Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007744.1 Hibiscus syriacus cultivar Beakdansim tig00110007_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: 4276731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 16
Found at i:3545678 original size:21 final size:21
Alignment explanation
Indices: 3545653--3545721 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 21
3545643 TTAATATACA
3545653 AATCAAATTTATTAATCTAAT
1 AATCAAATTTATTAATCTAAT
* * * *
3545674 GATC--ATAT-TTAATATAAA
1 AATCAAATTTATTAATCTAAT
3545692 AAT-AAATTTATTAATCTAAT
1 AATCAAATTTATTAATCTAAT
3545712 AATCATAATT
1 AATCA-AATT
3545722 AAATTTATTG
Statistics
Matches: 35, Mismatches: 8, Indels: 9
0.67 0.15 0.17
Matches are distributed among these distances:
18 10 0.29
19 6 0.17
20 11 0.31
21 4 0.11
22 4 0.11
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (21 bp):
AATCAAATTTATTAATCTAAT
Found at i:3545708 original size:38 final size:39
Alignment explanation
Indices: 3545614--3545723 Score: 159
Period size: 39 Copynumber: 2.8 Consensus size: 39
3545604 TAATGGTCAT
* * * *
3545614 AATCAGATTTTTTAATCTCATGATCATAATTAATATACA
1 AATCAAATTTATTAATCTAATGATCATAATTAATATAAA
*
3545653 AATCAAATTTATTAATCTAATGATCATATTTAATATAAA
1 AATCAAATTTATTAATCTAATGATCATAATTAATATAAA
*
3545692 AAT-AAATTTATTAATCTAATAATCATAATTAA
1 AATCAAATTTATTAATCTAATGATCATAATTAA
3545724 ATTTATTGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
38 27 0.42
39 37 0.58
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (39 bp):
AATCAAATTTATTAATCTAATGATCATAATTAATATAAA
Found at i:3545725 original size:27 final size:27
Alignment explanation
Indices: 3545694--3545750 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
3545684 AATATAAAAA
3545694 TAAATTTATTAATCTAATAATCATAAT
1 TAAATTTATTAATCTAATAATCATAAT
* * *
3545721 TAAATTTATTGATCTAATGATTATAAT
1 TAAATTTATTAATCTAATAATCATAAT
3545748 TAA
1 TAA
3545751 TAATTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (27 bp):
TAAATTTATTAATCTAATAATCATAAT
Found at i:3547193 original size:18 final size:18
Alignment explanation
Indices: 3547170--3547213 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
3547160 TTCATGCATC
3547170 TAGTTCATTTAA-TAAAG
1 TAGTTCATTTAATTAAAG
3547187 TTAGTTCA-TTAATTAAAG
1 -TAGTTCATTTAATTAAAG
3547205 TAGTTCATT
1 TAGTTCATT
3547214 CATCAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (18 bp):
TAGTTCATTTAATTAAAG
Found at i:3547208 original size:17 final size:17
Alignment explanation
Indices: 3547170--3547231 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
3547160 TTCATGCATC
3547170 TAGTTCATTTAA-TAAAG
1 TAGTTCA-TTAATTAAAG
3547187 TTAGTTCATTAATTAAAG
1 -TAGTTCATTAATTAAAG
* * *
3547205 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAG
3547222 TAGTT-ATTAA
1 TAGTTCATTAA
3547232 CTAACTCTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
16 4 0.10
17 23 0.59
18 12 0.31
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAG
Found at i:3557818 original size:20 final size:20
Alignment explanation
Indices: 3557793--3557831 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3557783 AATAAAAGGT
3557793 CTGGTTACAAATGATGTTTG
1 CTGGTTACAAATGATGTTTG
3557813 CTGGTTACAAATGATGTTT
1 CTGGTTACAAATGATGTTT
3557832 ACTTTCCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (20 bp):
CTGGTTACAAATGATGTTTG
Found at i:3559289 original size:21 final size:21
Alignment explanation
Indices: 3559250--3559289 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3559240 GAAACGAGAG
*
3559250 TTGAAAAAGACATTGAGAGCA
1 TTGAAAAAGACATTAAGAGCA
3559271 TTGAAAAGAGA-ATTAAGAG
1 TTGAAAA-AGACATTAAGAG
3559290 TGAAAGTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.50, C:0.05, G:0.25, T:0.20
Consensus pattern (21 bp):
TTGAAAAAGACATTAAGAGCA
Found at i:3560815 original size:17 final size:17
Alignment explanation
Indices: 3560776--3560821 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
3560766 ATTCATGCAT
3560776 CTAGTTCATTTAATAAAG
1 CTAGTTCA-TTAATAAAG
*
3560794 TTAGTTCATTAATTAAA-
1 CTAGTTCATTAA-TAAAG
3560811 CTAGTT-ATTAA
1 CTAGTTCATTAA
3560822 ACTAACTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 5 0.20
17 9 0.36
18 11 0.44
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (17 bp):
CTAGTTCATTAATAAAG
Found at i:3563256 original size:15 final size:16
Alignment explanation
Indices: 3563236--3563273 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3563226 TACTTTGATA
*
3563236 TCATTTCTT-TCCATT
1 TCATTTCTTATCAATT
3563251 TCATTTCTTATCAATT
1 TCATTTCTTATCAATT
3563267 TACATTT
1 T-CATTT
3563274 ATTTAATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 6 0.30
17 5 0.25
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (16 bp):
TCATTTCTTATCAATT
Found at i:3563497 original size:25 final size:24
Alignment explanation
Indices: 3563469--3563524 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
3563459 CAAGTTCTGC
3563469 AACAAAAAGAAAA-AGAAAGAAGAAA
1 AACAAAAAGAAAATA-AAAGAAG-AA
*
3563494 AACAAAAGGAAAATTAAAAGAAGAA
1 AACAAAAAGAAAA-TAAAAGAAGAA
3563519 AACAAA
1 AACAAA
3563525 TTCAAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 20 0.71
26 7 0.25
27 1 0.04
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.04
Consensus pattern (24 bp):
AACAAAAAGAAAATAAAAGAAGAA
Found at i:3572267 original size:15 final size:15
Alignment explanation
Indices: 3572232--3572260 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3572222 GTGCTTCAAC
3572232 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
3572246 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
3572261 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:3574546 original size:13 final size:13
Alignment explanation
Indices: 3574528--3574552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3574518 GATACTATCT
3574528 TTCCATCACCATA
1 TTCCATCACCATA
3574541 TTCCATCACCAT
1 TTCCATCACCAT
3574553 TCACGCCTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.32
Consensus pattern (13 bp):
TTCCATCACCATA
Found at i:3574755 original size:15 final size:16
Alignment explanation
Indices: 3574709--3574755 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
3574699 ACTTTGATAT
*
3574709 CATTTCTTTCCATTT-
1 CATTTCTTTCAATTTC
3574724 CATTTCTTATCAATTTC
1 CATTTCTT-TCAATTTC
3574741 CATTTCTTT-AATTTC
1 CATTTCTTTCAATTTC
3574756 TTATTTCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 14 0.48
16 7 0.24
17 8 0.28
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.57
Consensus pattern (16 bp):
CATTTCTTTCAATTTC
Found at i:3575697 original size:50 final size:51
Alignment explanation
Indices: 3575600--3575698 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 51
3575590 ATGAATCATC
* **
3575600 CTCCCTTTGGCCGAATGGTGATATGTTGGTTCATCTTGGTGCCAAAGTTAT
1 CTCCCTTTGGCCGAATGATGATATGTTGGTTCATCTTGGCACCAAAGTTAT
* * * *
3575651 CTCCC-TTGGCTGAATGATGTTGTGTTGGTTCATCTTGGCACTAAAGTT
1 CTCCCTTTGGCCGAATGATGATATGTTGGTTCATCTTGGCACCAAAGTT
3575699 TTCATGTGCA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
50 36 0.88
51 5 0.12
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.38
Consensus pattern (51 bp):
CTCCCTTTGGCCGAATGATGATATGTTGGTTCATCTTGGCACCAAAGTTAT
Found at i:3595750 original size:23 final size:25
Alignment explanation
Indices: 3595698--3595752 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
3595688 TTTATTTTCT
3595698 TTTTCTTCCTTTTTGAGTGCGTTCA
1 TTTTCTTCCTTTTTGAGTGCGTTCA
* * *
3595723 ATTTCTT-C-TTTTGAGTGCTTTGA
1 TTTTCTTCCTTTTTGAGTGCGTTCA
3595746 TTTTCTT
1 TTTTCTT
3595753 TGCTAGACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 19 0.73
24 1 0.04
25 6 0.23
ACGTcount: A:0.09, C:0.16, G:0.15, T:0.60
Consensus pattern (25 bp):
TTTTCTTCCTTTTTGAGTGCGTTCA
Found at i:3597952 original size:10 final size:10
Alignment explanation
Indices: 3597929--3597968 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
3597919 TTAAAATGAG
*
3597929 AAATATTTCGA
1 AAATATTT-TA
*
3597940 AAATGTTTTA
1 AAATATTTTA
3597950 AAATATTTTA
1 AAATATTTTA
3597960 AAATATTTT
1 AAATATTTT
3597969 TTTGAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 19 0.73
11 7 0.27
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (10 bp):
AAATATTTTA
Found at i:3598406 original size:15 final size:16
Alignment explanation
Indices: 3598381--3598410 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3598371 ATCTAAGCTT
3598381 CATTCTTCTTCTTGCC
1 CATTCTTCTTCTTGCC
3598397 CATT-TTCTTCTTGC
1 CATTCTTCTTCTTGC
3598411 TTTATTGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.33, G:0.07, T:0.53
Consensus pattern (16 bp):
CATTCTTCTTCTTGCC
Found at i:3599642 original size:159 final size:159
Alignment explanation
Indices: 3599353--3599670 Score: 636
Period size: 159 Copynumber: 2.0 Consensus size: 159
3599343 TGGAAGTGTG
3599353 TGATCATTACGAGCATGTATACCATGACATGTTGGTTATGAATTATGATCGGAAGAATGTGAATA
1 TGATCATTACGAGCATGTATACCATGACATGTTGGTTATGAATTATGATCGGAAGAATGTGAATA
3599418 TTTGCAAAGAATGAAGTGTATGATATGTACATTGATGTTACTAGTTTGATACATTACGTTCAAAG
66 TTTGCAAAGAATGAAGTGTATGATATGTACATTGATGTTACTAGTTTGATACATTACGTTCAAAG
3599483 TATGACAAAAATTGTTATATGCGTGTTGT
131 TATGACAAAAATTGTTATATGCGTGTTGT
3599512 TGATCATTACGAGCATGTATACCATGACATGTTGGTTATGAATTATGATCGGAAGAATGTGAATA
1 TGATCATTACGAGCATGTATACCATGACATGTTGGTTATGAATTATGATCGGAAGAATGTGAATA
3599577 TTTGCAAAGAATGAAGTGTATGATATGTACATTGATGTTACTAGTTTGATACATTACGTTCAAAG
66 TTTGCAAAGAATGAAGTGTATGATATGTACATTGATGTTACTAGTTTGATACATTACGTTCAAAG
3599642 TATGACAAAAATTGTTATATGCGTGTTGT
131 TATGACAAAAATTGTTATATGCGTGTTGT
3599671 GTTACCTTTT
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 159 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (159 bp):
TGATCATTACGAGCATGTATACCATGACATGTTGGTTATGAATTATGATCGGAAGAATGTGAATA
TTTGCAAAGAATGAAGTGTATGATATGTACATTGATGTTACTAGTTTGATACATTACGTTCAAAG
TATGACAAAAATTGTTATATGCGTGTTGT
Found at i:3601586 original size:75 final size:76
Alignment explanation
Indices: 3601433--3601587 Score: 217
Period size: 75 Copynumber: 2.1 Consensus size: 76
3601423 CTAATATAAT
* * *
3601433 GAAATGGTAATTCACAAACTTATTATGAATACCATGGATGTGCACATAGTGCAGAAAGTACACAA
1 GAAATGGTAATTCACAAACTCATTATAAATACCATGGATGCGCACATAGTGCAGAAAGTACACAA
* * *
3601498 AGTATTGATAC
66 AATACTGAAAC
3601509 GAAATGGTAATTCAC-AACTCATTATAAATACCATGGATGCGCACATA-TGTCA-AAAGTACACA
1 GAAATGGTAATTCACAAACTCATTATAAATACCATGGATGCGCACATAGTG-CAGAAAGTACACA
3601571 AAATACTGAAAAC
65 AAATACTG-AAAC
3601584 GAAA
1 GAAA
3601588 ATGCAACATA
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
74 18 0.25
75 38 0.54
76 15 0.21
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (76 bp):
GAAATGGTAATTCACAAACTCATTATAAATACCATGGATGCGCACATAGTGCAGAAAGTACACAA
AATACTGAAAC
Found at i:3613454 original size:27 final size:27
Alignment explanation
Indices: 3613404--3613456 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
3613394 GAGGGAAGAA
*
3613404 GAAGAAATAAAAATAAAGTGAAAAAGT
1 GAAGAAATAAAAACAAAGTGAAAAAGT
* *
3613431 GAAGAAGATAAGAACAAAGTAAAAAA
1 GAAGAA-ATAAAAACAAAGTGAAAAA
3613457 ATAGGGGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.68, C:0.02, G:0.19, T:0.11
Consensus pattern (27 bp):
GAAGAAATAAAAACAAAGTGAAAAAGT
Found at i:3617259 original size:41 final size:42
Alignment explanation
Indices: 3617187--3617270 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
3617177 TGTTCTCGTG
3617187 TTTTTGAAAGGAATCTCTGGGTCAGTAACTTTTTCCTCGTCT
1 TTTTTGAAAGGAATCTCTGGGTCAGTAACTTTTTCCTCGTCT
3617229 TTTTTGAAAGGAATCTCTGGGTCAGT-ACTTTTTCCTCGTCT
1 TTTTTGAAAGGAATCTCTGGGTCAGTAACTTTTTCCTCGTCT
3617270 T
1 T
3617271 GCCCCTACAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 16 0.38
42 26 0.62
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (42 bp):
TTTTTGAAAGGAATCTCTGGGTCAGTAACTTTTTCCTCGTCT
Found at i:3617371 original size:32 final size:31
Alignment explanation
Indices: 3617329--3617392 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 31
3617319 GTAAATTCTG
3617329 GTCCATCGGAGTCCTTTACAATTAGCAAAGT
1 GTCCATCGGAGTCCTTTACAATTAGCAAAGT
3617360 GTCCATTCGGAGTCCTTTACAATTAGCAAAGT
1 GTCCA-TCGGAGTCCTTTACAATTAGCAAAGT
3617392 G
1 G
3617393 ATATATTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 5 0.16
32 27 0.84
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (31 bp):
GTCCATCGGAGTCCTTTACAATTAGCAAAGT
Found at i:3618739 original size:24 final size:24
Alignment explanation
Indices: 3618711--3618759 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3618701 AACATAAAAT
* *
3618711 AATTGGATGAAACAAAAAAAATGA
1 AATTGAATAAAACAAAAAAAATGA
* *
3618735 AATTGAATAAAATAAAATAAATGA
1 AATTGAATAAAACAAAAAAAATGA
3618759 A
1 A
3618760 GATAAAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.20
Consensus pattern (24 bp):
AATTGAATAAAACAAAAAAAATGA
Found at i:3618961 original size:28 final size:29
Alignment explanation
Indices: 3618929--3619000 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
3618919 AAATAGTAAT
3618929 AATAATAATAAATGAAAA-TAAAT-ATACA
1 AATAATAATAAATGAAAAGT-AATCATACA
* * * *
3618957 TATAATATTAAATAAAAAGTAATCATAGA
1 AATAATAATAAATGAAAAGTAATCATACA
3618986 AATAA-AATAAATGAA
1 AATAATAATAAATGAA
3619001 GTAAGAATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
28 26 0.74
29 9 0.26
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (29 bp):
AATAATAATAAATGAAAAGTAATCATACA
Found at i:3619068 original size:2 final size:2
Alignment explanation
Indices: 3619061--3619119 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
3619051 TAATAGATAA
3619061 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
3619103 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
3619120 AAATAATATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3619719 original size:34 final size:36
Alignment explanation
Indices: 3619640--3619737 Score: 119
Period size: 34 Copynumber: 2.8 Consensus size: 36
3619630 ATGCTTGTGG
* * *
3619640 ATCATATCTTTGGGAGTTTGAATCATAATAGAACTCT
1 ATCATATTTTTAGGAGTTTGAATCCT-ATAGAACTCT
* *
3619677 ATCCTATTTTTAGGAGTTTGAATCCTA-A-AATTCT
1 ATCATATTTTTAGGAGTTTGAATCCTATAGAACTCT
*
3619711 ATCATATTTTTAAGAGTTTGAATCCTA
1 ATCATATTTTTAGGAGTTTGAATCCTA
3619738 GTAGGACGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 30 0.56
35 1 0.02
36 1 0.02
37 22 0.41
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (36 bp):
ATCATATTTTTAGGAGTTTGAATCCTATAGAACTCT
Found at i:3624237 original size:13 final size:12
Alignment explanation
Indices: 3624216--3624255 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
3624206 AAAATATTGT
3624216 TTAAGTTATTAAA
1 TTAA-TTATTAAA
3624229 TTAATTTATTAAA
1 TTAA-TTATTAAA
3624242 -TAATTATTAAA
1 TTAATTATTAAA
3624253 TTA
1 TTA
3624256 TATTGAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 8 0.32
12 5 0.20
13 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (12 bp):
TTAATTATTAAA
Found at i:3624349 original size:22 final size:20
Alignment explanation
Indices: 3624309--3624361 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
3624299 AATTTATTAA
3624309 ATTTTCATAATATTACAATGATT
1 ATTTT-ATAATATTACAAT-A-T
3624332 ATTTTATAATAATT-CAATAT
1 ATTTTATAAT-ATTACAATAT
*
3624352 ATTTGATAAT
1 ATTTTATAAT
3624362 TGATTTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 10 0.36
21 1 0.04
22 9 0.32
23 8 0.29
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (20 bp):
ATTTTATAATATTACAATAT
Found at i:3625461 original size:48 final size:50
Alignment explanation
Indices: 3625409--3625507 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
3625399 ATCCCTTTAG
*
3625409 GGGACAGAGAAAAA-C-AAAGAGAGAGAGAAGAGGAGG-AGGAGAAAAATA
1 GGGACAGAGAAAAAGCGAAAGAGAGAGA-AAGAAGAGGAAGGAGAAAAATA
3625457 GGGACAGAGAAAAAGCGAAAGAGAGAGAAAGAAGAGGAAGGAGAAAAATA
1 GGGACAGAGAAAAAGCGAAAGAGAGAGAAAGAAGAGGAAGGAGAAAAATA
3625507 G
1 G
3625508 TGATTATAGG
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
48 14 0.30
49 9 0.19
50 24 0.51
ACGTcount: A:0.57, C:0.04, G:0.37, T:0.02
Consensus pattern (50 bp):
GGGACAGAGAAAAAGCGAAAGAGAGAGAAAGAAGAGGAAGGAGAAAAATA
Found at i:3627487 original size:27 final size:27
Alignment explanation
Indices: 3627448--3627515 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
3627438 GTTTTCTATT
*
3627448 ATTTGGCATCATCAATAACACTTTTTGC
1 ATTT-GCATCATCAATAACACCTTTTGC
3627476 ATTTGCATCATCAATAACACCTTTTGC
1 ATTTGCATCATCAATAACACCTTTTGC
*
3627503 ATTTGCATTATCA
1 ATTTGCATCATCA
3627516 TAAAAATACA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 34 0.89
28 4 0.11
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (27 bp):
ATTTGCATCATCAATAACACCTTTTGC
Found at i:3629572 original size:15 final size:16
Alignment explanation
Indices: 3629552--3629591 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
3629542 CCTTTGATAA
3629552 CATTTCTTTCCA-TTT
1 CATTTCTTTCCACTTT
3629567 CATTTCTTAT-CACTTT
1 CATTTCTT-TCCACTTT
3629583 -ATTTCTTTC
1 CATTTCTTTC
3629592 ATAATTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 17 0.77
16 4 0.18
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.60
Consensus pattern (16 bp):
CATTTCTTTCCACTTT
Found at i:3632677 original size:15 final size:15
Alignment explanation
Indices: 3632657--3632696 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3632647 CCTTTGATAA
*
3632657 CATTTCTTTCCATTT
1 CATTTCTTTCCAATT
3632672 CATTTCTTAT-CAATT
1 CATTTCTT-TCCAATT
3632687 CATTTCTTTC
1 CATTTCTTTC
3632697 ATAATTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.57
Consensus pattern (15 bp):
CATTTCTTTCCAATT
Found at i:3636846 original size:30 final size:30
Alignment explanation
Indices: 3636795--3636853 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3636785 CTTAGCTTTA
**
3636795 TATTATGTTACATATGTTTTAGAT-TCATT
1 TATTATGTTACATATCATTTAGATATCATT
*
3636824 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATG-TTACATATCATTTAGATATCAT
3636854 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
30 14 0.56
31 4 0.16
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (30 bp):
TATTATGTTACATATCATTTAGATATCATT
Found at i:3640846 original size:15 final size:15
Alignment explanation
Indices: 3640826--3640861 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3640816 AGAAATTAAG
*
3640826 AAGAAAGGAAATGGT
1 AAGAAAGGAAATGGA
3640841 AAGAAAGGAAATGGA
1 AAGAAAGGAAATGGA
3640856 AAGAAA
1 AAGAAA
3640862 TGTTATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.31, T:0.08
Consensus pattern (15 bp):
AAGAAAGGAAATGGA
Found at i:3648748 original size:41 final size:41
Alignment explanation
Indices: 3648691--3648849 Score: 273
Period size: 41 Copynumber: 3.9 Consensus size: 41
3648681 GTGTGTCATC
3648691 TGTTTGTGAGCTGTATATGTCTTCCAAATGCTCCACTAAGT
1 TGTTTGTGAGCTGTATATGTCTTCCAAATGCTCCACTAAGT
*
3648732 TGTTTGTGAGCTGTATATGTCTTCCAAATGCTCCACTAAGC
1 TGTTTGTGAGCTGTATATGTCTTCCAAATGCTCCACTAAGT
* * *
3648773 TGTTTGTGAGTTGTATATGTCTTCTAAATACTCCACTAAGT
1 TGTTTGTGAGCTGTATATGTCTTCCAAATGCTCCACTAAGT
*
3648814 TGTTTGTGAACTGTATATGTCTTCCAAATGCTCCAC
1 TGTTTGTGAGCTGTATATGTCTTCCAAATGCTCCAC
3648850 CAAGCTATCC
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 109 1.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (41 bp):
TGTTTGTGAGCTGTATATGTCTTCCAAATGCTCCACTAAGT
Found at i:3660035 original size:91 final size:91
Alignment explanation
Indices: 3659875--3660121 Score: 325
Period size: 91 Copynumber: 2.7 Consensus size: 91
3659865 CCTAGAACAC
** * * * * * * *
3659875 CCATGTGCCTTGCATATGACCATCCCCTATGTTCCTTGCATGTGGATCATTTAGGTGCTAAGATG
1 CCATGTGTTTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATA
3659940 AAGAGTTCTCTCCCTATTCGACCAAG
66 AAGAGTTCTCTCCCTATTCGACCAAG
*
3659966 CCATGTGTTTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATA
1 CCATGTGTTTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATA
*
3660031 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGACCAAG
* * * * *
3660057 CCATGTGTTTTGCATGTGATCAGCCCCCCATGTGCCTTGTAT-ATGGTTCATTTAGGGGCCAAGA
1 CCATGTGTTTTGCATATGACCAG-CCCCCATGTGCCTTGCATGA-GGATCATTTAGGCGCCAAGA
3660121 T
64 T
3660122 GAATGGCCAT
Statistics
Matches: 137, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
91 102 0.74
92 35 0.26
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (91 bp):
CCATGTGTTTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATA
AAGAGTTCTCTCCCTATTCGACCAAG
Found at i:3666019 original size:26 final size:27
Alignment explanation
Indices: 3665986--3666036 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
3665976 TCCTAGAACA
*
3665986 CCCATGTGGCTTGCATAT-GATCAACC
1 CCCATGTGCCTTGCATATGGATCAACC
*
3666012 CCCATGTGCCTTGCATGTGGATCAA
1 CCCATGTGCCTTGCATATGGATCAA
3666037 AAGACATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (27 bp):
CCCATGTGCCTTGCATATGGATCAACC
Found at i:3678496 original size:8 final size:8
Alignment explanation
Indices: 3678485--3678509 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3678475 TCTTTTTCTT
3678485 TTCTTTTC
1 TTCTTTTC
3678493 TTCTTTTC
1 TTCTTTTC
3678501 TTCTTTTC
1 TTCTTTTC
3678509 T
1 T
3678510 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:3678505 original size:27 final size:26
Alignment explanation
Indices: 3678475--3678543 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
3678465 TTTAAACTTC
*
3678475 TCTTTTTCTTTTCTTTTCTTCTTTTC
1 TCTTTTTCTTTTCTTTTCTTCTTTTG
*
3678501 T-TCTTTTCTGATTT-TTCTCTTCTTTTG
1 TCT-TTTTCT--TTTCTTTTCTTCTTTTG
3678528 TCTTTTTC-TTTCTTTT
1 TCTTTTTCTTTTCTTTT
3678544 TGCACTCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
24 3 0.09
25 4 0.11
26 7 0.20
27 17 0.49
28 4 0.11
ACGTcount: A:0.01, C:0.20, G:0.03, T:0.75
Consensus pattern (26 bp):
TCTTTTTCTTTTCTTTTCTTCTTTTG
Found at i:3682112 original size:19 final size:21
Alignment explanation
Indices: 3682088--3682139 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3682078 CGGCCAAGAG
*
3682088 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
3682107 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
3682128 CATGTATTTTCA
1 CATGTATTTTCA
3682140 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:3687168 original size:29 final size:29
Alignment explanation
Indices: 3687136--3687194 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3687126 AAAGATGAAA
3687136 AGAATTCATCCTTGAATTGCTTTGAATAG
1 AGAATTCATCCTTGAATTGCTTTGAATAG
3687165 AGAATTCATCCTTGAATTGCTTTGAATAG
1 AGAATTCATCCTTGAATTGCTTTGAATAG
3687194 A
1 A
3687195 AGCATTAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (29 bp):
AGAATTCATCCTTGAATTGCTTTGAATAG
Found at i:3687653 original size:33 final size:35
Alignment explanation
Indices: 3687588--3687661 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 35
3687578 TAGTTTGATT
* *
3687588 AATGAAATAGTATTATTCAATGAACTAAATGCATG
1 AATGAAATAGTATTATTAAATGAACTAAATGCATA
* *
3687623 AATGAATTAGT-TTATTAAAT-AACTAGATGCATA
1 AATGAAATAGTATTATTAAATGAACTAAATGCATA
3687656 AATGAA
1 AATGAA
3687662 CTACTTCCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 17 0.49
34 8 0.23
35 10 0.29
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (35 bp):
AATGAAATAGTATTATTAAATGAACTAAATGCATA
Found at i:3689705 original size:20 final size:21
Alignment explanation
Indices: 3689682--3689722 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3689672 CCCCTCTTTA
3689682 AATATTT-TTTTATTT-TTTTT
1 AATATTTATTTT-TTTCTTTTT
3689702 AATATTTATTTTTTTCTTTTT
1 AATATTTATTTTTTTCTTTTT
3689723 TTACTAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (21 bp):
AATATTTATTTTTTTCTTTTT
Found at i:3690847 original size:29 final size:29
Alignment explanation
Indices: 3690815--3690873 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3690805 AAAGATTAAA
*
3690815 AGAATTCATCCTTGAATTGCTTTGAATAG
1 AGAATTCATCCTTGAATTACTTTGAATAG
3690844 AGAATTCATCCTTGAATTACTTTGAATAG
1 AGAATTCATCCTTGAATTACTTTGAATAG
3690873 A
1 A
3690874 AGCATTAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (29 bp):
AGAATTCATCCTTGAATTACTTTGAATAG
Found at i:3696623 original size:23 final size:24
Alignment explanation
Indices: 3696577--3696631 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
3696567 TCCATTGAAG
3696577 TTCCAAAGGTTGGAACATTTGGTA
1 TTCCAAAGGTTGGAACATTTGGTA
*
3696601 TTTCAAAGGTTGGAA-ATTTGGTA
1 TTCCAAAGGTTGGAACATTTGGTA
3696624 TTCCAAAG
1 TTCCAAAG
3696632 AATGTGCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.35
Consensus pattern (24 bp):
TTCCAAAGGTTGGAACATTTGGTA
Found at i:3700157 original size:5 final size:5
Alignment explanation
Indices: 3700143--3700177 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
3700133 CTATTTTTTT
* *
3700143 CAAAA AAAAA CAAAA CAAAA CAAAA AAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA
3700178 AAGCCAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:3700162 original size:10 final size:10
Alignment explanation
Indices: 3700143--3700179 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
3700133 CTATTTTTTT
3700143 CAAAAAAAAA
1 CAAAAAAAAA
*
3700153 CAAAACAAAA
1 CAAAAAAAAA
3700163 CAAAAAAAAA
1 CAAAAAAAAA
3700173 CAAAAAA
1 CAAAAAA
3700180 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:3710032 original size:41 final size:41
Alignment explanation
Indices: 3709984--3710151 Score: 248
Period size: 41 Copynumber: 4.1 Consensus size: 41
3709974 AGTGTGTCAT
3709984 CTGTTTGTGAGATGTATATGTCTTCCAAATGCTCCACTAAG
1 CTGTTTGTGAGATGTATATGTCTTCCAAATGCTCCACTAAG
* * *
3710025 CTATTTGTGAGCTGTATATGTCTTCCAAATGATCCACTAAG
1 CTGTTTGTGAGATGTATATGTCTTCCAAATGCTCCACTAAG
* *
3710066 CTGTTTGTGAGCTGTATATGTCTTCCAAATGCTCCAATAAG
1 CTGTTTGTGAGATGTATATGTCTTCCAAATGCTCCACTAAG
* * *
3710107 CTGTTTGTGA-ACCGTATATGTCTTCCAAATGCTCTACCAAG
1 CTGTTTGTGAGA-TGTATATGTCTTCCAAATGCTCCACTAAG
3710148 CTGT
1 CTGT
3710152 CCCCATGTGT
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
41 115 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.36
Consensus pattern (41 bp):
CTGTTTGTGAGATGTATATGTCTTCCAAATGCTCCACTAAG
Found at i:3716900 original size:19 final size:20
Alignment explanation
Indices: 3716876--3716915 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3716866 ATCCTTTTTT
3716876 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
3716895 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
3716915 T
1 T
3716916 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:3717206 original size:11 final size:10
Alignment explanation
Indices: 3717182--3717244 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
3717172 ATTGGAGTGC
*
3717182 AAAAAGAAAG
1 AAAAAGAAAA
*
3717192 AAAAAGACAA
1 AAAAAGAAAA
3717202 AAAAAGAAGAGA
1 AAAAAGAA-A-A
**
3717214 AAAATCAAAA
1 AAAAAGAAAA
*
3717224 AAGAAGAAAA
1 AAAAAGAAAA
*
3717234 GAAAAGAAAA
1 AAAAAGAAAA
3717244 A
1 A
3717245 GAATTCAAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
10 31 0.77
11 2 0.05
12 7 0.17
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:3717211 original size:19 final size:19
Alignment explanation
Indices: 3717182--3717247 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 19
3717172 ATTGGAGTGC
3717182 AAAAAGAAAGAAAAAGACAA
1 AAAAAG-AAGAAAAAGACAA
3717202 AAAAAGAAGAGAAAA-ATC-A
1 AAAAAGAAGA-AAAAGA-CAA
*
3717221 AAAAAGAAG-AAAAGAAAA
1 AAAAAGAAGAAAAAGACAA
3717239 GAAAAAGAA
1 -AAAAAGAA
3717248 TTCAAAAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
17 4 0.10
18 2 0.05
19 23 0.57
20 11 0.28
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.02
Consensus pattern (19 bp):
AAAAAGAAGAAAAAGACAA
Found at i:3717225 original size:22 final size:20
Alignment explanation
Indices: 3717182--3717238 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
3717172 ATTGGAGTGC
* *
3717182 AAAAAGAAAGAAAAAGACAA
1 AAAAAGAAAGAAAAACAAAA
3717202 AAAAAGAAGAGAAAAATCAAAA
1 AAAAAGAA-AGAAAAA-CAAAA
*
3717224 AAGAAGAAAAGAAAA
1 AAAAAG-AAAGAAAA
3717239 GAAAAAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 8 0.26
21 7 0.23
22 14 0.45
23 2 0.06
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAGAAAAACAAAA
Found at i:3720242 original size:35 final size:35
Alignment explanation
Indices: 3720174--3720256 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
3720164 AAAGGCCAAA
* *
3720174 TCCATCACCATTTTCACGCCTATAACATCACCATCT
1 TCCATCACCA-TTGCACGACTATAACATCACCATCT
* * *
3720210 TCCATTACCATTGCACGACTATATCATTACCATCT
1 TCCATCACCATTGCACGACTATAACATCACCATCT
*
3720245 TCTATCACCATT
1 TCCATCACCATT
3720257 TCACCCTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 31 0.77
36 9 0.22
ACGTcount: A:0.28, C:0.35, G:0.04, T:0.34
Consensus pattern (35 bp):
TCCATCACCATTGCACGACTATAACATCACCATCT
Found at i:3731364 original size:35 final size:36
Alignment explanation
Indices: 3731279--3731387 Score: 125
Period size: 35 Copynumber: 3.1 Consensus size: 36
3731269 TAAGATACTA
*
3731279 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTGCACG
* * *
3731314 CTTATAACATCACCATCTTTCATTACCA-TTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTGCACG
* * * *
3731349 CCTATATCATTACCATCTTCTATCACCATTT-CACA
1 CCTATAACATCACCATCTTCCATCACCATTTGCACG
3731384 CCTA
1 CCTA
3731388 AATAACCACC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
35 38 0.62
36 23 0.38
ACGTcount: A:0.28, C:0.36, G:0.03, T:0.33
Consensus pattern (36 bp):
CCTATAACATCACCATCTTCCATCACCATTTGCACG
Found at i:3733959 original size:19 final size:20
Alignment explanation
Indices: 3733906--3733951 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
3733896 CTTAATAAAG
*
3733906 TGAATAATAATATTATAAGTAA
1 TGAA-AATAA-ATAATAAGTAA
3733928 TGAAAATAAATAATAAG-AA
1 TGAAAATAAATAATAAGTAA
3733947 TGAAA
1 TGAAA
3733952 TGAAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 7 0.30
21 5 0.22
22 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (20 bp):
TGAAAATAAATAATAAGTAA
Found at i:3742554 original size:19 final size:21
Alignment explanation
Indices: 3742530--3742581 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3742520 CAGCCAAGAG
*
3742530 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
3742549 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
3742570 CATGTATTTTCA
1 CATGTATTTTCA
3742582 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:3746673 original size:19 final size:21
Alignment explanation
Indices: 3746649--3746700 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3746639 CAGCCAAGAG
*
3746649 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
3746668 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
3746689 CATGTATTTTCA
1 CATGTATTTTCA
3746701 AAGTGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:3750044 original size:22 final size:20
Alignment explanation
Indices: 3750019--3750077 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 20
3750009 GAACTTCTTT
3750019 TCTTCTTTTTTTCTGATTTTTC
1 TCTTCTTTTTTTCT--TTTTTC
*
3750041 TCTTC-TTTTATC-TTTTTC
1 TCTTCTTTTTTTCTTTTTTC
3750059 T-TTCTTTTTTTCTTCTTTT
1 TCTTCTTTTTTTCTT-TTTT
3750078 TGCACTCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 3 0.09
18 13 0.41
19 1 0.03
20 4 0.12
21 6 0.19
22 5 0.16
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (20 bp):
TCTTCTTTTTTTCTTTTTTC
Found at i:3752141 original size:19 final size:20
Alignment explanation
Indices: 3752117--3752165 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
3752107 TATCCTTTTT
3752117 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
3752136 TTATTTCT-TTTCATTACTTA
1 TTATTT-TATTTCATTACTTA
3752156 -TATTATTATT
1 TTATT-TTATT
3752166 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:3753734 original size:24 final size:21
Alignment explanation
Indices: 3753699--3753741 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
3753689 GGCACATTCT
*
3753699 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
3753722 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
3753742 GTCTTATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:3757994 original size:2 final size:2
Alignment explanation
Indices: 3757981--3758043 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
3757971 TGGCAGCGGA
*
3757981 AT AT AT AC 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
3758023 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
3758044 AGTTGGTGAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3765250 original size:8 final size:8
Alignment explanation
Indices: 3765237--3765281 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
3765227 ATATTTTTCT
3765237 TTTTCTTC
1 TTTTCTTC
3765245 TTTTCTTC
1 TTTTCTTC
3765253 TTTTCTTC
1 TTTTCTTC
3765261 TTTT-TGTC
1 TTTTCT-TC
3765269 TTTTCTTTC
1 TTTTC-TTC
3765278 TTTT
1 TTTT
3765282 TGCACTCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.03
8 26 0.76
9 6 0.18
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTCTTC
Found at i:3777006 original size:2 final size:2
Alignment explanation
Indices: 3776999--3777026 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3776989 TATAGGCATA
3776999 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
3777027 GAAAATAACT
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:3779951 original size:19 final size:20
Alignment explanation
Indices: 3779927--3779977 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3779917 CGGCCAAGAG
* *
3779927 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
3779946 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
3779966 CATGTATTTTCA
1 CATGTATTTTCA
3779978 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:3781788 original size:12 final size:13
Alignment explanation
Indices: 3781769--3781802 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3781759 TGAAATCTTT
*
3781769 TTCTTTTTTTTTC
1 TTCTTTTTTTTCC
3781782 TTCTTTTTTTTCC
1 TTCTTTTTTTTCC
3781795 TTCTTTTT
1 TTCTTTTT
3781803 GTCTTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTCTTTTTTTTCC
Found at i:3781798 original size:26 final size:27
Alignment explanation
Indices: 3781769--3781819 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
3781759 TGAAATCTTT
*
3781769 TTCTTTTT-TTTTCTTCTTT-TTTTTCC
1 TTCTTTTTGTCTT-TTCTTTCTTTTTCC
3781795 TTCTTTTTGTCTTTTCTTTCTTTTT
1 TTCTTTTTGTCTTTTCTTTCTTTTT
3781820 GCACTCCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (27 bp):
TTCTTTTTGTCTTTTCTTTCTTTTTCC
Found at i:3783842 original size:9 final size:9
Alignment explanation
Indices: 3783828--3783852 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3783818 CCCACCATGG
3783828 TCTTCATTT
1 TCTTCATTT
3783837 TCTTCATTT
1 TCTTCATTT
3783846 TCTTCAT
1 TCTTCAT
3783853 CTTGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (9 bp):
TCTTCATTT
Found at i:3785414 original size:15 final size:15
Alignment explanation
Indices: 3785378--3785407 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3785368 GTACTTCCAC
3785378 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
3785392 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
3785407 T
1 T
3785408 CTTTTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:3793576 original size:10 final size:10
Alignment explanation
Indices: 3793561--3793586 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3793551 ACTCAAAAAG
3793561 AAGAAAAGGA
1 AAGAAAAGGA
3793571 AAGAAAAGGA
1 AAGAAAAGGA
3793581 AAGAAA
1 AAGAAA
3793587 GAAAGTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
AAGAAAAGGA
Found at i:3798143 original size:13 final size:13
Alignment explanation
Indices: 3798127--3798169 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
3798117 AAGTGCTATA
3798127 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
* *
3798140 AAAAAATAAAAAC
1 AAAAAAGAAAAAG
*
3798153 AAAAGAG-AAAAG
1 AAAAAAGAAAAAG
3798165 AAAAA
1 AAAAA
3798170 GACTCTTACA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:3798156 original size:18 final size:18
Alignment explanation
Indices: 3798135--3798169 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3798125 TAAAAAAAGA
*
3798135 AAAAGAAAAAATAAAAAC
1 AAAAGAAAAAAGAAAAAC
*
3798153 AAAAGAGAAAAGAAAAA
1 AAAAGAAAAAAGAAAAA
3798170 GACTCTTACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.83, C:0.03, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAAAGAAAAAC
Found at i:3802052 original size:15 final size:15
Alignment explanation
Indices: 3802032--3802071 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3802022 CCTTTGATAA
*
3802032 CATTTCTTTCCATTT
1 CATTTCTTTCCAATT
3802047 CATTTCTTAT-CAATT
1 CATTTCTT-TCCAATT
3802062 CATTTCTTTC
1 CATTTCTTTC
3802072 ATAATATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.57
Consensus pattern (15 bp):
CATTTCTTTCCAATT
Found at i:3806775 original size:15 final size:15
Alignment explanation
Indices: 3806755--3806802 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
3806745 TACTTTGATA
3806755 TCATTTCTTTACATT
1 TCATTTCTTTACATT
3806770 TCATTTC-TTATCAATT
1 TCATTTCTTTA-C-ATT
3806786 TCCATTTCTTT-CATT
1 T-CATTTCTTTACATT
3806801 TC
1 TC
3806803 TTATTTCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 4 0.14
15 12 0.41
16 5 0.17
17 6 0.21
18 2 0.07
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (15 bp):
TCATTTCTTTACATT
Found at i:3807332 original size:17 final size:17
Alignment explanation
Indices: 3807307--3807339 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3807297 GTCCTACCTT
3807307 TACCATAACCATTTCTA
1 TACCATAACCATTTCTA
*
3807324 TACCCTAACCATTTCT
1 TACCATAACCATTTCT
3807340 TTTAGCCGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (17 bp):
TACCATAACCATTTCTA
Found at i:3810960 original size:134 final size:134
Alignment explanation
Indices: 3810720--3810989 Score: 540
Period size: 134 Copynumber: 2.0 Consensus size: 134
3810710 TATTCGGCCA
3810720 TGCCCCTCCATTTCCTATAAATAGGAAAGCATATCTCAATTGTATAAAGACCTTTTTGTTTAATT
1 TGCCCCTCCATTTCCTATAAATAGGAAAGCATATCTCAATTGTATAAAGACCTTTTTGTTTAATT
3810785 AAAGTGAGATTATTCTCTTCCTTAAGTCATGGTGACTTTTATCGACTTATCAAGTATAATTTATA
66 AAAGTGAGATTATTCTCTTCCTTAAGTCATGGTGACTTTTATCGACTTATCAAGTATAATTTATA
3810850 CTTG
131 CTTG
3810854 TGCCCCTCCATTTCCTATAAATAGGAAAGCATATCTCAATTGTATAAAGACCTTTTTGTTTAATT
1 TGCCCCTCCATTTCCTATAAATAGGAAAGCATATCTCAATTGTATAAAGACCTTTTTGTTTAATT
3810919 AAAGTGAGATTATTCTCTTCCTTAAGTCATGGTGACTTTTATCGACTTATCAAGTATAATTTATA
66 AAAGTGAGATTATTCTCTTCCTTAAGTCATGGTGACTTTTATCGACTTATCAAGTATAATTTATA
3810984 CTTG
131 CTTG
3810988 TG
1 TG
3810990 GCGTCAACCC
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 136 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (134 bp):
TGCCCCTCCATTTCCTATAAATAGGAAAGCATATCTCAATTGTATAAAGACCTTTTTGTTTAATT
AAAGTGAGATTATTCTCTTCCTTAAGTCATGGTGACTTTTATCGACTTATCAAGTATAATTTATA
CTTG
Found at i:3815085 original size:19 final size:21
Alignment explanation
Indices: 3815061--3815112 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3815051 CGGCCAAGAG
*
3815061 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
3815080 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
3815101 CATGTATTTTCA
1 CATGTATTTTCA
3815113 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:3815871 original size:21 final size:21
Alignment explanation
Indices: 3815845--3815884 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3815835 CAAAAAGAAA
3815845 AGAAAAGATA-AAAAGAAAATT
1 AGAAAAGA-AGAAAAGAAAATT
3815866 AGAAAAGAAGAAAAGAAAA
1 AGAAAAGAAGAAAAGAAAA
3815885 AGAAGTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.07
Consensus pattern (21 bp):
AGAAAAGAAGAAAAGAAAATT
Found at i:3819059 original size:19 final size:21
Alignment explanation
Indices: 3819035--3819080 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3819025 CGGCCAAGAG
3819035 CATGTAACTTCA-TT-AAAAT
1 CATGTAACTTCATTTAAAAAT
**
3819054 CATGTATTTTCATTTAAAAAT
1 CATGTAACTTCATTTAAAAAT
3819075 CATGTA
1 CATGTA
3819081 TTTTCAAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 2 0.09
21 11 0.48
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (21 bp):
CATGTAACTTCATTTAAAAAT
Found at i:3819838 original size:21 final size:22
Alignment explanation
Indices: 3819812--3819865 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
3819802 GGAGTGCAAA
3819812 AAGAAAAGAAAAGACA-AAAAG
1 AAGAAAAGAAAAGACAGAAAAG
***
3819833 AAGAAAA-AAAATTTAGAAAAG
1 AAGAAAAGAAAAGACAGAAAAG
3819854 AAGAAAAGAAAA
1 AAGAAAAGAAAA
3819866 AGAAGTTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 19 0.68
22 4 0.14
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.06
Consensus pattern (22 bp):
AAGAAAAGAAAAGACAGAAAAG
Found at i:3822689 original size:19 final size:21
Alignment explanation
Indices: 3822665--3822716 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3822655 CGGCCAAGAG
*
3822665 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
3822684 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
3822705 CATGTATTTTCA
1 CATGTATTTTCA
3822717 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:3827028 original size:14 final size:15
Alignment explanation
Indices: 3827002--3827046 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 15
3826992 ATTTGGAGTG
3827002 CAAAAGAAAGAAAAT
1 CAAAAGAAAGAAAAT
3827017 CAAAAG-AAGAAAAT
1 CAAAAGAAAGAAAAT
3827031 CAAAAGCAAAAGAAAA
1 CAAAAG--AAAGAAAA
3827047 GTGAAGCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 14 0.52
15 6 0.22
17 7 0.26
ACGTcount: A:0.73, C:0.09, G:0.13, T:0.04
Consensus pattern (15 bp):
CAAAAGAAAGAAAAT
Found at i:3836592 original size:10 final size:10
Alignment explanation
Indices: 3836577--3836601 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3836567 GAAATTTCAG
3836577 TTTTTTTGTT
1 TTTTTTTGTT
3836587 TTTTTTTGTT
1 TTTTTTTGTT
3836597 TTTTT
1 TTTTT
3836602 ATTTTGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:3838271 original size:77 final size:77
Alignment explanation
Indices: 3838134--3838276 Score: 173
Period size: 77 Copynumber: 1.9 Consensus size: 77
3838124 TATGACCAGA
* * * * * * *
3838134 CCCCATGTGCCTTACATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCTCTCTCTATTCGTCCA
1 CCCCATGTACCTTACATATGGATCATTTAGGCACCAAGATGAAGAGTCCTCTATCCATTCGGCCA
3838199 AGCCATGTCAGC
66 AGCCATGTCAGC
* *
3838211 CCCCATGTACCTTGCATATGGTTCATTTAGGCACCAAGATGAATG-G-CCATCTATCCATTCGGC
1 CCCCATGTACCTTACATATGGATCATTTAGGCACCAAGATGAA-GAGTCC-TCTATCCATTCGGC
3838274 CAA
64 CAA
3838277 ACACCATTAC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
76 1 0.02
77 53 0.96
78 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (77 bp):
CCCCATGTACCTTACATATGGATCATTTAGGCACCAAGATGAAGAGTCCTCTATCCATTCGGCCA
AGCCATGTCAGC
Found at i:3840337 original size:24 final size:21
Alignment explanation
Indices: 3840303--3840345 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
3840293 TGCACAAGAT
*
3840303 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
3840325 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
3840346 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:3845756 original size:8 final size:8
Alignment explanation
Indices: 3845745--3845794 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
3845735 TTTTGAAATA
3845745 TTTTTC-T
1 TTTTTCTT
3845752 TTTTT-TT
1 TTTTTCTT
*
3845759 TTCTTCTT
1 TTTTTCTT
*
3845767 TTCTTCTT
1 TTTTTCTT
*
3845775 TTTGTCTT
1 TTTTTCTT
3845783 TTCTTTCTT
1 TT-TTTCTT
3845792 TTT
1 TTT
3845795 GCACTCCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 10 0.28
8 19 0.53
9 7 0.19
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:3845759 original size:11 final size:11
Alignment explanation
Indices: 3845745--3845794 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
3845735 TTTTGAAATA
3845745 TTTTTCTTTTT
1 TTTTTCTTTTT
*
3845756 TTTTTCTTCTT
1 TTTTTCTTTTT
*
3845767 TTCTTCTTTTT
1 TTTTTCTTTTT
3845778 GTCTTTTCTTTCTT
1 -T-TTTTCTTT-TT
3845792 TTT
1 TTT
3845795 GCACTCCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 19 0.59
12 3 0.09
13 8 0.25
14 2 0.06
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:3845782 original size:16 final size:17
Alignment explanation
Indices: 3845763--3845795 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3845753 TTTTTTTTCT
3845763 TCTTTTC-TTCTTTTTG
1 TCTTTTCTTTCTTTTTG
3845779 TCTTTTCTTTCTTTTTG
1 TCTTTTCTTTCTTTTTG
3845796 CACTCCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (17 bp):
TCTTTTCTTTCTTTTTG
Found at i:3850161 original size:19 final size:20
Alignment explanation
Indices: 3850137--3850187 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3850127 CGGCCAAGAG
* *
3850137 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
3850156 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
3850176 CATGTATTTTCA
1 CATGTATTTTCA
3850188 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:3854356 original size:19 final size:20
Alignment explanation
Indices: 3854332--3854382 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3854322 CGGCCAAGAG
* *
3854332 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
3854351 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
3854371 CATGTATTTTCA
1 CATGTATTTTCA
3854383 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:3860943 original size:14 final size:14
Alignment explanation
Indices: 3860924--3860954 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3860914 AGGATTCAGC
3860924 CATGAAGATATATT
1 CATGAAGATATATT
*
3860938 CATGAAGATTTATT
1 CATGAAGATATATT
3860952 CAT
1 CAT
3860955 TAATTCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (14 bp):
CATGAAGATATATT
Found at i:3868184 original size:36 final size:36
Alignment explanation
Indices: 3868111--3868214 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
3868101 ATTTATAAGT
*
3868111 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
3868146 TGGTGATGATATAGGCGTGATAATGGTGATTGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
3868182 TGGTGTTGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
3868215 CAGATTGTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 20 0.32
36 43 0.68
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:3877958 original size:19 final size:20
Alignment explanation
Indices: 3877916--3877967 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
3877906 GAAACCCCTT
*
3877916 TGAAAATACATGATTTTTTGA
1 TGAAAATACATGA-TTTTTAA
3877937 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
3877956 TGAAGATACATG
1 TGAAAATACATG
3877968 CTCTTGGCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:3880416 original size:19 final size:19
Alignment explanation
Indices: 3880385--3880435 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3880375 AGGGGATAAT
3880385 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
3880404 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATGAAATGA
*
3880423 AATA-AAGAAATGA
1 AATATAAGTAATGA
3880436 TAGAGATGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.10
18 5 0.17
19 18 0.60
20 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.24
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:3880881 original size:19 final size:20
Alignment explanation
Indices: 3880839--3880890 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
3880829 GAAACCCCTT
*
3880839 TGAAAATACATGATTTTTTGA
1 TGAAAATACATGA-TTTTTAA
3880860 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
3880879 TGAAGATACATG
1 TGAAAATACATG
3880891 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:3881726 original size:30 final size:31
Alignment explanation
Indices: 3881687--3881746 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
3881677 ACATGCTGTC
**
3881687 ATGATATCTAAATGATACGAAAACATAATAA
1 ATGATATCTAAAACATACGAAAACATAATAA
* *
3881718 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATACGAAAACATAATA
3881747 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACATACGAAAACATAATAA
Found at i:3883634 original size:292 final size:292
Alignment explanation
Indices: 3883084--3883646 Score: 884
Period size: 293 Copynumber: 1.9 Consensus size: 292
3883074 GGCATTTGTA
*
3883084 CCTTAACAATTGATTGTGGATCTAGGAAGGAAGCAAACAACCTGTACAAGTGAATGGCTCAAAAA
1 CCTTAACAATTGATTGTGGATCTAGGAAGGAAGCAAACAACCTGCACAAGTGAATGGCTCAAAAA
3883149 GAGATGGTTAAGGGTGGTAAACGTATGGGTGAATAGGTAGGCTATTTAAATGAGAGATGGAAGCG
66 GAGATGGTTAAGGGTGGTAAACGTATGGGTGAATAGGTAGGCTATTTAAATGAGAGATGGAAGCG
* *
3883214 GAAGATGATTGAAATGGATATGGGTTATGGTTGACGAAACAAAGGGATGGTTGTGAGGATAGTAT
131 AAAGATGATTGAAATGGATATGGGTTATGGTTGACGAAACAAAGGGATGGTTATGAGGATAGTAT
* *
3883279 CTCATAGAAGACTCAAAGAAGAACTAATGCTATAGAGAGCAAAGACCCTGACTTTATATTGCTTC
196 CTCAAAGAAGACTCAAAGAAGAACTAATGCTATAGAAAGCAAAGACCCTGACTTTATATTGCTTC
3883344 TTTAAGGGGTGTGATATAAGGCTCTTCTGATG
261 TTTAAGGGGTGTGATATAAGGCTCTTCTGATG
*
3883376 CCTTAACAAATTGATTGTGGATCTAGGAAGGAAGCAAAATAACCTGCA-AAGTGAATGGCTCAAA
1 CCTTAAC-AATTGATTGTGGATCTAGGAAGGAAGC-AAACAACCTGCACAAGTGAATGGCTCAAA
* * *
3883440 ACAGAG-TGGTTAAGGGTGGTAAACGTATGGGTGATTAGGTGGGCTATTTAATTGAGAGATGGAA
64 A-AGAGATGGTTAAGGGTGGTAAACGTATGGGTGAATAGGTAGGCTATTTAAATGAGAGATGGAA
* * * * * * *
3883504 GCGAAAGATGGTTGATATGGCTAT-GGTTATGGTTTATGGAACAAAGGGATGGTTATGAGGATTG
128 GCGAAAGATGATTGAAATGGATATGGGTTATGGTTGACGAAACAAAGGGATGGTTATGAGGATAG
* *
3883568 TATCTTAAAGAAGACTCAAAGAAGAA-TCAATGCTATATAAAGCAAAGA-CCTAGACTTTATATT
193 TATCTCAAAGAAGACTCAAAGAAGAACT-AATGCTATAGAAAGCAAAGACCCT-GACTTTATATT
3883631 GCTTCTTTAAGGGGTG
256 GCTTCTTTAAGGGGTG
3883647 GTATGAAGTA
Statistics
Matches: 248, Mismatches: 18, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
291 4 0.02
292 111 0.45
293 119 0.48
294 14 0.06
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.27
Consensus pattern (292 bp):
CCTTAACAATTGATTGTGGATCTAGGAAGGAAGCAAACAACCTGCACAAGTGAATGGCTCAAAAA
GAGATGGTTAAGGGTGGTAAACGTATGGGTGAATAGGTAGGCTATTTAAATGAGAGATGGAAGCG
AAAGATGATTGAAATGGATATGGGTTATGGTTGACGAAACAAAGGGATGGTTATGAGGATAGTAT
CTCAAAGAAGACTCAAAGAAGAACTAATGCTATAGAAAGCAAAGACCCTGACTTTATATTGCTTC
TTTAAGGGGTGTGATATAAGGCTCTTCTGATG
Found at i:3889655 original size:418 final size:415
Alignment explanation
Indices: 3888855--3889656 Score: 1197
Period size: 418 Copynumber: 1.9 Consensus size: 415
3888845 TTAACAATTA
* *
3888855 ATTGTGGATCTGGGAAGGAAGCAAACAACCTGCACAAGTGAATGGCTCAAAAAGAGATGGTTAAG
1 ATTGTGGATCTAGGAAGGAAGCAAACAACCTGCACAAGTGAATGGCTCAAAAAGAGATGGATAAG
* * *
3888920 GGTGGTAAATATATGGGTGAATAGGTGGGCTATTTAAATGAGAGATTGAAGCGGAAGATGATTGA
66 GGTGGTAAACATATGGGTGAATAGGTAGGCTATTTAAATGAGAGATGGAAGCGGAAGATGATTGA
* *
3888985 AATGGCTATGGGTTATGGCTGATGAAACAAAGGGATGGTTGTGAGGATAGTATCTCAAAGAAGAC
131 AATGGCTATGGGTTATGGCTGATGAAACAAAAGGAAGGTTGTGAGGATAGTATCTCAAAGAAGAC
* * *
3889050 ACAAAGAAGAACCAATGCTTTAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTTAAGGGGTGG
196 ACAAAAAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTCAAGGGGTGG
*
3889115 TATTAAGTACTTTGACCCACTAGTTATATGAACTAGGAACCAGAAGTATCAAGGTAAAAAGAAAG
261 TATTAAGTACTTTGACCCACTAGTTATATGAACTAGGAACCAGAAGTATCAAGATAAAAAGAAAG
* * * *
3889180 GGGTTGATGTCACAAGTATAAAGTACTTGATAAGTTGATAAAAGTCACCAAGACTTAAGGTGATG
326 GGGTTGACGACACAAGTATAAAATACTTGATAAGTCGATAAAAGTCACCAAGACTTAAGGTGATG
3889245 TAAGCTAATTCTACCTTCTCGTTTG
391 TAAGCTAATTCTACCTTCTCGTTTG
*
3889270 ATTGTGGATCTAGGAATGAAGCAAAACAACCTGCACAAGTGAATGGCTCAAAACAGA-ATGGATA
1 ATTGTGGATCTAGGAAGGAAGC-AAACAACCTGCACAAGTGAATGGCTCAAAA-AGAGATGGATA
* * *
3889334 AGGGTGGTAAACGTATGGTTTAATAGGTAGGCTATTTAATAAATGAGAGATGGAAGCGGAAGATG
64 AGGGTGGTAAACATATGGGTGAATAGGTAGGCTA-TT--TAAATGAGAGATGGAAGCGGAAGATG
* **
3889399 ATTGAAATGGTTAT-GGTTATGGC-GATGAAACAAAAAGGAAGGTTGTGAGGATAGTATCTTGAA
126 ATTGAAATGGCTATGGGTTATGGCTGATGAAAC-AAAAGGAAGGTTGTGAGGATAGTATCTCAAA
* **
3889462 GAATG-CTCAAAAAAGAACCAATGCTATAGAGAGCAAAGACCCA-ATCTTTATATTTTTTCTTCA
190 GAA-GACACAAAAAAGAACCAATGCTATAGAGAGCAAAGACCCAGA-CTTTATATTGCTTCTTCA
* * *
3889525 AGGGGTGGTGTTAAGTATTTTGACCCACTAGTTATATGAACTAGGAACCAGAAGTATCAAGAT-T
253 AGGGGTGGTATTAAGTACTTTGACCCACTAGTTATATGAACTAGGAACCAGAAGTATCAAGATAA
3889589 AAAGAATA-GGGTTGACGACACAAGTATAAAATACTTGATAAGTCGATAAAAAGTCA-CAAGGAC
318 AAAGAA-AGGGGTTGACGACACAAGTATAAAATACTTGATAAGTCGAT-AAAAGTCACCAA-GAC
3889652 TTAAG
380 TTAAG
3889657 AAAGAGAATA
Statistics
Matches: 348, Mismatches: 28, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
415 20 0.06
416 65 0.19
417 58 0.17
418 166 0.48
419 39 0.11
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (415 bp):
ATTGTGGATCTAGGAAGGAAGCAAACAACCTGCACAAGTGAATGGCTCAAAAAGAGATGGATAAG
GGTGGTAAACATATGGGTGAATAGGTAGGCTATTTAAATGAGAGATGGAAGCGGAAGATGATTGA
AATGGCTATGGGTTATGGCTGATGAAACAAAAGGAAGGTTGTGAGGATAGTATCTCAAAGAAGAC
ACAAAAAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTCAAGGGGTGG
TATTAAGTACTTTGACCCACTAGTTATATGAACTAGGAACCAGAAGTATCAAGATAAAAAGAAAG
GGGTTGACGACACAAGTATAAAATACTTGATAAGTCGATAAAAGTCACCAAGACTTAAGGTGATG
TAAGCTAATTCTACCTTCTCGTTTG
Found at i:3893121 original size:23 final size:24
Alignment explanation
Indices: 3893078--3893130 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
3893068 TTTTTTTCTT
3893078 TTTCTTCTTTTCGAGTCCTTTCAA
1 TTTCTTCTTTTCGAGTCCTTTCAA
* * *
3893102 TTTCTTCTTTT-GAGTGCTTTGAT
1 TTTCTTCTTTTCGAGTCCTTTCAA
3893125 TTTCTT
1 TTTCTT
3893131 TGCTGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.09, C:0.19, G:0.11, T:0.60
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTCCTTTCAA
Found at i:3898727 original size:22 final size:22
Alignment explanation
Indices: 3898701--3898751 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
3898691 GATATCATTT
3898701 ATTTCCATTTCATTTC-TTATC-A
1 ATTTCCATTTC-TTTCATT-TCTA
3898723 ATTTCCATTTCTTTCATTTCTA
1 ATTTCCATTTCTTTCATTTCTA
3898745 ATTTCCA
1 ATTTCCA
3898752 ATTAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTCCATTTCTTTCATTTCTA
Found at i:3911532 original size:11 final size:10
Alignment explanation
Indices: 3911516--3911583 Score: 68
Period size: 10 Copynumber: 6.7 Consensus size: 10
3911506 CTTTATTGGC
*
3911516 TTTTTTTGGT
1 TTTTTTTTGT
3911526 TTTTTTTTGCCT
1 TTTTTTTTG--T
3911538 TTTTTATTT-T
1 TTTTT-TTTGT
**
3911548 TTTTTAAT-T
1 TTTTTTTTGT
3911557 TTTTTTTTGT
1 TTTTTTTTGT
3911567 TTTTTTTTGT
1 TTTTTTTTGT
3911577 TTTTTTT
1 TTTTTTT
3911584 GAAAAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
9 8 0.16
10 32 0.65
12 6 0.12
13 3 0.06
ACGTcount: A:0.04, C:0.03, G:0.07, T:0.85
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:3911560 original size:31 final size:31
Alignment explanation
Indices: 3911525--3911583 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3911515 CTTTTTTTGG
3911525 TTTTTTTTTGCCTTTTTTAT-TTTTTTTTAAT
1 TTTTTTTTTG-CTTTTTTATGTTTTTTTTAAT
* *
3911556 TTTTTTTTTGTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTGCTTTTTTATGTTTTTTTT
3911584 GAAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.05, C:0.03, G:0.05, T:0.86
Consensus pattern (31 bp):
TTTTTTTTTGCTTTTTTATGTTTTTTTTAAT
Found at i:3914764 original size:24 final size:23
Alignment explanation
Indices: 3914737--3914781 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3914727 TAGGTGTGCA
*
3914737 ATAGTAATGAAAGATGGTGATGTT
1 ATAGGAATGAAA-ATGGTGATGTT
**
3914761 ATAGGCGTGAAAATGGTGATG
1 ATAGGAATGAAAATGGTGATG
3914782 GAAGATGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.36, C:0.02, G:0.33, T:0.29
Consensus pattern (23 bp):
ATAGGAATGAAAATGGTGATGTT
Found at i:3914789 original size:36 final size:35
Alignment explanation
Indices: 3914690--3914800 Score: 107
Period size: 35 Copynumber: 3.2 Consensus size: 35
3914680 TTGGTGGTTA
* * * *
3914690 TATAGGCGTGAAATGGTGATAAAAGATGGTTAGGA
1 TATAGGCGTGAAATGGTGATGAAAGATGGTGATGT
* * * * *
3914725 AATAGGTGTGCAATAGTAATGAAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGAAAGATGGTGATGT
* *
3914760 TATAGGCGTGAAAATGGTGATGGAAGATGGTGTTGT
1 TATAGGCGTG-AAATGGTGATGAAAGATGGTGATGT
3914796 T-TAGG
1 TATAGG
3914801 TAGTATCTTA
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
35 38 0.64
36 21 0.36
ACGTcount: A:0.33, C:0.03, G:0.35, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGAAAGATGGTGATGT
Found at i:3922441 original size:17 final size:17
Alignment explanation
Indices: 3922420--3922466 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
3922410 AAAAGACAAA
3922420 AAAAAGAAAA-AAATTC
1 AAAAAGAAAAGAAATTC
3922436 AGAAAAGAAAAAGAAATTC
1 A-AAAAG-AAAAGAAATTC
3922455 AAAAAGAGAAAG
1 AAAAAGA-AAAG
3922467 CAAGCCAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 6 0.22
18 13 0.48
19 7 0.26
ACGTcount: A:0.72, C:0.04, G:0.15, T:0.09
Consensus pattern (17 bp):
AAAAAGAAAAGAAATTC
Found at i:3922466 original size:18 final size:18
Alignment explanation
Indices: 3922418--3922466 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
3922408 ATAAAAGACA
* *
3922418 AAAAAAAGAAAAAAATTC
1 AAAAAGAGAAAGAAATTC
*
3922436 AGAAAAGAAAAAGAAATTC
1 A-AAAAGAGAAAGAAATTC
3922455 AAAAAGAGAAAG
1 AAAAAGAGAAAG
3922467 CAAGCCAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.73, C:0.04, G:0.14, T:0.08
Consensus pattern (18 bp):
AAAAAGAGAAAGAAATTC
Found at i:3932091 original size:1 final size:1
Alignment explanation
Indices: 3932087--3932153 Score: 62
Period size: 1 Copynumber: 67.0 Consensus size: 1
3932077 AAATTTTGGC
* * *** ** *
3932087 TTTTTTATTTTTTTTTTTTATTTTTTTTTTTTTTTTTGCCTTTTTTTTTTGGTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3932152 TT
1 TT
3932154 GGAAGAAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.03, C:0.03, G:0.06, T:0.88
Consensus pattern (1 bp):
T
Found at i:3932110 original size:20 final size:19
Alignment explanation
Indices: 3932087--3932153 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 19
3932077 AAATTTTGGC
3932087 TTTTTTATTTTTTTTTTTTA
1 TTTTTT-TTTTTTTTTTTTA
**
3932107 TTTTTTTTTTTTTTTTTGCC
1 TTTTTTTTTTTTTTTTT-TA
*
3932127 TTTTTTTTTTGGTTTTTTTTG
1 TTTTTTTTTT--TTTTTTTTA
3932148 TTTTTT
1 TTTTTT
3932154 GGAAGAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 11 0.28
20 16 0.40
21 6 0.15
22 7 0.17
ACGTcount: A:0.03, C:0.03, G:0.06, T:0.88
Consensus pattern (19 bp):
TTTTTTTTTTTTTTTTTTA
Found at i:3932122 original size:31 final size:31
Alignment explanation
Indices: 3932087--3932153 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
3932077 AAATTTTGGC
** * *
3932087 TTTTTTATTTTTTTTTTTTATTTTTTTTTTT
1 TTTTTTACCTTTTTTTTTTAGTTTTTTTTGT
* *
3932118 TTTTTTGCCTTTTTTTTTTGGTTTTTTTTGT
1 TTTTTTACCTTTTTTTTTTAGTTTTTTTTGT
3932149 TTTTT
1 TTTTT
3932154 GGAAGAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.03, C:0.03, G:0.06, T:0.88
Consensus pattern (31 bp):
TTTTTTACCTTTTTTTTTTAGTTTTTTTTGT
Found at i:3935120 original size:36 final size:35
Alignment explanation
Indices: 3935022--3935131 Score: 123
Period size: 35 Copynumber: 3.1 Consensus size: 35
3935012 TTGTGGTTAC
* ** * * *
3935022 ATAGGCGTGAAATGGTGATAAAAGATGGTTAGGAT
1 ATAGGCATGAAATGGTGATGGAAGATGGTGATGTT
* * *
3935057 ATAGGCATGCAATAGTAATGGAAGATGGTGATGTT
1 ATAGGCATGAAATGGTGATGGAAGATGGTGATGTT
3935092 ATAGGCATGAAAATGGTGATGGAAGATGGTGATGTT
1 ATAGGCATG-AAATGGTGATGGAAGATGGTGATGTT
3935128 -TAGG
1 ATAGG
3935132 TAGTATCTTA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
35 39 0.63
36 23 0.37
ACGTcount: A:0.35, C:0.04, G:0.35, T:0.27
Consensus pattern (35 bp):
ATAGGCATGAAATGGTGATGGAAGATGGTGATGTT
Found at i:3938189 original size:123 final size:123
Alignment explanation
Indices: 3937970--3938215 Score: 492
Period size: 123 Copynumber: 2.0 Consensus size: 123
3937960 TTCTGTCGAA
3937970 TTGCCACGGTCTTCCCAAAAGTATATGTCCAGTATCCATTGGTACAACATCACAAAGGACTTCAT
1 TTGCCACGGTCTTCCCAAAAGTATATGTCCAGTATCCATTGGTACAACATCACAAAGGACTTCAT
3938035 CTTGATATTTGCCAATTGAAAATGGAATGACAACTTGCTTTGTGATCCTTACTTCTCC
66 CTTGATATTTGCCAATTGAAAATGGAATGACAACTTGCTTTGTGATCCTTACTTCTCC
3938093 TTGCCACGGTCTTCCCAAAAGTATATGTCCAGTATCCATTGGTACAACATCACAAAGGACTTCAT
1 TTGCCACGGTCTTCCCAAAAGTATATGTCCAGTATCCATTGGTACAACATCACAAAGGACTTCAT
3938158 CTTGATATTTGCCAATTGAAAATGGAATGACAACTTGCTTTGTGATCCTTACTTCTCC
66 CTTGATATTTGCCAATTGAAAATGGAATGACAACTTGCTTTGTGATCCTTACTTCTCC
3938216 ACCGTCATTT
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (123 bp):
TTGCCACGGTCTTCCCAAAAGTATATGTCCAGTATCCATTGGTACAACATCACAAAGGACTTCAT
CTTGATATTTGCCAATTGAAAATGGAATGACAACTTGCTTTGTGATCCTTACTTCTCC
Found at i:3946692 original size:8 final size:8
Alignment explanation
Indices: 3946664--3946711 Score: 64
Period size: 8 Copynumber: 6.1 Consensus size: 8
3946654 AACTTTTCTA
3946664 TTCTTTTC
1 TTCTTTTC
3946672 TT-TTCTT-
1 TTCTT-TTC
3946679 TTCTTTTC
1 TTCTTTTC
*
3946687 TTCTTTTT
1 TTCTTTTC
3946695 TTCTTTTC
1 TTCTTTTC
3946703 TTCTTTTC
1 TTCTTTTC
3946711 T
1 T
3946712 GATTTTCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 6 0.17
8 29 0.83
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTCTTTTC
Found at i:3946698 original size:16 final size:16
Alignment explanation
Indices: 3946664--3946709 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
3946654 AACTTTTCTA
*
3946664 TTCTTTTCTT-TTCTT
1 TTCTTTTCTTCTTTTT
3946679 TTCTTTTCTTCTTTTT
1 TTCTTTTCTTCTTTTT
3946695 TTCTTTTCTTCTTTT
1 TTCTTTTCTTCTTTT
3946710 CTGATTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTCTTTTCTTCTTTTT
Found at i:3946698 original size:21 final size:21
Alignment explanation
Indices: 3946645--3946727 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
3946635 GCTTGCTTTA
*
3946645 TCTTTTTTTAACTTTTCTATTCT
1 TCTTTTTTT--CTTTTCTTTTCT
*
3946668 T-TTCTTTTCTTTTCTTTTCT
1 TCTTTTTTTCTTTTCTTTTCT
3946688 TCTTTTTTTCTTTTCTTCTT-T
1 TCTTTTTTTCTTTTCTT-TTCT
** *
3946709 TCTGATTTTCTCTTCTTTT
1 TCTTTTTTTCTTTTCTTTT
3946728 TGCACTCCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
20 14 0.27
21 29 0.56
22 8 0.15
23 1 0.02
ACGTcount: A:0.05, C:0.19, G:0.01, T:0.75
Consensus pattern (21 bp):
TCTTTTTTTCTTTTCTTTTCT
Found at i:3946711 original size:5 final size:5
Alignment explanation
Indices: 3946656--3946704 Score: 71
Period size: 5 Copynumber: 9.6 Consensus size: 5
3946646 CTTTTTTTAA
* *
3946656 CTTTT CTATT CTTTT CTTTT CTTTT CTTTT CTTCTT TTTTT CTTTT CTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTT-TT CTTTT CTTTT CTT
3946705 CTTTTCTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
5 35 0.90
6 4 0.10
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (5 bp):
CTTTT
Found at i:3948335 original size:21 final size:20
Alignment explanation
Indices: 3948294--3948336 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
3948284 TCTATTTTTT
*
3948294 AAAAAAAAAAAAAAAGGCAA
1 AAAAAAAAAAAAAAAGCCAA
*
3948314 AAAAAAAACAAAAAAATCCAA
1 AAAAAAAA-AAAAAAAGCCAA
3948335 AA
1 AA
3948337 TTTCAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.84, C:0.09, G:0.05, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAGCCAA
Found at i:3954114 original size:2 final size:2
Alignment explanation
Indices: 3954103--3954134 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3954093 TAACTATAGG
3954103 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3954135 GAAAATACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3969512 original size:23 final size:22
Alignment explanation
Indices: 3969480--3969522 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3969470 TTGGTGCTGG
3969480 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
* *
3969503 AAACATGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
3969523 AAAGGAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.16
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:3973535 original size:2 final size:2
Alignment explanation
Indices: 3973524--3973565 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3973514 TAACTATAGG
3973524 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3973565 T
1 T
3973566 GAAAATAACT
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:3977417 original size:18 final size:18
Alignment explanation
Indices: 3977396--3977434 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3977386 TATTTTGAAA
* *
3977396 TTTTGGCTTTTTTGTTTT
1 TTTTGCCTTTTTTATTTT
3977414 TTTTGCCTTTTTTATTTT
1 TTTTGCCTTTTTTATTTT
3977432 TTT
1 TTT
3977435 GAAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.08, G:0.10, T:0.79
Consensus pattern (18 bp):
TTTTGCCTTTTTTATTTT
Found at i:3977796 original size:23 final size:22
Alignment explanation
Indices: 3977764--3977806 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3977754 TTGGTGCTAG
3977764 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
* *
3977787 AAACATGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
3977807 AGAGGAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.16
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Done.