Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 62
Found at i:2472561 original size:31 final size:31
Alignment explanation
Indices: 2472523--2472616 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
2472513 AGGGTCGAGG
2472523 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2472554 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
2472585 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
2472616 G
1 G
2472617 GTCCTTCGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2473122 original size:21 final size:21
Alignment explanation
Indices: 2473097--2473139 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2473087 AAAGAATATA
2473097 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
2473118 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
2473139 T
1 T
2473140 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:2476027 original size:2 final size:2
Alignment explanation
Indices: 2476014--2476064 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2476004 AAGGGCCTCA
*
2476014 TC TC TC TA TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2476056 TC TC TC TC T
1 TC TC TC TC T
2476065 AAATCTTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2489634 original size:18 final size:19
Alignment explanation
Indices: 2489592--2489631 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
2489582 TTTGGTTTAC
2489592 GGAATGTAAGATTACAAGTG
1 GGAATGTAAGATTACAAG-G
*
2489612 GGAATGTAAGATTACCAGG
1 GGAATGTAAGATTACAAGG
2489631 G
1 G
2489632 AATAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.23
Consensus pattern (19 bp):
GGAATGTAAGATTACAAGG
Found at i:2489774 original size:18 final size:18
Alignment explanation
Indices: 2489751--2489798 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2489741 AAATTGTCCT
* *
2489751 TATTATATATTTGTATAA
1 TATTATATATTTGAAAAA
*
2489769 TATTATA-AGTTGAAAAA
1 TATTATATATTTGAAAAA
2489786 TATTTATATATTT
1 TA-TTATATATTT
2489799 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
TATTATATATTTGAAAAA
Found at i:2490948 original size:24 final size:24
Alignment explanation
Indices: 2490889--2490950 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
2490879 TATTTAATTT
* *
2490889 TTATTAAAATAAAAATATTTTAAA
1 TTATAAAAATAAAAATATTTCAAA
*
2490913 TTATAAATATAAAAATA-TTCAAA
1 TTATAAAAATAAAAATATTTCAAA
2490936 -TATTCAAAAATAAAA
1 TTA-T-AAAAATAAAA
2490951 TAAAAAATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 2 0.06
23 6 0.19
24 24 0.75
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (24 bp):
TTATAAAAATAAAAATATTTCAAA
Found at i:2501341 original size:35 final size:34
Alignment explanation
Indices: 2501268--2501374 Score: 110
Period size: 35 Copynumber: 3.1 Consensus size: 34
2501258 TGAAAGTATT
** **
2501268 AAAATGGTTTTC-AAGTTTGGTAACCAACTTTG-AA
1 AAAATGGTTTTCAAAGTTTGGTAA--ATGTTTGTTG
*
2501302 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTT-GTTG
* *
2501337 AAAATTGTTTTCAAAGTTTGGTAGATGTTTGTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTGTTG
2501371 AAAA
1 AAAA
2501375 ATGATAATGA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
33 4 0.06
34 19 0.31
35 39 0.63
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.41
Consensus pattern (34 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTGTTG
Found at i:2501376 original size:35 final size:36
Alignment explanation
Indices: 2501301--2501377 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 36
2501291 CCAACTTTGA
*
2501301 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCGTTG
* *
2501337 -AAAATTGTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCGTTG
2501371 AAAAATG
1 AAAAATG
2501378 ATAATGAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 3 0.08
35 33 0.92
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (36 bp):
AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCGTTG
Found at i:2505924 original size:37 final size:36
Alignment explanation
Indices: 2505825--2505943 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
2505815 TGGTAACCAA
2505825 CTTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
* *
2505862 CTTTG-AAAGTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
2505897 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
2505934 -GTTGAAAAAT
1 CTTTGAAAAAT
2505944 GATAATGGGA
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
35 33 0.45
36 14 0.19
37 27 0.36
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2507890 original size:21 final size:21
Alignment explanation
Indices: 2507865--2507908 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2507855 AATTTAGTTA
2507865 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
2507886 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
2507907 AT
1 AT
2507909 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:2507922 original size:28 final size:28
Alignment explanation
Indices: 2507885--2507938 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
2507875 TAGTATAAAT
*
2507885 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
*
2507913 TATTAATTTGTTTGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
2507939 ATTAGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:2508307 original size:5 final size:5
Alignment explanation
Indices: 2508297--2508324 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2508287 AAAGAAACAA
2508297 GAAAG GAAAG GAAAG GAAAG GAAAG GAA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAA
2508325 GAATGCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:2508371 original size:14 final size:14
Alignment explanation
Indices: 2508352--2508378 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2508342 GTAATTTATT
2508352 ATTTTTTGTTGTTC
1 ATTTTTTGTTGTTC
2508366 ATTTTTTGTTGTT
1 ATTTTTTGTTGTT
2508379 GTGTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
ATTTTTTGTTGTTC
Found at i:2508464 original size:17 final size:17
Alignment explanation
Indices: 2508442--2508480 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2508432 ATTTATTCCC
2508442 GTTTAAAAAAATATT-GT
1 GTTTAAAAAAAT-TTAGT
*
2508459 GTTTAAAAATATTTAGT
1 GTTTAAAAAAATTTAGT
2508476 GTTTA
1 GTTTA
2508481 TTTTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (17 bp):
GTTTAAAAAAATTTAGT
Found at i:2508501 original size:82 final size:84
Alignment explanation
Indices: 2508400--2508562 Score: 276
Period size: 84 Copynumber: 2.0 Consensus size: 84
2508390 AATTAGTTAG
* *
2508400 TTTATATTAGAGTATATAAAATTAATTTG-TTAATTTATTCCCGTTT-AAAAAAATATTGTGTTT
1 TTTATATTAGAGTATATAAAATTAATTTGTTTAATTTATTACAGTTTAAAAAAAATATTGTGTTT
2508463 AAAAATATTTAGTGTTTAT
66 AAAAATATTTAGTGTTTAT
* *
2508482 TTTATATTATATTATATAAAATTAATTTGTTTAATTTATTACAGTTTAAAAAAAATATTGTGTTT
1 TTTATATTAGAGTATATAAAATTAATTTGTTTAATTTATTACAGTTTAAAAAAAATATTGTGTTT
2508547 AAAAATATTTAGTGTT
66 AAAAATATTTAGTGTT
2508563 GTTTTAAAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
82 27 0.36
83 15 0.20
84 33 0.44
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (84 bp):
TTTATATTAGAGTATATAAAATTAATTTGTTTAATTTATTACAGTTTAAAAAAAATATTGTGTTT
AAAAATATTTAGTGTTTAT
Found at i:2510052 original size:14 final size:14
Alignment explanation
Indices: 2510033--2510075 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
2510023 TATGATTTAC
*
2510033 TAATGATTTTATAA
1 TAATGATTTAATAA
*
2510047 TAATGATTTAATAC
1 TAATGATTTAATAA
*
2510061 TAATAATTTAATAA
1 TAATGATTTAATAA
2510075 T
1 T
2510076 TATTACTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:2510186 original size:18 final size:18
Alignment explanation
Indices: 2510159--2510195 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2510149 GTCGAATTTA
*
2510159 TTAATGATTTTTAAATAT
1 TTAATAATTTTTAAATAT
2510177 TTAATAATTTTTAAATAT
1 TTAATAATTTTTAAATAT
2510195 T
1 T
2510196 GATACTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTAATAATTTTTAAATAT
Found at i:2510249 original size:24 final size:24
Alignment explanation
Indices: 2510201--2510245 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2510191 ATATTGATAC
*
2510201 TAATGATTTACTAATTATTATTAA
1 TAATGATTTACTAATTAATATTAA
*
2510225 TAATGATTTA-TTATTAATATT
1 TAATGATTTACTAATTAATATT
2510246 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATGATTTACTAATTAATATTAA
Found at i:2510252 original size:17 final size:17
Alignment explanation
Indices: 2510212--2510253 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2510202 AATGATTTAC
2510212 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
2510229 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
2510246 TAATTATT
1 TAATTATT
2510254 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:2512645 original size:27 final size:29
Alignment explanation
Indices: 2512610--2512674 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
2512600 AAAATATAAC
*
2512610 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
2512637 TTAAATA-TTAGACTAACTAACATACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
2512665 TTAATTATTT
1 TTAAATATTT
2512675 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:2512787 original size:21 final size:25
Alignment explanation
Indices: 2512729--2512784 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
2512719 TTTATGTATG
2512729 ATATAACTTAAACTAAACAAACAATA
1 ATATAACTTAAACTAAACAAAC-ATA
2512755 ATATAACTTAAACT-AACAAAC-TA
1 ATATAACTTAAACTAAACAAACATA
2512778 AT-TAACT
1 ATATAACT
2512785 AAAATTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.17
23 4 0.13
25 7 0.23
26 14 0.47
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (25 bp):
ATATAACTTAAACTAAACAAACATA
Found at i:2512945 original size:29 final size:29
Alignment explanation
Indices: 2512912--2512971 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
2512902 TCCATGCACA
* *
2512912 CTCCAAGCTCGCCTGGATGCCATGGCGAC
1 CTCCAAGCTCACCCGGATGCCATGGCGAC
2512941 CTCCAAGCTCACCCGGATGCCATGGCGAC
1 CTCCAAGCTCACCCGGATGCCATGGCGAC
2512970 CT
1 CT
2512972 ACATGGGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.18, C:0.40, G:0.25, T:0.17
Consensus pattern (29 bp):
CTCCAAGCTCACCCGGATGCCATGGCGAC
Found at i:2517191 original size:11 final size:11
Alignment explanation
Indices: 2517177--2517201 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2517167 TTAGATATTA
2517177 TTTAAATTAAT
1 TTTAAATTAAT
2517188 TTTAAATTAAT
1 TTTAAATTAAT
2517199 TTT
1 TTT
2517202 TTTTAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTAAATTAAT
Found at i:2519210 original size:21 final size:22
Alignment explanation
Indices: 2519186--2519228 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2519176 ATTTAGCTTA
*
2519186 TATAAATA-TATTATTTTTAAT
1 TATAAAAAGTATTATTTTTAAT
*
2519207 TATAAAAAGTTTTATTTTTAAT
1 TATAAAAAGTATTATTTTTAAT
2519229 GTATTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATAAAAAGTATTATTTTTAAT
Found at i:2529823 original size:30 final size:30
Alignment explanation
Indices: 2529775--2530033 Score: 152
Period size: 29 Copynumber: 8.6 Consensus size: 30
2529765 CACGTATTAA
* *
2529775 TATTAAAAATATTTTTATTTTTATTTTGAA-T
1 TATTAAATATA-TTTTATTTTTATCTT-AACT
* * *
2529806 TATTAAATATATTTTATTCTTGTCTTAACC
1 TATTAAATATATTTTATTTTTATCTTAACT
* * *
2529836 TA-AAAATAAATTTTATTTTTATTTTAACT
1 TATTAAATATATTTTATTTTTATCTTAACT
* * * * *
2529865 TA--AATTATATTATAATCTTATCCTAACT
1 TATTAAATATATTTTATTTTTATCTTAACT
* *
2529893 TA-AAAATATATTTTATTTTTATCTTAAAT
1 TATTAAATATATTTTATTTTTATCTTAACT
* * *
2529922 T-TTAAAAAGTATATATATTTTTTATTTTAACT
1 TATTAAATA-TAT-TTTA-TTTTTATCTTAACT
* * * *
2529954 TATTACATATATTATGATGTTCTTAACTTAAAT
1 TATTAAATATATT-TTAT-TT-TTATCTTAACT
* * * * * *
2529987 GATTAAATATATTCTAGTCTTACCTTAAAT
1 TATTAAATATATTTTATTTTTATCTTAACT
2530017 TATTAAATATATTTTAT
1 TATTAAATATATTTTAT
2530034 CCTTATTTTA
Statistics
Matches: 172, Mismatches: 46, Indels: 21
0.72 0.19 0.09
Matches are distributed among these distances:
28 21 0.12
29 50 0.29
30 41 0.24
31 16 0.09
32 20 0.12
33 24 0.14
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (30 bp):
TATTAAATATATTTTATTTTTATCTTAACT
Found at i:2529906 original size:57 final size:57
Alignment explanation
Indices: 2529777--2529919 Score: 173
Period size: 57 Copynumber: 2.5 Consensus size: 57
2529767 CGTATTAATA
* * * *
2529777 TTAAAAATAT-TTTTATTTTTATTTTGAATTATTAAATATATTTTATTCTTGTCTTAAC
1 TTAAAAATATATTTTATTTTTATTTT-AATTA-TAAATATATTATAATCTTATCCTAAC
* * *
2529835 CTAAAAATAAATTTTATTTTTATTTTAACTTA-AATTATATTATAATCTTATCCTAAC
1 TTAAAAATATATTTTATTTTTATTTTAA-TTATAAATATATTATAATCTTATCCTAAC
*
2529892 TTAAAAATATATTTTATTTTTATCTTAA
1 TTAAAAATATATTTTATTTTTATTTTAA
2529920 ATTTTAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
57 45 0.62
58 10 0.14
59 18 0.25
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.55
Consensus pattern (57 bp):
TTAAAAATATATTTTATTTTTATTTTAATTATAAATATATTATAATCTTATCCTAAC
Found at i:2530083 original size:30 final size:30
Alignment explanation
Indices: 2530018--2530091 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
2530008 ACCTTAAATT
2530018 ATTAAATATAT-T-TTATCCTTATTTTAAC
1 ATTAAATATATATATTATCCTTATTTTAAC
* * *
2530046 GTCAAATATATATATTATTCTTATTTTTAA-
1 ATTAAATATATATATTATCCTTA-TTTTAAC
*
2530076 ATTAAATATGTATATT
1 ATTAAATATATATATT
2530092 TTATTTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 9 0.24
29 1 0.03
30 21 0.57
31 6 0.16
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (30 bp):
ATTAAATATATATATTATCCTTATTTTAAC
Found at i:2530277 original size:27 final size:28
Alignment explanation
Indices: 2530174--2530308 Score: 96
Period size: 28 Copynumber: 4.6 Consensus size: 28
2530164 TTAAAATATT
*
2530174 ATAAGAATAAAATATAAATATTTAAGTTAAG
1 ATAAGAATAAAATAT--AT-TTTAAGTTAAA
* * * *
2530205 GTAAGAATAAATTATTTTTTAAAATTAATA
1 ATAAGAATAAAATATATTTT-AAGTTAA-A
*
2530235 A-AA-AATTAAAATATATATTTTAGGTTAAA
1 ATAAGAA-T-AAA-ATATATTTTAAGTTAAA
**
2530264 ATAAGAAT-AAATATATTTTTAAGTTATG
1 ATAAGAATAAAATATA-TTTTAAGTTAAA
2530292 ATAAGAATAAAATATAT
1 ATAAGAATAAAATATAT
2530309 AGTTTAATGT
Statistics
Matches: 82, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
27 5 0.06
28 25 0.30
29 19 0.23
30 11 0.13
31 22 0.27
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (28 bp):
ATAAGAATAAAATATATTTTAAGTTAAA
Found at i:2530321 original size:59 final size:56
Alignment explanation
Indices: 2530162--2530321 Score: 153
Period size: 59 Copynumber: 2.7 Consensus size: 56
2530152 TTTATCTTAG
* **
2530162 TTTTAAAATATTATAAGAATAAAATATAAATATTTAAGTTAAGGTAAGAATAAATTATT
1 TTTTAAAAT-TAATAAGAATAAAATAT--ATATTTAAGTTAAAATAAGAATAAATTATT
* *
2530221 TTTTAAAATTAATAAAAAATTAAAATATATATTTTAGGTTAAAATAAGAATAAA-TATAT
1 TTTTAAAATTAAT-AAGAA-TAAAATATATA-TTTAAGTTAAAATAAGAATAAATTAT-T
*
2530280 TTTT-AAGTTATGATAAGAATAAAATATATAGTTTAATGTTAA
1 TTTTAAAATTA--ATAAGAATAAAATATATA-TTTAA-GTTAA
2530322 GATGTTAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
58 29 0.34
59 46 0.54
60 10 0.12
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (56 bp):
TTTTAAAATTAATAAGAATAAAATATATATTTAAGTTAAAATAAGAATAAATTATT
Found at i:2530344 original size:18 final size:18
Alignment explanation
Indices: 2530311--2530360 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
2530301 AAATATATAG
*
2530311 TTTAATGTTAAGATGTTAA
1 TTTAAT-TTAAGATGTGAA
*
2530330 TTTAATTTAATATGTGAA
1 TTTAATTTAAGATGTGAA
*
2530348 TTTAAGTTAAGAT
1 TTTAATTTAAGAT
2530361 ATATAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (18 bp):
TTTAATTTAAGATGTGAA
Found at i:2531261 original size:23 final size:23
Alignment explanation
Indices: 2531235--2531279 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2531225 CACTACAGCT
*
2531235 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
2531258 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2531280 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:2533375 original size:23 final size:23
Alignment explanation
Indices: 2533349--2533393 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2533339 CACTACAGCT
*
2533349 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
2533372 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2533394 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:2535188 original size:64 final size:66
Alignment explanation
Indices: 2535090--2535214 Score: 193
Period size: 64 Copynumber: 1.9 Consensus size: 66
2535080 TAATGAAGGT
* *
2535090 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTTAATGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAATGGG
2535154 G
66 G
*
2535155 ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAA
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAA
2535215 ATTCATGCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
63 1 0.02
64 29 0.53
65 25 0.45
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (66 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAATGGG
G
Found at i:2535223 original size:64 final size:64
Alignment explanation
Indices: 2535090--2535232 Score: 184
Period size: 64 Copynumber: 2.2 Consensus size: 64
2535080 TAATGAAGGT
* * *
2535090 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCCATTCGATGTTTCTATTTAAT-GGC
*
2535155 ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAAT-
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCCATTCGATG-TTTCTATTT-AATG
*
2535217 TC
63 GC
2535219 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2535233 CTTAAACAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 43 0.61
65 23 0.33
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCCATTCGATGTTTCTATTTAATGGC
Found at i:2536380 original size:21 final size:21
Alignment explanation
Indices: 2536356--2536400 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2536346 TTTTGTTCGT
* *
2536356 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2536377 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2536398 TTG
1 TTG
2536401 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2544721 original size:3 final size:3
Alignment explanation
Indices: 2544713--2544738 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2544703 CTTTCGCAGT
2544713 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
2544739 GTTGATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2546605 original size:14 final size:14
Alignment explanation
Indices: 2546586--2546612 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2546576 GATGTGTTTG
2546586 AATTTAGAGATTTA
1 AATTTAGAGATTTA
2546600 AATTTAGAGATTT
1 AATTTAGAGATTT
2546613 TTAGGGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (14 bp):
AATTTAGAGATTTA
Found at i:2546825 original size:22 final size:23
Alignment explanation
Indices: 2546794--2546840 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
2546784 TTAGAATAAT
*
2546794 AATAATAATTTTAAAATTTTTTA
1 AATAATAATTTTAAAATTTTATA
2546817 AATAA-AATTTTAAAATTTTATA
1 AATAATAATTTTAAAATTTTATA
2546839 AA
1 AA
2546841 CATGTCACGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATAATTTTAAAATTTTATA
Found at i:2549018 original size:15 final size:15
Alignment explanation
Indices: 2548994--2549041 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
2548984 GAGAAATGAA
*
2548994 ATAAGGTATGTGATT
1 ATAAGATATGTGATT
*
2549009 ATAAGATATGTGATA
1 ATAAGATATGTGATT
* * *
2549024 ATAGGTTATATGATT
1 ATAAGATATGTGATT
2549039 ATA
1 ATA
2549042 TGATCATAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.40
Consensus pattern (15 bp):
ATAAGATATGTGATT
Found at i:2549532 original size:23 final size:23
Alignment explanation
Indices: 2549464--2549524 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
2549454 ACATTTTATA
2549464 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
2549487 TGACACTTCGATGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
2549510 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
2549525 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:2550464 original size:37 final size:37
Alignment explanation
Indices: 2550419--2550498 Score: 160
Period size: 37 Copynumber: 2.2 Consensus size: 37
2550409 ATATAATATT
2550419 TTAATTACTAAGATCGTTTAGTTTGTGTAATATTTTG
1 TTAATTACTAAGATCGTTTAGTTTGTGTAATATTTTG
2550456 TTAATTACTAAGATCGTTTAGTTTGTGTAATATTTTG
1 TTAATTACTAAGATCGTTTAGTTTGTGTAATATTTTG
2550493 TTAATT
1 TTAATT
2550499 TTAAATTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.53
Consensus pattern (37 bp):
TTAATTACTAAGATCGTTTAGTTTGTGTAATATTTTG
Found at i:2555899 original size:14 final size:14
Alignment explanation
Indices: 2555859--2555903 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
2555849 TTTGGCTTAA
2555859 TTGTCTTATCTTTATT
1 TTGT-TTATCTTT-TT
*
2555875 TTTTTTAATCTTTTT
1 TTGTTT-ATCTTTTT
2555890 TTGTTTATCTTTTT
1 TTGTTTATCTTTTT
2555904 GTTTTAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 8 0.31
15 9 0.35
16 9 0.35
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (14 bp):
TTGTTTATCTTTTT
Found at i:2555913 original size:14 final size:13
Alignment explanation
Indices: 2555873--2555913 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
2555863 CTTATCTTTA
2555873 TTTTTTTTAATCT
1 TTTTTTTTAATCT
*
2555886 TTTTTTGTTTATCT
1 TTTTTT-TTAATCT
2555900 TTTTGTTTTAATCT
1 TTTT-TTTTAATCT
2555914 CCATTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.25
14 16 0.67
15 2 0.08
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (13 bp):
TTTTTTTTAATCT
Found at i:2558807 original size:23 final size:23
Alignment explanation
Indices: 2558781--2558826 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2558771 CACCACAGCT
* *
2558781 CGTATAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
2558804 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2558827 TATAATGATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2559001 original size:150 final size:149
Alignment explanation
Indices: 2558804--2559108 Score: 547
Period size: 150 Copynumber: 2.0 Consensus size: 149
2558794 TGAAGTGCCA
* *
2558804 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
2558869 CATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGTTCCACAGAATAT
66 CATATACATATACTAGGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGTTCCAAAGAATAT
*
2558934 ATATATATCCCGAAGGACCG
130 ACATATATCCCGAAGGACCG
*
2558954 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAATGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
2559019 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
*
2559084 CATATGTCCCGAAGGACCG
131 CATATATCCCGAAGGACCG
2559103 CGTAGA
1 CGTAGA
2559109 CCCTCTACCC
Statistics
Matches: 149, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
149 52 0.35
150 97 0.65
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATATCCCGAAGGACCG
Found at i:2560278 original size:19 final size:17
Alignment explanation
Indices: 2560246--2560280 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
2560236 ACGTTTGGAG
2560246 AAGGAAGAGAAGAAGAT
1 AAGGAAGAGAAGAAGAT
2560263 AAGGAAGAAGGAAGAAGA
1 AAGGAAG-A-GAAGAAGA
2560281 AATGAGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (17 bp):
AAGGAAGAGAAGAAGAT
Found at i:2565835 original size:23 final size:23
Alignment explanation
Indices: 2565809--2565853 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2565799 CACCACAGCT
* *
2565809 CGTATAAATGCACTGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
2565832 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2565854 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:2567299 original size:19 final size:17
Alignment explanation
Indices: 2567267--2567301 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
2567257 ACGTTTGGAG
2567267 AAGGAAGAGAAGAAGAT
1 AAGGAAGAGAAGAAGAT
2567284 AAGGAAGAAGGAAGAAGA
1 AAGGAAG-A-GAAGAAGA
2567302 AATGAGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (17 bp):
AAGGAAGAGAAGAAGAT
Found at i:2571542 original size:14 final size:14
Alignment explanation
Indices: 2571521--2571556 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2571511 ACCGTCCAAT
2571521 GACCCTGCCATACA
1 GACCCTGCCATACA
*
2571535 GGCCCTGCCATACA
1 GACCCTGCCATACA
2571549 GACCCTGC
1 GACCCTGC
2571557 TAATGTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.44, G:0.19, T:0.14
Consensus pattern (14 bp):
GACCCTGCCATACA
Found at i:2573432 original size:13 final size:13
Alignment explanation
Indices: 2573414--2573438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2573404 TTGCGTTGTT
2573414 TATTTTAAATTTA
1 TATTTTAAATTTA
2573427 TATTTTAAATTT
1 TATTTTAAATTT
2573439 TTAATATTTT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTAAATTTA
Found at i:2573472 original size:20 final size:20
Alignment explanation
Indices: 2573421--2573477 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
2573411 GTTTATTTTA
* *
2573421 AATTTATATT-TTAAATTTTT
1 AATTTTTATTCTTAAA-TTAT
2573441 AATATTTT-TTCTTAAATTAT
1 AAT-TTTTATTCTTAAATTAT
*
2573461 AATTTTTATTCTAAAAT
1 AATTTTTATTCTTAAAT
2573478 AATTTTAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 4 0.13
20 19 0.61
21 8 0.26
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTTTTATTCTTAAATTAT
Found at i:2573891 original size:23 final size:23
Alignment explanation
Indices: 2573865--2573928 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
2573855 TCATAAATAA
*
2573865 TATTAATTTATGATT-ATTTATTT
1 TATTAATTT-TGATTAATATATTT
* *
2573888 TATTTATTTTTATTAATATATTT
1 TATTAATTTTGATTAATATATTT
*
2573911 TATTTAAATTTTAATTAA
1 TA-TT-AATTTTGATTAA
2573929 AGATACATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 4 0.12
23 17 0.52
24 2 0.06
25 10 0.30
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TATTAATTTTGATTAATATATTT
Found at i:2575419 original size:3 final size:3
Alignment explanation
Indices: 2575413--2575441 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2575403 TATTAGTAAC
2575413 TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2575442 AAATGTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2583570 original size:28 final size:28
Alignment explanation
Indices: 2583539--2583592 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
2583529 TTCATACATG
2583539 AATTCAAAACGAATGAAGAGTTTACACA
1 AATTCAAAACGAATGAAGAGTTTACACA
2583567 AATTCAAAACGAATGAAGAGTTTACA
1 AATTCAAAACGAATGAAGAGTTTACA
2583593 TCGATTACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.22
Consensus pattern (28 bp):
AATTCAAAACGAATGAAGAGTTTACACA
Found at i:2587877 original size:39 final size:39
Alignment explanation
Indices: 2587833--2587910 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
2587823 CCTTGCATGG
*
2587833 TAAGAAAGATCCACTTCCTAGGATAAACTGCAGTAAATT
1 TAAGAAAGATCAACTTCCTAGGATAAACTGCAGTAAATT
2587872 TAAGAAAGATCAACTTCCTAGGATAAACTGCAGTAAATT
1 TAAGAAAGATCAACTTCCTAGGATAAACTGCAGTAAATT
2587911 ATTTTAACTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (39 bp):
TAAGAAAGATCAACTTCCTAGGATAAACTGCAGTAAATT
Found at i:2593281 original size:22 final size:22
Alignment explanation
Indices: 2593251--2593297 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2593241 TATAATTGAG
*
2593251 TATATTATTATAATATTAAAAA
1 TATAATATTATAATATTAAAAA
*
2593273 TATAATATTATATTATTAAAAA
1 TATAATATTATAATATTAAAAA
2593295 TAT
1 TAT
2593298 TTTAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATAATATTATAATATTAAAAA
Found at i:2593351 original size:18 final size:19
Alignment explanation
Indices: 2593328--2593365 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2593318 TTTAAATGTT
2593328 ATTAAAATAT-TTTCTAAA
1 ATTAAAATATATTTCTAAA
*
2593346 ATTAAATTATATTTCTAAA
1 ATTAAAATATATTTCTAAA
2593365 A
1 A
2593366 AATATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTAAAATATATTTCTAAA
Found at i:2593526 original size:21 final size:20
Alignment explanation
Indices: 2593500--2593558 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
2593490 TTGAGTATAT
2593500 TATTATAATATTTTTAAATAA
1 TATTATAATATTTTTAAA-AA
*
2593521 TATTAT-AT-TATTTAAAAA
1 TATTATAATATTTTTAAAAA
2593539 TATTAATAAATATATTTTAA
1 TATT-AT-AATAT-TTTTAA
2593559 GTGTTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 6 0.19
19 9 0.29
20 2 0.06
21 8 0.26
22 1 0.03
23 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAATATTTTTAAAAA
Found at i:2593540 original size:18 final size:18
Alignment explanation
Indices: 2593507--2593543 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2593497 TATTATTATA
2593507 ATATTTTTAAATAATATT
1 ATATTTTTAAATAATATT
2593525 ATATTATTTAAA-AATATT
1 ATATT-TTTAAATAATATT
2593543 A
1 A
2593544 ATAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTTTTAAATAATATT
Found at i:2596214 original size:10 final size:10
Alignment explanation
Indices: 2596185--2596219 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
2596175 ACAATTTTAT
2596185 TTTAAAATAAA
1 TTTAAAA-AAA
2596196 TTT-AAAAAA
1 TTTAAAAAAA
2596205 TTTAAAAAAA
1 TTTAAAAAAA
2596215 TTTAA
1 TTTAA
2596220 GATATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.26
10 14 0.61
11 3 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:2596229 original size:19 final size:20
Alignment explanation
Indices: 2596187--2596229 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
2596177 AATTTTATTT
*
2596187 TAAAATAAATTTAAAAAATT
1 TAAAATAAATTTAAAAAATA
* *
2596207 TAAAA-AAATTTAAGATATA
1 TAAAATAAATTTAAAAAATA
2596226 TAAA
1 TAAA
2596230 TATATTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
TAAAATAAATTTAAAAAATA
Found at i:2596272 original size:25 final size:25
Alignment explanation
Indices: 2596213--2596272 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
2596203 AATTTAAAAA
*
2596213 AATTTAAGATATATAAATATATTATT
1 AATTTAA-ATATATAAATATATTAAT
** *
2596239 AATAAAAATATTTAAA-ATATATAAT
1 AATTTAAATATATAAATATAT-TAAT
2596264 AATTTAAAT
1 AATTTAAAT
2596273 TTATTATATT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
AATTTAAATATATAAATATATTAAT
Found at i:2598495 original size:22 final size:23
Alignment explanation
Indices: 2598467--2598509 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2598457 TATTAAATAA
2598467 ATAAATAA-TAAAACATTTATCT
1 ATAAATAATTAAAACATTTATCT
*
2598489 ATAAATAATTAAAATATTTAT
1 ATAAATAATTAAAACATTTAT
2598510 TTTAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAAATAATTAAAACATTTATCT
Found at i:2598642 original size:43 final size:43
Alignment explanation
Indices: 2598592--2598674 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 43
2598582 AAATAAAACT
*
2598592 AAAATAATATATATATATA-TATATAAT-TTAAAATATTTATGTA
1 AAAATAATATATATATA-ACT-TATAATAATAAAATATTTATGTA
2598635 AAAATAATATATATATAACTTATAATAATAAAATATTTAT
1 AAAATAATATATATATAACTTATAATAATAAAATATTTAT
2598675 TTAGAATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 7 0.19
43 30 0.81
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (43 bp):
AAAATAATATATATATAACTTATAATAATAAAATATTTATGTA
Found at i:2600346 original size:3 final size:3
Alignment explanation
Indices: 2600338--2600388 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
2600328 ATTATTTATT
2600338 TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
2600384 TAA TA
1 TAA TA
2600389 TATGAAAGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2612180 original size:21 final size:21
Alignment explanation
Indices: 2612091--2612203 Score: 101
Period size: 20 Copynumber: 5.6 Consensus size: 21
2612081 AAATGACCAA
**
2612091 CAAATTCGCAACGCGA-ACTC
1 CAAATTCGCAACGCGAGTTTC
** * *
2612111 CACTTTCACAACAC-AGTTTC
1 CAAATTCGCAACGCGAGTTTC
*
2612131 CAAATTCGCAACTC-AGTTTC
1 CAAATTCGCAACGCGAGTTTC
* *
2612151 TACAA-TCGCAACGCGATTTTC
1 CA-AATTCGCAACGCGAGTTTC
2612172 CAAATTCGCAACGCG-GTTTC
1 CAAATTCGCAACGCGAGTTTC
2612192 CAAATTCGCAAC
1 CAAATTCGCAAC
2612204 ACGGAATTTT
Statistics
Matches: 74, Mismatches: 15, Indels: 8
0.76 0.15 0.08
Matches are distributed among these distances:
19 1 0.01
20 55 0.74
21 18 0.24
ACGTcount: A:0.31, C:0.32, G:0.12, T:0.25
Consensus pattern (21 bp):
CAAATTCGCAACGCGAGTTTC
Found at i:2612191 original size:41 final size:43
Alignment explanation
Indices: 2612127--2612238 Score: 128
Period size: 41 Copynumber: 2.7 Consensus size: 43
2612117 CACAACACAG
* *
2612127 TTTCCAAATTCGCAACTCAGTTTCTACAA-TCGCAACGC-G-AT
1 TTTCCAAATTCGCAACTCGGTTTCTA-AATTCGCAACACGGAAT
* *
2612168 TTTCCAAATTCGCAACGCGGTTTCCAAATTCGCAACACGGAAT
1 TTTCCAAATTCGCAACTCGGTTTCTAAATTCGCAACACGGAAT
*
2612211 TTT---AATTCGCAACTCGGTTTCTGAATTC
1 TTTCCAAATTCGCAACTCGGTTTCTAAATTC
2612239 ACAATGCGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
40 24 0.39
41 31 0.51
42 1 0.02
43 5 0.08
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (43 bp):
TTTCCAAATTCGCAACTCGGTTTCTAAATTCGCAACACGGAAT
Found at i:2612237 original size:20 final size:19
Alignment explanation
Indices: 2612133--2612238 Score: 70
Period size: 20 Copynumber: 5.3 Consensus size: 19
2612123 ACAGTTTCCA
* *
2612133 AATTCGCAACTCAGTTTCT
1 AATTCGCAACGCGGTTTCT
* * *
2612152 ACAATCGCAACGCGATTTTCCA
1 A-ATTCGCAACGCG-GTTT-CT
*
2612174 AATTCGCAACGCGGTTTCCA
1 AATTCGCAACGCGGTTT-CT
*
2612194 AATTCGCAACACGGAATTT-T
1 AATTCGCAACGCGG--TTTCT
*
2612214 AATTCGCAACTCGGTTTCT
1 AATTCGCAACGCGGTTTCT
2612233 GAATTC
1 -AATTC
2612239 ACAATGCGAA
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
18 3 0.04
19 2 0.03
20 46 0.66
21 14 0.20
22 5 0.07
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (19 bp):
AATTCGCAACGCGGTTTCT
Found at i:2612304 original size:40 final size:40
Alignment explanation
Indices: 2612260--2612351 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 40
2612250 TTCTTTTTCA
*
2612260 CAACAC-AAGTTTCCTTTTCGCAAC-AAGATTTTCTAAATCG
1 CAACACGAA-TTTCCTTTTCGCAACTAA-ATTTTCGAAATCG
** * *
2612300 CAACACGAATTTTGTTTTCGCAACTCAATTTTCGAATTCG
1 CAACACGAATTTCCTTTTCGCAACTAAATTTTCGAAATCG
2612340 CAACACGAATTT
1 CAACACGAATTT
2612352 TAATTTCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
40 42 0.93
41 3 0.07
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (40 bp):
CAACACGAATTTCCTTTTCGCAACTAAATTTTCGAAATCG
Found at i:2612320 original size:20 final size:19
Alignment explanation
Indices: 2612297--2612385 Score: 74
Period size: 20 Copynumber: 4.6 Consensus size: 19
2612287 ATTTTCTAAA
**
2612297 TCGCAACACGAATTTTGTTT
1 TCGCAACAC-AATTTTAATT
*
2612317 TCGCAACTCAATTTTCGAA-T
1 TCGCAACACAATTTT--AATT
2612337 TCGCAACACGAATTTTAATT
1 TCGCAACAC-AATTTTAATT
* * *
2612357 TCGCAATA-ACTTTTATTT
1 TCGCAACACAATTTTAATT
2612375 TCGCAACACAA
1 TCGCAACACAA
2612386 ATGTTTTGGG
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
18 15 0.27
19 9 0.16
20 25 0.45
21 6 0.11
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.36
Consensus pattern (19 bp):
TCGCAACACAATTTTAATT
Found at i:2612352 original size:40 final size:40
Alignment explanation
Indices: 2612274--2612362 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
2612264 ACAAGTTTCC
* *
2612274 TTTTCGCAACAAGATTTTCTAAATCGCAACACGAATTTTG
1 TTTTCGCAACAAGATTTTCGAAATCGCAACACGAATTTTA
* *
2612314 TTTTCGCAACTCA-ATTTTCGAATTCGCAACACGAATTTTA
1 TTTTCGCAAC-AAGATTTTCGAAATCGCAACACGAATTTTA
*
2612354 ATTTCGCAA
1 TTTTCGCAA
2612363 TAACTTTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 42 0.98
41 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (40 bp):
TTTTCGCAACAAGATTTTCGAAATCGCAACACGAATTTTA
Found at i:2613172 original size:12 final size:12
Alignment explanation
Indices: 2613151--2613184 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2613141 ACCACATTTC
*
2613151 CAATACCAAACA
1 CAATATCAAACA
2613163 CAATATCAAACA
1 CAATATCAAACA
*
2613175 CAATCTCAAA
1 CAATATCAAA
2613185 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:2613361 original size:24 final size:24
Alignment explanation
Indices: 2613309--2613363 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2613299 AGTATTTGAA
*
2613309 ATTTT-ATCTTGGTCAATACCCGG
1 ATTTTGATCTTGGTCAATACCCAG
* *
2613332 ACTTTGATCTTGGTCAATACTCAG
1 ATTTTGATCTTGGTCAATACCCAG
2613356 ATTTTGAT
1 ATTTTGAT
2613364 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (24 bp):
ATTTTGATCTTGGTCAATACCCAG
Found at i:2615667 original size:18 final size:18
Alignment explanation
Indices: 2615634--2615669 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2615624 AAGCAAAAGG
**
2615634 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
2615652 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
2615670 CAACCGACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:2617555 original size:21 final size:21
Alignment explanation
Indices: 2617530--2617627 Score: 160
Period size: 21 Copynumber: 4.7 Consensus size: 21
2617520 GTGAATCGGG
* * *
2617530 CTCTTGAACGGTGTGAGGGAC
1 CTCTTGAACGATGAGAGGGGC
2617551 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
2617572 CTCTTGAACGATGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
2617593 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
2617614 CTCTTGAACGATGA
1 CTCTTGAACGATGA
2617628 CAAGTGAATC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:2618044 original size:21 final size:21
Alignment explanation
Indices: 2618020--2618069 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2618010 ACCATTGTCG
*
2618020 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
* **
2618041 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCACCGACCTCA
2618062 TCACGTAA
1 TCACGTAA
2618070 CTCCCCTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:2622794 original size:13 final size:13
Alignment explanation
Indices: 2622776--2622804 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2622766 CAAGTTAGAT
2622776 ACACTATAAACAG
1 ACACTATAAACAG
2622789 ACACTATAAACAG
1 ACACTATAAACAG
2622802 ACA
1 ACA
2622805 TGATATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.24, G:0.07, T:0.14
Consensus pattern (13 bp):
ACACTATAAACAG
Found at i:2623545 original size:22 final size:22
Alignment explanation
Indices: 2623511--2623559 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2623501 TAGAGAGGGG
* *
2623511 TCGCCGAATATGGGGACGAATT
1 TCGCCGAAGATGGGGACGAATA
* *
2623533 TCGCCGGAGATGGGGACGGATA
1 TCGCCGAAGATGGGGACGAATA
2623555 TCGCC
1 TCGCC
2623560 ATAGAGAGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.37, T:0.18
Consensus pattern (22 bp):
TCGCCGAAGATGGGGACGAATA
Found at i:2623737 original size:20 final size:20
Alignment explanation
Indices: 2623712--2623779 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
2623702 CACACTTTGT
*
2623712 GAATTTGACTTTTGTGTTGC
1 GAATTTGACTTCTGTGTTGC
2623732 GAATTTGACTTCTGTGTTGC
1 GAATTTGACTTCTGTGTTGC
*
2623752 G-ATTT-ACAAATTCTGTATTGC
1 GAATTTGAC---TTCTGTGTTGC
2623773 GAATTTG
1 GAATTTG
2623780 GAAAATCGCG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 20 0.49
21 11 0.27
22 4 0.10
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.46
Consensus pattern (20 bp):
GAATTTGACTTCTGTGTTGC
Found at i:2625909 original size:21 final size:21
Alignment explanation
Indices: 2625883--2625928 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2625873 TTTATAGAGG
2625883 TAAAATAGTTAAA-TTT-AATTT
1 TAAAATA--TAAATTTTAAATTT
2625904 TAAAATATAAATTTTAAATTT
1 TAAAATATAAATTTTAAATTT
2625925 TAAA
1 TAAA
2625929 TTTTGCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.17
20 3 0.13
21 16 0.70
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAAATATAAATTTTAAATTT
Found at i:2625921 original size:7 final size:7
Alignment explanation
Indices: 2625891--2625932 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
2625881 GGTAAAATAG
2625891 TTAAA-T
1 TTAAATT
2625897 TT-AATT
1 TTAAATT
*
2625903 TTAAAAT
1 TTAAATT
*
2625910 ATAAATT
1 TTAAATT
2625917 TTAAATT
1 TTAAATT
2625924 TTAAATT
1 TTAAATT
2625931 TT
1 TT
2625933 GCATTAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
5 2 0.07
6 5 0.17
7 23 0.77
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TTAAATT
Found at i:2627564 original size:64 final size:63
Alignment explanation
Indices: 2627496--2627656 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 63
2627486 TTGTTTAAGG
*
2627496 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCACATGCAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * * * *
2627560 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCACATGCAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
** *
2627624 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCA-CATGCAGTGCATCGATGCAT
2627657 ACCTCCATTA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 60 0.72
65 22 0.27
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCACATGCAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:2628281 original size:23 final size:23
Alignment explanation
Indices: 2628248--2628310 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
2628238 ATTATTATAT
2628248 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2628271 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
2628294 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
2628311 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2631750 original size:54 final size:55
Alignment explanation
Indices: 2631647--2631752 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 55
2631637 TACCTCTTGT
* *
2631647 TTTTTAGGTATATATTCTCATTTTTCACTGTTAATTTCAATCGCCTATTTTCATG
1 TTTTTAGCTATATATTCTCATTTTTCACTGTTAATCTCAATCGCCTATTTTCATG
* * * **
2631702 TTTTTAGCTATATCTTCTC-TTTTTTATTGTTAATCTCAATCGTTTATTTTC
1 TTTTTAGCTATATATTCTCATTTTTCACTGTTAATCTCAATCGCCTATTTTC
2631753 GTGCATCCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
54 27 0.61
55 17 0.39
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.57
Consensus pattern (55 bp):
TTTTTAGCTATATATTCTCATTTTTCACTGTTAATCTCAATCGCCTATTTTCATG
Found at i:2632202 original size:14 final size:15
Alignment explanation
Indices: 2632180--2632212 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2632170 TCCCGATTTT
2632180 ATTATTTTTATTATA
1 ATTATTTTTATTATA
*
2632195 ATTA-TTTTATTATT
1 ATTATTTTTATTATA
2632209 ATTA
1 ATTA
2632213 ATAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTATTTTTATTATA
Found at i:2634228 original size:21 final size:21
Alignment explanation
Indices: 2634204--2634261 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
2634194 TCCGAGTTAC
* *
2634204 CCGCGACAGCCGCAATAGCGT
1 CCGCGACGGCCGCAATAGCCT
* *
2634225 CCGCGATGGCCGCAATATCCT
1 CCGCGACGGCCGCAATAGCCT
2634246 CCGCGACGGCCGCAAT
1 CCGCGACGGCCGCAAT
2634262 CACGGTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.40, G:0.28, T:0.12
Consensus pattern (21 bp):
CCGCGACGGCCGCAATAGCCT
Found at i:2641893 original size:23 final size:23
Alignment explanation
Indices: 2641863--2641912 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
2641853 AATACTCATT
2641863 ATCATGCATC-GATGATTTATTTG
1 ATCATGCATCAG-TGATTTATTTG
*
2641886 ATCATGCATCAGTGATTTGTTTG
1 ATCATGCATCAGTGATTTATTTG
2641909 ATCA
1 ATCA
2641913 GTTCCGTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (23 bp):
ATCATGCATCAGTGATTTATTTG
Found at i:2649548 original size:15 final size:15
Alignment explanation
Indices: 2649510--2649548 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
2649500 ACATAAATAC
*
2649510 ATTTAAAAATTAAAA
1 ATTTAAATATTAAAA
2649525 A-TTATAATATTAAAA
1 ATTTA-AATATTAAAA
2649540 ATTTAAATA
1 ATTTAAATA
2649549 AACATAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 15 0.71
16 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTTAAATATTAAAA
Found at i:2650224 original size:3 final size:3
Alignment explanation
Indices: 2650204--2650238 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2650194 AGGGGCCGGC
* *
2650204 GGT GGC GGT GGT GAT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
2650239 AGGCTTAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.03, G:0.66, T:0.29
Consensus pattern (3 bp):
GGT
Found at i:2654721 original size:21 final size:21
Alignment explanation
Indices: 2654673--2654721 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2654663 GTTTATTGCG
* * *
2654673 ATTGCGACCATAGCGGGTGCT
1 ATTGCGGCCATAGCAGGCGCT
2654694 ATTGCGGCCATAGCAGGCGCT
1 ATTGCGGCCATAGCAGGCGCT
2654715 ATTGCGG
1 ATTGCGG
2654722 TATATCGGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.22
Consensus pattern (21 bp):
ATTGCGGCCATAGCAGGCGCT
Found at i:2659093 original size:5 final size:5
Alignment explanation
Indices: 2659083--2659112 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2659073 CAACGCATGC
*
2659083 CTTTG CTTTG CTTTG CTTTG CTTTA CTTTG
1 CTTTG CTTTG CTTTG CTTTG CTTTG CTTTG
2659113 GGCATCATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.20, G:0.17, T:0.60
Consensus pattern (5 bp):
CTTTG
Found at i:2662534 original size:58 final size:58
Alignment explanation
Indices: 2662420--2662536 Score: 146
Period size: 58 Copynumber: 2.0 Consensus size: 58
2662410 CAATTGTTAT
** * *
2662420 CGGTTAACTGTTTCTTAATAATTAGATTATGATTAGTAAAATTCAGTAACCATTATAA
1 CGGTTAACCATTTCCTAATAATTAGATTATGATTAGTAAAATTCAATAACCATTATAA
* * **
2662478 CGGTTAACCATTTCCTAATGATTA-AGTTATGATTAGTAAAATTTAATAACTGTTATAA
1 CGGTTAACCATTTCCTAATAATTAGA-TTATGATTAGTAAAATTCAATAACCATTATAA
2662536 C
1 C
2662537 AATTAATCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
57 1 0.02
58 49 0.98
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (58 bp):
CGGTTAACCATTTCCTAATAATTAGATTATGATTAGTAAAATTCAATAACCATTATAA
Found at i:2663949 original size:60 final size:60
Alignment explanation
Indices: 2663837--2663950 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
2663827 ATATTATATG
* * *
2663837 TCCCAAAACTATAATCCTCAATTTAAATTAGTCCTTAAAATTTAGAATATTCTAATTCAA
1 TCCCAAAACTATAATCCTCAATGTAAACTAGTCCTTAAAATTTAGAACATTCTAATTCAA
* * *
2663897 TCCCAAAACTATAA-CTCTC-ATGGTAAACTAGTCCTTAAACTTTTGGACATTCTA
1 TCCCAAAACTATAATC-CTCAAT-GTAAACTAGTCCTTAAAATTTAGAACATTCTA
2663951 GTAATACCCC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 3 0.07
60 43 0.93
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (60 bp):
TCCCAAAACTATAATCCTCAATGTAAACTAGTCCTTAAAATTTAGAACATTCTAATTCAA
Found at i:2664223 original size:18 final size:18
Alignment explanation
Indices: 2664200--2664236 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2664190 CCAACGCTCC
*
2664200 CATAATATCTCATCCACT
1 CATAATATCTCACCCACT
2664218 CATAATATCTCACCCACT
1 CATAATATCTCACCCACT
2664236 C
1 C
2664237 TTCTTCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.38, G:0.00, T:0.30
Consensus pattern (18 bp):
CATAATATCTCACCCACT
Found at i:2669576 original size:24 final size:24
Alignment explanation
Indices: 2669544--2669596 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
2669534 CAGAGATTTC
2669544 GAGGGCCATATTCTCGGTAGACTA
1 GAGGGCCATATTCTCGGTAGACTA
2669568 GAGGGCCATATTCTCGGTAGACTA
1 GAGGGCCATATTCTCGGTAGACTA
*
2669592 AAGGG
1 GAGGG
2669597 GTATGTGTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (24 bp):
GAGGGCCATATTCTCGGTAGACTA
Found at i:2669997 original size:60 final size:61
Alignment explanation
Indices: 2669890--2670064 Score: 185
Period size: 60 Copynumber: 2.9 Consensus size: 61
2669880 GTATATATGT
* * * *
2669890 ATAATTT-GGGATAAAATTAAAATGTTCTAAAAGTTTGGGGACCAATTTAGAATGAAT-TTC
1 ATAATTTAGGGATAAAATTGAAATGTT-TAAAAGTTTGAGGACTAATTTAGAATGAATAGTC
* * * *
2669950 ATAGTTTGGGGATGAAATTGAATTGTTTAAAAGTTTGAGGACTAATTTAGAATG-ATAGTC
1 ATAATTTAGGGATAAAATTGAAATGTTTAAAAGTTTGAGGACTAATTTAGAATGAATAGTC
* * * * * * *
2670010 ATAATTTAAGGATTAAATTGAAATATTTAAAAATTTAAGGATTAATTTAAAATGA
1 ATAATTTAGGGATAAAATTGAAATGTTTAAAAGTTTGAGGACTAATTTAGAATGA
2670065 GGGTCATACT
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
59 2 0.02
60 77 0.81
61 16 0.17
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (61 bp):
ATAATTTAGGGATAAAATTGAAATGTTTAAAAGTTTGAGGACTAATTTAGAATGAATAGTC
Found at i:2672316 original size:19 final size:17
Alignment explanation
Indices: 2672284--2672323 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 17
2672274 CTCTGGCACC
2672284 TTCTGGCAAACCCATTT
1 TTCTGGCAAACCCATTT
2672301 TTCTGAGCAGAACCCATTT
1 TTCTG-GCA-AACCCATTT
2672320 TTCT
1 TTCT
2672324 TTTCTTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.24
18 3 0.14
19 13 0.62
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.38
Consensus pattern (17 bp):
TTCTGGCAAACCCATTT
Found at i:2679022 original size:25 final size:24
Alignment explanation
Indices: 2678972--2679027 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
2678962 TTAAATGATT
*
2678972 AATTTTAATTTGTTTTAATATTTA
1 AATTTTAATTTGTTTTAATATCTA
*
2678996 AATTTTTATTT-TTTTAAATATACTA
1 AATTTTAATTTGTTTT-AATAT-CTA
*
2679021 AAGTTTA
1 AATTTTA
2679028 GTTTTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 4 0.15
24 15 0.58
25 7 0.27
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (24 bp):
AATTTTAATTTGTTTTAATATCTA
Found at i:2680891 original size:22 final size:22
Alignment explanation
Indices: 2680863--2680931 Score: 59
Period size: 23 Copynumber: 3.1 Consensus size: 22
2680853 AGTTCTTCCA
2680863 TTTCTTCACCGTTTCGCTAGGT
1 TTTCTTCACCGTTTCGCTAGGT
* ** * *
2680885 TTTCTTCGTCTTTTTCTCTAAGT
1 TTTCTTC-ACCGTTTCGCTAGGT
*
2680908 TTTCTTCACCGATTT-GCTGGGT
1 TTTCTTCACCG-TTTCGCTAGGT
2680930 TT
1 TT
2680932 CTTGCTTTTC
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.09, C:0.23, G:0.16, T:0.52
Consensus pattern (22 bp):
TTTCTTCACCGTTTCGCTAGGT
Found at i:2694972 original size:40 final size:39
Alignment explanation
Indices: 2694885--2695000 Score: 119
Period size: 40 Copynumber: 3.0 Consensus size: 39
2694875 AATTATTGTC
* * * *
2694885 GTCACAAATTACCAACTAAAACTAATTAAAAAAATATTA
1 GTCACAAATAACCAACTAAGACTAGTGAAAAAAATATTA
* *
2694924 GTCACAAATCACCAACTAAGACTAGTGACAAACAATTATT-
1 GTCACAAATAACCAACTAAGACTAGTGA-AAA-AAATATTA
* * *
2694964 GTCACAAATAATCAACAAAGACTAGTG-ATAAAATATT
1 GTCACAAATAACCAACTAAGACTAGTGAAAAAAATATT
2695001 TTCATCACAA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
37 6 0.09
38 2 0.03
39 24 0.37
40 27 0.42
41 6 0.09
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.24
Consensus pattern (39 bp):
GTCACAAATAACCAACTAAGACTAGTGAAAAAAATATTA
Found at i:2702707 original size:66 final size:66
Alignment explanation
Indices: 2702598--2702728 Score: 217
Period size: 66 Copynumber: 2.0 Consensus size: 66
2702588 TAAATTTGTC
* *
2702598 ATTTTTGTTAAATAATTGGTGGTCATTTGAGTTTGATGCTAGGGATAGAGTGAGTGAGTGAGTGA
1 ATTTTTGTTAAATAATTGATAGTCATTTGAGTTTGATGCTAGGGATAGAGTGAGTGAGTGAGTGA
2702663 A
66 A
* * *
2702664 ATTTTTGTTAAATAATTGATAGTCATTTGAGTTTGATGTTAGGGATATATTGAGTGAGTGAGTGA
1 ATTTTTGTTAAATAATTGATAGTCATTTGAGTTTGATGCTAGGGATAGAGTGAGTGAGTGAGTGA
2702729 GTGAGGACAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.28, C:0.02, G:0.29, T:0.40
Consensus pattern (66 bp):
ATTTTTGTTAAATAATTGATAGTCATTTGAGTTTGATGCTAGGGATAGAGTGAGTGAGTGAGTGA
A
Found at i:2706202 original size:19 final size:19
Alignment explanation
Indices: 2706178--2706233 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
2706168 ATGACCAATA
2706178 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
*
2706197 AAATCGCAATGCAATCTCT
1 AAATCGCAATGCGATCTCT
*
2706216 AAATCGCAACGCGATCTC
1 AAATCGCAATGCGATCTC
2706234 CAGTATCGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:2706303 original size:21 final size:21
Alignment explanation
Indices: 2706278--2706331 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
2706268 GTTTTTGACT
2706278 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTCCAAA
* * *
2706299 TTCGCGTTGCGATTTTCTAAA
1 ATCGCATTGCGATTTTCCAAA
*
2706320 ATCGCAATGCGA
1 ATCGCATTGCGA
2706332 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (21 bp):
ATCGCATTGCGATTTTCCAAA
Found at i:2706979 original size:19 final size:19
Alignment explanation
Indices: 2706957--2707000 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
2706947 AAATCGCAAC
*
2706957 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCATT
2706976 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCATT
2706995 GCGATT
1 GCGATT
2707001 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (19 bp):
GCGATTTTCATTTCGCATT
Found at i:2707030 original size:20 final size:20
Alignment explanation
Indices: 2707005--2707053 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2706995 GCGATTATCT
2707005 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
2707025 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
2707045 TGTTGCGAT
1 CGTTGCGAT
2707054 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2707059 original size:20 final size:20
Alignment explanation
Indices: 2707036--2707076 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2707026 GTTGCAATAG
2707036 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
2707056 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
2707076 T
1 T
2707077 AAGTTTCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.15, G:0.20, T:0.56
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:2707083 original size:20 final size:20
Alignment explanation
Indices: 2707040--2707083 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2707030 CAATAGTCAT
* *
2707040 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
2707060 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
2707080 TTTC
1 TTTC
2707084 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:2708707 original size:21 final size:21
Alignment explanation
Indices: 2708669--2708708 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2708659 CATGGCGTGA
* *
2708669 TGAGGTATCTACTTTACGTAG
1 TGAGGTATCCACTCTACGTAG
*
2708690 TGAGGTATCCGCTCTACGT
1 TGAGGTATCCACTCTACGT
2708709 GAGATGGTAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (21 bp):
TGAGGTATCCACTCTACGTAG
Found at i:2709016 original size:20 final size:20
Alignment explanation
Indices: 2708993--2709055 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
2708983 CTTAAAATCA
2708993 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
*
2709013 CAACGCGGAAATGACTATCG
1 CAACGCGAAAATGACTATCG
**
2709033 CAACGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
2709053 CAA
1 CAA
2709056 TGGGATAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:2709691 original size:21 final size:21
Alignment explanation
Indices: 2709624--2709694 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
2709614 CCTGTTATCA
* * * *
2709624 TTCAAGAGGCCTCTCCTATCG
1 TTCAAGAGTCCCCTCCCACCG
**
2709645 TTCAAGAGTCCCCTATCATCC-
1 TTCAAGAGTCCCCTCCCA-CCG
*
2709666 CTCAAGAGTCCCCTCCCACCG
1 TTCAAGAGTCCCCTCCCACCG
2709687 TTCAAGAG
1 TTCAAGAG
2709695 GCCCTTGTCA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
20 2 0.05
21 35 0.92
22 1 0.03
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.24
Consensus pattern (21 bp):
TTCAAGAGTCCCCTCCCACCG
Found at i:2709706 original size:42 final size:42
Alignment explanation
Indices: 2709625--2709736 Score: 107
Period size: 42 Copynumber: 2.7 Consensus size: 42
2709615 CTGTTATCAT
* * * *
2709625 TCAAGAGGCCTCTCCTATCGTTCAAGAGTCCCCTATCATCCC
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* * * **
2709667 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCTTGTCATCGT
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* * * *
2709709 TGAAGAGGTCCCTTCCACCATTCAAGAG
1 TCAAGAGGCCCCTCCCACCGTTCAAGAG
2709737 CCCGATTCAC
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:2709735 original size:21 final size:21
Alignment explanation
Indices: 2709667--2709736 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
2709657 CTATCATCCC
*
2709667 TCAAGA-GTCCCCTCCCACCGT
1 TCAAGAGGT-CCCTTCCACCGT
* *
2709688 TCAAGAGG-CCCTTGTCATCGT
1 TCAAGAGGTCCCTT-CCACCGT
* *
2709709 TGAAGAGGTCCCTTCCACCAT
1 TCAAGAGGTCCCTTCCACCGT
2709730 TCAAGAG
1 TCAAGAG
2709737 CCCGATTCAC
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
20 4 0.11
21 28 0.74
22 6 0.16
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (21 bp):
TCAAGAGGTCCCTTCCACCGT
Found at i:2711322 original size:20 final size:20
Alignment explanation
Indices: 2711249--2711322 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
2711239 AGGTATACTT
*
2711249 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
** *
2711269 TCGCAATACGAAAGTCAAAA
1 TCGCAACGCGAAAGCCAAAA
*
2711289 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
*
2711309 TCGCAACGCAAAAG
1 TCGCAACGCGAAAG
2711323 TCAATTCGCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.46, C:0.26, G:0.16, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:2711423 original size:20 final size:20
Alignment explanation
Indices: 2711398--2711554 Score: 242
Period size: 20 Copynumber: 7.8 Consensus size: 20
2711388 GCGATTTTCT
*
2711398 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
2711418 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
2711438 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
2711458 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
2711478 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2711498 TGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2711518 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2711538 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
2711555 GAATGTGTAA
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 127 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2711453 original size:40 final size:40
Alignment explanation
Indices: 2711345--2711554 Score: 247
Period size: 40 Copynumber: 5.4 Consensus size: 40
2711335 GCGATTTTCA
* *
2711345 CGTTGCGAAAGTC-AATTCGCGTTGCGATAGTCTAATAT-G
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAT-TCG
* * *
2711384 CTTTGCGAT--T----TTCTCGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
* *
2711418 CGTTGCGATAGTCAAATTCCCGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
*
2711458 CGTTGCGATAGTCAAATTTGCGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
* * *
2711498 TGTTACGATAGTCAAATTCGCGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
*
2711538 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
2711555 GAATGTGTAA
Statistics
Matches: 146, Mismatches: 18, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
33 1 0.01
34 27 0.18
36 1 0.01
37 1 0.01
39 7 0.05
40 109 0.75
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (40 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
Found at i:2713809 original size:14 final size:14
Alignment explanation
Indices: 2713790--2713826 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2713780 TCCTGTGGCA
2713790 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
2713804 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
2713818 TTCTTCTTC
1 TT-TTCTTC
2713827 AGGGTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:2714068 original size:24 final size:24
Alignment explanation
Indices: 2714017--2714068 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2714007 ATCCGAGTAT
** *
2714017 TGACCAAGATCAAAGTCTGGGTAT
1 TGACCAAGATCAAAGTCTGAATAC
* *
2714041 TGACCAAGATCAAATTTTGAATAC
1 TGACCAAGATCAAAGTCTGAATAC
2714065 TGAC
1 TGAC
2714069 TATTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCTGAATAC
Found at i:2714730 original size:17 final size:17
Alignment explanation
Indices: 2714708--2714745 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2714698 CGGATGGGGA
2714708 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
2714725 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
2714742 AGGA
1 AGGA
2714746 ACGGATGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.37, T:0.32
Consensus pattern (17 bp):
AGGATGTCGTTGGATAT
Found at i:2714754 original size:22 final size:20
Alignment explanation
Indices: 2714705--2714755 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 20
2714695 TGCCGGATGG
2714705 GGAAGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
2714725 ---AGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
2714742 AGGAACGGATGTCG
1 -GGAA-GGATGTCG
2714756 CCGGAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 17 0.65
21 1 0.04
22 8 0.31
ACGTcount: A:0.25, C:0.08, G:0.39, T:0.27
Consensus pattern (20 bp):
GGAAGGATGTCGTTGGATAT
Found at i:2714989 original size:21 final size:20
Alignment explanation
Indices: 2714945--2714993 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
2714935 GCGATTTTCT
* *
2714945 AAAATCGCAATGCGAATTTGA
1 AAAATCGCAATGCGAATGT-C
2714966 AAAATCGCAATGCG-ATAGTC
1 AAAATCGCAATGCGAAT-GTC
2714986 AAAATCGC
1 AAAATCGC
2714994 GTTGCGAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGAATGTC
Done.