Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000417.1 Hibiscus syriacus cultivar Beakdansim tig00000764_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: 2005044
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:952333 original size:18 final size:20
Alignment explanation
Indices: 952298--952334 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
952288 TTCCTTTTGT
*
952298 TTTTTTTTTCGGTATCACTG
1 TTTTTTTTTCGCTATCACTG
952318 TTTTTTTTT-GCT-TCACT
1 TTTTTTTTTCGCTATCACT
952335 TCGAATATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 2 0.12
20 9 0.56
ACGTcount: A:0.08, C:0.16, G:0.11, T:0.65
Consensus pattern (20 bp):
TTTTTTTTTCGCTATCACTG
Found at i:952459 original size:12 final size:12
Alignment explanation
Indices: 952444--952469 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
952434 TGGTCCCCCC
952444 TCCTCCCTGTCT
1 TCCTCCCTGTCT
952456 TCCTCCCTGTCT
1 TCCTCCCTGTCT
952468 TC
1 TC
952470 TCTCTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.50, G:0.08, T:0.42
Consensus pattern (12 bp):
TCCTCCCTGTCT
Found at i:953001 original size:3 final size:3
Alignment explanation
Indices: 952993--953056 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
952983 CAAAACAGTG
* * **
952993 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TGA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
953037 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
953057 CGAAAAAACC
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.09
3 45 0.85
4 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:958941 original size:226 final size:225
Alignment explanation
Indices: 958541--958979 Score: 763
Period size: 226 Copynumber: 1.9 Consensus size: 225
958531 TATCTATCCT
* *
958541 TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGTTAATAT
1 TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTTAATAT
**
958606 TGTTAAATTTAAAATCTAAATAAGATTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
66 TGTTAAATTTAAAATCTAAATAAGATTTATAAAATATCAAAACAATCAAATAAAATTTTGTGTAA
*
958671 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
131 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAACATA
958736 AATTACATAACTTTCAAAAAAGTATATATCA
196 AATTACATAACTTT-AAAAAAGTATATATCA
*
958767 TTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGGTTAATA
1 TTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAGTTAATA
* *
958832 TTGTTAAATTTAAATTCTAAATAATATTTATAAAATATC-AAACAATCAAATAAAATTTTGTGTA
65 TTGTTAAATTTAAAATCTAAATAAGATTTATAAAATATCAAAACAATCAAATAAAATTTTGTGTA
* *
958896 AATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATTGAAACAT
130 AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAACAT
958961 AAATTACATAACTTTAAAA
195 AAATTACATAACTTTAAAA
958980 GCAGTTTTAA
Statistics
Matches: 202, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
225 4 0.02
226 131 0.65
227 67 0.33
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.39
Consensus pattern (225 bp):
TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTTAATAT
TGTTAAATTTAAAATCTAAATAAGATTTATAAAATATCAAAACAATCAAATAAAATTTTGTGTAA
ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAACATA
AATTACATAACTTTAAAAAAGTATATATCA
Found at i:959226 original size:20 final size:19
Alignment explanation
Indices: 959203--959249 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
959193 CGATATAACA
*
959203 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
959223 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
959243 GGTAAAA
1 GGTAAAA
959250 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:961596 original size:31 final size:32
Alignment explanation
Indices: 961544--961606 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
961534 AAATAGATGG
*
961544 AGTGGTGAAGAAGTAGAGGTG-TGAGGGGTGA
1 AGTGGTGAAGAAGTAGAGGTGTTAAGGGGTGA
***
961575 AGTGGTGAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAGAAGTAGAGGTGTTAAGGGGTGA
961607 TATTAAGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.27, C:0.02, G:0.48, T:0.24
Consensus pattern (32 bp):
AGTGGTGAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:963996 original size:23 final size:23
Alignment explanation
Indices: 963965--964027 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
963955 ATAGGTAAAC
*
963965 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
963988 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
964011 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
964028 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:964035 original size:23 final size:23
Alignment explanation
Indices: 963965--964037 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
963955 ATAGGTAAAC
* * **
963965 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
963988 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
964011 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
964034 ATAT
1 ATAT
964038 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:964425 original size:23 final size:23
Alignment explanation
Indices: 964394--964456 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
964384 ATAGGTAAAC
*
964394 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
964417 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
964440 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
964457 ATGGTATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:964702 original size:429 final size:430
Alignment explanation
Indices: 963869--965161 Score: 2514
Period size: 429 Copynumber: 3.0 Consensus size: 430
963859 AATTCGCAGT
963869 ACACTGTT-AAAAAATTGAAACATAAATTACATAAG-TTTAAAAAAAGTATCGATCC-TTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
963931 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
963996 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCC-TTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
964060 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATC-TTTGAGTGAGTTTT
196 AAAAGTGTCCATAC-TTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
964124 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
260 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
964189 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
325 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
964254 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
390 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
964295 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
964360 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
964425 TAATAGGTATCGTTTATATAATGTAATAGGTAATGG-TATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
964489 AAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
196 AAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
964554 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTA
261 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTA
964619 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
326 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
964684 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
964724 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
964789 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
964854 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
964919 AAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
196 AAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
964984 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGG--TATA-TATTA
261 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTA
965046 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
326 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
965111 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
965151 ACACTGTTAAA
1 ACACTGTTAAA
965162 GTATCGATCC
Statistics
Matches: 861, Mismatches: 0, Indels: 11
0.99 0.00 0.01
Matches are distributed among these distances:
426 8 0.01
427 148 0.17
428 80 0.09
429 479 0.56
430 146 0.17
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.39
Consensus pattern (430 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTA
TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:964854 original size:23 final size:23
Alignment explanation
Indices: 964823--964885 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
964813 ATAGGTAAAC
*
964823 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
964846 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
964869 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
964886 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:964893 original size:23 final size:23
Alignment explanation
Indices: 964823--964895 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
964813 ATAGGTAAAC
* * **
964823 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
964846 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
964869 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
964892 ATAT
1 ATAT
964896 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:970252 original size:20 final size:20
Alignment explanation
Indices: 970229--970275 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
970219 CTTTCCAATT
*
970229 TCGCAATGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
970249 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
970269 TCGCAAC
1 TCGCAAC
970276 ATATAAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:970292 original size:20 final size:20
Alignment explanation
Indices: 970269--970335 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
970259 AATTTGTAAA
* *
970269 TCGCAACATATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
970289 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
970309 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
970329 TCGCAAC
1 TCGCAAC
970336 GCGTGCTGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.45, C:0.25, G:0.12, T:0.18
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:970485 original size:24 final size:24
Alignment explanation
Indices: 970453--970505 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
970443 ATTTGATGTT
970453 TGTTGGTTTTAGATGTGTAGAAAG
1 TGTTGGTTTTAGATGTGTAGAAAG
970477 TGTTGGTTTTAGATGTGTAGAAAG
1 TGTTGGTTTTAGATGTGTAGAAAG
970501 TGTTG
1 TGTTG
970506 TTTGAGCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.43
Consensus pattern (24 bp):
TGTTGGTTTTAGATGTGTAGAAAG
Found at i:970756 original size:66 final size:66
Alignment explanation
Indices: 970597--970777 Score: 251
Period size: 66 Copynumber: 2.7 Consensus size: 66
970587 TGAGGTTCAC
**
970597 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTT-TAATTGATGAGGAAATA
1 TTTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTGTTTTTGATGAGGAAATA
970660 AGAATTA
60 AGAATTA
* *
970667 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTGTTTTTGATGTGTAAATAAGAATT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTGTTTTTGATGAGGAAATAAGAATT
970731 A
66 A
970732 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTGTTTT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTGTTTT
970778 AAATTCAATC
Statistics
Matches: 104, Mismatches: 4, Indels: 10
0.88 0.03 0.08
Matches are distributed among these distances:
64 14 0.13
65 20 0.19
66 45 0.43
67 1 0.01
68 4 0.04
69 20 0.19
ACGTcount: A:0.26, C:0.02, G:0.18, T:0.54
Consensus pattern (66 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTGTTTTTGATGAGGAAATAAGAATT
A
Found at i:970845 original size:20 final size:20
Alignment explanation
Indices: 970820--970861 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
970810 AGACATGTTG
970820 AAGGTAAATTCGCAACGCGA
1 AAGGTAAATTCGCAACGCGA
970840 AAGGTAAATTCGCAACGCGA
1 AAGGTAAATTCGCAACGCGA
970860 AA
1 AA
970862 TAAGCGTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (20 bp):
AAGGTAAATTCGCAACGCGA
Found at i:970989 original size:20 final size:20
Alignment explanation
Indices: 970942--970991 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
970932 GCAACACTTA
*
970942 TTTCGCGATGCAAATTTGAC
1 TTTCGCGTTGCAAATTTGAC
*
970962 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCAAATTTGAC
970982 TTTCGCGTTG
1 TTTCGCGTTG
970992 ATCACAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCAAATTTGAC
Found at i:971934 original size:18 final size:18
Alignment explanation
Indices: 971911--971947 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
971901 CGAAATTTAT
971911 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
971929 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
971947 A
1 A
971948 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:974951 original size:3 final size:3
Alignment explanation
Indices: 974943--974967 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
974933 TCTTCGGGGA
974943 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
974968 AGGGTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:975945 original size:21 final size:21
Alignment explanation
Indices: 975904--975945 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
975894 TTCTGGGCTG
* *
975904 GGGGAATCGGTACCCATTCAA
1 GGGGAATCGATACCCACTCAA
*
975925 GGGGAATCGATACCCCCTCAA
1 GGGGAATCGATACCCACTCAA
975946 CGAATATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGGAATCGATACCCACTCAA
Found at i:976651 original size:23 final size:23
Alignment explanation
Indices: 976625--976678 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
976615 TGGCACTACA
976625 GTGCAATTCTACGCGGCACTCT-G
1 GTGCAATTCTACGCGGCACT-TAG
*
976648 GTGCAATTCTACGTGGCACTTAG
1 GTGCAATTCTACGCGGCACTTAG
976671 GTGCAATT
1 GTGCAATT
976679 ATATGAGCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
GTGCAATTCTACGCGGCACTTAG
Found at i:983479 original size:23 final size:23
Alignment explanation
Indices: 983447--983508 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
983437 TTATTATATG
983447 GCACTACGGTGCAATTCTACGCA
1 GCACTACGGTGCAATTCTACGCA
* * **
983470 GCACTCCGGTGTAATTCTACGTG
1 GCACTACGGTGCAATTCTACGCA
983493 GCACTTA-GGTGCAATT
1 GCAC-TACGGTGCAATT
983509 ATATGAGCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACGCA
Found at i:984261 original size:12 final size:12
Alignment explanation
Indices: 984240--984273 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
984230 TGTTGTGGGT
*
984240 TTTGAGATTGTG
1 TTTGATATTGTG
984252 TTTGATATTGTG
1 TTTGATATTGTG
*
984264 TTTGGTATTG
1 TTTGATATTG
984274 GAAATGTGGT
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:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:985078 original size:20 final size:19
Alignment explanation
Indices: 985042--985151 Score: 141
Period size: 19 Copynumber: 5.7 Consensus size: 19
985032 ACTAAAACCT
* *
985042 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTC-A
*
985061 GTTGCAAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
985080 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
985099 GTTGCAAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
985118 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-C-A
985139 GTTGCGAATTTGA
1 GTTGCGAATTTGA
985152 CTTTTGTGTT
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 61 0.75
20 7 0.09
21 13 0.16
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:985086 original size:38 final size:39
Alignment explanation
Indices: 985042--985151 Score: 161
Period size: 38 Copynumber: 2.8 Consensus size: 39
985032 ACTAAAACCT
* *
985042 GTTGCGAAATT-AAATTCGTGTTGCAAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCGAGTTGCAAATTTGAAATTCA
985080 GTTGCGAATTTGAAATTC-AGTTGCAAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCGAGTTGCAAATTTGAAATTCA
* *
985118 GTTGCGAATTTGAAATTCCGCGTTGCGAATTTGA
1 GTTGCGAATTTGAAATT-CGAGTTGCAAATTTGA
985152 CTTTTGTGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
38 46 0.71
39 7 0.11
40 12 0.18
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (39 bp):
GTTGCGAATTTGAAATTCGAGTTGCAAATTTGAAATTCA
Found at i:985164 original size:20 final size:20
Alignment explanation
Indices: 985139--985265 Score: 141
Period size: 20 Copynumber: 6.3 Consensus size: 20
985129 GAAATTCCGC
985139 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
*
985159 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
985179 GTTACG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGAC--TTTTGT
985199 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* *
985219 GTTGCGAATTTGACTATTGC
1 GTTGCGAATTTGACTTTTGT
* *
985239 GTTGCGAATTTGACTTCTAT
1 GTTGCGAATTTGACTTTTGT
985259 GTTGCGA
1 GTTGCGA
985266 TTTACAAATT
Statistics
Matches: 87, Mismatches: 16, Indels: 8
0.78 0.14 0.07
Matches are distributed among these distances:
18 2 0.02
19 4 0.05
20 75 0.86
21 4 0.05
22 2 0.02
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:985211 original size:40 final size:40
Alignment explanation
Indices: 985159--985322 Score: 203
Period size: 40 Copynumber: 4.1 Consensus size: 40
985149 TGACTTTTGT
*
985159 GTTGCGAATTTGACTTCTGTGTTACGATTTACAAATTCGC
1 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGC
* *
985199 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGAC-TATT-GC
1 GTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGC
* *
985239 GTTGCGAATTTGACTTCTATGTTGCGATTTACAAATTCGT
1 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGC
985279 GTTGCG-ATTT-ACAAATTC-GTGTTGCGATTTACAAATTCGC
1 GTTGCGAATTTGAC---TTCTGTGTTGCGATTTACAAATTCGC
985319 GTTG
1 GTTG
985323 TTAAACTGGA
Statistics
Matches: 108, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
38 4 0.04
39 11 0.10
40 81 0.75
41 10 0.09
42 2 0.02
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.41
Consensus pattern (40 bp):
GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGC
Found at i:985281 original size:20 final size:20
Alignment explanation
Indices: 985258--985322 Score: 121
Period size: 20 Copynumber: 3.2 Consensus size: 20
985248 TTGACTTCTA
985258 TGTTGCGATTTACAAATTCG
1 TGTTGCGATTTACAAATTCG
985278 TGTTGCGATTTACAAATTCG
1 TGTTGCGATTTACAAATTCG
985298 TGTTGCGATTTACAAATTCG
1 TGTTGCGATTTACAAATTCG
*
985318 CGTTG
1 TGTTG
985323 TTAAACTGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (20 bp):
TGTTGCGATTTACAAATTCG
Found at i:985321 original size:80 final size:80
Alignment explanation
Indices: 985042--985322 Score: 242
Period size: 80 Copynumber: 3.5 Consensus size: 80
985032 ACTAAAACCT
* * * *
985042 GTTGCGAAATT-AAATTCGTGTTGCAAATTTGA-AATT-CAGTTGCGAATTTGAAATTC-A-GTT
1 GTTGCGAATTTGACATTCGTGTTGCGAATTTGACAATTGC-GTTGCGAATTTG-ACTTCTATGTT
* * * *
985102 GCAAATTT-GAAATTC-A
64 AC-GATTTACAAATTCGC
* * ** * *
985118 GTTGCGAATTTGAAATTCCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCTGTGTTA
1 GTTGCGAATTTGACATT-CGTGTTGCGAATTTGACAATTGCGTTGCGAATTTGACTTCTATGTTA
985183 CGATTTACAAATTCGC
65 CGATTTACAAATTCGC
* * * *
985199 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATTGCGTTGCGAATTTGACTTCTATGTTGC
1 GTTGCGAATTTGACATTCGTGTTGCGAATTTGACAATTGCGTTGCGAATTTGACTTCTATGTTAC
*
985264 GATTTACAAATTCGT
66 GATTTACAAATTCGC
985279 GTTGCG-ATTT-ACAAATTCGTGTTGCG-ATTT-ACAAATTCGCGTTG
1 GTTGCGAATTTGAC--ATTCGTGTTGCGAATTTGAC-AATT-GCGTTG
985323 TTAAACTGGA
Statistics
Matches: 169, Mismatches: 24, Indels: 20
0.79 0.11 0.09
Matches are distributed among these distances:
76 10 0.06
77 5 0.03
78 22 0.13
79 29 0.17
80 88 0.52
81 15 0.09
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (80 bp):
GTTGCGAATTTGACATTCGTGTTGCGAATTTGACAATTGCGTTGCGAATTTGACTTCTATGTTAC
GATTTACAAATTCGC
Found at i:988382 original size:29 final size:29
Alignment explanation
Indices: 988350--988409 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
988340 TAAAATTAGA
988350 TTACGACCTTATCTCAATCTAATTCAACT
1 TTACGACCTTATCTCAATCTAATTCAACT
988379 TTACGACCTTATCTCAATCTAATTCAACT
1 TTACGACCTTATCTCAATCTAATTCAACT
988408 TT
1 TT
988410 CTCTTCAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (29 bp):
TTACGACCTTATCTCAATCTAATTCAACT
Found at i:989758 original size:166 final size:167
Alignment explanation
Indices: 989484--989813 Score: 608
Period size: 166 Copynumber: 2.0 Consensus size: 167
989474 TTCCTTCTAG
* *
989484 TGATGGAGTATGTTTGGGTACCTTTTCCAAGAGGTAAGTTGTCACCAATGATGCATGTAGAGCTG
1 TGATGGAGTATGTTTGGGTACATTTTCCAAGAGGTAAGTTGTCACCAATGATGAATGTAGAGCTG
*
989549 CGTCATATGAAAATACATCTTCATTAACTCTATAGTAGGGTGAATGCCCCGAATGAAATGGTCCT
66 CGTCATATGAAAATACATCTTCATTAACTCTATAGTAGGGTGAATGCCCCAAATGAAATGGTCCT
989614 AAGTTTCA-TTTTCATTCCAAGGAGGAGGAGGAGATA
131 AAGTTTCATTTTTCATTCCAAGGAGGAGGAGGAGATA
*
989650 TGATGGAGTATGTTTGGGTATATTTTCCAAGAGGTAAGTTGTCACCAATGATGAATGTAGAGCTG
1 TGATGGAGTATGTTTGGGTACATTTTCCAAGAGGTAAGTTGTCACCAATGATGAATGTAGAGCTG
989715 CGTCATATGAAAATACATCTTCATTAACTCTATAGTAGGGTGAATGCCCCAAATGAAATGGTCCT
66 CGTCATATGAAAATACATCTTCATTAACTCTATAGTAGGGTGAATGCCCCAAATGAAATGGTCCT
*
989780 AAGTTTCATTTTTCATTCCGAGGAGGAGGAGGAG
131 AAGTTTCATTTTTCATTCCAAGGAGGAGGAGGAG
989814 GAGGAGGAGG
Statistics
Matches: 158, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
166 134 0.85
167 24 0.15
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (167 bp):
TGATGGAGTATGTTTGGGTACATTTTCCAAGAGGTAAGTTGTCACCAATGATGAATGTAGAGCTG
CGTCATATGAAAATACATCTTCATTAACTCTATAGTAGGGTGAATGCCCCAAATGAAATGGTCCT
AAGTTTCATTTTTCATTCCAAGGAGGAGGAGGAGATA
Found at i:989807 original size:3 final size:3
Alignment explanation
Indices: 989799--989864 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
989789 TTTTCATTCC
989799 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
989847 GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG
989865 TCAAACGGTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:995042 original size:23 final size:23
Alignment explanation
Indices: 995007--995052 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
994997 TTATTGATAA
* *
995007 TATATTTTTGTCTCTTAAAATAT
1 TATATGTTCGTCTCTTAAAATAT
*
995030 TATATGTTCGTCTCTTATAATAT
1 TATATGTTCGTCTCTTAAAATAT
995053 GCTAGACCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.54
Consensus pattern (23 bp):
TATATGTTCGTCTCTTAAAATAT
Found at i:997091 original size:38 final size:39
Alignment explanation
Indices: 997049--997142 Score: 138
Period size: 39 Copynumber: 2.4 Consensus size: 39
997039 ATCTATAAAT
*
997049 ATATTAAAAATATAATTAAAT-TAATAA-TTTGTGATTGA
1 ATATTATAAA-ATAATTAAATATAATAATTTTGTGATTGA
**
997087 ATATTATAAAATAATTATTTATAATAATTTTGTGATTGA
1 ATATTATAAAATAATTAAATATAATAATTTTGTGATTGA
997126 ATATTATAAAATAATTA
1 ATATTATAAAATAATTA
997143 TTTATAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
37 8 0.16
38 15 0.29
39 28 0.55
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (39 bp):
ATATTATAAAATAATTAAATATAATAATTTTGTGATTGA
Found at i:997119 original size:39 final size:38
Alignment explanation
Indices: 997070--997150 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 38
997060 ATAATTAAAT
997070 TAATAATTTGTGATTGAATATTATAAAATAATTATTTA
1 TAATAATTTGTGATTGAATATTATAAAATAATTATTTA
997108 TAATAATTTTGTGATTGAATATTATAAAATAATTATTTA
1 TAATAA-TTTGTGATTGAATATTATAAAATAATTATTTA
997147 TAAT
1 TAAT
997151 TTAATCATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 6 0.14
39 36 0.86
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (38 bp):
TAATAATTTGTGATTGAATATTATAAAATAATTATTTA
Found at i:999019 original size:31 final size:31
Alignment explanation
Indices: 998979--999101 Score: 176
Period size: 31 Copynumber: 4.0 Consensus size: 31
998969 GTGTCGATGG
*
998979 TTACTTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
999010 TTATCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
999041 TTACCTATGTTCTTCGGGATATATGGACTTT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
999072 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
999102 GTCCTTCAGG
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 82 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1001192 original size:24 final size:23
Alignment explanation
Indices: 1001168--1001253 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
1001158 TCGTATAAAT
*
1001168 TTGCACCGAAGTGTCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
1001191 TT-TATCCCGAAG-GACCACCTAGAA
1 TTGCA--CCGAAGTG-CCACGTAGAA
*
1001215 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
1001238 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
1001254 TATAAGATTG
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
22 1 0.02
23 32 0.64
24 16 0.32
25 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:1004932 original size:23 final size:23
Alignment explanation
Indices: 1004901--1004967 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
1004891 GTCGAGGGTT
* *
1004901 CTATATGGTCATTCGAGACAAAC
1 CTATGTGGTCATTCGGGACAAAC
1004924 CTATGTGGTCATTCGGGACAAAC
1 CTATGTGGTCATTCGGGACAAAC
*
1004947 CTATGTAGTCATTCGGGACAA
1 CTATGTGGTCATTCGGGACAA
1004968 TTATGTGGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAAAC
Found at i:1008772 original size:18 final size:18
Alignment explanation
Indices: 1008740--1008794 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
1008730 CACTTAAAAC
* *
1008740 TTGTCCCGAATGACCACT
1 TTGTCACGAAGGACCACT
*
1008758 TTGTCATGAAGGACCACT
1 TTGTCACGAAGGACCACT
* * *
1008776 ATGTCCCGAATGACCACT
1 TTGTCACGAAGGACCACT
1008794 T
1 T
1008795 GTAATCCCTT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (18 bp):
TTGTCACGAAGGACCACT
Found at i:1011574 original size:52 final size:52
Alignment explanation
Indices: 1011496--1011597 Score: 186
Period size: 52 Copynumber: 2.0 Consensus size: 52
1011486 TTATAATATT
1011496 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATAC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATAC
* *
1011548 CTTGTAATTAGTTGTAATCCCCTAACTCTATGCTAGTTTCCTATTTCTAT
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTAT
1011598 GTGTCCAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.43
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATAC
Found at i:1016168 original size:52 final size:52
Alignment explanation
Indices: 1016090--1016192 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
1016080 TTATAATATT
1016090 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGATAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGATAGTCTCCTATTTCTATGC
* *
1016142 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGATAGTCTCCTATTTCTATG
1016193 TGTCCAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGATAGTCTCCTATTTCTATGC
Found at i:1016977 original size:20 final size:19
Alignment explanation
Indices: 1016939--1016977 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1016929 TCTGTTACAA
*
1016939 CTATAGTTATAGTCTATGG
1 CTATAGTTATAGACTATGG
*
1016958 CTATGGTTATAAGACTATGG
1 CTATAGTTAT-AGACTATGG
1016978 TTAGAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.38
Consensus pattern (19 bp):
CTATAGTTATAGACTATGG
Found at i:1017898 original size:32 final size:33
Alignment explanation
Indices: 1017827--1017898 Score: 130
Period size: 32 Copynumber: 2.2 Consensus size: 33
1017817 TCAACATTTA
1017827 TACAAATTATTCTTACTAAAGTAATCGAGAATT
1 TACAAATTATTCTTACTAAAGTAATCGAGAATT
1017860 TA-AAATTATTCTTACTAAAGTAATCGAGAA-T
1 TACAAATTATTCTTACTAAAGTAATCGAGAATT
1017891 TACAAATT
1 TACAAATT
1017899 TTAAATTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
31 3 0.08
32 33 0.87
33 2 0.05
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (33 bp):
TACAAATTATTCTTACTAAAGTAATCGAGAATT
Found at i:1018014 original size:22 final size:23
Alignment explanation
Indices: 1017979--1018023 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1017969 AAGTCTCATC
* *
1017979 TAATTTAAAGAT-AATTATAGAA
1 TAATTTAAACATAAAATATAGAA
*
1018001 TAATTTTAACATAAAATATAGAA
1 TAATTTAAACATAAAATATAGAA
1018024 GAAGACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
TAATTTAAACATAAAATATAGAA
Found at i:1019476 original size:12 final size:12
Alignment explanation
Indices: 1019459--1019484 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1019449 TATATGATAC
1019459 GTTTTGCAATGG
1 GTTTTGCAATGG
1019471 GTTTTGCAATGG
1 GTTTTGCAATGG
1019483 GT
1 GT
1019485 ACCATTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.35, T:0.42
Consensus pattern (12 bp):
GTTTTGCAATGG
Found at i:1022190 original size:29 final size:29
Alignment explanation
Indices: 1022153--1022225 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
1022143 CCAACTCATA
* * * * *
1022153 GTCGTCATGCCCTCCGGGCGACCTTGTAG
1 GTCGTCATGCACGCCAGGCGACATGGTAG
*
1022182 GTCGCCATGCACGCCAGGCGACATGGTAG
1 GTCGTCATGCACGCCAGGCGACATGGTAG
1022211 GTCGTCATGCACGCC
1 GTCGTCATGCACGCC
1022226 CAGCGACCTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.15, C:0.34, G:0.32, T:0.19
Consensus pattern (29 bp):
GTCGTCATGCACGCCAGGCGACATGGTAG
Found at i:1022271 original size:20 final size:20
Alignment explanation
Indices: 1022245--1022316 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
1022235 TGTCCTGCGC
*
1022245 CCTGCTCCCCTGTATGCTCG
1 CCTGCTCCCCTGCATGCTCG
* *
1022265 TCTGCTCCCATGCATGCTCG
1 CCTGCTCCCCTGCATGCTCG
1022285 CCTGCTCCCCACTGCATGCTCG
1 CCTGCT-CCC-CTGCATGCTCG
1022307 CCTGCTCCCC
1 CCTGCTCCCC
1022317 ACTGCTCCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
20 23 0.51
21 6 0.13
22 16 0.36
ACGTcount: A:0.07, C:0.49, G:0.18, T:0.26
Consensus pattern (20 bp):
CCTGCTCCCCTGCATGCTCG
Found at i:1022303 original size:22 final size:21
Alignment explanation
Indices: 1022245--1022321 Score: 104
Period size: 22 Copynumber: 3.7 Consensus size: 21
1022235 TGTCCTGCGC
*
1022245 CCTGCTCCC-CTGTATGCTCG
1 CCTGCTCCCACTGCATGCTCG
*
1022265 TCTGCTCCCA-TGCATGCTCG
1 CCTGCTCCCACTGCATGCTCG
1022285 CCTGCTCCCCACTGCATGCTCG
1 CCTGCT-CCCACTGCATGCTCG
1022307 CCTGCTCCCCACTGC
1 CCTGCT-CCCACTGC
1022322 TCCATGCACC
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
20 22 0.43
21 4 0.08
22 25 0.49
ACGTcount: A:0.08, C:0.48, G:0.18, T:0.26
Consensus pattern (21 bp):
CCTGCTCCCACTGCATGCTCG
Found at i:1022875 original size:28 final size:30
Alignment explanation
Indices: 1022841--1022907 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
1022831 AATTAAAAAA
1022841 TTTATTAGTT-AAG-TATATTAAAGAATAG
1 TTTATTAGTTGAAGTTATATTAAAGAATAG
1022869 TTTATTAGTTGAAGTTATATTAAAGAATAG
1 TTTATTAGTTGAAGTTATATTAAAGAATAG
*
1022899 CTTATTAGT
1 TTTATTAGT
1022908 GTTTAAGGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 10 0.28
29 3 0.08
30 23 0.64
ACGTcount: A:0.39, C:0.01, G:0.15, T:0.45
Consensus pattern (30 bp):
TTTATTAGTTGAAGTTATATTAAAGAATAG
Found at i:1022988 original size:15 final size:16
Alignment explanation
Indices: 1022960--1022993 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1022950 GTTTGTTACT
1022960 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
1022976 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
1022991 TTA
1 TTA
1022994 ATTTTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:1025007 original size:47 final size:47
Alignment explanation
Indices: 1024938--1025031 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
1024928 GGCATCAAAT
1024938 GCCCCCAATGAATAAGGAGGATGGGTACCAT-CTCCTGAGCAAACCGC
1 GCCCCCAATGAATAAGGAGGATGGGTACCATACTCCTGAGC-AACCGC
1024985 GCCCCCAATGAATAAGGAGGATGGGTACCATACTCCTGAGCAACCGC
1 GCCCCCAATGAATAAGGAGGATGGGTACCATACTCCTGAGCAACCGC
1025032 AACGACCACA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 37 0.80
48 9 0.20
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.15
Consensus pattern (47 bp):
GCCCCCAATGAATAAGGAGGATGGGTACCATACTCCTGAGCAACCGC
Found at i:1025219 original size:11 final size:11
Alignment explanation
Indices: 1025203--1025280 Score: 54
Period size: 11 Copynumber: 7.0 Consensus size: 11
1025193 CATTACTAAT
1025203 AATCATTAGTA
1 AATCATTAGTA
1025214 AATCATTAGT-
1 AATCATTAGTA
* *
1025224 -ATCAATAATTA
1 AATC-ATTAGTA
*
1025235 AAT-ATTTAATA
1 AATCA-TTAGTA
*
1025246 AATCATTATTAA
1 AATCATTAGT-A
*
1025258 TAATAATTAGTA
1 -AATCATTAGTA
1025270 AATCATTAGTA
1 AATCATTAGTA
1025281 TCAAATCATT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
9 3 0.06
10 5 0.10
11 31 0.60
12 5 0.10
13 8 0.15
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (11 bp):
AATCATTAGTA
Found at i:1025251 original size:32 final size:32
Alignment explanation
Indices: 1025212--1025309 Score: 106
Period size: 32 Copynumber: 3.3 Consensus size: 32
1025202 TAATCATTAG
1025212 TAAATCATTAGTATCAATAATTAAATATTTAA
1 TAAATCATTAGTATCAATAATTAAATATTTAA
*
1025244 TAAATCATTA-T-T-AATAA-T--A-A-TTAG
1 TAAATCATTAGTATCAATAATTAAATATTTAA
*
1025268 TAAATCATTAGTATCAAATCATTAAATATTTAA
1 TAAATCATTAGTATC-AATAATTAAATATTTAA
1025301 -AAATCATTA
1 TAAATCATTA
1025310 ATAAATTCGA
Statistics
Matches: 54, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
24 13 0.24
25 2 0.04
26 2 0.04
28 5 0.09
29 6 0.11
30 1 0.02
31 2 0.04
32 20 0.37
33 3 0.06
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (32 bp):
TAAATCATTAGTATCAATAATTAAATATTTAA
Found at i:1025261 original size:56 final size:56
Alignment explanation
Indices: 1025192--1025309 Score: 193
Period size: 56 Copynumber: 2.1 Consensus size: 56
1025182 TCATATAATT
*
1025192 TCATTACTAATAATCATTAGTAAATCATTAGTATC-AATAATTAAATATTTAATAAA
1 TCATTACTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTTAA-AAA
* *
1025248 TCATTATTAATAATAATTAGTAAATCATTAGTATCAAATCATTAAATATTTAAAAA
1 TCATTACTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAAAA
1025304 TCATTA
1 TCATTA
1025310 ATAAATTCGA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
56 42 0.72
57 16 0.28
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (56 bp):
TCATTACTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAAAA
Found at i:1025414 original size:11 final size:11
Alignment explanation
Indices: 1025394--1025658 Score: 171
Period size: 11 Copynumber: 23.3 Consensus size: 11
1025384 ATTAGTAATA
*
1025394 ATTATTAAATT
1 ATTATTAAATC
*
1025405 ATTATAAAATC
1 ATTATTAAATC
*
1025416 ATTACTAAATC
1 ATTATTAAATC
*
1025427 ATTATTAAATT
1 ATTATTAAATC
*
1025438 ACTATTAAATC
1 ATTATTAAATC
*
1025449 ATTATTATAATG
1 ATTATTA-AATC
1025461 ATTATTAAATC
1 ATTATTAAATC
** *
1025472 ATTATTGTATT
1 ATTATTAAATC
1025483 ATTATTAAATC
1 ATTATTAAATC
*
1025494 ATTATTATAATT
1 ATTATTA-AATC
*
1025506 ATTATCAAATC
1 ATTATTAAATC
* *
1025517 ATTACTAAATT
1 ATTATTAAATC
* * * * *
1025528 ATCAATCATTA
1 ATTATTAAATC
*
1025539 AATATTAAAGTC
1 ATTATTAAA-TC
1025551 ATTATTAAATC
1 ATTATTAAATC
*
1025562 ATTATTATAATG
1 ATTATTA-AATC
1025574 ATTATTACTAATC
1 ATTATTA--AATC
*
1025587 A-T-TTAAATT
1 ATTATTAAATC
1025596 ATAATATTAAAATC
1 AT--TATT-AAATC
*
1025610 ATTACTAAATC
1 ATTATTAAATC
1025621 ATCAAATCATTAAAT-
1 AT----T-ATTAAATC
1025636 ATTA--AAATC
1 ATTATTAAATC
1025645 ATTATTAAATC
1 ATTATTAAATC
1025656 ATT
1 ATT
1025659 TTTATGGTTA
Statistics
Matches: 195, Mismatches: 41, Indels: 36
0.72 0.15 0.13
Matches are distributed among these distances:
8 4 0.02
9 8 0.04
10 1 0.01
11 117 0.60
12 43 0.22
13 7 0.04
14 6 0.03
15 3 0.02
16 6 0.03
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:1025489 original size:45 final size:45
Alignment explanation
Indices: 1025394--1025619 Score: 192
Period size: 45 Copynumber: 5.0 Consensus size: 45
1025384 ATTAGTAATA
* * *
1025394 ATTATTAAATTATTA-TAAAATCATTACTAAATCATTATTAAATT
1 ATTATTAAATCATTATTATAATCATTATTAAATCATTATTAAATT
* * **
1025438 ACTATTAAATCATTATTATAATGATTATTAAATCATTATTGTATT
1 ATTATTAAATCATTATTATAATCATTATTAAATCATTATTAAATT
* * *
1025483 ATTATTAAATCATTATTATAATTATTATCAAATCATTACTAAATT
1 ATTATTAAATCATTATTATAATCATTATTAAATCATTATTAAATT
* * * * * * *
1025528 ATCAATCATTAAATATTA-AAGTCATTATTAAATCATTATTATAATG
1 ATTATTAAATCATTATTATAA-TCATTATTAAATCATTATTA-AATT
*
1025574 ATTATTACTAATCATTTAAATTATAAT-ATTA--AAATCATTACTAAAT
1 ATTATTA--AATCA-TT--ATTATAATCATTATTAAATCATTATTAAAT
1025620 CATCAAATCA
Statistics
Matches: 143, Mismatches: 30, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
44 15 0.10
45 92 0.64
46 7 0.05
47 3 0.02
48 14 0.10
49 1 0.01
50 4 0.03
51 5 0.03
52 2 0.01
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (45 bp):
ATTATTAAATCATTATTATAATCATTATTAAATCATTATTAAATT
Found at i:1025643 original size:8 final size:9
Alignment explanation
Indices: 1025601--1025658 Score: 50
Period size: 8 Copynumber: 6.3 Consensus size: 9
1025591 AAATTATAAT
1025601 ATTAAAATC
1 ATTAAAATC
1025610 ATTACTAAATC
1 ATTA--AAATC
*
1025621 A-TCAAATC
1 ATTAAAATC
1025629 ATT-AAAT-
1 ATTAAAATC
1025636 ATTAAAATC
1 ATTAAAATC
1025645 ATTATTAAATC
1 ATTA--AAATC
1025656 ATT
1 ATT
1025659 TTTATGGTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
7 3 0.07
8 14 0.34
9 9 0.22
10 1 0.02
11 14 0.34
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (9 bp):
ATTAAAATC
Found at i:1025643 original size:16 final size:17
Alignment explanation
Indices: 1025593--1025649 Score: 64
Period size: 16 Copynumber: 3.3 Consensus size: 17
1025583 AATCATTTAA
1025593 ATTATAATATTAAAATC
1 ATTATAATATTAAAATC
*
1025610 ATTACTAA-ATCATCAAATC
1 ATTA-TAATAT--TAAAATC
1025629 ATTA-AATATTAAAATC
1 ATTATAATATTAAAATC
1025645 ATTAT
1 ATTAT
1025650 TAAATCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 10 0.30
17 8 0.24
18 5 0.15
19 10 0.30
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTATAATATTAAAATC
Found at i:1025971 original size:48 final size:48
Alignment explanation
Indices: 1025863--1026112 Score: 374
Period size: 48 Copynumber: 5.4 Consensus size: 48
1025853 ATTACTAATA
* * * *
1025863 ATTACTAATCATTACTATCAAATCATTAAAATTAACAAT-A-TTAATT
1 ATTACTAATCATTACTACCAAATCATTAATATTAATAATAATTTCATT
1025909 ATTACTAATCATTACTACCAAATCATTAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAATATTAATAATAATTTCATT
1025957 ATTACTAATCATTACTACCAAATCA-TAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAATATTAATAATAATTTCATT
1026004 ATTACT-ATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATT-AATATTAATAATAATTTCATT
*
1026052 A-T--TAAT-ATTACTATC-AATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATT-AATATTAATAATAATTTCATT
1026096 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
1026113 AATAATTATT
Statistics
Matches: 190, Mismatches: 5, Indels: 16
0.90 0.02 0.08
Matches are distributed among these distances:
44 30 0.16
45 10 0.05
46 56 0.29
47 35 0.18
48 59 0.31
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.42
Consensus pattern (48 bp):
ATTACTAATCATTACTACCAAATCATTAATATTAATAATAATTTCATT
Found at i:1026050 original size:22 final size:22
Alignment explanation
Indices: 1026025--1026096 Score: 87
Period size: 22 Copynumber: 3.3 Consensus size: 22
1026015 TACTACCAAA
1026025 TCATTAAATATTAATAATAATT
1 TCATTAAATATTAATAATAATT
*
1026047 TCATTATTAATATTACT-ATCAA--
1 TCATTA--AATATTAATAAT-AATT
1026069 TCATTAAATATTAATAATAATT
1 TCATTAAATATTAATAATAATT
1026091 TCATTA
1 TCATTA
1026097 TTACTAATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
20 10 0.24
21 2 0.05
22 18 0.43
23 2 0.05
24 10 0.24
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (22 bp):
TCATTAAATATTAATAATAATT
Found at i:1026154 original size:48 final size:47
Alignment explanation
Indices: 1025863--1026155 Score: 276
Period size: 48 Copynumber: 6.2 Consensus size: 47
1025853 ATTACTAATA
* *
1025863 ATTACTAATCATTACT-ATCAAATCATTAAA-ATTAACAAT-A-TTAATT
1 ATTAC-AATCATTACTAAT--AATCATTAAATATTAATAATAATTTCATT
1025909 ATTACTAATCATTACTACCA-AATCATT-AATATTAATAATAATTTCATT
1 ATTAC-AATCATTACTA--ATAATCATTAAATATTAATAATAATTTCATT
1025957 ATTACTAATCATTACTACCA-AATCA-T-AATATTAATAATAATTTCATT
1 ATTAC-AATCATTACTA--ATAATCATTAAATATTAATAATAATTTCATT
*
1026004 ATTACTATCATTACTACCA-AATCATTAAATATTAATAATAATTTCATT
1 ATTACAATCATTACTA--ATAATCATTAAATATTAATAATAATTTCATT
1026052 ATT--AAT-ATTACT-ATCAATCATTAAATATTAATAATAATTTCATT
1 ATTACAATCATTACTAAT-AATCATTAAATATTAATAATAATTTCATT
* * *
1026096 ATTACTAATCATTACTAAATAATTATTATAATTTTAA-ATATAAATTCATT
1 ATTAC-AATCATTACT-AATAATCATTA-AATATTAATA-ATAATTTCATT
1026146 ATTA-AATCAT
1 ATTACAATCAT
1026156 GATTAAATCA
Statistics
Matches: 222, Mismatches: 7, Indels: 34
0.84 0.03 0.13
Matches are distributed among these distances:
42 1 0.00
44 32 0.14
45 8 0.04
46 51 0.23
47 32 0.14
48 66 0.30
49 9 0.04
50 23 0.10
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (47 bp):
ATTACAATCATTACTAATAATCATTAAATATTAATAATAATTTCATT
Found at i:1026160 original size:11 final size:11
Alignment explanation
Indices: 1026091--1026176 Score: 57
Period size: 11 Copynumber: 7.3 Consensus size: 11
1026081 AATAATAATT
1026091 TCATTATTACTAA
1 TCATTATTA--AA
*
1026104 TCATTACTAAA
1 TCATTATTAAA
*
1026115 TAATTATTATAA
1 TCATTATTA-AA
*
1026127 T-TTTAAATATAAA
1 TCATT--AT-TAAA
1026140 TTCATTATTAAA
1 -TCATTATTAAA
*
1026152 TCATGATTAAA
1 TCATTATTAAA
*
1026163 TCATTACTAAA
1 TCATTATTAAA
1026174 TCA
1 TCA
1026177 AATCATCATT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
11 33 0.56
12 7 0.12
13 14 0.24
14 3 0.05
15 2 0.03
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.43
Consensus pattern (11 bp):
TCATTATTAAA
Found at i:1027039 original size:31 final size:32
Alignment explanation
Indices: 1026989--1027052 Score: 121
Period size: 31 Copynumber: 2.0 Consensus size: 32
1026979 ATATTGTGTT
1026989 AAACCGCAATTAAAAAAACCACGTAAAAATGC
1 AAACCGCAATTAAAAAAACCACGTAAAAATGC
1027021 AAACCGCAATT-AAAAAACCACGTAAAAATGC
1 AAACCGCAATTAAAAAAACCACGTAAAAATGC
1027052 A
1 A
1027053 CAAATATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.66
32 11 0.34
ACGTcount: A:0.56, C:0.22, G:0.09, T:0.12
Consensus pattern (32 bp):
AAACCGCAATTAAAAAAACCACGTAAAAATGC
Found at i:1029775 original size:28 final size:30
Alignment explanation
Indices: 1029735--1029797 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
1029725 ATTTTTTATA
*
1029735 TAATATAATATATAACTTAAACTAACAAAT
1 TAATATAATATATAACTTAAACTAACAAAC
1029765 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1029793 TAATA
1 TAATA
1029798 ATTTACACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1029807 original size:21 final size:21
Alignment explanation
Indices: 1029774--1029822 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1029764 TTAATATAAT
1029774 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1029795 ATAATTTACACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1029816 ATTAACT
1 A-TAACT
1029823 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1030308 original size:114 final size:114
Alignment explanation
Indices: 1030108--1030333 Score: 398
Period size: 114 Copynumber: 2.0 Consensus size: 114
1030098 CATTTAACAA
*
1030108 CTAAATTAACGATGCAATAATGCAGCTAGGGATACAGGAATCTCCCAGCTATGGATGCAACGCAT
1 CTAAATTAACGATGCAATAATACAGCTAGGGATACAGGAATCTCCCAGCTATGGATGCAACGCAT
*
1030173 GCATGAGGGAGCAAAGGGTTAAAGCTTGGTCGCCGGGTAGGAATCTCTG
66 GCATGAGGGAGCAAAGGGTTAAAGCTTGGTCGCCGGGCAGGAATCTCTG
* *
1030222 CTAAATTAACGATGCAATAATACAGCTAGGGATGCAGGAATCTCCCATCTATGGATGCAACGCAT
1 CTAAATTAACGATGCAATAATACAGCTAGGGATACAGGAATCTCCCAGCTATGGATGCAACGCAT
* *
1030287 GCATGAGGGAGCAGAGGGTTAAAGCTTGGTCGTCGGGCAGGAATCTC
66 GCATGAGGGAGCAAAGGGTTAAAGCTTGGTCGCCGGGCAGGAATCTC
1030334 CCCACTATGG
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (114 bp):
CTAAATTAACGATGCAATAATACAGCTAGGGATACAGGAATCTCCCAGCTATGGATGCAACGCAT
GCATGAGGGAGCAAAGGGTTAAAGCTTGGTCGCCGGGCAGGAATCTCTG
Found at i:1030911 original size:23 final size:23
Alignment explanation
Indices: 1030868--1030912 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1030858 TTTATGAATT
*
1030868 TAATATTAATAAATATTTTAATA
1 TAATATTAATAAATATATTAATA
*
1030891 TAATTTTAATCAAA-ATATTAAT
1 TAATATTAAT-AAATATATTAAT
1030913 TATTAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATATTAATAAATATATTAATA
Found at i:1030984 original size:29 final size:33
Alignment explanation
Indices: 1030932--1031002 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
1030922 ATTTAAGATG
*
1030932 TATTTATTAATATTTCTAATAATA-AA-A-ATTA
1 TATTT-TTAATATTTATAATAATATAAGATATTA
1030963 TATTTTTAATA-TTATAATAATATAAGATATTA
1 TATTTTTAATATTTATAATAATATAAGATATTA
1030995 TATTTTTA
1 TATTTTTA
1031003 TTTTAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 10 0.28
30 8 0.22
31 6 0.17
32 12 0.33
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (33 bp):
TATTTTTAATATTTATAATAATATAAGATATTA
Found at i:1031004 original size:29 final size:29
Alignment explanation
Indices: 1030948--1031015 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
1030938 TTAATATTTC
1030948 TAATAATA-AAAATTATATTTTTAATATTA
1 TAATAATATAAAATTATATTTTT-ATATTA
1030977 TAATAATATAAGATATTATATTTTTAT-TT-
1 TAATAATATAA-A-ATTATATTTTTATATTA
*
1031006 TAAAAATATA
1 TAATAATATA
1031016 TAATAAATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 17 0.49
30 4 0.11
31 3 0.09
32 11 0.31
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TAATAATATAAAATTATATTTTTATATTA
Found at i:1031299 original size:22 final size:22
Alignment explanation
Indices: 1031274--1031357 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 22
1031264 TATTAACAAA
1031274 ATTATAAAAATAATATTTTAAT
1 ATTATAAAAATAATATTTTAAT
1031296 ATTA-AATAAAT--TATTTTAAT
1 ATTATAA-AAATAATATTTTAAT
* *
1031316 ATTTTAAAAATAATAATATTAAGT
1 ATTATAAAAATAAT-ATTTTAA-T
* *
1031340 TTTATGATAAATAATATT
1 ATTAT-AAAAATAATATT
1031358 ATTTATTGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
20 16 0.33
21 4 0.08
22 9 0.18
23 6 0.12
24 6 0.12
25 8 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTATAAAAATAATATTTTAAT
Found at i:1031479 original size:15 final size:15
Alignment explanation
Indices: 1031456--1031485 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1031446 TCGTAAAACG
1031456 TTTTCCAGAAAATGT
1 TTTTCCAGAAAATGT
*
1031471 TTTTTCAGAAAATGT
1 TTTTCCAGAAAATGT
1031486 AATTCATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (15 bp):
TTTTCCAGAAAATGT
Found at i:1034607 original size:3 final size:3
Alignment explanation
Indices: 1034601--1034658 Score: 57
Period size: 3 Copynumber: 19.0 Consensus size: 3
1034591 TTATGATTAT
*
1034601 TAA TAA TAA TAA GTAA -AGA TAA TAA TTAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA -TAA TA-A TAA TAA -TAA TAA TAA TAA TAA TAA TAA
*
1034648 -AT TAA TAA TAA
1 TAA TAA TAA TAA
1034659 AAAATGGTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
2 2 0.04
3 37 0.80
4 7 0.15
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1034624 original size:13 final size:13
Alignment explanation
Indices: 1034601--1034647 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1034591 TTATGATTAT
1034601 TAATAATAATAAG
1 TAATAATAATAAG
*
1034614 TAA-AGATAATAAT
1 TAATA-ATAATAAG
1034627 TAATAATAATAA-
1 TAATAATAATAAG
*
1034639 TTATAATAA
1 TAATAATAA
1034648 ATTAATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 9 0.30
13 20 0.67
14 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (13 bp):
TAATAATAATAAG
Found at i:1034628 original size:26 final size:23
Alignment explanation
Indices: 1034599--1034658 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 23
1034589 TATTATGATT
1034599 ATTAATAATAATAAGTAAAGATAATA
1 ATTAATAATAATAAGTAAA-AT-A-A
* *
1034625 ATTAATAATAATAATTATAATAA
1 ATTAATAATAATAAGTAAAATAA
1034648 ATTAATAATAA
1 ATTAATAATAA
1034659 AAAATGGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 12 0.38
24 1 0.03
25 2 0.06
26 17 0.53
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (23 bp):
ATTAATAATAATAAGTAAAATAA
Found at i:1034634 original size:23 final size:23
Alignment explanation
Indices: 1034604--1034658 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1034594 TGATTATTAA
1034604 TAATAATAAGTAAAGATAAT-AAT
1 TAATAATAA-TAAAGATAATAAAT
**
1034627 TAATAATAATAATTATAATAAAT
1 TAATAATAATAAAGATAATAAAT
1034650 TAATAATAA
1 TAATAATAA
1034659 AAAATGGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
TAATAATAATAAAGATAATAAAT
Found at i:1038699 original size:36 final size:36
Alignment explanation
Indices: 1038335--1038697 Score: 424
Period size: 36 Copynumber: 10.1 Consensus size: 36
1038325 TAGCCCCAGA
* * * * *
1038335 TTCAGTAGCCAATTCATCTTGAGGCTCAGCCCGTGG
1 TTCAGTAGCTAATTCATGTTGAGGCTTAGCCTGAGG
*
1038371 TTCAGTTA-CTAATTCATGTTTG-GGCTCAGCCTGAGG
1 TTCAG-TAGCTAATTCATG-TTGAGGCTTAGCCTGAGG
* * *
1038407 TTTAGTAGCTAATTCATGTTTAGGCTTAGCCAGAGG
1 TTCAGTAGCTAATTCATGTTGAGGCTTAGCCTGAGG
* ** *
1038443 TTCAGTAGCTAATTCTTGCCGAGGCTTAGCATGAGG
1 TTCAGTAGCTAATTCATGTTGAGGCTTAGCCTGAGG
* ** *
1038479 TTCAGTAGCTAATTCTTGCCGAGGCTTAGCATGAGG
1 TTCAGTAGCTAATTCATGTTGAGGCTTAGCCTGAGG
** *
1038515 TTCAGTAGCTAATTCATGACGAGGCTTTGCCTGAGG
1 TTCAGTAGCTAATTCATGTTGAGGCTTAGCCTGAGG
** * *
1038551 TTCAGTAGCTAATTCATGCCGAGGCTTTGCCTGAGT
1 TTCAGTAGCTAATTCATGTTGAGGCTTAGCCTGAGG
*
1038587 TTCAGTAGCTAATTCATGTTTAGGCTTAGCCTGAGG
1 TTCAGTAGCTAATTCATGTTGAGGCTTAGCCTGAGG
* * * *
1038623 TTCGGTAGTTAATTCAAGTTGAGGCTTAGCCAGAGG
1 TTCAGTAGCTAATTCATGTTGAGGCTTAGCCTGAGG
*
1038659 TTCGGTAGCTAATTCATGTTGAGGCTTAGCCTGAGG
1 TTCAGTAGCTAATTCATGTTGAGGCTTAGCCTGAGG
1038695 TTC
1 TTC
1038698 GGGATCAAAC
Statistics
Matches: 289, Mismatches: 34, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
35 4 0.01
36 280 0.97
37 5 0.02
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (36 bp):
TTCAGTAGCTAATTCATGTTGAGGCTTAGCCTGAGG
Found at i:1040590 original size:2 final size:2
Alignment explanation
Indices: 1040583--1040610 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1040573 TGACATTTTA
1040583 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
1040611 TATCAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1040785 original size:19 final size:19
Alignment explanation
Indices: 1040751--1040787 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1040741 ATGACCAACA
* *
1040751 AAATCGCAATGTGATCTCT
1 AAATCGCAACGCGATCTCT
1040770 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1040788 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1040917 original size:20 final size:20
Alignment explanation
Indices: 1040894--1041027 Score: 96
Period size: 20 Copynumber: 6.7 Consensus size: 20
1040884 GAATATGTAA
1040894 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
1040914 ATCGCAACGCGA-TCTCCAGT
1 ATCGCAACGCGATTCT-GACT
** * *
1040934 ATCGCAAATCAGTTTCCAGA-T
1 ATCGCAACGC-GATT-CTGACT
1040955 -TCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* ** *
1040974 ATCGCAACTCGATAAT-ACAAA
1 ATCGCAACGCGATTCTGAC--T
*
1040995 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1041015 ATCGCAACGCGAT
1 ATCGCAACGCGAT
1041028 AATACATAAT
Statistics
Matches: 84, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
18 3 0.04
19 9 0.11
20 53 0.63
21 14 0.17
22 4 0.05
23 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1041007 original size:41 final size:41
Alignment explanation
Indices: 1040955--1041169 Score: 152
Period size: 41 Copynumber: 5.1 Consensus size: 41
1040945 GTTTCCAGAT
1040955 TCGCAACGCGATTCTGACTATCGCAACTCGATAATACAAAA
1 TCGCAACGCGATTCTGACTATCGCAACTCGATAATACAAAA
* * *
1040996 TCGCAATGCGATTCTGACTATCGCAACGCGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACTCGATAATACAAAA
*** * * ** **
1041037 TCGCGTTGTTGCAATTTTAGAAAATCGCAA-TGCG--AATATGTAAA
1 TCGC---AACGCGATTCT-GACTATCGCAACT-CGATAATA-CAAAA
* * * *
1041081 TTGCAACGCGGTTCTGACTATCGCATCGCGATAATACAAAA
1 TCGCAACGCGATTCTGACTATCGCAACTCGATAATACAAAA
**
1041122 TCGCAACGCGATAAT-ACATAATCGCAA-TGCGATAATACAAAA
1 TCGCAACGCGATTCTGAC-T-ATCGCAACT-CGATAATACAAAA
1041164 TCGCAA
1 TCGCAA
1041170 TGTGATTTTC
Statistics
Matches: 130, Mismatches: 32, Indels: 23
0.70 0.17 0.12
Matches are distributed among these distances:
40 12 0.09
41 62 0.48
42 29 0.22
43 4 0.03
44 12 0.09
45 11 0.08
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAACTCGATAATACAAAA
Found at i:1041039 original size:142 final size:142
Alignment explanation
Indices: 1040772--1041040 Score: 337
Period size: 142 Copynumber: 1.9 Consensus size: 142
1040762 TGATCTCTAA
*
1040772 ATCGCAACGCGATCTCCAGTATCGCAAATCAGTTTACAGATTCGCAACGCGATTTTGACTATCGC
1 ATCGCAACGCGATCTCCAGTATCGCAAATCAGTTTACAGATTCGCAACGCGATTCTGACTATCGC
* * ** * * ** * * **
1040837 ATTGTGATTTTCCAAATTCGCGTTGCGATTTTAGAAAATCACAATGCGAATATGTAAATCGCAAC
66 ACTGCGATAATACAAAATCGCAATGCGATTCTAGAAAATCACAACGCGAATACATAAATCGCAAC
1040902 GCGATTCTGACT
131 GCGATTCTGACT
*
1040914 ATCGCAACGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTCTGACTATCGC
1 ATCGCAACGCGATCTCCAGTATCGCAAATCAGTTTACAGATTCGCAACGCGATTCTGACTATCGC
** *
1040979 AACT-CGATAATACAAAATCGCAATGCGATTCT-GACTATCGCAACGCGATAATACAT-AATCGC
66 -ACTGCGATAATACAAAATCGCAATGCGATTCTAGAAAATCACAACGCG--AATACATAAATCGC
1041041 GTTGTTGCAA
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
141 11 0.10
142 89 0.83
143 7 0.07
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (142 bp):
ATCGCAACGCGATCTCCAGTATCGCAAATCAGTTTACAGATTCGCAACGCGATTCTGACTATCGC
ACTGCGATAATACAAAATCGCAATGCGATTCTAGAAAATCACAACGCGAATACATAAATCGCAAC
GCGATTCTGACT
Found at i:1041183 original size:21 final size:21
Alignment explanation
Indices: 1041100--1041171 Score: 110
Period size: 21 Copynumber: 3.4 Consensus size: 21
1041090 GGTTCTGACT
1041100 ATCGC-ATCGCGATAATACAAA
1 ATCGCAAT-GCGATAATACAAA
* *
1041121 ATCGCAACGCGATAATACATA
1 ATCGCAATGCGATAATACAAA
1041142 ATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATAATACAAA
1041163 ATCGCAATG
1 ATCGCAATG
1041172 TGATTTTCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 45 0.98
22 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.19
Consensus pattern (21 bp):
ATCGCAATGCGATAATACAAA
Found at i:1041619 original size:19 final size:19
Alignment explanation
Indices: 1041595--1041703 Score: 101
Period size: 19 Copynumber: 5.4 Consensus size: 19
1041585 TTATTTTGGA
1041595 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
1041614 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
1041636 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
1041658 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
* * *
1041677 ATTTTAACTATTGCAACAC
1 TTTTTCACTATCGCAACAC
1041696 ATTTTTCA
1 -TTTTTCA
1041704 AAATCGCGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
19 43 0.57
20 5 0.07
21 4 0.05
22 12 0.16
23 6 0.08
25 6 0.08
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.36
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:1042791 original size:21 final size:21
Alignment explanation
Indices: 1042758--1042799 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1042748 AAATCAAAAT
*
1042758 TTAATATTATAATTAA-ATTAA
1 TTAAAATTATAA-TAATATTAA
*
1042779 TTAAAATTTTAATAATATTAA
1 TTAAAATTATAATAATATTAA
1042800 CATTATACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAAATTATAATAATATTAA
Found at i:1050513 original size:2 final size:2
Alignment explanation
Indices: 1050506--1050532 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1050496 TTGGTGGAAT
1050506 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1050533 TCCAACTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1051939 original size:15 final size:15
Alignment explanation
Indices: 1051919--1051954 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1051909 CCAAGACTAC
1051919 TCGAACTGTTGTTAG
1 TCGAACTGTTGTTAG
1051934 TCGAACTGTTGTTAG
1 TCGAACTGTTGTTAG
1051949 TCGAAC
1 TCGAAC
1051955 CACAGGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (15 bp):
TCGAACTGTTGTTAG
Found at i:1052380 original size:22 final size:22
Alignment explanation
Indices: 1052352--1052404 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1052342 ACTATATTGT
1052352 ATGAACAGTGCCATGAACA-TCA
1 ATGAACAGTGCCATGAACAGT-A
* * *
1052374 ATGAACAATGTCGTGAACAGTA
1 ATGAACAGTGCCATGAACAGTA
1052396 ATGAACAGT
1 ATGAACAGT
1052405 TAAAAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (22 bp):
ATGAACAGTGCCATGAACAGTA
Found at i:1059031 original size:119 final size:119
Alignment explanation
Indices: 1058853--1059067 Score: 301
Period size: 119 Copynumber: 1.8 Consensus size: 119
1058843 GTTTCTTCTG
* ** * *
1058853 ATGACCCGACTGTAAGCAACGGTGCTTCACAGACAAGACAAAGGTATATAATTCATTTTTGTTCT
1 ATGACCCGACTGTAAGCAACAGTGAGTCACAGACAAGACAAAGATATAGAATTCATTTTTGTTCT
*
1058918 CTCT-TAAATTTCAATTCTTAAACCCTAATTTTTCCAAGTACTCAATTTCATTCA
66 AT-TGTAAATTTCAATTCTTAAACCCTAATTTTTCCAAGTACTCAATTTCATTCA
*
1058972 ATGACCCGACTGTAA-CAGACAGTGAGTCACAGACAAGACAAAGATATCGAATTTC-TTTTTGTT
1 ATGACCCGACTGTAAGCA-ACAGTGAGTCACAGACAAGACAAAGATATAGAA-TTCATTTTTGTT
* *
1059035 TTATTGTAAATTTCAATTCTTAAACCTTAATTT
64 CTATTGTAAATTTCAATTCTTAAACCCTAATTT
1059068 CCCCATTGAT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
118 3 0.04
119 78 0.93
120 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (119 bp):
ATGACCCGACTGTAAGCAACAGTGAGTCACAGACAAGACAAAGATATAGAATTCATTTTTGTTCT
ATTGTAAATTTCAATTCTTAAACCCTAATTTTTCCAAGTACTCAATTTCATTCA
Found at i:1075894 original size:3 final size:3
Alignment explanation
Indices: 1075888--1075926 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
1075878 AATTTTTTTT
* *
1075888 TTA TTA TTA TTA TTA ATG TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1075927 ATAATTACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1078969 original size:30 final size:31
Alignment explanation
Indices: 1078928--1078988 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
1078918 ATGAGTGAAC
*
1078928 ACATCAGTGATTAAAATGTAAT-AATCAATA
1 ACATAAGTGATTAAAATGTAATAAATCAATA
* *
1078958 ACATAAGTGATTAAATTTTAATAAATCAATA
1 ACATAAGTGATTAAAATGTAATAAATCAATA
1078989 GTGTAAGTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (31 bp):
ACATAAGTGATTAAAATGTAATAAATCAATA
Found at i:1079759 original size:31 final size:31
Alignment explanation
Indices: 1079721--1079781 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1079711 TTATACGGCG
1079721 TAGAATAGTCGTGCTCAACCCCAAATTGGCA
1 TAGAATAGTCGTGCTCAACCCCAAATTGGCA
* *
1079752 TAGAATAGTCGTGCTCAACCTCGAATTGGC
1 TAGAATAGTCGTGCTCAACCCCAAATTGGC
1079782 GAATTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (31 bp):
TAGAATAGTCGTGCTCAACCCCAAATTGGCA
Found at i:1082476 original size:153 final size:153
Alignment explanation
Indices: 1082198--1082512 Score: 526
Period size: 153 Copynumber: 2.1 Consensus size: 153
1082188 CCAAGCATTG
* * *
1082198 AATTTGTGTACTAAAAAAATCAACATCGTGCTTGCATAATTTCTAATTGAAGTTGTTGTCCAAAA
1 AATTTGTGTACTAAAAAAATCAACATCGTGCTTACATAATTTCTAATTGAAATTATTGTCCAAAA
**
1082263 CAATGTAGTTGCATTTAATTAATTTATTTTTATTATACCCTAAATTAGTGGGGGTCATAACTCCC
66 CAATGTAGTTGCATTTAATTAATTTATTTTTATTATACCCTAAATTAGTGACGGTCATAACTCCC
1082328 ACCTAAACCCAATTTCAATTAGA
131 ACCTAAACCCAATTTCAATTAGA
1082351 AATTTGTGTACTAAAGAAAA-CAACATCGTGCTTACATAATTTCTAATTGAAATTATTGTCCAAA
1 AATTTGTGTACTAAA-AAAATCAACATCGTGCTTACATAATTTCTAATTGAAATTATTGTCCAAA
* *
1082415 ATAGT-TCAGTTGCATTTAATTAATTTATTTTTATTATACCCTAAATTAGTGACGGTCATAACTC
65 ACAATGT-AGTTGCATTTAATTAATTTATTTTTATTATACCCTAAATTAGTGACGGTCATAACTC
1082479 CCACCTAAACCCAATTTCAATTAGA
129 CCACCTAAACCCAATTTCAATTAGA
1082504 AATTATGTG
1 AATT-TGTG
1082513 AGCACGATGT
Statistics
Matches: 152, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
152 1 0.01
153 143 0.94
154 8 0.05
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (153 bp):
AATTTGTGTACTAAAAAAATCAACATCGTGCTTACATAATTTCTAATTGAAATTATTGTCCAAAA
CAATGTAGTTGCATTTAATTAATTTATTTTTATTATACCCTAAATTAGTGACGGTCATAACTCCC
ACCTAAACCCAATTTCAATTAGA
Found at i:1083450 original size:56 final size:56
Alignment explanation
Indices: 1083385--1083500 Score: 205
Period size: 56 Copynumber: 2.1 Consensus size: 56
1083375 GATGAGCATT
*
1083385 ATTAATTTAATTTATAAAAAATTAAAATTCTAAAAAGGCTCAACGTATAATTATAA
1 ATTAATTTAATTTATAAAAAATTAAAATTCTAAAAAGGCCCAACGTATAATTATAA
* *
1083441 ATTAATTTAATTTATAAAAATTTAAAATTTTAAAAAGGCCCAACGTATAATTATAA
1 ATTAATTTAATTTATAAAAAATTAAAATTCTAAAAAGGCCCAACGTATAATTATAA
1083497 ATTA
1 ATTA
1083501 GTATGATATA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (56 bp):
ATTAATTTAATTTATAAAAAATTAAAATTCTAAAAAGGCCCAACGTATAATTATAA
Found at i:1083711 original size:23 final size:24
Alignment explanation
Indices: 1083679--1083730 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
1083669 CAAATGTAGT
*
1083679 TTTTTAAAAATATATAATATAT-A
1 TTTTTAAAAACATATAATATATAA
* *
1083702 TTTTTGAAAACGTATAATATATAA
1 TTTTTAAAAACATATAATATATAA
1083726 TTTTT
1 TTTTT
1083731 TTAATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (24 bp):
TTTTTAAAAACATATAATATATAA
Found at i:1083767 original size:25 final size:25
Alignment explanation
Indices: 1083738--1083800 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
1083728 TTTTTAATAT
* *
1083738 TTTTTGAAAATATATAATATATAGC
1 TTTTTAAAAATATATAATATATAAC
** *
1083763 TTTTTAAAAACGTATAATATATAAT
1 TTTTTAAAAATATATAATATATAAC
*
1083788 TTTTTTAAAATAT
1 TTTTTAAAAATAT
1083801 TTTTGAAACG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (25 bp):
TTTTTAAAAATATATAATATATAAC
Found at i:1083767 original size:36 final size:37
Alignment explanation
Indices: 1083697--1083767 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
1083687 AATATATAAT
* *
1083697 ATATATTTTTGAAAACGTATAATATATAATTTTTTTA
1 ATATATTTTTGAAAACATATAATATATAACTTTTTTA
* *
1083734 ATAT-TTTTTGAAAATATATAATATATAGCTTTTT
1 ATATATTTTTGAAAACATATAATATATAACTTTTT
1083768 AAAAACGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 26 0.87
37 4 0.13
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (37 bp):
ATATATTTTTGAAAACATATAATATATAACTTTTTTA
Found at i:1083776 original size:61 final size:60
Alignment explanation
Indices: 1083678--1083833 Score: 217
Period size: 61 Copynumber: 2.6 Consensus size: 60
1083668 TCAAATGTAG
* * *
1083678 TTTTTTAAAAATATATAATATATA-TTTTTGAAAACGTATAATATATAATTTTTTTAATA
1 TTTTTTGAAAATATATAATATATAGTTTTTAAAAACGTATAATATATAATTTTTTTAAAA
1083737 TTTTTTGAAAATATATAATATATAGCTTTTTAAAAACGTATAATATATAATTTTTTTAAAA
1 TTTTTTGAAAATATATAATATATAG-TTTTTAAAAACGTATAATATATAATTTTTTTAAAA
** *
1083798 TATTTTTG-AAACGTATAATATATGGTTTTCTAAAAA
1 T-TTTTTGAAAATATATAATATATAGTTTT-TAAAAA
1083834 ATATTTTTGA
Statistics
Matches: 87, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
59 23 0.26
60 4 0.05
61 54 0.62
62 6 0.07
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (60 bp):
TTTTTTGAAAATATATAATATATAGTTTTTAAAAACGTATAATATATAATTTTTTTAAAA
Found at i:1083857 original size:38 final size:36
Alignment explanation
Indices: 1083763--1083900 Score: 134
Period size: 38 Copynumber: 3.7 Consensus size: 36
1083753 AATATATAGC
* **
1083763 TTTTTAAAAACGTATAATATATAATTTTTTTAAAATA
1 TTTTTGAAAACGTATAATATAT-ATTTTTAAAAAATA
*
1083800 TTTTTG-AAACGTATAATATATGGTTTTCTAAAAAATA
1 TTTTTGAAAACGTATAATATAT-ATTTT-TAAAAAATA
* **
1083837 TTTTTGAAAACGTACAATATATATATTTTTAAAAACGA
1 TTTTTGAAAACGTA-TA-ATATATATTTTTAAAAAATA
* *
1083875 TTTTTGAAAACATGTAATATAATATT
1 TTTTTGAAAACGTATAATAT-ATATT
1083901 ATATAGTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
36 23 0.27
37 24 0.29
38 26 0.31
39 5 0.06
40 6 0.07
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.44
Consensus pattern (36 bp):
TTTTTGAAAACGTATAATATATATTTTTAAAAAATA
Found at i:1083922 original size:20 final size:19
Alignment explanation
Indices: 1083897--1083934 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1083887 TGTAATATAA
*
1083897 TATTATATAGTTTTTATTTT
1 TATTATATA-TTATTATTTT
1083917 TATTATATATTATTATTT
1 TATTATATATTATTATTT
1083935 AGTTAGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TATTATATATTATTATTTT
Found at i:1088580 original size:64 final size:63
Alignment explanation
Indices: 1088511--1088665 Score: 163
Period size: 64 Copynumber: 2.4 Consensus size: 63
1088501 TAATGAAGGT
**
1088511 ATGCATCGATGCACTACTTGTGCATC-AGTGCA-TAAAATGCATTCGATGTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGA-TGCACT-AAATGCATTCGATGTTTTATT-TTAAAAG
1088574 A
63 A
* * * * * *
1088575 ATGCATTGATGCA-TGCCTTATTCATCGATGCACTAATTGCATTCGATTTTTTATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTATTTTAAAAGA
* *
1088638 GTGCATCGATGCACTACCTGTGCATCGA
1 ATGCATCGATGCACTACTTGTGCATCGA
1088666 AACACTTTCA
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
63 27 0.37
64 44 0.60
65 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTATTTTAAAAGA
Found at i:1090777 original size:18 final size:17
Alignment explanation
Indices: 1090756--1090816 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 17
1090746 TGGTCCTTCA
1090756 GGACATAGTGGTCATTTG
1 GGACATAGTGGTC-TTTG
*
1090774 GGACATATACAGAGGTCTTTCG
1 GGAC--AT--AGTGGTCTTT-G
1090796 GGACATAGTGGTCCTTTG
1 GGACATAGTGGT-CTTTG
1090814 GGA
1 GGA
1090817 TAAATATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
18 13 0.37
19 4 0.11
20 4 0.11
21 3 0.09
22 11 0.31
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.30
Consensus pattern (17 bp):
GGACATAGTGGTCTTTG
Found at i:1090800 original size:40 final size:40
Alignment explanation
Indices: 1090738--1090816 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
1090728 GAGTCGAGGG
*
1090738 ATATACAGTGGTCCTTCAGGACATAGTGGTCATTTGGGAC
1 ATATACAGAGGTCCTTCAGGACATAGTGGTCATTTGGGAC
* * *
1090778 ATATACAGAGGTCTTTCGGGACATAGTGGTCCTTTGGGA
1 ATATACAGAGGTCCTTCAGGACATAGTGGTCATTTGGGA
1090817 TAAATATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.30
Consensus pattern (40 bp):
ATATACAGAGGTCCTTCAGGACATAGTGGTCATTTGGGAC
Found at i:1091345 original size:11 final size:11
Alignment explanation
Indices: 1091326--1091360 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1091316 GTAAATGTAT
*
1091326 AGTATTGTAGC
1 AGTACTGTAGC
*
1091337 AGTACTGTAGT
1 AGTACTGTAGC
1091348 AGTACTGTAGC
1 AGTACTGTAGC
1091359 AG
1 AG
1091361 GGGAATCAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (11 bp):
AGTACTGTAGC
Found at i:1092508 original size:18 final size:17
Alignment explanation
Indices: 1092485--1092519 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1092475 AGTTATTAAG
*
1092485 ATTAAATTATTTTAATAT
1 ATTAAATT-TTTAAATAT
1092503 ATTAAATTTTTAAATAT
1 ATTAAATTTTTAAATAT
1092520 CGAACTTGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTAAATTTTTAAATAT
Found at i:1092942 original size:12 final size:12
Alignment explanation
Indices: 1092927--1092972 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1092917 CGGTTTTTTT
*
1092927 ACCGGATAAAAA
1 ACCGGTTAAAAA
1092939 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
1092954 ACCGGTTAAAAA
1 ACCGGTTAAAAA
1092966 ACCGGTT
1 ACCGGTT
1092973 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:1092954 original size:15 final size:13
Alignment explanation
Indices: 1092933--1092973 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
1092923 TTTTACCGGA
1092933 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1092946 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
1092960 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1092973 T
1 T
1092974 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:1095289 original size:21 final size:21
Alignment explanation
Indices: 1095265--1095304 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1095255 TTTATTTTAT
1095265 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1095286 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1095305 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1095352 original size:33 final size:33
Alignment explanation
Indices: 1095299--1095397 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1095289 TTTGTTTCAA
1095299 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1095331 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1095364 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1095397 T
1 T
1095398 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1095426 original size:13 final size:13
Alignment explanation
Indices: 1095383--1095437 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1095373 TTGGAAGTAT
1095383 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1095396 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1095410 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
1095423 TTAAGTATTTGAA
1 TTAAGTATTTCAA
1095436 TT
1 TT
1095438 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1095685 original size:21 final size:21
Alignment explanation
Indices: 1095633--1095689 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1095623 TGGAGCATGG
**
1095633 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTTCCTCTCATA
1095654 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTTCCTCTCATA
1095675 GGGAATCGGTTTCCT
1 GGGAATCGGTTTCCT
1095690 AAGTGTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (21 bp):
GGGAATCGGTTTCCTCTCATA
Found at i:1095906 original size:15 final size:15
Alignment explanation
Indices: 1095854--1095907 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
1095844 ATCTGGAATA
*
1095854 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1095869 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
1095884 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
1095901 TTAAAAC
1 TTAAAAC
1095908 TGAAACCGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 19 0.59
17 13 0.41
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1095918 original size:21 final size:18
Alignment explanation
Indices: 1095873--1095906 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1095863 GTTTTTTTAT
1095873 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
1095890 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
1095907 CTGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:1096027 original size:15 final size:17
Alignment explanation
Indices: 1096001--1096032 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1095991 TTCTATGGGA
1096001 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1096017 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1096033 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1096435 original size:2 final size:2
Alignment explanation
Indices: 1096428--1096468 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1096418 ACTTGTAAAA
1096428 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1096469 AGGACAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1098262 original size:13 final size:13
Alignment explanation
Indices: 1098233--1098267 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1098223 ATAACTAATA
*
1098233 ATATTAAAT-ATT
1 ATATTAAATAAAT
1098245 ATATTAAATAAAT
1 ATATTAAATAAAT
1098258 ATATTAAATA
1 ATATTAAATA
1098268 TTTATGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:1101574 original size:126 final size:126
Alignment explanation
Indices: 1101369--1101971 Score: 1165
Period size: 126 Copynumber: 4.8 Consensus size: 126
1101359 CTATAATCGG
1101369 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
1101433 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1101494 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
1101559 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
1101620 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1101685 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1101746 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1101811 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1101872 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1101936 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
1101972 ATAACTTAAA
Statistics
Matches: 474, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
125 100 0.21
126 374 0.79
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:1102420 original size:33 final size:34
Alignment explanation
Indices: 1102359--1102458 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
1102349 AAATTTAATG
*
1102359 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
1102393 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
1102426 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
1102459 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:1103064 original size:21 final size:21
Alignment explanation
Indices: 1102977--1103069 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
1102967 TATGGTATAA
*
1102977 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1102998 AA-CCTG-GCGGCTAGGCATGT
1 AACCCTGCG-GGCTAGGAATGT
1103018 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1103039 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1103060 AACCCTGCGG
1 AACCCTGCGG
1103070 AGATGGCATA
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
19 1 0.02
20 21 0.32
21 40 0.61
22 4 0.06
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1103099 original size:21 final size:21
Alignment explanation
Indices: 1103073--1103120 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1103063 CCTGCGGAGA
*
1103073 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1103094 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1103115 GGGCAT
1 TGGCAT
1103121 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Done.