Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007754.1 Hibiscus syriacus cultivar Beakdansim tig00110020_pilon, whole genome shotgun sequence
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: 3698414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 15
Found at i:2660414 original size:24 final size:24
Alignment explanation
Indices: 2660382--2660436 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
2660372 ATATATATAT
* * *
2660382 ATACCCGACCCGATTCTCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
*
2660406 ATACCCGACCCAATACCCGGCCTA
1 ATACCCGACCCAATACCCGGCCCA
2660430 ATACCCG
1 ATACCCG
2660437 TTTAAATAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.45, G:0.15, T:0.15
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGGCCCA
Found at i:2660419 original size:12 final size:12
Alignment explanation
Indices: 2660382--2660436 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
2660372 ATATATATAT
*
2660382 ATACCCGACCCG
1 ATACCCGACCCA
* * *
2660394 ATTCTCGGCCCA
1 ATACCCGACCCA
2660406 ATACCCGACCCA
1 ATACCCGACCCA
* *
2660418 ATACCCGGCCTA
1 ATACCCGACCCA
2660430 ATACCCG
1 ATACCCG
2660437 TTTAAATAAC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.25, C:0.45, G:0.15, T:0.15
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:2661830 original size:24 final size:24
Alignment explanation
Indices: 2661779--2661830 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2661769 ATCTGAGTAT
** *
2661779 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
2661803 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
2661827 TGAC
1 TGAC
2661831 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:2662685 original size:20 final size:20
Alignment explanation
Indices: 2662660--2662724 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
2662650 ATTCAGTATC
2662660 GCGATAGTCAGAATCTCGTT
1 GCGATAGTCAGAATCTCGTT
2662680 GCGATAGTCAGAATCTCGTT
1 GCGATAGTCAGAATCTCGTT
* *
2662700 GCGATAGTCAGATTCGCGTT
1 GCGATAGTCAGAATCTCGTT
2662720 GCGAT
1 GCGAT
2662725 TTACGTATTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (20 bp):
GCGATAGTCAGAATCTCGTT
Found at i:2662734 original size:20 final size:20
Alignment explanation
Indices: 2662711--2662885 Score: 206
Period size: 20 Copynumber: 8.7 Consensus size: 20
2662701 CGATAGTCAG
*
2662711 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2662731 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
2662751 ATTCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
2662771 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
2662792 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
2662812 ATTCGCATTGTGATTTATGT
1 ATTCGCATTGCGATTTACGT
* * **
2662832 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
2662853 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2662873 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2662886 ATTAGGAAAA
Statistics
Matches: 126, Mismatches: 27, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
20 97 0.77
21 29 0.23
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2662742 original size:40 final size:38
Alignment explanation
Indices: 2662698--2662826 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 38
2662688 CAGAATCTCG
2662698 TTGCGATAGTCAGATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGAT--TCAGATTCGCGTTGCGATTTACGTATTCGCA
* * * *
2662738 TTGCGATTTACGTATTCGCATTGTGATTTACGTAATCGCA
1 TTGCGATTCA-G-ATTCGCGTTGCGATTTACGTATTCGCA
*
2662778 TTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGA--TT-CAGATTCGCGTTGCGATTTACGTATTCGCA
*
2662819 TTGTGATT
1 TTGCGATT
2662827 TATGTAATCG
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
38 2 0.03
39 3 0.04
40 37 0.50
41 29 0.39
42 2 0.03
43 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (38 bp):
TTGCGATTCAGATTCGCGTTGCGATTTACGTATTCGCA
Found at i:2662812 original size:61 final size:61
Alignment explanation
Indices: 2662731--2662882 Score: 286
Period size: 61 Copynumber: 2.5 Consensus size: 61
2662721 CGATTTACGT
*
2662731 ATTCGCATTGCGATTTACGTATTCGCATTGTGATTTACGTAATCGCATTGCGATTTTCCAA
1 ATTCGCGTTGCGATTTACGTATTCGCATTGTGATTTACGTAATCGCATTGCGATTTTCCAA
*
2662792 ATTCGCGTTGCGATTTACGTATTCGCATTGTGATTTATGTAATCGCATTGCGATTTTCCAA
1 ATTCGCGTTGCGATTTACGTATTCGCATTGTGATTTACGTAATCGCATTGCGATTTTCCAA
2662853 ATTCGCGTTGCGATTTACGTATTCGCATTG
1 ATTCGCGTTGCGATTTACGTATTCGCATTG
2662883 CGAATTAGGA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 89 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (61 bp):
ATTCGCGTTGCGATTTACGTATTCGCATTGTGATTTACGTAATCGCATTGCGATTTTCCAA
Found at i:2662877 original size:81 final size:81
Alignment explanation
Indices: 2662711--2662885 Score: 226
Period size: 81 Copynumber: 2.2 Consensus size: 81
2662701 CGATAGTCAG
* * **
2662711 ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGTGATTTACGTAATCG
1 ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCAAATCG
*
2662776 CATTGCGATTTTCCAA
66 CATTGCGATTTTACAA
* * *
2662792 ATTCGCGTTGCGATTTACGTATTCGCATTGTGATTTATGTAATCGCATTGCGATTTTCCAAATTC
1 ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCAAA-TC
* **
2662857 GCGTTGCGA-TTTACGT
65 GCATTGCGATTTTACAA
*
2662873 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
2662886 ATTAGGAAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 71 0.88
82 10 0.12
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (81 bp):
ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCAAATCG
CATTGCGATTTTACAA
Found at i:2663711 original size:21 final size:21
Alignment explanation
Indices: 2663659--2663712 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2663649 GTTTGTCTTC
*
2663659 AAATTTTATTTTGATTTTTATT
1 AAATTTTA-TTTGAGTTTTATT
** *
2663681 GTATTATATTTGAGTTTTATT
1 AAATTTTATTTGAGTTTTATT
2663702 AAATTTTATTT
1 AAATTTTATTT
2663713 TATTTCACAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (21 bp):
AAATTTTATTTGAGTTTTATT
Found at i:2664722 original size:10 final size:10
Alignment explanation
Indices: 2664707--2664746 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
2664697 TTTATCACAC
2664707 CAAATTCTCT
1 CAAATTCTCT
2664717 CAAATTCTCT
1 CAAATTCTCT
2664727 -AAATTTCTCT
1 CAAA-TTCTCT
*
2664737 CAAATACTCT
1 CAAATTCTCT
2664747 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:2664826 original size:17 final size:18
Alignment explanation
Indices: 2664789--2664829 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2664779 CTATTATGTA
*
2664789 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
2664807 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
2664824 TTTACT
1 TTTACT
2664830 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:2665079 original size:111 final size:111
Alignment explanation
Indices: 2664885--2665112 Score: 375
Period size: 111 Copynumber: 2.1 Consensus size: 111
2664875 CTCGGATAGA
* * **
2664885 AATTATATATCTCTACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAT
1 AATTAAATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAT
* * *
2664950 TAGTAATATTTATTTGATTTATTTAATGCATAATTATTAGATTAAG
66 TAGTAATAATTAGTTGATTTATTTAATGCATAATTATTAAATTAAG
*
2664996 AATTAAATATCTCGGCACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAT
1 AATTAAATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAT
*
2665061 TAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAAATTAAG
66 TAGTAATAATTAGTTGATTTATTTAATGCATAATTATTAAATTAAG
2665107 AATTAA
1 AATTAA
2665113 TTTTTGTAAT
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (111 bp):
AATTAAATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAT
TAGTAATAATTAGTTGATTTATTTAATGCATAATTATTAAATTAAG
Found at i:2667999 original size:29 final size:29
Alignment explanation
Indices: 2667942--2668019 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
2667932 CTACTACGGG
* *
2667942 TGTTAGATTAAAAAAATATAATCTGATCGA
1 TGTTAAATT-AAAAAATATAATCTAATCGA
*
2667972 TGTTAAATTAAAAAATATAATTTAATCGA
1 TGTTAAATTAAAAAATATAATCTAATCGA
* *
2668001 TGTTAAATCAATAAATATA
1 TGTTAAATTAAAAAATATA
2668020 CTAATCATCG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 35 0.81
30 8 0.19
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (29 bp):
TGTTAAATTAAAAAATATAATCTAATCGA
Found at i:2671066 original size:37 final size:37
Alignment explanation
Indices: 2671025--2671103 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
2671015 TATACATATT
2671025 ATACATACATACATGCATGCATGCATTTGTGATATAC
1 ATACATACATACATGCATGCATGCATTTGTGATATAC
*
2671062 ATACATACATGCATGCATGCATGCATTTGTGATATAC
1 ATACATACATACATGCATGCATGCATTTGTGATATAC
2671099 ATACA
1 ATACA
2671104 ATTAGTGTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (37 bp):
ATACATACATACATGCATGCATGCATTTGTGATATAC
Found at i:2687933 original size:21 final size:21
Alignment explanation
Indices: 2687890--2687933 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2687880 CTAAATTCTA
* *
2687890 TTTTTATTATTTATTTTATAT
1 TTTTTATAATTTATTGTATAT
2687911 TTTTTATAATTTTATTGTA-AT
1 TTTTTATAA-TTTATTGTATAT
2687932 TT
1 TT
2687934 ATATCAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTTATAATTTATTGTATAT
Found at i:2688354 original size:2 final size:2
Alignment explanation
Indices: 2688347--2688386 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2688337 AAAATTAAAT
2688347 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2688387 CAGTTAACCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2698811 original size:18 final size:18
Alignment explanation
Indices: 2698759--2698803 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
2698749 TGTTATACAG
2698759 AGTATTTAAATTTAAATA
1 AGTATTTAAATTTAAATA
2698777 AGTATTTAAATTTAAATA
1 AGTATTTAAATTTAAATA
2698795 AGTATTTAA
1 AGTATTTAA
2698804 GTATAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (18 bp):
AGTATTTAAATTTAAATA
Found at i:2699818 original size:21 final size:19
Alignment explanation
Indices: 2699792--2699860 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 19
2699782 CATATTCGTA
2699792 TTGCGATAATCCAAGTTCACG
1 TTGCGATAATCCAAGTT--CG
**
2699813 TTGCGATTTTCCAAGTTCG
1 TTGCGATAATCCAAGTTCG
*
2699832 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATA--ATCCAAGTTCG
2699853 TTGCGATA
1 TTGCGATA
2699861 GTCTCCAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.21
21 33 0.79
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (19 bp):
TTGCGATAATCCAAGTTCG
Found at i:2699861 original size:21 final size:21
Alignment explanation
Indices: 2699801--2699884 Score: 109
Period size: 21 Copynumber: 4.0 Consensus size: 21
2699791 ATTGCGATAA
*
2699801 TCCAAGTTCACGTTGCGAT--TT
1 TCCAAGTT--CGTTGCGATAGTC
2699822 TCCAAGTTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
2699843 TCCAAGTTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
* *
2699864 TCCAAATTCATTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
2699885 CAAAATCGCA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
19 9 0.16
21 49 0.84
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (21 bp):
TCCAAGTTCGTTGCGATAGTC
Found at i:2699887 original size:40 final size:39
Alignment explanation
Indices: 2699791--2699887 Score: 106
Period size: 42 Copynumber: 2.4 Consensus size: 39
2699781 ACATATTCGT
* * *
2699791 ATTGCGATAATCCAAGTTCACGTTGCGATTTTCCAAGTTC
1 ATTGCGATAGTCCAAGTT-ACGTTGCGATTCTCCAAATTC
*
2699831 GTTGCGATAGTCTCCAAGTT-CGTTGCGATAGTCTCCAAATTC
1 ATTGCGATAG--TCCAAGTTACGTTGCGAT--TCTCCAAATTC
2699873 ATTGCGATAGTCCAA
1 ATTGCGATAGTCCAA
2699888 AATCGCAACG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
40 22 0.46
42 26 0.54
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (39 bp):
ATTGCGATAGTCCAAGTTACGTTGCGATTCTCCAAATTC
Found at i:2700570 original size:21 final size:21
Alignment explanation
Indices: 2700544--2700654 Score: 195
Period size: 21 Copynumber: 5.3 Consensus size: 21
2700534 CAAATGCAAT
* *
2700544 AACGAACTCGAAGACTATCGC
1 AACGAACTTGGAGACTATCGC
2700565 AACGAACTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
2700586 AACGAACTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
2700607 AACGAACTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
2700628 AACGAACTTGGAGACTATCAC
1 AACGAACTTGGAGACTATCGC
2700649 AACGAA
1 AACGAA
2700655 GTTGACGAAG
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 87 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (21 bp):
AACGAACTTGGAGACTATCGC
Found at i:2700592 original size:42 final size:42
Alignment explanation
Indices: 2700544--2700795 Score: 342
Period size: 42 Copynumber: 5.8 Consensus size: 42
2700534 CAAATGCAAT
* *
2700544 AACGAACTCGAAGACTATCGCAACGAACTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGC
2700586 AACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGC
* *
2700628 AACGAACTTGGAGACTATCACAACGAAGTTGACGAAGTTGGAGACTATCGT
1 AACGAACTTGGAGACTATCGCAACG-A----AC----TTGGAGACTATCGC
* * *
2700679 AACGAAGTTGGAGACTATCACAACGAACTTGGAGACTATTGC
1 AACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGC
* *
2700721 AACGAAATTGGAGACTATCGCAATGAACTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGC
2700763 AACGAACTTGGAGACTATCGCAACGAACTTGGA
1 AACGAACTTGGAGACTATCGCAACGAACTTGGA
2700796 AAATCGCAAC
Statistics
Matches: 188, Mismatches: 13, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
42 145 0.77
43 1 0.01
46 2 0.01
47 2 0.01
50 1 0.01
51 37 0.20
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (42 bp):
AACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGC
Found at i:2700643 original size:63 final size:63
Alignment explanation
Indices: 2700544--2700795 Score: 342
Period size: 63 Copynumber: 3.9 Consensus size: 63
2700534 CAAATGCAAT
* *
2700544 AACGAACTCGAAGACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGC
*
2700607 AACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCACAACGAAGTTGACGAAGTTGGAGA
1 AACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGCAACG-A----AC----TTGGAGA
*
2700672 CTATCGT
57 CTATCGC
* * * *
2700679 AACGAAGTTGGAGACTATCACAACGAACTTGGAGACTATTGCAACGAAATTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGC
*
2700742 AATGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGA
1 AACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGA
2700796 AAATCGCAAC
Statistics
Matches: 165, Mismatches: 15, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
63 105 0.64
64 1 0.01
67 1 0.01
68 2 0.01
71 1 0.01
72 55 0.33
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (63 bp):
AACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGC
Found at i:2700669 original size:30 final size:30
Alignment explanation
Indices: 2700629--2700688 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2700619 GACTATCGCA
2700629 ACGAACTTGGAGACTATCACAACGAAGTTG
1 ACGAACTTGGAGACTATCACAACGAAGTTG
* **
2700659 ACGAAGTTGGAGACTATCGTAACGAAGTTG
1 ACGAACTTGGAGACTATCACAACGAAGTTG
2700689 GAGACTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.22
Consensus pattern (30 bp):
ACGAACTTGGAGACTATCACAACGAAGTTG
Found at i:2700685 original size:21 final size:21
Alignment explanation
Indices: 2700659--2700795 Score: 211
Period size: 21 Copynumber: 6.5 Consensus size: 21
2700649 AACGAAGTTG
* *
2700659 ACGAAGTTGGAGACTATCGTA
1 ACGAACTTGGAGACTATCGCA
* *
2700680 ACGAAGTTGGAGACTATCACA
1 ACGAACTTGGAGACTATCGCA
*
2700701 ACGAACTTGGAGACTATTGCA
1 ACGAACTTGGAGACTATCGCA
*
2700722 ACGAAATTGGAGACTATCGCA
1 ACGAACTTGGAGACTATCGCA
*
2700743 ATGAACTTGGAGACTATCGCA
1 ACGAACTTGGAGACTATCGCA
2700764 ACGAACTTGGAGACTATCGCA
1 ACGAACTTGGAGACTATCGCA
2700785 ACGAACTTGGA
1 ACGAACTTGGA
2700796 AAATCGCAAC
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 106 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (21 bp):
ACGAACTTGGAGACTATCGCA
Found at i:2700749 original size:114 final size:114
Alignment explanation
Indices: 2700555--2700768 Score: 365
Period size: 114 Copynumber: 1.9 Consensus size: 114
2700545 ACGAACTCGA
* *
2700555 AGACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAG
1 AGACTATCGCAACGAACTTGGAGACTATCACAACGAACTTGGAGACTATCGCAACGAAATTGGAG
2700620 ACTATCGCAACGAACTTGGAGACTATCACAACGAAGTTGACGAAGTTGG
66 ACTATCGCAACGAACTTGGAGACTATCACAACGAAGTTGACGAAGTTGG
* * *
2700669 AGACTATCGTAACGAAGTTGGAGACTATCACAACGAACTTGGAGACTATTGCAACGAAATTGGAG
1 AGACTATCGCAACGAACTTGGAGACTATCACAACGAACTTGGAGACTATCGCAACGAAATTGGAG
* *
2700734 ACTATCGCAATGAACTTGGAGACTATCGCAACGAA
66 ACTATCGCAACGAACTTGGAGACTATCACAACGAA
2700769 CTTGGAGACT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 93 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.20
Consensus pattern (114 bp):
AGACTATCGCAACGAACTTGGAGACTATCACAACGAACTTGGAGACTATCGCAACGAAATTGGAG
ACTATCGCAACGAACTTGGAGACTATCACAACGAAGTTGACGAAGTTGG
Found at i:2701292 original size:38 final size:38
Alignment explanation
Indices: 2701249--2701324 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2701239 TCTCCTACGG
2701249 AAGCTGCTCTCAACCTAGTGTTGGGGGCATCCTACTAT
1 AAGCTGCTCTCAACCTAGTGTTGGGGGCATCCTACTAT
2701287 AAGCTGCTCTCAACCTAGTGTTGGGGGCATCCTACTAT
1 AAGCTGCTCTCAACCTAGTGTTGGGGGCATCCTACTAT
2701325 CTTACCTCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (38 bp):
AAGCTGCTCTCAACCTAGTGTTGGGGGCATCCTACTAT
Found at i:2702039 original size:28 final size:28
Alignment explanation
Indices: 2701978--2702039 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
2701968 TATGTTTTAA
2701978 TTAAAAATATAAATAATGTTAAATGGTT
1 TTAAAAATATAAATAATGTTAAATGGTT
* * **
2702006 TCAAAAAT-TAAATAATAGTTTAATTTTT
1 TTAAAAATATAAATAAT-GTTAAATGGTT
2702034 TTAAAA
1 TTAAAA
2702040 TACTACTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (28 bp):
TTAAAAATATAAATAATGTTAAATGGTT
Found at i:2708300 original size:2 final size:2
Alignment explanation
Indices: 2708293--2708323 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2708283 AATGATTTTA
2708293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2708324 ATTATCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2710380 original size:27 final size:27
Alignment explanation
Indices: 2710336--2710391 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
2710326 TCCCATCCGT
2710336 ATCTCTCTCTACCCTTCAAATTTCACC
1 ATCTCTCTCTACCCTTCAAATTTCACC
* *
2710363 ATCTCTCTCTGCCTTTCAAATTTCACC
1 ATCTCTCTCTACCCTTCAAATTTCACC
2710390 AT
1 AT
2710392 TCGGTTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.21, C:0.38, G:0.02, T:0.39
Consensus pattern (27 bp):
ATCTCTCTCTACCCTTCAAATTTCACC
Found at i:2714018 original size:26 final size:26
Alignment explanation
Indices: 2713989--2714052 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 26
2713979 GTCGAGTCAC
2713989 ATTATACTCGAGAAAACA-AACTTA-TA
1 ATTATACTCGAGAAAA-AGAA-TTATTA
2714015 ATTATA-T-GAGAAAAAGAATTATTA
1 ATTATACTCGAGAAAAAGAATTATTA
2714039 A-TA-ACTCGAGAAAA
1 ATTATACTCGAGAAAA
2714053 TTTCGTGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
22 1 0.03
23 7 0.21
24 19 0.56
25 1 0.03
26 6 0.18
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (26 bp):
ATTATACTCGAGAAAAAGAATTATTA
Found at i:2715069 original size:20 final size:20
Alignment explanation
Indices: 2715044--2715114 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
2715034 CACGAAATGT
*
2715044 AAGATTATCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
* *
2715064 AAGATTACCATTGAGAATAA
1 AAGATTACCAGTGGGAATAA
2715084 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
2715104 AAGATTACCAG
1 AAGATTACCAG
2715115 GGAATAGGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:2729412 original size:48 final size:48
Alignment explanation
Indices: 2729360--2729462 Score: 179
Period size: 48 Copynumber: 2.1 Consensus size: 48
2729350 TTCGATAATC
*
2729360 TTCAACAGCGGCATCTGCCTCGGGAAACTGATAAGAATTCCTATCATA
1 TTCAACAGCAGCATCTGCCTCGGGAAACTGATAAGAATTCCTATCATA
*
2729408 TTCAACAGCAGCATCTGTCTCGGGAAACTGATAAGAATTCCTATCATA
1 TTCAACAGCAGCATCTGCCTCGGGAAACTGATAAGAATTCCTATCATA
*
2729456 GTCAACA
1 TTCAACA
2729463 ACCGCTGTCT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (48 bp):
TTCAACAGCAGCATCTGCCTCGGGAAACTGATAAGAATTCCTATCATA
Found at i:2729776 original size:2 final size:2
Alignment explanation
Indices: 2729769--2729796 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2729759 CGTAGTGTAC
2729769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2729797 GTTTTATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2733328 original size:153 final size:153
Alignment explanation
Indices: 2733060--2733342 Score: 386
Period size: 153 Copynumber: 1.8 Consensus size: 153
2733050 CATCGGTCTC
**
2733060 TGGAAGATTATCAGAGTTCAGATCATCTTCAACAACAGGATCAACCTCTTGAGAGTTTGAGTTTT
1 TGGAAGATTATCAGAGTTCAGATCATCTTCAACAACAACATCAACCTCTTGAGAGTTTGAGTTTT
* * * * *
2733125 GATCATCCTTCTCTACAGTTGGCTCAAAGATATTTTGAGGAGCATGTTCAAAGTCATGAAAGTTC
66 GATCATCCTTCGCTACAGCTGCCACAAAGATACTTTGAGGAGCATGTTCAAAGTCATGAAAGTTC
2733190 TCTTGACCAAAAGCATCGGCCAT
131 TCTTGACCAAAAGCATCGGCCAT
* * ** *
2733213 TGGAAGGTTATCAGAGTTCCGATCATCTTCGCCAGCAACATCAACCTCTTGAGAGTTTGAGTTTT
1 TGGAAGATTATCAGAGTTCAGATCATCTTCAACAACAACATCAACCTCTTGAGAGTTTGAGTTTT
*** * ** * *
2733278 GATCATCCTTCGCTACAGCTGCCACGGCGATACTTTGAGGGGTTTGTTCAAAGTTATGAGAGTTC
66 GATCATCCTTCGCTACAGCTGCCACAAAGATACTTTGAGGAGCATGTTCAAAGTCATGAAAGTTC
2733343 CCTTCACCGA
Statistics
Matches: 110, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
153 110 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (153 bp):
TGGAAGATTATCAGAGTTCAGATCATCTTCAACAACAACATCAACCTCTTGAGAGTTTGAGTTTT
GATCATCCTTCGCTACAGCTGCCACAAAGATACTTTGAGGAGCATGTTCAAAGTCATGAAAGTTC
TCTTGACCAAAAGCATCGGCCAT
Found at i:2736027 original size:16 final size:16
Alignment explanation
Indices: 2736006--2736049 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
2735996 ACATAAATAG
2736006 TGTCTCGGATTCCCTT
1 TGTCTCGGATTCCCTT
2736022 TGTCTCGGATTCCCTT
1 TGTCTCGGATTCCCTT
2736038 TGTCTCGGATTC
1 TGTCTCGGATTC
2736050 ATCTCGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.07, C:0.30, G:0.20, T:0.43
Consensus pattern (16 bp):
TGTCTCGGATTCCCTT
Found at i:2739227 original size:63 final size:63
Alignment explanation
Indices: 2739128--2739255 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
2739118 ATGAGTTATC
* *
2739128 TGTAAAGATGAGTCAGTCTTCTCAAGGGTCGCCCTTCATGGATGCCAATCAACGGAACCAGGT
1 TGTAAAGATGAGTCAGTCTTCTCAAGGGTCACCCTTCATGGATGCCAATCAAAGGAACCAGGT
2739191 TGTAAAGATGAGTCAGTCTTCTCAAGGGTCACCCTTCATGGATGCCAATCAAAGGAACCAGGT
1 TGTAAAGATGAGTCAGTCTTCTCAAGGGTCACCCTTCATGGATGCCAATCAAAGGAACCAGGT
2739254 TG
1 TG
2739256 ATGATTGCAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (63 bp):
TGTAAAGATGAGTCAGTCTTCTCAAGGGTCACCCTTCATGGATGCCAATCAAAGGAACCAGGT
Found at i:2739409 original size:48 final size:48
Alignment explanation
Indices: 2739322--2739598 Score: 184
Period size: 48 Copynumber: 5.8 Consensus size: 48
2739312 CGGCATCAGG
** * * *
2739322 AAAGTTATCAGAGCTCTGGTCATCTTCAACAAC-GACATCAGTCTTGGA
1 AAAGTTATCAGAATTCTGATAATCTTCAACAACAG-CATCAGACTTGGA
* ** *
2739370 AAAGTTTTCAGAATTCTGATAATCTTCAACAACAGCATCATCCTAAGG-
1 AAAGTTATCAGAATTCTGATAATCTTCAACAACAGCATCAGACT-TGGA
* * * * * **
2739418 AAAGTTATCAGAGTTCTGATCATCTCCAGCAACAGAATCAGAC-TCAA
1 AAAGTTATCAGAATTCTGATAATCTTCAACAACAGCATCAGACTTGGA
* * * * * **
2739465 GAAAGTGATCAGAACTCTGACAATCTTCAACAAAAGCATC-GACCTAAA
1 -AAAGTTATCAGAATTCTGATAATCTTCAACAACAGCATCAGACTTGGA
* * * * * * * * *
2739513 GAAAGTTATCTGAGTTCCGATCATCTTAAACAACAGAATCAGCCTCGGG
1 -AAAGTTATCAGAATTCTGATAATCTTCAACAACAGCATCAGACTTGGA
* *
2739562 AAAGTTATCAAAATCCTGATAATCTTCAACAACAGCA
1 AAAGTTATCAGAATTCTGATAATCTTCAACAACAGCA
2739599 GGCTGTAGTT
Statistics
Matches: 170, Mismatches: 53, Indels: 12
0.72 0.23 0.05
Matches are distributed among these distances:
47 3 0.02
48 162 0.95
49 5 0.03
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (48 bp):
AAAGTTATCAGAATTCTGATAATCTTCAACAACAGCATCAGACTTGGA
Found at i:2739470 original size:96 final size:96
Alignment explanation
Indices: 2739319--2739598 Score: 332
Period size: 96 Copynumber: 2.9 Consensus size: 96
2739309 CAACGGCATC
* * * * *
2739319 AGGAAAGTTATCAGAGCTCTGGTCATCTTCAACAAC-GACATCAGTCT-TGGAAAAGTTTTCAGA
1 AGGAAAGTTATCAGAGTTCTGATCATCTTCAACAACAGA-ATCAGACTCAGG-AAAGTTATCAGA
2739382 ATTCTGATAATCTTCAACAACAGCATC-ATCCTA
64 ATTCTGATAATCTTCAACAACAGCATCGA-CCTA
* * * * *
2739415 AGGAAAGTTATCAGAGTTCTGATCATCTCCAGCAACAGAATCAGACTCAAGAAAGTGATCAGAAC
1 AGGAAAGTTATCAGAGTTCTGATCATCTTCAACAACAGAATCAGACTCAGGAAAGTTATCAGAAT
* *
2739480 TCTGACAATCTTCAACAAAAGCATCGACCTA
66 TCTGATAATCTTCAACAACAGCATCGACCTA
* * * * * * *
2739511 AAGAAAGTTATCTGAGTTCCGATCATCTTAAACAACAGAATCAGCCTCGGGAAAGTTATCAAAAT
1 AGGAAAGTTATCAGAGTTCTGATCATCTTCAACAACAGAATCAGACTCAGGAAAGTTATCAGAAT
*
2739576 CCTGATAATCTTCAACAACAGCA
66 TCTGATAATCTTCAACAACAGCA
2739599 GGCTGTAGTT
Statistics
Matches: 154, Mismatches: 27, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
96 150 0.97
97 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (96 bp):
AGGAAAGTTATCAGAGTTCTGATCATCTTCAACAACAGAATCAGACTCAGGAAAGTTATCAGAAT
TCTGATAATCTTCAACAACAGCATCGACCTA
Found at i:2740618 original size:20 final size:20
Alignment explanation
Indices: 2740565--2740618 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
2740555 ACCAACAAAT
* * **
2740565 TCGCAACGCGAACTCTAATT
1 TCGCAACGCAAATTCTAAAA
*
2740585 TCGCAACACAAATTCTAAAA
1 TCGCAACGCAAATTCTAAAA
*
2740605 TCGCAACGCTAATT
1 TCGCAACGCAAATT
2740619 ACCGATATAG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (20 bp):
TCGCAACGCAAATTCTAAAA
Found at i:2740673 original size:57 final size:57
Alignment explanation
Indices: 2740605--2740755 Score: 284
Period size: 57 Copynumber: 2.6 Consensus size: 57
2740595 AATTCTAAAA
*
2740605 TCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAATGCGATTTTCAAAT
1 TCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTTCAAAT
2740662 TCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTTCAAAT
1 TCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTTCAAAT
*
2740719 TCGCAACGCTAATTACCGATATAGGTAAACATTACTA
1 TCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
2740756 AAATCCGCGT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 92 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (57 bp):
TCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTTCAAAT
Found at i:2740846 original size:19 final size:19
Alignment explanation
Indices: 2740804--2740852 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
2740794 TGGAAACTGT
* *
2740804 GTTGCGAAATTGGAGTTCGA
1 GTTGCG-AATTCGAGATCGA
*
2740824 GTTGCGAATTCGAGATCGC
1 GTTGCGAATTCGAGATCGA
*
2740843 GTTGCAAATT
1 GTTGCGAATT
2740853 TGTTGTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (19 bp):
GTTGCGAATTCGAGATCGA
Found at i:2747609 original size:20 final size:20
Alignment explanation
Indices: 2747572--2747609 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2747562 TCTCAGTCAT
*
2747572 TCCTTCCTCCAAGGTCTGTA
1 TCCTTCCTCCAAGCTCTGTA
2747592 TCCTTCCCTCC-AGCTCTG
1 TCCTT-CCTCCAAGCTCTG
2747610 CTTTCTGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.11, C:0.42, G:0.13, T:0.34
Consensus pattern (20 bp):
TCCTTCCTCCAAGCTCTGTA
Found at i:2749798 original size:66 final size:66
Alignment explanation
Indices: 2749690--2749822 Score: 185
Period size: 66 Copynumber: 2.0 Consensus size: 66
2749680 ACCAGCAAAT
* * * *
2749690 TAATACAATAAGAATCAAAGAATTACATTTTGTGGTTAATCGATAATATAAATGATAATAATGTA
1 TAATACAATAAAAATCAAAGAATTACATTTTATGATTAATCGATAATATAAATGATAATAATATA
2749755 G
66 G
* * * * *
2749756 TAATATAATAAAAATCAATGAATTACATTTTATGATTTATCGATAATATAAATTATCATAATATA
1 TAATACAATAAAAATCAAAGAATTACATTTTATGATTAATCGATAATATAAATGATAATAATATA
2749821 G
66 G
2749822 T
1 T
2749823 TTTAAAAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (66 bp):
TAATACAATAAAAATCAAAGAATTACATTTTATGATTAATCGATAATATAAATGATAATAATATA
G
Found at i:2752023 original size:18 final size:19
Alignment explanation
Indices: 2751988--2752023 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2751978 AATCAATATC
*
2751988 AAATAACTAAAATATAATA
1 AAATAACAAAAATATAATA
2752007 AAATAACAAAAAT-TAAT
1 AAATAACAAAAATATAAT
2752024 TCAACGTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (19 bp):
AAATAACAAAAATATAATA
Found at i:2768392 original size:24 final size:24
Alignment explanation
Indices: 2768343--2768417 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 24
2768333 TTTCATTTGA
*
2768343 ATATTATATATATAATTATTATTATT
1 ATATTATA-AT-TAATAATTATTATT
2768369 ATAATTATAATT-ATAATTATTATT
1 AT-ATTATAATTAATAATTATTATT
* * *
2768393 ATTTTATTATTAATAAATATTATT
1 ATATTATAATTAATAATTATTATT
2768417 A
1 A
2768418 CATATTACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
23 7 0.16
24 25 0.58
25 1 0.02
26 4 0.09
27 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATATTATAATTAATAATTATTATT
Found at i:2768406 original size:21 final size:22
Alignment explanation
Indices: 2768344--2768417 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
2768334 TTCATTTGAA
2768344 TATTA-TATATATAATTATT-AT
1 TATTATTAT-TATAATTATTAAT
*
2768365 TATTATAATTATAATTA-TAAT
1 TATTATTATTATAATTATTAAT
*
2768386 TATTATTATT-TTATTATTAAT
1 TATTATTATTATAATTATTAAT
* *
2768407 AAATATTATTA
1 TATTATTATTA
2768418 CATATTACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 6 0.14
21 36 0.82
22 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTATTATTATAATTATTAAT
Found at i:2768417 original size:3 final size:3
Alignment explanation
Indices: 2768344--2768404 Score: 63
Period size: 3 Copynumber: 20.7 Consensus size: 3
2768334 TTCATTTGAA
* * * *
2768344 TAT TA- TAT ATAT AAT TAT TAT TAT TAT AAT TAT AAT TAT AAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2768389 TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TA
2768405 ATAAATATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 4 0.09
3 40 0.85
4 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:2770082 original size:22 final size:22
Alignment explanation
Indices: 2770043--2770085 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
2770033 CATTTTCTGA
2770043 TATTTTTAAATAAATATATATCC
1 TATTTTT-AATAAATATATATCC
2770066 TATTTTT-ATAAATTATATAT
1 TATTTTTAATAAA-TATATAT
2770086 TAATCTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTTAATAAATATATATCC
Found at i:2771365 original size:100 final size:100
Alignment explanation
Indices: 2771158--2771365 Score: 224
Period size: 101 Copynumber: 2.1 Consensus size: 100
2771148 TAAATTTAGT
* * * *
2771158 ATTTCAATTTTAGGAGGCGTTAGATATTTGAGCAAAGTTAATGTTTAAATTCTGAAATTGTAAAC
1 ATTTCTATTTTAGGAGGCGTTAGATATTTGAACAAAGTTAAAGTTTAAATTCTGAAATTATAAAC
* *
2771223 AGAGTAAATTAGATCGAGATAGTTGTCTTTAATAA
66 AGAGTAAATTAGATCAAGATAGTTGTCCTTAATAA
** * * * * *
2771258 ACCTCTATTTTAGGAGGTGTTAGATTTTTTAACAAAGTTAAAAGTTTGAATTCTTG-CATTATAA
1 ATTTCTATTTTAGGAGGCGTTAGATATTTGAACAAAGTT-AAAGTTTAAATTC-TGAAATTATAA
* *
2771322 A-TGAAGTAAATTAGATCAAGATGGTTGTCCTT-ATAA
64 ACAG-AGTAAATTAGATCAAGATAGTTGTCCTTAATAA
*
2771358 TTTTCTAT
1 ATTTCTAT
2771366 AATATTTTAT
Statistics
Matches: 87, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
100 42 0.48
101 43 0.49
102 2 0.02
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.39
Consensus pattern (100 bp):
ATTTCTATTTTAGGAGGCGTTAGATATTTGAACAAAGTTAAAGTTTAAATTCTGAAATTATAAAC
AGAGTAAATTAGATCAAGATAGTTGTCCTTAATAA
Found at i:2774326 original size:5 final size:5
Alignment explanation
Indices: 2774316--2774346 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
2774306 ATATATTTAT
2774316 TAATA TAATA TAATA TAATA TAATAA TAATA
1 TAATA TAATA TAATA TAATA TAAT-A TAATA
2774347 ATATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAATA
Found at i:2774392 original size:26 final size:24
Alignment explanation
Indices: 2774329--2774409 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 24
2774319 TATAATATAA
*
2774329 TATAATATAATAATAATA-A-TAT
1 TATATTATAATAATAATATACTAT
* *
2774351 TATTATTATTACAATAATATACTCAAT
1 TA-TATTATAATAATAATATACT--AT
2774378 TATATTATAATAATATATGATACTAT
1 TATATTATAATAATA-AT-ATACTAT
2774404 TATATT
1 TATATT
2774410 CTTATTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
22 2 0.04
23 13 0.28
24 1 0.02
25 1 0.02
26 19 0.40
27 6 0.13
28 5 0.11
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (24 bp):
TATATTATAATAATAATATACTAT
Found at i:2774762 original size:23 final size:22
Alignment explanation
Indices: 2774735--2774797 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
2774725 ATAAATAGTA
2774735 TTAAATAAATTATT-TTAATGTTT
1 TTAAATAAA-TATTATTAA-GTTT
2774758 TTAAA-ATAATATTATTAAGTTT
1 TTAAATA-AATATTATTAAGTTT
* *
2774780 TTATAATAAGTAATATTA
1 TTA-AATAAATATTATTA
2774798 TTTATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 12 0.35
23 21 0.62
24 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TTAAATAAATATTATTAAGTTT
Found at i:2774779 original size:22 final size:24
Alignment explanation
Indices: 2774745--2774797 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
2774735 TTAAATAAAT
2774745 TATT-TTAATGTTTTTAAAATAA-
1 TATTATTAATGTTTTTAAAATAAG
*
2774767 TATTATTAA-GTTTTTATAATAAG
1 TATTATTAATGTTTTTAAAATAAG
*
2774790 TAATATTA
1 TATTATTA
2774798 TTTATTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (24 bp):
TATTATTAATGTTTTTAAAATAAG
Found at i:2775421 original size:23 final size:23
Alignment explanation
Indices: 2775386--2775436 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
2775376 TTTTTCGTAT
*
2775386 GTGTTTCGTATACCTCTACGGTC
1 GTGTTTCGAATACCTCTACGGTC
*
2775409 TTGTTTCGAATACCTCTACGGTC
1 GTGTTTCGAATACCTCTACGGTC
2775432 GTGTT
1 GTGTT
2775437 AATGCTCGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.41
Consensus pattern (23 bp):
GTGTTTCGAATACCTCTACGGTC
Found at i:2775930 original size:20 final size:20
Alignment explanation
Indices: 2775893--2775930 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2775883 ATAAATTTAT
* *
2775893 ATTTGATAAGTTATGATTCG
1 ATTTGATAAGATAAGATTCG
2775913 ATTTGATAAGATAAGATT
1 ATTTGATAAGATAAGATT
2775931 TTTTAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTTGATAAGATAAGATTCG
Found at i:2779891 original size:16 final size:16
Alignment explanation
Indices: 2779870--2779903 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2779860 AAGAGATCAC
2779870 TGGATTTACTATAGGT
1 TGGATTTACTATAGGT
2779886 TGGATTTACTATAGGT
1 TGGATTTACTATAGGT
2779902 TG
1 TG
2779904 CCTTCCAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (16 bp):
TGGATTTACTATAGGT
Found at i:2783260 original size:8 final size:9
Alignment explanation
Indices: 2783249--2783283 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
2783239 TTTATTAATC
2783249 TATTATA-A
1 TATTATATA
2783257 TATTATATA
1 TATTATATA
2783266 TATATATATA
1 TAT-TATATA
2783276 TATTATAT
1 TATTATAT
2783284 TTTCATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 7 0.28
9 9 0.36
10 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TATTATATA
Found at i:2783765 original size:23 final size:22
Alignment explanation
Indices: 2783729--2783793 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
2783719 AATATTGTAT
* *
2783729 TTTAATTAAATTATATTTAGATT
1 TTTAA-TAATTTATATTTAGATG
* * *
2783752 TTTAACTAGTTTATAATTATATG
1 TTTAA-TAATTTATATTTAGATG
2783775 TTTAATAATTTATAATTTA
1 TTTAATAATTTAT-ATTTA
2783794 ACATTTTATA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
22 7 0.21
23 26 0.79
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTAATAATTTATATTTAGATG
Found at i:2785586 original size:96 final size:97
Alignment explanation
Indices: 2785360--2785660 Score: 370
Period size: 96 Copynumber: 3.0 Consensus size: 97
2785350 CTGTTTGTGC
* * *
2785360 AAGTGTAGAAGCCCAGGTACGTTTCAATCATGTATATAGTAAGGATTAGGAATGGACATAGGATT
1 AAGTGTAGAAGCCCAGGTACGTTTCAATCATGTACATAGTAAGGATTAGGGATGGACATGGGATT
* *
2785425 CAAAGTACCATATATTTCAATTACATCATAGTTATA
66 -AAAGTACC--A-ATTTCAATTCCATCATATTTATA
* * * *
2785461 AAGTGTAGAAGCCCAAGTGCATTTCAATCATGTACATAGTAAGGATTAGGGACGGACATGGGATT
1 AAGTGTAGAAGCCCAGGTACGTTTCAATCATGTACATAGTAAGGATTAGGGATGGACATGGGATT
* *
2785526 AAAGCACC-ACTTCAATTCCATCATATTTATA
66 AAAGTACCAATTTCAATTCCATCATATTTATA
* * * * * *
2785557 AAGTGTAGAAGTCCGGGTACGTTTCAATCATGTACATAGTAAAGATCAGGGATAGACATGAGATT
1 AAGTGTAGAAGCCCAGGTACGTTTCAATCATGTACATAGTAAGGATTAGGGATGGACATGGGATT
*
2785622 CAAGTACCTCAGATTTCAATTCCATCATATTTATA
66 AAAGTA-C-CA-ATTTCAATTCCATCATATTTATA
2785657 AAGT
1 AAGT
2785661 TTTTTTTCTT
Statistics
Matches: 172, Mismatches: 24, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
96 79 0.46
97 1 0.01
98 1 0.01
100 33 0.19
101 58 0.34
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (97 bp):
AAGTGTAGAAGCCCAGGTACGTTTCAATCATGTACATAGTAAGGATTAGGGATGGACATGGGATT
AAAGTACCAATTTCAATTCCATCATATTTATA
Found at i:2791730 original size:24 final size:24
Alignment explanation
Indices: 2791702--2791757 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
2791692 AAATATATAT
*
2791702 TTAAAAAATCCATTTTTTCAAATC
1 TTAAAAAAGCCATTTTTTCAAATC
* *
2791726 TTAAAAAGGCTATTTTTTCAAATC
1 TTAAAAAAGCCATTTTTTCAAATC
2791750 TTAAAAAA
1 TTAAAAAA
2791758 AGCTCAGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (24 bp):
TTAAAAAAGCCATTTTTTCAAATC
Found at i:2793238 original size:69 final size:69
Alignment explanation
Indices: 2793127--2793261 Score: 216
Period size: 69 Copynumber: 2.0 Consensus size: 69
2793117 GCCCCAAAAC
* *
2793127 GCCAAAACCTCATTAACGCACACACATCCCTCTCGACATACATACATACATACATATATATATAT
1 GCCAAAACCGCATTAACGCACACACATCCCTCTCGACATACATACATACATACATATATAAATAT
2793192 ATAA
66 ATAA
* * * *
2793196 GCCAAAGCCGCATTAATGCACACACATCTCTCTCTACATACATACATACATACATATATAAATAT
1 GCCAAAACCGCATTAACGCACACACATCCCTCTCGACATACATACATACATACATATATAAATAT
2793261 A
66 A
2793262 CGTTTATCTA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.41, C:0.28, G:0.05, T:0.25
Consensus pattern (69 bp):
GCCAAAACCGCATTAACGCACACACATCCCTCTCGACATACATACATACATACATATATAAATAT
ATAA
Found at i:2812471 original size:22 final size:22
Alignment explanation
Indices: 2812453--2812499 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2812443 ATAATTTTTG
*
2812453 ATAAGTTTAATGTTTATTTTATA
1 ATAA-TTTAATGATTATTTTATA
*
2812476 ATAATTTAATGATTATTTTGTA
1 ATAATTTAATGATTATTTTATA
2812498 AT
1 AT
2812500 TGTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (22 bp):
ATAATTTAATGATTATTTTATA
Found at i:2813042 original size:21 final size:21
Alignment explanation
Indices: 2813016--2813061 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2813006 TAATAGAGCT
* * *
2813016 CAATAGTGCCTGCAACGGCCG
1 CAATAGCGCCCGCAACGGCCA
*
2813037 CAATAGCGCCCGCGACGGCCA
1 CAATAGCGCCCGCAACGGCCA
2813058 CAAT
1 CAAT
2813062 CACGGTAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (21 bp):
CAATAGCGCCCGCAACGGCCA
Found at i:2814352 original size:33 final size:33
Alignment explanation
Indices: 2814315--2814380 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
2814305 CAAAGAATAA
2814315 ACCAAAAATTTTTCCTGCATATCTCTCTCACTT
1 ACCAAAAATTTTTCCTGCATATCTCTCTCACTT
* *
2814348 ACCAAAATTTTTTCCTGCATATCTTTCTCACTT
1 ACCAAAAATTTTTCCTGCATATCTCTCTCACTT
2814381 CCTCTTTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.42
Consensus pattern (33 bp):
ACCAAAAATTTTTCCTGCATATCTCTCTCACTT
Found at i:2818606 original size:23 final size:23
Alignment explanation
Indices: 2818562--2818606 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2818552 AAAAGTAGAA
*
2818562 GAAAACGTATCATAAAGGCAGAG
1 GAAAACGTATCATAAAGACAGAG
*
2818585 GAAAACGTGTCATACAA-ACAGA
1 GAAAACGTATCATA-AAGACAGA
2818607 CTTATTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.13
Consensus pattern (23 bp):
GAAAACGTATCATAAAGACAGAG
Found at i:2820595 original size:2 final size:2
Alignment explanation
Indices: 2820588--2820626 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2820578 AGAAGTGATT
2820588 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2820627 TAAGTGTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2823664 original size:2 final size:2
Alignment explanation
Indices: 2823657--2823690 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2823647 GGAGACTGTA
2823657 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2823691 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2823695 original size:2 final size:2
Alignment explanation
Indices: 2823690--2823716 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2823680 TCTCTCTCTC
2823690 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2823717 GGAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2846595 original size:2 final size:2
Alignment explanation
Indices: 2846588--2846612 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2846578 AAATCGTTCT
2846588 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2846613 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2856043 original size:19 final size:21
Alignment explanation
Indices: 2856014--2856054 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2856004 CACACGACTG
*
2856014 AAATCATACCA-AAAGACAAA
1 AAATCATACCATAAAAACAAA
2856034 AAAT-ATACCATAAAAACAAA
1 AAATCATACCATAAAAACAAA
2856054 A
1 A
2856055 TAAAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.68, C:0.17, G:0.02, T:0.12
Consensus pattern (21 bp):
AAATCATACCATAAAAACAAA
Found at i:2861891 original size:18 final size:17
Alignment explanation
Indices: 2861871--2861911 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
2861861 TCCTTAAAAT
*
2861871 AAATAAATAAATATTAATA
1 AAAT-AATAAA-AATAATA
2861890 AAATAATAAAAATAATA
1 AAATAATAAAAATAATA
2861907 AAATA
1 AAATA
2861912 TTAGATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.52
18 6 0.29
19 4 0.19
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAATAAAAATAATA
Found at i:2862186 original size:2 final size:2
Alignment explanation
Indices: 2862179--2862224 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2862169 AATTAAACAA
2862179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2862221 AT AT
1 AT AT
2862225 GACTAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2863637 original size:3 final size:3
Alignment explanation
Indices: 2863629--2863682 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
2863619 ATTTTATTTA
2863629 AAT AAT AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2863675 AA- AAT AAT
1 AAT AAT AAT
2863683 TTTAATGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2864049 original size:76 final size:76
Alignment explanation
Indices: 2863846--2864563 Score: 1186
Period size: 76 Copynumber: 9.4 Consensus size: 76
2863836 AGGTCCTAAA
* * * * *
2863846 AAACATCATGCACTGAATGG-CTTAAAGATGGCCCTAAGGTTTTGAAAACATAAAAAAGCTCCCG
1 AAACATCATGCACTGCA-GGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
2863910 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* * * *
2863922 AAACAACATCATGCACTGTAGGACTTACAGATGGCCCTAAGGTTTTAAAAACATCAAAAAGCTCC
1 --A-AACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCC
2863987 CGAAGGCTTTTTGG
63 CGAAGGCTTTTTGG
*
2864001 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2864066 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2864077 AAACATCATGCACTACAGGAATTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
2864142 AGGCTTTTTAG
66 AGGCTTTTTGG
* * *
2864153 AAACATCATGCACTGCATGACTTACAGATGACCCTAAGGCTTTGGAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2864218 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2864229 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGGAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2864294 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2864305 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2864370 AGGCTTTTTTGG
66 AGGC-TTTTTGG
2864382 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2864447 AGGCTTTTTGG
66 AGGCTTTTTGG
* **
2864458 AAACATCATGCACTGTACAACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2864523 AGGCTTTTTGG
66 AGGCTTTTTGG
2864534 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
2864564 TGGGAAATAG
Statistics
Matches: 607, Mismatches: 30, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
76 461 0.76
77 75 0.12
78 3 0.00
79 68 0.11
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:2865295 original size:22 final size:22
Alignment explanation
Indices: 2865243--2865296 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
2865233 AAAGTTTTCC
* *
2865243 TCTTTGAAAAGAGAATCTATTA
1 TCTTTGAAGAGAGAATCTATCA
*
2865265 TCTTTGAAGAGATAATCTATCA
1 TCTTTGAAGAGAGAATCTATCA
2865287 TCTTTGAAGA
1 TCTTTGAAGA
2865297 ATGTAGATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (22 bp):
TCTTTGAAGAGAGAATCTATCA
Found at i:2869773 original size:9 final size:9
Alignment explanation
Indices: 2869756--2869800 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
2869746 CTTGATTCAA
*
2869756 TTTTCCTTT
1 TTTTTCTTT
2869765 TTTTTCTTT
1 TTTTTCTTT
2869774 TTTTTC--T
1 TTTTTCTTT
2869781 TTTTTC--T
1 TTTTTCTTT
2869788 TTTTTCTTT
1 TTTTTCTTT
2869797 TTTT
1 TTTT
2869801 CCCTTTTCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
7 14 0.42
9 19 0.58
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:2869774 original size:7 final size:7
Alignment explanation
Indices: 2869773--2869799 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2869763 TTTTTTTCTT
2869773 TTTTTTC
1 TTTTTTC
2869780 TTTTTTC
1 TTTTTTC
2869787 TTTTTTC
1 TTTTTTC
2869794 TTTTTT
1 TTTTTT
2869800 TCCCTTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:2869807 original size:23 final size:23
Alignment explanation
Indices: 2869764--2869813 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
2869754 AATTTTCCTT
* * *
2869764 TTTTTTCTTTTTTTTCTTTTTTC
1 TTTTTTCTTTTTTTCCCTTTTCC
2869787 TTTTTTCTTTTTTTCCCTTTTCC
1 TTTTTTCTTTTTTTCCCTTTTCC
2869810 TTTT
1 TTTT
2869814 CCTTTTCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTTCTTTTTTTCCCTTTTCC
Found at i:2869829 original size:8 final size:8
Alignment explanation
Indices: 2869764--2869831 Score: 58
Period size: 8 Copynumber: 9.2 Consensus size: 8
2869754 AATTTTCCTT
*
2869764 TTTTTTCT
1 TTTTTTCC
*
2869772 TTTTTTTC
1 TTTTTTCC
2869780 TTTTTT-C
1 TTTTTTCC
*
2869787 TTTTTTCT
1 TTTTTTCC
2869795 TTTTTTCC
1 TTTTTTCC
*
2869803 -CTTTTCC
1 TTTTTTCC
2869810 --TTTTCC
1 TTTTTTCC
2869816 --TTTTCC
1 TTTTTTCC
2869822 TTTTTTCC
1 TTTTTTCC
2869830 TT
1 TT
2869832 CTTCTTTCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
6 12 0.23
7 13 0.25
8 27 0.52
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCC
Found at i:2869838 original size:14 final size:13
Alignment explanation
Indices: 2869756--2869838 Score: 62
Period size: 14 Copynumber: 6.1 Consensus size: 13
2869746 CTTGATTCAA
2869756 TTTTCCTTTT-TT
1 TTTTCCTTTTCTT
**
2869768 TTCTTTTTTTTCTT
1 TT-TTCCTTTTCTT
*
2869782 TTTTCTTTTTTCTTT
1 TTTTC-CTTTTC-TT
*
2869797 TTTTCCCTTTTC-C
1 TTTT-CCTTTTCTT
2869810 TTTTCCTTTTCCTT
1 TTTTCCTTTT-CTT
2869824 TTTTCCTTCTTCTT
1 TTTTCCTT-TTCTT
2869838 T
1 T
2869839 CTTTGCTGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
12 8 0.14
13 13 0.23
14 22 0.39
15 13 0.23
16 1 0.02
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCCTTTTCTT
Found at i:2875316 original size:2 final size:2
Alignment explanation
Indices: 2875298--2875339 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
2875288 TTTAAAGAAA
*
2875298 AT AT AT -T A- AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2875338 AT
1 AT
2875340 TCTTAACATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2876304 original size:3 final size:3
Alignment explanation
Indices: 2876296--2876352 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
2876286 ATTTTATTTA
* *
2876296 AAT AAT AAT ATAT AAT ATT AAT ATT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2876342 AAT AA- AAT AAT
1 AAT AAT AAT AAT
2876353 TTTAATGAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:2876698 original size:60 final size:59
Alignment explanation
Indices: 2876553--2876698 Score: 163
Period size: 60 Copynumber: 2.5 Consensus size: 59
2876543 AATATTGGGT
* * *
2876553 AAAG-TACACAAATAGTCTCTCAACTATAGGGCATTACTTTGTGAGTCCCTCGACTATTA
1 AAAGTTACA-AAATGGTCACTCAACTATAGGGCATTACTTTGTGAGTCACTCGACTATTA
* * * * *
2876612 AAAGTTACAAAATGATCCCTCGACTATAGGATGC-TT-CTTTGTTGAGTCATTCGGCTATTA
1 AAAGTTACAAAATGGTCACTCAACTATAGG--GCATTACTTTG-TGAGTCACTCGACTATTA
2876672 AAAGTTACAAAATGGTCACTCAACTAT
1 AAAGTTACAAAATGGTCACTCAACTAT
2876699 CATATGTTCC
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
59 26 0.36
60 45 0.62
61 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCACTCAACTATAGGGCATTACTTTGTGAGTCACTCGACTATTA
Found at i:2885423 original size:24 final size:24
Alignment explanation
Indices: 2885395--2885469 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
2885385 TCAACTCTAA
*
2885395 ACTCCGATAAGACAGTCCTTGACT
1 ACTCCGATAACACAGTCCTTGACT
2885419 ACTCCGATAACACAGTCCTTGACT
1 ACTCCGATAACACAGTCCTTGACT
*
2885443 ACTCCGATAACACAGTCCTTGATT
1 ACTCCGATAACACAGTCCTTGACT
2885467 ACT
1 ACT
2885470 TTTTCTCCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (24 bp):
ACTCCGATAACACAGTCCTTGACT
Found at i:2905573 original size:190 final size:189
Alignment explanation
Indices: 2905243--2905669 Score: 678
Period size: 190 Copynumber: 2.3 Consensus size: 189
2905233 ATGTTAGTCT
* * ** * * **
2905243 TTTCTCGAACTCTATTTGTCAATGGCTATCATGGCGGGCATTGTTTATTCAAGGATGTCCAGGCA
1 TTTCTCAAACTCTATTTGCCGTTGGCTATCATGACAGGCATTGTTTATTCAAGGACATCCAGGCA
*
2905308 TGAGTTAGATCAACATGTTTATAGTTACAGGACGGGAACCTGTTTCGATACTTTCCTTTTCCTTT
66 TGAGTTAGATCAACATGTTTATAGTTACAGGACAGGAACCTGTTTCGATACTTTCCTTTTCCTTT
2905373 ATGGACTAGGTATTAGAGTTTTCGGTATGTGCATCTTGAAAAGCTAAGCAAGGAGTCTCC
131 ATGGACTAGGTATTAGAGTTTTCGGTATGTGCAT-TTGAAAAGCTAAGCAAGGAGTCTCC
*
2905433 TTTCTCAAACTCTATTTGCCGTTGGCTATCATGACAGGCATTGTTTATTCAAGGGCATCCAGGCA
1 TTTCTCAAACTCTATTTGCCGTTGGCTATCATGACAGGCATTGTTTATTCAAGGACATCCAGGCA
* *
2905498 TGAGTTAGATCGACATGTTTATAGTTATTAGGACAGGAACCTGTTTCGATACTTTCCTTTT-CTT
66 TGAGTTAGATCAACATGTTTATAGTTA-CAGGACAGGAACCTGTTTCGATACTTTCCTTTTCCTT
*
2905562 TATGGACTAGGTATTAGAGTTTTCGGTATGTGCATTTGAAATGCTAAGCAAGGAGTCTCC
130 TATGGACTAGGTATTAGAGTTTTCGGTATGTGCATTTGAAAAGCTAAGCAAGGAGTCTCC
* **
2905622 TTTCTCAAACTCTATTTACCGTCAGCTATCATGACAGGCATT-TTTATT
1 TTTCTCAAACTCTATTTGCCGTTGGCTATCATGACAGGCATTGTTTATT
2905670 ATGACAGGAA
Statistics
Matches: 220, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
188 6 0.03
189 63 0.29
190 120 0.55
191 31 0.14
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (189 bp):
TTTCTCAAACTCTATTTGCCGTTGGCTATCATGACAGGCATTGTTTATTCAAGGACATCCAGGCA
TGAGTTAGATCAACATGTTTATAGTTACAGGACAGGAACCTGTTTCGATACTTTCCTTTTCCTTT
ATGGACTAGGTATTAGAGTTTTCGGTATGTGCATTTGAAAAGCTAAGCAAGGAGTCTCC
Found at i:2914723 original size:19 final size:20
Alignment explanation
Indices: 2914699--2914749 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2914689 AATGACCAAT
2914699 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
2914718 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
2914738 AAAATCGCAACG
1 AAAATCGCAACG
2914750 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:2914743 original size:20 final size:20
Alignment explanation
Indices: 2914699--2915036 Score: 214
Period size: 20 Copynumber: 16.6 Consensus size: 20
2914689 AATGACCAAT
* *
2914699 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
2914718 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
2914738 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
** *
2914758 AAAATCGCAACG-G-TCAAAAA
1 AAAATCGCAACGCGAT--TTAG
* **
2914778 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
2914799 AAGTTCGCAACGCGATTTAAAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2914822 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
2914842 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
2914862 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* *
2914882 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
2914902 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2914925 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
2914945 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
2914965 AGAATCGCAACGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
2914985 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
2915005 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
2915025 AAAATCGCAACG
1 AAAATCGCAACG
2915037 GTCAAAAGAA
Statistics
Matches: 265, Mismatches: 42, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
19 17 0.06
20 205 0.77
21 14 0.05
23 29 0.11
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:2914875 original size:40 final size:40
Alignment explanation
Indices: 2914824--2915034 Score: 242
Period size: 40 Copynumber: 5.2 Consensus size: 40
2914814 TTTAAAAGAA
* * *
2914824 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAG
* *
2914864 AATCGCAATGCGATTTATAGAATCGCAACGCGATTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAG
* * * * *
2914904 AGTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGA-TT-G-AGAGAATCGCAACGCGATTGAGAG
* *
2914947 AATCGCAATGCGACTGAGAGAATCGCAACGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAG
* * * * *
2914987 AATCGCAACGCGATTTAGAAAATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAG
2915027 AATCGCAA
1 AATCGCAA
2915035 CGGTCAAAAG
Statistics
Matches: 146, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
40 111 0.76
41 3 0.02
42 1 0.01
43 31 0.21
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAG
Found at i:2914931 original size:83 final size:80
Alignment explanation
Indices: 2914824--2915034 Score: 269
Period size: 83 Copynumber: 2.6 Consensus size: 80
2914814 TTTAAAAGAA
* * * * * * * *
2914824 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATCG
1 AATCGCAACGCGATTTAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAATCG
*
2914889 CAACGCGATTGAGAG
66 CAACGCGACTGAGAG
* *
2914904 AGTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAA
1 AATCGCAACGCGATTT---AGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAA
2914969 TCGCAACGCGACTGAGAG
63 TCGCAACGCGACTGAGAG
* * *
2914987 AATCGCAACGCGATTTAGAAAATCGCAACGCGATTTAGAAAATCGCAA
1 AATCGCAACGCGATTTAGAAAATCGCAATGCGATTGAGAGAATCGCAA
2915035 CGGTCAAAAG
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
80 41 0.37
83 71 0.63
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (80 bp):
AATCGCAACGCGATTTAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAATCG
CAACGCGACTGAGAG
Found at i:2914949 original size:103 final size:103
Alignment explanation
Indices: 2914803--2915026 Score: 340
Period size: 103 Copynumber: 2.2 Consensus size: 103
2914793 GCTTCCAAGT
* * * * *
2914803 TCGCAACGCGATTTAAAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
* * * * * *
2914868 GCAATGCGATTTATAGAATCGCAACGCGATTGAGAGAG
66 GCAACGCGACTGAGAGAATCGCAACGCGATTGAGAAAA
2914906 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
*
2914971 GCAACGCGACTGAGAGAATCGCAACGCGATTTAGAAAA
66 GCAACGCGACTGAGAGAATCGCAACGCGATTGAGAAAA
2915009 TCGCAACGCGATTTAGAA
1 TCGCAACGCGATTTAGAA
2915027 AATCGCAACG
Statistics
Matches: 109, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (103 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAACGCGACTGAGAGAATCGCAACGCGATTGAGAAAA
Found at i:2915135 original size:6 final size:6
Alignment explanation
Indices: 2915124--2915185 Score: 117
Period size: 6 Copynumber: 10.5 Consensus size: 6
2915114 GACACGTATT
2915124 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2915172 ACCACG ACC-CG ACC
1 ACCACG ACCACG ACC
2915186 CGAGACGAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.09
6 51 0.91
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2915909 original size:6 final size:6
Alignment explanation
Indices: 2915873--2915939 Score: 99
Period size: 6 Copynumber: 12.0 Consensus size: 6
2915863 TCTCGTCTCG
2915873 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2915916 GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT
2915940 ACGTGTCTTC
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 25 0.41
6 36 0.59
ACGTcount: A:0.00, C:0.18, G:0.54, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:2916096 original size:20 final size:20
Alignment explanation
Indices: 2916046--2916113 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
2916036 ATTTTCGACG
* * *
2916046 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAGTCGCA
2916066 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAGTCGCA
*
2916086 TTGCGATTCTCTCAGTCGCG
1 TTGCGATTCTCTCAGTCGCA
2916106 TTGCGATT
1 TTGCGATT
2916114 TTCTTTTGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTCTCAGTCGCA
Found at i:2916127 original size:20 final size:20
Alignment explanation
Indices: 2916104--2916157 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
2916094 CTCTCAGTCG
* *
2916104 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTCAA
*
2916124 CGTTGCGATTTTATTTTCAA
1 CGTTGCGATTTTCTTTTCAA
2916144 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
2916158 AAATCGCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.50
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTCAA
Found at i:2916167 original size:20 final size:20
Alignment explanation
Indices: 2916144--2916318 Score: 113
Period size: 20 Copynumber: 8.6 Consensus size: 20
2916134 TTATTTTCAA
2916144 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
2916164 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
2916184 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
2916207 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
2916228 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
2916246 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
2916268 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
2916288 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
2916307 CGTTGCGATTTT
1 CGTTGCGATTTT
2916319 ATTGGTCATT
Statistics
Matches: 119, Mismatches: 28, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
18 2 0.02
19 17 0.14
20 69 0.58
21 13 0.11
22 4 0.03
23 14 0.12
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:2916187 original size:100 final size:100
Alignment explanation
Indices: 2916014--2916193 Score: 324
Period size: 100 Copynumber: 1.8 Consensus size: 100
2916004 TTTTTAACTA
*
2916014 TTCTTTTGACCGTTGCGATTTTATTTTCGACGTTGCGATTCTATAAATCGCATTGCGATTCTCTC
1 TTCTTTTGACCGTTGCGATTTTATTTTCAACGTTGCGATTCTATAAATCGCATTGCGATTCTCTC
2916079 AGTCGCATTGCGATTCTCTCAGTCGCGTTGCGATT
66 AGTCGCATTGCGATTCTCTCAGTCGCGTTGCGATT
* * *
2916114 TTCTTTTGACCGTTGCGATTTTATTTTCAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTC
1 TTCTTTTGACCGTTGCGATTTTATTTTCAACGTTGCGATTCTATAAATCGCATTGCGATTCTCTC
2916179 AGTCGCATTGCGATT
66 AGTCGCATTGCGATT
2916194 TTCTTCTAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 76 1.00
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.42
Consensus pattern (100 bp):
TTCTTTTGACCGTTGCGATTTTATTTTCAACGTTGCGATTCTATAAATCGCATTGCGATTCTCTC
AGTCGCATTGCGATTCTCTCAGTCGCGTTGCGATT
Found at i:2916308 original size:19 final size:20
Alignment explanation
Indices: 2916268--2916318 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2916258 TTCTTTTTAA
*
2916268 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
2916288 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
2916307 CGTTGCGATTTT
1 CGTTGCGATTTT
2916319 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:2916868 original size:26 final size:26
Alignment explanation
Indices: 2916819--2916868 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2916809 TGTTAGGACG
* *
2916819 AAAATTTTTAAAAAAAGGTGAGGGCC
1 AAAATGTTTAAAAAAAGATGAGGGCC
*
2916845 AAAATGTTTAAAAAAAGATTAGGG
1 AAAATGTTTAAAAAAAGATGAGGG
2916869 ACTTTGAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.50, C:0.04, G:0.22, T:0.24
Consensus pattern (26 bp):
AAAATGTTTAAAAAAAGATGAGGGCC
Found at i:2921598 original size:26 final size:27
Alignment explanation
Indices: 2921548--2921598 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
2921538 CGTTAGAAAG
*
2921548 AAAATGTTTAAAAAAAAGGTGAGGGCC
1 AAAATGTTTAAAAAAAAGATGAGGGCC
*
2921575 AAAATGTTT-AAAAAAAGATTAGGG
1 AAAATGTTTAAAAAAAAGATGAGGG
2921599 ACTTTGAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.51, C:0.04, G:0.24, T:0.22
Consensus pattern (27 bp):
AAAATGTTTAAAAAAAAGATGAGGGCC
Found at i:2924014 original size:3 final size:3
Alignment explanation
Indices: 2924006--2924037 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2923996 AAAGTAACAT
2924006 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2924038 GTATAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2926377 original size:39 final size:39
Alignment explanation
Indices: 2926333--2926441 Score: 128
Period size: 39 Copynumber: 2.8 Consensus size: 39
2926323 AGTTAAAAGA
*
2926333 AATAATTTAGATTGTTATGGTGAAATAATTTAAAAAATT
1 AATAATTTAGAATGTTATGGTGAAATAATTTAAAAAATT
* ** *
2926372 AATAATTTAGAATGTTATAGTGAAATGGTTTAAGAAATT
1 AATAATTTAGAATGTTATGGTGAAATAATTTAAAAAATT
** * * *
2926411 AGGAATTTAAAATGTTAGGGTGTAATAATTT
1 AATAATTTAGAATGTTATGGTGAAATAATTT
2926442 GAGAATTAGG
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.39
Consensus pattern (39 bp):
AATAATTTAGAATGTTATGGTGAAATAATTTAAAAAATT
Found at i:2929935 original size:23 final size:23
Alignment explanation
Indices: 2929915--2929959 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2929905 TATGTTTTTA
2929915 TATGTCTTCATGACACATTTTCT
1 TATGTCTTCATGACACATTTTCT
* * *
2929938 TCTGTCTTTATGGCACATTTTC
1 TATGTCTTCATGACACATTTTC
2929960 GGTCGTTTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.22, G:0.11, T:0.49
Consensus pattern (23 bp):
TATGTCTTCATGACACATTTTCT
Found at i:2930911 original size:35 final size:35
Alignment explanation
Indices: 2930862--2930973 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
2930852 AAAACAATCC
*
2930862 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * *
2930897 TCAATTTCACTCTAAACCCTAAATTCTAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** * *
2930932 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
2930967 TTAATTT
1 TCAATTT
2930974 AAGGTTTAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:2933083 original size:35 final size:35
Alignment explanation
Indices: 2933035--2933144 Score: 148
Period size: 35 Copynumber: 3.1 Consensus size: 35
2933025 TATAAACCTT
* * *
2933035 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
2933070 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* * *
2933105 AAATTAAATTACTTTGGAATTTGGGGTTTAGAATA
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
2933140 AAATT
1 AAATT
2933145 AAGGACTATT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
Found at i:2933954 original size:14 final size:14
Alignment explanation
Indices: 2933937--2933965 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2933927 GCGTTTAATA
2933937 TAAGAATTTTAACT
1 TAAGAATTTTAACT
2933951 TAAGAATTTTAACT
1 TAAGAATTTTAACT
2933965 T
1 T
2933966 TTTGGAAGAA
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:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TAAGAATTTTAACT
Found at i:2934570 original size:24 final size:24
Alignment explanation
Indices: 2934541--2934588 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2934531 TAATGGGTTC
2934541 GGACCCGTGCCTATAATGTTTAAT
1 GGACCCGTGCCTATAATGTTTAAT
*
2934565 GGACCCGTGTCTATAATGTTTAAT
1 GGACCCGTGCCTATAATGTTTAAT
2934589 ATGTAATAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (24 bp):
GGACCCGTGCCTATAATGTTTAAT
Found at i:2946153 original size:17 final size:18
Alignment explanation
Indices: 2946116--2946156 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2946106 ATATTATGTA
*
2946116 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
2946134 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
2946151 TTTACT
1 TTTACT
2946157 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:2948436 original size:26 final size:24
Alignment explanation
Indices: 2948365--2948436 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
2948355 TTATATTTGT
2948365 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
2948390 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
2948412 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
2948437 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:2950213 original size:21 final size:21
Alignment explanation
Indices: 2950187--2950231 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2950177 GATTTCTGGG
* *
2950187 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2950208 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2950229 CAA
1 CAA
2950232 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2950836 original size:18 final size:18
Alignment explanation
Indices: 2950813--2950847 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2950803 CTAGGAGATT
2950813 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2950831 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2950848 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2950933 original size:21 final size:22
Alignment explanation
Indices: 2950904--2950947 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2950894 GTTGTATGAT
2950904 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
2950925 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
2950947 A
1 A
2950948 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:2951903 original size:149 final size:149
Alignment explanation
Indices: 2951723--2952026 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
2951713 GAGTCGAGGG
2951723 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
2951788 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
2951853 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2951872 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
2951937 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
2952002 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2952021 TCTACG
1 TCTACG
2952027 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:2952049 original size:23 final size:23
Alignment explanation
Indices: 2952005--2952049 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2951995 ATCATTATAT
*
2952005 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
2952028 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2952050 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:2958790 original size:6 final size:6
Alignment explanation
Indices: 2958779--2958804 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2958769 AGTACGTCAG
2958779 CAACAC CAACAC CAACAC CAACAC CA
1 CAACAC CAACAC CAACAC CAACAC CA
2958805 TCCGCAAGTG
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:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (6 bp):
CAACAC
Found at i:2959206 original size:7 final size:7
Alignment explanation
Indices: 2959194--2959233 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
2959184 GGTACTTCAT
2959194 TTTGCAA
1 TTTGCAA
2959201 TTTGCAA
1 TTTGCAA
2959208 TTTGCAA
1 TTTGCAA
2959215 TTTGCAA
1 TTTGCAA
2959222 TTTGCAA
1 TTTGCAA
2959229 TTTGC
1 TTTGC
2959234 GTATGCTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (7 bp):
TTTGCAA
Found at i:2962298 original size:26 final size:25
Alignment explanation
Indices: 2962269--2962349 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
2962259 TTAATTTAAA
2962269 CTAAACTACTTAGTAGTTATCCTTAT
1 CTAAACTACTTAGTAGTTAT-CTTAT
* * *
2962295 CT-AACTTTCTAAG-AGTTAAT-TTAAA
1 CTAAAC-TACTTAGTAGTT-ATCTT-AT
2962320 CTAAACTACTTAGTAGTTATCTTTAT
1 CTAAACTACTTAGTAGTTATC-TTAT
2962346 CTAA
1 CTAA
2962350 CTTTCTAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 2 0.05
25 17 0.40
26 21 0.50
27 2 0.05
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (25 bp):
CTAAACTACTTAGTAGTTATCTTAT
Found at i:2962311 original size:25 final size:24
Alignment explanation
Indices: 2962283--2962363 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
2962273 ACTACTTAGT
2962283 AGTTATCCTTATCTAACTTTCTAAG
1 AGTTAT-CTTATCTAACTTTCTAAG
* * *
2962308 AGTTAAT-TTAAACTAAAC-TACTTAG
1 AGTT-ATCTT-ATCT-AACTTTCTAAG
2962333 TAGTTATCTTTATCTAACTTTCTAAG
1 -AGTTATC-TTATCTAACTTTCTAAG
2962359 AGTTA
1 AGTTA
2962364 GTGTTATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
24 2 0.05
25 22 0.51
26 17 0.40
27 2 0.05
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (24 bp):
AGTTATCTTATCTAACTTTCTAAG
Found at i:2962335 original size:51 final size:51
Alignment explanation
Indices: 2962259--2962400 Score: 203
Period size: 51 Copynumber: 2.8 Consensus size: 51
2962249 GAACAAGTAT
2962259 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
*
2962310 TTAATTTAAACTAAACTACTTAGTAGTTATCTTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
* * * * * * *
2962361 TTAGTGTTATATTAAAATACTAATTAATTATCCTTATCTA
1 TTAAT-TTAAACTAAACTACTTAGTAGTTATCCTTATCTA
2962401 TCGCATAGCC
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 54 0.67
52 27 0.33
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (51 bp):
TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
Found at i:2966499 original size:26 final size:25
Alignment explanation
Indices: 2966470--2966550 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 25
2966460 TTAATTTAAA
2966470 CTAAACTACTTAGTAGTTATCCTTAT
1 CTAAACTACTTAGTAGTTAT-CTTAT
* * *
2966496 CT-AACTTTCTAAG-AGTTAAT-TTAAA
1 CTAAAC-TACTTAGTAGTT-ATCTT-AT
*
2966521 CTAAACTACTTGGTAGTTATCTTTAT
1 CTAAACTACTTAGTAGTTATC-TTAT
2966547 CTAA
1 CTAA
2966551 CTTTCTAAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 2 0.05
25 16 0.39
26 21 0.51
27 2 0.05
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (25 bp):
CTAAACTACTTAGTAGTTATCTTAT
Done.