Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 24
Found at i:3429838 original size:44 final size:44
Alignment explanation
Indices: 3429756--3429963 Score: 193
Period size: 44 Copynumber: 4.7 Consensus size: 44
3429746 CATAAACCGT
* * * *
3429756 TCACATTTTCAGATATTCACATAGTTCAGTATCACATAGCTTATA
1 TCACATGTTCACATAATCACATAGATCA-TATCACATAGCTTATA
* *
3429801 TCATATGTTCACATAATAACATAGATCATATCACATAGCTTATA
1 TCACATGTTCACATAATCACATAGATCATATCACATAGCTTATA
* * * *
3429845 TCACATGTTTACATAATCACTTAGATCATATTATATAGCTTATA
1 TCACATGTTCACATAATCACATAGATCATATCACATAGCTTATA
* * ** * * *
3429889 TCACATTTTCATATGTTCACGTAGTTTAGTATCACATAGCTTATA
1 TCACATGTTCACATAATCACATAGATCA-TATCACATAGCTTATA
* * *
3429934 TCA-TTTTTCTCATATATCCACATAGATCAT
1 TCACATGTTCACATA-AT-CACATAGATCAT
3429964 GTAACACATA
Statistics
Matches: 130, Mismatches: 30, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
44 81 0.62
45 41 0.32
46 8 0.06
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (44 bp):
TCACATGTTCACATAATCACATAGATCATATCACATAGCTTATA
Found at i:3429849 original size:89 final size:90
Alignment explanation
Indices: 3429756--3429976 Score: 216
Period size: 89 Copynumber: 2.5 Consensus size: 90
3429746 CATAAACCGT
* * *
3429756 TCACATTTTCAGATATTCACATAGTTCAGTATCACATAGCTTATATCATATGTTCACATAATAAC
1 TCACATTTTCACATATTCACATAGATCAGTATCACATAGCTTATATCACATGTTCACATAATAAC
3429821 ATAGATCA-TATCACATAGCTTATA
66 ATAGATCAGTATCACATAGCTTATA
* * * * * * ** *
3429845 TCACATGTTT-ACATAATCACTTAGATCA-TATTATATAGCTTATATCACATTTTCATATGTTCA
1 TCACAT-TTTCACATATTCACATAGATCAGTATCACATAGCTTATATCACATGTTCACATAATAA
* * *
3429908 CGTAGTTTAGTATCACATAGCTTATA
65 CATAGATCAGTATCACATAGCTTATA
* * *
3429934 TCA-TTTTTCTCATATATCCACATAGATCATGTAACACATAGCT
1 TCACATTTTCACATAT-T-CACATAGATCA-GTATCACATAGCT
3429977 CATGTATGAC
Statistics
Matches: 103, Mismatches: 22, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
87 3 0.03
88 38 0.37
89 40 0.39
90 13 0.13
92 9 0.09
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.38
Consensus pattern (90 bp):
TCACATTTTCACATATTCACATAGATCAGTATCACATAGCTTATATCACATGTTCACATAATAAC
ATAGATCAGTATCACATAGCTTATA
Found at i:3429973 original size:16 final size:16
Alignment explanation
Indices: 3429952--3429982 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3429942 CTCATATATC
3429952 CACATAGATCATGTAA
1 CACATAGATCATGTAA
*
3429968 CACATAGCTCATGTA
1 CACATAGATCATGTA
3429983 TGACAATGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (16 bp):
CACATAGATCATGTAA
Found at i:3430631 original size:57 final size:57
Alignment explanation
Indices: 3430543--3430660 Score: 236
Period size: 57 Copynumber: 2.1 Consensus size: 57
3430533 CGACACCCAA
3430543 ACCCAAATCTCACCTATTTTTATTTTGAAGTATCGGTATTGTTCATTTAGTACCGAT
1 ACCCAAATCTCACCTATTTTTATTTTGAAGTATCGGTATTGTTCATTTAGTACCGAT
3430600 ACCCAAATCTCACCTATTTTTATTTTGAAGTATCGGTATTGTTCATTTAGTACCGAT
1 ACCCAAATCTCACCTATTTTTATTTTGAAGTATCGGTATTGTTCATTTAGTACCGAT
3430657 ACCC
1 ACCC
3430661 CTTTCCCATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (57 bp):
ACCCAAATCTCACCTATTTTTATTTTGAAGTATCGGTATTGTTCATTTAGTACCGAT
Found at i:3436615 original size:13 final size:15
Alignment explanation
Indices: 3436585--3436616 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
3436575 AGAGGGCAAA
3436585 AGAAAAATATACGAG
1 AGAAAAATATACGAG
3436600 AGAAAAA-ATA-GAG
1 AGAAAAATATACGAG
3436613 AGAA
1 AGAA
3436617 TTGAGAGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.66, C:0.03, G:0.22, T:0.09
Consensus pattern (15 bp):
AGAAAAATATACGAG
Found at i:3441993 original size:128 final size:128
Alignment explanation
Indices: 3441835--3442090 Score: 512
Period size: 128 Copynumber: 2.0 Consensus size: 128
3441825 GGTTGGATTT
3441835 TTTTGTTAAATTTAATAAAAAAGTTAAATTCTTTTTAGAGACAACTTGTCTTTGTCAAATAATAT
1 TTTTGTTAAATTTAATAAAAAAGTTAAATTCTTTTTAGAGACAACTTGTCTTTGTCAAATAATAT
3441900 TTTTTTTATAAATTCAACGTGTTTTTTATCATATATTAATATTTTATTTAAATTATAGATATA
66 TTTTTTTATAAATTCAACGTGTTTTTTATCATATATTAATATTTTATTTAAATTATAGATATA
3441963 TTTTGTTAAATTTAATAAAAAAGTTAAATTCTTTTTAGAGACAACTTGTCTTTGTCAAATAATAT
1 TTTTGTTAAATTTAATAAAAAAGTTAAATTCTTTTTAGAGACAACTTGTCTTTGTCAAATAATAT
3442028 TTTTTTTATAAATTCAACGTGTTTTTTATCATATATTAATATTTTATTTAAATTATAGATATA
66 TTTTTTTATAAATTCAACGTGTTTTTTATCATATATTAATATTTTATTTAAATTATAGATATA
3442091 GAAAAAAGAT
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (128 bp):
TTTTGTTAAATTTAATAAAAAAGTTAAATTCTTTTTAGAGACAACTTGTCTTTGTCAAATAATAT
TTTTTTTATAAATTCAACGTGTTTTTTATCATATATTAATATTTTATTTAAATTATAGATATA
Found at i:3442153 original size:3 final size:3
Alignment explanation
Indices: 3442145--3442270 Score: 231
Period size: 3 Copynumber: 43.0 Consensus size: 3
3442135 CCAATAATTC
3442145 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3442193 TCT TCT TCT TCT TCT TCT TCT T-T TCT TCT TCT TCT TCT TCT TC- TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3442239 TCT TCT TCT TCT TCT T-T TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3442271 CACAGAGTTT
Statistics
Matches: 120, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
2 6 0.05
3 114 0.95
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:3442450 original size:3 final size:3
Alignment explanation
Indices: 3442442--3442522 Score: 162
Period size: 3 Copynumber: 27.0 Consensus size: 3
3442432 AAGATGTGAG
3442442 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3442490 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3442523 GTAGTCATTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3443338 original size:19 final size:19
Alignment explanation
Indices: 3443314--3443391 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
3443304 AATGCATTTT
3443314 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
*
3443333 ATGCATCGATGCACTCAGTACATTTG
1 ATGCATCGATGCA--CA-TAC----C
3443359 ATGCATCGATGCACA-AGCC
1 ATGCATCGATGCACATA-CC
3443378 ATGCATCGATGCAC
1 ATGCATCGATGCAC
3443392 TCTGGCTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
19 27 0.55
21 2 0.04
22 4 0.08
23 1 0.02
24 2 0.04
26 13 0.27
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:3443357 original size:45 final size:45
Alignment explanation
Indices: 3443308--3443393 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
3443298 ACATCAAATG
*
3443308 CATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTCAGTA
1 CATTTGATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGTA
3443353 CATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTC
1 CATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTC
3443394 TGGCTATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (45 bp):
CATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGTA
Found at i:3454164 original size:31 final size:31
Alignment explanation
Indices: 3454126--3454195 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
3454116 CTTTTAAAAC
*
3454126 TTGCAATACAAT-CCTCCAACATTTAGTCCGT
1 TTGCAATACAATCCCT-CAACATTTAGTCCAT
*** *
3454157 TTGCAATATGGTCCCTCAACATTTAGTCTAT
1 TTGCAATACAATCCCTCAACATTTAGTCCAT
3454188 TTGCAATA
1 TTGCAATA
3454196 TGGTCCATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 30 0.91
32 3 0.09
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (31 bp):
TTGCAATACAATCCCTCAACATTTAGTCCAT
Found at i:3454196 original size:31 final size:31
Alignment explanation
Indices: 3454142--3454201 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3454132 TACAATCCTC
*
3454142 CAACATTTAGTCCGTTTGCAATATGGTCCCT
1 CAACATTTAGTCCATTTGCAATATGGTCCCT
*
3454173 CAACATTTAGTCTATTTGCAATATGGTCC
1 CAACATTTAGTCCATTTGCAATATGGTCC
3454202 ATGATGTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (31 bp):
CAACATTTAGTCCATTTGCAATATGGTCCCT
Found at i:3455651 original size:31 final size:31
Alignment explanation
Indices: 3455616--3455682 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
3455606 TTAAAACTTA
3455616 CAATACAATCCCCCAATATTTAGTCCATTTG
1 CAATACAATCCCCCAATATTTAGTCCATTTG
*** * *
3455647 CAATATGGTCCCTCAATATTTAGTCCGTTTG
1 CAATACAATCCCCCAATATTTAGTCCATTTG
3455678 CAATA
1 CAATA
3455683 TGGTCCCGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.34
Consensus pattern (31 bp):
CAATACAATCCCCCAATATTTAGTCCATTTG
Found at i:3455683 original size:31 final size:31
Alignment explanation
Indices: 3455624--3455689 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
3455614 TACAATACAA
3455624 TCCCCCAATATTTAGTCCATTTGCAATATGG
1 TCCCCCAATATTTAGTCCATTTGCAATATGG
* *
3455655 TCCCTCAATATTTAGTCCGTTTGCAATATGG
1 TCCCCCAATATTTAGTCCATTTGCAATATGG
3455686 TCCC
1 TCCC
3455690 GATGTAACTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (31 bp):
TCCCCCAATATTTAGTCCATTTGCAATATGG
Found at i:3458484 original size:37 final size:37
Alignment explanation
Indices: 3458405--3458487 Score: 91
Period size: 37 Copynumber: 2.2 Consensus size: 37
3458395 GATAATCTAT
*
3458405 TAATATATCAAACAAAATATATAAATTTATATACTAC
1 TAATATATCAAACAAAATATATAAATTGATATACTAC
* *
3458442 CAATATATCAAATATAAATAT-TAAAATTGATATTA-TA-
1 TAATATATCAAACA-AAATATAT-AAATTGATA-TACTAC
3458479 TAATATATC
1 TAATATATC
3458488 TTTTAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
37 21 0.54
38 16 0.41
39 2 0.05
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.37
Consensus pattern (37 bp):
TAATATATCAAACAAAATATATAAATTGATATACTAC
Found at i:3459230 original size:16 final size:17
Alignment explanation
Indices: 3459209--3459249 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
3459199 ACGATTTGAC
*
3459209 ATTTATATTATATTT-T
1 ATTTATATCATATTTAT
3459225 ATTTATATCATATTTAT
1 ATTTATATCATATTTAT
3459242 ATTTATAT
1 ATTTATAT
3459250 AGCATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTATATCATATTTAT
Found at i:3459245 original size:6 final size:6
Alignment explanation
Indices: 3459209--3459249 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
3459199 ACGATTTGAC
*
3459209 ATTTAT A-TTAT ATTT-T ATTTAT A-TCAT ATTTAT ATTTAT AT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
3459250 AGCATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 14 0.47
6 16 0.53
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (6 bp):
ATTTAT
Found at i:3461077 original size:2 final size:2
Alignment explanation
Indices: 3461072--3461096 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3461062 TATATATATA
3461072 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3461097 TAGTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3462054 original size:3 final size:3
Alignment explanation
Indices: 3462046--3462076 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3462036 TAGCTGCTCC
*
3462046 TGA TGA TGA CGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
3462077 AGGAGTGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:3464372 original size:23 final size:23
Alignment explanation
Indices: 3464346--3464393 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
3464336 CACTACAATT
3464346 CAATTCTACGCGGCACTTCAGTG
1 CAATTCTACGCGGCACTTCAGTG
* * *
3464369 CAATTCTATGTGGCACTTCGGTG
1 CAATTCTACGCGGCACTTCAGTG
3464392 CA
1 CA
3464394 TTTATGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (23 bp):
CAATTCTACGCGGCACTTCAGTG
Found at i:3464624 original size:3 final size:3
Alignment explanation
Indices: 3464616--3464668 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
3464606 CATTTCCTTG
3464616 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3464664 -TA TTA
1 TTA TTA
3464669 CCTCACTAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3470923 original size:23 final size:23
Alignment explanation
Indices: 3470885--3470944 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
3470875 CATCTTATAT
* *
3470885 GGCACTACGGTACAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
3470908 GGCACTTTGGTGCAATTCTATGT
1 GGCACTTCGGTGCAATTCTACGC
3470931 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
3470945 TTTATACGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:3489342 original size:15 final size:15
Alignment explanation
Indices: 3489318--3489351 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3489308 TCGTAGGACC
*
3489318 ACTACATCCCGAATG
1 ACTACATCCCGAAGG
*
3489333 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
3489348 ACTA
1 ACTA
3489352 TTATGCCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:3489482 original size:29 final size:29
Alignment explanation
Indices: 3489436--3489516 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
3489426 TTCCATATGT
3489436 TCATGTA-CTCATGCCATTTCTCTTGTGA
1 TCATGTAGCTCATGCCATTTCTCTTGTGA
*
3489464 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGCCATTTCTCTTGTGA
*
3489493 TCATGTAGCTCATGGCATGTTCTC
1 TCATGTAGCTCATGCCAT-TTCTC
3489517 ATATCACATA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 7 0.14
29 37 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (29 bp):
TCATGTAGCTCATGCCATTTCTCTTGTGA
Found at i:3489962 original size:64 final size:64
Alignment explanation
Indices: 3489893--3490053 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 64
3489883 TAATGAAGGC
* * **
3489893 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATGTTT-TATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATACACT-AAATGCATTCGATGTTTATATT-TTAAAAG
3489956 A
64 A
* * *
3489957 ATGCATCGATGCA-TGCCTTATGCATCGATACACTAATTGCATTCGATGTTTATATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATACACTAAATGCATTCGATGTTTATATTTTAAAAGA
* *
3490021 GTGCATCGATGCACTACCTGTGCATCGATACAC
1 ATGCATCGATGCACTACTTGTGCATCGATACAC
3490054 CTTCAAACAA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
63 1 0.01
64 75 0.91
65 6 0.07
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATACACTAAATGCATTCGATGTTTATATTTTAAAAGA
Found at i:3493404 original size:23 final size:25
Alignment explanation
Indices: 3493351--3493409 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
3493341 CATTATATTT
* *
3493351 AGAAGATATATAATTTATTTTTACA
1 AGAAAATATATAATTTATTTCTACA
3493376 AGAAAATATATAA-TTACTTTCTACA
1 AGAAAATATATAATTTA-TTTCTACA
*
3493401 A-AAATTATA
1 AGAAAATATA
3493410 AACACGTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (25 bp):
AGAAAATATATAATTTATTTCTACA
Found at i:3497950 original size:182 final size:182
Alignment explanation
Indices: 3497579--3498242 Score: 766
Period size: 182 Copynumber: 3.6 Consensus size: 182
3497569 TTGTCGGTTT
* * * * *
3497579 GTGTCGATAC-AAATGAAAAATGTATCGCTCCATAGCAATATAATAGGTAAAAATATGATAAAAC
1 GTGTCGATACTTAAT-AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
* * ** ** ** * * * *
3497643 CGGGTTCATTATGATAAAATTGGTAAACCGCTACTGGATATATCGAAAGTATCGATTAGATTTAA
65 C-AGTACAAAATGATAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGA-TA-AATTAA
*
3497708 -ATAAGTATCGACAC-TTTTGAAATTTAAAAGAGAAGAAGTAATAACGCCTATAAA
127 TATAAGTATCGACACTTTTTGAAATTTAAAAGAGAAGAAGTTATAACGCCTATAAA
* * * *
3497762 GTGTCGATACTTAATAAAAACGTATCGATCCATAACAATATAACAGGTATAAGTATGATAAAACC
1 GTGTCGATACTTAATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACC
**
3497827 AGTCACAAAATGATAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACCTTAATAT
66 AGT-ACAAAATGATAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATAAATTAATAT
*
3497892 AAGTATCGACACTTTTTG-AATTTAAAAGAGAAGAAGTTATAGCGCCTATAAA
130 AAGTATCGACACTTTTTGAAATTTAAAAGAGAAGAAGTTATAACGCCTATAAA
* * * * * * *
3497944 GTGTCGATACTTTATACAAATGTATTGATCTATAGCAATATAACATGTAAGAATATGACAAAA-C
1 GTGTCGATACTTAATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACC
* * *
3498008 AGGT-CTAGAAATGATAAAACCGGTAAAAAGCTATCGAATATATTGAAAGTGTCGATAAATTAAT
66 A-GTAC-A-AAATGATAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATAAATTAAT
* * *
3498072 ATAAGTATCGACA-TTTTCGTAATTTAAAAGAGAAGAAGTTATAACGCCTAAAAA
128 ATAAGTATCGACACTTTTTGAAATTTAAAAGAGAAGAAGTTATAACGCCTATAAA
* * * *
3498126 GTGTTGATACTTTATGAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACC
1 GTGTCGATACTTAATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACC
* * * * * *
3498191 GGTATCGAAATGACAAAACCGGTAAAGCGCTACCGGTTATGTTGAAAGTGTC
66 AGTA-CAAAATGATAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTC
3498243 AGTGCTTTAA
Statistics
Matches: 411, Mismatches: 59, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
180 1 0.00
181 12 0.03
182 294 0.72
183 100 0.24
184 4 0.01
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (182 bp):
GTGTCGATACTTAATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACC
AGTACAAAATGATAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATA
AGTATCGACACTTTTTGAAATTTAAAAGAGAAGAAGTTATAACGCCTATAAA
Found at i:3500147 original size:22 final size:22
Alignment explanation
Indices: 3500096--3500151 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
3500086 TGTTTTTGGT
*
3500096 TTTTTTTATATAAAATGATGGTA
1 TTTTATTATATAAAATGAT-GTA
*
3500119 TAGTTATTATATAAAATGAT-TAA
1 T-TTTATTATATAAAATGATGT-A
3500142 TTTTATTATA
1 TTTTATTATA
3500152 AATTCAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 3 0.11
24 16 0.57
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTTTATTATATAAAATGATGTA
Found at i:3500823 original size:18 final size:18
Alignment explanation
Indices: 3500800--3500838 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3500790 GAGAAAATTT
3500800 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
3500818 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
3500836 GAA
1 GAA
3500839 ATGAGGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:3501162 original size:17 final size:17
Alignment explanation
Indices: 3501140--3501175 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3501130 TTTAAATATT
3501140 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
3501157 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
3501174 TC
1 TC
3501176 CTAATGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (17 bp):
TCATGAAAAGATATTAA
Found at i:3502375 original size:19 final size:19
Alignment explanation
Indices: 3502325--3502377 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
3502315 AATGTAGGGT
* *
3502325 TAATTTTGTATAAGATTTT
1 TAATTTTGTATACGATTTA
3502344 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
3502363 TAATTTTGTATACGA
1 TAATTTTGTATACGA
3502378 ACGTAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:3503045 original size:198 final size:198
Alignment explanation
Indices: 3502707--3503671 Score: 1627
Period size: 198 Copynumber: 4.9 Consensus size: 198
3502697 GGTAAACATA
*
3502707 TGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATTGAGACCCATAATTATAATGTAAT
1 TGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAAT
* *
3502772 AGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACATGTCTACATAAAGT
66 AGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGT
3502837 ATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGG
131 ATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGG
3502902 AAC
196 AAC
*
3502905 TGTGTCGATACATTTATAAAAAGTATCAATCCCAAAAACATCGAGACCCATAATTATAATGTAAT
1 TGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAAT
* *
3502970 AGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAAGTATACATAAAGT
66 AGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGT
*
3503035 ATCAACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGG
131 ATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGG
*
3503100 AAA
196 AAC
* *
3503103 TATGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAAT
1 TGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAAT
3503168 AGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGT
66 AGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGT
*
3503233 ATTGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGG
131 ATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGG
3503298 AAC
196 AAC
*
3503301 TGTGTTGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAAT
1 TGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAAT
* * * * * * *
3503366 AAGTAAATTATCAATCTAATCGGTCTAAATATACCAGTTTATGAAAAAACATGTGTACATAAAGT
66 AGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGT
* *
3503431 ATCGACACTTGTTTAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCA
131 ATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAA-GT--GCA
3503496 T--AA-
193 TGGAAC
* * *
3503499 TGTGTCGATACAATTATAAAAAGTATCAATCCC-AAAATATCGAGACCCATAATTATAATGTAAT
1 TGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAAT
3503563 AGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGT
66 AGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGT
3503628 ATCGACACTCT-TTGAATTTGTGTCGATACGTTT-TGTCCAGAATG
131 ATCGACACT-TGTTGAATTTGTGTCGATAC-TTTGTGTCCAGAATG
3503672 TAAATGGTCA
Statistics
Matches: 723, Mismatches: 39, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
197 125 0.17
198 591 0.82
199 4 0.01
201 3 0.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (198 bp):
TGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAAT
AGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGT
ATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGG
AAC
Found at i:3504167 original size:15 final size:15
Alignment explanation
Indices: 3504147--3504198 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
3504137 AGAATCGGGG
*
3504147 CTCTTCTCAACCCAT
1 CTCTTCTCAACCCAC
3504162 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAC
*
3504177 CTCTTCTCAACCCAG
1 CTCTTCTCAACCCAC
3504192 CTCTTCT
1 CTCTTCT
3504199 GAGGAAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.17, C:0.48, G:0.02, T:0.33
Consensus pattern (15 bp):
CTCTTCTCAACCCAC
Found at i:3505381 original size:9 final size:9
Alignment explanation
Indices: 3505341--3505380 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
3505331 CAAGCGGTCA
3505341 ATGAAGATG
1 ATGAAGATG
*
3505350 ATGAAGAAG
1 ATGAAGATG
*
3505359 ATGAAAATG
1 ATGAAGATG
*
3505368 ATGATGATG
1 ATGAAGATG
3505377 ATGA
1 ATGA
3505381 TCCAAACAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (9 bp):
ATGAAGATG
Found at i:3508451 original size:21 final size:21
Alignment explanation
Indices: 3508413--3508452 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3508403 CAATGGGATT
*
3508413 AGGATTAGGAATTAGATTTTG
1 AGGATTAGGAAGTAGATTTTG
* *
3508434 AGGATTTGGAAGTGGATTT
1 AGGATTAGGAAGTAGATTT
3508453 GGTTGACGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.38
Consensus pattern (21 bp):
AGGATTAGGAAGTAGATTTTG
Found at i:3509215 original size:20 final size:20
Alignment explanation
Indices: 3509186--3509223 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3509176 CCCCTTCAAA
*
3509186 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
3509206 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
3509224 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:3512921 original size:20 final size:21
Alignment explanation
Indices: 3512883--3512922 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3512873 GAAGTTTTAA
* *
3512883 GATCATCAATTGTCTTTTGAT
1 GATCATCAATTGACCTTTGAT
3512904 GATCATC-ATTGACCTTTGA
1 GATCATCAATTGACCTTTGA
3512923 AAGTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (21 bp):
GATCATCAATTGACCTTTGAT
Found at i:3513056 original size:21 final size:22
Alignment explanation
Indices: 3513032--3513074 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3513022 GAGCTTATTT
3513032 TCATTTTTCA-ATTTTA-AAACA
1 TCATTTTT-ATATTTTATAAACA
3513053 TCATTTTTATATTTTATAAACA
1 TCATTTTTATATTTTATAAACA
3513075 ATTTCTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 14 0.70
22 5 0.25
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (22 bp):
TCATTTTTATATTTTATAAACA
Found at i:3517674 original size:16 final size:14
Alignment explanation
Indices: 3517636--3517667 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3517626 ACAATGTAAC
3517636 CGGTCTAAATATAT
1 CGGTCTAAATATAT
3517650 CGGTCTAAATATAT
1 CGGTCTAAATATAT
3517664 CGGT
1 CGGT
3517668 TATTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (14 bp):
CGGTCTAAATATAT
Found at i:3517709 original size:22 final size:21
Alignment explanation
Indices: 3517684--3517729 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3517674 AAAAGAAACG
*
3517684 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
3517706 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
3517727 TAT
1 TAT
3517730 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:3517910 original size:22 final size:21
Alignment explanation
Indices: 3517884--3517929 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3517874 AAAAGAAAGG
*
3517884 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
3517906 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
3517927 TAT
1 TAT
3517930 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:3518142 original size:398 final size:395
Alignment explanation
Indices: 3517095--3518502 Score: 1666
Period size: 398 Copynumber: 3.5 Consensus size: 395
3517085 TTATTCATTC
* **
3517095 GTGTCGATACATGTTGTCCATAATGTATTTCCAAACCAAGTGCACGAACAAAGTGTCGATACATT
1 GTGTCGACACATGTTGTCCATAATAAATTTCCAAACCAAGTGCACGAA-AAAGTGTCGATACATT
* * * *
3517160 TATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAAATAACAA
65 TATAAAAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAA
* * * * * *
3517225 TGTAACCGGTCTAAATATACCGATTTATGAGAAAAGAGATATACATAAAGTATCGACACTTTATA
130 TGTAACCGGTCTAAATATACCG-GTTATTAAAAAAAAGGTATACATAATGTATCGACACTTTATA
* * * **
3517290 CATTTATGTCGATACTTTGTGTCCATAATGTATTTTCCAACCAAAACAAGTTCAC-AAATAAGTG
194 CATTTGTGTCGACACTTTATGTCCATAATAAATTTT----CC-AAACAAGTTCACGAAA-AAGTG
* * *
3517354 TCGATACATTTATATCAAGTGTCGATCCCAAAAACATCGAAACCCGTAACTATAATGTAATAGGT
253 TCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACGTAATTATAATGTAATAGGT
* * * * * * * * * *
3517419 CACTTTACAATGTAACCAGTTTAAATTTACCAGTT-TTATGAGAAAATAGGTCTACA-ATATGTA
318 AACATAACAATGTAACCGGTCTAAATATACCGGTTATTA--AAAAAAAAGGTATACATA-ATGTA
3517482 TCGACACTTTATTAATTT
380 TCGA-ACTTTA-TAATTT
* * ** *
3517500 GTGTCGATACATGTTGTCCAAAATGTATTTCCAAACCAAGTGCACGAAAAAAGTGTCAATACATT
1 GTGTCGACACATGTTGTCCATAATAAATTTCCAAACCAAGTGCACG-AAAAAGTGTCGATACATT
*
3517565 TATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAA
65 TATAAAAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAA
*
3517630 TGTAACCGGTCTAAATATATCGGTCTAAATATATCGGTTATTAAAAAAGAAACGTATACATAATG
130 TGTAACCGGTCTAAATATA-----C---------CGGTTATT-AAAAA-AAAGGTATACATAATG
*
3517695 TATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
179 TATCGACACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
*
3517760 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
244 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACGTAATTATAAT
*
3517825 GTAATAGGTAACATAACAATGTAACCGGTCTAAATATACTGGTTATTAAAAAAGAAAGGTATACA
309 GTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAA-AAAGGTATACA
3517890 TAATGTATCGATACTTTATACATTT
373 TAATGTATCGA-ACTTTATA-ATTT
* *
3517915 GTGTCGACAC-TTTATGTCCATAATAAATTTTCCAAA-CAAGTTCACGAAAAAGTGTCGATACAT
1 GTGTCGACACATGT-TGTCCATAATAAA-TTTCCAAACCAAGTGCACGAAAAAGTGTCGATACAT
*
3517978 TTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACA
64 TTATAAAAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACA
*
3518043 ATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACATAATGTATCGATACTTTATA
129 ATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACATAATGTATCGACACTTTATA
*
3518108 CATTTGTGTCAACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATA
194 CATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATA
* * *
3518173 CTTTTATAACAAGCGTCGATCCCAAAAACATCGAAACACGTAATTATAATGTAATAGTTAACATA
259 CATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACGTAATTATAATGTAATAGGTAACATA
3518238 ACAATGTAACCGGTCTAAATATACCGGTTATT-AAAAAAAAGGTATACATAATGTATCG-AC---
324 ACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAAGGTATACATAATGTATCGAACTTT
*
3518298 ---A-CT
389 ATAATTT
*
3518301 -T-T------A---TGTCCATAATAAATTTTCCAAA-CAAGTTCACGAAAAAGTGTCGATACATT
1 GTGTCGACACATGTTGTCCATAATAAA-TTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATT
* * * * * * *
3518354 TAGAAAAAATGTCGATCCTAAAAACATCGAAAC-CTGTAATTATAATGTAATAGGTCACTTTACA
65 TATAAAAAGTGTCGATCCCAAAAACATCGAAACAC-ATAATTATAATGTAATAGGTAACATAACA
* * * *
3518418 ATGTAACCGGTTTAAATTTACTGGTT-TTATGAGAAAATAGGTATACATAATGTATCGACACTTT
129 ATGTAACCGGTCTAAATATACCGGTTATTA--A-AAAAAAGGTATACATAATGTATCGACACTTT
* * * *
3518482 TTAAATTAGTGTCGATACTTT
191 ATACATTTGTGTCGACACTTT
3518503 TTAAAATTAC
Statistics
Matches: 905, Mismatches: 69, Indels: 86
0.85 0.07 0.08
Matches are distributed among these distances:
374 4 0.00
375 127 0.14
376 1 0.00
377 45 0.05
384 1 0.00
385 1 0.00
386 1 0.00
387 1 0.00
394 2 0.00
396 21 0.02
397 5 0.01
398 186 0.21
399 5 0.01
400 8 0.01
405 139 0.15
406 2 0.00
409 1 0.00
410 1 0.00
414 109 0.12
415 161 0.18
416 17 0.02
418 4 0.00
419 6 0.01
420 57 0.06
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (395 bp):
GTGTCGACACATGTTGTCCATAATAAATTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTT
ATAAAAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAAT
GTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACATAATGTATCGACACTTTATACA
TTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACA
TTTATAACAAGTGTCGATCCCAAAAACATCGAAACACGTAATTATAATGTAATAGGTAACATAAC
AATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAAGGTATACATAATGTATCGAACTTTAT
AATTT
Found at i:3518219 original size:198 final size:200
Alignment explanation
Indices: 3517650--3518304 Score: 1201
Period size: 198 Copynumber: 3.3 Consensus size: 200
3517640 CTAAATATAT
* *
3517650 CGGTCTAAATATATCGGTTATTAAAAAAGAAACGTATACATAATGTATCGATACTTTATACATTT
1 CGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAATGTATCGATACTTTATACATTT
3517715 GTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTT
66 GTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTT
3517780 ATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAAT
131 ATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAAT
3517845 GTAAC
196 GTAAC
*
3517850 CGGTCTAAATATACTGGTTATTAAAAAAGAAAGGTATACATAATGTATCGATACTTTATACATTT
1 CGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAATGTATCGATACTTTATACATTT
3517915 GTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTT
66 GTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTT
3517980 ATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAAT
131 ATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAAT
3518045 GTAAC
196 GTAAC
3518050 CGGTCTAAATATACCGGTTATT-AAAAA-AAAGGTATACATAATGTATCGATACTTTATACATTT
1 CGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAATGTATCGATACTTTATACATTT
* *
3518113 GTGTCAACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACTTTT
66 GTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTT
* * *
3518178 ATAACAAGCGTCGATCCCAAAAACATCGAAACACGTAATTATAATGTAATAGTTAACATAACAAT
131 ATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAAT
3518243 GTAAC
196 GTAAC
*
3518248 CGGTCTAAATATACCGGTTATT-AAAAA-AAAGGTATACATAATGTATCGACACTTTAT
1 CGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAATGTATCGATACTTTAT
3518305 GTCCATAATA
Statistics
Matches: 445, Mismatches: 10, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
198 222 0.50
199 5 0.01
200 218 0.49
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (200 bp):
CGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAATGTATCGATACTTTATACATTT
GTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTT
ATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAAT
GTAAC
Found at i:3518320 original size:177 final size:178
Alignment explanation
Indices: 3518119--3518481 Score: 552
Period size: 177 Copynumber: 2.0 Consensus size: 178
3518109 ATTTGTGTCA
* * *
3518119 ACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACTTTTATAACA
1 ACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTTAGAAAA
* *
3518184 AGCGTCGATCCCAAAAACATCGAAACAC-GTAATTATAATGTAATAGTTAACATAACAATGTAAC
66 AACGTCGATCCCAAAAACATCGAAAC-CTGTAATTATAATGTAATAGGTAACATAACAATGTAAC
3518248 CGGTCTAAATATACCGGTTATTA-A-AAAAAAGGTATACATAATGTATCG
130 CGGTCTAAATATACCGGTT-TTAGAGAAAAAAGGTATACATAATGTATCG
3518296 ACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTTAGAAAA
1 ACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTTAGAAAA
* * * * *
3518361 AATGTCGATCCTAAAAACATCGAAACCTGTAATTATAATGTAATAGGTCACTTTACAATGTAACC
66 AACGTCGATCCCAAAAACATCGAAACCTGTAATTATAATGTAATAGGTAACATAACAATGTAACC
* * * *
3518426 GGTTTAAATTTACTGGTTTTATGAGAAAATAGGTATACATAATGTATCG
131 GGTCTAAATATACCGGTTTTA-GAGAAAAAAGGTATACATAATGTATCG
3518475 ACACTTT
1 ACACTTT
3518482 TTAAATTAGT
Statistics
Matches: 168, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
176 4 0.02
177 133 0.79
178 1 0.01
179 30 0.18
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (178 bp):
ACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTTAGAAAA
AACGTCGATCCCAAAAACATCGAAACCTGTAATTATAATGTAATAGGTAACATAACAATGTAACC
GGTCTAAATATACCGGTTTTAGAGAAAAAAGGTATACATAATGTATCG
Found at i:3518369 original size:198 final size:198
Alignment explanation
Indices: 3517760--3518369 Score: 418
Period size: 200 Copynumber: 3.1 Consensus size: 198
3517750 ACAAGTTCAC
3517760 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
1 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
*
3517825 GTAATAGGTAACATAACAATGTAACCGGTCTAAATATACTGGTTATTAAAAAAGAAAGGTATACA
66 GTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATT-AAAAA-AAAGGTATACA
* * * * * * * * * *
3517890 TAATGTATCGATACTTTA--TACAT--T---TGTGTCGACACTTTATGTCCA-TAATAAATTTTC
129 TAATGTATCGACACTTTATGTCCATAATAAAT-TTTCCAAAC---AAGTTCACGAA-AAAGTGTC
* * *
3517947 CAAACAAGTTCA
189 GATAC-A-TTTA
3517959 CGAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAA
1 -GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAA
3518024 TGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACAT
65 TGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACAT
*
3518089 AATGTATCGATACTTTATACATTTGTGTCAACACTTTATGTCCATAATAAATTTTCCAAACAAGT
130 AATGTATCG--AC-----AC-TTTATGT---C-C---A--T----AATAAATTTTCCAAACAAGT
*
3518154 TCACGAAAAAGTGTCGATACTTTTA
174 TCACGAAAAAGTGTCGATACATTTA
* * * ** * * ** *
3518179 TAACAAGCGTCGAT-C--CCA-AA-AA----C-AT--C-GAAACA-CGTAA-TTATAA-TGTAAT
1 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
* ** * *
3518228 AGTTAACA--TAAC--AA-TGT-AAC-CGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACA
66 -G-TAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACA
3518286 TAATGTATCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATAC
129 TAATGTATCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATAC
3518351 ATTTA
194 ATTTA
*
3518356 GAAAAAATGTCGAT
1 GAAAAAGTGTCGAT
3518370 CCTAAAAACA
Statistics
Matches: 342, Mismatches: 37, Indels: 85
0.74 0.08 0.18
Matches are distributed among these distances:
177 54 0.16
181 1 0.00
183 1 0.00
186 1 0.00
187 1 0.00
190 6 0.02
191 2 0.01
196 2 0.01
198 69 0.20
199 6 0.02
200 113 0.33
201 2 0.01
203 9 0.03
204 5 0.01
205 10 0.03
206 8 0.02
207 1 0.00
208 1 0.00
209 2 0.01
210 1 0.00
212 1 0.00
214 2 0.01
215 3 0.01
216 1 0.00
217 1 0.00
218 1 0.00
219 11 0.03
220 3 0.01
222 14 0.04
223 3 0.01
225 6 0.02
226 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (198 bp):
GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
GTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACATA
ATGTATCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACAT
TTA
Found at i:3519019 original size:37 final size:36
Alignment explanation
Indices: 3518944--3519019 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
3518934 TTTTTATATT
*
3518944 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
3518980 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
3519017 TTT
1 TTT
3519020 TTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:3519182 original size:18 final size:19
Alignment explanation
Indices: 3519159--3519202 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3519149 CCAGTAATCC
* *
3519159 TATTCC-CTGTTAATCTTT
1 TATTCCACTGGTAATCTTA
3519177 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
3519197 TATTCC
1 TATTCC
3519203 GTAAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.20, C:0.25, G:0.07, T:0.48
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:3530847 original size:23 final size:23
Alignment explanation
Indices: 3530821--3530868 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3530811 AAGTCATCTA
3530821 TGGTGGGTTCCAGTTTGAAGTTT
1 TGGTGGGTTCCAGTTTGAAGTTT
3530844 TGGTGGGTTCCAGTTTGAAGTTT
1 TGGTGGGTTCCAGTTTGAAGTTT
3530867 TG
1 TG
3530869 TTTATAGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.08, G:0.35, T:0.44
Consensus pattern (23 bp):
TGGTGGGTTCCAGTTTGAAGTTT
Found at i:3535061 original size:2 final size:2
Alignment explanation
Indices: 3535054--3535093 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3535044 ATCCAAATTA
3535054 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
3535094 TTAATTAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3537132 original size:21 final size:21
Alignment explanation
Indices: 3537097--3537144 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3537087 CGCGAATATG
3537097 TAAATT-GCATTGCGATTTTC
1 TAAATTCGCATTGCGATTTTC
*
3537117 TAAATTCGCGTTGCGATTTTC
1 TAAATTCGCATTGCGATTTTC
*
3537138 CAAATTC
1 TAAATTC
3537145 ACAACGCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (21 bp):
TAAATTCGCATTGCGATTTTC
Found at i:3537188 original size:20 final size:20
Alignment explanation
Indices: 3537160--3537308 Score: 96
Period size: 20 Copynumber: 7.5 Consensus size: 20
3537150 GCGAATCTGT
*
3537160 AAATT-GCAACACATAAGTC
1 AAATTCGCAACGCATAAGTC
** *
3537179 AAATTCGCAATACAAAAGTC
1 AAATTCGCAACGCATAAGTC
*
3537199 AAATTCGCAACGCGAATATGT-
1 AAATTCGCAACGC--ATAAGTC
* **
3537220 AAA-TCGGAACGCGAATTTGT-
1 AAATTCGCAACGC--ATAAGTC
** *
3537240 AAA-TCGCAATACAGAAGTC
1 AAATTCGCAACGCATAAGTC
3537259 AAATTCGCAACGCA-ATAGTC
1 AAATTCGCAACGCATA-AGTC
3537279 AAATTCGCAACGCGAT-AGTC
1 AAATTCGCAACGC-ATAAGTC
3537299 AAATTCGCAA
1 AAATTCGCAA
3537309 AGCGCGTTTA
Statistics
Matches: 106, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
18 3 0.03
19 9 0.08
20 86 0.81
21 4 0.04
22 4 0.04
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACGCATAAGTC
Found at i:3537221 original size:60 final size:60
Alignment explanation
Indices: 3537076--3537308 Score: 206
Period size: 60 Copynumber: 3.9 Consensus size: 60
3537066 ACCCAGTTTC
** ** ** * * ***
3537076 CAAATTCGCAACGCGAATATGTAAATTGCATTGCGATTTTCTAAATTCGCGTTGCGATTTT
1 CAAATTCGCAACGCGAATATGTAAATTGCAACGCGATAGTC-AAATTCGCAATACAAAAGT
* * *
3537137 CCAAATTCACAACGCGAATCTGTAAATTGCAACAC-ATAAGTCAAATTCGCAATACAAAAGT
1 -CAAATTCGCAACGCGAATATGTAAATTGCAACGCGAT-AGTCAAATTCGCAATACAAAAGT
* * * *
3537198 CAAATTCGCAACGCGAATATGTAAATCGGAACGCGAATTTGT-AAA-TCGCAATACAGAAGT
1 CAAATTCGCAACGCGAATATGTAAATTGCAACGCG-A-TAGTCAAATTCGCAATACAAAAGT
3537258 CAAATTCGCAACGC-AATA-GTCAAATTCGCAACGCGATAGTCAAATTCGCAA
1 CAAATTCGCAACGCGAATATGT-AAATT-GCAACGCGATAGTCAAATTCGCAA
3537309 AGCGCGTTTA
Statistics
Matches: 139, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
58 5 0.04
59 12 0.09
60 70 0.50
61 17 0.12
62 34 0.24
63 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (60 bp):
CAAATTCGCAACGCGAATATGTAAATTGCAACGCGATAGTCAAATTCGCAATACAAAAGT
Found at i:3537969 original size:24 final size:24
Alignment explanation
Indices: 3537935--3537988 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3537925 CTGAAACGTC
3537935 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3537959 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3537983 ATCAAA
1 ATCAAA
3537989 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3538002 original size:24 final size:24
Alignment explanation
Indices: 3537935--3538002 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
3537925 CTGAAACGTC
* * *
3537935 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
3537959 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
3537983 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
3538003 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:3538752 original size:16 final size:15
Alignment explanation
Indices: 3538730--3538768 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3538720 GAAATCATTG
3538730 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
3538746 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
3538761 AAAAATTA
1 AAAAATTA
3538769 GAGATGGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:3538945 original size:18 final size:19
Alignment explanation
Indices: 3538893--3538949 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
3538883 TACCCAAAAC
*
3538893 ATTTGTGTTGCGAAACTAA
1 ATTTGTGTTGCGAAATTAA
**
3538912 AACT-TGTTGCGAAATTAA
1 ATTTGTGTTGCGAAATTAA
*
3538930 ATTTGTGTTGCGAATTTAA
1 ATTTGTGTTGCGAAATTAA
3538949 A
1 A
3538950 AATCGAGTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (19 bp):
ATTTGTGTTGCGAAATTAA
Found at i:3538961 original size:20 final size:20
Alignment explanation
Indices: 3538936--3539028 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
3538926 TTAAATTTGT
*
3538936 GTTGCGAATTTAAAAATCGA
1 GTTGCGAATTTGAAAATCGA
*
3538956 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAAATCGA
* *
3538975 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAAATC-GA
** *
3538996 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGAAAATCGA
3539016 GTTGCGAATTTGA
1 GTTGCGAATTTGA
3539029 CTTTTGTGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
19 19 0.30
20 30 0.47
21 15 0.23
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGA
Found at i:3538977 original size:19 final size:19
Alignment explanation
Indices: 3538936--3539008 Score: 101
Period size: 19 Copynumber: 3.7 Consensus size: 19
3538926 TTAAATTTGT
* *
3538936 GTTGCGAATTTAAAAATCGA
1 GTTGCGAATTTGAAATTC-A
3538956 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
3538975 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
3538994 GTGTTGCGAATTTGA
1 --GTTGCGAATTTGA
3539009 CTATCGCGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
19 20 0.41
20 16 0.33
21 13 0.27
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:3539029 original size:20 final size:20
Alignment explanation
Indices: 3538996--3539107 Score: 99
Period size: 20 Copynumber: 5.6 Consensus size: 20
3538986 GAAATTCAGT
3538996 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
* * *
3539016 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGC
*
3539036 GTTGCGAATTTGACT-TCTGT
1 GTTGCGAATTTGACTATC-GC
*
3539056 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC-TA-TCGC
3539076 GTTGCG-ATTT-ACATATTCGC
1 GTTGCGAATTTGAC-TA-TCGC
3539096 GTTGCGAATTTG
1 GTTGCGAATTTG
3539108 GAAACTGGGT
Statistics
Matches: 79, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
18 2 0.03
19 5 0.06
20 66 0.84
21 6 0.08
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:3539058 original size:60 final size:59
Alignment explanation
Indices: 3538916--3539066 Score: 162
Period size: 60 Copynumber: 2.6 Consensus size: 59
3538906 AACTAAAACT
* *
3538916 TGTTGCGAAATTAAATT-TGTGTTGCGAATTTAAAAATCGAGTTGCGAATTTGAAATTC
1 TGTTGCGAATTTGAATTCTGTGTTGCGAATTTAAAAATCGAGTTGCGAATTTGAAATTC
* * * ** * ** *
3538974 AGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTG
1 TGTTGCGAATTTG-AATTCTGTGTTGCGAATTTAAAAATCGAGTTGCGAATTTGA-AATTC
*
3539035 TGTTGCGAATTTGACTTCTGTGTTGCG-ATTTA
1 TGTTGCGAATTTGAATTCTGTGTTGCGAATTTA
3539067 CAGATTCGCG
Statistics
Matches: 75, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
58 10 0.13
59 8 0.11
60 43 0.57
61 14 0.19
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.40
Consensus pattern (59 bp):
TGTTGCGAATTTGAATTCTGTGTTGCGAATTTAAAAATCGAGTTGCGAATTTGAAATTC
Found at i:3539060 original size:40 final size:41
Alignment explanation
Indices: 3538936--3539107 Score: 130
Period size: 40 Copynumber: 4.3 Consensus size: 41
3538926 TTAAATTTGT
* * * * *
3538936 GTTGCGAATTTAAAAATC-GAGTTGCGAATTTGA-AATTC-A
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTA-TCGC
3538975 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGC
* ** *
3539016 GTTGCGAATTTG-ACTTTTGTGTTGCGAATTTGACT-TCTGT
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATC-GC
*
3539056 GTTGCG-ATTT-ACAGATTC-GCGTTGCG-ATTT-ACATATTCGC
1 GTTGCGAATTTGA-A-ATTCAGTGTTGCGAATTTGAC-TA-TCGC
3539096 GTTGCGAATTTG
1 GTTGCGAATTTG
3539108 GAAACTGGGT
Statistics
Matches: 108, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
38 2 0.02
39 27 0.25
40 58 0.54
41 21 0.19
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (41 bp):
GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGC
Found at i:3539076 original size:60 final size:61
Alignment explanation
Indices: 3538917--3539107 Score: 150
Period size: 60 Copynumber: 3.2 Consensus size: 61
3538907 ACTAAAACTT
* * * ** * *
3538917 GTTGCGAAATT-AAATT-TGTGTTGCGAATTTAAAAATCGAGTTGCGAATTTGA-A-ATTC-A
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACGATCGCGTTGCG-ATTT-ACATATTCGC
* * *
3538975 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGAC-T-TTTGT
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACGATCGCGTTGCG-ATTT-ACATATTCGC
* *
3539036 GTTGCGAATTTG-ACTTCTGTGTTGCG-ATTT-ACAGATTCGCGTTGCGATTTACATATTCGC
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGAC-GA-TCGCGTTGCGATTTACATATTCGC
3539096 GTTGCGAATTTG
1 GTTGCGAATTTG
3539108 GAAACTGGGT
Statistics
Matches: 111, Mismatches: 13, Indels: 16
0.79 0.09 0.11
Matches are distributed among these distances:
58 14 0.13
59 15 0.14
60 70 0.63
61 12 0.11
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (61 bp):
GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACGATCGCGTTGCGATTTACATATTCGC
Found at i:3539333 original size:15 final size:15
Alignment explanation
Indices: 3539328--3539370 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 15
3539318 TTATGTAAAA
3539328 TAAAATAAAATATTATT
1 TAAAAT-AAA-ATTATT
3539345 TAAAATAAAATTATT
1 TAAAATAAAATTATT
3539360 TAAAATAAAAT
1 TAAAATAAAAT
3539371 ATTAATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 17 0.65
16 3 0.12
17 6 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAATAAAATTATT
Found at i:3539350 original size:17 final size:17
Alignment explanation
Indices: 3539328--3539379 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 17
3539318 TTATGTAAAA
3539328 TAAAATAAAATATTATT
1 TAAAATAAAATATTATT
3539345 TAAAAT-AAA-ATTATT
1 TAAAATAAAATATTATT
*
3539360 TAAAATAAAATATTAAT
1 TAAAATAAAATATTATT
3539377 TAA
1 TAA
3539380 GTTATTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 12 0.38
16 6 0.19
17 14 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATAAAATATTATT
Found at i:3548275 original size:18 final size:17
Alignment explanation
Indices: 3548221--3548269 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3548211 TTGGACCCTT
* *
3548221 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
3548239 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
3548257 AGTGCATTCGATG
1 AGTGCA-TCGATG
3548270 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:3557117 original size:65 final size:64
Alignment explanation
Indices: 3556919--3557128 Score: 219
Period size: 65 Copynumber: 3.2 Consensus size: 64
3556909 TACACTAAGA
* * * * *
3556919 GTGCATCGATGCATCAAGTGTATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCCATAGTGCATCGATGCATGGTTG
* * **
3556983 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGCTGCATGGTAA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCATAGTGCATCGATGCATGGTTG
* ** * * *
3557048 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATAGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCCATAGTGCATCGATGCATGG-TT
3557112 G
64 G
3557113 GTGCATC-AGTGCATCA
1 GTGCATCGA-TGCATCA
3557129 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
63 3 0.02
64 49 0.40
65 66 0.55
66 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCATAGTGCATCGATGCATGGTTG
Found at i:3560771 original size:2 final size:2
Alignment explanation
Indices: 3560764--3560788 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3560754 TTTGAAAATA
3560764 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3560789 ATCACCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3566398 original size:18 final size:18
Alignment explanation
Indices: 3566377--3566414 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
3566367 TGACGACCCA
3566377 GAGGATGGA-GATGACGAT
1 GAGGAT-GACGATGACGAT
3566395 GAGGATGACGATGACGAT
1 GAGGATGACGATGACGAT
3566413 GA
1 GA
3566415 TGACGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.34, C:0.08, G:0.42, T:0.16
Consensus pattern (18 bp):
GAGGATGACGATGACGAT
Found at i:3566401 original size:12 final size:12
Alignment explanation
Indices: 3566386--3566428 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
3566376 AGAGGATGGA
3566386 GATGACGATGAG
1 GATGACGATGAG
3566398 GATGACGATGACG
1 GATGACGATGA-G
*
3566411 ATGATGACGATGAT
1 --GATGACGATGAG
3566425 GATG
1 GATG
3566429 GAGGTGAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 15 0.56
13 1 0.04
15 11 0.41
ACGTcount: A:0.33, C:0.09, G:0.37, T:0.21
Consensus pattern (12 bp):
GATGACGATGAG
Found at i:3566418 original size:9 final size:9
Alignment explanation
Indices: 3566386--3566426 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
3566376 AGAGGATGGA
3566386 GATGACGAT
1 GATGACGAT
* * *
3566395 GAGGATGAC
1 GATGACGAT
3566404 GATGACGAT
1 GATGACGAT
3566413 GATGACGAT
1 GATGACGAT
3566422 GATGA
1 GATGA
3566427 TGGAGGTGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.37, T:0.20
Consensus pattern (9 bp):
GATGACGAT
Found at i:3568075 original size:16 final size:15
Alignment explanation
Indices: 3568051--3568081 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
3568041 AATATAAAAT
3568051 AAATAAACAATAAAC
1 AAATAAACAATAAAC
3568066 AAATAGAACAATAAAC
1 AAATA-AACAATAAAC
3568082 CAATTTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.71, C:0.13, G:0.03, T:0.13
Consensus pattern (15 bp):
AAATAAACAATAAAC
Found at i:3574579 original size:2 final size:2
Alignment explanation
Indices: 3574574--3574600 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3574564 TATATGATTA
3574574 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 A
3574601 AATAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3580514 original size:34 final size:34
Alignment explanation
Indices: 3580476--3580560 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
3580466 CCCGACCCCG
* *
3580476 AAAATATTTTATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
3580510 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
3580544 AAAATATTATATATATA
1 AAAATATTATATATATA
3580561 TATATATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:3589468 original size:25 final size:25
Alignment explanation
Indices: 3589434--3589506 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 25
3589424 AGTTTTATCA
* *
3589434 ACCAACTTGTTACATACAAAAAAAG
1 ACCACCTTGTTTCATACAAAAAAAG
** *
3589459 AGTACCTTGTTTTATACAAAATAAAAG
1 ACCACCTTGTTTCATAC-AAA-AAAAG
*
3589486 ACCAGCTTGTTTCATACAAAA
1 ACCACCTTGTTTCATACAAAA
3589507 CATACCAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
25 13 0.35
26 6 0.16
27 18 0.49
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (25 bp):
ACCACCTTGTTTCATACAAAAAAAG
Found at i:3589947 original size:23 final size:22
Alignment explanation
Indices: 3589916--3589969 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
3589906 AGAATTATAC
3589916 CAAAT-ATTTCAGACAATTT-GA
1 CAAATAATTTCA-ACAATTTAGA
3589937 CAAGATAATTTCAACAATTTCAGA
1 CAA-ATAATTTCAACAATTT-AGA
3589961 CAAATAATT
1 CAAATAATT
3589970 AACCAACTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.10
22 9 0.31
23 12 0.41
24 5 0.17
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (22 bp):
CAAATAATTTCAACAATTTAGA
Found at i:3590182 original size:18 final size:18
Alignment explanation
Indices: 3590159--3590197 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3590149 AGTAGAACTT
*
3590159 GATGTGGTTGATTTCTTC
1 GATGTGGTTGACTTCTTC
3590177 GATGTGGTTGACTTCTTC
1 GATGTGGTTGACTTCTTC
3590195 GAT
1 GAT
3590198 TTGGCTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.13, G:0.28, T:0.46
Consensus pattern (18 bp):
GATGTGGTTGACTTCTTC
Found at i:3593141 original size:3 final size:3
Alignment explanation
Indices: 3593133--3593205 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
3593123 TCCAGAATGT
3593133 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3593181 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3593206 AAGAGTAGAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3593445 original size:82 final size:80
Alignment explanation
Indices: 3593347--3593510 Score: 249
Period size: 82 Copynumber: 2.0 Consensus size: 80
3593337 TGTTCTTTTC
* * * *
3593347 CTTCCAACAACGTTTACCTGTGAGAAT-AAAAACAAAAGAGAAAGTTAAACAAAATAGTTCAAAA
1 CTTCCAACAACATTTACATGTGAG-ATCAAAAACAAAAGAGAAAGTTAAACAAAACAATTCAAAA
3593411 AGGTAAAAAAATTGATTT
65 AGGT-AAAAAATT-ATTT
3593429 CTTCCAACAACATTTACATGTGAGATCAAAAACAAAAGAGAAAGTTAAACAAAACAATTCAAAAA
1 CTTCCAACAACATTTACATGTGAGATCAAAAACAAAAGAGAAAGTTAAACAAAACAATTCAAAAA
*
3593494 GGTAGAAAATTATTT
66 GGTAAAAAATTATTT
3593509 CT
1 CT
3593511 CGAAACAAAC
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
80 6 0.08
81 9 0.12
82 61 0.80
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.23
Consensus pattern (80 bp):
CTTCCAACAACATTTACATGTGAGATCAAAAACAAAAGAGAAAGTTAAACAAAACAATTCAAAAA
GGTAAAAAATTATTT
Found at i:3593845 original size:24 final size:24
Alignment explanation
Indices: 3593817--3593878 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
3593807 CGTTCGTGAA
3593817 CGTTCAGTTATGTTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
* *
3593841 TGTTCGGTTATGTTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
* *
3593865 CATTCATTTATGTT
1 CGTTCAGTTATGTT
3593879 TAACCCAATC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.13, C:0.11, G:0.19, T:0.56
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATGTT
Found at i:3594737 original size:21 final size:21
Alignment explanation
Indices: 3594711--3594759 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
3594701 GTTTTCATTA
3594711 TGGGTTTGAATCAAGGTTTTC
1 TGGGTTTGAATCAAGGTTTTC
3594732 TGGGTTTGAATCAAGGTTTTC
1 TGGGTTTGAATCAAGGTTTTC
3594753 TGGGTTT
1 TGGGTTT
3594760 AAGTTTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.08, G:0.31, T:0.45
Consensus pattern (21 bp):
TGGGTTTGAATCAAGGTTTTC
Found at i:3596919 original size:2 final size:2
Alignment explanation
Indices: 3596914--3596941 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3596904 ACACACACAC
3596914 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
3596942 TGTACTCTTG
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):
AT
Found at i:3597451 original size:36 final size:36
Alignment explanation
Indices: 3597402--3597479 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
3597392 TAACTCAAAT
* * * *
3597402 GATCAATTGAATAAATTTAGCTCAAATATCAGAAAA
1 GATCGATTAAATAAATTCAGCTCAAAGATCAGAAAA
* *
3597438 GATCGATTAAATAACTTCAGCTCAAAGATCAGAAAT
1 GATCGATTAAATAAATTCAGCTCAAAGATCAGAAAA
3597474 GATCGA
1 GATCGA
3597480 ACGTGATCGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (36 bp):
GATCGATTAAATAAATTCAGCTCAAAGATCAGAAAA
Found at i:3602593 original size:24 final size:23
Alignment explanation
Indices: 3602562--3602614 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
3602552 AGAACGACGA
*
3602562 TTTAAA-TTCACATCTCTTAAAAT
1 TTTAAATTTCACAT-TCGTAAAAT
*
3602585 TTTATAATTTGACATTCGTAAAA-
1 TTTA-AATTTCACATTCGTAAAAT
3602608 TTTAAAT
1 TTTAAAT
3602615 ATAATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 3 0.12
23 8 0.31
24 9 0.35
25 6 0.23
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (23 bp):
TTTAAATTTCACATTCGTAAAAT
Found at i:3605901 original size:23 final size:24
Alignment explanation
Indices: 3605855--3605915 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 24
3605845 ATGTTCACGA
* * *
3605855 ATAAATTCATGTATCGACTCATTT
1 ATAAACTCATTTATCCACTCATTT
* *
3605879 ATAAA-TCGTTTATCCACTTATTT
1 ATAAACTCATTTATCCACTCATTT
3605902 ATAAACTCATTTAT
1 ATAAACTCATTTAT
3605916 TAATTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 19 0.61
24 12 0.39
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.44
Consensus pattern (24 bp):
ATAAACTCATTTATCCACTCATTT
Found at i:3613406 original size:3 final size:3
Alignment explanation
Indices: 3613398--3613423 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3613388 TTTTTAAATG
3613398 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
3613424 CATTTGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3613618 original size:5 final size:5
Alignment explanation
Indices: 3613581--3613617 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
3613571 AGTCTATTAT
*
3613581 ATATA AGTATA ATATA ATATA ATATA ATATA AAATA A
1 ATATA A-TATA ATATA ATATA ATATA ATATA ATATA A
3613618 ACATATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:3615053 original size:14 final size:15
Alignment explanation
Indices: 3615025--3615056 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3615015 TAAATATTAT
*
3615025 AATTTAATTTAAAAA
1 AATTAAATTTAAAAA
3615040 AATTAAATTTAAAAA
1 AATTAAATTTAAAAA
3615055 AA
1 AA
3615057 AATATTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTAAATTTAAAAA
Found at i:3615392 original size:31 final size:32
Alignment explanation
Indices: 3615350--3615409 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
3615340 ATAAAGTATA
**
3615350 ATTAATCATAGAAAATGAA-GGACAAAATATG
1 ATTAATCATAGAAAACAAAGGGACAAAATATG
*
3615381 ATTAATTATAGAAAACAAAGGGACAAAAT
1 ATTAATCATAGAAAACAAAGGGACAAAAT
3615410 CAAAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.22
Consensus pattern (32 bp):
ATTAATCATAGAAAACAAAGGGACAAAATATG
Found at i:3620050 original size:15 final size:15
Alignment explanation
Indices: 3620030--3620104 Score: 59
Period size: 15 Copynumber: 4.9 Consensus size: 15
3620020 AGTATGTATA
3620030 TATTTATTTTATTAT
1 TATTTATTTTATTAT
3620045 TATTTATTTT-TT-T
1 TATTTATTTTATTAT
3620058 TATCTAATATTTTA-TAT
1 TAT-T--TATTTTATTAT
*
3620075 GTATATATTTTTATTAT
1 -TATTTA-TTTTATTAT
*
3620092 T-TTTACTTTATTA
1 TATTTATTTTATTA
3620105 CATATTTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
13 4 0.08
14 10 0.20
15 15 0.31
16 13 0.27
17 4 0.08
18 3 0.06
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (15 bp):
TATTTATTTTATTAT
Found at i:3620052 original size:19 final size:19
Alignment explanation
Indices: 3620006--3620060 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
3619996 TTCCTTACTT
* *
3620006 TTATTTATTTA-GTTAGTA
1 TTATTTATTTATTTTATTA
*
3620024 TGTATATATTTATTTTATTA
1 T-TATTTATTTATTTTATTA
*
3620044 TTATTTATTTTTTTTAT
1 TTATTTATTTATTTTAT
3620061 CTAATATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 23 0.77
20 6 0.20
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTATTTATTTATTTTATTA
Found at i:3620091 original size:44 final size:42
Alignment explanation
Indices: 3620039--3620124 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
3620029 ATATTTATTT
* *
3620039 TATTATTATTTATTTTT--TTTATCTA-ATATTTTATATGTATA
1 TATTTTTA-TTATTTTTACTTTAT-TACATATTTTATATATATA
3620080 TATTTTTATTATTTTTACTTTATTACATATTTTATATATATA
1 TATTTTTATTATTTTTACTTTATTACATATTTTATATATATA
3620122 TAT
1 TAT
3620125 ATATATATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
40 8 0.20
41 9 0.22
42 23 0.57
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (42 bp):
TATTTTTATTATTTTTACTTTATTACATATTTTATATATATA
Found at i:3620120 original size:40 final size:40
Alignment explanation
Indices: 3620039--3620122 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
3620029 ATATTTATTT
3620039 TATTATTATTTATTTTTTTTATCTAATATTTTATATGTATA
1 TATTATTATTTATTTTTTTTATCTAATATTTTATA-GTATA
*
3620080 TATTTTTA-TTATTTTTACTTTAT-TACATATTTTATA-TATA
1 TATTATTATTTATTTTT--TTTATCTA-ATATTTTATAGTATA
3620120 TAT
1 TAT
3620123 ATATATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
40 15 0.38
41 9 0.23
42 15 0.38
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (40 bp):
TATTATTATTTATTTTTTTTATCTAATATTTTATAGTATA
Found at i:3624862 original size:2 final size:2
Alignment explanation
Indices: 3624855--3624880 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3624845 TTCATGGTCT
3624855 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
3624881 CACGGGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3628074 original size:32 final size:33
Alignment explanation
Indices: 3628029--3628096 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
3628019 ACTAGTAAAG
*
3628029 GAAATGTTGGAGAA-ATAGCGAAACCTGCAGCA
1 GAAATGTTGGAGAAGACAGCGAAACCTGCAGCA
*
3628061 GAAACTGTT-GAGAAGACGGCGAAACCTGCAGCA
1 GAAA-TGTTGGAGAAGACAGCGAAACCTGCAGCA
3628094 GAA
1 GAA
3628097 GAAACCGTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 9 0.28
33 23 0.72
ACGTcount: A:0.40, C:0.18, G:0.29, T:0.13
Consensus pattern (33 bp):
GAAATGTTGGAGAAGACAGCGAAACCTGCAGCA
Found at i:3628997 original size:41 final size:41
Alignment explanation
Indices: 3628887--3628996 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
3628877 CAAACACCGT
* * *
3628887 AATAGTGTTAATCATTAGTAGCG-TTTTTAGATAAACGCCAC
1 AATAGTG-TAATCAATAGTGGCGTTTTTTAGACAAACGCCAC
* *
3628928 AATAGTTTTAATCAATAGTGACGTTTTTTA-ACAAACGCCAC
1 AATAG-TGTAATCAATAGTGGCGTTTTTTAGACAAACGCCAC
3628969 AATAGTGTAATCAATAGTGGCGTTTTTT
1 AATAGTGTAATCAATAGTGGCGTTTTTT
3628997 TGTATAAACG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
40 21 0.35
41 32 0.53
42 7 0.12
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (41 bp):
AATAGTGTAATCAATAGTGGCGTTTTTTAGACAAACGCCAC
Found at i:3629409 original size:41 final size:41
Alignment explanation
Indices: 3629364--3629477 Score: 122
Period size: 41 Copynumber: 2.7 Consensus size: 41
3629354 AAGTTGTACT
* **
3629364 TTAGTGGCGTTTTTGACATAAACGCCGCAATAGTGT-GTCCC
1 TTAGTGGCATTTTTGA-ATAAACGCCGCAATAGAATAGTCCC
* * *
3629405 TTAGTGGCATTTTCGTAATAAACGCCGTAATAGAATAGTTCC
1 TTAGTGGCATTTTTG-AATAAACGCCGCAATAGAATAGTCCC
* *
3629447 TTTGTGGCATTTTTAATATAAACGCCGCAAT
1 TTAGTGGCATTTTTGA-ATAAACGCCGCAAT
3629478 TATCCTTTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
41 30 0.50
42 30 0.50
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (41 bp):
TTAGTGGCATTTTTGAATAAACGCCGCAATAGAATAGTCCC
Found at i:3629468 original size:42 final size:39
Alignment explanation
Indices: 3629362--3629477 Score: 106
Period size: 42 Copynumber: 2.8 Consensus size: 39
3629352 AAAAGTTGTA
* **
3629362 CTTTAGTGGCGTTTTTGACATAAACGCCGCAATAGTGTGTCC
1 CTTT-GTGGCATTTTT-A-ATAAACGCCGCAATAGAATGTCC
* * *
3629404 CTTAGTGGCATTTTCGTAATAAACGCCGTAATAGAATAGTTC
1 CTTTGTGGCATTTT--TAATAAACGCCGCAATAGAAT-GTCC
3629446 CTTTGTGGCATTTTTAATATAAACGCCGCAAT
1 CTTTGTGGCATTTTT-A-ATAAACGCCGCAAT
3629478 TATCCTTTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
40 1 0.02
41 26 0.43
42 33 0.54
43 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (39 bp):
CTTTGTGGCATTTTTAATAAACGCCGCAATAGAATGTCC
Found at i:3636521 original size:21 final size:21
Alignment explanation
Indices: 3636497--3636582 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
3636487 ATGAAGCAAG
*
3636497 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
3636518 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
3636539 AGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
3636560 GGCAGCACAGAGAG-AGTCAGC
1 GGAAGCAGAGAGAGCAG-CAGC
3636581 GG
1 GG
3636583 CAGAACAGAG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 2 0.04
21 52 0.96
ACGTcount: A:0.38, C:0.20, G:0.40, T:0.02
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:3636583 original size:21 final size:20
Alignment explanation
Indices: 3636505--3636595 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 20
3636495 AGGGAAACAG
*
3636505 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAG-AGCAGCGGCAGCA-C
* * * *
3636527 TAGAG-CAGCAGCAGAAGCAG
1 -AGAGAGAGCAGCGGCAGCAC
3636547 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAG-AGCAGCGGCAGCAC
*
3636568 AGAGAGAGTCAGCGGCAGAAC
1 AGAGAGAG-CAGCGGCAGCAC
3636589 AGAGAGA
1 AGAGAGA
3636596 AGTAATATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.07
20 2 0.04
21 47 0.82
23 4 0.07
ACGTcount: A:0.40, C:0.20, G:0.38, T:0.02
Consensus pattern (20 bp):
AGAGAGAGCAGCGGCAGCAC
Found at i:3637100 original size:43 final size:43
Alignment explanation
Indices: 3637018--3637162 Score: 150
Period size: 43 Copynumber: 3.4 Consensus size: 43
3637008 AAATAAACAT
* * * * *
3637018 CTATTGCGGCGTTTGTGAAG-AAAACGTCGCTAAACATCAATGA-
1 CTATTGCGGCGTTTGT-ATGCCAAACGCCACTAAATATCAA-GAC
* * ** *
3637061 CTATTGCGGCGTTTGTCTGCCAAATGCCGTTAAATATCAACAC
1 CTATTGCGGCGTTTGTATGCCAAACGCCACTAAATATCAAGAC
*
3637104 CTATTGCGGCGTTTTTATGCCAAACGCCACTAAATATCAAGAC
1 CTATTGCGGCGTTTGTATGCCAAACGCCACTAAATATCAAGAC
*
3637147 CTTTTGCGGCGTTTGT
1 CTATTGCGGCGTTTGT
3637163 TGAACAATCG
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
42 2 0.02
43 82 0.98
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (43 bp):
CTATTGCGGCGTTTGTATGCCAAACGCCACTAAATATCAAGAC
Found at i:3644841 original size:151 final size:151
Alignment explanation
Indices: 3644627--3644916 Score: 438
Period size: 151 Copynumber: 1.9 Consensus size: 151
3644617 TAAATATATT
** * * *
3644627 AATTTTTTAACTATCATGTCATATTCTACGTCAAATGTTAATGACGAGTGACTAGATTGTCAATG
1 AATTTTTTAACTATCACATCATATTCTACGTCAAATATTAACGACGAGTGACTAGATTATCAATG
* * *
3644692 TTTAAATAATTAAGTGGTCTGATTGAAA-AAAATGAAAGATTAGTAATCAAAACAAAATCTTGTC
66 TTTAAATAATTAAGTGGCCTGATT-AAAGAAAATGAAAGATCAGTAATCAAAACAAAATCTCGTC
3644756 ATAATTAAGTGACTTGATTGTC
130 ATAATTAAGTGACTTGATTGTC
* * * *
3644778 AATTTTTTAACTATCACATCATCTTTTCCGTCAAATATTAACGACGAGTGACTTGATTATCAATG
1 AATTTTTTAACTATCACATCATATTCTACGTCAAATATTAACGACGAGTGACTAGATTATCAATG
* *
3644843 TTTAAATAATTAAGTGGCCTGGTTAAAGAAAATGAAAGATCAGTAATCAAAATAAAATCTCGTCA
66 TTTAAATAATTAAGTGGCCTGATTAAAGAAAATGAAAGATCAGTAATCAAAACAAAATCTCGTCA
3644908 TAATTAAGT
131 TAATTAAGT
3644917 ATCATAGGTG
Statistics
Matches: 124, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
150 3 0.02
151 121 0.98
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (151 bp):
AATTTTTTAACTATCACATCATATTCTACGTCAAATATTAACGACGAGTGACTAGATTATCAATG
TTTAAATAATTAAGTGGCCTGATTAAAGAAAATGAAAGATCAGTAATCAAAACAAAATCTCGTCA
TAATTAAGTGACTTGATTGTC
Found at i:3653009 original size:23 final size:23
Alignment explanation
Indices: 3652982--3653082 Score: 103
Period size: 23 Copynumber: 4.3 Consensus size: 23
3652972 CACCACAGCT
*
3652982 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
* *
3653005 TATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGGAGTGCCA
* * *
3653028 CGTAGAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGGAGTGCCA
* * *
3653051 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
3653074 TATAATAAT
1 CAT-ATAAT
3653083 GTCCATAAGG
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
23 62 0.94
24 4 0.06
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGGAGTGCCA
Found at i:3653260 original size:103 final size:103
Alignment explanation
Indices: 3653089--3653306 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
3653079 TAATGTCCAT
* **
3653089 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCA
*
3653154 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
*
3653192 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCA
*
3653257 GACTTCACACATATTCTAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
3653295 AAGGACCACATA
1 AAGGACCACATA
3653307 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCA
GACTTCACACATATTCCAAAGAATACATATATGTCCCG
Found at i:3655206 original size:32 final size:32
Alignment explanation
Indices: 3655127--3655207 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
3655117 GTTTTTTTCG
** *
3655127 GATCGATTGATTTTTTAGTCGGGTTAATAAAT
1 GATCGATTGATTTTCGAGTCAGGTTAATAAAT
* *
3655159 GATCGATTAGA-TTTCGAGTCATGTTAATATCA-
1 GATCGATT-GATTTTCGAGTCAGGTTAATA-AAT
3655191 GATCGATTGATTTTCGA
1 GATCGATTGATTTTCGA
3655208 TTTGGGTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
31 2 0.05
32 36 0.88
33 3 0.07
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (32 bp):
GATCGATTGATTTTCGAGTCAGGTTAATAAAT
Found at i:3655599 original size:16 final size:16
Alignment explanation
Indices: 3655580--3655610 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3655570 TCAGTTAAAT
3655580 TTTGGATCGGGTATGG
1 TTTGGATCGGGTATGG
*
3655596 TTTGGGTCGGGTATG
1 TTTGGATCGGGTATG
3655611 ATTCGAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.45, T:0.39
Consensus pattern (16 bp):
TTTGGATCGGGTATGG
Found at i:3656817 original size:28 final size:28
Alignment explanation
Indices: 3656761--3656819 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
3656751 TTTAGTAACC
* *
3656761 AAACCATTATTTTAAAACTTCAGTGACT
1 AAACCATTATTTTAAAACCTCAATGACT
*
3656789 AAACCATTATTTTTGAAACCTCAAT-ACT
1 AAACCATTA-TTTTAAAACCTCAATGACT
3656817 AAA
1 AAA
3656820 AAAGAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.34
Consensus pattern (28 bp):
AAACCATTATTTTAAAACCTCAATGACT
Found at i:3662164 original size:23 final size:23
Alignment explanation
Indices: 3662119--3662166 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
3662109 ATTTTAAAAA
**
3662119 TTAAATATTTTTAAAAGGTAATT
1 TTAAATATTTTTAAAAGAAAATT
* *
3662142 TTAAGTATTTTTAAAATAAAATT
1 TTAAATATTTTTAAAAGAAAATT
3662165 TT
1 TT
3662167 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (23 bp):
TTAAATATTTTTAAAAGAAAATT
Found at i:3663250 original size:21 final size:20
Alignment explanation
Indices: 3663211--3663253 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3663201 AAAGTTAAAA
*
3663211 TTCAAAGTTTGGCAATGATT
1 TTCAAAGTTTGGAAATGATT
*
3663231 TTCAAAGTTTGATAAATGATT
1 TTCAAAGTTTG-GAAATGATT
3663252 TT
1 TT
3663254 TTGAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (20 bp):
TTCAAAGTTTGGAAATGATT
Found at i:3663286 original size:20 final size:20
Alignment explanation
Indices: 3663211--3663286 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
3663201 AAAGTTAAAA
**
3663211 TTCAAAGTTTG-GCAATGATT
1 TTCAAAGTTTGATAAATG-TT
*
3663231 TTCAAAGTTTGATAAATGAT
1 TTCAAAGTTTGATAAATGTT
3663251 TT-----TTTGA-AAATAGTT
1 TTCAAAGTTTGATAAAT-GTT
3663266 TTCAAAGTTTGATAAATGTT
1 TTCAAAGTTTGATAAATGTT
3663286 T
1 T
3663287 CTTTGAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
14 4 0.09
15 9 0.20
20 23 0.52
21 8 0.18
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (20 bp):
TTCAAAGTTTGATAAATGTT
Found at i:3663329 original size:36 final size:35
Alignment explanation
Indices: 3663229--3663333 Score: 142
Period size: 35 Copynumber: 2.9 Consensus size: 35
3663219 TTGGCAATGA
3663229 TTTTCAAAGTTTGATAAATGATTTTTTG-AAAATAG
1 TTTTCAAAGTTTGATAAATG-TTTTTTGAAAAATAG
3663264 TTTTCAAAGTTTGATAAATGTTTCTTTGAAAAATAG
1 TTTTCAAAGTTTGATAAATGTTT-TTTGAAAAATAG
* *
3663300 TTTTTCAAAGTTT-AGTAGATGTTTATTGAAAAAT
1 -TTTTCAAAGTTTGA-TAAATGTTTTTTGAAAAAT
3663334 GATAATAGGA
Statistics
Matches: 64, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
34 3 0.05
35 24 0.38
36 17 0.27
37 20 0.31
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.46
Consensus pattern (35 bp):
TTTTCAAAGTTTGATAAATGTTTTTTGAAAAATAG
Found at i:3663782 original size:32 final size:33
Alignment explanation
Indices: 3663741--3663804 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
3663731 TATTCACATA
3663741 AATAGTGAATTTTGTGAATAGT-AAATTTTGTG
1 AATAGTGAATTTTGTGAATAGTAAAATTTTGTG
3663773 AATAGTGAATTTTGTGAATAGTAAAATTTTGT
1 AATAGTGAATTTTGTGAATAGTAAAATTTTGT
3663805 CGGCGATACG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 22 0.71
33 9 0.29
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (33 bp):
AATAGTGAATTTTGTGAATAGTAAAATTTTGTG
Found at i:3663802 original size:17 final size:16
Alignment explanation
Indices: 3663741--3663804 Score: 101
Period size: 16 Copynumber: 3.9 Consensus size: 16
3663731 TATTCACATA
*
3663741 AATAGTGAATTTTGTG
1 AATAGTAAATTTTGTG
3663757 AATAGTAAATTTTGTG
1 AATAGTAAATTTTGTG
*
3663773 AATAGTGAATTTTGTG
1 AATAGTAAATTTTGTG
3663789 AATAGTAAAATTTTGT
1 AATAGT-AAATTTTGT
3663805 CGGCGATACG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
16 36 0.82
17 8 0.18
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (16 bp):
AATAGTAAATTTTGTG
Found at i:3664575 original size:15 final size:15
Alignment explanation
Indices: 3664551--3664582 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3664541 TGGCAGATCC
*
3664551 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
3664566 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
3664581 AA
1 AA
3664583 TAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:3667887 original size:21 final size:20
Alignment explanation
Indices: 3667863--3667926 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
3667853 AACTTTGAAA
3667863 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
3667884 AAATGTTTT-----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
3667898 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
3667919 AAATGTTT
1 AAATGTTT
3667927 CTTTTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
20 11 0.32
21 10 0.29
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:3667901 original size:35 final size:35
Alignment explanation
Indices: 3667862--3667971 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 35
3667852 CAACTTTGAA
3667862 AAAATGATTTTCAAAGTTTGGTAAATGTTTTTTTG
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTTTTTG
* *
3667897 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTTA
1 AAAATGATTTTCAAAGTTTGGTAAATGTTT-TTTTG
* * *
3667933 AAAATAGTTTTTCAAAGTTTGTTAGATG-TTTTTTG
1 AAAAT-GATTTTCAAAGTTTGGTAAATGTTTTTTTG
3667968 AAAA
1 AAAA
3667972 ATAATAATGG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
35 37 0.55
36 11 0.16
37 19 0.28
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (35 bp):
AAAATGATTTTCAAAGTTTGGTAAATGTTTTTTTG
Found at i:3670093 original size:61 final size:59
Alignment explanation
Indices: 3669963--3670154 Score: 280
Period size: 61 Copynumber: 3.2 Consensus size: 59
3669953 ATAGTACCAA
* * * *
3669963 TACTAATAACGATTTATTATTAATATTTAATTATTTGATATTTAATGATTTAATAACGAT
1 TACTAATAATGATTTATTATTAATATTTAATGATTTGATA-TTAATGATTTAGTAATGAT
3670023 TACTAATAATGATTTATTATTAATATTTAATGATTT-AGTAATGGT-ATGATTTAGTAATGAT
1 TACTAATAATGATTTATTATTAATATTTAATGATTTGA-T-AT--TAATGATTTAGTAATGAT
*
3670084 TACTAATAATTATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
1 TACTAATAATGATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
3670143 TACTAATAATGA
1 TACTAATAATGA
3670155 AATTATAATA
Statistics
Matches: 120, Mismatches: 6, Indels: 13
0.86 0.04 0.09
Matches are distributed among these distances:
58 1 0.01
59 28 0.23
60 38 0.32
61 51 0.43
62 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (59 bp):
TACTAATAATGATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
Found at i:3670154 original size:13 final size:13
Alignment explanation
Indices: 3670136--3670193 Score: 75
Period size: 13 Copynumber: 4.6 Consensus size: 13
3670126 AATGATTTAG
3670136 TAATGATTACTAA
1 TAATGATTACTAA
* *
3670149 TAATGA--AATTA
1 TAATGATTACTAA
*
3670160 TAATAATTACTAA
1 TAATGATTACTAA
3670173 TAATGATTACTAA
1 TAATGATTACTAA
3670186 TAATGATT
1 TAATGATT
3670194 TATTATTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 8 0.22
13 29 0.78
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (13 bp):
TAATGATTACTAA
Found at i:3671890 original size:23 final size:23
Alignment explanation
Indices: 3671838--3671892 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
3671828 ATCCATTAGT
*
3671838 AATCATTATTAGAAATTATTATA
1 AATCATTATTAGAAATCATTATA
* *
3671861 ATTTCATTA-TAGTAATCATTACTA
1 A-ATCATTATTAGAAATCATTA-TA
3671885 AATCATTA
1 AATCATTA
3671893 GTATCAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (23 bp):
AATCATTATTAGAAATCATTATA
Found at i:3671958 original size:13 final size:13
Alignment explanation
Indices: 3671901--3671965 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
3671891 TAGTATCAAA
3671901 TAAT-TAAAT-AT
1 TAATATAAATCAT
3671912 TAATAATAAATCAT
1 TAAT-ATAAATCAT
* * *
3671926 TATTATTAATAAT
1 TAATATAAATCAT
*
3671939 T-A-CTAAATCAT
1 TAATATAAATCAT
3671950 TAATATAAATCAT
1 TAATATAAATCAT
3671963 TAA
1 TAA
3671966 AATATTAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
11 11 0.27
12 1 0.02
13 24 0.59
14 5 0.12
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (13 bp):
TAATATAAATCAT
Found at i:3671964 original size:24 final size:23
Alignment explanation
Indices: 3671917--3671986 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
3671907 AATATTAATA
* * *
3671917 ATAAATCATTATTATTAATAATT
1 ATAAATCATTAATATAAATCATT
3671940 ACTAAATCATTAATATAAATCATT
1 A-TAAATCATTAATATAAATCATT
3671964 A-AAAT-ATTAATAATAAATCATT
1 ATAAATCATTAAT-ATAAATCATT
3671986 A
1 A
3671987 GTAGTACGGC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.14
22 15 0.36
23 1 0.02
24 20 0.48
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAAATCATTAATATAAATCATT
Done.