Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 31
Found at i:3596608 original size:2 final size:2
Alignment explanation
Indices: 3596603--3596649 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3596593 CACACACACA
3596603 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3596645 AT AT A
1 AT AT A
3596650 CACACATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3598357 original size:123 final size:124
Alignment explanation
Indices: 3598107--3598357 Score: 283
Period size: 123 Copynumber: 2.0 Consensus size: 124
3598097 TCTTACTTTG
* * * * * *
3598107 TCCTTTAAAGGACTCTAAGTCGTAATTTGGGATGATCTACTCCTTTTATTGAAGGATGTTGAATC
1 TCCTCTAAAGGACTCTAAGTCGTAATTTGGGATGATCCAATCCTTTTATTAAAGGACGTTAAATC
* * *
3598172 TGGTGACGATCTGACTCTTTCCTCTAAACAACGCTGAGTCTTTGAACAATTTTACCCCT
66 TGGTGACGATCTGACTCTTTCCTCTAAACAACGCTGAGTCATGGAACAATTTTACCCAT
* * *
3598231 TCCTCTAAATGACTCTAAGTTGTAA-TTGGGGTGATCCAATCCTTTTGA-TAAAGGACGTTAAAT
1 TCCTCTAAAGGACTCTAAGTCGTAATTTGGGATGATCCAATCCTTTT-ATTAAAGGACGTTAAAT
* * * * * ** *
3598294 CTGGTGATGATCTTACTCTTTCCTTTGAAA-GACGTTGAGTCATGGAATGATTTTACTCAT
65 CTGGTGACGATCTGACTCTTTCCTCT-AAACAACGCTGAGTCATGGAACAATTTTACCCAT
3598354 TCCT
1 TCCT
3598358 ATAACTAAAG
Statistics
Matches: 105, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
123 79 0.75
124 26 0.25
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (124 bp):
TCCTCTAAAGGACTCTAAGTCGTAATTTGGGATGATCCAATCCTTTTATTAAAGGACGTTAAATC
TGGTGACGATCTGACTCTTTCCTCTAAACAACGCTGAGTCATGGAACAATTTTACCCAT
Found at i:3598420 original size:84 final size:84
Alignment explanation
Indices: 3598279--3598441 Score: 290
Period size: 84 Copynumber: 1.9 Consensus size: 84
3598269 ATCCTTTTGA
* *
3598279 TAAAGGACGTTAAATCTGGTGATGATCTTACTCTTTCCTTTGAAAGACGTTGAGTCATGGAATGA
1 TAAAGGACCTTAAATCTAGTGATGATCTTACTCTTTCCTTTGAAAGACGTTGAGTCATGGAATGA
3598344 TTTTACTCATTCCTATAAC
66 TTTTACTCATTCCTATAAC
*
3598363 TAAAGGACCTTAAATCTAGTGTTGATCTTACTCTTTCCTTTGAAAGACGTTGAGTCATGGAATGA
1 TAAAGGACCTTAAATCTAGTGATGATCTTACTCTTTCCTTTGAAAGACGTTGAGTCATGGAATGA
*
3598428 TTTTACTCGTTCCT
66 TTTTACTCATTCCT
3598442 CTAAAGGACG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (84 bp):
TAAAGGACCTTAAATCTAGTGATGATCTTACTCTTTCCTTTGAAAGACGTTGAGTCATGGAATGA
TTTTACTCATTCCTATAAC
Found at i:3598441 original size:40 final size:40
Alignment explanation
Indices: 3598279--3598458 Score: 136
Period size: 40 Copynumber: 4.4 Consensus size: 40
3598269 ATCCTTTTGA
* *
3598279 TAAAGGACGTTAAATC-TGGTGATGATCTTACTCTTTCCTT
1 TAAAGGACGTTAAGTCATGG-AATGATCTTACTCTTTCCTT
* * *
3598319 TGAAA-GACGTTGAGTCATGGAATGATTTTACTCATTCCTAT
1 T-AAAGGACGTTAAGTCATGGAATGATCTTACTCTTTCCT-T
* * *
3598360 AACTAAAGGACCTTAAATC-TAGTG-TTGATCTTACTCTTTCCTT
1 ---TAAAGGACGTTAAGTCAT-G-GAATGATCTTACTCTTTCCTT
* * * *
3598403 TGAAA-GACGTTGAGTCATGGAATGATTTTACTCGTTCCTC
1 T-AAAGGACGTTAAGTCATGGAATGATCTTACTCTTTCCTT
3598443 TAAAGGACGTTAAGTC
1 TAAAGGACGTTAAGTC
3598459 GTAATTCGGG
Statistics
Matches: 108, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
39 4 0.04
40 62 0.57
41 11 0.10
43 5 0.05
44 25 0.23
45 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (40 bp):
TAAAGGACGTTAAGTCATGGAATGATCTTACTCTTTCCTT
Found at i:3598814 original size:40 final size:40
Alignment explanation
Indices: 3598749--3598844 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
3598739 GAATCTGGTG
* * *
3598749 ACGATCTCACTCTTTCCTCTGAAAGACCCTGAGTTATGGA
1 ACGATCTTACTCTTTCCTCTAAAAGACCCTGAGTCATGGA
* *
3598789 ACGATCTTACTCCTTT-CTCTAAAAGACGCTGAGTCATGGG
1 ACGATCTTACT-CTTTCCTCTAAAAGACCCTGAGTCATGGA
* *
3598829 ATGATCTTACTTTTTC
1 ACGATCTTACTCTTTC
3598845 TTCTGAAGGA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.06
40 40 0.85
41 4 0.09
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (40 bp):
ACGATCTTACTCTTTCCTCTAAAAGACCCTGAGTCATGGA
Found at i:3598863 original size:264 final size:264
Alignment explanation
Indices: 3598386--3598992 Score: 657
Period size: 264 Copynumber: 2.3 Consensus size: 264
3598376 ATCTAGTGTT
* * * * * * * * *
3598386 GATCTTACTCTTTCCTTTGAAAGACGTTGAGTCATGGAATGATTTTACTCGTTCCTCTAAAGGAC
1 GATCTCACTCTTTCATATGAAAGACGCTAAGTCATGGGACGATCTTACTCCTTCCTCTAAAGGAC
* * * * *
3598451 GTTAAGTCGTAATTCGGGGTCACTGAATCTAGTGACGATATCACTCTTTTCTATGAAAGATAATG
66 GCTAAATCGTAATTCGGGATCACTGAATCTAGTGACGATATCACTCTTTCCTATGAAAGACAATG
* * * * * *
3598516 AGTCGTGGGATGATCTTACTCATTCCTTTAAAGGATGCTAAGTTGAGGAACTATCTTACTCCTTT
131 AGTCATGGAACGATCTTACTCATTCCTCTAAAAGACGCTAAGTTGAGGAACTATCTTACTCCTTT
* ** * * **
3598581 CTCTGAAAGGTATTAAGTTGTGATTAGGGTGATTCACTCCTTTTGTTGAAGGGTGAGAAATCTGG
196 CTCTGAAAGGTATTAAGTTGTAATTAGGGTGATTCACTCCTTTTACTGAAGGATGAAAAATCTAA
3598646 TGAC
261 TGAC
* * * * * *
3598650 GATCTCACTCTTTCCTCTGAAAGACGCTAATTTATGGGGCGATCTTACTCCTTCCTCTAAAGGAT
1 GATCTCACTCTTTCATATGAAAGACGCTAAGTCATGGGACGATCTTACTCCTTCCTCTAAAGGAC
* * * * **
3598715 GCTAAATCATAATTCGGGATCACTGAATCTGGTGACGATCTCACTCTTTCCTCTGAAAGACCCTG
66 GCTAAATCGTAATTCGGGATCACTGAATCTAGTGACGATATCACTCTTTCCTATGAAAGACAATG
* * * * *
3598780 AGTTATGGAACGATCTTACTCCTTTCTCTAAAAGACGCTGAGTCATG-GG-A-TGATCTTACT-T
131 AGTCATGGAACGATCTTACTCATTCCTCTAAAAGACGCTAAGT--TGAGGAACT-ATCTTACTCC
* * * *
3598841 TTTCTTCTG-AAGGATGTTAAGTTGTAATTGGGGTGGTTCACTTCTTTTACTGAAGGATGAAAAA
193 TTTC-TCTGAAAGG-TATTAAGTTGTAATTAGGGTGATTCACTCCTTTTACTGAAGGATGAAAAA
3598905 TCTAATGAC
256 TCTAATGAC
* * * *
3598914 GATCTCACTCTTTCATATTAAAGATGCTAAGTCGTGGGATGATCTTACTCCTTCCTCTAAAGGAC
1 GATCTCACTCTTTCATATGAAAGACGCTAAGTCATGGGACGATCTTACTCCTTCCTCTAAAGGAC
*
3598979 ACTAAATCGTAATT
66 GCTAAATCGTAATT
3598993 GAATGATTGT
Statistics
Matches: 281, Mismatches: 57, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
263 9 0.03
264 268 0.95
265 2 0.01
266 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (264 bp):
GATCTCACTCTTTCATATGAAAGACGCTAAGTCATGGGACGATCTTACTCCTTCCTCTAAAGGAC
GCTAAATCGTAATTCGGGATCACTGAATCTAGTGACGATATCACTCTTTCCTATGAAAGACAATG
AGTCATGGAACGATCTTACTCATTCCTCTAAAAGACGCTAAGTTGAGGAACTATCTTACTCCTTT
CTCTGAAAGGTATTAAGTTGTAATTAGGGTGATTCACTCCTTTTACTGAAGGATGAAAAATCTAA
TGAC
Found at i:3599466 original size:45 final size:43
Alignment explanation
Indices: 3599334--3599473 Score: 124
Period size: 45 Copynumber: 3.1 Consensus size: 43
3599324 AATCAGGTTG
* *
3599334 AAGAAATACATCACTGAAAAGTTGACTCATC--TACGCAAGAAATTC
1 AAGAAAGACATCACT-AAAAGTTGACTCATCTTTA-G--AGAAAGTC
* * * *
3599379 AAGAATGAAATCACTACAAGGTTGACTCCTCATTGTAG-GAAAGTC
1 AAGAAAGACATCACTA-AAAGTTGACTCATC-TT-TAGAGAAAGTC
3599424 AAGAAAGACATCACTAAAAGATTGACTCATCTTTATGAGAAAGTC
1 AAGAAAGACATCACTAAAAG-TTGACTCATCTTTA-GAGAAAGTC
3599469 AAGAA
1 AAGAA
3599474 TGGCATACTT
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
43 2 0.03
44 7 0.09
45 65 0.84
48 1 0.01
49 2 0.03
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (43 bp):
AAGAAAGACATCACTAAAAGTTGACTCATCTTTAGAGAAAGTC
Found at i:3602563 original size:20 final size:20
Alignment explanation
Indices: 3602535--3602572 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3602525 TGATACATTT
3602535 AAAACATAAATAAAACAATC
1 AAAACATAAATAAAACAATC
*
3602555 AAAAGATAAATAAAACAA
1 AAAACATAAATAAAACAA
3602573 ACTCATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.11, G:0.03, T:0.13
Consensus pattern (20 bp):
AAAACATAAATAAAACAATC
Found at i:3603862 original size:29 final size:29
Alignment explanation
Indices: 3603798--3603855 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
3603788 CAATAGACTG
3603798 AAATAAATACAGCATACAAATTAGAAACC
1 AAATAAATACAGCATACAAATTAGAAACC
3603827 AAATAAATACAAG-ATACAAATTAGAAACC
1 AAATAAATAC-AGCATACAAATTAGAAACC
3603856 GATTAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.60, C:0.16, G:0.07, T:0.17
Consensus pattern (29 bp):
AAATAAATACAGCATACAAATTAGAAACC
Found at i:3606913 original size:12 final size:12
Alignment explanation
Indices: 3606896--3606928 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3606886 GAATACCCGG
3606896 GTATCGGGCCGA
1 GTATCGGGCCGA
*
3606908 GTATCGGGCCGG
1 GTATCGGGCCGA
3606920 GTATCGGGC
1 GTATCGGGC
3606929 GGGGATTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.24, G:0.45, T:0.18
Consensus pattern (12 bp):
GTATCGGGCCGA
Found at i:3611010 original size:45 final size:45
Alignment explanation
Indices: 3610945--3611388 Score: 430
Period size: 45 Copynumber: 9.9 Consensus size: 45
3610935 CCTGAAGGAT
* * * * ** * *
3610945 ATCACTAAAAGATTGTCTCCTTTTCATGAGAAACTCAAGAATGGC
1 ATCACTTAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATGAC
**
3610990 ATCACTTAAAGGTTGACTCCTCTTCATGAGAAAGTCAAGAATGAC
1 ATCACTTAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATGAC
* * *
3611035 ATCAC-TAAAGAGTTGACTACTCTTCGCGATAAAGTCAATAATGAC
1 ATCACTTAAAG-GTTGACTCCTCTTCGCGAGAAAGTCAAGAATGAC
* * * ** * * *
3611080 AACACTGAAAGATTGACAACTCTTTGCGAGAAAGTCAAAAAATGAT
1 ATCACTTAAAGGTTGACTCCTCTTCGCGAGAAAGTC-AAGAATGAC
* * * * * ** *
3611126 ATCACTAAAAGGTTGACTCATATTTGCAAGAAACCCAAGAATAAC
1 ATCACTTAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATGAC
* * * *
3611171 ATCACTAAAATGTTAACTCCTCTTCGTGAGAAAGTCAAGAATGAC
1 ATCACTTAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATGAC
3611216 ATCAC-T-AAGAGTTGACTCCTCTTCGCGAGAAAGTCAAGAATGAC
1 ATCACTTAAAG-GTTGACTCCTCTTCGCGAGAAAGTCAAGAATGAC
* ** * *
3611260 ATCA-TTGGAAGACTGACTCCTCTTCGCGAGAAAGTCAAGAATAAA
1 ATCACTT-AAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATGAC
* *
3611305 ATCA-TTGAAAGGTTGACTTCTCTTCGCGAGAAATTCAAGAATGAC
1 ATCACTT-AAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATGAC
* *
3611350 ATCACTGAAAGGTTGACTCCTCTTCGCAAGAAAGTCAAG
1 ATCACTTAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAG
3611389 TTGATGTTTT
Statistics
Matches: 330, Mismatches: 61, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
43 2 0.01
44 42 0.13
45 245 0.74
46 41 0.12
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (45 bp):
ATCACTTAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATGAC
Found at i:3614217 original size:21 final size:20
Alignment explanation
Indices: 3614191--3614238 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3614181 AAAAATCCTG
* **
3614191 TTTAATTGTTTATATTATTTT
1 TTTAATTATTTAT-TTAAATT
3614212 TTTAATTATTTATTTAAATT
1 TTTAATTATTTATTTAAATT
3614232 TTTAATT
1 TTTAATT
3614239 TTTTTAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTAATTATTTATTTAAATT
Found at i:3622134 original size:19 final size:19
Alignment explanation
Indices: 3622060--3622136 Score: 77
Period size: 19 Copynumber: 4.1 Consensus size: 19
3622050 TGCATTGGGC
*
3622060 TATGAATTTGAAAATAA-T
1 TATGAATCTGAAAATAAGT
* *
3622078 CTATGAATCT-AACAGTAAGC
1 -TATGAATCTGAA-AATAAGT
*
3622098 TATGAGTCTGAAAATAAGT
1 TATGAATCTGAAAATAAGT
*
3622117 TATGAATCTGGAAATAAGT
1 TATGAATCTGAAAATAAGT
3622136 T
1 T
3622137 TTGATTTAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
18 2 0.04
19 43 0.91
20 2 0.04
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (19 bp):
TATGAATCTGAAAATAAGT
Found at i:3628723 original size:24 final size:24
Alignment explanation
Indices: 3628691--3628767 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 24
3628681 AATTCATTAG
3628691 AGAT-ATTTCCTAATAAATTGCAA
1 AGATAATTTCCTAATAAATTGCAA
* **
3628714 AGGTAATTT-CTAA-AAATCACAA
1 AGATAATTTCCTAATAAATTGCAA
*
3628736 CATATAA-TTCCTAATAAATTGCAAA
1 -AGATAATTTCCTAATAAATTGC-AA
3628761 AGATAAT
1 AGATAAT
3628768 ACCTCAATGT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 9 0.22
23 15 0.38
24 14 0.35
25 2 0.05
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (24 bp):
AGATAATTTCCTAATAAATTGCAA
Found at i:3631954 original size:9 final size:9
Alignment explanation
Indices: 3631942--3631979 Score: 58
Period size: 9 Copynumber: 4.0 Consensus size: 9
3631932 TATTTGTTTA
3631942 ATTCTTATT
1 ATTCTTATT
3631951 ATTCTTATT
1 ATTCTTATT
3631960 CAATTCTTATT
1 --ATTCTTATT
3631971 ATTCTTATT
1 ATTCTTATT
3631980 CTTATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 18 0.67
11 9 0.33
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (9 bp):
ATTCTTATT
Found at i:3631966 original size:20 final size:20
Alignment explanation
Indices: 3631941--3631980 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3631931 TTATTTGTTT
3631941 AATTCTTATTATTCTTATTC
1 AATTCTTATTATTCTTATTC
3631961 AATTCTTATTATTCTTATTC
1 AATTCTTATTATTCTTATTC
3631981 TTATTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTCTTATTATTCTTATTC
Found at i:3639341 original size:17 final size:16
Alignment explanation
Indices: 3639310--3639343 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3639300 CACGTGAGGA
3639310 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
3639326 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
3639343 T
1 T
3639344 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:3645659 original size:19 final size:21
Alignment explanation
Indices: 3645622--3645664 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
3645612 TAACTTTTTC
3645622 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
3645642 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
3645662 TTT
1 TTT
3645665 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:3645670 original size:19 final size:20
Alignment explanation
Indices: 3645621--3645670 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3645611 TTAACTTTTT
*
3645621 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
3645641 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
3645660 CTTTTACCTTT
1 CTTTTACCTTT
3645671 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:3649514 original size:17 final size:16
Alignment explanation
Indices: 3649483--3649516 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3649473 CACGTGAGGA
3649483 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
3649499 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
3649516 T
1 T
3649517 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:3653757 original size:65 final size:65
Alignment explanation
Indices: 3653624--3653780 Score: 185
Period size: 65 Copynumber: 2.4 Consensus size: 65
3653614 ACTAAGAGAG
* * *
3653624 CATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGTG
1 CATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGTA
* * * * * *
3653688 CATCGATGCATCAAATGCATTTGATGTTTTCATAAA-ATCCTCAGTGCATTGGTGCATGG-TATG
1 CATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-GG
3653751 TA
64 TA
*
3653753 CATCGATGCATGAAATGCATTCGATGTT
1 CATCGATGCATCAAATGCATTCGATGTT
3653781 CAATTTAATT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 25 0.32
65 51 0.65
66 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
CATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGTA
Found at i:3660043 original size:117 final size:117
Alignment explanation
Indices: 3659837--3660070 Score: 452
Period size: 117 Copynumber: 2.0 Consensus size: 117
3659827 ACCTTTTTCA
3659837 AAACTTTTTGTTCCAGCCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGATAATTATC
1 AAACTTTTTGTTCCAGCCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGATAATTATC
3659902 ATGAACTTTTGAAAGTAAGTTATGCAAATCAGTATTTT-TCTTTCAAAATCAT
66 ATGAACTTTTGAAAGTAAGTTATGCAAATCAGTATTTTCT-TTTCAAAATCAT
3659954 AAACTTTTTGTTCCAGCCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGATAATTATC
1 AAACTTTTTGTTCCAGCCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGATAATTATC
3660019 ATGAACTTTTGAAAGTAAGTTATGCAAATCAGTATTTTCTTTTCAAAATCAT
66 ATGAACTTTTGAAAGTAAGTTATGCAAATCAGTATTTTCTTTTCAAAATCAT
3660071 TAATTTTGAT
Statistics
Matches: 116, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
117 115 0.99
118 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (117 bp):
AAACTTTTTGTTCCAGCCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGATAATTATC
ATGAACTTTTGAAAGTAAGTTATGCAAATCAGTATTTTCTTTTCAAAATCAT
Found at i:3662200 original size:65 final size:65
Alignment explanation
Indices: 3662070--3662227 Score: 169
Period size: 65 Copynumber: 2.4 Consensus size: 65
3662060 ACTAAGAGTA
* * * * *
3662070 CATCGATACATCAAGTGTATTCGATG-TTTCAAAATAGCCAGATTGCATCGATGCATGGCTGGTG
1 CATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACACTGCATCGATGCATGGCTGGTG
* * * *
3662134 CATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCACTGCATCGGTGCATGG-TATG
1 CATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACACTGCATCGATGCATGGCT-GG
3662197 TG
64 TG
* * *
3662199 CATCGGTGCATAAAACGCATTCGATGTTT
1 CATCGATGCATCAAATGCATTCGATGTTT
3662228 AATTTAATTC
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
64 24 0.30
65 52 0.66
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (65 bp):
CATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACACTGCATCGATGCATGGCTGGTG
Found at i:3665022 original size:23 final size:23
Alignment explanation
Indices: 3664962--3665026 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
3664952 AGAGATAGAA
* *
3664962 CCTAATAAATT-CAAAGATAATG
1 CCTAATAAATTGTAAAGATATTG
*
3664984 CCTAA-AAA-TGAATAAAGATATTT
1 CCTAATAAATTG--TAAAGATATTG
3665007 CCTAATAAATTGTAAA-ATAT
1 CCTAATAAATTGTAAAGATAT
3665027 AATCCATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
20 1 0.03
21 3 0.09
22 9 0.26
23 17 0.49
24 3 0.09
25 2 0.06
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.31
Consensus pattern (23 bp):
CCTAATAAATTGTAAAGATATTG
Found at i:3673759 original size:13 final size:14
Alignment explanation
Indices: 3673743--3673772 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3673733 TTAAAATTGG
3673743 AAAATAAAG-AAAT
1 AAAATAAAGAAAAT
3673756 AAAATAAAGAAAAT
1 AAAATAAAGAAAAT
3673770 AAA
1 AAA
3673773 CACATAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAATAAAGAAAAT
Found at i:3679721 original size:20 final size:20
Alignment explanation
Indices: 3679706--3679748 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
3679696 AGAGCTTGCC
3679706 TAGAAACTTTCAAGCTTCCT
1 TAGAAACTTTCAAGCTTCCT
3679726 TAGAAACTTTCAAGCTTCCT
1 TAGAAACTTTCAAGCTTCCT
3679746 TAG
1 TAG
3679749 GGATAGACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
TAGAAACTTTCAAGCTTCCT
Found at i:3680812 original size:31 final size:31
Alignment explanation
Indices: 3680766--3680827 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
3680756 AGGTACAATG
* * *
3680766 CTTAGTGTTCTAGAGAAATTAAGTGAAGATC
1 CTTAGTATTCCAGAGAAACTAAGTGAAGATC
*
3680797 CTTAGTATTCCAGAGAAACTAGGTGAAGATC
1 CTTAGTATTCCAGAGAAACTAAGTGAAGATC
3680828 AACTTGAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (31 bp):
CTTAGTATTCCAGAGAAACTAAGTGAAGATC
Found at i:3696938 original size:31 final size:31
Alignment explanation
Indices: 3696860--3696938 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
3696850 TCAAAAAACA
* **
3696860 TAAGTTTTGGTCACTTACGTTATTGTTTTAT
1 TAAGTTTTGGTCACTTGCGTTATCATTTTAT
*
3696891 TAAGTTTTGGTCACTTGTGTTATCATTTTAT
1 TAAGTTTTGGTCACTTGCGTTATCATTTTAT
3696922 TAAGTTTTGGTCACTTG
1 TAAGTTTTGGTCACTTG
3696939 GACATTGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.19, C:0.10, G:0.18, T:0.53
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTGCGTTATCATTTTAT
Found at i:3697598 original size:20 final size:20
Alignment explanation
Indices: 3697573--3697612 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3697563 TTCTTAAAGC
3697573 ACATTTAGG-TACATATAGTT
1 ACATTTAGGAT-CATATAGTT
3697593 ACATTTAGGATCATATAGTT
1 ACATTTAGGATCATATAGTT
3697613 TCATGTGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (20 bp):
ACATTTAGGATCATATAGTT
Found at i:3699903 original size:31 final size:31
Alignment explanation
Indices: 3699868--3699942 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
3699858 AACATCCAAT
*
3699868 TGACCAAAACTTAATAAAACGATAATGTAAG
1 TGACCAAAACTTAATAAAACGATAACGTAAG
* *
3699899 TGACCAAAACATAATAAAATGATAACGTAAG
1 TGACCAAAACTTAATAAAACGATAACGTAAG
3699930 TGACCAAAACTTA
1 TGACCAAAACTTA
3699943 TATTTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (31 bp):
TGACCAAAACTTAATAAAACGATAACGTAAG
Found at i:3700585 original size:31 final size:31
Alignment explanation
Indices: 3700516--3700590 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
3700506 TAAGGAAAAG
*
3700516 CGATTTTGATCTTTTACATTATCAATCATTT
1 CGATTTTGATCCTTTACATTATCAATCATTT
**
3700547 -GATTTTGATCCTTTACATTATCGGT-ATGTT
1 CGATTTTGATCCTTTACATTATCAATCAT-TT
3700577 CGATTTTGATCCTT
1 CGATTTTGATCCTT
3700591 CAGCCATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 2 0.05
30 24 0.62
31 13 0.33
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (31 bp):
CGATTTTGATCCTTTACATTATCAATCATTT
Found at i:3701888 original size:13 final size:14
Alignment explanation
Indices: 3701864--3701892 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3701854 ACTATAACAA
3701864 AAATATAAAAATAC
1 AAATATAAAAATAC
3701878 AAATA-AAAAATAC
1 AAATATAAAAATAC
3701891 AA
1 AA
3701893 TTATTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (14 bp):
AAATATAAAAATAC
Found at i:3706055 original size:15 final size:16
Alignment explanation
Indices: 3706019--3706056 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3706009 AGAGCCTTTG
*
3706019 AATCATTCAGCATTTA
1 AATCATTCAGCACTTA
*
3706035 AATCATTCAGCGCTT-
1 AATCATTCAGCACTTA
3706050 AATCATT
1 AATCATT
3706057 TTGAAGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (16 bp):
AATCATTCAGCACTTA
Found at i:3708473 original size:18 final size:18
Alignment explanation
Indices: 3708450--3708484 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3708440 GTGAATCCCA
3708450 CGCCTTTCATGCACCTCG
1 CGCCTTTCATGCACCTCG
*
3708468 CGCCTTTCATGCGCCTC
1 CGCCTTTCATGCACCTC
3708485 AAGGCTCCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.46, G:0.17, T:0.29
Consensus pattern (18 bp):
CGCCTTTCATGCACCTCG
Found at i:3717921 original size:2 final size:2
Alignment explanation
Indices: 3717896--3718071 Score: 74
Period size: 2 Copynumber: 90.5 Consensus size: 2
3717886 AAACTTGTGC
*
3717896 AT AT A- AT AT AA AT AT AT ACT -T AT AT A- AGT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT
* * *
3717935 AT -T AT AC AT -T AT ACT -T AT A- AT AT AT GT AC AT A- AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
3717973 ACT -T AT TT AT AT AT AT AA AT AA AGT AT A- AT AT TT AT AA ACT
1 A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T
* *
3718014 AT AA AGT AT A- AGT AT AT AA AT -T AT AT AGT AT AT AT AT AT AT
1 AT AT A-T AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
3718055 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
3718072 AACTATAAAG
Statistics
Matches: 129, Mismatches: 22, Indels: 46
0.65 0.11 0.23
Matches are distributed among these distances:
1 14 0.11
2 105 0.81
3 10 0.08
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3717948 original size:34 final size:37
Alignment explanation
Indices: 3717896--3717971 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 37
3717886 AAACTTGTGC
*
3717896 ATATAATATAAATATATACTTAT-ATA-A-GTATATA
1 ATATAATATAAATATATACTTATAATATATGTACATA
*
3717930 ATATAATTATACAT-TATACTTATAATATATGTACATA
1 ATATAA-TATAAATATATACTTATAATATATGTACATA
3717967 ATATA
1 ATATA
3717972 TACTTATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
34 15 0.42
35 9 0.25
36 1 0.03
37 11 0.31
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (37 bp):
ATATAATATAAATATATACTTATAATATATGTACATA
Found at i:3718040 original size:9 final size:9
Alignment explanation
Indices: 3718026--3718112 Score: 56
Period size: 9 Copynumber: 9.7 Consensus size: 9
3718016 AAAGTATAAG
3718026 TATATAAAT
1 TATATAAAT
*
3718035 TATATAGTAT
1 TATATA-AAT
*
3718045 ATATATATAT
1 -TATATAAAT
*
3718055 ATATATATAT
1 -TATATAAAT
3718065 ATATATAAA-
1 -TATATAAAT
* *
3718074 -CTATAAAG
1 TATATAAAT
*
3718082 CATATAAA-
1 TATATAAAT
3718090 T-TATAAAT
1 TATATAAAT
3718098 TATATAAAT
1 TATATAAAT
3718107 TATATA
1 TATATA
3718113 TATATTGTAC
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
7 12 0.18
8 1 0.01
9 25 0.37
10 23 0.34
11 6 0.09
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (9 bp):
TATATAAAT
Found at i:3718045 original size:16 final size:15
Alignment explanation
Indices: 3718013--3718117 Score: 80
Period size: 16 Copynumber: 7.2 Consensus size: 15
3718003 ATTTATAAAC
*
3718013 TATAAAGTATA-AGTA
1 TATAAATTATATA-TA
3718028 TATAAATTATATAGTA
1 TATAAATTATATA-TA
3718044 TAT--A-TATATATA
1 TATAAATTATATATA
3718056 TAT--A-TATATATA
1 TATAAATTATATATA
* * *
3718068 TATAAACTATAAAGCA
1 TATAAATTATATA-TA
*
3718084 TATAAATTATAAATTA
1 TATAAATTATATA-TA
3718100 TATAAATTATATATA
1 TATAAATTATATATA
3718115 TAT
1 TAT
3718118 TGTACACTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
12 17 0.22
13 6 0.08
14 2 0.03
15 20 0.26
16 33 0.42
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (15 bp):
TATAAATTATATATA
Found at i:3718168 original size:2 final size:2
Alignment explanation
Indices: 3718161--3718193 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3718151 TTTATTTTAT
3718161 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3718194 GTTTGCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3718218 original size:46 final size:44
Alignment explanation
Indices: 3718170--3718362 Score: 162
Period size: 42 Copynumber: 4.6 Consensus size: 44
3718160 TTATATATAT
* *
3718170 ATATATATATATATATATTATATAGTTTGCAAATGATTTTTG--A
1 ATATATATATATATATA-TATATAGTTTGAAAACGATTTTTGAAA
*
3718213 A-ATATATATA-ATATATA-GT--TTTGAAAACGATTTTTGAAA
1 ATATATATATATATATATATATAGTTTGAAAACGATTTTTGAAA
*
3718252 TATATATATATATATATATATATAGTTTTGAAAACAATTTTTG-AA
1 -ATATATATATATATATATATATAG-TTTGAAAACGATTTTTGAAA
* ** *
3718297 A-ATGTATATAT-TATATAGCT--TTTAAAAAC-A-TTTTGAAA
1 ATATATATATATATATATATATAGTTTGAAAACGATTTTTGAAA
* *
3718335 ACATATATATATATATATAATATGGTTT
1 ATATATATATATATATAT-ATATAGTTT
3718363 TTTGAAACAT
Statistics
Matches: 123, Mismatches: 12, Indels: 30
0.75 0.07 0.18
Matches are distributed among these distances:
37 20 0.16
38 4 0.03
39 19 0.15
40 8 0.07
41 16 0.13
42 23 0.19
43 14 0.11
44 1 0.01
45 2 0.02
46 16 0.13
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (44 bp):
ATATATATATATATATATATATAGTTTGAAAACGATTTTTGAAA
Found at i:3718228 original size:36 final size:37
Alignment explanation
Indices: 3718178--3718267 Score: 137
Period size: 37 Copynumber: 2.4 Consensus size: 37
3718168 ATATATATAT
* * *
3718178 ATATATATATTATATAG-TTTGCAAATGATTTTTGAA
1 ATATATATAATATATAGTTTTGAAAACGATTTTTGAA
3718214 ATATATATAATATATAGTTTTGAAAACGATTTTTGAA
1 ATATATATAATATATAGTTTTGAAAACGATTTTTGAA
3718251 ATATATATATATATATA
1 ATATATATA-ATATATA
3718268 TATATATAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
36 16 0.33
37 26 0.53
38 7 0.14
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTGAAAACGATTTTTGAA
Found at i:3718258 original size:2 final size:2
Alignment explanation
Indices: 3718251--3718275 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3718241 GATTTTTGAA
3718251 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
3718276 GTTTTGAAAA
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:3718325 original size:39 final size:37
Alignment explanation
Indices: 3718261--3718676 Score: 238
Period size: 36 Copynumber: 11.3 Consensus size: 37
3718251 ATATATATAT
* *
3718261 ATATATATATATATAGTTTTGAAAACAATTTTTGAAAAT
1 ATATATATATATATAGTTTTAAAAAC-A-TTTTGAAAAC
*
3718300 GTATATAT-TATATAGCTTTTAAAAACATTTTGAAAAC
1 ATATATATATATATAG-TTTTAAAAACATTTTGAAAAC
** *****
3718337 ATATATATATATATA-TAAT-ATGGTTTTTTG-AAAC
1 ATATATATATATATAGTTTTAAAAACATTTTGAAAAC
* * * **
3718371 ATTTTTATA-ATATGGTTTTTAAAAA-AAATTGAAAAC
1 ATATATATATATATAG-TTTTAAAAACATTTTGAAAAC
*
3718407 ATATATA-ATATATGGTTTTTTTAAAAAAATCATTTTGAAAA-
1 ATATATATATATATAG---TTTT--AAAAA-CATTTTGAAAAC
* * *
3718448 AAATATATAATATATAGTTTTTGAAAACATTTTAAAAAC
1 ATATATAT-ATATATAG-TTTTAAAAACATTTTGAAAAC
* * * * *
3718487 TTATATA-ATATATAATATTGAAATCATTTTGAAAAC
1 ATATATATATATATAGTTTTAAAAACATTTTGAAAAC
* *
3718523 TTATATA-ATATATTGTTTT-AAAACATTTTTGAAAAC
1 ATATATATATATATAGTTTTAAAAACA-TTTTGAAAAC
* * *
3718559 ATTTATA-ATATAT-GGTATAAAAACATTTTG-AAA-
1 ATATATATATATATAGTTTTAAAAACATTTTGAAAAC
* * * *
3718592 ATCATATA-ATATATAGTTTTGAAAACTTTTTAAAAAA
1 AT-ATATATATATATAGTTTTAAAAACATTTTGAAAAC
* * * *
3718629 ATATGTATAATATATAGTTTT-AAAATATCTT-AAAAT
1 ATATATAT-ATATATAGTTTTAAAAACATTTTGAAAAC
3718665 ATATATATATAT
1 ATATATATATAT
3718677 TATTTATTTT
Statistics
Matches: 297, Mismatches: 56, Indels: 52
0.73 0.14 0.13
Matches are distributed among these distances:
33 6 0.02
34 24 0.08
35 41 0.14
36 97 0.33
37 32 0.11
38 41 0.14
39 25 0.08
40 5 0.02
41 11 0.04
42 8 0.03
43 7 0.02
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (37 bp):
ATATATATATATATAGTTTTAAAAACATTTTGAAAAC
Found at i:3718331 original size:83 final size:83
Alignment explanation
Indices: 3718168--3718363 Score: 256
Period size: 83 Copynumber: 2.4 Consensus size: 83
3718158 TATTATATAT
* **
3718168 ATATATATATATATATATATTATATAG-TTTGCAAATGATTTTTGAAATATATATAATATATAGT
1 ATATATATATATATATATA-TATATAGTTTTGAAAACAATTTTTGAAATATATATAATATATAGT
*
3718232 TTTGAAAACGATTTTTGAA
65 TTTAAAAACGATTTTTGAA
* *
3718251 ATATATATATATATATATATATATAGTTTTGAAAACAATTTTTGAAAATGTATATATTATATAGC
1 ATATATATATATATATATATATATAGTTTTGAAAACAATTTTTG-AAATATATATAATATATAG-
3718316 TTTTAAAAAC-A-TTTTGAA
64 TTTTAAAAACGATTTTTGAA
* *
3718334 A-ACATATATATATATATATAATATGGTTTT
1 ATATATATATATATATATAT-ATATAGTTTT
3718364 TTGAAACATT
Statistics
Matches: 101, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
82 24 0.24
83 50 0.50
84 18 0.18
85 9 0.09
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (83 bp):
ATATATATATATATATATATATATAGTTTTGAAAACAATTTTTGAAATATATATAATATATAGTT
TTAAAAACGATTTTTGAA
Found at i:3718371 original size:84 final size:81
Alignment explanation
Indices: 3718170--3718376 Score: 215
Period size: 84 Copynumber: 2.5 Consensus size: 81
3718160 TTATATATAT
* * * **
3718170 ATATATATATATATATATTATATAGTTTGCAAATGATTTTTGAAATATATATAATATATAGTTTT
1 ATATATATATATATATAATATGT-TTTTG-AAAACATTTTTGAAATATATATAATATATAGTTTT
* *
3718235 GAAAACGATTTTTGAAAT
64 AAAAACGATTTTTGAAAC
* *
3718253 ATATATATATATATATATATATAG-TTTTGAAAACAATTTTTGAAAATGTATATATTATATAGCT
1 ATATATATATATATATA-ATAT-GTTTTTGAAAAC-ATTTTTG-AAATATATATAATATATAG-T
3718317 TTTAAAAAC-A-TTTTGAAAAC
61 TTTAAAAACGATTTTTG-AAAC
3718337 ATATATATATATATATAATATGGTTTTTTG-AAACATTTTT
1 ATATATATATATATATAATAT-G-TTTTTGAAAACATTTTT
3718377 ATAATATGGT
Statistics
Matches: 106, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
82 3 0.03
83 44 0.42
84 45 0.42
85 14 0.13
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (81 bp):
ATATATATATATATATAATATGTTTTTGAAAACATTTTTGAAATATATATAATATATAGTTTTAA
AAACGATTTTTGAAAC
Found at i:3718530 original size:150 final size:141
Alignment explanation
Indices: 3718290--3718644 Score: 337
Period size: 150 Copynumber: 2.4 Consensus size: 141
3718280 TGAAAACAAT
* * *
3718290 TTTTGAAAATGTATATATTATATAGCTTTTAAAAACATTTTGAAAACATATATATATATATATAA
1 TTTTGAAAA--TATATAATATATAG-TTTTGAAAACATTTTAAAAACATATATATATATATATAA
* * * * *
3718355 TATGGTTTTTTGAAACATTTTTATAATATGGT-TTTTAAAA-AAAATTGAAAACATATATAATAT
63 TATGATATTTTGAAACACTTATATAATATAGTGTTTTAAAACAAAATTGAAAACATATATAATAT
3718418 ATGGTTTTTTTAAAAAAATCA
128 ATGG------TAAAAAAA-CA
3718439 TTTTGAAAAAAATATATAATATATAGTTTTTGAAAACATTTTAAAAAC-T-TATATA-ATATATA
1 TTTTG---AAAATATATAATATATAG-TTTTGAAAACATTTTAAAAACATATATATATATATATA
* *** *
3718501 ATATTGAAATCATTTTGAAA-ACTTATATAATATATTGTTTTAAAACATTTTTGAAAACATTTAT
62 ATA-TG--AT-ATTTTGAAACACTTATATAATATAGTGTTTTAAAACAAAATTGAAAACATATAT
*
3718565 AATATATGGTATAAAAACA
123 AATATATGGTAAAAAAACA
* * *
3718584 TTTTGAAAATCATATAATATATAGTTTTGAAAACTTTTTAAAAAAATATGTATA-ATATATA
1 TTTTGAAAAT-ATATAATATATAGTTTTGAAAACATTTTAAAAACATATATATATATATATA
3718645 GTTTTAAAAT
Statistics
Matches: 176, Mismatches: 18, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
142 24 0.14
143 14 0.08
144 12 0.07
145 7 0.04
146 7 0.04
147 10 0.06
148 8 0.05
149 6 0.03
150 45 0.26
151 16 0.09
152 27 0.15
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (141 bp):
TTTTGAAAATATATAATATATAGTTTTGAAAACATTTTAAAAACATATATATATATATATAATAT
GATATTTTGAAACACTTATATAATATAGTGTTTTAAAACAAAATTGAAAACATATATAATATATG
GTAAAAAAACA
Found at i:3718640 original size:72 final size:69
Alignment explanation
Indices: 3718447--3718676 Score: 225
Period size: 71 Copynumber: 3.2 Consensus size: 69
3718437 CATTTTGAAA
* * * *
3718447 AAAATATATAATATATAGTTTTTGAAAACATTTTAAAAACTTATATAATATATAATATTGAAATC
1 AAAATATATAATATATAG-TTTTGAAAACTTTTTAAAAAATT-TATAATATATAATATTAAAAAC
3718512 ATTTTG
64 ATTTTG
* * **
3718518 AAAACTTATATAATATATTGTTTT-AAAACATTTTTGAAAACATTTATAATATATGGTA-TAAAA
1 AAAA--TATATAATATATAGTTTTGAAAAC-TTTTT-AAAAAATTTATAATATATAATATTAAAA
3718581 ACATTTTG
62 ACATTTTG
* *
3718589 AAAATCATATAATATATAGTTTTGAAAACTTTTTAAAAAAATATGTATAATATATAGT-TTTAAA
1 AAAAT-ATATAATATATAGTTTTGAAAACTTTTT-AAAAAAT-T-TATAATATATAATATTAAAA
* *
3718653 ATATCTT-
62 ACATTTTG
3718660 AAAATATATATATATAT
1 AAAATATATA-ATATAT
3718677 TATTTATTTT
Statistics
Matches: 134, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
69 1 0.01
70 32 0.24
71 41 0.31
72 41 0.31
73 19 0.14
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (69 bp):
AAAATATATAATATATAGTTTTGAAAACTTTTTAAAAAATTTATAATATATAATATTAAAAACAT
TTTG
Found at i:3718714 original size:14 final size:14
Alignment explanation
Indices: 3718684--3718735 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
3718674 TATTATTTAT
*
3718684 TTTTA-TTTATCTTA
1 TTTTATTTTAT-TAA
3718698 TTTTATTTTATTAA
1 TTTTATTTTATTAA
* *
3718712 TTTCATTTTTTTAA
1 TTTTATTTTATTAA
3718726 TTTTTATTTT
1 -TTTTATTTT
3718736 GGTCCAGGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTTATTAA
Found at i:3719819 original size:19 final size:19
Alignment explanation
Indices: 3719803--3719846 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3719793 CTTTTTTTTC
3719803 TTTATTTGTTTCCTTTTAT
1 TTTATTTGTTTCCTTTTAT
*
3719822 TTTATTTGTTTCCTTTGA-
1 TTTATTTGTTTCCTTTTAT
3719840 TTTATTT
1 TTTATTT
3719847 AGTATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.11, C:0.09, G:0.07, T:0.73
Consensus pattern (19 bp):
TTTATTTGTTTCCTTTTAT
Found at i:3719875 original size:37 final size:38
Alignment explanation
Indices: 3719816--3719892 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 38
3719806 ATTTGTTTCC
* *
3719816 TTTTATTTTATTTGTTTCCTTTGATTTATTTAGTATTT
1 TTTTATTTTATTTCTTTCCTTTGAATTATTTAGTATTT
**
3719854 TTTTCATTTT-TTTCTTT-CTTTGAATTATTTTTTATTT
1 TTTT-ATTTTATTTCTTTCCTTTGAATTATTTAGTATTT
3719891 TT
1 TT
3719893 ATGTTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 19 0.56
38 10 0.29
39 5 0.15
ACGTcount: A:0.14, C:0.06, G:0.05, T:0.74
Consensus pattern (38 bp):
TTTTATTTTATTTCTTTCCTTTGAATTATTTAGTATTT
Found at i:3719907 original size:19 final size:19
Alignment explanation
Indices: 3719883--3719921 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3719873 TTGAATTATT
3719883 TTTTATTT-TTATGTTTTTA
1 TTTTATTTATTAT-TTTTTA
3719902 TTTTATTTATTATTTTTTA
1 TTTTATTTATTATTTTTTA
3719921 T
1 T
3719922 CTAACATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTTATTTATTATTTTTTA
Found at i:3720230 original size:2 final size:2
Alignment explanation
Indices: 3720223--3720268 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3720213 CGGTTGTTAC
*
3720223 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3720265 AT AT
1 AT AT
3720269 GTAATTATGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3720506 original size:16 final size:18
Alignment explanation
Indices: 3720472--3720513 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
3720462 AGAACATAAA
3720472 ATATATAAATTATATAGT
1 ATATATAAATTATATAGT
*
3720490 ATATATATA-TATA-AGT
1 ATATATAAATTATATAGT
*
3720506 ACATATAA
1 ATATATAA
3720514 GTATATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.43
17 4 0.19
18 8 0.38
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (18 bp):
ATATATAAATTATATAGT
Found at i:3720858 original size:19 final size:20
Alignment explanation
Indices: 3720818--3720861 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3720808 TCTCTATTCT
*
3720818 CTCTAAATTTTCCAATTACC
1 CTCTAAATTCTCCAATTACC
*
3720838 CTCTAAATTCT-CAATTTCC
1 CTCTAAATTCTCCAATTACC
3720857 CTCTA
1 CTCTA
3720862 TTATCAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (20 bp):
CTCTAAATTCTCCAATTACC
Found at i:3722144 original size:26 final size:26
Alignment explanation
Indices: 3722115--3722168 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
3722105 TTAATGTTAG
*
3722115 TTATCGACTGTTAATATTATTTATTT
1 TTATCGACTGTTAATATTATATATTT
* * * *
3722141 TTATCTATTTTTTATATTATATATTT
1 TTATCGACTGTTAATATTATATATTT
3722167 TT
1 TT
3722169 TATTTTATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.65
Consensus pattern (26 bp):
TTATCGACTGTTAATATTATATATTT
Found at i:3722165 original size:16 final size:16
Alignment explanation
Indices: 3722141--3722176 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3722131 TTATTTATTT
*
3722141 TTATCTATTTTTTATA
1 TTATATATTTTTTATA
*
3722157 TTATATATTTTTTATT
1 TTATATATTTTTTATA
3722173 TTAT
1 TTAT
3722177 TAAAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTATATATTTTTTATA
Found at i:3722813 original size:13 final size:12
Alignment explanation
Indices: 3722783--3722817 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
3722773 AATTTAAAAA
3722783 TATTTTAATTAT
1 TATTTTAATTAT
3722795 TAATTTTCAATTAT
1 T-ATTTT-AATTAT
3722809 TATTTTAAT
1 TATTTTAAT
3722818 AACATGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.19
13 10 0.48
14 7 0.33
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:3723854 original size:7 final size:7
Alignment explanation
Indices: 3723842--3723866 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3723832 ATAACTATTA
3723842 TAATAAT
1 TAATAAT
3723849 TAATAAT
1 TAATAAT
3723856 TAATAAT
1 TAATAAT
3723863 TAAT
1 TAAT
3723867 TTTATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATAAT
Found at i:3723881 original size:29 final size:29
Alignment explanation
Indices: 3723839--3723898 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
3723829 TAGATAACTA
* * *
3723839 TTATAATAATTAATAATTAA-TAATTAATT
1 TTATAAAAAATAAT-ATTAATTAAATAATT
*
3723868 TTATAAAAAATAATTTTAATTAAATAATT
1 TTATAAAAAATAATATTAATTAAATAATT
3723897 TT
1 TT
3723899 TATACTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTATAAAAAATAATATTAATTAAATAATT
Found at i:3725180 original size:5 final size:5
Alignment explanation
Indices: 3725158--3725196 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
3725148 GCAAAGTCTA
* *
3725158 ATGAT ATGAAA ATGAT ATAAT ATGAT ATGAT ATGAT ATG
1 ATGAT ATG-AT ATGAT ATGAT ATGAT ATGAT ATGAT ATG
3725197 CATGTTCACT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (5 bp):
ATGAT
Found at i:3732153 original size:13 final size:13
Alignment explanation
Indices: 3732133--3732194 Score: 62
Period size: 14 Copynumber: 4.9 Consensus size: 13
3732123 TTATTTGAAT
3732133 GATTATAATTAA-
1 GATTATAATTAAG
3732145 GATTTATAATATAAG
1 GA-TTATAAT-TAAG
3732160 GATTATAATT-A-
1 GATTATAATTAAG
3732171 -A-TATAATATAAG
1 GATTATAAT-TAAG
3732183 GATTATAATTAA
1 GATTATAATTAA
3732195 TATAAAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
9 6 0.14
10 2 0.05
11 1 0.02
12 3 0.07
13 12 0.29
14 16 0.38
15 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (13 bp):
GATTATAATTAAG
Found at i:3732175 original size:23 final size:23
Alignment explanation
Indices: 3732149--3732199 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
3732139 AATTAAGATT
3732149 TATAATATAAGGATTATAATTAA
1 TATAATATAAGGATTATAATTAA
3732172 TATAATATAAGGATTATAATTAA
1 TATAATATAAGGATTATAATTAA
3732195 TATAA
1 TATAA
3732200 AAAATAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (23 bp):
TATAATATAAGGATTATAATTAA
Found at i:3736506 original size:5 final size:5
Alignment explanation
Indices: 3736484--3736522 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
3736474 GCAAAGTCTA
* *
3736484 ATGAT ATGAAA ATGAT ATAAT ATGAT ATGAT ATGAT ATG
1 ATGAT ATG-AT ATGAT ATGAT ATGAT ATGAT ATGAT ATG
3736523 CATGTTCACT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (5 bp):
ATGAT
Found at i:3738995 original size:14 final size:14
Alignment explanation
Indices: 3738976--3739003 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3738966 AAATTACTCC
3738976 CCTTACTTTAATAT
1 CCTTACTTTAATAT
3738990 CCTTACTTTAATAT
1 CCTTACTTTAATAT
3739004 TTCTCCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (14 bp):
CCTTACTTTAATAT
Found at i:3740406 original size:24 final size:24
Alignment explanation
Indices: 3740362--3740411 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3740352 ATAAAGAACC
*
3740362 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
3740386 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
3740410 AA
1 AA
3740412 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:3748837 original size:24 final size:24
Alignment explanation
Indices: 3748793--3748842 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3748783 ATAAAGAACC
*
3748793 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
3748817 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
3748841 AA
1 AA
3748843 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:3749065 original size:24 final size:25
Alignment explanation
Indices: 3749017--3749065 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3749007 CCACGAACCA
* *
3749017 CCTAGCTCGCTAGCTCCTTTCAGCT
1 CCTAGCTCGCCAGCTCCTTGCAGCT
*
3749042 CCTAGCTCGCCA-CTCCTTGGAGCT
1 CCTAGCTCGCCAGCTCCTTGCAGCT
3749066 TTATCAATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.12, C:0.41, G:0.18, T:0.29
Consensus pattern (25 bp):
CCTAGCTCGCCAGCTCCTTGCAGCT
Found at i:3750821 original size:27 final size:27
Alignment explanation
Indices: 3750783--3750835 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
3750773 TGGGAATTGT
* *
3750783 TTTTTTGAAAAACAATAGTTTATATAA
1 TTTTATGAAAAACAATAGTATATATAA
3750810 TTTTATGAAAAACAATAGTATATATA
1 TTTTATGAAAAACAATAGTATATATA
3750836 TATATATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42
Consensus pattern (27 bp):
TTTTATGAAAAACAATAGTATATATAA
Found at i:3751274 original size:20 final size:20
Alignment explanation
Indices: 3751245--3751282 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3751235 GCCTAAAACG
* *
3751245 TCGAGTAGTATCGGTACTCC
1 TCGAGGAGTATCGATACTCC
3751265 TCGAGGAGTATCGATACT
1 TCGAGGAGTATCGATACT
3751283 TCAAGGCAAA
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:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (20 bp):
TCGAGGAGTATCGATACTCC
Found at i:3751404 original size:42 final size:42
Alignment explanation
Indices: 3751358--3751452 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
3751348 GGATGAACAA
* ** *
3751358 TATCGATACTAAGTAAGAACAGTATTGATACTATATGAGTAG
1 TATCGATACTAAGCAAGAACAGTATCAATACTACATGAGTAG
* **
3751400 TATCGATACCAAGCAAGAGTAGTATCAATACTACATGAGTAG
1 TATCGATACTAAGCAAGAACAGTATCAATACTACATGAGTAG
*
3751442 TATCAATACTA
1 TATCGATACTA
3751453 GATGAGTAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (42 bp):
TATCGATACTAAGCAAGAACAGTATCAATACTACATGAGTAG
Found at i:3751407 original size:20 final size:20
Alignment explanation
Indices: 3751378--3751472 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
3751368 AAGTAAGAAC
* *
3751378 AGTATTGATACTATATGAGT
1 AGTATCGATACTACATGAGT
* *
3751398 AGTATCGATACCAAGCAAGAGT
1 AGTATCGATA-CTA-CATGAGT
*
3751420 AGTATCAATACTACATGAGT
1 AGTATCGATACTACATGAGT
* *
3751440 AGTATCAATACTAGATGAGT
1 AGTATCGATACTACATGAGT
3751460 AGTATCGATACTA
1 AGTATCGATACTA
3751473 AGTGCATAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
20 46 0.72
21 4 0.06
22 14 0.22
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTACATGAGT
Found at i:3760143 original size:15 final size:16
Alignment explanation
Indices: 3760118--3760159 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3760108 TAATAAATAA
*
3760118 ACGATCATAAACGAAC
1 ACGAACATAAACGAAC
* *
3760134 ATG-ACATAAATGAAC
1 ACGAACATAAACGAAC
3760149 ACGAACATAAA
1 ACGAACATAAA
3760160 AACATAAACG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.55, C:0.19, G:0.12, T:0.14
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3761208 original size:14 final size:14
Alignment explanation
Indices: 3761191--3761270 Score: 104
Period size: 14 Copynumber: 6.3 Consensus size: 14
3761181 AATGAACATA
3761191 AACGAACATAACCG
1 AACGAACATAACCG
3761205 AACGAACAT-A---
1 AACGAACATAACCG
3761215 AACGAACATAACCG
1 AACGAACATAACCG
3761229 AACGAACAT-A---
1 AACGAACATAACCG
3761239 AACGAACATAACCG
1 AACGAACATAACCG
3761253 AACGAACATAACCG
1 AACGAACATAACCG
3761267 AACG
1 AACG
3761271 TTCACGAACG
Statistics
Matches: 58, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
10 18 0.31
11 2 0.03
13 2 0.03
14 36 0.62
ACGTcount: A:0.53, C:0.26, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:3761269 original size:10 final size:10
Alignment explanation
Indices: 3761184--3761255 Score: 63
Period size: 10 Copynumber: 6.4 Consensus size: 10
3761174 ATAAATGAAT
3761184 GAACATAAAC
1 GAACATAAAC
3761194 GAACATAACCGAAC
1 GAACAT-A---AAC
3761208 GAACATAAAC
1 GAACATAAAC
3761218 GAACATAACCGAAC
1 GAACAT-A---AAC
3761232 GAACATAAAC
1 GAACATAAAC
*
3761242 GAACATAACC
1 GAACATAAAC
3761252 GAAC
1 GAAC
3761256 GAACATAACC
Statistics
Matches: 53, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
10 31 0.58
11 2 0.04
13 2 0.04
14 18 0.34
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:3761280 original size:24 final size:24
Alignment explanation
Indices: 3761184--3761269 Score: 163
Period size: 24 Copynumber: 3.6 Consensus size: 24
3761174 ATAAATGAAT
3761184 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
3761208 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
3761232 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
3761256 GAACATAACCGAAC
1 GAACATAAACGAAC
3761270 GTTCACGAAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.53, C:0.26, G:0.13, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:3762930 original size:26 final size:27
Alignment explanation
Indices: 3762891--3762941 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
3762881 TCCCTCTAAA
* *
3762891 TTCTCGATTCCCTT-TATTCTCAAAAT
1 TTCTCAATTCCCTTAAATTCTCAAAAT
*
3762917 TTCTCAATTTCCTTAAATTCTCAAA
1 TTCTCAATTCCCTTAAATTCTCAAA
3762942 TAAACTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.45
Consensus pattern (27 bp):
TTCTCAATTCCCTTAAATTCTCAAAAT
Found at i:3763239 original size:24 final size:25
Alignment explanation
Indices: 3763181--3763241 Score: 90
Period size: 25 Copynumber: 2.4 Consensus size: 25
3763171 TTATTTGAAT
3763181 GATTATAATTAAGATTATAATATCAG
1 GATTAT-ATTAAGATTATAATATCAG
3763207 GATTATATTAAGATT-TAAATATCA-
1 GATTATATTAAGATTAT-AATATCAG
3763231 GATTATATTAA
1 GATTATATTAA
3763242 TATAAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 12 0.35
25 16 0.47
26 6 0.18
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (25 bp):
GATTATATTAAGATTATAATATCAG
Found at i:3763251 original size:25 final size:25
Alignment explanation
Indices: 3763181--3763249 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
3763171 TTATTTGAAT
* *
3763181 GATTATAATTAAGATTATAATATCAG
1 GATTAT-ATTAAGATAAAAATATCAG
**
3763207 GATTATATTAAGATTTAAATATCA-
1 GATTATATTAAGATAAAAATATCAG
*
3763231 GATTATATTAATATAAAAA
1 GATTATATTAAGATAAAAA
3763250 ATTTATTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
24 16 0.42
25 16 0.42
26 6 0.16
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (25 bp):
GATTATATTAAGATAAAAATATCAG
Found at i:3763483 original size:16 final size:16
Alignment explanation
Indices: 3763464--3763505 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
3763454 TAATATTAGA
*
3763464 TCAGGTTAATATCAAG
1 TCAGGTTAATAACAAG
*
3763480 TCAGGTTGATAACAAG
1 TCAGGTTAATAACAAG
3763496 TCAGG-TAATA
1 TCAGGTTAATA
3763506 CCAGTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (16 bp):
TCAGGTTAATAACAAG
Found at i:3775964 original size:19 final size:20
Alignment explanation
Indices: 3775923--3775970 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3775913 GTGCTAATAT
* *
3775923 TATCGATACTTACCCTTGGG
1 TATCGATACTTAACCTTGAG
3775943 TATCGATAC-TAACCTTGAG
1 TATCGATACTTAACCTTGAG
*
3775962 TATCAATAC
1 TATCGATAC
3775971 AAAAAATAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (20 bp):
TATCGATACTTAACCTTGAG
Found at i:3778206 original size:21 final size:22
Alignment explanation
Indices: 3778182--3778222 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3778172 TCCTTTTAGA
*
3778182 AAAGGGATCGATC-TTTTTTGC
1 AAAGAGATCGATCATTTTTTGC
3778203 AAAGAGATCGATCATTTTTT
1 AAAGAGATCGATCATTTTTT
3778223 CTAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (22 bp):
AAAGAGATCGATCATTTTTTGC
Found at i:3806287 original size:11 final size:11
Alignment explanation
Indices: 3806261--3806294 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3806251 CCAGTTCTTA
3806261 ACCGACT-TTG
1 ACCGACTGTTG
*
3806271 AACGACTGTTG
1 ACCGACTGTTG
3806282 ACCGACTGTTG
1 ACCGACTGTTG
3806293 AC
1 AC
3806295 TTTTTTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (11 bp):
ACCGACTGTTG
Found at i:3807976 original size:59 final size:59
Alignment explanation
Indices: 3807792--3808023 Score: 286
Period size: 60 Copynumber: 3.9 Consensus size: 59
3807782 GCCTGTTTTG
* *
3807792 ATCTTCAATATTGGAATCCTAGATCCTAGTGGTCTAGAGTAAGTCCTTATGGATGCATGT
1 ATCTTCCATATTGGACTCCTAGATCCTAGTGGTCTAG-GTAAGTCCTTATGGATGCATGT
* * * *
3807852 ATCTTTCATAATGGACTCCTAGATCATAGTAGTCTAGGTTAAGTCCTTATGGATGCATGT
1 ATCTTCCATATTGGACTCCTAGATCCTAGTGGTCTAGG-TAAGTCCTTATGGATGCATGT
* * * * * * *
3807912 ATCTTCCATATTAGACTCCTAAATCCTAGTGGCCTAAGGTAACT-CTTATGTATACTTGT
1 ATCTTCCATATTGGACTCCTAGATCCTAGTGGTCT-AGGTAAGTCCTTATGGATGCATGT
* *
3807971 ATCTTCTATATTGGACTCCTAGATCCTAGGGGTCTAGGGTAAGTCCTTATGGA
1 ATCTTCCATATTGGACTCCTAGATCCTAGTGGTCTA-GGTAAGTCCTTATGGA
3808024 CTCCTGTTAT
Statistics
Matches: 144, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
58 1 0.01
59 49 0.34
60 91 0.63
61 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (59 bp):
ATCTTCCATATTGGACTCCTAGATCCTAGTGGTCTAGGTAAGTCCTTATGGATGCATGT
Found at i:3808006 original size:119 final size:120
Alignment explanation
Indices: 3807792--3808023 Score: 299
Period size: 119 Copynumber: 1.9 Consensus size: 120
3807782 GCCTGTTTTG
* * * * *
3807792 ATCTTCAATATTGGAATCCTAGATCCTAGTGGTCTAGAGTAAGTCCTTATGGATGCATGTATCTT
1 ATCTTCAATATTAGAATCCTAAATCCTAGTGGCCTAGAGTAACTCCTTATGGATACATGTATCTT
* *
3807857 TCATAATGGACTCCTAGATCATAGTAGTCTAGGTTAAGTCCTTATGGATGCATGT
66 TCATAATGGACTCCTAGATCATAGGAGTCTAGGGTAAGTCCTTATGGATGCATGT
* * * *
3807912 ATCTTCCATATTAGACTCCTAAATCCTAGTGGCCTA-AGGTAACT-CTTATGTATACTTGTATC-
1 ATCTTCAATATTAGAATCCTAAATCCTAGTGGCCTAGA-GTAACTCCTTATGGATACATGTATCT
* * *
3807974 TTCTATATTGGACTCCTAGATCCTAGGGGTCTAGGGTAAGTCCTTATGGA
65 TTC-ATAATGGACTCCTAGATCATAGGAGTCTAGGGTAAGTCCTTATGGA
3808024 CTCCTGTTAT
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
118 3 0.03
119 57 0.59
120 36 0.38
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (120 bp):
ATCTTCAATATTAGAATCCTAAATCCTAGTGGCCTAGAGTAACTCCTTATGGATACATGTATCTT
TCATAATGGACTCCTAGATCATAGGAGTCTAGGGTAAGTCCTTATGGATGCATGT
Found at i:3810372 original size:20 final size:21
Alignment explanation
Indices: 3810342--3810391 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
3810332 CTTGAGTCGA
* *
3810342 GTCGTTGACCAGCATTGACCT
1 GTCGTTAACCAGCATTGACCG
3810363 G-CGTTAACCAGCATTGACCG
1 GTCGTTAACCAGCATTGACCG
3810383 GTCGTTAAC
1 GTCGTTAAC
3810392 AGACGTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (21 bp):
GTCGTTAACCAGCATTGACCG
Found at i:3812000 original size:60 final size:60
Alignment explanation
Indices: 3811936--3812168 Score: 299
Period size: 60 Copynumber: 3.9 Consensus size: 60
3811926 TGCTTGTTTG
* * *
3811936 ATCTTCCATATTGGACTCCTAGATTCTAATAGTCTAGGGTAAGTCCTTATAGATTCATGT
1 ATCTTCCATATTGGACTCCTAGATCCTAATAGTCTAGGGTAAGTCCTTATGGATACATGT
* * * *
3811996 ATCTTCTATATTGGACTCCTAGATTCTAGTGGTCTAGGGTAAGTCCTTATGGATACATGT
1 ATCTTCCATATTGGACTCCTAGATCCTAATAGTCTAGGGTAAGTCCTTATGGATACATGT
* * * * * *
3812056 ATCTTCTATATTGGACTCCTAGATCCTAGTAGCCTAGGGTAACTCC-TATGGATGCTTGT
1 ATCTTCCATATTGGACTCCTAGATCCTAATAGTCTAGGGTAAGTCCTTATGGATACATGT
* * *
3812115 ATCTTCCATATTGAACTACTAGATCCTAGA-GGTCTAGGGTAAGTCCTTATGGAT
1 ATCTTCCATATTGGACTCCTAGATCCTA-ATAGTCTAGGGTAAGTCCTTATGGAT
3812169 GCTTGTTTTG
Statistics
Matches: 153, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
59 49 0.32
60 104 0.68
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (60 bp):
ATCTTCCATATTGGACTCCTAGATCCTAATAGTCTAGGGTAAGTCCTTATGGATACATGT
Found at i:3812155 original size:119 final size:120
Alignment explanation
Indices: 3811936--3812168 Score: 342
Period size: 119 Copynumber: 1.9 Consensus size: 120
3811926 TGCTTGTTTG
* * * *
3811936 ATCTTCCATATTGGACTCCTAGATTCTAATAGTCTAGGGTAAGTCCTTATAGATTCATGTATCTT
1 ATCTTCCATATTGGACTCCTAGATCCTAATAGCCTAGGGTAACTCCTTATAGATGCATGTATCTT
* * * * *
3812001 CTATATTGGACTCCTAGATTCTAGTGGTCTAGGGTAAGTCCTTATGGATACATGT
66 CCATATTGAACTACTAGATCCTAGAGGTCTAGGGTAAGTCCTTATGGATACATGT
* * * *
3812056 ATCTTCTATATTGGACTCCTAGATCCTAGTAGCCTAGGGTAACTCC-TATGGATGCTTGTATCTT
1 ATCTTCCATATTGGACTCCTAGATCCTAATAGCCTAGGGTAACTCCTTATAGATGCATGTATCTT
3812120 CCATATTGAACTACTAGATCCTAGAGGTCTAGGGTAAGTCCTTATGGAT
66 CCATATTGAACTACTAGATCCTAGAGGTCTAGGGTAAGTCCTTATGGAT
3812169 GCTTGTTTTG
Statistics
Matches: 100, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
119 59 0.59
120 41 0.41
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (120 bp):
ATCTTCCATATTGGACTCCTAGATCCTAATAGCCTAGGGTAACTCCTTATAGATGCATGTATCTT
CCATATTGAACTACTAGATCCTAGAGGTCTAGGGTAAGTCCTTATGGATACATGT
Found at i:3818047 original size:93 final size:92
Alignment explanation
Indices: 3817888--3818073 Score: 250
Period size: 93 Copynumber: 2.0 Consensus size: 92
3817878 CGAATTAAAT
* * * *
3817888 TGATCTCCATCTACAGTTTTAACTTTCTGTGCAGTATGTGTTGTCGTTGGGACCAATTCATTTCC
1 TGATCTCCATCTACAGCTTTAACTTTCGGTGCAGTATGTGTTGCCATTGGGACCAATTCATTTCC
**
3817953 AATTTC-TCTATTTGGTTTTTTATGCATG
66 AATTTCTTC-A-TTCATTTTTTATGCATG
* **
3817981 TGATCTCCATCTGCAGCTTTGCCTTTCGGTGCA-TCATGTGTTGCCATTGGGACCAATTCATTTC
1 TGATCTCCATCTACAGCTTTAACTTTCGGTGCAGT-ATGTGTTGCCATTGGGACCAATTCATTTC
3818045 CAATTTCTTCATTCATTTTTTATGCATG
65 CAATTTCTTCATTCATTTTTTATGCATG
3818073 T
1 T
3818074 TTATGGCATT
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
92 17 0.21
93 63 0.77
94 2 0.02
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.45
Consensus pattern (92 bp):
TGATCTCCATCTACAGCTTTAACTTTCGGTGCAGTATGTGTTGCCATTGGGACCAATTCATTTCC
AATTTCTTCATTCATTTTTTATGCATG
Found at i:3819270 original size:2 final size:2
Alignment explanation
Indices: 3819265--3819306 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3819255 CTTTTTTGTT
3819265 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
3819307 CATTATACTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3822282 original size:42 final size:43
Alignment explanation
Indices: 3822235--3822348 Score: 119
Period size: 42 Copynumber: 2.7 Consensus size: 43
3822225 CAGGAAGAGA
*
3822235 TCGATCATTTTCATCGAGGGATCGATCCTTTTGGTGAA-GGCT
1 TCGATCATTTTCATCGAGGGATCGATCCTTTTGGTGAAGGGAT
* * * * * *
3822277 TCGATCCTTTTCCTCGAGGGGTTGAT-ATTTTTGTGAAGGGAT
1 TCGATCATTTTCATCGAGGGATCGATCCTTTTGGTGAAGGGAT
*
3822319 TCGATCATTTT-A-CTAAGGGATCGATCCTTT
1 TCGATCATTTTCATC-GAGGGATCGATCCTTT
3822349 GAGCAAAACA
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
40 1 0.02
41 17 0.30
42 38 0.68
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (43 bp):
TCGATCATTTTCATCGAGGGATCGATCCTTTTGGTGAAGGGAT
Found at i:3823046 original size:23 final size:23
Alignment explanation
Indices: 3823014--3823070 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
3823004 TGTGACATGT
* *
3823014 TCTCTACCTTTATGGCACGTTTA
1 TCTCTGCCTTTATGACACGTTTA
*
3823037 TCTCTGCCTTTATGACACGTTTT
1 TCTCTGCCTTTATGACACGTTTA
3823060 TCTCTGCCTTT
1 TCTCTGCCTTT
3823071 TGGTAACTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.12, C:0.28, G:0.12, T:0.47
Consensus pattern (23 bp):
TCTCTGCCTTTATGACACGTTTA
Found at i:3824683 original size:19 final size:19
Alignment explanation
Indices: 3824661--3824701 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3824651 GTCACGTTCT
* *
3824661 TATATATATTTTTTAAAAA
1 TATAAATATTATTTAAAAA
3824680 TATAAATATTATTTAAAAA
1 TATAAATATTATTTAAAAA
3824699 TAT
1 TAT
3824702 TTTTTAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATAAATATTATTTAAAAA
Found at i:3825007 original size:6 final size:6
Alignment explanation
Indices: 3824997--3825040 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
3824987 AATTGAAAAC
*
3824997 GAGAGC GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG AGAGAGG G
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG -GAGAGG G
3825041 TGGGCTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.34, C:0.02, G:0.64, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:3829305 original size:19 final size:19
Alignment explanation
Indices: 3829260--3829305 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
3829250 TAAAGCATAA
3829260 AAGAAA-GAAAGAGAGAAG
1 AAGAAAGGAAAGAGAGAAG
3829278 AGAGAAAGGAAAG-GAAGAAG
1 A-AGAAAGGAAAGAG-AGAAG
3829298 AAGAAAGG
1 AAGAAAGG
3829306 GAGATAAGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.04
19 13 0.52
20 11 0.44
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (19 bp):
AAGAAAGGAAAGAGAGAAG
Found at i:3829500 original size:36 final size:39
Alignment explanation
Indices: 3829449--3829546 Score: 100
Period size: 36 Copynumber: 2.5 Consensus size: 39
3829439 TACATAAATA
3829449 AAAAATTATTTAATTAGTTTGTTTGATAGTTA-TATATAT-T
1 AAAAA-TA-TTAATTAGTTTGTTTGATAGTTAGT-TATATCT
3829489 AAAAAATAATTAATTAGTTTG-TT--T-GTTAGTTATATCT
1 -AAAAAT-ATTAATTAGTTTGTTTGATAGTTAGTTATATCT
3829526 AAAAATATTTAATTAGTTTGT
1 AAAAATA-TTAATTAGTTTGT
3829547 GTTAGTTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
35 1 0.02
36 27 0.52
37 3 0.06
39 2 0.04
40 13 0.25
41 6 0.12
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.50
Consensus pattern (39 bp):
AAAAATATTAATTAGTTTGTTTGATAGTTAGTTATATCT
Found at i:3829504 original size:40 final size:37
Alignment explanation
Indices: 3829447--3829546 Score: 130
Period size: 40 Copynumber: 2.6 Consensus size: 37
3829437 CATACATAAA
*
3829447 TAAAAAATTATTTAATTAGTTTGTTTGATAGTTATATATAT
1 TAAAAAA-TATTTAATTAGTTTGTTTGATAG-T-TATAT-C
* *
3829488 TAAAAAATAATTAATTAGTTTGTTTGTTAGTTATATC
1 TAAAAAATATTTAATTAGTTTGTTTGATAGTTATATC
3829525 T-AAAAATATTTAATTAGTTTGT
1 TAAAAAATATTTAATTAGTTTGT
3829547 GTTAGTTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
36 20 0.36
37 1 0.02
38 5 0.09
39 1 0.02
40 21 0.38
41 7 0.13
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.50
Consensus pattern (37 bp):
TAAAAAATATTTAATTAGTTTGTTTGATAGTTATATC
Found at i:3829764 original size:16 final size:16
Alignment explanation
Indices: 3829731--3829776 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3829721 TTTTAAAAAG
*
3829731 ATTAGTTTGTTAGT-TT
1 ATTAGTTTATTA-TATT
3829747 ATTAGTTTATTATATT
1 ATTAGTTTATTATATT
*
3829763 ATAAG-TTATTATAT
1 ATTAGTTTATTATAT
3829777 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (16 bp):
ATTAGTTTATTATATT
Found at i:3831838 original size:21 final size:21
Alignment explanation
Indices: 3831809--3831858 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
3831799 ACGTTTGCAA
*
3831809 GTGGGATGGAAGAGCA-AACTG
1 GTGGAATGGAAGAGCATAA-TG
*
3831830 GTGGAATGGCAGAGCATAATG
1 GTGGAATGGAAGAGCATAATG
3831851 GTTGGAAT
1 G-TGGAAT
3831859 ATATTTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.32, C:0.08, G:0.40, T:0.20
Consensus pattern (21 bp):
GTGGAATGGAAGAGCATAATG
Found at i:3832133 original size:17 final size:15
Alignment explanation
Indices: 3832111--3832150 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
3832101 GTTACATATG
3832111 TTAAATATTATTAAAA
1 TTAAATATTA-TAAAA
*
3832127 CTTAAATATTATAATA
1 -TTAAATATTATAAAA
3832143 TTAAATAT
1 TTAAATAT
3832151 GCATGTCTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATTATAAAA
Found at i:3832219 original size:16 final size:16
Alignment explanation
Indices: 3832200--3832238 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3832190 TATTTATAAA
* *
3832200 TATATATTCGACTAGT
1 TATAAATTCAACTAGT
*
3832216 TATAAATTCAACTATT
1 TATAAATTCAACTAGT
3832232 TATAAAT
1 TATAAAT
3832239 CCGATTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (16 bp):
TATAAATTCAACTAGT
Found at i:3832369 original size:14 final size:14
Alignment explanation
Indices: 3832308--3832371 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
3832298 AATCATTATT
*
3832308 AAATCATTAGTTTC
1 AAATCATTAGTATC
* *
3832322 AAATAATTATTAT-
1 AAATCATTAGTATC
* *
3832335 AATTTCATTATTA-C
1 AA-ATCATTAGTATC
*
3832349 TAATCATTAGTATC
1 AAATCATTAGTATC
3832363 AAATCATTA
1 AAATCATTA
3832372 AATATTAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
13 10 0.26
14 28 0.74
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (14 bp):
AAATCATTAGTATC
Found at i:3832816 original size:20 final size:21
Alignment explanation
Indices: 3832766--3832816 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
3832756 AAATAGAAAT
* *
3832766 AATTCAATTAAAAATGAACTTA
1 AATTCTATTAAAAA-GAACATA
3832788 AATAT-TATTAAAAA-AACATA
1 AAT-TCTATTAAAAAGAACATA
3832808 AATTCTATT
1 AATTCTATT
3832817 TAATAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 1 0.04
20 12 0.48
22 11 0.44
23 1 0.04
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (21 bp):
AATTCTATTAAAAAGAACATA
Found at i:3834155 original size:155 final size:154
Alignment explanation
Indices: 3833778--3834088 Score: 498
Period size: 155 Copynumber: 2.0 Consensus size: 154
3833768 CCAATTCCTT
* * * * * *
3833778 TATCGAATATCAAGCAAACTCCATCTTCACGAACGACATATTGACGTAGATTAGTCATAAAGAAA
1 TATCCAATATCAAGCAAACTACAAC-TCACGAACCACATATTGACATAGATGAGTCATAAAGAAA
3833843 TCCCAGGCATCTATTATCTCTCCCTCAACAATGGCAAATGCAATTGGGAAGATATTTTCGCTCAC
65 TCCCAGGCATCTATTATCTCTCCCTCAACAATGGCAAATGCAATTGGGAAGATATTTTCGCTCAC
3833908 CATCTTACGCAACTGCCATCAAGAG
130 CATCTTACGCAACTGCCATCAAGAG
* * * * *
3833933 TATCGAATATCAAGCAAACTCCATCTTCACGAACGACATATTGACGTAGATGAGTCATAAAGAAA
1 TATCCAATATCAAGCAAACTACAAC-TCACGAACCACATATTGACATAGATGAGTCATAAAGAAA
3833998 TCCCAGGCATCTATTATCTCTCCCTCAACAATGGCAAATGCAATTGGGAAGATA-TTTCGCTCAC
65 TCCCAGGCATCTATTATCTCTCCCTCAACAATGGCAAATGCAATTGGGAAGATATTTTCGCTCAC
3834062 CATCTTACGCAACTGCCATCAAGAG
130 CATCTTACGCAACTGCCATCAAGAG
3834087 TA
1 TA
3834089 CATGCCTATA
Statistics
Matches: 155, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
154 37 0.24
155 118 0.76
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (154 bp):
TATCCAATATCAAGCAAACTACAACTCACGAACCACATATTGACATAGATGAGTCATAAAGAAAT
CCCAGGCATCTATTATCTCTCCCTCAACAATGGCAAATGCAATTGGGAAGATATTTTCGCTCACC
ATCTTACGCAACTGCCATCAAGAG
Found at i:3836004 original size:19 final size:21
Alignment explanation
Indices: 3835966--3836006 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3835956 TAAATTAAAC
*
3835966 AAATATTTTTTAAGCAACAAT
1 AAATATTTTTTAAACAACAAT
3835987 AAATA-TTTTTAAAC-ACAAT
1 AAATATTTTTTAAACAACAAT
3836006 A
1 A
3836007 TTTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 8 0.42
21 5 0.26
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATATTTTTTAAACAACAAT
Found at i:3836556 original size:28 final size:29
Alignment explanation
Indices: 3836514--3836576 Score: 110
Period size: 28 Copynumber: 2.2 Consensus size: 29
3836504 ATTTTTTATA
3836514 TAATATAATAAATAACTTAAACTAACAAAC
1 TAATATAAT-AATAACTTAAACTAACAAAC
3836544 TAATATAAT-ATAACTTAAACTAACAAAC
1 TAATATAATAATAACTTAAACTAACAAAC
3836572 TAATA
1 TAATA
3836577 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 24 0.73
30 9 0.27
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.29
Consensus pattern (29 bp):
TAATATAATAATAACTTAAACTAACAAAC
Found at i:3836586 original size:21 final size:21
Alignment explanation
Indices: 3836553--3836601 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3836543 CTAATATAAT
3836553 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
3836574 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
3836595 ATTAACT
1 A-TAACT
3836602 AAAAATGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:3836753 original size:16 final size:15
Alignment explanation
Indices: 3836705--3836750 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
3836695 TTGAGCCTTA
*
3836705 TCTCCCTCTC-TTCT
1 TCTCCCTTTCTTTCT
*
3836719 TCTTCCTTTCCTTTCT
1 TCTCCCTTT-CTTTCT
3836735 TCTCCCTTTCTTTCT
1 TCTCCCTTTCTTTCT
3836750 T
1 T
3836751 TCTTATGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 7 0.26
15 8 0.30
16 12 0.44
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
TCTCCCTTTCTTTCT
Found at i:3838647 original size:98 final size:101
Alignment explanation
Indices: 3838476--3838679 Score: 335
Period size: 98 Copynumber: 2.0 Consensus size: 101
3838466 AATTTGATGG
3838476 ATAATGGAAAACTTGAGATTTTTTTCATTGCATTTTTTTGATGCTGTATGCCCTTATCCATAGGA
1 ATAATGGAAAACTTGAGA--TTTTTCATTGCATTTTTTTGATGCTGTATGCCCTTATCCATAGGA
3838541 GCTGCATTG-AGGA-TTTGCCTAAATTCCATTAA-TTA
64 GCTGCATTGAAGGATTTTGCCTAAATTCCATTAATTTA
*
3838576 ATAATGGAAAACTTGAGA-TTTTCATTGCATTTTTTTTGATGCTGTATGTCCTTATCCATAGGAG
1 ATAATGGAAAACTTGAGATTTTTCATTGCA-TTTTTTTGATGCTGTATGCCCTTATCCATAGGAG
*
3838640 CTGCATTGAATGATTTTGCCTAAATTCCATTAATTTA
65 CTGCATTGAAGGATTTTGCCTAAATTCCATTAATTTA
3838677 ATA
1 ATA
3838680 TTGATGTTTA
Statistics
Matches: 98, Mismatches: 2, Indels: 7
0.92 0.02 0.07
Matches are distributed among these distances:
97 11 0.11
98 41 0.42
99 3 0.03
100 37 0.38
101 6 0.06
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (101 bp):
ATAATGGAAAACTTGAGATTTTTCATTGCATTTTTTTGATGCTGTATGCCCTTATCCATAGGAGC
TGCATTGAAGGATTTTGCCTAAATTCCATTAATTTA
Found at i:3841441 original size:15 final size:15
Alignment explanation
Indices: 3841421--3841449 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3841411 ATTATTATAT
3841421 ATTAAGTACATGAAC
1 ATTAAGTACATGAAC
3841436 ATTAAGTACATGAA
1 ATTAAGTACATGAA
3841450 TCTTCTAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (15 bp):
ATTAAGTACATGAAC
Found at i:3842692 original size:21 final size:21
Alignment explanation
Indices: 3842645--3842694 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3842635 TGGTTATATT
* *
3842645 TATAAAATTATATTTAATACT
1 TATAAAATTATATCTAATACA
3842666 TA-AAAATTAATATCTAA-ACA
1 TATAAAATT-ATATCTAATACA
3842686 TATAAAATT
1 TATAAAATT
3842695 TAAAATTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (21 bp):
TATAAAATTATATCTAATACA
Found at i:3846739 original size:2 final size:2
Alignment explanation
Indices: 3846732--3846764 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3846722 TTCTTCTTAA
3846732 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 A
3846765 ATTTTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3847267 original size:30 final size:30
Alignment explanation
Indices: 3847186--3847250 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
3847176 ATGGAAAATA
* ** *
3847186 ATTTACATAAAATGGATTACCTGAAAACTG
1 ATTTACGTAAAATAAATTACATGAAAACTG
*
3847216 TTTTACGTAAAATAAATTACATGAAAACTG
1 ATTTACGTAAAATAAATTACATGAAAACTG
3847246 ATTTA
1 ATTTA
3847251 TGTTAAGTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (30 bp):
ATTTACGTAAAATAAATTACATGAAAACTG
Found at i:3847739 original size:17 final size:17
Alignment explanation
Indices: 3847717--3847750 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3847707 ATATATTAAT
3847717 ATAATATTAAAAATATA
1 ATAATATTAAAAATATA
*
3847734 ATAATATTAAAATTATA
1 ATAATATTAAAAATATA
3847751 TTATATGTAT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATATTAAAAATATA
Found at i:3852253 original size:17 final size:19
Alignment explanation
Indices: 3852215--3852255 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
3852205 TAATAAAATA
3852215 AAATA-AATAAATATTTCT
1 AAATATAATAAATATTTCT
3852233 -AATATAAT-AATATTT-T
1 AAATATAATAAATATTTCT
3852249 AAATATA
1 AAATATA
3852256 TGATAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.05
17 17 0.81
18 3 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATATAATAAATATTTCT
Found at i:3853584 original size:3 final size:3
Alignment explanation
Indices: 3853576--3853670 Score: 77
Period size: 3 Copynumber: 32.0 Consensus size: 3
3853566 CTGTAATATG
* * * *
3853576 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
3853621 TTA TAA TAA TTA TAA CAA TTA TAA TAA TTA TAA TAA TAA AAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3853668 TAA
1 TAA
3853671 GCAAAAATTT
Statistics
Matches: 71, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
2 4 0.06
3 65 0.92
4 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3854032 original size:58 final size:58
Alignment explanation
Indices: 3853939--3854054 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
3853929 TGAAAATGTT
* *
3853939 GATGCTAATCTATCTCCTTCTATGATAGATTATACAAAAGGTTGAACAAGCTCTTCTC
1 GATGCTAATCTATCTCCTTCTATGATAGATCATACAAAAGGTTGAACAAACTCTTCTC
* *
3853997 GATGCTAATCTATCTCCTTCTGTGATAGATCATACAAAAGGTTGAACAAATTCTTCTC
1 GATGCTAATCTATCTCCTTCTATGATAGATCATACAAAAGGTTGAACAAACTCTTCTC
3854055 ATTATAAACT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (58 bp):
GATGCTAATCTATCTCCTTCTATGATAGATCATACAAAAGGTTGAACAAACTCTTCTC
Found at i:3854241 original size:124 final size:124
Alignment explanation
Indices: 3854004--3854496 Score: 773
Period size: 124 Copynumber: 4.0 Consensus size: 124
3853994 CTCGATGCTA
* * *
3854004 ATCTATCTCCTTCTGTGATAGA-TCATAC-AAAAGGTTGAACAAATTCTTCTCATTATAAACTTC
1 ATCTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAACTCTTCTCATTATGAA---C
*
3854067 TTCTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
63 TTCTTCTTC--CTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGGAAAAGTTGATGTTG
*
3854132 ATCTATCTCCTTCTGTGATAGAGTCATGC-AAAAGGTTGAACAAACTCTTCTAATTATGAACTTC
1 ATCTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAACTCTTCTCATTATGAACTTC
3854196 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATGTTG
66 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGGAAAAGTTGATGTTG
* * *
3854256 ATTTATCTTCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAACTCTTCTCATTATGAACTTC
*
3854321 -T-TT-CTTCTTCAGATGAGTTCTTCGTATTATGAACTTCTCTGGAAAAGTTGATGTTG
66 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGTTGATGTTG
* * *
3854377 ATGTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAGCTCTTCTCATTATGAATTTC
1 ATCTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAACTCTTCTCATTATGAACTTC
3854442 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGTTGAT
66 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGTTGAT
3854497 CTATCGAATG
Statistics
Matches: 346, Mismatches: 14, Indels: 14
0.93 0.04 0.04
Matches are distributed among these distances:
121 84 0.24
122 31 0.09
123 4 0.01
124 129 0.37
125 33 0.10
126 10 0.03
128 22 0.06
129 33 0.10
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (124 bp):
ATCTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAACTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGTTGATGTTG
Found at i:3854474 original size:246 final size:246
Alignment explanation
Indices: 3854007--3854610 Score: 776
Period size: 246 Copynumber: 2.5 Consensus size: 246
3853997 GATGCTAATC
*
3854007 TATCTCCTTCTGTGATAGATCATACAAAAGGTTGAACAAATTCTTCTCATTATAAACTTCTTCTT
1 TATCTCCTTCTGTGATAGATCATACAAAAGGTTGAACAAACTCTTCTCATTATAAA-----TCTT
3854072 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTA
61 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTA
3854137 TCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAACTCTTCTAATTATGAACTTCTTCTTC
126 TCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAACTCTTCTAATTATGAACTTCTTCTTC
3854202 CTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATGTTGATT
191 CTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGGAAAAGTTGATGTTGATT
* * * *
3854259 TATCTTCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAGCTCTTCTCATTATGAA-CTTC-T
1 TATCTCCTTCTGTGATAGA-TCATAC-AAAAGGTTGAACAAACTCTTCTCATTATAAATCTTCTT
*
3854322 -TTCTTCTTCAGATGAGTTCTTCGT-ATTATGAAC-TTCTCTGGAAAAGTTGATGTTGATGTATC
64 CTTCTTCTTCAGATGAGTTCTTC-TCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATC
* * *
3854384 TCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCC
128 TCCTTCTGTGATAGAGTCATGC-AAAAGGTTGAACAAACTCTTCTAATTATGAACTTCTTCTTCC
*
3854449 TTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGG-AAA----A-GTTGATC
192 TTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGTTGATGTTGATT
*** * * * * *
3854498 TA--T-CGAATGATGA-A-TTCAAATAAAAGGTTTGAACAAATTCTTCTCATTATGAAT-TTCTT
1 TATCTCCTTCTG-TGATAGATCATACAAAAGG-TTGAACAAACTCTTCTCATTATAAATCTTCTT
* *
3854557 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTT-TCTAGAAATGTTGAT
64 CTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGAT
3854611 CCATCGAATG
Statistics
Matches: 318, Mismatches: 21, Indels: 40
0.84 0.06 0.11
Matches are distributed among these distances:
233 6 0.02
234 29 0.09
235 1 0.00
236 7 0.02
237 33 0.10
238 13 0.04
239 10 0.03
240 1 0.00
244 3 0.01
245 58 0.18
246 100 0.31
247 2 0.01
248 4 0.01
252 18 0.06
253 5 0.02
254 28 0.09
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (246 bp):
TATCTCCTTCTGTGATAGATCATACAAAAGGTTGAACAAACTCTTCTCATTATAAATCTTCTTCT
TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCC
TTCTGTGATAGAGTCATGCAAAAGGTTGAACAAACTCTTCTAATTATGAACTTCTTCTTCCTTCT
TCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGTTGATGTTGATT
Found at i:3854540 original size:113 final size:113
Alignment explanation
Indices: 3854407--3854628 Score: 356
Period size: 113 Copynumber: 2.0 Consensus size: 113
3854397 GAGTCATGCA
* *
3854407 AAAAGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAACTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
3854472 TATGAACT-TCTCTGGAAAAGTTGATCTATCGAATGATGAATTCAAAT
66 TATGAACTCTCTCTAGAAAAGTTGATCCATCGAATGATGAATTCAAAT
*
3854519 AAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAGG-TTGAACAAACTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
3854584 TTATGAACTCTTTCTAGAAATGTTGATCCATCGAATGATGGATTC
65 TTATGAACTCTCTCTAGAAAAGTTGATCCATCGAATGATGAATTC
3854629 GAATCTTTGC
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
112 6 0.06
113 64 0.64
114 30 0.30
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (113 bp):
AAAAGGTTGAACAAACTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTCTCTAGAAAAGTTGATCCATCGAATGATGAATTCAAAT
Found at i:3855791 original size:18 final size:18
Alignment explanation
Indices: 3855768--3855802 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3855758 TATATGAAAC
3855768 AAATTGAATTTCAAAAAT
1 AAATTGAATTTCAAAAAT
3855786 AAATTGAATTTCAAAAA
1 AAATTGAATTTCAAAAA
3855803 GATAAACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTGAATTTCAAAAAT
Done.