Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009460.1 Hibiscus syriacus cultivar Beakdansim tig00113722_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: 2853300
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 13 of 14
Found at i:2523253 original size:66 final size:66
Alignment explanation
Indices: 2523143--2523301 Score: 246
Period size: 66 Copynumber: 2.4 Consensus size: 66
2523133 ACTTAACTTG
* * * *
2523143 GATTTCAACTTCTCGACGAAGGATATCCAATTCAAGGTTTAACTTCACGACGAAGGGGTCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCATCCA
2523208 C
66 C
* * * *
2523209 GATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAATGAATGGGTCATTCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCATCCA
2523274 C
66 C
2523275 GATTTCAACTTCACGACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
2523302 GTGCTCATTT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 85 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (66 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCATCCA
C
Found at i:2523464 original size:84 final size:83
Alignment explanation
Indices: 2523330--2523736 Score: 291
Period size: 84 Copynumber: 4.8 Consensus size: 83
2523320 GCTCAAGGTA
* * *
2523330 AGAAGGGTTATCTGCTAACAAAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCATT
1 AGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTA-ACTTAGCTCAAAGGCACATCATT
*
2523395 TGTAGTATAGCTTAAGTCG
65 TGCAGTATAGCTTAAGTCG
* * * * *
2523414 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGATT-GACTACGCTTAGCTCCAAGGCACGTCAT
1 AGAAGGGCTATCTGCCAACAAAAGACCTTCGAG-TTCGATTA-ACTTAGCTCAAAGGCACATCAT
* * * * *
2523478 TTGCAGCATAACTCAAGGCT
64 TTGCAGTATAGCTTAAGTCG
* * * * * *
2523498 AGAAGGGTTATCTGTCAATAAAAGACCTTCGAGTTCAATTATA-TTCAGCTCAAAGGAATATCAT
1 AGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTA-ACTT-AGCTCAAAGGCACATCAT
*
2523562 TTGCAGTATAGCTTAAGTTG
64 TTGCAGTATAGCTTAAGTCG
* * * * * * * * * * *
2523582 AGAAGAGCTATCTGTCATC-AAATACCTTCAATATTCAATT-TCATTCAGTTCCAAGGCACGTCA
1 AGAAGGGCTATCTGCCAACAAAAGACCTTCGA-GTTCGATTAAC-TT-AGCTCAAAGGCACATCA
* * * * *
2523645 TTTGCAGCATAACTCAAGGCT
63 TTTGCAGTATAGCTTAAGTCG
* * * * * * * *
2523666 AGAAGGGTTATCTGTCAACAAAAGACCTTTTGAGTTCGATTACACTCAGTTTAAAGACACATCTT
1 AGAAGGGCTATCTGCCAACAAAAGACC-TTCGAGTTCGATTA-ACTTAGCTCAAAGGCACATCAT
2523731 TTGCAG
64 TTGCAG
2523737 CATAACTCAA
Statistics
Matches: 246, Mismatches: 67, Indels: 19
0.74 0.20 0.06
Matches are distributed among these distances:
83 14 0.06
84 194 0.79
85 33 0.13
86 4 0.02
87 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (83 bp):
AGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTAACTTAGCTCAAAGGCACATCATTT
GCAGTATAGCTTAAGTCG
Found at i:2523594 original size:168 final size:168
Alignment explanation
Indices: 2523306--2523736 Score: 539
Period size: 168 Copynumber: 2.6 Consensus size: 168
2523296 GATATCGTGC
* * *
2523306 TCATTTGCAGCTTAGCTCAAGG-TAAGAAGGGTTATCTG-CTAACAAAAGACCTTCGAGTTCGAT
1 TCATTTGCAGCATAACTCAAGGCT-AGAAGGGTTATCTGTC-AACAAAAGACCTTCGAGTTCAAT
* * *
2523369 TATACTCAGCTCAAAGGCACATCATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAACC
64 TATACTCAGCTCAAAGGAACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCC-ACC
* * *
2523434 AAAGACCTTCGAGATT-GACTACGCTT-AGCTCCAAGGCACG
128 AAAGACCTTCAAGATTCAACTAC-ATTCAGCTCCAAGGCACG
*
2523474 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAATAAAAGACCTTCGAGTTCAATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCAATTA
* * * * *
2523539 TATTCAGCTCAAAGGAATATCATTTGCAGTATAGCTTAAGTTGAGAAGAGCTATCTGTCATCAAA
66 TACTCAGCTCAAAGGAACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCACCAAA
* * * * *
2523604 TACCTTCAATATTCAATTTCATTCAGTTCCAAGGCACG
131 GACCTTCAAGATTCAACTACATTCAGCTCCAAGGCACG
* *
2523642 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTTTGAGTTCGATT
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACC-TTCGAGTTCAATT
* * * *
2523707 ACACTCAGTTTAAA-GACACATCTTTTGCAG
65 ATACTCAGCTCAAAGGA-ACATCATTTGCAG
2523737 CATAACTCAA
Statistics
Matches: 228, Mismatches: 29, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
167 17 0.07
168 177 0.78
169 34 0.15
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (168 bp):
TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCAATTA
TACTCAGCTCAAAGGAACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCACCAAA
GACCTTCAAGATTCAACTACATTCAGCTCCAAGGCACG
Found at i:2527997 original size:22 final size:20
Alignment explanation
Indices: 2527959--2527998 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
2527949 ATCACTACAA
2527959 AAATTTGAAATTTTAATATT
1 AAATTTGAAATTTTAATATT
2527979 AAATTTAGAAATGTTTAATA
1 AAATTT-GAAAT-TTTAATA
2527999 AATTATGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
AAATTTGAAATTTTAATATT
Found at i:2531227 original size:15 final size:16
Alignment explanation
Indices: 2531207--2531248 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2531197 TAATTATTTT
*
2531207 TATTTTCTTTTTA-AA
1 TATTTTATTTTTATAA
*
2531222 TATTTTAATTTTATAA
1 TATTTTATTTTTATAA
2531238 TATTTTATTTT
1 TATTTTATTTT
2531249 AAAGTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTTATTTTTATAA
Found at i:2531249 original size:15 final size:15
Alignment explanation
Indices: 2531215--2531251 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2531205 TTTATTTTCT
2531215 TTTTAAATATTTTAA
1 TTTTAAATATTTTAA
2531230 TTTTATAATATTTT-A
1 TTTTA-AATATTTTAA
2531245 TTTTAAA
1 TTTTAAA
2531252 GTAAAATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 11 0.52
16 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAATATTTTAA
Found at i:2535907 original size:22 final size:22
Alignment explanation
Indices: 2535861--2535925 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
2535851 AACATAAGTG
*
2535861 TATATATAAGCATACATATAAA
1 TATATATATGCATACATATAAA
* * *
2535883 TATATATATGCATGCATGTACA
1 TATATATATGCATACATATAAA
* *
2535905 TATGTATGATGCATATATATA
1 TATATAT-ATGCATACATATA
2535926 CATACTTATA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 24 0.71
23 10 0.29
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (22 bp):
TATATATATGCATACATATAAA
Found at i:2537242 original size:16 final size:16
Alignment explanation
Indices: 2537221--2537251 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2537211 TTAATTATAG
2537221 GTCAGGTTCATAACAT
1 GTCAGGTTCATAACAT
2537237 GTCAGGTTCATAACA
1 GTCAGGTTCATAACA
2537252 GGTCGGGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (16 bp):
GTCAGGTTCATAACAT
Found at i:2540067 original size:23 final size:23
Alignment explanation
Indices: 2540033--2540078 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2540023 ACATATTATA
2540033 TGGCACTACGGTCCAATTCTACG
1 TGGCACTACGGTCCAATTCTACG
* * *
2540056 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTCCAATTCTACG
2540079 CGGTCCTTTG
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:0.17, C:0.28, G:0.24, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTCCAATTCTACG
Found at i:2540120 original size:24 final size:24
Alignment explanation
Indices: 2540047--2540121 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
2540037 ACTACGGTCC
*
2540047 AATTCTACGTGGCACTTCGGTGC-
1 AATTCTACGTGGTACTTCGGTGCA
* * * * *
2540070 ATTTCTACGCGGTCCTTTGG-GAAA
1 AATTCTACGTGGTACTTCGGTG-CA
2540094 AATTCTACGTGGTACTTCGGTGCA
1 AATTCTACGTGGTACTTCGGTGCA
2540118 AATT
1 AATT
2540122 TATATAAGCC
Statistics
Matches: 38, Mismatches: 11, Indels: 5
0.70 0.20 0.09
Matches are distributed among these distances:
22 1 0.03
23 15 0.39
24 21 0.55
25 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (24 bp):
AATTCTACGTGGTACTTCGGTGCA
Found at i:2540767 original size:25 final size:25
Alignment explanation
Indices: 2540733--2540783 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
2540723 TTTGTGTAAT
2540733 CGGTACTGTAGCAAGTTACTGTTTA
1 CGGTACTGTAGCAAGTTACTGTTTA
* *
2540758 CGGTATTGTAGCAGGTTACTGTTTA
1 CGGTACTGTAGCAAGTTACTGTTTA
2540783 C
1 C
2540784 ACGTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (25 bp):
CGGTACTGTAGCAAGTTACTGTTTA
Found at i:2546920 original size:11 final size:11
Alignment explanation
Indices: 2546904--2546948 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
2546894 TAAAATAATG
*
2546904 ATAATATTTAT
1 ATAATATATAT
2546915 ATAATATATAT
1 ATAATATATAT
2546926 ATAATATATA-
1 ATAATATATAT
*
2546936 AT-ATATAAAT
1 ATAATATATAT
2546946 ATA
1 ATA
2546949 TGTTTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 6 0.20
10 4 0.13
11 20 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATAATATATAT
Found at i:2548242 original size:64 final size:63
Alignment explanation
Indices: 2548174--2548351 Score: 189
Period size: 64 Copynumber: 2.8 Consensus size: 63
2548164 GAACACTTGA
* *
2548174 TGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-G
1 TGCATCGATGCA-CAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAG
** * **
2548238 TGCATCGATGCA-TGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGA
1 TGCATCGATGCACAAG--TGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGA
2548302 G
63 G
* * * *
2548303 TGCATCGATGCATAGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCACA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
2548352 CAATTAATTC
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
64 50 0.53
65 43 0.45
67 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (63 bp):
TGCATCGATGCACAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAG
Found at i:2548325 original size:65 final size:65
Alignment explanation
Indices: 2548192--2548351 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
2548182 TGCACCAAGT
* * ***
2548192 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATAGAGA
* **
2548256 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATAGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATAGAG
2548320 A
65 A
* *
2548321 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
2548352 CAATTAATTC
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 36 0.43
65 47 0.57
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATAGAGA
Found at i:2548391 original size:65 final size:65
Alignment explanation
Indices: 2548193--2548400 Score: 198
Period size: 65 Copynumber: 3.2 Consensus size: 65
2548183 GCACCAAGTG
* * ** *
2548193 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
2548256 G-
64 GA
* * * *
2548257 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATAGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
2548320 A
65 A
* *
2548321 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
2548383 CTGA
62 CTGA
2548387 TGCATCGGTGCATG
1 TGCATCGGTGCATG
2548401 CCTTTGAATA
Statistics
Matches: 122, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.07
64 50 0.41
65 59 0.48
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:2548768 original size:31 final size:31
Alignment explanation
Indices: 2548730--2548809 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
2548720 ATCGATTTTG
2548730 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
2548761 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
** * *
2548792 TTAAATTTTCTCCCCCTT
1 AAAAACTTACTCCCCCTT
2548810 TTTGTTAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (31 bp):
AAAAACTTACTCCCCCTTACTATAGCACATC
Found at i:2554418 original size:22 final size:21
Alignment explanation
Indices: 2554392--2554438 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
2554382 AAGGCCAAAA
*
2554392 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
2554414 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
2554434 ATCAA
1 ATCAA
2554439 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:2556538 original size:45 final size:46
Alignment explanation
Indices: 2556474--2556578 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 46
2556464 TGCACCAAGT
* *
2556474 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTG-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATAGCCAGA
* **
2556519 GTGCATCGATGCATCAAATGTATTCGATGTTTTGAAAATATTCAGA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGA
2556565 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2556579 GGAGAGTGCA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 35 0.66
46 18 0.34
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.31
Consensus pattern (46 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGA
Found at i:2556586 original size:19 final size:19
Alignment explanation
Indices: 2556562--2556600 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2556552 GAAAATATTC
2556562 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2556581 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2556600 A
1 A
2556601 ATTCATTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2557086 original size:37 final size:36
Alignment explanation
Indices: 2557028--2557282 Score: 165
Period size: 36 Copynumber: 7.3 Consensus size: 36
2557018 ACCAAAAGAT
** *
2557028 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA
* * * **
2557064 TTTAGTTCCAAAAGAAACTGTCTCAAGGGATACGTAA
1 TTT-GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA
* * *
2557101 TTTGTTTC-AAGGAAAATAGAT-TC---AGAG----AT
1 TTTGTTTCAAAAGAAACT-G-TCTCAAGAGAGACAAAA
* **
2557130 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAGG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA
** *
2557166 TTTGCTTT-ACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTG-TTTCAAAAGAAACTGTCTCAAGAGAGACAAAA
* * * *
2557202 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACACAA
1 -TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA
** *
2557239 TTTGTTTCAAGGGAAACTCTCTC-A-AGAGACAAAA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA
2557273 TTTGTTTCAA
1 TTTGTTTCAA
2557283 GGGAGACGTT
Statistics
Matches: 167, Mismatches: 37, Indels: 32
0.71 0.16 0.14
Matches are distributed among these distances:
28 1 0.01
29 12 0.07
30 6 0.04
32 4 0.02
33 2 0.01
34 18 0.11
35 8 0.05
36 58 0.35
37 58 0.35
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA
Found at i:2557104 original size:102 final size:102
Alignment explanation
Indices: 2556934--2557163 Score: 276
Period size: 102 Copynumber: 2.3 Consensus size: 102
2556924 AAAGGTTTTG
* * * * *
2556934 TGTTTCAAGAGAAACTGTCTCAAG-G-GAGATAA--T-GTT-TAAGAGAAACTGTCTCGAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTAGTTCCAAAAGAAACTGTCTCAAGAGAG
2556993 ACGAAATTTGTTTAAAGGAAAACAGA-CCAAAAGATTT
66 ACGAAATTTGTTTAAAGGAAAACAGATCC-AAAGATTT
* * * *
2557030 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTAGTTCCAAAAGAAACTGTCTCAAGGGAT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTAGTTCCAAAAGAAACTGTCTCAAGAGAG
* * * * *
2557095 ACGTAATTTGTTTCAAGGAAAATAGATTCAGAGATTT
66 ACGAAATTTGTTTAAAGGAAAACAGATCCAAAGATTT
2557132 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
2557164 GGTTTGCTTT
Statistics
Matches: 111, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
96 22 0.20
97 1 0.01
98 5 0.05
100 1 0.01
101 3 0.03
102 78 0.70
103 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.27
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTAGTTCCAAAAGAAACTGTCTCAAGAGAG
ACGAAATTTGTTTAAAGGAAAACAGATCCAAAGATTT
Found at i:2557262 original size:36 final size:36
Alignment explanation
Indices: 2557130--2557390 Score: 186
Period size: 36 Copynumber: 7.5 Consensus size: 36
2557120 ATTCAGAGAT
**
2557130 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
2557166 TTTGCTTT-ACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTG-TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
2557202 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACACAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
2557239 TTTGTTTCAAGGGAAACTCTCTC-A-AGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
2557273 TTTGTTTCAAGGGAGAC-GTTTTC-A-A-TG-----T
1 TTTGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAA
* *
2557301 TTATGTTTCAAGAGAAACTGACTCAAGGGAGACAAAA
1 TT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
2557338 TTTGTTTCAAGGGAAATTATCTCAAGAGAGATAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
2557374 TTTGTTCCAAGGGAAAC
1 TTTGTTTCAAGAGAAAC
2557391 AATCTCAAAG
Statistics
Matches: 173, Mismatches: 38, Indels: 28
0.72 0.16 0.12
Matches are distributed among these distances:
28 2 0.01
29 15 0.09
30 2 0.01
32 1 0.01
33 1 0.01
34 29 0.17
35 1 0.01
36 91 0.53
37 31 0.18
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:2557396 original size:36 final size:36
Alignment explanation
Indices: 2557322--2557398 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
2557312 GAGAAACTGA
* * **
2557322 CTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTAT
1 CTCAAGAGAGACAAAATTTGTTCCAAGGGAAACAAT
*
2557358 CTCAAGAGAGATAAAATTTGTTCCAAGGGAAACAAT
1 CTCAAGAGAGACAAAATTTGTTCCAAGGGAAACAAT
2557394 CTCAA
1 CTCAA
2557399 AGGTTTTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (36 bp):
CTCAAGAGAGACAAAATTTGTTCCAAGGGAAACAAT
Found at i:2557612 original size:84 final size:84
Alignment explanation
Indices: 2557398--2558111 Score: 576
Period size: 84 Copynumber: 8.6 Consensus size: 84
2557388 AACAATCTCA
* * * * * * *
2557398 AAGGT-TTTTGTTGACAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAGA
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTC-GA
*
2557462 GCTGAGTGTAATCGAACTCG
65 GCTGAGCGTAATCGAACTCG
* * * * * * *
2557482 -GGGGC-CT--TTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTGTAAATGATGTGCCTTAGAG
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTCGAG
* * *
2557543 CTGAGCATAGTCAAACTCG
66 CTGAGCGTAATCGAACTCG
* * * * * *
2557562 GAGGTCTTTGGTTGGTAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAA
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTCG-A
* *
2557627 GCTGAGTGTAATCGAACTTG
65 GCTGAGCGTAATCGAACTCG
* * * * * *
2557647 AAGGTCTTTGGTT-ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGAGCCCTCGAA
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTCG-A
*
2557711 GCTGAGTGTAATCGAACTCG
65 GCTGAGCGTAATCGAACTCG
* * * * * * * *
2557731 AGGGTC--T--TTAGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATGTCGTT-GA
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG-CCTTCGA
* *
2557791 GCTGAGCGTAGTCGAACTCA
65 GCTGAGCGTAATCGAACTCG
* * * * * * * *
2557811 AAGGTATTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGTAAATGATGCGCCATGGAG
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTCGAG
*
2557876 CTGAGCGTAGTCGAACTCG
66 CTGAGCGTAATCGAACTCG
* * * * * * ** * ** * ** *
2557895 AAGGTATTTGGTTGGAAAATAGCCCTTCTTGCCTCGAGCTATATTGCAAATGATACGCCCTCGAA
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTCG-A
*
2557960 GCTGAGTGTAATCGAACTCG
65 GCTGAGCGTAATCGAACTCG
* * ** * *
2557980 AGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGCGCCTTGGAG
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTCGAG
* *
2558041 CTGAGCGTAGTCAAACTCG
66 CTGAGCGTAATCGAACTCG
* *
2558060 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
1 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATG
2558112 TTGTAAAAAA
Statistics
Matches: 499, Mismatches: 113, Indels: 36
0.77 0.17 0.06
Matches are distributed among these distances:
80 65 0.13
81 117 0.23
82 6 0.01
83 6 0.01
84 254 0.51
85 51 0.10
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (84 bp):
AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTCGAG
CTGAGCGTAATCGAACTCG
Found at i:2557755 original size:165 final size:162
Alignment explanation
Indices: 2557406--2558111 Score: 612
Period size: 165 Copynumber: 4.3 Consensus size: 162
2557396 CAAAGGTTTT
* * * * * *
2557406 TGTTGACAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTC-AGAGCTGAGTG
1 TGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATATGCCCTCGA-AGCTGAGTG
** * * * *
2557470 TAATCGAACTCGGGGGCCTTTGGCAGATAGCCCTTCTCA-ACTTAAGCTATGCTGTAAATGATGT
65 TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCT-AGACTTAAGTTATGCTGTAAATGATGC
* * *
2557534 GCCTTAGAGCTGAGCATAGTCAAACTCG-GAGGTC
129 GCCCTGGAGCTGAGCGTAGTCAAACTCGAG-GGTC
* * ** *
2557568 TTTGGTTGGTAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAG
1 --T-GTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATATGCCCTCGAAGCTGAG
* * *
2557633 TGTAATCGAACTTGAAGGTCTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
63 TGTAATCGAACTCGAAGGTCTTTGG---CAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATG
* * * * *
2557698 ATGAGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC
125 ATGCGCCCT-GGAGCTGAGCGTAGTCAAACTCGAGGGTC
* * * * * * * * *
2557737 T-TTAGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATGTCGTTG-AGCTGAGCGT
1 TGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGT
* * * * *
2557800 AGTCGAACTCAAAGGTATTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGTAAATGAT
66 AATCGAACTCGAAGG---TCT-TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGAT
* * * *
2557865 GCGCCATGGAGCTGAGCGTAGTCGAACTCGAAGGTATT
127 GCGCCCTGGAGCTGAGCGTAGTCAAACTCG-AGG-GTC
* * * * * ** *
2557903 TGGTTGGAAAATAGCCCTTCTTGCCTCGAGCTATATTGCAAATGATACGCCCTCGAAGCTGAGTG
1 T-GTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATATGCCCTCGAAGCTGAGTG
* * * **
2557968 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGCG
65 TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGCG
* *
2558033 CCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC
130 CCCTGGAGCTGAGCGTAGTCAAACTCGAGGGTC
** * *
2558066 TTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
1 --T-GTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATG
2558112 TTGTAAAAAA
Statistics
Matches: 433, Mismatches: 90, Indels: 37
0.77 0.16 0.07
Matches are distributed among these distances:
163 1 0.00
164 44 0.10
165 255 0.59
166 5 0.01
167 4 0.01
168 81 0.19
169 42 0.10
170 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (162 bp):
TGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGT
AATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGCGC
CCTGGAGCTGAGCGTAGTCAAACTCGAGGGTC
Found at i:2557863 original size:249 final size:248
Alignment explanation
Indices: 2557398--2558111 Score: 934
Period size: 249 Copynumber: 2.9 Consensus size: 248
2557388 AACAATCTCA
* * *
2557398 AAGGTTTTTGTTGACAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTC-AGA
1 AAGGTTTTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGAGCCCTCGA-A
* * * *
2557462 GCTGAGTGTAATCGAACTCGGGGGCCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTGTAA
65 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAA
* * *
2557527 ATGATGTGCCTTAGAGCTGAGCATAGTCAAACTCGGAGGTCTTTGGTTGGTAGATAACCCTTCTC
130 ATGATGTGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTC
* * * * * * *
2557592 GCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTG
195 GACTTAAGTTATGCTGTAAATGATGCGCCAT-GAAGCTGAGCGTAATCGAACTCG
2557647 AAGGTCTTTGGTT-ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGAGCCCTCGAA
1 AAGGT-TTTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGAGCCCTCGAA
* *
2557711 GCTGAGTGTAATCGAACTCGAGGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAA
65 GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAA
* * * * * * *
2557776 ATGATATGTCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTATTTTGTTGGCAGACAACCCTTCT
130 ATGATGTG-CCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
* * * *
2557840 AGACTTAAGTTGTGCTGTAAATGATGCGCCATGGAGCTGAGCGTAGTCGAACTCG
194 CGACTTAAGTTATGCTGTAAATGATGCGCCATGAAGCTGAGCGTAATCGAACTCG
* * * * * ** *
2557895 AAGGTATTTGGTTGGA-AAATAGCCCTTCTTGCCTCGAGCTATATTGCAAATGAT-ACGCCCTCG
1 AAGGT-TTTGGTT-GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGA-GCCCTCG
* *
2557958 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTAC
63 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
* *
2558023 AAATGATGCGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
128 AAATGATGTGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* *
2558088 TCGATTTAAGTTATGCTGCAAATG
193 TCGACTTAAGTTATGCTGTAAATG
2558112 TTGTAAAAAA
Statistics
Matches: 403, Mismatches: 55, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
248 35 0.09
249 357 0.89
250 11 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (248 bp):
AAGGTTTTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGAGCCCTCGAAG
CTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAA
TGATGTGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
ACTTAAGTTATGCTGTAAATGATGCGCCATGAAGCTGAGCGTAATCGAACTCG
Found at i:2567023 original size:23 final size:23
Alignment explanation
Indices: 2566992--2567060 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
2566982 CACCACAGCT
* *
2566992 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
2567015 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
2567038 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
2567061 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:2567255 original size:103 final size:103
Alignment explanation
Indices: 2567076--2567288 Score: 390
Period size: 103 Copynumber: 2.1 Consensus size: 103
2567066 TAATGTCCAT
* *
2567076 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
2567141 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
*
2567179 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
2567244 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
2567282 AAGGACC
1 AAGGACC
2567289 GCGTAGACCC
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:2567559 original size:13 final size:13
Alignment explanation
Indices: 2567543--2567574 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2567533 TTCATATATC
2567543 TCATATCTTGTGA
1 TCATATCTTGTGA
2567556 TCATATCTTGTGA
1 TCATATCTTGTGA
2567569 TCATAT
1 TCATAT
2567575 AATCATGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (13 bp):
TCATATCTTGTGA
Found at i:2568692 original size:22 final size:21
Alignment explanation
Indices: 2568667--2568726 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
2568657 TTCGTTTGAG
*
2568667 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
2568689 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
2568709 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
2568727 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:2569513 original size:39 final size:39
Alignment explanation
Indices: 2569469--2569592 Score: 114
Period size: 39 Copynumber: 3.2 Consensus size: 39
2569459 TCGTCCTCGA
2569469 ATTTTCACTGCATGCCTTTATAATATCACATCTTCTAAT
1 ATTTTCACTGCATGCCTTTATAATATCACATCTTCTAAT
* * * * * *
2569508 ATTTTCATATTGCCT-CCTTTA-AAGA--AAATTCGTCCACGA-
1 ATTTTC--ACTGCATGCCTTTATAATATCACA-TCTTCTA--AT
2569547 ATTTTCACTGCATGCCTTTATAATATCACATCTTCTAAT
1 ATTTTCACTGCATGCCTTTATAATATCACATCTTCTAAT
2569586 ATTTTCA
1 ATTTTCA
2569593 TATTGCTTCC
Statistics
Matches: 63, Mismatches: 12, Indels: 20
0.66 0.13 0.21
Matches are distributed among these distances:
37 7 0.11
38 12 0.19
39 25 0.40
40 12 0.19
41 7 0.11
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (39 bp):
ATTTTCACTGCATGCCTTTATAATATCACATCTTCTAAT
Found at i:2569537 original size:78 final size:78
Alignment explanation
Indices: 2569442--2569607 Score: 305
Period size: 78 Copynumber: 2.1 Consensus size: 78
2569432 ACAAATCTTC
*
2569442 CCTCCTTTAAAGAAAATTCGTCCTCGAATTTTCACTGCATGCCTTTATAATATCACATCTTCTAA
1 CCTCCTTTAAAGAAAATTCGTCCACGAATTTTCACTGCATGCCTTTATAATATCACATCTTCTAA
2569507 TATTTTCATATTG
66 TATTTTCATATTG
2569520 CCTCCTTTAAAGAAAATTCGTCCACGAATTTTCACTGCATGCCTTTATAATATCACATCTTCTAA
1 CCTCCTTTAAAGAAAATTCGTCCACGAATTTTCACTGCATGCCTTTATAATATCACATCTTCTAA
2569585 TATTTTCATATTG
66 TATTTTCATATTG
* *
2569598 CTTCCCTTAA
1 CCTCCTTTAA
2569608 TATTTCTTGC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 85 1.00
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.40
Consensus pattern (78 bp):
CCTCCTTTAAAGAAAATTCGTCCACGAATTTTCACTGCATGCCTTTATAATATCACATCTTCTAA
TATTTTCATATTG
Found at i:2572338 original size:23 final size:23
Alignment explanation
Indices: 2572312--2572380 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
2572302 CACCACAGCT
*
2572312 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
2572335 CGTAGAATTACACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
2572358 CGTAGAATTGCACCGTAA-TGCCA
1 CGTAGAATTGCACCG-AAGTGCCA
2572381 TATAATAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 37 0.97
24 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:2572567 original size:103 final size:103
Alignment explanation
Indices: 2572396--2572608 Score: 365
Period size: 103 Copynumber: 2.1 Consensus size: 103
2572386 TAATGTCCAT
* *
2572396 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
2572461 GACTTCACACATA-TTCCAAAGAATACATATATGTCTCG
66 GACTTCACACA-AGTTCCAAAGAATACATATATGTCCCG
* *
2572499 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
2572564 GACTTCACACAAGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACAAGTTCCAAAGAATACATATATGTCCCG
2572602 AAGGACC
1 AAGGACC
2572609 GCGTAGACCC
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
102 1 0.01
103 102 0.99
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACAAGTTCCAAAGAATACATATATGTCCCG
Found at i:2574011 original size:22 final size:21
Alignment explanation
Indices: 2573986--2574045 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
2573976 TTCGTTTGAG
2573986 GGGTATCGATTCCCCATTGAAT
1 GGGTATCGATTCCCC-TTGAAT
2574008 GGGTATCGATT-CCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
*
2574028 GGGTACCGATTCCCCTTG
1 GGGTATCGATTCCCCTTG
2574046 CCCAAAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 16 0.44
21 9 0.25
22 11 0.31
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTGAAT
Found at i:2575161 original size:23 final size:23
Alignment explanation
Indices: 2575133--2575204 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
2575123 ACTATGGTCT
2575133 AATTCTACGTGGCACTTCGGTGC
1 AATTCTACGTGGCACTTCGGTGC
* *
2575156 ATTTCTACGCGGTC-CTTCGG-GAC
1 AATTCTACGTGG-CACTTCGGTG-C
*
2575179 AAATTCTACGTGGTACTTCGGTGC
1 -AATTCTACGTGGCACTTCGGTGC
2575203 AA
1 AA
2575205 ATTTATATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
22 1 0.03
23 19 0.49
24 18 0.46
25 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
AATTCTACGTGGCACTTCGGTGC
Found at i:2575187 original size:24 final size:24
Alignment explanation
Indices: 2575133--2575207 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
2575123 ACTATGGTCT
* *
2575133 AATTCTACGTGGCACTTCGGTGC-
1 AATTCTACGCGGTACTTCGGTGCA
* *
2575156 ATTTCTACGCGGTCCTTCGG-GACA
1 AATTCTACGCGGTACTTCGGTG-CA
*
2575180 AATTCTACGTGGTACTTCGGTGCA
1 AATTCTACGCGGTACTTCGGTGCA
2575204 AATT
1 AATT
2575208 TATATGAGCT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
22 1 0.02
23 17 0.40
24 23 0.55
25 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (24 bp):
AATTCTACGCGGTACTTCGGTGCA
Found at i:2577553 original size:21 final size:21
Alignment explanation
Indices: 2577510--2577565 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
2577500 TTTGTGAAAG
* *
2577510 GGATCGATCCTTCTAGTGAAT
1 GGATCGATCCTTTTACTGAAT
2577531 GGATCGATCCTTTTACTCG-AT
1 GGATCGATCCTTTTACT-GAAT
* *
2577552 GGGTCAATCCTTTT
1 GGATCGATCCTTTT
2577566 TGTAAAGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (21 bp):
GGATCGATCCTTTTACTGAAT
Found at i:2577666 original size:20 final size:20
Alignment explanation
Indices: 2577597--2577668 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
2577587 CCTACTGGAA
*
2577597 TCTAAGGGATTGATTCTTTT
1 TCTAAGGGATCGATTCTTTT
2577617 TC-AAGGGGATCGA-TCTTTT
1 TCTAA-GGGATCGATTCTTTT
* *
2577636 GGTCAAAGGGATCGATTCATTT
1 --TCTAAGGGATCGATTCTTTT
2577658 TCTAAGGGATC
1 TCTAAGGGATC
2577669 AATCATTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
19 8 0.18
20 19 0.43
21 10 0.23
22 7 0.16
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.38
Consensus pattern (20 bp):
TCTAAGGGATCGATTCTTTT
Found at i:2577667 original size:41 final size:41
Alignment explanation
Indices: 2577600--2577677 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
2577590 ACTGGAATCT
* * * *
2577600 AAGGGATTGATTCTTTTTCAAGGGGATCGATCTTTTGGTCA
1 AAGGGATCGATTCATTTTCAAGGGGATCAATCATTTGGTCA
2577641 AAGGGATCGATTCATTTTCTAA-GGGATCAATCATTTG
1 AAGGGATCGATTCATTTTC-AAGGGGATCAATCATTTG
2577678 AGCCAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 30 0.94
42 2 0.06
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (41 bp):
AAGGGATCGATTCATTTTCAAGGGGATCAATCATTTGGTCA
Found at i:2579242 original size:13 final size:14
Alignment explanation
Indices: 2579224--2579256 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
2579214 TGTCACATTC
2579224 ATATTTTTTAAA-A
1 ATATTTTTTAAATA
2579237 ATA-TTTTTAAATA
1 ATATTTTTTAAATA
2579250 ATATTTT
1 ATATTTT
2579257 ATTTTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 7 0.39
14 3 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATTTTTTAAATA
Found at i:2584071 original size:24 final size:24
Alignment explanation
Indices: 2584039--2584096 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
2584029 GGATTGTGGG
2584039 ATTCCCATGTGATGGGAATCTCAC
1 ATTCCCATGTGATGGGAATCTCAC
*
2584063 ATTCCCATGGGATGGGAATCTCAC
1 ATTCCCATGTGATGGGAATCTCAC
2584087 ATTCCCATGT
1 ATTCCCATGT
2584097 TTGGTTAGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (24 bp):
ATTCCCATGTGATGGGAATCTCAC
Found at i:2584496 original size:37 final size:37
Alignment explanation
Indices: 2584420--2584496 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
2584410 TTTTTATATT
*
2584420 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
2584457 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
2584494 TTT
1 TTT
2584497 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:2587616 original size:20 final size:19
Alignment explanation
Indices: 2587591--2587641 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
2587581 TCGGATGATC
*
2587591 AGTATCGATACTGATTGAAG
1 AGTATCGATACT-AATGAAG
*
2587611 AGTATCGATACTAATGTAG
1 AGTATCGATACTAATGAAG
2587630 AGGTATCGATAC
1 A-GTATCGATAC
2587642 CAAGAGGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (19 bp):
AGTATCGATACTAATGAAG
Found at i:2588282 original size:21 final size:22
Alignment explanation
Indices: 2588209--2588283 Score: 98
Period size: 23 Copynumber: 3.4 Consensus size: 22
2588199 GTCGAGGGTT
*
2588209 CTATGCGGTCCTTCGGGACAAA
1 CTATGTGGTCCTTCGGGACAAA
*
2588231 CCTATGTGGTCCTTCGAGACAAAA
1 -CTATGTGGTCCTTCGGGAC-AAA
*
2588255 CTATGTGGTCATTCGGGACAAA
1 CTATGTGGTCCTTCGGGACAAA
2588277 -TATGTGG
1 CTATGTGG
2588284 CACTTCAGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.15
22 3 0.06
23 34 0.72
24 3 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (22 bp):
CTATGTGGTCCTTCGGGACAAA
Found at i:2600769 original size:22 final size:21
Alignment explanation
Indices: 2600725--2600765 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2600715 ATATAAGTTC
2600725 ATTTTCTATTTTTAACAATTA
1 ATTTTCTATTTTTAACAATTA
*
2600746 ATTTTCT-TTCTTTTACAATT
1 ATTTTCTATT-TTTAACAATT
2600766 TAATCCTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTCTATTTTTAACAATTA
Found at i:2601720 original size:39 final size:40
Alignment explanation
Indices: 2601662--2601743 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 40
2601652 TCTAAAAGAC
*
2601662 ATTCTTATTTTCATTAAATT-TTGACAC-TATAACGTTCTAA
1 ATTCTTAATTTCATTAAATTATT-ACACAT-TAACGTTCTAA
*
2601702 ATTCTTAATTTC-TTAAATTATTTCACATTAACGTTCTAA
1 ATTCTTAATTTCATTAAATTATTACACATTAACGTTCTAA
2601741 ATT
1 ATT
2601744 ATTTTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
39 24 0.63
40 14 0.37
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.49
Consensus pattern (40 bp):
ATTCTTAATTTCATTAAATTATTACACATTAACGTTCTAA
Found at i:2613634 original size:2 final size:2
Alignment explanation
Indices: 2613627--2613666 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2613617 GTTTGTTTTG
2613627 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2613666 T
1 T
2613667 TTTTATATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2613667 original size:8 final size:9
Alignment explanation
Indices: 2613627--2613675 Score: 59
Period size: 8 Copynumber: 5.7 Consensus size: 9
2613617 GTTTGTTTTG
2613627 TATATATA-
1 TATATATAT
2613635 TATATATAT
1 TATATATAT
2613644 ATATATATAT
1 -TATATATAT
2613654 TATAT-TAT
1 TATATATAT
*
2613662 TATAT-TTT
1 TATATATAT
2613670 TATATA
1 TATATA
2613676 CTAATAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
8 23 0.62
9 5 0.14
10 9 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TATATATAT
Found at i:2617175 original size:22 final size:21
Alignment explanation
Indices: 2617150--2617194 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2617140 TTTTAAATTT
2617150 AATTTTAAT-AAAAATAAAATAA
1 AATTTT-ATGAAAAA-AAAATAA
*
2617172 AATTTTATGAAAAAAAGATAA
1 AATTTTATGAAAAAAAAATAA
2617193 AA
1 AA
2617195 AAATATTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
AATTTTATGAAAAAAAAATAA
Found at i:2617184 original size:21 final size:22
Alignment explanation
Indices: 2617150--2617194 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2617140 TTTTAAATTT
2617150 AATTTTAATAAAAATAAA-ATAA
1 AATTTTAATAAAAA-AAAGATAA
*
2617172 AATTTT-ATGAAAAAAAGATAA
1 AATTTTAATAAAAAAAAGATAA
2617193 AA
1 AA
2617195 AAATATTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 12 0.57
22 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (22 bp):
AATTTTAATAAAAAAAAGATAA
Found at i:2638357 original size:3 final size:3
Alignment explanation
Indices: 2638349--2638378 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2638339 TATTTAACTC
2638349 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2638379 AAGGAATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2647189 original size:25 final size:24
Alignment explanation
Indices: 2647146--2647193 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
2647136 AAATATCTAA
*
2647146 AATTATAATAAAATTTATAATTAT
1 AATTATAATAAAATATATAATTAT
*
2647170 AATTATAAATTAAATATATAATTA
1 AATTAT-AATAAAATATATAATTA
2647194 AGACTTGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AATTATAATAAAATATATAATTAT
Found at i:2647192 original size:12 final size:11
Alignment explanation
Indices: 2647145--2647194 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 11
2647135 AAAATATCTA
*
2647145 AAATTATAATA
1 AAATTATAATT
2647156 AAATTTATAATT
1 AAA-TTATAATT
2647168 ATAATTATAAATT
1 A-AATTAT-AATT
2647181 AAATATATAATT
1 AAAT-TATAATT
2647193 AA
1 AA
2647195 GACTTGTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
11 3 0.09
12 21 0.62
13 10 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTATAATT
Found at i:2647271 original size:172 final size:173
Alignment explanation
Indices: 2647093--2647433 Score: 585
Period size: 172 Copynumber: 2.0 Consensus size: 173
2647083 AACCATAATA
* * *
2647093 ATTTATTATTTTTATAGGATTTCGTTAATTTTATTTAAAATTAAAATATCTAAAATTATAATAAA
1 ATTTATTATTTTTATAGAATTTCGTTAATTTTATTAAAAATTAAAATATCTAAAATAATAATAAA
* *
2647158 ATTTATAATTATAATTATAAATTAAA-TATATAATTAAGACTTGTTCAATGATCACTGATATAAG
66 ATTTATAATTATAATTATAAATTAAATTATATAATTAAGACTTCTTCAATAATCACTGATATAAG
*
2647222 AAATTAATAATTTAAAATTATATAAAGACTATGCAAGATTATT
131 AAATTAATAATTTAAAATTATATAAAGACTATACAAGATTATT
2647265 ATTTATTATTTTTATAGAATTTCGTTAATTTTATTAAAAATTAAAATATCTAAAATAATAATAAA
1 ATTTATTATTTTTATAGAATTTCGTTAATTTTATTAAAAATTAAAATATCTAAAATAATAATAAA
*
2647330 ATTTATAATTATAATTATAAATTAAATTTATATAATTAAGACTTCTTCAATAATCACTTATATAA
66 ATTTATAATTATAATTATAAATTAAA-TTATATAATTAAGACTTCTTCAATAATCACTGATATAA
* *
2647395 GAAATTAATTATTTAAAATTATATAAATACTATACAAGA
130 GAAATTAATAATTTAAAATTATATAAAGACTATACAAGA
2647434 AAATTATTAA
Statistics
Matches: 158, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
172 88 0.56
174 70 0.44
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (173 bp):
ATTTATTATTTTTATAGAATTTCGTTAATTTTATTAAAAATTAAAATATCTAAAATAATAATAAA
ATTTATAATTATAATTATAAATTAAATTATATAATTAAGACTTCTTCAATAATCACTGATATAAG
AAATTAATAATTTAAAATTATATAAAGACTATACAAGATTATT
Found at i:2666849 original size:12 final size:12
Alignment explanation
Indices: 2666832--2666863 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
2666822 CCATCTACCC
2666832 TCGAATGACTCG
1 TCGAATGACTCG
2666844 TCGAATGACTCG
1 TCGAATGACTCG
2666856 TCGAATGA
1 TCGAATGA
2666864 TTCATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (12 bp):
TCGAATGACTCG
Found at i:2668495 original size:30 final size:29
Alignment explanation
Indices: 2668448--2668782 Score: 207
Period size: 30 Copynumber: 11.0 Consensus size: 29
2668438 TTAAGTTTAC
*
2668448 ATCTTAACATTAAAAATACATTTTATTTTT
1 ATCTTAAC-TTAAAAATATATTTTATTTTT
* * *
2668478 ATATTAACTTATTAAATATATTTTATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTTTT
2668508 ATCTTAAAC-TAAAAATATATTTTATTTTT
1 ATCTT-AACTTAAAAATATATTTTATTTTT
* *
2668537 ATAC-TAACTTAAAAATATATTGTAGTCTTT
1 AT-CTTAACTTAAAAATATATTTTA-TTTTT
* *
2668567 ATCTTAACTTAAATATATATTTTATTCTT
1 ATCTTAACTTAAAAATATATTTTATTTTT
* * *
2668596 ATCTTAACTTATTACATAAATTATTAAATATATTCT
1 ATCTTAACTTA-AAAATATATT-TT--AT-T-TT-T
* * * *
2668632 ATTCTTACCCTAAATTATTAAATATAATTATTTGTT
1 A-TCTTAACTTAAA--A--ATATAT-TTTATTT-TT
* * *
2668668 ATTTTAACTTACAATATATATTTTATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTTTT
2668698 ATCTTAACTTAAAAATATATTTT-TATTTT
1 ATCTTAACTTAAAAATATATTTTAT-TTTT
** *
2668727 A-AAT-AC--AAAAATATATTTTATTATT
1 ATCTTAACTTAAAAATATATTTTATTTTT
* *
2668752 ATCTTAACTACAAAAAATATATTATATTTTT
1 ATCTTAACT--TAAAAATATATTTTATTTTT
2668783 TAACGTAAAT
Statistics
Matches: 235, Mismatches: 41, Indels: 57
0.71 0.12 0.17
Matches are distributed among these distances:
25 17 0.07
26 2 0.01
27 4 0.02
28 5 0.02
29 66 0.28
30 72 0.31
31 27 0.11
32 5 0.02
33 2 0.01
34 1 0.00
35 8 0.03
36 8 0.03
37 10 0.04
38 2 0.01
40 6 0.03
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (29 bp):
ATCTTAACTTAAAAATATATTTTATTTTT
Found at i:2668524 original size:59 final size:60
Alignment explanation
Indices: 2668448--2668609 Score: 204
Period size: 59 Copynumber: 2.7 Consensus size: 60
2668438 TTAAGTTTAC
* * * *
2668448 ATCTTAACATTAAAAATACATTTTATTTTTATATTAACTTATTAAATATATTTTATTC-TT
1 ATCTTAA-ACTAAAAATATATTTTATTTTTATATTAACTTATTAAATATATTGTAGTCTTT
* *
2668508 ATCTTAAACTAAAAATATATTTTATTTTTATACTAACTTA-AAAATATATTGTAGTCTTT
1 ATCTTAAACTAAAAATATATTTTATTTTTATATTAACTTATTAAATATATTGTAGTCTTT
* * *
2668567 ATCTT-AACTTAAATATATATTTTATTCTTATCTTAACTTATTA
1 ATCTTAAAC-TAAAAATATATTTTATTTTTATATTAACTTATTA
2668610 CATAAATTAT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
58 16 0.18
59 64 0.73
60 8 0.09
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (60 bp):
ATCTTAAACTAAAAATATATTTTATTTTTATATTAACTTATTAAATATATTGTAGTCTTT
Found at i:2668636 original size:42 final size:43
Alignment explanation
Indices: 2668581--2668663 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 43
2668571 TAACTTAAAT
* * * * *
2668581 ATATATTTTATTCTTATCTTAACTTATTACATA-AATTATTAA
1 ATATATTCTATTCTTACCCTAAATTATTAAATATAATTATTAA
2668623 ATATATTCTATTCTTACCCTAAATTATTAAATATAATTATT
1 ATATATTCTATTCTTACCCTAAATTATTAAATATAATTATT
2668664 TGTTATTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 28 0.80
43 7 0.20
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.51
Consensus pattern (43 bp):
ATATATTCTATTCTTACCCTAAATTATTAAATATAATTATTAA
Found at i:2668726 original size:54 final size:56
Alignment explanation
Indices: 2668660--2668774 Score: 155
Period size: 54 Copynumber: 2.1 Consensus size: 56
2668650 TAAATATAAT
* * * *
2668660 TATTTGTTATTTTAACTTAC-AATATATATTTTATTCTTATCTTAACT-TAAAAATA
1 TATTTGTTATTTTAA-ATACAAAAATATATTTTATTATTATCTTAACTAAAAAAATA
2668715 TATTT-TTATTTTAAATACAAAAATATATTTTATTATTATCTTAACTACAAAAAATA
1 TATTTGTTATTTTAAATACAAAAATATATTTTATTATTATCTTAACTA-AAAAAATA
2668771 TATT
1 TATT
2668775 ATATTTTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
53 3 0.06
54 34 0.64
55 5 0.09
56 11 0.21
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.50
Consensus pattern (56 bp):
TATTTGTTATTTTAAATACAAAAATATATTTTATTATTATCTTAACTAAAAAAATA
Found at i:2669606 original size:16 final size:16
Alignment explanation
Indices: 2669585--2669618 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2669575 CGATGAACGG
*
2669585 CATGAAAGCTGGGAAC
1 CATGAAAGATGGGAAC
2669601 CATGAAAGATGGGAAC
1 CATGAAAGATGGGAAC
2669617 CA
1 CA
2669619 GAGAACACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.29, T:0.12
Consensus pattern (16 bp):
CATGAAAGATGGGAAC
Found at i:2670106 original size:32 final size:32
Alignment explanation
Indices: 2670059--2670145 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
2670049 GAACAATGGG
* *
2670059 GGCATCTTTGAAGATTCAACATCAAATGTTGA
1 GGCATCTTTGGAGATTCAACATCAAATATTGA
* * *
2670091 GGCAT-TTTCGGAGATTAAACATCGAATATTGG
1 GGCATCTTT-GGAGATTCAACATCAAATATTGA
*
2670123 GGCATCTTTGGGGATTCAACATC
1 GGCATCTTTGGAGATTCAACATC
2670146 TAGATGTGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 3 0.07
32 40 0.87
33 3 0.07
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (32 bp):
GGCATCTTTGGAGATTCAACATCAAATATTGA
Found at i:2670978 original size:36 final size:36
Alignment explanation
Indices: 2670921--2671073 Score: 225
Period size: 36 Copynumber: 4.2 Consensus size: 36
2670911 TAATTTACTC
*
2670921 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTATCTCTCTTGAGACAGTTTCTCTT
2670958 AAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTT
* * * *
2670994 ATAGCAAATTTTGTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTT
* *
2671030 AAAACAAATTTTATCTCTCTTGAGACAATTTCCCTT
1 AAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTT
*
2671066 GAAACAAA
1 AAAACAAA
2671074 ATCTTTGAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 97 0.92
37 8 0.08
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.40
Consensus pattern (36 bp):
AAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTT
Found at i:2671020 original size:72 final size:73
Alignment explanation
Indices: 2670925--2671061 Score: 249
Period size: 72 Copynumber: 1.9 Consensus size: 73
2670915 TTACTCAAAA
*
2670925 CAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTATCTCTCTTGAGACAGTTTC
1 CAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTATCTCTCTTGAGACAATTTC
2670990 TCTTATAG
66 TCTTATAG
*
2670998 CAAA-TTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTATCTCTCTTGAGACAATTTC
1 CAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTATCTCTCTTGAGACAATTTC
2671062 CCTTGAAACA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
72 58 0.94
73 4 0.06
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (73 bp):
CAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTATCTCTCTTGAGACAATTTC
TCTTATAG
Found at i:2671186 original size:36 final size:36
Alignment explanation
Indices: 2671088--2671417 Score: 340
Period size: 36 Copynumber: 9.3 Consensus size: 36
2671078 TTGAATCTAT
* * *
2671088 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGATAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * * *
2671123 TTTCTTTTGGAACTAAGTTTTGGCTCTCTTTAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
2671160 TTTCTATTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
2671196 TTTCCCTT-AAATCAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAA-CAAATTTTGTCTCTCTTGAGACAG
* **
2671232 TTTCTCTTGAAACAAA------ATCT-TTGA-ATTTG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGA-CAG
* * *
2671261 TTT-TCCTTTAAACAAATTTCGTCTCTCTCGAGACAG
1 TTTCT-CTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2671297 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
2671334 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
2671370 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
2671407 TTTCTCTTGAA
1 TTTCTCTTGAA
2671418 GCATCAACCT
Statistics
Matches: 242, Mismatches: 36, Indels: 32
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 18 0.07
30 3 0.01
35 10 0.04
36 116 0.48
37 93 0.38
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:2671214 original size:174 final size:173
Alignment explanation
Indices: 2670922--2671417 Score: 726
Period size: 174 Copynumber: 2.8 Consensus size: 173
2670912 AATTTACTCA
* * ** * *
2670922 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAC-AAATTTTATCTCTCTTGAGACAG
1 AAACAAA-TTTCGTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
* * * *
2670986 TTTCTCTT-ATAGCAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTATCTCTCT
65 TTTCTCTTGA-AACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-AAACAAATTTTGTCTCTCT
* *
2671050 TGAGACAATTTCCCTTGAAACAAAATCTTTGAATCTATTTTCCTTG
128 TGAGACAGTTTCTCTTGAAACAAAATCTTTGAATCTATTTTCCTTG
* * * *
2671096 AAACAAATTTCGTCTCCCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGGCTCTCTTTAGACAGT
1 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
*
2671161 TTCTATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAATCAAATTTTGTCTCTCTTG
66 TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAA-CAAATTTTGTCTCTCTTG
* * *
2671226 AGACAGTTTCTCTTGAAACAAAATCTTTGAATTTGTTTTCCTTT
130 AGACAGTTTCTCTTGAAACAAAATCTTTGAATCTATTTTCCTTG
*
2671270 AAACAAATTTCGTCTCTCTCGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
1 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
2671335 TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTT
66 TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-AAACAAA-TTTTGTCTCTCTT
*
2671400 GAGATAGTTTCTCTTGAA
129 GAGACAGTTTCTCTTGAA
2671418 GCATCAACCT
Statistics
Matches: 290, Mismatches: 27, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
173 30 0.10
174 226 0.78
175 34 0.12
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (173 bp):
AAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAACAAATTTTGTCTCTCTTGA
GACAGTTTCTCTTGAAACAAAATCTTTGAATCTATTTTCCTTG
Found at i:2671331 original size:37 final size:36
Alignment explanation
Indices: 2671262--2671417 Score: 206
Period size: 37 Copynumber: 4.3 Consensus size: 36
2671252 TTGAATTTGT
* * * *
2671262 TTTC-CTTTAAACAAATTTCGTCTCTCTCGAGACAG
1 TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
* *
2671297 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAG
*
2671334 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
* *
2671370 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAG
2671407 TTTCTCTTGAA
1 TTTCTCTTGAA
2671418 GCATCAACCT
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
35 4 0.04
36 39 0.37
37 62 0.59
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
Found at i:2671389 original size:73 final size:73
Alignment explanation
Indices: 2671262--2671417 Score: 233
Period size: 73 Copynumber: 2.2 Consensus size: 73
2671252 TTGAATTTGT
* ** * *
2671262 TTTC-CTTTAAACAAATTTCGTCTCTCTCGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
2671326 TGAGACAG
66 TGAGACAG
* *
2671334 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
*
2671399 TGAGATAG
66 TGAGACAG
2671407 TTTCTCTTGAA
1 TTTCTCTTGAA
2671418 GCATCAACCT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
72 4 0.05
73 71 0.95
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
TGAGACAG
Found at i:2673403 original size:22 final size:22
Alignment explanation
Indices: 2673378--2673420 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2673368 CAATTCATTT
2673378 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
2673400 ATCTTATTTTTATCTTGTTTT
1 ATCTTATTTTTATCTTGTTTT
2673421 CAGCACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:2679592 original size:16 final size:16
Alignment explanation
Indices: 2679573--2679603 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2679563 CATTTATCAC
2679573 TTTAAAACACACTTAT
1 TTTAAAACACACTTAT
2679589 TTTAAAACACACTTA
1 TTTAAAACACACTTA
2679604 AAACACACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (16 bp):
TTTAAAACACACTTAT
Found at i:2681392 original size:2 final size:2
Alignment explanation
Indices: 2681385--2681409 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2681375 TTAAGAAACA
2681385 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 A
2681410 GTTTTCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2681882 original size:21 final size:21
Alignment explanation
Indices: 2681857--2681937 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
2681847 CAGAACCCCA
* *
2681857 GGGGGTATCGATTCCCTTGTG
1 GGGGGAATCGATTCCCTTATG
* **
2681878 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCCTT-ATG
* *
2681901 GGGGGAATCGGTTCCCTCATG
1 GGGGGAATCGATTCCCTTATG
2681922 GGGGG-ATCGATTCCCT
1 GGGGGAATCGATTCCCT
2681938 CTGCACAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 10 0.20
21 17 0.35
22 9 0.18
23 13 0.27
ACGTcount: A:0.15, C:0.23, G:0.36, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTTATG
Found at i:2689613 original size:22 final size:22
Alignment explanation
Indices: 2689588--2689629 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2689578 CAATTCATTT
2689588 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
2689610 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
2689630 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:2690553 original size:32 final size:32
Alignment explanation
Indices: 2690506--2690599 Score: 109
Period size: 32 Copynumber: 2.9 Consensus size: 32
2690496 GAACAATGGG
*
2690506 GGCATCTTTGAAGATTCAACATCAAATGTTGA
1 GGCATCTTTGGAGATTCAACATCAAATGTTGA
* * * *
2690538 GGCAT-TTTCGGAGATTAAACATCGAATATTGG
1 GGCATCTTT-GGAGATTCAACATCAAATGTTGA
*
2690570 GGCATCTTTGGGGATTCAACATCCAAATGT
1 GGCATCTTTGGAGATTCAACAT-CAAATGT
2690600 GAAATGACCA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
31 3 0.06
32 39 0.78
33 8 0.16
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (32 bp):
GGCATCTTTGGAGATTCAACATCAAATGTTGA
Found at i:2691424 original size:36 final size:36
Alignment explanation
Indices: 2691367--2691519 Score: 216
Period size: 36 Copynumber: 4.2 Consensus size: 36
2691357 TAATTTACTC
*
2691367 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTATCTCTCTTGAGACAGTTTCTCTT
* *
2691404 AAAACAAATTTTATCTCTCTTTAGACAATTTCTCTT
1 AAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTT
* * * *
2691440 ATAGCAAATTTTCTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTT
*
2691476 AAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTT
*
2691512 GAAACAAA
1 AAAACAAA
2691520 ATCTTTGAAT
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 94 0.92
37 8 0.08
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (36 bp):
AAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTT
Found at i:2691632 original size:36 final size:36
Alignment explanation
Indices: 2691534--2691863 Score: 331
Period size: 36 Copynumber: 9.3 Consensus size: 36
2691524 TTGAATCTAT
* * * *
2691534 TTTC-CTTGAAGCAAATTTCGTCTCCCTTGAGATAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * * *
2691569 TTTCTTTTGGAACTAAGTTTTGGCTCTCTTTAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
2691606 TTTCTATTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
2691642 TTTCCCTT-AAATCAAATTTTGTATCTCTTGAGACAG
1 TTTCTCTTGAAA-CAAATTTTGTCTCTCTTGAGACAG
* **
2691678 TTTCTCTTGAAACAAA------ATCT-TTGA-ATTTG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGA-CAG
* *
2691707 TTT-TCCTTTAAACAAATTTTGTCTCTCTCGAGACAG
1 TTTCT-CTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2691743 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
2691780 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
2691816 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
2691853 TTTCTCTTGAA
1 TTTCTCTTGAA
2691864 GCATCAACCT
Statistics
Matches: 242, Mismatches: 36, Indels: 32
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 18 0.07
30 4 0.02
35 10 0.04
36 114 0.47
37 94 0.39
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:2691713 original size:174 final size:173
Alignment explanation
Indices: 2691368--2691863 Score: 663
Period size: 174 Copynumber: 2.8 Consensus size: 173
2691358 AATTTACTCA
* * * * ** * ** *
2691368 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAC-AAATTTTATCTCTCTTTAGACAA
1 AAACAAA-TTTCGTCTCCCTCGAGACAGTTTCTTTTGGAACTAAGTTTTGGCTCTCTTTAGACAG
* * * * *
2691432 TTTCTCTT-ATAGCAAATTTTCTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTATCTCTCT
65 TTTCTCTTGA-AACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-AAACAAATTTTGTCTCTCT
*
2691496 TGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTATTTTCCTTG
128 TGAGACAGTTTCTCTTGAAACAAAATCTTTGAATCTATTTTCCTTG
* * *
2691542 AAGCAAATTTCGTCTCCCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGGCTCTCTTTAGACAGT
1 AAACAAATTTCGTCTCCCTCGAGACAGTTTCTTTTGGAACTAAGTTTTGGCTCTCTTTAGACAGT
* *
2691607 TTCTATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAATCAAATTTTGTATCTCTTG
66 TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAA-CAAATTTTGTCTCTCTTG
* * *
2691672 AGACAGTTTCTCTTGAAACAAAATCTTTGAATTTGTTTTCCTTT
130 AGACAGTTTCTCTTGAAACAAAATCTTTGAATCTATTTTCCTTG
* * * *
2691716 AAACAAATTTTGTCTCTCTCGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
1 AAACAAATTTCGTCTCCCTCGAGACAGTTTCTTTTGGAACTAAGTTTTGGCTCTCTTTAGACAGT
2691781 TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTT
66 TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-AAACAAA-TTTTGTCTCTCTT
*
2691846 GAGATAGTTTCTCTTGAA
129 GAGACAGTTTCTCTTGAA
2691864 GCATCAACCT
Statistics
Matches: 285, Mismatches: 32, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
173 30 0.11
174 222 0.78
175 33 0.12
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.42
Consensus pattern (173 bp):
AAACAAATTTCGTCTCCCTCGAGACAGTTTCTTTTGGAACTAAGTTTTGGCTCTCTTTAGACAGT
TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAACAAATTTTGTCTCTCTTGA
GACAGTTTCTCTTGAAACAAAATCTTTGAATCTATTTTCCTTG
Found at i:2691777 original size:37 final size:36
Alignment explanation
Indices: 2691708--2691863 Score: 215
Period size: 37 Copynumber: 4.3 Consensus size: 36
2691698 TTGAATTTGT
* * *
2691708 TTTC-CTTTAAACAAATTTTGTCTCTCTCGAGACAG
1 TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
* *
2691743 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAG
*
2691780 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
* *
2691816 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAG
2691853 TTTCTCTTGAA
1 TTTCTCTTGAA
2691864 GCATCAACCT
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
35 4 0.04
36 39 0.37
37 63 0.59
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (36 bp):
TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
Found at i:2691835 original size:73 final size:73
Alignment explanation
Indices: 2691708--2691863 Score: 242
Period size: 73 Copynumber: 2.2 Consensus size: 73
2691698 TTGAATTTGT
* ** * *
2691708 TTTC-CTTTAAACAAATTTTGTCTCTCTCGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTCGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
2691772 TGAGACAG
66 TGAGACAG
*
2691780 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTCGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
*
2691845 TGAGATAG
66 TGAGACAG
2691853 TTTCTCTTGAA
1 TTTCTCTTGAA
2691864 GCATCAACCT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
72 4 0.05
73 72 0.95
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTCGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
TGAGACAG
Found at i:2693758 original size:15 final size:16
Alignment explanation
Indices: 2693737--2693773 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2693727 TCAATTCCCT
2693737 TATTTATTTTTATTTC
1 TATTTATTTTTATTTC
*
2693753 -ATTTATTTTTGTTTC
1 TATTTATTTTTATTTC
2693768 TATTTA
1 TATTTA
2693774 CTTATTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (16 bp):
TATTTATTTTTATTTC
Found at i:2693794 original size:23 final size:23
Alignment explanation
Indices: 2693768--2693811 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2693758 TTTTTGTTTC
2693768 TATT-TACTTATTCATTTTATTAT
1 TATTATACTT-TTCATTTTATTAT
*
2693791 TATTATGCTTTTCATTTTATT
1 TATTATACTTTTCATTTTATT
2693812 TATTTTCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (23 bp):
TATTATACTTTTCATTTTATTAT
Found at i:2693883 original size:22 final size:21
Alignment explanation
Indices: 2693858--2693925 Score: 50
Period size: 21 Copynumber: 3.1 Consensus size: 21
2693848 TTTTATTATA
2693858 TTTATCTCATTTATTTATTTCT
1 TTTA-CTCATTTATTTATTTCT
* *
2693880 TTTAC-CTTTTTATTTACTT-T
1 TTTACTC-ATTTATTTATTTCT
*
2693900 TCTACTCATTTCATTTTATTTTCT
1 TTTACTCATTT-A-TTTA-TTTCT
2693924 TT
1 TT
2693926 ATTTTAGTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
20 9 0.26
21 13 0.38
22 8 0.24
23 2 0.06
24 2 0.06
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTACTCATTTATTTATTTCT
Found at i:2694323 original size:29 final size:29
Alignment explanation
Indices: 2694286--2694375 Score: 126
Period size: 29 Copynumber: 3.1 Consensus size: 29
2694276 GGTTCCGACA
* * *
2694286 TTAAGTTAATATAAGAATAAATTATATTT
1 TTAAATTAAAATAAGAATAAAATATATTT
* * *
2694315 TTAATTTAAGATAAGATTAAAATATATTT
1 TTAAATTAAAATAAGAATAAAATATATTT
2694344 TTAAATTAAAATAAGAATAAAATATATTT
1 TTAAATTAAAATAAGAATAAAATATATTT
2694373 TTA
1 TTA
2694376 GGATACGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (29 bp):
TTAAATTAAAATAAGAATAAAATATATTT
Found at i:2694388 original size:29 final size:27
Alignment explanation
Indices: 2694298--2694401 Score: 91
Period size: 29 Copynumber: 3.6 Consensus size: 27
2694288 AAGTTAATAT
* * *
2694298 AAGAATAAATTATATTTTTAATTTAAGAT
1 AAGAATAAAATATATTTTTAA-AT-AGAA
* *
2694327 AAGATTAAAATATATTTTTAAATTAAAA
1 AAGAATAAAATATATTTTTAAA-TAGAA
*
2694355 TAAGAATAAAATATATTTTTAGGATACGAA
1 -AAGAATAAAATATATTTTTA-AATA-GAA
*
2694385 AAGAATAACATATATTT
1 AAGAATAAAATATATTT
2694402 AATAAGTTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
28 2 0.03
29 57 0.92
30 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (27 bp):
AAGAATAAAATATATTTTTAAATAGAA
Found at i:2694398 original size:58 final size:58
Alignment explanation
Indices: 2694286--2694401 Score: 142
Period size: 58 Copynumber: 2.0 Consensus size: 58
2694276 GGTTCCGACA
* * * ** * *
2694286 TTAAGTTAATATAAGAATAAATTATATTTTTAATTTAAGATAAGATTAAAATATATTT
1 TTAAATTAAAATAAGAATAAAATATATTTTTAAGATAAGAAAAGAATAAAATATATTT
* * *
2694344 TTAAATTAAAATAAGAATAAAATATATTTTTAGGATACGAAAAGAATAACATATATTT
1 TTAAATTAAAATAAGAATAAAATATATTTTTAAGATAAGAAAAGAATAAAATATATTT
2694402 AATAAGTTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (58 bp):
TTAAATTAAAATAAGAATAAAATATATTTTTAAGATAAGAAAAGAATAAAATATATTT
Found at i:2694461 original size:18 final size:18
Alignment explanation
Indices: 2694420--2694466 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2694410 AAGATAATTT
2694420 TTTAATGTTAATATGTAAA
1 TTTAAT-TTAATATGTAAA
* *
2694439 ATTAATTTAATATGTGAA
1 TTTAATTTAATATGTAAA
*
2694457 TTTAAATTAA
1 TTTAATTTAA
2694467 GATATATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.47
Consensus pattern (18 bp):
TTTAATTTAATATGTAAA
Found at i:2696983 original size:15 final size:15
Alignment explanation
Indices: 2696965--2696995 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2696955 GGGAACCGAA
*
2696965 AAAGGAAATATATAT
1 AAAGAAAATATATAT
2696980 AAAGAAAATATATAT
1 AAAGAAAATATATAT
2696995 A
1 A
2696996 GATGAAAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (15 bp):
AAAGAAAATATATAT
Found at i:2701376 original size:17 final size:17
Alignment explanation
Indices: 2701321--2701377 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
2701311 AACTAACTGA
2701321 CACTACACACTAAGTGG
1 CACTACACACTAAGTGG
** * * * *
2701338 CAAAAATAAACTAACTGA
1 C-ACTACACACTAAGTGG
2701356 CACTACACACTAAGTGG
1 CACTACACACTAAGTGG
2701373 CACTA
1 CACTA
2701378 AAATAGGAGT
Statistics
Matches: 27, Mismatches: 12, Indels: 2
0.66 0.29 0.05
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.18
Consensus pattern (17 bp):
CACTACACACTAAGTGG
Found at i:2702324 original size:11 final size:11
Alignment explanation
Indices: 2702308--2702334 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2702298 TAGTGCATCG
2702308 GTGCACTAAGT
1 GTGCACTAAGT
2702319 GTGCACTAAGT
1 GTGCACTAAGT
2702330 GTGCA
1 GTGCA
2702335 TCGATGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (11 bp):
GTGCACTAAGT
Found at i:2702463 original size:56 final size:56
Alignment explanation
Indices: 2702339--2702464 Score: 168
Period size: 57 Copynumber: 2.2 Consensus size: 56
2702329 TGTGCATCGA
* * *
2702339 TGCATAAAATGTATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTGG
1 TGCATCAAATGCATTCGATGTTTCAAAATACCCTGAGTGCATCGATGCATGGCTGG
*
2702395 TGCATCAAATGCATTCGATGTTTTCATAAAT-CCCTGAGTGCATCGATGCATGG-TATG
1 TGCATCAAATGCATTCGATG-TTTCA-AAATACCCTGAGTGCATCGATGCATGGCT-GG
2702452 TGCATC-AATGCAT
1 TGCATCAAATGCAT
2702465 GAAATGCATT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
56 26 0.41
57 33 0.52
58 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (56 bp):
TGCATCAAATGCATTCGATGTTTCAAAATACCCTGAGTGCATCGATGCATGGCTGG
Found at i:2711067 original size:64 final size:65
Alignment explanation
Indices: 2711018--2711141 Score: 189
Period size: 64 Copynumber: 1.9 Consensus size: 65
2711008 TGCATTAAGT
* * *
2711018 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAGCCTGAGTGCATCGATACATGGCT
1 GTGCATCGATGCATAAAATACATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATACATAGCT
2711081 G
65 G
*
2711082 GTGCATCGATGCATCAAATACATTCGATGTTTTCATAAAACCCTGAGTGCATCGATACAT
1 GTGCATCGATGCATAAAATACATTCGATGTTTTCATAAAACCCTGAGTGCATCGATACAT
2711142 GAAATGCATT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 27 0.49
65 25 0.45
66 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATACATTCGATGTTTTCATAAAACCCTGAGTGCATCGATACATAGCTG
Found at i:2711155 original size:64 final size:64
Alignment explanation
Indices: 2711019--2711156 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 64
2711009 GCATTAAGTG
* * ***
2711019 TGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATACATGGCTGG
1 TGCATCGATGCATAAAATACATTCGATGTTTCAAAATACCCTGAGTGCATCGATACATGGCAAA
*
2711083 TGCATCGATGCATCAAATACATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATACAT-G-AA
1 TGCATCGATGCATAAAATACATTCGATG-TTTCA-AAATACCCTGAGTGCATCGATACATGGCAA
2711145 A
64 A
2711146 TGCATTCGATG
1 TGCA-TCGATG
2711157 TTCAATTTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
63 4 0.06
64 33 0.51
65 25 0.38
66 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATAAAATACATTCGATGTTTCAAAATACCCTGAGTGCATCGATACATGGCAAA
Found at i:2714287 original size:2 final size:2
Alignment explanation
Indices: 2714282--2714331 Score: 91
Period size: 2 Copynumber: 24.5 Consensus size: 2
2714272 TTAATCATTA
2714282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2714324 AT GAT AT A
1 AT -AT AT A
2714332 ATTACTTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2716907 original size:34 final size:35
Alignment explanation
Indices: 2716864--2716934 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
2716854 TATAGACTCT
*
2716864 CAGAAACAAACTAACT-ACACTATACACTAAGTGG
1 CAGAAACAAACTAACTGACACTACACACTAAGTGG
*
2716898 CAGAAACAAACTAACTGACACTACACATTAAGTGG
1 CAGAAACAAACTAACTGACACTACACACTAAGTGG
2716933 CA
1 CA
2716935 CTAAAATAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 16 0.47
35 18 0.53
ACGTcount: A:0.46, C:0.24, G:0.13, T:0.17
Consensus pattern (35 bp):
CAGAAACAAACTAACTGACACTACACACTAAGTGG
Found at i:2719427 original size:21 final size:23
Alignment explanation
Indices: 2719381--2719433 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
2719371 AACAAGTAAT
*
2719381 TATAAATTAGTTAAAAATCTAAA
1 TATAAATTAGTTAAAAATCGAAA
*
2719404 TATAAATTA-TTTAAAAT-GAAA
1 TATAAATTAGTTAAAAATCGAAA
*
2719425 TATTAATTA
1 TATAAATTA
2719434 CATTACTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 11 0.41
22 7 0.26
23 9 0.33
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
TATAAATTAGTTAAAAATCGAAA
Found at i:2720142 original size:43 final size:45
Alignment explanation
Indices: 2720088--2720172 Score: 131
Period size: 44 Copynumber: 1.9 Consensus size: 45
2720078 ATAAATATAA
2720088 AATTTTAAATTATATATGA-TAAAAAT-AATTTTTAATATTTATTT
1 AATTTTAAATTATATATGATTAAAAATAAATTTTTAA-ATTTATTT
*
2720132 AATTTT-AATTATATATGATTATAAATAAATTTTTAAATTTA
1 AATTTTAAATTATATATGATTAAAAATAAATTTTTAAATTTA
2720173 AATTTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
43 12 0.32
44 17 0.45
45 9 0.24
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (45 bp):
AATTTTAAATTATATATGATTAAAAATAAATTTTTAAATTTATTT
Found at i:2720181 original size:43 final size:41
Alignment explanation
Indices: 2720079--2720182 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 41
2720069 ATCAATTAAA
* * *
2720079 TAAATATAAAATTTTAAATTATATATGATAAAAATAATTTT
1 TAAATTTAAATTTTTTAATTATATATGATAAAAATAATTTT
* *
2720120 TAATATTT-ATTTAATTTTAATTATATATGATTATAAATAAATTTT
1 TAA-ATTTAAATT--TTTTAATTATATATGA-TAAAAAT-AATTTT
2720165 TAAATTTAAATTTTTTAA
1 TAAATTTAAATTTTTTAA
2720183 AAGTTTAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
41 5 0.10
42 3 0.06
43 21 0.41
44 10 0.20
45 12 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (41 bp):
TAAATTTAAATTTTTTAATTATATATGATAAAAATAATTTT
Found at i:2723341 original size:22 final size:21
Alignment explanation
Indices: 2723290--2723338 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
2723280 AAACCAGATT
*
2723290 AATTTTTATCAGATTCGGATC
1 AATTTTTATCAGATCCGGATC
2723311 AATTTTTAT-ATGATCCGGATC
1 AATTTTTATCA-GATCCGGATC
2723332 AATTTTT
1 AATTTTT
2723339 TATCGGACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (21 bp):
AATTTTTATCAGATCCGGATC
Found at i:2725242 original size:69 final size:68
Alignment explanation
Indices: 2725103--2725232 Score: 185
Period size: 68 Copynumber: 1.9 Consensus size: 68
2725093 GTGATTTAGA
* *
2725103 AAAAAATTCTCAAATGTTAGGATTTTTAATTAGATTTAAATTAGAGTGTTACACCAATTTTATAA
1 AAAAAATACTCAAATGTTAGGATTTTTAATTAGAGTTAAATTAGAGTGTTACA-CAATTTTATAA
2725168 TTTT
65 TTTT
*
2725172 AAAAAATACTTAAATGTTAGGA-TTTTAATTAGAGTTAAATTAG-GATGTTACA-ATATTTTAT
1 AAAAAATACTCAAATGTTAGGATTTTTAATTAGAGTTAAATTAGAG-TGTTACACA-ATTTTAT
2725233 TTGTGTTTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
66 1 0.02
67 8 0.14
68 27 0.48
69 20 0.36
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (68 bp):
AAAAAATACTCAAATGTTAGGATTTTTAATTAGAGTTAAATTAGAGTGTTACACAATTTTATAAT
TTT
Found at i:2725435 original size:75 final size:75
Alignment explanation
Indices: 2725248--2725451 Score: 213
Period size: 75 Copynumber: 2.8 Consensus size: 75
2725238 TTTAATATTT
* *
2725248 TTCTAGACTTAATATTATGGTTTGAGTCTT-AAGATTTAATACTTTAATATTATGATTTCATTAT
1 TTCTAGACTTAATATTATGGTTTGAGTCTTGAA-ATTTGACACTTTAATATTATGATTTCATTAT
*
2725312 GGATTTTATTA
65 GGATTTTACTA
* * * * * * * **
2725323 TTCTAGAGTTAATATTTTAGTTTGAATCTTGAAATTTGACATTTTAATATTGTGGTTTGTTTATG
1 TTCTAGACTTAATATTATGGTTTGAGTCTTGAAATTTGACACTTTAATATTATGATTTCATTATG
*
2725388 GATTTTACTG
66 GATTTTACTA
* *
2725398 TTCTA-ATCTTAATATTGTGGTTTGAGTCTTGATATTTG--ACTTT-AT-TTATGATTT
1 TTCTAGA-CTTAATATTATGGTTTGAGTCTTGAAATTTGACACTTTAATATTATGATTT
2725452 TATATATATA
Statistics
Matches: 106, Mismatches: 21, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
71 7 0.07
72 2 0.02
73 4 0.04
74 1 0.01
75 90 0.85
76 2 0.02
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.52
Consensus pattern (75 bp):
TTCTAGACTTAATATTATGGTTTGAGTCTTGAAATTTGACACTTTAATATTATGATTTCATTATG
GATTTTACTA
Found at i:2733704 original size:17 final size:17
Alignment explanation
Indices: 2733679--2733712 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2733669 ATATGAATAA
2733679 TTGGATGATCATTTTAT
1 TTGGATGATCATTTTAT
*
2733696 TTGGGTGATCATTTTAT
1 TTGGATGATCATTTTAT
2733713 ACTTTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.21, T:0.53
Consensus pattern (17 bp):
TTGGATGATCATTTTAT
Found at i:2737555 original size:3 final size:3
Alignment explanation
Indices: 2737549--2737597 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
2737539 ACTTTTTTTT
2737549 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
2737593 TTA TT
1 TTA TT
2737598 GGATAATCCC
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2737577 original size:23 final size:23
Alignment explanation
Indices: 2737550--2737596 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
2737540 CTTTTTTTTT
2737550 TATTATTATTA-TTATTATTATTA
1 TATTATTATTATTTATTA-TATTA
2737573 TATTATTATTATTTATTATATTA
1 TATTATTATTATTTATTATATTA
2737596 T
1 T
2737597 TGGATAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTATTATTATTTATTATATTA
Found at i:2740229 original size:20 final size:21
Alignment explanation
Indices: 2740175--2740229 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
2740165 GATACTGAAA
*
2740175 GGAGTATCGATACCATAGTAG
1 GGAGTACCGATACCATAGTAG
*
2740196 GGAAGTATCGATACCATA-TAAG
1 GG-AGTACCGATACCATAGT-AG
2740218 GG-GTACCGATAC
1 GGAGTACCGATAC
2740230 TAATATGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 9 0.29
21 3 0.10
22 19 0.61
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (21 bp):
GGAGTACCGATACCATAGTAG
Found at i:2740628 original size:54 final size:54
Alignment explanation
Indices: 2740543--2740986 Score: 584
Period size: 54 Copynumber: 8.4 Consensus size: 54
2740533 ATATGTGTAC
*
2740543 TATCGACACTATGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGACCG
1 TATCGACACTATGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
* * *
2740597 TATCGACACTATGTGTGCATCCCACGGAATTCATAATAAGTTTATGAATGACCG
1 TATCGACACTATGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
* * * * * * *
2740651 TATCGACACTATGTATGCAACTCACATAATTTATAATAAGTTTATAAATGATCG
1 TATCGACACTATGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
*
2740705 TATC-AGCACTA-------AACCCACGGAATTCATAATAAGTTTATGAACGACCG
1 TATCGA-CACTATGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
* * *
2740752 TATCGGCACTATGCGTGCAACCCACAGAATTCAGAATAAGTTTATGAACGACCG
1 TATCGACACTATGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
* **
2740806 TATC-AGCACTATGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGGTCG
1 TATCGA-CACTATGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
*
2740860 TATCGACACTATGTGTGCAACCCA-AGAAATTCATAATAAGTTTATGAATGACCG
1 TATCGACACTATGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACCG
* *
2740914 TATCGACACTATGTGTGCAACCCACTGAATTCATAATAAGTTTATGAACGATCG
1 TATCGACACTATGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
* *
2740968 TATCGGCACTACGTGTGCA
1 TATCGACACTATGTGTGCA
2740987 CCCGAAAGAA
Statistics
Matches: 340, Mismatches: 37, Indels: 26
0.84 0.09 0.06
Matches are distributed among these distances:
47 38 0.11
53 2 0.01
54 298 0.88
55 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (54 bp):
TATCGACACTATGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
Found at i:2750944 original size:53 final size:54
Alignment explanation
Indices: 2750881--2751131 Score: 343
Period size: 53 Copynumber: 4.7 Consensus size: 54
2750871 CTATGTGTAC
2750881 TATCGACACTATGTGTGCAACCCACAGAATTCATAATAAG-TTATGAACGACCA
1 TATCGACACTATGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCA
*
2750934 TATCGACACTATGTGTGCAACCCA-TGAAATTCATAATAAG-TTATGAACGACCA
1 TATCGACACTATGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACCA
*
2750987 TATCGACACTATGTGTGCAACCCAC-GAAATTCATAATAAGTTTATGAACGACCG
1 TATCGACACTATGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACCA
* * *
2751041 TATC-AGCACTATGTATGCAACCCACATAATTCATAATAAGTTTATGAACGACCG
1 TATCGA-CACTATGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCA
* * * *
2751095 TATCGGCACTACGTGTGCACCCCAAAGAACTT-ATAAT
1 TATCGACACTATGTGTGCAACCCACAGAA-TTCATAAT
2751132 GTTTTGAAAA
Statistics
Matches: 181, Mismatches: 10, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
52 1 0.01
53 90 0.50
54 88 0.49
55 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (54 bp):
TATCGACACTATGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCA
Found at i:2751078 original size:107 final size:107
Alignment explanation
Indices: 2750881--2751131 Score: 350
Period size: 107 Copynumber: 2.3 Consensus size: 107
2750871 CTATGTGTAC
2750881 TATCGACACTATGTGTGCAACCCACAGAATTCATAATAAGTTATGAACGACCATATCGACACTAT
1 TATCGACACTATGTGTGCAACCCACAGAATTCATAATAAGTTATGAACGACCATATCGACACTAT
* *
2750946 GTGTGCAACCCATGAAATTCATAATAAG-TTATGAACGACCA
66 GTATGCAACCCATCAAATTCATAATAAGTTTATGAACGACCA
*
2750987 TATCGACACTATGTGTGCAACCCAC-GAAATTCATAATAAGTTTATGAACGACCGTATC-AGCAC
1 TATCGACACTATGTGTGCAACCCACAG-AATTCATAATAAG-TTATGAACGACCATATCGA-CAC
*
2751050 TATGTATGCAACCCA-CATAATTCATAATAAGTTTATGAACGACCG
63 TATGTATGCAACCCATCA-AATTCATAATAAGTTTATGAACGACCA
* * * *
2751095 TATCGGCACTACGTGTGCACCCCAAAGAACTT-ATAAT
1 TATCGACACTATGTGTGCAACCCACAGAA-TTCATAAT
2751132 GTTTTGAAAA
Statistics
Matches: 130, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
105 1 0.01
106 40 0.31
107 46 0.35
108 40 0.31
109 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (107 bp):
TATCGACACTATGTGTGCAACCCACAGAATTCATAATAAGTTATGAACGACCATATCGACACTAT
GTATGCAACCCATCAAATTCATAATAAGTTTATGAACGACCA
Found at i:2755610 original size:41 final size:40
Alignment explanation
Indices: 2755565--2755774 Score: 116
Period size: 41 Copynumber: 5.1 Consensus size: 40
2755555 TATTGTAGCA
*
2755565 TTTTTATGTAAACGCCGCGATAGAGTAGCACTGTAGAGGCG
1 TTTTTATGTAAACGCCGCGATAGAGTAGAACT-TAGAGGCG
** * ** * * *
2755606 TTTTTATACAAATGCCGTAAAAGAGTTGAACATTAGTGGCG
1 TTTTTATGTAAACGCCGCGATAGAGTAGAAC-TTAGAGGCG
* * *
2755647 TTTTTTTTGTAAACGCCGAGATAGAGTAGAACTATAAAGGCG
1 -TTTTTATGTAAACGCCGCGATAGAGTAGAACT-TAGAGGCG
* * * * * * **
2755689 TTTTCATAG-AAACGCCTCTATAGAGTTGGACTTTTGTTGCG
1 TTTTTAT-GTAAACGCCGCGATAGAGTAGAAC-TTAGAGGCG
* * * * *
2755730 TTTTTTTGATAAACGTCGGGATAGATTAGAACTATATAGGCG
1 TTTTTATG-TAAACGCCGCGATAGAGTAGAACT-TAGAGGCG
2755772 TTT
1 TTT
2755775 GGTTTACTAA
Statistics
Matches: 118, Mismatches: 43, Indels: 15
0.67 0.24 0.09
Matches are distributed among these distances:
40 1 0.01
41 63 0.53
42 54 0.46
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (40 bp):
TTTTTATGTAAACGCCGCGATAGAGTAGAACTTAGAGGCG
Found at i:2755689 original size:42 final size:42
Alignment explanation
Indices: 2755565--2755692 Score: 118
Period size: 42 Copynumber: 3.1 Consensus size: 42
2755555 TATTGTAGCA
* * *
2755565 TTTTTATGTAAACGCCGCGATAGAGTAGCACTGTAGAGGCG-
1 TTTTTATGTAAACGCCGAGATAGAGTAGAACTATAGAGGCGT
** * * * *
2755606 TTTTTATACAAATGCCGTA-AAAGAGTTGAAC-ATTAGTGGCGT
1 TTTTTATGTAAACGCCG-AGATAGAGTAGAACTA-TAGAGGCGT
* *
2755648 TTTTTTTGTAAACGCCGAGATAGAGTAGAACTATAAAGGCGT
1 TTTTTATGTAAACGCCGAGATAGAGTAGAACTATAGAGGCGT
2755690 TTT
1 TTT
2755693 CATAGAAACG
Statistics
Matches: 65, Mismatches: 17, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
41 31 0.48
42 33 0.51
43 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.32
Consensus pattern (42 bp):
TTTTTATGTAAACGCCGAGATAGAGTAGAACTATAGAGGCGT
Found at i:2755714 original size:83 final size:82
Alignment explanation
Indices: 2755565--2755774 Score: 224
Period size: 83 Copynumber: 2.5 Consensus size: 82
2755555 TATTGTAGCA
* * * * * * *
2755565 TTTTTATGTAAACGCCGCGATAGAGTAGCACTGTAGAGGCGTTTTTATACAAATGCCGTAAAAGA
1 TTTTTTTGTAAACGCCGAGATAGAGTAGAACTATAAAGGCGTTTTCATACAAACGCCGTAAAAGA
2755630 GTTGAACATTAGTGGCG
66 GTTGAACATTAGTGGCG
* * *
2755647 TTTTTTTTGTAAACGCCGAGATAGAGTAGAACTATAAAGGCGTTTTCATAGAAACGCC-TCTATA
1 -TTTTTTTGTAAACGCCGAGATAGAGTAGAACTATAAAGGCGTTTTCATACAAACGCCGT-AAAA
* * * *
2755711 GAGTTGGACTTTTGTTGCG
64 GAGTTGAACATTAGTGGCG
* * * *
2755730 TTTTTTTGATAAACGTCGGGATAGATTAGAACTATATAGGCGTTT
1 TTTTTTTG-TAAACGCCGAGATAGAGTAGAACTATAAAGGCGTTT
2755775 GGTTTACTAA
Statistics
Matches: 107, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
82 9 0.08
83 98 0.92
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (82 bp):
TTTTTTTGTAAACGCCGAGATAGAGTAGAACTATAAAGGCGTTTTCATACAAACGCCGTAAAAGA
GTTGAACATTAGTGGCG
Found at i:2755986 original size:75 final size:75
Alignment explanation
Indices: 2755859--2756080 Score: 338
Period size: 75 Copynumber: 3.0 Consensus size: 75
2755849 CTATTACCCT
* *
2755859 CCATCAGTTCTTTGTGCTGCCTCACAACACAAACACAAACGTCGATTGCAGTCGCCACCATTCAC
1 CCATCAGTTCTCTGTGCTACCTCACAACACAAACACAAACGTCGATTGCAGTCGCCACCATTCAC
2755924 GCCGTCGGTC
66 GCCGTCGGTC
* * * *
2755934 CCATCATTTCTCTGTGTTACCTCACAACACAAACACAAACGTTGATTACAGTCGCCACCATTCAC
1 CCATCAGTTCTCTGTGCTACCTCACAACACAAACACAAACGTCGATTGCAGTCGCCACCATTCAC
*
2755999 GCCGTCGGTT
66 GCCGTCGGTC
* * *
2756009 CCATCAGTTCTCTGTGCTCCCTCACAACACAAAAACAATA-ATCGATTGCAGTCGCCACCATTCA
1 CCATCAGTTCTCTGTGCTACCTCACAACACAAACACAA-ACGTCGATTGCAGTCGCCACCATTCA
2756073 CGCCGTCG
65 CGCCGTCG
2756081 TGCCATCTGT
Statistics
Matches: 132, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
75 131 0.99
76 1 0.01
ACGTcount: A:0.26, C:0.35, G:0.15, T:0.24
Consensus pattern (75 bp):
CCATCAGTTCTCTGTGCTACCTCACAACACAAACACAAACGTCGATTGCAGTCGCCACCATTCAC
GCCGTCGGTC
Found at i:2756956 original size:31 final size:31
Alignment explanation
Indices: 2756920--2756978 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2756910 AACTTAAAAG
* *
2756920 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
2756951 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
2756979 CATACAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2757028 original size:22 final size:22
Alignment explanation
Indices: 2757002--2757044 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2756992 TAATAAATTA
2757002 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2757024 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2757045 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2757053 original size:22 final size:22
Alignment explanation
Indices: 2757004--2757052 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2756994 ATAAATTATT
**
2757004 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2757026 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2757049 TAAA
1 TAAA
2757053 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2757055 original size:54 final size:54
Alignment explanation
Indices: 2756992--2757290 Score: 294
Period size: 54 Copynumber: 5.6 Consensus size: 54
2756982 ACAACTACAA
2756992 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
2757046 TAATAAATTATTTAAAATAAATCAATCAATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** **
2757103 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
* * *
2757158 -AACTACA--A--T--AATAAATCAATCTATATTTTAAAATAAATCAACCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
2757206 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
2757260 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
2757291 CAACTACAAT
Statistics
Matches: 200, Mismatches: 28, Indels: 34
0.76 0.11 0.13
Matches are distributed among these distances:
48 29 0.14
49 4 0.02
50 6 0.03
51 1 0.00
52 1 0.00
53 1 0.00
54 112 0.56
55 6 0.03
56 5 0.03
57 13 0.06
58 22 0.11
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:2757094 original size:80 final size:79
Alignment explanation
Indices: 2757006--2757568 Score: 526
Period size: 80 Copynumber: 6.8 Consensus size: 79
2756996 AAATTATTTA
2757006 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
*
2757071 TCAATACAACTACAAT
66 TCCATA-AACTA-AAT
2757087 -AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
2757151 TCCATACAACTACAAT
66 TCCATA-AACTA-AAT
* *
2757167 -AATAAATCAATCTATATTTTAAAATAAATCAACCCATACTAATAAATTATTTAAAATAAATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
***
2757231 TCCATATTTTAAAAT
66 TCCATAAACT-AAAT
* * *
2757246 AAATCAATTC-ATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACA--A--T--AA
1 AAAT-AAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAA
* **
2757303 TAAATCAATCCAT--ATTTTA-
58 TAAATCAATCCATAAACTAAAT
2757322 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT-AATTATTTAAAATAAATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
***
2757386 TCCATATTTTAAAAT
66 TCCATAAACT-AAAT
* * *
2757401 AAATCAATCCATACTAATAAATTAGTTAAAATAAATCAATCCATAACTACAATAATCAATCCATA
1 AAATAAATCAAT-C-CAT--ATT--TTAAAATAAATCAATCCAT-ACT--AAT-A--AAT---TA
2757466 TTTTAAAATAAATCAATCCATACTAA-TAAATTTTT
51 -TTTAAAATAAATCAATCCATA--AACTAAA----T
2757501 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 -AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
2757566 ATC
65 ATC
2757569 ATATTTAAAA
Statistics
Matches: 409, Mismatches: 27, Indels: 88
0.78 0.05 0.17
Matches are distributed among these distances:
69 1 0.00
70 23 0.06
71 4 0.01
72 1 0.00
73 1 0.00
74 2 0.00
75 20 0.05
76 6 0.01
77 3 0.01
78 3 0.01
79 14 0.03
80 169 0.41
81 7 0.02
82 3 0.01
83 3 0.01
84 2 0.00
85 39 0.10
86 29 0.07
88 3 0.01
89 3 0.01
91 1 0.00
92 6 0.01
94 3 0.01
95 21 0.05
96 24 0.06
97 4 0.01
99 2 0.00
100 2 0.00
101 10 0.02
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (79 bp):
AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
TCCATAAACTAAAT
Found at i:2757133 original size:22 final size:22
Alignment explanation
Indices: 2757061--2757133 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
2757051 AATTATTTAA
* *
2757061 AATAAATCAATCAATACA-ACT
1 AATAAATAAATCAATCCATACT
2757082 ACA-ATAATAAATCAATCCATA-T
1 A-ATA-AATAAATCAATCCATACT
**
2757104 TTTAAAATAAATCAATCCATACT
1 AAT-AAATAAATCAATCCATACT
2757127 AATAAAT
1 AATAAAT
2757134 TATTTAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
21 2 0.05
22 34 0.85
23 4 0.10
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
AATAAATAAATCAATCCATACT
Found at i:2757242 original size:22 final size:22
Alignment explanation
Indices: 2757216--2757258 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2757206 TAATAAATTA
2757216 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
2757238 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
2757259 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2757267 original size:22 final size:22
Alignment explanation
Indices: 2757218--2757266 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2757208 ATAAATTATT
**
2757218 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
2757240 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2757263 TAAA
1 TAAA
2757267 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2757422 original size:22 final size:22
Alignment explanation
Indices: 2757272--2757367 Score: 102
Period size: 22 Copynumber: 4.1 Consensus size: 22
2757262 ATAAATTATT
*
2757272 TAAAATAAATCAATCCATACAA
1 TAAAATAAATCAATCCATATAA
**
2757294 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
**
2757320 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2757342 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2757365 TAA
1 TAA
2757368 TTATTTAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
22 38 0.59
23 7 0.11
25 3 0.05
26 16 0.25
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Done.