Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008475.1 Hibiscus syriacus cultivar Beakdansim tig00111303_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: 982705
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 3 of 4
Found at i:580117 original size:36 final size:36
Alignment explanation
Indices: 580077--580149 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
580067 CATAGATTCC
580077 TTCACGTGCTCCCCGCTGCATGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATGCCTACACCTCCCAA
580113 TTCACGTGCTCCCCGCTGCATGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATGCCTACACCTCCCAA
580149 T
1 T
580150 GCATGCATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.16, C:0.47, G:0.14, T:0.23
Consensus pattern (36 bp):
TTCACGTGCTCCCCGCTGCATGCCTACACCTCCCAA
Found at i:580319 original size:23 final size:23
Alignment explanation
Indices: 580291--580336 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
580281 AAAAGAAAGA
580291 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
580314 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
580337 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:580351 original size:25 final size:23
Alignment explanation
Indices: 580291--580351 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
580281 AAAAGAAAGA
**
580291 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
580314 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
580337 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
580352 AGAAAAGGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:580557 original size:41 final size:41
Alignment explanation
Indices: 580512--580600 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
580502 TATATGATTG
* *
580512 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
580553 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
580594 TTAGTTT
1 TTAGTTT
580601 GTATTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:580644 original size:46 final size:48
Alignment explanation
Indices: 580581--580672 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
580571 TTATATAGTT
580581 AAAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
* *
580626 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATAT
580673 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 6 0.15
46 17 0.41
47 3 0.07
48 7 0.17
49 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
Found at i:580890 original size:28 final size:30
Alignment explanation
Indices: 580850--580912 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
580840 ATTTTTTATA
*
580850 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
580880 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
580908 TAATA
1 TAATA
580913 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:580919 original size:28 final size:28
Alignment explanation
Indices: 580854--580919 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
580844 TTTATATAAT
*
580854 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
580882 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
580910 ATAATTTATA
1 ATAATATATA
580920 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:580922 original size:21 final size:21
Alignment explanation
Indices: 580889--580937 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
580879 CTAATATAAT
580889 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
580910 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
580931 ATTAACT
1 A-TAACT
580938 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:582462 original size:6 final size:6
Alignment explanation
Indices: 582447--582477 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
582437 AATCGGGCAT
*
582447 AAAGAC AAAGAG AAAGAG AAAGAG AAAGAG A
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG A
582478 GACTAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:584140 original size:20 final size:20
Alignment explanation
Indices: 584117--584312 Score: 144
Period size: 20 Copynumber: 9.7 Consensus size: 20
584107 GTTTCCAGAT
584117 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
584137 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
** * *
584157 TTCGCGTTGCGATTTTCCGACAA
1 -TCGCAATGCGA--TTCTGACTA
* * *
584180 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* *
584200 TCGCAATGCGAGTATGACTA
1 TCGCAATGCGATTCTGACTA
*
584220 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* * *
584240 TCGCAACGAGATTATGACTA
1 TCGCAATGCGATTCTGACTA
* *
584260 TCGCAACGCGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
* *
584280 TCGCAACGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
584300 TCGCAATGCGATT
1 TCGCAATGCGATT
584313 TTCAAAGCGC
Statistics
Matches: 142, Mismatches: 27, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 114 0.80
21 11 0.08
22 9 0.06
23 4 0.03
24 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:584512 original size:22 final size:22
Alignment explanation
Indices: 584487--584529 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
584477 GGCAACATCC
584487 GTCCCCATCTCCGAAGAAATCA
1 GTCCCCATCTCCGAAGAAATCA
*
584509 GTCCCCATCTCCGGAGAAATC
1 GTCCCCATCTCCGAAGAAATC
584530 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.37, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGAAGAAATCA
Found at i:584704 original size:24 final size:24
Alignment explanation
Indices: 584677--584724 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
584667 TATTGAAATT
584677 GATGATAAGTTTACTGGTAATTTC
1 GATGATAAGTTTACTGGTAATTTC
584701 GATGATAAGTTTACTGGTAATTTC
1 GATGATAAGTTTACTGGTAATTTC
584725 AATAATAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (24 bp):
GATGATAAGTTTACTGGTAATTTC
Found at i:584975 original size:20 final size:20
Alignment explanation
Indices: 584931--585004 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
584921 GCGATTTTAG
*
584931 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
584951 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* * **
584971 TTTCGTGTTGCGGTTTTCAT
1 TTTCGCGTTGCGATAGTCAT
*
584991 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
585005 TTTAAGTTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.14, C:0.18, G:0.26, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:585007 original size:20 final size:20
Alignment explanation
Indices: 584920--585007 Score: 79
Period size: 20 Copynumber: 4.5 Consensus size: 20
584910 AGAGTCGCAA
*
584920 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
584939 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
584959 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
* *
584979 TGCGGTTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
584999 TGCGATTTT
1 TGCGATTTT
585008 AAGTTTCAGA
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
19 7 0.12
20 50 0.88
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.45
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:585014 original size:20 final size:20
Alignment explanation
Indices: 584971--585014 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
584961 CGATAGTCAT
* * *
584971 TTTCGTGTTGCGGTTTTCAT
1 TTTCGTGTTGCGATTTTAAG
584991 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
585011 TTTC
1 TTTC
585015 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.14, G:0.23, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:585110 original size:28 final size:28
Alignment explanation
Indices: 585073--585149 Score: 145
Period size: 28 Copynumber: 2.8 Consensus size: 28
585063 TTCAACAATA
*
585073 AAACTACTACTCTTTAAGTTTGAAGAAT
1 AAACTACTACTCTTTATGTTTGAAGAAT
585101 AAACTACTACTCTTTATGTTTGAAGAAT
1 AAACTACTACTCTTTATGTTTGAAGAAT
585129 AAACTACTACTCTTTATGTTT
1 AAACTACTACTCTTTATGTTT
585150 ATTGTTCTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (28 bp):
AAACTACTACTCTTTATGTTTGAAGAAT
Found at i:586942 original size:20 final size:20
Alignment explanation
Indices: 586917--586964 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
586907 TATTTTACTT
586917 TCGCAACGCGAAA-ATGACTA
1 TCGCAACGC-AAATATGACTA
*
586937 TCGCAACGCAAATTTGACTA
1 TCGCAACGCAAATATGACTA
586957 TCGCAACG
1 TCGCAACG
586965 AAAGAATCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCAAATATGACTA
Found at i:587018 original size:20 final size:19
Alignment explanation
Indices: 586990--587059 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
586980 GAAATGAAAA
*
586990 TCGCATTGCGATAGTCAAAT
1 TCGCGTTGCGATAGTC-AAT
*
587010 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATAGTCA-AT
* *
587030 TCACGTTGCAATAGTC-AT
1 TCGCGTTGCGATAGTCAAT
*
587048 TCGTGTTGCGAT
1 TCGCGTTGCGAT
587060 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 10 0.24
19 1 0.02
20 30 0.73
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCAAT
Found at i:587590 original size:18 final size:19
Alignment explanation
Indices: 587551--587592 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
587541 CTCACCTGTC
587551 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
587572 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
587590 ATC
1 ATC
587593 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:587646 original size:42 final size:43
Alignment explanation
Indices: 587546--587656 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 43
587536 TCCGACTCAC
* * * *
587546 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGTCTCCTCCCACCGTTCAAGAGGCCA
* ** *
587588 CTATCATCCCTCAAGA-GTCTCCTCCCACCGTTCAAGATGCCA
1 CTGTCATCGTTCAAGAGGTCTCCTCCCACCGTTCAAGAGGCCA
*
587630 CTGTCATCGTTGAAGAGGTC-CCTCCCA
1 CTGTCATCGTTCAAGAGGTCTCCTCCCA
587657 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 5 0.09
42 47 0.85
43 3 0.05
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (43 bp):
CTGTCATCGTTCAAGAGGTCTCCTCCCACCGTTCAAGAGGCCA
Found at i:588741 original size:14 final size:14
Alignment explanation
Indices: 588707--588768 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
588697 AGGCTTGTTT
*
588707 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
588721 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
588735 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
588750 TATTGATGTGTAAA
1 AATTGATTTGTAAA
588764 TAATT
1 -AATT
588769 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:588919 original size:20 final size:20
Alignment explanation
Indices: 588882--588920 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
588872 ACACTAAACT
*
588882 CAAAATCGCAATGCGAAAGA
1 CAAAATCGCAACGCGAAAGA
*
588902 CAAAATCGCAACGTGAAAG
1 CAAAATCGCAACGCGAAAG
588921 TCAATTCGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.10
Consensus pattern (20 bp):
CAAAATCGCAACGCGAAAGA
Found at i:588990 original size:20 final size:20
Alignment explanation
Indices: 588963--589221 Score: 187
Period size: 20 Copynumber: 13.8 Consensus size: 20
588953 GCGATTTTCT
* *
588963 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
588983 CATTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
589003 CGTTGCGATACTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
589023 CGTCGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
589043 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
* *
589057 CATTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
589076 CCGTTGCGATAGTCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
*
589097 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
589111 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
589131 TGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
589151 CGTTGC-A-A-T---TTTTG
1 CGTTGCGATAGTCAAATTCG
* * * *
589165 AGTTGTGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
589185 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
589205 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
589222 GAATGTGTAA
Statistics
Matches: 183, Mismatches: 36, Indels: 40
0.71 0.14 0.15
Matches are distributed among these distances:
14 30 0.16
15 1 0.01
16 3 0.02
17 2 0.01
18 3 0.02
19 2 0.01
20 140 0.77
21 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:589049 original size:94 final size:94
Alignment explanation
Indices: 588923--589105 Score: 294
Period size: 94 Copynumber: 1.9 Consensus size: 94
588913 CGTGAAAGTC
* * * *
588923 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCATTG
1 AATTCGCGTCGCGATAGTCAAATACGCGTTGCGATTTTCTCATTGCGATAGTCAAATACCCATTG
588988 CGATAATCAAATTCGCGTTGCGATACTCA
66 CGATAATCAAATTCGCGTTGCGATACTCA
* * *
589017 AATTCGCGTCGCGATAGTCAAATTCGCGTTGCGATTTTCTCATTGCGATAGTCAAATAGCCGTTG
1 AATTCGCGTCGCGATAGTCAAATACGCGTTGCGATTTTCTCATTGCGATAGTCAAATACCCATTG
*
589082 CGATAGTCAAATTCGCGTTGCGAT
66 CGATAATCAAATTCGCGTTGCGAT
589106 TTTTGCGTTG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
94 81 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (94 bp):
AATTCGCGTCGCGATAGTCAAATACGCGTTGCGATTTTCTCATTGCGATAGTCAAATACCCATTG
CGATAATCAAATTCGCGTTGCGATACTCA
Found at i:589087 original size:54 final size:53
Alignment explanation
Indices: 589005--589213 Score: 258
Period size: 54 Copynumber: 3.9 Consensus size: 53
588995 CAAATTCGCG
* **
589005 TTGCGATACTCAAATTCGCGTCGCGATAGTCAAATTCGCGTTGCGATTTTCTCA
1 TTGCGATAGTCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATTTT-TCA
* * *
589059 TTGCGATAGTCAAA-TAGCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCG
1 TTGCGATAGTCAAATTCG-CGTTACGATAGTCAAATTCGCGTTGCGATTTTT-CA
* * * *
589113 TTGCGATAGTCATATTCGTGTTACGATAGTCAAATTCGCGTTGCAATTTTTGA
1 TTGCGATAGTCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATTTTTCA
* * *
589166 GTTGTGATAATCAAATTCACGTTACGATAGTCAAATTCGCGTTGCGAT
1 -TTGCGATAGTCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGAT
589214 ATTCAAATGA
Statistics
Matches: 134, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
53 3 0.02
54 129 0.96
55 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (53 bp):
TTGCGATAGTCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATTTTTCA
Found at i:589151 original size:108 final size:108
Alignment explanation
Indices: 589002--589213 Score: 293
Period size: 108 Copynumber: 2.0 Consensus size: 108
588992 AATCAAATTC
* *
589002 GCGTTGCGATACTCAAATTCGCGTCGCGATAGTCAAATTCGCGTTGCGATTTTCTCA-TTGCGAT
1 GCGTTGCGATACTCAAATTCGCGTCACGATAGTCAAATTCGCGTTGCAATTTT-TCAGTTGCGAT
* *
589066 AGTCAAATAGC-CGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
65 AATCAAAT-GCACGTTACGATAGTCAAATTCGCGTTGCGATTTTT
* * * * * *
589110 GCGTTGCGATAGTCATATTCGTGTTACGATAGTCAAATTCGCGTTGCAATTTTTGAGTTGTGATA
1 GCGTTGCGATACTCAAATTCGCGTCACGATAGTCAAATTCGCGTTGCAATTTTTCAGTTGCGATA
*
589175 ATCAAATTCACGTTACGATAGTCAAATTCGCGTTGCGAT
66 ATCAAATGCACGTTACGATAGTCAAATTCGCGTTGCGAT
589214 ATTCAAATGA
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 3 0.03
108 88 0.97
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (108 bp):
GCGTTGCGATACTCAAATTCGCGTCACGATAGTCAAATTCGCGTTGCAATTTTTCAGTTGCGATA
ATCAAATGCACGTTACGATAGTCAAATTCGCGTTGCGATTTTT
Found at i:589155 original size:74 final size:72
Alignment explanation
Indices: 588919--589156 Score: 198
Period size: 74 Copynumber: 3.2 Consensus size: 72
588909 GCAACGTGAA
* * * * *
588919 AGTC-AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACC
1 AGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TCGTTGCGATAGTCATAT-TC
*
588983 CATTGCGAT
64 TATTGCGAT
* * * ** * * *
588992 AATCAAATTCGCGTTGCGATACTCAAATTCGCGTCGCGA-TAGTCAAATTCGCG-TTG-CGATTT
1 AGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTC--GTT-GCGATAGTC-ATAT
589054 TCTCATTGCGAT
62 TCT-ATTGCGAT
*
589066 AGTCAAA-TAGCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGCGATAGTCATATTC
1 AGTCAAATTCG-CGTTGCGATAGTCAAATTCGCGTTGCGATTTTT-CGTTGCGATAGTCATATTC
* *
589130 GTGTTACGAT
64 -TATTGCGAT
589140 AGTCAAATTCGCGTTGC
1 AGTCAAATTCGCGTTGC
589157 AATTTTTGAG
Statistics
Matches: 126, Mismatches: 26, Indels: 25
0.71 0.15 0.14
Matches are distributed among these distances:
72 2 0.02
73 11 0.09
74 103 0.82
75 9 0.07
76 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.34
Consensus pattern (72 bp):
AGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTCGTTGCGATAGTCATATTCTA
TTGCGAT
Found at i:592695 original size:20 final size:20
Alignment explanation
Indices: 592652--592718 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
592642 AAATTCAGTG
* *
592652 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
* *
592672 TTGCTATAGTCAGAATCACA
1 TTGCGATAGTCAGAATCGCA
* *
592692 TTGCGATAATCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
592712 TTGCGAT
1 TTGCGAT
592719 TTACATATTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:592725 original size:20 final size:20
Alignment explanation
Indices: 592702--592778 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
592692 TTGCGATAAT
*
592702 CATAATCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
592722 CATATTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
592742 CATATTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
**
592762 CATATTTACATTGCGAT
1 CATATTCGCATTGCGAT
592779 AGTCGGAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (20 bp):
CATATTCGCATTGCGATTTA
Found at i:592734 original size:40 final size:41
Alignment explanation
Indices: 592687--592779 Score: 136
Period size: 40 Copynumber: 2.3 Consensus size: 41
592677 ATAGTCAGAA
592687 TCACATTGCGATAAT-CATAATCGCATTGCGATTTACATAT
1 TCACATTGCGATAATACATAATCGCATTGCGATTTACATAT
* * *
592727 TCGCATTGCGAT-TTACATATTCGCATTGCGATTTACATAT
1 TCACATTGCGATAATACATAATCGCATTGCGATTTACATAT
*
592767 TTACATTGCGATA
1 TCACATTGCGATA
592780 GTCGGAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 1 0.02
40 45 0.98
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (41 bp):
TCACATTGCGATAATACATAATCGCATTGCGATTTACATAT
Found at i:593329 original size:31 final size:31
Alignment explanation
Indices: 593282--593423 Score: 221
Period size: 31 Copynumber: 4.6 Consensus size: 31
593272 ATATAGATTT
* *
593282 CGAAGAACCTAGGTAAATAATCCATATGTCC
1 CGAAGAACATAGGTAAACAATCCATATGTCC
* * *
593313 CGATGAACATAGGTAAACAGTGCATATGTCC
1 CGAAGAACATAGGTAAACAATCCATATGTCC
*
593344 CAAAGAACATAGGTAAACAATCCATATGTCC
1 CGAAGAACATAGGTAAACAATCCATATGTCC
*
593375 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAATCCATATGTCC
593406 CGAAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
593424 CCTCGACCCT
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 100 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAATCCATATGTCC
Found at i:595274 original size:35 final size:35
Alignment explanation
Indices: 595218--595314 Score: 126
Period size: 35 Copynumber: 2.8 Consensus size: 35
595208 GAATGGGTTA
** *
595218 TGAATTT-GAGGTTGGGCATGTAATTGAAGTATTT
1 TGAATTTAGAGGTTTAGAATGTAATTGAAGTATTT
*
595252 TGGAATTT-GATGTTTAGAATGTAATTGAAGTATTT
1 T-GAATTTAGAGGTTTAGAATGTAATTGAAGTATTT
*
595287 TGAATTTAGGGGTTTAGAATGTAATTGA
1 TGAATTTAGAGGTTTAGAATGTAATTGA
595315 TGAATGTGTT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
34 7 0.13
35 48 0.87
ACGTcount: A:0.30, C:0.01, G:0.27, T:0.42
Consensus pattern (35 bp):
TGAATTTAGAGGTTTAGAATGTAATTGAAGTATTT
Found at i:595668 original size:12 final size:13
Alignment explanation
Indices: 595641--595666 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
595631 CTTATTTCAC
595641 TAAAAAATAATTT
1 TAAAAAATAATTT
595654 TAAAAAATAATTT
1 TAAAAAATAATTT
595667 AAGTAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAAAATAATTT
Found at i:596109 original size:6 final size:6
Alignment explanation
Indices: 596100--596134 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
596090 CCAAAACCTT
596100 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCT
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCT
596135 TTCCTTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
TCCCTC
Found at i:599399 original size:63 final size:63
Alignment explanation
Indices: 599320--599571 Score: 373
Period size: 63 Copynumber: 4.0 Consensus size: 63
599310 AGAGTCGAGG
* * *
599320 AGTATACCTATGTTCTACGGAACATATGGATAGAATTACCTATGTCTTTCGGGACATGTAGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
*
599383 AGTATACATATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
* * *
599446 AGTATACCTATGTTCAACGGAACATATTGACAGAATTACCTATGTCTTTCGGAACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
* * * * *
599509 AGTATACCTATGTTTTAAGGAACATATGGACAG-TTTACCTAGGT-TCTTCGGGACCTATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCT-TTCGGGACATATGGAC
599571 A
1 A
599572 ATTGCCGAGG
Statistics
Matches: 172, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
61 1 0.01
62 24 0.14
63 147 0.85
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (63 bp):
AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
Found at i:599415 original size:31 final size:31
Alignment explanation
Indices: 599320--599571 Score: 240
Period size: 31 Copynumber: 8.0 Consensus size: 31
599310 AGAGTCGAGG
*
599320 AGTATACCTATGTTCTACGGAACATATGGAT
1 AGTATACCTATGTTCTACGGAACATATGGAC
* * * * *
599351 AGAATTACCTATG-TCTTTCGGGACATGTAGAC
1 AGTA-TACCTATGTTC-TACGGAACATATGGAC
*
599383 AGTATACATATGTTCTACGGAACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGAC
* * *
599414 AGAATTACCTATG-TCTTTCGGGACATATGGAC
1 AGTA-TACCTATGTTC-TACGGAACATATGGAC
* *
599446 AGTATACCTATGTTCAACGGAACATATTGAC
1 AGTATACCTATGTTCTACGGAACATATGGAC
* *
599477 AGAATTACCTATG-TCTTTCGGAACATATGGAC
1 AGTA-TACCTATGTTC-TACGGAACATATGGAC
* *
599509 AGTATACCTATGTTTTAAGGAACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGAC
* * * * *
599540 AGTTTACCTAGGTTCTTCGGGACCTATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGAC
599571 A
1 A
599572 ATTGCCGAGG
Statistics
Matches: 176, Mismatches: 36, Indels: 18
0.77 0.16 0.08
Matches are distributed among these distances:
31 101 0.57
32 75 0.43
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
AGTATACCTATGTTCTACGGAACATATGGAC
Found at i:602803 original size:63 final size:63
Alignment explanation
Indices: 602730--602951 Score: 347
Period size: 63 Copynumber: 3.5 Consensus size: 63
602720 AGAGTCGAGG
* *
602730 AGTATACCTATGTTCTAAGGAACATATGGATAGAATTACCTATGTCTTTCGGGACATATGGAC
1 AGTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCAGGACATATGGAC
* * * *
602793 AGTATACCTATGTTCTACGGAACATATGGACATAATTACCTATGTCTTTCAGGATATATAGAC
1 AGTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCAGGACATATGGAC
*
602856 AGTATACCTATGTTC-AACGGAACATATGGACAGAATTACCTATGTCTTTCTGGACATATGGAC
1 AGTATACCTATGTTCTAA-GGAACATATGGACAGAATTACCTATGTCTTTCAGGACATATGGAC
* *
602919 AATATACCTATGTTCTAAGGAACATATGAACAG
1 AGTATACCTATGTTCTAAGGAACATATGGACAG
602952 TTTACATAGG
Statistics
Matches: 144, Mismatches: 13, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
62 1 0.01
63 141 0.98
64 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (63 bp):
AGTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCAGGACATATGGAC
Found at i:602804 original size:31 final size:31
Alignment explanation
Indices: 602730--602983 Score: 201
Period size: 31 Copynumber: 8.1 Consensus size: 31
602720 AGAGTCGAGG
** * *
602730 AGTATACCTATGTTCTAAGGAACATATGGAT
1 AGTATACCTATGTTCTTCGGGACATATGGAC
*
602761 AGAATTACCTATG-TCTTTCGGGACATATGGAC
1 AGTA-TACCTATGTTC-TTCGGGACATATGGAC
* *
602793 AGTATACCTATGTTCTACGGAACATATGGAC
1 AGTATACCTATGTTCTTCGGGACATATGGAC
* * *
602824 A-TAATTACCTATG-TCTTTCAGGATATATAGAC
1 AGT-A-TACCTATGTTC-TTCGGGACATATGGAC
** *
602856 AGTATACCTATGTTCAACGGAACATATGGAC
1 AGTATACCTATGTTCTTCGGGACATATGGAC
* *
602887 AGAATTACCTATG-TCTTTCTGGACATATGGAC
1 AGTA-TACCTATGTTC-TTCGGGACATATGGAC
* ** * *
602919 AATATACCTATGTTCTAAGGAACATATGAAC
1 AGTATACCTATGTTCTTCGGGACATATGGAC
* * * *
602950 AGTTTACATAGGTTCTTCGGGACCTATGGAC
1 AGTATACCTATGTTCTTCGGGACATATGGAC
602981 AGT
1 AGT
602984 TTTCGAGGTT
Statistics
Matches: 172, Mismatches: 40, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
30 1 0.01
31 98 0.57
32 72 0.42
33 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (31 bp):
AGTATACCTATGTTCTTCGGGACATATGGAC
Found at i:606090 original size:35 final size:33
Alignment explanation
Indices: 606041--606119 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 33
606031 TTTAAATTCG
* * *
606041 TAATATTTTTATATTTAATTTTTTAAATATCTTAA
1 TAATTTTTTTATATTTAATATTTTAAAT-T-TAAA
*
606076 TAATTTTTTTATATTTTATATTTTAAATTTAAA
1 TAATTTTTTTATATTTAATATTTTAAATTTAAA
606109 T-ATTTTTTTAT
1 TAATTTTTTTAT
606120 TTTCTAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.25
33 4 0.10
34 1 0.03
35 25 0.62
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (33 bp):
TAATTTTTTTATATTTAATATTTTAAATTTAAA
Found at i:610634 original size:39 final size:39
Alignment explanation
Indices: 610590--610668 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
610580 ATTGTAACAA
610590 CAACAGAAATTCAAATCTGAGTTTCAAAACGCCGTAGAT
1 CAACAGAAATTCAAATCTGAGTTTCAAAACGCCGTAGAT
610629 CAACAGAAATTCAAATCTGAGTTTCAAAACGCCGTAGAT
1 CAACAGAAATTCAAATCTGAGTTTCAAAACGCCGTAGAT
610668 C
1 C
610669 TAAAATCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.23
Consensus pattern (39 bp):
CAACAGAAATTCAAATCTGAGTTTCAAAACGCCGTAGAT
Found at i:611439 original size:17 final size:18
Alignment explanation
Indices: 611389--611439 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 18
611379 TATGAATACA
* *
611389 CATAATTAAAATTAGAAT
1 CATAATTAAAATAATAAT
*
611407 CA-AATCAAAA-AATAAT
1 CATAATTAAAATAATAAT
611423 -ATAATTAAAATAATAAT
1 CATAATTAAAATAATAAT
611440 TAAAATATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 1 0.04
16 11 0.41
17 13 0.48
18 2 0.07
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (18 bp):
CATAATTAAAATAATAAT
Found at i:611597 original size:2 final size:2
Alignment explanation
Indices: 611586--611643 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
611576 CTTCTAGAAC
611586 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
611627 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
611644 TGTTGAAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:611724 original size:29 final size:29
Alignment explanation
Indices: 611690--611748 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
611680 CCTAAATTAA
611690 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
611719 TTTGATGTCATTGGTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
611748 T
1 T
611749 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:616408 original size:29 final size:29
Alignment explanation
Indices: 616374--616432 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
616364 CCTAAATTAA
616374 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
616403 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
616432 T
1 T
616433 AGGTGAAAAT
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:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:617493 original size:14 final size:14
Alignment explanation
Indices: 617470--617507 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
617460 TCTGTCTATA
*
617470 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
617483 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
617498 TGCAGGGATT
1 TGCAGGGATT
617508 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:635965 original size:13 final size:13
Alignment explanation
Indices: 635947--635982 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
635937 ACGATAAACG
635947 GGTCGGGTCAACA
1 GGTCGGGTCAACA
*
635960 GGTCGGGTCAACG
1 GGTCGGGTCAACA
*
635973 GGTCAGGTCA
1 GGTCGGGTCA
635983 GACCGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.19, C:0.22, G:0.42, T:0.17
Consensus pattern (13 bp):
GGTCGGGTCAACA
Found at i:642781 original size:19 final size:20
Alignment explanation
Indices: 642757--642794 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
642747 CACCATCAGG
642757 CACTATTT-CGGTCGCCAAT
1 CACTATTTACGGTCGCCAAT
*
642776 CACTATTTACGGTGGCCAA
1 CACTATTTACGGTCGCCAA
642795 AAAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (20 bp):
CACTATTTACGGTCGCCAAT
Found at i:643798 original size:137 final size:137
Alignment explanation
Indices: 643483--644044 Score: 878
Period size: 137 Copynumber: 4.1 Consensus size: 137
643473 AGATCCAACT
* * * * *
643483 GGTGTATGATATTGTTCCTTCATGATGAGGAAGTCTGGCCATCTTTGAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * * *
643548 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATAACTCTT-C-C-TACGTGATGAGGAG
66 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGA-TGTTGCTCATTCGTGATGAGGAA
643610 TTCTGATC
130 TTCTGATC
* * *
643618 AGTGGATGACTTTGTCCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* *
643683 CGGTTCCTTCGTAATGAGGACGTCTGGCTATCTAAGAATGATGTTGCTCATTCGTGATGAGGAAT
66 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCATTCGTGATGAGGAAT
643748 TCTGATC
131 TCTGATC
643755 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* ** * *
643820 CGGTTCCTTCGTGATGAGAATGTCTGGCTATCTAAGAATGATGTTGCTCCTTCATGATGAGGAAT
66 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCATTCGTGATGAGGAAT
643885 TCTGATC
131 TCTGATC
* *
643892 GGTGGATGACATTGTTCCTTCGTGATAAGGACGTATGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * *
643957 CGGTTCTTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCATTTGTGATGAGGAGT
66 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCATTCGTGATGAGGAAT
644022 TCTGATC
131 TCTGATC
644029 GGTGGATGACATTGTT
1 GGTGGATGACATTGTT
644045 GTTGGTGGAC
Statistics
Matches: 392, Mismatches: 32, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
134 3 0.01
135 96 0.24
136 1 0.00
137 292 0.74
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (137 bp):
GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCATTCGTGATGAGGAAT
TCTGATC
Found at i:644610 original size:103 final size:103
Alignment explanation
Indices: 644426--644622 Score: 306
Period size: 103 Copynumber: 1.9 Consensus size: 103
644416 TGGTGGACAC
* *
644426 GATATCCTTCGTCTTGAAGTTGAAATCCAATCTTTCATTGTATTGCTTTGAGTTCAATATCCTTC
1 GATATCCTTCATCTTGAAGTTGAAATCCAATCTTTCATTGTATTGATTTGAGTTCAATATCCTTC
* * *
644491 GCTGTGAATTTTAAATTGACTCTAAATGATTTGAATTT
66 GCTGTAAAGTTGAAATTGACTCTAAATGATTTGAATTT
**
644529 GATATCCTTCAT-TGTGAAGTTGAAATCCAATCTTTGGTTGTATTGATTTGAGTTCAATATCCTT
1 GATATCCTTCATCT-TGAAGTTGAAATCCAATCTTTCATTGTATTGATTTGAGTTCAATATCCTT
*
644593 CGCTGTAAAGTTGAAATTGACTCTGAATGA
65 CGCTGTAAAGTTGAAATTGACTCTAAATGA
644623 AACTGAAAAG
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
102 1 0.01
103 84 0.99
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.42
Consensus pattern (103 bp):
GATATCCTTCATCTTGAAGTTGAAATCCAATCTTTCATTGTATTGATTTGAGTTCAATATCCTTC
GCTGTAAAGTTGAAATTGACTCTAAATGATTTGAATTT
Found at i:644699 original size:58 final size:58
Alignment explanation
Indices: 644604--644726 Score: 203
Period size: 58 Copynumber: 2.1 Consensus size: 58
644594 GCTGTAAAGT
* *
644604 TGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAG-CCTAATATCCTTCGCTG
1 TGAAGTTGACTCTGAATGAAACTGAAAAGTTATTTGTTGAGTCC-AATATCCTTCGCTG
*
644662 TGAAGTTGACTCTGAATGAAATTGAAAAGTTATTTGTTGAGTCCAATATCCTTCGCTG
1 TGAAGTTGACTCTGAATGAAACTGAAAAGTTATTTGTTGAGTCCAATATCCTTCGCTG
644720 TGAAGTT
1 TGAAGTT
644727 AAAATTGACT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
58 59 0.97
59 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (58 bp):
TGAAGTTGACTCTGAATGAAACTGAAAAGTTATTTGTTGAGTCCAATATCCTTCGCTG
Found at i:649674 original size:3 final size:3
Alignment explanation
Indices: 649666--649694 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
649656 ATTTATTTTT
649666 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
649695 TGATAGTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:650237 original size:17 final size:17
Alignment explanation
Indices: 650211--650243 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
650201 CGAAAAACCT
650211 AAAATATGACTTTTTGA
1 AAAATATGACTTTTTGA
*
650228 AAAATTTGACTTTTTG
1 AAAATATGACTTTTTG
650244 GGTCAAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
AAAATATGACTTTTTGA
Found at i:650343 original size:24 final size:23
Alignment explanation
Indices: 650288--650350 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
650278 GGAGTCAATG
* *
650288 GGTCAGGTCGGGTCAAACAGTTC
1 GGTCGGGTCAGGTCAAACAGTTC
* * *
650311 GAGTTGGGTCTGGTCAAATAGTTC
1 G-GTCGGGTCAGGTCAAACAGTTC
650335 AGGTCGGGTCAGGTCA
1 -GGTCGGGTCAGGTCA
650351 GCGGTTCGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 1 0.03
24 30 0.94
25 1 0.03
ACGTcount: A:0.21, C:0.17, G:0.37, T:0.25
Consensus pattern (23 bp):
GGTCGGGTCAGGTCAAACAGTTC
Found at i:669021 original size:16 final size:16
Alignment explanation
Indices: 668987--669028 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
668977 TCGTTCATTT
668987 AATAAAT-AA-ACGAA
1 AATAAATGAACACGAA
669001 AATAAATGAACACGAA
1 AATAAATGAACACGAA
*
669017 CATAAATGAACA
1 AATAAATGAACA
669029 TAAACGTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 7 0.28
15 2 0.08
16 16 0.64
ACGTcount: A:0.64, C:0.12, G:0.10, T:0.14
Consensus pattern (16 bp):
AATAAATGAACACGAA
Found at i:670138 original size:14 final size:14
Alignment explanation
Indices: 670121--670173 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
670111 ATAAATGAAT
670121 GAACATAACCGAAC
1 GAACATAACCGAAC
*
670135 GAACAT-A---AAT
1 GAACATAACCGAAC
*
670145 GAACATAACTGAAC
1 GAACATAACCGAAC
*
670159 GAACATAACCAAAC
1 GAACATAACCGAAC
670173 G
1 G
670174 TTCACGAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
10 8 0.26
11 1 0.03
13 1 0.03
14 21 0.68
ACGTcount: A:0.53, C:0.23, G:0.13, T:0.11
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:670150 original size:24 final size:24
Alignment explanation
Indices: 670118--670166 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
670108 AATATAAATG
670118 AATGAACATAACCGAACGAACATA
1 AATGAACATAACCGAACGAACATA
*
670142 AATGAACATAACTGAACGAACATA
1 AATGAACATAACCGAACGAACATA
670166 A
1 A
670167 CCAAACGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.18, G:0.12, T:0.14
Consensus pattern (24 bp):
AATGAACATAACCGAACGAACATA
Found at i:672563 original size:14 final size:14
Alignment explanation
Indices: 672544--672573 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
672534 CTACTTTGCT
672544 GTAGAAAGTTGCCG
1 GTAGAAAGTTGCCG
672558 GTAGAAAGTTGCCG
1 GTAGAAAGTTGCCG
672572 GT
1 GT
672574 GGGAGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.37, T:0.23
Consensus pattern (14 bp):
GTAGAAAGTTGCCG
Found at i:676753 original size:27 final size:27
Alignment explanation
Indices: 676699--676754 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
676689 CCGCCATCAC
* *
676699 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCACAACAT
*
676726 CACTTTGAACTTGAAAGTCCACAACAT
1 CACTTTGAACTTGAAACTCCACAACAT
676753 CA
1 CA
676755 AGATCTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.27
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCACAACAT
Found at i:677028 original size:30 final size:30
Alignment explanation
Indices: 676966--677030 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
676956 CAAAATTGGT
* * *
676966 GGTTCACACCGGTTTTATCGGTTTCTAGCC
1 GGTTCACACCGATTTTACCGGTTCCTAGCC
*
676996 GGTTCACACCGATTTTGCCGGTTCCCTA-CC
1 GGTTCACACCGATTTTACCGGTT-CCTAGCC
677026 GGTTC
1 GGTTC
677031 TACTGGTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.12, C:0.31, G:0.23, T:0.34
Consensus pattern (30 bp):
GGTTCACACCGATTTTACCGGTTCCTAGCC
Found at i:678628 original size:21 final size:21
Alignment explanation
Indices: 678585--678657 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
678575 TTTTCCCAAT
** *
678585 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
*
678605 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
678626 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
678647 TCGCAATGCGA
1 TCGCAATGCGA
678658 TACTTACTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 11 0.23
21 36 0.77
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTGGGAAAA
Found at i:678688 original size:41 final size:41
Alignment explanation
Indices: 678643--678720 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
678633 GCGAATTGGG
* * * *
678643 AAAATCGCAATGCGATACTTACTATCGTAATGCGATAATAC
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
*
678684 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATA
678721 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
Found at i:678736 original size:20 final size:20
Alignment explanation
Indices: 678688--678739 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
678678 TAATACAAAA
* *
678688 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
678708 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
678728 TCGCAACGCGAT
1 TCGCAACGCGAT
678740 TTACATAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:679302 original size:19 final size:19
Alignment explanation
Indices: 679257--679304 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
679247 TTCGAGAATG
*
679257 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGCGGAAAC
*
679276 AACTATCGCAACGC-GAAACC
1 AA-AATCGCAACGCGGAAA-C
679296 AAAATCGCA
1 AAAATCGCA
679305 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGGAAAC
Found at i:679322 original size:19 final size:19
Alignment explanation
Indices: 679300--679450 Score: 177
Period size: 19 Copynumber: 8.1 Consensus size: 19
679290 GAAACCAAAA
*
679300 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
679319 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
679338 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
679357 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
679377 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
679393 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
679410 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
679429 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
679449 TC
1 TC
679451 AACCAAAAGA
Statistics
Matches: 114, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 65 0.57
20 35 0.31
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:679377 original size:39 final size:38
Alignment explanation
Indices: 679300--679450 Score: 177
Period size: 39 Copynumber: 4.1 Consensus size: 38
679290 GAAACCAAAA
*
679300 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
679338 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
679377 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
679410 TCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
679449 TC
1 TC
679451 AACCAAAAGA
Statistics
Matches: 94, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
33 27 0.29
35 1 0.01
36 1 0.01
37 1 0.01
38 21 0.22
39 43 0.46
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:681514 original size:42 final size:42
Alignment explanation
Indices: 681454--681576 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
681444 GCCCGACTCG
* * *
681454 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
681496 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
681538 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
681577 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:681534 original size:21 final size:21
Alignment explanation
Indices: 681510--681576 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
681500 TCATTCCTCG
681510 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
681531 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
681552 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
681573 AGAG
1 AGAG
681577 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:682952 original size:14 final size:14
Alignment explanation
Indices: 682933--682968 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
682923 ATTGTTTAAT
682933 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
682947 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
682961 TGATTTGT
1 TGATTTGT
682969 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:683132 original size:20 final size:19
Alignment explanation
Indices: 683075--683142 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
683065 CAAAAGTACT
683075 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
683094 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
683108 ATCGCAATGCGAAAATGAAA
1 ATCGCAATGCG-AAATGAAA
*
683128 ATCGCAACGCGAAAT
1 ATCGCAATGCGAAAT
683143 TAAATTCGCG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:683169 original size:19 final size:19
Alignment explanation
Indices: 683147--683277 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
683137 CGAAATTAAA
*
683147 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
683166 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
683182 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
683199 TTCGCATTGCGAAATT-A-
1 TTCGCATTGCGATTTTCAT
*
683216 -GCGC--TGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
683232 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
* *
683248 CTCG--TTGCGATTTTTAT
1 TTCGCATTGCGATTTTCAT
683265 TTCGCATTGCGAT
1 TTCGCATTGCGAT
683278 GGACATTAAG
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 19 0.23
15 1 0.01
16 15 0.18
17 16 0.19
18 1 0.01
19 31 0.37
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:683193 original size:33 final size:32
Alignment explanation
Indices: 683151--683277 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
683141 ATTAAATTCG
683151 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
683184 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
683217 CGCTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
683250 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
683278 GGACATTAAG
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:683240 original size:66 final size:66
Alignment explanation
Indices: 683144--683276 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
683134 ACGCGAAATT
* *
683144 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGCTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
683209 G
66 G
* *
683210 AAATTAGCGCTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTTATTTCGCATTGC
1 AAATTAGCGCTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
683275 G
66 G
683276 A
1 A
683277 TGGACATTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGCTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:685563 original size:12 final size:12
Alignment explanation
Indices: 685546--685570 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
685536 TCTTCGGGGA
685546 CTTTTTCTTCTT
1 CTTTTTCTTCTT
685558 CTTTTTCTTCTT
1 CTTTTTCTTCTT
685570 C
1 C
685571 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:685779 original size:24 final size:24
Alignment explanation
Indices: 685745--685798 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
685735 CTGAAACATC
* *
685745 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
685769 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
685793 ATCAAA
1 ATCAAA
685799 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:686858 original size:20 final size:20
Alignment explanation
Indices: 686833--686890 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
686823 ATTCATTTGA
686833 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
686853 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
686873 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
686891 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:686950 original size:19 final size:19
Alignment explanation
Indices: 686909--687029 Score: 180
Period size: 19 Copynumber: 6.6 Consensus size: 19
686899 GAAATGAAAA
686909 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
686925 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
686942 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
686961 TCGCATTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
686980 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
686999 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
687018 TCGCGTTGCGAT
1 TCGCATTGCGAT
687030 AGTCTGTTTT
Statistics
Matches: 96, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
14 11 0.11
16 3 0.03
17 3 0.03
19 79 0.82
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:689053 original size:20 final size:19
Alignment explanation
Indices: 689018--689084 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
689008 GAAACTTAAA
689018 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
689037 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
689057 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
689076 ATCGCAACG
1 ATCGCAACG
689085 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:689092 original size:14 final size:14
Alignment explanation
Indices: 689073--689130 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
689063 ATGCGAAATG
689073 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
689087 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
689103 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
689119 AAAATCGCAACG
1 AAAATCGCAACG
689131 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:689115 original size:32 final size:33
Alignment explanation
Indices: 689057--689135 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
689047 GGAAATGGCT
*
689057 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
689090 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
689122 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
689136 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:689164 original size:19 final size:16
Alignment explanation
Indices: 689142--689237 Score: 65
Period size: 19 Copynumber: 5.7 Consensus size: 16
689132 GAAACACAAA
689142 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTT-ATT
*
689161 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
689177 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTT-ATT
*
689193 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
689209 TCG-TTGCGATTTTTATT
1 TCGCTTGCGA--TTTATT
689226 TCGCATTGCGAT
1 TCGC-TTGCGAT
689238 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 15 0.24
16 15 0.24
17 5 0.08
18 12 0.19
19 16 0.25
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (16 bp):
TCGCTTGCGATTTATT
Found at i:689183 original size:14 final size:14
Alignment explanation
Indices: 689164--689221 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
689154 TTTCATTTCG
689164 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
689178 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
689194 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
689210 CGTTGCGATTTT
1 CGTTGCGATTTT
689222 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:689194 original size:32 final size:33
Alignment explanation
Indices: 689147--689237 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
689137 ACAAATCGCA
689147 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
689180 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
689212 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
689238 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:689256 original size:20 final size:19
Alignment explanation
Indices: 689223--689275 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
689213 TGCGATTTTT
*
689223 ATTTCGCATTGCGATAGCC
1 ATTTCGCGTTGCGATAGCC
*
689242 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGATAGCC
*
689262 ATTTCGTGTTGCGA
1 ATTTCGCGTTGCGA
689276 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.36
Consensus pattern (19 bp):
ATTTCGCGTTGCGATAGCC
Found at i:689774 original size:18 final size:18
Alignment explanation
Indices: 689748--689792 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
689738 GTCGATCAGA
* *
689748 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
689766 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
689784 TGATGGCTC
1 TGATGGCTC
689793 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:691351 original size:22 final size:22
Alignment explanation
Indices: 691326--691369 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
691316 GATTTAGATA
691326 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
691348 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
691370 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:691650 original size:20 final size:20
Alignment explanation
Indices: 691537--691650 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
691527 CGCTTTGAAA
691537 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
691557 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * *
691577 ATCGCGTTGCAAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
691597 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
691618 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
691638 ATCGCATTGCGAT
1 ATCGCATTGCGAT
691651 TTTCCCAATT
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 54 0.72
21 12 0.16
22 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:691668 original size:21 final size:21
Alignment explanation
Indices: 691639--691714 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
691629 ATAGTAAGTA
*
691639 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* **
691660 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
691680 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
691701 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
691715 ACTTATTCGC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:691669 original size:41 final size:41
Alignment explanation
Indices: 691578--691712 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
691568 AAAGTCAGTA
* * * ** *
691578 TCGCGTTGCAAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCGTTGCGATTTTCCCAAT
* *
691618 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCGTTGCGATTTTCCCAAT
* **
691660 TCGCGTTGCGAT-TTACTTATTCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCGTTGCGATTTTCCCAAT
691701 TCGCGTTGCGAT
1 TCGCGTTGCGAT
691713 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCGTTGCGATTTTCCCAAT
Found at i:691683 original size:20 final size:20
Alignment explanation
Indices: 691658--691731 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
691648 GATTTTCCCA
691658 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* **
691678 ATTCGCGTTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
691699 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
*
691719 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
691732 ATTGGGAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
20 29 0.63
21 17 0.37
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:691713 original size:41 final size:41
Alignment explanation
Indices: 691639--691731 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
691629 ATAGTAAGTA
691639 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
691680 TCGCGTTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
691721 TCGCATTGCGA
1 TCGCATTGCGA
691732 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:702343 original size:60 final size:60
Alignment explanation
Indices: 702264--702435 Score: 177
Period size: 60 Copynumber: 2.9 Consensus size: 60
702254 AACTATAATT
* * * * *
702264 TCATTTTAAA-TAATCCTTAAACTTTTAAATATTTTAATTTCATTCTCAAATTATGACTC
1 TCATTCTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATTCCCAAATTATGACCC
* * * *
702323 TCATTCTAAATTAATCCTTAAAGTTTTGCACATTCTAATTTCA-TCCCTAAACTATGACCC
1 TCATTCTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATTCCC-AAATTATGACCC
* * ** * * *
702383 TCTTTCTAGATTGGTCCTCAAACTTTTGAATATTCCAGTTTCATTCCCAAATT
1 TCATTCTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATTCCCAAATT
702436 CATCCAAATA
Statistics
Matches: 90, Mismatches: 20, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
59 12 0.13
60 74 0.82
61 4 0.04
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (60 bp):
TCATTCTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATTCCCAAATTATGACCC
Found at i:707934 original size:16 final size:16
Alignment explanation
Indices: 707913--707944 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
707903 TAATTGGCAC
707913 TGAAAGGGCAGTACAA
1 TGAAAGGGCAGTACAA
707929 TGAAAGGGCAGTACAA
1 TGAAAGGGCAGTACAA
707945 GGGTGCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.31, T:0.12
Consensus pattern (16 bp):
TGAAAGGGCAGTACAA
Found at i:710821 original size:18 final size:18
Alignment explanation
Indices: 710807--710842 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
710797 AACAAAAAGA
710807 AAAAAGAGAAAAAAAAAT
1 AAAAAGAGAAAAAAAAAT
710825 AAAAAGAGAAAATAAAAA
1 AAAAAGAGAAAA-AAAAA
710843 GATAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (18 bp):
AAAAAGAGAAAAAAAAAT
Found at i:710853 original size:25 final size:25
Alignment explanation
Indices: 710801--710854 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 25
710791 AATCAGAACA
*
710801 AAAAGAAAAAAGAGAAAAAAAAATA
1 AAAAGAAAAAAGAGAAAAAAAAACA
* * *
710826 AAAAGAGAAAATA-AAAAGATAAACA
1 AAAAGAAAAAAGAGAAAA-AAAAACA
710851 AAAA
1 AAAA
710855 ACAAAGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (25 bp):
AAAAGAAAAAAGAGAAAAAAAAACA
Found at i:710855 original size:13 final size:13
Alignment explanation
Indices: 710820--710844 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
710810 AAGAGAAAAA
710820 AAAATAAAAAGAG
1 AAAATAAAAAGAG
710833 AAAATAAAAAGA
1 AAAATAAAAAGA
710845 TAAACAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (13 bp):
AAAATAAAAAGAG
Found at i:711935 original size:33 final size:32
Alignment explanation
Indices: 711898--711974 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
711888 TGGAGGCATC
*
711898 TTTGAAAATTCAACATCAAATGTTAGGGCATTT
1 TTTG-AAATTCAACATCAAATATTAGGGCATTT
* * * *
711931 TTTGAGATTCAACATCGAATATTGGGGCATAT
1 TTTGAAATTCAACATCAAATATTAGGGCATTT
* *
711963 TTGGGAATTCAA
1 TTTGAAATTCAA
711975 TATCCTGATG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
32 32 0.89
33 4 0.11
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTGAAATTCAACATCAAATATTAGGGCATTT
Found at i:712659 original size:64 final size:64
Alignment explanation
Indices: 712553--712810 Score: 426
Period size: 64 Copynumber: 4.0 Consensus size: 64
712543 AAGTTGTCTG
* * * * *
712553 TCAATAAACAACTGTCCAGTTTCATTCAGAGTTAATTTCAACTTCGCAGCGAAGGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
712617 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
*
712681 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
* * * *
712745 TCAACAAACAACTTTCTAGTTTTATTTAGAGTCAATTTCAACTTCACAACGAATGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
712809 TC
1 TC
712811 GAAACAACGC
Statistics
Matches: 183, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 183 1.00
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (64 bp):
TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
Found at i:713174 original size:83 final size:84
Alignment explanation
Indices: 713003--713254 Score: 335
Period size: 83 Copynumber: 3.0 Consensus size: 84
712993 TCCCAGCCTA
* * * *
713003 TTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAA-ACCATCGAGTTCGATTACATTC
*
713068 AGCTCAAAGGCATACCAAAT
65 AGCTCAAAGGCATATCAAAT
* * * *
713088 TTACAGCATAACTCAAGGTGAGAAGGGTTATCTGTCAAC-AAACCCTCGAGTTCAATTACATTCA
1 TTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAACCATCGAGTTCGATTACATTCA
*
713152 GCTCAAGGGCATATCAAAT
66 GCTCAAAGGCATATCAAAT
* * *
713171 TTACAGCATAGCTCAAGGCGATAAGGGTTATCTGTCAACAAAAAACTATCGAGTTCGATTCCATT
1 TTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC--AAAACCATCGAGTTCGATTACATT
* *
713236 CAGCTCAATGACATATCAA
64 CAGCTCAAAGGCATATCAA
713255 CCGCATGGTA
Statistics
Matches: 146, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
83 73 0.50
84 2 0.01
85 35 0.24
86 36 0.25
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (84 bp):
TTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAACCATCGAGTTCGATTACATTCA
GCTCAAAGGCATATCAAAT
Found at i:722457 original size:78 final size:79
Alignment explanation
Indices: 722313--722473 Score: 270
Period size: 78 Copynumber: 2.1 Consensus size: 79
722303 CAACAACAAA
* * *
722313 AATCAATCCATTTTTGTTCAAATTATGTCATGTATTAATATGAATAATTAACACCATACTTAGTT
1 AATCAATCAATTTTAGTTCAAAATATGTCATGTATTAATATGAATAATTAACACCATACTTAGTT
722378 GTCCTTGTTTACTT
66 GTCCTTGTTTACTT
* *
722392 AATCAATCAATTTTAGTTCAAAATATGTCAT-TATTAATATGAATAATTAACACCATTCTTGGTT
1 AATCAATCAATTTTAGTTCAAAATATGTCATGTATTAATATGAATAATTAACACCATACTTAGTT
722456 GTCCTTGTTTACTT
66 GTCCTTGTTTACTT
722470 AATC
1 AATC
722474 GCTCGTGAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
78 49 0.64
79 28 0.36
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (79 bp):
AATCAATCAATTTTAGTTCAAAATATGTCATGTATTAATATGAATAATTAACACCATACTTAGTT
GTCCTTGTTTACTT
Found at i:724966 original size:15 final size:15
Alignment explanation
Indices: 724942--724977 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
724932 TTAATTTTAA
724942 ACCC-AACCAAAAAT
1 ACCCAAACCAAAAAT
724956 ACCCAAACCAAAAAT
1 ACCCAAACCAAAAAT
724971 ACCCAAA
1 ACCCAAA
724978 TCAATTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.58, C:0.36, G:0.00, T:0.06
Consensus pattern (15 bp):
ACCCAAACCAAAAAT
Found at i:737503 original size:7 final size:7
Alignment explanation
Indices: 737491--737532 Score: 57
Period size: 7 Copynumber: 5.6 Consensus size: 7
737481 CTTTATGATA
737491 ATATTAT
1 ATATTAT
737498 ATATTATAT
1 ATA-T-TAT
737507 ATTATTAT
1 A-TATTAT
737515 ATATTAT
1 ATATTAT
737522 ATATTAT
1 ATATTAT
737529 ATAT
1 ATAT
737533 ATGTGCCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 20 0.62
8 5 0.16
9 5 0.16
10 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTAT
Found at i:737514 original size:17 final size:17
Alignment explanation
Indices: 737492--737534 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
737482 TTTATGATAA
737492 TATTATATATTATATAT
1 TATTATATATTATATAT
737509 TATTATATATTATATAT
1 TATTATATATTATATAT
737526 TA-TATATAT
1 TATTATATAT
737535 GTGCCACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATATATTATATAT
Found at i:738532 original size:15 final size:14
Alignment explanation
Indices: 738512--738548 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
738502 TTCGATAATC
738512 TGTTCGTTTATTTGA
1 TGTTCGTTTATTT-A
738527 TGTTCGTTTATTTA
1 TGTTCGTTTATTTA
*
738541 TATTCGTT
1 TGTTCGTT
738549 CAGTTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.14, C:0.08, G:0.16, T:0.62
Consensus pattern (14 bp):
TGTTCGTTTATTTA
Found at i:738548 original size:14 final size:14
Alignment explanation
Indices: 738514--738558 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
738504 CGATAATCTG
*
738514 TTCGTTTATTTGATG
1 TTCGTTTATTT-ATA
738529 TTCGTTTATTTATA
1 TTCGTTTATTTATA
* *
738543 TTCGTTCAGTTATA
1 TTCGTTTATTTATA
738557 TT
1 TT
738559 TAATTCAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.18, C:0.09, G:0.13, T:0.60
Consensus pattern (14 bp):
TTCGTTTATTTATA
Found at i:748710 original size:4 final size:4
Alignment explanation
Indices: 748696--748732 Score: 65
Period size: 4 Copynumber: 9.0 Consensus size: 4
748686 TATGGATTGT
748696 TATG ATATG TATG TATG TATG TATG TATG TATG TATG
1 TATG -TATG TATG TATG TATG TATG TATG TATG TATG
748733 GCCTAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:749377 original size:29 final size:31
Alignment explanation
Indices: 749341--749407 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
749331 AATTGTTTTG
749341 ATCATTGAATTT-TTAAA-AATTATAAAATA
1 ATCATTGAATTTATTAAATAATTATAAAATA
* *
749370 ATCATTGAATTTATTAAATTATTATAAAATG
1 ATCATTGAATTTATTAAATAATTATAAAATA
749401 ATCATTG
1 ATCATTG
749408 CAGTGTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 12 0.35
30 5 0.15
31 17 0.50
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (31 bp):
ATCATTGAATTTATTAAATAATTATAAAATA
Found at i:755857 original size:21 final size:21
Alignment explanation
Indices: 755815--755857 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
755805 TTTCTGGGCT
* *
755815 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
755836 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
755857 A
1 A
755858 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:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:756624 original size:31 final size:30
Alignment explanation
Indices: 756585--756681 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
756575 AGTCGAGGGT
756585 TTACCTATGTCTTTCGAGACATATGGACAG
1 TTACCTATGTCTTTCGAGACATATGGACAG
*** *
756615 TATACCTATGTTCTAAGGA-ACATATGGATAG
1 T-TACCTATG-TCTTTCGAGACATATGGACAG
* *
756646 TTTACCTAGGT-TCTTCGAGACCTATGGACAG
1 -TTACCTATGTCT-TTCGAGACATATGGACAG
756677 TTACC
1 TTACC
756682 GAGGATCTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
29 1 0.02
30 9 0.17
31 36 0.69
32 6 0.12
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (30 bp):
TTACCTATGTCTTTCGAGACATATGGACAG
Found at i:756698 original size:30 final size:30
Alignment explanation
Indices: 756664--756822 Score: 266
Period size: 30 Copynumber: 5.3 Consensus size: 30
756654 GGTTCTTCGA
*
756664 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
756694 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
756724 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
756754 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * * *
756784 GACCTCTGGACAGTTATCG-GGGTGTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
756813 GACCTCTGGA
1 GACCTCTGGA
756823 TAGGTCCTTT
Statistics
Matches: 124, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 17 0.14
30 107 0.86
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:760604 original size:21 final size:21
Alignment explanation
Indices: 760562--760604 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
760552 TTTCTGGGCT
* *
760562 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
760583 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
760604 A
1 A
760605 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:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:761418 original size:31 final size:31
Alignment explanation
Indices: 761329--761424 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
761319 AGAGTCGAGG
*
761329 GTTTACCTATG-TCTTTCGAGACATATGGATA
1 GTTTACCTATGTTC-TTCGGGACATATGGATA
* ** *
761360 GTATACCTATGTTCTAAGGAACATATGGATA
1 GTTTACCTATGTTCTTCGGGACATATGGATA
* * *
761391 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGATA
761422 GTT
1 GTT
761425 ACCGAGGATC
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
31 50 0.96
32 2 0.04
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGATA
Found at i:761444 original size:30 final size:30
Alignment explanation
Indices: 761410--761568 Score: 284
Period size: 30 Copynumber: 5.3 Consensus size: 30
761400 GGTTCTTCGG
*
761410 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
761440 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
761470 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
761500 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* *
761530 GACCTCTGGACAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
761559 GACCTCTGGA
1 GACCTCTGGA
761569 TAGGTCCTTT
Statistics
Matches: 126, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
29 18 0.14
30 108 0.86
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:766585 original size:31 final size:30
Alignment explanation
Indices: 766550--766615 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 30
766540 TTTATTCTTT
*
766550 TTCTCAAATCGGTACCTTAAA-TTAAAACAAA
1 TTCTCAAATCGCTA-CTTAAACTTAAAA-AAA
*
766581 TTCTCAAATTGCTACTTAAACTTTAAAAAAA
1 TTCTCAAATCGCTACTTAAAC-TTAAAAAAA
766612 TTCT
1 TTCT
766616 TAGATTGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.19
31 19 0.61
32 6 0.19
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.35
Consensus pattern (30 bp):
TTCTCAAATCGCTACTTAAACTTAAAAAAA
Found at i:769899 original size:37 final size:37
Alignment explanation
Indices: 769858--769930 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
769848 TAATTTAGCC
769858 CCTAAATCATCACTTATTTTGGACTTTTATTACTTAT
1 CCTAAATCATCACTTATTTTGGACTTTTATTACTTAT
*
769895 CCTAAATCATCACTTATTTTGGAGTTTTATTACTTA
1 CCTAAATCATCACTTATTTTGGACTTTTATTACTTA
769931 ATGGAATCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (37 bp):
CCTAAATCATCACTTATTTTGGACTTTTATTACTTAT
Found at i:786425 original size:18 final size:18
Alignment explanation
Indices: 786399--786444 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
786389 TTAAAATGAA
*
786399 CATCAAATGCATTTTATG
1 CATCGAATGCATTTTATG
786417 CATCGAATGCATTTTATG
1 CATCGAATGCATTTTATG
786435 CATCG-ATGCA
1 CATCGAATGCA
786445 CATACCATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (18 bp):
CATCGAATGCATTTTATG
Found at i:786463 original size:45 final size:45
Alignment explanation
Indices: 786414--786511 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
786404 AATGCATTTT
* *
786414 ATGCA-TCGAATGCATTTTATGCATCGATGCACATA-CCATGCATCG
1 ATGCACTC-AATGCATTTGATGCATCGATACACA-AGCCATGCATCG
* *
786459 ATGCACTCAGTGCATTTGATGCATCGATACACAAGCCATGTATCG
1 ATGCACTCAATGCATTTGATGCATCGATACACAAGCCATGCATCG
786504 ATGCACTC
1 ATGCACTC
786512 TGGCTATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 1 0.02
45 44 0.94
46 2 0.04
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (45 bp):
ATGCACTCAATGCATTTGATGCATCGATACACAAGCCATGCATCG
Found at i:809282 original size:20 final size:20
Alignment explanation
Indices: 809257--809305 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
809247 CTCAATTCGA
809257 TCCGTTTTTCGCAATTAAGC
1 TCCGTTTTTCGCAATTAAGC
809277 TCCGTTTTTCGCAATTAAGC
1 TCCGTTTTTCGCAATTAAGC
809297 TCCGTTTTT
1 TCCGTTTTT
809306 ATGAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.45
Consensus pattern (20 bp):
TCCGTTTTTCGCAATTAAGC
Found at i:811681 original size:62 final size:62
Alignment explanation
Indices: 811592--811760 Score: 234
Period size: 62 Copynumber: 2.7 Consensus size: 62
811582 CTAATATGAC
* * *
811592 TCTTGGGTAGG-CTC-TGCGACCCCGAGATCATTCTTGGGTAGGCCCTGCGACCTTGGGATTTT
1 TCTTGGGTAGGCCTCGTG-G-CCCTGAGATCATTCTTGGGTAGGCCCTGCGACCTTGAGATCTT
* *
811654 TCTTGGGTAGGCCTCGTGGCCCTGAGATCATTCTTGGGTAGGCCTTGCGGCCTTGAGATCTT
1 TCTTGGGTAGGCCTCGTGGCCCTGAGATCATTCTTGGGTAGGCCCTGCGACCTTGAGATCTT
* * *
811716 TCTTGGGTAGGCCCCGTGGCCCTGAGAACTTTCTTGGGTAGGCCC
1 TCTTGGGTAGGCCTCGTGGCCCTGAGATCATTCTTGGGTAGGCCC
811761 ATAAGCCCCA
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
62 90 0.94
63 4 0.04
64 2 0.02
ACGTcount: A:0.12, C:0.26, G:0.32, T:0.30
Consensus pattern (62 bp):
TCTTGGGTAGGCCTCGTGGCCCTGAGATCATTCTTGGGTAGGCCCTGCGACCTTGAGATCTT
Found at i:811759 original size:31 final size:31
Alignment explanation
Indices: 811592--811760 Score: 167
Period size: 31 Copynumber: 5.5 Consensus size: 31
811582 CTAATATGAC
* * * * * *
811592 TCTTGGGTAGGCTCTGCGACCCCGAGATCAT
1 TCTTGGGTAGGCCCCGTGGCCCTGAGATCTT
* * * * * *
811623 TCTTGGGTAGGCCCTGCGACCTTGGGATTTT
1 TCTTGGGTAGGCCCCGTGGCCCTGAGATCTT
* *
811654 TCTTGGGTAGGCCTCGTGGCCCTGAGATCAT
1 TCTTGGGTAGGCCCCGTGGCCCTGAGATCTT
** * *
811685 TCTTGGGTAGGCCTTGCGGCCTTGAGATCTT
1 TCTTGGGTAGGCCCCGTGGCCCTGAGATCTT
*
811716 TCTTGGGTAGGCCCCGTGGCCCTGAGAACTT
1 TCTTGGGTAGGCCCCGTGGCCCTGAGATCTT
811747 TCTTGGGTAGGCCC
1 TCTTGGGTAGGCCC
811761 ATAAGCCCCA
Statistics
Matches: 115, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 115 1.00
ACGTcount: A:0.12, C:0.26, G:0.32, T:0.30
Consensus pattern (31 bp):
TCTTGGGTAGGCCCCGTGGCCCTGAGATCTT
Found at i:837220 original size:35 final size:35
Alignment explanation
Indices: 837180--837259 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
837170 AACACAATCA
*
837180 TCAATTACATTCTAAACCCCAAATTTCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
* * *
837215 TCAATTATATTTTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
837250 TCAATTACAT
1 TCAATTACAT
837260 ACTTAGCCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATACT
Done.