Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 38 of 356
Found at i:12521399 original size:13 final size:14
Alignment explanation
Indices: 12521381--12521409 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12521371 GATTAACTTC
12521381 ATAAATATTTT-TA
1 ATAAATATTTTCTA
12521394 ATAAATATTTTCTA
1 ATAAATATTTTCTA
12521408 AT
1 AT
12521410 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:12521670 original size:26 final size:27
Alignment explanation
Indices: 12521628--12521679 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
12521618 ATTATGAGAA
*
12521628 AAATTAAATAAAACAAAAAAATAACTT
1 AAATTAAATAAAACAAAAAAAAAACTT
12521655 AAATTAAA-AAAACAAAAAAAAAACT
1 AAATTAAATAAAACAAAAAAAAAACT
12521680 AAACATATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (27 bp):
AAATTAAATAAAACAAAAAAAAAACTT
Found at i:12524081 original size:23 final size:23
Alignment explanation
Indices: 12524055--12524152 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
12524045 ATAAGTGCCA
12524055 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12524078 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
12524101 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
12524123 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12524146 CACTGAT
1 CACTGAT
12524153 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:12524120 original size:45 final size:45
Alignment explanation
Indices: 12524062--12524150 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
12524052 CCACACTGAT
* *
12524062 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
12524107 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
12524151 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:12524387 original size:75 final size:75
Alignment explanation
Indices: 12524301--12524448 Score: 296
Period size: 75 Copynumber: 2.0 Consensus size: 75
12524291 CTATTCCTAA
12524301 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
1 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
12524366 CAACTTTCAT
66 CAACTTTCAT
12524376 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
1 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
12524441 CAACTTTC
66 CAACTTTC
12524449 CTTCCACATT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (75 bp):
GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
CAACTTTCAT
Found at i:12529638 original size:23 final size:23
Alignment explanation
Indices: 12529612--12529709 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
12529602 ATAAGTGCCA
12529612 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12529635 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
12529658 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
12529680 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12529703 CACTGAT
1 CACTGAT
12529710 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:12529677 original size:45 final size:45
Alignment explanation
Indices: 12529619--12529707 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
12529609 CCACACTGAT
* *
12529619 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
12529664 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
12529708 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:12529944 original size:75 final size:75
Alignment explanation
Indices: 12529858--12530005 Score: 296
Period size: 75 Copynumber: 2.0 Consensus size: 75
12529848 CTATTCCTAA
12529858 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
1 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
12529923 CAACTTTCAT
66 CAACTTTCAT
12529933 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
1 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
12529998 CAACTTTC
66 CAACTTTC
12530006 CTTCCACATT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (75 bp):
GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
CAACTTTCAT
Found at i:12532401 original size:24 final size:25
Alignment explanation
Indices: 12532355--12532403 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
12532345 TTGCCCGGGC
*
12532355 CCCAACAAGCCCAAAACTAAACCTA
1 CCCAACAAGCCCAAAACCAAACCTA
*
12532380 CCCAAC-AGCCCAAAACCCAACCTA
1 CCCAACAAGCCCAAAACCAAACCTA
12532404 TCCTAACCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.45, C:0.45, G:0.04, T:0.06
Consensus pattern (25 bp):
CCCAACAAGCCCAAAACCAAACCTA
Found at i:12533502 original size:3 final size:3
Alignment explanation
Indices: 12533494--12533638 Score: 55
Period size: 3 Copynumber: 47.0 Consensus size: 3
12533484 TAATTTAATA
* * * * *
12533494 TAT TAT TAT TGCT TAT TAT T-T TAC TAT TAT TGT CTAA TA- TAT TAG
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * * * * *
12533539 GAT TAT CAC TAT TAT TAT TAC T-T TAC TAT TAT AAT T-T AAT GTAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
** *
12533583 TAT CGT TAT TATT TATT TATT TATT TATT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TA-T TA-T TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT
12533630 TAT TAT TAT
1 TAT TAT TAT
12533639 CTTAGGACTA
Statistics
Matches: 105, Mismatches: 29, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
2 6 0.06
3 75 0.71
4 24 0.23
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:12533600 original size:4 final size:4
Alignment explanation
Indices: 12533591--12533615 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12533581 ATTATCGTTA
12533591 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
12533616 ATTATTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:12533845 original size:3 final size:3
Alignment explanation
Indices: 12533839--12533890 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
12533829 TTGTTGTGTC
* * *
12533839 ATT ATT ATT GTT ACT GTT ATT ATT CATGT ATAT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -AT-T AT-T ATT ATT ATT ATT ATT
12533887 ATT A
1 ATT A
12533891 CCACATTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
3 32 0.80
4 7 0.17
5 1 0.03
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:12546300 original size:68 final size:68
Alignment explanation
Indices: 12546190--12546398 Score: 337
Period size: 68 Copynumber: 3.1 Consensus size: 68
12546180 GCTGGGAATT
* * * * *
12546190 ACGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTTGAAGCCATAACAGATTTTCTTGAAGTT
1 ACGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTT
12546255 TCA
66 TCA
* *
12546258 ACGGATCTCTTCTCCCTAAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTT
1 ACGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTT
12546323 TCA
66 TCA
*
12546326 GCGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTT
1 ACGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTT
12546391 TCA
66 TCA
*
12546394 GCGGA
1 ACGGA
12546399 GTAGATTGAA
Statistics
Matches: 131, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 131 1.00
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (68 bp):
ACGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTT
TCA
Found at i:12546415 original size:34 final size:34
Alignment explanation
Indices: 12546377--12546443 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
12546367 GCCACAGCAG
* * *
12546377 ATCTCCTTGAAGTTTCAGCGGAGTAGATTGAAGT
1 ATCTCCCTGAAGTTGCAGCGGAGTAGACTGAAGT
*
12546411 ATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAG
1 ATCTCCCTGAAGTTGCAGCGGAGTAGACTGAAG
12546444 ATAGCACATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (34 bp):
ATCTCCCTGAAGTTGCAGCGGAGTAGACTGAAGT
Found at i:12546551 original size:41 final size:41
Alignment explanation
Indices: 12546505--12546607 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 41
12546495 ATCATAGGTT
* * *
12546505 TTATCTCTCTGAAGTTGCAGTAGAACAAATCAAAACAAGTC
1 TTATCTCCCTAAAGTTGCAGTAGAACAAATCAAAACAAATC
* *
12546546 TTATCTCCCTAAAGTTGCAGTAGAGCAGATCAAAACAAATC
1 TTATCTCCCTAAAGTTGCAGTAGAACAAATCAAAACAAATC
* *
12546587 TCATCTCCCTAAAGTGGCAGT
1 TTATCTCCCTAAAGTTGCAGT
12546608 GGAGCAGATT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (41 bp):
TTATCTCCCTAAAGTTGCAGTAGAACAAATCAAAACAAATC
Found at i:12548050 original size:3 final size:3
Alignment explanation
Indices: 12548042--12548091 Score: 55
Period size: 3 Copynumber: 15.3 Consensus size: 3
12548032 TGTATTGTCG
*
12548042 TTA TTA TTA TTTA TTTA TTTA TTTA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA -TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
12548091 T
1 T
12548092 CTTAGTACTA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 29 0.66
4 15 0.34
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12548315 original size:18 final size:18
Alignment explanation
Indices: 12548292--12548362 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 18
12548282 TTGTTGTGTC
*
12548292 ATTATTATTGTTACTGTT
1 ATTATTATTGTTACTATT
12548310 ATTATTCA-TGTATA-TATT
1 ATTATT-ATTGT-TACTATT
* * *
12548328 ATTATTATTATTACCA-C
1 ATTATTATTGTTACTATT
*
12548345 ATTATT-TTATTACTATT
1 ATTATTATTGTTACTATT
12548362 A
1 A
12548363 ACACTCTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
16 8 0.19
17 10 0.24
18 21 0.50
19 3 0.07
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.56
Consensus pattern (18 bp):
ATTATTATTGTTACTATT
Found at i:12550852 original size:40 final size:40
Alignment explanation
Indices: 12550776--12550870 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 40
12550766 CCATCTCCGA
* * *
12550776 CTAACCCAACACACC-ATGTGGGGATAGAATCGACCCA-C
1 CTAACCCTACACACCAATATGGGGATAGAATCAACCCATC
*
12550814 CTAACCCTACACACCAAGTATGGGGATATAATCAACCCATC
1 CTAACCCTACACACCAA-TATGGGGATAGAATCAACCCATC
12550855 C-AACCCTACACACCAA
1 CTAACCCTACACACCAA
12550871 AAGGTACCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 14 0.28
39 1 0.02
40 33 0.66
41 2 0.04
ACGTcount: A:0.37, C:0.36, G:0.13, T:0.15
Consensus pattern (40 bp):
CTAACCCTACACACCAATATGGGGATAGAATCAACCCATC
Found at i:12555841 original size:31 final size:31
Alignment explanation
Indices: 12555800--12555861 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
12555790 GCTGAAACTG
12555800 ATGCCATGTTTCATTTATTTTGTTTAAGCTT
1 ATGCCATGTTTCATTTATTTTGTTTAAGCTT
*
12555831 ATGCCGTGTTTCATTTATTTTGTTTAAGCTT
1 ATGCCATGTTTCATTTATTTTGTTTAAGCTT
12555862 CTATGTACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.55
Consensus pattern (31 bp):
ATGCCATGTTTCATTTATTTTGTTTAAGCTT
Found at i:12571115 original size:19 final size:18
Alignment explanation
Indices: 12571070--12571116 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
12571060 AATTCAAATG
* *
12571070 AAATATTTTAAAATTTTA
1 AAATAATTTAAAATTTAA
12571088 AAATCAATTTAAAATTTAA
1 AAAT-AATTTAAAATTTAA
12571107 ACAATAATTT
1 A-AATAATTT
12571117 GAGAACCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.16
19 18 0.72
20 3 0.12
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAATTTAAAATTTAA
Found at i:12573472 original size:21 final size:21
Alignment explanation
Indices: 12573448--12573491 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
12573438 AGATCAACTA
12573448 GTGGTTGAGGGTTCGATCCTC
1 GTGGTTGAGGGTTCGATCCTC
12573469 GTGGTTGAGGGTTCGATCCTC
1 GTGGTTGAGGGTTCGATCCTC
12573490 GT
1 GT
12573492 ATTGGGTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.39, T:0.34
Consensus pattern (21 bp):
GTGGTTGAGGGTTCGATCCTC
Found at i:12574527 original size:19 final size:18
Alignment explanation
Indices: 12574493--12574528 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12574483 TAACTCTTAG
*
12574493 AAAATAATATATATGATA
1 AAAATAATATAAATGATA
12574511 AAAATATATATAAATGAT
1 AAAATA-ATATAAATGAT
12574529 TAATGGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
AAAATAATATAAATGATA
Found at i:12577792 original size:26 final size:26
Alignment explanation
Indices: 12577754--12577811 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
12577744 CATGAAATTC
12577754 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
12577780 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
12577806 TTATCA
1 TTATCA
12577812 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:12582658 original size:24 final size:25
Alignment explanation
Indices: 12582604--12582658 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
12582594 AATAAAATAA
*
12582604 TCAAACTATAATTAAATATTTTTAT
1 TCAAACTATAATTAAATAGTTTTAT
** * *
12582629 AAAAACTTTAATT-ATTAGTTTTAT
1 TCAAACTATAATTAAATAGTTTTAT
12582653 TCAAAC
1 TCAAAC
12582659 AATTTTGTCT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (25 bp):
TCAAACTATAATTAAATAGTTTTAT
Found at i:12594148 original size:49 final size:47
Alignment explanation
Indices: 12594076--12594170 Score: 127
Period size: 49 Copynumber: 2.0 Consensus size: 47
12594066 TGTATGGTAG
* * * *
12594076 TTGTTATAATTAGTTATTTCATTACTTTCTTTTTACAGATTATTCTTTA
1 TTGTTATAATTAGTAATTCCATTAC-AT-TTTTCACAGATTATTCTTTA
*
12594125 TTGTTATAATTAGTAATTCCATTACATTTTTCCCAGATTATTCTTT
1 TTGTTATAATTAGTAATTCCATTACATTTTTCACAGATTATTCTTT
12594171 CATATAGATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
47 17 0.41
48 1 0.02
49 23 0.56
ACGTcount: A:0.25, C:0.13, G:0.06, T:0.56
Consensus pattern (47 bp):
TTGTTATAATTAGTAATTCCATTACATTTTTCACAGATTATTCTTTA
Found at i:12603151 original size:12 final size:12
Alignment explanation
Indices: 12603134--12603159 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12603124 GAATTTGGAT
12603134 GAGGATGAGGAA
1 GAGGATGAGGAA
12603146 GAGGATGAGGAA
1 GAGGATGAGGAA
12603158 GA
1 GA
12603160 TCCTTTGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.50, T:0.08
Consensus pattern (12 bp):
GAGGATGAGGAA
Found at i:12616236 original size:4 final size:4
Alignment explanation
Indices: 12616227--12616285 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
12616217 TCTTTTCATA
12616227 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12616275 TATG TATG TAT
1 TATG TATG TAT
12616286 ATGTGCATGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:12629936 original size:27 final size:27
Alignment explanation
Indices: 12629904--12629960 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
12629894 GAACTATTGA
* *
12629904 CATGGGGGGCTTGCATGTCAAATGGAC
1 CATGGGGGACTTGCATATCAAATGGAC
12629931 CATGGGGGACTTGCATATCAAATGGAC
1 CATGGGGGACTTGCATATCAAATGGAC
12629958 CAT
1 CAT
12629961 TTTTAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (27 bp):
CATGGGGGACTTGCATATCAAATGGAC
Found at i:12631715 original size:38 final size:39
Alignment explanation
Indices: 12631645--12631758 Score: 133
Period size: 40 Copynumber: 2.9 Consensus size: 39
12631635 ATTTGATGTG
* *
12631645 TATCCGGGCTTAAAGGT-CCGCAGACTTCGTGCTGGTATTA
1 TATCCGGG-TTAAA-GTCCCGCAGGCTTAGTGCTGGTATTA
12631685 TATCCGGGTTAAA-TCCCGCAGGCTTAGTGCTGGTATTA
1 TATCCGGGTTAAAGTCCCGCAGGCTTAGTGCTGGTATTA
* * * *
12631723 TATTCGAGCTTAAAGTCCCGCAGGTTTTGTGCTGGT
1 TATCCG-GGTTAAAGTCCCGCAGGCTTAGTGCTGGT
12631759 GGCTGGATTC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
37 1 0.02
38 26 0.40
39 11 0.17
40 27 0.42
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.32
Consensus pattern (39 bp):
TATCCGGGTTAAAGTCCCGCAGGCTTAGTGCTGGTATTA
Found at i:12631755 original size:40 final size:38
Alignment explanation
Indices: 12631645--12631758 Score: 122
Period size: 38 Copynumber: 2.9 Consensus size: 38
12631635 ATTTGATGTG
* *
12631645 TATCCGGGCTTAAAGGT-CCGCAGACTTCGTGCTGGTATTA
1 TATCC-GGCTTAAA--TCCCGCAGGCTTAGTGCTGGTATTA
*
12631685 TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTATTA
1 TATCCGGCTTAAATCCCGCAGGCTTAGTGCTGGTATTA
* * *
12631723 TATTCGAGCTTAAAGTCCCGCAGGTTTTGTGCTGGT
1 TATCCG-GCTTAAA-TCCCGCAGGCTTAGTGCTGGT
12631759 GGCTGGATTC
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
37 1 0.02
38 26 0.41
39 13 0.20
40 24 0.38
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.32
Consensus pattern (38 bp):
TATCCGGCTTAAATCCCGCAGGCTTAGTGCTGGTATTA
Found at i:12635080 original size:40 final size:40
Alignment explanation
Indices: 12635025--12635256 Score: 245
Period size: 40 Copynumber: 5.8 Consensus size: 40
12635015 ATAACCACAA
* * * * *
12635025 GCACAATTACCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
12635065 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * *
12635105 GTACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* * * *
12635145 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* * * * *
12635185 GCATAAATGCCTTTGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
12635225 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
12635257 CATTCAAATG
Statistics
Matches: 177, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.01
40 172 0.97
41 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:12635153 original size:80 final size:79
Alignment explanation
Indices: 12635024--12635256 Score: 297
Period size: 80 Copynumber: 2.9 Consensus size: 79
12635014 TATAACCACA
* * * * * * * * *
12635024 AGCACAATTACCTTCGGGTCTTAACCCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTCTTAG
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAGCATAAATGCCTTCGGGACTTAG
12635088 CCCGGATATATCAACT
65 CCCGGATATATC-ACT
* *
12635104 CGTACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGC
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGC
*
12635169 CCGGATAAAATCACT
66 CCGGAT-ATATCACT
* * *
12635184 AGCATAAATGCCTTTGGGACTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGC
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGC
12635249 CCGGATAT
66 CCGGATAT
12635257 CATTCAAATG
Statistics
Matches: 133, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
79 1 0.01
80 125 0.94
81 7 0.05
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (79 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGC
CCGGATATATCACT
Found at i:12642767 original size:38 final size:39
Alignment explanation
Indices: 12642705--12642856 Score: 202
Period size: 38 Copynumber: 3.9 Consensus size: 39
12642695 ATTTGATGTG
12642705 TATCCGGGCTTAAAGGT-CCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGG-TTAAA-GTCCCGCAGGCTTCGTGCTGGTATTA
12642745 TATCCGGGTTAAA-TCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAAGTCCCGCAGGCTTCGTGCTGGTATTA
* *
12642783 TATCCGGGTTAAA-TCCCGCAGGCTTAGTGCTAGTATTA
1 TATCCGGGTTAAAGTCCCGCAGGCTTCGTGCTGGTATTA
* * * *
12642821 TATTCGAGCTTAAAGTCCCGCAGGTTTTGTGCTGGT
1 TATCCG-GGTTAAAGTCCCGCAGGCTTCGTGCTGGT
12642857 GGCTGGATTC
Statistics
Matches: 102, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
37 1 0.01
38 64 0.63
39 11 0.11
40 26 0.25
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (39 bp):
TATCCGGGTTAAAGTCCCGCAGGCTTCGTGCTGGTATTA
Found at i:12642805 original size:76 final size:79
Alignment explanation
Indices: 12642705--12642856 Score: 204
Period size: 78 Copynumber: 1.9 Consensus size: 79
12642695 ATTTGATGTG
* * *
12642705 TATCCGGGCTTAAAGGTCCGCAGGCTTCGTGCTGGTATTATATCCG-GGTTAAA-TCCCGCAGGC
1 TATCCGGGCTTAAA-GTCCGCAGGCTTAGTGCTAGTATTATATCCGAGCTTAAAGTCCCGCAGGC
12642768 TTCGTGCTGGTATTA
65 TTCGTGCTGGTATTA
* *
12642783 TATCCGGG-TTAAA-TCCCGCAGGCTTAGTGCTAGTATTATATTCGAGCTTAAAGTCCCGCAGGT
1 TATCCGGGCTTAAAGT-CCGCAGGCTTAGTGCTAGTATTATATCCGAGCTTAAAGTCCCGCAGGC
*
12642846 TTTGTGCTGGT
65 TTCGTGCTGGT
12642857 GGCTGGATTC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
75 1 0.02
76 26 0.40
77 11 0.17
78 27 0.42
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (79 bp):
TATCCGGGCTTAAAGTCCGCAGGCTTAGTGCTAGTATTATATCCGAGCTTAAAGTCCCGCAGGCT
TCGTGCTGGTATTA
Found at i:12644006 original size:8 final size:8
Alignment explanation
Indices: 12643993--12644017 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12643983 ATTAGGGACT
12643993 AAAATGTG
1 AAAATGTG
12644001 AAAATGTG
1 AAAATGTG
12644009 AAAATGTG
1 AAAATGTG
12644017 A
1 A
12644018 GGGCTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AAAATGTG
Found at i:12644548 original size:43 final size:42
Alignment explanation
Indices: 12644393--12644554 Score: 155
Period size: 43 Copynumber: 3.8 Consensus size: 42
12644383 TGTGTTTTCC
* * ** *
12644393 TGTAAGACCACATTTGGGACGTTGGCATCGGCTTATGATTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGTATT-TGA-TTACA
* * * *
12644437 TGTAAGACCATGTCTGGGACATCGGCATCGTATTTGATTTCA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGTATTTGATTACA
** * *
12644479 TGTAAGACCTTGTATGAGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCACGTCTGGGAC-GTTGGCATCG-TATTTGATTACA
*
12644522 TGTAAGACCACGTCTGGGACGTTGGCATTGTAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGTAT
12644555 GAGCTTTTCA
Statistics
Matches: 95, Mismatches: 20, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
42 31 0.33
43 37 0.39
44 27 0.28
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGTATTTGATTACA
Found at i:12644732 original size:18 final size:19
Alignment explanation
Indices: 12644701--12644740 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
12644691 GTACATGTGC
*
12644701 AAGTGATGATATATGATAT
1 AAGTGATGAAATATGATAT
*
12644720 AAGT-ATGAAATATGCTAT
1 AAGTGATGAAATATGATAT
12644738 AAG
1 AAG
12644741 AGTAAATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.33
Consensus pattern (19 bp):
AAGTGATGAAATATGATAT
Found at i:12650537 original size:20 final size:20
Alignment explanation
Indices: 12650512--12650554 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
12650502 GATTTACTGC
12650512 GATTGTTTTTCCTTAATTGA
1 GATTGTTTTTCCTTAATTGA
12650532 GATTGTTTTTCCTTAATTGA
1 GATTGTTTTTCCTTAATTGA
12650552 GAT
1 GAT
12650555 ATGCAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.09, G:0.16, T:0.53
Consensus pattern (20 bp):
GATTGTTTTTCCTTAATTGA
Found at i:12651310 original size:16 final size:18
Alignment explanation
Indices: 12651289--12651325 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12651279 CCATCAAAAC
12651289 AAATTGA-AAAA-TATAA
1 AAATTGAGAAAATTATAA
12651305 AAATTGAGAAAATTATAA
1 AAATTGAGAAAATTATAA
12651323 AAA
1 AAA
12651326 ATATATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 4 0.21
18 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
AAATTGAGAAAATTATAA
Found at i:12651428 original size:18 final size:18
Alignment explanation
Indices: 12651405--12651439 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12651395 CATTCTAGAC
12651405 ATATTTTTTAATAATTTT
1 ATATTTTTTAATAATTTT
*
12651423 ATATTTTTTTATAATTT
1 ATATTTTTTAATAATTT
12651440 CAAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATATTTTTTAATAATTTT
Found at i:12654577 original size:22 final size:22
Alignment explanation
Indices: 12654542--12654594 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
12654532 AATAAAATGA
*
12654542 AATTTATTTAATTACTATATATT
1 AATTT-TTAAATTACTATATATT
* *
12654565 AATTTTTAAATTATTATATTTT
1 AATTTTTAAATTACTATATATT
*
12654587 TATTTTTA
1 AATTTTTA
12654595 TAATGATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
AATTTTTAAATTACTATATATT
Found at i:12654603 original size:23 final size:22
Alignment explanation
Indices: 12654557--12654614 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
12654547 ATTTAATTAC
* * *
12654557 TATATATTAATTTTTAAATTAT
1 TATATTTTTATTTTTAAATGAT
12654579 TATATTTTTATTTTTATAATGAT
1 TATATTTTTATTTTTA-AATGAT
* *
12654602 TAAATTTATATTT
1 TATATTTTTATTT
12654615 ATCATATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TATATTTTTATTTTTAAATGAT
Found at i:12662935 original size:3 final size:3
Alignment explanation
Indices: 12662927--12662961 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
12662917 TTTTCTACAT
12662927 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
12662962 TTGACTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:12666356 original size:30 final size:30
Alignment explanation
Indices: 12666321--12666378 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
12666311 TAGGCACTTC
*
12666321 CACACGGGT-GATTCACACACCCGTGTGTTA
1 CACACGGGTAGA-CCACACACCCGTGTGTTA
*
12666351 CACACGGGTAGACCACACGCCCGTGTGT
1 CACACGGGTAGACCACACACCCGTGTGT
12666379 CATGGCCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.22, C:0.33, G:0.26, T:0.19
Consensus pattern (30 bp):
CACACGGGTAGACCACACACCCGTGTGTTA
Found at i:12671589 original size:131 final size:130
Alignment explanation
Indices: 12671100--12671592 Score: 383
Period size: 131 Copynumber: 3.8 Consensus size: 130
12671090 TGGTTTAAGA
* * * * * * * * **
12671100 CGAGATTCGATATTTGGCAATTCGCGGAATAGTGCCCTAACGTGTTGGGTTGCAATTTCGCGA-T
1 CGAG-TTCGATGTTTGGCAATTCG-AGAATCGAGCCCTATCGTGCTAGGTTGCGATTTTTC-ATT
* * * * * **
12671164 TGCTCGAAATAATCGAATATCACTTC-AAATTTCACTCATATCTT-TTAAAATCCCTT-AAACGA
63 TGCTCAAAATAATCGAATATCCCTTCGGAATTTCACTCATGTCTTCTAAAAATCTTTTAAAACGA
*
12671226 AGA
128 AGG
* * * * * * * * *
12671229 CGAGATTTGATGTTTGGCAATTCGAGGAATCGTGCTCTAACGTGTTGGGTCGCAATTTTGCATTT
1 CGAG-TTCGATGTTTGGCAATTCGA-GAATCGAGCCCTATCGTGCTAGGTTGCGATTTTTCATTT
* * * * *
12671294 GCTCAAAATAATCGAATATCACTTCGAAATTCCCCTCATGTCTTCTAAAAATCTTTTAAAACAAA
64 GCTCAAAATAATCGAATATCCCTTCGGAATTTCACTCATGTCTTCTAAAAATCTTTTAAAACGAA
12671359 GG
129 GG
* ** * * **
12671361 CGA-TACTCGGTGTTTGATAATTCGGGAATC-ATGCCCTATCGTGCTAGGTTGTGATTACTCATT
1 CGAGT--TCGATGTTTGGCAATTCGAGAATCGA-GCCCTATCGTGCTAGGTTGCGATTTTTCATT
* * * * *
12671424 TACTCAAAATAATCGAATATTCCTTTAGG-TTTTCACTCATGT-TTATTAAAAAT-TTTTCAAAA
63 TGCTCAAAATAATCGAATA-TCCCTTCGGAATTTCACTCATGTCTT-CTAAAAATCTTTT-AAAA
12671486 CGAAGG
125 CGAAGG
* *
12671492 CGACGTTCGATGTTTGGCAATTTGAGAATCGAGCCCTATCGTGCTAGGTTGCGCTTTTTCATTTG
1 CGA-GTTCGATGTTTGGCAATTCGAGAATCGAGCCCTATCGTGCTAGGTTGCGATTTTTCATTTG
* *
12671557 CTCAAAACAATCAAATATCCCTTCGGAATTTCACTC
65 CTCAAAATAATCGAATATCCCTTCGGAATTTCACTC
12671593 GTATTTTCTA
Statistics
Matches: 292, Mismatches: 57, Indels: 28
0.77 0.15 0.07
Matches are distributed among these distances:
128 1 0.00
129 79 0.27
130 29 0.10
131 152 0.52
132 30 0.10
133 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (130 bp):
CGAGTTCGATGTTTGGCAATTCGAGAATCGAGCCCTATCGTGCTAGGTTGCGATTTTTCATTTGC
TCAAAATAATCGAATATCCCTTCGGAATTTCACTCATGTCTTCTAAAAATCTTTTAAAACGAAGG
Found at i:12683169 original size:45 final size:45
Alignment explanation
Indices: 12683119--12683433 Score: 193
Period size: 45 Copynumber: 7.1 Consensus size: 45
12683109 AATCCCACAG
* *
12683119 ATCTTGTTTCCCTGAAGTTACAGTGGAGTAGATCGAAGACGACGA
1 ATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATTGAAGACGACGA
* * * * *
12683164 ATCTTGACTTT--CTGAAGTTGCAGTGAAGCAGATTTAAGTC-ACTA
1 ATCTTG--TTTCCCTGAAGTTGCAGTGGAGTAGATTGAAGACGACGA
* * * * * * **
12683208 ACCTAG-CTCCCTAAAGTTGTAGTGGAGTAGGTTGAA-ATTAC-A
1 ATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATTGAAGACGACGA
* * * *
12683250 GATCTTGTTTCCCTGAAGTCGTAGTGGAGTAGATCGAAGACGATGA
1 -ATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATTGAAGACGACGA
* * * * * * *
12683296 ATCTTGACTT-CCTGAAGTTGCAATGAAGCAGATTTAAGTC-ACTA
1 ATCTTG-TTTCCCTGAAGTTGCAGTGGAGTAGATTGAAGACGACGA
* * * * * * **
12683340 ACCTAG-CTCCCTAAAGTTGTAGTGGAGTAGGTTGAA-ATTAC-A
1 ATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATTGAAGACGACGA
*
12683382 GATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATCGAAGACGACGA
1 -ATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATTGAAGACGACGA
12683428 ATCTTG
1 ATCTTG
12683434 ACTTTCTGAT
Statistics
Matches: 194, Mismatches: 60, Indels: 32
0.68 0.21 0.11
Matches are distributed among these distances:
41 1 0.01
42 3 0.02
43 52 0.27
44 63 0.32
45 68 0.35
46 4 0.02
47 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (45 bp):
ATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATTGAAGACGACGA
Found at i:12683278 original size:44 final size:45
Alignment explanation
Indices: 12683215--12683415 Score: 146
Period size: 44 Copynumber: 4.6 Consensus size: 45
12683205 CTAACCTAGC
* *
12683215 TCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTAC-AGATCTTGTT
1 TCCCTGAAGTTGTAGTGGAGTAGATTGAAATTACGAGATCTTGTT
* * * *
12683259 TCCCTGAAGTCGTAGTGGAGTAGATCG-AA-GACGATGAATCTTGACT
1 TCCCTGAAGTTGTAGTGGAGTAGATTGAAATTACGA-G-ATCTTG-TT
* * * * * * * * * * *
12683305 T-CCTGAAGTTGCAATGAAGCAGATTTAAGTCACTA-ACCTAG-C
1 TCCCTGAAGTTGTAGTGGAGTAGATTGAAATTACGAGATCTTGTT
* *
12683347 TCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTAC-AGATCTTGTT
1 TCCCTGAAGTTGTAGTGGAGTAGATTGAAATTACGAGATCTTGTT
*
12683391 TCCCTGAAGTTGCAGTGGAGTAGAT
1 TCCCTGAAGTTGTAGTGGAGTAGAT
12683416 CGAAGACGAC
Statistics
Matches: 114, Mismatches: 34, Indels: 18
0.69 0.20 0.11
Matches are distributed among these distances:
42 4 0.04
43 30 0.26
44 50 0.44
45 24 0.21
46 3 0.03
47 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.31
Consensus pattern (45 bp):
TCCCTGAAGTTGTAGTGGAGTAGATTGAAATTACGAGATCTTGTT
Found at i:12683330 original size:132 final size:133
Alignment explanation
Indices: 12683115--12683767 Score: 895
Period size: 132 Copynumber: 4.9 Consensus size: 133
12683105 GGCGAATCCC
** *
12683115 ACAGATCTTGTTTCCCTGAAGTTACAGTGGAGTAGATCGAAGACGACGAATCTTGACTTTCTGAA
1 ACAGATCTTGTTTCCCTGAAGTTGTAGTGGAGTAGATCGAAGACGACGAATCTTGACTTCCTGAA
* *
12683180 GTTGCAGTGAAGCAGATTTAAGTCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAA-
66 GTTGCAGCGAAGCAGATTTAAGTCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAG
12683244 ATT
131 ATT
* *
12683247 ACAGATCTTGTTTCCCTGAAGTCGTAGTGGAGTAGATCGAAGACGATGAATCTTGACTTCCTGAA
1 ACAGATCTTGTTTCCCTGAAGTTGTAGTGGAGTAGATCGAAGACGACGAATCTTGACTTCCTGAA
** *
12683312 GTTGCAATGAAGCAGATTTAAGTCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAA-
66 GTTGCAGCGAAGCAGATTTAAGTCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAG
12683376 ATT
131 ATT
* * *
12683379 ACAGATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATCGAAGACGACGAATCTTGACTTTCTGAT
1 ACAGATCTTGTTTCCCTGAAGTTGTAGTGGAGTAGATCGAAGACGACGAATCTTGACTTCCTGAA
* * *
12683444 GTTGCAGCGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAG
66 GTTGCAGCGAAGCAGATTTAAGTCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAG
12683509 ATT
131 ATT
* * * * * **
12683512 GCAGATCTTGTTTCTCTG-AGATTGTAGTGGA-TCAGATCGAAGACGGCGGATCTAGGTTTCCTG
1 ACAGATCTTGTTTCCCTGAAG-TTGTAGTGGAGT-AGATCGAAGACGACGAATCTTGACTTCCTG
* *
12683575 ATGTTGCAGCGAAGCAGATTTAAGTCACCACCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGA
64 AAGTTGCAGCGAAGCAGATTTAAGTCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGA
12683640 AGATT
129 AGATT
** * * * * * ** *
12683645 GTAGATCTTGTTTCCCTG-AGATTGTAGTGGAGCAGATCGAAGATGGCGGATCTAGGTTTCTTGA
1 ACAGATCTTGTTTCCCTGAAG-TTGTAGTGGAGTAGATCGAAGACGACGAATCTTGACTTCCTGA
* *
12683709 TA-TTGCAGCGAAGCAGATTTAAGTCACCACCCTAGCTCCCTGAAGTTGTAGTGGAGTAG
65 -AGTTGCAGCGAAGCAGATTTAAGTCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAG
12683768 ACCCAAGATT
Statistics
Matches: 480, Mismatches: 36, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
132 247 0.51
133 233 0.49
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (133 bp):
ACAGATCTTGTTTCCCTGAAGTTGTAGTGGAGTAGATCGAAGACGACGAATCTTGACTTCCTGAA
GTTGCAGCGAAGCAGATTTAAGTCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAG
ATT
Found at i:12687237 original size:131 final size:131
Alignment explanation
Indices: 12686811--12687240 Score: 311
Period size: 131 Copynumber: 3.3 Consensus size: 131
12686801 AATTTCGCGA
* * * * * ** *
12686811 TTGCTCGAAATAATCGAATATCACTTCA-AATTTCACTCATATCTT-TTAAAATCCCTT-AAACG
1 TTGCTCAAAACAATCGAATATCCCTTCAGAATTTCACTCATGTCTTCTAAAAATCTTTTAAAACA
* * * * * * * * * * * * * *
12686873 AAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCTCTAACGTGTTGGGTCGCAATT-TTG
66 AAGGCGATACTCGATGTTTGACAATTCG-AGAATCATGCCCTATCGTGCTAGGTTGCGATTACT-
12686937 CAT
129 CAT
* * * * *
12686940 TTGCTCAAAATAATCGAATATCACTTCAAAATTCCCCTCATGTCTTCTAAAAATCTTTTAAAACA
1 TTGCTCAAAACAATCGAATATCCCTTCAGAATTTCACTCATGTCTTCTAAAAATCTTTTAAAACA
* * * *
12687005 AAGGCGATACTCGGTGTTTGATAATTCGGGAATCATGCCCTATCGTGCTAGGTTGTGATTACTCA
66 AAGGCGATACTCGATGTTTGACAATTCGAGAATCATGCCCTATCGTGCTAGGTTGCGATTACTCA
12687070 T
131 T
* * * ** *
12687071 TTACTCAAAACAATCGAATATTCCTTTAGGTTTTCACTCATGT-TTATTAAAAAT-TTTTCAAAA
1 TTGCTCAAAACAATCGAATATCCCTTCAGAATTTCACTCATGTCTT-CTAAAAATCTTTT-AAAA
* * * * *
12687134 CGAAGGC-A-ACGTTCGATGTTTGGCAATTTGAGAATCGA-GCCCTATCGTGCTGGGTTGCGCTT
64 CAAAGGCGATAC--TCGATGTTTGACAATTCGAGAATC-ATGCCCTATCGTGCTAGGTTGCGATT
** *
12687196 TTTTAT
126 ACTCAT
* *
12687202 TTGCTCAAAACAATCAAAGATCCCTTCAGAATTTCACTC
1 TTGCTCAAAACAATCGAATATCCCTTCAGAATTTCACTC
12687241 GTATTTTCTA
Statistics
Matches: 238, Mismatches: 54, Indels: 16
0.77 0.18 0.05
Matches are distributed among these distances:
129 29 0.12
130 21 0.09
131 161 0.68
132 27 0.11
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (131 bp):
TTGCTCAAAACAATCGAATATCCCTTCAGAATTTCACTCATGTCTTCTAAAAATCTTTTAAAACA
AAGGCGATACTCGATGTTTGACAATTCGAGAATCATGCCCTATCGTGCTAGGTTGCGATTACTCA
T
Found at i:12690422 original size:6 final size:6
Alignment explanation
Indices: 12690411--12690436 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12690401 ATTTATTTTA
12690411 TTTCTT TTTCTT TTTCTT TTTCTT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TT
12690437 ATTTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:12692310 original size:30 final size:30
Alignment explanation
Indices: 12692270--12692359 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
12692260 TAGGCACTTC
* *
12692270 CACACAGGTGATTCATACACCAGTGTGTCA
1 CACACGGGTGATTCACACACCAGTGTGTCA
* * *
12692300 CACACGGGTGATTTACACGCCCGTGTGTCA
1 CACACGGGTGATTCACACACCAGTGTGTCA
* *
12692330 CACACGGGTAGA-CCACACACCCGTGTGTCA
1 CACACGGGT-GATTCACACACCAGTGTGTCA
12692360 TGGCCGTGTC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 49 0.96
31 2 0.04
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (30 bp):
CACACGGGTGATTCACACACCAGTGTGTCA
Found at i:12694105 original size:8 final size:8
Alignment explanation
Indices: 12694092--12694119 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
12694082 TCGTTTCAGA
12694092 GCAAATTG
1 GCAAATTG
12694100 GCAAATTG
1 GCAAATTG
12694108 GCAAATTG
1 GCAAATTG
12694116 GCAA
1 GCAA
12694120 CTTGCAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (8 bp):
GCAAATTG
Found at i:12703099 original size:14 final size:14
Alignment explanation
Indices: 12703080--12703108 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12703070 CCCTTTCATG
12703080 AGTCCTAATTAAAA
1 AGTCCTAATTAAAA
12703094 AGTCCTAATTAAAA
1 AGTCCTAATTAAAA
12703108 A
1 A
12703109 CTAAGTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (14 bp):
AGTCCTAATTAAAA
Found at i:12703488 original size:17 final size:17
Alignment explanation
Indices: 12703468--12703547 Score: 124
Period size: 17 Copynumber: 4.5 Consensus size: 17
12703458 AATGATATGT
12703468 AATCTTAGATATGATAC
1 AATCTTAGATATGATAC
12703485 AATCTTAGATATGATAC
1 AATCTTAGATATGATAC
*
12703502 AATCTTAGATATGATTGC
1 AATCTTAGATATGA-TAC
12703520 AATCTTAGATATGATATAC
1 AATCTTAGATATG--ATAC
12703539 AATCTTAGA
1 AATCTTAGA
12703548 AGATATGATT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
17 31 0.53
18 15 0.26
19 11 0.19
20 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (17 bp):
AATCTTAGATATGATAC
Found at i:12703530 original size:35 final size:35
Alignment explanation
Indices: 12703468--12703547 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
12703458 AATGATATGT
12703468 AATCTTAGATATGATACAATCTTAGATATG-ATAC
1 AATCTTAGATATGATACAATCTTAGATATGAATAC
*
12703502 AATCTTAGATATGATTGCAATCTTAGATATGATATAC
1 AATCTTAGATATGA-TACAATCTTAGATATGA-ATAC
12703539 AATCTTAGA
1 AATCTTAGA
12703548 AGATATGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
34 14 0.33
35 15 0.36
37 13 0.31
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (35 bp):
AATCTTAGATATGATACAATCTTAGATATGAATAC
Found at i:12703867 original size:12 final size:11
Alignment explanation
Indices: 12703852--12703885 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
12703842 TATTTTTAAT
12703852 TTATTATATATA
1 TTATT-TATATA
12703864 TTATTTATTATA
1 TTATTTA-TATA
12703876 TTATTTATAT
1 TTATTTATAT
12703886 TTTCAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTTATATA
Found at i:12703877 original size:21 final size:21
Alignment explanation
Indices: 12703853--12703961 Score: 61
Period size: 21 Copynumber: 5.3 Consensus size: 21
12703843 ATTTTTAATT
12703853 TATTATATATATTATTTATTA
1 TATTATATATATTATTTATTA
* *
12703874 TATTATTTATATT-TTCA--A
1 TATTATATATATTATTTATTA
* * *
12703892 AATT-TGTAAATTA-TTATTA
1 TATTATATATATTATTTATTA
* *
12703911 TA-TATTATATTTTAACTTATATA
1 TATTA-TATATATT-ATTTAT-TA
*
12703934 TCTTATATAT-TTATTTATTTA
1 TATTATATATATTATTTA-TTA
12703955 TATTATA
1 TATTATA
12703962 CATTATTTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 20
0.66 0.13 0.20
Matches are distributed among these distances:
17 8 0.12
18 5 0.08
19 2 0.03
20 8 0.12
21 25 0.38
22 7 0.11
23 8 0.12
24 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.60
Consensus pattern (21 bp):
TATTATATATATTATTTATTA
Found at i:12703883 original size:16 final size:16
Alignment explanation
Indices: 12703850--12703880 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12703840 CTTATTTTTA
12703850 ATTTATTATATATATT
1 ATTTATTATATATATT
12703866 ATTTATTATAT-TATT
1 ATTTATTATATATATT
12703881 TATATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATTATATATATT
Found at i:12706096 original size:23 final size:23
Alignment explanation
Indices: 12706065--12706119 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
12706055 CTATATGTTT
* * *
12706065 CCCTAGTGGCTTATTTTGTTTGG
1 CCCTTGTGGCGTACTTTGTTTGG
12706088 CCCTTGTGGCGTACTTTGTTTGG
1 CCCTTGTGGCGTACTTTGTTTGG
12706111 CCCTTGTGG
1 CCCTTGTGG
12706120 TGAATTATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.05, C:0.22, G:0.29, T:0.44
Consensus pattern (23 bp):
CCCTTGTGGCGTACTTTGTTTGG
Found at i:12712258 original size:46 final size:46
Alignment explanation
Indices: 12712090--12712271 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
12712080 TTCGACATGA
* * * * *
12712090 TGCCATAGTATCTTTCAACTATGGTCTTACTCGTTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACAC-ATTTCATGTCAGGT
* ** * *
12712136 TGCCATGGTATCTTTCCACCATGGTCTTATTCATTTTATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
*
12712182 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
*
12712228 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAG
12712272 AGAGCACACT
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
45 3 0.02
46 118 0.98
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
Found at i:12712690 original size:23 final size:23
Alignment explanation
Indices: 12712664--12712772 Score: 107
Period size: 23 Copynumber: 4.7 Consensus size: 23
12712654 CCATATCGTA
12712664 AAGCTCACGAAGAGCCTATCGGG
1 AAGCTCACGAAGAGCCTATCGGG
12712687 AAGCTC-CGAATG-GCCATATATCGGG
1 AAGCTCACGAA-GAGCC---TATCGGG
* * *
12712712 AAGTTCAAG-CGAGCACTATCGGG
1 AAGCTCACGAAGAGC-CTATCGGG
* *
12712735 AGGCTCACAAAGAGCCTATCGGG
1 AAGCTCACGAAGAGCCTATCGGG
12712758 AAGCTCACGAAGAGC
1 AAGCTCACGAAGAGC
12712773 TGTATTTCGG
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
22 7 0.10
23 40 0.59
24 5 0.07
25 14 0.21
26 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.29, T:0.15
Consensus pattern (23 bp):
AAGCTCACGAAGAGCCTATCGGG
Found at i:12714893 original size:18 final size:18
Alignment explanation
Indices: 12714845--12714893 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 18
12714835 ATAATATAAT
12714845 TATTTAATTAATAAATATC
1 TATTTAA-TAATAAATATC
*
12714864 TTTTATAAAATAATAAATATC
1 TATT-T--AATAATAAATATC
12714885 TATTTAATA
1 TATTTAATA
12714894 TCTAATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
20 2 0.08
21 14 0.56
22 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTTAATAATAAATATC
Found at i:12723095 original size:12 final size:12
Alignment explanation
Indices: 12723078--12723113 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12723068 AAAAAATATC
12723078 AATATTTTTTGA
1 AATATTTTTTGA
12723090 AATATTTTTTGA
1 AATATTTTTTGA
* *
12723102 AAAATTCTTTGA
1 AATATTTTTTGA
12723114 GTACTCGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (12 bp):
AATATTTTTTGA
Found at i:12728005 original size:8 final size:9
Alignment explanation
Indices: 12727964--12728006 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
12727954 CCATTTAGGC
12727964 CTTTTAAAA
1 CTTTTAAAA
*
12727973 TTTTTAAAA
1 CTTTTAAAA
12727982 CTTTTAAAA
1 CTTTTAAAA
12727991 CTTTTAAAA
1 CTTTTAAAA
12728000 -TTTTAAA
1 CTTTTAAA
12728007 TTAGTAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 7 0.22
9 25 0.78
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (9 bp):
CTTTTAAAA
Found at i:12728456 original size:14 final size:15
Alignment explanation
Indices: 12728423--12728460 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
12728413 ACTATTTTAA
*
12728423 GGTTTATGGATTATG
1 GGTTTAAGGATTATG
*
12728438 GGTTTAAGGGTTA-G
1 GGTTTAAGGATTATG
12728452 GGTTTAAGG
1 GGTTTAAGG
12728461 TTGATGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (15 bp):
GGTTTAAGGATTATG
Found at i:12729132 original size:22 final size:22
Alignment explanation
Indices: 12729036--12729132 Score: 73
Period size: 22 Copynumber: 4.5 Consensus size: 22
12729026 TTTAAACAGC
12729036 AAACCC-TAAATCTCAAATCAT
1 AAACCCTTAAATCTCAAATCAT
* *
12729057 AAACCCTTAAAACT-ATAAACGAT
1 AAACCCTTAAATCTCA-AATC-AT
*
12729080 AAA-CCTT-AATC-CTAACA-CCT
1 AAACCCTTAAATCTC-AA-ATCAT
12729100 GAAACCC-TAAATCTCAAATCAT
1 -AAACCCTTAAATCTCAAATCAT
12729122 AAACCCTTAAA
1 AAACCCTTAAA
12729133 ACTCTAACCC
Statistics
Matches: 59, Mismatches: 5, Indels: 23
0.68 0.06 0.26
Matches are distributed among these distances:
20 1 0.02
21 23 0.39
22 29 0.49
23 6 0.10
ACGTcount: A:0.47, C:0.28, G:0.02, T:0.23
Consensus pattern (22 bp):
AAACCCTTAAATCTCAAATCAT
Found at i:12729265 original size:28 final size:27
Alignment explanation
Indices: 12729199--12729266 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
12729189 AACTAACCTT
12729199 TAAACCCATAAACTATAGATCATAAATC
1 TAAACCC-TAAACTATAGATCATAAATC
**
12729227 CCAACCTCTAAACTATA-ACTCATAAATC
1 TAAACC-CTAAACTATAGA-TCATAAATC
12729255 ATAAACCCTAAA
1 -TAAACCCTAAA
12729267 ATCTAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 1 0.03
28 27 0.82
29 5 0.15
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.24
Consensus pattern (27 bp):
TAAACCCTAAACTATAGATCATAAATC
Found at i:12729450 original size:8 final size:8
Alignment explanation
Indices: 12729415--12729467 Score: 52
Period size: 8 Copynumber: 6.1 Consensus size: 8
12729405 TTTATATGTT
*
12729415 AATTTAAA
1 AATTAAAA
12729423 AATTATAAA
1 AATTA-AAA
12729432 AATCTTCAAAA
1 AA--TT-AAAA
12729443 AATTAAAA
1 AATTAAAA
12729451 AATTAAAA
1 AATTAAAA
*
12729459 ACTTAAAA
1 AATTAAAA
12729467 A
1 A
12729468 TGTAATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 24 0.62
9 7 0.18
11 7 0.18
12 1 0.03
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (8 bp):
AATTAAAA
Found at i:12729601 original size:18 final size:17
Alignment explanation
Indices: 12729574--12729617 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
12729564 TTTTGAAAGA
*
12729574 AAAAATAAAAAAAAGTT
1 AAAAATAAAAAAAAATT
12729591 AAAAATGAAAAAAAAATT
1 AAAAAT-AAAAAAAAATT
*
12729609 AAAATTAAA
1 AAAAATAAA
12729618 CAATAGTGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAAATAAAAAAAAATT
Found at i:12730795 original size:153 final size:154
Alignment explanation
Indices: 12730516--12730822 Score: 580
Period size: 153 Copynumber: 2.0 Consensus size: 154
12730506 GTAAGATAGA
*
12730516 TTGATTTCACTAATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAGTTTGCTTCCTTCATCA
1 TTGATTTCACTAATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAATTTGCTTCCTTCATCA
12730581 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGGTGTATAGTTTTTA
66 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGGTGTATAGTTTTTA
12730646 TTTTATCTTATATTCTGCAGAATG
131 TTTTATCTTATATTCTGCAGAATG
*
12730670 TTGATTTCACTGATTTTAGGCTTGAATTTTACGTTCTTC-AAGAAAAAATTTGCTTCCTTCATCA
1 TTGATTTCACTAATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAATTTGCTTCCTTCATCA
*
12730734 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGTTGTATAGTTTTTA
66 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGGTGTATAGTTTTTA
12730799 TTTTATCTTATATTCTGCAGAATG
131 TTTTATCTTATATTCTGCAGAATG
12730823 GGGATGATTC
Statistics
Matches: 150, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
153 112 0.75
154 38 0.25
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (154 bp):
TTGATTTCACTAATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAATTTGCTTCCTTCATCA
ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGGTGTATAGTTTTTA
TTTTATCTTATATTCTGCAGAATG
Found at i:12733477 original size:152 final size:152
Alignment explanation
Indices: 12733201--12733660 Score: 848
Period size: 152 Copynumber: 3.0 Consensus size: 152
12733191 AAGTTTTGCG
* *
12733201 CTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGATATCATTTATTTCATTAGCAAACATC
1 CTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATC
*
12733266 GTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTATTG
66 GTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTG
*
12733331 CACAGAGGTATATCTATGTGCT
131 CACTGAGGTATATCTATGTGCT
*
12733353 CTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAGACATC
1 CTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATC
*
12733418 GTGCAATATTTTAACTAATACTATTAGCATTTACCATACGCTTTTTTTCACTATAAGTTTTGTTG
66 GTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTG
*
12733483 CACTGAGGTATATCTATGTACT
131 CACTGAGGTATATCTATGTGCT
*
12733505 CTATTGCATGCTAGCTGATCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATC
1 CTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATC
12733570 GTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTG
66 GTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTG
12733635 CACTGAGGTATATCTATGTGCT
131 CACTGAGGTATATCTATGTGCT
12733657 CTAT
1 CTAT
12733661 AGATATCGTG
Statistics
Matches: 297, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 297 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (152 bp):
CTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATC
GTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTG
CACTGAGGTATATCTATGTGCT
Found at i:12733736 original size:98 final size:98
Alignment explanation
Indices: 12733567--12733758 Score: 357
Period size: 98 Copynumber: 2.0 Consensus size: 98
12733557 ATTAGCAAAC
*
12733567 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTG
1 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTG
*
12733632 TTGCACTGAGGTATATCTATGTGCTCTATAGAT
66 TTGCACTGAAGTATATCTATGTGCTCTATAGAT
12733665 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTG
1 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTG
*
12733730 TTGCACTGAAGTATATCTATGTGTTCTAT
66 TTGCACTGAAGTATATCTATGTGCTCTAT
12733759 TGCATGCTGG
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (98 bp):
ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTG
TTGCACTGAAGTATATCTATGTGCTCTATAGAT
Found at i:12733856 original size:250 final size:250
Alignment explanation
Indices: 12733415--12733910 Score: 902
Period size: 250 Copynumber: 2.0 Consensus size: 250
12733405 ATTAGCAGAC
*
12733415 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATACGCTTTTTTTCACTATAAGTTTTG
1 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATACGCTTTTCTTCACTATAAGTTTTG
*
12733480 TTGCACTGAGGTATATCTATGTACTCTATTGCATGCTAGCTGATCTTTAAAATGATGTTAAGGAT
66 TTGCACTGAAGTATATCTATGTACTCTATTGCATGCTAGCTGATCTTTAAAATGATGTTAAGGAT
*
12733545 ATCCTTTTTTTCATTAGCAAACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATG
131 ATCCTTATTTTCATTAGCAAACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATG
*
12733610 CTTTTTTTCACTATAAGTTTTGTTGCACTGAGGTATATCTATGTGCTCTATAGAT
196 CTTTTTTCCACTATAAGTTTTGTTGCACTGAGGTATATCTATGTGCTCTATAGAT
*
12733665 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTG
1 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATACGCTTTTCTTCACTATAAGTTTTG
** *
12733730 TTGCACTGAAGTATATCTATGTGTTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGAT
66 TTGCACTGAAGTATATCTATGTACTCTATTGCATGCTAGCTGATCTTTAAAATGATGTTAAGGAT
* *
12733795 ATCCTTATTTTCATTAGTAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATG
131 ATCCTTATTTTCATTAGCAAACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATG
12733860 CTTTTTTCCACTATAAGTTTTGTTGCACTGAGGTATATCTATGTGCTCTAT
196 CTTTTTTCCACTATAAGTTTTGTTGCACTGAGGTATATCTATGTGCTCTAT
12733911 TGCATGCTGG
Statistics
Matches: 236, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
250 236 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (250 bp):
ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATACGCTTTTCTTCACTATAAGTTTTG
TTGCACTGAAGTATATCTATGTACTCTATTGCATGCTAGCTGATCTTTAAAATGATGTTAAGGAT
ATCCTTATTTTCATTAGCAAACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATG
CTTTTTTCCACTATAAGTTTTGTTGCACTGAGGTATATCTATGTGCTCTATAGAT
Found at i:12733941 original size:152 final size:150
Alignment explanation
Indices: 12733660--12734016 Score: 633
Period size: 152 Copynumber: 2.4 Consensus size: 150
12733650 ATGTGCTCTA
*
12733660 TAGATATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAG
1 TAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTT-TTCACTATAAG
*
12733725 TTTTGTTGCACTGAAGTATATCTATGTGTTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTA
65 TTTTGTTGCACTGAAGTATATCTATGTGCTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTA
12733790 AGGATATCCTTATTTTCATTAG
130 A-GATATCCTTATTTTCATTAG
12733812 TAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTCCACTATAAG
1 TAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTT-CACTATAAG
*
12733877 TTTTGTTGCACTGAGGTATATCTATGTGCTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTA
65 TTTTGTTGCACTGAAGTATATCTATGTGCTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTA
*
12733942 AGATATCCTTTTTTTCATTAG
130 AGATATCCTTATTTTCATTAG
* *
12733963 CAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATTTGCTTTTT
1 TAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTT
12734017 ACATGAATCC
Statistics
Matches: 198, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
151 73 0.37
152 125 0.63
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (150 bp):
TAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTCACTATAAGT
TTTGTTGCACTGAAGTATATCTATGTGCTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTAA
GATATCCTTATTTTCATTAG
Found at i:12735005 original size:43 final size:43
Alignment explanation
Indices: 12734886--12734990 Score: 156
Period size: 43 Copynumber: 2.4 Consensus size: 43
12734876 GCGGCGTTTT
** *
12734886 GGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCAGTGTTTGC
1 GGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCAACGATTGC
* * *
12734929 GGGAAAAGCGTCGTTAAAGGTCAAGGTCTTTAGCAACGATTGC
1 GGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCAACGATTGC
12734972 GGGAAAAGCGCCGCTAAAG
1 GGGAAAAGCGCCGCTAAAG
12734991 ACCATGACCT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.29, C:0.18, G:0.32, T:0.21
Consensus pattern (43 bp):
GGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCAACGATTGC
Found at i:12736645 original size:26 final size:26
Alignment explanation
Indices: 12736616--12736672 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
12736606 TGATACAAAT
12736616 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12736642 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12736668 TGATA
1 TGATA
12736673 GGAATTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:12743319 original size:26 final size:26
Alignment explanation
Indices: 12743290--12743345 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
12743280 TGATACAAAT
12743290 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12743316 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12743342 TGAT
1 TGAT
12743346 GGGAATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:12744861 original size:26 final size:26
Alignment explanation
Indices: 12744831--12744883 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
12744821 TTTATAGTTT
12744831 TACCCCTAGTAGTTAAATT-ACCGAAA
1 TACCCCTAG-AGTTAAATTGACCGAAA
* *
12744857 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGTTAAATTGACCGAAA
12744883 T
1 T
12744884 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (26 bp):
TACCCCTAGAGTTAAATTGACCGAAA
Found at i:12748749 original size:3 final size:3
Alignment explanation
Indices: 12748743--12748769 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12748733 CCTTCTTCTT
12748743 CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC
12748770 TTCTTCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:12750438 original size:29 final size:30
Alignment explanation
Indices: 12750359--12750438 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
12750349 AAAAAATAAA
***
12750359 TTTTAAAGTTTTCTAAATTTTTTTTACTAAT
1 TTTTAAA-TTTTCTAAAGAATTTTTACTAAT
* *
12750390 TTTTATA-TTTGTAAAGAATTTTTAC-AACT
1 TTTTAAATTTTCTAAAGAATTTTTACTAA-T
12750419 TTTTAAATTTTCTAAA-AATT
1 TTTTAAATTTTCTAAAGAATT
12750439 ATATATTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
28 2 0.05
29 25 0.62
30 7 0.17
31 6 0.15
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (30 bp):
TTTTAAATTTTCTAAAGAATTTTTACTAAT
Found at i:12759983 original size:5 final size:5
Alignment explanation
Indices: 12759973--12760004 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
12759963 TTGTGTGTTC
12759973 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
12760005 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:12759987 original size:9 final size:9
Alignment explanation
Indices: 12759973--12760003 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
12759963 TTGTGTGTTC
12759973 TTTATTTTA
1 TTTATTTTA
12759982 TTTATTTTA
1 TTTATTTTA
12759991 TTTTATTTTA
1 -TTTATTTTA
12760001 TTT
1 TTT
12760004 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:12764424 original size:5 final size:5
Alignment explanation
Indices: 12764414--12764445 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
12764404 TTGTGTGTTC
12764414 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
12764446 TCACAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:12764428 original size:9 final size:9
Alignment explanation
Indices: 12764414--12764444 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
12764404 TTGTGTGTTC
12764414 TTTATTTTA
1 TTTATTTTA
12764423 TTTATTTTA
1 TTTATTTTA
12764432 TTTTATTTTA
1 -TTTATTTTA
12764442 TTT
1 TTT
12764445 TTCACAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:12767516 original size:45 final size:45
Alignment explanation
Indices: 12767452--12767542 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
12767442 TATGACAAAG
12767452 GGTTAACTGAATCTGAATCTGAATCGAAGCAAGAAACTATGGTAA
1 GGTTAACTGAATCTGAATCTGAATCGAAGCAAGAAACTATGGTAA
12767497 GGTTAACTGAATCTGAATCTGAATCGAAGCAAGAAACTATGGTAA
1 GGTTAACTGAATCTGAATCTGAATCGAAGCAAGAAACTATGGTAA
12767542 G
1 G
12767543 CAATGGTAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (45 bp):
GGTTAACTGAATCTGAATCTGAATCGAAGCAAGAAACTATGGTAA
Found at i:12770580 original size:22 final size:21
Alignment explanation
Indices: 12770543--12770594 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
12770533 ATCACCCCAA
*
12770543 TTTT-ATTTTATTTTATTTAT
1 TTTTAATTTTATCTTATTTAT
12770563 TTTTAATTGTTATCTTATTTAT
1 TTTTAATT-TTATCTTATTTAT
*
12770585 CTTT-ATTTTA
1 TTTTAATTTTA
12770595 CTAATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 7 0.25
21 6 0.21
22 15 0.54
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTAATTTTATCTTATTTAT
Found at i:12770683 original size:6 final size:6
Alignment explanation
Indices: 12770672--12770696 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12770662 ATATATTTTA
12770672 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
12770697 GCTATTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:12773877 original size:29 final size:29
Alignment explanation
Indices: 12773845--12773900 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
12773835 TTACTTGATA
* * *
12773845 CACACAGCTGTGTCGCAGACCGTGTATGG
1 CACACAACCGTGTCGCAGACCATGTATGG
12773874 CACACAACCGTGTCGCAGACCATGTAT
1 CACACAACCGTGTCGCAGACCATGTAT
12773901 AGCAGACGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (29 bp):
CACACAACCGTGTCGCAGACCATGTATGG
Found at i:12776801 original size:46 final size:46
Alignment explanation
Indices: 12776751--12777104 Score: 548
Period size: 46 Copynumber: 7.7 Consensus size: 46
12776741 GATAGAAAAT
*
12776751 GTGTAAGACCATGGTTGAAAGATACCATGGCAATCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
*
12776797 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
12776843 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
* *
12776889 GTGTAAGACCATGGTTGAAAGATACCTTGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
*
12776935 GTGTAAGACCATAGTTGAAAGATACCATGGCAACCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
* * *
12776981 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
* * *
12777027 GTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAAC
* * * * *
12777073 GAGTAAAACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
12777105 TCATGTCGAA
Statistics
Matches: 289, Mismatches: 18, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
45 1 0.00
46 288 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
Found at i:12786150 original size:19 final size:19
Alignment explanation
Indices: 12786128--12786165 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12786118 TATATATAGG
12786128 TTAGCTTTTTTACTTGTTT
1 TTAGCTTTTTTACTTGTTT
12786147 TTAGCTTTTTTACTTGTTT
1 TTAGCTTTTTTACTTGTTT
12786166 AGTTGCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.68
Consensus pattern (19 bp):
TTAGCTTTTTTACTTGTTT
Found at i:12787775 original size:21 final size:21
Alignment explanation
Indices: 12787732--12787782 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
12787722 TAAGAATGTT
**
12787732 ATTAAATTATATATTATTTTA
1 ATTAAATTATATATTATAATA
12787753 ATTAAATTATAT-TTAATAATA
1 ATTAAATTATATATT-ATAATA
*
12787774 ATTAGATTA
1 ATTAAATTA
12787783 AAATATGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTAAATTATATATTATAATA
Found at i:12787776 original size:16 final size:16
Alignment explanation
Indices: 12787744--12787830 Score: 56
Period size: 16 Copynumber: 5.5 Consensus size: 16
12787734 TAAATTATAT
*
12787744 ATTAT-TTTAATTA-A
1 ATTATATTTAATAATA
12787758 ATTATATTTAATAATA
1 ATTATATTTAATAATA
*
12787774 ATTAGA-TTAA-AATA
1 ATTATATTTAATAATA
* ** *
12787788 TGATTAAATTTTTTATTAA
1 --ATTATATTTAATAAT-A
12787807 ATTATATTTAATAATA
1 ATTATATTTAATAATA
*
12787823 ATTCTATT
1 ATTATATT
12787831 AAAATTTAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
14 9 0.16
15 11 0.20
16 19 0.35
17 13 0.24
18 2 0.04
19 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (16 bp):
ATTATATTTAATAATA
Found at i:12787783 original size:59 final size:52
Alignment explanation
Indices: 12787736--12787840 Score: 144
Period size: 49 Copynumber: 2.1 Consensus size: 52
12787726 AATGTTATTA
12787736 AATTATATATTATTTTAATTAAATTATATTTAATAATAATTAGATTAAAATAT
1 AATTATATATTATTTT-ATTAAATTATATTTAATAATAATTAGATTAAAATAT
* ** *
12787789 GATTA-A-ATT-TTTTATTAAATTATATTTAATAATAATTCTATTAAAATTT
1 AATTATATATTATTTTATTAAATTATATTTAATAATAATTAGATTAAAATAT
12787838 AAT
1 AAT
12787841 AACAAACAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 35 0.74
50 4 0.09
51 3 0.06
52 1 0.02
53 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (52 bp):
AATTATATATTATTTTATTAAATTATATTTAATAATAATTAGATTAAAATAT
Found at i:12788023 original size:16 final size:16
Alignment explanation
Indices: 12788002--12788036 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12787992 TGAATTATTG
*
12788002 ATTACAACTCTATTTT
1 ATTACAACTCTATTCT
*
12788018 ATTACAACTTTATTCT
1 ATTACAACTCTATTCT
12788034 ATT
1 ATT
12788037 CCCCCCAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTACAACTCTATTCT
Found at i:12791136 original size:22 final size:23
Alignment explanation
Indices: 12791111--12791156 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12791101 CAACCAAATC
12791111 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
12791133 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
12791156 A
1 A
12791157 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:12791162 original size:23 final size:23
Alignment explanation
Indices: 12791118--12791162 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12791108 ATCAATTCAA
*
12791118 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
12791141 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
12791163 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:12798857 original size:22 final size:23
Alignment explanation
Indices: 12798832--12798877 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12798822 CAACCAAATC
12798832 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
12798854 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
12798877 A
1 A
12798878 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:12798883 original size:23 final size:23
Alignment explanation
Indices: 12798839--12798883 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12798829 ATCAATTCAA
*
12798839 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
12798862 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
12798884 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:12801647 original size:46 final size:46
Alignment explanation
Indices: 12801594--12801692 Score: 137
Period size: 46 Copynumber: 2.2 Consensus size: 46
12801584 GGCCATTACA
* **
12801594 TGAAAGATACCACGGCAACCTGACATG-AAATGAATAAGACCATGGT
1 TGAAAGATACCACGGCAACATGACA-GAAAATGAATAAGACCATAAT
* *
12801640 TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAAT
1 TGAAAGATACCACGGCAACATGACAGAAAATGAATAAGACCATAAT
12801686 TGAAAGA
1 TGAAAGA
12801693 CACTATGGCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 1 0.02
46 46 0.98
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.17
Consensus pattern (46 bp):
TGAAAGATACCACGGCAACATGACAGAAAATGAATAAGACCATAAT
Found at i:12802007 original size:16 final size:17
Alignment explanation
Indices: 12801986--12802018 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12801976 TTGATGGTGC
12801986 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
12802002 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
12802019 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:12803050 original size:14 final size:15
Alignment explanation
Indices: 12803021--12803051 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12803011 TTTAAGTTTG
12803021 ATTTTTCTTTTCTAA
1 ATTTTTCTTTTCTAA
12803036 ATTTTTCTTTT-TAA
1 ATTTTTCTTTTCTAA
12803050 AT
1 AT
12803052 GCTTCTGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTCTTTTCTAA
Found at i:12803342 original size:29 final size:30
Alignment explanation
Indices: 12803295--12803362 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
12803285 TGGCCCAAGA
* * *
12803295 GTAAATACTCAAAATTTGAGGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
12803325 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
12803355 GCAAATAT
1 GTAAATAT
12803363 TTTAAGGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:12810810 original size:18 final size:17
Alignment explanation
Indices: 12810765--12810814 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
12810755 AGTCCATTTA
12810765 TTTCATTATTATTATTAAT
1 TTTCATT-TTATT-TTAAT
*
12810784 TTTTATTTTTATTTTAAT
1 TTTCA-TTTTATTTTAAT
*
12810802 TTTCCTTTTATTT
1 TTTCATTTTATTT
12810815 ATTTTTGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 8 0.30
18 8 0.30
19 9 0.33
20 2 0.07
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTCATTTTATTTTAAT
Found at i:12814807 original size:31 final size:31
Alignment explanation
Indices: 12814765--12814828 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
12814755 CCTTTTCATA
*
12814765 TTTCATTTTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
12814796 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
12814827 TT
1 TT
12814829 ACTATAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:12815074 original size:24 final size:24
Alignment explanation
Indices: 12815036--12815187 Score: 227
Period size: 24 Copynumber: 6.4 Consensus size: 24
12815026 CTAGAGGCCT
*
12815036 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
*
12815061 AGCCCTTTTTATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
12815085 AGCCC-TTTAATAACTGGGGCGTA
1 AGCCCTTTTAATAACTGGGGCATA
* *
12815108 AGCCCTTTTGATAATTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
12815132 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
12815156 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
12815179 AGCCCTTTT
1 AGCCCTTTT
12815188 TCACTTCCTC
Statistics
Matches: 116, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
23 43 0.37
24 69 0.59
25 4 0.03
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:12815096 original size:47 final size:47
Alignment explanation
Indices: 12815043--12815186 Score: 218
Period size: 47 Copynumber: 3.1 Consensus size: 47
12815033 CCTAGCCTCT
* *
12815043 TTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
* * *
12815090 TTTAATAACTGGGGCGTAAGCCCTTTTGATAATTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
*
12815137 TTTTGATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
12815184 TTT
1 TTT
12815187 TTCACTTCCT
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
46 3 0.03
47 64 0.73
48 21 0.24
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (47 bp):
TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
Found at i:12815127 original size:71 final size:71
Alignment explanation
Indices: 12815036--12815187 Score: 250
Period size: 71 Copynumber: 2.1 Consensus size: 71
12815026 CTAGAGGCCT
*
12815036 AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAAGCCCTTTAATAACTG
1 AGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTG
*
12815101 GGGCGTA
65 GGGCATA
* * *
12815108 AGCCCTTTTGATAATTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGG
1 AGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGG
12815173 GGCATA
66 GGCATA
12815179 AGCCCTTTT
1 AGCCCTTTT
12815188 TCACTTCCTC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 71 0.95
72 4 0.05
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (71 bp):
AGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGG
GGCATA
Found at i:12815264 original size:20 final size:20
Alignment explanation
Indices: 12815241--12815303 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
12815231 GAACATCTCG
12815241 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
* *
12815261 TGTGCATATCCTACATGTCA
1 TGTGCATATCATACATATCA
12815281 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
12815301 TGT
1 TGT
12815304 TTATCAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:12815368 original size:25 final size:25
Alignment explanation
Indices: 12815340--12815387 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12815330 ATATATAAAC
* * *
12815340 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
12815365 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
12815388 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:12816597 original size:27 final size:27
Alignment explanation
Indices: 12816545--12816633 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
12816535 GGGCATATTC
* *
12816545 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACA
*
12816572 GTTATTTTACCCTACAGGGGCT-TTACA
1 GTCATTTTACCCTACAGGGG-TATTACA
* * **
12816599 GTCACTTTACCCTAATAGGGGTATTTTA
1 GTCATTTTACCCT-ACAGGGGTATTACA
12816627 GTCATTT
1 GTCATTT
12816634 CATCCTATAA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
27 34 0.68
28 16 0.32
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTACA
Found at i:12816759 original size:56 final size:54
Alignment explanation
Indices: 12816662--12816893 Score: 180
Period size: 54 Copynumber: 4.3 Consensus size: 54
12816652 TGGTAAATCA
* * * * *
12816662 ACAAACCAAAGGTATTTCAATAATTTTGTAAACCAATGGTATTTCTA-TAATTTTT
1 ACAAATCAAGGGTATTTCAGTAACTTTGTAAACCAAGGGTATTT-TAGTAA-TTTT
* * * *
12816717 AGAAAGTCAAGGGTATTTCTGTAACTTTGTAAATCAGGGGTATTTTAGTAATTTT
1 ACAAA-TCAAGGGTATTTCAGTAACTTTGTAAACCAAGGGTATTTTAGTAATTTT
* * ** *
12816772 ACAAATTAAGGGTATTTCGGTAA-TTTCACAAACCAAGGGTATTTTGGTAATTTT
1 ACAAATCAAGGGTATTTCAGTAACTTT-GTAAACCAAGGGTATTTTAGTAATTTT
* * ** * ** * *
12816826 ACAAATTAGGGGTATTTTGGTAATTTTACAAACCAATGGTGTTTTAGTAATTTT
1 ACAAATCAAGGGTATTTCAGTAACTTTGTAAACCAAGGGTATTTTAGTAATTTT
** *
12816880 GTAAATCGAGGGTA
1 ACAAATCAAGGGTA
12816894 AAATAGTAAT
Statistics
Matches: 146, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
53 3 0.02
54 92 0.63
55 17 0.12
56 34 0.23
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (54 bp):
ACAAATCAAGGGTATTTCAGTAACTTTGTAAACCAAGGGTATTTTAGTAATTTT
Found at i:12816777 original size:27 final size:27
Alignment explanation
Indices: 12816662--12816920 Score: 162
Period size: 27 Copynumber: 9.5 Consensus size: 27
12816652 TGGTAAATCA
* * * *
12816662 ACAAACCAAAGGTATTTCAATAATTTT
1 ACAAATCAAGGGTATTTTAGTAATTTT
** * *
12816689 GTAAACCAATGGTATTTCTA-TAATTTTT
1 ACAAATCAAGGGTATTT-TAGTAA-TTTT
* *
12816717 AGAAAGTCAAGGGTATTTCT-GTAACTTT
1 ACAAA-TCAAGGGTATTT-TAGTAATTTT
** *
12816745 GTAAATCAGGGGTATTTTAGTAATTTT
1 ACAAATCAAGGGTATTTTAGTAATTTT
* ** *
12816772 ACAAATTAAGGGTATTTCGGTAATTTC
1 ACAAATCAAGGGTATTTTAGTAATTTT
* *
12816799 ACAAACCAAGGGTATTTTGGTAATTTT
1 ACAAATCAAGGGTATTTTAGTAATTTT
* * *
12816826 ACAAATTAGGGGTATTTTGGTAATTTT
1 ACAAATCAAGGGTATTTTAGTAATTTT
* * *
12816853 ACAAACCAATGGTGTTTTAGTAATTTT
1 ACAAATCAAGGGTATTTTAGTAATTTT
** * *** *
12816880 GTAAATCGAGGGTAAAATAGTAATTCT
1 ACAAATCAAGGGTATTTTAGTAATTTT
**
12816907 GTAAATCAAGGGTA
1 ACAAATCAAGGGTA
12816921 AAACAGTAAT
Statistics
Matches: 183, Mismatches: 44, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
26 1 0.01
27 153 0.84
28 14 0.08
29 15 0.08
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (27 bp):
ACAAATCAAGGGTATTTTAGTAATTTT
Found at i:12816812 original size:54 final size:53
Alignment explanation
Indices: 12816691--12816879 Score: 200
Period size: 54 Copynumber: 3.5 Consensus size: 53
12816681 ATAATTTTGT
* * * * **
12816691 AAACCAATGGTATTTCTA-TAATTTTTAGAAAGTCAAGGGTATTTCTGTAACTTTGT
1 AAACCAAGGGTATTT-TAGTAA-TTTTACAAA-TTAAGGGTATTTCGGTAA-TTTAC
* *
12816747 AAATCAGGGGTATTTTAGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCAC
1 AAACCAAGGGTATTTTAGTAATTTTACAAATTAAGGGTATTTCGGTAATTT-AC
* * *
12816801 AAACCAAGGGTATTTTGGTAATTTTACAAATTAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTTAGTAATTTTACAAATTAAGGGTATTTCGGTAA-TTTAC
* *
12816855 AAACCAATGGTGTTTTAGTAATTTT
1 AAACCAAGGGTATTTTAGTAATTTT
12816880 GTAAATCGAG
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
53 3 0.03
54 83 0.73
55 13 0.11
56 15 0.13
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (53 bp):
AAACCAAGGGTATTTTAGTAATTTTACAAATTAAGGGTATTTCGGTAATTTAC
Found at i:12816892 original size:81 final size:80
Alignment explanation
Indices: 12816672--12816893 Score: 196
Period size: 81 Copynumber: 2.7 Consensus size: 80
12816662 ACAAACCAAA
* * **
12816672 GGTATTTCAATAATTTTGTAAACCAATGGTATTTCTA-TAATTTTTAGAAAGTCAAGGGTATTTC
1 GGTATTTTAGTAATTTTACAAACCAATGGTATTT-TAGTAATTTTT--AAA-TCAAGGGTATTTC
**
12816736 TGTAACTTTGTAAATCAGG
62 TGTAACTTTACAAATCAGG
** * ** ** *
12816755 GGTATTTTAGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTT-TGG
1 GGTATTTTAGTAATTTTACAAACCAATGGTATTTTAGTAATTT-TTAAATCAAGGGTATTTCT-G
* *
12816819 TAATTTTACAAATTAGG
64 TAACTTTACAAATCAGG
* * *
12816836 GGTATTTTGGTAATTTTACAAACCAATGGTGTTTTAGTAATTTTGTAAATCGAGGGTA
1 GGTATTTTAGTAATTTTACAAACCAATGGTATTTTAGTAATTTT-TAAATCAAGGGTA
12816894 AAATAGTAAT
Statistics
Matches: 108, Mismatches: 27, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
80 1 0.01
81 71 0.66
82 3 0.03
83 33 0.31
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.41
Consensus pattern (80 bp):
GGTATTTTAGTAATTTTACAAACCAATGGTATTTTAGTAATTTTTAAATCAAGGGTATTTCTGTA
ACTTTACAAATCAGG
Found at i:12816921 original size:27 final size:27
Alignment explanation
Indices: 12816870--12817003 Score: 164
Period size: 27 Copynumber: 5.0 Consensus size: 27
12816860 AATGGTGTTT
*
12816870 TAGTAATTTTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
*
12816897 TAGTAATTCTGTAAATCAAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* * **
12816924 CAGTAATTCTATAAATCGACAGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
12816951 T-GATAATTCTGTAAATCGAGGGTAAAA
1 TAG-TAATTCTGTAAATCGAGGGTAAAA
* *
12816978 -CGATAATTCTGTAAGTCGAGGGTAAA
1 TAG-TAATTCTGTAAATCGAGGGTAAA
12817004 TCAGGGGTAA
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 92 0.99
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (27 bp):
TAGTAATTCTGTAAATCGAGGGTAAAA
Found at i:12817015 original size:65 final size:65
Alignment explanation
Indices: 12816945--12817066 Score: 181
Period size: 65 Copynumber: 1.9 Consensus size: 65
12816935 TAAATCGACA
* * *
12816945 GTAAAATGATAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAGTCGAGGGTAAATCAGGG
1 GTAAAATGATAATTATATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAATCAGGG
* * * *
12817010 GTAAAATGGTAATTATATAAATCGGGGGTAAAATGGTAATTCTGTAAATCGAGGGTA
1 GTAAAATGATAATTATATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTA
12817067 TTTTGGTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 50 1.00
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (65 bp):
GTAAAATGATAATTATATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAATCAGGG
Found at i:12817023 original size:38 final size:38
Alignment explanation
Indices: 12816961--12817041 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
12816951 TGATAATTCT
* * *
12816961 GTAAATCGAGGGTAAAACGATAATTCTGTAAGTCGAGG
1 GTAAATCGAGGGTAAAACGATAATTATATAAATCGAGG
* * *
12816999 GTAAATC-AGGGGTAAAATGGTAATTATATAAATCGGGG
1 GTAAATCGA-GGGTAAAACGATAATTATATAAATCGAGG
12817037 GTAAA
1 GTAAA
12817042 ATGGTAATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
37 1 0.03
38 35 0.97
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (38 bp):
GTAAATCGAGGGTAAAACGATAATTATATAAATCGAGG
Found at i:12817038 original size:27 final size:27
Alignment explanation
Indices: 12817000--12817066 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
12816990 AAGTCGAGGG
*
12817000 TAAATCAGGGGTAAAATGGTAATTATA
1 TAAATCGGGGGTAAAATGGTAATTATA
* *
12817027 TAAATCGGGGGTAAAATGGTAATTCTG
1 TAAATCGGGGGTAAAATGGTAATTATA
*
12817054 TAAATCGAGGGTA
1 TAAATCGGGGGTA
12817067 TTTTGGTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.39, C:0.06, G:0.27, T:0.28
Consensus pattern (27 bp):
TAAATCGGGGGTAAAATGGTAATTATA
Found at i:12817073 original size:27 final size:26
Alignment explanation
Indices: 12817016--12817124 Score: 85
Period size: 27 Copynumber: 4.0 Consensus size: 26
12817006 AGGGGTAAAA
* ***
12817016 TGGTAATTATATAAATCGGGGGTAAAA
1 TGGTAATT-TATAAATCGAGGGTATTT
*
12817043 TGGTAATTCTGTAAATCGAGGGTATTT
1 TGGTAATT-TATAAATCGAGGGTATTT
*
12817070 TGGTAATTT-TACAAGTCGAAGGTATTT
1 TGGTAATTTATA-AA-TCGAGGGTATTT
** *
12817097 CAGTAATTTTACAAATCGAGGGTATTT
1 TGGTAA-TTTATAAATCGAGGGTATTT
12817124 T
1 T
12817125 AGTATTTTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
25 2 0.03
26 3 0.05
27 55 0.83
28 5 0.08
29 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (26 bp):
TGGTAATTTATAAATCGAGGGTATTT
Found at i:12817086 original size:92 final size:92
Alignment explanation
Indices: 12816907--12817093 Score: 221
Period size: 92 Copynumber: 2.0 Consensus size: 92
12816897 TAGTAATTCT
*
12816907 GTAAATCAAGGGTAAAACAGTAATTCTATAAATCGACAGTAAAATGATAATTCTGTAAATCGAGG
1 GTAAATCAAGGGTAAAACAGTAATTATATAAATCGACAGTAAAATGATAATTCTGTAAATCGAGG
** *
12816972 GTAAAACGATAATTCTGTAAGTCGAGG
66 GTAAAACGATAATTCTACAAGTCGAAG
* ** *** *
12816999 GTAAATCAGGGGTAAAATGGTAATTATATAAATCGGGGGTAAAATGGTAATTCTGTAAATCGAGG
1 GTAAATCAAGGGTAAAACAGTAATTATATAAATCGACAGTAAAATGATAATTCTGTAAATCGAGG
**** * *
12817064 GTATTTTGGTAATTTTACAAGTCGAAG
66 GTAAAACGATAATTCTACAAGTCGAAG
12817091 GTA
1 GTA
12817094 TTTCAGTAAT
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
92 78 1.00
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.29
Consensus pattern (92 bp):
GTAAATCAAGGGTAAAACAGTAATTATATAAATCGACAGTAAAATGATAATTCTGTAAATCGAGG
GTAAAACGATAATTCTACAAGTCGAAG
Done.