Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 78
Found at i:3749720 original size:18 final size:18
Alignment explanation
Indices: 3749697--3749734 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3749687 GTAATATGGG
3749697 GGATCAATGGTTGAGAAA
1 GGATCAATGGTTGAGAAA
*
3749715 GGATCAATGGTTGATAAA
1 GGATCAATGGTTGAGAAA
3749733 GG
1 GG
3749735 CATATCAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.34, T:0.24
Consensus pattern (18 bp):
GGATCAATGGTTGAGAAA
Found at i:3753395 original size:19 final size:19
Alignment explanation
Indices: 3753371--3753408 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3753361 AAATTTATTT
3753371 TCCTTCCA-CTTCTCCACTC
1 TCCTTCCATCTT-TCCACTC
3753390 TCCTTCCATCTTTCCACTC
1 TCCTTCCATCTTTCCACTC
3753409 AACCAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.11, C:0.50, G:0.00, T:0.39
Consensus pattern (19 bp):
TCCTTCCATCTTTCCACTC
Found at i:3755666 original size:16 final size:16
Alignment explanation
Indices: 3755645--3755675 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3755635 TGAATTTGAG
3755645 GCACTCTGCTTTTCCT
1 GCACTCTGCTTTTCCT
*
3755661 GCACTCTTCTTTTCC
1 GCACTCTGCTTTTCC
3755676 ATTTGGATAG
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:0.06, C:0.39, G:0.10, T:0.45
Consensus pattern (16 bp):
GCACTCTGCTTTTCCT
Found at i:3759164 original size:3 final size:3
Alignment explanation
Indices: 3759156--3759182 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3759146 TTCCCTATCT
3759156 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
3759183 AGAGCATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3764138 original size:2 final size:2
Alignment explanation
Indices: 3764131--3764166 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3764121 ATTTTACCTA
3764131 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
3764167 TTAAGTCGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3764452 original size:14 final size:14
Alignment explanation
Indices: 3764433--3764460 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3764423 ATATAAATGT
3764433 AAAATCATTTTAAG
1 AAAATCATTTTAAG
3764447 AAAATCATTTTAAG
1 AAAATCATTTTAAG
3764461 TATGTTTTTA
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:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
AAAATCATTTTAAG
Found at i:3767538 original size:28 final size:28
Alignment explanation
Indices: 3767506--3767565 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
3767496 ATTTATAATG
3767506 TCATTAGTTAATCCAAATTGTTAGAATA
1 TCATTAGTTAATCCAAATTGTTAGAATA
3767534 TCATTAGTTAATCCAAATTGTTAGAATA
1 TCATTAGTTAATCCAAATTGTTAGAATA
3767562 TCAT
1 TCAT
3767566 GACCAACGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (28 bp):
TCATTAGTTAATCCAAATTGTTAGAATA
Found at i:3772593 original size:15 final size:15
Alignment explanation
Indices: 3772550--3772594 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
3772540 CTAAATTTAG
*
3772550 TCACTTA-GTTATCG
1 TCACTTACGTTATCA
3772564 TCACTTACGTTATCA
1 TCACTTACGTTATCA
3772579 TCACTTACGTTATCA
1 TCACTTACGTTATCA
3772594 T
1 T
3772595 TTTATTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 7 0.24
15 22 0.76
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (15 bp):
TCACTTACGTTATCA
Found at i:3773720 original size:30 final size:30
Alignment explanation
Indices: 3773686--3773743 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3773676 GACGTAACTT
3773686 ATTTTTATTAATATATAAAGATGATATAAC
1 ATTTTTATTAATATATAAAGATGATATAAC
* **
3773716 ATTTTTATTAATATTTAATTATGATATA
1 ATTTTTATTAATATATAAAGATGATATA
3773744 TAAAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (30 bp):
ATTTTTATTAATATATAAAGATGATATAAC
Found at i:3774635 original size:36 final size:37
Alignment explanation
Indices: 3774550--3774668 Score: 131
Period size: 33 Copynumber: 3.3 Consensus size: 37
3774540 TAAACCCTAA
* *
3774550 ACCCGACCCAAATATCGCACTTAAAAAAA----TCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCGTCCG
*
3774583 ACCCGACCCGAATATCACACTTAAAAAAACCCGTCTG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCGTCCG
* * *
3774620 ACCC-ACCCGAATATCAAACTTAAATAAACCCGACCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG-TCCG
*
3774657 ACCCGAACCGAA
1 ACCCGACCCGAA
3774669 CCTGATTTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
33 27 0.38
36 26 0.36
37 13 0.18
38 6 0.08
ACGTcount: A:0.40, C:0.36, G:0.10, T:0.13
Consensus pattern (37 bp):
ACCCGACCCGAATATCACACTTAAAAAAACCCGTCCG
Found at i:3775752 original size:18 final size:18
Alignment explanation
Indices: 3775729--3775765 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3775719 CGAAATTTAT
3775729 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
3775747 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
3775765 A
1 A
3775766 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:3776184 original size:25 final size:25
Alignment explanation
Indices: 3776152--3776201 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3776142 CATTATTTTC
* *
3776152 CAAATAATGTATCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
3776177 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
3776202 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:3776334 original size:14 final size:14
Alignment explanation
Indices: 3776290--3776334 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
3776280 GCGAAAGTCA
3776290 AATTT-GCGTTGCG
1 AATTTCGCGTTGCG
*
3776303 ATTTTCG-GTTTGCG
1 AATTTCGCG-TTGCG
3776317 -ATTTCGCGTTGCG
1 AATTTCGCGTTGCG
3776330 AATTT
1 AATTT
3776335 AACTTTCGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.13, C:0.16, G:0.27, T:0.44
Consensus pattern (14 bp):
AATTTCGCGTTGCG
Found at i:3776343 original size:20 final size:20
Alignment explanation
Indices: 3776318--3776364 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
3776308 CGGTTTGCGA
*
3776318 TTTCGCGTTGCGAATTTAAC
1 TTTCGCATTGCGAATTTAAC
*
3776338 TTTCGCATTGCGAATTTGAC
1 TTTCGCATTGCGAATTTAAC
3776358 TTTCGCA
1 TTTCGCA
3776365 ACGCTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (20 bp):
TTTCGCATTGCGAATTTAAC
Found at i:3776701 original size:6 final size:6
Alignment explanation
Indices: 3776692--3776745 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
3776682 TTGTGATTGG
** ** **
3776692 GATTTT GATTTT GATTGC GATTGA GATTTT GATTTT GATTGC GATTTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT
3776740 GATTTT
1 GATTTT
3776746 CCTTTTGCTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.19, C:0.04, G:0.22, T:0.56
Consensus pattern (6 bp):
GATTTT
Found at i:3776708 original size:18 final size:18
Alignment explanation
Indices: 3776698--3776745 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
3776688 TTGGGATTTT
**
3776698 GATTTTGATTGCGATTGA
1 GATTTTGATTTTGATTGA
*
3776716 GATTTTGATTTTGATTGC
1 GATTTTGATTTTGATTGA
3776734 GATTTTGATTTT
1 GATTTTGATTTT
3776746 CCTTTTGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.19, C:0.04, G:0.23, T:0.54
Consensus pattern (18 bp):
GATTTTGATTTTGATTGA
Found at i:3776745 original size:24 final size:24
Alignment explanation
Indices: 3776686--3776737 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
3776676 AGCCAGTTGT
*
3776686 GATTGGGATTTTGATTTTGATTGC
1 GATTGAGATTTTGATTTTGATTGC
3776710 GATTGAGATTTTGATTTTGATTGC
1 GATTGAGATTTTGATTTTGATTGC
3776734 GATT
1 GATT
3776738 TTGATTTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.04, G:0.27, T:0.50
Consensus pattern (24 bp):
GATTGAGATTTTGATTTTGATTGC
Found at i:3776751 original size:24 final size:24
Alignment explanation
Indices: 3776686--3776752 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
3776676 AGCCAGTTGT
* *
3776686 GATTGGGATTTTGATTTTGATTGC
1 GATTGAGATTTTCATTTTGATTGC
*
3776710 GATTGAGATTTTGATTTTGATTGC
1 GATTGAGATTTTCATTTTGATTGC
** *
3776734 GATTTTGATTTTCCTTTTG
1 GATTGAGATTTTCATTTTG
3776753 CTTGGCACCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.16, C:0.06, G:0.24, T:0.54
Consensus pattern (24 bp):
GATTGAGATTTTCATTTTGATTGC
Found at i:3778769 original size:24 final size:24
Alignment explanation
Indices: 3778735--3778788 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3778725 CCATCACATC
3778735 ATCAAAATCCGAGTATTGAACAAG
1 ATCAAAATCCGAGTATTGAACAAG
* * * *
3778759 GTCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGAACAAG
3778783 ATCAAA
1 ATCAAA
3778789 TTTCGAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGAACAAG
Found at i:3779747 original size:19 final size:19
Alignment explanation
Indices: 3779705--3779752 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3779695 CAAAACATTT
3779705 GTGTTGCGAAACTAAAACC
1 GTGTTGCGAAACTAAAACC
* * **
3779724 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAACTAAAACC
3779743 GTGTTGCGAA
1 GTGTTGCGAA
3779753 TTCGAAAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (19 bp):
GTGTTGCGAAACTAAAACC
Found at i:3779786 original size:19 final size:20
Alignment explanation
Indices: 3779749--3779801 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
3779739 ATTCGTGTTG
* *
3779749 CGAATTCGAAAATCTAGTTA
1 CGAATTTGAAATTCTAGTTA
*
3779769 CGAATTTGAAATTC-AGTTG
1 CGAATTTGAAATTCTAGTTA
3779788 CGAATTTGAAATTC
1 CGAATTTGAAATTC
3779802 CGCGTTGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (20 bp):
CGAATTTGAAATTCTAGTTA
Found at i:3779814 original size:21 final size:19
Alignment explanation
Indices: 3779771--3779815 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3779761 TCTAGTTACG
*
3779771 AATTTGAAATTCAGTTGCG
1 AATTTGAAATTCAGTTGCA
*
3779790 AATTTGAAATTCCGCGTTGCA
1 AATTTGAAATT-C-AGTTGCA
3779811 AATTT
1 AATTT
3779816 AACTTTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 1 0.05
21 10 0.45
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (19 bp):
AATTTGAAATTCAGTTGCA
Found at i:3779840 original size:20 final size:20
Alignment explanation
Indices: 3779805--3779887 Score: 85
Period size: 20 Copynumber: 4.2 Consensus size: 20
3779795 GAAATTCCGC
* *
3779805 GTTGCAAATTTAACTTTTGT
1 GTTGCGAATTTGACTTTTGT
*
3779825 GCTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * * * *
3779845 GTTGTGCATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
3779865 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
3779885 GTT
1 GTT
3779888 ACGATTTACA
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:3779908 original size:40 final size:40
Alignment explanation
Indices: 3779827--3779909 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
3779817 ACTTTTGTGC
* ** *
3779827 TGCGAATTTGACTTTTGTGTTGTGCATTTGACTATCGCGT
1 TGCGAATTTGACTTATGTGTTACGCATTTGACTATCACGT
3779867 TGCGAATTTGACTTATGTGTTACG-ATTT-ACATATTCACGT
1 TGCGAATTTGACTTATGTGTTACGCATTTGAC-TA-TCACGT
3779907 TGC
1 TGC
3779910 AAAATTGGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 2 0.05
39 6 0.16
40 29 0.78
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (40 bp):
TGCGAATTTGACTTATGTGTTACGCATTTGACTATCACGT
Found at i:3779929 original size:20 final size:19
Alignment explanation
Indices: 3779904--3779953 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
3779894 TACATATTCA
*
3779904 CGTTGCAAAATTGGAGTTCG
1 CGTTGC-AAATTGGAGATCG
* *
3779924 CGTTGCGAATTTGAGATCG
1 CGTTGCAAATTGGAGATCG
*
3779943 CGTTGCGAATT
1 CGTTGCAAATT
3779954 TGTTGGTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
CGTTGCAAATTGGAGATCG
Found at i:3782264 original size:120 final size:122
Alignment explanation
Indices: 3782022--3782266 Score: 295
Period size: 120 Copynumber: 2.0 Consensus size: 122
3782012 TAATGGAAAG
* * *
3782022 TATTTTGTGAAATTAATGCGCAGAGCAAAGACAAAATAATATAATGTGCCATATCATAATGTTAT
1 TATTTTATGAAATTAATGCGCAGAGCAAAGACAAAAGAATATAACGTGCCATATCATAATGTTAT
* * *
3782087 TAGTGAATTTGACGGTGCAGTGATCAAAACAAGAGTAATTGAAAAGTTTAATTATTAAA
66 TAATGAATTTAACGGTGCA--GATCAAAACAAGAGTAATTGAAAAGTATAATTATTAAA
* * *
3782146 TATTTTATGAAATTAATGCGCAGAGCAAAGACGTAAGAGATTATAACGTGCCATGTCATAATGGT
1 TATTTTATGAAATTAATGCGCAGAGCAAAGAC--AAAAGAATATAACGTGCCATATCATAAT-GT
* *
3782211 T-TTAAT-AGATTTAAC-GTG-A-A-CAAAATAAGAGTAATTTAAAAGTATAATTATTAAA
63 TATTAATGA-ATTTAACGGTGCAGATCAAAACAAGAGTAATTGAAAAGTATAATTATTAAA
3782266 T
1 T
3782267 TAAAAAATTT
Statistics
Matches: 106, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
120 33 0.31
121 1 0.01
124 32 0.30
125 4 0.04
126 33 0.31
127 3 0.03
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (122 bp):
TATTTTATGAAATTAATGCGCAGAGCAAAGACAAAAGAATATAACGTGCCATATCATAATGTTAT
TAATGAATTTAACGGTGCAGATCAAAACAAGAGTAATTGAAAAGTATAATTATTAAA
Found at i:3787451 original size:96 final size:96
Alignment explanation
Indices: 3787326--3787516 Score: 262
Period size: 96 Copynumber: 2.0 Consensus size: 96
3787316 TAACACGCAA
*
3787326 TTGTGTGTCATAAATCTATGACACACATTTATAACAGACATTTACGACGTGCATTGCGTGTCATT
1 TTGTGTGTCATAAATCTATGACACACATTTATAACAGACATTTACGACGTACATTGCGTGTCATT
* *
3787391 GAAGCCCCCGTCA-TAAATGAAA-ATGACACAT
66 GAAGCACACGTCATTAAA--AAAGATGACACAT
* ** * *
3787422 TTGTGTGTCATAAAGT-TATGACACGCATTTATGGCATACATTTACGACTTACATTGCGTGTCAT
1 TTGTGTGTCATAAA-TCTATGACACACATTTATAACAGACATTTACGACGTACATTGCGTGTCAT
3787486 TGAAGCACACGTCATTAAAAAAGATGACACA
65 TGAAGCACACGTCATTAAAAAAGATGACACA
3787517 CATTCGTGTG
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
95 3 0.04
96 76 0.90
97 5 0.06
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (96 bp):
TTGTGTGTCATAAATCTATGACACACATTTATAACAGACATTTACGACGTACATTGCGTGTCATT
GAAGCACACGTCATTAAAAAAGATGACACAT
Found at i:3787555 original size:2 final size:2
Alignment explanation
Indices: 3787548--3787601 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
3787538 TGTCGTAAAT
3787548 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3787589 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
3787602 GTAGATTGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3802013 original size:18 final size:18
Alignment explanation
Indices: 3801990--3802060 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
3801980 AGGAATTATC
3801990 AGTGGTCTTTCGGGACAT
1 AGTGGTCTTTCGGGACAT
3802008 AGTGGTCCTTT-GGGACAT
1 AGTGGT-CTTTCGGGACAT
*
3802026 AGTGGT-TATTCGGGAGAT
1 AGTGGTCT-TTCGGGACAT
* *
3802044 AGTGGTCCTACGGGACA
1 AGTGGTCTTTCGGGACA
3802061 AATTCTACGC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.02
17 2 0.04
18 38 0.84
19 4 0.09
ACGTcount: A:0.20, C:0.15, G:0.35, T:0.30
Consensus pattern (18 bp):
AGTGGTCTTTCGGGACAT
Found at i:3802059 original size:36 final size:36
Alignment explanation
Indices: 3801990--3802060 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
3801980 AGGAATTATC
**
3801990 AGTGGTCTTTCGGGACATAGTGGTCCTTTGGGACAT
1 AGTGGTCTTTCGGGACATAGTGGTCCTACGGGACAT
*
3802026 AGTGGT-TATTCGGGAGATAGTGGTCCTACGGGACA
1 AGTGGTCT-TTCGGGACATAGTGGTCCTACGGGACA
3802061 AATTCTACGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.20, C:0.15, G:0.35, T:0.30
Consensus pattern (36 bp):
AGTGGTCTTTCGGGACATAGTGGTCCTACGGGACAT
Found at i:3803246 original size:21 final size:20
Alignment explanation
Indices: 3803217--3803255 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3803207 TTTTTTTCGT
3803217 GAAAGGATCAATCATTTTGA
1 GAAAGGATCAATCATTTTGA
*
3803237 GAAAGTGATCAATCCTTTT
1 GAAAG-GATCAATCATTTT
3803256 TAAAATTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (20 bp):
GAAAGGATCAATCATTTTGA
Found at i:3806751 original size:2 final size:2
Alignment explanation
Indices: 3806746--3806787 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3806736 AATCTTCTAG
3806746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
3806787 T
1 T
3806788 GTACGAGACA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3810141 original size:20 final size:20
Alignment explanation
Indices: 3810116--3810175 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
3810106 AAGAAAGGGA
*
3810116 GAAGAAAGAAGATAAAAGAG
1 GAAGAAAGAAGAGAAAAGAG
3810136 GAAGAAAGAAGAGAAAAGAG
1 GAAGAAAGAAGAGAAAAGAG
3810156 GAAGAAAGAAGAGAAAAGAG
1 GAAGAAAGAAGAGAAAAGAG
3810176 AAGGAAGTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (20 bp):
GAAGAAAGAAGAGAAAAGAG
Found at i:3810143 original size:10 final size:10
Alignment explanation
Indices: 3810106--3810164 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
3810096 GAGTGAAAGA
*
3810106 AAGAAAGGGAG
1 AAGAAAGAG-G
*
3810117 AAGAAAGAAG
1 AAGAAAGAGG
3810127 ATA-AAAGAGG
1 A-AGAAAGAGG
*
3810137 AAGAAAGAAG
1 AAGAAAGAGG
3810147 -AGAAAAGAGG
1 AAG-AAAGAGG
3810157 AAGAAAGA
1 AAGAAAGA
3810165 AGAGAAAAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
9 3 0.08
10 26 0.67
11 10 0.26
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (10 bp):
AAGAAAGAGG
Found at i:3810160 original size:40 final size:39
Alignment explanation
Indices: 3810100--3810175 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
3810090 CACCGGGAGT
* *
3810100 GAAAGAAAGAAAGGGAGAAGAAAGAAGATAAAAGAGGAA
1 GAAAGAAAGAAAGAGAGAAGAAAGAAGAGAAAAGAGGAA
3810139 GAAAGAAGAGAAA-AGAGGAAGAAAGAAGAGAAAAGAG
1 GAAAGAA-AGAAAGAGA-GAAGAAAGAAGAGAAAAGAG
3810176 AAGGAAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 9 0.27
40 24 0.73
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.01
Consensus pattern (39 bp):
GAAAGAAAGAAAGAGAGAAGAAAGAAGAGAAAAGAGGAA
Found at i:3811411 original size:264 final size:263
Alignment explanation
Indices: 3810942--3811471 Score: 1006
Period size: 264 Copynumber: 2.0 Consensus size: 263
3810932 CAGTCCAGAT
3810942 AGATATGATACAATACTAGTTGAAGAAGATGATGATATTGAAACCATAATTAGATTACACGAGTC
1 AGATATGATACAATACTAGTTGAAGAAGATGATGATATTGAAACCATAATTAGATTACACGAGTC
3811007 AACAAATATTTTAGTTATTGAGTTATTTGTTGATGTGCATAAGATATTTGATGTTCCTATGTCAT
66 AACAAATATTTTAGTTATTGAGTTATTTGTTGATGTGCATAAGATATTTGATGTTCCTATGTCAT
3811072 CAAGAAATGTGGCTGGAGATTCATCTCAAATGGCTTTCGGAAATGAGTTTGAAAACCCGACATAC
131 CAAGAAATGTGGCTGGAGATTCATCTCAAATGGCTTTCGGAAATGAGTTTGAAAACCCGACATAC
*
3811137 ATATCAATAAACAATTTTATGACGCTATTGGAAAGTGGAAATAAAGTCGATAGAACATCCGCAGC
196 ATATCAATAAACAATTTTATGACGCTATTGGAAAGTGGAAATAAAGTCGATAGAACATCAGCAGC
3811202 AGC
261 AGC
* *
3811205 AGATATGATACAGTACTAGTTGAAGAAGATGATGATATTGAAACCATAATTGGATTACACCGAGT
1 AGATATGATACAATACTAGTTGAAGAAGATGATGATATTGAAACCATAATTAGATTACA-CGAGT
3811270 CAACAAATATTTTAGTTATTGAGTTATTTGTTGATGTGCATAAGATATTTGATGTTCCTATGTCA
65 CAACAAATATTTTAGTTATTGAGTTATTTGTTGATGTGCATAAGATATTTGATGTTCCTATGTCA
*
3811335 TCAAGAAATGTGGTTGGAGATTCATCTCAAATGGCTTTCGGAAATGAGTTTGAAAACCCGACATA
130 TCAAGAAATGTGGCTGGAGATTCATCTCAAATGGCTTTCGGAAATGAGTTTGAAAACCCGACATA
*
3811400 CATATCAATAAACAATTTTATGGCGCTATTGGAAAGTGGAAATAAAGTCGATAGAACATCAGCAG
195 CATATCAATAAACAATTTTATGACGCTATTGGAAAGTGGAAATAAAGTCGATAGAACATCAGCAG
3811465 CAGC
260 CAGC
3811469 AGA
1 AGA
3811472 GTACAAGAAG
Statistics
Matches: 261, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
263 57 0.22
264 204 0.78
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (263 bp):
AGATATGATACAATACTAGTTGAAGAAGATGATGATATTGAAACCATAATTAGATTACACGAGTC
AACAAATATTTTAGTTATTGAGTTATTTGTTGATGTGCATAAGATATTTGATGTTCCTATGTCAT
CAAGAAATGTGGCTGGAGATTCATCTCAAATGGCTTTCGGAAATGAGTTTGAAAACCCGACATAC
ATATCAATAAACAATTTTATGACGCTATTGGAAAGTGGAAATAAAGTCGATAGAACATCAGCAGC
AGC
Found at i:3813721 original size:23 final size:23
Alignment explanation
Indices: 3813693--3813736 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3813683 TAACTTTATT
3813693 TTATAAAAAATTATGTATTTTTA
1 TTATAAAAAATTATGTATTTTTA
* * *
3813716 TTATAATAATTTATGTGTTTT
1 TTATAAAAAATTATGTATTTT
3813737 AAGTTTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (23 bp):
TTATAAAAAATTATGTATTTTTA
Found at i:3815597 original size:9 final size:10
Alignment explanation
Indices: 3815564--3815597 Score: 54
Period size: 9 Copynumber: 3.6 Consensus size: 10
3815554 ATTAAATTAA
3815564 ATTATATATT
1 ATTATATATT
3815574 ATTAT-TATT
1 ATTATATATT
3815583 ATTATATA-T
1 ATTATATATT
3815592 ATTATA
1 ATTATA
3815598 AAATATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTATATATT
Found at i:3817179 original size:17 final size:18
Alignment explanation
Indices: 3817147--3817185 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3817137 GAATTCAATT
*
3817147 TAAAGATTACATTTAATA
1 TAAACATTACATTTAATA
*
3817165 TAAACATTA-ATTTAATC
1 TAAACATTACATTTAATA
3817182 TAAA
1 TAAA
3817186 AATAATCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAACATTACATTTAATA
Found at i:3817581 original size:18 final size:19
Alignment explanation
Indices: 3817548--3817583 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3817538 TCTCTTTTCT
*
3817548 TTTCTTTCTTCTCCCATTC
1 TTTCTTTCTACTCCCATTC
3817567 TTTCTTTC-ACTCCCATT
1 TTTCTTTCTACTCCCATT
3817584 GTAACCCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTCTTTCTACTCCCATTC
Found at i:3821702 original size:165 final size:166
Alignment explanation
Indices: 3821392--3821713 Score: 558
Period size: 165 Copynumber: 1.9 Consensus size: 166
3821382 ATAAAAATTA
*
3821392 AATATTCTTTAATTCAAAAAAACAGTTTCTAATTAATTTAAATAATATATAATTATAAAATAAAA
1 AATATTCTTTAATTCAAAAAAACAGTTTCTAATTAATTTAAATAATATACAATTATAAAATAAAA
3821457 ATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGAATCTTAAATT
66 ATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGAATCTTAAATT
*
3821522 ATTATTTGGGTTTTAAATGGTTTGGGCAATATATTT
131 ATTAATTGGGTTTTAAATGGTTTGGGCAATATATTT
* *
3821558 AATATTTTTTAATTCAAAAAAATAGTTTAC-AATTAATTTAAATAATATACAATTATAAAATAAA
1 AATATTCTTTAATTCAAAAAAACAGTTT-CTAATTAATTTAAATAATATACAATTATAAAATAAA
* * *
3821622 AATTTTATAT-AAATTTTTAATTAATTAATATTGATTTAGGTTTAAAATTTATTGGATCTTAAAT
65 AATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGAATCTTAAAT
3821686 TATTAATTGGGTTTTAAATGGTTTGGGC
130 TATTAATTGGGTTTTAAATGGTTTGGGC
3821714 TGAGCCCATA
Statistics
Matches: 148, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
165 78 0.53
166 69 0.47
167 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (166 bp):
AATATTCTTTAATTCAAAAAAACAGTTTCTAATTAATTTAAATAATATACAATTATAAAATAAAA
ATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGAATCTTAAATT
ATTAATTGGGTTTTAAATGGTTTGGGCAATATATTT
Found at i:3822065 original size:2 final size:2
Alignment explanation
Indices: 3822058--3822082 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3822048 AGACTTTGGA
3822058 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
3822083 ATTCTAAAAA
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:3822797 original size:25 final size:25
Alignment explanation
Indices: 3822769--3822817 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
3822759 TATGAGATTA
3822769 CATGCAATAGAATCATGTATGCATG
1 CATGCAATAGAATCATGTATGCATG
*
3822794 CATGCAATATAATCATGTATGCAT
1 CATGCAATAGAATCATGTATGCAT
3822818 AAACGGACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (25 bp):
CATGCAATAGAATCATGTATGCATG
Found at i:3828194 original size:3 final size:3
Alignment explanation
Indices: 3828186--3828238 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
3828176 CAAAAACCTG
* * *
3828186 TAA TAA TAA TAAA TAA TAA TAA TAG TAG TAA TAA TTAA TAT TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
3828233 TAA TAA
1 TAA TAA
3828239 CTCGAATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3828940 original size:250 final size:252
Alignment explanation
Indices: 3828438--3829560 Score: 1260
Period size: 259 Copynumber: 4.5 Consensus size: 252
3828428 ACAATTTTGG
* *
3828438 AAATAGTTTACTAAGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATGTCATTTTCTG
1 AAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTG
*
3828503 AAAATATTAAATGAGAAACTTTGAAAATTGCTTTTCTTATTTTTCACAAACATCATATGAAAACA
66 AAAATATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCA-AAACATCATATGAAAACA
* * * ** *
3828568 TC-TTCCCTGAAGGTCTTATAAATGGCCCGAATGACTTATCATCTCACTCGAAAGATTGACAGAT
130 TCATGCCC-GAAGGTCTTATAGATGGCCCAAATGACTTATCATCTTGCTCGAAAGACTGACAGAT
* * *
3828632 GACCCGAAGAATTTAATCATCATGCTCGGAAGACTTACTAATGGCCCGAAATACTTACC
194 GACCCGAAGAATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTACC
* * * *
3828691 -AATAGTTTACTAGGTAAGAAACTTTGTAAATCGCTTTCTTTCTTTTCAAAAATTTTATTTTCTT
1 AAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTG
* * *
3828755 AAAATATTAAATGAGAAACTTTGAAAATTGCTTTTCTTATTTTTCGAAA-ATCATGTGAAAACAT
66 AAAATATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCAAAACATCATATGAAAACAT
*
3828819 CATGCCCGAAGGTCTTATAGATGGCCCAAATGACTTATCATCTTGCTCGAAAGACTGATAGATGA
131 CATGCCCGAAGGTCTTATAGATGGCCCAAATGACTTATCATCTTGCTCGAAAGACTGACAGATGA
** * *
3828884 CCCGAATTATTTAATCATCATGCTCGAAAGACTTATTGGTGGCCCGAAAGACTTACC
196 CCCGAAGAATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTACC
*
3828941 AATTTTGAAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTT
1 --------AAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTC-AAAAATTT
* * * *
3829006 CATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATT-TTTTTCTCATTTTTCAAAA-TTAATG
57 CATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCAAAACATCATA
* *
3829069 TGAAAACATCATGCCCGAAGGTCTTATAGATGACCCAAAGGACTTATCATCTTGCTCGAAAGACT
122 TGAAAACATCATGCCCGAAGGTCTTATAGATGGCCCAAATGACTTATCATCTTGCTCGAAAGACT
* * * * * * * *
3829134 AACAAATGACCCGAAGGATTTAATCATAATGTTCGAAAGACTTCCTGATAGCCCGAAGGACTTAC
187 GACAGATGACCCGAAGAATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTAC
3829199 C
252 C
* * *
3829200 AATTTTGAAAATAGTTTACTAGGTAAGAAACTTTGGAAATTGCTTTATTACTGTTCAAAAATTTC
1 --------AAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTC
* *
3829265 ATTTTTTGAAAACATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCAAAAACATCATA
58 ATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTC-AAAACATCATA
* * *
3829330 TGAAAGCATCTTGCCC----G------A-A-GG-----A-G--TTATCATCTCGCTCGAAAGACT
122 TGAAAACATCATGCCCGAAGGTCTTATAGATGGCCCAAATGACTTATCATCTTGCTCGAAAGACT
* * * * * *
3829375 GACAGATGGCCCAAAGGATTTAATCATCTTACTTGAAAGACTTACTGATGGCCC-AAAGGACTTA
187 GACAGATGACCCGAAGAATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAA-GACTTA
3829439 -C
251 CC
* *
3829440 --------T-C-A-GTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCATTTTTTG
1 AAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTG
* * *
3829494 AAAACATGAAATGAGAAACTTTAAAAATTGCTTTTCTCATTTTTCACAAACATCATATGAAAACA
66 AAAATATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCA-AAACATCATATGAAAACA
3829559 TC
130 TC
3829561 TTGATGGTCG
Statistics
Matches: 775, Mismatches: 79, Indels: 64
0.84 0.09 0.07
Matches are distributed among these distances:
220 1 0.00
221 109 0.14
222 1 0.00
223 1 0.00
224 1 0.00
240 3 0.00
241 70 0.09
243 1 0.00
244 1 0.00
249 1 0.00
250 118 0.15
251 8 0.01
252 103 0.13
257 1 0.00
258 44 0.06
259 247 0.32
260 48 0.06
261 17 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (252 bp):
AAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTG
AAAATATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCAAAACATCATATGAAAACAT
CATGCCCGAAGGTCTTATAGATGGCCCAAATGACTTATCATCTTGCTCGAAAGACTGACAGATGA
CCCGAAGAATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTACC
Found at i:3829096 original size:259 final size:258
Alignment explanation
Indices: 3828382--3829350 Score: 1314
Period size: 259 Copynumber: 3.8 Consensus size: 258
3828372 AACCTAAAAG
* * * * *
3828382 ATTTAATCATCATGCTCGAAATACTTACTGATAGCCTGGAGGACTTA-CAATTTTGGAAATAGTT
1 ATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAAGACTTACCAATTTTGAAAATAGTT
* *
3828446 TACTAAGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATGTCATTTTCTGAAAATATT
66 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATT
* * *
3828511 AAATGAGAAACTTTGAAAATTGCTTTTCTTATTTTTCACAAACATCATATGAAAACATC-TTCCC
131 AAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTT--CAAA-ATCATGTGAAAACATCATGCCC
* * ** *
3828575 TGAAGGTCTTATAAATGGCCCGAATGACTTATCATCTCACTCGAAAGATTGACAGATGACCCGAA
193 -GAAGGTCTTATAGATGGCCCAAATGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAA
3828640 GA
257 GA
* * * *
3828642 ATTTAATCATCATGCTCGGAAGACTTACTAATGGCCCGAAATACTTACC---------AATAGTT
1 ATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAAGACTTACCAATTTTGAAAATAGTT
* * * *
3828698 TACTAGGTAAGAAACTTTGTAAATCGCTTTCTTTCTTTTCAAAAATTTTATTTTCTTAAAATATT
66 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATT
*
3828763 AAATGAGAAACTTTGAAAATTGCTTTTCTTATTTTTCGAAAATCATGTGAAAACATCATGCCCGA
131 AAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTC-AAAATCATGTGAAAACATCATGCCCGA
* **
3828828 AGGTCTTATAGATGGCCCAAATGACTTATCATCTTGCTCGAAAGACTGATAGATGACCCGAATT
195 AGGTCTTATAGATGGCCCAAATGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGA
* * *
3828892 ATTTAATCATCATGCTCGAAAGACTTATTGGTGGCCCGAAAGACTTACCAATTTTGAAAATAGTT
1 ATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAAGACTTACCAATTTTGAAAATAGTT
*
3828957 TACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTTCATTTTCTGAAAATAT
66 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTC-AAAAATTTCATTTTCTGAAAATAT
* *
3829022 TAAATGAGAAACTTTGAAAATT-TTTTTCTCATTTTTCAAAATTAATGTGAAAACATCATGCCCG
130 TAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCAAAA-TCATGTGAAAACATCATGCCCG
* * * * *
3829086 AAGGTCTTATAGATGACCCAAAGGACTTATCATCTTGCTCGAAAGACTAACAAATGACCCGAAGG
194 AAGGTCTTATAGATGGCCCAAATGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGA
* * * *
3829151 ATTTAATCATAATGTTCGAAAGACTTCCTGATAGCCCGAAGGACTTACCAATTTTGAAAATAGTT
1 ATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAAGACTTACCAATTTTGAAAATAGTT
* * * * *
3829216 TACTAGGTAAGAAACTTTGGAAATTGCTTTATTACTGTTCAAAAATTTCATTTTTTGAAAACATT
66 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATT
* * *
3829281 AAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCAAAAACATCATATGAAAGCATCTTGCCC
131 AAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTC--AAA-ATCATGTGAAAACATCATGCCC
3829346 GAAGG
193 GAAGG
3829351 AGTTATCATC
Statistics
Matches: 629, Mismatches: 62, Indels: 35
0.87 0.09 0.05
Matches are distributed among these distances:
250 118 0.19
251 7 0.01
252 102 0.16
258 48 0.08
259 244 0.39
260 83 0.13
261 26 0.04
262 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (258 bp):
ATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAAGACTTACCAATTTTGAAAATAGTT
TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATT
AAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCAAAATCATGTGAAAACATCATGCCCGAA
GGTCTTATAGATGGCCCAAATGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGA
Found at i:3832528 original size:17 final size:17
Alignment explanation
Indices: 3832506--3832555 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
3832496 AAATTATTCT
3832506 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
3832523 AACA-T--TA-ATACTCA
1 AACATTCATAGAAAC-CA
3832537 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
3832554 AA
1 AA
3832556 ACATAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 3 0.12
14 8 0.31
15 1 0.04
16 1 0.04
17 10 0.38
18 3 0.12
ACGTcount: A:0.54, C:0.22, G:0.04, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:3832576 original size:31 final size:31
Alignment explanation
Indices: 3832506--3832566 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
3832496 AAATTATTCT
* * *
3832506 AACATTCATAGAAACCAAACATTAATACTCA
1 AACATTCATAGAAACCAAACATAAACAATCA
3832537 AACATTCATAGAAACCAAAACATAAACAAT
1 AACATTCATAGAAACC-AAACATAAACAAT
3832567 AAATTTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.20
Consensus pattern (31 bp):
AACATTCATAGAAACCAAACATAAACAATCA
Found at i:3832886 original size:30 final size:30
Alignment explanation
Indices: 3832850--3832911 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
3832840 TTATTTTTTA
3832850 ATATATATATATATATAATATAATATATAT
1 ATATATATATATATATAATATAATATATAT
3832880 ATATATATATATATATAATATAATATATAT
1 ATATATATATATATATAATATAATATATAT
3832910 AT
1 AT
3832912 GGATGGATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
ATATATATATATATATAATATAATATATAT
Found at i:3832926 original size:30 final size:30
Alignment explanation
Indices: 3832862--3832926 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
3832852 ATATATATAT
* * *
3832862 ATATAATATAATATATATATATATATATAT
1 ATATAATATAATATATATATAGATAGATAG
* * *
3832892 ATATAATATAATATATATATGGATGGATGG
1 ATATAATATAATATATATATAGATAGATAG
3832922 ATATA
1 ATATA
3832927 TTAATGGGTG
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:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (30 bp):
ATATAATATAATATATATATAGATAGATAG
Found at i:3832927 original size:2 final size:2
Alignment explanation
Indices: 3832850--3832911 Score: 96
Period size: 2 Copynumber: 33.0 Consensus size: 2
3832840 TTATTTTTTA
3832850 AT AT AT AT AT AT AT AT A- AT AT A- 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
3832890 AT AT AT A- AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
3832912 GGATGGATGG
Statistics
Matches: 56, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
1 4 0.07
2 52 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3835036 original size:221 final size:226
Alignment explanation
Indices: 3834646--3835097 Score: 709
Period size: 221 Copynumber: 2.0 Consensus size: 226
3834636 TAATGTTGCG
*
3834646 CTCCTAATTCTTTTCGAAGTGAAGTGGCTCCTTTGCTTGGCCTCAGCACAGTTCATTGATATCTG
1 CTCCTAATCCTTTTCGAAGTGAAGTGGCTCCTTT-CTTGGCCT-AGCACAGTTCATTGATATCTG
* ** *
3834711 CACTCCGGTTGATTGTCAGTTTGCTCCTTTGATTTCAGGCTCGTCTTTGCGTCCTGTTTCTCTGC
64 CACTCCGGTTGATTGTCAGTTTGCTCCTTCGATTTCAGGCTCGTCTTTGCGTCCAATTTCTCTAC
*
3834776 TACTCCTTGTTTGGCTCTTCATTTTTCAAATCTGGTGAGATCGCTCCTTTACTGCTCTCGGTTGT
129 TACTCCTTGTTTGGCTCTTCATTTTTCAAATATGGTGAGATCGCTCCTTTACTGCTCTCGGTTGT
3834841 TTTGGCATACTGTTTTTCAATTTATGGTTACTA
194 TTTGGCATACTGTTTTTCAATTTATGGTTACTA
* * * *
3834874 CTCCTAATCCTTTTCGAAGTGAAGTGGCT-C-TT-TT-G-CT-TCACAGTTCGTTGATCTTTGCA
1 CTCCTAATCCTTTTCGAAGTGAAGTGGCTCCTTTCTTGGCCTAGCACAGTTCATTGATATCTGCA
* *
3834933 CTCCGGTTGATTGTCGGTTTGCTCCTTCGATTTTAGGCTGCGTCTTTGCGTCCAATTTCTCTACT
66 CTCCGGTTGATTGTCAGTTTGCTCCTTCGATTTCAGGCT-CGTCTTTGCGTCCAATTTCTCTACT
*
3834998 ACTCCTTGTTTGGCTCTTCGTTTTTCAAATATGGTGAGATCGCTCCTTTACTGCTCTCGGTTGTT
130 ACTCCTTGTTTGGCTCTTCATTTTTCAAATATGGTGAGATCGCTCCTTTACTGCTCTCGGTTGTT
*
3835063 TTGGCATACTGTTTTTTAATTTATGGTTACTA
195 TTGGCATACTGTTTTTCAATTTATGGTTACTA
3835095 CTC
1 CTC
3835098 TCCATTAATC
Statistics
Matches: 209, Mismatches: 14, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
220 54 0.26
221 119 0.57
222 2 0.01
223 1 0.00
224 2 0.01
226 2 0.01
227 1 0.00
228 28 0.13
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (226 bp):
CTCCTAATCCTTTTCGAAGTGAAGTGGCTCCTTTCTTGGCCTAGCACAGTTCATTGATATCTGCA
CTCCGGTTGATTGTCAGTTTGCTCCTTCGATTTCAGGCTCGTCTTTGCGTCCAATTTCTCTACTA
CTCCTTGTTTGGCTCTTCATTTTTCAAATATGGTGAGATCGCTCCTTTACTGCTCTCGGTTGTTT
TGGCATACTGTTTTTCAATTTATGGTTACTA
Found at i:3836312 original size:15 final size:15
Alignment explanation
Indices: 3836289--3836359 Score: 79
Period size: 15 Copynumber: 4.7 Consensus size: 15
3836279 ACCTCAAATT
*
3836289 CCTCGATTTTCTGCA
1 CCTCAATTTTCTGCA
*
3836304 CCTCAATTTTATGCA
1 CCTCAATTTTCTGCA
* *
3836319 ACTCAATTTTCTGTA
1 CCTCAATTTTCTGCA
* *
3836334 CCTTAATTTTATGCA
1 CCTCAATTTTCTGCA
*
3836349 CCTCAAATTTC
1 CCTCAATTTTC
3836360 CTACAACATG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.24, C:0.27, G:0.07, T:0.42
Consensus pattern (15 bp):
CCTCAATTTTCTGCA
Found at i:3836330 original size:30 final size:30
Alignment explanation
Indices: 3836294--3836359 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
3836284 AAATTCCTCG
3836294 ATTTTCTGCACCTCAATTTTATGCAACTCA
1 ATTTTCTGCACCTCAATTTTATGCAACTCA
* * *
3836324 ATTTTCTGTACCTTAATTTTATGCACCTCA
1 ATTTTCTGCACCTCAATTTTATGCAACTCA
*
3836354 AATTTC
1 ATTTTC
3836360 CTACAACATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
ATTTTCTGCACCTCAATTTTATGCAACTCA
Found at i:3836881 original size:22 final size:22
Alignment explanation
Indices: 3836853--3836904 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
3836843 TAATGTCAGT
3836853 TGCATGTTTACTGATGATGAAA
1 TGCATGTTTACTGATGATGAAA
*
3836875 TGCATGTTTACTTATGATGAAA
1 TGCATGTTTACTGATGATGAAA
3836897 TGCATGTT
1 TGCATGTT
3836905 AATAATTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (22 bp):
TGCATGTTTACTGATGATGAAA
Found at i:3838226 original size:18 final size:17
Alignment explanation
Indices: 3838185--3838228 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3838175 ACTAATTTAT
* *
3838185 CACCATCATCATTACCA
1 CACCTTCATCACTACCA
3838202 CATCCTTCATCACTACCA
1 CA-CCTTCATCACTACCA
3838220 CCACCTTCA
1 -CACCTTCA
3838229 CCATCATCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 19 0.83
19 2 0.09
ACGTcount: A:0.30, C:0.45, G:0.00, T:0.25
Consensus pattern (17 bp):
CACCTTCATCACTACCA
Found at i:3843937 original size:62 final size:62
Alignment explanation
Indices: 3843840--3843966 Score: 211
Period size: 62 Copynumber: 2.0 Consensus size: 62
3843830 GACTAACCTA
* *
3843840 AACTAAACTCATACACTCTATCATTCCATTTGTGAAGACTACGATCATCACTGAACATCTTC
1 AACTAAACTCATACACTCTATCATTCCATTTGTGAAGACTACGATAATCACCGAACATCTTC
*
3843902 AACTAAACTCAT-CGACTCTATCATTCCATTTGTGAAGACTACGATAATCACCGAACGTCTTC
1 AACTAAACTCATAC-ACTCTATCATTCCATTTGTGAAGACTACGATAATCACCGAACATCTTC
3843964 AAC
1 AAC
3843967 AGAAGTGTAG
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 1 0.02
62 60 0.98
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.29
Consensus pattern (62 bp):
AACTAAACTCATACACTCTATCATTCCATTTGTGAAGACTACGATAATCACCGAACATCTTC
Found at i:3853740 original size:21 final size:21
Alignment explanation
Indices: 3853714--3853753 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3853704 CCCCCTTTGA
*
3853714 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
3853735 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3853754 CTGGGGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:3862636 original size:19 final size:19
Alignment explanation
Indices: 3862598--3862636 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3862588 TACTTTTTTA
*
3862598 TTTTTATATAAATTTATTT
1 TTTTTATATAAATCTATTT
*
3862617 TTTTTAT-TAAATCTACTT
1 TTTTTATATAAATCTATTT
3862635 TT
1 TT
3862637 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTATATAAATCTATTT
Found at i:3863466 original size:2 final size:2
Alignment explanation
Indices: 3863459--3863504 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3863449 ATAAAATAAG
3863459 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
3863501 AT AT
1 AT AT
3863505 TGTAAATGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3865078 original size:7 final size:7
Alignment explanation
Indices: 3865056--3865211 Score: 89
Period size: 7 Copynumber: 22.4 Consensus size: 7
3865046 ATTTGTAATG
3865056 AACCCTA
1 AACCCTA
* *
3865063 AATCTTA
1 AACCCTA
3865070 AACCCTA
1 AACCCTA
3865077 AACCCTA
1 AACCCTA
* *
3865084 AGCCATA
1 AACCCTA
**
3865091 AATACTA
1 AACCCTA
3865098 AACCCTA
1 AACCCTA
*
3865105 AACTCTA
1 AACCCTA
*
3865112 ATCCCTA
1 AACCCTA
*
3865119 AATCCTA
1 AACCCTA
* *
3865126 AGCCATA
1 AACCCTA
*
3865133 AACACTA
1 AACCCTA
3865140 AACCCTA
1 AACCCTA
*
3865147 AGCCCTA
1 AACCCTA
*
3865154 AA-CCTT
1 AACCCTA
***
3865160 AATTTTA
1 AACCCTA
*
3865167 AACACTA
1 AACCCTA
* * *
3865174 AGCCATT
1 AACCCTA
* *
3865181 AGCACTA
1 AACCCTA
3865188 AACCCTA
1 AACCCTA
*
3865195 AAACCTA
1 AACCCTA
3865202 AACCCTA
1 AACCCTA
3865209 AAC
1 AAC
3865212 TCAGTTATAT
Statistics
Matches: 104, Mismatches: 44, Indels: 2
0.69 0.29 0.01
Matches are distributed among these distances:
6 5 0.05
7 99 0.95
ACGTcount: A:0.44, C:0.32, G:0.03, T:0.21
Consensus pattern (7 bp):
AACCCTA
Found at i:3865118 original size:42 final size:42
Alignment explanation
Indices: 3865056--3865147 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
3865046 ATTTGTAATG
*
3865056 AACCCTAAATCTTAAACCCTAAACCCTAAGCCATAAATACTA
1 AACCCTAAATCTTAAACCCTAAACCCTAAGCCATAAACACTA
* *
3865098 AACCCTAAA-CTCTAATCCCTAAATCCTAAGCCATAAACACTA
1 AACCCTAAATCT-TAAACCCTAAACCCTAAGCCATAAACACTA
3865140 AACCCTAA
1 AACCCTAA
3865148 GCCCTAAACC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 2 0.04
42 44 0.96
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.21
Consensus pattern (42 bp):
AACCCTAAATCTTAAACCCTAAACCCTAAGCCATAAACACTA
Found at i:3865148 original size:21 final size:21
Alignment explanation
Indices: 3865068--3865156 Score: 99
Period size: 21 Copynumber: 4.2 Consensus size: 21
3865058 CCCTAAATCT
*
3865068 TAAACCCTAAACCCTAAGCCA
1 TAAACACTAAACCCTAAGCCA
* *
3865089 TAAATACTAAACCCTAAACTC-
1 TAAACACTAAACCCTAAGC-CA
* * *
3865110 TAATCCCTAAATCCTAAGCCA
1 TAAACACTAAACCCTAAGCCA
*
3865131 TAAACACTAAACCCTAAGCCC
1 TAAACACTAAACCCTAAGCCA
3865152 TAAAC
1 TAAAC
3865157 CTTAATTTTA
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 1 0.02
21 52 0.96
22 1 0.02
ACGTcount: A:0.44, C:0.34, G:0.03, T:0.19
Consensus pattern (21 bp):
TAAACACTAAACCCTAAGCCA
Found at i:3866667 original size:23 final size:23
Alignment explanation
Indices: 3866641--3866711 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
3866631 TAACTCGTTT
3866641 TCGAGCTCAAAATCGAGCTTGAA
1 TCGAGCTCAAAATCGAGCTTGAA
*
3866664 TCGAG--C----TCGAGTTTGAA
1 TCGAGCTCAAAATCGAGCTTGAA
* *
3866681 TTGAGCTTAAAATCGAGCTTGAA
1 TCGAGCTCAAAATCGAGCTTGAA
3866704 TCGAGCTC
1 TCGAGCTC
3866712 GAGTTTGAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
17 14 0.39
21 1 0.03
23 21 0.58
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (23 bp):
TCGAGCTCAAAATCGAGCTTGAA
Found at i:3866679 original size:17 final size:17
Alignment explanation
Indices: 3866653--3866727 Score: 60
Period size: 17 Copynumber: 4.1 Consensus size: 17
3866643 GAGCTCAAAA
3866653 TCGAGCTTGAATCGAGC
1 TCGAGCTTGAATCGAGC
* *
3866670 TCGAGTTTGAATTGAGC
1 TCGAGCTTGAATCGAGC
3866687 TTAAAATCGAGCTTGAATCGAGC
1 ------TCGAGCTTGAATCGAGC
* *
3866710 TCGAGTTTGAATTGAGC
1 TCGAGCTTGAATCGAGC
3866727 T
1 T
3866728 TAAAATCGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
17 31 0.67
23 15 0.33
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (17 bp):
TCGAGCTTGAATCGAGC
Found at i:3866687 original size:40 final size:40
Alignment explanation
Indices: 3866643--3866748 Score: 194
Period size: 40 Copynumber: 2.6 Consensus size: 40
3866633 ACTCGTTTTC
*
3866643 GAGCTCAAAATCGAGCTTGAATCGAGCTCGAGTTTGAATT
1 GAGCTTAAAATCGAGCTTGAATCGAGCTCGAGTTTGAATT
3866683 GAGCTTAAAATCGAGCTTGAATCGAGCTCGAGTTTGAATT
1 GAGCTTAAAATCGAGCTTGAATCGAGCTCGAGTTTGAATT
*
3866723 GAGCTTAAAATCGAGTTTGAATCGAG
1 GAGCTTAAAATCGAGCTTGAATCGAG
3866749 TTTTGAGTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.28
Consensus pattern (40 bp):
GAGCTTAAAATCGAGCTTGAATCGAGCTCGAGTTTGAATT
Found at i:3866799 original size:16 final size:16
Alignment explanation
Indices: 3866778--3866809 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3866768 TCTTGATTTT
3866778 TTTTTGAATTCGAGTC
1 TTTTTGAATTCGAGTC
*
3866794 TTTTTGAGTTCGAGTC
1 TTTTTGAATTCGAGTC
3866810 GAGTTTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.22, T:0.50
Consensus pattern (16 bp):
TTTTTGAATTCGAGTC
Found at i:3869089 original size:195 final size:195
Alignment explanation
Indices: 3868747--3869136 Score: 593
Period size: 195 Copynumber: 2.0 Consensus size: 195
3868737 CGACAGGCTC
** * * * *
3868747 GGACGACATCGACGACGGTTTGGTTACAGAATACGAGGTCTTGTTCTTTCAAGACTTCTTTCGCG
1 GGACGACATCGACGACGGTACGGTTACAGAAGACGAGGTCCTATTCTTTCAAGACTTCTTTCACG
* * * * *
3868812 GTTTTTTTCGATGAAACGACGACGGTGAATAAGCTGCCGAGTTGGAGACCCATAACGGTGTCGTG
66 GTTTTTCTCGATAAAACGACGACGGTGAATAAGCTACCGAGTTGGAGACCCATAACGGGGCCGTG
* *
3868877 AACCTGAGCGAGCTTAGCCAATAATCTGTGGGGTTTATCGCCAAGATCGAAGAGGTTGCCGAAGA
131 AACCTAAGCGAGCTTAGCCAATAACCTGTGGGGTTTATCGCCAAGATCGAAGAGGTTGCCGAAGA
*
3868942 GGACGACATCGACGATGGTACGGTTACAGAAGACGAGGTCCTATTCTTTCAAGACTTCTTTCACG
1 GGACGACATCGACGACGGTACGGTTACAGAAGACGAGGTCCTATTCTTTCAAGACTTCTTTCACG
* *
3869007 GTTGTTTCT-GATAAAACGACGACGGTGAATAAGCTATCGAGTTGGAGACCCATAACGGGGCCTT
66 GTT-TTTCTCGATAAAACGACGACGGTGAATAAGCTACCGAGTTGGAGACCCATAACGGGGCCGT
* * *
3869071 GAACCTAAGCGTGCTTAGCCAATGACCTGTGGGGTTTATCGCCAAGATCGAAGAGGTTGTCGAAG
130 GAACCTAAGCGAGCTTAGCCAATAACCTGTGGGGTTTATCGCCAAGATCGAAGAGGTTGCCGAAG
3869136 A
195 A
3869137 TCGGCAGCCA
Statistics
Matches: 175, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
195 171 0.98
196 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (195 bp):
GGACGACATCGACGACGGTACGGTTACAGAAGACGAGGTCCTATTCTTTCAAGACTTCTTTCACG
GTTTTTCTCGATAAAACGACGACGGTGAATAAGCTACCGAGTTGGAGACCCATAACGGGGCCGTG
AACCTAAGCGAGCTTAGCCAATAACCTGTGGGGTTTATCGCCAAGATCGAAGAGGTTGCCGAAGA
Found at i:3870056 original size:55 final size:55
Alignment explanation
Indices: 3869972--3870079 Score: 135
Period size: 55 Copynumber: 2.0 Consensus size: 55
3869962 AAAAACTTAC
* * * * * **
3869972 GTGTAAATTCCACGTCAGCACATATTAGTGACGTGGACATGCCATGTCATCATTT
1 GTGTAAATTCCACATCAGCACAAAATAGTGACATGGAAATGCCACATCATCATTT
* *
3870027 GTGTAAATTTCACATCAGCATAAAATAGTGACATGGAAATGCCACATCATCAT
1 GTGTAAATTCCACATCAGCACAAAATAGTGACATGGAAATGCCACATCATCAT
3870080 CGATGACCAC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (55 bp):
GTGTAAATTCCACATCAGCACAAAATAGTGACATGGAAATGCCACATCATCATTT
Found at i:3873329 original size:37 final size:37
Alignment explanation
Indices: 3873276--3873380 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
3873266 CATTTTCGTC
3873276 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
3873313 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
3873350 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3873381 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:3873699 original size:24 final size:23
Alignment explanation
Indices: 3873656--3873701 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
3873646 CATGTAATAT
*
3873656 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
3873679 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
3873702 TAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:3873766 original size:2 final size:2
Alignment explanation
Indices: 3873759--3873784 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3873749 TTTATTAATT
3873759 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
3873785 CCTTTTTTAT
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:3873868 original size:21 final size:20
Alignment explanation
Indices: 3873844--3873914 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
3873834 ATTATTATTT
3873844 TATTTATTTGTT-TTATTTCTA
1 TATTTATTT-TTATT-TTTCTA
* * *
3873865 TATTTTTTTCTTCTTTTTCTT
1 TATTTATTT-TTATTTTTCTA
*
3873886 TA-TTATTTTTATTTTTTTA
1 TATTTATTTTTATTTTTCTA
3873905 TATTTATTTT
1 TATTTATTTT
3873915 ACTTACTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 10 0.24
20 12 0.29
21 17 0.41
22 2 0.05
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.77
Consensus pattern (20 bp):
TATTTATTTTTATTTTTCTA
Found at i:3878255 original size:183 final size:183
Alignment explanation
Indices: 3877947--3878483 Score: 959
Period size: 183 Copynumber: 2.9 Consensus size: 183
3877937 ATTAAATCCG
3877947 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
3878012 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
3878077 TTGTCAGGCCAAAGACTTTGTGATAAGATGAACCCTTCAGTGATTTATCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTATCCCTC
3878130 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* * *
3878195 ATAGATTATGTTCAAACTATGACACTGCTCGAACACTTGACAATTCGGTGTTTGCTCCACTGTTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* * *
3878260 TTGTTAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTATCCCTC
3878313 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
3878378 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
3878442 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
3878484 TAAACCTGAT
Statistics
Matches: 337, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
182 1 0.00
183 336 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTATCCCTC
Found at i:3879680 original size:36 final size:34
Alignment explanation
Indices: 3879640--3879753 Score: 86
Period size: 36 Copynumber: 3.2 Consensus size: 34
3879630 CACTCAAATT
3879640 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * * ** *
3879676 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACA-ATTTGTCTCACTTGAGAC
*
3879712 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
*
3879748 CGTTTT
1 TGTTTT
3879754 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 49 0.83
37 5 0.08
38 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:3879716 original size:72 final size:75
Alignment explanation
Indices: 3879624--3879798 Score: 218
Period size: 72 Copynumber: 2.4 Consensus size: 75
3879614 ATGCAGATGA
* * * *
3879624 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
3879686 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
3879696 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
3879761 AAGAAGGCAT
66 AAGAAGGCAT
**
3879771 TTCATTTCACTCAAGGCTGTTTTT-TTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
3879799 GAAGATTTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
71 1 0.01
72 50 0.56
73 11 0.12
74 1 0.01
75 8 0.09
76 19 0.21
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:3879833 original size:73 final size:72
Alignment explanation
Indices: 3879640--3879835 Score: 177
Period size: 72 Copynumber: 2.7 Consensus size: 72
3879630 CACTCAAATT
* * * * *
3879640 TGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTCGAAAGAAGATTTATTTC
1 TGTTTTTCTT-AAACA-AGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTC
*
3879703 ACTCAAGAT
64 ACTCAAGAC
* *
3879712 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TGTTTTTCTT-AAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAA-G-ATTT-ATT
*
3879777 TCACTCAAGGC
62 TCACTCAAGAC
* * * *
3879788 TGTTTTT-TT-AAGAAGATTTTATCTTGCTTGAGATAG-TTTCCCTCGAAA
1 TGTTTTTCTTAAACAAGA-TTTATCTCGCTTGAGACAGTTTTCACTCGAAA
3879836 CAGAAAATTT
Statistics
Matches: 106, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
71 1 0.01
72 37 0.35
73 27 0.25
74 16 0.15
75 6 0.06
76 19 0.18
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (72 bp):
TGTTTTTCTTAAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTCAC
TCAAGAC
Found at i:3879857 original size:39 final size:39
Alignment explanation
Indices: 3879814--3879949 Score: 103
Period size: 39 Copynumber: 3.2 Consensus size: 39
3879804 TTTTATCTTG
3879814 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * * *
3879853 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGATAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-C
*
3879905 C-TGAGATAGTTTCCCTCGAAACATAAAATTTTGTCTCC
1 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
3879943 CTTGAGA
1 CTTGAGA
3879950 CAATTTCTCT
Statistics
Matches: 74, Mismatches: 9, Indels: 28
0.67 0.08 0.25
Matches are distributed among these distances:
38 2 0.03
39 31 0.42
40 5 0.07
41 2 0.03
48 1 0.01
49 2 0.03
50 5 0.07
51 24 0.32
52 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (39 bp):
CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:3880038 original size:105 final size:104
Alignment explanation
Indices: 3879869--3880187 Score: 493
Period size: 105 Copynumber: 3.1 Consensus size: 104
3879859 ACAGTTTCTC
* *
3879869 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAT-AAAA
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAAC-TGAAAA
3879933 TTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACA
65 TTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACA
* *
3879973 TTGAAAACATTTCCATTGAAATGATTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACTGAAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACTGAAAA
3880038 TTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACA
65 TTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACA
* * *
3880078 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACTGAAAAT
* ** *
3880140 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACA
3880179 TTGAAAACA
1 TTGAAAACA
3880188 ATTTAACGAA
Statistics
Matches: 200, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
101 47 0.23
103 1 0.00
104 53 0.26
105 99 0.50
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACTGAAAAT
TTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACA
Found at i:3880134 original size:36 final size:36
Alignment explanation
Indices: 3880087--3880162 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
3880077 ATTGAAAACA
* * *
3880087 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
3880123 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
3880159 TTTC
1 TTTC
3880163 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:3880689 original size:100 final size:104
Alignment explanation
Indices: 3880362--3880782 Score: 582
Period size: 105 Copynumber: 4.0 Consensus size: 104
3880352 ATATCGTGAC
3880362 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-CCA
3880427 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
3880467 ATTCCAGACAACGCAAGTTCAACTTCAAGACGAAGGGACCGCTGCTTGTCAACAACAACCTCCCA
1 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA-CTTCCA
3880532 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
3880572 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCACTGCTTGTCAACAA-AA-TTTC-A
1 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAA
* *
3880634 T-TCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 TCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
3880672 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTT-CC
** *
3880737 GGT-TCCAGAGCCAATTTCAACTTCACAACGGAGGATATTGG
64 AATCT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
3880778 ACTCG
1 ACTCG
3880783 GAACAATGCT
Statistics
Matches: 283, Mismatches: 26, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
100 80 0.28
101 4 0.01
102 4 0.01
103 2 0.01
104 3 0.01
105 150 0.53
106 40 0.14
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (104 bp):
ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAA
TCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:3880694 original size:205 final size:211
Alignment explanation
Indices: 3880362--3880781 Score: 604
Period size: 205 Copynumber: 2.0 Consensus size: 211
3880352 ATATCGTGAC
* * *
3880362 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACACAAGTTCAACTCCACGACGAAGGGACCACTGCTTGTCAACAACAACTTCCCA
* *
3880427 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTT
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTT
3880492 CA-AGACGAAGGGACCGCTGCTTGTCAAC-AACAACCTCCCAA-TCTCAGAGCCAATTTCAACTT
131 CACA-ACGAAGGGACCGCTGCTTGTCAACAAACAACCTCCCAATTC-CAGAGCCAATTTCAACTT
3880554 CACAACGAAGGATATTGG
194 CACAACGAAGGATATTGG
* *
3880572 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCACTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACACAAGTTCAACTCCACGACGAAGGGACCACTGCTTGTCAACAACAACTTCCCA
* * *
3880633 AT-TCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTT
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTT
* * * ** **
3880697 CACAACGAATGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCA
131 CACAACGAAGGGACCGCTGCTTGTCAACAAACAACCTCCCAATTCCAGAGCCAATTTCAACTTCA
*
3880762 CAACGGAGGATATTGG
196 CAACGAAGGATATTGG
3880778 ACTC
1 ACTC
3880782 GGAACAATGC
Statistics
Matches: 189, Mismatches: 18, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
205 80 0.42
206 51 0.27
207 3 0.02
208 2 0.01
209 2 0.01
210 51 0.27
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (211 bp):
ACTCCAGACAACACAAGTTCAACTCCACGACGAAGGGACCACTGCTTGTCAACAACAACTTCCCA
ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTT
CACAACGAAGGGACCGCTGCTTGTCAACAAACAACCTCCCAATTCCAGAGCCAATTTCAACTTCA
CAACGAAGGATATTGG
Found at i:3881727 original size:23 final size:23
Alignment explanation
Indices: 3881701--3881765 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
3881691 TCATGTAATA
*
3881701 TTTTTACATTT-TATGTATTTT-T
1 TTTTTAC-TTTATATATATTTTAT
3881723 TTTTTACTTTAGTATATATTTTTAT
1 TTTTTACTTTA-TATATA-TTTTAT
**
3881748 TTTTTAGATTATATATAT
1 TTTTTACTTTATATATAT
3881766 AAATATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 3 0.08
22 7 0.19
23 6 0.17
24 10 0.28
25 10 0.28
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTTTACTTTATATATATTTTAT
Found at i:3881845 original size:36 final size:36
Alignment explanation
Indices: 3881761--3881871 Score: 116
Period size: 36 Copynumber: 3.0 Consensus size: 36
3881751 TTAGATTATA
* * * * *
3881761 TATATAAATATATTTTTTTTATTATCAGTTTTATTAATT
1 TATATATATATATTTCTTTT-TTA-C-TTTTTTTTATTT
3881800 TATATATATATATTTACTTTTTTA-TTTTTTTTATTT
1 TATATATATATATTT-CTTTTTTACTTTTTTTTATTT
*
3881836 TATATATATATATTTTTTTTTTACTTTTTTATTATT
1 TATATATATATATTTCTTTTTTACTTTTTT-TTATT
3881872 ATTTTATTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
35 7 0.11
36 30 0.48
37 5 0.08
39 17 0.27
40 4 0.06
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (36 bp):
TATATATATATATTTCTTTTTTACTTTTTTTTATTT
Found at i:3881865 original size:12 final size:11
Alignment explanation
Indices: 3881846--3881937 Score: 69
Period size: 13 Copynumber: 7.8 Consensus size: 11
3881836 TATATATATA
3881846 TATTTTTTTTT
1 TATTTTTTTTT
3881857 TACTTTTTTATTAT
1 TA-TTTTTT-TT-T
3881871 TATTTTATTTATT
1 TATTTT-TTT-TT
* *
3881884 TGTTTTATTTCTA
1 TATTTT-TTT-TT
*
3881897 TATTTTTTTCT
1 TATTTTTTTTT
*
3881908 T-CTTTTTTTT
1 TATTTTTTTTT
3881918 TATTTTTTTTT
1 TATTTTTTTTT
*
3881929 AATTTTTTT
1 TATTTTTTT
3881938 ATATTTATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
10 8 0.12
11 19 0.29
12 9 0.14
13 23 0.35
14 6 0.09
ACGTcount: A:0.14, C:0.04, G:0.01, T:0.80
Consensus pattern (11 bp):
TATTTTTTTTT
Found at i:3881876 original size:21 final size:22
Alignment explanation
Indices: 3881852--3881925 Score: 53
Period size: 24 Copynumber: 3.3 Consensus size: 22
3881842 TATATATTTT
3881852 TTTTTTACTT-TTTTATTATTA
1 TTTTTTACTTCTTTTATTATTA
* * *
3881873 TTTTATTTATTTGTTTTATTTCTATA
1 -TTT-TTTACTTCTTTTA-TTAT-TA
* *
3881899 TTTTTTTCTTCTTTT-TTTTTA
1 TTTTTTACTTCTTTTATTATTA
3881920 TTTTTT
1 TTTTTT
3881926 TTTAATTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
21 8 0.19
22 6 0.14
23 6 0.14
24 14 0.33
25 6 0.14
26 2 0.05
ACGTcount: A:0.14, C:0.05, G:0.01, T:0.80
Consensus pattern (22 bp):
TTTTTTACTTCTTTTATTATTA
Found at i:3881926 original size:21 final size:21
Alignment explanation
Indices: 3881895--3881948 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3881885 GTTTTATTTC
*
3881895 TATATTTTTTTCTT-CTTTTTT
1 TATATTTTTTT-TTAATTTTTT
*
3881916 TTTATTTTTTTTTAATTTTTT
1 TATATTTTTTTTTAATTTTTT
*
3881937 TATATTTATTTT
1 TATATTTTTTTT
3881949 ACTTACTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (21 bp):
TATATTTTTTTTTAATTTTTT
Found at i:3881944 original size:6 final size:5
Alignment explanation
Indices: 3881819--3881949 Score: 59
Period size: 5 Copynumber: 27.0 Consensus size: 5
3881809 ATATTTACTT
* *
3881819 TTTTA TTTT- TTTTA TTTTA TATATATA TATT- TTTT- TTTTA -CTT-
1 TTTTA TTTTA TTTTA TTTTA T-T-T-TA TTTTA TTTTA TTTTA TTTTA
* *
3881862 TTTTA TTATTA TTTTA -TTTA -TTTG TTTTA TTTCTA TATTT- TTTTC
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTT-TA T-TTTA TTTTA
* * *
3881907 TTCT- TTTT- TTTTA TTTTT TTTTA ATTT- TTTTA TATTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA
3881950 CTTACTATTT
Statistics
Matches: 99, Mismatches: 12, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
4 35 0.35
5 42 0.42
6 16 0.16
7 3 0.03
8 3 0.03
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:3885517 original size:131 final size:130
Alignment explanation
Indices: 3885175--3887397 Score: 2047
Period size: 130 Copynumber: 17.1 Consensus size: 130
3885165 AGTGATTTTT
* * * * * * * * *
3885175 GAAGATCAAATCTG-AAGAGAGATCTGCTCCGCTTCTCTTCAGGGTATATCAGATATGGAAACTT
1 GAAGATCAAATCTGAAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGTT
* * * * **
3885239 TGATTCACTTTACTTG-TTTTTAGGGAATG-TTGAATC-AGGGTTGATTCACTT-CACTGCTCTT
66 TGATTCACTTCAC-TGCTCTTCAGGGAA-GATTGAATCGA-GGTAGATT-TGTTCCACTGCTCTT
3885300 CAGG
127 CAGG
* * * * *
3885304 GAAGATCAAATCTGAAAAAAGGATTTGCTCCGCTGCAT-TTCAGGATAGATCGGAT-TTGGAAAG
1 GAAGATCAAATCTGAAAAAGGGATATGCTCTGCTGC-TCTTCAGGGTAGATCAGATCTT-GAAAG
* * * *
3885367 TTTGATTCACTTCATTGCTCTTCAGGGAAAATTGAATCGAGGTGGATTTGCTT-CATTGCTCTTC
64 TTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTG-TTCCACTGCTCTTC
*
3885431 AGA
128 AGG
* * * **
3885434 GAATATCAAATCTAGAAATAGGGACATGCTCTGCTGCTCTTCAATGTAGATCAGATCTTGAAAGT
1 GAAGATCAAATCT-GAAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGT
* * * * *
3885499 TTGATTCACTTCACTGCTCTTCAGAGAAGATTGAATCGAGGCAGATTTGTTCCACTGTTCCTCAT
65 TTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCTTCAG
3885564 G
130 G
* * * * * * **
3885565 GAAGATCAAATCTGAAAAAGGGATCTACTCCGCTGCTCTTGAGGGTAGATCACATCTAGAAACAT
1 GAAGATCAAATCTGAAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGTT
* * *
3885630 TGATTCACTTCACTGCTCTTCAGGGAAGATTGAATTGAGGTATATTTGCTT-CACTGCCCTTCAG
66 TGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTG-TTCCACTGCTCTTCAG
3885694 G
130 G
* * * ** * *
3885695 GAAGATTAAATATGAAAAAGGGGATATGGTCCACTGCTCTTCAAGGTAGATCAGATCCTGAAAGT
1 GAAGATCAAATCTGAAAAA-GGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGT
* * * *
3885760 TTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTTGTTGCACCGCTCCTCAG
65 TTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCTTCAG
3885825 G
130 G
* * * * * *
3885826 GAAGATCAAATCTGATAAAGGGATCTACTCCGCTACTCTTCATGGTAGATCAGATCTTGAAAGTT
1 GAAGATCAAATCTGAAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGTT
* * * ** * * * * *
3885891 TGATTCAATACACTGCTCTTTAGGGAAGATTGAATCGAGACAGATTTGTTACATTACTCCTCATG
66 TGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCTTCAGG
* * * * * **
3885956 GAAGATCAAATCTGAAAAAGAGATCTGCTCTACTGCTATTCAGGGTAGATCAGATCTAGAAACAT
1 GAAGATCAAATCTGAAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGTT
* * * * * *
3886021 TGATTCACTTTACTTCTCTTCAAGGAAGATTTAATCGAGGTAGATTTGCTT-CACCGCCCTTCAG
66 TGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTG-TTCCACTGCTCTTCAG
3886085 G
130 G
* * *
3886086 GAAGATCAAATCTGAAAAAGGG----G--AT-CTGCTCTTCAGGGTAGATTAGATATTGAAAGTT
1 GAAGATCAAATCTGAAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGTT
* * * * *
3886144 TGATTCACTTCACTACTCTTCAGGGAAGATTAAATCGAGGTAGATTTTTTCCACTACT-TCTCAA
66 TGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCT-TCAG
3886208 G
130 G
* * ** * * * *
3886209 GAATATCAAATCTGAAAAAAGGGATCTATTTTGTTGCTCTTCAGGGTTGATCAGATCTAGAAACG
1 GAAGATCAAATCTG-AAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAA-G
* ** * * *
3886274 -TTGATTTACTTTGCTGCTCTTTAGGGAAGGTTGAATCGAGGTATATTTGTTCCACTGCTCCTT-
64 TTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCT-CTTC
3886337 AGG
128 AGG
* * ** * * * **
3886340 GAAGATCAAATCTAAAAAAGGGATTTTATTCT-CTACTATTCAGGGTAGATCAGATCTAGAAACA
1 GAAGATCAAATCTGAAAAAGGGA-TATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGT
* * ** * *
3886404 TTGATTCACTTCACTGCTCTTGAGGGAAGATTGAATCTAGGTAGATTTGTTTTATTTCTCTTCAG
65 TTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCTTCAG
*
3886469 A
130 G
* * * * * ** * *
3886470 GAAGATCAAACCTAAAAAAGGGGATCTGCTCCGTTATTTTTCAGGGTAGATTAGATCTTGAAAGT
1 GAAGATCAAATCTGAAAAA-GGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGT
* * * * ** * *
3886535 TTGATCCACTTCACTGATCTTTAGGGAAGATTAAATCGAGACATATTTGTTCCACTGCTCCTCAG
65 TTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCTTCAG
3886600 G
130 G
* ** * ** * * *
3886601 GAAGATCAAGTCTGAAAAAATGATATGTTCCACTACTCTTCAGGGTAGATTAGATCTTGAAAATT
1 GAAGATCAAATCTGAAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGTT
*
3886666 TGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGCTT-CACTACTCTTCAG
66 TGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTG-TTCCACTGCTCTTCAG
3886730 G
130 G
*
3886731 GAAGATCAAATCTGAAAAAAGGGATATGCTCTGCTACTCTTCAGGGTAGATCAGATCTTGAAAGT
1 GAAGATCAAATCTG-AAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGT
* * * * * * * * *
3886796 TTAATTCACATCACTACTCTTTAGGGATGATTAAATCGAGGCAGATTTGTTCCACTACTCCTCAG
65 TTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCTTCAG
3886861 G
130 G
* * * * * *
3886862 GAAGATTAAATCT-AAAAACGAGATATGCATC-ACT-ATTTTCAGGGTAGATCATATCTTGAAAG
1 GAAGATCAAATCTGAAAAA-GGGATATGC-TCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAG
* * * * * *
3886924 TTTGATTTACTTCACTACTCTTCAGGGAAGATTGAATCGAGGCATATTTGTTCCACTACTCCTCA
64 TTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCTTCA
*
3886989 AG
129 GG
* * * * * * * * * * *
3886991 AAAGATAAAATATGAAAAAAAATGGATTTTCTCTACTGTTCTTCAAGGTAGGTCAGATCTAGAAA
1 GAAGATCAAATCTG---AAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAA
* * * * *
3887056 CG-TTGATTCACTTAACTTCTCTTCAGGGAAGATGGAATCGAGGTAGATTTGTTTCACT-TTCCT
63 -GTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCT-CT
3887119 TCAGG
126 TCAGG
* * * * * * *
3887124 GAATATCAAATTTAAAAAAGGGGATATGTTCTGTTGCTTTTCAGGGTAGATCAAATCTTGAAAGT
1 GAAGATCAAATCTGAAAAA-GGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGT
* * * *
3887189 TTGATTCACTTCACTGCTCTTCAAGGAAGATTGAATCGAGGAAGATTTGTTCCACTACTCCTCA-
65 TTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCTTCAG
*
3887253 T
130 G
* * * * * * *
3887254 GAAGATTAAATCTGAAAAAGGGATCTGCTTTACTGTTCTTCAGAGTATATCAGATCTTGAAAGTT
1 GAAGATCAAATCTGAAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGTT
* * ** ** *
3887319 TGATTCACTTTAATGCTCTTCAGTAAAGATTGAATCGAGGTAGATTTGCTT-CACTATTCTTCAT
66 TGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTG-TTCCACTGCTCTTCAG
3887383 G
130 G
3887384 GAAGATCAAATCTG
1 GAAGATCAAATCTG
3887398 GAGGAAAATT
Statistics
Matches: 1711, Mismatches: 332, Indels: 101
0.80 0.15 0.05
Matches are distributed among these distances:
122 3 0.00
123 91 0.05
124 9 0.01
126 1 0.00
129 207 0.12
130 688 0.40
131 607 0.35
132 14 0.01
133 90 0.05
134 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (130 bp):
GAAGATCAAATCTGAAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTTGAAAGTT
TGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCTTCAGG
Found at i:3885679 original size:261 final size:261
Alignment explanation
Indices: 3885290--3887397 Score: 2040
Period size: 261 Copynumber: 8.1 Consensus size: 261
3885280 TGATTCACTT
* * * * *
3885290 CACTGCTCTTCAGGGAAGATCAAATCTGAAAAAAGGATTTGCTCCGCTGCAT-TTCAGGATAGAT
1 CACTGCTCCTCAGGGAAGATCAAATCTGAAAAAGGGATATACTCCGCTGC-TCTTCAGGGTAGAT
* * * *
3885354 CGGAT-TTGGAAAGTTTGATTCACTTCATTGCTCTTCAGGGAAAATTGAATCGAGGTGGATTTGC
65 CAGATCTT-GAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTG-
* * * * * *
3885418 TT-CATTGCTCTTCAGAGAATATCAAATCTAGAAATAGGGA-CATGCTCTGCTGCTCTTCAATGT
128 TTCCACTACTCTTCAGAGAAGATCAAATCT-GAAAAAGGGATCATGCTCTACTGCTCTTCAAGGT
*
3885481 AGATCAGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGAGAAGATTGAATCGAGGCAGATT
192 AGATCAGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATT
3885546 TGTTC
257 TGTTC
* * * *
3885551 CACTGTTCCTCATGGAAGATCAAATCTGAAAAAGGGATCTACTCCGCTGCTCTTGAGGGTAGATC
1 CACTGCTCCTCAGGGAAGATCAAATCTGAAAAAGGGATATACTCCGCTGCTCTTCAGGGTAGATC
* * ** * *
3885616 ACATCTAGAAACATTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATTGAGGTATATTTGCTT
66 AGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTG-TT
* * * * * * *
3885681 -CACTGCCCTTCAGGGAAGATTAAATATGAAAAAGGGGAT-ATGGTCCACTGCTCTTCAAGGTAG
130 CCACTACTCTTCAGAGAAGATCAAATCTGAAAAA-GGGATCATGCTCTACTGCTCTTCAAGGTAG
*
3885744 ATCAGATCCTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTTG
194 ATCAGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTTG
*
3885809 TTG
259 TTC
* * * * *
3885812 CACCGCTCCTCAGGGAAGATCAAATCTGATAAAGGGATCTACTCCGCTACTCTTCATGGTAGATC
1 CACTGCTCCTCAGGGAAGATCAAATCTGAAAAAGGGATATACTCCGCTGCTCTTCAGGGTAGATC
* * * ** *
3885877 AGATCTTGAAAGTTTGATTCAATACACTGCTCTTTAGGGAAGATTGAATCGAGACAGATTTGTTA
66 AGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTC
* * * * *
3885942 CATTACTCCTCATG-GAAGATCAAATCTGAAAAAGAGATC-TGCTCTACTGCTATTCAGGGTAGA
131 CACTACTCTTCA-GAGAAGATCAAATCTGAAAAAGGGATCATGCTCTACTGCTCTTCAAGGTAGA
* ** * * * * *
3886005 TCAGATCTAGAAACATTGATTCACTTTACTTCTCTTCAAGGAAGATTTAATCGAGGTAGATTTGC
195 TCAGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTTG-
3886070 TT-
259 TTC
* *
3886072 CACCGC-CCTTCAGGGAAGATCAAATCTGAAAAAGGG---GA-T---CTGCTCTTCAGGGTAGAT
1 CACTGCTCC-TCAGGGAAGATCAAATCTGAAAAAGGGATATACTCCGCTGCTCTTCAGGGTAGAT
* * * * *
3886129 TAGATATTGAAAGTTTGATTCACTTCACTACTCTTCAGGGAAGATTAAATCGAGGTAGATTTTTT
65 CAGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTT
* * ** *
3886194 CCACTACT-TCTCA-AGGAATATCAAATCTGAAAAAAGGGATCTAT--TTTGTTGCTCTTCAGGG
130 CCACTACTCT-TCAGA-GAAGATCAAATCTG-AAAAAGGGATC-ATGCTCTACTGCTCTTCAAGG
* * * ** * * * *
3886255 TTGATCAGATCTAGAAACG-TTGATTTACTTTGCTGCTCTTTAGGGAAGGTTGAATCGAGGTATA
191 TAGATCAGATCTTGAAA-GTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGA
3886319 TTTGTTC
255 TTTGTTC
* * * * * * *
3886326 CACTGCTCCTTAGGGAAGATCAAATCTAAAAAAGGGATTTTA-TTCTCTACTATTCAGGGTAGAT
1 CACTGCTCCTCAGGGAAGATCAAATCTGAAAAAGGGA-TATACTCCGCTGCTCTTCAGGGTAGAT
* ** * *
3886390 CAGATCTAGAAACATTGATTCACTTCACTGCTCTTGAGGGAAGATTGAATCTAGGTAGATTTGTT
65 CAGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTT
** * * * * *** ** * *
3886455 TTATTTCTCTTCAGAGAAGATCAAACCTAAAAAAGGGGATC-TGCTCCGTTATTTTTCAGGGTAG
130 CCACTACTCTTCAGAGAAGATCAAATCTGAAAAA-GGGATCATGCTCTACTGCTCTTCAAGGTAG
* * * * * * *
3886519 ATTAGATCTTGAAAGTTTGATCCACTTCACTGATCTTTAGGGAAGATTAAATCGAGACATATTTG
194 ATCAGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTTG
3886584 TTC
259 TTC
* ** ** * * *
3886587 CACTGCTCCTCAGGGAAGATCAAGTCTGAAAAAATGATATGTTCCACTACTCTTCAGGGTAGATT
1 CACTGCTCCTCAGGGAAGATCAAATCTGAAAAAGGGATATACTCCGCTGCTCTTCAGGGTAGATC
*
3886652 AGATCTTGAAAATTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGCTT
66 AGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTG-TT
* * * *
3886717 -CACTACTCTTCAGGGAAGATCAAATCTGAAAAAAGGGAT-ATGCTCTGCTACTCTTCAGGGTAG
130 CCACTACTCTTCAGAGAAGATCAAATCTG-AAAAAGGGATCATGCTCTACTGCTCTTCAAGGTAG
* * * * * *
3886780 ATCAGATCTTGAAAGTTTAATTCACATCACTACTCTTTAGGGATGATTAAATCGAGGCAGATTTG
194 ATCAGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTTG
3886845 TTC
259 TTC
* * * * * * *
3886848 CACTACTCCTCAGGGAAGATTAAATCT-AAAAACGAGATATGCAT-CACT-ATTTTCAGGGTAGA
1 CACTGCTCCTCAGGGAAGATCAAATCTGAAAAA-GGGATATAC-TCCGCTGCTCTTCAGGGTAGA
* * * * *
3886910 TCATATCTTGAAAGTTTGATTTACTTCACTACTCTTCAGGGAAGATTGAATCGAGGCATATTTGT
64 TCAGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGT
* * * * * * *
3886975 TCCACTACTCCTCA-AGAAAGATAAAATATGAAAAAAAATGGAT-TTTCTCTACTGTTCTTCAAG
129 TCCACTACTCTTCAGAG-AAGATCAAATCTG---AAAAAGGGATCATGCTCTACTGCTCTTCAAG
* * * * * *
3887038 GTAGGTCAGATCTAGAAACG-TTGATTCACTTAACTTCTCTTCAGGGAAGATGGAATCGAGGTAG
190 GTAGATCAGATCTTGAAA-GTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGCAG
*
3887102 ATTTGTTT
254 ATTTGTTC
* * * * ** * * *
3887110 CACT-TTCCTTCAGGGAATATCAAATTTAAAAAAGGGGATATGTTCTGTTGCTTTTCAGGGTAGA
1 CACTGCTCC-TCAGGGAAGATCAAATCTGAAAAA-GGGATATACTCCGCTGCTCTTCAGGGTAGA
* * *
3887174 TCAAATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAAGGAAGATTGAATCGAGGAAGATTTGT
64 TCAGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGT
* * * * *
3887239 TCCACTACTCCTCA-TGAAGATTAAATCTGAAAAAGGGATC-TGCTTTACTGTTCTTC-AGAGTA
129 TCCACTACTCTTCAGAGAAGATCAAATCTGAAAAAGGGATCATGCTCTACTGCTCTTCAAG-GTA
* * * ** *
3887301 TATCAGATCTTGAAAGTTTGATTCACTTTAATGCTCTTCAGTAAAGATTGAATCGAGGTAGATTT
193 GATCAGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTT
3887366 GCTT-
258 G-TTC
** * *
3887370 CACTATTCTTCATGGAAGATCAAATCTG
1 CACTGCTCCTCAGGGAAGATCAAATCTG
3887398 GAGGAAAATT
Statistics
Matches: 1543, Mismatches: 253, Indels: 103
0.81 0.13 0.05
Matches are distributed among these distances:
253 95 0.06
254 110 0.07
255 2 0.00
256 2 0.00
257 1 0.00
258 2 0.00
259 9 0.01
260 323 0.21
261 773 0.50
262 114 0.07
263 25 0.02
264 87 0.06
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (261 bp):
CACTGCTCCTCAGGGAAGATCAAATCTGAAAAAGGGATATACTCCGCTGCTCTTCAGGGTAGATC
AGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTC
CACTACTCTTCAGAGAAGATCAAATCTGAAAAAGGGATCATGCTCTACTGCTCTTCAAGGTAGAT
CAGATCTTGAAAGTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTTGTT
C
Found at i:3886685 original size:45 final size:44
Alignment explanation
Indices: 3886509--3886696 Score: 129
Period size: 45 Copynumber: 4.3 Consensus size: 44
3886499 TCCGTTATTT
* * * *
3886509 TTCAGGGTAGATTAGATCTTGAAAGTTTGATCCACTTCACTGATC
1 TTCAGGGAAGATTAGATCTTGAAAATTTGAT-TACTTCACTGCTC
* * ** *
3886554 TTTAGGGAAGATTAAATCGAGACATATTTG-TT-C--CACTGCTC
1 TTCAGGGAAGATTAGATCTTGA-AAATTTGATTACTTCACTGCTC
* * ** * *
3886595 CTCAGGGAAGATCA-AGTC-TGAAAAAATGA-TATGTTCCACTACTC
1 TTCAGGGAAGATTAGA-TCTTGAAAATTTGATTA-CTT-CACTGCTC
*
3886639 TTCAGGGTAGATTAGATCTTGAAAATTTGATTCACTTCACTGCTC
1 TTCAGGGAAGATTAGATCTTGAAAATTTGATT-ACTTCACTGCTC
3886684 TTCAGGGAAGATT
1 TTCAGGGAAGATT
3886697 GAATCGAGGT
Statistics
Matches: 105, Mismatches: 26, Indels: 24
0.68 0.17 0.15
Matches are distributed among these distances:
39 5 0.05
40 3 0.03
41 20 0.19
43 1 0.01
44 20 0.19
45 47 0.45
46 8 0.08
47 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (44 bp):
TTCAGGGAAGATTAGATCTTGAAAATTTGATTACTTCACTGCTC
Found at i:3888717 original size:45 final size:45
Alignment explanation
Indices: 3888105--3888719 Score: 588
Period size: 45 Copynumber: 13.8 Consensus size: 45
3888095 GACATAATTA
* * * *
3888105 AAAAG-TTAACTCCTCTTC-CTTAGAAAGTCAAGAAAGACAACAAT
1 AAAAGATTGACTCCTCTTCAC-GAGAAAGTCAAGAAGGACAACACT
* * *
3888149 AAAAGATTGACTCCTCTTCGCGAG--A---AA-AATGACATCACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACT
* * * * **
3888188 AAAAGGTTGACTCATCTTCATGAGAAAGTCAAAAAATACAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACT
* ** *
3888233 AAAATATTCTCTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACT
* ** ** *
3888278 AAAAGATTGACTCCTCTTCGCGAGATGGTCCAA-AATAACATCACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGT-CAAGAAGGACAACACT
*
3888323 AAAAGATTAACTCCTCTTCACGAGAAAGTCAAGGAA-GACAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAA-GAAGGACAACACT
** * *
3888368 AAAAGATTGAGACCTCTTCACGAGAAAGTCAAGAAAGACATCACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACT
* * *
3888413 AAAAGATTAACTCCTCTTCGCAAGAAAGTCAAGAAGGACAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACT
* * *
3888458 AAAAGGTCGACTCCTCTTCACGAGAAAGTCAAGAAGGAAAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACT
* * * * *
3888503 AAAA-ATCGACTTCTCTTCACGAGAAAGTCAATAATGAAAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACT
* * * * *
3888547 GAAAGATTGACTCTTCTTCGCGAGAAAGTGAAGAAGGATAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACT
* * * ** * *
3888592 AAAATATTGACTTCTCTTCATGAGAAAGTCAA-ACATAACATCATT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA-AGGACAACACT
** *
3888637 AAAAGATTGACTCCTCTTCGTGAGAAATTCAAGAAGGACAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACT
** * *
3888682 AAAAGATCAACTTCTCTTTACGAGAAAGTCAAGAAGGA
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGA
3888720 TAAAAATGAA
Statistics
Matches: 463, Mismatches: 93, Indels: 29
0.79 0.16 0.05
Matches are distributed among these distances:
39 29 0.06
40 2 0.00
41 1 0.00
43 1 0.00
44 53 0.11
45 370 0.80
46 7 0.02
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (45 bp):
AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACT
Found at i:3888827 original size:38 final size:36
Alignment explanation
Indices: 3888712--3888828 Score: 117
Period size: 37 Copynumber: 3.1 Consensus size: 36
3888702 CGAGAAAGTC
* * * *
3888712 AAGAAGGATAAAAATGAATTTTTAAAGAAACTATCCT
1 AAGAAGGACAAGAATGAATTTCTAAGGAAAC-ATCCT
*
3888749 AAGAAGGACAAGAATGAATTTCTAGGGAAAGCATCCT
1 AAGAAGGACAAGAATGAATTTCTAAGGAAA-CATCCT
* * * *
3888786 AAGAAGGACTAGAGTGAGGTTTCTAAGGAAACAATCTT
1 AAGAAGGACAAGAATGA-ATTTCTAAGGAAAC-ATCCT
3888824 AAGAA
1 AAGAA
3888829 AAATAAAATG
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
37 46 0.69
38 21 0.31
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.22
Consensus pattern (36 bp):
AAGAAGGACAAGAATGAATTTCTAAGGAAACATCCT
Found at i:3889759 original size:19 final size:18
Alignment explanation
Indices: 3889735--3889806 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 18
3889725 ACTTGATTTG
3889735 TTCTCTTTCTTCTTCTTT
1 TTCTCTTTCTTCTTCTTT
3889753 CTTCTCTTT-TTC-TCTTT
1 -TTCTCTTTCTTCTTCTTT
* *
3889770 TTCTCTTATATTTTTCTTT
1 TTCTCTT-TCTTCTTCTTT
3889789 TTCT-TTTCATT-TTCTTT
1 TTCTCTTTC-TTCTTCTTT
3889806 T
1 T
3889807 CTTTTTTATC
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
16 7 0.15
17 14 0.30
18 9 0.19
19 17 0.36
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (18 bp):
TTCTCTTTCTTCTTCTTT
Found at i:3889767 original size:8 final size:9
Alignment explanation
Indices: 3889735--3889776 Score: 61
Period size: 8 Copynumber: 4.8 Consensus size: 9
3889725 ACTTGATTTG
3889735 TTCTCTTTC
1 TTCTCTTTC
3889744 TTCTTCTTTC
1 TTC-TCTTTC
3889754 TTCTCTTT-
1 TTCTCTTTC
3889762 TTCTCTTT-
1 TTCTCTTTC
3889770 TTCTCTT
1 TTCTCTT
3889777 ATATTTTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 15 0.47
9 8 0.25
10 9 0.28
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (9 bp):
TTCTCTTTC
Found at i:3889791 original size:6 final size:6
Alignment explanation
Indices: 3889738--3889834 Score: 51
Period size: 6 Copynumber: 15.8 Consensus size: 6
3889728 TGATTTGTTC
* * *
3889738 TCTTTCT TCTTCTT TCTTCTCT T-TTTC TCTTTT TCTCTTA TATTTT TCTTTT
1 TCTTT-T TCTT-TT TCTT-T-T TCTTTT TCTTTT TCT-TTT TCTTTT TCTTTT
* *
3889790 TC-TTT TCATTT TC-TTT TCTTTTT TATCTTT TC-TTT T-TTTT TCTTT
1 TCTTTT TCTTTT TCTTTT TC-TTTT TCT-TTT TCTTTT TCTTTT TCTTT
3889835 GTTTTTCTTG
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
5 19 0.26
6 25 0.35
7 25 0.35
8 3 0.04
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (6 bp):
TCTTTT
Found at i:3889795 original size:5 final size:5
Alignment explanation
Indices: 3889781--3889843 Score: 67
Period size: 5 Copynumber: 12.4 Consensus size: 5
3889771 TCTCTTATAT
* *
3889781 TTTTC TTTTTC TTTTC ATTTTC TTTTC TTTT- TTATC TTTTC TTTTT TTTTC
1 TTTTC -TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
3889832 TTTGT- TTTTC TT
1 TTT-TC TTTTC TT
3889844 GAATGTGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
4 4 0.08
5 34 0.69
6 11 0.22
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:3889818 original size:25 final size:23
Alignment explanation
Indices: 3889740--3889839 Score: 78
Period size: 24 Copynumber: 4.1 Consensus size: 23
3889730 ATTTGTTCTC
*
3889740 TTTCTTCTTC-TTTCTTCTCTTTT
1 TTTCTT-TTCTTTTCTTTTCTTTT
* * *
3889763 TCTCTTTTTCTCTTATATTTT-TCTT
1 TTTC-TTTTCT-TT-TCTTTTCTTTT
3889788 TTTCTTTTCATTTTCTTTTCTTTT
1 TTTCTTTTC-TTTTCTTTTCTTTT
*
3889812 TTATCTTTTCTTTTTTTTTCTTTGT
1 TT-TCTTTTCTTTTCTTTTCTTT-T
3889837 TTT
1 TTT
3889840 TCTTGAATGT
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
23 11 0.18
24 27 0.44
25 19 0.31
26 4 0.07
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.77
Consensus pattern (23 bp):
TTTCTTTTCTTTTCTTTTCTTTT
Found at i:3889820 original size:14 final size:14
Alignment explanation
Indices: 3889787--3889827 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
3889777 ATATTTTTCT
*
3889787 TTTTCTTTTCATTTTC
1 TTTTCTTTT--TTATC
3889803 TTTTCTTTTTTATC
1 TTTTCTTTTTTATC
3889817 TTTTCTTTTTT
1 TTTTCTTTTTT
3889828 TTTCTTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 15 0.62
16 9 0.38
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTCTTTTTTATC
Found at i:3889830 original size:10 final size:10
Alignment explanation
Indices: 3889740--3889843 Score: 64
Period size: 10 Copynumber: 9.6 Consensus size: 10
3889730 ATTTGTTCTC
* *
3889740 TTTCTTCTTC
1 TTTCTTTTTT
*
3889750 TTTCTTCTCTT
1 TTTCTT-TTTT
*
3889761 TTTCTCTTTT
1 TTTCTTTTTT
* *
3889771 TCTCTTATATT
1 TTTCTT-TTTT
3889782 TTTCTTTTTCT
1 TTTCTTTTT-T
3889793 TTTCATTTTCTT
1 TTTC-TTTT-TT
*
3889805 TTCTTTTTTATCT
1 TT-TCTTTT-T-T
3889818 TTTCTTTTTT
1 TTTCTTTTTT
*
3889828 TTTCTTTGTT
1 TTTCTTTTTT
3889838 TTTCTT
1 TTTCTT
3889844 GAATGTGAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
10 31 0.42
11 20 0.27
12 17 0.23
13 5 0.07
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.77
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:3889839 original size:14 final size:13
Alignment explanation
Indices: 3889780--3889840 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 13
3889770 TTCTCTTATA
*
3889780 TTTTTCTTTTTCT
1 TTTTTTTTTTTCT
3889793 TTTCATTTTCTTTTCT
1 TTT--TTTT-TTTTCT
*
3889809 TTTTTATCTTTTCT
1 TTTTT-TTTTTTCT
*
3889823 TTTTTTTTCTTTGT
1 TTTTTTTT-TTTCT
3889837 TTTT
1 TTTT
3889841 CTTGAATGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 5 0.13
14 21 0.54
15 4 0.10
16 9 0.23
ACGTcount: A:0.03, C:0.13, G:0.02, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTTTCT
Found at i:3889843 original size:25 final size:25
Alignment explanation
Indices: 3889786--3889843 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
3889776 TATATTTTTC
3889786 TTTTTCTTTTCATTTTCTTTTCTTT
1 TTTTTCTTTTCATTTTCTTTTCTTT
* *
3889811 TTTATCTTTTC-TTTTTTTTTCTTT
1 TTTTTCTTTTCATTTTCTTTTCTTT
3889835 GTTTTTCTT
1 -TTTTTCTT
3889844 GAATGTGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (25 bp):
TTTTTCTTTTCATTTTCTTTTCTTT
Found at i:3890322 original size:14 final size:14
Alignment explanation
Indices: 3890303--3890330 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3890293 CATGATATAA
3890303 TTATTTCAATCATT
1 TTATTTCAATCATT
3890317 TTATTTCAATCATT
1 TTATTTCAATCATT
3890331 CCCTTTATTT
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:0.14, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTTCAATCATT
Found at i:3893319 original size:2 final size:2
Alignment explanation
Indices: 3893312--3893339 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3893302 ATTAATGTGC
3893312 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
3893340 TATTGTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3893620 original size:18 final size:18
Alignment explanation
Indices: 3893597--3893649 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
3893587 AGGTATTATC
*
3893597 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGAAAT
* *
3893615 AGTGGTCCTGCGAGAAAT
1 AGTGGTCCTTCGGGAAAT
3893633 AGTGGTCCTTCGGGAAA
1 AGTGGTCCTTCGGGAAA
3893650 AAATTCAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGAAAT
Found at i:3903514 original size:15 final size:15
Alignment explanation
Indices: 3903491--3903523 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3903481 CGTAGGACTC
3903491 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
3903506 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
3903521 CTA
1 CTA
3903524 TTATACCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:3903702 original size:12 final size:12
Alignment explanation
Indices: 3903668--3903702 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3903658 TATCATGTTC
**
3903668 TCATATCACAGG
1 TCATATCACATA
3903680 TCATATCACATA
1 TCATATCACATA
3903692 TCATATCACAT
1 TCATATCACAT
3903703 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:3904208 original size:64 final size:64
Alignment explanation
Indices: 3904078--3904219 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 64
3904068 TGTTGGGATT
* * * *
3904078 CATCGATGCACTCCTTATGCATCGATGCACCGATTACATTCGATGTTTTACTATTAATGAGATG
1 CATCGATGCACTACTTATGCATCGATACACCGATTACATTCGATGCTTTACTATTAAAGAGATG
* * * *
3904142 CATCGATGCACTACTTATGCATCGATACA-TGAATTGCATTTGATGCCTTTA-TTTTAAA-AGAG
1 CATCGATGCACTACTTATGCATCGATACACCG-ATTACATTCGATG-CTTTACTATTAAAGAGA-
3904204 TG
63 TG
3904206 CATCGATGCACTAC
1 CATCGATGCACTAC
3904220 CAATGTATTG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 4 0.06
64 59 0.88
65 4 0.06
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (64 bp):
CATCGATGCACTACTTATGCATCGATACACCGATTACATTCGATGCTTTACTATTAAAGAGATG
Found at i:3908376 original size:18 final size:18
Alignment explanation
Indices: 3908353--3908405 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
3908343 AGGTATTATC
*
3908353 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGAAAT
* *
3908371 AGTGGTCCTGCGAGAAAT
1 AGTGGTCCTTCGGGAAAT
3908389 AGTGGTCCTTCGGGAAA
1 AGTGGTCCTTCGGGAAA
3908406 AAATTCAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGAAAT
Found at i:3908613 original size:2 final size:2
Alignment explanation
Indices: 3908563--3908595 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
3908553 TCATTCGTGC
3908563 AT AT CAT 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
3908596 GTTATAGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3909057 original size:20 final size:20
Alignment explanation
Indices: 3909034--3909092 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
3909024 GTTGGGGGTG
3909034 TTACATACAGTATCGATACC
1 TTACATACAGTATCGATACC
*
3909054 TTAC-T-CTTAGTATCTATACC
1 TTACATAC--AGTATCGATACC
*
3909074 -TCCATATCAGTATCGATAC
1 TTACATA-CAGTATCGATAC
3909093 TACTTCAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
18 1 0.03
19 3 0.10
20 26 0.84
22 1 0.03
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (20 bp):
TTACATACAGTATCGATACC
Found at i:3910256 original size:23 final size:22
Alignment explanation
Indices: 3910220--3910262 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3910210 ACAACACAAG
3910220 TGAAATAAAGCTTCATGATGGA
1 TGAAATAAAGCTTCATGATGGA
*
3910242 TGAAATTATAGCTTCATGATG
1 TGAAA-TAAAGCTTCATGATG
3910263 AAATTATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (22 bp):
TGAAATAAAGCTTCATGATGGA
Found at i:3910264 original size:19 final size:19
Alignment explanation
Indices: 3910240--3910276 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3910230 CTTCATGATG
3910240 GATGAAATTATAGCTTCAT
1 GATGAAATTATAGCTTCAT
*
3910259 GATGAAATTATATCTTCA
1 GATGAAATTATAGCTTCA
3910277 AAATAAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (19 bp):
GATGAAATTATAGCTTCAT
Found at i:3910675 original size:462 final size:462
Alignment explanation
Indices: 3909811--3910720 Score: 1775
Period size: 462 Copynumber: 2.0 Consensus size: 462
3909801 TTTCAATCTA
3909811 TTCAAAATAAACCACCAAATTTTAAATCCTTAAATTTTAATCACTGACCCAAAGTTTGGGGTATT
1 TTCAAAATAAACCACCAAATTTTAAATCCTTAAATTTTAATCACTGACCCAAAGTTTGGGGTATT
3909876 ACAGAGAAGGTAAAATTATGAACTTGGTGTCTCAAAAAAGGTAAGGGTATGACATTAGAGTATGA
66 ACAGAGAAGGTAAAATTATGAACTTGGTGTCTCAAAAAAGGTAAGGGTATGACATTAGAGTATGA
3909941 AATAGAGTTAATGTCAAGATAAAGAATCTAGTGATTGTACTTTTGGCTTTGGACGGGATACGAAA
131 AATAGAGTTAATGTCAAGATAAAGAATCTAGTGATTGTACTTTTGGCTTTGGACGGGATACGAAA
3910006 GGTCTAATCTTGTCACTTGCCAAAGATCTATAATTCTTGAAAAATTGAAAGAATCTTTAATTCAT
196 GGTCTAATCTTGTCACTTGCCAAAGATCTATAATTCTTGAAAAATTGAAAGAATCTTTAATTCAT
3910071 CAATATTCAAAGAAATTCAAGATTAAAACTTATTTCATTACTTATAACCCTAGAATAAGGTATGA
261 CAATATTCAAAGAAATTCAAGATTAAAACTTATTTCATTACTTATAACCCTAGAATAAGGTATGA
*
3910136 GTTCAATCACCAAACATTTTTACAAAATATTTAGGTAAATAAAGAAAGAAATAACAATAACAAAC
326 GTTCAATCACCAAACATTTTTACAAAATATTTAGGTAAATAAAGAAAGAAATAACAAAAACAAAC
3910201 TCAAATAAGACAACACAAGTGAAATAAAGCTTCATGATGGATGAAATTATAGCTTCATGATGAAA
391 TCAAATAAGACAACACAAGTGAAATAAAGCTTCATGATGGATGAAATTATAGCTTCATGATGAAA
3910266 TTATATC
456 TTATATC
3910273 TTCAAAATAAACCACCAAATTTTAAATCCTTAAATTTTAATCACTGACCCAAAGTTTGGGGTATT
1 TTCAAAATAAACCACCAAATTTTAAATCCTTAAATTTTAATCACTGACCCAAAGTTTGGGGTATT
* *
3910338 ACAGATAAGGTAAAATTATGAACTTGGTGTCTCAAAAGAGGTAAGGGTATGACATTAGAGTATGA
66 ACAGAGAAGGTAAAATTATGAACTTGGTGTCTCAAAAAAGGTAAGGGTATGACATTAGAGTATGA
3910403 AATAGAGTTAATGTCAAGATAAAGAATCTAGTGATTGTACTTTTGGCTTTGGACGGGATACGAAA
131 AATAGAGTTAATGTCAAGATAAAGAATCTAGTGATTGTACTTTTGGCTTTGGACGGGATACGAAA
3910468 GGTCTAATCTTGTCACTTGCCAAAGATCTATAATTCTTGAAAAATTGAAAGAATCTTTAATTCAT
196 GGTCTAATCTTGTCACTTGCCAAAGATCTATAATTCTTGAAAAATTGAAAGAATCTTTAATTCAT
3910533 CAATATTCAAAGAAATTCAAGATTAAAACTTATTTCATTACTTATAACCCTAGAATAAGGTATGA
261 CAATATTCAAAGAAATTCAAGATTAAAACTTATTTCATTACTTATAACCCTAGAATAAGGTATGA
*
3910598 GTTCAATCACCAAACATTTTTACAAAATATTTAGGTAAATAAAGAAAGAAATAACAAAAACAAGC
326 GTTCAATCACCAAACATTTTTACAAAATATTTAGGTAAATAAAGAAAGAAATAACAAAAACAAAC
*
3910663 TCAAATAAGACAACACAAGTGAAATAAAGCTTCATGATGGATGAAATTATATCTTCAT
391 TCAAATAAGACAACACAAGTGAAATAAAGCTTCATGATGGATGAAATTATAGCTTCAT
3910721 AATTAGGATG
Statistics
Matches: 443, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
462 443 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (462 bp):
TTCAAAATAAACCACCAAATTTTAAATCCTTAAATTTTAATCACTGACCCAAAGTTTGGGGTATT
ACAGAGAAGGTAAAATTATGAACTTGGTGTCTCAAAAAAGGTAAGGGTATGACATTAGAGTATGA
AATAGAGTTAATGTCAAGATAAAGAATCTAGTGATTGTACTTTTGGCTTTGGACGGGATACGAAA
GGTCTAATCTTGTCACTTGCCAAAGATCTATAATTCTTGAAAAATTGAAAGAATCTTTAATTCAT
CAATATTCAAAGAAATTCAAGATTAAAACTTATTTCATTACTTATAACCCTAGAATAAGGTATGA
GTTCAATCACCAAACATTTTTACAAAATATTTAGGTAAATAAAGAAAGAAATAACAAAAACAAAC
TCAAATAAGACAACACAAGTGAAATAAAGCTTCATGATGGATGAAATTATAGCTTCATGATGAAA
TTATATC
Found at i:3911729 original size:23 final size:23
Alignment explanation
Indices: 3911692--3911753 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
3911682 CAGCTCGTAT
3911692 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
* * * *
3911715 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACATAG
*
3911738 AAATGCACCAAAGTGC
1 AAATGCACCGAAGTGC
3911754 TATATAAGGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:3912791 original size:2 final size:2
Alignment explanation
Indices: 3912784--3912833 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3912774 TCTTATGTTC
3912784 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
3912826 AT AT AT AT
1 AT AT AT AT
3912834 CAATGGTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3916161 original size:2 final size:2
Alignment explanation
Indices: 3916154--3916211 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
3916144 ATTGTTTAAA
3916154 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
3916196 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3916212 TATTTTAATG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3918504 original size:2 final size:2
Alignment explanation
Indices: 3918499--3918572 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
3918489 CTGTTTTTGA
3918499 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
*
3918541 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3918573 GGTTTTGAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3918615 original size:24 final size:24
Alignment explanation
Indices: 3918569--3918616 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3918559 ATATATATAA
* *
3918569 ATATGGTTTTGAAAACACGTTTTT
1 ATATAGTTTTGAAAACACATTTTT
*
3918593 ATATAGTTTTGAAAACATATTTTT
1 ATATAGTTTTGAAAACACATTTTT
3918617 GAAAACATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (24 bp):
ATATAGTTTTGAAAACACATTTTT
Found at i:3918618 original size:14 final size:14
Alignment explanation
Indices: 3918599--3918626 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3918589 TTTTATATAG
3918599 TTTTGAAAACATAT
1 TTTTGAAAACATAT
3918613 TTTTGAAAACATAT
1 TTTTGAAAACATAT
3918627 ATAATATATA
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:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTTGAAAACATAT
Done.