Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 38
Found at i:2246897 original size:11 final size:11
Alignment explanation
Indices: 2246881--2246910 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2246871 AGGGGCTCTC
2246881 GGCCAGTGGGT
1 GGCCAGTGGGT
2246892 GGCCAGTGGGT
1 GGCCAGTGGGT
*
2246903 GGTCAGTG
1 GGCCAGTG
2246911 TTGTGGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.17, G:0.53, T:0.20
Consensus pattern (11 bp):
GGCCAGTGGGT
Found at i:2247903 original size:99 final size:96
Alignment explanation
Indices: 2247708--2247906 Score: 276
Period size: 99 Copynumber: 2.0 Consensus size: 96
2247698 TACTAATTTC
*
2247708 TAACTCTAACTTTTTATTAATTTGTTCAAATTATTATATGACCTTGCGGTGACCCGATCCGGGAT
1 TAACTCTAACTTTTTATTAATTTGTTCAAATTATTATACGACCTTGCGGTGACCCGATCCGGGAT
** *
2247773 ACGACAAGCATTATTATGGTCCAGGCTCTAT
66 ACGACAAGCATTATTACAGTCCAGGCCCTAT
**
2247804 TAACTCCTAACATTTTTCATTAATTTGTTTGAATTATTATACGACCTTGCGGTGACCCGATCCGG
1 TAACT-CTAAC-TTTTT-ATTAATTTGTTCAAATTATTATACGACCTTGCGGTGACCCGATCCGG
*
2247869 GATACGATACA-CATTATTACAGT-CAGGACCCTAT
63 GATACGACA-AGCATTATTACAGTCCAGG-CCCTAT
2247903 TAAC
1 TAAC
2247907 AACTAATTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
96 5 0.05
97 5 0.05
98 9 0.10
99 71 0.78
100 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (96 bp):
TAACTCTAACTTTTTATTAATTTGTTCAAATTATTATACGACCTTGCGGTGACCCGATCCGGGAT
ACGACAAGCATTATTACAGTCCAGGCCCTAT
Found at i:2248171 original size:14 final size:14
Alignment explanation
Indices: 2248152--2248190 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2248142 TACTTTTTAT
*
2248152 TTATTTAGTTTCAG
1 TTATTTAATTTCAG
2248166 TTATTTAATTTCA-
1 TTATTTAATTTCAG
2248179 TTACTTTAATTT
1 TTA-TTTAATTT
2248191 ACTATTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 3 0.13
14 20 0.87
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (14 bp):
TTATTTAATTTCAG
Found at i:2251571 original size:9 final size:9
Alignment explanation
Indices: 2251557--2251620 Score: 60
Period size: 9 Copynumber: 7.0 Consensus size: 9
2251547 TTGACAACGC
2251557 AGAAAAAAG
1 AGAAAAAAG
2251566 AGAAAAAA-
1 AGAAAAAAG
2251574 AGAAGAAAA-
1 AGAA-AAAAG
2251583 AGAGAAAAAG
1 AGA-AAAAAG
*
2251593 AAAAAAAAG
1 AGAAAAAAG
* *
2251602 AAGAAGATAG
1 -AGAAAAAAG
2251612 AGAAAAAAG
1 AGAAAAAAG
2251621 TAAAAGTGAG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
8 4 0.09
9 32 0.71
10 9 0.20
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:2251577 original size:8 final size:8
Alignment explanation
Indices: 2251557--2251599 Score: 59
Period size: 8 Copynumber: 5.1 Consensus size: 8
2251547 TTGACAACGC
2251557 AGAAAAAA
1 AGAAAAAA
2251565 GAGAAAAAA
1 -AGAAAAAA
2251574 AGAAGAAAA
1 AGAA-AAAA
*
2251583 AGAGAAAA
1 AGAAAAAA
2251591 AGAAAAAA
1 AGAAAAAA
2251599 A
1 A
2251600 AGAAGAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 16 0.52
9 15 0.48
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:2251584 original size:19 final size:18
Alignment explanation
Indices: 2251559--2251619 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
2251549 GACAACGCAG
*
2251559 AAAAAAGAGAAAAAAAGA
1 AAAAAAGAGAAAAAGAGA
2251577 AGAAAAAGAGAAAAAGA-A
1 A-AAAAAGAGAAAAAGAGA
*
2251595 AAAAAAGAAGAAGATAGAGA
1 AAAAAAG-AGAA-AAAGAGA
2251615 AAAAA
1 AAAAA
2251620 GTAAAAGTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 6 0.16
18 7 0.19
19 18 0.49
20 6 0.16
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAAAGAGAAAAAGAGA
Found at i:2251590 original size:17 final size:18
Alignment explanation
Indices: 2251559--2251602 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
2251549 GACAACGCAG
2251559 AAAAAAGAGAAAAAAAGAA
1 AAAAAAGAG-AAAAAAGAA
*
2251578 GAAAAAGAG-AAAAAGAA
1 AAAAAAGAGAAAAAAGAA
2251595 AAAAAAGA
1 AAAAAAGA
2251603 AGAAGATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
19 8 0.35
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAGAGAAAAAAGAA
Found at i:2251597 original size:26 final size:28
Alignment explanation
Indices: 2251560--2251618 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 28
2251550 ACAACGCAGA
2251560 AAAAAGAGAAAAAAAGAAGAA-AAAGAG
1 AAAAAGAGAAAAAAAGAAGAAGAAAGAG
*
2251587 AAAAAGA-AAAAAAAGAAGAAGATAGAG
1 AAAAAGAGAAAAAAAGAAGAAGAAAGAG
2251614 AAAAA
1 AAAAA
2251619 AGTAAAAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (28 bp):
AAAAAGAGAAAAAAAGAAGAAGAAAGAG
Found at i:2251625 original size:27 final size:26
Alignment explanation
Indices: 2251560--2251625 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
2251550 ACAACGCAGA
2251560 AAAAAGAGAAAAAAAGAAGAAAAAGAG
1 AAAAA-AGAAAAAAAGAAGAAAAAGAG
*
2251587 -AAAAAGAAAAAAAAGAAGAAGATAGAG
1 AAAAAAG-AAAAAAAGAAGAA-AAAGAG
*
2251614 AAAAAAGTAAAA
1 AAAAAAGAAAAA
2251626 GTGAGAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 2 0.06
26 17 0.50
27 9 0.26
28 6 0.18
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (26 bp):
AAAAAAGAAAAAAAGAAGAAAAAGAG
Found at i:2251667 original size:20 final size:20
Alignment explanation
Indices: 2251557--2251667 Score: 77
Period size: 21 Copynumber: 5.3 Consensus size: 20
2251547 TTGACAACGC
*
2251557 AGAAAAAAGAGAAA-AAAAGA
1 AGAAAAGAGAGAAAGAAAA-A
*
2251577 AGAAAAAGAGAAAAAGAAAAA
1 AG-AAAAGAGAGAAAGAAAAA
2251598 A-AAGAAGA-AGATAGAGAAAAA
1 AGAA-AAGAGAGA-A-AGAAAAA
**
2251619 AGTAAAAGTGAGAGAAAAGAAATC
1 AG-AAAA--GAGAG-AAAGAAAAA
2251643 A-AAAAGAGAGAAAGAAAAA
1 AGAAAAGAGAGAAAGAAAAA
2251662 AGAAAA
1 AGAAAA
2251668 TAGATCAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
19 12 0.17
20 16 0.22
21 20 0.28
22 10 0.14
23 2 0.03
24 8 0.11
25 3 0.04
26 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.22, T:0.04
Consensus pattern (20 bp):
AGAAAAGAGAGAAAGAAAAA
Found at i:2253638 original size:54 final size:51
Alignment explanation
Indices: 2253575--2253740 Score: 156
Period size: 54 Copynumber: 3.1 Consensus size: 51
2253565 CCAAACAATG
*
2253575 TGATGTTTTCAAATGAATTTTGAGAGAAACTAAGCCTAGTTTTTAGGGTTTTCT
1 TGAT-TTTTCAAATGAATTTTGA-AGAAACTAAGCCTA-TTTTTAGGGGTTTCT
* *
2253629 TGATATTTTCAAATGGATTTTGTAATG-AACTAATCCATATTTTTAGGGGTTTCT
1 TGAT-TTTTCAAATGAATTTTG-AA-GAAACTAAGCC-TATTTTTAGGGGTTTCT
* ** *
2253683 TGATTACTTCTGATGAATTTTTAA-AATAGCTAAGCCTAATTTTTAGGGGTTTCT
1 TGATT-TTTCAAATGAATTTTGAAGAA-A-CTAAGCCT-ATTTTTAGGGGTTTCT
2253737 TGAT
1 TGAT
2253741 GATAACCATA
Statistics
Matches: 94, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
52 1 0.01
53 5 0.05
54 84 0.89
55 4 0.04
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.45
Consensus pattern (51 bp):
TGATTTTTCAAATGAATTTTGAAGAAACTAAGCCTATTTTTAGGGGTTTCT
Found at i:2254703 original size:38 final size:36
Alignment explanation
Indices: 2254661--2254745 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 36
2254651 TACTTTGTCT
* *
2254661 TTCTTAGGATAATTTTTTTAGAAAAT-TCATTTGAGTCA
1 TTCTTAGGAT-ATTTATCTAG--AATGTCATTTGAGTCA
* *
2254699 TTCTTATGACTATTTATCTAGAATGTCGTTTGAGTCA
1 TTCTTAGGA-TATTTATCTAGAATGTCATTTGAGTCA
2254736 TTCTTAGGAT
1 TTCTTAGGAT
2254746 TGTGTCCCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
36 4 0.10
37 19 0.47
38 16 0.40
39 1 0.03
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.47
Consensus pattern (36 bp):
TTCTTAGGATATTTATCTAGAATGTCATTTGAGTCA
Found at i:2255421 original size:139 final size:139
Alignment explanation
Indices: 2255251--2255866 Score: 710
Period size: 137 Copynumber: 4.5 Consensus size: 139
2255241 GAATGGAACG
* * *
2255251 TAATGAGAAGAACTCGTCTAATAAGGGAGAAGAAGTTCATAATGAGAATAAATAT-TTCAACCTT
1 TAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTCATAATGAGAATAACT-TGTTCAACCTT
* * * * * *
2255315 AGCTCTATTTATAGTATATGGAGTTGAATCAGCGACAACTCACTAGAGGGATCAACATCTCCAAT
65 AGCTCGATTCATAGCATATGGAGTTGAATCAGCAACACCTCACTAGAGGGATCAACATTTCCAAT
*
2255380 TGAGAGTTCA
130 GGAGAGTTCA
* * *
2255390 TAATAAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATTAGAATAACTTGTTCAACCTTA
1 TAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTTA
* * *
2255455 GCTCGATTCATCGCATATGGAGTTGAATCAACAACACCTCACTCA-AGGGATCAACATTTCCAGT
66 GCTCGATTCATAGCATATGGAGTTGAATCAGCAACACCTCACT-AGAGGGATCAACATTTCCAAT
*
2255519 GTAGAGTTCA
130 GGAGAGTTCA
* ** * ** *
2255529 TAATGATAAGAACTCGTCTGATGA--GAGAAAAAAATCATAATGAGAAGAACTTGTTCAACCTTA
1 TAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTTA
* ** * *
2255592 GCTCGATTCATCGCATATGGAGTTGAATCAGTGACACCTAACCT-GAGGGATCAACGTTTCCAAT
66 GCTCGATTCATAGCATATGGAGTTGAATCAGCAACACCTCA-CTAGAGGGATCAACATTTCCAAT
2255656 GGAGAGTTCA
130 GGAGAGTTCA
* * * * *
2255666 TAATGAGAAAAACTCGTCCGATGAGGGAGAAGAAGTTCATAATAAG-A-AACCTGTTCAACATTA
1 TAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTTA
* * * * * *
2255729 GCTCAATTAATCA-TATATGGAGTTGAATCAGCAACACCTTACTCGAGGGATCAACATTTCCAGT
66 GCTCGATTCAT-AGCATATGGAGTTGAATCAGCAACACCTCACTAGAGGGATCAACATTTCCAAT
*
2255793 GGAGAGTTTA
130 GGAGAGTTCA
* * * * *
2255803 TAATGAGAAGAACTCATCCGAA-CAAGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTT
1 TAATGAGAAGAACTCGTCC-AATGAGGGAGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTT
2255867 TACTCAAATC
Statistics
Matches: 404, Mismatches: 62, Indels: 22
0.83 0.13 0.05
Matches are distributed among these distances:
136 2 0.00
137 229 0.57
138 6 0.01
139 166 0.41
140 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (139 bp):
TAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTTA
GCTCGATTCATAGCATATGGAGTTGAATCAGCAACACCTCACTAGAGGGATCAACATTTCCAATG
GAGAGTTCA
Found at i:2255835 original size:276 final size:278
Alignment explanation
Indices: 2255251--2255866 Score: 823
Period size: 276 Copynumber: 2.2 Consensus size: 278
2255241 GAATGGAACG
* * * *
2255251 TAATGAGAAGAACTCGT-CTAATAAGGGAGAAGAAGTTCATAATGAGAATAAATAT-TTCAACCT
1 TAATGAGAAGAACTCGTCCGAATAA-GGAGAAAAAGTTCATAATGAGAAGAACT-TGTTCAACCT
* * * *
2255314 TAGCTCTATTTATAGTATATGGAGTTGAATCAGCGACAACTCACTAGAGGGATCAACATCTCCAA
64 TAGCTCGATTCATAGCATATGGAGTTGAATCAGCGACAACTAACTAGAGGGATCAACATCTCCAA
* * * *
2255379 TTGAGAGTTCATAATAAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATTAGAATAACTT
129 TGGAGAGTTCATAATAAGAAAAACTCATCCAATGAGGGAGAAGAAGTTCATAATAAGAATAACCT
* * * *
2255444 GTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAACACCTCACTCAAGGGATCAA
194 GTTCAACATTAGCTCAATTAATCACATATGGAGTTGAATCAACAACACCTCACTCAAGGGATCAA
*
2255509 CATTTCCAGTGTAGAGTTCA
259 CATTTCCAGTGGAGAGTTCA
* * * **
2255529 TAATGATAAGAACTCGTCTG-ATGA-GAGAAAAAAATCATAATGAGAAGAACTTGTTCAACCTTA
1 TAATGAGAAGAACTCGTCCGAATAAGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
* * * * *
2255592 GCTCGATTCATCGCATATGGAGTTGAATCAGTGACACCTAACCT-GAGGGATCAACGTTTCCAAT
66 GCTCGATTCATAGCATATGGAGTTGAATCAGCGACAACTAA-CTAGAGGGATCAACATCTCCAAT
* * *
2255656 GGAGAGTTCATAATGAGAAAAACTCGTCCGATGAGGGAGAAGAAGTTCATAATAAG-A-AACCTG
130 GGAGAGTTCATAATAAGAAAAACTCATCCAATGAGGGAGAAGAAGTTCATAATAAGAATAACCTG
* * * *
2255719 TTCAACATTAGCTCAATTAATCATATATGGAGTTGAATCAGCAACACCTTACTCGAGGGATCAAC
195 TTCAACATTAGCTCAATTAATCACATATGGAGTTGAATCAACAACACCTCACTCAAGGGATCAAC
*
2255784 ATTTCCAGTGGAGAGTTTA
260 ATTTCCAGTGGAGAGTTCA
* *
2255803 TAATGAGAAGAACTCATCCGAACAAGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTT
1 TAATGAGAAGAACTCGTCCGAATAAGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTT
2255867 TACTCAAATC
Statistics
Matches: 291, Mismatches: 42, Indels: 12
0.84 0.12 0.03
Matches are distributed among these distances:
274 96 0.33
275 4 0.01
276 170 0.58
277 2 0.01
278 19 0.07
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (278 bp):
TAATGAGAAGAACTCGTCCGAATAAGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
GCTCGATTCATAGCATATGGAGTTGAATCAGCGACAACTAACTAGAGGGATCAACATCTCCAATG
GAGAGTTCATAATAAGAAAAACTCATCCAATGAGGGAGAAGAAGTTCATAATAAGAATAACCTGT
TCAACATTAGCTCAATTAATCACATATGGAGTTGAATCAACAACACCTCACTCAAGGGATCAACA
TTTCCAGTGGAGAGTTCA
Found at i:2256658 original size:29 final size:30
Alignment explanation
Indices: 2256626--2256695 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
2256616 TTTATTCTGA
* * *
2256626 ATTAACTACTGACT-TTTATTTTATTGCAT
1 ATTAACCACTGAATCTTTATTTTACTGCAT
*
2256655 ATTAACCATTGAATCTTTATTTTACTGCAT
1 ATTAACCACTGAATCTTTATTTTACTGCAT
* *
2256685 TTTAGCCACTG
1 ATTAACCACTG
2256696 TTTAATTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 11 0.33
30 22 0.67
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.47
Consensus pattern (30 bp):
ATTAACCACTGAATCTTTATTTTACTGCAT
Found at i:2259531 original size:19 final size:20
Alignment explanation
Indices: 2259493--2259538 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
2259483 AAAGCATTTG
*
2259493 GAAAATACATCATTTTTAAT
1 GAAAATACATCATATTTAAT
*
2259513 GAAAATACATGA-ATTTAAT
1 GAAAATACATCATATTTAAT
2259532 GAAAATA
1 GAAAATA
2259539 AATGCTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.33
Consensus pattern (20 bp):
GAAAATACATCATATTTAAT
Found at i:2263326 original size:20 final size:19
Alignment explanation
Indices: 2263297--2263343 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2263287 GAAATCCCTT
*
2263297 TGAAAATACAAGATTTTTAA
1 TGAAAATACAAGA-CTTTAA
* *
2263317 TGAAACTACATGACTTTAA
1 TGAAAATACAAGACTTTAA
2263336 TGAAAATA
1 TGAAAATA
2263344 AATGCTCTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (19 bp):
TGAAAATACAAGACTTTAA
Found at i:2264290 original size:21 final size:21
Alignment explanation
Indices: 2264241--2264290 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
2264231 TGCTGCCATG
2264241 ATATGTAAATGATCTACAAAC
1 ATATGTAAATGATCTACAAAC
*
2264262 ATA-ATAAATGAATCTA-AAAC
1 ATATGTAAATG-ATCTACAAAC
2264282 ATATGTAAA
1 ATATGTAAA
2264291 ACATAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (21 bp):
ATATGTAAATGATCTACAAAC
Found at i:2270412 original size:23 final size:23
Alignment explanation
Indices: 2270383--2270436 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
2270373 TCGTTTAGCG
*
2270383 TTCGTTTAATGTTCGCGAACATA
1 TTCGTTTAATGTTCGCGAACACA
*
2270406 TTCGTTTAATGTTCGCGAACACG
1 TTCGTTTAATGTTCGCGAACACA
2270429 TTCGTTTA
1 TTCGTTTA
2270437 TATCCTCACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (23 bp):
TTCGTTTAATGTTCGCGAACACA
Found at i:2270420 original size:34 final size:34
Alignment explanation
Indices: 2270353--2270420 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
2270343 AACAAATTCA
* * *
2270353 TTTAATGTTTACGAACATGTTCGTTTAGCGTTCG
1 TTTAATGTTCACGAACATATTCGTTTAACGTTCG
* *
2270387 TTTAATGTTCGCGAACATATTCGTTTAATGTTCG
1 TTTAATGTTCACGAACATATTCGTTTAACGTTCG
2270421 CGAACACGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (34 bp):
TTTAATGTTCACGAACATATTCGTTTAACGTTCG
Found at i:2270527 original size:22 final size:22
Alignment explanation
Indices: 2270469--2270527 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
2270459 AACATGTTCT
* *
2270469 TTTAGCTTTCATTTAGTGTTCG
1 TTTAGCATTCATTTAGTATTCG
** *
2270491 TTTAGCATTGTTTTAGTATTTG
1 TTTAGCATTCATTTAGTATTCG
*
2270513 TTTATCATTCATTTA
1 TTTAGCATTCATTTA
2270528 TTTATTCAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.10, G:0.14, T:0.58
Consensus pattern (22 bp):
TTTAGCATTCATTTAGTATTCG
Found at i:2273084 original size:24 final size:24
Alignment explanation
Indices: 2273056--2273101 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2273046 GTTTGTTTAT
2273056 ATTCA-TTACCAAGCTCATTTATCA
1 ATTCATTTA-CAAGCTCATTTATCA
*
2273080 ATTCATTTATAAGCTCATTTAT
1 ATTCATTTACAAGCTCATTTAT
2273102 TCGACTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (24 bp):
ATTCATTTACAAGCTCATTTATCA
Found at i:2273097 original size:12 final size:13
Alignment explanation
Indices: 2273065--2273101 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
2273055 TATTCATTAC
2273065 CAAGCTCATTTAT
1 CAAGCTCATTTAT
*
2273078 CAA-TTCATTTAT
1 CAAGCTCATTTAT
2273090 -AAGCTCATTTAT
1 CAAGCTCATTTAT
2273102 TCGACTCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
11 2 0.10
12 16 0.76
13 3 0.14
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.43
Consensus pattern (13 bp):
CAAGCTCATTTAT
Found at i:2273359 original size:22 final size:22
Alignment explanation
Indices: 2273324--2273394 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
2273314 AAATGAATAA
2273324 TTCACAAACGTTAAACAAACATG
1 TTCACAAAC-TTAAACAAACATG
2273347 TTCACAAACTTAAACAAACATG
1 TTCACAAACTTAAACAAACATG
*
2273369 TTCACAAACTTAAACAAACATA
1 TTCACAAACTTAAACAAACATG
2273391 TTCA
1 TTCA
2273395 TGAAAGTTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 38 0.81
23 9 0.19
ACGTcount: A:0.49, C:0.23, G:0.04, T:0.24
Consensus pattern (22 bp):
TTCACAAACTTAAACAAACATG
Found at i:2278566 original size:20 final size:20
Alignment explanation
Indices: 2278526--2278564 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2278516 CATTGTAGGA
*
2278526 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
2278546 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
2278565 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:2279404 original size:31 final size:30
Alignment explanation
Indices: 2279360--2279422 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
2279350 CAAAATTTTT
2279360 AAGTTAAGTGACCAAAGTATAAACTTTGGAA
1 AAGTTAAGTGACCAAAGTATAAACTTT-GAA
2279391 AAGTTCAAG-GACCAAAGTATAAACTTTGAA
1 AAGTT-AAGTGACCAAAGTATAAACTTTGAA
2279421 AA
1 AA
2279423 TATTTAGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 5 0.16
31 23 0.74
32 3 0.10
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (30 bp):
AAGTTAAGTGACCAAAGTATAAACTTTGAA
Found at i:2279434 original size:31 final size:31
Alignment explanation
Indices: 2279369--2279437 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
2279359 TAAGTTAAGT
*
2279369 GACCAAAGTATAAACTTTGGAAAAGTTCAAG
1 GACCAAAGTATAAACTTTGGAAAAATTCAAG
* *
2279400 GACCAAAGTATAAACTTT-GAAAATATTTAGG
1 GACCAAAGTATAAACTTTGGAAAA-ATTCAAG
2279431 GACCAAA
1 GACCAAA
2279438 ATGGTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 5 0.15
31 29 0.85
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.23
Consensus pattern (31 bp):
GACCAAAGTATAAACTTTGGAAAAATTCAAG
Found at i:2280412 original size:29 final size:30
Alignment explanation
Indices: 2280380--2280449 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
2280370 AAGATTTTAA
* * *
2280380 AAAAATTGTG-GACCATTCTATAATTTTTG
1 AAAAATTGTGAGACAATTCAATAATTTTGG
*
2280409 AAAAGA-TGGGAGACAATTCAATAATTTTGG
1 AAAA-ATTGTGAGACAATTCAATAATTTTGG
*
2280439 AAAAGTTGTGA
1 AAAAATTGTGA
2280450 ATGATTGTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (30 bp):
AAAAATTGTGAGACAATTCAATAATTTTGG
Found at i:2282260 original size:40 final size:40
Alignment explanation
Indices: 2282211--2282322 Score: 197
Period size: 40 Copynumber: 2.8 Consensus size: 40
2282201 CAAGATGGGT
*
2282211 AAAGCTTGACCTCAGCACTACGGTGCAATATTAGGTGACC
1 AAAGCTTGACCTCAGCACTGCGGTGCAATATTAGGTGACC
*
2282251 AAAGCTTGACCTCAGCACTGCGGTGCAATATTAGGTGAGC
1 AAAGCTTGACCTCAGCACTGCGGTGCAATATTAGGTGACC
*
2282291 AAAGCTCGACCTCAGCACTGCGGTGCAATATT
1 AAAGCTTGACCTCAGCACTGCGGTGCAATATT
2282323 TGACTCCTAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (40 bp):
AAAGCTTGACCTCAGCACTGCGGTGCAATATTAGGTGACC
Found at i:2286003 original size:31 final size:31
Alignment explanation
Indices: 2285965--2286029 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
2285955 TTAAGTGACC
2285965 AAAGTATAAACTTTGGAAAAGTTCAGGGACT
1 AAAGTATAAACTTTGGAAAAGTTCAGGGACT
* *
2285996 AAAGTATAAACTTTGGAAATGTTTAGGGACT
1 AAAGTATAAACTTTGGAAAAGTTCAGGGACT
2286027 AAA
1 AAA
2286030 ATGGTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.28
Consensus pattern (31 bp):
AAAGTATAAACTTTGGAAAAGTTCAGGGACT
Found at i:2297112 original size:17 final size:17
Alignment explanation
Indices: 2297072--2297112 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2297062 CGACTAAAAG
* *
2297072 GGATAGATTCTAGAGTG
1 GGATAGATGCTAGAGTA
*
2297089 GGTTAGATGCTAGAGTA
1 GGATAGATGCTAGAGTA
2297106 GGATAGA
1 GGATAGA
2297113 CAATGACTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.37, T:0.27
Consensus pattern (17 bp):
GGATAGATGCTAGAGTA
Found at i:2297720 original size:86 final size:87
Alignment explanation
Indices: 2297565--2297738 Score: 224
Period size: 86 Copynumber: 2.0 Consensus size: 87
2297555 TGAGGAGTCG
* * * * * * * *
2297565 ATAACTCACTTACCCTATATTACTTGATTTGATTGTGTATACCTGCATAGAATTATTTTCCTTAT
1 ATAACTCACTTAACCTATATTACTTGATTCGATTGTCTATACCTGAACAGAATTACTTGCCTTAG
2297630 CATATACATTTACAAGCGATCA
66 CATATACATTTACAAGCGATCA
* * *
2297652 ATAACT-ACTTAACCTTTATTACTTGATTCGATTGTCTATACTTGAACAGAATTGCTTGCCTTAG
1 ATAACTCACTTAACCTATATTACTTGATTCGATTGTCTATACCTGAACAGAATTACTTGCCTTAG
* *
2297716 CATATACATTTCCAAGGGATCA
66 CATATACATTTACAAGCGATCA
2297738 A
1 A
2297739 GTTTTTGACG
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
86 68 0.92
87 6 0.08
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.39
Consensus pattern (87 bp):
ATAACTCACTTAACCTATATTACTTGATTCGATTGTCTATACCTGAACAGAATTACTTGCCTTAG
CATATACATTTACAAGCGATCA
Found at i:2303600 original size:16 final size:17
Alignment explanation
Indices: 2303576--2303616 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
2303566 TATGCACTAG
2303576 TTATCTGTTTCACTTTAT
1 TTAT-TGTTTCACTTTAT
*
2303594 TT-TTG-TTCATTTTAT
1 TTATTGTTTCACTTTAT
2303609 TTATTGTT
1 TTATTGTT
2303617 GGCTTGCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 11 0.55
16 5 0.25
17 2 0.10
18 2 0.10
ACGTcount: A:0.15, C:0.10, G:0.07, T:0.68
Consensus pattern (17 bp):
TTATTGTTTCACTTTAT
Found at i:2307975 original size:16 final size:17
Alignment explanation
Indices: 2307951--2307991 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
2307941 TATGCACTAG
2307951 TTATCTGTTTCACTTTAT
1 TTAT-TGTTTCACTTTAT
*
2307969 TT-TTG-TTCATTTTAT
1 TTATTGTTTCACTTTAT
2307984 TTATTGTT
1 TTATTGTT
2307992 GGCTTGCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 11 0.55
16 5 0.25
17 2 0.10
18 2 0.10
ACGTcount: A:0.15, C:0.10, G:0.07, T:0.68
Consensus pattern (17 bp):
TTATTGTTTCACTTTAT
Found at i:2314045 original size:20 final size:21
Alignment explanation
Indices: 2313999--2314046 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2313989 ACAAATATAA
*
2313999 ATAATAAATAATATTATTTATT
1 ATAA-AAACAATATTATTTATT
2314021 ATAAAAACAATATTA-TTATT
1 ATAAAAACAATATTATTTATT
*
2314041 TTAAAA
1 ATAAAA
2314047 TATTAGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
21 10 0.42
22 4 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAAAACAATATTATTTATT
Found at i:2318405 original size:2 final size:2
Alignment explanation
Indices: 2318395--2318443 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
2318385 ATTTTTTTTA
*
2318395 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2318435 AA AT AT AT A
1 AT AT AT AT A
2318444 ATTTCTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2318739 original size:2 final size:2
Alignment explanation
Indices: 2318734--2318766 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
2318724 GAGAGTTTTG
2318734 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
2318767 TATGAGATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2321034 original size:3 final size:3
Alignment explanation
Indices: 2321028--2321063 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2321018 AATATTTGTT
2321028 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2321064 GTCTCATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2324626 original size:54 final size:54
Alignment explanation
Indices: 2324544--2324649 Score: 151
Period size: 54 Copynumber: 2.0 Consensus size: 54
2324534 GTGGAAATAG
*
2324544 GTTTGTGTTACTGTCGTGTTTGTGTTTGGAATTAGG-AGAAAGTTGAAGTTTGTT
1 GTTTGTGTTACTATCGTGTTTGTGTTTGGAA-TAGGTAGAAAGTTGAAGTTTGTT
* * * *
2324598 GTTTGTGTTACTATTGTGTTTGTTTTTGGAATGGGTTGAAAGTTGAAGTTTG
1 GTTTGTGTTACTATCGTGTTTGTGTTTGGAATAGGTAGAAAGTTGAAGTTTG
2324650 GTTATTGGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 3 0.07
54 43 0.93
ACGTcount: A:0.18, C:0.03, G:0.31, T:0.48
Consensus pattern (54 bp):
GTTTGTGTTACTATCGTGTTTGTGTTTGGAATAGGTAGAAAGTTGAAGTTTGTT
Found at i:2328591 original size:47 final size:45
Alignment explanation
Indices: 2328537--2328634 Score: 151
Period size: 47 Copynumber: 2.1 Consensus size: 45
2328527 GAATAAATGT
*
2328537 ATGCGAACTAGAAATCATGCGGTTAGGTATATTTTCTCGAACAAAGC
1 ATGCGAACTAGAAATCACGCGGTTAGGTATATTTTC-CGAACAAA-C
* *
2328584 ATGCGAACTAGAAATCACGCGGTTATGTTTATTTTCCGAACAAAC
1 ATGCGAACTAGAAATCACGCGGTTAGGTATATTTTCCGAACAAAC
2328629 ATGCGA
1 ATGCGA
2328635 TTAGGTTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
45 7 0.15
46 8 0.17
47 33 0.69
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (45 bp):
ATGCGAACTAGAAATCACGCGGTTAGGTATATTTTCCGAACAAAC
Found at i:2331677 original size:2 final size:2
Alignment explanation
Indices: 2331670--2331694 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2331660 ATCCCTTCAA
2331670 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 A
2331695 CCCCTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2334661 original size:36 final size:36
Alignment explanation
Indices: 2334620--2334690 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
2334610 GCAAAGTCAA
* * * * *
2334620 TCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACCG
1 TCTTAAGCATGCACCAAAGAATAATGAAGCAAACCG
2334656 TCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
1 TCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
2334691 ATTGTGTCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.20
Consensus pattern (36 bp):
TCTTAAGCATGCACCAAAGAATAATGAAGCAAACCG
Found at i:2335250 original size:54 final size:54
Alignment explanation
Indices: 2335106--2335792 Score: 864
Period size: 54 Copynumber: 12.9 Consensus size: 54
2335096 AGTGAAGCAA
* * *
2335106 AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * *
2335160 AAG-A-TTGTTCGAGTTTCATACT-CCT-GAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTG
* * ** * * *
2335211 AAGAAGAGGTACGAGTTTTATACTCCTTAAAGAAAGAGGGAGCGAACCAGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * *
2335265 AAGAAGATGTCCGAGTTCTATACTCCTTAGAGAAAGAGGAAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
2335319 AAGAAAATATCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
2335373 AAGAAGATGTACGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
2335427 AAGAAGATGTCCGAGTTCTATACTCCCTAGAG-AA-AGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
2335479 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * *
2335533 AAGAAGATTTCCAAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCG--TG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * * *
2335585 -TGAAGATAT-CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
**
2335637 -A-AAGATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * *
2335689 AAGAAGATTTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGTGAACCCCG--T-
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAA-CCCGTTTG
* * * * *
2335741 AAGAAGATTATTCGAGTTCTATACTGCCTGAAAGAAAGAGGGAGCGAACCCG
1 AAGAAGA-TGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCG
2335793 ATTGTTGAAT
Statistics
Matches: 563, Mismatches: 55, Indels: 31
0.87 0.08 0.05
Matches are distributed among these distances:
50 35 0.06
51 42 0.07
52 116 0.21
53 43 0.08
54 323 0.57
55 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.21
Consensus pattern (54 bp):
AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
Found at i:2335552 original size:160 final size:158
Alignment explanation
Indices: 2335106--2335792 Score: 843
Period size: 160 Copynumber: 4.3 Consensus size: 158
2335096 AGTGAAGCAA
* * * * *
2335106 AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTTTGAAG-A-TTGTT
1 AAGAAGATATCCGAGTTCTATACTCCCTAGAG--AAAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * **
2335169 CGAGTTTCATACT-CCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGAGGTACGAGTTTTAT
64 CGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTACGAGTTCCAT
* * *
2335232 ACTCCTTAAAGAAAGAGGGAGCGAACCAGTTTG
128 ACTCCCTAGAGAAAGAGGGAGCGAACCCG--TG
* * * *
2335265 AAGAAGATGTCCGAGTTCTATACTCCTTAGAGAAAGAGGAAGCGAACCCGTTTGAAGAAAATATC
1 AAGAAGATATCCGAGTTCTATACTCCCTAGAGAAAG-GG-AGCGAACCCGTTTGAAGAAGATGTC
2335330 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTACGAGTTCCATA
64 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTACGAGTTCCATA
2335395 CTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
129 CTCCCTAGAGAAAGAGGGAGCGAACCCG--TG
*
2335427 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
1 AAGAAGATATCCGAGTTCTATACTCCCTAGAGAAAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
* * * * *
2335492 AGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATTTCCAAGTTCCATACT
66 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTACGAGTTCCATACT
*
2335557 TCCTAGAGAAAGAGGGAGCGAACCCGTG
131 CCCTAGAGAAAGAGGGAGCGAACCCGTG
* * * * *
2335585 -TGAAGATAT-CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AAGATGTT
1 AAGAAGATATCCGAGTTCTATACTCCCTAGAGAAAG--GGAGCGAACCCGTTTGAAGAAGATGTC
* * *
2335646 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTTTCGAGTTCCATA
64 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTACGAGTTCCATA
* *
2335711 CTTCCTAGAGAAAGAGGGAGTGAACCCCGT-
129 CTCCCTAGAGAAAGAGGGAGCGAA-CCCGTG
* * *
2335741 AAGAAGATTATTCGAGTTCTATACTGCCTGAAAGAAAGAGGGAGCGAACCCG
1 AAGAAGA-TATCCGAGTTCTATACTCCCT-AGAG-AA-AGGGAGCGAACCCG
2335793 ATTGTTGAAT
Statistics
Matches: 474, Mismatches: 39, Indels: 29
0.87 0.07 0.05
Matches are distributed among these distances:
156 112 0.24
157 22 0.05
158 23 0.05
159 59 0.12
160 127 0.27
161 18 0.04
162 112 0.24
163 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.21
Consensus pattern (158 bp):
AAGAAGATATCCGAGTTCTATACTCCCTAGAGAAAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTACGAGTTCCATACT
CCCTAGAGAAAGAGGGAGCGAACCCGTG
Found at i:2335912 original size:55 final size:55
Alignment explanation
Indices: 2335743--2336014 Score: 320
Period size: 55 Copynumber: 4.9 Consensus size: 55
2335733 AACCCCGTAA
* * * *
2335743 GAAGATTATTCGAGT-TCTATACTGC-CTGAAAGAAAGAGGGAGC-GAACCCGATTGTT
1 GAAGATTGTTCGAGTCT-TATACT-CTCTG-AAGAAATAGGGAGCAG-ACACGATCGTT
* *
2335799 GAATATTGTTCGAGTCTTATACTCTCTCTGAAGAAATAGGGAGTAGACACGA-CTGTT
1 GAAGATTGTTCGAGTCTTATA--CTCTCTGAAGAAATAGGGAGCAGACACGATC-GTT
2335856 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
* * **
2335911 GAAGATTGTTCGAGTCTTATACTCTTTGAAGGAATAGGGAGCAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
* * *
2335966 GAAGATTGTTTGAGTCTTATACTCTCTGAA-AGAATAGAGAGCGGACACG
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGACACG
2336015 TTTTCCGAAG
Statistics
Matches: 191, Mismatches: 17, Indels: 17
0.85 0.08 0.08
Matches are distributed among these distances:
55 125 0.65
56 18 0.09
57 42 0.22
58 6 0.03
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
Found at i:2340777 original size:12 final size:12
Alignment explanation
Indices: 2340760--2340786 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2340750 TTAATTGCGA
2340760 AAATTGAAATTT
1 AAATTGAAATTT
2340772 AAATTGAAATTT
1 AAATTGAAATTT
2340784 AAA
1 AAA
2340787 AACTCGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATTGAAATTT
Found at i:2342156 original size:21 final size:21
Alignment explanation
Indices: 2342120--2342175 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
2342110 ACAAAAATCA
*
2342120 AATAAAAGAA-AAATAATATT
1 AATAAAATAATAAATAATATT
2342140 AATAAAATAATAAATAATATT
1 AATAAAATAATAAATAATATT
*
2342161 AATATAATATATAAA
1 AATAAAATA-ATAAA
2342176 AAATCGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 9 0.28
21 18 0.56
22 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
AATAAAATAATAAATAATATT
Found at i:2342225 original size:40 final size:38
Alignment explanation
Indices: 2342174--2342278 Score: 110
Period size: 40 Copynumber: 2.8 Consensus size: 38
2342164 ATAATATATA
* * * *
2342174 AAAAATCGTTTTTAAAACTATATATCATATTTGTTTTTTT
1 AAAAATTGTTTTTAAAAC-ATATAT-ATATTTATATTTTC
*
2342214 AAAAATTGTTTTCAAAACCATATA-ATA--TATATTTTC
1 AAAAATTGTTTTTAAAA-CATATATATATTTATATTTTC
2342250 AAAAATTGTTTTT-AAACATATATATATTT
1 AAAAATTGTTTTTAAAACATATATATATTT
2342279 TCAACAATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
34 6 0.11
35 6 0.11
36 18 0.33
37 1 0.02
38 3 0.05
40 20 0.36
41 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.48
Consensus pattern (38 bp):
AAAAATTGTTTTTAAAACATATATATATTTATATTTTC
Found at i:2342309 original size:37 final size:36
Alignment explanation
Indices: 2342268--2342556 Score: 262
Period size: 37 Copynumber: 7.5 Consensus size: 36
2342258 TTTTTAAACA
2342268 TATATATATTTTCAACAATATTTTCAAAACTATATAT
1 TATATATATTTTCAA-AATATTTTCAAAACTATATAT
* *
2342305 TATATACATCTTCAAAAATATTTTCAAAACTATATAT
1 TATATATATTTTC-AAAATATTTTCAAAACTATATAT
*
2342342 TATATATATTTTCAAAATATTTTTAAAAACTATATATTATAT
1 TATATATATTTTCAAAATA-TTTTCAAAAC----TA-TATAT
* *
2342384 ATATATATATATATATGTAAAATGTTTTCAAAAACTATATAT
1 -TATATATAT-T-T-T-CAAAATATTTTC-AAAACTATATAT
*
2342426 TATATATATGTTTTCAAAATATTTTTAAAAACTATAT-T
1 TATATATA--TTTTCAAAATA-TTTTCAAAACTATATAT
*
2342464 ATATATATATATTT-AAAATGTTTTCAAAAACTATATAT
1 -TATATATAT-TTTCAAAATATTTTC-AAAACTATATAT
2342502 TATATATATGTTTTCAAAAAATATTTTCAAAA-T-TATAT
1 TATATATA--TTTTC--AAAATATTTTCAAAACTATATAT
*
2342540 AATATATATTTTCAAAA
1 TATATATATTTTCAAAA
2342557 CTATATGTTA
Statistics
Matches: 212, Mismatches: 15, Indels: 53
0.76 0.05 0.19
Matches are distributed among these distances:
34 4 0.02
36 15 0.07
37 76 0.36
38 22 0.10
39 25 0.12
40 9 0.04
41 21 0.10
42 11 0.05
43 12 0.06
44 1 0.00
45 1 0.00
46 5 0.02
47 10 0.05
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (36 bp):
TATATATATTTTCAAAATATTTTCAAAACTATATAT
Found at i:2342396 original size:123 final size:122
Alignment explanation
Indices: 2342267--2342510 Score: 329
Period size: 123 Copynumber: 2.0 Consensus size: 122
2342257 GTTTTTAAAC
*
2342267 ATATATATAT-TTTCAACAATATTTTC-AAAACTATATATTATATACA-TCTTCAAAA-ATATTT
1 ATATATATATATGT-AA-AATATTTTCAAAAACTATATATTATATACAGTCTTCAAAATAT-TTT
* *
2342328 TCAAAACTATA-TAT-TATATATATTTTCAAAATATTTTTAAAAACTATATATTATATATAT
63 TAAAAACTATATTATATATATATA-TTT-AAAATATTTTCAAAAACTATATATTATATATAT
* * *
2342388 ATATATATATATGTAAAATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAATATTTTTA
1 ATATATATATATGTAAAATATTTTCAAAAACTATATATTATATACA-GTCTTCAAAATATTTTTA
*
2342453 AAAACTATATTATATATATATATTTAAAATGTTTTCAAAAACTATATATTATATATAT
65 AAAACTATATTATATATATATATTTAAAATATTTTCAAAAACTATATATTATATATAT
2342511 GTTTTCAAAA
Statistics
Matches: 109, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
120 8 0.07
121 31 0.28
122 2 0.02
123 52 0.48
124 8 0.07
125 8 0.07
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (122 bp):
ATATATATATATGTAAAATATTTTCAAAAACTATATATTATATACAGTCTTCAAAATATTTTTAA
AAACTATATTATATATATATATTTAAAATATTTTCAAAAACTATATATTATATATAT
Found at i:2342488 original size:76 final size:77
Alignment explanation
Indices: 2342381--2342548 Score: 275
Period size: 76 Copynumber: 2.2 Consensus size: 77
2342371 CTATATATTA
*
2342381 TATATATATATATATATATGTAAAATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAAT
1 TATAT-TATATATATATATGTAAAATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAAA
2342446 AT-TTTTAAAAAC
65 ATATTTTAAAAAC
*
2342458 TATATTATATATATATATTTAAAATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAAAA
1 TATATTATATATATATATGTAAAATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAAAA
* *
2342523 TATTTTCAAAAT
66 TATTTTAAAAAC
*
2342535 TATATAATATATAT
1 TATATTATATATAT
2342549 TTTCAAAACT
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
76 59 0.69
77 26 0.31
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (77 bp):
TATATTATATATATATATGTAAAATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAAAA
TATTTTAAAAAC
Found at i:2342549 original size:23 final size:23
Alignment explanation
Indices: 2342522--2342581 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2342512 TTTTCAAAAA
2342522 ATATTTTCAAAATTATATAATAT
1 ATATTTTCAAAATTATATAATAT
* **
2342545 ATATTTTCAAAACTATATGTTAT
1 ATATTTTCAAAATTATATAATAT
2342568 ATATTTTCGAAAAT
1 ATATTTTC-AAAAT
2342582 CGATTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 28 0.88
24 4 0.12
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (23 bp):
ATATTTTCAAAATTATATAATAT
Found at i:2342623 original size:23 final size:22
Alignment explanation
Indices: 2342522--2342623 Score: 77
Period size: 23 Copynumber: 4.5 Consensus size: 22
2342512 TTTTCAAAAA
*
2342522 ATATTTTCAAAATTATATAATAT
1 ATATTTTCAAAA-TATATATTAT
*
2342545 ATATTTTCAAAACTATATGTTAT
1 ATATTTTCAAAA-TATATATTAT
**
2342568 ATATTTTCGAAAATCGAT-TT-T
1 ATATTTTC-AAAATATATATTAT
*
2342589 -T-TTTTAAAAAAAGTATATATTAT
1 ATATTTT--CAAAA-TATATATTAT
2342612 ATATTTTCAAAA
1 ATATTTTCAAAA
2342624 AACCATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
19 4 0.06
20 5 0.08
21 4 0.06
22 4 0.06
23 36 0.58
24 5 0.08
25 4 0.06
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (22 bp):
ATATTTTCAAAATATATATTAT
Found at i:2343405 original size:85 final size:84
Alignment explanation
Indices: 2343256--2343572 Score: 339
Period size: 85 Copynumber: 3.7 Consensus size: 84
2343246 TCATCAAGCA
* * * *** *
2343256 GAATGGAATCGAACTCGACAGTTTTTTATTAACAAATATCCCTTCTCGTAATGAGTTATGTTGTA
1 GAATGGAATCGAACTCGA-AGTTTTTTGTTAACAAATAGCCCTTCTTGCCTTGAGCTATGTTGTA
*
2343321 AATTGGATATGCCCTCGAGCT
65 AATT-GATATGCCCTTGAGCT
* * * *
2343342 GAATGGAATCGAACTTGAAGATTTTTGTTTACATATAGCCCTTCTTGCCTTGAGCTATGTTGTAA
1 GAATGGAATCGAACTCGAAGTTTTTTGTTAACAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAA
* *
2343407 ACTTGATAAGCCCTTTGAGTT
66 A-TTGATATGCCC-TTGAGCT
* * * * * **
2343428 GAATGAAATCAAACTCGAAAGTTTTTTGCTGACAAATAGCCCTTGTTGCCTTGAGCTATACTGTA
1 GAATGGAATCGAACTCG-AAGTTTTTTGTTAACAAATAGCCCTTCTTGCCTTGAGCTATGTTGTA
2343493 AATTTGATATGCCCTTGAGCT
65 AA-TTGATATGCCCTTGAGCT
* * * *
2343514 GAATGTAATCGAACTCGAAGGTTTTTGTTAACAGATAGCCCTT-TTCTCCTTGAGCTATG
1 GAATGGAATCGAACTCGAAGTTTTTTGTTAACAAATAGCCCTTCTT-GCCTTGAGCTATG
2343573 CTGCGAACAG
Statistics
Matches: 192, Mismatches: 35, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
84 2 0.01
85 79 0.41
86 59 0.31
87 52 0.27
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (84 bp):
GAATGGAATCGAACTCGAAGTTTTTTGTTAACAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAA
ATTGATATGCCCTTGAGCT
Found at i:2348971 original size:12 final size:13
Alignment explanation
Indices: 2348954--2348982 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2348944 CTTAATTGCG
2348954 AAAATTAAAA-TT
1 AAAATTAAAATTT
2348966 AAAATTAAAATTT
1 AAAATTAAAATTT
2348979 AAAA
1 AAAA
2348983 ACTCGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:2349158 original size:17 final size:17
Alignment explanation
Indices: 2349138--2349170 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2349128 GAATATTAAA
2349138 ATAAAAAAAATAAAAAT
1 ATAAAAAAAATAAAAAT
*
2349155 ATAAAAACAATAAAAA
1 ATAAAAAAAATAAAAA
2349171 AGTTAAATTT
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:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (17 bp):
ATAAAAAAAATAAAAAT
Found at i:2350394 original size:5 final size:5
Alignment explanation
Indices: 2350355--2350423 Score: 65
Period size: 5 Copynumber: 14.0 Consensus size: 5
2350345 AAAAAAATTA
* *
2350355 ATAAA ATAAT A-AAT A-AAA ATAA- ATAAT ATTAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT
2350403 ATAAT A-ATAT ATATAT ATAAT
1 ATAAT ATA-AT ATA-AT ATAAT
2350424 CATTTTTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
4 12 0.21
5 33 0.58
6 12 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:2350411 original size:13 final size:13
Alignment explanation
Indices: 2350353--2350423 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 13
2350343 GAAAAAAAAT
*
2350353 TAATAAAATAATA
1 TAATAATATAATA
2350366 -AATAA-A-AATA
1 TAATAATATAATA
2350376 -AATAATATTAATA
1 TAATAATA-TAATA
2350389 TAATATAATATAATA
1 T-A-ATAATATAATA
2350404 TAATAATAT-ATA
1 TAATAATATAATA
2350416 TATATAAT
1 TA-ATAAT
2350424 CATTTTTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.18
11 2 0.04
12 10 0.20
13 16 0.31
14 1 0.02
15 7 0.14
16 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:2350508 original size:37 final size:36
Alignment explanation
Indices: 2350462--2350801 Score: 244
Period size: 37 Copynumber: 9.1 Consensus size: 36
2350452 TTTTTTAAAA
* * *
2350462 AAAATGTTTTCAAAACCATATAATATATATATATTC
1 AAAATATTTTCAAAACTATATAATATATATATTTTC
* * *
2350498 AAAATTGTTTTTATAACTATAT-A-ATATATATTTTC
1 AAAA-TATTTTCAAAACTATATAATATATATATTTTC
* * *
2350533 AACAATATTTTCAAAACTATATATTATATACATCTTC
1 AA-AATATTTTCAAAACTATATAATATATATATTTTC
* * * *
2350570 AAAAACTATATATTTTTAAAATTTTTAAAACTATATATTATGTTTTC
1 ---AA--A-ATATTTTCAAAA-CTATATAA-TATATA-TA--TTTTC
*
2350617 AAAATATTTTTAAAACTATAT-ATATATATATTTT-
1 AAAATATTTTCAAAACTATATAATATATATATTTTC
* *
2350651 AAAATGTTTTCAAAAACTATATATTATATATATGTTTTC
1 AAAATATTTTC-AAAACTATATA--ATATATATATTTTC
*
2350690 AAAATATTTTGAAAACTATATAATATATATATTTTC
1 AAAATATTTTCAAAACTATATAATATATATATTTTC
* * *
2350726 AAAAATATTTTCAAAATTATATATTATATAT-TTTTG
1 -AAAATATTTTCAAAACTATATAATATATATATTTTC
** * *
2350762 AAAATCTATTTTTTAAAGTATAT-AT-TATATGTTTTC
1 AAAA--TATTTTCAAAACTATATAATATATATATTTTC
2350798 AAAA
1 AAAA
2350802 AACCATTTTC
Statistics
Matches: 245, Mismatches: 36, Indels: 46
0.75 0.11 0.14
Matches are distributed among these distances:
34 9 0.04
35 50 0.20
36 33 0.13
37 67 0.27
38 29 0.12
39 10 0.04
40 5 0.02
41 13 0.05
42 12 0.05
43 4 0.02
44 8 0.03
45 1 0.00
47 4 0.02
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (36 bp):
AAAATATTTTCAAAACTATATAATATATATATTTTC
Found at i:2350599 original size:26 final size:25
Alignment explanation
Indices: 2350522--2350608 Score: 77
Period size: 25 Copynumber: 3.3 Consensus size: 25
2350512 AACTATATAA
*
2350522 TATATATTTTCAACAATATTTTCAAAAC
1 TATATATTTTTAA-AAT-TTTT-AAAAC
* * **
2350550 TATATA-TTATATACATCTTCAAAAAC
1 TATATATTTTTA-AAAT-TTTTAAAAC
2350576 TATATATTTTTAAAATTTTTAAAAC
1 TATATATTTTTAAAATTTTTAAAAC
2350601 TATATATT
1 TATATATT
2350609 ATGTTTTCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
25 15 0.32
26 14 0.30
27 11 0.23
28 7 0.15
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (25 bp):
TATATATTTTTAAAATTTTTAAAAC
Found at i:2350605 original size:25 final size:26
Alignment explanation
Indices: 2350522--2350639 Score: 87
Period size: 27 Copynumber: 4.3 Consensus size: 26
2350512 AACTATATAA
*
2350522 TATATATTTTCAACAATATTTTCAAAAC
1 TATATATTTTTAA-AATATTTT-AAAAC
* * * **
2350550 TATATA-TTATATACATCTTCAAAAAC
1 TATATATTTTTA-AAATATTTTAAAAC
2350576 TATATATTTTTAAAAT-TTTTAAAAC
1 TATATATTTTTAAAATATTTTAAAAC
2350601 TATATATTATGTTTTCAAAATATTTTTAAAAC
1 --TATA-TAT-TTTT-AAAATA-TTTTAAAAC
2350633 TATATAT
1 TATATAT
2350640 ATATATATTT
Statistics
Matches: 71, Mismatches: 10, Indels: 17
0.72 0.10 0.17
Matches are distributed among these distances:
25 7 0.10
26 14 0.20
27 15 0.21
28 10 0.14
29 7 0.10
30 9 0.13
32 9 0.13
ACGTcount: A:0.43, C:0.09, G:0.01, T:0.47
Consensus pattern (26 bp):
TATATATTTTTAAAATATTTTAAAAC
Found at i:2350693 original size:27 final size:27
Alignment explanation
Indices: 2350641--2350693 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
2350631 ACTATATATA
*
2350641 TATATATTTTAAAATGTTTTCAAAAAC
1 TATATATTATAAAATGTTTTCAAAAAC
*
2350668 TATATATTATATATATGTTTTCAAAA
1 TATATATTATA-AAATGTTTTCAAAA
2350694 TATTTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (27 bp):
TATATATTATAAAATGTTTTCAAAAAC
Found at i:2350705 original size:73 final size:74
Alignment explanation
Indices: 2350462--2350756 Score: 251
Period size: 73 Copynumber: 3.9 Consensus size: 74
2350452 TTTTTTAAAA
* * * * * * * *
2350462 AAAATGTTTTCAAAACCATATAATATATATATATTCAAAATTGTTTTTATAACTATATA--ATAT
1 AAAATATTTTGAAAACTATATAATATATATAT-TTTAAAAATATTTTCAAAACTATATATTATAT
2350525 ATA--TTTTC
65 ATATGTTTTC
* * * * * * *
2350533 AACAATATTTTCAAAACTATATATTATATACATCTTCAAAAACTATATATTTTTAAAATTTTTAA
1 AA-AATATTTTGAAAACTATATAATATATATAT-TT--TAAA--A-ATATTTTCAAAA-CTAT-A
* *
2350598 AACTATATATTATGTTTTC
57 TATTATATA-TATGTTTTC
* *
2350617 AAAATATTTTTAAAACTATAT-ATATATATATTTT-AAAATGTTTTCAAAAACTATATATTATAT
1 AAAATATTTTGAAAACTATATAATATATATATTTTAAAAATATTTTC-AAAACTATATATTATAT
2350680 ATATGTTTTC
65 ATATGTTTTC
*
2350690 AAAATATTTTGAAAACTATATAATATATATATTTTCAAAAATATTTTCAAAATTATATATTATAT
1 AAAATATTTTGAAAACTATATAATATATATATTTT-AAAAATATTTTCAAAACTATATATTATAT
2350755 AT
65 AT
2350757 TTTTGAAAAT
Statistics
Matches: 182, Mismatches: 25, Indels: 30
0.77 0.11 0.13
Matches are distributed among these distances:
71 2 0.01
72 28 0.15
73 29 0.16
74 24 0.13
75 26 0.14
76 16 0.09
77 9 0.05
78 4 0.02
79 2 0.01
81 7 0.04
82 10 0.05
83 18 0.10
84 7 0.04
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (74 bp):
AAAATATTTTGAAAACTATATAATATATATATTTTAAAAATATTTTCAAAACTATATATTATATA
TATGTTTTC
Found at i:2350810 original size:37 final size:37
Alignment explanation
Indices: 2350706--2350815 Score: 107
Period size: 37 Copynumber: 3.0 Consensus size: 37
2350696 TTTTGAAAAC
* * *
2350706 TATATAATATATATATTTTC-AAAAA-TATTTTCAAAAT
1 TATAT-AT-TATATATTTTCAAAAAACCATTTTCTAAAG
** * * *
2350743 TATATATTATATATTTTTGAAAATCTATTTTTTAAAG
1 TATATATTATATATTTTCAAAAAACCATTTTCTAAAG
*
2350780 TATATATTATATGTTTTCAAAAAACCATTTTCTAAA
1 TATATATTATATATTTTCAAAAAACCATTTTCTAAA
2350816 AACTATAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
35 10 0.17
36 6 0.10
37 44 0.73
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (37 bp):
TATATATTATATATTTTCAAAAAACCATTTTCTAAAG
Found at i:2351304 original size:16 final size:16
Alignment explanation
Indices: 2351283--2351314 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2351273 GTATCCACAT
2351283 GGAAATTTCGAAACTA
1 GGAAATTTCGAAACTA
2351299 GGAAATTTCGAAACTA
1 GGAAATTTCGAAACTA
2351315 TTGTATCAAT
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:0.19, T:0.25
Consensus pattern (16 bp):
GGAAATTTCGAAACTA
Found at i:2354584 original size:22 final size:22
Alignment explanation
Indices: 2354554--2354619 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
2354544 TTCATGAACA
*
2354554 TGTTCGTTTAGCGTTCATTTAT
1 TGTTTGTTTAGCGTTCATTTAT
** *
2354576 TGTTTGTTTAGCGTTGTTTTAG
1 TGTTTGTTTAGCGTTCATTTAT
* **
2354598 TATTTGTTTATTGTTCATTTAT
1 TGTTTGTTTAGCGTTCATTTAT
2354620 ATATTTGATT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.14, C:0.08, G:0.18, T:0.61
Consensus pattern (22 bp):
TGTTTGTTTAGCGTTCATTTAT
Found at i:2355259 original size:3 final size:3
Alignment explanation
Indices: 2355251--2355303 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
2355241 ATTTATTTAT
* * *
2355251 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTTA TTT TTA TTT TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
2355296 TTA TTA TT
1 TTA TTA TT
2355304 TAATATAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:2357270 original size:15 final size:15
Alignment explanation
Indices: 2357250--2357278 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2357240 TTTTTATCTT
2357250 TTAAAATTATTTTTC
1 TTAAAATTATTTTTC
2357265 TTAAAATTATTTTT
1 TTAAAATTATTTTT
2357279 AAATGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAAAATTATTTTTC
Found at i:2367812 original size:91 final size:93
Alignment explanation
Indices: 2367698--2367879 Score: 262
Period size: 96 Copynumber: 2.0 Consensus size: 93
2367688 TCCCGAATAT
* * * *
2367698 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAA-AA-AA-TAAAATCTCTAATATGA
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAACAAAAAACCCTAATATGA
*
2367760 TTAGGGTAACTTGGATATAAAAGGATTA
66 CTAGGGTAACTTGGATATAAAAGGATTA
2367788 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAGCCAAAAAACCCTAATA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAA--CAAAAAACCCTAATA
*
2367853 TGACTAGGGTAACTTGGCTATAAAAGG
63 TGACTAGGGTAACTTGGATATAAAAGG
2367880 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
90 7 0.09
91 33 0.41
92 2 0.03
93 2 0.03
96 36 0.45
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (93 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAACAAAAAACCCTAATATGA
CTAGGGTAACTTGGATATAAAAGGATTA
Found at i:2368605 original size:17 final size:17
Alignment explanation
Indices: 2368585--2368617 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2368575 ATATTTATTT
2368585 ATAT-AAAATATAATATA
1 ATATGAAAA-ATAATATA
2368602 ATATGAAAAATAATAT
1 ATATGAAAAATAATAT
2368618 TATGGTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATGAAAAATAATATA
Found at i:2371883 original size:26 final size:26
Alignment explanation
Indices: 2371835--2371885 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2371825 TTGGAATAAC
* *
2371835 ATTTTATTTAAAAGTATTTTATTTTT
1 ATTTTATTTAAAAATATTATATTTTT
2371861 ATTTTCATTTAAAAATA-TATATTTT
1 ATTTT-ATTTAAAAATATTATATTTT
2371886 ATGTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTTTATTTAAAAATATTATATTTTT
Found at i:2376348 original size:2 final size:2
Alignment explanation
Indices: 2376343--2376391 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2376333 CTAAAACGTG
2376343 TA TA TA 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
2376385 TA TA TA T
1 TA TA TA T
2376392 TTTAGTAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2380694 original size:19 final size:19
Alignment explanation
Indices: 2380659--2380701 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2380649 TTTTATCTAC
*
2380659 ATTTTTATGTCATTATTTG
1 ATTTTTATGTAATTATTTG
*
2380678 ATTTTTA-GTAATATATTTT
1 ATTTTTATGTAAT-TATTTG
2380697 ATTTT
1 ATTTT
2380702 GTATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (19 bp):
ATTTTTATGTAATTATTTG
Found at i:2386572 original size:13 final size:13
Alignment explanation
Indices: 2386554--2386580 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2386544 GTCGCTCAAC
2386554 GCACGTCATAAAT
1 GCACGTCATAAAT
2386567 GCACGTCATAAAT
1 GCACGTCATAAAT
2386580 G
1 G
2386581 TGTGTCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (13 bp):
GCACGTCATAAAT
Found at i:2388826 original size:45 final size:45
Alignment explanation
Indices: 2388688--2389047 Score: 347
Period size: 45 Copynumber: 8.0 Consensus size: 45
2388678 TATTGTGCAC
* * * *
2388688 TTTCAACTATAACAT-CTTTAT-TGTTGATAATGTACTCATATGCA
1 TTTCAACCATAGCATACTTT-TCTGTTGATAATGTACCCATATACA
* * *
2388732 TTTCAACTATAGTATACTTTT-TATTGATAATGTACCCATATACA
1 TTTCAACCATAGCATACTTTTCTGTTGATAATGTACCCATATACA
* *
2388776 TTTCAACCATAGTATACTTTTCTGTTGACAATGTACCCATATACA
1 TTTCAACCATAGCATACTTTTCTGTTGATAATGTACCCATATACA
* * * * * *
2388821 ATTCAACTC-TAGCATGCTCTTCTATTGATAATGCACCCATATGCA
1 TTTCAAC-CATAGCATACTTTTCTGTTGATAATGTACCCATATACA
* * *
2388866 TTTCAACTC-TAGCACACTTTTCTGTTGATAATGCACCCATATGCA
1 TTTCAAC-CATAGCATACTTTTCTGTTGATAATGTACCCATATACA
*
2388911 TTTCAACTC-TAGCATACTTTTCTGTTGACAATGTACCCATATACA
1 TTTCAAC-CATAGCATACTTTTCTGTTGATAATGTACCCATATACA
* ** ** *
2388956 TTTCAACTATAATATGTTTTTCTGTTGATAATGTACCTATATACA
1 TTTCAACCATAGCATACTTTTCTGTTGATAATGTACCCATATACA
* * * * * *
2389001 TTTCAACTATAGCAT-CCTTTCATGCTAATAATGCACCCATATGCA
1 TTTCAACCATAGCATACTTTTC-TGTTGATAATGTACCCATATACA
2389046 TT
1 TT
2389048 AATATTTTCA
Statistics
Matches: 270, Mismatches: 41, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
44 58 0.21
45 211 0.78
46 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (45 bp):
TTTCAACCATAGCATACTTTTCTGTTGATAATGTACCCATATACA
Found at i:2388869 original size:90 final size:89
Alignment explanation
Indices: 2388709--2389047 Score: 385
Period size: 90 Copynumber: 3.8 Consensus size: 89
2388699 ACATCTTTAT
* * * * *
2388709 TGTTGATAATGTACTCATATGCATTTCAACTATAGTATACTTTTTATTGATAATGTACCCATATA
1 TGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTCTATTGATAATGCACCCATATA
2388774 CATTTCAACCATAGTATACTTTTC
66 CATTTCAACCATAGTATACTTTTC
* * * *
2388798 TGTTGACAATGTACCCATATACAATTCAACTCTAGCATGCTCTTCTATTGATAATGCACCCATAT
1 TGTTGATAATGTACCCATATACATTTCAACTATAGCATACT-TTCTATTGATAATGCACCCATAT
* * *
2388863 GCATTTCAACTC-TAGCACACTTTTC
65 ACATTTCAAC-CATAGTATACTTTTC
* * * * * *
2388888 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTCTGTTGACAATGTACCCATAT
1 TGTTGATAATGTACCCATATACATTTCAACTATAGCATAC-TTTCTATTGATAATGCACCCATAT
* * **
2388953 ACATTTCAACTATAATATGTTTTTC
65 ACATTTCAACCATAGTATACTTTTC
* * *
2388978 TGTTGATAATGTACCTATATACATTTCAACTATAGCATCCTTTC-ATGCTAATAATGCACCCATA
1 TGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTCTAT--TGATAATGCACCCATA
*
2389042 TGCATT
64 TACATT
2389048 AATATTTTCA
Statistics
Matches: 207, Mismatches: 37, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
88 1 0.00
89 38 0.18
90 166 0.80
91 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.39
Consensus pattern (89 bp):
TGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTCTATTGATAATGCACCCATATA
CATTTCAACCATAGTATACTTTTC
Found at i:2388928 original size:135 final size:135
Alignment explanation
Indices: 2388689--2389047 Score: 442
Period size: 135 Copynumber: 2.7 Consensus size: 135
2388679 ATTGTGCACT
* * * * *
2388689 TTCAACTATAACAT-CT-TTATTGTTGATAATGTACTCATATGCATTTCAACTATAGTATACTTT
1 TTCAACTATAACATGCTCTT-CTATTGATAATGTACCCATATGCATTTCAACTATAGCACACTTT
* * * *
2388752 T-TATTGATAATGTACCCATATACATTTCAACCATAGTATACTTTTCTGTTGACAATGTACCCAT
65 TCTGTTGATAATGCACCCATATGCATTTCAACCATAGCATACTTTTCTGTTGACAATGTACCCAT
2388816 ATACAA
130 ATACAA
* * * *
2388822 TTCAACTCTAGCATGCTCTTCTATTGATAATGCACCCATATGCATTTCAACTCTAGCACACTTTT
1 TTCAACTATAACATGCTCTTCTATTGATAATGTACCCATATGCATTTCAACTATAGCACACTTTT
2388887 CTGTTGATAATGCACCCATATGCATTTCAACTC-TAGCATACTTTTCTGTTGACAATGTACCCAT
66 CTGTTGATAATGCACCCATATGCATTTCAAC-CATAGCATACTTTTCTGTTGACAATGTACCCAT
*
2388951 ATACAT
130 ATACAA
* * * * * *
2388957 TTCAACTATAATATGTTTTTCTGTTGATAATGTACCTATATACATTTCAACTATAGCATC-C-TT
1 TTCAACTATAACATGCTCTTCTATTGATAATGTACCCATATGCATTTCAACTATAGCA-CACTTT
* *
2389020 TCATGCTAATAATGCACCCATATGCATT
65 TC-TGTTGATAATGCACCCATATGCATT
2389048 AATATTTTCA
Statistics
Matches: 194, Mismatches: 26, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
133 12 0.06
134 44 0.23
135 136 0.70
136 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (135 bp):
TTCAACTATAACATGCTCTTCTATTGATAATGTACCCATATGCATTTCAACTATAGCACACTTTT
CTGTTGATAATGCACCCATATGCATTTCAACCATAGCATACTTTTCTGTTGACAATGTACCCATA
TACAA
Found at i:2389421 original size:22 final size:20
Alignment explanation
Indices: 2389380--2389435 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 20
2389370 TGACCCTTCA
2389380 GTATCGATACCCCTACTATG
1 GTATCGATACCCCTACTATG
*
2389400 GTATCGATACTACCCTATTATG
1 GTATCGATAC--CCCTACTATG
*
2389422 GTAACGATACCCCT
1 GTATCGATACCCCT
2389436 TCCAGTATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.44
22 18 0.56
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:2389503 original size:20 final size:20
Alignment explanation
Indices: 2389474--2389525 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2389464 ATGTAGTCTT
2389474 GTATCGATACCCTCACCATG
1 GTATCGATACCCTCACCATG
*
2389494 GTATCAATACCCTCACCATG
1 GTATCGATACCCTCACCATG
2389514 GTATCGATACCC
1 GTATCGATACCC
2389526 CCTTAGGTAT
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:0.35, G:0.13, T:0.25
Consensus pattern (20 bp):
GTATCGATACCCTCACCATG
Found at i:2389542 original size:92 final size:93
Alignment explanation
Indices: 2389379--2389594 Score: 246
Period size: 92 Copynumber: 2.3 Consensus size: 93
2389369 CTGACCCTTC
* **
2389379 AGTATCGATACCC-CTACTATGGTATCGATACTACCCTATTATGGTAACGATACCCCTTCCAGTA
1 AGTATCGATACCCTC-ACCATGGTATCGATACTACCCTACCATGGTAACGATACCCCTT-CAGTA
* *
2389443 TCAATACCAAAATTAGCTTTGATGTAGT-CT
64 TCAATACCAAAATTAGATTCGATGT-GTACT
* *
2389473 TGTATCGATACCCTCACCATGGTATC-A-A-TACCCTCACCATGGTATCGATACCCCCTT-AGGT
1 AGTATCGATACCCTCACCATGGTATCGATACTACCCT-ACCATGGTAACGATA-CCCCTTCA-GT
* *
2389534 ATCGATACCAAAATTAGATTCGATGTTTACT
63 ATCAATACCAAAATTAGATTCGATGTGTACT
*
2389565 AGTATCGATACCCTTACCATGGTATCGATA
1 AGTATCGATACCCTCACCATGGTATCGATA
2389595 ACATATCGCT
Statistics
Matches: 104, Mismatches: 11, Indels: 14
0.81 0.09 0.11
Matches are distributed among these distances:
91 8 0.08
92 64 0.62
93 8 0.08
94 23 0.22
95 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (93 bp):
AGTATCGATACCCTCACCATGGTATCGATACTACCCTACCATGGTAACGATACCCCTTCAGTATC
AATACCAAAATTAGATTCGATGTGTACT
Found at i:2395561 original size:45 final size:45
Alignment explanation
Indices: 2395443--2395783 Score: 334
Period size: 45 Copynumber: 7.6 Consensus size: 45
2395433 ATAACATAGG
* * * *
2395443 TTCTGTTGATAATGCACCCTTATGCATTTCAACTATAGTATACTT
1 TTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATACTT
2395488 TT-TGTTGATAATGTACCCATATACATTTCAACCATAGTATACTT
1 TTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATACTT
* * * * * *
2395532 TTCTCTTAACAATGTACCCATATACATTTCAA-CATAGCATGCTC
1 TTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATACTT
* ** *
2395576 TTCTGTTGATAATGCACCCATATGTATTTCAACTC-TAGCATACTT
1 TTCTGTTGATAATGTACCCATATACATTTCAAC-CATAGTATACTT
* * * *
2395621 TTATGTTGATAATGCATCCATATGCATTTCAACTC-TA-TCATACTT
1 TTCTGTTGATAATGTACCCATATACATTTCAAC-CATAGT-ATACTT
* * * *
2395666 TTCTGTTGACAATGTACCCATATACATTTCAACTATAATATGCTT
1 TTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATACTT
* * * *
2395711 TTATGTTGATAATGTACCCATATACATTTCAACTATAGCAT-CCT
1 TTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATACTT
* * * *
2395755 TTCATGCTAATAATGCACCCATATGCATT
1 TTC-TGTTGATAATGTACCCATATACATT
2395784 AATATTTTCA
Statistics
Matches: 250, Mismatches: 39, Indels: 14
0.83 0.13 0.05
Matches are distributed among these distances:
44 79 0.32
45 169 0.68
46 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (45 bp):
TTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATACTT
Found at i:2395619 original size:89 final size:89
Alignment explanation
Indices: 2395446--2395783 Score: 374
Period size: 90 Copynumber: 3.8 Consensus size: 89
2395436 ACATAGGTTC
* * * * *
2395446 TGTTGATAATGCACCCTTATGCATTTCAACTATAGTATACTTTTTGTTGATAATGTACCCATATA
1 TGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTCTGTTGATAATGCACCCATATA
*
2395511 CATTTCAAC-CATAGTATACTTTTC
66 CATTTCAACTC-TAGTATACTTTTA
* * * * *
2395535 TCTTAACAATGTACCCATATACATTTCAAC-ATAGCATGCTCTTCTGTTGATAATGCACCCATAT
1 TGTTGATAATGCACCCATATACATTTCAACTATAGCATACT-TTCTGTTGATAATGCACCCATAT
** *
2395599 GTATTTCAACTCTAGCATACTTTTA
65 ACATTTCAACTCTAGTATACTTTTA
* * * * * *
2395624 TGTTGATAATGCATCCATATGCATTTCAACTCTATCATACTTTTCTGTTGACAATGTACCCATAT
1 TGTTGATAATGCACCCATATACATTTCAACTATAGCATAC-TTTCTGTTGATAATGCACCCATAT
* * *
2395689 ACATTTCAACTATAATATGCTTTTA
65 ACATTTCAACTCTAGTATACTTTTA
* * * *
2395714 TGTTGATAATGTACCCATATACATTTCAACTATAGCATCCTTTCATGCTAATAATGCACCCATAT
1 TGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTC-TGTTGATAATGCACCCATAT
*
2395779 GCATT
65 ACATT
2395784 AATATTTTCA
Statistics
Matches: 202, Mismatches: 42, Indels: 9
0.80 0.17 0.04
Matches are distributed among these distances:
88 8 0.04
89 92 0.46
90 101 0.50
91 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (89 bp):
TGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTCTGTTGATAATGCACCCATATA
CATTTCAACTCTAGTATACTTTTA
Found at i:2395802 original size:135 final size:134
Alignment explanation
Indices: 2395446--2395783 Score: 403
Period size: 135 Copynumber: 2.5 Consensus size: 134
2395436 ACATAGGTTC
* * * * * * *
2395446 TGTTGATAATGCACCCTTATGCATTTCAACTATAGTATACTTT-TTGTTGATAATGTACCCATAT
1 TGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTCATGCTAATAATGCACCCATAT
* * *
2395510 ACATTTCAAC-CATAGT-ATACTTTTCTCTTAACAATGTACCCATATACATTTCAACATAGCATG
66 GCATTTAAACTC-TA-TCATACTTTTCTCTTAACAATGTACCCATATACATTTCAACATAACATG
*
2395573 CTCTTC
129 CTCTTA
** * * * * *
2395579 TGTTGATAATGCACCCATATGTATTTCAACTCTAGCATACTTTTATGTTGATAATGCATCCATAT
1 TGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTCATGCTAATAATGCACCCATAT
* * * *
2395644 GCATTTCAACTCTATCATACTTTTCTGTTGACAATGTACCCATATACATTTCAACTATAATATGC
66 GCATTTAAACTCTATCATACTTTTCTCTTAACAATGTACCCATATACATTTCAAC-ATAACATGC
*
2395709 TTTTA
130 TCTTA
* *
2395714 TGTTGATAATGTACCCATATACATTTCAACTATAGCATCCTTTCATGCTAATAATGCACCCATAT
1 TGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTCATGCTAATAATGCACCCATAT
2395779 GCATT
66 GCATT
2395784 AATATTTTCA
Statistics
Matches: 178, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
133 40 0.22
134 66 0.37
135 72 0.40
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (134 bp):
TGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTCATGCTAATAATGCACCCATAT
GCATTTAAACTCTATCATACTTTTCTCTTAACAATGTACCCATATACATTTCAACATAACATGCT
CTTA
Found at i:2399509 original size:59 final size:59
Alignment explanation
Indices: 2399435--2399901 Score: 674
Period size: 59 Copynumber: 7.9 Consensus size: 59
2399425 GATTACCAAA
* * *
2399435 AGAGCACTAAGTGTGCTAAAATGATAGGGAAATCGTATTAAATGTATGAATTTCCAGAT
1 AGAGCACTAAGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
2399494 GGAGCACTAAGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTTTGAATTTCCAGAT
1 AGAGCACTAAGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
2399553 AGAGCACTAAGTGTGCT-AAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGAGCACTAAGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
2399611 GGAGCACTAAGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTACGAATTTCCAGAT
1 AGAGCACTAAGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * **
2399670 AGAGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGTATTTATAGAT
1 AGAGCACTAAGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * *
2399729 A-AGGCACTTCA-CGTGCTAAAATGATAGGGAAATCATACTAAATGTATGAATTTCCAAAT
1 AGA-GCAC-TAAGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
2399788 AG-GACACTTCA-TGTGCTAAAATGATAGGGAAATCATACTAAGTGTATGAATTTTCAGAT
1 AGAG-CAC-TAAGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
2399847 AGAGCACTAAGTGTGCTAAAATGATAAGGAAATCATAGTAATTGTATGAATTTCC
1 AGAGCACTAAGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATGAATTTCC
2399902 TATGGGAATT
Statistics
Matches: 367, Mismatches: 34, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
58 59 0.16
59 305 0.83
60 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (59 bp):
AGAGCACTAAGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:2409217 original size:200 final size:202
Alignment explanation
Indices: 2408871--2409275 Score: 778
Period size: 200 Copynumber: 2.0 Consensus size: 202
2408861 TGTTGCCTAA
*
2408871 ACGAGTCACACACTTCAAGCAAATCTCGCACATATTGTCTAGCATCTTCACTAGGAAAGCCCCCA
1 ACGAGTCACACACTTCAAGCAAA-CTCGCACATATTGTCTAGCATCTTCACTAGGAAAGCCCCAA
2408936 AACTGACATATAGAATTGAACATGTTGAACATCACCGGTTTGAGTTCAAAGTGGGATGCCTGTAT
65 AACTGACATATAGAATTGAACATGTTGAACATCACCGGTTTGAGTTCAAAGTGGGATGCCTGTAT
2409001 TTCTAGTGCCACTATTCTAGGGTTGAGATCATCGATAATAGGATTTAAGTTATCTCGTATCGCTT
130 TTCTAGTGCCACTATTCTAGGGTTGAGATCATCGATAATAGGATTTAAGTTATCTCGTATCGCTT
2409066 GTGGTCTT
195 GTGGTCTT
2409074 ACGAGTCACACACTTCAAGCAAA-TCGCACATATTGTCTAGCATCTTCACTAGGAAAG-CCCAAA
1 ACGAGTCACACACTTCAAGCAAACTCGCACATATTGTCTAGCATCTTCACTAGGAAAGCCCCAAA
2409137 ACTGACATATAGAATTGAACATGTTGAACATCACCGGTTTGAGTTCAAAGTGGGATGCCTGTATT
66 ACTGACATATAGAATTGAACATGTTGAACATCACCGGTTTGAGTTCAAAGTGGGATGCCTGTATT
2409202 TCTAGTGCCACTATTCTAGGGTTGAGATCATCGATAATAGGATTTAAGTTATCTCGTATCGCTTG
131 TCTAGTGCCACTATTCTAGGGTTGAGATCATCGATAATAGGATTTAAGTTATCTCGTATCGCTTG
2409267 TGGTCTT
196 TGGTCTT
2409274 AC
1 AC
2409276 AACATTTTGA
Statistics
Matches: 201, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
200 144 0.72
201 34 0.17
203 23 0.11
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (202 bp):
ACGAGTCACACACTTCAAGCAAACTCGCACATATTGTCTAGCATCTTCACTAGGAAAGCCCCAAA
ACTGACATATAGAATTGAACATGTTGAACATCACCGGTTTGAGTTCAAAGTGGGATGCCTGTATT
TCTAGTGCCACTATTCTAGGGTTGAGATCATCGATAATAGGATTTAAGTTATCTCGTATCGCTTG
TGGTCTT
Found at i:2411927 original size:21 final size:22
Alignment explanation
Indices: 2411897--2411938 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2411887 TTAGGATCAA
*
2411897 TGGGATTAGGAATAGGATTTGG
1 TGGGATTAGGAAGAGGATTTGG
2411919 TGGGA-TAGGAAGAGGATTTG
1 TGGGATTAGGAAGAGGATTTG
2411939 TAGGAGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.29
Consensus pattern (22 bp):
TGGGATTAGGAAGAGGATTTGG
Found at i:2419507 original size:18 final size:18
Alignment explanation
Indices: 2419484--2419519 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2419474 ACTTGGGTTG
2419484 AATTTTTCTATGGCTAGA
1 AATTTTTCTATGGCTAGA
*
2419502 AATTTTTCTATGTCTAGA
1 AATTTTTCTATGGCTAGA
2419520 GTGATTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (18 bp):
AATTTTTCTATGGCTAGA
Found at i:2421685 original size:2 final size:2
Alignment explanation
Indices: 2421680--2421723 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2421670 TTTTTTTCTA
2421680 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
2421722 AT
1 AT
2421724 TTTTTAGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2426887 original size:14 final size:14
Alignment explanation
Indices: 2426868--2426895 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2426858 GATGATGGAG
2426868 GATGGTGATGGAAA
1 GATGGTGATGGAAA
2426882 GATGGTGATGGAAA
1 GATGGTGATGGAAA
2426896 TAGATAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GATGGTGATGGAAA
Found at i:2428932 original size:24 final size:24
Alignment explanation
Indices: 2428905--2428950 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2428895 GATGTCAACA
*
2428905 GACACAACTCTTGGCACTTCAAGT
1 GACACAACTCTTGGAACTTCAAGT
***
2428929 GACATTTCTCTTGGAACTTCAA
1 GACACAACTCTTGGAACTTCAA
2428951 ACGACATTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (24 bp):
GACACAACTCTTGGAACTTCAAGT
Found at i:2428956 original size:24 final size:24
Alignment explanation
Indices: 2428912--2428958 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2428902 ACAGACACAA
* **
2428912 CTCTTGGCACTTCAAGTGACATTT
1 CTCTTGGAACTTCAAACGACATTT
2428936 CTCTTGGAACTTCAAACGACATT
1 CTCTTGGAACTTCAAACGACATT
2428959 ATCGTTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (24 bp):
CTCTTGGAACTTCAAACGACATTT
Found at i:2430062 original size:26 final size:25
Alignment explanation
Indices: 2430023--2430074 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
2430013 TAGAAAAGGT
2430023 TAAGAAAACAGAAA-AAGTAATGAAAA
1 TAAGAAAACAGAAAGAA-TAA-GAAAA
2430049 TAAGAAAA-ATGAAAGAATAAGAAAA
1 TAAGAAAACA-GAAAGAATAAGAAAA
2430074 T
1 T
2430075 GAAATAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.29
26 15 0.62
27 2 0.08
ACGTcount: A:0.69, C:0.02, G:0.15, T:0.13
Consensus pattern (25 bp):
TAAGAAAACAGAAAGAATAAGAAAA
Found at i:2430075 original size:16 final size:16
Alignment explanation
Indices: 2430047--2430094 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
2430037 AAGTAATGAA
2430047 AATAAGAAAAATGAAAG
1 AATAAG-AAAATGAAAG
*
2430064 AATAAGAAAATGAAAT
1 AATAAGAAAATGAAAG
*
2430080 AGTAAGAAAATGAAA
1 AATAAGAAAATGAAA
2430095 ATAACTTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 23 0.79
17 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
AATAAGAAAATGAAAG
Found at i:2430730 original size:14 final size:14
Alignment explanation
Indices: 2430711--2430738 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2430701 GATGATGGAG
2430711 GATGGTGATGGAAA
1 GATGGTGATGGAAA
2430725 GATGGTGATGGAAA
1 GATGGTGATGGAAA
2430739 TAGACCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GATGGTGATGGAAA
Found at i:2439682 original size:31 final size:31
Alignment explanation
Indices: 2439645--2439709 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
2439635 ATACTCTAGC
2439645 GTCTATCCTACTCTAGCGTCTATCCATTTTA
1 GTCTATCCTACTCTAGCGTCTATCCATTTTA
*
2439676 GTCTATCCTACTCTAGCGTCTATCCCTTTTA
1 GTCTATCCTACTCTAGCGTCTATCCATTTTA
2439707 GTC
1 GTC
2439710 GATTGGATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (31 bp):
GTCTATCCTACTCTAGCGTCTATCCATTTTA
Found at i:2439700 original size:17 final size:17
Alignment explanation
Indices: 2439628--2439700 Score: 98
Period size: 17 Copynumber: 4.5 Consensus size: 17
2439618 TATAGGCGTT
*
2439628 GTCTATCATACTCTAGC
1 GTCTATCCTACTCTAGC
2439645 GTCTATCCTACTCTAGC
1 GTCTATCCTACTCTAGC
* *
2439662 GTCTATCC-ATTTTA--
1 GTCTATCCTACTCTAGC
2439676 GTCTATCCTACTCTAGC
1 GTCTATCCTACTCTAGC
2439693 GTCTATCC
1 GTCTATCC
2439701 CTTTTAGTCG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
14 8 0.17
15 4 0.08
16 4 0.08
17 32 0.67
ACGTcount: A:0.19, C:0.32, G:0.11, T:0.38
Consensus pattern (17 bp):
GTCTATCCTACTCTAGC
Found at i:2442777 original size:20 final size:20
Alignment explanation
Indices: 2442752--2442790 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2442742 AAATTAATCC
*
2442752 CCAACGGCTCCAAACAACCT
1 CCAACGGCTACAAACAACCT
*
2442772 CCAACGGCTAGAAACAACC
1 CCAACGGCTACAAACAACC
2442791 ACAACAACAT
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:0.38, C:0.41, G:0.13, T:0.08
Consensus pattern (20 bp):
CCAACGGCTACAAACAACCT
Found at i:2446059 original size:20 final size:21
Alignment explanation
Indices: 2446034--2446073 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2446024 CTCTATATAG
2446034 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
*
2446054 TAGTATGGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
2446074 CCCAACGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:2451445 original size:2 final size:2
Alignment explanation
Indices: 2451438--2451462 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2451428 ATTATGTATT
2451438 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2451463 TTAATACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2453682 original size:25 final size:25
Alignment explanation
Indices: 2453653--2453709 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
2453643 TTACAAGCCT
*
2453653 AAAATAAAAAATCGGGTCCCTTCAC
1 AAAATAAAAAATCGGGCCCCTTCAC
* * *
2453678 AAAAT-GAAAATGGGGCCCCTTTAC
1 AAAATAAAAAATCGGGCCCCTTCAC
*
2453702 AAACTAAA
1 AAAATAAA
2453710 GCCCATACAC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.19
Consensus pattern (25 bp):
AAAATAAAAAATCGGGCCCCTTCAC
Found at i:2459878 original size:19 final size:20
Alignment explanation
Indices: 2459841--2459879 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2459831 AGGTAAAGGA
*
2459841 AGTATCGATACTCACTAGGT
1 AGTACCGATACTCACTAGGT
2459861 AGTACCGATACT-ACTAGGT
1 AGTACCGATACTCACTAGGT
2459880 TTGCTCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (20 bp):
AGTACCGATACTCACTAGGT
Found at i:2459971 original size:20 final size:21
Alignment explanation
Indices: 2459946--2459985 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
2459936 CTCTATATAG
2459946 TAGTATCGATACCA-TAGGCA
1 TAGTATCGATACCATTAGGCA
2459966 TAGTATCGATACCATTAGGC
1 TAGTATCGATACCATTAGGC
2459986 CCCAATAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATTAGGCA
Found at i:2463442 original size:18 final size:18
Alignment explanation
Indices: 2463419--2463465 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2463409 ATGCAAAAAT
*
2463419 GGTACTGATACACAAAGG
1 GGTACTGATACACAAAGC
*
2463437 GGTACTGATACACAGAGC
1 GGTACTGATACACAAAGC
*
2463455 GGTACCGATAC
1 GGTACTGATAC
2463466 TACTCTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (18 bp):
GGTACTGATACACAAAGC
Found at i:2465941 original size:90 final size:91
Alignment explanation
Indices: 2465822--2465999 Score: 259
Period size: 90 Copynumber: 2.0 Consensus size: 91
2465812 TAATCCAGAA
* * *** *
2465822 TATTTAATTTCAATTAATTAAATAGAGATTTAATTAATTTGAAATAAT-AAAATTTCTGATATGA
1 TATTAAATTCCAATTAATTAAATAGAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
*
2465886 TTAGGGTAACTTGGATATAAAAGGAT
66 CTAGGGTAACTTGGATATAAAAGGAT
*
2465912 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAAACCCTAATATG
1 TATTAAATTCCAATTAATTAAATAGAGATTTAATTAATTTGAAATAAT-AAAAAACCCTAATATG
*
2465977 ACTAGGGTAACTTGGCTATAAAA
65 ACTAGGGTAACTTGGATATAAAA
2466000 TGGTGTGTTA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 45 0.58
92 32 0.42
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (91 bp):
TATTAAATTCCAATTAATTAAATAGAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
CTAGGGTAACTTGGATATAAAAGGAT
Found at i:2472509 original size:90 final size:91
Alignment explanation
Indices: 2472389--2472567 Score: 288
Period size: 90 Copynumber: 2.0 Consensus size: 91
2472379 TAATCCCGAA
* * * * *
2472389 TATTTAATTTCAATTAATTAATTATAGATTTAATTAATTTGAAATAAT-AAAATCCCTGATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
*
2472453 TTAGGGTAACTTGGATATAAAAGGAT
66 CTAGGGTAACTTGGATATAAAAGGAT
2472479 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
*
2472544 CTAGGGTAACTTGGCTATAAAAGG
66 CTAGGGTAACTTGGATATAAAAGG
2472568 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 45 0.56
91 36 0.44
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (91 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
CTAGGGTAACTTGGATATAAAAGGAT
Found at i:2473320 original size:11 final size:11
Alignment explanation
Indices: 2473299--2473328 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2473289 TATAAATAAC
2473299 AATATAAACCCA
1 AATA-AAACCCA
2473311 AATAAAACCCA
1 AATAAAACCCA
2473322 AATAAAA
1 AATAAAA
2473329 TCCCCAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.67, C:0.20, G:0.00, T:0.13
Consensus pattern (11 bp):
AATAAAACCCA
Found at i:2478163 original size:27 final size:27
Alignment explanation
Indices: 2478129--2478187 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
2478119 TTATAACCAA
2478129 ACCTCATCTAGAGAATTTAGTAAACCT
1 ACCTCATCTAGAGAATTTAGTAAACCT
2478156 ACCTCATCTAGAGAATTTAGTAAACCT
1 ACCTCATCTAGAGAATTTAGTAAACCT
2478183 ACCTC
1 ACCTC
2478188 GCTAGACCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (27 bp):
ACCTCATCTAGAGAATTTAGTAAACCT
Found at i:2484714 original size:59 final size:60
Alignment explanation
Indices: 2484621--2484778 Score: 165
Period size: 59 Copynumber: 2.6 Consensus size: 60
2484611 ATGTTTTCAT
* * * * *
2484621 ATTTCCTATTGCTCAATTCACGGCATTTTGAATCAGCAATGCCTCACTTGAGGAATCAAC
1 ATTTCCTATTGCTCGATTCACGACATTTCGAATCAGCAACGCCCCACTTGAGGAATCAAC
* * ** * * *
2484681 ATTTCCT-TTGCTCGATTCATGATATTTCGAATCAGTGACGCCCCGCTTGAGGGATTAAC
1 ATTTCCTATTGCTCGATTCACGACATTTCGAATCAGCAACGCCCCACTTGAGGAATCAAC
* * * *
2484740 ATGTCCTATTGGTCGATTCACGCCATTTCGAATAAGCAA
1 ATTTCCTATTGCTCGATTCACGACATTTCGAATCAGCAA
2484779 AAGTTCTTTG
Statistics
Matches: 77, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
59 46 0.60
60 31 0.40
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (60 bp):
ATTTCCTATTGCTCGATTCACGACATTTCGAATCAGCAACGCCCCACTTGAGGAATCAAC
Found at i:2491855 original size:3 final size:3
Alignment explanation
Indices: 2491847--2491894 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
2491837 TACTCGTAGG
*
2491847 ATT ATT ATT ATT ATT CATAT GTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT -AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
2491894 A
1 A
2491895 GGATTTCGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 37 0.90
4 3 0.07
5 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2498072 original size:39 final size:39
Alignment explanation
Indices: 2498029--2498120 Score: 139
Period size: 39 Copynumber: 2.4 Consensus size: 39
2498019 TCTATGACTT
*
2498029 GTAAGTCCTTACCGTAAGCTCCTCAGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAAGCTCCTCAGCTTTGTGCTCAGG
* * *
2498068 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTTAGG
1 GTAAGTCCTTACCGCAAGCTCCTCAGCTTTGTGCTCAGG
*
2498107 GTAAGTTCTTACCG
1 GTAAGTCCTTACCG
2498121 AAAGTCTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.16, C:0.27, G:0.25, T:0.32
Consensus pattern (39 bp):
GTAAGTCCTTACCGCAAGCTCCTCAGCTTTGTGCTCAGG
Found at i:2498945 original size:20 final size:20
Alignment explanation
Indices: 2498920--2498957 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2498910 ACTAATATCT
* *
2498920 TCGTCAAATGGTCTTAACTC
1 TCGTCAAAAGGTCATAACTC
2498940 TCGTCAAAAGGTCATAAC
1 TCGTCAAAAGGTCATAAC
2498958 CTTTTGATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (20 bp):
TCGTCAAAAGGTCATAACTC
Found at i:2498988 original size:2 final size:2
Alignment explanation
Indices: 2498981--2499018 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2498971 TTCCTCTCCC
2498981 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
2499019 GTTAGTTAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2505872 original size:12 final size:12
Alignment explanation
Indices: 2505855--2505885 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2505845 ATATATTGAT
2505855 AATCAAATGAAA
1 AATCAAATGAAA
2505867 AATCAAATGAAA
1 AATCAAATGAAA
*
2505879 AAACAAA
1 AATCAAA
2505886 CCTGAGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (12 bp):
AATCAAATGAAA
Found at i:2516388 original size:31 final size:31
Alignment explanation
Indices: 2516362--2516465 Score: 190
Period size: 31 Copynumber: 3.4 Consensus size: 31
2516352 CCATATCACA
* *
2516362 TGTACTTTTCACATATTCACTTCATATAACT
1 TGTACTTTTCACATATTCACATCACATAACT
2516393 TGTACTTTTCACATATTCACATCACATAACT
1 TGTACTTTTCACATATTCACATCACATAACT
2516424 TGTACTTTTCACATATTCACATCACATAACT
1 TGTACTTTTCACATATTCACATCACATAACT
2516455 TGTACTTTTCA
1 TGTACTTTTCA
2516466 TTTCATTTCA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.42
Consensus pattern (31 bp):
TGTACTTTTCACATATTCACATCACATAACT
Found at i:2516437 original size:18 final size:18
Alignment explanation
Indices: 2516382--2516465 Score: 53
Period size: 18 Copynumber: 5.2 Consensus size: 18
2516372 ACATATTCAC
*
2516382 TTCATATAACTTGTACTT
1 TTCACATAACTTGTACTT
*
2516400 TTCACAT-A-TT-CAC--
1 TTCACATAACTTGTACTT
*
2516413 ATCACATAACTTGTACTT
1 TTCACATAACTTGTACTT
*
2516431 TTCACAT-A-TT-CAC--
1 TTCACATAACTTGTACTT
*
2516444 ATCACATAACTTGTACTT
1 TTCACATAACTTGTACTT
2516462 TTCA
1 TTCA
2516466 TTTCATTTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 20
0.62 0.12 0.26
Matches are distributed among these distances:
13 12 0.26
14 2 0.04
15 8 0.17
16 8 0.17
17 2 0.04
18 15 0.32
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.42
Consensus pattern (18 bp):
TTCACATAACTTGTACTT
Found at i:2516734 original size:24 final size:24
Alignment explanation
Indices: 2516676--2516734 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
2516666 ACAATGGTAT
* *
2516676 TAATACGAGAGTGCACGAATGCAC
1 TAATACAAGATTGCACGAATGCAC
2516700 TAATACAAGATTGCACGAATGCAC
1 TAATACAAGATTGCACGAATGCAC
2516724 TAATACAAGAT
1 TAATACAAGAT
2516735 CAATCGATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (24 bp):
TAATACAAGATTGCACGAATGCAC
Found at i:2530428 original size:24 final size:24
Alignment explanation
Indices: 2530399--2530470 Score: 108
Period size: 24 Copynumber: 2.9 Consensus size: 24
2530389 CTATTCTTTC
2530399 GCTTCAATTGAACTCAAATTTTAG
1 GCTTCAATTGAACTCAAATTTTAG
*
2530423 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAACTCAAATTTTAG
*
2530447 GCTTCAATCGAACTTCTAAATTTT
1 GCTTCAATTGAAC-TC-AAATTTT
2530471 TTTTTTGAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 34 0.79
25 2 0.05
26 7 0.16
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAACTCAAATTTTAG
Found at i:2531224 original size:16 final size:16
Alignment explanation
Indices: 2531205--2531258 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
2531195 GTTAGTTTAT
2531205 ATTATTTTTAGATTAA
1 ATTATTTTTAGATTAA
*
2531221 ATTATTTTT-GTTTAA
1 ATTATTTTTAGATTAA
* * *
2531236 ATTAATGTTTATATCAA
1 ATT-ATTTTTAGATTAA
2531253 ATTATT
1 ATTATT
2531259 GTAGTTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 8 0.27
16 16 0.53
17 6 0.20
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (16 bp):
ATTATTTTTAGATTAA
Found at i:2532348 original size:14 final size:16
Alignment explanation
Indices: 2532316--2532353 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
2532306 TATATTATTA
2532316 TTTATAATTACTAATTT
1 TTTATAATTAC-AATTT
2532333 TTTATAATTA-AATTT
1 TTTATAATTACAATTT
2532348 TATTAT
1 T-TTAT
2532354 TTATTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 4 0.20
17 10 0.50
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATAATTACAATTT
Found at i:2533347 original size:24 final size:24
Alignment explanation
Indices: 2533320--2533386 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
2533310 ATAATGGTTT
2533320 AATTCTGTTTAATTTATTTATGTA
1 AATTCTGTTTAATTTATTTATGTA
* *
2533344 AATTCTATTTAATTTATGTATGTA
1 AATTCTGTTTAATTTATTTATGTA
* * *
2533368 AATTCCGCTTAATTCATTT
1 AATTCTGTTTAATTTATTT
2533387 CAAACCATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (24 bp):
AATTCTGTTTAATTTATTTATGTA
Done.