Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 29
Found at i:3383316 original size:53 final size:53
Alignment explanation
Indices: 3383245--3383448 Score: 311
Period size: 53 Copynumber: 3.8 Consensus size: 53
3383235 CTAAAAAAAA
* * * *
3383245 GGGTTTGCTCCCTATTGCTTCAGGGAGTAGAACTTGAACAATCTTC-GACCAAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG-CCTAC
*
3383298 GAGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* *
3383351 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGTCTAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* *
3383404 GGGTTCGCTCCCTCTTGTTTCAGGGAGTAGAACTTGAACAATCTT
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTT
3383449 ATGGTGTGAT
Statistics
Matches: 139, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
53 138 0.99
54 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (53 bp):
GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
Found at i:3384052 original size:42 final size:42
Alignment explanation
Indices: 3383872--3384270 Score: 228
Period size: 42 Copynumber: 9.4 Consensus size: 42
3383862 ACATCCTACC
* * * * *
3383872 CGAAGGACTTA-TGGATAACCCGAAAGATTT-ATTATCTTGCT
1 CGAAAGACTTACT-GATGACCCGAAGGATTTCATCATCATGCT
* *** * * *
3383913 CGAAAGACTCAAAAATGACCTGAATGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGACCCGAAGGATTTCATCATCATGCT
* * * * *
3383955 CGAAAGACTTACTTATGGCCTGAATGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGACCCGAAGGATTTCATCATCATGCT
*
3383997 CGAAAGACTTACTGATGACCCGAAGGACTTCATCATCATGCT
1 CGAAAGACTTACTGATGACCCGAAGGATTTCATCATCATGCT
* *
3384039 CGAAAGACTTACTGAT-A---G-A--TTTTCTTCA-CTACT-CTT
1 CGAAAGACTTACTGATGACCCGAAGGATTTCATCATC-A-TGC-T
* * ** * *
3384075 CGGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCT
1 C-G-AAAGACTTACTGATGACCCGAAGGATTTCATCATCATGCT
* * * *
3384119 CGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCA-CTATTCTT
1 CGAAAGACTTACTGAT-G-AC---CCGAAGGATTT-CATCATC-ATGC-T
* * ** * *
3384168 CGGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCT
1 C-G-AAAGACTTACTGATGACCCGAAGGATTTCATCATCATGCT
* *
3384212 CGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCT
1 CGAAAGACTTACTGATGACCCGAAGGATTTCATCATCATGCT
3384254 CGAAAGACTTACTGATG
1 CGAAAGACTTACTGATG
3384271 GGTTTGCTTC
Statistics
Matches: 273, Mismatches: 58, Indels: 53
0.71 0.15 0.14
Matches are distributed among these distances:
34 1 0.00
35 8 0.03
36 3 0.01
37 2 0.01
38 11 0.04
39 1 0.00
41 23 0.08
42 158 0.58
43 3 0.01
44 7 0.03
45 14 0.05
46 11 0.04
47 10 0.04
48 6 0.02
49 4 0.01
50 1 0.00
51 10 0.04
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (42 bp):
CGAAAGACTTACTGATGACCCGAAGGATTTCATCATCATGCT
Found at i:3384143 original size:13 final size:13
Alignment explanation
Indices: 3384125--3384149 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3384115 TGCTCGAAAG
3384125 ACTTACTGATGGC
1 ACTTACTGATGGC
3384138 ACTTACTGATGG
1 ACTTACTGATGG
3384150 ATTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:3384204 original size:93 final size:93
Alignment explanation
Indices: 3384045--3384230 Score: 345
Period size: 93 Copynumber: 2.0 Consensus size: 93
3384035 TGCTCGAAAG
*
3384045 ACTTACTGATAGATTTTCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
1 ACTTACTGATAGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
3384110 CATCATGCTCGAAAGACTTACTGATGGC
66 CATCATGCTCGAAAGACTTACTGATGGC
* *
3384138 ACTTACTGATGGATTTGCTTCACTATTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
1 ACTTACTGATAGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
3384203 CATCATGCTCGAAAGACTTACTGATGGC
66 CATCATGCTCGAAAGACTTACTGATGGC
3384231 CCGAAGGACT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (93 bp):
ACTTACTGATAGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
CATCATGCTCGAAAGACTTACTGATGGC
Found at i:3384262 original size:22 final size:21
Alignment explanation
Indices: 3384201--3384264 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
3384191 GAAGGATTTA
3384201 ATCATCATGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
3384222 A-C-TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
3384242 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
3384264 A
1 A
3384265 CTGATGGGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.09
20 12 0.36
21 3 0.09
22 12 0.36
23 3 0.09
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:3384360 original size:122 final size:122
Alignment explanation
Indices: 3384138--3384363 Score: 380
Period size: 122 Copynumber: 1.9 Consensus size: 122
3384128 TACTGATGGC
* * * *
3384138 ACTTACTGATGGATTTGCTTCACTATTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGATGAAGGCTTACAAATTACCCGAAAGACTTAAT
*
3384203 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAG
66 CATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTCATCATCATGCTCGAAAG
* *
3384260 ACTTACTGATGGGTTTGCTTCACTACTCTTCGATGAAGGCTTACAAATTACCTGAAAGACTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGATGAAGGCTTACAAATTACCCGAAAGACTTAAT
*
3384325 CATCATGCTCGAAAGCCTTACTGATGGCCCAAAGGACTT
66 CATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTT
3384364 AGATTGTTTA
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
122 96 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (122 bp):
ACTTACTGATGGATTTGCTTCACTACTCTTCGATGAAGGCTTACAAATTACCCGAAAGACTTAAT
CATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTCATCATCATGCTCGAAAG
Found at i:3392787 original size:2 final size:2
Alignment explanation
Indices: 3392780--3392817 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3392770 ATAAATTTAA
3392780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3392818 TAAAAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3393184 original size:16 final size:17
Alignment explanation
Indices: 3393163--3393196 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
3393153 TAATATAAAT
3393163 ATTAAACCT-AAACTAA
1 ATTAAACCTAAAACTAA
3393179 ATTAAACCTAAAACTAA
1 ATTAAACCTAAAACTAA
3393196 A
1 A
3393197 CCCCATTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
ATTAAACCTAAAACTAA
Found at i:3395649 original size:15 final size:17
Alignment explanation
Indices: 3395623--3395658 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
3395613 ATTGTGTCAC
3395623 AATATGATAA-TTTAAA
1 AATATGATAATTTTAAA
3395639 AATAT-ATAATTTTAAA
1 AATATGATAATTTTAAA
3395655 AATA
1 AATA
3395659 AAATTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AATATGATAATTTTAAA
Found at i:3397683 original size:18 final size:20
Alignment explanation
Indices: 3397657--3397699 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
3397647 TATACCTCTA
*
3397657 TTTTAAATT-CTAATTT-TT
1 TTTTTAATTGCTAATTTATT
*
3397675 TTTTTAATTGGTAATTTATT
1 TTTTTAATTGCTAATTTATT
3397695 TTTTT
1 TTTTT
3397700 TGATTCTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 6 0.29
20 7 0.33
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTTAATTGCTAATTTATT
Found at i:3398520 original size:155 final size:155
Alignment explanation
Indices: 3398238--3398547 Score: 620
Period size: 155 Copynumber: 2.0 Consensus size: 155
3398228 CTGTGGGTTT
3398238 TAGGTGAAAGGAAGTCGGGTCAGTCCGGGTTTGAGTACAACAGAACCGGTATTAACTGCAAAGAT
1 TAGGTGAAAGGAAGTCGGGTCAGTCCGGGTTTGAGTACAACAGAACCGGTATTAACTGCAAAGAT
3398303 TAGCCTCGTGTTCCTTATCTCTTTCCCTCCATCAGTCCCAACAATTTCTGGATTTCAGTAACAAT
66 TAGCCTCGTGTTCCTTATCTCTTTCCCTCCATCAGTCCCAACAATTTCTGGATTTCAGTAACAAT
3398368 TGTTTGAGAGGGTGTTGAACATTCA
131 TGTTTGAGAGGGTGTTGAACATTCA
3398393 TAGGTGAAAGGAAGTCGGGTCAGTCCGGGTTTGAGTACAACAGAACCGGTATTAACTGCAAAGAT
1 TAGGTGAAAGGAAGTCGGGTCAGTCCGGGTTTGAGTACAACAGAACCGGTATTAACTGCAAAGAT
3398458 TAGCCTCGTGTTCCTTATCTCTTTCCCTCCATCAGTCCCAACAATTTCTGGATTTCAGTAACAAT
66 TAGCCTCGTGTTCCTTATCTCTTTCCCTCCATCAGTCCCAACAATTTCTGGATTTCAGTAACAAT
3398523 TGTTTGAGAGGGTGTTGAACATTCA
131 TGTTTGAGAGGGTGTTGAACATTCA
3398548 ACATGTACTC
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 155 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (155 bp):
TAGGTGAAAGGAAGTCGGGTCAGTCCGGGTTTGAGTACAACAGAACCGGTATTAACTGCAAAGAT
TAGCCTCGTGTTCCTTATCTCTTTCCCTCCATCAGTCCCAACAATTTCTGGATTTCAGTAACAAT
TGTTTGAGAGGGTGTTGAACATTCA
Found at i:3411215 original size:21 final size:20
Alignment explanation
Indices: 3411129--3411286 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
3411119 AAATGACCAA
**
3411129 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
3411148 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
3411168 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
3411188 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
3411209 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3411230 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3411250 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3411271 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3411287 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3411315 original size:20 final size:20
Alignment explanation
Indices: 3411253--3411446 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3411243 CGATTTTCCA
* ** *
3411253 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
3411273 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
3411293 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3411313 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
3411333 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
3411353 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3411373 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
3411393 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
3411413 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
3411434 AAATCGCAACGCG
1 AAATCGCAACGCG
3411447 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3411337 original size:60 final size:60
Alignment explanation
Indices: 3411253--3411446 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3411243 CGATTTTCCA
* ** * *
3411253 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
3411313 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
3411373 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
3411434 AAATCGCAACGCG
1 AAATCGCAACGCG
3411447 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:3411617 original size:22 final size:22
Alignment explanation
Indices: 3411592--3411646 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
3411582 CTCTCTACGG
*
3411592 CGAAGAAATCTGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
3411614 CGAAGATTTCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
3411636 CGGCGAAATCC
1 CGAAGAAATCC
3411647 CTCACAACCA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.38, G:0.16, T:0.22
Consensus pattern (22 bp):
CGAAGAAATCCGTCCCCATCTC
Found at i:3411866 original size:33 final size:33
Alignment explanation
Indices: 3411827--3411897 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
3411817 TTCACTTAGA
* *
3411827 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
3411860 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
3411893 TTTCA
1 TTTCA
3411898 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:3412021 original size:20 final size:20
Alignment explanation
Indices: 3411977--3412086 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
3411967 TGCAGAAGAG
*
3411977 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
3411998 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
3412018 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
3412039 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
3412053 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
3412072 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
3412087 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:3412034 original size:41 final size:38
Alignment explanation
Indices: 3411970--3412086 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
3411960 TTCAATTTGC
* *
3411970 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
3412008 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
3412049 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
3412082 AGAAT
1 AGAAT
3412087 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:3412056 original size:14 final size:14
Alignment explanation
Indices: 3412037--3412093 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3412027 GAGAAATGAA
3412037 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3412051 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3412070 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3412084 AATCGCAACG
1 AATCGCAACG
3412094 CGAACCAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3412069 original size:33 final size:33
Alignment explanation
Indices: 3412029--3412097 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
3412019 CGCAACGAGA
3412029 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3412062 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3412095 GAA
1 GAA
3412098 CCAAATCGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.46, C:0.20, G:0.25, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3414030 original size:93 final size:93
Alignment explanation
Indices: 3413871--3414344 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
3413861 TAGATTGCTT
*
3413871 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3413936 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3413964 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3414029 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
3414057 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3414122 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3414150 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3414215 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3414243 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3414308 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3414336 AGTAAATTT
1 AGTAAATTT
3414345 ATCCATTCAA
Statistics
Matches: 378, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 378 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3414446 original size:18 final size:19
Alignment explanation
Indices: 3414388--3414515 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
3414378 TAGTTTACTT
* *
3414388 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3414408 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3414427 TCGCAACGCG-AATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3414445 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
3414459 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
3414478 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
3414492 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3414511 TCGCA
1 TCGCA
3414516 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 6 0.07
17 2 0.02
18 14 0.16
19 33 0.37
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3414483 original size:33 final size:32
Alignment explanation
Indices: 3414424--3414515 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
3414414 CGCGAAACCA
**
3414424 AAATCGCAACGCG-AATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
3414455 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
3414488 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
3414516 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
31 1 0.02
32 13 0.23
33 42 0.75
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:3414533 original size:19 final size:19
Alignment explanation
Indices: 3414511--3414644 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
3414501 GAAACCAAAA
*
3414511 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3414530 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
3414546 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3414563 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3414579 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
**
3414595 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3414614 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3414634 TCGTGTTGCGA
1 TCGCGTTGCGA
3414645 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
15 3 0.03
16 10 0.11
17 9 0.10
18 8 0.09
19 37 0.39
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3414552 original size:14 final size:14
Alignment explanation
Indices: 3414533--3414589 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3414523 TTTCATTTCG
3414533 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3414547 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3414564 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
3414580 CGTTGCGATT
1 CGTTGCGATT
3414590 TCATTTCGCG
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3414597 original size:32 final size:33
Alignment explanation
Indices: 3414516--3414607 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
3414506 CAAAATCGCA
*
3414516 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
3414549 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3414582 TTGCGA-TTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3414608 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 19 0.34
33 37 0.66
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3414616 original size:51 final size:47
Alignment explanation
Indices: 3414533--3414626 Score: 125
Period size: 51 Copynumber: 1.9 Consensus size: 47
3414523 TTTCATTTCG
3414533 CGTTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTGT
1 CGTTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTGT
** *
3414580 CGTTGCGATTTCATTTCGCGTTGCGATTTTGGTTTCGCGTTGCGATT
1 CGTTGCGA-TTC-TTT--CGTTGCGATTTTCATTTCGCATTGCGATT
3414627 TTAAGTTTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
47 8 0.20
48 3 0.08
49 3 0.08
51 26 0.65
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (47 bp):
CGTTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTGT
Found at i:3416587 original size:14 final size:14
Alignment explanation
Indices: 3416568--3416603 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3416558 ATTGTTTAAT
3416568 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3416582 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3416596 TGATTTGT
1 TGATTTGT
3416604 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3416733 original size:19 final size:19
Alignment explanation
Indices: 3416709--3416808 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
3416699 AAAATTGACT
*
3416709 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3416728 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3416747 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3416761 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3416780 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3416800 ATCGCAATG
1 ATCGCAATG
3416809 GGAGAATCGC
Statistics
Matches: 72, Mismatches: 3, Indels: 11
0.84 0.03 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3416838 original size:53 final size:53
Alignment explanation
Indices: 3416709--3416825 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
3416699 AAAATTGACT
*
3416709 ATCGCAACGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
3416761 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
3416814 ATCGCAATGCGA
1 ATCGCAATGCGA
3416826 TTTTAATTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 28 0.46
53 33 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:3416843 original size:19 final size:19
Alignment explanation
Indices: 3416815--3416982 Score: 177
Period size: 19 Copynumber: 9.6 Consensus size: 19
3416805 AATGGGAGAA
* *
3416815 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
3416834 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
3416850 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3416867 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3416886 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
3416902 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3416919 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3416938 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
3416954 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3416971 TCCGCATTGCGA
1 T-CGCATTGCGA
3416983 AATGTAATGG
Statistics
Matches: 125, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 18 0.14
16 21 0.17
17 18 0.14
18 2 0.02
19 60 0.48
20 6 0.05
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3416858 original size:33 final size:33
Alignment explanation
Indices: 3416821--3416982 Score: 159
Period size: 33 Copynumber: 4.7 Consensus size: 33
3416811 AGAATCGCAA
*
3416821 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
3416854 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
3416892 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
3416925 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
3416958 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
3416983 AATGTAATGG
Statistics
Matches: 104, Mismatches: 13, Indels: 23
0.74 0.09 0.16
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 49 0.47
34 10 0.10
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:3416878 original size:52 final size:52
Alignment explanation
Indices: 3416815--3416982 Score: 309
Period size: 52 Copynumber: 3.2 Consensus size: 52
3416805 AATGGGAGAA
* *
3416815 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
3416867 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
3416919 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
3416971 TCCGCATTGCGA
1 T-CGCATTGCGA
3416983 AATGTAATGG
Statistics
Matches: 113, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 103 0.91
53 10 0.09
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:3417065 original size:19 final size:19
Alignment explanation
Indices: 3417041--3417189 Score: 187
Period size: 19 Copynumber: 8.4 Consensus size: 19
3417031 AAAATTGACT
3417041 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3417060 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3417079 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3417093 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3417112 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3417132 ATCGCAA--CG--A-G--A
1 ATCGCAATGCGAAATGAAA
3417144 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3417163 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3417183 ATCGCAA
1 ATCGCAA
3417190 CGAGAGATCG
Statistics
Matches: 114, Mismatches: 2, Indels: 27
0.80 0.01 0.19
Matches are distributed among these distances:
12 8 0.07
14 13 0.11
15 2 0.02
16 3 0.03
17 4 0.04
18 2 0.02
19 50 0.44
20 32 0.28
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3417101 original size:33 final size:34
Alignment explanation
Indices: 3417059--3417207 Score: 141
Period size: 33 Copynumber: 4.4 Consensus size: 34
3417049 GCGAAATGAA
3417059 AATCGCAATGCGAAATGAAAATCGCAA-CGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAGAG
3417092 AATCGCAATGCGAAATGAAAATCGCAATGCG-GA-
1 AATCGCAATGCGAAATGAAAATCGCAA-GCGAGAG
* * * * *
3417125 AAT-GAAAAT-CGCAACGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGAAAATCGCAA-GCG--A-GAG
3417162 AATCGCAATGCGGAAATGAAAATCGCAA-CGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAAGCGAGAG
3417196 -ATCGCAATGCGA
1 AATCGCAATGCGA
3417208 TTTTCATTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
32 21 0.22
33 43 0.45
34 4 0.04
35 3 0.03
36 2 0.02
37 8 0.08
38 2 0.02
39 13 0.14
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAAGCGAGAG
Found at i:3417165 original size:51 final size:51
Alignment explanation
Indices: 3417041--3417207 Score: 300
Period size: 51 Copynumber: 3.2 Consensus size: 51
3417031 AAAATTGACT
3417041 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAAC--GAGA
3417093 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA
3417144 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA
3417195 GATCGCAATGCGA
1 -ATCGCAATGCGA
3417208 TTTTCATTTC
Statistics
Matches: 113, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
51 55 0.49
52 41 0.36
53 17 0.15
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (51 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA
Found at i:3419538 original size:12 final size:12
Alignment explanation
Indices: 3419521--3419545 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3419511 TCTTCGGGGA
3419521 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3419533 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3419545 C
1 C
3419546 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3419754 original size:24 final size:24
Alignment explanation
Indices: 3419720--3419766 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3419710 CTGAAACATC
3419720 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3419744 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3419767 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:3420477 original size:20 final size:20
Alignment explanation
Indices: 3420449--3420678 Score: 246
Period size: 20 Copynumber: 11.5 Consensus size: 20
3420439 AAATTTCAGT
* * *
3420449 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
3420469 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATTCGC
**
3420489 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
3420509 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
3420529 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
3420549 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
3420569 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
3420589 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
3420609 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
3420629 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
3420649 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
3420669 GTTGCGATTT
1 GTTGCGATTT
3420679 TGGAAAATCG
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 183 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:3420695 original size:21 final size:21
Alignment explanation
Indices: 3420665--3420747 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3420655 ATTTTCATAT
*
3420665 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
3420686 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3420707 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
3420728 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3420748 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3420738 original size:42 final size:43
Alignment explanation
Indices: 3420645--3420743 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3420635 ATTTATGTGT
* *
3420645 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
3420686 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
3420728 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3420744 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:3423501 original size:37 final size:37
Alignment explanation
Indices: 3423425--3423501 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
3423415 TTTTTATATT
*
3423425 TTTAATTTTGTGAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTGAAAAAAATTATATAAATATTATCAA
* *
3423462 TTTAATTTT-TTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTGAAA-AAAATTATATAAATATTAT-CAA
3423499 TTT
1 TTT
3423502 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 17 0.49
37 18 0.51
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTGAAAAAAATTATATAAATATTATCAA
Found at i:3424398 original size:98 final size:97
Alignment explanation
Indices: 3424228--3424418 Score: 265
Period size: 98 Copynumber: 2.0 Consensus size: 97
3424218 AAAAAGTAAT
* * * * *
3424228 TAATTTATATGATTACCATTATAATAAATTAATTCAATGCACAGAAAATTGTAAATAAATAGATT
1 TAATTTATATGATAACCATTATAAAAAATTAATTCAATGCACAAAAAATTATAAATAAATAGACT
* *
3424293 TATAATCGTCAACAATTTATAGAGTAATTGAC
66 TAGAATCGTCAACAATCTATAGAGTAATTGAC
* * * * *
3424325 TAATTTATATGATAACTATTATAAAAAAATTAGTTTAATGCACAAAAAATTATAAATGAATGGAC
1 TAATTTATATGATAACCATTAT-AAAAAATTAATTCAATGCACAAAAAATTATAAATAAATAGAC
3424390 TTAGAATCGTCAACAATCTATAGAGTAAT
65 TTAGAATCGTCAACAATCTATAGAGTAAT
3424419 CGCTTAAATA
Statistics
Matches: 81, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
97 20 0.25
98 61 0.75
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.35
Consensus pattern (97 bp):
TAATTTATATGATAACCATTATAAAAAATTAATTCAATGCACAAAAAATTATAAATAAATAGACT
TAGAATCGTCAACAATCTATAGAGTAATTGAC
Found at i:3424893 original size:30 final size:32
Alignment explanation
Indices: 3424846--3424914 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 32
3424836 AATATATACT
*
3424846 AATTTTTAAAAATTATTTTTGAAAATAGCA-C
1 AATTTTTAAAAATTATTTATGAAAATAGCATC
*
3424877 -ATTTTTCAAAAA-TATTTATGATAATAGCATC
1 AATTTTT-AAAAATTATTTATGAAAATAGCATC
3424908 AATTTTT
1 AATTTTT
3424915 GTTACATAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 21 0.64
31 6 0.18
32 6 0.18
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (32 bp):
AATTTTTAAAAATTATTTATGAAAATAGCATC
Found at i:3427582 original size:20 final size:21
Alignment explanation
Indices: 3427557--3427597 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3427547 TTAATTAATG
3427557 ATAATTG-TTAGTTTTATTAA
1 ATAATTGTTTAGTTTTATTAA
3427577 ATAATTGTTTAGTTTTATTAA
1 ATAATTGTTTAGTTTTATTAA
3427598 TTAAAGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (21 bp):
ATAATTGTTTAGTTTTATTAA
Found at i:3427632 original size:45 final size:42
Alignment explanation
Indices: 3427576--3427668 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 42
3427566 AGTTTTATTA
* **
3427576 AATAATTGTTTAGTTTTATTAATTAAAGATGAATTTTTAATTAAT
1 AATAATCGTTTAGTTTTATTAAAAAAAGATG-ATTTTT--TTAAT
*
3427621 AATAATCGTTTAGTTTTATTAAAAAAATATGATTTTTTTAAT
1 AATAATCGTTTAGTTTTATTAAAAAAAGATGATTTTTTTAAT
3427663 AATAAT
1 AATAAT
3427669 GTATGCTCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 11 0.25
44 6 0.14
45 27 0.61
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (42 bp):
AATAATCGTTTAGTTTTATTAAAAAAAGATGATTTTTTTAAT
Found at i:3428253 original size:2 final size:2
Alignment explanation
Indices: 3428246--3428288 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3428236 CAATATTGAT
3428246 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
3428288 T
1 T
3428289 GATCCACCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3428406 original size:2 final size:2
Alignment explanation
Indices: 3428345--3428393 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3428335 AATCTTCAAT
3428345 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
3428387 TA TA TA T
1 TA TA TA T
3428394 TGTTAGAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3429121 original size:59 final size:58
Alignment explanation
Indices: 3429019--3429181 Score: 213
Period size: 59 Copynumber: 2.8 Consensus size: 58
3429009 ATTACCAAAT
* * *
3429019 GGCACTTCGTGTGC-AGTATGTTAAGTAATTCATACTAAGTGTATGAATTTCAGTATAG
1 GGCACTTCGTGTGCTA-AATGATAAGAAATTCATACTAAGTGTATGAATTTCAGTATAG
* * *
3429077 GGCACTTCGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATAAATTTCTGTATTG
1 GGCACTTCGTGTGCTAA-ATGATAAGAAATTCATACTAAGTGTATGAATTTCAGTATAG
* *
3429136 GGCACCTT-GTGTGCTAAAGGATAAGAAATTCATACTAAGGGTATGA
1 GGCA-CTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGA
3429182 TTTTTCGTAT
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
58 40 0.43
59 50 0.54
60 3 0.03
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (58 bp):
GGCACTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCAGTATAG
Found at i:3429645 original size:32 final size:32
Alignment explanation
Indices: 3429541--3429645 Score: 90
Period size: 32 Copynumber: 3.2 Consensus size: 32
3429531 TGACAGGCAT
3429541 GTGTCATTTATGCCAGTTAGATGAAAGACTAA
1 GTGTCATTTATGCCAGTTAGATGAAAGACTAA
* ** *
3429573 GTGTC-TTTGAGGCCTAACT-G-TGCATATGACATAAA
1 GTGTCATTT-ATGCC-AGTTAGATG-A-AAGAC-T-AA
3429608 TGTGTCATTTATGCCAGTTAGATGAAAGACTAA
1 -GTGTCATTTATGCCAGTTAGATGAAAGACTAA
3429641 GTGTC
1 GTGTC
3429646 TTTGAGACCT
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
31 5 0.09
32 16 0.29
33 8 0.15
34 2 0.04
35 8 0.15
36 11 0.20
37 5 0.09
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32
Consensus pattern (32 bp):
GTGTCATTTATGCCAGTTAGATGAAAGACTAA
Found at i:3429787 original size:68 final size:68
Alignment explanation
Indices: 3429517--3429769 Score: 373
Period size: 68 Copynumber: 3.7 Consensus size: 68
3429507 GATCAAGAGG
***
3429517 CCTAACTGTGCATATGACAGGCATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTG
1 CCTAACTGTGCATATGACAAAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTG
*
3429582 AGG
66 AGA
*
3429585 CCTAACTGTGCATATGACATAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTG
1 CCTAACTGTGCATATGACAAAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTG
3429650 AGA
66 AGA
* *
3429653 CCTAACTGTGCATATGACAAAAATGTGTCATTTATGCCAATTAGATGAAAGACCAAGTGTCTTTG
1 CCTAACTGTGCATATGACAAAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTG
3429718 AGA
66 AGA
* * * * * *
3429721 CCTAATTGTGTATATGATAGAAA-GATGTCAATTATGTCAGTTAGATGAA
1 CCTAACTGTGCATATGACAAAAATG-TGTCATTTATGCCAGTTAGATGAA
3429770 TGGTTAAGTA
Statistics
Matches: 170, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
67 1 0.01
68 169 0.99
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (68 bp):
CCTAACTGTGCATATGACAAAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCTTTG
AGA
Found at i:3429873 original size:80 final size:80
Alignment explanation
Indices: 3429739--3430005 Score: 419
Period size: 80 Copynumber: 3.3 Consensus size: 80
3429729 TGTATATGAT
3429739 AGAAAGATGTCAATTATGTCAGTTAGATGAATGGTTAAGTATCGTTGAGTAAAAGAATAATGGCC
1 AGAAAGATGTCAATTATGTCAGTTAGATGAATGGTTAAGTATCGTTGAGTAAAAGAATAATGGCC
*
3429804 TAACTGTGCATTGGC
66 TAAATGTGCATTGGC
* * *
3429819 TGAAAGGTGTCAATTATG-CTAGTTAGATGAATAGTTAAGTATCGTTGAGTAAAAGAATAATGGC
1 AGAAAGATGTCAATTATGTC-AGTTAGATGAATGGTTAAGTATCGTTGAGTAAAAGAATAATGGC
*
3429883 CTAATTGTGCATTGGC
65 CTAAATGTGCATTGGC
* * * *
3429899 AGAAATATGTCAATTATGTCAGTTAGATGAACGGTTAAGTACCGTTAAGTAAAAGAATAATGGCC
1 AGAAAGATGTCAATTATGTCAGTTAGATGAATGGTTAAGTATCGTTGAGTAAAAGAATAATGGCC
3429964 TAAATGTGCATTGGC
66 TAAATGTGCATTGGC
* *
3429979 AGAAAGGTGTCAATTATGCCAGTTAGA
1 AGAAAGATGTCAATTATGTCAGTTAGA
3430006 CGAACGTTAA
Statistics
Matches: 170, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
79 1 0.01
80 168 0.99
81 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (80 bp):
AGAAAGATGTCAATTATGTCAGTTAGATGAATGGTTAAGTATCGTTGAGTAAAAGAATAATGGCC
TAAATGTGCATTGGC
Found at i:3430011 original size:80 final size:80
Alignment explanation
Indices: 3429739--3430037 Score: 413
Period size: 80 Copynumber: 3.8 Consensus size: 80
3429729 TGTATATGAT
* *
3429739 AGAAAGATGTCAATTATGTCAGTTAGATGAATGGTTAAGTATCGTTGAGTAAAAGAATAATGGCC
1 AGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAGTATCGTTGAGTAAAAGAATAATGGCC
*
3429804 TAACTGTGCATTGGC
66 TAAATGTGCATTGGC
* * * **
3429819 TGAAAGGTGTCAATTATGCTAGTTAGATGAATAGTTAAGTATCGTTGAGTAAAAGAATAATGGCC
1 AGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAGTATCGTTGAGTAAAAGAATAATGGCC
*
3429884 TAATTGTGCATTGGC
66 TAAATGTGCATTGGC
* * * *
3429899 AGAAATATGTCAATTATGTCAGTTAGATGAACGGTTAAGTACCGTTAAGTAAAAGAATAATGGCC
1 AGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAGTATCGTTGAGTAAAAGAATAATGGCC
3429964 TAAATGTGCATTGGC
66 TAAATGTGCATTGGC
* * ** *
3429979 AGAAAGGTGTCAATTATGCCAGTTAGACGAAC-GTTAAACA-CGGTTGAGTAAGAGAATAA
1 AGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAGTATC-GTTGAGTAAAAGAATAA
3430038 AGAAATTTTA
Statistics
Matches: 194, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
78 1 0.01
79 21 0.11
80 172 0.89
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.29
Consensus pattern (80 bp):
AGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAGTATCGTTGAGTAAAAGAATAATGGCC
TAAATGTGCATTGGC
Found at i:3432725 original size:31 final size:31
Alignment explanation
Indices: 3432687--3432747 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3432677 AAGGACCACT
*
3432687 GTCCATATGTTCCGAAGAACATAGGTAACCG
1 GTCCATATGTCCCGAAGAACATAGGTAACCG
* *
3432718 GTCCATATGTCCCGAAGGACATATGTAACC
1 GTCCATATGTCCCGAAGAACATAGGTAACC
3432748 ATCAACTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (31 bp):
GTCCATATGTCCCGAAGAACATAGGTAACCG
Found at i:3434457 original size:64 final size:64
Alignment explanation
Indices: 3434389--3434545 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
3434379 TTGAAGGTGT
** * *
3434389 ATCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGTAATGCATCGATGCATC-CCTATAATAATA-AAACATCGAATGCATATTA-T
3434451 GC
63 GC
* * *
3434453 ATCGATGCATAAGTCATGCATCGATGCATCCCTATAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
* * *
3434517 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
3434546 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
64 71 0.90
65 8 0.10
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
Found at i:3434898 original size:18 final size:18
Alignment explanation
Indices: 3434863--3434898 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3434853 AAAATGGGTA
* *
3434863 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
3434881 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
3434899 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:3436097 original size:22 final size:18
Alignment explanation
Indices: 3436055--3436124 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
3436045 TTAATGAGTA
*
3436055 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
3436073 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
*
3436095 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
3436113 GTCCTACGGGAC
1 GTCCTACGGGAC
3436125 GAATACTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 26 0.58
20 4 0.09
22 15 0.33
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:3439861 original size:18 final size:18
Alignment explanation
Indices: 3439826--3439861 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3439816 AAAATGGGTA
* *
3439826 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
3439844 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
3439862 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:3441060 original size:22 final size:18
Alignment explanation
Indices: 3441018--3441087 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
3441008 TTAAGGAGTA
*
3441018 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
3441036 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
*
3441058 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
3441076 GTCCTACGGGAC
1 GTCCTACGGGAC
3441088 GAATATTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 26 0.58
20 4 0.09
22 15 0.33
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:3443473 original size:16 final size:17
Alignment explanation
Indices: 3443454--3443495 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 17
3443444 TAATTAAGAC
3443454 TAAATATTAAAATCA-T
1 TAAATATTAAAATCATT
3443470 T-AA-ATTAAAATCATT
1 TAAATATTAAAATCATT
3443485 TAAAT-TTAAAA
1 TAAATATTAAAA
3443496 ATAAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 10 0.43
15 4 0.17
16 9 0.39
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATATTAAAATCATT
Found at i:3443478 original size:14 final size:15
Alignment explanation
Indices: 3443459--3443495 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
3443449 AAGACTAAAT
3443459 ATTAAAATCA-TTAA
1 ATTAAAATCATTTAA
3443473 ATTAAAATCATTTAA
1 ATTAAAATCATTTAA
3443488 ATTTAAAA
1 A-TTAAAA
3443496 ATAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.48
15 5 0.24
16 6 0.29
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAAATCATTTAA
Found at i:3443497 original size:23 final size:24
Alignment explanation
Indices: 3443471--3443517 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
3443461 TAAAATCATT
* *
3443471 AAATTAAAATCAT-TTAAATTTAA
1 AAATAAAAATAATATTAAATTTAA
*
3443494 AAATAAAAATAATATTTAATTTAA
1 AAATAAAAATAATATTAAATTTAA
3443518 TTAGTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATAAAAATAATATTAAATTTAA
Found at i:3444729 original size:10 final size:10
Alignment explanation
Indices: 3444710--3444763 Score: 72
Period size: 10 Copynumber: 5.3 Consensus size: 10
3444700 TTAATTTTAC
*
3444710 AAATATAAAA
1 AAATACAAAA
3444720 AAATACAAAA
1 AAATACAAAA
3444730 AAATACAAAAA
1 AAATAC-AAAA
*
3444741 AAATCCAAAA
1 AAATACAAAA
*
3444751 AATTACAAAA
1 AAATACAAAA
3444761 AAA
1 AAA
3444764 ATAGTATGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
10 29 0.76
11 9 0.24
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (10 bp):
AAATACAAAA
Found at i:3444733 original size:20 final size:20
Alignment explanation
Indices: 3444710--3444766 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
3444700 TTAATTTTAC
*
3444710 AAATATAAAAAAATACAAAA
1 AAATAAAAAAAAATACAAAA
*
3444730 AAATACAAAAAAAATCCAAAA
1 AAATA-AAAAAAAATACAAAA
*
3444751 AATTACAAAAAAAATA
1 AAATA-AAAAAAAATA
3444767 GTATGATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 5 0.16
21 27 0.84
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (20 bp):
AAATAAAAAAAAATACAAAA
Found at i:3444742 original size:21 final size:21
Alignment explanation
Indices: 3444716--3444766 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3444706 TTACAAATAT
3444716 AAAAAAATACAAAAAAATACA
1 AAAAAAATACAAAAAAATACA
* *
3444737 AAAAAAATCCAAAAAATTACA
1 AAAAAAATACAAAAAAATACA
3444758 AAAAAAATA
1 AAAAAAATA
3444767 GTATGATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAAAAATACAAAAAAATACA
Found at i:3444797 original size:10 final size:10
Alignment explanation
Indices: 3444784--3444828 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
3444774 TATTTATCTA
3444784 ATTTTAATAT
1 ATTTTAATAT
* *
3444794 ATTTTTATCT
1 ATTTTAATAT
3444804 ATTTT-ATA-
1 ATTTTAATAT
3444812 A-TTTAATAT
1 ATTTTAATAT
3444821 ATTTTAAT
1 ATTTTAAT
3444829 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
7 3 0.10
8 4 0.14
9 3 0.10
10 19 0.66
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:3446721 original size:24 final size:24
Alignment explanation
Indices: 3446694--3446800 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
3446684 AAACGGAGAT
*
3446694 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
3446718 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
3446742 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
3446766 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
3446790 ATCAGAAATCA
1 ATCAGAAATCA
3446801 GATAAATATT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:3446800 original size:48 final size:48
Alignment explanation
Indices: 3446694--3446802 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
3446684 AAACGGAGAT
* * * *
3446694 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
3446742 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
3446790 ATCAGAAATCAGA
1 ATCAGAAATCAGA
3446803 TAAATATTCA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:3447948 original size:18 final size:18
Alignment explanation
Indices: 3447927--3447962 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3447917 ATTCCATCCG
*
3447927 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
3447945 ATCTTATCATTTAATTCA
1 ATCTTATCATTTAATTCA
3447963 GTCCTTTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:3449297 original size:13 final size:13
Alignment explanation
Indices: 3449279--3449339 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 13
3449269 TCCGGTCAAC
3449279 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3449292 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
3449310 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
3449323 GGTAAACGGGTCG
1 GGTCAACGGGTCG
3449336 GGTC
1 GGTC
3449340 GGGTCGTGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 28 0.68
18 13 0.32
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3449316 original size:31 final size:31
Alignment explanation
Indices: 3449279--3449344 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
3449269 TCCGGTCAAC
*
3449279 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
3449310 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
3449341 GGTC
1 GGTC
3449345 GTGACCGGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
Found at i:3449343 original size:18 final size:18
Alignment explanation
Indices: 3449285--3449325 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
3449275 CAACGGTCAA
3449285 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
3449303 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
3449321 CGGGT
1 CGGGT
3449326 AAACGGGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:3451496 original size:24 final size:24
Alignment explanation
Indices: 3451469--3451575 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
3451459 AAACGGAGAT
*
3451469 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
3451493 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
3451517 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
3451541 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
3451565 ATCAGAAATCA
1 ATCAGAAATCA
3451576 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:3451575 original size:48 final size:48
Alignment explanation
Indices: 3451469--3451577 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
3451459 AAACGGAGAT
* * * *
3451469 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
3451517 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
3451565 ATCAGAAATCAGA
1 ATCAGAAATCAGA
3451578 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:3452723 original size:18 final size:18
Alignment explanation
Indices: 3452702--3452737 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3452692 ATTCCATCCG
*
3452702 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
3452720 ATCTTATCATTTAATTCA
1 ATCTTATCATTTAATTCA
3452738 GTCCTTTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:3454069 original size:13 final size:13
Alignment explanation
Indices: 3454051--3454111 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 13
3454041 TCCGGTCAAC
3454051 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3454064 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
3454082 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
3454095 GGTAAACGGGTCG
1 GGTCAACGGGTCG
3454108 GGTC
1 GGTC
3454112 GGGTCGTGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 28 0.68
18 13 0.32
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3454088 original size:31 final size:31
Alignment explanation
Indices: 3454051--3454116 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
3454041 TCCGGTCAAC
*
3454051 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
3454082 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
3454113 GGTC
1 GGTC
3454117 GTGACCGGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
Found at i:3454115 original size:18 final size:18
Alignment explanation
Indices: 3454057--3454097 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
3454047 CAACGGTCAA
3454057 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
3454075 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
3454093 CGGGT
1 CGGGT
3454098 AAACGGGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:3455206 original size:24 final size:24
Alignment explanation
Indices: 3455179--3455285 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
3455169 AAACGGAGAT
*
3455179 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
3455203 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
3455227 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
3455251 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
3455275 ATCAGAAATCA
1 ATCAGAAATCA
3455286 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:3455285 original size:48 final size:48
Alignment explanation
Indices: 3455179--3455287 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
3455169 AAACGGAGAT
* * * *
3455179 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
3455227 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
3455275 ATCAGAAATCAGA
1 ATCAGAAATCAGA
3455288 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:3456435 original size:18 final size:18
Alignment explanation
Indices: 3456414--3456449 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3456404 ATTCCATCCG
*
3456414 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
3456432 ATCTTATCATTTAATTCA
1 ATCTTATCATTTAATTCA
3456450 GTCCTTTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:3457784 original size:13 final size:13
Alignment explanation
Indices: 3457766--3457826 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 13
3457756 TCCGGTCAAC
3457766 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3457779 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
3457797 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
3457810 GGTAAACGGGTCG
1 GGTCAACGGGTCG
3457823 GGTC
1 GGTC
3457827 GGGTCGTGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 28 0.68
18 13 0.32
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3457803 original size:31 final size:31
Alignment explanation
Indices: 3457766--3457831 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
3457756 TCCGGTCAAC
*
3457766 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
3457797 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
3457828 GGTC
1 GGTC
3457832 GTGACCGGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
Found at i:3457830 original size:18 final size:18
Alignment explanation
Indices: 3457772--3457812 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
3457762 CAACGGTCAA
3457772 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
3457790 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
3457808 CGGGT
1 CGGGT
3457813 AAACGGGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:3459228 original size:42 final size:42
Alignment explanation
Indices: 3459182--3459333 Score: 132
Period size: 41 Copynumber: 3.7 Consensus size: 42
3459172 TAAAAATGCT
3459182 GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGCC
1 GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGCC
* *** * *
3459224 GCAATAG-GGTGGTTTATTGCGGCGTTTTT-TAACAAACGCC
1 GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGCC
* * * * * * *
3459264 GCAATAGAGTGGTAAAT-TAGCGGCATTTATACCATAAACGCT
1 GCAATAGAGTTG-ACATATAGCGGCGTTTTTACAACAAACGCC
* *
3459306 GCAATAGA-TTAACATATAGTGGCGTTTT
1 GCAATAGAGTTGACATATAGCGGCGTTTT
3459334 AGCCAAAACG
Statistics
Matches: 82, Mismatches: 24, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
40 20 0.24
41 39 0.48
42 23 0.28
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (42 bp):
GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGCC
Found at i:3459286 original size:82 final size:83
Alignment explanation
Indices: 3459159--3459312 Score: 188
Period size: 82 Copynumber: 1.9 Consensus size: 83
3459149 TGATACTTTA
* * * * * *
3459159 GCGGCGTTTGTTGTAAAAATGCTGCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGCC
1 GCGGCGTTTGTTGTAAAAACGCCGCAATAGAGTGGAAATATAGCGGCATTTATACAACAAACGCC
3459224 GCAATAGGGTGGTTTATT
66 GCAATAGGGTGGTTTATT
* *
3459242 GCGGCGTTT-TT-TAACAAACGCCGCAATAGAGTGGTAAAT-TAGCGGCATTTATACCATAAACG
1 GCGGCGTTTGTTGTAA-AAACGCCGCAATAGAGTGG-AAATATAGCGGCATTTATACAACAAACG
*
3459304 CTGCAATAG
64 CCGCAATAG
3459313 ATTAACATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
81 3 0.05
82 45 0.75
83 12 0.20
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (83 bp):
GCGGCGTTTGTTGTAAAAACGCCGCAATAGAGTGGAAATATAGCGGCATTTATACAACAAACGCC
GCAATAGGGTGGTTTATT
Found at i:3459330 original size:82 final size:85
Alignment explanation
Indices: 3459244--3459415 Score: 230
Period size: 82 Copynumber: 2.1 Consensus size: 85
3459234 GGTTTATTGC
* *
3459244 GGCGTTTTTTA-AC-AAACGCCGCAATAGAGT-GGTAAATTAGCGGCATTTATACCATAAACGCT
1 GGCGTTTTTTAGACAAAACGCCGCAATAGA-TCGGTAAATTAGCAGCATTTATACCATAAACGCC
3459306 GCAATAGATTA-ACATATAGT
65 GCAATAGATTATACATATAGT
* * *
3459326 GGCG--TTTTAGCCAAAACGTCGCAATAGATCGGTAAATTAGCAGCGTTTATACCATAAACGCCG
1 GGCGTTTTTTAGACAAAACGCCGCAATAGATCGGTAAATTAGCAGCATTTATACCATAAACGCCG
*
3459389 TAATAGATTATACATATAGT
66 CAATAGATTATACATATAGT
*
3459409 GGTGTTT
1 GGCGTTT
3459416 ATTCCTAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
80 5 0.06
81 2 0.03
82 57 0.74
83 12 0.16
85 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (85 bp):
GGCGTTTTTTAGACAAAACGCCGCAATAGATCGGTAAATTAGCAGCATTTATACCATAAACGCCG
CAATAGATTATACATATAGT
Found at i:3459394 original size:42 final size:41
Alignment explanation
Indices: 3459199--3459396 Score: 158
Period size: 40 Copynumber: 4.8 Consensus size: 41
3459189 AGTTGACATA
* * * * **
3459199 TAGCGGCGTTTTTACAACAAACGCCGCAATAGGGTGGTTTAT
1 TAGCGGCGTTTATACCATAAACGCCGCAATA-GATGGTAAAT
* *
3459241 T-GCGGCGTTTTTTA--ACAAACGCCGCAATAGAGTGGTAAAT
1 TAGCGGCG-TTTATACCATAAACGCCGCAATAGA-TGGTAAAT
* *
3459281 TAGCGGCATTTATACCATAAACGCTGCAATAGAT--TAACAT
1 TAGCGGCGTTTATACCATAAACGCCGCAATAGATGGTAA-AT
* *
3459321 ATAGTGGCGTTT-TAGCCA-AAACGTCGCAATAGATCGGTAAAT
1 -TAGCGGCGTTTATA-CCATAAACGCCGCAATAGAT-GGTAAAT
* *
3459363 TAGCAGCGTTTATACCATAAACGCCGTAATAGAT
1 TAGCGGCGTTTATACCATAAACGCCGCAATAGAT
3459397 TATACATATA
Statistics
Matches: 128, Mismatches: 15, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
39 4 0.03
40 45 0.35
41 36 0.28
42 40 0.31
43 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (41 bp):
TAGCGGCGTTTATACCATAAACGCCGCAATAGATGGTAAAT
Found at i:3459416 original size:42 final size:42
Alignment explanation
Indices: 3459257--3459436 Score: 138
Period size: 42 Copynumber: 4.3 Consensus size: 42
3459247 GTTTTTTAAC
** * * *
3459257 AAACGCCGCAATAGAGTGGTAAAT-TAGCGGCATTTATACCAT
1 AAACGCCGCAATAGA-TTATACATATAGTGGCGTTTATACCAT
*
3459299 AAACGCTGCAATAGATTA-ACATATAGTGGCGTTT-TAGCCA-
1 AAACGCCGCAATAGATTATACATATAGTGGCGTTTATA-CCAT
* ** * **
3459339 AAACGTCGCAATAGATCGGTAAAT-TAGCAGCGTTTATACCAT
1 AAACGCCGCAATAGAT-TATACATATAGTGGCGTTTATACCAT
* * *
3459381 AAACGCCGTAATAGATTATACATATAGTGGTGTTTATTCC-T
1 AAACGCCGCAATAGATTATACATATAGTGGCGTTTATACCAT
*
3459422 AAAATGCCGCAATAG
1 -AAACGCCGCAATAG
3459437 TGATAATAAA
Statistics
Matches: 106, Mismatches: 24, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
40 19 0.18
41 30 0.28
42 57 0.54
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (42 bp):
AAACGCCGCAATAGATTATACATATAGTGGCGTTTATACCAT
Found at i:3459478 original size:41 final size:41
Alignment explanation
Indices: 3459427--3459581 Score: 197
Period size: 41 Copynumber: 3.8 Consensus size: 41
3459417 TTCCTAAAAT
* *
3459427 GCCGCAATAGTGATAATAAATAGTGGCATTTTTAGACAAAC
1 GCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGACAAAC
* *
3459468 GCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGAAAAAT
1 GCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGACAAAC
* *
3459509 GTCGCAATAGTTTTAATCAATAGTGGCATTGTTTTA-ACAAAC
1 GCCGCAATAGTGTTAATCAATAGTGGCA-T-TTTTAGACAAAC
* * *
3459551 GCCACAATAGTG-TAATTAATAGTGGCGTTTT
1 GCCGCAATAGTGTTAATCAATAGTGGCATTTT
3459582 CTTTGTATAA
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.03
40 1 0.01
41 76 0.77
42 14 0.14
43 5 0.05
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (41 bp):
GCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGACAAAC
Found at i:3459491 original size:83 final size:82
Alignment explanation
Indices: 3459404--3459581 Score: 216
Period size: 82 Copynumber: 2.2 Consensus size: 82
3459394 GATTATACAT
* * *
3459404 ATAGTGGTGTTTATTCCTAAAATGCCGCAATAGTGATAATAAATAGTGGCA-T-TTTTAGACAAA
1 ATAGTGGCGTTT-TTACAAAAATGCCGCAATAGTGATAATAAATAGTGGCATTGTTTTA-ACAAA
*
3459467 CGCCGCAATAGTGTTAATCA
64 CGCCACAATAGTG-TAATCA
* * * ** *
3459487 ATAGTGGCATTTTTAGAAAAATGTCGCAATAGTTTTAATCAATAGTGGCATTGTTTTAACAAACG
1 ATAGTGGCGTTTTTACAAAAATGCCGCAATAGTGATAATAAATAGTGGCATTGTTTTAACAAACG
*
3459552 CCACAATAGTGTAATTA
66 CCACAATAGTGTAATCA
3459569 ATAGTGGCGTTTT
1 ATAGTGGCGTTTT
3459582 CTTTGTATAA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
82 48 0.59
83 28 0.35
84 5 0.06
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (82 bp):
ATAGTGGCGTTTTTACAAAAATGCCGCAATAGTGATAATAAATAGTGGCATTGTTTTAACAAACG
CCACAATAGTGTAATCA
Found at i:3459531 original size:82 final size:82
Alignment explanation
Indices: 3459422--3459581 Score: 225
Period size: 82 Copynumber: 2.0 Consensus size: 82
3459412 GTTTATTCCT
*
3459422 AAAATGCCGCAATAGTGATAATAAATAGTGGCA-T-TTTTAGACAAACGCCGCAATAGTGTTAAT
1 AAAATGCCGCAATAGTGATAATAAATAGTGGCATTGTTTTA-ACAAACGCCACAATAGTG-TAAT
3459485 CAATAGTGGCATTTTTAGA
64 CAATAGTGGCATTTTTAGA
* ** * *
3459504 AAAATGTCGCAATAGTTTTAATCAATAGTGGCATTGTTTTAACAAACGCCACAATAGTGTAATTA
1 AAAATGCCGCAATAGTGATAATAAATAGTGGCATTGTTTTAACAAACGCCACAATAGTGTAATCA
*
3459569 ATAGTGGCGTTTT
66 ATAGTGGCATTTT
3459582 CTTTGTATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
82 46 0.67
83 18 0.26
84 5 0.07
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (82 bp):
AAAATGCCGCAATAGTGATAATAAATAGTGGCATTGTTTTAACAAACGCCACAATAGTGTAATCA
ATAGTGGCATTTTTAGA
Found at i:3461099 original size:42 final size:42
Alignment explanation
Indices: 3461008--3461127 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 42
3460998 AAAATACTCT
* *
3461008 TAATTTAGTGGCGTTTGTT-AC-CAAACGCCGCTAA-AAAGTTG
1 TAATTTAGTGGCGTTT-TTGACATAAACGCCG-TAATAGAGTTG
* *
3461049 TACTTTAGTGGCGTTTTTGACATAAACACCGTAATAGAGTTG
1 TAATTTAGTGGCGTTTTTGACATAAACGCCGTAATAGAGTTG
* *
3461091 TAATTTAGTGGCATTTTTGTA-ATAAACGCCGCAATAG
1 TAATTTAGTGGCGTTTTTG-ACATAAACGCCGTAATAG
3461128 TATGTCCCTT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
40 2 0.03
41 20 0.30
42 44 0.66
43 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (42 bp):
TAATTTAGTGGCGTTTTTGACATAAACGCCGTAATAGAGTTG
Found at i:3464560 original size:21 final size:21
Alignment explanation
Indices: 3464515--3464617 Score: 109
Period size: 21 Copynumber: 4.9 Consensus size: 21
3464505 GAAGCAAGGG
* *
3464515 AAGCAGAGAGAGCAGCAAC-A
1 AAGCAGAGAGAGAAGCAGCGA
**
3464535 GAAGCAGCTAGAGAAGCAGCGA
1 -AAGCAGAGAGAGAAGCAGCGA
*
3464557 AAGCAGAGAAAGAAGCAGCGA
1 AAGCAGAGAGAGAAGCAGCGA
* *
3464578 TAGCATAGAGAGAAGCAGCGA
1 AAGCAGAGAGAGAAGCAGCGA
* *
3464599 CAGCACAGAGAGAAGCAGC
1 AAGCAGAGAGAGAAGCAGC
3464618 ATATCAGTAG
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
21 68 0.99
22 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.33, T:0.03
Consensus pattern (21 bp):
AAGCAGAGAGAGAAGCAGCGA
Found at i:3465090 original size:43 final size:43
Alignment explanation
Indices: 3465037--3465238 Score: 192
Period size: 43 Copynumber: 4.7 Consensus size: 43
3465027 GCAAAAATGT
*
3465037 CGCAAAACATCAATACCTACTGCGGCATTTGTGAGAAAAAAAC
1 CGCAAAACATCAAAACCTACTGCGGCATTTGTGAGAAAAAAAC
* * * *
3465080 CGTAAAACATCAAAACCTACTGCAGCGTTTGTGAGAAAAACAC
1 CGCAAAACATCAAAACCTACTGCGGCATTTGTGAGAAAAAAAC
* **
3465123 CGCAAAACATCAACACCTACTGCGGCATTT-TAGAGAAAAACGC
1 CGCAAAACATCAAAACCTACTGCGGCATTTGT-GAGAAAAAAAC
* * * * * * **
3465166 CGCTAAACATCATAACCTATTGCAGCGTTTGTCTA-AAAAACGC
1 CGCAAAACATCAAAACCTACTGCGGCATTTGT-GAGAAAAAAAC
* * * *
3465209 CGCTAAATATCAACACCTATTGCGGCATTT
1 CGCAAAACATCAAAACCTACTGCGGCATTT
3465239 TTCTGACAAA
Statistics
Matches: 134, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
42 1 0.01
43 131 0.98
44 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.21
Consensus pattern (43 bp):
CGCAAAACATCAAAACCTACTGCGGCATTTGTGAGAAAAAAAC
Found at i:3465174 original size:86 final size:85
Alignment explanation
Indices: 3465037--3465239 Score: 266
Period size: 86 Copynumber: 2.4 Consensus size: 85
3465027 GCAAAAATGT
*
3465037 CGCAAAACATCAATACCTACTGCGGCATTTGTGAGAAAAAAACCGTAAAACATCAAAACCTACTG
1 CGCAAAACATCAACACCTACTGCGGCATTT-TGAGAAAAAAACCGTAAAACATCAAAACCTACTG
3465102 CAGCGTTTGT-GAGAAAAACAC
65 CAGCGTTTGTCGA-AAAAACAC
** * *
3465123 CGCAAAACATCAACACCTACTGCGGCATTTTAGAGAAAAACGCCGCT-AAACATCATAACCTATT
1 CGCAAAACATCAACACCTACTGCGGCATTTT-GAGAAAAAAACCG-TAAAACATCAAAACCTACT
* *
3465187 GCAGCGTTTGTCTAAAAAACGC
64 GCAGCGTTTGTCGAAAAAACAC
* * *
3465209 CGCTAAATATCAACACCTATTGCGGCATTTT
1 CGCAAAACATCAACACCTACTGCGGCATTTT
3465240 TCTGACAAAC
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
85 1 0.01
86 101 0.97
87 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (85 bp):
CGCAAAACATCAACACCTACTGCGGCATTTTGAGAAAAAAACCGTAAAACATCAAAACCTACTGC
AGCGTTTGTCGAAAAAACAC
Found at i:3465250 original size:43 final size:43
Alignment explanation
Indices: 3465041--3465266 Score: 168
Period size: 43 Copynumber: 5.3 Consensus size: 43
3465031 AAATGTCGCA
* * * ** **
3465041 AAACATCAATACCTACTGCGGCATTTGTGAGAAAAAAACCG-T
1 AAACATCAACACCTATTGCGGCATTTTTCTGAAAAACGCCGCT
* * * * * ** * *
3465083 AAAACATCAAAACCTACTGCAGCGTTTGTGAGAAAAACACCGCA
1 -AAACATCAACACCTATTGCGGCATTTTTCTGAAAAACGCCGCT
* ***
3465127 AAACATCAACACCTACTGCGGCATTTTAGAGAAAAACGCCGCT
1 AAACATCAACACCTATTGCGGCATTTTTCTGAAAAACGCCGCT
* * * *
3465170 AAACATCATA-ACCTATTGCAGCGTTTGTCTAAAAAACGCCGCT
1 AAACATCA-ACACCTATTGCGGCATTTTTCTGAAAAACGCCGCT
* * *
3465213 AAATATCAACACCTATTGCGGCATTTTTCTGACAAACGCCACT
1 AAACATCAACACCTATTGCGGCATTTTTCTGAAAAACGCCGCT
*
3465256 AAATATCAACA
1 AAACATCAACA
3465267 AACGCCGCTA
Statistics
Matches: 153, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.01
43 151 0.99
44 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.22
Consensus pattern (43 bp):
AAACATCAACACCTATTGCGGCATTTTTCTGAAAAACGCCGCT
Found at i:3465250 original size:86 final size:86
Alignment explanation
Indices: 3465037--3465264 Score: 246
Period size: 86 Copynumber: 2.7 Consensus size: 86
3465027 GCAAAAATGT
* * ** *
3465037 CGCAAAACATCAATACCTACTGCGGCATTTGT-GAGAAAAAAACC-GTAAAACATCAAAACCTAC
1 CGCAAAACATCAACACCTACTGCGGCATTT-TACAGAAAAACGCCACT-AAACATCAAAACCTAC
3465100 TGCAGCGTTTGTGAGAAAAACAC
64 TGCAGCGTTTGTGAGAAAAACAC
* * * *
3465123 CGCAAAACATCAACACCTACTGCGGCATTTTAGAGAAAAACGCCGCTAAACATCATAACCTATTG
1 CGCAAAACATCAACACCTACTGCGGCATTTTACAGAAAAACGCCACTAAACATCAAAACCTACTG
* *
3465188 CAGCGTTTGTCTA-AAAAACGC
66 CAGCGTTTGT-GAGAAAAACAC
* * * * * * *
3465209 CGCTAAATATCAACACCTATTGCGGCATTTTTCTGACAAACGCCACTAAATATCAA
1 CGCAAAACATCAACACCTACTGCGGCATTTTACAGAAAAACGCCACTAAACATCAA
3465265 CAAACGCCGC
Statistics
Matches: 121, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
85 1 0.01
86 118 0.98
87 2 0.02
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.21
Consensus pattern (86 bp):
CGCAAAACATCAACACCTACTGCGGCATTTTACAGAAAAACGCCACTAAACATCAAAACCTACTG
CAGCGTTTGTGAGAAAAACAC
Found at i:3465269 original size:20 final size:20
Alignment explanation
Indices: 3465244--3465284 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3465234 CATTTTTCTG
3465244 ACAAACGCCACTAAATATCA
1 ACAAACGCCACTAAATATCA
*
3465264 ACAAACGCCGCTAAATATCA
1 ACAAACGCCACTAAATATCA
3465284 A
1 A
3465285 TTCCTATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.29, G:0.07, T:0.15
Consensus pattern (20 bp):
ACAAACGCCACTAAATATCA
Found at i:3467344 original size:52 final size:52
Alignment explanation
Indices: 3467280--3467381 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 52
3467270 AGTCCTATAT
* *
3467280 AAATCAAGCAATAAATTAACTCGTGTTTTAAACATAGTTAATGTTATATACG
1 AAATCAAACAATAAATTAACTCGTGTTTTAAACATAGTTAATATTATATACG
* * *
3467332 AAATCAAACAATAGATTAACTCTTGTTTTAAACATATTTAATATTATATA
1 AAATCAAACAATAAATTAACTCGTGTTTTAAACATAGTTAATATTATATA
3467382 TGAATCGACA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (52 bp):
AAATCAAACAATAAATTAACTCGTGTTTTAAACATAGTTAATATTATATACG
Found at i:3468242 original size:3 final size:3
Alignment explanation
Indices: 3468227--3468256 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3468217 GCATGATAGT
*
3468227 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3468257 CTACTACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3468934 original size:26 final size:28
Alignment explanation
Indices: 3468905--3468969 Score: 64
Period size: 31 Copynumber: 2.3 Consensus size: 28
3468895 GTAGTTTTAT
3468905 AAATTTTTG-AGTTTTCTT-A-TTAAACA
1 AAATTTTTGAAGTTTT-TTAATTTAAACA
*
3468931 AAATATCATTTGAAGTTTTTTAATTTAAATA
1 AAAT-T--TTTGAAGTTTTTTAATTTAAACA
3468962 AAATTTTT
1 AAATTTTT
3468970 AAATTTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
26 4 0.12
27 1 0.03
28 3 0.09
29 6 0.19
30 8 0.25
31 10 0.31
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.51
Consensus pattern (28 bp):
AAATTTTTGAAGTTTTTTAATTTAAACA
Found at i:3471579 original size:11 final size:11
Alignment explanation
Indices: 3471563--3471587 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3471553 TGATATCAAT
3471563 AATTATAAAAA
1 AATTATAAAAA
3471574 AATTATAAAAA
1 AATTATAAAAA
3471585 AAT
1 AAT
3471588 ATCGATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATTATAAAAA
Found at i:3477749 original size:17 final size:18
Alignment explanation
Indices: 3477727--3477766 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3477717 ATTTTAAAGG
* *
3477727 CTATTTGTATTCTTT-CT
1 CTATTTGTAATATTTCCT
3477744 CTATTTGTAATATTTCCT
1 CTATTTGTAATATTTCCT
3477762 CTATT
1 CTATT
3477767 AGTGAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.17, C:0.17, G:0.05, T:0.60
Consensus pattern (18 bp):
CTATTTGTAATATTTCCT
Found at i:3484886 original size:23 final size:24
Alignment explanation
Indices: 3484846--3484891 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
3484836 TACTCTCCCA
*
3484846 AATCCCTAACCCTTCTTTCTCCAG
1 AATCCCTAACCCTCCTTTCTCCAG
3484870 AATCCC-AACCCTCCTTTCTCCA
1 AATCCCTAACCCTCCTTTCTCCA
3484892 TTCCCAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.22, C:0.46, G:0.02, T:0.30
Consensus pattern (24 bp):
AATCCCTAACCCTCCTTTCTCCAG
Found at i:3490036 original size:24 final size:24
Alignment explanation
Indices: 3490003--3490056 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
3489993 CCCAATTTAC
*
3490003 TCTCCCGAATCCCTAACCCTCCTT
1 TCTCCAGAATCCCTAACCCTCCTT
3490027 TCTCCAGAATCCCTAACCCTCCTT
1 TCTCCAGAATCCCTAACCCTCCTT
3490051 TCTCCA
1 TCTCCA
3490057 TTCCCAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.19, C:0.48, G:0.04, T:0.30
Consensus pattern (24 bp):
TCTCCAGAATCCCTAACCCTCCTT
Found at i:3493900 original size:2 final size:2
Alignment explanation
Indices: 3493893--3493923 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3493883 GCTACCCAAC
3493893 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3493924 GGCGTCATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3495163 original size:21 final size:21
Alignment explanation
Indices: 3495139--3495207 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
3495129 AAATCTAATG
3495139 TTAGTGTTTTATAGTTTTGGT
1 TTAGTGTTTTATAGTTTTGGT
*
3495160 TTAG-GATTTTATAGTTTTGATT
1 TTAGTG-TTTTATAGTTTTG-GT
* *
3495182 TTA-TATTTTATATTTTATGGT
1 TTAGTGTTTTATAGTTT-TGGT
3495203 TTAGT
1 TTAGT
3495208 TATTTTTAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
20 1 0.03
21 31 0.79
22 7 0.18
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.62
Consensus pattern (21 bp):
TTAGTGTTTTATAGTTTTGGT
Found at i:3495183 original size:14 final size:15
Alignment explanation
Indices: 3495159--3495204 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
3495149 ATAGTTTTGG
3495159 TTTAGGATTTTATAGT
1 TTTA-GATTTTATAGT
3495175 TTT-GATTTTATA-T
1 TTTAGATTTTATAGT
* *
3495188 TTTATATTTTATGGT
1 TTTAGATTTTATAGT
3495203 TT
1 TT
3495205 AGTTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 4 0.15
14 16 0.62
15 3 0.12
16 3 0.12
ACGTcount: A:0.22, C:0.00, G:0.13, T:0.65
Consensus pattern (15 bp):
TTTAGATTTTATAGT
Found at i:3507420 original size:3 final size:3
Alignment explanation
Indices: 3507412--3507438 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3507402 TAAAATATGC
3507412 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
3507439 GAGTTTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3509652 original size:20 final size:20
Alignment explanation
Indices: 3509624--3509661 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3509614 CAATTTATTC
*
3509624 ATTGGTGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
*
3509644 ATTGATGCATCGGTGCAT
1 ATTGATGCATCGATGCAT
3509662 TCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:3511670 original size:22 final size:21
Alignment explanation
Indices: 3511634--3511675 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3511624 AACAACCTTT
3511634 CTGTTTTTTTATTTCCAATCTG
1 CTGTTTTTTTATTT-CAATCTG
3511656 CTGTTTTTTCT-TTTCAATCT
1 CTGTTTTTT-TATTTCAATCT
3511676 ATTGCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 12 0.63
23 1 0.05
ACGTcount: A:0.12, C:0.19, G:0.07, T:0.62
Consensus pattern (21 bp):
CTGTTTTTTTATTTCAATCTG
Found at i:3514332 original size:25 final size:25
Alignment explanation
Indices: 3514286--3514333 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
3514276 TTTCTCGAGC
* * **
3514286 TCGAGTTGAGCTTTAATTTTTTATT
1 TCGAGTTGAACTTGAAAATTTTATT
3514311 TCGAGTTGAACTTGAAAATTTTA
1 TCGAGTTGAACTTGAAAATTTTA
3514334 AGCTCGTAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (25 bp):
TCGAGTTGAACTTGAAAATTTTATT
Found at i:3515721 original size:20 final size:19
Alignment explanation
Indices: 3515693--3515730 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3515683 ATTCAAAATT
*
3515693 AAAAAAGAAAACTAAAGAA
1 AAAAAAGAAAACAAAAGAA
3515712 AAAAAGAGAAAACAAAAGA
1 AAAAA-AGAAAACAAAAGA
3515731 CATAGCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (19 bp):
AAAAAAGAAAACAAAAGAA
Found at i:3522386 original size:29 final size:32
Alignment explanation
Indices: 3522341--3522426 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
3522331 ATAATTTTTA
*
3522341 TAATTTTCAAATATTTATAAAATTA-TA-AAAT
1 TAATTTTTAAA-ATTTATAAAATTATTATAAAT
*
3522372 T-ATTTTTAAAATTTATTAAATTATTATAAAT
1 TAATTTTTAAAATTTATAAAATTATTATAAAT
*
3522403 TAATTATTAAAATTT-TAATAATTA
1 TAATTTTTAAAATTTATAA-AATTA
3522427 AAATAATCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 12 0.26
30 10 0.21
31 8 0.17
32 17 0.36
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (32 bp):
TAATTTTTAAAATTTATAAAATTATTATAAAT
Found at i:3522401 original size:20 final size:20
Alignment explanation
Indices: 3522352--3522401 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3522342 AATTTTCAAA
3522352 TATTTATAAAATTATAAAAT
1 TATTTATAAAATTATAAAAT
* *
3522372 TATTTTTAAAATTTATTAAAT
1 TATTTATAAAA-TTATAAAAT
3522393 TA-TTATAAA
1 TATTTATAAA
3522402 TTAATTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTTATAAAATTATAAAAT
Found at i:3524612 original size:2 final size:2
Alignment explanation
Indices: 3524605--3524639 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3524595 CTGCCCCGAT
3524605 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3524640 TTTTTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3524674 original size:34 final size:34
Alignment explanation
Indices: 3524625--3524709 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
3524615 TATATATATA
*
3524625 TATATATATATATATTTTTTATTTTTTATATTAAT
1 TATATATATA-ATATTTTATATTTTTTATATTAAT
3524660 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
3524694 TATATATA-AATATTTT
1 TATATATATAATATTTT
3524710 CGGGTTCGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 8 0.16
34 31 0.63
35 10 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:3524697 original size:43 final size:43
Alignment explanation
Indices: 3524603--3524698 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 43
3524593 CCCTGCCCCG
3524603 ATTATATATATATATATATATATATATATATATATATTTTTTATTT
1 ATTATAT-TA-AT-TATATATATATATATATATATATTTTTTATTT
* *
3524649 TTTATATTAATTATATATATA-ATAT-TTTATATTTTTTATATT
1 ATTATATTAATTATATATATATATATATATATATTTTTTAT-TT
3524691 AATTATAT
1 -ATTATAT
3524699 ATAAATATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
41 13 0.29
42 6 0.13
43 16 0.36
44 2 0.04
45 2 0.04
46 6 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (43 bp):
ATTATATTAATTATATATATATATATATATATATTTTTTATTT
Found at i:3524732 original size:20 final size:20
Alignment explanation
Indices: 3524702--3524739 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3524692 ATTATATATA
3524702 AATATTTTCGGGTTCGGGTAT
1 AATATTTTCGGG-TCGGGTAT
3524723 AATA-TTTCGGGTCGGGT
1 AATATTTTCGGGTCGGGT
3524740 TCGGGGACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.18, C:0.11, G:0.32, T:0.39
Consensus pattern (20 bp):
AATATTTTCGGGTCGGGTAT
Done.