Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007808.1 Hibiscus syriacus cultivar Beakdansim tig00110129_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1698870
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:333921 original size:16 final size:16
Alignment explanation
Indices: 333902--333943 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 16
333892 TATTCTCTTT
333902 TTATTTATATATTATA
1 TTATTTATATATTATA
333918 TTATTT-T-TATTATA
1 TTATTTATATATTATA
333932 TATATCTTATAT
1 T-TAT-TTATAT
333944 CATTGTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.36
15 4 0.18
16 8 0.36
17 1 0.05
18 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTTATATATTATA
Found at i:333941 original size:25 final size:24
Alignment explanation
Indices: 333899--333978 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 24
333889 CTATATTCTC
333899 TTTTTATT-TATATA-TTATATTA
1 TTTTTATTATATATATTTATATTA
*
333921 TTTTTATTATATATATCTTATATCA
1 TTTTTATTATATATAT-TTATATTA
* *
333946 TTGTGTATATATATATATATATGTATTA
1 TT-T-T-TAT-TATATATATTTATATTA
333974 TTTTT
1 TTTTT
333979 TCTCCATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
22 8 0.17
23 6 0.13
25 10 0.21
26 2 0.04
27 2 0.04
28 10 0.21
29 9 0.19
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTTTATTATATATATTTATATTA
Found at i:334066 original size:27 final size:26
Alignment explanation
Indices: 334028--334080 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
334018 ATGTATATCT
334028 TTATTTTTTATT-TGTTTTACTTAGTA
1 TTATTTTTTATTAT-TTTTACTTAGTA
*
334054 TTATATTTTTATTATTTTTATTTAGTA
1 TTAT-TTTTTATTATTTTTACTTAGTA
334081 AATACTACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 19 0.79
28 1 0.04
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.70
Consensus pattern (26 bp):
TTATTTTTTATTATTTTTACTTAGTA
Found at i:347604 original size:21 final size:21
Alignment explanation
Indices: 347558--347604 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
347548 TTTTCTTCTT
* *
347558 ATTTTATTTATTTTATTTATC
1 ATTTTATTTATGTTATTTACC
*
347579 TTTTTATTTACTGTT-TTTACC
1 ATTTTATTTA-TGTTATTTACC
347600 ATTTT
1 ATTTT
347605 TCATTGCCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (21 bp):
ATTTTATTTATGTTATTTACC
Found at i:351754 original size:31 final size:31
Alignment explanation
Indices: 351716--351804 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 31
351706 GAATCTTTGA
351716 AGATTTAACATCAAATGTTGGGGCATTTTTT
1 AGATTTAACATCAAATGTTGGGGCATTTTTT
* * *
351747 AGATTTAACATCAATTGTTGGCGTATTTTTTT
1 AGATTTAACATCAAATGTTGGGGCA-TTTTTT
* * *
351779 AGATTCAACATCGAATATTGGGGCAT
1 AGATTTAACATCAAATGTTGGGGCAT
351805 CTTTGGGAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
31 23 0.48
32 25 0.52
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (31 bp):
AGATTTAACATCAAATGTTGGGGCATTTTTT
Found at i:352609 original size:106 final size:106
Alignment explanation
Indices: 352399--352595 Score: 250
Period size: 106 Copynumber: 1.9 Consensus size: 106
352389 ATATCGTGCC
* * * * *
352399 ACTCGAGACAACTCAAGTTCAACTCCACAACGAAGGGACGACTAGTTGTCAATAAACAATTTCCT
1 ACTCGAGACAACACAAGCTCAACTCCACAACGAAGGGACGACTAGCTATCAACAAACAATTTCCT
*
352464 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGA
66 AATTCCAGAGCCAATTTCAACTTCACATCGAAGGATATTGA
* * * ** * *
352505 ACTCGAGACAGCACAAGCTCAACTTCACAACGAAGGGGCGGTTGGCTATCAACAAACAATTTCTT
1 ACTCGAGACAACACAAGCTCAACTCCACAACGAAGGGACGACTAGCTATCAACAAACAATTTCCT
* * *
352570 AGTTCCATAGCCAATTTTAACTTCAC
66 AATTCCAGAGCCAATTTCAACTTCAC
352596 GGTGGAGGAT
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
106 75 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (106 bp):
ACTCGAGACAACACAAGCTCAACTCCACAACGAAGGGACGACTAGCTATCAACAAACAATTTCCT
AATTCCAGAGCCAATTTCAACTTCACATCGAAGGATATTGA
Found at i:352902 original size:36 final size:36
Alignment explanation
Indices: 352803--352918 Score: 117
Period size: 36 Copynumber: 3.2 Consensus size: 36
352793 GTTTTATTTG
* * * *
352803 AAACAAATTTCATCTCC-CATGAGACAGTTTCTTTTC
1 AAACAAATTTCGTC-CCTCTTGAGACAGTTTCTCTTA
* * * *
352839 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTA
1 AAAC-AAATTTCGTCCCTCTTGAGACAGTTTCTCTTA
* *
352876 AAACAAATTTCGTCCCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTCGTCCCTCTTGAGACAGTTTCTCTTA
352912 AAACAAA
1 AAACAAA
352919 ATCTTTGAAT
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
36 38 0.59
37 26 0.41
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.35
Consensus pattern (36 bp):
AAACAAATTTCGTCCCTCTTGAGACAGTTTCTCTTA
Found at i:353013 original size:67 final size:67
Alignment explanation
Indices: 352867--353047 Score: 226
Period size: 67 Copynumber: 2.7 Consensus size: 67
352857 CTTGAGACAG
* * **
352867 TTTCTCTTAAAACAAATTTCGTC-CCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAAT
1 TTTCTCTTAAAACAAATTTTGTCTCC-CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAAT
352929 TAA
65 TAA
* *
352932 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
1 TTTCTCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
*
352997 TA
66 AA
* * * *
352999 TTTTTCTTAAAACAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACA
1 TTTCTCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
353048 ACAGATATCT
Statistics
Matches: 100, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
65 38 0.38
66 13 0.13
67 49 0.49
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (67 bp):
TTTCTCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
AA
Found at i:353831 original size:110 final size:110
Alignment explanation
Indices: 353633--353871 Score: 317
Period size: 110 Copynumber: 2.2 Consensus size: 110
353623 GCTTCCTAGT
* * *
353633 TTCAGAGCCAATTTCAACTTCACAACGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAACATCA
*
353698 CAACGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTCTCA
66 CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTCTCA
* ** *
353743 TTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGAACTCAAGATAACACAAGCTCAACATCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAACATCA
* * * *
353808 CAACGAAGGGGTGGCTGGCTGTCAACAAACAA-TTTCCCAGT-TC-
66 CAACGAAGGGGCGACTGACTGTCAACAAACAACTTT-TCAGTCTCA
*
353851 --CAAAGCCAATTTCAACTTCAC
1 TTCAGAGCCAATTTCAACTTCAC
353872 GACGGACGAT
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
106 19 0.17
109 5 0.04
110 90 0.79
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAACATCA
CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTCTCA
Found at i:355231 original size:18 final size:17
Alignment explanation
Indices: 355210--355308 Score: 89
Period size: 18 Copynumber: 5.6 Consensus size: 17
355200 TTTCGTCCCC
355210 TATATATATATTTTTAAT
1 TATATATATATTTTT-AT
355228 TATAT-T-T-TTATTTAT
1 TATATATATATT-TTTAT
*
355243 TACTATAT-TCTTTTTAT
1 TA-TATATATATTTTTAT
355260 TATATATATTATTTTTAT
1 TATATATA-TATTTTTAT
*
355278 TATATATATATATCATTAT
1 TATATATATAT-T-TTTAT
355297 GTATATATATAT
1 -TATATATATAT
355309 ATATATGTAT
Statistics
Matches: 70, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
15 6 0.09
16 12 0.17
17 13 0.19
18 24 0.34
19 4 0.06
20 11 0.16
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (17 bp):
TATATATATATTTTTAT
Found at i:355250 original size:32 final size:33
Alignment explanation
Indices: 355214--355284 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
355204 GTCCCCTATA
*
355214 TATATAT-TTTTAATTATAT-TTTTATTTATTAC
1 TATATATCTTTTAATTATATATATTATTT-TTAC
* *
355246 TATAT-TCTTTTTATTATATATATTATTTTTAT
1 TATATATCTTTTAATTATATATATTATTTTTAC
355278 TATATAT
1 TATATAT
355285 ATATATCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
31 1 0.03
32 24 0.73
33 8 0.24
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (33 bp):
TATATATCTTTTAATTATATATATTATTTTTAC
Found at i:355267 original size:2 final size:2
Alignment explanation
Indices: 355260--355319 Score: 54
Period size: 2 Copynumber: 31.0 Consensus size: 2
355250 TTCTTTTTAT
* * *
355260 TA TA TA TA T- TA TT TT TA T- TA TA TA TA TA TA TCA T- TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
*
355300 TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA
355320 GATGTATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
1 3 0.06
2 43 0.90
3 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (2 bp):
TA
Found at i:365219 original size:26 final size:26
Alignment explanation
Indices: 365169--365232 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
365159 CTTGGCTTGC
365169 TTTTCTCTTTT-TGAAATATTTTTCT
1 TTTTCTCTTTTCTGAAATATTTTTCT
365194 TTTTCTTCTTTTCTG-AAT-TTTCTTCT
1 TTTTC-TCTTTTCTGAAATATTT-TTCT
*
365220 TTTTGTCTTTTCT
1 TTTTCTCTTTTCT
365233 TTCTTTTTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 16 0.46
26 17 0.49
27 2 0.06
ACGTcount: A:0.09, C:0.16, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTTCTCTTTTCTGAAATATTTTTCT
Found at i:365880 original size:21 final size:20
Alignment explanation
Indices: 365846--365886 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
365836 AAAAAATGTT
**
365846 ATAAAAAATTTAAAAGAAAAA
1 ATAAAAAAAATAAAA-AAAAA
365867 ATAAAAAAAATAAAAAAAAA
1 ATAAAAAAAATAAAAAAAAA
365887 TATTAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (20 bp):
ATAAAAAAAATAAAAAAAAA
Found at i:365983 original size:16 final size:14
Alignment explanation
Indices: 365964--365997 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
365954 AAGAAGTGGG
365964 AAAATAAAGATAAAA
1 AAAATAAA-ATAAAA
365979 CAAAATAAAATAAAA
1 -AAAATAAAATAAAA
365994 AAAA
1 AAAA
365998 GAAGTGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 6 0.33
16 8 0.44
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (14 bp):
AAAATAAAATAAAA
Found at i:366055 original size:12 final size:12
Alignment explanation
Indices: 366040--366066 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
366030 AGAAAAAAAT
366040 AAAGGTATAATA
1 AAAGGTATAATA
366052 AAAGGTATAATA
1 AAAGGTATAATA
366064 AAA
1 AAA
366067 TAAAAGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (12 bp):
AAAGGTATAATA
Found at i:366152 original size:18 final size:18
Alignment explanation
Indices: 366131--366173 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
366121 GTTGTTTTTA
*
366131 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
366149 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
*
366167 TAATAAA
1 AAATAAA
366174 TAATCTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:373771 original size:24 final size:24
Alignment explanation
Indices: 373742--373787 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
373732 TTCAATTCTC
*
373742 TCATTTGCAACCCCAACGTTTTCA
1 TCATTTGCAACCCCAACATTTTCA
* *
373766 TCATTTTCAACTCCAACATTTT
1 TCATTTGCAACCCCAACATTTT
373788 GTTCAACTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (24 bp):
TCATTTGCAACCCCAACATTTTCA
Found at i:377782 original size:14 final size:15
Alignment explanation
Indices: 377762--377803 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
377752 AACCGGAGCG
377762 ATTCTTTATTTTTCT
1 ATTCTTTATTTTTCT
377777 -TTCTTTTAATTTTTCT
1 ATTC-TTT-ATTTTTCT
377793 ATT-TTTATTTT
1 ATTCTTTATTTT
377804 AATAGGGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 8 0.33
15 6 0.25
16 8 0.33
17 2 0.08
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTCTTTATTTTTCT
Found at i:399251 original size:55 final size:55
Alignment explanation
Indices: 399162--399605 Score: 642
Period size: 55 Copynumber: 8.1 Consensus size: 55
399152 GTATATGTTG
* *
399162 GAATTTTCGTATTGACACTATGTGCT-CAACCTCACGAAATTCACAATGAGTTTAT
1 GAATTTTCGTATTGGCACTATGTG-TGCAACCTCACGAAATTCATAATGAGTTTAT
* *
399217 GAATTTAT-GTATTGGCACTATGTGTGCAATCTCACGAAATTCATAATTAGTTTAT
1 GAATTT-TCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
* *
399272 GAATTTTCGCATTGGCACTATGTGTGCAACCTCACGAAATTCACAATGAGTTTAT
1 GAATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
* *
399327 GAATTTTCGTATTGGTACTATGTGTGCAACCTCACGAAATTCACAATGAGTTTAT
1 GAATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
* * *
399382 GAATTTTTGTATTGGCACTATGTGTACAACCTCACGAAATTCATACTGAGTTTAT
1 GAATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
* * *
399437 GAATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTTATAACGAGTTTAT
1 GAATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
* * *
399492 GAATTTTCGCATTGGCATTATGTGTACAACCTCACGAAATTCATAATGAGTTTAT
1 GAATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
* * * ** *
399547 GAATTTT-TTATTGCCACTATGTGTGCAACCCCACCTAATTCATAATGAGTTTGT
1 GAATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
399601 GAATT
1 GAATT
399606 ACCGTATCAG
Statistics
Matches: 350, Mismatches: 36, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
54 45 0.13
55 304 0.87
56 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (55 bp):
GAATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
Found at i:401495 original size:19 final size:17
Alignment explanation
Indices: 401460--401560 Score: 80
Period size: 19 Copynumber: 5.6 Consensus size: 17
401450 TTTTATTTAT
* *
401460 TTTTCTTCTTATTCTTC
1 TTTTCTTTTTTTTCTTC
401477 TTTTCCTTTTTTGTTCTTC
1 TTTT-CTTTTTT-TTCTTC
*
401496 -TTTCTTTCTTTTCTTTTC
1 TTTTCTTT-TTTT-TCTTC
*
401514 TTTTCTTTTTTATCTTTTC
1 TTTTCTTTTTT-T-TCTTC
401533 TTTT-TTCTTTTTTCTTC
1 TTTTCTT-TTTTTTCTTC
401550 TTTTTCTTTTT
1 -TTTTCTTTTT
401561 AATTTTTTAT
Statistics
Matches: 71, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
17 13 0.18
18 28 0.39
19 30 0.42
ACGTcount: A:0.02, C:0.19, G:0.01, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTTTTTCTTC
Found at i:401515 original size:14 final size:13
Alignment explanation
Indices: 401474--401597 Score: 85
Period size: 14 Copynumber: 9.2 Consensus size: 13
401464 CTTCTTATTC
*
401474 TTCTTTTCCTTTT
1 TTCTTTTCTTTTT
* *
401487 TTGTTCTTCTTTCT
1 TTCTT-TTCTTTTT
401501 TTCTTTTC---TT
1 TTCTTTTCTTTTT
401511 TTCTTTTCTTTTT
1 TTCTTTTCTTTTT
401524 TATCTTTTCTTTTT
1 T-TCTTTTCTTTTT
*
401538 TCTTTTTTCTTCTTT
1 T-TCTTTTCTT-TTT
*
401553 TTCTTTTTAATTTTT
1 TTC-TTTT-CTTTTT
*
401568 TATATTTGTCTTTTT
1 T-TCTTT-TCTTTTT
401583 TT-TTCTTCTTTTT
1 TTCTT-TTCTTTTT
401596 TT
1 TT
401598 TCCTTTTTTT
Statistics
Matches: 89, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
10 9 0.10
13 21 0.24
14 34 0.38
15 21 0.24
16 4 0.04
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (13 bp):
TTCTTTTCTTTTT
Found at i:401524 original size:37 final size:36
Alignment explanation
Indices: 401459--401614 Score: 124
Period size: 37 Copynumber: 4.2 Consensus size: 36
401449 ATTTTATTTA
* *
401459 TTTTTCTTCTTATTCTTCTTTTCCTTTTTTGT-TCTTCT
1 TTTTTCTT-TT-TTCTTCTTTT-CTTTTTTATCTTTTCT
401497 TTCTTTCTTTTCTT-TTCTTTTCTTTTTTATCTTTTCT
1 TT-TTTCTTTT-TTCTTCTTTTCTTTTTTATCTTTTCT
* * *
401534 TTTTTCTTTTTTCTTCTTTTTCTTTTTAATTTTTTAT
1 TTTTTCTTTTTTCTTC-TTTTCTTTTTTATCTTTTCT
* * *
401571 ATTTGTCTTTTTTTTTCTTCTT-TTTTTT-CCTTTT-T
1 -TTTTTCTTTTTTCTTCTT-TTCTTTTTTATCTTTTCT
401606 TTTCTTCTT
1 TTT-TTCTT
401615 CAGGCAAAGT
Statistics
Matches: 99, Mismatches: 12, Indels: 17
0.77 0.09 0.13
Matches are distributed among these distances:
34 3 0.03
35 7 0.07
36 23 0.23
37 38 0.38
38 22 0.22
39 6 0.06
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (36 bp):
TTTTTCTTTTTTCTTCTTTTCTTTTTTATCTTTTCT
Found at i:401538 original size:51 final size:48
Alignment explanation
Indices: 401475--401611 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 48
401465 TTCTTATTCT
**
401475 TCTTTTCCTTTTTTGTTCTTCTTTCTTTCTTTTCTTTTCTTTTCTTTTTTA
1 TCTTTT-CTTTTTT-TTCTTCTTTCTTTCTTTT-TTTTCTTTAATTTTTTA
* *
401526 TCTTTTC--TTTTTTCTTTTTTC-TTCTTTTTCTT-TTTAATTTTTTA
1 TCTTTTCTTTTTTTTCTTCTTTCTTTCTTTTTTTTCTTTAATTTTTTA
* *
401570 TATTTGTCTTTTTTTTTCTTCTTTTTTTTCCTTTTTTTTCTT
1 TCTTT-TC-TTTTTTTTCTTC-TTTCTTT-CTTTTTTTTCTT
401612 CTTCAGGCAA
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
44 14 0.20
45 5 0.07
46 7 0.10
47 9 0.13
48 13 0.19
49 3 0.04
50 3 0.04
51 14 0.20
52 2 0.03
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.79
Consensus pattern (48 bp):
TCTTTTCTTTTTTTTCTTCTTTCTTTCTTTTTTTTCTTTAATTTTTTA
Found at i:401541 original size:44 final size:43
Alignment explanation
Indices: 401493--401608 Score: 132
Period size: 44 Copynumber: 2.7 Consensus size: 43
401483 TTTTTTGTTC
*
401493 TTCTTTCTTTCTTTTCTTTTCTTTTCTTTTTTATCTTT-TCTTTT
1 TTCTTTCTTTCTTTT-TTTTCTTTT-TTTTTTATATTTGTCTTTT
*
401537 TTCTTT-TTTCTTCTTTTTCTTTTTAATTTTTTATATTTGTCTTTT
1 TTCTTTCTTTCTTTTTTTTC-TTTT--TTTTTTATATTTGTCTTTT
*
401582 TT-TTTC-TTCTTTTTTTTCCTTTTTTTT
1 TTCTTTCTTTCTTTTTTTTCTTTTTTTTT
401609 CTTCTTCAGG
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
41 5 0.08
42 5 0.08
43 14 0.22
44 31 0.49
45 8 0.13
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.80
Consensus pattern (43 bp):
TTCTTTCTTTCTTTTTTTTCTTTTTTTTTTATATTTGTCTTTT
Found at i:401551 original size:22 final size:22
Alignment explanation
Indices: 401459--401614 Score: 87
Period size: 21 Copynumber: 7.0 Consensus size: 22
401449 ATTTTATTTA
401459 TTTTTCTTCTTATTCTTCTTTTCCT
1 TTTTTCTTCTT-TTCTT-TTTT-CT
*
401484 TTTTTGTTC--TTCTTTCTTTCT
1 TTTTTCTTCTTTTCTTT-TTTCT
*
401505 TTTCTT-TTCTTTTCTTTTTTAT
1 TTT-TTCTTCTTTTCTTTTTTCT
*
401527 CTTTTCTT-TTTTCTTTTTTCTT
1 TTTTTCTTCTTTTCTTTTTTC-T
** *
401549 CTTTTTCTT-TTTAATTTTTTAT
1 -TTTTTCTTCTTTTCTTTTTTCT
* *
401571 ATTTGTCTT-TTTT-TTTCTTCT
1 -TTTTTCTTCTTTTCTTTTTTCT
401592 TTTTT-TTCCTTTT-TTTTCTTCT
1 TTTTTCTT-CTTTTCTTTT-TTCT
401614 T
1 T
401615 CAGGCAAAGT
Statistics
Matches: 106, Mismatches: 15, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
19 2 0.02
20 4 0.04
21 35 0.33
22 35 0.33
23 22 0.21
25 8 0.08
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (22 bp):
TTTTTCTTCTTTTCTTTTTTCT
Found at i:401608 original size:14 final size:13
Alignment explanation
Indices: 401500--401598 Score: 81
Period size: 15 Copynumber: 6.9 Consensus size: 13
401490 TTCTTCTTTC
401500 TTTCTTTTCTTTTCT
1 TTTCTTTT-TTTT-T
*
401515 TTTCTTTTTTATCT
1 TTTCTTTTTT-TTT
401529 TTTCTTTTTTCTTT
1 TTTCTTTTTT-TTT
401543 TTTCTTCTTTTTCTT
1 TTTCTT-TTTTT-TT
*
401558 TTTAATTTTTTATATT
1 TTT-CTTTTTT-T-TT
*
401574 TGTCTTTTTTTTT
1 TTTCTTTTTTTTT
*
401587 CTTCTTTTTTTT
1 TTTCTTTTTTTT
401599 CCTTTTTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
13 12 0.17
14 23 0.33
15 28 0.40
16 7 0.10
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.81
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:403008 original size:31 final size:32
Alignment explanation
Indices: 402972--403060 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 32
402962 GTTATCATTA
402972 AATGCGTACAATTAAATCAAAATTAAAATTTT
1 AATGCGTACAATTAAATCAAAATTAAAATTTT
* * * * *
403004 -ATGCGTACAGTTTAATCATAATCAGAATTTT
1 AATGCGTACAATTAAATCAAAATTAAAATTTT
* * *
403035 AATGTGTACAACTAAAT-TAAATTAAA
1 AATGCGTACAATTAAATCAAAATTAAA
403061 GTTTCATACA
Statistics
Matches: 43, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
31 31 0.72
32 12 0.28
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (32 bp):
AATGCGTACAATTAAATCAAAATTAAAATTTT
Found at i:408287 original size:133 final size:133
Alignment explanation
Indices: 407957--408564 Score: 757
Period size: 133 Copynumber: 4.6 Consensus size: 133
407947 TAGAGAAATG
* * ** *
407957 TTGATTCA-TTCCACTGTTCTTCAGGGAAGATTCAATCGGAATCGATTTGCTTCACTGCTCTTCG
1 TTGATTCACTT-CACTGCTCTTCAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCA
* * * * *
408021 GGAATACCAAATTTGAAAGAAGAAAAATATGCTCCACTACTCTTTAGGGGAGATCAAACTCAAGA
65 GGAAGACCAAATCTGAAAGAAGAAGAATATGATCCACTACTCTTTAGGGGAGATCAAACTCGAGA
408086 AAAC
130 AAAC
* * *
408090 TTTGATCCACTTTACTGCTCTTCAGGGAAGATTGAAT-AAGAATCGATTTGCTTTACTGCTCTTC
1 -TTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAA-AATCGATTTGCTTCACTGCTCTTC
* * * *
408154 AGGAAGACCAAATCTGAAAGAAGAAGAATCTGAACCACTACTCTTTAGGGGAGATCAGATTCGAG
64 AGGAAGACCAAATCTGAAAGAAGAAGAATATGATCCACTACTCTTTAGGGGAGATCAAACTCGAG
408219 AAAAC
129 AAAAC
* *
408224 TTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAAAATTGATTTGATTCACTGCTCTTCAG
1 TTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCAG
* *
408289 GAAGACCAAATCTAAAAGAAGAAGAATCT-ACTCCACTACTCTTTAGGGGAGATCAAACTCGAGA
66 GAAGACCAAATCTGAAAGAAGAAGAATATGA-TCCACTACTCTTTAGGGGAGATCAAACTCGAGA
408353 AAAC
130 AAAC
* * * *
408357 TTGATTCACTTC-GTCGCTCTTCAGGGAAGATTGAATCATAATCGATTTGCTTCACTTCTCTTTA
1 TTGATTCACTTCACT-GCTCTTCAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCA
* * *
408421 GGAAGACCAAATCTTAAAGAA-AGAGAATATGCT-CA-TACTCTTTAGGGGAGATCAGACT-GAA
65 GGAAGACCAAATCTGAAAGAAGA-AGAATATGATCCACTACTCTTTAGGGGAGATCAAACTCG-A
*
408482 GAAAATT
128 GAAAA-C
* * * * *
408489 TTGATCCACTTCTCTGCTCTTGAAGGAAGATTGAATCGAACAT-GATTTGCTTCACTGCTCTTCA
1 TTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATC-AAAATCGATTTGCTTCACTGCTCTTCA
*
408553 AGAAGACCAAAT
65 GGAAGACCAAAT
408565 ATGCTCCACT
Statistics
Matches: 417, Mismatches: 46, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
130 1 0.00
131 28 0.07
132 66 0.16
133 206 0.49
134 114 0.27
135 2 0.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (133 bp):
TTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCAG
GAAGACCAAATCTGAAAGAAGAAGAATATGATCCACTACTCTTTAGGGGAGATCAAACTCGAGAA
AAC
Found at i:409365 original size:14 final size:14
Alignment explanation
Indices: 409348--409392 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
409338 ACAATCTCTA
409348 AAATATAAAGAAAT
1 AAATATAAAGAAAT
*
409362 AAATTTAAAGACAA-
1 AAATATAAAGA-AAT
*
409376 AATTATAAAGAAAT
1 AAATATAAAGAAAT
409390 AAA
1 AAA
409393 GTAATTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 2 0.08
14 21 0.84
15 2 0.08
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (14 bp):
AAATATAAAGAAAT
Found at i:410985 original size:53 final size:52
Alignment explanation
Indices: 410897--411010 Score: 158
Period size: 53 Copynumber: 2.2 Consensus size: 52
410887 TTTTTTTATT
* * * *
410897 ATTTTTTTAACATTTCCGGTAAAAAATTACCTAAAACATTATTATTTCTACC-
1 ATTTTGTTAACATATCCGATAAAAAACTACCTAAAACATTATT-TTTCTACCG
*
410949 AGTTTTGTTAACATATCCGATAAAGAACTACCTAAAACATTATTTTTCTACCG
1 A-TTTTGTTAACATATCCGATAAAAAACTACCTAAAACATTATTTTTCTACCG
411002 ATTTTGTTA
1 ATTTTGTTA
411011 TTATTGGGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
52 17 0.31
53 38 0.69
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (52 bp):
ATTTTGTTAACATATCCGATAAAAAACTACCTAAAACATTATTTTTCTACCG
Found at i:411302 original size:3 final size:3
Alignment explanation
Indices: 411294--411372 Score: 51
Period size: 3 Copynumber: 27.0 Consensus size: 3
411284 TTTTGTATAT
* * * *
411294 ATA ATA ATA AGT- ATA TTA ATT ATA ATA ACTA A-A A-A ATG GTA AATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA A-TA
*
411339 ATA ATA ATA ATA ATA ATA A-A ATT AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
411373 TACTAATTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
2 9 0.15
3 44 0.73
4 7 0.12
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:411697 original size:18 final size:17
Alignment explanation
Indices: 411669--411711 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
411659 TTAATGAATT
*
411669 TTAAGATTTTATATTTGA
1 TTAA-ATTTTATATTCGA
411687 TTCAAATTTTATATTCGA
1 TT-AAATTTTATATTCGA
411705 TTAAATT
1 TTAAATT
411712 AGTCGAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 16 0.70
19 2 0.09
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (17 bp):
TTAAATTTTATATTCGA
Found at i:411986 original size:24 final size:23
Alignment explanation
Indices: 411940--412016 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 23
411930 TACCCTACAC
* **
411940 AGTATCGATACCATTATACATAGT
1 AGTACCGATACCATGGT-CATAGT
* *
411964 AGTACTGATACCATGTTCA-A-T
1 AGTACCGATACCATGGTCATAGT
411985 AGTACCGATACCATGGTCA-A-T
1 AGTACCGATACCATGGTCATAGT
412006 AGTACCGATAC
1 AGTACCGATAC
412017 TACCCTTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 31 0.66
22 1 0.02
23 2 0.04
24 13 0.28
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (23 bp):
AGTACCGATACCATGGTCATAGT
Found at i:412264 original size:45 final size:45
Alignment explanation
Indices: 412215--412542 Score: 321
Period size: 45 Copynumber: 7.7 Consensus size: 45
412205 AAAGAATGAA
* *
412215 TTCTCTTCGCGAGAAAGTCAAGAATAACAATAATGAACGATTAAC
1 TTCTCTTCACGAGAAAGTCAAGAATAACAATATTGAACGATTAAC
* ** * * * * * *
412260 TTCTCTTAATAAGAAAGTAAATAATGACAATACTGAATGATTGAC
1 TTCTCTTCACGAGAAAGTCAAGAATAACAATATTGAACGATTAAC
*
412305 TTCTCTTCACGATAAAGTCAAGAATAACAATATTGAACGATTAAC
1 TTCTCTTCACGAGAAAGTCAAGAATAACAATATTGAACGATTAAC
*
412350 TTCTCTTCACGAGAAATTCAAGAATAACAATATTGAACGATTAAC
1 TTCTCTTCACGAGAAAGTCAAGAATAACAATATTGAACGATTAAC
* * *
412395 TTCTCTTCACGAGAAATTCAAGAATAAC---ATTGAAAGATTGAC
1 TTCTCTTCACGAGAAAGTCAAGAATAACAATATTGAACGATTAAC
* ** *
412437 TCCTCTTCACGAGGGAGTCAAGAATAAC---A---AA-GATTGAC
1 TTCTCTTCACGAGAAAGTCAAGAATAACAATATTGAACGATTAAC
* * *
412475 TTCTTTTCATGAGGAAGTCAAGAATAAC---A---AA-GATTAAC
1 TTCTCTTCACGAGAAAGTCAAGAATAACAATATTGAACGATTAAC
*
412513 TTCTCTTCACGAGGAAGTCAAGAATAACAA
1 TTCTCTTCACGAGAAAGTCAAGAATAACAA
412543 AGATTGAATT
Statistics
Matches: 246, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
38 66 0.27
39 2 0.01
42 37 0.15
45 141 0.57
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (45 bp):
TTCTCTTCACGAGAAAGTCAAGAATAACAATATTGAACGATTAAC
Found at i:412494 original size:38 final size:38
Alignment explanation
Indices: 412388--413005 Score: 653
Period size: 38 Copynumber: 15.9 Consensus size: 38
412378 AATATTGAAC
* * * *
412388 GATTAACTTCTCTTCACGAGAAATTCAAGAATAACATTGAAA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAAC----AAA
* * *
412430 GATTGACTCCTCTTCACGAGGGAGTCAAGAATAACAAA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAA
*
412468 GATTGACTTCTTTTCATGAGGAAGTCAAGAATAACAAA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAA
* *
412506 GATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAAA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAA
* * * *
412544 GATTGAATTCTCTTCTTGAGGAAGTCAAAAATATCAAA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAA
* * * * **
412582 GATTGAATTCTCTTCATGAGGAAGTCATGGATAATATT
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAA
* * * *
412620 GATCGACCTCTCTTCATGATGAAGTGAAGAATAACAAA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAA
* * * *
412658 GATTGACTTCTCTTTACGAGGAAGTCAAAAATGATAATGAAA
1 GATTGACTTCTCTTCATGAGGAAGTC-AAGA--ATAA-CAAA
* * * * *
412700 GATTAACTCCTCTTCACGAGGGAGCCAAGAATAACAAA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAA
**
412738 GATTGACTTCTCTTCACAAGGAAGTCAAGAATAACAAA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAA
*
412776 TATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATTTAAA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAAC----AAA
* * * *
412818 GATTGAATCCTCTTCATGA-TAGAGTCAATAATAACAAA
1 GATTGACTTCTCTTCATGAGGA-AGTCAAGAATAACAAA
* * * * *
412856 GATCGACTTCTCTTTATGAGGAAGTTACGAATAAAAAA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAA
*
412894 GATTGATTTCTCTTCATGAGGAAGTCAAGAATAACAAA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAA
* * *
412932 TATTGACTTCTCTTCACGAGGAAGTCAAGAATGACAAA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAA
* *
412970 GATCGACTTCTCTTCACGAGGAAGTCAAGAATAACA
1 GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACA
413006 TTGAAAGATT
Statistics
Matches: 480, Mismatches: 86, Indels: 24
0.81 0.15 0.04
Matches are distributed among these distances:
38 379 0.79
39 8 0.02
41 8 0.02
42 85 0.18
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (38 bp):
GATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAA
Found at i:413039 original size:194 final size:193
Alignment explanation
Indices: 412388--413040 Score: 803
Period size: 194 Copynumber: 3.4 Consensus size: 193
412378 AATATTGAAC
* * * *
412388 GATTAACTTCTCTTCACGAGAAATTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACCCCTCTTCACGAGGGA
*
412453 GTCAAGAATAACAAAGATTGACTTCT-TTTCATGAGGAAGTCAAGAATAACAAAGATTAACTTCT
66 GTCAAGAATAACAAAGATTGACTTCTCTTT-ATGAGGAAGTCAAGAATAAAAAAGATTAACTTCT
* ** *
412517 CTTCACGAGGAAGTCAAGAATAACAAAGATTGAATTCTCTTCTTGAGGAAGTCAAAAATATCAAA
130 CTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATA-CAAA
* * * * * * * * * *
412582 GATTGAATTCTCTTCATGAGGAAGTCATGGATAATATT----GATCGACCTCTCTTCATGATGAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACCCCTCTTCACGAGGGA
* * *
412643 GTGAAGAATAACAAAGATTGACTTCTCTTTACGAGGAAGTCAAAAATGATAATGAAAGATTAACT
66 GTCAAGAATAACAAAGATTGACTTCTCTTTATGAGGAAGTCAAGAAT-A-AA--AAAGATTAACT
* * * *
412708 CCTCTTCACGAGGGAGCCAAGAATAACAAAGATTGACTTCTCTTCACAAGGAAGTCAAGAATAAC
127 TCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-AC
412773 AAA
191 AAA
* * * ** * **
412776 TATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATTTAAAGATTGAATCCTCTTCATGATAGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACCCCTCTTCACGAGGGA
* * * * * *
412841 GTCAATAATAACAAAGATCGACTTCTCTTTATGAGGAAGTTACGAATAAAAAAGATTGATTTCTC
66 GTCAAGAATAACAAAGATTGACTTCTCTTTATGAGGAAGTCAAGAATAAAAAAGATTAACTTCTC
* *
412906 TTCATGAGGAAGTCAAGAATAACAAATATTGACTTCTCTTCACGAGGAAGTCAAGAATGACAAA
131 TTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-ACAAA
* *
412970 GATCGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACCCCTCTTCGCGAGGGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACCCCTCTTCACGAGGGA
413035 GTCAAG
66 GTCAAG
413041 TTGAAGCTTC
Statistics
Matches: 385, Mismatches: 64, Indels: 20
0.82 0.14 0.04
Matches are distributed among these distances:
190 57 0.15
191 4 0.01
192 1 0.00
194 262 0.68
195 1 0.00
196 2 0.01
197 1 0.00
198 57 0.15
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (193 bp):
GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACCCCTCTTCACGAGGGA
GTCAAGAATAACAAAGATTGACTTCTCTTTATGAGGAAGTCAAGAATAAAAAAGATTAACTTCTC
TTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATACAAA
Found at i:415218 original size:9 final size:9
Alignment explanation
Indices: 415206--415268 Score: 64
Period size: 9 Copynumber: 7.6 Consensus size: 9
415196 ATTTGATTTA
415206 TTTTTTCTC
1 TTTTTTCTC
415215 --TTTTCTC
1 TTTTTTCTC
*
415222 TTTTTTTTC
1 TTTTTTCTC
415231 -TTTTTCTC
1 TTTTTTCTC
*
415239 TCTTTT-TC
1 TTTTTTCTC
*
415247 -TTTTTCTA
1 TTTTTTCTC
415255 TTTTTTCTC
1 TTTTTTCTC
415264 TTTTT
1 TTTTT
415269 CTTAATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
7 11 0.26
8 10 0.23
9 22 0.51
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:415227 original size:16 final size:16
Alignment explanation
Indices: 415206--415271 Score: 82
Period size: 16 Copynumber: 4.1 Consensus size: 16
415196 ATTTGATTTA
415206 TTTTTTCTCTTTTCTC
1 TTTTTTCTCTTTTCTC
*
415222 TTTTTTTTCTTTTTCTC
1 TTTTTTCTC-TTTTCTC
*
415239 TCTTTTTCT-TTTTCTA
1 T-TTTTTCTCTTTTCTC
415255 TTTTTTCTCTTTT-TC
1 TTTTTTCTCTTTTCTC
415270 TT
1 TT
415272 AATTTTTTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
15 10 0.23
16 19 0.44
17 8 0.19
18 6 0.14
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTCTCTTTTCTC
Found at i:415228 original size:17 final size:17
Alignment explanation
Indices: 415206--415297 Score: 79
Period size: 17 Copynumber: 5.6 Consensus size: 17
415196 ATTTGATTTA
415206 TTTTTTCTCTTTTCTCT
1 TTTTTTCTCTTTTCTCT
415223 TTTTTT-TCTTTTTCTCT
1 TTTTTTCTC-TTTTCTCT
* *
415240 CTTTTTCT-TTTTCT-A
1 TTTTTTCTCTTTTCTCT
415255 TTTTTTCTCTTTT-TCT
1 TTTTTTCTCTTTTCTCT
*
415271 TAATTTTT-TCTTCT-TCT
1 T--TTTTTCTCTTTTCTCT
*
415288 TTTTATCTCT
1 TTTTTTCTCT
415298 ATATTTTTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
15 12 0.19
16 16 0.26
17 28 0.45
18 6 0.10
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTCTCTTTTCTCT
Found at i:415259 original size:33 final size:34
Alignment explanation
Indices: 415207--415270 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
415197 TTTGATTTAT
* *
415207 TTTTTCTCTTTTCTCTTTTTTTTCTTTTTCTCTC
1 TTTTTCTCTTTTCTATTTTTTCTCTTTTTCTCTC
415241 TTTTTCT-TTTTCTATTTTTTCTCTTTTTCT
1 TTTTTCTCTTTTCTATTTTTTCTCTTTTTCT
415271 TAATTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (34 bp):
TTTTTCTCTTTTCTATTTTTTCTCTTTTTCTCTC
Found at i:415278 original size:33 final size:33
Alignment explanation
Indices: 415204--415297 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 33
415194 ATATTTGATT
*
415204 TATTTTTTCTCTTTTCTCTTTTTTTTCTTTTTCTC
1 TATTTTTTCT-TTTTCT-TTTTTTCTCTTTTTCTC
*
415239 T-CTTTTTCTTTTTCTATTTTTTCTCTTTTTCT-
1 TATTTTTTCTTTTTCT-TTTTTTCTCTTTTTCTC
* *
415271 TAATTTTTTCTTCTTCTTTTTATCTCT
1 T-ATTTTTTCTTTTTCTTTTTTTCTCT
415298 ATATTTTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
32 1 0.02
33 30 0.59
34 19 0.37
35 1 0.02
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (33 bp):
TATTTTTTCTTTTTCTTTTTTTCTCTTTTTCTC
Found at i:415287 original size:25 final size:23
Alignment explanation
Indices: 415208--415295 Score: 74
Period size: 25 Copynumber: 3.7 Consensus size: 23
415198 TTGATTTATT
*
415208 TTTTCTCTTTTCTCTTTTTTTTC
1 TTTTCTCTTTTATCTTTTTTTTC
*
415231 TTTTTCTCTCTTTTTCTTTTTCTATT-
1 -TTTTCTCT-TTTATCTTTTT-T-TTC
415257 TTTTCTCTTTT-TCTTAATTTTTTC
1 TTTTCTCTTTTATCTT--TTTTTTC
415281 TTCTTCT-TTTTATCT
1 TT-TTCTCTTTTATCT
415296 CTATATTTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
23 6 0.11
24 18 0.33
25 28 0.51
26 1 0.02
27 2 0.04
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTCTCTTTTATCTTTTTTTTC
Found at i:419767 original size:24 final size:24
Alignment explanation
Indices: 419739--419811 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
419729 AAAAGTGTAT
419739 TGGTAAAATAAGCTTACGAGATTA
1 TGGTAAAATAAGCTTACGAGATTA
* * *
419763 TGGTAAAA-ATG-GTA--AGTATTT
1 TGGTAAAATAAGCTTACGAG-ATTA
*
419784 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTACGAGATTA
419808 TGGT
1 TGGT
419812 TAATAAATGG
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
20 2 0.05
21 11 0.30
22 4 0.11
23 4 0.11
24 14 0.38
25 2 0.05
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (24 bp):
TGGTAAAATAAGCTTACGAGATTA
Found at i:424516 original size:3 final size:3
Alignment explanation
Indices: 424503--424535 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
424493 AAATAAACGT
*
424503 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
424536 CGGGTCTCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:424594 original size:14 final size:13
Alignment explanation
Indices: 424573--424614 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
424563 ACAATTTTTA
424573 AAATTAATATTAT
1 AAATTAATATTAT
*
424586 AAATATAATAATA-
1 AAAT-TAATATTAT
*
424599 AAATTATTATTAT
1 AAATTAATATTAT
424612 AAA
1 AAA
424615 AATAGTAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 6 0.25
13 11 0.46
14 7 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTAATATTAT
Found at i:425746 original size:86 final size:87
Alignment explanation
Indices: 425649--425817 Score: 268
Period size: 86 Copynumber: 2.0 Consensus size: 87
425639 AAGTAATGTT
* * * *
425649 TATATGTATTTTAATATTTTATAACACCAGCCCCATTGAATTCAATTAAGAGTACTAGAAGAAAA
1 TATATGAATTTTAATATTTTATAACACCACCCCCATTGAATTAAATTAAGAATACTAGAAGAAAA
*
425714 T-GTGTTTTCTTTATAAATCTA
66 TGGGGTTTTCTTTATAAATCTA
* *
425735 TATATGAATTTTAATATTTTATAACACCACCCCCGTTGAATTAAATTAAGAATACTAGAAGAAAC
1 TATATGAATTTTAATATTTTATAACACCACCCCCATTGAATTAAATTAAGAATACTAGAAGAAAA
425800 TGGGGTTTTCTTTATAAA
66 TGGGGTTTTCTTTATAAA
425818 AATTAGTTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
86 60 0.80
87 15 0.20
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (87 bp):
TATATGAATTTTAATATTTTATAACACCACCCCCATTGAATTAAATTAAGAATACTAGAAGAAAA
TGGGGTTTTCTTTATAAATCTA
Found at i:430827 original size:15 final size:16
Alignment explanation
Indices: 430807--430836 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
430797 CTTAATAGAA
430807 AAAAATAT-TTTATAT
1 AAAAATATATTTATAT
430822 AAAAATATATTTATA
1 AAAAATATATTTATA
430837 ACAATACATT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAAATATATTTATAT
Found at i:430831 original size:17 final size:18
Alignment explanation
Indices: 430790--430833 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
430780 TTTATCACAT
430790 ATATATTCTTAATAGAAAA
1 ATATATT-TTAATAGAAAA
* *
430809 AAATATTTT-ATATAAAA
1 ATATATTTTAATAGAAAA
430826 ATATATTT
1 ATATATTT
430834 ATAACAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 2 0.09
19 6 0.27
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
ATATATTTTAATAGAAAA
Found at i:441626 original size:54 final size:54
Alignment explanation
Indices: 441554--442250 Score: 1015
Period size: 54 Copynumber: 12.9 Consensus size: 54
441544 GTATACCCAA
* * * * * * *
441554 TGCCAATATGGAAGTTCATAAACTTCTTATGAATTTCTTAGGTTGCACATACAT
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* * * * *
441608 TACCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGAACACAGAA
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* *
441662 TGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTTCACACACAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* *
441716 TG-CAATAC-ATAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* * *
441768 TGGCAATACAAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAA
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* * *
441822 TGCCAATACAAAAATTCATAAACTTATTATGAATTTCTTAAGTTGTACACATAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* *
441876 TGCCAATAC-ATAAATTCATAAACTTATTATGAATTTATTAAGTTGTACACACAG
1 TGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
*
441930 TGGCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* * *
441984 TTCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACATACAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* *
442038 TGCCAATACAAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAT
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
442092 TGCCAATAC-AGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
1 TGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* * * *
442146 TGCCAATACGAAAATTCATAAACTTATTACGAATTTCTTAAGTTGCATAAACAA
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* * *
442200 TGCCAATATGGAAATTCTTAAACTTATTATGAATTTCTTAAGTTGCACACA
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACA
442251 TAGTACCCAT
Statistics
Matches: 583, Mismatches: 54, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
52 42 0.07
53 14 0.02
54 525 0.90
55 2 0.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (54 bp):
TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
Found at i:443415 original size:18 final size:18
Alignment explanation
Indices: 443378--443411 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
443368 TTTTAAGATT
*
443378 TTATATTTTATTCAAATA
1 TTATATTTGATTCAAATA
443396 TTATATTTGATT-AAAT
1 TTATATTTGATTCAAAT
443412 TATTCGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TTATATTTGATTCAAATA
Found at i:448213 original size:15 final size:15
Alignment explanation
Indices: 448193--448222 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
448183 GCACATTGAA
448193 ATTAGACATCATTTC
1 ATTAGACATCATTTC
*
448208 ATTAGAGATCATTTC
1 ATTAGACATCATTTC
448223 TCAAAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (15 bp):
ATTAGACATCATTTC
Found at i:451331 original size:7 final size:6
Alignment explanation
Indices: 451312--451351 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
451302 GTGCTGCAAC
* *
451312 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG CAAAAG AAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAA
451352 GGACTCCTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:451333 original size:13 final size:13
Alignment explanation
Indices: 451315--451352 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
451305 CTGCAACAAA
451315 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
*
451328 AAGAAAAACAAA-
1 AAGAAAAAGAAAG
*
451340 AAGCAAAAGAAAG
1 AAGAAAAAGAAAG
451353 GACTCCTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAG
Found at i:462956 original size:22 final size:22
Alignment explanation
Indices: 462931--462987 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
462921 ATTCTATGCA
462931 CTTAGTATCGATACT-TTTCTTG
1 CTTAGTATCGATACTATTTC-TG
462953 CTTAGTATCGATACTATTTCTG
1 CTTAGTATCGATACTATTTCTG
462975 CTTAGTATCGATA
1 CTTAGTATCGATA
462988 TTGTTCATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 30 0.88
23 4 0.12
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.46
Consensus pattern (22 bp):
CTTAGTATCGATACTATTTCTG
Found at i:470695 original size:54 final size:54
Alignment explanation
Indices: 470586--470859 Score: 363
Period size: 54 Copynumber: 4.9 Consensus size: 54
470576 GCATACCCAA
* * *
470586 TGCCAATACGAAAATTCATAAACTT-TTATGAATTTTTTAGGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* * *
470639 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTATGTTTCACACACAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
**
470693 TGCCAATATAAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACAGTTGCACAAACAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTG--CA----CAC--ACAG
*
470755 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
*
470809 TGCCAATACAAAAATTCATAAA-TATATTATGAATTTCTTAAGTTGCACACA
1 TGCCAATACGAAAATTCATAAACT-TATTATGAATTTCTTAAGTTGCACACA
470860 TAGTTCCCAT
Statistics
Matches: 197, Mismatches: 14, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
53 25 0.13
54 115 0.58
56 5 0.03
60 5 0.03
62 47 0.24
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.34
Consensus pattern (54 bp):
TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
Found at i:470830 original size:116 final size:116
Alignment explanation
Indices: 470626--470857 Score: 385
Period size: 116 Copynumber: 2.0 Consensus size: 116
470616 AATTTTTTAG
* * * *
470626 GTTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTATGTTTCACACAC
1 GTTGCACAAACAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
*
470691 AGTGCCAATATAAAAATTCATAAACT-TATTATGAATTTCTTAAGTTGCACA
66 AGTGCCAATACAAAAATTCATAAA-TATATTATGAATTTCTTAAGTTGCACA
* *
470742 GTTGCACAAACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAT
1 GTTGCACAAACAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
470807 AGTGCCAATACAAAAATTCATAAATATATTATGAATTTCTTAAGTTGCACA
66 AGTGCCAATACAAAAATTCATAAATATATTATGAATTTCTTAAGTTGCACA
470858 CATAGTTCCC
Statistics
Matches: 108, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
115 1 0.01
116 107 0.99
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (116 bp):
GTTGCACAAACAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
AGTGCCAATACAAAAATTCATAAATATATTATGAATTTCTTAAGTTGCACA
Found at i:471306 original size:32 final size:33
Alignment explanation
Indices: 471249--471321 Score: 121
Period size: 32 Copynumber: 2.2 Consensus size: 33
471239 TTGCCTTTCA
**
471249 GTATCAATACCATTTCTATATTATGGATCCATG
1 GTATCAATACCAAATCTATATTATGGATCCATG
471282 GTATCAATACCAAAT-TATATTATGGATCCATG
1 GTATCAATACCAAATCTATATTATGGATCCATG
471314 GTATCAAT
1 GTATCAAT
471322 TCCTTCTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 25 0.66
33 13 0.34
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (33 bp):
GTATCAATACCAAATCTATATTATGGATCCATG
Found at i:471785 original size:18 final size:18
Alignment explanation
Indices: 471762--471802 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
471752 TTTTTCTTCA
471762 ATCTCAAAGAATTCATCC
1 ATCTCAAAGAATTCATCC
471780 ATCTCAAAGAATTCATCC
1 ATCTCAAAGAATTCATCC
471798 ATCTC
1 ATCTC
471803 TTACTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (18 bp):
ATCTCAAAGAATTCATCC
Found at i:476595 original size:54 final size:54
Alignment explanation
Indices: 476526--476745 Score: 307
Period size: 54 Copynumber: 4.1 Consensus size: 54
476516 GCATACCCAA
* * * * *
476526 TGCCAATATGGAAATTCACAAACTTCTTATGAATTTCTTAGGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAG
* * * * *
476580 TGCCAATACGAAAATTCTTAAACTCATTCTGAATTTCTTCAGTTACACACATAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAG
*
476634 TGCCAATAC-AGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
1 TGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAG
* *
476688 TGCCAATACGAAAATTAATTAACTTATTATGAATTTCTTAAGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAG
476742 TGCC
1 TGCC
476746 CATTCGGTAA
Statistics
Matches: 145, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
53 1 0.01
54 143 0.99
55 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (54 bp):
TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAG
Found at i:476865 original size:54 final size:54
Alignment explanation
Indices: 476778--477104 Score: 530
Period size: 54 Copynumber: 6.1 Consensus size: 54
476768 GCATACCCAA
* * *
476778 TGCCAATACGAAAATTCATAAACTTCTTATGAATTTCTTAGGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* * * *
476832 TGCTAATACGGAAATTCATAAACTCATTTTGAATTTCTTAAGTTGCACACACAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
*
476886 TGCCAATACGAAAATTCATAAACTTGTTATGAATTTCTTAAGTTGCACACACAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
*
476940 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACAAACAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* * *
476994 TGCCAATACGGAAATTGATATACTTATTATGAATTTCTTAAGTTGCACACACAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
*
477048 TGCCAA-ACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
477101 TGCC
1 TGCC
477105 CATTCGATAA
Statistics
Matches: 251, Mismatches: 22, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
53 47 0.19
54 204 0.81
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (54 bp):
TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
Found at i:476918 original size:198 final size:198
Alignment explanation
Indices: 476580--476943 Score: 597
Period size: 198 Copynumber: 1.8 Consensus size: 198
476570 GCACACATAG
* *
476580 TGCCAATACGAAAATTCTTAAACTCATTCTGAATTTCTTCAGTTACACACATAGTGCCAATACAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTCAGTTACACACATAGTGCCAATACAG
* *
476645 AAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTAATTAA
66 AAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTAATAAA
*
476710 CTTATTATGAATTTCTTAAGTTGCACACATAGTGCCCATTCGGTAATTACTTGGGGATGCATACC
131 CTTATTATGAATTTCTTAAGTTGCACACACAGTGCCCATTCGGTAATTACTTGGGGATGCATACC
476775 CAA
196 CAA
* *
476778 TGCCAATACGAAAATTCATAAACTTC-TTATGAATTTCTT-AGGTTGCACACATAGTGCTAATAC
1 TGCCAATACGAAAATTCATAAAC-TCATTATGAATTTCTTCA-GTTACACACATAGTGCCAATAC
* * *
476841 GGAAATTCATAAACTCATTTTGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTCATA
64 AGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTAATA
*
476906 AACTTGTTATGAATTTCTTAAGTTGCACACACAGTGCC
129 AACTTATTATGAATTTCTTAAGTTGCACACACAGTGCC
476944 AATACGAAAA
Statistics
Matches: 153, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
197 1 0.01
198 150 0.98
199 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (198 bp):
TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTCAGTTACACACATAGTGCCAATACAG
AAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTAATAAA
CTTATTATGAATTTCTTAAGTTGCACACACAGTGCCCATTCGGTAATTACTTGGGGATGCATACC
CAA
Found at i:476947 original size:252 final size:252
Alignment explanation
Indices: 476502--476997 Score: 841
Period size: 252 Copynumber: 2.0 Consensus size: 252
476492 CCTCATTAGG
* *
476502 AATTACTTGGGGATGCATACCCAATGCCAATATGGAAATTCACAAACTTCTTATGAATTTCTTAG
1 AATTACTTGGGGATGCATACCCAATGCCAATACGAAAATTCACAAACTTCTTATGAATTTCTTAG
* * *
476567 GTTGCACACATAGTGCCAATACGAAAATTCTTAAACTCATTCTGAATTTCTTCAGTTACACACAT
66 GTTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTCTGAATTTCTTAAGTTACACACAC
476632 AGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
131 AGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
* * *
476697 GAAAATTAATTAACTTATTATGAATTTCTTAAGTTGCACACATAGTGCCCATTCGGT
196 GAAAATTAATAAACTTATTATGAATTTCTTAAGTTGCACAAACAGTGCCCATTCGGT
*
476754 AATTACTTGGGGATGCATACCCAATGCCAATACGAAAATTCATAAACTTCTTATGAATTTCTTAG
1 AATTACTTGGGGATGCATACCCAATGCCAATACGAAAATTCACAAACTTCTTATGAATTTCTTAG
* * * *
476819 GTTGCACACATAGTGCTAATACGGAAATTCATAAACTCATTTTGAATTTCTTAAGTTGCACACAC
66 GTTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTCTGAATTTCTTAAGTTACACACAC
*
476884 AGTGCCAATAC-GAAAATTCATAAACTTGTTATGAATTTCTTAAGTTGCACACACAGTGCCAATA
131 AGTGCCAATACAG-AAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATA
*
476948 CGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACAAACAGTGCC
195 CGAAAATTAATAAACTTATTATGAATTTCTTAAGTTGCACAAACAGTGCC
476998 AATACGGAAA
Statistics
Matches: 228, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
251 1 0.00
252 227 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (252 bp):
AATTACTTGGGGATGCATACCCAATGCCAATACGAAAATTCACAAACTTCTTATGAATTTCTTAG
GTTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTCTGAATTTCTTAAGTTACACACAC
AGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
GAAAATTAATAAACTTATTATGAATTTCTTAAGTTGCACAAACAGTGCCCATTCGGT
Found at i:477465 original size:22 final size:22
Alignment explanation
Indices: 477437--477485 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
477427 ACCCTTACCA
477437 TGGTATCGATACTTCTATATTG
1 TGGTATCGATACTTCTATATTG
477459 TGGTATCGATACTTCTATATTG
1 TGGTATCGATACTTCTATATTG
477481 TGGTA
1 TGGTA
477486 CCCATACTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.45
Consensus pattern (22 bp):
TGGTATCGATACTTCTATATTG
Found at i:477492 original size:22 final size:22
Alignment explanation
Indices: 477445--477493 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
477435 CATGGTATCG
* *
477445 ATACTTCTATATTGTGGTATCG
1 ATACTTCTATATTGTGGTACCC
477467 ATACTTCTATATTGTGGTACCC
1 ATACTTCTATATTGTGGTACCC
477489 ATACT
1 ATACT
477494 CCCTTTCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.43
Consensus pattern (22 bp):
ATACTTCTATATTGTGGTACCC
Found at i:477544 original size:33 final size:33
Alignment explanation
Indices: 477502--477613 Score: 197
Period size: 33 Copynumber: 3.4 Consensus size: 33
477492 CTCCCTTTCA
477502 GTATCGATACCTTTTCTACATTCTGGATCCATG
1 GTATCGATACCTTTTCTACATTCTGGATCCATG
* * *
477535 GTATCGATACATTTTCTACATTCTAGAACCATG
1 GTATCGATACCTTTTCTACATTCTGGATCCATG
477568 GTATCGATACCTTTTCTACATTCTGGATCCATG
1 GTATCGATACCTTTTCTACATTCTGGATCCATG
477601 GTATCGATACCTT
1 GTATCGATACCTT
477614 CCTTCTAGTT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (33 bp):
GTATCGATACCTTTTCTACATTCTGGATCCATG
Found at i:482481 original size:136 final size:137
Alignment explanation
Indices: 482236--482500 Score: 381
Period size: 136 Copynumber: 1.9 Consensus size: 137
482226 GAAATAAGTA
* *
482236 AAAATCACATCAAAGGATGTCTTACTGTTATTGTAATATACTCTTCGATGCTTGGTGTTGCTCAA
1 AAAATCACATCAAAGGATGTCTTACTGATATTGTAATATACTATTCGATGCTTGGTGTTGCTCAA
* * * * *
482301 TATTACTTACTCCTATTGCTTCTTCTTACCTACGCGTGAAAATCATCACACGCTAAGTATATACT
66 TACTACCTACTCCTACTCCTTCTTCTTACCTACGCGTGAAAATCATCACACGCTAAGTACATACT
482366 TATAGTC
131 TATAGTC
* * *
482373 AAAATCACATCAAAGGATGTCTTACTGATATTGTAAT-TACTATTC-ACTTCTTGGTGTTTCTTA
1 AAAATCACATCAAAGGATGTCTTACTGATATTGTAATATACTATTCGA-TGCTTGGTGTTGCTCA
* * * *
482436 GTACTCCCTACTCCTACTCCTTCTTCTTACCTACGCGTGAAAATCATCATATGCTAAGTACATAC
65 ATACTACCTACTCCTACTCCTTCTTCTTACCTACGCGTGAAAATCATCACACGCTAAGTACATAC
482501 CTAGTGAGGT
Statistics
Matches: 113, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
135 1 0.01
136 76 0.67
137 36 0.32
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (137 bp):
AAAATCACATCAAAGGATGTCTTACTGATATTGTAATATACTATTCGATGCTTGGTGTTGCTCAA
TACTACCTACTCCTACTCCTTCTTCTTACCTACGCGTGAAAATCATCACACGCTAAGTACATACT
TATAGTC
Found at i:483612 original size:24 final size:24
Alignment explanation
Indices: 483583--483631 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
483573 ATGATGAAAT
*
483583 TTCACATCCTAATACTCATTTAAA
1 TTCACATCCTAACACTCATTTAAA
483607 TTCACATCCTAACACTCATTTAAA
1 TTCACATCCTAACACTCATTTAAA
483631 T
1 T
483632 ATACAAACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (24 bp):
TTCACATCCTAACACTCATTTAAA
Found at i:488764 original size:61 final size:61
Alignment explanation
Indices: 488651--488765 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
488641 CTAGCTCTAA
* * * *
488651 ACCTACACTAAGCTTACGCTCTAGTGCTAATCCGGATATGATACGTAGGGTCGTACCCACC
1 ACCTACACTAAGCTTACGCTCTAGTGCTAATCCGAATATGAGACATAAGGTCGTACCCACC
* * *
488712 ACCTACACTAGGTTTA-GACTCTAGTGCTCATCCGAATATGAGACATAAGGTCGT
1 ACCTACACTAAGCTTACG-CTCTAGTGCTAATCCGAATATGAGACATAAGGTCGT
488766 GCCTTCCATA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 1 0.02
61 45 0.98
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGCTCTAGTGCTAATCCGAATATGAGACATAAGGTCGTACCCACC
Found at i:494286 original size:30 final size:30
Alignment explanation
Indices: 494252--494311 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
494242 GCTAGGATAA
494252 TATCTATACTAAGATTATGATATCGATACT
1 TATCTATACTAAGATTATGATATCGATACT
*
494282 TATCTATACTAGGATTATGATATCGATACT
1 TATCTATACTAAGATTATGATATCGATACT
494312 ACTATGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (30 bp):
TATCTATACTAAGATTATGATATCGATACT
Found at i:496530 original size:190 final size:190
Alignment explanation
Indices: 496207--496561 Score: 559
Period size: 190 Copynumber: 1.9 Consensus size: 190
496197 GCAATATGCT
**
496207 ACCTTAGGGCCCTCTGTTATGCATGTGTTCTTGCATCAATCCAATACAAAAAATATCATTAGAGC
1 ACCTTAGGGCCCTCTGTTATGCATGTGTAATTGCATCAATCCAATACAAAAAATATCATTAGAGC
* * *
496272 ATGGCTTAATGGCTATGTGAGACCGACCCAATGCTTTAGTTGAGTGGGAATTATATCGATGCTAT
66 ATGGCTTAATGGCTATATGAGACAGACCCAATGCTTTAGTTGAGTGGGAATTATACCGATGCTAT
* *
496337 GTGACATCGAGTTCCCTCTCTATGATCTACCTGATAGTTATATGATTATCAAATTATATG
131 GTGACATCGAGTTCCCCCTCCATGATCTACCTGATAGTTATATGATTATCAAATTATATG
* * * * *
496397 ACCTTAGGGCCCT-TAGTTATGCATGTGTAATTGCGTCAGTCCAATACAACATATATCCTTAGAG
1 ACCTTAGGGCCCTCT-GTTATGCATGTGTAATTGCATCAATCCAATACAAAAAATATCATTAGAG
* * *
496461 CATGGCTTAATGGCTATATGAGACAGAGCCAATGCTTTAGTTGAGTGGGAATTGTACCGATGTTA
65 CATGGCTTAATGGCTATATGAGACAGACCCAATGCTTTAGTTGAGTGGGAATTATACCGATGCTA
496526 TGTGACATCGAGTTCCCCCTCCATGATCTACCTGAT
130 TGTGACATCGAGTTCCCCCTCCATGATCTACCTGAT
496562 GGCTATGTGA
Statistics
Matches: 149, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
189 1 0.01
190 148 0.99
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (190 bp):
ACCTTAGGGCCCTCTGTTATGCATGTGTAATTGCATCAATCCAATACAAAAAATATCATTAGAGC
ATGGCTTAATGGCTATATGAGACAGACCCAATGCTTTAGTTGAGTGGGAATTATACCGATGCTAT
GTGACATCGAGTTCCCCCTCCATGATCTACCTGATAGTTATATGATTATCAAATTATATG
Found at i:500741 original size:34 final size:34
Alignment explanation
Indices: 500702--500779 Score: 156
Period size: 34 Copynumber: 2.3 Consensus size: 34
500692 AAAGGGAAAA
500702 TATCGATACCATGGATAACAGAATGCCAAAATGG
1 TATCGATACCATGGATAACAGAATGCCAAAATGG
500736 TATCGATACCATGGATAACAGAATGCCAAAATGG
1 TATCGATACCATGGATAACAGAATGCCAAAATGG
500770 TATCGATACC
1 TATCGATACC
500780 TAAAGGGTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (34 bp):
TATCGATACCATGGATAACAGAATGCCAAAATGG
Found at i:501267 original size:54 final size:54
Alignment explanation
Indices: 501204--501597 Score: 482
Period size: 54 Copynumber: 7.3 Consensus size: 54
501194 ATTACCAAAT
**
501204 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAATAGTTTC
1 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
*
501258 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACTGTTTC
1 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
*** * * * * *
501312 AAAACTATGTGTGCAACGCACGGAATTCATCATATATTGATCAACAATCGTTTT
1 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* *
501366 GGTACTATGTGTGCAACTCATGGAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * * * *
501420 GACACTATGTTTGTAACTCACGGAATTCATCACATGTTGATGAAAAACCGTTTC
1 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * * * ** * * * *
501474 AGTACTATGTTTGAAACTCACAAAATTTATCATATATTGATGAACAACCATTTT
1 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * * *
501528 GGCACTATGTATGCAACTCACAGAATTCATCATATATTGATCAACAACCGTTTC
1 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* *
501582 GACACTTTGTGTGCAA
1 GGCACTATGTGTGCAA
501598 AACTAAGAAA
Statistics
Matches: 289, Mismatches: 51, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 289 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (54 bp):
GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
Found at i:501293 original size:27 final size:26
Alignment explanation
Indices: 501209--501346 Score: 68
Period size: 27 Copynumber: 5.1 Consensus size: 26
501199 CAAATGGCAC
501209 TATGTGTGCAACTCACGGAATTCATCA
1 TATGTGTGCAAC-CACGGAATTCATCA
* ** * **
501236 TATGTTGATG-AACAATAG-TTTCGGCA
1 TATG-TG-TGCAACCACGGAATTCATCA
501262 CTATGTGTGCAACTCACGGAATTCATCA
1 -TATGTGTGCAAC-CACGGAATTCATCA
* * * **
501290 TATGTTGATG-AACAACTG-TTTCAAAA
1 TATG-TG-TGCAACCACGGAATTCATCA
501316 CTATGTGTGCAACGCACGGAATTCATCA
1 -TATGTGTGCAAC-CACGGAATTCATCA
501344 TAT
1 TAT
501347 ATTGATCAAC
Statistics
Matches: 77, Mismatches: 22, Indels: 24
0.63 0.18 0.20
Matches are distributed among these distances:
25 4 0.05
26 20 0.26
27 29 0.38
28 20 0.26
29 4 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (26 bp):
TATGTGTGCAACCACGGAATTCATCA
Found at i:501483 original size:162 final size:162
Alignment explanation
Indices: 501203--501597 Score: 556
Period size: 162 Copynumber: 2.4 Consensus size: 162
501193 GATTACCAAA
** *
501203 TGGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAATAGTTTCGGCACTATGT
1 TGGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGT
* * * *
501268 GTGCAACTCACGGAATTCATCATATGTTGATGAACAACTGTTTCAAAACTATGTGTGCAACGCAC
66 GTGCAACTCACGGAATTCATCACATGTTGATGAAAAACCGTTTCAAAACTATGTGTGAAACGCAC
** * *
501333 GGAATTCATCATATATTGATCAACAATCGTTT
131 AAAATTCATCATATATTGATCAACAACCATTT
* *
501365 TGGTACTATGTGTGCAACTCATGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGT
1 TGGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGT
* * ** * *
501430 TTGTAACTCACGGAATTCATCACATGTTGATGAAAAACCGTTTCAGTACTATGTTTGAAACTCAC
66 GTGCAACTCACGGAATTCATCACATGTTGATGAAAAACCGTTTCAAAACTATGTGTGAAACGCAC
* *
501495 AAAATTTATCATATATTGATGAACAACCATTT
131 AAAATTCATCATATATTGATCAACAACCATTT
* * * * *
501527 TGGCACTATGTATGCAACTCACAGAATTCATCATATATTGATCAACAACCGTTTCGACACTTTGT
1 TGGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGT
501592 GTGCAA
66 GTGCAA
501598 AACTAAGAAA
Statistics
Matches: 203, Mismatches: 30, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
162 203 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (162 bp):
TGGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGT
GTGCAACTCACGGAATTCATCACATGTTGATGAAAAACCGTTTCAAAACTATGTGTGAAACGCAC
AAAATTCATCATATATTGATCAACAACCATTT
Found at i:501703 original size:54 final size:54
Alignment explanation
Indices: 501590--501748 Score: 185
Period size: 54 Copynumber: 2.9 Consensus size: 54
501580 TCGACACTTT
* * * * **
501590 GTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCATTTT
1 GTGTGCAAAACT-AGAAATTCATAATAAGTTTATGAATTTCCGTATTGGTAGTGA
501645 GTGTGCAAAACTAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGTAGTGA
1 GTGTGCAAAACTAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGTAGTGA
* * ** * *
501699 GTGTGGAAACCGCGTAAATT-ATAATAAGTTTGTGAATTACCGTATTGGTA
1 GTGTGCAAAACTAG-AAATTCATAATAAGTTTATGAATTTCCGTATTGGTA
501749 CTACATGTGC
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
54 74 0.81
55 17 0.19
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (54 bp):
GTGTGCAAAACTAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGTAGTGA
Found at i:505215 original size:38 final size:38
Alignment explanation
Indices: 505170--505263 Score: 145
Period size: 38 Copynumber: 2.5 Consensus size: 38
505160 CACTGAATAT
505170 TTGTTCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTTCCGAAGGACCACTATGTCCCGAAGGACCACTGA
* * *
505208 TTGTTCCGAAGAACCACTATGTCCTGAAGGACCACTGT
1 TTGTTCCGAAGGACCACTATGTCCCGAAGGACCACTGA
505246 TTG-TCCTGAAGGACCACT
1 TTGTTCC-GAAGGACCACT
505264 GATAATCCCT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
37 3 0.06
38 48 0.94
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (38 bp):
TTGTTCCGAAGGACCACTATGTCCCGAAGGACCACTGA
Found at i:505218 original size:20 final size:20
Alignment explanation
Indices: 505170--505266 Score: 107
Period size: 20 Copynumber: 5.0 Consensus size: 20
505160 CACTGAATAT
505170 TTGTTCCGAAGGACCACT-A
1 TTGTTCCGAAGGACCACTGA
*
505189 -TGTCCCGAAGGACCACTGA
1 TTGTTCCGAAGGACCACTGA
*
505208 TTGTTCCGAAGAACCACT-A
1 TTGTTCCGAAGGACCACTGA
*
505227 -TG-TCCTGAAGGACCACTGT
1 TTGTTCC-GAAGGACCACTGA
505246 TTG-TCCTGAAGGACCACTGA
1 TTGTTCC-GAAGGACCACTGA
505266 T
1 T
505267 AATCCCTCGA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.04
18 28 0.42
19 2 0.03
20 34 0.51
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (20 bp):
TTGTTCCGAAGGACCACTGA
Found at i:506235 original size:2 final size:2
Alignment explanation
Indices: 506228--506267 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
506218 CATGAATTAG
506228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
506268 TCATATAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:509887 original size:54 final size:54
Alignment explanation
Indices: 509822--510159 Score: 380
Period size: 54 Copynumber: 6.3 Consensus size: 54
509812 ATTACCAAAT
* * *
509822 GGCACTATGTGTGCAACTCACGGAATTCAACATATATTGATGAACAACTATTTC
1 GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACTATTTC
* * * **
509876 GACACTATGTGTGCAACACACATAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACTATTTC
* * * *
509930 GGCACTATGTGTACAACTCACATAATTCATCATATGTTGATGAAAAACCT-TTTT
1 GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAA-CTATTTC
*
509984 GGCACTATGTGTGCAACTCACAGAATTAATCATATGTTGATGAACAACCT-TTTC
1 GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAA-CTATTTC
* * * * * * *
510038 GGGACTATGTGTGCAACTCAC-GGATTCATGATAAGTTGATGAACTACCATTTT
1 GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACTATTTC
* ** *
510091 TGCACTATGTGTGCAACTCATGGAATTCATCATATG-TGATGAA-AAATCATTTC
1 GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACT-ATTTC
* *
510144 GACACTTTGTGTGCAA
1 GGCACTATGTGTGCAA
510160 AACTAATAAA
Statistics
Matches: 240, Mismatches: 40, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
52 2 0.01
53 65 0.27
54 172 0.72
55 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (54 bp):
GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACTATTTC
Found at i:510593 original size:46 final size:46
Alignment explanation
Indices: 510542--510629 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
510532 TTAGATGAAC
* **
510542 AACAATGCATAATTGACATGAAAGGATGTCGTAAATGAAAATGTAT
1 AACAATGCATAATTAACATGAAAGGATGTCACAAATGAAAATGTAT
510588 AACAATGCATAATTAACATGAAAGGATGTCACAAATGAAAAT
1 AACAATGCATAATTAACATGAAAGGATGTCACAAATGAAAAT
510630 ACATAGTGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (46 bp):
AACAATGCATAATTAACATGAAAGGATGTCACAAATGAAAATGTAT
Found at i:525568 original size:19 final size:20
Alignment explanation
Indices: 525544--525589 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
525534 CAAAGTGATC
*
525544 CAATTTCA-CACTCTAACAT
1 CAATTTCATCACTCGAACAT
*
525563 CAATTTCATCATTCGAACAT
1 CAATTTCATCACTCGAACAT
525583 CAATTTC
1 CAATTTC
525590 TAGCATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (20 bp):
CAATTTCATCACTCGAACAT
Found at i:526555 original size:27 final size:27
Alignment explanation
Indices: 526517--526572 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
526507 AAATCCAATG
526517 ATCCATATTATTTTCCATCATTTTAAC
1 ATCCATATTATTTTCCATCATTTTAAC
526544 ATCCATATTATTTTCCATCATTTTAAC
1 ATCCATATTATTTTCCATCATTTTAAC
526571 AT
1 AT
526573 GTGAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (27 bp):
ATCCATATTATTTTCCATCATTTTAAC
Found at i:535966 original size:72 final size:73
Alignment explanation
Indices: 535848--535999 Score: 270
Period size: 72 Copynumber: 2.1 Consensus size: 73
535838 AGAGACCATT
*
535848 AACCAATTGTGTCGAACCATAAAAACATTATCTAGATAAAAAGAACAACAATTATTCTTAATAAT
1 AACCAATTGTGTCGAACCATAAAAACATTATCGAGATAAAAAGAACAACAATTATTCTTAATAAT
535913 AATCTCAA
66 AATCTCAA
* *
535921 AACCAATTGTGTCGAATCAT-AATACATTATCGAGATAAAAAGAACAACAATTATTCTTAATAAT
1 AACCAATTGTGTCGAACCATAAAAACATTATCGAGATAAAAAGAACAACAATTATTCTTAATAAT
535985 AATCTCAA
66 AATCTCAA
535993 AACCAAT
1 AACCAAT
536000 CTTATTCAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 57 0.75
73 19 0.25
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (73 bp):
AACCAATTGTGTCGAACCATAAAAACATTATCGAGATAAAAAGAACAACAATTATTCTTAATAAT
AATCTCAA
Found at i:537510 original size:16 final size:16
Alignment explanation
Indices: 537489--537526 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
537479 AGTTATTACC
537489 TATATCTCAACTAGTG
1 TATATCTCAACTAGTG
*
537505 TATATCTTAACTAGTG
1 TATATCTCAACTAGTG
*
537521 AATATC
1 TATATC
537527 ACTTGCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (16 bp):
TATATCTCAACTAGTG
Found at i:540258 original size:11 final size:12
Alignment explanation
Indices: 540232--540262 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
540222 TGGTTAAGGA
540232 TTTTCCTGATGT
1 TTTTCCTGATGT
*
540244 TTTTCTTGATGT
1 TTTTCCTGATGT
540256 TTTTCCT
1 TTTTCCT
540263 AAAGAGCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.06, C:0.16, G:0.13, T:0.65
Consensus pattern (12 bp):
TTTTCCTGATGT
Found at i:542925 original size:11 final size:11
Alignment explanation
Indices: 542909--542950 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
542899 ACTCTCATTC
542909 TTCATTTCATA
1 TTCATTTCATA
*
542920 TTCATTTCTTA
1 TTCATTTCATA
* *
542931 TTGATTT-ATG
1 TTCATTTCATA
542941 TTCATTTCAT
1 TTCATTTCAT
542951 CTCTATTTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (11 bp):
TTCATTTCATA
Found at i:546037 original size:12 final size:13
Alignment explanation
Indices: 546000--546040 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
545990 GTCAAGGTTG
546000 GACTAGTGGGCAT
1 GACTAGTGGGCAT
546013 GACTAGTGGGCAT
1 GACTAGTGGGCAT
*
546026 GACTTG-GGGCAT
1 GACTAGTGGGCAT
546038 GAC
1 GAC
546041 GCGTCTGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.22, C:0.17, G:0.39, T:0.22
Consensus pattern (13 bp):
GACTAGTGGGCAT
Found at i:549448 original size:23 final size:22
Alignment explanation
Indices: 549422--549473 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
549412 TAATATTTTT
*
549422 AATAAAATTTAAAATATACAAAA
1 AATAAAATATAAAAT-TACAAAA
*
549445 AAT-AAATATAAAATTACTAAA
1 AATAAAATATAAAATTACAAAA
549466 AATGAAAA
1 AAT-AAAA
549474 CTAAATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 9 0.36
22 10 0.40
23 6 0.24
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (22 bp):
AATAAAATATAAAATTACAAAA
Found at i:550486 original size:3 final size:3
Alignment explanation
Indices: 550478--550510 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
550468 CTATACTTTA
550478 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
550511 TTCTTAAGAA
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):
ATT
Found at i:551967 original size:32 final size:32
Alignment explanation
Indices: 551905--551967 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
551895 TTCGTCCCAA
* * **
551905 TATTTCATCAAAATGAAAAATTATGGCAAATT
1 TATTTAATAAAAATGAAAAATTATAACAAATT
551937 TATTTAATAAAAAT-AACAAATTATAACAAAT
1 TATTTAATAAAAATGAA-AAATTATAACAAAT
551968 ATTAATTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 2 0.08
32 24 0.92
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (32 bp):
TATTTAATAAAAATGAAAAATTATAACAAATT
Found at i:552042 original size:198 final size:197
Alignment explanation
Indices: 551602--552046 Score: 574
Period size: 197 Copynumber: 2.3 Consensus size: 197
551592 CATTCAATTG
* * *
551602 AAATAATATTCTTTCAAAATAGC-AATGTGTAACAAATTTATTTAGTTACAATAACATAGTAAAT
1 AAATAATATTCTTTCAAAATAACAAAT-TGTAACAAATTTATTTAGTCACAATAACACAGTAAAT
** * * *
551666 TTAGTCAAAATAAAATTTTATGTCAAATTTATTTTGTCACAATATTTTATCGAAATAAAAAATTG
65 TTAGTCAAAATAAAAAGTTATGTCAAATTTATTTCGTCACAATATTTCATCAAAATAAAAAATTG
* *
551731 TAAAATGTATTTAATAAAAATAATCATTTATAAAAAAATATTAATTTCTCATTATAAAAAATTGT
130 GAAAATGTATTTAATAAAAATAATCAATTATAAAAAAATATTAATTTCTCATTATAAAAAATTGT
551796 GAC
195 GAC
* * * * * * * *
551799 AAGTAATGTTCTTTCATAATAACAAATTGCAACAAAATGATTTAGTCACAATAACACATTAAGTT
1 AAATAATATTCTTTCAAAATAACAAATTGTAACAAATTTATTTAGTCACAATAACACAGTAA-AT
* * * *
551864 TTA-TCATAGTAAAAAGTTATGTCAAATTTATTTCGTCCCAATATTTCATCAAAATGAAAAATTA
65 TTAGTCAAAATAAAAAGTTATGTCAAATTTATTTCGTCACAATATTTCATCAAAAT-AAAAAAT-
* * *
551928 TGGCAAATTTATTTAATAAAAATAA-CAAATTAT-AACAAATATTAATTTCTCATTATAAAAAAT
128 TGGAAAATGTATTTAATAAAAATAATC-AATTATAAAAAAATATTAATTTCTCATTATAAAAAAT
551991 TGTGAC
192 TGTGAC
* *
551997 AAATAATATTCTTTCACAATAATAAATTGTAACAAATTTATTTAGTCACA
1 AAATAATATTCTTTCAAAATAACAAATTGTAACAAATTTATTTAGTCACA
552047 GTAAAAAGTT
Statistics
Matches: 211, Mismatches: 32, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
197 92 0.44
198 92 0.44
199 27 0.13
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (197 bp):
AAATAATATTCTTTCAAAATAACAAATTGTAACAAATTTATTTAGTCACAATAACACAGTAAATT
TAGTCAAAATAAAAAGTTATGTCAAATTTATTTCGTCACAATATTTCATCAAAATAAAAAATTGG
AAAATGTATTTAATAAAAATAATCAATTATAAAAAAATATTAATTTCTCATTATAAAAAATTGTG
AC
Found at i:556557 original size:19 final size:20
Alignment explanation
Indices: 556521--556558 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
556511 GCTCCTATAT
*
556521 CAAACAAGAGAGTGCAAAAA
1 CAAACAAGAAAGTGCAAAAA
*
556541 CAAA-AAGAAAGTTCAAAA
1 CAAACAAGAAAGTGCAAAA
556559 GGAAGAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.63, C:0.13, G:0.16, T:0.08
Consensus pattern (20 bp):
CAAACAAGAAAGTGCAAAAA
Found at i:561064 original size:14 final size:14
Alignment explanation
Indices: 561041--561099 Score: 93
Period size: 14 Copynumber: 4.3 Consensus size: 14
561031 CCTTAAACCA
561041 TTTC-TTTTATCCT
1 TTTCATTTTATCCT
561054 TTTCATTTTATCCT
1 TTTCATTTTATCCT
*
561068 TTTCATTTTATTCT
1 TTTCATTTTATCCT
*
561082 TTTCATTTTATTCT
1 TTTCATTTTATCCT
561096 TTTC
1 TTTC
561100 CTCTCCAAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
13 4 0.09
14 40 0.91
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTCATTTTATCCT
Found at i:567401 original size:13 final size:13
Alignment explanation
Indices: 567383--567408 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
567373 TTTATTCCCT
567383 TTTATTCATTTTA
1 TTTATTCATTTTA
567396 TTTATTCATTTTA
1 TTTATTCATTTTA
567409 ATTACTTATC
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:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATTCATTTTA
Found at i:574401 original size:21 final size:22
Alignment explanation
Indices: 574371--574411 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
574361 GGTTAAAATA
574371 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
574393 AAAAA-AAGAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
574412 CAAATTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:574421 original size:21 final size:19
Alignment explanation
Indices: 574366--574434 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 19
574356 GTTATGGTTA
574366 AAATAAAAAAT-AAGAATT
1 AAATAAAAAATAAAGAATT
*
574384 AAATAAAAGAAAAAAAGAATT
1 AAAT-AAA-AAATAAAGAATT
574405 AAATAAACAAATTAAAGAAATT
1 AAATAAA-AAA-TAAAG-AATT
574427 AAGATAAA
1 AA-ATAAA
574435 GAGAAACTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 4 0.10
19 3 0.07
20 9 0.21
21 15 0.36
22 6 0.14
23 5 0.12
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.19
Consensus pattern (19 bp):
AAATAAAAAATAAAGAATT
Found at i:581058 original size:13 final size:13
Alignment explanation
Indices: 581040--581065 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
581030 ATATTAAAAT
581040 AAAAGAAAAATAA
1 AAAAGAAAAATAA
581053 AAAAGAAAAATAA
1 AAAAGAAAAATAA
581066 TATAATAATA
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:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAAGAAAAATAA
Found at i:581163 original size:23 final size:24
Alignment explanation
Indices: 581126--581176 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
581116 AAGTTGTGGT
581126 TAAAAGAAAAAAATAAGAATTAAA
1 TAAAAGAAAAAAATAAGAATTAAA
*
581150 TAAAAG-AAAAAATAATAATTAAA
1 TAAAAGAAAAAAATAAGAATTAAA
581173 TAAA
1 TAAA
581177 CAAATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.20
Consensus pattern (24 bp):
TAAAAGAAAAAAATAAGAATTAAA
Found at i:581604 original size:36 final size:36
Alignment explanation
Indices: 581557--581631 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
581547 TCACGTTTGG
581557 AATTGAGCCTTCGCTTTAGTCTTCGGCTTGAAAGAA
1 AATTGAGCCTTCGCTTTAGTCTTCGGCTTGAAAGAA
581593 AATTGAGCCTTCGCTTTAGTCTTCGGCTTGAAAGAA
1 AATTGAGCCTTCGCTTTAGTCTTCGGCTTGAAAGAA
581629 AAT
1 AAT
581632 CTGAAGCGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (36 bp):
AATTGAGCCTTCGCTTTAGTCTTCGGCTTGAAAGAA
Found at i:595334 original size:77 final size:79
Alignment explanation
Indices: 595230--595379 Score: 191
Period size: 77 Copynumber: 1.9 Consensus size: 79
595220 AATTAATAAA
595230 TAAAATATTATTTAATTAATTCAAATTAAATAT-ACACT-AAAGACTTGTAATATAAATTACAAT
1 TAAAATATTATTTAATTAATTCAAATTAAATATCA-ACTAAAAGACTTGTAATATAAATTACAAT
595293 C-TTTAATGTTTATT
65 CTTTTAATGTTTATT
* * * * * * *
595307 TAAAATCTTATTTAATT-ATTCTGAATTATATATCAATTAAAAGAGTTGTAATCTAAATTACATT
1 TAAAATATTATTTAATTAATTC-AAATTAAATATCAACTAAAAGACTTGTAATATAAATTACAAT
595371 CTTTTAATG
65 CTTTTAATG
595380 CATACTTACT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
76 4 0.06
77 27 0.44
78 24 0.39
79 7 0.11
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (79 bp):
TAAAATATTATTTAATTAATTCAAATTAAATATCAACTAAAAGACTTGTAATATAAATTACAATC
TTTTAATGTTTATT
Found at i:606483 original size:24 final size:24
Alignment explanation
Indices: 606455--606528 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
606445 TATCGATCGA
606455 TTTTGTTTAATGCATAAGTTGCAT
1 TTTTGTTTAATGCATAAGTTGCAT
* * * * *
606479 TTTTGTATGATG-ATTA-TCGATCAA
1 TTTTGTTTAATGCATAAGTTG--CAT
606503 TTTTGTTTAATGCATAAGTTGC-T
1 TTTTGTTTAATGCATAAGTTGCAT
606526 TTT
1 TTT
606529 CCATATGATG
Statistics
Matches: 36, Mismatches: 10, Indels: 9
0.65 0.18 0.16
Matches are distributed among these distances:
22 2 0.06
23 6 0.17
24 23 0.64
25 3 0.08
26 2 0.06
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.51
Consensus pattern (24 bp):
TTTTGTTTAATGCATAAGTTGCAT
Found at i:606506 original size:48 final size:48
Alignment explanation
Indices: 606437--606581 Score: 213
Period size: 48 Copynumber: 3.0 Consensus size: 48
606427 TACTTTGTGG
*
606437 ATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTTTGT
1 ATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTTCGT
* * *
606485 ATGATGATTATCGATCAATTTTGTTTAATGCATAAGTTGC-TTTTCCAT
1 ATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTT-CGT
* *
606533 ATGATGGTTATCGATTGA-TTTGTTTAATGCATATGTTGCATTTTCGT
1 ATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTTCGT
606580 AT
1 AT
606582 CAATACTATA
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
47 28 0.33
48 58 0.67
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.48
Consensus pattern (48 bp):
ATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTTCGT
Found at i:606685 original size:53 final size:53
Alignment explanation
Indices: 606597--606705 Score: 148
Period size: 53 Copynumber: 2.1 Consensus size: 53
606587 CTATATGTAC
*
606597 TTTCGGCACTATGTGTGCACCCATGGTATTCATAATGAGTTTATGAATGACCA
1 TTTCGGCACTATGTGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCA
* * * * *
606650 TTTCGGCATTATTTGTGCATCCATGGAATGT-ATAATGAGTTTTTGAATTACCA
1 TTTCGGCACTATGTGTGCACCCATGGAAT-TCATAATGAGTTTATGAATGACCA
606703 TTT
1 TTT
606706 ATGCACTTAG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
53 48 0.98
54 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (53 bp):
TTTCGGCACTATGTGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCA
Found at i:607137 original size:29 final size:29
Alignment explanation
Indices: 607104--607179 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
607094 ATTAGATGGC
*
607104 ATGTAATTGACTTATGATAATACTCTGGA
1 ATGTAATTGACTTATGATAATACTCTAGA
* *
607133 ATGTAATCGACTTATGATAATGCTCTAGA
1 ATGTAATTGACTTATGATAATACTCTAGA
607162 ATGTAATTGACTTATGAT
1 ATGTAATTGACTTATGAT
607180 GATTTTAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (29 bp):
ATGTAATTGACTTATGATAATACTCTAGA
Found at i:613665 original size:47 final size:46
Alignment explanation
Indices: 613575--613720 Score: 211
Period size: 47 Copynumber: 3.1 Consensus size: 46
613565 CATACTATGT
613575 GTATGATTGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTTC
1 GTATGA-TGTTATCGATCGATTTT-TTTAATGCATAAGTTGCATTTTC
*
613623 GTATGATGATTATCGATCGATGTTTTTAATGCATAAGTTGCATTTTC
1 GTATGATG-TTATCGATCGATTTTTTTAATGCATAAGTTGCATTTTC
* * * *
613670 GTATGATGGTTATCAATCAATTTTTTTAATGCATATGTTGCATTTTT
1 GTATGAT-GTTATCGATCGATTTTTTTAATGCATAAGTTGCATTTTC
613717 GTAT
1 GTAT
613721 CGGTACTATA
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
47 69 0.77
48 21 0.23
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.48
Consensus pattern (46 bp):
GTATGATGTTATCGATCGATTTTTTTAATGCATAAGTTGCATTTTC
Found at i:613825 original size:53 final size:53
Alignment explanation
Indices: 613742--613851 Score: 159
Period size: 53 Copynumber: 2.1 Consensus size: 53
613732 GTACTTTCGA
* *
613742 CACTATGTGTGCACCCATGGTATTAGTAATGAGTTTATGAATGACCATTTCAG
1 CACTATGTGTGCACCCATGATATTAATAATGAGTTTATGAATGACCATTTCAG
* * *
613795 CACTATGTGTGCATCCAT-ATAATTAATAATGAGTTTGTGAATTACCATTTCAG
1 CACTATGTGTGCACCCATGAT-ATTAATAATGAGTTTATGAATGACCATTTCAG
613848 CACT
1 CACT
613852 TAGGAGCAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 1 0.02
53 50 0.98
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (53 bp):
CACTATGTGTGCACCCATGATATTAATAATGAGTTTATGAATGACCATTTCAG
Found at i:614287 original size:29 final size:29
Alignment explanation
Indices: 614245--614320 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
614235 ATTTAATGGC
* * *
614245 ATGTAATCGACTTATGATAAAGCTTTGGA
1 ATGTAATCGACTTATGATAAAGATCTAGA
* *
614274 ATGTAATCAACTTATGATAATGATCTAGA
1 ATGTAATCGACTTATGATAAAGATCTAGA
*
614303 ATGTAATTGACTTATGAT
1 ATGTAATCGACTTATGAT
614321 GATTGTAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (29 bp):
ATGTAATCGACTTATGATAAAGATCTAGA
Found at i:617826 original size:11 final size:12
Alignment explanation
Indices: 617810--617838 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
617800 AAAGAAATGT
617810 ACAAAAAG-AAA
1 ACAAAAAGAAAA
617821 ACAAAAAGAAAA
1 ACAAAAAGAAAA
617833 ACAAAA
1 ACAAAA
617839 TTAAAGCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (12 bp):
ACAAAAAGAAAA
Found at i:626494 original size:81 final size:81
Alignment explanation
Indices: 626357--626991 Score: 828
Period size: 81 Copynumber: 8.0 Consensus size: 81
626347 GTTTTAAAAG
* * *
626357 AAAAGATTAAATGCCTAGTTTTGCATTTGACAGAAAGCTGTCAATCATGCCAGTTAGATAAAAGG
1 AAAAGATTAAATGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGG
626422 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * *
626438 ACAAGATTAAATGTCTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGTCAGTTAGATGAAAGG
1 AAAAGATTAAATGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGG
626503 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * * *
626519 AAAAGATT-AATGTCTAGCTATGCATTTGACAGAAAGATGTCAATCATGCCAGTT--A-G--A--
1 AAAAGATTAAATGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGG
626576 -T-AATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * *
626590 AAAAGATTAAATGCATAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCTGCTAGATGAAAGG
1 AAAAGATTAAATGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGG
* *
626655 TTAAATACCATTGACT
66 TTAAATACCTTTGAGT
* * * *
626671 AAAAGATTAAATGCCTAGCTGTGCATTTGAAAGAAAGGTGTCAATCGTGTCA-TGTAGATGAAAG
1 AAAAGATTAAATGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGT-TAGATGAAAG
*
626735 GTTAAATACATTTGAG-
65 GTTAAATACCTTTGAGT
** * * *
626751 AAAATGATTAAATGCCTAAATGTGTATTTGACATAAATGTGTCAATCATGCCAGTTAGATGAAAG
1 AAAA-GATTAAATGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
*
626816 GTTAAATACCTTTGAGA
65 GTTAAATACCTTTGAGT
* * * *
626833 AAAAGATTAAATGCCTA-TGTGTGCATTTGAAATAAAGGTTTCAATCATGCCAGTTAGATGAAGG
1 AAAAGATTAAATGCCTAGT-TGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
626897 GTTAAATACCTTTGAGT
65 GTTAAATACCTTTGAGT
* ** * * *
626914 AAAAGATTAAATGTCTAACTGTGCACTTGACAGAAATGTGTCAATCATGCAAGTTAGATGAAAGG
1 AAAAGATTAAATGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGG
626979 TTAAATACCTTTG
66 TTAAATACCTTTG
626992 CGATGAAAGA
Statistics
Matches: 483, Mismatches: 55, Indels: 32
0.85 0.10 0.06
Matches are distributed among these distances:
71 21 0.04
72 40 0.08
74 1 0.00
75 2 0.00
77 2 0.00
78 1 0.00
80 47 0.10
81 364 0.75
82 5 0.01
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (81 bp):
AAAAGATTAAATGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGG
TTAAATACCTTTGAGT
Found at i:627118 original size:49 final size:49
Alignment explanation
Indices: 627023--627145 Score: 113
Period size: 49 Copynumber: 2.5 Consensus size: 49
627013 ATTGTTCTTT
* * * *** ** *
627023 TTGGCAGAAAAGTACCATTAATGCAAGATAGATGCCTAACGGTGCAT-T
1 TTGGCAGAAAGGTGCCACTAATGCAAGATAGATGAAGAACAATGCATAA
*
627071 TCTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAGAACAATGCATAA
1 T-TGGCAGAAAGGTGCCACTAATGCAAGATAGATGAAGAACAATGCATAA
*
627121 TTGGCATGAAAGGATGCCACAAATG
1 TTGGCA-GAAAGG-TGCCACTAATG
627146 AAAATGTATA
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
48 1 0.02
49 42 0.70
50 7 0.12
51 10 0.17
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (49 bp):
TTGGCAGAAAGGTGCCACTAATGCAAGATAGATGAAGAACAATGCATAA
Found at i:631209 original size:19 final size:19
Alignment explanation
Indices: 631170--631211 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
631160 ATCTAATTTT
*
631170 GGTATCGATACCGGTAAAG
1 GGTATCGATACCGCTAAAG
631189 GGTATCGATACC-CTAATAG
1 GGTATCGATACCGCTAA-AG
631208 GGTA
1 GGTA
631212 GTATCGATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.24
Consensus pattern (19 bp):
GGTATCGATACCGCTAAAG
Found at i:631290 original size:75 final size:75
Alignment explanation
Indices: 631137--631291 Score: 168
Period size: 75 Copynumber: 2.1 Consensus size: 75
631127 ATGATAAGGG
* * * *
631137 GTATTGATACCAAGAAACATCGAATCTAATTTTGGTATCGATACCGGTAAAGGGTATCGATACCC
1 GTATCGATACCAAGAAACATCAAACCTAATTTTGGTATCGATACCGGTAAAGGGTATCGATACCA
* *
631202 TAATAGGGTA
66 TAATAGAGAA
* * * * * *
631212 GTATCGATACCAGGCAACATCAAACCTATTTTTGGTATCGATACCTG-AATGGGGTATCGGTACC
1 GTATCGATACCAAGAAACATCAAACCTAATTTTGGTATCGATACCGGTAA-AGGGTATCGATACC
* *
631276 ATAGTATAGAA
65 ATAATAGAGAA
631287 GTATC
1 GTATC
631292 AGTACTAGGG
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
74 2 0.03
75 63 0.97
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (75 bp):
GTATCGATACCAAGAAACATCAAACCTAATTTTGGTATCGATACCGGTAAAGGGTATCGATACCA
TAATAGAGAA
Found at i:632178 original size:68 final size:68
Alignment explanation
Indices: 632095--632249 Score: 215
Period size: 68 Copynumber: 2.3 Consensus size: 68
632085 AAAGGTGTTG
* * * *
632095 TTTATGCCAGCTAGATGAAAGACTAAGTTTCTTTGTGGCCTAACTGTGC-ATATGACATAAATA-
1 TTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTGAGGCCTAACTGTGCAAT-TAACATAAA-AG
632158 TGTCA
64 TGTCA
* *
632163 TTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTGAGGTCTAACTGTGGAATTAACATAAAAGTG
1 TTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTGAGGCCTAACTGTGCAATTAACATAAAAGTG
632228 TCA
66 TCA
*
632231 ATTATGCCAGTTAGATGAA
1 TTTATGCCAGTTAGATGAA
632250 CGGTTAAGTA
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
67 1 0.01
68 75 0.96
69 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (68 bp):
TTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTGAGGCCTAACTGTGCAATTAACATAAAAGTG
TCA
Found at i:632338 original size:81 final size:81
Alignment explanation
Indices: 632199--632742 Score: 736
Period size: 81 Copynumber: 6.7 Consensus size: 81
632189 GTGTCTTTGA
* * * *
632199 GGTCTAACTGTGGAATTAACATAAAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
1 GGTCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
632264 TGAGTAAAAGAAAAAT
66 TGAGTAAAAGAAAAAT
* *
632280 GGTCTAACTATGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACCGT
1 GGTCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
632345 TGAGTAAAAGAAAAAT
66 TGAGTAAAAGAAAAAT
*
632361 GGCCTAGA-TGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCG
1 GGTCTA-ACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCG
632425 TTGAGTAAAAGAAAAAT
65 TTGAGTAAAAGAAAAAT
* * * * * *
632442 GGCCTAGCTGTGTAATTGATAGAAAGGTGTCAATTATGCCAGTTGGATGAATGGTTAAGTACCGT
1 GGTCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
632507 TGAGTAAAAGAAAAAAT
66 TGAGTAAAAG-AAAAAT
* ** * * *
632524 GGCCTAGTTGTGCAATTGACAGAGAGGTGTCAATTATGTCAGCTAGATGAACGGTTAAGTACCGT
1 GGTCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
632589 TGAGTAAAAGAAAAAT
66 TGAGTAAAAGAAAAAT
* * * * * * * *
632605 -GTGCTAGA-TGTACAATTGATAGAAAGGTATCAATTTTGCTAGTTAGATGAACGATTAAATACT
1 GGT-CTA-ACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACC
632668 GTTGAGTAAAAGAAAAAT
64 GTTGAGTAAAAGAAAAAT
* * * * *
632686 TGTCTAGCTATGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGACGAAC-GTTAA
1 GGTCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAA
632743 ACATTTTTGA
Statistics
Matches: 411, Mismatches: 45, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
80 5 0.01
81 330 0.80
82 76 0.18
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.27
Consensus pattern (81 bp):
GGTCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
TGAGTAAAAGAAAAAT
Found at i:632653 original size:244 final size:243
Alignment explanation
Indices: 632225--632742 Score: 779
Period size: 244 Copynumber: 2.1 Consensus size: 243
632215 TAACATAAAA
*
632225 GTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGTCTAACTA
1 GTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTAACTA
*
632290 TGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAG
66 TGCAATTGACAGAAAGGTGTCAATTATGCCAGCTAGATGAACGATTAAGTACCGTTGAGTAAAAG
* * * *
632355 AAAAATGGCCTAGATGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAG
131 AAAAATGGCCTAGATGTACAATTGACAGAAAGGTATCAATTATGCCAGTTAGATGAACGATTAAA
* * *
632420 TACCGTTGAGTAAAAGAAAAATGGCCTAGCTGTGTAATTGATAGAAAG
196 TACCGTTGAGTAAAAGAAAAATGGCCTAGCTATGCAATTGACAGAAAG
* * **
632468 GTGTCAATTATGCCAGTTGGATGAATGGTTAAGTACCGTTGAGTAAAAGAAAAAATGGCCTAGTT
1 GTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAG-AAAAATGGCCTAACT
* * * *
632533 GTGCAATTGACAGAGAGGTGTCAATTATGTCAGCTAGATGAACGGTTAAGTACCGTTGAGTAAAA
65 ATGCAATTGACAGAAAGGTGTCAATTATGCCAGCTAGATGAACGATTAAGTACCGTTGAGTAAAA
* * *
632598 GAAAAATGTG-CTAGATGTACAATTGATAGAAAGGTATCAATTTTGCTAGTTAGATGAACGATTA
130 GAAAAATG-GCCTAGATGTACAATTGACAGAAAGGTATCAATTATGCCAGTTAGATGAACGATTA
* * * *
632662 AATACTGTTGAGTAAAAGAAAAATTGTCTAGCTATGCAATTGGCAGAAAG
194 AATACCGTTGAGTAAAAGAAAAATGGCCTAGCTATGCAATTGACAGAAAG
*
632712 GTGTCAATTATGCCAGTTAGACGAAC-GTTAA
1 GTGTCAATTATGCCAGTTAGATGAACGGTTAA
632743 ACATTTTTGA
Statistics
Matches: 246, Mismatches: 27, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
243 52 0.21
244 193 0.78
245 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (243 bp):
GTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTAACTA
TGCAATTGACAGAAAGGTGTCAATTATGCCAGCTAGATGAACGATTAAGTACCGTTGAGTAAAAG
AAAAATGGCCTAGATGTACAATTGACAGAAAGGTATCAATTATGCCAGTTAGATGAACGATTAAA
TACCGTTGAGTAAAAGAAAAATGGCCTAGCTATGCAATTGACAGAAAG
Found at i:639141 original size:103 final size:103
Alignment explanation
Indices: 638755--639413 Score: 511
Period size: 103 Copynumber: 6.4 Consensus size: 103
638745 TATTCGAAAT
*** * * * * *
638755 TATTATCAATATAAATCACGATAAATTTGTTTGACACTAAAAAC-ATATTTTGTGACCATCAATA
1 TATTATCAATA-AAATTGTGATGAATTTTTTTGACACT-GAAACTATATTTAGTGACCATCAATG
* * * *
638819 TTATCACACTAAGTATTTTTTAACGATCAAATGTTCGACTC
64 TTGTCACACTAAGTA-TTTTTAATGACCAAATGTTCGACAC
* * * * *
638860 TATTATCAATACAAATAT-TGATGAATTGTTTTGACACTGAGAGTATATTTTGTGACCACCAATG
1 TATTATCAATA-AAAT-TGTGATGAATTTTTTTGACACTGAAACTATATTTAGTGACCATCAATG
638924 TTGTCACACTAAGTATTTTTAAATGACCAAATGTTCGACAC
64 TTGTCACACTAAGTATTTTT-AATGACCAAATGTTCGACAC
* * * * * * *
638965 TATTATCAATAAAAATGTGTTG-ATTTTATT-ATACTGAAAGTATAATTAGTGATCA-CTAATGT
1 TATTATCAATAAAATTGTGATGAATTTTTTTGACACTGAAACTATATTTAGTGACCATC-AATGT
* * * *
639027 TGTCACACTAAGTGTTTTTAGTGACCAAATGTTAGGCA-
65 TGTCACACTAAGTATTTTTAATGACCAAATGTTCGACAC
* *
639065 TCATTATCAATAGAAATTGTGAT-AATTTTTTTGGCATTGAAACTATATTTAGTGACCATCAATG
1 T-ATTATCAATA-AAATTGTGATGAATTTTTTTGACACTGAAACTATATTTAGTGACCATCAATG
* *
639129 TTGTCACACTAAGTATTTTTAGTGACAAAATGTTCGACAC
64 TTGTCACACTAAGTATTTTTAATGACCAAATGTTCGACAC
* *** * *
639169 TATTATCAATAAAAATTGTGATGAATTTGTACAACATTGAAA-TATATTT-GTGACCA-CTACTG
1 TATTATCAAT-AAAATTGTGATGAATTTTTTTGACACTGAAACTATATTTAGTGACCATC-AATG
* * * ** *
639231 TTGTCATAC-AAGGTGTTTTTTAATAATTAAATATT-GAACAC
64 TTGTCACACTAA-GT-ATTTTTAATGACCAAATGTTCG-ACAC
* * * * * * * *
639272 TATTATCAGTAGAAATTATGATGAATTTATTTGACAGT-AACAATATATTT-GTTG-TCATTAGT
1 TATTATCAATA-AAATTGTGATGAATTTTTTTGACACTGAA-ACTATATTTAG-TGACCATCAAT
** * * * *
639334 GTTACCACATTAAGTATCTTTTAGTGACTAAATGTTTGACAC
63 GTTGTCACACTAAGTAT-TTTTAATGACCAAATGTTCGACAC
*
639376 TATTATCAATAGAAATTGTGATGAATTTATTTGACACT
1 TATTATCAATA-AAATTGTGATGAATTTTTTTGACACT
639414 AATTTTATGT
Statistics
Matches: 453, Mismatches: 76, Indels: 51
0.78 0.13 0.09
Matches are distributed among these distances:
100 1 0.00
101 30 0.07
102 82 0.18
103 140 0.31
104 104 0.23
105 96 0.21
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (103 bp):
TATTATCAATAAAATTGTGATGAATTTTTTTGACACTGAAACTATATTTAGTGACCATCAATGTT
GTCACACTAAGTATTTTTAATGACCAAATGTTCGACAC
Found at i:639235 original size:205 final size:206
Alignment explanation
Indices: 638859--639614 Score: 563
Period size: 207 Copynumber: 3.6 Consensus size: 206
638849 ATGTTCGACT
* * * * *
638859 CTATTATCAATACAAATATTGATGAATTGTTTTGACACTGAGAGTATATTTTGTGACCACCAATG
1 CTATTATCAATAGAAAT-TTGATGAATTTTTTTGACACTGAAAATATA-TTTGTGACCATCAATG
* * *
638924 TTGTCACACTAAGTATTTTTAAATGACCAAATGTTCGACACTATTATCAATAAAAA-TGTGTTG-
64 TTGTCACACTAAGTATTTTT-AGTGACAAAATGTTCGACACTATTATCAATAAAAATTGTGATGA
** * * * *
638987 ATTTTATTATACTGAAAGTATAATTAGTGATCACTAATGTTGTCACACTAA-GTG-TTTTTAGTG
128 ATTTTACAACACTGAAAGTATAATTAGTGACCACTAATGTTGTCACAC-AAGGTGTTTTTTAATA
* *
639050 ACCAAATGTT-AGGCA
192 ACCAAATATTGA-ACA
* * *
639065 -TCATTATCAATAGAAATTGTGAT-AATTTTTTTGGCATTGAAACTATATTTAGTGACCATCAAT
1 CT-ATTATCAATAGAAATT-TGATGAATTTTTTTGACACTGAAAATATATTT-GTGACCATCAAT
639128 GTTGTCACACTAAGTATTTTTAGTGACAAAATGTTCGACACTATTATCAATAAAAATTGTGATGA
63 GTTGTCACACTAAGTATTTTTAGTGACAAAATGTTCGACACTATTATCAATAAAAATTGTGATGA
* * * *
639193 ATTTGTACAACATTGAAA-TAT-ATTTGTGACCACTACTGTTGTCATACAAGGTGTTTTTTAATA
128 ATTT-TACAACACTGAAAGTATAATTAGTGACCACTAATGTTGTCACACAAGGTGTTTTTTAATA
**
639256 ATTAAATATTGAACA
192 ACCAAATATTGAACA
* * * * * *
639271 CTATTATCAGTAGAAATTATGATGAATTTATTTGACAGT-AACAATATATTTGTTG-TCATTAGT
1 CTATTATCAATAGAAATT-TGATGAATTTTTTTGACACTGAA-AATATATTTG-TGACCATCAAT
** * * * *
639334 GTTACCACATTAAGTATCTTTTAGTGACTAAATGTTTGACACTATTATCAATAGAAATTGTGATG
63 GTTGTCACACTAAGTAT-TTTTAGTGACAAAATGTTCGACACTATTATCAATAAAAATTGTGATG
*** ** ** * ** * *
639399 AATTTATTTGACACT-AATTTTATGTTTTGTGACCA-TAGATGTTACCACAATAAGAAT-TTTTT
127 AATTT-TACAACACTGAA-AGTATAATTAGTGACCACTA-ATGTTGTCAC-ACAAG-GTGTTTTT
**
639461 TAATAATTAAATATTGAACA
187 TAATAACCAAATATTGAACA
** * * * * * * * *
639481 CTATTATCGGTTGAAATTATGATGAATTTATTTGCCAGT-AACAATATATTTTTTCG-TCATTAG
1 CTATTATCAATAGAAATT-TGATGAATTTTTTTGACACTGAA-AATATA-TTTGT-GACCATCAA
* ** * * * * * *
639544 TGATAACACATTTAGTATCTTTTAGTGACTAAATGTTTGACATTATTATCAATAGAAATTGTGAT
62 TGTTGTCACACTAAGTAT-TTTTAGTGACAAAATGTTCGACACTATTATCAATAAAAATTGTGAT
639609 GAATTT
126 GAATTT
639615 ATTTGACACT
Statistics
Matches: 468, Mismatches: 60, Indels: 39
0.83 0.11 0.07
Matches are distributed among these distances:
204 38 0.08
205 84 0.18
206 84 0.18
207 87 0.19
208 5 0.01
209 16 0.03
210 75 0.16
211 79 0.17
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (206 bp):
CTATTATCAATAGAAATTTGATGAATTTTTTTGACACTGAAAATATATTTGTGACCATCAATGTT
GTCACACTAAGTATTTTTAGTGACAAAATGTTCGACACTATTATCAATAAAAATTGTGATGAATT
TTACAACACTGAAAGTATAATTAGTGACCACTAATGTTGTCACACAAGGTGTTTTTTAATAACCA
AATATTGAACA
Found at i:639522 original size:210 final size:210
Alignment explanation
Indices: 639246--639703 Score: 744
Period size: 211 Copynumber: 2.2 Consensus size: 210
639236 ATACAAGGTG
639246 TTTTTTAATAATTAAATATTGAACACTATTATCAGTAGAAATTATGATGAATTTATTTGACAGTA
1 TTTTTTAATAATTAAATATTGAACACTATTATCAGTAGAAATTATGATGAATTTATTTGACAGTA
* *
639311 ACAATATATTTGTT-GTCATTAGTGTTACCACATTAAGTATCTTTTAGTGACTAAATGTTTGACA
66 ACAATATATTTGTTCGTCATTAGTGATAACACATTAAGTATCTTTTAGTGACTAAATGTTTGACA
* *
639375 CTATTATCAATAGAAATTGTGATGAATTTATTTGACACTAATTTTATGTTTTGTGACCAT-AGAT
131 CTATTATCAATAGAAATTGTGATGAATTTATTTGACACTAATCTTATGTTTTGTGAACATCA-AT
639439 GTTACCACAATAAGAAT
195 GTTACCACAATAAG-AT
* * *
639456 TTTTTTAATAATTAAATATTGAACACTATTATCGGTTGAAATTATGATGAATTTATTTGCCAGTA
1 TTTTTTAATAATTAAATATTGAACACTATTATCAGTAGAAATTATGATGAATTTATTTGACAGTA
* *
639521 ACAATATATTTTTTCGTCATTAGTGATAACACATTTAGTATCTTTTAGTGACTAAATGTTTGACA
66 ACAATATATTTGTTCGTCATTAGTGATAACACATTAAGTATCTTTTAGTGACTAAATGTTTGACA
*
639586 TTATTATCAATAGAAATTGTGATGAATTTATTTGACACTAATCTTATGTTTTGTGAACATCAATG
131 CTATTATCAATAGAAATTGTGATGAATTTATTTGACACTAATCTTATGTTTTGTGAACATCAATG
* *
639651 TTACCACACTGAGAT
196 TTACCACAATAAGAT
*
639666 TTTTTTAATAATTAAATATTTG-ACA-TATTATCAATAGA
1 TTTTTTAATAATTAAATA-TTGAACACTATTATCAGTAGA
639704 TATTCAGACA
Statistics
Matches: 230, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
209 10 0.04
210 98 0.43
211 121 0.53
212 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (210 bp):
TTTTTTAATAATTAAATATTGAACACTATTATCAGTAGAAATTATGATGAATTTATTTGACAGTA
ACAATATATTTGTTCGTCATTAGTGATAACACATTAAGTATCTTTTAGTGACTAAATGTTTGACA
CTATTATCAATAGAAATTGTGATGAATTTATTTGACACTAATCTTATGTTTTGTGAACATCAATG
TTACCACAATAAGAT
Found at i:639602 original size:105 final size:104
Alignment explanation
Indices: 639268--639622 Score: 417
Period size: 106 Copynumber: 3.4 Consensus size: 104
639258 TAAATATTGA
* *
639268 ACACTATTATCAGTAGAAATTATGATGAATTTATTTGACAGTAACAATATATTTGTTGTCATTAG
1 ACACTATTATCAATAGAAATTATGATGAATTTATTTGACAGTAACAATATATTTTTTGTCATTAG
639333 TGTTACCACATTAAGTATCTTTTAGTGACTAAATGTTTG
66 TGTTACCACATTAAGTATCTTTTAGTGACTAAATGTTTG
* * *** * * *
639372 ACACTATTATCAATAGAAATTGTGATGAATTTATTTGACACTAATTTTATGTTTTGTGACCA-TA
1 ACACTATTATCAATAGAAATTATGATGAATTTATTTGACAGTAACAATATATTTTTTG-TCATTA
* * * * * * *
639436 GATGTTACCACAATAAGAATTTTTTTAATAATTAAAT-ATTG
65 G-TGTTACCACATTAAGTA-TCTTTTAGTGACTAAATGTTTG
** * *
639477 AACACTATTATCGGTTGAAATTATGATGAATTTATTTGCCAGTAACAATATATTTTTTCGTCATT
1 -ACACTATTATCAATAGAAATTATGATGAATTTATTTGACAGTAACAATATATTTTTT-GTCATT
* * *
639542 AGTGATAACACATTTAGTATCTTTTAGTGACTAAATGTTTG
64 AGTGTTACCACATTAAGTATCTTTTAGTGACTAAATGTTTG
* *
639583 ACATTATTATCAATAGAAATTGTGATGAATTTATTTGACA
1 ACACTATTATCAATAGAAATTATGATGAATTTATTTGACA
639623 CTAATCTTAT
Statistics
Matches: 199, Mismatches: 45, Indels: 13
0.77 0.18 0.05
Matches are distributed among these distances:
104 52 0.26
105 67 0.34
106 76 0.38
107 4 0.02
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (104 bp):
ACACTATTATCAATAGAAATTATGATGAATTTATTTGACAGTAACAATATATTTTTTGTCATTAG
TGTTACCACATTAAGTATCTTTTAGTGACTAAATGTTTG
Done.