Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015269.1 Kokia drynarioides strain JFW-HI SEQ_130314, 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: 664642
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 122 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:267687 original size:49 final size:49
Alignment explanation
Indices: 267634--267776 Score: 128
Period size: 49 Copynumber: 3.1 Consensus size: 49
267624 AGTTAAAATC
267634 TATTTATTTGTTTCAATCAAACTCTGATTAGTATAAATTATTTTATTAT
1 TATTTATTTGTTTCAATCAAACTCTGATTAGTATAAATTATTTTATTAT
* * * * *
267683 TATTTCCTTT-TGTC--T-ACA-T-T-ATT--TAT-TATTATTTAAATT-T
1 TATTT-ATTTGTTTCAATCAAACTCTGATTAGTATAAATTATTT-TATTAT
* *
267723 TATTTATTTGTTTCAATCAAACTCTGATTAGTCTAGATTATTTTATTAT
1 TATTTATTTGTTTCAATCAAACTCTGATTAGTATAAATTATTTTATTAT
267772 TATTT
1 TATTT
267777 GACTTATGAA
Statistics
Matches: 70, Mismatches: 11, Indels: 26
0.65 0.10 0.24
Matches are distributed among these distances:
39 3 0.04
40 16 0.23
41 6 0.09
42 1 0.01
43 5 0.07
44 2 0.03
45 2 0.03
46 5 0.07
47 1 0.01
48 5 0.07
49 21 0.30
50 3 0.04
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.57
Consensus pattern (49 bp):
TATTTATTTGTTTCAATCAAACTCTGATTAGTATAAATTATTTTATTAT
Found at i:270277 original size:3 final size:3
Alignment explanation
Indices: 270271--270315 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
270261 TAATTTAATA
270271 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
270316 ATTGTCTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:270352 original size:22 final size:23
Alignment explanation
Indices: 270305--270352 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
270295 TATTATTATT
*
270305 ATTATTATTATATTGTCTATTTA
1 ATTATTATTATATTGTCAATTTA
*
270328 ATTATT-TTATTTTGT-AATTTGA
1 ATTATTATTATATTGTCAATTT-A
270350 ATT
1 ATT
270353 TGATTGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 4 0.18
22 12 0.55
23 6 0.27
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (23 bp):
ATTATTATTATATTGTCAATTTA
Found at i:276104 original size:45 final size:46
Alignment explanation
Indices: 276008--276187 Score: 183
Period size: 45 Copynumber: 4.0 Consensus size: 46
275998 CAAAAATACC
* * *
276008 AATCTTTTACCCTTAAGTTAAGAGGGACAGATTGAAA---ACCAT-T
1 AATCTTTTACCCCTAAGTCAAGAGGGGCAGATT-AAAGCCACCATCT
276051 CAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTAAAGCCACCATCT
1 -AATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGCCACCATCT
* * * ** *
276097 AATCTTTTACCCTTAA-TTAAGAGGGGTAGATCGAAGCCACCATCC
1 AATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGCCACCATCT
* * * *
276142 AATCTTTTACCACAAAGTCAAGAGGGGCAGATTGAAGCTACCATCT
1 AATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGCCACCATCT
276188 TACAGAAGCG
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
42 3 0.03
43 14 0.12
44 15 0.13
45 57 0.50
46 25 0.22
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (46 bp):
AATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGCCACCATCT
Found at i:276185 original size:91 final size:89
Alignment explanation
Indices: 276008--276187 Score: 245
Period size: 91 Copynumber: 2.0 Consensus size: 89
275998 CAAAAATACC
* * * *
276008 AATCTTTTACCCTTAAGTTAAGAGGGACAGATTGAAAACCATTCAATCTTTTACCCCTAATCAAG
1 AATCTTTTACCCTTAAGTTAAGAGGGACAGATCGAAAACCATCCAATCTTTTACCACAAATCAAG
276073 AGGGGCAGATTAAAGCCACCATCT
66 AGGGGCAGATTAAAGCCACCATCT
** *
276097 AATCTTTTACCCTTAA-TTAAGAGGGGTAGATCGAAGCCACCATCCAATCTTTTACCACAAAGTC
1 AATCTTTTACCCTTAAGTTAAGAGGGACAGATCGAA--AACCATCCAATCTTTTACCACAAA-TC
* *
276161 AAGAGGGGCAGATTGAAGCTACCATCT
63 AAGAGGGGCAGATTAAAGCCACCATCT
276188 TACAGAAGCG
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
88 16 0.20
89 16 0.20
90 20 0.25
91 27 0.34
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (89 bp):
AATCTTTTACCCTTAAGTTAAGAGGGACAGATCGAAAACCATCCAATCTTTTACCACAAATCAAG
AGGGGCAGATTAAAGCCACCATCT
Found at i:277634 original size:29 final size:30
Alignment explanation
Indices: 277602--277688 Score: 74
Period size: 28 Copynumber: 3.0 Consensus size: 30
277592 TTTTTTACTT
*
277602 AAAACTATTT-TTTGTTTT-AATTTAACCCC
1 AAAA-TATTTATTTCTTTTAAATTTAACCCC
* *
277631 AAAATTTTTATTTCTTTTAAATTTGACCCC
1 AAAATATTTATTTCTTTTAAATTTAACCCC
** * *
277661 --TTTATTTATTTATTTTAAATTAAACCCC
1 AAAATATTTATTTCTTTTAAATTTAACCCC
277689 TTTTATTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 26 0.55
29 11 0.23
30 10 0.21
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (30 bp):
AAAATATTTATTTCTTTTAAATTTAACCCC
Found at i:277676 original size:28 final size:29
Alignment explanation
Indices: 277637--277714 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
277627 CCCCAAAATT
* **
277637 TTTATTTCTTTTAAATTTGACCCC-TTTA
1 TTTATTTATTTTAAATTAAACCCCTTTTA
277665 TTTATTTATTTTAAATTAAACCCCTTTTA
1 TTTATTTATTTTAAATTAAACCCCTTTTA
*
277694 TTT-TTCATTTTTCAAATTAAA
1 TTTATTTA-TTTT-AAATTAAA
277715 TCTTTTATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 24 0.56
29 11 0.26
30 8 0.19
ACGTcount: A:0.28, C:0.14, G:0.01, T:0.56
Consensus pattern (29 bp):
TTTATTTATTTTAAATTAAACCCCTTTTA
Found at i:277705 original size:29 final size:28
Alignment explanation
Indices: 277641--277726 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
277631 AAAATTTTTA
**
277641 TTTC-TTTTAAATTTGACCCC-TTTATT
1 TTTCATTTTAAATTAAACCCCTTTTATT
*
277667 TATTTATTTTAAATTAAACCCCTTTTATT
1 T-TTCATTTTAAATTAAACCCCTTTTATT
*
277696 TTTCATTTTTCAAATTAAA--TCTTTTATT
1 TTTCA-TTTT-AAATTAAACCCCTTTTATT
277724 TTT
1 TTT
277727 ATTCTTTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 1 0.02
27 2 0.04
28 28 0.56
29 11 0.22
30 8 0.16
ACGTcount: A:0.26, C:0.14, G:0.01, T:0.59
Consensus pattern (28 bp):
TTTCATTTTAAATTAAACCCCTTTTATT
Found at i:277776 original size:8 final size:8
Alignment explanation
Indices: 277765--277809 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
277755 TGTTTTTTTA
*
277765 ATTTTAAT
1 ATTTTATT
277773 ATTTTATTT
1 ATTTTA-TT
277782 ACTTTTATT
1 A-TTTTATT
277791 ATTTTATT
1 ATTTTATT
277799 ATTTTA-T
1 ATTTTATT
277806 ATTT
1 ATTT
277810 ATACTTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
7 5 0.15
8 19 0.56
9 5 0.15
10 5 0.15
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (8 bp):
ATTTTATT
Found at i:277787 original size:18 final size:17
Alignment explanation
Indices: 277765--277809 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
277755 TGTTTTTTTA
277765 ATTTTAATATTTTATTT
1 ATTTTAATATTTTATTT
*
277782 ACTTTTATTATTTTA-TT
1 A-TTTTAATATTTTATTT
277799 ATTTT-ATATTT
1 ATTTTAATATTT
277810 ATACTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.20
16 4 0.16
17 4 0.16
18 12 0.48
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTAATATTTTATTT
Found at i:281726 original size:18 final size:18
Alignment explanation
Indices: 281703--281737 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
281693 AGTAATTATG
* *
281703 AAATATTGAATAAAATAA
1 AAATATTAAAAAAAATAA
281721 AAATATTAAAAAAAATA
1 AAATATTAAAAAAAATA
281738 CACAACTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAATATTAAAAAAAATAA
Found at i:281871 original size:12 final size:12
Alignment explanation
Indices: 281854--281894 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
281844 TTTAAAATCC
281854 ATTTTTAAACTG
1 ATTTTTAAACTG
281866 ATTTTTTAATA-T-
1 A-TTTTTAA-ACTG
281878 ATTTTTAAACTG
1 ATTTTTAAACTG
281890 ATTTT
1 ATTTT
281895 ATTGTCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 1 0.04
11 8 0.32
12 7 0.28
13 8 0.32
14 1 0.04
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (12 bp):
ATTTTTAAACTG
Found at i:292963 original size:205 final size:205
Alignment explanation
Indices: 292609--293018 Score: 766
Period size: 205 Copynumber: 2.0 Consensus size: 205
292599 TAGTAAATTT
292609 CTTTTAATAAACTTATAGATTCTTGAAGCCAAGTTCAATAAATGGCAATACTTAATAATGAATAA
1 CTTTTAATAAACTTATAGATTCTTGAAGCCAAGTTCAATAAATGGCAATACTTAATAATGAATAA
*
292674 AGTGGCAATGCTTAAGAAGAAAAAACCAAAGAAATGTCATAAAACACTCCAATGCTTAGAACTGC
66 AGTGGCAAGGCTTAAGAAGAAAAAACCAAAGAAATGTCATAAAACACTCCAATGCTTAGAACTGC
** *
292739 TGAATAGGTCATTAACATTTTGTTTGCTTCATTGTGTTATTGATTAGAAAAGTAAGCTCAAGTAA
131 TGAATAGGTCAGCAACATTTTGTTTGCTTCATTGTGTTATTGATTAGAAAAATAAGCTCAAGTAA
292804 GAGTGTGTAA
196 GAGTGTGTAA
*
292814 CTTTTAATAAACTTATAGATTCTTGAATCCAAGTTCAATAAATGGCAATACTTAATAATGAATAA
1 CTTTTAATAAACTTATAGATTCTTGAAGCCAAGTTCAATAAATGGCAATACTTAATAATGAATAA
292879 AGTGGCAAGGCTTAAGAAGAAAAAACCAAAGAAATGTCATAAAACACTCCAATGCTTAGAACTGC
66 AGTGGCAAGGCTTAAGAAGAAAAAACCAAAGAAATGTCATAAAACACTCCAATGCTTAGAACTGC
*
292944 TGAATAGGTCAGCAACATTTTGTTTGCTTCATTGTTTTATTGATTAGAAAAATAAGCTCAAGTAA
131 TGAATAGGTCAGCAACATTTTGTTTGCTTCATTGTGTTATTGATTAGAAAAATAAGCTCAAGTAA
293009 GAGTGTGTAA
196 GAGTGTGTAA
293019 AAAGTAGTTT
Statistics
Matches: 199, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
205 199 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (205 bp):
CTTTTAATAAACTTATAGATTCTTGAAGCCAAGTTCAATAAATGGCAATACTTAATAATGAATAA
AGTGGCAAGGCTTAAGAAGAAAAAACCAAAGAAATGTCATAAAACACTCCAATGCTTAGAACTGC
TGAATAGGTCAGCAACATTTTGTTTGCTTCATTGTGTTATTGATTAGAAAAATAAGCTCAAGTAA
GAGTGTGTAA
Found at i:306573 original size:22 final size:22
Alignment explanation
Indices: 306548--306591 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
306538 ATTTTAAATA
306548 TAAT-TTATTTATTATTATTTTT
1 TAATATTATTTATT-TTATTTTT
*
306570 TAATATTTTTTATTTTATTTTT
1 TAATATTATTTATTTTATTTTT
306592 ACTCACGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (22 bp):
TAATATTATTTATTTTATTTTT
Found at i:310377 original size:22 final size:22
Alignment explanation
Indices: 310346--310395 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
310336 ACATTTTATC
* *
310346 TTTTTCTTCTTCTTTCTTCCAT
1 TTTTTTTTCTTCTTTCTTCAAT
*
310368 TTTTTTTTCTTCTTTTTTCAAT
1 TTTTTTTTCTTCTTTCTTCAAT
310390 TTTTTT
1 TTTTTT
310396 CAACTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTTTTCTTCTTTCTTCAAT
Found at i:311357 original size:6 final size:6
Alignment explanation
Indices: 311346--311383 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
311336 TTGCATAATT
* *
311346 AAAATA AAAATA AAAATA AAAATA AATATG AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
311384 TATACTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:311384 original size:12 final size:12
Alignment explanation
Indices: 311345--311387 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
311335 ATTGCATAAT
311345 TAAA-ATAAAAA
1 TAAATATAAAAA
*
311356 TAAAAATAAAAA
1 TAAATATAAAAA
*
311368 TAAATATGAAAA
1 TAAATATAAAAA
311380 TAAATATA
1 TAAATATA
311388 CTAATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 4 0.14
12 24 0.86
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (12 bp):
TAAATATAAAAA
Found at i:312037 original size:43 final size:43
Alignment explanation
Indices: 311974--312114 Score: 185
Period size: 43 Copynumber: 3.3 Consensus size: 43
311964 TTATGAGGAA
*
311974 AAACGCCGCTATAGAACATGGTCTTTAGCGGCACTTTTTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTTTTCCAC
* * * * * *
312017 AAACGTCGGTAAAGACCATGGTCTTTAGCGGCGCTTTTCCCGC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTTTTCCAC
*
312060 AAACGCCGCTAAAGAACATGGTCTTTAGCGGGA-TTTTTCCTAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTTTTCC-AC
*
312103 AAACGCCACTAA
1 AAACGCCGCTAA
312115 TATTAACAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 6 0.07
43 76 0.93
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTTTTCCAC
Found at i:315006 original size:13 final size:14
Alignment explanation
Indices: 314983--315011 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
314973 TCAATAGTAC
314983 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
314997 AAAAAG-AAAAGAA
1 AAAAAGAAAAAGAA
315010 AA
1 AA
315012 TGATTACAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:315391 original size:41 final size:41
Alignment explanation
Indices: 315346--315443 Score: 135
Period size: 41 Copynumber: 2.4 Consensus size: 41
315336 GCGCTTAGGG
* *** *
315346 GCTCTGACCTTTAGCGGCGCTTTTCCA-TAAGCGTTGTTAAT
1 GCTCTGACCTTTAGCGGCGC-TTTCCAGTAAACACCGCTAAT
315387 GCTCTGACCTTTAGCGGCGCTTTCCAGTAAACACCGCTAAT
1 GCTCTGACCTTTAGCGGCGCTTTCCAGTAAACACCGCTAAT
315428 GCTCTGACCTTTAGCG
1 GCTCTGACCTTTAGCG
315444 ACCCTTAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 6 0.12
41 45 0.88
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.32
Consensus pattern (41 bp):
GCTCTGACCTTTAGCGGCGCTTTCCAGTAAACACCGCTAAT
Found at i:315460 original size:25 final size:27
Alignment explanation
Indices: 315424--315502 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 27
315414 TAAACACCGC
*
315424 TAATGCTCTGACCTTTAGCGAC-C-CT
1 TAATGCTTTGACCTTTAGCGACGCTCT
*
315449 TAATGCTTTGACCTTTAGCGGCGCTTTCT
1 TAATGCTTTGACCTTTAGCGACGC--TCT
* *
315478 CAATGCTTTGACCTTTAGCGGCGCT
1 TAATGCTTTGACCTTTAGCGACGCT
315503 TTCCCCTAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 20 0.43
26 1 0.02
27 1 0.02
29 25 0.53
ACGTcount: A:0.16, C:0.28, G:0.20, T:0.35
Consensus pattern (27 bp):
TAATGCTTTGACCTTTAGCGACGCTCT
Found at i:315492 original size:29 final size:29
Alignment explanation
Indices: 315450--315505 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
315440 AGCGACCCTT
315450 AATGCTTTGACCTTTAGCGGCGCTTTCTC
1 AATGCTTTGACCTTTAGCGGCGCTTTCTC
315479 AATGCTTTGACCTTTAGCGGCGCTTTC
1 AATGCTTTGACCTTTAGCGGCGCTTTC
315506 CCCTAAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.27, G:0.21, T:0.38
Consensus pattern (29 bp):
AATGCTTTGACCTTTAGCGGCGCTTTCTC
Found at i:315536 original size:41 final size:41
Alignment explanation
Indices: 315479--315675 Score: 259
Period size: 41 Copynumber: 4.8 Consensus size: 41
315469 GCGCTTTCTC
* * ****
315479 AATGCTTTGACCTTTAGCGGCGCTTTCCCCTAAGTGTTGCT
1 AATGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCACCGCT
* * * *
315520 AATGCTCTGAACTTTAGCAGCGTTTTCCCATAAGCGCCGCT
1 AATGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCACCGCT
* *
315561 AATGCTCTGACCTTTAGCGACGCTTTTCCATAAGCACCGCT
1 AATGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCACCGCT
* *
315602 AATGCTTTGACCTTTAGCGGCACTTTCCCATAAGCACCGCT
1 AATGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCACCGCT
*
315643 AATGCTCTGACCTTTAGCGGCGCTTTCTCATAA
1 AATGCTCTGACCTTTAGCGGCGCTTTCCCATAA
315676 ACTTCACTAT
Statistics
Matches: 135, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 135 1.00
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.31
Consensus pattern (41 bp):
AATGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCACCGCT
Found at i:315560 original size:136 final size:133
Alignment explanation
Indices: 315315--315581 Score: 367
Period size: 136 Copynumber: 2.0 Consensus size: 133
315305 ATAAGCACCG
* *
315315 TTAATGCTTTGACCTTTAGCGGCGCTTAGGGGCTCTGACCTTTAGCGGCGCTTTTCCATAAGCGT
1 TTAATGCTTTGACCTTTAGCGGCGCTTAGAGGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGT
* * *
315380 TGTTAATGCTCTGACCTTTAGCGGCGCTTTCCAGTAAACACCGCTAATGCTCTGACCTTTAGCGA
66 TGCTAATGCTCTGAACTTTAGCAGCGCTTTCCAGTAAACACCGCTAATGCTCTGACCTTTAGCGA
315445 CCC
131 CCC
* * *
315448 TTAATGCTTTGACCTTTAGCGGCGCTTTCTCA-ATGCTTTGACCTTTAGCGGCGCTTTCCCCTAA
1 TTAATGCTTTGACCTTTAGCGGCGC--T-T-AGAGGCTCTGACCTTTAGCGGCGCTTTCCCATAA
* * * *
315512 GTGTTGCTAATGCTCTGAACTTTAGCAGCGTTTTCCCA-TAAGCGCCGCTAATGCTCTGACCTTT
62 GCGTTGCTAATGCTCTGAACTTTAGCAGCGCTTT-CCAGTAAACACCGCTAATGCTCTGACCTTT
315576 AGCGAC
126 AGCGAC
315582 GCTTTTCCAT
Statistics
Matches: 117, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
133 25 0.21
135 1 0.01
136 87 0.74
137 4 0.03
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (133 bp):
TTAATGCTTTGACCTTTAGCGGCGCTTAGAGGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGT
TGCTAATGCTCTGAACTTTAGCAGCGCTTTCCAGTAAACACCGCTAATGCTCTGACCTTTAGCGA
CCC
Found at i:315690 original size:82 final size:82
Alignment explanation
Indices: 315479--315697 Score: 246
Period size: 82 Copynumber: 2.7 Consensus size: 82
315469 GCGCTTTCTC
* * * * * * * **
315479 AATGCTTTGACCTTTAGCGGCGCTTTCCCCT-AAGTGTTGCTAATGCTCTGAACTTTAGCAGCGT
1 AATGCTCTGACCTTTAGCGGCGCTTTCTCATAAACT-TCGCTAATGCTTTGACCTTTAGCAGCAC
*
315543 TTTCCCATAAGCGCCGCT
65 TTTCCCATAAGCACCGCT
* * ** *
315561 AATGCTCTGACCTTTAGCGACGCTTT-TCCATAAGCACCGCTAATGCTTTGACCTTTAGCGGCAC
1 AATGCTCTGACCTTTAGCGGCGCTTTCT-CATAAACTTCGCTAATGCTTTGACCTTTAGCAGCAC
315625 TTTCCCATAAGCACCGCT
65 TTTCCCATAAGCACCGCT
* *
315643 AATGCTCTGACCTTTAGCGGCGCTTTCTCATAAACTTCACTATTGCTTT-ACCTTT
1 AATGCTCTGACCTTTAGCGGCGCTTTCTCATAAACTTCGCTAATGCTTTGACCTTT
315698 TGCGACGTTT
Statistics
Matches: 113, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
81 6 0.05
82 105 0.93
83 2 0.02
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.33
Consensus pattern (82 bp):
AATGCTCTGACCTTTAGCGGCGCTTTCTCATAAACTTCGCTAATGCTTTGACCTTTAGCAGCACT
TTCCCATAAGCACCGCT
Found at i:315726 original size:123 final size:123
Alignment explanation
Indices: 315479--315709 Score: 293
Period size: 123 Copynumber: 1.9 Consensus size: 123
315469 GCGCTTTCTC
* * **** *
315479 AATGCTTTGACCTTTAGCGGCGCTTTCCCCTAAGTGTTGCTAATGCTCTGAACTTTAGCAGCGTT
1 AATGCTTTGACCTTTAGCGGCACTTTCCCATAAGCACCGCTAATGCTCTGAACTTTAGCAGCGCT
* *
315544 TTCCCATAAGCGCCGCTAATGCTCTGACCTTTAGCGACGCTTTTCCATAAGCACCGCT
66 TTCCCATAAACGCCACTAATGCTCTGACCTTTAGCGACGCTTTTCCATAAGCACCGCT
* *
315602 AATGCTTTGACCTTTAGCGGCACTTTCCCATAAGCACCGCTAATGCTCTGACCTTTAGCGGCGCT
1 AATGCTTTGACCTTTAGCGGCACTTTCCCATAAGCACCGCTAATGCTCTGAACTTTAGCAGCGCT
* ** * * * *
315667 TTCTCATAAACTTCACTATTGCT-TTACCTTTTGCGACGTTTTT
66 TTCCCATAAACGCCACTAATGCTCTGACCTTTAGCGACGCTTTT
315710 TGTCCAAACC
Statistics
Matches: 90, Mismatches: 18, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
122 17 0.19
123 73 0.81
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (123 bp):
AATGCTTTGACCTTTAGCGGCACTTTCCCATAAGCACCGCTAATGCTCTGAACTTTAGCAGCGCT
TTCCCATAAACGCCACTAATGCTCTGACCTTTAGCGACGCTTTTCCATAAGCACCGCT
Found at i:317296 original size:22 final size:22
Alignment explanation
Indices: 317271--317314 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
317261 AAATCCCTAC
317271 TGCCTTCAAAGGTTTTACTCTT
1 TGCCTTCAAAGGTTTTACTCTT
*
317293 TGCCTTCACAGGTTTTACTCTT
1 TGCCTTCAAAGGTTTTACTCTT
317315 GTAACTTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.25, G:0.14, T:0.45
Consensus pattern (22 bp):
TGCCTTCAAAGGTTTTACTCTT
Found at i:320691 original size:6 final size:6
Alignment explanation
Indices: 320658--320690 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
320648 CTTTACATTA
*
320658 TATATT TATATT TATATT TATATT TATGTT TAT
1 TATATT TATATT TATATT TATATT TATATT TAT
320691 GAATGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:321404 original size:25 final size:23
Alignment explanation
Indices: 321376--321422 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
321366 GTTGAATCCA
*
321376 AATTGAATTCTAAAAAGATAATTAT
1 AATTAAATT-TAAAAA-ATAATTAT
*
321401 AATTAAATTTAAACAATAATTA
1 AATTAAATTTAAAAAATAATTA
321423 CCCCATTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 5 0.25
25 8 0.40
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (23 bp):
AATTAAATTTAAAAAATAATTAT
Found at i:321545 original size:16 final size:17
Alignment explanation
Indices: 321526--321565 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
321516 TAATTCTAAG
*
321526 AAATAGAGTTTAATTT-
1 AAATAAAGTTTAATTTC
*
321542 AAATAAAGTTTTATTTC
1 AAATAAAGTTTAATTTC
321559 AAATAAA
1 AAATAAA
321566 TCTTTTCCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (17 bp):
AAATAAAGTTTAATTTC
Found at i:332612 original size:22 final size:22
Alignment explanation
Indices: 332585--332646 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
332575 CTTTGTTTAT
332585 TAGCACATTAGTGCTCTCCGT-
1 TAGCACATTAGTGCTCTCCGTA
*
332606 TCAGCACATTCA-TGCTCTTCGTA
1 T-AGCACATT-AGTGCTCTCCGTA
* *
332629 TAGCACCTTAGTGTTCTC
1 TAGCACATTAGTGCTCTC
332647 TGTCCATTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.35
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCCGTA
Found at i:333502 original size:104 final size:104
Alignment explanation
Indices: 333356--333564 Score: 409
Period size: 104 Copynumber: 2.0 Consensus size: 104
333346 TTGGATAAGT
*
333356 AATTCCAGATTGCATCCAGGATTGTCATCGCATCTGACAGTTATCCAGATAAGAACATAAATGTG
1 AATTCCAGATTGCATCCAGGATTGTCATCGCATCTGACAGTTATCCAGATAAGAACAGAAATGTG
333421 TAAGCTGTCCAGTCTGGTATAACCAACTAGTACGACCAA
66 TAAGCTGTCCAGTCTGGTATAACCAACTAGTACGACCAA
333460 AATTCCAGATTGCATCCAGGATTGTCATCGCATCTGACAGTTATCCAGATAAGAACAGAAATGTG
1 AATTCCAGATTGCATCCAGGATTGTCATCGCATCTGACAGTTATCCAGATAAGAACAGAAATGTG
333525 TAAGCTGTCCAGTCTGGTATAACCAACTAGTACGACCAA
66 TAAGCTGTCCAGTCTGGTATAACCAACTAGTACGACCAA
333564 A
1 A
333565 GACAGCTTGA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (104 bp):
AATTCCAGATTGCATCCAGGATTGTCATCGCATCTGACAGTTATCCAGATAAGAACAGAAATGTG
TAAGCTGTCCAGTCTGGTATAACCAACTAGTACGACCAA
Found at i:337437 original size:26 final size:26
Alignment explanation
Indices: 337408--337458 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
337398 AATTTTTACG
337408 AATCGAGTCGAGTGAGATAGAATTCA
1 AATCGAGTCGAGTGAGATAGAATTCA
**
337434 AATCGAGTTTAGTGAGATAGAATTC
1 AATCGAGTCGAGTGAGATAGAATTC
337459 GAATATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.27
Consensus pattern (26 bp):
AATCGAGTCGAGTGAGATAGAATTCA
Found at i:337649 original size:34 final size:34
Alignment explanation
Indices: 337611--337682 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
337601 AGTAAACAAC
* *
337611 ATTTGGGTAAGGTAAAAGATAAAATATTAAAAAT
1 ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
*
337645 ATTTGGGTAAGATAAAAGGTAAAAAATTAAAAAT
1 ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
337679 ATTT
1 ATTT
337683 TGGTTTAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (34 bp):
ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
Found at i:337845 original size:18 final size:18
Alignment explanation
Indices: 337822--337860 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
337812 TAACATAGTT
337822 TTATTCG-GTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
337840 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
337858 TTA
1 TTA
337861 AAAAATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:337925 original size:31 final size:31
Alignment explanation
Indices: 337842--337926 Score: 80
Period size: 35 Copynumber: 2.5 Consensus size: 31
337832 TATTCGAATT
* *
337842 ATTCGAGTTATTCGAATTAAAAAATTCAACTCA
1 ATTCGAATAATTCGAA--AAAAAATTCAACTCA
* *
337875 ATTCAAACTTGAAATTCGAAAAAAAATTCAACTCG
1 ATTCGAA--T--AATTCGAAAAAAAATTCAACTCA
337910 ATTCGAATAATTCGAAA
1 ATTCGAATAATTCGAAA
337927 TTCATTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.21
33 6 0.14
35 21 0.49
37 7 0.16
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.29
Consensus pattern (31 bp):
ATTCGAATAATTCGAAAAAAAATTCAACTCA
Found at i:340256 original size:29 final size:29
Alignment explanation
Indices: 340224--340375 Score: 163
Period size: 29 Copynumber: 5.4 Consensus size: 29
340214 TAGCCTTGTT
* * *
340224 GAACTTTCTACATATTAGATAGTCCTAAC
1 GAACTTTCCACATATCAGATAGTCCTCAC
*
340253 GAAC-TTCTCACATATCAGATTGTCCTCAC
1 GAACTTTC-CACATATCAGATAGTCCTCAC
340282 GAAC-TTCCACATA--AGATAGTCCT-ATC
1 GAACTTTCCACATATCAGATAGTCCTCA-C
* *
340308 GAAATTTCCACATATCAGATAGTCCTCAT
1 GAACTTTCCACATATCAGATAGTCCTCAC
* *
340337 GGACTTCCCACATATCAGATAGTCCTCAC
1 GAACTTTCCACATATCAGATAGTCCTCAC
*
340366 AAAC-TTCCAC
1 GAACTTTCCAC
340376 GTATTCGGTA
Statistics
Matches: 103, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
25 1 0.01
26 13 0.13
27 9 0.09
28 14 0.14
29 65 0.63
30 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.11, T:0.29
Consensus pattern (29 bp):
GAACTTTCCACATATCAGATAGTCCTCAC
Found at i:340281 original size:84 final size:84
Alignment explanation
Indices: 340176--340375 Score: 258
Period size: 84 Copynumber: 2.4 Consensus size: 84
340166 GGCGGTCTTT
* * * * * * *
340176 CCACATATCAGATAATACTCACAAACTTCCACATAACATAG-CCTTGTTGAACTTTCTACATATT
1 CCACATATCAGATAGTCCTCACAAACTTCCACATAACATAGTCC-TATCGAAATTTCCACATATC
340240 AGATAGTCCTAACGAACTTC
65 AGATAGTCCTAACGAACTTC
* * * *
340260 TCACATATCAGATTGTCCTCACGAACTTCCACATAAGATAGTCCTATCGAAATTTCCACATATCA
1 CCACATATCAGATAGTCCTCACAAACTTCCACATAACATAGTCCTATCGAAATTTCCACATATCA
* * *
340325 GATAGTCCTCATGGACTTC
66 GATAGTCCTAACGAACTTC
340344 CCACATATCAGATAGTCCTCACAAACTTCCAC
1 CCACATATCAGATAGTCCTCACAAACTTCCAC
340376 GTATTCGGTA
Statistics
Matches: 98, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
84 96 0.98
85 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (84 bp):
CCACATATCAGATAGTCCTCACAAACTTCCACATAACATAGTCCTATCGAAATTTCCACATATCA
GATAGTCCTAACGAACTTC
Found at i:340299 original size:55 final size:58
Alignment explanation
Indices: 340240--340372 Score: 166
Period size: 55 Copynumber: 2.3 Consensus size: 58
340230 TCTACATATT
*
340240 AGATAGTCCTAACGAACTTCT-CACATATCAGATTGTCCTCACGAACTT-CCACATA-
1 AGATAGTCCTAACGAACTTCTCCACATATCAGATAGTCCTCACGAACTTCCCACATAC
* * * *
340295 AGATAGTCCTATCGAAATT-TCCACATATCAGATAGTCCTCATGGACTTCCCACATATC
1 AGATAGTCCTAACGAACTTCTCCACATATCAGATAGTCCTCACGAACTTCCCACATA-C
* *
340353 AGATAGTCCTCACAAACTTC
1 AGATAGTCCTAACGAACTTC
340373 CACGTATTCG
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 41 0.64
56 7 0.11
58 15 0.23
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.28
Consensus pattern (58 bp):
AGATAGTCCTAACGAACTTCTCCACATATCAGATAGTCCTCACGAACTTCCCACATAC
Found at i:340436 original size:22 final size:22
Alignment explanation
Indices: 340406--340467 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
340396 CATGATTTTC
340406 CATAAATCCCATAAAGGGCTCT
1 CATAAATCCCATAAAGGGCTCT
* * * *
340428 CATACATCCTATGAGGGGCTCT
1 CATAAATCCCATAAAGGGCTCT
*
340450 CA-AATGTCCCATAAAGGG
1 CATAA-ATCCCATAAAGGG
340468 GCCAGATCTC
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (22 bp):
CATAAATCCCATAAAGGGCTCT
Found at i:351106 original size:15 final size:16
Alignment explanation
Indices: 351088--351124 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
351078 ACATTTTTGA
*
351088 TATATTTAT-TTAAAG
1 TATATTTATATTAAAC
351103 TATATTTATATTAAAC
1 TATATTTATATTAAAC
351119 TATATT
1 TATATT
351125 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (16 bp):
TATATTTATATTAAAC
Found at i:351126 original size:26 final size:28
Alignment explanation
Indices: 351097--351166 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 28
351087 ATATATTTAT
* *
351097 TTAAAGTATATTTATATTAAACT-AT-A
1 TTAAAATATATTTATATTAAAATAATAA
* *
351123 TTAAAATAAAATTATATTAAAATAATAA
1 TTAAAATATATTTATATTAAAATAATAA
351151 TTAAAAATATATTTAT
1 TT-AAAATATATTTAT
351167 GATAATTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
26 19 0.54
27 2 0.06
28 3 0.09
29 11 0.31
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (28 bp):
TTAAAATATATTTATATTAAAATAATAA
Found at i:351138 original size:16 final size:17
Alignment explanation
Indices: 351119--351153 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
351109 TATATTAAAC
351119 TATATTAAAATAA-AAT
1 TATATTAAAATAATAAT
351135 TATATTAAAATAATAAT
1 TATATTAAAATAATAAT
351152 TA
1 TA
351154 AAAATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATATTAAAATAATAAT
Found at i:362855 original size:18 final size:16
Alignment explanation
Indices: 362823--362866 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
362813 ATAGGATGAG
362823 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
362839 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
362853 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
362867 ACCTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:363151 original size:12 final size:12
Alignment explanation
Indices: 363132--363162 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
363122 ATCAAAAGGA
363132 AAGAAGATGAAG
1 AAGAAGATGAAG
*
363144 ATGAAGATGAAG
1 AAGAAGATGAAG
363156 AAGAAGA
1 AAGAAGA
363163 AGAGAGGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.32, T:0.10
Consensus pattern (12 bp):
AAGAAGATGAAG
Found at i:363866 original size:31 final size:31
Alignment explanation
Indices: 363831--363929 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
363821 TAACAACCTG
363831 ATGACTTAAATAAAAACTTTCGAATAATTCA
1 ATGACTTAAATAAAAACTTTCGAATAATTCA
* * * *
363862 ATGACTTCAATAAAAACTTTTGATTAGTTCA
1 ATGACTTAAATAAAAACTTTCGAATAATTCA
* * * *
363893 ATGCCTTAAATGAAAACTTTCAAATTATTCA
1 ATGACTTAAATAAAAACTTTCGAATAATTCA
363924 ATGACT
1 ATGACT
363930 ATTTTGTAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.35
Consensus pattern (31 bp):
ATGACTTAAATAAAAACTTTCGAATAATTCA
Found at i:364166 original size:7 final size:6
Alignment explanation
Indices: 364146--364178 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
364136 CTTCAATAGC
*
364146 TTTTCT TTTTCT TTTTC- CTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
364179 TCATTTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:364178 original size:24 final size:23
Alignment explanation
Indices: 364146--364191 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
364136 CTTCAATAGC
* *
364146 TTTTCTTTTTCTTTTTCCTTTCT
1 TTTTCTTTTTCATTTTCATTTCT
364169 TTTTCTTTTTTCATTTTCATTTC
1 TTTTC-TTTTTCATTTTCATTTC
364192 AATAGCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTCTTTTTCATTTTCATTTCT
Found at i:364646 original size:29 final size:30
Alignment explanation
Indices: 364613--364707 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 30
364603 GTTTCATGTA
364613 CAATTGTATACAT-AAACTTTAATTTGGTGT
1 CAATTGTATACATGAAACTTTAATTTGGT-T
* *
364643 -AATTATATACATGAAACTTTCATTATGGTT
1 CAATTGTATACATGAAACTTTAATT-TGGTT
* * *
364673 CAAATGTATGCATGAAACTTTAATTTTGATT
1 CAATTGTATACATGAAACTTTAA-TTTGGTT
364704 CAAT
1 CAAT
364708 CATACATATT
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
29 11 0.21
30 11 0.21
31 29 0.55
32 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.42
Consensus pattern (30 bp):
CAATTGTATACATGAAACTTTAATTTGGTT
Found at i:373918 original size:2 final size:2
Alignment explanation
Indices: 373911--373942 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
373901 CTTCCCCAGG
373911 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
373943 AGCTCTATTT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:381484 original size:7 final size:7
Alignment explanation
Indices: 381472--381504 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
381462 TTATTGGTAA
381472 TGGTGAG
1 TGGTGAG
381479 TGGTGAG
1 TGGTGAG
381486 TGGTGAG
1 TGGTGAG
381493 TGGTGAG
1 TGGTGAG
381500 TGGTG
1 TGGTG
381505 TTGGTTGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.58, T:0.30
Consensus pattern (7 bp):
TGGTGAG
Found at i:387388 original size:95 final size:95
Alignment explanation
Indices: 387220--387395 Score: 291
Period size: 95 Copynumber: 1.9 Consensus size: 95
387210 AATGAGGCAC
* * *
387220 TGGGTGCCAAATTACTTCGGTTTAATCGATGAGACACTGGGTGTCAACCTTATTATAGCGTTGGG
1 TGGGTGCCAAATTACTTCAGTTTAATCGATGAGACACTGGGTGTCAACATTATTATAGCGTTGGA
*
387285 CGCGTTTTATTACTTCAGACGATAAATCAT
66 CGCATTTTATTACTTCAGACGATAAATCAT
*
387315 TGGGTGCCAAATTACTTCAGTTTAA-CTGATGAGACACTGGGTGTTAACATTATTATAGCGTTGG
1 TGGGTGCCAAATTACTTCAGTTTAATC-GATGAGACACTGGGTGTCAACATTATTATAGCGTTGG
387379 ACGCATTTTATTACTTC
65 ACGCATTTTATTACTTC
387396 GGATGTATCC
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
94 1 0.01
95 74 0.99
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (95 bp):
TGGGTGCCAAATTACTTCAGTTTAATCGATGAGACACTGGGTGTCAACATTATTATAGCGTTGGA
CGCATTTTATTACTTCAGACGATAAATCAT
Found at i:397601 original size:51 final size:52
Alignment explanation
Indices: 397490--397726 Score: 352
Period size: 52 Copynumber: 4.6 Consensus size: 52
397480 TAAATCAAAA
* * * *
397490 AGGTCCGATGATTATGTGTCATCATAAGTATACGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGATTCCTTTACGGATTATG
* *
397542 AGGTCCGATGACTATGTGTCATTATGAGTATATGA-TCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGATTCCTTTACGGATTATG
*
397593 AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGATTCCTTTACGGATTATG
* * * *
397645 AAGTTCGATGACTATGTGTCATCATGAGTATATGATTCCTTTACGAATTAAG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGATTCCTTTACGGATTATG
*
397697 AGGTCCGATGACTA-GTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCATGAGTAT
397727 TAAATGAAAT
Statistics
Matches: 168, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
51 63 0.38
52 105 0.62
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCATGAGTATATGATTCCTTTACGGATTATG
Found at i:397672 original size:103 final size:104
Alignment explanation
Indices: 397490--397726 Score: 361
Period size: 103 Copynumber: 2.3 Consensus size: 104
397480 TAAATCAAAA
* * * *
397490 AGGTCCGATGATTATGTGTCATCATAAGTATACGAATCCTTTACGGATTATGAGGTCCGATGACT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTATGAAGTCCGATGACT
* * * *
397555 ATGTGTCATTATGAGTATATGA-TCCTTTATGGATTATG
66 ATGTGTCATCATGAGTATATGATTCCTTTACGAATTAAG
* * *
397593 AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTATGAAGTTCGATGACT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTATGAAGTCCGATGACT
397658 ATGTGTCATCATGAGTATATGATTCCTTTACGAATTAAG
66 ATGTGTCATCATGAGTATATGATTCCTTTACGAATTAAG
397697 AGGTCCGATGACTA-GTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
397727 TAAATGAAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
103 95 0.78
104 27 0.22
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (104 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTATGAAGTCCGATGACT
ATGTGTCATCATGAGTATATGATTCCTTTACGAATTAAG
Found at i:403159 original size:52 final size:52
Alignment explanation
Indices: 402995--403231 Score: 334
Period size: 52 Copynumber: 4.6 Consensus size: 52
402985 TAAATCAAAA
* * *
402995 AGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTATG
* ** * *
403047 AGGTCCAATGACTATGTGTCATTATGATTATATGA-TCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTATG
*
403098 AGGTCCGATGACTATGTGTCATCATGAGTATATGATTCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTATG
* * * * *
403150 AGGTTCGATGACTATGTGTCATCGTGAGTACATGATTCCCTTACGAATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTATG
403202 AGGTCCGATGACTA-GTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
403232 TAAATGAAAT
Statistics
Matches: 167, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
51 63 0.38
52 104 0.62
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTATG
Found at i:403185 original size:103 final size:104
Alignment explanation
Indices: 402995--403231 Score: 334
Period size: 103 Copynumber: 2.3 Consensus size: 104
402985 TAAATCAAAA
*
402995 AGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTATGGATTATGAGGTCCAATGACT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTATGAGGTCCAATGACT
* * * * * * *
403060 ATGTGTCATTATGATTATATGA-TCCTTTATGGATTATG
66 ATGTGTCATCATGAGTACATGATTCCCTTACGAATTAAG
* * * * *
403098 AGGTCCGATGACTATGTGTCATCATGAGTATATGATTCCTTTACGGATTATGAGGTTCGATGACT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTATGAGGTCCAATGACT
*
403163 ATGTGTCATCGTGAGTACATGATTCCCTTACGAATTAAG
66 ATGTGTCATCATGAGTACATGATTCCCTTACGAATTAAG
403202 AGGTCCGATGACTA-GTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
403232 TAAATGAAAT
Statistics
Matches: 118, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
103 92 0.78
104 26 0.22
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (104 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTATGAGGTCCAATGACT
ATGTGTCATCATGAGTACATGATTCCCTTACGAATTAAG
Found at i:409460 original size:27 final size:27
Alignment explanation
Indices: 409428--409481 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
409418 CTTTTAAATG
*
409428 ATATTTTCATTAAATA-ATTATTATTTA
1 ATATTTT-ATTAAATATATTAGTATTTA
*
409455 ATATTTTATTTAATATATTAGTATTTA
1 ATATTTTATTAAATATATTAGTATTTA
409482 TTAATTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
ATATTTTATTAAATATATTAGTATTTA
Found at i:409465 original size:12 final size:12
Alignment explanation
Indices: 409428--409470 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
409418 CTTTTAAATG
*
409428 ATATTTTCATTAA
1 ATATTTT-ATTTA
409441 ATAATTATTATTTA
1 AT-ATT-TTATTTA
409455 ATATTTTATTTA
1 ATATTTTATTTA
409467 ATAT
1 ATAT
409471 ATTAGTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 11 0.41
13 5 0.19
14 9 0.33
15 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATTTTATTTA
Found at i:409488 original size:14 final size:15
Alignment explanation
Indices: 409440--409501 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 15
409430 ATTTTCATTA
*
409440 AATA-ATTATTATTT
1 AATATATTACTATTT
409454 AATAT-TT--TATTT
1 AATATATTACTATTT
*
409466 AATATATTAGTATTT
1 AATATATTACTATTT
*
409481 ATTA-ATTACTATTAT
1 AATATATTACTATT-T
409496 AATATA
1 AATATA
409502 AACAAAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
12 10 0.26
13 2 0.05
14 14 0.36
15 12 0.31
16 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
AATATATTACTATTT
Found at i:410724 original size:27 final size:27
Alignment explanation
Indices: 410686--410765 Score: 135
Period size: 27 Copynumber: 3.0 Consensus size: 27
410676 TTATTATTGT
*
410686 TAGCCTCAATT-CCTATAGGGTCGTGGG
1 TAGCCCCAATTCCCTA-AGGGTCGTGGG
410713 TAGCCCCAATTCCCTAAGGGTCGTGGG
1 TAGCCCCAATTCCCTAAGGGTCGTGGG
410740 TAGCCCCAATTCCCTAAGGGTCGTGG
1 TAGCCCCAATTCCCTAAGGGTCGTGG
410766 ACTACTCTGA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 47 0.92
28 4 0.08
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.25
Consensus pattern (27 bp):
TAGCCCCAATTCCCTAAGGGTCGTGGG
Found at i:411580 original size:3 final size:3
Alignment explanation
Indices: 411572--411605 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
411562 TTCAAAAATA
*
411572 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
411606 GAAAAGTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:413725 original size:9 final size:9
Alignment explanation
Indices: 413707--413737 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
413697 CATGTCACCA
*
413707 AAAGAGTTG
1 AAAGAATTG
413716 AAAGAATTG
1 AAAGAATTG
413725 AAAGAATTG
1 AAAGAATTG
413734 AAAG
1 AAAG
413738 TAAAATTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (9 bp):
AAAGAATTG
Found at i:418095 original size:27 final size:27
Alignment explanation
Indices: 418028--418098 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
418018 TATTGTTAGC
* * * *
418028 CCCAATTTCCAGAGAGTTGTGGGTAGT
1 CCCAATTCCCTGAGGGTTATGGGTAGT
418055 CCCAATTCCCTGAGGGTTATGGGTAGT
1 CCCAATTCCCTGAGGGTTATGGGTAGT
*
418082 CCCAATTCCTTGAGGGT
1 CCCAATTCCCTGAGGGT
418099 CGTGGACTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.30
Consensus pattern (27 bp):
CCCAATTCCCTGAGGGTTATGGGTAGT
Found at i:418577 original size:13 final size:13
Alignment explanation
Indices: 418550--418592 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
418540 TGTTTTTAAG
*
418550 AAGTGCTTTTAAA
1 AAGTGCTTTTGAA
*
418563 AAGTGCTTTGGAA
1 AAGTGCTTTTGAA
* *
418576 AAATACTTTTGAA
1 AAGTGCTTTTGAA
418589 AAGT
1 AAGT
418593 TTGGTTTAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.35
Consensus pattern (13 bp):
AAGTGCTTTTGAA
Found at i:430215 original size:18 final size:18
Alignment explanation
Indices: 430180--430222 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
430170 AATAAATATA
430180 AATACAATTTAAATTTAAT
1 AATA-AATTTAAATTTAAT
430199 AATAAATTGTAAA-TTAAT
1 AATAAATT-TAAATTTAAT
430217 AA-AAAT
1 AATAAAT
430223 AAATGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 11 0.48
19 8 0.35
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
AATAAATTTAAATTTAAT
Found at i:433058 original size:19 final size:19
Alignment explanation
Indices: 433034--433076 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
433024 AAACATAAAT
433034 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
433053 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
433072 TAAAT
1 TAAAT
433077 CGTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:434598 original size:6 final size:6
Alignment explanation
Indices: 434587--434624 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
434577 ATAAAATAGA
434587 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
434625 CTGGGTTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:435652 original size:21 final size:21
Alignment explanation
Indices: 435607--435653 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
435597 ATGCCTTAGT
* *
435607 TTGCTTTTGAAAATCTGCAGT
1 TTGCTTTTGAAAATCTACAGA
* *
435628 TTGCTTTTGAAAATTTATAGA
1 TTGCTTTTGAAAATCTACAGA
435649 TTGCT
1 TTGCT
435654 GCTGAAATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.47
Consensus pattern (21 bp):
TTGCTTTTGAAAATCTACAGA
Found at i:444850 original size:8 final size:8
Alignment explanation
Indices: 444837--444863 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
444827 TAGGTACTTC
444837 CTTATAAA
1 CTTATAAA
444845 CTTATAAA
1 CTTATAAA
444853 CTTATAAA
1 CTTATAAA
444861 CTT
1 CTT
444864 GAACAAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (8 bp):
CTTATAAA
Found at i:449138 original size:16 final size:16
Alignment explanation
Indices: 449113--449148 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
449103 TGATCTGGGG
*
449113 GAAAATAAAAATAAAA
1 GAAAACAAAAATAAAA
*
449129 GAAAACAAAATTAAAA
1 GAAAACAAAAATAAAA
449145 GAAA
1 GAAA
449149 TAGAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (16 bp):
GAAAACAAAAATAAAA
Found at i:449959 original size:19 final size:19
Alignment explanation
Indices: 449935--449977 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
449925 AAACATAAAT
449935 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
449954 TAAATAATATCTTAAATAC
1 TAAATAAAATCTTAAATAA
449973 TAAAT
1 TAAAT
449978 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:454127 original size:42 final size:42
Alignment explanation
Indices: 454063--454198 Score: 231
Period size: 42 Copynumber: 3.3 Consensus size: 42
454053 ATGAGTCATA
454063 AGTCTTCCTTT-ATCATATTCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTTAATCATATTCTCATTCTCATCTCGAGACATG
454104 AGTCTTCCTTTAATCATATTCTCATTC-CAATCTCGAGACATG
1 AGTCTTCCTTTAATCATATTCTCATTCTC-ATCTCGAGACATG
* *
454146 AGTCTTCCTTTAATTATATTCTCATTCTCATCTCGAGACATA
1 AGTCTTCCTTTAATCATATTCTCATTCTCATCTCGAGACATG
454188 AGTCTTCCTTT
1 AGTCTTCCTTT
454199 TTACATCAAA
Statistics
Matches: 90, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
41 12 0.13
42 77 0.86
43 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.09, T:0.42
Consensus pattern (42 bp):
AGTCTTCCTTTAATCATATTCTCATTCTCATCTCGAGACATG
Found at i:459286 original size:18 final size:18
Alignment explanation
Indices: 459250--459289 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
459240 CCTAGATAAT
**
459250 ATGCGATCACATGACTAG
1 ATGCGATCACAAAACTAG
*
459268 ATGCGATCACAAAATTAG
1 ATGCGATCACAAAACTAG
459286 ATGC
1 ATGC
459290 ATTCATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (18 bp):
ATGCGATCACAAAACTAG
Found at i:465778 original size:21 final size:21
Alignment explanation
Indices: 465740--465779 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
465730 TGTTGACTCC
*
465740 AAGGACAAGAAAAGAAAGAGG
1 AAGGACAAGAAAAAAAAGAGG
465761 AAGGACAA-AAAGAAAAAGA
1 AAGGACAAGAAA-AAAAAGA
465780 AGCACAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.68, C:0.05, G:0.28, T:0.00
Consensus pattern (21 bp):
AAGGACAAGAAAAAAAAGAGG
Found at i:465781 original size:18 final size:19
Alignment explanation
Indices: 465749--465787 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
465739 CAAGGACAAG
* *
465749 AAAAGAAAGAGGAAGGACA
1 AAAAGAAAGAAGAAGCACA
465768 AAAAGAAA-AAGAAGCACA
1 AAAAGAAAGAAGAAGCACA
465786 AA
1 AA
465788 GAGGAGCGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.69, C:0.08, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAGAAAGAAGAAGCACA
Found at i:465908 original size:16 final size:17
Alignment explanation
Indices: 465887--465925 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
465877 GCATGCATCT
465887 CATTTTA-TTGTCGTTG
1 CATTTTAGTTGTCGTTG
*
465903 CATTTTAGTTGTTGTTG
1 CATTTTAGTTGTCGTTG
465920 CATTTT
1 CATTTT
465926 CATTTTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.13, C:0.10, G:0.18, T:0.59
Consensus pattern (17 bp):
CATTTTAGTTGTCGTTG
Found at i:484586 original size:240 final size:238
Alignment explanation
Indices: 484153--484628 Score: 747
Period size: 240 Copynumber: 2.0 Consensus size: 238
484143 TAAAAAAAGC
* *
484153 CTCCAATTAACTTGTAATTTGACTAAGACGTGTTCACCAAACTTATCTAATTTAAAAATTAAATT
1 CTCCAATTAACTTGTAACTTGACTAAAACGTGTTCACCAAACTTATCTAATTTAAAAATTAAATT
* * **
484218 AAATATTTTTACTCCTAATAAGAACCTTAAAAGATACCTAAATAATTCTAGTAAAATATTTTCAA
66 AAACATTTTTACTCCTAATAAGAACCCTAAAAGATACCTAAATAATTCTAGTAAAATACCTTCAA
*
484283 TTCTTAAAATTAATTCTATTTTCGAATCCTAAAAAAACCTAAAAAAAATTACTAATAAATTAAGA
131 TTCTTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCT--AAAAAATTACTAATAAATTAAGA
*
484348 GAAATATTAAAGTTCATCTACAACTTATTCGATCTTTTATCTTTA
194 GAAATATTAAAATTCATCTACAACTTATTCGATCTTTTATCTTTA
* * * *
484393 CTCCGATTTACTTGTAACTTGACTAAAACGTGTTTACCAAACTTATCTAATTTAAAACTTAAATT
1 CTCCAATTAACTTGTAACTTGACTAAAACGTGTTCACCAAACTTATCTAATTTAAAAATTAAATT
*
484458 AAACATTTTTATTCCTAATAAGAACCCTAAAAGATACCTAAATAATTCTAGTAAAATACCTTCAA
66 AAACATTTTTACTCCTAATAAGAACCCTAAAAGATACCTAAATAATTCTAGTAAAATACCTTCAA
* * *
484523 TTCTTAAGATTAATTCTATTTTAGAATCCTAAAAAAAAAGCCT-AAAAGTTACTAATGAATTAAG
131 TTCTTAAAATTAATTCTATTTTAGAATCCT--AAAAAAA-CCTAAAAAATTACTAATAAATTAAG
*
484587 AGAAATATTAAAATTTATCTACAACTTATTCGATCTTTTATC
193 AGAAATATTAAAATTCATCTACAACTTATTCGATCTTTTATC
484629 ATTATTATGA
Statistics
Matches: 216, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
240 206 0.95
242 7 0.03
243 3 0.01
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.37
Consensus pattern (238 bp):
CTCCAATTAACTTGTAACTTGACTAAAACGTGTTCACCAAACTTATCTAATTTAAAAATTAAATT
AAACATTTTTACTCCTAATAAGAACCCTAAAAGATACCTAAATAATTCTAGTAAAATACCTTCAA
TTCTTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAAATTACTAATAAATTAAGAGA
AATATTAAAATTCATCTACAACTTATTCGATCTTTTATCTTTA
Found at i:485907 original size:152 final size:151
Alignment explanation
Indices: 485672--486273 Score: 817
Period size: 157 Copynumber: 4.0 Consensus size: 151
485662 TTGATTAAAC
* *
485672 AAAAATCACTATTTTACTTAAAAATCCAAATTTTTATTTTGAAATAATTAAAAAAAATCAAAACT
1 AAAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATT-AAAAAAATCAAAACT
* * * * * *
485737 TTGTAAAAAATTTAAACTTTTTTTTTTAAATAACTAAAAAAACAGATTTTTATTTTTTAAAAATC
65 TTGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAAAAACAGATTTTTATTTTTTAAAAATA
*
485802 TAA-ACTTTCTCTTTTTTTTGAA
130 TAAGATTTTCTCTTTTTTTT-AA
*
485824 GAAAATCACTATTTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACT
1 AAAAATCACTA-TTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACT
* *
485889 TTGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAGAAAACAAATTTTTATTTTTTAAAAAAT
65 TTGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAAAAACAGATTTTTATTTTTT-AAAAAT
* *
485954 ATAAGTTTTTTTCTTTTTTTTTTTAA
129 ATAAG--ATTTTC-TCTTTTTTTTAA
* *
485980 ACAAAATCACTATTTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAAT
1 A-AAAATCACTA-TTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAATCAAAAC
* * * **
486045 TTTGTTAAAAATCTAAACTTTTTCTCCAAAATAACTAAGAAAACATATTTTTATTTTTTTTAAAT
64 TTTGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAAAAACAGATTTTTATTTTTTAAAAAT
486110 ATAAGATTTT-TC-TTTTTTTAA
129 ATAAGATTTTCTCTTTTTTTTAA
* * * **
486131 AAAAATTACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTTTAAAAA--AAAACTT
1 AAAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTT
486194 TGTTAAAAATCTAAA-TTTTTCT-TGAAAATAACTAAAAAAACAGATTTTTA-TTTTTAAAAATA
66 TGTTAAAAATCTAAACTTTTTCTCT-AAAATAACTAAAAAAACAGATTTTTATTTTTTAAAAATA
486256 TAA-ATTTTCTCTTTTTTT
130 TAAGATTTTCTCTTTTTTT
486274 CTTTTTTTTT
Statistics
Matches: 407, Mismatches: 33, Indels: 26
0.87 0.07 0.06
Matches are distributed among these distances:
144 5 0.01
145 15 0.04
146 37 0.09
147 21 0.05
149 42 0.10
150 9 0.02
151 10 0.02
152 77 0.19
153 45 0.11
154 4 0.01
156 15 0.04
157 127 0.31
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (151 bp):
AAAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTT
TGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAAAAACAGATTTTTATTTTTTAAAAATAT
AAGATTTTCTCTTTTTTTTAA
Found at i:485996 original size:31 final size:32
Alignment explanation
Indices: 485935--485996 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 32
485925 AGAAAACAAA
* *
485935 TTTTTATTTTTTAAAAAATATAAGTTTTTTTC
1 TTTTTATTTTTTAAAAAATATAACTATTTTTC
*
485967 TTTTT-TTTTTTAAACAAA-ATCACTATTTTT
1 TTTTTATTTTTTAAA-AAATATAACTATTTTT
485997 ACTTAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (32 bp):
TTTTTATTTTTTAAAAAATATAACTATTTTTC
Found at i:486063 original size:50 final size:50
Alignment explanation
Indices: 485689--486067 Score: 147
Period size: 50 Copynumber: 7.4 Consensus size: 50
485679 ACTATTTTAC
* * *
485689 TTAAAAATCCAAA-TTTTTATTTTGAAATAATTAAAAAAAATCAAAACTTTG
1 TTAAAAATCTAAACTTTTT-TTCTGAAATAATT-AAAAAAATCAAAATTTTG
* * * * * *
485740 TAAAAAATTTAAACTTTTTTTTTTAAATAACTAAAAAAA-CAGATTTTTATTTT-
1 TTAAAAATCTAAACTTTTTTTCTGAAATAATTAAAAAAATCA-A----AATTTTG
* * * * *
485793 TTAAAAATCTAAACTTTCTCTTT-T----T-TTTGAAGAAAATCACTATTTTTAC
1 TTAAAAATCTAAACTTT-T-TTTCTGAAATAATT-AAAAAAATCA-AAATTTT-G
* *
485842 TTAAAAATCCAAACTTTTATTTC-GAAATAATTAAAAAAATCAAAACTTTG
1 TTAAAAATCTAAACTTTT-TTTCTGAAATAATTAAAAAAATCAAAATTTTG
* * * *
485892 TTAAAAATCTAAACTTTTTCTCTAAAATAACTAAGAAAA-CAAATTTTTATTTT-
1 TTAAAAATCTAAACTTTTTTTCTGAAATAATTAAAAAAATCAAA-----ATTTTG
* * **** ** * * *
485945 TTAAAAA-ATATAAGTTTTTTTCTTTTTTTTTTTAAACAAAATCACTATTTTTAC
1 TTAAAAATCTA-AACTTTTTTTC-TGAAATAATTAAA-AAAATCA-AAATTTT-G
* *
485999 TTAAAAATCCAAACTTTTATTTC-GAAATAGTTAAAAAAATCAAAATTTTG
1 TTAAAAATCTAAACTTTT-TTTCTGAAATAATTAAAAAAATCAAAATTTTG
486049 TTAAAAATCTAAACTTTTT
1 TTAAAAATCTAAACTTTTT
486068 CTCCAAAATA
Statistics
Matches: 239, Mismatches: 56, Indels: 68
0.66 0.15 0.19
Matches are distributed among these distances:
47 4 0.02
48 4 0.02
49 27 0.11
50 62 0.26
51 32 0.13
52 28 0.12
53 39 0.16
54 28 0.12
55 12 0.05
56 2 0.01
57 1 0.00
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (50 bp):
TTAAAAATCTAAACTTTTTTTCTGAAATAATTAAAAAAATCAAAATTTTG
Found at i:486249 original size:309 final size:309
Alignment explanation
Indices: 485666--486364 Score: 824
Period size: 309 Copynumber: 2.2 Consensus size: 309
485656 TTTCATTTGA
* * *
485666 TTAAACAAAAATCACTA-TTTTACTTAAAAATCCAAATTTTTATTTTGAAATAATTAAAAAAAAT
1 TTAAAC-AAAATCACTATTTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTT-AAAAAAAT
* * ***
485730 CAAAACTTTGTAAAAAATTTAAACTTTTTTTTTTAAATAACTAAAAAAACAGATTTTTATTTTTT
64 CAAAACTTTGTAAAAAATCTAAACTTTTTCTCCAAAATAACTAAAAAAACAGATTTTTATTTTTT
* *
485795 AAAAATCTAAACTTTCTCTTTTTTTTGAAGAAAATCACTATTTTTACTTAAAAATCCAAACTTTT
129 AAAAATATAAACTTTCTCTTTTTTTTGAAAAAAATCACTATTTTTACTTAAAAATCCAAACTTTT
485860 ATTTCGAAATAATTAAAAAAATCAAAACTTTGTTAAAAATCTAAACTTTTTCTCTAAAATAACTA
194 ATTTCGAAATAATTAAAAAAA-CAAAACTTTGTTAAAAATCTAAACTTTTTCTCTAAAATAACTA
* **** *
485925 AGAAAACAAATTTTTATTTTTTAAAAAATATAAGTTTTTTTC-TTTTT-TTTT
258 AAAAAACAAATTTTTA-AAAATAAAAAATATAACTTTTTTTCTTTTTTCTTTT
485976 TTAAACAAAATCACTATTTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCA
1 TTAAACAAAATCACTATTTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCA
* * * * **
486041 AAATTTTGTTAAAAATCTAAACTTTTTCTCCAAAATAACTAAGAAAACATATTTTTATTTTTTTT
66 AAACTTTGTAAAAAATCTAAACTTTTTCTCCAAAATAACTAAAAAAACAGATTTTTATTTTTTAA
* * *
486106 AAATATAAGA-TTTTTC-TTTTTTT-AAAAAAATTACTA-TTTTACTTAAAAATTCAAACTTTTA
131 AAATATAA-ACTTTCTCTTTTTTTTGAAAAAAATCACTATTTTTACTTAAAAATCCAAACTTTTA
* **
486167 TTTCGAAATAGTTTTAAAAA-AAAACTTTGTTAAAAATCTAAA-TTTTTCT-TGAAAATAACTAA
195 TTTCGAAATAATTAAAAAAACAAAACTTTGTTAAAAATCTAAACTTTTTCTCT-AAAATAACTAA
* * * **
486229 AAAAACAGATTTTTATTTTTAAAAATATAAATTTTCTCTTTTTTTCTTTTTTTTTCTTTT
259 AAAAACA-A-----ATTTTTAAAAATAAAAAATATAACTTTTTTTC---TTTTTTCTTTT
* * *
486289 TTAAAGAAAATCACTATTTTTACTTAAAAAAATCAAAACTTTTATTTCGAAATTGTTTAAAAAAA
1 TTAAACAAAATCACTATTTTTACTT--AAAAATCCAAACTTTTATTTCGAAATAG-TTAAAAAAA
*
486354 CCCAAAACTTT
63 -TCAAAACTTT
486365 TCTCAAAATC
Statistics
Matches: 333, Mismatches: 38, Indels: 29
0.83 0.09 0.07
Matches are distributed among these distances:
302 1 0.00
303 24 0.07
304 23 0.07
306 41 0.12
307 11 0.03
308 22 0.07
309 93 0.28
310 42 0.13
312 5 0.02
313 28 0.08
315 26 0.08
316 9 0.03
317 8 0.02
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (309 bp):
TTAAACAAAATCACTATTTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCA
AAACTTTGTAAAAAATCTAAACTTTTTCTCCAAAATAACTAAAAAAACAGATTTTTATTTTTTAA
AAATATAAACTTTCTCTTTTTTTTGAAAAAAATCACTATTTTTACTTAAAAATCCAAACTTTTAT
TTCGAAATAATTAAAAAAACAAAACTTTGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAA
AAACAAATTTTTAAAAATAAAAAATATAACTTTTTTTCTTTTTTCTTTT
Found at i:487218 original size:42 final size:42
Alignment explanation
Indices: 487147--487563 Score: 568
Period size: 42 Copynumber: 9.9 Consensus size: 42
487137 AAAAAATAAA
** * * * *
487147 TAAATGGACCTGTACGCCTAGGCCACTAAATGCAATAAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
** * * *
487189 TAAATGGGTCTCCACACTTGAGCCTCTAAATACAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
487231 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* * *
487273 TAAATGGGCCTCCACACCTGGGCCTCTAAATGTAAAGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
*
487315 TAAATGAACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* * *
487357 TAAATGGGCCTCCACACCTGAGCCTCTGAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* *
487399 TAAATAGG-CCTCCACACCTGGACCTCTGAATGCGAA-GAAAAG
1 TAAAT-GGACCTCCACACCTGGGCCTCTAAATGC-AATGAAAAG
*
487441 TAAATGGACCTCCAGACCTGGGCCTCTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* * *
487483 TAAATGGACCACCACACCTGGGCCTCTGAATGCGATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* *
487525 TAAATTGACCTCCACACCTAGGCCTCTAAATGCAATGAA
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
487564 TGCTTTTCTT
Statistics
Matches: 330, Mismatches: 41, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
41 4 0.01
42 322 0.98
43 4 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (42 bp):
TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
Found at i:488003 original size:16 final size:16
Alignment explanation
Indices: 487965--488003 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
487955 TGCTCTCTCT
*
487965 TTCTATTTTTTCTTTG
1 TTCTTTTTTTTCTTTG
487981 TTCTTTTTTTTCTTT-
1 TTCTTTTTTTTCTTTG
487996 TT-TTTTTT
1 TTCTTTTTT
488004 GTATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.27
15 2 0.09
16 14 0.64
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.85
Consensus pattern (16 bp):
TTCTTTTTTTTCTTTG
Found at i:488004 original size:24 final size:24
Alignment explanation
Indices: 487964--488013 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
487954 TTGCTCTCTC
*
487964 TTTCTATTTTTTCTTTGTTCTTTTT
1 TTTCTATTTTTTCTTTG-TATTTTT
*
487989 TTTCT-TTTTTTTTTTGTATTTTT
1 TTTCTATTTTTTCTTTGTATTTTT
488012 TT
1 TT
488014 CTTGATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 10 0.43
25 5 0.22
ACGTcount: A:0.04, C:0.08, G:0.04, T:0.84
Consensus pattern (24 bp):
TTTCTATTTTTTCTTTGTATTTTT
Found at i:492116 original size:301 final size:301
Alignment explanation
Indices: 491562--492164 Score: 1048
Period size: 301 Copynumber: 2.0 Consensus size: 301
491552 AGATGAAACG
* * *
491562 AGACACGTAATTTAACCGTCCGAAAAAACTTCTTACCTCCTTTTGAGTCTTAGGGGTGTCAAATC
1 AGACACATAATTTAACCGTCCCAAAAAACCTCTTACCTCCTTTTGAGTCTTAGGGGTGTCAAATC
491627 TTGAATTGCTCGAACCTTGTCCGGATCTATTTCAATTCCTCGTTCACTCACTATGAAACCCAACA
66 TTGAATTGCTCGAACCTTGTCCGGATCTATTTCAATTCCTCGTTCACTCACTATGAAACCCAACA
*
491692 ACTTCCTCGACTTTACCCCGAAAGTACATTTTACTGGATTTAATCTCAATTTGTATTTCCTCTAT
131 ACTTCCTCGACTTTACCCCGAAAGTACATTTTACTGGATTTAATCTCAATTTGTATTTCCTCAAT
* *
491757 CTTTCAAATAATTTGCGGAGGTTCTCCACATGACCTTCCTTCCTAACAAACTTTGCTATCATATC
196 CTTTCAAATAATTTGCGGAGGTTCTCCACATGACCTTCCTCCCTAACAAACCTTGCTATCATATC
*
491822 GTCAACATAAACTTCAATCTCTTTATGTATCGTGTCATGAA
261 GTCAACATAAACTTCAATCTCTTTATGTATCATGTCATGAA
*
491863 AGACACATAATTTAACCGTCCCAAAAAACCTCTTACCTCTTTTTGAGTCTT-GAGGGTGTCAAAT
1 AGACACATAATTTAACCGTCCCAAAAAACCTCTTACCTCCTTTTGAGTCTTAG-GGGTGTCAAAT
491927 CTTGAATTGCTCGAACCTTGTCCGGATCTATTTCAATTCCTCGTTCACTCACTATGAAACCCAAC
65 CTTGAATTGCTCGAACCTTGTCCGGATCTATTTCAATTCCTCGTTCACTCACTATGAAACCCAAC
* *
491992 AACTTTCC-CGACTTTACCTCGAAAGTACATTTTGCTGGATTTAATCTCAATTTGTATTTCCTCA
130 AAC-TTCCTCGACTTTACCCCGAAAGTACATTTTACTGGATTTAATCTCAATTTGTATTTCCTCA
**
492056 ATCTTTCAAATAATTTGCGGAGGTTCTCCACATGACCTTCCTCCCTAATGAACCTTGCTATCATA
194 ATCTTTCAAATAATTTGCGGAGGTTCTCCACATGACCTTCCTCCCTAACAAACCTTGCTATCATA
* *
492121 TTGTCACCATAAACTTCAATCTCTTTATGTATCATGTCATGAA
259 TCGTCAACATAAACTTCAATCTCTTTATGTATCATGTCATGAA
492164 A
1 A
492165 CAGTGTCACT
Statistics
Matches: 286, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
300 1 0.00
301 281 0.98
302 4 0.01
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.35
Consensus pattern (301 bp):
AGACACATAATTTAACCGTCCCAAAAAACCTCTTACCTCCTTTTGAGTCTTAGGGGTGTCAAATC
TTGAATTGCTCGAACCTTGTCCGGATCTATTTCAATTCCTCGTTCACTCACTATGAAACCCAACA
ACTTCCTCGACTTTACCCCGAAAGTACATTTTACTGGATTTAATCTCAATTTGTATTTCCTCAAT
CTTTCAAATAATTTGCGGAGGTTCTCCACATGACCTTCCTCCCTAACAAACCTTGCTATCATATC
GTCAACATAAACTTCAATCTCTTTATGTATCATGTCATGAA
Found at i:492762 original size:35 final size:35
Alignment explanation
Indices: 492716--492788 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
492706 TTGACTTTGC
492716 TCTGGTATGAGAGTGGTTCTAATCCTAATTTCCTT
1 TCTGGTATGAGAGTGGTTCTAATCCTAATTTCCTT
492751 TCTGGTATGAGAGTGGTTCTAATCCTAATTTCCTT
1 TCTGGTATGAGAGTGGTTCTAATCCTAATTTCCTT
492786 TCT
1 TCT
492789 TACCTCATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (35 bp):
TCTGGTATGAGAGTGGTTCTAATCCTAATTTCCTT
Found at i:496420 original size:12 final size:12
Alignment explanation
Indices: 496403--496432 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
496393 ACAAATGACT
496403 GAATGAACGAAC
1 GAATGAACGAAC
*
496415 GAATGAACGAAT
1 GAATGAACGAAC
496427 GAATGA
1 GAATGA
496433 TTGAATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.27, T:0.13
Consensus pattern (12 bp):
GAATGAACGAAC
Found at i:501484 original size:152 final size:151
Alignment explanation
Indices: 501246--501922 Score: 694
Period size: 152 Copynumber: 4.4 Consensus size: 151
501236 TGATTATACA
* * * ** *
501246 AAAATCACTA-CTTTACTT-AAAAGTCAAAGTTTTTATTTTTAAATAATTAAAAAAAAATCAAAA
1 AAAATCACTATTTTTACTTAAAAATTCAAA-CTTTTATTTCGAAATAGTT--AAAAAAATCAAAA
* * * *
501309 CTTTGTTAAAATTTTAAACTTTTTCTTTAAAATAACTAAAAAAATAGATTTTTATTTTTTAAAAA
63 CTTTGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAAAAACAGATTTTTATTTTTTAAAAA
* *
501374 TCTAAACTTTCTC-TTTTTTGAAG
128 TATAAACTTTCTCTTTTTTTAAAG
*
501397 AAAATCACTATTTTTACTTAAAAATTCAAACTTTTATTTCTAAATAGTTAAAAAAATCAAAACTT
1 AAAATCACTATTTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTT
* *
501462 TGTTAAAAATCTAAACTTTTTTTCTAAAATAACTAATAAAACAGATTTTTATTTTTTTTTTAAAA
66 TGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAAAAACAGATTTTTA----TTTTTTAAAA
**
501527 ATATAAGTTTTTTCTTCTTTTTTTTTTTTAAAG
127 ATATAA--ACTTTC-TC-----TTTTTTTAAAG
501560 AAAATCACTATTTTTACTTAAAAA-TCTAAACTTTTATTTCGAAATAGTTAAAAAAAAAAATC-A
1 AAAATCACTATTTTTACTTAAAAATTC-AAACTTTTATTTCGAAATAGTT----AAAAAAATCAA
* * * * * * * *
501623 AATTTTGTTAAAAATTTAAAATTTTTCTCCAAAATAACTAAGAAAACATATTTTAATTTTTT-TA
61 AACTTTGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAAAAACAGATTTTTATTTTTTAAA
* *
501687 AATATAAGCTTTTTC-TTTTTTAAAG
126 AATATAAACTTTCTCTTTTTTTAAAG
* * *
501712 AAAATCATTA-TTTAACTTAAAAATTCAAACTTTTATTTCGAAATAGTT-AAAAAATCTAAACTT
1 AAAATCACTATTTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTT
*
501775 TGTTAAAAATCTAAAC-TTTTCTCTAAAATAACT-AAAAAAGAGATTTTTA-TTTTTAAAAATAT
66 TGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAAAAACAGATTTTTATTTTTTAAAAATAT
501837 AAACTTTCTCCTTTTTTTTTTTTAAAG
131 AAACTTTCT-C-----TTTTTTTAAAG
* * * *
501864 AAAATCACTATTTTTACTTAAAAAAATCAAAATTTTTATTTCAAAATTATTTAAAAAAA
1 AAAATCACTATTTTTACTT-AAAAATTC-AAACTTTTATTTCGAAA-TAGTTAAAAAAA
501923 AACCCAAATT
Statistics
Matches: 444, Mismatches: 47, Indels: 64
0.80 0.08 0.12
Matches are distributed among these distances:
144 5 0.01
145 25 0.06
146 25 0.06
147 19 0.04
150 61 0.14
151 44 0.10
152 63 0.14
153 16 0.04
154 22 0.05
155 15 0.03
156 8 0.02
157 8 0.02
158 2 0.00
159 3 0.01
161 8 0.02
162 8 0.02
163 54 0.12
166 49 0.11
167 9 0.02
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (151 bp):
AAAATCACTATTTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTT
TGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAAAAACAGATTTTTATTTTTTAAAAATAT
AAACTTTCTCTTTTTTTAAAG
Found at i:501700 original size:146 final size:140
Alignment explanation
Indices: 501550--501843 Score: 333
Period size: 151 Copynumber: 2.0 Consensus size: 140
501540 CTTCTTTTTT
*
501550 TTTTTTAAAGAAAATCACTATTTTTACTTAAAAA-TCTAAACTTTTATTTCGAAATAGTTAAAAA
1 TTTTTTAAAGAAAATCACTA-TTTAACTTAAAAATTC-AAACTTTTATTTCGAAATAGTT-----
* * * *
501614 AAAAAATC-AAATTTTGTTAAAAATTTAAAATTTTTCTCCAAAATAACTAAGAAAACATATTTTA
59 AAAAAATCTAAACTTTGTTAAAAATCT-AAACTTTTCTCCAAAATAACTAA-AAAACAGATTTTA
** *
501678 ATTTTTTTAAATATAAGCTTTTTC
122 ATTTTTAAAAATATAA-----ATC
*
501702 TTTTTTAAAGAAAATCATTATTTAACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAT
1 TTTTTTAAAGAAAATCACTATTTAACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAT
* * *
501767 CTAAACTTTGTTAAAAATCTAAACTTTTCTCTAAAATAACTAAAAAAGAGATTTTTATTTTTAAA
66 CTAAACTTTGTTAAAAATCTAAACTTTTCTCCAAAATAACTAAAAAACAGATTTTAATTTTTAAA
501832 AATATAAA-C
131 AATATAAATC
501841 TTT
1 TTT
501844 CTCCTTTTTT
Statistics
Matches: 128, Mismatches: 12, Indels: 17
0.82 0.08 0.11
Matches are distributed among these distances:
139 4 0.03
145 24 0.19
146 29 0.23
147 16 0.12
151 34 0.27
152 21 0.16
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.41
Consensus pattern (140 bp):
TTTTTTAAAGAAAATCACTATTTAACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAT
CTAAACTTTGTTAAAAATCTAAACTTTTCTCCAAAATAACTAAAAAACAGATTTTAATTTTTAAA
AATATAAATC
Found at i:501909 original size:23 final size:22
Alignment explanation
Indices: 501851--501909 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
501841 TTTCTCCTTT
* **
501851 TTTTTTTTTAAAGAAAATCACTA
1 TTTTTATTTAAA-AAAATCAAAA
*
501874 TTTTTACTTAAAAAAATCAAAA
1 TTTTTATTTAAAAAAATCAAAA
*
501896 TTTTTATTTCAAAA
1 TTTTTATTTAAAAA
501910 TTATTTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (22 bp):
TTTTTATTTAAAAAAATCAAAA
Found at i:502242 original size:16 final size:16
Alignment explanation
Indices: 502221--502251 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
502211 TATTGTTCAT
502221 TAATCTTGTTTATCTG
1 TAATCTTGTTTATCTG
*
502237 TAATCTTTTTTATCT
1 TAATCTTGTTTATCT
502252 TGTTTCATTT
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:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (16 bp):
TAATCTTGTTTATCTG
Found at i:502724 original size:19 final size:19
Alignment explanation
Indices: 502702--502746 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
502692 TTTTATTAGG
502702 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
502721 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
502740 ATTTAAT
1 ATTTAAT
502747 TTATGTTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:503586 original size:21 final size:22
Alignment explanation
Indices: 503539--503596 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
503529 AACACCTTTA
503539 TTTTCTATTT-TTTTTAATTCTG
1 TTTTCT-TTTATTTTTAATTCTG
*
503561 TTTTCTTTTATTTTTAATTTTG
1 TTTTCTTTTATTTTTAATTCTG
503583 -TTTCTTTTATTTTT
1 TTTTCTTTTATTTTT
503597 CCTCAGATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.12, C:0.07, G:0.03, T:0.78
Consensus pattern (22 bp):
TTTTCTTTTATTTTTAATTCTG
Found at i:512663 original size:21 final size:22
Alignment explanation
Indices: 512627--512673 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
512617 TTTTTATTTC
512627 TTTTAATTCTGTTTTCTTTTAT
1 TTTTAATTCTGTTTTCTTTTAT
*
512649 TTTTAATTCTG-TTTCTTTTGT
1 TTTTAATTCTGTTTTCTTTTAT
512670 TTTT
1 TTTT
512674 CCTCAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.11, C:0.09, G:0.06, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTGTTTTCTTTTAT
Found at i:519597 original size:12 final size:13
Alignment explanation
Indices: 519573--519601 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
519563 GGTTGCAACA
519573 AAGGGGAAAGGGG
1 AAGGGGAAAGGGG
519586 AAGGGG-AAGGGG
1 AAGGGGAAAGGGG
519598 AAGG
1 AAGG
519602 TAAAAGAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (13 bp):
AAGGGGAAAGGGG
Found at i:520994 original size:40 final size:40
Alignment explanation
Indices: 520950--521034 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
520940 ATATTTCATT
* * * *
520950 AAAAGGTTGAAAATGATATTATCCAAAAGGATAATAGATG
1 AAAAGGTTAAAAAGGATATTATCCAAAAGGATAACAAATG
* * *
520990 AAAAGGTTAAAAAGGATGTTATTCGAAAGGATAACAAATG
1 AAAAGGTTAAAAAGGATATTATCCAAAAGGATAACAAATG
521030 AAAAG
1 AAAAG
521035 ATCGAAAAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.22
Consensus pattern (40 bp):
AAAAGGTTAAAAAGGATATTATCCAAAAGGATAACAAATG
Found at i:521793 original size:13 final size:13
Alignment explanation
Indices: 521775--521812 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
521765 ATGGTAAATC
*
521775 GAAATGGTTATAT
1 GAAATGGTTATAA
*
521788 GCAATGGTTATAA
1 GAAATGGTTATAA
521801 GAAATGGTTATA
1 GAAATGGTTATA
521813 GGGAATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (13 bp):
GAAATGGTTATAA
Found at i:534706 original size:21 final size:22
Alignment explanation
Indices: 534666--534707 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
534656 TCATAATTAG
534666 CTTTATTAATCTCTTATTTAAC
1 CTTTATTAATCTCTTATTTAAC
534688 CTTTAATTAATC-C-TATTTAA
1 CTTT-ATTAATCTCTTATTTAA
534708 TATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (22 bp):
CTTTATTAATCTCTTATTTAAC
Found at i:534714 original size:2 final size:2
Alignment explanation
Indices: 534707--534740 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
534697 ATCCTATTTA
534707 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
534741 CATGATATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:538079 original size:13 final size:13
Alignment explanation
Indices: 538063--538088 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
538053 TTGTATAGTA
538063 TTATACTATATAT
1 TTATACTATATAT
538076 TTATACTATATAT
1 TTATACTATATAT
538089 AGTATAATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATACTATATAT
Found at i:539208 original size:15 final size:15
Alignment explanation
Indices: 539188--539218 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
539178 GACGGTTCCG
539188 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
539203 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
539218 T
1 T
539219 ACTCATACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
TGTGCTCTGATTCAT
Found at i:542429 original size:20 final size:20
Alignment explanation
Indices: 542393--542430 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
542383 ATTTATGATT
*
542393 CCTTATTTCTATCTCATTAG
1 CCTTATTTCAATCTCATTAG
*
542413 CCTTATTTCAATTTCATT
1 CCTTATTTCAATCTCATT
542431 TCGTATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.53
Consensus pattern (20 bp):
CCTTATTTCAATCTCATTAG
Found at i:542687 original size:16 final size:16
Alignment explanation
Indices: 542661--542700 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
542651 ATTCTATTAT
*
542661 ATATTTATATATTCTA
1 ATATATATATATTCTA
*
542677 TTATATATATATTCTA
1 ATATATATATATTCTA
542693 ATATATAT
1 ATATATAT
542701 TAGAATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATATATATATTCTA
Found at i:542720 original size:12 final size:12
Alignment explanation
Indices: 542662--542746 Score: 51
Period size: 12 Copynumber: 7.4 Consensus size: 12
542652 TTCTATTATA
542662 TATTTATATATT
1 TATTTATATATT
*
542674 CTA-TTATATATA
1 -TATTTATATATT
*
542686 TATTCTA-ATATA
1 TATT-TATATATT
*
542698 TA-TTAGA-ATT
1 TATTTATATATT
542708 TATTTATATATT
1 TATTTATATATT
542720 T-TATTA-AT-TT
1 TAT-TTATATATT
542730 T-TTTATATATTT
1 TATTTATATA-TT
542742 TATTT
1 TATTT
542747 CTAATATATT
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
9 3 0.05
10 12 0.20
11 11 0.19
12 26 0.44
13 7 0.12
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (12 bp):
TATTTATATATT
Found at i:542734 original size:21 final size:21
Alignment explanation
Indices: 542662--542745 Score: 80
Period size: 21 Copynumber: 3.8 Consensus size: 21
542652 TTCTATTATA
*
542662 TATTTATATATTCTATTATATAT
1 TATTTATATATTTTATTA-AT-T
* *
542685 ATATTCTAATATATATTA-GAATT
1 -TATT-T-ATATATTTTATTAATT
542708 TATTTATATATTTTATTAATT
1 TATTTATATATTTTATTAATT
*
542729 TTTTTATATATTTTATT
1 TATTTATATATTTTATT
542746 TCTAATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 9 0.18
21 21 0.41
22 4 0.08
23 1 0.02
24 6 0.12
25 2 0.04
26 8 0.16
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (21 bp):
TATTTATATATTTTATTAATT
Found at i:542795 original size:57 final size:56
Alignment explanation
Indices: 542695--542804 Score: 136
Period size: 57 Copynumber: 1.9 Consensus size: 56
542685 ATATTCTAAT
* *
542695 ATATATTAGAATTTATTTATATATTTTATTAATTTTTTTATATATTT-TATTTCTA
1 ATATATTAGAATTTATTTATATATTTTATTAATTTATTGATATATTTCTATTTCTA
*
542750 ATATATTAGAATATTATATTA-ATATTATT-TTTATATTATTGATATATTTCTATTT
1 ATATATTAGAAT-TTAT-TTATATATT-TTATTAAT-TTATTGATATATTTCTATTT
542805 TATTTATTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
55 12 0.26
56 13 0.28
57 17 0.36
58 5 0.11
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (56 bp):
ATATATTAGAATTTATTTATATATTTTATTAATTTATTGATATATTTCTATTTCTA
Found at i:542820 original size:39 final size:39
Alignment explanation
Indices: 542777--542853 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
542767 ATTAATATTA
*
542777 TTTTTATATTATTGATATATTTCTATTTTATTTATTTCC
1 TTTTTATATTATTGATATATTTCTATTTCATTTATTTCC
* * *
542816 TTTTTATATTATTTATCTATTTTTATTTCATTTATTTC
1 TTTTTATATTATTGATATATTTCTATTTCATTTATTTC
542854 ATTTGCATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.22, C:0.08, G:0.01, T:0.69
Consensus pattern (39 bp):
TTTTTATATTATTGATATATTTCTATTTCATTTATTTCC
Found at i:542857 original size:20 final size:19
Alignment explanation
Indices: 542776--542857 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 19
542766 TATTAATATT
* *
542776 ATTTTTATATTATTGATAT-
1 ATTTTTAT-TTATTTATTTC
*
542795 ATTTCTATTTTATTTATTTC
1 ATTTTTA-TTTATTTATTTC
* *
542815 CTTTTTATATTATTTATCT-
1 ATTTTTAT-TTATTTATTTC
542834 ATTTTTATTTCATTTATTTC
1 ATTTTTATTT-ATTTATTTC
542854 ATTT
1 ATTT
542858 GCATTTAGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
18 2 0.04
19 29 0.58
20 19 0.38
ACGTcount: A:0.23, C:0.07, G:0.01, T:0.68
Consensus pattern (19 bp):
ATTTTTATTTATTTATTTC
Found at i:547258 original size:17 final size:17
Alignment explanation
Indices: 547236--547270 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
547226 TATAGACTCG
*
547236 TTTAGATATACTTAGTA
1 TTTAGATATAATTAGTA
547253 TTTAGATATAATTAGTA
1 TTTAGATATAATTAGTA
547270 T
1 T
547271 AATATACGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (17 bp):
TTTAGATATAATTAGTA
Found at i:547784 original size:12 final size:12
Alignment explanation
Indices: 547767--547793 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
547757 ATTCCTTCTA
547767 AAAGTTCATATC
1 AAAGTTCATATC
547779 AAAGTTCATATC
1 AAAGTTCATATC
547791 AAA
1 AAA
547794 ATAGTACTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (12 bp):
AAAGTTCATATC
Found at i:557110 original size:6 final size:6
Alignment explanation
Indices: 557095--557124 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
557085 GCTTGCAATA
557095 TTTT-C TTTTGC TTTTGC TTTTGC TTTTGC T
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC T
557125 ATATATTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.00, C:0.17, G:0.13, T:0.70
Consensus pattern (6 bp):
TTTTGC
Found at i:557827 original size:17 final size:18
Alignment explanation
Indices: 557792--557827 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
557782 AGTTAATTTA
*
557792 ATTAAAAAATTAAATATC
1 ATTAAAAAAATAAATATC
557810 ATTAAAAAAATAAA-ATC
1 ATTAAAAAAATAAATATC
557827 A
1 A
557828 AATTATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
ATTAAAAAAATAAATATC
Found at i:558785 original size:18 final size:16
Alignment explanation
Indices: 558753--558796 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
558743 ATGGAATAAG
558753 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
558769 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
558783 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
558797 ACCCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:559020 original size:6 final size:6
Alignment explanation
Indices: 559009--559035 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
558999 GAATCAAAAG
559009 AGATGA AGATGA AGATGA AGATGA AGA
1 AGATGA AGATGA AGATGA AGATGA AGA
559036 AGACAAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (6 bp):
AGATGA
Found at i:559340 original size:89 final size:89
Alignment explanation
Indices: 559189--559368 Score: 351
Period size: 89 Copynumber: 2.0 Consensus size: 89
559179 CGTTAGGGAG
*
559189 ATAACGAAACTTAACGGCAGAGTTATCATTTCGTAACAAAATAATTACATAAGTGACTAAAATGT
1 ATAACGAAACTTAACGGCAGAGTTATCATTTCGTAACAAAATAATTACATAAATGACTAAAATGT
559254 AACCTAAAACAAATAAAAGTGACT
66 AACCTAAAACAAATAAAAGTGACT
559278 ATAACGAAACTTAACGGCAGAGTTATCATTTCGTAACAAAATAATTACATAAATGACTAAAATGT
1 ATAACGAAACTTAACGGCAGAGTTATCATTTCGTAACAAAATAATTACATAAATGACTAAAATGT
559343 AACCTAAAACAAATAAAAGTGACT
66 AACCTAAAACAAATAAAAGTGACT
559367 AT
1 AT
559369 TTTTATAGTT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (89 bp):
ATAACGAAACTTAACGGCAGAGTTATCATTTCGTAACAAAATAATTACATAAATGACTAAAATGT
AACCTAAAACAAATAAAAGTGACT
Found at i:560130 original size:2 final size:2
Alignment explanation
Indices: 560123--560170 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
560113 TTAAAAGAAT
560123 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
560165 TA TA TA
1 TA TA TA
560171 CTAAACTCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:567345 original size:77 final size:77
Alignment explanation
Indices: 567218--567373 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 77
567208 TGGTCCAAGA
567218 TAAAAACCAAGCATCATGGCAGATACGGACACAATACCACAACTTATCCCACTTTTGGTATAATC
1 TAAAAACCAAGCATCATGGCAGATACGGACACAATACCACAACTTATCCCACTTTTGGTATAATC
567283 CAACAGGAGCTT
66 CAACAGGAGCTT
*
567295 TAAAAACCAAGCATCATGGCAGATACGGACACAATACCACAACTTATCCCACTTTTGTTATAATC
1 TAAAAACCAAGCATCATGGCAGATACGGACACAATACCACAACTTATCCCACTTTTGGTATAATC
567360 CAACAGGAGCTT
66 CAACAGGAGCTT
567372 TA
1 TA
567374 GATTCTTGAA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (77 bp):
TAAAAACCAAGCATCATGGCAGATACGGACACAATACCACAACTTATCCCACTTTTGGTATAATC
CAACAGGAGCTT
Found at i:570604 original size:14 final size:14
Alignment explanation
Indices: 570585--570612 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
570575 TTTTTTTTAA
570585 TTTTTACCCAATTT
1 TTTTTACCCAATTT
570599 TTTTTACCCAATTT
1 TTTTTACCCAATTT
570613 GGTACCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTTACCCAATTT
Found at i:570681 original size:59 final size:60
Alignment explanation
Indices: 570596--570738 Score: 200
Period size: 59 Copynumber: 2.4 Consensus size: 60
570586 TTTTACCCAA
*
570596 TTTTTTTTACCCAATTTGGTACCTGAACTTGACACTTTTTT-CTAATTTGATACCTAAAC
1 TTTTTTTGACCCAATTTGGTACCTGAACTTGACACTTTTTTCCTAATTTGATACCTAAAC
* * * *
570655 TTTTTTTGACCTAATTTGGTATCTGAACTTGACATTTTTTTCCTAATTTGGTACCTAAAC
1 TTTTTTTGACCCAATTTGGTACCTGAACTTGACACTTTTTTCCTAATTTGATACCTAAAC
**
570715 TTTTTTAT-ATTCAATTTGGTACCT
1 TTTTTT-TGACCCAATTTGGTACCT
570739 AAATTTATTA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
59 37 0.51
60 35 0.48
61 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (60 bp):
TTTTTTTGACCCAATTTGGTACCTGAACTTGACACTTTTTTCCTAATTTGATACCTAAAC
Found at i:570998 original size:90 final size:90
Alignment explanation
Indices: 570895--571067 Score: 267
Period size: 90 Copynumber: 1.9 Consensus size: 90
570885 GATTAGGTGC
* ** *
570895 CAAATTAGGAAAAAGGGTCAAGTTT-AGGTACCAAATTGGACCCCAAAAAGTTTAAGTGCCAACT
1 CAAATTAGGAAAAAGGGTCAAATTTGA-GTACCAAATTGGACCAAAAAAAGTTTAAGTGCCAAAT
570959 TAAAAAAAAGTGTCAAGTTTAGGCAT
65 TAAAAAAAAGTGTCAAGTTTAGGCAT
* *
570985 CAAATTAGGAAAAAGTGTCAAATTTGAGTACCAAATTGGACCAAAAAAAGTTTAGGTGCCAAATT
1 CAAATTAGGAAAAAGGGTCAAATTTGAGTACCAAATTGGACCAAAAAAAGTTTAAGTGCCAAATT
*
571050 AAAAAAAAGTGTTAAGTT
66 AAAAAAAAGTGTCAAGTT
571068 CAAGTACCAA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
90 74 0.99
91 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (90 bp):
CAAATTAGGAAAAAGGGTCAAATTTGAGTACCAAATTGGACCAAAAAAAGTTTAAGTGCCAAATT
AAAAAAAAGTGTCAAGTTTAGGCAT
Done.