Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008170.1 Hibiscus syriacus cultivar Beakdansim tig00110761_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: 686002
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:475121 original size:16 final size:18
Alignment explanation
Indices: 475100--475133 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
475090 ATTTCTTATT
475100 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
475116 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
475134 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:475780 original size:24 final size:24
Alignment explanation
Indices: 475749--475814 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
475739 TTTTCATTTA
*
475749 TTGTGTTCGTTTACATTCTTTCGT
1 TTGTGTTCGTTTACATTCGTTCGT
*
475773 TTGTGTTCGTTTACGTTCGTTCGT
1 TTGTGTTCGTTTACATTCGTTCGT
* *
475797 TTTTGTTCGTTAACATTC
1 TTGTGTTCGTTTACATTC
475815 ATTTATTGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.09, C:0.17, G:0.18, T:0.56
Consensus pattern (24 bp):
TTGTGTTCGTTTACATTCGTTCGT
Found at i:475875 original size:24 final size:24
Alignment explanation
Indices: 475720--475881 Score: 76
Period size: 24 Copynumber: 6.8 Consensus size: 24
475710 AAAAATCTAT
* * *
475720 ATTCATTTATGTTTGTTTATTTTC
1 ATTCATTTGTGTTCGTTTATGTTC
* **
475744 ATTTA-TTGTGTTCGTTTACATTC
1 ATTCATTTGTGTTCGTTTATGTTC
* * *
475767 TTTCGTTTGTGTTCGTTTACGTTC
1 ATTCATTTGTGTTCGTTTATGTTC
* * * * **
475791 GTTCGTTTTTGTTCGTTAACATTC
1 ATTCATTTGTGTTCGTTTATGTTC
* ** *
475815 ATTTA-TTGTGTTTATTTATGTTT
1 ATTCATTTGTGTTCGTTTATGTTC
* * ****
475838 GTTTATACCCGTTCGTTTATGTTC
1 ATTCATTTGTGTTCGTTTATGTTC
*
475862 ATTCATTTGTGTTCATTTAT
1 ATTCATTTGTGTTCGTTTAT
475882 CATTTAAATG
Statistics
Matches: 98, Mismatches: 38, Indels: 4
0.70 0.27 0.03
Matches are distributed among these distances:
23 31 0.32
24 67 0.68
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.59
Consensus pattern (24 bp):
ATTCATTTGTGTTCGTTTATGTTC
Found at i:477177 original size:17 final size:17
Alignment explanation
Indices: 477137--477184 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
477127 TGATTCAATT
* *
477137 TATATTTAAATTTATGA
1 TATATTTATATTTTTGA
477154 -ATCATTTATATTTTTGA
1 TAT-ATTTATATTTTTGA
477171 TATATTT-TATTTTT
1 TATATTTATATTTTT
477185 CTTGTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.33
17 16 0.59
18 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (17 bp):
TATATTTATATTTTTGA
Found at i:477348 original size:16 final size:18
Alignment explanation
Indices: 477316--477349 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
477306 TATTAATGTA
477316 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
477334 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
477350 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:478019 original size:130 final size:130
Alignment explanation
Indices: 477815--478062 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
477805 AATTTTCTTC
* * * *
477815 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGCGGTGACATGGGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
477880 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* *
477945 TAATTAGGCGGTGACATGGGTCACCAATGACACATGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGCGGTGACATGGGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
478010 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
478063 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGCGGTGACATGGGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:478496 original size:35 final size:35
Alignment explanation
Indices: 478457--478532 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
478447 AATTGAATTT
* * *
478457 AATTGATTTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
478492 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
478527 AATTGA
1 AATTGA
478533 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.34, C:0.01, G:0.24, T:0.41
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:478847 original size:14 final size:13
Alignment explanation
Indices: 478828--479030 Score: 148
Period size: 14 Copynumber: 15.7 Consensus size: 13
478818 TCGTTCGGAG
478828 ATATATTATAGTAT
1 ATATATTATA-TAT
*
478842 ATATATTAATTATGTT
1 ATATATT-A-TAT-AT
478858 ATATAGTTAT-TAT
1 ATATA-TTATATAT
**
478871 -GCTATTATATAT
1 ATATATTATATAT
478883 AT-TATTATATAGT
1 ATATATTATATA-T
478896 -TATA-TAT-T-T
1 ATATATTATATAT
478905 -TATATTATATAT
1 ATATATTATATAT
478917 AT-TATTATATAGTT
1 ATATATTATATA--T
478931 ATATATTATATCAT
1 ATATATTATAT-AT
478945 ATATA-TAT-TAT
1 ATATATTATATAT
478956 ATATTATTATATAT
1 ATA-TATTATATAT
478970 ATTATATTATATAT
1 A-TATATTATATAT
478984 ATTATATTATATAT
1 A-TATATTATATAT
478998 AT-TATTAT-TATT
1 ATATATTATATA-T
479010 ATTATATTATAT-T
1 A-TATATTATATAT
479023 AT-TATTAT
1 ATATATTAT
479031 TATTTTTTAT
Statistics
Matches: 160, Mismatches: 5, Indels: 51
0.74 0.02 0.24
Matches are distributed among these distances:
9 5 0.03
10 3 0.02
11 19 0.12
12 40 0.25
13 15 0.09
14 52 0.32
15 14 0.09
16 10 0.06
17 2 0.01
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (13 bp):
ATATATTATATAT
Found at i:478860 original size:16 final size:16
Alignment explanation
Indices: 478831--478909 Score: 58
Period size: 17 Copynumber: 4.8 Consensus size: 16
478821 TTCGGAGATA
478831 TATTATAGTATATATA-T
1 TATTAT-GT-TATATAGT
478848 TAATTATGTTATATAGT
1 T-ATTATGTTATATAGT
*
478865 TATTATGCTATTATA-T
1 TATTATGTTA-TATAGT
478881 ATATTA--TTATATAGT
1 -TATTATGTTATATAGT
*
478896 TATATATTTTATAT
1 TAT-TATGTTATAT
478910 TATATATATT
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 7 0.13
15 5 0.10
16 15 0.29
17 20 0.38
18 5 0.10
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (16 bp):
TATTATGTTATATAGT
Found at i:478869 original size:34 final size:33
Alignment explanation
Indices: 478831--479044 Score: 166
Period size: 34 Copynumber: 6.5 Consensus size: 33
478821 TTCGGAGATA
*
478831 TATTATAGTATATATATTAATTATGTTATATAGT
1 TATTATATTATATATATTAATTATGTTATATA-T
*
478865 TATTATGCTATTATATATATTATTATATAGTTATATAT
1 TATTA---TATTATATATATTAAT-TAT-GTTATATAT
*
478903 T-TTATATTATATATATTATTATATAGTTATATAT
1 TATTATATTATATATATTAAT-TAT-GTTATATAT
*
478937 TA-TATCA-TATATATATT-A-TATATTATTATAT
1 TATTAT-ATTATATATATTAATTATGTTA-TATAT
478968 ATATTATATTATATATATT-A-TAT-TATATATAT
1 -TATTATATTATATATATTAATTATGT-TATATAT
479000 TATTATTATTAT-TATATTATATTA--TTAT-TAT
1 TATTA-TATTATATATATTA-ATTATGTTATATAT
*
479031 TATT-TTTTATATAT
1 TATTATATTATATAT
479045 TTTATTAACC
Statistics
Matches: 158, Mismatches: 5, Indels: 38
0.79 0.02 0.19
Matches are distributed among these distances:
29 5 0.03
30 6 0.04
31 26 0.16
32 18 0.11
33 21 0.13
34 51 0.32
35 1 0.01
37 17 0.11
38 5 0.03
39 8 0.05
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (33 bp):
TATTATATTATATATATTAATTATGTTATATAT
Found at i:478881 original size:2 final size:2
Alignment explanation
Indices: 478876--479021 Score: 102
Period size: 2 Copynumber: 82.5 Consensus size: 2
478866 ATTATGCTAT
*
478876 TA TA TA TA T- TA T- TA TA TA GT- TA TA TA T- TT TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
478914 TA TA T- TA T- TA TA TA GT- TA TA TA T- TA TA TCA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA T-A TA TA TA TA TA
478953 TA TA TA T- TA T- TA TA TA TA T- TA TA T- TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
478990 T- TA TA TA TA T- TA T- TA T- TA T- TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
479022 TATTATTATT
Statistics
Matches: 118, Mismatches: 1, Indels: 50
0.70 0.01 0.30
Matches are distributed among these distances:
1 22 0.19
2 92 0.78
3 4 0.03
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (2 bp):
TA
Found at i:479049 original size:19 final size:20
Alignment explanation
Indices: 478873--479051 Score: 98
Period size: 22 Copynumber: 8.4 Consensus size: 20
478863 GTTATTATGC
*
478873 TATTATATATATTATTATATAGT
1 TATTAT-TAT-TTTTTATATA-T
*
478896 TA-TA-TATTTTATATTATAT
1 TATTATTATTTTTTA-TATAT
**
478915 ATATTATTATATAGTTATATAT
1 -TATTATTAT-TTTTTATATAT
* *
478937 TATATCATATATATATTATATAT
1 TAT-T-AT-TATTTTTTATATAT
478960 TATTATATATATTATATTATATA-
1 TATTAT-TAT-TT-T-TTATATAT
* *
478983 TATTA-TATTATATATATTAT
1 TATTATTATTTTTTATA-TAT
*
479003 TATTATTATTATATTATATTAT
1 TATTATTATT-TTTTATA-TAT
479025 TATTATTATTTTTTATATAT
1 TATTATTATTTTTTATATAT
479045 T-TTATTA
1 TATTATTA
479052 ACCATTTCAA
Statistics
Matches: 125, Mismatches: 16, Indels: 34
0.71 0.09 0.19
Matches are distributed among these distances:
18 4 0.03
19 14 0.11
20 19 0.15
21 24 0.19
22 31 0.25
23 23 0.18
24 10 0.08
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.60
Consensus pattern (20 bp):
TATTATTATTTTTTATATAT
Found at i:479050 original size:28 final size:27
Alignment explanation
Indices: 478873--479051 Score: 103
Period size: 28 Copynumber: 6.2 Consensus size: 27
478863 GTTATTATGC
* * *
478873 TATTATATATATTATTATATAGTTATATAT
1 TATTATAT-TATTATTTTTTA--TATATTT
*
478903 T-TTATATTATATATATTATTATATAGTTAT
1 TATTATATTAT-TAT-TTTTTATATA-TT-T
* * *
478933 ATATTATATCATATATATATTATATA--T
1 -TATTATATTAT-TATTTTTTATATATTT
* * *
478960 TATTATATATATTATATTATATATATTA
1 TATTATAT-TATTATTTTTTATATATTT
*
478988 TATTATATATATTATTATTATTATTATATTA
1 TATTATAT-TATTATT-TT-TTA-TATATTT
479019 TATTATTATTATTATTTTTTATATATTT
1 TATTA-TATTATTATTTTTTATATATTT
479047 TATTA
1 TATTA
479052 ACCATTTCAA
Statistics
Matches: 123, Mismatches: 13, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
26 19 0.15
27 3 0.02
28 33 0.27
29 15 0.12
30 9 0.07
31 29 0.24
32 15 0.12
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.60
Consensus pattern (27 bp):
TATTATATTATTATTTTTTATATATTT
Found at i:482161 original size:66 final size:66
Alignment explanation
Indices: 482055--482186 Score: 196
Period size: 66 Copynumber: 2.0 Consensus size: 66
482045 TTAAAACAGC
* *
482055 GGCCGACGTAATTGCCGAAACTACATTTATTGAGGTTGAGG-GAGAAATGGAGAGAGAAGGGAAG
1 GGCCGACGTAATGGCCGAAACTACAATTATTGAGGTTGAGGAGAG-AATGGAGAGAGAAGGGAAG
482119 AA
65 AA
* *
482121 GGCCGACGTAATGGCTGAAAACTA-AATTATTGAGGTTGAGGAGAGAGTGGAGAGAGAAGGGAAG
1 GGCCGACGTAATGGCCG-AAACTACAATTATTGAGGTTGAGGAGAGAATGGAGAGAGAAGGGAAG
482185 AA
65 AA
482187 TAAATAGAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
66 51 0.85
67 9 0.15
ACGTcount: A:0.37, C:0.09, G:0.36, T:0.17
Consensus pattern (66 bp):
GGCCGACGTAATGGCCGAAACTACAATTATTGAGGTTGAGGAGAGAATGGAGAGAGAAGGGAAGA
A
Found at i:483939 original size:21 final size:20
Alignment explanation
Indices: 483915--483990 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 20
483905 GCAACGATGG
*
483915 CAACAACACGAACAACGTCGT
1 CAACAACACG-ACAACATCGT
*
483936 CAACAACAAC-AGCAATATCGT
1 CAACAAC-ACGA-CAACATCGT
483957 CAACAACA-G-CAACATCGT
1 CAACAACACGACAACATCGT
483975 CAACAAACAACGACAA
1 CAAC-AAC-ACGACAA
483991 AGCAACAGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
18 12 0.27
19 3 0.07
20 3 0.07
21 22 0.49
22 5 0.11
ACGTcount: A:0.49, C:0.32, G:0.11, T:0.09
Consensus pattern (20 bp):
CAACAACACGACAACATCGT
Found at i:491602 original size:20 final size:18
Alignment explanation
Indices: 491562--491605 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
491552 CCTTAGAGTT
*
491562 TTTTAAAAATAAATTATAA
1 TTTT-AAAATAAATTAAAA
491581 TTTTAAAATAAATTTTAAAA
1 TTTTAAAATAAA--TTAAAA
491601 TTTTA
1 TTTTA
491606 TAAGCATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 4 0.18
20 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTTAAAATAAATTAAAA
Found at i:491730 original size:18 final size:17
Alignment explanation
Indices: 491690--491732 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
491680 ATAATTATTT
491690 AATTTAAAAAACTTTAA
1 AATTTAAAAAACTTTAA
491707 ATATTTAAAATTAA-TTTAA
1 A-ATTTAAAA--AACTTTAA
491726 AATTTAA
1 AATTTAA
491733 TTTTAAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 14 0.61
19 6 0.26
20 2 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAAAAAACTTTAA
Found at i:491959 original size:29 final size:29
Alignment explanation
Indices: 491927--491987 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
491917 AATATAACAG
**
491927 AAAAAATATTAAATAATT-ATTTTAATTTA
1 AAAAAAT-TTAAATAATTAAAATTAATTTA
* *
491956 AAAAACTTTAAATATTTAAAATTAATTTA
1 AAAAAATTTAAATAATTAAAATTAATTTA
491985 AAA
1 AAA
491988 TTTAATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAAAATTTAAATAATTAAAATTAATTTA
Found at i:491966 original size:28 final size:29
Alignment explanation
Indices: 491927--491987 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
491917 AATATAACAG
**
491927 AAAAAATATTAAATAATT-ATTTTAATTT
1 AAAAAATATTAAATAATTAAAATTAATTT
*
491955 AAAAAACT-TTAAATATTTAAAATTAATTT
1 AAAAAA-TATTAAATAATTAAAATTAATTT
491984 AAAA
1 AAAA
491988 TTTAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAAAATATTAAATAATTAAAATTAATTT
Found at i:491985 original size:11 final size:12
Alignment explanation
Indices: 491969--491998 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
491959 AACTTTAAAT
491969 ATTTAAAA-TTA
1 ATTTAAAATTTA
491980 ATTTAAAATTTA
1 ATTTAAAATTTA
491992 ATTTAAA
1 ATTTAAA
491999 CACTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTTAAAATTTA
Found at i:491990 original size:18 final size:17
Alignment explanation
Indices: 491950--491992 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
491940 TAATTATTTT
491950 AATTTAAAAAACTTTAA
1 AATTTAAAAAACTTTAA
491967 ATATTTAAAATTAA-TTTAA
1 A-ATTTAAAA--AACTTTAA
491986 AATTTAA
1 AATTTAA
491993 TTTAAACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 14 0.61
19 6 0.26
20 2 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAAAAAACTTTAA
Found at i:493309 original size:48 final size:48
Alignment explanation
Indices: 493233--493330 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
493223 AGTTGAGTCT
* *
493233 TGGTGGGCAGAATAATTTGATGAATAAGGAAGGTGTTCGAAAGGAGGC
1 TGGTGGCCAGAATAATTTGATGAATAAGGAAGGTGTTCGAAACGAGGC
* * * * *
493281 TGGTGGCCAGGATAATTTGATTAGTAAGGATGGTGTTGGAAACGAGGC
1 TGGTGGCCAGAATAATTTGATGAATAAGGAAGGTGTTCGAAACGAGGC
493329 TG
1 TG
493331 TTGTTGTGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.30, C:0.07, G:0.38, T:0.26
Consensus pattern (48 bp):
TGGTGGCCAGAATAATTTGATGAATAAGGAAGGTGTTCGAAACGAGGC
Found at i:493457 original size:30 final size:30
Alignment explanation
Indices: 493421--493488 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
493411 GGAGCAGGAT
493421 GAACAAGATGAACAAGAGGAGCAGCATGAA
1 GAACAAGATGAACAAGAGGAGCAGCATGAA
493451 GAACAAGATGAACAAGAGGAGCAGCATGAA
1 GAACAAGATGAACAAGAGGAGCAGCATGAA
493481 GAACAAGA
1 GAACAAGA
493489 GGAGCAGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.51, C:0.13, G:0.29, T:0.06
Consensus pattern (30 bp):
GAACAAGATGAACAAGAGGAGCAGCATGAA
Found at i:493485 original size:21 final size:21
Alignment explanation
Indices: 493460--493501 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
493450 AGAACAAGAT
493460 GAACAAGAGGAGCAGCATGAA
1 GAACAAGAGGAGCAGCATGAA
*
493481 GAACAAGAGGAGCAGTATGAA
1 GAACAAGAGGAGCAGCATGAA
493502 CACAGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.33, T:0.07
Consensus pattern (21 bp):
GAACAAGAGGAGCAGCATGAA
Found at i:493529 original size:49 final size:51
Alignment explanation
Indices: 493430--493537 Score: 166
Period size: 49 Copynumber: 2.2 Consensus size: 51
493420 TGAACAAGAT
*
493430 GAACAAGAGGAGCAGCATGAAGAACAAGATGAACAAGAGGAGCAGCATGAA
1 GAACAAGAGGAGCAGCATGAAGAACAAGATGAACAAGAAGAGCAGCATGAA
* * *
493481 GAACAAGAGGAGCAGTATGAA-CAC-AGATGAACAAGAAGAGCAGGATGAA
1 GAACAAGAGGAGCAGCATGAAGAACAAGATGAACAAGAAGAGCAGCATGAA
493530 GAACAAGA
1 GAACAAGA
493538 TGAGTATGAG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 31 0.58
50 2 0.04
51 20 0.38
ACGTcount: A:0.50, C:0.13, G:0.31, T:0.06
Consensus pattern (51 bp):
GAACAAGAGGAGCAGCATGAAGAACAAGATGAACAAGAAGAGCAGCATGAA
Found at i:502320 original size:22 final size:22
Alignment explanation
Indices: 502271--502323 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
502261 GAGGAGATAG
502271 TTTT-AAATATGGATTAATTTA
1 TTTTAAAATATGGATTAATTTA
*
502292 -TTTAAAATATGGATTGATTTA
1 TTTTAAAATATGGATTAATTTA
502313 TTTTAAAATAT
1 TTTTAAAATAT
502324 TATTATTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 3 0.10
21 16 0.55
22 10 0.34
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TTTTAAAATATGGATTAATTTA
Found at i:502399 original size:31 final size:31
Alignment explanation
Indices: 502342--502400 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
502332 TAGTTGTAGG
*
502342 ATTATTTAAATTTCAATATTATAAAACTAAA
1 ATTATTTAAATTTCAATATTACAAAACTAAA
* *
502373 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAATATTACAAAACT
502401 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTACAAAACTAAA
Found at i:507958 original size:29 final size:29
Alignment explanation
Indices: 507913--508067 Score: 283
Period size: 29 Copynumber: 5.3 Consensus size: 29
507903 GCATAATATC
* **
507913 ATATCATGCTGCAGTCATAATGCTGCCTG
1 ATATCATGCTGCGGTCATAATGCTATCTG
507942 ATATCATGCTGCGGTCATAATGCTATCTG
1 ATATCATGCTGCGGTCATAATGCTATCTG
507971 ATATCATGCTGCGGTCATAATGCTATCTG
1 ATATCATGCTGCGGTCATAATGCTATCTG
508000 ATATCATGCTGCGGTCATAATGCTATCTG
1 ATATCATGCTGCGGTCATAATGCTATCTG
508029 ATATCATGCTGCGGTCATAATGCTATCTG
1 ATATCATGCTGCGGTCATAATGCTATCTG
508058 ATATCATGCT
1 ATATCATGCT
508068 TATACACAGT
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 123 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (29 bp):
ATATCATGCTGCGGTCATAATGCTATCTG
Found at i:521581 original size:20 final size:20
Alignment explanation
Indices: 521558--521625 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
521548 GTTTCCAATT
521558 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
** * * **
521578 TCGCATTGCGATTTTCCAAA
1 TCGCAACGCGAATATGTAAA
* *
521598 TTCGAAACGCGAATCTGTAAA
1 -TCGCAACGCGAATATGTAAA
521619 TCGCAAC
1 TCGCAAC
521626 ACATAAGTCA
Statistics
Matches: 33, Mismatches: 14, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
20 20 0.61
21 13 0.39
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:521644 original size:20 final size:20
Alignment explanation
Indices: 521619--521686 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
521609 AATCTGTAAA
521619 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
521639 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
*
521659 TCGCAACACAAAAGTCAAATT
1 TCGCAACACATAAGTCAAA-T
521680 TCGCAAC
1 TCGCAAC
521687 GCGGAATTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.02
20 31 0.74
21 10 0.24
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.19
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:521649 original size:40 final size:40
Alignment explanation
Indices: 521594--521707 Score: 126
Period size: 40 Copynumber: 2.8 Consensus size: 40
521584 TGCGATTTTC
* * *
521594 CAAATTCGAAACGCGAATCTGT-AAA-TCGCAACACATAAGT
1 CAAATTCGCAACGCG-AT-AGTCAAATTCGCAACACAAAAGT
521634 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
*
521674 CAAATTTCGCAACGCGGA-ATTTCAAATTCGCAAC
1 CAAA-TTCGCAACGC-GATA-GTCAAATTCGCAAC
521708 TGAATTTGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
38 2 0.03
39 5 0.08
40 32 0.49
41 11 0.17
42 15 0.23
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
Found at i:521759 original size:20 final size:19
Alignment explanation
Indices: 521690--521765 Score: 107
Period size: 19 Copynumber: 3.9 Consensus size: 19
521680 TCGCAACGCG
521690 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
* *
521709 GAATTTGAAATTCACAACT
1 GAATTTCAAATTCGCAACT
521728 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
* *
521747 AGATTTTCGAATTCGCAAC
1 -GAATTTCAAATTCGCAAC
521766 ACGAATTTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
19 34 0.68
20 16 0.32
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (19 bp):
GAATTTCAAATTCGCAACT
Found at i:521957 original size:14 final size:15
Alignment explanation
Indices: 521938--521975 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
521928 TCCCCATCTC
521938 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
521952 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
521968 TAATTTTT
1 TAATTTTT
521976 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:522881 original size:20 final size:20
Alignment explanation
Indices: 522842--522881 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
522832 TGCGATTTTG
* * *
522842 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
522862 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
522882 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:523234 original size:26 final size:22
Alignment explanation
Indices: 523209--523255 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
523199 TTTGAGAGAT
523209 GGAGAT-A-GACGGATTTCGCC
1 GGAGATGATGACGGATTTCGCC
*
523229 GGAGATGATTACGGATTTCGCC
1 GGAGATGATGACGGATTTCGCC
523251 GGAGA
1 GGAGA
523256 GAGTGAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (22 bp):
GGAGATGATGACGGATTTCGCC
Found at i:523403 original size:20 final size:20
Alignment explanation
Indices: 523348--523485 Score: 163
Period size: 20 Copynumber: 6.8 Consensus size: 20
523338 ATATTGTGTT
*
523348 TCGCGTTGCGAATTTGA-AA
1 TCGCGTTGCGAATTTGACTA
*
523367 TTCAGTGTTGCGAATTTGACTA
1 -TC-GCGTTGCGAATTTGACTA
* *
523389 TCGCTTTGTGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
523409 TCGCGTTGCGGATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
523429 TCGCGTTGCGGATTTGACTA
1 TCGCGTTGCGAATTTGACTA
523449 TCGCGTTGCGAATTTGACT-
1 TCGCGTTGCGAATTTGACTA
* *
523468 TCTGTGTTGCGAAATTGA
1 TC-GCGTTGCGAATTTGA
523486 AAATTTGGTT
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 85 0.82
21 16 0.15
22 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:523497 original size:60 final size:60
Alignment explanation
Indices: 523348--523524 Score: 162
Period size: 60 Copynumber: 2.9 Consensus size: 60
523338 ATATTGTGTT
* * * * *
523348 TCGCGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCTTTGTGAATTTGACTA
1 TCGCGTTGCGAAATTGAAAATC-GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTA
* * ** *
523409 TCGCGTTGCGGATTTGACTATCGCGTTGCGGATTTGACTATCGCGTTGCGAATTTGACT-
1 TCGCGTTGCGAAATTGAAAATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTA
* * * * *
523468 TCTGTGTTGCGAAATTGAAAATTTG-GTTGCGAAATTGGAGT-TCGTGTTGCGAATTTG
1 TC-GCGTTGCGAAATTGAAAA-TCGCGTTGCG-AATTTGACTATCGCGTTGCGAATTTG
523525 TTGGTCATTT
Statistics
Matches: 95, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
59 2 0.02
60 67 0.71
61 26 0.27
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGAAATTGAAAATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTA
Found at i:523516 original size:20 final size:20
Alignment explanation
Indices: 523453--523520 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
523443 TGACTATCGC
* *
523453 GTTGCG-AATTTGACTTCTGT
1 GTTGCGAAATTGGAATTC-GT
* *
523473 GTTGCGAAATTGAAAATTTG-
1 GTTGCGAAATTG-GAATTCGT
*
523493 GTTGCGAAATTGGAGTTCGT
1 GTTGCGAAATTGGAATTCGT
523513 GTTGCGAA
1 GTTGCGAA
523521 TTTGTTGGTC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 4 0.11
20 26 0.68
21 5 0.13
22 3 0.08
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.37
Consensus pattern (20 bp):
GTTGCGAAATTGGAATTCGT
Found at i:523906 original size:27 final size:27
Alignment explanation
Indices: 523869--523940 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
523859 GTTGTTAAAT
*
523869 TTAATTATAATTAGAAATCGGAAAAAA
1 TTAATTCTAATTAGAAATCGGAAAAAA
523896 TTAATTCTAATTAGAAATCGGAAAAAA
1 TTAATTCTAATTAGAAATCGGAAAAAA
*
523923 ATAATTCTAATTAGAAAT
1 TTAATTCTAATTAGAAAT
523941 GATTCCTTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.32
Consensus pattern (27 bp):
TTAATTCTAATTAGAAATCGGAAAAAA
Found at i:527323 original size:10 final size:10
Alignment explanation
Indices: 527287--527316 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
527277 TCCGACGGGT
527287 TTCGATCCGA
1 TTCGATCCGA
527297 TTCGATCCGA
1 TTCGATCCGA
527307 TTCGATCCGA
1 TTCGATCCGA
527317 CCCGATCGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (10 bp):
TTCGATCCGA
Found at i:528934 original size:2 final size:2
Alignment explanation
Indices: 528927--528977 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
528917 TCAATCTAAA
528927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
528969 AT AT AT AT A
1 AT AT AT AT A
528978 GGTTTCCTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:529836 original size:23 final size:22
Alignment explanation
Indices: 529767--529836 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
529757 TTATGAAAAA
*
529767 TAATATAATTAATAATT-TATTT
1 TAAT-TAATTTATAATTATATTT
* ** *
529789 TAAATAATTTATCGTTAGATTTT
1 TAATTAATTTATAATTATA-TTT
529812 TAATTAATTTATAATTATATGTT
1 TAATTAATTTATAATTATAT-TT
529835 TA
1 TA
529837 GTCTTTTAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
21 9 0.25
22 5 0.14
23 22 0.61
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (22 bp):
TAATTAATTTATAATTATATTT
Found at i:530219 original size:16 final size:15
Alignment explanation
Indices: 530181--530232 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
530171 ATAAATTTTA
530181 AAAATAATATTAAAAGTT
1 AAAA-AATA-TAAAA-TT
* *
530199 TAAAATTATAAAACTT
1 AAAAAATATAAAA-TT
530215 AAAAAATATAAAATT
1 AAAAAATATAAAATT
530230 AAA
1 AAA
530233 TGATTAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 5 0.17
16 18 0.62
17 3 0.10
18 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAAAATATAAAATT
Found at i:531594 original size:23 final size:23
Alignment explanation
Indices: 531568--531612 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
531558 AAAAGTTAGG
*
531568 AAAAATATGCCACAAAGACAGAA
1 AAAAACATGCCACAAAGACAGAA
* *
531591 AAAAACATGTCATAAAGACAGA
1 AAAAACATGCCACAAAGACAGA
531613 GCTATTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.60, C:0.16, G:0.13, T:0.11
Consensus pattern (23 bp):
AAAAACATGCCACAAAGACAGAA
Found at i:532059 original size:21 final size:21
Alignment explanation
Indices: 532030--532069 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
532020 AATAAAGCGC
* *
532030 TACCTAAAACATTATTTTTTA
1 TACCGAAAACATTAATTTTTA
*
532051 TACCGAAAATATTAATTTT
1 TACCGAAAACATTAATTTT
532070 AGACGCTATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (21 bp):
TACCGAAAACATTAATTTTTA
Found at i:532105 original size:14 final size:14
Alignment explanation
Indices: 532086--532115 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
532076 TATCTAAAAT
532086 GTTTAAAATTTCCG
1 GTTTAAAATTTCCG
532100 GTTTAAAATTTCCG
1 GTTTAAAATTTCCG
532114 GT
1 GT
532116 AAAACCTTAC
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:0.17, T:0.43
Consensus pattern (14 bp):
GTTTAAAATTTCCG
Found at i:537088 original size:33 final size:33
Alignment explanation
Indices: 537051--537144 Score: 116
Period size: 34 Copynumber: 2.8 Consensus size: 33
537041 TAATGACTTA
* * *
537051 TAATTTCTTATGTATATGTATAATATATGTTTG
1 TAATTTCTTAAGTATATGTACAATATATCTTTG
* *
537084 TAATTTCTTACGTATATGTAGAATATAATCTTTG
1 TAATTTCTTAAGTATATGTACAATAT-ATCTTTG
* *
537118 TAAATTCTTAAGCATATGTACAATATA
1 TAATTTCTTAAGTATATGTACAATATA
537145 ATTAGTCTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 25 0.47
34 28 0.53
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.47
Consensus pattern (33 bp):
TAATTTCTTAAGTATATGTACAATATATCTTTG
Found at i:539885 original size:51 final size:51
Alignment explanation
Indices: 539813--539919 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 51
539803 ATTTCAATCA
539813 ATTCCAAGGATTCTTGCTGGTACCAATACTGATACTGCTACTATCCCTTCC
1 ATTCCAAGGATTCTTGCTGGTACCAATACTGATACTGCTACTATCCCTTCC
* *
539864 ATTCCTAGGATTCTTGCTGGTACTAATACTGATACTGCTACTATCCCTTCC
1 ATTCCAAGGATTCTTGCTGGTACCAATACTGATACTGCTACTATCCCTTCC
539915 ATTCC
1 ATTCC
539920 CAGTATTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.36
Consensus pattern (51 bp):
ATTCCAAGGATTCTTGCTGGTACCAATACTGATACTGCTACTATCCCTTCC
Found at i:550319 original size:21 final size:21
Alignment explanation
Indices: 550295--550334 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
550285 CCCCCTTTGA
*
550295 AGGGGAACCGATCCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
550316 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
550335 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.42, G:0.25, T:0.07
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:555667 original size:14 final size:13
Alignment explanation
Indices: 555643--555680 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
555633 TTTTATAATT
555643 TAAACTTAATATAA
1 TAAA-TTAATATAA
555657 GTAAATTAATATAA
1 -TAAATTAATATAA
555671 -AAATTAATAT
1 TAAATTAATAT
555681 TAAACCCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
14 9 0.39
15 4 0.17
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (13 bp):
TAAATTAATATAA
Found at i:564136 original size:21 final size:21
Alignment explanation
Indices: 564110--564155 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
564100 ACTTATATAT
564110 AAAAAAAATTCAATTAATACC
1 AAAAAAAATTCAATTAATACC
* *
564131 AAAAAAATTTCAATTAATATC
1 AAAAAAAATTCAATTAATACC
564152 AAAA
1 AAAA
564156 GTAGTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAAAATTCAATTAATACC
Found at i:572043 original size:374 final size:374
Alignment explanation
Indices: 570772--572649 Score: 3641
Period size: 374 Copynumber: 5.0 Consensus size: 374
570762 GCTTCGGCTG
*
570772 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAATTGAAAACCCAATGAAGGATTGGATCA
1 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
570837 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
66 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
570902 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
131 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
570967 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
196 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
571032 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
261 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
571097 AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAA
326 AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAA
571146 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
1 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
571211 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
66 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
571276 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
131 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
571341 CTTCCAGCCATATCCATATCCTTGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTC
196 CTTCCAGCCATATCC--A----TGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTC
*
571406 TATCTCCTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGATGACTAATAAACAGT
255 TATCTCCTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGT
571471 TCGTTTAGGCTTTTAGCCCATTTGACGGAGGAGCTAACATG-AAGTTAAAAATAA
320 TCGTTTAGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAA
571525 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
1 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
*
571590 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCATGATAAGCTTTATG
66 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
571655 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
131 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
571720 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
196 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
571785 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
261 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
*
571850 AGGCTTTTAGCCCATTTGACGTAGGAGCTAACATGAAAGTTAAAAATAA
326 AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAA
571899 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
1 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
571964 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
66 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
572029 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
131 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
* *
572094 ATTCCAGCCATATCCATGCCATTCTCTTTCTTTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
196 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
572159 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
261 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
572224 AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAA
326 AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAA
572273 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
1 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
572338 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
66 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
572403 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
131 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
572468 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
196 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
572533 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
261 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
572598 AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAA
326 AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAA
572647 TTT
1 TTT
572650 TATATTCACA
Statistics
Matches: 1486, Mismatches: 11, Indels: 14
0.98 0.01 0.01
Matches are distributed among these distances:
373 147 0.10
374 967 0.65
376 1 0.00
377 1 0.00
379 222 0.15
380 148 0.10
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (374 bp):
TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAA
Found at i:572626 original size:748 final size:749
Alignment explanation
Indices: 570772--572649 Score: 3643
Period size: 753 Copynumber: 2.5 Consensus size: 749
570762 GCTTCGGCTG
*
570772 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAATTGAAAACCCAATGAAGGATTGGATCA
1 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
570837 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
66 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
570902 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
131 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
570967 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
196 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
571032 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
261 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
571097 AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAATTTGGAATTTCATTTT
326 AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAATTTGGAATTTCATTTT
571162 TATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCAAAGATTTCATATTTTA
391 TATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCAAAGATTTCATATTTTA
571227 AATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATGGATGAAATACTGAGCA
456 AATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATGGATGAAATACTGAGCA
*
571292 TTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTGCTTCCAGCCATATCCA
521 TTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTGATTCCAGCCATATCCA
571357 TATCCTTGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTCCTAAATTTCT
586 -A--C-TGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTCCTAAATTTCT
*
571422 TCCTTCATATGCCCTCTAATTCAGGTCCGAGTGATGACTAATAAACAGTTCGTTTAGGCTTTTAG
647 TCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTTAGGCTTTTAG
571487 CCCATTTGACGGAGGAGCTAACATGAAGTTAAAAATAA
712 CCCATTTGACGGAGGAGCTAACATGAAGTTAAAAATAA
571525 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
1 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
*
571590 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCATGATAAGCTTTATG
66 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
571655 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
131 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
571720 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
196 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
571785 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
261 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
*
571850 AGGCTTTTAGCCCATTTGACGTAGGAGCTAACATGAAAGTTAAAAATAATTTGGAATTTCATTTT
326 AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAATTTGGAATTTCATTTT
571915 TATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCAAAGATTTCATATTTTA
391 TATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCAAAGATTTCATATTTTA
571980 AATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATGGATGAAATACTGAGCA
456 AATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATGGATGAAATACTGAGCA
572045 TTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTGATTCCAGCCATATCC-
521 TTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTGATTCCAGCCATATCCA
*
572109 A-TGCCATTCTCTTTCTTTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTCCTAAATTTCTTCCT
586 ACTGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTCCTAAATTTCTTCCT
572173 TCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTTAGGCTTTTAGCCCA
651 TCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTTAGGCTTTTAGCCCA
572238 TTTGACGGAGGAGCTAACATGAAAGTTAAAAATAA
716 TTTGACGGAGGAGCTAACATG-AAGTTAAAAATAA
572273 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
1 TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
572338 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
66 AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
572403 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
131 GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
572468 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
196 CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
572533 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
261 CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
572598 AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAATTT
326 AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAATTT
572650 TATATTCACA
Statistics
Matches: 1116, Mismatches: 8, Indels: 7
0.99 0.01 0.01
Matches are distributed among these distances:
747 147 0.13
748 388 0.35
751 1 0.00
753 580 0.52
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (749 bp):
TTTGGAATTTCATTTTTATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCA
AAGATTTCATATTTTAAATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATG
GATGAAATACTGAGCATTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTG
CTTCCAGCCATATCCATGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTC
CTAAATTTCTTCCTTCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTT
AGGCTTTTAGCCCATTTGACGGAGGAGCTAACATGAAAGTTAAAAATAATTTGGAATTTCATTTT
TATCGAACGATTTCAATCAAAACTGAAAACCCAATGAAGGATTGGATCAAAGATTTCATATTTTA
AATTAGAAAAAGGAAAAGGGAAACAAACCCGGCCGTGATAAGCTTTATGGATGAAATACTGAGCA
TTGCCCATTACACAGAGCATTCCAGCTATGATCCCCAGGGGAAGTGCTGATTCCAGCCATATCCA
ACTGCCATTCTCTTTCTGTTTTTCTTCTGTGCTTCTCCCTTTTTCTATCTCCTAAATTTCTTCCT
TCATATGCCCTCTAATTCAGGTCCGAGTGACGACTAATAAACAGTTCGTTTAGGCTTTTAGCCCA
TTTGACGGAGGAGCTAACATGAAGTTAAAAATAA
Found at i:587176 original size:21 final size:22
Alignment explanation
Indices: 587152--587198 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
587142 AGAAGCTCGT
*
587152 AAAATTAGCAACCAAAA-AAAA
1 AAAATTAACAACCAAAAGAAAA
*
587173 AAAATTAACAAGCAAAAGAAAA
1 AAAATTAACAACCAAAAGAAAA
587195 AAAA
1 AAAA
587199 ATCAAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.74, C:0.11, G:0.06, T:0.09
Consensus pattern (22 bp):
AAAATTAACAACCAAAAGAAAA
Found at i:592184 original size:23 final size:24
Alignment explanation
Indices: 592137--592185 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
592127 TTCGCGAACA
*
592137 AATGTGTTCATTTATATGTTCACG
1 AATGTGTTCATTTATAAGTTCACG
592161 AATGTGTTCATTTA-AAGTTCACG
1 AATGTGTTCATTTATAAGTTCACG
592184 AA
1 AA
592186 CATGTTCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (24 bp):
AATGTGTTCATTTATAAGTTCACG
Found at i:592191 original size:23 final size:24
Alignment explanation
Indices: 592141--592193 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
592131 CGAACAAATG
* **
592141 TGTTCATTTATATGTTCACGAATG
1 TGTTCATTTATAAGTTCACGAACA
592165 TGTTCATTTA-AAGTTCACGAACA
1 TGTTCATTTATAAGTTCACGAACA
592188 TGTTCA
1 TGTTCA
592194 CTTACGGTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (24 bp):
TGTTCATTTATAAGTTCACGAACA
Found at i:597944 original size:2 final size:2
Alignment explanation
Indices: 597937--597964 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
597927 GGTGCAAGTT
597937 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
597965 AATTTATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:600884 original size:183 final size:184
Alignment explanation
Indices: 600573--600959 Score: 638
Period size: 183 Copynumber: 2.1 Consensus size: 184
600563 TTTTCTAATT
* * * *
600573 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
*
600637 TATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
600702 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 GAATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTAAGCCCATATGTTA
600756 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAAATAATTTAAATAATATATAA
* *
600820 TTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAAATTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
*
600884 TGAATCTTAAATTATTAATTTGGTTTTAAATGATTTGGGTTAAGCCCATATGTTA
130 TGAATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTAAGCCCATATGTTA
600939 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
600960 AAAATTTAAT
Statistics
Matches: 191, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
182 2 0.01
183 124 0.65
184 65 0.34
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GAATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTAAGCCCATATGTTA
Found at i:603009 original size:30 final size:30
Alignment explanation
Indices: 602975--603047 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
602965 GTCAAATTGA
602975 TATTTTATATAAACTTT-AAGATTAAATTAG
1 TATTTTATATAAACTTTAAAGA-TAAATTAG
* *
603005 TATTTTATGTAAAGTTTAAAGATAAATTAG
1 TATTTTATATAAACTTTAAAGATAAATTAG
* *
603035 TATATTATCTAAA
1 TATTTTATATAAA
603048 ATTCATGGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 34 0.89
31 4 0.11
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (30 bp):
TATTTTATATAAACTTTAAAGATAAATTAG
Found at i:603267 original size:14 final size:14
Alignment explanation
Indices: 603248--603276 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
603238 TCCTTAGACT
603248 TGAATCAACGTCGG
1 TGAATCAACGTCGG
603262 TGAATCAACGTCGG
1 TGAATCAACGTCGG
603276 T
1 T
603277 TTACTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (14 bp):
TGAATCAACGTCGG
Found at i:612387 original size:14 final size:14
Alignment explanation
Indices: 612368--612397 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
612358 CGAAAGTTTT
612368 TTCTTTTCAAGTTA
1 TTCTTTTCAAGTTA
612382 TTCTTTTCAAGTTA
1 TTCTTTTCAAGTTA
612396 TT
1 TT
612398 GACAACCATA
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:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (14 bp):
TTCTTTTCAAGTTA
Found at i:614892 original size:77 final size:76
Alignment explanation
Indices: 614765--614927 Score: 245
Period size: 77 Copynumber: 2.1 Consensus size: 76
614755 ATATGTTTAA
* * *
614765 ATTTATAATATCTTAAATATGGATGGGCCAAGTGTCACATTGGACCATCAAAACGATCACAACTA
1 ATTTATAATACCTTAAATATGGATGGGCCAAGTGTCACACTGGACCATCAAAACGATCAAAACTA
614830 TAAATTTATTCT
66 T-AATTTATTCT
* * * *
614842 ATTTATAATACCTTAAATTTGGATGTGCCTAGTGTTACACTGGACCATCAAAACGATCAAAACTA
1 ATTTATAATACCTTAAATATGGATGGGCCAAGTGTCACACTGGACCATCAAAACGATCAAAACTA
614907 TAATTTATTCT
66 TAATTTATTCT
*
614918 ATTTAAAATA
1 ATTTATAATA
614928 TTGTGACACA
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
76 19 0.24
77 59 0.76
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (76 bp):
ATTTATAATACCTTAAATATGGATGGGCCAAGTGTCACACTGGACCATCAAAACGATCAAAACTA
TAATTTATTCT
Found at i:616287 original size:26 final size:26
Alignment explanation
Indices: 616210--616296 Score: 99
Period size: 26 Copynumber: 3.4 Consensus size: 26
616200 TCTACAGTAA
616210 ATTTTTAATTTTTAATTTAAATATAT
1 ATTTTTAATTTTTAATTTAAATATAT
* **
616236 A-TTCTAA--AATAATCCTTAAATATAT
1 ATTTTTAATTTTTAAT--TTAAATATAT
616261 ATTTTTAATTTTTAATTTAAATATAT
1 ATTTTTAATTTTTAATTTAAATATAT
*
616287 ATTTATAATT
1 ATTTTTAATT
616297 AAACATTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
23 4 0.08
25 16 0.33
26 25 0.51
28 4 0.08
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTTTTAATTTTTAATTTAAATATAT
Found at i:616306 original size:51 final size:51
Alignment explanation
Indices: 616210--616306 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
616200 TCTACAGTAA
* *
616210 ATTTTTAATTTTTAATTTAAATATATATTCTAAAATAATCCTTAAATATAT
1 ATTTTTAATTTTTAATTTAAATATATATTCTAAAATAAACATTAAATATAT
*
616261 ATTTTTAATTTTTAATTTAAATATATATT-TATAATTAAACATTAAA
1 ATTTTTAATTTTTAATTTAAATATATATTCTA-AAATAAACATTAAA
616307 CATCTAGTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
50 2 0.05
51 40 0.95
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (51 bp):
ATTTTTAATTTTTAATTTAAATATATATTCTAAAATAAACATTAAATATAT
Found at i:616322 original size:51 final size:51
Alignment explanation
Indices: 616216--616328 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
616206 GTAAATTTTT
* * * * **
616216 AATTTTTAATTTAAATATATATTCTAAAATAATCCTTAAATATATATTTTT
1 AATTTTTAATTTAAATATATATTCTAAAATAAACATTAAACATATAGTTGA
* *
616267 AATTTTTAATTTAAATATATATT-TATAATTAAACATTAAACATCTAGTTGA
1 AATTTTTAATTTAAATATATATTCTA-AAATAAACATTAAACATATAGTTGA
616318 AATTTTTAATT
1 AATTTTTAATT
616329 GAAAATAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 2 0.04
51 51 0.96
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (51 bp):
AATTTTTAATTTAAATATATATTCTAAAATAAACATTAAACATATAGTTGA
Found at i:616332 original size:13 final size:13
Alignment explanation
Indices: 616314--616355 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
616304 AAACATCTAG
616314 TTGAAATTTTTAA
1 TTGAAATTTTTAA
* **
616327 TTGAAA-ATAAAA
1 TTGAAATTTTTAA
616339 TTGAAATTTTTAA
1 TTGAAATTTTTAA
616352 TTGA
1 TTGA
616356 GTATAAAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (13 bp):
TTGAAATTTTTAA
Found at i:616342 original size:25 final size:25
Alignment explanation
Indices: 616314--616365 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
616304 AAACATCTAG
616314 TTGAAATTTTTAATTGAAAATAAAA
1 TTGAAATTTTTAATTGAAAATAAAA
**
616339 TTGAAATTTTTAATTGAGTATAAAA
1 TTGAAATTTTTAATTGAAAATAAAA
616364 TT
1 TT
616366 TATAATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (25 bp):
TTGAAATTTTTAATTGAAAATAAAA
Found at i:623392 original size:2 final size:2
Alignment explanation
Indices: 623382--623413 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
623372 TATTTTTTTA
623382 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
623414 ATAGCTTGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:642813 original size:75 final size:75
Alignment explanation
Indices: 642734--642966 Score: 210
Period size: 75 Copynumber: 3.1 Consensus size: 75
642724 CTAACACATC
642734 TGCTTGTTCAGTCCCCGTGCTATTTGGTTTCTTTCCAGTATCTGTATTCTCTTTCTTCTCCTCTT
1 TGCTTGTTCAGTCCCCGTGCTATTTGGTTTCTTTCCAGTATCTGTATTCTCTTTCTTCTCCTCTT
642799 TAGCCTTCAA
66 TAGCCTTCAA
** ** * * * * * *
642809 TGCTT-TATCA-T--TGGTGGAATTTGAAGTTGAATTGTTTCTACTA-CTTGCATTATTTTTCTT
1 TGCTTGT-TCAGTCCCCGTGCTATTTG--G-T---TTCTTTCCAGTATC-TGTATTCTCTTTCTT
* * *
642869 CTCCTCCTCTAACACATC--
58 CTCCT-CTTTAGC-CTTCAA
642887 TGCTTGTTCAGTCCCCGTGCTATTTGGTTTCTTTCCAGTATCTGTATTCTCTTTCTTCTCCTCTT
1 TGCTTGTTCAGTCCCCGTGCTATTTGGTTTCTTTCCAGTATCTGTATTCTCTTTCTTCTCCTCTT
642952 TAGCCTTCAA
66 TAGCCTTCAA
642962 TGCTT
1 TGCTT
642967 TATCATTGGT
Statistics
Matches: 115, Mismatches: 26, Indels: 34
0.66 0.15 0.19
Matches are distributed among these distances:
72 8 0.07
73 3 0.03
74 8 0.07
75 40 0.35
76 1 0.01
77 1 0.01
78 35 0.30
79 8 0.07
80 3 0.03
81 8 0.07
ACGTcount: A:0.14, C:0.25, G:0.13, T:0.48
Consensus pattern (75 bp):
TGCTTGTTCAGTCCCCGTGCTATTTGGTTTCTTTCCAGTATCTGTATTCTCTTTCTTCTCCTCTT
TAGCCTTCAA
Found at i:642989 original size:153 final size:153
Alignment explanation
Indices: 642711--643027 Score: 625
Period size: 153 Copynumber: 2.1 Consensus size: 153
642701 CTTCTTCTTA
*
642711 TTCTTATCCTCCTCTAACACATCTGCTTGTTCAGTCCCCGTGCTATTTGGTTTCTTTCCAGTATC
1 TTCTTCTCCTCCTCTAACACATCTGCTTGTTCAGTCCCCGTGCTATTTGGTTTCTTTCCAGTATC
642776 TGTATTCTCTTTCTTCTCCTCTTTAGCCTTCAATGCTTTATCATTGGTGGAATTTGAAGTTGAAT
66 TGTATTCTCTTTCTTCTCCTCTTTAGCCTTCAATGCTTTATCATTGGTGGAATTTGAAGTTGAAT
642841 TGTTTCTACTACTTGCATTATTT
131 TGTTTCTACTACTTGCATTATTT
642864 TTCTTCTCCTCCTCTAACACATCTGCTTGTTCAGTCCCCGTGCTATTTGGTTTCTTTCCAGTATC
1 TTCTTCTCCTCCTCTAACACATCTGCTTGTTCAGTCCCCGTGCTATTTGGTTTCTTTCCAGTATC
642929 TGTATTCTCTTTCTTCTCCTCTTTAGCCTTCAATGCTTTATCATTGGTGGAATTTGAAGTTGAAT
66 TGTATTCTCTTTCTTCTCCTCTTTAGCCTTCAATGCTTTATCATTGGTGGAATTTGAAGTTGAAT
642994 TGTTTCTACTACTTGCATTATTT
131 TGTTTCTACTACTTGCATTATTT
643017 TTCTTCTCCTC
1 TTCTTCTCCTC
643028 GTTATCCTCC
Statistics
Matches: 163, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 163 1.00
ACGTcount: A:0.15, C:0.25, G:0.13, T:0.47
Consensus pattern (153 bp):
TTCTTCTCCTCCTCTAACACATCTGCTTGTTCAGTCCCCGTGCTATTTGGTTTCTTTCCAGTATC
TGTATTCTCTTTCTTCTCCTCTTTAGCCTTCAATGCTTTATCATTGGTGGAATTTGAAGTTGAAT
TGTTTCTACTACTTGCATTATTT
Found at i:644554 original size:14 final size:14
Alignment explanation
Indices: 644535--644591 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
644525 TTATACTTTC
644535 ATAATATTTAAAAA
1 ATAATATTTAAAAA
*
644549 ATAATAATTTTAAAA
1 ATAAT-ATTTAAAAA
* * *
644564 GTAAAAATTAAAAA
1 ATAATATTTAAAAA
*
644578 ATATATATATAAAA
1 ATA-ATATTTAAAA
644592 GTCCGTCGTT
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
14 14 0.44
15 18 0.56
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
ATAATATTTAAAAA
Found at i:647080 original size:10 final size:10
Alignment explanation
Indices: 647065--647099 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
647055 AAAGTTTTGA
647065 TAGTTTAGAT
1 TAGTTTAGAT
647075 TAGTTTAGAT
1 TAGTTTAGAT
647085 TAGTTTAGAT
1 TAGTTTAGAT
647095 TAGTT
1 TAGTT
647100 CGTTTTAGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (10 bp):
TAGTTTAGAT
Found at i:648396 original size:26 final size:26
Alignment explanation
Indices: 648364--648425 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
648354 TGGATTTGTA
* *
648364 AAATGACCAAAATACTCCTAATATGG
1 AAATGACCAAAATACCCCTAATATGC
**
648390 AAATGACCAAAATACCCCTGGTATGC
1 AAATGACCAAAATACCCCTAATATGC
648416 AAATGACCAA
1 AAATGACCAA
648426 GAATTTCACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (26 bp):
AAATGACCAAAATACCCCTAATATGC
Found at i:651215 original size:60 final size:60
Alignment explanation
Indices: 651151--651280 Score: 152
Period size: 60 Copynumber: 2.2 Consensus size: 60
651141 TAGAAAAAGG
** * *
651151 GTCATAGTTTAGGAATGAAAATAGAACATTCAAATTTTTAAGGATTAATTTATAATGAGA
1 GTCATAGTTTAGGAATGAAAATAGAACATTCAAAAGTTTAAGGATCAATTTAAAATGAGA
* * * * * * *
651211 GTCATAGTTTGGGGATGAAATTGGAGCATTTAAAAGTTTAAGGATCAATTTAAAATGAGG
1 GTCATAGTTTAGGAATGAAAATAGAACATTCAAAAGTTTAAGGATCAATTTAAAATGAGA
*
651271 GTTATAGTTT
1 GTCATAGTTT
651281 GGGGACATAT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (60 bp):
GTCATAGTTTAGGAATGAAAATAGAACATTCAAAAGTTTAAGGATCAATTTAAAATGAGA
Found at i:660929 original size:22 final size:20
Alignment explanation
Indices: 660904--660949 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
660894 TTTATTTATG
660904 TATTAAAACAAAAATACCATAA
1 TATT-AAACAAAAATACCAT-A
*
660926 TATTATACAAAAATACCATA
1 TATTAAACAAAAATACCATA
660946 TATT
1 TATT
660950 TTTTATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 14 0.61
22 4 0.17
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (20 bp):
TATTAAACAAAAATACCATA
Found at i:660948 original size:20 final size:21
Alignment explanation
Indices: 660911--660949 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
660901 ATGTATTAAA
660911 ACAAAAATACCATAATATTAT
1 ACAAAAATACCATAATATTAT
660932 ACAAAAATACCAT-ATATT
1 ACAAAAATACCATAATATT
660950 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ACAAAAATACCATAATATTAT
Found at i:664891 original size:14 final size:14
Alignment explanation
Indices: 664872--664902 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
664862 AAAGATAATG
664872 AGAAGAAGCTGTTC
1 AGAAGAAGCTGTTC
664886 AGAAGAAGCTGTTC
1 AGAAGAAGCTGTTC
664900 AGA
1 AGA
664903 GTGAGAGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.29, T:0.19
Consensus pattern (14 bp):
AGAAGAAGCTGTTC
Found at i:668506 original size:21 final size:21
Alignment explanation
Indices: 668480--668519 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
668470 CGAATTAAAT
668480 GTAGTAATTACGGGCAACCAC
1 GTAGTAATTACGGGCAACCAC
668501 GTAGTAATTACGGGCAACC
1 GTAGTAATTACGGGCAACC
668520 GTCACCTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (21 bp):
GTAGTAATTACGGGCAACCAC
Done.