Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008424.1 Hibiscus syriacus cultivar Beakdansim tig00111207_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: 4198033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 16
Found at i:3601506 original size:90 final size:91
Alignment explanation
Indices: 3601352--3601533 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
3601342 CCTAGAACAC
*
3601352 CCATGTGCCTTGCATATGACCAGCCTCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCTCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATG
* *
3601417 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTATCTCCCTATTCGGCCAAG
** * * * * *
3601443 CCATGTGTTTTGCATGTGAACAGCC-CCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCTCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATG
3601507 AAGAGCTATCTCCCTATTCGGCCAAG
66 AAGAGCTATCTCCCTATTCGGCCAAG
3601533 C
1 C
3601534 ATCATTTCCC
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 60 0.74
91 21 0.26
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCTCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATG
AAGAGCTATCTCCCTATTCGGCCAAG
Found at i:3602371 original size:24 final size:23
Alignment explanation
Indices: 3602312--3602372 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
3602302 AAAATTCAGC
3602312 AAAGAAAACA-AAAGCACTCAAAA
1 AAAGAAAA-AGAAAGCACTCAAAA
* ** *
3602335 GAAGAAATTGAAAGCACTTGAAAA
1 AAAGAAAAAGAAAGCAC-TCAAAA
3602359 AAAGAAAAAGAAAG
1 AAAGAAAAAGAAAG
3602373 AAAGAAAAGT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 13 0.45
24 16 0.55
ACGTcount: A:0.66, C:0.10, G:0.16, T:0.08
Consensus pattern (23 bp):
AAAGAAAAAGAAAGCACTCAAAA
Found at i:3607952 original size:14 final size:15
Alignment explanation
Indices: 3607923--3607967 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 15
3607913 CTTGCTTCAC
3607923 TTTTCTTTTGCTTTTGA
1 TTTTC-TTT-CTTTTGA
3607940 TTTTC-TTCTTTTGA
1 TTTTCTTTCTTTTGA
3607954 TTTTCTTTCTTTTG
1 TTTTCTTTCTTTTG
3607968 CGCTCCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 12 0.44
15 10 0.37
17 5 0.19
ACGTcount: A:0.04, C:0.13, G:0.09, T:0.73
Consensus pattern (15 bp):
TTTTCTTTCTTTTGA
Found at i:3608461 original size:35 final size:37
Alignment explanation
Indices: 3608415--3608494 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
3608405 TTTGAGAATT
* *
3608415 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTAATAATGGAAGATGGACTA
*
3608450 TGGTGATGATATAGGCGTAATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTAATAATGGAAGATGGACTA
3608487 TGGTGATG
1 TGGTGATG
3608495 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTAATAATGGAAGATGGACTA
Found at i:3614009 original size:90 final size:91
Alignment explanation
Indices: 3613854--3614027 Score: 242
Period size: 90 Copynumber: 1.9 Consensus size: 91
3613844 CCTAGAACAC
* * *
3613854 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCATGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATG
* *
3613919 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTATCTCCCTATTCGGCCAAG
** * * * *
3613945 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATG
3614009 AAGAGCTATCTCCCTATTC
66 AAGAGCTATCTCCCTATTC
3614028 ATCCAAGTAT
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
90 53 0.74
91 19 0.26
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATG
AAGAGCTATCTCCCTATTCGGCCAAG
Found at i:3618535 original size:11 final size:11
Alignment explanation
Indices: 3618521--3618576 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
3618511 TCTTTTTGAA
3618521 TTCTTTTTCTT
1 TTCTTTTTCTT
3618532 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
3618545 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
3618558 TGTCTTTTTC-T
1 T-TCTTTTTCTT
3618569 TTCTTTTT
1 TTCTTTTT
3618577 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:3618545 original size:19 final size:18
Alignment explanation
Indices: 3618521--3618576 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
3618511 TCTTTTTGAA
3618521 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
3618539 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
3618558 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
3618576 T
1 T
3618577 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:3628668 original size:13 final size:12
Alignment explanation
Indices: 3628649--3628734 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
3628639 ATATAGGCGT
3628649 GATATGGTGATG
1 GATATGGTGATG
3628661 GAATATGGTGAT-
1 G-ATATGGTGATG
*
3628673 GATATAGGCG-T-
1 GATAT-GGTGATG
3628684 GATAATGGTGATG
1 GAT-ATGGTGATG
3628697 GACTATGGTGAT-
1 GA-TATGGTGATG
*
3628709 GATATAGGCG-T-
1 GATAT-GGTGATG
3628720 GATAATGGTGATG
1 GAT-ATGGTGATG
3628733 GA
1 GA
3628735 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:3628704 original size:36 final size:36
Alignment explanation
Indices: 3628631--3628735 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
3628621 ATTTATAAGT
* *
3628631 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
3628666 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
3628702 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
3628736 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:3629123 original size:19 final size:20
Alignment explanation
Indices: 3629076--3629126 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
3629066 GAAACCCCTT
**
3629076 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
3629096 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
3629115 TGAAGATACATG
1 TGAAAATACATG
3629127 TTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:3632456 original size:13 final size:12
Alignment explanation
Indices: 3632437--3632522 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
3632427 ATATAGGCGT
3632437 GATATGGTGATG
1 GATATGGTGATG
3632449 GAATATGGTGAT-
1 G-ATATGGTGATG
*
3632461 GATATAGGCG-T-
1 GATAT-GGTGATG
3632472 GATAATGGTGATG
1 GAT-ATGGTGATG
3632485 GACTATGGTGAT-
1 GA-TATGGTGATG
*
3632497 GATATAGGCG-T-
1 GATAT-GGTGATG
3632508 GATAATGGTGATG
1 GAT-ATGGTGATG
3632521 GA
1 GA
3632523 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:3632492 original size:36 final size:36
Alignment explanation
Indices: 3632419--3632523 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
3632409 ATTTATAAGT
* *
3632419 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
3632454 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
3632490 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
3632524 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:3633502 original size:13 final size:13
Alignment explanation
Indices: 3633480--3633522 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3633470 AAAAGTAACA
3633480 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
* * *
3633493 AAAGAAGAAATAC
1 AAAAAAGAAAAAG
*
3633506 AAAAAAGAGAAAG
1 AAAAAAGAAAAAG
3633519 AAAA
1 AAAA
3633523 GACTCATATA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:3633817 original size:17 final size:17
Alignment explanation
Indices: 3633795--3633827 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3633785 ATCCTACCCA
3633795 TATACCATAACCATTTC
1 TATACCATAACCATTTC
*
3633812 TATACCCTAACCATTT
1 TATACCATAACCATTT
3633828 TTTTAAGCCG
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:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (17 bp):
TATACCATAACCATTTC
Found at i:3637316 original size:13 final size:13
Alignment explanation
Indices: 3637298--3637323 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3637288 ACTATCTGTT
3637298 CATCACCATTTTC
1 CATCACCATTTTC
3637311 CATCACCATTTTC
1 CATCACCATTTTC
3637324 ACGCCTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (13 bp):
CATCACCATTTTC
Found at i:3646786 original size:16 final size:16
Alignment explanation
Indices: 3646765--3646797 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3646755 TTCTTCCACC
3646765 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
3646781 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
3646797 T
1 T
3646798 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:3648593 original size:15 final size:16
Alignment explanation
Indices: 3648542--3648594 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
3648532 TGATAGTGAA
3648542 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
3648559 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
3648576 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
3648591 ATAA
1 ATAA
3648595 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:3649253 original size:35 final size:36
Alignment explanation
Indices: 3649207--3649286 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 36
3649197 AAATGCAATT
**
3649207 TGGTGATGATATAGGCGTGAT-ATGATGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGATGATGGAAGA
*
3649242 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGATGATGGAAGA
3649278 TGGTGATGA
1 TGGTGATGA
3649287 ACAGATTGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 21 0.51
36 20 0.49
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGATGATGGAAGA
Found at i:3649675 original size:19 final size:20
Alignment explanation
Indices: 3649628--3649678 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
3649618 GAAACCCCTT
**
3649628 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
3649648 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
3649667 TGAAGATACATG
1 TGAAAATACATG
3649679 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:3656554 original size:24 final size:21
Alignment explanation
Indices: 3656519--3656561 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
3656509 GGCTCATTCT
*
3656519 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
3656542 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
3656562 ATCTTGTGCA
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:3657821 original size:27 final size:28
Alignment explanation
Indices: 3657791--3657852 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
3657781 ATTTTCTTTG
* *
3657791 CTTTTCTTCTTTTTGAATGC-TGAATTT
1 CTTTTCTTCTTTTGGAATGCTTCAATTT
* *
3657818 CTTTTTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTCTTCTTTTGGAATGCTTCAATTT
3657846 CTTTTCT
1 CTTTTCT
3657853 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.11, C:0.16, G:0.11, T:0.61
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAATGCTTCAATTT
Found at i:3663936 original size:123 final size:124
Alignment explanation
Indices: 3663749--3663993 Score: 377
Period size: 123 Copynumber: 2.0 Consensus size: 124
3663739 TAAATAGCCC
* *
3663749 ACCTATTCACCCATACGTTTACCACCCTTAACCATCTTTTTTTGAGCCATTCACTTGTGCAGGTT
1 ACCTATTCACCCATACGTTTACCACACTTAACCATCTTCTTTTGAGCCATTCACTTGTGCAGGTT
* * *
3663814 GTTTGCTTCCTTCCTAGATCCGCAATCAATTTGTTAAGGTACAAGTGCCTTACATCACT
66 GTTTGCTTCCTTCCTAGATCCACAATCAATTTGTTAAGGTACAAATACCTTACATCACT
* * *
3663873 ACCTATTTCACCTATACGTTTACCA-ACTTAACCATC-TCTTTTGAGCTATTCACTTTTGCAGGT
1 ACCTA-TTCACCCATACGTTTACCACACTTAACCATCTTCTTTTGAGCCATTCACTTGTGCAGGT
* *
3663936 TGTTTGTTTCCTTCCTAGATCCATAATCAATTTGTTAAGGTACAAATACCTTACATCA
65 TGTTTGCTTCCTTCCTAGATCCACAATCAATTTGTTAAGGTACAAATACCTTACATCA
3663994 AGTGGTAATC
Statistics
Matches: 110, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
123 77 0.70
124 15 0.14
125 18 0.16
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.38
Consensus pattern (124 bp):
ACCTATTCACCCATACGTTTACCACACTTAACCATCTTCTTTTGAGCCATTCACTTGTGCAGGTT
GTTTGCTTCCTTCCTAGATCCACAATCAATTTGTTAAGGTACAAATACCTTACATCACT
Found at i:3665475 original size:24 final size:25
Alignment explanation
Indices: 3665429--3665483 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
3665419 ACAGTTATGC
*
3665429 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
3665453 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
3665478 CA-TTGA
1 CACTTGA
3665484 GGCTCTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:3666809 original size:148 final size:148
Alignment explanation
Indices: 3666541--3666837 Score: 558
Period size: 148 Copynumber: 2.0 Consensus size: 148
3666531 AAGGTATTTA
*
3666541 GCTCATAACAGCTCAATATCATGGACTTACCTTGTTTCCTTGCACATATAGGTACATTGGAGTGT
1 GCTCATAACAGCTCAATATCATGGACTTACATTGTTTCCTTGCACATATAGGTACATTGGAGTGT
3666606 GATGCACGATGAGGCAGCTTGGTAGAGTATTTGGACGTCATATGCAGCTCAGAAACAACTCACAA
66 GATGCACGATGAGGCAGCTTGGTAGAGTATTTGGACGTCATATGCAGCTCAGAAACAACTCACAA
3666671 ATATCATGGCAGCTCGTG
131 ATATCATGGCAGCTCGTG
3666689 GCTCATAACAGCTCAATATCATGGACTTACATTGTTTCCTTGCACATATAGGTACATTGGAGTGT
1 GCTCATAACAGCTCAATATCATGGACTTACATTGTTTCCTTGCACATATAGGTACATTGGAGTGT
* *
3666754 GATGCATGATGAGGCAGCTTGGTAGAGTATTTGGACGTCATATGCAGCTCAGAAACAGCTCACAA
66 GATGCACGATGAGGCAGCTTGGTAGAGTATTTGGACGTCATATGCAGCTCAGAAACAACTCACAA
*
3666819 ATTTCATGGCAGCTCGTG
131 ATATCATGGCAGCTCGTG
3666837 G
1 G
3666838 AACACTAAGG
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
148 145 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (148 bp):
GCTCATAACAGCTCAATATCATGGACTTACATTGTTTCCTTGCACATATAGGTACATTGGAGTGT
GATGCACGATGAGGCAGCTTGGTAGAGTATTTGGACGTCATATGCAGCTCAGAAACAACTCACAA
ATATCATGGCAGCTCGTG
Found at i:3666935 original size:20 final size:22
Alignment explanation
Indices: 3666906--3666945 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
3666896 AGGAGAGCTT
3666906 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
3666926 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
3666946 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:3675771 original size:25 final size:25
Alignment explanation
Indices: 3675755--3675813 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
3675745 AAGCAACAAG
*
3675755 AAAGAAGAAGAAAAAAACAAAAAGA
1 AAAGAAAAAGAAAAAAACAAAAAGA
* * *
3675780 AAAGAAAAAG-AAGAATCAAAAAGC
1 AAAGAAAAAGAAAAAAACAAAAAGA
3675804 AAAGAAAAAG
1 AAAGAAAAAG
3675814 TGAAGCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 21 0.70
25 9 0.30
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (25 bp):
AAAGAAAAAGAAAAAAACAAAAAGA
Found at i:3675793 original size:14 final size:15
Alignment explanation
Indices: 3675752--3675794 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
3675742 CAAAAGCAAC
*
3675752 AAGAAAGAAGAAGAA
1 AAGAAACAAGAAGAA
*
3675767 AA-AAACAAAAAGAA
1 AAGAAACAAGAAGAA
3675781 AAGAAA-AAGAAGAA
1 AAGAAACAAGAAGAA
3675795 TCAAAAAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (15 bp):
AAGAAACAAGAAGAA
Found at i:3675830 original size:24 final size:24
Alignment explanation
Indices: 3675745--3675823 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
3675735 GCTACAACAA
* * *
3675745 AAGCAACAAG-AAAGAAGAAGAAAA
1 AAGCAAAAAGCAAAGAAAAAG-AAG
* *
3675769 AAACAAAAAGAAAAGAAAAAGAAG
1 AAGCAAAAAGCAAAGAAAAAGAAG
* *
3675793 AATCAAAAAGCAAAGAAAAAG-TG
1 AAGCAAAAAGCAAAGAAAAAGAAG
3675816 AAGCAAAA
1 AAGCAAAA
3675824 TTGCAAATAC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
23 8 0.17
24 29 0.63
25 9 0.20
ACGTcount: A:0.72, C:0.08, G:0.18, T:0.03
Consensus pattern (24 bp):
AAGCAAAAAGCAAAGAAAAAGAAG
Found at i:3678564 original size:13 final size:13
Alignment explanation
Indices: 3678546--3678605 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
3678536 TATAGGCGTG
3678546 ATATGGTGATGGA
1 ATATGGTGATGGA
3678559 ATATGGTGAT-G-
1 ATATGGTGATGGA
*
3678570 ATATAGGCG-T-GA
1 ATAT-GGTGATGGA
*
3678582 TTATGGTGATGGA
1 ATATGGTGATGGA
*
3678595 CTATGGTGATG
1 ATATGGTGATG
3678606 ATATAGGCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 9 0.23
12 8 0.21
13 22 0.56
ACGTcount: A:0.27, C:0.03, G:0.37, T:0.33
Consensus pattern (13 bp):
ATATGGTGATGGA
Found at i:3678631 original size:36 final size:35
Alignment explanation
Indices: 3678527--3678631 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 35
3678517 ATTTATAAGT
* *
3678527 TGGTGATAATATAGGCGTGATATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGACTA
3678562 TGGTGATGATATAGGCGTGATTATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGA-TATGGTGATGGACTA
3678598 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGAC
3678632 AGATTGTATC
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.31
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGACTA
Found at i:3684080 original size:19 final size:20
Alignment explanation
Indices: 3684056--3684106 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3684046 CGGCCAAGAG
* *
3684056 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
3684075 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
3684095 CATGTATTTTCA
1 CATGTATTTTCA
3684107 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:3684543 original size:14 final size:14
Alignment explanation
Indices: 3684523--3684561 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
3684513 CTTTTTATTT
3684523 ATTTCATTTCTATTC
1 ATTTCATTTCT-TTC
3684538 -TTTCATTTCTTTC
1 ATTTCATTTCTTTC
3684551 TATTTCATTTC
1 -ATTTCATTTC
3684562 CTTTATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.14
14 10 0.45
15 9 0.41
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTCATTTCTTTC
Found at i:3686440 original size:14 final size:13
Alignment explanation
Indices: 3686423--3686472 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
3686413 GTGCAAAAAG
3686423 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
3686437 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
3686450 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
3686461 AAAGAAAAAGAA
1 AAAGAAAAAGAA
3686473 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:3686469 original size:19 final size:18
Alignment explanation
Indices: 3686417--3686472 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
3686407 ATTGGAGTGC
3686417 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
3686434 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
3686453 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
3686472 A
1 A
3686473 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:3686470 original size:11 final size:11
Alignment explanation
Indices: 3686417--3686472 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
3686407 ATTGGAGTGC
3686417 AAAAAG-AAAG
1 AAAAAGAAAAG
3686427 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
3686441 AAGAAGAAAAG
1 AAAAAGAAAAG
3686452 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
3686465 AAAAAGAA
1 AAAAAGAA
3686473 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:3694636 original size:16 final size:16
Alignment explanation
Indices: 3694615--3694654 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 16
3694605 TTTTTTTTTC
3694615 AAAAAAACAAAAAAAA
1 AAAAAAACAAAAAAAA
3694631 AAAAAAACAAAAAAAA
1 AAAAAAACAAAAAAAA
3694647 AACAAAAA
1 AA-AAAAA
3694655 AAAGCCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAAAAAA
Found at i:3694666 original size:1 final size:1
Alignment explanation
Indices: 3694615--3694657 Score: 59
Period size: 1 Copynumber: 43.0 Consensus size: 1
3694605 TTTTTTTTTC
* * *
3694615 AAAAAAACAAAAAAAAAAAAAAACAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3694658 GCCAAAAAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3694666 original size:12 final size:11
Alignment explanation
Indices: 3694616--3694657 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
3694606 TTTTTTTTCA
*
3694616 AAAAAACAAAAA
1 AAAAAA-AAAAC
3694628 AAAAAAAAAAC
1 AAAAAAAAAAC
3694639 AAAAAAAAAAC
1 AAAAAAAAAAC
3694650 AAAAAAAA
1 AAAAAAAA
3694658 GCCAAAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 23 0.79
12 6 0.21
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:3703320 original size:937 final size:939
Alignment explanation
Indices: 3701100--3703527 Score: 4326
Period size: 939 Copynumber: 2.6 Consensus size: 939
3701090 CTTCCCTATC
* *
3701100 ATAAAGTGTGGATCTTTGCTCTCTATAGAATTGGTTCTTCTTTGAGACTTCTTCAAGATACAATC
1 ATAAAGTATGGGTCTTTGCTCTCTATAGAATTGGTTCTTCTTTGAGACTTCTTCAAGATACAATC
3701165 CTCACTACAATCCCTTTTGTTTCATCGCCATAACCATAGCCATATAAACCATCTTTCACTTCCAT
66 CTCACTACAATCCCTTTTGTTTCATCGCCATAACCATAGCCATATAAACCATCTTTCACTTCCAT
*
3701230 TATTTATTATTTAAATAGCCTACCTATTTTACCTATACGTTTACCACCTTAATCATCTCTTTTGA
131 TATTTATTATTTAAATAGCCTACCTATTTCACCTATACGTTTACCACCTTAATCATCTCTTTTGA
* * *
3701295 GCCGTTCACTTGTGGATGTTGTTTGCTTTCTTCCTAGATCCACAATCAATTTGTTAAGGTACAAA
196 GCCATTCACTTGTGCAGGTTGTTTGCTTTCTTCCTAGATCCACAATCAATTTGTTAAGGTACAAA
3701360 TGCCTTACATCATGAACATGTTGTTAAGGAGCTCACAAGGACTTGGCTTGGAAGCTTGTTCACAA
261 TGCCTTACATCATGAACATGTTGTTAAGGAGCTCACAAGGACTTGGCTTGGAAGCTTGTTCACAA
*
3701425 ATAGCCCATGCTTGTTAAGTAGCTCCACACTCAAGCTAGCTTGGAAGGAGACACATGCACGCCCA
326 ATAGCCCATGCTTGTTAACTAGCTCCACACTCAAGCTAGCTTGGAAGGAGACACATGCACGCCCA
* *
3701490 AGATGGAGCACATGACCAGCCATCATCCCATGCACAAGGTTGCACCACAAGGTTCCCTAGAACAC
391 AGATGGAGCACATGACCAACCATCATCCCATGCACAAGGCTGCACCACAAGGTTCCCTAGAACAC
* *
3701555 CCATGTGTGTGCCATATGACCAGCCCCCATGTGCCTTGCATGTGGTCTAATTTAGGCACCAAGAT
456 CCATGTGCGTGCCATATGACCAGCCCCCATGTGCCTTGCATGTGGTCTAATTTAGGCGCCAAGAT
3701620 GAAGAGCCCTCTCCCTATTTGGCCAAGCATCATCTCCCATCCAATTTGGCGCCAACATGAAGAGA
521 GAAGAGCCCTCTCCCTATTTGGCCAAGCATCATCTCCCATCCAATTTGGCGCCAACATGAAGAGA
*
3701685 CACAAGAGCTATTCGGCCAAGGGTTATCACCCTCCATTTAAACTGAACCACATCTCTATTTTGTA
586 CACAAGAGCTATTCGGCCAAGGGTTATCACCCTCCATTTAAACTAAACCACATCTCTATTTTGTA
* *
3701750 ATTAATTATATCTCTATAGGAAGGCACAAGGCTGGTTGAATCCCCTTGTAACCATTCGGCCATGC
651 ATTAATTATATCTCTATAAGAAGGCACAAGGCTGGCTGAATCCCCTTGTAACCATTCGGCCATGC
* ** * ** * *
3701815 CTCTCCATTTCCTATAAATAGGTCATCATATTTCATTTGTAATCATACCTTTTTGATTCATATAA
716 CTATCCATTTCCTATAAATAGGAAAACATACATAATTTGTAATCAGACCTTTTTGATTCATATAA
* *
3701880 GTGAGAGCATTCTCTTTCTTAAGTCCTGGTGACTTTTATCGACTTATCAAATATTTTATACTTAT
781 GTGAGAGCATTCTCTTCCTTAAGTCCTGGGGACTTTTATCGACTTATCAAATATTTTATACTTAT
* *
3701945 GGCGTCAACCCCCTTTTTTACCTTGATACTTCTGGTTCCTAGTTCTTATAACTAGTGGGTCAAAG
846 GGCGTCAACCCCCTTTTTCACCTTGATACTTCTGGTTCATAGTTCTTATAACTAGTGGGTCAAAG
*
3702010 TCCTTAATACCACCCCTTGAAGAAGCAAT
911 TCCTTAATACCACCACTTGAAGAAGCAAT
3702039 ATAAAGTATGGGTCTTTGCTCTCTATAGAATTGGTTCTTCTTTGAGACTTCTTCAAGATACAATC
1 ATAAAGTATGGGTCTTTGCTCTCTATAGAATTGGTTCTTCTTTGAGACTTCTTCAAGATACAATC
* *
3702104 CTCACTACAATCCCTTTTGTTTCATCGCCATAACCATAGCCAAATAAACCATCTTTCGCTTCCAT
66 CTCACTACAATCCCTTTTGTTTCATCGCCATAACCATAGCCATATAAACCATCTTTCACTTCCAT
*
3702169 TATTTATTATTTAAATAGCCTACCTATTTCACCTATACGTTTACCACTTTAATCATCTCTTTTGA
131 TATTTATTATTTAAATAGCCTACCTATTTCACCTATACGTTTACCACCTTAATCATCTCTTTTGA
*
3702234 GCCATTCACTTGTGCAGGTTGTTTGCTTTCTTCCTATATCCACAATCAATTTGTTAAGGTACAAA
196 GCCATTCACTTGTGCAGGTTGTTTGCTTTCTTCCTAGATCCACAATCAATTTGTTAAGGTACAAA
3702299 TGCCTTACATCATGAACATGTTGTTAAGGAGCTCACAAGGACTTGGCTTGGAAGCTTGTTCACAA
261 TGCCTTACATCATGAACATGTTGTTAAGGAGCTCACAAGGACTTGGCTTGGAAGCTTGTTCACAA
3702364 ATAGCCCATGCTTGTTAACTAGCTCCACACTCAAGCTAGCTTGGAAGGAGACACATGCACGCCCA
326 ATAGCCCATGCTTGTTAACTAGCTCCACACTCAAGCTAGCTTGGAAGGAGACACATGCACGCCCA
3702429 AGATGGAGCACATGACCAACCATCATCCCATGCACAAGGCTGCACCACAAGGTTCCCTAGAACAC
391 AGATGGAGCACATGACCAACCATCATCCCATGCACAAGGCTGCACCACAAGGTTCCCTAGAACAC
* *
3702494 CCATGTGCGTGCCATATGACCAGCCCCCATGTGCCTTACATGTTGTCTAATTTAGGCGCCAAGAT
456 CCATGTGCGTGCCATATGACCAGCCCCCATGTGCCTTGCATGTGGTCTAATTTAGGCGCCAAGAT
3702559 GAAGAGCCCTCTCCCTATTTGGCCAAGCATCATCTCCCATCCAATTTGGCGCCAACATGAAGAGA
521 GAAGAGCCCTCTCCCTATTTGGCCAAGCATCATCTCCCATCCAATTTGGCGCCAACATGAAGAGA
*
3702624 CACAAGAGCTATTTGGCCAAGGGTTATCACCCTCCATTTAAACTAAACCATCATCTCTATTTTGT
586 CACAAGAGCTATTCGGCCAAGGGTTATCACCCTCCATTTAAACTAAACCA-CATCTCTATTTTGT
*
3702689 AATTAATTATGTCTCTATAAGAAGGCACAAGGCTGGCTGAATCCCCTTGTAACCATTCGGCCATG
650 AATTAATTATATCTCTATAAGAAGGCACAAGGCTGGCTGAATCCCCTTGTAACCATTCGGCCATG
3702754 CCTATCCATTTCCTATAAATAGGAAAACATACATAATTTGTAATCAGACC-TTTTGA-TCAATAT
715 CCTATCCATTTCCTATAAATAGGAAAACATACATAATTTGTAATCAGACCTTTTTGATTC-ATAT
** *
3702817 AAGTGAGATTATTCTCTTCCTTAAGTCCTGGGGACTTTTATCGACTTATCAAGTATTTTATACTT
779 AAGTGAGAGCATTCTCTTCCTTAAGTCCTGGGGACTTTTATCGACTTATCAAATATTTTATACTT
*
3702882 GTGGCGTCAA-CCCC-TTTTCACCTTGATACTTCTGGTTCATAGTTCTTATAACTAGTGGGTCAA
844 ATGGCGTCAACCCCCTTTTTCACCTTGATACTTCTGGTTCATAGTTCTTATAACTAGTGGGTCAA
*
3702945 AGTCCTTAATACCATCACTTGAAGAAGCAAT
909 AGTCCTTAATACCACCACTTGAAGAAGCAAT
* *
3702976 ATAAAGTCTGGGTCTTTGCTCTCTATAGCATTGGTTCTTCTTTGAGACTTCTTCAAGATACAATC
1 ATAAAGTATGGGTCTTTGCTCTCTATAGAATTGGTTCTTCTTTGAGACTTCTTCAAGATACAATC
*
3703041 CTCACTACCATCCCTTTTGTTTCATCGCCATAACCATAGCCATATAAACCATCTTTCACTTCCAT
66 CTCACTACAATCCCTTTTGTTTCATCGCCATAACCATAGCCATATAAACCATCTTTCACTTCCAT
*
3703106 TATTTATTATTTAAATAGCCTACCTATTTCACCTATACGTTTACCACCTTAATAATCTCTTTTGA
131 TATTTATTATTTAAATAGCCTACCTATTTCACCTATACGTTTACCACCTTAATCATCTCTTTTGA
*
3703171 GCCATTCACTTGTGCAGGTTGTTTTCTTTCTTCCTAGATCCACAATCAATTTGTTAAGGTACAAA
196 GCCATTCACTTGTGCAGGTTGTTTGCTTTCTTCCTAGATCCACAATCAATTTGTTAAGGTACAAA
*
3703236 TGCCTTACATCATGAACATGTTGTTAAGGAGCTCACAAGGACTTGGCTTGGAAGCTTATTCACAA
261 TGCCTTACATCATGAACATGTTGTTAAGGAGCTCACAAGGACTTGGCTTGGAAGCTTGTTCACAA
* *
3703301 ACAGTCCATGCTTGTTAACTAGCTCCACACTCAAGCTAGCTTGGAAGGAGACACATGCACGCCCA
326 ATAGCCCATGCTTGTTAACTAGCTCCACACTCAAGCTAGCTTGGAAGGAGACACATGCACGCCCA
* ** *
3703366 AGATGGAGAACATGACCAACCATCAT-CCGGGCACAAGGCTGTACCACAAGGTTCCCTAGAACAC
391 AGATGGAGCACATGACCAACCATCATCCCATGCACAAGGCTGCACCACAAGGTTCCCTAGAACAC
*
3703430 CCATGTGCGTGCCATATGACCAGCCCCTATGTGCCTTGCATGTGGTCTAATTTAGGCGCCAAGAT
456 CCATGTGCGTGCCATATGACCAGCCCCCATGTGCCTTGCATGTGGTCTAATTTAGGCGCCAAGAT
3703495 GAAGAGCCCTCTCCCTATTTGGCCAAGCATCAT
521 GAAGAGCCCTCTCCCTATTTGGCCAAGCATCAT
3703528 GATACGATCA
Statistics
Matches: 1428, Mismatches: 59, Indels: 7
0.96 0.04 0.00
Matches are distributed among these distances:
936 130 0.09
937 479 0.34
938 6 0.00
939 695 0.49
940 118 0.08
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (939 bp):
ATAAAGTATGGGTCTTTGCTCTCTATAGAATTGGTTCTTCTTTGAGACTTCTTCAAGATACAATC
CTCACTACAATCCCTTTTGTTTCATCGCCATAACCATAGCCATATAAACCATCTTTCACTTCCAT
TATTTATTATTTAAATAGCCTACCTATTTCACCTATACGTTTACCACCTTAATCATCTCTTTTGA
GCCATTCACTTGTGCAGGTTGTTTGCTTTCTTCCTAGATCCACAATCAATTTGTTAAGGTACAAA
TGCCTTACATCATGAACATGTTGTTAAGGAGCTCACAAGGACTTGGCTTGGAAGCTTGTTCACAA
ATAGCCCATGCTTGTTAACTAGCTCCACACTCAAGCTAGCTTGGAAGGAGACACATGCACGCCCA
AGATGGAGCACATGACCAACCATCATCCCATGCACAAGGCTGCACCACAAGGTTCCCTAGAACAC
CCATGTGCGTGCCATATGACCAGCCCCCATGTGCCTTGCATGTGGTCTAATTTAGGCGCCAAGAT
GAAGAGCCCTCTCCCTATTTGGCCAAGCATCATCTCCCATCCAATTTGGCGCCAACATGAAGAGA
CACAAGAGCTATTCGGCCAAGGGTTATCACCCTCCATTTAAACTAAACCACATCTCTATTTTGTA
ATTAATTATATCTCTATAAGAAGGCACAAGGCTGGCTGAATCCCCTTGTAACCATTCGGCCATGC
CTATCCATTTCCTATAAATAGGAAAACATACATAATTTGTAATCAGACCTTTTTGATTCATATAA
GTGAGAGCATTCTCTTCCTTAAGTCCTGGGGACTTTTATCGACTTATCAAATATTTTATACTTAT
GGCGTCAACCCCCTTTTTCACCTTGATACTTCTGGTTCATAGTTCTTATAACTAGTGGGTCAAAG
TCCTTAATACCACCACTTGAAGAAGCAAT
Found at i:3711792 original size:16 final size:16
Alignment explanation
Indices: 3711768--3711808 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
3711758 TTTTCCTTGA
3711768 TGTTGGAAAGAATACT
1 TGTTGGAAAGAATACT
*
3711784 TGTTAGAAAGAATACT
1 TGTTGGAAAGAATACT
3711800 TGTTGGAAA
1 TGTTGGAAA
3711809 ATCTATCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (16 bp):
TGTTGGAAAGAATACT
Found at i:3714074 original size:33 final size:33
Alignment explanation
Indices: 3713995--3714098 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
3713985 ATACAATCTG
* *
3713995 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
3714031 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
3714064 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
3714097 TC
1 TC
3714099 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:3718545 original size:33 final size:33
Alignment explanation
Indices: 3718501--3718569 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
3718491 CATCACCATA
*
3718501 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
3718534 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
3718567 TTC
1 TTC
3718570 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:3721995 original size:13 final size:12
Alignment explanation
Indices: 3721976--3722061 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
3721966 ATATAGGCGT
3721976 GATATGGTGATG
1 GATATGGTGATG
3721988 GAATATGGTGAT-
1 G-ATATGGTGATG
*
3722000 GATATAGGCG-T-
1 GATAT-GGTGATG
3722011 GATAATGGTGATG
1 GAT-ATGGTGATG
3722024 GACTATGGTGAT-
1 GA-TATGGTGATG
*
3722036 GATATAGGCG-T-
1 GATAT-GGTGATG
3722047 GATAATGGTGATG
1 GAT-ATGGTGATG
3722060 GA
1 GA
3722062 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:3722031 original size:36 final size:36
Alignment explanation
Indices: 3721958--3722062 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
3721948 ATTTATAAGT
* *
3721958 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
3721993 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
3722029 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
3722063 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:3722451 original size:19 final size:20
Alignment explanation
Indices: 3722404--3722454 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
3722394 GAAACCCCTT
**
3722404 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
3722424 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
3722443 TGAAGATACATG
1 TGAAAATACATG
3722455 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:3725637 original size:15 final size:15
Alignment explanation
Indices: 3725610--3725651 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
3725600 TGGATTCACT
*
3725610 TTTTCTTTGTTTTT-
1 TTTTCTTTCTTTTTC
3725624 TTATTC-TTCTTTTTC
1 TT-TTCTTTCTTTTTC
3725639 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
3725652 GCACTCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:3726139 original size:13 final size:12
Alignment explanation
Indices: 3726120--3726205 Score: 67
Period size: 11 Copynumber: 7.2 Consensus size: 12
3726110 ATATAGGCGT
3726120 GATATGGTGATG
1 GATATGGTGATG
3726132 GAATATGGTGAT-
1 G-ATATGGTGATG
*
3726144 GATATAGGCG-T-
1 GATAT-GGTGATG
3726155 GATAATGGTGATG
1 GAT-ATGGTGATG
3726168 GACTATGGTGAT-
1 GA-TATGGTGATG
3726180 GATATAGGTG-T-
1 GATAT-GGTGATG
3726191 GATAATGGTGATG
1 GAT-ATGGTGATG
3726204 GA
1 GA
3726206 CATATTGTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 22 0.35
12 17 0.27
13 22 0.35
14 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:3726175 original size:36 final size:36
Alignment explanation
Indices: 3726102--3726206 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
3726092 ATTTATAAGT
* *
3726102 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
3726137 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
3726173 TGGTGATGATATAGGTGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
3726207 ATATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:3747443 original size:25 final size:25
Alignment explanation
Indices: 3747415--3747473 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
3747405 AATGATGCTT
3747415 GGCACATGGGGTTGTTCACATGCAA
1 GGCACATGGGGTTGTTCACATGCAA
3747440 GGCACATGGGGTTGTTCACATGCAA
1 GGCACATGGGGTTGTTCACATGCAA
**
3747465 AACACATGG
1 GGCACATGG
3747474 CTTGGCAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (25 bp):
GGCACATGGGGTTGTTCACATGCAA
Found at i:3748991 original size:11 final size:11
Alignment explanation
Indices: 3748968--3749052 Score: 75
Period size: 11 Copynumber: 7.2 Consensus size: 11
3748958 ACAATCTGTC
3748968 CATCACCATTAT
1 CATCACCA-TAT
3748980 CA-CACCTATAT
1 CATCACC-ATAT
3748991 CATCACCATAGTT
1 CATCACCATA--T
3749004 CATCACCATTAT
1 CATCACCA-TAT
*
3749016 CA-CGCCTATAT
1 CATCACC-ATAT
3749027 CATCACCATATT
1 CATCACCATA-T
3749039 CCATCACCATAT
1 -CATCACCATAT
3749051 CA
1 CA
3749053 CGCCTTTATT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 25 0.40
12 16 0.26
13 19 0.31
14 2 0.03
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:3749015 original size:36 final size:36
Alignment explanation
Indices: 3748966--3749069 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
3748956 ATACAATCTG
*
3748966 TCCATCACCATTATCACACCTATATCATCACCATAGT
1 TCCATCACCATTATCACGCCTATATCATCACCATA-T
3749003 T-CATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
* *
3749038 TCCATCACCA-TATCACGCCTTTATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
3749070 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
35 22 0.35
36 40 0.63
37 1 0.02
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.31
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:3749469 original size:24 final size:22
Alignment explanation
Indices: 3749438--3749484 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 22
3749428 GTGCTACAAC
3749438 AAAAAAAAGA-AACAAGAAAGAAG
1 AAAAAAAAGAGAA-AAGAAA-AAG
3749461 AAAACAAAAGAGAAAAGAAAAAG
1 AAAA-AAAAGAGAAAAGAAAAAG
3749484 A
1 A
3749485 CTCCTACATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.36
24 12 0.55
25 2 0.09
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAAAAAGAGAAAAGAAAAAG
Found at i:3749540 original size:14 final size:15
Alignment explanation
Indices: 3749506--3749552 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
3749496 AATTTGGTGT
3749506 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
3749521 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
3749535 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
3749552 G
1 G
3749553 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:3749731 original size:25 final size:25
Alignment explanation
Indices: 3749703--3749753 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
3749693 TTACTATTTC
*
3749703 ATTTCATTTTCTT-TCATCTTTTCTT
1 ATTTCATTTCCTTATCATC-TTTCTT
3749728 ATTTCATTTCCTTATCATCTTTCTT
1 ATTTCATTTCCTTATCATCTTTCTT
3749753 A
1 A
3749754 ACATTTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTCATTTCCTTATCATCTTTCTT
Found at i:3754768 original size:35 final size:36
Alignment explanation
Indices: 3754678--3754778 Score: 170
Period size: 36 Copynumber: 2.8 Consensus size: 36
3754668 CAATATGTCT
3754678 ATCACCATTATCACGCCTATATCATCACCATAGTTC
1 ATCACCATTATCACGCCTATATCATCACCATAGTTC
3754714 ATCACCATTATCACGCCTATATCATCACCATA-TTCC
1 ATCACCATTATCACGCCTATATCATCACCATAGTT-C
*
3754750 ATCACCA-TATCACGCCTATATTATCACCA
1 ATCACCATTATCACGCCTATATCATCACCA
3754779 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
35 23 0.37
36 40 0.63
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.30
Consensus pattern (36 bp):
ATCACCATTATCACGCCTATATCATCACCATAGTTC
Found at i:3757323 original size:36 final size:35
Alignment explanation
Indices: 3757272--3757381 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
3757262 TAAAATAATA
3757272 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* * *
3757307 CCTATAACATCACCATCTTCCATTACTATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * *
3757342 CCTATATCCTAACCATCTT-CATCACCATTTCACT
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
3757376 CCTATA
1 CCTATA
3757382 TAACCACCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 17 0.27
35 26 0.41
36 21 0.33
ACGTcount: A:0.28, C:0.37, G:0.03, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:3758671 original size:18 final size:18
Alignment explanation
Indices: 3758636--3758685 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
3758626 TTAGTAAAGG
3758636 AAAATAAATGAAAT--AAT
1 AAAATAAA-GAAATGAAAT
3758653 AAAGAT-AAGAAATGAAAT
1 AAA-ATAAAGAAATGAAAT
3758671 AAAATAAAGAAATGA
1 AAAATAAAGAAATGA
3758686 TAGAGATAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.17
17 7 0.24
18 17 0.59
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (18 bp):
AAAATAAAGAAATGAAAT
Found at i:3759821 original size:21 final size:21
Alignment explanation
Indices: 3759788--3759940 Score: 136
Period size: 21 Copynumber: 7.3 Consensus size: 21
3759778 TGAGCTCATG
* *
3759788 TAAGGTAAAATGTATATAAGC
1 TAAGATAACATGTATATAAGC
*
3759809 TAAGATAACATGTATATGAGC
1 TAAGATAACATGTATATAAGC
* * *
3759830 TATGAATGATCATCTA-A-AAGC
1 TAAG-AT-AACATGTATATAAGC
3759851 TAAGATAACATGTATATAAGC
1 TAAGATAACATGTATATAAGC
* *
3759872 TAAGATAACATGTATATGAGT
1 TAAGATAACATGTATATAAGC
* * *
3759893 TATGAATGATCATCTA-A-AAGC
1 TAAG-AT-AACATGTATATAAGC
3759914 TAAGATAACATGTATATAAGC
1 TAAGATAACATGTATATAAGC
3759935 T-AGATA
1 TAAGATA
3759941 GAAGGCATAG
Statistics
Matches: 104, Mismatches: 20, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
19 12 0.12
20 11 0.11
21 63 0.61
22 6 0.06
23 12 0.12
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.29
Consensus pattern (21 bp):
TAAGATAACATGTATATAAGC
Found at i:3759897 original size:63 final size:63
Alignment explanation
Indices: 3759788--3759940 Score: 272
Period size: 63 Copynumber: 2.4 Consensus size: 63
3759778 TGAGCTCATG
* *
3759788 TAAGGTAAAATGTATATAAGCTAAGATAACATGTATATGAGCTATGAATGATCATCTAAAAGC
1 TAAGATAACATGTATATAAGCTAAGATAACATGTATATGAGCTATGAATGATCATCTAAAAGC
*
3759851 TAAGATAACATGTATATAAGCTAAGATAACATGTATATGAGTTATGAATGATCATCTAAAAGC
1 TAAGATAACATGTATATAAGCTAAGATAACATGTATATGAGCTATGAATGATCATCTAAAAGC
3759914 TAAGATAACATGTATATAAGCT-AGATA
1 TAAGATAACATGTATATAAGCTAAGATA
3759941 GAAGGCATAG
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 5 0.06
63 82 0.94
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.29
Consensus pattern (63 bp):
TAAGATAACATGTATATAAGCTAAGATAACATGTATATGAGCTATGAATGATCATCTAAAAGC
Found at i:3760270 original size:13 final size:13
Alignment explanation
Indices: 3760229--3760271 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3760219 ATAATAAAGG
*
3760229 AAATGAAATAGAAA
1 AAATGAAATA-AAT
* *
3760243 AAATGAAAGATAT
1 AAATGAAATAAAT
3760256 AAATGAAATAAAT
1 AAATGAAATAAAT
3760269 AAA
1 AAA
3760272 AAGATAGAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.19
Consensus pattern (13 bp):
AAATGAAATAAAT
Found at i:3764168 original size:10 final size:9
Alignment explanation
Indices: 3764154--3764200 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
3764144 TTTTGAATTC
3764154 TTTTTCTTT
1 TTTTTCTTT
3764163 TCTTTTCTTT
1 T-TTTTCTTT
*
3764173 TTCTTC-TT
1 TTTTTCTTT
*
3764181 TTTGTCTTT
1 TTTTTCTTT
*
3764190 TTCTTCTTT
1 TTTTTCTTT
3764199 TT
1 TT
3764201 GCACTCCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
8 6 0.19
9 16 0.52
10 9 0.29
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:3764192 original size:17 final size:17
Alignment explanation
Indices: 3764152--3764201 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
3764142 CTTTTTGAAT
3764152 TCTTTTTCTT-TTCTTT-
1 TCTTTTTCTTCTT-TTTG
3764168 TCTTTTTCTTCTTTTTG
1 TCTTTTTCTTCTTTTTG
3764185 TCTTTTTCTTCTTTTTG
1 TCTTTTTCTTCTTTTTG
3764202 CACTCCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (17 bp):
TCTTTTTCTTCTTTTTG
Found at i:3765978 original size:30 final size:31
Alignment explanation
Indices: 3765937--3765994 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
3765927 ACATGCTGCC
**
3765937 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
3765968 ATGA-ATCTAAAACATATGTAAACATAA
1 ATGATATCTAAAACATATGCAAACATAA
3765995 AATAAAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:3768705 original size:18 final size:18
Alignment explanation
Indices: 3768670--3768719 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
3768660 TTAGTAAAGG
3768670 AAAATAAATGAAAT--AAT
1 AAAATAAA-GAAATGAAAT
3768687 AAAGAT-AAGAAATGAAAT
1 AAA-ATAAAGAAATGAAAT
3768705 AAAATAAAGAAATGA
1 AAAATAAAGAAATGA
3768720 TAGAGATGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.17
17 7 0.24
18 17 0.59
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (18 bp):
AAAATAAAGAAATGAAAT
Found at i:3768960 original size:176 final size:177
Alignment explanation
Indices: 3768665--3769020 Score: 705
Period size: 176 Copynumber: 2.0 Consensus size: 177
3768655 TATGATTAGT
3768665 AAAGGAAAATAAATGAAATAATAAAGATAAGAAATGAAATAAAATAAAGAAATGATAGAGATGGC
1 AAAGGAAAATAAATGAAATAATAAAGATAAGAAATGAAATAAAATAAAGAAATGATAGAGATGGC
3768730 TGCGGAATTGATGGAAGAGATGGATGATGTTGATGATGAAATGGCAATGGTGGTGATGTTGATGT
66 TGCGGAATTGATGGAAGAGATGGATGATGTTGATGATGAAATGGCAATGGTGGTGATGTTGATGT
3768795 AAGGTAATTCTACCTTCTCGTTTGATTGTGGATCTAGGAAGGAAGCA
131 AAGGTAATTCTACCTTCTCGTTTGATTGTGGATCTAGGAAGGAAGCA
3768842 AAAGGAAAATAAATGAAATAATAAAGATAAG-AATGAAATAAAATAAAGAAATGATAGAGATGGC
1 AAAGGAAAATAAATGAAATAATAAAGATAAGAAATGAAATAAAATAAAGAAATGATAGAGATGGC
3768906 TGCGGAATTGATGGAAGAGATGGATGATGTTGATGATGAAATGGCAATGGTGGTGATGTTGATGT
66 TGCGGAATTGATGGAAGAGATGGATGATGTTGATGATGAAATGGCAATGGTGGTGATGTTGATGT
3768971 AAGGTAATTCTACCTTCTCGTTTGATTGTGGATCTAGGAAGGAAGCA
131 AAGGTAATTCTACCTTCTCGTTTGATTGTGGATCTAGGAAGGAAGCA
3769018 AAA
1 AAA
3769021 CAACCTGCAC
Statistics
Matches: 179, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
176 148 0.83
177 31 0.17
ACGTcount: A:0.41, C:0.06, G:0.28, T:0.26
Consensus pattern (177 bp):
AAAGGAAAATAAATGAAATAATAAAGATAAGAAATGAAATAAAATAAAGAAATGATAGAGATGGC
TGCGGAATTGATGGAAGAGATGGATGATGTTGATGATGAAATGGCAATGGTGGTGATGTTGATGT
AAGGTAATTCTACCTTCTCGTTTGATTGTGGATCTAGGAAGGAAGCA
Found at i:3771650 original size:13 final size:13
Alignment explanation
Indices: 3771628--3771657 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3771618 ACTAAACACC
3771628 TTTC-ACATACCT
1 TTTCAACATACCT
3771640 TTTCAACATACCT
1 TTTCAACATACCT
3771653 TTTCA
1 TTTCA
3771658 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:3774462 original size:23 final size:24
Alignment explanation
Indices: 3774406--3774464 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
3774396 ACTTTTCTTT
*
3774406 CTTTC-TTTTCTTCTTTTCGAGTG
1 CTTTCATTTTCTTCTTTTAGAGTG
*
3774429 CTTTCAATTTCTTC-TTTAGAGTG
1 CTTTCATTTTCTTCTTTTAGAGTG
**
3774452 CTTTTGTTTTCTT
1 CTTTCATTTTCTT
3774465 TGCTGAACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.08, C:0.19, G:0.12, T:0.61
Consensus pattern (24 bp):
CTTTCATTTTCTTCTTTTAGAGTG
Found at i:3775410 original size:90 final size:91
Alignment explanation
Indices: 3775257--3775428 Score: 256
Period size: 90 Copynumber: 1.9 Consensus size: 91
3775247 GGAAATGATT
* * *
3775257 CTTGGCCGAATAGGGAGATAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGACACAT-G
1 CTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGACACATGG
*
3775321 GGGCTGTTCACATGCAAAACACATGG
66 GGGCTGGTCACATGCAAAACACATGG
* * * *
3775347 CTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCTCATGCAAGGCACATGG
1 CTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGACACATGG
*
3775412 GGGCTGGTCATATGCAA
66 GGGCTGGTCACATGCAA
3775429 GGAACATGGG
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 56 0.78
91 16 0.22
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (91 bp):
CTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGACACATGG
GGGCTGGTCACATGCAAAACACATGG
Found at i:3781348 original size:30 final size:30
Alignment explanation
Indices: 3781312--3781378 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
3781302 TCGTTTGAAA
* *
3781312 TTTTTTGAAATTTTGGC-TTTTTTGGCTTTT
1 TTTTTTG-AATTTTGCCTTTTTTTGCCTTTT
**
3781342 TTTTTTGTTTTTTGCCTTTTTTTGCCTTTT
1 TTTTTTGAATTTTGCCTTTTTTTGCCTTTT
3781372 TTTTTTG
1 TTTTTTG
3781379 TTTTTTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.04, C:0.09, G:0.13, T:0.73
Consensus pattern (30 bp):
TTTTTTGAATTTTGCCTTTTTTTGCCTTTT
Found at i:3781361 original size:9 final size:10
Alignment explanation
Indices: 3781349--3781374 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3781339 TTTTTTTTTG
3781349 TTTTTTGCCT
1 TTTTTTGCCT
3781359 TTTTTTGCCT
1 TTTTTTGCCT
3781369 TTTTTT
1 TTTTTT
3781375 TTTGTTTTTT
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:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (10 bp):
TTTTTTGCCT
Found at i:3782698 original size:35 final size:36
Alignment explanation
Indices: 3782618--3782718 Score: 132
Period size: 35 Copynumber: 2.8 Consensus size: 36
3782608 TGCATGTATC
3782618 ACATCACCATCTTCCATCACCATTTACACGCCTATA
1 ACATCACCATCTTCCATCACCATTTACACGCCTATA
* *
3782654 ACATCACCATCTTCCATTACCA-TTGCACGCCTATA
1 ACATCACCATCTTCCATCACCATTTACACGCCTATA
* * * *
3782689 TCATTACCATCTTCTATCACCGTTTCACAC
1 ACATCACCATCTTCCATCACCATTT-ACAC
3782719 CTAAATAACC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
35 29 0.53
36 23 0.42
37 3 0.05
ACGTcount: A:0.28, C:0.38, G:0.04, T:0.31
Consensus pattern (36 bp):
ACATCACCATCTTCCATCACCATTTACACGCCTATA
Found at i:3794762 original size:30 final size:31
Alignment explanation
Indices: 3794721--3794780 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
3794711 ACATGCTGCC
**
3794721 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
3794752 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
3794781 TAAAACTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:3796261 original size:21 final size:23
Alignment explanation
Indices: 3796230--3796272 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3796220 TCTTCAGTTG
*
3796230 CATTGTCTTTAA-GTTTTTCTTT
1 CATTGTCTTTAATGTTCTTCTTT
3796252 CATTG-CTTTAATGTTCTTCTT
1 CATTGTCTTTAATGTTCTTCTT
3796273 CAAGGTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.14, C:0.16, G:0.09, T:0.60
Consensus pattern (23 bp):
CATTGTCTTTAATGTTCTTCTTT
Found at i:3797223 original size:13 final size:12
Alignment explanation
Indices: 3797183--3797224 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
3797173 TTGGCTTGCT
3797183 TTTTCTTTTTGAA
1 TTTTCTTTTTG-A
*
3797196 TTTTCTTTTT-C
1 TTTTCTTTTTGA
3797207 TTTTCTTTTCTGA
1 TTTTCTTTT-TGA
3797220 TTTTC
1 TTTTC
3797225 ATTCCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTTCTTTTTGA
Found at i:3797234 original size:24 final size:23
Alignment explanation
Indices: 3797181--3797234 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
3797171 CCTTGGCTTG
*
3797181 CTTTTTCTTTTTGAATTTTCTTT
1 CTTTTTCTTTTTGAATTTTCTTC
*
3797204 TTCTTTTCTTTTCTG-ATTTTCATTC
1 CT-TTTTCTTTT-TGAATTTTC-TTC
3797229 CTTTTT
1 CTTTTT
3797235 ACACTCTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 1 0.04
24 19 0.76
25 5 0.20
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (23 bp):
CTTTTTCTTTTTGAATTTTCTTC
Found at i:3797528 original size:18 final size:18
Alignment explanation
Indices: 3797481--3797530 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
3797471 TTAGTAAAGG
3797481 AAAATAAATGAAAT--AAT
1 AAAATAAA-GAAATGAAAT
*
3797498 AAAGAT-AATAAATGAAAT
1 AAA-ATAAAGAAATGAAAT
3797516 AAAATAAAGAAATGA
1 AAAATAAAGAAATGA
3797531 TAGAGATGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 16 0.59
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (18 bp):
AAAATAAAGAAATGAAAT
Found at i:3798932 original size:30 final size:31
Alignment explanation
Indices: 3798891--3798950 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
3798881 ACATGCTACC
**
3798891 ATGATATCTAAATGATATGAAAACATAATAA
1 ATGATATCTAAAACATATGAAAACATAATAA
*
3798922 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGAAAACATAATA
3798951 TAAAACTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGAAAACATAATAA
Found at i:3805960 original size:18 final size:19
Alignment explanation
Indices: 3805923--3805960 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3805913 AACCCCTTTG
*
3805923 AAAATACATGATTTTTTAAT
1 AAAATACATGA-TATTTAAT
3805943 AAAATACATGA-ATTTAAT
1 AAAATACATGATATTTAAT
3805961 GAAGAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (19 bp):
AAAATACATGATATTTAAT
Found at i:3818152 original size:746 final size:746
Alignment explanation
Indices: 3816721--3818214 Score: 2952
Period size: 746 Copynumber: 2.0 Consensus size: 746
3816711 CTGAGTTGCC
3816721 AAAAGTGATGTCAAAGGTAGCTATTTGGAGCTGAGTTGCCAACACATAACCATTCGGCCAAGAGC
1 AAAAGTGATGTCAAAGGTAGCTATTTGGAGCTGAGTTGCCAACACATAACCATTCGGCCAAGAGC
*
3816786 ATGTATCTTCATTTAAATCATGTATTTTCATCAAAAATCATGTATTTTCAAAGGGGTTTCAACCT
66 ATGTATCTTCATTTAAATCATGTATTTTCATCAAAAATCATATATTTTCAAAGGGGTTTCAACCT
3816851 TGGCCGAACCATCAAGTATTTATTCAGCCTAAACCCTTTTAAAACTATATATAGGCCATCATATT
131 TGGCCGAACCATCAAGTATTTATTCAGCCTAAACCCTTTTAAAACTATATATAGGCCATCATATT
3816916 TCATTTGTAATCAGACCTTTTTGATTCATATAAGTGAGAGTATTCTCTTTCTTAAGTCCTGCTGA
196 TCATTTGTAATCAGACCTTTTTGATTCATATAAGTGAGAGTATTCTCTTTCTTAAGTCCTGCTGA
3816981 CTTTTATCGACTTGTCAAGTATTTTATACTTGTGGCATCAACCCCTTTTTTCACCATGATACTTC
261 CTTTTATCGACTTGTCAAGTATTTTATACTTGTGGCATCAACCCCTTTTTTCACCATGATACTTC
3817046 TAGTTCCTAGTTCATATAACTAGTGGGTCAAAGTACTTAATACCACCCCTTGTAGAAGCAATATA
326 TAGTTCCTAGTTCATATAACTAGTGGGTCAAAGTACTTAATACCACCCCTTGTAGAAGCAATATA
*
3817111 AAGTATGGGTCTTTTCTCTCTATAACATTGGTTCTTCTTTGAGACTTCTTCAAGATACTATCCTC
391 AAGTATGGGTCTTTGCTCTCTATAACATTGGTTCTTCTTTGAGACTTCTTCAAGATACTATCCTC
3817176 ACTACCGTCCCTTTTGTTTCATCGCCATAACCATAGTCATATCAACCATTTTCCACTTCCATCAT
456 ACTACCGTCCCTTTTGTTTCATCGCCATAACCATAGTCATATCAACCATTTTCCACTTCCATCAT
3817241 TTATTATTTAAACATCCCTCCTATTCACCTATACGTTTACCACCCTTAACCCTCTCTTTTTGAGC
521 TTATTATTTAAACATCCCTCCTATTCACCTATACGTTTACCACCCTTAACCCTCTCTTTTTGAGC
3817306 CATTCACTTGTGCAGGTTGTTTGCTTCCTTCCTAGATCCACAACCAATTTGTTAAGGTACAAATG
586 CATTCACTTGTGCAGGTTGTTTGCTTCCTTCCTAGATCCACAACCAATTTGTTAAGGTACAAATG
*
3817371 CCTTACATCAAGCGGTAATCAGAGCTTTGGTGGAAGAAAGCAATGTGCAACAACAACGAAAAGAA
651 CCTTACATCAAGCGGTAATCAGAGCTTTGGTGGAAGAAAGCAATGTGCAACAACAACAAAAAGAA
3817436 AAATACAAAAAGAAGTGCAAAGTGAAGTGCA
716 AAATACAAAAAGAAGTGCAAAGTGAAGTGCA
3817467 AAAAGTGATGTCAAAGGTAGCTATTTGGAGCTGAGTTGCCAACACATAACCATTCGGCCAAGAGC
1 AAAAGTGATGTCAAAGGTAGCTATTTGGAGCTGAGTTGCCAACACATAACCATTCGGCCAAGAGC
3817532 ATGTATCTTCATTTAAATCATGTATTTTCATCAAAAATCATATATTTTCAAAGGGGTTTCAACCT
66 ATGTATCTTCATTTAAATCATGTATTTTCATCAAAAATCATATATTTTCAAAGGGGTTTCAACCT
3817597 TGGCCGAACCATCAAGTATTTATTCAGCCTAAACCCTTTTAAAACTATATATAGGCCATCATATT
131 TGGCCGAACCATCAAGTATTTATTCAGCCTAAACCCTTTTAAAACTATATATAGGCCATCATATT
3817662 TCATTTGTAATCAGACCTTTTTGATTCATATAAGTGAGAGTATTCTCTTTCTTAAGTCCTGCTGA
196 TCATTTGTAATCAGACCTTTTTGATTCATATAAGTGAGAGTATTCTCTTTCTTAAGTCCTGCTGA
3817727 CTTTTATCGACTTGTCAAGTATTTTATACTTGTGGCATCAACCCCTTTTTTCACCATGATACTTC
261 CTTTTATCGACTTGTCAAGTATTTTATACTTGTGGCATCAACCCCTTTTTTCACCATGATACTTC
3817792 TAGTTCCTAGTTCATATAACTAGTGGGTCAAAGTACTTAATACCACCCCTTGTAGAAGCAATATA
326 TAGTTCCTAGTTCATATAACTAGTGGGTCAAAGTACTTAATACCACCCCTTGTAGAAGCAATATA
3817857 AAGTATGGGTCTTTGCTCTCTATAACATTGGTTCTTCTTTGAGACTTCTTCAAGATACTATCCTC
391 AAGTATGGGTCTTTGCTCTCTATAACATTGGTTCTTCTTTGAGACTTCTTCAAGATACTATCCTC
3817922 ACTACCGTCCCTTTTGTTTCATCGCCATAACCATAGTCATATCAACCATTTTCCACTTCCATCAT
456 ACTACCGTCCCTTTTGTTTCATCGCCATAACCATAGTCATATCAACCATTTTCCACTTCCATCAT
3817987 TTATTATTTAAACATCCCTCCTATTCACCTATACGTTTACCACCCTTAACCCTCTCTTTTTGAGC
521 TTATTATTTAAACATCCCTCCTATTCACCTATACGTTTACCACCCTTAACCCTCTCTTTTTGAGC
3818052 CATTCACTTGTGCAGGTTGTTTGCTTCCTTCCTAGATCCACAACCAATTTGTTAAGGTACAAATG
586 CATTCACTTGTGCAGGTTGTTTGCTTCCTTCCTAGATCCACAACCAATTTGTTAAGGTACAAATG
3818117 CCTTACATCAAGCGGTAATCAGAGCTTTGGTGGAAGAAAGCAATGTGCAACAACAACAAAAAGAA
651 CCTTACATCAAGCGGTAATCAGAGCTTTGGTGGAAGAAAGCAATGTGCAACAACAACAAAAAGAA
*
3818182 AAATACAGAAAGAAGTGCAAAGTGAAGTGCA
716 AAATACAAAAAGAAGTGCAAAGTGAAGTGCA
3818213 AA
1 AA
3818215 GTCAAGGAAT
Statistics
Matches: 744, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
746 744 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (746 bp):
AAAAGTGATGTCAAAGGTAGCTATTTGGAGCTGAGTTGCCAACACATAACCATTCGGCCAAGAGC
ATGTATCTTCATTTAAATCATGTATTTTCATCAAAAATCATATATTTTCAAAGGGGTTTCAACCT
TGGCCGAACCATCAAGTATTTATTCAGCCTAAACCCTTTTAAAACTATATATAGGCCATCATATT
TCATTTGTAATCAGACCTTTTTGATTCATATAAGTGAGAGTATTCTCTTTCTTAAGTCCTGCTGA
CTTTTATCGACTTGTCAAGTATTTTATACTTGTGGCATCAACCCCTTTTTTCACCATGATACTTC
TAGTTCCTAGTTCATATAACTAGTGGGTCAAAGTACTTAATACCACCCCTTGTAGAAGCAATATA
AAGTATGGGTCTTTGCTCTCTATAACATTGGTTCTTCTTTGAGACTTCTTCAAGATACTATCCTC
ACTACCGTCCCTTTTGTTTCATCGCCATAACCATAGTCATATCAACCATTTTCCACTTCCATCAT
TTATTATTTAAACATCCCTCCTATTCACCTATACGTTTACCACCCTTAACCCTCTCTTTTTGAGC
CATTCACTTGTGCAGGTTGTTTGCTTCCTTCCTAGATCCACAACCAATTTGTTAAGGTACAAATG
CCTTACATCAAGCGGTAATCAGAGCTTTGGTGGAAGAAAGCAATGTGCAACAACAACAAAAAGAA
AAATACAAAAAGAAGTGCAAAGTGAAGTGCA
Found at i:3818270 original size:28 final size:26
Alignment explanation
Indices: 3818238--3818298 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 26
3818228 GCATATAATC
*
3818238 AGAAAAGAAAGTGAAGCACTCAAAAGA
1 AGAAAAGAAA-TCAAGCACTCAAAAGA
* *
3818265 A-AGAA-AAATCCAGCACTCAAAAGA
1 AGAAAAGAAATCAAGCACTCAAAAGA
3818289 AGAAAAGAAA
1 AGAAAAGAAA
3818299 AGAAAGAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
24 15 0.54
25 6 0.21
26 6 0.21
27 1 0.04
ACGTcount: A:0.62, C:0.13, G:0.18, T:0.07
Consensus pattern (26 bp):
AGAAAAGAAATCAAGCACTCAAAAGA
Found at i:3826078 original size:19 final size:20
Alignment explanation
Indices: 3826054--3826093 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3826044 TATCCCATCC
3826054 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
3826073 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
3826093 T
1 T
3826094 ATTATTATCC
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:3827097 original size:16 final size:15
Alignment explanation
Indices: 3827076--3827121 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
3827066 TGAATATATA
3827076 ATAAAGGAAATGAAAT
1 ATAAA-GAAATGAAAT
*
3827092 ATAAAGAAATGAAAG
1 ATAAAGAAATGAAAT
*
3827107 A-ATAGAAATGAAAT
1 ATAAAGAAATGAAAT
3827121 A
1 A
3827122 AATAAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 12 0.44
15 10 0.37
16 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAGAAATGAAAT
Found at i:3827105 original size:20 final size:20
Alignment explanation
Indices: 3827062--3827110 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3827052 ATGGTCTTAA
*
3827062 GAAATGAATATATAATAAAG
1 GAAATGAATATATAAGAAAG
*
3827082 GAAATGAA-ATATAAAGAAAT
1 GAAATGAATATAT-AAGAAAG
3827102 GAAA-GAATA
1 GAAATGAATA
3827111 GAAATGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.63, C:0.00, G:0.16, T:0.20
Consensus pattern (20 bp):
GAAATGAATATATAAGAAAG
Found at i:3827577 original size:19 final size:21
Alignment explanation
Indices: 3827534--3827585 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
3827524 GAAACCCCTT
3827534 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
3827555 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
3827574 TGAAGATACATG
1 TGAAAATACATG
3827586 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:3830891 original size:11 final size:11
Alignment explanation
Indices: 3830877--3830932 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
3830867 TCTTTTTGAA
3830877 TTCTTTTTCTT
1 TTCTTTTTCTT
3830888 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
3830901 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
3830914 TGTCTTTTTC-T
1 T-TCTTTTTCTT
3830925 TTCTTTTT
1 TTCTTTTT
3830933 GTACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:3830901 original size:19 final size:18
Alignment explanation
Indices: 3830877--3830932 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
3830867 TCTTTTTGAA
3830877 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
3830895 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
3830914 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
3830932 T
1 T
3830933 GTACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:3831703 original size:19 final size:21
Alignment explanation
Indices: 3831660--3831711 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
3831650 GAAACCCCTT
3831660 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
3831681 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
3831700 TGAAGATACATG
1 TGAAAATACATG
3831712 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:3832555 original size:22 final size:23
Alignment explanation
Indices: 3832518--3832561 Score: 72
Period size: 22 Copynumber: 1.9 Consensus size: 23
3832508 AACTATATAA
3832518 TGCATATAATATAATGATGTGATG
1 TGCATAT-ATATAATGATGTGATG
3832542 TGCATAT-TATAATGATGTGA
1 TGCATATATATAATGATGTGA
3832562 ACTATAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (23 bp):
TGCATATATATAATGATGTGATG
Found at i:3833793 original size:19 final size:20
Alignment explanation
Indices: 3833756--3833808 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
3833746 TTCGGCCAAG
* *
3833756 ATCATTTATCTTCAGT-AAA
1 ATCATGTATTTTCAGTAAAA
* *
3833775 ATTATGTATTTTCATTAAAA
1 ATCATGTATTTTCAGTAAAA
*
3833795 ATCATGTGTTTTCA
1 ATCATGTATTTTCA
3833809 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (20 bp):
ATCATGTATTTTCAGTAAAA
Found at i:3834516 original size:14 final size:14
Alignment explanation
Indices: 3834497--3834523 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3834487 ATGATAGAGA
3834497 ATGGTGATGAAAAG
1 ATGGTGATGAAAAG
3834511 ATGGTGATGAAAA
1 ATGGTGATGAAAA
3834524 TAGATAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (14 bp):
ATGGTGATGAAAAG
Found at i:3834968 original size:16 final size:16
Alignment explanation
Indices: 3834934--3834980 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 16
3834924 ATAACATCTC
*
3834934 TATCCATTTTATTTCT
1 TATCCATTTCATTTCT
3834950 TATCC-TTTCATTTCT
1 TATCCATTTCATTTCT
3834965 T-T--ATTTCATTTCT
1 TATCCATTTCATTTCT
3834978 TAT
1 TAT
3834981 TTCCAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.39
14 2 0.07
15 10 0.36
16 5 0.18
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (16 bp):
TATCCATTTCATTTCT
Found at i:3834982 original size:12 final size:13
Alignment explanation
Indices: 3834955--3834983 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3834945 TTTCTTATCC
3834955 TTTCATTTCTTTA
1 TTTCATTTCTTTA
3834968 TTTCATTTC-TTA
1 TTTCATTTCTTTA
3834980 TTTC
1 TTTC
3834984 CAATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:3839285 original size:24 final size:21
Alignment explanation
Indices: 3839250--3839292 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
3839240 GGCTCATTCT
*
3839250 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
3839273 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
3839293 ATCTTGTGCA
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:3847007 original size:13 final size:13
Alignment explanation
Indices: 3846989--3847049 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
3846979 TATAGGCGTG
3846989 ATATGGTGATGAA
1 ATATGGTGATGAA
*
3847002 ATATGGTGATGAT
1 ATATGGTGATGAA
* *
3847015 ATA-GGCG-TGAT
1 ATATGGTGATGAA
*
3847026 A-ATGGTGATGGA
1 ATATGGTGATGAA
*
3847038 CTATGGTGATGA
1 ATATGGTGATGA
3847050 TATAGGCGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
10 1 0.03
11 8 0.21
12 5 0.13
13 24 0.63
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.31
Consensus pattern (13 bp):
ATATGGTGATGAA
Found at i:3847043 original size:36 final size:36
Alignment explanation
Indices: 3846970--3847085 Score: 171
Period size: 36 Copynumber: 3.2 Consensus size: 36
3846960 ATTTAGAAGT
* *
3846970 TGGTGATAATATAGGCGTGAT-ATGGTGATGAAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
3847005 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
3847041 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGG-TGATGGAATA
3847078 TGGTGATG
1 TGGTGATG
3847086 GAAATAGTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
35 20 0.27
36 38 0.51
37 16 0.22
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:3852725 original size:13 final size:13
Alignment explanation
Indices: 3852707--3852767 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
3852697 TATAGGCGTG
3852707 ATATGGTGATGAA
1 ATATGGTGATGAA
*
3852720 ATATGGTGATGAT
1 ATATGGTGATGAA
* *
3852733 ATA-GGCG-TGAT
1 ATATGGTGATGAA
*
3852744 A-ATGGTGATGGA
1 ATATGGTGATGAA
*
3852756 CTATGGTGATGA
1 ATATGGTGATGA
3852768 TATAGGCGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
10 1 0.03
11 8 0.21
12 5 0.13
13 24 0.63
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.31
Consensus pattern (13 bp):
ATATGGTGATGAA
Found at i:3852761 original size:36 final size:36
Alignment explanation
Indices: 3852688--3852802 Score: 169
Period size: 36 Copynumber: 3.2 Consensus size: 36
3852678 ATTTAGAAGT
* *
3852688 TGGTGATAATATAGGCGTGAT-ATGGTGATGAAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
3852723 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
3852759 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGG-TGATGGAATA
3852796 TGGTGAT
1 TGGTGAT
3852803 TGAAATAGTA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.27
36 38 0.52
37 15 0.21
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:3854818 original size:9 final size:9
Alignment explanation
Indices: 3854804--3854843 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
3854794 AAATGGAAAT
3854804 AAGAAATGA
1 AAGAAATGA
3854813 AAGAAA-GA
1 AAGAAATGA
3854821 AATGAAATGA
1 AA-GAAATGA
3854831 TAAGAAATGA
1 -AAGAAATGA
3854841 AAG
1 AAG
3854844 GGATAGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 4 0.14
9 13 0.46
10 9 0.32
11 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (9 bp):
AAGAAATGA
Found at i:3854837 original size:15 final size:14
Alignment explanation
Indices: 3854802--3854843 Score: 68
Period size: 13 Copynumber: 3.0 Consensus size: 14
3854792 TTAAATGGAA
3854802 ATAAGAAATGAAAG
1 ATAAGAAATGAAAG
3854816 A-AAGAAATGAAATG
1 ATAAGAAATGAAA-G
3854830 ATAAGAAATGAAAG
1 ATAAGAAATGAAAG
3854844 GGATAGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.14
Consensus pattern (14 bp):
ATAAGAAATGAAAG
Found at i:3856686 original size:18 final size:19
Alignment explanation
Indices: 3856649--3856686 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3856639 AACCCCTTTG
*
3856649 AAAATACATGATTTTTTAAT
1 AAAATACATGA-TATTTAAT
3856669 AAAATACATGA-ATTTAAT
1 AAAATACATGATATTTAAT
3856687 GAAGAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (19 bp):
AAAATACATGATATTTAAT
Found at i:3864324 original size:20 final size:19
Alignment explanation
Indices: 3864280--3864325 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
3864270 TATTTTTTTT
*
3864280 CAAAAAAACAAAAAAAAGG
1 CAAAAAAACAAAAAAAAGC
3864299 CAAAAAAACAAAAAAAAAGC
1 CAAAAAAAC-AAAAAAAAGC
*
3864319 CCAAAAA
1 CAAAAAA
3864326 GCCAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (19 bp):
CAAAAAAACAAAAAAAAGC
Found at i:3864325 original size:19 final size:19
Alignment explanation
Indices: 3864280--3864318 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3864270 TATTTTTTTT
*
3864280 CAAAAAAACAAAAAAAAGG
1 CAAAAAAACAAAAAAAAAG
3864299 CAAAAAAACAAAAAAAAAG
1 CAAAAAAACAAAAAAAAAG
3864318 C
1 C
3864319 CCAAAAAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.79, C:0.13, G:0.08, T:0.00
Consensus pattern (19 bp):
CAAAAAAACAAAAAAAAAG
Found at i:3864332 original size:21 final size:20
Alignment explanation
Indices: 3864280--3864325 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
3864270 TATTTTTTTT
*
3864280 CAAAAAAAC-AAAAAAAAGG
1 CAAAAAAACAAAAAAAAAGC
3864299 CAAAAAAACAAAAAAAAAGCC
1 CAAAAAAACAAAAAAAAAG-C
3864320 CAAAAA
1 CAAAAA
3864326 GCCAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 9 0.38
20 9 0.38
21 6 0.25
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (20 bp):
CAAAAAAACAAAAAAAAAGC
Found at i:3870121 original size:50 final size:50
Alignment explanation
Indices: 3870055--3870175 Score: 233
Period size: 50 Copynumber: 2.4 Consensus size: 50
3870045 AGGATCAGAT
3870055 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAGTTA
3870105 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAGTTA
*
3870155 TTATTATTTTATTAAGAATTA
1 TTATTATTTTATTAGGAATTA
3870176 GAGTTAAAAC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.50
Consensus pattern (50 bp):
TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAGTTA
Found at i:3871786 original size:5 final size:5
Alignment explanation
Indices: 3871768--3871797 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
3871758 GTGCTTCAAC
3871768 TTTCT TTT-T TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
3871798 CTTTTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTCT
Found at i:3874044 original size:28 final size:26
Alignment explanation
Indices: 3874012--3874072 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 26
3874002 GAATATAATC
*
3874012 AGAAAAGAAAGTGAAGCACTCAAAAGA
1 AGAAAAGAAA-TCAAGCACTCAAAAGA
* *
3874039 A-AGAA-AAATCCAGCACTCAAAAGA
1 AGAAAAGAAATCAAGCACTCAAAAGA
3874063 AGAAAAGAAA
1 AGAAAAGAAA
3874073 AGAAAGAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
24 15 0.54
25 6 0.21
26 6 0.21
27 1 0.04
ACGTcount: A:0.62, C:0.13, G:0.18, T:0.07
Consensus pattern (26 bp):
AGAAAAGAAATCAAGCACTCAAAAGA
Found at i:3880022 original size:36 final size:36
Alignment explanation
Indices: 3879970--3880118 Score: 237
Period size: 36 Copynumber: 4.2 Consensus size: 36
3879960 GATACTATTT
* *
3879970 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
3880006 TCATCACCATAGTCCATCACCATTATCACGTCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
3880042 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
* *
3880078 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
3880113 ACATCA
1 TCATCA
3880119 TCCTTCCATT
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 17 0.16
36 89 0.84
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACGCCTATA
Found at i:3880025 original size:13 final size:11
Alignment explanation
Indices: 3879970--3880104 Score: 80
Period size: 13 Copynumber: 11.3 Consensus size: 11
3879960 GATACTATTT
3879970 TCATCACCATAA
1 TCATCACCAT-A
*
3879982 TCCATCTCCATTA
1 T-CATCACCA-TA
*
3879995 TCA-CGCCTATA
1 TCATCACC-ATA
3880006 TCATCACCATA
1 TCATCACCATA
3880017 GTCCATCACCAT-
1 -T-CATCACCATA
3880029 T-ATCACGTCTATA
1 TCATCAC--C-ATA
3880042 TCATCACCATA
1 TCATCACCATA
3880053 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
3880067 TCA-CGCCTATA
1 TCATCACC-ATA
3880078 TCATCACCATA
1 TCATCACCATA
3880089 TTCCATCACCATA
1 -T-CATCACCATA
3880102 TCA
1 TCA
3880105 CGCCAATAAC
Statistics
Matches: 100, Mismatches: 5, Indels: 37
0.70 0.04 0.26
Matches are distributed among these distances:
9 5 0.05
11 29 0.29
12 20 0.20
13 38 0.38
14 8 0.08
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:3880133 original size:33 final size:33
Alignment explanation
Indices: 3879982--3880157 Score: 99
Period size: 36 Copynumber: 5.1 Consensus size: 33
3879972 ATCACCATAA
* * *
3879982 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* * *
3880016 AGTCCATCACCATTATCACGTCTATATCATCA-CCAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
3880052 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
3880090 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
3880123 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
3880156 TC
1 TC
3880158 ATTCATCAAC
Statistics
Matches: 127, Mismatches: 9, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
33 24 0.19
34 7 0.06
35 17 0.13
36 77 0.61
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:3883848 original size:24 final size:25
Alignment explanation
Indices: 3883815--3883870 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
3883805 TTTTCTTTGC
*
3883815 TTTTTC-TTCTTTTGAGTG-CTGGA
1 TTTTTCTTTCTTTGGAGTGCCTGGA
*
3883838 TTTTTCTTTCTTTGGAGTGCCTTGA
1 TTTTTCTTTCTTTGGAGTGCCTGGA
3883863 -TTTTCTTT
1 TTTTTCTTT
3883871 ACTGGTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.21
24 19 0.66
25 4 0.14
ACGTcount: A:0.07, C:0.14, G:0.18, T:0.61
Consensus pattern (25 bp):
TTTTTCTTTCTTTGGAGTGCCTGGA
Found at i:3884561 original size:19 final size:20
Alignment explanation
Indices: 3884514--3884564 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
3884504 GAAACCGTTT
**
3884514 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
3884534 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
3884553 TGAAGATACATG
1 TGAAAATACATG
3884565 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:3887838 original size:25 final size:23
Alignment explanation
Indices: 3887782--3887840 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
3887772 TTTCTTTGCT
*
3887782 TTTTCTTCT-TTTGAGTGCTGGA
1 TTTTCTTTTCTTTGAGTGCTGGA
*
3887804 TTTT-TATTTCTTTGTAGTGCTTTGA
1 TTTTCT-TTTCTTTG-AGTGC-TGGA
3887829 TTTTCTTTTCTT
1 TTTTCTTTTCTT
3887841 GATTTTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 1 0.03
22 6 0.20
23 4 0.13
24 5 0.17
25 13 0.43
26 1 0.03
ACGTcount: A:0.08, C:0.12, G:0.15, T:0.64
Consensus pattern (23 bp):
TTTTCTTTTCTTTGAGTGCTGGA
Found at i:3888518 original size:19 final size:20
Alignment explanation
Indices: 3888471--3888521 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
3888461 GAAACCCTTT
**
3888471 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
3888491 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
3888510 TGAAGATACATG
1 TGAAAATACATG
3888522 CTCTTGCCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:3892663 original size:13 final size:13
Alignment explanation
Indices: 3892639--3892671 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3892629 AACAAAAAAA
*
3892639 CAAAAAAAAAAGG
1 CAAAAAAAAAAGC
3892652 CAAAAAAAAAAGC
1 CAAAAAAAAAAGC
3892665 CAAAAAA
1 CAAAAAA
3892672 TCCAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAGC
Found at i:3892669 original size:12 final size:12
Alignment explanation
Indices: 3892632--3892671 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
3892622 AAAAAAAAAC
3892632 AAAAAAA-CAAA
1 AAAAAAAGCAAA
3892643 AAAAAAAGGCAAA
1 AAAAAAA-GCAAA
3892656 AAAAAAAGCCAAA
1 AAAAAAAG-CAAA
3892669 AAA
1 AAA
3892672 TCCAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.27
12 1 0.04
13 18 0.69
ACGTcount: A:0.82, C:0.10, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAGCAAA
Found at i:3898014 original size:21 final size:21
Alignment explanation
Indices: 3897988--3898035 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3897978 GATGTAGGAG
*
3897988 TCTTTTTCTTTTCTTT-TTGTT
1 TCTTTTT-TCTTCTTTCTTGTT
3898009 TCTTTTTTCTTCTTTCTTGTT
1 TCTTTTTTCTTCTTTCTTGTT
*
3898030 GCTTTT
1 TCTTTT
3898036 GTTGTAGCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (21 bp):
TCTTTTTTCTTCTTTCTTGTT
Found at i:3898450 original size:35 final size:36
Alignment explanation
Indices: 3898411--3898490 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 36
3898401 AAATGGAATT
**
3898411 TGGTGATGATATAGGCGTGAT-ATGATGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGATGATGGAAGA
*
3898446 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGATGATGGAAGA
3898482 TGGTGATGA
1 TGGTGATGA
3898491 ACAGATTGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 21 0.51
36 20 0.49
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGATGATGGAAGA
Found at i:3898876 original size:19 final size:20
Alignment explanation
Indices: 3898831--3898879 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
3898821 AACCCCTTTC
**
3898831 AAAATACATGATTTTTGATG
1 AAAATACATGATTTTAAATG
3898851 AAAATACATGA-TTTAAATG
1 AAAATACATGATTTTAAATG
*
3898870 AAGATACATG
1 AAAATACATG
3898880 CTCTTCGCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
AAAATACATGATTTTAAATG
Found at i:3900754 original size:30 final size:31
Alignment explanation
Indices: 3900702--3900761 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
3900692 CTTAGCTTTA
**
3900702 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
3900732 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
3900762 GGCAGCATGT
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:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:3901613 original size:19 final size:21
Alignment explanation
Indices: 3901589--3901640 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3901579 CGGCCAAGAG
*
3901589 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
3901608 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
3901629 CATGTATTTTCA
1 CATGTATTTTCA
3901641 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
Done.