Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004117.1 Hibiscus syriacus cultivar Beakdansim tig00009009_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: 2456583
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 9
Found at i:339073 original size:77 final size:76
Alignment explanation
Indices: 338932--339074 Score: 205
Period size: 77 Copynumber: 1.9 Consensus size: 76
338922 ATCGTACTTT
* * * * *
338932 TTACTTTTATAATTGAGGCTCCTAATTTTTCAATCTCGCTTTCTACATTTATAATTGAGGCCCCT
1 TTACCTTTATAATTGAGACCCCTAATTTTTCAATCTCACTTTCTACATTTATAATTGAGACCCCT
338997 ACTTTTTTTAA
66 ACTTTTTTTAA
* * *
339008 TTACCTTTATAATTGAGACCCCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGATACCCC
1 TTACCTTTATAATTGAGACCCCTAA-TTTTTCAATCTCACTTTCTACATTTATAATTGAGACCCC
339073 TA
65 TA
339075 ATTTAATAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
76 22 0.38
77 36 0.62
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.46
Consensus pattern (76 bp):
TTACCTTTATAATTGAGACCCCTAATTTTTCAATCTCACTTTCTACATTTATAATTGAGACCCCT
ACTTTTTTTAA
Found at i:339680 original size:18 final size:18
Alignment explanation
Indices: 339659--339697 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
339649 ATTGAAAATC
*
339659 AAAAAATAAAT-CAAAGA
1 AAAAAAAAAATGCAAAGA
*
339676 AAAAAAAAGATGCAAAGA
1 AAAAAAAAAATGCAAAGA
339694 AAAA
1 AAAA
339698 TATATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.77, C:0.05, G:0.10, T:0.08
Consensus pattern (18 bp):
AAAAAAAAAATGCAAAGA
Found at i:365509 original size:30 final size:29
Alignment explanation
Indices: 365450--365515 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
365440 CATGATTTGG
*
365450 TTGTAACAATCAATTAATTGGATGACTTAA
1 TTGTAACAATCAATTAATCGGAT-ACTTAA
365480 TTGTAACAATCAATTAATC-GAGTATCTTAA
1 TTGTAACAATCAATTAATCGGA-TA-CTTAA
365510 TTGTAA
1 TTGTAA
365516 AATACTTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (29 bp):
TTGTAACAATCAATTAATCGGATACTTAA
Found at i:379347 original size:30 final size:29
Alignment explanation
Indices: 379288--379353 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
379278 CATGATTTGG
*
379288 TTGTAACAATCAATTAATTGGATGACTTAA
1 TTGTAACAATCAATTAATCGGAT-ACTTAA
379318 TTGTAACAATCAATTAATC-GAGTATCTTAA
1 TTGTAACAATCAATTAATCGGA-TA-CTTAA
379348 TTGTAA
1 TTGTAA
379354 AATACTTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (29 bp):
TTGTAACAATCAATTAATCGGATACTTAA
Found at i:383975 original size:15 final size:15
Alignment explanation
Indices: 383955--383985 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
383945 GATATGCATA
383955 GTGATAATGCACATG
1 GTGATAATGCACATG
*
383970 GTGATAATGCGCATG
1 GTGATAATGCACATG
383985 G
1 G
383986 GACCGAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (15 bp):
GTGATAATGCACATG
Found at i:384528 original size:24 final size:24
Alignment explanation
Indices: 384499--384544 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
384489 TATTGGGAGC
*
384499 CACACCGCTTGGACTTGGAGCAGT
1 CACACCGCTTGAACTTGGAGCAGT
*
384523 CACACCGTTTGAACTTGGAGCA
1 CACACCGCTTGAACTTGGAGCA
384545 ATGTCCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (24 bp):
CACACCGCTTGAACTTGGAGCAGT
Found at i:391247 original size:10 final size:10
Alignment explanation
Indices: 391234--391259 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
391224 AAAGGTAGGA
391234 AAACATACAT
1 AAACATACAT
391244 AAACATACAT
1 AAACATACAT
391254 AAACAT
1 AAACAT
391260 GCGCCCTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (10 bp):
AAACATACAT
Found at i:392083 original size:20 final size:19
Alignment explanation
Indices: 392058--392321 Score: 251
Period size: 20 Copynumber: 13.1 Consensus size: 19
392048 TTGACATAAG
*
392058 TGGAACCGCGTTGCGATTCT
1 TGGAATCGCGTTGCGATT-T
*
392078 TGGAACCGCGTTGCGATTT
1 TGGAATCGCGTTGCGATTT
* *
392097 TCTGAATCGCATTGCGATTCT
1 T-GGAATCGCGTTGCGATT-T
392118 TGGAATCGCGTTGCGATTT
1 TGGAATCGCGTTGCGATTT
* *
392137 TCTGAATCGCATTGCGATTCT
1 T-GGAATCGCGTTGCGATT-T
392158 TGGAAGATCGCGTTGCGATTT
1 TGG-A-ATCGCGTTGCGATTT
* *
392179 TCTGAATCGCATTGCGATTCT
1 T-GGAATCGCGTTGCGATT-T
392200 TGGAATCGCGTTGCGATTT
1 TGGAATCGCGTTGCGATTT
* *
392219 TCTGAATCGCATTGCGATTCT
1 T-GGAATCGCGTTGCGATT-T
*
392240 TGGAAGATCGCGTTGCGCTTT
1 TGG-A-ATCGCGTTGCGATTT
* *
392261 TCTGAATCGCATTGCGATTCT
1 T-GGAATCGCGTTGCGATT-T
*
392282 TGGAATCGCGTTGCGGTTT
1 TGGAATCGCGTTGCGATTT
392301 T-GATATCGCGTTGCGATTT
1 TGGA-ATCGCGTTGCGATTT
392320 TG
1 TG
392322 TTGGTCATTT
Statistics
Matches: 203, Mismatches: 25, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
18 2 0.01
19 23 0.11
20 133 0.66
21 18 0.09
22 27 0.13
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (19 bp):
TGGAATCGCGTTGCGATTT
Found at i:392112 original size:40 final size:40
Alignment explanation
Indices: 392068--392318 Score: 407
Period size: 40 Copynumber: 6.2 Consensus size: 40
392058 TGGAACCGCG
*
392068 TTGCGATTCTTGGAACCGCGTTGCGATTTTCTGAATCGCA
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCA
392108 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCA
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCA
392148 TTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCA
1 TTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTGAATCGCA
392190 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCA
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCA
*
392230 TTGCGATTCTTGGAAGATCGCGTTGCGCTTTTCTGAATCGCA
1 TTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTGAATCGCA
* *
392272 TTGCGATTCTTGGAATCGCGTTGCG-GTTT-TGATATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTGA-ATCGCA
392311 TTGCGATT
1 TTGCGATT
392319 TTGTTGGTCA
Statistics
Matches: 202, Mismatches: 4, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
38 3 0.01
39 16 0.08
40 102 0.50
41 4 0.02
42 77 0.38
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCA
Found at i:392180 original size:82 final size:82
Alignment explanation
Indices: 392068--392318 Score: 429
Period size: 82 Copynumber: 3.1 Consensus size: 82
392058 TGGAACCGCG
*
392068 TTGCGATTCTTGG-A-ACCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAATCGCGTTG
1 TTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAATCGCGTTG
392131 CGATTTTCTGAATCGCA
66 CGATTTTCTGAATCGCA
392148 TTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAATCGCGTTG
1 TTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAATCGCGTTG
392213 CGATTTTCTGAATCGCA
66 CGATTTTCTGAATCGCA
*
392230 TTGCGATTCTTGGAAGATCGCGTTGCGCTTTTCTGAATCGCATTGCGATTCTTGGAATCGCGTTG
1 TTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAATCGCGTTG
* *
392295 CG-GTTT-TGATATCGCG
66 CGATTTTCTGA-ATCGCA
392311 TTGCGATT
1 TTGCGATT
392319 TTGTTGGTCA
Statistics
Matches: 164, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
80 16 0.10
81 17 0.10
82 131 0.80
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (82 bp):
TTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAATCGCGTTG
CGATTTTCTGAATCGCA
Found at i:393823 original size:2 final size:2
Alignment explanation
Indices: 393816--393854 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
393806 TATGAAGGCA
393816 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
393855 CACACACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:402203 original size:99 final size:100
Alignment explanation
Indices: 402031--402237 Score: 380
Period size: 99 Copynumber: 2.1 Consensus size: 100
402021 AGCAGGTATG
*
402031 ACATGACTCGGTTATGGGGGGAAAATATCAACCATAGAAGATAGCCCCAAGTATACGCATTGAAC
1 ACATGACTCGGTTATGGGGGAAAAATATCAACCATAGAAGATAGCCCCAAGTATACGCATTGAAC
402096 TAAAGCGTGGAAAATGCAAATCATAGCCAGTAGCC
66 TAAAGCGTGGAAAATGCAAATCATAGCCAGTAGCC
* *
402131 ACATGACTCGGTTAT-GGGGAAAAATATCAACCATAGAAGCTAGCCCCGAGTATACGCATTGAAC
1 ACATGACTCGGTTATGGGGGAAAAATATCAACCATAGAAGATAGCCCCAAGTATACGCATTGAAC
402195 TAAAGCGTGGAAAATGCAAATCATAGCCAGTAGCC
66 TAAAGCGTGGAAAATGCAAATCATAGCCAGTAGCC
402230 ACATGACT
1 ACATGACT
402238 TTGAAAGAAA
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
99 89 0.86
100 15 0.14
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (100 bp):
ACATGACTCGGTTATGGGGGAAAAATATCAACCATAGAAGATAGCCCCAAGTATACGCATTGAAC
TAAAGCGTGGAAAATGCAAATCATAGCCAGTAGCC
Found at i:404677 original size:7 final size:7
Alignment explanation
Indices: 404665--404695 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
404655 GTCAAAGAAA
404665 GTCAACG
1 GTCAACG
404672 GTCAACG
1 GTCAACG
404679 GTCAACG
1 GTCAACG
404686 GTCAACG
1 GTCAACG
404693 GTC
1 GTC
404696 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:404713 original size:22 final size:22
Alignment explanation
Indices: 404685--404727 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
404675 AACGGTCAAC
404685 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
404707 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
404728 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:404748 original size:19 final size:19
Alignment explanation
Indices: 404726--404823 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
404716 TCGGGTCGGG
404726 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
404745 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
404764 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
404783 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
404803 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
404823 T
1 T
404824 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 39 0.57
20 17 0.25
21 9 0.13
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:404754 original size:10 final size:9
Alignment explanation
Indices: 404724--404822 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
404714 GGTCGGGTCG
*
404724 GGTCAGACC
1 GGTCAAACC
404733 GGTCAAACC
1 GGTCAAACC
*
404742 GGTTCAGACC
1 GG-TCAAACC
404752 GGTCAAACC
1 GGTCAAACC
*
404761 GGTTCGAACC
1 GG-TCAAACC
*
404771 GGTTGAAACC
1 GG-TCAAACC
404781 GGTCAAACC
1 GGTCAAACC
404790 GGTCAGAACC
1 GGTCA-AACC
*
404800 GGTTGAAAACC
1 GG-T-CAAACC
*
404811 GGTTAAACC
1 GGTCAAACC
404820 GGT
1 GGT
404823 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:404781 original size:29 final size:28
Alignment explanation
Indices: 404725--404822 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
404715 GTCGGGTCGG
* * *
404725 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTGAAACCG
*
404753 GTCAAACCGGTTCGAACCGGTTGAAACCG
1 GTCAAACCGG-TCAAACCGGTTGAAACCG
404782 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTTG-AAACCG
*
404812 GTTAAACCGGT
1 GTCAAACCGGT
404823 TTCCAGCAGC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 11 0.18
29 34 0.56
30 16 0.26
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTGAAACCG
Found at i:411894 original size:7 final size:7
Alignment explanation
Indices: 411882--411912 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
411872 GTCAAAGAAA
411882 GTCAACG
1 GTCAACG
411889 GTCAACG
1 GTCAACG
411896 GTCAACG
1 GTCAACG
411903 GTCAACG
1 GTCAACG
411910 GTC
1 GTC
411913 GGGTCAGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:411930 original size:22 final size:22
Alignment explanation
Indices: 411902--411966 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
411892 AACGGTCAAC
*
411902 GGTCAACGGTCGGGTCAGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
411924 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
411946 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
411967 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:411939 original size:5 final size:5
Alignment explanation
Indices: 411909--411966 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
411899 AACGGTCAAC
* * *
411909 GGTCG GGTCA GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
411958 GGTCG GGTC
1 GGTCG GGTC
411967 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 35 0.81
7 8 0.19
ACGTcount: A:0.09, C:0.22, G:0.50, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:411987 original size:19 final size:19
Alignment explanation
Indices: 411965--412062 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
411955 TCGGGTCGGG
411965 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
411984 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
412003 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
412022 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
412042 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
412062 T
1 T
412063 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 39 0.57
20 17 0.25
21 9 0.13
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:411993 original size:10 final size:9
Alignment explanation
Indices: 411963--412061 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
411953 GGTCGGGTCG
*
411963 GGTCAGACC
1 GGTCAAACC
411972 GGTCAAACC
1 GGTCAAACC
*
411981 GGTTCAGACC
1 GG-TCAAACC
411991 GGTCAAACC
1 GGTCAAACC
*
412000 GGTTCGAACC
1 GG-TCAAACC
*
412010 GGTTGAAACC
1 GG-TCAAACC
412020 GGTCAAACC
1 GGTCAAACC
412029 GGTCAGAACC
1 GGTCA-AACC
*
412039 GGTTGAAAACC
1 GG-T-CAAACC
*
412050 GGTTAAACC
1 GGTCAAACC
412059 GGT
1 GGT
412062 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:412020 original size:29 final size:28
Alignment explanation
Indices: 411964--412061 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
411954 GTCGGGTCGG
* * *
411964 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTGAAACCG
*
411992 GTCAAACCGGTTCGAACCGGTTGAAACCG
1 GTCAAACCGG-TCAAACCGGTTGAAACCG
412021 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTTG-AAACCG
*
412051 GTTAAACCGGT
1 GTCAAACCGGT
412062 TTCCAGCAGC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 11 0.18
29 34 0.56
30 16 0.26
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTGAAACCG
Found at i:419242 original size:22 final size:20
Alignment explanation
Indices: 419205--419276 Score: 62
Period size: 22 Copynumber: 3.6 Consensus size: 20
419195 GGAATGAATG
419205 AAAT-AATAATAA-AATATCAA
1 AAATGAATAA-AAGAATAT-AA
419225 AAATGAAATAAAAGAATATAA
1 AAATG-AATAAAAGAATATAA
*
419246 TAAATG-AT-AAAGAATATGA
1 -AAATGAATAAAAGAATATAA
*
419265 AAATGTATAAAA
1 AAATGAATAAAA
419277 TGATTGCCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
18 5 0.11
19 12 0.27
20 9 0.20
21 4 0.09
22 15 0.33
ACGTcount: A:0.67, C:0.01, G:0.08, T:0.24
Consensus pattern (20 bp):
AAATGAATAAAAGAATATAA
Found at i:419259 original size:19 final size:19
Alignment explanation
Indices: 419235--419275 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
419225 AAATGAAATA
419235 AAAGAATATAATAAATG-AT
1 AAAGAATATAA-AAATGTAT
*
419254 AAAGAATATGAAAATGTAT
1 AAAGAATATAAAAATGTAT
419273 AAA
1 AAA
419276 ATGATTGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (19 bp):
AAAGAATATAAAAATGTAT
Found at i:426762 original size:39 final size:39
Alignment explanation
Indices: 426708--426783 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
426698 GAGTGCATGC
426708 AGGGGAGAGACGCATGGAGTGCAATGCGTCTTCGGGGGG
1 AGGGGAGAGACGCATGGAGTGCAATGCGTCTTCGGGGGG
* *
426747 AGGGGATAGACGCATGGAGTGCAATGCGTCTTTGGGG
1 AGGGGAGAGACGCATGGAGTGCAATGCGTCTTCGGGG
426784 TGTACTGTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.21, C:0.14, G:0.46, T:0.18
Consensus pattern (39 bp):
AGGGGAGAGACGCATGGAGTGCAATGCGTCTTCGGGGGG
Found at i:426988 original size:39 final size:37
Alignment explanation
Indices: 426938--427041 Score: 145
Period size: 39 Copynumber: 2.7 Consensus size: 37
426928 CCCAAAGACG
* *
426938 CATTGCACTCCATGCGTCTCTCCCATTTCCCCCCTAAGA
1 CATTGCACTCCATGCGTCTCTCCC--CTCCCCCCGAAGA
*
426977 CATTGCACTCCATGCGTCTATCCCCTCCCCCCGAAGA
1 CATTGCACTCCATGCGTCTCTCCCCTCCCCCCGAAGA
427014 CGTATTGCACTCCATGCGTCTCTCCCCT
1 C--ATTGCACTCCATGCGTCTCTCCCCT
427042 GCATGCACTC
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
37 12 0.20
39 47 0.80
ACGTcount: A:0.16, C:0.44, G:0.12, T:0.27
Consensus pattern (37 bp):
CATTGCACTCCATGCGTCTCTCCCCTCCCCCCGAAGA
Found at i:427093 original size:12 final size:12
Alignment explanation
Indices: 427078--427142 Score: 84
Period size: 12 Copynumber: 5.6 Consensus size: 12
427068 GACACTGCCC
427078 CTGCATGGCAGT
1 CTGCATGGCAGT
427090 CTGCAT-GCA-T
1 CTGCATGGCAGT
427100 GCTGCATGGCAGT
1 -CTGCATGGCAGT
427113 CTGCAT-GCA-T
1 CTGCATGGCAGT
427123 GCTGCATGGCAGT
1 -CTGCATGGCAGT
427136 CTGCATG
1 CTGCATG
427143 CATGCTGCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
10 2 0.04
11 18 0.38
12 25 0.53
13 2 0.04
ACGTcount: A:0.17, C:0.26, G:0.31, T:0.26
Consensus pattern (12 bp):
CTGCATGGCAGT
Found at i:427104 original size:23 final size:23
Alignment explanation
Indices: 427078--427157 Score: 153
Period size: 23 Copynumber: 3.5 Consensus size: 23
427068 GACACTGCCC
427078 CTGCATGGCAGTCTGCATGCATG
1 CTGCATGGCAGTCTGCATGCATG
427101 CTGCATGGCAGTCTGCATGCATG
1 CTGCATGGCAGTCTGCATGCATG
427124 CTGCATGGCAGTCTGCATGCATG
1 CTGCATGGCAGTCTGCATGCATG
427147 CTGCAT-GCAGT
1 CTGCATGGCAGT
427158 AATAACAGCA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 5 0.09
23 52 0.91
ACGTcount: A:0.17, C:0.26, G:0.30, T:0.26
Consensus pattern (23 bp):
CTGCATGGCAGTCTGCATGCATG
Found at i:427106 original size:11 final size:11
Alignment explanation
Indices: 427090--427155 Score: 82
Period size: 11 Copynumber: 5.8 Consensus size: 11
427080 GCATGGCAGT
427090 CTGCATGCATG
1 CTGCATGCATG
427101 CTGCATGGCA-G
1 CTGCAT-GCATG
427112 TCTGCATGCATG
1 -CTGCATGCATG
427124 CTGCATGGCA-G
1 CTGCAT-GCATG
427135 TCTGCATGCATG
1 -CTGCATGCATG
427147 CTGCATGCA
1 CTGCATGCA
427156 GTAATAACAG
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
11 29 0.59
12 20 0.41
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.26
Consensus pattern (11 bp):
CTGCATGCATG
Found at i:434394 original size:3 final size:3
Alignment explanation
Indices: 434386--434431 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
434376 ACATATATTA
*
434386 AAT AAT AAT AAT AAT AAT AAT -AT AGTT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
434431 A
1 A
434432 TTAAAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:434723 original size:43 final size:42
Alignment explanation
Indices: 434657--434884 Score: 132
Period size: 40 Copynumber: 5.4 Consensus size: 42
434647 ATAACTCGGT
* * *
434657 TCCTACGTGATGAGGACGGCTGGTTAACTGTGGTTGACACGGC
1 TCCTACGTGATGAAGA-GTCTGGTTAACTGTGGATGACACGGC
* *
434700 TCCTACGTGATGAAGAGATCTGG-T--C-GGGGAATGACATGGC
1 TCCTACGTGATGAAGAG-TCTGGTTAACTGTGG-ATGACACGGC
* ** * *
434740 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT-GATAACACGGT
1 TCCTACGTGATGAAGAG-TCTGG---T-TAACTGTGGATGACACGGC
* * * * *
434786 TCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAAGA-GTCTGGTTAACTGTGGATGACACGGC
* *
434829 TCCTACGTGATGAAGAGATCTGG-T--C-GGGGAATGACATGGC
1 TCCTACGTGATGAAGAG-TCTGGTTAACTGTGG-ATGACACGGC
*
434869 TCATACGTGATGAAGA
1 TCCTACGTGATGAAGA
434885 CGGCTGGCCA
Statistics
Matches: 142, Mismatches: 29, Indels: 31
0.70 0.14 0.15
Matches are distributed among these distances:
39 5 0.04
40 54 0.38
42 7 0.05
43 47 0.33
45 1 0.01
46 25 0.18
47 2 0.01
48 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (42 bp):
TCCTACGTGATGAAGAGTCTGGTTAACTGTGGATGACACGGC
Found at i:434747 original size:40 final size:41
Alignment explanation
Indices: 434691--434884 Score: 139
Period size: 40 Copynumber: 4.6 Consensus size: 41
434681 TAACTGTGGT
434691 TGACACGGCTCCTACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGATCAGGGG-A
* * * *
434731 TGACATGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGG--ATC---AGGGGA
* * * * * *
434777 TAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTA-TGGT
1 TGACACGGCTCCTACGTGATGAAGA-GATCTGG--ATC-AGGGGA
434820 TGACACGGCTCCTACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGATCAGGGG-A
* *
434860 TGACATGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAAGA
434885 CGGCTGGCCA
Statistics
Matches: 119, Mismatches: 24, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
39 2 0.02
40 54 0.45
42 1 0.01
43 29 0.24
44 1 0.01
46 28 0.24
47 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (41 bp):
TGACACGGCTCCTACGTGATGAAGAGATCTGGATCAGGGGA
Found at i:434839 original size:129 final size:131
Alignment explanation
Indices: 434604--434897 Score: 486
Period size: 129 Copynumber: 2.2 Consensus size: 131
434594 GGACGACACT
* *
434604 GCTCATACGTGATGAAGAGTTCGGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATG
1 GCTCATACGTGATGAAGAGTTCTGGCCATC--TA-GAAGGGTGATAACACGGTTCCTACGTGATG
*
434669 AGGACGGCTGGTTAACTGTGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGA
63 AGGACGGCTGGTTAACTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGA
434734 CATG
128 CATG
434738 GCTCATACGTGATGAAGAGTTCTGGCCATCTA-AA-GGTGATAACACGGTTCCTACGTGATGAGG
1 GCTCATACGTGATGAAGAGTTCTGGCCATCTAGAAGGGTGATAACACGGTTCCTACGTGATGAGG
*
434801 ACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACAT
66 ACGGCTGGTTAACTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACAT
434866 G
131 G
*
434867 GCTCATACGTGATGAAGACG-GCTGGCCATCT
1 GCTCATACGTGATGAAGA-GTTCTGGCCATCT
434898 TTAGGAGTTA
Statistics
Matches: 154, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
129 120 0.78
130 3 0.02
132 2 0.01
134 29 0.19
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (131 bp):
GCTCATACGTGATGAAGAGTTCTGGCCATCTAGAAGGGTGATAACACGGTTCCTACGTGATGAGG
ACGGCTGGTTAACTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACAT
G
Found at i:435661 original size:66 final size:65
Alignment explanation
Indices: 435549--435740 Score: 176
Period size: 66 Copynumber: 2.9 Consensus size: 65
435539 TATTTCTAGA
* * * **
435549 AAAAAAAATTGTCTCAAGGGATACAAAA-TTTGTTTTAATAGAAACAATCTCAAAGATGGGTATT
1 AAAAGAAATTGTCTCAA--GAGACAAAATTTTGTTTCAA-AGAAACAA-CTCAAAGATGGAAATT
435613 T-TC
62 TCTC
* * **
435616 AAAAGAAGTTGTCTCAAGAGACAAAATTTTGTTTCAAAGGAAACAAACTTAAA-A-AAAAATTTC
1 AAAAGAAATTGTCTCAAGAGACAAAATTTTGTTTCAAA-GAAAC-AACTCAAAGATGGAAATTTC
435679 TC
64 TC
* *
435681 AAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGA
1 AAAAGAAATTGTC-TCAAGAGACAAAATTTTGTTTC-AAAGAAACA-ACTCAAAGATGGA
435741 TCACATCTTA
Statistics
Matches: 101, Mismatches: 15, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
64 4 0.04
65 25 0.25
66 50 0.50
67 21 0.21
68 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (65 bp):
AAAAGAAATTGTCTCAAGAGACAAAATTTTGTTTCAAAGAAACAACTCAAAGATGGAAATTTCTC
Found at i:436024 original size:37 final size:37
Alignment explanation
Indices: 435968--436160 Score: 155
Period size: 37 Copynumber: 5.6 Consensus size: 37
435958 GAAACAGATT
435968 CAAAGATTTT-TTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAA-ATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
* ** * *
436005 CAAAATTTTGTTTCCAAAGAAACAAAC-TCA-A-AG-
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
*
436038 ---ATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
* ** * *
436072 CAAAATTTTGTTTCCAAAGAAACAAAC-TCA-A-AG-
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
*
436105 ---ATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
*
436139 CAAAATTTTGTTTCCAAAGAAA
1 CAAAATTTTGTTTCAAAAGAAA
436161 CAAACTCAAA
Statistics
Matches: 116, Mismatches: 25, Indels: 30
0.68 0.15 0.18
Matches are distributed among these distances:
30 38 0.33
31 4 0.03
32 2 0.02
33 4 0.03
34 4 0.03
35 2 0.02
36 9 0.08
37 53 0.46
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
Found at i:436051 original size:29 final size:29
Alignment explanation
Indices: 436010--436384 Score: 136
Period size: 30 Copynumber: 12.1 Consensus size: 29
436000 AGAGACAAAA
436010 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTT-CAAAGAAACAAACTCAAAGAT
** * * *
436040 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTC-AAAGAAACAAAC-TCA-A-AG----AT
436077 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTT-CAAAGAAACAAACTCAAAGAT
** * * *
436107 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTC-AAAGAAACAAAC-TCA-A-AG----AT
436144 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTT-CAAAGAAACAAACTCAAAGAT
** * *
436174 TTTTGTTTCAAAAGAAATTATCTTAAAGAT
1 TTTTGTTTC-AAAGAAACAAACTCAAAGAT
* **** *
436204 TTTT-TTTCACA-AAATTGTCTCAAGAGAGACAAAA
1 TTTTGTTTCAAAGAAACAAACTC-A-A-AG----AT
* * *
436238 CTTTGTTTCAAAGTAAATAGACTCAAAGA-
1 TTTTGTTTCAAAG-AAACAAACTCAAAGAT
*
436267 TTTT-TTTCAAACGAAAC-AACTCACAGAT
1 TTTTGTTTCAAA-GAAACAAACTCAAAGAT
* * * *
436295 TTTTATTCCAAAGGAACAAACTCCAAGAT
1 TTTTGTTTCAAAGAAACAAACTCAAAGAT
* *
436324 TTTT-ATTCAAAAGGAACAAACTCAAAGA-
1 TTTTGTTTC-AAAGAAACAAACTCAAAGAT
*
436352 TTTT-TTTCAAGAGGAACAAACTCAAAGAT
1 TTTTGTTTCAA-AGAAACAAACTCAAAGAT
436381 TTTT
1 TTTT
436385 CCTCAAAAGA
Statistics
Matches: 265, Mismatches: 44, Indels: 73
0.69 0.12 0.19
Matches are distributed among these distances:
27 18 0.07
28 47 0.18
29 53 0.20
30 67 0.25
31 4 0.02
32 2 0.01
33 4 0.02
34 10 0.04
35 9 0.03
36 5 0.02
37 44 0.17
38 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (29 bp):
TTTTGTTTCAAAGAAACAAACTCAAAGAT
Found at i:436063 original size:67 final size:67
Alignment explanation
Indices: 435957--436199 Score: 454
Period size: 67 Copynumber: 3.7 Consensus size: 67
435947 TCATTTTAAG
* *
435957 AGAAACAGATTCAAAGA-TTTT-TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
436020 AA
66 AA
436022 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
436087 AA
66 AA
436089 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
436154 AA
66 AA
436156 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAA
436200 AGATTTTTTT
Statistics
Matches: 174, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
65 15 0.09
66 4 0.02
67 155 0.89
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.32
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:436246 original size:94 final size:97
Alignment explanation
Indices: 436077--436298 Score: 269
Period size: 94 Copynumber: 2.4 Consensus size: 97
436067 AGAGACAAAA
* *
436077 TTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAA
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTCAAGAGAGACAA
*
436142 AATTTTGTTTCCAAAG-AAACAAACTCAAAGAT
66 AACTTTGTTT-CAAAGTAAACAAACTCAAAGAT
** * * * *
436174 TTTTGTTTCAAAAGAAATTATCTTAAAGATTTTT-TTTC-ACA-AAATTGTCTCAAGAGAGACAA
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTCAAGAGAGACAA
* *
436236 AACTTTGTTTCAAAGTAAATAGACTCAAAGA-
66 AACTTTGTTTCAAAGTAAACAAACTCAAAGAT
* *
436267 TTTT-TTTCAAACGAAAC-AACTCACAGATTTTT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
436299 ATTCCAAAGG
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
91 12 0.11
92 11 0.10
93 9 0.08
94 41 0.38
95 2 0.02
96 4 0.04
97 29 0.27
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (97 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTCAAGAGAGACAA
AACTTTGTTTCAAAGTAAACAAACTCAAAGAT
Found at i:436274 original size:28 final size:27
Alignment explanation
Indices: 436258--436384 Score: 166
Period size: 29 Copynumber: 4.5 Consensus size: 27
436248 AAGTAAATAG
*
436258 ACTCAAAGATTTTTTTCAAACGAA-ACA
1 ACTCAAAGATTTTTTTCAAAGGAACA-A
*
436285 ACTCACAGATTTTTATTCCAAAGGAACAA
1 ACTCAAAGATTTTT-TT-CAAAGGAACAA
*
436314 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-TTC-AAAGGAACAA
436343 ACTCAAAGATTTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTTCAA-AGGAACAA
436371 ACTCAAAGATTTTT
1 ACTCAAAGATTTTT
436385 CCTCAAAAGA
Statistics
Matches: 90, Mismatches: 5, Indels: 9
0.87 0.05 0.09
Matches are distributed among these distances:
27 15 0.17
28 28 0.31
29 46 0.51
30 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (27 bp):
ACTCAAAGATTTTTTTCAAAGGAACAA
Found at i:436334 original size:57 final size:56
Alignment explanation
Indices: 436258--436396 Score: 183
Period size: 57 Copynumber: 2.4 Consensus size: 56
436248 AAGTAAATAG
* *
436258 ACTCAAAGATTTTTTTCAAACGAAAC-AACTCACAGATTTTTATTCCAA-AGGAACAA
1 ACTCAAAGATTTTTTTCAAAAGAAACAAACTCAAAGATTTTT-TT-CAAGAGGAACAA
* *
436314 ACTCCAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGAAACAAACTCAAAGATTTTTTTCAAGAGGAACAA
*
436371 ACTCAAAGATTTTTCCTCAAAAGAAA
1 ACTCAAAGATTTTT-TTCAAAAGAAA
436397 TTGTCTTTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
56 16 0.22
57 42 0.58
58 14 0.19
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (56 bp):
ACTCAAAGATTTTTTTCAAAAGAAACAAACTCAAAGATTTTTTTCAAGAGGAACAA
Found at i:436419 original size:22 final size:22
Alignment explanation
Indices: 436389--436432 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
436379 ATTTTTCCTC
* *
436389 AAAAGAAATTGTCTTTAAGAGAT
1 AAAAGAAATCGT-TTTAAAAGAT
436412 AAAA-AAATCGTTTTAAAAGAT
1 AAAAGAAATCGTTTTAAAAGAT
436433 TCAAATATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 6 0.32
23 4 0.21
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.30
Consensus pattern (22 bp):
AAAAGAAATCGTTTTAAAAGAT
Found at i:436721 original size:36 final size:36
Alignment explanation
Indices: 436637--436740 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
436627 GAGAAAATGA
* * *
436637 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
436671 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
436707 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
436741 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:436768 original size:36 final size:36
Alignment explanation
Indices: 436638--436756 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
436628 AGAAAATGAT
* * * *
436638 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
436672 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
436708 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
436743 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
436757 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 19 0.28
35 12 0.17
36 38 0.55
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:436887 original size:105 final size:101
Alignment explanation
Indices: 436708--436940 Score: 258
Period size: 105 Copynumber: 2.3 Consensus size: 101
436698 TAGAGAAATT
*
436708 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
* * *
436772 GTGAAACAAATTCGAAATTTAG-ATCTCAAAGGGATAAG
64 GTGAAACAAATTCAAAATTT-GTATCTCAAAGGAAAAAG
* *
436810 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTGTTT
* * *
436874 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
61 AAT-GTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAAG
* *
436915 GTCTCAAACGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
436941 AAAATTCTCA
Statistics
Matches: 112, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 6 0.05
105 78 0.70
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGTATCTCAAAGGAAAAAG
Found at i:437447 original size:4 final size:4
Alignment explanation
Indices: 437398--437435 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
437388 TTTATGTATC
*
437398 ATGT ATGT ATG- -TGT ATGT ATGT ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
437436 GTTGATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:437760 original size:66 final size:66
Alignment explanation
Indices: 437675--437813 Score: 253
Period size: 66 Copynumber: 2.1 Consensus size: 66
437665 GAGATTATCT
*
437675 TGTTTAAAAGTGTTTTTCTTCTTCTTTTATTTTCAAAAGTCTGGCAATATCAATAGTTTTGAAAA
1 TGTTTAAAAGTGTTTTTCTTCTTCTTTTATTTTCAAAAGTCTGACAATATCAATAGTTTTGAAAA
437740 A
66 A
437741 TGTTTGAAAA-TGTTTTTCTTCTTCTTTTATTTTCAAAAGTCTGACAATATCAATAGTTTTGAAA
1 TGTTT-AAAAGTGTTTTTCTTCTTCTTTTATTTTCAAAAGTCTGACAATATCAATAGTTTTGAAA
437805 AA
65 AA
437807 TGTTTAA
1 TGTTTAA
437814 TCAAAAGATT
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
65 2 0.03
66 65 0.92
67 4 0.06
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (66 bp):
TGTTTAAAAGTGTTTTTCTTCTTCTTTTATTTTCAAAAGTCTGACAATATCAATAGTTTTGAAAA
A
Found at i:438693 original size:11 final size:11
Alignment explanation
Indices: 438679--438716 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
438669 CCTCTTTTTG
438679 TTCTTTGCTTT
1 TTCTTTGCTTT
438690 TTCTTTGCTTT
1 TTCTTTGCTTT
*
438701 TTGCTTTGATTT
1 TT-CTTTGCTTT
438713 TTCT
1 TTCT
438717 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.03, C:0.16, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGCTTT
Found at i:438703 original size:25 final size:26
Alignment explanation
Indices: 438672--438738 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
438662 TCTTTGTCCT
438672 CTTTTTGTTCTTTGCTTTT-TCTTTG
1 CTTTTTGTTCTTTGCTTTTCTCTTTG
*
438697 CTTTTTG--CTTTGATTTTTCTCTTTG
1 CTTTTTGTTCTTTG-CTTTTCTCTTTG
* *
438722 CTCTTTGTT-TTTTCTTT
1 CTTTTTGTTCTTTGCTTT
438739 GGTTTGATCT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
23 5 0.15
24 4 0.12
25 22 0.65
26 3 0.09
ACGTcount: A:0.01, C:0.16, G:0.10, T:0.72
Consensus pattern (26 bp):
CTTTTTGTTCTTTGCTTTTCTCTTTG
Found at i:438721 original size:18 final size:17
Alignment explanation
Indices: 438700--438746 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
438690 TTCTTTGCTT
438700 TTTGCTTTGATTTTTCTC
1 TTTGCTTTGATTTTT-TC
438718 TTTGCTCTTTG-TTTTTTC
1 TTTG--CTTTGATTTTTTC
*
438736 TTTGGTTTGAT
1 TTTGCTTTGAT
438747 CTTTGCACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.16
17 1 0.04
18 10 0.40
19 5 0.20
20 5 0.20
ACGTcount: A:0.04, C:0.13, G:0.15, T:0.68
Consensus pattern (17 bp):
TTTGCTTTGATTTTTTC
Found at i:439369 original size:26 final size:24
Alignment explanation
Indices: 439339--439409 Score: 78
Period size: 26 Copynumber: 3.0 Consensus size: 24
439329 CAAGGTGGAA
439339 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
* *
439363 AGGGAATGTTTCAAGGTC-GAAA-A-
1 A--GAATATTTCAAGGTCTCAAAGAG
439386 A-AATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
439409 A
1 A
439410 TAGAATGCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
20 13 0.34
21 3 0.08
22 1 0.03
23 2 0.05
24 2 0.05
25 3 0.08
26 14 0.37
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (24 bp):
AGAATATTTCAAGGTCTCAAAGAG
Found at i:439416 original size:46 final size:45
Alignment explanation
Indices: 439324--439416 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 45
439314 ATAAATACAG
* * *
439324 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAAAATATTTCAAGGTCTCAAAGAGAGAGAA
*
439369 TGTTTCAAGGTCGAAAAAAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAAAATATTTCAAGGTCTCAAAGAGAGAGAA
439415 TG
1 TG
439417 CCAAAAATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 11 0.26
46 32 0.74
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.26
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAAAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:440875 original size:31 final size:32
Alignment explanation
Indices: 440819--440880 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
440809 TGACAAAATG
440819 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
440851 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
440881 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:444360 original size:3 final size:3
Alignment explanation
Indices: 444352--444397 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
444342 ACATATATTA
*
444352 AAT AAT AAT AAT AAT AAT AAT -AT AGTT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
444397 A
1 A
444398 TTAAAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:447196 original size:30 final size:29
Alignment explanation
Indices: 447137--447202 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
447127 CATGATTTGG
*
447137 TTGTAACAATCAATTAATTGGATGACTTAA
1 TTGTAACAATCAATTAATCGGAT-ACTTAA
*
447167 TTGTGACAATCAATTAATC-GAGTATCTTAA
1 TTGTAACAATCAATTAATCGGA-TA-CTTAA
447197 TTGTAA
1 TTGTAA
447203 AATACTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (29 bp):
TTGTAACAATCAATTAATCGGATACTTAA
Found at i:450055 original size:16 final size:16
Alignment explanation
Indices: 450034--450067 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
450024 TTACTATTCA
*
450034 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
450050 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
450066 CG
1 CG
450068 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:459772 original size:3 final size:3
Alignment explanation
Indices: 459764--459827 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
459754 TACCCATATC
* * *
459764 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATC ATT ATT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
459812 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
459828 AATATATTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:459876 original size:10 final size:10
Alignment explanation
Indices: 459858--459890 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
459848 AAATATTATT
459858 ATAAAAAATA
1 ATAAAAAATA
*
459868 ATAATAAATA
1 ATAAAAAATA
459878 ATAAAAAATA
1 ATAAAAAATA
459888 ATA
1 ATA
459891 TTTACAGGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:463024 original size:83 final size:84
Alignment explanation
Indices: 462781--463272 Score: 773
Period size: 83 Copynumber: 5.9 Consensus size: 84
462771 TTATCTTAGT
* *
462781 CCAATCATTGAATCT-GAAAAATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTA
1 CCAATCATTGAATTTAG-AAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTA
** *
462845 TCTGATCTGGTTTAACGGAA
65 TCTGATCTGGTTTGGCAGAA
* * * *
462865 CCAATCATT-AACTGA-AAGATGAATGTGCTCAATAGCATCTTTTGGAAGCGTTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTAT
*
462928 CTGATCTGGTTTGGCAAAA
66 CTGATCTGGTTTGGCAGAA
**
462947 CCAATCATTGAATTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTATTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTAT
*
463011 CTGATCTGATTTGGCAGAA
66 CTGATCTGGTTTGGCAGAA
*
463030 CCAATCATTGAATTT-GAAAGATGAATTTGCTCAATAACATCTTCTGGAAGCGTTCTTTGAGTTA
1 CCAATCATTGAATTTAG-AAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTA
463094 TCTGATCTGGTTTGGCAGAA
65 TCTGATCTGGTTTGGCAGAA
*
463114 CCAATCATTGAATTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTAT
463178 CTGATCTGGTTTGGCAGAA
66 CTGATCTGGTTTGGCAGAA
*
463197 CCAATCATTGAATTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTAT
463261 CTGATCTGGTTT
66 CTGATCTGGTTT
463273 AGTAAAAATT
Statistics
Matches: 378, Mismatches: 24, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
82 70 0.19
83 209 0.55
84 98 0.26
85 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (84 bp):
CCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTAT
CTGATCTGGTTTGGCAGAA
Found at i:463104 original size:167 final size:167
Alignment explanation
Indices: 462781--463272 Score: 796
Period size: 167 Copynumber: 3.0 Consensus size: 167
462771 TTATCTTAGT
* * *
462781 CCAATCATTGAATCT-GAAAAATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTA
1 CCAATCATTGAATTTAG-AAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
** * * * *
462845 TCTGATCTGGTTTAACGGAACCAATCATT-AA-CTGAAAGATGAATGTGCTCAATAGCATCTTTT
64 TCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGAAAGATGAATTTGCTCAATAGCATCTTCT
462908 GGAAGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
129 GGAAGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
*
462947 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* *
463012 TGATCTGATTTGGCAGAACCAATCATTGAATTTGAAAGATGAATTTGCTCAATAACATCTTCTGG
66 TGATCTGGTTTGGCAGAACCAATCATTGAATTTGAAAGATGAATTTGCTCAATAGCATCTTCTGG
*
463077 AAGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
131 AAGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
463114 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
463179 TGATCTGGTTTGGCAGAACCAATCATTGAATTT-AGAAGATGAATTTGC-CAATAGCATCTTCTG
66 TGATCTGGTTTGGCAGAACCAATCATTGAATTTGA-AAGATGAATTTGCTCAATAGCATCTTCTG
*
463242 GAAGTGTTCTTTGAGTTATCTGATCTGGTTT
130 GAAGCGTTCTTTGAGTTATCTGATCTGGTTT
463273 AGTAAAAATT
Statistics
Matches: 305, Mismatches: 17, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
165 56 0.18
166 73 0.24
167 176 0.58
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (167 bp):
CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTGGCAGAACCAATCATTGAATTTGAAAGATGAATTTGCTCAATAGCATCTTCTGG
AAGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
Found at i:463233 original size:250 final size:249
Alignment explanation
Indices: 462781--463268 Score: 834
Period size: 250 Copynumber: 2.0 Consensus size: 249
462771 TTATCTTAGT
*
462781 CCAATCATTGAATCTGAAAAATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTAT
1 CCAATCATTGAATCTGAAAAATGAATTTGCTCAATAACATCTTCTGGAAGCGTTCTTTGAGTTAT
* *
462846 CTGATCTGGTTTAACGGAACCAATCATTAACTGAAAGATGAATGTGCTCAATAGCATCTTTTGGA
66 CTGATCTGGTTTAACAGAACCAATCATTAACTGAAAGATGAATGTGCTCAATAGCATCTTCTGGA
462911 AGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATTTAGAAGATGAATTTG
131 AGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATTTAGAAGATGAATTTG
462976 CCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTTGGCAGAA
196 CCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTTGGCAGAA
* *
463030 CCAATCATTGAATTTGAAAGATGAATTTGCTCAATAACATCTTCTGGAAGCGTTCTTTGAGTTAT
1 CCAATCATTGAATCTGAAAAATGAATTTGCTCAATAACATCTTCTGGAAGCGTTCTTTGAGTTAT
** * * *
463095 CTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTGC-CAATAGCATCTTCTG
66 CTGATCTGGTTTAACAGAACCAATCATT-AACTGA-AAGATGAATGTGCTCAATAGCATCTTCTG
* *
463159 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATT
129 GAAGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATTTAGAAGATGAATT
*
463224 TGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
194 TGCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
463269 GTTTAGTAAA
Statistics
Matches: 224, Mismatches: 13, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
249 87 0.39
250 125 0.56
251 12 0.05
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (249 bp):
CCAATCATTGAATCTGAAAAATGAATTTGCTCAATAACATCTTCTGGAAGCGTTCTTTGAGTTAT
CTGATCTGGTTTAACAGAACCAATCATTAACTGAAAGATGAATGTGCTCAATAGCATCTTCTGGA
AGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATTTAGAAGATGAATTTG
CCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTTGGCAGAA
Found at i:464475 original size:116 final size:113
Alignment explanation
Indices: 463855--464602 Score: 1111
Period size: 113 Copynumber: 6.5 Consensus size: 113
463845 GCAAAGATTC
463855 GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
463920 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
*
463968 GAATCCATCATTTGATAGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
464033 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
464081 GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
464146 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
*
464194 GAATCCATCATTTTATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
**
464259 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTACTT
* * * *** * * *
464308 GAATTCATCACTTGATGGATTATTGTTGCCAGAGGTAGAGTTCATAATGAGAAAAACTCGTCATC
1 GAATCCATCATTTGATGGATCAGCCTTTCCAGA-G-AAAGTTCATAATGAGAAGAA--C-TCATC
* *
464373 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
61 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
* * * * * * *
464426 AAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAAAAATCGTCATCT
1 GAATCCATCATTTGATGGATCAGCCTTTCCAGAG-AAAGTTCATAATGAG-AAGAA-C-TCATCT
* * *
464490 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTT
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
* * * ** *
464542 GAATTCATCATTTGATGGATCATCATCCCCAGCAGGAAGTTCATAATGAGAAGAACTCATC
1 GAATCCATCATTTGATGGATCAGCCTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATC
464603 AAGAGCTTAT
Statistics
Matches: 593, Mismatches: 33, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
113 328 0.55
114 36 0.06
115 2 0.00
116 125 0.21
117 18 0.03
118 35 0.06
119 49 0.08
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (113 bp):
GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
Found at i:464852 original size:3 final size:3
Alignment explanation
Indices: 464844--464938 Score: 163
Period size: 3 Copynumber: 31.7 Consensus size: 3
464834 TTTTTACCCA
464844 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
464892 TAT TAT TAT CAT CAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
464939 AATATATTAA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:464985 original size:10 final size:10
Alignment explanation
Indices: 464968--464999 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
464958 TAAATATTAT
464968 TAAAAAATAA
1 TAAAAAATAA
*
464978 TAATAAATAA
1 TAAAAAATAA
464988 TAAAAAATAA
1 TAAAAAATAA
464998 TA
1 TA
465000 TTTACAGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
TAAAAAATAA
Found at i:465483 original size:18 final size:18
Alignment explanation
Indices: 465460--465496 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
465450 ACAGAACTAG
465460 AGAGAAAGAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAC
465478 AGAGAAAGAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAC
465496 A
1 A
465497 ACAACAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.00
Consensus pattern (18 bp):
AGAGAAAGAAAAAAAAAC
Found at i:466329 original size:22 final size:23
Alignment explanation
Indices: 466297--466340 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
466287 TTAATTAGGA
466297 ATTAGATTTAG-T-TTTATTTTT
1 ATTAGATTTAGTTATTTATTTTT
466318 ATTAGAATTTAGTTATTTATTTT
1 ATTAG-ATTTAGTTATTTATTTT
466341 ATATGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 6 0.30
23 1 0.05
24 8 0.40
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (23 bp):
ATTAGATTTAGTTATTTATTTTT
Found at i:466428 original size:20 final size:21
Alignment explanation
Indices: 466391--466431 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
466381 GATATTTTTA
**
466391 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
466412 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
466432 ACATATAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:479206 original size:83 final size:84
Alignment explanation
Indices: 478963--479454 Score: 773
Period size: 83 Copynumber: 5.9 Consensus size: 84
478953 TTATCTTAGT
* *
478963 CCAATCATTGAATCT-GAAAAATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTA
1 CCAATCATTGAATTTAG-AAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTA
** *
479027 TCTGATCTGGTTTAACGGAA
65 TCTGATCTGGTTTGGCAGAA
* * * *
479047 CCAATCATT-AACTGA-AAGATGAATGTGCTCAATAGCATCTTTTGGAAGCGTTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTAT
*
479110 CTGATCTGGTTTGGCAAAA
66 CTGATCTGGTTTGGCAGAA
**
479129 CCAATCATTGAATTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTATTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTAT
*
479193 CTGATCTGATTTGGCAGAA
66 CTGATCTGGTTTGGCAGAA
*
479212 CCAATCATTGAATTT-GAAAGATGAATTTGCTCAATAACATCTTCTGGAAGCGTTCTTTGAGTTA
1 CCAATCATTGAATTTAG-AAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTA
479276 TCTGATCTGGTTTGGCAGAA
65 TCTGATCTGGTTTGGCAGAA
*
479296 CCAATCATTGAATTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTAT
479360 CTGATCTGGTTTGGCAGAA
66 CTGATCTGGTTTGGCAGAA
*
479379 CCAATCATTGAATTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTAT
479443 CTGATCTGGTTT
66 CTGATCTGGTTT
479455 AGTAAAAATT
Statistics
Matches: 378, Mismatches: 24, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
82 70 0.19
83 209 0.55
84 98 0.26
85 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (84 bp):
CCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTAT
CTGATCTGGTTTGGCAGAA
Found at i:479286 original size:167 final size:167
Alignment explanation
Indices: 478963--479454 Score: 796
Period size: 167 Copynumber: 3.0 Consensus size: 167
478953 TTATCTTAGT
* * *
478963 CCAATCATTGAATCT-GAAAAATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTA
1 CCAATCATTGAATTTAG-AAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
** * * * *
479027 TCTGATCTGGTTTAACGGAACCAATCATT-AA-CTGAAAGATGAATGTGCTCAATAGCATCTTTT
64 TCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGAAAGATGAATTTGCTCAATAGCATCTTCT
479090 GGAAGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
129 GGAAGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
*
479129 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* *
479194 TGATCTGATTTGGCAGAACCAATCATTGAATTTGAAAGATGAATTTGCTCAATAACATCTTCTGG
66 TGATCTGGTTTGGCAGAACCAATCATTGAATTTGAAAGATGAATTTGCTCAATAGCATCTTCTGG
*
479259 AAGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
131 AAGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
479296 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
479361 TGATCTGGTTTGGCAGAACCAATCATTGAATTT-AGAAGATGAATTTGC-CAATAGCATCTTCTG
66 TGATCTGGTTTGGCAGAACCAATCATTGAATTTGA-AAGATGAATTTGCTCAATAGCATCTTCTG
*
479424 GAAGTGTTCTTTGAGTTATCTGATCTGGTTT
130 GAAGCGTTCTTTGAGTTATCTGATCTGGTTT
479455 AGTAAAAATT
Statistics
Matches: 305, Mismatches: 17, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
165 56 0.18
166 73 0.24
167 176 0.58
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (167 bp):
CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTGGCAGAACCAATCATTGAATTTGAAAGATGAATTTGCTCAATAGCATCTTCTGG
AAGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
Found at i:479415 original size:250 final size:249
Alignment explanation
Indices: 478963--479450 Score: 834
Period size: 250 Copynumber: 2.0 Consensus size: 249
478953 TTATCTTAGT
*
478963 CCAATCATTGAATCTGAAAAATGAATTTGCTCAATAGCATCTTCTGGAAGCGTTCTTTGAGTTAT
1 CCAATCATTGAATCTGAAAAATGAATTTGCTCAATAACATCTTCTGGAAGCGTTCTTTGAGTTAT
* *
479028 CTGATCTGGTTTAACGGAACCAATCATTAACTGAAAGATGAATGTGCTCAATAGCATCTTTTGGA
66 CTGATCTGGTTTAACAGAACCAATCATTAACTGAAAGATGAATGTGCTCAATAGCATCTTCTGGA
479093 AGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATTTAGAAGATGAATTTG
131 AGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATTTAGAAGATGAATTTG
479158 CCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTTGGCAGAA
196 CCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTTGGCAGAA
* *
479212 CCAATCATTGAATTTGAAAGATGAATTTGCTCAATAACATCTTCTGGAAGCGTTCTTTGAGTTAT
1 CCAATCATTGAATCTGAAAAATGAATTTGCTCAATAACATCTTCTGGAAGCGTTCTTTGAGTTAT
** * * *
479277 CTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTGC-CAATAGCATCTTCTG
66 CTGATCTGGTTTAACAGAACCAATCATT-AACTGA-AAGATGAATGTGCTCAATAGCATCTTCTG
* *
479341 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATT
129 GAAGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATTTAGAAGATGAATT
*
479406 TGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
194 TGCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
479451 GTTTAGTAAA
Statistics
Matches: 224, Mismatches: 13, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
249 87 0.39
250 125 0.56
251 12 0.05
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (249 bp):
CCAATCATTGAATCTGAAAAATGAATTTGCTCAATAACATCTTCTGGAAGCGTTCTTTGAGTTAT
CTGATCTGGTTTAACAGAACCAATCATTAACTGAAAGATGAATGTGCTCAATAGCATCTTCTGGA
AGCGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATTTAGAAGATGAATTTG
CCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTTGGCAGAA
Found at i:480657 original size:116 final size:113
Alignment explanation
Indices: 480037--480784 Score: 1111
Period size: 113 Copynumber: 6.5 Consensus size: 113
480027 GCAAAGATTC
480037 GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
480102 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
*
480150 GAATCCATCATTTGATAGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
480215 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
480263 GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
480328 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
*
480376 GAATCCATCATTTTATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
**
480441 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTACTT
* * * *** * * *
480490 GAATTCATCACTTGATGGATTATTGTTGCCAGAGGTAGAGTTCATAATGAGAAAAACTCGTCATC
1 GAATCCATCATTTGATGGATCAGCCTTTCCAGA-G-AAAGTTCATAATGAGAAGAA--C-TCATC
* *
480555 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
61 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
* * * * * * *
480608 AAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAAAAATCGTCATCT
1 GAATCCATCATTTGATGGATCAGCCTTTCCAGAG-AAAGTTCATAATGAG-AAGAA-C-TCATCT
* * *
480672 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTT
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
* * * ** *
480724 GAATTCATCATTTGATGGATCATCATCCCCAGCAGGAAGTTCATAATGAGAAGAACTCATC
1 GAATCCATCATTTGATGGATCAGCCTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATC
480785 AAGAGCTTAT
Statistics
Matches: 593, Mismatches: 33, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
113 328 0.55
114 36 0.06
115 2 0.00
116 125 0.21
117 18 0.03
118 35 0.06
119 49 0.08
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (113 bp):
GAATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTT
Found at i:481034 original size:3 final size:3
Alignment explanation
Indices: 481026--481105 Score: 133
Period size: 3 Copynumber: 26.7 Consensus size: 3
481016 TTTTTACCCA
* *
481026 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
481074 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
481106 AATATATTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:481113 original size:15 final size:13
Alignment explanation
Indices: 481026--481114 Score: 100
Period size: 12 Copynumber: 7.2 Consensus size: 13
481016 TTTTTACCCA
481026 TATTAT-TATTAT
1 TATTATATATTAT
481038 TATTAT-TATTAT
1 TATTATATATTAT
481050 TATTAT-TATTAT
1 TATTATATATTAT
481062 TATTATCATCATTAT
1 TATTAT-AT-ATTAT
*
481077 TATTAT-TATCAT
1 TATTATATATTAT
481089 TATTAT-TATTAT
1 TATTATATATTAT
*
481101 TATTAAATA-TAT
1 TATTATATATTAT
481113 TA
1 TA
481115 AATACATATA
Statistics
Matches: 70, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
12 55 0.79
13 3 0.04
14 1 0.01
15 11 0.16
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:482203 original size:22 final size:23
Alignment explanation
Indices: 482171--482214 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
482161 TTAATTAGGA
482171 ATTAGATTTAG-T-TTTATTTTT
1 ATTAGATTTAGTTATTTATTTTT
482192 ATTAGAATTTAGTTATTTATTTT
1 ATTAG-ATTTAGTTATTTATTTT
482215 ATATGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 6 0.30
23 1 0.05
24 8 0.40
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (23 bp):
ATTAGATTTAGTTATTTATTTTT
Found at i:482302 original size:20 final size:21
Alignment explanation
Indices: 482265--482305 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
482255 GATATTTTTA
**
482265 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
482286 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
482306 ACATATAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:484113 original size:30 final size:29
Alignment explanation
Indices: 484054--484119 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
484044 CATGATTTGG
*
484054 TTGTAACAATCAATTAATTGGATGACTTAA
1 TTGTAACAATCAATTAATCGGAT-ACTTAA
484084 TTGTAACAATCAATTAATC-GAGTATCTTAA
1 TTGTAACAATCAATTAATCGGA-TA-CTTAA
484114 TTGTAA
1 TTGTAA
484120 AATACTTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (29 bp):
TTGTAACAATCAATTAATCGGATACTTAA
Found at i:492150 original size:3 final size:3
Alignment explanation
Indices: 492142--492196 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
492132 TCTAATTTTA
*
492142 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATGT -TT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT -ATT ATT ATT
492188 ATT ATT ATT
1 ATT ATT ATT
492197 TTTGCAGGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 42 0.89
4 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:494008 original size:19 final size:19
Alignment explanation
Indices: 493967--494009 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
493957 ATTCCTTTTG
* **
493967 TATGTACTTATTTTTATGT
1 TATGTACTTATTTATATCA
*
493986 TATGTATTTATTTATATCA
1 TATGTACTTATTTATATCA
494005 TATGT
1 TATGT
494010 GAATTAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (19 bp):
TATGTACTTATTTATATCA
Found at i:498926 original size:30 final size:31
Alignment explanation
Indices: 498890--498950 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
498880 GACGCAGAGT
**
498890 GCAAAGATCAAACCAAAG-AAAAAACAAAGA
1 GCAAAGAGAAAACCAAAGCAAAAAACAAAGA
* *
498920 GCAAAGAGAAAATCAAAGCAAAAATCAAAGA
1 GCAAAGAGAAAACCAAAGCAAAAAACAAAGA
498951 AAAAGCAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.66, C:0.15, G:0.15, T:0.05
Consensus pattern (31 bp):
GCAAAGAGAAAACCAAAGCAAAAAACAAAGA
Found at i:498943 original size:12 final size:11
Alignment explanation
Indices: 498921--498962 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
498911 AAACAAAGAG
498921 CAAAGAGAAAAT
1 CAAAGA-AAAAT
498933 CAAAGCAAAAAT
1 CAAAG-AAAAAT
*
498945 CAAAGAAAAAG
1 CAAAGAAAAAT
498956 CAAAGAA
1 CAAAGAA
498963 CAAAAGAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 12 0.43
12 15 0.54
13 1 0.04
ACGTcount: A:0.69, C:0.12, G:0.14, T:0.05
Consensus pattern (11 bp):
CAAAGAAAAAT
Found at i:500156 original size:4 final size:4
Alignment explanation
Indices: 500149--500214 Score: 118
Period size: 4 Copynumber: 17.0 Consensus size: 4
500139 ATACATTAAC
500149 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
500197 ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT
500215 GATACATAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
4 58 0.97
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:500617 original size:36 final size:36
Alignment explanation
Indices: 500557--500665 Score: 128
Period size: 38 Copynumber: 2.9 Consensus size: 36
500547 TAAAAAAAAA
* * * *
500557 AAAAACAAAGTGTCGTCTCACTTGAGACAGTTTTCTT
1 AAAAACAAA-TTTTGTCTCGCTTGAGACACTTTTCTT
500594 AAAAACAAATTTTGTCTCGCTTGAGACAACTTTCTCTT
1 AAAAACAAATTTTGTCTCGCTTGAGAC-ACTTT-TCTT
* * *
500632 TAAAACAAATTATGTCTCGCTTGAGACATTTTTC
1 AAAAACAAATTTTGTCTCGCTTGAGACACTTTTC
500666 CACAAATTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
36 17 0.27
37 17 0.27
38 29 0.46
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (36 bp):
AAAAACAAATTTTGTCTCGCTTGAGACACTTTTCTT
Found at i:500707 original size:66 final size:66
Alignment explanation
Indices: 500617--500748 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
500607 GTCTCGCTTG
*
500617 AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAGAAT
1 AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAAAAT
500682 T
66 T
500683 AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAAAAT
1 AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAAAAT
500748 T
66 T
500749 TTAAAACAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (66 bp):
AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAAAAT
T
Found at i:500938 original size:105 final size:102
Alignment explanation
Indices: 500751--500989 Score: 288
Period size: 105 Copynumber: 2.3 Consensus size: 102
500741 TGAAAATTTT
* * *
500751 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
*
500816 AAAAACAAAATTAATCTCACCTT-AGATTCTTGTTTCTTTC-
66 AAAAACAAAATTAATCTCA-CTTGAGA-TCAT-TTTC--TCA
* * *
500856 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
* * *
500920 ATTAAACAAAGTTGATCTCACTTGAGATCATTTTCTCA
66 A-AAAACAAAATTAATCTCACTTGAGATCATTTTCTCA
*
500958 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
500990 TCTAAAAACA
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
101 2 0.02
102 26 0.22
103 7 0.06
104 7 0.06
105 76 0.64
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
AAAAACAAAATTAATCTCACTTGAGATCATTTTCTCA
Found at i:500980 original size:36 final size:36
Alignment explanation
Indices: 500935--501053 Score: 118
Period size: 36 Copynumber: 3.4 Consensus size: 36
500925 ACAAAGTTGA
*
500935 TCTCACTTGAGATCATTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
500971 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * * * *
501007 TCTCATTTGAGACTATATCT-T-AAAGCAAAGTTCG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
*
501041 TCTCGCTTGAGAC
1 TCTCACTTGAGAC
501054 GTCATTTTCT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 21 0.30
35 9 0.13
36 40 0.57
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:501336 original size:29 final size:28
Alignment explanation
Indices: 501303--501367 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
501293 CAGTTTCTCG
501303 TGAATAAAAATCTTGGAGTTTGTTCCTTT
1 TGAATAAAAATCTTGGAG-TTGTTCCTTT
* * *
501332 TGAATAAATATCTTTGAGTTGTTTCTTT
1 TGAATAAAAATCTTGGAGTTGTTCCTTT
501360 TGAA-AAAA
1 TGAATAAAA
501368 TCTGTGAGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 3 0.09
28 13 0.41
29 16 0.50
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (28 bp):
TGAATAAAAATCTTGGAGTTGTTCCTTT
Found at i:501362 original size:28 final size:27
Alignment explanation
Indices: 501303--501376 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 27
501293 CAGTTTCTCG
*
501303 TGAATAAAAATCTTGGAGTTTGTTCCTTT
1 TGAAT-AAAATCTTTGAG-TTGTTCCTTT
*
501332 TGAATAAATATCTTTGAGTTGTTTCTTT
1 TGAATAAA-ATCTTTGAGTTGTTCCTTT
*
501360 TGAA-AAAATCTGTGAGT
1 TGAATAAAATCTTTGAGT
501377 CTATTTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 9 0.22
27 3 0.07
28 16 0.39
29 13 0.32
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.45
Consensus pattern (27 bp):
TGAATAAAATCTTTGAGTTGTTCCTTT
Found at i:501438 original size:119 final size:119
Alignment explanation
Indices: 501262--501538 Score: 421
Period size: 119 Copynumber: 2.3 Consensus size: 119
501252 TATTTGAATC
* *
501262 TTTTAAAACGATTTTTTTTATCTCTTAAAGACAGTTTCTCGTGAATAAAAATCTTGGAGTTTGTT
1 TTTTAAAACGA-TTTTTGTATCTCTT-GAGACAGTTTCTCGTGAATAAAAATCTTGGAGTTTGTT
501327 CCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAATCTGTGAGTCTATTTA
64 CCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTG-AAAAATCTGTGAGTCTATTTA
* *
501384 TTTTAAAACGATTTTTGTGTCTCTTGAGACAGTTTCTCTTGAA-AAAAATCTTGGAGTTTGTTCC
1 TTTTAAAACGATTTTTGTATCTCTTGAGACAGTTTCTCGTGAATAAAAATCTTGGAGTTTGTTCC
*
501448 TTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTATTTA
66 TTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTGTGAGTCTATTTA
* * * * *
501502 TTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTC
1 TTTTAAAAC-GATTTTTGTATCTCTTGAGACAGTTTC
501539 GTGAAAAATC
Statistics
Matches: 144, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
118 28 0.19
119 77 0.53
120 16 0.11
121 12 0.08
122 11 0.08
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (119 bp):
TTTTAAAACGATTTTTGTATCTCTTGAGACAGTTTCTCGTGAATAAAAATCTTGGAGTTTGTTCC
TTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTGTGAGTCTATTTA
Found at i:501464 original size:29 final size:27
Alignment explanation
Indices: 501422--501486 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 27
501412 ACAGTTTCTC
*
501422 TTGAAAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAATATCTTGGAG-TTGTTCCTT
* *
501450 TTGAATAAATATCTTTGAGTTGTTTCTT
1 TTGAA-AAATATCTTGGAGTTGTTCCTT
501478 TTGAAAAAT
1 TTGAAAAAT
501487 CTTTGAGTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 4 0.12
28 18 0.55
29 11 0.33
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (27 bp):
TTGAAAAATATCTTGGAGTTGTTCCTT
Found at i:501494 original size:25 final size:25
Alignment explanation
Indices: 501427--501509 Score: 85
Period size: 26 Copynumber: 3.1 Consensus size: 25
501417 TTCTCTTGAA
* *
501427 AAAAATCTTGGAGTTTGTTCCTTTTG
1 AAAAATCTTTGAG-TTGTTTCTTTTG
501453 AATAAATATCTTTGAGTTGTTTCTTTTG
1 -A-AAA-ATCTTTGAGTTGTTTCTTTTG
* *
501481 AAAAATCTTTGAGTCTATTTATTTTG
1 AAAAATCTTTGAGT-TGTTTCTTTTG
501507 AAA
1 AAA
501510 CAAAGTTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
25 10 0.20
26 15 0.31
27 2 0.04
28 14 0.29
29 8 0.16
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.48
Consensus pattern (25 bp):
AAAAATCTTTGAGTTGTTTCTTTTG
Found at i:501583 original size:52 final size:53
Alignment explanation
Indices: 501505--501608 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
501495 CTATTTATTT
501505 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
501557 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
501609 ATTGTTTCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 36 0.73
54 13 0.27
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:501630 original size:30 final size:30
Alignment explanation
Indices: 501596--501860 Score: 161
Period size: 30 Copynumber: 8.1 Consensus size: 30
501586 ATTTTGTGAA
* *
501596 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
1 AAAAATCTTTAAGATTGTTTCTTTGGAAAC
*
501626 AAAAATCTTTAAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTAAGATTGTTTCTTTGGAAAC
* ** *
501656 AAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATCT-TTAAGATTGTTTCTTTGGAAAC
*
501693 AAAAATCTTTAAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTAAGATTGTTTCTTTGGAAAC
* ** *
501723 AAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATCT-TTAAGATTGTTTCTTTGGAAAC
* *
501760 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTAAGATTGTTTCTTTGGAAAC
* ** *
501790 AAAATTTTGTCTCTTTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATC-TTTAAGATTGTTTCTTTGGAAAC
* *
501827 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTAAGATTGTTTCTTTGGAAAC
501857 AAAA
1 AAAA
501861 TTTTGTCTCT
Statistics
Matches: 178, Mismatches: 36, Indels: 42
0.70 0.14 0.16
Matches are distributed among these distances:
30 96 0.54
31 8 0.04
36 8 0.04
37 66 0.37
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (30 bp):
AAAAATCTTTAAGATTGTTTCTTTGGAAAC
Found at i:501688 original size:67 final size:67
Alignment explanation
Indices: 501613--501892 Score: 533
Period size: 67 Copynumber: 4.2 Consensus size: 67
501603 TTTGAGATTG
501613 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
501678 AA
66 AA
501680 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
501745 AA
66 AA
* *
501747 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
501812 AA
66 AA
*
501814 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
501879 AA
66 AA
501881 TTTCTTTTGAAA
1 TTTCTTTTGAAA
501893 AAATCTTTGA
Statistics
Matches: 210, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 210 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:502222 original size:64 final size:63
Alignment explanation
Indices: 502143--502267 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 63
502133 GATGAGATCC
* *
502143 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
* * **
502207 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
502268 TACCAACCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 19 0.35
64 36 0.65
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:502447 original size:15 final size:15
Alignment explanation
Indices: 502424--502482 Score: 100
Period size: 15 Copynumber: 3.9 Consensus size: 15
502414 TTTTGAGTCG
*
502424 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
502439 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
502454 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
502469 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
502483 AGATCATCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:502956 original size:40 final size:41
Alignment explanation
Indices: 502897--503272 Score: 219
Period size: 43 Copynumber: 8.7 Consensus size: 41
502887 TAGATGGCCA
* *
502897 ACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAG
1 ACCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAG
* * * **
502938 ATC-TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG
1 ACCGTCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAG
*
502981 -CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCA-
1 ACCGTCCTCATCACGTAGGAACCGTGTCAT--CC--CC---AGA---CCAG
* *
503030 ACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAG
1 ACCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAG
* * * **
503071 ATC-TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG
1 ACCGTCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAG
*
503114 -CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCA-
1 ACCGTCCTCATCACGTAGGAACCGTGTCAT--CC--CC---AGA---CCAG
* *
503163 ACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAG
1 ACCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAG
* * * **
503204 ATC-TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCA-
1 ACCGTCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAG
*
503246 ACCGTACTCATCACGTAGGAACCGTGT
1 ACCGTCCTCATCACGTAGGAACCGTGT
503273 TATCACCTTC
Statistics
Matches: 257, Mismatches: 42, Indels: 70
0.70 0.11 0.19
Matches are distributed among these distances:
40 84 0.33
41 6 0.02
42 4 0.02
43 87 0.34
45 4 0.02
46 4 0.02
47 2 0.01
48 4 0.02
50 62 0.24
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (41 bp):
ACCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAG
Found at i:502991 original size:43 final size:43
Alignment explanation
Indices: 502898--503272 Score: 234
Period size: 40 Copynumber: 8.6 Consensus size: 43
502888 AGATGGCCAA
* * **
502898 CCGTCCTCATCATGTAGGAATCGTGTCATCCCCAG---ACCAG
1 CCGTCCTCATCACGTAGGAACCGTGTCATCCATAGATAACCAG
* * *
502938 ATC-TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG
1 -CCGTCCTCATCACGTAGGAACCGTGTCATCCATAGATAACCAG
* ** *
502981 CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCAA
1 CCGTCCTCATCACGTAGGAACCGTG---TCA---TCC-ATAGATAACCAG
* * **
503031 CCGTCCTCATCATGTAGGAATCGTGTCATCCCCAG---ACCAG
1 CCGTCCTCATCACGTAGGAACCGTGTCATCCATAGATAACCAG
* * *
503071 ATC-TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG
1 -CCGTCCTCATCACGTAGGAACCGTGTCATCCATAGATAACCAG
* ** *
503114 CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCAA
1 CCGTCCTCATCACGTAGGAACCGTG---TCA---TCC-ATAGATAACCAG
* * **
503164 CCGTCCTCATCATGTAGGAATCGTGTCATCCCCAG---ACCAG
1 CCGTCCTCATCACGTAGGAACCGTGTCATCCATAGATAACCAG
* * * *
503204 ATC-TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAA
1 -CCGTCCTCATCACGTAGGAACCGTGTCATCCATAGATAACCAG
*
503247 CCGTACTCATCACGTAGGAACCGTGT
1 CCGTCCTCATCACGTAGGAACCGTGT
503273 TATCACCTTC
Statistics
Matches: 255, Mismatches: 51, Indels: 54
0.71 0.14 0.15
Matches are distributed among these distances:
40 84 0.33
41 3 0.01
42 3 0.01
43 81 0.32
44 6 0.02
46 6 0.02
47 6 0.02
49 4 0.02
50 62 0.24
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.22
Consensus pattern (43 bp):
CCGTCCTCATCACGTAGGAACCGTGTCATCCATAGATAACCAG
Found at i:503056 original size:50 final size:48
Alignment explanation
Indices: 502981--503312 Score: 182
Period size: 50 Copynumber: 7.3 Consensus size: 48
502971 AGATAACCAG
502981 CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCAA
1 CCGTCCTCATCACGTAGGAACCGTGTTATCACC-TCC-AAAGATGGCCAA
* * *
503031 CCGTCCTCATCATGTAGGAATCGTGTCAT--CC-CC--AGA---CCAGA
1 CCGTCCTCATCACGTAGGAACCGTGTTATCACCTCCAAAGATGGCCA-A
* * * * ** *
503072 TC-TCCTCATCACGTAGGAGCCGTG---TCA--ACCATAGATAACCAG
1 CCGTCCTCATCACGTAGGAACCGTGTTATCACCTCCAAAGATGGCCAA
503114 CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCAA
1 CCGTCCTCATCACGTAGGAACCGTGTTATCACC-TCC-AAAGATGGCCAA
* * *
503164 CCGTCCTCATCATGTAGGAATCGTGTCAT--CC-CC--AGA---CCAGA
1 CCGTCCTCATCACGTAGGAACCGTGTTATCACCTCCAAAGATGGCCA-A
* * * * **
503205 TC-TCCTCATCACGTAGGAGCCGTG---TCA--ACCATAGATAACCAA
1 CCGTCCTCATCACGTAGGAACCGTGTTATCACCTCCAAAGATGGCCAA
*
503247 CCGTACTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCAGA
1 CCGTCCTCATCACGTAGGAACCGTGTTATCACC-TCC-AAAGATGGCCA-A
* *
503298 AC-TCTTCATCACGTA
1 CCGTCCTCATCACGTA
503313 TGAGCAGTGT
Statistics
Matches: 215, Mismatches: 32, Indels: 70
0.68 0.10 0.22
Matches are distributed among these distances:
37 2 0.01
38 4 0.02
40 50 0.23
41 4 0.02
42 3 0.01
43 53 0.25
46 10 0.05
48 4 0.02
49 4 0.02
50 79 0.37
51 2 0.01
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (48 bp):
CCGTCCTCATCACGTAGGAACCGTGTTATCACCTCCAAAGATGGCCAA
Found at i:503330 original size:133 final size:133
Alignment explanation
Indices: 502888--503295 Score: 798
Period size: 133 Copynumber: 3.1 Consensus size: 133
502878 TAACTCCTTT
502888 AGATGGCCAACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
1 AGATGGCCAACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
502953 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCC
66 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCC
503018 TAA
131 TAA
503021 AGATGGCCAACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
1 AGATGGCCAACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
503086 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCC
66 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCC
503151 TAA
131 TAA
503154 AGATGGCCAACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
1 AGATGGCCAACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
* *
503219 AGGAGCCGTGTCAACCATAGATAACCAACCGTACTCATCACGTAGGAACCGTGTTATCACCTTCC
66 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCC
503284 TAA
131 TAA
503287 AGATGGCCA
1 AGATGGCCA
503296 GAACTCTTCA
Statistics
Matches: 273, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 273 1.00
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (133 bp):
AGATGGCCAACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCC
TAA
Found at i:503497 original size:3 final size:3
Alignment explanation
Indices: 503489--503543 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
503479 TCTAATTTTA
*
503489 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATGT -TT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT -ATT ATT ATT
503535 ATT ATT ATT
1 ATT ATT ATT
503544 TTTGCAGGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 42 0.89
4 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:504128 original size:10 final size:9
Alignment explanation
Indices: 504111--504137 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
504101 GGGGGTTTCC
504111 AGAAAAAAA
1 AGAAAAAAA
504120 AGAAAAAAA
1 AGAAAAAAA
504129 AGAAAAAAA
1 AGAAAAAAA
504138 GAGAGTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:505352 original size:19 final size:19
Alignment explanation
Indices: 505311--505353 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
505301 ATTCCTTTTG
* **
505311 TATGTACTTATTTTTATGT
1 TATGTACTTATTTATATCA
*
505330 TATGTATTTATTTATATCA
1 TATGTACTTATTTATATCA
505349 TATGT
1 TATGT
505354 GAATTAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (19 bp):
TATGTACTTATTTATATCA
Found at i:511725 original size:22 final size:22
Alignment explanation
Indices: 511699--511752 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
511689 TTACATTTCC
511699 ATAATGCATACGTTTTATTATA
1 ATAATGCATACGTTTTATTATA
511721 ATAATGCATACGTTTTATTATA
1 ATAATGCATACGTTTTATTATA
511743 ATAATGCATA
1 ATAATGCATA
511753 ATAATGATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (22 bp):
ATAATGCATACGTTTTATTATA
Found at i:539351 original size:30 final size:30
Alignment explanation
Indices: 539317--539373 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
539307 ATGGTAACAC
**
539317 ATGATTTGGTTGTAACAATCAATTAATTGG
1 ATGATTTAATTGTAACAATCAATTAATTGG
*
539347 ATGATTTAATTGTGACAATCAATTAAT
1 ATGATTTAATTGTAACAATCAATTAAT
539374 CGAGTATCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (30 bp):
ATGATTTAATTGTAACAATCAATTAATTGG
Found at i:539386 original size:30 final size:30
Alignment explanation
Indices: 539317--539391 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
539307 ATGGTAACAC
** *
539317 ATGATTTGGTTGTAACAATCAATTAATTGG
1 ATGATTTAATTGTAACAATCAATTAATCGG
*
539347 ATGATTTAATTGTGACAATCAATTAATC-G
1 ATGATTTAATTGTAACAATCAATTAATCGG
539376 A-GTATCTTAATTGTAA
1 ATG-AT-TTAATTGTAA
539392 AATACTTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 1 0.03
29 4 0.11
30 33 0.87
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (30 bp):
ATGATTTAATTGTAACAATCAATTAATCGG
Found at i:540807 original size:11 final size:11
Alignment explanation
Indices: 540792--540827 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
540782 AGATGTTGCT
540792 GTTCGGTTGTG
1 GTTCGGTTGTG
* *
540803 TTTCGATTGTG
1 GTTCGGTTGTG
540814 GTTCGGTTGTG
1 GTTCGGTTGTG
540825 GTT
1 GTT
540828 GGTCTTCGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.03, C:0.08, G:0.39, T:0.50
Consensus pattern (11 bp):
GTTCGGTTGTG
Found at i:546740 original size:2 final size:2
Alignment explanation
Indices: 546733--546763 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
546723 TATGAAGGCA
546733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
546764 CACACAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:560908 original size:30 final size:30
Alignment explanation
Indices: 560874--560939 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
560864 CATGATTTGG
560874 TTGTAACAATCAATTAATTCGA-TGA-CTTAA
1 TTGTAACAATCAATTAA-TCGAGT-ATCTTAA
560904 TTGTAACAATCAATTAATCGAGTATCTTAA
1 TTGTAACAATCAATTAATCGAGTATCTTAA
560934 TTGTAA
1 TTGTAA
560940 AATACTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (30 bp):
TTGTAACAATCAATTAATCGAGTATCTTAA
Found at i:571487 original size:39 final size:40
Alignment explanation
Indices: 571433--571549 Score: 173
Period size: 39 Copynumber: 2.9 Consensus size: 40
571423 GAGTGCATGC
571433 AGGGGAGAGACGCATGGAGTGCAATGCGTCTTCGGGGGG-
1 AGGGGAGAGACGCATGGAGTGCAATGCGTCTTCGGGGGGA
*
571472 AGGGGATAGACGCATGGAGTGCAATGCGTCTTCGGGGGGAA
1 AGGGGAGAGACGCATGGAGTGCAATGCGTCTTCGGGGGG-A
* * * *
571513 AGGGGAGGGACACATGAAGTGCAATGCGTCTTTGGGG
1 AGGGGAGAGACGCATGGAGTGCAATGCGTCTTCGGGG
571550 TGTACTGTAG
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
39 38 0.54
41 32 0.46
ACGTcount: A:0.23, C:0.15, G:0.45, T:0.17
Consensus pattern (40 bp):
AGGGGAGAGACGCATGGAGTGCAATGCGTCTTCGGGGGGA
Found at i:571706 original size:41 final size:40
Alignment explanation
Indices: 571644--571760 Score: 191
Period size: 39 Copynumber: 2.9 Consensus size: 40
571634 CTACAGTACA
*
571644 CCCCAAAGACGCATTGCACTCCATGCGTCTCTCCCCTTTCC
1 CCCCGAAGACGCATTGCACTCCATGCGTCTCTCCCC-TTCC
*
571685 CCCCGAAGACGCATTGCACTCCATGCGTCTATCCCC-TCC
1 CCCCGAAGACGCATTGCACTCCATGCGTCTCTCCCCTTCC
*
571724 CCCCGAAGACGTATTGCACTCCATGCGTCTCTCCCCT
1 CCCCGAAGACGCATTGCACTCCATGCGTCTCTCCCCT
571761 GCATGCACTC
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
39 37 0.52
41 34 0.48
ACGTcount: A:0.17, C:0.45, G:0.15, T:0.23
Consensus pattern (40 bp):
CCCCGAAGACGCATTGCACTCCATGCGTCTCTCCCCTTCC
Found at i:571758 original size:34 final size:36
Alignment explanation
Indices: 571644--571759 Score: 119
Period size: 41 Copynumber: 3.1 Consensus size: 36
571634 CTACAGTACA
* *
571644 CCCCAAAGACGCATTGCACTCCATGCGTCTCTCCCCTTTCC
1 CCCCGAAGACGCATTGCACTCCATGCGTC-AT--CC--TCC
571685 CCCCGAAGACGCATTGCACTCCATGCGTCTATCCCCTCC
1 CCCCGAAGACGCATTGCACTCCATGCGTC-AT--CCTCC
*
571724 CCCCGAAGACGTATTGCACTCCATGCGTC-T-CTCC
1 CCCCGAAGACGCATTGCACTCCATGCGTCATCCTCC
571758 CC
1 CC
571760 TGCATGCACT
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
34 6 0.08
37 1 0.01
39 31 0.43
41 34 0.47
ACGTcount: A:0.17, C:0.46, G:0.15, T:0.22
Consensus pattern (36 bp):
CCCCGAAGACGCATTGCACTCCATGCGTCATCCTCC
Found at i:578685 original size:30 final size:30
Alignment explanation
Indices: 578651--578716 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
578641 CATGATTTGG
578651 TTGTAACAATCAATTAATTCGA-TGA-CTTAA
1 TTGTAACAATCAATTAA-TCGAGT-ATCTTAA
578681 TTGTAACAATCAATTAATCGAGTATCTTAA
1 TTGTAACAATCAATTAATCGAGTATCTTAA
578711 TTGTAA
1 TTGTAA
578717 AATACTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (30 bp):
TTGTAACAATCAATTAATCGAGTATCTTAA
Found at i:594429 original size:16 final size:16
Alignment explanation
Indices: 594408--594440 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
594398 GAACGCCATG
594408 TGCAGATCCCCAGAAA
1 TGCAGATCCCCAGAAA
594424 TGCAGATCCCCAGAAA
1 TGCAGATCCCCAGAAA
594440 T
1 T
594441 CCCCAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.15
Consensus pattern (16 bp):
TGCAGATCCCCAGAAA
Found at i:598706 original size:22 final size:22
Alignment explanation
Indices: 598678--598720 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
598668 AACGGTCAAC
598678 GGTCAAC-GATCGGGTCGGGTCG
1 GGTCAACAG-TCGGGTCGGGTCG
598700 GGTCAACAGTCGGGTCGGGTC
1 GGTCAACAGTCGGGTCGGGTC
598721 AGACCGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.14, C:0.23, G:0.44, T:0.19
Consensus pattern (22 bp):
GGTCAACAGTCGGGTCGGGTCG
Found at i:598743 original size:19 final size:19
Alignment explanation
Indices: 598719--598777 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
598709 TCGGGTCGGG
598719 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
598738 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
598757 TCAAAACAGGTCAAACCGGT
1 TC-AGACCGGTCAAACCGGT
598777 T
1 T
598778 TTCCAGCAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:598747 original size:10 final size:9
Alignment explanation
Indices: 598717--598776 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
598707 AGTCGGGTCG
*
598717 GGTCAGACC
1 GGTCAAACC
598726 GGTCAAACC
1 GGTCAAACC
*
598735 GGTTCAGACC
1 GG-TCAAACC
598745 GGTCAAACC
1 GGTCAAACC
*
598754 GGTTCAAAACA
1 GG-TC-AAACC
598765 GGTCAAACC
1 GGTCAAACC
598774 GGT
1 GGT
598777 TTTCCAGCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 25 0.58
10 12 0.28
11 6 0.14
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:600174 original size:30 final size:30
Alignment explanation
Indices: 600140--600205 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
600130 CATGATTTGG
600140 TTGTAACAATCAATTAATTCGA-TGA-CTTAA
1 TTGTAACAATCAATTAA-TCGAGT-ATCTTAA
600170 TTGTAACAATCAATTAATCGAGTATCTTAA
1 TTGTAACAATCAATTAATCGAGTATCTTAA
600200 TTGTAA
1 TTGTAA
600206 AATACTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (30 bp):
TTGTAACAATCAATTAATCGAGTATCTTAA
Found at i:602123 original size:29 final size:29
Alignment explanation
Indices: 602089--602147 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
602079 CCTAAATTAA
*
602089 TTTGATGTTATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
602118 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
602147 T
1 T
602148 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:604845 original size:15 final size:15
Alignment explanation
Indices: 604825--604859 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
604815 TCGTAGGACC
604825 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
604840 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
604855 ACTAC
1 ACTAC
604860 AATACCCACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:617883 original size:29 final size:28
Alignment explanation
Indices: 617840--617899 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 28
617830 CACACCTAAA
*
617840 TTAATTTAATGTCATTGCTTACATTAAT
1 TTAATTTAATGTCATTGCTTACATCAAT
*
617868 TTAATTTTGATGTCATTGCTTACATCAAT
1 TTAA-TTTAATGTCATTGCTTACATCAAT
617897 TTA
1 TTA
617900 GTTAGGTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (28 bp):
TTAATTTAATGTCATTGCTTACATCAAT
Done.