Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 136 of 193
Found at i:42782753 original size:21 final size:21
Alignment explanation
Indices: 42782729--42782770 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
42782719 GCGATGGTGG
42782729 TTGTGGCTAATATATAGAGGT
1 TTGTGGCTAATATATAGAGGT
42782750 TTGTGGCTAATATATAGAGGT
1 TTGTGGCTAATATATAGAGGT
42782771 AATATGGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.38
Consensus pattern (21 bp):
TTGTGGCTAATATATAGAGGT
Found at i:42784276 original size:19 final size:18
Alignment explanation
Indices: 42784244--42784279 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42784234 ATATATGATT
*
42784244 TTTTTAAAATTTTAAATC
1 TTTTCAAAATTTTAAATC
42784262 TTTTCAAAATATTTAAAT
1 TTTTCAAAAT-TTTAAAT
42784280 TATAAATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTCAAAATTTTAAATC
Found at i:42789778 original size:31 final size:31
Alignment explanation
Indices: 42789709--42789778 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
42789699 TATTAAAATA
* * * *
42789709 AATATTGAAATCAAATTCAAGTACTAAATTG
1 AATATTAAAATCAAATCCAAGTACCAAATGG
* *
42789740 AACATTAAAATCAAATCCAAGTACCAAGTGG
1 AATATTAAAATCAAATCCAAGTACCAAATGG
*
42789771 TATATTAA
1 AATATTAA
42789779 TCCTGTTGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.29
Consensus pattern (31 bp):
AATATTAAAATCAAATCCAAGTACCAAATGG
Found at i:42789962 original size:2 final size:2
Alignment explanation
Indices: 42789955--42789980 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42789945 GAATTTGGTC
42789955 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
42789981 GGTAAACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42791192 original size:31 final size:31
Alignment explanation
Indices: 42791122--42791192 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
42791112 TGTATAACAG
* * * *
42791122 GTACCAAAATGAACATTGAAGCCAAACTCAA
1 GTACCAAATTGAACATTAAAACCAAACCCAA
42791153 GTACCAAATTGAACATTAAAACCAAACCCAA
1 GTACCAAATTGAACATTAAAACCAAACCCAA
*
42791184 GTATCAAAT
1 GTACCAAAT
42791193 GGCATATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.49, C:0.23, G:0.10, T:0.18
Consensus pattern (31 bp):
GTACCAAATTGAACATTAAAACCAAACCCAA
Found at i:42792881 original size:24 final size:24
Alignment explanation
Indices: 42792853--42792932 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
42792843 TAGACTAATA
* *
42792853 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAATTCAAACAAATAAAC
*
42792877 AGAGTTTAATTTAAACAAATAAAC
1 AGAGTTTAATTCAAACAAATAAAC
* * * *
42792901 ATAGTTTAATTGAAATAATTAAAC
1 AGAGTTTAATTCAAACAAATAAAC
42792925 AGAGTTTA
1 AGAGTTTA
42792933 GCTGAAAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (24 bp):
AGAGTTTAATTCAAACAAATAAAC
Found at i:42792938 original size:24 final size:23
Alignment explanation
Indices: 42792872--42792944 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 23
42792862 CTCAAACAAA
* *
42792872 TAAACAGAGTTTAATTTAAACAAA
1 TAAACAGAGTTTAATTGAAA-AAT
*
42792896 TAAACATAGTTTAATTGAAATAAT
1 TAAACAGAGTTTAATTGAAA-AAT
**
42792920 TAAACAGAGTTTAGCTGAAAAAT
1 TAAACAGAGTTTAATTGAAAAAT
42792943 TA
1 TA
42792945 TTTCTCAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 5 0.12
24 37 0.88
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.32
Consensus pattern (23 bp):
TAAACAGAGTTTAATTGAAAAAT
Found at i:42794926 original size:24 final size:24
Alignment explanation
Indices: 42794877--42794927 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
42794867 AGTTTGACTC
*
42794877 AAACAAATAAACAGAATTTAATTG
1 AAACAAATAAACAGAATTTAACTG
* *
42794901 AAACAAATAAACAGAGTTTAGCTG
1 AAACAAATAAACAGAATTTAACTG
42794925 AAA
1 AAA
42794928 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAACTG
Found at i:42798310 original size:30 final size:30
Alignment explanation
Indices: 42798267--42798547 Score: 363
Period size: 30 Copynumber: 9.4 Consensus size: 30
42798257 GTTGAGGGTG
* *
42798267 AAATGGTAATTTTTG-AAAGTTTTGGGGTAA
1 AAAT-GTAATTTTGGAAAAGTTTTGGGGTTA
* *
42798297 AAATGTAATTTTTTGAAAA-TTTAGGGGTTA
1 AAATGTAA-TTTTGGAAAAGTTTTGGGGTTA
* * *
42798327 AAATATGATTTTGGAAAAGTTTTGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
*
42798357 AAATGTAATTTTGGAAAAGTTTTAGGGTTA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
* *
42798387 AAATGTAATTTTTGAAAAGTTTTGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
* * * **
42798417 AAATGTAATTTT-TAGAAAGTTTTGAGATCG
1 AAATGTAATTTTGGA-AAAGTTTTGGGGTTA
42798447 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
*
42798477 AAATATAATTTTGGAAAAGTTTTGGGGTT-
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
42798506 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
42798536 AAATGTAATTTT
1 AAATGTAATTTT
42798548 TGGATAATTT
Statistics
Matches: 220, Mismatches: 25, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
29 42 0.19
30 174 0.79
31 4 0.02
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (30 bp):
AAATGTAATTTTGGAAAAGTTTTGGGGTTA
Found at i:42802432 original size:30 final size:30
Alignment explanation
Indices: 42802389--42802669 Score: 318
Period size: 30 Copynumber: 9.4 Consensus size: 30
42802379 GTTGAGGGTG
* * *
42802389 AAATGGTAATTTTTG-AAAGTTTCGGGGTAA
1 AAAT-GTAATTTTGGAAAAGTTTTGGGGTTA
* *
42802419 AAATGTAATTTTTTTGAAAA--TTTGGGGTCA
1 AAATGTAA--TTTTGGAAAAGTTTTGGGGTTA
* * *
42802449 AAATATGATTTTGGAAAAGTTTTAGGGTTA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
*
42802479 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
** * * **
42802509 AAATGTAATTTTTAAAAAGTTTTGAGATCG
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
* * * *
42802539 AAATGTATTTTTAG-AAAGTTTTGAGGTTG
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
42802568 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
* *
42802598 AAATATAATTTTGGAAAAGTTTTAGGGTTA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
42802628 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTTA
42802658 AAATGTAATTTT
1 AAATGTAATTTT
42802670 TAGATAATTT
Statistics
Matches: 216, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
28 9 0.04
29 29 0.13
30 169 0.78
31 6 0.03
32 3 0.01
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (30 bp):
AAATGTAATTTTGGAAAAGTTTTGGGGTTA
Found at i:42802560 original size:89 final size:89
Alignment explanation
Indices: 42802446--42802669 Score: 281
Period size: 89 Copynumber: 2.5 Consensus size: 89
42802436 AAATTTGGGG
* * *
42802446 TCAAAATATGATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAA
1 TCAAAATGTAATTTTAGAAAAGTTTT-GGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAA
* *
42802511 ATGTAATTTTTAAAAAGTTTT-GAGA
65 ATATAATTTTGAAAAAGTTTTAG-GA
* * * *
42802536 TCGAAATGTATTTTTAG-AAAGTTTTGAGGTTGAAATGTAATTTTGGAAAAGTTTTGGGGTTAAA
1 TCAAAATGTAATTTTAGAAAAGTTTTG-GGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAA
* *
42802600 ATATAATTTTGGAAAAGTTTTAGGG
65 ATATAATTTTGAAAAAGTTTTAGGA
* *
42802625 TTAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTT
1 TCAAAATGTAATTTTAGAAAAGTTTT-GGGTTAAAATGTAATTTT
42802670 TAGATAATTT
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
88 1 0.01
89 75 0.66
90 37 0.32
91 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (89 bp):
TCAAAATGTAATTTTAGAAAAGTTTTGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAA
TATAATTTTGAAAAAGTTTTAGGA
Found at i:42802592 original size:149 final size:149
Alignment explanation
Indices: 42802388--42802671 Score: 439
Period size: 149 Copynumber: 1.9 Consensus size: 149
42802378 AGTTGAGGGT
* *
42802388 GAAATGGTAATTTTTGAAAGTTTCGGGGTAAAAATGTAATTTTTTTGAAAATTTGGGGTCAAAAT
1 GAAATGGTAATTTTTGAAAGTTTCGAGGTAAAAATGTAA-TTTTTGGAAAATTTGGGGTCAAAAT
*
42802453 ATGATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAAT
65 ATAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAAT
42802518 TTTTAAAAAGTTTTGAGATC
130 TTTTAAAAAGTTTTGAGATC
* ** *
42802538 GAAAT-GT-ATTTTTAGAAAGTTTTGAGGTTGAAATGTAA-TTTTGGAAAAGTTTTGGGGTTAAA
1 GAAATGGTAATTTTT-GAAAGTTTCGAGGTAAAAATGTAATTTTTGGAAAA--TTTGGGGTCAAA
*
42802600 ATATAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATGTA
63 ATATAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTA
42802665 ATTTTTA
128 ATTTTTA
42802672 GATAATTTAG
Statistics
Matches: 123, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
147 9 0.07
148 6 0.05
149 103 0.84
150 5 0.04
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.40
Consensus pattern (149 bp):
GAAATGGTAATTTTTGAAAGTTTCGAGGTAAAAATGTAATTTTTGGAAAATTTGGGGTCAAAATA
TAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATT
TTTAAAAAGTTTTGAGATC
Found at i:42803802 original size:20 final size:20
Alignment explanation
Indices: 42803777--42803814 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42803767 GTATTTCTTT
42803777 TTTATTATT-TTAAATATTTA
1 TTTATTATTATT-AATATTTA
42803797 TTTATTATTATTAATATT
1 TTTATTATTATTAATATT
42803815 ATAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATTATTATTAATATTTA
Found at i:42804585 original size:11 final size:11
Alignment explanation
Indices: 42804526--42804596 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 11
42804516 TATTCAAATT
42804526 TAAATTTAAAA
1 TAAATTTAAAA
*
42804537 TAAACTTAAATAA
1 TAAA-TTTAA-AA
* *
42804550 GTAATTTTAAATTT
1 -TAAATTTAAA--A
42804564 TAAATTTTAAAA
1 TAAA-TTTAAAA
42804576 TAAATTTAAAA
1 TAAATTTAAAA
*
42804587 TTAATTTAAA
1 TAAATTTAAA
42804597 CTCAAAGCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
11 20 0.43
12 9 0.19
13 9 0.19
14 9 0.19
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:42804774 original size:30 final size:29
Alignment explanation
Indices: 42804705--42804880 Score: 192
Period size: 29 Copynumber: 6.0 Consensus size: 29
42804695 CCCTAGAAGT
*
42804705 CCTTAAACTATCCAAAAATTACATTTTTAC
1 CCTTAAACT-TCCAAAAATTCCATTTTTAC
*
42804735 CCTTGAACTTCCAAAAATTCCATTTTTGAC
1 CCTTAAACTTCCAAAAATTCCATTTTT-AC
* * *
42804765 CCTAAAACTTCTAAAAATTACATTTTTAC
1 CCTTAAACTTCCAAAAATTCCATTTTTAC
* * *
42804794 CCCTAAACTTCTAAAAATTCTATTTTTGAC
1 CCTTAAACTTCCAAAAATTCCATTTTT-AC
** *
42804824 CCCGAAACTTGCAAAAATTACCA-TTTTAC
1 CCTTAAACTTCCAAAAATT-CCATTTTTAC
**
42804853 CCTTGGACTTCCAAAAATTCCATTTTTA
1 CCTTAAACTTCCAAAAATTCCATTTTTA
42804881 ATCCTGATTT
Statistics
Matches: 123, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
28 3 0.02
29 63 0.51
30 55 0.45
31 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
CCTTAAACTTCCAAAAATTCCATTTTTAC
Found at i:42804810 original size:59 final size:58
Alignment explanation
Indices: 42804717--42804879 Score: 229
Period size: 59 Copynumber: 2.8 Consensus size: 58
42804707 TTAAACTATC
*
42804717 CAAAAATTACATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCTAAAACTT
1 CAAAAATTACATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTT
* * * * *
42804775 CTAAAAATTACATTTTTACCCCTAAACTTCTAAAAATTCTATTTTTGACCCCGAAACTT
1 C-AAAAATTACATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTT
*
42804834 GCAAAAATTACCA-TTTTACCCTTGGACTTCCAAAAATTCCATTTTT
1 -CAAAAATTA-CATTTTTACCCTTGAACTTCCAAAAATTCCATTTTT
42804880 AATCCTGATT
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
58 1 0.01
59 87 0.96
60 3 0.03
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (58 bp):
CAAAAATTACATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTT
Found at i:42804900 original size:59 final size:59
Alignment explanation
Indices: 42804718--42804909 Score: 217
Period size: 59 Copynumber: 3.2 Consensus size: 59
42804708 TAAACTATCC
* *
42804718 AAAAATTACATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCT
1 AAAAATTACATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCTGAAATTTCT
* * * * * *
42804777 AAAAATTACATTTTTACCCCTAAACTTCTAAAAATTCTATTTTTGACCCCGAAACTTGC-
1 AAAAATTACATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCTGAAA-TTTCT
* * * **
42804836 AAAAATTACCA-TTTTACCCTTGGACTTCCAAAAATTCCATTTTTAATCCTGATTTTTCT
1 AAAAATTA-CATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCTGAAATTTCT
*
42804895 TAAAATTACCATTTT
1 AAAAATTA-CATTTT
42804910 GCCCCTTAAA
Statistics
Matches: 109, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
58 3 0.03
59 99 0.91
60 7 0.06
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.39
Consensus pattern (59 bp):
AAAAATTACATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCTGAAATTTCT
Found at i:42805413 original size:16 final size:16
Alignment explanation
Indices: 42805392--42805423 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42805382 CACGTGTCCG
42805392 AGGATCGTGTTTTAAA
1 AGGATCGTGTTTTAAA
42805408 AGGATCGTGTTTTAAA
1 AGGATCGTGTTTTAAA
42805424 CTCAGTACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (16 bp):
AGGATCGTGTTTTAAA
Found at i:42806662 original size:28 final size:28
Alignment explanation
Indices: 42806631--42806684 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
42806621 AATAAATAAA
42806631 TAAA-CAAACAAGATAATAACAATAAAGG
1 TAAATCAAACAA-ATAATAACAATAAAGG
* * *
42806659 TAAATTAAATAAATAATAATAATAAA
1 TAAATCAAACAAATAATAACAATAAA
42806685 TTGCATGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 17 0.77
29 5 0.23
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (28 bp):
TAAATCAAACAAATAATAACAATAAAGG
Found at i:42806727 original size:31 final size:32
Alignment explanation
Indices: 42806692--42806771 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 32
42806682 AAATTGCATG
42806692 AAAATAAATAATAACAAGA-T-AAATAAACAAA-
1 AAAATAAA-AATAA-AAGATTAAAATAAACAAAT
* *
42806723 AAAATAAAAATTAAATATTAAAATAAACAAAT
1 AAAATAAAAATAAAAGATTAAAATAAACAAAT
42806755 AAATATAAACAATAAAA
1 AAA-ATAAA-AATAAAA
42806772 ATAATTGAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 3 0.07
30 5 0.12
31 19 0.46
32 3 0.07
33 5 0.12
34 6 0.15
ACGTcount: A:0.74, C:0.05, G:0.01, T:0.20
Consensus pattern (32 bp):
AAAATAAAAATAAAAGATTAAAATAAACAAAT
Found at i:42806745 original size:19 final size:19
Alignment explanation
Indices: 42806722--42806773 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
42806712 AAATAAACAA
42806722 AAAAATAAAAATTAAATAT
1 AAAAATAAAAATTAAATAT
* *
42806741 TAAAATAAACAAATAAATAT
1 AAAAATAAA-AATTAAATAT
42806761 AAACAATAAAAAT
1 AAA-AATAAAAAT
42806774 AATTGAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 8 0.30
20 13 0.48
21 6 0.22
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATAAAAATTAAATAT
Found at i:42806775 original size:13 final size:12
Alignment explanation
Indices: 42806692--42806775 Score: 53
Period size: 13 Copynumber: 6.6 Consensus size: 12
42806682 AAATTGCATG
42806692 AAAATAAATAATA
1 AAAATAAA-AATA
* * *
42806705 ACAAGATAAATA
1 AAAATAAAAATA
42806717 AACAA-AAAAATA
1 AA-AATAAAAATA
* *
42806729 AAAATTAAATATT
1 AAAA-TAAAAATA
42806742 AAAATAAACAAATA
1 AAAAT-AA-AAATA
*
42806756 AATATAAACAATA
1 AAAATAAA-AATA
42806769 AAAATAA
1 AAAATAA
42806776 TTGAGATTAG
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
11 2 0.04
12 15 0.28
13 30 0.56
14 7 0.13
ACGTcount: A:0.74, C:0.05, G:0.01, T:0.20
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:42807540 original size:10 final size:10
Alignment explanation
Indices: 42807521--42807585 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
42807511 AAATTATTTT
*
42807521 AAAAACTATA
1 AAAAATTATA
42807531 AAAAATTATA
1 AAAAATTATA
* *
42807541 TAAAATTAAA
1 AAAAATTATA
*
42807551 TAAAAACTAT-
1 -AAAAATTATA
* **
42807561 CAAAATGGTA
1 AAAAATTATA
42807571 AAAAATTATA
1 AAAAATTATA
42807581 AAAAA
1 AAAAA
42807586 AATTAAAATT
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
9 5 0.12
10 29 0.73
11 6 0.15
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (10 bp):
AAAAATTATA
Found at i:42807584 original size:19 final size:19
Alignment explanation
Indices: 42807528--42807584 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
42807518 TTTAAAAACT
*
42807528 ATAAAAAATTATATAAAATT
1 ATAAAAAATTATA-AAAATG
* * *
42807548 AAATAAAAACTATCAAAATG
1 ATA-AAAAATTATAAAAATG
*
42807568 GTAAAAAATTATAAAAA
1 ATAAAAAATTATAAAAA
42807585 AAATTAAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
19 12 0.43
20 8 0.29
21 8 0.29
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.26
Consensus pattern (19 bp):
ATAAAAAATTATAAAAATG
Found at i:42812927 original size:15 final size:15
Alignment explanation
Indices: 42812875--42812932 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
42812865 CAAAGTTTGG
*
42812875 ATTTGTTTACATAAT
1 ATTTTTTTACATAAT
**
42812890 ATTTTTTT-TGTAATT
1 ATTTTTTTACATAA-T
*
42812905 ATTATTTTACATAAT
1 ATTTTTTTACATAAT
42812920 ATTTTTTTA-ATAA
1 ATTTTTTTACATAA
42812933 AAAAAAAGTG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
14 7 0.21
15 24 0.71
16 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (15 bp):
ATTTTTTTACATAAT
Found at i:42812993 original size:23 final size:23
Alignment explanation
Indices: 42812967--42813013 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
42812957 TTGATATTGA
42812967 TATTCAATTTTAAAGTTGAGCTT
1 TATTCAATTTTAAAGTTGAGCTT
42812990 TATTCAATTTTAAAGTTGAGCTT
1 TATTCAATTTTAAAGTTGAGCTT
42813013 T
1 T
42813014 CTCTTTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.49
Consensus pattern (23 bp):
TATTCAATTTTAAAGTTGAGCTT
Found at i:42825980 original size:12 final size:12
Alignment explanation
Indices: 42825960--42825990 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
42825950 CTAACGACAG
*
42825960 ATATATATATAT
1 ATATGTATATAT
42825972 ATATGTATATAT
1 ATATGTATATAT
42825984 ATATGTA
1 ATATGTA
42825991 GTTCCTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:42826642 original size:30 final size:30
Alignment explanation
Indices: 42826588--42826652 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
42826578 ATTAATTGAT
42826588 ATTTTTATTATTTTTAAAAAGTTAAATCA-A
1 ATTTTTATTATTTTTAAAAAGTTAAAT-ATA
** **
42826618 ATTTTTATTATTTTTGGAGGGTTAAATATA
1 ATTTTTATTATTTTTAAAAAGTTAAATATA
42826648 ATTTT
1 ATTTT
42826653 AACTTTACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (30 bp):
ATTTTTATTATTTTTAAAAAGTTAAATATA
Found at i:42826764 original size:27 final size:27
Alignment explanation
Indices: 42826729--42826788 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
42826719 TGGACTTTTC
*
42826729 GTTTAATTTAGAGTTAAATTGATTTTAA
1 GTTT-ATTTAAAGTTAAATTGATTTTAA
* *
42826757 GTTTATTTAAATTTAAATTTATTTTAA
1 GTTTATTTAAAGTTAAATTGATTTTAA
*
42826784 ATTTA
1 GTTTA
42826789 AATTTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (27 bp):
GTTTATTTAAAGTTAAATTGATTTTAA
Found at i:42826770 original size:6 final size:6
Alignment explanation
Indices: 42826761--42826851 Score: 78
Period size: 6 Copynumber: 15.0 Consensus size: 6
42826751 TTTTAAGTTT
*
42826761 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* * ** * *
42826809 CTTTGA ATTTAA ATTTAA ATAAAA ATTAAA ATACTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA
42826852 CATTAAAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
5 8 0.12
6 51 0.74
7 4 0.06
8 6 0.09
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:42826820 original size:17 final size:16
Alignment explanation
Indices: 42826752--42826825 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
42826742 TTAAATTGAT
*
42826752 TTTAAGTTTATTTAAA
1 TTTAAATTTATTTAAA
42826768 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
*
42826785 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
*
42826799 TTTAAATTTACTTTGAA
1 TTTAAATTTA-TTTAAA
42826816 TTTAAATTTA
1 TTTAAATTTA
42826826 AATAAAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.22
15 2 0.04
16 11 0.22
17 27 0.53
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:42826907 original size:23 final size:23
Alignment explanation
Indices: 42826877--42826931 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
42826867 AGTTCAATGT
42826877 CCAAATACATGACCCACTTGGAC
1 CCAAATACATGACCCACTTGGAC
*
42826900 CCAAATACATGGCCCACTTGGAC
1 CCAAATACATGACCCACTTGGAC
42826923 CCAAATACA
1 CCAAATACA
42826932 AACCCAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.35, G:0.13, T:0.16
Consensus pattern (23 bp):
CCAAATACATGACCCACTTGGAC
Found at i:42827729 original size:22 final size:22
Alignment explanation
Indices: 42827688--42827729 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42827678 TAATGTTTTA
* *
42827688 AATAATAATAATCATTAATATT
1 AATAATAATAATAATAAATATT
*
42827710 AATATTAATAATAATAAATA
1 AATAATAATAATAATAAATA
42827730 AAAAGGGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAATAATAATAATAAATATT
Found at i:42828094 original size:21 final size:21
Alignment explanation
Indices: 42828048--42828095 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
42828038 AGGGGTTTTG
42828048 AAATAAAGAACAAAAAATGAA
1 AAATAAAGAACAAAAAATGAA
*
42828069 GAATAAAGAACAAAAGAA-GAA
1 AAATAAAGAACAAAA-AATGAA
42828090 AAATAA
1 AAATAA
42828096 GAAAGAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.75, C:0.04, G:0.12, T:0.08
Consensus pattern (21 bp):
AAATAAAGAACAAAAAATGAA
Found at i:42828598 original size:11 final size:11
Alignment explanation
Indices: 42828575--42828637 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
42828565 TCAAATTTAT
42828575 TTTAATCTTAAA
1 TTTAAT-TTAAA
*
42828587 TTTATTTTAAA
1 TTTAATTTAAA
*
42828598 TTCAATTTAAA
1 TTTAATTTAAA
*
42828609 TTTAAATTTGAA
1 TTT-AATTTAAA
42828621 TTTAATTTAAA
1 TTTAATTTAAA
42828632 TTTAAT
1 TTTAAT
42828638 GTTATTATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
11 29 0.66
12 15 0.34
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:42828634 original size:17 final size:16
Alignment explanation
Indices: 42828585--42828653 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 16
42828575 TTTAATCTTA
* *
42828585 AATTTATTTTAAATTC
1 AATTTAATTTAAATTT
42828601 AATTTAAATTTAAATTT
1 AATTT-AATTTAAATTT
42828618 GAATTTAATTTAAATTT
1 -AATTTAATTTAAATTT
42828635 AATGTT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
42828652 AA
1 AA
42828654 AAAGAAAGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
16 11 0.23
17 31 0.66
18 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:42828654 original size:6 final size:6
Alignment explanation
Indices: 42828582--42828636 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
42828572 TATTTTAATC
* * *
42828582 TTAAAT TT-ATT TTAAA- TTCAAT TTAAAT TTAAAT TTGAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
42828627 TTAAAT TTAA
1 TTAAAT TTAA
42828637 TGTTATTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
5 13 0.32
6 28 0.68
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:42828701 original size:14 final size:14
Alignment explanation
Indices: 42828682--42828717 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
42828672 TGGCCCAGGG
*
42828682 CCCAATTACAATGA
1 CCCAATTACAAAGA
*
42828696 CCCAATTACAAAGG
1 CCCAATTACAAAGA
42828710 CCCAATTA
1 CCCAATTA
42828718 AGGGCCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (14 bp):
CCCAATTACAAAGA
Found at i:42830398 original size:160 final size:163
Alignment explanation
Indices: 42830223--42830535 Score: 483
Period size: 160 Copynumber: 1.9 Consensus size: 163
42830213 CTTTTCAATT
* *
42830223 TAGTCCTTTGACTGTTTGACTGTACCATAGGCTGCCACGTGTCA-C-TTTTGGATTATTTATGCA
1 TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTATGCA
**
42830286 TTTAGTCCTTTTTATTTTT-ATTTGTTTTAATTTAATCC-CAAATCAAC-TTTATTTTAATTATG
66 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTA-TTTAATTACA
*
42830348 AAATTGGCCCCAATAATTTTTCAAGGTTTATAAAC
130 AAATTGG-CCCAAAAATTTTTCAAGGTTTATAAAC
* *
42830383 TAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATCTTTTTGGATTATTTCTGCA
1 TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTATGCA
* *
42830448 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACAA
66 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAA
*
42830513 AATTGGTCCAAAAATTTTTCAAG
131 AATTGGCCCAAAAATTTTTCAAG
42830536 ATTTTCAAAT
Statistics
Matches: 138, Mismatches: 10, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
160 41 0.30
161 1 0.01
162 36 0.26
163 34 0.25
164 22 0.16
165 4 0.03
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (163 bp):
TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTATGCA
TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAA
AATTGGCCCAAAAATTTTTCAAGGTTTATAAAC
Found at i:42830583 original size:162 final size:159
Alignment explanation
Indices: 42830223--42830589 Score: 413
Period size: 163 Copynumber: 2.3 Consensus size: 159
42830213 CTTTTCAATT
* * * * *
42830223 TAGTCCTTTGACTGTTTGACTGTACCATAGGCTGCCACGTGTCACTTTTGGATTATTTATGCATT
1 TAGTCCCTTGACTGCTGGACT-CACCAGAGGCTGCCACGTGTCACTTTTGGATTATTTATGCATT
**
42830288 TAGTCCTTTTTATTTTTATTTGTTTTAATTTAATCCCAAATCAACTTTATTTTAATTATGAAATT
65 TAGTCCTTTTTATTTTTATTTGTTTTAATTTAATCCCAAATCAACTTTATTTTAATTACAAAATT
* *
42830353 GGCCCCAATAATTTTTCAAGGTTTATAAAC
130 GGCCCCAAAAATTTTTCAAGATTTATAAAC
* * * * *
42830383 TAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATCTTTTTGGATTATTTCTGCA
1 TAGTCCCTTGACTGCTGGACT-CACCAGAGGCTGCCACGTGTCA-C-TTTTGGATTATTTATGCA
* *
42830448 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTT-TATTTAATTACA
63 TTTAGTCCTTTTTATTTTT-ATTTGTTTTAATTTAATCC-CAAATCAACTTTAT-TTTAATTACA
* *
42830512 AAATTGG-TCCAAAAATTTTTCAAGATTT-TCAAAT
125 AAATTGGCCCCAAAAATTTTTCAAGATTTAT-AAAC
* *
42830546 TGGTCCCTTGACCT-CTGGA-T-ACCTGTAGGGCTGCCACGTGTCAC
1 TAGTCCCTTGA-CTGCTGGACTCACCAG-A-GGCTGCCACGTGTCAC
42830590 CTGTTTTTGG
Statistics
Matches: 180, Mismatches: 18, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
160 45 0.25
161 3 0.02
162 52 0.29
163 53 0.29
164 27 0.15
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (159 bp):
TAGTCCCTTGACTGCTGGACTCACCAGAGGCTGCCACGTGTCACTTTTGGATTATTTATGCATTT
AGTCCTTTTTATTTTTATTTGTTTTAATTTAATCCCAAATCAACTTTATTTTAATTACAAAATTG
GCCCCAAAAATTTTTCAAGATTTATAAAC
Found at i:42830668 original size:30 final size:30
Alignment explanation
Indices: 42830632--42830950 Score: 482
Period size: 30 Copynumber: 10.6 Consensus size: 30
42830622 AAATTGTCCA
* *
42830632 AAAATTACATTTTGACCCTAACACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
42830662 AAAATTACATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
42830692 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
42830722 AAAATTATATTTTGACCCCGAAACTTTAT-C
1 AAAATTACATTTTGACCCCAAAACTTT-TCC
*
42830752 AAAATTACATTTTGATCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
42830782 AAAATTACATTTTAAACCCCAAAACTTTTCC
1 AAAATTACATTTT-GACCCCAAAACTTTTCC
* * *
42830813 AAAATTATATTTTGACCCCGAAACTTTACC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
42830843 AAAATTACATTTTGATCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
42830873 AAAATTACATTTTGACCCCAAAACTTTAT-C
1 AAAATTACATTTTGACCCCAAAACTTT-TCC
42830903 AAAATTACATTTTGA-CCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
42830932 AAAATTACATTTTAACCCC
1 AAAATTACATTTTGACCCC
42830951 GATTTCACCA
Statistics
Matches: 262, Mismatches: 21, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
28 1 0.00
29 27 0.10
30 205 0.78
31 29 0.11
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:42830816 original size:151 final size:149
Alignment explanation
Indices: 42830632--42830950 Score: 530
Period size: 151 Copynumber: 2.1 Consensus size: 149
42830622 AAATTGTCCA
* * * *
42830632 AAAATTACATTTTGACCCTAACACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAAT
1 AAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTACCAAAAT
* *
42830697 TACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCGAAACTTTATCAAAATTACAT
66 TACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTATCAAAATTACAT
42830762 TTTGATCCCAAAACTTTTCC
131 TTTGA-CCCAAAACTTTTCC
* * *
42830782 AAAATTACATTTTAAACCCCAAAACTTTTCCAAAATTATATTTTGACCCCGAAACTTTACCAAAA
1 AAAATTACATTTT-AACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTACCAAAA
*
42830847 TTACATTTTGATCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTATCAAAATTACA
65 TTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTATCAAAATTACA
42830912 TTTTGACCCAAAACTTTTCC
130 TTTTGACCCAAAACTTTTCC
42830932 AAAATTACATTTTAACCCC
1 AAAATTACATTTTAACCCC
42830951 GATTTCACCA
Statistics
Matches: 158, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
149 6 0.04
150 40 0.25
151 112 0.71
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.34
Consensus pattern (149 bp):
AAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTACCAAAAT
TACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTATCAAAATTACAT
TTTGACCCAAAACTTTTCC
Found at i:42830838 original size:91 final size:89
Alignment explanation
Indices: 42830632--42830944 Score: 486
Period size: 91 Copynumber: 3.5 Consensus size: 89
42830622 AAATTGTCCA
* * *
42830632 AAAATTACATTTTGACCCTAACACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAAT
1 AAAATTACATTTTGACCCGAA-ACTTTTCCAAAATTACATTTTGATCCCAAAACTTTTCCAAAAT
42830697 TACATTTTGACCCCAAAACTTTTCC
65 TACATTTTGACCCCAAAACTTTTCC
*
42830722 AAAATTATATTTTGACCCCGAAACTTTAT-CAAAATTACATTTTGATCCCAAAACTTTTCCAAAA
1 AAAATTACATTTTGA-CCCGAAACTTT-TCCAAAATTACATTTTGATCCCAAAACTTTTCCAAAA
*
42830786 TTACATTTTAAACCCCAAAACTTTTCC
64 TTACATTTT-GACCCCAAAACTTTTCC
* *
42830813 AAAATTATATTTTGACCCCGAAACTTTACCAAAATTACATTTTGATCCCAAAACTTTTCCAAAAT
1 AAAATTACATTTTGA-CCCGAAACTTTTCCAAAATTACATTTTGATCCCAAAACTTTTCCAAAAT
42830878 TACATTTTGACCCCAAAACTTTAT-C
65 TACATTTTGACCCCAAAACTTT-TCC
*
42830903 AAAATTACATTTTGACCCAAAACTTTTCCAAAATTACATTTT
1 AAAATTACATTTTGACCCGAAACTTTTCCAAAATTACATTTT
42830945 AACCCCGATT
Statistics
Matches: 208, Mismatches: 10, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
89 25 0.12
90 89 0.43
91 94 0.45
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (89 bp):
AAAATTACATTTTGACCCGAAACTTTTCCAAAATTACATTTTGATCCCAAAACTTTTCCAAAATT
ACATTTTGACCCCAAAACTTTTCC
Found at i:42830973 original size:59 final size:56
Alignment explanation
Indices: 42830660--42831270 Score: 420
Period size: 59 Copynumber: 10.4 Consensus size: 56
42830650 TAACACTTTT
* * *
42830660 CCAAAATTA-CATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTT-T
1 CCAAAATTACCATTTT-ACCCCAAAACTTTT--AAAATTACATTTTAACCCC--GA-TTTCA
* * * ** *
42830720 CCAAAATTA-TATTTTGACCCCGAAACTTTATCAAAATTACATTTTGATCCCAAAACTTT-T
1 CCAAAATTACCATTTT-ACCCCAAAACTTT-T-AAAATTACATTTT-AACCC-CGA-TTTCA
* *
42830780 CCAAAATTA-CATTTTAAACCCCAAAACTTTTCCAAAATTATATTTTGACCCCGAAACTTT-A
1 CCAAAATTACCATTTT--ACCCCAAAACTTTT--AAAATTACATTTTAACCCCG--A-TTTCA
* * *
42830841 CCAAAATTA-CATTTTGATCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTT-A
1 CCAAAATTACCATTTT-ACCCCAAAACTTTT--AAAATTACATTTTAACCCC--GA-TTTCA
*
42830901 TCAAAATTA-CATTTTGA-CCCAAAACTTTTCCAAAATTACATTTTAACCCCGATTTCA
1 CCAAAATTACCATTTT-ACCCCAAAACTTTT--AAAATTACATTTTAACCCCGATTTCA
* * *
42830958 CCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCA
1 CC-AAAATTACCATTTTA-CCCCAAAACTTTTAAAATTACA-TTTTAACCCCGATTTCA
* * * *
42831017 TCAAAAATTACCATTTTACCCTCGAATC-TTTAAAATTCCATTTTTAACCCCGATTTCA
1 -CCAAAATTACCATTTTACCC-CAAAACTTTTAAAATTACA-TTTTAACCCCGATTTCA
** * *
42831075 CCGAAAATTACCATTTTACCCTTGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCA
1 CC-AAAATTACCATTTTACCC-CAAAACTTTTAAAATTACA-TTTTAACCCCGATTTCA
* ** * *
42831134 TCGAAAATTACCATTTTACCCCCGAA-TCTTTAAAATTCCGTTTTTAA-CCCGATTTCA
1 -CCAAAATTACCATTTTACCCCAAAACT-TTTAAAATTAC-ATTTTAACCCCGATTTCA
* * * *
42831191 CTGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCA
1 C-CAAAATTACCATTTTA-CCCCAAAACTTTTAAAATTACA-TTTTAACCCCGATTTCA
*
42831250 CCAAAATTACCATTTTGCCCC
1 CCAAAATTACCATTTTACCCC
42831271 CGGGTATCTA
Statistics
Matches: 483, Mismatches: 41, Indels: 57
0.83 0.07 0.10
Matches are distributed among these distances:
56 4 0.01
57 35 0.07
58 127 0.26
59 136 0.28
60 132 0.27
61 49 0.10
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (56 bp):
CCAAAATTACCATTTTACCCCAAAACTTTTAAAATTACATTTTAACCCCGATTTCA
Found at i:42831001 original size:58 final size:59
Alignment explanation
Indices: 42830932--42831272 Score: 548
Period size: 58 Copynumber: 5.9 Consensus size: 59
42830922 AAACTTTTCC
* *
42830932 AAAATTACA-TTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* * *
42830990 AAAATTCCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCTCGAATC-TTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
**
42831048 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTTGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
*
42831107 AAAATTCCATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCCGAATC-TTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* *
42831165 AAAATTCCGTTTTTAA-CCCGATTTCACTGAAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
*
42831223 AAAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTGCCCCCG
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCG
42831273 GGTATCTATA
Statistics
Matches: 264, Mismatches: 15, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
57 36 0.14
58 119 0.45
59 109 0.41
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
Found at i:42831062 original size:117 final size:117
Alignment explanation
Indices: 42830932--42831272 Score: 571
Period size: 117 Copynumber: 2.9 Consensus size: 117
42830922 AAACTTTTCC
* *
42830932 AAAATTACA-TTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
*
42830996 CCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCTCGAATCTTT
66 CCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAATCTTT
**
42831048 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTTGAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
*
42831113 CCATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCCGAATCTTT
66 CCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAATCTTT
* *
42831165 AAAATTCCGTTTTTAA-CCCGATTTCACTGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
* *
42831229 CCATTTTTAACCCCGATTTCA-CCAAAATTACCATTTTGCCCCCG
66 CCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCG
42831273 GGTATCTATA
Statistics
Matches: 212, Mismatches: 12, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
115 21 0.10
116 74 0.35
117 117 0.55
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.36
Consensus pattern (117 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
CCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAATCTTT
Found at i:42846113 original size:68 final size:68
Alignment explanation
Indices: 42846004--42846611 Score: 882
Period size: 68 Copynumber: 8.9 Consensus size: 68
42845994 ACATCGTTCC
**
42846004 CTTGAAATTGAAGTAGAGTGGATAACACGT-TTCCATCTCTGAAATTGAAGTAAGAGCAATTTCA
1 CTTGAAATTGAAGTAGAGTGGATAACACGTCTT-CATCTCTGAAATTGAAGTAAGAGCAACGTCA
42846068 TCCT
65 TCCT
42846072 CTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCAT
1 CTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCAT
42846137 CCT
66 CCT
* * *
42846140 CTTGAAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTC
1 CTTG-AAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTC
42846205 ATTCC-
64 A-TCCT
* *
42846210 CTTGAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAATGTCAT
1 CTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCAT
42846275 CC-
66 CCT
* **
42846277 CTTTGAAATTGAAGTAAAGTGGATAACACGT-TTCCATCTCTGAAATTGAAGTAAGAGCAATTTC
1 C-TTGAAATTGAAGTAGAGTGGATAACACGTCTT-CATCTCTGAAATTGAAGTAAGAGCAACGTC
42846341 ATCCT
64 ATCCT
42846346 CTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCAT
1 CTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCAT
42846411 CCT
66 CCT
* * *
42846414 CTTGAAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTC
1 CTTG-AAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTC
*
42846479 GTCCT
64 ATCCT
** ** * * *
42846484 CTTGAAATTGAAGTAGAGTTGGATATTAAATCTTTATCTCTGAAATTGGAGTAAAAGCAACGTCA
1 CTTGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCA
*
42846549 TCCC
65 TCCT
* * *
42846553 CTCGAAATTGAAATAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 CTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
42846612 GATCATTTCC
Statistics
Matches: 497, Mismatches: 33, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
67 6 0.01
68 269 0.54
69 122 0.25
70 97 0.20
71 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (68 bp):
CTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCAT
CCT
Found at i:42846456 original size:206 final size:202
Alignment explanation
Indices: 42846000--42846611 Score: 899
Period size: 206 Copynumber: 3.0 Consensus size: 202
42845990 CTCAACATCG
* *
42846000 TTCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGCAATT
1 TTCCCTTGAAATTGAAGTAGAGTGGATAACACGTTT-TATCTCTGAAATTGAAGTAAGAGCAATG
42846065 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
65 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGT-TTCATCTCTGAAATTGAAGTAAGAGCA
* *
42846130 ACGTCATCCTCTTGAAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAA
129 ACGTCATCCTCTTG-AAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAA
42846195 GAGCAACGTCA
192 GAGCAACGTCA
42846206 TTCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAATG
1 TTCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTT-ATCTCTGAAATTGAAGTAAGAGCAATG
*
42846271 TCATCC-CTTTGAAATTGAAGTAAAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGC
65 TCATCCTC-TTGAAATTGAAGTAGAGTGGATAACACGTTT-CATCTCTGAAATTGAAGTAAGAGC
** *
42846335 AATTTCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAG
128 AACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAG
42846400 AGCAACGTCA
193 AGCAACGTCA
* *
42846410 -TCCTCTTGAAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 TTCC-CTTG-AAATTGAAGTAGAG-TGGATAACACGT-TTTATCTCTGAAATTGAAGTAAGAGCA
* * * *
42846474 ACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATTAAATC-TTT-ATCTCTGAAATTGGAGTA
62 ATGTCATCCTCTTGAAATTGAAGTAGAG-TGGATA--ACA-CGTTTCATCTCTGAAATTGAAGTA
* * * *
42846537 AAAGCAACGTCATCCCCTCGAAATTGAAATAGAGTGGATAACACGTCTTTATCTCTGAAATTGAA
123 AGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAA
42846602 GTAAGAGCAA
188 GTAAGAGCAA
42846612 GATCATTTCC
Statistics
Matches: 372, Mismatches: 22, Indels: 23
0.89 0.05 0.06
Matches are distributed among these distances:
203 3 0.01
204 47 0.13
205 31 0.08
206 190 0.51
207 95 0.26
209 5 0.01
210 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (202 bp):
TTCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTTATCTCTGAAATTGAAGTAAGAGCAATGT
CATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTTTCATCTCTGAAATTGAAGTAAGAGCAAC
GTCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGC
AACGTCA
Found at i:42846494 original size:274 final size:274
Alignment explanation
Indices: 42846001--42846611 Score: 1041
Period size: 274 Copynumber: 2.2 Consensus size: 274
42845991 TCAACATCGT
42846001 TCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGCAATTT
1 TCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGCAATTT
42846066 CATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
66 CATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
42846131 CGTCATCCTCTTGAAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAG
131 CGTCATCCTCTTGAAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAG
* **
42846196 AGCAACGTCATTCCCTTGAAATTGAAGTAGAG-TGGATAACACGT-TTTCATCTCTGAAATTGAA
196 AGCAACGTCAGTCCCTTGAAATTGAAGTAGAGTTGGATAACAAATCTTT-ATCTCTGAAATTGAA
* *
42846259 GTAAGAGCAATGTCA
260 GTAAAAGCAACGTCA
*
42846274 TCCCTTTGAAATTGAAGTAAAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGCAATT
1 TCCC-TTGAAATTGAAGTAGAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGCAATT
42846339 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
65 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
42846404 ACGTCATCCTCTTGAAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAA
130 ACGTCATCCTCTTGAAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAA
** *
42846469 GAGCAACGTC-GTCCTCTTGAAATTGAAGTAGAGTTGGATATTAAATCTTTATCTCTGAAATTGG
195 GAGCAACGTCAGTCC-CTTGAAATTGAAGTAGAGTTGGATAACAAATCTTTATCTCTGAAATTGA
42846533 AGTAAAAGCAACGTCA
259 AGTAAAAGCAACGTCA
* * *
42846549 TCCCCTCGAAATTGAAATAGAGTGGATAACACGTCTT-TATCTCTGAAATTGAAGTAAGAGCAA
1 T-CCCTTGAAATTGAAGTAGAGTGGATAACACGT-TTCCATCTCTGAAATTGAAGTAAGAGCAA
42846612 GATCATTTCC
Statistics
Matches: 319, Mismatches: 13, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
273 7 0.02
274 217 0.68
275 87 0.27
276 8 0.03
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (274 bp):
TCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGCAATTT
CATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
CGTCATCCTCTTGAAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAG
AGCAACGTCAGTCCCTTGAAATTGAAGTAGAGTTGGATAACAAATCTTTATCTCTGAAATTGAAG
TAAAAGCAACGTCA
Found at i:42847011 original size:21 final size:21
Alignment explanation
Indices: 42846965--42847012 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
42846955 AGGGGTTTTG
42846965 AAATAAAGAACAAAAAATGAA
1 AAATAAAGAACAAAAAATGAA
*
42846986 GAATAAAGAACAAAAGAA-GAA
1 AAATAAAGAACAAAA-AATGAA
42847007 AAATAA
1 AAATAA
42847013 GAAAGAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.75, C:0.04, G:0.12, T:0.08
Consensus pattern (21 bp):
AAATAAAGAACAAAAAATGAA
Found at i:42847515 original size:11 final size:11
Alignment explanation
Indices: 42847492--42847554 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
42847482 TCAAATTTAT
42847492 TTTAATCTTAAA
1 TTTAAT-TTAAA
*
42847504 TTTATTTTAAA
1 TTTAATTTAAA
*
42847515 TTCAATTTAAA
1 TTTAATTTAAA
*
42847526 TTTAAATTTGAA
1 TTT-AATTTAAA
42847538 TTTAATTTAAA
1 TTTAATTTAAA
42847549 TTTAAT
1 TTTAAT
42847555 GTTATTATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
11 29 0.66
12 15 0.34
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:42847551 original size:17 final size:16
Alignment explanation
Indices: 42847502--42847570 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 16
42847492 TTTAATCTTA
* *
42847502 AATTTATTTTAAATTC
1 AATTTAATTTAAATTT
42847518 AATTTAAATTTAAATTT
1 AATTT-AATTTAAATTT
42847535 GAATTTAATTTAAATTT
1 -AATTTAATTTAAATTT
42847552 AATGTT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
42847569 AA
1 AA
42847571 AAAGAATGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
16 11 0.23
17 31 0.66
18 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:42847571 original size:6 final size:6
Alignment explanation
Indices: 42847499--42847553 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
42847489 TATTTTAATC
* * *
42847499 TTAAAT TT-ATT TTAAA- TTCAAT TTAAAT TTAAAT TTGAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
42847544 TTAAAT TTAA
1 TTAAAT TTAA
42847554 TGTTATTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
5 13 0.32
6 28 0.68
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:42847616 original size:14 final size:14
Alignment explanation
Indices: 42847597--42847643 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
42847587 CATGGCCTAG
42847597 GGCCCAATTACAAA
1 GGCCCAATTACAAA
*
42847611 GGCCCAATT--AAG
1 GGCCCAATTACAAA
*
42847623 GGCCCAATTACAAT
1 GGCCCAATTACAAA
42847637 GGCCCAA
1 GGCCCAA
42847644 ATCCCTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 11 0.38
14 18 0.62
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.15
Consensus pattern (14 bp):
GGCCCAATTACAAA
Found at i:42847775 original size:15 final size:15
Alignment explanation
Indices: 42847755--42847785 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42847745 GCTTATGCCG
42847755 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
42847770 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
42847785 C
1 C
42847786 CATCCACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.55, G:0.13, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:42849314 original size:160 final size:163
Alignment explanation
Indices: 42849141--42849450 Score: 493
Period size: 163 Copynumber: 1.9 Consensus size: 163
42849131 TTCAATTTAA
* * *
42849141 TCCTTTGACTGTTTGACTGTACCATAGGCTGCCACGTGTCA-CTTTTTGGATTATTTATGCATTT
1 TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGCCATCTTTTTGGATTATTTATGCATTT
*
42849205 AGTCCTTTTTATTTTT-ATTTGTTTTAATTTAAT-CTCAAATCAAC-TTTATTTTAATTACGAAA
66 AGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTA-TTTAATTACAAAA
*
42849267 TTGGCCCAATAATTTTTCAAGGTTTATAAACTAG
130 TTGGCCCAAAAATTTTTCAAGGTTTATAAACTAG
* *
42849301 TCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGCCATCTTTTTGGATTATTTCTGCATTT
1 TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGCCATCTTTTTGGATTATTTATGCATTT
* *
42849366 AGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACAAAAT
66 AGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAAAT
*
42849431 TGGTCCAAAAATTTTTCAAG
131 TGGCCCAAAAATTTTTCAAG
42849451 ATTTTCAAAT
Statistics
Matches: 136, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
160 37 0.27
161 38 0.28
162 17 0.12
163 40 0.29
164 4 0.03
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (163 bp):
TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGCCATCTTTTTGGATTATTTATGCATTT
AGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAAAT
TGGCCCAAAAATTTTTCAAGGTTTATAAACTAG
Found at i:42849583 original size:30 final size:30
Alignment explanation
Indices: 42849547--42849897 Score: 495
Period size: 30 Copynumber: 11.6 Consensus size: 30
42849537 AAATTATCCA
*
42849547 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* ** *
42849577 AAAATTACATTTTAACCCCAAATTTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCC
42849607 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
42849637 AAAATTAGATTTTTGACCCCGAAACTTTACC
1 AAAATTACA-TTTTGACCCCAAAACTTTTCC
*
42849668 AAAATTACATTTTGATCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
42849698 AAAATTACATTTTAACCTCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
42849728 AAAATTATATTTTTGACCCCGAAACTTTACC
1 AAAATTACA-TTTTGACCCCAAAACTTTTCC
* *
42849759 AAAATTACATTTTGATCTCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
42849789 AAAATTACATTTTGATCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
** *
42849819 AAAATTACATTTTGACCCTGAAACTTTACC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
42849849 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
42849879 AAAATTACATTTTAACCCC
1 AAAATTACATTTTGACCCC
42849898 GATTTCACCG
Statistics
Matches: 281, Mismatches: 38, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
30 229 0.81
31 52 0.19
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:42849652 original size:91 final size:90
Alignment explanation
Indices: 42849547--42849897 Score: 531
Period size: 91 Copynumber: 3.9 Consensus size: 90
42849537 AAATTATCCA
** * * ** *
42849547 AAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTAACCCCAAATTTTTTCTAAAAT
1 AAAATTACATTTTGACCCCGAAACTTTACCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
*
42849612 TACATTTTGACCCCAAAACTTTTCC
66 TACATTTTAACCCCAAAACTTTTCC
* *
42849637 AAAATTAGATTTTTGACCCCGAAACTTTACCAAAATTACATTTTGATCCCAAAACTTTTCCAAAA
1 AAAATTACA-TTTTGACCCCGAAACTTTACCAAAATTACATTTTGACCCCAAAACTTTTCCAAAA
*
42849702 TTACATTTTAACCTCAAAACTTTTCC
65 TTACATTTTAACCCCAAAACTTTTCC
* * *
42849728 AAAATTATATTTTTGACCCCGAAACTTTACCAAAATTACATTTTGATCTCAAAACTTTTCCAAAA
1 AAAATTACA-TTTTGACCCCGAAACTTTACCAAAATTACATTTTGACCCCAAAACTTTTCCAAAA
* *
42849793 TTACATTTTGATCCCAAAACTTTTCC
65 TTACATTTTAACCCCAAAACTTTTCC
*
42849819 AAAATTACATTTTGACCCTGAAACTTTACCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
1 AAAATTACATTTTGACCCCGAAACTTTACCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
42849884 TACATTTTAACCCC
66 TACATTTTAACCCC
42849898 GATTTCACCG
Statistics
Matches: 238, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
90 73 0.31
91 165 0.69
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (90 bp):
AAAATTACATTTTGACCCCGAAACTTTACCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
TACATTTTAACCCCAAAACTTTTCC
Found at i:42849921 original size:60 final size:59
Alignment explanation
Indices: 42849547--42850219 Score: 482
Period size: 60 Copynumber: 11.3 Consensus size: 59
42849537 AAATTATCCA
* * ** *
42849547 AAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACA-TTTTAACCCCAAATTTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTTAACCCC-GA-TTTCACC
* *
42849607 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTAGATTTTTGACCCCGAAACTTT-ACC
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTTAACCCCG--A-TTTCACC
* ** *
42849668 AAAATTACATTTTGATCCCAAAACTTTTCCAAAATTACA-TTTTAACCTCAAAACTTT-TCC
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTTAACC-C-CGA-TTTCACC
* * * * * *** *
42849728 AAAATTATATTTTTGACCCCGAAACTTTACCAAAATTACATTTTGATCTCAAAACTTT-TCC
1 AAAATTACA-TTTTGACCCCAAAACTTTTCCAAAATTACATTTTTAAC-CCCGA-TTTCACC
* * *
42849789 AAAATTACATTTTGATCCCAAAACTTTTCCAAAATTACA-TTTTGACCCTGAAACTTT-ACC
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTTAACCCCG--A-TTTCACC
42849849 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACA-TTTTAACCCCGATTTCACC
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTTAACCCCGATTTCACC
* * **
42849907 GAAAATTACTATTTT-ACCCCCGAATCTTTT--AAAATT-CTATTTTTAACCCCGATTTCATTG
1 -AAAATTAC-ATTTTGA-CCCCAAAACTTTTCCAAAATTAC-ATTTTTAACCCCGATTTCA-CC
** * *
42849967 AAAATTACCATTTT-ACCCCCGAA-TCTTT--AAAATTCCATTTTTAACCTCGATTTCACC
1 AAAATTA-CATTTTGACCCCAAAACT-TTTCCAAAATTACATTTTTAACCCCGATTTCACC
* * *
42850024 GAAAATTACCATTTT-ACCCCTGAATCTTTT--AAAATT-CTATTTTTAACCCCGATTTCATCA
1 -AAAATTA-CATTTTGACCCC-AAAACTTTTCCAAAATTAC-ATTTTTAACCCCGATTTCA-CC
** * *
42850084 AAAATTACCATTTT-ACCCCCGAA-TCTTT--AAAATTCCATTTTTAACCCCGATTTCATCA
1 AAAATTA-CATTTTGACCCCAAAACT-TTTCCAAAATTACATTTTTAACCCCGATTTCA-CC
* * * *
42850142 AAAATTACCATTTT-ACCCCCGAATCTTTT--AAAATTCCATTTTTAACCCTGATTTCACC
1 AAAATTA-CATTTTGA-CCCCAAAACTTTTCCAAAATTACATTTTTAACCCCGATTTCACC
*
42850200 AAAATTACCATTTTGCCCCC
1 AAAATTA-CATTTTGACCCC
42850220 GGGTATCCAT
Statistics
Matches: 525, Mismatches: 58, Indels: 62
0.81 0.09 0.10
Matches are distributed among these distances:
57 6 0.01
58 130 0.25
59 126 0.24
60 160 0.30
61 93 0.18
62 9 0.02
63 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (59 bp):
AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTTAACCCCGATTTCACC
Found at i:42849998 original size:58 final size:59
Alignment explanation
Indices: 42849849--42850220 Score: 531
Period size: 58 Copynumber: 6.4 Consensus size: 59
42849839 AAACTTTACC
* * * *
42849849 AAAATTA-CATTTTGA-CCCCAAAACTTTTCCAAAATTACA-TTTTAACCCCGATTTCACCG
1 AAAATTACCATTTT-ACCCCCGAATCTTTT--AAAATTCCATTTTTAACCCCGATTTCATCG
* * *
42849908 AAAATTACTATTTTACCCCCGAATCTTTTAAAATTCTATTTTTAACCCCGATTTCATTG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCATCG
* *
42849967 AAAATTACCATTTTACCCCCGAATC-TTTAAAATTCCATTTTTAACCTCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCATCG
* * *
42850025 AAAATTACCATTTTACCCCTGAATCTTTTAAAATTCTATTTTTAACCCCGATTTCATCA
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCATCG
*
42850084 AAAATTACCATTTTACCCCCGAATC-TTTAAAATTCCATTTTTAACCCCGATTTCATCA
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCATCG
* *
42850142 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCTGATTTCA-CC
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCATCG
*
42850200 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
42850221 GGTATCCATA
Statistics
Matches: 286, Mismatches: 22, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
58 138 0.48
59 132 0.46
60 16 0.06
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCATCG
Found at i:42850029 original size:117 final size:117
Alignment explanation
Indices: 42849879--42850220 Score: 562
Period size: 117 Copynumber: 2.9 Consensus size: 117
42849869 AAACTTTTCC
* *
42849879 AAAATTACA-TTTTAACCCCGATTTCACCGAAAATTACTATTTTACCCCCGAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
**
42849943 CTATTTTTAACCCCGATTTCATTGAAAATTACCATTTTACCCCCGAATCTTT
66 CTATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAATCTTT
* *
42849995 AAAATTCCATTTTTAACCTCGATTTCACCGAAAATTACCATTTTACCCCTGAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
42850060 CTATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAATCTTT
66 CTATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAATCTTT
* *
42850112 AAAATTCCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
* * * *
42850177 CCATTTTTAACCCTGATTTCA-CCAAAATTACCATTTTGCCCCCG
66 CTATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCG
42850221 GGTATCCATA
Statistics
Matches: 211, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
116 29 0.14
117 182 0.86
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (117 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
CTATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAATCTTT
Found at i:42851665 original size:30 final size:30
Alignment explanation
Indices: 42851628--42851857 Score: 313
Period size: 30 Copynumber: 7.7 Consensus size: 30
42851618 CTTTTGTAAG
*
42851628 CCCCAAAA-TTGTCCAGAAATTACATTTTGA
1 CCCCAAAACTTTTCCA-AAATTACATTTTGA
* * *
42851658 CCTCAAAACTTTTTCAAAATTACATTTTAA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
* *
42851688 CCCTAAAACTTTTCTAAAATTACATTTTGA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
*
42851718 CCCCAAAACTTTTCCAAAATTACATTTTAA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
**
42851748 CCCTGAAACTTTTCCAAAATTACATTTTGA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
42851778 CCCCAAAACTTTTCCAAAATTACATTTTGA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
** *
42851808 -CCTGAAACTTTTCCAAAATTATATTTTGA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
*
42851837 CCCCAAAAC-TTTCAAAAATTA
1 CCCCAAAACTTTTCCAAAATTA
42851858 TGATTTACCC
Statistics
Matches: 175, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
29 37 0.21
30 133 0.76
31 5 0.03
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (30 bp):
CCCCAAAACTTTTCCAAAATTACATTTTGA
Found at i:42851717 original size:60 final size:60
Alignment explanation
Indices: 42851639--42851857 Score: 352
Period size: 60 Copynumber: 3.7 Consensus size: 60
42851629 CCCAAAATTG
* * *
42851639 TCCAGAAATTACATTTTGACCTCAAAACTTTTTCAAAATTACATTTTAACCCTAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCTGAAACTTT
*
42851700 TCTAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCTGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCTGAAACTTT
*
42851760 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGA-CCTGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCTGAAACTTT
* *
42851819 TCCAAAATTATATTTTGACCCCAAAAC-TTTCAAAAATTA
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTA
42851858 TGATTTACCC
Statistics
Matches: 150, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
58 11 0.07
59 37 0.25
60 99 0.66
61 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (60 bp):
TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCTGAAACTTT
Found at i:42859040 original size:30 final size:30
Alignment explanation
Indices: 42858986--42859050 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
42858976 ATTAATTGAT
42858986 ATTTTTATTATTTTTAAAAAGTTAAATCA-A
1 ATTTTTATTATTTTTAAAAAGTTAAAT-ATA
** **
42859016 ATTTTTATTATTTTTGGAGGGTTAAATATA
1 ATTTTTATTATTTTTAAAAAGTTAAATATA
42859046 ATTTT
1 ATTTT
42859051 AACTTTACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (30 bp):
ATTTTTATTATTTTTAAAAAGTTAAATATA
Found at i:42859162 original size:27 final size:27
Alignment explanation
Indices: 42859127--42859186 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
42859117 TGGATTTTTC
*
42859127 GTTTAATTTAGAGTTAAATTGATTTTAA
1 GTTT-ATTTAAAGTTAAATTGATTTTAA
* *
42859155 GTTTATTTAAATTTAAATTTATTTTAA
1 GTTTATTTAAAGTTAAATTGATTTTAA
*
42859182 ATTTA
1 GTTTA
42859187 AATTTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (27 bp):
GTTTATTTAAAGTTAAATTGATTTTAA
Found at i:42859168 original size:6 final size:6
Alignment explanation
Indices: 42859159--42859249 Score: 78
Period size: 6 Copynumber: 15.0 Consensus size: 6
42859149 TTTTAAGTTT
*
42859159 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* * ** * *
42859207 CTTTGA ATTTAA ATTTAA ATAAAA ATTAAA ATACTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA
42859250 CATTAAAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
5 8 0.12
6 51 0.74
7 4 0.06
8 6 0.09
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:42859218 original size:17 final size:16
Alignment explanation
Indices: 42859150--42859223 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
42859140 TTAAATTGAT
*
42859150 TTTAAGTTTATTTAAA
1 TTTAAATTTATTTAAA
42859166 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
*
42859183 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
*
42859197 TTTAAATTTACTTTGAA
1 TTTAAATTTA-TTTAAA
42859214 TTTAAATTTA
1 TTTAAATTTA
42859224 AATAAAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.22
15 2 0.04
16 11 0.22
17 27 0.53
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:42860104 original size:22 final size:22
Alignment explanation
Indices: 42860063--42860104 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42860053 TAACGTTTTA
*
42860063 AATAATAATAATCATTAATATT
1 AATAATAATAATCATAAATATT
* *
42860085 AATATTAATAATGATAAATA
1 AATAATAATAATCATAAATA
42860105 AAAAGGGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AATAATAATAATCATAAATATT
Found at i:42861164 original size:30 final size:29
Alignment explanation
Indices: 42861128--42861410 Score: 361
Period size: 30 Copynumber: 9.4 Consensus size: 29
42861118 AAATTGTCCA
*
42861128 AAAATTACATTTTAACCTCAAAACTTTTCC
1 AAAATTACATTTTGACC-CAAAACTTTTCC
*
42861158 AAAATTACATTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCC-AAAACTTTTCC
*
42861188 AAAATTACATTTTGACCCTAAAAATTTTCC
1 AAAATTACATTTTGACCC-AAAACTTTTCC
* *
42861218 AAAATTACCTTTTAACCCCAAAAACTTTTCC
1 AAAATTACATTTTGA-CCC-AAAACTTTTCC
42861249 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGA-CCCAAAACTTTTCC
*
42861279 AAAATTACATTTTGACCCCAAAATTTTTCC
1 AAAATTACATTTTGA-CCCAAAACTTTTCC
*
42861309 ACAATTACATTTTGACCCAAAACTTTTCC
1 AAAATTACATTTTGACCCAAAACTTTTCC
* *
42861338 AAAATTACATTTTAAACCCTAAAACTTTTCT
1 AAAATTACATTTT-GACCC-AAAACTTTTCC
* *
42861369 AAAATTATATTTTGACCCCAAAAC-TTTCA
1 AAAATTACATTTTGA-CCCAAAACTTTTCC
42861398 AAAATTACCATTT
1 AAAATTA-CATTT
42861411 ACCCCCAAAC
Statistics
Matches: 229, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
29 37 0.16
30 137 0.60
31 55 0.24
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTGACCCAAAACTTTTCC
Found at i:42861271 original size:19 final size:19
Alignment explanation
Indices: 42861247--42861303 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
42861237 AAAAACTTTT
42861247 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
42861266 CC-AAA--AC-TTTT----
1 CCAAAATTACATTTTGACC
42861277 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
42861296 CCAAAATT
1 CCAAAATT
42861304 TTTCCACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
11 2 0.07
12 3 0.10
14 2 0.07
15 8 0.27
16 2 0.07
18 3 0.10
19 10 0.33
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.32
Consensus pattern (19 bp):
CCAAAATTACATTTTGACC
Found at i:42861273 original size:91 final size:89
Alignment explanation
Indices: 42861118--42861419 Score: 410
Period size: 91 Copynumber: 3.3 Consensus size: 89
42861108 GTAAGCCCCT
* *
42861118 AAATTGTCCAAAAATTACATTTTAACCTCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACT
1 AAATTTTCC-AAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACT
42861183 TTTCCAAAATTACATTTTGACCCTAA
65 TTTCCAAAATTACATTTTGACCC-AA
* * *
42861209 AAATTTTCCAAAATTACCTTTTAACCCCAAAAACTTTTCCAAAATTACATTTTGACCCCAAAACT
1 AAATTTTCCAAAATTACATTTTAACCCC-AAAACTTTTCCAAAATTACATTTTAACCCTAAAACT
42861274 TTTCCAAAATTACATTTTGACCCCAA
65 TTTCCAAAATTACATTTTGA-CCCAA
* * *
42861300 AATTTTTCCACAATTACATTTTGA-CCCAAAACTTTTCCAAAATTACATTTTAAACCCTAAAACT
1 AAATTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTT-AACCCTAAAACT
* * *
42861364 TTTCTAAAATTATATTTTGACCCCA
65 TTTCCAAAATTACATTTTGACCCAA
* * *
42861389 AAACTTTCAAAAATTACCA-TTTACCCCCAAA
1 AAATTTTCCAAAATTA-CATTTTAACCCCAAA
42861420 CTTCCCTAAA
Statistics
Matches: 186, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
89 43 0.23
90 56 0.30
91 84 0.45
92 3 0.02
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.34
Consensus pattern (89 bp):
AAATTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTT
TTCCAAAATTACATTTTGACCCAA
Found at i:42861496 original size:59 final size:59
Alignment explanation
Indices: 42861402--42861587 Score: 155
Period size: 59 Copynumber: 3.2 Consensus size: 59
42861392 CTTTCAAAAA
* * *
42861402 TTACCA-TTTA-CCCCCAAACTTCCCTAAATCCCATTTTTAACCCCGATTTCACCGAAAC
1 TTACCATTTTAGCCTCCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCACCGAAAC
* * * * ** * ** * *
42861460 TTACCGTTTT-GCCTCCGAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTGCCTAAAT
1 TTACCATTTTAGCCTCCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCACCGAAAC
** * * *
42861519 TTACCATTTTATTCTCCAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA-CAAAAA
1 TTACCATTTTAGCCTCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCACCGAAAC
42861577 TTACCATTTTA
1 TTACCATTTTA
42861588 CCCCTAAAAC
Statistics
Matches: 96, Mismatches: 29, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
58 20 0.21
59 64 0.67
60 12 0.12
ACGTcount: A:0.27, C:0.29, G:0.05, T:0.39
Consensus pattern (59 bp):
TTACCATTTTAGCCTCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCACCGAAAC
Found at i:42870457 original size:4 final size:4
Alignment explanation
Indices: 42870448--42870475 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
42870438 TTAGATCAAC
42870448 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
42870476 TTCATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:42872404 original size:21 final size:20
Alignment explanation
Indices: 42872356--42872396 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
42872346 CAATTTTTTA
*
42872356 TTTTATTAT-TTGTATATAT
1 TTTTATTTTATTGTATATAT
42872375 TTTTATTTTATTGTA-ATAT
1 TTTTATTTTATTGTATATAT
42872394 TTT
1 TTT
42872397 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTATTTTATTGTATATAT
Found at i:42872408 original size:29 final size:29
Alignment explanation
Indices: 42872351--42872405 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
42872341 GAGCCCAATT
* *
42872351 TTTTATTTTATTATTTGTATATATTTTTA
1 TTTTATTGTAATATTTGTATATATTTTTA
42872380 TTTTATTGTAATATTT-TATA-ATTTTT
1 TTTTATTGTAATATTTGTATATATTTTT
42872406 TTAAAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 4 0.17
29 14 0.58
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (29 bp):
TTTTATTGTAATATTTGTATATATTTTTA
Found at i:42875330 original size:23 final size:24
Alignment explanation
Indices: 42875292--42875337 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
42875282 TATTTGATCA
* *
42875292 ATAATTTTTTAGAAGAATAAAATT
1 ATAAATTTTTAGAAGAACAAAATT
42875316 ATAAATTTTTA-AAGAACAAAAT
1 ATAAATTTTTAGAAGAACAAAAT
42875338 ACAATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (24 bp):
ATAAATTTTTAGAAGAACAAAATT
Found at i:42876907 original size:16 final size:16
Alignment explanation
Indices: 42876862--42876933 Score: 83
Period size: 16 Copynumber: 4.5 Consensus size: 16
42876852 TGTTTGGTTC
*
42876862 GCTGTAATGTAATAGA
1 GCTGTAATGGAATAGA
* * * *
42876878 GATGCAACGAAATAGA
1 GCTGTAATGGAATAGA
42876894 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
42876910 GCTGTAATGGAATA-A
1 GCTGTAATGGAATAGA
42876925 GGCTGTAAT
1 -GCTGTAAT
42876934 CAATAATTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
15 1 0.02
16 46 0.98
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:42877123 original size:58 final size:59
Alignment explanation
Indices: 42877061--42877211 Score: 209
Period size: 58 Copynumber: 2.6 Consensus size: 59
42877051 ATTTAATAAG
* *
42877061 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTTTTAACATA
* * *
42877119 ATTATTATTAAATACAATTTAAT-AAAATAATATATAATTTAATAACATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTTTTAACATA
*
42877177 ATTATTATTAAAATATGAA-TTAATAAAAATTATAA
1 ATTATTATT-AAATAT-AATTTAATAAAAATAATAA
42877212 TATATAAAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
57 21 0.26
58 40 0.49
59 10 0.12
60 10 0.12
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTTTTAACATA
Found at i:42881144 original size:12 final size:12
Alignment explanation
Indices: 42881106--42881146 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
42881096 CAGATCTTTT
42881106 TTAAATAAAAAC
1 TTAAATAAAAAC
42881118 TTAATAGTCAAAAAC
1 TTAA-A-T-AAAAAC
42881133 TTAAATAAAAAC
1 TTAAATAAAAAC
42881145 TT
1 TT
42881147 TTGAATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.46
13 2 0.08
14 2 0.08
15 10 0.38
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (12 bp):
TTAAATAAAAAC
Found at i:42881605 original size:28 final size:30
Alignment explanation
Indices: 42881555--42881619 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
42881545 GTTTTTCAAT
*
42881555 TATATAATATGTTATATTATAAAAATT-AAA
1 TATATAATA-GTTATAGTATAAAAATTGAAA
* *
42881585 TATATAATA-TTATAGTGTAAATATTGAAA
1 TATATAATAGTTATAGTATAAAAATTGAAA
*
42881614 AATATA
1 TATATA
42881620 CTAATTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 13 0.43
29 8 0.27
30 9 0.30
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (30 bp):
TATATAATAGTTATAGTATAAAAATTGAAA
Found at i:42882457 original size:17 final size:18
Alignment explanation
Indices: 42882443--42882483 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
42882433 TAATATAACT
42882443 TATTTAATAAAATAAATA
1 TATTTAATAAAATAAATA
* *
42882461 TTTTTAATAAAGTAAATTA
1 TATTTAATAAAATAAA-TA
42882480 TATT
1 TATT
42882484 ATTTGAAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TATTTAATAAAATAAATA
Found at i:42882934 original size:23 final size:23
Alignment explanation
Indices: 42882889--42882934 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
42882879 TGGGACAAAG
* **
42882889 AAAAACTCAAGTATCAATTTGAA
1 AAAAACTCAAGTACCAAACTGAA
*
42882912 AAAAACTCATGTACCAAACTGAA
1 AAAAACTCAAGTACCAAACTGAA
42882935 CATCAAAGCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.22
Consensus pattern (23 bp):
AAAAACTCAAGTACCAAACTGAA
Found at i:42890260 original size:20 final size:21
Alignment explanation
Indices: 42890237--42890275 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42890227 TAAAAAATTG
*
42890237 ATTGATT-CTCATTTGAATCC
1 ATTGATTCCCCATTTGAATCC
*
42890257 ATTGTTTCCCCATTTGAAT
1 ATTGATTCCCCATTTGAAT
42890276 TTTTAGTCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (21 bp):
ATTGATTCCCCATTTGAATCC
Found at i:42893192 original size:18 final size:18
Alignment explanation
Indices: 42893171--42893208 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
42893161 TGAATTTTCG
*
42893171 AATTTGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
42893189 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
42893207 AA
1 AA
42893209 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:42895385 original size:30 final size:30
Alignment explanation
Indices: 42895351--42895412 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
42895341 ACATAAGTTA
42895351 GTGTAGTGTTTATTTTCCCAACAATTTATT
1 GTGTAGTGTTTATTTTCCCAACAATTTATT
42895381 GTGTAGTGTTTATTTTCCCAACAATTTATT
1 GTGTAGTGTTTATTTTCCCAACAATTTATT
42895411 GT
1 GT
42895413 TGTTCTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.50
Consensus pattern (30 bp):
GTGTAGTGTTTATTTTCCCAACAATTTATT
Found at i:42895691 original size:24 final size:23
Alignment explanation
Indices: 42895630--42895691 Score: 54
Period size: 24 Copynumber: 2.6 Consensus size: 23
42895620 ATTCCTTGGA
*
42895630 TTAAATTATTAAATTAATATTAAT
1 TTAAATTA-TAAAATAATATTAAT
* * *
42895654 TAAAATTCTTAAATAA-ATTAAAAT
1 TTAAATTATAAAATAATATT--AAT
42895678 TTAAATTATAAAAT
1 TTAAATTATAAAAT
42895692 TAAAGCGGTA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
22 3 0.10
23 6 0.21
24 20 0.69
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAAATTATAAAATAATATTAAT
Found at i:42896717 original size:6 final size:6
Alignment explanation
Indices: 42896696--42896785 Score: 71
Period size: 6 Copynumber: 15.0 Consensus size: 6
42896686 TTAAATTGAT
*
42896696 TTTAAA TTT-TA TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
* * * *
42896744 TTTAAA TTT-AC CTTAAG TTTAAA TTTAAA TTAAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
42896786 ACGAATTTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
4 2 0.03
5 9 0.13
6 45 0.67
7 5 0.07
8 6 0.09
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:42896776 original size:11 final size:11
Alignment explanation
Indices: 42896686--42896781 Score: 52
Period size: 11 Copynumber: 8.7 Consensus size: 11
42896676 AATTGAGAAG
* *
42896686 TTAAATTGATT
1 TTAAATTAAAT
**
42896697 TTAAATTTTAT
1 TTAAATTAAAT
42896708 TTAAATTTAAAT
1 TTAAA-TTAAAT
**
42896720 TTATCTTAAAT
1 TTAAATTAAAT
*
42896731 TTAAATTTAA-
1 TTAAATTAAAT
*
42896741 TT-ATTTAAAT
1 TTAAATTAAAT
** *
42896751 TTACCTTAAGT
1 TTAAATTAAAT
42896762 TTAAATTTAAAT
1 TTAAA-TTAAAT
*
42896774 TAAAATTA
1 TTAAATTA
42896782 TAAAACGAAT
Statistics
Matches: 62, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
9 5 0.08
10 4 0.06
11 37 0.60
12 16 0.26
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:42896776 original size:17 final size:17
Alignment explanation
Indices: 42896686--42896777 Score: 82
Period size: 17 Copynumber: 5.6 Consensus size: 17
42896676 AATTGAGAAG
* *
42896686 TTAAATTGATTTTAAAT
1 TTAAATTAAATTTAAAT
* *
42896703 TTTATTTAAATTTAAAT
1 TTAAATTAAATTTAAAT
**
42896720 TTATCTTAAATTTAAAT
1 TTAAATTAAATTTAAAT
42896737 TT-AATT--ATTTAAAT
1 TTAAATTAAATTTAAAT
** *
42896751 TTACCTTAAGTTTAAAT
1 TTAAATTAAATTTAAAT
42896768 TTAAATTAAA
1 TTAAATTAAA
42896778 ATTATAAAAC
Statistics
Matches: 57, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
14 10 0.18
15 2 0.04
16 2 0.04
17 43 0.75
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.52
Consensus pattern (17 bp):
TTAAATTAAATTTAAAT
Found at i:42898548 original size:161 final size:162
Alignment explanation
Indices: 42898367--42898704 Score: 516
Period size: 162 Copynumber: 2.1 Consensus size: 162
42898357 AGTTTTCAAT
* ***
42898367 TTAATCCTTTGACTGTTTGACTGCACTAGAGGCTGCCACGTGTTTTTTTTTG-CTTATTTATGCA
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGCCTTATTTATGCA
* ** * *
42898431 TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCTTAGATCAACTTTTATTTAATTACAA
66 CTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTCTTATTTAATTACAA
* *
42898496 AATTGGCCCAAGAATTTTTCAAGGTTTATAAA
131 AATTGGCCCAAGAATTTTTCAAGATTTACAAA
* *
42898528 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGCCTTATTTCTGCA
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGCCTTATTTATGCA
* *
42898593 CTTAGTCCCTGATATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTCTTATTTAATTATAA
66 CTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTCTTATTTAATTACAA
*
42898658 AATTGGCCCAAGAATTTTTCAAGATTTACAAT
131 AATTGGCCCAAGAATTTTTCAAGATTTACAAA
*
42898690 TTAATCCCTTGACTG
1 TTAATCCTTTGACTG
42898705 CTGGATGCCT
Statistics
Matches: 158, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
161 47 0.30
162 111 0.70
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (162 bp):
TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGCCTTATTTATGCA
CTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTCTTATTTAATTACAA
AATTGGCCCAAGAATTTTTCAAGATTTACAAA
Found at i:42898839 original size:29 final size:28
Alignment explanation
Indices: 42898807--42898876 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 28
42898797 AAATTTCAGG
42898807 AAATTATATTTTGA-CCTCGAAAC-TTCCAA
1 AAATTATATTTT-ACCCTC-AAACTTTCC-A
*
42898836 AAATTACCATTTTACCCTCAAACTTTCCA
1 AAATTA-TATTTTACCCTCAAACTTTCCA
*
42898865 AAATTCTATTTT
1 AAATTATATTTT
42898877 TAATCTCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
28 5 0.14
29 17 0.49
30 13 0.37
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.39
Consensus pattern (28 bp):
AAATTATATTTTACCCTCAAACTTTCCA
Found at i:42898877 original size:29 final size:29
Alignment explanation
Indices: 42898830--42899199 Score: 197
Period size: 29 Copynumber: 12.6 Consensus size: 29
42898820 ACCTCGAAAC
42898830 TTCCAAAAATTACCA-TTTTACCCTCAAACT
1 TTCCAAAAATT-CCATTTTTACCCTC-AACT
* ** *
42898860 TTCC-AAAATTCTATTTTTAATCTCGA-T
1 TTCCAAAAATTCCATTTTTACCCTCAACT
42898887 TTCACCAAAAATTACCA-TTTTATCCC-CAAACT
1 TT--CCAAAAATT-CCATTTTTA-CCCTC-AACT
*
42898919 TTCC-AAAATTCCATTTTTAACCC-CGA-T
1 TTCCAAAAATTCCATTTTT-ACCCTCAACT
*
42898946 TTCACCAAAAATTACCA-TTTTACCCTAAACT
1 TT--CCAAAAATT-CCATTTTTACCCTCAACT
* * *
42898977 TTCC-AAAATTCCATTTTAACCC-CGATT
1 TTCCAAAAATTCCATTTTTACCCTCAACT
*
42899004 TTACCAAAAATTACCA-TTTTACCCTTGAACT
1 TT-CCAAAAATT-CCATTTTTACCC-TCAACT
* *
42899035 TTCC-AAAATTCCATTTTTAACCTCGA-T
1 TTCCAAAAATTCCATTTTTACCCTCAACT
* *
42899062 TTCACCGAAAATTACCA-TTTTACCCCCGAACT
1 TT--CCAAAAATT-CCATTTTTACCCTC-AACT
*
42899094 TTCC-AAAATTCCATTTTTAACCC-CGA-T
1 TTCCAAAAATTCCATTTTT-ACCCTCAACT
*
42899121 TTCACCAAAAATTACCA-TTTTACCCCCAAACT
1 TT--CCAAAAATT-CCATTTTTACCCTC-AACT
* *
42899153 TTCC-AAAATTCCATTTTTAACC-CAAAT
1 TTCCAAAAATTCCATTTTTACCCTCAACT
*
42899180 TTCACCAAAATTACCATTTT
1 TTC-CAAAAATT-CCATTTT
42899200 GCCCCTGGGT
Statistics
Matches: 269, Mismatches: 29, Indels: 84
0.70 0.08 0.22
Matches are distributed among these distances:
27 25 0.09
28 36 0.13
29 102 0.38
30 75 0.28
31 22 0.08
32 9 0.03
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTACCCTCAACT
Found at i:42898898 original size:59 final size:59
Alignment explanation
Indices: 42898832--42899199 Score: 582
Period size: 59 Copynumber: 6.3 Consensus size: 59
42898822 CTCGAAACTT
* * *
42898832 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCTATTTTTAATCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
42898891 CCAAAAATTACCATTTTATCCC-CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTA-CCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
42898950 CCAAAAATTACCATTTTACCCT-AAACTTTCCAAAATTCCA-TTTTAACCCCGATTTTA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
** *
42899007 CCAAAAATTACCATTTTACCCTTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
42899066 CCGAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* **
42899125 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCAAATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
42899184 CC-AAAATTACCATTTT
1 CCAAAAATTACCATTTT
42899200 GCCCCTGGGT
Statistics
Matches: 290, Mismatches: 15, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
57 38 0.13
58 52 0.18
59 197 0.68
60 3 0.01
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:42899067 original size:175 final size:177
Alignment explanation
Indices: 42898832--42899199 Score: 616
Period size: 175 Copynumber: 2.1 Consensus size: 177
42898822 CTCGAAACTT
* *
42898832 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCTATTTTTAATCTCGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAA
*
42898897 ATTACCATTTTATCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACC
66 ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACC
* ** *
42898962 ATTTTA-CCCTAAACTTTCCAAAATTCCA-TTTTAACCCCGATTTTA
131 ATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCAAATTTCA
** *
42899007 CCAAAAATTACCATTTTACCCTTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCGAAA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAA
*
42899072 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACC
66 ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACC
42899137 ATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCAAATTTCA
131 ATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCAAATTTCA
42899184 CC-AAAATTACCATTTT
1 CCAAAAATTACCATTTT
42899200 GCCCCTGGGT
Statistics
Matches: 180, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
175 129 0.72
176 35 0.19
177 16 0.09
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (177 bp):
CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAA
ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACC
ATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCAAATTTCA
Found at i:42899217 original size:175 final size:175
Alignment explanation
Indices: 42898832--42899241 Score: 592
Period size: 175 Copynumber: 2.3 Consensus size: 175
42898822 CTCGAAACTT
* * * *
42898832 CCAAAAATTACCATTTTA-CCCTCAAACTTTCCAAAATTCTATTTTTAATCTCGATTTCACCAAA
1 CCAAAAATTACCATTTTACCCCT-GAACTATCCAAAATTCCATTTTTAACCTCGATTTCACCAAA
*
42898896 AATTACCATTTTATCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTAC
65 AATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTAC
* ** *
42898961 CATTTTACCCTAAACTTTCCAAAATTCCATTTTAACCCCGATTTTA
130 CATTTTACCCCAAACTTTCCAAAATTCCATTTTAACCCAAATTTCA
* * *
42899007 CCAAAAATTACCATTTTACCCTTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCGAAA
1 CCAAAAATTACCATTTTACCCCTGAACTATCCAAAATTCCATTTTTAACCTCGATTTCACCAAAA
*
42899072 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACC
66 ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACC
42899137 ATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCAAATTTCA
131 ATTTTA-CCCCAAACTTTCCAAAATTCCA-TTTTAACCCAAATTTCA
* ** * * *
42899184 CC-AAAATTACCATTTTGCCCCTG-GGTATCCAAAAGTCCCATTTTTCACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTATCCAAAA-TTCCATTTTTAACCTCGATTTCA
42899242 TCGTTTCTTA
Statistics
Matches: 212, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
175 133 0.63
176 63 0.30
177 16 0.08
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (175 bp):
CCAAAAATTACCATTTTACCCCTGAACTATCCAAAATTCCATTTTTAACCTCGATTTCACCAAAA
ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACC
ATTTTACCCCAAACTTTCCAAAATTCCATTTTAACCCAAATTTCA
Found at i:42899225 original size:58 final size:58
Alignment explanation
Indices: 42898832--42899241 Score: 529
Period size: 59 Copynumber: 7.0 Consensus size: 58
42898822 CTCGAAACTT
** * * *
42898832 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCTATTTTTAATCTCGATTTCA
1 CCAAAAATTACCATTTTACCC-CTGACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
**
42898891 CCAAAAATTACCATTTTATCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTA-CCCCTGACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
42898950 CCAAAAATTACCATTTTA-CCCTAAACTTTCCAAAATTCCA-TTTTAACCCCGATTTTA
1 CCAAAAATTACCATTTTACCCCT-GACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
42899007 CCAAAAATTACCATTTTACCCTTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTG-ACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
42899066 CCGAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTG-ACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
** **
42899125 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCAAATTTCA
1 CCAAAAATTACCATTTTA-CCCCTGACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* ** * * *
42899184 CC-AAAATTACCATTTTGCCCCTGGGTATCCAAAAGTCCCATTTTTCACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGACTTTCCAAAA-TTCCATTTTTAACCCCGATTTCA
42899242 TCGTTTCTTA
Statistics
Matches: 316, Mismatches: 28, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
57 49 0.16
58 69 0.22
59 191 0.60
60 7 0.02
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCTGACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:42911408 original size:38 final size:37
Alignment explanation
Indices: 42911366--42912344 Score: 235
Period size: 38 Copynumber: 26.2 Consensus size: 37
42911356 TATCCCCTTC
42911366 AAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTG
1 AAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTG
* * * **
42911404 AAATTGAAGTA-AGAGCA-AGATCATG-CCATATCCTCTTG
1 AAATTGAAGTAGAGTGGATA-A-CAAGTCTTTAT-CTC-TG
*
42911442 AAATTGAAGTAGAGTGG--AACACGTCTTTATCTCTG
1 AAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTG
* * *** * *
42911477 AAATTGAAGTAG-GAGCA-AGATCTTTTCCTGT-CCTCTTG
1 AAATTGAAGTAGAGTGGATA-A-CAAGT-CTTTATCTC-TG
*
42911515 AAATTGAAGTAGAGTGG--AACACGTCTTTATCTCTG
1 AAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTG
* *** * *
42911550 AAATTGAAGTAGGAGCGAGAT--CTTTTC-CTATCCGCTTG
1 AAATTGAAGTA-GAGTG-GATAACAAGTCTTTAT-CTC-TG
* *
42911588 AAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTG
1 AAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTG
* * ****
42911625 AAATTGAAGTA-AG-AG-CAAC--GTCACCCTCT-TG
1 AAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTG
* *
42911656 AAATTGAAGTAGAGTTGGATGACACGTCTTTATCTCTG
1 AAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTG
* * * **
42911694 AAATTGAAGTA-AG-AG-CAAC--GTCATCCTCT-TG
1 AAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTG
*
42911725 AAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTG
1 AAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTG
* * *
42911762 AAATTGAAGTA-AGAGCA-AGATAA-T-TTCCTATCCTCTTG
1 AAATTGAAGTAGAGTGGATA-ACAAGTCTT--TAT-CTC-TG
* **
42911800 AAATTGAAGTAAAGCTGGATATTAAGTCTTTATCTCTG
1 AAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTG
42911838 AAATTGAAGTA-A---G--AACAAGATCATTTCCTATCCTCTTG
1 AAATTGAAGTAGAGTGGATAACAAG-TC--TT--TAT-CTC-TG
*
42911876 AAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTTTG
1 AAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTC--TG
* * * * *
42911916 AAATTGAA--AGA-TGAAGCACCAACATCATTTTCGTCCATCTG
1 AAATTGAAGTAGAGTGGA-TAACAA-GTC--TTT-AT-C-TCTG
42911957 AAATTGAAGTA-A---G--AACAAGATCATTTCCTATCCTCTTG
1 AAATTGAAGTAGAGTGGATAACAAG-TC--TT--TAT-CTC-TG
* * ***
42911995 AAATTGAAGTA-AGGCTGGGTATCAAGTCGCCATCTCTG
1 AAATTGAAGTAGA-G-TGGATAACAAGTCTTTATCTCTG
* ** *
42912033 AAATTGAAGTAAGAGCAAGG-T--CATTTC-CTATCCTCTTG
1 AAATTGAAGT-AGAG--TGGATAACAAGTCTTTAT-CTC-TG
42912071 AAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTG
1 AAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTG
* * *
42912109 AAATTGAAGTA-AG-AG-CAACATCGT-TTCCTATCCTCTTG
1 AAATTGAAGTAGAGTGGATAACA-AGTCTT--TAT-CTC-TG
42912147 AAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTG
1 AAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTG
* * ** *
42912185 AAATTGAAGTA-AGAGCA-AAGTCATTTC-CTATCCTCTTG
1 AAATTGAAGTAGAGTGGATAA--CAAGTCTTTAT-CTC-TG
* * * *
42912223 AAATGGAAGTAGAGTTGGACAACAAGTCGTCATCTCTG
1 AAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTG
* * * *
42912261 AAATTGAAGTA-AG-AG-CAAC--GTCATTTCCTACCCACTTG
1 AAATTGAAGTAGAGTGGATAACAAGTC--TT--TA-TCTC-TG
*
42912299 AAATTGAAGTAGAGTTGGATAACAAGTATTTATCTCTG
1 AAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTG
42912337 AAATTGAA
1 AAATTGAA
42912345 TAAGAGCAAG
Statistics
Matches: 700, Mismatches: 122, Indels: 238
0.66 0.12 0.22
Matches are distributed among these distances:
31 30 0.04
32 23 0.03
33 2 0.00
34 26 0.04
35 44 0.06
36 67 0.10
37 116 0.17
38 244 0.35
39 48 0.07
40 42 0.06
41 19 0.03
42 17 0.02
43 5 0.01
44 6 0.01
45 11 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (37 bp):
AAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTG
Found at i:42911434 original size:76 final size:74
Alignment explanation
Indices: 42911264--42911923 Score: 753
Period size: 76 Copynumber: 8.9 Consensus size: 74
42911254 ATCAGACCGC
* * * * *
42911264 AGCAAGATTATTGCCTTTCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTC-TTATCACTTTG
1 AGCAAGATCATT-CCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTAT--CTCTG
42911328 AAATTGAAGTAAG
62 AAATTGAAGTAAG
* * * * *
42911341 AGCTAGATCTTTTCATATCCCCTTCAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATC-ATTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAA
42911406 ATTGAAGTAAG
64 ATTGAAGTAAG
* *
42911417 AGCAAGATCATGCCATATCCTCTTGAAATTGAAGTAGAGTGG--AACACGTCTTTATCTCTGAAA
1 AGCAAGATCATTCC-TATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAA
*
42911480 TTGAAGTAGG
65 TTGAAGTAAG
* * *
42911490 AGCAAGATCTTTTCCTGTCCTCTTGAAATTGAAGTAGAGTGG--AACACGTCTTTATCTCTGAAA
1 AGCAAGATC-ATTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAA
*
42911553 TTGAAGTAGG
65 TTGAAGTAAG
* * * * *
42911563 AGCGAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAA
1 AGCAAGATC-ATTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAA
42911628 TTGAAGTAAG
65 TTGAAGTAAG
* *
42911638 AGCAACG-TCA---C---CCTCTTGAAATTGAAGTAGAGTTGGATGACACGTCTTTATCTCTGAA
1 AGCAA-GATCATTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAA
42911696 ATTGAAGTAAG
64 ATTGAAGTAAG
* *
42911707 AGC-A-A-C-GT-C-ATCCTCTTGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAAT
1 AGCAAGATCATTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAAT
42911766 TGAAGTAAG
66 TGAAGTAAG
* * **
42911775 AGCAAGATAATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATTAAGTCTTTATCTCTGAA
1 AGCAAGATCA-TTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAA
42911840 ATTGAAGTAAG
64 ATTGAAGTAAG
* *
42911851 AACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTTTG
1 AGCAAGATCA-TTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTC--TG
42911916 AAATTGAA
62 AAATTGAA
42911924 AGATGAAGCA
Statistics
Matches: 516, Mismatches: 44, Indels: 45
0.85 0.07 0.07
Matches are distributed among these distances:
66 1 0.00
67 1 0.00
68 58 0.11
69 59 0.11
70 1 0.00
71 1 0.00
73 135 0.26
74 4 0.01
75 62 0.12
76 138 0.27
77 40 0.08
78 16 0.03
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (74 bp):
AGCAAGATCATTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAAT
TGAAGTAAG
Found at i:42911495 original size:73 final size:73
Alignment explanation
Indices: 42911264--42911923 Score: 681
Period size: 73 Copynumber: 8.9 Consensus size: 73
42911254 ATCAGACCGC
* * * *
42911264 AGCAAGATTATTGCCTTTCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTC-TTATCACTTTG
1 AGCAAGATCATT-CCTATCCTCTTGAAATTGAAGTAGAGCTGGA-A-CAAGTCTTTAT--CTCTG
42911328 AAATTGAAGTAAG
61 AAATTGAAGTAAG
* * * * * *
42911341 AGCTAGATCTTTTCATATCCCCTTCAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATC-ATTCCTATCCTCTTGAAATTGAAGTAGAGCTGG--AACAAGTCTTTATCTCTGAA
42911406 ATTGAAGTAAG
63 ATTGAAGTAAG
* *
42911417 AGCAAGATCATGCCATATCCTCTTGAAATTGAAGTAGAG-TGGAACACGTCTTTATCTCTGAAAT
1 AGCAAGATCATTCC-TATCCTCTTGAAATTGAAGTAGAGCTGGAACAAGTCTTTATCTCTGAAAT
*
42911481 TGAAGTAGG
65 TGAAGTAAG
* * *
42911490 AGCAAGATCTTTTCCTGTCCTCTTGAAATTGAAGTAGAG-TGGAACACGTCTTTATCTCTGAAAT
1 AGCAAGATC-ATTCCTATCCTCTTGAAATTGAAGTAGAGCTGGAACAAGTCTTTATCTCTGAAAT
*
42911554 TGAAGTAGG
65 TGAAGTAAG
* * * * *
42911563 AGCGAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAA
1 AGCAAGATC-ATTCCTATCCTCTTGAAATTGAAGTAGAGCTGG--AACAAGTCTTTATCTCTGAA
42911627 ATTGAAGTAAG
63 ATTGAAGTAAG
* *
42911638 AGCAACG-TCA---C---CCTCTTGAAATTGAAGTAGAGTTGGATGACACGTCTTTATCTCTGAA
1 AGCAA-GATCATTCCTATCCTCTTGAAATTGAAGTAGAGCTGGA--ACAAGTCTTTATCTCTGAA
42911696 ATTGAAGTAAG
63 ATTGAAGTAAG
* *
42911707 AGC-A-A-C-GT-C-ATCCTCTTGAAATTGAAGTAGAG-TGGATAACATGTCTTTATCTCTGAAA
1 AGCAAGATCATTCCTATCCTCTTGAAATTGAAGTAGAGCTGG--AACAAGTCTTTATCTCTGAAA
42911765 TTGAAGTAAG
64 TTGAAGTAAG
* * *
42911775 AGCAAGATAATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATTAAGTCTTTATCTCTGAA
1 AGCAAGATCA-TTCCTATCCTCTTGAAATTGAAGTAGAGCTGGA-A-CAAGTCTTTATCTCTGAA
42911840 ATTGAAGTAAG
63 ATTGAAGTAAG
* *
42911851 AACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTTTG
1 AGCAAGATCA-TTCCTATCCTCTTGAAATTGAAGTAGAGCTGG--AACAAGTCTTTATCTC--TG
42911916 AAATTGAA
61 AAATTGAA
42911924 AGATGAAGCA
Statistics
Matches: 511, Mismatches: 39, Indels: 65
0.83 0.06 0.11
Matches are distributed among these distances:
66 1 0.00
67 2 0.00
68 56 0.11
69 57 0.11
70 2 0.00
71 1 0.00
73 135 0.26
74 5 0.01
75 63 0.12
76 132 0.26
77 38 0.07
78 18 0.04
79 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (73 bp):
AGCAAGATCATTCCTATCCTCTTGAAATTGAAGTAGAGCTGGAACAAGTCTTTATCTCTGAAATT
GAAGTAAG
Found at i:42911658 original size:31 final size:31
Alignment explanation
Indices: 42911616--42911735 Score: 111
Period size: 31 Copynumber: 3.7 Consensus size: 31
42911606 TAACACGTCT
42911616 TCAT-CTC-TGAAATTGAAGTAAGAGCAACG
1 TCATCCTCTTGAAATTGAAGTAAGAGCAACG
*
42911645 TCACCCTCTTGAAATTGAAGTAGAGTTGGATG-ACACG
1 TCATCCTCTTGAAATTGAAGTA-A----GA-GCA-ACG
* **
42911682 TCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAACG
42911714 TCATCCTCTTGAAATTGAAGTA
1 TCATCCTCTTGAAATTGAAGTA
42911736 GAGTGGATAA
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
29 3 0.04
30 3 0.04
31 26 0.36
32 11 0.15
33 3 0.04
36 3 0.04
37 10 0.14
38 13 0.18
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (31 bp):
TCATCCTCTTGAAATTGAAGTAAGAGCAACG
Found at i:42912042 original size:76 final size:76
Alignment explanation
Indices: 42911953--42912356 Score: 582
Period size: 76 Copynumber: 5.3 Consensus size: 76
42911943 TTTTCGTCCA
* * * *
42911953 TCTGAAATTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTA-AGGCTGGGTAT
1 TCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGA-GTTGGATAA
*
42912017 CAAGTCGCCATC
65 CAAGTCGTCATC
*
42912029 TCTGAAATTGAAGTAAGAGCAAGGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC
1 TCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC
* *
42912094 AAGTCTTTATC
66 AAGTCGTCATC
* *
42912105 TCTGAAATTGAAGTAAGAGCAACATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC
1 TCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC
* *
42912170 AAGTCTTTATC
66 AAGTCGTCATC
* *
42912181 TCTGAAATTGAAGTAAGAGCAA-AGTCATTTCCTATCCTCTTGAAATGGAAGTAGAGTTGGACAA
1 TCTGAAATTGAAGTAAGAGCAAGA-TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAA
42912245 CAAGTCGTCATC
65 CAAGTCGTCATC
* *
42912257 TCTGAAATTGAAGTAAGAGCAACG-TCATTTCCTACCCACTTGAAATTGAAGTAGAGTTGGATAA
1 TCTGAAATTGAAGTAAGAGCAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAA
** *
42912321 CAAGTATTTATC
65 CAAGTCGTCATC
42912333 TCTGAAATTGAA-TAAGAGCAAGAT
1 TCTGAAATTGAAGTAAGAGCAAGAT
42912357 GAAGCCTCGA
Statistics
Matches: 300, Mismatches: 23, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
74 1 0.00
75 11 0.04
76 287 0.96
77 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (76 bp):
TCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC
AAGTCGTCATC
Found at i:42912092 original size:195 final size:193
Alignment explanation
Indices: 42911758--42912116 Score: 592
Period size: 195 Copynumber: 1.8 Consensus size: 193
42911748 TGTCTTTATC
* *
42911758 TCTGAAATTGAAGTAAGAGCAAGATAATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATT
1 TCTGAAATTGAAGTAAGAACAAGATAATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATC
***
42911823 AAGTCTTTATCTCTGAAATTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAA
66 AAGTCGCCATCTCTGAAATTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAA
42911888 AGCTGGATAACAAGTCTTTATCTCTTTGAAATTGAAAGATGAAGCACCAACATCATTTTCGTCCA
131 AGCTGGATAACAAGTCTTTATCTC--TGAAATTGAAAGATGAAGCACCAACATCATTTTCGTCCA
* * *
42911953 TCTGAAATTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAGGCTGGGTATC
1 TCTGAAATTGAAGTAAGAACAAGATAATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATC
* * *
42912018 AAGTCGCCATCTCTGAAATTGAAGTAAGAGCAAGGTCATTTCCTATCCTCTTGAAATTGAAGTAG
66 AAGTCGCCATCTCTGAAATTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAA
*
42912083 AGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
131 AGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
42912117 GTAAGAGCAA
Statistics
Matches: 152, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
193 10 0.07
195 142 0.93
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (193 bp):
TCTGAAATTGAAGTAAGAACAAGATAATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATC
AAGTCGCCATCTCTGAAATTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAA
AGCTGGATAACAAGTCTTTATCTCTGAAATTGAAAGATGAAGCACCAACATCATTTTCGTCCA
Found at i:42912665 original size:6 final size:6
Alignment explanation
Indices: 42912644--42912733 Score: 71
Period size: 6 Copynumber: 15.0 Consensus size: 6
42912634 TTAAATTGAT
*
42912644 TTTAAA TTT-TA TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
* * * *
42912692 TTTAAA TTT-AC CTTAAG TTTAAA TTTAAA TTAAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
42912734 ACGAATTTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
4 2 0.03
5 9 0.13
6 45 0.67
7 5 0.07
8 6 0.09
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:42912724 original size:11 final size:11
Alignment explanation
Indices: 42912634--42912729 Score: 52
Period size: 11 Copynumber: 8.7 Consensus size: 11
42912624 AATTGAGAAG
* *
42912634 TTAAATTGATT
1 TTAAATTAAAT
**
42912645 TTAAATTTTAT
1 TTAAATTAAAT
42912656 TTAAATTTAAAT
1 TTAAA-TTAAAT
**
42912668 TTATCTTAAAT
1 TTAAATTAAAT
*
42912679 TTAAATTTAA-
1 TTAAATTAAAT
*
42912689 TT-ATTTAAAT
1 TTAAATTAAAT
** *
42912699 TTACCTTAAGT
1 TTAAATTAAAT
42912710 TTAAATTTAAAT
1 TTAAA-TTAAAT
*
42912722 TAAAATTA
1 TTAAATTA
42912730 TAAAACGAAT
Statistics
Matches: 62, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
9 5 0.08
10 4 0.06
11 37 0.60
12 16 0.26
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:42912724 original size:17 final size:17
Alignment explanation
Indices: 42912634--42912725 Score: 82
Period size: 17 Copynumber: 5.6 Consensus size: 17
42912624 AATTGAGAAG
* *
42912634 TTAAATTGATTTTAAAT
1 TTAAATTAAATTTAAAT
* *
42912651 TTTATTTAAATTTAAAT
1 TTAAATTAAATTTAAAT
**
42912668 TTATCTTAAATTTAAAT
1 TTAAATTAAATTTAAAT
42912685 TT-AATT--ATTTAAAT
1 TTAAATTAAATTTAAAT
** *
42912699 TTACCTTAAGTTTAAAT
1 TTAAATTAAATTTAAAT
42912716 TTAAATTAAA
1 TTAAATTAAA
42912726 ATTATAAAAC
Statistics
Matches: 57, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
14 10 0.18
15 2 0.04
16 2 0.04
17 43 0.75
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.52
Consensus pattern (17 bp):
TTAAATTAAATTTAAAT
Found at i:42914500 original size:162 final size:162
Alignment explanation
Indices: 42914318--42914656 Score: 525
Period size: 162 Copynumber: 2.1 Consensus size: 162
42914308 AGTTTTCAAT
* ** **
42914318 TTAATCCTTTGACTGTTTGACTGCACTAGAGGCTGCCACGTGTCTTTTTTTTGCTTATTTATGCA
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTACCTTATTTATGCA
* ** * *
42914383 TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCTTAGATCAACTTTTATTTAATTACAA
66 CTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTCTTATTTAATTACAA
* *
42914448 AATTGGCCCAAGAATTTTTCAAGGTTTATAAA
131 AATTGGCCCAAGAATTTTTCAAGATTTACAAA
*
42914480 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTACCTTATTTATGCA
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTACCTTATTTATGCA
* *
42914545 CTTAGTCCCTGATATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTCTTATTTAATTATAA
66 CTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTCTTATTTAATTACAA
*
42914610 AATTGGCCCAAGAATTTTTCAAGATTTACAAT
131 AATTGGCCCAAGAATTTTTCAAGATTTACAAA
*
42914642 TTAATCCCTTGACTG
1 TTAATCCTTTGACTG
42914657 CTGGATGCCT
Statistics
Matches: 159, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
162 159 1.00
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.43
Consensus pattern (162 bp):
TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTACCTTATTTATGCA
CTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTCTTATTTAATTACAA
AATTGGCCCAAGAATTTTTCAAGATTTACAAA
Found at i:42914791 original size:29 final size:28
Alignment explanation
Indices: 42914727--42914887 Score: 103
Period size: 29 Copynumber: 5.5 Consensus size: 28
42914717 CCAAACAGTC
* * *
42914727 CAAAAATTGCATTTTGACCCTAAAATTT
1 CAAAAATTACATTTTGACCCCAAACTTT
* * *
42914755 CAGGAAATTATATTTTGACCTCGAAACTTT
1 CA-AAAATTACATTTTGACC-CCAAACTTT
42914785 CAAAAATTACCATTTT-ACCCCCAAACTTT
1 CAAAAATTA-CATTTTGA-CCCCAAACTTT
* * * * *
42914814 CCAAAATTCCATTTTTAACCCAGA-TTT
1 CAAAAATTACATTTTGACCCCAAACTTT
42914841 CACCAAAAATTACCATTTT-ACCCCTAAACTTT
1 ---CAAAAATTA-CATTTTGACCCC-AAACTTT
* *
42914873 CCAAAATTCCATTTT
1 CAAAAATTACATTTT
42914888 TAACCTCGAT
Statistics
Matches: 104, Mismatches: 18, Indels: 22
0.72 0.12 0.15
Matches are distributed among these distances:
27 3 0.03
28 19 0.18
29 44 0.42
30 27 0.26
31 8 0.08
32 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (28 bp):
CAAAAATTACATTTTGACCCCAAACTTT
Found at i:42914850 original size:59 final size:58
Alignment explanation
Indices: 42914785--42915099 Score: 506
Period size: 59 Copynumber: 5.4 Consensus size: 58
42914775 TCGAAACTTT
42914785 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCAGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCC-GATTTCAC
*
42914844 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACC-CGATTTCAC
42914903 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACC-CGATTTCAC
* *
42914962 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCTATTTTTAACCCTGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCC-GATTTCAC
* * * *
42915021 CGAAAATTACCATTTTACCCTCAAACTTTCTAAAATTCCATTTTTAACCCCGATTTTAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA-CCCGATTTCAC
*
42915080 C-AAAATTACCATTTTGCCCC
1 CAAAAATTACCATTTTACCCC
42915100 TGGGTATCCA
Statistics
Matches: 241, Mismatches: 12, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
58 18 0.07
59 219 0.91
60 4 0.02
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.35
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCGATTTCAC
Found at i:42917316 original size:28 final size:28
Alignment explanation
Indices: 42917276--42917467 Score: 168
Period size: 28 Copynumber: 7.1 Consensus size: 28
42917266 TAAACGTGTG
* *
42917276 CAAGCTAACGAGCGTAAATGCATATGTA
1 CAAGCTGACGAGCGTAAACGCATATGTA
42917304 CAAGCTGACGAGCGTAAACGCATATGTA
1 CAAGCTGACGAGCGTAAACGCATATGTA
* * *
42917332 TAAGCTGACAAGCGTAAACG----TGTG
1 CAAGCTGACGAGCGTAAACGCATATGTA
* * *
42917356 CAAGTTGGCGAGCGTAAATGCATATGTA
1 CAAGCTGACGAGCGTAAACGCATATGTA
*
42917384 CAAGCT-AGCGAGTGTAAACGCATATGTA
1 CAAGCTGA-CGAGCGTAAACGCATATGTA
* * ** * *
42917412 TAAGTTGGTGAGCGT-AA---ATGTGTG
1 CAAGCTGACGAGCGTAAACGCATATGTA
*
42917436 CAAGCTGACGAGCGTAAACGCATATGTG
1 CAAGCTGACGAGCGTAAACGCATATGTA
42917464 CAAG
1 CAAG
42917468 TTGGCGCAGG
Statistics
Matches: 127, Mismatches: 27, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
24 34 0.27
25 2 0.02
27 2 0.02
28 89 0.70
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.22
Consensus pattern (28 bp):
CAAGCTGACGAGCGTAAACGCATATGTA
Found at i:42917401 original size:80 final size:80
Alignment explanation
Indices: 42917262--42917467 Score: 297
Period size: 80 Copynumber: 2.6 Consensus size: 80
42917252 TTAGCTAACG
*
42917262 AGCGTAAACGTGTGCAAGCTAACGAGCGTAAATGCATATGTACAAGCTGACGAGCGTAAACGCAT
1 AGCGTAAACGTGTGCAAGCTGACGAGCGTAAATGCATATGTACAAGCTGACGAGCGTAAACGCAT
42917327 ATGTATAAGCTGACA
66 ATGTATAAGCTGACA
* * *
42917342 AGCGTAAACGTGTGCAAGTTGGCGAGCGTAAATGCATATGTACAAGCT-AGCGAGTGTAAACGCA
1 AGCGTAAACGTGTGCAAGCTGACGAGCGTAAATGCATATGTACAAGCTGA-CGAGCGTAAACGCA
* ***
42917406 TATGTATAAGTTGGTG
65 TATGTATAAGCTGACA
* * *
42917422 AGCGTAAATGTGTGCAAGCTGACGAGCGTAAACGCATATGTGCAAG
1 AGCGTAAACGTGTGCAAGCTGACGAGCGTAAATGCATATGTACAAG
42917468 TTGGCGCAGG
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
79 1 0.01
80 111 0.99
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (80 bp):
AGCGTAAACGTGTGCAAGCTGACGAGCGTAAATGCATATGTACAAGCTGACGAGCGTAAACGCAT
ATGTATAAGCTGACA
Found at i:42917440 original size:52 final size:53
Alignment explanation
Indices: 42917260--42917473 Score: 181
Period size: 52 Copynumber: 4.0 Consensus size: 53
42917250 AATTAGCTAA
* * * * * *
42917260 CGAGCGTAAACG-TGTGCAAGCTAACGAGCGTAAATGCATATGTACAAGCTGA
1 CGAGCGTAAATGATGTACAAGCTGACGAGCGTAAACGCATATGTACAAGTTGG
* * * *
42917312 CGAGCGTAAACGCATATGTATAAGCTGACAAGCGTAAACG----TGTGCAAGTTGG
1 CGAGCGTAAATG---ATGTACAAGCTGACGAGCGTAAACGCATATGTACAAGTTGG
* *
42917364 CGAGCGTAAATGCATATGTACAAGCT-AGCGAGTGTAAACGCATATGTATAAGTTGG
1 CGAGCGTAAATG---ATGTACAAGCTGA-CGAGCGTAAACGCATATGTACAAGTTGG
* * *
42917420 TGAGCGTAAATG-TGTGCAAGCTGACGAGCGTAAACGCATATGTGCAAGTTGG
1 CGAGCGTAAATGATGTACAAGCTGACGAGCGTAAACGCATATGTACAAGTTGG
42917472 CG
1 CG
42917474 CAGGGGCGAA
Statistics
Matches: 132, Mismatches: 20, Indels: 20
0.77 0.12 0.12
Matches are distributed among these distances:
51 1 0.01
52 90 0.68
53 1 0.01
56 40 0.30
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (53 bp):
CGAGCGTAAATGATGTACAAGCTGACGAGCGTAAACGCATATGTACAAGTTGG
Found at i:42923157 original size:13 final size:13
Alignment explanation
Indices: 42923139--42923163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42923129 TATCCCTTGA
42923139 AGAAGTTTCAGGC
1 AGAAGTTTCAGGC
42923152 AGAAGTTTCAGG
1 AGAAGTTTCAGG
42923164 TCGGAGCTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (13 bp):
AGAAGTTTCAGGC
Found at i:42931443 original size:19 final size:20
Alignment explanation
Indices: 42931399--42931443 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
42931389 GGTGTTTTTG
42931399 TTTT-AATTAGGTTTAAGAT
1 TTTTAAATTAGGTTTAAGAT
42931418 TTTTAAATTAGTGTTT-AG-T
1 TTTTAAATTAG-GTTTAAGAT
42931437 TTTTAAA
1 TTTTAAA
42931444 AATTAGGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.50
20 8 0.33
21 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (20 bp):
TTTTAAATTAGGTTTAAGAT
Found at i:42932372 original size:18 final size:18
Alignment explanation
Indices: 42932349--42932383 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
42932339 ACTAGAAAAT
42932349 GGAAACATATAAGGGTTA
1 GGAAACATATAAGGGTTA
42932367 GGAAACATATAAGGGTT
1 GGAAACATATAAGGGTT
42932384 TTGATACGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.29, T:0.23
Consensus pattern (18 bp):
GGAAACATATAAGGGTTA
Found at i:42933057 original size:29 final size:29
Alignment explanation
Indices: 42933011--42933099 Score: 169
Period size: 29 Copynumber: 3.1 Consensus size: 29
42933001 CTATGTTATG
*
42933011 TATATATAGTTTAGAATTAAATAAAGACT
1 TATATATAGTTTAAAATTAAATAAAGACT
42933040 TATATATAGTTTAAAATTAAATAAAGACT
1 TATATATAGTTTAAAATTAAATAAAGACT
42933069 TATATATAGTTTAAAATTAAATAAAGACT
1 TATATATAGTTTAAAATTAAATAAAGACT
42933098 TA
1 TA
42933100 CATGCGCTTC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (29 bp):
TATATATAGTTTAAAATTAAATAAAGACT
Found at i:42934041 original size:18 final size:17
Alignment explanation
Indices: 42934020--42934068 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 17
42934010 TAAATTATAA
42934020 AAATCATATAAAATAATT
1 AAAT-ATATAAAATAATT
42934038 AAATATTATTAAAAATAATT
1 AAATA-TA-T-AAAATAATT
42934058 AAAT-TATAAAA
1 AAATATATAAAA
42934069 ATAAAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.14
17 2 0.07
18 8 0.29
19 1 0.04
20 13 0.46
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATATATAAAATAATT
Found at i:42934069 original size:17 final size:20
Alignment explanation
Indices: 42934029--42934072 Score: 67
Period size: 17 Copynumber: 2.4 Consensus size: 20
42934019 AAAATCATAT
42934029 AAAATAATTAAATATTATTA
1 AAAATAATTAAATATTATTA
42934049 AAAATAATT-AA-ATTA-TA
1 AAAATAATTAAATATTATTA
42934066 AAAATAA
1 AAAATAA
42934073 AATGAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.38
18 4 0.17
19 2 0.08
20 9 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATAATTAAATATTATTA
Found at i:42934069 original size:18 final size:20
Alignment explanation
Indices: 42934029--42934069 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
42934019 AAAATCATAT
*
42934029 AAAATAATTAAATATTATTA
1 AAAATAATTAAATATTATAA
42934049 AAAATAATT-AA-ATTATAA
1 AAAATAATTAAATATTATAA
42934067 AAA
1 AAA
42934070 TAAAATGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATAATTAAATATTATAA
Found at i:42942652 original size:11 final size:11
Alignment explanation
Indices: 42942592--42942653 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 11
42942582 CAACTGTCAA
*
42942592 CGGTCAACGGT
1 CGGTCAACGCT
*
42942603 TGGTCAACGCT
1 CGGTCAACGCT
42942614 -GGATCAACGCT
1 CGG-TCAACGCT
*
42942625 CGGTCAACGAT
1 CGGTCAACGCT
* *
42942636 CAGTCAACGTT
1 CGGTCAACGCT
42942647 CGGTCAA
1 CGGTCAA
42942654 AGGTTTGGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
10 2 0.05
11 39 0.91
12 2 0.05
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.21
Consensus pattern (11 bp):
CGGTCAACGCT
Found at i:42945121 original size:16 final size:14
Alignment explanation
Indices: 42945089--42945122 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
42945079 TTATAAGTTT
42945089 TTAAAATTAAATAA
1 TTAAAATTAAATAA
42945103 TTAAAATATAAATTAA
1 TTAAAAT-TAAA-TAA
42945119 TTAA
1 TTAA
42945123 TAGTTTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 4 0.22
16 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAAATTAAATAA
Done.