Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 71 of 171
Found at i:25535624 original size:49 final size:49
Alignment explanation
Indices: 25535542--25535707 Score: 190
Period size: 51 Copynumber: 3.4 Consensus size: 49
25535532 TCCCTTCAAA
* ** * *
25535542 TCTTCGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCTTGTG
1 TCTTCGCGGTACTGGATCTACCATTACGGTCTTAGATCTTTCCCTTGTG
* *
25535590 TCTTCGCGGTACTGGATCTATCATTACGGTCTTAGATCTTTCCCTTCTGTA
1 TCTTCGCGGTACTGGATCTACCATTACGGTCTTAGATCTTTCCC-T-TGTG
* * * * *
25535641 TCTTTGTGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCTTGTG
1 TCTTCGCGGTACTGGATCTACCATTACGGTCTTAGATCTTTCCCTTGTG
*
25535690 TCTTCGCGATACTGGATC
1 TCTTCGCGGTACTGGATC
25535708 CACCGTTGCA
Statistics
Matches: 98, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
48 23 0.23
49 32 0.33
50 2 0.02
51 41 0.42
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.40
Consensus pattern (49 bp):
TCTTCGCGGTACTGGATCTACCATTACGGTCTTAGATCTTTCCCTTGTG
Found at i:25535725 original size:49 final size:49
Alignment explanation
Indices: 25535542--25535783 Score: 240
Period size: 49 Copynumber: 4.9 Consensus size: 49
25535532 TCCCTTCAAA
* *
25535542 TCTTCGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCTTGTG
1 TCTTCGCGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCCCTTGTG
* * * * *
25535590 TCTTCGCGGTACTGGATCTATCATTACGGTCTTAGATCTTTCCCTTCTGTA
1 TCTTCGCGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCCC-T-TGTG
* * **
25535641 TCTTTGTGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCTTGTG
1 TCTTCGCGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCCCTTGTG
* *
25535690 TCTTCGCGATACTGGATCCACCGTTGCAG-CATTAGATCTTT-CCTGTCGTG
1 TCTTCGCGGTACTGGATCCACCGTTGCGGTC-TTAGATCTTTCCCT-T-GTG
* * * * * *
25535740 TTTTTGTGGTACTGGATCCGCAGTCGCGG-CTTAGATCTTTCCCT
1 TCTTCGCGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCCCT
25535784 GTCAAACCTG
Statistics
Matches: 159, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
48 27 0.17
49 61 0.38
50 30 0.19
51 41 0.26
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.39
Consensus pattern (49 bp):
TCTTCGCGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCCCTTGTG
Found at i:25535725 original size:100 final size:100
Alignment explanation
Indices: 25535541--25535783 Score: 334
Period size: 99 Copynumber: 2.5 Consensus size: 100
25535531 TTCCCTTCAA
* *
25535541 ATCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTGTCTTCGCGGTACTGGA
1 ATCTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTGTCTTCGCGATACTGGA
* * *
25535606 TCTATCATTACGGTCTTAGATCTTTCCCT-TC-TGT
66 TCCACCATTACAGTCTTAGATCTTT-CCTGTCGTGT
*
25535640 ATCTTTGTGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCTTGTGTCTTCGCGATACTGG
1 ATCTTTGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCTTGTGTCTTCGCGATACTGG
* *
25535705 ATCCACCGTTGCAG-CATTAGATCTTTCCTGTCGTGT
65 ATCCACCATTACAGTC-TTAGATCTTTCCTGTCGTGT
* *
25535741 -T-TTTGTGGTACTGGATCCGCAGTCGCGGCTTAGATCTTTCCCT
1 ATCTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCT
25535784 GTCAAACCTG
Statistics
Matches: 129, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
98 15 0.12
99 56 0.43
100 55 0.43
101 3 0.02
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.39
Consensus pattern (100 bp):
ATCTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTGTCTTCGCGATACTGGA
TCCACCATTACAGTCTTAGATCTTTCCTGTCGTGT
Found at i:25541829 original size:58 final size:59
Alignment explanation
Indices: 25541686--25541951 Score: 176
Period size: 59 Copynumber: 4.6 Consensus size: 59
25541676 TGAAACTTTA
* * * * * *
25541686 GACATCCGAGGGTAAAACGGTAACTTTAT-AAAAAATCAGGAT-AAAAA-ACGTTATTTTTG
1 GACATTCGAGGGTAAAAAGGTAA-TTTTTGAAAGAATCGGGATCAAAAATA-G-AATTTTTG
*
25541745 GACA-TCTGAGGGTAAAATGGTAATTTTTAGAAA-AATCGGGATCAAAAATAGAA-TTTTG
1 GACATTC-GAGGGTAAAAAGGTAATTTTT-GAAAGAATCGGGATCAAAAATAGAATTTTTG
* * ** * *
25541803 GACATTCGGGGGTAAAAGGGTAA-TTTTGAAAGTTTTGGGGTCAAAAATAGAATTTTTG
1 GACATTCGAGGGTAAAAAGGTAATTTTTGAAAGAATCGGGATCAAAAATAGAATTTTTG
* * * ** * * *
25541861 GA-AGTTCGAGGGTAAAAATGTAATTTTGGGAAGGTTTGGGGTCAAAAATGGAATTTTTG
1 GACA-TTCGAGGGTAAAAAGGTAATTTTTGAAAGAATCGGGATCAAAAATAGAATTTTTG
* *
25541920 GA-AGTTCTG-GGGT-AAAATGTAATTTTTAAAAG
1 GACA-TTC-GAGGGTAAAAAGGTAATTTTTGAAAG
25541952 TTTTAGGGTC
Statistics
Matches: 175, Mismatches: 21, Indels: 23
0.80 0.10 0.11
Matches are distributed among these distances:
56 4 0.02
57 21 0.12
58 67 0.38
59 72 0.41
60 10 0.06
61 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (59 bp):
GACATTCGAGGGTAAAAAGGTAATTTTTGAAAGAATCGGGATCAAAAATAGAATTTTTG
Found at i:25541866 original size:30 final size:28
Alignment explanation
Indices: 25541826--25542014 Score: 150
Period size: 30 Copynumber: 6.4 Consensus size: 28
25541816 AAAAGGGTAA
*
25541826 TTTTGAAAGTTTTGGGGTCAAAAATAGAAT
1 TTTTGGAAGTTTTGGGGT-AAAAAT-GAAT
*
25541856 TTTTGGAAG-TTCGAGGGTAAAAATGTAAT
1 TTTTGGAAGTTTTG-GGGTAAAAATG-AAT
* *
25541885 TTTGGGAAGGTTTGGGGTCAAAAATGGAAT
1 TTTTGGAAGTTTTGGGGT-AAAAAT-GAAT
*
25541915 TTTTGGAAGTTCTGGGGT-AAAATGTAAT
1 TTTTGGAAGTTTTGGGGTAAAAATG-AAT
** *
25541943 TTTTAAAAGTTTTAGGGTCAAAAATGGAAT
1 TTTTGGAAGTTTTGGGGT-AAAAAT-GAAT
* * *
25541973 TTTTAGAAG-TTCGGAGGTAAAAATATAAT
1 TTTTGGAAGTTTTGG-GGTAAAAAT-GAAT
25542002 TTTTGGACAGTTT
1 TTTTGGA-AGTTT
25542015 AGGGACCTTC
Statistics
Matches: 130, Mismatches: 17, Indels: 23
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.01
28 23 0.18
29 42 0.32
30 60 0.46
31 4 0.03
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.37
Consensus pattern (28 bp):
TTTTGGAAGTTTTGGGGTAAAAATGAAT
Found at i:25541965 original size:58 final size:58
Alignment explanation
Indices: 25541786--25542006 Score: 270
Period size: 58 Copynumber: 3.8 Consensus size: 58
25541776 AAAATCGGGA
**
25541786 TCAAAAATAGAA-TTTTGGACA-TTCGGGGGTAAAAGGGTAA-TTTTGAAAGTTTTGGGG
1 TCAAAAATAGAATTTTTGGA-AGTTC-GGGGTAAAAATGTAATTTTTGAAAGTTTTGGGG
* * *
25541843 TCAAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTGGGAAGGTTTGGGG
1 TCAAAAATAGAATTTTTGGAAGTTCG-GGGTAAAAATGTAATTTTTGAAAGTTTTGGGG
* * *
25541902 TCAAAAATGGAATTTTTGGAAGTTCTGGGGT-AAAATGTAATTTTTAAAAGTTTTAGGG
1 TCAAAAATAGAATTTTTGGAAGTTC-GGGGTAAAAATGTAATTTTTGAAAGTTTTGGGG
* * *
25541960 TCAAAAATGGAATTTTTAGAAGTTCGGAGGTAAAAATATAATTTTTG
1 TCAAAAATAGAATTTTTGGAAGTTCGG-GGTAAAAATGTAATTTTTG
25542007 GACAGTTTAG
Statistics
Matches: 143, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
57 16 0.11
58 71 0.50
59 55 0.38
60 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.34
Consensus pattern (58 bp):
TCAAAAATAGAATTTTTGGAAGTTCGGGGTAAAAATGTAATTTTTGAAAGTTTTGGGG
Found at i:25541974 original size:117 final size:116
Alignment explanation
Indices: 25541786--25542004 Score: 309
Period size: 117 Copynumber: 1.9 Consensus size: 116
25541776 AAAATCGGGA
* *
25541786 TCAAAAATAGAATTTTGGACATTCGGGGGTAAAAGGGTAATTTTGAAAGTTTTGGGGTCAAAAAT
1 TCAAAAATAGAATTTTGGACATTCGGGGGTAAAAGGGTAATTTTAAAAGTTTTAGGGTCAAAAAT
* *
25541851 AGAATTTTTGGAAGTTC-GAGGGTAAAAATGTAATTTTGGGAAGGTTTGGGG
66 AGAATTTTTAGAAGTTCGGA-GGTAAAAATATAATTTTGGGAAGGTTTGGGG
* * *
25541902 TCAAAAATGGAATTTTTGGA-AGTTCTGGGGTAAAA-TGTAATTTTTAAAAGTTTTAGGGTCAAA
1 TCAAAAATAGAA-TTTTGGACA-TTCGGGGGTAAAAGGGTAA-TTTTAAAAGTTTTAGGGTCAAA
*
25541965 AATGGAATTTTTAGAAGTTCGGAGGTAAAAATATAATTTT
63 AATAGAATTTTTAGAAGTTCGGAGGTAAAAATATAATTTT
25542005 TGGACAGTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
116 16 0.18
117 73 0.80
118 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (116 bp):
TCAAAAATAGAATTTTGGACATTCGGGGGTAAAAGGGTAATTTTAAAAGTTTTAGGGTCAAAAAT
AGAATTTTTAGAAGTTCGGAGGTAAAAATATAATTTTGGGAAGGTTTGGGG
Found at i:25543109 original size:3 final size:3
Alignment explanation
Indices: 25543101--25543155 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
25543091 TCTTTTTTAA
*
25543101 TAT TAT TAT T-T TAT TAA TAT TAT TAAT T-T TAT TA- TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TA-T TAT TAT
25543145 TAT TAT TAT TA
1 TAT TAT TAT TA
25543156 AAACGTTCTG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 6 0.13
3 34 0.76
4 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:25543119 original size:17 final size:17
Alignment explanation
Indices: 25543093--25543152 Score: 79
Period size: 18 Copynumber: 3.5 Consensus size: 17
25543083 TCTTCAAATC
25543093 TTTT-TTAATATTATTA
1 TTTTATTAATATTATTA
25543109 TTTTATTAATATTATTAA
1 TTTTATTAATATTATT-A
25543127 TTTTATT-ATATTTATTA
1 TTTTATTAATA-TTATTA
25543144 TTATTATTA
1 TT-TTATTA
25543153 TTAAAACGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.10
17 17 0.44
18 18 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATTAATATTATTA
Found at i:25549608 original size:18 final size:19
Alignment explanation
Indices: 25549568--25549608 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
25549558 ATAAGCTTTG
*
25549568 TAATCAATTTAAAATCACT
1 TAATCAATTTAAAATCACA
*
25549587 TAATCAATTT-AATTCACA
1 TAATCAATTTAAAATCACA
25549605 TAAT
1 TAAT
25549609 AAGGAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATCAATTTAAAATCACA
Found at i:25551052 original size:15 final size:16
Alignment explanation
Indices: 25551032--25551067 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
25551022 TAAATAATAA
25551032 AATATTATTATTAA-T
1 AATATTATTATTAATT
25551047 AATATTATTATTAATT
1 AATATTATTATTAATT
25551063 AATAT
1 AATAT
25551068 ATCATTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATATTATTATTAATT
Found at i:25557470 original size:29 final size:30
Alignment explanation
Indices: 25557411--25557485 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
25557401 AGATATAGTT
*
25557411 AGGTATTTTATAGTATTTTTTTTTTGTGAAA
1 AGGTATTTTATAGTA-TTTTTTTTGGTGAAA
*
25557442 AGGTATTTTGTAGTA-TTTTTTTGGTGAAA
1 AGGTATTTTATAGTATTTTTTTTGGTGAAA
*
25557471 AGTTATTTTATAGTA
1 AGGTATTTTATAGTA
25557486 GGCTTAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 26 0.65
31 14 0.35
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.55
Consensus pattern (30 bp):
AGGTATTTTATAGTATTTTTTTTGGTGAAA
Found at i:25557572 original size:57 final size:59
Alignment explanation
Indices: 25557499--25557618 Score: 156
Period size: 59 Copynumber: 2.1 Consensus size: 59
25557489 TTAATATAAC
* * *
25557499 ATTTGGTACATGAACTTGACA-TTTTT-TAAATTTTGTACCTAAACCTTTTTT-GACTCA
1 ATTTAGTACATGAACTTAACATTTTTTCTAAATTTGGTACCTAAA-CTTTTTTAGACTCA
* * *
25557556 ATTTAGTACTTGAACTTAACATTTTTTCTTAATTTGGTACCTAAACTTTTTTAGATTCA
1 ATTTAGTACATGAACTTAACATTTTTTCTAAATTTGGTACCTAAACTTTTTTAGACTCA
25557615 ATTT
1 ATTT
25557619 GATACCTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
57 18 0.33
58 12 0.22
59 24 0.44
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.48
Consensus pattern (59 bp):
ATTTAGTACATGAACTTAACATTTTTTCTAAATTTGGTACCTAAACTTTTTTAGACTCA
Found at i:25557890 original size:32 final size:33
Alignment explanation
Indices: 25557847--25557918 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
25557837 GTACCAATAT
* *
25557847 AAAAAAGTGTCAAGTTT-AGATACCAAATT-AGG
1 AAAAAAATGTCAAGTTTGAG-TACCAAATTGAGC
*
25557879 AAAAAAATGTCAAGTTTGAGTATCAAATTGAGC
1 AAAAAAATGTCAAGTTTGAGTACCAAATTGAGC
25557912 AAAAAAA
1 AAAAAAA
25557919 ATTTAGAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 24 0.69
33 11 0.31
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.24
Consensus pattern (33 bp):
AAAAAAATGTCAAGTTTGAGTACCAAATTGAGC
Found at i:25558524 original size:3 final size:3
Alignment explanation
Indices: 25558518--25558562 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
25558508 TTATTATGAG
*
25558518 TAA TAA TAA TAG TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
25558563 CACATTCGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:25558543 original size:20 final size:20
Alignment explanation
Indices: 25558520--25558560 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
25558510 ATTATGAGTA
*
25558520 ATAATAATAGTAATAATAAT
1 ATAATAATAATAATAATAAT
25558540 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
25558560 A
1 A
25558561 ATCACATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
ATAATAATAATAATAATAAT
Found at i:25558544 original size:23 final size:23
Alignment explanation
Indices: 25558518--25558562 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
25558508 TTATTATGAG
*
25558518 TAATAATAATAGTAATAATAATA
1 TAATAATAATAATAATAATAATA
25558541 TAATAATAATAATAATAATAAT
1 TAATAATAATAATAATAATAAT
25558563 CACATTCGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATAATAATAATAATAATAATA
Found at i:25559136 original size:22 final size:21
Alignment explanation
Indices: 25559110--25559158 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
25559100 AGTTCTTCGT
* *
25559110 GAAAACCCTAATTTTTTCTTGA
1 GAAAACCC-AACTTTTTATTGA
*
25559132 GAAAACTCAACTTTTTATTGA
1 GAAAACCCAACTTTTTATTGA
25559153 -AAAACC
1 GAAAACC
25559159 TAAAATTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 5 0.22
21 11 0.48
22 7 0.30
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (21 bp):
GAAAACCCAACTTTTTATTGA
Found at i:25559485 original size:5 final size:6
Alignment explanation
Indices: 25559463--25559496 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
25559453 CTTTTATCAA
25559463 AAAAAGT AAAAAT AAAAAT AAAAAT ATAAAAT AA
1 AAAAA-T AAAAAT AAAAAT AAAAAT A-AAAAT AA
25559497 TTTTTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 15 0.58
7 11 0.42
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:25559606 original size:21 final size:20
Alignment explanation
Indices: 25559553--25559606 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
25559543 ATTTTTACAG
*
25559553 AAAAAACTAAAATTAATATT
1 AAAAAAATAAAATTAATATT
** *
25559573 AAAAAAAGCAAATTAAATTTT
1 AAAAAAATAAAATT-AATATT
*
25559594 AAAAATATAAAAT
1 AAAAAAATAAAAT
25559607 GAGTTATCAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAAAATAAAATTAATATT
Found at i:25560102 original size:19 final size:18
Alignment explanation
Indices: 25560054--25560108 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 18
25560044 ATTTAAGAAA
25560054 TTATTTTTAATAATAATATT
1 TTATTTTTAAT-AT-ATATT
25560074 TTAGTTTTTAGATATATATT
1 TTA-TTTTTA-ATATATATT
25560094 TTATTTTTAA-ATATA
1 TTATTTTTAATATATA
25560109 ATTATATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
17 5 0.15
18 1 0.03
19 6 0.18
20 11 0.33
21 8 0.24
22 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TTATTTTTAATATATATT
Found at i:25561565 original size:24 final size:24
Alignment explanation
Indices: 25561525--25561570 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25561515 TGATCGCCAC
* *
25561525 AGGGATAGGGATAGAGATAAGGGT
1 AGGGATAGGGACAGAGAAAAGGGT
*
25561549 AGGGATAGGGACCGAGAAAAGG
1 AGGGATAGGGACAGAGAAAAGG
25561571 ATCGTGATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.04, G:0.46, T:0.11
Consensus pattern (24 bp):
AGGGATAGGGACAGAGAAAAGGGT
Found at i:25569788 original size:96 final size:96
Alignment explanation
Indices: 25569624--25569805 Score: 253
Period size: 96 Copynumber: 1.9 Consensus size: 96
25569614 TTTGGAAAAG
** *
25569624 GATTATCTCGATTTAAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAATA
1 GATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAATA
25569689 T-AAAGAAACATTGCCTCGATTAAGGGTATTT
66 TAAAAG-AACATTGCCTCGATTAAGGGTATTT
* * *
25569720 GATTATTTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCCA-AACTCGAA
1 GATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTT-CAGAA-TCGAA
*
25569784 -ATAAAAGAATATTGCCTCGATT
64 TATAAAAGAACATTGCCTCGATT
25569806 TTAAAGTTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
96 65 0.86
97 11 0.14
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (96 bp):
GATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAATA
TAAAAGAACATTGCCTCGATTAAGGGTATTT
Found at i:25570244 original size:58 final size:59
Alignment explanation
Indices: 25570113--25570257 Score: 186
Period size: 58 Copynumber: 2.5 Consensus size: 59
25570103 TGAAACTTTA
* * * *
25570113 GACATCCGGGGGTAAAACGGTAACTTTTAGAAAAAATCAGAATCAAAAACGTTATTTTTG
1 GACATCCGGGGGTAAAATGGTAATTTTTAGAAAAAATCAGAATCAAAAAC-TGAATTTTG
* * *
25570173 GACATCCGAGGGTAAAATGGTAATTTTTA-AAAAAATCGGGATCAAAAA-TAGAATTTTG
1 GACATCCGGGGGTAAAATGGTAATTTTTAGAAAAAATCAGAATCAAAAACT-GAATTTTG
*
25570231 GACATTCGGGGGTAAAATGGTAATTTT
1 GACATCCGGGGGTAAAATGGTAATTTT
25570258 GAAATTTTCA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
57 1 0.01
58 31 0.41
59 17 0.23
60 26 0.35
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.28
Consensus pattern (59 bp):
GACATCCGGGGGTAAAATGGTAATTTTTAGAAAAAATCAGAATCAAAAACTGAATTTTG
Found at i:25570288 original size:30 final size:29
Alignment explanation
Indices: 25570244--25570407 Score: 114
Period size: 30 Copynumber: 5.5 Consensus size: 29
25570234 ATTCGGGGGT
**
25570244 AAAATGGTAA-TTTTGAAATTTTCAAGGTTA
1 AAAATGG-AATTTTTGAAATTTT-GGGGTTA
* * *
25570274 AAAATGGAATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGAAATTTTGGGGTTA
* * *
25570303 AAAATGAAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTT-GAAATTTTGGGGTTA
* * * *
25570333 AAACTAGAATTTTTAGAAGTTTTGGGGGTCA
1 AAAATGGAATTTTT-GAAATTTT-GGGGTTA
* * ***
25570364 AAAATGGAATTTTTGGAAGTTCAAGGTTA
1 AAAATGGAATTTTTGAAATTTTGGGGTTA
*
25570393 AAAATGTAATTTTTG
1 AAAATGGAATTTTTG
25570408 GACAGTTCAG
Statistics
Matches: 106, Mismatches: 25, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
29 37 0.35
30 50 0.47
31 19 0.18
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGAAATTTTGGGGTTA
Found at i:25570304 original size:29 final size:29
Alignment explanation
Indices: 25570272--25570414 Score: 160
Period size: 29 Copynumber: 4.8 Consensus size: 29
25570262 TTTTCAAGGT
25570272 TAAAAATGGAATTTTTGGAAGTTTGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTGGGGG
* *
25570301 TAAAAATGAAATTTTTGGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTTGGGGG
* * *
25570330 TCAAAACTAGAATTTTTAGAAGTTTTGGGGG
1 T-AAAAATGGAATTTTTGGAAG-TTTGGGGG
*** *
25570361 TCAAAAATGGAATTTTTGGAAGTTCAAGGT
1 T-AAAAATGGAATTTTTGGAAGTTTGGGGG
*
25570391 TAAAAATGTAATTTTTGGACAGTT
1 TAAAAATGGAATTTTTGGA-AGTT
25570415 CAGGGACCTC
Statistics
Matches: 96, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
29 45 0.47
30 25 0.26
31 26 0.27
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTGGGGG
Found at i:25570364 original size:31 final size:30
Alignment explanation
Indices: 25570273--25570384 Score: 149
Period size: 31 Copynumber: 3.7 Consensus size: 30
25570263 TTTCAAGGTT
25570273 AAAAATGGAATTTTTGGAAG-TTTGGGGGT-
1 AAAAAT-GAATTTTTGGAAGTTTTGGGGGTC
25570302 AAAAATGAAATTTTTGGAAGTTTT-GGGGTC
1 AAAAATG-AATTTTTGGAAGTTTTGGGGGTC
* *
25570332 AAAACTAGAATTTTTAGAAGTTTTGGGGGTC
1 AAAAAT-GAATTTTTGGAAGTTTTGGGGGTC
25570363 AAAAATGGAATTTTTGGAAGTT
1 AAAAAT-GAATTTTTGGAAGTT
25570385 CAAGGTTAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
28 1 0.01
29 23 0.32
30 23 0.32
31 26 0.36
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.36
Consensus pattern (30 bp):
AAAAATGAATTTTTGGAAGTTTTGGGGGTC
Found at i:25571575 original size:17 final size:17
Alignment explanation
Indices: 25571549--25571601 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 17
25571539 TCTTCAAATC
25571549 TTTT-TTAATATTATTA
1 TTTTATTAATATTATTA
25571565 TTTTATTAATATTATTA
1 TTTTATTAATATTATTA
25571582 TATTTATT-ATATTTATTA
1 T-TTTATTAATA-TTATTA
25571600 TT
1 TT
25571602 AAAACGTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.12
17 17 0.50
18 13 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATTAATATTATTA
Found at i:25571581 original size:9 final size:8
Alignment explanation
Indices: 25571556--25571600 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 8
25571546 ATCTTTTTTA
25571556 ATATTATT
1 ATATTATT
*
25571564 ATTTTATT
1 ATATTATT
25571572 AATATTATT
1 -ATATTATT
25571581 ATATTTATT
1 ATA-TTATT
25571590 ATATTTATT
1 ATA-TTATT
25571599 AT
1 AT
25571601 TAAAACGTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
8 10 0.30
9 23 0.70
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
ATATTATT
Found at i:25572351 original size:11 final size:11
Alignment explanation
Indices: 25572335--25572361 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
25572325 ACATTAAAGC
25572335 TTGGATTGTAA
1 TTGGATTGTAA
25572346 TTGGATTGTAA
1 TTGGATTGTAA
25572357 TTGGA
1 TTGGA
25572362 CATTAAAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (11 bp):
TTGGATTGTAA
Found at i:25573044 original size:206 final size:202
Alignment explanation
Indices: 25572690--25573276 Score: 804
Period size: 206 Copynumber: 2.9 Consensus size: 202
25572680 TCTTGTTTTA
* * ** *
25572690 TTGATTTGGTTTTCTTCTCAGTATCTCATCAGGAAGATAACCGCATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
* *
25572755 CTCTATGT-T-TCATCAGGAAGACGGATTTGG-CTCACTTCTCCGTATCTCATCAGGAAGCTAAC
66 CT-T-TGTATCTCATCAGGAAGACGAATTTGGTC-CACTTCTCAGTATCTCATCAGGAAGCTAAC
*
25572817 CATTTTATTGCTTCGACCTGCTTCTCAGTATCACATCAGGAAGCTAGGGTTCGAAGATTTGCTCA
128 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGATTTGCTCA
25572882 CATCGAGCGTGGG
192 CATCGA--GTGGG
*
25572895 TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCT
1 -TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCT
25572960 TCTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
65 TCTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
*
25573025 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGTTCACA
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTG-GGTTCGAAGATTTGCTCACA
* *
25573090 TTGAGTTGG
194 TCGAGTGGG
* ** *
25573099 -TG---T--ACTTC-TCT--GTATCTCATCAAAAAGATGACCATC-TCACTTGTTTCAATCCGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACC-GCATCACTTGTTTCAATCCGCT
* * * *
25573154 TCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATGTCTCATCAGGAAGCTAACCA
65 TCTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
*
25573219 TTTTATTGCTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGATTT
25573277 CTTCGCATTG
Statistics
Matches: 353, Mismatches: 22, Indels: 24
0.88 0.06 0.06
Matches are distributed among these distances:
194 154 0.44
195 2 0.01
196 3 0.01
197 4 0.01
199 1 0.00
202 2 0.01
204 7 0.02
205 3 0.01
206 176 0.50
207 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (202 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
CTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCACATC
GAGTGGG
Found at i:25573245 original size:194 final size:194
Alignment explanation
Indices: 25572909--25573336 Score: 678
Period size: 194 Copynumber: 2.2 Consensus size: 194
25572899 ATTTGGTCTT
* ** * * *
25572909 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTTTGTATCTCAT
1 CTTCTCTGTATCTCATCAAAAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTACCTCAT
*
25572974 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* *
25573039 CCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGTTCACATTGAGTTGGTGTA
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTCTTCACATTGAGTTGGTATA
*
25573103 CTTCTCTGTATCTCATCAAAAAGATGACCATC-TCACTTGTTTCAATCCGCTTCTCTGTACCTCA
1 CTTCTCTGTATCTCATCAAAAAGATGACC-GCATCACTTGTTTCAATCCGCTTCTCTGTACCTCA
* *
25573167 TCAGGAAGACGAATTTGGTCCACTTCTCAATGTCTCATCAGGAAGCTAACCATTTTATTGCTTTG
65 TCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
* *
25573232 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTCTTCGCATTGAGTTGGTATA
130 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTCTTCACATTGAGTTGGTATA
** * *
25573297 CTTCTCTGTATCTCATCAGGAAGATAACCGCCTCACTTGT
1 CTTCTCTGTATCTCATCAAAAAGATGACCGCATCACTTGT
25573337 GGATAATCGC
Statistics
Matches: 214, Mismatches: 18, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
193 1 0.00
194 212 0.99
195 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.34
Consensus pattern (194 bp):
CTTCTCTGTATCTCATCAAAAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTACCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
CCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTCTTCACATTGAGTTGGTATA
Found at i:25573560 original size:50 final size:50
Alignment explanation
Indices: 25573386--25573561 Score: 187
Period size: 49 Copynumber: 3.5 Consensus size: 50
25573376 CGATTGATAT
* * * *
25573386 CGTTGCGGTCTTAGATCTTTTCCTTTTGTATCTTTGTGGTACTGGATCTGC
1 CGTTGCGG-CTTAGATCTTTCCCTGTCGTATCTTTGTGGTACTGGATCCGC
* * * * *
25573437 CGTTGCGATCTTAGATCTTTCCCT-T-GTGTCTTCGCGATACTGGATCCGC
1 CGTTGCG-GCTTAGATCTTTCCCTGTCGTATCTTTGTGGTACTGGATCCGC
*
25573486 CGTTGCGGCCTTAGATCTTT-CCTGTCGTATTTTTGTGGTACTGGATCCGC
1 CGTTGCGG-CTTAGATCTTTCCCTGTCGTATCTTTGTGGTACTGGATCCGC
* * *
25573536 AGTCGCGGGTTAGATCTTTCCCTGTC
1 CGTTGCGGCTTAGATCTTTCCCTGTC
25573562 AAACCTGTAG
Statistics
Matches: 104, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
48 3 0.03
49 48 0.46
50 32 0.31
51 21 0.20
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.40
Consensus pattern (50 bp):
CGTTGCGGCTTAGATCTTTCCCTGTCGTATCTTTGTGGTACTGGATCCGC
Found at i:25574789 original size:9 final size:8
Alignment explanation
Indices: 25574771--25574839 Score: 50
Period size: 8 Copynumber: 8.0 Consensus size: 8
25574761 CGACCTCTCC
25574771 TTTTCTTT
1 TTTTCTTT
*
25574779 TTTTCCTT
1 TTTTCTTT
*
25574787 TTTTGTTT
1 TTTTCTTT
25574795 TTTTCTTTTGCT
1 TTTTC--TT--T
25574807 TTTTCTTCT
1 TTTTCTT-T
*
25574816 TCTTCTTCT
1 TTTTCTT-T
25574825 TTTTC-TT
1 TTTTCTTT
25574832 TTTTCTTT
1 TTTTCTTT
25574840 ATTCATTGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
7 6 0.12
8 20 0.40
9 14 0.28
10 4 0.08
12 6 0.12
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (8 bp):
TTTTCTTT
Found at i:25574795 original size:16 final size:15
Alignment explanation
Indices: 25574771--25574839 Score: 70
Period size: 16 Copynumber: 4.5 Consensus size: 15
25574761 CGACCTCTCC
25574771 TTTTCTTTTTTTCCTT
1 TTTTCTTTTTTT-CTT
*
25574787 TTTTGTTTTTTTC-T
1 TTTTCTTTTTTTCTT
*
25574801 TTTGCTTTTTCTTC-T
1 TTTTCTTTTT-TTCTT
*
25574816 TCTTCTTCTTTTTCTT
1 TTTTCTT-TTTTTCTT
25574832 TTTTCTTT
1 TTTTCTTT
25574840 ATTCATTGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
14 9 0.20
15 14 0.32
16 21 0.48
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTTTCTT
Found at i:25574810 original size:15 final size:14
Alignment explanation
Indices: 25574770--25574833 Score: 65
Period size: 15 Copynumber: 4.4 Consensus size: 14
25574760 TCGACCTCTC
*
25574770 CTTTTCTTTTTTTC
1 CTTTTCTTTTTTTT
*
25574784 CTTTTTTGTTTTTTT
1 CTTTTCT-TTTTTTT
*
25574799 CTTTTGCTTTTTCTT
1 CTTTT-CTTTTTTTT
*
25574814 CTTCTTCTTCTTTTT
1 CTT-TTCTTTTTTTT
25574829 CTTTT
1 CTTTT
25574834 TTCTTTATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.20
15 30 0.73
16 3 0.07
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (14 bp):
CTTTTCTTTTTTTT
Found at i:25575668 original size:53 final size:54
Alignment explanation
Indices: 25575587--25575702 Score: 180
Period size: 53 Copynumber: 2.1 Consensus size: 54
25575577 TCACTCTCTT
*
25575587 TTTTTCTTTTTTTTTAATTGGGTTTTTAAAATACCTTTTGCGAATTTTCGACCCA
1 TTTTT-TTATTTTTTAATTGGGTTTTTAAAATACCTTTTGCGAATTTTCGACCCA
* *
25575642 TTTTTTTATTTTTT-ATTGGGTTTTTAAAATGCCTTTTGCGAATTTTCGACCTA
1 TTTTTTTATTTTTTAATTGGGTTTTTAAAATACCTTTTGCGAATTTTCGACCCA
25575695 TCTTTTTT
1 T-TTTTTT
25575703 TTTGTTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
53 38 0.67
54 14 0.25
55 5 0.09
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (54 bp):
TTTTTTTATTTTTTAATTGGGTTTTTAAAATACCTTTTGCGAATTTTCGACCCA
Found at i:25580664 original size:58 final size:58
Alignment explanation
Indices: 25580524--25580726 Score: 168
Period size: 58 Copynumber: 3.5 Consensus size: 58
25580514 TGAAACTTTA
* * * *
25580524 GACATCCGAGGGTAAAACGGTAACTTTTATA-AAAAATCAGGAT-AAAAA-ACGTTATTTTTG
1 GACATTCGAGGGTAAAAAGGTAA-TTTT-TAGAAAAATCGGGATCAAAAATA-G--AATTTTG
*
25580584 GACA-TCTGAGGGTAAAATGGTAATTTTTAGAAAAATCGGGATCAAAAATAGAATTTTG
1 GACATTC-GAGGGTAAAAAGGTAATTTTTAGAAAAATCGGGATCAAAAATAGAATTTTG
* ** * *
25580642 GACATTCGAGGGTAAAAGGGTAA-TTTT-GAAAGTTTTGGGGTCAAAAATAGAATTTTTG
1 GACATTCGAGGGTAAAAAGGTAATTTTTAGAAA-AATCGGGATCAAAAATAGAA-TTTTG
* *
25580700 GA-AGTTCGGGGGTAAAAATGTAATTTT
1 GACA-TTCGAGGGTAAAAAGGTAATTTT
25580727 GGGAAGGTTT
Statistics
Matches: 122, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
56 4 0.03
57 21 0.17
58 50 0.41
59 21 0.17
60 25 0.20
61 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (58 bp):
GACATTCGAGGGTAAAAAGGTAATTTTTAGAAAAATCGGGATCAAAAATAGAATTTTG
Found at i:25580705 original size:30 final size:28
Alignment explanation
Indices: 25580665--25580853 Score: 157
Period size: 30 Copynumber: 6.4 Consensus size: 28
25580655 AAAAGGGTAA
*
25580665 TTTTGAAAGTTTTGGGGTCAAAAATAGAAT
1 TTTTGGAAGTTTTGGGGT-AAAAAT-GAAT
**
25580695 TTTTGGAAGTTCGGGGGTAAAAATGTAAT
1 TTTTGGAAGTTTTGGGGTAAAAATG-AAT
* *
25580724 TTTGGGAAGGTTTGGGGTCAAAAATGGAAT
1 TTTTGGAAGTTTTGGGGT-AAAAAT-GAAT
*
25580754 TTTTGGAAGTTCTGGGGT-AAAATGTAAT
1 TTTTGGAAGTTTTGGGGTAAAAATG-AAT
* **
25580782 TTTTGAAAGTTTTAGGGCCAAAAATGGAAT
1 TTTTGGAAGTTTT-GGGGTAAAAAT-GAAT
* * *
25580812 TTTTAGAAG-TTCGGAGGTAAAAATATAAT
1 TTTTGGAAGTTTTGG-GGTAAAAAT-GAAT
25580841 TTTTGGACAGTTT
1 TTTTGGA-AGTTT
25580854 AGGGACCTTC
Statistics
Matches: 127, Mismatches: 22, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.01
28 22 0.17
29 44 0.35
30 56 0.44
31 4 0.03
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (28 bp):
TTTTGGAAGTTTTGGGGTAAAAATGAAT
Found at i:25580758 original size:59 final size:58
Alignment explanation
Indices: 25580625--25580843 Score: 273
Period size: 58 Copynumber: 3.8 Consensus size: 58
25580615 AAAATCGGGA
* **
25580625 TCAAAAATAGAA-TTTTGGACA-TTCGAGGGTAAAAGGGTAATTTTGAAAGTTTTGGGG
1 TCAAAAATAGAATTTTTGGA-AGTTCGGGGGTAAAAATGTAATTTTGAAAGTTTTGGGG
* *
25580682 TCAAAAATAGAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTGGGAAGGTTTGGGG
1 TCAAAAATAGAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTT-GAAAGTTTTGGGG
* * *
25580741 TCAAAAATGGAATTTTTGGAAGTTCTGGGGT-AAAATGTAATTTTTGAAAGTTTTAGGG
1 TCAAAAATAGAATTTTTGGAAGTTCGGGGGTAAAAATGTAA-TTTTGAAAGTTTTGGGG
* * * * *
25580799 CCAAAAATGGAATTTTTAGAAGTTCGGAGGTAAAAATATAATTTT
1 TCAAAAATAGAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTT
25580844 TGGACAGTTT
Statistics
Matches: 142, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
57 13 0.09
58 77 0.54
59 52 0.37
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (58 bp):
TCAAAAATAGAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTGAAAGTTTTGGGG
Found at i:25580813 original size:117 final size:116
Alignment explanation
Indices: 25580625--25580843 Score: 309
Period size: 117 Copynumber: 1.9 Consensus size: 116
25580615 AAAATCGGGA
* *
25580625 TCAAAAATAGAATTTTGGACATTCGAGGGTAAAAGGGTAATTTTGAAAGTTTTGGGGTCAAAAAT
1 TCAAAAATAGAATTTTGGACATTCGAGGGTAAAAGGGTAATTTTGAAAGTTTTAGGGCCAAAAAT
* * *
25580690 AGAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTGGGAAGGTTTGGGG
66 AGAATTTTTAGAAGTTCGGAGGTAAAAATATAATTTTGGGAAGGTTTGGGG
* *
25580741 TCAAAAATGGAATTTTTGGA-AGTTCTG-GGGTAAAA-TGTAATTTTTGAAAGTTTTAGGGCCAA
1 TCAAAAATAGAA-TTTTGGACA-TTC-GAGGGTAAAAGGGTAA-TTTTGAAAGTTTTAGGGCCAA
*
25580803 AAATGGAATTTTTAGAAGTTCGGAGGTAAAAATATAATTTT
62 AAATAGAATTTTTAGAAGTTCGGAGGTAAAAATATAATTTT
25580844 TGGACAGTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
116 16 0.18
117 74 0.81
118 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (116 bp):
TCAAAAATAGAATTTTGGACATTCGAGGGTAAAAGGGTAATTTTGAAAGTTTTAGGGCCAAAAAT
AGAATTTTTAGAAGTTCGGAGGTAAAAATATAATTTTGGGAAGGTTTGGGG
Found at i:25581966 original size:3 final size:3
Alignment explanation
Indices: 25581958--25582025 Score: 81
Period size: 3 Copynumber: 23.7 Consensus size: 3
25581948 TCTTTTTTAA
* *
25581958 TAT TAT TAT T-T TAT TA- TAT TAT TAA TAT TAT TAA T-T TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25582002 TAT TATT TAT TAT TAT TAT TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TA
25582026 AAACGTTCTG
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
2 7 0.12
3 46 0.82
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:25581976 original size:16 final size:16
Alignment explanation
Indices: 25581960--25582024 Score: 78
Period size: 16 Copynumber: 4.0 Consensus size: 16
25581950 TTTTTTAATA
* *
25581960 TTATTATTTTATTATA
1 TTATTATATTATTATT
*
25581976 TTATTAATATTATTAAT
1 TTATT-ATATTATTATT
25581993 TTATTATATTATTA-T
1 TTATTATATTATTATT
25582008 TTATTATTATTATTATT
1 TTATTA-TATTATTATT
25582025 AAAACGTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
15 7 0.16
16 22 0.51
17 14 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTATATTATTATT
Found at i:25581982 original size:25 final size:25
Alignment explanation
Indices: 25581954--25582025 Score: 108
Period size: 25 Copynumber: 2.8 Consensus size: 25
25581944 CAAATCTTTT
25581954 TTAATATTATTATTTTATTATATTA
1 TTAATATTATTATTTTATTATATTA
*
25581979 TTAATATTATTAATTTATTATATTA
1 TTAATATTATTATTTTATTATATTA
*
25582004 TTATTTATTATTATTATTATTA
1 TTA-ATATTATTATT-TTATTA
25582026 AAACGTTCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
25 27 0.64
26 9 0.21
27 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TTAATATTATTATTTTATTATATTA
Found at i:25582829 original size:17 final size:17
Alignment explanation
Indices: 25582807--25582843 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
25582797 CTTTAATTTT
25582807 ATTTTAATTTAAAATAA
1 ATTTTAATTTAAAATAA
*
25582824 ATTTTAATTTAAAGTAA
1 ATTTTAATTTAAAATAA
25582841 ATT
1 ATT
25582844 CAAACTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
ATTTTAATTTAAAATAA
Found at i:25588507 original size:18 final size:19
Alignment explanation
Indices: 25588467--25588507 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
25588457 ATAAGCTTTG
*
25588467 TAATCAATTTAAAATCACT
1 TAATCAATTTAAAATCACA
*
25588486 TAATCAATTT-AATTCACA
1 TAATCAATTTAAAATCACA
25588504 TAAT
1 TAAT
25588508 AAGGAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATCAATTTAAAATCACA
Found at i:25589975 original size:18 final size:18
Alignment explanation
Indices: 25589935--25589969 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25589925 TAAATAATAA
*
25589935 AATATTATTATTTATTAT
1 AATATTATTATTAATTAT
25589953 AATATTATTATTAATTA
1 AATATTATTATTAATTA
25589970 ATATATCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTATTATTAATTAT
Found at i:25596426 original size:29 final size:30
Alignment explanation
Indices: 25596367--25596441 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
25596357 AGATATAGTT
*
25596367 AGGTATTTTATAGTATTTTTTTTTTGTGAAA
1 AGGTATTTTATAGTA-TTTTTTTTGGTGAAA
*
25596398 AGGTATTTTGTAGTA-TTTTTTTGGTGAAA
1 AGGTATTTTATAGTATTTTTTTTGGTGAAA
*
25596427 AGTTATTTTATAGTA
1 AGGTATTTTATAGTA
25596442 GGCTTAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 26 0.65
31 14 0.35
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.55
Consensus pattern (30 bp):
AGGTATTTTATAGTATTTTTTTTGGTGAAA
Found at i:25596528 original size:57 final size:57
Alignment explanation
Indices: 25596455--25596563 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
25596445 TTAATATAAC
* *
25596455 ATTTGGTACATGAACTTGACATTTTTT-AAATTTTG-TACCTAAACCTTTTTTGACTCA
1 ATTTAGTACATGAACTTAACATTTTTTCAAA-TTTGATACCTAAA-CTTTTTTGACTCA
* *
25596512 ATTTAGTACCTGAACTTAACATTTTTTCCTAATTTGATACCTAAACTTTTTT
1 ATTTAGTACATGAACTTAACATTTTTT-CAAATTTGATACCTAAACTTTTTT
25596564 AAATTCAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
57 24 0.53
58 11 0.24
59 10 0.22
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (57 bp):
ATTTAGTACATGAACTTAACATTTTTTCAAATTTGATACCTAAACTTTTTTGACTCA
Found at i:25596579 original size:28 final size:27
Alignment explanation
Indices: 25596542--25596594 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
25596532 ATTTTTTCCT
*
25596542 AATTTGATACCTAAACTTTTTTAAATTC
1 AATTTGATACCTAAA-TTTATTAAATTC
25596570 AATTTGATACCTAAATTTATTAAAT
1 AATTTGATACCTAAATTTATTAAAT
25596595 ATTATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (27 bp):
AATTTGATACCTAAATTTATTAAATTC
Found at i:25596581 original size:59 final size:57
Alignment explanation
Indices: 25596455--25596581 Score: 134
Period size: 57 Copynumber: 2.2 Consensus size: 57
25596445 TTAATATAAC
* * * *
25596455 ATTTGGTACATGAACTTGACATTTTTTAAATTTTGTACCTAAACCTTTTTTGACTCA
1 ATTTGATACCTGAACTTAACATTTTTTAAATTTTGTACCTAAACCTTTTTTAACTCA
* *
25596512 ATTT-AGTACCTGAACTTAACATTTTTTCCTAA-TTTGATACCTAAA-CTTTTTTAAATTCA
1 ATTTGA-TACCTGAACTTAACATTTTTT--AAATTTTG-TACCTAAACCTTTTTT-AACTCA
25596571 ATTTGATACCT
1 ATTTGATACCT
25596582 AAATTTATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
57 23 0.40
58 11 0.19
59 23 0.40
60 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.46
Consensus pattern (57 bp):
ATTTGATACCTGAACTTAACATTTTTTAAATTTTGTACCTAAACCTTTTTTAACTCA
Found at i:25596966 original size:11 final size:11
Alignment explanation
Indices: 25596952--25597020 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
25596942 CTCATCTTAA
25596952 CTTTCTCTTTT
1 CTTTCTCTTTT
* *
25596963 CTTTTTCTCATT
1 CTTTCTCT-TTT
25596975 CATTTCT-TATTT
1 C-TTTCTCT-TTT
25596987 CTTTCTCTTTT
1 CTTTCTCTTTT
*
25596998 CTTTTCTATTTT
1 C-TTTCTCTTTT
*
25597010 CTTCCTCTTTT
1 CTTTCTCTTTT
25597021 AATCACACTT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
11 24 0.52
12 18 0.39
13 4 0.09
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTTCTCTTTT
Found at i:25597010 original size:23 final size:22
Alignment explanation
Indices: 25596953--25597020 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 22
25596943 TCATCTTAAC
* *
25596953 TTTCTCTTTTCTTTTTCTCATTCA
1 TTTCT-TTTTCTTTCTCT-TTTCA
*
25596977 TTTCTTATTTCTTTCTCTTTTCT
1 TTTCTT-TTTCTTTCTCTTTTCA
*
25597000 TTTCTATTTTCTTCCTCTTTT
1 TTTCT-TTTTCTTTCTCTTTT
25597021 AATCACACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 22 0.58
24 16 0.42
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTCTTTTTCTTTCTCTTTTCA
Found at i:25597427 original size:21 final size:22
Alignment explanation
Indices: 25597391--25597437 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
25597381 ACCCATTAAG
25597391 CCCAAATTCTATTTAAACCAAA
1 CCCAAATTCTATTTAAACCAAA
25597413 CCCAAATTC-ATTTAAACCAAA
1 CCCAAATTCTATTTAAACCAAA
25597434 CCCA
1 CCCA
25597438 TTTGAACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (22 bp):
CCCAAATTCTATTTAAACCAAA
Found at i:25597439 original size:15 final size:15
Alignment explanation
Indices: 25597421--25597450 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25597411 AACCCAAATT
25597421 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
25597436 CATTTGAACCAAACC
1 CATTTAAACCAAACC
25597451 AAATGAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:25597512 original size:20 final size:20
Alignment explanation
Indices: 25597485--25597541 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
25597475 CAAGTCAAAC
25597485 CATTGACCGACGTTGACTAG
1 CATTGACCGACGTTGACTAG
* ** * *
25597505 CGTTGACCGATATTGATTGG
1 CATTGACCGACGTTGACTAG
25597525 CATTGACCGACGTTGAC
1 CATTGACCGACGTTGAC
25597542 CGACCGTTGA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (20 bp):
CATTGACCGACGTTGACTAG
Found at i:25597555 original size:7 final size:7
Alignment explanation
Indices: 25597543--25597600 Score: 82
Period size: 7 Copynumber: 8.4 Consensus size: 7
25597533 GACGTTGACC
25597543 GACCGTT
1 GACCGTT
25597550 GACCGTT
1 GACCGTT
*
25597557 GA-CTTT
1 GACCGTT
*
25597563 GATCGTT
1 GACCGTT
*
25597570 GATCGTT
1 GACCGTT
25597577 GACCGTT
1 GACCGTT
25597584 GACCGTT
1 GACCGTT
25597591 GACCGTT
1 GACCGTT
25597598 GAC
1 GAC
25597601 TTGTTCGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
6 5 0.11
7 42 0.89
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.33
Consensus pattern (7 bp):
GACCGTT
Found at i:25604066 original size:11 final size:11
Alignment explanation
Indices: 25604046--25604120 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
25604036 AAGCCTCTCA
*
25604046 TCTTTCCTTTC
1 TCTTTTCTTTC
*
25604057 TCTTTTCTTTT
1 TCTTTTCTTTC
*
25604068 TCTCATTCATTTC
1 TCT-TTTC-TTTC
25604081 T-TATTTCTTTC
1 TCT-TTTCTTTC
25604092 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
25604104 TATTTTCTTCC
1 TCTTTTCTTTC
25604115 TCTTTT
1 TCTTTT
25604121 AATCACACTT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
11 29 0.57
12 18 0.35
13 4 0.08
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.69
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:25604107 original size:22 final size:22
Alignment explanation
Indices: 25604053--25604117 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
25604043 TCATCTTTCC
*
25604053 TTTCTCTTTTCTTTTTCTCATTCA
1 TTTCT-TTTTCTTTCTCTC-TTCA
* *
25604077 TTTCTTATTTCTTTCTCTTTTCT
1 TTTCTT-TTTCTTTCTCTCTTCA
*
25604100 TTTCTATTTTCTTCCTCT
1 TTTCT-TTTTCTTTCTCT
25604118 TTTAATCACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTTTTTCTTTCTCTCTTCA
Found at i:25604527 original size:21 final size:21
Alignment explanation
Indices: 25604491--25604558 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
25604481 ACCCATTAAG
25604491 CCCAAATTCTATTTAAACCAAA
1 CCCAAATTC-ATTTAAACCAAA
*
25604513 CCCACATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
*
25604534 CTCAAATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
25604555 CCCA
1 CCCA
25604559 TTTGAACCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 34 0.81
22 8 0.19
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (21 bp):
CCCAAATTCATTTAAACCAAA
Found at i:25604560 original size:15 final size:15
Alignment explanation
Indices: 25604542--25604571 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25604532 AACTCAAATT
25604542 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
25604557 CATTTGAACCAAACC
1 CATTTAAACCAAACC
25604572 AAATTAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:25604597 original size:25 final size:25
Alignment explanation
Indices: 25604565--25604623 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
25604555 CCCATTTGAA
*
25604565 CCAAACCAAATTAACCAAGTTCAAC
1 CCAAACCAAATGAACCAAGTTCAAC
25604590 CCAAACCAAATGAACCAAGTTCAAC
1 CCAAACCAAATGAACCAAGTTCAAC
25604615 CCAAACCAA
1 CCAAACCAA
25604624 GTCAAACCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.49, C:0.34, G:0.05, T:0.12
Consensus pattern (25 bp):
CCAAACCAAATGAACCAAGTTCAAC
Found at i:25604646 original size:10 final size:10
Alignment explanation
Indices: 25604633--25604678 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
25604623 AGTCAAACCA
25604633 TTGACCGACG
1 TTGACCGACG
* *
25604643 TTGACTGGCG
1 TTGACCGACG
*
25604653 TTGACCGACA
1 TTGACCGACG
25604663 TTGACCGACCG
1 TTGACCGA-CG
25604674 TTGAC
1 TTGAC
25604679 TTTGATCGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
10 23 0.79
11 6 0.21
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.24
Consensus pattern (10 bp):
TTGACCGACG
Found at i:25604690 original size:13 final size:13
Alignment explanation
Indices: 25604669--25604721 Score: 79
Period size: 13 Copynumber: 4.0 Consensus size: 13
25604659 GACATTGACC
25604669 GACCGTTGACTTT
1 GACCGTTGACTTT
* *
25604682 GATCGTTGATCGTT
1 GACCGTTGA-CTTT
25604696 GACCGTTGACTTT
1 GACCGTTGACTTT
25604709 GACCGTTGACTTT
1 GACCGTTGACTTT
25604722 TTCAAAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 24 0.69
14 11 0.31
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (13 bp):
GACCGTTGACTTT
Found at i:25604692 original size:7 final size:7
Alignment explanation
Indices: 25604669--25604718 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
25604659 GACATTGACC
25604669 GACCGTT
1 GACCGTT
*
25604676 GA-CTTT
1 GACCGTT
*
25604682 GATCGTT
1 GACCGTT
*
25604689 GATCGTT
1 GACCGTT
25604696 GACCGTT
1 GACCGTT
*
25604703 GA-CTTT
1 GACCGTT
25604709 GACCGTT
1 GACCGTT
25604716 GAC
1 GAC
25604719 TTTTTCAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 10 0.28
7 26 0.72
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (7 bp):
GACCGTT
Found at i:25605777 original size:3 final size:3
Alignment explanation
Indices: 25605769--25605806 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
25605759 TCTATTCTAT
25605769 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
25605807 TTGGGATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25606138 original size:33 final size:34
Alignment explanation
Indices: 25606094--25606168 Score: 100
Period size: 33 Copynumber: 2.2 Consensus size: 34
25606084 GTACTAATAT
* *
25606094 AAAAAAGTGTCAAGTTT-AGATACCAAATT-AGGA
1 AAAAAAATGTCAAGTTTGAG-TACCAAATTGAGCA
*
25606127 AAAAAAATGTCAAGTTTGAGTATCAAATTGAGCA
1 AAAAAAATGTCAAGTTTGAGTACCAAATTGAGCA
25606161 AAAAAAAT
1 AAAAAAAT
25606169 TTAGAAACCA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 24 0.65
34 13 0.35
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (34 bp):
AAAAAAATGTCAAGTTTGAGTACCAAATTGAGCA
Found at i:25606775 original size:3 final size:3
Alignment explanation
Indices: 25606765--25606800 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
25606755 TTATTATGAG
25606765 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
25606801 CACATTCGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:25607384 original size:21 final size:22
Alignment explanation
Indices: 25607349--25607400 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
25607339 AGTTCTTCGT
*
25607349 GAAAACTCTAATTTTTTCTTGA
1 GAAAACTCTAATTTTTTATTGA
25607371 GAAAACTC-AATTTTTTATTGA
1 GAAAACTCTAATTTTTTATTGA
25607392 -AAAAC-CTAA
1 GAAAACTCTAA
25607401 AATTTTCCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 7 0.25
21 12 0.43
22 8 0.29
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (22 bp):
GAAAACTCTAATTTTTTATTGA
Found at i:25607844 original size:21 final size:20
Alignment explanation
Indices: 25607791--25607844 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
25607781 GTTTTTACAG
*
25607791 AAAAAACTAAAATTAATATT
1 AAAAAAATAAAATTAATATT
** *
25607811 AAAAAAAGCAAATTAAATTTT
1 AAAAAAATAAAATT-AATATT
*
25607832 AAAAATATAAAAT
1 AAAAAAATAAAAT
25607845 GAGTTATCAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAAAATAAAATTAATATT
Found at i:25607872 original size:16 final size:16
Alignment explanation
Indices: 25607848--25607893 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
25607838 ATAAAATGAG
*
25607848 TTATCAAAATAAAAAT
1 TTATTAAAATAAAAAT
*
25607864 TTATTAAAAT-TAAA-
1 TTATTAAAATAAAAAT
*
25607878 TAATTAAAATAAAAAT
1 TTATTAAAATAAAAAT
25607894 AATTGTTGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 9 0.38
15 6 0.25
16 9 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
TTATTAAAATAAAAAT
Found at i:25607893 original size:15 final size:15
Alignment explanation
Indices: 25607853--25607897 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
25607843 ATGAGTTATC
*
25607853 AAAATAAAAATTTATT
1 AAAATAAAAA-TAATT
*
25607869 AAAAT-TAAATAATT
1 AAAATAAAAATAATT
25607883 AAAATAAAAATAATT
1 AAAATAAAAATAATT
25607898 GTTGACGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.36
15 11 0.44
16 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATAAAAATAATT
Found at i:25608342 original size:19 final size:18
Alignment explanation
Indices: 25608294--25608348 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 18
25608284 ATTTAAGAAA
25608294 TTATTTTTAATAATAATATT
1 TTATTTTTAAT-AT-ATATT
25608314 TTAGTTTTTAGATATATATT
1 TTA-TTTTTA-ATATATATT
25608334 TTATTTTTAA-ATATA
1 TTATTTTTAATATATA
25608349 ATTATATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
17 5 0.15
18 1 0.03
19 6 0.18
20 11 0.33
21 8 0.24
22 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TTATTTTTAATATATATT
Found at i:25609622 original size:39 final size:39
Alignment explanation
Indices: 25609547--25609624 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
25609537 TTATGCCTGT
* * * *
25609547 TCTACATTTGGGCTTTTAGTGTTATGGATTACATGCAAC
1 TCTACATTTGGGCTCTTAGTGATATAGATTAAATGCAAC
*
25609586 TCTACATTTGGTCTCTTAGTGATATA-AGTTAAATGCAAC
1 TCTACATTTGGGCTCTTAGTGATATAGA-TTAAATGCAAC
25609625 CTTAACTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (39 bp):
TCTACATTTGGGCTCTTAGTGATATAGATTAAATGCAAC
Found at i:25614895 original size:2 final size:2
Alignment explanation
Indices: 25614888--25614932 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
25614878 CCAAATAAAT
25614888 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
25614930 AC A
1 AC A
25614933 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:25620788 original size:96 final size:96
Alignment explanation
Indices: 25620624--25620805 Score: 262
Period size: 96 Copynumber: 1.9 Consensus size: 96
25620614 TTTGGAAAAG
** *
25620624 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAATA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAATA
25620689 T-AAAGAAACATTGCCTCGATTAAGGGTATTT
66 TAAAAG-AACATTGCCTCGATTAAGGGTATTT
* *
25620720 GATTATTTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCCA-AACTCGAA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTT-CAGAA-TCGAA
*
25620784 -ATAAAAGAATATTGCCTCGATT
64 TATAAAAGAACATTGCCTCGATT
25620806 TTAAAGTTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
96 66 0.86
97 11 0.14
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAATA
TAAAAGAACATTGCCTCGATTAAGGGTATTT
Found at i:25621199 original size:28 final size:28
Alignment explanation
Indices: 25621167--25621258 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
25621157 AATAAACGTT
25621167 ATTTTTGGACATCGAGGGTAAAATGGTA
1 ATTTTTGGACATCGAGGGTAAAATGGTA
* * * *
25621195 ATTTTTAGAAAAATCGA-GATCAAAAATAG-A
1 ATTTTT-G-GACATCGAGGGT--AAAATGGTA
*
25621225 A-TTTTGGACATCCGAGGGTAAAAGGGTA
1 ATTTTTGGACAT-CGAGGGTAAAATGGTA
25621253 ATTTTT
1 ATTTTT
25621259 AAAGTTTCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 15
0.66 0.13 0.21
Matches are distributed among these distances:
27 8 0.17
28 12 0.26
29 13 0.28
30 8 0.17
31 6 0.13
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.32
Consensus pattern (28 bp):
ATTTTTGGACATCGAGGGTAAAATGGTA
Found at i:25621284 original size:29 final size:30
Alignment explanation
Indices: 25621252--25621418 Score: 189
Period size: 30 Copynumber: 5.7 Consensus size: 30
25621242 GTAAAAGGGT
* *
25621252 AATTTTT-AAAGTTTCAAGGTTAAAAATGG
1 AATTTTTGGAAGTTTCAGGGTTAAAAATGG
* * *
25621281 AATTTTTGGAAG-TTCGGGGGTAAAAATGA
1 AATTTTTGGAAGTTTCAGGGTTAAAAATGG
* * *
25621310 AATTTTTGGAAGTTTCGGGGTTAAAACTAG
1 AATTTTTGGAAGTTTCAGGGTTAAAAATGG
* *
25621340 AATTTTTGGAAGTTTTAGGGTCAAAAATGG
1 AATTTTTGGAAGTTTCAGGGTTAAAAATGG
* *
25621370 AATTTTTGGAAG-TTCAAGGTTAAAAATGT
1 AATTTTTGGAAGTTTCAGGGTTAAAAATGG
25621399 AATTTTTGGACAG-TTCAGGG
1 AATTTTTGGA-AGTTTCAGGG
25621419 ACCTTTAGAG
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
29 55 0.47
30 61 0.53
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (30 bp):
AATTTTTGGAAGTTTCAGGGTTAAAAATGG
Found at i:25621329 original size:30 final size:30
Alignment explanation
Indices: 25621237--25621413 Score: 150
Period size: 29 Copynumber: 6.0 Consensus size: 30
25621227 TTTGGACATC
** * *
25621237 CGAGGGTAAAAGGGTAATTTTT-AAAGTTT
1 CGAGGGTAAAAATGAAATTTTTGGAAGTTT
* * *
25621266 CAAGGTTAAAAATGGAATTTTTGGAAG-TT
1 CGAGGGTAAAAATGAAATTTTTGGAAGTTT
*
25621295 CGGGGGTAAAAATGAAATTTTTGGAAGTTT
1 CGAGGGTAAAAATGAAATTTTTGGAAGTTT
*
25621325 CG-GGGTTAAAACT-AGAATTTTTGGAAGTTT
1 CGAGGG-TAAAAATGA-AATTTTTGGAAGTTT
* *
25621355 -TAGGGTCAAAAATGGAATTTTTGGAAG-TT
1 CGAGGGT-AAAAATGAAATTTTTGGAAGTTT
* * *
25621384 CAAGGTTAAAAATGTAATTTTTGGACAGTT
1 CGAGGGTAAAAATGAAATTTTTGGA-AGTT
25621414 CAGGGACCTT
Statistics
Matches: 121, Mismatches: 17, Indels: 18
0.78 0.11 0.12
Matches are distributed among these distances:
29 66 0.55
30 54 0.45
31 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (30 bp):
CGAGGGTAAAAATGAAATTTTTGGAAGTTT
Found at i:25621345 original size:59 final size:59
Alignment explanation
Indices: 25621252--25621418 Score: 198
Period size: 59 Copynumber: 2.8 Consensus size: 59
25621242 GTAAAAGGGT
* *
25621252 AATTTTT-AAAGTTTCAAGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGT-AAAAATGA
1 AATTTTTGGAAGTTTCAAGGTTAAAAAT-GAATTTTTGGAAGTTCGAGGGTCAAAAATGA
** * ** *
25621310 AATTTTTGGAAGTTTCGGGGTTAAAACTAGAATTTTTGGAAGTTTTAGGGTCAAAAATGG
1 AATTTTTGGAAGTTTCAAGGTTAAAAAT-GAATTTTTGGAAGTTCGAGGGTCAAAAATGA
25621370 AATTTTTGGAAG-TTCAAGGTTAAAAATGTAATTTTTGGACAGTTC-AGGG
1 AATTTTTGGAAGTTTCAAGGTTAAAAATG-AATTTTTGGA-AGTTCGAGGG
25621419 ACCTTTAGAG
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
58 8 0.09
59 61 0.66
60 23 0.25
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (59 bp):
AATTTTTGGAAGTTTCAAGGTTAAAAATGAATTTTTGGAAGTTCGAGGGTCAAAAATGA
Found at i:25622572 original size:17 final size:17
Alignment explanation
Indices: 25622546--25622601 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
25622536 TCTTCAAATC
25622546 TTTT-TTAATATTATTA
1 TTTTATTAATATTATTA
25622562 TTTTATTAATATTATTA
1 TTTTATTAATATTATTA
*
25622579 TATTA-T-AT-TTATTA
1 TTTTATTAATATTATTA
25622593 TATTTATTA
1 T-TTTATTA
25622602 TTAAAACGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 7 0.21
15 5 0.15
16 6 0.18
17 16 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAATATTATTA
Found at i:25622574 original size:14 final size:13
Alignment explanation
Indices: 25622557--25622604 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
25622547 TTTTTAATAT
*
25622557 TATTATTTTATTAA
1 TATTATTATATT-A
25622571 TATTATTATATTA
1 TATTATTATATTA
25622584 TATTTATTATATT-
1 TA-TTATTATATTA
25622597 TATTATTA
1 TATTATTA
25622605 AAACGTTCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 6 0.19
13 5 0.16
14 21 0.66
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:25622591 original size:9 final size:9
Alignment explanation
Indices: 25622556--25622602 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
25622546 TTTTTTAATA
25622556 TTATTAT-T
1 TTATTATAT
25622564 TTATTA-A-
1 TTATTATAT
25622571 -TATTAT-T
1 TTATTATAT
*
25622578 ATATTATAT
1 TTATTATAT
25622587 TTATTATAT
1 TTATTATAT
25622596 TTATTAT
1 TTATTAT
25622603 TAAAACGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
6 5 0.15
8 12 0.36
9 16 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTATTATAT
Found at i:25623408 original size:17 final size:17
Alignment explanation
Indices: 25623383--25623453 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 17
25623373 CTTTAATTTT
*
25623383 ATTTTAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
25623400 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
* * * *
25623417 ATTCAAACTCAAAATGA
1 ATTTAAATTTAAAATAA
*
25623434 ATTTGAATTTAAAATAA
1 ATTTAAATTTAAAATAA
25623451 ATT
1 ATT
25623454 CAAACTTATT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:25623431 original size:34 final size:34
Alignment explanation
Indices: 25623393--25623459 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
25623383 ATTTTAATTT
*
25623393 AAAATAAATTTAAATTTAAAGTAAATTCAAACTC
1 AAAATAAATTTAAATTTAAAATAAATTCAAACTC
* *
25623427 AAAATGAATTTGAATTTAAAATAAATTCAAACT
1 AAAATAAATTTAAATTTAAAATAAATTCAAACT
25623460 TATTTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.33
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATTCAAACTC
Found at i:25624520 original size:39 final size:39
Alignment explanation
Indices: 25624454--25624621 Score: 131
Period size: 39 Copynumber: 4.3 Consensus size: 39
25624444 CCGTGATCAA
* * * *
25624454 GGTAAGGAGATCGATTGATGGTGATCTGCCTCAGGCTTGG
1 GGTAA-GAGATCGAATGATGGTAATCTGCCCCAGGCTCGG
* *
25624494 GGTAAGAGATCGAATGATTGTAATCTGCCCCTGGCTCGG
1 GGTAAGAGATCGAATGATGGTAATCTGCCCCAGGCTCGG
* ** * * * * *
25624533 GGTAAGAGACTTGGTTAAAGATGATCTGCCCCAGGCTCGA
1 GGTAAGAGA-TCGAATGATGGTAATCTGCCCCAGGCTCGG
* * * * *
25624573 GGTAAAAGATCAAATGGCT-GTAACCTGCCCCAGGCTCAG
1 GGTAAGAGATCGAAT-GATGGTAATCTGCCCCAGGCTCGG
25624612 GGTAAGAGAT
1 GGTAAGAGAT
25624622 TGGTTGATGA
Statistics
Matches: 96, Mismatches: 30, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
39 63 0.66
40 33 0.34
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (39 bp):
GGTAAGAGATCGAATGATGGTAATCTGCCCCAGGCTCGG
Found at i:25624568 original size:79 final size:78
Alignment explanation
Indices: 25624475--25624626 Score: 205
Period size: 79 Copynumber: 1.9 Consensus size: 78
25624465 CGATTGATGG
* * * * * * * * *
25624475 TGATCTGCCTCAGGCTTGGGGTAAGAGATCGAATGATTGTAATCTGCCCCTGGCTCGGGGTAAGA
1 TGATCTGCCCCAGGCTCGAGGTAAAAGATCAAATGACTGTAACCTGCCCCAGGCTCAGGGTAAGA
25624540 GACTTGGTTAAAGA
66 GA-TTGGTTAAAGA
*
25624554 TGATCTGCCCCAGGCTCGAGGTAAAAGATCAAATGGCTGTAACCTGCCCCAGGCTCAGGGTAAGA
1 TGATCTGCCCCAGGCTCGAGGTAAAAGATCAAATGACTGTAACCTGCCCCAGGCTCAGGGTAAGA
25624619 GATTGGTT
66 GATTGGTT
25624627 GATGATGTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
78 6 0.10
79 57 0.90
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.24
Consensus pattern (78 bp):
TGATCTGCCCCAGGCTCGAGGTAAAAGATCAAATGACTGTAACCTGCCCCAGGCTCAGGGTAAGA
GATTGGTTAAAGA
Found at i:25625021 original size:49 final size:49
Alignment explanation
Indices: 25624939--25625180 Score: 310
Period size: 49 Copynumber: 4.9 Consensus size: 49
25624929 TCCCTTCAAA
25624939 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCT-TGTG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTCTGTG
* * *
25624987 TCTTCGTGGTACTGGATCTGTCGTTGCGGTCTTAGATCTTTCCCTTCTGTA
1 TCTTCGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCC-TCTGTG
* *
25625038 TCTTTGTGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCT-TGTG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCTCTGTG
* * *
25625087 TCTTCGCGATACTGGATCCGCCGTTGCGGCCTTAGATCTTT-CCTGTCGTG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCTCT-GTG
* * * *
25625137 TTTTTGTGGTACTGGATCCGCAGTCGCGGCTTAGATCTTTCCCT
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCT
25625181 GTCAAACCTG
Statistics
Matches: 171, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
48 30 0.18
49 65 0.38
50 31 0.18
51 45 0.26
ACGTcount: A:0.10, C:0.26, G:0.26, T:0.39
Consensus pattern (49 bp):
TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTCTGTG
Found at i:25625100 original size:100 final size:100
Alignment explanation
Indices: 25624938--25625180 Score: 359
Period size: 100 Copynumber: 2.5 Consensus size: 100
25624928 TTCCCTTCAA
* * *
25624938 ATCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTGGA
1 ATCTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTGTCTTCGCGATACTGGA
* * *
25625003 TCTGTCGTTGCGGTCTTAGATCTTTCCCT-TC-TGT
66 TCCGCCGTTGCGGCCTTAGATCTTT-CCTGTCGTGT
*
25625037 ATCTTTGTGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCTTGTGTCTTCGCGATACTGG
1 ATCTTTGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCTTGTGTCTTCGCGATACTGG
25625102 ATCCGCCGTTGCGGCCTTAGATCTTTCCTGTCGTGT
65 ATCCGCCGTTGCGGCCTTAGATCTTTCCTGTCGTGT
* *
25625138 -T-TTTGTGGTACTGGATCCGCAGTCGCGGCTTAGATCTTTCCCT
1 ATCTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCT
25625181 GTCAAACCTG
Statistics
Matches: 131, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
98 15 0.11
99 55 0.42
100 58 0.44
101 3 0.02
ACGTcount: A:0.10, C:0.26, G:0.26, T:0.39
Consensus pattern (100 bp):
ATCTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTGTCTTCGCGATACTGGA
TCCGCCGTTGCGGCCTTAGATCTTTCCTGTCGTGT
Found at i:25626399 original size:9 final size:8
Alignment explanation
Indices: 25626381--25626451 Score: 67
Period size: 8 Copynumber: 9.0 Consensus size: 8
25626371 CGACCTCTCC
25626381 TTTTCTTT
1 TTTTCTTT
*
25626389 TTTTCCTT
1 TTTTCTTT
*
25626397 TTTTGTTT
1 TTTTCTTT
25626405 TTTTC--T
1 TTTTCTTT
*
25626411 TTTGCTTT
1 TTTTCTTT
25626419 TTCTTCTTCT
1 TT-TTCTT-T
*
25626429 TCTTC-TT
1 TTTTCTTT
25626436 TTTTCTTT
1 TTTTCTTT
25626444 TTTTCTTT
1 TTTTCTTT
25626452 ATTCATTGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
6 5 0.10
7 5 0.10
8 31 0.62
9 7 0.14
10 2 0.04
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (8 bp):
TTTTCTTT
Found at i:25626413 original size:13 final size:15
Alignment explanation
Indices: 25626388--25626444 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 15
25626378 TCCTTTTCTT
25626388 TTTTTCCTT-TTTTG-
1 TTTTT-CTTCTTTTGC
25626402 TTTTT-TTCTTTTGC
1 TTTTTCTTCTTTTGC
25626416 TTTTTCTTCTTCTT-C
1 TTTTTCTTCTT-TTGC
*
25626431 TTCTTTTTTCTTTT
1 TT-TTTCTTCTTTT
25626445 TTTCTTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
12 2 0.05
13 5 0.14
14 10 0.27
15 10 0.27
16 10 0.27
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTTTCTTCTTTTGC
Found at i:25626420 original size:15 final size:14
Alignment explanation
Indices: 25626380--25626444 Score: 67
Period size: 15 Copynumber: 4.4 Consensus size: 14
25626370 TCGACCTCTC
*
25626380 CTTTTCTTTTTTTC
1 CTTTTCTTTTTTTT
*
25626394 CTTTTTTGTTTTTTT
1 CTTTTCT-TTTTTTT
*
25626409 CTTTTGCTTTTTCTT
1 CTTTT-CTTTTTTTT
25626424 CTTCTTCTTCTTTTTT
1 CTT-TTCTT-TTTTTT
25626440 CTTTT
1 CTTTT
25626445 TTTCTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
14 6 0.14
15 25 0.60
16 11 0.26
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.78
Consensus pattern (14 bp):
CTTTTCTTTTTTTT
Found at i:25627187 original size:11 final size:11
Alignment explanation
Indices: 25627173--25627218 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
25627163 TCATCTTGAC
25627173 TTTTTCTTTCT
1 TTTTTCTTTCT
**
25627184 TTTTTCACTCT
1 TTTTTCTTTCT
25627195 TTTTT-TTTCT
1 TTTTTCTTTCT
25627205 TTTTTCTTT-T
1 TTTTTCTTTCT
25627215 TTTT
1 TTTT
25627219 AATTGGGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 13 0.43
11 17 0.57
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:25627280 original size:54 final size:54
Alignment explanation
Indices: 25627204--25627328 Score: 189
Period size: 54 Copynumber: 2.3 Consensus size: 54
25627194 TTTTTTTTTC
25627204 TTTTTTCTTTTTTTTAATTGGGTTTTTAAAATACCTTTTGCGAATTTTCGACCCA
1 TTTTTT-TTTTTTTTAATTGGGTTTTTAAAATACCTTTTGCGAATTTTCGACCCA
* *
25627259 TTTTTTTGTTTTTTT-ATTGGGTTTTTAAAATGCCTTTTGCGAATTTTCGACCTA
1 TTTTTTT-TTTTTTTAATTGGGTTTTTAAAATACCTTTTGCGAATTTTCGACCCA
25627313 TCTTTTTTTTTGTTTT
1 T-TTTTTTTTT-TTTT
25627329 TTTATAACAC
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
54 42 0.65
55 23 0.35
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.60
Consensus pattern (54 bp):
TTTTTTTTTTTTTTAATTGGGTTTTTAAAATACCTTTTGCGAATTTTCGACCCA
Found at i:25632273 original size:58 final size:58
Alignment explanation
Indices: 25632143--25632341 Score: 184
Period size: 58 Copynumber: 3.5 Consensus size: 58
25632133 TGAAACTTTA
* * *
25632143 GACATCCGAGGGTAAAACGGTAACTTTTATA-AAAAATCAGGAT-AAAAA-ACG--TTTTG
1 GACATTCGAGGGTAAAATGGTAA-TTTT-TAGAAAAATCGGGATCAAAAATA-GAATTTTG
25632199 GACA-TCTGAGGGTAAAATGGTAATTTTTAGAAAAATCGGGATCAAAAATAGAATTTTG
1 GACATTC-GAGGGTAAAATGGTAATTTTTAGAAAAATCGGGATCAAAAATAGAATTTTG
* ** * *
25632257 GACATTCGAGGGTAAAAGGGTAA-TTTT-GAAAGTTTTGGGGTCAAAAATAGAATTTTTG
1 GACATTCGAGGGTAAAATGGTAATTTTTAGAAA-AATCGGGATCAAAAATAGAA-TTTTG
25632315 GA-AGTTCGAGGGTAAAAAT-GTAATTTT
1 GACA-TTCGAGGGT-AAAATGGTAATTTT
25632342 GGGAAGGTTT
Statistics
Matches: 122, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
54 2 0.02
55 16 0.13
56 29 0.24
57 22 0.18
58 44 0.36
59 9 0.07
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.30
Consensus pattern (58 bp):
GACATTCGAGGGTAAAATGGTAATTTTTAGAAAAATCGGGATCAAAAATAGAATTTTG
Found at i:25632331 original size:29 final size:29
Alignment explanation
Indices: 25632252--25632466 Score: 165
Period size: 29 Copynumber: 7.4 Consensus size: 29
25632242 AAAAATAGAA
**
25632252 TTTTGGACA-TTCGAGGGTAAAAGGGTAA-
1 TTTTGGA-AGTTCGAGGGTAAAAATGTAAT
* *
25632280 TTTTGAAAGTTTTG-GGGTCAAAAATAG-AAT
1 TTTTGGAAG-TTCGAGGGT-AAAAAT-GTAAT
25632310 TTTTGGAAGTTCGAGGGTAAAAATGTAAT
1 TTTTGGAAGTTCGAGGGTAAAAATGTAAT
* * * *
25632339 TTTGGGAAGGTTTG-GGTTAAAAATGGAAT
1 TTTTGGAA-GTTCGAGGGTAAAAATGTAAT
* *
25632368 TTTTTGAAGTTCTAGGGT-AAAATGTAAT
1 TTTTGGAAGTTCGAGGGTAAAAATGTAAT
* ** *
25632396 TTTTGAAAGTTTTAGGGCCAAAAATGTAAT
1 TTTTGGAAGTTCGAGGG-TAAAAATGTAAT
* *
25632426 TTTTAGAAGTTCG-GAGGTAAAAATATAAT
1 TTTTGGAAGTTCGAG-GGTAAAAATGTAAT
25632455 TTTTGGACAGTT
1 TTTTGGA-AGTT
25632467 TAGGGACCTT
Statistics
Matches: 147, Mismatches: 27, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
27 1 0.01
28 37 0.25
29 67 0.46
30 42 0.29
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
TTTTGGAAGTTCGAGGGTAAAAATGTAAT
Found at i:25632342 original size:58 final size:57
Alignment explanation
Indices: 25632240--25632457 Score: 239
Period size: 58 Copynumber: 3.8 Consensus size: 57
25632230 AAAATCGGGA
**
25632240 TCAAAAATAGAA-TTTTGGACA-TTCGAGGGTAAAAGGGTAATTTTGAAAGTTTTGGGG
1 TCAAAAATAGAATTTTTGGA-AGTTCGAGGGTAAAAATGTAATTTTGAAAGTTTT-GGG
* *
25632297 TCAAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTGGGAAGGTTTGGG
1 TCAAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTT-GAAAGTTTTGGG
* * * *
25632355 TTAAAAATGGAATTTTTTGAAGTTCTAGGGT-AAAATGTAATTTTTGAAAGTTTTAGGG
1 TCAAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATGTAA-TTTTGAAAGTTTT-GGG
* * *
25632413 CCAAAAAT-GTAATTTTTAGAAGTTCG-GAGGTAAAAATATAATTTT
1 TCAAAAATAG-AATTTTTGGAAGTTCGAG-GGTAAAAATGTAATTTT
25632458 TGGACAGTTT
Statistics
Matches: 138, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
57 31 0.22
58 92 0.67
59 15 0.11
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.35
Consensus pattern (57 bp):
TCAAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTGAAAGTTTTGGG
Found at i:25633581 original size:3 final size:3
Alignment explanation
Indices: 25633573--25633627 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
25633563 TCTTTTTTAA
* *
25633573 TAT TAT TAT T-T TAT TAA TAT TAT TAAT T-T TTT TA- TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TA-T TAT TAT
25633617 TAT TAT TAT TA
1 TAT TAT TAT TA
25633628 AAACGTTCTG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
2 6 0.14
3 33 0.75
4 5 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:25633591 original size:17 final size:16
Alignment explanation
Indices: 25633565--25633617 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 16
25633555 TCTTCAAATC
25633565 TTTTTTAATATTATTA
1 TTTTTTAATATTATTA
25633581 TTTTATTAATATTATTAA
1 TTTT-TTAATATTATT-A
*
25633599 TTTTTTTATATTTATTA
1 TTTTTTAATA-TTATTA
25633616 TT
1 TT
25633618 ATTATTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 4 0.12
17 19 0.58
18 10 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTAATATTATTA
Found at i:25634432 original size:17 final size:17
Alignment explanation
Indices: 25634410--25634446 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
25634400 CTTTAATTTT
25634410 ATTTTAATTTAAAATAA
1 ATTTTAATTTAAAATAA
*
25634427 ATTTTAATTTAAAGTAA
1 ATTTTAATTTAAAATAA
25634444 ATT
1 ATT
25634447 GAAACTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
ATTTTAATTTAAAATAA
Found at i:25640035 original size:11 final size:11
Alignment explanation
Indices: 25640019--25640045 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
25640009 CGTATAAATC
25640019 ATTAAATATAG
1 ATTAAATATAG
25640030 ATTAAATATAG
1 ATTAAATATAG
25640041 ATTAA
1 ATTAA
25640046 TTAATAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (11 bp):
ATTAAATATAG
Found at i:25640119 original size:18 final size:19
Alignment explanation
Indices: 25640079--25640119 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
25640069 ATAAGCTTTG
*
25640079 TAATCAATTTAAAATCACT
1 TAATCAATTTAAAATCACA
*
25640098 TAATCAATTT-AATTCACA
1 TAATCAATTTAAAATCACA
25640116 TAAT
1 TAAT
25640120 AAGGAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATCAATTTAAAATCACA
Found at i:25647464 original size:182 final size:183
Alignment explanation
Indices: 25647157--25647737 Score: 926
Period size: 182 Copynumber: 3.2 Consensus size: 183
25647147 TGATACCAAG
* * * * *
25647157 GTGATTACTGCAACAATGGAAAGCAGGAAGTTAGTGCGTTATTTCTTCATTGATCACG--TACGA
1 GTGATTACTGCAACAATGCAAAGCAGGAATTTAGTGCGTGATTTCTCCATTGA-C-CGTCTATGA
* *
25647220 AACTGATAGTGCAGTCGAGTGGTATGAAGCGTCA-GAAAATAGACTGTACAGAAATTAAACAGTC
64 AACTGATAGTGCAGTCGAGTGGTATGAGGCGTCAGGAAAAGAGACTGTACAGAAATTAAACAGTC
25647284 TAGTAGTTGAGTGGTAACCAAGCCAACGTGTTCATTCTTTGTGAACATATAAAAC
129 TAGTAGTTGAGTGGTAACCAAGCCAACGTGTTCATTCTTTGTGAACATATAAAAC
*
25647339 GTGATTACTGCAACAATGCAAAGCAGGAATTTCGTGCGTGATTTCTCCATTGACCGTCTATGAAA
1 GTGATTACTGCAACAATGCAAAGCAGGAATTTAGTGCGTGATTTCTCCATTGACCGTCTATGAAA
*
25647404 CTGATAGTGCAGTCGAGT-GTATGAGGCGTCAGGAAAAGAGACTGTATAGAAATTAAACAGTCTA
66 CTGATAGTGCAGTCGAGTGGTATGAGGCGTCAGGAAAAGAGACTGTACAGAAATTAAACAGTCTA
* *
25647468 GTAGTTGAGTGGTAACCAAGCCAGCGTGTTCATTCTTTGTGAACATATAAAAG
131 GTAGTTGAGTGGTAACCAAGCCAACGTGTTCATTCTTTGTGAACATATAAAAC
25647521 GTGATTACTGCAACAATGCAAAGCAGGAATTTAGTGCGTGATTTCTCCATTGACCGTCTATGAAA
1 GTGATTACTGCAACAATGCAAAGCAGGAATTTAGTGCGTGATTTCTCCATTGACCGTCTATGAAA
* *
25647586 CTGATAGTGCAGTCGAATGGTATGAGGCGTCAGAAAAAGAGACTGTACAGAAATT--A-A-TCTA
66 CTGATAGTGCAGTCGAGTGGTATGAGGCGTCAGGAAAAGAGACTGTACAGAAATTAAACAGTCTA
* *
25647647 GTAGTTGAGTGGTAACCAAGCCAACGTGTTCATTCTTTGCGAACAAATAAAAC
131 GTAGTTGAGTGGTAACCAAGCCAACGTGTTCATTCTTTGTGAACATATAAAAC
* * *
25647700 GTGATTACTGCAATAATACATAGCAGGAATTTAGTGCG
1 GTGATTACTGCAACAATGCAAAGCAGGAATTTAGTGCG
25647738 CAATTGTATT
Statistics
Matches: 373, Mismatches: 22, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
179 88 0.24
180 3 0.01
181 14 0.04
182 234 0.63
183 34 0.09
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (183 bp):
GTGATTACTGCAACAATGCAAAGCAGGAATTTAGTGCGTGATTTCTCCATTGACCGTCTATGAAA
CTGATAGTGCAGTCGAGTGGTATGAGGCGTCAGGAAAAGAGACTGTACAGAAATTAAACAGTCTA
GTAGTTGAGTGGTAACCAAGCCAACGTGTTCATTCTTTGTGAACATATAAAAC
Found at i:25648201 original size:15 final size:15
Alignment explanation
Indices: 25648183--25648217 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
25648173 TCAAATGAAG
25648183 AATTTAAAAATAATA
1 AATTTAAAAATAATA
* *
25648198 AATTCAAAAATTATA
1 AATTTAAAAATAATA
25648213 AATTT
1 AATTT
25648218 GAAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTTAAAAATAATA
Found at i:25648351 original size:16 final size:16
Alignment explanation
Indices: 25648313--25648357 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
25648303 TTTGGTTCGC
*
25648313 TGTAATAGAATAGAGG
1 TGTAATGGAATAGAGG
*
25648329 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGG
*
25648345 TGTAATGAAATAG
1 TGTAATGGAATAG
25648358 GACTGTAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:25648612 original size:57 final size:58
Alignment explanation
Indices: 25648536--25648662 Score: 177
Period size: 57 Copynumber: 2.2 Consensus size: 58
25648526 AATTTTAATG
* * * *
25648536 ATTATTATTAAATATAATTTAATAAAAATATTA-ATTATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATACAATTTAAT-AAAATAATATATAATTTAATAATATTTTTAACATA
* *
25648593 ATTCTTATTAAATACAATTTAATAAAATAATATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAATATTTTTAACATA
25648651 ATTATTATTAAA
1 ATTATTATTAAA
25648663 ATATGAATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
56 8 0.13
57 33 0.54
58 20 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (58 bp):
ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAATATTTTTAACATA
Found at i:25648683 original size:25 final size:24
Alignment explanation
Indices: 25648654--25648704 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
25648644 TAATATAATT
*
25648654 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
25648679 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
25648703 AT
1 AT
25648705 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:25653714 original size:2 final size:2
Alignment explanation
Indices: 25653707--25653738 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25653697 TTATAAGTAC
25653707 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
25653739 TCAATCATAC
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:25658193 original size:3 final size:3
Alignment explanation
Indices: 25658187--25658211 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25658177 ATTGTGTTCT
25658187 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
25658212 ATAGGTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25660090 original size:22 final size:22
Alignment explanation
Indices: 25660065--25660106 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
25660055 AAGCTTTGAT
25660065 TTTAAAATTAGGTTTAAATTAA
1 TTTAAAATTAGGTTTAAATTAA
* **
25660087 TTTAAATTTATTTTTAAATT
1 TTTAAAATTAGGTTTAAATT
25660107 TAAATCTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTAAAATTAGGTTTAAATTAA
Found at i:25660121 original size:16 final size:15
Alignment explanation
Indices: 25660077--25660132 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 15
25660067 TAAAATTAGG
25660077 TTTAAATTAATTTAAA
1 TTTAAATTAA-TTAAA
*
25660093 TTT--ATT-TTTAAA
1 TTTAAATTAATTAAA
25660105 TTTAAATCTAATTAAA
1 TTTAAAT-TAATTAAA
*
25660121 TTTGAATTAATT
1 TTTAAATTAATT
25660133 TAAAACTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
12 8 0.24
14 5 0.15
15 6 0.18
16 14 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTAAATTAATTAAA
Found at i:25662160 original size:29 final size:29
Alignment explanation
Indices: 25662126--25662340 Score: 220
Period size: 29 Copynumber: 7.3 Consensus size: 29
25662116 TCCCTAATTG
25662126 TCCAAAAATTATATTTTGACCCCTAAACT
1 TCCAAAAATTATATTTTGACCCCTAAACT
* * *
25662155 TTCAAAAATTATATTTTTAACCCTAAAACT
1 TCCAAAAATTATATTTTGACCCCT-AAACT
* * *
25662185 TCTAAAAATTACATTTTTACCCCTAAACT
1 TCCAAAAATTATATTTTGACCCCTAAACT
* * * *
25662214 TCCAAAAATTACATTTTAACCTCGAAACT
1 TCCAAAAATTATATTTTGACCCCTAAACT
*
25662243 TCCAAAAATTATATTTTTG-CCCTCGAAACT
1 TCCAAAAATTATA-TTTTGACCC-CTAAACT
**
25662273 TCCAAAAATTCCATTCTTGA-CCCTAAACT
1 TCCAAAAATTATATT-TTGACCCCTAAACT
* * *
25662302 TCTAAAAATTCTAGTTTT-AACCCTAAACT
1 TCCAAAAATTATA-TTTTGACCCCTAAACT
25662331 TCCAAAAATT
1 TCCAAAAATT
25662341 CCATTTTAAC
Statistics
Matches: 159, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
28 1 0.01
29 104 0.65
30 54 0.34
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTATATTTTGACCCCTAAACT
Found at i:25662223 original size:88 final size:88
Alignment explanation
Indices: 25662126--25662380 Score: 281
Period size: 88 Copynumber: 2.9 Consensus size: 88
25662116 TCCCTAATTG
*
25662126 TCCAAAAATTATATTTTGACCCCTAAACTTTCAAAAATTATATTTTTAACCCT-AAAACTTCTAA
1 TCCAAAAATTATATTTT-ACCCCTAAACTTCCAAAAATTATATTTTTAACCCTCAAAACTTCTAA
25662190 AAATTACATTTTTACCCCTAAACT
65 AAATTACATTTTTACCCCTAAACT
* * * * * *
25662214 TCCAAAAATTACATTTTAACCTCGAAACTTCCAAAAATTATATTTTT-GCCCTCGAAACTTCCAA
1 TCCAAAAATTATATTTT-ACCCCTAAACTTCCAAAAATTATATTTTTAACCCTCAAAACTTCTAA
* *
25662278 AAATTCCATTCTTGA-CCCTAAACT
65 AAATTACATT-TTTACCCCTAAACT
* * * ** *
25662302 TCTAAAAATTCTAGTTTTAACCCTAAACTTCCAAAAATTCCA-TTTTAA-CCTCAAAACTCCT-A
1 TCCAAAAATTATA-TTTTACCCCTAAACTTCCAAAAATTATATTTTTAACCCTCAAAACTTCTAA
25662364 AAATTACCA-TTTTACCC
65 AAATTA-CATTTTTACCC
25662381 TCGAATGTCT
Statistics
Matches: 137, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
85 3 0.02
86 9 0.07
87 20 0.15
88 98 0.72
89 7 0.05
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (88 bp):
TCCAAAAATTATATTTTACCCCTAAACTTCCAAAAATTATATTTTTAACCCTCAAAACTTCTAAA
AATTACATTTTTACCCCTAAACT
Found at i:25662332 original size:117 final size:116
Alignment explanation
Indices: 25662126--25662369 Score: 332
Period size: 117 Copynumber: 2.1 Consensus size: 116
25662116 TCCCTAATTG
* * * *
25662126 TCCAAAAATTATATTTTGACCCCTAAACTTTCAAAAATTATATTTTTAACCCTAAAACTTCTAAA
1 TCCAAAAATTATATTTTGACCCCGAAACTTCCAAAAATTACATTCTTAACCCTAAAACTTCTAAA
* * *
25662191 AATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTAACCTCGAAAC
66 AATTACAGTTTTAACCCTAAACTTCCAAAAATTACATTTTAACCTCAAAAC
* *
25662242 TTCCAAAAATTATATTTTTG-CCCTCGAAACTTCCAAAAATTCCATTCTTGACCCT-AAACTTCT
1 -TCCAAAAATTATA-TTTTGACCC-CGAAACTTCCAAAAATTACATTCTTAACCCTAAAACTTCT
*
25662305 AAAAATT-CTAGTTTTAACCCTAAACTTCCAAAAATTCCATTTTAACCTCAAAAC
63 AAAAATTAC-AGTTTTAACCCTAAACTTCCAAAAATTACATTTTAACCTCAAAAC
*
25662359 TCCTAAAATTA
1 TCCAAAAATTA
25662370 CCATTTTACC
Statistics
Matches: 113, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
116 11 0.10
117 72 0.64
118 30 0.27
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (116 bp):
TCCAAAAATTATATTTTGACCCCGAAACTTCCAAAAATTACATTCTTAACCCTAAAACTTCTAAA
AATTACAGTTTTAACCCTAAACTTCCAAAAATTACATTTTAACCTCAAAAC
Found at i:25662341 original size:29 final size:28
Alignment explanation
Indices: 25662126--25662381 Score: 214
Period size: 29 Copynumber: 8.8 Consensus size: 28
25662116 TCCCTAATTG
* *
25662126 TCCAAAAATTATATTTTGACCCCTAAACT
1 TCCAAAAATTCTATTTT-AACCCTAAACT
* *
25662155 TTCAAAAATTATATTTTTAACCCTAAAACT
1 TCCAAAAATTCTA-TTTTAACCCT-AAACT
* *
25662185 TCTAAAAATTAC-ATTTTTACCCCTAAACT
1 TCCAAAAATT-CTA-TTTTAACCCTAAACT
*
25662214 TCCAAAAATTAC-ATTTTAACCTCGAAACT
1 TCCAAAAATT-CTATTTTAACC-CTAAACT
* **
25662243 TCCAAAAATTATATTTTTGCCCTCGAAACT
1 TCCAAAAATTCTATTTTAACCCT--AAACT
* *
25662273 TCCAAAAATTCCATTCTTGACCCTAAACT
1 TCCAAAAATTCTATT-TTAACCCTAAACT
*
25662302 TCTAAAAATTCTAGTTTTAACCCTAAACT
1 TCCAAAAATTCTA-TTTTAACCCTAAACT
* *
25662331 TCCAAAAATTCCATTTTAACCTCAAAAC-
1 TCCAAAAATTCTATTTTAACC-CTAAACT
* *
25662359 TCCTAAAATTACCATTTT-ACCCT
1 TCCAAAAATT-CTATTTTAACCCT
25662382 CGAATGTCTA
Statistics
Matches: 191, Mismatches: 25, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.01
28 28 0.15
29 108 0.57
30 48 0.25
31 6 0.03
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (28 bp):
TCCAAAAATTCTATTTTAACCCTAAACT
Found at i:25663336 original size:61 final size:61
Alignment explanation
Indices: 25663241--25663363 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
25663231 GCTGTAAAAG
*
25663241 GAAAGGCCTTAGTAATTGAGCCAGAAGAAAAAGAGACTGACAAGCCAGGACCGATAAATGA
1 GAAAGGCCTTAGCAATTGAGCCAGAAGAAAAAGAGACTGACAAGCCAGGACCGATAAATGA
25663302 GAAAGGCCTTAGCAATTGAGCCAGAAGAAAAAGAGACTGACAAGCCAGGACCGATAAATGA
1 GAAAGGCCTTAGCAATTGAGCCAGAAGAAAAAGAGACTGACAAGCCAGGACCGATAAATGA
25663363 G
1 G
25663364 CCAGTCACGG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.44, C:0.17, G:0.27, T:0.12
Consensus pattern (61 bp):
GAAAGGCCTTAGCAATTGAGCCAGAAGAAAAAGAGACTGACAAGCCAGGACCGATAAATGA
Found at i:25669481 original size:92 final size:92
Alignment explanation
Indices: 25669324--25670101 Score: 1297
Period size: 92 Copynumber: 8.5 Consensus size: 92
25669314 ATCAAAATAA
* *
25669324 CAAGTCTTTATCTCTTTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATAAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCC
*
25669389 TCTTGAAGTTGTAGTAAAGTTAGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
*
25669416 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAATTTCAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCC
25669481 TCTTGAAGTTGTAGTAAAGTTGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
* * *
25669508 CAAGTCTTTTTCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGCTTCAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCC
* *
25669573 TCTTAAAGTTGTAGTGAAGTTGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
* * *
25669600 CAAGTTTTTATCTCTCTGAAGTTGTAGTAAGAGCAGGATGAAGTTTCAAACATCATTTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCC
*
25669665 TCTTGAAGTTGTAGTAAAGTTGGATAA
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
* * * *
25669692 CAAGTCTTTATCTCTCTGAAGTTGCAGTAGGAGTAAGATGAAGCTTCAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCC
25669757 TCTTGAAGTTGTAGTAAAGTTGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
*
25669784 CAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCC
* *
25669849 TCTTGAAGTTATAGTGAAGTTGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
* *
25669876 CAAGTCTTTACCTCTCTGAAGTTGTAGT-AGAGCAAGATGGAGTTTCAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCC
**
25669940 TCTTGAAGTTGTAGTAAAGAGGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
* *
25669967 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGTAGTTTCAAACACCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCC
25670032 TCTTGAAGTTGTAGTAAAGTTGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
* *
25670059 CAAGTCTTTATCTCTCTAAAGTTGTAGTAAGAACAAGATGAAG
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAG
25670102 CCTCGACATC
Statistics
Matches: 636, Mismatches: 49, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
91 85 0.13
92 551 0.87
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (92 bp):
CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCC
TCTTGAAGTTGTAGTAAAGTTGGATAG
Found at i:25670393 original size:22 final size:22
Alignment explanation
Indices: 25670368--25670409 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
25670358 AAGCTTTGAT
25670368 TTTAAAGTTAGGTTTAAATTAA
1 TTTAAAGTTAGGTTTAAATTAA
* **
25670390 TTTAAATTTATTTTTAAATT
1 TTTAAAGTTAGGTTTAAATT
25670410 TAAATTTATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
TTTAAAGTTAGGTTTAAATTAA
Found at i:25670411 original size:18 final size:20
Alignment explanation
Indices: 25670388--25670436 Score: 84
Period size: 18 Copynumber: 2.5 Consensus size: 20
25670378 GGTTTAAATT
25670388 AATTTAAATTTAT-TTTT-A
1 AATTTAAATTTATCTTTTAA
25670406 AATTTAAATTTATCTTTTAA
1 AATTTAAATTTATCTTTTAA
25670426 AATTTAAATTT
1 AATTTAAATTT
25670437 GCTTTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.45
19 4 0.14
20 12 0.41
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTTAAATTTATCTTTTAA
Found at i:25670468 original size:39 final size:38
Alignment explanation
Indices: 25670384--25670474 Score: 89
Period size: 39 Copynumber: 2.4 Consensus size: 38
25670374 GTTAGGTTTA
**
25670384 AATT-AATTTAAATTTATTTTTAAATTTAAATTTATCT
1 AATTAAATTTAAATTTAGCTTTAAATTTAAATTTATCT
* *
25670421 -TTTAAAATTTAAATTT-GCTTTAATTTTAAATTTTTATCT
1 AATT-AAATTTAAATTTAGCTTTAAATTTAAA--TTTATCT
*
25670460 AATTAAATTTGAATT
1 AATTAAATTTAAATT
25670475 AATTTAAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
36 2 0.05
37 11 0.26
38 11 0.26
39 17 0.40
40 2 0.05
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.56
Consensus pattern (38 bp):
AATTAAATTTAAATTTAGCTTTAAATTTAAATTTATCT
Done.