1 TTTTGGTCCTTTATAGAAT
* *
647679 TTTTTGTCCTTTATAGCAT
1 TTTTGGTCCTTTATAGAAT
647698 TT
1 TT
647700 AAATTTGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (19 bp):
TTTTGGTCCTTTATAGAAT
Found at i:647883 original size:10 final size:10
Alignment explanation
Indices: 647870--647894 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
647860 AAAAAGTACA
647870 AAAATATTTT
1 AAAATATTTT
647880 AAAATATTTT
1 AAAATATTTT
647890 AAAAT
1 AAAAT
647895 TAATTAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AAAATATTTT
Found at i:654462 original size:24 final size:24
Alignment explanation
Indices: 654430--654481 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
654420 CCTGATATAT
654430 GTAAAATGGATTTAGCCCGGACGG
1 GTAAAATGGATTTAGCCCGGACGG
*
654454 GTAAAATGGATTTAGCCTGGACGG
1 GTAAAATGGATTTAGCCCGGACGG
654478 GTAA
1 GTAA
654482 TCTGAACTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.23
Consensus pattern (24 bp):
GTAAAATGGATTTAGCCCGGACGG
Found at i:655229 original size:14 final size:14
Alignment explanation
Indices: 655206--655235 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
655196 TTGAAAATAT
655206 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
655220 GTTGATTTGGATTG
1 GTTGAATTGGATTG
655234 GT
1 GT
655236 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:661046 original size:14 final size:14
Alignment explanation
Indices: 661002--661046 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
660992 AAATCATGTT
* *
661002 AATTATTTATTTTT
1 AATTATTTATATTA
*
661016 AATTATTTA-AATA
1 AATTATTTATATTA
661029 AATTATTTATATTA
1 AATTATTTATATTA
661043 AATT
1 AATT
661047 TAACTTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTATTTATATTA
Found at i:671692 original size:23 final size:23
Alignment explanation
Indices: 671634--671694 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 23
671624 AACTGTCATG
*
671634 ATTATAGGGATTATAAGCTGTAA
1 ATTATAGAGATTATAAGCTGTAA
* * * * *
671657 AATGTAGAAATTATATGTTGTAA
1 ATTATAGAGATTATAAGCTGTAA
*
671680 ATTATAGTGATTATA
1 ATTATAGAGATTATA
671695 GGCTCAATTT
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.39
Consensus pattern (23 bp):
ATTATAGAGATTATAAGCTGTAA
Found at i:687690 original size:20 final size:20
Alignment explanation
Indices: 687652--687690 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
687642 GTCCATTATC
*
687652 TGTCCAGATTACATGCCCGT
1 TGTCCAGATTACATACCCGT
687672 TGTCCA-ATTACATAACCCG
1 TGTCCAGATTACAT-ACCCG
687691 AGCCCAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTCCAGATTACATACCCGT
Found at i:687952 original size:20 final size:21
Alignment explanation
Indices: 687909--687958 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
687899 CCTCGTACCT
*
687909 GCAAAAACATACAAACGCACA
1 GCAAAAACAAACAAACGCACA
*
687930 GCAAATACAAACAAACG-ACA
1 GCAAAAACAAACAAACGCACA
687950 GCAAAAACA
1 GCAAAAACA
687959 GCAAACAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.60, C:0.26, G:0.10, T:0.04
Consensus pattern (21 bp):
GCAAAAACAAACAAACGCACA
Found at i:690550 original size:130 final size:130
Alignment explanation
Indices: 690307--690560 Score: 377
Period size: 130 Copynumber: 2.0 Consensus size: 130
690297 AAATTCTTCA
* * * * *
690307 AAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCGAT
1 AAACGAAAACGAGATTCGATATTTAGCAATTCACGGAATCGTGCCCTAACGTGTTGGGTTGCGAT
* * *
690372 TTCGCATTTGCTCAAAATAATCGAATATCACTTTAAAATTTCTCTCATATCTTTTAAAATCCCTT
66 TTCGCATTTGCTCAAAATAATCGAATATCACTTCAAAAATTCTCTCATATCTTCTAAAATCCCTT
*
690437 AAACGAAAACGAGATTCGATATTTAGCAATTCACGGGATCGTGCCCTAACGTGTTGGGTTGC-AG
1 AAACGAAAACGAGATTCGATATTTAGCAATTCACGGAATCGTGCCCTAACGTGTTGGGTTGCGA-
* *
690501 TTTCGCATTTGCTCAAAATAATCGAGTATCCCTTCAAAAATTCAT-TCATATCTTCTAAAA
65 TTTCGCATTTGCTCAAAATAATCGAATATCACTTCAAAAATTC-TCTCATATCTTCTAAAA
690561 ATTATTTAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
129 1 0.01
130 109 0.98
131 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (130 bp):
AAACGAAAACGAGATTCGATATTTAGCAATTCACGGAATCGTGCCCTAACGTGTTGGGTTGCGAT
TTCGCATTTGCTCAAAATAATCGAATATCACTTCAAAAATTCTCTCATATCTTCTAAAATCCCTT
Found at i:690785 original size:129 final size:131
Alignment explanation
Indices: 690612--690889 Score: 325
Period size: 129 Copynumber: 2.1 Consensus size: 131
690602 GGTATCATGC
* * * * *
690612 CCTATCGTGCTGGGTTGTGATTCTCGTTTGCTCAAAACAATCGAATATTCCTTC-AGGTTTTCAC
1 CCTATCGTGCTGGGTTGCGATTCTCATTTGCTCAAAACAATCGAAGATCCCTTCGAAG-TTTCAC
* * *
690676 TCATG-TTTATAAAAAACCTTTCAAAA-CAAAGGA-TGTTCGATGTTTGGC-GATTT-GAGAATC
65 TCACGTTTTATAAAAAACCTTT-AAAATCAAAGAAGTGTTCGATGTTTGGCAG-TTTGGAGAATA
690736 GTGT
128 GTGT
* * * * *
690740 CCTATCGTGCTGGGTTGCGCTTTTTCATTTGTTCTAAACAATCGAAGATCCCTTCGAAGTTTCAT
1 CCTATCGTGCTGGGTTGCG-ATTCTCATTTGCTCAAAACAATCGAAGATCCCTTCGAAGTTTCAC
* * * *
690805 TCACGTTTTCTAAAAACCCTTTAAAATGAAAGAAGTGTTCGATGTTTGGCAGTTTGGGGAATAGT
65 TCACGTTTTATAAAAAACCTTTAAAATCAAAGAAGTGTTCGATGTTTGGCAGTTTGGAGAATAGT
690870 GT
130 GT
690872 CCTATCGTGCTGGGTTGC
1 CCTATCGTGCTGGGTTGC
690890 AATCTCCCGT
Statistics
Matches: 126, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
128 18 0.14
129 41 0.33
130 21 0.17
131 18 0.14
132 28 0.22
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (131 bp):
CCTATCGTGCTGGGTTGCGATTCTCATTTGCTCAAAACAATCGAAGATCCCTTCGAAGTTTCACT
CACGTTTTATAAAAAACCTTTAAAATCAAAGAAGTGTTCGATGTTTGGCAGTTTGGAGAATAGTG
T
Found at i:691766 original size:20 final size:20
Alignment explanation
Indices: 691742--691846 Score: 84
Period size: 20 Copynumber: 5.0 Consensus size: 20
691732 TATAGAATGC
691742 GCCACAAAGGCTAACAGAAT
1 GCCACAAAGGCTAACAGAAT
* * **
691762 CCCACAATGGCTATTTTAGAAT
1 GCCACAAAGGCTA--ACAGAAT
* *
691784 GCCACAAAGGCTAATAAAAT
1 GCCACAAAGGCTAACAGAAT
** * *
691804 GCCACAAAAACCATATCATAAT
1 GCCAC-AAAGGC-TAACAGAAT
691826 GCCACAAAGGCTAACAGAAT
1 GCCACAAAGGCTAACAGAAT
691846 G
1 G
691847 AGCCATAAAG
Statistics
Matches: 64, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
20 29 0.45
21 8 0.12
22 27 0.42
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.17
Consensus pattern (20 bp):
GCCACAAAGGCTAACAGAAT
Found at i:691791 original size:42 final size:42
Alignment explanation
Indices: 691742--691845 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
691732 TATAGAATGC
*** * * *
691742 GCCACAAAGGCTAACAGAATCCCACAATGGCTATTTTAGAAT
1 GCCACAAAGGCTAACAGAATCCCACAAAAACCATATCAGAAT
* * * *
691784 GCCACAAAGGCTAATAAAATGCCACAAAAACCATATCATAAT
1 GCCACAAAGGCTAACAGAATCCCACAAAAACCATATCAGAAT
691826 GCCACAAAGGCTAACAGAAT
1 GCCACAAAGGCTAACAGAAT
691846 GAGCCATAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.17
Consensus pattern (42 bp):
GCCACAAAGGCTAACAGAATCCCACAAAAACCATATCAGAAT
Found at i:693986 original size:16 final size:17
Alignment explanation
Indices: 693965--693997 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
693955 TTAGGTTGAG
693965 AAAATT-ATTTAATTAA
1 AAAATTAATTTAATTAA
*
693981 AAAATTAATTTAGTTAA
1 AAAATTAATTTAATTAA
693998 TTTAACTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AAAATTAATTTAATTAA
Found at i:695972 original size:37 final size:35
Alignment explanation
Indices: 695895--695983 Score: 88
Period size: 37 Copynumber: 2.4 Consensus size: 35
695885 GATTATTATT
* *
695895 AAATATAATTTAATAAAAATAATTTAATCATATTT
1 AAATATAATTTAATAAAAATAATTTAATCAAATTA
* * * *
695930 TAATATAATTAGTACTAAATATAATTTAATTAAATTAA
1 AAATATAATT--TAATAAAAATAATTTAATCAAATT-A
695968 AATATATAATTTAATA
1 AA-ATATAATTTAATA
695984 TCATTCTTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
35 9 0.21
37 24 0.57
38 1 0.02
39 8 0.19
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (35 bp):
AAATATAATTTAATAAAAATAATTTAATCAAATTA
Found at i:696292 original size:28 final size:28
Alignment explanation
Indices: 696252--696315 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
696242 ATTACTGTCT
696252 AAATCAAGGAGATAACAAGAAACGCACA
1 AAATCAAGGAGATAACAAGAAACGCACA
696280 AAATCAAGGAGATAACAAGAAACGCACA
1 AAATCAAGGAGATAACAAGAAACGCACA
*
696308 AAAACAAG
1 AAATCAAG
696316 TTCTATGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.59, C:0.17, G:0.17, T:0.06
Consensus pattern (28 bp):
AAATCAAGGAGATAACAAGAAACGCACA
Found at i:696440 original size:77 final size:78
Alignment explanation
Indices: 696352--696499 Score: 280
Period size: 78 Copynumber: 1.9 Consensus size: 78
696342 TAAAAAAGGG
*
696352 GCTTGATTACAGGGAAATGT-AAACAAAAAGGTTTAAAAGAAATCTATAAGGAAAATTTGTTCTG
1 GCTTGATTACAGGGAAATGTAAAACAAAAAGGTTTAAAAGAAATCGATAAGGAAAATTTGTTCTG
696416 TGCATCATCCAAC
66 TGCATCATCCAAC
696429 GCTTGATTACAGGGAAATGTAAAACAAAAAGGTTTAAAAGAAATCGATAAGGAAAATTTGTTCTG
1 GCTTGATTACAGGGAAATGTAAAACAAAAAGGTTTAAAAGAAATCGATAAGGAAAATTTGTTCTG
696494 TGCATC
66 TGCATC
696500 TTCGAACTTT
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
77 20 0.29
78 49 0.71
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (78 bp):
GCTTGATTACAGGGAAATGTAAAACAAAAAGGTTTAAAAGAAATCGATAAGGAAAATTTGTTCTG
TGCATCATCCAAC
Found at i:697908 original size:15 final size:15
Alignment explanation
Indices: 697885--697915 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
697875 AGTAAACTTC
697885 CTTGCTCACATGCAT
1 CTTGCTCACATGCAT
*
697900 CTTGTTCACATGCAT
1 CTTGCTCACATGCAT
697915 C
1 C
697916 GAGCCACCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.35
Consensus pattern (15 bp):
CTTGCTCACATGCAT
Found at i:701844 original size:23 final size:23
Alignment explanation
Indices: 701818--701892 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
701808 TCTACAAACC
701818 TATTATTAAGCAAGTCTAAGGCA
1 TATTATTAAGCAAGTCTAAGGCA
* * * *
701841 TATTCTTAA-CAA-TATTTA--CC
1 TATTATTAAGCAAGT-CTAAGGCA
701861 TATTATTAAGCAAGTCTAAGGCA
1 TATTATTAAGCAAGTCTAAGGCA
*
701884 TATTCTTAA
1 TATTATTAA
701893 CAATATTTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
20 9 0.24
21 6 0.16
22 6 0.16
23 17 0.45
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (23 bp):
TATTATTAAGCAAGTCTAAGGCA
Found at i:701876 original size:43 final size:43
Alignment explanation
Indices: 701815--701901 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
701805 TGATCTACAA
701815 ACCTATTATTAAGCAAGTCTAAGGCATATTCTTAACAATATTT
1 ACCTATTATTAAGCAAGTCTAAGGCATATTCTTAACAATATTT
701858 ACCTATTATTAAGCAAGTCTAAGGCATATTCTTAACAATATTT
1 ACCTATTATTAAGCAAGTCTAAGGCATATTCTTAACAATATTT
701901 A
1 A
701902 TGTAATTTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (43 bp):
ACCTATTATTAAGCAAGTCTAAGGCATATTCTTAACAATATTT
Found at i:701985 original size:27 final size:27
Alignment explanation
Indices: 701926--701988 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
701916 ATTCGAAGTG
* * *
701926 TTTTAATGTGGGGTTTTAATTTCTATA
1 TTTTAGTGTAGGGTCTTAATTTCTATA
701953 TTTTAGTGTAGGGTCTTAATTTCTATA
1 TTTTAGTGTAGGGTCTTAATTTCTATA
701980 TTTTAGTGT
1 TTTTAGTGT
701989 TAAAGCGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.21, C:0.05, G:0.19, T:0.56
Consensus pattern (27 bp):
TTTTAGTGTAGGGTCTTAATTTCTATA
Found at i:702662 original size:25 final size:26
Alignment explanation
Indices: 702611--702665 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
702601 TGTAATATAT
*
702611 TAAATATTATAAATTTAAAAAAATTA
1 TAAATATTATAAATTCAAAAAAATTA
702637 TAAATA-TA-AAATTCATAAAAAATTA
1 TAAATATTATAAATTCA-AAAAAATTA
702662 TAAA
1 TAAA
702666 AAAATTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 6 0.22
25 15 0.56
26 6 0.22
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAATATTATAAATTCAAAAAAATTA
Found at i:702676 original size:22 final size:25
Alignment explanation
Indices: 702611--702679 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 25
702601 TGTAATATAT
*
702611 TAAATATTATAAATTTA-AAAAAATTA
1 TAAATA-TA-AAATTAATAAAAAATTA
*
702637 TAAATATAAAATTCATAAAAAATTA
1 TAAATATAAAATTAATAAAAAATTA
702662 T-AA-A-AAAATTAATAAAAA
1 TAAATATAAAATTAATAAAAA
702680 TCTTTACCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
22 13 0.32
23 1 0.03
24 8 0.20
25 12 0.30
26 6 0.15
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (25 bp):
TAAATATAAAATTAATAAAAAATTA
Found at i:711126 original size:100 final size:100
Alignment explanation
Indices: 710953--711150 Score: 378
Period size: 100 Copynumber: 2.0 Consensus size: 100
710943 TAGTTGCTAG
*
710953 ATCTATGAGTTGATGGTCAATAGCATGAATCGTATAGACCAAAGCAGAGTTTAGGTCGTGTTGAT
1 ATCTATGAGTTGATGGTCAATAGCATGAATCGTATAGACCAAAGCAGAGTTTAGGTAGTGTTGAT
711018 CCTGATAAGTTCCATTTTCTAGCAGTTTTTTCTAA
66 CCTGATAAGTTCCATTTTCTAGCAGTTTTTTCTAA
*
711053 ATCTATGAGTTGATGGTCAATAGCATGAATCGTTTAGACCAAAGCAGAGTTTAGGTAGTGTTGAT
1 ATCTATGAGTTGATGGTCAATAGCATGAATCGTATAGACCAAAGCAGAGTTTAGGTAGTGTTGAT
711118 CCTGATAAGTTCCATTTTCTAGCAGTTTTTTCT
66 CCTGATAAGTTCCATTTTCTAGCAGTTTTTTCT
711151 CGTCTTTTTT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (100 bp):
ATCTATGAGTTGATGGTCAATAGCATGAATCGTATAGACCAAAGCAGAGTTTAGGTAGTGTTGAT
CCTGATAAGTTCCATTTTCTAGCAGTTTTTTCTAA
Found at i:723670 original size:2 final size:2
Alignment explanation
Indices: 723663--723698 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
723653 AGATTAAACA
723663 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
723699 GGGAGGAATC
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):
AT
Found at i:726509 original size:118 final size:118
Alignment explanation
Indices: 726349--726579 Score: 390
Period size: 118 Copynumber: 2.0 Consensus size: 118
726339 TATTTCCGGT
726349 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
* *
726414 CCTACCCCGGTTACTCAGTCAGTCACGATTTGAGCCATACTCATAACCTCGGC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
****
726467 TAGCGGAGTTTTACTTGTCACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
**
726532 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCTGTACTCATAACC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACC
726580 ATGGAAAACA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 105 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (118 bp):
TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
Found at i:728569 original size:60 final size:60
Alignment explanation
Indices: 728476--728595 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 60
728466 ATTGCCACTT
* * *
728476 TCTCCTACGGAATTCATCCGTCCTCCATACCTAATTTCATGTAATTATTCACATAAACTC
1 TCTCCTACGGAACTCATCCATCCTCCATACCTAATTTCATGTAATCATTCACATAAACTC
* *
728536 TCTCCTACTGAACTCATCTATCCTCCATACCTAATTTCATGTAATCATTCACATAAACTC
1 TCTCCTACGGAACTCATCCATCCTCCATACCTAATTTCATGTAATCATTCACATAAACTC
728596 AGTATATCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.29, C:0.31, G:0.05, T:0.35
Consensus pattern (60 bp):
TCTCCTACGGAACTCATCCATCCTCCATACCTAATTTCATGTAATCATTCACATAAACTC
Found at i:728823 original size:26 final size:26
Alignment explanation
Indices: 728793--728911 Score: 89
Period size: 28 Copynumber: 4.5 Consensus size: 26
728783 CAGGGTCACA
728793 CATACAGGGTTCGCATGTAGGGTTCG
1 CATACAGGGTTCGCATGTAGGGTTCG
*** *
728819 CATACA-AAATCACATG-AGGGTTCG
1 CATACAGGGTTCGCATGTAGGGTTCG
* * * *
728843 CACATAGGGTTCACATATAGGGTTCG
1 CATACAGGGTTCGCATGTAGGGTTCG
* * *
728869 AACATACAGAGTTGGCATGTAGGGTTTGCA
1 --CATACAGGGTTCGCATGTAGGG-TT-CG
728899 CATACAGGGTTCG
1 CATACAGGGTTCG
728912 GATACTAAGT
Statistics
Matches: 68, Mismatches: 19, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
24 12 0.18
25 12 0.18
26 14 0.21
28 27 0.40
29 2 0.03
30 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (26 bp):
CATACAGGGTTCGCATGTAGGGTTCG
Found at i:728853 original size:13 final size:13
Alignment explanation
Indices: 728829--728874 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
728819 CATACAAAAT
728829 CACATGAGGGTTCG
1 CACAT-AGGGTTCG
*
728843 CACATAGGGTTCA
1 CACATAGGGTTCG
*
728856 CATATAGGGTTCG
1 CACATAGGGTTCG
*
728869 AACATA
1 CACATA
728875 CAGAGTTGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (13 bp):
CACATAGGGTTCG
Found at i:728994 original size:24 final size:24
Alignment explanation
Indices: 728977--729065 Score: 110
Period size: 24 Copynumber: 3.8 Consensus size: 24
728967 AATCGTATAG
728977 GGGTTCGCATACTAAATCCATA--A
1 GGGTTCGCATACTAAAT-CATATTA
729000 GGGTTCGCATACTAAATCATATTA
1 GGGTTCGCATACTAAATCATATTA
** * * *
729024 AAGTTTGCATATTAAAACATATTA
1 GGGTTCGCATACTAAATCATATTA
729048 GGGTTCGCATACTAAATC
1 GGGTTCGCATACTAAATC
729066 CATAAGGGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
22 4 0.07
23 17 0.31
24 33 0.61
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (24 bp):
GGGTTCGCATACTAAATCATATTA
Found at i:729007 original size:23 final size:24
Alignment explanation
Indices: 728972--729080 Score: 109
Period size: 24 Copynumber: 4.6 Consensus size: 24
728962 AACATAATCG
728972 TATAGGGGTTCGCATACTAAATCCA
1 TATA-GGGTTCGCATACTAAATCCA
728997 TA-AGGGTTCGCATACTAAAT-CA
1 TATAGGGTTCGCATACTAAATCCA
** * * *
729019 TATTAAAGTTTGCATATTAAA-ACA
1 TA-TAGGGTTCGCATACTAAATCCA
729043 TATTAGGGTTCGCATACTAAATCCA
1 TA-TAGGGTTCGCATACTAAATCCA
*
729068 TA-AGGGTTTGCAT
1 TATAGGGTTCGCAT
729081 GAGGGTTCGC
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
22 4 0.06
23 27 0.39
24 33 0.47
25 6 0.09
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (24 bp):
TATAGGGTTCGCATACTAAATCCA
Found at i:730675 original size:15 final size:15
Alignment explanation
Indices: 730657--730713 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
730647 ATATTGAAAG
*
730657 TATATATATACATAA
1 TATACATATACATAA
* *
730672 TATATATATATATAA
1 TATACATATACATAA
730687 -A-ACATATACGAT-A
1 TATACATATAC-ATAA
730700 TATACATATACATA
1 TATACATATACATA
730714 GAAATGATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
13 7 0.20
14 6 0.17
15 22 0.63
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.37
Consensus pattern (15 bp):
TATACATATACATAA
Found at i:730938 original size:2 final size:2
Alignment explanation
Indices: 730931--731035 Score: 57
Period size: 2 Copynumber: 56.0 Consensus size: 2
730921 TACTTCACAA
* * * *
730931 AT AT AT AT AT ACT AA AA AT AT AC AT A- AT A- AT AT AT A- AA AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
730971 AT A- AT AT -T AA AA AC AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
731010 GA- AA AT AT AT AT AT AT A- AT AT A- AT AT
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
731036 TAAAATATTT
Statistics
Matches: 83, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
1 9 0.11
2 71 0.86
3 3 0.04
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (2 bp):
AT
Found at i:730970 original size:21 final size:22
Alignment explanation
Indices: 730931--731031 Score: 79
Period size: 21 Copynumber: 4.6 Consensus size: 22
730921 TACTTCACAA
730931 ATATATAT-ATACTA-AAAATAT
1 ATATATATAATA-TATAAAATAT
*
730952 ACATA-ATAATATATAAAATAT
1 ATATATATAATATATAAAATAT
* * *
730973 A-ATAT-TAA-AAACATATATAT
1 ATATATATAATATATA-AAATAT
730993 ATATATATATATAATATGAAAATAT
1 ATATATATA-AT-ATAT-AAAATAT
731018 ATATATATAATATA
1 ATATATATAATATA
731032 ATATTAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
19 3 0.05
20 16 0.25
21 19 0.30
22 2 0.03
23 4 0.06
24 2 0.03
25 16 0.25
26 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (22 bp):
ATATATATAATATATAAAATAT
Found at i:730987 original size:31 final size:30
Alignment explanation
Indices: 730952--731040 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 30
730942 CTAAAAATAT
730952 ACATAATAATATATAAAATATAATATTAAAA
1 ACAT-ATAATATATAAAATATAATATTAAAA
* *
730983 ACATATATATATATATATATATAATA-T-GAA
1 ACATATA-ATATATA-AAATATAATATTAAAA
*
731013 A-ATAT-ATATATATAATATAATATTAAAA
1 ACATATAATATATAAAATATAATATTAAAA
731041 TATTTACAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
26 8 0.16
27 8 0.16
28 2 0.04
29 4 0.08
30 6 0.12
31 12 0.24
32 9 0.18
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (30 bp):
ACATATAATATATAAAATATAATATTAAAA
Done.