Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008003.1 Hibiscus syriacus cultivar Beakdansim tig00110462_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: 3297763
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 14
Found at i:2622080 original size:19 final size:19
Alignment explanation
Indices: 2622056--2622094 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2622046 CTGGCATCAC
2622056 ACTAACTTTCCTTTCAGCT
1 ACTAACTTTCCTTTCAGCT
2622075 ACTAACTTTCCTTTCAGCT
1 ACTAACTTTCCTTTCAGCT
2622094 A
1 A
2622095 TTGAGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.31, G:0.05, T:0.41
Consensus pattern (19 bp):
ACTAACTTTCCTTTCAGCT
Found at i:2625626 original size:8 final size:9
Alignment explanation
Indices: 2625605--2625629 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2625595 AGAGTTAATT
2625605 TTTTTATTA
1 TTTTTATTA
2625614 TTTTTATTA
1 TTTTTATTA
2625623 TTTTTAT
1 TTTTTAT
2625630 ATATGGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTATTA
Found at i:2626221 original size:21 final size:21
Alignment explanation
Indices: 2626188--2626243 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2626178 TTGAAATTTG
* * *
2626188 AAATTTTAGAAAATAATCATTA
1 AAATTTCA-AAAAAAATAATTA
*
2626210 ACATTTCAAAAAAAATAATTA
1 AAATTTCAAAAAAAATAATTA
2626231 AAATTTCAAAAAA
1 AAATTTCAAAAAA
2626244 TAGAAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (21 bp):
AAATTTCAAAAAAAATAATTA
Found at i:2655107 original size:23 final size:27
Alignment explanation
Indices: 2655074--2655138 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 27
2655064 AATGATTCAG
*
2655074 TGCTGACTGATTCAGCA-A-AA-TA-A
1 TGCTGAATGATTCAGCACATAAGTACA
*
2655097 TGCTGAATGATTCAACACATAAGTACA
1 TGCTGAATGATTCAGCACATAAGTACA
*
2655124 TTCTGAATGATTCAG
1 TGCTGAATGATTCAG
2655139 AGTCATTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 15 0.44
24 1 0.03
25 2 0.06
26 2 0.06
27 14 0.41
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (27 bp):
TGCTGAATGATTCAGCACATAAGTACA
Found at i:2655451 original size:18 final size:19
Alignment explanation
Indices: 2655416--2655452 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2655406 CACGGAATGT
2655416 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2655436 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2655453 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2655641 original size:36 final size:37
Alignment explanation
Indices: 2655592--2655667 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 37
2655582 ATAATATTAC
*
2655592 AAATTGTAAAATATTTATATATTTTTTTTAAAAAATT
1 AAATTGTAAAATATTTATATAATTTTTTTAAAAAATT
* *
2655629 AAATT-TATAATATTTATATAATTTTTTTACAAAATT
1 AAATTGTAAAATATTTATATAATTTTTTTAAAAAATT
2655665 AAA
1 AAA
2655668 AATATAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 31 0.86
37 5 0.14
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (37 bp):
AAATTGTAAAATATTTATATAATTTTTTTAAAAAATT
Found at i:2658726 original size:21 final size:20
Alignment explanation
Indices: 2658697--2658745 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
2658687 TATCAAACGG
*
2658697 TTATAAAATAATCATTAAATT
1 TTATCAAATAATCATTAAA-T
* *
2658718 TTATCAAATAGTTATTAAAT
1 TTATCAAATAATCATTAAAT
2658738 TTATCAAA
1 TTATCAAA
2658746 GATCATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (20 bp):
TTATCAAATAATCATTAAAT
Found at i:2658732 original size:32 final size:31
Alignment explanation
Indices: 2658636--2658737 Score: 118
Period size: 32 Copynumber: 3.2 Consensus size: 31
2658626 CTTGAAGTAA
2658636 ATAAAATAAAT-ATTAAATTTATCAAATTA-TT
1 ATAAAAT-AATCATTAAATTTATCAAA-TAGTT
* **
2658667 ATAAAACAATCATTAAAATTTATCAAACGGTT
1 ATAAAATAATCATT-AAATTTATCAAATAGTT
2658699 ATAAAATAATCATTAAATTTTATCAAATAGTT
1 ATAAAATAATCATTAAA-TTTATCAAATAGTT
*
2658731 ATTAAAT
1 ATAAAAT
2658738 TTATCAAAGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
30 3 0.05
31 12 0.20
32 45 0.75
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (31 bp):
ATAAAATAATCATTAAATTTATCAAATAGTT
Found at i:2660316 original size:90 final size:90
Alignment explanation
Indices: 2660203--2660376 Score: 208
Period size: 90 Copynumber: 1.9 Consensus size: 90
2660193 AAATCAAGGA
* ** * * * *
2660203 AACTAAAGCTAAACACATGCAAAATAGATAT-GACTAACTTTGGCCAGAATAAACCTTCCTTG-T
1 AACTAAAGCTAAAAACAAACAAAACAAATATAG-CTAACTTTGCCCAGAATAAACCTTCCTCGCT
*
2660266 TCAGTATACTGTGTTGATCAAGAAGTT
65 T-AGTATACTGGGTTGATCAAGAAGTT
* **
2660293 AACTAAAGCTAAAAACAAACAAAACAAATCTAGCTAACTTTGCCCAGAATGTACCTTCCTCGCTT
1 AACTAAAGCTAAAAACAAACAAAACAAATATAGCTAACTTTGCCCAGAATAAACCTTCCTCGCTT
*
2660358 AGTATATTGGGTTGATCAA
66 AGTATACTGGGTTGATCAA
2660377 CCAAAAGTTG
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
90 67 0.96
91 3 0.04
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (90 bp):
AACTAAAGCTAAAAACAAACAAAACAAATATAGCTAACTTTGCCCAGAATAAACCTTCCTCGCTT
AGTATACTGGGTTGATCAAGAAGTT
Found at i:2664677 original size:3 final size:3
Alignment explanation
Indices: 2664669--2664785 Score: 99
Period size: 3 Copynumber: 35.3 Consensus size: 3
2664659 CGATTTTAGG
* * *
2664669 AGA AGA AGA AGG AGG AGG AGA AGA AGGA AGA AGGA AGA AGGA AGA AGGA
1 AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA A-GA AGA A-GA AGA A-GA
*
2664718 AGA AGAA AGA AGA GGA AGA AGA AGAA AGA AGGA AGA AGGA AGA AGGA
1 AGA AG-A AGA AGA AGA AGA AGA AG-A AGA A-GA AGA A-GA AGA A-GA
2664765 AGA AGAA AGA AGGA AGA AGA A
1 AGA AG-A AGA A-GA AGA AGA A
2664786 TGCGGTTAAC
Statistics
Matches: 99, Mismatches: 4, Indels: 22
0.79 0.03 0.18
Matches are distributed among these distances:
3 66 0.67
4 33 0.33
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2664700 original size:7 final size:7
Alignment explanation
Indices: 2664669--2664783 Score: 146
Period size: 7 Copynumber: 16.7 Consensus size: 7
2664659 CGATTTTAGG
2664669 AGAA-GA
1 AGAAGGA
2664675 AGAAGGA
1 AGAAGGA
* *
2664682 GGAGGAGA
1 AGAAG-GA
2664690 AGAAGGA
1 AGAAGGA
2664697 AGAAGGA
1 AGAAGGA
2664704 AGAAGGA
1 AGAAGGA
2664711 AGAAGGA
1 AGAAGGA
*
2664718 AGAAGAA
1 AGAAGGA
2664725 AGAA-GA
1 AGAAGGA
*
2664731 GGAA-GA
1 AGAAGGA
*
2664737 AGAAGAA
1 AGAAGGA
2664744 AGAAGGA
1 AGAAGGA
2664751 AGAAGGA
1 AGAAGGA
2664758 AGAAGGA
1 AGAAGGA
*
2664765 AGAAGAA
1 AGAAGGA
2664772 AGAAGGA
1 AGAAGGA
2664779 AGAAG
1 AGAAG
2664784 AATGCGGTTA
Statistics
Matches: 94, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
6 13 0.14
7 76 0.81
8 5 0.05
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
AGAAGGA
Found at i:2664960 original size:20 final size:19
Alignment explanation
Indices: 2664936--2664989 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2664926 AACTTCGATT
*
2664936 TCGCAACACAGTTTTTAAA
1 TCGCAACACAGTTTGTAAA
* *
2664955 TACGCAACGCGAATTTGTAAA
1 T-CGCAACAC-AGTTTGTAAA
2664976 TCGCAACACAGTTT
1 TCGCAACACAGTTT
2664990 CCAAAATCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 5 0.18
20 14 0.50
21 9 0.32
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (19 bp):
TCGCAACACAGTTTGTAAA
Found at i:2665190 original size:20 final size:20
Alignment explanation
Indices: 2665164--2665212 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2665154 TCGATAATTT
2665164 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
*
2665184 TCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
2665204 GCGTTGCGA
1 GCGTTGCGA
2665213 TTTACATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:2668065 original size:23 final size:23
Alignment explanation
Indices: 2668030--2668084 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
2668020 ACTAATTTTT
* *
2668030 ATAATAATTAAAATCATTAACAG
1 ATAATTATCAAAATCATTAACAG
* *
2668053 ATAATTATCAAAATTATTAACAT
1 ATAATTATCAAAATCATTAACAG
2668076 ATAATTATC
1 ATAATTATC
2668085 TATATAGTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAATTATCAAAATCATTAACAG
Found at i:2679034 original size:20 final size:20
Alignment explanation
Indices: 2678995--2679033 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2678985 ATATTATAAA
* *
2678995 AATATAATATTTTATATTTT
1 AATATAAAATATTATATTTT
2679015 AATATAAAATATTAT-TTTT
1 AATATAAAATATTATATTTT
2679034 TCGACCTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATATAAAATATTATATTTT
Found at i:2680699 original size:2 final size:2
Alignment explanation
Indices: 2680694--2680731 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2680684 TTTTTCTTTG
2680694 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
2680732 AATGATACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2681303 original size:14 final size:14
Alignment explanation
Indices: 2681284--2681319 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2681274 TTGCGTTCGT
2681284 AATATAATATAGAG
1 AATATAATATAGAG
2681298 AATATAATATAGAG
1 AATATAATATAGAG
*
2681312 AAAATAAT
1 AATATAAT
2681320 TTCAGTGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (14 bp):
AATATAATATAGAG
Found at i:2681547 original size:21 final size:21
Alignment explanation
Indices: 2681479--2681540 Score: 115
Period size: 21 Copynumber: 3.0 Consensus size: 21
2681469 AACTATCACA
2681479 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
2681500 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
*
2681521 TTGCGATTTTCCTAATTCGC
1 TTGCGATTTTCCAAATTCGC
2681541 AATGCGAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCG
Found at i:2681562 original size:20 final size:20
Alignment explanation
Indices: 2681537--2681629 Score: 159
Period size: 20 Copynumber: 4.7 Consensus size: 20
2681527 TTTTCCTAAT
2681537 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2681557 TCGCAATGCGAATACGTACA
1 TCGCAATGCGAATACGTAAA
2681577 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2681597 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2681617 TTGCAACGCGAAT
1 TCGCAATGCGAAT
2681630 CTGACTATCA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2681643 original size:20 final size:20
Alignment explanation
Indices: 2681619--2681702 Score: 105
Period size: 20 Copynumber: 4.2 Consensus size: 20
2681609 TACGTAAATT
* *
2681619 GCAACGCGAATCTGACTATC
1 GCAACGAGATTCTGACTATC
*
2681639 ACAACGAGATTCTGACTATC
1 GCAACGAGATTCTGACTATC
* * *
2681659 GTAAGGAGATTATGACTATC
1 GCAACGAGATTCTGACTATC
*
2681679 GCAACGCGATTCTGACTATC
1 GCAACGAGATTCTGACTATC
2681699 GCAA
1 GCAA
2681703 TACTGAATTT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
GCAACGAGATTCTGACTATC
Found at i:2682624 original size:20 final size:19
Alignment explanation
Indices: 2682599--2682691 Score: 141
Period size: 20 Copynumber: 4.7 Consensus size: 19
2682589 CAACGTGGAA
2682599 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAA-ATGACT
*
2682619 ATCGCAACACGGAAATGACT
1 ATCGCAACGC-GAAATGACT
2682639 ATCGCAACGCGAAATTGACT
1 ATCGCAACGCGAAA-TGACT
2682659 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
2682679 ATCGCAACGCGAA
1 ATCGCAACGCGAA
2682692 TTTAGTTTCG
Statistics
Matches: 68, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
19 7 0.10
20 54 0.79
21 7 0.10
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:2682658 original size:40 final size:41
Alignment explanation
Indices: 2682599--2682691 Score: 163
Period size: 40 Copynumber: 2.3 Consensus size: 41
2682589 CAACGTGGAA
2682599 ATCGCAACGCG-AATATGACTATCGCAACACGGAAATGACT
1 ATCGCAACGCGAAATATGACTATCGCAACACGGAAATGACT
*
2682639 ATCGCAACGCGAAAT-TGACTATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAATATGACTATCGCAACACGGAAATGACT
2682679 ATCGCAACGCGAA
1 ATCGCAACGCGAA
2682692 TTTAGTTTCG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 48 0.94
41 3 0.06
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.16
Consensus pattern (41 bp):
ATCGCAACGCGAAATATGACTATCGCAACACGGAAATGACT
Found at i:2682722 original size:20 final size:19
Alignment explanation
Indices: 2682697--2682753 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 19
2682687 GCGAATTTAG
*
2682697 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
2682716 TTTTCGCATTGCGATTTTCA
1 -TTTCGCATTGCGATTTTCA
2682736 TTTCGCATTGCGATTTTC
1 TTTCGCATTGCGATTTTC
2682754 TCGTTGCGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:2682761 original size:33 final size:34
Alignment explanation
Indices: 2682715--2682783 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 34
2682705 TGCGATTTTC
**
2682715 ATTTTCGCATTGCGATTTTCA-TTTCGCATTGCG
1 ATTTTCGCATTGCGATAGTCATTTTCGCATTGCG
* * *
2682748 ATTTTCTCGTTGCGATAGTCATTTTCGCGTTGCG
1 ATTTTCGCATTGCGATAGTCATTTTCGCATTGCG
2682782 AT
1 AT
2682784 AGTCTGTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 17 0.57
34 13 0.43
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (34 bp):
ATTTTCGCATTGCGATAGTCATTTTCGCATTGCG
Found at i:2682773 original size:20 final size:20
Alignment explanation
Indices: 2682748--2682787 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2682738 TCGCATTGCG
*
2682748 ATTTTCTCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
2682768 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
2682788 TGTTTTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGTC
Found at i:2682908 original size:14 final size:14
Alignment explanation
Indices: 2682889--2682925 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2682879 CATCAATTAA
2682889 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2682903 ACAAATCATCTTTT
1 ACAAATCAACATTT
2682917 ACAAATCAA
1 ACAAATCAA
2682926 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2684406 original size:42 final size:42
Alignment explanation
Indices: 2684308--2684419 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
2684298 TCTAGAATGT
* * * *
2684308 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGA-CTCTTGAACGATGATAGGGGCCTCTTGAACGA
* **
2684350 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACGA
*
2684392 TAGGG-GAGGCCTCTTGAACGATGATAGG
1 T-GGGAGAGGACTCTTGAACGATGATAGG
2684420 TGAGTCGAGC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
42 52 0.90
43 6 0.10
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACGA
Found at i:2685046 original size:20 final size:20
Alignment explanation
Indices: 2684902--2685039 Score: 153
Period size: 20 Copynumber: 7.1 Consensus size: 20
2684892 ACTTAAAATT
2684902 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
*
2684922 GCAACGTGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
*
2684942 GCAATGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
* * **
2684962 GTAATGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
*
2684982 GCAA--CG-AGA-GA--ATC
1 GCAACGCGAAAATGACTATC
2684996 GCAATGCGCGAAAATGACTATC
1 GCAA--CGCGAAAATGACTATC
2685018 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
2685038 GC
1 GC
2685040 GTTGCGATTT
Statistics
Matches: 100, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
14 7 0.07
16 2 0.02
17 1 0.01
18 4 0.04
19 2 0.02
20 77 0.77
22 7 0.07
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:2687047 original size:20 final size:20
Alignment explanation
Indices: 2686997--2687049 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2686987 GAAACTTTAA
* **
2686997 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATTTGACT
2687017 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
2687037 ATCGCAGCGCGAA
1 ATCGCAACGCGAA
2687050 ATGAAAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:2687462 original size:22 final size:22
Alignment explanation
Indices: 2687400--2687469 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 22
2687390 TGACCGTAAA
* *
2687400 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
2687422 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
2687444 TGATTTCGTCGGAGATGGGGAT
1 TGATTTCGTCGGAGATGGGGAC
2687466 TGAT
1 TGAT
2687470 GTCATCTTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.21, C:0.13, G:0.39, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:2687714 original size:21 final size:21
Alignment explanation
Indices: 2687690--2687735 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2687680 TATTCGCATT
2687690 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
2687711 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2687732 GCGA
1 GCGA
2687736 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2691340 original size:2 final size:2
Alignment explanation
Indices: 2691329--2691369 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2691319 TAGCTAAAAG
2691329 AT AT -T 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
2691370 TTAAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2691669 original size:126 final size:125
Alignment explanation
Indices: 2691439--2691686 Score: 376
Period size: 126 Copynumber: 2.0 Consensus size: 125
2691429 TGTAAACACT
* *
2691439 TCCCGAATCCAACCTGACTCGCTGTCTAAATAATCGGCTAATCATGGCTTGCATCAATAGAGGTG
1 TCCCAAATCCAACCTGACTCGCTGTCCAAATAATCGGCTAATCATGGCTTGCATCAATAGAGGTG
* *
2691504 CCGGTCCTGGCCTGTGAGATGCTATTGCCATAAACTGTAACCAGCCTCAACTTTGTGAGA
66 CCGGTCCTGGCCTGTGAGATCCTATTGCCATAAACTGTAACCAGCCTCAACTGTGTGAGA
*
2691564 TCCCAAATCCGACCTGACTCGCTGTCCAAATGAA-CTGGCTAATCATGGCTTGCATCAATAG-GA
1 TCCCAAATCCAACCTGACTCGCTGTCCAAAT-AATC-GGCTAATCATGGCTTGCATCAATAGAG-
* *
2691627 GTGCCGGTCCTGGCCTGTGAGATCCTATTTG-CATAAATTGTAACCAGCTTCAACTGTGTG
63 GTGCCGGTCCTGGCCTGTGAGATCCTA-TTGCCATAAACTGTAACCAGCCTCAACTGTGTG
2691687 CTGTTAAGCC
Statistics
Matches: 112, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
125 30 0.27
126 79 0.71
127 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (125 bp):
TCCCAAATCCAACCTGACTCGCTGTCCAAATAATCGGCTAATCATGGCTTGCATCAATAGAGGTG
CCGGTCCTGGCCTGTGAGATCCTATTGCCATAAACTGTAACCAGCCTCAACTGTGTGAGA
Found at i:2709544 original size:2 final size:2
Alignment explanation
Indices: 2709537--2709575 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2709527 CTAACCACCG
2709537 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
2709576 TCGACTTCAT
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:2711969 original size:42 final size:42
Alignment explanation
Indices: 2711917--2711997 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
2711907 ATACAAATTG
* * *
2711917 CCAGTTATGCAGGAAGTTGATCCCTTAGCTTCTTGTTCCGTA
1 CCAGCTATGCAGGAAGCTGATCCCCTAGCTTCTTGTTCCGTA
2711959 CCAGCTATGCAGGAAGCTGATCCCCTAGCTTCTTGTTCC
1 CCAGCTATGCAGGAAGCTGATCCCCTAGCTTCTTGTTCC
2711998 TTACTACTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.32
Consensus pattern (42 bp):
CCAGCTATGCAGGAAGCTGATCCCCTAGCTTCTTGTTCCGTA
Found at i:2718430 original size:11 final size:11
Alignment explanation
Indices: 2718414--2718446 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
2718404 TCATATTAGA
2718414 GTAAAAGTATT
1 GTAAAAGTATT
2718425 GTAAAAGTATT
1 GTAAAAGTATT
2718436 GTAAAAGTATT
1 GTAAAAGTATT
2718447 TCTACCTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (11 bp):
GTAAAAGTATT
Found at i:2723439 original size:15 final size:16
Alignment explanation
Indices: 2723408--2723440 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2723398 TTTTAATAGA
2723408 ATAGACTATGTTAATT
1 ATAGACTATGTTAATT
*
2723424 ATAGACTTTG-TAATT
1 ATAGACTATGTTAATT
2723439 AT
1 AT
2723441 TGGGGTATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (16 bp):
ATAGACTATGTTAATT
Found at i:2724664 original size:4 final size:4
Alignment explanation
Indices: 2724655--2724680 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2724645 AGTTATCATG
2724655 TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TG
2724681 CATGATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:2728153 original size:22 final size:24
Alignment explanation
Indices: 2728109--2728160 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
2728099 AAAAACCAAG
*
2728109 ACCGGTTTTTTTACCGGATAAAAA
1 ACCGGTTTTTATACCGGATAAAAA
*
2728133 ACCGGTTTTTAT-CCTGA-AAAAA
1 ACCGGTTTTTATACCGGATAAAAA
2728155 ACCGGT
1 ACCGGT
2728161 CTGGGTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 11 0.42
23 4 0.15
24 11 0.42
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (24 bp):
ACCGGTTTTTATACCGGATAAAAA
Found at i:2729607 original size:21 final size:21
Alignment explanation
Indices: 2729583--2729624 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2729573 AGTTTATTTT
2729583 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
2729604 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
2729625 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:2729673 original size:33 final size:32
Alignment explanation
Indices: 2729619--2729717 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
2729609 TTTGTTTCAA
2729619 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
2729651 TTATCGAACTTGTAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTG-AAGTTTTTAAGTATTTGAAT
* * *
2729684 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
2729717 T
1 T
2729718 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 12 0.19
33 49 0.79
34 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:2730851 original size:15 final size:15
Alignment explanation
Indices: 2730824--2730862 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2730814 TTTAATAATA
*
2730824 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
2730839 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
2730854 TTAAAACCG
1 TTAAAACCG
2730863 AAACCGCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:2730978 original size:15 final size:17
Alignment explanation
Indices: 2730952--2730983 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2730942 TTCTATGGGA
2730952 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
2730968 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
2730984 CTGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:2744723 original size:41 final size:39
Alignment explanation
Indices: 2744686--2744767 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
2744676 TTAAATTAAT
*
2744686 TCAAACT-TTTTAAAATATTTTATATCAGTTCTCAAATTA
1 TCAAACTATTTTAAAATATTTT-TATCAATTCTCAAATTA
* ** * *
2744725 TGATCCTATTTTAAAATATTTTTATCAATTCTCGAACTA
1 TCAAACTATTTTAAAATATTTTTATCAATTCTCAAATTA
2744764 TCAA
1 TCAA
2744768 TATCATTCTA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
39 20 0.59
40 14 0.41
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.45
Consensus pattern (39 bp):
TCAAACTATTTTAAAATATTTTTATCAATTCTCAAATTA
Found at i:2745037 original size:16 final size:15
Alignment explanation
Indices: 2745011--2745044 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
2745001 CGTCACATTG
2745011 TATAAATGAAATTTA
1 TATAAATGAAATTTA
2745026 TATAACATGAAATTTA
1 TATAA-ATGAAATTTA
2745042 TAT
1 TAT
2745045 TAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (15 bp):
TATAAATGAAATTTA
Found at i:2745100 original size:37 final size:33
Alignment explanation
Indices: 2745052--2745136 Score: 109
Period size: 37 Copynumber: 2.5 Consensus size: 33
2745042 TATTAAAATT
*
2745052 ATTATTATAAATCTAATTTGAATGAAATTGTAATAAA
1 ATTATTATAAATATAATTTGAAT-AAA-T-T-ATAAA
2745089 ATTATTATAAATATAATTTGAATAAATTATAAA
1 ATTATTATAAATATAATTTGAATAAATTATAAA
*
2745122 ATTATTA-ATATATAA
1 ATTATTATAAATATAA
2745137 ATGAAATTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
32 7 0.15
33 12 0.26
34 1 0.02
35 1 0.02
36 3 0.07
37 22 0.48
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (33 bp):
ATTATTATAAATATAATTTGAATAAATTATAAA
Found at i:2747228 original size:4 final size:4
Alignment explanation
Indices: 2747221--2747281 Score: 122
Period size: 4 Copynumber: 15.2 Consensus size: 4
2747211 TGATGTATAT
2747221 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2747269 ATAC ATAC ATAC A
1 ATAC ATAC ATAC A
2747282 CATCAACACT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:2748504 original size:58 final size:59
Alignment explanation
Indices: 2748439--2748569 Score: 144
Period size: 58 Copynumber: 2.2 Consensus size: 59
2748429 CGAGTGAGTC
* * * *
2748439 AAGTCATAATTTGATAATAAAATTGA-AATATTCAAAAATT-TAAGGAATAATTTAAAAT-
1 AAGTCATAATTTGAGAACAAAATTGAGAACATCCAAAAATTGT-A-GAATAATTTAAAATA
* *
2748497 AAGTCATAATTT-AGGACAAAATTGAGAACATCCAAAAATTGTAGACTAATTTAAAATAA
1 AAGTCATAATTTGAGAACAAAATTGAGAACATCCAAAAATTGTAGAATAATTTAAAAT-A
*
2748556 AAATCATAATTTGA
1 AAGTCATAATTTGA
2748570 AGATATGTGT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
57 23 0.38
58 25 0.41
59 12 0.20
60 1 0.02
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (59 bp):
AAGTCATAATTTGAGAACAAAATTGAGAACATCCAAAAATTGTAGAATAATTTAAAATA
Found at i:2748791 original size:46 final size:46
Alignment explanation
Indices: 2748724--2748818 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
2748714 AACTTAACTC
*
2748724 GATAGGATCAATGTGGCAGATTCGAATGAAGATAATATGCTTCTCA
1 GATAGGATCAATGTAGCAGATTCGAATGAAGATAATATGCTTCTCA
*
2748770 GATAGGATCAATGTATCAGATTCGAATGAAGATAATATGCTTCTCA
1 GATAGGATCAATGTAGCAGATTCGAATGAAGATAATATGCTTCTCA
2748816 GAT
1 GAT
2748819 CGGGTTAATC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (46 bp):
GATAGGATCAATGTAGCAGATTCGAATGAAGATAATATGCTTCTCA
Found at i:2752952 original size:27 final size:27
Alignment explanation
Indices: 2752922--2752988 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
2752912 TTTGTTTATT
2752922 AAGCATGGAGTGATCGAAGAAAGAAAA
1 AAGCATGGAGTGATCGAAGAAAGAAAA
2752949 AAGCATGGAGTGATCGAAGAAAGAAAA
1 AAGCATGGAGTGATCGAAGAAAGAAAA
2752976 AAGCATGGAGTGA
1 AAGCATGGAGTGA
2752989 AAGAAAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.49, C:0.07, G:0.31, T:0.12
Consensus pattern (27 bp):
AAGCATGGAGTGATCGAAGAAAGAAAA
Found at i:2753515 original size:31 final size:31
Alignment explanation
Indices: 2753479--2753537 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2753469 AACTTAAAAG
* * *
2753479 AGTTTTGCTATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
2753510 AGTTTTACAATATTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
2753538 CTATACAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2753587 original size:22 final size:22
Alignment explanation
Indices: 2753562--2753604 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2753552 TAATAAATTA
2753562 TTTAAAATAAAACAATCCATAT
1 TTTAAAATAAAACAATCCATAT
* *
2753584 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAAACAATCCATA
2753605 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAAACAATCCATAT
Found at i:2753621 original size:54 final size:54
Alignment explanation
Indices: 2753552--2753852 Score: 332
Period size: 54 Copynumber: 5.5 Consensus size: 54
2753542 ACAACTAAAA
*
2753552 TAATAAATTATTTAAAATAAAACAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
* *** * *
2753606 TAATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-AAT-AAATCA-ATC
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATTCATA-C
2753659 T-AT--A-T-TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAA-TCTATAC
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATTC-ATAC
*
2753718 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
*
2753772 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
*
2753826 AAATAAATTATTTAAAATAAATCAATC
1 TAATAAATTATTTAAAATAAATCAATC
2753853 TATACTAATA
Statistics
Matches: 209, Mismatches: 17, Indels: 42
0.78 0.06 0.16
Matches are distributed among these distances:
48 16 0.08
49 2 0.01
50 1 0.00
52 3 0.01
53 7 0.03
54 131 0.63
55 8 0.04
56 2 0.01
57 5 0.02
58 7 0.03
59 5 0.02
60 3 0.01
62 1 0.00
63 2 0.01
64 16 0.08
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
Found at i:2753703 original size:14 final size:14
Alignment explanation
Indices: 2753686--2753739 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
2753676 CAATCCATAC
2753686 AAATAAATTATTTA
1 AAATAAATTATTTA
*
2753700 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
2753717 CTAATAAATTATTTA
1 -AAATAAATTATTTA
2753732 AAATAAAT
1 AAATAAAT
2753740 CAATCTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:2753808 original size:22 final size:22
Alignment explanation
Indices: 2753782--2753824 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2753772 TAATAAATTA
2753782 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2753804 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2753825 CAAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2753833 original size:22 final size:22
Alignment explanation
Indices: 2753784--2753832 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2753774 ATAAATTATT
***
2753784 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATAAAA
2753806 TAAAATAAATCAATCCATACAAA
1 TAAAATAAATCAATCCATA-AAA
2753829 TAAA
1 TAAA
2753833 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATAAAA
Found at i:2753843 original size:14 final size:14
Alignment explanation
Indices: 2753826--2753879 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
2753816 CAATCCATAC
2753826 AAATAAATTATTTA
1 AAATAAATTATTTA
*
2753840 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
2753857 CTAATAAATTATTTA
1 -AAATAAATTATTTA
2753872 AAATAAAT
1 AAATAAAT
2753880 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:2753894 original size:22 final size:22
Alignment explanation
Indices: 2753868--2753912 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2753858 TAATAAATTA
2753868 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2753890 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2753912 T
1 T
2753913 AATAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2753894 original size:54 final size:54
Alignment explanation
Indices: 2753836--2754209 Score: 455
Period size: 54 Copynumber: 6.9 Consensus size: 54
2753826 AAATAAATTA
2753836 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
2753890 TTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
2753944 TTTAAAATAAATCAAT-TCATACTAATAAATTATTTAAAATAAATCAATCAATACA
1 TTTAAAATAAATCAATCT-ATACTAATAAATTATTTAAAATAAATCAATCCATA-T
** * * *
2753999 ACTACAAT-AATAAATCAAT-C-AAT--A-T-TTTAAAATAAATCAATCCATACAAATAAATT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T
2754055 ATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 -TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
2754110 TTTAAAATAAATCAATCCATATTAATAAATTATTT-AAATAAATCAAT-CATAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
2754162 TTTAAAGTAAATCAATCTATACTAAT-AATTATTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATC
2754210 TATACAACTA
Statistics
Matches: 275, Mismatches: 24, Indels: 43
0.80 0.07 0.13
Matches are distributed among these distances:
48 16 0.06
49 2 0.01
50 1 0.00
51 8 0.03
52 43 0.16
53 13 0.05
54 144 0.52
55 6 0.02
56 2 0.01
57 5 0.02
58 11 0.04
59 1 0.00
60 4 0.01
62 1 0.00
63 2 0.01
64 16 0.06
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:2753916 original size:18 final size:20
Alignment explanation
Indices: 2753866--2753964 Score: 79
Period size: 22 Copynumber: 5.1 Consensus size: 20
2753856 ACTAATAAAT
2753866 TATTTAAAATAAATCAATCCA
1 TATTT-AAATAAATCAATCCA
2753887 TATTTTAAAATAAATCAATCCA
1 TA-TTT-AAATAAATCAATCCA
2753909 TA-TT-AATAAAT---T--A
1 TATTTAAATAAATCAATCCA
*
2753922 T-TTAAAATAAATCAATCCA
1 TATTTAAATAAATCAATCCA
*
2753941 TATTTTAAAATAAATCAATTCA
1 TA-TTT-AAATAAATCAATCCA
2753963 TA
1 TA
2753965 CTAATAAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
13 3 0.05
14 7 0.11
15 1 0.02
17 1 0.02
18 7 0.11
19 2 0.03
20 2 0.03
21 4 0.06
22 37 0.58
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (20 bp):
TATTTAAATAAATCAATCCA
Found at i:2753919 original size:22 final size:22
Alignment explanation
Indices: 2753866--2753918 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
2753856 ACTAATAAAT
2753866 TATT-TAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
*
2753887 TATTTTAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
2753909 TATTAATAAA
1 TATT-ATAAA
2753919 TTATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (22 bp):
TATTATAAAATAAATCAATCCA
Found at i:2753973 original size:22 final size:22
Alignment explanation
Indices: 2753924--2753972 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2753914 ATAAATTATT
**
2753924 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
2753946 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2753969 TAAA
1 TAAA
2753973 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2754014 original size:220 final size:218
Alignment explanation
Indices: 2753567--2754283 Score: 980
Period size: 220 Copynumber: 3.3 Consensus size: 218
2753557 AATTATTTAA
* * *
2753567 AATAAAACAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
* * **
2753632 CTATAC-AACTACA--A--T--AATAAATCAATCTATATTTTAAAATAAATCAATCCATACAAAT
66 CTATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTAAT
** * * * * *
2753690 AAATTATTTAAAATAAATCAATC-TATACT--AATAAAT-TATTTAAAATAAATCAATCTATATT
130 AAATTATTTAAAATAAATCAATCATATTTTAAAATAAATCAATTCATACT-AAT-AA-AT-TA-T
*
2753751 TTAAAATAAATCAATTCATACTAA-TAAATTATTT
190 TTAAAATAAATCAA-TCATAC-AACTACA--A--T
2753785 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCA
2753850 ATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTAA
64 ATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTAA
2753915 TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTA
129 TAAATTATTTAAAATAAATCAAT-CATATTTTAAAATAAATCAATTCATACTAATAAATTATTTA
2753980 AAATAAATCAATCAATACAACTACAAT
193 AAATAAATCAATC-ATACAACTACAAT
*
2754007 AATAAATCAATCAATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
2754072 CTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTAATA
66 CTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTAATA
*
2754137 AATTATTT-AAATAAATCAATCATATTTTAAAGTAAATCAA-TCTATACTAAT-AATTATTTAAA
131 AATTATTTAAAATAAATCAATCATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAA
2754199 ATAAATCAATCTATACAACTACAAT
195 ATAAATCAATC-ATACAACTACAAT
* * *
2754224 AAT-AATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAAT
2754284 TATTTTAAAA
Statistics
Matches: 461, Mismatches: 21, Indels: 34
0.89 0.04 0.07
Matches are distributed among these distances:
216 54 0.12
217 40 0.09
218 27 0.06
219 12 0.03
220 208 0.45
221 2 0.00
222 2 0.00
224 2 0.00
225 4 0.01
226 84 0.18
227 3 0.01
228 5 0.01
229 2 0.00
230 10 0.02
231 6 0.01
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.35
Consensus pattern (218 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
CTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTAATA
AATTATTTAAAATAAATCAATCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAA
TAAATCAATCATACAACTACAAT
Found at i:2754060 original size:32 final size:32
Alignment explanation
Indices: 2754024--2754214 Score: 167
Period size: 32 Copynumber: 6.7 Consensus size: 32
2754014 CAATCAATAT
*
2754024 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
2754056 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2754088 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
2754110 TTTAAAATAAATCAATCCATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2754142 TTT-AAATAAATCAAT-CATA-T--T---TTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
2754166 ---AAG-TAAATCAATCTATACTAAT-AATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
2754193 TTTAAAATAAATCAATCTATAC
1 TTTAAAATAAATCAATCCATAC
2754215 AACTACAATA
Statistics
Matches: 131, Mismatches: 7, Indels: 43
0.72 0.04 0.24
Matches are distributed among these distances:
21 9 0.07
22 20 0.15
23 3 0.02
24 4 0.03
25 1 0.01
26 2 0.02
27 4 0.03
28 3 0.02
29 1 0.01
30 7 0.05
31 28 0.21
32 49 0.37
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.37
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:2754063 original size:14 final size:14
Alignment explanation
Indices: 2754046--2754099 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
2754036 CAATCCATAC
2754046 AAATAAATTATTTA
1 AAATAAATTATTTA
*
2754060 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
2754077 CTAATAAATTATTTA
1 -AAATAAATTATTTA
2754092 AAATAAAT
1 AAATAAAT
2754100 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:2754114 original size:22 final size:22
Alignment explanation
Indices: 2754088--2754132 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2754078 TAATAAATTA
2754088 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2754110 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2754132 T
1 T
2754133 AATAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2754136 original size:18 final size:20
Alignment explanation
Indices: 2754086--2754178 Score: 71
Period size: 22 Copynumber: 4.9 Consensus size: 20
2754076 ACTAATAAAT
2754086 TATTTAAAATAAATCAATCCA
1 TATTT-AAATAAATCAATCCA
2754107 TATTTTAAAATAAATCAATCCA
1 TA-TTT-AAATAAATCAATCCA
2754129 TA-TT-AAT--A--AAT---
1 TATTTAAATAAATCAATCCA
2754140 TATTTAAATAAATCAAT-CA
1 TATTTAAATAAATCAATCCA
2754159 TATTTTAAAGTAAATCAATC
1 TA-TTTAAA-TAAATCAATC
2754179 TATACTAATA
Statistics
Matches: 60, Mismatches: 0, Indels: 23
0.72 0.00 0.28
Matches are distributed among these distances:
11 2 0.03
12 2 0.03
13 3 0.05
14 3 0.05
15 1 0.02
16 1 0.02
17 3 0.05
18 3 0.05
19 2 0.03
20 8 0.13
21 11 0.18
22 21 0.35
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.38
Consensus pattern (20 bp):
TATTTAAATAAATCAATCCA
Found at i:2754139 original size:22 final size:22
Alignment explanation
Indices: 2754086--2754138 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
2754076 ACTAATAAAT
2754086 TATT-TAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
*
2754107 TATTTTAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
2754129 TATTAATAAA
1 TATT-ATAAA
2754139 TTATTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (22 bp):
TATTATAAAATAAATCAATCCA
Found at i:2754292 original size:15 final size:15
Alignment explanation
Indices: 2754263--2754380 Score: 148
Period size: 15 Copynumber: 7.5 Consensus size: 15
2754253 AATTCATACT
2754263 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
2754277 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
2754292 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
2754314 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
2754329 AATAAATTATTTTAT
1 AATAAATTATTTTAA
2754344 AATAAATTATTTTAA
1 AATAAATTATTTTAA
2754359 AATAAATTATTTTAA
1 AATAAATTATTTTAA
2754374 AATAAAT
1 AATAAAT
2754381 AACCTTATTA
Statistics
Matches: 92, Mismatches: 4, Indels: 15
0.83 0.04 0.14
Matches are distributed among these distances:
14 9 0.10
15 65 0.71
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:2754370 original size:45 final size:43
Alignment explanation
Indices: 2754265--2754402 Score: 146
Period size: 45 Copynumber: 3.3 Consensus size: 43
2754255 TTCATACTAA
*
2754265 TAAATTA-TTTAAAATAAATTATTTTAAAATAAAT---C--AA
1 TAAATTATTTTAAAATAAATTATTTTAAAATAAATAACCTTAT
** * * **
2754302 TCCA-TATTTTATAATAAATTATTTTAAAATAAATTATTTTAT
1 TAAATTATTTTAAAATAAATTATTTTAAAATAAATAACCTTAT
2754344 AATAAATTATTTTAAAATAAATTATTTTAAAATAAATAACCTTAT
1 --TAAATTATTTTAAAATAAATTATTTTAAAATAAATAACCTTAT
2754389 TAAATTATTTTAAA
1 TAAATTATTTTAAA
2754403 TTATTTTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
36 2 0.02
37 28 0.35
42 1 0.01
43 14 0.17
44 2 0.02
45 34 0.42
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (43 bp):
TAAATTATTTTAAAATAAATTATTTTAAAATAAATAACCTTAT
Found at i:2754436 original size:82 final size:81
Alignment explanation
Indices: 2754262--2754424 Score: 217
Period size: 82 Copynumber: 2.0 Consensus size: 81
2754252 CAATTCATAC
2754262 TAATAAATTA-TTTAAAATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTT
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTT
* *
2754326 TAAAATAAATTATTTTA
66 T-AAATAAATAACTTTA
* **
2754343 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAAT-AA-CCTTATTAAATTATTTTAAATTA
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATCAATCCATATT---TTATAATAAATTA
2754406 TTTT-AATAAATAACTTTA
63 TTTTAAATAAATAACTTTA
2754424 T
1 T
2754425 TTTATAATTA
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
80 6 0.08
81 25 0.34
82 27 0.37
83 15 0.21
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.47
Consensus pattern (81 bp):
TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTT
TAAATAAATAACTTTA
Found at i:2783269 original size:22 final size:26
Alignment explanation
Indices: 2783224--2783279 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
2783214 ATTTAGTTTC
2783224 TAATAAAATTAAGTTCTTTGATAAA-
1 TAATAAAATTAAGTTCTTTGATAAAT
2783249 TAATAAAATTAAG-T-TTT-ATAAAT
1 TAATAAAATTAAGTTCTTTGATAAAT
2783272 TAA-AAAAT
1 TAATAAAAT
2783280 AATAATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.33
23 6 0.20
24 1 0.03
25 13 0.43
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (26 bp):
TAATAAAATTAAGTTCTTTGATAAAT
Found at i:2784401 original size:474 final size:471
Alignment explanation
Indices: 2783506--2784428 Score: 1503
Period size: 474 Copynumber: 1.9 Consensus size: 471
2783496 CTTTTTTTAC
*
2783506 AAAAACGACTCTTTGTATTTTTATATTTAAAAATATTGATTTCTTCTCTAATTATAATTAATTTT
1 AAAAACGACTCTTTGTATTTTTATATTTAAAAATATTGATTTCTTATCTAATTATAATTAATTTT
*
2783571 ATTATTAATTATTGATTTGACATTTATAAGTAAAGCAAAACTATTTTTTTTTTATCTTTATACGT
66 ATTATTAATTATTGATTTGACATCTATAAGTAAAGCAAAACTATTTTTTTTTTATCTTTATACGT
* *
2783636 TTATATTTTTTATCCGCTTCCTCGCCCCTATAAGATTGTAGAAAAAATAATTTTTTTCATATAAG
131 TTATATTTTTTATCCGCTTCCTCGCCCCTATAAAATTGTAAAAAAAATAATTTTTTTCATATAAG
*
2783701 ATATTCACCATATTATTTCCCGAAATAAGATTTTTTATTAGTATGAAGGCGACGTGCATTCTTGG
196 ATATTCACCATATTATTTCCCGAAATAAGATTTTTTATTAGTACGAAGGCGACGTGCATTCTTGG
* *
2783766 GGTCTTATCTGTTTACCTGAAGAAGCCATGCAGTCGTAGGGTCTTCTTTATTTGCCTGAATACGT
261 GGTCTTATCTATTTACCTGAAGAAGACATGCAGTCGTAGGGTCTTCTTTATTTGCCTGAATAC-T
* *
2783831 CATGCAATCGTGGAGTCTTCATATTTACCTTGAAGACGCGTGGAGCACCGATCATCTTTAAATTG
325 CA-GCAATCGTGGAGTCTTCATATTTAACTTGAAGACGCATGGAGCACCGATCATCTTTAAATTG
* * *
2783896 ATAATGTACATTTTACCCTAGATGAGGAAATAATCCTCAGTTTGAATTATATTGTGAATGAGTCT
389 ATAATGTACATTTCACCCTAGATGAGGAAATAATCCTAAATTTGAATTATATTGTGAATGAGTCT
2783961 TTATATTTATTTAAAAAA
454 TTATATTTATTTAAAAAA
* *
2783979 AAAAATGAGTCTTTGTATTTTTATATTTAAAAATATTGATTTCTTATCTAATTATAATTAATTTT
1 AAAAACGACTCTTTGTATTTTTATATTTAAAAATATTGATTTCTTATCTAATTATAATTAATTTT
2784044 ATTATTAATTATTGATTTTGACATCTATAAGTAAAGCAAAACTATTATTATTTTTTTATCTTTAT
66 ATTATTAATTATTGA-TTTGACATCTATAAGTAAAGCAAAACTA-T-TT-TTTTTTTATCTTTAT
*
2784109 ACGTTTATATTTTTTATCTGCTTCCTCGCCCCTATAAAATTGTGAAAAAAAATAA-TTTTTTCAT
127 ACGTTTATATTTTTTATCCGCTTCCTCGCCCCTATAAAATTGT-AAAAAAAATAATTTTTTTCAT
*
2784173 ATAAGATATTCACCATATTATTTTCCGAAATAAGATTTTTTTTATTAGTACGAAGGCGACGTGCA
191 ATAAGATATTCACCATATTATTTCCCGAAATAAGA--TTTTTTATTAGTACGAAGGCGACGTGCA
* * * *
2784238 TTCTTGGGGTTTTCTCTATTTGCCTGAAGAAGACATGCAGTCGTAGGGTCTTCTTTGTTTGCCTG
254 TTCTTGGGGTCTTATCTATTTACCTGAAGAAGACATGCAGTCGTAGGGTCTTCTTTATTTGCCTG
* *
2784303 AATA-T-A-CAATCGTGGAGTCTTCATATTTAACTTGAAGACGCATGGAGCACCGATCGTTTTTA
319 AATACTCAGCAATCGTGGAGTCTTCATATTTAACTTGAAGACGCATGGAGCACCGATCATCTTTA
* * * *
2784365 AATTGATATTGTGCATTTCACCCTAGATGGGGAAATAATCTTAAATTTGAATTATATTGTGAAT
384 AATTGATAATGTACATTTCACCCTAGATGAGGAAATAATCCTAAATTTGAATTATATTGTGAAT
2784429 TAAAAAATCT
Statistics
Matches: 417, Mismatches: 26, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
473 77 0.18
474 136 0.33
475 1 0.00
476 3 0.01
477 100 0.24
478 10 0.02
479 90 0.22
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (471 bp):
AAAAACGACTCTTTGTATTTTTATATTTAAAAATATTGATTTCTTATCTAATTATAATTAATTTT
ATTATTAATTATTGATTTGACATCTATAAGTAAAGCAAAACTATTTTTTTTTTATCTTTATACGT
TTATATTTTTTATCCGCTTCCTCGCCCCTATAAAATTGTAAAAAAAATAATTTTTTTCATATAAG
ATATTCACCATATTATTTCCCGAAATAAGATTTTTTATTAGTACGAAGGCGACGTGCATTCTTGG
GGTCTTATCTATTTACCTGAAGAAGACATGCAGTCGTAGGGTCTTCTTTATTTGCCTGAATACTC
AGCAATCGTGGAGTCTTCATATTTAACTTGAAGACGCATGGAGCACCGATCATCTTTAAATTGAT
AATGTACATTTCACCCTAGATGAGGAAATAATCCTAAATTTGAATTATATTGTGAATGAGTCTTT
ATATTTATTTAAAAAA
Found at i:2795963 original size:50 final size:50
Alignment explanation
Indices: 2795888--2795985 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 50
2795878 AAGATTGCAA
*
2795888 ATGATAATTTCTTGTGCTTTACCTGAAGGTGAGGATATGGTCGGAACTGG
1 ATGATAATTTATTGTGCTTTACCTGAAGGTGAGGATATGGTCGGAACTGG
*
2795938 ATGATAATTTATTGTTCTTTACCTGAAGGTGAGGATATGGTCGGAACT
1 ATGATAATTTATTGTGCTTTACCTGAAGGTGAGGATATGGTCGGAACT
2795986 CCATCGGAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.36
Consensus pattern (50 bp):
ATGATAATTTATTGTGCTTTACCTGAAGGTGAGGATATGGTCGGAACTGG
Found at i:2798723 original size:42 final size:42
Alignment explanation
Indices: 2798655--2798766 Score: 172
Period size: 42 Copynumber: 2.7 Consensus size: 42
2798645 CAGGCACACA
* * *
2798655 ATTTCCAGACTTCTCA-TTCGAGAACTTGGATGAAGATTGGGC
1 ATTTCTAGACTTCTCACTTGGA-AACTTGGATGAAGAGTGGGC
*
2798697 ATTTCTATACTTCTCACTTGGAAACTTGGATGAAGAGTGGGC
1 ATTTCTAGACTTCTCACTTGGAAACTTGGATGAAGAGTGGGC
2798739 ATTTCTAGACTTCTCACTTGGAAACTTG
1 ATTTCTAGACTTCTCACTTGGAAACTTG
2798767 ACAGAATAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 60 0.94
43 4 0.06
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (42 bp):
ATTTCTAGACTTCTCACTTGGAAACTTGGATGAAGAGTGGGC
Found at i:2798778 original size:42 final size:42
Alignment explanation
Indices: 2798655--2798781 Score: 159
Period size: 42 Copynumber: 3.0 Consensus size: 42
2798645 CAGGCACACA
* * * *
2798655 ATTTCCAGACTTCTCA-TTCGAGAACTTGGATGAAGATTGGGC
1 ATTTCTAGACTTCTCACTTGGA-AACTTGGAAGAAGAGTGGGC
* *
2798697 ATTTCTATACTTCTCACTTGGAAACTTGGATGAAGAGTGGGC
1 ATTTCTAGACTTCTCACTTGGAAACTTGGAAGAAGAGTGGGC
*
2798739 ATTTCTAGACTTCTCACTTGGAAACTT-GACAGAATAGTGGGC
1 ATTTCTAGACTTCTCACTTGGAAACTTGGA-AGAAGAGTGGGC
2798781 A
1 A
2798782 GGACAAAGCA
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.03
42 70 0.92
43 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (42 bp):
ATTTCTAGACTTCTCACTTGGAAACTTGGAAGAAGAGTGGGC
Found at i:2801640 original size:20 final size:20
Alignment explanation
Indices: 2801615--2801699 Score: 68
Period size: 20 Copynumber: 4.2 Consensus size: 20
2801605 GAAATCTAAT
2801615 TTCGCAACACAGTTTCCAAA
1 TTCGCAACACAGTTTCCAAA
* *
2801635 TTCGCAACGCGATTTTCCCAAA
1 TTCGCAACAC-AGTTT-CCAAA
* *
2801657 TTCGCTACTCAGTTTCTGC-AA
1 TTCGCAACACAGTTTC--CAAA
2801678 -TCGCAACAC-GATTTCCAAA
1 TTCGCAACACAG-TTTCCAAA
2801697 TTC
1 TTC
2801700 ACAATACGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
18 1 0.02
19 3 0.06
20 23 0.45
21 10 0.20
22 14 0.27
ACGTcount: A:0.28, C:0.31, G:0.12, T:0.29
Consensus pattern (20 bp):
TTCGCAACACAGTTTCCAAA
Found at i:2801774 original size:20 final size:21
Alignment explanation
Indices: 2801738--2801779 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
2801728 AATTTCTGAA
*
2801738 TTTGCAACGCGAATTT-CTTT
1 TTTGCAACACGAATTTCCTTT
2801758 TTTGCAACAC-AAGTTTCCTTT
1 TTTGCAACACGAA-TTTCCTTT
2801779 T
1 T
2801780 CGTAACAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 2 0.11
20 12 0.63
21 5 0.26
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (21 bp):
TTTGCAACACGAATTTCCTTT
Found at i:2801850 original size:20 final size:20
Alignment explanation
Indices: 2801827--2801866 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2801817 TTTCATAATT
2801827 CGAATTTCGAA-TTCGCAACA
1 CGAATTT-GAATTTCGCAACA
*
2801847 CGAATTTTAATTTCGCAACA
1 CGAATTTGAATTTCGCAACA
2801867 GCTTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (20 bp):
CGAATTTGAATTTCGCAACA
Found at i:2802024 original size:22 final size:22
Alignment explanation
Indices: 2801982--2802025 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2801972 CTCTCTCCGG
*
2801982 CGACATCCGTTCTTATATCTAA
1 CGACATCCGTTCTCATATCTAA
*
2802004 CGACATCC-TTCCTCATCTCTAA
1 CGACATCCGTT-CTCATATCTAA
2802026 TTTTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.25, C:0.34, G:0.07, T:0.34
Consensus pattern (22 bp):
CGACATCCGTTCTCATATCTAA
Found at i:2802042 original size:14 final size:15
Alignment explanation
Indices: 2802023--2802060 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
2802013 TCCTCATCTC
2802023 TAATTTTTTT-TATA
1 TAATTTTTTTCTATA
2802037 TAATTTTATTTCTATA
1 TAATTTT-TTTCTATA
2802053 TAATTTTT
1 TAATTTTT
2802061 CAATGATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.32
15 4 0.18
16 11 0.50
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TAATTTTTTTCTATA
Found at i:2802829 original size:24 final size:24
Alignment explanation
Indices: 2802802--2802855 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2802792 GTATTCGAAA
2802802 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
2802826 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
2802850 TTTGAT
1 TTTGAT
2802856 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:2806886 original size:21 final size:21
Alignment explanation
Indices: 2806860--2806935 Score: 134
Period size: 21 Copynumber: 3.6 Consensus size: 21
2806850 CATGTGAATC
2806860 GGCCTCTTGAACGGTGGGAGG
1 GGCCTCTTGAACGGTGGGAGG
2806881 GGCCTCTTGAACGGTGGGAGG
1 GGCCTCTTGAACGGTGGGAGG
* *
2806902 GGCCTCTTGAACGATGAGAGG
1 GGCCTCTTGAACGGTGGGAGG
2806923 GGCCTCTTGAACG
1 GGCCTCTTGAACG
2806936 ATATGAGAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.17, C:0.21, G:0.42, T:0.20
Consensus pattern (21 bp):
GGCCTCTTGAACGGTGGGAGG
Found at i:2806936 original size:21 final size:21
Alignment explanation
Indices: 2806860--2806960 Score: 132
Period size: 21 Copynumber: 4.8 Consensus size: 21
2806850 CATGTGAATC
* *
2806860 GGCCTCTTGAACGGTGGGAGG
1 GGCCTCTTGAACGATGAGAGG
* *
2806881 GGCCTCTTGAACGGTGGGAGG
1 GGCCTCTTGAACGATGAGAGG
2806902 GGCCTCTTGAACGATGAGAGG
1 GGCCTCTTGAACGATGAGAGG
*
2806923 GGCCTCTTGAACGAT-ATGAGA
1 GGCCTCTTGAACGATGA-GAGG
*
2806944 AGCCTCTTGAACGATGA
1 GGCCTCTTGAACGATGA
2806961 CATGTGAATC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
20 1 0.01
21 72 0.97
22 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.21
Consensus pattern (21 bp):
GGCCTCTTGAACGATGAGAGG
Found at i:2807389 original size:21 final size:21
Alignment explanation
Indices: 2807365--2807417 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2807355 TGCACCATTG
**
2807365 TCATCACGTAAAGTACCGACC
1 TCATCACGTAAAACACCGACC
*
2807386 TCATCACGTAAAACACTGACC
1 TCATCACGTAAAACACCGACC
2807407 TCATCACGTAA
1 TCATCACGTAA
2807418 CTCTCCTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.32, G:0.11, T:0.21
Consensus pattern (21 bp):
TCATCACGTAAAACACCGACC
Found at i:2807611 original size:42 final size:42
Alignment explanation
Indices: 2807532--2807630 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
2807522 GTGATGGAAT
* * * *
2807532 AGGTGATGGCTCTCGTTGTGGAAGTGTATAATCGGCTCAATC
1 AGGTGATGGCTCTCGGTGTCGAAGTGTAGAATAGGCTCAATC
* *
2807574 AGGTGATGGCTCTGGGTGTCG-AGCTGTAGAATAGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAAG-TGTAGAATAGGCTCAATC
2807616 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
2807631 AAATGGGGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 2 0.04
42 47 0.96
ACGTcount: A:0.19, C:0.17, G:0.35, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAAGTGTAGAATAGGCTCAATC
Found at i:2809153 original size:20 final size:20
Alignment explanation
Indices: 2809130--2809171 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2809120 AAACTTAAAT
2809130 TCGCAACACGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
*
2809150 TCGCAACGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
2809170 TC
1 TC
2809172 CGATTTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.21, G:0.17, T:0.12
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:2809569 original size:22 final size:22
Alignment explanation
Indices: 2809541--2809632 Score: 166
Period size: 22 Copynumber: 4.2 Consensus size: 22
2809531 ATAGAGGGGG
*
2809541 GTCGCCGGATATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
2809563 GTCGCCGGAGATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
*
2809585 GTCGCCGGAGATGAGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
2809607 GTCGCCGGAGATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
2809629 GTCG
1 GTCG
2809633 TCGTAGAGAG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 67 1.00
ACGTcount: A:0.18, C:0.18, G:0.48, T:0.15
Consensus pattern (22 bp):
GTCGCCGGAGATGGGGACGGAT
Found at i:2809808 original size:20 final size:20
Alignment explanation
Indices: 2809783--2809831 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2809773 TTAACGCGCT
2809783 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
*
2809803 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTATGTG
*
2809823 TTACGAATT
1 TTGCGAATT
2809832 ACAAATTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:2814359 original size:19 final size:18
Alignment explanation
Indices: 2814337--2814372 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2814327 TTAAAGGCTA
*
2814337 TTTGTACTATTTCTCTCTC
1 TTTGTAATATTTC-CTCTC
2814356 TTTGTAATATTTCCTCT
1 TTTGTAATATTTCCTCT
2814373 ATTAGTGAAA
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:0.14, C:0.22, G:0.06, T:0.58
Consensus pattern (18 bp):
TTTGTAATATTTCCTCTC
Found at i:2820268 original size:2 final size:2
Alignment explanation
Indices: 2820261--2820285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2820251 AACTGTTTTC
2820261 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 A
2820286 AACTTACCTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2823555 original size:20 final size:20
Alignment explanation
Indices: 2823530--2823576 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2823520 GGTAATTAGA
2823530 GTTGCGAATTTGAAAATCGC
1 GTTGCGAATTTGAAAATCGC
*
2823550 GTTGCGAATTTTAAAATCGC
1 GTTGCGAATTTGAAAATCGC
*
2823570 ATTGCGA
1 GTTGCGA
2823577 TAGTACTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGC
Found at i:2823587 original size:77 final size:77
Alignment explanation
Indices: 2823480--2823768 Score: 366
Period size: 77 Copynumber: 3.7 Consensus size: 77
2823470 GCAACGAGAT
* * **
2823480 TTTTCAAATTCGCGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGAGTTGCGAATTTGAAA
1 TTTT-AAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTAGAGTTGCGAATTTGAAA
2823545 ATCGCGTTGCGAA
65 ATCGCGTTGCGAA
* * *
2823558 TTTTAAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTACGAATTTGATAA
1 TTTTAAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTAGAGTTGCGAATTTGAAAA
2823623 TCGCGTTGCGAA
66 TCGCGTTGCGAA
* *
2823635 TTTGAAAATCGCATTGCGATAGTATTGTTTACCTATATCGGTAATTA-ACGTTGCGAATTTGAAA
1 TTTTAAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTAGA-GTTGCGAATTTGAAA
**
2823699 ATCGTATTGC-AA
65 ATCGCGTTGCGAA
** * * ** * *
2823711 TAGTACTATTTACATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGATGCGAA
1 TTTTA-AAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTAGAGTTGCGAA
2823769 CGCGATTTTC
Statistics
Matches: 184, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
76 4 0.02
77 176 0.96
78 4 0.02
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (77 bp):
TTTTAAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTAGAGTTGCGAATTTGAAAA
TCGCGTTGCGAA
Found at i:2823634 original size:20 final size:20
Alignment explanation
Indices: 2823605--2823653 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2823595 TCGGTAATTA
* *
2823605 GCGTTACGAATTTGATAATC
1 GCGTTGCGAATTTGAAAATC
2823625 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
*
2823645 GCATTGCGA
1 GCGTTGCGA
2823654 TAGTATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:2823727 original size:20 final size:20
Alignment explanation
Indices: 2823704--2823743 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2823694 TGAAAATCGT
2823704 ATTGCAATAGTACTATTTAC
1 ATTGCAATAGTACTATTTAC
* *
2823724 ATTGCGATAGTACTGTTTAC
1 ATTGCAATAGTACTATTTAC
2823744 CTATATCGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
ATTGCAATAGTACTATTTAC
Found at i:2824774 original size:23 final size:23
Alignment explanation
Indices: 2824748--2824791 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2824738 TTTTTGGTTC
2824748 AATTAAAATTTAAATATTATTAA
1 AATTAAAATTTAAATATTATTAA
*
2824771 AATTAAAATTTAAATGTTATT
1 AATTAAAATTTAAATATTATT
2824792 TGATTGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AATTAAAATTTAAATATTATTAA
Found at i:2832231 original size:2 final size:2
Alignment explanation
Indices: 2832226--2832261 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2832216 TTGATAAACA
2832226 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
2832262 GTAATACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2834785 original size:17 final size:17
Alignment explanation
Indices: 2834760--2834793 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2834750 TATTTTAAAA
2834760 ATATATAATATATTTTT
1 ATATATAATATATTTTT
* *
2834777 ATATGTAATCTATTTTT
1 ATATATAATATATTTTT
2834794 TTAATAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
ATATATAATATATTTTT
Found at i:2843137 original size:40 final size:40
Alignment explanation
Indices: 2843067--2843144 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
2843057 ATTGGAGAGG
* ***
2843067 TTTTAAAATATTCTAGAGCTTTCTGTAGAAGTGTAGAATT
1 TTTTAAAATATTCCAGAGAACTCTGTAGAAGTGTAGAATT
2843107 TTTTAAAATATTCCAGAGAACTCTAG-AGAAGTGTAGAA
1 TTTTAAAATATTCCAGAGAACTCT-GTAGAAGTGTAGAA
2843145 CTCTCTAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (40 bp):
TTTTAAAATATTCCAGAGAACTCTGTAGAAGTGTAGAATT
Found at i:2843232 original size:10 final size:10
Alignment explanation
Indices: 2843209--2843275 Score: 59
Period size: 10 Copynumber: 6.9 Consensus size: 10
2843199 TGTGGAACCT
2843209 TATGGAA-AA
1 TATGGAAGAA
2843218 GTATGGAAGAA
1 -TATGGAAGAA
*
2843229 TATGAAAGAA
1 TATGGAAGAA
*
2843239 -ATGGAAGAG
1 TATGGAAGAA
*
2843248 CATGGAAGAA
1 TATGGAAGAA
* *
2843258 TATGAAAGGA
1 TATGGAAGAA
2843268 -ATGGAAGA
1 TATGGAAGA
2843276 GTGTAGAGCT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
9 13 0.28
10 31 0.67
11 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.31, T:0.16
Consensus pattern (10 bp):
TATGGAAGAA
Found at i:2843252 original size:29 final size:29
Alignment explanation
Indices: 2843210--2843276 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
2843200 GTGGAACCTT
* *
2843210 ATGGAAAAGTATGGAAGAATATGAAAGAA
1 ATGGAAGAGCATGGAAGAATATGAAAGAA
*
2843239 ATGGAAGAGCATGGAAGAATATGAAAGGA
1 ATGGAAGAGCATGGAAGAATATGAAAGAA
2843268 ATGGAAGAG
1 ATGGAAGAG
2843277 TGTAGAGCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.51, C:0.01, G:0.33, T:0.15
Consensus pattern (29 bp):
ATGGAAGAGCATGGAAGAATATGAAAGAA
Found at i:2843256 original size:19 final size:20
Alignment explanation
Indices: 2843210--2843275 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 20
2843200 GTGGAACCTT
2843210 ATGGAA-AAGTATGGAAGA-A
1 ATGGAAGAA-TATGGAAGAGA
* *
2843229 TATGAAAGAA-ATGGAAGAGC
1 -ATGGAAGAATATGGAAGAGA
*
2843249 ATGGAAGAATATGAAAG-GA
1 ATGGAAGAATATGGAAGAGA
2843268 ATGGAAGA
1 ATGGAAGA
2843276 GTGTAGAGCT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 25 0.66
20 11 0.29
21 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.32, T:0.15
Consensus pattern (20 bp):
ATGGAAGAATATGGAAGAGA
Found at i:2860994 original size:106 final size:106
Alignment explanation
Indices: 2860807--2861002 Score: 275
Period size: 106 Copynumber: 1.8 Consensus size: 106
2860797 TTAAAAAGGC
* * * * *
2860807 GAAGAAATGATGATATAAAAGCGAAAAATAAATAATATTTTAATCATTATAAGCTTCTCATTCAC
1 GAAGAAAAGATGATATAAAAGCGAAAAATAAATAATATTTTAATAAGTACAAACTTCTCATTCAC
* *
2860872 GTTAAACAACATAACACCCAAAAAAATGGTTGTGCATCATT
66 CTTAAACAACACAACACCCAAAAAAATGGTTGTGCATCATT
* ** * *
2860913 GAAGAAAAGATGATGTAAAAGTTAAAAGTAAATAATATTTTAATAAGTACAAACTTCTCATTTAC
1 GAAGAAAAGATGATATAAAAGCGAAAAATAAATAATATTTTAATAAGTACAAACTTCTCATTCAC
*
2860978 CTTAAACAATACAACACCCAAAAAA
66 CTTAAACAACACAACACCCAAAAAA
2861003 TGAGTGTGCA
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
106 77 1.00
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (106 bp):
GAAGAAAAGATGATATAAAAGCGAAAAATAAATAATATTTTAATAAGTACAAACTTCTCATTCAC
CTTAAACAACACAACACCCAAAAAAATGGTTGTGCATCATT
Found at i:2864875 original size:9 final size:10
Alignment explanation
Indices: 2864850--2864879 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2864840 AAAATCAAAA
2864850 TTCCCGATTT
1 TTCCCGATTT
2864860 TTCCCGATTT
1 TTCCCGATTT
2864870 TT-CCGATTT
1 TTCCCGATTT
2864879 T
1 T
2864880 CAGCCGGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.10, C:0.27, G:0.10, T:0.53
Consensus pattern (10 bp):
TTCCCGATTT
Found at i:2870927 original size:24 final size:24
Alignment explanation
Indices: 2870900--2870949 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2870890 ATAAAGAACC
2870900 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAATCTTAAACAT-CCATTA
*
2870924 AAAATAAATTTTAAACATCCATTA
1 AAAATAAATCTTAAACATCCATTA
2870948 AA
1 AA
2870950 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAATAAATCTTAAACATCCATTA
Found at i:2874682 original size:2 final size:2
Alignment explanation
Indices: 2874675--2874706 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2874665 GTTAACTTTA
2874675 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
2874707 TATTTGTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2878316 original size:23 final size:25
Alignment explanation
Indices: 2878289--2878336 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
2878279 AAAAAAACAT
2878289 ATTTAAAAATTAAT-AA-ATTTATA
1 ATTTAAAAATTAATGAAGATTTATA
**
2878312 ATTTATCAATTAATGAAGATTTATA
1 ATTTAAAAATTAATGAAGATTTATA
2878337 TATATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 2 0.10
25 7 0.33
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (25 bp):
ATTTAAAAATTAATGAAGATTTATA
Found at i:2882272 original size:3 final size:3
Alignment explanation
Indices: 2882266--2882308 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
2882256 TTTTTTTCTT
* *
2882266 TTA TTA TTA TTA TTA TTA TTA TTA TTT TTCA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
2882309 CCATCATCGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 33 0.94
4 2 0.06
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2896089 original size:14 final size:14
Alignment explanation
Indices: 2896070--2896100 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2896060 AAAGAAATGT
2896070 AATTTAAAATAAAA
1 AATTTAAAATAAAA
*
2896084 AATTTATAATAAAA
1 AATTTAAAATAAAA
2896098 AAT
1 AAT
2896101 ATAATGATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATTTAAAATAAAA
Found at i:2898491 original size:12 final size:12
Alignment explanation
Indices: 2898471--2898504 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2898461 TTCGTGCGAT
2898471 TTTTCGTTATAAA
1 TTTT-GTTATAAA
2898484 TTTTGTTATAAA
1 TTTTGTTATAAA
*
2898496 TTTTTTTAT
1 TTTTGTTAT
2898505 TATACTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (12 bp):
TTTTGTTATAAA
Found at i:2903088 original size:18 final size:17
Alignment explanation
Indices: 2903056--2903101 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2903046 AAATTATATT
2903056 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
*
2903073 AGTAAAATGCTTAAATAA
1 AGTAAAAT-ATTAAATAA
*
2903091 ATTAAATATAT
1 AGTAAA-ATAT
2903102 AATATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.33
18 14 0.58
19 2 0.08
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:2909881 original size:210 final size:212
Alignment explanation
Indices: 2909508--2909918 Score: 790
Period size: 210 Copynumber: 1.9 Consensus size: 212
2909498 GCTGCTGGTT
*
2909508 TTAGGGATAGCCTTAGGCCCTTAGCTATAGATGCTAACTAGCTCTATCTGGTTTGTGTTTTTCCT
1 TTAGGGATACCCTTAGGCCCTTAGCTATAGATGCTAACTAGCTCTATCTGGTTTGTGTTTTTCCT
2909573 TCAAAATTCAAGTGGAATTTAGGGTCAGCAATTAGATTTCGTTCGTCGGGAAAGTGTACAACAGG
66 TCAAAATTCAAGTGGAATTTAGGGTCAGCAATTAGATTTCGTTCGTCGGGAAAGTGTACAACAGG
*
2909638 GCAGAAAACCTTGAAATATTTCGAAAAACTAGTGCCTGTGATGGGTCCAAGATTAAGAACAAACA
131 GCAGAAAACCTTGAAATATTTCGAAAAACTAGTGCCTGTGATGGGTACAAGATTAAGAACAAACA
2909703 ATTGACGCCTTAGGCCC
196 ATTGACGCCTTAGGCCC
2909720 TTAGGGAT-CCCTTAGGCCCTTAGCTATAGATGCTAACTAGCTCTATCTGGTTTGTG-TTTTCCT
1 TTAGGGATACCCTTAGGCCCTTAGCTATAGATGCTAACTAGCTCTATCTGGTTTGTGTTTTTCCT
2909783 TCAAAATTCAAGTGGAATTTAGGGTCAGCAATTAGATTTCGTTCGTCGGGAAAGTGTACAACAGG
66 TCAAAATTCAAGTGGAATTTAGGGTCAGCAATTAGATTTCGTTCGTCGGGAAAGTGTACAACAGG
2909848 GCAGAAAACCTTGAAATATTTCGAAAAACTAGTGCCTGTGATGGGTACAAGATTAAGAACAAACA
131 GCAGAAAACCTTGAAATATTTCGAAAAACTAGTGCCTGTGATGGGTACAAGATTAAGAACAAACA
2909913 ATTGAC
196 ATTGAC
2909919 AACAAATATA
Statistics
Matches: 197, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
210 142 0.72
211 47 0.24
212 8 0.04
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (212 bp):
TTAGGGATACCCTTAGGCCCTTAGCTATAGATGCTAACTAGCTCTATCTGGTTTGTGTTTTTCCT
TCAAAATTCAAGTGGAATTTAGGGTCAGCAATTAGATTTCGTTCGTCGGGAAAGTGTACAACAGG
GCAGAAAACCTTGAAATATTTCGAAAAACTAGTGCCTGTGATGGGTACAAGATTAAGAACAAACA
ATTGACGCCTTAGGCCC
Found at i:2929040 original size:11 final size:11
Alignment explanation
Indices: 2929024--2929051 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2929014 ATAAAATAAA
2929024 AAATAAACAAT
1 AAATAAACAAT
2929035 AAATAAACAAT
1 AAATAAACAAT
2929046 AAATAA
1 AAATAA
2929052 TAATTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (11 bp):
AAATAAACAAT
Found at i:2929040 original size:18 final size:18
Alignment explanation
Indices: 2929017--2929059 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2929007 AAAAATTATA
2929017 AAATAAAAAATAAACAAT
1 AAATAAAAAATAAACAAT
* *
2929035 AAATAAACAATAAATAAT
1 AAATAAAAAATAAACAAT
*
2929053 AATTAAA
1 AAATAAA
2929060 TTTATACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (18 bp):
AAATAAAAAATAAACAAT
Found at i:2929530 original size:2 final size:2
Alignment explanation
Indices: 2929519--2929548 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2929509 TCTGCATTTT
2929519 TA TA -A 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 T
2929549 GTATTAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2930837 original size:2 final size:2
Alignment explanation
Indices: 2930830--2930873 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2930820 TATGCCTTTA
2930830 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
2930872 AT
1 AT
2930874 CATTTTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2932055 original size:5 final size:5
Alignment explanation
Indices: 2932038--2932067 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
2932028 CACTAACTCT
2932038 TTTTA TCTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA T-TTTA TTTTA TTTTA TTTTA TTTT
2932068 CATCACTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:2934720 original size:22 final size:22
Alignment explanation
Indices: 2934690--2934740 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2934680 CCCCATCAAT
*
2934690 CCTTGGAGCATCAAACACCAAA
1 CCTTTGAGCATCAAACACCAAA
**
2934712 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAACACCAAA
2934734 CCTTTGA
1 CCTTTGA
2934741 TCAAACGCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.22
Consensus pattern (22 bp):
CCTTTGAGCATCAAACACCAAA
Found at i:2935178 original size:18 final size:18
Alignment explanation
Indices: 2935143--2935178 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2935133 TCAACATCAA
**
2935143 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCCTTGG
2935161 ATATTGGGGCATCCTTGG
1 ATATTGGGGCATCCTTGG
2935179 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.33, T:0.39
Consensus pattern (18 bp):
ATATTGGGGCATCCTTGG
Found at i:2935468 original size:19 final size:20
Alignment explanation
Indices: 2935431--2935468 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2935421 GAATGCTCGG
2935431 AGGGAACCGATTCCCCCCCA
1 AGGGAACCGATTCCCCCCCA
*
2935451 AGGGTACCGATTCCCCCC
1 AGGGAACCGATTCCCCCC
2935469 TGTTCAACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.13
Consensus pattern (20 bp):
AGGGAACCGATTCCCCCCCA
Done.