Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000526.1 Hibiscus syriacus cultivar Beakdansim tig00001008_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: 100901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3351 original size:25 final size:25
Alignment explanation
Indices: 3315--3413 Score: 146
Period size: 25 Copynumber: 4.0 Consensus size: 25
3305 GAGTTGAGGG
* *
3315 TTCTACGCGGTCCTTCGGGATAAAT
1 TTCTACGTGGTCCTTCGGGACAAAT
*
3340 TTCTACGTGGTCCTTCGGGATAAAT
1 TTCTACGTGGTCCTTCGGGACAAAT
* *
3365 TTTTATGTGGTCCTTCGGGACAAA-
1 TTCTACGTGGTCCTTCGGGACAAAT
3389 TTCTACGTGGTCCTTCGGGACAAAT
1 TTCTACGTGGTCCTTCGGGACAAAT
3414 CTATGTGGCC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 22 0.33
25 45 0.67
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.34
Consensus pattern (25 bp):
TTCTACGTGGTCCTTCGGGACAAAT
Found at i:3403 original size:24 final size:24
Alignment explanation
Indices: 3315--3461 Score: 140
Period size: 25 Copynumber: 6.1 Consensus size: 24
3305 GAGTTGAGGG
* *
3315 TTCTACGCGGTCCTTCGGGATAAA
1 TTCTACGTGGTCCTTCGGGACAAA
*
3339 TTTCTACGTGGTCCTTCGGGATAAA
1 -TTCTACGTGGTCCTTCGGGACAAA
* *
3364 TTTTTATGTGGTCCTTCGGGACAAA
1 -TTCTACGTGGTCCTTCGGGACAAA
3389 TTCTACGTGGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
* * * *
3413 -TCTATGTGGCCCTTCGATG-CATA
1 TTCTACGTGGTCCTTCG-GGACAAA
3436 TTCTACGTGG-CACTTCGGTG-CAAA
1 TTCTACGTGGTC-CTTCGG-GACAAA
3460 TT
1 TT
3462 ATATGAGCAG
Statistics
Matches: 105, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
23 18 0.17
24 42 0.40
25 45 0.43
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:3439 original size:47 final size:48
Alignment explanation
Indices: 3326--3466 Score: 146
Period size: 47 Copynumber: 2.9 Consensus size: 48
3316 TCTACGCGGT
* * * *
3326 CCTTCGGGATAAATTTCTACGTGGTCCTTCGGGATAAATTTTTATGTGGT
1 CCTTCGGGACAAA-TTCTACGTGGTCCTTCGGGACAAA-TTCTATGTGGC
3376 CCTTCGGGACAAATTCTACGTGGTCCTTCGGGACAAA-TCTATGTGGC
1 CCTTCGGGACAAATTCTACGTGGTCCTTCGGGACAAATTCTATGTGGC
* * *
3423 CCTTCGATG-CATATTCTACGTGG-CACTTCGGTG-CAAATTATATG
1 CCTTCG-GGACAAATTCTACGTGGTC-CTTCGG-GACAAATTCTATG
3467 AGCAGTGGTG
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
46 1 0.01
47 37 0.46
48 7 0.09
49 23 0.29
50 12 0.15
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (48 bp):
CCTTCGGGACAAATTCTACGTGGTCCTTCGGGACAAATTCTATGTGGC
Found at i:4991 original size:138 final size:139
Alignment explanation
Indices: 4849--5203 Score: 459
Period size: 139 Copynumber: 2.6 Consensus size: 139
4839 GCACTAGCTA
* * ** * * * *
4849 TGAAATTAAACATAAAATGTAGGCTCTAAAAATTATCCTAATTAATTTTAACTATTTAATTGATT
1 TGAAATTAAGCCTAAAATGTAGGCTCTAATTATTAACCTAGTCAATTTTAACTAATTAATTGATT
*
4914 C-AATAATTAAAATAGA-ATCTCGAGCAAAAACGAGGACCAAATTAAAAATTCCACTAAATTTAA
66 CGAATAATTAAAATA-ACAACTCGAGCAAAAACGAGGACCAAATTAAAAATTCCACTAAATTTAA
4977 GGACTAAGTG
130 GGACTAAGTG
* * * * *
4987 TGAAATTAAGCCTAAAAT-TGATGCTCTATTTGTTAACCTAGTCAATTTTAACCAATTATTTGAT
1 TGAAATTAAGCCTAAAATGT-AGGCTCTAATTATTAACCTAGTCAATTTTAACTAATTAATTGAT
* *
5051 TCGAATAATTAAAATAACAACTCGAGCAAAAGCGAGGACCAAATTAAAAATTCCTCTAAATTTAA
65 TCGAATAATTAAAATAACAACTCGAGCAAAAACGAGGACCAAATTAAAAATTCCACTAAATTTAA
*
5116 GGACTAAGTT
130 GGACTAAGTG
* * *
5126 TGAAATTAAGCCTAAGATGAAGGCTCTAATTATTAACCTAGTCAA-TTTAATTAATT-ATGTGAT
1 TGAAATTAAGCCTAAAATGTAGGCTCTAATTATTAACCTAGTCAATTTTAACTAATTAAT-TGAT
*
5189 TCTAATAATTAAAAT
65 TCGAATAATTAAAAT
5204 GAAACCTTGG
Statistics
Matches: 186, Mismatches: 26, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
137 2 0.01
138 79 0.42
139 105 0.56
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (139 bp):
TGAAATTAAGCCTAAAATGTAGGCTCTAATTATTAACCTAGTCAATTTTAACTAATTAATTGATT
CGAATAATTAAAATAACAACTCGAGCAAAAACGAGGACCAAATTAAAAATTCCACTAAATTTAAG
GACTAAGTG
Found at i:5098 original size:139 final size:137
Alignment explanation
Indices: 4849--5240 Score: 473
Period size: 138 Copynumber: 2.8 Consensus size: 137
4839 GCACTAGCTA
* * * ** * * * * *
4849 TGAAATTAAACATAAAATGTAGGCTCTAAAAATTATCCTAATTAATTTTAACTATTTAATTGATT
1 TGAAATTAAGCCTAAAATGAAGGCTCTAATTATTAACCTAGTCAATTTTAACTAATTATTTGATT
* *
4914 CAATAATTAAAATAGAATCTCGAGCAAAAACGAGGACCAAATTAAAAATTCCACTAAATTTAAGG
66 CAATAATTAAAATA-AAACTCGAGCAAAAGCGAGGACCAAATTAAAAATTCCACTAAATTTAAGG
4979 ACTAAGTG
130 ACTAAGTG
* * * *
4987 TGAAATTAAGCCTAAAATTG-ATGCTCTATTTGTTAACCTAGTCAATTTTAACCAATTATTTGAT
1 TGAAATTAAGCCTAAAA-TGAAGGCTCTAATTATTAACCTAGTCAATTTTAACTAATTATTTGAT
*
5051 TCGAATAATTAAAATAACAACTCGAGCAAAAGCGAGGACCAAATTAAAAATTCCTCTAAATTTAA
65 TC-AATAATTAAAATAA-AACTCGAGCAAAAGCGAGGACCAAATTAAAAATTCCACTAAATTTAA
*
5116 GGACTAAGTT
128 GGACTAAGTG
* * *
5126 TGAAATTAAGCCTAAGATGAAGGCTCTAATTATTAACCTAGTCAA-TTTAATTAATTATGTGATT
1 TGAAATTAAGCCTAAAATGAAGGCTCTAATTATTAACCTAGTCAATTTTAACTAATTATTTGATT
* * * * * *
5190 CTAATAATTAAAATGAAACCTTGGGCAAAAGTGATGACCAAATTTAAAATT
66 C-AATAATTAAAAT-AAAACTCGAGCAAAAGCGAGGACCAAATTAAAAATT
5241 TCCTAATTAA
Statistics
Matches: 218, Mismatches: 31, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
138 110 0.50
139 108 0.50
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (137 bp):
TGAAATTAAGCCTAAAATGAAGGCTCTAATTATTAACCTAGTCAATTTTAACTAATTATTTGATT
CAATAATTAAAATAAAACTCGAGCAAAAGCGAGGACCAAATTAAAAATTCCACTAAATTTAAGGA
CTAAGTG
Found at i:7515 original size:3 final size:3
Alignment explanation
Indices: 7507--7536 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
7497 ACTAGAAACA
7507 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
7537 TCTCACCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:8856 original size:33 final size:33
Alignment explanation
Indices: 8813--8876 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
8803 CTTTTTATAA
*
8813 TTTACTTCAAATCTTATAAATCACATTATAAAT
1 TTTACTTCAAACCTTATAAATCACATTATAAAT
* * *
8846 TTTATTTCAAACCTTATAAATTATATTATAA
1 TTTACTTCAAACCTTATAAATCACATTATAA
8877 TCTCCAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (33 bp):
TTTACTTCAAACCTTATAAATCACATTATAAAT
Found at i:9707 original size:27 final size:26
Alignment explanation
Indices: 9636--9708 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 26
9626 GATAAAATAA
*
9636 TTAATTTAGATT-TTTTATAATATTAT
1 TTAATTTAG-TTAATTTATAATATTAT
* * * *
9662 TTACTTTAGTTATTCTTATAATGTTTT
1 TTAATTTAGTTAAT-TTATAATATTAT
9689 TTAATTTATGTTAATTTATA
1 TTAATTTA-GTTAATTTATA
9709 TAAATATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.05
26 10 0.26
27 22 0.56
28 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (26 bp):
TTAATTTAGTTAATTTATAATATTAT
Found at i:18703 original size:20 final size:20
Alignment explanation
Indices: 18680--18719 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
18670 AATTTAATCC
* *
18680 TATAATTTTATATTTTTAAG
1 TATAATTTGATATATTTAAG
18700 TATAATTTGATATATTTAAG
1 TATAATTTGATATATTTAAG
18720 GATGATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TATAATTTGATATATTTAAG
Found at i:19005 original size:2 final size:2
Alignment explanation
Indices: 18998--19022 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18988 TATAAAACCC
18998 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19023 TAGTTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19570 original size:26 final size:25
Alignment explanation
Indices: 19523--19573 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
19513 TTGAGAATTC
19523 TGATTTATTTAATTTGTAATTCTTT
1 TGATTTATTTAATTTGTAATTCTTT
* * *
19548 TGATTTCTTTCAATTTTTTATTCTTT
1 TGATTTATTT-AATTTGTAATTCTTT
19574 ATTATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.20, C:0.08, G:0.06, T:0.67
Consensus pattern (25 bp):
TGATTTATTTAATTTGTAATTCTTT
Found at i:20230 original size:23 final size:23
Alignment explanation
Indices: 20204--20249 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
20194 AGATACCATG
*
20204 GTAGATATGCTCTTTTCTTTCCA
1 GTAGATATGCTATTTTCTTTCCA
*
20227 GTAGATATGTTATTTTCTTTCCA
1 GTAGATATGCTATTTTCTTTCCA
20250 TTAATTGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (23 bp):
GTAGATATGCTATTTTCTTTCCA
Found at i:22707 original size:6 final size:6
Alignment explanation
Indices: 22696--22759 Score: 62
Period size: 6 Copynumber: 10.7 Consensus size: 6
22686 TTCAAATTTC
* *
22696 AAAAAG AAAAAG AAAAA- AAAGAG -AAAGG AAAAAGG AAAAAGG AAAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G AAAAA-G -AAAAAG
22745 AAAAAG AAAAA- AAAA
1 AAAAAG AAAAAG AAAA
22760 GTTACTACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
5 11 0.22
6 25 0.50
7 9 0.18
8 5 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:22742 original size:8 final size:7
Alignment explanation
Indices: 22696--22755 Score: 61
Period size: 7 Copynumber: 8.7 Consensus size: 7
22686 TTCAAATTTC
22696 AAAAA-G
1 AAAAAGG
*
22702 AAAAAGAA
1 AAAAAG-G
*
22710 AAAAAAG
1 AAAAAGG
*
22717 AGAAAGG
1 AAAAAGG
22724 AAAAAGG
1 AAAAAGG
22731 AAAAAGG
1 AAAAAGG
*
22738 AAAAAAG
1 AAAAAGG
22745 AAAAA-G
1 AAAAAGG
22751 AAAAA
1 AAAAA
22756 AAAAGTTACT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
6 11 0.24
7 29 0.64
8 5 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:22757 original size:14 final size:14
Alignment explanation
Indices: 22696--22757 Score: 79
Period size: 14 Copynumber: 4.4 Consensus size: 14
22686 TTCAAATTTC
22696 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAG-AA
* *
22711 AAAAAGAGAAAGGA
1 AAAAAGAAAAAGAA
* *
22725 AAAAGGAAAAAGGA
1 AAAAAGAAAAAGAA
22739 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
22753 AAAAA
1 AAAAA
22758 AAGTTACTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 30 0.73
15 11 0.27
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:25499 original size:20 final size:21
Alignment explanation
Indices: 25466--25505 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
25456 TTTTAACGTA
**
25466 ATTGATATTCATTTT-AAACC
1 ATTGATATAAATTTTCAAACC
25486 ATTGATATAAATTTTCAAAC
1 ATTGATATAAATTTTCAAAC
25506 AATTTGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATAAATTTTCAAACC
Found at i:28860 original size:21 final size:21
Alignment explanation
Indices: 28823--28905 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
28813 TTTTGGTGCA
*
28823 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
28843 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
28864 GAAGGGGAACCGATTCCCCCCAT
1 G-A-GGGAACCGATTCCCCCCAT
* * *
28887 AAGGGAATCGATACCCCCC
1 GAGGGAACCGATTCCCCCC
28906 TGGGGTTCTG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 10 0.19
21 23 0.44
22 2 0.04
23 17 0.33
ACGTcount: A:0.25, C:0.35, G:0.24, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:33907 original size:123 final size:123
Alignment explanation
Indices: 33688--34312 Score: 928
Period size: 123 Copynumber: 5.1 Consensus size: 123
33678 CACTTGAGAG
* * *
33688 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAGGAACTCATTTGAAGAGGAATAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
33753 ATCTGAAAAACTTATTCAACTTTTTGGTCGACTCTATCGCAGAATGAGATAGAGCAAC
66 ATCTGAAGAACTTATTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * *
33811 ATCAACATTTCCAGAAGGAGTTCTTAATAAGAAGAACTCATCTAAAGAGGAAAAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
33876 ATCTGAAGAACTTATTCAACATTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
66 ATCTGAAGAACTTATTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * *
33934 ATCAACATTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* *
33999 ATCTGAAGAACTTATTCAAGC-TTTTGCTCGGCTCTATCGCAGAAGGAGATAGAGCAGC
66 ATCTGAAGAACTTATTCAA-CTTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* *
34057 ATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAACTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * *
34122 ATCTGAAGAACTTATTCAAGTTTTTGCTCAACCCTATCCCAGAAGGAGATAGAGCAAC
66 ATCTGAAGAACTTATTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* *
34180 ATCAACATTTCCAGAAAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGGAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * * ** ** **
34245 ATCTGAAGAACTTATTAAACCTTTTGTTCAATTCTATTACAGAAAAAGATAGAGCATT
66 ATCTGAAGAACTTATTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
34303 ATCAACATTT
1 ATCAACATTT
34313 TCGTCTTAAT
Statistics
Matches: 461, Mismatches: 39, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
123 460 1.00
124 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (123 bp):
ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATCTGAAGAACTTATTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
Found at i:34495 original size:3 final size:3
Alignment explanation
Indices: 34427--34479 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
34417 CCTTTTTTAT
* *
34427 TTA TTA TTT TTA -TA TTA TTA TTA TTA TTTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
34472 TTA TTA TT
1 TTA TTA TT
34480 CAAATAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:37370 original size:29 final size:29
Alignment explanation
Indices: 37328--37386 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
37318 CTTACGCTCA
37328 ACCATCGATGCAAGTCTCAAATTACTGGT
1 ACCATCGATGCAAGTCTCAAATTACTGGT
37357 ACCATCGATGCAAGTCTCAAATTACTGGT
1 ACCATCGATGCAAGTCTCAAATTACTGGT
37386 A
1 A
37387 ATCCGAGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (29 bp):
ACCATCGATGCAAGTCTCAAATTACTGGT
Found at i:44696 original size:19 final size:19
Alignment explanation
Indices: 44689--44736 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
44679 CTGGAAGCTG
44689 TTGAGGCGGCTGGAAACCA
1 TTGAGGCGGCTGGAAACCA
44708 TTGAGGCGGCTGGAAACCA
1 TTGAGGCGGCTGGAAACCA
44727 TTGAGGCGGC
1 TTGAGGCGGC
44737 GGCATGTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.40, T:0.17
Consensus pattern (19 bp):
TTGAGGCGGCTGGAAACCA
Found at i:44866 original size:3 final size:3
Alignment explanation
Indices: 44858--44932 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
44848 TTAATGTATT
* * * * *
44858 TAA TAA TAA TAA TTA TAA TAA TAA TAT TAT TTA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
44906 TAA TAT TTA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
44933 ATTAATTAAT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:44870 original size:18 final size:16
Alignment explanation
Indices: 44834--44930 Score: 71
Period size: 18 Copynumber: 6.1 Consensus size: 16
44824 AATTTTTATT
*
44834 ATTATTTATAATATTTA
1 ATTATTTATAATA-ATA
44851 ATGTATTTAATAATAATA
1 AT-TATTT-ATAATAATA
*
44869 ATTA-TAATAATAAT-
1 ATTATTTATAATAATA
44883 ATTA-TT-T-ATAATA
1 ATTATTTATAATAATA
*
44896 ATTA-TAATAATAATA
1 ATTATTTATAATAATA
*
44911 TTTATAATTATAATAATA
1 ATTAT--TTATAATAATA
44929 AT
1 AT
44931 AAATTAATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
12 5 0.08
13 6 0.09
14 6 0.09
15 17 0.26
16 1 0.02
17 4 0.06
18 20 0.31
19 6 0.09
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (16 bp):
ATTATTTATAATAATA
Found at i:44893 original size:27 final size:29
Alignment explanation
Indices: 44854--44932 Score: 110
Period size: 27 Copynumber: 2.8 Consensus size: 29
44844 ATATTTAATG
*
44854 TATTTA-ATAATAATAATTATAATAATAA
1 TATTTATATTATAATAATTATAATAATAA
44882 TA-TTAT-TTATAATAATTATAATAATAA
1 TATTTATATTATAATAATTATAATAATAA
*
44909 TATTTATAATTATAATAATAATAA
1 TATTTAT-ATTATAATAATTATAA
44933 ATTAATTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 25 0.56
28 6 0.13
30 14 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TATTTATATTATAATAATTATAATAATAA
Found at i:44904 original size:24 final size:24
Alignment explanation
Indices: 44866--44932 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
44856 TTTAATAATA
*
44866 ATAATTATAATAATAATATTATTT
1 ATAATTATAATAATAATAATATTT
* *
44890 ATAATAATTATAATAATAATATTT
1 ATAATTATAATAATAATAATATTT
44914 ATAATTATAATAATAATAA
1 ATAATTATAATAATAATAA
44933 ATTAATTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATAATTATAATAATAATAATATTT
Found at i:44942 original size:24 final size:23
Alignment explanation
Indices: 44864--44938 Score: 87
Period size: 24 Copynumber: 3.2 Consensus size: 23
44854 TATTTAATAA
*
44864 TAATAATTATAATAATAATATTAT
1 TAATAATTATAATAATAATA-AAT
* * *
44888 TTATAATAATTATAATAATAATAT
1 TAATAATTATAATAATAATAA-AT
*
44912 TTATAATTATAATAATAATAAAT
1 TAATAATTATAATAATAATAAAT
44935 TAAT
1 TAAT
44939 TAATATGGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 5 0.12
24 38 0.88
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAATAATTATAATAATAATAAAT
Found at i:45275 original size:113 final size:113
Alignment explanation
Indices: 45078--45728 Score: 1052
Period size: 113 Copynumber: 5.7 Consensus size: 113
45068 GTTGAATAAA
* * * * ** *
45078 TTCTTC-TCTTTCTCCAGATGAGTTCTTCTCATTACGAACTTTCTGCTGGGGATGATGTTCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTGGTAATGATGATCCATC
* *
45142 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 AAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* *
45191 TTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGATGATCCATCA
45256 AGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 AGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* *
45304 TTCTCCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-C-TTCTCTGGTAATGATGATC
45369 CATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
61 CATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
45422 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGATGATCCATCA
45487 AGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 AGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
45535 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGATGATCCATCA
45600 AGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 AGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
45648 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTT-CTCTGGTAATGATGATC
45713 CATCAAGTGATGAATT
61 CATCAAGTGATGAATT
45729 TGAATCTTTG
Statistics
Matches: 509, Mismatches: 18, Indels: 17
0.94 0.03 0.03
Matches are distributed among these distances:
113 290 0.57
114 35 0.07
115 20 0.04
116 40 0.08
117 4 0.01
118 120 0.24
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGATGATCCATCA
AGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
Found at i:45546 original size:231 final size:227
Alignment explanation
Indices: 45087--45728 Score: 1063
Period size: 231 Copynumber: 2.8 Consensus size: 227
45077 ATTCTTCTCT
* * ** * *
45087 TTCTCCAGATGAGTTCTTCTCATTACGAA-CTTTCTGCTGGGGATGATGTTCCATCAAATGATGA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACCTTTCT-CTGGAAATGATGATCCATCAAGTGATGA
* *
45151 ATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGAGTT
65 ATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
45216 CTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTG
130 CTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTG
45281 AACAAGTTCTTCTCATTATGAACTTCTCCTTCC
195 AACAAGTTCTTCTCATTATGAACTTCTCCTTCC
45314 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGA
1 TTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTTCTCTGGAAATGATGATCCATCAAGTGA
45379 TGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
62 TGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
45444 GTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAGTGATGAATTCAAGCAAAAGG
127 GTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAGTGATGAATTCAAGCAAAAGG
*
45509 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
192 TTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCC
* *
45545 TTCTTCAGATGAGTTCTTCTCATTATGAACC-TTCTCTGGTAATGTTGATCCATCAAGTGATGAA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACCTTTCTCTGGAAATGATGATCCATCAAGTGATGAA
45609 TTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAG
66 TTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAG
* *
45674 TTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAGTGATGAATT
128 TTCTTCTCATTATGAAC-CTT-CTCTGGTAATGTTGATCCATCAAGTGATGAATT
45729 TGAATCTTTG
Statistics
Matches: 392, Mismatches: 13, Indels: 16
0.93 0.03 0.04
Matches are distributed among these distances:
226 90 0.23
227 10 0.03
228 20 0.05
229 20 0.05
230 21 0.05
231 225 0.57
232 6 0.02
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (227 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACCTTTCTCTGGAAATGATGATCCATCAAGTGATGAA
TTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
TTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGA
ACAAGTTCTTCTCATTATGAACTTCTCCTTCC
Found at i:45705 original size:344 final size:344
Alignment explanation
Indices: 45078--45728 Score: 1169
Period size: 344 Copynumber: 1.9 Consensus size: 344
45068 GTTGAATAAA
* * * *
45078 TTCTTCTCTTTCTCCAGATGAGTTCTTCTCATTACGAACTTTCTGCTGGGGATGATGTTCCATCA
1 TTCTTCTCCTTCTCCAGATGAGTTCTTCTCATTACGAACCTTCTGCTGGGAATGATGATCCATCA
45143 AATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCA
66 AATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCA
45208 GATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAGTGATGAATTCAAGCA
131 GATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAGTGATGAATTCAAGCA
45273 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGACGAGTTCTTCTC
196 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGACGAGTTCTTCTC
*
45338 ATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
261 ATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
45403 AGTTCTTCTCATTATGAAC
326 AGTTCTTCTCATTATGAAC
* * * *
45422 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTGGTAATGTTGATCCATC
1 TTCTTC-TCCTTCTCCAGATGAGTTCTTCTCATTACGAACCTTCTGCTGGGAATGATGATCCATC
* * *
45486 AAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
65 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTC
45551 AGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAGTGATGAATTCAAGC
130 AGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAGTGATGAATTCAAGC
*
45616 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCT
195 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGACGAGTTCTTCT
45681 CATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAGTGATGAATT
260 CATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAGTGATGAATT
45729 TGAATCTTTG
Statistics
Matches: 293, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
344 259 0.88
345 34 0.12
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (344 bp):
TTCTTCTCCTTCTCCAGATGAGTTCTTCTCATTACGAACCTTCTGCTGGGAATGATGATCCATCA
AATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCA
GATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAGTGATGAATTCAAGCA
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGACGAGTTCTTCTC
ATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
AGTTCTTCTCATTATGAAC
Found at i:46489 original size:52 final size:52
Alignment explanation
Indices: 46364--46863 Score: 890
Period size: 51 Copynumber: 9.8 Consensus size: 52
46354 TATGTCCAAT
46364 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG--T--C
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
*
46412 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
46464 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
*
46515 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGTTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
*
46567 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
*
46619 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATATTCT-TCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
46670 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
46721 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
*
46772 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGTTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
*
46824 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
46864 TGAGCACATA
Statistics
Matches: 435, Mismatches: 11, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
48 46 0.11
51 199 0.46
52 190 0.44
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (52 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
Found at i:46562 original size:103 final size:103
Alignment explanation
Indices: 46364--46863 Score: 884
Period size: 103 Copynumber: 4.9 Consensus size: 103
46354 TATGTCCAAT
*
46364 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC-TGT--CCAGATCAGATAACT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAACCAGATCAGATAACT
*
46426 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAAC
66 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
46464 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAACCAGATCAGATAACT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAACCAGATCAGATAACT
*
46529 CAAAGAACACTTCCAGAAGATACTATGTTCTGTCTAAC
66 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
*
46567 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAACCAGATCAGATAAC
*
46632 TCAAAGAACACTTCCAGAAGATGCTATATTCT-TCTAAC
65 TCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
46670 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAACCAGATCAGATAACT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAACCAGATCAGATAACT
46735 CAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
66 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
* *
46772 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGTTCTGTCTAACCAGATCAAATAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAACCAGATCAGATAAC
46837 TCAAAGAACACTTCCAGAAGATGCTAT
65 TCAAAGAACACTTCCAGAAGATGCTAT
46864 TGAGCACATA
Statistics
Matches: 385, Mismatches: 10, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
100 44 0.11
101 2 0.01
102 99 0.26
103 192 0.50
104 48 0.12
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (103 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAACCAGATCAGATAACT
CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
Found at i:47828 original size:13 final size:13
Alignment explanation
Indices: 47810--47871 Score: 65
Period size: 12 Copynumber: 4.8 Consensus size: 13
47800 ACCCCCTTTC
47810 TTTTTCTTCTCTT
1 TTTTTCTTCTCTT
*
47823 TTTTTCATTTTCTAT
1 TTTTTC-TTCTCT-T
47838 TTTTTCTT-TCTT
1 TTTTTCTTCTCTT
*
47850 TTTTT-TTTTCTT
1 TTTTTCTTCTCTT
*
47862 TTTTTTTTCT
1 TTTTTCTTCT
47872 TCAAGCATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
11 2 0.05
12 15 0.35
13 12 0.28
14 7 0.16
15 7 0.16
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTCTTCTCTT
Found at i:47835 original size:25 final size:23
Alignment explanation
Indices: 47806--47872 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 23
47796 CTTGACCCCC
47806 TTTCTTTTTCTTC-TCTTTTTTTCAT
1 TTTCTTTTT-TTCTTCTTTTTTT--T
47831 TTTCTATTTTTTCTTTCTTTTTTTT
1 TTTCT-TTTTTTC-TTCTTTTTTTT
*
47856 TTTCTTTTTTTTTTCTT
1 TTTCTTTTTTTCTTCTT
47873 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
23 5 0.13
24 6 0.16
25 14 0.37
26 4 0.11
27 9 0.24
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTCTTTTTTTCTTCTTTTTTTT
Found at i:47849 original size:27 final size:24
Alignment explanation
Indices: 47810--47872 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 24
47800 ACCCCCTTTC
47810 TTTTTCTTCTCTTTTTTTCATTTTCTAT
1 TTTTTCTT-TCTTTTTTT--TTTTCT-T
47838 TTTTTCTTTCTTTTTTTTTTTCTT
1 TTTTTCTTTCTTTTTTTTTTTCTT
47862 TTTTT-TTTCTT
1 TTTTTCTTTCTT
47873 CAAGCATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.17
24 6 0.17
25 6 0.17
27 9 0.26
28 8 0.23
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTCTTTCTTTTTTTTTTTCTT
Found at i:47856 original size:16 final size:17
Alignment explanation
Indices: 47805--47867 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 17
47795 CCTTGACCCC
*
47805 CTTTCTTTTTCTTCTCTTT
1 CTTTCTTTTTATT-T-TTT
*
47824 TTTTCATTTTCTATTTTTT
1 CTTTC-TTTT-TATTTTTT
47843 CTTTCTTTTT-TTTTTT
1 CTTTCTTTTTATTTTTT
47859 CTTT-TTTTT
1 CTTTCTTTTT
47868 TTCTTCAAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 5 0.13
16 10 0.26
17 1 0.03
18 4 0.10
19 11 0.28
20 5 0.13
21 3 0.08
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (17 bp):
CTTTCTTTTTATTTTTT
Found at i:47868 original size:16 final size:16
Alignment explanation
Indices: 47806--47869 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
47796 CTTGACCCCC
47806 TTTCTTTTTCTTCTCTTTT
1 TTTCTTTTT-TT-T-TTTT
* * *
47825 TTTC-ATTTTCTATTT
1 TTTCTTTTTTTTTTTT
*
47840 TTTCTTTCTTTTTTTT
1 TTTCTTTTTTTTTTTT
47856 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
47870 CTTCAAGCAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
15 7 0.19
16 21 0.58
17 1 0.03
18 3 0.08
19 4 0.11
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTCTTTTTTTTTTTT
Found at i:60364 original size:19 final size:19
Alignment explanation
Indices: 60357--60404 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
60347 CTGGAAGCTG
60357 TTGAGGCGGCTGGAAACCA
1 TTGAGGCGGCTGGAAACCA
60376 TTGAGGCGGCTGGAAACCA
1 TTGAGGCGGCTGGAAACCA
60395 TTGAGGCGGC
1 TTGAGGCGGC
60405 GGCATGTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.40, T:0.17
Consensus pattern (19 bp):
TTGAGGCGGCTGGAAACCA
Found at i:60518 original size:19 final size:21
Alignment explanation
Indices: 60491--60541 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
60481 ATCTGGCTTG
*
60491 TAATTTTTATTAT-TATTT-A
1 TAATATTTATTATGTATTTAA
60510 TAATATTTA--ATGTATTTAA
1 TAATATTTATTATGTATTTAA
*
60529 TAATAATTATTAT
1 TAATATTTATTAT
60542 AATAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 2 0.08
18 5 0.19
19 17 0.65
21 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TAATATTTATTATGTATTTAA
Found at i:60534 original size:3 final size:3
Alignment explanation
Indices: 60526--60600 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
60516 TTAATGTATT
* * * * * *
60526 TAA TAA TAA TTA TTA TAA TAA TAA TAT TAT TTA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
60574 TAA TAT TTA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
60601 ATAAATTAAT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (3 bp):
TAA
Found at i:60559 original size:21 final size:21
Alignment explanation
Indices: 60491--60599 Score: 86
Period size: 21 Copynumber: 5.2 Consensus size: 21
60481 ATCTGGCTTG
* *
60491 TAATTTTTATTATTAT--TTA
1 TAATATTTATTATTATAATAA
60510 TAATATTTAATGTATT-TAATAA
1 TAATATTT-AT-TATTATAATAA
*
60532 T-A-A-TTATTATAATAATAA
1 TAATATTTATTATTATAATAA
*
60550 TATTATTTATAATAATTATAATAA
1 TAATATTTAT--T-ATTATAATAA
*
60574 TAATATTTATAATTATAATAA
1 TAATATTTATTATTATAATAA
60595 TAATA
1 TAATA
60600 AATAAATTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
17 3 0.04
18 9 0.12
19 9 0.12
20 5 0.07
21 24 0.33
22 3 0.04
23 1 0.01
24 18 0.25
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (21 bp):
TAATATTTATTATTATAATAA
Found at i:60561 original size:27 final size:25
Alignment explanation
Indices: 60531--60603 Score: 103
Period size: 24 Copynumber: 2.9 Consensus size: 25
60521 GTATTTAATA
60531 ATAATTATTATAATAATAATATTATTT
1 ATAATTATTATAATAATAA-A-TATTT
*
60558 ATAATAATTATAATAAT-AATATTT
1 ATAATTATTATAATAATAAATATTT
*
60582 ATAATTATAATAATAATAAATA
1 ATAATTATTATAATAATAAATA
60604 AATTAATATG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
24 20 0.48
25 5 0.12
26 1 0.02
27 16 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAATTATTATAATAATAAATATTT
Found at i:60564 original size:30 final size:28
Alignment explanation
Indices: 60522--60600 Score: 97
Period size: 27 Copynumber: 2.8 Consensus size: 28
60512 ATATTTAATG
* * *
60522 TATTTAATAATAATTATTATAATAATAA
1 TATTTATTTATAATAATTATAATAATAA
60550 TA-TTATTTATAATAATTATAATAATAA
1 TATTTATTTATAATAATTATAATAATAA
*
60577 TATTTATAATTATAATAATAATAA
1 TATTTAT--TTATAATAATTATAA
60601 ATAAATTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 24 0.55
28 6 0.14
30 14 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TATTTATTTATAATAATTATAATAATAA
Found at i:60578 original size:15 final size:15
Alignment explanation
Indices: 60526--60600 Score: 84
Period size: 15 Copynumber: 5.2 Consensus size: 15
60516 TTAATGTATT
*
60526 TAATAATAATTATTA
1 TAATAATAATAATTA
60541 TAATAATAAT-ATTA
1 TAATAATAATAATTA
*
60555 T--TTATAATAATTA
1 TAATAATAATAATTA
*
60568 TAATAATAATATTTA
1 TAATAATAATAATTA
* *
60583 TAATTATAATAATAA
1 TAATAATAATAATTA
60598 TAA
1 TAA
60601 ATAAATTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
12 6 0.12
13 5 0.10
14 5 0.10
15 35 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:61849 original size:60 final size:59
Alignment explanation
Indices: 61772--61942 Score: 170
Period size: 60 Copynumber: 2.9 Consensus size: 59
61762 ATCCTCTATT
* * *
61772 TAAATTGGTCC-CTAAACTTTTTAACATTCCAATTTCATCCCTAAACTATGAT-TATCATTC
1 TAAATTTGTCCTC-AAACTTTTTAACATTTCAATTTCATCCCCAAACTAT-ATCT-TCATTC
* * * *
61832 TAAATTTGTCCTCAAACTTTTGAATATTTTATTTTCATCCCCAAACTATATCCTTCATTC
1 TAAATTTGTCCTCAAACTTTTTAACATTTCAATTTCATCCCCAAACTATAT-CTTCATTC
* * *
61892 TAAATTAT-TCCTCAAATTTTTTCACCATTTCAATTTCAT-CCCAAATTATAT
1 TAAATT-TGTCCTCAAACTTTTT-AACATTTCAATTTCATCCCCAAACTATAT
61943 GTATATACTA
Statistics
Matches: 92, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
59 2 0.02
60 75 0.82
61 15 0.16
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.43
Consensus pattern (59 bp):
TAAATTTGTCCTCAAACTTTTTAACATTTCAATTTCATCCCCAAACTATATCTTCATTC
Found at i:62240 original size:60 final size:60
Alignment explanation
Indices: 62101--62250 Score: 151
Period size: 60 Copynumber: 2.5 Consensus size: 60
62091 AATTTGGGGT
* ** * * * * * *
62101 CAATTTAGAATACGGGTCATACTTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAGGAC
1 CAATTTAGAATGCGAATCATAGTTTGAGGATAAAACTGAAATATTCAAAAATTTAAGGAC
* * *
62161 TAATTTAGAATG-AATATCATAGTTTGATGATAAAACTGAAATATTCAAAAATTT-AGTGAC
1 CAATTTAGAATGCGA-ATCATAGTTTGAGGATAAAACTGAAATATTCAAAAATTTAAG-GAC
*
62221 CAATTTAGAATGCGAATCATAGTTTAAGGA
1 CAATTTAGAATGCGAATCATAGTTTGAGGA
62251 CATATGATGC
Statistics
Matches: 71, Mismatches: 16, Indels: 6
0.76 0.17 0.06
Matches are distributed among these distances:
59 2 0.03
60 68 0.96
61 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.32
Consensus pattern (60 bp):
CAATTTAGAATGCGAATCATAGTTTGAGGATAAAACTGAAATATTCAAAAATTTAAGGAC
Found at i:62930 original size:60 final size:61
Alignment explanation
Indices: 62866--63000 Score: 182
Period size: 61 Copynumber: 2.2 Consensus size: 61
62856 AATTATAATT
* * * * * * * *
62866 CTCATTTTAAATTTATCTTTTAA-TTTTTGAATATTTTACTTTCATCCCTAAATTATGACC
1 CTCATTTTAAATTAATCTTTAAATTTTTTAAAAATTCTAATTCCATCCCTAAACTATGACC
62926 CTCATTTTAAATTAATCTTTAAATTTTTTAAAAATTCTAATTCCATCCCTAAACTATGACC
1 CTCATTTTAAATTAATCTTTAAATTTTTTAAAAATTCTAATTCCATCCCTAAACTATGACC
*
62987 CTCTTTTTAAATTA
1 CTCATTTTAAATTA
63001 GTCCCAAGAC
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
60 21 0.32
61 44 0.68
ACGTcount: A:0.32, C:0.18, G:0.02, T:0.48
Consensus pattern (61 bp):
CTCATTTTAAATTAATCTTTAAATTTTTTAAAAATTCTAATTCCATCCCTAAACTATGACC
Found at i:63706 original size:60 final size:60
Alignment explanation
Indices: 63605--63738 Score: 173
Period size: 60 Copynumber: 2.2 Consensus size: 60
63595 TTTATTGGAT
* ** * *
63605 AAAGTGTAC-AAATGGTCCCTTGACTATAGGGTGATGTTTTGTTGAGTCCCTCGATTATTA
1 AAAGT-TACAAAATGGTCCCTTAACTATAGGGTGATACTTTGTTGAGTCCCTCAACTATTA
* *
63665 AAAGTTTCAAAATGGT-CCTTCAACTATAGGGTGTTACTTTGTTGAGTCCCTCAACTATTA
1 AAAGTTACAAAATGGTCCCTT-AACTATAGGGTGATACTTTGTTGAGTCCCTCAACTATTA
63725 AAAGTTACAAAATG
1 AAAGTTACAAAATG
63739 ATCACTCAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 6 0.09
60 58 0.91
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCTTAACTATAGGGTGATACTTTGTTGAGTCCCTCAACTATTA
Found at i:64478 original size:60 final size:60
Alignment explanation
Indices: 64377--64525 Score: 176
Period size: 60 Copynumber: 2.5 Consensus size: 60
64367 GATATTATTA
*
64377 GAATATTCAAAAGTTTGAGGACTAATTTAGAATAAGGGTCATAGTTTGAGGATGATTTTG
1 GAATATTCAAAAGTTTAAGGACTAATTTAGAATAAGGGTCATAGTTTGAGGATGATTTTG
* * * * * ** *
64437 GAATGTTCAAAAGTTTAAGGACTATTTTAGAAT-GGGAGTCATAGTTTGGGGATTAAATTA
1 GAATATTCAAAAGTTTAAGGACTAATTTAGAATAAGG-GTCATAGTTTGAGGATGATTTTG
*
64497 AAATATTCAAAAGTTT-AGAGACTAATTTA
1 GAATATTCAAAAGTTTAAG-GACTAATTTA
64526 ACATAAAAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
59 4 0.05
60 71 0.95
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (60 bp):
GAATATTCAAAAGTTTAAGGACTAATTTAGAATAAGGGTCATAGTTTGAGGATGATTTTG
Found at i:65058 original size:29 final size:29
Alignment explanation
Indices: 64993--65065 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
64983 AAAATGAGAG
* **
64993 TCATAGTTTAAGAATGAAATTAAAATATT
1 TCATAGTTTAAGGATGAAATTAAAATAAA
* * * *
65022 TAAAAGTTTAAGGATTAATTTAAAATAAA
1 TCATAGTTTAAGGATGAAATTAAAATAAA
65051 TCATAGTTTAAGGAT
1 TCATAGTTTAAGGAT
65066 ATATGTTGCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.37
Consensus pattern (29 bp):
TCATAGTTTAAGGATGAAATTAAAATAAA
Found at i:68243 original size:2 final size:2
Alignment explanation
Indices: 68236--68261 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
68226 GGTGGAATTA
68236 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
68262 TAGGATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69834 original size:38 final size:38
Alignment explanation
Indices: 69790--69867 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
69780 AGTCGCTAGA
69790 AACTATTGACACAA-AAAATTAGTCACTTGAGATCATAT
1 AACTATTGACACAAGAAAATT-GTCACTTGAGATCATAT
* * *
69828 AACTATTGACACAAGAAACTTGTCTCTTTAGATCATAT
1 AACTATTGACACAAGAAAATTGTCACTTGAGATCATAT
69866 AA
1 AA
69868 GGATTAAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 31 0.86
39 5 0.14
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (38 bp):
AACTATTGACACAAGAAAATTGTCACTTGAGATCATAT
Found at i:71768 original size:60 final size:58
Alignment explanation
Indices: 71656--71842 Score: 186
Period size: 60 Copynumber: 3.1 Consensus size: 58
71646 TACATGTCCT
* *
71656 CAAAGTATGAGAC-TCATTTTAAATTGGTACCT-AAACTTTT-AAATGTTCCAATTTCATCC
1 CAAACTATGA-ACTTCATTCTAAATTGGT-CCTCAAACTTTTGAAAT-TT-CAATTTCATCC
*
71715 CTAAACTAT-AACTATCATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATTTCATCCC
1 C-AAACTATGAACT-TCATTCTAAATTGGTCCTCAAACTTTTGAA-ATTTCAATTTCAT-CC
* * *
71776 CAAAATATGACCTTCATTCTAAATTGGTCCCCAAACTTTTTG-AATATTCTAATTTCATCC
1 CAAACTATGAACTTCATTCTAAATTGGTCCTCAAAC-TTTTGAAAT-TTC-AATTTCATCC
71836 CAAACTA
1 CAAACTA
71843 CACGTATATA
Statistics
Matches: 109, Mismatches: 8, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
58 2 0.02
59 7 0.06
60 75 0.69
61 23 0.21
62 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.37
Consensus pattern (58 bp):
CAAACTATGAACTTCATTCTAAATTGGTCCTCAAACTTTTGAAATTTCAATTTCATCC
Found at i:72067 original size:60 final size:60
Alignment explanation
Indices: 71963--72128 Score: 201
Period size: 60 Copynumber: 2.8 Consensus size: 60
71953 ATTTGGTTGG
* * * *
71963 ATTTAAGGATGAAATTGGGATATTCAAAAGTTTAGGGAGC-AATTTAGAAAGATG-GTCATA
1 ATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGA-CTAATTTAGAAAGA-GAGTCATA
* * *
72023 GTTTAGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATA
1 ATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATA
* * * *
72083 ATTTGGGGGTGAAATTAGAATATTTAAAAGTTTAAGGATTAATTTA
1 ATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTA
72129 AAATGAATGT
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 2 0.02
60 89 0.98
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (60 bp):
ATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATA
Found at i:72148 original size:60 final size:60
Alignment explanation
Indices: 71969--72148 Score: 197
Period size: 60 Copynumber: 3.0 Consensus size: 60
71959 TTGGATTTAA
* * * *
71969 GGATGAAATTGGGATATTCAAAAGTTTAGGGAGC-AATTTAGAAA-G-ATGGTCATAGTTTAG
1 GGATGAAATTAGAATATTCAAAAGTTTAAGGA-CTAATTTA-AAATGAAT-GTCATAGTTTGG
* * *
72029 GGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGA-GTCATAATTTGG
1 GGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGA-ATGTCATAGTTTGG
* * * *
72089 GGGTGAAATTAGAATATTTAAAAGTTTAAGGATTAATTTAAAATGAATGTTATAGTTTGG
1 GGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAATGTCATAGTTTGG
72149 AGACATATAA
Statistics
Matches: 101, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
59 4 0.04
60 96 0.95
62 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.33
Consensus pattern (60 bp):
GGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAATGTCATAGTTTGG
Found at i:77492 original size:2 final size:2
Alignment explanation
Indices: 77485--77514 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
77475 AAATTTTGGG
77485 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
77515 TAGTATTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83879 original size:44 final size:44
Alignment explanation
Indices: 83816--83903 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
83806 TTTAAATGGT
*
83816 CGGTTAGGACTTGTTCAAAATTAACATGCGGGGTAGAGATCATG
1 CGGTTAGGACTTGTTCAAAATTAACATGCGGGGTACAGATCATG
83860 CGGTTAGGACTTGTTCAAAATTAACATGCGGGGTACAGATCATG
1 CGGTTAGGACTTGTTCAAAATTAACATGCGGGGTACAGATCATG
83904 TCCGAGTAGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (44 bp):
CGGTTAGGACTTGTTCAAAATTAACATGCGGGGTACAGATCATG
Found at i:86097 original size:14 final size:14
Alignment explanation
Indices: 86065--86129 Score: 68
Period size: 14 Copynumber: 4.8 Consensus size: 14
86055 AAAGAAGAAA
86065 AAAGAG-AAAAAAC
1 AAAGAGAAAAAAAC
86078 -AA-AGAAAAAAAC
1 AAAGAGAAAAAAAC
86090 AAAGAGAAAATAAA-
1 AAAGAGAAAA-AAAC
86104 AAAGAGAAACAAAAAC
1 AAAGAG-AA-AAAAAC
86120 AAAG-GAAAAA
1 AAAGAGAAAAA
86130 GTGAAGAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
11 2 0.04
12 9 0.20
13 5 0.11
14 14 0.31
15 9 0.20
16 6 0.13
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (14 bp):
AAAGAGAAAAAAAC
Found at i:86105 original size:30 final size:29
Alignment explanation
Indices: 86071--86128 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
86061 GAAAAAAGAG
86071 AAAAAACA-AAGAAAAAAACAAAGAGAAAAT
1 AAAAAACAGAA-AAAAAAACAAAG-GAAAAT
* *
86101 AAAAAAGAGAAACAAAAACAAAGGAAAA
1 AAAAAACAGAAAAAAAAACAAAGGAAAA
86129 AGTGAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 18 0.72
31 2 0.08
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (29 bp):
AAAAAACAGAAAAAAAAACAAAGGAAAAT
Found at i:86117 original size:12 final size:12
Alignment explanation
Indices: 86057--86118 Score: 63
Period size: 12 Copynumber: 4.9 Consensus size: 12
86047 AAAAGAGAAA
*
86057 AGAAGAAAAAAG
1 AGAAAAAAAAAG
86069 AGAAAAAACAAAG
1 AGAAAAAA-AAAG
86082 A-AAAAAACAAAG
1 AGAAAAAA-AAAG
86094 AGAAAATAAAAAAG
1 AG-AAA-AAAAAAG
*
86108 AGAAACAAAAA
1 AGAAAAAAAAA
86119 CAAAGGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 24 0.55
13 8 0.18
14 9 0.20
15 3 0.07
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.02
Consensus pattern (12 bp):
AGAAAAAAAAAG
Found at i:86118 original size:42 final size:42
Alignment explanation
Indices: 86048--86129 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
86038 ATCAGAACAA
*
86048 AAAGAGAAAAGAAGAAAAAAGAGAAAAAACAAAGAAAAAAAC
1 AAAGAGAAAAGAAGAAAAAAGAAAAAAAACAAAGAAAAAAAC
* * *
86090 AAAGAGAAAATAA-AAAAGAGAAACAAAAACAAAGGAAAAA
1 AAAGAGAAAAGAAGAAAAAAGAAA-AAAAACAAAGAAAAAA
86130 GTGAAGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 8 0.23
42 27 0.77
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.01
Consensus pattern (42 bp):
AAAGAGAAAAGAAGAAAAAAGAAAAAAAACAAAGAAAAAAAC
Found at i:86129 original size:12 final size:13
Alignment explanation
Indices: 86065--86112 Score: 71
Period size: 12 Copynumber: 3.7 Consensus size: 13
86055 AAAGAAGAAA
86065 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
86078 AAAGA-AAAAAAC
1 AAAGAGAAAAAAC
*
86090 AAAGAGAAAATAAA
1 AAAGAGAAAA-AAC
86104 AAAGAGAAA
1 AAAGAGAAA
86113 CAAAAACAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 12 0.38
13 9 0.28
14 11 0.34
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:87049 original size:24 final size:25
Alignment explanation
Indices: 86994--87056 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
86984 AGAAAGGGGC
*
86994 AATATTTTCAAAA--CTTTTGATTA
1 AATATTTTCAAAACTCTTTTAATTA
*
87017 AACATTTTTCAAAACTCTTTTAATT-
1 AATA-TTTTCAAAACTCTTTTAATTA
*
87042 AATATTTTCAGAACT
1 AATATTTTCAAAACT
87057 TTGAAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 3 0.09
24 19 0.58
25 3 0.09
26 8 0.24
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (25 bp):
AATATTTTCAAAACTCTTTTAATTA
Found at i:87247 original size:31 final size:31
Alignment explanation
Indices: 87194--87277 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
87184 ATGAACAATG
* * *
87194 GGGGCATCTTTGAATATTCAACATTAAATGTT
1 GGGGCATCTTTG-AGATTCAACATCAAATATT
* *
87226 GGGGCATTTTTGAGATTCAACATCGAATATT
1 GGGGCATCTTTGAGATTCAACATCAAATATT
*
87257 GGGGCATCTTTGGGAATTCAA
1 GGGGCATCTTTGAG-ATTCAA
87278 TATCCTGATG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 27 0.61
32 17 0.39
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.35
Consensus pattern (31 bp):
GGGGCATCTTTGAGATTCAACATCAAATATT
Found at i:93036 original size:22 final size:22
Alignment explanation
Indices: 93011--93054 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
93001 CCACCAAATA
93011 AGGTTAAGTCATGGTGGGGTTC
1 AGGTTAAGTCATGGTGGGGTTC
93033 AGGTTAAGTCATGGTGGGGTTC
1 AGGTTAAGTCATGGTGGGGTTC
93055 GAATCATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.41, T:0.32
Consensus pattern (22 bp):
AGGTTAAGTCATGGTGGGGTTC
Found at i:96253 original size:15 final size:15
Alignment explanation
Indices: 96233--96262 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
96223 TGGAGTGTTG
96233 GTTCAGCTTAGAGAT
1 GTTCAGCTTAGAGAT
96248 GTTCAGCTTAGAGAT
1 GTTCAGCTTAGAGAT
96263 ACTGGAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (15 bp):
GTTCAGCTTAGAGAT
Found at i:96584 original size:26 final size:27
Alignment explanation
Indices: 96555--96621 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
96545 GAATATGAAG
* *
96555 AAATGAGATAGGAAAAGAAAAAGTT-A
1 AAATGAGAGAGAAAAAGAAAAAGTTAA
*
96581 AAATGAAAGAGAAAAAGAAAAAGTTAA
1 AAATGAGAGAGAAAAAGAAAAAGTTAA
*
96608 AAATGAGAGGGAAA
1 AAATGAGAGAGAAA
96622 TTGGTGATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
26 22 0.63
27 13 0.37
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (27 bp):
AAATGAGAGAGAAAAAGAAAAAGTTAA
Found at i:96609 original size:14 final size:14
Alignment explanation
Indices: 96567--96610 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
96557 ATGAGATAGG
96567 AAAAGAAAAAGTTA
1 AAAAGAAAAAGTTA
* *
96581 AAATGAAAGAG--A
1 AAAAGAAAAAGTTA
96593 AAAAGAAAAAGTTA
1 AAAAGAAAAAGTTA
96607 AAAA
1 AAAA
96611 TGAGAGGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 10 0.42
14 14 0.58
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAAGAAAAAGTTA
Done.