Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold44
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: 3265628
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.28
Warning! 491382 characters in sequence are not A, C, G, or T
File 3 of 17
Found at i:344936 original size:17 final size:17
Alignment explanation
Indices: 344916--344967 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
344906 TGTATTTATA
344916 TTATATTTATATTATTT
1 TTATATTTATATTATTT
* * *
344933 TTATATTAAAATTATTA
1 TTATATTTATATTATTT
*
344950 TT-TATTTATATAATTT
1 TTATATTTATATTATTT
344966 TT
1 TT
344968 GAAACAATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTTATATTATTT
Found at i:345963 original size:15 final size:15
Alignment explanation
Indices: 345922--345965 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
345912 TGTACTTTTG
*
345922 TAATATAATTTATAAA
1 TAAT-TAATTTTTAAA
*
345938 TAATTAATTTTTACA
1 TAATTAATTTTTAAA
*
345953 TATTTAATTTTTA
1 TAATTAATTTTTA
345966 TAATTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTAATTTTTAAA
Found at i:346764 original size:43 final size:44
Alignment explanation
Indices: 346716--346804 Score: 108
Period size: 47 Copynumber: 2.0 Consensus size: 44
346706 ATGCAAAAGT
**
346716 TACATA-TAAAGAAGGTTTATAATTTTATCTATATAAAAATTAA
1 TACATATTAAAGAAGGTTTATAACCTTATCTATATAAAAATTAA
* *
346759 TACATATTTGTTAAGAAGGTTTGTAACCTTATCTATATAAAAATTA
1 TACATA--T-TAAAGAAGGTTTATAACCTTATCTATATAAAAATTA
346805 TAAGATGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 6 0.16
47 32 0.84
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (44 bp):
TACATATTAAAGAAGGTTTATAACCTTATCTATATAAAAATTAA
Found at i:350041 original size:3 final size:3
Alignment explanation
Indices: 350033--350091 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
350023 TATAGCAGAA
350033 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
350081 AAT AAT AAT AA
1 AAT AAT AAT AA
350092 CAAGTAATTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:353866 original size:20 final size:20
Alignment explanation
Indices: 353841--353880 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
353831 GGTTTATAAT
353841 TTTATCCATATAAAAATTAC
1 TTTATCCATATAAAAATTAC
*
353861 TTTATCCATATAAAATTTAC
1 TTTATCCATATAAAAATTAC
353881 AAATTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTATCCATATAAAAATTAC
Found at i:353936 original size:47 final size:47
Alignment explanation
Indices: 353885--353974 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 47
353875 ATTTACAAAT
* *
353885 TATTTATGAAGTA-AGTTTGTAACTTTGTATGTGCAAAAGTTATGAGA
1 TATTTATG-AGGAGAGTTTGTAACTTTATATGTGCAAAAGTTATGAGA
* * * *
353932 TATTTGTGAGGAGATTTTGTAGCTTTATATGTGCAATAGTTAT
1 TATTTATGAGGAGAGTTTGTAACTTTATATGTGCAAAAGTTAT
353975 AAGTGCTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
46 3 0.08
47 33 0.92
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.43
Consensus pattern (47 bp):
TATTTATGAGGAGAGTTTGTAACTTTATATGTGCAAAAGTTATGAGA
Found at i:357405 original size:26 final size:26
Alignment explanation
Indices: 357376--357427 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
357366 CTATTTACTT
357376 TGAAGTCGATTTTAAACCTTTTTCAA
1 TGAAGTCGATTTTAAACCTTTTTCAA
357402 TGAAGTCGATTTTAAACCTTTTTCAA
1 TGAAGTCGATTTTAAACCTTTTTCAA
357428 CTGTATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (26 bp):
TGAAGTCGATTTTAAACCTTTTTCAA
Found at i:359408 original size:20 final size:19
Alignment explanation
Indices: 359375--359414 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
359365 AAAAATCTTG
359375 AAATTTTATCATTTTTTATT
1 AAATTTTATCA-TTTTTATT
359395 AAATTCTTAT-ATTTTTATT
1 AAATT-TTATCATTTTTATT
359414 A
1 A
359415 CGAACTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.47
20 6 0.32
21 4 0.21
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
AAATTTTATCATTTTTATT
Found at i:360373 original size:2 final size:2
Alignment explanation
Indices: 360366--360398 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
360356 ATAAAAACTT
360366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
360399 TACATATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:361277 original size:20 final size:20
Alignment explanation
Indices: 361249--361286 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
361239 ATCTAAATTG
361249 ATAAAATTTAATTTAATTAT
1 ATAAAATTTAATTTAATTAT
*
361269 ATAATATTTAATTTAATT
1 ATAAAATTTAATTTAATT
361287 TTAATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAAAATTTAATTTAATTAT
Found at i:361291 original size:11 final size:11
Alignment explanation
Indices: 361270--361299 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
361260 TTTAATTATA
361270 TAATATTTAATT
1 TAAT-TTTAATT
361282 TAATTTTAATT
1 TAATTTTAATT
361293 TAATTTT
1 TAATTTT
361300 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TAATTTTAATT
Found at i:361895 original size:6 final size:7
Alignment explanation
Indices: 361879--361905 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
361869 AATAATATAT
361879 AAAATTA
1 AAAATTA
361886 AAAATTA
1 AAAATTA
361893 AAAATTA
1 AAAATTA
361900 AAAATT
1 AAAATT
361906 CTAAAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAATTA
Found at i:363357 original size:14 final size:15
Alignment explanation
Indices: 363332--363360 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
363322 TGTGTGATTG
363332 ATTTTTTATAAAATT
1 ATTTTTTATAAAATT
363347 ATTTTTT-TAAAATT
1 ATTTTTTATAAAATT
363361 TTTAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTTTATAAAATT
Found at i:364040 original size:147 final size:147
Alignment explanation
Indices: 363846--364138 Score: 435
Period size: 149 Copynumber: 2.0 Consensus size: 147
363836 GGGAAAAAAC
* * * **
363846 ATATATAAGTGCTTTAATTAGAACATATGAAAATATATTCATGATTAATTAG-TTTTTTATTTAG
1 ATATATAAGGGCTTTAATTAAAACATATGAAAATATACTCACAATTAATTAGTTTTTTTATTTAG
* *
363910 TTTCTTATTTAATTTTGTTATTGATAAATTAATTATAACTTATTTCTATAAGATAAGAACATTCG
66 TTTCTTATTTAATTTTGTTACTGATAAATTAATTATAACTTATTTATATAAGATAAGAACATTCG
363975 ATATTTTAAAAGGTAAGA
131 ATA-TTTAAAAGGTAAGA
* *
363993 ATATATGAGGGCTTTAATTAAAAGATATGAAAATATACTCACAATTAATTAGTTTTTTTTATTTA
1 ATATATAAGGGCTTTAATTAAAACATATGAAAATATACTCACAATTAATTAG-TTTTTTTATTTA
* * * * *
364058 GTTTCTTATTTAATTTTGTTACTGATAAATTAATTGTAACTTATTTATGTAAGCTAAGAATATTG
65 GTTTCTTATTTAATTTTGTTACTGATAAATTAATTATAACTTATTTATATAAGATAAGAACATTC
364123 GATATTTAAAAGGTAA
130 GATATTTAAAAGGTAA
364139 TAAATCTAAT
Statistics
Matches: 130, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
147 45 0.35
148 12 0.09
149 73 0.56
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45
Consensus pattern (147 bp):
ATATATAAGGGCTTTAATTAAAACATATGAAAATATACTCACAATTAATTAGTTTTTTTATTTAG
TTTCTTATTTAATTTTGTTACTGATAAATTAATTATAACTTATTTATATAAGATAAGAACATTCG
ATATTTAAAAGGTAAGA
Found at i:365495 original size:64 final size:64
Alignment explanation
Indices: 365368--365487 Score: 186
Period size: 64 Copynumber: 1.9 Consensus size: 64
365358 TTACTTATTG
* * *
365368 CAAAGCCCACACAAACTGGTGGCACCTATCTACTTTAGTCCATAAAGAGTTGGACTCATTTTCT
1 CAAAGCCCACACAAACTGGTGGCACCTATCTACCTTAGTCAACAAAGAGTTGGACTCATTTTCT
* * *
365432 CAAAGCCCACACAAGCTTGTGGCACTTATCTACCTTAGTCAACAAAGAGTTGGACT
1 CAAAGCCCACACAAACTGGTGGCACCTATCTACCTTAGTCAACAAAGAGTTGGACT
365488 TGTTTTCTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (64 bp):
CAAAGCCCACACAAACTGGTGGCACCTATCTACCTTAGTCAACAAAGAGTTGGACTCATTTTCT
Found at i:369882 original size:36 final size:36
Alignment explanation
Indices: 369833--369901 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
369823 TCGGTATTGG
369833 CATCTCTCCAGTGCCTAATATAGAACATCCAAATTT
1 CATCTCTCCAGTGCCTAATATAGAACATCCAAATTT
*
369869 CATCTCTCTAGTGCCTAATATAGAACATCCAAA
1 CATCTCTCCAGTGCCTAATATAGAACATCCAAA
369902 ATTTAACTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.35, C:0.28, G:0.09, T:0.29
Consensus pattern (36 bp):
CATCTCTCCAGTGCCTAATATAGAACATCCAAATTT
Found at i:372700 original size:16 final size:14
Alignment explanation
Indices: 372677--372715 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
372667 TAAATTTTCT
372677 TTTTTAAAATATAAA
1 TTTTTAAAAT-TAAA
*
372692 TTATTTAAAATTATA
1 TT-TTTAAAATTAAA
372707 TTTTTAAAA
1 TTTTTAAAA
372716 ATTATATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 7 0.32
16 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTTTTAAAATTAAA
Found at i:372718 original size:15 final size:14
Alignment explanation
Indices: 372677--372722 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
372667 TAAATTTTCT
*
372677 TTTTTAAAATATAAA
1 TTTTTAAAAT-TATA
372692 TTATTTAAAATTATA
1 TT-TTTAAAATTATA
372707 TTTTTAAAAATTATA
1 TTTTT-AAAATTATA
372722 T
1 T
372723 CTAATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 3 0.11
15 17 0.61
16 8 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTTAAAATTATA
Found at i:373007 original size:26 final size:27
Alignment explanation
Indices: 372978--373028 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
372968 TAAAATTTTC
* *
372978 TTTCTTTTCTTTTTTCTTTT-TTCTAT
1 TTTCCTTTCTTTTCTCTTTTGTTCTAT
373004 TTTCCTTTCTTTTCTCTTTTGTTCT
1 TTTCCTTTCTTTTCTCTTTTGTTCT
373029 CACATCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTCCTTTCTTTTCTCTTTTGTTCTAT
Found at i:373261 original size:19 final size:19
Alignment explanation
Indices: 373225--373260 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
373215 GAGGGAAATT
*
373225 GGGAGAAAATGAAGAAAAG
1 GGGAGAAAATAAAGAAAAG
373244 GGGAGAAAA-AAAGAAAA
1 GGGAGAAAATAAAGAAAA
373261 AAAAAAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (19 bp):
GGGAGAAAATAAAGAAAAG
Found at i:373265 original size:13 final size:14
Alignment explanation
Indices: 373249--373281 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
373239 AAAAGGGGAG
373249 AAAAAAAGAAAAA-
1 AAAAAAAGAAAAAT
*
373262 AAAAAGAGAAAAAT
1 AAAAAAAGAAAAAT
373276 AAAAAA
1 AAAAAA
373282 TTTATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAAAAT
Found at i:377475 original size:51 final size:51
Alignment explanation
Indices: 377397--377527 Score: 185
Period size: 51 Copynumber: 2.6 Consensus size: 51
377387 AATTAACTAG
* *
377397 ATCGATAC-ATTAAAGAATGTATTGATACATTTGGGTTAAAAACCCAG-ATGT
1 ATCGATACGA-TAAAGAATGTATCGATACATTT-GGATAAAAACCCAGAATGT
* *
377448 ATCGATACGATGAAGAATGTATCGATACATTTGGATCAAAACCCAGAATGT
1 ATCGATACGATAAAGAATGTATCGATACATTTGGATAAAAACCCAGAATGT
*
377499 ATCGATATGATAAAGAATGTATCGATACA
1 ATCGATACGATAAAGAATGTATCGATACA
377528 ATAAAAATGT
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
50 12 0.17
51 59 0.82
52 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (51 bp):
ATCGATACGATAAAGAATGTATCGATACATTTGGATAAAAACCCAGAATGT
Found at i:377538 original size:19 final size:20
Alignment explanation
Indices: 377492--377546 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
377482 ATCAAAACCC
**
377492 AGAATGTATCGATATGATAA
1 AGAATGTATCGATACAATAA
377512 AGAATGTATCGATACAATAA
1 AGAATGTATCGATACAATAA
377532 A-AATGTATCGATACA
1 AGAATGTATCGATACA
377547 TTTTCTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.27
Consensus pattern (20 bp):
AGAATGTATCGATACAATAA
Found at i:377966 original size:21 final size:20
Alignment explanation
Indices: 377940--377980 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
377930 ATTAGGACCT
*
377940 TGTATCGATACATGTAAGGCA
1 TGTATCAATACATGT-AGGCA
377961 TGTATCAATACATGTAGGCA
1 TGTATCAATACATGTAGGCA
377981 AAATGTACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (20 bp):
TGTATCAATACATGTAGGCA
Found at i:392484 original size:21 final size:21
Alignment explanation
Indices: 392460--392515 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
392450 AATTTATCCA
*
392460 AATGTATCGATATATTTGTAG
1 AATGTATCGATACATTTGTAG
*
392481 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
392502 AATGTATCGATACA
1 AATGTATCGATACA
392516 ATCTACAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:392665 original size:13 final size:13
Alignment explanation
Indices: 392647--392672 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
392637 CATTTTTCTG
392647 TGTATCGATACAT
1 TGTATCGATACAT
392660 TGTATCGATACAT
1 TGTATCGATACAT
392673 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:392690 original size:34 final size:33
Alignment explanation
Indices: 392630--392693 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
392620 AAGGGAATGC
*
392630 ATCGATACATTTTTCTGTGTATCGATACATTGT
1 ATCGATACATTATTCTGTGTATCGATACATTGT
*
392663 ATCGATACATCTATTCTTTGTATCGATACAT
1 ATCGATACAT-TATTCTGTGTATCGATACAT
392694 CTAGGAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (33 bp):
ATCGATACATTATTCTGTGTATCGATACATTGT
Found at i:395231 original size:31 final size:28
Alignment explanation
Indices: 395149--395220 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
395139 TTCACAATCG
*
395149 GGGATACTCCAACCCCGTTA-ATCATTG--
1 GGGATACTCCAACCCCGTTATTTC--TGAA
395176 GGGATACTCCAACCCCGTTATTTCTGAA
1 GGGATACTCCAACCCCGTTATTTCTGAA
395204 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
395221 ACTTTATTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 2 0.05
27 20 0.49
28 19 0.46
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCTGAA
Found at i:395415 original size:52 final size:51
Alignment explanation
Indices: 395036--395421 Score: 273
Period size: 51 Copynumber: 7.4 Consensus size: 51
395026 CTCAATTCTC
* * *
395036 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAAC-CCTAA-TTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACC-AATTTTT
* *
395086 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTATTTCC--AAAACACCAATTT-TT
* **** * *
395141 CACAATCGGGGATACTCCAACCCCG-TTAATCATTGGGGATACTCCAACCCCGTTATTT
1 CACAATCGGGGATACTCCAACCCCGATT--TTATTTCCAAAACACCAA-----TT-TTT
** * * * ***
395199 CTGAA---GGGATACTCCAACCCCGACTTTATTTCTAAAATATTGATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
* * * * *
395247 CATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
* * *
395298 CCACAATC-GGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTC
1 -CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
** * * *
395349 CTTTAATTGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTT
*
395402 CACAATCGAGGATACTCCAA
1 CACAATCGGGGATACTCCAA
395422 TCTCGTTATT
Statistics
Matches: 262, Mismatches: 52, Indels: 42
0.74 0.15 0.12
Matches are distributed among these distances:
48 6 0.02
49 2 0.01
50 2 0.01
51 110 0.42
52 46 0.18
53 30 0.11
54 33 0.13
55 24 0.09
56 1 0.00
58 7 0.03
59 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
Found at i:395442 original size:28 final size:28
Alignment explanation
Indices: 395406--395482 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
395396 ATTTTTCACA
* * *
395406 ATCGAGGATACTCCAATCTCGTTATTTC
1 ATCGGGGATACTCCAATCCCGTTACTTC
*
395434 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAATCCCGTTACTTC
***
395462 CGAGGGGATACTCCAATCCCG
1 ATCGGGGATACTCCAATCCCG
395483 ATTTTTTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAATCCCGTTACTTC
Found at i:396647 original size:33 final size:32
Alignment explanation
Indices: 396605--396666 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
396595 CAAACCCAGG
396605 TGTATCGATACATATTGCTTAGTATCGATAAAT
1 TGTATCGATACATATT-CTTAGTATCGATAAAT
* *
396638 TGTATCGATACATGTTCTTGGTATCGATA
1 TGTATCGATACATATTCTTAGTATCGATA
396667 CACACTGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATATTCTTAGTATCGATAAAT
Found at i:399417 original size:18 final size:18
Alignment explanation
Indices: 399394--399431 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
399384 AAGACTCTAA
399394 AAGGTAAATGTTTGTAGG
1 AAGGTAAATGTTTGTAGG
**
399412 AAGGTAGGTGTTTGTAGG
1 AAGGTAAATGTTTGTAGG
399430 AA
1 AA
399432 TTTAAGTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.37, T:0.32
Consensus pattern (18 bp):
AAGGTAAATGTTTGTAGG
Found at i:400914 original size:16 final size:16
Alignment explanation
Indices: 400893--400923 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
400883 CCCATCACTT
*
400893 ATAAAAAATAATAAAA
1 ATAAAAAACAATAAAA
400909 ATAAAAAACAATAAA
1 ATAAAAAACAATAAA
400924 TTTTTATCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (16 bp):
ATAAAAAACAATAAAA
Found at i:401165 original size:2 final size:2
Alignment explanation
Indices: 401158--401182 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
401148 AAATAATAGA
401158 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
401183 CTAAAACTAA
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:402690 original size:20 final size:20
Alignment explanation
Indices: 402667--402706 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
402657 TAAAAAAGAA
402667 TAAAAAAATAAAAAAAAATG
1 TAAAAAAATAAAAAAAAATG
* *
402687 TAAATAAATAAAATAAAATG
1 TAAAAAAATAAAAAAAAATG
402707 AAATGAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (20 bp):
TAAAAAAATAAAAAAAAATG
Found at i:407723 original size:103 final size:106
Alignment explanation
Indices: 407598--407793 Score: 274
Period size: 106 Copynumber: 1.9 Consensus size: 106
407588 CTTAAAAAAA
*
407598 ATTTAAATAATTATGCTATGTAA-AGTGATATCAGTTGCCAT-CATTTGT-TTATTATTAAACAT
1 ATTTAAATAATTATGCTATGTAATA-TGATATCAGTTGCCATGCATTTGTATTATTATTAAAAAT
407660 AAATTATTTTACAAAAATAAGAAAATTATCTGCTCAAAATAT
65 AAATTATTTTACAAAAATAAGAAAATTATCTGCTCAAAATAT
* * ** *
407702 ATTT-AATAATTATGCTATGTAATATGATATTAGTTGCTATGGTTTTTTTATTATTATTAAAAAT
1 ATTTAAATAATTATGCTATGTAATATGATATCAGTTGCCAT-GCATTTGTATTATTATTAAAAAT
* *
407766 AAATTATTTTACAAATATAAGATAATTA
65 AAATTATTTTACAAAAATAAGAAAATTA
407794 ACATGTAACA
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
103 32 0.40
104 5 0.06
105 4 0.05
106 39 0.49
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (106 bp):
ATTTAAATAATTATGCTATGTAATATGATATCAGTTGCCATGCATTTGTATTATTATTAAAAATA
AATTATTTTACAAAAATAAGAAAATTATCTGCTCAAAATAT
Found at i:407957 original size:22 final size:21
Alignment explanation
Indices: 407932--407990 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
407922 AATATTTTTA
407932 TTATTAATAAAATTTATTACA-T
1 TTATTAATAAAATTT-TTA-ATT
*
407954 TTATAAATAAGAA-TTTTAATT
1 TTATTAATAA-AATTTTTAATT
407975 TTATTAA-AAAATTTTT
1 TTATTAATAAAATTTTT
407991 TAAATGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.06
20 7 0.22
21 10 0.31
22 11 0.34
23 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTATTAATAAAATTTTTAATT
Found at i:408191 original size:18 final size:18
Alignment explanation
Indices: 408170--408207 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
408160 ATATATAAAA
408170 TTTTAGAA-ATAAATAATT
1 TTTTAGAATATAAAT-ATT
*
408188 TTTTATAATATAAATATT
1 TTTTAGAATATAAATATT
408206 TT
1 TT
408208 ATATTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTTAGAATATAAATATT
Found at i:408216 original size:18 final size:19
Alignment explanation
Indices: 408178--408218 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
408168 AATTTTAGAA
*
408178 ATAAATAATTTTTTATAAT
1 ATAAATAATTTTATATAAT
*
408197 ATAAAT-ATTTTATATTAT
1 ATAAATAATTTTATATAAT
408215 ATAA
1 ATAA
408219 TTAGTGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAAATAATTTTATATAAT
Found at i:410412 original size:2 final size:2
Alignment explanation
Indices: 410405--410434 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
410395 ACAATTAGAT
*
410405 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
410435 CCAAATTAAA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:414625 original size:17 final size:17
Alignment explanation
Indices: 414593--414631 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
414583 ATATATTTCA
*
414593 TATTTTAAAATTATTAG
1 TATTTTAAAATCATTAG
414610 -ATTTTAAAAATCATTAG
1 TATTTT-AAAATCATTAG
414627 TATTT
1 TATTT
414632 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 5 0.26
17 10 0.53
18 4 0.21
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (17 bp):
TATTTTAAAATCATTAG
Found at i:415612 original size:23 final size:23
Alignment explanation
Indices: 415562--415605 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
415552 CTTTTGGTTG
* *
415562 AATTAGTATTAAAAATTTGATTC
1 AATTAGTATTAAAAATTTAAGTC
415585 AATTAGTATTAAAAA-TTAAGT
1 AATTAGTATTAAAAATTTAAGT
415606 GATATTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (23 bp):
AATTAGTATTAAAAATTTAAGTC
Found at i:416784 original size:17 final size:18
Alignment explanation
Indices: 416762--416808 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
416752 TTAGAGATGC
416762 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
416779 AATTATATTATTTA-TTT
1 AATTATATTATTTATTTT
*
416796 ATTTAT-TTATTTA
1 AATTATATTATTTA
416809 CTAATATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 7 0.25
17 17 0.61
18 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:422348 original size:32 final size:32
Alignment explanation
Indices: 422303--422365 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
422293 TAGCTAATTA
* *
422303 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCAACACAACACTTATGTATCGATACAT
*
422335 TGTATCAACACAACACTTTTGTATCGATACA
1 TGTATCAACACAACACTTATGTATCGATACA
422366 AATCGTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (32 bp):
TGTATCAACACAACACTTATGTATCGATACAT
Found at i:422366 original size:19 final size:19
Alignment explanation
Indices: 422303--422366 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
422293 TAGCTAATTA
*
422303 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTT
422322 TGTATCGAT---ACA---T
1 TGTATCGATACAACACTTT
* *
422335 TGTATCAACACAACACTTT
1 TGTATCGATACAACACTTT
422354 TGTATCGATACAA
1 TGTATCGATACAA
422367 ATCGTTGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 12
0.67 0.10 0.24
Matches are distributed among these distances:
13 7 0.21
16 6 0.18
19 21 0.62
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTT
Found at i:426556 original size:36 final size:36
Alignment explanation
Indices: 426459--426571 Score: 122
Period size: 36 Copynumber: 3.1 Consensus size: 36
426449 AAGGATTTTT
*
426459 TAATATTCTGATTACAATTACAAGATCA-TAATCTTC
1 TAATATTCTGATTACAATTACAGGAT-AGTAATCTTC
**
426495 TAATATTCTGATTATGATTACAGGATAGTAATCTTC
1 TAATATTCTGATTACAATTACAGGATAGTAATCTTC
* * * *
426531 -ATATATTCTGATTACAACTATAGGATCGCAATCTTC
1 TA-ATATTCTGATTACAATTACAGGATAGTAATCTTC
426567 GTAAT
1 -TAAT
426572 TTGATTCTGT
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
35 2 0.03
36 59 0.92
37 2 0.03
38 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (36 bp):
TAATATTCTGATTACAATTACAGGATAGTAATCTTC
Found at i:429209 original size:20 final size:20
Alignment explanation
Indices: 429136--429211 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
429126 TTTTACCCAG
429136 ATGTATCGATACA-TTTTTA
1 ATGTATCGATACATTTTTTA
* * * *
429155 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTTA
*
429175 ATGTATTGATACATTTTTTA
1 ATGTATCGATACATTTTTTA
429195 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
429212 ATCTTTTTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
19 12 0.26
20 34 0.74
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTA
Found at i:429246 original size:14 final size:14
Alignment explanation
Indices: 429227--429253 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
429217 TTTATCCAGA
429227 TGTATCGATACATT
1 TGTATCGATACATT
429241 TGTATCGATACAT
1 TGTATCGATACAT
429254 CTAGTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (14 bp):
TGTATCGATACATT
Found at i:430194 original size:19 final size:19
Alignment explanation
Indices: 430158--430198 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
430148 TTTGATCATT
430158 CATTTTTACTATGTTCCATG
1 CATTTTTACTATGTTCCA-G
430178 CATTTTTAAC-ATG-TCCAG
1 CATTTTT-ACTATGTTCCAG
430196 CAT
1 CAT
430199 CTCATTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.20
19 4 0.20
20 10 0.50
21 2 0.10
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (19 bp):
CATTTTTACTATGTTCCAG
Found at i:430804 original size:13 final size:13
Alignment explanation
Indices: 430786--430810 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
430776 CATAAAGTGT
430786 TGTATCGATACAA
1 TGTATCGATACAA
430799 TGTATCGATACA
1 TGTATCGATACA
430811 TATTTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:430826 original size:32 final size:33
Alignment explanation
Indices: 430766--430831 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
430756 TTCAACGATT
430766 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
** *
430799 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
430831 T
1 T
430832 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:430890 original size:13 final size:13
Alignment explanation
Indices: 430872--430896 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
430862 ATCACTTAAA
430872 TGTATCGATACAT
1 TGTATCGATACAT
430885 TGTATCGATACA
1 TGTATCGATACA
430897 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:436801 original size:20 final size:20
Alignment explanation
Indices: 436740--436803 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 20
436730 AACCAAAAAT
*
436740 TTTA-TCTTATATTAATTA-G
1 TTTATTCTT-TATTAATTATA
*
436759 TTTATCCTTTATT-ATTATA
1 TTTATTCTTTATTAATTATA
436778 ---ATTCTTTATTAATTATA
1 TTTATTCTTTATTAATTATA
436795 TTTATTCTT
1 TTTATTCTT
436804 GTTTAACACC
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
16 9 0.25
17 6 0.17
18 4 0.11
19 8 0.22
20 9 0.25
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTATTCTTTATTAATTATA
Found at i:441240 original size:20 final size:22
Alignment explanation
Indices: 441217--441259 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
441207 CAAAGCAATA
*
441217 TGTATTGATAC-TTCT-GGGTT
1 TGTATCGATACTTTCTAGGGTT
441237 TGTATCGATACTTTCTAGGGTT
1 TGTATCGATACTTTCTAGGGTT
441259 T
1 T
441260 TGACCTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.16, C:0.12, G:0.23, T:0.49
Consensus pattern (22 bp):
TGTATCGATACTTTCTAGGGTT
Found at i:442895 original size:97 final size:97
Alignment explanation
Indices: 442638--442884 Score: 404
Period size: 97 Copynumber: 2.5 Consensus size: 97
442628 TTTTGATTGA
* * *
442638 AAAAACGGGGTTGGAGTATCCCCTCAGAGGAATGGGATTGGAATGTCCCCGATGATGACAATTTA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGATTGGAGTGTCCCCGATGATGACAATTTA
* *
442703 AGCGAGAATAAGATTTGAATCTTGATAAGTTT
66 AGCGAGAACAAGATTTGAATCTTGACAAGTTT
* * * *
442735 AAAAGTGGGGTTGGAGTATCTCCTCGGAGGAATGGGGTTGGAGTGTCCCCAATGATGACAATTTA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGATTGGAGTGTCCCCGATGATGACAATTTA
442800 AGCGAGAACAAGATTTGAATCTTGACAAGTTT
66 AGCGAGAACAAGATTTGAATCTTGACAAGTTT
*
442832 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGATTGGAGTATCCCCGAT
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGATTGGAGTGTCCCCGAT
442885 TAATGAAATT
Statistics
Matches: 136, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 136 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (97 bp):
AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGATTGGAGTGTCCCCGATGATGACAATTTA
AGCGAGAACAAGATTTGAATCTTGACAAGTTT
Found at i:445062 original size:20 final size:20
Alignment explanation
Indices: 445036--445086 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
445026 AAAACGATAG
*
445036 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
445056 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
445076 AATGTATCGAT
1 AATGTATCGAT
445087 GCATCTGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:446026 original size:16 final size:16
Alignment explanation
Indices: 446005--446040 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
445995 TTCATTAAGG
**
446005 AAAGTTAAGTACAAGC
1 AAAGTTAAAAACAAGC
446021 AAAGTTAAAAACAAGC
1 AAAGTTAAAAACAAGC
446037 AAAG
1 AAAG
446041 AACCAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.11, G:0.17, T:0.14
Consensus pattern (16 bp):
AAAGTTAAAAACAAGC
Found at i:447746 original size:68 final size:68
Alignment explanation
Indices: 447666--447798 Score: 221
Period size: 68 Copynumber: 2.0 Consensus size: 68
447656 CCTTGTATTG
* *
447666 ATACTATAAACATAGTATCGATGCATCTAGGTTTTTCTAGATGTATCAATACATCATTCAATGTA
1 ATACTATAAACATAGTATCGATACATCTAGGTTTTTCCAGATGTATCAATACATCATTCAATGTA
447731 TCA
66 TCA
* * *
447734 ATACTATGAACATAGTATCTATACATCTGGGTTTTTCCAGATGTATCAATACATCATTCAATGTA
1 ATACTATAAACATAGTATCGATACATCTAGGTTTTTCCAGATGTATCAATACATCATTCAATGTA
447799 ATGATATGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (68 bp):
ATACTATAAACATAGTATCGATACATCTAGGTTTTTCCAGATGTATCAATACATCATTCAATGTA
TCA
Found at i:451679 original size:21 final size:21
Alignment explanation
Indices: 451655--451701 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
451645 ACTAACTTGC
451655 AATTCAATTATCTTCTTTTCT
1 AATTCAATTATCTTCTTTTCT
* * *
451676 AATTCACTTATTTTCTTTTTT
1 AATTCAATTATCTTCTTTTCT
451697 AATTC
1 AATTC
451702 TTCTTCCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTCAATTATCTTCTTTTCT
Found at i:452182 original size:3 final size:3
Alignment explanation
Indices: 452168--452205 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
452158 CAAGTCAACT
*
452168 TCA TCA TTA TCA TCA TCA TCA TCA TCA TC- TCCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T-CA TCA TC
452206 TTTGATGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 29 0.94
4 1 0.03
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:453123 original size:22 final size:22
Alignment explanation
Indices: 453079--453124 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
453069 CAATCTCTTC
*
453079 AAGAATTATACCCCAAATTTTT
1 AAGAATTATACCCCAAATATTT
*
453101 AAGAGATTATAGCCCAAA-ATTT
1 AAGA-ATTATACCCCAAATATTT
453123 AA
1 AA
453125 TGCAACCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (22 bp):
AAGAATTATACCCCAAATATTT
Found at i:454397 original size:20 final size:20
Alignment explanation
Indices: 454374--454446 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
454364 ACAATTCAAA
454374 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
454394 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
454415 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
454435 GTATCGATACAT
1 GTATCGATACAT
454447 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:454417 original size:21 final size:21
Alignment explanation
Indices: 454391--454467 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
454381 TACATGTTGC
454391 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
454412 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
454432 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
454452 GGATGTATCGATACAT
1 -AATGTATCGATACAT
454468 TTCTTAGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:454425 original size:41 final size:41
Alignment explanation
Indices: 454374--454467 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
454364 ACAATTCAAA
454374 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
454415 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
454456 GTATCGATACAT
1 GTATCGATACAT
454468 TTCTTAGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:454524 original size:13 final size:13
Alignment explanation
Indices: 454506--454531 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
454496 TACAGCAAGT
454506 ATGTATCGATACA
1 ATGTATCGATACA
454519 ATGTATCGATACA
1 ATGTATCGATACA
454532 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:458583 original size:15 final size:15
Alignment explanation
Indices: 458563--458593 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
458553 TAAAAATGTC
*
458563 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
458578 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
458593 C
1 C
458594 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:460690 original size:13 final size:13
Alignment explanation
Indices: 460672--460710 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
460662 ACATTTTTCC
460672 TTGTATCGATACA
1 TTGTATCGATACA
460685 TTGTATCGATACA
1 TTGTATCGATACA
*
460698 CTGTATCGATACA
1 TTGTATCGATACA
460711 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:463176 original size:20 final size:20
Alignment explanation
Indices: 463153--463225 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
463143 ACAATTCAAA
463153 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
463173 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
463194 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
463214 GTATCGATACAT
1 GTATCGATACAT
463226 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:463196 original size:21 final size:21
Alignment explanation
Indices: 463170--463246 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
463160 TACATGTTGC
463170 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
463191 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
463211 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
463231 GGATGTATCGATACAT
1 -AATGTATCGATACAT
463247 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:463204 original size:41 final size:41
Alignment explanation
Indices: 463153--463246 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
463143 ACAATTCAAA
463153 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
463194 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
463235 GTATCGATACAT
1 GTATCGATACAT
463247 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:463303 original size:13 final size:13
Alignment explanation
Indices: 463285--463310 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
463275 TACAGCAAGT
463285 ATGTATCGATACA
1 ATGTATCGATACA
463298 ATGTATCGATACA
1 ATGTATCGATACA
463311 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:468580 original size:23 final size:23
Alignment explanation
Indices: 468554--468599 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
468544 TAACAATAAT
*
468554 ATGTTTTATTCAATTAAATTTTG
1 ATGTGTTATTCAATTAAATTTTG
**
468577 ATGTGTTATTTGATTAAATTTTG
1 ATGTGTTATTCAATTAAATTTTG
468600 TGATTTTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (23 bp):
ATGTGTTATTCAATTAAATTTTG
Found at i:468780 original size:20 final size:20
Alignment explanation
Indices: 468754--468831 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
468744 AATGTCCAAA
468754 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* *
468774 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACA--T-G--TTTCT
*
468799 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
468819 TTGTATCGATACA
1 ATGTATCGATACA
468832 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 28 0.60
22 1 0.02
23 2 0.04
25 16 0.34
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:468838 original size:13 final size:13
Alignment explanation
Indices: 468820--468857 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
468810 CATTTTTCTT
468820 TGTATCGATACAA
1 TGTATCGATACAA
*
468833 TGTATCGATACAC
1 TGTATCGATACAA
468846 TGTATCGATACA
1 TGTATCGATACA
468858 GGGTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:471360 original size:20 final size:20
Alignment explanation
Indices: 471337--471409 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
471327 ACAATTCAAA
471337 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
471357 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
471378 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
471398 GTATCGATACAT
1 GTATCGATACAT
471410 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:471381 original size:21 final size:21
Alignment explanation
Indices: 471355--471430 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
471345 ACATGTTGCA
471355 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
471376 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
471396 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
471417 ATGTATCGATACAT
1 ATGTATCGATACAT
471431 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:471388 original size:41 final size:41
Alignment explanation
Indices: 471337--471430 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
471327 ACAATTCAAA
*
471337 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
471378 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
471419 GTATCGATACAT
1 GTATCGATACAT
471431 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:471487 original size:13 final size:13
Alignment explanation
Indices: 471469--471494 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
471459 TACAGCAAGT
471469 ATGTATCGATACA
1 ATGTATCGATACA
471482 ATGTATCGATACA
1 ATGTATCGATACA
471495 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:473512 original size:13 final size:13
Alignment explanation
Indices: 473480--473533 Score: 90
Period size: 13 Copynumber: 4.0 Consensus size: 13
473470 CACACCCAGA
473480 TGTATCGATACATTT
1 TGTATCGATACA--T
473495 TGTATCGATACAT
1 TGTATCGATACAT
473508 TGTATCGATACAT
1 TGTATCGATACAT
473521 TGTATCGATACAT
1 TGTATCGATACAT
473534 GGACAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 27 0.69
15 12 0.31
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:473621 original size:13 final size:13
Alignment explanation
Indices: 473600--473630 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
473590 CGAAACATGG
*
473600 TACAATGTATCGA
1 TACATTGTATCGA
473613 TACATTGTATCGA
1 TACATTGTATCGA
473626 TACAT
1 TACAT
473631 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:473621 original size:33 final size:32
Alignment explanation
Indices: 473584--473650 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
473574 CTATCACTAT
473584 TTGTATCGAAACATG-GTACAATGTATCGATACA
1 TTGTATCGAAACATGAG-A-AATGTATCGATACA
*
473617 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGAAACATG-AGAAATGTATCGATACA
473650 T
1 T
473651 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Consensus pattern (32 bp):
TTGTATCGAAACATGAGAAATGTATCGATACA
Found at i:479970 original size:24 final size:22
Alignment explanation
Indices: 479943--479987 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
479933 TCATCAAATT
*
479943 TTCAACAAATTTTCACTTTTTCAC
1 TTCAA-AAACTTTCA-TTTTTCAC
*
479967 TTCAAATACTTTCATTTTTCA
1 TTCAAAAACTTTCATTTTTCA
479988 TCAAAATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (22 bp):
TTCAAAAACTTTCATTTTTCAC
Found at i:482323 original size:13 final size:13
Alignment explanation
Indices: 482305--482331 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
482295 ACATGCTGCT
482305 TTGTATCGATACA
1 TTGTATCGATACA
482318 TTGTATCGATACA
1 TTGTATCGATACA
482331 T
1 T
482332 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:482328 original size:33 final size:32
Alignment explanation
Indices: 482286--482350 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
482276 CACACCCAGA
*
482286 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATG-TGCATTGTATCGATACAT
*
482319 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTGCATTGTATCGATACAT
482351 GGACAAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGTATCGATACAT
Found at i:482362 original size:21 final size:19
Alignment explanation
Indices: 482315--482372 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
482305 TTGTATCGAT
*
482315 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
482334 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
482353 ACAAATTGTATCGATACATG
1 AC--ATTGTATCGATACATG
482373 AAACTAGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:482438 original size:13 final size:13
Alignment explanation
Indices: 482417--482447 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
482407 CGATACATGG
*
482417 TACAATGTATCGA
1 TACATTGTATCGA
482430 TACATTGTATCGA
1 TACATTGTATCGA
482443 TACAT
1 TACAT
482448 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:482443 original size:33 final size:32
Alignment explanation
Indices: 482401--482467 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
482391 CTATCACTAT
482401 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
482434 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
482467 T
1 T
482468 AGTTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:483629 original size:31 final size:31
Alignment explanation
Indices: 483594--483703 Score: 84
Period size: 31 Copynumber: 3.5 Consensus size: 31
483584 ACAATCCTTT
483594 TCAAAGTTCACACAAGTTGGTAGCACCCTCA
1 TCAAAGTTCACACAAGTTGGTAGCACCCTCA
* * **
483625 TCAAA-TTC-CACATGAATTGGTAGCAACCTTT
1 TCAAAGTTCACACA--AGTTGGTAGCACCCTCA
* * * *
483656 TCAAAGTCCACATAAGTTGGTGGCACGC-CA
1 TCAAAGTTCACACAAGTTGGTAGCACCCTCA
483686 TTCAAAG-TCTACACAAGT
1 -TCAAAGTTC-ACACAAGT
483704 CGTGGTACAA
Statistics
Matches: 59, Mismatches: 14, Indels: 12
0.69 0.16 0.14
Matches are distributed among these distances:
29 4 0.07
30 4 0.07
31 46 0.78
32 2 0.03
33 3 0.05
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (31 bp):
TCAAAGTTCACACAAGTTGGTAGCACCCTCA
Found at i:483691 original size:62 final size:63
Alignment explanation
Indices: 483584--483811 Score: 187
Period size: 64 Copynumber: 3.6 Consensus size: 63
483574 CCACCCCCAC
* * * * * *
483584 ACAATCCTTTTCAAAGTTCACACAAGTTGGTAGCACCCTCA-TCAAATTCCACATGAA-T-TGGT
1 ACAAACCTTTTCAAAGTCCACATAAGTTGGTGGCACCC-CATTCAAAGTCCACA-CAAGTCTGGT
* *
483646 AGC-AACCTTTTCAAAGTCCACATAAGTTGGTGGCACGCCATTCAAAGTCTACACAAGTCGTGGT
1 A-CAAACCTTTTCAAAGTCCACATAAGTTGGTGGCACCCCATTCAAAGTCCACACAAGTC-TGGT
* * * * *
483710 ACAAACTTTTTCAAAGTCCACATAGGTTGGTGTCACCCCATTCAAAGTCTATACAAGT-TCGAAG
1 ACAAACCTTTTCAAAGTCCACATAAGTTGGTGGCACCCCATTCAAAGTCCACACAAGTCT-G--G
*
483774 CA
63 -T
* * *
483776 ACCAAACATTTTCAAAGTCCACACAAGTTAGTGGCA
1 A-CAAACCTTTTCAAAGTCCACATAAGTTGGTGGCA
483812 ACTAAACTTT
Statistics
Matches: 136, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
61 4 0.03
62 43 0.32
63 3 0.02
64 55 0.40
65 1 0.01
66 1 0.01
67 29 0.21
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (63 bp):
ACAAACCTTTTCAAAGTCCACATAAGTTGGTGGCACCCCATTCAAAGTCCACACAAGTCTGGT
Found at i:483724 original size:64 final size:67
Alignment explanation
Indices: 483653--483811 Score: 207
Period size: 64 Copynumber: 2.4 Consensus size: 67
483643 GGTAGCAACC
* * **
483653 TTTTCAAAGTCCACATAAGTTGGTGGCACGCCATTCAAAGTCTACACAAG-TCG-TGGTA-CAAA
1 TTTTCAAAGTCCACATAAGTTGGTGGCACCCCATTCAAAGTCTACACAAGTTCGAAGCAACCAAA
*
483715 CT
66 CA
* * *
483717 TTTTCAAAGTCCACATAGGTTGGTGTCACCCCATTCAAAGTCTATACAAGTTCGAAGCAACCAAA
1 TTTTCAAAGTCCACATAAGTTGGTGGCACCCCATTCAAAGTCTACACAAGTTCGAAGCAACCAAA
483782 CA
66 CA
* *
483784 TTTTCAAAGTCCACACAAGTTAGTGGCA
1 TTTTCAAAGTCCACATAAGTTGGTGGCA
483812 ACTAAACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 46 0.57
65 3 0.04
66 2 0.03
67 29 0.36
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (67 bp):
TTTTCAAAGTCCACATAAGTTGGTGGCACCCCATTCAAAGTCTACACAAGTTCGAAGCAACCAAA
CA
Found at i:483802 original size:36 final size:36
Alignment explanation
Indices: 483686--483944 Score: 145
Period size: 36 Copynumber: 7.5 Consensus size: 36
483676 TGGCACGCCA
* * *
483686 TTCAAAGTCTACACAAG-TCGTGG-TA-CAAACTTT
1 TTCAAAGTCCACACAAGTTCGTGGCAACCAAACATT
* * * * *
483719 TTCAAAGTCCACATAGGTTGGTGTC-ACC--CCA--
1 TTCAAAGTCCACACAAGTTCGTGGCAACCAAACATT
* * **
483750 TTCAAAGTCTATACAAGTTCGAAGCAACCAAACATT
1 TTCAAAGTCCACACAAGTTCGTGGCAACCAAACATT
* * *
483786 TTCAAAGTCCACACAAGTTAGTGGCAACTAAACTTTT
1 TTCAAAGTCCACACAAGTTCGTGGCAACCAAAC-ATT
* ** *
483823 TTTAAAGTCCACATGAGTTGGTGGCAACC---CA--
1 TTCAAAGTCCACACAAGTTCGTGGCAACCAAACATT
* * *
483854 TTCAAAGTCTACATAAG-TCGGTGGCAACCAAACCTT
1 TTCAAAGTCCACACAAGTTC-GTGGCAACCAAACATT
*
483890 TTCAAAGTCCACACAAG-TCAGTGGCAATCAAACCA-T
1 TTCAAAGTCCACACAAGTTC-GTGGCAACCAAA-CATT
*
483926 TTCTAAAGTCCACAAAAGT
1 TTC-AAAGTCCACACAAGT
483945 CGATGGAACA
Statistics
Matches: 168, Mismatches: 40, Indels: 31
0.70 0.17 0.13
Matches are distributed among these distances:
30 1 0.01
31 40 0.24
32 3 0.02
33 15 0.09
34 9 0.05
35 1 0.01
36 59 0.35
37 40 0.24
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (36 bp):
TTCAAAGTCCACACAAGTTCGTGGCAACCAAACATT
Found at i:483862 original size:104 final size:103
Alignment explanation
Indices: 483686--483939 Score: 295
Period size: 104 Copynumber: 2.5 Consensus size: 103
483676 TGGCACGCCA
* * * * * *
483686 TTCAAAGTCTACACAAG-TCGTGG-TAC-AAACTTTTTCAAAGTCCACATAGGTTGGTGTCACCC
1 TTCAAAGTCCACACAAGTTAGTGGCAACTAAACTTTTTTAAAGTCCACATAGGTTGGTGGCAACC
*
483748 CATTCAAAGTCTATACAAGTTC-GAAGCAACCAAACATT
66 CATTCAAAGTCTACACAAG-TCGGAAGCAACCAAACATT
483786 TTCAAAGTCCACACAAGTTAGTGGCAACTAAACTTTTTTTAAAGTCCACAT-GAGTTGGTGGCAA
1 TTCAAAGTCCACACAAGTTAGTGGCAACTAAAC-TTTTTTAAAGTCCACATAG-GTTGGTGGCAA
* ** *
483850 CCCATTCAAAGTCTACATAAGTCGGTGGCAACCAAACCTT
64 CCCATTCAAAGTCTACACAAGTCGGAAGCAACCAAACATT
* * *
483890 TTCAAAGTCCACACAAGTCAGTGGCAA-TCAAACCATTTCTAAAGTCCACA
1 TTCAAAGTCCACACAAGTTAGTGGCAACT-AAA-CTTTTTTAAAGTCCACA
483940 AAAGTCGATG
Statistics
Matches: 132, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
100 16 0.12
101 5 0.04
102 2 0.02
103 8 0.06
104 100 0.76
105 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (103 bp):
TTCAAAGTCCACACAAGTTAGTGGCAACTAAACTTTTTTAAAGTCCACATAGGTTGGTGGCAACC
CATTCAAAGTCTACACAAGTCGGAAGCAACCAAACATT
Found at i:483945 original size:37 final size:36
Alignment explanation
Indices: 483773--483986 Score: 133
Period size: 36 Copynumber: 6.1 Consensus size: 36
483763 CAAGTTCGAA
* *
483773 GCAACCAAA-CATTTTCAAAGTCCACACAAGTTAGTG
1 GCAACCAAACCA-TTTCAAAGTCCACAAAAGTCAGTG
* ** * ** **
483809 GCAACTAAACTTTTTTTAAAGTCCACATGAGTTGGTG
1 GCAACCAAAC-CATTTCAAAGTCCACAAAAGTCAGTG
* * *
483846 GCAA-C---CCA-TTCAAAGTCTACATAAGTCGGTG
1 GCAACCAAACCATTTCAAAGTCCACAAAAGTCAGTG
* *
483877 GCAACCAAACCTTTTCAAAGTCCACACAAGTCAGTG
1 GCAACCAAACCATTTCAAAGTCCACAAAAGTCAGTG
*
483913 GCAATCAAACCATTTCTAAAGTCCACAAAAGTC-GATG
1 GCAACCAAACCATTTC-AAAGTCCACAAAAGTCAG-TG
* * * *
483950 G-AA-CAACCCCAGTT-AAAGTCGACATAAGTCAGTG
1 GCAACCAA-ACCATTTCAAAGTCCACAAAAGTCAGTG
483984 GCA
1 GCA
483987 TTCCATTCAA
Statistics
Matches: 141, Mismatches: 25, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
31 23 0.16
32 1 0.01
33 1 0.01
34 17 0.12
35 7 0.05
36 50 0.35
37 42 0.30
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (36 bp):
GCAACCAAACCATTTCAAAGTCCACAAAAGTCAGTG
Found at i:484024 original size:29 final size:29
Alignment explanation
Indices: 483975--484318 Score: 212
Period size: 29 Copynumber: 12.2 Consensus size: 29
483965 AAGTCGACAT
* *
483975 AAGTCAGTGGCATTCC-ATTCAAAGCCCAC
1 AAGTCAGTGGCA-CCCTTTTCAAAGCCCAC
* *
484004 AAGTCAGTGGTACCCTTTTCAAAGCTCAC
1 AAGTCAGTGGCACCCTTTTCAAAGCCCAC
*
484033 AAGTCAATGGCACCC-TTTCAAAGCCCAC
1 AAGTCAGTGGCACCCTTTTCAAAGCCCAC
* * *
484061 AAGTCAGTGGTATCATTTTC--A---CAC
1 AAGTCAGTGGCACCCTTTTCAAAGCCCAC
* *
484085 AA-TCAGTAGCAACCC-TTACAAAGCCCAC
1 AAGTCAGTGGC-ACCCTTTTCAAAGCCCAC
* * * *
484113 AAGTTAATGGCACCTTTTTCAAAGCCAAC
1 AAGTCAGTGGCACCCTTTTCAAAGCCCAC
* * *
484142 AAGTCAATGGCA-CATTTTCAAAGCCTAC
1 AAGTCAGTGGCACCCTTTTCAAAGCCCAC
* * * *
484170 AAGTCAATGGCACCATTTTCAAAACCCAT
1 AAGTCAGTGGCACCCTTTTCAAAGCCCAC
*** *
484199 AAGTCAGTAATACTC-TTTCAAAGCCCAC
1 AAGTCAGTGGCACCCTTTTCAAAGCCCAC
** ** * *
484227 AAGTCAGTCACACATTTTTCAAAGCTCAT
1 AAGTCAGTGGCACCCTTTTCAAAGCCCAC
* * *
484256 AAGTTAAT--CACACCTTTTGCAAAGCTCAC
1 AAGTCAGTGGCAC-CCTTTT-CAAAGCCCAC
* * * *
484285 AAATCAGTGACA-CATTTTCAAAGCTCAC
1 AAGTCAGTGGCACCCTTTTCAAAGCCCAC
484313 AAGTCA
1 AAGTCA
484319 ATCAAAGCCC
Statistics
Matches: 247, Mismatches: 52, Indels: 33
0.74 0.16 0.10
Matches are distributed among these distances:
23 9 0.04
24 7 0.03
25 1 0.00
27 4 0.02
28 100 0.40
29 124 0.50
31 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.25
Consensus pattern (29 bp):
AAGTCAGTGGCACCCTTTTCAAAGCCCAC
Found at i:484064 original size:57 final size:57
Alignment explanation
Indices: 483992--484320 Score: 275
Period size: 57 Copynumber: 5.9 Consensus size: 57
483982 TGGCATTCCA
* * *
483992 TTCAAAGCCCACAAGTCAGTGGTACCCTTTTCAAAGCTCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCATTTTCAAAGCTCACAAGTCAATAGCACCCT
* * *
484049 TTCAAAGCCCACAAGTCAGTGGTATCATTTTC--A---CACAA-TCAGTAGCAACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCATTTTCAAAGCTCACAAGTCAATAGC-ACCCT
* * * * * **
484101 TACAAAGCCCACAAGTTAATGGCACCTTTTTCAAAGC-CAACAAGTCAATGGCACATT
1 TTCAAAGCCCACAAGTCAGTGGCACCATTTTCAAAGCTC-ACAAGTCAATAGCACCCT
* * * * * * ** *
484158 TTCAAAGCCTACAAGTCAATGGCACCATTTTCAAAACCCATAAGTCAGTAATACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCATTTTCAAAGCTCACAAGTCAATAGCACCCT
* * *
484215 TTCAAAGCCCACAAGTCAGT--CACACATTTTTCAAAGCTCATAAGTTAATCA-CACCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CA-TTTTCAAAGCTCACAAGTCAAT-AGCACCCT
* * *
484272 TTGCAAAGCTCACAAATCAGTGACA-CATTTTCAAAGCTCACAAGTCAAT
1 TT-CAAAGCCCACAAGTCAGTGGCACCATTTTCAAAGCTCACAAGTCAAT
484321 CAAAGCCCAT
Statistics
Matches: 219, Mismatches: 39, Indels: 28
0.77 0.14 0.10
Matches are distributed among these distances:
51 6 0.03
52 36 0.16
54 1 0.00
55 4 0.02
56 3 0.01
57 141 0.64
58 26 0.12
60 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.25
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCACCATTTTCAAAGCTCACAAGTCAATAGCACCCT
Found at i:484172 original size:109 final size:109
Alignment explanation
Indices: 483994--484190 Score: 288
Period size: 109 Copynumber: 1.8 Consensus size: 109
483984 GCATTCCATT
* * *
483994 CAAAGCCCACAAGTCAGTGGTACCCTTTTCAAAGCTCACAAGTCAATGGCACCCTTTCAAAGCCC
1 CAAAGCCCACAAGTCAATGGCACCCTTTTCAAAGCTCACAAGTCAATGGCACACTTTCAAAGCCC
* * *
484059 ACAAGTCAGTGGTATCATTTTCACACAATCAGTAGCAACCCTTA
66 ACAAGTCAATGGCACCATTTTCACACAATCAGTAGCAACCCTTA
* * *
484103 CAAAGCCCACAAGTTAATGGCACCTTTTTCAAAGC-CAACAAGTCAATGGCACATTTTCAAAGCC
1 CAAAGCCCACAAGTCAATGGCACCCTTTTCAAAGCTC-ACAAGTCAATGGCACACTTTCAAAGCC
*
484167 TACAAGTCAATGGCACCATTTTCA
65 CACAAGTCAATGGCACCATTTTCA
484191 AAACCCATAA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
108 1 0.01
109 76 0.99
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (109 bp):
CAAAGCCCACAAGTCAATGGCACCCTTTTCAAAGCTCACAAGTCAATGGCACACTTTCAAAGCCC
ACAAGTCAATGGCACCATTTTCACACAATCAGTAGCAACCCTTA
Found at i:491941 original size:2 final size:2
Alignment explanation
Indices: 491934--491970 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
491924 TTCATATGTC
491934 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
491971 TACTTTGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:492660 original size:2 final size:2
Alignment explanation
Indices: 492649--492684 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
492639 CTTCATACAA
492649 AT AT AT -T 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 A
492685 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:495717 original size:3 final size:3
Alignment explanation
Indices: 495711--495775 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
495701 GATGGAAGCC
*
495711 CTT CTT CTT CTT CTT CCT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
495759 CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CT
495776 ACCACATCTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:499710 original size:3 final size:3
Alignment explanation
Indices: 499692--499727 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
499682 ATTTTTTAAA
*
499692 TAT TTT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
499728 TTAATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:499742 original size:21 final size:21
Alignment explanation
Indices: 499718--499759 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
499708 TTATTATTAT
* *
499718 TATTATTATTTTAATTTAAAA
1 TATTAATATTTAAATTTAAAA
499739 TATTAATATTTAAATTTAAAA
1 TATTAATATTTAAATTTAAAA
499760 ATTCCTCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTAATATTTAAATTTAAAA
Found at i:503336 original size:27 final size:27
Alignment explanation
Indices: 503295--503363 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
503285 ATAACATGTT
*
503295 ACCATTTTTGACAAATA-AAAAGAAACT
1 ACCATTTTTGACAAATACAAAA-AAACC
* *
503322 ACTATTTTTGACAAATACAAAATAACC
1 ACCATTTTTGACAAATACAAAAAAACC
503349 ACCATTTTTGACAAA
1 ACCATTTTTGACAAA
503364 CAAAGAGTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 33 0.89
28 4 0.11
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.29
Consensus pattern (27 bp):
ACCATTTTTGACAAATACAAAAAAACC
Found at i:507915 original size:27 final size:26
Alignment explanation
Indices: 507855--507935 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
507845 AATAACATGT
* *
507855 CACCATTTTTGATAAATAAAAAGAAAC
1 CACCATTTTTGATAAACAAAAA-TAAC
*
507882 TACCATTTTTGATAAACACAAAATAAC
1 CACCATTTTTGATAAACA-AAAATAAC
* * *
507909 CATCATTTTTTACAAACAAAAGATAAC
1 CACCATTTTTGATAAACAAAA-ATAAC
507936 TTTTGTTGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 3 0.07
27 38 0.84
28 4 0.09
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.28
Consensus pattern (26 bp):
CACCATTTTTGATAAACAAAAATAAC
Found at i:514316 original size:34 final size:34
Alignment explanation
Indices: 514248--514465 Score: 251
Period size: 34 Copynumber: 6.4 Consensus size: 34
514238 TACCATGATT
*
514248 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * * *
514281 TTGTTGATTAAATGGGTGATTTGATGGTTTGCCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * *
514315 TTGTTGACTAAATGGGAGATTTGGTAACTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* **
514349 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* ** *
514383 TTATTGATTAAATTAGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * *
514417 TTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGT-GATTTGGTAGCTTACCA
514451 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
514466 TGGTTTTTAC
Statistics
Matches: 156, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
33 15 0.10
34 140 0.90
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
Found at i:514381 original size:102 final size:101
Alignment explanation
Indices: 514248--514465 Score: 310
Period size: 102 Copynumber: 2.1 Consensus size: 101
514238 TACCATGATT
** * * * * *
514248 TTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGATGGTTTGC
1 TTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTGATGGCTTAC
514313 CATTGTTGACTAAATGGGAGATTTGGTAACTTACCA
66 CATTGTTGACTAAATGGGAGATTTGGTAACTTACCA
* *
514349 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATTAGTGATTTGGTGGCTTA
1 TTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTGATGGCTTA
* ** *
514414 CCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCA
65 CCATTGTTGACTAAATGGGAGATTTGGTAACTTACCA
514451 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
514466 TGGTTTTTAC
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 15 0.15
102 88 0.85
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (101 bp):
TTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTGATGGCTTAC
CATTGTTGACTAAATGGGAGATTTGGTAACTTACCA
Found at i:519895 original size:52 final size:51
Alignment explanation
Indices: 519810--519933 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
519800 ATATGAAAAG
* *
519810 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
519861 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
519913 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
519934 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:519946 original size:51 final size:51
Alignment explanation
Indices: 519810--519953 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
519800 ATATGAAAAG
*
519810 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
519862 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
519913 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
519954 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:519960 original size:13 final size:13
Alignment explanation
Indices: 519942--519966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
519932 CAAAGATCAG
519942 TGTATCGATACAA
1 TGTATCGATACAA
519955 TGTATCGATACA
1 TGTATCGATACA
519967 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:520044 original size:33 final size:33
Alignment explanation
Indices: 520007--520073 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
519997 AGTAGCTTAA
520007 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
520040 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
520073 A
1 A
520074 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:520047 original size:13 final size:13
Alignment explanation
Indices: 520029--520053 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
520019 CAAAAAAATA
520029 TGTATCGATACAT
1 TGTATCGATACAT
520042 TGTATCGATACA
1 TGTATCGATACA
520054 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:522318 original size:34 final size:34
Alignment explanation
Indices: 522256--522474 Score: 246
Period size: 34 Copynumber: 6.5 Consensus size: 34
522246 AAGTGGGAGA
*
522256 ATTGTTGATTAAAT-GGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
* * * *
522289 ATTGTTAATTAAATGGGTGATTTGATGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
* * **
522323 ATTGTTGACTAAATGGGAGATTTGGTAACTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
* ** *
522357 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
* *
522391 ATTATTGATTAAATGGGTGATTTGGTGGCCTACC
1 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
* *
522425 ATTGTTGACTAAAT-GGTAGATTTGGTAGG-TTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGT-GGCTTACC
522459 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
522475 TGGTTTTTAC
Statistics
Matches: 156, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
33 16 0.10
34 137 0.88
35 3 0.02
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
Found at i:522431 original size:102 final size:101
Alignment explanation
Indices: 522256--522474 Score: 303
Period size: 102 Copynumber: 2.2 Consensus size: 101
522246 AAGTGGGAGA
** * * * ** *
522256 ATTGTTGATTAAATGGTGATTTGGTGGTTTACCATTGTTAATTAAATGGGTGATTTGATGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTAATTAAATGGGTGATTTGATGGCCTA
522321 CCATTGTTGACTAAATGGGAGATTTGGTAACTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAACTTACC
* *
522357 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCCT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTAATTAAATGGGTGATTTGATGGCCT
* ** *
522422 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAACTTACC
522459 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
522475 TGGTTTTTAC
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
101 16 0.16
102 87 0.84
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTAATTAAATGGGTGATTTGATGGCCTA
CCATTGTTGACTAAATGGGAGATTTGGTAACTTACC
Found at i:525477 original size:11 final size:11
Alignment explanation
Indices: 525442--525485 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
525432 TTTGGATGAT
525442 TTATATTTAT-
1 TTATATTTATA
525452 TTA-ATTTATTA
1 TTATATTTA-TA
525463 TTATATTTATA
1 TTATATTTATA
525474 TTATATTTATA
1 TTATATTTATA
525485 T
1 T
525486 AAATTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 5 0.16
10 4 0.13
11 17 0.55
12 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATATTTATA
Found at i:525477 original size:17 final size:16
Alignment explanation
Indices: 525440--525505 Score: 50
Period size: 15 Copynumber: 4.2 Consensus size: 16
525430 TGTTTGGATG
525440 ATTTA-TATTTATTTA
1 ATTTATTATTTATTTA
525455 ATTTATTATTATATTT-
1 ATTTATTATT-TATTTA
*
525471 ATATTA-TATTTATATA
1 AT-TTATTATTTATTTA
* * *
525487 AATTA-TATATATTAA
1 ATTTATTATTTATTTA
525502 ATTT
1 ATTT
525506 TAAATAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
15 22 0.54
16 11 0.27
17 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTATTTATTTA
Found at i:525513 original size:25 final size:24
Alignment explanation
Indices: 525470--525516 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
525460 TTATTATATT
* *
525470 TATATTATATTTATATAAATTATA
1 TATATTAAATTTAAATAAATTATA
525494 TATATTAAATTTTAAATAAATTA
1 TATATTAAA-TTTAAATAAATTA
525517 AAAATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATATTAAATTTAAATAAATTATA
Found at i:525523 original size:25 final size:25
Alignment explanation
Indices: 525471--525529 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
525461 TATTATATTT
* * * *
525471 ATATTATA-TTTATATAAATTATAT
1 ATATTAAATTTTAAATAAATTAAAA
525495 ATATTAAATTTTAAATAAATTAAAA
1 ATATTAAATTTTAAATAAATTAAAA
*
525520 ATATTTAATT
1 ATATTAAATT
525530 ATTTATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATTAAATTTTAAATAAATTAAAA
Found at i:525802 original size:3 final size:3
Alignment explanation
Indices: 525794--525827 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
525784 TAACGTACTT
*
525794 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
525828 GCAGTCGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:527947 original size:3 final size:3
Alignment explanation
Indices: 527939--527969 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
527929 TAATCTTTTG
*
527939 TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
527970 CTTTAGGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:535643 original size:18 final size:18
Alignment explanation
Indices: 535622--535656 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
535612 AATAAGATAA
535622 GGAGTTTTCATGGTTTAG
1 GGAGTTTTCATGGTTTAG
535640 GGAGTTTTCATGGTTTA
1 GGAGTTTTCATGGTTTA
535657 ACAAGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.06, G:0.31, T:0.46
Consensus pattern (18 bp):
GGAGTTTTCATGGTTTAG
Found at i:535663 original size:18 final size:18
Alignment explanation
Indices: 535624--535665 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
535614 TAAGATAAGG
***
535624 AGTTTTCATGGTTTAGGG
1 AGTTTTCATGGTTTAACA
535642 AGTTTTCATGGTTTAACA
1 AGTTTTCATGGTTTAACA
535660 AGTTTT
1 AGTTTT
535666 TATAAAAGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.07, G:0.24, T:0.48
Consensus pattern (18 bp):
AGTTTTCATGGTTTAACA
Done.