Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_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: 4978262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 24
Found at i:3870897 original size:23 final size:23
Alignment explanation
Indices: 3870867--3870927 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
3870857 ATATTTTATA
* *
3870867 TATATTAACTTAAAAATGTTTTT
1 TATATTAACTTAAAAATATATTT
*
3870890 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA-AAAATATATTT
3870914 TATTATTAACTTAA
1 TA-TATTAACTTAA
3870928 TTTAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 12 0.38
24 10 0.31
25 10 0.31
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (23 bp):
TATATTAACTTAAAAATATATTT
Found at i:3871636 original size:2 final size:2
Alignment explanation
Indices: 3871629--3871667 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3871619 AAAAATCTAG
3871629 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3871668 GTATCAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3878750 original size:55 final size:55
Alignment explanation
Indices: 3878685--3878796 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
3878675 CACATCACTC
3878685 ATATAACATACATAGCATATCGTGTAACGTTCTCATAAAAACACATATGAGTCAT
1 ATATAACATACATAGCATATCGTGTAACGTTCTCATAAAAACACATATGAGTCAT
*
3878740 ATATAACATACATAGCATATCGTGTAACGTTCTCATAGAAACACATATGAGTCAT
1 ATATAACATACATAGCATATCGTGTAACGTTCTCATAAAAACACATATGAGTCAT
3878795 AT
1 AT
3878797 CACTTTCACA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (55 bp):
ATATAACATACATAGCATATCGTGTAACGTTCTCATAAAAACACATATGAGTCAT
Found at i:3879371 original size:63 final size:64
Alignment explanation
Indices: 3879298--3879419 Score: 160
Period size: 63 Copynumber: 1.9 Consensus size: 64
3879288 CACCACACCC
* *
3879298 TGCATCGATGCAT-AAAT-CCTATTCGATGTTTACA-TTTAAGAGAGTGCATCGATGCACTAATT
1 TGCATCGATGC-TCAAATGCC-ATTCGATGTTTACATTTTAAAAGAGTACATCGATGCACTAATT
3879360 G
64 G
** *
3879361 TGCATCGATGCTCTGATGGCATTCGATGTTTACATTTTAAAAGAGTACATCGATGCACT
1 TGCATCGATGCTCAAATGCCATTCGATGTTTACATTTTAAAAGAGTACATCGATGCACT
3879420 TCAGGTGCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
62 1 0.02
63 27 0.53
64 23 0.45
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
TGCATCGATGCTCAAATGCCATTCGATGTTTACATTTTAAAAGAGTACATCGATGCACTAATTG
Found at i:3880320 original size:21 final size:21
Alignment explanation
Indices: 3880295--3880346 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
3880285 CCGTTGATCA
3880295 GGGGGAATCGATACCCCATTG
1 GGGGGAATCGATACCCCATTG
*
3880316 GGGGGAATCGATACCCCCTTG
1 GGGGGAATCGATACCCCATTG
3880337 GGGGGAATCG
1 GGGGGAATCG
3880347 GTTCCCTCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.38, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGATACCCCATTG
Found at i:3881761 original size:19 final size:20
Alignment explanation
Indices: 3881718--3881765 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3881708 CTAAATCATT
*
3881718 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
3881738 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
3881757 TTTTCAAAA
1 TTTTCAAAA
3881766 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:3883920 original size:17 final size:17
Alignment explanation
Indices: 3883898--3883939 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
3883888 AGTATTAAAT
3883898 TAAAGTTGTAACAAGGG
1 TAAAGTTGTAACAAGGG
3883915 TAAAGTTGTAACAAGGG
1 TAAAGTTGTAACAAGGG
*
3883932 AAAAGTTG
1 TAAAGTTG
3883940 AGGACTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (17 bp):
TAAAGTTGTAACAAGGG
Found at i:3885696 original size:26 final size:26
Alignment explanation
Indices: 3885677--3885739 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
3885667 CAAGCCCTGG
3885677 AATAAATAAATACCCTCAAGCTCCGA
1 AATAAATAAATACCCTCAAGCTCCGA
* *
3885703 AATAACTAAATACCCTCAAGCACCGA
1 AATAAATAAATACCCTCAAGCTCCGA
*
3885729 AATGAATAAAT
1 AATAAATAAAT
3885740 TAACCTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.49, C:0.24, G:0.08, T:0.19
Consensus pattern (26 bp):
AATAAATAAATACCCTCAAGCTCCGA
Found at i:3891115 original size:2 final size:2
Alignment explanation
Indices: 3891108--3891160 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3891098 ATCAATCAAC
3891108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3891150 TA TA TA TA TA T
1 TA TA TA TA TA T
3891161 GGCCACAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3891192 original size:20 final size:21
Alignment explanation
Indices: 3891167--3891213 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
3891157 ATATGGCCAC
*
3891167 AATTATTAA-ACAGAATATGT
1 AATTATTAATACACAATATGT
*
3891187 AATTATTAATACACAATATAT
1 AATTATTAATACACAATATGT
3891208 -ATTATT
1 AATTATT
3891214 TATATATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (21 bp):
AATTATTAATACACAATATGT
Found at i:3892411 original size:16 final size:17
Alignment explanation
Indices: 3892377--3892422 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
3892367 AATTATTTTT
3892377 TATTA-ATTGTTATTTAA
1 TATTATATT-TTATTTAA
3892394 TATTATATTTTA-TTAA
1 TATTATATTTTATTTAA
*
3892410 TATATTTATTTTA
1 TAT-TATATTTTA
3892423 AGTTAACAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 7 0.27
17 16 0.62
18 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATTATATTTTATTTAA
Found at i:3894223 original size:20 final size:20
Alignment explanation
Indices: 3894187--3894224 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3894177 AAGAAAACTA
*
3894187 AAAAAAATATGAGAAAAAGG
1 AAAAAAATATGAAAAAAAGG
3894207 AAAAAAATGA-GAAAAAAA
1 AAAAAAAT-ATGAAAAAAA
3894225 TCCAGAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (20 bp):
AAAAAAATATGAAAAAAAGG
Found at i:3896255 original size:20 final size:20
Alignment explanation
Indices: 3896230--3896279 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
3896220 ACCATTTTTC
*
3896230 GTATCGGTACCAAGAGTAGA
1 GTATCGATACCAAGAGTAGA
*
3896250 GTATCGATACCAAGGGTAGA
1 GTATCGATACCAAGAGTAGA
3896270 GTATCGATAC
1 GTATCGATAC
3896280 TCCCTAGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (20 bp):
GTATCGATACCAAGAGTAGA
Found at i:3897882 original size:54 final size:54
Alignment explanation
Indices: 3897824--3897926 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
3897814 CGAAATGGAA
* *
3897824 ATTCACAAACTCATTATGAAT-TCCATGTATTGCACACATAGTGTCGAAATAATT
1 ATTCACAAACACATTATGAATAT-CATGGATTGCACACATAGTGTCGAAATAATT
* * **
3897878 ATTCATAAACACATTATGAATATCATGGGTTGCACATTTAGTGTCGAAA
1 ATTCACAAACACATTATGAATATCATGGATTGCACACATAGTGTCGAAA
3897927 ATACACCGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 41 0.98
55 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.33
Consensus pattern (54 bp):
ATTCACAAACACATTATGAATATCATGGATTGCACACATAGTGTCGAAATAATT
Found at i:3899285 original size:21 final size:21
Alignment explanation
Indices: 3899260--3899309 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
3899250 CTTTTTCCCA
*
3899260 ATTTATTTCTTGTACTTTACC
1 ATTTATTCCTTGTACTTTACC
3899281 ATTTATTCCTTGTACTTTACC
1 ATTTATTCCTTGTACTTTACC
3899302 ATTTATTC
1 ATTTATTC
3899310 AATTTAATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.56
Consensus pattern (21 bp):
ATTTATTCCTTGTACTTTACC
Found at i:3899717 original size:21 final size:20
Alignment explanation
Indices: 3899692--3899740 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
3899682 CATGAAACAT
3899692 CAAAAACATAA-AAACTTAAAA
1 CAAAAACATAACAAAC--AAAA
3899713 CAAAAACA-AACAAACAAAA
1 CAAAAACATAACAAACAAAA
*
3899732 CTAAAACAT
1 CAAAAACAT
3899741 GAGAAAGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 11 0.44
20 2 0.08
21 12 0.48
ACGTcount: A:0.71, C:0.18, G:0.00, T:0.10
Consensus pattern (20 bp):
CAAAAACATAACAAACAAAA
Found at i:3902800 original size:202 final size:202
Alignment explanation
Indices: 3902403--3902806 Score: 792
Period size: 202 Copynumber: 2.0 Consensus size: 202
3902393 ATAAATAATG
3902403 AATAGTTTAATTCTTACCACAATCCCTCTAACTTTGAAGTGTAATTCATTTTGCTCACTCATTGT
1 AATAGTTTAATTCTTACCACAATCCCTCTAACTTTGAAGTGTAATTCATTTTGCTCACTCATTGT
3902468 AAATTTACCCTGTAATATCGAATCAATTCAATTTAGTCCAATCTATTTTTGTAATTTTGCAATTT
66 AAATTTACCCTGTAATATCGAATCAATTCAATTTAGTCCAATCTATTTTTGTAATTTTGCAATTT
3902533 AACCCCACAACCTTGCTTTTCTCCTTGTAGCTTTCAATTAATTCAATTTGGTCCTCGATTTTTTA
131 AACCCCACAACCTTGCTTTTCTCCTTGTAGCTTTCAATTAATTCAATTTGGTCCTCGATTTTTTA
3902598 TTCTTTC
196 TTCTTTC
3902605 AATAGTTTAATTCTTACCACAATCCCTCTAACTTTGAAGTGTAATTCATTTTGCTCACTCATTGT
1 AATAGTTTAATTCTTACCACAATCCCTCTAACTTTGAAGTGTAATTCATTTTGCTCACTCATTGT
3902670 AAATTTACCCTGTAATATCGAATCAATTCAATTTAGTCCAATCTATTTTTGTAATTTTGCAATTT
66 AAATTTACCCTGTAATATCGAATCAATTCAATTTAGTCCAATCTATTTTTGTAATTTTGCAATTT
3902735 AACCCCACAACCTTTGCTTTTCTCCTTGTAGCTTTCAATTAATTCAATTTGGTCCTCGA-TTTTT
131 AACCCCACAACC-TTGCTTTTCTCCTTGTAGCTTTCAATTAATTCAATTTGGTCCTCGATTTTTT
3902799 ATTCTTTC
195 ATTCTTTC
3902807 TAATTTTAAG
Statistics
Matches: 201, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
202 155 0.77
203 46 0.23
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.44
Consensus pattern (202 bp):
AATAGTTTAATTCTTACCACAATCCCTCTAACTTTGAAGTGTAATTCATTTTGCTCACTCATTGT
AAATTTACCCTGTAATATCGAATCAATTCAATTTAGTCCAATCTATTTTTGTAATTTTGCAATTT
AACCCCACAACCTTGCTTTTCTCCTTGTAGCTTTCAATTAATTCAATTTGGTCCTCGATTTTTTA
TTCTTTC
Found at i:3903959 original size:15 final size:16
Alignment explanation
Indices: 3903923--3903963 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3903913 AAATTGGGAA
*
3903923 TTAGGGA-TTTATATT
1 TTAGGGATTTTATAAT
*
3903938 TTGGGGATTTTA-AAT
1 TTAGGGATTTTATAAT
3903953 TTAGGGATTTT
1 TTAGGGATTTT
3903964 GGGTGACGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (16 bp):
TTAGGGATTTTATAAT
Found at i:3904322 original size:3 final size:3
Alignment explanation
Indices: 3904314--3904347 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3904304 AGCATTATCT
3904314 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3904348 AAAACTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3922138 original size:29 final size:30
Alignment explanation
Indices: 3922096--3922169 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
3922086 GTCAACCATT
* *
3922096 TTACAAAAATAGCACCCT-TTTTAAATTAA
1 TTACTAAAATAGCACCCTATTTCAAATTAA
*
3922125 TTACTAAAATAGCA-CCTATTTCGAATTAA
1 TTACTAAAATAGCACCCTATTTCAAATTAA
3922154 TTACTAAAATAGCACC
1 TTACTAAAATAGCACC
3922170 TCAGTCAACG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 3 0.08
29 36 0.90
30 1 0.03
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.32
Consensus pattern (30 bp):
TTACTAAAATAGCACCCTATTTCAAATTAA
Found at i:3932520 original size:15 final size:15
Alignment explanation
Indices: 3932488--3932525 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3932478 GAAACTTTAA
3932488 TTATAATATTTTTATT
1 TTATAA-ATTTTTATT
3932504 TTATAAATTGTTT-TT
1 TTATAAATT-TTTATT
3932519 TTATAAA
1 TTATAAA
3932526 GAATCAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TTATAAATTTTTATT
Found at i:3932549 original size:3 final size:3
Alignment explanation
Indices: 3932543--3932567 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3932533 GGTGTAGTAG
3932543 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
3932568 TTGATTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3933542 original size:36 final size:35
Alignment explanation
Indices: 3933491--3933561 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
3933481 AACATCTACC
*
3933491 AAACTTTACCAAACTTTGAAAAATATTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
3933526 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAAG
3933562 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:3933560 original size:21 final size:21
Alignment explanation
Indices: 3933500--3933560 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
3933490 CAAACTTTAC
*
3933500 CAAACTTTGAAAAATATTTTT
1 CAAACTTTGAAAAACATTTTT
**
3933521 CAAA----G--AAACATTTAC
1 CAAACTTTGAAAAACATTTTT
3933536 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
3933557 CAAA
1 CAAA
3933561 GTTGGTTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 12
0.63 0.11 0.26
Matches are distributed among these distances:
15 11 0.38
17 1 0.03
19 1 0.03
21 16 0.55
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:3937518 original size:35 final size:35
Alignment explanation
Indices: 3937474--3937543 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
3937464 AACATCTACC
3937474 AAACTTTACCAAACTTTAAAAAACA-TTTTCAAAG
1 AAACTTTACCAAACTTTAAAAAACATTTTTCAAAG
*
3937508 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAAC-TTTACCAAACTTTAAAAAACATTTTTCAAAG
3937544 TTGGTTGTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 4 0.12
35 20 0.61
36 9 0.27
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30
Consensus pattern (35 bp):
AAACTTTACCAAACTTTAAAAAACATTTTTCAAAG
Found at i:3938014 original size:22 final size:23
Alignment explanation
Indices: 3937979--3938021 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3937969 ACGTTTTGAC
* *
3937979 TTTTTTTTTCTTCTTTTGTTCGG
1 TTTTTTCTTCTTCTCTTGTTCGG
3938002 TTTTTTCTT-TTCTCTTGTTC
1 TTTTTTCTTCTTCTCTTGTTC
3938022 AGAGAAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.74
Consensus pattern (23 bp):
TTTTTTCTTCTTCTCTTGTTCGG
Found at i:3939000 original size:22 final size:22
Alignment explanation
Indices: 3938972--3939013 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3938962 TAAAATATCG
*
3938972 GGGGATCACTACGGTTATTTTT
1 GGGGATCACCACGGTTATTTTT
*
3938994 GGGGATCCCCACGGTTATTT
1 GGGGATCACCACGGTTATTT
3939014 ACACAGATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.36
Consensus pattern (22 bp):
GGGGATCACCACGGTTATTTTT
Found at i:3939871 original size:132 final size:132
Alignment explanation
Indices: 3939634--3939898 Score: 485
Period size: 132 Copynumber: 2.0 Consensus size: 132
3939624 CCCCCATTTC
* *
3939634 CCTCCCCTCTCCCGTCTTGTTCATCCCCTCCCCCTCACCATGCAATCTTCTACAATTCTTCAAAT
1 CCTCCCCTCTCCCGTCTTGTTCAGCCCCTCCCCCTCACCATGCAATCTCCTACAATTCTTCAAAT
*
3939699 CTTGCAAAAGTCACCTATTGCTAATCATATAACGGCTTAAATAGCTGCAAATCATCTGCAAATTA
66 CTTGCAAAAATCACCTATTGCTAATCATATAACGGCTTAAATAGCTGCAAATCATCTGCAAATTA
3939764 CA
131 CA
*
3939766 CCTCCCCTCTCCCGTCTTGTTCAGCCCCTCCCCCTCACTATGCAATCTCCTACAATTCTTCAAAT
1 CCTCCCCTCTCCCGTCTTGTTCAGCCCCTCCCCCTCACCATGCAATCTCCTACAATTCTTCAAAT
*
3939831 CTTGCAAAAATCATCTATTGCTAATCATATAACGGCTTAAATAGCTGCAAATCATCTGCAAATTA
66 CTTGCAAAAATCACCTATTGCTAATCATATAACGGCTTAAATAGCTGCAAATCATCTGCAAATTA
3939896 CA
131 CA
3939898 C
1 C
3939899 GATCGACAAT
Statistics
Matches: 128, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 128 1.00
ACGTcount: A:0.28, C:0.34, G:0.08, T:0.30
Consensus pattern (132 bp):
CCTCCCCTCTCCCGTCTTGTTCAGCCCCTCCCCCTCACCATGCAATCTCCTACAATTCTTCAAAT
CTTGCAAAAATCACCTATTGCTAATCATATAACGGCTTAAATAGCTGCAAATCATCTGCAAATTA
CA
Found at i:3939966 original size:22 final size:22
Alignment explanation
Indices: 3939927--3939984 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
3939917 GGATTAGGGG
* *
3939927 TAGAGATTTAGGGATTAAGGTT
1 TAGAGATTTAAGGATTAAGATT
**
3939949 TAGAGATTTAAGTTTTAAGATT
1 TAGAGATTTAAGGATTAAGATT
* *
3939971 TACAAATTTAAGGA
1 TAGAGATTTAAGGA
3939985 GATTTTGACG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (22 bp):
TAGAGATTTAAGGATTAAGATT
Found at i:3944434 original size:32 final size:32
Alignment explanation
Indices: 3944392--3944457 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
3944382 TATGGTAGTA
3944392 AACCACATGTCCATCATCTCCATGAAAGTATG
1 AACCACATGTCCATCATCTCCATGAAAGTATG
*
3944424 AACCATATGTCCATCATCTCCATGAAAGTATG
1 AACCACATGTCCATCATCTCCATGAAAGTATG
3944456 AA
1 AA
3944458 AGTAAGGAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (32 bp):
AACCACATGTCCATCATCTCCATGAAAGTATG
Found at i:3945640 original size:2 final size:2
Alignment explanation
Indices: 3945633--3945694 Score: 72
Period size: 2 Copynumber: 30.5 Consensus size: 2
3945623 TTACGCGCAC
*
3945633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT CAGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -A-T
* *
3945676 AT GT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
3945695 AGTTAAAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
1 1 0.02
2 48 0.92
3 2 0.04
4 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3945690 original size:31 final size:30
Alignment explanation
Indices: 3945648--3945711 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
3945638 TATATATATA
*
3945648 TATATATATATATATATA-TAAAATCAGTATG
1 TATATAAATATATATA-AGTAAAAT-AGTATG
3945679 TATATAAATATATATAAGTTAAAATAGTATG
1 TATATAAATATATATAAG-TAAAATAGTATG
3945710 TA
1 TA
3945712 AAAAACACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 1 0.03
31 23 0.77
32 6 0.20
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.41
Consensus pattern (30 bp):
TATATAAATATATATAAGTAAAATAGTATG
Found at i:3949785 original size:2 final size:2
Alignment explanation
Indices: 3949780--3949807 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3949770 TATTAAAAAG
3949780 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3949808 AATAAAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3949787 original size:39 final size:39
Alignment explanation
Indices: 3949710--3949787 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
3949700 CGCATTCCTC
* *
3949710 ATGTATTAAGTAAAAACAATATATGTATATATACATATA
1 ATGTATTAAGTAAAAACAATATATGTAAAAATACATATA
* *
3949749 ATGTA-TACGTAAAAACATATATAT-TAAAAAGTATATATA
1 ATGTATTAAGTAAAAACA-ATATATGTAAAAA-TACATATA
3949788 TATATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
38 15 0.45
39 18 0.55
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.35
Consensus pattern (39 bp):
ATGTATTAAGTAAAAACAATATATGTAAAAATACATATA
Found at i:3952214 original size:41 final size:40
Alignment explanation
Indices: 3952152--3952616 Score: 243
Period size: 41 Copynumber: 11.4 Consensus size: 40
3952142 AATCGAGTCT
**
3952152 TGGTAGCATATAATAGTTCATCATTCAACTTGATTCGATCA
1 TGGTAGCATGCAATAGTTCATCATTCAA-TTGATTCGATCA
** *
3952193 TGGTAGCATGCAATAAATCATCATTCATCTTGATTCGATCA
1 TGGTAGCATGCAATAGTTCATCATTCA-ATTGATTCGATCA
* * * * * * *
3952234 TGATAACATGTAATAATTCA-CTATTCGATTCAATTCAATCA
1 TGGTAGCATGCAATAGTTCATC-ATTCAATT-GATTCGATCA
* ** * ** * *
3952275 AGACAACATATAATAGTTCTTCATTCAATTTGTTTCGATCA
1 TGGTAGCATGCAATAGTTCATCATTCAA-TTGATTCGATCA
* *
3952316 TGGTAGCATGCAATAGATCATCATTCAAATTGATTCAATCA
1 TGGTAGCATGCAATAGTTCATCATTC-AATTGATTCGATCA
* * * * * * *
3952357 TGGTAACATGAAATAATTCAACATTCGATTCAATTCAATCA
1 TGGTAGCATGCAATAGTTCATCATTCAATT-GATTCGATCA
* * ** * * *
3952398 AGGTAGCTTATAATTGTTTATCCTTCAATT-AGTTCGATCA
1 TGGTAGCATGCAATAGTTCATCATTCAATTGA-TTCGATCA
* * * *** * *
3952438 TGGTAGAATGCAATAATTCAACATTTGGTTCAATTCAATCA
1 TGGTAGCATGCAATAGTTCATCATTCAATT-GATTCGATCA
* ** * *
3952479 AGGTAGCATATAATAGTTTATCCTTCAATTTGATTCGATCA
1 TGGTAGCATGCAATAGTTCATCATTCAA-TTGATTCGATCA
* * * *
3952520 TGGTAGCATGCAATAGATCATCATTCGATTCAATTCAATCA
1 TGGTAGCATGCAATAGTTCATCATTCAATT-GATTCGATCA
* ** ** * *
3952561 AGACATG-ATATAATAGTTCATCATCCAATTGGATTCAATCA
1 TGGTA-GCATGCAATAGTTCATCATTCAATT-GATTCGATCA
*
3952602 TGGTAGTATGCAATA
1 TGGTAGCATGCAATA
3952617 ACCAATTTAT
Statistics
Matches: 308, Mismatches: 102, Indels: 28
0.70 0.23 0.06
Matches are distributed among these distances:
39 1 0.00
40 33 0.11
41 265 0.86
42 9 0.03
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (40 bp):
TGGTAGCATGCAATAGTTCATCATTCAATTGATTCGATCA
Found at i:3952357 original size:123 final size:122
Alignment explanation
Indices: 3952158--3952462 Score: 398
Period size: 123 Copynumber: 2.5 Consensus size: 122
3952148 GTCTTGGTAG
* * **
3952158 CATATAATAGTTCATCATTCAACTTGATTCGATCATGGTAGCATGCAATAAATCATCATTCATCT
1 CATATAATAGTTCTTCATTCAATTTG-TTCGATCATGGTAGCATGCAATAAATCATCATTCAAAT
* *
3952223 TGATTCGATCATGATAACATGTAATAATTC-ACTATTCGATTCAATTCAATCAAGACAA
65 TGATTCAATCATGATAACATGAAATAATTCAAC-ATTCGATTCAATTCAATCAAGACAA
*
3952281 CATATAATAGTTCTTCATTCAATTTGTTTCGATCATGGTAGCATGCAATAGATCATCATTCAAAT
1 CATATAATAGTTCTTCATTCAATTTG-TTCGATCATGGTAGCATGCAATAAATCATCATTCAAAT
* ** *
3952346 TGATTCAATCATGGTAACATGAAATAATTCAACATTCGATTCAATTCAATCAAGGTAG
65 TGATTCAATCATGATAACATGAAATAATTCAACATTCGATTCAATTCAATCAAGACAA
* * * * * * *
3952404 CTTATAATTGTT-TATCCTTCAATTAGTTCGATCATGGTAGAATGCAATAATTCAACATT
1 CATATAATAGTTCT-TCATTCAATTTGTTCGATCATGGTAGCATGCAATAAATCATCATT
3952463 TGGTTCAATT
Statistics
Matches: 160, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
122 30 0.19
123 128 0.80
124 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (122 bp):
CATATAATAGTTCTTCATTCAATTTGTTCGATCATGGTAGCATGCAATAAATCATCATTCAAATT
GATTCAATCATGATAACATGAAATAATTCAACATTCGATTCAATTCAATCAAGACAA
Found at i:3952403 original size:82 final size:82
Alignment explanation
Indices: 3952153--3952617 Score: 336
Period size: 82 Copynumber: 5.7 Consensus size: 82
3952143 ATCGAGTCTT
* * * * *
3952153 GGTAGCATATAATAGTTCATCATTCAACTTGATTCGATCATGGTAGCATGCAATAAATCATCATT
1 GGTAGCATATAATAGTTCATCATTCAAATTGATTCAATCATGGTAACATGCAATAATTCAACATT
** * *
3952218 C-ATCTTGATTCGATCAT
66 CGAT-TCAATTCAATCAA
* * * * * * * ** ** * **
3952235 GATAACATGTAATAATTCA-CTATTC-GATTCAATTCAATCAAGACAACATATAATAGTTCTTCA
1 GGTAGCATATAATAGTTCATC-ATTCAAATT-GATTCAATCATGGTAACATGCAATAATTCAACA
* *** * *
3952298 TTCAATTTGTTTCGATCAT
64 TTCGATTCAATTCAATCAA
** * *
3952317 GGTAGCATGCAATAGATCATCATTCAAATTGATTCAATCATGGTAACATGAAATAATTCAACATT
1 GGTAGCATATAATAGTTCATCATTCAAATTGATTCAATCATGGTAACATGCAATAATTCAACATT
3952382 CGATTCAATTCAATCAA
66 CGATTCAATTCAATCAA
* * * * *
3952399 GGTAGCTTATAATTGTTTATCCTTC-AATT-AGTTCGATCATGGTAGA-ATGCAATAATTCAACA
1 GGTAGCATATAATAGTTCATCATTCAAATTGA-TTCAATCATGGTA-ACATGCAATAATTCAACA
* *
3952461 TTTGGTTCAATTCAATCAA
64 TTCGATTCAATTCAATCAA
* * * * * *
3952480 GGTAGCATATAATAGTTTATCCTTCAATTTGATTCGATCATGGTAGCATGCAATAGA-TCATCAT
1 GGTAGCATATAATAGTTCATCATTCAAATTGATTCAATCATGGTAACATGCAATA-ATTCAACAT
3952544 TCGATTCAATTCAATCAA
65 TCGATTCAATTCAATCAA
** * **
3952562 GACATG-ATATAATAGTTCATCA-TCCAATTGGATTCAATCATGGTAGTATGCAATAA
1 GGTA-GCATATAATAGTTCATCATTCAAATT-GATTCAATCATGGTAACATGCAATAA
3952618 CCAATTTATC
Statistics
Matches: 305, Mismatches: 65, Indels: 27
0.77 0.16 0.07
Matches are distributed among these distances:
80 1 0.00
81 80 0.26
82 215 0.70
83 9 0.03
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (82 bp):
GGTAGCATATAATAGTTCATCATTCAAATTGATTCAATCATGGTAACATGCAATAATTCAACATT
CGATTCAATTCAATCAA
Found at i:3952599 original size:204 final size:203
Alignment explanation
Indices: 3952226--3952607 Score: 479
Period size: 204 Copynumber: 1.9 Consensus size: 203
3952216 TTCATCTTGA
*
3952226 TTCGATCATGATAACATGTAATAATTCACTATTCGATTCAATTCAATCAAGACAACATATAATAG
1 TTCGATCATGATAACATGCAATAATTCACTATTCGATTCAATTCAATCAAGACAACATATAATAG
* *
3952291 TTCTTCATTCAATTTGTTTCGATCATGGTAGCATGCAATAGATCATCATTCAAATTGATTCAATC
66 TTCTTCATTCAATTTGATTCGATCATGGTAGCATGCAATAGATCATCATTCAAATTAATTCAATC
* * *
3952356 ATGGTAACATGAAATAATTCAACATTCGATTCAATTCAATCAAGGTAGCTTATAATTGTTTATCC
131 ATAG-AACATGAAATAATTCAACATCCAATTCAATTCAATCAAGGTAGCTTATAATTGTTTATCC
3952421 TTCAATTAG
195 TTCAATTAG
* * * ** *
3952430 TTCGATCATGGTAGA-ATGCAATAATTCAAC-ATTTGGTTCAATTCAATCAAGGTAGCATATAAT
1 TTCGATCATGATA-ACATGCAATAATTC-ACTATTCGATTCAATTCAATCAAGACAACATATAAT
* *
3952493 AGTT-TATCCTTCAATTTGATTCGATCATGGTAGCATGCAATAGATCATCATTC-GATTCAATTC
64 AGTTCT-TCATTCAATTTGATTCGATCATGGTAGCATGCAATAGATCATCATTCAAATT-AATTC
* * ** *
3952556 AATCA-AG-ACATGATATAATAGTTCATCATCCAATTGGATTCAATCATGGTAG
127 AATCATAGAACATG--A-AATAATTCAACATCCAATTCAATTCAATCAAGGTAG
3952608 TATGCAATAA
Statistics
Matches: 152, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
201 5 0.03
203 6 0.04
204 138 0.91
205 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (203 bp):
TTCGATCATGATAACATGCAATAATTCACTATTCGATTCAATTCAATCAAGACAACATATAATAG
TTCTTCATTCAATTTGATTCGATCATGGTAGCATGCAATAGATCATCATTCAAATTAATTCAATC
ATAGAACATGAAATAATTCAACATCCAATTCAATTCAATCAAGGTAGCTTATAATTGTTTATCCT
TCAATTAG
Found at i:3958245 original size:3 final size:3
Alignment explanation
Indices: 3958237--3958268 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3958227 TATCTGAACG
3958237 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3958269 TTAAATAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3960065 original size:13 final size:13
Alignment explanation
Indices: 3960047--3960124 Score: 111
Period size: 13 Copynumber: 6.0 Consensus size: 13
3960037 GTCATAAATC
*
3960047 TATGACGTGCATT
1 TATGACGCGCATT
*
3960060 TATGACGCACATT
1 TATGACGCGCATT
3960073 TATGACGCGCATT
1 TATGACGCGCATT
*
3960086 TATGACGCGTATT
1 TATGACGCGCATT
*
3960099 TATGACGCGTATT
1 TATGACGCGCATT
*
3960112 TATGACGCTCATT
1 TATGACGCGCATT
3960125 GCGCGTCATT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 59 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:3964699 original size:70 final size:70
Alignment explanation
Indices: 3964466--3964677 Score: 424
Period size: 70 Copynumber: 3.0 Consensus size: 70
3964456 GTATATTTTC
3964466 TTGTAGTGTTTATTGATTATTTTCATTTTTAATATTTGTAATATTTAGTATTTATGATTTTAGTT
1 TTGTAGTGTTTATTGATTATTTTCATTTTTAATATTTGTAATATTTAGTATTTATGATTTTAGTT
3964531 CTAGT
66 CTAGT
3964536 TTGTAGTGTTTATTGATTATTTTCATTTTTAATATTTGTAATATTTAGTATTTATGATTTTAGTT
1 TTGTAGTGTTTATTGATTATTTTCATTTTTAATATTTGTAATATTTAGTATTTATGATTTTAGTT
3964601 CTAGT
66 CTAGT
3964606 TTGTAGTGTTTATTGATTATTTTCATTTTTAATATTTGTAATATTTAGTATTTATGATTTTAGTT
1 TTGTAGTGTTTATTGATTATTTTCATTTTTAATATTTGTAATATTTAGTATTTATGATTTTAGTT
3964671 CTAGT
66 CTAGT
3964676 TT
1 TT
3964678 ATTTAAAACT
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 142 1.00
ACGTcount: A:0.24, C:0.03, G:0.13, T:0.60
Consensus pattern (70 bp):
TTGTAGTGTTTATTGATTATTTTCATTTTTAATATTTGTAATATTTAGTATTTATGATTTTAGTT
CTAGT
Found at i:3972611 original size:90 final size:90
Alignment explanation
Indices: 3972458--3972713 Score: 440
Period size: 90 Copynumber: 2.8 Consensus size: 90
3972448 CTAATGTGTT
*
3972458 TTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCTTTCGGGCCATCCATAGGACCTT
1 TTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCTTTCGGGCCATCCATAAGACCTT
*
3972523 TAGTGCAGGATGTTTTCAAATGAGA
66 CAGTGCAGGATGTTTTCAAATGAGA
*
3972548 TTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCTTTCGGGCCATCTATAAGACCTT
1 TTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCTTTCGGGCCATCCATAAGACCTT
*
3972613 CAGTGCATGATGTTTTCAAATGAGA
66 CAGTGCAGGATGTTTTCAAATGAGA
* * *
3972638 TTTTAGAAACAAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAATACCTT
1 TTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCTTTCGGGCCATCCATAAGACCTT
*
3972703 CAATGCAGGAT
66 CAGTGCAGGAT
3972714 AAAAATTGAG
Statistics
Matches: 156, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 156 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (90 bp):
TTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCTTTCGGGCCATCCATAAGACCTT
CAGTGCAGGATGTTTTCAAATGAGA
Found at i:3972737 original size:72 final size:72
Alignment explanation
Indices: 3972650--3972785 Score: 227
Period size: 72 Copynumber: 1.9 Consensus size: 72
3972640 TTAGAAACAA
* * *
3972650 AGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAATACCTTCAATGCAGGATA
1 AGCCTTCGAGGGTTTCTTGATTTATAAGTCCTTCGGGCCATCCATAAGACCTTCAATGCAGGATA
3972715 AAAATTG
66 AAAATTG
* *
3972722 AGCCTTCGAGGGTTTCTTGATTTATAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCTGGAT
1 AGCCTTCGAGGGTTTCTTGATTTATAAGTCCTTCGGGCCATCCATAAGACCTTCAATGCAGGAT
3972786 GTTTTCAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (72 bp):
AGCCTTCGAGGGTTTCTTGATTTATAAGTCCTTCGGGCCATCCATAAGACCTTCAATGCAGGATA
AAAATTG
Found at i:3973049 original size:136 final size:136
Alignment explanation
Indices: 3972805--3973334 Score: 782
Period size: 136 Copynumber: 3.9 Consensus size: 136
3972795 AATTTCGTTG
**
3972805 CTCGATTCATGGCATTTCAAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCTAATAGAGAGT
1 CTCGATTCATGGCATTTCAAATCAGTGACACCTCGCTTGAGGGATTGACATTTCTAATAGAGAGT
* * *
3972870 TCATAATGAGAAGAACTCATCCGACAGAGGTAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAAC
66 TCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGAC
3972935 CTATCA
131 CTATCA
* * * * *
3972941 CTCGATTCGTGACATTTTAAATCAGTGACACTTCGCTTGAGGGATTGACATTTCTAATAGAGAGA
1 CTCGATTCATGGCATTTCAAATCAGTGACACCTCGCTTGAGGGATTGACATTTCTAATAGAGAGT
* *
3973006 TCATAATAAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGAC
66 TCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGAC
3973071 CTATCA
131 CTATCA
* * * *
3973077 CTCGATTAACGGCATTTCGAATTAGTGACACCTCGCTTGAGGGATTGACATTTCTAATAGAGAGT
1 CTCGATTCATGGCATTTCAAATCAGTGACACCTCGCTTGAGGGATTGACATTTCTAATAGAGAGT
* * * *
3973142 TCAAAATGAGATGAACTCATCCGAAAGGGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGAC
66 TCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGAC
3973207 CTATCA
131 CTATCA
* * ** *
3973213 CTCGATTCACGGTATTTTGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCTAATTGAGAGT
1 CTCGATTCATGGCATTTCAAATCAGTGACACCTCGCTTGAGGGATTGACATTTCTAATAGAGAGT
* *
3973278 TCATAATGAGAAGAACTCATCCTA-A-A-GGAG-A-AAGTTCATAATGAGAAGAACTTGTTC
66 TCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
3973335 CTTTCAAATT
Statistics
Matches: 357, Mismatches: 37, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
131 25 0.07
132 1 0.00
133 4 0.01
135 1 0.00
136 326 0.91
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (136 bp):
CTCGATTCATGGCATTTCAAATCAGTGACACCTCGCTTGAGGGATTGACATTTCTAATAGAGAGT
TCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGAC
CTATCA
Found at i:3973458 original size:105 final size:105
Alignment explanation
Indices: 3973273--3973548 Score: 394
Period size: 105 Copynumber: 2.6 Consensus size: 105
3973263 TTTCTAATTG
*
3973273 AGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTT
1 AGAGTTCATAATGAGAAGAACTCATCCTAAAGAAGAAAGTTCATAATGAGAAGAACTTGTTCCTT
*
3973338 TCAAATTCACTACAGAAGGAGGTGAACCAACATTTCCAGA
66 TCAAATCCACTACAGAAGGAGGTGAACCAACATTTCCAGA
* *
3973378 AGAGTTCATAATGAGAAGAACTCATCCTAAAGAAGAAATTTTATAATGAGAAGAACTTGTTCCTT
1 AGAGTTCATAATGAGAAGAACTCATCCTAAAGAAGAAAGTTCATAATGAGAAGAACTTGTTCCTT
* * *
3973443 TCAAGTCCA-TCACAGAAGGAGGTGGATCAACATTTCCAGA
66 TCAAATCCACT-ACAGAAGGAGGTGAACCAACATTTCCAGA
* * *
3973483 AGAGTTCAAAATAAGAAGAACTCATCC-AGCGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCCTA---AAGAAG-A-AAGTTCATAATGAGAAGAACTTGT
3973547 TC
61 TC
3973549 AACCTTGCAT
Statistics
Matches: 153, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
104 2 0.01
105 121 0.79
107 5 0.03
108 1 0.01
109 24 0.16
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (105 bp):
AGAGTTCATAATGAGAAGAACTCATCCTAAAGAAGAAAGTTCATAATGAGAAGAACTTGTTCCTT
TCAAATCCACTACAGAAGGAGGTGAACCAACATTTCCAGA
Found at i:3973579 original size:91 final size:89
Alignment explanation
Indices: 3973474--3973641 Score: 264
Period size: 91 Copynumber: 1.9 Consensus size: 89
3973464 GTGGATCAAC
* * * *
3973474 ATTTCCAGAAGAGTTCAAAATAAGAAGAACTCATCCAGCGAGGAAGAAGAAGTTCATAATGAGAA
1 ATTTCCAGAAGAGTTCAAAATAAGAAGAAATCATCCAACAAGAAAGAAGAAGTTCATAATGAGAA
3973539 GAACTTGTTCAACCTTGCATCAGT
66 GAACTTGTTCAACCTTGCATCAGT
* *
3973563 ATTTCCAATGAAGAGTTCATAATGAGAAGAAATCATCCAACAAGAAAGAAGAAGTTCATAATGAG
1 ATTTCC-A-GAAGAGTTCAAAATAAGAAGAAATCATCCAACAAGAAAGAAGAAGTTCATAATGAG
3973628 AAGAACTTGTTCAA
64 AAGAACTTGTTCAA
3973642 TCCAACGATG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
89 6 0.08
90 1 0.01
91 64 0.90
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (89 bp):
ATTTCCAGAAGAGTTCAAAATAAGAAGAAATCATCCAACAAGAAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTTGCATCAGT
Found at i:3977778 original size:12 final size:12
Alignment explanation
Indices: 3977763--3977789 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3977753 AGAGACACCA
3977763 AAGGAGAAGAAG
1 AAGGAGAAGAAG
3977775 AAGGAGAAGAAG
1 AAGGAGAAGAAG
3977787 AAG
1 AAG
3977790 AAAAACATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
AAGGAGAAGAAG
Found at i:3987118 original size:20 final size:20
Alignment explanation
Indices: 3987093--3987134 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3987083 TTAGGTTTAA
3987093 ATAATTGATTGTTTGGTTGC
1 ATAATTGATTGTTTGGTTGC
3987113 ATAATTGATTGTTTGGTTGC
1 ATAATTGATTGTTTGGTTGC
3987133 AT
1 AT
3987135 CATTTATCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.05, G:0.24, T:0.50
Consensus pattern (20 bp):
ATAATTGATTGTTTGGTTGC
Found at i:3991542 original size:35 final size:35
Alignment explanation
Indices: 3991493--3991565 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
3991483 CCTAACAATT
3991493 GTTAAAGGGATATAACTTTCAAAATTTAAAGAGTA
1 GTTAAAGGGATATAACTTTCAAAATTTAAAGAGTA
*
3991528 GTTAAAGGGTTATAACTTTCAAAATTTAAAGAGTA
1 GTTAAAGGGATATAACTTTCAAAATTTAAAGAGTA
3991563 GTT
1 GTT
3991566 GATTCTTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.34
Consensus pattern (35 bp):
GTTAAAGGGATATAACTTTCAAAATTTAAAGAGTA
Found at i:3992367 original size:117 final size:116
Alignment explanation
Indices: 3992220--3992435 Score: 285
Period size: 117 Copynumber: 1.9 Consensus size: 116
3992210 GGAAGGGTTC
* * * * *
3992220 ATAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTCATAATGATAAGAG-TTTCTTTAACC-
1 ATAATGAGAAGAACTCATCCAATAAGGGAGAAGAAGTTCAAAATGAGAAGAGCTTT-TTCAACCT
3992283 TTGGTTCA-TCCATCACAGAATGAGGTGGATCAACATTTCCAGTAGAATGAGTTA
65 TTGGTTCATTCCATCACAG---GAGGTGGATCAACATTTCCAGTAGAATGAGTTA
* *
3992337 ATAATGAGAAGAACTCATCTAATAAGGGAGAATAAGTTCAAAATGAGAAGAGCTTTTTCAACCTT
1 ATAATGAGAAGAACTCATCCAATAAGGGAGAAGAAGTTCAAAATGAGAAGAGCTTTTTCAACCTT
* * *
3992402 TGTTTGATTCCATCACAGGAGGTTGATCAACATT
66 TGGTTCATTCCATCACAGGAGGTGGATCAACATT
3992436 GATAGAGAAG
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
116 15 0.17
117 52 0.60
118 9 0.10
119 10 0.12
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (116 bp):
ATAATGAGAAGAACTCATCCAATAAGGGAGAAGAAGTTCAAAATGAGAAGAGCTTTTTCAACCTT
TGGTTCATTCCATCACAGGAGGTGGATCAACATTTCCAGTAGAATGAGTTA
Found at i:3992548 original size:117 final size:117
Alignment explanation
Indices: 3992407--3992649 Score: 486
Period size: 117 Copynumber: 2.1 Consensus size: 117
3992397 ACCTTTGTTT
3992407 GATTCCATCACAGGAGGTTGATCAACATTGATAGAGAAGAAGTTCATAACGATAAGAACTTGTTC
1 GATTCCATCACAGGAGGTTGATCAACATTGATAGAGAAGAAGTTCATAACGATAAGAACTTGTTC
3992472 AAACTTTGACTCATCCATCACATAAGGAGTTGGATCAACATCACCTCTGCTC
66 AAACTTTGACTCATCCATCACATAAGGAGTTGGATCAACATCACCTCTGCTC
3992524 GATTCCATCACAGGAGGTTGATCAACATTGATAGAGAAGAAGTTCATAACGATAAGAACTTGTTC
1 GATTCCATCACAGGAGGTTGATCAACATTGATAGAGAAGAAGTTCATAACGATAAGAACTTGTTC
3992589 AAACTTTGACTCATCCATCACATAAGGAGTTGGATCAACATCACCTCTGCTC
66 AAACTTTGACTCATCCATCACATAAGGAGTTGGATCAACATCACCTCTGCTC
3992641 GATTCCATC
1 GATTCCATC
3992650 GGTAAAAGAA
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 126 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (117 bp):
GATTCCATCACAGGAGGTTGATCAACATTGATAGAGAAGAAGTTCATAACGATAAGAACTTGTTC
AAACTTTGACTCATCCATCACATAAGGAGTTGGATCAACATCACCTCTGCTC
Found at i:4001925 original size:2 final size:2
Alignment explanation
Indices: 4001918--4001989 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
4001908 ATTTGACCAT
*
4001918 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4001960 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4001990 ATGATGAACC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4024202 original size:21 final size:22
Alignment explanation
Indices: 4024178--4024219 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4024168 AATTTTCGGG
4024178 AAAAA-AATTGTTTTTGATTTT
1 AAAAAGAATTGTTTTTGATTTT
* *
4024199 AAAAAGTATTGTTTTTTATTT
1 AAAAAGAATTGTTTTTGATTT
4024220 AATTATGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (22 bp):
AAAAAGAATTGTTTTTGATTTT
Found at i:4033652 original size:21 final size:21
Alignment explanation
Indices: 4033626--4033673 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
4033616 ACATGTTTTT
4033626 CTACCCTTATTAGGTTAAATC
1 CTACCCTTATTAGGTTAAATC
4033647 CTACCCTTATTAGGTTAAATC
1 CTACCCTTATTAGGTTAAATC
4033668 CTACCC
1 CTACCC
4033674 AAAACATGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.35
Consensus pattern (21 bp):
CTACCCTTATTAGGTTAAATC
Found at i:4036046 original size:44 final size:44
Alignment explanation
Indices: 4035998--4036105 Score: 198
Period size: 44 Copynumber: 2.5 Consensus size: 44
4035988 AAGAAAGTAA
4035998 AGTGACAAAATCAAAAATAAATAAAACAAGAAATATAACATGTT
1 AGTGACAAAATCAAAAATAAATAAAACAAGAAATATAACATGTT
4036042 AGTGACAAAATCAAAAATAAATAAAACAAGAAATATAACATGTT
1 AGTGACAAAATCAAAAATAAATAAAACAAGAAATATAACATGTT
* *
4036086 AGTGACTAAATTAAAAATAA
1 AGTGACAAAATCAAAAATAA
4036106 TGAAACTGAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 62 1.00
ACGTcount: A:0.61, C:0.08, G:0.09, T:0.21
Consensus pattern (44 bp):
AGTGACAAAATCAAAAATAAATAAAACAAGAAATATAACATGTT
Found at i:4038905 original size:75 final size:74
Alignment explanation
Indices: 4038809--4038958 Score: 239
Period size: 75 Copynumber: 2.0 Consensus size: 74
4038799 CCCTAGTATC
*
4038809 TCATATAAGTCATCATCCACACAATCTAATCGATAAAAGTTAAATAATATATG-TTCTAATCAAG
1 TCATATAAGTCATCATCCACACAATCTAATCAATAAAAGTTAAATAATATATGTTTC-AATC-AG
*
4038873 TGATGGTATAT
64 TGATGGCATAT
* *
4038884 TCATATAAGTCATCATCCACACAATCTCATCAATAAAAGTTAAATAGTATATGTTTCAATCAGTG
1 TCATATAAGTCATCATCCACACAATCTAATCAATAAAAGTTAAATAATATATGTTTCAATCAGTG
4038949 ATGGCATAT
66 ATGGCATAT
4038958 T
1 T
4038959 AGAAAGTCTA
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
74 13 0.19
75 54 0.77
76 3 0.04
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (74 bp):
TCATATAAGTCATCATCCACACAATCTAATCAATAAAAGTTAAATAATATATGTTTCAATCAGTG
ATGGCATAT
Found at i:4039811 original size:17 final size:17
Alignment explanation
Indices: 4039785--4039818 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4039775 AATGTGTTGA
4039785 TCTGTATGTTTTCTTGG
1 TCTGTATGTTTTCTTGG
*
4039802 TCTGTTTGTTTTCTTGG
1 TCTGTATGTTTTCTTGG
4039819 CACAGGGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.12, G:0.24, T:0.62
Consensus pattern (17 bp):
TCTGTATGTTTTCTTGG
Found at i:4042343 original size:19 final size:19
Alignment explanation
Indices: 4042316--4042352 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4042306 TAGCATTGTT
4042316 TATAAGATGAACTTAAATC
1 TATAAGATGAACTTAAATC
*
4042335 TATAGGATGAACTTAAAT
1 TATAAGATGAACTTAAAT
4042353 AAATAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (19 bp):
TATAAGATGAACTTAAATC
Found at i:4042460 original size:48 final size:48
Alignment explanation
Indices: 4042404--4042552 Score: 289
Period size: 48 Copynumber: 3.1 Consensus size: 48
4042394 TTAAACTTGT
*
4042404 ATATTTGCCATCTGTTTAACAGTCGAACCTAAATTGAATGGACAAAGG
1 ATATTTGCCATCTGTTTAACAGTCGAACCTGAATTGAATGGACAAAGG
4042452 ATATTTGCCATCTGTTTAACAGTCGAACCTGAATTGAATGGACAAAGG
1 ATATTTGCCATCTGTTTAACAGTCGAACCTGAATTGAATGGACAAAGG
4042500 ATATTTGCCATCTGTTTAACAGTCGAACCTGAATTGAATGGACAAAGG
1 ATATTTGCCATCTGTTTAACAGTCGAACCTGAATTGAATGGACAAAGG
4042548 ATATT
1 ATATT
4042553 GAAGCTAATT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 100 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (48 bp):
ATATTTGCCATCTGTTTAACAGTCGAACCTGAATTGAATGGACAAAGG
Found at i:4048051 original size:52 final size:52
Alignment explanation
Indices: 4047973--4048080 Score: 216
Period size: 52 Copynumber: 2.1 Consensus size: 52
4047963 TGTGAAACTA
4047973 TCAAATTGTTTGCCTTGAGGAATGACTCCCACGAGATTATTCCAAGAAAGGT
1 TCAAATTGTTTGCCTTGAGGAATGACTCCCACGAGATTATTCCAAGAAAGGT
4048025 TCAAATTGTTTGCCTTGAGGAATGACTCCCACGAGATTATTCCAAGAAAGGT
1 TCAAATTGTTTGCCTTGAGGAATGACTCCCACGAGATTATTCCAAGAAAGGT
4048077 TCAA
1 TCAA
4048081 CACTGCTAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (52 bp):
TCAAATTGTTTGCCTTGAGGAATGACTCCCACGAGATTATTCCAAGAAAGGT
Found at i:4051194 original size:37 final size:37
Alignment explanation
Indices: 4051144--4051218 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
4051134 CATTAAACAT
** *
4051144 TTTTATATTTTTAATTTTTTTAAA-AAAATTATATAAA
1 TTTTATAAATTTAAATTTTTTAAAGAAAA-TATATAAA
4051181 TTTTATAAATTTAAATTTTTTAAAGAAAATATATAAA
1 TTTTATAAATTTAAATTTTTTAAAGAAAATATATAAA
4051218 T
1 T
4051219 ATTTTCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 30 0.88
38 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTATAAATTTAAATTTTTTAAAGAAAATATATAAA
Found at i:4051398 original size:20 final size:19
Alignment explanation
Indices: 4051359--4051432 Score: 112
Period size: 20 Copynumber: 3.8 Consensus size: 19
4051349 AACATTCCCA
*
4051359 GTAATTTTACATTCCACTG
1 GTAATCTTACATTCCACTG
4051378 GTAATCTTACATTCTCACTG
1 GTAATCTTACATTC-CACTG
4051398 GTAATCTTACATTCCCACTG
1 GTAATCTTACATT-CCACTG
*
4051418 ATAATCTTACATTCC
1 GTAATCTTACATTCC
4051433 GTGAACCAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 15 0.29
20 35 0.69
21 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.39
Consensus pattern (19 bp):
GTAATCTTACATTCCACTG
Found at i:4054464 original size:10 final size:10
Alignment explanation
Indices: 4054449--4054482 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4054439 GGACCAGCTG
*
4054449 AAAACCAGAA
1 AAAACCGGAA
*
4054459 AAAACCGGGA
1 AAAACCGGAA
4054469 AAAACCGGAA
1 AAAACCGGAA
4054479 AAAA
1 AAAA
4054483 TCGCATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.65, C:0.18, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAACCGGAA
Found at i:4056561 original size:28 final size:28
Alignment explanation
Indices: 4056530--4056585 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
4056520 CAATAACTGT
4056530 CCATATGGTTAACAGTTTCTCAAACTCC
1 CCATATGGTTAACAGTTTCTCAAACTCC
*
4056558 CCATATGGTTAATAGTTTCTCAAACTCC
1 CCATATGGTTAACAGTTTCTCAAACTCC
4056586 GTTTCTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (28 bp):
CCATATGGTTAACAGTTTCTCAAACTCC
Found at i:4058822 original size:24 final size:24
Alignment explanation
Indices: 4058791--4058894 Score: 71
Period size: 24 Copynumber: 4.5 Consensus size: 24
4058781 TTTTATCTTT
4058791 GTATTTTAATTTAAATAGGTTTTA
1 GTATTTTAATTTAAATAGGTTTTA
* *
4058815 GTATTTTAA-TTAATCTTTAGGATATTA
1 GTATTTTAATTTAA---ATAGG-TTTTA
*
4058842 -T-TTTTATATTT-TATA---TTT-
1 GTATTTTA-ATTTAAATAGGTTTTA
*
4058860 GTATTTTAGTTTAAATAGGTTTTA
1 GTATTTTAATTTAAATAGGTTTTA
4058884 GTATTTTAATT
1 GTATTTTAATT
4058895 AGGATTTAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 26
0.63 0.09 0.28
Matches are distributed among these distances:
19 6 0.10
20 8 0.14
23 9 0.15
24 19 0.32
25 5 0.08
26 6 0.10
27 6 0.10
ACGTcount: A:0.30, C:0.01, G:0.11, T:0.59
Consensus pattern (24 bp):
GTATTTTAATTTAAATAGGTTTTA
Found at i:4058873 original size:69 final size:68
Alignment explanation
Indices: 4058776--4058972 Score: 252
Period size: 69 Copynumber: 2.9 Consensus size: 68
4058766 ATTTTAAACA
* * ** *
4058776 TTATATTTTATCTTTGTATTTTAATTTAAATAGGTTTTAGTATTTTAATTAATCTTTAGGATATT
1 TTATATTTTATATTTGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATT
4058841 ATTT
66 A-TT
*
4058845 TTATATTTTATATTTGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATT
1 TTATATTTTATATTTGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATT
4058910 ATT
66 ATT
* * * * *
4058913 TTAAATATTATTTTTAGGTATTTTAGTTTAAATA-GTTTTAAATGTTTTAATTAAGATTTA
1 TTATATTTTATATTT--GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATTTA
4058973 AGATGTTTTA
Statistics
Matches: 113, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
68 14 0.12
69 65 0.58
70 34 0.30
ACGTcount: A:0.31, C:0.01, G:0.10, T:0.57
Consensus pattern (68 bp):
TTATATTTTATATTTGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATT
ATT
Found at i:4059585 original size:18 final size:18
Alignment explanation
Indices: 4059562--4059604 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4059552 CTTTAATTTA
* *
4059562 TTTATTTATTTATTTTCT
1 TTTATTTAATTATTATCT
*
4059580 TTTATTTAATTGTTATCT
1 TTTATTTAATTATTATCT
4059598 TTTATTT
1 TTTATTT
4059605 TAAAACAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:4059664 original size:15 final size:14
Alignment explanation
Indices: 4059644--4059705 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
4059634 TCTTTACTAC
4059644 TATTATTTATTATTT
1 TATTA-TTATTATTT
* *
4059659 TATTATTTTTCCTTT
1 TATTATTATT-ATTT
*
4059674 TATTATTATTTTATT
1 TATTATTATTAT-TT
4059689 TATTATTATCTATTT
1 TATTATTAT-TATTT
4059704 TA
1 TA
4059706 ATTCATTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 5 0.13
15 32 0.82
16 2 0.05
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTATTATTT
Found at i:4059694 original size:18 final size:18
Alignment explanation
Indices: 4059644--4059705 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
4059634 TCTTTACTAC
4059644 TATTA-TTTA-TTATT-T
1 TATTATTTTATTTATTAT
4059659 TATTATTTT-TCCTT-TTAT
1 TATTATTTTAT--TTATTAT
4059677 TATTATTTTATTTATTAT
1 TATTATTTTATTTATTAT
4059695 TATCTATTTTA
1 TAT-TATTTTA
4059706 ATTCATTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
15 5 0.13
16 3 0.08
17 4 0.10
18 19 0.49
19 8 0.21
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTATTTTATTTATTAT
Found at i:4061435 original size:36 final size:35
Alignment explanation
Indices: 4061377--4061452 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 35
4061367 TCGCGAATTT
*
4061377 TCGAGTCGAGTCCATTTCAGAGTTTTCGAGTCGAG
1 TCGAGTCGAGTCCATTTCAGAGTTTTCGAGTCAAG
* *
4061412 TCGAGTCGAGCTCCATTTTAGAGTTTTGGAGTCAAG
1 TCGAGTCGAG-TCCATTTCAGAGTTTTCGAGTCAAG
4061448 TCGAG
1 TCGAG
4061453 CTCAGCAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 10 0.27
36 27 0.73
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (35 bp):
TCGAGTCGAGTCCATTTCAGAGTTTTCGAGTCAAG
Found at i:4062951 original size:2 final size:2
Alignment explanation
Indices: 4062944--4062980 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4062934 TGCACGTCAA
4062944 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 A
4062981 GACACCTTTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4064618 original size:22 final size:23
Alignment explanation
Indices: 4064564--4064623 Score: 86
Period size: 24 Copynumber: 2.6 Consensus size: 23
4064554 GTATGAACAG
4064564 TACCGTGAATAGTGATATACAAAA
1 TACCGTGAATAGTGATATAC-AAA
*
4064588 TACCGTGAACAGTGATATAC-AA
1 TACCGTGAATAGTGATATACAAA
*
4064610 TACCATGAATAGTG
1 TACCGTGAATAGTG
4064624 TTACAGTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 14 0.42
24 19 0.58
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (23 bp):
TACCGTGAATAGTGATATACAAA
Found at i:4065423 original size:22 final size:22
Alignment explanation
Indices: 4065378--4065427 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
4065368 ATTTGTCATG
* * *
4065378 AGGACCTATGTATTTGCCCCGA
1 AGGACCAATGTATTTACCCAGA
*
4065400 AGGACCAATGTATTTATCCAGA
1 AGGACCAATGTATTTACCCAGA
4065422 AGGACC
1 AGGACC
4065428 GCGTAGACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (22 bp):
AGGACCAATGTATTTACCCAGA
Found at i:4065744 original size:21 final size:22
Alignment explanation
Indices: 4065702--4065745 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
4065692 TTGTTCATAT
***
4065702 ACATATGTCATATATTGTTCAC
1 ACATATGTCATATATACATCAC
4065724 ACATA-GTCATATATACATCAC
1 ACATATGTCATATATACATCAC
4065745 A
1 A
4065746 TAGCACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (22 bp):
ACATATGTCATATATACATCAC
Found at i:4068703 original size:2 final size:2
Alignment explanation
Indices: 4068698--4068731 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4068688 ATTAATTGAC
*
4068698 TA TA TA TA TA TA TA TA TA TA TA T- TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4068732 CTGATCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4073473 original size:23 final size:23
Alignment explanation
Indices: 4073447--4073491 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4073437 GGTTTTATAA
*
4073447 AAGTT-TTCTCTTTTTTACTTTTC
1 AAGTTCTTCTCATTTTT-CTTTTC
*
4073470 AAGTTCTTTTCATTTTTCTTTT
1 AAGTTCTTCTCATTTTTCTTTT
4073492 ATTTTCAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.13, C:0.16, G:0.04, T:0.67
Consensus pattern (23 bp):
AAGTTCTTCTCATTTTTCTTTTC
Found at i:4075451 original size:2 final size:2
Alignment explanation
Indices: 4075434--4075483 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
4075424 ACGTTTTAAG
* *
4075434 CT CT C- CT CT CT TT CT CT CT CT CT CA CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4075475 CT CT CT CT C
1 CT CT CT CT C
4075484 ATTTCTTCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4076637 original size:7 final size:7
Alignment explanation
Indices: 4076625--4076661 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
4076615 AGAAGCTCTC
4076625 TCCGTTT
1 TCCGTTT
4076632 TCCGTTT
1 TCCGTTT
4076639 TCCGTTT
1 TCCGTTT
4076646 TCCGTTT
1 TCCGTTT
4076653 TCCGTTT
1 TCCGTTT
4076660 TC
1 TC
4076662 TTTGATCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.00, C:0.30, G:0.14, T:0.57
Consensus pattern (7 bp):
TCCGTTT
Found at i:4084013 original size:467 final size:469
Alignment explanation
Indices: 4083245--4084171 Score: 1402
Period size: 467 Copynumber: 2.0 Consensus size: 469
4083235 GGACTATCGG
* *
4083245 GACCATCAATGATTCAAGGTGTAATCTTAGATACAGGTCATCTCAGGTGAATCATAGACGTTCGA
1 GACCATCAACGATTCAAGGTGTAATCTTAGATACAGGTCATCTCAGGTGAAGCATAGACGTTCGA
* *
4083310 TGAAATGATTATGAGAAAAAAATGTGGTTAAAATATAGAGTTGACAAATACTACTAAGATAAACT
66 TGAAATGATTATGAGAAAAAAATGAGGTTAAAATACAGAGTTGACAAATACTACTAAGATAAACT
* *
4083375 AAGTATCATTGTTGAAAGTCACCAACAAAGCTAGAATTATTTTGTGTAAATGACATATAACAATT
131 AAGTATCATTGTTGAAAGTCACCAACAAAACTAGAATTATTTTGTATAAATGACATATAACAATT
* *
4083440 TCTTCTTTTAATCCTTGTGGTTAAAGATTTTCCAACAGATGATCAAATATAATGAAATCCCAAAC
196 TCTTCTTTTAATACTTGTGGTTAAAGATTTACCAACAGATGATCAAATATAATGAAATCCCAAAC
* * * * *
4083505 AACTCATTCACCTCTCAGTTTCTTTTGCTCATATTCACTCTCGTTTAGTTT-TTTTCTTCAATTT
261 AACTCATTCACCTCTCAGTCTCTTTCGCTCACATGCACTCTCGTTTAGTTTGTGTTCTTCAATTT
* * * *
4083569 TCCACTATGTAAATTGTAAACCCAAGCAGTGCTCTGTCTTTTAGCTTTTTATTTACAAAGAAAAA
326 TCCACTATGTAAATTGTAAACCCAAGCAGTGCTATATCTTTCA--ATTTT-TTTACAAAGAAAAA
*
4083634 ATGGAGGA-AAAGTTGTTAGAACGCAACACCGATTGTATTTATTTCTTAGCCTCTC-CCATCACT
388 ATGGAGGATAAA-TTGTTAGAACGCAACACCGATTGCATTTATTTCTTAGCCTCTCGCC-TCACT
4083697 TACAAGAAGGGGCTATCAA
451 TACAAGAAGGGGCTATCAA
* * * *
4083716 GACCATCAACGATTCAATGTGTAATGTTAGATACATGTCATCTCAGGTGAAGCATAGATGTT-GA
1 GACCATCAACGATTCAAGGTGTAATCTTAGATACAGGTCATCTCAGGTGAAGCATAGACGTTCGA
* * *
4083780 TGAAATGATTGTGAG-AAAAAATGAGGTTAAAATACAGAGTTGACAAATACTATTAAGATGAACT
66 TGAAATGATTATGAGAAAAAAATGAGGTTAAAATACAGAGTTGACAAATACTACTAAGATAAACT
* *
4083844 AAGTATCATTGTTGAAAGTCACCAACAAAACT-GAATTATTTTGTATACATGACATATAATAATT
131 AAGTATCATTGTTGAAAGTCACCAACAAAACTAGAATTATTTTGTATAAATGACATATAACAATT
* *
4083908 TCTT-TGTTTAATAC-TGTGGTTAAAGATTTACCAACAGATGATCAAATATAATGAAATCTCAAG
196 TCTTCT-TTTAATACTTGTGGTTAAAGATTTACCAACAGATGATCAAATATAATGAAATCCCAAA
* *
4083971 CAACTCATTCATCTCTCAGTCTCTTTCGCTCACATGCACTCTCGTTTGGTTTGTGTTCTTCAATT
260 CAACTCATTCACCTCTCAGTCTCTTTCGCTCACATGCACTCTCGTTTAGTTTGTGTTCTTCAATT
*
4084036 TTCCACTATGTAAATTGTAAACCCAAGCAGTGCTATATCTTTCAATTTTTTTACAAAGGAAAAAT
325 TTCCACTATGTAAATTGTAAACCCAAGCAGTGCTATATCTTTCAATTTTTTTACAAAGAAAAAAT
* * * * * *
4084101 GGAGGATGAATTGTTGGAATGCAACACCGATTGCGTTTATTTCTTAGCCTCTCGCCTTACTTGCA
390 GGAGGATAAATTGTTAGAACGCAACACCGATTGCATTTATTTCTTAGCCTCTCGCCTCACTTACA
4084166 AGAAGG
455 AGAAGG
4084172 TACTTATTTT
Statistics
Matches: 414, Mismatches: 38, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
465 73 0.18
466 8 0.02
467 93 0.22
468 92 0.22
469 76 0.18
470 16 0.04
471 56 0.14
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (469 bp):
GACCATCAACGATTCAAGGTGTAATCTTAGATACAGGTCATCTCAGGTGAAGCATAGACGTTCGA
TGAAATGATTATGAGAAAAAAATGAGGTTAAAATACAGAGTTGACAAATACTACTAAGATAAACT
AAGTATCATTGTTGAAAGTCACCAACAAAACTAGAATTATTTTGTATAAATGACATATAACAATT
TCTTCTTTTAATACTTGTGGTTAAAGATTTACCAACAGATGATCAAATATAATGAAATCCCAAAC
AACTCATTCACCTCTCAGTCTCTTTCGCTCACATGCACTCTCGTTTAGTTTGTGTTCTTCAATTT
TCCACTATGTAAATTGTAAACCCAAGCAGTGCTATATCTTTCAATTTTTTTACAAAGAAAAAATG
GAGGATAAATTGTTAGAACGCAACACCGATTGCATTTATTTCTTAGCCTCTCGCCTCACTTACAA
GAAGGGGCTATCAA
Found at i:4092596 original size:17 final size:17
Alignment explanation
Indices: 4092574--4092610 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
4092564 TTGAATATCG
4092574 ATATTTGCAATTTTTTC
1 ATATTTGCAATTTTTTC
4092591 ATATTTGCAATTTTTTC
1 ATATTTGCAATTTTTTC
4092608 ATA
1 ATA
4092611 AAATAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (17 bp):
ATATTTGCAATTTTTTC
Found at i:4095833 original size:20 final size:20
Alignment explanation
Indices: 4095775--4095834 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
4095765 AGATTAGTTT
*
4095775 GGGTTGACTCAGGTCGGTTC
1 GGGTTGACTCAGATCGGTTC
* * * *
4095795 GTGTTAACTCAGTTTGGTTC
1 GGGTTGACTCAGATCGGTTC
*
4095815 GGGTTGACTCAGACCGGTTC
1 GGGTTGACTCAGATCGGTTC
4095835 AAACAGGTTC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.20, G:0.33, T:0.33
Consensus pattern (20 bp):
GGGTTGACTCAGATCGGTTC
Found at i:4097798 original size:16 final size:16
Alignment explanation
Indices: 4097779--4097826 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
4097769 TTTTAAATAG
4097779 ACCGAAAGTAAACCGA
1 ACCGAAAGTAAACCGA
*
4097795 ACCGAAA-TTAACTCGA
1 ACCGAAAGTAAAC-CGA
*
4097811 TCCGAAAG-AAACCGA
1 ACCGAAAGTAAACCGA
4097826 A
1 A
4097827 TTGAAAACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.48, C:0.25, G:0.17, T:0.10
Consensus pattern (16 bp):
ACCGAAAGTAAACCGA
Found at i:4098244 original size:16 final size:16
Alignment explanation
Indices: 4098219--4098280 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
4098209 AATTGAAATC
* *
4098219 AACCCAAACCAAAAGA
1 AACCCGAACCAAAAGT
4098235 AACCCGAACCAAAAGT
1 AACCCGAACCAAAAGT
*
4098251 TACCCGAACCGAAAA-T
1 AACCCGAACC-AAAAGT
*
4098267 AACCTGAACCAAAA
1 AACCCGAACCAAAA
4098281 TCAACCTGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
15 4 0.10
16 32 0.80
17 4 0.10
ACGTcount: A:0.53, C:0.31, G:0.10, T:0.06
Consensus pattern (16 bp):
AACCCGAACCAAAAGT
Found at i:4098290 original size:16 final size:15
Alignment explanation
Indices: 4098214--4098286 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 15
4098204 AATTGAATTG
*
4098214 AAATCAACCCAAACCA
1 AAAT-AACCCGAACCA
*
4098230 AAAGAAACCCGAACCA
1 AAA-TAACCCGAACCA
*
4098246 AAAGTTACCCGAACCGA
1 AAA-TAACCCGAACC-A
*
4098263 AAATAACCTGAACCA
1 AAATAACCCGAACCA
4098278 AAATCAACC
1 AAAT-AACC
4098287 TGAATTTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
15 5 0.10
16 39 0.81
17 4 0.08
ACGTcount: A:0.52, C:0.32, G:0.08, T:0.08
Consensus pattern (15 bp):
AAATAACCCGAACCA
Found at i:4098384 original size:12 final size:13
Alignment explanation
Indices: 4098367--4098402 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
4098357 TGAACAAATA
4098367 ATTTATTTATT-T
1 ATTTATTTATTAT
4098379 ATTTATTTATTAT
1 ATTTATTTATTAT
4098392 A-TTA-TTATTAT
1 ATTTATTTATTAT
4098403 CTATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.30
12 14 0.61
13 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTATTTATTAT
Found at i:4099392 original size:45 final size:47
Alignment explanation
Indices: 4099296--4099397 Score: 140
Period size: 46 Copynumber: 2.2 Consensus size: 47
4099286 ACGGTTGAAA
* *
4099296 TAAACCAAAATCAACTTGAATTGACAAGAAAATCTAAAGGTTGACGC
1 TAAACCAAAACCAACCTGAATTGACAAGAAAATCTAAAGGTTGACGC
4099343 -AAACCAAAACCAACCTGAATTGATC-A-AAAATCTAAAGGTTGAC-C
1 TAAACCAAAACCAACCTGAATTGA-CAAGAAAATCTAAAGGTTGACGC
4099387 TAAACCGAAAA
1 TAAACC-AAAA
4099398 AAACTGACCC
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
44 1 0.02
45 22 0.44
46 26 0.52
47 1 0.02
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.19
Consensus pattern (47 bp):
TAAACCAAAACCAACCTGAATTGACAAGAAAATCTAAAGGTTGACGC
Found at i:4111404 original size:37 final size:37
Alignment explanation
Indices: 4111346--4111441 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 37
4111336 CCTTTTCGTC
*
4111346 CTACTAGAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
4111383 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
4111420 CTACTATGATTTAAACTCCTAA
1 CTACTAGGATTCAAACTCCTAA
4111442 GGATATGATC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:4111534 original size:21 final size:23
Alignment explanation
Indices: 4111505--4111546 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
4111495 ACGATTTACA
*
4111505 GAAAGAATACAGAGG-AAAGCAC
1 GAAAGAATACAAAGGCAAAGCAC
4111527 GAAA-AATACAAAGGCAAAGC
1 GAAAGAATACAAAGGCAAAGC
4111547 TATTGTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.57, C:0.14, G:0.24, T:0.05
Consensus pattern (23 bp):
GAAAGAATACAAAGGCAAAGCAC
Found at i:4112204 original size:10 final size:10
Alignment explanation
Indices: 4112166--4112225 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 10
4112156 TATGTATACT
*
4112166 TTTATATTTGG
1 TTTAT-TTTTG
*
4112177 TTTATATGTTTA
1 TTTAT-T-TTTG
4112189 TTTATTTTTG
1 TTTATTTTTG
4112199 TTTATTTTTG
1 TTTATTTTTG
4112209 TTTATTTATTTG
1 TTTA-TT-TTTG
4112221 TTTAT
1 TTTAT
4112226 ATTATATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
10 17 0.40
11 11 0.26
12 15 0.35
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (10 bp):
TTTATTTTTG
Found at i:4112228 original size:24 final size:24
Alignment explanation
Indices: 4112183--4112228 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4112173 TTGGTTTATA
*
4112183 TGTTTATTTATTTTTGTTTATTTT
1 TGTTTATTTATTTTTGTATATTTT
4112207 TGTTTATTTATTTGTT-TATATT
1 TGTTTATTTATTT-TTGTATATT
4112229 ATATTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (24 bp):
TGTTTATTTATTTTTGTATATTTT
Found at i:4112238 original size:24 final size:23
Alignment explanation
Indices: 4112170--4112239 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 23
4112160 TATACTTTTA
4112170 TATTTGGTTTATATGTTTATTTA-T
1 TATTT-GTTTATAT-TTTATTTATT
*
4112194 T-TTTGTTTAT-TTTTGTTTATT
1 TATTTGTTTATATTTTATTTATT
*
4112215 TATTTGTTTATATTATATTATATT
1 TATTTGTTTATATTTTATT-TATT
4112239 T
1 T
4112240 TCATATTACT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 7 0.18
21 3 0.08
22 15 0.38
23 8 0.21
24 6 0.15
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (23 bp):
TATTTGTTTATATTTTATTTATT
Found at i:4112322 original size:4 final size:4
Alignment explanation
Indices: 4112309--4112338 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
4112299 TATATATTTA
4112309 TATT TCATT TATT TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT T
4112339 TTCCTTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:4112365 original size:12 final size:12
Alignment explanation
Indices: 4112350--4112384 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
4112340 TCCTTTCCTT
4112350 TTATTTTTTTAC
1 TTATTTTTTTAC
*
4112362 TTATTTTTATAC
1 TTATTTTTTTAC
4112374 TTCATTTTTTT
1 TT-ATTTTTTT
4112385 CATTTATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATTTTTTTAC
Found at i:4116808 original size:31 final size:31
Alignment explanation
Indices: 4116769--4116848 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
4116759 AGATTCAATC
* * * *
4116769 AGAA-CAAAAAGGGCAAAAAGAAAAAAGAAA
1 AGAAGCAAAAAAGGAAAAAACAAAAAAAAAA
4116799 AGAAGCAAAAAAGGAAAAAACAAAAAAAAAA
1 AGAAGCAAAAAAGGAAAAAACAAAAAAAAAA
* * *
4116830 AAAAGAAAAAAAAGAAAAA
1 AGAAGCAAAAAAGGAAAAA
4116849 GCACATGCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 4 0.10
31 38 0.90
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (31 bp):
AGAAGCAAAAAAGGAAAAAACAAAAAAAAAA
Found at i:4116817 original size:9 final size:8
Alignment explanation
Indices: 4116783--4116848 Score: 73
Period size: 8 Copynumber: 8.4 Consensus size: 8
4116773 CAAAAAGGGC
4116783 AAAAAG-A
1 AAAAAGAA
4116790 AAAAAGAA
1 AAAAAGAA
* *
4116798 AAGAAGCA
1 AAAAAGAA
*
4116806 AAAAAGGA
1 AAAAAGAA
*
4116814 AAAAACAA
1 AAAAAGAA
4116822 AAAAA-AA
1 AAAAAGAA
4116829 AAAAAGAAA
1 AAAAAG-AA
4116838 AAAAAGAA
1 AAAAAGAA
4116846 AAA
1 AAA
4116849 GCACATGCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
7 13 0.26
8 29 0.58
9 8 0.16
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:4116841 original size:15 final size:15
Alignment explanation
Indices: 4116783--4116849 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
4116773 CAAAAAGGGC
*
4116783 AAAAAGAAAAAAGAA
1 AAAAAGAAAAAAAAA
* **
4116798 AAGAAGCAAAAAAGGA
1 AAAAAG-AAAAAAAAA
*
4116814 AAAAACAAAAAAAAA
1 AAAAAGAAAAAAAAA
*
4116829 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAA
4116844 AAAAAG
1 AAAAAG
4116850 CACATGCAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
15 31 0.72
16 12 0.28
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAA
Found at i:4116848 original size:7 final size:7
Alignment explanation
Indices: 4116783--4116840 Score: 62
Period size: 7 Copynumber: 7.7 Consensus size: 7
4116773 CAAAAAGGGC
4116783 AAAAAGA
1 AAAAAGA
4116790 AAAAAGA
1 AAAAAGA
4116797 AAAGAAGCA
1 AAA-AAG-A
4116806 AAAAAGGA
1 AAAAA-GA
*
4116814 AAAAACAA
1 AAAAA-GA
*
4116822 AAAAAAA
1 AAAAAGA
4116829 AAAAAGA
1 AAAAAGA
4116836 AAAAA
1 AAAAA
4116841 AAGAAAAAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
7 23 0.51
8 17 0.38
9 5 0.11
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:4117470 original size:22 final size:22
Alignment explanation
Indices: 4117439--4117494 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
4117429 AGCTACCCCT
*
4117439 TCAAAACTTTGAGCATCAAATG
1 TCAAACCTTTGAGCATCAAATG
*
4117461 -CTAAACCTTTTAGCATCAAATG
1 TC-AAACCTTTGAGCATCAAATG
4117483 TCAAACCTTTGA
1 TCAAACCTTTGA
4117495 CCAAGCACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (22 bp):
TCAAACCTTTGAGCATCAAATG
Found at i:4118572 original size:106 final size:106
Alignment explanation
Indices: 4118447--4119812 Score: 2026
Period size: 106 Copynumber: 13.0 Consensus size: 106
4118437 GTGCCACTTG
* ** * *
4118447 AGACAACACAAGTTCAACTTCACGACGAAGGGACAACTGGTCGTCAACAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
* * *
4118512 AAGAGCCAATTTCAACTTCCCAGTGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
4118553 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
* *
4118618 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGATTCT
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * *
4118659 AGACAACGCAAGTTCAACTTCACGTCGAAGGGACCACTGGTTGTCAATAAGCAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
*
4118724 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACACC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
4118765 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
4118830 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
4118871 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
*
4118936 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
4118977 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTTTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
*
4119042 CAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
4119083 AGACAACGCAAGTTCAAATTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
*
4119148 CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * * *
4119189 AAACAACGAAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
* *
4119254 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * *
4119295 AGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTATCAA-CAACAATTTCCCAATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTCCCAATT
* *
4119358 TCAGAGCCAGTTTCAACTTCACAGCAAAGGATATTGGACTCC
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
4119400 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC-ATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
4119464 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
4119505 AGACAACGCAAGTTCAACTTCACGACGAAGAGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
* *
4119570 CAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGGAC-CC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
** ** * * *
4119610 AAGACAATACAAGCCCAACTTCACGACGAAGGG-GCGACTGATTGTCAA-CAA-AATTT--C-A-
1 -AGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTCCCAAT
* * ** *
4119668 TTC--AGTCAATTTCAACTTCACAGCAAAGGATATTAAACTCG
64 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * **
4119709 AGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCGGTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTCCCAATT
* **
4119773 CCA-AGCCAATTTCAACTTCAC-GACGCTGGATATTGGACTC
65 TCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
4119813 GGAACAATGC
Statistics
Matches: 1148, Mismatches: 96, Indels: 33
0.90 0.08 0.03
Matches are distributed among these distances:
98 70 0.06
99 3 0.00
100 8 0.01
101 1 0.00
102 2 0.00
104 7 0.01
105 231 0.20
106 826 0.72
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
Found at i:4120568 original size:37 final size:37
Alignment explanation
Indices: 4120510--4120614 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
4120500 CCTTTTCGTC
* *
4120510 CTACTAGAATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
4120547 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
4120584 CTAATATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
4120615 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:4121171 original size:21 final size:21
Alignment explanation
Indices: 4121081--4121172 Score: 82
Period size: 21 Copynumber: 4.3 Consensus size: 21
4121071 TTTTTTACAC
4121081 TATATA-TTATTATTATATATA
1 TATATATTTATTATT-TATATA
* * *
4121102 CATATATTTTTTATTTATTTA
1 TATATATTTATTATTTATATA
* *
4121123 TAT-TCATTTGGTTATTTTTA-A
1 TATAT-ATTT-ATTATTTATATA
4121144 TACTATATTTATTATTTATATA
1 TA-TATATTTATTATTTATATA
4121166 TATATAT
1 TATATAT
4121173 ACTTTTTTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
20 1 0.02
21 32 0.57
22 22 0.39
23 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (21 bp):
TATATATTTATTATTTATATA
Found at i:4121411 original size:12 final size:12
Alignment explanation
Indices: 4121373--4121421 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
4121363 TATTTGTTTA
4121373 TATTAT-ATTA-
1 TATTATCATTAT
*
4121383 TATTTTCA-TAT
1 TATTATCATTAT
4121394 TATTATCATTAT
1 TATTATCATTAT
* *
4121406 TGTTATGATTAT
1 TATTATCATTAT
4121418 TATT
1 TATT
4121422 TTTCTATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 7 0.23
11 8 0.26
12 16 0.52
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (12 bp):
TATTATCATTAT
Found at i:4121446 original size:2 final size:2
Alignment explanation
Indices: 4121439--4121468 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4121429 TTTACTCATT
4121439 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4121469 CATTTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4121488 original size:9 final size:9
Alignment explanation
Indices: 4121476--4121563 Score: 53
Period size: 9 Copynumber: 10.1 Consensus size: 9
4121466 ATACATTTTA
4121476 TATTTCATT
1 TATTTCATT
4121485 TATTT-ATT
1 TATTTCATT
4121493 TATTT-ATT
1 TATTTCATT
* *
4121501 TTTTTCCTTT
1 TATTT-CATT
*
4121511 TATTTTATT
1 TATTTCATT
* *
4121520 TATTTTACT
1 TATTTCATT
4121529 TA-TT--TT
1 TATTTCATT
4121535 TATTCTTCATT
1 TA-T-TTCATT
*
4121546 TTTTTCATT
1 TATTTCATT
4121555 TA-TTCATT
1 TATTTCATT
4121563 T
1 T
4121564 TTCCCTCTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
6 3 0.05
8 24 0.38
9 26 0.41
10 7 0.11
11 3 0.05
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTTCATT
Found at i:4121518 original size:31 final size:30
Alignment explanation
Indices: 4121471--4121565 Score: 90
Period size: 30 Copynumber: 3.1 Consensus size: 30
4121461 TATATATACA
4121471 TTTTATAT-TTCA-TTTATTTATTTATTTAT
1 TTTTAT-TCTTCATTTTATTTATTTATTTAT
* *
4121500 TTTT-TTCCTTTTATTTTATTTATTTTACTTAT
1 TTTTATT-C-TTCATTTTATTTA-TTTATTTAT
*
4121532 TTTTATTCTTCATTTT-TTTCATTTATTCAT
1 TTTTATTCTTCATTTTATTT-ATTTATTTAT
4121562 TTTT
1 TTTT
4121566 CCCTCTAACA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
27 1 0.02
28 1 0.02
29 4 0.07
30 17 0.31
31 16 0.30
32 13 0.24
33 2 0.04
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (30 bp):
TTTTATTCTTCATTTTATTTATTTATTTAT
Found at i:4121519 original size:19 final size:20
Alignment explanation
Indices: 4121471--4121538 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 20
4121461 TATATATACA
4121471 TTTTATATTTCATTTA-TTTA-
1 TTTTAT-TTT-ATTTATTTTAC
*
4121491 -TTTA-TTTATTT-TTTTCC
1 TTTTATTTTATTTATTTTAC
4121508 TTTTATTTTATTTATTTTAC
1 TTTTATTTTATTTATTTTAC
*
4121528 TTAT-TTTTATT
1 TTTTATTTTATT
4121539 CTTCATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
16 7 0.17
17 3 0.08
18 4 0.10
19 18 0.45
20 8 0.20
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTATTTTATTTATTTTAC
Found at i:4121534 original size:23 final size:22
Alignment explanation
Indices: 4121487--4121534 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
4121477 ATTTCATTTA
* *
4121487 TTTATTTATTTATTTTTTTCCT
1 TTTATTTATTTATTTTCTTCAT
4121509 TTTATTTTATTTATTTTACTT-AT
1 TTTA-TTTATTTATTTT-CTTCAT
4121532 TTT
1 TTT
4121535 TATTCTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 16 0.73
24 2 0.09
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTATTTATTTATTTTCTTCAT
Found at i:4124379 original size:9 final size:9
Alignment explanation
Indices: 4124365--4124423 Score: 73
Period size: 9 Copynumber: 6.0 Consensus size: 9
4124355 AACCCCACAT
4124365 AAAAAGAAA
1 AAAAAGAAA
4124374 AAAAAGAAA
1 AAAAAGAAA
4124383 AAAAAGAAGAA
1 AAAAAG-A-AA
4124394 GAAGAAAGAAA
1 -AA-AAAGAAA
4124405 GAAAAAGAAA
1 -AAAAAGAAA
4124415 AAAAAGAAA
1 AAAAAGAAA
4124424 TAGAAGTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
9 24 0.52
10 8 0.17
11 7 0.15
12 3 0.07
13 4 0.09
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:4131429 original size:3 final size:3
Alignment explanation
Indices: 4131416--4131483 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
4131406 TTTTATTAAT
*
4131416 TTA TT- TTA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
*
4131460 TTA TTA TTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
4131484 CAGGCCCAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 4 0.07
3 51 0.88
4 3 0.05
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4132718 original size:20 final size:20
Alignment explanation
Indices: 4132680--4132719 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4132670 AAATTTAATC
*
4132680 ATATAATTTTATATTTTTAA
1 ATATAATTTTATATGTTTAA
4132700 ATATAATTTCT-TATGTTTAA
1 ATATAATTT-TATATGTTTAA
4132720 TAATTTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
ATATAATTTTATATGTTTAA
Found at i:4132852 original size:13 final size:15
Alignment explanation
Indices: 4132820--4132865 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
4132810 AATATCATAA
* *
4132820 TTATATAAATTATAT
1 TTATTTAAATTATTT
*
4132835 ATATTT-AATT-TTT
1 TTATTTAAATTATTT
4132848 TTATTTAAATTATTT
1 TTATTTAAATTATTT
4132863 TTA
1 TTA
4132866 AATGATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.28
14 8 0.32
15 10 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTTAAATTATTT
Found at i:4136968 original size:15 final size:15
Alignment explanation
Indices: 4136948--4136977 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4136938 TCAATACCTC
4136948 TTGCATACATTCATT
1 TTGCATACATTCATT
4136963 TTGCATACATTCATT
1 TTGCATACATTCATT
4136978 ACTCATTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (15 bp):
TTGCATACATTCATT
Found at i:4144353 original size:6 final size:6
Alignment explanation
Indices: 4144342--4144398 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
4144332 ATGCTTGAAG
* * *
4144342 AAGAAA AAG-AA AAGAAAA AAAACAA AAGAAA AAGAGA AAGAGA AAGAAA
1 AAGAAA AAGAAA AAG-AAA AAGA-AA AAGAAA AAGAAA AAGAAA AAGAAA
*
4144391 AGGAAA AA
1 AAGAAA AA
4144399 ATAGAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 5 0.12
6 28 0.67
7 9 0.21
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:4144362 original size:14 final size:14
Alignment explanation
Indices: 4144339--4144397 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
4144329 ATTATGCTTG
*
4144339 AAGAAGAAAAAGAA
1 AAGAAAAAAAAGAA
*
4144353 AAGAAAAAAAACAA
1 AAGAAAAAAAAGAA
*
4144367 AAG-AAAAAGAGAA
1 AAGAAAAAAAAGAA
*
4144380 AGAGAAAGAAAAGGAA
1 A-AGAAA-AAAAAGAA
4144396 AA
1 AA
4144398 AATAGAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
13 9 0.25
14 17 0.47
15 3 0.08
16 7 0.19
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAGAA
Found at i:4144415 original size:33 final size:32
Alignment explanation
Indices: 4144342--4144416 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 32
4144332 ATGCTTGAAG
4144342 AAGAAAAAGA-AAAGAAAAAAAACAAAAGAAA
1 AAGAAAAAGAGAAAGAAAAAAAACAAAAGAAA
* *
4144373 AAGAGAAAGAGAAAGAAAAGGAAAA-AATAGAAA
1 AAGAAAAAGAGAAAGAAAA--AAAACAAAAGAAA
4144406 ATA-AAAAAGAG
1 A-AGAAAAAGAG
4144417 GGTCTAGATG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.24
32 8 0.22
33 15 0.41
34 5 0.14
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (32 bp):
AAGAAAAAGAGAAAGAAAAAAAACAAAAGAAA
Found at i:4145790 original size:123 final size:123
Alignment explanation
Indices: 4145295--4145990 Score: 1001
Period size: 123 Copynumber: 5.7 Consensus size: 123
4145285 CTCGATGGAT
* *
4145295 CAACATTTCCAG-GTGGAGTTCATAATGAGAAGAACTCATCTG-AGAAGGAAGAAGAAGTTCATA
1 CAACATTTCCAGAG-AGAATTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATA
* * * * *
4145358 ATGAGAAGAACTTGTACAACTTTTTGCTCGACT-TATCATAGAATGAGATAGATCAGCAC
64 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAGCAC
* * *
4145417 CAACATTTTCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* *
4145482 GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGGGATAGATCAGCAC
66 GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAGCAC
* *
4145540 CAATATTTCCAGAGAG-ATGCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* * * *
4145604 --G-AGAACTTATTTAACCTTTTTCTCGACTCTATCACAAAAGGAGATAGATCAACAC
66 GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAGCAC
*
4145659 CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAACAAGTTCATAAT
1 CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* * *
4145724 GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGAAAATAGATCATCAC
66 GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAGCAC
* * * *
4145782 CAATATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAAAAGTTCTTAAT
1 CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* * * * *
4145847 GAGAAGAACTTGTTCAACCTTTTTCTCGACTCTATCATAGAAGGAGATAGATCATCAT
66 GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAGCAC
* * *
4145905 CAACATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* *
4145970 AAGAAGAACTTGTTCGACCTT
66 GAGAAGAACTTGTTCAACCTT
4145991 AACTTGATTA
Statistics
Matches: 522, Mismatches: 45, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
119 63 0.12
120 47 0.09
122 132 0.25
123 280 0.54
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (123 bp):
CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAGCAC
Found at i:4145946 original size:246 final size:245
Alignment explanation
Indices: 4145313--4145990 Score: 1053
Period size: 242 Copynumber: 2.8 Consensus size: 245
4145303 CCAGGTGGAG
*
4145313 TTCATAATGAGAAGAACTCATCTG-AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTACAA
1 TTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* * *
4145377 -CTTTTTGCTCGACT-TATCATAGAATGAGATAGATCAGCACCAACATTTTCAGAGAGAGTTCAT
65 CCTTTTT-CTCGACTCTATCATAGAAGGAGATAGATCAACACCAACATTTCCAGAGAGAGTTCAT
*
4145440 AATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
129 AATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
* ***
4145505 GCTCGACTCTATCACAGAAGGGGATAGATCAGCACCAATATTTCCAGAGAGA
194 GCTCGACTCTATCACAAAAGAAAATAGATCAGCACCAATATTTCCAGAGAGA
* * * *
4145557 TGCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT--G-AGAACTTATTTAAC
1 TTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* * *
4145619 CTTTTTCTCGACTCTATCACAAAAGGAGATAGATCAACACCAACATTTCCAGAGAGAATTCATAA
66 CTTTTTCTCGACTCTATCATAGAAGGAGATAGATCAACACCAACATTTCCAGAGAGAGTTCATAA
* *
4145684 TGAGAAGAACTCATCTGAAGAGGAAGAACAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
131 TGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
4145749 TCGACTCTATCACAAAAGAAAATAGATCATCACCAATATTTCCAGAGAGAA
196 TCGACTCTATCACAAAAGAAAATAGATCAGCACCAATATTTCCAGAGAG-A
* *
4145800 TTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAAAAGTTCTTAATGAGAAGAACTTGTTCAAC
1 TTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* * *
4145865 CTTTTTCTCGACTCTATCATAGAAGGAGATAGATCATCATCAACATTTCCAGATAGAGTTCATAA
66 CTTTTTCTCGACTCTATCATAGAAGGAGATAGATCAACACCAACATTTCCAGAGAGAGTTCATAA
* *
4145930 TGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCGACCTT
131 TGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
4145991 AACTTGATTA
Statistics
Matches: 393, Mismatches: 34, Indels: 12
0.90 0.08 0.03
Matches are distributed among these distances:
241 17 0.04
242 159 0.40
243 44 0.11
244 41 0.10
245 4 0.01
246 128 0.33
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (245 bp):
TTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
CTTTTTCTCGACTCTATCATAGAAGGAGATAGATCAACACCAACATTTCCAGAGAGAGTTCATAA
TGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
TCGACTCTATCACAAAAGAAAATAGATCAGCACCAATATTTCCAGAGAGA
Found at i:4146350 original size:80 final size:80
Alignment explanation
Indices: 4146216--4146396 Score: 326
Period size: 80 Copynumber: 2.3 Consensus size: 80
4146206 GAGGAAGAAT
* *
4146216 AAGTTCATAATGTGAAGAAATTGTTCAACCTTTTGCTAGATTTCATCGCAGAAGGAGATAAGTTA
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTAGATTTCATCGCAGAAGGAGATAAGTTA
4146281 TCATTCCCAGTGGAA
66 TCATTCCCAGTGGAA
* *
4146296 GAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTAGATTTCATCGCAGAAGGAGATATGTTA
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTAGATTTCATCGCAGAAGGAGATAAGTTA
4146361 TCATTCCCAGTGGAA
66 TCATTCCCAGTGGAA
4146376 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
4146397 AGCCTCAAAG
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 96 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (80 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTAGATTTCATCGCAGAAGGAGATAAGTTA
TCATTCCCAGTGGAA
Found at i:4146584 original size:3 final size:3
Alignment explanation
Indices: 4146578--4146638 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
4146568 ATTTTTTTAT
* *
4146578 TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA TTA TAA TTAA TTA -AA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
4146623 TTA TTA TTA CTA TTA T
1 TTA TTA TTA TTA TTA T
4146639 AGGTCCAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 3 0.06
3 39 0.81
4 6 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:4146599 original size:18 final size:19
Alignment explanation
Indices: 4146568--4146611 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
4146558 TTTTTTTCCC
4146568 ATTTT-TTTATTTATTATT
1 ATTTTATTTATTTATTATT
4146586 ATTTTATTTA-TTATTATT
1 ATTTTATTTATTTATTATT
4146604 ATTATTAT
1 ATT-TTAT
4146612 AATTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTTATTTATTTATTATT
Done.