Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007906.1 Hibiscus syriacus cultivar Beakdansim tig00110300_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: 551901
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:273841 original size:14 final size:13
Alignment explanation
Indices: 273806--273852 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 13
273796 TATATAAAAT
273806 ATAAAATAAA--A
1 ATAAAATAAATCA
*
273817 AT-AAATCAATCA
1 ATAAAATAAATCA
273829 ATCAAAATAAATCA
1 AT-AAAATAAATCA
273843 ATAAAATAAA
1 ATAAAATAAA
273853 ATAAAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 6 0.20
11 2 0.07
12 3 0.10
13 8 0.27
14 11 0.37
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (13 bp):
ATAAAATAAATCA
Found at i:273896 original size:20 final size:20
Alignment explanation
Indices: 273855--273896 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
273845 AAAATAAAAT
*
273855 AAAAATATTAAATAAACCAA
1 AAAAATATTAAATAAAACAA
*
273875 AAAAATA-TAAGATAAAAGAA
1 AAAAATATTAA-ATAAAACAA
273895 AA
1 AA
273897 GAAAAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.17
Consensus pattern (20 bp):
AAAAATATTAAATAAAACAA
Found at i:273928 original size:2 final size:2
Alignment explanation
Indices: 273923--273950 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
273913 GAAGTAAATA
273923 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
273951 GGAAAAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:274011 original size:18 final size:18
Alignment explanation
Indices: 273988--274026 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
273978 ACGAAATTAA
* *
273988 AAATAAAATATTAAAAAT
1 AAATAAAACATGAAAAAT
274006 AAATAAAACATGAAAAAT
1 AAATAAAACATGAAAAAT
274024 AAA
1 AAA
274027 AAGAGGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
AAATAAAACATGAAAAAT
Found at i:275160 original size:20 final size:20
Alignment explanation
Indices: 275115--275167 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
275105 CGAACTGAAA
275115 AAATAAAAATAAAAAAGGAAT
1 AAATAAAAATAAAAAA-GAAT
* *
275136 TAATAAAAATATAAACA-AAT
1 AAATAAAAATA-AAAAAGAAT
*
275156 AAATAATAATAA
1 AAATAAAAATAA
275168 TAATAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 12 0.44
21 10 0.37
22 4 0.15
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (20 bp):
AAATAAAAATAAAAAAGAAT
Found at i:275285 original size:36 final size:36
Alignment explanation
Indices: 275237--275552 Score: 315
Period size: 37 Copynumber: 8.6 Consensus size: 36
275227 AGTTTTCAAA
* * *
275237 TATATATTATATAGTTTTCAAAACG-TTTTAAAAAA
1 TATATATTATATAATTTTCAAAATGTTTTTAAAAAC
*
275272 TCATATATTATATACATTTTCAAAATGCTTTTTTAAAAC
1 T-ATATATTATATA-ATTTTCAAAATG-TTTTTAAAAAC
* *
275311 TATATATTATATAAATTTTTAAAATGATTTT-AAAAC
1 TATATATTATAT-AATTTTCAAAATGTTTTTAAAAAC
*
275347 TATATATTATA-AGTTTTTCAAATCAAAT-TTTTTAAAAAC
1 TATATATTATATA-ATTTTC--A--AAATGTTTTTAAAAAC
*
275386 TATATATTATAT-ATTTTCAAAATATTTTTAAAAAC
1 TATATATTATATAATTTTCAAAATGTTTTTAAAAAC
* *
275421 TATATATTATATAATTTTTAAAATATTTTTTAAAAAC
1 TATATATTATATAATTTTCAAAAT-GTTTTTAAAAAC
* *
275458 TATATATTATAT--TTTTTAAAATG-TGTTAAAAAC
1 TATATATTATATAATTTTCAAAATGTTTTTAAAAAC
** *
275491 TATATATTATATATATTTTCAAAATACTTTCAAAAAC
1 TATATATTATATA-ATTTTCAAAATGTTTTTAAAAAC
*
275528 TATACATTATATATATGTTTCAAAA
1 TATATATTATATA-AT-TTTCAAAA
275553 ATCATTTGTA
Statistics
Matches: 242, Mismatches: 19, Indels: 37
0.81 0.06 0.12
Matches are distributed among these distances:
33 21 0.09
34 5 0.02
35 38 0.16
36 48 0.20
37 61 0.25
38 39 0.16
39 30 0.12
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (36 bp):
TATATATTATATAATTTTCAAAATGTTTTTAAAAAC
Found at i:275451 original size:37 final size:37
Alignment explanation
Indices: 275237--275540 Score: 285
Period size: 36 Copynumber: 8.4 Consensus size: 37
275227 AGTTTTCAAA
* * ** *
275237 TATATATTATAT-AGTTTTCAAA-ACGTTTTAAAAAA
1 TATATATTATATAATTTTTAAAATATTTTTTAAAAAC
* *
275272 TCATATATTATATACATTTTCAAAATGCTTTTTT-AAAAC
1 T-ATATATTATATA-ATTTTTAAAAT-ATTTTTTAAAAAC
275311 TATATATTATATAAATTTTTAAAATGA--TTTT-AAAAC
1 TATATATTATAT-AATTTTTAAAAT-ATTTTTTAAAAAC
* *
275347 TATATATTATA-AGTTTTTCAAATCAAATTTTTTAAAAAC
1 TATATATTATATAATTTTT-AAA--ATATTTTTTAAAAAC
*
275386 TATATATTATAT-ATTTTCAAAATA-TTTTTAAAAAC
1 TATATATTATATAATTTTTAAAATATTTTTTAAAAAC
275421 TATATATTATATAATTTTTAAAATATTTTTTAAAAAC
1 TATATATTATATAATTTTTAAAATATTTTTTAAAAAC
* *
275458 TATATATTATAT--TTTTT-AAA-ATGTGTTAAAAAC
1 TATATATTATATAATTTTTAAAATATTTTTTAAAAAC
* * *
275491 TATATATTATATATATTTTCAAAATA-CTTTCAAAAAC
1 TATATATTATATA-ATTTTTAAAATATTTTTTAAAAAC
*
275528 TATACATTATATA
1 TATATATTATATA
275541 TATGTTTCAA
Statistics
Matches: 227, Mismatches: 22, Indels: 38
0.79 0.08 0.13
Matches are distributed among these distances:
33 23 0.10
34 9 0.04
35 32 0.14
36 49 0.22
37 47 0.21
38 37 0.16
39 26 0.11
40 4 0.02
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (37 bp):
TATATATTATATAATTTTTAAAATATTTTTTAAAAAC
Found at i:275541 original size:37 final size:37
Alignment explanation
Indices: 275193--275552 Score: 302
Period size: 37 Copynumber: 9.8 Consensus size: 37
275183 AAAGAAATTT
* * *
275193 AAAACTATATATTATATATAATTTTATTAACAAAAGTTTT-
1 AAAACTATATATTATATAT-A-TTT-TCAA-AATACTTTTA
* *
275233 CAAA-TATATATTATATA-GTTTTC-AAA-ACGTTTTA
1 AAAACTATATATTATATATATTTTCAAAATAC-TTTTA
* * * *
275267 AAAAATCATATATTATATACATTTTCAAAATGCTTTTTT
1 AAAACT-ATATATTATATATATTTTCAAAATAC-TTTTA
* *
275306 AAAACTATATATTATATAAATTTTTAAAATGA-TTTT-
1 AAAACTATATATTATATATATTTTCAAAAT-ACTTTTA
* *
275342 AAAACTATATATTATA-AGT-TTTTCAAATCAAATTTTTTA
1 AAAACTATATATTATATA-TATTTTCAAA--ATA-CTTTTA
*
275381 AAAACTATATA-T-TATATATTTTCAAAATATTTTTA
1 AAAACTATATATTATATATATTTTCAAAATACTTTTA
* *
275416 AAAACTATATATTATATA-ATTTTTAAAATATTTTTTA
1 AAAACTATATATTATATATATTTTCAAAATA-CTTTTA
* *
275453 AAAACTATATATTATAT-T-TTTT-AAAAT-GTGTTA
1 AAAACTATATATTATATATATTTTCAAAATACTTTTA
*
275486 AAAACTATATATTATATATATTTTCAAAATACTTTCA
1 AAAACTATATATTATATATATTTTCAAAATACTTTTA
*
275523 AAAACTATACATTATATATATGTTTCAAAA
1 AAAACTATATATTATATATAT-TTTCAAAA
275553 ATCATTTGTA
Statistics
Matches: 271, Mismatches: 24, Indels: 52
0.78 0.07 0.15
Matches are distributed among these distances:
32 1 0.00
33 27 0.10
34 5 0.02
35 36 0.13
36 55 0.20
37 63 0.23
38 47 0.17
39 34 0.13
40 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.46
Consensus pattern (37 bp):
AAAACTATATATTATATATATTTTCAAAATACTTTTA
Found at i:281286 original size:24 final size:24
Alignment explanation
Indices: 281254--281305 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
281244 CCTCCACTAT
*
281254 CACCTCCTCTGTTATACCCGCTGC
1 CACCTCCTCTGTTATACCCACTGC
281278 CACCTCCTCTGTTATACCCACTGC
1 CACCTCCTCTGTTATACCCACTGC
281302 CACC
1 CACC
281306 ACGATCACCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.15, C:0.48, G:0.10, T:0.27
Consensus pattern (24 bp):
CACCTCCTCTGTTATACCCACTGC
Found at i:281616 original size:15 final size:15
Alignment explanation
Indices: 281596--281627 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
281586 TCCACCACGG
281596 CCGCCACCTCTTCCA
1 CCGCCACCTCTTCCA
281611 CCGCCACCTCTTCCA
1 CCGCCACCTCTTCCA
281626 CC
1 CC
281628 ACGGTCTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.62, G:0.06, T:0.19
Consensus pattern (15 bp):
CCGCCACCTCTTCCA
Found at i:284415 original size:59 final size:59
Alignment explanation
Indices: 284313--284481 Score: 152
Period size: 59 Copynumber: 2.8 Consensus size: 59
284303 ATGATCTTGT
* * *
284313 TTCTAAATTGACCCTTAAAC-TTCT-AA-ATGTTCAAATTTCATCCCTAAATTATAT-CATCA
1 TTCTAAATTGATCCTCAAACTTTATCAACAT-TTC-AATTT-ATCCC-AAATTATATCCATCA
* * * ** *
284372 TTCTAAATTTG-TCCTCAAACTTT-TTAACATTTTATTTTAATCCCCAAACCATATCCTTCA
1 TTCTAAA-TTGATCCTCAAACTTTATCAACATTTCAATTT-AT-CCCAAATTATATCCATCA
284432 TTCTAAATTGATCCTCAAACTTTATCAACATTTCAATTTATCCCAAATTA
1 TTCTAAATTGATCCTCAAACTTTATCAACATTTCAATTTATCCCAAATTA
284482 CGTGTATATA
Statistics
Matches: 89, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
59 38 0.43
60 37 0.42
61 14 0.16
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (59 bp):
TTCTAAATTGATCCTCAAACTTTATCAACATTTCAATTTATCCCAAATTATATCCATCA
Found at i:284709 original size:60 final size:58
Alignment explanation
Indices: 284610--284783 Score: 161
Period size: 60 Copynumber: 2.9 Consensus size: 58
284600 GATGAATTTG
* * * * *
284610 GGATGAAATTAGAAG-ATTTAAAAGTTTGGGGACCAATTTAGAATGAGGGTCATAGTTTAA
1 GGATGAAATTAG-AGTATTTAAAAGTTT-AGGA-CTATTTAGAATGAAGATCATAGCTTAA
* * * * * *
284670 GGATGAAATTGGATTGTTTAAAAGTTTAAGGACTTATTTAAAATGAATATCATAGCTTGA
1 GGATGAAATTAGAGTATTTAAAAGTTT-AGGAC-TATTTAGAATGAAGATCATAGCTTAA
* * *
284730 GGATGAAATTAGAGTATTCAAAGGTTTAGGAACTATTTAGAATGAAAATCATAG
1 GGATGAAATTAGAGTATTTAAAAGTTTAGG-ACTATTTAGAATGAAGATCATAG
284784 TATGGGGACA
Statistics
Matches: 92, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
59 24 0.26
60 68 0.74
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (58 bp):
GGATGAAATTAGAGTATTTAAAAGTTTAGGACTATTTAGAATGAAGATCATAGCTTAA
Found at i:286640 original size:4 final size:4
Alignment explanation
Indices: 286631--286660 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
286621 GATAGAATGG
286631 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
286661 AGGGTTGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:287742 original size:66 final size:66
Alignment explanation
Indices: 287636--287763 Score: 256
Period size: 66 Copynumber: 1.9 Consensus size: 66
287626 ATTACACCTT
287636 CTAAATCAATACTTCTTGTGTGCTTTACTTCACCCTTTATATATACGCTTTTATAAATAGTTTTG
1 CTAAATCAATACTTCTTGTGTGCTTTACTTCACCCTTTATATATACGCTTTTATAAATAGTTTTG
287701 A
66 A
287702 CTAAATCAATACTTCTTGTGTGCTTTACTTCACCCTTTATATATACGCTTTTATAAATAGTT
1 CTAAATCAATACTTCTTGTGTGCTTTACTTCACCCTTTATATATACGCTTTTATAAATAGTT
287764 GCAGTTGTAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.45
Consensus pattern (66 bp):
CTAAATCAATACTTCTTGTGTGCTTTACTTCACCCTTTATATATACGCTTTTATAAATAGTTTTG
A
Found at i:290325 original size:50 final size:51
Alignment explanation
Indices: 290200--290325 Score: 182
Period size: 51 Copynumber: 2.5 Consensus size: 51
290190 TTAGCAGTAA
**
290200 AGCGCGCCCCCTGCACCGCGCTATACGATGATTTGGCGTCACGTGGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGTCACGTGGGGTAT
* *
290251 AGCGCGCCCCCTGCACCGCACTATACGGTGAGCTGGCGTCACGT-GGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGTCACGTGGGGTAT
* * *
290301 AGCGCGGCCCCTGCAGCGTGCTATA
1 AGCGCGCCCCCTGCACCGCGCTATA
290326 TATGTATATC
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 27 0.40
51 40 0.60
ACGTcount: A:0.16, C:0.33, G:0.32, T:0.19
Consensus pattern (51 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGTCACGTGGGGTAT
Found at i:290479 original size:20 final size:19
Alignment explanation
Indices: 290448--290486 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
290438 TTATCACACC
*
290448 AAATTTTCTCAAATTCTCT
1 AAATTTTCTCAAACTCTCT
290467 AAATTTCTCTCAAACTCTCT
1 AAATTT-TCTCAAACTCTCT
290487 TTTTAAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTTTCTCAAACTCTCT
Found at i:290748 original size:110 final size:111
Alignment explanation
Indices: 290608--290828 Score: 390
Period size: 110 Copynumber: 2.0 Consensus size: 111
290598 TGGAAATCAT
* *
290608 ATATCTCTACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
290673 TATTTAGTT-ATTTATTTAATGTATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
290718 ATATCTCGACACTTTACTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
290783 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
290829 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
110 71 0.68
111 34 0.32
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:294122 original size:26 final size:26
Alignment explanation
Indices: 294051--294122 Score: 62
Period size: 26 Copynumber: 2.8 Consensus size: 26
294041 ATGTTTGTAT
**
294051 TTACTTTATTTTGTTAAATTGTAATTT
1 TTACTTTATTTTGTTAAATT-TAATAC
*
294078 TTA--TTATTATT-TCT-CATTTAATAC
1 TTACTTTATT-TTGT-TAAATTTAATAC
294102 TTACTTTATTTTGTTAAATTT
1 TTACTTTATTTTGTTAAATTT
294123 GTTGGACTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
24 7 0.20
25 12 0.34
26 13 0.37
27 3 0.09
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (26 bp):
TTACTTTATTTTGTTAAATTTAATAC
Found at i:295043 original size:51 final size:46
Alignment explanation
Indices: 294930--295048 Score: 123
Period size: 51 Copynumber: 2.5 Consensus size: 46
294920 TATACAAAAC
** *
294930 GCGGTACCTGATCCGCGCTATATAAAATTATGTTTAAAGGTATGTT
1 GCGGTACCTGATCCGCGCTATATAAAATTATGAGTAAAGGTATGTA
**
294976 GCGGTACCTGCCCCGCGCTATATAAAATTAAGTCAGGAGTAAAGGTATAG-A
1 GCGGTACCTGATCCGCGCTATATAAAATT-A-T---GAGTAAAGGTAT-GTA
*
295027 GCGGTACATGATCCGCGCTATA
1 GCGGTACCTGATCCGCGCTATA
295049 CCCCTACGTG
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
46 27 0.46
47 1 0.02
48 1 0.02
51 29 0.49
52 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (46 bp):
GCGGTACCTGATCCGCGCTATATAAAATTATGAGTAAAGGTATGTA
Found at i:301422 original size:14 final size:13
Alignment explanation
Indices: 301399--301453 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 13
301389 TGTTCATGAA
301399 CGTTGGTTATGTT
1 CGTTGGTTATGTT
301412 CGTTCGGTTATGTT
1 CGTT-GGTTATGTT
301426 CG-T--TTATGTT
1 CGTTGGTTATGTT
*
301436 CGTTCGGTAATGTT
1 CGTT-GGTTATGTT
301450 CGTT
1 CGTT
301454 TATGTTCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 5 0.14
14 21 0.58
ACGTcount: A:0.09, C:0.13, G:0.27, T:0.51
Consensus pattern (13 bp):
CGTTGGTTATGTT
Found at i:301432 original size:10 final size:10
Alignment explanation
Indices: 301413--301460 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
301403 GGTTATGTTC
*
301413 GTTCGGTTAT
1 GTTCGTTTAT
301423 GTTCGTTTAT
1 GTTCGTTTAT
301433 GTTCGTTCGGTAAT
1 GTTCGTT---T-AT
301447 GTTCGTTTAT
1 GTTCGTTTAT
301457 GTTC
1 GTTC
301461 ATTCATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.10, C:0.12, G:0.25, T:0.52
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:301473 original size:24 final size:24
Alignment explanation
Indices: 301405--301460 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
301395 TGAACGTTGG
301405 TTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCGT
*
301429 TTATGTTCGTTCGGTAATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCGT
301453 TTATGTTC
1 TTATGTTC
301461 ATTCATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (24 bp):
TTATGTTCGTTCGGTTATGTTCGT
Found at i:301900 original size:16 final size:16
Alignment explanation
Indices: 301879--301945 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
301869 GTCTCCAACG
301879 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
301895 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
301911 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
301927 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
301941 TTTAT
1 TTTAT
301946 TAAATGAACA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:301918 original size:32 final size:32
Alignment explanation
Indices: 301877--301937 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
301867 GGGTCTCCAA
301877 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
*
301909 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
301938 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:302031 original size:16 final size:16
Alignment explanation
Indices: 302007--302047 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
301997 AAAAAAATTT
302007 TGTTAGTTTATGTTCG
1 TGTTAGTTTATGTTCG
*
302023 TGTTCGTTTATGTTCG
1 TGTTAGTTTATGTTCG
302039 T-TTA-TTTAT
1 TGTTAGTTTAT
302048 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.07, G:0.20, T:0.61
Consensus pattern (16 bp):
TGTTAGTTTATGTTCG
Found at i:303452 original size:18 final size:20
Alignment explanation
Indices: 303431--303471 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
303421 TTCTATTTTA
303431 ATTTTAA-TTA-TTGTTAAT
1 ATTTTAATTTATTTGTTAAT
*
303449 ATTTTAATTTATTTTTTAAT
1 ATTTTAATTTATTTGTTAAT
303469 ATT
1 ATT
303472 AGTTTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 3 0.15
20 10 0.50
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTTTAATTTATTTGTTAAT
Found at i:303468 original size:30 final size:30
Alignment explanation
Indices: 303432--303488 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
303422 TCTATTTTAA
*
303432 TTTTAATTATT-GTTAATATTTTAATTTATT
1 TTTTAA-TATTAGTTAATATATTAATTTATT
*
303462 TTTTAATATTAGTTTATATATTAATTT
1 TTTTAATATTAGTTAATATATTAATTT
303489 TTATAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (30 bp):
TTTTAATATTAGTTAATATATTAATTTATT
Found at i:304980 original size:18 final size:17
Alignment explanation
Indices: 304944--304977 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
304934 TTACGAGTGG
304944 TTTAATAGGAATAAAAA
1 TTTAATAGGAATAAAAA
304961 TTTAATAGGAATAAAAA
1 TTTAATAGGAATAAAAA
304978 ATTGTTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (17 bp):
TTTAATAGGAATAAAAA
Found at i:305516 original size:3 final size:3
Alignment explanation
Indices: 305508--305550 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
305498 CCTGCTCCTA
* * *
305508 ATG ATG ATG ATG ATA ATG ACG GTG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
305551 CATAATGAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.02, G:0.33, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:307424 original size:26 final size:26
Alignment explanation
Indices: 307392--307441 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
307382 ATAAACATTA
307392 CTTTTCAGTGGTAGAGCGATCGACAT
1 CTTTTCAGTGGTAGAGCGATCGACAT
307418 CTTTTCAGTGGTAGAGCGATCGAC
1 CTTTTCAGTGGTAGAGCGATCGAC
307442 TTAACTGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (26 bp):
CTTTTCAGTGGTAGAGCGATCGACAT
Found at i:309116 original size:44 final size:44
Alignment explanation
Indices: 309053--309142 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
309043 GGATTAAATC
309053 CCGCAAGAAAGGGTACTAGATCGGTAAAATTTGGTGAAACGATG
1 CCGCAAGAAAGGGTACTAGATCGGTAAAATTTGGTGAAACGATG
309097 CCGCAAGAAAGGGTACTAGATCGGTAAAATTTGGTGAAACGATG
1 CCGCAAGAAAGGGTACTAGATCGGTAAAATTTGGTGAAACGATG
309141 CC
1 CC
309143 TGACAGATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.20
Consensus pattern (44 bp):
CCGCAAGAAAGGGTACTAGATCGGTAAAATTTGGTGAAACGATG
Found at i:309746 original size:11 final size:12
Alignment explanation
Indices: 309723--309755 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
309713 TAATTTAAAA
309723 TATAAATAGTTT
1 TATAAATAGTTT
309735 TATAAA-AGTTT
1 TATAAATAGTTT
*
309746 TATAACTAGT
1 TATAAATAGT
309756 ATTTTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (12 bp):
TATAAATAGTTT
Found at i:310073 original size:68 final size:68
Alignment explanation
Indices: 309999--310139 Score: 282
Period size: 68 Copynumber: 2.1 Consensus size: 68
309989 TTATTTTGTA
309999 TTTTTTAAAATTAATATTAGAAAGAATATTGTAAATATATAGGTGATATTTTTTAGTTTTACATT
1 TTTTTTAAAATTAATATTAGAAAGAATATTGTAAATATATAGGTGATATTTTTTAGTTTTACATT
310064 CTT
66 CTT
310067 TTTTTTAAAATTAATATTAGAAAGAATATTGTAAATATATAGGTGATATTTTTTAGTTTTACATT
1 TTTTTTAAAATTAATATTAGAAAGAATATTGTAAATATATAGGTGATATTTTTTAGTTTTACATT
310132 CTT
66 CTT
310135 TTTTT
1 TTTTT
310140 ATTGAATTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 73 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (68 bp):
TTTTTTAAAATTAATATTAGAAAGAATATTGTAAATATATAGGTGATATTTTTTAGTTTTACATT
CTT
Found at i:310328 original size:11 final size:10
Alignment explanation
Indices: 310307--310365 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
310297 CTCTCATATT
310307 TAAAAATCAA
1 TAAAAATCAA
310317 TAAAAATACAA
1 TAAAAAT-CAA
**
310328 TATAAAAAGAA
1 TA-AAAATCAA
*
310339 TTAAAAATGAA
1 -TAAAAATCAA
*
310350 TAAAATTCAA
1 TAAAAATCAA
310360 TAAAAA
1 TAAAAA
310366 AAAGAATGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
10 20 0.50
11 14 0.35
12 6 0.15
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.22
Consensus pattern (10 bp):
TAAAAATCAA
Found at i:310343 original size:33 final size:33
Alignment explanation
Indices: 310306--310377 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
310296 ACTCTCATAT
*
310306 TTAAAAATCAATAAAAATACAAT-ATAAAAAGAA
1 TTAAAAATCAAT-AAAATACAATAAAAAAAAGAA
* *
310339 TTAAAAATGAATAAAATTCAATAAAAAAAAGAA
1 TTAAAAATCAATAAAATACAATAAAAAAAAGAA
310372 TGTAAA
1 T-TAAA
310378 GCTAAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 9 0.26
33 21 0.62
34 4 0.12
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.22
Consensus pattern (33 bp):
TTAAAAATCAATAAAATACAATAAAAAAAAGAA
Found at i:310557 original size:12 final size:12
Alignment explanation
Indices: 310525--310557 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
310515 GTAAAAAAAT
*
310525 ACTAGTTATAAA
1 ACTATTTATAAA
310537 ACT-TTTATAAA
1 ACTATTTATAAA
310548 ACTATTTATA
1 ACTATTTATA
310558 TTTTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.42
Consensus pattern (12 bp):
ACTATTTATAAA
Found at i:312557 original size:12 final size:12
Alignment explanation
Indices: 312540--312568 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
312530 ATCCCTAACC
312540 ACCACGATGGAA
1 ACCACGATGGAA
312552 ACCACGATGGAA
1 ACCACGATGGAA
312564 ACCAC
1 ACCAC
312569 AACAACAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.31, G:0.21, T:0.07
Consensus pattern (12 bp):
ACCACGATGGAA
Found at i:314198 original size:27 final size:27
Alignment explanation
Indices: 314168--314223 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
314158 TATTTTTAGA
*
314168 TATTAAATTTAAAATTTATAATATAAT
1 TATTAAATTTAAAATTTATAATAAAAT
*
314195 TATTAAATTTAAAATTTATCATAAAAT
1 TATTAAATTTAAAATTTATAATAAAAT
314222 TA
1 TA
314224 ATGTCACACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
TATTAAATTTAAAATTTATAATAAAAT
Found at i:314978 original size:33 final size:31
Alignment explanation
Indices: 314941--315011 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 31
314931 AAGAAATTTA
* * *
314941 TTTTTATGTTAGTATTT-TTTAAATAGTTATT
1 TTTTTATATTAATATTTATGTAAATA-TTATT
314972 ACTTTTTATATTAATATTTATGTAAATATTATT
1 --TTTTTATATTAATATTTATGTAAATATTATT
315005 TTTTTAT
1 TTTTTAT
315012 TAAAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.21
33 20 0.59
34 7 0.21
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (31 bp):
TTTTTATATTAATATTTATGTAAATATTATT
Found at i:315205 original size:17 final size:17
Alignment explanation
Indices: 315183--315236 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
315173 AATGTTAATA
315183 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
315200 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
315217 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
315234 TTT
1 TTT
315237 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:316799 original size:21 final size:21
Alignment explanation
Indices: 316769--316816 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
316759 GTAGGGGTAC
* *
316769 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
316790 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
316811 ATGCCA
1 ATGCCA
316817 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:316846 original size:21 final size:21
Alignment explanation
Indices: 316820--316913 Score: 118
Period size: 21 Copynumber: 4.5 Consensus size: 21
316810 TATGCCATCT
316820 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
* * *
316841 CCGCAGGGTTATACTCTGAGC
1 CCGCAGGGTTACATTCCGAGC
*
316862 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
316883 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
316904 CCGCAGGGTT
1 CCGCAGGGTT
316914 TTATACCATA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 2 0.03
21 59 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:316853 original size:42 final size:41
Alignment explanation
Indices: 316796--316913 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 41
316786 TCATATGCCA
* * *
316796 AGCCCACCAGTTTATATGCCATCTCCGCAGGGTTACATTCCG
1 AGCCCGCCAGGTTATATGCCAGC-CCGCAGGGTTACATTCCG
* *
316838 AGCCCG-CAGGGTTATACT-CTGAGCCCGCAGGGTTACATTCCT
1 AGCCCGCCA-GGTTATA-TGC-CAGCCCGCAGGGTTACATTCCG
*
316880 AGCCCGCCAGGTTACATGCCTAGCCCGCAGGGTT
1 AGCCCGCCAGGTTATATGCC-AGCCCGCAGGGTT
316914 TTATACCATA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
41 3 0.05
42 55 0.87
43 5 0.08
ACGTcount: A:0.19, C:0.33, G:0.25, T:0.23
Consensus pattern (41 bp):
AGCCCGCCAGGTTATATGCCAGCCCGCAGGGTTACATTCCG
Found at i:323451 original size:35 final size:35
Alignment explanation
Indices: 323405--323477 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
323395 GGGTATCGAT
*
323405 ATTAACTCTTAAAATTTAACCTTTCATCGCTATAC
1 ATTAACTCTTAAAATTTAACCTTTCACCGCTATAC
323440 ATTAACTCTTAAAATTTAACCTTTCACCGCTATAC
1 ATTAACTCTTAAAATTTAACCTTTCACCGCTATAC
323475 ATT
1 ATT
323478 TATCATTTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (35 bp):
ATTAACTCTTAAAATTTAACCTTTCACCGCTATAC
Found at i:324096 original size:23 final size:23
Alignment explanation
Indices: 324070--324130 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
324060 CACCACAGCT
*
324070 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
324093 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
324116 CGTAGAAATACACCG
1 CGTAGAAATGCACCG
324131 TAGTTCCATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:327130 original size:17 final size:17
Alignment explanation
Indices: 327092--327133 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
327082 TAACACATAC
*
327092 GATGTATCCAAAATAAT
1 GATGTATCCAAAATAAG
* *
327109 AATGTATCCAAAATAGG
1 GATGTATCCAAAATAAG
327126 GATGTATC
1 GATGTATC
327134 ACATGTGTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (17 bp):
GATGTATCCAAAATAAG
Found at i:327221 original size:29 final size:29
Alignment explanation
Indices: 327189--327244 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
327179 CCTCCAACAG
*
327189 GCTTCCACCATCCCATTTCTTTCCACCAA
1 GCTTCCACCATCACATTTCTTTCCACCAA
* *
327218 GCTTCCACTATCATATTTCTTTCCACC
1 GCTTCCACCATCACATTTCTTTCCACC
327245 CACTCCACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.20, C:0.41, G:0.04, T:0.36
Consensus pattern (29 bp):
GCTTCCACCATCACATTTCTTTCCACCAA
Found at i:328609 original size:2 final size:2
Alignment explanation
Indices: 328604--328640 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
328594 GTTAATCCGA
328604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
328641 AATTTACTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:338235 original size:19 final size:19
Alignment explanation
Indices: 338204--338240 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
338194 TCTCACAATG
338204 TTTCATTTATTTTTTTTAT
1 TTTCATTTATTTTTTTTAT
338223 TTTCGATTT-TTTTTTTTA
1 TTTC-ATTTATTTTTTTTA
338241 AAATGATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTCATTTATTTTTTTTAT
Found at i:344356 original size:77 final size:76
Alignment explanation
Indices: 344112--344505 Score: 436
Period size: 77 Copynumber: 5.1 Consensus size: 76
344102 ATCTCATTGG
* * * ** *
344112 AGATTGTTTTTCTTAAAAC-AGACTTTATCTCACTTGAGA-TTGTTTTACTTGAAAGAATACATT
1 AGATTGTTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGACATGTTTTACTCAAAAGAAGACATT
*
344175 TCATTTTACTCA
65 TCATTTCACTCA
* * * * *
344187 AGATTGTTTTTCTTAAAATAAAATTTGTCTCGCTTGAGACAGGTTTTATTCAAAACAAGACATTT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACATGTTTTACTCAAAAGAAGACATTT
*
344252 CACTTCACTACA
66 CATTTCACT-CA
* * * * *
344264 TG-TTGGTTTTCTTAAAACAAGATTTGTCTCGCTTGAGATGATTTTTTACTCGAAAGAAGACATT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGA-CATGTTTTACTCAAAAGAAGACATT
*
344328 TCATTTGACTCA
65 TCATTTCACTCA
* * * * * *
344340 AGATTGTTTTTCTTAAAGCAAAATTTTTTCTCGCTTGAGACAGGTTTTATTCAAAACAAGACATT
1 AGATTGTTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGACATGTTTTACTCAAAAGAAGACATT
*
344405 TCACTTCACTACA
65 TCATTTCACT-CA
* * *
344418 TG-TTGTTTTTCTTAAAACAAGATTTGTCTTGCTTGAGACGATTTTTTTACTCAAAAGAAGACAT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC-A-TGTTTTACTCAAAAGAAGACAT
344482 TTCATTTCACTCA
64 TTCATTTCACTCA
344495 AGATTGTTTTT
1 AGATTGTTTTT
344506 AAAGAAGATT
Statistics
Matches: 260, Mismatches: 49, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
75 32 0.12
76 78 0.30
77 96 0.37
78 54 0.21
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.41
Consensus pattern (76 bp):
AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACATGTTTTACTCAAAAGAAGACATTT
CATTTCACTCA
Found at i:344421 original size:154 final size:153
Alignment explanation
Indices: 344119--344505 Score: 600
Period size: 154 Copynumber: 2.5 Consensus size: 153
344109 TGGAGATTGT
* * * * *
344119 TTTTCTTAAAAC-AGACTTTATCTCACTTGAGAT--TGTTTTACTTGAAAGAATACATTTCATTT
1 TTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGATGATTTTTTACTCGAAAGAAGACATTTCATTT
* *
344181 TACTCAAGATTGTTTTTCTTAAAATAAAATTTGTCTCGCTTGAGACAGGTTTTATTCAAAACAAG
65 CACTCAAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGGTTTTATTCAAAACAAG
344246 ACATTTCACTTCACTACATGTTGG
130 ACATTTCACTTCACTACATGTTGG
*
344270 TTTTCTTAAAACAAGATTTGTCTCGCTTGAGATGATTTTTTACTCGAAAGAAGACATTTCATTTG
1 TTTTCTTAAAACAAGATTTGTCTCGCTTGAGATGATTTTTTACTCGAAAGAAGACATTTCATTTC
* *
344335 ACTCAAGATTGTTTTTCTTAAAGCAAAATTTTTTCTCGCTTGAGACAGGTTTTATTCAAAACAAG
66 ACTCAAGATTGTTTTTCTTAAAACAAAA-TTTGTCTCGCTTGAGACAGGTTTTATTCAAAACAAG
*
344400 ACATTTCACTTCACTACATGTTGT
130 ACATTTCACTTCACTACATGTTGG
* * *
344424 TTTTCTTAAAACAAGATTTGTCTTGCTTGAGACGATTTTTTTACTCAAAAGAAGACATTTCATTT
1 TTTTCTTAAAACAAGATTTGTCTCGCTTGAGATGA-TTTTTTACTCGAAAGAAGACATTTCATTT
344489 CACTCAAGATTGTTTTT
65 CACTCAAGATTGTTTTT
344506 AAAGAAGATT
Statistics
Matches: 217, Mismatches: 14, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
151 27 0.12
152 3 0.01
153 52 0.24
154 91 0.42
155 44 0.20
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (153 bp):
TTTTCTTAAAACAAGATTTGTCTCGCTTGAGATGATTTTTTACTCGAAAGAAGACATTTCATTTC
ACTCAAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGGTTTTATTCAAAACAAGA
CATTTCACTTCACTACATGTTGG
Found at i:344563 original size:39 final size:39
Alignment explanation
Indices: 344508--345066 Score: 621
Period size: 39 Copynumber: 14.7 Consensus size: 39
344498 TTGTTTTTAA
*
344508 AGAAGATTTTATCTCGCTTTAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
344547 AAAAGATTTTATCTCGCTTGAGATAATTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
344586 AGAAGATTTTATCTCACTTAAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
344625 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
344664 AGAAGATTTTATCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * **
344703 AAAAGGTTTTATCTTTCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
344742 AGAATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
344781 AGAAGATTTTATCTTGCTTGAGATAGATTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
344820 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* ** * *
344859 -G-AG-TTTTGTCTCTATTGAGACAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * *
344895 --AA-ATTTTGTCTCTCTTGTGACAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* **
344931 --AA-ATTTTGTCTCGCTTGAGATAGTTTCCCTTTAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* ** * *
344967 -G-AG-TTTTGTCTCTTTTGAGACAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * *
345003 --AA-ATTTTGTCTCTCTAGAGACAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
345039 AAGAA-A-TGTATCTCACTTGAGATGGTTT
1 -AGAAGATTTTATCTCGCTTGAGATAGTTT
345067 TTCTTAAAAC
Statistics
Matches: 460, Mismatches: 51, Indels: 19
0.87 0.10 0.04
Matches are distributed among these distances:
36 154 0.33
37 2 0.00
38 17 0.04
39 287 0.62
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.36
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:345158 original size:75 final size:73
Alignment explanation
Indices: 344999--345158 Score: 171
Period size: 75 Copynumber: 2.1 Consensus size: 73
344989 GTTTCCCTTG
* * * *
344999 AAACAAATTTTGTCTCTCTAGAGACAGTTTCCCTTGAAACAAGAAATGTATCTCACTTGAGATGG
1 AAAC-AATTTCGTCTCGCTAGAGACAGTTTCCCATGAAACAAGAAATGTATCTCACTCGAGATGG
* *
345064 TTTTTCTTA
65 CTTCTCTTA
* * *
345073 AAACCAATTTCGTCTCGCTTGAGACAATTTTCCCATGAAACAAGAAATTTTATCTCACTCGAGA-
1 AAA-CAATTTCGTCTCGCTAGAGAC-AGTTTCCCATGAAACAAGAAA-TGTATCTCACTCGAGAT
345137 GAGCTTCTCTT-
63 G-GCTTCTCTTA
345148 AAACAGATTTC
1 AAACA-ATTTC
345159 TTATTCATTT
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
74 22 0.31
75 29 0.40
76 21 0.29
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.34
Consensus pattern (73 bp):
AAACAATTTCGTCTCGCTAGAGACAGTTTCCCATGAAACAAGAAATGTATCTCACTCGAGATGGC
TTCTCTTA
Found at i:345850 original size:29 final size:29
Alignment explanation
Indices: 345817--345880 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
345807 ATGCCCATCC
* * *
345817 TCCACCAAGCTTCCACCATCCCATTTGTT
1 TCCACCAACCTTCCACCATCACATTTCTT
* *
345846 TCCACCAACCTTCCACTATCATATTTCTT
1 TCCACCAACCTTCCACCATCACATTTCTT
345875 TCCACC
1 TCCACC
345881 CACTCCACCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.22, C:0.42, G:0.03, T:0.33
Consensus pattern (29 bp):
TCCACCAACCTTCCACCATCACATTTCTT
Found at i:347696 original size:14 final size:14
Alignment explanation
Indices: 347677--347716 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
347667 TTTTGTCTTA
347677 AAAAATTATTTTTT
1 AAAAATTATTTTTT
347691 AAAAATTA-TTTTT
1 AAAAATTATTTTTT
347704 AAAAGA-TATTTTT
1 AAAA-ATTATTTTT
347717 AGGTATTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
AAAAATTATTTTTT
Found at i:347702 original size:13 final size:13
Alignment explanation
Indices: 347677--347717 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
347667 TTTTGTCTTA
347677 AAAAATTATTTTTT
1 AAAAATTA-TTTTT
347691 AAAAATTATTTTT
1 AAAAATTATTTTT
347704 AAAAGA-TATTTTT
1 AAAA-ATTATTTTT
347717 A
1 A
347718 GGTATTCGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:348668 original size:185 final size:184
Alignment explanation
Indices: 348350--348738 Score: 622
Period size: 185 Copynumber: 2.1 Consensus size: 184
348340 AACCGAAATT
*
348350 AAATATTAAATATTTTATATATAACATATGGGTTCAACCTAAACCATTTAAAACCAAATTAATAA
1 AAATATTAAATATTTTATATATAACATATGGGCTCAACCTAAACCATTTAAAACCAAATTAATAA
348415 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
* *
348480 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
* * * *
348535 AAATATTAAATATATTATATATAACATATGGGCT-AAGCTCAAACTATTTAAAACCCAATTAATA
1 AAATATTAAATATTTTATATATAACATATGGGCTCAACCT-AAACCATTTAAAACCAAATTAATA
* * *
348599 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTGAAA-T
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATT
348663 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
129 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
* *
348719 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATTTTATATA
348739 AATTAGAAAA
Statistics
Matches: 189, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
183 8 0.04
184 26 0.14
185 152 0.80
186 3 0.02
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATTTTATATATAACATATGGGCTCAACCTAAACCATTTAAAACCAAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:348899 original size:15 final size:15
Alignment explanation
Indices: 348881--348922 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
348871 TTATGGTTAA
348881 TTCGATTCGGTTCGG
1 TTCGATTCGGTTCGG
348896 TTCGATTCGGTTCGG
1 TTCGATTCGGTTCGG
*
348911 TTCAATTCGGTT
1 TTCGATTCGGTT
348923 TTAACTGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.43
Consensus pattern (15 bp):
TTCGATTCGGTTCGG
Found at i:348919 original size:20 final size:19
Alignment explanation
Indices: 348865--348919 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 19
348855 AATTCGATTA
*
348865 ATTCGGTTATGGTTAATTCG
1 ATTCGGTT-CGGTTAATTCG
348885 ATTCGGTTCGG----TTCG
1 ATTCGGTTCGGTTAATTCG
348900 ATTCGGTTCGGTTCAATTCG
1 ATTCGGTTCGGTT-AATTCG
348920 GTTTTAACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
15 15 0.52
19 2 0.07
20 12 0.41
ACGTcount: A:0.15, C:0.16, G:0.27, T:0.42
Consensus pattern (19 bp):
ATTCGGTTCGGTTAATTCG
Found at i:350114 original size:3 final size:3
Alignment explanation
Indices: 350106--350144 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
350096 CTACAATGTT
*
350106 TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
350145 AGGTGAGAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:353397 original size:4 final size:4
Alignment explanation
Indices: 353388--353413 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
353378 TGGTATATGG
353388 AATC AATC AATC AATC AATC AATC AA
1 AATC AATC AATC AATC AATC AATC AA
353414 CCAGTCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (4 bp):
AATC
Found at i:354608 original size:13 final size:13
Alignment explanation
Indices: 354590--354614 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
354580 TTGGTCAAGG
354590 AATTTAGAAACAC
1 AATTTAGAAACAC
354603 AATTTAGAAACA
1 AATTTAGAAACA
354615 AGGTACTGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (13 bp):
AATTTAGAAACAC
Found at i:360079 original size:13 final size:14
Alignment explanation
Indices: 360061--360111 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 14
360051 CTTCATATAA
360061 AATTT-ATTATTTT
1 AATTTAATTATTTT
360074 AATTTAATTA-TTT
1 AATTTAATTATTTT
360087 AATATT-A-TATTTT
1 AAT-TTAATTATTTT
*
360100 ACTTTAATTATT
1 AATTTAATTATT
360112 CTTCTAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
12 4 0.12
13 18 0.56
14 10 0.31
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTTAATTATTTT
Found at i:363426 original size:20 final size:21
Alignment explanation
Indices: 363389--363431 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
363379 ATATGAAGCA
*
363389 TTTGAGCTGAAATGAAGTAATT
1 TTTGAGCTCAAA-GAAGTAATT
*
363411 TTTGAGCTCAAA-AAGTGATT
1 TTTGAGCTCAAAGAAGTAATT
363431 T
1 T
363432 ATGGGCAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (21 bp):
TTTGAGCTCAAAGAAGTAATT
Found at i:364589 original size:32 final size:32
Alignment explanation
Indices: 364541--364601 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
364531 GAGTCGATGG
* * * *
364541 TTACCTATGTCTTTCGGGATATATTGACAATA
1 TTACCTATATCATTCGGGACATATGGACAATA
364573 TTACCTATATCATTCGGGACATATGGACA
1 TTACCTATATCATTCGGGACATATGGACA
364602 GTTACCTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (32 bp):
TTACCTATATCATTCGGGACATATGGACAATA
Found at i:367905 original size:30 final size:31
Alignment explanation
Indices: 367838--367926 Score: 117
Period size: 32 Copynumber: 2.9 Consensus size: 31
367828 GAGTCGAGGG
* *
367838 TTACCTATGTCTTTCGGGACATATGGATAGTA
1 TTACCTATGTCCTTCGGGACATATGGACAG-A
367870 TTACCTATGTCCTTCGGGACATATGGACA-A
1 TTACCTATGTCCTTCGGGACATATGGACAGA
* * *
367900 TTACCTATGTTCTTAGGAACATATGGA
1 TTACCTATGTCCTTCGGGACATATGGA
367927 TAGGTTCTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
30 25 0.48
32 27 0.52
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (31 bp):
TTACCTATGTCCTTCGGGACATATGGACAGA
Found at i:369452 original size:18 final size:18
Alignment explanation
Indices: 369429--369468 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
369419 TGTCATTTGG
*
369429 GACATAGTGGTCCTTCGA
1 GACATAGTGGTCATTCGA
*
369447 GACATAGTGGTCATTCGG
1 GACATAGTGGTCATTCGA
369465 GACA
1 GACA
369469 AATTTTCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (18 bp):
GACATAGTGGTCATTCGA
Found at i:371267 original size:56 final size:54
Alignment explanation
Indices: 371214--371318 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 54
371204 GACATATACA
*
371214 ATCTAATGATTGAGA-AAAATAACGATTTTAACAATCGATTAATATATATATATAAG
1 ATCTAATGA-T-AGATAAAATAACGATTTTAACAATCGATTAAAATA-ATATATAAG
* * **
371270 ATTTATTGATAGATAAAATAACGATTTTAACGGTCGATTAAAATAATAT
1 ATCTAATGATAGATAAAATAACGATTTTAACAATCGATTAAAATAATAT
371319 TATCATATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
54 7 0.16
55 29 0.67
56 7 0.16
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (54 bp):
ATCTAATGATAGATAAAATAACGATTTTAACAATCGATTAAAATAATATATAAG
Found at i:371571 original size:2 final size:2
Alignment explanation
Indices: 371564--371602 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
371554 ACTAACTAAC
371564 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
371603 CTCCATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:381601 original size:10 final size:10
Alignment explanation
Indices: 381586--381611 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
381576 TCACACCAAA
381586 TTCTCTCAAT
1 TTCTCTCAAT
381596 TTCTCTCAAT
1 TTCTCTCAAT
381606 TTCTCT
1 TTCTCT
381612 TAAATACTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (10 bp):
TTCTCTCAAT
Found at i:381699 original size:17 final size:18
Alignment explanation
Indices: 381669--381704 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
381659 ATGTATGTAA
381669 TTTATTTAAGTATTTTAC
1 TTTATTTAAGTATTTTAC
381687 TTTATTTAA-TATTTTAC
1 TTTATTTAAGTATTTTAC
381704 T
1 T
381705 AATATAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTATTTAAGTATTTTAC
Found at i:383785 original size:3 final size:3
Alignment explanation
Indices: 383770--383810 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
383760 ACCTGCTCAT
* *
383770 GAC GAC GAA GAC GAC GAT GAC GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
383811 TGATGACAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.37, C:0.27, G:0.34, T:0.02
Consensus pattern (3 bp):
GAC
Found at i:384071 original size:35 final size:33
Alignment explanation
Indices: 384032--384116 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
384022 ATATTTCAGT
384032 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
384067 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
384102 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
384117 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:385549 original size:171 final size:171
Alignment explanation
Indices: 385264--385607 Score: 661
Period size: 171 Copynumber: 2.0 Consensus size: 171
385254 CAATGTGTCG
* *
385264 GAGATAATACCTATGTTGGACAAAATTTGGTTACTACATTGGACCCAAAGACTCCATTACTGCTT
1 GAGATAATACCTATGTTGGACAAAATTTGGTTACCACATTAGACCCAAAGACTCCATTACTGCTT
*
385329 TGATTCCAGCTCCACGATCTGAAATGACACAAATGTTTTCCCTCGTGATAACATGTGCACGTAAA
66 TGATCCCAGCTCCACGATCTGAAATGACACAAATGTTTTCCCTCGTGATAACATGTGCACGTAAA
385394 TTTAGAAGGAAAAAAACCCAAGAATCTGTATCTTCTCCTTC
131 TTTAGAAGGAAAAAAACCCAAGAATCTGTATCTTCTCCTTC
385435 GAGATAATACCTATGTTGGACAAAATTTGGTTACCACATTAGACCCAAAGACTCCATTACTGCTT
1 GAGATAATACCTATGTTGGACAAAATTTGGTTACCACATTAGACCCAAAGACTCCATTACTGCTT
385500 TGATCCCAGCTCCACGATCTGAAATGACACAAATGTTTTCCCTCGTGATAACATGTGCACGTAAA
66 TGATCCCAGCTCCACGATCTGAAATGACACAAATGTTTTCCCTCGTGATAACATGTGCACGTAAA
385565 TTTAGAAGGAAAAAAACCCAAGAATCTGTATCTTCTCCTTC
131 TTTAGAAGGAAAAAAACCCAAGAATCTGTATCTTCTCCTTC
385606 GA
1 GA
385608 CAAGAGAAAA
Statistics
Matches: 170, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
171 170 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (171 bp):
GAGATAATACCTATGTTGGACAAAATTTGGTTACCACATTAGACCCAAAGACTCCATTACTGCTT
TGATCCCAGCTCCACGATCTGAAATGACACAAATGTTTTCCCTCGTGATAACATGTGCACGTAAA
TTTAGAAGGAAAAAAACCCAAGAATCTGTATCTTCTCCTTC
Found at i:388107 original size:30 final size:29
Alignment explanation
Indices: 388045--388107 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
388035 TACTGCTACG
* *
388045 GGTGTTAGATCGGGAAATATAATATGACT
1 GGTGTCAGATCGGGAAATATAATATCACT
*
388074 GGTGTCAGATCGGTAAATATACCA-ATCACT
1 GGTGTCAGATCGGGAAATATA--ATATCACT
388104 GGTG
1 GGTG
388108 ATTTTTCAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 19 0.66
30 9 0.31
31 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (29 bp):
GGTGTCAGATCGGGAAATATAATATCACT
Found at i:390505 original size:5 final size:5
Alignment explanation
Indices: 390497--390529 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
390487 ATAAATATCT
390497 GATGA GATGA GATGA GATGA GATGA GATTGA GA
1 GATGA GATGA GATGA GATGA GATGA GA-TGA GA
390530 AAACAATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (5 bp):
GATGA
Found at i:394083 original size:6 final size:6
Alignment explanation
Indices: 394074--394141 Score: 85
Period size: 6 Copynumber: 12.3 Consensus size: 6
394064 CTCTCTTTTC
*
394074 TCTCTG TCTCTG TCTCT- T-T-TA TCTCTG TCTCTG TCTCT- T-T-TG
1 TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG
394116 TCTCTG TCTCTG TCTCTG TCTCTG TC
1 TCTCTG TCTCTG TCTCTG TCTCTG TC
394142 CCTTTTTTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
3 2 0.04
4 4 0.07
5 4 0.07
6 45 0.82
ACGTcount: A:0.01, C:0.31, G:0.13, T:0.54
Consensus pattern (6 bp):
TCTCTG
Found at i:394089 original size:21 final size:21
Alignment explanation
Indices: 394056--394132 Score: 122
Period size: 21 Copynumber: 3.8 Consensus size: 21
394046 TTTTTTTCGG
*
394056 CTCTGTCTC--TCTCTTTTCT
1 CTCTGTCTCTGTCTCTTTTAT
394075 CTCTGTCTCTGTCTCTTTTAT
1 CTCTGTCTCTGTCTCTTTTAT
*
394096 CTCTGTCTCTGTCTCTTTTGT
1 CTCTGTCTCTGTCTCTTTTAT
394117 CTCTGTCTCTGTCTCT
1 CTCTGTCTCTGTCTCT
394133 GTCTCTGTCC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
19 9 0.17
21 45 0.83
ACGTcount: A:0.01, C:0.32, G:0.10, T:0.56
Consensus pattern (21 bp):
CTCTGTCTCTGTCTCTTTTAT
Found at i:394110 original size:27 final size:27
Alignment explanation
Indices: 394074--394147 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
394064 CTCTCTTTTC
394074 TCTCTGTCTCTGTCTCTTTTATCTCTG
1 TCTCTGTCTCTGTCTCTTTTATCTCTG
* * * *
394101 TCTCTGTCTCT-TTTGTCTCTGTCTCTG
1 TCTCTGTCTCTGTCTCT-TTTATCTCTG
*
394128 TCTCTGTCTCTGTCCCTTTT
1 TCTCTGTCTCTGTCTCTTTT
394148 TTTTGCTCGC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.08
27 32 0.86
28 2 0.05
ACGTcount: A:0.01, C:0.31, G:0.12, T:0.55
Consensus pattern (27 bp):
TCTCTGTCTCTGTCTCTTTTATCTCTG
Found at i:394548 original size:12 final size:13
Alignment explanation
Indices: 394533--394597 Score: 82
Period size: 12 Copynumber: 5.1 Consensus size: 13
394523 TGGGCTTGTA
394533 ATATTA-AATAAT
1 ATATTATAATAAT
394545 ATATTAATAATAAT
1 ATATT-ATAATAAT
*
394559 ATAATTATAATTAT
1 AT-ATTATAATAAT
394573 A-ATTATAATAAT
1 ATATTATAATAAT
394585 A-ATTATAATAAT
1 ATATTATAATAAT
394597 A
1 A
394598 ATAATATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
12 28 0.58
13 1 0.02
14 16 0.33
15 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTATAATAAT
Found at i:394555 original size:3 final size:3
Alignment explanation
Indices: 394539--394615 Score: 72
Period size: 3 Copynumber: 26.7 Consensus size: 3
394529 TGTAATATTA
* * * *
394539 AAT AAT -AT ATT AAT AAT AAT -AT AAT TAT AAT TAT AAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
394585 AAT TAT AAT AAT AAT AAT -AT AAAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
394616 AAAATGAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
2 8 0.14
3 49 0.83
4 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:395460 original size:113 final size:113
Alignment explanation
Indices: 394900--395466 Score: 814
Period size: 113 Copynumber: 5.0 Consensus size: 113
394890 ATAGAATTAT
* * *
394900 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
394965 ATTATGAACTTC--TCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGA
66 ATTATGAAC-TCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
395012 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * * * * * * **
395077 CTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAA
63 CTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * *
395128 ACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * * * *
395193 ATTATGAACTCTACCTGGCAATGTTGATCCCTCAAATGATGGATCTGA
66 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
395241 GCAAAAGGTTGGACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
395306 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
395354 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
395419 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
395467 ATCTTTGCTA
Statistics
Matches: 411, Mismatches: 39, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
112 49 0.12
113 266 0.65
114 2 0.00
115 20 0.05
116 74 0.18
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:396353 original size:83 final size:83
Alignment explanation
Indices: 396251--396669 Score: 741
Period size: 83 Copynumber: 5.0 Consensus size: 83
396241 CTTATTTCTA
*
396251 CTATGAGCAAATTCATCTTCCAAATTCAATGGTTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGGTTGGTTCTGCCAAACCAGATCAGATAACTCAAA
396316 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
396334 CTATGAGCAAATTCATCTTCTAAATTCAATGGTTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGGTTGGTTCTGCCAAACCAGATCAGATAACTCAAA
*
396399 GAACACTTCTAGAAGATG
66 GAACACTTCCAGAAGATG
* * * *
396417 CTATGAGCAAATTTATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGGTTGGTTCTGCCAAACCAGATCAGATAACTCAAA
396482 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
396500 CTATGAGCAAATTCATCTTCTAAATTCAATGGTTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGGTTGGTTCTGCCAAACCAGATCAGATAACTCAAA
396565 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * *
396583 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGATTCTGTCC-AACCAGATCAAATAACTCAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGGTTGGTTCTG-CCAAACCAGATCAGATAACTCAA
396647 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
396666 CTAT
1 CTAT
396670 TAGTATATTG
Statistics
Matches: 321, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
83 319 0.99
84 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCTAAATTCAATGGTTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:408586 original size:6 final size:7
Alignment explanation
Indices: 408567--408591 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
408557 TAAATATATA
408567 AATTTTT
1 AATTTTT
408574 AATTTTT
1 AATTTTT
408581 AATTTTT
1 AATTTTT
408588 AATT
1 AATT
408592 AATGGAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:410185 original size:6 final size:6
Alignment explanation
Indices: 410176--410255 Score: 66
Period size: 6 Copynumber: 14.2 Consensus size: 6
410166 TTTTTTTCGG
* * *
410176 CTCTGT CTCTCT CT-TTT CTCTCTGT CTCTGT CTCT-T -T-TAT CTCTGT
1 CTCTGT CTCTGT CTCTGT CTC--TGT CTCTGT CTCTGT CTCTGT CTCTGT
410222 CTCTGT CTCT-T -T-TGT CTCTGT CTCTGT CTCTGT C
1 CTCTGT CTCTGT CTCTGT CTCTGT CTCTGT CTCTGT C
410256 CCTTTTTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
3 2 0.03
4 4 0.07
5 8 0.13
6 42 0.69
8 5 0.08
ACGTcount: A:0.01, C:0.33, G:0.11, T:0.55
Consensus pattern (6 bp):
CTCTGT
Found at i:410230 original size:27 final size:21
Alignment explanation
Indices: 410176--410252 Score: 122
Period size: 21 Copynumber: 3.8 Consensus size: 21
410166 TTTTTTTCGG
*
410176 CTCTGTCTC--TCTCTTTTCT
1 CTCTGTCTCTGTCTCTTTTAT
410195 CTCTGTCTCTGTCTCTTTTAT
1 CTCTGTCTCTGTCTCTTTTAT
*
410216 CTCTGTCTCTGTCTCTTTTGT
1 CTCTGTCTCTGTCTCTTTTAT
410237 CTCTGTCTCTGTCTCT
1 CTCTGTCTCTGTCTCT
410253 GTCCCTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
19 9 0.17
21 45 0.83
ACGTcount: A:0.01, C:0.32, G:0.10, T:0.56
Consensus pattern (21 bp):
CTCTGTCTCTGTCTCTTTTAT
Found at i:410667 original size:3 final size:3
Alignment explanation
Indices: 410653--410728 Score: 77
Period size: 3 Copynumber: 25.7 Consensus size: 3
410643 TGTAATATTA
* * *
410653 AAT AAT ATAT AAT AAT AAT -AT TAT AAT TAT AAT TAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
410698 AAT TAT AAT AAT AAT AAT -AT AAAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
410729 AAAATGAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.10
3 50 0.82
4 5 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:418194 original size:19 final size:20
Alignment explanation
Indices: 418170--418207 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
418160 AAACTATTAA
*
418170 TATTATTATTTTA-AAATAT
1 TATTATAATTTTATAAATAT
418189 TATTATAATTTTATAAATA
1 TATTATAATTTTATAAATA
418208 AAAATACTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTATAATTTTATAAATAT
Found at i:418511 original size:19 final size:18
Alignment explanation
Indices: 418465--418513 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
418455 TTAATTTTAT
*
418465 TAAAA-AATACTAAATAA
1 TAAAATAATATTAAATAA
* *
418482 TATATTAATATTAAATATA
1 TAAAATAATATTAAATA-A
418501 TAAAATAATATTA
1 TAAAATAATATTA
418514 TTTCATGTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 3 0.12
18 10 0.40
19 12 0.48
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATAATATTAAATAA
Found at i:431377 original size:10 final size:10
Alignment explanation
Indices: 431375--431413 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
431365 TTTGGCTTTT
431375 TTTTTTTGCC
1 TTTTTTTGCC
431385 TTTTTTTTGCC
1 -TTTTTTTGCC
**
431396 TTTTTTTGTT
1 TTTTTTTGCC
431406 TTTTTTTG
1 TTTTTTTG
431414 AAAAAAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.79
Consensus pattern (10 bp):
TTTTTTTGCC
Found at i:431388 original size:11 final size:11
Alignment explanation
Indices: 431374--431402 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
431364 TTTTGGCTTT
431374 TTTTTTTTGCC
1 TTTTTTTTGCC
431385 TTTTTTTTGCC
1 TTTTTTTTGCC
431396 TTTTTTT
1 TTTTTTT
431403 GTTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGCC
Found at i:436076 original size:11 final size:11
Alignment explanation
Indices: 436056--436106 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
436046 TTTTTTGAAA
*
436056 TTTTGGCTTTT
1 TTTTGACTTTT
436067 TTTTGACTTTT
1 TTTTGACTTTT
*
436078 TTTTGGCTTTTT
1 TTTTGAC-TTTT
**
436090 TTTTGTTTTTT
1 TTTTGACTTTT
436101 TTTTGA
1 TTTTGA
436107 AAAAAATAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
11 25 0.74
12 9 0.26
ACGTcount: A:0.04, C:0.06, G:0.14, T:0.76
Consensus pattern (11 bp):
TTTTGACTTTT
Found at i:440274 original size:19 final size:19
Alignment explanation
Indices: 440250--440286 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
440240 ATGACCAACA
*
440250 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
440269 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
440287 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:440335 original size:20 final size:20
Alignment explanation
Indices: 440312--440446 Score: 78
Period size: 20 Copynumber: 6.6 Consensus size: 20
440302 GTTTCCAGAT
440312 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTTTGACTA
* *
440332 TCGC-ACTGCGATTTT-CCAAA
1 TCGCAAC-GCGATTTTGAC-TA
*** **
440352 TTCGCGTTGCGATTTTAGAAAA
1 -TCGCAACGCGATTTT-GACTA
* * *
440374 CCGCAATGCGATTCTGACTA
1 TCGCAACGCGATTTTGACTA
**
440394 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTTTGAC-T-A
*
440415 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTTTGACTA
440435 TCGCAACGCGAT
1 TCGCAACGCGAT
440447 AATACAAAAT
Statistics
Matches: 88, Mismatches: 18, Indels: 18
0.71 0.15 0.15
Matches are distributed among these distances:
19 5 0.06
20 41 0.47
21 38 0.43
22 4 0.05
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTTTGACTA
Found at i:440419 original size:21 final size:21
Alignment explanation
Indices: 440393--440467 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
440383 GATTCTGACT
440393 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
**
440414 ATCGCAACGCGATTCTGAC-T-
1 ATCGCAACGCGATAAT-ACATA
*
440434 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACATA
* *
440455 ATCTCAATGCGAT
1 ATCGCAACGCGAT
440468 TTTCAAAGCG
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 2 0.05
20 14 0.32
21 26 0.59
22 2 0.05
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGATAATACATA
Found at i:440467 original size:41 final size:41
Alignment explanation
Indices: 440370--440468 Score: 162
Period size: 41 Copynumber: 2.4 Consensus size: 41
440360 GCGATTTTAG
*
440370 AAAACCGCAATGCGATTCTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATTCTGACTATCGCAACGCGATAATAC
* *
440411 ATAATCGCAACGCGATTCTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATTCTGACTATCGCAACGCGATAATAC
*
440452 AAAATCTCAATGCGATT
1 AAAATCGCAATGCGATT
440469 TTCAAAGCGC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAATCGCAATGCGATTCTGACTATCGCAACGCGATAATAC
Found at i:441133 original size:20 final size:20
Alignment explanation
Indices: 441027--441135 Score: 79
Period size: 20 Copynumber: 5.8 Consensus size: 20
441017 GATAGTCAAA
* **
441027 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
*
441047 TTCGTGTTGCAATTTTCA-T
1 TTCGTGTTGCGATTTTCATT
*
441066 TTCGCGTTGCGA--TT-A-T
1 TTCGTGTTGCGATTTTCATT
* **
441082 CTC--GTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
*
441100 TTTGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
441120 TTCGTGTTGTGATTTT
1 TTCGTGTTGCGATTTT
441136 AAGTTTCAGA
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
14 7 0.10
16 5 0.07
17 3 0.04
18 2 0.03
19 11 0.16
20 41 0.59
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:441142 original size:20 final size:20
Alignment explanation
Indices: 441103--441142 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
441093 AGTCATTTTT
* *
441103 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGATTTTAAGTTTC
*
441123 GTGTTGTGATTTTAAGTTTC
1 GTGTTGCGATTTTAAGTTTC
441143 AGAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.12, C:0.10, G:0.23, T:0.55
Consensus pattern (20 bp):
GTGTTGCGATTTTAAGTTTC
Found at i:443072 original size:20 final size:20
Alignment explanation
Indices: 443047--443135 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
443037 AAACTTAAAA
443047 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
443067 ATCGCAGCGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
443087 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
**
443107 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
443127 ATTGCAACG
1 ATCGCAACG
443136 GGATAATCGC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:443177 original size:33 final size:34
Alignment explanation
Indices: 443130--443202 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 34
443120 TTTGACTATT
*
443130 GCAACGGGATAATCGCAATGCG-AAATAAAAATC
1 GCAACGGGAAAATCGCAATGCGAAAATAAAAATC
* *
443163 GCAACGTGAAAATCGCAATGCGAAAATGAAAATC
1 GCAACGGGAAAATCGCAATGCGAAAATAAAAATC
443197 GCAACG
1 GCAACG
443203 CGAATTTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 20 0.56
34 16 0.44
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (34 bp):
GCAACGGGAAAATCGCAATGCGAAAATAAAAATC
Found at i:443192 original size:20 final size:20
Alignment explanation
Indices: 443169--443206 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
443159 AATCGCAACG
*
443169 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
443189 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
443207 TTTAGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:443224 original size:19 final size:19
Alignment explanation
Indices: 443202--443292 Score: 103
Period size: 19 Copynumber: 4.7 Consensus size: 19
443192 AAATCGCAAC
* *
443202 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCATT
*
443221 GCGATTTTGGTTTCGCATT
1 GCGATTTTAGTTTCGCATT
443240 GCGATTTTTA-TTTCGCATT
1 GCGA-TTTTAGTTTCGCATT
* **
443259 GCGATTTAAGTTTCGTGTT
1 GCGATTTTAGTTTCGCATT
443278 GCGATTTTAAGTTTC
1 GCGATTTT-AGTTTC
443293 AGAAACTATT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.07
19 47 0.77
20 10 0.16
ACGTcount: A:0.15, C:0.14, G:0.23, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCATT
Found at i:443865 original size:21 final size:21
Alignment explanation
Indices: 443769--443872 Score: 79
Period size: 21 Copynumber: 5.0 Consensus size: 21
443759 GACTCACCTG
* *
443769 TCATCGTTCAAGAGGCCTCT-
1 TCATCCTTCAAGAGGCCCCTA
* *
443789 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCCTTCAAGAGGCCCCTA
* *
443811 TCATCCCTCAAGAGTCCCCT-
1 TCATCCTTCAAGAGGCCCCTA
443831 TCCA-CCGTTCAAGAGGCCCCTA
1 T-CATCC-TTCAAGAGGCCCCTA
* * *
443853 TCATCTTTGAAGAGGTCCCT
1 TCATCCTTCAAGAGGCCCCT
443873 CCCACCATTC
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
20 4 0.06
21 60 0.90
22 3 0.04
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (21 bp):
TCATCCTTCAAGAGGCCCCTA
Found at i:443866 original size:42 final size:42
Alignment explanation
Indices: 443776--443887 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
443766 CTGTCATCGT
* *
443776 TCAAGAGG-CCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGGTCC-CTCCCACCGTTCAAGAGGCCCCTATCATCCC
* **
443818 TCAAGA-GTCCCCTTCCACCGTTCAAGAGGCCCCTATCATCTT
1 TCAAGAGGT-CCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* *
443860 TGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCAAGAGGTCCCTCCCACCGTTCAAGAG
443888 CTCGATTCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.02
42 54 0.92
43 4 0.07
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
TCAAGAGGTCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:443886 original size:21 final size:21
Alignment explanation
Indices: 443796--443887 Score: 53
Period size: 21 Copynumber: 4.4 Consensus size: 21
443786 TCTCCTATCG
* *
443796 TTCAAGAGGCCCCTATCATCC-
1 TTCAAGAGGTCCCTACCA-CCA
* * *
443817 CTCAAGA-GTCCCCTTCCACCG
1 TTCAAGAGGT-CCCTACCACCA
* * * *
443838 TTCAAGAGGCCCCTATCATCT
1 TTCAAGAGGTCCCTACCACCA
* *
443859 TTGAAGAGGTCCCTCCCACCA
1 TTCAAGAGGTCCCTACCACCA
443880 TTCAAGAG
1 TTCAAGAG
443888 CTCGATTCAT
Statistics
Matches: 51, Mismatches: 17, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
20 3 0.06
21 47 0.92
22 1 0.02
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGTCCCTACCACCA
Found at i:445263 original size:72 final size:67
Alignment explanation
Indices: 445185--445408 Score: 239
Period size: 67 Copynumber: 3.3 Consensus size: 67
445175 GGGGTACACT
*
445185 TTTTTTGATTGTTTAATTGATTCT-TAAAAGTCTGATTTGTTTAATTGATGA-G-GAAAATAAGA
1 TTTTTTGCTTGTTTAATTGATT-TATAAAAGT-TGATTTGTTTAATTGATGATGTGAAAAT---A
445247 ATTATTAGCA
61 ATTATT---A
* * *
445257 TTTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTGTTTAATTAATTGATGTGTAAATAATTC
1 TTTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTGTTTAATTGA-TGATGTGAAAATAATTA
445322 TTA
65 TTA
* *
445325 -TTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATG-TGT--AAATAATTCT
1 TTTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTGTTTAATTGATGATGTGAAAATAATTAT
445386 TA
66 TA
* *
445388 -TTTGTGCTTATTTAATTGATT
1 TTTTTTGCTTGTTTAATTGATT
445409 GAAATGTAAA
Statistics
Matches: 140, Mismatches: 8, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
63 31 0.22
65 3 0.02
66 2 0.01
67 44 0.31
68 1 0.01
71 22 0.16
72 31 0.22
73 1 0.01
74 5 0.04
ACGTcount: A:0.29, C:0.04, G:0.15, T:0.52
Consensus pattern (67 bp):
TTTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTGTTTAATTGATGATGTGAAAATAATTAT
TA
Found at i:445345 original size:67 final size:63
Alignment explanation
Indices: 445258--445408 Score: 239
Period size: 63 Copynumber: 2.3 Consensus size: 63
445248 TTATTAGCAT
445258 TTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTGTTTAATTAATTGATGTGTAAATAATTCT
1 TTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTG--T--TTAATTGATGTGTAAATAATTCT
445323 TA
62 TA
*
445325 TTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA
1 TTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA
* *
445388 TTTGTGCTTATTTAATTGATT
1 TTTTTGCTTGTTTAATTGATT
445409 GAAATGTAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
63 44 0.54
65 1 0.01
67 36 0.44
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.55
Consensus pattern (63 bp):
TTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA
Found at i:445350 original size:36 final size:35
Alignment explanation
Indices: 445300--445407 Score: 106
Period size: 36 Copynumber: 3.3 Consensus size: 35
445290 ATTTGTTTAA
445300 TTAATTGATGTGTAAATAATTCTTATTTTTGCTTGT
1 TTAATTGATGTGTAAATAATTCTTA-TTTTGCTTGT
* * *
445336 TTAATTGATTTGT-AA-AAGT-TGA---T--TTGT
1 TTAATTGATGTGTAAATAATTCTTATTTTGCTTGT
*
445363 TTAATTGATGTGTAAATAATTCTTATTTGTGCTTAT
1 TTAATTGATGTGTAAATAATTCTTATTT-TGCTTGT
445399 TTAATTGAT
1 TTAATTGAT
445408 TGAAATGTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
27 16 0.29
28 2 0.04
29 4 0.07
30 2 0.04
33 2 0.04
34 4 0.07
35 2 0.04
36 24 0.43
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.54
Consensus pattern (35 bp):
TTAATTGATGTGTAAATAATTCTTATTTTGCTTGT
Found at i:445402 original size:63 final size:63
Alignment explanation
Indices: 445262--445430 Score: 239
Period size: 67 Copynumber: 2.6 Consensus size: 63
445252 TAGCATTTTT
*
445262 TGCTTGTTTAATTGATTTATAAAAGTTGATTTGTTTAATTAATTGATGTGTAAATAATTCTTATT
1 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTG--T--TTAATTGATGTGTAAATAATTCTTATT
*
445327 TT
62 TG
445329 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
1 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
*
445392 TGCTTATTTAATTGATTGAAATGTAAAAGTTGATTTGTT
1 TGCTTGTTTAATTGATT----TGTAAAAGTTGATTTGTT
445431 GATTTCAATC
Statistics
Matches: 95, Mismatches: 3, Indels: 8
0.90 0.03 0.08
Matches are distributed among these distances:
63 44 0.46
65 1 0.01
67 50 0.53
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (63 bp):
TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
Found at i:445507 original size:20 final size:20
Alignment explanation
Indices: 445482--445559 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
445472 AGGTACACTT
*
445482 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
445502 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
*
445522 TCGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
*
445542 TCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAACTCAA
445560 TTCGCGTTGC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:445526 original size:40 final size:40
Alignment explanation
Indices: 445482--445559 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
445472 AGGTACACTT
* *
445482 TCGCAACGCTAAA-CTCAAAATCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGC-CAAAATCGCAACGCGAAAGTCAAAA
*
445522 TCGCAATGCGAAAGCCAAAATCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAAGCCAAAATCGCAACGCGAAAGTCAA
445560 TTCGCGTTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.13
Consensus pattern (40 bp):
TCGCAACGCGAAAGCCAAAATCGCAACGCGAAAGTCAAAA
Found at i:445629 original size:34 final size:34
Alignment explanation
Indices: 445563--445657 Score: 102
Period size: 34 Copynumber: 2.8 Consensus size: 34
445553 AAGTCAATTC
* * * ** *
445563 GCGTTGCGATAGTCTAATACGTTTTGCGATTTTCT
1 GCGTTGCGATAATCAAATTCGCGTTGCAATTTT-T
* *
445598 -CGTTGCGGTAGTCAAATTCGCGTTGCAATTTTT
1 GCGTTGCGATAATCAAATTCGCGTTGCAATTTTT
445631 GCGTTGCGATAATCAAATTCGCGTTGC
1 GCGTTGCGATAATCAAATTCGCGTTGC
445658 GATAATCAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
33 1 0.02
34 50 0.98
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (34 bp):
GCGTTGCGATAATCAAATTCGCGTTGCAATTTTT
Found at i:445656 original size:20 final size:20
Alignment explanation
Indices: 445631--445782 Score: 190
Period size: 20 Copynumber: 7.9 Consensus size: 20
445621 TGCAATTTTT
*
445631 GCGTTGCGATAATCAAATTC
1 GCGTTGCGATAGTCAAATTC
*
445651 GCGTTGCGATAATCAAATTC
1 GCGTTGCGATAGTCAAATTC
*
445671 ACGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
*
445691 ACGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
*
445711 GCGTTGCGAT--T----TTT
1 GCGTTGCGATAGTCAAATTC
*
445725 GAGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
445745 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
* *
445765 ACGTTGCGATATTCAAAT
1 GCGTTGCGATAGTCAAAT
445783 GAATATGTAA
Statistics
Matches: 117, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
14 11 0.09
16 1 0.01
18 1 0.01
20 104 0.89
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:445715 original size:94 final size:94
Alignment explanation
Indices: 445598--445782 Score: 316
Period size: 94 Copynumber: 2.0 Consensus size: 94
445588 GCGATTTTCT
* *
445598 CGTTGCGGTAGTCAAATTCGCGTTGCAATTTTTGCGTTGCGATAATCAAATTCGCGTTGCGATAA
1 CGTTGCGATAGTCAAATTCGCGTTGCAATTTTTGAGTTGCGATAATCAAATTCGCGTTGCGATAA
445663 TCAAATTCACGTTGCGATAGTCAAATTCA
66 TCAAATTCACGTTGCGATAGTCAAATTCA
* * *
445692 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTGCGATAGTCAAATTCGCGTTGCGATAG
1 CGTTGCGATAGTCAAATTCGCGTTGCAATTTTTGAGTTGCGATAATCAAATTCGCGTTGCGATAA
*
445757 TCAAATTCACGTTGCGATATTCAAAT
66 TCAAATTCACGTTGCGATAGTCAAAT
445783 GAATATGTAA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 85 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (94 bp):
CGTTGCGATAGTCAAATTCGCGTTGCAATTTTTGAGTTGCGATAATCAAATTCGCGTTGCGATAA
TCAAATTCACGTTGCGATAGTCAAATTCA
Found at i:445755 original size:54 final size:57
Alignment explanation
Indices: 445631--445776 Score: 199
Period size: 54 Copynumber: 2.6 Consensus size: 57
445621 TGCAATTTTT
*
445631 GCGTTGCGATAATCAAATTCGCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTCGCGTTGCGAT-AT--AATTCACGTTGCGATAGTCAAATTC
* * *
445691 ACGTTGCGATAGTCAAATTCGCGTTGCGAT-T-TTTGA-GTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATATAATTCACGTTGCGATAGTCAAATTC
*
445745 GCGTTGCGATAGTCAAATTCACGTTGCGATAT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAT
445777 TCAAATGAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
54 46 0.58
55 4 0.05
58 1 0.01
60 28 0.35
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (57 bp):
GCGTTGCGATAGTCAAATTCGCGTTGCGATATAATTCACGTTGCGATAGTCAAATTC
Found at i:446008 original size:140 final size:140
Alignment explanation
Indices: 445753--446035 Score: 505
Period size: 140 Copynumber: 2.0 Consensus size: 140
445743 TCGCGTTGCG
*
445753 ATAGTCAAATTCACGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCACGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAAATCA
445818 TAGCAATGTTCAAACTCAAGTCACTAATACATGCCTAACTGAAAAAGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTCACTAATACATGCCTAACTGAAAAAGTTAAAAGTTTACACATAA
*
445883 AATACACTTA
131 AATACACATA
* *
445893 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
1 ATAGTCAAATTCACGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAAATCA
*
445958 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACT-AAAAATGTTAAAAGTTTACACATA
66 TAGCAATGTTCAAACTCAAGTCACTAATACATGCCTAACTGAAAAA-GTTAAAAGTTTACACATA
446022 AAATACACATA
130 AAATACACATA
446033 ATA
1 ATA
446036 CAACGTTTGC
Statistics
Matches: 137, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
139 5 0.04
140 132 0.96
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCACGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAAATCA
TAGCAATGTTCAAACTCAAGTCACTAATACATGCCTAACTGAAAAAGTTAAAAGTTTACACATAA
AATACACATA
Found at i:448412 original size:24 final size:24
Alignment explanation
Indices: 448378--448431 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
448368 CTGAAACATC
448378 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
448402 ATCAAAGTCCGGGTATTGACTAAG
1 ATCAAAATCCGAGTATTGACCAAG
448426 ATCAAA
1 ATCAAA
448432 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:453391 original size:20 final size:20
Alignment explanation
Indices: 453366--453404 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
453356 GGATTAGAAT
453366 CGGGTATGTATCAATGTATA
1 CGGGTATGTATCAATGTATA
453386 CGGGTATGTATCAATGTAT
1 CGGGTATGTATCAATGTAT
453405 TACTATGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (20 bp):
CGGGTATGTATCAATGTATA
Found at i:459413 original size:20 final size:21
Alignment explanation
Indices: 459388--459467 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 21
459378 CCAGAACCCC
*
459388 AGGGGGTATCGATTCCCCT-A
1 AGGGGGAATCGATTCCCCTCA
* *
459408 AGGGGGAATTGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCC-TC-A
*
459431 AGGGGGAATCGGTT-CCCTCA
1 AGGGGGAATCGATTCCCCTCA
* *
459451 TGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
459468 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 27 0.55
21 5 0.10
22 3 0.06
23 14 0.29
ACGTcount: A:0.19, C:0.24, G:0.33, T:0.25
Consensus pattern (21 bp):
AGGGGGAATCGATTCCCCTCA
Found at i:464713 original size:204 final size:206
Alignment explanation
Indices: 464354--464766 Score: 803
Period size: 204 Copynumber: 2.0 Consensus size: 206
464344 AGGGGGTGAA
464354 TTGGCAATAAAAATTTTGGTGGAAGCTTTTGCAGAAAATTGAAAGAAATTGCACATCGATTTAGA
1 TTGGCAATAAAAATTTTGGTGGAAGCTTTTGCAGAAAATTGAAAGAAATTGCACATCGATTTAGA
464419 GTAGTTCGACTTTCTCAACCAAAGTATACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCC
66 GTAGTTCGACTTTCTCAACCAAAGTATACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCC
464484 ACAAATTCACTAATTTGTCTTTCTTTTGAGGATAAAGAGTAACCTTACAAACCCTCAAGAATTAT
131 ACAAATTCACTAATTTGTCTTTCTTTTGAGGATAAAGAGTAACCTTACAAACCCTCAAGAATTAT
464549 A-CCCAAATTC
196 ACCCCAAATTC
464559 TTGGCAAT-AAAATTTTGGTGGAAGCTTTTGCAGAAAATTGAAAGAAATTGCACATCGATTTAGA
1 TTGGCAATAAAAATTTTGGTGGAAGCTTTTGCAGAAAATTGAAAGAAATTGCACATCGATTTAGA
*
464623 GTAGTTCGACTTTCTCAACCAAAGTCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCC
66 GTAGTTCGACTTTCTCAACCAAAGTATACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCC
464688 ACAAATTCACTAATTTGTCTTTCTTTTGAGGATAAAGAGTAACCTTACAAACCCTCAAGAATTAT
131 ACAAATTCACTAATTTGTCTTTCTTTTGAGGATAAAGAGTAACCTTACAAACCCTCAAGAATTAT
464753 ACCCCAAATTC
196 ACCCCAAATTC
464764 TTG
1 TTG
464767 AGAACACTCT
Statistics
Matches: 206, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
204 186 0.90
205 20 0.10
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (206 bp):
TTGGCAATAAAAATTTTGGTGGAAGCTTTTGCAGAAAATTGAAAGAAATTGCACATCGATTTAGA
GTAGTTCGACTTTCTCAACCAAAGTATACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCC
ACAAATTCACTAATTTGTCTTTCTTTTGAGGATAAAGAGTAACCTTACAAACCCTCAAGAATTAT
ACCCCAAATTC
Done.