Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 133 of 161
Found at i:41426163 original size:59 final size:57
Alignment explanation
Indices: 41426012--41426192 Score: 177
Period size: 59 Copynumber: 3.1 Consensus size: 57
41426002 TTTTTACGAA
* * * *
41426012 TTTTATATTTTCTTTACATTTTTTATAATTTTCTTATGA-CTTTATAAAATTTGATAATTT
1 TTTTATA-TTT-TTTACAATTTTTATAATTTTTTTATGATTTTTATAAAATTTAAT-A-TT
* * * *
41426072 TTTTCTATATTTCTA-TATATTTTATAATTTTTTTATGATTTTTATAAAATTTTATATT
1 TTTTATAT-TTTTTACAAT-TTTTATAATTTTTTTATGATTTTTATAAAATTTAATATT
* *
41426130 TTTTATATTTTTTACAATTTTTATAATTTTTTTTCTAATTTTTAATAAAATTTAAATATT
1 TTTTATATTTTTTACAATTTTTATAA-TTTTTTTATGATTTTT-ATAAAATTT-AATATT
41426190 TTT
1 TTT
41426193 ATTAAAATAT
Statistics
Matches: 101, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
57 13 0.13
58 26 0.26
59 32 0.32
60 30 0.30
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (57 bp):
TTTTATATTTTTTACAATTTTTATAATTTTTTTATGATTTTTATAAAATTTAATATT
Found at i:41426214 original size:20 final size:20
Alignment explanation
Indices: 41426167--41426214 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
41426157 TTTTTTTCTA
* *
41426167 ATTTTTAATAAAATTTAAAT
1 ATTTTTATTAAAATATAAAT
41426187 ATTTTTATTAAAATAT-AAT
1 ATTTTTATTAAAATATAAAT
41426206 CATTTTTAT
1 -ATTTTTAT
41426215 AACTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTTATTAAAATATAAAT
Found at i:41426638 original size:85 final size:84
Alignment explanation
Indices: 41426349--41426641 Score: 338
Period size: 84 Copynumber: 3.4 Consensus size: 84
41426339 TCAAAGGGCT
* * * *
41426349 TTTTTGATGCATTTTGGCAA-TTCAAGTACCCAATTTAGTGGGGGGAAAACTGGGGCTTAATTGC
1 TTTTTGATGCATTTT-GAAAGTTCAAGTACCCAATTGAAT---GGGAAAACAGGGGCTTAATTGC
* *
41426413 TTTTTTTGAAAAAGTTTGAGGGGC
62 TTTTTTTGAAAAAGTTT-AAGGTC
* * * * ** * * *
41426437 ATTTTGGTGCATTTTGAAAGTTCAAGCACCCAATTGAGTGAAAAAAAAGGGGATTAATTGTTTTT
1 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGGGAAAACAGGGGCTTAATTGCTTTT
* *
41426502 TTTGGAAAAGTTTGAGAGT-
66 TTTGAAAAAGTTTAAG-GTC
41426521 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGGGAAAACAGGGGCTTAATTGCTTTT
1 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGGGAAAACAGGGGCTTAATTGCTTTT
41426586 TTTGAAAAAGTTTAAAGGTC
66 TTTGAAAAAGTTT-AAGGTC
**
41426606 TTTTTGATATATTTTGAAAGTTCAAGTACCCAATTG
1 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTG
41426642 GGTGCAAAAA
Statistics
Matches: 173, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
84 71 0.41
85 69 0.40
87 3 0.02
88 30 0.17
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (84 bp):
TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGGGAAAACAGGGGCTTAATTGCTTTT
TTTGAAAAAGTTTAAGGTC
Found at i:41437475 original size:14 final size:14
Alignment explanation
Indices: 41437458--41437502 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
41437448 TAGGGGGAAA
41437458 GGGAATTAGGGATT
1 GGGAATTAGGGATT
**
41437472 GGGAA--AGGGAAA
1 GGGAATTAGGGATT
41437484 GGGAATTAGGGATT
1 GGGAATTAGGGATT
41437498 GGGAA
1 GGGAA
41437503 GAGGAAGAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.47, T:0.18
Consensus pattern (14 bp):
GGGAATTAGGGATT
Found at i:41437514 original size:26 final size:26
Alignment explanation
Indices: 41437452--41437502 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
41437442 TGCATTTAGG
41437452 GGGAAAGGGAATTAGGGATTGGGAAA
1 GGGAAAGGGAATTAGGGATTGGGAAA
41437478 GGGAAAGGGAATTAGGGATTGGGAA
1 GGGAAAGGGAATTAGGGATTGGGAA
41437503 GAGGAAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.47, T:0.16
Consensus pattern (26 bp):
GGGAAAGGGAATTAGGGATTGGGAAA
Found at i:41444137 original size:14 final size:14
Alignment explanation
Indices: 41444118--41444156 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
41444108 ATAATGGTGA
41444118 TAATAATAATAAAT
1 TAATAATAATAAAT
*
41444132 TAATAATAATAGAT
1 TAATAATAATAAAT
41444146 TAATAATAATA
1 TAATAATAATA
41444157 TTACTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TAATAATAATAAAT
Found at i:41444139 original size:17 final size:17
Alignment explanation
Indices: 41444117--41444156 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
41444107 AATAATGGTG
41444117 ATAATAATA-ATAAATTA
1 ATAATAATAGATAAA-TA
*
41444134 ATAATAATAGATTAATA
1 ATAATAATAGATAAATA
41444151 ATAATA
1 ATAATA
41444157 TTACTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
ATAATAATAGATAAATA
Found at i:41448110 original size:20 final size:20
Alignment explanation
Indices: 41448085--41448122 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41448075 CTTATCATGT
*
41448085 TAAAAATAAATTGTTATTTA
1 TAAAAATAAATTATTATTTA
41448105 TAAAAATAAATTATTATT
1 TAAAAATAAATTATTATT
41448123 GGTGTAAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TAAAAATAAATTATTATTTA
Found at i:41448349 original size:9 final size:9
Alignment explanation
Indices: 41448335--41448365 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
41448325 CATCTGGTCA
41448335 ACAACAATC
1 ACAACAATC
41448344 ACAACAATC
1 ACAACAATC
41448353 ACAACAATC
1 ACAACAATC
41448362 ACAA
1 ACAA
41448366 ACATTTGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.58, C:0.32, G:0.00, T:0.10
Consensus pattern (9 bp):
ACAACAATC
Found at i:41461448 original size:21 final size:23
Alignment explanation
Indices: 41461422--41461467 Score: 78
Period size: 21 Copynumber: 2.1 Consensus size: 23
41461412 ACACAACTCT
41461422 AATGGATCTCAAAAAA-AAA-AA
1 AATGGATCTCAAAAAAGAAATAA
41461443 AATGGATCTCAAAAAAGAAATAA
1 AATGGATCTCAAAAAAGAAATAA
41461466 AA
1 AA
41461468 AGGTTGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 16 0.70
22 3 0.13
23 4 0.17
ACGTcount: A:0.65, C:0.09, G:0.11, T:0.15
Consensus pattern (23 bp):
AATGGATCTCAAAAAAGAAATAA
Found at i:41472457 original size:4 final size:4
Alignment explanation
Indices: 41472444--41472482 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
41472434 ACCCAAAACT
* * *
41472444 ATAC ATAT ATAT ATAC ATAC ATGC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
41472483 TATATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.31
Consensus pattern (4 bp):
ATAC
Found at i:41472460 original size:12 final size:12
Alignment explanation
Indices: 41472443--41472494 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
41472433 AACCCAAAAC
*
41472443 TATACATATATA
1 TATACATACATA
*
41472455 TATACATACATG
1 TATACATACATA
*
41472467 CATACATACATA
1 TATACATACATA
* * *
41472479 CATATATATATA
1 TATACATACATA
41472491 TATA
1 TATA
41472495 ATAAGGGACA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (12 bp):
TATACATACATA
Found at i:41472491 original size:8 final size:8
Alignment explanation
Indices: 41472443--41472494 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
41472433 AACCCAAAAC
41472443 TATACATA
1 TATACATA
*
41472451 TATATATA
1 TATACATA
* *
41472459 CATACATG
1 TATACATA
*
41472467 CATACATA
1 TATACATA
*
41472475 CATACATA
1 TATACATA
*
41472483 TATATATA
1 TATACATA
41472491 TATA
1 TATA
41472495 ATAAGGGACA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (8 bp):
TATACATA
Found at i:41478034 original size:20 final size:20
Alignment explanation
Indices: 41478009--41478050 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
41477999 CTTTTAAGGA
41478009 TTATTTCTTTGTTTGTTTCT
1 TTATTTCTTTGTTTGTTTCT
41478029 TTATTTCTTTGTTTGTTTCT
1 TTATTTCTTTGTTTGTTTCT
41478049 TT
1 TT
41478051 GTATCTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.05, C:0.10, G:0.10, T:0.76
Consensus pattern (20 bp):
TTATTTCTTTGTTTGTTTCT
Found at i:41480759 original size:52 final size:48
Alignment explanation
Indices: 41480740--41480942 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
41480730 TGACAAGTGG
* *
41480740 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
41480786 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
41480838 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
41480884 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
41480930 AAAGTGATAAGTG
1 AAAGTGATAAGTG
41480943 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:41480794 original size:98 final size:98
Alignment explanation
Indices: 41480674--41480942 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
41480664 TTTGAGTACT
*
41480674 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
41480739 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
41480772 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
41480837 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
41480870 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
41480935 GATAAGTG
65 GAAAAGTG
41480943 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:41480950 original size:37 final size:37
Alignment explanation
Indices: 41480906--41481051 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
41480896 GATAGCTTTA
*
41480906 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
41480943 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
41480980 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
41481017 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
41481052 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:41482367 original size:49 final size:49
Alignment explanation
Indices: 41482306--41482449 Score: 225
Period size: 49 Copynumber: 2.9 Consensus size: 49
41482296 ATGTGAACAT
* *
41482306 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
41482356 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
41482405 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCG
41482450 AGAAAACGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 84 0.95
50 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.33
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:41485660 original size:52 final size:48
Alignment explanation
Indices: 41485641--41485843 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
41485631 TGACAAGTGG
* *
41485641 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
41485687 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
41485739 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
41485785 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
41485831 AAAGTGATAAGTG
1 AAAGTGATAAGTG
41485844 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:41485695 original size:98 final size:98
Alignment explanation
Indices: 41485575--41485843 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
41485565 TTTGAGTACT
*
41485575 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
41485640 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
41485673 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
41485738 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
41485771 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
41485836 GATAAGTG
65 GAAAAGTG
41485844 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:41485851 original size:37 final size:37
Alignment explanation
Indices: 41485807--41485952 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
41485797 GATAGCTTTA
*
41485807 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
41485844 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
41485881 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
41485918 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
41485953 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:41491859 original size:14 final size:14
Alignment explanation
Indices: 41491840--41491874 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
41491830 TATGTCAAAG
41491840 ATAACAACACCTTA
1 ATAACAACACCTTA
41491854 ATAACAACACCTTA
1 ATAACAACACCTTA
41491868 ATAACAA
1 ATAACAA
41491875 TATCAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (14 bp):
ATAACAACACCTTA
Found at i:41492311 original size:7 final size:7
Alignment explanation
Indices: 41492293--41492326 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
41492283 CACATCTCAA
41492293 TTCATCAT
1 TTCAT-AT
41492301 TTCATAT
1 TTCATAT
41492308 TTCATAT
1 TTCATAT
41492315 TTCATAT
1 TTCATAT
41492322 TTCAT
1 TTCAT
41492327 CTCATAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.81
8 5 0.19
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (7 bp):
TTCATAT
Found at i:41492375 original size:43 final size:43
Alignment explanation
Indices: 41492323--41492405 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 43
41492313 ATTTCATATT
41492323 TCATCTCATAATCATTTCTCATCATTT-CCATTTCAATATCTTC
1 TCATCTCATAATCATTTCTCATC-TTTGCCATTTCAATATCTTC
* *
41492366 TCATCTCATATTTATTTCTCATCTTTGCCATTTCAATATC
1 TCATCTCATAATCATTTCTCATCTTTGCCATTTCAATATC
41492406 AATCACATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.24, C:0.27, G:0.01, T:0.48
Consensus pattern (43 bp):
TCATCTCATAATCATTTCTCATCTTTGCCATTTCAATATCTTC
Found at i:41506805 original size:19 final size:19
Alignment explanation
Indices: 41506781--41506834 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
41506771 AATCTTCAAG
*
41506781 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41506800 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41506819 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
41506835 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:41506856 original size:23 final size:22
Alignment explanation
Indices: 41506794--41506857 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 22
41506784 ATGTAATCTT
41506794 AGATATGATATGCAATCTT---
1 AGATATGATATGCAATCTTAGA
41506813 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATCTTAGA
* *
41506835 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGCAATCTTAGA
41506858 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.49
22 8 0.21
23 12 0.31
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATCTTAGA
Found at i:41507085 original size:23 final size:23
Alignment explanation
Indices: 41507041--41507085 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
41507031 TCTTATTTTG
* *
41507041 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
41507064 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
41507086 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:41507261 original size:23 final size:24
Alignment explanation
Indices: 41507220--41507266 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
41507210 CCTCTATTTG
*
41507220 TTATTTTAGTTTTATTATTATTAAA
1 TTATTTTA-TTTTAATATTATTAAA
41507245 TTATTTT-TTTTAATATTATTAA
1 TTATTTTATTTTAATATTATTAA
41507267 CACAATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
25 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TTATTTTATTTTAATATTATTAAA
Found at i:41507563 original size:23 final size:22
Alignment explanation
Indices: 41507537--41507579 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
41507527 TAATTCACAC
* *
41507537 ACATATTTATTTTTCTTATATGT
1 ACATATATATATTT-TTATATGT
41507560 ACATATATATATTTTTATAT
1 ACATATATATATTTTTATAT
41507580 TTTATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (22 bp):
ACATATATATATTTTTATATGT
Found at i:41507569 original size:27 final size:27
Alignment explanation
Indices: 41507507--41507588 Score: 69
Period size: 27 Copynumber: 2.9 Consensus size: 27
41507497 ATGTATAGTT
41507507 ATATATATTTTATTTTTTTATAATTCAC
1 ATATATA-TTTATTTTTTTATAATTCAC
* *
41507535 ACACATATTTATTTTTCTTAT-ATGT-AC
1 ATATATATTTATTTTT-TTATAAT-TCAC
*
41507562 ATATATATATTTTTATATTTTATAATT
1 ATATATAT-TTATT-T-TTTTATAATT
41507589 TTTATCTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
27 19 0.44
28 14 0.33
29 6 0.14
30 4 0.09
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (27 bp):
ATATATATTTATTTTTTTATAATTCAC
Found at i:41507728 original size:271 final size:271
Alignment explanation
Indices: 41507380--41507918 Score: 1078
Period size: 271 Copynumber: 2.0 Consensus size: 271
41507370 TTATAATATA
41507380 TATACATATACGTACACATTTTTTAATTTTTATAAATATATATATACACATACTTTTATATATTT
1 TATACATATACGTACACATTTTTTAATTTTTATAAATATATATATACACATACTTTTATATATTT
41507445 TCTATGTTTCATAATTTTATATACATACTTATATATATTTACAAATTAAAATATGTATAGTTATA
66 TCTATGTTTCATAATTTTATATACATACTTATATATATTTACAAATTAAAATATGTATAGTTATA
41507510 TATATTTTATTTTTTTATAATTCACACACATATTTATTTTTCTTATATGTACATATATATATTTT
131 TATATTTTATTTTTTTATAATTCACACACATATTTATTTTTCTTATATGTACATATATATATTTT
41507575 TATATTTTATAATTTTTATCTATTTTCTTTGTTATTATTATCGCTTTACTTGATGTTTATTTATT
196 TATATTTTATAATTTTTATCTATTTTCTTTGTTATTATTATCGCTTTACTTGATGTTTATTTATT
41507640 TATTTATTCAC
261 TATTTATTCAC
41507651 TATACATATACGTACACATTTTTTAATTTTTATAAATATATATATACACATACTTTTATATATTT
1 TATACATATACGTACACATTTTTTAATTTTTATAAATATATATATACACATACTTTTATATATTT
41507716 TCTATGTTTCATAATTTTATATACATACTTATATATATTTACAAATTAAAATATGTATAGTTATA
66 TCTATGTTTCATAATTTTATATACATACTTATATATATTTACAAATTAAAATATGTATAGTTATA
41507781 TATATTTTATTTTTTTATAATTCACACACATATTTATTTTTCTTATATGTACATATATATATTTT
131 TATATTTTATTTTTTTATAATTCACACACATATTTATTTTTCTTATATGTACATATATATATTTT
41507846 TATATTTTATAATTTTTATCTATTTTCTTTGTTATTATTATCGCTTTACTTGATGTTTATTTATT
196 TATATTTTATAATTTTTATCTATTTTCTTTGTTATTATTATCGCTTTACTTGATGTTTATTTATT
41507911 TATTTATT
261 TATTTATT
41507919 TATTCACATG
Statistics
Matches: 268, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
271 268 1.00
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.55
Consensus pattern (271 bp):
TATACATATACGTACACATTTTTTAATTTTTATAAATATATATATACACATACTTTTATATATTT
TCTATGTTTCATAATTTTATATACATACTTATATATATTTACAAATTAAAATATGTATAGTTATA
TATATTTTATTTTTTTATAATTCACACACATATTTATTTTTCTTATATGTACATATATATATTTT
TATATTTTATAATTTTTATCTATTTTCTTTGTTATTATTATCGCTTTACTTGATGTTTATTTATT
TATTTATTCAC
Found at i:41507834 original size:23 final size:22
Alignment explanation
Indices: 41507808--41507850 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
41507798 TAATTCACAC
* *
41507808 ACATATTTATTTTTCTTATATGT
1 ACATATATATATTT-TTATATGT
41507831 ACATATATATATTTTTATAT
1 ACATATATATATTTTTATAT
41507851 TTTATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (22 bp):
ACATATATATATTTTTATATGT
Found at i:41507840 original size:27 final size:27
Alignment explanation
Indices: 41507778--41507859 Score: 69
Period size: 27 Copynumber: 2.9 Consensus size: 27
41507768 ATGTATAGTT
41507778 ATATATATTTTATTTTTTTATAATTCAC
1 ATATATA-TTTATTTTTTTATAATTCAC
* *
41507806 ACACATATTTATTTTTCTTAT-ATGT-AC
1 ATATATATTTATTTTT-TTATAAT-TCAC
*
41507833 ATATATATATTTTTATATTTTATAATT
1 ATATATAT-TTATT-T-TTTTATAATT
41507860 TTTATCTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
27 19 0.44
28 14 0.33
29 6 0.14
30 4 0.09
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (27 bp):
ATATATATTTATTTTTTTATAATTCAC
Found at i:41508038 original size:3 final size:3
Alignment explanation
Indices: 41508032--41508091 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
41508022 TTATCTTTTC
41508032 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41508080 ATT ATT ATT ATT
1 ATT ATT ATT ATT
41508092 GTTGTTGTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41513546 original size:34 final size:34
Alignment explanation
Indices: 41513503--41513572 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
41513493 AGTTTAAAGG
41513503 TTGGTAATCTGAGAAGGAAGAGTCTAAATTAAGA
1 TTGGTAATCTGAGAAGGAAGAGTCTAAATTAAGA
41513537 TTGGTAATCTGAGAAGGAAGAGTCTAAATTAAGA
1 TTGGTAATCTGAGAAGGAAGAGTCTAAATTAAGA
41513571 TT
1 TT
41513573 ATCTCTTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.29
Consensus pattern (34 bp):
TTGGTAATCTGAGAAGGAAGAGTCTAAATTAAGA
Found at i:41514220 original size:44 final size:44
Alignment explanation
Indices: 41514171--41514256 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
41514161 AAACCATAAA
* *
41514171 TCCTAGCT-CTCTGAACAGCAGTGGAATAGGTGGAAGATTGTAAG
1 TCCTAGCTCCT-TGAACAGCAATGGAATAAGTGGAAGATTGTAAG
* *
41514215 TCCTAGCTCCTTGAATAGTAATGGAATAAGTGGAAGATTGTA
1 TCCTAGCTCCTTGAACAGCAATGGAATAAGTGGAAGATTGTA
41514257 GATCCTGTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 35 0.95
45 2 0.05
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (44 bp):
TCCTAGCTCCTTGAACAGCAATGGAATAAGTGGAAGATTGTAAG
Found at i:41514751 original size:50 final size:50
Alignment explanation
Indices: 41514689--41514798 Score: 157
Period size: 50 Copynumber: 2.2 Consensus size: 50
41514679 AAAGCTGTGG
* * *
41514689 GCAGCGAGTCCTATCTCTTTGGCATTACAGTGGAATAGGTTGAAGCTACA
1 GCAGCGAATCCTATCTCTTTGGCATTACAGTGAAATAGATTGAAGCTACA
* *
41514739 GCAGCGAATCCTATCTCTTTGGCATTGCAGTTAAATAGATTGAAGCTACA
1 GCAGCGAATCCTATCTCTTTGGCATTACAGTGAAATAGATTGAAGCTACA
**
41514789 ATAGCGAATC
1 GCAGCGAATC
41514799 TTACTTCCCT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (50 bp):
GCAGCGAATCCTATCTCTTTGGCATTACAGTGAAATAGATTGAAGCTACA
Found at i:41514996 original size:310 final size:311
Alignment explanation
Indices: 41514421--41515024 Score: 904
Period size: 310 Copynumber: 1.9 Consensus size: 311
41514411 AAAGCTGTGG
* * * *
41514421 GCAGCGAATCCTATCACTTTGGCATTATAGTGGAATAGATTGAAGCTACAATGGTGAATCTTACC
1 GCAGCGAATCCTATCACTTTGGCATTACAGTGAAATAGATTGAAGCTACAATAGCGAATCTTACC
* * *
41514486 TCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGATAGCGAATCTTGGTTCCCCGACATTGCAG
66 TCCCTGACAGTGTAGTGGAACAGATTGAAGCTACGACAGCGAATCTTGGTTCCCCGACAATGC--
* * *
41514551 TTAAAGAGATTGAAGCCAAAACGGTGAATCTTACTTCCCTGACGTTATAGCGGAGCAGATTAAAG
129 ----A-AGATTAAAGCCAAAACGATGAATCTTACTTCCCTGACGTTATAGCAGAGCAGATTAAAG
41514616 CTGAGGACAGTGAATCTTATCTCCATGGCGTTAAGACTTGAAATAGCTGAAGTGGAGCAGATTAA
189 CTGAGGACAGTGAATCTTATCTCCATGGCGTTAAGACTTGAAATAGCTGAAGTGGAGCAGATTAA
*
41514681 AGCTGTGGGCAGCGAGTCCTATCTCTTTGGCATTACAGTGGAATAGGTTGAAGCTACA
254 AGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACAGTGGAATAGGTTGAAGCTACA
* * * *
41514739 GCAGCGAATCCTATCTCTTTGGCATTGCAGTTAAATAGATTGAAGCTACAATAGCGAATCTTACT
1 GCAGCGAATCCTATCACTTTGGCATTACAGTGAAATAGATTGAAGCTACAATAGCGAATCTTACC
* * * **
41514804 TCCCTGACGGTGTAGTGGAACAGATTGAAGCTACGACGGTGAATCTTGGTTTTCCGACAATGC-A
66 TCCCTGACAGTGTAGTGGAACAGATTGAAGCTACGACAGCGAATCTTGGTTCCCCGACAATGCAA
* *
41514868 GATTAAAGCCAAAACGATGAATCTTACTTCCCTGACGTTATAGTAGAGCAGATTAAAGCTGAGGG
131 GATTAAAGCCAAAACGATGAATCTTACTTCCCTGACGTTATAGCAGAGCAGATTAAAGCTGAGGA
* * *
41514933 CAGTGAATCTTATCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGGAGCGGATTGAAGCTGTG
196 CAGTGAATCTTATCTCCATGGCGTTAAGACTTGAAATAGCTGAAGTGGAGCAGATTAAAGCTGTG
*
41514998 GGCAGGGAATCCTATCTCTTTGGCATT
261 GGCAGCGAATCCTATCTCTTTGGCATT
41515025 GTAGTTAAAT
Statistics
Matches: 260, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
310 148 0.57
318 112 0.43
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (311 bp):
GCAGCGAATCCTATCACTTTGGCATTACAGTGAAATAGATTGAAGCTACAATAGCGAATCTTACC
TCCCTGACAGTGTAGTGGAACAGATTGAAGCTACGACAGCGAATCTTGGTTCCCCGACAATGCAA
GATTAAAGCCAAAACGATGAATCTTACTTCCCTGACGTTATAGCAGAGCAGATTAAAGCTGAGGA
CAGTGAATCTTATCTCCATGGCGTTAAGACTTGAAATAGCTGAAGTGGAGCAGATTAAAGCTGTG
GGCAGCGAATCCTATCTCTTTGGCATTACAGTGGAATAGGTTGAAGCTACA
Found at i:41515089 original size:50 final size:50
Alignment explanation
Indices: 41515035--41515210 Score: 163
Period size: 50 Copynumber: 3.5 Consensus size: 50
41515025 GTAGTTAAAT
* *
41515035 AGATTGAAGATACAATAGCAAATCTTACTTCCCTGACGGTGTAGTGGAAC
1 AGATTGAAGCTACAACAGCAAATCTTACTTCCCTGACGGTGTAGTGGAAC
* * ** ** * ** * ** *
41515085 AGATTGAAGCTACGACGGTGAATCTTGGTTCCCCGACATTGCAGTTAAAT
1 AGATTGAAGCTACAACAGCAAATCTTACTTCCCTGACGGTGTAGTGGAAC
* * * * *
41515135 AGATTGAAGCTACAATAGCGAATCTTACTTTCCTGGCGGTATAGTGGAAC
1 AGATTGAAGCTACAACAGCAAATCTTACTTCCCTGACGGTGTAGTGGAAC
*
41515185 AAATTGAAGCTACAACAGCAAATCTT
1 AGATTGAAGCTACAACAGCAAATCTT
41515211 GTTTCCTCGA
Statistics
Matches: 92, Mismatches: 34, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
50 92 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCAAATCTTACTTCCCTGACGGTGTAGTGGAAC
Found at i:41515110 original size:310 final size:311
Alignment explanation
Indices: 41514448--41515160 Score: 863
Period size: 310 Copynumber: 2.3 Consensus size: 311
41514438 TTTGGCATTA
*
41514448 TAGTGGAATAGATTGAAGCTACAATGGTGAATCTTACCTCCCTGGCAGTGTAGTGGAACAGATTG
1 TAGTGGAATAGATTGAAGCTACAATGGTGAATCTTACCTCCCTGACAGTGTAGTGGAACAGATTG
* * * *
41514513 AAGCTACGATAGCGAATCTTGGTTCCCCGACATTGCAGTTAAAGAGATTGAAGCCAAAACGGTGA
66 AAGCTACGACAGCGAATCTTGGTTCCCCGACAATGC------A-AGATTAAAGCCAAAACGATGA
*
41514578 ATCTTACTTCCCTGACGTTATAGCGGAGCAGATTAAAGCTGAGGACAGTGAATCTTATCTCCATG
124 ATCTTACTTCCCTGACGTTATAGCAGAGCAGATTAAAGCTGAGGACAGTGAATCTTATCTCCATG
*
41514643 GCGTTAAGACTTGAAATAGCTGAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAGTCCTATCTCTT
189 GCGTTAAGACTTGAAATAGCTGAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTT
* * * * * ** * *
41514708 TGGCATTACAGTGGAATAGGTTGAAGCTACAGCAGCGAATCCTATCTCTTTGGCATTG
254 TGGCATTACAGTGAAATAGATTGAAGATACAACAGCAAATCCTATCTCCCTGACAGTG
* ** * * * *
41514766 CAGTTAAATAGATTGAAGCTACAATAGCGAATCTTACTTCCCTGACGGTGTAGTGGAACAGATTG
1 TAGTGGAATAGATTGAAGCTACAATGGTGAATCTTACCTCCCTGACAGTGTAGTGGAACAGATTG
* * **
41514831 AAGCTACGACGGTGAATCTTGGTTTTCCGACAATGC-AGATTAAAGCCAAAACGATGAATCTTAC
66 AAGCTACGACAGCGAATCTTGGTTCCCCGACAATGCAAGATTAAAGCCAAAACGATGAATCTTAC
* * *
41514895 TTCCCTGACGTTATAGTAGAGCAGATTAAAGCTGAGGGCAGTGAATCTTATCTCCCTGGCGTTAA
131 TTCCCTGACGTTATAGCAGAGCAGATTAAAGCTGAGGACAGTGAATCTTATCTCCATGGCGTTAA
* * *
41514960 GACTTGAAATAGCTGAAGTGGAGCGGATTGAAGCTGTGGGCAGGGAATCCTATCTCTTTGGCATT
196 GACTTGAAATAGCTGAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATT
** * * * *
41515025 GTAGTTAAATAGATTGAAGATACAATAGCAAATCTTA-CTTCCCTGACGGTG
261 ACAGTGAAATAGATTGAAGATACAACAGCAAATCCTATC-TCCCTGACAGTG
* * * *** * * * ** *
41515076 TAGTGGAACAGATTGAAGCTACGACGGTGAATCTTGGTTCCCCGACATTGCAGTTAAATAGATTG
1 TAGTGGAATAGATTGAAGCTACAATGGTGAATCTTACCTCCCTGACAGTGTAGTGGAACAGATTG
* *
41515141 AAGCTACAATAGCGAATCTT
66 AAGCTACGACAGCGAATCTT
41515161 ACTTTCCTGG
Statistics
Matches: 334, Mismatches: 60, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
309 1 0.00
310 246 0.74
318 87 0.26
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (311 bp):
TAGTGGAATAGATTGAAGCTACAATGGTGAATCTTACCTCCCTGACAGTGTAGTGGAACAGATTG
AAGCTACGACAGCGAATCTTGGTTCCCCGACAATGCAAGATTAAAGCCAAAACGATGAATCTTAC
TTCCCTGACGTTATAGCAGAGCAGATTAAAGCTGAGGACAGTGAATCTTATCTCCATGGCGTTAA
GACTTGAAATAGCTGAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATT
ACAGTGAAATAGATTGAAGATACAACAGCAAATCCTATCTCCCTGACAGTG
Found at i:41515150 original size:100 final size:100
Alignment explanation
Indices: 41515021--41515239 Score: 312
Period size: 100 Copynumber: 2.2 Consensus size: 100
41515011 ATCTCTTTGG
* *
41515021 CATTGTAGTTAAATAGATTGAAGATACAATAGCAAATCTTACTTCCCTGACGGTGTAGTGGAACA
1 CATTGCAGTTAAATAGATTGAAGATACAATAGCAAATCTTACTTCCCTGACGGTATAGTGGAACA
* * * **
41515086 GATTGAAGCTACGACGGTGAATCTTGGTTCCCCGA
66 AATTGAAGCTACAACAGCAAATCTTGGTTCCCCGA
* * * *
41515121 CATTGCAGTTAAATAGATTGAAGCTACAATAGCGAATCTTACTTTCCTGGCGGTATAGTGGAACA
1 CATTGCAGTTAAATAGATTGAAGATACAATAGCAAATCTTACTTCCCTGACGGTATAGTGGAACA
* *
41515186 AATTGAAGCTACAACAGCAAATCTTGTTTCCTCGA
66 AATTGAAGCTACAACAGCAAATCTTGGTTCCCCGA
*
41515221 CATTGCAGTTAAACAGATT
1 CATTGCAGTTAAATAGATT
41515240 AAAGTTACGA
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 105 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (100 bp):
CATTGCAGTTAAATAGATTGAAGATACAATAGCAAATCTTACTTCCCTGACGGTATAGTGGAACA
AATTGAAGCTACAACAGCAAATCTTGGTTCCCCGA
Found at i:41515539 original size:130 final size:132
Alignment explanation
Indices: 41515253--41515599 Score: 572
Period size: 130 Copynumber: 2.6 Consensus size: 132
41515243 GTTACGAATT
* *
41515253 ACCAATCCTATCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTGTCTCCCCAAGC
1 ACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCCAAGC
41515318 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCCTCCCAATGTAGTAGGGAAACAGATTTAAG
66 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCCTCCCAATGTAGTAGGGAAACAGATTTAAG
41515383 CC
131 CC
* * *
41515385 ACCAATCCTATCTCCCTAAGCAGCAGTAGAGTAAGTTGAAGATTGTAGATCCTGTCTCCCCAAGC
1 ACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCCAAGC
* * *
41515450 AAT-GTGGAGCAGATCGAAGACGGTGAATCTTATCCTCCCAA-GTAGTAGGGAAGCAGATTTAAG
66 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCCTCCCAATGTAGTAGGGAAACAGATTTAAG
41515513 CC
131 CC
* *
41515515 ACCAATCCTATCTCTCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGC
1 ACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCCAAGC
* *
41515580 AGTAGTAGAGCATATCGAAG
66 AGTAGTGGAGCAGATCGAAG
41515600 GCAGCAAATC
Statistics
Matches: 198, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
130 85 0.43
131 51 0.26
132 62 0.31
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (132 bp):
ACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCCAAGC
AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCCTCCCAATGTAGTAGGGAAACAGATTTAAG
CC
Found at i:41521478 original size:42 final size:42
Alignment explanation
Indices: 41521419--41521502 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
41521409 AAACCCGAAA
* *
41521419 AGAGCGGCTCAAATTTTGATTAGAAT-AGGACATGAGGTGATC
1 AGAGCAGCTCAAATTTTGATCAGAATGAGG-CATGAGGTGATC
* *
41521461 AGAGCAGCTCAAATTTTGATCAGATTGAGGCATGTGGTGATC
1 AGAGCAGCTCAAATTTTGATCAGAATGAGGCATGAGGTGATC
41521503 TTGCTATACT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 34 0.92
43 3 0.08
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (42 bp):
AGAGCAGCTCAAATTTTGATCAGAATGAGGCATGAGGTGATC
Found at i:41522966 original size:50 final size:50
Alignment explanation
Indices: 41522912--41523095 Score: 190
Period size: 50 Copynumber: 3.7 Consensus size: 50
41522902 TTGGCATTAC
* * *
41522912 AGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTAT
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGT
* * ** * ** *
41522962 AGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCTCC-AACATTGC
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTC-CCTAGCGGTGT
** * *
41523012 AGTTAAATAGATTAAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGT
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGT
* * *
41523062 AGTGGAACAAATTGAAGCTACGACGGCGAATCTT
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTT
41523096 GGTTCCCCGA
Statistics
Matches: 102, Mismatches: 30, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
49 2 0.02
50 98 0.96
51 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (50 bp):
AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGT
Found at i:41523044 original size:100 final size:100
Alignment explanation
Indices: 41522917--41523180 Score: 375
Period size: 100 Copynumber: 2.6 Consensus size: 100
41522907 ATTACAGTGG
41522917 AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTATAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTATAGTGGAACAGATTGAAGCTA
* * *
41522982 CGACGGCGAATCTTGTTTCTCCAACATTGCAGTTA
66 CGACGGCGAATCTTGGTTCCCCAACATTGCAGTCA
* * * *
41523017 AATAGATTAAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGTAGTGGAACAAATTGAAGCTA
1 AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTATAGTGGAACAGATTGAAGCTA
*
41523082 CGACGGCGAATCTTGGTTCCCCGACATTGCAGTCA
66 CGACGGCGAATCTTGGTTCCCCAACATTGCAGTCA
* * * ** * * * *
41523117 ACTATATTGAAGCCAAAACGGCGAATCTTACTTTTCTGACGTTATAGTGGAGCAGATTAAAGCT
1 AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTATAGTGGAACAGATTGAAGCT
41523181 GAGGGCAGCG
Statistics
Matches: 143, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 143 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (100 bp):
AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTATAGTGGAACAGATTGAAGCTA
CGACGGCGAATCTTGGTTCCCCAACATTGCAGTCA
Found at i:41523126 original size:50 final size:50
Alignment explanation
Indices: 41522972--41523145 Score: 143
Period size: 50 Copynumber: 3.5 Consensus size: 50
41522962 AGTGGAACAG
* * * * * * *
41522972 ATTGAAGCTACGACGGCGAATCTTGTTTCTCCAACATTGCAGTTAAATAG
1 ATTGAAGCCACAACGGCGAATCTTGCTTCCCCAACATTGCAGTCAACTAA
* * * * ** * *
41523022 ATTAAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGTAGTGGAAC-AA
1 ATTGAAGCCACAACGGCGAATCTTGCTTCCCCAACATTGCAGT-CAACTAA
* * * * *
41523072 ATTGAAGCTACGACGGCGAATCTTGGTTCCCCGACATTGCAGTCAACTAT
1 ATTGAAGCCACAACGGCGAATCTTGCTTCCCCAACATTGCAGTCAACTAA
*
41523122 ATTGAAGCCAAAACGGCGAATCTT
1 ATTGAAGCCACAACGGCGAATCTT
41523146 ACTTTTCTGA
Statistics
Matches: 92, Mismatches: 30, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
49 3 0.03
50 87 0.95
51 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (50 bp):
ATTGAAGCCACAACGGCGAATCTTGCTTCCCCAACATTGCAGTCAACTAA
Found at i:41523365 original size:168 final size:168
Alignment explanation
Indices: 41523106--41523499 Score: 565
Period size: 168 Copynumber: 2.3 Consensus size: 168
41523096 GGTTCCCCGA
* * ** **
41523106 CATTGCAGTCAACTATATTGAAGCCAAAACGGCGAATCTTACTTTTCTGACGTTATAGTGGAGCA
1 CATTGCAGTCAAATAGATTGAAGCCAAAACGGCGAATCTTACTTCCCTGACGTTATAGCAGAGCA
* *
41523171 GATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTAGCGTTAAGACTT-GAAATAGCTGAAGTGGA
66 GATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTAGCGTTAAGACTTAG-AATAGATGAAGTGGA
*
41523235 GCGGATTGAAGCTGTGGGCAGCGAATCCTATCTCTTTGG
130 GCGGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGG
* * *
41523274 CATTGCAGTCAAATAGATTGAAGCCAAAACGGCTAATCTCACTTCCCTGACGTTATAGCAGAGTA
1 CATTGCAGTCAAATAGATTGAAGCCAAAACGGCGAATCTTACTTCCCTGACGTTATAGCAGAGCA
* *
41523339 GATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTAGATTAGATGAAGTGGAG
66 GATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTAGCGTTAAGACTTAGAATAGATGAAGTGGAG
*
41523404 CGGATTAAAGCTGTGGGCAGCGAATCTTATCTCTTTGG
131 CGGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGG
** ** * * * *
41523442 CATTATAGTGGAATAGATTGAAGCCACAACGTCGAATCTTACTTCCCTGGCGGTATAG
1 CATTGCAGTCAAATAGATTGAAGCCAAAACGGCGAATCTTACTTCCCTGACGTTATAG
41523500 TGGAACAGAT
Statistics
Matches: 200, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
168 199 1.00
169 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (168 bp):
CATTGCAGTCAAATAGATTGAAGCCAAAACGGCGAATCTTACTTCCCTGACGTTATAGCAGAGCA
GATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTAGCGTTAAGACTTAGAATAGATGAAGTGGAG
CGGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGG
Found at i:41523571 original size:100 final size:99
Alignment explanation
Indices: 41523453--41523839 Score: 492
Period size: 100 Copynumber: 3.9 Consensus size: 99
41523443 ATTATAGTGG
* * *
41523453 AATAGATTGAAGCCACAACGTCGAATCTTACTTCCCTGGCGGTATAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTATAATGGAACAGATTAAAGCTA
41523518 CGACGGCGAATCTTGTTTCTCCAACATTGCAGTTA
66 CGACGGCGAATCTTGTTTC-CCAACATTGCAGTTA
* * * * * *
41523553 AATAGATTGAAGCCACAACGG-GAAATCTTACTTCCTTGGCAGTGTAGTGGAACAAATTGAAGCT
1 AATAGATTGAAGCCACAACGGCG-AATCTTACTTCCCTGGCGGTATAATGGAACAGATTAAAGCT
* *
41523617 ACGACGGTGGATCTTGTTTCCCCAACATTGCAGTTA
65 ACGACGGCGAATCTTGTTT-CCCAACATTGCAGTTA
*
41523653 AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAATGGAACAGATTAAAGCTA
1 AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTATAATGGAACAGATTAAAGCTA
* *
41523718 CGACGGCGAATCTGGTTTCCCTGACATTGCAGTTA
66 CGACGGCGAATCTTGTTTCCC-AACATTGCAGTTA
* * * * * *
41523753 AATAGATTAAAGCCACAACGGCAAATCTTA-TCTCCTTGGCGTTACAATAGAACAGATTAAAGCT
1 AATAGATTGAAGCCACAACGGCGAATCTTACT-TCCCTGGCGGTATAATGGAACAGATTAAAGCT
* *
41523817 A-AAGGTAGCGAATCTTGTTTCCC
65 ACGACG--GCGAATCTTGTTTCCC
41523840 TGGCATTACA
Statistics
Matches: 254, Mismatches: 26, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
99 7 0.03
100 230 0.91
101 17 0.07
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (99 bp):
AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTATAATGGAACAGATTAAAGCTA
CGACGGCGAATCTTGTTTCCCAACATTGCAGTTA
Found at i:41523760 original size:50 final size:50
Alignment explanation
Indices: 41523453--41523781 Score: 212
Period size: 50 Copynumber: 6.6 Consensus size: 50
41523443 ATTATAGTGG
* ** * ** ** **
41523453 AATAGATTGAAGCCACAACGTCGAATCTTACTTCCCTGGCGGTATAGTGG
1 AATAGATTGAAGCCACAACGGCGAATCTTGTTTCCCTGACATTGCAGTTA
* * * *
41523503 AACAGATTGAAGCTACGACGGCGAATCTTGTTTCTCC-AACATTGCAGTTA
1 AATAGATTGAAGCCACAACGGCGAATCTTGTTTC-CCTGACATTGCAGTTA
** * * * * **
41523553 AATAGATTGAAGCCACAACGG-GAAATCTTACTTCCTTGGCAGTGTAGTGG
1 AATAGATTGAAGCCACAACGGCG-AATCTTGTTTCCCTGACATTGCAGTTA
* * * * * * **
41523603 AACAAATTGAAGCTACGACGGTGGATCTTGTTTCCCCAACATTGCAGTTA
1 AATAGATTGAAGCCACAACGGCGAATCTTGTTTCCCTGACATTGCAGTTA
** * ** * * **
41523653 AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAATGG
1 AATAGATTGAAGCCACAACGGCGAATCTTGTTTCCCTGACATTGCAGTTA
* * * * *
41523703 AACAGATTAAAGCTACGACGGCGAATCTGGTTTCCCTGACATTGCAGTTA
1 AATAGATTGAAGCCACAACGGCGAATCTTGTTTCCCTGACATTGCAGTTA
* *
41523753 AATAGATTAAAGCCACAACGGCAAATCTT
1 AATAGATTGAAGCCACAACGGCGAATCTT
41523782 ATCTCCTTGG
Statistics
Matches: 198, Mismatches: 77, Indels: 8
0.70 0.27 0.03
Matches are distributed among these distances:
49 2 0.01
50 193 0.97
51 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (50 bp):
AATAGATTGAAGCCACAACGGCGAATCTTGTTTCCCTGACATTGCAGTTA
Found at i:41524632 original size:19 final size:19
Alignment explanation
Indices: 41524608--41524686 Score: 113
Period size: 19 Copynumber: 4.0 Consensus size: 19
41524598 AATCTTCAAG
41524608 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41524627 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41524646 GATATGCAATCTTAGAGATAT
1 GATATGCAATCTT--AGATAT
* *
41524667 GATTTTGTAATCTTAGATAT
1 GA-TATGCAATCTTAGATAT
41524687 TTAATTTGTA
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
19 32 0.58
20 6 0.11
21 8 0.15
22 9 0.16
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:41524651 original size:38 final size:40
Alignment explanation
Indices: 41524608--41524686 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
41524598 AATCTTCAAG
41524608 GATATGCAATCTT-AGATATGA-TATGCAATCTTAGATAT
1 GATATGCAATCTTAAGATATGATTATGCAATCTTAGATAT
* *
41524646 GATATGCAATCTTAGAGATATGATTTTGTAATCTTAGATAT
1 GATATGCAATCTTA-AGATATGATTATGCAATCTTAGATAT
41524687 TTAATTTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 13 0.36
40 8 0.22
41 15 0.42
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.39
Consensus pattern (40 bp):
GATATGCAATCTTAAGATATGATTATGCAATCTTAGATAT
Found at i:41524931 original size:23 final size:23
Alignment explanation
Indices: 41524887--41524931 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
41524877 TCTTATTTTG
* *
41524887 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
41524910 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
41524932 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:41525381 original size:25 final size:25
Alignment explanation
Indices: 41525344--41525410 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
41525334 GTATATTTAT
41525344 ATATATTATTTTTTATAAT-TCACACAC
1 ATATA-TA-TTTTTATAATAT-ACACAC
* * * *
41525371 ATATATATTTTTCTTATATATACAT
1 ATATATATTTTTATAATATACACAC
41525396 ATATATATTTTTATA
1 ATATATATTTTTATA
41525411 TTTTATAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 25 0.76
26 3 0.09
27 5 0.15
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (25 bp):
ATATATATTTTTATAATATACACAC
Found at i:41525399 original size:23 final size:22
Alignment explanation
Indices: 41525369--41525411 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
41525359 TAATTCACAC
*
41525369 ACATATATATTTTTCTTATATAT
1 ACATATATATATTT-TTATATAT
41525392 ACATATATATATTTTTATAT
1 ACATATATATATTTTTATAT
41525412 TTTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (22 bp):
ACATATATATATTTTTATATAT
Found at i:41528363 original size:54 final size:53
Alignment explanation
Indices: 41528281--41528395 Score: 194
Period size: 54 Copynumber: 2.1 Consensus size: 53
41528271 CAACATTATT
*
41528281 TTCGAATATCGGTCTTCTACCTCTCTGTAGAGTTGTCATCGATTTTGTAACCTA
1 TTCGAATATCGGTCTTCTACCTCTCTGTAAAGTTGTCATCGATTTTGT-ACCTA
*
41528335 TTCGAATATCGGTGTTCTACCTCTCTGTAAAGTTGTCATCGATTTTGTACCTA
1 TTCGAATATCGGTCTTCTACCTCTCTGTAAAGTTGTCATCGATTTTGTACCTA
41528388 TTCTGAAT
1 TTC-GAAT
41528396 TAGTCTCAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
53 8 0.14
54 50 0.86
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (53 bp):
TTCGAATATCGGTCTTCTACCTCTCTGTAAAGTTGTCATCGATTTTGTACCTA
Found at i:41532936 original size:18 final size:18
Alignment explanation
Indices: 41532910--41532950 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
41532900 GATGAAAAAT
*
41532910 TTTGACTGAAAGGCCTAG
1 TTTGCCTGAAAGGCCTAG
41532928 TTTGCCTGAAAGGCCTAG
1 TTTGCCTGAAAGGCCTAG
41532946 TTTGC
1 TTTGC
41532951 TCTTTGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (18 bp):
TTTGCCTGAAAGGCCTAG
Found at i:41535990 original size:41 final size:41
Alignment explanation
Indices: 41535933--41536016 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
41535923 GAAAAACCTT
41535933 AAGACTAATTAAATAATATAACATGAAGGATCCAACAAGAC
1 AAGACTAATTAAATAATATAACATGAAGGATCCAACAAGAC
41535974 AAGACTAATTAAATAATATAACATGAAGGATCCAACAAGAC
1 AAGACTAATTAAATAATATAACATGAAGGATCCAACAAGAC
41536015 AA
1 AA
41536017 CAAACAAGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.55, C:0.14, G:0.12, T:0.19
Consensus pattern (41 bp):
AAGACTAATTAAATAATATAACATGAAGGATCCAACAAGAC
Found at i:41537485 original size:18 final size:18
Alignment explanation
Indices: 41537462--41537496 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41537452 TATTATACAC
*
41537462 ATATACATATACATATAG
1 ATATACAAATACATATAG
*
41537480 ATATACAAATATATATA
1 ATATACAAATACATATA
41537497 TAACTATGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.34
Consensus pattern (18 bp):
ATATACAAATACATATAG
Found at i:41541108 original size:14 final size:14
Alignment explanation
Indices: 41541089--41541116 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41541079 TAACATGATG
41541089 TTTAACATTTTCAA
1 TTTAACATTTTCAA
41541103 TTTAACATTTTCAA
1 TTTAACATTTTCAA
41541117 ACAATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAACATTTTCAA
Found at i:41542435 original size:27 final size:28
Alignment explanation
Indices: 41542379--41542445 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
41542369 ATTACCAAAG
*
41542379 TACCCTCGA-TT-TACAGAATTACCATTT
1 TACCCTCGATTTATACAGAATTACCA-GT
*
41542406 TACCCTCGATTTATATAGAATTACC-GT
1 TACCCTCGATTTATACAGAATTACCAGT
41542433 TACCCTCGATTTA
1 TACCCTCGATTTA
41542446 NACCCTCAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 23 0.64
28 2 0.06
29 11 0.31
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.37
Consensus pattern (28 bp):
TACCCTCGATTTATACAGAATTACCAGT
Found at i:41542464 original size:67 final size:65
Alignment explanation
Indices: 41542380--41542512 Score: 187
Period size: 67 Copynumber: 2.0 Consensus size: 65
41542370 TTACCAAAGT
* *
41542380 ACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATATAGAATTACCG-TTACCCTCGATT
1 ACCCTCAATTTACAGAATTACCATTTTACCCTCGA-TT-TACAGAATTACCGTTTACCCTCGATT
41542444 TA
64 TA
* *
41542446 NACCCTCAATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATT
1 -ACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCG-TTTACCCTCGATT
41542511 TA
64 TA
41542513 CAAAATTACT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
65 12 0.20
66 2 0.03
67 46 0.77
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37
Consensus pattern (65 bp):
ACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTACCCTCGATTTA
Found at i:41542484 original size:27 final size:27
Alignment explanation
Indices: 41542447--41542521 Score: 123
Period size: 27 Copynumber: 2.8 Consensus size: 27
41542437 CTCGATTTAN
* *
41542447 ACCCTCAATTTATAGAATTACCGTTTT
1 ACCCTCGATTTACAGAATTACCGTTTT
41542474 ACCCTCGATTTACAGAATTACCGTTTT
1 ACCCTCGATTTACAGAATTACCGTTTT
*
41542501 ACCCTCGATTTACAAAATTAC
1 ACCCTCGATTTACAGAATTAC
41542522 TAAAATACCC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (27 bp):
ACCCTCGATTTACAGAATTACCGTTTT
Found at i:41542530 original size:27 final size:27
Alignment explanation
Indices: 41542473--41542667 Score: 139
Period size: 27 Copynumber: 7.2 Consensus size: 27
41542463 ATTACCGTTT
* ****
41542473 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACCAAAA
*
41542500 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
* *
41542527 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
* *
41542554 TATCCCTAGCTTGT--AAAATTACCAAAA
1 TA-CCCTCGATT-TACAAAATTACCAAAA
* *** *
41542581 TACCACT-GGTTTGTGAAATTACCGAAA
1 TACC-CTCGATTTACAAAATTACCAAAA
* **
41542608 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
*
41542635 TACCC-CTGATTTAGAAAATTA-CAGAAA
1 TACCCTC-GATTTACAAAATTACCA-AAA
41542662 TACCCT
1 TACCCT
41542668 TGACTTTCTA
Statistics
Matches: 138, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
25 1 0.01
26 10 0.07
27 119 0.86
28 7 0.05
29 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCAAAA
Found at i:41542572 original size:54 final size:53
Alignment explanation
Indices: 41542514--41542752 Score: 187
Period size: 54 Copynumber: 4.4 Consensus size: 53
41542504 CTCGATTTAC
*
41542514 AAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATATCCCTAGCTTGT
1 AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATA-CCCTAGCTTGT
*** * **
41542568 AAAATTACCAAAATACCAC-TGGTTTGTGAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACC-CTTGGTTTACAAAATTACCAAAATACCCT-AGCTTGT
* * * * *
41542622 AAAATTACCAAAATACCCCTGATTTAGAAAATTA-CAGAAATACCCTTGACTTTCT
1 AAAATTACCAAAATACCCTTGGTTTACAAAATTACCA-AAATACCCTAG-C-TTGT
* * ** * *
41542677 AAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTTGT
1 -AAAATTACCA-AAATACCCTTGGTTTACAAAATTACCAAAATACCC-TAGCTTGT
* * *
41542732 AGATTTACCAAAACACCCTTG
1 AAAATTACCAAAATACCCTTG
41542753 TAGGATGAAA
Statistics
Matches: 143, Mismatches: 31, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
53 6 0.04
54 91 0.64
55 9 0.06
56 35 0.24
57 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (53 bp):
AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTAGCTTGT
Found at i:41542717 original size:27 final size:27
Alignment explanation
Indices: 41542500--41542752 Score: 149
Period size: 27 Copynumber: 9.3 Consensus size: 27
41542490 ATTACCGTTT
* * *
41542500 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
41542527 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
* *
41542554 TATCCCTAGCTTGT--AAAATTACCAAAA
1 TA-CCCTTGGTT-TACAAAATTACCAAAA
*** *
41542581 TACCAC-TGGTTTGTGAAATTACCGAAA
1 TACC-CTTGGTTTACAAAATTACCAAAA
*** **
41542608 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
* * *
41542635 TACCCCTGATTTAGAAAATTA-CAGAAA
1 TACCCTTGGTTTACAAAATTACCA-AAA
* *
41542662 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTG-GTTTAC--AAAATTACCA-AAA
* **
41542691 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
** * *
41542718 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
*
41542745 CACCCTTG
1 TACCCTTG
41542753 TAGGATGAAA
Statistics
Matches: 180, Mismatches: 34, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
25 1 0.01
26 8 0.04
27 136 0.76
28 14 0.08
29 21 0.12
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
TACCCTTGGTTTACAAAATTACCAAAA
Found at i:41542732 original size:110 final size:108
Alignment explanation
Indices: 41542482--41542723 Score: 247
Period size: 108 Copynumber: 2.2 Consensus size: 108
41542472 TTACCCTCGA
* *** * ** * * *
41542482 TTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATT
1 TTTACAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATT
*
41542547 ACCAAAATATCCCTAGCTTGTAAAATTACCAAAATACCACTGG
66 ACCAAAATATCCCTAGCTTCTAAAATTACCAAAATACCACTGG
*** *
41542590 TTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTAGAAAATT
1 TTTACAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATT
* * *
41542655 A-CAGAAATA-CCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGG
66 ACCA-AAATATCCCTAG-C-TTCT-AAAATTACCA-AAATACCACTGG
*
41542700 TTTACAAAATTACTGAAATACCCT
1 TTTACAAAATTACCGAAATACCCT
41542724 TGGTTTGTAG
Statistics
Matches: 107, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
107 7 0.07
108 58 0.54
109 4 0.04
110 38 0.36
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (108 bp):
TTTACAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATT
ACCAAAATATCCCTAGCTTCTAAAATTACCAAAATACCACTGG
Found at i:41543728 original size:24 final size:25
Alignment explanation
Indices: 41543652--41543721 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
41543642 AGGAAGTGCT
* * * *
41543652 AAAAGGGCTATGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
41543677 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
* *
41543702 AAAAGTGCTTTGCCTCAGTT
1 AAAAGGGCTTTGCCCCAGTT
41543722 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:41543989 original size:31 final size:31
Alignment explanation
Indices: 41543940--41544022 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
41543930 TGCTTACAGT
41543940 AAAGGCTTCGG-CCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
41543970 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
41544001 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
41544023 TCGAGACTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 16 0.31
31 36 0.69
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:41547711 original size:17 final size:17
Alignment explanation
Indices: 41547691--41547727 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
41547681 TTATCGTTTG
41547691 TTTATTTTTCTTATTTA
1 TTTATTTTTCTTATTTA
*
41547708 TTTATTTTTGTTATTTA
1 TTTATTTTTCTTATTTA
41547725 TTT
1 TTT
41547728 GTATCTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTATTTTTCTTATTTA
Found at i:41549897 original size:22 final size:22
Alignment explanation
Indices: 41549869--41549913 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
41549859 ATCAAAATTA
*
41549869 TAACATAAACAGTGTGTGTGGC
1 TAACATAAACAGTATGTGTGGC
41549891 TAACATAAACAGTATGTGTGGC
1 TAACATAAACAGTATGTGTGGC
41549913 T
1 T
41549914 TTCTCTGAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (22 bp):
TAACATAAACAGTATGTGTGGC
Found at i:41550223 original size:27 final size:26
Alignment explanation
Indices: 41550175--41550226 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
41550165 GCGAGGCTGC
*
41550175 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
41550201 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
41550227 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:41550826 original size:26 final size:27
Alignment explanation
Indices: 41550797--41550850 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
41550787 TCACACAAGT
*
41550797 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
41550823 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
41550850 T
1 T
41550851 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:41550881 original size:27 final size:26
Alignment explanation
Indices: 41550851--41550965 Score: 99
Period size: 27 Copynumber: 4.3 Consensus size: 26
41550841 GGGGCAAAAT
*
41550851 GGTAATTTTACTCCACAAGGGTATCTC
1 GGTAATTTTAC-CCACAAGGGTATTTC
* * *
41550878 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTTTACC-CACAAGGGTATTTC
41550905 GGT-ATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCC-ACAAGGGTATTTC
* * *
41550932 GATAATTCTACCTTAC-AGAGGTATTTC
1 GGTAATTTTACC-CACAAG-GGTATTTC
41550959 GGTAATT
1 GGTAATT
41550966 CTACAACTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
26 6 0.08
27 62 0.87
28 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (26 bp):
GGTAATTTTACCCACAAGGGTATTTC
Found at i:41550938 original size:54 final size:54
Alignment explanation
Indices: 41550851--41550969 Score: 177
Period size: 54 Copynumber: 2.2 Consensus size: 54
41550841 GGGGCAAAAT
* * *
41550851 GGTAATTTTACTCC-ACAAGGGTATCTCGGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTAC-CCTACAAGGGTATCTCGATAATTCTACCTTACAGAGGTATTTC
* *
41550905 GGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCTTACAGAGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATCTCGATAATTCTACCTTACAGAGGTATTTC
41550959 GGTAATTCTAC
1 GGTAATTCTAC
41550970 AACTTATCCA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 2 0.03
54 56 0.97
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATCTCGATAATTCTACCTTACAGAGGTATTTC
Found at i:41550966 original size:27 final size:27
Alignment explanation
Indices: 41550870--41550969 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
41550860 ACTCCACAAG
* *
41550870 GGTATCTCGGTAATTCTACCTTACAGG
1 GGTATTTCGGTAATTCTACCTTACAGA
* *
41550897 GGTATTTCGGTATTTCTACCCTACA-A
1 GGTATTTCGGTAATTCTACCTTACAGA
*
41550923 GGGTATTTCGATAATTCTACCTTACAGA
1 -GGTATTTCGGTAATTCTACCTTACAGA
41550951 GGTATTTCGGTAATTCTAC
1 GGTATTTCGGTAATTCTAC
41550970 AACTTATCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
27 62 0.98
28 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (27 bp):
GGTATTTCGGTAATTCTACCTTACAGA
Found at i:41554962 original size:13 final size:13
Alignment explanation
Indices: 41554926--41554962 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
41554916 GAAAAATGAA
*
41554926 TATATGAAAAGGT
1 TATATGAAATGGT
*
41554939 TATATGGAATGGT
1 TATATGAAATGGT
41554952 TATATGAAATG
1 TATATGAAATG
41554963 AATATTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (13 bp):
TATATGAAATGGT
Found at i:41557291 original size:3 final size:3
Alignment explanation
Indices: 41557283--41557309 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
41557273 GGCTGGAGAA
41557283 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
41557310 TTGGTGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41557949 original size:20 final size:19
Alignment explanation
Indices: 41557913--41557963 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
41557903 ACGGGCTATT
*
41557913 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
41557932 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
41557952 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
41557964 GTTACTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:41562404 original size:27 final size:26
Alignment explanation
Indices: 41562356--41562415 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
41562346 GCGAGGCTGC
*
41562356 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
41562383 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
41562409 CAGATAT
1 CAGATAT
41562416 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:41562460 original size:71 final size:67
Alignment explanation
Indices: 41562383--41562524 Score: 203
Period size: 67 Copynumber: 2.1 Consensus size: 67
41562373 TCACCAGATA
* * *
41562383 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGA
41562448 GGCTGC
62 GGCTGC
* *
41562454 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
41562519 GC
66 GC
41562521 CAGA
1 CAGA
41562525 ACGCTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
67 41 0.62
71 25 0.38
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.18
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
GC
Found at i:41562502 original size:27 final size:26
Alignment explanation
Indices: 41562454--41562505 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
41562444 GCGAGGCTGC
*
41562454 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
41562480 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
41562506 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:41563204 original size:54 final size:54
Alignment explanation
Indices: 41563146--41563248 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
41563136 TTAACACCCT
41563146 AGGGGCAAAATGGTAATTT-TACCCCACAAGGGTATCTCGATAATTCTACCCTAC
1 AGGGGCAAAATGGT-ATTTCTACCCCACAAGGGTATCTCGATAATTCTACCCTAC
* *** * * *
41563200 AGGGGTATTTTGGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTAC
1 AGGGGCAAAATGGTATTTCTACCCCACAAGGGTATCTCGATAATTCTAC
41563249 AACTTGGGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 4 0.10
54 37 0.90
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (54 bp):
AGGGGCAAAATGGTATTTCTACCCCACAAGGGTATCTCGATAATTCTACCCTAC
Found at i:41563246 original size:27 final size:27
Alignment explanation
Indices: 41563157--41563248 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
41563147 GGGGCAAAAT
* * *
41563157 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
41563184 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
41563211 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
41563238 GGTAATTCTAC
1 GGTAATTCTAC
41563249 AACTTGGGCC
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:41569240 original size:40 final size:40
Alignment explanation
Indices: 41569178--41569313 Score: 177
Period size: 40 Copynumber: 3.4 Consensus size: 40
41569168 AAACCAAGTA
* * * * * *
41569178 CCTTCGGGATTTA-ACCGGATATAGCCACTGGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
41569217 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
41569257 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTCACTAGCACAAATG
41569297 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
41569314 CGTTATCATC
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 13 0.15
40 73 0.85
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:41573785 original size:177 final size:177
Alignment explanation
Indices: 41573489--41573843 Score: 710
Period size: 177 Copynumber: 2.0 Consensus size: 177
41573479 AATTCCTCTA
41573489 ATCCTCAAGCAACTTCCGTTGTCATGCTTGTTAGCTTGAACTGTCACTGCACTTTCCAGTGTCAA
1 ATCCTCAAGCAACTTCCGTTGTCATGCTTGTTAGCTTGAACTGTCACTGCACTTTCCAGTGTCAA
41573554 TGACCGCAATAACACTTTCATGCTAAAAACATTCAAACTCAAAGATTAAACAGTAGAAGCAAGAT
66 TGACCGCAATAACACTTTCATGCTAAAAACATTCAAACTCAAAGATTAAACAGTAGAAGCAAGAT
41573619 TGAATAAAATAATATTTAACCCAGAAATCATATATACTTTCGTACAG
131 TGAATAAAATAATATTTAACCCAGAAATCATATATACTTTCGTACAG
41573666 ATCCTCAAGCAACTTCCGTTGTCATGCTTGTTAGCTTGAACTGTCACTGCACTTTCCAGTGTCAA
1 ATCCTCAAGCAACTTCCGTTGTCATGCTTGTTAGCTTGAACTGTCACTGCACTTTCCAGTGTCAA
41573731 TGACCGCAATAACACTTTCATGCTAAAAACATTCAAACTCAAAGATTAAACAGTAGAAGCAAGAT
66 TGACCGCAATAACACTTTCATGCTAAAAACATTCAAACTCAAAGATTAAACAGTAGAAGCAAGAT
41573796 TGAATAAAATAATATTTAACCCAGAAATCATATATACTTTCGTACAG
131 TGAATAAAATAATATTTAACCCAGAAATCATATATACTTTCGTACAG
41573843 A
1 A
41573844 CATGAAATAG
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 178 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (177 bp):
ATCCTCAAGCAACTTCCGTTGTCATGCTTGTTAGCTTGAACTGTCACTGCACTTTCCAGTGTCAA
TGACCGCAATAACACTTTCATGCTAAAAACATTCAAACTCAAAGATTAAACAGTAGAAGCAAGAT
TGAATAAAATAATATTTAACCCAGAAATCATATATACTTTCGTACAG
Found at i:41579990 original size:25 final size:25
Alignment explanation
Indices: 41579956--41580006 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
41579946 CCCTTATAAT
*
41579956 GTGAAAATGACCT-TTTTACCCCTAG
1 GTGAAAATGA-CTATTATACCCCTAG
41579981 GTGAAAATGACTATTATACCCCTAG
1 GTGAAAATGACTATTATACCCCTAG
41580006 G
1 G
41580007 GTTATGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (25 bp):
GTGAAAATGACTATTATACCCCTAG
Found at i:41580065 original size:10 final size:10
Alignment explanation
Indices: 41580050--41580084 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
41580040 TTTGTACATA
41580050 ATATGCCATG
1 ATATGCCATG
41580060 ATATGCACATG
1 ATATGC-CATG
41580071 ATATGCCATG
1 ATATGCCATG
41580081 ATAT
1 ATAT
41580085 ATACATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (10 bp):
ATATGCCATG
Found at i:41580069 original size:21 final size:21
Alignment explanation
Indices: 41580045--41580084 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41580035 ACTGATTTGT
41580045 ACATAATATGCCATGATATGC
1 ACATAATATGCCATGATATGC
*
41580066 ACATGATATGCCATGATAT
1 ACATAATATGCCATGATAT
41580085 ATACATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (21 bp):
ACATAATATGCCATGATATGC
Found at i:41580090 original size:21 final size:20
Alignment explanation
Indices: 41580044--41580096 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
41580034 TACTGATTTG
*
41580044 TACATAATATGCCATGATATG
1 TACAT-ATATGCCATGATATA
*
41580065 CACATGATATGCCATGATATA
1 TACAT-ATATGCCATGATATA
41580086 TACATATATGC
1 TACATATATGC
41580097 ACGGGTTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (20 bp):
TACATATATGCCATGATATA
Found at i:41585472 original size:40 final size:39
Alignment explanation
Indices: 41585428--41585532 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
41585418 AGTGACCATA
*
41585428 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
41585468 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
41585506 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGACTAAG-CCCGAAGGCATTTG
41585533 AACGAGTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.03
39 32 0.55
40 24 0.41
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:41585489 original size:39 final size:40
Alignment explanation
Indices: 41585388--41585532 Score: 165
Period size: 40 Copynumber: 3.6 Consensus size: 40
41585378 TTGAATGATG
* *
41585388 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATA
*
41585428 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA
*
41585467 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
* *
41585507 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41585533 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 7, Indels: 14
0.81 0.06 0.12
Matches are distributed among these distances:
39 34 0.37
40 46 0.51
41 10 0.11
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
Found at i:41594732 original size:44 final size:42
Alignment explanation
Indices: 41594664--41594833 Score: 119
Period size: 43 Copynumber: 4.0 Consensus size: 42
41594654 ATCCGATATG
* ** * *
41594664 TGTTTTCGTGTAAGCCCACATCTGGGACTTTGGCATCG-ACTTC
1 TGTTTTCGTGTAAGACCATGTCTGGGACATTGACATCGTA--TC
41594707 TGTTTTACGTGTAAGACCATGTCTGGGACATTGACATCGTATC
1 TGTTTT-CGTGTAAGACCATGTCTGGGACATTGACATCGTATC
* * ** * * *
41594750 T-TATTTCGTGTAAAACCTTGTCTGGGACAGCGGCATCGATGTT
1 TGT-TTTCGTGTAAGACCATGTCTGGGACATTGACATCG-TATC
* * * * * *
41594793 TGATTGCATGTAAGACCACGTCTGGGACATTGGCATTGTAT
1 TGTTTTCGTGTAAGACCATGTCTGGGACATTGACATCGTAT
41594834 ATGCTTCTCG
Statistics
Matches: 100, Mismatches: 22, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
42 30 0.30
43 42 0.42
44 27 0.27
45 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (42 bp):
TGTTTTCGTGTAAGACCATGTCTGGGACATTGACATCGTATC
Found at i:41594828 original size:43 final size:42
Alignment explanation
Indices: 41594670--41594828 Score: 131
Period size: 42 Copynumber: 3.7 Consensus size: 42
41594660 TATGTGTTTT
* * * * *
41594670 CGTGTAAGCCCACATCTGGGACTTTGGCATCGACTTCTGTTTTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGA-TTTTG-ATTA
* * * *
41594714 CGTGTAAGACCATGTCTGGGACATTGACATCGTATCTT-ATTT
1 CGTGTAAGACCACGTCTGGGACATTGGCATCG-ATTTTGATTA
* ** ** *
41594756 CGTGTAAAACCTTGTCTGGGACAGCGGCATCGATGTTTGATTG
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGAT-TTTGATTA
*
41594799 CATGTAAGACCACGTCTGGGACATTGGCAT
1 CGTGTAAGACCACGTCTGGGACATTGGCAT
41594829 TGTATATGCT
Statistics
Matches: 90, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
41 2 0.02
42 31 0.34
43 27 0.30
44 29 0.32
45 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGATTTTGATTA
Found at i:41607687 original size:6 final size:6
Alignment explanation
Indices: 41607676--41607715 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
41607666 TAGGTTTCTA
* *
41607676 GAAATG GAAATG GAAAT- GAAATG AAAATT GAAATG GAAAT
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAAT
41607716 AATCCATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (6 bp):
GAAATG
Found at i:41611409 original size:17 final size:17
Alignment explanation
Indices: 41611387--41611420 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41611377 GCAAAGACTG
41611387 ACAAGGTAAATCCTAAC
1 ACAAGGTAAATCCTAAC
41611404 ACAAGGTAAATCCTAAC
1 ACAAGGTAAATCCTAAC
41611421 TTACTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (17 bp):
ACAAGGTAAATCCTAAC
Found at i:41615383 original size:27 final size:26
Alignment explanation
Indices: 41615335--41615394 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
41615325 GCGAGGCTGC
*
41615335 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
41615362 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
41615388 CAGATAT
1 CAGATAT
41615395 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:41615439 original size:71 final size:66
Alignment explanation
Indices: 41615362--41615500 Score: 188
Period size: 66 Copynumber: 2.0 Consensus size: 66
41615352 TCACCAGATA
* * *
41615362 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGCGA
1 CAGATATTGTGACAAAGCCACCAGAACAG----ATATATGTGGCG-AGCCACCAGATTGCAGCGA
41615427 GGCTGC
61 GGCTGC
* *
41615433 CAGATATTGTGACAAAGTCAGCAGAACAGATATATGTGGCGAGCCACCAGATTGCAGCGAGGCTG
1 CAGATATTGTGACAAAGCCACCAGAACAGATATATGTGGCGAGCCACCAGATTGCAGCGAGGCTG
41615498 C
66 C
41615499 CA
1 CA
41615501 AAACGCTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
66 27 0.43
67 12 0.19
71 24 0.38
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (66 bp):
CAGATATTGTGACAAAGCCACCAGAACAGATATATGTGGCGAGCCACCAGATTGCAGCGAGGCTG
C
Found at i:41616267 original size:27 final size:27
Alignment explanation
Indices: 41616135--41616281 Score: 161
Period size: 27 Copynumber: 5.4 Consensus size: 27
41616125 GAGGCTAAAT
* * *
41616135 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
41616162 GGTAATTCTACCCTACAGGGGGATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
41616189 AGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
41616216 GGTAATTCTATACCCTACAAGGGTATTTC
1 GGTAATTC--TACCCTACAAGGGTATTTC
* *
41616245 GGTAATTCTATCCTA-TAGAGGTATTTC
1 GGTAATTCTACCCTACAAG-GGTATTTC
**
41616272 AATAATTCTA
1 GGTAATTCTA
41616282 GTACTTATCC
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
26 2 0.02
27 73 0.72
29 27 0.26
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:41616268 original size:56 final size:56
Alignment explanation
Indices: 41616136--41616281 Score: 163
Period size: 56 Copynumber: 2.6 Consensus size: 56
41616126 AGGCTAAATG
* * * *
41616136 GTAATTTTACCCCACAAGGGTATCTCGGTAATTC--TACCCTACAGGGGGATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTATACCCTACAAGGGGATTTCA
* * *
41616190 GTATTTCTACCCTACAAGGGTATTTCGGTAATTCTATACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTATACCCTACAAGGGGATTTCA
* * **
41616246 GTAATTCTATCCTA-TAGAGGTATTTCAATAATTCTA
1 GTAATTCTACCCTACAAG-GGTATTTCGGTAATTCTA
41616282 GTACTTATCC
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 30 0.39
55 2 0.03
56 45 0.58
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (56 bp):
GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTATACCCTACAAGGGGATTTCA
Found at i:41623013 original size:70 final size:67
Alignment explanation
Indices: 41622935--41623075 Score: 167
Period size: 67 Copynumber: 2.1 Consensus size: 67
41622925 TCACTAGATA
* * * *
41622935 CAGATATTGTGGCTAGGCCACC-GAACAGATATATATCTGTGGCGAAGCCAGCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG--ATATA--TGTGGCGAAGCCAGCAGATTGCAACGA
41622999 GGCTAC
62 GGCTAC
* * *
41623005 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCATCAGATTGCAACGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCAGCAGATTGCAACGAGGCT
*
41623070 GC
66 AC
41623072 CAGA
1 CAGA
41623076 ATGCTTCCTC
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
67 33 0.53
69 5 0.08
70 18 0.29
71 6 0.10
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.19
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCAGCAGATTGCAACGAGGCT
AC
Found at i:41623781 original size:54 final size:54
Alignment explanation
Indices: 41623712--41623825 Score: 176
Period size: 54 Copynumber: 2.1 Consensus size: 54
41623702 AAAAATGGTA
*
41623712 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGT
1 ATTTCTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAAT
* * *
41623765 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTATCCTACAGGGGTATTTCAAT
1 ATTTCTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAAT
*
41623819 AATTCTA
1 ATTTCTA
41623826 GTACTTATCC
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 4 0.07
54 51 0.93
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (54 bp):
ATTTCTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAAT
Found at i:41623821 original size:27 final size:27
Alignment explanation
Indices: 41623709--41623825 Score: 144
Period size: 27 Copynumber: 4.3 Consensus size: 27
41623699 GAGAAAAATG
* * * * *
41623709 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
41623736 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
41623763 GTATTTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
*
41623790 GTAATTCTATCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
41623817 ATAATTCTA
1 GTAATTCTA
41623826 GTACTTATCC
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:41627276 original size:10 final size:9
Alignment explanation
Indices: 41627258--41627289 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
41627248 TAATAAATTA
41627258 ATGAAATAT
1 ATGAAATAT
41627267 ATGAAA-AT
1 ATGAAATAT
41627275 ATGAAA-AT
1 ATGAAATAT
41627283 ATGAAAT
1 ATGAAAT
41627290 TGGGACATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.28
Consensus pattern (9 bp):
ATGAAATAT
Found at i:41627945 original size:18 final size:18
Alignment explanation
Indices: 41627905--41627961 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
41627895 TCTCTTTTCT
*
41627905 AATCATCCCTCATCCCTC
1 AATCATCCCTCATCACTC
*
41627923 AATCATCCCTCACTCATTC
1 AATCATCCCTCA-TCACTC
* *
41627942 -ATCATTCTCTCATCTCTC
1 AATCA-TCCCTCATCACTC
41627960 AA
1 AA
41627962 CTCACTTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 20 0.65
19 11 0.35
ACGTcount: A:0.25, C:0.42, G:0.00, T:0.33
Consensus pattern (18 bp):
AATCATCCCTCATCACTC
Found at i:41629401 original size:28 final size:28
Alignment explanation
Indices: 41629319--41629404 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
41629309 TAGCATGGCT
*
41629319 ACCAGAAT-AGATA-TTGTGACAGAGCC
1 ACCAGAATCAGATATTTGTGGCAGAGCC
* *
41629345 ACCA-AATACAGATATTTGTGGTAGTGCC
1 ACCAGAAT-CAGATATTTGTGGCAGAGCC
*
41629373 ACCAGAATCAGATATTTGTGGCACAGCC
1 ACCAGAATCAGATATTTGTGGCAGAGCC
41629401 ACCA
1 ACCA
41629405 AAACTCTTCC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
25 3 0.06
26 4 0.08
27 5 0.10
28 35 0.70
29 3 0.06
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (28 bp):
ACCAGAATCAGATATTTGTGGCAGAGCC
Found at i:41631569 original size:12 final size:12
Alignment explanation
Indices: 41631552--41631576 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41631542 CTAGACATAC
41631552 AAAATAATAATA
1 AAAATAATAATA
41631564 AAAATAATAATA
1 AAAATAATAATA
41631576 A
1 A
41631577 CATTCAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:41637619 original size:28 final size:28
Alignment explanation
Indices: 41637587--41637690 Score: 136
Period size: 28 Copynumber: 3.7 Consensus size: 28
41637577 AGTTTGCATA
*
41637587 TTGTGACAGAGTCACCAGAAACAGATAT
1 TTGTGACAGAGCCACCAGAAACAGATAT
** * **
41637615 TTGTGGTAGTGCCACCAGAATGAGATAT
1 TTGTGACAGAGCCACCAGAAACAGATAT
*
41637643 TTGTGGCAGAGCCACCAGAAACAGATAT
1 TTGTGACAGAGCCACCAGAAACAGATAT
*
41637671 TTGTGACATAGCCACCAGAA
1 TTGTGACAGAGCCACCAGAA
41637691 CGCTTCCTCC
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (28 bp):
TTGTGACAGAGCCACCAGAAACAGATAT
Found at i:41656709 original size:40 final size:40
Alignment explanation
Indices: 41656635--41656856 Score: 313
Period size: 40 Copynumber: 5.6 Consensus size: 40
41656625 AACCCAAGTA
* * *
41656635 CCTTCGGGATTTAG-CCGGATAT-AGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAA-TAGCACAAATG
* * *
41656674 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
*
41656714 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
*
41656754 CCTTCGGGACTTAGCCTGGATATAATCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
* *
41656794 CCTTCGGGACTTAGCCCGGATATAATCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
* *
41656834 CCTTCGGGACTTAACCCAGATAT
1 CCTTCGGGACTTAGCCCGGATAT
41656857 CATTCGAATA
Statistics
Matches: 164, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 12 0.07
40 149 0.91
41 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
Found at i:41660247 original size:42 final size:42
Alignment explanation
Indices: 41660185--41660280 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
41660175 TAGCCCAACC
* *
41660185 ATGGTCTTACATGAAATCTCACATCGATGCCATATCCAAGAT
1 ATGGTCTTACACGAAATCTCACATCAATGCCATATCCAAGAT
* * *
41660227 ATGGTCTTACACGAAGTCTCATATCAATGCCATATCCCAGAT
1 ATGGTCTTACACGAAATCTCACATCAATGCCATATCCAAGAT
41660269 ATGGTCTTACAC
1 ATGGTCTTACAC
41660281 ATAATCTTAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (42 bp):
ATGGTCTTACACGAAATCTCACATCAATGCCATATCCAAGAT
Found at i:41660885 original size:20 final size:20
Alignment explanation
Indices: 41660847--41660885 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
41660837 TGTTTCTCTA
*
41660847 ACCATAAACATGCATAATAT
1 ACCATAAACATGCAAAATAT
41660867 ACCATTAAACAT-CAAAATA
1 ACCA-TAAACATGCAAAATA
41660886 CACAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.54, C:0.21, G:0.03, T:0.23
Consensus pattern (20 bp):
ACCATAAACATGCAAAATAT
Found at i:41683764 original size:27 final size:26
Alignment explanation
Indices: 41683726--41683776 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
41683716 CTCGCTGCAA
*
41683726 TCTGGTGGCTTCGCCACATATATCTAT
1 TCTGGTGACTTCGCCACA-ATATCTAT
*
41683753 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACTTCGCCACAATATCT
41683777 GGCAGCCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (26 bp):
TCTGGTGACTTCGCCACAATATCTAT
Found at i:41683902 original size:102 final size:102
Alignment explanation
Indices: 41683738--41683999 Score: 499
Period size: 102 Copynumber: 2.6 Consensus size: 102
41683728 TGGTGGCTTC
*
41683738 GCCACATATATCTAT-TCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATTTGGTGGC
1 GCCACA-ATATCTATATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATTTGGTGGC
41683802 TTCTCCACACATATATATATATCTGTTCTGGTCGGCTA
65 TTCTCCACACATATATATATATCTGTTCTGGTCGGCTA
41683840 GCCACAATATCTATATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATTTGGTGGCT
1 GCCACAATATCTATATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATTTGGTGGCT
41683905 TCTCCACACATATATATATATCTGTTCTGGTCGGCTA
66 TCTCCACACATATATATATATCTGTTCTGGTCGGCTA
41683942 GCCACAATATCTATATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATTT
1 GCCACAATATCTATATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATTT
41684000 CTGTGGTGTG
Statistics
Matches: 158, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
101 8 0.05
102 150 0.95
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (102 bp):
GCCACAATATCTATATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATTTGGTGGCT
TCTCCACACATATATATATATCTGTTCTGGTCGGCTA
Found at i:41693000 original size:18 final size:19
Alignment explanation
Indices: 41692977--41693012 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41692967 TAACAGGTAA
41692977 ACTAAAAGCAAA-TAAAAT
1 ACTAAAAGCAAATTAAAAT
*
41692995 ACTAAAATCAAATTAAAA
1 ACTAAAAGCAAATTAAAA
41693013 ATTAAAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.67, C:0.11, G:0.03, T:0.19
Consensus pattern (19 bp):
ACTAAAAGCAAATTAAAAT
Found at i:41698639 original size:31 final size:31
Alignment explanation
Indices: 41698596--41698661 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
41698586 ACTGTTGCTG
*
41698596 TTCAATACTGTTTTAATGTTAATTTCAGTTT
1 TTCAATACTGTTTTAATGCTAATTTCAGTTT
*
41698627 TTCAATATTGTTTTAATGCTAATTTCAGTTT
1 TTCAATACTGTTTTAATGCTAATTTCAGTTT
41698658 TTCA
1 TTCA
41698662 TGATTTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.55
Consensus pattern (31 bp):
TTCAATACTGTTTTAATGCTAATTTCAGTTT
Found at i:41699499 original size:55 final size:54
Alignment explanation
Indices: 41699424--41699562 Score: 154
Period size: 55 Copynumber: 2.6 Consensus size: 54
41699414 TGAACTCACT
** * *
41699424 AATGCCACACCTTGGAATGGTCTTACATG-GGACCTTTACCTTATAGTGACACATC
1 AATGCCATGCCTTGGCATGGTCTTACATGAGGACC-TTACCTTATAGAG-CACATC
* *** * **
41699479 AATGCCATGTCTTGGCATGGTCTTACATGATTTCCTTGCCTTATAGAGCTTATC
1 AATGCCATGCCTTGGCATGGTCTTACATGAGGACCTTACCTTATAGAGCACATC
41699533 AATGCCATGCCTTGGCATGGTCTTACATGA
1 AATGCCATGCCTTGGCATGGTCTTACATGA
41699563 TATCCTTATC
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
54 33 0.46
55 36 0.51
56 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (54 bp):
AATGCCATGCCTTGGCATGGTCTTACATGAGGACCTTACCTTATAGAGCACATC
Found at i:41699605 original size:47 final size:47
Alignment explanation
Indices: 41699548--41699669 Score: 190
Period size: 47 Copynumber: 2.6 Consensus size: 47
41699538 CATGCCTTGG
*
41699548 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
* * *
41699595 CATGGCCTTACATGGCATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
* *
41699642 CATGGTCTTACATGGTATCTTTCTCTTA
1 CATGGTCTTACATGGTATCCTTATCTTA
41699670 GTGCCAATGG
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.35
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
Found at i:41699745 original size:47 final size:47
Alignment explanation
Indices: 41699684--41699805 Score: 135
Period size: 45 Copynumber: 2.6 Consensus size: 47
41699674 CAATGGCACA
* * * *
41699684 TCTTGATATGGTCTTACATGGATTCCTTAATCAATGCCGATGCCATG
1 TCTTGACATGGTCTTACATGGATTCCTTAAGCAATACCAATGCCATG
* **
41699731 TCTTGACATGGTCTTACACGGGA-TCCTT--GCCTTACCAATGCCATG
1 TCTTGACATGGTCTTACA-TGGATTCCTTAAGCAATACCAATGCCATG
41699776 TCTTGACATGGTCTTACATGG-TATCCTTAA
1 TCTTGACATGGTCTTACATGGAT-TCCTTAA
41699806 CCGTCAATTC
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
44 2 0.03
45 35 0.56
47 22 0.35
48 3 0.05
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (47 bp):
TCTTGACATGGTCTTACATGGATTCCTTAAGCAATACCAATGCCATG
Found at i:41706136 original size:53 final size:54
Alignment explanation
Indices: 41706068--41706275 Score: 213
Period size: 53 Copynumber: 3.9 Consensus size: 54
41706058 TTTCCTTTTT
* * * *
41706068 GAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * *
41706121 GAACTCACCAATGCCATGCCTTCACATGGTCGTACATGGGA-CCTTTGCCTTATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATA
* * * * *
41706175 GTGACTCATCAATGCCATGTCTTGGCATGGTCTTACGTGGTATCCTTGCCTTATA
1 G-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * * * ** *
41706230 GAGCTTATCAATTCCATGCCTTGGTATGGTCTTACATGATATCCTT
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
41706276 ATCTTACCAA
Statistics
Matches: 128, Mismatches: 23, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
52 2 0.02
53 43 0.34
54 38 0.30
55 43 0.34
56 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (54 bp):
GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
Found at i:41706259 original size:54 final size:54
Alignment explanation
Indices: 41706079--41706275 Score: 218
Period size: 55 Copynumber: 3.6 Consensus size: 54
41706069 AACTTACCAT
* * * * *
41706079 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAGCTCATCAA
** * * *
41706132 TGCCATGCCTTCACATGGTCGTACATGGGA-CCTTTGCCTTATAGTGACTCATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGGTATCC-TTGCCTTATAGAG-CTCATCAA
* * *
41706187 TGCCATGTCTTGGCATGGTCTTACGTGGTATCCTTGCCTTATAGAGCTTATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAGCTCATCAA
* * *
41706241 TTCCATGCCTTGGTATGGTCTTACATGATATCCTT
1 TGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
41706276 ATCTTACCAA
Statistics
Matches: 119, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
52 2 0.02
53 34 0.29
54 38 0.32
55 43 0.36
56 2 0.02
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.36
Consensus pattern (54 bp):
TGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAGCTCATCAA
Found at i:41706307 original size:47 final size:47
Alignment explanation
Indices: 41706255--41706375 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
41706245 ATGCCTTGGT
*
41706255 ATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAAC
1 ATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAAC
* * * *
41706302 ATGGTCTTACATGGCATCCTTGTCCTACTAAATGCCATGTTCCAAAC
1 ATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAAC
*
41706349 ATGGTCTTACATGGTATCCTTCTCTTA
1 ATGGTCTTACATGGTATCCTTATCTTA
41706376 GTGCCAATGC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (47 bp):
ATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAAC
Done.