Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 132 of 141
Found at i:39642967 original size:27 final size:26
Alignment explanation
Indices: 39642883--39642969 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 26
39642873 CTGACCGATT
* * *
39642883 TACCCCCACAAGGTAACATGACTGAA
1 TACCCCCACAGGGTAAAATGACTGTA
* **
39642909 TTACCCCCACAGGATAAAATGAAC-AAA
1 -TACCCCCACAGGGTAAAATG-ACTGTA
39642936 TTACCCCCACAGGGTAAAATGACTGTTA
1 -TACCCCCACAGGGTAAAATGACTG-TA
39642964 TACCCC
1 TACCCC
39642970 TAGGAGATGA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.04
27 45 0.90
28 3 0.06
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.18
Consensus pattern (26 bp):
TACCCCCACAGGGTAAAATGACTGTA
Found at i:39644519 original size:24 final size:24
Alignment explanation
Indices: 39644478--39644546 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
39644468 CAAATGAAAA
*
39644478 AATAATAATATAGT-ATAACTTTTA-
1 AATAATAATACA-TAATAA-TTTTAG
*
39644502 AGTAATAATACATAATAATTTTAG
1 AATAATAATACATAATAATTTTAG
* *
39644526 AATAATAATACACAATGATTT
1 AATAATAATACATAATAATTT
39644547 CGAAAATATG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 6 0.16
24 32 0.84
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
AATAATAATACATAATAATTTTAG
Found at i:39647830 original size:6 final size:6
Alignment explanation
Indices: 39647819--39647856 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
39647809 AAGCATGTTA
39647819 TATCTG TATCTG TATCTG TATCTG TATTCTG TATCTG T
1 TATCTG TATCTG TATCTG TATCTG TA-TCTG TATCTG T
39647857 TTTTGGGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (6 bp):
TATCTG
Found at i:39648077 original size:21 final size:21
Alignment explanation
Indices: 39648053--39648093 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39648043 ATGGTAGGAT
39648053 TCTGTATATT-TGATCTGCATA
1 TCTGTA-ATTGTGATCTGCATA
*
39648074 TCTGTAATTGTTATCTGCAT
1 TCTGTAATTGTGATCTGCAT
39648094 CTAAAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.49
Consensus pattern (21 bp):
TCTGTAATTGTGATCTGCATA
Found at i:39651538 original size:193 final size:193
Alignment explanation
Indices: 39651223--39651708 Score: 532
Period size: 195 Copynumber: 2.5 Consensus size: 193
39651213 ATGTCGTTTT
* * * * *
39651223 TAATATTGCACGTGTTTTGCAAAGAACAATCTTATAATTTATGTAATTTATGGGGTTCAAATATA
1 TAATATTACACGTGTTTTGCAAAGATCAATATTATAATTTATTTAATTTAT-GGATTCAAATATA
* * * ** * *
39651288 AATTATTGT-GTTCATTCATTCATATGCAATTCTTTACGTTACACGTACTTGTGAAGATTGATCA
65 AATTATTGTCG-TCATTCATTCATATGTAGTTATCAACATTACACGTACTTGTGAAGATCGATCA
* * * *
39651352 GATAGTGGATTTGA-TTTT-GTGTTAAAATAAAAACTATAGTATTCATTTATTCTTATGCAGTTC
129 GATAATGGATTTGATTTTTAGAGTTAAAATAAAAACCATAGTATTCATTTATTATTATGCAGTT-
39651415 C
193 C
* ** *
39651416 TAATATTACATGTGTTTTGCAAAGATGGATATTATAATTTATTTAATTTACGAGATTCAAATATA
1 TAATATTACACGTGTTTTGCAAAGATCAATATTATAATTTATTTAATTTATG-GATTCAAATATA
* * * **
39651481 AATTATTATCGTCATGT-ATTCATATGTAGTTATCAATATTACTCGTGTTTGTGAAGATCGATCA
65 AATTATTGTCGTCAT-TCATTCATATGTAGTTATCAACATTACACGTACTTGTGAAGATCGATCA
* * * * * * * *
39651545 TATAATTGATTTTATTTTTAGAGTTCAAATACAAACCATCGTCTTCATTTATTATTATGTAGTTC
129 GATAATGGATTTGATTTTTAGAGTTAAAATAAAAACCATAGTATTCATTTATTATTATGCAGTTC
* * *
39651610 TCAATATTACACGTGTTTTGTC-AATATCAATAATATAGTTTATTTAATTTATTGGATTCAAATA
1 T-AATATTACACGTGTTTTG-CAAAGATCAATATTATAATTTATTTAATTTA-TGGATTCAAATA
*
39651674 TAAATTATTGTCGTCATTCATTCATACGTAGTTAT
63 TAAATTATTGTCGTCATTCATTCATATGTAGTTAT
39651709 TTAAATTACA
Statistics
Matches: 242, Mismatches: 42, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
192 1 0.00
193 112 0.46
194 9 0.04
195 118 0.49
196 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.44
Consensus pattern (193 bp):
TAATATTACACGTGTTTTGCAAAGATCAATATTATAATTTATTTAATTTATGGATTCAAATATAA
ATTATTGTCGTCATTCATTCATATGTAGTTATCAACATTACACGTACTTGTGAAGATCGATCAGA
TAATGGATTTGATTTTTAGAGTTAAAATAAAAACCATAGTATTCATTTATTATTATGCAGTTC
Found at i:39651705 original size:98 final size:97
Alignment explanation
Indices: 39651417--39651708 Score: 297
Period size: 97 Copynumber: 3.0 Consensus size: 97
39651407 TGCAGTTCCT
* * * *
39651417 AATATTACATGTGTTTTG-CAAAGATGGATATTATAATTTATTTAATTTA-CGAGATTCAAATAT
1 AATATTACACGTGTTTTGTC-AAGATCGATAATATAATTTATTTAATTTATTG-GATTCAAATAT
*
39651480 AAATTATTATCGTCATGTATTCATATGTAGTTATC
64 AAATTATTGTCGTCAT-TATTCATATGTAGTTATC
* * * * * * *
39651515 AATATTACTCGTG-TTTGTGAAGATCGATCATATAATTGATTTTATTT-TTAGAGTTCAAATACA
1 AATATTACACGTGTTTTGTCAAGATCGATAATATAATTTATTTAATTTATTGGA-TTCAAATATA
** * * *
39651578 AACCATCGTCTTCATTTATT-ATTATGTAGTTCTC
65 AATTATTGTCGTCA-TTATTCA-TATGTAGTTATC
* * *
39651612 AATATTACACGTGTTTTGTCAATATCAATAATATAGTTTATTTAATTTATTGGATTCAAATATAA
1 AATATTACACGTGTTTTGTCAAGATCGATAATATAATTTATTTAATTTATTGGATTCAAATATAA
*
39651677 ATTATTGTCGTCATTCATTCATACGTAGTTAT
66 ATTATTGTCGTCATT-ATTCATATGTAGTTAT
39651709 TTAAATTACA
Statistics
Matches: 152, Mismatches: 33, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
96 3 0.02
97 74 0.49
98 70 0.46
99 5 0.03
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.45
Consensus pattern (97 bp):
AATATTACACGTGTTTTGTCAAGATCGATAATATAATTTATTTAATTTATTGGATTCAAATATAA
ATTATTGTCGTCATTATTCATATGTAGTTATC
Found at i:39651724 original size:98 final size:97
Alignment explanation
Indices: 39651417--39651724 Score: 297
Period size: 98 Copynumber: 3.2 Consensus size: 97
39651407 TGCAGTTCCT
* * *
39651417 AATATTACATGTGTTTTG-CAAAGATGGATATTATAATTTATTTAATTTA-CGAGATTCAAATAT
1 AATATTACATGTGTTTTGTC-AAGATCGATAATATAATTTATTTAATTTATTG-GATTCAAATAT
*
39651480 AAATTATTATCGTCATGTATTCATATGTAGTTATC
64 AAATTATTGTCGTCAT-TATTCATATGTAGTTATC
* * * * * *
39651515 AATATTAC-TCGTG-TTTGTGAAGATCGATCATATAATTGATTTTATTT-TTAGAGTTCAAATAC
1 AATATTACAT-GTGTTTTGTCAAGATCGATAATATAATTTATTTAATTTATTGGA-TTCAAATAT
** * * *
39651577 AAACCATCGTCTTCATTTATT-ATTATGTAGTTCTC
64 AAATTATTGTCGTCA-TTATTCA-TATGTAGTTATC
* * * *
39651612 AATATTACACGTGTTTTGTCAATATCAATAATATAGTTTATTTAATTTATTGGATTCAAATATAA
1 AATATTACATGTGTTTTGTCAAGATCGATAATATAATTTATTTAATTTATTGGATTCAAATATAA
* *
39651677 ATTATTGTCGTCATTCATTCATACGTAGTTATTT
66 ATTATTGTCGTCATT-ATTCATATGTAGTTA-TC
39651711 AA-ATTACATGTGTT
1 AATATTACATGTGTT
39651725 CATGCAAACA
Statistics
Matches: 165, Mismatches: 33, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
96 3 0.02
97 74 0.45
98 80 0.48
99 8 0.05
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (97 bp):
AATATTACATGTGTTTTGTCAAGATCGATAATATAATTTATTTAATTTATTGGATTCAAATATAA
ATTATTGTCGTCATTATTCATATGTAGTTATC
Found at i:39652656 original size:24 final size:23
Alignment explanation
Indices: 39652616--39652661 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
39652606 CAATTATTTG
*
39652616 TAATGTTATTTGGTAACTTTTTT
1 TAATGTTATTTGGTAACATTTTT
**
39652639 TAATAGTTATTTTTTAACATTTT
1 TAAT-GTTATTTGGTAACATTTT
39652662 CTTTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (23 bp):
TAATGTTATTTGGTAACATTTTT
Found at i:39652749 original size:26 final size:26
Alignment explanation
Indices: 39652720--39652769 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
39652710 TGAGTTGTCA
*
39652720 AAAATCACATATATGGTTATGAATCT
1 AAAATCAAATATATGGTTATGAATCT
*
39652746 AAAATCAAATATTTGGTTATGAAT
1 AAAATCAAATATATGGTTATGAAT
39652770 ATGTCCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (26 bp):
AAAATCAAATATATGGTTATGAATCT
Found at i:39656893 original size:18 final size:18
Alignment explanation
Indices: 39656870--39656904 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39656860 TTAACTTTCA
*
39656870 TCAAATCAACCCTAAAAT
1 TCAAATCAACACTAAAAT
39656888 TCAAATCAACACTAAAA
1 TCAAATCAACACTAAAA
39656905 AGTTAGCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (18 bp):
TCAAATCAACACTAAAAT
Found at i:39661164 original size:27 final size:27
Alignment explanation
Indices: 39661134--39661463 Score: 354
Period size: 27 Copynumber: 12.2 Consensus size: 27
39661124 AGAGGTTAGT
* **
39661134 AAATGACAGAAATACCCTTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39661161 AAATGACTGAAATACCCCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39661188 ACATGACCGAAATACACTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
39661215 AAATGACCGAAATACCCCCGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
** **
39661242 AAATGATTGAAATACCCTAATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39661269 AAATGACCGAAATACCCTCGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * ** *
39661296 GAATAACTGAAATACCATCATAGGGTT
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39661323 GAATGATCAAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39661350 GAATGACCGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39661377 GAATGACCGAAATACCCCCATATGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39661404 GAATGACCGTAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39661431 AAATGATCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
39661458 AAATGA
1 AAATGA
39661464 ATGTTATACC
Statistics
Matches: 254, Mismatches: 49, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 254 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:39661218 original size:54 final size:54
Alignment explanation
Indices: 39661135--39661463 Score: 390
Period size: 54 Copynumber: 6.1 Consensus size: 54
39661125 GAGGTTAGTA
* * * *
39661135 AATGACAGAAATACCCTTATAGGGTAAAATGACTGAAATACCCCCATAGGATA-
1 AATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAG
* * *
39661188 ACATGACCGAAATACACTCATAGGGTAAAATGACCGAAATACCCCCGTAGGGTAA
1 A-ATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAG
** * * *
39661243 AATGATTGAAATACCCTAATAGGGTAAAATGACCGAAATACCCTCGTAGGGTAG
1 AATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAG
* * * ** * *
39661297 AATAACTGAAATACCATCATAGGGTTGAATGATCAAAATACCCCCATAGGGTAG
1 AATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAG
* * * * *
39661351 AATGACCGAAATACCCCCATAAGGTAGAATGACCGAAATACCCCCATATGATAG
1 AATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAG
* * * *
39661405 AATGACCGTAATACCCTCATAGGGTAAAATGATCGAAATACCCCTATAGGGTAA
1 AATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAG
39661459 AATGA
1 AATGA
39661464 ATGTTATACC
Statistics
Matches: 233, Mismatches: 41, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
53 1 0.00
54 231 0.99
55 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (54 bp):
AATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAG
Found at i:39661472 original size:27 final size:27
Alignment explanation
Indices: 39661418--39661498 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
39661408 GACCGTAATA
**
39661418 CCCTCATAGGGTAAAATG-ATCGAAATAC
1 CCCT-ATAGGGTAAAATGAAT-GTTATAC
39661446 CCCTATAGGGTAAAATGAATGTTATAC
1 CCCTATAGGGTAAAATGAATGTTATAC
*
39661473 CCC--TAGGAGATAAAATGACTGTTATA
1 CCCTATAGG-G-TAAAATGAATGTTATA
39661499 GCCTTATGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
25 4 0.09
26 1 0.02
27 36 0.77
28 6 0.13
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (27 bp):
CCCTATAGGGTAAAATGAATGTTATAC
Found at i:39664954 original size:27 final size:27
Alignment explanation
Indices: 39664915--39665425 Score: 439
Period size: 27 Copynumber: 19.1 Consensus size: 27
39664905 AAAGGTCAAT
* * *
39664915 AAATGCCCGAAATACCCCCATAGAGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
39664942 AAATGATCAAAATACCCCCATATGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* * * **
39664969 AACTGACCGAGAT-CCCCTGTAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
39664995 AAATGACCAAAATACCCCTATAGGATA
1 AAATGACCAAAATACCCCCATAGGGTA
** *
39665022 AAATGACTGAAATACCCTCGA-AGGGTA
1 AAATGACCAAAATACCC-CCATAGGGTA
* *
39665049 AAATGACCAAAATA-CCCCGTAAGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* * *
39665075 AAATGA-TAGACATACCCCTATAGGGTA
1 AAATGACCA-AAATACCCCCATAGGGTA
* * *
39665102 AATTGATCGAAATA-CCCCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* ** *
39665128 GAATGACTGAAATA-CCCTATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* * *
39665154 GAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
39665181 GAATGA-CAGAAATACCCCCATAGCGTA
1 AAATGACCA-AAATACCCCCATAGGGTA
* * *
39665208 AAATGA-TAGAAACACCCTCATAGGGTA
1 AAATGACCA-AAATACCCCCATAGGGTA
* * *
39665235 GAATGACCAAAATA-CCCCATAAGATA
1 AAATGACCAAAATACCCCCATAGGGTA
* * * * *
39665261 GAATGATCGAAATACCCTCATAAGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
*
39665288 AAATGACCAAAATACCCCTATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* * **
39665315 AAATGACGAAAATA-ACCCATATAGTA
1 AAATGACCAAAATACCCCCATAGGGTA
*
39665341 AAATGACCAAAATACCCCCATAAGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* * *
39665368 GAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
*
39665395 AAATGACAAAAATACCCCCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
39665422 AAAT
1 AAAT
39665426 ACATCGATTT
Statistics
Matches: 388, Mismatches: 85, Indels: 22
0.78 0.17 0.04
Matches are distributed among these distances:
25 2 0.01
26 125 0.32
27 258 0.66
28 3 0.01
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATGACCAAAATACCCCCATAGGGTA
Found at i:39665049 original size:80 final size:79
Alignment explanation
Indices: 39664915--39665425 Score: 425
Period size: 80 Copynumber: 6.4 Consensus size: 79
39664905 AAAGGTCAAT
* * * * * * *
39664915 AAATGCCCGAAATACCCCCATAGAGTAAAATGA-TCAAAATACCCCCATATGGTAAACTGACCGA
1 AAATGACCAAAATACCCCTATAGGGTAAAATGACT-GAAATA-CCCCATAGGGTAAAATGACCGA
* *
39664979 GATCCCCTGTAGGGTA
64 AATCCCCTATAGGGTA
* *
39664995 AAATGACCAAAATACCCCTATAGGATAAAATGACTGAAATACCCTCGA-AGGGTAAAATGACCAA
1 AAATGACCAAAATACCCCTATAGGGTAAAATGACTGAAATACCC-C-ATAGGGTAAAATGACCGA
39665059 AATACCCCGTA-A-GGTA
64 AAT-CCCC-TATAGGGTA
* * * * *
39665075 AAATGA-TAGACATACCCCTATAGGGTAAATTGA-TCGAAATACCCCATAGGGTAGAATGACTGA
1 AAATGACCA-AAATACCCCTATAGGGTAAAATGACT-GAAATACCCCATAGGGTAAAATGACCGA
*
39665138 AATACCCTATAGGGTA
64 AATCCCCTATAGGGTA
* * * * * **
39665154 GAATGACCGAAATA-CCCTCATAGGGTAGAATGACAGAAATACCCCCATAGCGTAAAATGATAGA
1 AAATGACCAAAATACCCCT-ATAGGGTAAAATGACTGAAATA-CCCCATAGGGTAAAATGACCGA
39665218 AA-CACCCTCATAGGGTA
64 AATC-CCCT-ATAGGGTA
* * * * * *
39665235 GAATGACCAAAATACCCC-ATAAGATAGAATGA-TCGAAATACCCTCATAAGGTAAAATGACCAA
1 AAATGACCAAAATACCCCTATAGGGTAAAATGACT-GAAATACCC-CATAGGGTAAAATGACCGA
39665298 AATACCCCTATAGGGTA
64 AAT-CCCCTATAGGGTA
* * ** * *
39665315 AAATGACGAAAATAACCCATATA--GTAAAATGACCAAAATACCCCCATAAGGTAGAATGACCGA
1 AAATGACCAAAAT-ACCCCTATAGGGTAAAATGACTGAAATA-CCCCATAGGGTAAAATGACCGA
*
39665378 AATACCCTCATAGGGTA
64 AATCCCCT-ATAGGGTA
* *
39665395 AAATGACAAAAATACCCCCATAGGGTAAAAT
1 AAATGACCAAAATACCCCTATAGGGTAAAAT
39665426 ACATCGATTT
Statistics
Matches: 350, Mismatches: 53, Indels: 55
0.76 0.12 0.12
Matches are distributed among these distances:
77 2 0.01
78 9 0.03
79 67 0.19
80 218 0.62
81 46 0.13
82 8 0.02
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.19
Consensus pattern (79 bp):
AAATGACCAAAATACCCCTATAGGGTAAAATGACTGAAATACCCCATAGGGTAAAATGACCGAAA
TCCCCTATAGGGTA
Found at i:39665100 original size:53 final size:54
Alignment explanation
Indices: 39664915--39665425 Score: 426
Period size: 53 Copynumber: 9.6 Consensus size: 54
39664905 AAAGGTCAAT
* * * *
39664915 AAATG-CCCGAAATACCCCCATAGAGTAAAATGATCAAAATACCCCCATATGGTA
1 AAATGACCAGAAATACCCCCATAGGGTAAAATGACCAAAATA-CCCCATAAGGTA
* * **
39664969 AACTGACC-GAGAT-CCCCTGTAGGGTAAAATGACCAAAATACCCC-TATAGGATA
1 AAATGACCAGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCATA-AGG-TA
* * *
39665022 AAATGA-CTGAAATACCCTCGA-AGGGTAAAATGACCAAAATACCCCGTAAGGTA
1 AAATGACCAGAAATACCC-CCATAGGGTAAAATGACCAAAATACCCCATAAGGTA
* * * * * * *
39665075 AAATGA-TAGACATACCCCTATAGGGTAAATTGATCGAAATACCCCATAGGGTA
1 AAATGACCAGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCATAAGGTA
* * * * * *
39665128 GAATGA-CTGAAATA-CCCTATAGGGTAGAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCAGAAATACCCCCATAGGGTAAAATGACCAAAATACCC-CATAAGGTA
* * * * *
39665181 GAATGA-CAGAAATACCCCCATAGCGTAAAATGA-TAGAAACACCCTCATAGGGTA
1 AAATGACCAGAAATACCCCCATAGGGTAAAATGACCA-AAATACCC-CATAAGGTA
* * * * * *
39665235 GAATGACCA-AAATA-CCCCATAAGATAGAATGATCGAAATACCCTCATAAGGTA
1 AAATGACCAGAAATACCCCCATAGGGTAAAATGACCAAAATACCC-CATAAGGTA
* * *
39665288 AAATGACCA-AAATACCCCTATAGGGTAAAATGACGAAAATAACCCATATA-GTA
1 AAATGACCAGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCATA-AGGTA
* * * *
39665341 AAATGACCA-AAATACCCCCATAAGGTAGAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCAGAAATACCCCCATAGGGTAAAATGACCAAAATACCC-CATAAGGTA
*
39665395 AAATGA-CAAAAATACCCCCATAGGGTAAAAT
1 AAATGACCAGAAATACCCCCATAGGGTAAAAT
39665426 ACATCGATTT
Statistics
Matches: 379, Mismatches: 60, Indels: 36
0.80 0.13 0.08
Matches are distributed among these distances:
51 2 0.01
52 35 0.09
53 199 0.53
54 136 0.36
55 7 0.02
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.19
Consensus pattern (54 bp):
AAATGACCAGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCATAAGGTA
Found at i:39667434 original size:97 final size:97
Alignment explanation
Indices: 39667333--39667545 Score: 223
Period size: 97 Copynumber: 2.2 Consensus size: 97
39667323 ATCTACAAAT
* * * *
39667333 TTCAAATATAAATTATTGTCGTCATTTATTCATATGTAGTTCTAAATATTACACATGTTTGTG-A
1 TTCAAATAAAAATTATTATCGTCATTTATTCATATGCAGTTCTAAATATCACACATGTTT-TGAA
*
39667397 AGATCAATCGTATAATTGATTTAATTTTTA-GA
65 AGATCAATCGTATAATTGATTTAATTTATAGGA
* ** * * * * * *
39667429 GTTCAAATACAAACCATCATCTTCATTTATTCTTCTGCAGTTCTTAATATCACACGTGTTTTGCA
1 -TTCAAATAAAAATTATTATCGTCATTTATTCATATGCAGTTCTAAATATCACACATGTTTTG-A
* * * *
39667494 AATATCAATCTTATAGTTTATTTAATTTATAGGA
64 AAGATCAATCGTATAATTGATTTAATTTATAGGA
39667528 TTCAAATAAAAATTATTA
1 TTCAAATAAAAATTATTA
39667546 ACATCATGAA
Statistics
Matches: 92, Mismatches: 21, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
96 2 0.02
97 48 0.52
98 40 0.43
99 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (97 bp):
TTCAAATAAAAATTATTATCGTCATTTATTCATATGCAGTTCTAAATATCACACATGTTTTGAAA
GATCAATCGTATAATTGATTTAATTTATAGGA
Found at i:39669266 original size:24 final size:23
Alignment explanation
Indices: 39669235--39669377 Score: 83
Period size: 26 Copynumber: 5.9 Consensus size: 23
39669225 AAAACAAAAT
* * *
39669235 AATATATAGAACAATTTGAGGTA
1 AATATATAAAACAATTTAAAGTA
39669258 AATAGTATAAAACAATTTAAAGTA
1 AATA-TATAAAACAATTTAAAGTA
* *
39669282 AATAATACGTAAAACAAATTAAAATA
1 AAT-ATA--TAAAACAATTTAAAGTA
* * *
39669308 AATAATATACCAAGCAATTCAAAATA
1 AAT-ATATA--AAACAATTTAAAGTA
* *
39669334 AATAACATATAAGACAATTTAAAAT-
1 AAT---ATATAAAACAATTTAAAGTA
*
39669359 AATATATAAAA-AGTTTAAA
1 AATATATAAAACAATTTAAA
39669378 ACAAATAATA
Statistics
Matches: 98, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
21 7 0.07
22 7 0.07
23 4 0.04
24 23 0.23
25 4 0.04
26 48 0.49
28 5 0.05
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (23 bp):
AATATATAAAACAATTTAAAGTA
Found at i:39669383 original size:25 final size:24
Alignment explanation
Indices: 39669354--39669438 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 24
39669344 AAGACAATTT
*
39669354 AAAATAATATATAAAAAGTTTAAA
1 AAAATAATATAAAAAAAGTTTAAA
39669378 ACAAATAATATGTAAAAAGAAGTTTCAAA
1 A-AAATAATA--TAAAAA-AAGTTT-AAA
* *
39669407 TAAATAATATACAAAACAGTTTAAA
1 AAAATAATATA-AAAAAAGTTTAAA
39669432 AAAATAA
1 AAAATAA
39669439 ATGATATGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
24 1 0.02
25 17 0.33
26 7 0.14
27 9 0.18
28 14 0.27
29 3 0.06
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.26
Consensus pattern (24 bp):
AAAATAATATAAAAAAAGTTTAAA
Found at i:39669422 original size:28 final size:28
Alignment explanation
Indices: 39669369--39669438 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
39669359 AATATATAAA
**
39669369 AAGTTTAAAACAAATAATATGTAAAAAG
1 AAGTTTAAAACAAATAATATACAAAAAG
* *
39669397 AAGTTTCAAATAAATAATATAC-AAAA-
1 AAGTTTAAAACAAATAATATACAAAAAG
*
39669423 CAGTTTAAAA-AAATAA
1 AAGTTTAAAACAAATAA
39669439 ATGATATGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
25 6 0.17
26 8 0.22
27 4 0.11
28 18 0.50
ACGTcount: A:0.61, C:0.06, G:0.07, T:0.26
Consensus pattern (28 bp):
AAGTTTAAAACAAATAATATACAAAAAG
Found at i:39669475 original size:25 final size:26
Alignment explanation
Indices: 39669258--39669507 Score: 136
Period size: 26 Copynumber: 9.4 Consensus size: 26
39669248 ATTTGAGGTA
* *
39669258 AATAGTATAAAACAATTTAAAGTAAAT
1 AATA-TATAAAACAATTCAAAATAAAT
**
39669285 AATACGTAAAACAAATT-AAAATAAAT
1 AATATATAAAAC-AATTCAAAATAAAT
** *
39669311 AATATACCAAGCAATTCAAAATAAAT
1 AATATATAAAACAATTCAAAATAAAT
* * *
39669337 AACATATAAGACAATT---TA-AAAT
1 AATATATAAAACAATTCAAAATAAAT
* * *
39669359 AATATATAAAA-AGTTTAAAACAAAT
1 AATATATAAAACAATTCAAAATAAAT
* *
39669384 AATATGTAAAAAGAAGTTTC-AAATAAAT
1 AATATAT-AAAACAA--TTCAAAATAAAT
* * *
39669412 AATATACAAAACAGTTTAAAAAAATAAAT
1 AATATATAAAACA-ATT--CAAAATAAAT
*
39669441 GATATGTATAAAAACAATTCAAAATAAAT
1 -A-ATATAT-AAAACAATTCAAAATAAAT
** * *
39669470 AATATATATGACAGTTTAAAAATAAAT
1 AATATATAAAACA-ATTCAAAATAAAT
39669497 AATATATAAAA
1 AATATATAAAA
39669508 AAATGGATAA
Statistics
Matches: 167, Mismatches: 38, Indels: 36
0.69 0.16 0.15
Matches are distributed among these distances:
21 3 0.02
22 13 0.08
23 1 0.01
24 1 0.01
25 14 0.08
26 51 0.31
27 39 0.23
28 13 0.08
29 19 0.11
30 1 0.01
31 6 0.04
32 6 0.04
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (26 bp):
AATATATAAAACAATTCAAAATAAAT
Found at i:39669479 original size:33 final size:33
Alignment explanation
Indices: 39669414--39669479 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
39669404 AAATAAATAA
* *
39669414 TATACAAAACAGTTTAAAAAAATAAATGATATG
1 TATACAAAACAATTCAAAAAAATAAATGATATG
39669447 TATA-AAAACAATTCAAAATAAATAATAT-ATATG
1 TATACAAAACAATTCAAAA-AAATAA-ATGATATG
39669480 ACAGTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 12 0.41
33 15 0.52
34 2 0.07
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (33 bp):
TATACAAAACAATTCAAAAAAATAAATGATATG
Found at i:39669588 original size:25 final size:24
Alignment explanation
Indices: 39669560--39669648 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 24
39669550 GGAAAACTTG
39669560 AAATAAATAATAATAAAACAATTTA
1 AAATAAATAATAATAAAA-AATTTA
39669585 AAATAAATAATACATAAGAAAAAGGTTTA
1 AAATAAATAATA-AT-A-AAAAA--TTTA
*
39669614 AAATAAATAAATGAATAAAAAATTCAA
1 AAATAAAT-AAT-AATAAAAAATT-TA
39669641 AAATAAAT
1 AAATAAAT
39669649 TGAAATCAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
25 12 0.22
26 4 0.07
27 12 0.22
28 8 0.15
29 13 0.24
30 5 0.09
31 1 0.02
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.25
Consensus pattern (24 bp):
AAATAAATAATAATAAAAAATTTA
Found at i:39670509 original size:17 final size:16
Alignment explanation
Indices: 39670469--39670519 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
39670459 GAGACGCAAG
* * *
39670469 AAAGAAAAAAATAATA
1 AAAGAAAAGAGTAAAA
39670485 AAAGAAAAGAGTAGAAA
1 AAAGAAAAGAGTA-AAA
*
39670502 AAATAAAAGAGTAAAA
1 AAAGAAAAGAGTAAAA
39670518 AA
1 AA
39670520 GACACCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 16 0.53
17 14 0.47
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (16 bp):
AAAGAAAAGAGTAAAA
Found at i:39670941 original size:18 final size:18
Alignment explanation
Indices: 39670913--39670957 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
39670903 CATTTGTTTC
*
39670913 CAAAACATTATTC-ATTT
1 CAAAACGTTATTCAATTT
*
39670930 ACAAATCGTTATTCAATTT
1 -CAAAACGTTATTCAATTT
39670949 CAAAACGTT
1 CAAAACGTT
39670958 TTCTTATTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (18 bp):
CAAAACGTTATTCAATTT
Found at i:39672455 original size:17 final size:16
Alignment explanation
Indices: 39672415--39672465 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
39672405 GAGACGCAAG
* * *
39672415 AAAGAAAAAAATAATA
1 AAAGAAAAGAGTAAAA
39672431 AAAGAAAAGAGTAGAAA
1 AAAGAAAAGAGTA-AAA
*
39672448 AAATAAAAGAGTAAAA
1 AAAGAAAAGAGTAAAA
39672464 AA
1 AA
39672466 GACACCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 16 0.53
17 14 0.47
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (16 bp):
AAAGAAAAGAGTAAAA
Found at i:39672887 original size:18 final size:18
Alignment explanation
Indices: 39672859--39672903 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
39672849 CATTTGTTTC
*
39672859 CAAAACATTATTC-ATTT
1 CAAAACGTTATTCAATTT
*
39672876 ACAAATCGTTATTCAATTT
1 -CAAAACGTTATTCAATTT
39672895 CAAAACGTT
1 CAAAACGTT
39672904 TTCTTATTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (18 bp):
CAAAACGTTATTCAATTT
Found at i:39673875 original size:17 final size:18
Alignment explanation
Indices: 39673844--39673877 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
39673834 CATGATGTTT
39673844 GCCCGTGTGGGCCCACAC
1 GCCCGTGTGGGCCCACAC
39673862 GCCCGTGT-GGCCCACA
1 GCCCGTGTGGGCCCACA
39673878 TGACCCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.12, C:0.44, G:0.32, T:0.12
Consensus pattern (18 bp):
GCCCGTGTGGGCCCACAC
Found at i:39679178 original size:25 final size:25
Alignment explanation
Indices: 39679150--39679197 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39679140 TATAGTCTAT
* *
39679150 CTATAGTAGTCTCAGTATATACTGC
1 CTATAGCAGTCTCAGGATATACTGC
*
39679175 CTATAGCAGTTTCAGGATATACT
1 CTATAGCAGTCTCAGGATATACT
39679198 ATCAAAGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (25 bp):
CTATAGCAGTCTCAGGATATACTGC
Found at i:39679517 original size:19 final size:18
Alignment explanation
Indices: 39679495--39679550 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
39679485 TCTTATGTTA
39679495 ATTT-CAAATCGTGTCATTC
1 ATTTACAAATCGT-T-ATTC
* * *
39679514 ATTTCCAAAACATTATTC
1 ATTTACAAATCGTTATTC
39679532 ATTTACAAATCGTTATTC
1 ATTTACAAATCGTTATTC
39679550 A
1 A
39679551 ATTTCAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 20 0.65
19 5 0.16
20 6 0.19
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (18 bp):
ATTTACAAATCGTTATTC
Found at i:39679560 original size:19 final size:18
Alignment explanation
Indices: 39679495--39679560 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
39679485 TCTTATGTTA
39679495 ATTTC-AAATCGTGTCATTC
1 ATTTCAAAATCGT-T-ATTC
*
39679514 ATTTCCAAAA-CATTATTC
1 ATTT-CAAAATCGTTATTC
39679532 ATTT-ACAAATCGTTATTC
1 ATTTCA-AAATCGTTATTC
39679550 AATTTCAAAAT
1 -ATTTCAAAAT
39679561 GTTTTCTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
16 1 0.03
17 3 0.08
18 15 0.38
19 13 0.33
20 4 0.10
21 3 0.08
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (18 bp):
ATTTCAAAATCGTTATTC
Found at i:39682695 original size:29 final size:29
Alignment explanation
Indices: 39682611--39682699 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 29
39682601 GACTGAATCA
* * *
39682611 AAATTAAAGTTTCATGTTTACATATGAACC
1 AAATTAAAGTTTCATGTATAAAT-TGCACC
* *
39682641 ACAATCAAAGTTTCATATATATAATTGCACC
1 A-AATTAAAGTTTCATGTATA-AATTGCACC
39682672 AAATTAAAG-TTCATGTATCAAATTGCAC
1 AAATTAAAGTTTCATGTAT-AAATTGCAC
39682700 ATTAAAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
29 16 0.33
30 9 0.18
31 22 0.45
32 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.34
Consensus pattern (29 bp):
AAATTAAAGTTTCATGTATAAATTGCACC
Found at i:39693382 original size:35 final size:35
Alignment explanation
Indices: 39693336--39693405 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
39693326 ACCTCTAGAG
39693336 TTAGACCGTATCCATGATGTGTTTCACGTCTCGAT
1 TTAGACCGTATCCATGATGTGTTTCACGTCTCGAT
39693371 TTAGACCGTATCCATGATGTGTTTCACGTCTCGAT
1 TTAGACCGTATCCATGATGTGTTTCACGTCTCGAT
39693406 GTTGAGGCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (35 bp):
TTAGACCGTATCCATGATGTGTTTCACGTCTCGAT
Found at i:39704080 original size:50 final size:51
Alignment explanation
Indices: 39703955--39704196 Score: 179
Period size: 50 Copynumber: 4.7 Consensus size: 51
39703945 AATAATAACA
* * ** *
39703955 TGCCAAAGCCATGTCCCAGACATTGTCTTACATGGGATGTT-TCTTATAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTCTCATAT-CGG
* * * * *
39704004 TGCCGATGTCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTCTCATATCGG
* ** * * * *
39704054 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGA-CATCGCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTCTCATATCGG
* * * * * *
39704104 TGCCAACGCAATGTCCCAGACATGGTCTTATATGGGACCTATCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-TC-TCATATC---GG
*
39704160 TGCCAATGCCATGTCCCAGACATGGTCTTACACGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
39704197 TCTCATCACC
Statistics
Matches: 151, Mismatches: 33, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
48 4 0.03
49 36 0.24
50 70 0.46
51 1 0.01
52 2 0.01
53 5 0.03
56 33 0.22
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.27
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTCTCATATCGG
Found at i:39718630 original size:14 final size:15
Alignment explanation
Indices: 39718597--39718631 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39718587 ATTAATTAAT
*
39718597 TTTTTTAATGTTCAA
1 TTTTTTAATATTCAA
*
39718612 TTTTTTAATATTCGA
1 TTTTTTAATATTCAA
39718627 TTTTT
1 TTTTT
39718632 CTTTTGCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (15 bp):
TTTTTTAATATTCAA
Found at i:39723990 original size:130 final size:130
Alignment explanation
Indices: 39723770--39724017 Score: 311
Period size: 130 Copynumber: 1.9 Consensus size: 130
39723760 ATTGTCTTAA
* *
39723770 ATTTTGAAGCAGATAAAGAAGTGTCGATCATCCTTGGGAGACCTTTCTTAGCCACGAGAAGAACA
1 ATTTTGAAGCAGATAAAGAAGTGTCGATCATCCTTAGGAGACCTTTCCTAGCCACGAGAAGAACA
* * * * * * *
39723835 TTAATTGATGTGTAGAAAGGTGAACTCACCATGCGAGTTGAAGACGATCAAGTTCATTATGTTAG
66 TTAATAGATGTGCAAAAAGGAGAACTCACAATGAGAGTTCAAGACGATCAAGTTCATTATGTTAG
* * * * *
39723900 ATTTTGAAGTAGAT-AAGCAAGCT-TCGGTCATCTTTAGGAGACCTTTCCTAGCTACGGGAAGAA
1 ATTTTGAAGCAGATAAAG-AAG-TGTCGATCATCCTTAGGAGACCTTTCCTAGCCACGAGAAGAA
* * *
39723963 CGTTGATAGATGTGCAAAAAGGAGAACTCACAATGAGAGTTCAAGATGATCAAGT
64 CATTAATAGATGTGCAAAAAGGAGAACTCACAATGAGAGTTCAAGACGATCAAGT
39724018 AATGTTTAAT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
129 3 0.03
130 95 0.96
131 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (130 bp):
ATTTTGAAGCAGATAAAGAAGTGTCGATCATCCTTAGGAGACCTTTCCTAGCCACGAGAAGAACA
TTAATAGATGTGCAAAAAGGAGAACTCACAATGAGAGTTCAAGACGATCAAGTTCATTATGTTAG
Found at i:39724920 original size:38 final size:38
Alignment explanation
Indices: 39724869--39724944 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
39724859 CCCCAAAAGA
*
39724869 CCAGCGTAAAATTGGTTTTACTTTCCCATACGGTACAT
1 CCAGCGTAAAATTGCTTTTACTTTCCCATACGGTACAT
39724907 CCAGCGTAAAATTGCTTTTACTTTCCCATACGGTACAT
1 CCAGCGTAAAATTGCTTTTACTTTCCCATACGGTACAT
39724945 TTGCTTTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.34
Consensus pattern (38 bp):
CCAGCGTAAAATTGCTTTTACTTTCCCATACGGTACAT
Found at i:39727276 original size:18 final size:17
Alignment explanation
Indices: 39727233--39727279 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
39727223 TAAATTTGAA
*
39727233 ATTTTATTTTTATTTTA
1 ATTTTATTTTTATTTTT
39727250 ATTTCTATTTTTAATGTTTT
1 ATTT-TATTTTT-AT-TTTT
39727270 -TTTTATTTTT
1 ATTTTATTTTT
39727280 TTACGTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.15
18 14 0.54
19 5 0.19
20 3 0.12
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (17 bp):
ATTTTATTTTTATTTTT
Found at i:39731294 original size:13 final size:13
Alignment explanation
Indices: 39731266--39731315 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
39731256 CGTTATATTG
39731266 ATTTCTTAACTTTTT
1 ATTT-TTAA-TTTTT
39731281 ATTTTTAATTTTT
1 ATTTTTAATTTTT
39731294 ATTTTATCAA--TTT
1 ATTTT-T-AATTTTT
39731307 ATTTTTAAT
1 ATTTTTAAT
39731316 CTTAAACCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
11 2 0.06
12 1 0.03
13 18 0.56
14 5 0.16
15 6 0.19
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTTAATTTTT
Found at i:39736443 original size:28 final size:28
Alignment explanation
Indices: 39736392--39736445 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
39736382 TAGTAACAGT
* *
39736392 ACAGTGTGGGCCTTAGCGCAATACAGAA
1 ACAGTGTGGGCCTAAGCCCAATACAGAA
*
39736420 ACAGTGTGGGCCTAAGCCCGATACAG
1 ACAGTGTGGGCCTAAGCCCAATACAG
39736446 TATCAATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.24, G:0.30, T:0.17
Consensus pattern (28 bp):
ACAGTGTGGGCCTAAGCCCAATACAGAA
Found at i:39736672 original size:31 final size:32
Alignment explanation
Indices: 39736637--39736774 Score: 129
Period size: 32 Copynumber: 4.4 Consensus size: 32
39736627 GAATGGCTAC
* *
39736637 AAGCCATAAG-AACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
39736668 AAGCCATTAGTAGCAGTGATAT-ATCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
39736699 CAA-CCATCAGTAACGGTAATATGACCGGCACA
1 -AAGCCATCAGTAACAGTAATATGATCGGCACA
* * ** *
39736731 AAGCTATCAGCAACAGTAATATGATCGATAAA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
39736763 AAGCCATCAGTA
1 AAGCCATCAGTA
39736775 GCATCGCAGC
Statistics
Matches: 83, Mismatches: 20, Indels: 7
0.75 0.18 0.06
Matches are distributed among these distances:
31 33 0.40
32 50 0.60
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:39736794 original size:26 final size:26
Alignment explanation
Indices: 39736765--39736821 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
39736755 TCGATAAAAA
* * *
39736765 GCCATCAGTAGCATCGCAGCAAAGCT
1 GCCAACAGCAGCACCGCAGCAAAGCT
* *
39736791 GCCAACAGCAGTACCGCAGTAAAGCT
1 GCCAACAGCAGCACCGCAGCAAAGCT
39736817 GCCAA
1 GCCAA
39736822 TAATAATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.32, G:0.23, T:0.12
Consensus pattern (26 bp):
GCCAACAGCAGCACCGCAGCAAAGCT
Found at i:39736966 original size:23 final size:23
Alignment explanation
Indices: 39736919--39736981 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
39736909 CCATGCTCAG
* * *
39736919 AATCAGTCATTCAAATCACAGACA
1 AATCAGTCATT-TAACCACAAACA
39736943 AATCAGTCATTTAACCACAAACA
1 AATCAGTCATTTAACCACAAACA
*
39736966 AATCAATCATTTAACC
1 AATCAGTCATTTAACC
39736982 TCGAGGGGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 24 0.69
24 11 0.31
ACGTcount: A:0.46, C:0.25, G:0.05, T:0.24
Consensus pattern (23 bp):
AATCAGTCATTTAACCACAAACA
Found at i:39736995 original size:27 final size:26
Alignment explanation
Indices: 39736965--39737017 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
39736955 AACCACAAAC
*
39736965 AAATCAATCATTTAACCTCGAGGGGCA
1 AAAT-AATCATTTAACCTCCAGGGGCA
* *
39736992 AAATAGTCATTTATCCTCCAGGGGCA
1 AAATAATCATTTAACCTCCAGGGGCA
39737018 TTATAGTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (26 bp):
AAATAATCATTTAACCTCCAGGGGCA
Found at i:39737001 original size:26 final size:26
Alignment explanation
Indices: 39736972--39737029 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
39736962 AACAAATCAA
*
39736972 TCATTTAACCTCGAGGGGCAAAATAG
1 TCATTTAACCTCCAGGGGCAAAATAG
* **
39736998 TCATTTATCCTCCAGGGGCATTATAG
1 TCATTTAACCTCCAGGGGCAAAATAG
39737024 TCATTT
1 TCATTT
39737030 TACATTATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (26 bp):
TCATTTAACCTCCAGGGGCAAAATAG
Found at i:39737041 original size:27 final size:27
Alignment explanation
Indices: 39736997--39737491 Score: 514
Period size: 27 Copynumber: 18.4 Consensus size: 27
39736987 GGGCAAAATA
* * * *
39736997 GTCA-TTTATCCTCCAGGGGCATTATA
1 GTCATTTTACCCTACAGGGGTATTATG
** *
39737023 GTCATTTTACATTATAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTATG
*
39737050 GTCATTTTACCCTACATGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTATG
* * *
39737077 GTCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTATG
* * *
39737104 GCCATTTTACCTTACAGGGGTATTACGG
1 GTCATTTTACCCTACAGGGGTATTA-TG
* * * *
39737132 GT-ATTTTACCCTATAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTATG
*
39737158 GTCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTATG
* * **
39737185 GTTATTTTACCCTACAAGGGTATTACA
1 GTCATTTTACCCTACAGGGGTATTATG
*
39737212 GTCAATTTACCCTACAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTATG
* * * * *
39737239 ATCATTTTACCTTACAAGGGTCTTACG
1 GTCATTTTACCCTACAGGGGTATTATG
* * *
39737266 GTCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTATG
* * *
39737293 GTCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTATG
* *
39737320 GTCA-TTTACCCTATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTATG
*
39737346 GTCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTATG
* *
39737373 GTCATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTATG
*
39737400 GTCATTTTACCCTA-TGAGGGTATTATG
1 GTCATTTTACCCTACAG-GGGTATTATG
* *
39737427 GTTATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTATG
* *
39737454 GTCATTTTATCCTA-TGCGGGTATTATG
1 GTCATTTTACCCTACAG-GGGTATTATG
*
39737481 GTCATTATACC
1 GTCATTTTACC
39737492 TATTTTAGGG
Statistics
Matches: 399, Mismatches: 63, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
26 32 0.08
27 364 0.91
28 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTATG
Found at i:39737083 original size:54 final size:54
Alignment explanation
Indices: 39736997--39737491 Score: 577
Period size: 54 Copynumber: 9.2 Consensus size: 54
39736987 GGGCAAAATA
* * * ** ** *
39736997 GTCA-TTTATCCTCCAGGGGCATTATAGTCATTTTACATTATAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATAGGGGTATTACG
* * *
39737050 GTCATTTTACCCTACATGGGTATTATGGTCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATAGGGGTATTACG
* * * *
39737104 GCCATTTTACCTTACAGGGGTATTACGGGT-ATTTTACCCTATAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTAC-GGTCATTTTACCCTATAGGGGTATTACG
* * * *
39737158 GTCATTTTACCCTACAGGGGTATTACGGTTATTTTACCCTACAAGGGTATTACA
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATAGGGGTATTACG
* * * * * * *
39737212 GTCAATTTACCCTACAGGGGTATTATGATCATTTTACCTTACAAGGGTCTTACG
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATAGGGGTATTACG
* * * * *
39737266 GTCATTTTACCCTACAAGGGCATTACGGTCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATAGGGGTATTACG
* *
39737320 GTCA-TTTACCCTATAGGGGTATTACGGTCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATAGGGGTATTACG
* *
39737373 GTCATTTTACCCTATAGGGGTATTACGGTCATTTTACCCTAT-GAGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATAG-GGGTATTACG
* * *
39737427 GTTATTTTACCCTACAGGGGTATTACGGTCATTTTATCCTAT-GCGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATAG-GGGTATTACG
*
39737481 GTCATTATACC
1 GTCATTTTACC
39737492 TATTTTAGGG
Statistics
Matches: 390, Mismatches: 47, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
53 56 0.14
54 331 0.85
55 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (54 bp):
GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATAGGGGTATTACG
Found at i:39742386 original size:14 final size:14
Alignment explanation
Indices: 39742367--39742393 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39742357 CTAAAGAAAA
39742367 TAACTAGAATAAAC
1 TAACTAGAATAAAC
39742381 TAACTAGAATAAA
1 TAACTAGAATAAA
39742394 TAGCAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (14 bp):
TAACTAGAATAAAC
Found at i:39745252 original size:24 final size:24
Alignment explanation
Indices: 39745190--39745241 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
39745180 TTTCTAGAAG
* *
39745190 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGTATTTATTAGCATAATAT
39745214 ATTTAGTATTTATTAGCATAATAT
1 ATTTAGTATTTATTAGCATAATAT
39745238 ATTT
1 ATTT
39745242 GACTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTAGTATTTATTAGCATAATAT
Found at i:39748896 original size:130 final size:130
Alignment explanation
Indices: 39748663--39748922 Score: 520
Period size: 130 Copynumber: 2.0 Consensus size: 130
39748653 GGGTACATTG
39748663 GGAATGTTCTTTGCAGGTTCAATATGCAAAGTGCTAAGCCTGTTAGTACTCCTTTAGCAGCCAAT
1 GGAATGTTCTTTGCAGGTTCAATATGCAAAGTGCTAAGCCTGTTAGTACTCCTTTAGCAGCCAAT
39748728 TTCAAGCTTCCATCAGCTTTGTCTCCACAATCAGATGATGAGATTGAGTACATGTCACATGTTTC
66 TTCAAGCTTCCATCAGCTTTGTCTCCACAATCAGATGATGAGATTGAGTACATGTCACATGTTTC
39748793 GGAATGTTCTTTGCAGGTTCAATATGCAAAGTGCTAAGCCTGTTAGTACTCCTTTAGCAGCCAAT
1 GGAATGTTCTTTGCAGGTTCAATATGCAAAGTGCTAAGCCTGTTAGTACTCCTTTAGCAGCCAAT
39748858 TTCAAGCTTCCATCAGCTTTGTCTCCACAATCAGATGATGAGATTGAGTACATGTCACATGTTTC
66 TTCAAGCTTCCATCAGCTTTGTCTCCACAATCAGATGATGAGATTGAGTACATGTCACATGTTTC
39748923 ATACTCTAGT
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 130 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (130 bp):
GGAATGTTCTTTGCAGGTTCAATATGCAAAGTGCTAAGCCTGTTAGTACTCCTTTAGCAGCCAAT
TTCAAGCTTCCATCAGCTTTGTCTCCACAATCAGATGATGAGATTGAGTACATGTCACATGTTTC
Found at i:39756444 original size:13 final size:13
Alignment explanation
Indices: 39756426--39756450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39756416 AGCCCAATCC
39756426 AAAATAAACCAAA
1 AAAATAAACCAAA
39756439 AAAATAAACCAA
1 AAAATAAACCAA
39756451 TCCAAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.16, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAATAAACCAAA
Found at i:39757489 original size:6 final size:6
Alignment explanation
Indices: 39757478--39757513 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
39757468 CTGTCGTGAT
39757478 TTTTAG TTTTAG ACTTTTAG TTTTAG TTTTAG TTTT
1 TTTTAG TTTTAG --TTTTAG TTTTAG TTTTAG TTTT
39757514 GGAATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 22 0.79
8 6 0.21
ACGTcount: A:0.17, C:0.03, G:0.14, T:0.67
Consensus pattern (6 bp):
TTTTAG
Found at i:39757497 original size:14 final size:12
Alignment explanation
Indices: 39757478--39757513 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 12
39757468 CTGTCGTGAT
39757478 TTTTAGTTTTAG
1 TTTTAGTTTTAG
39757490 ACTTTTAGTTTTAG
1 --TTTTAGTTTTAG
39757504 TTTTAGTTTT
1 TTTTAGTTTT
39757514 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.17, C:0.03, G:0.14, T:0.67
Consensus pattern (12 bp):
TTTTAGTTTTAG
Found at i:39762629 original size:19 final size:18
Alignment explanation
Indices: 39762597--39762632 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
39762587 AACCCACAGA
*
39762597 ATTTTTTTATTTTTTCAT
1 ATTTTTTTACTTTTTCAT
39762615 ATTTTTTATACTTTTTCA
1 ATTTTTT-TACTTTTTCA
39762633 ATCACTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTTTTACTTTTTCAT
Found at i:39766064 original size:20 final size:20
Alignment explanation
Indices: 39766039--39766084 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
39766029 TTATGAAATT
39766039 AAAATTATCAAAAAATT-ATA
1 AAAATTATC-AAAAATTAATA
*
39766059 AAAATTATCAATAATTAATA
1 AAAATTATCAAAAATTAATA
39766079 AAAATT
1 AAAATT
39766085 TCTAACAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTATCAAAAATTAATA
Found at i:39770898 original size:15 final size:15
Alignment explanation
Indices: 39770878--39770913 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
39770868 TCCCAAAAAC
*
39770878 CACATTTCTAGTAAT
1 CACATTTCAAGTAAT
39770893 CACATTTCAAGTAAT
1 CACATTTCAAGTAAT
39770908 CACATT
1 CACATT
39770914 CCATTGGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (15 bp):
CACATTTCAAGTAAT
Found at i:39772448 original size:27 final size:27
Alignment explanation
Indices: 39772412--39772486 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 27
39772402 TTACGGAGTT
* * *
39772412 CGCCGCAAAGTCATTCCTTTCATATTC
1 CGCCACAAAGGCATTCCTTTCATATTA
* * * *
39772439 CGCCATAAAGGCTTTTCTTTCATGTTA
1 CGCCACAAAGGCATTCCTTTCATATTA
* *
39772466 CGCCACAAAGGCTTTTCTTTC
1 CGCCACAAAGGCATTCCTTTC
39772487 TTGACATGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.36
Consensus pattern (27 bp):
CGCCACAAAGGCATTCCTTTCATATTA
Found at i:39774394 original size:2 final size:2
Alignment explanation
Indices: 39774387--39774417 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39774377 AATAGGAGGG
39774387 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
39774418 CAGCAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39780156 original size:32 final size:32
Alignment explanation
Indices: 39780120--39780190 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
39780110 TAATTTGATT
*
39780120 AATTTTACTTTTTTTTGTTATTCGAATTTTAA
1 AATTTCACTTTTTTTTGTTATTCGAATTTTAA
*
39780152 AATTTCAGTTTTTTTTGTTATTCGAATTTTAA
1 AATTTCACTTTTTTTTGTTATTCGAATTTTAA
39780184 AATTTCA
1 AATTTCA
39780191 GTCTTGATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (32 bp):
AATTTCACTTTTTTTTGTTATTCGAATTTTAA
Found at i:39780191 original size:32 final size:32
Alignment explanation
Indices: 39780128--39780192 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
39780118 TTAATTTTAC
39780128 TTTTTTTTGTTATTCGAATTTTAAAATTTCAG
1 TTTTTTTTGTTATTCGAATTTTAAAATTTCAG
39780160 TTTTTTTTGTTATTCGAATTTTAAAATTTCAG
1 TTTTTTTTGTTATTCGAATTTTAAAATTTCAG
39780192 T
1 T
39780193 CTTGATTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.06, G:0.09, T:0.60
Consensus pattern (32 bp):
TTTTTTTTGTTATTCGAATTTTAAAATTTCAG
Found at i:39786275 original size:50 final size:51
Alignment explanation
Indices: 39786172--39786413 Score: 217
Period size: 50 Copynumber: 4.7 Consensus size: 51
39786162 GGTAAAGAGA
* *
39786172 TCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCATTGAGATTATGAGAAG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-T-AG---ATGAGAAG
* *
39786228 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCA-AGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGATGAGAAG
* * * * *
39786278 TCCTC-CGTAAGACCATGTCTGGGACATGACATGGGCACCA-ATATGAGAAC
1 TCC-CATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGATGAGAAG
* * * * ** *
39786328 TCCCATGTAAGACCATATCTGGGATATGACATTGGTAGTATAG--GA-AACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGATGAGAA-G
* *
39786377 TCCTATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39786414 TATTATTATC
Statistics
Matches: 156, Mismatches: 26, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
48 2 0.01
49 34 0.22
50 79 0.51
51 2 0.01
53 2 0.01
56 37 0.24
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (51 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGATGAGAAG
Found at i:39794672 original size:123 final size:124
Alignment explanation
Indices: 39794466--39794705 Score: 347
Period size: 123 Copynumber: 1.9 Consensus size: 124
39794456 TCTCTATCAT
* * *
39794466 CTTTAAAAATTTATGAAAGCAATGAGTTAAAACTTCCCATTCGTTATTAAAGATGCTTAATGCAC
1 CTTTAAAAATTTATAAAAGCAATGAGTTAAAACTCCCCATTCATTATTAAAGATGCTTAATGCAC
*
39794531 GTGTTAATGAAGAAGTTAAATAAGCTTCATTTATTAATGTTGCATTGAATGTTTATAAC
66 GTGTTAATGAAGAAGTTAAATAAGCTTCATTTATTAATGATGCATTGAATGTTTATAAC
* * * * * **
39794590 CTTTAAACATTTATAAAAGTAATGAGTTGAATC-CCCCATTCATTATTAAAGATGTTTAATGTTC
1 CTTTAAAAATTTATAAAAGCAATGAGTTAAAACTCCCCATTCATTATTAAAGATGCTTAATGCAC
* * *
39794654 GTGTTAATGAAGCAGTTAAATAAGCTTCATTTATTTATGATGTATTGAATGT
66 GTGTTAATGAAGAAGTTAAATAAGCTTCATTTATTAATGATGCATTGAATGT
39794706 CAATGGCTTA
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
123 74 0.73
124 28 0.27
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.39
Consensus pattern (124 bp):
CTTTAAAAATTTATAAAAGCAATGAGTTAAAACTCCCCATTCATTATTAAAGATGCTTAATGCAC
GTGTTAATGAAGAAGTTAAATAAGCTTCATTTATTAATGATGCATTGAATGTTTATAAC
Found at i:39804900 original size:59 final size:61
Alignment explanation
Indices: 39804830--39804946 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 61
39804820 ATCATTTTAA
* * * *
39804830 TATTAAATTAATATAATACT-TA-T-CGAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATA-TGTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
39804889 TATTAAATTAATAGAATATGTATCTACAAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAATTAATAGAATATGTA-CTACAAGATAAACATTAAATTAAATTTAATATTAA
39804947 GATAATCATA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
58 1 0.02
59 19 0.38
61 1 0.02
62 29 0.58
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (61 bp):
TATTAAATTAATAGAATATGTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:39805033 original size:37 final size:37
Alignment explanation
Indices: 39804954--39805033 Score: 85
Period size: 37 Copynumber: 2.2 Consensus size: 37
39804944 TAAGATAATC
* *
39804954 ATATT-AATATTAAATTAATAAAATACTATTAAGATA
1 ATATTAAATATTAAATTAATAAAATACTACTAAAATA
*
39804990 AGTATTAAAT-TTAATTTAATATTAAAT-CTACTAAAATA
1 A-TATTAAATATTAAATTAATA--AAATACTACTAAAATA
39805028 ATATTA
1 ATATTA
39805034 TTTTTGGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
36 1 0.03
37 19 0.51
38 13 0.35
39 4 0.11
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (37 bp):
ATATTAAATATTAAATTAATAAAATACTACTAAAATA
Found at i:39806067 original size:31 final size:31
Alignment explanation
Indices: 39806025--39806083 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
39806015 TTTCAAAATT
* *
39806025 TTAAATAAAAACTTTCGAATAGTTTAGTAAC
1 TTAAATAAAAACTTTCAAATAATTTAGTAAC
*
39806056 TTAAATGAAAACTTTCAAATAATTTAGT
1 TTAAATAAAAACTTTCAAATAATTTAGT
39806084 GATCATTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (31 bp):
TTAAATAAAAACTTTCAAATAATTTAGTAAC
Found at i:39808291 original size:20 final size:20
Alignment explanation
Indices: 39808268--39808333 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
39808258 GAAGTACAAA
39808268 CAGGGGCACGTATGTACATT
1 CAGGGGCACGTATGTACATT
* * **
39808288 CAGGGGTACCG-AAGTACAAA
1 CAGGGGCA-CGTATGTACATT
**
39808308 CAGGGGCACGTATGTGGATT
1 CAGGGGCACGTATGTACATT
39808328 CAGGGG
1 CAGGGG
39808334 TACCGAAGTA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.18
Consensus pattern (20 bp):
CAGGGGCACGTATGTACATT
Found at i:39808306 original size:40 final size:40
Alignment explanation
Indices: 39808219--39808343 Score: 180
Period size: 40 Copynumber: 3.1 Consensus size: 40
39808209 AAGGATTATT
* * * * *
39808219 GAAGTACAAACAGAGGCACATATATACACTCA-GGGTACT
1 GAAGTACAAACAGGGGCACGTATGTACATTCAGGGGTACC
39808258 GAAGTACAAACAGGGGCACGTATGTACATTCAGGGGTACC
1 GAAGTACAAACAGGGGCACGTATGTACATTCAGGGGTACC
**
39808298 GAAGTACAAACAGGGGCACGTATGTGGATTCAGGGGTACC
1 GAAGTACAAACAGGGGCACGTATGTACATTCAGGGGTACC
39808338 GAAGTA
1 GAAGTA
39808344 AATTCACACA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 28 0.36
40 50 0.64
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (40 bp):
GAAGTACAAACAGGGGCACGTATGTACATTCAGGGGTACC
Found at i:39808348 original size:20 final size:20
Alignment explanation
Indices: 39808285--39808349 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
39808275 ACGTATGTAC
39808285 ATTCAGGGGTACCGAAGTACA
1 ATTCAGGGGTACCGAAGTA-A
* * * **
39808306 A-ACAGGGGCA-CGTATGTGG
1 ATTCAGGGGTACCG-AAGTAA
39808325 ATTCAGGGGTACCGAAGTAA
1 ATTCAGGGGTACCGAAGTAA
39808345 ATTCA
1 ATTCA
39808350 CACATATATA
Statistics
Matches: 31, Mismatches: 10, Indels: 7
0.65 0.21 0.15
Matches are distributed among these distances:
19 3 0.10
20 25 0.81
21 3 0.10
ACGTcount: A:0.32, C:0.17, G:0.31, T:0.20
Consensus pattern (20 bp):
ATTCAGGGGTACCGAAGTAA
Found at i:39811598 original size:25 final size:24
Alignment explanation
Indices: 39811559--39811606 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
39811549 GATTTTAGGC
39811559 CAATGAAAATGTTTTTTCTTTAAA
1 CAATGAAAATGTTTTTTCTTTAAA
39811583 CAATGAAAATGTTTTTTCTTTAAA
1 CAATGAAAATGTTTTTTCTTTAAA
39811607 TGTTTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (24 bp):
CAATGAAAATGTTTTTTCTTTAAA
Found at i:39821162 original size:10 final size:10
Alignment explanation
Indices: 39821147--39821179 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
39821137 TTACTTATTC
39821147 ATTTATTTTT
1 ATTTATTTTT
39821157 ATTTA-TTTT
1 ATTTATTTTT
*
39821166 AATTATTTTT
1 ATTTATTTTT
39821176 ATTT
1 ATTT
39821180 TTTAAAGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:39824045 original size:21 final size:23
Alignment explanation
Indices: 39824007--39824050 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
39823997 TAATTTATTT
39824007 TATTTTATGATGTAAAAA-TAAA
1 TATTTTATGATGTAAAAAGTAAA
*
39824029 TATTTTAT-ATTTAAAAAGTAAA
1 TATTTTATGATGTAAAAAGTAAA
39824051 AAAACTTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (23 bp):
TATTTTATGATGTAAAAAGTAAA
Found at i:39825056 original size:24 final size:24
Alignment explanation
Indices: 39825023--39825068 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
39825013 TCACAAATGA
* * *
39825023 GAAAGGTAAGGCATGTATATATGT
1 GAAAGATAAGGCACGCATATATGT
39825047 GAAAGATAAGGCACGCATATAT
1 GAAAGATAAGGCACGCATATAT
39825069 TTATAAAAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (24 bp):
GAAAGATAAGGCACGCATATATGT
Found at i:39828889 original size:10 final size:10
Alignment explanation
Indices: 39828874--39828898 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
39828864 ATCCTGAATT
39828874 TTTTTTTCTC
1 TTTTTTTCTC
39828884 TTTTTTTCTC
1 TTTTTTTCTC
39828894 TTTTT
1 TTTTT
39828899 GCATTAGTTT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:39833570 original size:50 final size:50
Alignment explanation
Indices: 39833503--39833631 Score: 179
Period size: 50 Copynumber: 2.6 Consensus size: 50
39833493 GATGCAAACT
* *
39833503 TTAACTAATATGGGAGTTACATAATGCATGACATAATTTATGATACA-ATC
1 TTAACTAACATGAGAGTTACATAATGCATGACATAATTTATGATACATA-C
* * *
39833553 TTAACTAACATGAGAGTTACATAATGCATGTCATTATTTATGATGCATAC
1 TTAACTAACATGAGAGTTACATAATGCATGACATAATTTATGATACATAC
* *
39833603 GTAACTAACATGAAAGTTACATAATGCAT
1 TTAACTAACATGAGAGTTACATAATGCAT
39833632 AACTTTATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 70 0.99
51 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (50 bp):
TTAACTAACATGAGAGTTACATAATGCATGACATAATTTATGATACATAC
Found at i:39837336 original size:22 final size:24
Alignment explanation
Indices: 39837302--39837345 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
39837292 CTTGGACCAA
39837302 GATTTTCAAGA-T-TTGAAATCTT
1 GATTTTCAAGATTCTTGAAATCTT
**
39837324 GATTTTCTCGATTCTTGAAATC
1 GATTTTCAAGATTCTTGAAATC
39837346 GCTCCAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 1 0.06
24 8 0.44
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (24 bp):
GATTTTCAAGATTCTTGAAATCTT
Found at i:39841901 original size:20 final size:21
Alignment explanation
Indices: 39841878--39841921 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
39841868 AATGGTTATA
*
39841878 GGTTTGATGTTTGAG-TTTAG
1 GGTTTGAGGTTTGAGATTTAG
*
39841898 GGTTTGGGGTTTGAGATTTAG
1 GGTTTGAGGTTTGAGATTTAG
39841919 GGT
1 GGT
39841922 AAAAAAGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.45
Consensus pattern (21 bp):
GGTTTGAGGTTTGAGATTTAG
Found at i:39841908 original size:27 final size:26
Alignment explanation
Indices: 39841846--39841912 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
39841836 GGGTTACGAA
*
39841846 TTTGGGGTTTAGAGTTTGAGTTAATGG
1 TTTGGGGTTT-GAGTTTGAGTTAAGGG
* *
39841873 TTAT-AGGTTTGATGTTTGAGTTTAGGG
1 TT-TGGGGTTTGA-GTTTGAGTTAAGGG
39841900 TTTGGGGTTTGAG
1 TTTGGGGTTTGAG
39841913 ATTTAGGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
26 4 0.12
27 28 0.85
28 1 0.03
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.46
Consensus pattern (26 bp):
TTTGGGGTTTGAGTTTGAGTTAAGGG
Found at i:39846026 original size:15 final size:15
Alignment explanation
Indices: 39846006--39846035 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39845996 TTCACAAAGA
39846006 CAACTTAAAAATAGG
1 CAACTTAAAAATAGG
39846021 CAACTTAAAAATAGG
1 CAACTTAAAAATAGG
39846036 TGGAATGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (15 bp):
CAACTTAAAAATAGG
Found at i:39847591 original size:26 final size:27
Alignment explanation
Indices: 39847539--39847601 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
39847529 TTTAAAATAC
* * *
39847539 TTTTAAAATGATTTTTTATTTTTTTTAT
1 TTTTAAAATAATTTTTTA-TATGTTTAT
39847567 TTTTAAAATAATTTTTTA-ATGTTTAT
1 TTTTAAAATAATTTTTTATATGTTTAT
*
39847593 TTTAAAAAT
1 TTTTAAAAT
39847602 GGGCCTGGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 14 0.45
28 17 0.55
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (27 bp):
TTTTAAAATAATTTTTTATATGTTTAT
Found at i:39852617 original size:41 final size:41
Alignment explanation
Indices: 39852560--39852776 Score: 398
Period size: 41 Copynumber: 5.3 Consensus size: 41
39852550 AATTTAACAT
* *
39852560 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* *
39852601 ATTCATATCACCGGCACTTAGCCTACTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
39852642 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
39852683 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
39852724 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
39852765 ATTCAGATCACC
1 ATTCAGATCACC
39852777 AATTTCAAAC
Statistics
Matches: 170, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 170 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:39856520 original size:20 final size:20
Alignment explanation
Indices: 39856495--39856534 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39856485 CGTAAAATAA
*
39856495 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
39856515 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
39856535 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:39856524 original size:34 final size:35
Alignment explanation
Indices: 39856480--39856546 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
39856470 CAGTAAAATG
* *
39856480 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTAGAAAATATTTTAC
* *
39856514 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTAGAAAATATTTT
39856547 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTAGAAAATATTTTAC
Found at i:39860037 original size:41 final size:42
Alignment explanation
Indices: 39859981--39860083 Score: 115
Period size: 41 Copynumber: 2.5 Consensus size: 42
39859971 TGATTCAGTA
* * *
39859981 CACCGGC-TTTAAGCCTGCTAGACTTATAGTTTGAATTG-TTT
1 CACCGGCATTTAAGCCTGCTAGACGTAAAGTCTGAA-TGATTT
39860022 CACCGGCATTT-AGCCTGCTAGACGTAAAGTCTGAATGATTT
1 CACCGGCATTTAAGCCTGCTAGACGTAAAGTCTGAATGATTT
* * *
39860063 CATCGGCA-ATAAGCCTACTAG
1 CACCGGCATTTAAGCCTGCTAG
39860084 GCACTGAGCC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
40 3 0.06
41 47 0.89
42 3 0.06
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (42 bp):
CACCGGCATTTAAGCCTGCTAGACGTAAAGTCTGAATGATTT
Found at i:39866307 original size:22 final size:22
Alignment explanation
Indices: 39866261--39866318 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
39866251 ACTATTTTTG
* * *
39866261 TTGTTG-TTTACTATTGTTATG
1 TTGTTGTTTTGCTACTGTTATA
39866282 TTGTTGTTTTGCTACTGTTATA
1 TTGTTGTTTTGCTACTGTTATA
39866304 TTGTTGTTTTGCTAC
1 TTGTTGTTTTGCTAC
39866319 CATTTCACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 6 0.18
22 27 0.82
ACGTcount: A:0.12, C:0.09, G:0.19, T:0.60
Consensus pattern (22 bp):
TTGTTGTTTTGCTACTGTTATA
Found at i:39868181 original size:102 final size:102
Alignment explanation
Indices: 39868055--39868281 Score: 427
Period size: 102 Copynumber: 2.2 Consensus size: 102
39868045 AGGTTTAGGG
* * *
39868055 TTAAAGTGTTCGGTTATTTTCTGCCATGTGCATGGTAGAAATGGATGTGTTTGTATTAAATTGTT
1 TTAAATTGTTTGGTTATTGTCTGCCATGTGCATGGTAGAAATGGATGTGTTTGTATTAAATTGTT
39868120 TTTGTATTGGTTATTGTTTGTCATTGCATATGTTGTA
66 TTTGTATTGGTTATTGTTTGTCATTGCATATGTTGTA
39868157 TTAAATTGTTTGGTTATTGTCTGCCATGTGCATGGTAGAAATGGATGTGTTTGTATTAAATTGTT
1 TTAAATTGTTTGGTTATTGTCTGCCATGTGCATGGTAGAAATGGATGTGTTTGTATTAAATTGTT
39868222 TTTGTATTGGTTATTGTTTGTCATTGCATATGTTGTA
66 TTTGTATTGGTTATTGTTTGTCATTGCATATGTTGTA
39868259 TTAAATTGTTTGGTTATTGTCTG
1 TTAAATTGTTTGGTTATTGTCTG
39868282 GCTTTATTGA
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 122 1.00
ACGTcount: A:0.20, C:0.06, G:0.23, T:0.50
Consensus pattern (102 bp):
TTAAATTGTTTGGTTATTGTCTGCCATGTGCATGGTAGAAATGGATGTGTTTGTATTAAATTGTT
TTTGTATTGGTTATTGTTTGTCATTGCATATGTTGTA
Found at i:39868978 original size:21 final size:21
Alignment explanation
Indices: 39868939--39868980 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39868929 GCATCTAGAT
*
39868939 GTGTTCACACTAACAATTAAA
1 GTGTTCACACAAACAATTAAA
39868960 GTGTTCACACAAAGC-ATTAAA
1 GTGTTCACACAAA-CAATTAAA
39868981 ATTCTATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (21 bp):
GTGTTCACACAAACAATTAAA
Found at i:39873296 original size:20 final size:20
Alignment explanation
Indices: 39873271--39873315 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
39873261 CTTTGAGCAA
* *
39873271 ATTTG-ACTTGTTTGAAAATT
1 ATTTGAACTTGGTT-AAAATC
39873291 ATTTGAACTTGGTTAAAATC
1 ATTTGAACTTGGTTAAAATC
39873311 ATTTG
1 ATTTG
39873316 CATTTGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTTGAACTTGGTTAAAATC
Found at i:39881141 original size:45 final size:44
Alignment explanation
Indices: 39881004--39881141 Score: 111
Period size: 44 Copynumber: 3.1 Consensus size: 44
39880994 TGGCTTCGAT
* *
39881004 CTGCTTCACTATCGATGCAGGAAGGCAAGACCTACTATCTTCAAC
1 CTGCTTCAC-CTCGATGCAGGAAGGCAAGACCTGCTATCTTCAAC
* ** * * * * * *
39881049 CTGCTCCA-CTAC-AACCAAGGGAGGCAAGGCTTG-TGTCTTCGAT
1 CTGCTTCACCT-CGATGC-AGGAAGGCAAGACCTGCTATCTTCAAC
*
39881092 CTGCTTCACCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAAC
1 CTGCTTCACC-TCGATGCAGGAAGGCAAGACCTGCTATCTTCAAC
39881137 CTGCT
1 CTGCT
39881142 CCACTGCTGC
Statistics
Matches: 66, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
43 17 0.26
44 27 0.41
45 22 0.33
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (44 bp):
CTGCTTCACCTCGATGCAGGAAGGCAAGACCTGCTATCTTCAAC
Found at i:39881200 original size:44 final size:44
Alignment explanation
Indices: 39881141--39881653 Score: 614
Period size: 44 Copynumber: 11.7 Consensus size: 44
39881131 TTCAACCTGC
* * *
39881141 TCCACTGCTGCTCAGGGAGCTAGGACTTACAATCTTCTGTCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCCGCCTAT
* * * **
39881185 TCCACTACTGTTCAGGAAGCTAGGACTTACAGTCTTCTACCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCCGCCTAT
* * *
39881229 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCTGCCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCCGCCTAT
* * *
39881273 TCCACTGCTGTTCAGGGAGCTAGGACTTATAGTCTTCCACCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCCGCCTAT
* * * *
39881317 TCCACTACTGGTCAGGGATCTAGGATTTACAATCTTCCGCCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCCGCCTAT
* * *
39881361 TCCACTGCTGTTCAGGGAGCTAGGACTTTCAGTCTTCCACCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCCGCCTAT
* *
39881405 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCCGCCTAT
* ** * * * *
39881449 TCCGCTATTGTTTAGGGAGCTAGGACTTTCAGTCTTCCACCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCCGCCTAT
* *
39881493 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCCGCCTAT
** * * *
39881537 TCCACTATTGTTCAGGGAGCTAGGACTTTCAGTCTTCCACCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCCGCCTAT
* * ** * * *
39881581 TCCACTTCTGGTCAATGAGCTAGTA-TTCATAATCTTCTGCCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTT-ACAATCTTCCGCCTAT
39881625 TCCACTGCTGTTCAGGGAGCTAGGACTTA
1 TCCACTGCTGTTCAGGGAGCTAGGACTTA
39881654 TAGTTTCACC
Statistics
Matches: 389, Mismatches: 78, Indels: 4
0.83 0.17 0.01
Matches are distributed among these distances:
43 2 0.01
44 385 0.99
45 2 0.01
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (44 bp):
TCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCCGCCTAT
Found at i:39881652 original size:88 final size:88
Alignment explanation
Indices: 39881141--39881652 Score: 792
Period size: 88 Copynumber: 5.8 Consensus size: 88
39881131 TTCAACCTGC
* * * * *
39881141 TCCACTGCTGCTCAGGGAGCTAGGACTTACAATCTTCTGTCTATTCCACTACTGTTCAGGAAGCT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTACTGTTCAGGGAGCT
* *
39881206 AGGACTTACAGTCTTCTACCTAT
66 AGGACTTTCAGTCTTCCACCTAT
* *
39881229 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCTGCCTATTCCACTGCTGTTCAGGGAGCT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTACTGTTCAGGGAGCT
39881294 AGGACTTAT-AGTCTTCCACCTAT
66 AGGACTT-TCAGTCTTCCACCTAT
* * *
39881317 TCCACTACTGGTCAGGGATCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGTTCAGGGAGCT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTACTGTTCAGGGAGCT
39881382 AGGACTTTCAGTCTTCCACCTAT
66 AGGACTTTCAGTCTTCCACCTAT
* * *
39881405 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCGCTATTGTTTAGGGAGCT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTACTGTTCAGGGAGCT
39881470 AGGACTTTCAGTCTTCCACCTAT
66 AGGACTTTCAGTCTTCCACCTAT
*
39881493 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTATTGTTCAGGGAGCT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTACTGTTCAGGGAGCT
39881558 AGGACTTTCAGTCTTCCACCTAT
66 AGGACTTTCAGTCTTCCACCTAT
* ** * * * * *
39881581 TCCACTTCTGGTCAATGAGCTAGTATTCATAATCTTCTGCCTATTCCACTGCTGTTCAGGGAGCT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTACTGTTCAGGGAGCT
39881646 AGGACTT
66 AGGACTT
39881653 ATAGTTTCAC
Statistics
Matches: 395, Mismatches: 27, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
87 1 0.00
88 394 1.00
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (88 bp):
TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTACTGTTCAGGGAGCT
AGGACTTTCAGTCTTCCACCTAT
Found at i:39883801 original size:6 final size:6
Alignment explanation
Indices: 39883790--39883829 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
39883780 TTCATTTGTT
39883790 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTT
39883830 CCCTTCCCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (6 bp):
ATTTTG
Found at i:39883861 original size:10 final size:10
Alignment explanation
Indices: 39883838--39883906 Score: 88
Period size: 10 Copynumber: 6.8 Consensus size: 10
39883828 TTCCCTTCCC
39883838 TTTTTTCTTGA
1 TTTTTT-TTGA
39883849 TTTTTTTT-A
1 TTTTTTTTGA
*
39883858 ATTTTTTTGA
1 TTTTTTTTGA
39883868 -TTTTTTTGA
1 TTTTTTTTGA
39883877 TTTTTTTTGA
1 TTTTTTTTGA
39883887 TTTTTTGATTGA
1 TTTTTT--TTGA
39883899 TTTTTTTT
1 TTTTTTTT
39883907 TGAAAATTAG
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
9 17 0.32
10 20 0.38
11 6 0.11
12 10 0.19
ACGTcount: A:0.12, C:0.01, G:0.09, T:0.78
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:39883862 original size:19 final size:19
Alignment explanation
Indices: 39883839--39883892 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
39883829 TCCCTTCCCT
*
39883839 TTTTTCTTGATTTTTTTTAA
1 TTTTT-TTGATTTTTTTGAA
*
39883859 TTTTTTTGATTTTTTTGAT
1 TTTTTTTGATTTTTTTGAA
39883878 TTTTTTTGATTTTTT
1 TTTTTTTGATTTTTT
39883893 GATTGATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 27 0.84
20 5 0.16
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTTTTTGATTTTTTTGAA
Found at i:39883871 original size:8 final size:9
Alignment explanation
Indices: 39883839--39883896 Score: 73
Period size: 9 Copynumber: 6.2 Consensus size: 9
39883829 TCCCTTCCCT
39883839 TTTTTCTTGA
1 TTTTT-TTGA
*
39883849 TTTTTTTTAA
1 -TTTTTTTGA
39883859 TTTTTTTGA
1 TTTTTTTGA
39883868 TTTTTTTGA
1 TTTTTTTGA
39883877 TTTTTTTTGA
1 -TTTTTTTGA
39883887 -TTTTTTGA
1 TTTTTTTGA
39883895 TT
1 TT
39883897 GATTTTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
8 8 0.19
9 18 0.42
10 12 0.28
11 5 0.12
ACGTcount: A:0.12, C:0.02, G:0.09, T:0.78
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:39883902 original size:19 final size:19
Alignment explanation
Indices: 39883845--39883903 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 19
39883835 CCCTTTTTTC
*
39883845 TTGATTTTTTTTAATT-TTT
1 TTGA-TTTTTTTGATTATTT
*
39883864 TTGATTTTTTTGATTTTTT
1 TTGATTTTTTTGATTATTT
39883883 TTGA-TTTTTTGATTGATTT
1 TTGATTTTTTTGATT-ATTT
39883902 TT
1 TT
39883904 TTTTGAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 20 0.56
19 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (19 bp):
TTGATTTTTTTGATTATTT
Found at i:39884568 original size:13 final size:13
Alignment explanation
Indices: 39884550--39884574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39884540 TATTTTAATA
39884550 TTATTTTGTGTGT
1 TTATTTTGTGTGT
39884563 TTATTTTGTGTG
1 TTATTTTGTGTG
39884575 CATTCGATGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:39886314 original size:41 final size:41
Alignment explanation
Indices: 39886107--39886303 Score: 317
Period size: 41 Copynumber: 4.8 Consensus size: 41
39886097 TTTATCGTTA
* * * *
39886107 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39886148 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39886189 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39886230 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
39886271 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
39886304 AAGAGCCGGT
Statistics
Matches: 148, Mismatches: 4, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 143 0.97
42 2 0.01
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:39886576 original size:33 final size:32
Alignment explanation
Indices: 39886520--39886583 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
39886510 AGATATGTAT
39886520 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
39886552 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
39886584 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:39886600 original size:33 final size:33
Alignment explanation
Indices: 39886527--39886600 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
39886517 TATATATATA
* * **
39886527 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
39886559 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
39886592 TGTATGTAT
1 TATATGTAT
39886601 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:39895247 original size:41 final size:41
Alignment explanation
Indices: 39894712--39895236 Score: 973
Period size: 41 Copynumber: 12.8 Consensus size: 41
39894702 TTTATCGTTA
* * * *
39894712 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39894753 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39894794 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39894835 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39894876 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39894917 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39894958 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39894999 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39895040 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39895081 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39895122 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
39895163 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
39895204 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
39895237 AAGAGCCGGT
Statistics
Matches: 476, Mismatches: 4, Indels: 8
0.98 0.01 0.02
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 471 0.99
42 2 0.00
43 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:39895507 original size:33 final size:32
Alignment explanation
Indices: 39895451--39895514 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
39895441 ATAGATATGT
39895451 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
39895483 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
39895515 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:39895531 original size:33 final size:33
Alignment explanation
Indices: 39895458--39895531 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
39895448 TGTATATATA
* * **
39895458 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
39895490 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
39895523 TGTATGTAT
1 TATATGTAT
39895532 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:39905988 original size:45 final size:45
Alignment explanation
Indices: 39905905--39905993 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
39905895 AGGAGGGATC
*
39905905 AAGGTGAAAACCCAAAAAGGGCGCTTTGAATCCTAAAAAGAAACT
1 AAGGTGAAAACCCAAAAAGGGCGCTTTGAATCCTAAAAACAAACT
** * *
39905950 AAGGTGAAAACCCGCAAAGGGTGCTTTGAGT-CTAAAAAACAAAC
1 AAGGTGAAAACCCAAAAAGGGCGCTTTGAATCCT-AAAAACAAAC
39905994 AAATAAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 2 0.05
45 36 0.95
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (45 bp):
AAGGTGAAAACCCAAAAAGGGCGCTTTGAATCCTAAAAACAAACT
Found at i:39907295 original size:45 final size:45
Alignment explanation
Indices: 39907241--39907876 Score: 439
Period size: 44 Copynumber: 14.4 Consensus size: 45
39907231 TATCTCTTTA
* * *
39907241 AAGTTGCAGTGGAGCGGATTGAGGATAGCAAGTCTTATCTCCCTG
1 AAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTG
* * *
39907286 AGGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATC-CACCTG
1 AAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTC-CCTG
* * * * * *
39907331 AAGTTTCAGTGGGGCTGGTTGAAGATA-CAAATCCTATCTTCCTG
1 AAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTG
* * *
39907375 AAGTTTCAGTGGAGCAGATTGAATATAGCAAGTCTTATCTCCCTG
1 AAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTG
* * *
39907420 AAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCCTATCTCCCTG
1 AAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTG
* * *
39907465 AAGTTGCAGTGGAGCGGATTAAAGATAGCAAGTCTTATCTCCCTG
1 AAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTG
* * * * *
39907510 ATGTTGCAGCGGAGTAGACTGAATA-AGCAAATCTTATCTCCCTG
1 AAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTG
* ** *
39907554 AAGTTGCAGTGGAGCAGATTAAAGCCA--ATAATCCTATCTCCCTG
1 AAGTTGCAGTGGAGCAGATTGAAGATAGCA-AATCTTATCTCCCTG
* * * * * * * *
39907598 AAGTTGTAGCGGAACAAACTGAATAAATG--AATCTTATCCCCCTG
1 AAGTTGCAGTGGAGCAGATTGAAGATA-GCAAATCTTATCTCCCTG
* * * * * *
39907642 AAGTTACAGTGGGGCAAATTAAAGCA-AGCGAATCTTAGCTCCCTG
1 AAGTTGCAGTGGAGCAGATTGAAG-ATAGCAAATCTTATCTCCCTG
* * ** * * *
39907687 AAGTTGCAGTGGATCAGATTAAAGCCA--ATAATCATATTTCCCTA
1 AAGTTGCAGTGGAGCAGATTGAAGATAGCA-AATCTTATCTCCCTG
* * * * * *
39907731 AAGTTGTAGCGGAGCGGATTAAAG-T-GACAGATCTTATCTCTCTG
1 AAGTTGCAGTGGAGCAGATTGAAGATAG-CAAATCTTATCTCCCTG
* * * * * *
39907775 AAGTTGCAG-AGAGTAGATCG--CAT--CTAATCTTATCTCCCTA
1 AAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTG
** * * * *
39907815 AAGTTGCAGCAGAGCAAACT-AAGCA-AGCAGATTTTATAC-CCCTG
1 AAGTTGCAGTGGAGCAGATTGAAG-ATAGCAAATCTTAT-CTCCCTG
39907859 AAGTTGCAGTGGAGCAGA
1 AAGTTGCAGTGGAGCAGA
39907877 CAGAAGAAAG
Statistics
Matches: 454, Mismatches: 114, Indels: 47
0.74 0.19 0.08
Matches are distributed among these distances:
40 22 0.05
41 6 0.01
42 1 0.00
43 9 0.02
44 210 0.46
45 206 0.45
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (45 bp):
AAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTG
Found at i:39907384 original size:44 final size:45
Alignment explanation
Indices: 39907224--39907706 Score: 408
Period size: 45 Copynumber: 10.8 Consensus size: 45
39907214 GGTGAAACCA
** * * *
39907224 CAAATCCTATCTCTTTAAAGTTGCAGTGGAGCGGATTGAGGATAG
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * *
39907269 CAAGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAAGATAG
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * *
39907314 CAAA-CCTTATC-CACCTGAAGTTTCAGTGGGGCTGGTTGAAGATA-
1 CAAATCC-TATCTC-CCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * *
39907358 CAAATCCTATCTTCCTGAAGTTTCAGTGGAGCAGATTGAATATAG
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * *
39907403 CAAGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAG
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* *
39907448 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGATAG
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * * * * *
39907493 CAAGTCTTATCTCCCTGATGTTGCAGCGGAGTAGACTGAATA-AG
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * **
39907537 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * * * * *
39907581 -ATAATCCTATCTCCCTGAAGTTGTAGCGGAACAAACTGAATAAATG
1 CA-AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-G
* * * * * *
39907627 --AATCTTATCCCCCTGAAGTTACAGTGGGGCAAATTAAAGCA-AG
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-ATAG
* * * *
39907670 CGAATCTTAGCTCCCTGAAGTTGCAGTGGATCAGATT
1 CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATT
39907707 AAAGCCAATA
Statistics
Matches: 348, Mismatches: 78, Indels: 24
0.77 0.17 0.05
Matches are distributed among these distances:
43 2 0.01
44 135 0.39
45 211 0.61
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (45 bp):
CAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
Found at i:39907465 original size:134 final size:134
Alignment explanation
Indices: 39907223--39907603 Score: 452
Period size: 134 Copynumber: 2.9 Consensus size: 134
39907213 CGGTGAAACC
* * * **
39907223 ACAAATCCTATC-TCTTTAAAGTTGCAGTGGAGCGGATTGAGGATAGCAAGTCTTATCTCCCTGA
1 ACAAATCCTATCTTC-CTGAAGTTGCAGTGGAGCAGATTGAATATAGCAAGTCTTATCTCCCTGA
* * *
39907287 GGTTGCAGTGGAGCAGACTGAAGATAGCAAA-CCTTATC-CACCTGAAGTTTCAGTGGGGCTGG-
65 AGTTGCAGTGGAGCAGACTGAAGATAGCAAATCC-TATCTC-CCTGAAGTTGCAGTGGAGC-GGA
*
39907349 TTGAAGAT
127 TTAAAGAT
*
39907357 ACAAATCCTATCTTCCTGAAGTTTCAGTGGAGCAGATTGAATATAGCAAGTCTTATCTCCCTGAA
1 ACAAATCCTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAATATAGCAAGTCTTATCTCCCTGAA
*
39907422 GTTGCAGCGGAGCAGACTGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA
66 GTTGCAGTGGAGCAGACTGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA
39907487 AGAT
131 AGAT
* * * * * * * *
39907491 AGCAAGTCTTATCTCCCTGATGTTGCAGCGGAGTAGACTGAATA-AGCAAATCTTATCTCCCTGA
1 A-CAAATCCTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAATATAGCAAGTCTTATCTCCCTGA
* * **
39907555 AGTTGCAGTGGAGCAGATTAAAGCCA--ATAATCCTATCTCCCTGAAGTTG
65 AGTTGCAGTGGAGCAGACTGAAGATAGCA-AATCCTATCTCCCTGAAGTTG
39907604 TAGCGGAACA
Statistics
Matches: 216, Mismatches: 25, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
132 1 0.00
133 23 0.11
134 153 0.71
135 39 0.18
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (134 bp):
ACAAATCCTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAATATAGCAAGTCTTATCTCCCTGAA
GTTGCAGTGGAGCAGACTGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA
AGAT
Found at i:39908148 original size:23 final size:23
Alignment explanation
Indices: 39908108--39908154 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
39908098 ACTCGCATAC
*
39908108 ACAAAGAAAATAATAAACCAAAT
1 ACAAAGAAAATAAAAAACCAAAT
39908131 ACAAA-AAAATATAAAAACCAAAT
1 ACAAAGAAAATA-AAAAACCAAAT
39908154 A
1 A
39908155 AATAAAGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.72, C:0.13, G:0.02, T:0.13
Consensus pattern (23 bp):
ACAAAGAAAATAAAAAACCAAAT
Found at i:39909488 original size:3 final size:3
Alignment explanation
Indices: 39909480--39909520 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
39909470 ACTTCGTTAA
* *
39909480 TAT TAT TAT TAC TAT TAT TAT TTT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39909521 AGTTTTCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:39913814 original size:20 final size:20
Alignment explanation
Indices: 39913777--39913830 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
39913767 CCTGGAGCAA
*
39913777 ATTTG-ACTTGTTTGAAAATC
1 ATTTGAACTTGGTT-AAAATC
*
39913797 ATTTTAACTTGGTTAAAATC
1 ATTTGAACTTGGTTAAAATC
*
39913817 ATTTGCACTTGGTT
1 ATTTGAACTTGGTT
39913831 TTAAGATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (20 bp):
ATTTGAACTTGGTTAAAATC
Found at i:39917086 original size:15 final size:15
Alignment explanation
Indices: 39917066--39917096 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39917056 GAATCTCTAT
39917066 TTTTTCTTCTTCTTC
1 TTTTTCTTCTTCTTC
39917081 TTTTTCTTCTTCTTC
1 TTTTTCTTCTTCTTC
39917096 T
1 T
39917097 ACTGTCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTCTTCTTCTTC
Found at i:39928806 original size:50 final size:50
Alignment explanation
Indices: 39928749--39928850 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
39928739 TAATTGACAC
39928749 GTATTTGATATTTTAGGTAATAAAGAAAAAGGTATGAGACGGTGAGGTTT
1 GTATTTGATATTTTAGGTAATAAAGAAAAAGGTATGAGACGGTGAGGTTT
39928799 GTATTTGATATTTTAGGTAATAAAGAAAAAGGTATGAGACGGTGAGGTTT
1 GTATTTGATATTTTAGGTAATAAAGAAAAAGGTATGAGACGGTGAGGTTT
39928849 GT
1 GT
39928851 GCGAAGAGAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (50 bp):
GTATTTGATATTTTAGGTAATAAAGAAAAAGGTATGAGACGGTGAGGTTT
Found at i:39934820 original size:125 final size:124
Alignment explanation
Indices: 39934631--39934868 Score: 354
Period size: 125 Copynumber: 1.9 Consensus size: 124
39934621 AAATAGTGGG
** * * * * *
39934631 AAATCGCTTCTACTAGGATGTTATTTAAGAAGAAATTGTGAAATAGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
39934696 TCGCTACAG-TGGTCATGT-GAGAAATAATTTTTTTTTGACGTTTTCTGAGGAAATAGTATA
66 TCGCTACAGTTGGTCATGTAG-GAAATAA-TTTTTTTTGACG-TTTCTGAGGAAATAGTATA
* *
39934756 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
39934821 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACGTTTCTGAG
66 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACGTTTCTGAG
39934869 CAAACAGTGT
Statistics
Matches: 102, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
124 8 0.08
125 77 0.75
126 16 0.16
127 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (124 bp):
AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACGTTTCTGAGGAAATAGTATA
Found at i:39947658 original size:23 final size:23
Alignment explanation
Indices: 39947628--39947676 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
39947618 TTCGAAGGTT
39947628 AACCAACCTCATGGAAATCAACC
1 AACCAACCTCATGGAAATCAACC
*
39947651 AACCAACCTCATGGAAATTAACC
1 AACCAACCTCATGGAAATCAACC
39947674 AAC
1 AAC
39947677 TACTGTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.45, C:0.33, G:0.08, T:0.14
Consensus pattern (23 bp):
AACCAACCTCATGGAAATCAACC
Found at i:39950139 original size:21 final size:21
Alignment explanation
Indices: 39950115--39950202 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
39950105 AGCTTTCACA
* *
39950115 AGTTTCTGTTTAACTCATATG
1 AGTTTCCGTTTAACTCTTATG
39950136 AGTTTCCGTTTAAC-CTTATG
1 AGTTTCCGTTTAACTCTTATG
* * * *
39950156 GGTTTCCGTTCAGCTCTTTTG
1 AGTTTCCGTTTAACTCTTATG
* * *
39950177 AGCTTCTGTTTAACCCTTATG
1 AGTTTCCGTTTAACTCTTATG
*
39950198 GGTTT
1 AGTTT
39950203 TCATTCAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
20 16 0.31
21 35 0.69
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.47
Consensus pattern (21 bp):
AGTTTCCGTTTAACTCTTATG
Found at i:39950202 original size:42 final size:42
Alignment explanation
Indices: 39950132--39950270 Score: 172
Period size: 42 Copynumber: 3.3 Consensus size: 42
39950122 GTTTAACTCA
* *
39950132 TATGAGTTTCCGTTTAA-CCTTATGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
* * *
39950173 TTTGAGCTTCTGTTTAACCCTTATGGGTTTTCATTCAGCTCT
1 TATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
* * * * *
39950215 TACGAGCTTTTGTTCAACCCTTACGGGTTTCCGTTTAGCTCT
1 TATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
*
39950257 CATGAGCTTCTGTT
1 TATGAGCTTCTGTT
39950271 CAGCCTTCGG
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 14 0.17
42 67 0.83
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (42 bp):
TATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
Found at i:39950230 original size:21 final size:21
Alignment explanation
Indices: 39950206--39950274 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 21
39950196 TGGGTTTTCA
39950206 TTCAGCTCTTACGAGCTTTTG
1 TTCAGCTCTTACGAGCTTTTG
* * * *
39950227 TTCAACCCTTACG-GGTTTCCG
1 TTCAGCTCTTACGAGCTTT-TG
* * * *
39950248 TTTAGCTCTCATGAGCTTCTG
1 TTCAGCTCTTACGAGCTTTTG
39950269 TTCAGC
1 TTCAGC
39950275 CTTCGGGCTT
Statistics
Matches: 33, Mismatches: 13, Indels: 4
0.66 0.26 0.08
Matches are distributed among these distances:
20 4 0.12
21 26 0.79
22 3 0.09
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39
Consensus pattern (21 bp):
TTCAGCTCTTACGAGCTTTTG
Found at i:39956404 original size:77 final size:77
Alignment explanation
Indices: 39956277--39956438 Score: 306
Period size: 77 Copynumber: 2.1 Consensus size: 77
39956267 TGAGACAATC
*
39956277 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
1 TTAAAGTGTTATGCCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
39956342 CAAGTTCAATTA
66 CAAGTTCAATTA
39956354 TTAAAGTGTTATGCCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
1 TTAAAGTGTTATGCCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
*
39956419 CAAGTTTAATTA
66 CAAGTTCAATTA
39956431 TTAAAGTG
1 TTAAAGTG
39956439 GACAAAAAAT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 83 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (77 bp):
TTAAAGTGTTATGCCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
CAAGTTCAATTA
Found at i:39956825 original size:24 final size:24
Alignment explanation
Indices: 39956798--39956875 Score: 58
Period size: 26 Copynumber: 3.3 Consensus size: 24
39956788 TATATATTTT
39956798 TTATTAAATTATATTTAATAATAA
1 TTATTAAATTATATTTAATAATAA
* *
39956822 TTATTTTAAATTAT-TATTAA-ATTAT
1 TTA--TTAAATTATAT-TTAATAATAA
* *
39956847 TTATT-ATTTATA-TTAATAAT-C
1 TTATTAAATTATATTTAATAATAA
39956868 TTATTAAA
1 TTATTAAA
39956876 ATTTAATAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
21 9 0.21
22 8 0.19
23 2 0.05
24 3 0.07
25 7 0.17
26 13 0.31
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATTAAATTATATTTAATAATAA
Found at i:39956839 original size:56 final size:57
Alignment explanation
Indices: 39956730--39956862 Score: 155
Period size: 56 Copynumber: 2.3 Consensus size: 57
39956720 TATATTATTA
* *
39956730 TATATTATGATTTTAGTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAAT
1 TATA-TATTATTTTATTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAAT
* * *
39956788 TATATATT-TTTTATTAAATTATATTTAATAATAATTAT-TTTA-AATTATTATTAAAT
1 TATATATTATTTTATTAAATTA-ATATAAGAATAATTATATTAAGAATT-TTATTAAAT
*
39956844 TATTTATTATTTATATTAA
1 TATATATTATTT-TATTAA
39956863 TAATCTTATT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
55 4 0.06
56 31 0.48
57 20 0.31
58 10 0.15
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (57 bp):
TATATATTATTTTATTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAAT
Found at i:39956847 original size:11 final size:11
Alignment explanation
Indices: 39956820--39956852 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
39956810 ATTTAATAAT
39956820 AATTATT-TTA
1 AATTATTATTA
39956830 AATTATTATTA
1 AATTATTATTA
39956841 AATTATTTATTA
1 AATTA-TTATTA
39956853 TTTATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 8 0.38
12 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATTATTATTA
Done.