Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000081.1 Hibiscus syriacus cultivar Beakdansim tig00000145_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: 136242
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2882 original size:2 final size:2
Alignment explanation
Indices: 2871--2902 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2861 CAATGCTTTA
2871 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2903 CTGGTAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5616 original size:43 final size:43
Alignment explanation
Indices: 5560--5689 Score: 111
Period size: 47 Copynumber: 2.9 Consensus size: 43
5550 AAATTTATTT
*
5560 ATTTAGTTCAAGCAATACATTAATAAAATTATGATATTTTACTA
1 ATTTA-TTTAAGCAATACATTAATAAAATTATGATATTTTACTA
* ** * * *
5604 ATTT-TTTAAAGCATTAAATCAATTAATTTTAATTATGA-AATTTATTT
1 ATTTATTT-AAGCA--ATA-C-ATTAA-TAAAATTATGATATTTTACTA
5651 ATTTAGTTTAAGCAATACATTAATAAAATTATGATATTT
1 ATTTA-TTTAAGCAATACATTAATAAAATTATGATATTT
5690 CGAGTTCGAG
Statistics
Matches: 66, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
42 2 0.03
43 14 0.21
44 12 0.18
45 3 0.05
46 3 0.05
47 15 0.23
48 14 0.21
49 3 0.05
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (43 bp):
ATTTATTTAAGCAATACATTAATAAAATTATGATATTTTACTA
Found at i:12920 original size:2 final size:2
Alignment explanation
Indices: 12913--12948 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12903 TAATGTAAGA
12913 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12949 GCCTGGTTTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18419 original size:22 final size:22
Alignment explanation
Indices: 18394--18459 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
18384 ATACAATATA
* *
18394 TAAACGAACGATAAACAAACAT
1 TAAACGAACGCTAAACGAACAT
*
18416 TAAAAC-AACGCTAAACGAACAC
1 T-AAACGAACGCTAAACGAACAT
*
18438 TAAATGAACGCTAAACGAACAT
1 TAAACGAACGCTAAACGAACAT
18460 GTTCTTGAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 3 0.08
22 30 0.81
23 4 0.11
ACGTcount: A:0.55, C:0.21, G:0.11, T:0.14
Consensus pattern (22 bp):
TAAACGAACGCTAAACGAACAT
Found at i:25058 original size:75 final size:77
Alignment explanation
Indices: 24969--25142 Score: 228
Period size: 76 Copynumber: 2.3 Consensus size: 77
24959 GGTAATATAA
* * * *
24969 TAGGTTGCTCCTAAAATGTTATAAACG-TAAAAAAATA-AGTTATAAATGTTAAATGTTATTAGT
1 TAGGTTGCGCCTAAAATGTTATAAACGATAAAAAAATAGA-TTATAAATGATAAATGTTATGAAT
25032 ATT-TTAACAATT
65 ATTATTAACAATT
* * * *
25044 TAGGTTGCGCCTAAAATGATATAAACGATAAGAAAATTGATTATAAATGATGAATGTTATGAATA
1 TAGGTTGCGCCTAAAATGTTATAAACGATAAAAAAATAGATTATAAATGATAAATGTTATGAATA
*
25109 TTATTAACATTT
66 TTATTAACAATT
*
25121 TAGGTTGCGCCTAAAATATTAT
1 TAGGTTGCGCCTAAAATGTTAT
25143 TAGAGTTTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
75 25 0.29
76 31 0.36
77 29 0.34
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.37
Consensus pattern (77 bp):
TAGGTTGCGCCTAAAATGTTATAAACGATAAAAAAATAGATTATAAATGATAAATGTTATGAATA
TTATTAACAATT
Found at i:25677 original size:72 final size:69
Alignment explanation
Indices: 25443--25680 Score: 266
Period size: 68 Copynumber: 3.4 Consensus size: 69
25433 ACTTAACTCT
* * * * *
25443 GATATTTGTGGAAAAGT-TCGATACTTTACAACCTTCCCATATTCCATTTTTTTTTAAATTTGAA
1 GATACTTGTGGAAAAGTATCGATACTTTGC-ATCTTCTCATTTTCCA-TTTTTTTTAAATTTGAA
25507 AGTATC
64 AGTATC
* * * **
25513 AATATTTGTGGAAAAATATCGATACTTTGCATCATTCTCATTTTCCA-TTTTTTT-AATTCAAAA
1 GATACTTGTGGAAAAGTATCGATACTTTGCATC-TTCTCATTTTCCATTTTTTTTAAATTTGAAA
*
25576 GTATT
65 GTATC
* *
25581 GATACTTGTGGAAAAGTATGGATACTTTGTAGTCTTCTCATTTTCCATGTTTTTTTAAAATTTGA
1 GATACTTGTGGAAAAGTATCGATACTTTGCA-TCTTCTCATTTTCCAT-TTTTTTT-AAATTTGA
25646 AAGTATC
63 AAGTATC
* *
25653 GATACTAGTAGAAAAGTATCGATACTTT
1 GATACTTGTGGAAAAGTATCGATACTTT
25681 CAAATTTTTT
Statistics
Matches: 141, Mismatches: 20, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
68 50 0.35
69 9 0.06
70 24 0.17
71 22 0.16
72 36 0.26
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (69 bp):
GATACTTGTGGAAAAGTATCGATACTTTGCATCTTCTCATTTTCCATTTTTTTTAAATTTGAAAG
TATC
Found at i:27189 original size:29 final size:28
Alignment explanation
Indices: 27157--27239 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 28
27147 CATACAAAAA
27157 CAGAACGGAGAATAAATCCCATGCAGAGT
1 CAGAACGG-GAATAAATCCCATGCAGAGT
* *
27186 CAGAACATGGAATAAATCCCACGCAGAGT
1 CAGAAC-GGGAATAAATCCCATGCAGAGT
* *
27215 CAAAACGGGGAATAAATTCCATGCA
1 CAGAAC-GGGAATAAATCCCATGCA
27240 TAATCGAGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
29 45 0.98
30 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14
Consensus pattern (28 bp):
CAGAACGGGAATAAATCCCATGCAGAGT
Found at i:38182 original size:10 final size:9
Alignment explanation
Indices: 38147--38258 Score: 89
Period size: 10 Copynumber: 11.7 Consensus size: 9
38137 GCTCCTGGAA
*
38147 ACCGGTTTA
1 ACCGGTTTG
*
38156 ACCGGTTTTCA
1 ACCGG-TTT-G
38167 ACCGGTTCTG
1 ACCGGTT-TG
38177 ACCGGTTTG
1 ACCGGTTTG
*
38186 ACCGGTTTCA
1 ACCGGTTT-G
*
38196 ACCGGTTCG
1 ACCGGTTTG
*
38205 AACCAGTTTG
1 -ACCGGTTTG
*
38215 ACCGGTCTG
1 ACCGGTTTG
*
38224 AATCGGTTTG
1 -ACCGGTTTG
*
38234 ACCGGTCTG
1 ACCGGTTTG
38243 AGCCGGTTTG
1 A-CCGGTTTG
38253 ACCGGT
1 ACCGGT
38259 CCGACCCGAC
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
9 35 0.42
10 41 0.49
11 7 0.08
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:38259 original size:19 final size:19
Alignment explanation
Indices: 38146--38259 Score: 106
Period size: 19 Copynumber: 5.9 Consensus size: 19
38136 GGCTCCTGGA
* * *
38146 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TCTG
*
38166 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
*
38186 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
*
38205 AACCAGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
38224 AATCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
38243 AGCCGGTTTGACCGGTC
1 AACCGGTTTGACCGGTC
38260 CGACCCGACC
Statistics
Matches: 80, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
18 2 0.03
19 53 0.66
20 19 0.24
21 6 0.08
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:38264 original size:9 final size:9
Alignment explanation
Indices: 38167--38264 Score: 54
Period size: 9 Copynumber: 10.3 Consensus size: 9
38157 CCGGTTTTCA
38167 ACCGGTTCTG
1 ACCGG-TCTG
*
38177 ACCGGTTTG
1 ACCGGTCTG
* *
38186 ACCGGTTTCA
1 ACCGGTCT-G
38196 ACCGGT-TCG
1 ACCGGTCT-G
* *
38205 AACCAGTTTG
1 -ACCGGTCTG
38215 ACCGGTCTG
1 ACCGGTCTG
* *
38224 AATCGGTTTG
1 -ACCGGTCTG
38234 ACCGGTCTG
1 ACCGGTCTG
*
38243 AGCCGGTTTG
1 A-CCGGTCTG
*
38253 ACCGGTCCG
1 ACCGGTCTG
38262 ACC
1 ACC
38265 CGACCCGACC
Statistics
Matches: 70, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
9 37 0.53
10 32 0.46
11 1 0.01
ACGTcount: A:0.15, C:0.29, G:0.30, T:0.27
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:38269 original size:5 final size:5
Alignment explanation
Indices: 38259--38323 Score: 76
Period size: 5 Copynumber: 12.2 Consensus size: 5
38249 TTTGACCGGT
* *
38259 CCGAC CCGAC CCGAC CCGAC CGTTGAC CCGAC CCGAC CCGAC CGTTGAC
1 CCGAC CCGAC CCGAC CCGAC C--CGAC CCGAC CCGAC CCGAC C--CGAC
38308 CCGAC CCGAC CCGAC C
1 CCGAC CCGAC CCGAC C
38324 GTTGACCGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
5 44 0.85
7 8 0.15
ACGTcount: A:0.18, C:0.54, G:0.22, T:0.06
Consensus pattern (5 bp):
CCGAC
Found at i:38287 original size:22 final size:22
Alignment explanation
Indices: 38261--38330 Score: 140
Period size: 22 Copynumber: 3.2 Consensus size: 22
38251 TGACCGGTCC
38261 GACCCGACCCGACCCGACCGTT
1 GACCCGACCCGACCCGACCGTT
38283 GACCCGACCCGACCCGACCGTT
1 GACCCGACCCGACCCGACCGTT
38305 GACCCGACCCGACCCGACCGTT
1 GACCCGACCCGACCCGACCGTT
38327 GACC
1 GACC
38331 GTTGACCGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCCGACCGTT
Found at i:39315 original size:63 final size:63
Alignment explanation
Indices: 39213--39336 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
39203 CTAATGTGAC
* ** * *
39213 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
39276 TCTTAGGTAGGCCCCACGGCCCCGAAATC-TATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCAT-TCTCGGGTAGGCCCTCAGGCCCTAAGATGT
39337 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:45580 original size:29 final size:30
Alignment explanation
Indices: 45517--45591 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
45507 GGCTGCTGGA
*
45517 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
45548 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
45576 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
45592 CTGAATTGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:45628 original size:9 final size:9
Alignment explanation
Indices: 45518--45629 Score: 80
Period size: 10 Copynumber: 11.7 Consensus size: 9
45508 GCTGCTGGAA
*
45518 ACCGGTTTA
1 ACCGGTTTG
*
45527 ACCGGTTTTCA
1 ACCGG-TTT-G
45538 ACCGGTTCTG
1 ACCGGTT-TG
45548 ACCGGTTTG
1 ACCGGTTTG
*
45557 ACCGGTTTCA
1 ACCGGTTT-G
*
45567 ACCGGTTCG
1 ACCGGTTTG
45576 AACCGGTTTG
1 -ACCGGTTTG
*
45586 ACCGGTCTG
1 ACCGGTTTG
**
45595 AATTGGTTTG
1 -ACCGGTTTG
* *
45605 ACTGGTCTG
1 ACCGGTTTG
45614 AGCCGGTTTG
1 A-CCGGTTTG
45624 ACCGGT
1 ACCGGT
45630 CCGACCCGAC
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
9 36 0.43
10 40 0.48
11 7 0.08
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:45630 original size:19 final size:19
Alignment explanation
Indices: 45517--45630 Score: 97
Period size: 19 Copynumber: 5.9 Consensus size: 19
45507 GGCTGCTGGA
* * *
45517 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TCTG
*
45537 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
*
45557 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
45576 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
** *
45595 AATTGGTTTGACTGGTCTG
1 AACCGGTTTGACCGGTCTG
*
45614 AGCCGGTTTGACCGGTC
1 AACCGGTTTGACCGGTC
45631 CGACCCGACC
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.03
19 50 0.64
20 20 0.26
21 6 0.08
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.31
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:45656 original size:22 final size:22
Alignment explanation
Indices: 45630--45691 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
45620 TTTGACCGGT
45630 CCGACCCGACCCGACCGTT---
1 CCGACCCGACCCGACCGTTGAC
45649 --GACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
*
45669 CCGACCCGACTCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
45691 C
1 C
45692 GTTGACTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 17 0.46
22 20 0.54
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:45691 original size:17 final size:17
Alignment explanation
Indices: 45632--45678 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
45622 TGACCGGTCC
45632 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
45649 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
45666 GACCCGACCCGAC
1 GACCCGACCCGAC
45679 TCGACCGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:46629 original size:63 final size:63
Alignment explanation
Indices: 46561--46684 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
46551 CTAATGTGAC
* ** * *
46561 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
46624 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
46685 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:48098 original size:16 final size:17
Alignment explanation
Indices: 48077--48109 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
48067 ACACACTAAA
*
48077 TCGGTTA-CGGTTTTTT
1 TCGGTTATCGATTTTTT
48093 TCGGTTATCGATTTTTT
1 TCGGTTATCGATTTTTT
48110 GGATCGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (17 bp):
TCGGTTATCGATTTTTT
Found at i:49140 original size:15 final size:15
Alignment explanation
Indices: 49116--49151 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
49106 TCAAAAGTAC
*
49116 AAAACACTCGAAGTG
1 AAAACCCTCGAAGTG
49131 AAAACCCTCGAAGTG
1 AAAACCCTCGAAGTG
49146 AAAACC
1 AAAACC
49152 AGTGTGTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (15 bp):
AAAACCCTCGAAGTG
Found at i:53714 original size:17 final size:17
Alignment explanation
Indices: 53694--53749 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
53684 AACTTCATGC
53694 AACTTGCCTTTTTTATT
1 AACTTGCCTTTTTTATT
** *
53711 AACTTG-CTTCATGA-T
1 AACTTGCCTTTTTTATT
* *
53726 AACTAGCCATTTTTATT
1 AACTTGCCTTTTTTATT
53743 AACTTGC
1 AACTTGC
53750 AGCTCCAGAA
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (17 bp):
AACTTGCCTTTTTTATT
Found at i:53721 original size:31 final size:32
Alignment explanation
Indices: 53686--53749 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
53676 AAACTTTGAA
* *
53686 CTTCATG-CAACTTGCCTTTTTTATTAACTTG
1 CTTCATGACAACTAGCCATTTTTATTAACTTG
*
53717 CTTCATGATAACTAGCCATTTTTATTAACTTG
1 CTTCATGACAACTAGCCATTTTTATTAACTTG
53749 C
1 C
53750 AGCTCCAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.45
Consensus pattern (32 bp):
CTTCATGACAACTAGCCATTTTTATTAACTTG
Found at i:54275 original size:24 final size:24
Alignment explanation
Indices: 54243--54295 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
54233 TTGTCGTTTC
54243 AGCAGGATCAAGCAATACAGAAAG
1 AGCAGGATCAAGCAATACAGAAAG
54267 AGCAGGATCAAGCAATACAGAAAG
1 AGCAGGATCAAGCAATACAGAAAG
54291 AGCAG
1 AGCAG
54296 AAACAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.49, C:0.17, G:0.26, T:0.08
Consensus pattern (24 bp):
AGCAGGATCAAGCAATACAGAAAG
Found at i:57929 original size:37 final size:36
Alignment explanation
Indices: 57784--57956 Score: 197
Period size: 36 Copynumber: 4.8 Consensus size: 36
57774 TTTAATATTT
* *
57784 TTTTTCTTAAAACATATTTTATC-CTACTTGAGATTG
1 TTTTTCTTAAAACAAATTTTATCTC-ACTTGAGAGTG
* * * *
57820 TTTTTCATAAAACATATTTTATCTCACTTGAGATTA
1 TTTTTCTTAAAACAAATTTTATCTCACTTGAGAGTG
* *
57856 TTTTTCTTAAAATAGATTTTATCTCACTTGAGAGTG
1 TTTTTCTTAAAACAAATTTTATCTCACTTGAGAGTG
* *
57892 TTTTTCCTTAAAATAAATTTTATCTCACTTGAAAGTG
1 TTTTT-CTTAAAACAAATTTTATCTCACTTGAGAGTG
* *
57929 TTTATCTTGAAACAAATTTT-TCCTCACT
1 TTTTTCTTAAAACAAATTTTAT-CTCACT
57957 CAATGCAATT
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
35 1 0.01
36 87 0.71
37 34 0.28
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.47
Consensus pattern (36 bp):
TTTTTCTTAAAACAAATTTTATCTCACTTGAGAGTG
Found at i:57948 original size:73 final size:72
Alignment explanation
Indices: 57788--57956 Score: 189
Period size: 73 Copynumber: 2.3 Consensus size: 72
57778 ATATTTTTTT
* * * *
57788 TCTTAAAACATATTTTATC-CTACTTGAGATTGTTTTTCATAAAACATATTTTATCTCACTTGAG
1 TCTTAAAACAAATTTTATCTC-ACTTGAGAGTGTTTTTCATAAAACAAATTTTATCTCACTTGAA
* *
57852 ATTATTTT
65 AGTATTTA
* * * *
57860 TCTTAAAATAGATTTTATCTCACTTGAGAGTGTTTTTCCTTAAAATAAATTTTATCTCACTTGAA
1 TCTTAAAACAAATTTTATCTCACTTGAGAGTGTTTTT-CATAAAACAAATTTTATCTCACTTGAA
*
57925 AGTGTTTA
65 AGTATTTA
*
57933 TCTTGAAACAAATTTT-TCCTCACT
1 TCTTAAAACAAATTTTAT-CTCACT
57957 CAATGCAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
72 33 0.41
73 48 0.59
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (72 bp):
TCTTAAAACAAATTTTATCTCACTTGAGAGTGTTTTTCATAAAACAAATTTTATCTCACTTGAAA
GTATTTA
Found at i:59879 original size:17 final size:19
Alignment explanation
Indices: 59843--59880 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
59833 CGCATTAATT
*
59843 TTTTTTTGTATAATTCAAA
1 TTTTTTTATATAATTCAAA
59862 TTTTTTTATA-AATT-AAA
1 TTTTTTTATATAATTCAAA
59879 TT
1 TT
59881 AAATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 4 0.22
19 9 0.50
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTTTTATATAATTCAAA
Found at i:63347 original size:50 final size:49
Alignment explanation
Indices: 63293--63400 Score: 139
Period size: 48 Copynumber: 2.2 Consensus size: 49
63283 AGATACCTAG
* * *
63293 GTATAGCGCGA-ATCAGGGGGCGCGCTATACTCACGTGGCGTCAAATCACC
1 GTATAACGCGAGATCA-GGGG-GCGCTATACCCACGTGGCGCCAAATCACC
* *
63343 GTATATCGC-AGATCAGGGGGCGTTATACCCACGTGGCGCCAAATCACC
1 GTATAACGCGAGATCAGGGGGCGCTATACCCACGTGGCGCCAAATCACC
63391 GTATAACGCG
1 GTATAACGCG
63401 GTTCAGGAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
48 34 0.67
49 5 0.10
50 12 0.24
ACGTcount: A:0.25, C:0.28, G:0.29, T:0.19
Consensus pattern (49 bp):
GTATAACGCGAGATCAGGGGGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:63407 original size:48 final size:49
Alignment explanation
Indices: 63304--63399 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 49
63294 TATAGCGCGA
* * *
63304 ATCAGGGGGCGCGCTATACTCACGTGGCGTCAAATCACCGTATATCGCAG
1 ATCA-GGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAACGCAG
*
63354 ATCAGGGG-GCGTTATACCCACGTGGCGCCAAATCACCGTATAACGC
1 ATCAGGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAACGC
63400 GGTTCAGGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 34 0.81
49 4 0.10
50 4 0.10
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (49 bp):
ATCAGGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAACGCAG
Found at i:76043 original size:14 final size:14
Alignment explanation
Indices: 76009--76045 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
75999 TTGCAAACTT
*
76009 ACAAGGAAAACCTC
1 ACAAGGCAAACCTC
76023 ACAAGGCAAACCTC
1 ACAAGGCAAACCTC
76037 ACAAGGCAA
1 ACAAGGCAA
76046 TATGTTTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.30, G:0.16, T:0.05
Consensus pattern (14 bp):
ACAAGGCAAACCTC
Found at i:76558 original size:65 final size:64
Alignment explanation
Indices: 76440--76585 Score: 201
Period size: 65 Copynumber: 2.3 Consensus size: 64
76430 TGCATCGGAT
76440 AAAATGCATTCGATGTTTTAAAATAGCCCGAGTGCATCAATGCATGGCTTGTGCATCGATGCATC
1 AAAATGCATTCGATGTTTTAAAATAGCCCGAGTGCATCAATGCATGGCTTGTGCATCGATGCA-C
* *
76505 -AAATGCATTCGATGTTTTCATAAA-A-CCATGAGTGCATCGATGCATGG-TATGTGCATCGATG
1 AAAATGCATTCGATGTTTT-A-AAATAGCC-CGAGTGCATCAATGCATGGCT-TGTGCATCGATG
76566 CAC
62 CAC
76569 AAAATGCATTCGATGTT
1 AAAATGCATTCGATGTT
76586 CAATTAATTC
Statistics
Matches: 74, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
64 22 0.30
65 49 0.66
66 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (64 bp):
AAAATGCATTCGATGTTTTAAAATAGCCCGAGTGCATCAATGCATGGCTTGTGCATCGATGCAC
Found at i:76624 original size:65 final size:63
Alignment explanation
Indices: 76441--76632 Score: 178
Period size: 65 Copynumber: 3.0 Consensus size: 63
76431 GCATCGGATA
* * * *
76441 AAATGCATTCGATGTTTTA-AAATAGCC-CGAGTGCATCAATGCATGGCTTGTGCATCGATGCAT
1 AAATGCATTCGATGTTTCATAAA-A-CCATGAGTGCATCGATGCAT-GATTGTGCATCGATGCAT
76504 C
63 C
*
76505 AAATGCATTCGATGTTTTCATAAAACCATGAGTGCATCGATGCATGGTATGTGCATCGATGCA-C
1 AAATGCATTCGATG-TTTCATAAAACCATGAGTGCATCGATGCATGAT-TGTGCATCGATGCATC
* ** *
76569 AAAATGCATTCGATG-TTCAATTAATTCATTG-GTGCATCGATGCATGAATTGGTGCATCGGTGC
1 -AAATGCATTCGATGTTTC-ATAAAACCA-TGAGTGCATCGATGCATG-ATT-GTGCATCGATGC
76632 A
61 A
76633 GCCTTTTGAA
Statistics
Matches: 110, Mismatches: 9, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
63 3 0.03
64 41 0.37
65 63 0.57
66 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (63 bp):
AAATGCATTCGATGTTTCATAAAACCATGAGTGCATCGATGCATGATTGTGCATCGATGCATC
Found at i:84124 original size:14 final size:15
Alignment explanation
Indices: 84100--84132 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
84090 ATTTTAGTGA
84100 TCATCTCCTCAAGAG
1 TCATCTCCTCAAGAG
84115 TCAT-TCCTCAAGAG
1 TCATCTCCTCAAGAG
84129 TCAT
1 TCAT
84133 GTTTCTCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.30
Consensus pattern (15 bp):
TCATCTCCTCAAGAG
Found at i:87417 original size:2 final size:2
Alignment explanation
Indices: 87410--87437 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
87400 GTCCGATTAC
87410 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
87438 TATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88438 original size:4 final size:4
Alignment explanation
Indices: 88429--88476 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
88419 TTTAATCCTT
* * * *
88429 TTTA TTTA TTTA TTATA TATA TATA TATA TATA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
88477 TTATTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
4 38 0.93
5 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:89112 original size:24 final size:23
Alignment explanation
Indices: 89069--89114 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
89059 TTTTATATTA
*
89069 AAAGTGAACTCTTAATATTTTAG
1 AAAGTGAACTCTTAAGATTTTAG
89092 AAAGATGAA-TCTATAAGATTTTA
1 AAAG-TGAACTCT-TAAGATTTTA
89115 TATGACGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (23 bp):
AAAGTGAACTCTTAAGATTTTAG
Found at i:92814 original size:2 final size:2
Alignment explanation
Indices: 92809--92835 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
92799 ATAAAAAATC
92809 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
92836 AAATTAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:93119 original size:21 final size:21
Alignment explanation
Indices: 93073--93120 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
93063 ATTTAACAAA
*
93073 TAAATTAAGTTTTATATTTAC
1 TAAATTAAGTTTTATATGTAC
* *
93094 AAAATTAAGTTTT-TAGTGTAG
1 TAAATTAAGTTTTATA-TGTAC
93115 TAAATT
1 TAAATT
93121 GTGAACATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (21 bp):
TAAATTAAGTTTTATATGTAC
Found at i:96912 original size:4 final size:4
Alignment explanation
Indices: 96905--96930 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
96895 TTTGATATTT
96905 ATTC ATTC ATTC ATTC ATTC ATTC AT
1 ATTC ATTC ATTC ATTC ATTC ATTC AT
96931 CATCACATAT
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:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTC
Found at i:97244 original size:182 final size:182
Alignment explanation
Indices: 96749--97304 Score: 950
Period size: 182 Copynumber: 3.0 Consensus size: 182
96739 GAAATTGTTT
*
96749 TATAGTTTAAGTGCAATGCACTGTCGATGGTCATTCATGAAAAAAAGGTGCAGATAAGATCTTGT
1 TATAGTTTAAGTGCAATGCACTGTCAATGGTCATTCATGAAAAAAAGGTGCAGATAAGATCTTGT
96814 TTATTACATGCAGATACCGAGTGCTTTTCAATCAACGATCTGAGTATGTATTTCAATCTTCATAA
66 TTATTACATGCAGATACCGAGTGCTTTTCAATCAACGATCTGAGTATGTATTTCAATCTTCATAA
* *
96879 CAGGTTACATAAATGTTTTGATATTTATTCATTCATTCATTCATTCATTCATCATCACATATAGC
131 CAGGTTACATAAATGTTTTGATATTTA-T-A---A--AAAT-A-T-ATT-AT-A--A-ATATAGC
96944 TC
181 TC
96946 TATAGTTTAAGTGCAATGCACTGTCAATGGTCATTCATGAAAAAAAGGTGCAGATAAGATCTTGT
1 TATAGTTTAAGTGCAATGCACTGTCAATGGTCATTCATGAAAAAAAGGTGCAGATAAGATCTTGT
97011 TTATTACATGCAGATACCGAGTGCTTTTCAATCAACGATCTGAGTATGTATTTCAATCTTCATAA
66 TTATTACATGCAGATACCGAGTGCTTTTCAATCAACGATCTGAGTATGTATTTCAATCTTCATAA
97076 CAGGTTACATAAATGTTTTGATATTTATAAAAATATATTATAAATATAGCTC
131 CAGGTTACATAAATGTTTTGATATTTATAAAAATATATTATAAATATAGCTC
97128 TATAGTTTAAGTGCAATGCACTGTCAATGGTCATTCATGAAAAAAAGGTGCAGATAAGATCTTGT
1 TATAGTTTAAGTGCAATGCACTGTCAATGGTCATTCATGAAAAAAAGGTGCAGATAAGATCTTGT
97193 TTATTACATGCAGATACCGAGTGCTTTTCAATCAACGATCTGAGTATGTATTTCAATCTTCATAA
66 TTATTACATGCAGATACCGAGTGCTTTTCAATCAACGATCTGAGTATGTATTTCAATCTTCATAA
97258 CAGGTTACATAAATGTTTTGATATTTATAAAAATATATTATAAATAT
131 CAGGTTACATAAATGTTTTGATATTTATAAAAATATATTATAAATAT
97305 TTTGAATACA
Statistics
Matches: 356, Mismatches: 3, Indels: 15
0.95 0.01 0.04
Matches are distributed among these distances:
182 186 0.52
183 1 0.00
185 1 0.00
186 2 0.01
187 3 0.01
188 1 0.00
189 1 0.00
190 2 0.01
192 1 0.00
195 1 0.00
196 1 0.00
197 156 0.44
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (182 bp):
TATAGTTTAAGTGCAATGCACTGTCAATGGTCATTCATGAAAAAAAGGTGCAGATAAGATCTTGT
TTATTACATGCAGATACCGAGTGCTTTTCAATCAACGATCTGAGTATGTATTTCAATCTTCATAA
CAGGTTACATAAATGTTTTGATATTTATAAAAATATATTATAAATATAGCTC
Found at i:98728 original size:18 final size:19
Alignment explanation
Indices: 98694--98734 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
98684 AAAATATTAT
98694 ATTA-TTATTTTTGGATA-
1 ATTATTTATTTTTGGATAG
98711 ATTATTTATTTTAT-GATAG
1 ATTATTTATTTT-TGGATAG
98730 ATTAT
1 ATTAT
98735 AATTATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.19
18 11 0.52
19 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (19 bp):
ATTATTTATTTTTGGATAG
Found at i:99475 original size:27 final size:30
Alignment explanation
Indices: 99417--99486 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 30
99407 TTTGACGACT
* *
99417 AAATTAGAATGAGAGTCATAATTTAGGTAC
1 AAATTAGAATGAGAGTCAAAATTTAGGGAC
99447 AAATTAGAATGA-A-T-AAAATTTAGGGAC
1 AAATTAGAATGAGAGTCAAAATTTAGGGAC
*
99474 AAAGTTAAAATGA
1 AAA-TTAGAATGA
99487 TTCATAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 14 0.39
28 9 0.25
29 1 0.03
30 12 0.33
ACGTcount: A:0.50, C:0.04, G:0.19, T:0.27
Consensus pattern (30 bp):
AAATTAGAATGAGAGTCAAAATTTAGGGAC
Found at i:101083 original size:20 final size:20
Alignment explanation
Indices: 101058--101108 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
101048 TGGAGCGTGG
101058 GGGGAATCGGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
*
101078 GGGGAATCAGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
101098 GGGGAATCGGT
1 GGGGAATCGGT
101109 TCCCTAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (20 bp):
GGGGAATCGGTACCCCCTAT
Found at i:103007 original size:21 final size:21
Alignment explanation
Indices: 102965--103007 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
102955 TTTCTGGGCT
* *
102965 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
102986 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
103007 A
1 A
103008 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:104169 original size:31 final size:31
Alignment explanation
Indices: 104131--104322 Score: 377
Period size: 31 Copynumber: 6.2 Consensus size: 31
104121 AAGGAACATA
104131 TGGATAGTTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
104162 TGGATAGTTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
104193 TGGATAGTTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
104224 TGGATAGTTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
104255 TGGATAGTTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
104286 TGGATAG-TTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
104316 TGGATAG
1 TGGATAG
104323 GTCCTTCGGA
Statistics
Matches: 161, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
30 30 0.19
31 131 0.81
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (31 bp):
TGGATAGTTTACCGAGGATCTTTATGACCTC
Found at i:108571 original size:4 final size:4
Alignment explanation
Indices: 108562--108590 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
108552 AAATGATGAC
108562 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
108591 ATGGTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:108855 original size:31 final size:31
Alignment explanation
Indices: 108817--109099 Score: 536
Period size: 31 Copynumber: 9.2 Consensus size: 31
108807 AAGGAACATA
108817 TGGATAGTTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
108848 TGGATAGTTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
*
108879 TGGATAGTTTACCGATGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
108910 TGGATAGTTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
108941 TGGATAGTTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
108972 TGGATAGTTTACCGAGGATCTTTATGA-C-C
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
109001 TGGATAGTTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
109032 TGGATAGTTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
109063 TGGATAG-TTACCGAGGATCTTTATGACCTC
1 TGGATAGTTTACCGAGGATCTTTATGACCTC
109093 TGGATAG
1 TGGATAG
109100 GTCCTTCGGA
Statistics
Matches: 248, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
29 28 0.11
30 32 0.13
31 188 0.76
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (31 bp):
TGGATAGTTTACCGAGGATCTTTATGACCTC
Found at i:111340 original size:21 final size:21
Alignment explanation
Indices: 111314--111353 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
111304 CAGAACCCCA
*
111314 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
111335 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
111354 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:121808 original size:43 final size:43
Alignment explanation
Indices: 121747--121833 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
121737 CTAGACTGAT
121747 TGAACATTTCTGCCTGATGTTATATTGTACGGTTAAAGGCCTA
1 TGAACATTTCTGCCTGATGTTATATTGTACGGTTAAAGGCCTA
121790 TGAACATTTCTGCCTGATGTTATATTGTACGGTTAAAGGCCTA
1 TGAACATTTCTGCCTGATGTTATATTGTACGGTTAAAGGCCTA
121833 T
1 T
121834 CAACGGTAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (43 bp):
TGAACATTTCTGCCTGATGTTATATTGTACGGTTAAAGGCCTA
Found at i:128228 original size:20 final size:22
Alignment explanation
Indices: 128203--128244 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
128193 TTCTATCAAA
128203 ATAAGTTT-A-AAAAAATAATT
1 ATAAGTTTGATAAAAAATAATT
*
128223 ATAAGTTTGATAATAAATAATT
1 ATAAGTTTGATAAAAAATAATT
128245 TGTGTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (22 bp):
ATAAGTTTGATAAAAAATAATT
Done.