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 16 of 16
Found at i:3981759 original size:17 final size:15
Alignment explanation
Indices: 3981725--3981767 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
3981715 ACTTTGATAT
*
3981725 CATTTCTTTCCATTC
1 CATTTCTTTCAATTC
3981740 CATTTCTTATCAATTTC
1 CATTTCTT-TCAA-TTC
3981757 CATTTCTTTCA
1 CATTTCTTTCA
3981768 TTTCTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 8 0.32
16 6 0.24
17 11 0.44
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.53
Consensus pattern (15 bp):
CATTTCTTTCAATTC
Found at i:3986098 original size:173 final size:173
Alignment explanation
Indices: 3985773--3986128 Score: 669
Period size: 172 Copynumber: 2.1 Consensus size: 173
3985763 AGAAGACTCA
* *
3985773 AAGAAGAACCAATGTTAAAGAACAAAGACCCAGACTTTATATTGCTTCTTTAAGGGCTGGTAAAC
1 AAGAATAAACAATGTTAAAGAACAAAGACCCAGACTTTATATTGCTTCTTTAAGGGCTGGTAAAC
3985838 AAGGAATTTGACCCACTATCTATAAAGACATAGGAACCAGAAGTATCAGGGTGAATAGATAGGGG
66 AAGGAATTTGACCCACTATCTATAAAGACATAGGAACCAGAAGTATCAGGGTGAATAGATAGGGG
3985903 TGACGCCACAAGCATAAGCTTGATAAGTTGATAAAGTTCACTT
131 TGACGCCACAAGCATAAGCTTGATAAGTTGATAAAGTTCACTT
3985946 AAGAATAAACAATGTTAAAGAA-AAAGACCCAGACTTTATATTGCTTCTTTAAGGGCTGGTAAAC
1 AAGAATAAACAATGTTAAAGAACAAAGACCCAGACTTTATATTGCTTCTTTAAGGGCTGGTAAAC
3986010 AAGGAATTTGACCCACTATCTATAAAGACATAGGAACCAGAAGTATCAGGGTGACATAGATAGGG
66 AAGGAATTTGACCCACTATCTATAAAGACATAGGAACCAGAAGTATCAGGGTGA-ATAGATAGGG
3986075 GTGACGCCACAAGCATAAGCTTGATAAGTTGATAAAGTTCACTT
130 GTGACGCCACAAGCATAAGCTTGATAAGTTGATAAAGTTCACTT
3986119 AAGAACTAAA
1 AAGAA-TAAA
3986129 GATAGAAACT
Statistics
Matches: 179, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
172 96 0.54
173 79 0.44
174 4 0.02
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (173 bp):
AAGAATAAACAATGTTAAAGAACAAAGACCCAGACTTTATATTGCTTCTTTAAGGGCTGGTAAAC
AAGGAATTTGACCCACTATCTATAAAGACATAGGAACCAGAAGTATCAGGGTGAATAGATAGGGG
TGACGCCACAAGCATAAGCTTGATAAGTTGATAAAGTTCACTT
Found at i:3991059 original size:23 final size:24
Alignment explanation
Indices: 3991017--3991069 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
3991007 TTTCTTTCTT
3991017 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
3991041 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
3991064 TTTCTT
1 TTTCTT
3991070 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:3997168 original size:17 final size:17
Alignment explanation
Indices: 3997146--3997179 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3997136 CTATCTACCC
3997146 CTATACCATAACCATTT
1 CTATACCATAACCATTT
*
3997163 CTATACCCTAACCATTT
1 CTATACCATAACCATTT
3997180 TTTAAGTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (17 bp):
CTATACCATAACCATTT
Found at i:4017039 original size:19 final size:21
Alignment explanation
Indices: 4017015--4017066 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
4017005 CGGCCAAGAG
*
4017015 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
4017034 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
4017055 CATGTATTTTCA
1 CATGTATTTTCA
4017067 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:4025447 original size:35 final size:37
Alignment explanation
Indices: 4025401--4025480 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
4025391 TTTGAGAATT
*
4025401 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
* *
4025436 TGGTGATGATATAGGCTTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
4025473 TGGGGATG
1 TGGTGATG
4025481 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:4029519 original size:35 final size:37
Alignment explanation
Indices: 4029473--4029552 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
4029463 TTTGAGAATT
*
4029473 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
4029508 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
4029545 TGGGGATG
1 TGGTGATG
4029553 GAAATAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:4047620 original size:17 final size:17
Alignment explanation
Indices: 4047598--4047668 Score: 88
Period size: 17 Copynumber: 4.2 Consensus size: 17
4047588 ACAATTGAGT
4047598 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
4047615 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
4047632 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* **
4047649 TACTTCCATAAATGAAC
1 TAGTTTAATAAATGAAC
4047666 TAG
1 TAG
4047669 ATGATTTAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:4047637 original size:34 final size:34
Alignment explanation
Indices: 4047598--4047668 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
4047588 ACAATTGAGT
* ** *
4047598 TAGTTTAATAAATGAACTAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAACTACTTCCATAAATGAAC
*
4047632 TAGTTTAATTAATGAACTACTTCCATAAATGAAC
1 TAGTTTAATAAATGAACTACTTCCATAAATGAAC
4047666 TAG
1 TAG
4047669 ATGATTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (34 bp):
TAGTTTAATAAATGAACTACTTCCATAAATGAAC
Found at i:4048558 original size:60 final size:61
Alignment explanation
Indices: 4048416--4048560 Score: 175
Period size: 61 Copynumber: 2.4 Consensus size: 61
4048406 AAAAATAAGA
** * *
4048416 TCATGCCCACCACATGCACTAAGTTTACACTCTAGTGCTAATCCGAAAATGACAGATAAGG
1 TCATGCCCACCACATGCACTAAGTTTACACTCTAGCACTAATCCGAAAATGACACACAAGG
* * * * * *
4048477 TTATGCCCAACACCTGCACTAAGTTTACACTCTAGCATTGAT-CGAATATGACACACAAGG
1 TCATGCCCACCACATGCACTAAGTTTACACTCTAGCACTAATCCGAAAATGACACACAAGG
* *
4048537 TCGTGCCCACCACATGTACTAAGT
1 TCATGCCCACCACATGCACTAAGT
4048561 GTCCTTACAC
Statistics
Matches: 69, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 34 0.49
61 35 0.51
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (61 bp):
TCATGCCCACCACATGCACTAAGTTTACACTCTAGCACTAATCCGAAAATGACACACAAGG
Found at i:4059980 original size:121 final size:121
Alignment explanation
Indices: 4059766--4060008 Score: 486
Period size: 121 Copynumber: 2.0 Consensus size: 121
4059756 GGAGAAAATT
4059766 TGGTTGCCGAATGAATGGTTCGATTGTATGCAAACTCCACGTGTGGTAGGCATTCTTCCCACGTC
1 TGGTTGCCGAATGAATGGTTCGATTGTATGCAAACTCCACGTGTGGTAGGCATTCTTCCCACGTC
4059831 TTGATATTTTTCTTGATGATGGATCATAGTAGTGTTGATAAAACTCTATTAACTAC
66 TTGATATTTTTCTTGATGATGGATCATAGTAGTGTTGATAAAACTCTATTAACTAC
4059887 TGGTTGCCGAATGAATGGTTCGATTGTATGCAAACTCCACGTGTGGTAGGCATTCTTCCCACGTC
1 TGGTTGCCGAATGAATGGTTCGATTGTATGCAAACTCCACGTGTGGTAGGCATTCTTCCCACGTC
4059952 TTGATATTTTTCTTGATGATGGATCATAGTAGTGTTGATAAAACTCTATTAACTAC
66 TTGATATTTTTCTTGATGATGGATCATAGTAGTGTTGATAAAACTCTATTAACTAC
4060008 T
1 T
4060009 TCAGTTTGAC
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (121 bp):
TGGTTGCCGAATGAATGGTTCGATTGTATGCAAACTCCACGTGTGGTAGGCATTCTTCCCACGTC
TTGATATTTTTCTTGATGATGGATCATAGTAGTGTTGATAAAACTCTATTAACTAC
Found at i:4069171 original size:24 final size:23
Alignment explanation
Indices: 4069144--4069203 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
4069134 ACTTCTCTTT
4069144 CTTTCTTTTTCTTCTTTTCGAGTG
1 CTTTCTTTTTCTTCTTTT-GAGTG
**
4069168 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCTTTTTCTTCTTTTGAGTG
4069191 CTTT-TATTTTCTT
1 CTTTCT-TTTTCTT
4069204 TGCTGATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.08, C:0.18, G:0.10, T:0.63
Consensus pattern (23 bp):
CTTTCTTTTTCTTCTTTTGAGTG
Found at i:4069193 original size:23 final size:24
Alignment explanation
Indices: 4069151--4069203 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
4069141 TTTCTTTCTT
4069151 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
4069175 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
4069198 TTTCTT
1 TTTCTT
4069204 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:4072555 original size:21 final size:21
Alignment explanation
Indices: 4072531--4072570 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4072521 CTCATTTTCA
4072531 CTCTCAAT-TCTCTTTTCAATG
1 CTCTCAATGTCT-TTTTCAATG
4072552 CTCTCAATGTCTTTTTCAA
1 CTCTCAATGTCTTTTTCAA
4072571 CTCTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.20, C:0.28, G:0.05, T:0.47
Consensus pattern (21 bp):
CTCTCAATGTCTTTTTCAATG
Found at i:4072576 original size:19 final size:19
Alignment explanation
Indices: 4072525--4072576 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
4072515 AATATGCTCA
4072525 TTTTC-ACTCTCAATTCTC
1 TTTTCAACTCTCAATTCTC
4072543 TTTTCAATGCTCTCAATGTCT-
1 TTTTCAA--CTCTCAAT-TCTC
4072564 TTTTCAACTCTCA
1 TTTTCAACTCTCA
4072577 TTTTTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.17
19 7 0.23
21 15 0.50
22 3 0.10
ACGTcount: A:0.19, C:0.29, G:0.04, T:0.48
Consensus pattern (19 bp):
TTTTCAACTCTCAATTCTC
Found at i:4074973 original size:15 final size:15
Alignment explanation
Indices: 4074955--4074984 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4074945 CATATATAAC
4074955 AGCATATAATATTCA
1 AGCATATAATATTCA
4074970 AGCATATAATATTCA
1 AGCATATAATATTCA
4074985 TTATGAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
AGCATATAATATTCA
Found at i:4076494 original size:20 final size:19
Alignment explanation
Indices: 4076459--4076499 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
4076449 AGCATTTATC
*
4076459 TTCATTAAAATTATGTATT
1 TTCATTAAAATCATGTATT
*
4076478 TTCATTAAAAATCATGTGTT
1 TTCATT-AAAATCATGTATT
4076498 TT
1 TT
4076500 TAAAGGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (19 bp):
TTCATTAAAATCATGTATT
Found at i:4080115 original size:13 final size:13
Alignment explanation
Indices: 4080097--4080122 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4080087 ACTATATGTT
4080097 CATCACCATTTTC
1 CATCACCATTTTC
4080110 CATCACCATTTTC
1 CATCACCATTTTC
4080123 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:4080574 original size:15 final size:16
Alignment explanation
Indices: 4080556--4080588 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
4080546 CAACAAAAGC
4080556 AACAAAAAGAAAA-AA
1 AACAAAAAGAAAAGAA
4080571 AACAAAAAGAAAAGAA
1 AACAAAAAGAAAAGAA
4080587 AA
1 AA
4080589 AGACTCTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (16 bp):
AACAAAAAGAAAAGAA
Found at i:4093724 original size:142 final size:142
Alignment explanation
Indices: 4093464--4093767 Score: 565
Period size: 142 Copynumber: 2.1 Consensus size: 142
4093454 ATGAGTGAAC
*
4093464 CTTC-ATGGATGAGTGTTCATACTTTAAGTAGATACAAAGCATGGCTTAGGTGAATGAATTTTGA
1 CTTCTATGGATGAATGTTCATACTTTAAGTAGATACAAAGCATGGCTTAGGTGAATGAATTTTGA
4093528 TGAATGGATATTCATCTTTTAATGGAATACATCCTTTGGACGAATTCATCCCACCTTGTGTGAAC
66 TGAATGGATATTCATCTTTTAATGGAATACATCCTTTGGACGAATTCATCCCACCTTGTGTGAAC
4093593 TTGTTGATTTGT
131 TTGTTGATTTGT
4093605 CTTCTATGGATGAATGTTCATACTTTAAGTAGATACAAAGCATGGCTTAGGTGAATGAATTTTGA
1 CTTCTATGGATGAATGTTCATACTTTAAGTAGATACAAAGCATGGCTTAGGTGAATGAATTTTGA
*
4093670 TGAATGGATATTCATCTTTTAATGGAATACATCCTTTGGCCGAATTCATCCCACCTTGTGTGAAC
66 TGAATGGATATTCATCTTTTAATGGAATACATCCTTTGGACGAATTCATCCCACCTTGTGTGAAC
*
4093735 TTGTTGATTTTT
131 TTGTTGATTTGT
*
4093747 CTTCTATGGATGAATTTTCAT
1 CTTCTATGGATGAATGTTCAT
4093768 GAATGTATCT
Statistics
Matches: 158, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
141 4 0.03
142 154 0.97
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.39
Consensus pattern (142 bp):
CTTCTATGGATGAATGTTCATACTTTAAGTAGATACAAAGCATGGCTTAGGTGAATGAATTTTGA
TGAATGGATATTCATCTTTTAATGGAATACATCCTTTGGACGAATTCATCCCACCTTGTGTGAAC
TTGTTGATTTGT
Found at i:4096854 original size:16 final size:15
Alignment explanation
Indices: 4096828--4096879 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
4096818 GAGTTGTAAG
4096828 TTATC-TTCATTTTT
1 TTATCTTTCATTTTT
*
4096842 TTATCATTTCATTTAT
1 TTATC-TTTCATTTTT
4096858 TTATTCTTTCATCTTTT
1 TTA-TCTTTCAT-TTTT
4096875 CTTAT
1 -TTAT
4096880 TTCATTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
16 17 0.55
17 6 0.19
18 3 0.10
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATCTTTCATTTTT
Found at i:4101438 original size:2 final size:2
Alignment explanation
Indices: 4101427--4101478 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
4101417 TAACTATAGG
4101427 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
4101468 TA TA TA TA TA T
1 TA TA TA TA TA T
4101479 GAAAATAACT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4101953 original size:13 final size:13
Alignment explanation
Indices: 4101935--4101960 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4101925 TTATAGGCGT
4101935 GAAAATGGTGATG
1 GAAAATGGTGATG
4101948 GAAAATGGTGATG
1 GAAAATGGTGATG
4101961 AACAGATAGT
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:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (13 bp):
GAAAATGGTGATG
Found at i:4102350 original size:19 final size:20
Alignment explanation
Indices: 4102303--4102350 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
4102293 GAAACCCCTT
**
4102303 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTCAA
4102323 TGAAAATACATGA-TTTCAA
1 TGAAAATACATGATTTTCAA
*
4102342 TGAAGATAC
1 TGAAAATAC
4102351 TTGCTCTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTCAA
Found at i:4102722 original size:23 final size:23
Alignment explanation
Indices: 4102677--4102722 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4102667 TTATACCTAT
*
4102677 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
4102700 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
4102723 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:4104299 original size:8 final size:8
Alignment explanation
Indices: 4104288--4104339 Score: 61
Period size: 8 Copynumber: 6.2 Consensus size: 8
4104278 GAGAAAAATC
4104288 AGAAAAGA
1 AGAAAAGA
4104296 AGAAAAGA
1 AGAAAAGA
*
4104304 AGAAAATA
1 AGAAAAGA
4104312 AGAAAAGAAA
1 AGAAAAG--A
4104322 AGAAAAGA
1 AGAAAAGA
4104330 A-AAAGAGA
1 AGAAA-AGA
4104338 AG
1 AG
4104340 TTAAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
7 3 0.08
8 27 0.71
10 8 0.21
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (8 bp):
AGAAAAGA
Found at i:4104335 original size:6 final size:5
Alignment explanation
Indices: 4104295--4104332 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
4104285 ATCAGAAAAG
4104295 AAGAA AAGAA GAA-AA TAAGAA AAGAA AAGAA AAGAA AA
1 AAGAA AAGAA -AAGAA -AAGAA AAGAA AAGAA AAGAA AA
4104333 AGAGAAGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
AAGAA
Found at i:4104335 original size:21 final size:21
Alignment explanation
Indices: 4104295--4104335 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4104285 ATCAGAAAAG
*
4104295 AAGAAAAGAAGAAAATAAGAA
1 AAGAAAAGAAGAAAAAAAGAA
4104316 AAGAAAAGAA-AAGAAAAAGA
1 AAGAAAAGAAGAA-AAAAAGA
4104336 GAAGTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (21 bp):
AAGAAAAGAAGAAAAAAAGAA
Found at i:4107266 original size:23 final size:23
Alignment explanation
Indices: 4107221--4107266 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4107211 TTATACCTAT
*
4107221 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
4107244 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
4107267 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:4112340 original size:19 final size:20
Alignment explanation
Indices: 4112318--4112360 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4112308 AGCATTTATC
*
4112318 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
4112337 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
4112357 TTCA
1 TTCA
4112361 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:4112911 original size:15 final size:16
Alignment explanation
Indices: 4112886--4112918 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4112876 GATAACATTT
4112886 TTATCCATTTCAATTC
1 TTATCCATTTCAATTC
*
4112902 TTAT-CATTTCATTTC
1 TTATCCATTTCAATTC
4112917 TT
1 TT
4112919 CTTCCATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATCCATTTCAATTC
Found at i:4118235 original size:17 final size:16
Alignment explanation
Indices: 4118213--4118272 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
4118203 AAATTGGAGT
4118213 ACAAAAAGAAAGAAAAG
1 ACAAAAAG-AAGAAAAG
*
4118230 ACAAAAAGAAGAAAAT
1 ACAAAAAGAAGAAAAG
*
4118246 TCAGAAAAGAAGAAAAAG
1 ACA-AAAAGAAG-AAAAG
*
4118264 AAAAAAAGA
1 ACAAAAAGA
4118273 TTTCAAAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 9 0.25
17 22 0.61
18 5 0.14
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.03
Consensus pattern (16 bp):
ACAAAAAGAAGAAAAG
Found at i:4118475 original size:16 final size:16
Alignment explanation
Indices: 4118454--4118486 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4118444 TTGTCTTCAA
4118454 CCATTTCT-TTACCTTT
1 CCATTTCTATT-CCTTT
4118470 CCATTTCTATTCCTTT
1 CCATTTCTATTCCTTT
4118486 C
1 C
4118487 TACCCTAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.55
Consensus pattern (16 bp):
CCATTTCTATTCCTTT
Found at i:4122891 original size:21 final size:19
Alignment explanation
Indices: 4122841--4122891 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
4122831 CGGCCTAGAG
4122841 CATGTATTTTCATTAAAGT
1 CATGTATTTTCATTAAAGT
* *
4122860 CTTGTTTTTTTCATTAAAAGT
1 CATG-TATTTTCATT-AAAGT
4122881 CATGTCATTTT
1 CATGT-ATTTT
4122892 AGGAAGGTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.12
20 10 0.40
21 12 0.48
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (19 bp):
CATGTATTTTCATTAAAGT
Found at i:4123758 original size:25 final size:25
Alignment explanation
Indices: 4123721--4123768 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
4123711 GATGTAGGAG
*
4123721 TCTTTTTCTTTTTGTTTTTTGTTTT
1 TCTTTTTCTTTTTGCTTTTTGTTTT
4123746 TCTTCTTTC-TTTTGCTTTTTGTT
1 TCTT-TTTCTTTTTGCTTTTTGTT
4123769 GCAGCACTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.79
Consensus pattern (25 bp):
TCTTTTTCTTTTTGCTTTTTGTTTT
Found at i:4123764 original size:19 final size:20
Alignment explanation
Indices: 4123722--4123765 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
4123712 ATGTAGGAGT
* *
4123722 CTTTTTCTTTTTGTTTTTTG
1 CTTTTTCTTCTTGTCTTTTG
4123742 -TTTTTCTTCTT-TCTTTTG
1 CTTTTTCTTCTTGTCTTTTG
4123760 CTTTTT
1 CTTTTT
4123766 GTTGCAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (20 bp):
CTTTTTCTTCTTGTCTTTTG
Found at i:4130263 original size:46 final size:44
Alignment explanation
Indices: 4130193--4130291 Score: 137
Period size: 46 Copynumber: 2.2 Consensus size: 44
4130183 TAGTAGGAAT
*
4130193 AGAAAATAAAATATAATGAGAAAGGTGACTTAGAAATAAAAAGA
1 AGAAAATAAAATATAATGAAAAAGGTGACTTAGAAATAAAAAGA
* * *
4130237 AGAAAATGCAAATAATAATGAAAAAGGTGGCTTAGAAATAGAAAGA
1 AGAAAAT-AAAAT-ATAATGAAAAAGGTGACTTAGAAATAAAAAGA
4130283 AG-AAATAAA
1 AGAAAATAAA
4130292 GGGGTTACTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 9 0.19
45 8 0.17
46 31 0.65
ACGTcount: A:0.61, C:0.03, G:0.19, T:0.17
Consensus pattern (44 bp):
AGAAAATAAAATATAATGAAAAAGGTGACTTAGAAATAAAAAGA
Found at i:4131246 original size:30 final size:30
Alignment explanation
Indices: 4131198--4131254 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
4131188 TTCTTTGTGA
* *
4131198 GCTGTTTATGTCTCCCAAATGCTCCACCAG
1 GCTGTATATATCTCCCAAATGCTCCACCAG
*
4131228 GCTGTATATATCTTCCAAATGCTCCAC
1 GCTGTATATATCTCCCAAATGCTCCAC
4131255 TAAGCTATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.32
Consensus pattern (30 bp):
GCTGTATATATCTCCCAAATGCTCCACCAG
Found at i:4134623 original size:27 final size:27
Alignment explanation
Indices: 4134555--4134626 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 27
4134545 CCTTTTCAAA
*
4134555 ATCATAAATAGGTTCTTCAGATTCTTC
1 ATCATAAATAGGTTCTTCAGATTCCTC
*
4134582 ATC-T---T-GGATTGCTTCAGGTTCCTC
1 ATCATAAATAGG-TT-CTTCAGATTCCTC
4134606 ATCATAAATAGGTTCTTCAGA
1 ATCATAAATAGGTTCTTCAGA
4134627 ATCAGAGACA
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
22 2 0.06
23 3 0.09
24 14 0.40
25 1 0.03
26 1 0.03
27 9 0.26
28 3 0.09
29 2 0.06
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (27 bp):
ATCATAAATAGGTTCTTCAGATTCCTC
Found at i:4137954 original size:22 final size:23
Alignment explanation
Indices: 4137906--4137954 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
4137896 AATTCATCTT
**
4137906 GAAAATTCAAAAAAAAAAAATCC
1 GAAAATTCAAAAAAAAAAAATAA
4137929 GAAAATTCAAAAAAAAAAAA-AA
1 GAAAATTCAAAAAAAAAAAATAA
4137951 GAAA
1 GAAA
4137955 TTCTGGTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.76, C:0.08, G:0.06, T:0.10
Consensus pattern (23 bp):
GAAAATTCAAAAAAAAAAAATAA
Found at i:4145385 original size:15 final size:15
Alignment explanation
Indices: 4145374--4145402 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4145364 ACTCAAAAAG
4145374 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
4145389 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
4145403 GTTGAAGCAC
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:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:4148153 original size:19 final size:21
Alignment explanation
Indices: 4148110--4148161 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
4148100 GAAACCCCTT
4148110 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
4148131 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
4148150 TGAAGATACATG
1 TGAAAATACATG
4148162 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:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:4149002 original size:17 final size:18
Alignment explanation
Indices: 4148968--4149004 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
4148958 AACTATATAA
*
4148968 TGCATATATATAATGATG
1 TGCATATATATAAAGATG
4148986 TGCATAT-TATAAAGATG
1 TGCATATATATAAAGATG
4149003 TG
1 TG
4149005 AACTATAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (18 bp):
TGCATATATATAAAGATG
Found at i:4151252 original size:26 final size:25
Alignment explanation
Indices: 4151220--4151279 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
4151210 CTTGGCTTGC
*
4151220 TTTCTTTTTGAATTTTTCT-TTTTTT
1 TTTCTTTTTG-ATTTTTCTCTTCTTT
*
4151245 TTTCCTTTCTGATTTTTCTCTTCTTT
1 TTT-CTTTTTGATTTTTCTCTTCTTT
4151271 TTTCTTTTT
1 TTTCTTTTT
4151280 CGTTCTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 16 0.53
26 14 0.47
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (25 bp):
TTTCTTTTTGATTTTTCTCTTCTTT
Found at i:4152775 original size:30 final size:30
Alignment explanation
Indices: 4152741--4152801 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
4152731 TGGCTTCGAA
4152741 TCTGGTAACTCCATGTCTCCTTGAATCATC
1 TCTGGTAACTCCATGTCTCCTTGAATCATC
4152771 TCTGGTAACTCCATGTCTCCTTGAATCATC
1 TCTGGTAACTCCATGTCTCCTTGAATCATC
4152801 T
1 T
4152802 ATCCTTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.38
Consensus pattern (30 bp):
TCTGGTAACTCCATGTCTCCTTGAATCATC
Found at i:4174967 original size:10 final size:10
Alignment explanation
Indices: 4174954--4174984 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
4174944 GAAAAACACT
4174954 AAAAAGAAAA
1 AAAAAGAAAA
4174964 AAAAAGAAAAA
1 AAAAAG-AAAA
4174975 AAAAAGAAAA
1 AAAAAGAAAA
4174985 GTTGGAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:4174974 original size:11 final size:11
Alignment explanation
Indices: 4174954--4174984 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
4174944 GAAAAACACT
4174954 AAAAAG-AAAA
1 AAAAAGAAAAA
4174964 AAAAAGAAAAA
1 AAAAAGAAAAA
4174975 AAAAAGAAAA
1 AAAAAGAAAA
4174985 GTTGGAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:4177079 original size:23 final size:23
Alignment explanation
Indices: 4177034--4177079 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4177024 TTATACCTAT
*
4177034 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
4177057 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
4177080 TAATATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:4178708 original size:16 final size:16
Alignment explanation
Indices: 4178681--4178728 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
4178671 AATTGGAGTG
4178681 CAAAAAGAAAGAAAAGA
1 CAAAAAG-AAGAAAAGA
**
4178698 CAAAAAGAAGAAAATT
1 CAAAAAGAAGAAAAGA
4178714 CATAAAAGAAGAAAA
1 CA-AAAAGAAGAAAA
4178729 AAAAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.73, C:0.06, G:0.15, T:0.06
Consensus pattern (16 bp):
CAAAAAGAAGAAAAGA
Found at i:4178749 original size:29 final size:28
Alignment explanation
Indices: 4178699--4178756 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 28
4178689 AAGAAAAGAC
4178699 AAAAAGAAGAAAATTCATAAAAGAAGAAA
1 AAAAAGAAGAAAATTCATAAAAG-AGAAA
4178728 AAAAAGAA-AAAGATTTCA-AAAAGAGAAA
1 AAAAAGAAGAAA-A-TTCATAAAAGAGAAA
4178756 A
1 A
4178757 GCAAGCCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 9 0.33
29 14 0.52
30 4 0.15
ACGTcount: A:0.72, C:0.03, G:0.14, T:0.10
Consensus pattern (28 bp):
AAAAAGAAGAAAATTCATAAAAGAGAAA
Found at i:4181672 original size:23 final size:23
Alignment explanation
Indices: 4181627--4181672 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4181617 TTATACCTAT
*
4181627 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
4181650 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
4181673 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:4193572 original size:16 final size:16
Alignment explanation
Indices: 4193551--4193589 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
4193541 ATAATTAAGA
4193551 AAAGAAATAGAAATGG
1 AAAGAAATAGAAATGG
*
4193567 AAAG-AATCGAAATGG
1 AAAGAAATAGAAATGG
*
4193582 AAATAAAT
1 AAAGAAAT
4193590 TTTATCAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.62, C:0.03, G:0.21, T:0.15
Consensus pattern (16 bp):
AAAGAAATAGAAATGG
Found at i:4199340 original size:23 final size:24
Alignment explanation
Indices: 4199305--4199358 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
4199295 AAAATCAGAA
4199305 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
4199328 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
*
4199352 CAGAAAA
1 AAGAAAA
4199359 AGAAAGAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.61, C:0.13, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:4228096 original size:14 final size:14
Alignment explanation
Indices: 4228077--4228116 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
4228067 TTCACTTTTC
4228077 TTTTTCTTTTGATT
1 TTTTTCTTTTGATT
**
4228091 TTTTTCTTTTTCTT
1 TTTTTCTTTTGATT
4228105 TTCTTTCTTTTG
1 TT-TTTCTTTTG
4228117 CATTCCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.03, C:0.12, G:0.05, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTTGATT
Found at i:4228115 original size:20 final size:21
Alignment explanation
Indices: 4228071--4228115 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
4228061 ACTTGCTTCA
4228071 CTTTTCTTTTTCTTTTGATTT
1 CTTTTCTTTTTCTTTTGATTT
*
4228092 -TTTTCTTTTTCTTTT-CTTT
1 CTTTTCTTTTTCTTTTGATTT
4228111 CTTTT
1 CTTTT
4228116 GCATTCCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (21 bp):
CTTTTCTTTTTCTTTTGATTT
Found at i:4241465 original size:23 final size:24
Alignment explanation
Indices: 4241437--4241490 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
4241427 AAAATTAGCA
4241437 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
4241460 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
4241484 AAGAAAA
1 AAGAAAA
4241491 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:4241495 original size:24 final size:23
Alignment explanation
Indices: 4241437--4241496 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
4241427 AAAATTAGCA
4241437 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
4241460 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
4241484 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
4241497 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:4245739 original size:23 final size:24
Alignment explanation
Indices: 4245704--4245757 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
4245694 AAAATCAGAA
4245704 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
4245727 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
4245751 AAGAAAA
1 AAGAAAA
4245758 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:4245762 original size:24 final size:23
Alignment explanation
Indices: 4245704--4245763 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
4245694 AAAATCAGAA
4245704 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
4245727 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
4245751 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
4245764 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:4249995 original size:23 final size:24
Alignment explanation
Indices: 4249960--4250013 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
4249950 AAAATCAGAA
4249960 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
4249983 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
4250007 AAGAAAA
1 AAGAAAA
4250014 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:4250018 original size:24 final size:23
Alignment explanation
Indices: 4249960--4250019 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
4249950 AAAATCAGAA
4249960 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
4249983 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
4250007 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
4250020 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:4255410 original size:15 final size:15
Alignment explanation
Indices: 4255390--4255429 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4255380 AAGAAATTAT
*
4255390 GAAAGAAATG-AATT
1 GAAAGAAATGAAATG
4255404 GATAAGAAATGAAATG
1 GA-AAGAAATGAAATG
4255420 GAAAGAAATG
1 GAAAGAAATG
4255430 TTATCAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (15 bp):
GAAAGAAATGAAATG
Done.