Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008413.1 Hibiscus syriacus cultivar Beakdansim tig00111191_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: 2772818
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:2280119 original size:15 final size:15
Alignment explanation
Indices: 2280088--2280134 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
2280078 ACCCCCTTTC
2280088 TTTTTCTTCTCTCTTTT
1 TTTTTCTT-TCT-TTTT
2280105 TTTTTCTTTCTTTTT
1 TTTTTCTTTCTTTTT
*
2280120 TTTTCCTTT-TTTTT
1 TTTTTCTTTCTTTTT
2280134 T
1 T
2280135 CTTCAAGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 6 0.21
15 12 0.41
16 3 0.10
17 8 0.28
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTCTTTCTTTTT
Found at i:2280120 original size:16 final size:17
Alignment explanation
Indices: 2280083--2280123 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2280073 CCTTGACCCC
*
2280083 CTTTCTTTTTCTTCTCT
1 CTTTTTTTTTCTTCTCT
2280100 CTTTTTTTTTCTT-TCT
1 CTTTTTTTTTCTTCTCT
2280116 -TTTTTTTT
1 CTTTTTTTT
2280124 CCTTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.35
16 3 0.13
17 12 0.52
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
CTTTTTTTTTCTTCTCT
Found at i:2290791 original size:17 final size:17
Alignment explanation
Indices: 2290751--2290792 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2290741 ATACTTGCAA
*
2290751 ATAAAACATATAAATATT
1 ATAAAA-ATATAAATATC
2290769 ATAAAAATAATAAATA-C
1 ATAAAAAT-ATAAATATC
2290786 ATAAAAA
1 ATAAAAA
2290793 ATTTGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATATAAATATC
Found at i:2291507 original size:20 final size:21
Alignment explanation
Indices: 2291484--2291528 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2291474 CATTATATGT
**
2291484 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
2291504 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
2291525 ATAT
1 ATAT
2291529 CACTAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:2292962 original size:3 final size:3
Alignment explanation
Indices: 2292954--2293063 Score: 157
Period size: 3 Copynumber: 36.7 Consensus size: 3
2292944 TTAATATATT
* * * *
2292954 TAA TAA TAA TAG TAA AAA TAA TAA TAA TAA TAA AAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
2293002 TAA TAA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2293050 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
2293064 TGGATAAAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2294184 original size:18 final size:18
Alignment explanation
Indices: 2294163--2294197 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2294153 AGTTAGTTTG
2294163 TTGTATTCTGTTACACCT
1 TTGTATTCTGTTACACCT
2294181 TTGTATTCTGTTACACC
1 TTGTATTCTGTTACACC
2294198 AGATTACCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (18 bp):
TTGTATTCTGTTACACCT
Found at i:2316443 original size:41 final size:41
Alignment explanation
Indices: 2316396--2316496 Score: 175
Period size: 41 Copynumber: 2.5 Consensus size: 41
2316386 ATTCGCGTTA
*
2316396 CATTTCGCGGTGCGATAGTTGAAAATCGCGTTGCAATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTC
* *
2316437 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTC
2316478 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
2316497 CTACAGTTGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTC
Found at i:2316446 original size:20 final size:20
Alignment explanation
Indices: 2316421--2316493 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
2316411 TAGTTGAAAA
*
2316421 TCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
2316441 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
2316462 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
2316482 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2316494 AGTCTACAGT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:2316467 original size:21 final size:21
Alignment explanation
Indices: 2316400--2316473 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
2316390 GCGTTACATT
*
2316400 TCGCGGTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
2316421 TCGCGTTGCAAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
2316441 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
2316462 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2316474 TTTTCATTTC
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:2316543 original size:20 final size:20
Alignment explanation
Indices: 2316509--2316594 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
2316499 ACAGTTGTCA
2316509 TTGCGATTTTT-CAAATTCG
1 TTGCGATTTTTCCAAATTCG
2316528 TTGCGATTTTTCCAAATTCG
1 TTGCGATTTTTCCAAATTCG
* * * **
2316548 TTGCGATAGTCTACAGTTGTCG
1 TTGCGAT-TTTTCCAAAT-TCG
*
2316570 TTGCGA-TTTTCCAAATTTG
1 TTGCGATTTTTCCAAATTCG
2316589 TTGCGA
1 TTGCGA
2316595 AAATTCGTTG
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
19 19 0.36
20 20 0.38
21 5 0.09
22 9 0.17
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (20 bp):
TTGCGATTTTTCCAAATTCG
Found at i:2317208 original size:41 final size:42
Alignment explanation
Indices: 2317124--2317210 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
2317114 CACTATTGGG
2317124 AATGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGA
1 AATGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGA
* * *
2317166 AATGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGA
1 AATGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGA
2317207 AATG
1 AATG
2317211 CAATGCGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
41 23 0.56
42 18 0.44
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (42 bp):
AATGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGA
Found at i:2318819 original size:160 final size:157
Alignment explanation
Indices: 2318556--2319100 Score: 732
Period size: 159 Copynumber: 3.4 Consensus size: 157
2318546 TTAGTCCATG
* * ** * *
2318556 ATTTCTTCAATTCCTCCTCCATTTTAAGTTCATTTTTACCAAATTTAAACTACATGCTCCTAAAC
1 ATTTCTTCAATTCGTCATTTATTTTAAGTTCTTTTTTACCAAATTTAAACCACATGCTCCTAAAC
* *
2318621 CATAGTAGAATACATGTTTACTTTCAATTCCTCTTTTTGATAACAATAATTTTTTAATTTTCAAT
66 CATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAAT--TTTTTTATTTTTCAAT
* *
2318686 TTAGTCATTCAATTTTTTATAATCTTCTT
129 TTAGTCCTTCAATTTTTTATAATCTCCTT
* * **
2318715 ATTTCTTCAATTCGTCATTTATTTTAAGTCTGTTTTTTACCAAATTTGAATTACATGCTCCTAAA
1 ATTTCTTCAATTCGTCATTTATTTTAAGT-TCTTTTTTACCAAATTTAAACCACATGCTCCTAAA
*
2318780 CCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAATTTTTTTATTTTTCAATT
65 CCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAATTTTTTTATTTTTCAATT
* * *
2318845 TAATCCTTAAATTTTTTATAATCCCCTT
130 TAGTCCTTCAATTTTTTATAATCTCCTT
* * * * *
2318873 ATTT-TTCAATTCATCATTTATTTTAAGTCCCTTTTTTTTACCAAATTTGAGCCATATGCTCCTA
1 ATTTCTTCAATTCGTCATTTATTTTAAGT---TCTTTTTTACCAAATTTAAACCACATGCTCCTA
* *
2318937 AACCATAGTAGAATACATGTGCACTTTCAATTTCTCTTTTTGATAACAATTTTTTTATTTTTCAA
63 AACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAATTTTTTTATTTTTCAA
* * *
2319002 TTTAGTCCTTCAATTTTTCATAATATCCTA
128 TTTAGTCCTTCAATTTTTTATAATCTCCTT
* * * * *
2319032 ATTCCTTCAATTTGTCATTTATTTTAAGTTCTTTTTTACCAAATTTAAATCACATGCTCATATAC
1 ATTTCTTCAATTCGTCATTTATTTTAAGTTCTTTTTTACCAAATTTAAACCACATGCTCCTAAAC
2319097 CATA
66 CATA
2319101 ATAAAATATA
Statistics
Matches: 341, Mismatches: 41, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
157 56 0.16
158 43 0.13
159 143 0.42
160 99 0.29
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.48
Consensus pattern (157 bp):
ATTTCTTCAATTCGTCATTTATTTTAAGTTCTTTTTTACCAAATTTAAACCACATGCTCCTAAAC
CATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAATTTTTTTATTTTTCAATTT
AGTCCTTCAATTTTTTATAATCTCCTT
Found at i:2322896 original size:20 final size:21
Alignment explanation
Indices: 2322859--2322898 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2322849 TTTTTTCTAC
2322859 GGAAGAAGACACAATTTGGTG
1 GGAAGAAGACACAATTTGGTG
*
2322880 GGAAGACGACA-AATTTGGT
1 GGAAGAAGACACAATTTGGT
2322899 TCCTGGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.38, C:0.10, G:0.33, T:0.20
Consensus pattern (21 bp):
GGAAGAAGACACAATTTGGTG
Found at i:2330399 original size:2 final size:2
Alignment explanation
Indices: 2330392--2330423 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2330382 TTATTGTAAT
2330392 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
2330424 GTGTTAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2335318 original size:42 final size:42
Alignment explanation
Indices: 2335272--2335360 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
2335262 GGTAGAAAGT
*
2335272 ATTTTCCGAAAAATATTTTCCTA-TGTTTGATAGCTT-TAATTG
1 ATTTTACGAAAAATATTTT-CTAGTGTTTGATAG-TTGTAATTG
*
2335314 ATTTTACGAAAAATATTTTTTAGTGTTTGATAGTTGTAATTG
1 ATTTTACGAAAAATATTTTCTAGTGTTTGATAGTTGTAATTG
2335356 ATTTT
1 ATTTT
2335361 TCTTAATGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 39 0.91
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (42 bp):
ATTTTACGAAAAATATTTTCTAGTGTTTGATAGTTGTAATTG
Found at i:2336058 original size:30 final size:30
Alignment explanation
Indices: 2336018--2336074 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2336008 TTATAAAATA
2336018 TAATTCATTTTACGTAAAATAATTTTTAAG
1 TAATTCATTTTACGTAAAATAATTTTTAAG
* * * *
2336048 TAATTTATTTTATGTAAATTATTTTTT
1 TAATTCATTTTACGTAAAATAATTTTT
2336075 TAAAAACCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (30 bp):
TAATTCATTTTACGTAAAATAATTTTTAAG
Found at i:2338208 original size:27 final size:27
Alignment explanation
Indices: 2338178--2338232 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2338168 ACCCTAATTT
2338178 TAATTAAATTAAATAAATTTAATCATC
1 TAATTAAATTAAATAAATTTAATCATC
2338205 TAATTAAATTAAATAAATTTAATCATC
1 TAATTAAATTAAATAAATTTAATCATC
2338232 T
1 T
2338233 TGTATTATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (27 bp):
TAATTAAATTAAATAAATTTAATCATC
Found at i:2338335 original size:25 final size:26
Alignment explanation
Indices: 2338299--2338350 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
2338289 ATATATCTTT
2338299 TATTTTTGTTTTAACTTA-TTAAATA
1 TATTTTTGTTTTAACTTATTTAAATA
*
2338324 TATTTTAT-TTTTATCTTATTTAAATA
1 TATTTT-TGTTTTAACTTATTTAAATA
2338350 T
1 T
2338351 CTTAACTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TATTTTTGTTTTAACTTATTTAAATA
Found at i:2340697 original size:6 final size:6
Alignment explanation
Indices: 2340686--2340727 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
2340676 AGAGAGGAAA
*
2340686 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG G-GAAG GAGAGG G
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG G
2340728 GTTGGGTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:2340707 original size:18 final size:17
Alignment explanation
Indices: 2340676--2340727 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
2340666 AACAATGGGA
* *
2340676 AGAGAGGAAAGAGAGGG
1 AGAGGGGAAGGAGAGGG
*
2340693 AGAGGGAGAGGGAGAGGG
1 AGAGGG-GAAGGAGAGGG
2340711 AGAGGGGAAGGAGAGGG
1 AGAGGGGAAGGAGAGGG
2340728 GTTGGGTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (17 bp):
AGAGGGGAAGGAGAGGG
Found at i:2344026 original size:22 final size:24
Alignment explanation
Indices: 2344001--2344044 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
2343991 ACATCATTTT
*
2344001 ATTTTTTTTTA-T-TTTTTTTCTA
1 ATTTATTTTTAGTCTTTTTTTCTA
2344023 ATTTATTTTTAGTCTTTTTTTC
1 ATTTATTTTTAGTCTTTTTTTC
2344045 GAGTTATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (24 bp):
ATTTATTTTTAGTCTTTTTTTCTA
Found at i:2347664 original size:32 final size:28
Alignment explanation
Indices: 2347628--2347741 Score: 108
Period size: 27 Copynumber: 4.0 Consensus size: 28
2347618 GCTCAACTCG
2347628 TGCTCATTAAAACATTTTGTTGCTCGACTCAT
1 TGCTCATTAAAA-A--TT-TTGCTCGACTCAT
*
2347660 TGCTCGTT-AAAATTTTGCTCGACTCAT
1 TGCTCATTAAAAATTTTGCTCGACTCAT
* *
2347687 TCCTCATT-AAAATTTTGCTCGACTC-G
1 TGCTCATTAAAAATTTTGCTCGACTCAT
* *
2347713 TGCTCTTTAAAAAAATTTTGCTCAACTCA
1 TGCTCATT--AAAAATTTTGCTCGACTCA
2347742 ACTCGTTGCT
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
26 6 0.08
27 36 0.51
28 2 0.03
29 16 0.23
30 1 0.01
31 3 0.04
32 7 0.10
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.39
Consensus pattern (28 bp):
TGCTCATTAAAAATTTTGCTCGACTCAT
Found at i:2347679 original size:27 final size:27
Alignment explanation
Indices: 2347647--2347724 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
2347637 AAACATTTTG
*
2347647 TTGCTCGACTCATTGCTCGTTAAAATT
1 TTGCTCGACTCATTGCTCATTAAAATT
*
2347674 TTGCTCGACTCATTCCTCATTAAAATT
1 TTGCTCGACTCATTGCTCATTAAAATT
* *
2347701 TTGCTCGACTC-GTGCTCTTTAAAA
1 TTGCTCGACTCATTGCTCATTAAAA
2347725 AAATTTTGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 10 0.22
27 36 0.78
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (27 bp):
TTGCTCGACTCATTGCTCATTAAAATT
Found at i:2353578 original size:27 final size:26
Alignment explanation
Indices: 2353547--2353605 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
2353537 AATTTGAATA
2353547 TAAAA-AAAGTATTTTTTTTATTTGGGT
1 TAAAATAAAGTA--TTTTTTATTTGGGT
**
2353574 TAAAATTTAGTATTTTTTATTTGGGT
1 TAAAATAAAGTATTTTTTATTTGGGT
2353600 TAAAAT
1 TAAAAT
2353606 TTAATTAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 20 0.69
27 5 0.17
28 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (26 bp):
TAAAATAAAGTATTTTTTATTTGGGT
Found at i:2357702 original size:23 final size:23
Alignment explanation
Indices: 2357669--2357715 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2357659 ATATTATTTA
*
2357669 AGAAACATTTTTTTTAATATAATT
1 AGAAACATTTTATTTAAT-TAATT
2357693 AGAAA-ATTTTATTTAATTAATT
1 AGAAACATTTTATTTAATTAATT
2357715 A
1 A
2357716 AAATCGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 11 0.50
24 5 0.23
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
AGAAACATTTTATTTAATTAATT
Found at i:2359885 original size:21 final size:21
Alignment explanation
Indices: 2359859--2359903 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2359849 GATTTCTGGG
* *
2359859 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2359880 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2359901 CAA
1 CAA
2359904 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2378677 original size:13 final size:15
Alignment explanation
Indices: 2378659--2378691 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
2378649 ATAAAATGTG
2378659 ATATATAT-TGTAA-
1 ATATATATGTGTAAC
2378672 ATATATATGTGTAAC
1 ATATATATGTGTAAC
2378687 ATATA
1 ATATA
2378692 GAAAGATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 5 0.28
15 5 0.28
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (15 bp):
ATATATATGTGTAAC
Found at i:2384506 original size:59 final size:59
Alignment explanation
Indices: 2384404--2384517 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 59
2384394 GCATATACCA
* * ** *
2384404 ATAGTTTGGGATGAAATTGAAATGTTCAAGAGTTTGGGGATTAATTTTA-AATGAGGGTT
1 ATAGTTTGGGATGAAATGGAAATGTTCAAAAGTTTAAGAATTAA-TTTAGAATGAGGGTT
*
2384463 ATAGTTTGGGATGAAATGGGAA-GTTCCAAAAGTTTAAGAATTAATTTAGAATGAG
1 ATAGTTTGGGATGAAATGGAAATGTT-CAAAAGTTTAAGAATTAATTTAGAATGAG
2384518 AATAATTCTA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 7 0.15
59 40 0.85
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATGGAAATGTTCAAAAGTTTAAGAATTAATTTAGAATGAGGGTT
Found at i:2384904 original size:16 final size:16
Alignment explanation
Indices: 2384885--2384915 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2384875 TCTAATTTGA
*
2384885 TAATGACACATATCAC
1 TAATGACAAATATCAC
2384901 TAATGACAAATATCA
1 TAATGACAAATATCA
2384916 TCACATGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (16 bp):
TAATGACAAATATCAC
Found at i:2385418 original size:23 final size:24
Alignment explanation
Indices: 2385372--2385424 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2385362 AAGAAACGTA
*
2385372 CCACAAGAGCATAGAAAAAGTGTG
1 CCACAAGAGCAGAGAAAAAGTGTG
2385396 CCACAAGAGCAGAGAAAAA-TGTG
1 CCACAAGAGCAGAGAAAAAGTGTG
*
2385419 TCACAA
1 CCACAA
2385425 TGACATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (24 bp):
CCACAAGAGCAGAGAAAAAGTGTG
Found at i:2387752 original size:223 final size:223
Alignment explanation
Indices: 2387362--2387804 Score: 613
Period size: 223 Copynumber: 2.0 Consensus size: 223
2387352 ATATGCATGG
* * *
2387362 TGATAGCATAGGCAGCACACTTGAAAGCTTTATGCTTTACGTCTCTTTTTAAATTTTTAGGTAAA
1 TGATAGCAGAGGCAGCACACTTGAAAGCTTTATGCTTTACATCTCTTTTTAAATTTTCAGGTAAA
* *
2387427 CTAAATATTTAATACCTAAACTATCAATTTTGATTCGTTATAGTACCTAAACTTTTAGTTTTTTC
66 CTAAATATTTAATACCTAAACGATCAATTTTGATTCGTTATAGTACCTAAACTTTTAATTTTTTC
* * * *
2387492 AAAATTATACCTCTCGTTTAGTTATTGTTTCATTTTAGTACCCCGCTAAAAACTTAACGTTAAG-
131 AAAATCATACCTATCATTTAGTTATTGTTTCATTTTAGTA-CCCGCTAAAAACTTAACATTAAGT
*
2387556 TTTT-AAA-AAAATTGAAAGTTTAGGCGC
195 TTTTAAAAGAAAATTAAAAGTTTAGGCGC
* *
2387583 TGATAGCAGAGGCAGCAGAGTTGAAAGCTTTATGCTTTTACATCTCTTTTTAAAATTTTCAGGTA
1 TGATAGCAGAGGCAGCACACTTGAAAGCTTTATGC-TTTACATCTCTTTTT-AAATTTTCAGGTA
** * * * * * * *
2387648 AACTACGTGTTTAGTATCTAAACGATCAGTTTTGGTTTGTTATAGTACTTAAACTTTTAATTTTT
64 AACTAAATATTTAATACCTAAACGATCAATTTTGATTCGTTATAGTACCTAAACTTTTAATTTTT
* * * *
2387713 TCAAAATCATTCCTATCATTTAGTTTTTGTTTTATTTTAGTACCCGTTAAAAACTTAACATTAAG
129 TCAAAATCATACCTATCATTTAGTTATTGTTTCATTTTAGTACCCGCTAAAAACTTAACATTAAG
2387778 TTTTTAAAAGAAAATTAAAAGTTTAGG
194 TTTTTAAAAGAAAATTAAAAGTTTAGG
2387805 TACTAAAACA
Statistics
Matches: 192, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
221 32 0.17
222 35 0.18
223 106 0.55
224 3 0.02
225 16 0.08
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (223 bp):
TGATAGCAGAGGCAGCACACTTGAAAGCTTTATGCTTTACATCTCTTTTTAAATTTTCAGGTAAA
CTAAATATTTAATACCTAAACGATCAATTTTGATTCGTTATAGTACCTAAACTTTTAATTTTTTC
AAAATCATACCTATCATTTAGTTATTGTTTCATTTTAGTACCCGCTAAAAACTTAACATTAAGTT
TTTAAAAGAAAATTAAAAGTTTAGGCGC
Found at i:2391462 original size:21 final size:21
Alignment explanation
Indices: 2391433--2391477 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2391423 ATTCTGACTA
2391433 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
2391454 TCGCGTTGCGATTTTTCTAAT
1 TCGCATTGCGATTTTCCAAAT
2391475 TCG
1 TCG
2391478 TAATGCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:2391507 original size:20 final size:20
Alignment explanation
Indices: 2391479--2391565 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
2391469 TCTAATTCGT
2391479 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* *
2391499 AATGTGAATACGTAAATTGC
1 AATGCGAATACGTAAATCGC
2391519 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
*
2391539 AACGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
*
2391559 AACGCGA
1 AATGCGA
2391566 TTATGACAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Found at i:2391523 original size:40 final size:40
Alignment explanation
Indices: 2391479--2391585 Score: 144
Period size: 40 Copynumber: 2.7 Consensus size: 40
2391469 TCTAATTCGT
* * *
2391479 AATGCGAATACGTAAATCGCAATGTGAATACGTAAATTGC
1 AATGCGAATACGTAAATCGCAACGCGAATACGTAAATCGC
2391519 AATGCGAATACGTAAATCGCAACGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGCAACGCGAATACGTAAATCGC
* * *
2391559 AACGCGATTATG-ACAATCGCAACGCGA
1 AATGCGAATACGTA-AATCGCAACGCGA
2391586 TTATGACTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.02
40 59 0.98
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (40 bp):
AATGCGAATACGTAAATCGCAACGCGAATACGTAAATCGC
Found at i:2391576 original size:20 final size:20
Alignment explanation
Indices: 2391554--2391660 Score: 178
Period size: 20 Copynumber: 5.3 Consensus size: 20
2391544 GAATACGTAA
*
2391554 ATCGCAACGCGATTATGACA
1 ATCGCAACGCGATTATGACT
2391574 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTATGACT
*
2391594 ATCGCAACGAGATTATGACT
1 ATCGCAACGCGATTATGACT
*
2391614 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
*
2391634 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
2391654 ATCGCAA
1 ATCGCAA
2391661 TACTGAATTT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:2391598 original size:60 final size:60
Alignment explanation
Indices: 2391534--2391660 Score: 175
Period size: 60 Copynumber: 2.1 Consensus size: 60
2391524 GAATACGTAA
*
2391534 ATCGCAACGCGAATACGTA-AATCGCAACGCGATTATGACAATCGCAACGCGATTATGACT
1 ATCGCAACGAGAATACG-ACAATCGCAACGCGATTATGACAATCGCAACGCGATTATGACT
* * * * * *
2391594 ATCGCAACGAGATTATGACTATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGAGAATACGACAATCGCAACGCGATTATGACAATCGCAACGCGATTATGACT
2391654 ATCGCAA
1 ATCGCAA
2391661 TACTGAATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 1 0.02
60 58 0.98
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (60 bp):
ATCGCAACGAGAATACGACAATCGCAACGCGATTATGACAATCGCAACGCGATTATGACT
Found at i:2392555 original size:24 final size:24
Alignment explanation
Indices: 2392497--2392543 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2392487 AGTCAGTATT
*
2392497 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
2392521 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
2392544 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:2395046 original size:40 final size:40
Alignment explanation
Indices: 2394988--2395074 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
2394978 CAACGCGGAA
2394988 ATCGCAATGCGAATATGACTATCGCAACAAAGAAATGACT
1 ATCGCAATGCGAATATGACTATCGCAACAAAGAAATGACT
***
2395028 ATCGCAATGCGGAA-ATGACTATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAATATGACTATCGCAACAAAGAAATGACT
*
2395068 ATTGCAA
1 ATCGCAA
2395075 CGAGAGAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 39 0.93
41 3 0.07
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (40 bp):
ATCGCAATGCGAATATGACTATCGCAACAAAGAAATGACT
Found at i:2395075 original size:20 final size:20
Alignment explanation
Indices: 2394988--2395076 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
2394978 CAACGCGGAA
*
2394988 ATCGCAATGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
***
2395008 ATCGCAACAAAGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
2395028 ATCGCAATGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
2395048 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
2395068 ATTGCAACG
1 ATCGCAACG
2395077 AGAGAATCGC
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 56 0.95
21 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:2395098 original size:33 final size:33
Alignment explanation
Indices: 2395048--2395127 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
2395038 GGAAATGACT
* ** *
2395048 ATCGCAACGCGGAAATGACTATTGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
2395082 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2395115 ATCGCAATGCGAA
1 ATCGCAATGCGAA
2395128 TTTAATTTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 33 0.79
34 9 0.21
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2395144 original size:19 final size:20
Alignment explanation
Indices: 2395116--2395165 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2395106 AACGAGAGAA
*
2395116 TCGCAATGCGAATTT-AATT
1 TCGCATTGCGAATTTCAATT
* * *
2395135 TCGCGTTGCGATTTTCATTT
1 TCGCATTGCGAATTTCAATT
2395155 TCGCATTGCGA
1 TCGCATTGCGA
2395166 TTCTCTCGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGAATTTCAATT
Found at i:2395199 original size:20 final size:20
Alignment explanation
Indices: 2395122--2395200 Score: 57
Period size: 20 Copynumber: 4.3 Consensus size: 20
2395112 AGAATCGCAA
* * *
2395122 TGCGAATTTAATTTC-GCGT
1 TGCGATTTTCATTTCTGCAT
2395141 TGCGATTTTCATTT-TCGCAT
1 TGCGATTTTCATTTCT-GCAT
*
2395161 TGCGA--TTC---TCT-CGT
1 TGCGATTTTCATTTCTGCAT
2395175 TGCGATTTTCATTTCTGCAT
1 TGCGATTTTCATTTCTGCAT
2395195 TGCGAT
1 TGCGAT
2395201 AGTCTGTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 17
0.68 0.07 0.25
Matches are distributed among these distances:
14 7 0.15
15 1 0.02
16 4 0.09
18 3 0.07
19 15 0.33
20 16 0.35
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCATTTCTGCAT
Found at i:2395325 original size:14 final size:14
Alignment explanation
Indices: 2395306--2395342 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2395296 CATCAATTAA
2395306 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2395320 ACAAATCATCTTTT
1 ACAAATCAACATTT
2395334 ACAAATCAA
1 ACAAATCAA
2395343 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2396779 original size:21 final size:22
Alignment explanation
Indices: 2396755--2396831 Score: 65
Period size: 21 Copynumber: 3.7 Consensus size: 22
2396745 TGACAGTGGC
2396755 CTCTTGAACGG-TGAGAGGGGA
1 CTCTTGAACGGATGAGAGGGGA
* * *
2396776 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGGATGAGAGGGGA
* *
2396797 CTCTTGAAC-GAT-AGGGGAGGC
1 CTCTTGAACGGATGAGAGG-GGA
2396818 CTCTTGAAC-GATGA
1 CTCTTGAACGGATGA
2396832 CAGGTGAGTC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 6 0.13
21 38 0.83
22 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (22 bp):
CTCTTGAACGGATGAGAGGGGA
Found at i:2396822 original size:42 final size:42
Alignment explanation
Indices: 2396743--2396835 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
2396733 CCTTTTCAAC
* *
2396743 GATGACAGTGGCCTCTTGAACGGTGAGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGAGAGGGGACTCTTGAGG
* * * **
2396785 GATGATAGGGGCCTCTTGAACGAT-AGGGGAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGATGAGAGG-GGACTCTTGAGG
2396827 GATGACAGG
1 GATGACAGG
2396836 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGAGAGGGGACTCTTGAGG
Found at i:2397436 original size:20 final size:20
Alignment explanation
Indices: 2397315--2397427 Score: 172
Period size: 20 Copynumber: 5.7 Consensus size: 20
2397305 GAAACTTAAA
*
2397315 ATCGCAACGCGAAAATAACT
1 ATCGCAACGCGAAAATGACT
2397335 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
2397355 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
2397375 ATCGCAACGCGAAAATTACT
1 ATCGCAACGCGAAAATGACT
* **
2397395 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
2397415 ATCGCAATGCGAA
1 ATCGCAACGCGAA
2397428 TTTAACTATT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2397542 original size:20 final size:20
Alignment explanation
Indices: 2397488--2397644 Score: 108
Period size: 20 Copynumber: 8.5 Consensus size: 20
2397478 GATTCTTTCG
**
2397488 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
2397508 TTACGATAGTTATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
**
2397528 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCA
2397548 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
** *
2397562 TTGCGATTTTCA-TTTCGTA
1 TTGCGATAGTCATTTTCGCA
*
2397581 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
2397595 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
2397615 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
2397635 TTGCGATAGT
1 TTGCGATAGT
2397645 AAACTATTCT
Statistics
Matches: 112, Mismatches: 11, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
14 14 0.12
16 12 0.11
17 6 0.05
18 5 0.04
19 7 0.06
20 68 0.61
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2397608 original size:33 final size:33
Alignment explanation
Indices: 2397528--2397609 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
2397518 TATTTTCGCA
* * * *
2397528 TTGCGATAGTCATTTTCGTGTTGCGATTTTGTTG
1 TTGCGATAGTCA-TTTCGTATTGCGATTCTCTCG
**
2397562 TTGCGATTTTCATTTCGTATTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGTATTGCGATTCTCTCG
2397595 TTGCGATAGTCATTT
1 TTGCGATAGTCATTT
2397610 TCGCGTTGCG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 30 0.75
34 10 0.25
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGTATTGCGATTCTCTCG
Found at i:2399392 original size:20 final size:20
Alignment explanation
Indices: 2399337--2399427 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
2399327 TCTGAAACTT
* *
2399337 AAAATCGCAACACAAAAATG
1 AAAATCGCAACGCGAAAATG
*
2399357 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
2399377 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
2399397 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
2399416 AAAATCGCAACG
1 AAAATCGCAACG
2399428 ACAGAATCGC
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 13 0.21
20 48 0.79
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:2399798 original size:22 final size:22
Alignment explanation
Indices: 2399764--2399851 Score: 149
Period size: 22 Copynumber: 4.0 Consensus size: 22
2399754 TGACCGTGAA
* *
2399764 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
2399786 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
2399808 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
2399830 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
2399852 GAATGTCGCC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:2400073 original size:20 final size:20
Alignment explanation
Indices: 2400050--2400102 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
2400040 CGATAGTCAG
*
2400050 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2400070 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2400090 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2400103 ATTAGGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2400975 original size:2 final size:2
Alignment explanation
Indices: 2400968--2401020 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2400958 CATATAACAA
2400968 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
2401010 AT AT AT AT AT A
1 AT AT AT AT AT A
2401021 GCTACAATGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2403252 original size:19 final size:20
Alignment explanation
Indices: 2403230--2403268 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2403220 ATATTTATTT
2403230 CTTT-CATATACTGTTATAA
1 CTTTACATATACTGTTATAA
*
2403249 CTTTCACATTTACTGTTATA
1 CTTT-ACATATACTGTTATA
2403269 GCCCAATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (20 bp):
CTTTACATATACTGTTATAA
Found at i:2403627 original size:18 final size:18
Alignment explanation
Indices: 2403565--2403630 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
2403555 TTATTAATCT
*
2403565 ACGTCTGATAACTGTAAA
1 ACGTATGATAACTGTAAA
* *
2403583 ACATATGATAACTGAAAA
1 ACGTATGATAACTGTAAA
*
2403601 ACGTCTGATAACTGTAAA
1 ACGTATGATAACTGTAAA
* *
2403619 ATGTTTGATAAC
1 ACGTATGATAAC
2403631 AATAAATATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (18 bp):
ACGTATGATAACTGTAAA
Found at i:2429559 original size:14 final size:15
Alignment explanation
Indices: 2429542--2429578 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2429532 TATTATAATT
2429542 AATATTTTA-TTTTA
1 AATATTTTATTTTTA
*
2429556 AATAATTTATTTTTA
1 AATATTTTATTTTTA
2429571 AA-ATTTTA
1 AATATTTTA
2429579 ATTAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATATTTTATTTTTA
Found at i:2431201 original size:60 final size:60
Alignment explanation
Indices: 2431038--2431202 Score: 179
Period size: 60 Copynumber: 2.8 Consensus size: 60
2431028 TTTGGATGAA
* * ** * *
2431038 TTTAGGGATAAAATTGGAATATTCAAAAGTTTGGGGACCAATTTCGAAAGAGGATCATAG
1 TTTATGGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGGATAATAG
* * ** ** **
2431098 TTTATGGATGAAACTAGAATGCTCAAAAGTTTAAGGATTAATTTAGACTGAGTG-TAATAG
1 TTTATGGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAG-GATAATAG
*
2431158 TTTGTGGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTA
1 TTTATGGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTA
2431203 AGATGAGGGC
Statistics
Matches: 83, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
60 82 0.99
61 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.32
Consensus pattern (60 bp):
TTTATGGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGGATAATAG
Found at i:2431218 original size:60 final size:60
Alignment explanation
Indices: 2431043--2431221 Score: 177
Period size: 60 Copynumber: 3.0 Consensus size: 60
2431033 ATGAATTTAG
* ** * * *
2431043 GGATAAAATTGGAATATTCAAAAGTTTGGGGACCAATTTCGAA-A-GAGGATCATAGTTTAT
1 GGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTT--AAGATGAGGGTAATAGTTTGT
* * ** ** *
2431103 GGATGAAACTAGAATGCTCAAAAGTTTAAGGATTAATTT-AGACTGAGTGTAATAGTTTGT
1 GGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAGA-TGAGGGTAATAGTTTGT
2431163 GGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAGATGAGGGCT-ATAGTTTG
1 GGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAGATGAGGG-TAATAGTTTG
2431222 GGGACATGTG
Statistics
Matches: 94, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
57 1 0.01
58 1 0.01
60 88 0.94
61 4 0.04
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (60 bp):
GGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAGATGAGGGTAATAGTTTGT
Found at i:2434286 original size:21 final size:21
Alignment explanation
Indices: 2434262--2434330 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
2434252 ATTAATCTGT
*
2434262 CACCCTGGATTACCACGTTAG
1 CACCATGGATTACCACGTTAG
* * * * *
2434283 CACCATGAACTATCACATCAG
1 CACCATGGATTACCACGTTAG
* *
2434304 CACCGTGGATTGCCACGTTAG
1 CACCATGGATTACCACGTTAG
2434325 CACCAT
1 CACCAT
2434331 AATAATCAGC
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (21 bp):
CACCATGGATTACCACGTTAG
Found at i:2435831 original size:39 final size:39
Alignment explanation
Indices: 2435775--2435857 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
2435765 ATCATGATGT
* **
2435775 TATCAAAACCATAATAAACAATATTATTTATAATAGTCA
1 TATCAAAACCATAATAAACAATATCATACATAATAGTCA
* * *
2435814 TATCAAAGCCATGATAAACATTATCATACATAATAGTCA
1 TATCAAAACCATAATAAACAATATCATACATAATAGTCA
2435853 TATCA
1 TATCA
2435858 TATTCTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (39 bp):
TATCAAAACCATAATAAACAATATCATACATAATAGTCA
Found at i:2436027 original size:19 final size:19
Alignment explanation
Indices: 2435996--2436056 Score: 88
Period size: 19 Copynumber: 3.3 Consensus size: 19
2435986 GTTTCCGGAC
*
2435996 TCATAACTT-ATTTCAGAT
1 TCATAACTTAATTTCAAAT
2436014 TCATAACTTAATTTCAAAT
1 TCATAACTTAATTTCAAAT
* *
2436033 TCATAACTTATTTTCAAGT
1 TCATAACTTAATTTCAAAT
2436052 TCATA
1 TCATA
2436057 GCCCAATGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
18 9 0.23
19 30 0.77
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.44
Consensus pattern (19 bp):
TCATAACTTAATTTCAAAT
Found at i:2437419 original size:2 final size:2
Alignment explanation
Indices: 2437412--2437507 Score: 55
Period size: 2 Copynumber: 52.0 Consensus size: 2
2437402 TCGGGCCGGG
* * * *
2437412 TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- 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
* * * * *
2437452 TA TA TA TA T- TT TA -A TT TA AA T- TA AA TT TA T- TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2437488 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
2437508 ATAATTATTT
Statistics
Matches: 69, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
1 8 0.12
2 61 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2437471 original size:44 final size:44
Alignment explanation
Indices: 2437421--2437504 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
2437411 GTATATATAT
2437421 ATTTAAATTAAATATATAAATATTATATATATATATATATTTTA
1 ATTTAAATTAAATATATAAATATTATATATATATATATATTTTA
* *
2437465 ATTTAAATTAAATTTATTAATATTATATATATATATATAT
1 ATTTAAATTAAATATATAAATATTATATATATATATATAT
2437505 ATAATAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (44 bp):
ATTTAAATTAAATATATAAATATTATATATATATATATATTTTA
Found at i:2437612 original size:29 final size:29
Alignment explanation
Indices: 2437579--2437634 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
2437569 CCCGTCCCCA
2437579 TCCCCGTTTAGCATAAACGGTTTTTCCTG
1 TCCCCGTTTAGCATAAACGGTTTTTCCTG
*
2437608 TCCCCGTTTAGTATAAACGGTTTTTCC
1 TCCCCGTTTAGCATAAACGGTTTTTCC
2437635 CCGTCCCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.39
Consensus pattern (29 bp):
TCCCCGTTTAGCATAAACGGTTTTTCCTG
Found at i:2443487 original size:10 final size:10
Alignment explanation
Indices: 2443471--2443563 Score: 55
Period size: 10 Copynumber: 9.0 Consensus size: 10
2443461 TTATAGAATA
2443471 ATTATTAAAT
1 ATTATTAAAT
*
2443481 GTTATTAAATT
1 ATTATTAAA-T
* *
2443492 ATTATAAAAA
1 ATTATTAAAT
2443502 ATTATTAAAT
1 ATTATTAAAT
*
2443512 -TTATGAAATT
1 ATTATTAAA-T
*
2443522 ATTATAAAAT
1 ATTATTAAAT
*
2443532 GATCATTATAAT
1 -ATTATTA-AAT
*
2443544 GTTA-TAATAT
1 ATTATTAA-AT
*
2443554 ATTAATAAAT
1 ATTATTAAAT
2443564 TTCTAATTAA
Statistics
Matches: 63, Mismatches: 13, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
9 8 0.13
10 27 0.43
11 25 0.40
12 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (10 bp):
ATTATTAAAT
Found at i:2443489 original size:30 final size:30
Alignment explanation
Indices: 2443455--2443563 Score: 98
Period size: 31 Copynumber: 3.5 Consensus size: 30
2443445 AAAAAAAGTG
2443455 TTAAA-ATTATAGAATAATTATTAAATGTTA
1 TTAAATATTATA-AATAATTATTAAATGTTA
*
2443485 TTAAATTATTATAAAAAATTATTAAAT-TTA
1 TTAAA-TATTATAAATAATTATTAAATGTTA
* * *
2443515 TGAAATTATTATAAAATGATCATTATAATGTTA
1 TTAAA-TATTAT-AAATAATTATTA-AATGTTA
2443548 -TAATATATTAATAAAT
1 TTAA-ATATT-ATAAAT
2443564 TTCTAATTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
30 19 0.29
31 22 0.33
32 19 0.29
33 6 0.09
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (30 bp):
TTAAATATTATAAATAATTATTAAATGTTA
Found at i:2456914 original size:23 final size:25
Alignment explanation
Indices: 2456879--2456926 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
2456869 ACATATATAT
2456879 ATATATATAATATAGTTTTGAAAAC
1 ATATATATAATATAGTTTTGAAAAC
*
2456904 ATATA-AT-ATATAGTTTTTAAAAC
1 ATATATATAATATAGTTTTGAAAAC
2456927 GGTTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.68
24 2 0.09
25 5 0.23
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (25 bp):
ATATATATAATATAGTTTTGAAAAC
Found at i:2457045 original size:70 final size:71
Alignment explanation
Indices: 2456895--2457159 Score: 222
Period size: 71 Copynumber: 3.7 Consensus size: 71
2456885 ATAATATAGT
* * * * * * *
2456895 TTTGAAAACATATAATATATAG-TTTT---TAAAACGGTTTTAAAAACGTGTA-TAATTTAG-TT
1 TTTGAAAACATATAATATATAGATTTTAAAAAAAATGATTTTGAAAACATATAGT-ATATAGTTT
* *
2456954 AAGACGG
65 AAAACGA
** *
2456961 TTTGAAAATGTATAATATATA-ATTTTAAAAAAAATGATTTTGAAAATATATAGTATATAGTTTA
1 TTTGAAAACATATAATATATAGATTTTAAAAAAAATGATTTTGAAAACATATAGTATATAGTTTA
2457025 AAACGA
66 AAACGA
* *
2457031 TTTGAAAACATATAATATATAGTTTTTAAAAAAATTGATTTTGAAAACATATAGTATATAGTTTT
1 TTTGAAAACATATAATATATAGATTTTAAAAAAAATGATTTTGAAAACATATAGTATATAG--TT
*
2457096 TAAAAACGGTT
64 T-AAAAC-G-A
* ** ** *
2457107 TTTGGAAAACATATTATATATAG-TTTTTTAAAAACGGTTTTTGAAAACATATA
1 TTT-GAAAACATATAATATATAGATTTTAAAAAAAATGATTTTGAAAACATATA
2457160 TAATATATCA
Statistics
Matches: 162, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
66 23 0.14
69 21 0.13
70 27 0.17
71 36 0.22
73 3 0.02
74 5 0.03
75 1 0.01
76 28 0.17
77 18 0.11
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.40
Consensus pattern (71 bp):
TTTGAAAACATATAATATATAGATTTTAAAAAAAATGATTTTGAAAACATATAGTATATAGTTTA
AAACGA
Found at i:2457074 original size:39 final size:39
Alignment explanation
Indices: 2456961--2457159 Score: 168
Period size: 38 Copynumber: 5.4 Consensus size: 39
2456951 GTTAAGACGG
** * *
2456961 TTTGAAAATGTATAATATATA-ATTTTAAAAAAAATGAT
1 TTTGAAAACATATAATATATAGTTTTTAAAAAAATTGAT
* * *
2456999 TTTGAAAATATATAGTATATAG--TTT---AAAA-CGA-
1 TTTGAAAACATATAATATATAGTTTTTAAAAAAATTGAT
2457031 TTTGAAAACATATAATATATAGTTTTTAAAAAAATTGAT
1 TTTGAAAACATATAATATATAGTTTTTAAAAAAATTGAT
* **
2457070 TTTGAAAACATATAGTATATAGTTTTTAAAAACGGTT--T
1 TTTGAAAACATATAATATATAGTTTTTAAAAA-AATTGAT
* * * ** *
2457108 TTGGAAAACATATTATATATAGTTTTT-TAAAAACGGTT
1 TTTGAAAACATATAATATATAGTTTTTAAAAAAATTGAT
2457146 TTTGAAAACATATA
1 TTTGAAAACATATA
2457160 TAATATATCA
Statistics
Matches: 131, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
32 20 0.15
33 2 0.02
34 7 0.05
37 10 0.08
38 59 0.45
39 31 0.24
40 2 0.02
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.40
Consensus pattern (39 bp):
TTTGAAAACATATAATATATAGTTTTTAAAAAAATTGAT
Found at i:2457115 original size:38 final size:37
Alignment explanation
Indices: 2456894--2457159 Score: 186
Period size: 39 Copynumber: 7.4 Consensus size: 37
2456884 TATAATATAG
*
2456894 TTTTGAAAACATATAATATATAGTTTTT-AAAACGG-
1 TTTTGAAAACATATAGTATATAGTTTTTAAAAACGGT
** *
2456929 TTTT-AAAA-ACGT-GTATA-A-TTTAGTT-AAGACGG-
1 TTTTGAAAACATATAGTATATAGTTT--TTAAAAACGGT
** * * * ** *
2456961 -TTTGAAAATGTATAATATATAATTTTAAAAAAAATGA
1 TTTTGAAAACATATAGTATATAGTTTT-TAAAAACGGT
*
2456998 TTTTGAAAATATATAGTATATAG--TTT-AAAAC-G-
1 TTTTGAAAACATATAGTATATAGTTTTTAAAAACGGT
* * ** *
2457030 ATTTGAAAACATATAATATATAGTTTTTAAAAAAATTGA
1 TTTTGAAAACATATAGTATATAGTTTTT--AAAAACGGT
2457069 TTTTGAAAACATATAGTATATAGTTTTTAAAAACGGT
1 TTTTGAAAACATATAGTATATAGTTTTTAAAAACGGT
2457106 TTTTGGAAAACATATTA-TATATAGTTTTTTAAAAACGGT
1 TTTT-GAAAACATA-TAGTATATAG-TTTTTAAAAACGGT
2457145 TTTTGAAAACATATA
1 TTTTGAAAACATATA
2457160 TAATATATCA
Statistics
Matches: 184, Mismatches: 26, Indels: 40
0.74 0.10 0.16
Matches are distributed among these distances:
30 3 0.02
31 4 0.02
32 36 0.20
33 4 0.02
34 16 0.09
35 5 0.03
36 9 0.05
37 16 0.09
38 45 0.24
39 46 0.25
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (37 bp):
TTTTGAAAACATATAGTATATAGTTTTTAAAAACGGT
Found at i:2457166 original size:38 final size:39
Alignment explanation
Indices: 2457031--2457181 Score: 175
Period size: 39 Copynumber: 3.8 Consensus size: 39
2457021 TTTAAAACGA
* ** *
2457031 TTTGAAAACATATA-ATATATAGTTTTTAAAAAAATTGAT
1 TTTGAAAACATATATATATATAGTTTTT-TAAAAACGGTT
*
2457070 TTTGAAAACATATA-GTATATAG-TTTTTAAAAACGGTT
1 TTTGAAAACATATATATATATAGTTTTTTAAAAACGGTT
2457107 TTTGGAAAACATAT-TATATATAGTTTTTTAAAAACGGTT
1 TTT-GAAAACATATATATATATAGTTTTTTAAAAACGGTT
*
2457146 TTTGAAAACATATATAATATATCATGTTTTTGAAAA
1 TTTGAAAACATATAT-ATATAT-A-GTTTTTTAAAA
2457182 CATAATATAT
Statistics
Matches: 98, Mismatches: 7, Indels: 11
0.84 0.06 0.09
Matches are distributed among these distances:
37 10 0.10
38 31 0.32
39 40 0.41
40 6 0.06
41 1 0.01
42 10 0.10
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.42
Consensus pattern (39 bp):
TTTGAAAACATATATATATATAGTTTTTTAAAAACGGTT
Found at i:2457193 original size:2 final size:2
Alignment explanation
Indices: 2457186--2457243 Score: 54
Period size: 2 Copynumber: 30.0 Consensus size: 2
2457176 TGAAAACATA
2457186 AT AT AT AT AT AT -T AT AGT AT AGT AT AT AGT AT -T AT AT -T AT
1 AT AT AT AT AT AT AT AT A-T AT A-T AT AT A-T AT AT AT AT AT AT
2457226 AT AT AT -T AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT
2457244 TATGGTATAG
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
1 5 0.10
2 37 0.77
3 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2457244 original size:5 final size:5
Alignment explanation
Indices: 2457187--2457291 Score: 56
Period size: 5 Copynumber: 20.2 Consensus size: 5
2457177 GAAAACATAA
* *
2457187 TATAT ATATAT TATAG TATAG TATA- TAGTAT TATAT TATA- TATATT
1 TATAT -TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT TATA-T
** * *
2457233 ATATAT TATAT TATGG TATAG TATA- TATGT TATATGT TATAT GTATTAT
1 -TATAT TATAT TATAT TATAT TATAT TATAT TATA--T TATAT -TA-TAT
2457282 T-TAT TATAT T
1 TATAT TATAT T
2457292 TTTATTTAAC
Statistics
Matches: 82, Mismatches: 6, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
4 13 0.16
5 46 0.56
6 11 0.13
7 12 0.15
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:2462356 original size:21 final size:21
Alignment explanation
Indices: 2462308--2462449 Score: 124
Period size: 21 Copynumber: 6.6 Consensus size: 21
2462298 TCAGGAGTGA
* **
2462308 TCCTTTGGAACATATATGCAG
1 TCCTTTGGGACATATATGTGG
* *
2462329 TCATTTGGGACATATATTTGG
1 TCCTTTGGGACATATATGTGG
* *
2462350 TCCTTTGGAATATATATGTGG
1 TCCTTTGGGACATATATGTGG
* *
2462371 TCCTTAGGGACAATTCTATGTGG
1 TCCTTTGGGAC-A-TATATGTGG
* *
2462394 TCCTTAGGGACAATTCTATGTGG
1 TCCTTTGGGAC-A-TATATGTGG
*
2462417 TCC-TCGGGACATATATGTGG
1 TCCTTTGGGACATATATGTGG
*
2462437 TTCTTTGGGACAT
1 TCCTTTGGGACAT
2462450 TTCTACGTGG
Statistics
Matches: 101, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
20 10 0.10
21 50 0.50
22 7 0.07
23 34 0.34
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (21 bp):
TCCTTTGGGACATATATGTGG
Found at i:2462394 original size:23 final size:23
Alignment explanation
Indices: 2462364--2462474 Score: 138
Period size: 23 Copynumber: 5.0 Consensus size: 23
2462354 TTGGAATATA
2462364 TATGTGGTCCTTAGGGACAATTC
1 TATGTGGTCCTTAGGGACAATTC
2462387 TATGTGGTCCTTAGGGACAATTC
1 TATGTGGTCCTTAGGGACAATTC
* *
2462410 TATGTGGTCC-TCGGGAC-A-TA
1 TATGTGGTCCTTAGGGACAATTC
* * *
2462430 TATGTGGTTCTTTGGGACATTTC
1 TATGTGGTCCTTAGGGACAATTC
* *
2462453 TACGTGGTCCTTCGGGACAATT
1 TATGTGGTCCTTAGGGACAATT
2462475 TTATATGGCA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
20 10 0.13
21 7 0.09
22 6 0.08
23 52 0.69
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (23 bp):
TATGTGGTCCTTAGGGACAATTC
Found at i:2462447 original size:43 final size:44
Alignment explanation
Indices: 2462335--2462471 Score: 147
Period size: 43 Copynumber: 3.1 Consensus size: 44
2462325 GCAGTCATTT
* * *
2462335 GGGACATATATTTGGTCCTTT-GG--AATATATATGTGGTCCTTA
1 GGGACATATATGTGGTCCTTTGGGACAAT-TCTATGTGGTCCTTC
* *
2462377 GGGACAATTCTATGTGGTCCTTAGGGACAATTCTATGTGGTCC-TC
1 GGGAC-A-TATATGTGGTCCTTTGGGACAATTCTATGTGGTCCTTC
* * *
2462422 GGGACATATATGTGGTTCTTTGGGACATTTCTACGTGGTCCTTC
1 GGGACATATATGTGGTCCTTTGGGACAATTCTATGTGGTCCTTC
2462466 GGGACA
1 GGGACA
2462472 ATTTTATATG
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
42 5 0.06
43 31 0.39
44 21 0.27
45 8 0.10
46 11 0.14
47 3 0.04
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (44 bp):
GGGACATATATGTGGTCCTTTGGGACAATTCTATGTGGTCCTTC
Found at i:2467211 original size:18 final size:18
Alignment explanation
Indices: 2467188--2467226 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2467178 CCCTTAAAAA
2467188 TTTAAAATTATCATATAT
1 TTTAAAATTATCATATAT
* * *
2467206 TTTAAATTTTTTATATAT
1 TTTAAAATTATCATATAT
2467224 TTT
1 TTT
2467227 TTATTGAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAAATTATCATATAT
Found at i:2467611 original size:33 final size:33
Alignment explanation
Indices: 2467567--2467633 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2467557 CTAAATTAAA
* * *
2467567 CCTTAGACTGCATATATATTGATTAACATTATG
1 CCTTAGACTGCAGATATAGTAATTAACATTATG
*
2467600 CCTTAGCCTGCAGATATAGTAATTAACATTATG
1 CCTTAGACTGCAGATATAGTAATTAACATTATG
2467633 C
1 C
2467634 AAAATATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
CCTTAGACTGCAGATATAGTAATTAACATTATG
Found at i:2471143 original size:15 final size:16
Alignment explanation
Indices: 2471113--2471143 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2471103 TTTCTATTTC
2471113 TATTTTATATTTAAAT
1 TATTTTATATTTAAAT
2471129 TATTTTATA-TTAAAT
1 TATTTTATATTTAAAT
2471144 AATAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTATATTTAAAT
Found at i:2477125 original size:15 final size:15
Alignment explanation
Indices: 2477105--2477135 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2477095 TAAAAACTTG
2477105 AAAGTAAAACTAAAA
1 AAAGTAAAACTAAAA
*
2477120 AAAGTAAAAGTAAAA
1 AAAGTAAAACTAAAA
2477135 A
1 A
2477136 CTTTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAGTAAAACTAAAA
Found at i:2478727 original size:20 final size:20
Alignment explanation
Indices: 2478702--2478773 Score: 135
Period size: 20 Copynumber: 3.6 Consensus size: 20
2478692 CCTTCAAGAA
*
2478702 GTATCGATACTCGGAGTATG
1 GTATCGATACTCGGAGAATG
2478722 GTATCGATACTCGGAGAATG
1 GTATCGATACTCGGAGAATG
2478742 GTATCGATACTCGGAGAATG
1 GTATCGATACTCGGAGAATG
2478762 GTATCGATACTC
1 GTATCGATACTC
2478774 ATAGGGTTGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
GTATCGATACTCGGAGAATG
Found at i:2480777 original size:20 final size:20
Alignment explanation
Indices: 2480752--2480801 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2480742 TTGACTCAGT
2480752 AATATCGATATTGTTCATAG
1 AATATCGATATTGTTCATAG
* *
2480772 AATATCAATATTGTTCATCG
1 AATATCGATATTGTTCATAG
*
2480792 AGTATCGATA
1 AATATCGATA
2480802 CCCAATGGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (20 bp):
AATATCGATATTGTTCATAG
Found at i:2481118 original size:21 final size:20
Alignment explanation
Indices: 2481050--2481118 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
2481040 AGCAATTTTT
*
2481050 GTATCGATACCAAA-GGT-A
1 GTATCGATACTAAAGGGTCA
* *
2481068 CGTATCGATACTGAAGTGTCA
1 -GTATCGATACTAAAGGGTCA
* *
2481089 GTATTGATACTAAAGGGCTTA
1 GTATCGATACTAAAGGG-TCA
2481110 GTATCGATA
1 GTATCGATA
2481119 TCATCGTCCT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 12 0.31
20 16 0.41
21 11 0.28
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (20 bp):
GTATCGATACTAAAGGGTCA
Found at i:2489220 original size:28 final size:29
Alignment explanation
Indices: 2489186--2489263 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 29
2489176 TTTGGTTAAT
*
2489186 GACTAAAATGTAAGTTTTGAAA-GTTT-G
1 GACTAAAATATAAGTTTTGAAAGGTTTAG
* * *
2489213 GTGCTAAAATATAAGCTTTAAAAGGTTTAG
1 G-ACTAAAATATAAGTTTTGAAAGGTTTAG
2489243 GACTAAAATATAA-TTTTGAAA
1 GACTAAAATATAAGTTTTGAAA
2489264 AGTTATATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
27 1 0.02
28 23 0.56
29 15 0.37
30 2 0.05
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (29 bp):
GACTAAAATATAAGTTTTGAAAGGTTTAG
Found at i:2490153 original size:31 final size:32
Alignment explanation
Indices: 2490089--2490153 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
2490079 GGTTTTAAGA
* * **
2490089 GATGATTGGATTTGGATTGAATTTGGTGTTAG
1 GATGATTGGATTTGCATTGAATTTGATCATAG
*
2490121 GATGATTGGGTTTGCA-TGAATTTGATCATAG
1 GATGATTGGATTTGCATTGAATTTGATCATAG
2490152 GA
1 GA
2490154 GGTTGAATTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.25, C:0.03, G:0.32, T:0.40
Consensus pattern (32 bp):
GATGATTGGATTTGCATTGAATTTGATCATAG
Found at i:2492540 original size:22 final size:22
Alignment explanation
Indices: 2492500--2492541 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2492490 AGGGGAAGGG
*
2492500 TTTTTTTAAAAAGTTTTTTTTC
1 TTTTTTTAAAAAGTATTTTTTC
2492522 TTTTTTTAAATAA-TATTTTT
1 TTTTTTTAAA-AAGTATTTTT
2492542 ATTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTTTAAAAAGTATTTTTTC
Found at i:2497365 original size:32 final size:32
Alignment explanation
Indices: 2497329--2497391 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
2497319 GGAACGTTAA
2497329 CCAAAACGATTACATGACATGTGTCATGTCAT
1 CCAAAACGATTACATGACATGTGTCATGTCAT
** * *
2497361 CCAAAGTGATTATATGATATGTGTCATGTCA
1 CCAAAACGATTACATGACATGTGTCATGTCA
2497392 CATAAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (32 bp):
CCAAAACGATTACATGACATGTGTCATGTCAT
Found at i:2497411 original size:32 final size:32
Alignment explanation
Indices: 2497342--2497434 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
2497332 AAACGATTAC
* * *
2497342 ATGACATGTGTCATGTCATCCAAAGTGATTAT
1 ATGATATGTGTCATGTCATCCAAAATGATGAT
*
2497374 ATGATATGTGTCATGTCA-CATAAAATGATGAT
1 ATGATATGTGTCATGTCATC-CAAAATGATGAT
* * * *
2497406 GTGATATATGTTACGTCATCCAAAATGAT
1 ATGATATGTGTCATGTCATCCAAAATGAT
2497435 AATGTAACAC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
31 1 0.02
32 48 0.96
33 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (32 bp):
ATGATATGTGTCATGTCATCCAAAATGATGAT
Found at i:2497449 original size:32 final size:32
Alignment explanation
Indices: 2497395--2497455 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
2497385 CATGTCACAT
* * * *
2497395 AAAATGATGATGTGATATATGTTACGTCATCC
1 AAAATGATAATGTAACACATGTTACGTCATCC
*
2497427 AAAATGATAATGTAACACATGTTATGTCA
1 AAAATGATAATGTAACACATGTTACGTCA
2497456 AAAATTAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.33
Consensus pattern (32 bp):
AAAATGATAATGTAACACATGTTACGTCATCC
Found at i:2498161 original size:27 final size:27
Alignment explanation
Indices: 2498127--2498220 Score: 188
Period size: 27 Copynumber: 3.5 Consensus size: 27
2498117 GATAATGGCT
2498127 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
2498154 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
2498181 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
2498208 CTGAATCATTCAG
1 CTGAATCATTCAG
2498221 CACTGTTTTG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTGTG
Found at i:2499824 original size:60 final size:61
Alignment explanation
Indices: 2499741--2499862 Score: 142
Period size: 60 Copynumber: 2.0 Consensus size: 61
2499731 TTTTTACTCA
* * * *
2499741 CTAAATTCTGCCTCTCATTTTAAATTAGTCCTT-AAGC-TTTTGAACATTCTAATTTCATCC
1 CTAAATTATGCCTCTCATTTTAAATTAGT-CTTCAAACTTTTTAAACATTCAAATTTCATCC
* * *
2499801 CTAAATTATGACC-CTCTTTTTAAATTGGTCTTCAAACTTTTTAAACATTCAAATTTTATCC
1 CTAAATTATG-CCTCTCATTTTAAATTAGTCTTCAAACTTTTTAAACATTCAAATTTCATCC
2499862 C
1 C
2499863 AAGCTATACG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
59 3 0.06
60 26 0.50
61 23 0.44
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (61 bp):
CTAAATTATGCCTCTCATTTTAAATTAGTCTTCAAACTTTTTAAACATTCAAATTTCATCC
Found at i:2504952 original size:20 final size:19
Alignment explanation
Indices: 2504920--2504967 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2504910 GGGTATGTAT
*
2504920 TTAAATT-TTGTTATTTACA
1 TTAAATTATTGTTATATA-A
2504939 TTAAATTATTGTTATATAA
1 TTAAATTATTGTTATATAA
*
2504958 TTAAAATATT
1 TTAAATTATT
2504968 ATTTTGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
TTAAATTATTGTTATATAA
Found at i:2512172 original size:46 final size:47
Alignment explanation
Indices: 2512084--2512172 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 47
2512074 CATCTTTAAA
* * **
2512084 GGATGATAAATTCTAATTACCGATTTATAGACTGGTTTATCCTTAGC
1 GGATGATAAATTCTAATTACCGATTTACAGACTAGTGCATCCTTAGC
* **
2512131 GGATGGTAAATTC-AATTACCGATTTACAGGTTAGTGCATCCT
1 GGATGATAAATTCTAATTACCGATTTACAGACTAGTGCATCCT
2512173 CGTAGAATGG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
46 23 0.66
47 12 0.34
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (47 bp):
GGATGATAAATTCTAATTACCGATTTACAGACTAGTGCATCCTTAGC
Found at i:2512925 original size:29 final size:29
Alignment explanation
Indices: 2512891--2512986 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
2512881 ACCGCTCATA
2512891 ATCTAAGTTGGGTCTTTGATTAGACCCTT
1 ATCTAAGTTGGGTCTTTGATTAGACCCTT
* ** * *
2512920 ATCTAA--TGGTTAGTTGTTTACCGTCACTCATT
1 ATCTAAGTTGGGTCTTTGATTA--G--AC-CCTT
*
2512952 ATCTAAGTTGGGTCTTTGATTGGACCCTT
1 ATCTAAGTTGGGTCTTTGATTAGACCCTT
2512981 ATCTAA
1 ATCTAA
2512987 TGGTTCGTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
27 10 0.20
29 16 0.33
30 2 0.04
31 2 0.04
32 10 0.20
34 9 0.18
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (29 bp):
ATCTAAGTTGGGTCTTTGATTAGACCCTT
Found at i:2512940 original size:61 final size:61
Alignment explanation
Indices: 2512841--2513048 Score: 326
Period size: 61 Copynumber: 3.4 Consensus size: 61
2512831 CACAAATGCA
* *
2512841 GTCTTTGATTGGACCCTTATCTAATGGTTAGTTCTTTACCACCGCTCATAATCTAAGTTGG
1 GTCTTTGATTGGACCCTTATCTAATGGTTAGTTCTTTACCACCACTCATTATCTAAGTTGG
* * **
2512902 GTCTTTGATTAGACCCTTATCTAATGGTTAGTTGTTTACCGTCACTCATTATCTAAGTTGG
1 GTCTTTGATTGGACCCTTATCTAATGGTTAGTTCTTTACCACCACTCATTATCTAAGTTGG
* *
2512963 GTCTTTGATTGGACCCTTATCTAATGGTTCGTTTTTTACCACCACTCATTATCTAAGTTGG
1 GTCTTTGATTGGACCCTTATCTAATGGTTAGTTCTTTACCACCACTCATTATCTAAGTTGG
* *
2513024 GTTTTTGATTGGACACTTATCTAAT
1 GTCTTTGATTGGACCCTTATCTAAT
2513049 AATTAGCTTT
Statistics
Matches: 134, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 134 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (61 bp):
GTCTTTGATTGGACCCTTATCTAATGGTTAGTTCTTTACCACCACTCATTATCTAAGTTGG
Found at i:2517628 original size:19 final size:21
Alignment explanation
Indices: 2517604--2517645 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2517594 ATTTGTCACT
2517604 TACCCA-A-TCATAAAATGTA
1 TACCCACATTCATAAAATGTA
2517623 TACCCACCATTCATAAAATGTA
1 TACCCA-CATTCATAAAATGTA
2517645 T
1 T
2517646 GTATTTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
21 1 0.05
22 13 0.65
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.29
Consensus pattern (21 bp):
TACCCACATTCATAAAATGTA
Found at i:2523259 original size:31 final size:31
Alignment explanation
Indices: 2523183--2523263 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
2523173 CAACAGTTAC
* *
2523183 GTTG-GGGACCATATTGTAAACGGACTAAAT
1 GTTGAGGGACCATATTGCAAACAGACTAAAT
2523213 GTTGAGGGACCATATTGCAAACAGACTAAAT
1 GTTGAGGGACCATATTGCAAACAGACTAAAT
* **
2523244 GTTGGGGGATTATATTGCAA
1 GTTGAGGGACCATATTGCAA
2523264 GTTTTAAAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 4 0.09
31 41 0.91
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (31 bp):
GTTGAGGGACCATATTGCAAACAGACTAAAT
Found at i:2525476 original size:31 final size:31
Alignment explanation
Indices: 2525404--2525469 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
2525394 AGTTACGTCG
* *
2525404 GGGACCATATTGTAAATGGACTAAATGTTGA
1 GGGACCATATTATAAACGGACTAAATGTTGA
*
2525435 GGGACCATATTATAAACGGACTAAATGTTGG
1 GGGACCATATTATAAACGGACTAAATGTTGA
2525466 GGGA
1 GGGA
2525470 TTATATTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.26
Consensus pattern (31 bp):
GGGACCATATTATAAACGGACTAAATGTTGA
Found at i:2545515 original size:2 final size:2
Alignment explanation
Indices: 2545508--2545534 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2545498 GTTGTTTCCT
2545508 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
2545535 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2547240 original size:16 final size:16
Alignment explanation
Indices: 2547217--2547260 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
2547207 AATTCGAATA
2547217 ATTAAAAATTTATAAAT
1 ATTAAAAATTTAT-AAT
2547234 ATTAAAAATTTATAAT
1 ATTAAAAATTTATAAT
*
2547250 ATTATAAATTT
1 ATTAAAAATTT
2547261 GAATTCTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAAAATTTATAAT
Found at i:2557974 original size:2 final size:2
Alignment explanation
Indices: 2557967--2558002 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2557957 TAATTTTACT
2557967 TA TA TA TA TA TA TA TA TA TA TA TA TA 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 T
2558003 GTATGTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2561825 original size:29 final size:29
Alignment explanation
Indices: 2561784--2561844 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
2561774 AAATTATGGA
* * * * *
2561784 TTTAATCTTTATATTTTAATTTTATCAAT
1 TTTAATCTATATACTCTAATCTCATCAAT
*
2561813 TTTAGTCTATATACTCTAATCTCATCAAT
1 TTTAATCTATATACTCTAATCTCATCAAT
2561842 TTT
1 TTT
2561845 TAATTCCTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.13, G:0.02, T:0.56
Consensus pattern (29 bp):
TTTAATCTATATACTCTAATCTCATCAAT
Found at i:2565953 original size:15 final size:16
Alignment explanation
Indices: 2565933--2565965 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2565923 GGAACACAAA
*
2565933 TTCTTTCTTT-TTTTC
1 TTCTTTATTTATTTTC
2565948 TTCTTTATTTATTTTC
1 TTCTTTATTTATTTTC
2565964 TT
1 TT
2565966 TTCATGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (16 bp):
TTCTTTATTTATTTTC
Found at i:2566819 original size:22 final size:23
Alignment explanation
Indices: 2566779--2566821 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2566769 GCAAAAAACG
*
2566779 ACTTTGATTTTTTTATTTCTTGC
1 ACTTTGATTTTATTATTTCTTGC
*
2566802 ACTTTTATTTTATT-TTTCTT
1 ACTTTGATTTTATTATTTCTT
2566822 TCTTAATCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (23 bp):
ACTTTGATTTTATTATTTCTTGC
Found at i:2570016 original size:20 final size:21
Alignment explanation
Indices: 2569991--2570083 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
2569981 TTTTCCCAAT
*
2569991 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2570011 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
2570032 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2570052 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2570073 TCGCAATGCGA
1 TCGCAATGCGA
2570084 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2570036 original size:41 final size:41
Alignment explanation
Indices: 2569991--2570083 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
2569981 TTTTCCCAAT
2569991 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
2570032 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
2570073 TCGCAATGCGA
1 TCGCAATGCGA
2570084 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:2570096 original size:41 final size:41
Alignment explanation
Indices: 2570010--2570144 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
2570000 GAATAAGTAA
** *
2570010 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
2570051 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
2570092 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
2570133 TTCGCAACGCGA
1 ATCGCAACGCGA
2570145 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:2570097 original size:20 final size:20
Alignment explanation
Indices: 2570072--2570165 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
2570062 AATTGGGAAA
*
2570072 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
2570092 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
2570113 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
2570133 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
2570153 TTCGCAACGCGAT
1 ATCGCAACGCGAT
2570166 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:2570721 original size:19 final size:19
Alignment explanation
Indices: 2570683--2570749 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
2570673 TTCGAGAATG
2570683 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
2570703 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
2570722 AAAACCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
2570741 AAAATCGCA
1 AAAATCGCA
2570750 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:2570767 original size:19 final size:19
Alignment explanation
Indices: 2570745--2570895 Score: 177
Period size: 19 Copynumber: 8.1 Consensus size: 19
2570735 GAAACCAAAA
*
2570745 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2570764 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2570783 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
2570802 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
2570822 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
2570838 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
2570855 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
2570874 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2570894 TC
1 TC
2570896 AACCAAAAGA
Statistics
Matches: 114, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 65 0.57
20 35 0.31
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2570822 original size:39 final size:38
Alignment explanation
Indices: 2570745--2570895 Score: 177
Period size: 39 Copynumber: 4.1 Consensus size: 38
2570735 GAAACCAAAA
*
2570745 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
2570783 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
2570822 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
2570855 TCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
2570894 TC
1 TC
2570896 AACCAAAAGA
Statistics
Matches: 94, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
33 27 0.29
35 1 0.01
36 1 0.01
37 1 0.01
38 21 0.22
39 43 0.46
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:2574399 original size:14 final size:14
Alignment explanation
Indices: 2574380--2574415 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2574370 ATTGTTTAAT
2574380 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2574394 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2574408 TGATTTGT
1 TGATTTGT
2574416 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2574642 original size:33 final size:32
Alignment explanation
Indices: 2574600--2574725 Score: 182
Period size: 33 Copynumber: 3.8 Consensus size: 32
2574590 TTAAATTCGT
2574600 GTTGCGATTTTCATTTCGCATTGCGATTCCCTC
1 GTTGCGATTTTCATTTCGCATTGCGATT-CCTC
**
2574633 GTTGCGATTTTCATTTCGCATTGCGAAATT-AGC
1 GTTGCGATTTTCATTTCGCATTGCG--ATTCCTC
*
2574666 GTTGCGATTTTAATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTC-CTC
2574699 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
2574726 GGACATTAAG
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (32 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCCTC
Found at i:2574688 original size:66 final size:66
Alignment explanation
Indices: 2574600--2574724 Score: 232
Period size: 66 Copynumber: 1.9 Consensus size: 66
2574590 TTAAATTCGT
*
2574600 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
1 GTTGCGATTTTAATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
2574665 C
66 C
*
2574666 GTTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 GTTGCGATTTTAATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGA
2574725 TGGACATTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
GTTGCGATTTTAATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
C
Found at i:2577012 original size:12 final size:12
Alignment explanation
Indices: 2576995--2577019 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2576985 TCTTCGGGGA
2576995 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2577007 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2577019 C
1 C
2577020 GGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2577228 original size:24 final size:24
Alignment explanation
Indices: 2577194--2577250 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
2577184 CTGAAACATC
*
2577194 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
*
2577218 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
2577242 ATCAAAATC
1 ATCAAAATC
2577251 GCAATGCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAT
Found at i:2577281 original size:19 final size:19
Alignment explanation
Indices: 2577249--2577355 Score: 169
Period size: 19 Copynumber: 5.6 Consensus size: 19
2577239 AATATCAAAA
*
2577249 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2577268 TCGCATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
2577287 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2577306 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
2577325 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
2577344 TCGCGTTGCGAT
1 TCGCATTGCGAT
2577356 AGTCTGTTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 83 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2579371 original size:19 final size:19
Alignment explanation
Indices: 2579347--2579402 Score: 94
Period size: 20 Copynumber: 2.9 Consensus size: 19
2579337 GAAACTTAAA
2579347 ATCGCAATGCGAAATGACT
1 ATCGCAATGCGAAATGACT
*
2579366 ATCGCAATGCGAAAATGGCT
1 ATCGCAATGCG-AAATGACT
2579386 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
2579403 AAATCGCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (19 bp):
ATCGCAATGCGAAATGACT
Found at i:2579408 original size:19 final size:19
Alignment explanation
Indices: 2579344--2579481 Score: 100
Period size: 19 Copynumber: 7.8 Consensus size: 19
2579334 CACGAAACTT
2579344 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
**
2579363 ACTATCGCAATGCGAAAATG
1 AAAATCGCAATGCG-AAATG
***
2579383 GCTATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
2579402 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
*
2579416 AAAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
*
2579435 -AAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
*
2579448 AAAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
*
2579467 AAAATCGCATTGCGA
1 AAAATCGCAATGCGA
2579482 TTTTCATTTC
Statistics
Matches: 95, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
14 20 0.21
15 1 0.01
16 6 0.06
17 2 0.02
18 11 0.12
19 37 0.39
20 18 0.19
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.14
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:2579421 original size:14 final size:14
Alignment explanation
Indices: 2579402--2579459 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2579392 ATGCGAAATG
2579402 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2579416 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2579432 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2579448 AAAATCGCAACG
1 AAAATCGCAACG
2579460 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2579444 original size:32 final size:33
Alignment explanation
Indices: 2579386--2579475 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 33
2579376 GAAAATGGCT
*
2579386 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2579419 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2579451 ATCGCAACGCGAAATGAAAATCGCA
1 ATCGCAACGCGAAATGAAAATCGCA
2579476 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Done.