Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007817.1 Hibiscus syriacus cultivar Beakdansim tig00110152_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: 465523
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:236357 original size:39 final size:38
Alignment explanation
Indices: 236272--236368 Score: 131
Period size: 39 Copynumber: 2.5 Consensus size: 38
236262 GCTTATCGAT
* *
236272 TAAGCAGTTCAGTGCATATGGTGAGCAGACCTTATGTG
1 TAAGCACTTCAGTGCATATGGTGAGCAAACCTTATGTG
*
236310 TAATGCACTTCAGTGCATATGGTGGGCACAACCTTATGTG
1 TAA-GCACTTCAGTGCATATGGTGAGCA-AACCTTATGTG
* *
236350 TAAGCACTACGGTGCATAT
1 TAAGCACTTCAGTGCATAT
236369 ATTTGAATCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
38 3 0.06
39 36 0.69
40 13 0.25
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (38 bp):
TAAGCACTTCAGTGCATATGGTGAGCAAACCTTATGTG
Found at i:244488 original size:15 final size:15
Alignment explanation
Indices: 244468--244501 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
244458 TCCTAATGAT
*
244468 GTGAGAGAAGTCGAG
1 GTGAGAGAAGTCAAG
244483 GTGAGAGAAGTCAAG
1 GTGAGAGAAGTCAAG
244498 GTGA
1 GTGA
244502 CTAATAACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.44, T:0.15
Consensus pattern (15 bp):
GTGAGAGAAGTCAAG
Found at i:246230 original size:17 final size:17
Alignment explanation
Indices: 246208--246246 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
246198 ATACGAAAGA
246208 GAGACAAAGGATCAATC
1 GAGACAAAGGATCAATC
*
246225 GAGACAAAGGATCAATT
1 GAGACAAAGGATCAATC
246242 GAGAC
1 GAGAC
246247 TTCTTCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.26, T:0.13
Consensus pattern (17 bp):
GAGACAAAGGATCAATC
Found at i:249317 original size:14 final size:14
Alignment explanation
Indices: 249298--249325 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
249288 TCATTATCCA
249298 TTTTATTTTAATAT
1 TTTTATTTTAATAT
249312 TTTTATTTTAATAT
1 TTTTATTTTAATAT
249326 AGGCAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATTTTAATAT
Found at i:263012 original size:2 final size:2
Alignment explanation
Indices: 263005--263096 Score: 150
Period size: 2 Copynumber: 46.5 Consensus size: 2
262995 CTTACACTTG
* *
263005 TA TA TA TA TA TA CA -A AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
263046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
263088 TG TA TA TA T
1 TA TA TA TA T
263097 CTTACACATT
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
1 1 0.01
2 84 0.99
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:265512 original size:75 final size:75
Alignment explanation
Indices: 265427--265575 Score: 262
Period size: 75 Copynumber: 2.0 Consensus size: 75
265417 AAATTGAAAG
* *
265427 AGTCGTCATCGACCTTTAGATTAGGTAGGTCGAATACCTAAAAAAAGTCTTTTTAAAACAATTTT
1 AGTCGCCATCGACCTTCAGATTAGGTAGGTCGAATACCTAAAAAAAGTCTTTTTAAAACAATTTT
265492 AAGAAAAAAA
66 AAGAAAAAAA
* *
265502 AGTCGCCATCGACCTTCGGATTAGGTAGGTCGAATACCTAAAAAAAGTTTTTTTAAAACAATTTT
1 AGTCGCCATCGACCTTCAGATTAGGTAGGTCGAATACCTAAAAAAAGTCTTTTTAAAACAATTTT
265567 AAGAAAAAA
66 AAGAAAAAA
265576 TATTTTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (75 bp):
AGTCGCCATCGACCTTCAGATTAGGTAGGTCGAATACCTAAAAAAAGTCTTTTTAAAACAATTTT
AAGAAAAAAA
Found at i:267929 original size:3 final size:3
Alignment explanation
Indices: 267875--267914 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
267865 CAAAAATTTG
267875 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
267915 GTCATATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:268464 original size:133 final size:133
Alignment explanation
Indices: 268139--268480 Score: 463
Period size: 133 Copynumber: 2.6 Consensus size: 133
268129 TGGTCGTCTA
* * * *
268139 AGGGTGACACGGATCCTACATGATGAGGAAATCTGGTC-GAAGGATGACACTGCTCATATGTGAT
1 AGGGTGACACGGCTCCTACATGATGAGGAGATCTGGTCAG-GGGATGACACTGCTCATACGTGAT
** * * *
268203 GAAGAGTTCTTGTCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACTGCTGGT
65 GAAGAGTTC-TAACCATCTTTAAGAAGGGCGATAACACGGTTCCTACGCGATGAGGACTGCTGGT
268268 TATCT
129 TATCT
* * * * *
268273 ATGGGTGACACGGCTCTTACATGATGAGGAGGTCTGGTCAGGGAATGGCACGGCTCATACGTGAT
1 A-GGGTGACACGGCTCCTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGAT
* * *
268338 GAAGAGTTCTAACCATTTTTAAGAAGGGCGATAACACGGTTCCTACGTGATGAGG-GTGACTGGT
65 GAAGAGTTCTAACCATCTTTAAGAAGGGCGATAACACGGTTCCTACGCGATGAGGACTG-CTGGT
268402 TATCT
129 TATCT
**
268407 AGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATG
1 AGGGTGACACGGCTCCTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATG
268472 AAGAGTTCT
66 AAGAGTTCT
268481 TGGTTATCTT
Statistics
Matches: 181, Mismatches: 24, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
133 68 0.38
134 51 0.28
135 61 0.34
136 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (133 bp):
AGGGTGACACGGCTCCTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATG
AAGAGTTCTAACCATCTTTAAGAAGGGCGATAACACGGTTCCTACGCGATGAGGACTGCTGGTTA
TCT
Found at i:268902 original size:92 final size:91
Alignment explanation
Indices: 268688--268891 Score: 243
Period size: 92 Copynumber: 2.2 Consensus size: 91
268678 CTCAAACATT
* * * * *
268688 TTTCAAAAGGAACAGACTCAAAGAT-TTTTCTCAAGAAAAATTGTCTTAAGAGAGACAAAACTTT
1 TTTCAAAAGAAACA-ACTCAAAGATATTTT-T-TA-CAAAATTGTCTTAAGAGAAACAAAAATTT
* *
268752 GTTTCGAAAGAAACAAACTCAAAGATTTTGG
62 GTTTCAAAAGAAACAAACTCAAAGAATTT-G
**
268783 TTTCAAAAGAAATGACTCAAAGATATTTTTTACAAAATTGTCTTAAGAGAAACAAAAATTTGGTT
1 TTTCAAAAGAAACAACTCAAAGATATTTTTTACAAAATTGTCTTAAGAGAAACAAAAATTT-GTT
*
268848 T-AAAAGAAACAGACTCAAAGAATTT-
65 TCAAAAGAAACAAACTCAAAGAATTTG
268873 TTTCAAAAGAAACAACTCA
1 TTTCAAAAGAAACAACTCA
268892 GATTTTTATT
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
90 17 0.18
92 47 0.49
93 5 0.05
94 11 0.12
95 15 0.16
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (91 bp):
TTTCAAAAGAAACAACTCAAAGATATTTTTTACAAAATTGTCTTAAGAGAAACAAAAATTTGTTT
CAAAAGAAACAAACTCAAAGAATTTG
Found at i:269051 original size:66 final size:63
Alignment explanation
Indices: 268970--269125 Score: 163
Period size: 66 Copynumber: 2.4 Consensus size: 63
268960 TGTTTCAAGG
* * *
268970 GAAACA-ATCTCAAAGATGTTTGTTTTAAGCGAAATTGTCTTAAAAGAGACAAACCTTTGTTTTC
1 GAAACATA-CTCAAAGAT-TTT-TTTTAAG-GAAA-TGTCTCAAAAGAGACAAAACTTTGTTATC
*
269034 ATA
61 AAA
* * *
269037 -AAACATACTTAAAGATTTTTCTTCAAAAGGAAATGTCTCAAAAGAGACAAAATTTTGTTATCAA
1 GAAACATACTCAAAGATTTTT-TT--TAAGGAAATGTCTCAAAAGAGACAAAACTTTGTTATCAA
269101 A
63 A
269102 GAAACATACTCAAAGATTTTTTTT
1 GAAACATACTCAAAGATTTTTTTT
269126 CATTTTGTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
64 1 0.01
65 34 0.45
66 36 0.48
67 4 0.05
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (63 bp):
GAAACATACTCAAAGATTTTTTTTAAGGAAATGTCTCAAAAGAGACAAAACTTTGTTATCAAA
Found at i:269086 original size:65 final size:67
Alignment explanation
Indices: 269000--269127 Score: 179
Period size: 65 Copynumber: 1.9 Consensus size: 67
268990 TGTTTTAAGC
* * * * *
269000 GAAATTGTCTTAAAAGAGACAAACCTTTGTTTTCATA-AAACATACTTAAAGATTTTTCTTCAAA
1 GAAATTGTCTCAAAAGAGACAAAACTTTGTTATCAAAGAAACATACTCAAAGATTTTTCTTCAAA
269064 AG
66 AG
* *
269066 GAAA-TGTCTCAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTCAAAGATTTTTTTTCA
1 GAAATTGTCTCAAAAGAGACAAAACTTTGTTATCAAAGAAACATACTCAAAGATTTTTCTTCA
269128 TTTTGTTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 27 0.50
66 27 0.50
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (67 bp):
GAAATTGTCTCAAAAGAGACAAAACTTTGTTATCAAAGAAACATACTCAAAGATTTTTCTTCAAA
AG
Found at i:269335 original size:36 final size:36
Alignment explanation
Indices: 269288--269427 Score: 138
Period size: 36 Copynumber: 3.8 Consensus size: 36
269278 ATAATTTGGA
* *
269288 AAATTGTCTCAAGTGTGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * * *
269324 AAATTGTCTCAAACGAGACAAAAATTGTTTATAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * *
269360 AAATTGTCTCAAGCGAGACAACGTTTTTTTTTTTGAG
1 AAATTGTCTCAAGCGAGACAAC-ATTTGTTTTTAGAG
** *
269397 AAAACGATCTCAAGTGAGATCAAC-TTTGTTT
1 AAATTG-TCTCAAGCGAGA-CAACATTTGTTT
269428 AATGTGAAAA
Statistics
Matches: 84, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
36 50 0.60
37 19 0.23
38 11 0.13
39 4 0.05
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:269523 original size:107 final size:103
Alignment explanation
Indices: 269397--269710 Score: 409
Period size: 107 Copynumber: 3.0 Consensus size: 103
269387 TTTTTTTGAG
*
269397 AAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTGAAAACAAATTCGAAATTTGTATTCTCAA
1 AAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTG-AAACAAATTCGAAATTTGTA-TCTCAA
*
269462 AGGAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAAAA
64 AGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTT-AAAAA
* * * *
269503 AATAACAATCTCAAGTGAGATTAATTTTTGTTTCAA-GTGAATCAAATTCGAAATTTGTATATCA
1 AA-AACAATCTCAAGTGAGATCAA-CTTTGTTT-AATGTGAAACAAATTCGAAATTTGTATCTCA
* * * *
269567 AAGGAAAAAATGTCTCAAGCAAGACGAAGTTTGTTTTAAGAG
63 AAGG-AAAAATGTCTCAAGCGAGACGAAATTTGTTTTAAAAA
* * *
269609 AAAGCGATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTC-AAATTTTGTATCTCAAA
1 AAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAA-TTTGTATCTCAAA
*
269673 GGAAAAATGTCTCAAGTGAGACGAAATTTG-TTTAAAAA
65 GGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTAAAAA
269711 GAATTGTCTC
Statistics
Matches: 180, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
102 6 0.03
103 30 0.17
104 33 0.18
105 17 0.09
106 15 0.08
107 67 0.37
108 10 0.06
109 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (103 bp):
AAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTCAAAG
GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTAAAAA
Found at i:269758 original size:70 final size:71
Alignment explanation
Indices: 269674--269813 Score: 194
Period size: 71 Copynumber: 2.0 Consensus size: 71
269664 TATCTCAAAG
* * * *
269674 GAAAAATGTCTCAAGTGAGACGAAATTTG-TTT-AAAAAGAATTGTCTCAAGTGAGACAAATTTT
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAAAAA-AATTATCTCAAGCGAGACAAATTTT
269737 GTTTTTA
65 GTTTTTA
* * *
269744 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTGAGAAAAATTATCTCAAGCGAGACAAATTTTT
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAAAAAAATTATCTCAAGCGAGACAAATTTTG
269809 TTTTT
66 TTTTT
269814 TTAAATTCTC
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
70 26 0.43
71 31 0.51
72 4 0.07
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (71 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAAAAAAATTATCTCAAGCGAGACAAATTTTG
TTTTTA
Found at i:269792 original size:36 final size:35
Alignment explanation
Indices: 269674--269812 Score: 149
Period size: 35 Copynumber: 4.0 Consensus size: 35
269664 TATCTCAAAG
* *
269674 GAAAAA-TGTCTCAAGTGAGACGAAATTTG-TTTA
1 GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTA
* * *
269707 AAAAGAATTGTCTCAAGTGAGACAAATTTTGTTTTTA
1 GAAA-AATTGTCTCAAGCGAGACAAAATTTG-TTTTA
*
269744 G-AAAACTGTCTCAAGCGAGACAAAATTTGTTTTGA
1 GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTT-A
* * *
269779 GAAAAATTATCTCAAGCGAGACAAATTTTTTTTT
1 GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTT
269813 TTTAAATTCT
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
33 3 0.03
34 6 0.07
35 46 0.52
36 30 0.34
37 4 0.04
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (35 bp):
GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTA
Found at i:270102 original size:12 final size:11
Alignment explanation
Indices: 270069--270094 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
270059 GATGTCAAGA
270069 TGAAATTTATT
1 TGAAATTTATT
270080 TGAAATTTATT
1 TGAAATTTATT
270091 TGAA
1 TGAA
270095 GTTTTATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (11 bp):
TGAAATTTATT
Found at i:274074 original size:2 final size:2
Alignment explanation
Indices: 274067--274118 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
274057 CTTACACTTG
* * * *
274067 TA TA TA TA TA TA CA -A AA TA TA TA TA TA TA TA TA TA TG TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
274108 TA TG TA TA TA T
1 TA TA TA TA TA T
274119 CTTACACATT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:276534 original size:77 final size:76
Alignment explanation
Indices: 276447--276597 Score: 239
Period size: 77 Copynumber: 2.0 Consensus size: 76
276437 AAATTGAAAG
* * *
276447 AGTCGTCATCGACCTTTAGATTAGATAGGTCGAATACCTAAAAAAGGACTTTTTAAAACAATTTT
1 AGTCGCCATCGACCTTCAGATTAGATAGGTCGAATACCTAAAAAAAGACTTTTTAAAACAATTTT
276512 AAGAAGAAAAAA
66 AAGAA-AAAAAA
* * *
276524 AGTCGCCATCGACCTTCGGATTAGGTAGGTCGAATACCTAAAAAAAGTCTTTTTAAAACAATTTT
1 AGTCGCCATCGACCTTCAGATTAGATAGGTCGAATACCTAAAAAAAGACTTTTTAAAACAATTTT
276589 AAGAAAAAA
66 AAGAAAAAA
276598 TATTTTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
76 4 0.06
77 64 0.94
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (76 bp):
AGTCGCCATCGACCTTCAGATTAGATAGGTCGAATACCTAAAAAAAGACTTTTTAAAACAATTTT
AAGAAAAAAAA
Found at i:278649 original size:3 final size:3
Alignment explanation
Indices: 278598--278634 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
278588 CAAAAATTTG
*
278598 TAA T-A TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
278635 GTCATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:279190 original size:133 final size:133
Alignment explanation
Indices: 278859--279200 Score: 463
Period size: 133 Copynumber: 2.6 Consensus size: 133
278849 TGGTCGTCTA
* * * * * *
278859 AGGGTGACACGGATCCTACATAATGAGGAAATCTGGTC-GAAGGATGACACTGCTCATATGTGAT
1 AGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAG-GGGATGACACTGCTCATACGTGAT
* * * *
278923 GAAGAGTTCTTGTCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACTGCTGGT
65 GAAGAGTTC-TGACCATCTTTAAGAAGGGCGATAACACGGTTCCTACGCGATGAGGACTGCTGGT
278988 TATCT
129 TATCT
* * * * *
278993 ATGGGTGACACGGCTCTTACGTGATGAGGAGGTCTGGTCAGGGAATGGCACGGCTCATACGTGAT
1 A-GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGAT
* *
279058 GAAGAGTTCTGACCATTTTTAAGAAGGGCGATAACACGGTTCCTACGTGATGAGGAC-GACTGGT
65 GAAGAGTTCTGACCATCTTTAAGAAGGGCGATAACACGGTTCCTACGCGATGAGGACTG-CTGGT
279122 TATCT
129 TATCT
* *
279127 AGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCAGGGGATGACACTGCTTATACGTGATG
1 AGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATG
279192 AAGAGTTCT
66 AAGAGTTCT
279201 TGGTTATCTT
Statistics
Matches: 181, Mismatches: 24, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
133 67 0.37
134 54 0.30
135 59 0.33
136 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (133 bp):
AGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATG
AAGAGTTCTGACCATCTTTAAGAAGGGCGATAACACGGTTCCTACGCGATGAGGACTGCTGGTTA
TCT
Found at i:279601 original size:28 final size:26
Alignment explanation
Indices: 279569--279647 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 26
279559 ACTTTGGTTT
279569 AAAAGAAACAGACTCAAAGAATTTTTTC
1 AAAAGAAACA-ACTC-AAGAATTTTTTC
*
279597 AAAAGAAACAACTC-AGATTTTTATTTC
1 AAAAGAAACAACTCAAGA-ATTT-TTTC
*
279624 AAAAGAAACAACTCACAGACTTTT
1 AAAAGAAACAACTCA-AGAATTTT
279648 GTTTCAACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
25 3 0.07
26 3 0.07
27 23 0.51
28 13 0.29
29 3 0.07
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (26 bp):
AAAAGAAACAACTCAAGAATTTTTTC
Found at i:279622 original size:92 final size:91
Alignment explanation
Indices: 279393--279611 Score: 252
Period size: 92 Copynumber: 2.4 Consensus size: 91
279383 GTTAAGAGAC
* * * *
279393 ACAATCTCAAAG-A-TT-TTTCAAAAGGAACAGACTCAAAGAT-TTTTCTCAAGAAAAATTGTCT
1 ACAAACTCAAAGAATTTGTTTCAAAAGAAACA-ACTCAAAGATATTTT-T-TA-CAAAATTGTCT
* *
279454 TAAGAGAGACAAAACTTTGTTTCGAAAGAA
62 TAAGAGAAACAAAACTTTGTTTCAAAAGAA
* **
279484 ACAAACTCAAAGATTTTGGTTTCAAAAGAAATGACTCAAAGATATTTTTTACAAAATTGTCTTAA
1 ACAAACTCAAAGAATTT-GTTTCAAAAGAAACAACTCAAAGATATTTTTTACAAAATTGTCTTAA
279549 GAGAAACAAAACTTTGGTTT-AAAAGAA
65 GAGAAACAAAACTTT-GTTTCAAAAGAA
*
279576 ACAGACTCAAAGAATTT-TTTCAAAAGAAACAACTCA
1 ACAAACTCAAAGAATTTGTTTCAAAAGAAACAACTCA
279612 GATTTTTATT
Statistics
Matches: 109, Mismatches: 13, Indels: 13
0.81 0.10 0.10
Matches are distributed among these distances:
90 17 0.16
91 11 0.10
92 48 0.44
93 7 0.06
94 11 0.10
95 15 0.14
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.28
Consensus pattern (91 bp):
ACAAACTCAAAGAATTTGTTTCAAAAGAAACAACTCAAAGATATTTTTTACAAAATTGTCTTAAG
AGAAACAAAACTTTGTTTCAAAAGAA
Found at i:279801 original size:65 final size:65
Alignment explanation
Indices: 279725--279846 Score: 165
Period size: 65 Copynumber: 1.9 Consensus size: 65
279715 TAAGCGAACT
* * * * *
279725 TGTCTTAAAAGAGACAAACCTTTGTTTTCATA-AAACAGACTTAAAGATTTTTCTTCAAAAGGAA
1 TGTCTCAAAAGAGACAAAACTTTGTTATCAAAGAAACAGACTCAAAGATTTTT-TTCAAAAGGAA
279789 A
65 A
* *
279790 TGTCTCAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTCAAAGATTTTTTTCA
1 TGTCTCAAAAGAGACAAAACTTTGTTATCAAAGAAACAGACTCAAAGATTTTTTTCA
279847 TTTTGTTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
65 31 0.63
66 18 0.37
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (65 bp):
TGTCTCAAAAGAGACAAAACTTTGTTATCAAAGAAACAGACTCAAAGATTTTTTTCAAAAGGAAA
Found at i:279850 original size:38 final size:38
Alignment explanation
Indices: 279808--279880 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
279798 AAGAGACAAA
*
279808 ATTTTGTTATCA-AAGAAACATACTCAAAGATTTTTTTC
1 ATTTTGTT-TCAGAAGAAACAAACTCAAAGATTTTTTTC
* **
279846 ATTTTGTTTTAGGTGAAACAAACTCAAAGATTTTT
1 ATTTTGTTTCAGAAGAAACAAACTCAAAGATTTTT
279881 CAATAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 2 0.07
38 28 0.93
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (38 bp):
ATTTTGTTTCAGAAGAAACAAACTCAAAGATTTTTTTC
Found at i:280052 original size:36 final size:36
Alignment explanation
Indices: 280005--280108 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 36
279995 ATAATTTGGA
* *
280005 AAATTGTCTCAAGTGTGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * *
280041 AAATTGTCTCAAACGAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* *
280077 AAATTGTCTCAAGCGAGACAACGTTTTTTTTT
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTT
280109 TTTTGAGAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:280232 original size:108 final size:103
Alignment explanation
Indices: 280116--280449 Score: 402
Period size: 108 Copynumber: 3.2 Consensus size: 103
280106 TTTTTTTGAG
280116 AAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAAACAAATTCAAAATTTGTATTCTCAA
1 AAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTG-AAACAAATTCAAAATTTGTA-TCTCAA
*
280181 AGGAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAAAAA
64 AGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTT--AAAAA
* * * * * *
280223 AATAACAATCTCAGGTGAGATTAATTTTTGTTTCAA-GTGAATCAAATTCGAAATTTGTATATCA
1 AA-AACAATCTCAAGTGAGATCAA-CTTTGTTT-AATGTGAAACAAATTCAAAATTTGTATCTCA
* * * *
280287 AAGGAAAAAATGTCTCAAGCAAGACGAAGTTTGTTTTAAGAG
63 AAGG-AAAAATGTCTCAAGCGAGACGAAATTTGTTTTAAAAA
* * * *
280329 AAAGCGATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCAAATTTTGTATCTCAAAG
1 AAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAAAG
*
280394 GAAAAATGTCTCAAGTGAGACGAAATTTG-TTTAAAAA
66 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTAAAAA
* ***
280431 GAAATTGTCTCAAGTGAGA
1 AAAACAATCTCAAGTGAGA
280450 CAAATTTTGT
Statistics
Matches: 190, Mismatches: 32, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
102 19 0.10
103 27 0.14
104 35 0.18
105 16 0.08
106 5 0.03
107 10 0.05
108 66 0.35
109 10 0.05
110 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (103 bp):
AAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAAAG
GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTAAAAA
Found at i:280525 original size:36 final size:36
Alignment explanation
Indices: 280394--280534 Score: 153
Period size: 36 Copynumber: 3.9 Consensus size: 36
280384 TATCTCAAAG
* *
280394 GAAAAA-TGTCTCAAGTGAGACGAAATTTG-TTTAA
1 GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTAA
* * * *
280428 AAAGAAATTGTCTCAAGTGAGACAAATTTTGTTTTTA
1 GAA-AAATTGTCTCAAGCGAGACAAAATTTGTTTTAA
* *
280465 G-AAAACTGTCTCAAGCGAGACAAAATTTGTTTTGA
1 GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTAA
* *
280500 GAAAAATTATCTCAAGCGAGACAAAAATTTTTTTT
1 GAAAAATTGTCTCAAGCGAGAC-AAAATTTGTTTT
280535 TTAATTCTCA
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
34 2 0.02
35 33 0.37
36 40 0.44
37 15 0.17
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.33
Consensus pattern (36 bp):
GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTAA
Found at i:280534 original size:71 final size:71
Alignment explanation
Indices: 280394--280535 Score: 178
Period size: 71 Copynumber: 2.0 Consensus size: 71
280384 TATCTCAAAG
* * * * *
280394 GAAAAATGTCTCAAGTGAGACGAAATTTGTTTAAAAAGAAATTGTCTCAAGTGAGACAAATTTTG
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTAAAAAGAAATTATCTCAAGCGAGACAAAATTTG
280459 TTTTTA
66 TTTTTA
* * *
280465 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTGAGAA-AAATTATCTCAAGCGAGACAAAAATT
1 GAAAAATGTCTCAAGCGAGACAAAATTTG-TTTAAAAAGAAATTATCTCAAGCGAGAC-AAAATT
*
280529 TTTTTTT
64 TGTTTTT
280536 TAATTCTCAA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
71 43 0.72
72 17 0.28
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (71 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTAAAAAGAAATTATCTCAAGCGAGACAAAATTTG
TTTTTA
Found at i:280822 original size:12 final size:11
Alignment explanation
Indices: 280789--280814 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
280779 GATGTCAAGA
280789 TGAAATTTATT
1 TGAAATTTATT
280800 TGAAATTTATT
1 TGAAATTTATT
280811 TGAA
1 TGAA
280815 GTTTTATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (11 bp):
TGAAATTTATT
Found at i:284620 original size:2 final size:2
Alignment explanation
Indices: 284613--284650 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
284603 CTTACACTTG
* *
284613 TA TA TA TA TA TA CA -A AA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
284651 CTTACACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:288862 original size:3 final size:3
Alignment explanation
Indices: 288796--288847 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
288786 CAAAAATTTG
288796 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
288843 TAA TA
1 TAA TA
288848 GTCATATAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:289384 original size:133 final size:132
Alignment explanation
Indices: 289075--289416 Score: 452
Period size: 133 Copynumber: 2.6 Consensus size: 132
289065 TGGTCGTCTA
* * * * *
289075 AGGGTGACACGGATCCTACATGATGAGGAAATCTGGTCGAAGGATGACACTGCTCATATGTGATG
1 AGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTC-AGGGATGACACTGCTCATACGTGATG
* * * * * *
289140 AAGAGTTCTTGTCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACTGCTGGTT
65 AAGAGTTC-TGACCATCTTTAAGAAAGGCGATAACACGGTTCCTACGCGATGAGAACTGCTGGTT
289205 ATCT
129 ATCT
* * * * *
289209 ATGGGTGACACGGCTCTTACGTGATGAGGAGGTCTGGTCAGGGAATGGCACGGCTCATACATGAT
1 A-GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGG-ATGACACTGCTCATACGTGAT
* *
289274 GAAGAGTTCTGACCATTTTTAAGAAAGGCGATAACACGGTTCCTACGTGATGAGAAC-GACTGGT
64 GAAGAGTTCTGACCATCTTTAAGAAAGGCGATAACACGGTTCCTACGCGATGAGAACTG-CTGGT
289338 TATCT
128 TATCT
*
289343 AGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATG
1 AGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCA-GGGATGACACTGCTCATACGTGATG
289408 AAGAGTTCT
65 AAGAGTTCT
289417 TGGTTATCTT
Statistics
Matches: 180, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
133 64 0.36
134 58 0.32
135 58 0.32
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (132 bp):
AGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGATGACACTGCTCATACGTGATGA
AGAGTTCTGACCATCTTTAAGAAAGGCGATAACACGGTTCCTACGCGATGAGAACTGCTGGTTAT
CT
Found at i:289817 original size:28 final size:26
Alignment explanation
Indices: 289785--289863 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 26
289775 ACTTTGGTTT
289785 AAAAGAAACAGACTCAAAGAATTTTTTC
1 AAAAGAAACA-ACTC-AAGAATTTTTTC
*
289813 AAAAGAAACAACTC-AGATTTTTATTTC
1 AAAAGAAACAACTCAAGA-ATTT-TTTC
*
289840 AAAAGAAACAACTCACAGACTTTT
1 AAAAGAAACAACTCA-AGAATTTT
289864 GTTTCAACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
25 3 0.07
26 3 0.07
27 23 0.51
28 13 0.29
29 3 0.07
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (26 bp):
AAAAGAAACAACTCAAGAATTTTTTC
Found at i:289838 original size:92 final size:91
Alignment explanation
Indices: 289609--289827 Score: 252
Period size: 92 Copynumber: 2.4 Consensus size: 91
289599 GTTAAGAGAC
* * * *
289609 ACAATCTCAAAG-A-TT-TTTCAAAAGGAACAGACTCAAAGAT-TTTTCTCAAGAAAAATTGTCT
1 ACAAACTCAAAGAATTTGTTTCAAAAGAAACA-ACTCAAAGATATTTT-T-TA-CAAAATTGTCT
* *
289670 TAAGAGAGACAAAACTTTGTTTCGAAAGAA
62 TAAGAGAAACAAAACTTTGTTTCAAAAGAA
* **
289700 ACAAACTCAAAGATTTTGGTTTCAAAAGAAATGACTCAAAGATATTTTTTACAAAATTGTCTTAA
1 ACAAACTCAAAGAATTT-GTTTCAAAAGAAACAACTCAAAGATATTTTTTACAAAATTGTCTTAA
289765 GAGAAACAAAACTTTGGTTT-AAAAGAA
65 GAGAAACAAAACTTT-GTTTCAAAAGAA
*
289792 ACAGACTCAAAGAATTT-TTTCAAAAGAAACAACTCA
1 ACAAACTCAAAGAATTTGTTTCAAAAGAAACAACTCA
289828 GATTTTTATT
Statistics
Matches: 109, Mismatches: 13, Indels: 13
0.81 0.10 0.10
Matches are distributed among these distances:
90 17 0.16
91 11 0.10
92 48 0.44
93 7 0.06
94 11 0.10
95 15 0.14
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.28
Consensus pattern (91 bp):
ACAAACTCAAAGAATTTGTTTCAAAAGAAACAACTCAAAGATATTTTTTACAAAATTGTCTTAAG
AGAAACAAAACTTTGTTTCAAAAGAA
Found at i:290022 original size:65 final size:67
Alignment explanation
Indices: 289936--290063 Score: 170
Period size: 65 Copynumber: 1.9 Consensus size: 67
289926 TGTTTTAAGC
* * * * *
289936 GAAATTGTCTTAAAAGAGACAAACCTTTGTTTTCATA-AAACAGACTTAAAGATTTTTCTTCAAA
1 GAAATTGTCTCAAAAGAGACAAAACTTTGTTATCAAAGAAACAGACTCAAAGATTTTTCTTCAAA
290000 AG
66 AG
* * *
290002 GAAA-TGTCTCAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTCAAAGATTTTTTTTCA
1 GAAATTGTCTCAAAAGAGACAAAACTTTGTTATCAAAGAAACAGACTCAAAGATTTTTCTTCA
290064 TTTTGTTTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 27 0.51
66 26 0.49
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (67 bp):
GAAATTGTCTCAAAAGAGACAAAACTTTGTTATCAAAGAAACAGACTCAAAGATTTTTCTTCAAA
AG
Found at i:290271 original size:36 final size:36
Alignment explanation
Indices: 290222--290362 Score: 122
Period size: 36 Copynumber: 3.9 Consensus size: 36
290212 TCATAATTTG
* *
290222 GAAATTAGTCTCAAGTGTGACAACATTTGTTTTTACA
1 GAAATT-GTCTCAAGCGAGACAACATTTGTTTTTACA
* * * * *
290259 GAAATTTTCTCAAACGAGACAAAAATTGTTTTTAGA
1 GAAATTGTCTCAAGCGAGACAACATTTGTTTTTACA
* * **
290295 GAAATTGTCTCAAGCGAGACAACGTTTTTTTTTTGA
1 GAAATTGTCTCAAGCGAGACAACATTTGTTTTTACA
** *
290331 GAAAACGATCTCAAGTGAGATCAAC-TTTGTTT
1 GAAATTG-TCTCAAGCGAGA-CAACATTTGTTT
290363 AATGTGAAAA
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
36 57 0.68
37 23 0.27
38 4 0.05
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (36 bp):
GAAATTGTCTCAAGCGAGACAACATTTGTTTTTACA
Found at i:290458 original size:107 final size:103
Alignment explanation
Indices: 290332--290664 Score: 393
Period size: 107 Copynumber: 3.2 Consensus size: 103
290322 TTTTTTTGAG
*
290332 AAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTGAAAACAAATTCGAAATTTGTATTCTCAA
1 AAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTG-AAACAAATTCGAAATTTGTA-TCTCAA
*
290397 AGGAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAAAA
64 AGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTT-AAAAA
* * * * * *
290438 AATAACAATCTCAAGTGAGATTAA-TTTTTGTTACAAGTGAATCAAATTTGAAATTTGTATATCA
1 AA-AACAATCTCAAGTGAGATCAACTTTGT-TTA-ATGTGAAACAAATTCGAAATTTGTATCTCA
* * * *
290502 AAGGAAAAAATGTCTCAAGCAAGACGAAGTTTGTTTTAAGAG
63 AAGG-AAAAATGTCTCAAGCGAGACGAAATTTGTTTTAAAAA
* * *
290544 AAAGCGATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTC-AAATTTTGTATCTCAAA
1 AAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAA-TTTGTATCTCAAA
*
290608 GGAAAAATGTCTCAAGTGAGACGAAATTTG-TTTAAAAA
65 GGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTAAAAA
* ***
290646 GAAATTGTCTCAAGTGAGA
1 AAAACAATCTCAAGTGAGA
290665 CAAATTTTGT
Statistics
Matches: 189, Mismatches: 32, Indels: 16
0.80 0.14 0.07
Matches are distributed among these distances:
102 19 0.10
103 28 0.15
104 26 0.14
105 20 0.11
106 23 0.12
107 69 0.37
108 4 0.02
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (103 bp):
AAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTCAAAG
GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTAAAAA
Found at i:290730 original size:210 final size:211
Alignment explanation
Indices: 290222--290738 Score: 532
Period size: 212 Copynumber: 2.4 Consensus size: 211
290212 TCATAATTTG
* * * *
290222 GAAATTAGTCTCAAGTGTGACAACATTTGTTTTTACAGAAATTTTCTCAAACGAGACAAAAATTG
1 GAAATT-GTCTCAAGTGAGACAA-ATTTGTTTTTA-A-AAACTGTCTC-AACGAGACAAAATTTG
* * * ** *
290287 TTTTTAGAGAAATTGTCTCAAGCGAGACAACGTTTTTTTTTTGAGAAAACGATCTCAAGTGAGAT
61 TTTTAAGAAAAATTGTCTCAAGCGAGACAACGTTTGTTTTAAGAGAAAACGATCTCAAATGAGAT
290352 CAACTTTGTTTAATGTGAAAACAAATTCGAAATTTGTATTCTCAAAGGAAAAATGTCTCAAACGA
126 CAACTTTGTTTAATGTGAAAACAAATTCGAAATTTGTATTCTCAAAGGAAAAATGTCTCAAACGA
290417 GACGAAATTTGTTTTGAAAAA
191 GACGAAATTTGTTTTGAAAAA
* *** ** * * * ** ****
290438 AATAACAATCTCAAGTGAGATTAATTT-TTGTT-ACAAGTGAATCAA--ATTTGAAATTTGTATA
1 GA-AATTGTCTCAAGTGAGACAAATTTGTTTTTAAAAACTGTCTCAACGAGACAAAATTTGT-T-
* * * *
290499 TCAAAGGAAAAAATGTCTCAAGCAAGACGAA-GTTTGTTTTAAGAGAAAGCGATCTCAAATGAGA
63 T-TAA-GAAAAATTGTCTCAAGCGAGAC-AACGTTTGTTTTAAGAGAAAACGATCTCAAATGAGA
**
290563 TCAACTTTGTTTAATGTG-AAACAAATTC-AAATTTTGTA-TCTCAAAGGAAAAATGTCTCAAGT
125 TCAACTTTGTTTAATGTGAAAACAAATTCGAAA-TTTGTATTCTCAAAGGAAAAATGTCTCAAAC
290625 GAGACGAAATTTG-TTT-AAAAA
189 GAGACGAAATTTGTTTTGAAAAA
290646 GAAATTGTCTCAAGTGAGACAAATTTTGTTTTTAGAAAACTGTCTCAAGCGAGACAAAATTTGTT
1 GAAATTGTCTCAAGTGAGACAAA-TTTGTTTTTA-AAAACTGTCTCAA-CGAGACAAAATTTGTT
* *
290711 TTGAGAAAAATTATCTCAAGCGAGACAA
63 TTAAGAAAAATTGTCTCAAGCGAGACAA
290739 AAAAAAATTT
Statistics
Matches: 237, Mismatches: 50, Indels: 35
0.74 0.16 0.11
Matches are distributed among these distances:
207 16 0.07
208 17 0.07
209 10 0.04
210 60 0.25
211 32 0.14
212 67 0.28
213 3 0.01
214 13 0.05
215 4 0.02
216 13 0.05
217 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (211 bp):
GAAATTGTCTCAAGTGAGACAAATTTGTTTTTAAAAACTGTCTCAACGAGACAAAATTTGTTTTA
AGAAAAATTGTCTCAAGCGAGACAACGTTTGTTTTAAGAGAAAACGATCTCAAATGAGATCAACT
TTGTTTAATGTGAAAACAAATTCGAAATTTGTATTCTCAAAGGAAAAATGTCTCAAACGAGACGA
AATTTGTTTTGAAAAA
Found at i:290740 original size:36 final size:36
Alignment explanation
Indices: 290609--290740 Score: 153
Period size: 36 Copynumber: 3.7 Consensus size: 36
290599 TATCTCAAAG
* *
290609 GAAAAA-TGTCTCAAGTGAGACGAAATTTG-TTTAA
1 GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTAA
* * * *
290643 AAAGAAATTGTCTCAAGTGAGACAAATTTTGTTTTTA
1 GAA-AAATTGTCTCAAGCGAGACAAAATTTGTTTTAA
* *
290680 G-AAAACTGTCTCAAGCGAGACAAAATTTGTTTTGA
1 GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTAA
*
290715 GAAAAATTATCTCAAGCGAGACAAAA
1 GAAAAATTGTCTCAAGCGAGACAAAA
290741 AAAAATTTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
34 2 0.02
35 33 0.40
36 44 0.53
37 4 0.05
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (36 bp):
GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTAA
Found at i:291036 original size:12 final size:11
Alignment explanation
Indices: 291003--291028 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
290993 GATGTCAAGA
291003 TGAAATTTATT
1 TGAAATTTATT
291014 TGAAATTTATT
1 TGAAATTTATT
291025 TGAA
1 TGAA
291029 GTTTTATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (11 bp):
TGAAATTTATT
Found at i:295910 original size:75 final size:75
Alignment explanation
Indices: 295824--295972 Score: 271
Period size: 75 Copynumber: 2.0 Consensus size: 75
295814 TAAATTGAAA
*
295824 GAGTCGTCATCGACCTTTAGATTAGGTAGGTCGAATACCTAAAAAAAGTCTTTTAAAAACAATTT
1 GAGTCGCCATCGACCTTTAGATTAGGTAGGTCGAATACCTAAAAAAAGTCTTTTAAAAACAATTT
295889 TAAGAAAAAG
66 TAAGAAAAAG
* *
295899 GAGTCGCCATCGACCTTTGGATTAGGTAGGTCGAATACCTAAAAAAAGTCTTTTTAAAACAATTT
1 GAGTCGCCATCGACCTTTAGATTAGGTAGGTCGAATACCTAAAAAAAGTCTTTTAAAAACAATTT
295964 TAAGAAAAA
66 TAAGAAAAA
295973 ATATTTAAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (75 bp):
GAGTCGCCATCGACCTTTAGATTAGGTAGGTCGAATACCTAAAAAAAGTCTTTTAAAAACAATTT
TAAGAAAAAG
Found at i:298300 original size:3 final size:3
Alignment explanation
Indices: 298292--298383 Score: 109
Period size: 3 Copynumber: 31.0 Consensus size: 3
298282 TGTAATATAT
298292 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * * *
298341 -AA TAA TAA TAA TAG TCA T-A TAAA TAA TAT TAA TAT TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
298384 ATAAAAAGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
2 5 0.06
3 69 0.90
4 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:298635 original size:42 final size:42
Alignment explanation
Indices: 298584--298674 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
298574 CTGAAATCCT
* *
298584 GTGTTTGTTTAATGTAATTCGTTTTT-CGGAAAATGTTTTCCC
1 GTGTTTGTTTAACGTAATTC-TTTTTCCGGAAAATGTTTTCCA
*
298626 GTGTTTGTTTCACGTAATTCTTTTTCCGGAAAATGTTTTCCA
1 GTGTTTGTTTAACGTAATTCTTTTTCCGGAAAATGTTTTCCA
298668 GTGTTTG
1 GTGTTTG
298675 GTTGGAGGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 5 0.11
42 40 0.89
ACGTcount: A:0.18, C:0.13, G:0.20, T:0.49
Consensus pattern (42 bp):
GTGTTTGTTTAACGTAATTCTTTTTCCGGAAAATGTTTTCCA
Found at i:298974 original size:32 final size:36
Alignment explanation
Indices: 298899--298984 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 36
298889 AATATTTAAA
* *
298899 ATATATTTATTAATATTTATAATAATATAATATAAT
1 ATATATTTATTAATATTTATAATAAAATAATACAAT
298935 ATAATATTT-TTAATA-TTATAATAAAATAAT-CAAT
1 AT-ATATTTATTAATATTTATAATAAAATAATACAAT
*
298969 -TATATTATAATAATAT
1 ATATATT-TATTAATAT
298985 AAGATATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
32 5 0.12
33 2 0.05
34 8 0.19
35 14 0.33
36 8 0.19
37 6 0.14
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (36 bp):
ATATATTTATTAATATTTATAATAAAATAATACAAT
Found at i:299039 original size:26 final size:26
Alignment explanation
Indices: 299010--299071 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
299000 TATTTTAATA
299010 AATATATAATAATT-TTGTATATATTT
1 AATATATAATAATTATT-TATATATTT
*
299036 AATA-ATGAATGATTATTTATATATTT
1 AATATAT-AATAATTATTTATATATTT
299062 AATAT-TAATA
1 AATATATAATA
299072 TAATAATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
25 5 0.16
26 24 0.77
27 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (26 bp):
AATATATAATAATTATTTATATATTT
Found at i:299320 original size:21 final size:21
Alignment explanation
Indices: 299296--299348 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
299286 ATTCTGACTA
299296 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
299317 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
299338 TCGCAATGCGA
1 TCGCATTGCGA
299349 ATACGTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:299494 original size:20 final size:20
Alignment explanation
Indices: 299338--299491 Score: 222
Period size: 20 Copynumber: 7.7 Consensus size: 20
299328 TTTTCCTAAT
299338 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
299358 TCGCAACGCGAATTTA-GAAAA
1 TCGCAATGCGAA--TACGTAAA
*
299379 TCGCAAAGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
299399 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
299419 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
299439 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
299459 TCGCAACGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
*
299479 TCGCAACGCGAAT
1 TCGCAATGCGAAT
299492 CTGAACGAGA
Statistics
Matches: 124, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
19 3 0.02
20 104 0.84
21 15 0.12
22 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:299520 original size:20 final size:20
Alignment explanation
Indices: 299495--299536 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
299485 CGCGAATCTG
299495 AACGAGATTCTGACTATCGC
1 AACGAGATTCTGACTATCGC
299515 AACGAGATTCTGACTATCGC
1 AACGAGATTCTGACTATCGC
299535 AA
1 AA
299537 TACTGAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
AACGAGATTCTGACTATCGC
Found at i:299615 original size:20 final size:20
Alignment explanation
Indices: 299590--299682 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
299580 GGTTTTAGTT
*
299590 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
299610 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
299630 TTGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
299650 TCGCAACGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
*
299670 TCGCAACGCGAAT
1 TCGCAATGCGAAT
299683 CTGACTATCG
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 1 0.01
20 67 0.99
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:299692 original size:20 final size:20
Alignment explanation
Indices: 299649--299735 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
299639 GAATACGTAA
* *
299649 ATCGCAACGCGAATCTGTA-A
1 ATCGCAACGAGAATCTG-ACT
*
299669 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGAATCTGACT
*
299689 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGAATCTGACT
*
299709 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGAATCTGACT
299729 ATCGCAA
1 ATCGCAA
299736 TACTGAATTT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 1 0.02
20 62 0.98
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGAATCTGACT
Found at i:299788 original size:199 final size:191
Alignment explanation
Indices: 299399--299794 Score: 686
Period size: 199 Copynumber: 2.0 Consensus size: 191
299389 AATACGTAAA
299399 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCA
299464 ACGCGAATCTGTAAATCGCAACGCGAATCTGAACGAGATTCTGACTATCGCAACGAGATTCTGAC
66 ACGCGAATCTGTAAATCGCAACGCGAATCTGAACGAGATTCTGACTATCGCAACGAGATTCTGAC
299529 TATCGCAATACTGAATTTCAAATTCGCAACTCGATTTCTGAATTTGCAACAGGTTTTAGTT
131 TATCGCAATACTGAATTTCAAATTCGCAACTCGATTTCTGAATTTGCAACAGGTTTTAGTT
* *
299590 TCGCAATGTGAATACGTAAATCGCAATGCGAATACGTAAATTGCAATGCGAATACGTAAATCGCA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCA
299655 ACGCGAATCTGTAAATCGCAACGCGAATCTGACTATCGCAACGAGATTCTGACTATCGCAACGAG
66 ACGCGAATCTGTAAATCGCAACGCGAA--T--C--T-G-AACGAGATTCTGACTATCGCAACGAG
299720 ATTCTGACTATCGCAATACTGAATTTCAAATTCGCAACTCGATTTCTGAATTCT-CAACAGGTTT
123 ATTCTGACTATCGCAATACTGAATTTCAAATTCGCAACTCGATTTCTGAATT-TGCAACAGGTTT
299784 TAGTT
187 TAGTT
299789 TCGCAA
1 TCGCAA
299795 CACAAATGTT
Statistics
Matches: 194, Mismatches: 2, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
191 90 0.46
193 1 0.01
195 1 0.01
197 1 0.01
198 1 0.01
199 99 0.51
200 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (191 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCA
ACGCGAATCTGTAAATCGCAACGCGAATCTGAACGAGATTCTGACTATCGCAACGAGATTCTGAC
TATCGCAATACTGAATTTCAAATTCGCAACTCGATTTCTGAATTTGCAACAGGTTTTAGTT
Found at i:303080 original size:20 final size:19
Alignment explanation
Indices: 303055--303163 Score: 130
Period size: 20 Copynumber: 5.5 Consensus size: 19
303045 CAACGTGGAA
303055 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAA-ATGACT
303075 ATCGCAATACG-GAAATGACT
1 ATCGC-A-ACGCGAAATGACT
*
303095 ATCGCAACGCAGAATTGACT
1 ATCGCAACGC-GAAATGACT
303115 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
* *
303135 ATCGCAATGCGAAAATGGCT
1 ATCGCAACGCG-AAATGACT
303155 ATCGCAACG
1 ATCGCAACG
303164 AGAGAATCGT
Statistics
Matches: 78, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.04
19 2 0.03
20 66 0.85
21 4 0.05
22 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:303114 original size:40 final size:40
Alignment explanation
Indices: 303055--303162 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 40
303045 CAACGTGGAA
*
303055 ATCGCAACGCGAATATGACTATCGCAATACGGAAATGACT
1 ATCGCAACGCGAATATGACTATCGCAACACGGAAATGACT
*
303095 ATCGCAACGCAGAAT-TGACTATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAATATGACTATCGCAACACGGAAATGACT
* * *
303135 ATCGCAATGCGAAAATGGCTATCGCAAC
1 ATCGCAACGCGAATATGACTATCGCAAC
303163 GAGAGAATCG
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
39 3 0.05
40 54 0.89
41 4 0.07
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACTATCGCAACACGGAAATGACT
Found at i:303192 original size:33 final size:34
Alignment explanation
Indices: 303135--303230 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 34
303125 GGAAATGACT
* ***
303135 ATCGCAATGCGAAAATGGCTATCGCAACGAGA-GA
1 ATCGCAATGCAAAAATGAAAATCGCAACGA-ATGA
* *
303169 ATCGTAATGC-GAAATGAAAATCGCAACGAATGA
1 ATCGCAATGCAAAAATGAAAATCGCAACGAATGA
*
303202 ATCGCAATGCAAAAATGAAAATCACAACG
1 ATCGCAATGCAAAAATGAAAATCGCAACG
303231 CGAATTTAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
32 1 0.02
33 26 0.50
34 25 0.48
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.16
Consensus pattern (34 bp):
ATCGCAATGCAAAAATGAAAATCGCAACGAATGA
Found at i:303302 original size:33 final size:34
Alignment explanation
Indices: 303245--303312 Score: 111
Period size: 33 Copynumber: 2.0 Consensus size: 34
303235 TTTAGTTTCG
*
303245 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGAGATTCTCT
*
303279 CGTTGTGATTTTCA-TTTCGCATTGAGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGAGATTCTCT
303312 C
1 C
303313 TCTCATTGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 19 0.59
34 13 0.41
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGAGATTCTCT
Found at i:304973 original size:42 final size:41
Alignment explanation
Indices: 304867--304977 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 41
304857 TCTAGAATGT
* * *
304867 TGGGAG-GGACCTCTTCAACGATGACAGTGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGCCTCTTGAACGA
* * ** *
304908 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACA-GGGCCTCTTGAACGA
304950 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
304978 TGAGTCAGGC
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
41 20 0.36
42 32 0.58
43 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.21
Consensus pattern (41 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGCCTCTTGAACGA
Found at i:305483 original size:20 final size:20
Alignment explanation
Indices: 305457--305565 Score: 164
Period size: 20 Copynumber: 5.5 Consensus size: 20
305447 GAAACTTAAA
305457 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
305477 ATTGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
305497 ATCGCAACGCGAAAATAACT
1 ATCGCAACGCGAAAATGACT
*
305517 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
305537 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
305557 ATCGCAACG
1 ATCGCAACG
305566 AGAGAATCGC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:305641 original size:20 final size:20
Alignment explanation
Indices: 305610--305716 Score: 133
Period size: 20 Copynumber: 5.3 Consensus size: 20
305600 GATTCTTTCG
*
305610 TTGCGGTAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
*
305630 TTGTGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
305650 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
**
305670 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
305690 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
305710 TTGCGAT
1 TTGCGAT
305717 TTTGTTGTTG
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:305668 original size:40 final size:40
Alignment explanation
Indices: 305610--305716 Score: 151
Period size: 40 Copynumber: 2.7 Consensus size: 40
305600 GATTCTTTCG
* ** *
305610 TTGCGGTAGTCAAATTCGCATTGTGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCATTGCGATAGTCAAATTCGCA
**
305650 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCATTGCGATAGTCAAATTCGCA
*
305690 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
305717 TTTGTTGTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (40 bp):
TTGCGATAGTCATTTTCGCATTGCGATAGTCAAATTCGCA
Found at i:305780 original size:20 final size:20
Alignment explanation
Indices: 305755--305806 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
305745 GCGATTCTCT
305755 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCA
**
305775 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCA
*
305795 CATTGCGATAGT
1 CGTTGCGATAGT
305807 AAACTATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCA
Found at i:307713 original size:20 final size:20
Alignment explanation
Indices: 307690--307759 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
307680 TCTGAAACTT
307690 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
307710 AAAATCGCAACACGAAAAT-
1 AAAATCGCAACACGAAAATG
* *
307729 AACTATCGCAATACG-AAATG
1 AA-AATCGCAACACGAAAATG
307749 AAAATCGCAAC
1 AAAATCGCAAC
307760 GATAGAATCG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
19 13 0.30
20 31 0.70
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:308157 original size:22 final size:22
Alignment explanation
Indices: 308095--308160 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
308085 TGACCGTGAA
* *
308095 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
308117 TGATATCGTCAGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
308139 TTATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
308161 GGATGTCGCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:308380 original size:20 final size:20
Alignment explanation
Indices: 308339--308551 Score: 205
Period size: 20 Copynumber: 10.6 Consensus size: 20
308329 GCTATGTAAA
* *
308339 TCGCATTGCGATAGT-CAGAT
1 TCGCATTGCGAT-TTACATAT
*
308359 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* **
308379 TCACATTGCGATTTATGTAT
1 TCGCATTGCGATTTACATAT
308399 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
308419 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACATAT
** *
308439 TCGCATTGCGATTTATGTAA
1 TCGCATTGCGATTTACATAT
* * *
308459 TCACATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACATAT
* *
308480 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACATAT
* *
308500 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACATAT
* *
308521 TCACGTTGCGATTTACGA-AT
1 TCGCATTGCGATTTAC-ATAT
308541 TCGCATTGCGA
1 TCGCATTGCGA
308552 ATTAGGAAAA
Statistics
Matches: 156, Mismatches: 33, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
19 1 0.01
20 126 0.81
21 29 0.19
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:308428 original size:60 final size:59
Alignment explanation
Indices: 308331--308513 Score: 249
Period size: 60 Copynumber: 3.0 Consensus size: 59
308321 CGAATGGCGC
* * * *
308331 TATGTAAATCGCATTGCGATAGTCAGATTCGCGTTGCGATTTACATATTCACATTGCGATT
1 TATGT-AATCGCATTGCGAT-TTCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGATT
* * *
308392 TATGTATTCGCATTGCGATTTACATATTCGCATTGCGATTTACGTATTCGCATTGCGATT
1 TATGTAATCGCATTGCGATTT-CAAATTCGCGTTGCGATTTACGTATTCGCATTGCGATT
*
308452 TATGTAATCACATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGATT
1 TATGTAATCGCATTGCGA-TTT-CAAATTCGCGTTGCGATTTACGTATTCGCATTGCGATT
308513 T
1 T
308514 TCCAAATTCA
Statistics
Matches: 109, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
59 1 0.01
60 63 0.58
61 45 0.41
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (59 bp):
TATGTAATCGCATTGCGATTTCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGATT
Found at i:308536 original size:41 final size:40
Alignment explanation
Indices: 308339--308551 Score: 230
Period size: 40 Copynumber: 5.3 Consensus size: 40
308329 GCTATGTAAA
** * *
308339 TCGCATTGCGATAGTCAGATTCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTTCAAATTCGCGTTGCGATTTACGTAT
* ** * *
308379 TCACATTGCGATTTAT-GTATTCGCATTGCGATTTACATAT
1 TCGCATTGCGATTT-TCAAATTCGCGTTGCGATTTACGTAT
* ** * * *
308419 TCGCATTGCGATTTACGTATTCGCATTGCGATTTATGTAA
1 TCGCATTGCGATTTTCAAATTCGCGTTGCGATTTACGTAT
*
308459 TCACATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTT-CAAATTCGCGTTGCGATTTACGTAT
* *
308500 TCGCATTGCGATTTTCCAAATTCACGTTGCGATTTACGAAT
1 TCGCATTGCGATTTT-CAAATTCGCGTTGCGATTTACGTAT
308541 TCGCATTGCGA
1 TCGCATTGCGA
308552 ATTAGGAAAA
Statistics
Matches: 149, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
40 79 0.53
41 70 0.47
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (40 bp):
TCGCATTGCGATTTTCAAATTCGCGTTGCGATTTACGTAT
Found at i:308572 original size:21 final size:21
Alignment explanation
Indices: 308548--308593 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
308538 AATTCGCATT
308548 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
308569 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
308590 GCGA
1 GCGA
308594 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:309130 original size:20 final size:20
Alignment explanation
Indices: 309105--309154 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
309095 TCGAAAAACG
*
309105 TTTTCCATAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
309125 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
309145 TTTTCCAGAA
1 TTTTCCAGAA
309155 TTCAAATTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:309158 original size:14 final size:15
Alignment explanation
Indices: 309137--309209 Score: 76
Period size: 15 Copynumber: 4.9 Consensus size: 15
309127 TTCCAGAAAT
309137 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
309152 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
309166 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
* ** *
309181 ATAATTCAAATTACA
1 GTAATTCATTTTCCA
*
309196 ATAATTCATTTTCC
1 GTAATTCATTTTCC
309210 GGAAAATCAA
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
14 12 0.26
15 34 0.74
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:309162 original size:20 final size:20
Alignment explanation
Indices: 309105--309163 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
309095 TCGAAAAACG
* **
309105 TTTTCCATAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
**
309125 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
309145 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
309164 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:309179 original size:29 final size:30
Alignment explanation
Indices: 309137--309209 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
309127 TTCCAGAAAT
*
309137 GTAATTCATTTTCC-AGAATTCAAATTCCA
1 GTAATTCATTTTCCAAGAATTCAAATTACA
*
309166 GTAATTCATTTTCCAATAATTCAAATTACA
1 GTAATTCATTTTCCAAGAATTCAAATTACA
*
309196 ATAATTCATTTTCC
1 GTAATTCATTTTCC
309210 GGAAAATCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 14 0.35
30 26 0.65
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTCCAAGAATTCAAATTACA
Found at i:310581 original size:27 final size:27
Alignment explanation
Indices: 310543--310597 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
310533 AGTTGGTGAG
*
310543 GACTGTTATCCCTTGAGTAGAAGGAAA
1 GACTGTTATCCCTTGACTAGAAGGAAA
310570 GACTGTTATCCCTTGACTAGAAGGAAA
1 GACTGTTATCCCTTGACTAGAAGGAAA
310597 G
1 G
310598 GAAGAGGAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (27 bp):
GACTGTTATCCCTTGACTAGAAGGAAA
Found at i:313155 original size:13 final size:13
Alignment explanation
Indices: 313137--313164 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
313127 CACATATCTT
313137 TTCGCCTTTTATA
1 TTCGCCTTTTATA
313150 TTCGCCTTTTATA
1 TTCGCCTTTTATA
313163 TT
1 TT
313165 TACATGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (13 bp):
TTCGCCTTTTATA
Found at i:322286 original size:50 final size:48
Alignment explanation
Indices: 322052--322293 Score: 272
Period size: 49 Copynumber: 4.9 Consensus size: 48
322042 GAATACCATG
* *
322052 AGTGGCACCTTTTATGTCGGTAATGTACCATTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGTC-GAAATGCACCATTATGCATTTAA-TTTCATT
* * *
322102 AATGGCACCTTTTATG-CTAAAATGCATCATTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGTC-GAAATGCACCATTATGCATTTAA-TTTCATT
* * * *
322151 AGTGTCACCTTTTATGCCAAAATGCACTATTATGCATTTAATTTTCATT
1 AGTGGCACCTTTTATGTCGAAATGCACCATTATGCATTTAA-TTTCATT
* * *
322200 AATGGCACCTTTTAT-TCCGAAATGCACCGTTGTGCATTTAATTTACATT
1 AGTGGCACCTTTTATGT-CGAAATGCACCATTATGCATTTAATTT-CATT
* *
322249 AGTGGAACCTTTTTATGTCGAAATGCACCGTTATGCATTTAATTT
1 AGTGGCACC-TTTTATGTCGAAATGCACCATTATGCATTTAATTT
322294 GGCAATCATT
Statistics
Matches: 166, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
48 3 0.02
49 114 0.69
50 48 0.29
51 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (48 bp):
AGTGGCACCTTTTATGTCGAAATGCACCATTATGCATTTAATTTCATT
Found at i:329365 original size:49 final size:49
Alignment explanation
Indices: 329127--329367 Score: 275
Period size: 49 Copynumber: 4.9 Consensus size: 49
329117 GAATACCATG
* * * * *
329127 AGTGGCACCTTTTGTGTCGATAATGCATCGTTATGCATTTAACTGTCATT
1 AGTGGCACCTTTTATGCCGA-AATGCACCGTTATGCATTTAATTTTCATT
* * * * **
329177 AATGGCACCTTTTACGTCGAAATGCACCATTATGCATTTAACATTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTTTCATT
* * *
329226 AGTTGCACCTTTTATGCCTAAATGCACCGTTATGCATTTTATTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTTTCATT
* * * *
329275 AATGGCACCTTTTATGCCTAAATTCACCGTTATGCATTTAATTTTCTTT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTTTCATT
* * * *
329324 AGTGGTACATTTTATGCCGAAATTCACCGTTATGCCTTTAATTT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTT
329368 GGCAATCATT
Statistics
Matches: 165, Mismatches: 26, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
49 148 0.90
50 17 0.10
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (49 bp):
AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTTTCATT
Found at i:337077 original size:19 final size:18
Alignment explanation
Indices: 337055--337095 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
337045 AAAAAGCGAA
337055 AAAAATATGAAAAAGAACG
1 AAAAATAT-AAAAAGAACG
*
337074 AAAAATATAAAAAGAATG
1 AAAAATATAAAAAGAACG
337092 AAAA
1 AAAA
337096 GAAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (18 bp):
AAAAATATAAAAAGAACG
Found at i:338034 original size:18 final size:19
Alignment explanation
Indices: 338011--338053 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
338001 ATAGTTTAAC
*
338011 TATTTTCA-TTAGGATTTA
1 TATTTTCATTTAGGAATTA
*
338029 TATTTTTATTTTAGGAATTA
1 TATTTTCA-TTTAGGAATTA
338049 TATTT
1 TATTT
338054 CCTTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.60
Consensus pattern (19 bp):
TATTTTCATTTAGGAATTA
Found at i:340712 original size:21 final size:21
Alignment explanation
Indices: 340688--340739 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
340678 CGAACCTCAG
*
340688 TTTCCAAATTCGCATTGCGCT
1 TTTCCAAATTCGCATTGCGAT
*
340709 TTTCCAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCATTGCGAT
340730 TTTCCAAATT
1 TTTCCAAATT
340740 TACAACACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.40
Consensus pattern (21 bp):
TTTCCAAATTCGCATTGCGAT
Found at i:340802 original size:20 final size:20
Alignment explanation
Indices: 340779--340854 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
340769 GATTTCTAAA
*
340779 TTCGCAACGCGAATTTTGTT
1 TTCGCAACTCGAATTTTGTT
340799 TTCGCAACTCGAATTTTGTT
1 TTCGCAACTCGAATTTTGTT
*
340819 TTCTCAACTCGAATTTTGTT
1 TTCGCAACTCGAATTTTGTT
340839 TTCGCAACTCG-ATTTT
1 TTCGCAACTCGAATTTT
340855 CGAATTTGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 5 0.09
20 48 0.91
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (20 bp):
TTCGCAACTCGAATTTTGTT
Found at i:340804 original size:40 final size:39
Alignment explanation
Indices: 340759--340886 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 39
340749 GAATTTCAAA
*
340759 TTCGCAACTCGATTTCTAAATTCGCAACGCGAATTTTGTT
1 TTCGCAACTCGATTT-TGAATTCGCAACGCGAATTTTGTT
** * *
340799 TTCGCAACTCGAATTTTGTTTTCTCAACTCGAATTTTGTT
1 TTCGCAACTCG-ATTTTGAATTCGCAACGCGAATTTTGTT
*
340839 TTCGCAACTCGATTTTCGAATTTGCAACAG-GAATTTT-TAT
1 TTCGCAACTCGATTTT-GAATTCGCAAC-GCGAATTTTGT-T
340879 TTCGCAAC
1 TTCGCAAC
340887 AGGTTTTAGT
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
39 6 0.08
40 64 0.86
41 4 0.05
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (39 bp):
TTCGCAACTCGATTTTGAATTCGCAACGCGAATTTTGTT
Found at i:341063 original size:15 final size:16
Alignment explanation
Indices: 341043--341080 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
341033 TCCCCATCTC
*
341043 TAATTTTGTTT-TACA
1 TAATTTTATTTCTACA
*
341058 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
341074 TAATTTT
1 TAATTTT
341081 TCAATGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:341991 original size:64 final size:64
Alignment explanation
Indices: 341885--342037 Score: 202
Period size: 64 Copynumber: 2.4 Consensus size: 64
341875 AATTTAAAAC
* *
341885 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAACAATAAGAATTATTTAT-ACATTAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTT-TCACATCAATTA
* * *** *
341949 AACAAATCAACTTTTACAAATTAATTAAATAAGCAAAAAATAATTCTTATTTTCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTTCACATCAATTA
*
342013 AATAAATCAAC-TTTACAAATCAATT
1 AACAAATCAACTTTTACAAATCAATT
342038 GTAAATACAT
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
63 14 0.18
64 64 0.82
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTTCACATCAATTA
Found at i:343414 original size:21 final size:21
Alignment explanation
Indices: 343385--343473 Score: 90
Period size: 21 Copynumber: 4.2 Consensus size: 21
343375 GTGAATCGGT
* *
343385 CTCTCGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* **
343406 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
343427 CTCTTTAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
**
343448 CTCTTGAA-GGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
343469 CTCTT
1 CTCTT
343474 AAATGATAGG
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 2 0.04
21 53 0.96
ACGTcount: A:0.19, C:0.21, G:0.37, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:343451 original size:42 final size:42
Alignment explanation
Indices: 343391--343507 Score: 144
Period size: 42 Copynumber: 2.8 Consensus size: 42
343381 CGGTCTCTCG
* *
343391 AACGGTGGGAGGGACCTCTTGAACGATGACAGGGGCCTCTTT
1 AACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTA
* *
343433 AACGGTGGGAGGGGCCTCTTGAAGGATGATAGGGGCCTCTTA
1 AACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTA
* * * ** *
343475 AATGATAGGAGATGCCTCTTGAATGATGACAGG
1 AACGGTGGGAGGGGCCTCTTGAACGATGACAGG
343508 TGAATCGGGC
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.22
Consensus pattern (42 bp):
AACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTA
Found at i:343481 original size:18 final size:20
Alignment explanation
Indices: 343400--343503 Score: 77
Period size: 21 Copynumber: 5.0 Consensus size: 20
343390 GAACGGTGGG
* *
343400 AGGGACCTCTTGAACGATGAC
1 AGGGGCCTCTTGAA-GATGAT
* * **
343421 AGGGGCCTCTTTAACGGTGGG
1 AGGGGCCTCTTGAA-GATGAT
343442 AGGGGCCTCTTGAAGGATGAT
1 AGGGGCCTCTTGAA-GATGAT
343463 AGGGGCCTCTT-AA-ATGAT
1 AGGGGCCTCTTGAAGATGAT
343481 AGGAGATGCCTCTTGAATGATGA
1 AGG-G--GCCTCTTGAA-GATGA
343504 CAGGTGAATC
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
18 8 0.12
19 1 0.01
20 2 0.03
21 50 0.75
22 2 0.03
24 4 0.06
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (20 bp):
AGGGGCCTCTTGAAGATGAT
Found at i:343902 original size:21 final size:21
Alignment explanation
Indices: 343878--343927 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
343868 ACTATTGTCT
* *
343878 TCACGTAAAGTATTGACCTCC
1 TCACGTAAAGCATTGACCTCA
343899 TCACGTAAAGCATTGACCTCA
1 TCACGTAAAGCATTGACCTCA
343920 TCACGTAA
1 TCACGTAA
343928 CTCCCCTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (21 bp):
TCACGTAAAGCATTGACCTCA
Found at i:346011 original size:20 final size:21
Alignment explanation
Indices: 345986--346025 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
345976 TCTGAGAGAT
345986 GGAGAT-AGACGGATTTCGGC
1 GGAGATGAGACGGATTTCGGC
346006 GGAGATGGAGACGGATTTCG
1 GGAGAT-GAGACGGATTTCG
346026 TCATAGATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.25, C:0.12, G:0.42, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGGC
Found at i:346019 original size:22 final size:22
Alignment explanation
Indices: 345992--346043 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
345982 AGATGGAGAT
*
345992 AGACGGATTTCGGCGGAGATGG
1 AGACGGATTTCGGCAGAGATGG
* *
346014 AGACGGATTTCGTCATAGATGG
1 AGACGGATTTCGGCAGAGATGG
*
346036 GGACGGAT
1 AGACGGAT
346044 GTCACCGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.40, T:0.21
Consensus pattern (22 bp):
AGACGGATTTCGGCAGAGATGG
Found at i:348075 original size:20 final size:20
Alignment explanation
Indices: 348052--348116 Score: 105
Period size: 20 Copynumber: 3.2 Consensus size: 20
348042 TGCGATTTTC
348052 CAAATTCGCAACGCGGAAGT
1 CAAATTCGCAACGCGGAAGT
348072 CAAATTCGCAACGC-GATAGT
1 CAAATTCGCAACGCGGA-AGT
*
348092 CAAATTCGTAACGCGGAAGT
1 CAAATTCGCAACGCGGAAGT
348112 CAAAT
1 CAAAT
348117 ATAAATGCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 2 0.05
20 38 0.90
21 2 0.05
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGGAAGT
Found at i:348081 original size:41 final size:41
Alignment explanation
Indices: 347952--348116 Score: 128
Period size: 40 Copynumber: 4.1 Consensus size: 41
347942 AAATGACCAA
* * *
347952 CAAATTTGCAACGCGA-TCT-CAAATTCGCAACGC-GAATT
1 CAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGGAAGT
* * * * * *
347990 CCAATTTCGTAAC-CCAGTTTCCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGGA-A-GT
**
348033 -AAA-TCGCATTGCGATTTTCCAAATTCGCAACGCGGAAGT
1 CAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGGAAGT
** *
348072 CAAATTCGCAACGCGATAGT-CAAATTCGTAACGCGGAAGT
1 CAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGGAAGT
348112 CAAAT
1 CAAAT
348117 ATAAATGCAT
Statistics
Matches: 97, Mismatches: 21, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
38 2 0.02
39 13 0.13
40 45 0.46
41 35 0.36
42 1 0.01
43 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (41 bp):
CAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGGAAGT
Found at i:348808 original size:40 final size:39
Alignment explanation
Indices: 348749--348847 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 39
348739 AAGAGAGAGC
*
348749 ATTTC-ATTTGTGTTGCGAAAGTGAAATTCGCAACGTGA
1 ATTTCAATTTGTGTTGCGAAAGTGAAATTCGCAACGGGA
* * *
348787 ATTTCAATTGTGTGTTGCGAAATTGAAATTTGCAATGGGA
1 ATTTCAATT-TGTGTTGCGAAAGTGAAATTCGCAACGGGA
* *
348827 ATTTTAATTATATGTTGCGAA
1 ATTTCAATT-TGTGTTGCGAA
348848 TTTTATGTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
38 5 0.10
39 3 0.06
40 44 0.85
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.38
Consensus pattern (39 bp):
ATTTCAATTTGTGTTGCGAAAGTGAAATTCGCAACGGGA
Found at i:350145 original size:20 final size:21
Alignment explanation
Indices: 350129--350343 Score: 232
Period size: 20 Copynumber: 10.7 Consensus size: 21
350119 TACACAAATT
*
350129 CGCGTTGCG-ATTTACAAATC
1 CGCGTTGCGAATTTACAGATC
350149 CGCGTTGCGAATTT-CAGATC
1 CGCGTTGCGAATTTACAGATC
* **
350169 TGCGTTGCGAAAAT-CAGATC
1 CGCGTTGCGAATTTACAGATC
350189 CGCGTTGCGAATTT-CAGATC
1 CGCGTTGCGAATTTACAGATC
* *
350209 TGCGTTGCGAATTT-CAGATT
1 CGCGTTGCGAATTTACAGATC
**
350229 CGCGTTGCGAAAAT-CAGATC
1 CGCGTTGCGAATTTACAGATC
350249 CGCGTTGCGAATTT-CAGATC
1 CGCGTTGCGAATTTACAGATC
*
350269 CGCGTTGCGAA-TT-CATATC
1 CGCGTTGCGAATTTACAGATC
* *
350288 CGCGTTGCGTATTTACATATC
1 CGCGTTGCGAATTTACAGATC
* * *
350309 CGTGTTGCGAATTTACATATT
1 CGCGTTGCGAATTTACAGATC
*
350330 CGCGTTGCAAATTT
1 CGCGTTGCGAATTT
350344 GGAAAATCGC
Statistics
Matches: 170, Mismatches: 22, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.10
20 113 0.66
21 40 0.24
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (21 bp):
CGCGTTGCGAATTTACAGATC
Found at i:350198 original size:60 final size:60
Alignment explanation
Indices: 350129--350343 Score: 265
Period size: 60 Copynumber: 3.6 Consensus size: 60
350119 TACACAAATT
*
350129 CGCGTTGCG-ATTTACAAATCCGCGTTGCGAATTTCAGATCTGCGTTGCGAAAATCAGATC
1 CGCGTTGCGAATTT-CAGATCCGCGTTGCGAATTTCAGATCTGCGTTGCGAAAATCAGATC
*
350189 CGCGTTGCGAATTTCAGATCTGCGTTGCGAATTTCAGAT-TCGCGTTGCGAAAATCAGATC
1 CGCGTTGCGAATTTCAGATCCGCGTTGCGAATTTCAGATCT-GCGTTGCGAAAATCAGATC
* * * ** *
350249 CGCGTTGCGAATTTCAGATCCGCGTTGCGAA-TTCATATCCGCGTTGCGTATTTACATATC
1 CGCGTTGCGAATTTCAGATCCGCGTTGCGAATTTCAGATCTGCGTTGCGAAAAT-CAGATC
* * * *
350309 CGTGTTGCGAATTTACATATTCGCGTTGCAAATTT
1 CGCGTTGCGAATTT-CAGATCCGCGTTGCGAATTT
350344 GGAAAATCGC
Statistics
Matches: 136, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
59 17 0.12
60 99 0.73
61 18 0.13
62 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (60 bp):
CGCGTTGCGAATTTCAGATCCGCGTTGCGAATTTCAGATCTGCGTTGCGAAAATCAGATC
Found at i:350353 original size:21 final size:21
Alignment explanation
Indices: 350329--350369 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
350319 ATTTACATAT
*
350329 TCGCGTTGCAAATTTGGAAAA
1 TCGCATTGCAAATTTGGAAAA
**
350350 TCGCATTGTGAATTTGGAAA
1 TCGCATTGCAAATTTGGAAA
350370 CTGTATTGCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (21 bp):
TCGCATTGCAAATTTGGAAAA
Found at i:351429 original size:254 final size:258
Alignment explanation
Indices: 350933--351442 Score: 814
Period size: 254 Copynumber: 2.0 Consensus size: 258
350923 GGGTCGCTCG
*
350933 GTTTTTTTAAGTGTGATATTCGGTTCGAGTCGAGTTCGGGTTTAGGCTGAAAAATACCCAACCCG
1 GTTTTTTTAAGTGTGATATTCGGGTCGAGTCGAGTTCGGGTTTAGGCTGAAAAATACCCAACCCG
* * *
350998 AAAATATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATAACCCTCTATATATAAT
66 AAAAAATATATAATTTTACCTTATATACTTAGAAATAATTACAATAATAACCCCCTATATATAAT
* * * *
351063 TTTTTTCAATTAAGCTACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCAGGTC
131 ATTTTCCAATTAAGCTACTATTTTTATTGAATAAAAATAATTTTTTTATTATTTCCGGTCAGGTC
* *
351128 GAATTTCTAATTCATATATTCGGGTTGGGTCGGGTGAAACTTTATTTTGGTCAGGTCGGGTCA
196 GAATTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGTCGGGTCA
* * * *
351191 GTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCC-
1 GTTTTTTTAAGTGTGATATTCGGGTCGAGTCGAGTTCGGGTTTAGGCTGAAAAATACCCAACCCG
*
351255 AAAAAATATATAATTTTACCTTATATACTTAGGAATAATTACAATAAT-ACCCCCTATATAT-AT
66 AAAAAATATATAATTTTACCTTATATACTTAGAAATAATTACAATAATAACCCCCTATATATAAT
*
351318 ATTTTCCAATTAAG-TCACTATTTTTATTGAATAAAAAT-ATTTTTTTATTATTTCCGGTCGGGT
131 ATTTTCCAATTAAGCT-ACTATTTTTATTGAATAAAAATAATTTTTTTATTATTTCCGGTCAGGT
* *
351381 CGAGTTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGT
195 CGAATTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGTCGGGT
351443 GAACCCAAAA
Statistics
Matches: 233, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
254 82 0.35
255 35 0.15
256 12 0.05
257 45 0.19
258 59 0.25
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (258 bp):
GTTTTTTTAAGTGTGATATTCGGGTCGAGTCGAGTTCGGGTTTAGGCTGAAAAATACCCAACCCG
AAAAAATATATAATTTTACCTTATATACTTAGAAATAATTACAATAATAACCCCCTATATATAAT
ATTTTCCAATTAAGCTACTATTTTTATTGAATAAAAATAATTTTTTTATTATTTCCGGTCAGGTC
GAATTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGTCGGGTCA
Found at i:351805 original size:18 final size:18
Alignment explanation
Indices: 351760--351806 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
351750 TATGGAATTG
*
351760 GATTCCAATT-CTTGACA
1 GATTCCAATTCCTTCACA
*
351777 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
351795 TATTCCAATTCC
1 GATTCCAATTCC
351807 CTCAGAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.38
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:357782 original size:3 final size:3
Alignment explanation
Indices: 357767--357834 Score: 50
Period size: 3 Copynumber: 23.0 Consensus size: 3
357757 CCATTTTGAT
* ** * **
357767 TTA TTA CTA TTA TTA -TA GAA TTA TTA TTA TTA -CA TTA TTA CGAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
357811 ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
357835 AAAATAATTA
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 3 0.06
3 46 0.92
4 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:357844 original size:25 final size:25
Alignment explanation
Indices: 357767--357844 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
357757 CCATTTTGAT
* *
357767 TTATTACTATTATTATAGAATTATTA
1 TTATTA-TATTATTACAAAATTATTA
*
357793 TTATTACATTATTACGAAATATTATTA
1 TTATTATATTATTAC-AAA-ATTATTA
*
357820 TTATTATTATTATTA-AAAATAATTA
1 TTATTA-TATTATTACAAAATTATTA
357845 CATGCCCAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
25 13 0.30
26 11 0.25
27 13 0.30
28 7 0.16
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (25 bp):
TTATTATATTATTACAAAATTATTA
Found at i:361500 original size:14 final size:14
Alignment explanation
Indices: 361481--361523 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
361471 TTTTAAATAA
361481 TTTACATTTACATT
1 TTTACATTTACATT
* *
361495 TTTACATTCACATA
1 TTTACATTTACATT
*
361509 TTTACATTTGCATT
1 TTTACATTTACATT
361523 T
1 T
361524 GGCATTTGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.28, C:0.16, G:0.02, T:0.53
Consensus pattern (14 bp):
TTTACATTTACATT
Found at i:362680 original size:44 final size:44
Alignment explanation
Indices: 362621--362704 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
362611 CGTTGACAAC
362621 AAAACTCGACGAAGAGACAATGAAAGGGTTCGGATGGTCGGACA
1 AAAACTCGACGAAGAGACAATGAAAGGGTTCGGATGGTCGGACA
362665 AAAACTCGACGAAGAGACAATGAAAGGGTTCGGATGGTCG
1 AAAACTCGACGAAGAGACAATGAAAGGGTTCGGATGGTCG
362705 CTAACACAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.38, C:0.15, G:0.32, T:0.14
Consensus pattern (44 bp):
AAAACTCGACGAAGAGACAATGAAAGGGTTCGGATGGTCGGACA
Found at i:366538 original size:2 final size:2
Alignment explanation
Indices: 366533--366565 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
366523 GTGTGTGTGT
*
366533 GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
366566 GGTGTTTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:376502 original size:43 final size:43
Alignment explanation
Indices: 376437--376520 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
376427 AACTCGTTGC
* *
376437 TTTCGAGCCCATTGGTGTGAATGTGAGTGTGGATTTGTCTTGT
1 TTTCGAGCCCATTGGTGCGAATGTGAGCGTGGATTTGTCTTGT
376480 TTTCGAGCCCATTGGTGCGAATGTGAGCGTGGATTTGTCTT
1 TTTCGAGCCCATTGGTGCGAATGTGAGCGTGGATTTGTCTT
376521 CCGTCGGCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.14, C:0.14, G:0.32, T:0.39
Consensus pattern (43 bp):
TTTCGAGCCCATTGGTGCGAATGTGAGCGTGGATTTGTCTTGT
Found at i:377961 original size:12 final size:13
Alignment explanation
Indices: 377938--377969 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
377928 TACACGTGGG
377938 TTTTTTATTTTTA
1 TTTTTTATTTTTA
377951 TTTTTTA-TTTTA
1 TTTTTTATTTTTA
377963 TTTTTTA
1 TTTTTTA
377970 ATTGCCACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:378489 original size:19 final size:18
Alignment explanation
Indices: 378451--378489 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
378441 GGGTTTTAGA
*
378451 TTTGGAATTAGACCTCAG
1 TTTGGAATTAGACATCAG
*
378469 TTTGGAATTATGATATCAG
1 TTTGGAATTA-GACATCAG
378488 TT
1 TT
378490 GTATACTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (18 bp):
TTTGGAATTAGACATCAG
Found at i:387741 original size:7 final size:7
Alignment explanation
Indices: 387728--387825 Score: 115
Period size: 7 Copynumber: 14.0 Consensus size: 7
387718 TTGCAATGAG
387728 CCCTAAA
1 CCCTAAA
*
387735 TCCTAAA
1 CCCTAAA
387742 CCCTAAA
1 CCCTAAA
*
387749 CCCTAGA
1 CCCTAAA
*
387756 CCATAAA
1 CCCTAAA
* *
387763 CACTAAT
1 CCCTAAA
*
387770 CCATAAA
1 CCCTAAA
*
387777 CTCTAAA
1 CCCTAAA
387784 CCCTAAA
1 CCCTAAA
387791 CCCTAAA
1 CCCTAAA
387798 CCCTAAA
1 CCCTAAA
**
387805 CTATAAA
1 CCCTAAA
387812 CCCTAAA
1 CCCTAAA
387819 CCCTAAA
1 CCCTAAA
387826 TCCAATTATA
Statistics
Matches: 73, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 73 1.00
ACGTcount: A:0.45, C:0.36, G:0.01, T:0.18
Consensus pattern (7 bp):
CCCTAAA
Found at i:388167 original size:17 final size:17
Alignment explanation
Indices: 388138--388170 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
388128 AATTAAAATT
388138 ACAAGACATAATTGAAA
1 ACAAGACATAATTGAAA
388155 ACAAGCACA-AATTGAA
1 ACAAG-ACATAATTGAA
388171 TGAAATTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (17 bp):
ACAAGACATAATTGAAA
Found at i:392766 original size:7 final size:7
Alignment explanation
Indices: 392754--392821 Score: 57
Period size: 7 Copynumber: 9.7 Consensus size: 7
392744 TAAAAAAATT
392754 CTAAACC
1 CTAAACC
392761 CTAAACC
1 CTAAACC
392768 CTAAACC
1 CTAAACC
*
392775 CTAAAACA
1 CT-AAACC
*
392783 C-ATACC
1 CTAAACC
* *
392789 TTAAATC
1 CTAAACC
*
392796 CTAAATC
1 CTAAACC
*
392803 ATAAACC
1 CTAAACC
*
392810 CTAAACT
1 CTAAACC
392817 CTAAA
1 CTAAA
392822 GCTTAAATCT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
6 3 0.06
7 40 0.83
8 5 0.10
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:395721 original size:41 final size:41
Alignment explanation
Indices: 395660--395740 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
395650 TAGAATTATA
*
395660 AAAAATAAGGAATTAGGGGTATATTTTACCCATGAAATAAT
1 AAAAATAAGGAATTAAGGGTATATTTTACCCATGAAATAAT
* *
395701 AAAAATAAGGGATTAAGGGTATATTTTACCCCTGAAATAA
1 AAAAATAAGGAATTAAGGGTATATTTTACCCATGAAATAA
395741 ACCGAAATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (41 bp):
AAAAATAAGGAATTAAGGGTATATTTTACCCATGAAATAAT
Found at i:396800 original size:35 final size:36
Alignment explanation
Indices: 396750--396818 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
396740 AATAATTATT
* *
396750 AATTGATAATTTAGTAATT-TT-ATTATTTATTATAA
1 AATTCATAAATTAGTAATTATTAATT-TTTATTATAA
396785 AATTCATAAATTAGTAATTATTAATTTTTATTAT
1 AATTCATAAATTAGTAATTATTAATTTTTATTAT
396819 CTATTAGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 17 0.57
36 10 0.33
37 3 0.10
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (36 bp):
AATTCATAAATTAGTAATTATTAATTTTTATTATAA
Found at i:397374 original size:3 final size:3
Alignment explanation
Indices: 397366--397390 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
397356 CGGGTTTTAG
397366 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
397391 TTACATGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:398124 original size:20 final size:20
Alignment explanation
Indices: 398099--398137 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
398089 GCTAGAGGAT
398099 GGTGGCACACGGTGGCTGGA
1 GGTGGCACACGGTGGCTGGA
398119 GGTGGCACACGGTGGCTGG
1 GGTGGCACACGGTGGCTGG
398138 TGAGGGTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.13, C:0.21, G:0.51, T:0.15
Consensus pattern (20 bp):
GGTGGCACACGGTGGCTGGA
Found at i:399671 original size:132 final size:131
Alignment explanation
Indices: 399462--399830 Score: 497
Period size: 131 Copynumber: 2.8 Consensus size: 131
399452 TTGATATTGA
*
399462 AAATAGTAATATCTTTTCATTGT-GGTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGATCA
1 AAATAGTAATATCTTTTCATT-TCGGTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCA
* * * *
399526 ATTATTCTCGATTGGAAATCATTAGATTTTATCATTTTTCTCTTGAATAAGTATTGATTTTTAAG
65 TTTATTCTTGATTGGAAATCATTAGATATTATC-TTTTTCTCTTGAATAAGTATTGATTTGTAAG
399591 ACG
129 ACG
* * **
399594 AAATGGTAATATATTTTCATTTCGGTTGGAGTAATAAATGGTTGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTAATATCTTTTCATTTCGGTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
* ** *
399659 TTATTCTTGATTGGAAATCATTAGATATTATCGTTTTCTCTCAAATCAGTATTGATTTGTAAGAC
66 TTATTCTTGATTGGAAATCATTAGATATTATCTTTTTCTCTTGAATAAGTATTGATTTGTAAGAC
399724 G
131 G
* * ** * * * * *
399725 AAATACTGATATCTCCTCATTTCGGTTGGAGTAATAAATTACTGTTTTAACGCAAGAGAGGTCAT
1 AAATAGTAATATCTTTTCATTTCGGTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
* *
399790 TTATTCTTGATTGGAAATAATTAGATATTATCGTTTTCTCT
66 TTATTCTTGATTGGAAATCATTAGATATTATCTTTTTCTCT
399831 CTTAGAATTA
Statistics
Matches: 210, Mismatches: 26, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
131 123 0.59
132 87 0.41
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.41
Consensus pattern (131 bp):
AAATAGTAATATCTTTTCATTTCGGTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
TTATTCTTGATTGGAAATCATTAGATATTATCTTTTTCTCTTGAATAAGTATTGATTTGTAAGAC
G
Found at i:401259 original size:17 final size:17
Alignment explanation
Indices: 401237--401283 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
401227 TGTTTTATAT
* *
401237 TATTTTTATTTGTCTTA
1 TATTTTCATTTGCCTTA
401254 TATTTTCATTTGCCTTA
1 TATTTTCATTTGCCTTA
401271 TATTTTCATTTGC
1 TATTTTCATTTGC
401284 ATTTTCACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.17, C:0.13, G:0.06, T:0.64
Consensus pattern (17 bp):
TATTTTCATTTGCCTTA
Found at i:405862 original size:2 final size:2
Alignment explanation
Indices: 405855--405879 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
405845 GGTGATTGTA
405855 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
405880 CAATAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:407643 original size:41 final size:42
Alignment explanation
Indices: 407544--407643 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
407534 TTTCTTACTT
* * * * * * *
407544 AGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGGTGATTA
1 AGTCCTTCGGGCCATCTACAAGCCTTTCAAGCAAGATGATTA
* * *
407586 AATTCTTCGGGTCATCTACAAGCCTTTCAAGCAAGATGA-TA
1 AGTCCTTCGGGCCATCTACAAGCCTTTCAAGCAAGATGATTA
407627 AGTCCTTCGGGCCATCT
1 AGTCCTTCGGGCCATCT
407644 GTAAAACCTT
Statistics
Matches: 45, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
41 16 0.36
42 29 0.64
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (42 bp):
AGTCCTTCGGGCCATCTACAAGCCTTTCAAGCAAGATGATTA
Found at i:408054 original size:253 final size:253
Alignment explanation
Indices: 407544--408628 Score: 1319
Period size: 254 Copynumber: 4.3 Consensus size: 253
407534 TTTCTTACTT
* * * * * *
407544 AGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGGTGATTAAATTCTTCGGGTCATCTACAAGC
1 AGTCCTTCGGGCCATCAGTAAGTCTTT-TAGCATGATGATTAAATCCTTCGGGTCATCTATAAGC
* ** * * *
407609 CTTTCAAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAAACCTTCAGGTAGGATGTTTTCACAT
65 CTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAAGATGTTTTCACAT
* *
407674 GGTTTTCGAAAAATGATAAAACAATTTCTAAAGTTTCTCATTTAAA-ATTGAAAATTGAAATATT
130 -GTTTTCGAAAAATGAGAAAACAATTTCTAAAGTTTCTCATTGAAATA-TGAAAATTGAAAT-TT
407738 TT-AAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCT-AAATTGGTA
192 TTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCTAAAATTGGTA
* *
407798 AGTCCTTC-GGCTCATCAGTAAGTCTTTTAGCATGATGATTGAATCCTTCGGGTAATCTATAAGC
1 AGTCCTTCGGGC-CATCAGTAAGTCTTTTAGCATGATGATTAAATCCTTCGGGTCATCTATAAGC
* * * * * *
407862 CTTTCGAGCAAGATGATAAGTTCTTTGGGCCATCCGTAAGACCTTCGGGCAAGATGTTTTTATAT
65 CTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAAGATGTTTTCACAT
* * *
407927 GATTTTCAAAAAAATGAGAAAACAATTTCTAAAGTTTCTAAATGAAATATGAAAATTGAAATTTT
130 G-TTTTC-GAAAAATGAGAAAACAATTTCTAAAGTTTCTCATTGAAATATGAAAATTGAAATTTT
* * *
407992 TGAAAAATAAGAAAACGATTTCCAAAGTTT-TTACCTAGTAAGCTATTTCTAAAATT-GTA
193 TGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCTAAAATTGGTA
* * * * *
408051 AGTCTTTCGGGCCATCGGTAAGTCTTTTGAGCATGGTGATTAAATCTTTCGGGTCATCTATAAGT
1 AGTCCTTCGGGCCATCAGTAAGTCTTTT-AGCATGATGATTAAATCCTTCGGGTCATCTATAAGC
* * * * * ** * *
408116 ATTTTGAGTAAGATGATAAGTCCTTCAGGCCATTCATAAGACCTTGGGGCAGGATGTTTTCACTT
65 CTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAAGATGTTTTCACAT
* * * *
408181 GTTTGTTGAAAAATGAGAAAACAATTTGC-AAAGTTTGTCATTGAAATCTGAATATTGAAATTTT
130 GTTT-TCGAAAAATGAGAAAACAATTT-CTAAAGTTTCTCATTGAAATATGAAAATTGAAATTTT
* * *
408245 TTAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACATAGTAAGA-TA-TTCCAAAATTGGTA
193 TGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAA-ACTATTTCTAAAATTGGTA
* * * * * * *
408305 AGTTCTTTGGGCCATCAGCAAGTCTTTCGAGCATGTTGATTAAATCATTCTGGTCATCTATAAGC
1 AGTCCTTCGGGCCATCAGTAAGTCTTT-TAGCATGATGATTAAATCCTTCGGGTCATCTATAAGC
* * * * *
408370 CTTTCGAGTAAGATGATAAGTCATTCGGGCCATTCATAAGACCATCAGGC-AGAACGTTTTCACA
65 CTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAAG-ATGTTTTCACA
* * * * * *
408434 TGTTTTTCGAAAAATGAGAAAACGATTTCCAATGTTTCTCATTGAAATCTAAAAATTGAATTTTT
129 TG-TTTTCGAAAAATGAGAAAACAATTTCTAAAGTTTCTCATTGAAATATGAAAATTGAAATTTT
* * *
408499 TGGAAAGTAGGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAAAAATTGGTA
193 TGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCTAAAATTGGTA
408560 AGTCCTTCGGGCCATCAGTAAGT-TTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTATAAG
1 AGTCCTTCGGGCCATCAGTAAGTCTTTT--AGCATGATGATTAAATCCTTCGGGTCATCTATAAG
408624 CCTTT
64 CCTTT
408629 TCAAGAATGA
Statistics
Matches: 712, Mismatches: 98, Indels: 41
0.84 0.12 0.05
Matches are distributed among these distances:
252 1 0.00
253 233 0.33
254 404 0.57
255 74 0.10
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (253 bp):
AGTCCTTCGGGCCATCAGTAAGTCTTTTAGCATGATGATTAAATCCTTCGGGTCATCTATAAGCC
TTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAAGATGTTTTCACATG
TTTTCGAAAAATGAGAAAACAATTTCTAAAGTTTCTCATTGAAATATGAAAATTGAAATTTTTGA
AAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCTAAAATTGGTA
Found at i:408521 original size:507 final size:509
Alignment explanation
Indices: 407544--408633 Score: 1396
Period size: 507 Copynumber: 2.1 Consensus size: 509
407534 TTTCTTACTT
* * *
407544 AGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGGTGATTAAAT-TCTTCGGGTCATCTACAAG
1 AGTCATTCGGGCCATCAGTAAGTCTTTTGAGCATGGTGATTAAATCT-TTCGGGTCATCTATAAG
* * * *
407608 CCTTTCAAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAAACCTTCAGGTAGGATGTTTTCACA
65 CATTTCAAGCAAGATGATAAGTCCTTCAGGCCATCTATAAAACCTTCAGGCAGGATGTTTTCACA
*
407673 TGGTTTTCGAAAAATGATAAAACAATTTCTAAAGTTTCTCATTTAAAATTGAAAATTGAAATATT
130 TGGTTTTCGAAAAATGAGAAAACAATTTCTAAAGTTTCTCATTTAAAATTGAAAATTGAAATATT
* * *
407738 TTAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCTAAATTGGTAAGTCC
195 TTAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACATAGTAAACTATTCCAAAATTGGTAAGTCC
* * * *
407803 TTCGGCTCATCAGTAAGTCTTTTAGCATGATGATTGAATCCTTCGGGTAATCTATAAGCCTTTCG
260 TTCGGCTCATCAGCAAGTCTTTGAGCATGATGATTAAATCATTCGGGTAATCTATAAGCCTTTCG
* * * * * * *
407868 AGCAAGATGATAAGTTCTTTGGGCCATCCGTAAGACCTTCGGGCAAGATGTTTTTATATGATTTT
325 AGCAAGATGATAAGTTCTTCGGGCCATCCATAAGACCATCAGGCAAGACGTTTTCACATGATTTT
* *
407933 CAAAAAAATGAGAAAACAATTTCTAAAGTTTCTAAATGAAATATGAAAATTGAAATTTTTGAAAA
390 CAAAAAAATGAGAAAACAATTTCCAAAGTTTCTAAATGAAATATAAAAATTGAAATTTTTGAAAA
* *
407998 ATAAGAAAACGATTTCCAAAGTTT-TTACCTAGTAAGCTATTTCTAAAATT-GTA
455 ATAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAAAAATTGGTA
* * *
408051 AGTCTTTCGGGCCATCGGTAAGTCTTTTGAGCATGGTGATTAAATCTTTCGGGTCATCTATAAGT
1 AGTCATTCGGGCCATCAGTAAGTCTTTTGAGCATGGTGATTAAATCTTTCGGGTCATCTATAAGC
** * * **
408116 ATTTTGAGTAAGATGATAAGTCCTTCAGGCCAT-TCATAAGACCTTGGGGCAGGATGTTTTCAC-
66 ATTTCAAGCAAGATGATAAGTCCTTCAGGCCATCT-ATAAAACCTTCAGGCAGGATGTTTTCACA
* * * * *
408179 TTGTTTGTTGAAAAATGAGAAAACAATTTGC-AAAGTTTGTCA-TTGAAATCTGAATATTGAAAT
130 TGGTTT-TCGAAAAATGAGAAAACAATTT-CTAAAGTTTCTCATTTAAAAT-TGAAAATTGAAAT
*
408242 TTTTTAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACATAGTAAGA-TATTCCAAAATTGGTAA
192 ATTTTAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACATAGTAA-ACTATTCCAAAATTGGTAA
* * * * *
408306 GTTCTTTGGGC-CATCAGCAAGTCTTTCGAGCATGTTGATTAAATCATTCTGGTCATCTATAAGC
256 G-TCCTTCGGCTCATCAGCAAGTCTTT-GAGCATGATGATTAAATCATTCGGGTAATCTATAAGC
* *
408370 CTTTCGAGTAAGATGATAAG-TCATTCGGGCCATTCATAAGACCATCAGGC-AGAACGTTTTCAC
319 CTTTCGAGCAAGATGATAAGTTC-TTCGGGCCATCCATAAGACCATCAGGCAAG-ACGTTTTCAC
* * * * * * * *
408433 ATGTTTTTC-GAAAAATGAGAAAACGATTTCCAATGTTTCTCATTGAAATCTAAAAATTGAATTT
382 ATGATTTTCAAAAAAATGAGAAAACAATTTCCAAAGTTTCTAAATGAAATATAAAAATTGAAATT
* * * *
408497 TTTGGAAAGTAGGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAAAAATTGGTA
447 TTTGAAAAATAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAAAAATTGGTA
* * * *
408560 AGTCCTTCGGGCCATCAGTAAGT-TTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTATAAG
1 AGTCATTCGGGCCATCAGTAAGTCTTTT-GAGCATGGTGATTAAATCTTTCGGGTCATCTATAAG
*
408624 CCTTTTCAAG
65 -CATTTCAAG
408634 AATGATGTTT
Statistics
Matches: 500, Mismatches: 69, Indels: 25
0.84 0.12 0.04
Matches are distributed among these distances:
506 12 0.02
507 301 0.60
508 125 0.25
509 57 0.11
510 5 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (509 bp):
AGTCATTCGGGCCATCAGTAAGTCTTTTGAGCATGGTGATTAAATCTTTCGGGTCATCTATAAGC
ATTTCAAGCAAGATGATAAGTCCTTCAGGCCATCTATAAAACCTTCAGGCAGGATGTTTTCACAT
GGTTTTCGAAAAATGAGAAAACAATTTCTAAAGTTTCTCATTTAAAATTGAAAATTGAAATATTT
TAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACATAGTAAACTATTCCAAAATTGGTAAGTCCT
TCGGCTCATCAGCAAGTCTTTGAGCATGATGATTAAATCATTCGGGTAATCTATAAGCCTTTCGA
GCAAGATGATAAGTTCTTCGGGCCATCCATAAGACCATCAGGCAAGACGTTTTCACATGATTTTC
AAAAAAATGAGAAAACAATTTCCAAAGTTTCTAAATGAAATATAAAAATTGAAATTTTTGAAAAA
TAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAAAAATTGGTA
Found at i:408905 original size:15 final size:15
Alignment explanation
Indices: 408885--408918 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
408875 CAGGTTTTAG
*
408885 TATTATTTCAATTAT
1 TATTATTACAATTAT
408900 TATTATTACAATTAT
1 TATTATTACAATTAT
408915 TATT
1 TATT
408919 TTATTCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATTACAATTAT
Found at i:409278 original size:18 final size:16
Alignment explanation
Indices: 409245--409279 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
409235 ATATCATGTG
409245 AGAAAAAAAGAAAAGA
1 AGAAAAAAAGAAAAGA
409261 AGAAAATAAAGTAAAAGA
1 AGAAAA-AAAG-AAAAGA
409279 A
1 A
409280 AGGCCTAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 4 0.24
18 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (16 bp):
AGAAAAAAAGAAAAGA
Found at i:415958 original size:21 final size:20
Alignment explanation
Indices: 415932--415970 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
415922 TAAGGCATTA
415932 AACATCATAAACAAAACAAAT
1 AACATCATAAA-AAAACAAAT
*
415953 AACATCATACAAAAACAA
1 AACATCATAAAAAAACAA
415971 CCATCCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.67, C:0.21, G:0.00, T:0.13
Consensus pattern (20 bp):
AACATCATAAAAAAACAAAT
Found at i:417624 original size:16 final size:15
Alignment explanation
Indices: 417602--417641 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
417592 GTATATGTTC
417602 TATGTGAATAAATGA
1 TATGTGAATAAATGA
*
417617 TCATGTGAAT-AATGC
1 T-ATGTGAATAAATGA
417632 TATGTGAATA
1 TATGTGAATA
417642 CTTGTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 8 0.36
15 6 0.27
16 8 0.36
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (15 bp):
TATGTGAATAAATGA
Done.