Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_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: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 27
Found at i:3888745 original size:25 final size:26
Alignment explanation
Indices: 3888711--3888771 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
3888701 GGATGACATA
* *
3888711 TAAAGTTTTAAAAGTTTT-AGAAATT
1 TAAAATTTTAAAAATTTTGAGAAATT
3888736 TAAAATTTTAAAAATTTTGAGAAATT
1 TAAAATTTTAAAAATTTTGAGAAATT
*
3888762 AAAAACTTTT
1 TAAAA-TTTT
3888772 TACTTTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 16 0.52
26 11 0.35
27 4 0.13
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.43
Consensus pattern (26 bp):
TAAAATTTTAAAAATTTTGAGAAATT
Found at i:3888750 original size:16 final size:17
Alignment explanation
Indices: 3888717--3888752 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3888707 CATATAAAGT
*
3888717 TTTAAAAGTTTTAGAAA
1 TTTAAAAGTTTTAAAAA
3888734 TTTAAAA-TTTTAAAAA
1 TTTAAAAGTTTTAAAAA
3888750 TTT
1 TTT
3888753 TGAGAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TTTAAAAGTTTTAAAAA
Found at i:3891484 original size:20 final size:20
Alignment explanation
Indices: 3891447--3891485 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3891437 GAGTGACTTG
**
3891447 ATTGGTAAAAATTTAAAAAT
1 ATTGGTAAAAATGAAAAAAT
*
3891467 ATTGGTCAAAATGAAAAAA
1 ATTGGTAAAAATGAAAAAA
3891486 AGGCAATAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.13, T:0.28
Consensus pattern (20 bp):
ATTGGTAAAAATGAAAAAAT
Found at i:3900022 original size:21 final size:21
Alignment explanation
Indices: 3899998--3900073 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
3899988 CGAATATGTA
3899998 AATCGCAACGCGATAATACAT
1 AATCGCAACGCGATAATACAT
**
3900019 AATCGCAACGCGATTCTGAC-T
1 AATCGCAACGCGATAAT-ACAT
*
3900040 -ATCGCAACGCGATAATACAA
1 AATCGCAACGCGATAATACAT
*
3900060 AATCGCAATGCGAT
1 AATCGCAACGCGAT
3900074 TTTCAAAACG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.04
20 14 0.30
21 28 0.61
22 2 0.04
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (21 bp):
AATCGCAACGCGATAATACAT
Found at i:3900268 original size:22 final size:22
Alignment explanation
Indices: 3900212--3900269 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
3900202 TTACTCTCTA
* *
3900212 CGGCGACATCCGCCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
* *
3900234 CGACAAAATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
3900256 CGGCGAAATCCGTC
1 CGGCGAAATCCGTC
3900270 TATCTCCATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.47, G:0.17, T:0.16
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATCTC
Found at i:3900680 original size:24 final size:24
Alignment explanation
Indices: 3900629--3900680 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3900619 ATCTGAGTAT
** *
3900629 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
3900653 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
3900677 TGAC
1 TGAC
3900681 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:3901510 original size:20 final size:20
Alignment explanation
Indices: 3901485--3901574 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 20
3901475 TTGAAATTCA
*
3901485 GCGTTGCGGCAGTCAGAATC
1 GCGTTGCGACAGTCAGAATC
*
3901505 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGACAGTCAGAATC
* * **
3901525 GAGTTGCGATTATGT-ATTATC
1 GCGTTGCGA-CA-GTCAGAATC
* *
3901546 GCGTTGCGATAGTCAAAATC
1 GCGTTGCGACAGTCAGAATC
*
3901566 ACGTTGCGA
1 GCGTTGCGA
3901575 ATCTGGAAAC
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 40 0.69
21 14 0.24
22 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (20 bp):
GCGTTGCGACAGTCAGAATC
Found at i:3915281 original size:2 final size:2
Alignment explanation
Indices: 3915276--3915301 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3915266 AAAGTTAAAT
3915276 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
3915302 ATTTTAAATG
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3916886 original size:16 final size:16
Alignment explanation
Indices: 3916862--3916892 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3916852 TAAAAATACT
*
3916862 GATTTTTAGTAGATTA
1 GATTCTTAGTAGATTA
3916878 GATTCTTAGTAGATT
1 GATTCTTAGTAGATT
3916893 GTTTTTTTAT
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:0.29, C:0.03, G:0.19, T:0.48
Consensus pattern (16 bp):
GATTCTTAGTAGATTA
Found at i:3920608 original size:3 final size:3
Alignment explanation
Indices: 3920600--3920643 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
3920590 ATGTAAATTT
3920600 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA T
3920644 TAAAAAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3931192 original size:29 final size:29
Alignment explanation
Indices: 3931159--3931216 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3931149 GCTAATAAGT
3931159 GGGATGAGTCAAAAAATACTTTAGGCACC
1 GGGATGAGTCAAAAAATACTTTAGGCACC
3931188 GGGATGAGTCAAAAAATACTTTAGGCACC
1 GGGATGAGTCAAAAAATACTTTAGGCACC
3931217 TATCAGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (29 bp):
GGGATGAGTCAAAAAATACTTTAGGCACC
Found at i:3936638 original size:2 final size:2
Alignment explanation
Indices: 3936633--3936684 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3936623 TGTTTTTTAA
3936633 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
3936675 AT AT AT AT AT
1 AT AT AT AT AT
3936685 TTCGATATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3938568 original size:25 final size:24
Alignment explanation
Indices: 3938514--3938568 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
3938504 TAATAATACT
3938514 AAAAAAATATAATTTTTTGATTAAA
1 AAAAAAATATAATTTTTT-ATTAAA
* *
3938539 TAAAAAATATAATATTTTT-TTAAG
1 AAAAAAATATAAT-TTTTTATTAAA
3938563 AAAAAA
1 AAAAAA
3938569 GGGGGACTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 9 0.35
25 12 0.46
26 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
AAAAAAATATAATTTTTTATTAAA
Found at i:3945674 original size:84 final size:85
Alignment explanation
Indices: 3945532--3945689 Score: 237
Period size: 84 Copynumber: 1.9 Consensus size: 85
3945522 AATCCATTCA
*
3945532 ACAAGTAACCGATAATCTATTAAAAAAAATCAAAAGGAACTACAGGTTTTGTTACGTAAAAACAT
1 ACAAGTAACCGATAATCTATTAAAAAAAATCAAAAGGAACTACAGATTTTGTTACGTAAAAACAT
3945597 ATTAGGTATTTATGTGTTCT
66 ATTAGGTATTTATGTGTTCT
* * * * * * *
3945617 ACAAGTAACCGATAATCTATT-AAAAATATTAAAATGAGCTACATATTTTGTTCCGTAAATACAT
1 ACAAGTAACCGATAATCTATTAAAAAAAATCAAAAGGAACTACAGATTTTGTTACGTAAAAACAT
3945681 ATTAGGTAT
66 ATTAGGTAT
3945690 AGTACATAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 44 0.68
85 21 0.32
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (85 bp):
ACAAGTAACCGATAATCTATTAAAAAAAATCAAAAGGAACTACAGATTTTGTTACGTAAAAACAT
ATTAGGTATTTATGTGTTCT
Found at i:3945964 original size:40 final size:40
Alignment explanation
Indices: 3945909--3945990 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
3945899 AAGATATGAT
3945909 ATAATATGATCCCAAAATCTTAAACAACTATCATATCTCA
1 ATAATATGATCCCAAAATCTTAAACAACTATCATATCTCA
3945949 ATAATATGATCCCAAAATCTTAAACAACTATCATATCTCA
1 ATAATATGATCCCAAAATCTTAAACAACTATCATATCTCA
3945989 AT
1 AT
3945991 CAGTAGGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.30
Consensus pattern (40 bp):
ATAATATGATCCCAAAATCTTAAACAACTATCATATCTCA
Found at i:3948628 original size:3 final size:3
Alignment explanation
Indices: 3948614--3948671 Score: 64
Period size: 3 Copynumber: 18.7 Consensus size: 3
3948604 GGCCCTGCAA
* *
3948614 AAT AAA AAT AAT AAT AAT AAT AAT AAT ATT AAAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT
3948661 AAAT AA- AAT AA
1 -AAT AAT AAT AA
3948672 ATCCCAGACA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 37 0.77
4 9 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3948649 original size:22 final size:22
Alignment explanation
Indices: 3948623--3948671 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
3948613 AAATAAAAAT
*
3948623 AATAATAATAAT-AATAATATTA
1 AATAATAATAATAAATAA-ATAA
3948645 AATAATAATAATAAATAAATAA
1 AATAATAATAATAAATAAATAA
3948667 AATAA
1 AATAA
3948672 ATCCCAGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAATAATAATAAATAAATAA
Found at i:3948650 original size:19 final size:17
Alignment explanation
Indices: 3948613--3948671 Score: 72
Period size: 16 Copynumber: 3.7 Consensus size: 17
3948603 TGGCCCTGCA
*
3948613 AAATAAAAATAAT-AAT
1 AAATAATAATAATAAAT
*
3948629 -AATAATAATAAT-ATT
1 AAATAATAATAATAAAT
3948644 AAATAATAATAATAAAT
1 AAATAATAATAATAAAT
3948661 AAATAA-AATAA
1 AAATAATAATAA
3948672 ATCCCAGACA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 13 0.34
16 17 0.45
17 8 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAATAATAATAAAT
Found at i:3956335 original size:19 final size:19
Alignment explanation
Indices: 3956311--3956351 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
3956301 GGTATCCATG
3956311 GAAGAAAGGAGAGTGATAT
1 GAAGAAAGGAGAGTGATAT
3956330 GAAGAAAGGAGAGTGATAT
1 GAAGAAAGGAGAGTGATAT
3956349 GAA
1 GAA
3956352 TGAGTGGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.37, T:0.15
Consensus pattern (19 bp):
GAAGAAAGGAGAGTGATAT
Found at i:3958189 original size:21 final size:20
Alignment explanation
Indices: 3958103--3958260 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
3958093 AAATGACCAA
**
3958103 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
3958122 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
3958142 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
3958162 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
3958183 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3958204 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
3958224 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3958245 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3958261 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3958289 original size:20 final size:20
Alignment explanation
Indices: 3958228--3958436 Score: 199
Period size: 20 Copynumber: 10.4 Consensus size: 20
3958218 GATTTTCCAG
* ** *
3958228 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3958248 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3958268 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
3958288 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3958308 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3958328 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3958348 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3958368 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3958388 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3958408 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3958428 AATCACAAC
1 AATCGCAAC
3958437 ACTGAAATTT
Statistics
Matches: 157, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 153 0.97
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3959144 original size:24 final size:24
Alignment explanation
Indices: 3959105--3959151 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3959095 AAATTTGGTC
3959105 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3959129 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3959152 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3959343 original size:12 final size:12
Alignment explanation
Indices: 3959326--3959350 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3959316 ATATAATCCT
3959326 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3959338 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3959350 G
1 G
3959351 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3961715 original size:19 final size:19
Alignment explanation
Indices: 3961642--3961836 Score: 266
Period size: 19 Copynumber: 10.7 Consensus size: 19
3961632 GCAACGAGAG
3961642 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3961661 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
3961675 AATCGCAATGCGGAAATTAA
1 AATCGCAATGC-GAAATGAA
3961695 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3961714 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3961733 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3961752 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3961766 AATCGCAATGCGTAAATGAA
1 AATCGCAATGCG-AAATGAA
3961786 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3961805 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3961824 AATCGCATTGCGA
1 AATCGCAATGCGA
3961837 TTCTCTCGTT
Statistics
Matches: 157, Mismatches: 7, Indels: 24
0.84 0.04 0.13
Matches are distributed among these distances:
14 22 0.14
15 1 0.01
16 3 0.02
17 3 0.02
19 99 0.63
20 29 0.18
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3961770 original size:91 final size:91
Alignment explanation
Indices: 3961642--3961836 Score: 329
Period size: 91 Copynumber: 2.1 Consensus size: 91
3961632 GCAACGAGAG
*
3961642 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATTAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
3961707 AAATGAAAATCGCAATGCGAAATGAA
66 AAATGAAAATCGCAATGCGAAATGAA
* * *
3961733 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGTAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
3961797 GAAATGAAAATCGCAATGCGAAATGAA
65 GAAATGAAAATCGCAATGCGAAATGAA
*
3961824 AATCGCATTGCGA
1 AATCGCAATGCGA
3961837 TTCTCTCGTT
Statistics
Matches: 98, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
91 97 0.99
92 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (91 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAAAATCGCAATGCGAAATGAA
Found at i:3961783 original size:72 final size:71
Alignment explanation
Indices: 3961695--3961830 Score: 263
Period size: 72 Copynumber: 1.9 Consensus size: 71
3961685 CGGAAATTAA
3961695 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
3961760 CGAGAG
66 CGAGAG
3961766 AATCGCAATGCGTAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCG-AAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
3961831 TTGCGATTCT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
71 12 0.19
72 52 0.81
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
CGAGAG
Found at i:3961887 original size:53 final size:52
Alignment explanation
Indices: 3961826--3961943 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 52
3961816 GAAATGAAAA
3961826 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTACGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTACGATTTTCATT
* *
3961879 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATTTTCATT
3961931 TCCGCATTGCGAT
1 T-CGCATTGCGAT
3961944 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
52 17 0.27
53 45 0.73
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATTTTCATT
Found at i:3961951 original size:20 final size:19
Alignment explanation
Indices: 3961845--3961943 Score: 118
Period size: 19 Copynumber: 5.4 Consensus size: 19
3961835 GATTCTCTCG
3961845 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
3961865 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3961884 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
3961898 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
3961917 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3961937 TTGCGAT
1 TTGCGAT
3961944 AGTCATTTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 6 0.09
19 24 0.36
20 24 0.36
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3962069 original size:14 final size:14
Alignment explanation
Indices: 3962050--3962086 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3962040 CATCAATTAC
3962050 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3962064 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3962078 ACAAATCAA
1 ACAAATCAA
3962087 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3964084 original size:14 final size:14
Alignment explanation
Indices: 3964065--3964121 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3964055 GCGAACTGAA
*
3964065 AATCGCAACGACAG
1 AATCGCAACGAAAG
3964079 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
3964096 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
3964112 AATCGCAACG
1 AATCGCAACG
3964122 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3964092 original size:33 final size:33
Alignment explanation
Indices: 3964046--3964138 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
3964036 GCGAAACCAA
*
3964046 AATCGCAACGCGAACTGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
3964079 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
3964112 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3964139 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:3964103 original size:19 final size:19
Alignment explanation
Indices: 3964009--3964143 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
3963999 TAGTTTACTT
* *
3964009 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3964029 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
3964048 TCGCAACGCGAACTGAAAA
1 TCGCAACGCGAAATGAAAA
*
3964067 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3964081 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3964100 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
3964114 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3964133 TCGCAATGCGA
1 TCGCAACGCGA
3964144 TTTTGGTTTC
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 18 0.19
15 1 0.01
16 7 0.08
17 6 0.06
18 1 0.01
19 48 0.52
20 12 0.13
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3964174 original size:14 final size:14
Alignment explanation
Indices: 3964155--3964213 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
3964145 TTTGGTTTCG
3964155 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
3964169 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
3964186 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
3964202 CGTTGCGATTTT
1 CGTTGCGATTTT
3964214 CATTTCACGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3964181 original size:33 final size:33
Alignment explanation
Indices: 3964139--3964262 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
3964129 AAAATCGCAA
*
3964139 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
3964172 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** * *
3964205 TGCGATTTTCATTTCACGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
3964238 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
3964263 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 70 0.86
34 11 0.14
ACGTcount: A:0.10, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3964193 original size:19 final size:19
Alignment explanation
Indices: 3964139--3964197 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
3964129 AAAATCGCAA
3964139 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3964158 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3964172 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3964191 TGCGATT
1 TGCGATT
3964198 CTGTCGTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.34
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 19 0.54
ACGTcount: A:0.07, C:0.15, G:0.31, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3964240 original size:14 final size:14
Alignment explanation
Indices: 3964188--3964244 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3964178 TTTGGTTTCG
*
3964188 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
3964202 CGTTGCGATTTTCATTTCA
1 CGTTGCGA--TTC---TCT
3964221 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3964235 CGTTGCGATT
1 CGTTGCGATT
3964245 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3966207 original size:20 final size:20
Alignment explanation
Indices: 3966176--3966239 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
3966166 TTTTGGTTGA
3966176 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
3966196 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
3966216 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
3966237 AAT
1 AAT
3966240 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:3966228 original size:21 final size:21
Alignment explanation
Indices: 3966174--3966238 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
3966164 TTTTTTGGTT
3966174 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
3966195 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
3966215 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
3966236 GAA
1 GAA
3966239 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:3966312 original size:33 final size:33
Alignment explanation
Indices: 3966264--3966344 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
3966254 AAAATCGCAA
**
3966264 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
3966297 TGTGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3966330 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
3966345 TCTCGTTGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3966332 original size:14 final size:14
Alignment explanation
Indices: 3966280--3966336 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3966270 TTTGGTTTCG
3966280 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
3966294 CGTTGTGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3966313 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3966327 CGTTGCGATT
1 CGTTGCGATT
3966337 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3966347 original size:21 final size:21
Alignment explanation
Indices: 3966321--3966397 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
3966311 CGCGTTGCGA
3966321 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
3966342 TTCTCTCGTTGCAGATAGTCAT
1 TTCTCTCGTTGC-GATTTTCAT
*
3966364 TT-TCACGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
3966384 TTCTCTCGTTGCGA
1 TTCTCTCGTTGCGA
3966398 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.19
21 30 0.62
22 9 0.19
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:3966519 original size:33 final size:33
Alignment explanation
Indices: 3966477--3966547 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3966467 AATACTAACT
3966477 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
3966510 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
3966543 TGAAA
1 TGAAA
3966548 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:3966964 original size:20 final size:20
Alignment explanation
Indices: 3966928--3967080 Score: 184
Period size: 20 Copynumber: 7.6 Consensus size: 20
3966918 CTTTAAAAAT
*
3966928 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
3966948 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
3966969 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3966989 TGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3967009 CGCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
*
3967029 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3967049 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
3967069 CGCGTTGCGATT
1 CGCGTTGCGATT
3967081 CTGGAAAATC
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
20 105 0.91
21 10 0.09
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3969679 original size:16 final size:16
Alignment explanation
Indices: 3969658--3969688 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3969648 CTTCTAATTT
3969658 TTTTTGAGTTCAAGTC
1 TTTTTGAGTTCAAGTC
*
3969674 TTTTTGAGTTTAAGT
1 TTTTTGAGTTCAAGT
3969689 TTCAATATTA
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:0.19, C:0.06, G:0.19, T:0.55
Consensus pattern (16 bp):
TTTTTGAGTTCAAGTC
Found at i:3972121 original size:2 final size:2
Alignment explanation
Indices: 3972116--3972157 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3972106 CAACACACGC
3972116 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
3972158 GAAAGAGTGT
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):
AT
Found at i:3989683 original size:2 final size:2
Alignment explanation
Indices: 3989676--3989716 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
3989666 AGCTAATTTG
*
3989676 CT CT CT CT CT CT CT CT CT CT C- CT -T CT CT CT CT CT GT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3989716 C
1 C
3989717 GGGAATTGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3993936 original size:65 final size:65
Alignment explanation
Indices: 3993858--3993979 Score: 199
Period size: 65 Copynumber: 1.9 Consensus size: 65
3993848 TATAAAAATG
*
3993858 TTTAAAATATATTTAGTAATATTTCTAATAATAAAAAATTATATATATTTTATTTTAATAGAATA
1 TTTAAAATATATTTAGTAATATCTCTAATAATAAAAAATTATATATATTTTATTTTAATAGAATA
* * * *
3993923 TTTAAAATTTATTTATTAATATCTCTAATAATATAAAATTATATATTTTTTATTTTA
1 TTTAAAATATATTTAGTAATATCTCTAATAATAAAAAATTATATATATTTTATTTTA
3993980 TATTATAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (65 bp):
TTTAAAATATATTTAGTAATATCTCTAATAATAAAAAATTATATATATTTTATTTTAATAGAATA
Found at i:3994187 original size:23 final size:24
Alignment explanation
Indices: 3994161--3994213 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3994151 ATAATCTAAT
*
3994161 AATATTTTAA-TAAATATATTTAA
1 AATATATTAATTAAATATATTTAA
* * *
3994184 AATATATTAATTAATTCTTTTTAA
1 AATATATTAATTAAATATATTTAA
3994208 AATATA
1 AATATA
3994214 ATATAATATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
AATATATTAATTAAATATATTTAA
Found at i:3997867 original size:20 final size:19
Alignment explanation
Indices: 3997829--3997867 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3997819 ATTTATTTTC
*
3997829 AATTTTGATTTTTGAAATT
1 AATTTTGATATTTGAAATT
*
3997848 AATTTTGTATATTTGGAATT
1 AATTTTG-ATATTTGAAATT
3997868 CATGGTCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
AATTTTGATATTTGAAATT
Found at i:4000418 original size:14 final size:15
Alignment explanation
Indices: 4000392--4000420 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4000382 ATAAATACGG
4000392 GTAAAACTAAACTAA
1 GTAAAACTAAACTAA
4000407 GTAAAA-TAAACTAA
1 GTAAAACTAAACTAA
4000421 AAATAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (15 bp):
GTAAAACTAAACTAA
Found at i:4008443 original size:14 final size:15
Alignment explanation
Indices: 4008417--4008445 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4008407 ATAAATACAG
4008417 GTAAAACTAAACTAA
1 GTAAAACTAAACTAA
4008432 GTAAAA-TAAACTAA
1 GTAAAACTAAACTAA
4008446 AAATAGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (15 bp):
GTAAAACTAAACTAA
Found at i:4009096 original size:36 final size:35
Alignment explanation
Indices: 4009055--4009157 Score: 134
Period size: 36 Copynumber: 2.9 Consensus size: 35
4009045 ATGGTACTGG
*
4009055 ACATTGATACACGAATGTAGCAAAGCTGATATGATA
1 ACATTGATACACAAATGTA-CAAAGCTGATATGATA
* * *
4009091 TCATTGATACACAAATATACGAAAACTGATATGATA
1 ACATTGATACACAAATGTAC-AAAGCTGATATGATA
*
4009127 ACATTGATACACCAATGTACCAAAGCTGATA
1 ACATTGATACACAAATGTA-CAAAGCTGATA
4009158 ATGGATAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
35 1 0.02
36 55 0.96
37 1 0.02
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.25
Consensus pattern (35 bp):
ACATTGATACACAAATGTACAAAGCTGATATGATA
Found at i:4011912 original size:15 final size:16
Alignment explanation
Indices: 4011894--4011923 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4011884 GTTTTTTAAG
4011894 AATTTAATT-TTTTTT
1 AATTTAATTATTTTTT
4011909 AATTTAATTATTTTT
1 AATTTAATTATTTTT
4011924 CTACCACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
AATTTAATTATTTTTT
Found at i:4018844 original size:33 final size:33
Alignment explanation
Indices: 4018799--4018893 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
4018789 ACTTCAGGCG
4018799 TTGCCACAAGCATGTATGAGGAGACAATGCCCA
1 TTGCCACAAGCATGTATGAGGAGACAATGCCCA
* *
4018832 TTTCCACAAGCATGTATGAGGAGACATTGCCCA
1 TTGCCACAAGCATGTATGAGGAGACAATGCCCA
4018865 TTGCCACAAGCATGTATGAGG-GAGCAATG
1 TTGCCACAAGCATGTATGAGGAGA-CAATG
4018894 GATGTTGCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (33 bp):
TTGCCACAAGCATGTATGAGGAGACAATGCCCA
Found at i:4019293 original size:60 final size:60
Alignment explanation
Indices: 4019198--4019601 Score: 272
Period size: 60 Copynumber: 6.8 Consensus size: 60
4019188 AATCCTGTGA
* * * * **
4019198 CCTTGGCAGAAGAAATCCATACTACTCCCAGAACCTCAGGCGAAGAAACTCTAGCTATTT
1 CCTTGGCAGAAGAAACCCTTAGTATTCCCAGAACCTTGGGCGAAGAAACTCTAGCTATTT
* * * * *
4019258 CCTTGGCTGAAGAAACCCTTAGTGTTCCCATAACCTTGGGCGAAGAAACTCCAGCAATTT
1 CCTTGGCAGAAGAAACCCTTAGTATTCCCAGAACCTTGGGCGAAGAAACTCTAGCTATTT
* * * * * *
4019318 -GTGTGGCAGAAGAAACCCTTAGTATTTCCACAACCTTGGGTGAGGAAACTCCT-GCTATTC
1 CCT-TGGCAGAAGAAACCCTTAGTATTCCCAGAACCTTGGGCGAAGAAACT-CTAGCTATTT
* * * * * * * * *
4019378 CCTTGGCCGAAGCAACCCCTAGTATTCCCAGAACCTTGGGCGAAGACACGCCAACTGTTC
1 CCTTGGCAGAAGAAACCCTTAGTATTCCCAGAACCTTGGGCGAAGAAACTCTAGCTATTT
* * ** * ** *
4019438 CCCTGGCCA-AAGAAACCCTTAGTATTCACAGAACCTTGGATGAAGAAACACCGGCGATTAT
1 CCTTGG-CAGAAGAAACCCTTAGTATTCCCAGAACCTTGGGCGAAGAAACTCTAGCTATT-T
* * * * * * *
4019499 CC-TGACAGAAGAAATCCC-TAGTATTCCTAG------GAGCGAAGGAACTCCAGCCATCT
1 CCTTGGCAGAAGAAA-CCCTTAGTATTCCCAGAACCTTGGGCGAAGAAACTCTAGCTATTT
* * * * *
4019552 CCTTGGCTGAAGAAACCCCTAATATTCCAAGAACCTTAGGCGAAGAAACT
1 CCTTGGCAGAAGAAACCCTTAGTATTCCCAGAACCTTGGGCGAAGAAACT
4019602 TCAGCCATTC
Statistics
Matches: 262, Mismatches: 66, Indels: 32
0.73 0.18 0.09
Matches are distributed among these distances:
53 6 0.02
54 34 0.13
59 4 0.02
60 210 0.80
61 8 0.03
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (60 bp):
CCTTGGCAGAAGAAACCCTTAGTATTCCCAGAACCTTGGGCGAAGAAACTCTAGCTATTT
Found at i:4019730 original size:33 final size:33
Alignment explanation
Indices: 4019616--4019738 Score: 165
Period size: 33 Copynumber: 3.7 Consensus size: 33
4019606 CCATTCCTGA
4019616 AACCTCAAGTGGAGAAACTCCTACAATTCCTCC
1 AACCTCAAGTGGAGAAACTCCTACAATTCCTCC
* * * *
4019649 CACCTCAAATGGAGAAACTTCTACAATTACTCC
1 AACCTCAAGTGGAGAAACTCCTACAATTCCTCC
*
4019682 AGCCTCAAGTGGAGAAACTCCTACAATTCCTCC
1 AACCTCAAGTGGAGAAACTCCTACAATTCCTCC
* * **
4019715 AACTTCCAGCAGAGAAACTCCTAC
1 AACCTCAAGTGGAGAAACTCCTAC
4019739 CGTTCCCATA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.34, C:0.33, G:0.12, T:0.21
Consensus pattern (33 bp):
AACCTCAAGTGGAGAAACTCCTACAATTCCTCC
Found at i:4035268 original size:18 final size:18
Alignment explanation
Indices: 4035227--4035269 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
4035217 CGATCCCAGG
*
4035227 CCTTTGCTCTCTCCCTGTC
1 CCTTT-CTCTCTCCCTCTC
* *
4035246 TCTTTCTCTGTCCCTCTC
1 CCTTTCTCTCTCCCTCTC
4035264 CCTTTC
1 CCTTTC
4035270 CCGTTCCCTG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.00, C:0.47, G:0.07, T:0.47
Consensus pattern (18 bp):
CCTTTCTCTCTCCCTCTC
Found at i:4035280 original size:24 final size:24
Alignment explanation
Indices: 4035235--4035282 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4035225 GGCCTTTGCT
* * *
4035235 CTCTCCCTGTCTCTTTCTCTGTCC
1 CTCTCCCTGTCCCGTTCCCTGTCC
*
4035259 CTCTCCCTTTCCCGTTCCCTGTCC
1 CTCTCCCTGTCCCGTTCCCTGTCC
4035283 TTGCTCTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.08, T:0.42
Consensus pattern (24 bp):
CTCTCCCTGTCCCGTTCCCTGTCC
Found at i:4040617 original size:10 final size:10
Alignment explanation
Indices: 4040604--4040652 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
4040594 AAAACAAAAA
4040604 TCCCGGTTTT
1 TCCCGGTTTT
4040614 TCCCGG-TTT
1 TCCCGGTTTT
* *
4040623 TCCCCGATTT
1 TCCCGGTTTT
*
4040633 TCCTGGTTTT
1 TCCCGGTTTT
*
4040643 TTCCGGTTTT
1 TCCCGGTTTT
4040653 CAGCCGGTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
9 8 0.25
10 24 0.75
ACGTcount: A:0.02, C:0.29, G:0.18, T:0.51
Consensus pattern (10 bp):
TCCCGGTTTT
Found at i:4040652 original size:19 final size:19
Alignment explanation
Indices: 4040605--4040653 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
4040595 AAACAAAAAT
4040605 CCCGGTTTTTCCCGGTTTTC
1 CCCGG-TTTTCCCGGTTTTC
* * *
4040625 CCCGATTTTCCTGGTTTTT
1 CCCGGTTTTCCCGGTTTTC
*
4040644 TCCGGTTTTC
1 CCCGGTTTTC
4040654 AGCCGGTCTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.02, C:0.31, G:0.18, T:0.49
Consensus pattern (19 bp):
CCCGGTTTTCCCGGTTTTC
Found at i:4043778 original size:14 final size:15
Alignment explanation
Indices: 4043759--4043798 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
4043749 TTTCTGTCTA
*
4043759 TATGCAGAGATTT-T
1 TATGCAGGGATTTAT
4043773 TATGCAGGGATTTAT
1 TATGCAGGGATTTAT
4043788 T-TGCAGGGATT
1 TATGCAGGGATT
4043799 ACTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.25, C:0.07, G:0.28, T:0.40
Consensus pattern (15 bp):
TATGCAGGGATTTAT
Found at i:4044142 original size:16 final size:16
Alignment explanation
Indices: 4044121--4044167 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
4044111 ACGATGCTGA
4044121 CGTGATGATTCACTGG
1 CGTGATGATTCACTGG
4044137 CGTGATGATTCACTGG
1 CGTGATGATTCACTGG
4044153 CGTGATGATTCACTG
1 CGTGATGATTCACTG
4044168 TGGTTGGTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (16 bp):
CGTGATGATTCACTGG
Found at i:4045290 original size:13 final size:14
Alignment explanation
Indices: 4045272--4045306 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
4045262 ATCACGTCCA
4045272 AATTTTTTT-AAAT
1 AATTTTTTTAAAAT
4045285 AATTTTTTTAAAAT
1 AATTTTTTTAAAAT
4045299 AATATTTT
1 AAT-TTTT
4045307 ATTTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 7 0.35
15 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATTTTTTTAAAAT
Found at i:4045293 original size:14 final size:15
Alignment explanation
Indices: 4045273--4045306 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
4045263 TCACGTCCAA
*
4045273 ATTTTTTTAAATAAT
1 ATTTTTTAAAATAAT
4045288 -TTTTTTAAAATAAT
1 ATTTTTTAAAATAAT
4045302 ATTTT
1 ATTTT
4045307 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTTTAAAATAAT
Found at i:4045611 original size:2 final size:2
Alignment explanation
Indices: 4045604--4045684 Score: 148
Period size: 2 Copynumber: 41.5 Consensus size: 2
4045594 TATAATTTAT
4045604 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
4045646 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4045685 TATCATAGAA
Statistics
Matches: 77, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 75 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4047882 original size:13 final size:13
Alignment explanation
Indices: 4047864--4047889 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4047854 GCCGATGAAC
4047864 AGGGGTAATCTCA
1 AGGGGTAATCTCA
4047877 AGGGGTAATCTCA
1 AGGGGTAATCTCA
4047890 CTCTTGGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (13 bp):
AGGGGTAATCTCA
Found at i:4048243 original size:2 final size:2
Alignment explanation
Indices: 4048236--4048262 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4048226 TTAATATTAG
4048236 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4048263 TTAAGTATAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4048347 original size:2 final size:2
Alignment explanation
Indices: 4048342--4048376 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4048332 TTTTTTCTTT
4048342 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4048377 TATGTCATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4048503 original size:20 final size:21
Alignment explanation
Indices: 4048453--4048503 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
4048443 TTATATTTTG
*
4048453 TTCTATATATTTCTATATATAT
1 TTCT-TATTTTTCTATATATAT
4048475 TTCTTATTTTTCTAT-TATTAT
1 TTCTTATTTTTCTATATA-TAT
4048496 TT-TTATTT
1 TTCTTATTT
4048504 AATACTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 15 0.56
22 4 0.15
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.69
Consensus pattern (21 bp):
TTCTTATTTTTCTATATATAT
Found at i:4052730 original size:183 final size:183
Alignment explanation
Indices: 4052412--4052749 Score: 586
Period size: 183 Copynumber: 1.8 Consensus size: 183
4052402 ATTAAATTCG
*
4052412 TAAACCTGATCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAACCCTGGCTTTATGA
1 TAAACCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAACCCTGGCTTTATGA
** * *
4052477 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTGGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
4052542 TTGTCAGACCAAAGACTTTGTGATGGGACAAACCCTTCGGTGATTTATCCCTC
131 TTGTCAGACCAAAGACTTTGTGATGGGACAAACCCTTCGGTGATTTATCCCTC
* *
4052595 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAACCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAACCCTGGCTTTATGA
* *
4052660 ATATATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
4052725 TTGTCAGGCCAAAGACTTTGTGATG
131 TTGTCAGACCAAAGACTTTGTGATG
4052750 AGATGAACCC
Statistics
Matches: 145, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
183 145 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAACCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAACCCTGGCTTTATGA
ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGACCAAAGACTTTGTGATGGGACAAACCCTTCGGTGATTTATCCCTC
Found at i:4053863 original size:25 final size:24
Alignment explanation
Indices: 4053812--4053859 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
4053802 AACAGAAAGT
4053812 TTTTGTCTCACTTAAGACAGTTTC
1 TTTTGTCTCACTTAAGACAGTTTC
4053836 TTTTGTCTCA-TTAAGACAGTTTC
1 TTTTGTCTCACTTAAGACAGTTTC
4053859 T
1 T
4053860 CTTTAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (24 bp):
TTTTGTCTCACTTAAGACAGTTTC
Found at i:4053927 original size:34 final size:35
Alignment explanation
Indices: 4053884--4053966 Score: 105
Period size: 36 Copynumber: 2.4 Consensus size: 35
4053874 ATTGAAAACA
** * *
4053884 TTCCCTTGAAATGAATTTTGTCT-CTTGAGATAGT
1 TTCCCTTGAAACAAAATTTGTCTCCTTGAGACAGT
4053918 TTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGT
1 TTCCCTTGAAACAAAATTTGTCT-CCTTGAGACAGT
*
4053954 TTCTCTTGAAACA
1 TTCCCTTGAAACA
4053967 TAAACATTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 20 0.48
36 22 0.52
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (35 bp):
TTCCCTTGAAACAAAATTTGTCTCCTTGAGACAGT
Found at i:4053966 original size:98 final size:98
Alignment explanation
Indices: 4053849--4054028 Score: 281
Period size: 98 Copynumber: 1.8 Consensus size: 98
4053839 TGTCTCATTA
* ** *
4053849 AGACAGTTTCTCTTTAAACATAAACATTGAAAACATTCCCTTGAAATGAATTTTGTCT-CTTGAG
1 AGACAGTTTCTCTTGAAACATAAACATTGAAAACATT-CCTTGAAACAAAATTTGTCTCCTTGAG
*
4053913 ATAGTTTCCCTTGAAACAAAATTTGTCTCCCTTG
65 ACAGTTTCCCTTGAAACAAAATTTGTCTCCCTTG
*
4053947 AGACAGTTTCTCTTGAAACATAAACATTGAAAACATTCCTTGGAACAAAATTTGTCTCCTTGAGA
1 AGACAGTTTCTCTTGAAACATAAACATTGAAAACATTCCTTGAAACAAAATTTGTCTCCTTGAGA
*
4054012 CAGTTTCTCTTGAAACA
66 CAGTTTCCCTTGAAACA
4054029 TAAACATTGA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
97 16 0.22
98 58 0.78
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.34
Consensus pattern (98 bp):
AGACAGTTTCTCTTGAAACATAAACATTGAAAACATTCCTTGAAACAAAATTTGTCTCCTTGAGA
CAGTTTCCCTTGAAACAAAATTTGTCTCCCTTG
Found at i:4054024 original size:62 final size:64
Alignment explanation
Indices: 4053917--4054091 Score: 243
Period size: 63 Copynumber: 2.8 Consensus size: 64
4053907 CTTGAGATAG
*
4053917 TTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
1 TTTCCCTTGGAACAAAATTTGTCT-CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
4053982 -TT-CCTTGGAACAAAATTTGTCTCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGCA
1 TTTCCCTTGGAACAAAATTTGTCTCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
4054044 TTTCCCTT-GAA-ATAAA-TTGTCTCTCTTAAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-AAATTTGTCTC-CTTGAGACAGTTTCTCTTGAAACA
4054092 AAATTCTGTC
Statistics
Matches: 101, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
62 47 0.47
63 48 0.48
64 6 0.06
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (64 bp):
TTTCCCTTGGAACAAAATTTGTCTCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:4054061 original size:63 final size:62
Alignment explanation
Indices: 4053917--4054091 Score: 230
Period size: 62 Copynumber: 2.8 Consensus size: 62
4053907 CTTGAGATAG
4053917 TTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
1 TTTCCCTTG-AA-AAAATTTGTCT-CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
4053982 -TT-CCTTGGAACAAAATTTGTCTCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGCA
1 TTTCCCTT-GAA-AAAATTTGTCTCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
4054044 TTTCCCTTGAAATAAA-TTGTCTCTCTTAAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGAAA-AAATTTGTCTC-CTTGAGACAGTTTCTCTTGAAACA
4054092 AAATTCTGTC
Statistics
Matches: 101, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
62 47 0.47
63 47 0.47
64 7 0.07
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (62 bp):
TTTCCCTTGAAAAAATTTGTCTCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:4054126 original size:100 final size:101
Alignment explanation
Indices: 4053984--4054255 Score: 417
Period size: 100 Copynumber: 2.7 Consensus size: 101
4053974 TGAAAACATT
* * *
4053984 CCTTGGAACAAAATTTGTCT-CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGCATTTC
1 CCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACATTTC
4054048 CCTTGAAAT-AA-ATTGTCTCTCTTAAGATAGTTTC
66 CCTTGAAATGAATATTGTCTCTCTTAAGATAGTTTC
*
4054082 CCTTGAAACAAAATTCTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACTTTGAAAACATTT
1 CCTTGAAACAAAATT-TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACATTT
* *
4054147 CCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTC
65 CCCTTGAAATGAATATTGTCTCTCTTAAGATAGTTTC
* * * *
4054184 CCTTGAAACAAATTTTGTCTCCTTTGAGACAGTTTCTATTGAAACATAAACTTTGAAAACAGTT-
1 CCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACATTTC
4054248 CCTTGAAA
66 CCTTGAAA
4054256 CAAAATTTGA
Statistics
Matches: 159, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
98 14 0.09
99 5 0.03
100 58 0.36
101 47 0.30
102 35 0.22
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (101 bp):
CCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACATTTC
CCTTGAAATGAATATTGTCTCTCTTAAGATAGTTTC
Found at i:4054191 original size:36 final size:36
Alignment explanation
Indices: 4054144--4054229 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
4054134 TTTGAAAACA
** *
4054144 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
4054180 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
**
4054216 TTTCTATTGAAACA
1 TTTCCCTTGAAACA
4054230 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 42 0.95
37 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
Found at i:4054329 original size:263 final size:257
Alignment explanation
Indices: 4053849--4054391 Score: 652
Period size: 263 Copynumber: 2.1 Consensus size: 257
4053839 TGTCTCATTA
*
4053849 AGACAGTTTCTCTTTAAACATAAACATTGAAAACATTCCCTTGAAATGAATTTTGTCTCTTGAGA
1 AGACAGTTTCTCTTGAAACATAAACATTGAAAACATTCCCTTGAAATGAATTTTGTCTCTTGAGA
*
4053914 TAGTTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
66 TAGTTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTATTGAAACATAAACATTGAAA
* * ***
4053979 ACATTCCTTGGAACAAAATTTGTCTCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGCA
131 ACATTCCTTGAAACAAAATTTGTATCCTTGAGACAGTTAAAC-T-AAACATAAACATTGAAAGCA
* *
4054044 TTTCCCTTGAAATAAATTGTCTCTCTTAAGATA-GTTTCCCTTGAAACAAAATTCTGTCTCCCTT
194 TTTCCCTTGAAATAAATTGTCTCTCTTAAGACATGTTTCCCTTAAAACAAAATT-TGTCTCCC-T
4054108 G
257 G
* *
4054109 AGACAATTTCTCTTGAAACATAAACTTTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTG
1 AGACAGTTTCTCTTGAAACATAAACATTGAAAACA-TTCCCTTGAAATGAATTTTG--TCTCTTG
* * *
4054174 AGATAGTTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAGTTTCTATTGAAACATAAACTTTG
63 AGATAGTTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTATTGAAACATAAACATTG
* ** * ** *
4054239 AAAACAGTTCCTTGAAACAAAATTTGAATAT-GTT-TTACA-TTAAAC-AAATTCGT-CTCTCTT
128 AAAACA-TTCCTTGAAACAAAATTTG--TATCCTTGAGACAGTTAAACTAAA--CATAAAC-ATT
* * * **
4054299 GAGA-CAGTTTCTCTTGAACA-AATTTTGTCTCTCTTAAGACATGTTTTTCTTAAAACAAAATTT
187 GAAAGCA-TTTCCCTTGAA-ATAA-ATTGTCTCTCTTAAGACATGTTTCCCTTAAAACAAAATTT
4054362 GTCTCCCTG
249 GTCTCCCTG
4054371 AGACAGTTTCTCTTGAAACAT
1 AGACAGTTTCTCTTGAAACAT
4054392 CAATCCTTGA
Statistics
Matches: 243, Mismatches: 27, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
260 35 0.14
261 23 0.09
262 41 0.17
263 102 0.42
264 38 0.16
265 2 0.01
266 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (257 bp):
AGACAGTTTCTCTTGAAACATAAACATTGAAAACATTCCCTTGAAATGAATTTTGTCTCTTGAGA
TAGTTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTATTGAAACATAAACATTGAAA
ACATTCCTTGAAACAAAATTTGTATCCTTGAGACAGTTAAACTAAACATAAACATTGAAAGCATT
TCCCTTGAAATAAATTGTCTCTCTTAAGACATGTTTCCCTTAAAACAAAATTTGTCTCCCTG
Found at i:4054332 original size:35 final size:34
Alignment explanation
Indices: 4054281--4054387 Score: 126
Period size: 35 Copynumber: 3.1 Consensus size: 34
4054271 TTTTACATTA
*
4054281 AACAAATTCGTCTCTCTTGAGACAGTTTCTCTTG
1 AACAAATTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
4054315 AACAAATTTTGTCTCTCTTAAGACATGTTTTTCTTAA
1 AACAAA-TTTGTCTCTCTTGAGACA-GTTTCTCTT-G
*
4054352 AACAAAATTTGTCTC-CCTGAGACAGTTTCTCTTG
1 AAC-AAATTTGTCTCTCTTGAGACAGTTTCTCTTG
4054386 AA
1 AA
4054388 ACATCAATCC
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
34 8 0.13
35 24 0.39
36 15 0.25
37 11 0.18
38 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (34 bp):
AACAAATTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:4054507 original size:31 final size:32
Alignment explanation
Indices: 4054431--4054543 Score: 149
Period size: 31 Copynumber: 3.5 Consensus size: 32
4054421 CCTTGATACA
4054431 GTTTCTCTTGAAACACAAAATGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC--AA--AAACCTTTGAAATT
*
4054467 GTTTCTCTTGAAACACAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAACCTTTGAAATT
*
4054499 G-TTCTCTTGAAACAC-AAAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAACCTTTGAAATT
*
4054529 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
4054544 AATTCGTCTC
Statistics
Matches: 72, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
30 14 0.19
31 26 0.36
32 14 0.19
34 2 0.03
36 16 0.22
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (32 bp):
GTTTCTCTTGAAACACAAAAACCTTTGAAATT
Found at i:4054589 original size:66 final size:64
Alignment explanation
Indices: 4054499--4054686 Score: 205
Period size: 66 Copynumber: 2.8 Consensus size: 64
4054489 CTTTGAAAAT
*
4054499 GTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTCGTCTCCCTTGAGACA
1 GTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTCGTCT-CCTTGAGACA
* * * * *
4054564 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCCTTAAAACAAAATTTGTCTCCTTGAGGC
1 G-TTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTCGTCTCCTTGAGAC
*
4054629 C
64 A
* ** * * *
4054630 GTTCTCATGAAACAACATTTATCTTTAAGATCGTTTCCCTTGAAACGAATTCTGTCT
1 GTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATTC-GTCT
4054687 TTTTTAAGAC
Statistics
Matches: 101, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
65 12 0.12
66 55 0.54
67 34 0.34
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (64 bp):
GTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTCGTCTCCTTGAGACA
Found at i:4054859 original size:14 final size:15
Alignment explanation
Indices: 4054832--4054865 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
4054822 GATCAAGGAT
4054832 CAGAACTGAAGATTC
1 CAGAACTGAAGATTC
4054847 CAGAACT-AAGATTC
1 CAGAACTGAAGATTC
*
4054861 GAGAA
1 CAGAA
4054866 GCAACCGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (15 bp):
CAGAACTGAAGATTC
Found at i:4055184 original size:106 final size:107
Alignment explanation
Indices: 4054993--4055225 Score: 333
Period size: 106 Copynumber: 2.2 Consensus size: 107
4054983 GGTTTTAGCT
* *
4054993 AGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
** *
4055058 CGAAGGGACGACTGGTTGTCAAC-AAACAATTTCCCAATTTC
66 CGAAGGGACGACTGACTGTCAACAAAACAATTTCCCAATTCC
* ** * * *
4055099 GGAGCCAATTTCAACTTCACATTGAAGGGCATTGGACTCGAGACAGCACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
*
4055164 CGAAGGGACGACTGACTGTCAACAAAACAATTTCCCAGTTCC
66 CGAAGGGACGACTGACTGTCAACAAAACAATTTCCCAATTCC
* *
4055206 AGAACCAACTTCAACTTCAC
1 AGAGCCAATTTCAACTTCAC
4055226 GACAAAAGAT
Statistics
Matches: 111, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
106 78 0.70
107 33 0.30
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (107 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGACTGACTGTCAACAAAACAATTTCCCAATTCC
Found at i:4056549 original size:2 final size:2
Alignment explanation
Indices: 4056542--4056593 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
4056532 TTATTTATTT
4056542 TA TA TA TA -A TA T- TA -A 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
4056581 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
4056594 TATTTAAGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4057845 original size:60 final size:60
Alignment explanation
Indices: 4057763--4057906 Score: 146
Period size: 60 Copynumber: 2.4 Consensus size: 60
4057753 ATATGACCCT
* * * * ** * * **
4057763 AAACTAAGACTCTTATTTTAAATTAGTTTTTAAAATTTTAAATATT-ACAATTTCATCCTT
1 AAACTATGACTCTCATTCTAAATTAATCCTTAAAATTTTAAACATTCA-AATTGCATCCGC
* * *
4057823 AAATTATGACTCTCATTCTAAATTAATCCTTAAACTTTTGAACATTCAAATTGCATCCGC
1 AAACTATGACTCTCATTCTAAATTAATCCTTAAAATTTTAAACATTCAAATTGCATCCGC
*
4057883 AAACTATGAATCTCATTCTAAATT
1 AAACTATGACTCTCATTCTAAATT
4057907 GGTCCCTAAA
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
60 67 0.99
61 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.41
Consensus pattern (60 bp):
AAACTATGACTCTCATTCTAAATTAATCCTTAAAATTTTAAACATTCAAATTGCATCCGC
Found at i:4057940 original size:60 final size:59
Alignment explanation
Indices: 4057810--4057940 Score: 154
Period size: 60 Copynumber: 2.2 Consensus size: 59
4057800 TTAAATATTA
** * * *
4057810 CAATTTCATCCTTAAATTATGACTCTCATTCTAAATTAATCCTTAAACTTTTGAACATT
1 CAATTTCATCCGCAAACTATGAATCTCATTCTAAATTAATCCCTAAACTTTTGAACATT
* ** * *
4057869 CAAATTGCATCCGCAAACTATGAATCTCATTCTAAATTGGTCCCTAAACTTTTTGATCTTT
1 C-AATTTCATCCGCAAACTATGAATCTCATTCTAAATTAATCCCTAAAC-TTTTGAACATT
4057930 CAATTTCATCC
1 CAATTTCATCC
4057941 CTAAATTCAT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 1 0.02
60 48 0.81
61 10 0.17
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (59 bp):
CAATTTCATCCGCAAACTATGAATCTCATTCTAAATTAATCCCTAAACTTTTGAACATT
Found at i:4058408 original size:16 final size:16
Alignment explanation
Indices: 4058387--4058432 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
4058377 AATGAAAATT
4058387 AGGTTACTTTCGGTTC
1 AGGTTACTTTCGGTTC
*
4058403 AGGTTATTTTCGGTTC
1 AGGTTACTTTCGGTTC
* *
4058419 A-ATTGCTTTCGGTT
1 AGGTTACTTTCGGTT
4058433 TAACTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.13, C:0.15, G:0.24, T:0.48
Consensus pattern (16 bp):
AGGTTACTTTCGGTTC
Found at i:4059760 original size:129 final size:131
Alignment explanation
Indices: 4059496--4059760 Score: 417
Period size: 135 Copynumber: 2.0 Consensus size: 131
4059486 TCCCCATCAC
*
4059496 GAGGCGTTAGGCAATGAGTGGCTGCGAAATGGTAACTGTCCGATAGCCAAATCATAAAGGGCTAT
1 GAGGCGTTAGGCAATGAGTGGCTGCAAAATGGTAACTGTCCGATAG----ATCATAAAGGGCTAT
*
4059561 TAGCGGTGTTATGCCACTTGTTGCCAAGGTTTTAAAACCGCCTCCAGGGATGAAATTCAGGTGCC
62 TAGCGGCGTTATGCCACTTGTTGCCAAGGTTTTAAAACCGCCTCCAGGGATGAAATTCAGGTGCC
4059626 CACCT
127 CACCT
* * *
4059631 GAGGCGTTAGGCAATGAGTGGCTGCAAAATGGTAACTGTCCGTTAG-TTATATAGGGCTATTAGC
1 GAGGCGTTAGGCAATGAGTGGCTGCAAAATGGTAACTGTCCGATAGATCATAAAGGGCTATTAGC
* *
4059695 GGCGTTTTGTCACTTGTTGCCAAGG-TTTAAAACCGCCTCCAGGGATGAAATTCAGGTGCCCACC
66 GGCGTTATGCCACTTGTTGCCAAGGTTTTAAAACCGCCTCCAGGGATGAAATTCAGGTGCCCACC
4059759 T
131 T
4059760 G
1 G
4059761 CAGTAGTAGC
Statistics
Matches: 123, Mismatches: 7, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
129 41 0.33
130 38 0.31
135 44 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (131 bp):
GAGGCGTTAGGCAATGAGTGGCTGCAAAATGGTAACTGTCCGATAGATCATAAAGGGCTATTAGC
GGCGTTATGCCACTTGTTGCCAAGGTTTTAAAACCGCCTCCAGGGATGAAATTCAGGTGCCCACC
T
Found at i:4067135 original size:17 final size:17
Alignment explanation
Indices: 4067113--4067145 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4067103 AAAAATTTAA
*
4067113 ACAACAAAAGAAAAATC
1 ACAACAAAAAAAAAATC
4067130 ACAACAAAAAAAAAAT
1 ACAACAAAAAAAAAAT
4067146 AACACATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.15, G:0.03, T:0.06
Consensus pattern (17 bp):
ACAACAAAAAAAAAATC
Found at i:4069767 original size:17 final size:17
Alignment explanation
Indices: 4069737--4069774 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4069727 ATGAGATAAA
*
4069737 AAAAGATGATATTATTAT
1 AAAAGATGAAATTATT-T
4069755 AAAA-ATGAAATTATTT
1 AAAAGATGAAATTATTT
4069771 AAAA
1 AAAA
4069775 TAGCATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 10 0.53
18 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (17 bp):
AAAAGATGAAATTATTT
Found at i:4071578 original size:21 final size:19
Alignment explanation
Indices: 4071541--4071583 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
4071531 TATGAATCAG
*
4071541 ATGAATAATATCGATACTGA
1 ATGAATAATATCAATACT-A
*
4071561 ATGAAGTAGTATCAATACTA
1 ATGAA-TAATATCAATACTA
4071581 ATG
1 ATG
4071584 TGGAGGTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.30
Consensus pattern (19 bp):
ATGAATAATATCAATACTA
Found at i:4072245 original size:23 final size:23
Alignment explanation
Indices: 4072218--4072270 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
4072208 AAGTCGAGGG
* *
4072218 TTCTACGTGGTCCTTCGAGATAA
1 TTCTACGTGGTCATTCGAGACAA
* *
4072241 TTCTATGTGGTCATTCGGGACAA
1 TTCTACGTGGTCATTCGAGACAA
4072264 TTCTACG
1 TTCTACG
4072271 CGGCCCTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (23 bp):
TTCTACGTGGTCATTCGAGACAA
Found at i:4076089 original size:20 final size:20
Alignment explanation
Indices: 4076054--4076105 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
4076044 CTATCGCAAA
*
4076054 TTCGCGTTGCGATTTTTCAT
1 TTCGCGTTGCGATTTTTCAG
4076074 TTCGC-TTGCGATTTTTCAG
1 TTCGCGTTGCGATTTTTCAG
4076093 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
4076106 AGTCTACAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTTCAG
Found at i:4076142 original size:19 final size:19
Alignment explanation
Indices: 4076118--4076221 Score: 109
Period size: 19 Copynumber: 5.3 Consensus size: 19
4076108 TCTACAGTTG
4076118 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* *
4076137 TCGTTGCAATTTTTCAAAT
1 TCGTTGCGATTTTCCAAAT
* *
4076156 TCGTTGCAATTTTTCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
4076175 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
4076196 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
4076216 TCGTTG
1 TCGTTG
4076222 TGATAGTTAA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 51 0.72
20 5 0.07
21 5 0.07
22 10 0.14
ACGTcount: A:0.21, C:0.18, G:0.17, T:0.43
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:4076143 original size:41 final size:41
Alignment explanation
Indices: 4076097--4076228 Score: 171
Period size: 41 Copynumber: 3.3 Consensus size: 41
4076087 TTTCAGTTCG
4076097 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
* * * ** * *
4076138 CGTTGC-A-ATTTTTCAAAT-TCGTTGCAATTTTTCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
4076176 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
*
4076217 CGTTGTGATAGT
1 CGTTGCGATAGT
4076229 TAAAAAAAAA
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
38 24 0.33
39 7 0.10
40 7 0.10
41 35 0.48
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:4076197 original size:79 final size:79
Alignment explanation
Indices: 4076058--4076221 Score: 251
Period size: 79 Copynumber: 2.1 Consensus size: 79
4076048 CGCAAATTCG
* * * *
4076058 CGTTGCGATTTTTCATTTCGCTTGCGATTTTTCAGTTCGCGTTGCGATAGTCTACAGTTGTCGTT
1 CGTTGCAATTTTTCAATTCGCTTGCAATTTTTCAATTC-CGTTGCGATAGTCTACAGTTGTCGTT
4076123 GCGATTTTCCAAATT
65 GCGATTTTCCAAATT
4076138 CGTTGCAATTTTTCAAATTCG-TTGCAATTTTTCAAATT-CGTTGCGATAGTCTACAGTTGTCGT
1 CGTTGCAATTTTTC-AATTCGCTTGCAATTTTTC-AATTCCGTTGCGATAGTCTACAGTTGTCGT
4076201 TGCGATTTTCCAAATT
64 TGCGATTTTCCAAATT
4076217 CGTTG
1 CGTTG
4076222 TGATAGTTAA
Statistics
Matches: 78, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
79 46 0.59
80 24 0.31
81 8 0.10
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (79 bp):
CGTTGCAATTTTTCAATTCGCTTGCAATTTTTCAATTCCGTTGCGATAGTCTACAGTTGTCGTTG
CGATTTTCCAAATT
Found at i:4076928 original size:22 final size:22
Alignment explanation
Indices: 4076903--4076951 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
4076893 TGAAAAATCA
*
4076903 CAACGACAATTGTAGACTACCG
1 CAACGACAACTGTAGACTACCG
* *
4076925 CAACAACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTACCG
4076947 CAACG
1 CAACG
4076952 CAAAATGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.29, G:0.16, T:0.16
Consensus pattern (22 bp):
CAACGACAACTGTAGACTACCG
Found at i:4078993 original size:86 final size:86
Alignment explanation
Indices: 4078848--4079020 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
4078838 ATTTATAACA
4078848 ACTCAAAGGTAATACAAATAAGACGGGCAACTAGGAAATTGGTATCTGCAACTCGAACTCTTCCT
1 ACTCAAAGGTAATACAAATAAGACGGGCAACTAGGAAATTGGTATCTGCAACTCGAACTCTTCCT
4078913 TTTTCTAAAAACACCCTTACT
66 TTTTCTAAAAACACCCTTACT
4078934 ACTCAAAGGTAATACAAATAAGACGGGCAACTAGGAAATTGGTATCTGCAACTCGAACTCTTCCT
1 ACTCAAAGGTAATACAAATAAGACGGGCAACTAGGAAATTGGTATCTGCAACTCGAACTCTTCCT
4078999 TTTTCTAAAAACACCCTTACT
66 TTTTCTAAAAACACCCTTACT
4079020 A
1 A
4079021 AACACAAATG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (86 bp):
ACTCAAAGGTAATACAAATAAGACGGGCAACTAGGAAATTGGTATCTGCAACTCGAACTCTTCCT
TTTTCTAAAAACACCCTTACT
Found at i:4084932 original size:17 final size:17
Alignment explanation
Indices: 4084910--4084952 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
4084900 ATTGGAGTGG
4084910 ACTGCTGATGGTATTGA
1 ACTGCTGATGGTATTGA
* *
4084927 ACTGCTGATGGTTTTGC
1 ACTGCTGATGGTATTGA
*
4084944 ACTTCTGAT
1 ACTGCTGAT
4084953 CAGAAAGCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.40
Consensus pattern (17 bp):
ACTGCTGATGGTATTGA
Found at i:4090064 original size:75 final size:75
Alignment explanation
Indices: 4089941--4090090 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
4089931 ACAACGTACT
4089941 TCTTGATGCCAGCATCGTCCGCACCATACTTTTTATCGAGAGTATCCCATATTGCCTTGGCACTC
1 TCTTGATGCCAGCATCGTCCGCACCATACTTTTTATCGAGAGTATCCCATATTGCCTTGGCACTC
4090006 CTTTCTCTAA
66 CTTTCTCTAA
4090016 TCTTGATGCCAGCATCGTCCGCACCATACTTTTTATCGAGAGTATCCCATATTGCCTTGGCACTC
1 TCTTGATGCCAGCATCGTCCGCACCATACTTTTTATCGAGAGTATCCCATATTGCCTTGGCACTC
4090081 CTTTCTCTAA
66 CTTTCTCTAA
4090091 GGAACATGTC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.20, C:0.31, G:0.15, T:0.35
Consensus pattern (75 bp):
TCTTGATGCCAGCATCGTCCGCACCATACTTTTTATCGAGAGTATCCCATATTGCCTTGGCACTC
CTTTCTCTAA
Found at i:4100945 original size:15 final size:16
Alignment explanation
Indices: 4100925--4100956 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4100915 TTCGAACACC
4100925 ATGAACG-TCAATGTT
1 ATGAACGTTCAATGTT
4100940 ATGAACGTTCAATGTT
1 ATGAACGTTCAATGTT
4100956 A
1 A
4100957 AGTGGTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (16 bp):
ATGAACGTTCAATGTT
Found at i:4108968 original size:24 final size:25
Alignment explanation
Indices: 4108920--4108968 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
4108910 GAATAAACTA
4108920 AGTTTTAATTTATTTATTTTATATT
1 AGTTTTAATTTATTTATTTTATATT
4108945 AGTTTTAATTTATTT-TTTTATATT
1 AGTTTTAATTTATTTATTTTATATT
4108969 TCTTCAATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (25 bp):
AGTTTTAATTTATTTATTTTATATT
Found at i:4110189 original size:36 final size:37
Alignment explanation
Indices: 4110114--4110189 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 37
4110104 TTTTTATATT
*
4110114 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* *
4110151 TTTAATTTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
4110187 TTT
1 TTT
4110190 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 13 0.37
36 13 0.37
37 9 0.26
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:4117527 original size:30 final size:30
Alignment explanation
Indices: 4117456--4117515 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
4117446 ACAATTTAAG
4117456 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
4117486 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
4117516 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:4117623 original size:21 final size:21
Alignment explanation
Indices: 4117597--4117676 Score: 151
Period size: 21 Copynumber: 3.8 Consensus size: 21
4117587 AGGGTGTCAA
4117597 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
4117618 AGTGCATCCAAGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
4117639 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
4117660 AGTGCATCCATGCATCC
1 AGTGCATCCATGCATCC
4117677 AAACATCGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:4117722 original size:21 final size:21
Alignment explanation
Indices: 4117696--4117771 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
4117686 ATGCAATTAG
4117696 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
4117717 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
4117738 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
4117758 TGCATCCATGCATC
1 TGCATCGATGCATC
4117772 AGGGCTGCAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 18 0.33
21 36 0.67
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:4118174 original size:34 final size:32
Alignment explanation
Indices: 4118135--4118204 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
4118125 TTTTGTAAAG
* *
4118135 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
4118169 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
4118201 GGGA
1 GGGA
4118205 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:4121093 original size:30 final size:30
Alignment explanation
Indices: 4121022--4121081 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
4121012 ACAATTTAAG
4121022 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
4121052 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
4121082 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:4121189 original size:21 final size:21
Alignment explanation
Indices: 4121163--4121220 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
4121153 AGGGTGTCAA
4121163 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
4121184 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
4121205 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
4121221 TGCACTAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:4121309 original size:21 final size:21
Alignment explanation
Indices: 4121283--4121358 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
4121273 ATGCAATTAG
4121283 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
4121304 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
4121325 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
4121345 TGCATCCATGCATC
1 TGCATCGATGCATC
4121359 AAGGCTGCAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 18 0.33
21 36 0.67
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:4121752 original size:34 final size:32
Alignment explanation
Indices: 4121713--4121782 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
4121703 TTTTGTAAAG
* * *
4121713 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
4121747 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
4121779 GGGA
1 GGGA
4121783 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:4122724 original size:21 final size:21
Alignment explanation
Indices: 4122673--4122725 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
4122663 CGGTTGTCTT
* *
4122673 AATTGCAAAAATTAAAAAATTT
1 AATT-CAAAATTTAAAAAATTC
* *
4122695 AAATAAAAATTTAAAAAATTC
1 AATTCAAAATTTAAAAAATTC
4122716 AATTCAAAAT
1 AATTCAAAAT
4122726 AATTACCTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (21 bp):
AATTCAAAATTTAAAAAATTC
Found at i:4124001 original size:24 final size:26
Alignment explanation
Indices: 4123947--4124001 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
4123937 TATTAATAAT
4123947 AAATA-AATAAATAAATGTTTTAAAA
1 AAATATAATAAATAAATGTTTTAAAA
** *
4123972 CCATATAATATAT-AAT-TTTTAAAA
1 AAATATAATAAATAAATGTTTTAAAA
4123996 AAATAT
1 AAATAT
4124002 TTTTAAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
24 12 0.50
25 6 0.25
26 6 0.25
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (26 bp):
AAATATAATAAATAAATGTTTTAAAA
Found at i:4124017 original size:39 final size:41
Alignment explanation
Indices: 4123964--4124061 Score: 116
Period size: 39 Copynumber: 2.5 Consensus size: 41
4123954 TAAATAAATG
*
4123964 TTTT-AAAACCATATAATATATA-AT-TTTTAAAAAAATAT
1 TTTTAAAAACTATATAATATATACATATTTTAAAAAAATAT
* ** *
4124002 TTTTAAAAACTATAT-AT-TATACGTATTTTAAAAATGTTT
1 TTTTAAAAACTATATAATATATACATATTTTAAAAAAATAT
4124041 TTTTAAAAACTATATAATATA
1 TTTTAAAAACTATATAATATA
4124062 GATATATAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
37 4 0.08
38 7 0.14
39 35 0.70
40 2 0.04
41 2 0.04
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (41 bp):
TTTTAAAAACTATATAATATATACATATTTTAAAAAAATAT
Found at i:4124783 original size:20 final size:20
Alignment explanation
Indices: 4124743--4124783 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4124733 TTTGATCATG
*
4124743 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
4124763 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
4124783 A
1 A
4124784 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:4131770 original size:18 final size:18
Alignment explanation
Indices: 4131750--4131818 Score: 102
Period size: 18 Copynumber: 3.8 Consensus size: 18
4131740 TGCTATATAT
* * *
4131750 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACTACTAC
4131768 GTCCCGAAGGACTACTAC
1 GTCCCGAAGGACTACTAC
4131786 GTCCCGAAGGACTACTAC
1 GTCCCGAAGGACTACTAC
*
4131804 GTCCCGAATGACTAC
1 GTCCCGAAGGACTAC
4131819 AATACCCTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.19
Consensus pattern (18 bp):
GTCCCGAAGGACTACTAC
Found at i:4132176 original size:62 final size:66
Alignment explanation
Indices: 4132100--4132235 Score: 219
Period size: 68 Copynumber: 2.1 Consensus size: 66
4132090 ATAATATAAC
4132100 CTATACCCATTTCATGTA-T-ATGCACATATAAGAAT-C-ATCAAATAACATTTTAGGAGTCACT
1 CTATACCCATTTCATGTATTCATGCACATATAAGAATACAATCAAATAACATTTTAGGAGTCACT
4132161 T
66 T
4132162 CTATACCCATTTCATGTATTCATGCACATATAAGAATCACAAATCAAATAACATTTTAGGAGTCA
1 CTATACCCATTTCATGTATTCATGCACATATAAGAAT-AC-AATCAAATAACATTTTAGGAGTCA
4132227 CTT
64 CTT
4132230 CT-TACC
1 CTATACC
4132236 ATAGTAACTC
Statistics
Matches: 68, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
62 18 0.26
63 1 0.01
64 16 0.24
66 1 0.01
67 4 0.06
68 28 0.41
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (66 bp):
CTATACCCATTTCATGTATTCATGCACATATAAGAATACAATCAAATAACATTTTAGGAGTCACT
T
Found at i:4133829 original size:61 final size:61
Alignment explanation
Indices: 4133756--4133878 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
4133746 TGCCATATGC
4133756 AAAAGGATGCCCCATGTTGTCCTCACCTTATGAAAGGAAAAGTTTATATTGGTTAATTGCA
1 AAAAGGATGCCCCATGTTGTCCTCACCTTATGAAAGGAAAAGTTTATATTGGTTAATTGCA
4133817 AAAAGGATGCCCCATGTTGTCCTCACCTTATGAAAGGAAAAGTTTATATTGGTTAATTGCA
1 AAAAGGATGCCCCATGTTGTCCTCACCTTATGAAAGGAAAAGTTTATATTGGTTAATTGCA
4133878 A
1 A
4133879 GAGCAGGGTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (61 bp):
AAAAGGATGCCCCATGTTGTCCTCACCTTATGAAAGGAAAAGTTTATATTGGTTAATTGCA
Found at i:4137424 original size:19 final size:17
Alignment explanation
Indices: 4137398--4137441 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 17
4137388 CCTGGAAAAG
4137398 AAAAATAAAATGAATTAA
1 AAAAATAAAATGAA-TAA
4137416 AATAAATAAAATGAATAA
1 AA-AAATAAAATGAATAA
4137434 AAAAATAA
1 AAAAATAA
4137442 TATACTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (17 bp):
AAAAATAAAATGAATAA
Found at i:4137427 original size:9 final size:9
Alignment explanation
Indices: 4137400--4137441 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
4137390 TGGAAAAGAA
4137400 AAATAAAAT
1 AAATAAAAT
*
4137409 GAATTAAAAT
1 -AAATAAAAT
4137419 AAATAAAAT
1 AAATAAAAT
*
4137428 GAATAAAA-
1 AAATAAAAT
4137436 AAATAA
1 AAATAA
4137442 TATACTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 5 0.18
9 15 0.54
10 8 0.29
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Done.