Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 26
Found at i:3382195 original size:53 final size:53
Alignment explanation
Indices: 3382077--3382368 Score: 295
Period size: 53 Copynumber: 5.4 Consensus size: 53
3382067 ATTATGTTTG
3382077 ATTTTCAGGGGTTTCTTGATGATTATTTCAAATGAATTTTTG-AAGAAGCTAAGCCTAA
1 ATTTT-AGGGGTTTCTTGATG--T-TTTCAAATGAA--TTTGAAAGAAGCTAAGCCTAA
* *
3382135 TTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCATAA
1 ATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTAA
* * * **
3382188 ATTTTAGGGATTTCTTTATGTTTTCAAATGAGTTTGAAAGAAGCTAAG-CTTG
1 ATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTAA
* * *
3382240 ATTTTCAAGGGTTTCTTGATGTTTTCAAATGAATTTGAAAAAAAACTAAGCCTAA
1 ATTTT-AGGGGTTTCTTGATGTTTTCAAATGAATTTG-AAAGAAGCTAAGCCTAA
* * * * * *
3382295 TTTTTTGGGTTTTATTGATGTTTTCAAATGAAGTTTTTAAA-ATA-TTAAGCCTAA
1 ATTTTAGGGGTTTCTTGATGTTTTCAAATGAA--TTTGAAAGA-AGCTAAGCCTAA
* *
3382349 TTTTTAGGAGTTTCTTGATG
1 ATTTTAGGGGTTTCTTGATG
3382369 ATATCTGTAA
Statistics
Matches: 199, Mismatches: 28, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
52 10 0.05
53 86 0.43
54 70 0.35
55 11 0.06
56 3 0.02
57 15 0.08
58 4 0.02
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.42
Consensus pattern (53 bp):
ATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTAA
Found at i:3382759 original size:194 final size:197
Alignment explanation
Indices: 3382403--3382827 Score: 544
Period size: 194 Copynumber: 2.2 Consensus size: 197
3382393 GAATGATGCT
** *
3382403 TAAATCCTTCGGGTCTTCTATAAGTCTTTCGAGC-AGAATGATAAGTCCTTCGGGCCATCCATAA
1 TAAATCCTTCGGACCATCTATAAGTCTTTCGAGCAAGAATGATAAGTCCTTCGGGCCATCCATAA
* * *
3382467 GACCTTCGAACAGTTTGTTTTCACATGATTTTCAAAAAATGAGAAAGTGATTTCCAAATTTTCTC
66 GACCTTCGAACAGTATGTTTTCACAAGATTTTCAAAAAATGAGAAAGCGATTTCCAAATTTTCTC
*
3382532 ATTTAAATCTTTTCTAAAAATTGATTTTTGAAAA-TAAG-AAACAATTTCCAAACTTTCTTACTT
131 ATTTAAATCTTTTCTAAAAATTGATTTTTGAAAAGTAAGAAAACAATTTCCAAACTTTCTTACGT
*
3382595 AG
196 AC
* * * * *
3382597 TAAGTCCTTTGGACCATCTATAAGTCTTTCGAGCAAG-ATGATAATTCCTTTGGGCCATCTATAA
1 TAAATCCTTCGGACCATCTATAAGTCTTTCGAGCAAGAATGATAAGTCCTTCGGGCCATCCATAA
* ** *
3382661 GACCTTC-AGGCA-TGATGTTTTCACAAGATTTTTGAAAAATGAGAAAGCGATTT-CGAATGTTT
66 GACCTTCGA-ACAGT-ATGTTTTCACAAGATTTTCAAAAAATGAGAAAGCGATTTCCAAAT-TTT
* * *
3382723 CTCATTTAAATCTTTTTTAAAAATT-TTTTCTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTT
128 CTCATTTAAATCTTTTCTAAAAATTGATTT-TTGAAAAGTAAGAAAACAATTTCCAAACTTTCTT
3382787 ACGTAC
192 ACGTAC
* *
3382793 TAAATCCTTCGGGCCATC-AGTAAGTCTTTCAAGCA
1 TAAATCCTTCGGACCATCTA-TAAGTCTTTCGAGCA
3382828 TAATGCTTAA
Statistics
Matches: 199, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
193 9 0.05
194 130 0.65
195 7 0.04
196 53 0.27
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (197 bp):
TAAATCCTTCGGACCATCTATAAGTCTTTCGAGCAAGAATGATAAGTCCTTCGGGCCATCCATAA
GACCTTCGAACAGTATGTTTTCACAAGATTTTCAAAAAATGAGAAAGCGATTTCCAAATTTTCTC
ATTTAAATCTTTTCTAAAAATTGATTTTTGAAAAGTAAGAAAACAATTTCCAAACTTTCTTACGT
AC
Found at i:3383075 original size:242 final size:238
Alignment explanation
Indices: 3382615--3383089 Score: 691
Period size: 238 Copynumber: 2.0 Consensus size: 238
3382605 TTGGACCATC
* * * *
3382615 TATAAGTCTTTCGAGCAAGATGATAATTCCTTTGGGCCATCTATAAGACCTTCAGGCATGATGTT
1 TATAAGTCTTTCGAGCAAGATGATAAGTCCTCTGGGCCATCCATAAGACCTTCAGGCAGGATGTT
* ** * *
3382680 TTCACAAGATTTTTGAAAAATGAGAAAGCGATTTCGAATGTTTCTCATTTAAATCTTTTTTAAAA
66 ATCACAAGATTTTCAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTTTAAAA
*
3382745 ATTTTTTCTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACGTACTAAATCCTTCGGGCCAT
131 ATTTTTTCTTAAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACGTACTAAATCCTTCGGGCCAT
**
3382810 CAGTAAGTCTTTCAAGCATAATGCTTAAATCCTTCGGGTCATT
196 CAGTAAGTCTTTCAAGCATAATGCCCAAATCCTTCGGGTCATT
* **
3382853 TATAAGTCTTTGGAGCAAGATGATAAGTCCTCTGGGCCATCCATTAA-ACCTTTGGGCAGGATGT
1 TATAAGTCTTTCGAGCAAGATGATAAGTCCTCTGGGCCATCCA-TAAGACCTTCAGGCAGGATGT
*
3382917 TATCACATGATTTTCAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTTTGAA
65 TATCACAAGATTTTCAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTTT-AA
* * * * *
3382982 AATTGTTTTTTTCTTAAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGG
129 AA---ATTTTTTCTTAAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACGTACTAAATCCTTCGG
**
3383047 GCCATCAGTAAGTCTTTTGAGCATAATGCCCAAATCCTTCGGG
191 GCCATCAGTAAGTCTTTCAAGCATAATGCCCAAATCCTTCGGG
3383090 CATGATGAAA
Statistics
Matches: 209, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
238 109 0.52
239 7 0.03
242 93 0.44
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (238 bp):
TATAAGTCTTTCGAGCAAGATGATAAGTCCTCTGGGCCATCCATAAGACCTTCAGGCAGGATGTT
ATCACAAGATTTTCAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTTTAAAA
ATTTTTTCTTAAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACGTACTAAATCCTTCGGGCCAT
CAGTAAGTCTTTCAAGCATAATGCCCAAATCCTTCGGGTCATT
Found at i:3385305 original size:14 final size:14
Alignment explanation
Indices: 3385286--3385321 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3385276 TTTTTATTTA
*
3385286 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
3385300 TTTAATTTCATTAC
1 TTTAATTTCAGTAC
3385314 TTTAATTT
1 TTTAATTT
3385322 TCTATCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:3388918 original size:22 final size:22
Alignment explanation
Indices: 3388890--3388934 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3388880 TTTATTATGT
*
3388890 ACCTACTTTGAAAAGGAATATC
1 ACCTACTTTGAAAAGCAATATC
3388912 ACCTACTTTGAAAAGCAATATC
1 ACCTACTTTGAAAAGCAATATC
3388934 A
1 A
3388935 TCAGTCTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (22 bp):
ACCTACTTTGAAAAGCAATATC
Found at i:3390369 original size:36 final size:37
Alignment explanation
Indices: 3390320--3390403 Score: 127
Period size: 36 Copynumber: 2.3 Consensus size: 37
3390310 ATCGGGCCAG
3390320 ATAT-TTATATTTAAATTAAATATATAAATATTATAT
1 ATATATTATATTTAAATTAAATATATAAATATTATAT
* *
3390356 ATATATTA-ATTTAAATTAAATTTATTAATATTATAT
1 ATATATTATATTTAAATTAAATATATAAATATTATAT
3390392 ATATATATATAT
1 ATATAT-TATAT
3390404 AATAATTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 36 0.84
37 5 0.12
38 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
ATATATTATATTTAAATTAAATATATAAATATTATAT
Found at i:3390521 original size:6 final size:6
Alignment explanation
Indices: 3390506--3390536 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3390496 AAACGGTTTT
*
3390506 TCCCCA TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG T
3390537 TTATCATCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.65, G:0.13, T:0.19
Consensus pattern (6 bp):
TCCCCG
Found at i:3392139 original size:21 final size:22
Alignment explanation
Indices: 3392113--3392155 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3392103 CAAAGCAATT
*
3392113 TTATTATAT-AATAAATTGCAG
1 TTATTATATAAAAAAATTGCAG
3392134 TTATTATATAAAAAAATTGCAG
1 TTATTATATAAAAAAATTGCAG
3392156 CCACGTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (22 bp):
TTATTATATAAAAAAATTGCAG
Found at i:3394555 original size:2 final size:2
Alignment explanation
Indices: 3394532--3394591 Score: 77
Period size: 2 Copynumber: 30.5 Consensus size: 2
3394522 AACCTATTCG
* * *
3394532 AT AT AA AT AA AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3394574 AT A- AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT A
3394592 AGTTAAACAC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3396483 original size:3 final size:3
Alignment explanation
Indices: 3396469--3396515 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
3396459 AATATTGTAA
* * *
3396469 AAT AAT ATT AAT AAT AAT AAT AAT CAT ACT -AT AAT ATAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
3396514 AA
1 AA
3396516 ATATAATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 1 0.03
3 32 0.89
4 3 0.08
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:3396525 original size:24 final size:23
Alignment explanation
Indices: 3396466--3396525 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
3396456 GCAAATATTG
3396466 TAAA-ATAATATTAATAATAATAA
1 TAAATATAATA-TAATAATAATAA
*
3396489 T-AATCATACTATAATATATAATAA
1 TAAAT-ATAATATAATA-ATAATAA
3396513 TAAATATAATATA
1 TAAATATAATATA
3396526 CATTTTAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 2 0.06
23 6 0.19
24 20 0.65
25 3 0.10
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAATATAATATAATAATAATAA
Found at i:3396860 original size:90 final size:90
Alignment explanation
Indices: 3396726--3397199 Score: 768
Period size: 90 Copynumber: 5.3 Consensus size: 90
3396716 ATGGTTGCCT
* * *
3396726 GAAGGACTTTAAAAATCAAGAAACCCCTGAAGGTTTAGTTTCTTAAATCTCATTTGAAAACATCC
1 GAAGGAC-TTAAAAATCAAGAAACCCCTGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCC
3396791 TGCACTGAAGGTCTTACAGATGGCCC
65 TGCACTGAAGGTCTTACAGATGGCCC
* *
3396817 GAAGGACTTAAAAATCAAGAAACCCCTGAAGGCTCGGTTTCTTAGATCTCTTTTGAAAACATCCT
1 GAAGGACTTAAAAATCAAGAAACCCCTGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCCT
*
3396882 GCACTGAAGGTCTTACAGATGGTCC
66 GCACTGAAGGTCTTACAGATGGCCC
* *
3396907 GAAAGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCCT
1 GAAGGACTTAAAAATCAAGAAACCCCTGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCCT
**
3396972 GCACTGAAGGTCTTACAGATACCCC
66 GCACTGAAGGTCTTACAGATGGCCC
* * *
3396997 GAATGACTTAAAAATCAAGAAACCCCTGAAGGCTCAGTTTCTTAGATCTCATTTGAAAATATCAT
1 GAAGGACTTAAAAATCAAGAAACCCCTGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCCT
*
3397062 GCACTGAAGGTCTTACGGATGGCCC
66 GCACTGAAGGTCTTACAGATGGCCC
*
3397087 GAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCCT
1 GAAGGACTTAAAAATCAAGAAACCCCTGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCCT
** *
3397152 GCACTGAAGGTCTTATGGATGACCC
66 GCACTGAAGGTCTTACAGATGGCCC
*
3397177 GAAGAACTTAAAAATCAAGAAAC
1 GAAGGACTTAAAAATCAAGAAAC
3397200 TCTTGAAAAT
Statistics
Matches: 356, Mismatches: 27, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
90 349 0.98
91 7 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (90 bp):
GAAGGACTTAAAAATCAAGAAACCCCTGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCCT
GCACTGAAGGTCTTACAGATGGCCC
Found at i:3397348 original size:43 final size:43
Alignment explanation
Indices: 3397287--3397471 Score: 271
Period size: 43 Copynumber: 4.3 Consensus size: 43
3397277 AAATTTGTCT
* *
3397287 TCAAGGAACCTCTACATATCACGATGGTCCCTCAAGCTTTTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
** * *
3397330 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAACTTGTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
* *
3397373 TCAAGGAACACCTACATATCACGATGGTCCCTCAAGCTTTTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
** *
3397416 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTTTCT
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
3397459 TCAAGAAACCCCT
1 TCAAGAAACCCCT
3397472 GAAAATCAGG
Statistics
Matches: 125, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 125 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (43 bp):
TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
Found at i:3397420 original size:86 final size:86
Alignment explanation
Indices: 3397275--3397468 Score: 318
Period size: 86 Copynumber: 2.3 Consensus size: 86
3397265 CAAGTGTTCA
* *
3397275 TCAAATTTGTCTTCAAGGAACCTCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACC
1 TCAAACTTGTCATCAAGGAACCTCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACC
3397340 CCTACATATCACGATGGTTTC
66 CCTACATATCACGATGGTTTC
3397361 TCAAACTTGTCATCAAGGAACAC-CTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAAC
1 TCAAACTTGTCATCAAGGAAC-CTCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAAC
3397425 CCCTACATATCACGATGGTTTC
65 CCCTACATATCACGATGGTTTC
* * * *
3397447 TCAAGCTTTTCTTCAAGAAACC
1 TCAAACTTGTCATCAAGGAACC
3397469 CCTGAAAATC
Statistics
Matches: 101, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
85 1 0.01
86 99 0.98
87 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.29
Consensus pattern (86 bp):
TCAAACTTGTCATCAAGGAACCTCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACC
CCTACATATCACGATGGTTTC
Found at i:3397651 original size:36 final size:36
Alignment explanation
Indices: 3397521--3397640 Score: 159
Period size: 36 Copynumber: 3.3 Consensus size: 36
3397511 CGAAACTATC
* * *
3397521 TCAAGCGAGACTGTCTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAAACTGTCTCAAGTGAGACAAAATTTGTT
* * *
3397557 TCAAGGGAAACCGTCTCAAGAGAGATAAAATTTGTT
1 TCAAGGGAAACTGTCTCAAGTGAGACAAAATTTGTT
* * *
3397593 TCGAGAGAAACTGTCTCAAGTGAGACAGAATTTGTT
1 TCAAGGGAAACTGTCTCAAGTGAGACAAAATTTGTT
3397629 TCAAGGGAAACT
1 TCAAGGGAAACT
3397641 ATCTTGAGTG
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (36 bp):
TCAAGGGAAACTGTCTCAAGTGAGACAAAATTTGTT
Found at i:3397788 original size:76 final size:74
Alignment explanation
Indices: 3397600--3397790 Score: 204
Period size: 76 Copynumber: 2.5 Consensus size: 74
3397590 GTTTCGAGAG
* ** * *
3397600 AAACTGTCTCAAGTGAGACAGAATTTGTTTCAAGGGAAACTATCTTGAGTGAAATAAAATGTCTT
1 AAACAGTCTCAAGTGAGAC-GAATTTGTTTCAAGAAAAACAATCTTGAGTCAAATAAAATGTCTT
* *
3397665 GTTTTAAATA
65 CTTTCAAATA
* * * * ** *
3397675 AAACATGTCTCCAGCGAGACAAATCTTTTTTTGAGAAAAACAATCTTGAGTCAAATGAAATGTCT
1 AAACA-GTCTCAAGTGAGACGAAT-TTGTTTCAAGAAAAACAATCTTGAGTCAAATAAAATGTCT
*
3397740 TCTTTCAAGTA
64 TCTTTCAAATA
3397751 AAACAGTCTCAAGTGAGACGAATTTGTTTCAA-AAGAAACA
1 AAACAGTCTCAAGTGAGACGAATTTGTTTCAAGAA-AAACA
3397791 TACTCAAAAA
Statistics
Matches: 92, Mismatches: 21, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
73 2 0.02
74 11 0.12
75 22 0.24
76 57 0.62
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (74 bp):
AAACAGTCTCAAGTGAGACGAATTTGTTTCAAGAAAAACAATCTTGAGTCAAATAAAATGTCTTC
TTTCAAATA
Found at i:3397987 original size:34 final size:34
Alignment explanation
Indices: 3397943--3398097 Score: 222
Period size: 34 Copynumber: 4.6 Consensus size: 34
3397933 TCTCAGAGAA
* *
3397943 AAATTATCTCAAGCGAGACGAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACCAAATTTGTTTTGAG
3397977 AAATTGTCTCAAGCGAGACCAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACCAAATTTGTTTTGAG
*
3398011 AAATTGTCTCAAGCGAGACCAAATTTTTTTTGAG
1 AAATTGTCTCAAGCGAGACCAAATTTGTTTTGAG
* * *
3398045 AAATTGTCTCAA-CTAAGACAAAATTTATTTTGAG
1 AAATTGTCTCAAGC-GAGACCAAATTTGTTTTGAG
* *
3398079 AAATTGTCTCGAGTGAGAC
1 AAATTGTCTCAAGCGAGAC
3398098 AAAAAAAATT
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
33 1 0.01
34 109 0.99
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (34 bp):
AAATTGTCTCAAGCGAGACCAAATTTGTTTTGAG
Found at i:3398114 original size:68 final size:68
Alignment explanation
Indices: 3397974--3398115 Score: 160
Period size: 68 Copynumber: 2.1 Consensus size: 68
3397964 AATTTGTTTT
* * * * ****
3397974 GAGAAATTGTCTCAAGCGAGACCAAATTTGTTTTGAGAAATTGTCTCAAGCGAGACCAAATTTTT
1 GAGAAATTGTCTCAAGCAAGACAAAATTTATTTTGAGAAATTGTCTCAAGCGAGACAAAAAAAAT
**
3398039 TTT
66 TAA
* *
3398042 GAGAAATTGTCTCAA-CTAAGACAAAATTTATTTTGAGAAATTGTCTCGAGTGAGACAAAAAAAA
1 GAGAAATTGTCTCAAGC-AAGACAAAATTTATTTTGAGAAATTGTCTCAAGCGAGACAAAAAAAA
3398106 TTAA
65 TTAA
3398110 GAGAAA
1 GAGAAA
3398116 CAACATCAGA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
67 1 0.02
68 60 0.98
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (68 bp):
GAGAAATTGTCTCAAGCAAGACAAAATTTATTTTGAGAAATTGTCTCAAGCGAGACAAAAAAAAT
TAA
Found at i:3398293 original size:32 final size:32
Alignment explanation
Indices: 3398222--3398401 Score: 261
Period size: 32 Copynumber: 5.6 Consensus size: 32
3398212 GTATTCAATA
3398222 TTGAATCTCCAAAGATGCCCCAACATTTTGATG
1 TTGAATCTCCAAAGATGCCCCAACA-TTTGATG
* *
3398255 TTGAATCTCCAAAAATGCCCCAACATTTAATG
1 TTGAATCTCCAAAGATGCCCCAACATTTGATG
* * * *
3398287 TTGAATCTCCAAAGATACCCCAATATTCGATA
1 TTGAATCTCCAAAGATGCCCCAACATTTGATG
* *
3398319 TTGAATCTCCAAAGATGGCCCAACATTTTAATG
1 TTGAATCTCCAAAGATGCCCCAACA-TTTGATG
*
3398352 TTGAATCTCCAAAGATGCCTCAACATTTGATG
1 TTGAATCTCCAAAGATGCCCCAACATTTGATG
3398384 TTGAATCTCCAAAGATGC
1 TTGAATCTCCAAAGATGC
3398402 ATGTTGAATC
Statistics
Matches: 129, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
32 78 0.60
33 51 0.40
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.29
Consensus pattern (32 bp):
TTGAATCTCCAAAGATGCCCCAACATTTGATG
Found at i:3398308 original size:65 final size:65
Alignment explanation
Indices: 3398222--3398401 Score: 281
Period size: 65 Copynumber: 2.8 Consensus size: 65
3398212 GTATTCAATA
*
3398222 TTGAATCTCCAAAGATGCCCCAACATTTTGATGTTGAATCTCCAAAAATGCCCCAACA-TTTAAT
1 TTGAATCTCCAAAGATGCCCCAACA-TTTGATGTTGAATCTCCAAAGATGCCCCAACATTTTAAT
3398286 G
65 G
* * * * *
3398287 TTGAATCTCCAAAGATACCCCAATATTCGATATTGAATCTCCAAAGATGGCCCAACATTTTAATG
1 TTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCCCCAACATTTTAATG
*
3398352 TTGAATCTCCAAAGATGCCTCAACATTTGATGTTGAATCTCCAAAGATGC
1 TTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAGATGC
3398402 ATGTTGAATC
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
64 28 0.27
65 74 0.73
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.29
Consensus pattern (65 bp):
TTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCCCCAACATTTTAATG
Found at i:3398379 original size:97 final size:97
Alignment explanation
Indices: 3398213--3398399 Score: 320
Period size: 97 Copynumber: 1.9 Consensus size: 97
3398203 AATGCCACAG
*
3398213 TATTCAATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTTGAATCTCCAAAAATGCCCCAA
1 TATTCAATATTGAATCTCCAAAGATGCCCCAACATTTTAATGTTGAATCTCCAAAAATGCCCCAA
3398278 CATTTAATGTTGAATCTCCAAAGATACCCCAA
66 CATTTAATGTTGAATCTCCAAAGATACCCCAA
* * * *
3398310 TATTCGATATTGAATCTCCAAAGATGGCCCAACATTTTAATGTTGAATCTCCAAAGATGCCTCAA
1 TATTCAATATTGAATCTCCAAAGATGCCCCAACATTTTAATGTTGAATCTCCAAAAATGCCCCAA
*
3398375 CATTTGATGTTGAATCTCCAAAGAT
66 CATTTAATGTTGAATCTCCAAAGAT
3398400 GCATGTTGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 84 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.30
Consensus pattern (97 bp):
TATTCAATATTGAATCTCCAAAGATGCCCCAACATTTTAATGTTGAATCTCCAAAAATGCCCCAA
CATTTAATGTTGAATCTCCAAAGATACCCCAA
Found at i:3398407 original size:21 final size:21
Alignment explanation
Indices: 3398381--3398422 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3398371 TCAACATTTG
3398381 ATGTTGAATCTCCAAAGATGC
1 ATGTTGAATCTCCAAAGATGC
*
3398402 ATGTTGAATCTTCAAAGATGC
1 ATGTTGAATCTCCAAAGATGC
3398423 CCTCTATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (21 bp):
ATGTTGAATCTCCAAAGATGC
Found at i:3398607 original size:25 final size:24
Alignment explanation
Indices: 3398543--3398607 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
3398533 TTTTTTATTT
3398543 TCAAAAGTTTTG-AAAAATATCAA
1 TCAAAAGTTTTGAAAAAATATCAA
* * *
3398566 TTAGAAGAGTTTT-AAAAAATGTTTAA
1 TCA-AA-AGTTTTGAAAAAAT-ATCAA
3398592 TCAAAAGTTTTGAAAA
1 TCAAAAGTTTTGAAAA
3398608 TATTGCCACT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
23 2 0.06
24 8 0.24
25 18 0.55
26 5 0.15
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (24 bp):
TCAAAAGTTTTGAAAAAATATCAA
Found at i:3398809 original size:32 final size:32
Alignment explanation
Indices: 3398765--3398849 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
3398755 ACTCAGGTTA
*
3398765 TTGTGTTTGGTCAATGGTTTGAATGTCTCAGG
1 TTGTTTTTGGTCAATGGTTTGAATGTCTCAGG
3398797 TTGTTTTTGGTCAATGGTTTGAATGTCTCAGG
1 TTGTTTTTGGTCAATGGTTTGAATGTCTCAGG
*
3398829 TTGTTTTTGGTTAATGGTTTG
1 TTGTTTTTGGTCAATGGTTTG
3398850 GCCTTCTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.14, C:0.07, G:0.29, T:0.49
Consensus pattern (32 bp):
TTGTTTTTGGTCAATGGTTTGAATGTCTCAGG
Found at i:3400754 original size:6 final size:6
Alignment explanation
Indices: 3400737--3400775 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
3400727 AATGAATGTT
*
3400737 ATGCATA ATGCAA ATGCAG ATGCCAA ATGCAA ATGCAA A
1 ATGCA-A ATGCAA ATGCAA ATG-CAA ATGCAA ATGCAA A
3400776 AGGTCTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 19 0.66
7 10 0.34
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (6 bp):
ATGCAA
Found at i:3404903 original size:2 final size:2
Alignment explanation
Indices: 3404890--3404970 Score: 144
Period size: 2 Copynumber: 40.5 Consensus size: 2
3404880 AACCTATTCG
*
3404890 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3404932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3404971 AGTTAAACAC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3405127 original size:2 final size:2
Alignment explanation
Indices: 3405120--3405160 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3405110 GTAATATAAA
3405120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3405161 AAGCTAAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3408200 original size:13 final size:13
Alignment explanation
Indices: 3408171--3408205 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3408161 ATAACTAATA
*
3408171 ATATTAAAT-ATT
1 ATATTAAATAAAT
3408183 ATATTAAATAAAT
1 ATATTAAATAAAT
3408196 ATATTAAATA
1 ATATTAAATA
3408206 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:3411215 original size:8 final size:8
Alignment explanation
Indices: 3411202--3411242 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3411192 CTCATTTTCA
3411202 GAGAATTT
1 GAGAATTT
3411210 GAGAATTT
1 GAGAATTT
*
3411218 -AGAGTTT
1 GAGAATTT
*
3411225 GGGAATTT
1 GAGAATTT
3411233 GAGAATTT
1 GAGAATTT
3411241 GA
1 GA
3411243 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:3411535 original size:126 final size:126
Alignment explanation
Indices: 3411310--3411914 Score: 1201
Period size: 126 Copynumber: 4.8 Consensus size: 126
3411300 CTATAATCGG
3411310 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
3411375 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
3411436 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
3411501 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
3411562 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
3411627 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
3411688 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
3411753 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
3411814 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
3411879 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
3411915 ATAACTTAAA
Statistics
Matches: 478, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 478 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:3412363 original size:33 final size:34
Alignment explanation
Indices: 3412302--3412401 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
3412292 AAATTTAATG
*
3412302 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
3412336 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
3412369 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
3412402 AAAATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:3413009 original size:21 final size:21
Alignment explanation
Indices: 3412921--3413011 Score: 123
Period size: 21 Copynumber: 4.3 Consensus size: 21
3412911 TATGGTATAA
*
3412921 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
3412942 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
3412963 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
3412984 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
3413005 AACCCTG
1 AACCCTG
3413012 TGGAGATGGC
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
20 3 0.05
21 60 0.91
22 3 0.05
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:3413042 original size:21 final size:21
Alignment explanation
Indices: 3413018--3413065 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3413008 CCTGTGGAGA
*
3413018 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
3413039 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
3413060 GGGCAT
1 TGGCAT
3413066 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:3414828 original size:33 final size:32
Alignment explanation
Indices: 3414786--3414873 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 32
3414776 TTAATAATTC
*
3414786 TAAATAAATAATAATTATATAAATATTATT-TTAA
1 TAAA-AAATAATAATTATATAAATA-TATTAAT-A
* *
3414820 TAAAAAATAATATTTACATAAATATATTAATA
1 TAAAAAATAATAATTATATAAATATATTAATA
* *
3414852 TAAAAAATAATAACTATTTAAA
1 TAAAAAATAATAATTATATAAA
3414874 AAAATACTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
32 23 0.50
33 19 0.41
34 4 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAAATAATAATTATATAAATATATTAATA
Found at i:3414850 original size:30 final size:34
Alignment explanation
Indices: 3414786--3414864 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 34
3414776 TTAATAATTC
* *
3414786 TAAATAAATAATAATTATATAAATATTATTTTA-A
1 TAAA-AAATAATAATTACATAAATATTATTTAATA
*
3414820 TAAAAAATAATATTTACATAAATA-TA-TTAATA
1 TAAAAAATAATAATTACATAAATATTATTTAATA
3414852 TAAAAAATAATAA
1 TAAAAAATAATAA
3414865 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 3 0.08
32 15 0.38
33 18 0.45
34 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAAAAATAATAATTACATAAATATTATTTAATA
Found at i:3419386 original size:21 final size:20
Alignment explanation
Indices: 3419354--3419397 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3419344 TGTTTTGGTA
* *
3419354 AAAAGAGATTAAATAATAAT
1 AAAAGAGATTAAAGAAAAAT
*
3419374 AAAAGCGATTTAAAGAAAAAT
1 AAAAGAGA-TTAAAGAAAAAT
3419395 AAA
1 AAA
3419398 GAAAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.66, C:0.02, G:0.11, T:0.20
Consensus pattern (20 bp):
AAAAGAGATTAAAGAAAAAT
Found at i:3420109 original size:39 final size:39
Alignment explanation
Indices: 3420065--3420144 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
3420055 AGAAGAAGAA
* * *
3420065 TAAATTCTGATTTGTGTGTTTAGGCTTACTTCAAGAGGG
1 TAAATTATGAGTTGTGTGTTTAGGCTTACTTCAAGAAGG
3420104 TAAATTATGAGTTGTGTGTTTAGGCTTACTTCAAGAAGG
1 TAAATTATGAGTTGTGTGTTTAGGCTTACTTCAAGAAGG
3420143 TA
1 TA
3420145 TTTATAGTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.40
Consensus pattern (39 bp):
TAAATTATGAGTTGTGTGTTTAGGCTTACTTCAAGAAGG
Found at i:3420235 original size:33 final size:33
Alignment explanation
Indices: 3420197--3420259 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
3420187 ATTAAAATAA
3420197 CCCTAAAGATAATTCCAAATGTTTTCTAAAATT
1 CCCTAAAGATAATTCCAAATGTTTTCTAAAATT
3420230 CCCTAAAGATAATTCCAAATGTTTTCTAAA
1 CCCTAAAGATAATTCCAAATGTTTTCTAAA
3420260 TTCAAACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (33 bp):
CCCTAAAGATAATTCCAAATGTTTTCTAAAATT
Found at i:3420730 original size:33 final size:33
Alignment explanation
Indices: 3420688--3420754 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
3420678 CATTCGAGAA
* *
3420688 AGCAAGGTAGAGACCACAATAATTATCCAAGTC
1 AGCAAGGTAGACACCAAAATAATTATCCAAGTC
3420721 AGCAAGGTAGACACCAAAATAATTATCCAAGTC
1 AGCAAGGTAGACACCAAAATAATTATCCAAGTC
3420754 A
1 A
3420755 AGACACCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (33 bp):
AGCAAGGTAGACACCAAAATAATTATCCAAGTC
Found at i:3425951 original size:43 final size:42
Alignment explanation
Indices: 3425889--3425970 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 42
3425879 ATAGATAGAC
* *
3425889 AAACGTCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTATCAT
1 AAACGCCGCAATAAGTGTTGAGATTTAGCGG-GTTTTTATCAT
* *
3425932 AAACGCCGTAATAAGTGTTGAGATTTAGCGGTTTTTTAT
1 AAACGCCGCAATAAGTGTTGAGATTTAGCGGGTTTTTAT
3425971 GAAAACACCG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 7 0.20
43 28 0.80
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (42 bp):
AAACGCCGCAATAAGTGTTGAGATTTAGCGGGTTTTTATCAT
Found at i:3426027 original size:44 final size:44
Alignment explanation
Indices: 3425973--3426404 Score: 627
Period size: 44 Copynumber: 9.9 Consensus size: 44
3425963 TTTTTTATGA
* *
3425973 AAACACCGCTAAAAGG-ATGGTATATAGCGGCGTTTTTAGGATAC
1 AAACGCCGCT-AAAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
* * * *
3426017 AAATGCCGCTAAAGATTTGGTATATAGCGGCGTTTTTAAGATA-
1 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
* * * *
3426060 AAACGCCGCTATAGGTCTAGTACATAGCGGCATTTTTAGGATAC
1 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
** * *
3426104 AAACGTTGCTAATGGTCTGGTATATAGCGGTGTTTTTAGGATAC
1 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
*
3426148 AAACGACGCTAAAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
1 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
* *
3426192 AAACGTCGCTAAAGGTATGGTATATAGCGGCGTTTTTAGGATAC
1 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
*
3426236 AAACGCCGCTAAAGGTCTGGTATATAGCGGCATTTTTAGGATAC
1 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
3426280 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
1 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
* * *
3426324 AAACACCGCTAAAGGTCTGGTATATAGCGGCATTTTTAGGATAT
1 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
* *
3426368 AAACGCCGCTAAAGGT-TGGTATTTAGCGGCATTTTTA
1 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTA
3426405 TCAAAAATGT
Statistics
Matches: 350, Mismatches: 36, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
43 59 0.17
44 291 0.83
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (44 bp):
AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
Found at i:3426859 original size:21 final size:21
Alignment explanation
Indices: 3426827--3426913 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
3426817 CTGTTAATAT
*
3426827 GCTGCTTCTCTCTGTGCTGCC
1 GCTGCTTTTCTCTGTGCTGCC
* *
3426848 GCTTCTTTTCTCTGTGTTGCC
1 GCTGCTTTTCTCTGTGCTGCC
* *
3426869 ACTGCTTTTCTCTGTGTTGCC
1 GCTGCTTTTCTCTGTGCTGCC
* * * *
3426890 TCTGCTTCTCTCTGTACTTCC
1 GCTGCTTTTCTCTGTGCTGCC
3426911 GCT
1 GCT
3426914 ACTGCTCTGG
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.02, C:0.33, G:0.18, T:0.46
Consensus pattern (21 bp):
GCTGCTTTTCTCTGTGCTGCC
Found at i:3426930 original size:21 final size:21
Alignment explanation
Indices: 3426906--3426952 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
3426896 TCTCTCTGTA
*
3426906 CTTCCGCT-ACTGCTCTGGCTG
1 CTTCCGCTGA-TGCTCTCGCTG
* *
3426927 CTTCTGCTGATGCTCTCTCTG
1 CTTCCGCTGATGCTCTCGCTG
3426948 CTTCC
1 CTTCC
3426953 CTTGCTTCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.04, C:0.38, G:0.19, T:0.38
Consensus pattern (21 bp):
CTTCCGCTGATGCTCTCGCTG
Found at i:3433634 original size:20 final size:20
Alignment explanation
Indices: 3433609--3433656 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
3433599 TATGACTAAA
3433609 GGATTTTG-AAATTTTAAGTC
1 GGATTTTGCAAA-TTTAAGTC
3433629 GGATTTTGCAAATTTAAGTC
1 GGATTTTGCAAATTTAAGTC
3433649 GGATTTTG
1 GGATTTTG
3433657 GTCGAATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (20 bp):
GGATTTTGCAAATTTAAGTC
Found at i:3444358 original size:13 final size:14
Alignment explanation
Indices: 3444333--3444362 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3444323 TTATAATGAG
3444333 ATGATGATTTATGT
1 ATGATGATTTATGT
3444347 ATGATG-TTTATGT
1 ATGATGATTTATGT
3444360 ATG
1 ATG
3444363 TAAATCTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (14 bp):
ATGATGATTTATGT
Found at i:3446787 original size:172 final size:173
Alignment explanation
Indices: 3446490--3446833 Score: 633
Period size: 172 Copynumber: 2.0 Consensus size: 173
3446480 TTATTACATT
3446490 TGATGTTTTTTTCTTTTGAAAAAATATCATGCTAACCAGTTCTTTGTGCTTGCAGAAAGCAGTAA
1 TGATGTTTTTTTCTTTTGAAAAAATATCATGCTAACCAGTTCTTTGTGCTTGCAGAAAGCAGTAA
3446555 TATCAAAGGTAACACCAATCCTTGAAGATCCTTAGAGATATGTTCAAGGAAATGGCTCCAGCTTG
66 TATCAAAGGTAACACCAATCCTTGAAGATCCTTAGAGATATGTTCAAGGAAATGGCTCCAGCTTG
3446620 TATAAAGGTGGCAGACTTGGGTTGCTCTTCAGAA-CTAACACA
131 TATAAAGGTGGCAGACTTGGGTTGCTCTTCAGAACCTAACACA
3446662 TGATGTTTTTTTCTTTTTG-AAAAA-AT-ATGCTAACCAGTTCTTTGTGCTTGCAGAAAGCAGTA
1 TGATGTTTTTTTC-TTTTGAAAAAATATCATGCTAACCAGTTCTTTGTGCTTGCAGAAAGCAGTA
3446724 ATATCAAAGGTAACACCAATCCTTGAAGAATCCATTAGAGATATGTTCAAGGAAATGGCTCCAGC
65 ATATCAAAGGTAACACCAATCCTTGAAG-ATCC-TTAGAGATATGTTCAAGGAAATGGCTCCAGC
3446789 TTGTATAAAGGTGGCAGACTTGGGTTGCTCTTCAGAACCTAACAC
128 TTGTATAAAGGTGGCAGACTTGGGTTGCTCTTCAGAACCTAACAC
3446834 CTTCCACACT
Statistics
Matches: 168, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
170 64 0.38
171 6 0.04
172 86 0.51
173 12 0.07
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (173 bp):
TGATGTTTTTTTCTTTTGAAAAAATATCATGCTAACCAGTTCTTTGTGCTTGCAGAAAGCAGTAA
TATCAAAGGTAACACCAATCCTTGAAGATCCTTAGAGATATGTTCAAGGAAATGGCTCCAGCTTG
TATAAAGGTGGCAGACTTGGGTTGCTCTTCAGAACCTAACACA
Found at i:3447978 original size:10 final size:10
Alignment explanation
Indices: 3447963--3447990 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3447953 ATTAAAACCT
3447963 AAAATATCTC
1 AAAATATCTC
3447973 AAAATATCTC
1 AAAATATCTC
3447983 AAAATATC
1 AAAATATC
3447991 AACCAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATATCTC
Found at i:3449491 original size:15 final size:15
Alignment explanation
Indices: 3449471--3449501 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3449461 TAATAACCCG
3449471 CATACTTCTAAATAA
1 CATACTTCTAAATAA
3449486 CATACTTCTAAATAA
1 CATACTTCTAAATAA
3449501 C
1 C
3449502 CTTAACAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (15 bp):
CATACTTCTAAATAA
Found at i:3450396 original size:575 final size:575
Alignment explanation
Indices: 3449018--3452342 Score: 5812
Period size: 575 Copynumber: 5.8 Consensus size: 575
3449008 TAAACTTTAT
*
3449018 TGAATCCAAAAGCCACAAAGAGATTATCGTCACTCTTCGTTACTAAATCACACCATGGGTAGCAG
1 TGAATCCAAAAGCCACAAAGAGATTATCGTCACTCTTCGTTACTAAATCACACCATGGGCAGCAG
* * *
3449083 CACATCAAAGTATCCAAATAAATCATCTCCATAACAAAATCGCCTTGGTCGGAACCCGGTTGATG
66 CACATCAAAGTATCCAAATAAATCACCACCATAACAAAACCGCCTTGGTCGGAACCCGGTTGATG
* * *
3449148 ATAGTCATTGAAATAAAACTTTGGATGCGAGGAGGGAATTTTAGCTTCCATATTACATCAAAGTT
131 ATCGTCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTACATCAAAGTT
* * *
3449213 AAAACATGGACCCTCAATTGCATCATTTACCAGCTTTGCACAATGTTAATAAGGAATAATACACT
196 AAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATGTTAATAAGGCATAATACACT
*
3449278 TGCTAGAGTTATTAATGGCCAAAAATGATATATCTGACTAGGCGAGTTCTTAAAAAGTGACTGAA
261 TGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGAGTTCTTAAAAAGTGACTGAA
*
3449343 AATGCATAAATGGACTTTTAATCCATTTGACATTCTCAAATGTGAATTTTATAATGAGATGATGA
326 AATGCATAAATGGACTTTTAATCCATTTGACATGCTCAAATGTGAATTTTATAATGAGATGATGA
*
3449408 TTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAACACAAAAATTAATAACCCGCA
391 TTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAACACTAAAATTAATAA---G--
*
3449473 TACTTCTAAATAACATACTTCTAAATAACCTTAACAAAGAAACA--AAAA-ATAAATTACACAAG
451 --C--C------GCATACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTACACAAG
*
3449535 TCTCTAATTGATAAAGAGGCCTTTCAAGATAAATTCCACCAATCGAAAACACTGGACCGTAATAG
506 TCTCTAATTGATAAAGAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGTAATAG
3449600 CTTAG
571 CTTAG
3449605 TGAATCCAAAAGCCACAAAGAGATTATCGTCACTCTTCGTTACTAAATCACACCATGGGCAGCAG
1 TGAATCCAAAAGCCACAAAGAGATTATCGTCACTCTTCGTTACTAAATCACACCATGGGCAGCAG
* *
3449670 CACATCAAAGTATCCAAATAAATCA-CATCCATAACAAAACCTCCTTGGTCGGAACCCAGTTGAT
66 CACATCAAAGTATCCAAATAAATCACCA-CCATAACAAAACCGCCTTGGTCGGAACCCGGTTGAT
* *
3449734 GATCGTCATTGAAAGAAAACTTTGGATACGAGGAGGGAATTTTAGCTTCCATATTACATCAAAGT
130 GATCGTCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTACATCAAAGT
3449799 TAAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATGTTAATAAGGCATAATACAC
195 TAAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATGTTAATAAGGCATAATACAC
*
3449864 TTGCTAGAGTTATTAATGGCCAAAAATGATATATCTGACTAGGCGAGTTCTTAAAAAGTGACTGA
260 TTGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGAGTTCTTAAAAAGTGACTGA
*
3449929 AAATGCATAAATGGACTTTTAATCCATTTGACATTCTCAAATGTGAATTTTATAATGAGATGATG
325 AAATGCATAAATGGACTTTTAATCCATTTGACATGCTCAAATGTGAATTTTATAATGAGATGATG
*
3449994 ATTTATGTATGACATGTTATATGTATGTCAATCGATGTTCATTAACACTAAAATTAATAAGCCGC
390 ATTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAACACTAAAATTAATAAGCCGC
* *
3450059 ATACTTCAAAATAACCTTAACAAAGAAACATTAAAACATAAGTTACACAAGTCTCTAATTGATAA
455 ATACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTACACAAGTCTCTAATTGATAA
*
3450124 ATAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGTAATAGCTTAG
520 AGAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGTAATAGCTTAG
* *
3450180 TGAATCCAAAAGCCACAAAGAGATTATCATCACTCTTCATTACTAAATCACACCATGGGCAGCAG
1 TGAATCCAAAAGCCACAAAGAGATTATCGTCACTCTTCGTTACTAAATCACACCATGGGCAGCAG
*
3450245 CACATCAAAGTATCCAAATAAATCACCACCATAACAAAACCGCCTTGGTCAGAACCCGGTTGATG
66 CACATCAAAGTATCCAAATAAATCACCACCATAACAAAACCGCCTTGGTCGGAACCCGGTTGATG
3450310 ATCGTCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTACATCAAAGTT
131 ATCGTCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTACATCAAAGTT
*
3450375 AAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACAATGTTAATAAGGCATAATACACT
196 AAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATGTTAATAAGGCATAATACACT
3450440 TGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGAGTTCTTAAAAAGTGACTGAA
261 TGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGAGTTCTTAAAAAGTGACTGAA
* *
3450505 AATGCATAAATGGACTTTTAATCCATTTGACATGGTCAAATGTGAATTTTATAATGAGAAGATGA
326 AATGCATAAATGGACTTTTAATCCATTTGACATGCTCAAATGTGAATTTTATAATGAGATGATGA
*
3450570 TTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAACACTAAAATTGATAAGCCGCA
391 TTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAACACTAAAATTAATAAGCCGCA
* *
3450635 TACTTCTAAATAACCTTAACAAAGAAACGTTAAAACATAAATTACACAACTCTCTAATTGATAAA
456 TACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTACACAAGTCTCTAATTGATAAA
*
3450700 GAGTCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGTAATAGCTTAG
521 GAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGTAATAGCTTAG
*
3450755 TGAATCCAAAAGCCACAAAGAGATTATCGTCACTCTTCGTTACTAAATCACTCCATGGGCAGCAG
1 TGAATCCAAAAGCCACAAAGAGATTATCGTCACTCTTCGTTACTAAATCACACCATGGGCAGCAG
* * *
3450820 CACATCAAAGTATCGAAATAAATCACCTCCATAACAAAACCGCCTTTGTCGGAACCCGGTTGATG
66 CACATCAAAGTATCCAAATAAATCACCACCATAACAAAACCGCCTTGGTCGGAACCCGGTTGATG
* * *
3450885 ATCATCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGTTTCCATATTACATCAAATTT
131 ATCGTCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTACATCAAAGTT
*
3450950 AAAACATGGATCCTCAATTGCATTATTTACCAGCTTTGCACTATGTTAATAAGGCATAATACACT
196 AAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATGTTAATAAGGCATAATACACT
*
3451015 TGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGTGAGTTCTTAAAAAGTGACTGAA
261 TGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGAGTTCTTAAAAAGTGACTGAA
*
3451080 AATGCATAAATGGACTTTTAATCCATTTGACATTCTCAAATGTGAATTTTATAATGAGATGATGA
326 AATGCATAAATGGACTTTTAATCCATTTGACATGCTCAAATGTGAATTTTATAATGAGATGATGA
* *
3451145 TTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAACACTAAAATTAGTAAGTCGCA
391 TTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAACACTAAAATTAATAAGCCGCA
3451210 TACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTACACAAGTCTCTAATTGATAAA
456 TACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTACACAAGTCTCTAATTGATAAA
*
3451275 TAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGTAATAGCTTAG
521 GAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGTAATAGCTTAG
* * *
3451330 TGAATCCAAAAGCCACAAAGAGATTATCATCACTCTTCGTTAGTAAATCACACCATAGGCAGCAG
1 TGAATCCAAAAGCCACAAAGAGATTATCGTCACTCTTCGTTACTAAATCACACCATGGGCAGCAG
3451395 CACATCAAAGTATCCAAATAAATCACCACCATAACAAAACCGCCTTGGTCGGAACCCGGTTGATG
66 CACATCAAAGTATCCAAATAAATCACCACCATAACAAAACCGCCTTGGTCGGAACCCGGTTGATG
3451460 ATCGTCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTACATCAAAGTT
131 ATCGTCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTACATCAAAGTT
** *
3451525 AAAACAAAGATCCTCAATTGCATCATTTACCAGCTTTTCACTATGTTAATAAGGCATAATACACT
196 AAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATGTTAATAAGGCATAATACACT
3451590 TGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGAGTTCTTAAAAAGTGACTGAA
261 TGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGAGTTCTTAAAAAGTGACTGAA
3451655 AATGCATAAATGGACTTTTAATCCATTTGACATGCTCAAATGTGAATTTTATAATGAGATGATGA
326 AATGCATAAATGGACTTTTAATCCATTTGACATGCTCAAATGTGAATTTTATAATGAGATGATGA
3451720 TTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAACACTAAAATTAATAAGCCGCA
391 TTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAACACTAAAATTAATAAGCCGCA
* ** *
3451785 TACTTCTAAATAACCTTAACAATGAAATGTTAAAACATAAATTACACAACTCTCTAATTGATAAA
456 TACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTACACAAGTCTCTAATTGATAAA
* * **
3451850 GAGGTCGTTCAAGATAAATTCCACCATTCGAAAACGTTGGACCGTAATAGCTTAG
521 GAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGTAATAGCTTAG
* *
3451905 TGAATCCAAAAGCCACAAAGAGATTGTTGTCACTCTTCGTTACTAAATCACACCATGGGCAGCAG
1 TGAATCCAAAAGCCACAAAGAGATTATCGTCACTCTTCGTTACTAAATCACACCATGGGCAGCAG
* *
3451970 CACATCAAAGTATCCAAATAAATCACCTCCATAACAAAACCGCCTTGGTCGGAACTCGGTTGATG
66 CACATCAAAGTATCCAAATAAATCACCACCATAACAAAACCGCCTTGGTCGGAACCCGGTTGATG
* *
3452035 ATCATCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGTTTCCATATTACATCAAAGTT
131 ATCGTCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTACATCAAAGTT
**
3452100 AAAACATGGATCCTCAATTGCATTGTTTACCAGCTTTGCACTATGTTAATAAGGCATAATACACT
196 AAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATGTTAATAAGGCATAATACACT
*
3452165 TGCTAGAGTTGTTAATGGCCAAACATGATATATCTGACTAGGCGAGTTCTTAAAAAGTGACTGAA
261 TGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGAGTTCTTAAAAAGTGACTGAA
* *
3452230 AATGCATTAATGGACTTTTAATCCATTTGACATGCTCAAATGTGAATTTTATAATGAAATGATGA
326 AATGCATAAATGGACTTTTAATCCATTTGACATGCTCAAATGTGAATTTTATAATGAGATGATGA
*
3452295 TTTATGTATGACATGTTATATGTATGTCATTCTATGTTCATTAACACT
391 TTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAACACT
3452343 GATAACTCCG
Statistics
Matches: 2627, Mismatches: 106, Indels: 22
0.95 0.04 0.01
Matches are distributed among these distances:
572 30 0.01
574 4 0.00
575 2153 0.82
576 2 0.00
578 1 0.00
580 1 0.00
584 1 0.00
586 1 0.00
587 434 0.17
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (575 bp):
TGAATCCAAAAGCCACAAAGAGATTATCGTCACTCTTCGTTACTAAATCACACCATGGGCAGCAG
CACATCAAAGTATCCAAATAAATCACCACCATAACAAAACCGCCTTGGTCGGAACCCGGTTGATG
ATCGTCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTACATCAAAGTT
AAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATGTTAATAAGGCATAATACACT
TGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGAGTTCTTAAAAAGTGACTGAA
AATGCATAAATGGACTTTTAATCCATTTGACATGCTCAAATGTGAATTTTATAATGAGATGATGA
TTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAACACTAAAATTAATAAGCCGCA
TACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTACACAAGTCTCTAATTGATAAA
GAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGTAATAGCTTAG
Found at i:3460959 original size:18 final size:18
Alignment explanation
Indices: 3460890--3460949 Score: 120
Period size: 18 Copynumber: 3.3 Consensus size: 18
3460880 GAGAGTCCCC
3460890 AGCCTGCTGAAGCTGAAG
1 AGCCTGCTGAAGCTGAAG
3460908 AGCCTGCTGAAGCTGAAG
1 AGCCTGCTGAAGCTGAAG
3460926 AGCCTGCTGAAGCTGAAG
1 AGCCTGCTGAAGCTGAAG
3460944 AGCCTG
1 AGCCTG
3460950 ATGACCCTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.33, T:0.17
Consensus pattern (18 bp):
AGCCTGCTGAAGCTGAAG
Found at i:3468851 original size:10 final size:11
Alignment explanation
Indices: 3468838--3468888 Score: 66
Period size: 11 Copynumber: 4.4 Consensus size: 11
3468828 TTTTTTGAAA
*
3468838 TTTTGGCTTTT
1 TTTTGCCTTTT
3468849 TTTTGCCTTTTTT
1 TTTTGCC--TTTT
3468862 TTTTGCCTTTTT
1 TTTTGCC-TTTT
3468874 TTTTGCCTTTT
1 TTTTGCCTTTT
3468885 TTTT
1 TTTT
3468889 TTGAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
11 14 0.38
12 12 0.32
13 11 0.30
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (11 bp):
TTTTGCCTTTT
Found at i:3468862 original size:12 final size:12
Alignment explanation
Indices: 3468845--3468889 Score: 81
Period size: 12 Copynumber: 3.7 Consensus size: 12
3468835 AAATTTTGGC
3468845 TTTTTTTTGCCTT
1 TTTTTTTTGCC-T
3468858 TTTTTTTTGCCT
1 TTTTTTTTGCCT
3468870 TTTTTTTTGCCT
1 TTTTTTTTGCCT
3468882 TTTTTTTT
1 TTTTTTTT
3468890 TGAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 21 0.66
13 11 0.34
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTTTGCCT
Found at i:3468863 original size:13 final size:13
Alignment explanation
Indices: 3468845--3468891 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
3468835 AAATTTTGGC
3468845 TTTTTTTTGCCTT
1 TTTTTTTTGCCTT
3468858 TTTTTTTTGCC-T
1 TTTTTTTTGCCTT
3468870 TTTTTTTTGCCTT
1 TTTTTTTTGCCTT
3468883 TTTTTTTTG
1 TTTTTTTTG
3468892 AAAAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.36
13 21 0.64
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.79
Consensus pattern (13 bp):
TTTTTTTTGCCTT
Found at i:3481064 original size:14 final size:14
Alignment explanation
Indices: 3481028--3481054 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3481018 ATTTATTTTT
3481028 TAATTATATTTATA
1 TAATTATATTTATA
3481042 TAATTATATTTAT
1 TAATTATATTTAT
3481055 TATTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:3481325 original size:17 final size:17
Alignment explanation
Indices: 3481303--3481360 Score: 116
Period size: 17 Copynumber: 3.4 Consensus size: 17
3481293 GATAGCATGA
3481303 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGGT
3481320 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGGT
3481337 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGGT
3481354 CCGGTTC
1 CCGGTTC
3481361 TGAAAACCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.10, C:0.36, G:0.29, T:0.24
Consensus pattern (17 bp):
CCGGTTCGCTAACCGGT
Found at i:3486154 original size:14 final size:14
Alignment explanation
Indices: 3486118--3486144 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3486108 ATTTATTTTT
3486118 TAATTATATTTATA
1 TAATTATATTTATA
3486132 TAATTATATTTAT
1 TAATTATATTTAT
3486145 TATTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:3491209 original size:14 final size:14
Alignment explanation
Indices: 3491173--3491199 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3491163 ATTTATTTTT
3491173 TAATTATATTTATA
1 TAATTATATTTATA
3491187 TAATTATATTTAT
1 TAATTATATTTAT
3491200 TATTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:3491470 original size:17 final size:17
Alignment explanation
Indices: 3491448--3491505 Score: 116
Period size: 17 Copynumber: 3.4 Consensus size: 17
3491438 GATAGCATGA
3491448 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGGT
3491465 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGGT
3491482 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGGT
3491499 CCGGTTC
1 CCGGTTC
3491506 TGAAAACCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.10, C:0.36, G:0.29, T:0.24
Consensus pattern (17 bp):
CCGGTTCGCTAACCGGT
Found at i:3496890 original size:575 final size:575
Alignment explanation
Indices: 3494403--3496893 Score: 4377
Period size: 575 Copynumber: 4.3 Consensus size: 575
3494393 TCATAAATAA
** * *
3494403 TTAATAAGGCATGGTACACTTGCTAGAGTTGTTAATGGCAAAAAATGATATATCTGACTAGGTGA
1 TTAATAAGGCATAATACACTTGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGA
3494468 GTTCTTAAAAAGTGAC------TG-A-AAATGGACTTTTAATCCATTTGACATTCTCAAATGTGA
66 GTTCTTAAAAAGTGACTGAAAATGCATAAATGGACTTTTAATCCATTTGACATTCTCAAATGTGA
3494525 ATTTTATAATGAGATGATGATTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAAC
131 ATTTTATAATGAGATGATGATTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAAC
*
3494590 ACTGAAATTAATAAGCCGCATACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTAC
196 ACTAAAATTAATAAGCCGCATACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTAC
*
3494655 AAAAGTCTCTAATTGATAAAGAGGCCTTTCAAGATAAATTCCACCACTCGAAAACACTGGACCGT
261 AAAAGTCTCTAATTGATAAAGAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGT
* * *
3494720 AATAGTTTAGTGAATCCAAAAGCCACAAAGAGATTAGCGTCACTCTTCGTTACTAAATCACACCA
326 AATAGCTTAGTGAATCCAAAAGCCACAAAGAGATTATCATCACTCTTCGTTACTAAATCACACCA
*
3494785 TGGGCAGCAGCACATCAAAGTATCCAAATAAATCACCACCATAACAAAACCGCCTTGGTCGGAAC
391 TGGGCAGCAGCACATCAAAGTATCCAAATAAATCACCTCCATAACAAAACCGCCTTGGTCGGAAC
* * * *
3494850 CCGATTGATGATCGTCATTGAAAGAAAACTTCGGATGCGAGGAGGGACTTTTAACTTCCATATTA
456 CCGGTTGATGATCATCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTA
* * * * *
3494915 CATTAAAGTTAAAACACGGATCCTCAATGGCGTCATTTACCAGCTTTGCACTTTG
521 CATCAAAGTTAAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATG
3494970 TTAATAAGGCATAATACACTTGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGA
1 TTAATAAGGCATAATACACTTGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGA
* * *
3495035 GTTCTTAAAAAGTGACTGAAAAAGCATAAATTGACTTTTAATCCATTTGAAATTCTCAAATGTGA
66 GTTCTTAAAAAGTGACTGAAAATGCATAAATGGACTTTTAATCCATTTGACATTCTCAAATGTGA
* * *
3495100 ATTTTAAAATGAGATGATGATTTATGTATGACATGTTATATGTATGTCAATCTATATTCATTAAA
131 ATTTTATAATGAGATGATGATTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAAC
3495165 ACTAAAATTAATAAGCCGCATACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTAC
196 ACTAAAATTAATAAGCCGCATACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTAC
* *
3495230 ACAAGTCTCTAATTGATAAAGAGGCCTTTCAAGATAAATTCCACCAATCGAAAACACTGGACCGT
261 AAAAGTCTCTAATTGATAAAGAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGT
*
3495295 AATAGCTTAGTGAATCCAAAAGCCACAAAGAGATTATCGTCACTCTTCGTTACTAAATCACACCA
326 AATAGCTTAGTGAATCCAAAAGCCACAAAGAGATTATCATCACTCTTCGTTACTAAATCACACCA
*
3495360 TGGGCAGCAGCACATCAAAGTATCCAAATAAATCACATCCATAACAAAACCGCCTTGGTCGGAAC
391 TGGGCAGCAGCACATCAAAGTATCCAAATAAATCACCTCCATAACAAAACCGCCTTGGTCGGAAC
* * * *
3495425 CCGGTTGATGATCGTCATTGAAAGAAAACTTTGGATACGATGAGGGAATTTTAGCTTCCATATTA
456 CCGGTTGATGATCATCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTA
*
3495490 CATCAAAGTTAAAACATGGATCCTCAATTGCATCATTTACAAGCTTTGCACTATG
521 CATCAAAGTTAAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATG
3495545 TTAATAAGGCATAATACACTTGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGA
1 TTAATAAGGCATAATACACTTGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGA
*
3495610 GTTCTTAAAAAGTGACTGAAAAAGCATAAATGGACTTTTAATCCATTTGACATTCTCAAATGTGA
66 GTTCTTAAAAAGTGACTGAAAATGCATAAATGGACTTTTAATCCATTTGACATTCTCAAATGTGA
* *
3495675 ATTTTATAATGAGATGATTAATTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAAC
131 ATTTTATAATGAGATGATGATTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAAC
*
3495740 AATAAAATTAATAAGCCGCATACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAAATTA
196 ACTAAAATTAATAAGCCGCATACTTCTAAATAACCTTAACAAAGAAACATTAAAACAT-AAATTA
* *
3495805 CACAAGTCTCTAATTGATAAAGAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTAGACCG
260 CAAAAGTCTCTAATTGATAAAGAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCG
*
3495870 TAATAGCTTAGTGAATCCAAAAGCCGCAAAGAGATTATCATCACTCTTCGTTACTAAATCACACC
325 TAATAGCTTAGTGAATCCAAAAGCCACAAAGAGATTATCATCACTCTTCGTTACTAAATCACACC
*
3495935 ATGGGCAGCAGCACATCAAAGTATCCAAATAAATCACCTCCATAAGAAAACCGCCTTGGTCGGAA
390 ATGGGCAGCAGCACATCAAAGTATCCAAATAAATCACCTCCATAACAAAACCGCCTTGGTCGGAA
* *
3496000 CCCGGTTGATGATCATCATTAAAAGAAAACTTTGGATGCGAGGAGGGACATTTAGCTTCCATATT
455 CCCGGTTGATGATCATCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATT
*
3496065 ACATCAAAGTTAAAACATGGATCCTCAATTGCATCATTTACCACCTTTGCACTATG
520 ACATCAAAGTTAAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATG
*
3496121 TTAATAAGGCATAATACACTTGCTAGAGTTGTTAATGGCCCAAAATGATATATCTGACTAGGCGA
1 TTAATAAGGCATAATACACTTGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGA
* *
3496186 GTTCTTAAAAAGTGGCTGAAAATGCATAAATGGACTTTTAATCCATTTGACATGCTCAAATGTGA
66 GTTCTTAAAAAGTGACTGAAAATGCATAAATGGACTTTTAATCCATTTGACATTCTCAAATGTGA
3496251 ATTTTATAATGAGATGATGATTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAAC
131 ATTTTATAATGAGATGATGATTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAAC
* *
3496316 ACTAAAATTAATAAGCCGCATACTTCCAAATAACCTTAACAAAGAAACGTTAAAACATAAATTAC
196 ACTAAAATTAATAAGCCGCATACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTAC
* *
3496381 AAAACTCTCTAATTGATAAAGAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGC
261 AAAAGTCTCTAATTGATAAAGAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGT
*
3496446 AATAGCTTAGTGAATCCAAAAGCCACAAAGAGATTATCATCACTCTTCGTTACTAAATCATACCA
326 AATAGCTTAGTGAATCCAAAAGCCACAAAGAGATTATCATCACTCTTCGTTACTAAATCACACCA
3496511 TGGGCAGCAGCACATCAAAGTATCCAAATAAATCACCTCCATAACAAAACCGCCTTGGTCGGAAC
391 TGGGCAGCAGCACATCAAAGTATCCAAATAAATCACCTCCATAACAAAACCGCCTTGGTCGGAAC
3496576 CCGGTTGATGATCATCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTA
456 CCGGTTGATGATCATCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTA
* *
3496641 CATCAAAGTTAAAACATGGATCCTCAATTGCATTATTTACCAGCTTTACACTATG
521 CATCAAAGTTAAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATG
* *
3496696 TTAATAAGGCATAATACACTTGCTAGAGTTATTAATAGCCAAAAATGATATATCTGACTAGGCGA
1 TTAATAAGGCATAATACACTTGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGA
*
3496761 GTTCTTAAAAAGTGACTGAAAATGCATAAATGGACTTTTAATCCATTTGACATGCTCAAATGTGA
66 GTTCTTAAAAAGTGACTGAAAATGCATAAATGGACTTTTAATCCATTTGACATTCTCAAATGTGA
* *
3496826 ATTTTATAATGAGATGATGATTTATGTATGACATGTTATATGTATGTCATTATATGTTCATTAAC
131 ATTTTATAATGAGATGATGATTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAAC
3496891 ACT
196 ACT
3496894 GATAACTTCG
Statistics
Matches: 1837, Mismatches: 78, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
567 77 0.04
573 1 0.00
574 1 0.00
575 1206 0.66
576 552 0.30
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (575 bp):
TTAATAAGGCATAATACACTTGCTAGAGTTGTTAATGGCCAAAAATGATATATCTGACTAGGCGA
GTTCTTAAAAAGTGACTGAAAATGCATAAATGGACTTTTAATCCATTTGACATTCTCAAATGTGA
ATTTTATAATGAGATGATGATTTATGTATGACATGTTATATGTATGTCAATCTATGTTCATTAAC
ACTAAAATTAATAAGCCGCATACTTCTAAATAACCTTAACAAAGAAACATTAAAACATAAATTAC
AAAAGTCTCTAATTGATAAAGAGGCCTTTCAAGATAAATTCCACCATTCGAAAACACTGGACCGT
AATAGCTTAGTGAATCCAAAAGCCACAAAGAGATTATCATCACTCTTCGTTACTAAATCACACCA
TGGGCAGCAGCACATCAAAGTATCCAAATAAATCACCTCCATAACAAAACCGCCTTGGTCGGAAC
CCGGTTGATGATCATCATTGAAAGAAAACTTTGGATGCGAGGAGGGACTTTTAGCTTCCATATTA
CATCAAAGTTAAAACATGGATCCTCAATTGCATCATTTACCAGCTTTGCACTATG
Found at i:3513911 original size:14 final size:14
Alignment explanation
Indices: 3513892--3513920 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3513882 TATTCCTTTT
3513892 TTATTTATATTATA
1 TTATTTATATTATA
3513906 TTATTTATATTATA
1 TTATTTATATTATA
3513920 T
1 T
3513921 ATATATCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:3514033 original size:39 final size:41
Alignment explanation
Indices: 3513990--3514080 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 41
3513980 ATTTACTATG
*
3513990 TATATATATTTTTTCTTAATATTATATTTTATACA-TT-TT
1 TATATATATATTTTCTTAATATTATATTTTATACATTTATT
* **
3514029 TATATATATATTTTCTTAATATTCTATTTTATTTATTTATT
1 TATATATATATTTTCTTAATATTATATTTTATACATTTATT
3514070 TATATATATAT
1 TATATATATAT
3514081 ATATATTATA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 31 0.67
40 2 0.04
41 13 0.28
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (41 bp):
TATATATATATTTTCTTAATATTATATTTTATACATTTATT
Found at i:3514112 original size:18 final size:18
Alignment explanation
Indices: 3514086--3514123 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3514076 TATATATATA
3514086 TTATATTTTTACT-TTATT
1 TTATATTTTT-CTATTATT
*
3514104 TTATTTTTTTCTATTATT
1 TTATATTTTTCTATTATT
3514122 TT
1 TT
3514124 TTTAATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATATTTTTCTATTATT
Found at i:3514335 original size:19 final size:19
Alignment explanation
Indices: 3514304--3514354 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3514294 TCTGTGTCTT
*
3514304 TTTTTAATA-TTTTATTCA
1 TTTTTATTATTTTTATTCA
*
3514322 TTTTGT-TTATTTTTATTTA
1 TTTT-TATTATTTTTATTCA
3514341 TTTTTATTATTTTT
1 TTTTTATTATTTTT
3514355 TACGTGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTTATTATTTTTATTCA
Found at i:3514354 original size:9 final size:9
Alignment explanation
Indices: 3514304--3514354 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
3514294 TCTGTGTCTT
*
3514304 TTTTTAATA
1 TTTTTATTA
3514313 -TTTTATTCA
1 TTTTTATT-A
3514322 TTTTGT-TTA
1 TTTT-TATTA
3514331 TTTTTATTTA
1 TTTTTA-TTA
3514341 TTTTTATTA
1 TTTTTATTA
3514350 TTTTT
1 TTTTT
3514355 TACGTGTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
8 7 0.19
9 14 0.39
10 14 0.39
11 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTTTATTA
Found at i:3516238 original size:7 final size:7
Alignment explanation
Indices: 3516221--3516254 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3516211 GAACATTTCA
3516221 TGCATTTT
1 TGCA-TTT
3516229 TGCATTT
1 TGCATTT
3516236 TGCATTT
1 TGCATTT
*
3516243 TGCATCT
1 TGCATTT
3516250 TGCAT
1 TGCAT
3516255 CTACATTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.53
Consensus pattern (7 bp):
TGCATTT
Found at i:3517473 original size:10 final size:10
Alignment explanation
Indices: 3517458--3517482 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3517448 CAATCAAAAC
3517458 AAAAAGAGAA
1 AAAAAGAGAA
3517468 AAAAAGAGAA
1 AAAAAGAGAA
3517478 AAAAA
1 AAAAA
3517483 CAAAGAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGAGAA
Found at i:3517482 original size:13 final size:13
Alignment explanation
Indices: 3517466--3517533 Score: 84
Period size: 13 Copynumber: 5.1 Consensus size: 13
3517456 ACAAAAAGAG
3517466 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
3517479 AAAACAAAGAGAAA
1 AAAA-AAAGAGAAA
3517493 ATAAAAAGAGAGAAA
1 A-AAAAA-AGAGAAA
*
3517508 ATAAAAAGAGAAA
1 AAAAAAAGAGAAA
*
3517521 AAATAAAG-GAAA
1 AAAAAAAGAGAAA
3517533 A
1 A
3517534 TTGAAAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
12 5 0.10
13 17 0.35
14 16 0.33
15 11 0.22
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.04
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:3517506 original size:15 final size:15
Alignment explanation
Indices: 3517466--3517527 Score: 83
Period size: 15 Copynumber: 4.2 Consensus size: 15
3517456 ACAAAAAGAG
*
3517466 AAAAAAAGAGAAAA-
1 AAAAAGAGAGAAAAT
3517480 AAACAA-AGAGAAAAT
1 AAA-AAGAGAGAAAAT
3517495 AAAAAGAGAGAAAAT
1 AAAAAGAGAGAAAAT
*
3517510 AAAAAGAGAAAAAAT
1 AAAAAGAGAGAAAAT
3517525 AAA
1 AAA
3517528 GGAAAATTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
14 13 0.30
15 31 0.70
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.05
Consensus pattern (15 bp):
AAAAAGAGAGAAAAT
Found at i:3517541 original size:42 final size:40
Alignment explanation
Indices: 3517458--3517548 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 40
3517448 CAATCAAAAC
*
3517458 AAAAAGAGAA-AAAAAGAGAAAAAAACAAAGAGAAAATAA
1 AAAAAGAAAATAAAAAGAGAAAAAAACAAAGAGAAAATAA
*
3517497 AAAGAGAGAAAATAAAAAGAG-AAAAAATAAAG-GAAAATTGAA
1 AAA-A-AGAAAATAAAAAGAGAAAAAAACAAAGAGAAAA-T-AA
3517539 AAAAAGAAAA
1 AAAAAGAAAA
3517549 CAAGATGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
39 3 0.07
40 12 0.27
41 17 0.38
42 13 0.29
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.05
Consensus pattern (40 bp):
AAAAAGAAAATAAAAAGAGAAAAAAACAAAGAGAAAATAA
Found at i:3517722 original size:69 final size:69
Alignment explanation
Indices: 3517607--3517741 Score: 225
Period size: 69 Copynumber: 2.0 Consensus size: 69
3517597 TCAAACTATA
* * *
3517607 AGATTGATCAAGCACAATCATTTCTGAATCCCTAAACCACTTCACTCAAAGATCATAGAGCATCA
1 AGATTGATCAAGCACAATCATTTCTGAATCACTAAACCACTCCACTCAAAGACCATAGAGCATCA
3517672 AATG
66 AATG
* *
3517676 AGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCAAAGACCATAGAGCATCA
1 AGATTGATCAAGCACAATCATTTCTGAATCACTAAACCACTCCACTCAAAGACCATAGAGCATCA
3517741 A
66 A
3517742 GAGAGAGACA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (69 bp):
AGATTGATCAAGCACAATCATTTCTGAATCACTAAACCACTCCACTCAAAGACCATAGAGCATCA
AATG
Found at i:3518694 original size:32 final size:30
Alignment explanation
Indices: 3518658--3518763 Score: 86
Period size: 32 Copynumber: 3.3 Consensus size: 30
3518648 GGAACAATGA
* *
3518658 GGGCATCTTTGAAGATTTAACATCAAATCTCG
1 GGGCAT-TTTG-AGATTTAACATCAAATATTG
*** *
3518690 GGGCAATTTTTTTATTTAACATCAAATGTTG
1 GGGC-ATTTTGAGATTTAACATCAAATATTG
* *
3518721 GGGCATTTTTTGAGATTCAACATCGAATATTG
1 GGGCA--TTTTGAGATTTAACATCAAATATTG
3518753 GGGCATGTTTG
1 GGGCAT-TTTG
3518764 GGAATTCAAC
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
30 2 0.03
31 24 0.41
32 31 0.53
33 2 0.03
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (30 bp):
GGGCATTTTGAGATTTAACATCAAATATTG
Found at i:3518707 original size:31 final size:30
Alignment explanation
Indices: 3518672--3518731 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
3518662 ATCTTTGAAG
3518672 ATTTAACATCAAATCTCGGGGCAATTTTTTT
1 ATTTAACATCAAATCTCGGGGC-ATTTTTTT
* *
3518703 ATTTAACATCAAATGTTGGGGCATTTTTT
1 ATTTAACATCAAATCTCGGGGCATTTTTT
3518732 GAGATTCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (30 bp):
ATTTAACATCAAATCTCGGGGCATTTTTTT
Found at i:3518771 original size:32 final size:32
Alignment explanation
Indices: 3518707--3518776 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
3518697 TTTTTTATTT
* **
3518707 AACATCAAATGTTGGGGCATTTTTTGAGATTC
1 AACATCAAATATTGGGGCATTTTGGGAGATTC
*
3518739 AACATCGAATATTGGGGCATGTTTGGGA-ATTC
1 AACATCAAATATTGGGGCAT-TTTGGGAGATTC
3518771 AACATC
1 AACATC
3518777 CTGATACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 28 0.85
33 5 0.15
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (32 bp):
AACATCAAATATTGGGGCATTTTGGGAGATTC
Found at i:3519633 original size:110 final size:110
Alignment explanation
Indices: 3519435--3519692 Score: 307
Period size: 110 Copynumber: 2.4 Consensus size: 110
3519425 GCTTCCCAGT
*
3519435 TTCAGAGCCAATTTCAACTTCACATCGAGGAATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACATCGAGGAATATTGAACTCAAGACAACACAAGCTCAACTTCA
* *
3519500 CAATGAAGGGGCGACTGATTGTCAACAAATAACTTTTCAGTTTCA
66 CAACGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCA
* *
3519545 TTCAGAGTCAATTTCAACTTCACAGT-GAAGG-ATATTGAACTCGAGACAACACAAGCTCAACTT
1 TTCAGAGCCAATTTCAACTTCACA-TCG-AGGAATATTGAACTCAAGACAACACAAGCTCAACTT
* ** * *
3519608 CACAGCGAAGGGGCGGTTGGCTGTCAACAAATAA-TTTCCCAG-TTC-
64 CACAACGAAGGGGCGACTGACTGTCAACAAATAACTTT-TCAGTTTCA
* * *
3519653 --CAGAGCCAATTTTAACTTCACAACGGAGG-ATATTGGACTC
1 TTCAGAGCCAATTTCAACTTCACATC-GAGGAATATTGAACTC
3519693 GGAACAATAC
Statistics
Matches: 129, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
106 33 0.26
107 1 0.01
109 6 0.05
110 85 0.66
111 4 0.03
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACATCGAGGAATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCA
Found at i:3521051 original size:21 final size:19
Alignment explanation
Indices: 3521027--3521091 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
3521017 ATTTTTTAAT
3521027 TATAATATTTTATTTATTTA
1 TATAATATTTT-TTTATTTA
* *
3521047 CTATATTCCTTTTTTTATTTA
1 -TATAAT-ATTTTTTTATTTA
* *
3521068 TATTATATTATTTTATTATA
1 TATAATATTTTTTTATT-TA
3521088 TATA
1 TATA
3521092 TCTTATATCA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 9 0.26
20 9 0.26
21 13 0.37
22 4 0.11
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TATAATATTTTTTTATTTA
Found at i:3521086 original size:13 final size:14
Alignment explanation
Indices: 3521061--3521135 Score: 55
Period size: 16 Copynumber: 5.1 Consensus size: 14
3521051 ATTCCTTTTT
3521061 TTATTTATATTATA
1 TTATTTATATTATA
3521075 TTATTT-TATTATA
1 TTATTTATATTATA
*
3521088 TATATCTTATATCAT-
1 T-TAT-TTATATTATA
*
3521103 TATATATATATATATA
1 T-TATTTATAT-TATA
*
3521119 TATATATATATATATA
1 T-TATTTATAT-TATA
3521135 T
1 T
3521136 GTATAGATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
13 8 0.15
14 14 0.26
15 9 0.17
16 22 0.42
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:3521091 original size:2 final size:2
Alignment explanation
Indices: 3521084--3521140 Score: 73
Period size: 2 Copynumber: 29.0 Consensus size: 2
3521074 ATTATTTTAT
*
3521084 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
*
3521125 TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA
3521141 GATGTATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
1 2 0.04
2 45 0.92
3 2 0.04
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3521303 original size:19 final size:18
Alignment explanation
Indices: 3521268--3521306 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3521258 TATATATATA
3521268 TTATATTTTTACTTTATT
1 TTATATTTTTACTTTATT
* *
3521286 TTATTTTTTTTCTATTATT
1 TTATATTTTTACT-TTATT
3521305 TT
1 TT
3521307 TTAATATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TTATATTTTTACTTTATT
Found at i:3521581 original size:26 final size:28
Alignment explanation
Indices: 3521519--3521582 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 28
3521509 TTTGTTTATG
*
3521519 TTTATTTATGTTTATTATTTTTTACGTGT
1 TTTATTTAT-TTTATCATTTTTTACGTGT
* *
3521548 TTT-GTTATTTT-TCATTTTTT-CTTGT
1 TTTATTTATTTTATCATTTTTTACGTGT
3521573 TTTATTTATT
1 TTTATTTATT
3521583 ATTCTCACGT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
25 7 0.23
26 13 0.43
27 3 0.10
28 4 0.13
29 3 0.10
ACGTcount: A:0.14, C:0.05, G:0.08, T:0.73
Consensus pattern (28 bp):
TTTATTTATTTTATCATTTTTTACGTGT
Found at i:3524174 original size:3 final size:3
Alignment explanation
Indices: 3524168--3524200 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3524158 TTATAATAGC
3524168 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3524201 TATGATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3524211 original size:3 final size:3
Alignment explanation
Indices: 3524199--3524249 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
3524189 AATAATAATA
*
3524199 ATT ATG ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3524247 ATT
1 ATT
3524250 TTCTTAAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3527079 original size:3 final size:3
Alignment explanation
Indices: 3527073--3527191 Score: 109
Period size: 3 Copynumber: 40.0 Consensus size: 3
3527063 TATTATTATT
* *
3527073 TAA TAA TAA TAA TAA -AA TAA TAA AAA T-A TAA TTAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
* * * * * * *
3527117 T-A TAA TAA TAA TAA TAA TAA TAA TAA TAG TAG TAG TAG TAG TAG TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3527164 TAA TAG TAA TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA
3527192 GGATAATGAG
Statistics
Matches: 103, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
2 6 0.06
3 92 0.89
4 5 0.05
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3527114 original size:29 final size:29
Alignment explanation
Indices: 3527073--3527144 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
3527063 TATTATTATT
3527073 TAATAATAATAATAAAATAATAAAAAT-A
1 TAATAATAATAATAAAATAATAAAAATAA
* * *
3527101 TAATTATTAATAATAATATAATAATAATAA
1 TAA-TAATAATAATAAAATAATAAAAATAA
3527131 TAATAATAATAATA
1 TAATAATAATAATA
3527145 GTAGTAGTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 3 0.08
29 31 0.82
30 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
TAATAATAATAATAAAATAATAAAAATAA
Found at i:3527117 original size:32 final size:33
Alignment explanation
Indices: 3527076--3527137 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
3527066 TATTATTTAA
3527076 TAATAATAATAAAATAATAAAAAT-ATAATTAT
1 TAATAATAATAAAATAATAAAAATAATAATTAT
* *
3527108 TAATAATAATATAATAATAATAATAATAAT
1 TAATAATAATAAAATAATAAAAATAATAAT
3527138 AATAATAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (33 bp):
TAATAATAATAAAATAATAAAAATAATAATTAT
Found at i:3527509 original size:85 final size:85
Alignment explanation
Indices: 3527376--3527552 Score: 234
Period size: 85 Copynumber: 2.1 Consensus size: 85
3527366 TTCTTCTTAG
* *
3527376 TATGAACTCCTGTCTGGAAATGTTGATGCTACTCTATCTCCTTCTGCGATACAGTCGAGCAAAAA
1 TATGAACTCCTGTCTGGAAATGTTGATGCTAC-CTATCTCCTTATGCGATACAGTCAAGCAAAAA
*
3527441 -CTTAAATAAGTTCTTCAGAT
65 GCTTAAATAAGTTCTTCAGAC
* *
3527461 TATGAACTCCTGTCTGGAAATGGATCTGTTGC-A-CTATCTCCTTATGCGATAGAGTCAAGCAAA
1 TATGAACTCCTGTCTGGAAAT-G-T-TGATGCTACCTATCTCCTTATGCGATACAGTCAAGCAAA
* *
3527524 AAGGTTGAATAAGTTCTTCAGAC
63 AAGCTTAAATAAGTTCTTCAGAC
3527547 TATGAA
1 TATGAA
3527553 ATTCTTCTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
85 50 0.62
86 24 0.30
87 2 0.02
88 5 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (85 bp):
TATGAACTCCTGTCTGGAAATGTTGATGCTACCTATCTCCTTATGCGATACAGTCAAGCAAAAAG
CTTAAATAAGTTCTTCAGAC
Found at i:3527725 original size:73 final size:73
Alignment explanation
Indices: 3527605--3527863 Score: 396
Period size: 73 Copynumber: 3.6 Consensus size: 73
3527595 TATCTGGAAA
* * * * *
3527605 TGTTTTAAG-AAAACATTCTCAAGTGAGATAAAATGTTATTTCGAGTGAAACTTTCTCAAGCAAA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCAAGCGAG
3527669 AAAAAGTT
66 AAAAAGTT
* *
3527677 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGGGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCAAGCGAG
*
3527742 AACAAGTT
66 AAAAAGTT
* *
3527750 TGTTTTAAGGAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCTAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCAAGCGAG
3527815 AAAAAGTT
66 AAAAAGTT
* *
3527823 TATTTTAAGAAAAACAATCTCAAGTGAGATAAAAT-TTATTT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTT
3527864 GAAAACATCC
Statistics
Matches: 170, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
72 15 0.09
73 155 0.91
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCAAGCGAG
AAAAAGTT
Found at i:3527861 original size:36 final size:36
Alignment explanation
Indices: 3527607--3527863 Score: 182
Period size: 36 Copynumber: 7.1 Consensus size: 36
3527597 TCTGGAAATG
3527607 TTTTAAG-AAAACATTCTCAAGTGAGATAAAATGTTA
1 TTTTAAGTAAAACATTCTCAAGTGAGATAAAAT-TTA
** * * * * * *
3527643 TTTCGAGTGAAACTTTCTCAAG-CAAAAAAAAGTTTG
1 TTTTAAGTAAAACATTCTCAAGTGAGATAAAA-TTTA
* *
3527679 TTTTAAGAAAAACAATCTCAAGTGAGAT-AAATTGCTA
1 TTTTAAGTAAAACATTCTCAAGTGAGATAAAATT--TA
* * * * * *
3527716 TTTCAAGTGAAACTTTCTCAAGGGAGA-ACAAGTTTG
1 TTTTAAGTAAAACATTCTCAAGTGAGATA-AAATTTA
* * *
3527752 TTTTAAGGAAAACAATCTCAAGTGAGATAAATTGTTA
1 TTTTAAGTAAAACATTCTCAAGTGAGATAAAAT-TTA
* * * * *
3527789 TTTCAAGTGAAACTTTCTCTAGCGAGA-AAAAGTTTA
1 TTTTAAGTAAAACATTCTCAAGTGAGATAAAA-TTTA
* *
3527825 TTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTA
1 TTTTAAGTAAAACATTCTCAAGTGAGATAAAATTTA
3527861 TTT
1 TTT
3527864 GAAAACATCC
Statistics
Matches: 161, Mismatches: 49, Indels: 22
0.69 0.21 0.09
Matches are distributed among these distances:
35 2 0.01
36 90 0.56
37 65 0.40
38 4 0.02
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (36 bp):
TTTTAAGTAAAACATTCTCAAGTGAGATAAAATTTA
Found at i:3528158 original size:177 final size:176
Alignment explanation
Indices: 3527852--3528268 Score: 665
Period size: 177 Copynumber: 2.4 Consensus size: 176
3527842 TCAAGTGAGA
* *
3527852 TAAAATTTATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATCA
1 TAAAATTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATCA
*
3527917 AGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCATTTGTTAGGCTTAGCTTCCTTT
66 AGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCATTTGTTAGGCTTAGATTCCTTT
* * * *
3527982 AACAGCTCTTTTGAGATAATTAGTAGACCCCCGAAGGCTTGATTTC
131 AACAGATCTTTTAAGATAATTAGTAAACCCCCAAAGGCTTGATTTC
* *
3528028 TAAAATATCATTTGAAAACATCCTGCACTGAAGCTCTTATGGATGGCCCATAGGACTTACAAATC
1 TAAAAT-TCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
3528093 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAATCCC-TTTGTTAGGCTTAGATTCCT
65 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAA-CCCATTTGTTAGGCTTAGATTCCT
* * * *
3528157 TTAACATATCTTTTAAGGTAATTAGTAAACCCCTAAAGGCTTGGTTTC
129 TTAACAGATCTTTTAAGATAATTAGTAAACCCCCAAAGGCTTGATTTC
* *
3528205 TAAAATCTCATTTGAAAACATCATGCACTGAAGGTATTATGGATGGCCCGTAGGACTTACAAAT
1 TAAAAT-TCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
3528269 TTGGGAAATA
Statistics
Matches: 221, Mismatches: 18, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
176 6 0.03
177 212 0.96
178 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (176 bp):
TAAAATTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATCA
AGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCATTTGTTAGGCTTAGATTCCTTT
AACAGATCTTTTAAGATAATTAGTAAACCCCCAAAGGCTTGATTTC
Found at i:3529374 original size:54 final size:54
Alignment explanation
Indices: 3529274--3529378 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
3529264 CAATGGTTCA
* **
3529274 TAAAACATTTGACAACATATTCATCATTTCCTATGGCTTCTACCCAGATTTTCG
1 TAAAACATTTGACAACACATTCATCATTTCCTATGAATTCTACCCAGATTTTCG
* * * *
3529328 TAAAACATTTGACAACACATTCATCCTTTCTTGTGAATTCTTCCCAGATTT
1 TAAAACATTTGACAACACATTCATCATTTCCTATGAATTCTACCCAGATTT
3529379 CTTGTCAGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.38
Consensus pattern (54 bp):
TAAAACATTTGACAACACATTCATCATTTCCTATGAATTCTACCCAGATTTTCG
Found at i:3529979 original size:51 final size:51
Alignment explanation
Indices: 3529850--3530049 Score: 276
Period size: 51 Copynumber: 3.9 Consensus size: 51
3529840 ATATCCCAAC
* * *
3529850 CTTTTCATGCTGGTGTGAGCCTTCAAGATGCCCCACATGGATTACTTCTGTAT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATGCCCCAGATGGATTAC-T-TATAT
* * *
3529903 -TTTTCATTCTGATGCGAGCCTTCAAGATACCCCAGATGGATTACTTATAT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATGCCCCAGATGGATTACTTATAT
* * * *
3529953 CTTTTCATGCTAATGTGAGCCTTCAAGATGCCCCAAATAGATTACTTCTAT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATGCCCCAGATGGATTACTTATAT
*
3530004 CTTTTCATGCTGATGTGAGCTTTCAAGATGCCCCAGATGGATTACT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATGCCCCAGATGGATTACT
3530050 ACTATGTTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
50 4 0.03
51 86 0.67
52 39 0.30
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (51 bp):
CTTTTCATGCTGATGTGAGCCTTCAAGATGCCCCAGATGGATTACTTATAT
Found at i:3533481 original size:7 final size:7
Alignment explanation
Indices: 3533469--3533516 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
3533459 AAAATGTATG
3533469 AAAAAAT
1 AAAAAAT
3533476 AAAAAAT
1 AAAAAAT
3533483 AAAAAAT
1 AAAAAAT
*
3533490 AAATAAAA
1 AAA-AAAT
*
3533498 AAAATAAG
1 AAAA-AAT
3533506 AAAAAAT
1 AAAAAAT
3533513 AAAA
1 AAAA
3533517 TAGTTAGTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
7 24 0.67
8 12 0.33
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:3537659 original size:2 final size:2
Alignment explanation
Indices: 3537652--3537690 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3537642 ACTGGATTTA
*
3537652 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3537691 GGACTTTAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3539239 original size:25 final size:25
Alignment explanation
Indices: 3539211--3539258 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3539201 GGGATGAAAC
*
3539211 TTTATTTGAAAG-AAAGCCTAGTAAT
1 TTTACTTGAAAGTAAA-CCTAGTAAT
*
3539236 TTTACTTGGAAGTAAACCTAGTA
1 TTTACTTGAAAGTAAACCTAGTA
3539259 TATGTAAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (25 bp):
TTTACTTGAAAGTAAACCTAGTAAT
Found at i:3545089 original size:20 final size:20
Alignment explanation
Indices: 3545016--3545089 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
3545006 AAACTAGTCC
**
3545016 GAGTCAACTTGAACCAGAC-T
1 GAGTCAACTCAAACC-GACAT
* * *
3545036 GAGTCACCTCAAACCAAGAT
1 GAGTCAACTCAAACCGACAT
3545056 GAGTCAA-TGCAAACCGACAT
1 GAGTCAACT-CAAACCGACAT
*
3545076 GAGTCAACTTAAAC
1 GAGTCAACTCAAAC
3545090 TGGTATGACC
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
19 2 0.05
20 39 0.93
21 1 0.02
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.18
Consensus pattern (20 bp):
GAGTCAACTCAAACCGACAT
Found at i:3545168 original size:29 final size:23
Alignment explanation
Indices: 3545126--3545190 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
3545116 ACTATTGACC
*
3545126 TGACTAGCGTTGACTTTGACCTT
1 TGACTAACGTTGACTTTGACCTT
3545149 TGACTAACGTTGACTTTGACCTT
1 TGACTAACGTTGACTTTGACCTT
3545172 TGACTAACGTTGACTTTGA
1 TGACTAACGTTGACTTTGA
3545191 ATTTGACCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (23 bp):
TGACTAACGTTGACTTTGACCTT
Found at i:3545195 original size:29 final size:27
Alignment explanation
Indices: 3545135--3545198 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 27
3545125 CTGACTAGCG
3545135 TTGACTTTGACCTTTGACTAACGTTGAC
1 TTGA-TTTGACCTTTGACTAACGTTGAC
3545163 ----TTTGACCTTTGACTAACGTTGAC
1 TTGATTTGACCTTTGACTAACGTTGAC
3545186 TTTGAATTTGACC
1 -TTG-ATTTGACC
3545199 AAAAAGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
23 23 0.77
29 7 0.23
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (27 bp):
TTGATTTGACCTTTGACTAACGTTGAC
Found at i:3546929 original size:21 final size:23
Alignment explanation
Indices: 3546879--3546929 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
3546869 ATGTAGTATA
* *
3546879 TATGATTATTGATTTCTAATATT
1 TATGTTTATTGATTTCTAAGATT
*
3546902 AATGTTTATTG-TTT-TAAGATT
1 TATGTTTATTGATTTCTAAGATT
3546923 TATGTTT
1 TATGTTT
3546930 TATGGGCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 12 0.50
22 3 0.12
23 9 0.38
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (23 bp):
TATGTTTATTGATTTCTAAGATT
Found at i:3550642 original size:27 final size:27
Alignment explanation
Indices: 3550612--3550674 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3550602 GAAAGGATTG
**
3550612 AAATACCCCTAAACTCTAAAATG-ACT
1 AAATACCCCTAAACAATAAAATGAACT
* *
3550638 AAAATACCCTTAAACAATAGAATGAACT
1 -AAATACCCCTAAACAATAAAATGAACT
3550666 AAATACCCC
1 AAATACCCC
3550675 GAGCTCCTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.49, C:0.25, G:0.05, T:0.21
Consensus pattern (27 bp):
AAATACCCCTAAACAATAAAATGAACT
Found at i:3554745 original size:2 final size:2
Alignment explanation
Indices: 3554736--3554808 Score: 121
Period size: 2 Copynumber: 37.0 Consensus size: 2
3554726 CATTTAAAAA
3554736 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
3554777 AT AT AT AT AT AT AT TT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3554809 CAAATTCTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3555507 original size:13 final size:13
Alignment explanation
Indices: 3555465--3555501 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
3555455 ATATGACGCG
3555465 CATTTATGACACA
1 CATTTATGACACA
3555478 CATTTATGACACA
1 CATTTATGACACA
3555491 CATTTATGACA
1 CATTTATGACA
3555502 TGCATTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (13 bp):
CATTTATGACACA
Found at i:3555577 original size:30 final size:30
Alignment explanation
Indices: 3555541--3555609 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
3555531 GAAGCCCCCG
*
3555541 TCATAAATTAAGATGACATACATTTGTGCA
1 TCATAAATTAAGATGACACACATTTGTGCA
* *
3555571 TCATAAATTAAGATGACACATATTTGTGCG
1 TCATAAATTAAGATGACACACATTTGTGCA
3555601 TCATAAATT
1 TCATAAATT
3555610 TATGACATGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (30 bp):
TCATAAATTAAGATGACACACATTTGTGCA
Found at i:3555799 original size:2 final size:2
Alignment explanation
Indices: 3555792--3555828 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3555782 TTTCGTAAAT
3555792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3555829 TGTAGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3558154 original size:18 final size:18
Alignment explanation
Indices: 3558131--3558175 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
3558121 AACTCTTAGC
3558131 CTTGTCCTCATTTGTGCT
1 CTTGTCCTCATTTGTGCT
3558149 CTTGTCCTCATTTGTGCT
1 CTTGTCCTCATTTGTGCT
3558167 CTTGTCCTC
1 CTTGTCCTC
3558176 CTCCTTTGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.04, C:0.31, G:0.16, T:0.49
Consensus pattern (18 bp):
CTTGTCCTCATTTGTGCT
Found at i:3562149 original size:15 final size:15
Alignment explanation
Indices: 3562124--3562164 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3562114 CATGCTTTCT
*
3562124 TTTTCCTTCTTTTACA
1 TTTT-CTTCTTTGACA
*
3562140 TTTTCTTCTTTGACG
1 TTTTCTTCTTTGACA
3562155 TTTTCTTCTT
1 TTTTCTTCTT
3562165 AGATGTTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.07, C:0.22, G:0.05, T:0.66
Consensus pattern (15 bp):
TTTTCTTCTTTGACA
Found at i:3585806 original size:22 final size:23
Alignment explanation
Indices: 3585781--3585831 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
3585771 AACCTACCCG
3585781 TTTCCCATTTCTGCCT-TTCCCA
1 TTTCCCATTTCTGCCTCTTCCCA
* * * *
3585803 TTTCTCATTTTTGCGTCTTCCCC
1 TTTCCCATTTCTGCCTCTTCCCA
3585826 TTTCCC
1 TTTCCC
3585832 CATTCTTTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.06, C:0.39, G:0.06, T:0.49
Consensus pattern (23 bp):
TTTCCCATTTCTGCCTCTTCCCA
Found at i:3587162 original size:31 final size:31
Alignment explanation
Indices: 3587119--3587195 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
3587109 AGAAAAACTT
* *
3587119 TAAACTTTGTGACGGAACATGTGAACCTGTCA
1 TAAA-TTTGTGACGGAACATGTAAACCTATCA
* *
3587151 TAAATTTGTGACGGAATATGTAAATCTATCA
1 TAAATTTGTGACGGAACATGTAAACCTATCA
* *
3587182 GAAATTTATGACGG
1 TAAATTTGTGACGG
3587196 GTCTATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 35 0.90
32 4 0.10
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (31 bp):
TAAATTTGTGACGGAACATGTAAACCTATCA
Found at i:3590189 original size:17 final size:16
Alignment explanation
Indices: 3590158--3590191 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3590148 CACGTGAGGA
3590158 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
3590174 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
3590191 T
1 T
3590192 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:3595191 original size:219 final size:219
Alignment explanation
Indices: 3594813--3595250 Score: 844
Period size: 219 Copynumber: 2.0 Consensus size: 219
3594803 CATGATGAGA
3594813 AAATTTTATATGCCGCGGCAATCCCGTGGTACGCTTGACCTTGTTAATTTTTGTTAGTGGAATTG
1 AAATTTTATATGCCGCGGCAATCCCGTGGTACGCTTGACCTTGTTAATTTTTGTTAGTGGAATTG
3594878 TGCCTTTTGATTTGAATATTCAGGCTAAAAAGAAGTTCAAGCACGATGCAAGGCACTATTTTTGG
66 TGCCTTTTGATTTGAATATTCAGGCTAAAAAGAAGTTCAAGCACGATGCAAGGCACTATTTTTGG
3594943 GATGAGCCATATCTGTTCAAACATTATGCCAATCAGCTCATTAGACGATGTGTACCCGAAGAGGA
131 GATGAGCCATATCTGTTCAAACATTATGCCAATCAGCTCATTAGACGATGTGTACCCGAAGAGGA
3595008 GCAAAGTGATA-TTTATACCATTG
196 GCAAAGTGATATTTTATACCATTG
3595031 AAATTTTATATGCCGCGGCAATCCCGTGGTACGC-TGACCTTGTTAATTTTCTTGTTAGTGGAAT
1 AAATTTTATATGCCGCGGCAATCCCGTGGTACGCTTGACCTTGTTAA-TTT-TTGTTAGTGGAAT
3595095 TGTGCCTTTTGATTTGAATATTCAGGCTAAAAAGAAGTTCAAGCACGATGCAAGGCACTATTTTT
64 TGTGCCTTTTGATTTGAATATTCAGGCTAAAAAGAAGTTCAAGCACGATGCAAGGCACTATTTTT
3595160 GGGATGAGCCATATCTGTTCAAACATTATGCCAATCAGCTCATTAGACGATGTGTACCCGAAGAG
129 GGGATGAGCCATATCTGTTCAAACATTATGCCAATCAGCTCATTAGACGATGTGTACCCGAAGAG
3595225 GAGCAAAGTGATATTTTATACCATTG
194 GAGCAAAGTGATATTTTATACCATTG
3595251 TCATTCGGCC
Statistics
Matches: 217, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
217 12 0.06
218 37 0.17
219 156 0.72
220 12 0.06
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (219 bp):
AAATTTTATATGCCGCGGCAATCCCGTGGTACGCTTGACCTTGTTAATTTTTGTTAGTGGAATTG
TGCCTTTTGATTTGAATATTCAGGCTAAAAAGAAGTTCAAGCACGATGCAAGGCACTATTTTTGG
GATGAGCCATATCTGTTCAAACATTATGCCAATCAGCTCATTAGACGATGTGTACCCGAAGAGGA
GCAAAGTGATATTTTATACCATTG
Found at i:3596775 original size:20 final size:20
Alignment explanation
Indices: 3596733--3596776 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3596723 TTCTTTTATC
* *
3596733 TTTCATTATTAATTTTTCTT
1 TTTCATTATTAATTTTACCT
3596753 TTTCATT-TTAACTTTTACCT
1 TTTCATTATTAA-TTTTACCT
3596773 TTTC
1 TTTC
3596777 TCTTTCTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTCATTATTAATTTTACCT
Found at i:3598939 original size:12 final size:13
Alignment explanation
Indices: 3598916--3598944 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3598906 TAACAGTTAA
3598916 AAAAAATAAAAAT
1 AAAAAATAAAAAT
3598929 AAAAAAT-AAAAT
1 AAAAAATAAAAAT
3598941 AAAA
1 AAAA
3598945 TATCAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:3603811 original size:27 final size:27
Alignment explanation
Indices: 3603773--3603833 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
3603763 AATATTTTAT
* * *
3603773 AATGATATGTG-ACAATGTTCTACGTGA
1 AATGTTATGTGAAC-ATGTGCTAAGTGA
3603800 AATGTTATGTGAACATGTGCTAAGTGA
1 AATGTTATGTGAACATGTGCTAAGTGA
3603827 ATATGTT
1 A-ATGTT
3603834 CTATGGAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (27 bp):
AATGTTATGTGAACATGTGCTAAGTGA
Found at i:3604083 original size:23 final size:23
Alignment explanation
Indices: 3604049--3604170 Score: 140
Period size: 23 Copynumber: 5.3 Consensus size: 23
3604039 GTCAAGGGTT
3604049 CTATGTGGTCCTTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
* *
3604072 CTATGTGCTCCTTCGGGACAAAAT
1 CTATGTGGTCCTTCGGGAC-AAAC
* * *
3604096 TTATTTGGTCCTTCGAGACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
* *
3604119 CTATGTGGTCCTTCAGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAC
* *
3604142 CTATGTAGTCCTTCAGGACAAA-
1 CTATGTGGTCCTTCGGGACAAAC
3604164 -TATGTGG
1 CTATGTGG
3604171 CACTTATGTG
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
21 6 0.07
23 60 0.71
24 18 0.21
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAC
Found at i:3615185 original size:43 final size:43
Alignment explanation
Indices: 3615124--3615434 Score: 432
Period size: 43 Copynumber: 7.3 Consensus size: 43
3615114 TTAATTACCG
* *
3615124 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTCTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
3615167 TTACAGTTCTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * **
3615210 TTACAGTTTTCCCAAGTTTCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
3615253 TTACAGTT-TCCCAGGTTCTTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTCTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
3615295 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
3615338 TTATAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * * *
3615381 TTACAGCTTC-CCAAGAT-CTTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAG-TTCTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
3615423 TTACAGTT-TCCC
1 TTACAGTTCTCCC
3615435 CAGGCTCTTT
Statistics
Matches: 243, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
41 4 0.02
42 67 0.28
43 169 0.70
44 3 0.01
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.33
Consensus pattern (43 bp):
TTACAGTTCTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:3615318 original size:85 final size:86
Alignment explanation
Indices: 3615124--3615457 Score: 451
Period size: 85 Copynumber: 3.9 Consensus size: 86
3615114 TTAATTACCG
* *
3615124 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTCTCCCAGGTCCCTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCTCCCAGGTTCCTT
3615189 TGCTGTGTGCAAGGGTAAGCC
66 TGCTGTGTGCAAGGGTAAGCC
** * ** *
3615210 TTACAGTTTTCCCAAGTTTCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-TCCCAGGTTCTTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCTCCCAGGTTCCTT
*
3615274 TGTTGTGTGCAAGGGTAAGCC
66 TGCTGTGTGCAAGGGTAAGCC
* *
3615295 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTCCCCCAGGTTCCTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCTCCCAGGTTCCTT
3615360 TGCTGTGTGCAAGGGTAAGCC
66 TGCTGTGTGCAAGGGTAAGCC
* * * * * *
3615381 TTACAGCTT-CCCAAGAT-CTTTTGTTGTGTGCAAGGGTAAGCCTTACAGTT-TCCCCAGGCTCT
1 TTACAG-TTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCT-CCCAGGTTCC
* *
3615443 TTTCCTATGTGCAAG
64 TTTGCTGTGTGCAAG
3615458 TATAAGACCT
Statistics
Matches: 217, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
85 127 0.59
86 88 0.41
87 2 0.01
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.33
Consensus pattern (86 bp):
TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCTCCCAGGTTCCTT
TGCTGTGTGCAAGGGTAAGCC
Found at i:3615362 original size:128 final size:128
Alignment explanation
Indices: 3615124--3615438 Score: 504
Period size: 128 Copynumber: 2.5 Consensus size: 128
3615114 TTAATTACCG
* * * *
3615124 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTCTCCCAGGTCCCTT
1 TTACAGTT-TCCCAGGTTCTTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTT
** *
3615189 TGCTGTGTGCAAGGGTAAGCCTTACAGTTTTCCCAAGTTTCTTTGCTGTGTGCAAGGGTAAGCC
65 TGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAAGTTCCTTTGCTGTGTGCAAGGGTAAGCC
3615253 TTACAGTTTCCCAGGTTCTTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTT
1 TTACAGTTTCCCAGGTTCTTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTT
* *
3615318 GCTGTGTGCAAGGGTAAGCCTTATAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
66 GCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAAGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * * *
3615381 TTACAGCTTCCCAAGATCTTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGG
1 TTACAGTTTCCCAGGTTCTTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGG
3615439 CTCTTTTCCT
Statistics
Matches: 173, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
128 165 0.95
129 8 0.05
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (128 bp):
TTACAGTTTCCCAGGTTCTTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTT
GCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAAGTTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:3622825 original size:27 final size:27
Alignment explanation
Indices: 3622795--3622946 Score: 173
Period size: 27 Copynumber: 5.6 Consensus size: 27
3622785 TCCAAAGATT
3622795 GAATACTATGCATCACCCCGAAGGATG
1 GAATACTATGCATCACCCCGAAGGATG
***
3622822 GAATACTATGCATCACATTGAAAGG-TG
1 GAATACTATGCATCACCCCG-AAGGATG
*
3622849 GAATACTATGCATCACCCCGAAGGATA
1 GAATACTATGCATCACCCCGAAGGATG
** * * **
3622876 GCGTATTATGCACCACCTTGAAAGG-TG
1 GAATACTATGCATCACCCCG-AAGGATG
3622903 GAATACTATGCATCACCCCGAAGGATG
1 GAATACTATGCATCACCCCGAAGGATG
*
3622930 GAAAACTATGCATCACC
1 GAATACTATGCATCACC
3622947 TTGAAATGTG
Statistics
Matches: 100, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
26 8 0.08
27 84 0.84
28 8 0.08
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (27 bp):
GAATACTATGCATCACCCCGAAGGATG
Found at i:3622853 original size:54 final size:54
Alignment explanation
Indices: 3622795--3622959 Score: 258
Period size: 54 Copynumber: 3.1 Consensus size: 54
3622785 TCCAAAGATT
*
3622795 GAATACTATGCATCACCCCGAAGGATGGAATACTATGCATCACATTGAAAGGTG
1 GAATACTATGCATCACCCCGAAGGATGGAATACTATGCATCACCTTGAAAGGTG
* ** * *
3622849 GAATACTATGCATCACCCCGAAGGATAGCGTATTATGCACCACCTTGAAAGGTG
1 GAATACTATGCATCACCCCGAAGGATGGAATACTATGCATCACCTTGAAAGGTG
* *
3622903 GAATACTATGCATCACCCCGAAGGATGGAAAACTATGCATCACCTTGAAATGTG
1 GAATACTATGCATCACCCCGAAGGATGGAATACTATGCATCACCTTGAAAGGTG
3622957 GAA
1 GAA
3622960 CTTTGCATCT
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 98 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (54 bp):
GAATACTATGCATCACCCCGAAGGATGGAATACTATGCATCACCTTGAAAGGTG
Found at i:3634180 original size:18 final size:18
Alignment explanation
Indices: 3634157--3634192 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3634147 GCGATGGCAT
*
3634157 CATCATATATGGCTGCGG
1 CATCATAAATGGCTGCGG
3634175 CATCATAAATGGCTGCGG
1 CATCATAAATGGCTGCGG
3634193 TGGCTGCTGT
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:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (18 bp):
CATCATAAATGGCTGCGG
Found at i:3635903 original size:18 final size:17
Alignment explanation
Indices: 3635871--3635904 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3635861 AATTATATTA
*
3635871 GTAAAATATTAAATAAC
1 GTAAAATACTAAATAAC
3635888 GTAAAATACCTAAATAA
1 GTAAAATA-CTAAATAA
3635905 ATTAAATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (17 bp):
GTAAAATACTAAATAAC
Found at i:3637010 original size:2 final size:2
Alignment explanation
Indices: 3637003--3637068 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
3636993 AACATTTACG
3637003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3637045 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
3637069 GTTTACTATT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.