Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 16 of 25
Found at i:2356547 original size:19 final size:20
Alignment explanation
Indices: 2356523--2356575 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
2356513 TAATATTATA
2356523 AAATATATAAATATAA-AAT
1 AAATATATAAATATAATAAT
* * *
2356542 AAATATTTAAATTTAATTAT
1 AAATATATAAATATAATAAT
2356562 AAATATATTAAATA
1 AAATATA-TAAATA
2356576 AATTATATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 14 0.52
20 8 0.30
21 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATATATAAATATAATAAT
Found at i:2356579 original size:20 final size:20
Alignment explanation
Indices: 2356517--2356582 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
2356507 TGAATGTAAT
2356517 ATTATAAA-ATATATAAATATA
1 ATTATAAATATAT-TAAATA-A
* *
2356538 A-AATAAATAT-TTAAATTTA
1 ATTATAAATATATTAAA-TAA
2356557 ATTATAAATATATTAAATAA
1 ATTATAAATATATTAAATAA
2356577 ATTATA
1 ATTATA
2356583 TTAATTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.16
20 23 0.62
21 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTATAAATATATTAAATAA
Found at i:2356896 original size:2 final size:2
Alignment explanation
Indices: 2356889--2356926 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2356879 TTCTAGTGGC
2356889 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
2356927 GAAAGAGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2358066 original size:15 final size:16
Alignment explanation
Indices: 2358046--2358075 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2358036 TTTTTATTTT
2358046 TTTAAAAT-ATAATTG
1 TTTAAAATAATAATTG
2358061 TTTAAAATAATAATT
1 TTTAAAATAATAATT
2358076 TAAACTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TTTAAAATAATAATTG
Found at i:2359596 original size:24 final size:24
Alignment explanation
Indices: 2359536--2359597 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
2359526 AATAAAATGT
2359536 ATTTAAATTTATTTAAAAATTAATA
1 ATTTAAATTTATTTAAAAATT-ATA
*
2359561 ATTT-ATTTTATTTAATAAATT-TA
1 ATTTAAATTTATTTAA-AAATTATA
*
2359584 ATTTAAATATATTT
1 ATTTAAATTTATTT
2359598 TTAATTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 6 0.19
24 17 0.53
25 9 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTAAATTTATTTAAAAATTATA
Found at i:2359971 original size:6 final size:6
Alignment explanation
Indices: 2359960--2360062 Score: 60
Period size: 6 Copynumber: 17.3 Consensus size: 6
2359950 TTTTATTAAA
* *
2359960 AAATTT AAATTT GAA-TT -AATTT AAATTA AAATAATT AAATATAT AATTATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT--TT AAAT-T-T AA--ATTT
*
2360012 AAATTT AAAATTT ---TTT AAA-TT AAA-AT -AATTT AAATTT AAATTT
1 AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
2360055 AAATTT AA
1 AAATTT AA
2360063 TTGAAAGGTA
Statistics
Matches: 79, Mismatches: 5, Indels: 26
0.72 0.05 0.24
Matches are distributed among these distances:
3 3 0.04
4 4 0.05
5 11 0.14
6 39 0.49
7 8 0.10
8 11 0.14
9 1 0.01
10 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:2359982 original size:16 final size:16
Alignment explanation
Indices: 2359961--2360053 Score: 88
Period size: 16 Copynumber: 6.0 Consensus size: 16
2359951 TTTATTAAAA
*
2359961 AATTTAAATTTGAATT
1 AATTTAAATTTAAATT
*
2359977 AATTTAAA-TTAAAAT
1 AATTTAAATTTAAATT
*
2359992 AA-TTAAATATATAATT
1 AATTTAAATTTA-AATT
2360008 -ATTTAAATTTAAAATT
1 AATTTAAATTT-AAATT
* *
2360024 -TTTTAAA-TTAAAAT
1 AATTTAAATTTAAATT
2360038 AATTTAAATTTAAATT
1 AATTTAAATTTAAATT
2360054 TAAATTTAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
14 9 0.15
15 18 0.29
16 34 0.55
17 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (16 bp):
AATTTAAATTTAAATT
Found at i:2360013 original size:46 final size:41
Alignment explanation
Indices: 2359960--2360064 Score: 122
Period size: 46 Copynumber: 2.4 Consensus size: 41
2359950 TTTTATTAAA
2359960 AAATTTAAATTTGAATTAATTTAAATTAAAATAA-TTAAATATAT
1 AAATTTAAATTT-AATT-ATTTAAATTAAAATAATTTAAAT-T-T
*
2360004 AATTATTTAAATTTAAAATTTTTTAAATTAAAATAATTTAAATTT
1 AA--ATTTAAATTT--AATTATTTAAATTAAAATAATTTAAATTT
2360049 AAATTTAAATTTAATT
1 AAATTTAAATTTAATT
2360065 GAAAGGTACG
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
41 4 0.07
43 10 0.18
44 2 0.04
45 3 0.05
46 26 0.47
47 10 0.18
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (41 bp):
AAATTTAAATTTAATTATTTAAATTAAAATAATTTAAATTT
Found at i:2360020 original size:31 final size:31
Alignment explanation
Indices: 2359964--2360056 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
2359954 ATTAAAAAAT
**
2359964 TTAAATTTGAATTAATTTAAA-TTAAAA-TAA
1 TTAAATTAAAATT-ATTTAAATTTAAAATTAA
* **
2359994 TTAAATATATAATTATTTAAATTTAAAATTTT
1 TTAAAT-TAAAATTATTTAAATTTAAAATTAA
* *
2360026 TTAAATTAAAATAATTTAAATTTAAATTTAA
1 TTAAATTAAAATTATTTAAATTTAAAATTAA
2360057 ATTTAATTGA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
30 13 0.25
31 31 0.61
32 7 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TTAAATTAAAATTATTTAAATTTAAAATTAA
Found at i:2361373 original size:14 final size:14
Alignment explanation
Indices: 2361354--2361383 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2361344 AAAAAACTAA
2361354 AATAAAAGACTATT
1 AATAAAAGACTATT
*
2361368 AATAAAAGATTATT
1 AATAAAAGACTATT
2361382 AA
1 AA
2361384 ATTACCCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (14 bp):
AATAAAAGACTATT
Found at i:2362419 original size:17 final size:18
Alignment explanation
Indices: 2362397--2362439 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
2362387 TAATTTATAT
2362397 AATTTTAATTAAGA-GTC
1 AATTTTAATTAAGAGGTC
**
2362414 AATTTTTTTTAAGAGGTC
1 AATTTTAATTAAGAGGTC
2362432 AATTTTAA
1 AATTTTAA
2362440 AAAATAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.47
Consensus pattern (18 bp):
AATTTTAATTAAGAGGTC
Found at i:2363000 original size:25 final size:24
Alignment explanation
Indices: 2362945--2363001 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
2362935 TGATTGATTT
* *
2362945 TAATTTTAAATTTTTTTCGATAAT
1 TAATTTTAAATTTTTTTCAATAAC
* *
2362969 TCGATTTTAAATTTTTTTTAATCAAC
1 T-AATTTTAAATTTTTTTCAAT-AAC
2362995 TAATTTT
1 TAATTTT
2363002 TTTACATGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 1 0.04
25 22 0.85
26 3 0.12
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.58
Consensus pattern (24 bp):
TAATTTTAAATTTTTTTCAATAAC
Found at i:2363290 original size:20 final size:19
Alignment explanation
Indices: 2363261--2363298 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2363251 TGTATTTATG
*
2363261 TTATTTTTTATTTAAAATA
1 TTATTTTTTATATAAAATA
2363280 TTATATTTTTATATAAAAT
1 TTAT-TTTTTATATAAAAT
2363299 TTTTACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTTTTTATATAAAATA
Found at i:2363806 original size:16 final size:17
Alignment explanation
Indices: 2363785--2363832 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
2363775 TACACATATA
2363785 TATATTTTTATATT-TT
1 TATATTTTTATATTATT
* *
2363801 TATATTCTTATCTTATT
1 TATATTTTTATATTATT
*
2363818 CAT-TTTTTATATTAT
1 TATATTTTTATATTAT
2363833 GTTTTAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATTTTTATATTATT
Found at i:2363859 original size:23 final size:23
Alignment explanation
Indices: 2363819--2363874 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
2363809 TATCTTATTC
* *
2363819 ATTTTTTATATTATGTTTTAATT
1 ATTTTTTATATCAAGTTTTAATT
* *
2363842 ATTTTTTATGTCAAGTTTTTATT
1 ATTTTTTATATCAAGTTTTAATT
*
2363865 -TTTTGTATAT
1 ATTTTTTATAT
2363875 TTAAAGTAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (23 bp):
ATTTTTTATATCAAGTTTTAATT
Found at i:2364463 original size:18 final size:18
Alignment explanation
Indices: 2364437--2364471 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2364427 TTGTTTAAAG
*
2364437 TATTATAAATTTATATAA
1 TATTATAAATATATATAA
*
2364455 TATTTTAAATATATATA
1 TATTATAAATATATATA
2364472 TTTATATGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTATAAATATATATAA
Found at i:2364769 original size:17 final size:14
Alignment explanation
Indices: 2364725--2364767 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
2364715 CAGCCATGGG
* *
2364725 AGAAAAAGATGAAA
1 AGAAAAAAATGAGA
2364739 AGAAAAAAATGAGA
1 AGAAAAAAATGAGA
2364753 AGAAAGAAAATGAGA
1 AGAAA-AAAATGAGA
2364768 GAGAGATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (14 bp):
AGAAAAAAATGAGA
Found at i:2364935 original size:22 final size:21
Alignment explanation
Indices: 2364895--2364935 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2364885 CGTGTCATAT
* *
2364895 TTATTTTTTATTATGTTTTAA
1 TTATTTTTTATCATATTTTAA
2364916 TTATTTTTATATCATATTTT
1 TTATTTTT-TATCATATTTT
2364936 TATTTTTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (21 bp):
TTATTTTTTATCATATTTTAA
Found at i:2364990 original size:396 final size:388
Alignment explanation
Indices: 2364262--2365048 Score: 1226
Period size: 396 Copynumber: 2.0 Consensus size: 388
2364252 TTTATTAATA
* * * * *
2364262 ATATAAAATTAACTATATAAATAAATTTGGTGTTGACACATGTCTTACTTTTGAATTTATTTTTT
1 ATATAAAATTAACTATATAAATAAATTTGGCGATGACACATGTCCTACCTTTGAATTTATGTTTT
2364327 GGCAACCATGGGAGAGAAAAAAAAAAGAGAAGAAAGAAAATGAGAGAGAGAAATAAAAGAAAATT
66 GGCAACCATGGGAGAGAAAAAAAAAAGAGAAGAAAGAAAATGAGAGAGAGAAATAAAAGAAAATT
*
2364392 TTAATGTGTTTATATTTGTATTCATGTTTTTTTTATTGTTTAAAGTATTATAAATTTATATAATA
131 TTAATCTGTTTATATTTGTATTCATGTTTTTTTTATTGTTTAAAGTATTATAAATTTATATAATA
2364457 TTTTAAATATATATATTTATATGTTCTTATATTCGTATCATATTTATTTTTATTATGTTTTAATT
196 TTTTAAATATATATATTTATATGTTCTTATATTCGTATCATATTTATTTTTATTATGTTTTAATT
* *
2364522 ATTTTTATATCATATTTTTATTTTTCGTATATTTAAAGTAGTATAAATTTATATAAATTTTTATA
261 ATTTTTATATCATATTTTTATTTTTCGTATATTTAAAATAGTATAAATTTATATAAATTTTTACA
* * *
2364587 TATTAATTAATTATTTATGTATATTTTGACACGTTAGTATAATTAAATAATATATTTAAAATG
326 CATTAATTAATTATTTATGTATATATTGACACATTAGTATAATTAAATAATATATTTAAAATG
*
2364650 ATAT-AAATTAACTATATAAATAAATTTGGCGATGACACATGTCCTGCCTTTGAA-TT-TGTTTT
1 ATATAAAATTAACTATATAAATAAATTTGGCGATGACACATGTCCTACCTTTGAATTTATGTTTT
* *
2364712 GGACAGCCATGGGAGAAAAAGATGAAAAGAAAAAAATGAGAAGAAAGAAAATGAGAGAGAGATAT
66 GG-CAACCAT-GG-G----AGA-G-AAA-AAAAAAA-GAGAAGAAAGAAAATGAGAGAGAGAAAT
2364777 AAAAGAAAATTTTAATCTGTTTATATTTGTATTCATG-TTTTTTTATTGTTTAAAGTATTATAAA
120 AAAAGAAAATTTTAATCTGTTTATATTTGTATTCATGTTTTTTTTATTGTTTAAAGTATTATAAA
* *
2364841 TTTATATAATATTTTACACATATATATTTTTATAT-TT-TTATATTCGTGTCATATTTATTTTTT
185 TTTATATAATATTTTA-A-ATATATATATTTATATGTTCTTATATTCGTATCATATTTA-TTTTT
*
2364904 ATTATGTTTTAATTATTTTTATATCATATTTTTATTTTTCGTATATTTAAAATATTATAAATTTA
247 ATTATGTTTTAATTATTTTTATATCATATTTTTATTTTTCGTATATTTAAAATAGTATAAATTTA
* * *
2364969 TATAAATTTTTACACATTAATTATTTATTTATGTTTATATTGACACATTAGTATAATTAAATGAT
312 TATAAATTTTTACACATTAATTAATTATTTATGTATATATTGACACATTAGTATAATTAAATAAT
2365034 ATATTTAAAATG
377 ATATTTAAAATG
2365046 ATA
1 ATA
2365049 AATCCCCATG
Statistics
Matches: 365, Mismatches: 20, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
385 7 0.02
386 8 0.02
387 47 0.13
388 5 0.01
392 3 0.01
393 1 0.00
394 3 0.01
395 69 0.19
396 207 0.57
397 15 0.04
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (388 bp):
ATATAAAATTAACTATATAAATAAATTTGGCGATGACACATGTCCTACCTTTGAATTTATGTTTT
GGCAACCATGGGAGAGAAAAAAAAAAGAGAAGAAAGAAAATGAGAGAGAGAAATAAAAGAAAATT
TTAATCTGTTTATATTTGTATTCATGTTTTTTTTATTGTTTAAAGTATTATAAATTTATATAATA
TTTTAAATATATATATTTATATGTTCTTATATTCGTATCATATTTATTTTTATTATGTTTTAATT
ATTTTTATATCATATTTTTATTTTTCGTATATTTAAAATAGTATAAATTTATATAAATTTTTACA
CATTAATTAATTATTTATGTATATATTGACACATTAGTATAATTAAATAATATATTTAAAATG
Found at i:2365308 original size:28 final size:27
Alignment explanation
Indices: 2365239--2365312 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
2365229 ATAAAATGAT
2365239 TAAAATTTATTTT-TAATT-TTAAATA
1 TAAAATTTATTTTATAATTATTAAATA
* * * **
2365264 TACAAATTAAATATATAATTATTATTTAA
1 TA-AAATTTATTTTATAATTATTAAAT-A
2365293 TAAAATTTATTTTATAATTA
1 TAAAATTTATTTTATAATTA
2365313 AATTTTTATT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
25 2 0.05
26 8 0.22
27 5 0.14
28 19 0.51
29 3 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (27 bp):
TAAAATTTATTTTATAATTATTAAATA
Found at i:2365348 original size:21 final size:21
Alignment explanation
Indices: 2365306--2365344 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2365296 AATTTATTTT
*
2365306 ATAATTAAATTTTTATTAATA
1 ATAATTAAATTTTTATAAATA
2365327 ATAATTAAA-TTTTATAAA
1 ATAATTAAATTTTTATAAA
2365345 ATAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAATTAAATTTTTATAAATA
Found at i:2365654 original size:10 final size:10
Alignment explanation
Indices: 2365639--2365692 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
2365629 ACATATTTTT
2365639 TATATAATAA
1 TATATAATAA
2365649 TATATAATAA
1 TATATAATAA
*
2365659 -AAATAATAA
1 TATATAATAA
*
2365668 -AT-TAATAT
1 TATATAATAA
*
2365676 TTTATAATAA
1 TATATAATAA
*
2365686 AATATAA
1 TATATAA
2365693 AAGTGTAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
8 5 0.14
9 10 0.29
10 20 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TATATAATAA
Found at i:2365922 original size:23 final size:23
Alignment explanation
Indices: 2365898--2365942 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
2365888 TATTTTAATT
2365898 TTTTTAAT--ATATTTT-TTATA
1 TTTTTAATAAATATTTTATTATA
2365918 TTTTTAATAAATATTTTATTATA
1 TTTTTAATAAATATTTTATTATA
2365941 TT
1 TT
2365943 AAAATTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
22 7 0.32
23 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTAATAAATATTTTATTATA
Found at i:2375738 original size:3 final size:3
Alignment explanation
Indices: 2375719--2375764 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
2375709 ATTTTGTGAA
* * * *
2375719 ATT AAT ATT ACT ATT ATT ATT CTT ATT CTT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2375765 ATTCAAGCTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:2376854 original size:21 final size:23
Alignment explanation
Indices: 2376810--2376854 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
2376800 ATTAATTATT
*
2376810 TATAAATAAGAAATTATTTTAAA
1 TATAAATAAGAAATTATATTAAA
2376833 TATAAATAA-AAA-TATATTAAA
1 TATAAATAAGAAATTATATTAAA
2376854 T
1 T
2376855 GGCATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 3 0.14
23 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TATAAATAAGAAATTATATTAAA
Found at i:2377352 original size:21 final size:21
Alignment explanation
Indices: 2377323--2377366 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2377313 TCTTGAATCA
2377323 TAAAATAAAATA-TTTTTATT
1 TAAAATAAAATATTTTTTATT
*
2377343 TAAATATAAATTATTTTTTATT
1 TAAA-ATAAAATATTTTTTATT
2377365 TA
1 TA
2377367 TTACCAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 7 0.33
22 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAAATAAAATATTTTTTATT
Found at i:2379065 original size:4 final size:4
Alignment explanation
Indices: 2379056--2379080 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2379046 AGAATAAATT
2379056 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
2379081 ACTATAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:2379355 original size:19 final size:17
Alignment explanation
Indices: 2379333--2379371 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2379323 TTATTATTTA
2379333 ATTAATAAAAAATATTAAT
1 ATTAAT-AAAAATA-TAAT
*
2379352 ATTAATATAAATATAAT
1 ATTAATAAAAATATAAT
2379369 ATT
1 ATT
2379372 TTGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAATAAAAATATAAT
Found at i:2380136 original size:2 final size:2
Alignment explanation
Indices: 2380131--2380158 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2380121 ATTTTTTTTC
2380131 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
2380159 GATAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2380319 original size:21 final size:23
Alignment explanation
Indices: 2380302--2380345 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2380292 TTGTAAAATT
2380302 TTATT-ATCGATATATAAAATAA
1 TTATTCATCGATATATAAAATAA
**
2380324 TTATTCATTTATATATAAAATA
1 TTATTCATCGATATATAAAATA
2380346 TATGCCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (23 bp):
TTATTCATCGATATATAAAATAA
Found at i:2381969 original size:14 final size:14
Alignment explanation
Indices: 2381933--2381978 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
2381923 TGAAATAAAA
* *
2381933 AAAATTTAAATGTT
1 AAAATTTAATTTTT
2381947 AAAATTTAAATTTTT
1 AAAATTT-AATTTTT
2381962 AAAA-TTAATTTTT
1 AAAATTTAATTTTT
2381975 AAAA
1 AAAA
2381979 AATAACTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 11 0.38
14 9 0.31
15 9 0.31
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
AAAATTTAATTTTT
Found at i:2381973 original size:13 final size:15
Alignment explanation
Indices: 2381933--2381978 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
2381923 TGAAATAAAA
*
2381933 AAAATTTAAA-TGTT
1 AAAATTTAAATTTTT
2381947 AAAATTTAAATTTTT
1 AAAATTTAAATTTTT
2381962 AAAA-TT-AATTTTT
1 AAAATTTAAATTTTT
2381975 AAAA
1 AAAA
2381979 AATAACTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.37
14 12 0.40
15 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
AAAATTTAAATTTTT
Found at i:2382050 original size:28 final size:28
Alignment explanation
Indices: 2382019--2382073 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2382009 TTTAAATTTA
2382019 AATATGAAAATA-ATATATATATATAATT
1 AATAT-AAAATATATATATATATATAATT
*
2382047 AATATAAAATATTTATATATATATAAT
1 AATATAAAATATATATATATATATAAT
2382074 ATTTTGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
AATATAAAATATATATATATATATAATT
Found at i:2382063 original size:24 final size:24
Alignment explanation
Indices: 2382019--2382075 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
2382009 TTTAAATTTA
2382019 AATATGAAAATAATATATATATATAATT
1 AATAT-AAAAT-ATATATATATAT-A-T
*
2382047 AATATAAAATATTTATATATATAT
1 AATATAAAATATATATATATATAT
2382071 AATAT
1 AATAT
2382076 TTTGTATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 6 0.21
25 1 0.04
26 11 0.39
27 5 0.18
28 5 0.18
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
AATATAAAATATATATATATATAT
Found at i:2382944 original size:2 final size:2
Alignment explanation
Indices: 2382937--2382975 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2382927 AGTAACAAAA
2382937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2382976 AATGAAGTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2383193 original size:15 final size:15
Alignment explanation
Indices: 2383163--2383213 Score: 61
Period size: 14 Copynumber: 3.4 Consensus size: 15
2383153 ACATGTATTA
*
2383163 TTTTTAAAATAT-AT
1 TTTTTAAAATTTAAT
2383177 TTTTTAAAATTTAA-
1 TTTTTAAAATTTAAT
2383191 TTTTTAATAATTTAAT
1 TTTTTAA-AATTTAAT
2383207 ATTTTTA
1 -TTTTTA
2383214 TTAAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
14 18 0.56
15 8 0.25
17 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTAAAATTTAAT
Found at i:2383218 original size:34 final size:35
Alignment explanation
Indices: 2383170--2383252 Score: 116
Period size: 34 Copynumber: 2.4 Consensus size: 35
2383160 TTATTTTTAA
**
2383170 AATATATTTTTTAAAATTTAATTTTTAA-TAATTT
1 AATATATTTTTTAAAATTTAAAATTTAAGTAATTT
*
2383204 AATAT-TTTTATTAAATTTTAAAATTTAAGTAATTT
1 AATATATTTT-TTAAAATTTAAAATTTAAGTAATTT
2383239 AATATATTTTTTAA
1 AATATATTTTTTAA
2383253 TGTTTACACT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 4 0.09
34 20 0.47
35 15 0.35
36 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (35 bp):
AATATATTTTTTAAAATTTAAAATTTAAGTAATTT
Found at i:2383239 original size:26 final size:27
Alignment explanation
Indices: 2383187--2383248 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
2383177 TTTTTAAAAT
* *
2383187 TTAATTTTTAATAATTTAATATTTTTA
1 TTAAATTTTAATAATTTAATATATTTA
2383214 TTAAATTTTAA-AATTTAAGTA-ATTTA
1 TTAAATTTTAATAATTTAA-TATATTTA
* *
2383240 ATATATTTT
1 TTAAATTTT
2383249 TTAATGTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
TTAAATTTTAATAATTTAATATATTTA
Found at i:2384218 original size:19 final size:19
Alignment explanation
Indices: 2384205--2384272 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
2384195 TTAAATTTTT
2384205 ATAAAAAATATAAATTTAA
1 ATAAAAAATATAAATTTAA
* *
2384224 ATATAAAATATAAA--AAA
1 ATAAAAAATATAAATTTAA
* * *
2384241 ATTAAAAATTAAAAATTAAAA
1 A-TAAAAAATATAAATT-TAA
2384262 ATAAAAAATAT
1 ATAAAAAATAT
2384273 TTTTATAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
17 3 0.08
18 10 0.26
19 13 0.34
20 8 0.21
21 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAAAAAATATAAATTTAA
Found at i:2384247 original size:7 final size:7
Alignment explanation
Indices: 2384237--2384270 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
2384227 TAAAATATAA
2384237 AAAAATT
1 AAAAATT
2384244 AAAAATT
1 AAAAATT
2384251 AAAAATT
1 AAAAATT
*
2384258 AAAAATA
1 AAAAATT
2384265 AAAAAT
1 AAAAAT
2384271 ATTTTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:2384252 original size:29 final size:29
Alignment explanation
Indices: 2384207--2384269 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
2384197 AAATTTTTAT
* *
2384207 AAAAAATATAAATTTAAATA-TAAAATATA
1 AAAAAATATAAAATTAAAAATTAAAA-ATA
2384236 AAAAAAT-TAAAAATTAAAAATTAAAAATA
1 AAAAAATAT-AAAATTAAAAATTAAAAATA
2384265 AAAAA
1 AAAAA
2384270 TATTTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 24 0.80
30 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (29 bp):
AAAAAATATAAAATTAAAAATTAAAAATA
Found at i:2384256 original size:14 final size:14
Alignment explanation
Indices: 2384222--2384270 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 14
2384212 ATATAAATTT
2384222 AAATATAAAATATAAAA
1 AAAT-TAAAA-AT-AAA
*
2384239 AAATTAAAAATTAA
1 AAATTAAAAATAAA
2384253 AAATTAAAAATAAA
1 AAATTAAAAATAAA
2384267 AAAT
1 AAAT
2384271 ATTTTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 19 0.63
15 2 0.07
16 5 0.17
17 4 0.13
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATTAAAAATAAA
Found at i:2384271 original size:7 final size:7
Alignment explanation
Indices: 2384205--2384271 Score: 53
Period size: 7 Copynumber: 9.4 Consensus size: 7
2384195 TTAAATTTTT
2384205 ATAAAAA
1 ATAAAAA
*
2384212 ATATAAA
1 ATAAAAA
* * *
2384219 TTTAAAT
1 ATAAAAA
*
2384226 ATAAAAT
1 ATAAAAA
2384233 ATAAAAAA
1 AT-AAAAA
*
2384241 ATTAAAA
1 ATAAAAA
*
2384248 ATTAAAA
1 ATAAAAA
*
2384255 ATTAAAA
1 ATAAAAA
2384262 ATAAAAA
1 ATAAAAA
2384269 ATA
1 ATA
2384272 TTTTTATAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
7 43 0.88
8 6 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
ATAAAAA
Found at i:2384523 original size:24 final size:25
Alignment explanation
Indices: 2384510--2384558 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 25
2384500 AATAAATATT
2384510 AAATATA-TTAATTAATAAATAAAA
1 AAATATATTTAATTAATAAATAAAA
2384534 AAATATATTTAATTTAATAATATAA
1 AAATATATTTAA-TTAATAA-ATAA
2384559 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.32
25 4 0.18
26 7 0.32
27 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AAATATATTTAATTAATAAATAAAA
Found at i:2384538 original size:31 final size:31
Alignment explanation
Indices: 2384444--2384539 Score: 108
Period size: 31 Copynumber: 3.1 Consensus size: 31
2384434 ACTTGAATAA
*
2384444 ATTAAAT-TATTTAATTAAAAAAATAAATAAAT
1 ATTAAATATA-TTAATT-AATAAATAAATAAAT
*
2384476 ATTAAATATA-TAATTTTAAT-ATTAAATAAAT
1 ATTAAATATATTAA--TTAATAAATAAATAAAT
*
2384507 ATTAAATATATTAATTAATAAATAAAAAAAT
1 ATTAAATATATTAATTAATAAATAAATAAAT
2384538 AT
1 AT
2384540 ATTTAATTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
30 5 0.09
31 34 0.62
32 12 0.22
33 4 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTAAATATATTAATTAATAAATAAATAAAT
Found at i:2385237 original size:15 final size:15
Alignment explanation
Indices: 2385217--2385249 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2385207 TGGTAATATT
*
2385217 AATAATTAATTACAC
1 AATAATTAAATACAC
2385232 AATAATTAAATACAC
1 AATAATTAAATACAC
2385247 AAT
1 AAT
2385250 CAGGTCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAATTAAATACAC
Found at i:2385558 original size:11 final size:11
Alignment explanation
Indices: 2385540--2385586 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
2385530 GATTTAATTA
2385540 AAAT-AATAAT
1 AAATAAATAAT
2385550 AAATAAATAAT
1 AAATAAATAAT
*
2385561 AAATATAATAAA
1 AAATA-AATAAT
*
2385573 AAATTAATAA-
1 AAATAAATAAT
2385583 AAAT
1 AAAT
2385587 TCGTATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 8 0.24
11 16 0.48
12 9 0.27
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:2385560 original size:23 final size:23
Alignment explanation
Indices: 2385538--2385586 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2385528 TTGATTTAAT
*
2385538 TAAA-ATAATAATAAATAAATAA
1 TAAATATAATAAAAAATAAATAA
*
2385560 TAAATATAATAAAAAATTAATAA
1 TAAATATAATAAAAAATAAATAA
2385583 -AAAT
1 TAAAT
2385587 TCGTATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAATATAATAAAAAATAAATAA
Found at i:2385570 original size:20 final size:21
Alignment explanation
Indices: 2385540--2385583 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
2385530 GATTTAATTA
2385540 AAATAATAATAAATAAA-TAAT
1 AAATAATAATAAA-AAATTAAT
2385561 AAAT-ATAATAAAAAATTAAT
1 AAATAATAATAAAAAATTAAT
2385581 AAA
1 AAA
2385584 AATTCGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 15 0.68
21 4 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAATAATAAAAAATTAAT
Found at i:2388958 original size:17 final size:17
Alignment explanation
Indices: 2388921--2388958 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2388911 AAAAAATTAA
*
2388921 ATATATTTATGTTGAAT
1 ATATATTTATGTTGAAG
2388938 ATATATTTATGTCTG-AG
1 ATATATTTATGT-TGAAG
2388955 ATAT
1 ATAT
2388959 TTGAATTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (17 bp):
ATATATTTATGTTGAAG
Found at i:2399110 original size:12 final size:12
Alignment explanation
Indices: 2399093--2399118 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2399083 GCTCCCATTG
2399093 TAAGGTCTCGAT
1 TAAGGTCTCGAT
2399105 TAAGGTCTCGAT
1 TAAGGTCTCGAT
2399117 TA
1 TA
2399119 CAGCATCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (12 bp):
TAAGGTCTCGAT
Found at i:2399290 original size:26 final size:26
Alignment explanation
Indices: 2399254--2399309 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
2399244 TGGATGGTAA
2399254 AATTCGAGTCTAAACATATTAGATAT
1 AATTCGAGTCTAAACATATTAGATAT
*
2399280 AATTCGAGTCTAAACATGTTAGATAT
1 AATTCGAGTCTAAACATATTAGATAT
2399306 AATT
1 AATT
2399310 TTTTATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (26 bp):
AATTCGAGTCTAAACATATTAGATAT
Found at i:2399787 original size:17 final size:17
Alignment explanation
Indices: 2399767--2399823 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
2399757 AATTTTCATA
2399767 ATTAATAAATTATTTTT
1 ATTAATAAATTATTTTT
* *
2399784 ATTAATATAAATA-TTTC
1 ATTAATA-AATTATTTTT
*
2399801 ATTAAAAAATTAATTTATT
1 ATTAATAAATT-ATTT-TT
2399820 ATTA
1 ATTA
2399824 TTAATTAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 3 0.10
17 17 0.55
18 6 0.19
19 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAATAAATTATTTTT
Found at i:2400429 original size:17 final size:18
Alignment explanation
Indices: 2400404--2400437 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2400394 TTCTTCTTTC
2400404 TTTTGTTTTT-GTTTTTT
1 TTTTGTTTTTGGTTTTTT
*
2400421 TTTTTTTTTTGGTTTTT
1 TTTTGTTTTTGGTTTTT
2400438 GAGGTTCTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (18 bp):
TTTTGTTTTTGGTTTTTT
Found at i:2404784 original size:20 final size:19
Alignment explanation
Indices: 2404758--2404815 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
2404748 TTTGAATTTA
2404758 ATTGAGTTTTATTTTTAAAG
1 ATTGAGTTTTATTTTT-AAG
*
2404778 GTTGAGTTTGATATTATTT--G
1 ATTGAGTTT--TATT-TTTAAG
2404798 ATTGAGTTTTATTTTTAA
1 ATTGAGTTTTATTTTTAA
2404816 CTTTTGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
17 3 0.10
18 4 0.13
20 17 0.55
22 4 0.13
23 3 0.10
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (19 bp):
ATTGAGTTTTATTTTTAAG
Found at i:2404802 original size:40 final size:40
Alignment explanation
Indices: 2404753--2404838 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
2404743 TTAGATTTGA
*
2404753 ATTTAATTGAGTTTTATTTTTAAAGGTTGAGTTTGATATT
1 ATTTGATTGAGTTTTATTTTTAAAGGTTGAGTTTGATATT
***
2404793 ATTTGATTGAGTTTTATTTTTAACTTTTGAGTTTGATATT
1 ATTTGATTGAGTTTTATTTTTAAAGGTTGAGTTTGATATT
2404833 ATTTGA
1 ATTTGA
2404839 GTTTAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.26, C:0.01, G:0.16, T:0.57
Consensus pattern (40 bp):
ATTTGATTGAGTTTTATTTTTAAAGGTTGAGTTTGATATT
Found at i:2404839 original size:16 final size:16
Alignment explanation
Indices: 2404818--2404870 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2404808 ATTTTTAACT
*
2404818 TTTGAGTTTGATATTA
1 TTTGAGTTTAATATTA
*
2404834 TTTGAGTTTAAATTTTGA
1 TTTGAGTTT-AATATT-A
*
2404852 TTTCAGTTTAATATTA
1 TTTGAGTTTAATATTA
2404868 TTT
1 TTT
2404871 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 13 0.42
17 9 0.29
18 9 0.29
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.58
Consensus pattern (16 bp):
TTTGAGTTTAATATTA
Found at i:2404915 original size:14 final size:14
Alignment explanation
Indices: 2404898--2404929 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2404888 TTTAATAATT
2404898 TTAAATTTATTTAA
1 TTAAATTTATTTAA
*
2404912 TTAAATTTATTTAT
1 TTAAATTTATTTAA
2404926 TTAA
1 TTAA
2404930 TTAAAACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAATTTATTTAA
Found at i:2405149 original size:13 final size:13
Alignment explanation
Indices: 2405133--2405163 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2405123 TTTAAATTTA
2405133 TTTAACAAATATT
1 TTTAACAAATATT
2405146 TTTAACAAATATT
1 TTTAACAAATATT
2405159 TTTAA
1 TTTAA
2405164 AATTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAACAAATATT
Found at i:2407421 original size:25 final size:26
Alignment explanation
Indices: 2407393--2407446 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
2407383 CCCCGGGTTA
*
2407393 TTAATATA-T-ATCATTTTTTATATTT
1 TTAATATATTCATAATTTTTTA-ATTT
*
2407418 TTAATCTATTCATAATTTTTTAATTT
1 TTAATATATTCATAATTTTTTAATTT
2407444 TTA
1 TTA
2407447 TTTAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.28
26 8 0.32
27 10 0.40
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (26 bp):
TTAATATATTCATAATTTTTTAATTT
Found at i:2408679 original size:3 final size:3
Alignment explanation
Indices: 2408671--2408703 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2408661 TTTTCATGAC
2408671 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2408704 ATACTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2408908 original size:32 final size:31
Alignment explanation
Indices: 2408838--2408921 Score: 81
Period size: 33 Copynumber: 2.7 Consensus size: 31
2408828 AAAATTTTAA
2408838 AAATAA-ATATTA-TTTTAATAATATTAAATT
1 AAATAATAT-TTATTTTTAATAATATTAAATT
2408868 AGATATAATATTTATTTTTAAT-ATAATTAAATTT
1 A-A-ATAATATTTATTTTTAATAAT-ATTAAA-TT
2408902 AAATAAT-TTT-TTTTT-ATAAT
1 AAATAATATTTATTTTTAATAAT
2408922 TTTTCACTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
29 2 0.04
30 8 0.17
31 4 0.09
32 14 0.30
33 16 0.34
34 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (31 bp):
AAATAATATTTATTTTTAATAATATTAAATT
Found at i:2408949 original size:14 final size:15
Alignment explanation
Indices: 2408932--2408966 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2408922 TTTTCACTTA
2408932 TTTTATTTTTAATTT
1 TTTTATTTTTAATTT
*
2408947 TTTTAATTTT-ATTT
1 TTTTATTTTTAATTT
2408961 TTTTAT
1 TTTTAT
2408967 ATGCTGATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTTTTAATTT
Found at i:2408963 original size:23 final size:24
Alignment explanation
Indices: 2408905--2408965 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
2408895 TAAATTTAAA
*
2408905 TAATTTT-TTTTTATAATTTTTCACT
1 TAATTTTATTTTTTTAATTTTT--CT
2408930 T-ATTTTA--TTTTTAATTTTT-T
1 TAATTTTATTTTTTTAATTTTTCT
2408950 TAATTTTATTTTTTTA
1 TAATTTTATTTTTTTA
2408966 TATGCTGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
20 2 0.06
21 6 0.19
23 17 0.55
24 5 0.16
25 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (24 bp):
TAATTTTATTTTTTTAATTTTTCT
Found at i:2410204 original size:2 final size:2
Alignment explanation
Indices: 2410197--2410234 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2410187 TCCTCTGGAG
2410197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2410235 CAAATTTGCG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2410510 original size:2 final size:2
Alignment explanation
Indices: 2410503--2410531 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2410493 AGAATTAAAA
2410503 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2410532 GTTTTGTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2410906 original size:20 final size:21
Alignment explanation
Indices: 2410860--2410901 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2410850 ATGTCAATTA
2410860 AATTTATAATTTAATTAAACT
1 AATTTATAATTTAATTAAACT
2410881 AATTTAT-ATTTAA-TAAA-T
1 AATTTATAATTTAATTAAACT
2410899 AAT
1 AAT
2410902 ATTTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 4 0.19
20 6 0.29
21 7 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTTATAATTTAATTAAACT
Found at i:2411336 original size:20 final size:20
Alignment explanation
Indices: 2411311--2411351 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2411301 ACATTCATAA
2411311 TTATTTTACGATTTTTTATT
1 TTATTTTACGATTTTTTATT
***
2411331 TTATTTTTTTATTTTTTATT
1 TTATTTTACGATTTTTTATT
2411351 T
1 T
2411352 AATATTATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (20 bp):
TTATTTTACGATTTTTTATT
Found at i:2411408 original size:15 final size:15
Alignment explanation
Indices: 2411388--2411461 Score: 61
Period size: 15 Copynumber: 5.1 Consensus size: 15
2411378 ATTCATAAAC
2411388 ATAATTTTAATATAT
1 ATAATTTTAATATAT
2411403 ATAATTTT--T-TA-
1 ATAATTTTAATATAT
*
2411414 AT-ATTTAAAATATAAT
1 ATAATTT-TAATAT-AT
2411430 ATAATATTT-ATATAT
1 ATAAT-TTTAATATAT
*
2411445 ATGATTTTAATATAT
1 ATAATTTTAATATAT
2411460 AT
1 AT
2411462 CTAATATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 18
0.69 0.04 0.26
Matches are distributed among these distances:
10 4 0.09
11 2 0.04
12 2 0.04
13 2 0.04
14 4 0.09
15 23 0.49
16 6 0.13
17 2 0.04
18 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
ATAATTTTAATATAT
Found at i:2411460 original size:59 final size:60
Alignment explanation
Indices: 2411349--2411461 Score: 151
Period size: 57 Copynumber: 1.9 Consensus size: 60
2411339 TTATTTTTTA
*
2411349 TTTAATATTATAAAAATATATTATAATTTATTCATAAACATAATTTTAATATATATAATTT
1 TTTAATATTATAAAAATATAATATAA-TTATTCATAAACATAATTTTAATATATATAATTT
* * * *
2411410 TTTAATATT-T-AAAATATAATATAA-TATTTATATATATGATTTTAATATATAT
1 TTTAATATTATAAAAATATAATATAATTATTCATAAACATAATTTTAATATATAT
2411462 CTAATATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 24 0.51
59 13 0.28
60 1 0.02
61 9 0.19
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (60 bp):
TTTAATATTATAAAAATATAATATAATTATTCATAAACATAATTTTAATATATATAATTT
Found at i:2411480 original size:44 final size:42
Alignment explanation
Indices: 2411397--2411480 Score: 96
Period size: 44 Copynumber: 2.0 Consensus size: 42
2411387 CATAATTTTA
* * *
2411397 ATATATATAATTTTTTAATATTTAAAATATAATATAATATTT
1 ATATATATAATTTTATAATATCTAAAATATAATAAAATATTT
* * *
2411439 ATATATATGATTTTAATATATATCTAATATATATTAAAATAT
1 ATATATATAATTTT-ATA-ATATCTAAAATATAATAAAATAT
2411481 AAAAAGAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 13 0.38
43 2 0.06
44 19 0.56
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (42 bp):
ATATATATAATTTTATAATATCTAAAATATAATAAAATATTT
Found at i:2416311 original size:18 final size:19
Alignment explanation
Indices: 2416288--2416323 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2416278 TCCTTTCTAT
*
2416288 TTTTCT-TTTATCTCTAAG
1 TTTTCTGTTTAGCTCTAAG
2416306 TTTTCTGTTTAGCTCTAA
1 TTTTCTGTTTAGCTCTAA
2416324 ACCTTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.17, C:0.17, G:0.08, T:0.58
Consensus pattern (19 bp):
TTTTCTGTTTAGCTCTAAG
Found at i:2417311 original size:16 final size:17
Alignment explanation
Indices: 2417290--2417322 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2417280 TTTAAGCCTA
2417290 TATATAAT-AAATTTAC
1 TATATAATCAAATTTAC
2417306 TATATAATCAAATTTAC
1 TATATAATCAAATTTAC
2417323 ATTAAATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (17 bp):
TATATAATCAAATTTAC
Found at i:2417694 original size:21 final size:22
Alignment explanation
Indices: 2417670--2417714 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2417660 TTTATATTTC
* *
2417670 TATTTAAA-TAATATTTATTAT
1 TATTTAAATTAATAATTAGTAT
2417691 TA-TTAAATTAATAATTAGTAT
1 TATTTAAATTAATAATTAGTAT
2417712 TAT
1 TAT
2417715 AAAGGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TATTTAAATTAATAATTAGTAT
Found at i:2419717 original size:25 final size:25
Alignment explanation
Indices: 2419666--2419718 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
2419656 TATTATATGC
*
2419666 TAATTCAAAAAATAATTTTAATTTT
1 TAATTCAAAAAATAATATTAATTTT
* *
2419691 TAATTTAAGAAATAATATT-ATTATT
1 TAATTCAAAAAATAATATTAATT-TT
2419716 TAA
1 TAA
2419719 ATATTAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TAATTCAAAAAATAATATTAATTTT
Found at i:2424637 original size:20 final size:21
Alignment explanation
Indices: 2424612--2424668 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
2424602 CTAAATTATT
*
2424612 ATTTAATAATAAAA-AAATTA
1 ATTTAATAATAAAATAAATAA
2424632 ATTTAATAATATAAATAAATAA
1 ATTTAATAATA-AAATAAATAA
2424654 ATATTAAT-ATAAAAT
1 AT-TTAATAATAAAAT
2424669 TATTTTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 11 0.33
21 7 0.21
22 10 0.30
23 5 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTTAATAATAAAATAAATAA
Found at i:2425053 original size:21 final size:19
Alignment explanation
Indices: 2425006--2425054 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
2424996 TTTTATTTTA
2425006 TAATTTTTGAAAAGTAATT
1 TAATTTTTGAAAAGTAATT
* *
2425025 TATTTTTTTAGAAAAGCTACTT
1 TA-ATTTTT-GAAAAG-TAATT
2425047 TAATTTTT
1 TAATTTTT
2425055 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.08
20 5 0.21
21 11 0.46
22 6 0.25
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (19 bp):
TAATTTTTGAAAAGTAATT
Found at i:2425061 original size:22 final size:20
Alignment explanation
Indices: 2425009--2425061 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
2424999 TATTTTATAA
2425009 TTTTTGAAAAGTAATTTATT
1 TTTTTGAAAAGTAATTTATT
*
2425029 TTTTTAGAAAAGCTACTTTAATT
1 TTTTT-GAAAAG-TAATTT-ATT
*
2425052 TTTTTTAAAA
1 TTTTTGAAAA
2425062 AAATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.18
21 6 0.21
22 9 0.32
23 8 0.29
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTTTGAAAAGTAATTTATT
Found at i:2432129 original size:2 final size:2
Alignment explanation
Indices: 2432122--2432148 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2432112 ATAGATAGAT
2432122 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2432149 TCTAGCAGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2438860 original size:4 final size:4
Alignment explanation
Indices: 2438851--2438885 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2438841 AAATCAAACC
*
2438851 AAAG AAAG AAAG GAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
2438886 ACAACTTCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2439427 original size:20 final size:20
Alignment explanation
Indices: 2439402--2439439 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2439392 TAATAAAAAT
2439402 TAAAATATCAATTTAATTAA
1 TAAAATATCAATTTAATTAA
* *
2439422 TAAAATTTTAATTTAATT
1 TAAAATATCAATTTAATT
2439440 TTAAGCTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAATATCAATTTAATTAA
Found at i:2440272 original size:20 final size:20
Alignment explanation
Indices: 2440249--2440289 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2440239 AAAAATAATA
*
2440249 AATTATTATTAAAATATTTT
1 AATTAATATTAAAATATTTT
* *
2440269 AATTAATATTTATATATTTT
1 AATTAATATTAAAATATTTT
2440289 A
1 A
2440290 TAATTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTAATATTAAAATATTTT
Found at i:2443193 original size:32 final size:31
Alignment explanation
Indices: 2443156--2443223 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
2443146 AATAATTTTA
* * *
2443156 TTTAATTTTATTATAAA-ATATATAAATAATAT
1 TTTAATTATATAATAAATA-ATA-AAATAAAAT
2443188 TTTAATTATATAATAAATAATAAAATAAAAT
1 TTTAATTATATAATAAATAATAAAATAAAAT
2443219 TTTAA
1 TTTAA
2443224 ATTAATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 13 0.41
32 18 0.56
33 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTAATTATATAATAAATAATAAAATAAAAT
Found at i:2443206 original size:31 final size:32
Alignment explanation
Indices: 2443156--2443223 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
2443146 AATAATTTTA
* * *
2443156 TTTAATTTTATTATAAAAT-ATATAAATAATAT
1 TTTAATTATATAATAAAATAATA-AAATAAAAT
2443188 TTTAATTATATAAT-AAATAATAAAATAAAAT
1 TTTAATTATATAATAAAATAATAAAATAAAAT
2443219 TTTAA
1 TTTAA
2443224 ATTAATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 17 0.53
32 15 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
TTTAATTATATAATAAAATAATAAAATAAAAT
Found at i:2443238 original size:17 final size:19
Alignment explanation
Indices: 2443215--2443264 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 19
2443205 TAATAAAATA
2443215 AAATTTTAAATTAA-TTTT
1 AAATTTTAAATTAATTTTT
*
2443233 -AATTTTAAAATAATTTTT
1 AAATTTTAAATTAATTTTT
2443251 AAAATTTTAAATTA
1 -AAATTTTAAATTA
2443265 TAGATTAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 12 0.44
18 4 0.15
20 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATTTTAAATTAATTTTT
Found at i:2444899 original size:3 final size:3
Alignment explanation
Indices: 2444891--2444924 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2444881 AAAATATAGA
2444891 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2444925 GATTTCAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2446231 original size:2 final size:2
Alignment explanation
Indices: 2446226--2446255 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2446216 CACAGAAAAA
*
2446226 AC AC AC AC AC AC GC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2446256 TTGAAGGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2451271 original size:4 final size:4
Alignment explanation
Indices: 2451262--2451290 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2451252 AGCAGATAAA
2451262 TCAT TCAT TCAT TCAT TCAT TCAT TCAT T
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT T
2451291 TGATTTGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCAT
Found at i:2458446 original size:26 final size:26
Alignment explanation
Indices: 2458417--2458478 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
2458407 TAAATACAAA
*
2458417 ATTTAATTTAATTA-ATTTATATAATT
1 ATTTAATTTAATAATATTTA-ATAATT
*
2458443 ATTTAATATAATAATATTTAATAATT
1 ATTTAATTTAATAATATTTAATAATT
*
2458469 -TTAAATTTAA
1 ATTTAATTTAA
2458479 ATCTTCACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 8 0.26
26 18 0.58
27 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTAATTTAATAATATTTAATAATT
Found at i:2458945 original size:3 final size:3
Alignment explanation
Indices: 2458939--2458968 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2458929 TCTTCTTATA
*
2458939 AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2458969 CAAATGACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2459435 original size:27 final size:27
Alignment explanation
Indices: 2459396--2459450 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
2459386 AAAAAATAAA
*
2459396 TAATAAAAATT-AATTTATATTTGTAAT
1 TAATAAAAATTAAATTAATATTT-TAAT
* *
2459423 TAATAAGATTTAAATTAATATTTTAAT
1 TAATAAAAATTAAATTAATATTTTAAT
2459450 T
1 T
2459451 TTATATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
TAATAAAAATTAAATTAATATTTTAAT
Found at i:2459513 original size:17 final size:18
Alignment explanation
Indices: 2459470--2459514 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
2459460 AAATTATTTG
*
2459470 ATTA-ATTTAAATATATA
1 ATTATATTTAATTATATA
*
2459487 ATTTTA-TTAATTAT-TA
1 ATTATATTTAATTATATA
2459503 ATTATATTTAAT
1 ATTATATTTAAT
2459515 ATTTATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.30
17 15 0.65
18 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATATTTAATTATATA
Found at i:2459895 original size:3 final size:3
Alignment explanation
Indices: 2459889--2459918 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2459879 CATCATCATC
2459889 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2459919 CACTCAGTTG
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):
ATT
Found at i:2459997 original size:2 final size:2
Alignment explanation
Indices: 2459986--2460016 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2459976 AATTTCGAAA
2459986 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2460017 CCACATTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:2461127 original size:16 final size:15
Alignment explanation
Indices: 2461106--2461135 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2461096 TTTCTCAAAA
2461106 TTATAATTATTTTATG
1 TTATAATT-TTTTATG
2461122 TTATAATTTTTTAT
1 TTATAATTTTTTAT
2461136 CTTTTAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTATAATTTTTTATG
Found at i:2461532 original size:22 final size:22
Alignment explanation
Indices: 2461464--2461532 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
2461454 TATGATTATT
*
2461464 TTTGTACTTTTAAATAATAATA
1 TTTGTATTTTTAAATAATAATA
* ** *
2461486 TTTG-ATTTTCAACATGCTTAT-
1 TTTGTATTTTTAA-ATAATAATA
2461507 TTTGTATTTTTAAATAATAATA
1 TTTGTATTTTTAAATAATAATA
2461529 TTTG
1 TTTG
2461533 GTTTTCATAA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
21 15 0.43
22 20 0.57
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (22 bp):
TTTGTATTTTTAAATAATAATA
Found at i:2462065 original size:27 final size:27
Alignment explanation
Indices: 2462027--2462086 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
2462017 GATAATTTAT
*
2462027 ATTTATAT--ATTTTATTATATT-ATA
1 ATTTATATAAATTTTAATATATTAATA
2462051 ATTATATATAAATTTTAATATATTAATA
1 ATT-TATATAAATTTTAATATATTAATA
2462079 ATTTATAT
1 ATTTATAT
2462087 TAAAAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 3 0.10
25 5 0.16
27 17 0.55
28 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTTATATAAATTTTAATATATTAATA
Found at i:2462443 original size:18 final size:18
Alignment explanation
Indices: 2462420--2462475 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 18
2462410 AACAAGTCGA
2462420 TAATTAATTAATTAAAAT
1 TAATTAATTAATTAAAAT
2462438 TAATT-ATTAA-TAAAA-
1 TAATTAATTAATTAAAAT
*
2462453 AAATTAATATAAATATAAAAT
1 TAATTAAT-T-AAT-TAAAAT
2462474 TA
1 TA
2462476 TAAAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 4 0.13
16 7 0.23
17 6 0.20
18 7 0.23
20 5 0.17
21 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATTAATTAATTAAAAT
Found at i:2462448 original size:17 final size:18
Alignment explanation
Indices: 2462420--2462475 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
2462410 AACAAGTCGA
2462420 TAATTAATTAAT-TAAAAT
1 TAATT-ATTAATATAAAAT
*
2462438 TAATTATTAATAAAAAAAT
1 TAATTATTAAT-ATAAAAT
*
2462457 TAA-TATAAATATAAAAT
1 TAATTATTAATATAAAAT
2462474 TA
1 TA
2462476 TAAAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 14 0.42
18 11 0.33
19 8 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATTATTAATATAAAAT
Found at i:2462466 original size:29 final size:28
Alignment explanation
Indices: 2462425--2462487 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
2462415 GTCGATAATT
*
2462425 AATTAATTAAAAT-TAATTATTAATAAAAA
1 AATTAATTAAAATATAA-AATT-ATAAAAA
2462454 AATTAA-TATAAATATAAAATTATAAAAA
1 AATTAATTA-AAATATAAAATTATAAAAA
*
2462482 ATTTAA
1 AATTAA
2462488 AATTTAGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 14 0.47
29 13 0.43
30 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AATTAATTAAAATATAAAATTATAAAAA
Found at i:2462472 original size:19 final size:19
Alignment explanation
Indices: 2462433--2462472 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
2462423 TTAATTAATT
*
2462433 AAAATTAATTATTAATAAA
1 AAAATTAATTATAAATAAA
*
2462452 AAAATTAA-TATAAATATA
1 AAAATTAATTATAAATAAA
2462470 AAA
1 AAA
2462473 TTATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTAATTATAAATAAA
Found at i:2463175 original size:14 final size:14
Alignment explanation
Indices: 2463138--2463182 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
2463128 ATAAGGAAAG
*
2463138 AAAGGAAGATAAGGA
1 AAAGGAA-AAAAGGA
*
2463153 AAGGTGAAAAAAGGA
1 AAAG-GAAAAAAGGA
2463168 AAAGGAAAAAAGGA
1 AAAGGAAAAAAGGA
2463182 A
1 A
2463183 GGAAGAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 11 0.42
15 12 0.46
16 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.04
Consensus pattern (14 bp):
AAAGGAAAAAAGGA
Found at i:2464315 original size:4 final size:4
Alignment explanation
Indices: 2464308--2464333 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2464298 GAAAACAACC
2464308 AACA AACA AACA AACA AACA AACA AA
1 AACA AACA AACA AACA AACA AACA AA
2464334 AAAATCTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:2465636 original size:15 final size:15
Alignment explanation
Indices: 2465616--2465645 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2465606 CTAAGGCTTT
2465616 AAAAGAAATGAATGG
1 AAAAGAAATGAATGG
*
2465631 AAAAGAAATTAATGG
1 AAAAGAAATGAATGG
2465646 GAAGCAAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (15 bp):
AAAAGAAATGAATGG
Found at i:2467502 original size:15 final size:15
Alignment explanation
Indices: 2467484--2467515 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2467474 TCCCCCCCCC
2467484 CCCCCGGCCCCAAGG
1 CCCCCGGCCCCAAGG
2467499 CCCCCGGCCCCAAGG
1 CCCCCGGCCCCAAGG
2467514 CC
1 CC
2467516 AGCTTAAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.62, G:0.25, T:0.00
Consensus pattern (15 bp):
CCCCCGGCCCCAAGG
Found at i:2467536 original size:2 final size:2
Alignment explanation
Indices: 2467529--2467566 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2467519 TTAAGGCGCC
*
2467529 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2467567 GTGATTTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2468277 original size:25 final size:26
Alignment explanation
Indices: 2468237--2468293 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 26
2468227 ATTTATTCAA
2468237 ATTT-AATTTAACAAAAAATTTAAAT
1 ATTTAAATTTAACAAAAAATTTAAAT
*
2468262 ATTTAAATTTAA-AAAAATTTTAAAT
1 ATTTAAATTTAACAAAAAATTTAAAT
2468287 -TTTAAAT
1 ATTTAAAT
2468294 AGTTAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 7 0.23
25 16 0.53
26 7 0.23
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTTAAATTTAACAAAAAATTTAAAT
Found at i:2468301 original size:24 final size:24
Alignment explanation
Indices: 2468249--2468330 Score: 73
Period size: 24 Copynumber: 3.4 Consensus size: 24
2468239 TTAATTTAAC
2468249 AAAAAA-TTTAAATATTTAAATTT
1 AAAAAATTTTAAATATTTAAATTT
2468272 AAAAAAATTTTAAAT-TTTAAATAGTT
1 -AAAAAATTTTAAATATTTAAAT--TT
* *
2468298 --AAAATTTAAAATAGGTTTAAGTTT
1 AAAAAATTTTAAATA--TTTAAATTT
2468322 AAAAAATTT
1 AAAAAATTT
2468331 AAACTTAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
23 11 0.23
24 15 0.31
25 7 0.15
26 15 0.31
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (24 bp):
AAAAAATTTTAAATATTTAAATTT
Found at i:2468323 original size:32 final size:32
Alignment explanation
Indices: 2468255--2468324 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
2468245 TAACAAAAAA
* * *
2468255 TTTAAATATTTAAATTTAAAAAAATTTTAAAT
1 TTTAAATATTAAAATTTAAAAAAAGTTTAAAG
* *
2468287 TTTAAATAGTTAAAATTTAAAATAGGTTT-AAG
1 TTTAAATA-TTAAAATTTAAAAAAAGTTTAAAG
2468319 TTTAAA
1 TTTAAA
2468325 AAATTTAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 16 0.50
33 16 0.50
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (32 bp):
TTTAAATATTAAAATTTAAAAAAAGTTTAAAG
Found at i:2470966 original size:18 final size:20
Alignment explanation
Indices: 2470945--2470994 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2470935 ATAAAAATAT
2470945 AAATATATATAA-TTTT-TA
1 AAATATATATAATTTTTATA
*
2470963 AAATATATAAAATTTTTATA
1 AAATATATATAATTTTTATA
*
2470983 AAATAAATATAA
1 AAATATATATAA
2470995 ACTCGCATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 11 0.41
19 4 0.15
20 12 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATATATAATTTTTATA
Found at i:2470987 original size:20 final size:18
Alignment explanation
Indices: 2470945--2470980 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2470935 ATAAAAATAT
*
2470945 AAATATATATAATTTTTA
1 AAATATATAAAATTTTTA
2470963 AAATATATAAAATTTTTA
1 AAATATATAAAATTTTTA
2470981 TAAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATATATAAAATTTTTA
Found at i:2475511 original size:32 final size:30
Alignment explanation
Indices: 2475445--2475527 Score: 87
Period size: 32 Copynumber: 2.7 Consensus size: 30
2475435 TAAATATAAT
* * *
2475445 AATTAATATATTATAAATA-TATATTTTAA
1 AATTTATATAATATAAATATTATATATTAA
2475474 AATTTATATAATATAAATTATTAATATATTAA
1 AATTTATATAATATAAA-TATT-ATATATTAA
**
2475506 AATTTACCTAATATAAAATATT
1 AATTTATATAATAT-AAATATT
2475528 TTAAATATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 15 0.33
30 2 0.04
31 1 0.02
32 24 0.53
33 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
AATTTATATAATATAAATATTATATATTAA
Found at i:2475540 original size:47 final size:45
Alignment explanation
Indices: 2475434--2475541 Score: 119
Period size: 47 Copynumber: 2.3 Consensus size: 45
2475424 AACATATAAC
* * *
2475434 ATAAATATAATAATTAATATATTATAAATATATATTTTAAAATTT
1 ATAAATATAATTATTAATATATTATAAATATATAATATAAAATTT
*
2475479 ATATAATATAAATTATTAATATATTA-AAATTTACCTAATATAAAATATT
1 ATA-AATAT-AATTATTAATATATTATAAATATA--TAATATAAAAT-TT
*
2475528 TTAAATATAATTAT
1 ATAAATATAATTAT
2475542 ATAAAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
45 3 0.06
46 11 0.21
47 21 0.40
48 14 0.26
49 4 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (45 bp):
ATAAATATAATTATTAATATATTATAAATATATAATATAAAATTT
Found at i:2476222 original size:2 final size:2
Alignment explanation
Indices: 2476215--2476252 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2476205 GCTAACTAGC
*
2476215 AT AT AT AT AT AT AT AT AT AT AT AT GT 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
2476253 TATGCATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2476979 original size:71 final size:72
Alignment explanation
Indices: 2476850--2476993 Score: 254
Period size: 71 Copynumber: 2.0 Consensus size: 72
2476840 ATTATACACA
* *
2476850 AAATTATAAAAACATTTAAAATTAATCCAACTTCACCTCAATTTAAGTTAATCTCTTTATATATA
1 AAATTATAAAAACATTTAAAATTAATCCAACTTCACATCAATTTAAGTCAATCTCTTTATATATA
2476915 TATATAT
66 TATATAT
*
2476922 AAATTATAAAAACATTTAAAATTAAT-CAACTTTACATCAATTTAAGTCAATCTCTTTATATATA
1 AAATTATAAAAACATTTAAAATTAATCCAACTTCACATCAATTTAAGTCAATCTCTTTATATATA
2476986 TATATAT
66 TATATAT
2476993 A
1 A
2476994 TATATATATA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 43 0.62
72 26 0.38
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.40
Consensus pattern (72 bp):
AAATTATAAAAACATTTAAAATTAATCCAACTTCACATCAATTTAAGTCAATCTCTTTATATATA
TATATAT
Found at i:2476985 original size:2 final size:2
Alignment explanation
Indices: 2476978--2477007 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2476968 TCAATCTCTT
2476978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2477008 ATGTTTATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2478558 original size:2 final size:2
Alignment explanation
Indices: 2478553--2478580 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2478543 TTTTTAACAA
2478553 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
2478581 TCAATGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2478717 original size:20 final size:19
Alignment explanation
Indices: 2478692--2478729 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2478682 TACTTTACTC
2478692 TTAAAAATACTATTTAAATA
1 TTAAAAATACT-TTTAAATA
*
2478712 TTAAAATTACTTTTAAAT
1 TTAAAAATACTTTTAAAT
2478730 TATATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAAAATACTTTTAAATA
Found at i:2485651 original size:9 final size:9
Alignment explanation
Indices: 2485621--2485658 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2485611 AAACAATTTT
2485621 TTTTTCTTA
1 TTTTTCTTA
*
2485630 TTTTACTTA
1 TTTTTCTTA
2485639 TTTTTCTT-
1 TTTTTCTTA
*
2485647 TTTTTCTGA
1 TTTTTCTTA
2485656 TTT
1 TTT
2485659 CAATCCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTTTCTTA
Found at i:2486797 original size:44 final size:42
Alignment explanation
Indices: 2486671--2486842 Score: 209
Period size: 44 Copynumber: 3.9 Consensus size: 42
2486661 GAAACAAAAA
* * *
2486671 AGAATAAGGAAAGAGACAGAATGAAGGCATAAAGGAAAAATTGC
1 AGAAAAAGGAAAGAGACAGAATGAA--AAAAAAGGAAAAATTGC
2486715 AGGAAAAAAAGGAAAGAGACAGAATGAAAAAAAAGGAAAAATTTGC
1 A-G--AAAAAGGAAAGAGACAGAATGAAAAAAAAGGAAAAA-TTGC
* *
2486761 AGAAAAAGGAAGGAGACAGAATGAATAAAAAGGGAAAAAATTGC
1 AGAAAAAGGAAAGAGACAGAATGAA-AAAAAAGG-AAAAATTGC
*
2486805 CGAAAAAGGAAAGAGACAGAATGAAAACAAAAGGAAAA
1 AGAAAAAGGAAAGAGACAGAATGAAAA-AAAAGGAAAA
2486843 TATGGCATGT
Statistics
Matches: 113, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
43 28 0.25
44 40 0.35
45 18 0.16
46 5 0.04
47 22 0.19
ACGTcount: A:0.60, C:0.06, G:0.26, T:0.08
Consensus pattern (42 bp):
AGAAAAAGGAAAGAGACAGAATGAAAAAAAAGGAAAAATTGC
Done.