Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 117 of 143
Found at i:35525037 original size:152 final size:152
Alignment explanation
Indices: 35524761--35525086 Score: 580
Period size: 152 Copynumber: 2.1 Consensus size: 152
35524751 CACGTTCATT
* * *
35524761 TTCCTGATGAGATACTGAGAAGAATACCAACTCAACGCTCAATACGAGTAAATCTTTGAACCCTA
1 TTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAATACGAGCAAATCTTCGAACCCTA
35524826 GCTTCCTGATGAGATACAGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATAC
66 GCTTCCTGATGAGATACAGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATAC
*
35524891 TGAGAAGTGGACCAAGTTCGTC
131 TGAGAAGTGGACCAAATTCGTC
* * *
35524913 TTCCTAATGAGATACAGAGAAGAATACCAACTCAACGCTCGATGCGAGCAAATCTTCGAACCCTA
1 TTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAATACGAGCAAATCTTCGAACCCTA
35524978 GCTTCCTGATGAGATACAGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATAC
66 GCTTCCTGATGAGATACAGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATAC
35525043 TGAGAAGTGGACCAAATTCGTC
131 TGAGAAGTGGACCAAATTCGTC
*
35525065 TTCATGATGAGATACAGAGAAG
1 TTCCTGATGAGATACAGAGAAG
35525087 TGAATTGAAA
Statistics
Matches: 165, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
152 165 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (152 bp):
TTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAATACGAGCAAATCTTCGAACCCTA
GCTTCCTGATGAGATACAGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATAC
TGAGAAGTGGACCAAATTCGTC
Found at i:35525538 original size:206 final size:206
Alignment explanation
Indices: 35525182--35525714 Score: 879
Period size: 206 Copynumber: 2.6 Consensus size: 206
35525172 AACCCCAGCC
* *
35525182 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGACATAGAGAAGCGAATTG
1 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTG
* * *
35525247 AAACAATCGATGCAGTCATTTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAGGCTC
66 AAACAAGCGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAGGCTC
*
35525312 AATGCGAGCAAATCTTCGAACCTCAGCTTCTTGATGAGACACTAAGAAGCAGGTCGAAGCAATAA
131 AATGCGAGCAAATCTTCGAACCTCAGCTTCTTGATAAGACACTAAGAAGCAGGTCGAAGCAATAA
*
35525377 AATGGTTAGCT
196 AATGGTTAACT
*
35525388 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTA
1 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTG
* *
35525453 AAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAGGTTC
66 AAACAAGCGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAGGCTC
* *
35525518 AATGCGAGCAAATGTTCGAACCTCAGCTTCTTGATAAGACACTGAGAAGCAGGTCGAAGCAATAA
131 AATGCGAGCAAATCTTCGAACCTCAGCTTCTTGATAAGACACTAAGAAGCAGGTCGAAGCAATAA
35525583 AATGGTTAACT
196 AATGGTTAACT
* * * * *
35525594 TCCTGATAAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATAAGATACAGAGAAGCGAAGTG
1 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTG
*
35525659 AAACAAAG-GATTGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGGCCAAATCAA
66 AAAC-AAGCGA-TGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAA
35525715 TGAAACCAGA
Statistics
Matches: 305, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
206 259 0.85
207 46 0.15
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (206 bp):
TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTG
AAACAAGCGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAGGCTC
AATGCGAGCAAATCTTCGAACCTCAGCTTCTTGATAAGACACTAAGAAGCAGGTCGAAGCAATAA
AATGGTTAACT
Found at i:35526095 original size:17 final size:17
Alignment explanation
Indices: 35526029--35526104 Score: 68
Period size: 17 Copynumber: 4.5 Consensus size: 17
35526019 CAATGGGATA
*
35526029 TAAATTTATTTTTAAA-T
1 TAAATTTA-TTATAAATT
* *
35526046 TAAATTTATTTTGAATT
1 TAAATTTATTATAAATT
35526063 TAAATTTGCA-TA-AAATT
1 TAAATTT--ATTATAAATT
35526080 TAAATTTATTATAAATT
1 TAAATTTATTATAAATT
*
35526097 TGAATTTA
1 TAAATTTA
35526105 AAATTAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
15 1 0.02
16 8 0.16
17 39 0.78
18 1 0.02
19 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (17 bp):
TAAATTTATTATAAATT
Found at i:35527892 original size:30 final size:29
Alignment explanation
Indices: 35527852--35528256 Score: 289
Period size: 29 Copynumber: 13.8 Consensus size: 29
35527842 AGAGGTCCCT
*
35527852 AAACTGTCCAAAAATTATATTTTGACCCCG
1 AAACT-TCCAAAAATTACATTTTGACCCCG
*
35527882 AAAACTTCCAAAAATTACATTTTGCCCCCG
1 -AAACTTCCAAAAATTACATTTTGACCCCG
*
35527912 -AACTTCCAAAAATTATATTTTG-CCCTCG
1 AAACTTCCAAAAATTACATTTTGACCC-CG
* * *
35527940 -AACTTTCAAAAATTCCATTTTGACCTCG
1 AAACTTCCAAAAATTACATTTTGACCCCG
* *
35527968 AAACTTCCAAAAATT-CTATTTTTACCCCTA
1 AAACTTCCAAAAATTAC-ATTTTGACCCC-G
* * * *
35527998 AAACTTTCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTACA-TTTTGACCCCG
*
35528028 AAACTTCCAAAAATTACATTTTTGGCCCTCG
1 AAACTTCCAAAAATTACA-TTTTGACCC-CG
* * *
35528059 -AACTAT-CAAAAATTCCATTTTTGA-ACCT
1 AAACT-TCCAAAAATTACA-TTTTGACCCCG
35528087 AAACTTCCAAAAATTACATTTTTG-CCCCTG
1 AAACTTCCAAAAATTACA-TTTTGACCCC-G
*** * **
35528117 -AACTTTTTAAAATTCCATTTTGACCCTA
1 AAACTTCCAAAAATTACATTTTGACCCCG
35528145 AAACTTCCAAAAATTACATTTTTG-CCCTCG
1 AAACTTCCAAAAATTACA-TTTTGACCC-CG
* *
35528175 -AACTTTCAAAAATT-CAATTTTTGACCCCA
1 AAACTTCCAAAAATTAC-A-TTTTGACCCCG
* * *
35528204 AAATTTCCCAAAATTA-AGTTTTTACCCCCG
1 AAACTTCCAAAAATTACA-TTTTGA-CCCCG
* *
35528234 ACA-TTCCAAAAATTCCATTTTGA
1 AAACTTCCAAAAATTACATTTTGA
35528257 TCCTTACGCC
Statistics
Matches: 302, Mismatches: 49, Indels: 48
0.76 0.12 0.12
Matches are distributed among these distances:
27 3 0.01
28 53 0.18
29 121 0.40
30 108 0.36
31 17 0.06
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTGACCCCG
Found at i:35527973 original size:29 final size:30
Alignment explanation
Indices: 35527852--35528254 Score: 308
Period size: 30 Copynumber: 13.7 Consensus size: 30
35527842 AGAGGTCCCT
*
35527852 AAACTGTCCAAAAATTATA-TTTTGACCCCG
1 AAACT-TCCAAAAATTACATTTTTGACCCCG
*
35527882 AAAACTTCCAAAAATTACA-TTTTGCCCCCG
1 -AAACTTCCAAAAATTACATTTTTGACCCCG
*
35527912 -AACTTCCAAAAATTATA-TTTTG-CCCTCG
1 AAACTTCCAAAAATTACATTTTTGACCC-CG
* * *
35527940 -AACTTTCAAAAATTCCA-TTTTGACCTCG
1 AAACTTCCAAAAATTACATTTTTGACCCCG
*
35527968 AAACTTCCAAAAATT-CTATTTTT-ACCCCTA
1 AAACTTCCAAAAATTAC-ATTTTTGACCCC-G
* * * *
35527998 AAACTTTCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTACATTTTTGACCCCG
*
35528028 AAACTTCCAAAAATTACATTTTTGGCCCTCG
1 AAACTTCCAAAAATTACATTTTTGACCC-CG
* * *
35528059 -AACTAT-CAAAAATTCCATTTTTGA-ACCT
1 AAACT-TCCAAAAATTACATTTTTGACCCCG
35528087 AAACTTCCAAAAATTACATTTTTG-CCCCTG
1 AAACTTCCAAAAATTACATTTTTGACCCC-G
*** * **
35528117 -AACTTTTTAAAATTCCA-TTTTGACCCTA
1 AAACTTCCAAAAATTACATTTTTGACCCCG
35528145 AAACTTCCAAAAATTACATTTTTG-CCCTCG
1 AAACTTCCAAAAATTACATTTTTGACCC-CG
* *
35528175 -AACTTTCAAAAATT-CAATTTTTGACCCCA
1 AAACTTCCAAAAATTAC-ATTTTTGACCCCG
* *
35528204 AAATTTCCCAAAATTA-AGTTTTT-ACCCCCG
1 AAACTTCCAAAAATTACA-TTTTTGA-CCCCG
* *
35528234 ACA-TTCCAAAAATTCCATTTT
1 AAACTTCCAAAAATTACATTTT
35528255 GATCCTTACG
Statistics
Matches: 303, Mismatches: 44, Indels: 52
0.76 0.11 0.13
Matches are distributed among these distances:
27 3 0.01
28 53 0.17
29 112 0.37
30 122 0.40
31 13 0.04
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.34
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTGACCCCG
Found at i:35540528 original size:68 final size:68
Alignment explanation
Indices: 35540413--35540669 Score: 432
Period size: 68 Copynumber: 3.8 Consensus size: 68
35540403 CCTATGGTGA
* *
35540413 TTGTATTACTATATTTATTAATT-ATT-A--ATTTATTTTATGTACTTCCACCTACAAACCTGAC
1 TTGT-TTACTATATTTATTAATTAATTAATTATTTGTTTTATGTACTTCCACCTACCAACCTGAC
35540474 GTCT
65 GTCT
* *
35540478 TAGTTTACTATATTAATTAATTAATTAATTATTTGTTTTATGTACTTCCACCTACCAACCTGACG
1 TTGTTTACTATATTTATTAATTAATTAATTATTTGTTTTATGTACTTCCACCTACCAACCTGACG
35540543 TCT
66 TCT
*
35540546 TTGTTTACTATATTTATTAATTAATTAATTATTTGTTTTATGTACTTCCACCTACCAATCTGACG
1 TTGTTTACTATATTTATTAATTAATTAATTATTTGTTTTATGTACTTCCACCTACCAACCTGACG
35540611 TCT
66 TCT
35540614 TTGTTTACTATATTTATTAATTAATTAATTATTTGTTTTATGTACTTCCACCTACC
1 TTGTTTACTATATTTATTAATTAATTAATTATTTGTTTTATGTACTTCCACCTACC
35540670 TCTTAATTTG
Statistics
Matches: 181, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
64 17 0.09
65 6 0.03
66 1 0.01
68 157 0.87
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (68 bp):
TTGTTTACTATATTTATTAATTAATTAATTATTTGTTTTATGTACTTCCACCTACCAACCTGACG
TCT
Found at i:35540722 original size:17 final size:17
Alignment explanation
Indices: 35540702--35540736 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
35540692 GTTATAATGA
*
35540702 TAAATTTAATTTTTAAT
1 TAAATTTAATTATTAAT
*
35540719 TAAATTTGATTATTAAT
1 TAAATTTAATTATTAAT
35540736 T
1 T
35540737 TTTTAAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TAAATTTAATTATTAAT
Found at i:35541461 original size:17 final size:17
Alignment explanation
Indices: 35541439--35541508 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 17
35541429 AGCCCAACAG
35541439 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
35541456 ATTTAAGTTTATATTAA
1 ATTTAAATTTATTTTAA
** **
35541473 ATTTAAATCCATTTGGA
1 ATTTAAATTTATTTTAA
35541490 ATTTAAATTTA-TTTAA
1 ATTTAAATTTATTTTAA
35541506 ATT
1 ATT
35541509 AATGTCCAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
16 6 0.15
17 35 0.85
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:35543362 original size:31 final size:31
Alignment explanation
Indices: 35543326--35543408 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 31
35543316 CCCTAAACTG
*
35543326 TCCAAAAATCATATTTTAACCCTTAAACTTT
1 TCCAAAAATCATATTTTAACCCTCAAACTTT
* * *
35543357 TCCAAAATTC-TATTTTTGA-CCTCGAACTTT
1 TCCAAAAATCATA-TTTTAACCCTCAAACTTT
* *
35543387 TCAAAAAAT-ACATTTTAACCCT
1 TCCAAAAATCATATTTTAACCCT
35543409 ATTGTTTTCC
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
29 5 0.12
30 22 0.54
31 14 0.34
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (31 bp):
TCCAAAAATCATATTTTAACCCTCAAACTTT
Found at i:35543422 original size:30 final size:30
Alignment explanation
Indices: 35543384--35543440 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
35543374 GACCTCGAAC
35543384 TTTTCAAAAAATA-CATTTTAACCCTATTG
1 TTTTCAAAAAATACCATTTTAACCCTATTG
* *
35543413 TTTTCCAAAAATTACCATTTTACCCCTA
1 TTTT-CAAAAAATACCATTTTAACCCTA
35543441 AACTTCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 8 0.33
31 12 0.50
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (30 bp):
TTTTCAAAAAATACCATTTTAACCCTATTG
Found at i:35543447 original size:29 final size:29
Alignment explanation
Indices: 35543414--35543816 Score: 201
Period size: 29 Copynumber: 13.9 Consensus size: 29
35543404 ACCCTATTGT
35543414 TTTCCAAAAATTACCATTTTACCCCTAAA
1 TTTCCAAAAATTACCATTTTACCCCTAAA
* * * *
35543443 CTTCCAAAAATT-CCATTTTA-ACCTCGAT
1 TTTCCAAAAATTACCATTTTACCCCT-AAA
*
35543471 TTCTCCAAAAATTACCATTTTGCCCC-AAA
1 TT-TCCAAAAATTACCATTTTACCCCTAAA
* * *
35543500 CTTCCAAAAAATT-TCATTTTTGA-CCCTAATT
1 TTTCC-AAAAATTACCA-TTTT-ACCCCTAA-A
35543531 TTTCCAAAAATTACCATTTTACCCCTAAA
1 TTTCCAAAAATTACCATTTTACCCCTAAA
* * * * *
35543560 CTTCCAAAAATT-CCATTTTAACCTTGAT
1 TTTCCAAAAATTACCATTTTACCCCTAAA
** * *
35543588 TTTTTAAAAATTACCATTTTACCCTCGAAC
1 TTTCCAAAAATTACCATTTTACCC-CTAAA
* * *
35543618 TTT-CAAAAATT-TCATTTTTGA-CCTTAATT
1 TTTCCAAAAATTACCA-TTTT-ACCCCTAA-A
*
35543647 TTTCC-AAAATTACCATTTTACTCCC-GAA
1 TTTCCAAAAATTACCATTTTAC-CCCTAAA
* ** *
35543675 TGTT-TAAAAATT-CCATTTTAAAACCTGAAT
1 T-TTCCAAAAATTACCATTTT-ACCCCT-AAA
** * **
35543705 TTTTTAAAAATTATCATTTTACCTCC-GGA
1 TTTCCAAAAATTACCATTTTACC-CCTAAA
* * *
35543734 TGTCCAAAAATT-CCATTTTTGACCTCAAAA
1 TTTCCAAAAATTACCA-TTTT-ACCCCTAAA
35543764 TTTCC-AAAATTACCATTTTACCCCTAAAA
1 TTTCCAAAAATTACCATTTTACCCCT-AAA
* * *
35543793 TGTCC-AAATTTACCGTTTTACCCC
1 TTTCCAAAAATTACCATTTTACCCC
35543817 CCGAGCATCT
Statistics
Matches: 279, Mismatches: 62, Indels: 66
0.69 0.15 0.16
Matches are distributed among these distances:
27 3 0.01
28 57 0.20
29 145 0.52
30 58 0.21
31 16 0.06
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
TTTCCAAAAATTACCATTTTACCCCTAAA
Found at i:35543460 original size:59 final size:58
Alignment explanation
Indices: 35543388--35543800 Score: 339
Period size: 59 Copynumber: 7.1 Consensus size: 58
35543378 TCGAACTTTT
* *
35543388 CAAAAAATACATTTTAACCCTATTGTTTTCCAAAAATTACCATTTTACCCCTAAACTTC
1 CAAAAATTCCATTTTAACCCTATT-TTTTCCAAAAATTACCATTTTACCCCTAAACTTC
* * *
35543447 CAAAAATTCCATTTTAACCTCGA-TTTCTCCAAAAATTACCATTTTGCCCC-AAACTTC
1 CAAAAATTCCATTTTAACC-CTATTTTTTCCAAAAATTACCATTTTACCCCTAAACTTC
* * *
35543504 CAAAAAATTTCATTTTTGACCCTAATTTTTCCAAAAATTACCATTTTACCCCTAAACTTC
1 C-AAAAATTCCA-TTTTAACCCTATTTTTTCCAAAAATTACCATTTTACCCCTAAACTTC
* * *
35543564 CAAAAATTCCATTTTAACCTTGATTTTTT--AAAAATTACCATTTTA-CCCTCGAACTTT
1 CAAAAATTCCATTTTAACCCT-ATTTTTTCCAAAAATTACCATTTTACCCCT-AAACTTC
* * * * * **
35543621 CAAAAATTTCATTTTTGACCTTAATTTTTCC-AAAATTACCATTTTACTCCCGAATGTT-
1 CAAAAATTCCA-TTTTAACCCTATTTTTTCCAAAAATTACCATTTTAC-CCCTAAACTTC
* * * **
35543679 TAAAAATTCCATTTTAAAACCTGAATTTTTT--AAAAATTATCATTTTACCTCC-GGA-TGTC
1 CAAAAATTCCATTTT-AACCCT--ATTTTTTCCAAAAATTACCATTTTACC-CCTAAACT-TC
* *** *
35543738 CAAAAATTCCATTTTTGA-CCTCAAAATTTCC-AAAATTACCATTTTACCCCTAAAATGTC
1 CAAAAATTCCA-TTTTAACCCT-ATTTTTTCCAAAAATTACCATTTTACCCCTAAACT-TC
35543797 CAAA
1 CAAA
35543801 TTTACCGTTT
Statistics
Matches: 288, Mismatches: 42, Indels: 48
0.76 0.11 0.13
Matches are distributed among these distances:
56 4 0.01
57 56 0.19
58 101 0.35
59 104 0.36
60 23 0.08
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (58 bp):
CAAAAATTCCATTTTAACCCTATTTTTTCCAAAAATTACCATTTTACCCCTAAACTTC
Found at i:35543483 original size:58 final size:58
Alignment explanation
Indices: 35543413--35543800 Score: 355
Period size: 58 Copynumber: 6.7 Consensus size: 58
35543403 AACCCTATTG
*
35543413 TTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCA-TTTTAACCTCGA
1 TTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCAA
* * *
35543470 TTTCTCCAAAAATTACCATTTTGCCCC-AAACTTCCAAAAAATTTCATTTTTGACC-CTAA
1 TTT-TCCAAAAATTACCATTTTACCCCTAAACTTCC-AAAAATTCCATTTTTAACCTC-AA
**
35543529 TTTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCA-TTTTAACCTTGA
1 -TTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCAA
** * * * * *
35543587 TTTTTTAAAAATTACCATTTTA-CCCTCGAACTTTCAAAAATTTCATTTTTGACCTTAA
1 TTTTCCAAAAATTACCATTTTACCCCT-AAACTTCCAAAAATTCCATTTTTAACCTCAA
* ** * * *
35543645 TTTTTCC-AAAATTACCATTTTACTCCCGAATGTT-TAAAAATTCCATTTTAAAACCTGAA
1 -TTTTCCAAAAATTACCATTTTAC-CCCTAAACTTCCAAAAATTCCATTTT-TAACCTCAA
** * ** *
35543704 TTTTTTAAAAATTATCATTTTACCTCC-GGA-TGTCCAAAAATTCCATTTTTGACCTCAAA
1 TTTTCCAAAAATTACCATTTTACC-CCTAAACT-TCCAAAAATTCCATTTTTAACCTC-AA
* *
35543763 ATTTCC-AAAATTACCATTTTACCCCTAAAATGTCCAAA
1 TTTTCCAAAAATTACCATTTTACCCCTAAACT-TCCAAA
35543801 TTTACCGTTT
Statistics
Matches: 268, Mismatches: 43, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
56 4 0.01
57 49 0.18
58 105 0.39
59 96 0.36
60 14 0.05
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38
Consensus pattern (58 bp):
TTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCAA
Found at i:35543519 original size:117 final size:117
Alignment explanation
Indices: 35543399--35543800 Score: 446
Period size: 117 Copynumber: 3.4 Consensus size: 117
35543389 AAAAAATACA
* *
35543399 TTTTAACCCTATTGTTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTAA
1 TTTTGACCCTAAT-TTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTAA
*
35543464 CCTCGATTTCTCCAAAAATTACCATTTTGCCC-CAAACTTCCAAAAAATTTCAT
65 CCTCGATTT-TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAAATTTCAT
35543517 TTTTGACCCTAATTTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTAAC
1 TTTTGACCCTAATTTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTAAC
* ** * *
35543582 CTTGATTTTTTAAAAATTACCATTTTACCCTCGAACTTTC-AAAAATTTCAT
66 CTCGATTTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAAATTTCAT
* * ** *
35543633 TTTTGACCTTAATTTTTCC-AAAATTACCATTTTACTCCCGAATGTT-TAAAAATTCCATTTTAA
1 TTTTGACCCTAATTTTTCCAAAAATTACCATTTTAC-CCCTAAACTTCCAAAAATTCCATTTT--
** * ** *
35543696 AACCT-GAATTTTTTAAAAATTATCATTTTA-CCTCCGGA-TGTCC-AAAAATTCCAT
63 AACCTCG-ATTTTCCAAAAATTACCATTTTACCCT-CAAACT-TCCAAAAAATTTCAT
** *
35543750 TTTTGA-CCTCAAAATTTCC-AAAATTACCATTTTACCCCTAAAATGTCCAAA
1 TTTTGACCCT-AATTTTTCCAAAAATTACCATTTTACCCCTAAACT-TCCAAA
35543801 TTTACCGTTT
Statistics
Matches: 250, Mismatches: 24, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
115 30 0.12
116 68 0.27
117 138 0.55
118 14 0.06
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.39
Consensus pattern (117 bp):
TTTTGACCCTAATTTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTAAC
CTCGATTTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAAATTTCAT
Found at i:35555423 original size:21 final size:21
Alignment explanation
Indices: 35555397--35555440 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
35555387 GAAACATGGA
*
35555397 GGGAAAGGTTTAAGTCGTAAC
1 GGGAAAGGTTTAAGTCGCAAC
35555418 GGGAAAGGTTTAAGTCGCAAC
1 GGGAAAGGTTTAAGTCGCAAC
35555439 GG
1 GG
35555441 CGAACCTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.11, G:0.36, T:0.20
Consensus pattern (21 bp):
GGGAAAGGTTTAAGTCGCAAC
Found at i:35555530 original size:49 final size:49
Alignment explanation
Indices: 35555418--35556215 Score: 591
Period size: 49 Copynumber: 16.3 Consensus size: 49
35555408 AAGTCGTAAC
* * *
35555418 GGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTA-TACCTC-AGAGACATGAAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCC--AGTACCACGA-AGACAT-AAA
* ** *
35555468 GGGAAAGATTTAAGCCGTAACAACGAATCCAATACCACGAAGACATAAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAA
* * * *
35555517 GGGAAAGATTTAAGCCACAACGGCGAA-CCTAGTACCTCGGAGACATGTAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACGAAGACAT-AAA
* * * * ** *
35555567 -GGAAATATTTAAGCCGCAACGACGAATCTAGTACCGCGAAGACACGAG
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAA
* *
35555615 GGGAAAGGTTTAA-CTCGCAATGGCGAA-CCTTA-TACCTTA-GAAG-CATAAA
1 GGGAAAGATTTAAGC-CGCAACGGCGAATCC--AGTACC--ACGAAGACATAAA
* * *
35555664 GGGAAA-TTTTAAGTCGTAACGGCGAATCCAGTACCACGAAGACATAAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAA
* * * * ** *
35555712 GGGAAAGGTTTAAGTCGCAATGGTGAACTTTA-TACCTCAGAAG-CATAAA
1 GGGAAAGATTTAAGCCGCAACGGCGAA-TCCAGTACCAC-GAAGACATAAA
**
35555761 GGGAAAGATTTAAGCTACAACGGCGAATCCAGTACCACGAAGACATAAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAA
* *** * *
35555810 GGGAAAGGTTTAAGTTACAATGGCGAA-CCTAGTACCTTA-G-AGACATGAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACC--ACGAAGACATAAA
* ** * **
35555859 GGGAAAGATTTAAGCCGCAATGATGAATTCAGTACCACGAAGACACGAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAA
* * * *
35555908 GGGAAAGGTTTAAGTCGCAATGGCGAA-CCTTA-TACCTCAGAAG-CATAAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCC--AGTACCAC-GAAGACATAAA
* * * * *
35555957 GGGAAAGACTTAAGTCGCAATGACGAATCTAGTACCACGAAGACATAAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAA
* * * * *
35556006 GGGAAAGGTTTAAGTCGCAATGGCGAA-CCTTA-TACCTC-AGAGACATGAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCC--AGTACCACGA-AGACATAAA
*
35556055 GGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAGACATAAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAA
* * * * *
35556104 GGGAAAGGTTTAAGTCGCAATGGCGAA-CCTAGTACCTC-AGAGACATGAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACGA-AGACATAAA
* * *
35556153 GGGAAAGATTTAAGCCGTAACGGTGAATCCAGTACCACGAAGACACAAAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACA-TAAA
*
35556203 GGGAAAGGTTTAA
1 GGGAAAGATTTAA
35556216 CTCACAATGG
Statistics
Matches: 599, Mismatches: 104, Indels: 90
0.76 0.13 0.11
Matches are distributed among these distances:
46 1 0.00
47 6 0.01
48 57 0.10
49 455 0.76
50 76 0.13
51 4 0.01
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.18
Consensus pattern (49 bp):
GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAA
Found at i:35555627 original size:98 final size:99
Alignment explanation
Indices: 35555418--35556287 Score: 1090
Period size: 98 Copynumber: 8.9 Consensus size: 99
35555408 AAGTCGTAAC
*
35555418 GGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAGAGACATGAAAGGGAAAGATTTAAGC
1 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGACATGAAAGGGAAAGATTTAAGC
* ** *
35555483 CGTAACAACGAATCCAATACCACGAAGACATAAA
66 CGCAACGGCGAATCCAGTACCACGAAGACATAAA
* * * * * * *
35555517 GGGAAAGATTTAAGCCACAACGGCGAACC-TAGTACCTCGGAGACATGTAA-GGAAATATTTAAG
1 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTA-TACCTCAGAGACATGAAAGGGAAAGATTTAAG
* * * ** *
35555580 CCGCAACGACGAATCTAGTACCGCGAAGACACGAG
65 CCGCAACGGCGAATCCAGTACCACGAAGACATAAA
* * *
35555615 GGGAAAGGTTTAACTCGCAATGGCGAACCTTATACCTTAGA-AGCAT-AAAGGGAAA-TTTTAAG
1 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGA-CATGAAAGGGAAAGATTTAAG
* *
35555677 TCGTAACGGCGAATCCAGTACCACGAAGACATAAA
65 CCGCAACGGCGAATCCAGTACCACGAAGACATAAA
* *
35555712 GGGAAAGGTTTAAGTCGCAATGGTGAACTTTATACCTCAGA-AGCAT-AAAGGGAAAGATTTAAG
1 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGA-CATGAAAGGGAAAGATTTAAG
**
35555775 CTACAACGGCGAATCCAGTACCACGAAGACATAAA
65 CCGCAACGGCGAATCCAGTACCACGAAGACATAAA
** *
35555810 GGGAAAGGTTTAAGTTACAATGGCGAACC-TAGTACCTTAGAGACATG-AAGGGAAAGATTTAAG
1 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTA-TACCTCAGAGACATGAAAGGGAAAGATTTAAG
* ** * **
35555873 CCGCAATGATGAATTCAGTACCACGAAGACACGAA
65 CCGCAACGGCGAATCCAGTACCACGAAGACATAAA
*
35555908 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGA-AGCAT-AAAGGGAAAGACTTAAG
1 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGA-CATGAAAGGGAAAGATTTAAG
* * * *
35555971 TCGCAATGACGAATCTAGTACCACGAAGACATAAA
65 CCGCAACGGCGAATCCAGTACCACGAAGACATAAA
35556006 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGACATG-AAGGGAAAGATTTAAGC
1 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGACATGAAAGGGAAAGATTTAAGC
*
35556070 CGCAACGGTGAATCCAGTACCACGAAGACATAAA
66 CGCAACGGCGAATCCAGTACCACGAAGACATAAA
35556104 GGGAAAGGTTTAAGTCGCAATGGCGAACC-TAGTACCTCAGAGACATG-AAGGGAAAGATTTAAG
1 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTA-TACCTCAGAGACATGAAAGGGAAAGATTTAAG
* * *
35556167 CCGTAACGGTGAATCCAGTACCACGAAGACACAAAA
65 CCGCAACGGCGAATCCAGTACCACGAAGACA-TAAA
* * *
35556203 GGGAAAGGTTTAACTCACAATGGCAAACCTTATACCTCAGA-AGCATGAAA-GGAAA-ATTTAAG
1 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGA-CATGAAAGGGAAAGATTTAAG
* **
35556265 CCGCAACGGTGAATTTAGTACCA
65 CCGCAACGGCGAATCCAGTACCA
35556288 TGCAGATTAA
Statistics
Matches: 676, Mismatches: 77, Indels: 37
0.86 0.10 0.05
Matches are distributed among these distances:
97 92 0.14
98 485 0.72
99 95 0.14
100 4 0.01
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (99 bp):
GGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGACATGAAAGGGAAAGATTTAAGC
CGCAACGGCGAATCCAGTACCACGAAGACATAAA
Found at i:35556719 original size:17 final size:17
Alignment explanation
Indices: 35556697--35556784 Score: 106
Period size: 17 Copynumber: 5.2 Consensus size: 17
35556687 GGCCCAACAG
35556697 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
35556714 ATTTAAGTTTATATTAA
1 ATTTAAATTTATTTTAA
** *
35556731 ATTTAAATCCATTTGAA
1 ATTTAAATTTATTTTAA
*
35556748 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
35556765 AGTTTAAATTTA-TTTAA
1 A-TTTAAATTTATTTTAA
35556782 ATT
1 ATT
35556785 AATGTCCAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
16 2 0.03
17 46 0.79
18 10 0.17
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:35557596 original size:12 final size:12
Alignment explanation
Indices: 35557563--35557596 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35557553 TCATTCCAAC
*
35557563 CGCAGTCGCAGT
1 CGCAGTCGCCGT
35557575 CGCAGTCGCCGT
1 CGCAGTCGCCGT
*
35557587 CGCCGTCGCC
1 CGCAGTCGCC
35557597 AGAGCCGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.44, G:0.32, T:0.15
Consensus pattern (12 bp):
CGCAGTCGCCGT
Found at i:35558742 original size:29 final size:30
Alignment explanation
Indices: 35558703--35558969 Score: 100
Period size: 29 Copynumber: 9.1 Consensus size: 30
35558693 TCAAAACTTG
* *
35558703 CATTTTGACCCAGATTTTTCCAAAAATTAC
1 CATTTTAACCCAGATTCTTCCAAAAATTAC
* *
35558733 CATTTTACCCCCA-A-ACTTCCAAAAATT-C
1 CATTTTA-ACCCAGATTCTTCCAAAAATTAC
*
35558761 CATTTTTAACCTC-GATTCCTT-AAAAAATTAC
1 CA-TTTTAACC-CAGATT-CTTCCAAAAATTAC
* * * *
35558792 CATTTTACCCCTA-A-ACTT-CTAAAATTTC
1 CATTTTAACCC-AGATTCTTCCAAAAATTAC
* *
35558820 CATTTTTGAACCTA-ATT-TCTCCAAAAATTAT
1 CA-TTTT-AACCCAGATTCT-TCCAAAAATTAC
* * * *
35558851 CGTTTT-ACCCTGA-ACTTCTAAAAATT-C
1 CATTTTAACCCAGATTCTTCCAAAAATTAC
* * ** *
35558878 TATTTTGACCTTGATTTTTCCAAAAATTAC
1 CATTTTAACCCAGATTCTTCCAAAAATTAC
* *
35558908 CATTTTACCCTCA-A-ACTTCCAAAAATT-C
1 CATTTTAACC-CAGATTCTTCCAAAAATTAC
* *
35558936 TATTTTTAACCTCA-ATTTTTCCAAAAATTAC
1 CA-TTTTAACC-CAGATTCTTCCAAAAATTAC
35558967 CAT
1 CAT
35558970 CTTACCCCCA
Statistics
Matches: 172, Mismatches: 42, Indels: 46
0.66 0.16 0.18
Matches are distributed among these distances:
27 4 0.02
28 37 0.22
29 60 0.35
30 51 0.30
31 20 0.12
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.39
Consensus pattern (30 bp):
CATTTTAACCCAGATTCTTCCAAAAATTAC
Found at i:35558765 original size:58 final size:59
Alignment explanation
Indices: 35558705--35559149 Score: 449
Period size: 59 Copynumber: 7.6 Consensus size: 59
35558695 AAAACTTGCA
35558705 TTTTGACC-CAGATTTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCAT
1 TTTTGACCTCA-ATTTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCAT
* * * * * * *
35558764 TTTTAACCTCGATTCCTT-AAAAAATTACCATTTTACCCCTAAACTTCTAAAATTTCCAT
1 TTTTGACCTCAATT-TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCAT
* * * ** * *
35558823 TTTTGAACCT-AATTTCTCCAAAAATTATCGTTTTA-CCCTGAACTTCTAAAAATTCTA-
1 TTTTG-ACCTCAATTTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCAT
** * *
35558880 TTTTGACCTTGATTTTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTAT
1 TTTTGACCTCAATTTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCAT
* * * **
35558939 TTTTAACCTCAATTTTTCCAAAAATTACCATCTTACCCCCAAACTTTCAAAAATTTTAT
1 TTTTGACCTCAATTTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCAT
* ** *
35558998 TTTTGACCTCTATTTTTCC-AAAATTACCATTTTACCCCTTGAA-TGTCTAAAAATTCCAT
1 TTTTGACCTCAATTTTTCCAAAAATTACCATTTTACCCC-CAAACT-TCCAAAAATTCCAT
*** * * * *
35559057 TTCAAACGTCAAATTTTT-CAAAAATTACCATTTTACCCTCGAACGTCCAAAAATTCCAT
1 TTTTGACCTC-AATTTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCAT
**
35559116 TTTTGACCTCAAAATTTCC-AAAATTACCATTTTA
1 TTTTGACCTCAATTTTTCCAAAAATTACCATTTTA
35559150 GCCTTAAAAT
Statistics
Matches: 317, Mismatches: 56, Indels: 27
0.79 0.14 0.07
Matches are distributed among these distances:
56 4 0.01
57 26 0.08
58 77 0.24
59 179 0.56
60 31 0.10
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (59 bp):
TTTTGACCTCAATTTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCAT
Found at i:35559002 original size:175 final size:176
Alignment explanation
Indices: 35558703--35559145 Score: 542
Period size: 175 Copynumber: 2.5 Consensus size: 176
35558693 TCAAAACTTG
* *
35558703 CATTTTGACCCAGATTTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTT
1 CATTTTGACCTAGATTTTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTT
* * * * * *
35558768 AACCTCGATTCCTT-AAAAAATTACCATTTTACCCCTAAACTTCTAAAATTTCCATTTTTGAACC
66 AACCTCAATT-TTTCCAAAAATTACCATCTTACCCCCAAACTTCAAAAATTTCCATTTTTG-ACC
* *
35558832 T-AATTTCTCCAAAAATTATCGTTTTA-CCC-TGAACT-TCTAAAAATTC
129 TCAATTTCTCC-AAAATTACCATTTTACCCCTTGAA-TGTCTAAAAATTC
* * *
35558878 TATTTTGACCTTGATTTTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTT
1 CATTTTGACCTAGATTTTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTT
*
35558943 AACCTCAATTTTTCCAAAAATTACCATCTTACCCCCAAACTTTCAAAAATTT-TATTTTTGACCT
66 AACCTCAATTTTTCCAAAAATTACCATCTTACCCCCAAAC-TTCAAAAATTTCCATTTTTGACCT
* *
35559007 CTATTTTTCCAAAATTACCATTTTACCCCTTGAATGTCTAAAAATTC
130 CAATTTCTCCAAAATTACCATTTTACCCCTTGAATGTCTAAAAATTC
** * * * *
35559054 CATTTCAAACGTCAAATTTTT-CAAAAATTACCATTTTACCCTCGAACGTCCAAAAATTCCATTT
1 CATTT-TGACCT-AGATTTTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTT
* **
35559118 TTGACCTCAAAATTTCC-AAAATTACCAT
64 TTAACCTCAATTTTTCCAAAAATTACCAT
35559146 TTTAGCCTTA
Statistics
Matches: 232, Mismatches: 28, Indels: 15
0.84 0.10 0.05
Matches are distributed among these distances:
174 19 0.08
175 110 0.47
176 40 0.17
177 57 0.25
178 6 0.03
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (176 bp):
CATTTTGACCTAGATTTTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTT
AACCTCAATTTTTCCAAAAATTACCATCTTACCCCCAAACTTCAAAAATTTCCATTTTTGACCTC
AATTTCTCCAAAATTACCATTTTACCCCTTGAATGTCTAAAAATTC
Found at i:35559138 original size:29 final size:29
Alignment explanation
Indices: 35559077--35559178 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 29
35559067 AAATTTTTCA
* * *
35559077 AAAATTACCATTTTACCCTC-GAACGTCC
1 AAAATTACCATTTTAGCCTCAAAATGTCC
* *
35559105 AAAAATT-CCATTTTTGACCTCAAAATTTCC
1 -AAAATTACCATTTTAG-CCTCAAAATGTCC
*
35559135 AAAATTACCATTTTAGCCTTAAAATGTCC
1 AAAATTACCATTTTAGCCTCAAAATGTCC
* *
35559164 AAATTTACCTTTTTA
1 AAAATTACCATTTTA
35559179 CCCCCCAGGC
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 7 0.12
29 40 0.67
30 13 0.22
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAATTACCATTTTAGCCTCAAAATGTCC
Found at i:35564466 original size:29 final size:31
Alignment explanation
Indices: 35564434--35564522 Score: 92
Period size: 33 Copynumber: 2.9 Consensus size: 31
35564424 TTTAATATGT
*
35564434 AATTGTATACAT-AAACTTTAATTTGGTAC-
1 AATTATATACATGAAACTTTAATTTGGTACA
* * * *
35564463 AATTATACACATGAAACTCTAATTGTAGTTCA
1 AATTATATACATGAAACTTTAATT-TGGTACA
*
35564495 AATATATATACTTGAAACTTTAATTTGG
1 AAT-TATATACATGAAACTTTAATTTGG
35564523 ATTTAATCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 10 0.21
30 10 0.21
31 4 0.09
32 5 0.11
33 18 0.38
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (31 bp):
AATTATATACATGAAACTTTAATTTGGTACA
Found at i:35564718 original size:29 final size:31
Alignment explanation
Indices: 35564662--35564741 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
35564652 GAATTAGATC
*
35564662 AAATCAAAATTTCATGTATAAAATTGCA-A-A
1 AAATCAAAA-TTCATGTATAAAACTGCACATA
* * *
35564692 AAATCAAAATTAATGTATATAACTGCACATT
1 AAATCAAAATTCATGTATAAAACTGCACATA
*
35564723 AAATCATAATTCATGTATA
1 AAATCAAAATTCATGTATA
35564742 GTTTTGAGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.36
30 10 0.24
31 17 0.40
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (31 bp):
AAATCAAAATTCATGTATAAAACTGCACATA
Found at i:35570464 original size:18 final size:18
Alignment explanation
Indices: 35570441--35570483 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
35570431 AAATATATTT
35570441 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
35570459 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
35570477 TTAATTA
1 TTAATTA
35570484 TATCTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:35573749 original size:17 final size:17
Alignment explanation
Indices: 35573711--35573809 Score: 103
Period size: 17 Copynumber: 5.9 Consensus size: 17
35573701 TTTTTTAAAA
*
35573711 TTTAAATCTAAATTTA-
1 TTTAAATTTAAATTTAT
* *
35573727 TTTAAATTTGAATTTAC
1 TTTAAATTTAAATTTAT
*
35573744 TTTAAATTTAAACTTAT
1 TTTAAATTTAAATTTAT
* * ** *
35573761 TTTGAGTTTGGATTTAA
1 TTTAAATTTAAATTTAT
35573778 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
35573795 TTTAAA-TTAAATTTA
1 TTTAAATTTAAATTTA
35573810 AACTTTAAAT
Statistics
Matches: 66, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
16 23 0.35
17 43 0.65
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:35573782 original size:34 final size:34
Alignment explanation
Indices: 35573709--35573819 Score: 127
Period size: 34 Copynumber: 3.3 Consensus size: 34
35573699 ATTTTTTTAA
*
35573709 AATTTAAATCTAAATTTA-TTTAAATTTGAATTT
1 AATTTAAATTTAAATTTATTTTAAATTTGAATTT
* * * * *
35573742 ACTTTAAATTTAAACTTATTTTGAGTTTGGATTT
1 AATTTAAATTTAAATTTATTTTAAATTTGAATTT
*
35573776 AATTTAAATTTAAATTTATTTTAAA-TTAAATTT
1 AATTTAAATTTAAATTTATTTTAAATTTGAATTT
35573809 AAACTTTAAAT
1 -AA-TTTAAAT
35573820 GTCCAAAATA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
33 21 0.33
34 35 0.56
35 7 0.11
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.51
Consensus pattern (34 bp):
AATTTAAATTTAAATTTATTTTAAATTTGAATTT
Found at i:35573804 original size:22 final size:23
Alignment explanation
Indices: 35573773--35573816 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
35573763 TGAGTTTGGA
*
35573773 TTTAATTTAAATTTAAA-TTTAT
1 TTTAAATTAAATTTAAACTTTAT
35573795 TTTAAATTAAATTTAAACTTTA
1 TTTAAATTAAATTTAAACTTTA
35573817 AATGTCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAAATTAAATTTAAACTTTAT
Found at i:35573818 original size:7 final size:6
Alignment explanation
Indices: 35573708--35573819 Score: 76
Period size: 6 Copynumber: 19.7 Consensus size: 6
35573698 AATTTTTTTA
* * *
35573708 AAATTT AAATCT AAATTT --ATTT AAATTT GAATTT -ACTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * * * ** *
35573753 AAACTT -ATTTT GAGTTT GGATTT -AATTT AAATTT AAATTT -ATTTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
35573798 AAA-TT AAATTT AAACTTT AAAT
1 AAATTT AAATTT AAA-TTT AAAT
35573820 GTCCAAAATA
Statistics
Matches: 84, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
4 4 0.05
5 20 0.24
6 54 0.64
7 6 0.07
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:35574503 original size:9 final size:9
Alignment explanation
Indices: 35574489--35574550 Score: 61
Period size: 9 Copynumber: 6.6 Consensus size: 9
35574479 TTTTCATTGC
35574489 TAATATTAA
1 TAATATTAA
35574498 TAATATTAA
1 TAATATTAA
*
35574507 TAAGTTTTTAA
1 TAA--TATTAA
*
35574518 TAATAATAA
1 TAATATTAA
*
35574527 TAATAATTAG
1 TAAT-ATTAA
*
35574537 TAATATTAT
1 TAATATTAA
35574546 TAATA
1 TAATA
35574551 AAAAAGAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
9 29 0.66
10 7 0.16
11 8 0.18
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (9 bp):
TAATATTAA
Found at i:35575686 original size:29 final size:30
Alignment explanation
Indices: 35575649--35575920 Score: 125
Period size: 29 Copynumber: 9.3 Consensus size: 30
35575639 CCTAAACTTA
35575649 TCCAAAAA-TCATATTTTGACCCTC-AAACT
1 TCCAAAAATTCATATTTTGACCC-CAAAACT
*
35575678 TCCAAAAATTCCAT-TTTT-ACCCCTAAACT
1 TCCAAAAATT-CATATTTTGACCCCAAAACT
*
35575707 TCCAAAAATTC-CATTTTGACCCCAAAACT
1 TCCAAAAATTCATATTTTGACCCCAAAACT
* * * *
35575736 TCTAAAAATT-ACCATTTT-ACCTC-GAA-T
1 TCCAAAAATTCA-TATTTTGACCCCAAAACT
*
35575763 ATCAAAAAATTTCAT-TTTTGACCCCAAAACT
1 -TCCAAAAA-TTCATATTTTGACCCCAAAACT
* ***
35575794 T--ATAAAATT-ACCATTTT-ACCCTTGAA-T
1 TCCA-AAAATTCA-TATTTTGACCCCAAAACT
* *
35575821 GTCTAAAAATTCCAT-TTTTGACCTCAAAACT
1 -TCCAAAAATT-CATATTTTGACCCCAAAACT
* *
35575852 TCTAAAAATTACAT-TTTT-ACCCTC-GAACT
1 TCCAAAAATT-CATATTTTGACCC-CAAAACT
* * * *
35575881 TCCTAAAATTCCAT-TTTTGACCTCGAACCT
1 TCCAAAAATT-CATATTTTGACCCCAAAACT
35575911 TCCAAAAATT
1 TCCAAAAATT
35575921 ACCATTTTTC
Statistics
Matches: 189, Mismatches: 28, Indels: 51
0.71 0.10 0.19
Matches are distributed among these distances:
27 3 0.02
28 29 0.15
29 97 0.51
30 54 0.29
31 6 0.03
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (30 bp):
TCCAAAAATTCATATTTTGACCCCAAAACT
Found at i:35575871 original size:59 final size:60
Alignment explanation
Indices: 35575662--35575934 Score: 300
Period size: 58 Copynumber: 4.7 Consensus size: 60
35575652 AAAAATCATA
* * *
35575662 TTTTGACCCTC-AAACTTCCAAAAATT-CCATTTTTACCC-CTAAACTTCCAAAAATTCCA-
1 TTTTGA-CCTCAAAACTTCTAAAAATTACCATTTTTACCCTC-GAACTTCTAAAAATTCCAT
* * *
35575720 TTTTGACCCCAAAACTTCTAAAAATTACCA-TTTTA-CCTCGAA-TATCAAAAAATTTCAT
1 TTTTGACCTCAAAACTTCTAAAAATTACCATTTTTACCCTCGAACT-TCTAAAAATTCCAT
* * *
35575778 TTTTGACCCCAAAACTTAT-AAAATTACCA-TTTTACCCTTGAA-TGTCTAAAAATTCCAT
1 TTTTGACCTCAAAACTTCTAAAAATTACCATTTTTACCCTCGAACT-TCTAAAAATTCCAT
35575836 TTTTGACCTCAAAACTTCTAAAAATTA-CATTTTTACCCTCGAACTTCCT-AAAATTCCAT
1 TTTTGACCTCAAAACTTCTAAAAATTACCATTTTTACCCTCGAACTT-CTAAAAATTCCAT
* * * *
35575895 TTTTGACCTCGAACCTTCCAAAAATTACCATTTTTCCCCT
1 TTTTGACCTCAAAACTTCTAAAAATTACCATTTTTACCCT
35575935 GAGCATTCAA
Statistics
Matches: 187, Mismatches: 17, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
56 1 0.01
57 33 0.18
58 82 0.44
59 57 0.30
60 14 0.07
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (60 bp):
TTTTGACCTCAAAACTTCTAAAAATTACCATTTTTACCCTCGAACTTCTAAAAATTCCAT
Found at i:35575945 original size:29 final size:29
Alignment explanation
Indices: 35575911--35575976 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
35575901 CCTCGAACCT
*
35575911 TCCAAAAATTACCATTTT-TCCCCTGAGCA
1 TCCAAAAATTACCATTTTACCCCCTG-GCA
* *
35575940 TTC-AAAATTACCGTTTTACCCCCTGGCA
1 TCCAAAAATTACCATTTTACCCCCTGGCA
35575968 TCCAAAAAT
1 TCCAAAAAT
35575977 CACACTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.32, C:0.30, G:0.08, T:0.30
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCTGGCA
Found at i:35576915 original size:30 final size:30
Alignment explanation
Indices: 35576881--35577168 Score: 208
Period size: 29 Copynumber: 9.8 Consensus size: 30
35576871 CATTAGGGAG
35576881 TAAAATAGTAATTTTTGGAAAGTTTGGGGT
1 TAAAATAGTAATTTTTGGAAAGTTTGGGGT
** *
35576911 TAAAAATAG-AA-TTTTCAAAAGTTCGAGGGT
1 T-AAAATAGTAATTTTTGGAAAGTTTG-GGGT
*
35576941 AAAAATA-TAATTTTTGGAAAGTTTAGGGG-
1 TAAAATAGTAATTTTTGGAAAGTTT-GGGGT
* *
35576970 TAAAATA-TAATTTTTGGAAATTTTAGGG-
1 TAAAATAGTAATTTTTGGAAAGTTTGGGGT
* * * *
35576998 TAAAATGGTAATTTTTTG-AATTTTGGTGT
1 TAAAATAGTAATTTTTGGAAAGTTTGGGGT
* * *
35577027 TAAAA-ATGGAATCTTTGG-AAGTTTGGGGG
1 TAAAATA-GTAATTTTTGGAAAGTTTGGGGT
* ** * *
35577056 TAAAATGGTAA-TTTTCAAAAGTTTCGAGT
1 TAAAATAGTAATTTTTGGAAAGTTTGGGGT
*
35577085 ATAAAA-ATGTAATTTTTGG-AAGTTCGGGGT
1 -TAAAATA-GTAATTTTTGGAAAGTTTGGGGT
35577115 TAAAA-ATGTAATTTTTGGAAAGTTTAGGGGT
1 TAAAATA-GTAATTTTTGGAAAGTTT-GGGGT
* * *
35577146 CAAAATA-TGATTTTTGGATAGTT
1 TAAAATAGTAATTTTTGGAAAGTT
35577169 AAGAGACCTC
Statistics
Matches: 203, Mismatches: 39, Indels: 32
0.74 0.14 0.12
Matches are distributed among these distances:
28 20 0.10
29 105 0.52
30 56 0.28
31 21 0.10
32 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (30 bp):
TAAAATAGTAATTTTTGGAAAGTTTGGGGT
Found at i:35577151 original size:59 final size:58
Alignment explanation
Indices: 35576880--35577168 Score: 216
Period size: 59 Copynumber: 4.9 Consensus size: 58
35576870 CCATTAGGGA
* ***
35576880 GTAAAATAGTAATTTTTGGAAAGTTT-GGGGTTAAAAATAG-AATTTTCAAAAGTTCGAGG
1 GTAAAATGGTAATTTTTGGAAAGTTTAGGGG-TAAAAAT-GTAATTTTTGGAAGTTCG-GG
* * * **
35576939 GTAAAAAT-ATAATTTTTGGAAAGTTTAGGGGT-AAAATATAATTTTTGGAAATTTTAGG
1 GT-AAAATGGTAATTTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGG-AAGTTCGGG
* * * * * *
35576997 GTAAAATGGTAATTTTTTG-AA-TTTTGGTGTTAAAAATGGAATCTTTGGAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAAGTTTAGG-GGTAAAAATGTAATTTTTGGAAG-TTCGGG
** * **
35577055 GTAAAATGGTAA-TTTTCAAAAGTTTCGAGTATAAAAATGTAATTTTTGGAAGTTCGGG
1 GTAAAATGGTAATTTTTGGAAAGTTTAG-GGGTAAAAATGTAATTTTTGGAAGTTCGGG
* * *
35577113 GTTAAAAAT-GTAATTTTTGGAAAGTTTAGGGGTCAAAATATGATTTTTGGATAGTT
1 G-T-AAAATGGTAATTTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGA-AGTT
35577169 AAGAGACCTC
Statistics
Matches: 181, Mismatches: 34, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
56 5 0.03
57 15 0.08
58 61 0.34
59 69 0.38
60 31 0.17
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (58 bp):
GTAAAATGGTAATTTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTCGGG
Found at i:35578282 original size:9 final size:9
Alignment explanation
Indices: 35578263--35578322 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
35578253 ATTTTCTTTT
35578263 TTATTAATA
1 TTATTAATA
* *
35578272 ATATTACTAA
1 TTATTAAT-A
*
35578282 TTATTATTA
1 TTATTAATA
*
35578291 TTATTAAAGA
1 TTATT-AATA
35578301 CTTATTAATA
1 -TTATTAATA
35578311 TTATTAATA
1 TTATTAATA
35578320 TTA
1 TTA
35578323 GCAATGAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
9 24 0.59
10 12 0.29
11 5 0.12
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (9 bp):
TTATTAATA
Found at i:35579064 original size:16 final size:16
Alignment explanation
Indices: 35579015--35579065 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
35579005 TTTGGACTTT
35579015 TAAAGTTTAAATTTAAA
1 TAAA-TTTAAATTTAAA
* *
35579032 GTAAATTCAAATCTAAA
1 -TAAATTTAAATTTAAA
*
35579049 TAAATTTAGATTTAAA
1 TAAATTTAAATTTAAA
35579065 T
1 T
35579066 TTTAAAAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 14 0.50
17 10 0.36
18 4 0.14
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:35580048 original size:49 final size:49
Alignment explanation
Indices: 35579994--35580327 Score: 284
Period size: 49 Copynumber: 6.8 Consensus size: 49
35579984 GTAGTCGTAG
* * * *
35579994 CCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGTGGCTTAAA
1 CCTTTCCCTCCATATCTTCGAGGTACTAGATTCGCCGTTGCGACTTAAA
* * * ** * * *
35580043 TCTTTCTCTTCA-CGCTTCCGAGGTACAAGGTTC-CCATTGCGACTTAAA
1 CCTTTCCCTCCATATCTT-CGAGGTACTAGATTCGCCGTTGCGACTTAAA
* * * * *
35580091 CCTTTCCCTCCATATCTTCGTGATACTGGATTCACCGTTGCGGCTTAAA
1 CCTTTCCCTCCATATCTTCGAGGTACTAGATTCGCCGTTGCGACTTAAA
* * * * *
35580140 TCTTTCCCTTCAT-GCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAA
1 CCTTTCCCTCCATATCTTC-GAGGTACTAGATTCGCCGTTGCGACTTAAA
* * *
35580189 CCTTTCCCTCCATATCCTCGCA-GTACTAGATTCGTCGTTGCGGCTTAAA
1 CCTTTCCCTCCATATCTTCG-AGGTACTAGATTCGCCGTTGCGACTTAAA
* * * * *
35580238 TCTTTCCCTTCAT-GCTTCTGAGGTACTAGGTTCGCCATTGCGACTTAAA
1 CCTTTCCCTCCATATCTTC-GAGGTACTAGATTCGCCGTTGCGACTTAAA
* * *
35580287 CCTTTCCCTCCATATCTTC-ATGGTATTGGATTCGCCATTGC
1 CCTTTCCCTCCATATCTTCGA-GGTACTAGATTCGCCGTTGC
35580328 CCTTCATGCT
Statistics
Matches: 219, Mismatches: 56, Indels: 20
0.74 0.19 0.07
Matches are distributed among these distances:
48 42 0.19
49 169 0.77
50 8 0.04
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (49 bp):
CCTTTCCCTCCATATCTTCGAGGTACTAGATTCGCCGTTGCGACTTAAA
Found at i:35580111 original size:97 final size:98
Alignment explanation
Indices: 35579994--35580575 Score: 622
Period size: 98 Copynumber: 6.1 Consensus size: 98
35579984 GTAGTCGTAG
* * *
35579994 CCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGTGGCTTAAATCTTTCTCTTCACGCT
1 CCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCT
*
35580059 TCCGAGGTACAAGGTTC-CCATTGCGACTTAAA
66 TCTGAGGTACAAGGTTCGCCATTGCGACTTAAA
* * **
35580091 CCTTTCCCTCCATATCTTCGTGATACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCT
1 CCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCT
*
35580156 TCTGAGGTACAAGGTTCGCCGTTGCGACTTAAA
66 TCTGAGGTACAAGGTTCGCCATTGCGACTTAAA
* **
35580189 CCTTTCCCTCCATATCCTCGCAGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCT
1 CCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCT
*
35580254 TCTGAGGTACTAGGTTCGCCATTGCGACTTAAA
66 TCTGAGGTACAAGGTTCGCCATTGCGACTTAAA
* * * *
35580287 CCTTTCCCTCCATATCTTCATGGTATTGGA-T--TC---GC--C----A--TTGCCCTTCATGCT
1 CCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCT
* * * * *
35580338 TTTGAGCTACTAGGTTCGTCGTTGCGACTTAAA
66 TCTGAGGTACAAGGTTCGCCATTGCGACTTAAA
* * * * * *
35580371 CCTTCCCCTCCGTATCCTT-GTGGTACTAGATTCGCCATTACGGTTTAAATCTTTCCCTTCATGC
1 CCTTTCCCTCCATAT-CTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGC
* * * *
35580435 TTCTGAGGTGCAAGGTTTGCCGTTGTGACTTAAA
65 TTCTGAGGTACAAGGTTCGCCATTGCGACTTAAA
*** * * * ** * *
35580469 CCTTTCCCTTTGTGTCTTTGTGGTACTGGATTCACCGTTGCAGCTTAAATCTTTCCCTTTATGTC
1 CCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATG-C
* * *
35580534 TT-TAAGGTATAAGGTTCGCCATTGTGACTTAAA
65 TTCTGAGGTACAAGGTTCGCCATTGCGACTTAAA
35580567 CCTTTCCCT
1 CCTTTCCCT
35580576 TTGAATCTTC
Statistics
Matches: 406, Mismatches: 61, Indels: 35
0.81 0.12 0.07
Matches are distributed among these distances:
84 63 0.16
85 4 0.01
86 1 0.00
87 1 0.00
90 2 0.00
92 2 0.00
95 2 0.00
96 1 0.00
97 78 0.19
98 249 0.61
99 3 0.01
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (98 bp):
CCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCT
TCTGAGGTACAAGGTTCGCCATTGCGACTTAAA
Found at i:35580395 original size:84 final size:84
Alignment explanation
Indices: 35580243--35580409 Score: 237
Period size: 84 Copynumber: 2.0 Consensus size: 84
35580233 TTAAATCTTT
* *
35580243 CCCTTCATGCTTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTCCATATCTTCAT
1 CCCTTCATGCTTCTGAGCTACTAGGTTCGCCATTGCGACTTAAACCTTCCCCTCCATATCTTCAT
* *
35580308 GGTATTGGATTCGCCATTG
66 GGTACTAGATTCGCCATTG
* * * * *
35580327 CCCTTCATGCTTTTGAGCTACTAGGTTCGTCGTTGCGACTTAAACCTTCCCCTCCGTATCCTT-G
1 CCCTTCATGCTTCTGAGCTACTAGGTTCGCCATTGCGACTTAAACCTTCCCCTCCATAT-CTTCA
35580391 TGGTACTAGATTCGCCATT
65 TGGTACTAGATTCGCCATT
35580410 ACGGTTTAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 70 0.96
85 3 0.04
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.36
Consensus pattern (84 bp):
CCCTTCATGCTTCTGAGCTACTAGGTTCGCCATTGCGACTTAAACCTTCCCCTCCATATCTTCAT
GGTACTAGATTCGCCATTG
Found at i:35580467 original size:182 final size:182
Alignment explanation
Indices: 35580145--35580477 Score: 504
Period size: 182 Copynumber: 1.8 Consensus size: 182
35580135 TTAAATCTTT
* *
35580145 CCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCCTCGC
1 CCCTTCATGCTTCTGAGCTACAAGGTTCGCCGTTGCGACTTAAACCTTCCCCTCCATATCCTCGC
* * * *
35580210 AGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACTAGGTTCGCCA
66 AGTACTAGATTCGCCATTACGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCA
35580275 TTGCGACTTAAACCTTTCCCTCCATATCTTCATGGTATTGGATTCGCCATTG
131 TTGCGACTTAAACCTTTCCCTCCATATCTTCATGGTATTGGATTCGCCATTG
* * * * * *
35580327 CCCTTCATGCTTTTGAGCTACTAGGTTCGTCGTTGCGACTTAAACCTTCCCCTCCGTATCCTTGT
1 CCCTTCATGCTTCTGAGCTACAAGGTTCGCCGTTGCGACTTAAACCTTCCCCTCCATATCCTCGC
* * * * *
35580392 GGTACTAGATTCGCCATTACGGTTTAAATCTTTCCCTTCATGCTTCTGAGGTGCAAGGTTTGCCG
66 AGTACTAGATTCGCCATTACGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCA
*
35580457 TTGTGACTTAAACCTTTCCCT
131 TTGCGACTTAAACCTTTCCCT
35580478 TTGTGTCTTT
Statistics
Matches: 133, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
182 133 1.00
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.36
Consensus pattern (182 bp):
CCCTTCATGCTTCTGAGCTACAAGGTTCGCCGTTGCGACTTAAACCTTCCCCTCCATATCCTCGC
AGTACTAGATTCGCCATTACGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCA
TTGCGACTTAAACCTTTCCCTCCATATCTTCATGGTATTGGATTCGCCATTG
Found at i:35580507 original size:49 final size:48
Alignment explanation
Indices: 35580454--35580578 Score: 137
Period size: 49 Copynumber: 2.6 Consensus size: 48
35580444 GCAAGGTTTG
**
35580454 CCGTTGTGACTTAAACCTTTCCCTTTGTGTCTTTGTGGTACT-GGATTCA
1 CCGTTGTGACTTAAACCTTTCCCTTTGTGTCTTTAAGGTA-TAGG-TTCA
* * * *
35580503 CCGTTG-CAGCTTAAATCTTTCCCTTTATGTCTTTAAGGTATAAGGTTCG
1 CCGTTGTGA-CTTAAACCTTTCCCTTTGTGTCTTTAAGGTAT-AGGTTCA
*
35580552 CCATTGTGACTTAAACCTTTCCCTTTG
1 CCGTTGTGACTTAAACCTTTCCCTTTG
35580579 AATCTTCATG
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
48 2 0.03
49 57 0.92
50 3 0.05
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.42
Consensus pattern (48 bp):
CCGTTGTGACTTAAACCTTTCCCTTTGTGTCTTTAAGGTATAGGTTCA
Found at i:35581556 original size:23 final size:23
Alignment explanation
Indices: 35581529--35581573 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
35581519 CGACCTCTCC
*
35581529 TTTTATTTTTCTCGTTTTTTCTA
1 TTTTATTTTTCCCGTTTTTTCTA
*
35581552 TTTTATTTTTCCCTTTTTTTCT
1 TTTTATTTTTCCCGTTTTTTCT
35581574 TCTTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTATTTTTCCCGTTTTTTCTA
Found at i:35581610 original size:27 final size:27
Alignment explanation
Indices: 35581557--35581641 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
35581547 TTCTATTTTA
* *
35581557 TTTTTCCCTTTTTTTC-TTCTTTTTTCT
1 TTTTTCCCTTTTTTTCTTTC-CTCTTCT
35581584 TTTTTCCCTTTTTTTCTTTCCTCTTCT
1 TTTTTCCCTTTTTTTCTTTCCTCTTCT
*
35581611 TTTTT-TCTCTTTTTTCTTT-CTCTTCT
1 TTTTTCCCT-TTTTTTCTTTCCTCTTCT
35581637 TTTTT
1 TTTTT
35581642 ATTTATTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
26 14 0.26
27 36 0.68
28 3 0.06
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTTCCCTTTTTTTCTTTCCTCTTCT
Found at i:35581621 original size:10 final size:10
Alignment explanation
Indices: 35581534--35581625 Score: 50
Period size: 10 Copynumber: 9.4 Consensus size: 10
35581524 TCTCCTTTTA
35581534 TTTTTCTCGTT
1 TTTTTCTC-TT
* *
35581545 TTTTCTATTTT
1 TTTT-TCTCTT
*
35581556 ATTTTTCCCTT
1 -TTTTTCTCTT
*
35581567 TTTTTCT-TC
1 TTTTTCTCTT
35581576 TTTTT-TC-T
1 TTTTTCTCTT
*
35581584 TTTTTCCCTT
1 TTTTTCTCTT
35581594 TTTTTCT-TT
1 TTTTTCTCTT
** *
35581603 CCTCT-TCTT
1 TTTTTCTCTT
35581612 TTTTTCTCTT
1 TTTTTCTCTT
35581622 TTTT
1 TTTT
35581626 CTTTCTCTTC
Statistics
Matches: 58, Mismatches: 16, Indels: 15
0.65 0.18 0.17
Matches are distributed among these distances:
8 7 0.12
9 15 0.26
10 21 0.36
11 9 0.16
12 6 0.10
ACGTcount: A:0.02, C:0.21, G:0.01, T:0.76
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:35581630 original size:13 final size:13
Alignment explanation
Indices: 35581566--35581639 Score: 62
Period size: 14 Copynumber: 5.5 Consensus size: 13
35581556 ATTTTTCCCT
*
35581566 TTTTTTC-TTCTT
1 TTTTTTCTTTCTC
* *
35581578 TTTTCTTTTTTCCC
1 TTTT-TTCTTTCTC
35581592 TTTTTTTCTTTCCTC
1 -TTTTTTCTTT-CTC
35581607 TTCTTTT-TTTCTC
1 TT-TTTTCTTTCTC
35581620 TTTTTTCTTTCTC
1 TTTTTTCTTTCTC
35581633 TTCTTTT
1 TT-TTTT
35581640 TTATTTATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
12 8 0.16
13 15 0.30
14 17 0.34
15 10 0.20
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTCTTTCTC
Found at i:35581650 original size:26 final size:27
Alignment explanation
Indices: 35581583--35581655 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
35581573 TTCTTTTTTC
*
35581583 TTTTTTCCCTTTTTTTCTTTCCTCTTCT
1 TTTTTTCTC-TTTTTTCTTTCCTCTTCT
35581611 TTTTTTCTCTTTTTTCTTT-CTCTTCT
1 TTTTTTCTCTTTTTTCTTTCCTCTTCT
* *
35581637 TTTTTATTTATTTTTTCTT
1 TTTTT-TCTCTTTTTTCTT
35581656 CATTGCATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 12 0.29
27 21 0.51
28 8 0.20
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (27 bp):
TTTTTTCTCTTTTTTCTTTCCTCTTCT
Found at i:35581653 original size:23 final size:26
Alignment explanation
Indices: 35581596--35581654 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
35581586 TTTCCCTTTT
* *
35581596 TTTCTTTCCTCTTCTTTTTTTCTCTTT
1 TTTCTTT-CTCTTCTTTTTTTATCTTA
35581623 TTTCTTTCTCTTC-TTTTTTAT-TTA
1 TTTCTTTCTCTTCTTTTTTTATCTTA
35581647 TTT-TTTCT
1 TTTCTTTCT
35581655 TCATTGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 5 0.17
24 5 0.17
25 7 0.23
26 6 0.20
27 7 0.23
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTCTTTCTCTTCTTTTTTTATCTTA
Found at i:35581824 original size:35 final size:35
Alignment explanation
Indices: 35581785--35581857 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
35581775 TCCTTAGAAT
35581785 TCTTTTGTAATAAAGATCCTTTTCAAAACTAGAGC
1 TCTTTTGTAATAAAGATCCTTTTCAAAACTAGAGC
* *
35581820 TCTTTTGTAATCAATATCCTTTTCAAAACTAGAGC
1 TCTTTTGTAATAAAGATCCTTTTCAAAACTAGAGC
35581855 TCT
1 TCT
35581858 CTCGTGGAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.40
Consensus pattern (35 bp):
TCTTTTGTAATAAAGATCCTTTTCAAAACTAGAGC
Found at i:35583959 original size:18 final size:18
Alignment explanation
Indices: 35583936--35583981 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
35583926 TATGATGATA
35583936 TATATGTGATGA-ACAATG
1 TATATGTGATGAGA-AATG
*
35583954 TATATGTGAAGAGAAATG
1 TATATGTGATGAGAAATG
*
35583972 TAAATGTGAT
1 TATATGTGAT
35583982 ATATGAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (18 bp):
TATATGTGATGAGAAATG
Found at i:35584134 original size:23 final size:24
Alignment explanation
Indices: 35584084--35584144 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
35584074 CGCTAGCGCG
* *
35584084 CTTACTGTTCCACACTTCGTGTGT
1 CTTACTGTTCCGCACTTCGTCTGT
*
35584108 -TTACTATTCCGCACTTCGTCT-T
1 CTTACTGTTCCGCACTTCGTCTGT
*
35584130 CTTACTGTTTCGCAC
1 CTTACTGTTCCGCAC
35584145 CTTATGTGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.13, C:0.31, G:0.13, T:0.43
Consensus pattern (24 bp):
CTTACTGTTCCGCACTTCGTCTGT
Found at i:35584195 original size:22 final size:22
Alignment explanation
Indices: 35584149--35584227 Score: 104
Period size: 23 Copynumber: 3.5 Consensus size: 22
35584139 TCGCACCTTA
* *
35584149 TGTGCCTACTGATTTGCGCTATG
1 TGTGCCTACTGA-TTGCACTGTG
*
35584172 TGCGCCTACTGATTGCACTGTG
1 TGTGCCTACTGATTGCACTGTG
35584194 TGTGCCTACTAGATTGCACTGTG
1 TGTGCCTACT-GATTGCACTGTG
*
35584217 TGTGCTTACTG
1 TGTGCCTACTG
35584228 TTAAGTACTC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
22 18 0.36
23 32 0.64
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.37
Consensus pattern (22 bp):
TGTGCCTACTGATTGCACTGTG
Found at i:35590538 original size:16 final size:16
Alignment explanation
Indices: 35590517--35590549 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35590507 GTAATTAAGG
35590517 ATAAAACA-TTAATCAA
1 ATAAAACACTT-ATCAA
35590533 ATAAAACACTTATCAA
1 ATAAAACACTTATCAA
35590549 A
1 A
35590550 GATAGTGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (16 bp):
ATAAAACACTTATCAA
Found at i:35597169 original size:49 final size:49
Alignment explanation
Indices: 35596944--35597279 Score: 237
Period size: 49 Copynumber: 6.8 Consensus size: 49
35596934 TACAGGTTTA
* * * * *
35596944 AAGGGAAAGGTTTAAGCCACAACGGCGAACCTTGTACCTCAGGAGCACG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCACAGGAGCATG
* * * ** *
35596993 AAGGCAAAGATTTAAGCCGCAACGGCGAATCC-AATACCACGAAGATAACG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCAC-AGGAGCATG
* * * **
35597043 AAGGGAAAGATTTAAGCTGCAACGGTGAATCC-AGTACCACGAAGATAATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCAC-AGGAGCATG
** * * * * * *
35597093 GCGAGAAAGGTTTAAGCTGCAAAGGCGAACCTTGTACCTCAGGAGCATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCACAGGAGCATG
* * * *
35597142 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAC-GAAGATATA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCACAGGAG-CATG
* * * * * * * * *
35597191 AAAGGAAAGGTTTAAGTCGTAATGGCAAACCTTGTACCTCAGAAGCATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCACAGGAGCATG
* * * *
35597240 AAGGGAAAGATTTGAGCTGCAACGACGAATCTAGTACCAC
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCAC
35597280 GAAGATATGG
Statistics
Matches: 222, Mismatches: 60, Indels: 10
0.76 0.21 0.03
Matches are distributed among these distances:
48 3 0.01
49 133 0.60
50 86 0.39
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCACAGGAGCATG
Found at i:35597251 original size:98 final size:100
Alignment explanation
Indices: 35597042--35597287 Score: 347
Period size: 98 Copynumber: 2.5 Consensus size: 100
35597032 CGAAGATAAC
* * ***
35597042 GAAGGGAAAGATTTAAGCTGCAACGGTGAATCCAGTACCACGAAGATA-ATGGCGAGAAAGGTTT
1 GAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGATATATAAAGAGAAAGGTTT
* *
35597106 AAGCTGCAAAGGCGAACCTTGTACCTCAGGAGCAT
66 AAGCTGCAAAGGCAAACCTTGTACCTCAGAAGCAT
*
35597141 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATA-AAAG-GAAAGGTTT
1 GAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGATATATAAAGAGAAAGGTTT
* *
35597204 AAG-TCGTAATGGCAAACCTTGTACCTCAGAAGCAT
66 AAGCT-GCAAAGGCAAACCTTGTACCTCAGAAGCAT
* *
35597239 GAAGGGAAAGATTTGAGCTGCAACGACGAATCTAGTACCACGAAGATAT
1 GAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGATAT
35597288 GGAGTGAAGG
Statistics
Matches: 132, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
97 1 0.01
98 84 0.64
99 46 0.35
100 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.19
Consensus pattern (100 bp):
GAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGATATATAAAGAGAAAGGTTT
AAGCTGCAAAGGCAAACCTTGTACCTCAGAAGCAT
Found at i:35597327 original size:98 final size:96
Alignment explanation
Indices: 35597042--35597319 Score: 322
Period size: 98 Copynumber: 2.8 Consensus size: 96
35597032 CGAAGATAAC
* * * * *
35597042 GAAGGGAAAGATTTAAGCTGCAACGGTGAATCCAGTACCACGAAGATAATGGCGAGAAAGGTTTA
1 GAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGAT-ATGGAG-GAAGGGTTAA
* *
35597107 AGCTGCAAAGGCGAACCTTGTACCTCAGGAGCAT
64 ATC-GCAAAGGCGAACCTTGTACCTCAGAAGCAT
* ** *
35597141 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATAAAAGGAAAGGTTTAA
1 GAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGATAT-GGAGG-AAGGGTTAA
* * * *
35597206 GTCGTAATGGCAAACCTTGTACCTCAGAAGCAT
64 ATCGCAAAGGCGAACCTTGTACCTCAGAAGCAT
* *
35597239 GAAGGGAAAGATTTGAGCTGCAACGACGAATCTAGTACCACGAAGATATGGAGTGAAGGGTTACA
1 GAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGATATGGAG-GAAGGGTTA-A
* *
35597304 ATCGCAACGACGAACC
64 ATCGCAAAGGCGAACC
35597320 CGGTACCTTA
Statistics
Matches: 149, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
97 9 0.06
98 88 0.59
99 52 0.35
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (96 bp):
GAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGATATGGAGGAAGGGTTAAAT
CGCAAAGGCGAACCTTGTACCTCAGAAGCAT
Found at i:35606244 original size:51 final size:52
Alignment explanation
Indices: 35606146--35606319 Score: 190
Period size: 51 Copynumber: 3.3 Consensus size: 52
35606136 CCCATGGCTC
* ***
35606146 TTTTATCTGATAAAATATTTTTTTGTGTTGCTCAAGCCATAATCGACACCCT
1 TTTTATCTGATAAAATATTTTTTTGTGTTGCTCATGCCATGGCCGACACCCT
* * *
35606198 TTTTATTTGATAAAAT-TTTTTTTGTGTTGCCCATGCCACGGCCGACA-CCT
1 TTTTATCTGATAAAATATTTTTTTGTGTTGCTCATGCCATGGCCGACACCCT
* * * *
35606248 CCTTTATCTGATAAAAAAATATTTTTTTGGTGTCGCTCATGCCATGGCCGAGACCCC
1 -TTTTATCTGAT---AAAATATTTTTTT-GTGTTGCTCATGCCATGGCCGACACCCT
35606305 TTTTATCTGATAAAA
1 TTTTATCTGATAAAA
35606320 AAATTTTGTA
Statistics
Matches: 100, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
50 3 0.03
51 34 0.34
52 15 0.15
53 4 0.04
54 5 0.05
55 7 0.07
56 30 0.30
57 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (52 bp):
TTTTATCTGATAAAATATTTTTTTGTGTTGCTCATGCCATGGCCGACACCCT
Found at i:35606297 original size:56 final size:54
Alignment explanation
Indices: 35606145--35606326 Score: 169
Period size: 56 Copynumber: 3.4 Consensus size: 54
35606135 GCCCATGGCT
* * * * ****
35606145 CTTTTATCTGAT-AAAATA-TTTTTTTGTGTTGCTCAAGCCATAATCGACACCC
1 CTTTTATCTGATAAAAAAATTTTTTTTGTGTCGCCCATGCCACGGCCGACACCC
* * *
35606197 TTTTTATTTGAT---AAAATTTTTTTTGTGTTGCCCATGCCACGGCCGACACCTC
1 CTTTTATCTGATAAAAAAATTTTTTTTGTGTCGCCCATGCCACGGCCGACACC-C
* * *
35606249 C-TTTATCTGATAAAAAAATATTTTTTTGGTGTCGCTCATGCCATGGCCGAGACCC
1 CTTTTATCTGATAAAAAAAT-TTTTTTT-GTGTCGCCCATGCCACGGCCGACACCC
35606304 CTTTTATCTGATAAAAAAATTTT
1 CTTTTATCTGATAAAAAAATTTT
35606327 GTATCGTCCA
Statistics
Matches: 107, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
50 3 0.03
51 36 0.34
52 11 0.10
54 5 0.05
55 12 0.11
56 40 0.37
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (54 bp):
CTTTTATCTGATAAAAAAATTTTTTTTGTGTCGCCCATGCCACGGCCGACACCC
Found at i:35608293 original size:18 final size:18
Alignment explanation
Indices: 35608260--35608295 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35608250 GACACGTGTG
*
35608260 TATTTTTTTTAAATACGA
1 TATTTTTTTGAAATACGA
*
35608278 TATTTTTTTGATATACGA
1 TATTTTTTTGAAATACGA
35608296 AAATACGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (18 bp):
TATTTTTTTGAAATACGA
Found at i:35608521 original size:62 final size:62
Alignment explanation
Indices: 35608455--35608682 Score: 318
Period size: 61 Copynumber: 3.7 Consensus size: 62
35608445 TCGGCCATGC
* *
35608455 AAAAATTTCAATTTTTTTTTGTGTTGGCCATCAAATGGCCGACATCCCCTATTCTCGAGAAA
1 AAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACATCCCCTATTCTCGAGAAA
* * *
35608517 AAAAA-TTAAAATTTTTTTGGTGTTGGCCATCAAATGGTCGACACCCCCTATTCTCGAGAAA
1 AAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACATCCCCTATTCTCGAGAAA
* * * *
35608578 AAAAATTT-AAATTCTTTTGGTGTTGGCCATCAAATGGCTGACATCCCCTTTTTTCGA-ATAA
1 AAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACATCCCCTATTCTCGAGA-AA
* * *
35608639 AAAAATTCCAATTTTTTTTTGTGTTGGCCATCAAATGGCCGACA
1 AAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACA
35608683 CCAGCTTCTC
Statistics
Matches: 147, Mismatches: 16, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
60 1 0.01
61 108 0.73
62 38 0.26
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (62 bp):
AAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACATCCCCTATTCTCGAGAAA
Found at i:35612230 original size:12 final size:12
Alignment explanation
Indices: 35612188--35612235 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
35612178 TTTTGTGTAA
*
35612188 AAATTAATTTGA
1 AAATTAATTTGG
35612200 AAATTAATTTAAGTTG
1 AAATTAATTT--G--G
35612216 AAATTAATTTGG
1 AAATTAATTTGG
35612228 AAATTAAT
1 AAATTAAT
35612236 GAACATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
AAATTAATTTGG
Found at i:35612479 original size:72 final size:70
Alignment explanation
Indices: 35612401--35612625 Score: 220
Period size: 83 Copynumber: 3.0 Consensus size: 70
35612391 TATTGTATTA
* *
35612401 ATTTGACAATATATTATTTATCAAATTTTCATA-TTTAAAGT-ACAAATTATTATTATATTATAA
1 ATTTGACAATACATTATTTAT-AAATTTT-ATACTTTAAA-TAAAAAATT-TTATTATATTATAA
35612464 TTTTTATCG
62 TTTTTATCG
*
35612473 ATTTGACAATACATTATTTATTAATTTTATATCTTTAAATAAAAAATTTTATTATATTATAATTT
1 ATTTGACAATACATTATTTATAAATTTTATA-CTTTAAATAAAAAATTTTATTATATTATAATTT
35612538 TTATCATATAATGTGTTG
65 TTATC------------G
* * *
35612556 ATTTGACAATACATTATTTATTAATTTTGTATCTTTAAATAAAAAATTTTATTATATTACAATTT
1 ATTTGACAATACATTATTTATAAATTTTATA-CTTTAAATAAAAAATTTTATTATATTATAATTT
35612621 TTATC
65 TTATC
35612626 ATATTTTAAA
Statistics
Matches: 133, Mismatches: 5, Indels: 19
0.85 0.03 0.12
Matches are distributed among these distances:
70 3 0.02
71 29 0.22
72 32 0.24
83 69 0.52
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (70 bp):
ATTTGACAATACATTATTTATAAATTTTATACTTTAAATAAAAAATTTTATTATATTATAATTTT
TATCG
Found at i:35612565 original size:83 final size:83
Alignment explanation
Indices: 35612472--35612629 Score: 298
Period size: 83 Copynumber: 1.9 Consensus size: 83
35612462 AATTTTTATC
*
35612472 GATTTGACAATACATTATTTATTAATTTTATATCTTTAAATAAAAAATTTTATTATATTATAATT
1 GATTTGACAATACATTATTTATTAATTTTATATCTTTAAATAAAAAATTTTATTATATTACAATT
35612537 TTTATCATATAATGTGTT
66 TTTATCATATAATGTGTT
*
35612555 GATTTGACAATACATTATTTATTAATTTTGTATCTTTAAATAAAAAATTTTATTATATTACAATT
1 GATTTGACAATACATTATTTATTAATTTTATATCTTTAAATAAAAAATTTTATTATATTACAATT
35612620 TTTATCATAT
66 TTTATCATAT
35612630 TTTAAATTTA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (83 bp):
GATTTGACAATACATTATTTATTAATTTTATATCTTTAAATAAAAAATTTTATTATATTACAATT
TTTATCATATAATGTGTT
Found at i:35614347 original size:24 final size:24
Alignment explanation
Indices: 35614303--35614359 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
35614293 ATTTAGATTC
*
35614303 CGAGCCCGAGGATGAGCCCAATGA
1 CGAGCCCGAGGACGAGCCCAATGA
* * *
35614327 CGAGCCCGCGGACGAGGCCAATTA
1 CGAGCCCGAGGACGAGCCCAATGA
*
35614351 CTAGCCCGA
1 CGAGCCCGA
35614360 TTACGAGTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.33, G:0.32, T:0.09
Consensus pattern (24 bp):
CGAGCCCGAGGACGAGCCCAATGA
Found at i:35615832 original size:60 final size:59
Alignment explanation
Indices: 35615760--35616085 Score: 334
Period size: 61 Copynumber: 5.6 Consensus size: 59
35615750 AGGAGAAGTT
* * * * * *
35615760 GGTGTTGGCCATTTGATGGCCAATATAAAAAAATTAGAATTTTTTTATTCGAGAAAAGAG
1 GGTGTCGGCCATTTGATGGCCAACAAAAAAAAATTAGAATTTTTTT-CTCGAGAATAGGG
*
35615820 GGTGTCGACCATTTGATGGCCAACACAAAAAAAAATTAGAATTTTTTTCTCGAGAATAGGG
1 GGTGTCGGCCATTTGATGGCC-A-ACAAAAAAAAATTAGAATTTTTTTCTCGAGAATAGGG
* * *
35615881 GGTGTCGGCCATTTGGTGGCCAACACAAAAAAAATTTGAAAATTTTTTCTCGAGAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACA-AAAAAAAATTAG-AATTTTTTTCTCGAGAATAGGG
* * *
35615942 GGTGTCGGCCATTTGATGGCCAACACCAAAATAATTTA-AAATTTTTTCTCGAGAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACA--AAAAAAAATTAGAATTTTTTTCTCGAGAATAGGG
* * * *
35616002 GG-AT-GGCC----GA----C-ACCAAAAAAATTTAAAATTTTTTTCTCGAGAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACAAAAAAAAATTAGAATTTTTTTCTCGAGAATAGGG
*
35616050 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATT
1 GGTGTCGGCCATTTGATGGCCAACA-AAAAAAAATT
35616086 GGAACAACAC
Statistics
Matches: 225, Mismatches: 23, Indels: 36
0.79 0.08 0.13
Matches are distributed among these distances:
47 10 0.04
48 23 0.10
49 3 0.01
50 5 0.02
54 4 0.02
58 5 0.02
59 6 0.03
60 63 0.28
61 75 0.33
62 31 0.14
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (59 bp):
GGTGTCGGCCATTTGATGGCCAACAAAAAAAAATTAGAATTTTTTTCTCGAGAATAGGG
Found at i:35616015 original size:47 final size:48
Alignment explanation
Indices: 35615956--35616051 Score: 167
Period size: 47 Copynumber: 2.0 Consensus size: 48
35615946 TCGGCCATTT
*
35615956 GATGGCCAACACCAAAATAATTTAAAA-TTTTTTCTCGAGAATAGGGG
1 GATGGCCAACACCAAAAAAATTTAAAATTTTTTTCTCGAGAATAGGGG
*
35616003 GATGGCCGACACCAAAAAAATTTAAAATTTTTTTCTCGAGAATAGGGG
1 GATGGCCAACACCAAAAAAATTTAAAATTTTTTTCTCGAGAATAGGGG
35616051 G
1 G
35616052 TGTCGGCCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 25 0.54
48 21 0.46
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (48 bp):
GATGGCCAACACCAAAAAAATTTAAAATTTTTTTCTCGAGAATAGGGG
Found at i:35616146 original size:81 final size:81
Alignment explanation
Indices: 35616011--35616166 Score: 267
Period size: 81 Copynumber: 1.9 Consensus size: 81
35616001 GGGATGGCCG
*
35616011 ACACCAAAAAAATTTAAAATTTTTTTCTCGAGAATAGGGGGTGTCGGCCATTTGATGGCCAACAC
1 ACACCAAAAAAATTTAAAATTTTTTTCTCGAGAATAGAGGGTGTCGGCCATTTGATGGCCAACAC
35616076 CAAAAAAATTGGAACA
66 CAAAAAAATTGGAACA
* * **
35616092 ACACCAAAAAAATTTAGAATTTTTTTCTCGGGAATAGAGGGTGTCGGTTATTTGATGGCCAACAC
1 ACACCAAAAAAATTTAAAATTTTTTTCTCGAGAATAGAGGGTGTCGGCCATTTGATGGCCAACAC
35616157 CAAAAAAATT
66 CAAAAAAATT
35616167 TGAAAATTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (81 bp):
ACACCAAAAAAATTTAAAATTTTTTTCTCGAGAATAGAGGGTGTCGGCCATTTGATGGCCAACAC
CAAAAAAATTGGAACA
Found at i:35616338 original size:60 final size:57
Alignment explanation
Indices: 35616202--35616345 Score: 139
Period size: 58 Copynumber: 2.5 Consensus size: 57
35616192 GGTGTCGGCC
35616202 ATGTCGGCCATGCAATGGCTAACACCAAAAAATGCAATTTTTTTCTCGAGAAAAGGG
1 ATGTCGGCCATGCAATGGCTAACACCAAAAAATGCAATTTTTTTCTCGAGAAAAGGG
*** * * * *
35616259 AGTGTCGGCCATTTGATGGCTAATACCAAAAAATTTTG-AATTTTTTTTTTTGA-AACAGGGG
1 A-TGTCGGCCATGCAATGGCTAACACCAAAAAA---TGCAA-TTTTTTTCTCGAGAA-AAGGG
* *
35616320 ATGTCGACCATGCAATGGCCAACACC
1 ATGTCGGCCATGCAATGGCTAACACC
35616346 CCAAATTTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
57 1 0.01
58 27 0.40
60 23 0.34
61 17 0.25
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (57 bp):
ATGTCGGCCATGCAATGGCTAACACCAAAAAATGCAATTTTTTTCTCGAGAAAAGGG
Found at i:35619515 original size:26 final size:27
Alignment explanation
Indices: 35619468--35619522 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
35619458 AACTCGAATT
*
35619468 CTAAACCTCAAAACCCTGAACATTAAAC
1 CTAAACCT-AAAACCCTAAACATTAAAC
* *
35619496 CTAAACCT-AAACCTTAAACATTGAAC
1 CTAAACCTAAAACCCTAAACATTAAAC
35619522 C
1 C
35619523 CAAAACCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 16 0.67
28 8 0.33
ACGTcount: A:0.45, C:0.31, G:0.04, T:0.20
Consensus pattern (27 bp):
CTAAACCTAAAACCCTAAACATTAAAC
Found at i:35619933 original size:17 final size:17
Alignment explanation
Indices: 35619911--35620010 Score: 101
Period size: 17 Copynumber: 5.9 Consensus size: 17
35619901 TGTGGATTGT
*
35619911 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
*
35619928 TTTTAAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
* * *
35619945 TCTTAAATTTAAACTCA
1 TTTTAAATTTAAATTTA
* ***
35619962 CTTTGGGTTTAAATTTA
1 TTTTAAATTTAAATTTA
35619979 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
35619996 CTTTAAATTAAAATT
1 TTTTAAATTTAAATT
35620011 AAAAAAAGTC
Statistics
Matches: 64, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 64 1.00
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:35619999 original size:34 final size:34
Alignment explanation
Indices: 35619911--35620010 Score: 119
Period size: 34 Copynumber: 2.9 Consensus size: 34
35619901 TGTGGATTGT
* *
35619911 TTTTAAATTTTAATTTATTTTAAGTTTAAATTTA
1 TTTTAAATTTAAATTTACTTTAAGTTTAAATTTA
* * * **
35619945 TCTTAAATTTAAACTCACTTTGGGTTTAAATTTA
1 TTTTAAATTTAAATTTACTTTAAGTTTAAATTTA
* *
35619979 TTTTAAATTTAAATTTACTTTAAATTAAAATT
1 TTTTAAATTTAAATTTACTTTAAGTTTAAATT
35620011 AAAAAAAGTC
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.54
Consensus pattern (34 bp):
TTTTAAATTTAAATTTACTTTAAGTTTAAATTTA
Found at i:35620199 original size:26 final size:26
Alignment explanation
Indices: 35620169--35620229 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
35620159 TACCGCCACC
35620169 TCAGCAACTCAGAGTGCGCCATGTCA
1 TCAGCAACTCAGAGTGCGCCATGTCA
35620195 TCAGCAACTCAGAGTGCGCCATGTCA
1 TCAGCAACTCAGAGTGCGCCATGTCA
35620221 TCAGCAACT
1 TCAGCAACT
35620230 TGCCACCACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (26 bp):
TCAGCAACTCAGAGTGCGCCATGTCA
Found at i:35621857 original size:29 final size:30
Alignment explanation
Indices: 35621771--35621875 Score: 110
Period size: 30 Copynumber: 3.6 Consensus size: 30
35621761 GCCCTAAAGG
* * *
35621771 CCCCTAAACTATCCAAAAATTAT-ATTTTGA
1 CCCCTAAAATTTCCAAAAATT-TCATTTTTA
* *
35621801 CCCCTAAACTTTCCAAAAATTACATTTTTA
1 CCCCTAAAATTTCCAAAAATTTCATTTTTA
*
35621831 CCCCTAAAATTT-TAAAAATTTCATTTTTA
1 CCCCTAAAATTTCCAAAAATTTCATTTTTA
*
35621860 CCCC--AATTTTCCAAAA
1 CCCCTAAAATTTCCAAAA
35621876 TTACCATTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
27 5 0.08
28 4 0.06
29 19 0.29
30 37 0.57
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (30 bp):
CCCCTAAAATTTCCAAAAATTTCATTTTTA
Found at i:35622002 original size:45 final size:45
Alignment explanation
Indices: 35621946--35622035 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
35621936 TACTATTTTA
35621946 CCCCGGGTATCCAAAATCTCATTTTCAACTCCGATTGTTTTATCT
1 CCCCGGGTATCCAAAATCTCATTTTCAACTCCGATTGTTTTATCT
35621991 CCCCGGGTATCCAAAATCTCATTTTCAACTCCGATTGTTTTATCT
1 CCCCGGGTATCCAAAATCTCATTTTCAACTCCGATTGTTTTATCT
35622036 TTCTTCCTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.22, C:0.29, G:0.11, T:0.38
Consensus pattern (45 bp):
CCCCGGGTATCCAAAATCTCATTTTCAACTCCGATTGTTTTATCT
Found at i:35624483 original size:17 final size:17
Alignment explanation
Indices: 35624459--35624523 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
35624449 TTTTAATTCA
35624459 AAAATAAATTTAAATTT
1 AAAATAAATTTAAATTT
* ** * *
35624476 AAAGTAAATCCAAACTC
1 AAAATAAATTTAAATTT
* *
35624493 AAAATGAATTTGAATTT
1 AAAATAAATTTAAATTT
35624510 AAAATAAATTTAAA
1 AAAATAAATTTAAA
35624524 CTTATTTAAA
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAATAAATTTAAATTT
Found at i:35628957 original size:55 final size:55
Alignment explanation
Indices: 35628869--35628985 Score: 144
Period size: 55 Copynumber: 2.1 Consensus size: 55
35628859 ATGATTTTTT
* * ** * * * *
35628869 TTTATATGTTTAAGTCAATTGTCATGTTGAAATACAACTTTTTTTGAATCGATTG
1 TTTATATATTTAAATCAATTGTCATAATAAAATACAACTTCTTATGAATCGATTA
* *
35628924 TTTATATATTTAAATCGATTGTCATAATAAAATACTACTTCTTATGAATCGATTA
1 TTTATATATTTAAATCAATTGTCATAATAAAATACAACTTCTTATGAATCGATTA
35628979 TTTATAT
1 TTTATAT
35628986 GTTAAGCATG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.47
Consensus pattern (55 bp):
TTTATATATTTAAATCAATTGTCATAATAAAATACAACTTCTTATGAATCGATTA
Found at i:35632415 original size:16 final size:16
Alignment explanation
Indices: 35632394--35632448 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
35632384 GTTTAGTTCA
* *
35632394 CTGTAATGGAATAAAG
1 CTGTAATGAAATAGAG
*
35632410 CTGTAATAAAATAGAG
1 CTGTAATGAAATAGAG
*
35632426 CTGTAATGTAATAGAG
1 CTGTAATGAAATAGAG
*
35632442 ATGTAAT
1 CTGTAAT
35632449 CAGTAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (16 bp):
CTGTAATGAAATAGAG
Found at i:35632670 original size:19 final size:19
Alignment explanation
Indices: 35632646--35632689 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
35632636 TTAATAAAAA
*
35632646 TAATAAATAATTTAAAATT
1 TAATAAATAATATAAAATT
**
35632665 TAATAAATAATATGTAATT
1 TAATAAATAATATAAAATT
35632684 TAATAA
1 TAATAA
35632690 TATTTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TAATAAATAATATAAAATT
Found at i:35632682 original size:26 final size:27
Alignment explanation
Indices: 35632603--35632686 Score: 75
Period size: 26 Copynumber: 3.1 Consensus size: 27
35632593 ATTATTGCTA
* * *
35632603 TTAAAATTTAATAAAATTATTATTAAAT
1 TTAAAATTTAATAAAATAATAAAT-AAT
*
35632631 CT--AATTTAATAAAAATAATAAATAAT
1 TTAAAATTTAAT-AAAATAATAAATAAT
**
35632657 TTAAAATTTAAT-AAATAATATGTAAT
1 TTAAAATTTAATAAAATAATAAATAAT
35632683 TTAA
1 TTAA
35632687 TAATATTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
26 28 0.61
27 9 0.20
28 9 0.20
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (27 bp):
TTAAAATTTAATAAAATAATAAATAAT
Found at i:35637560 original size:21 final size:21
Alignment explanation
Indices: 35637534--35637580 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
35637524 TTTTTTTTGG
*
35637534 TAAAAAATCTTAGA-TCAGAC
1 TAAAAAATCTCAGATTCAGAC
*
35637554 TTAAAAATCTCAGATTCAGAC
1 TAAAAAATCTCAGATTCAGAC
35637575 TAAAAA
1 TAAAAA
35637581 GTAAAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.26
Consensus pattern (21 bp):
TAAAAAATCTCAGATTCAGAC
Found at i:35639040 original size:49 final size:49
Alignment explanation
Indices: 35638987--35639455 Score: 312
Period size: 49 Copynumber: 9.6 Consensus size: 49
35638977 TGATACTGGA
* * **
35638987 TTCGCTATTGCGGCTTAAATCTTTCCCTTCATGCTCCTGAGGTACAAGG
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTTATGCTTTTGAGGTACAAGG
* * * * * * *
35639036 TTCGCCATTACGACTTAAACCTTTCCCTTTAT-ATATTTGTGGTACTAGA
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTTATGCT-TTTGAGGTACAAGG
* * * *
35639085 TTGGGCATTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTGCAAGG
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTTATGCTTTTGAGGTACAAGG
* * * * * * * *
35639134 TTCGTCGTTACGACTTAAACCTTTCCCTTCATAT-C-TTCGTGGTAC-TGG
1 TTCGCCATTGCGGCTTAAATCTTTCCCTT--TATGCTTTTGAGGTACAAGG
* * *
35639182 ATTCGCCGTTACGGCTTAAATCTTTCCCTTTATGCTTCTGAGGTACAAGG
1 -TTCGCCATTGCGGCTTAAATCTTTCCCTTTATGCTTTTGAGGTACAAGG
* * * * * * * *
35639232 TTTGCCATTGCGACTTAAACCTTTCCCTTTAT-ATCTTCGTGGTACTAGA
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTTATGCT-TTTGAGGTACAAGG
*
35639281 TTCGCCATTGCAGCTTAAATCTTTCCCTTTATGCTTTTGAGGTACAAGG
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTTATGCTTTTGAGGTACAAGG
* * * * * * * *
35639330 TTCGTCGTTGTGACTTAAA-CTTCTCCCTCTATAT-C-TTCGTGG-AGCTAGA
1 TTCGCCATTGCGGCTTAAATCTT-TCCCT-T-TATGCTTTTGAGGTA-CAAGG
* * * * *
35639379 TTCACCGTTGCGGCTTAAATCTTT-CCTTTCATGCATCTAAGGTACAAGG
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTT-ATGCTTTTGAGGTACAAGG
* *
35639428 TTCGCCGTTGCGACTTAAA-CTTTTCCCT
1 TTCGCCATTGCGGCTTAAATC-TTTCCCT
35639456 CCAAACCTAT
Statistics
Matches: 318, Mismatches: 81, Indels: 41
0.72 0.18 0.09
Matches are distributed among these distances:
46 1 0.00
47 6 0.02
48 14 0.04
49 278 0.87
50 14 0.04
51 5 0.02
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (49 bp):
TTCGCCATTGCGGCTTAAATCTTTCCCTTTATGCTTTTGAGGTACAAGG
Found at i:35639095 original size:98 final size:98
Alignment explanation
Indices: 35638937--35639455 Score: 657
Period size: 98 Copynumber: 5.3 Consensus size: 98
35638927 GAGGTACCGA
* * * * * * *
35638937 GTTCGCCGTTGCGATCGT-AACCCTTCCTTTTATATTTTCGTGATACTGGATTCGCTATTGCGGC
1 GTTCGCCGTTGCGA-CTTAAACCTTTCCCTTTATATCTTCGTGGTACTAGATTCGCCATTGCGGC
*
35639001 TTAAATCTTTCCCTTCATGCTCCTGAGGTACAAG
65 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAAG
* * * * * *
35639035 GTTCGCCATTACGACTTAAACCTTTCCCTTTATATATTTGTGGTACTAGATTGGGCATTGCGGCT
1 GTTCGCCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGTGGTACTAGATTCGCCATTGCGGCT
* *
35639100 TAAATCTTTCCCTTCATGCTTTTGAGGTGCAAG
66 TAAATCTTTCCCTTCATGCTTCTGAGGTACAAG
* * * * * *
35639133 GTTCGTCGTTACGACTTAAACCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTACGGCT
1 GTTCGCCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGTGGTACTAGATTCGCCATTGCGGCT
*
35639198 TAAATCTTTCCCTTTATGCTTCTGAGGTACAAG
66 TAAATCTTTCCCTTCATGCTTCTGAGGTACAAG
* * *
35639231 GTTTGCCATTGCGACTTAAACCTTTCCCTTTATATCTTCGTGGTACTAGATTCGCCATTGCAGCT
1 GTTCGCCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGTGGTACTAGATTCGCCATTGCGGCT
* *
35639296 TAAATCTTTCCCTTTATGCTTTTGAGGTACAAG
66 TAAATCTTTCCCTTCATGCTTCTGAGGTACAAG
* * * * *
35639329 GTTCGTCGTTGTGACTTAAA-CTTCTCCCTCTATATCTTCGTGG-AGCTAGATTCACCGTTGCGG
1 GTTCGCCGTTGCGACTTAAACCTT-TCCCTTTATATCTTCGTGGTA-CTAGATTCGCCATTGCGG
* * *
35639392 CTTAAATCTTTCCTTTCATGCATCTAAGGTACAAG
64 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAG
*
35639427 GTTCGCCGTTGCGACTTAAACTTTTCCCT
1 GTTCGCCGTTGCGACTTAAACCTTTCCCT
35639456 CCAAACCTAT
Statistics
Matches: 363, Mismatches: 54, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
97 6 0.02
98 355 0.98
99 2 0.01
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.38
Consensus pattern (98 bp):
GTTCGCCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGTGGTACTAGATTCGCCATTGCGGCT
TAAATCTTTCCCTTCATGCTTCTGAGGTACAAG
Found at i:35639905 original size:18 final size:18
Alignment explanation
Indices: 35639878--35639914 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35639868 AATAATTGTC
* *
35639878 AAATATTTACAAGGAACA
1 AAATAATTACAAAGAACA
35639896 AAATAATTACAAAGAACA
1 AAATAATTACAAAGAACA
35639914 A
1 A
35639915 TATTAGATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.11, G:0.08, T:0.19
Consensus pattern (18 bp):
AAATAATTACAAAGAACA
Found at i:35641454 original size:12 final size:11
Alignment explanation
Indices: 35641411--35641463 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
35641401 TTTTACTTTG
*
35641411 AAATTAAATTT
1 AAATTAATTTT
**
35641422 ATTTTAATTTT
1 AAATTAATTTT
*
35641433 AAATTTATTTT
1 AAATTAATTTT
35641444 AAATTCAATTTT
1 AAATT-AATTTT
35641456 AAAATTAA
1 -AAATTAA
35641464 ATTTGAATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
11 21 0.64
12 7 0.21
13 5 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
AAATTAATTTT
Found at i:35641456 original size:17 final size:16
Alignment explanation
Indices: 35641411--35641454 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
35641401 TTTTACTTTG
35641411 AAATTAAATTTATTTT
1 AAATTAAATTTATTTT
*
35641427 AATTTTAAATTTATTTT
1 AA-ATTAAATTTATTTT
*
35641444 AAATTCAATTT
1 AAATTAAATTT
35641455 TAAAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATTAAATTTATTTT
Found at i:35641491 original size:29 final size:29
Alignment explanation
Indices: 35641414--35641491 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
35641404 TACTTTGAAA
* * *
35641414 TTAAATT-TATTTTAATTTTAAATTTATT
1 TTAAATTCAATTTTAATATTAAATTTAAT
*
35641442 TTAAATTCAATTTTAAAATTAAATTTGAAT
1 TTAAATTCAATTTTAATATTAAATTT-AAT
* *
35641472 TTAACTTGAA-TTTAATATTA
1 TTAAATTCAATTTTAATATTA
35641492 TTATAAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 7 0.17
29 24 0.59
30 10 0.24
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
TTAAATTCAATTTTAATATTAAATTTAAT
Found at i:35643258 original size:30 final size:29
Alignment explanation
Indices: 35643222--35643317 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 29
35643212 AAATTGTCCA
35643222 AAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAAC-TTTCC
*
35643252 AAAATTATATTTTGACCCTAAAA-TTTCC
1 AAAATTATATTTTGACCCCAAAACTTTCC
* * * *
35643280 AAAAAATTAAATTTTAACCCCGAAACTTTCA
1 --AAAATTATATTTTGACCCCAAAACTTTCC
35643311 AAAATTA
1 AAAATTA
35643318 CCATTTTACT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
28 5 0.09
29 7 0.12
30 41 0.72
31 4 0.07
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTATATTTTGACCCCAAAACTTTCC
Found at i:35643324 original size:60 final size:59
Alignment explanation
Indices: 35643208--35643324 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 59
35643198 CTCTGTAAGT
* * * *
35643208 CCCTAAATTGTCCAAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGA
1 CCCTAAATTGTCCAAAAATTAAATTTTAACCCCAAAACTTTTCAAAAATTACATTTTGA
*
35643267 CCCTAAAATT-TCCAAAAAATTAAATTTTAACCCCGAAAC-TTTCAAAAATTACCATTTT
1 CCCT-AAATTGTCC-AAAAATTAAATTTTAACCCCAAAACTTTTCAAAAATTA-CATTTT
35643325 ACTTTCGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
59 18 0.36
60 32 0.64
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.35
Consensus pattern (59 bp):
CCCTAAATTGTCCAAAAATTAAATTTTAACCCCAAAACTTTTCAAAAATTACATTTTGA
Found at i:35645260 original size:10 final size:10
Alignment explanation
Indices: 35645247--35645280 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
35645237 TCATTTTTTG
35645247 AATTTTTTCT
1 AATTTTTTCT
35645257 AATTTTTTCT
1 AATTTTTTCT
*
35645267 AATTTATTC-
1 AATTTTTTCT
35645276 AATTT
1 AATTT
35645281 AATCCCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (10 bp):
AATTTTTTCT
Found at i:35648060 original size:38 final size:38
Alignment explanation
Indices: 35648002--35648074 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
35647992 TAATTTAGCT
*
35648002 ATCAATTCAATCATATACTTAAATAATAGTATAGTAAA
1 ATCAATTCAATCATACACTTAAATAATAGTATAGTAAA
* *
35648040 ATCAATTTAATCGTACACTTAAATAATAGTATAGT
1 ATCAATTCAATCATACACTTAAATAATAGTATAGT
35648075 TGACAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.36
Consensus pattern (38 bp):
ATCAATTCAATCATACACTTAAATAATAGTATAGTAAA
Found at i:35652835 original size:42 final size:42
Alignment explanation
Indices: 35652770--35652861 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
35652760 TTTATTAATA
* * *
35652770 TTAGTGGCGTTTATGGAAAAAGCGTCGCTAAAGATCATGTT-T
1 TTAGCGGCGTTTATGGAAAAAGCGCCGCTAAA-ACCATGTTCT
* *
35652812 TTAGCGGCGTTTATGGGATAAGCGCCGCTAAAACCATGTTCT
1 TTAGCGGCGTTTATGGAAAAAGCGCCGCTAAAACCATGTTCT
35652854 TTAGCGGC
1 TTAGCGGC
35652862 ATTTTTCCTC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 7 0.16
42 37 0.84
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (42 bp):
TTAGCGGCGTTTATGGAAAAAGCGCCGCTAAAACCATGTTCT
Found at i:35658521 original size:22 final size:22
Alignment explanation
Indices: 35658491--35658542 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
35658481 GCGAAAATAA
* *
35658491 TACTATAATGCTTTTGAAAAGG
1 TACTCTAATGCTTTTGAAAAAG
35658513 TACTCTAATGCTTTTGAAAAAG
1 TACTCTAATGCTTTTGAAAAAG
35658535 TACTCTAA
1 TACTCTAA
35658543 AACAAGCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (22 bp):
TACTCTAATGCTTTTGAAAAAG
Found at i:35661042 original size:3 final size:3
Alignment explanation
Indices: 35661036--35661077 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
35661026 AGTAATAAAT
* *
35661036 ATA ATAA ATA ATA ATA ATA ATA ATA ATT TTA ATA ATA ATA AT
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
35661078 TTTTTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:35661042 original size:9 final size:10
Alignment explanation
Indices: 35661028--35661061 Score: 54
Period size: 9 Copynumber: 3.6 Consensus size: 10
35661018 TTATTAGTAG
35661028 TAATAAAT-A
1 TAATAAATAA
35661037 TAATAAATAA
1 TAATAAATAA
35661047 TAAT-AATAA
1 TAATAAATAA
35661056 TAATAA
1 TAATAA
35661062 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TAATAAATAA
Found at i:35661078 original size:15 final size:15
Alignment explanation
Indices: 35661036--35661080 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
35661026 AGTAATAAAT
**
35661036 ATAATAAATAATAATA
1 ATAAT-AATAATTTTA
35661052 ATAATAATAATTTTA
1 ATAATAATAATTTTA
35661067 ATAATAATAATTTT
1 ATAATAATAATTTT
35661081 TTTAAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATAATAATTTTA
Found at i:35661421 original size:17 final size:17
Alignment explanation
Indices: 35661387--35661428 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
35661377 TTCAACTTTG
* *
35661387 TTTTAAGTTTACACTTA
1 TTTTAAATTTAAACTTA
*
35661404 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAACTTA
35661421 -TTTAAATT
1 TTTTAAATT
35661429 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTTAAATTTAAACTTA
Found at i:35662004 original size:20 final size:20
Alignment explanation
Indices: 35661981--35662019 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
35661971 TCATTAAAGT
35661981 CATTTTTATTCTTAAGTTTA
1 CATTTTTATTCTTAAGTTTA
35662001 CATTTTTATTCTTAAGTTT
1 CATTTTTATTCTTAAGTTT
35662020 TTAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (20 bp):
CATTTTTATTCTTAAGTTTA
Found at i:35662987 original size:29 final size:30
Alignment explanation
Indices: 35662895--35663112 Score: 163
Period size: 29 Copynumber: 7.5 Consensus size: 30
35662885 CACAAATTAT
35662895 ATTTTTACCCTCGAACTTT-C-AAAATTCC
1 ATTTTTACCCTCGAACTTTCCAAAAATTCC
* * * *
35662923 ATCTTTAACCTCGATCTTTCCAAAAATTAC
1 ATTTTTACCCTCGAACTTTCCAAAAATTCC
* * *
35662953 AATTTTATCCTCAAACTTTCC-AAAATTCC
1 ATTTTTACCCTCGAACTTTCCAAAAATTCC
* **
35662982 ATTTTTGATCCT-GATTTTTCCAAAAATTACC
1 ATTTTT-ACCCTCGAACTTTCCAAAAATT-CC
*
35663013 A-TTTTACCCTCGAAC-TTCCAAAAATTAC
1 ATTTTTACCCTCGAACTTTCCAAAAATTCC
* *
35663041 ATTTTTGA-CC-CAAATTTTTCC-AAAATTACC
1 ATTTTT-ACCCTCGAA-CTTTCCAAAAATT-CC
**
35663071 A-TTTTACCCTTAAAC-TTCCAAAAATTCC
1 ATTTTTACCCTCGAACTTTCCAAAAATTCC
35663099 ATTTTTGA-CCTCGA
1 ATTTTT-ACCCTCGA
35663113 TTTTTAAAAA
Statistics
Matches: 149, Mismatches: 25, Indels: 31
0.73 0.12 0.15
Matches are distributed among these distances:
28 29 0.19
29 66 0.44
30 51 0.34
31 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.39
Consensus pattern (30 bp):
ATTTTTACCCTCGAACTTTCCAAAAATTCC
Found at i:35663002 original size:59 final size:59
Alignment explanation
Indices: 35662888--35663140 Score: 282
Period size: 58 Copynumber: 4.3 Consensus size: 59
35662878 AACTGTACAC
* * * * * * *
35662888 AAATTATATTTTTACCCTCGAACTTTC-AAAATTCCATCTTTAACCTCGATCTTTCCAA
1 AAATTACAATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCGATTTTTCCAA
*
35662946 AAATTACAATTTTATCCTCAAACTTTCC-AAAATTCCATTTTTGATCCT-GATTTTTCCAA
1 AAATTACAATTTTACCCTCAAAC-TTCCAAAAATTCCATTTTTGA-CCTCGATTTTTCCAA
* * * *
35663005 AAATTACCATTTTACCCTCGAACTTCCAAAAATTACATTTTTGACC-CAAATTTTTCC-A
1 AAATTACAATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTC-GATTTTTCCAA
* * **
35663063 AAATTACCATTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCTCGATTTTTAAAAA
1 AAATTACAATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCGATTTTT-CCAA
*
35663123 AAATTACTATTTTACCCT
1 AAATTACAATTTTACCCT
35663141 TGAATGTCTA
Statistics
Matches: 167, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
58 75 0.45
59 71 0.43
60 21 0.13
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.40
Consensus pattern (59 bp):
AAATTACAATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCGATTTTTCCAA
Found at i:35663071 original size:58 final size:57
Alignment explanation
Indices: 35662897--35663193 Score: 258
Period size: 58 Copynumber: 5.1 Consensus size: 57
35662887 CAAATTATAT
* * * * *
35662897 TTTTACCCTCGAACTTTC-AAAATTCCATCTTTAACCTCGATCTTTCCAAAAATTACAA
1 TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACC-CGATTTTTCC-AAAATTACCA
* * *
35662955 TTTTATCCTCAAACTTTCC-AAAATTCCATTTTTGATCCTGATTTTTCCAAAAATTACCA
1 TTTTACCCTCGAAC-TTCCAAAAATTCCATTTTTGA-CCCGATTTTTCC-AAAATTACCA
* *
35663014 TTTTACCCTCGAACTTCCAAAAATTACATTTTTGACCCAAATTTTTCCAAAATTACCA
1 TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCC-GATTTTTCCAAAATTACCA
** ** *
35663072 TTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCTCGATTTTTAAAAAAAATTACTA
1 TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACC-CGATTTTT--CCAAAATTACCA
* * *** * ** *
35663132 TTTTACCCTTGAA-TGTCTAAAAATTTTGTTTTTGACCCCAAACTTCCCAAAATTACCA
1 TTTTACCCTCGAACT-TCCAAAAATTCCATTTTTGA-CCCGATTTTTCCAAAATTACCA
35663190 TTTT
1 TTTT
35663194 GCCCCTAAGT
Statistics
Matches: 198, Mismatches: 32, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
58 81 0.41
59 72 0.36
60 43 0.22
61 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (57 bp):
TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCGATTTTTCCAAAATTACCA
Found at i:35663193 original size:29 final size:28
Alignment explanation
Indices: 35663161--35663226 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 28
35663151 AAAATTTTGT
35663161 TTTTGACCCCAAACT-TCCCAAAATTACCA
1 TTTTG-CCCCAAACTGT-CCAAAATTACCA
* *
35663190 TTTTGCCCCTAAGTGTCCAAAATTACCA
1 TTTTGCCCCAAACTGTCCAAAATTACCA
35663218 TTTTGCCCC
1 TTTTGCCCC
35663227 TAGATATCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 28 0.82
29 6 0.18
ACGTcount: A:0.27, C:0.33, G:0.08, T:0.32
Consensus pattern (28 bp):
TTTTGCCCCAAACTGTCCAAAATTACCA
Found at i:35663209 original size:118 final size:116
Alignment explanation
Indices: 35662897--35663221 Score: 313
Period size: 118 Copynumber: 2.8 Consensus size: 116
35662887 CAAATTATAT
* * * * * * *
35662897 TTTTACCCTCGAACTTTC-AAAATTCCATCTTTAACCTC-GATCTTTCCAAAAATTACAATTTTA
1 TTTTACCCTCGAACTTCCAAAAATTACATTTTTGACC-CAAATC-TTCCCAAAATTACCATTTTA
* **
35662960 -TCCTCAAACTTTCCAAAATTCCATTTTTGATCCTGATTTTTCCAAAAATTACCA
64 CCCCT-AAAC-TTCCAAAATTCCATTTTTGATCCTGATTTTTAAAAAAATTACCA
* *
35663014 TTTTACCCTCGAACTTCCAAAAATTACATTTTTGACCCAAATTTTTCCAAAATTACCATTTTACC
1 TTTTACCCTCGAACTTCCAAAAATTACATTTTTGACCCAAATCTTCCCAAAATTACCATTTTACC
* *
35663079 CTTAAACTTCCAAAAATTCCATTTTTGA-CCTCGATTTTTAAAAAAAATTACTA
66 CCTAAACTTCC-AAAATTCCATTTTTGATCCT-GATTTTT-AAAAAAATTACCA
* * *** *
35663132 TTTTACCCTTGAA-TGTCTAAAAATTTTGTTTTTGACCCCAAA-CTTCCCAAAATTACCATTTTG
1 TTTTACCCTCGAACT-TCCAAAAATTACATTTTTGA-CCCAAATCTTCCCAAAATTACCATTTTA
*
35663195 CCCCT-AAGTGTCCAAAATTACCATTTT
64 CCCCTAAACT-TCCAAAATT-CCATTTT
35663222 GCCCCTAGAT
Statistics
Matches: 174, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
116 7 0.04
117 72 0.41
118 89 0.51
119 6 0.03
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (116 bp):
TTTTACCCTCGAACTTCCAAAAATTACATTTTTGACCCAAATCTTCCCAAAATTACCATTTTACC
CCTAAACTTCCAAAATTCCATTTTTGATCCTGATTTTTAAAAAAATTACCA
Found at i:35663236 original size:28 final size:28
Alignment explanation
Indices: 35663178--35663239 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
35663168 CCCAAACTTC
*
35663178 CCAAAATTACCATTTTGCCCCTAAGTGT
1 CCAAAATTACCATTTTGCCCCTAAGTAT
35663206 CCAAAATTACCATTTTGCCCCT-AGATAT
1 CCAAAATTACCATTTTGCCCCTAAG-TAT
35663234 CCAAAA
1 CCAAAA
35663240 ATCTCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 2 0.06
28 30 0.94
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCTAAGTAT
Found at i:35664920 original size:29 final size:28
Alignment explanation
Indices: 35664882--35665244 Score: 116
Period size: 29 Copynumber: 12.4 Consensus size: 28
35664872 CAGAAACCAT
35664882 ATTTTAACCCTAAAACTTCCAAAAATTACC
1 ATTTT-ACCCTAAAACTTCCAAAAATT-CC
*
35664912 ATTTTACCCCT-AAACTTTCCAAAAATTGC
1 ATTTTA-CCCTAAAAC-TTCCAAAAATTCC
* * *
35664941 ATTTTTACCCCAAAACTTTCTAAAATTCC
1 A-TTTTACCCTAAAACTTCCAAAAATTCC
** ** * *
35664970 ATTTTTGA-TATCAAATTTTCTAAAAACTACC
1 A-TTTT-ACCCT-AAAACTTCCAAAAA-TTCC
* *
35665001 ATTTTACCTCT-AAA-TGCCCAAAAACTCC
1 ATTTTACC-CTAAAACT-TCCAAAAATTCC
* *
35665029 ATTTTTGATCCTAAAACTTCCAAAAATTATC
1 A-TTTT-ACCCTAAAACTTCCAAAAATT-CC
** *
35665060 ATTTTACCCTCGAA-TGTCGAAAAATTCC
1 ATTTTACCCTAAAACT-TCCAAAAATTCC
* *
35665088 ATTTTTGA-CCTCAAACTTTCC-AAAATTACT
1 A-TTTT-ACCCTAAAAC-TTCCAAAAATT-CC
** * * *
35665118 ATTTTACCCT-TGATTATCTAAAAACTCC
1 ATTTTACCCTAAAACT-TCCAAAAATTCC
** * *
35665146 ATTTTTGCCTCGAAATTTCCAAAAATTACC
1 ATTTTACCCT-AAAACTTCCAAAAATT-CC
* * *
35665176 ATTTTACCCTCGAAA-GTCCAAAAATTTC
1 ATTTTACCCT-AAAACTTCCAAAAATTCC
* *
35665204 ATTTTTTACCTTGAAA-TTCCCAAAAATTACC
1 A--TTTTACCCTAAAACTT-CCAAAAATT-CC
35665235 ATTTTACCCT
1 ATTTTACCCT
35665245 CTAATATCAA
Statistics
Matches: 249, Mismatches: 53, Indels: 63
0.68 0.15 0.17
Matches are distributed among these distances:
27 1 0.00
28 22 0.09
29 115 0.46
30 100 0.40
31 11 0.04
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (28 bp):
ATTTTACCCTAAAACTTCCAAAAATTCC
Found at i:35665141 original size:58 final size:57
Alignment explanation
Indices: 35664962--35665315 Score: 313
Period size: 58 Copynumber: 6.1 Consensus size: 57
35664952 AAAACTTTCT
** * * *
35664962 AAAATTCCATTTTTGATATCAAATTTTCTAAAAACTACCATTTTA-CCTCTAA-ATGCCCA
1 AAAATTCCATTTTTGACCTCAAA-TTTCCAAAAATTACCATTTTACCCTCGAATAT---CA
* * * * *
35665021 AAAACTCCATTTTTGATCCTAAAACTTCCAAAAATTATCATTTTACCCTCGAATGTCGA
1 AAAATTCCATTTTTGA-CCTCAAATTTCCAAAAATTACCATTTTACCCTCGAATATC-A
* * *
35665080 AAAATTCCATTTTTGACCTCAAACTTTCC-AAAATTACTATTTTACCCTTGATTATCTA
1 AAAATTCCATTTTTGACCTCAAA-TTTCCAAAAATTACCATTTTACCCTCGAATATC-A
*
35665138 AAAACTCCATTTTTG-CCTCGAAATTTCCAAAAATTACCATTTTACCCTCGAA-AGTCCA
1 AAAATTCCATTTTTGACCTC-AAATTTCCAAAAATTACCATTTTACCCTCGAATA-T-CA
* * * * *
35665196 AAAATTTCATTTTTTACCTTGAAATTCCCAAAAATTACCATTTTACCCTCTAATATCA
1 AAAATTCCATTTTTGACC-TCAAATTTCCAAAAATTACCATTTTACCCTCGAATATCA
* * * * * * *
35665254 AAAATTACATTTTTGCCCTCGAGTATCCAAAAATTATCATTTTACCCCCGAAGTATTCA
1 AAAATTCCATTTTTGACCTCAAATTTCCAAAAATTACCATTTTACCCTCGAA-TA-TCA
35665313 AAA
1 AAA
35665316 TTATTGTTTT
Statistics
Matches: 241, Mismatches: 40, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
57 36 0.15
58 100 0.41
59 92 0.38
60 12 0.05
61 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (57 bp):
AAAATTCCATTTTTGACCTCAAATTTCCAAAAATTACCATTTTACCCTCGAATATCA
Found at i:35665186 original size:116 final size:117
Alignment explanation
Indices: 35664962--35665305 Score: 357
Period size: 116 Copynumber: 2.9 Consensus size: 117
35664952 AAAACTTTCT
* * *
35664962 AAAATTCCATTTTTGA--TATCAAATTTTCTAAAAACTACCATTTTA-CCTCTAA-ATGCCCAAA
1 AAAATTCCATTTTTGACCT-TCAAA-TTCCCAAAAATTACCATTTTACCCTCTAATAT---CAAA
* * * *
35665023 AACTCCATTTTTGATCCT-AAAACTTCCAAAAATTATCATTTTACCCTCGAATGTCGA
61 AACTCCATTTTTGA-CCTCGAAATTTCCAAAAATTATCATTTTACCCTCGAAAGTCCA
* * *
35665080 AAAATTCCATTTTTGACC-TCAAACTTTCC-AAAATTACTATTTTACCCT-TGATTATCTAAAAA
1 AAAATTCCATTTTTGACCTTCAAA-TTCCCAAAAATTACCATTTTACCCTCT-AATATC-AAAAA
*
35665142 CTCCATTTTTG-CCTCGAAATTTCCAAAAATTACCATTTTACCCTCGAAAGTCCA
63 CTCCATTTTTGACCTCGAAATTTCCAAAAATTATCATTTTACCCTCGAAAGTCCA
* * * * *
35665196 AAAATTTCATTTTTTACCTTGAAATTCCCAAAAATTACCATTTTACCCTCTAATATCAAAAATTA
1 AAAATTCCATTTTTGACCTTCAAATTCCCAAAAATTACCATTTTACCCTCTAATATCAAAAACTC
* * * *
35665261 CATTTTTGCCCTCG-AGTATCCAAAAATTATCATTTTACCCCCGAA
66 CATTTTTGACCTCGAAATTTCCAAAAATTATCATTTTACCCTCGAA
35665306 GTATTCAAAA
Statistics
Matches: 193, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
115 3 0.02
116 96 0.50
117 62 0.32
118 30 0.16
119 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (117 bp):
AAAATTCCATTTTTGACCTTCAAATTCCCAAAAATTACCATTTTACCCTCTAATATCAAAAACTC
CATTTTTGACCTCGAAATTTCCAAAAATTATCATTTTACCCTCGAAAGTCCA
Found at i:35665257 original size:29 final size:29
Alignment explanation
Indices: 35664991--35665300 Score: 158
Period size: 29 Copynumber: 10.7 Consensus size: 29
35664981 CAAATTTTCT
* **
35664991 AAAAACTACCATTTTA-CCTCTAAATGCCC
1 AAAAATTACCATTTTACCCTC-AAATATCC
* * *
35665020 AAAAACT-CCATTTTTGATCCTAAAACT-TCC
1 AAAAATTACCA-TTTT-ACCCTCAAA-TATCC
* * * *
35665050 AAAAATTATCATTTTACCCTCGAATGTCG
1 AAAAATTACCATTTTACCCTCAAATATCC
*
35665079 AAAAATT-CCATTTTTGA-CCTCAAACTTTCC
1 AAAAATTACCA-TTTT-ACCCTCAAA-TATCC
* ** * *
35665109 -AAAATTACTATTTTACCCTTGATTATCT
1 AAAAATTACCATTTTACCCTCAAATATCC
* ** *
35665137 AAAAACT-CCATTTTTGCCTCGAAATTTCC
1 AAAAATTACCATTTTACCCTC-AAATATCC
*
35665166 AAAAATTACCATTTTACCCTCGAAA-GTCC
1 AAAAATTACCATTTTACCCTC-AAATATCC
* * *
35665195 AAAAATT-TCATTTTTTACCTTGAAAT-TCCC
1 AAAAATTACCA--TTTTACCCTCAAATAT-CC
*
35665225 AAAAATTACCATTTTACCCTCTAATAT-C
1 AAAAATTACCATTTTACCCTCAAATATCC
* * *
35665253 AAAAATTA-CATTTTTGCCCTCGAGTATCC
1 AAAAATTACCA-TTTTACCCTCAAATATCC
*
35665282 AAAAATTATCATTTTACCC
1 AAAAATTACCATTTTACCC
35665301 CCGAAGTATT
Statistics
Matches: 216, Mismatches: 42, Indels: 46
0.71 0.14 0.15
Matches are distributed among these distances:
27 2 0.01
28 43 0.20
29 106 0.49
30 57 0.26
31 8 0.04
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTCAAATATCC
Found at i:35665309 original size:30 final size:29
Alignment explanation
Indices: 35665047--35665319 Score: 165
Period size: 29 Copynumber: 9.4 Consensus size: 29
35665037 TCCTAAAACT
*
35665047 TCCAAAAATTATCATTTTACCCTCGAATG
1 TCCAAAAATTATCATTTTACCCTCGAATA
* * * *
35665076 TCGAAAAATT-CCATTTTTGA-CCTCAAACTT
1 TCCAAAAATTATCA-TTTT-ACCCTCGAA-TA
* *
35665106 TCC-AAAATTA-CTATTTTACCCTTGATTA
1 TCCAAAAATTATC-ATTTTACCCTCGAATA
* * * ** *
35665134 TCTAAAAACT-CCATTTTTGCCTCGAAATT
1 TCCAAAAATTATCATTTTACCCTCG-AATA
*
35665163 TCCAAAAATTACCATTTTACCCTCGAA-A
1 TCCAAAAATTATCATTTTACCCTCGAATA
*
35665191 GTCCAAAAATT-TCATTTTTTA-CCTTGAA-A
1 -TCCAAAAATTATCA--TTTTACCCTCGAATA
* *
35665220 TTCCCAAAAATTACCATTTTACCCTCTAATA
1 -T-CCAAAAATTATCATTTTACCCTCGAATA
* *
35665251 T-CAAAAATTA-CATTTTTGCCCTCGAGTA
1 TCCAAAAATTATCA-TTTTACCCTCGAATA
*
35665279 TCCAAAAATTATCATTTTACCCCCGAAGTA
1 TCCAAAAATTATCATTTTACCCTCGAA-TA
*
35665309 TTC-AAAATTAT
1 TCCAAAAATTAT
35665320 TGTTTTGCCC
Statistics
Matches: 189, Mismatches: 34, Indels: 42
0.71 0.13 0.16
Matches are distributed among these distances:
27 2 0.01
28 39 0.21
29 102 0.54
30 43 0.23
31 3 0.02
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.36
Consensus pattern (29 bp):
TCCAAAAATTATCATTTTACCCTCGAATA
Found at i:35669775 original size:16 final size:16
Alignment explanation
Indices: 35669749--35669786 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
35669739 CGTGTTATCA
35669749 AAAAAACAAAAAAAAGG
1 AAAAAACAAAAAAAA-G
*
35669766 AAAAAA-AAAAAGAAG
1 AAAAAACAAAAAAAAG
35669781 AAAAAA
1 AAAAAA
35669787 TGGGTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 7 0.35
17 6 0.30
ACGTcount: A:0.87, C:0.03, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAAAAAAG
Found at i:35670418 original size:13 final size:12
Alignment explanation
Indices: 35670385--35670454 Score: 59
Period size: 13 Copynumber: 5.2 Consensus size: 12
35670375 TAAATAAAGG
35670385 AAAAAAAAGAAA
1 AAAAAAAAGAAA
*
35670397 AAAGCAAAAGAAA
1 AAA-AAAAAGAAA
35670410 AAGAAAAAAGAGGAA
1 AA-AAAAAAGA--AA
35670425 AAAACAAGAAGAAA
1 AAAA-AA-AAGAAA
35670439 AACAAAAATAGAAA
1 AA-AAAAA-AGAAA
35670453 AA
1 AA
35670455 GGAAGAGGTC
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
12 3 0.06
13 17 0.35
14 16 0.33
15 8 0.17
16 4 0.08
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.01
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:35670426 original size:28 final size:29
Alignment explanation
Indices: 35670384--35670454 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
35670374 ATAAATAAAG
*
35670384 GAAAAAAAAGAAAAAAGCAA-AAGAAAAA
1 GAAAAAAAAGAAAAAAACAAGAAGAAAAA
* *
35670412 GAAAAAAGAGGAAAAAACAAGAAGAAAAA
1 GAAAAAAAAGAAAAAAACAAGAAGAAAAA
* *
35670441 -CAAAAATAGAAAAA
1 GAAAAAAAAGAAAAA
35670455 GGAAGAGGTC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 28 0.78
29 8 0.22
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.01
Consensus pattern (29 bp):
GAAAAAAAAGAAAAAAACAAGAAGAAAAA
Found at i:35671568 original size:50 final size:49
Alignment explanation
Indices: 35671441--35671878 Score: 309
Period size: 50 Copynumber: 8.9 Consensus size: 49
35671431 AAGCCCAATG
* * ** *
35671441 CCTTAGCAGATATTATGGGAAGGATTGAGGCCACAACGGCAAATTCGATT
1 CCTTAGCAGATATTATGGGAAGG-TTGAGGCCGCAACGGCGAACCCGATA
* * * * * *
35671491 CCATGAGGAAGA-A--ATGGGAAAGGTTGAGGCCACAATGGCGAACCTGGTA
1 CC-TTA-GCAGATATTATGGG-AAGGTTGAGGCCGCAACGGCGAACCCGATA
* * * ** * *
35671540 CCTTAGCAGATATAATGGGAAGGATTGAGGTCGCAACGGCAAATCTGGTTT
1 CCTTAGCAGATATTATGGGAAGG-TTGAGGCCGCAACGGCGAA-CCCGATA
* * * * * *
35671591 CATGAGGAAGA-A--ATGGTAAAGGTTGAGGCTGCAACGGCGAACCCGGTA
1 CCTTA-GCAGATATTATGG-GAAGGTTGAGGCCGCAACGGCGAACCCGATA
* * * * *
35671639 CCTTAGCAAATATTGTGGGAAGGATTAAGGCCGCAACGGCGAATCCGATT
1 CCTTAGCAGATATTATGGGAAGG-TTGAGGCCGCAACGGCGAACCCGATA
* * * * * *
35671689 CCATA-AAGATGA-AATAGGAAAGGTTGAGGCCGTAACGGTGAACCCGATA
1 CCTTAGCAGAT-ATTAT-GGGAAGGTTGAGGCCGCAACGGCGAACCCGATA
* * **
35671738 CCAT-GAAGATATTATGAAAAGGTTGAGGCCGCAACGGCGAACCCGATA
1 CCTTAGCAGATATTATGGGAAGGTTGAGGCCGCAACGGCGAACCCGATA
* *
35671786 CCGTAGCAAATATTATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATA
1 CCTTAGCAGATATTATGGG-AAGGTTGAGGCCGCAACGGCGAACCCGATA
* *
35671836 CCTTAGTAGATATTATGGGAAGGATTGAGGCCGTAACGGCGAA
1 CCTTAGCAGATATTATGGGAAGG-TTGAGGCCGCAACGGCGAA
35671879 TCCAGTACCA
Statistics
Matches: 302, Mismatches: 65, Indels: 42
0.74 0.16 0.10
Matches are distributed among these distances:
47 7 0.02
48 44 0.15
49 104 0.34
50 129 0.43
51 10 0.03
52 8 0.03
ACGTcount: A:0.33, C:0.18, G:0.30, T:0.19
Consensus pattern (49 bp):
CCTTAGCAGATATTATGGGAAGGTTGAGGCCGCAACGGCGAACCCGATA
Found at i:35671578 original size:99 final size:99
Alignment explanation
Indices: 35671407--35671881 Score: 510
Period size: 99 Copynumber: 4.8 Consensus size: 99
35671397 AAGATTTGAA
* ** * *
35671407 GGGAAAGGTTAAGGCCGCAAC-GATAAGCCCAATGCCTTAGCAGATATTATGGGAAGGATTGAGG
1 GGGAAAGGTTGAGGCCGCAACGGCGAA-CCCGATACCTTAGCAGATATTATGGGAAGGATTGAGG
* *
35671471 CCACAACGGCAAATTCGATTCCATGAGGAAGAAAT
65 CCGCAACGGCAAATCCGATTCCATGAGGAAGAAAT
* * * * * *
35671506 GGGAAAGGTTGAGGCCACAATGGCGAACCTGGTACCTTAGCAGATATAATGGGAAGGATTGAGGT
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGCAGATATTATGGGAAGGATTGAGGC
* * *
35671571 CGCAACGGCAAATCTGGTTTCATGAGGAAGAAAT
66 CGCAACGGCAAATCCGATTCCATGAGGAAGAAAT
* * * * * *
35671605 GGTAAAGGTTGAGGCTGCAACGGCGAACCCGGTACCTTAGCAAATATTGTGGGAAGGATTAAGGC
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGCAGATATTATGGGAAGGATTGAGGC
* * * *
35671670 CGCAACGGCGAATCCGATTCCATAAAGATGAAAT
66 CGCAACGGCAAATCCGATTCCATGAGGAAGAAAT
* * * * * **
35671704 AGGAAAGGTTGAGGCCGTAACGGTGAACCCGATACCAT-GAAGATATTATGAAAAGG-TTGAGGC
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGCAGATATTATGGGAAGGATTGAGGC
* * * * *
35671767 CGCAACGGCGAACCCGATACCGT-AGCAA-ATATTAT
66 CGCAACGGCAAATCCGATTCCATGAGGAAGA-A--AT
*
35671802 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGTAGATATTATGGGAAGGATTGAGGC
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGCAGATATTATGGGAAGGATTGAGGC
* *
35671867 CGTAACGGCGAATCC
66 CGCAACGGCAAATCC
35671882 AGTACCACAA
Statistics
Matches: 309, Mismatches: 61, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
95 1 0.00
96 3 0.01
97 26 0.08
98 49 0.16
99 207 0.67
100 23 0.07
ACGTcount: A:0.33, C:0.18, G:0.30, T:0.19
Consensus pattern (99 bp):
GGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGCAGATATTATGGGAAGGATTGAGGC
CGCAACGGCAAATCCGATTCCATGAGGAAGAAAT
Found at i:35672552 original size:29 final size:28
Alignment explanation
Indices: 35672518--35672902 Score: 217
Period size: 30 Copynumber: 13.1 Consensus size: 28
35672508 TAGCCTACCA
*
35672518 TTTTACCCTAAACTTTTCAAAAATTACAT
1 TTTTACCCTAAA-TTTCCAAAAATTACAT
* * *
35672547 TTTTACCCCCAAACTTT-CTAAAATTTCATT
1 TTTTA-CCCTAAA-TTTCCAAAAATTACA-T
* *
35672577 TTTTGACCCCAAATTTATCAAAAATTACCA-
1 TTTT-ACCCTAAATTT-CCAAAAATTA-CAT
* ** * *
35672607 TTTTACCCCCAAATGCCCAAAAACTCCAT
1 TTTTA-CCCTAAATTTCCAAAAATTACAT
* * *
35672636 TTTTGACCTCGAAACTTCCAAAGATTATCA-
1 TTTT-ACC-CTAAATTTCCAAAAATTA-CAT
* * * * *
35672666 TTTTACGCTCGAATGTCTAAAAATTTCAT
1 TTTTACCCT-AAATTTCCAAAAATTACAT
35672695 TTTTAACCCTAAAGTTTCCAAAAATTACAT
1 TTTT-ACCCTAAA-TTTCCAAAAATTACAT
35672725 TTTTACCTCTAAATTTTCC-AAAATTACAT
1 TTTTACC-CTAAA-TTTCCAAAAATTACAT
35672754 TTTTAACCCTAAACTTTCCAAAAATTACCA-
1 TTTT-ACCCTAAA-TTTCCAAAAATTA-CAT
* * *
35672784 TTTTACCCTCGAATATCCAAAAATTCCAT
1 TTTTACCCT-AAATTTCCAAAAATTACAT
* *
35672813 TTTTAACATCAAAATTTCCAAAAATTACCA-
1 TTTT-AC-CCTAAATTTCCAAAAATTA-CAT
* *
35672843 TTTTACCCTCGAATAT-CAAAAATTACAT
1 TTTTACCCT-AAATTTCCAAAAATTACAT
* * * *
35672871 TTTTGCCCTCGAGTGTCCAAAAATTACCAT
1 TTTTACCCT-AAATTTCCAAAAATTA-CAT
35672901 TT
1 TT
35672903 GCCCCCAAAG
Statistics
Matches: 281, Mismatches: 47, Indels: 55
0.73 0.12 0.14
Matches are distributed among these distances:
27 2 0.01
28 30 0.11
29 111 0.40
30 121 0.43
31 15 0.05
32 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (28 bp):
TTTTACCCTAAATTTCCAAAAATTACAT
Found at i:35672688 original size:59 final size:59
Alignment explanation
Indices: 35672595--35672902 Score: 263
Period size: 59 Copynumber: 5.3 Consensus size: 59
35672585 CCAAATTTAT
* * ** * * * *
35672595 CAAAAATTACCATTTTACCCCCAAATGCCCAAAAACTCCATTTTTGACCTCGAAACTTC
1 CAAAAATTACCATTTTACCCTCGAATATCTAAAAATTACATTTTTAACCTCGAAACTTC
* * * * * * *
35672654 CAAAGATTATCATTTTACGCTCGAATGTCTAAAAATTTCATTTTTAACC-CTAAAGTTTC
1 CAAAAATTACCATTTTACCCTCGAATATCTAAAAATTACATTTTTAACCTCGAAA-CTTC
* * * *
35672713 CAAAAATTA-CATTTTTA-CCTCTAA-ATTTTCCAAAATTACATTTTTAACC-CTAAACTTTC
1 CAAAAATTACCA-TTTTACCCTCGAATA-TCT-AAAAATTACATTTTTAACCTCGAAAC-TTC
* * * * *
35672772 CAAAAATTACCATTTTACCCTCGAATATCCAAAAATTCCATTTTTAACATCAAAATTTC
1 CAAAAATTACCATTTTACCCTCGAATATCTAAAAATTACATTTTTAACCTCGAAACTTC
** *
35672831 CAAAAATTACCATTTTACCCTCGAATATC-AAAAATTACATTTTTGCCCTCG--AGTGTC
1 CAAAAATTACCATTTTACCCTCGAATATCTAAAAATTACATTTTTAACCTCGAAACT-TC
35672888 CAAAAATTACCATTT
1 CAAAAATTACCATTT
35672903 GCCCCCAAAG
Statistics
Matches: 205, Mismatches: 34, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
56 2 0.01
57 17 0.08
58 30 0.15
59 142 0.69
60 13 0.06
61 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCTCGAATATCTAAAAATTACATTTTTAACCTCGAAACTTC
Found at i:35672722 original size:118 final size:117
Alignment explanation
Indices: 35672518--35672850 Score: 318
Period size: 118 Copynumber: 2.8 Consensus size: 117
35672508 TAGCCTACCA
* * * * * *
35672518 TTTT-ACCCTAAACTTTTCAAAAATTA-CATTTTTACCCCCAAACT-TTCTAAAATTTCATTTTT
1 TTTTAACCCGAAACTTTCCAAAAATTACCA-TTTTACCCTCGAA-TATCCAAAAATTTCA-TTTT
* * * *
35672580 TGACCCCAAATTTATCAAAAATTACCATTTTACCCCCAAA-TGCCCAAAAACTCCAT
63 TAACCCTAAATTT-CCAAAAATTACCATTTTACCCCCAAATTGCCC-AAAACTACAT
* * * * * *
35672636 TTTTGACCTCGAAAC-TTCCAAAGATTATCATTTTACGCTCGAATGTCTAAAAATTTCATTTTTA
1 TTTTAACC-CGAAACTTTCCAAAAATTACCATTTTACCCTCGAATATCCAAAAATTTCATTTTTA
* * ** *
35672700 ACCCTAAAGTTTCCAAAAATTA-CATTTTTACCTCTAAATTTTCCAAAATTACAT
65 ACCCTAAA-TTTCCAAAAATTACCA-TTTTACCCCCAAATTGCCCAAAACTACAT
* *
35672754 TTTTAACCCTAAACTTTCCAAAAATTACCATTTTACCCTCGAATATCCAAAAATTCCATTTTTAA
1 TTTTAACCCGAAACTTTCCAAAAATTACCATTTTACCCTCGAATATCCAAAAATTTCATTTTTAA
* *
35672819 CATCAAAATTTCCAAAAATTACCATTTTACCC
66 C-CCTAAATTTCCAAAAATTACCATTTTACCC
35672851 TCGAATATCA
Statistics
Matches: 176, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
117 7 0.04
118 117 0.66
119 45 0.26
120 7 0.04
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (117 bp):
TTTTAACCCGAAACTTTCCAAAAATTACCATTTTACCCTCGAATATCCAAAAATTTCATTTTTAA
CCCTAAATTTCCAAAAATTACCATTTTACCCCCAAATTGCCCAAAACTACAT
Found at i:35672903 original size:28 final size:29
Alignment explanation
Indices: 35672770--35672906 Score: 138
Period size: 28 Copynumber: 4.8 Consensus size: 29
35672760 CCCTAAACTT
*
35672770 TCCAAAAATTACCATTTTACCCTCGAATA
1 TCCAAAAATTACCATTTTGCCCTCGAATA
** * * *
35672799 TCCAAAAATT-CCATTTTTAACATCAAAATT
1 TCCAAAAATTACCA-TTTTGCCCTC-GAATA
*
35672829 TCCAAAAATTACCATTTTACCCTCGAATA
1 TCCAAAAATTACCATTTTGCCCTCGAATA
* *
35672858 T-CAAAAATTA-CATTTTTGCCCTCGAGTG
1 TCCAAAAATTACCA-TTTTGCCCTCGAATA
35672886 TCCAAAAATTACCA-TTTGCCC
1 TCCAAAAATTACCATTTTGCCC
35672907 CCAAAGTGTT
Statistics
Matches: 91, Mismatches: 11, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
27 2 0.02
28 32 0.35
29 31 0.34
30 23 0.25
31 3 0.03
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTGCCCTCGAATA
Found at i:35674131 original size:29 final size:31
Alignment explanation
Indices: 35674063--35674132 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 31
35674053 TAAATCATAG
* * *
35674063 TTAAAATATTCAATATACAATATAATTTTAT
1 TTAAAATAATCAATATACAATACAATATTAT
* * *
35674094 TTTATATAATCAATGTA-AA-ACAATATTAT
1 TTAAAATAATCAATATACAATACAATATTAT
35674123 TTAAAATAAT
1 TTAAAATAAT
35674133 AATTAATTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
29 16 0.52
30 2 0.06
31 13 0.42
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (31 bp):
TTAAAATAATCAATATACAATACAATATTAT
Found at i:35674133 original size:15 final size:15
Alignment explanation
Indices: 35674109--35674155 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
35674099 ATAATCAATG
* *
35674109 TAAAACAATATTATT
1 TAAAATAATATTAAT
35674124 TAAAATAATAATTAAT
1 TAAAATAAT-ATTAAT
*
35674140 TAACAT-ATATTAAT
1 TAAAATAATATTAAT
35674154 TA
1 TA
35674156 TTTTGACAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 8 0.29
15 10 0.36
16 10 0.36
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAATAATATTAAT
Done.