Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 106 of 206
Found at i:31370995 original size:18 final size:18
Alignment explanation
Indices: 31370954--31371002 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
31370944 ATATTTAAAC
31370954 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
31370972 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
31370988 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
31371003 TCTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:31371121 original size:67 final size:67
Alignment explanation
Indices: 31371050--31371262 Score: 163
Period size: 67 Copynumber: 3.1 Consensus size: 67
31371040 ATTGTTAATG
*
31371050 TTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATCTTAATCATATTTAAACATAAT
1 TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATATCTTAATCATATTTAAACATAAT
31371115 TA
66 TA
* * * * ***
31371117 TTATTAAATATATTTTAATTAAAATATATAATT-T-AAT-A-AAAT-TCTT-ATAATTAGCAGAA
1 TTATT---TAAATTTTAA-TAAGAT-TATTATTATCAATAATAAATATCTTAATCA-TA-TTTAA
** * *
31371176 ATTTGTTATTG
59 A--CATAATTA
*
31371187 TTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAAT-TTAATCATATTTAAACATAA
1 TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAAT-ATCTTAATCATATTTAAACATAA
31371251 TTA
65 TTA
31371254 TTA-TTAAAT
1 TTATTTAAAT
31371263 ACATTATAAT
Statistics
Matches: 106, Mismatches: 24, Indels: 33
0.65 0.15 0.20
Matches are distributed among these distances:
65 5 0.05
66 15 0.14
67 30 0.28
68 8 0.08
69 8 0.08
70 24 0.23
71 10 0.09
72 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (67 bp):
TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATATCTTAATCATATTTAAACATAAT
TA
Found at i:31371139 original size:156 final size:156
Alignment explanation
Indices: 31370855--31371182 Score: 611
Period size: 156 Copynumber: 2.1 Consensus size: 156
31370845 TAGAATACCC
* *
31370855 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
*
31370920 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATCTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
31370985 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
31371011 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
*
31371076 TTATCAGTAATAAATATCTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATCTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
31371141 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
*
31371167 TTAGCAGAAATTTGTT
1 TTAGCAGAAAATTGTT
31371183 ATTGTTATTT
Statistics
Matches: 167, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 167 1.00
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
TTATCAGTAATAAATATCTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTATAA
Found at i:31371145 original size:18 final size:17
Alignment explanation
Indices: 31371124--31371158 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31371114 TTATTATTAA
*
31371124 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
31371142 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
31371159 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:31371149 original size:137 final size:137
Alignment explanation
Indices: 31371041--31371300 Score: 387
Period size: 137 Copynumber: 1.9 Consensus size: 137
31371031 TAAATGATTA
* *
31371041 TTGTTAATGTTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAAT-ATCTTAATCATATT
1 TTGTTAATGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAAT-TTAATCATATT
* * * *
31371105 TAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTATAATTA
65 TAAACATAATTATTATTAAATACATTATAATTAAAATATATAATTTAAGAAAATTCTTATAAGTA
*
31371170 GCAGAAAT
130 GAAGAAAT
*
31371178 TTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTT
1 TTGTTAATGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTT
**** *
31371243 AAACATAATTATTATTAAATACATTATAATTTTGGTATATAATTTAATAAAATTCTTA
66 AAACATAATTATTATTAAATACATTATAATTAAAATATATAATTTAAGAAAATTCTTA
31371301 ATAATTCATA
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
137 111 0.98
138 2 0.02
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (137 bp):
TTGTTAATGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTT
AAACATAATTATTATTAAATACATTATAATTAAAATATATAATTTAAGAAAATTCTTATAAGTAG
AAGAAAT
Found at i:31371340 original size:137 final size:135
Alignment explanation
Indices: 31371062--31371340 Score: 332
Period size: 137 Copynumber: 2.0 Consensus size: 135
31371052 ATTTAAATTT
* *
31371062 TAATAAGATTATTATTATCAGTAATAAATATCTTAATCATATTTAAACATAATTATTATTAAATA
1 TAATAAGATTATTAATATCAATAATAAATATCTTAATCATATTTAAACATAATTATTATTAAATA
* * * *
31371127 TATTTTAATTAAAATATATAATTTAATAAAATTCTTATAATTAGCAGAAATTTGTTATTGTTATT
66 CATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTA-CA-AAATTTCTTATTGTTACT
* **
31371192 TAAATTT
129 CAAATCA
31371199 TAATAAGATTATTAATATCAATAATAAATAAT-TTAATCATATTTAAACATAATTATTATTAAAT
1 TAATAAGATTATTAATATCAATAATAAAT-ATCTTAATCATATTTAAACATAATTATTATTAAAT
**** *
31371263 ACATTATAATTTTGGTATATAATTTAATAAAATTCTTAATAATT-C-ATA-TTCTTATATGAATT
65 ACATTATAATTAAAATATATAATTTAATAAAATTCTT-ATAATTACAAAATTTCTTAT-TG---T
31371325 TACTCAAATCA
125 TACTCAAATCA
31371336 TAATA
1 TAATA
31371341 TAATGAAAAT
Statistics
Matches: 122, Mismatches: 14, Indels: 12
0.82 0.09 0.08
Matches are distributed among these distances:
133 6 0.05
134 4 0.03
136 1 0.01
137 103 0.84
138 8 0.07
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (135 bp):
TAATAAGATTATTAATATCAATAATAAATATCTTAATCATATTTAAACATAATTATTATTAAATA
CATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTACAAAATTTCTTATTGTTACTCA
AATCA
Found at i:31380309 original size:29 final size:30
Alignment explanation
Indices: 31380277--31380338 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
31380267 GTTTCACGTG
*
31380277 TATAATTGCATA-AAATTAAAGTTCATGTA
1 TATAATTGCATATAAATCAAAGTTCATGTA
*
31380306 TATAATTGCATATTAAATCAATGTTCATGTA
1 TATAATTGCATA-TAAATCAAAGTTCATGTA
31380337 TA
1 TA
31380339 ATTTTGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (30 bp):
TATAATTGCATATAAATCAAAGTTCATGTA
Found at i:31380339 original size:29 final size:27
Alignment explanation
Indices: 31380275--31380341 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 27
31380265 GAGTTTCACG
*
31380275 TGTATAATTGCATAAAATTAAAGTTCA
1 TGTATAATTGCATAAAATCAAAGTTCA
*
31380302 TGTATATAATTGCATATTAAATCAATGTTCA
1 TG--TATAATTGCATA--AAATCAAAGTTCA
31380333 TGTATAATT
1 TGTATAATT
31380342 TTGAGATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 2 0.06
29 19 0.56
31 13 0.38
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (27 bp):
TGTATAATTGCATAAAATCAAAGTTCA
Found at i:31380938 original size:2 final size:2
Alignment explanation
Indices: 31380931--31380976 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
31380921 CTCATGCTTT
31380931 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
31380972 AA TA T
1 TA TA T
31380977 GATGTTTGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31381626 original size:13 final size:13
Alignment explanation
Indices: 31381581--31381631 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
31381571 TAAAATTAAA
*
31381581 AAAATAGAATATT
1 AAAATATAATATT
31381594 AACAATATTAATATT
1 AA-AATA-TAATATT
31381609 AAAATA-AATATAT
1 AAAATATAATAT-T
31381622 AAAATA-AATA
1 AAAATATAATA
31381632 ATTTGTAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
12 5 0.15
13 13 0.38
14 8 0.24
15 8 0.24
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (13 bp):
AAAATATAATATT
Found at i:31381735 original size:16 final size:16
Alignment explanation
Indices: 31381714--31381744 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31381704 TTTTGTATTA
*
31381714 TTTTAATATTAAATAT
1 TTTTAAAATTAAATAT
31381730 TTTTAAAATTAAATA
1 TTTTAAAATTAAATA
31381745 ACATTAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAAATTAAATAT
Found at i:31382608 original size:9 final size:9
Alignment explanation
Indices: 31382579--31382663 Score: 125
Period size: 9 Copynumber: 9.4 Consensus size: 9
31382569 TTTGGTTAAA
31382579 AATTAACCG
1 AATTAACCG
* *
31382588 AATTATCTG
1 AATTAACCG
31382597 AATTAACCG
1 AATTAACCG
31382606 AATTAACCG
1 AATTAACCG
31382615 AATTAACCG
1 AATTAACCG
31382624 AATTAACCG
1 AATTAACCG
** *
31382633 GGTTACCCG
1 AATTAACCG
31382642 AATTAACCG
1 AATTAACCG
31382651 AATTAACCG
1 AATTAACCG
31382660 AATT
1 AATT
31382664 GAATCACTAC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 66 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:31389399 original size:20 final size:20
Alignment explanation
Indices: 31389374--31389413 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
31389364 TACCCATGTT
31389374 CAAATACCTGTTTGATACTC
1 CAAATACCTGTTTGATACTC
31389394 CAAATACCTGTTTGATACTC
1 CAAATACCTGTTTGATACTC
31389414 TTGCCGGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (20 bp):
CAAATACCTGTTTGATACTC
Found at i:31390957 original size:18 final size:19
Alignment explanation
Indices: 31390915--31390958 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
31390905 TCCATTGATG
31390915 TTTATAACTCCATTAATTA
1 TTTATAACTCCATTAATTA
31390934 TCTTATAA-TCC-TTAAATTA
1 T-TTATAACTCCATT-AATTA
31390953 TTTATA
1 TTTATA
31390959 GGGTACGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 7 0.30
19 10 0.43
20 6 0.26
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTATAACTCCATTAATTA
Found at i:31391112 original size:17 final size:18
Alignment explanation
Indices: 31391072--31391113 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
31391062 GAAAGCTGAA
* *
31391072 TCATCCTTTTATTTTTTT
1 TCATTCTTTTATTTTTGT
*
31391090 TTATTCTTTTA-TTTTGT
1 TCATTCTTTTATTTTTGT
31391107 TCATTCT
1 TCATTCT
31391114 ATAATTCTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.71
Consensus pattern (18 bp):
TCATTCTTTTATTTTTGT
Found at i:31396155 original size:47 final size:50
Alignment explanation
Indices: 31396062--31396157 Score: 126
Period size: 47 Copynumber: 2.0 Consensus size: 50
31396052 ATCCATGATA
* * * *
31396062 AATGGATGTCCATAACCCCTCTCAAATTTATTCTATTGTAATCCCTAAAG
1 AATGAATGTCCATAACCCCTCTCAAATTCATTATATTGTAACCCCTAAAG
*
31396112 AATGAATGTCCATAA-CCC-CT-AAATTCATTATCTTGTAACCCCTAAA
1 AATGAATGTCCATAACCCCTCTCAAATTCATTATATTGTAACCCCTAAA
31396158 TCATTTATAG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
47 22 0.54
48 2 0.05
49 3 0.07
50 14 0.34
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.32
Consensus pattern (50 bp):
AATGAATGTCCATAACCCCTCTCAAATTCATTATATTGTAACCCCTAAAG
Found at i:31407371 original size:22 final size:22
Alignment explanation
Indices: 31407346--31407389 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
31407336 GAAAACCCGA
31407346 AAACA-AAGAACTCTCAAAATGT
1 AAACACAA-AACTCTCAAAATGT
* *
31407368 AAACACAAAATTCTCTAAATGT
1 AAACACAAAACTCTCAAAATGT
31407390 GTTATGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.52, C:0.18, G:0.07, T:0.23
Consensus pattern (22 bp):
AAACACAAAACTCTCAAAATGT
Found at i:31415838 original size:29 final size:26
Alignment explanation
Indices: 31415786--31415853 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 26
31415776 ATAAAATTAA
* *
31415786 TAACTTTTAAAAATTTATACGAAATT
1 TAACTTTTAAAAATTTAAAAGAAATT
31415812 TAACATTTTAAATAATGTTAAAAGAAATT
1 TAAC-TTTTAAA-AAT-TTAAAAGAAATT
**
31415841 TATTTTTTAAAAA
1 TAACTTTTAAAAA
31415854 ACTTTATACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.11
27 9 0.26
28 10 0.29
29 12 0.34
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (26 bp):
TAACTTTTAAAAATTTAAAAGAAATT
Found at i:31415936 original size:21 final size:22
Alignment explanation
Indices: 31415888--31415938 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
31415878 TTAATTATTG
31415888 TTAAAAAT-TTTAAAATATATA
1 TTAAAAATATTTAAAATATATA
*
31415909 TT-TAAATATTT-AAATATACT-
1 TTAAAAATATTTAAAATATA-TA
31415929 TTAAAAATAT
1 TTAAAAATAT
31415939 ATTTTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAAAATATTTAAAATATATA
Found at i:31422638 original size:45 final size:46
Alignment explanation
Indices: 31422574--31422785 Score: 254
Period size: 45 Copynumber: 4.7 Consensus size: 46
31422564 TATCGGAGTG
* *
31422574 TGCCATGGTATCTTTCAACCATGGTATTATTTATTCTC-ATCTTGA
1 TGCCATAGTGTCTTTCAACCATGGTATTATTTATTCTCGATCTTGA
* *
31422619 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCG-TCTTGG
1 TGCCATAGTGTCTTTCAACCATGGTATTATTTATTCTCGATCTTGA
* *
31422664 TGCCACAGTGTCTTTCAACCATTGTCA-TATTTATTCTCGA-CTTGA
1 TGCCATAGTGTCTTTCAACCATGGT-ATTATTTATTCTCGATCTTGA
* * * * * *
31422709 TGCCATAGTGTCTTTCAAACATGGTTTTATTCATTTTCTG-TCGTGT
1 TGCCATAGTGTCTTTCAACCATGGTATTATTTATTCTC-GATCTTGA
*
31422755 TGCCATAGTGTCTTTCAACCATGGTCTTATT
1 TGCCATAGTGTCTTTCAACCATGGTATTATT
31422786 CATTTAATTT
Statistics
Matches: 143, Mismatches: 18, Indels: 11
0.83 0.10 0.06
Matches are distributed among these distances:
45 110 0.77
46 33 0.23
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (46 bp):
TGCCATAGTGTCTTTCAACCATGGTATTATTTATTCTCGATCTTGA
Found at i:31422726 original size:90 final size:91
Alignment explanation
Indices: 31422584--31422785 Score: 284
Period size: 90 Copynumber: 2.2 Consensus size: 91
31422574 TGCCATGGTA
*
31422584 TCTTTCAACCATGGT-ATTATTTATTCTCATCTTGATGCCATAGTGTCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCA-TATTTATTCTCATCTTGATGCCATAGTGTCTTTCAAACATGGTCTTA
* *
31422648 TTTATTCTC-GTCTTGGTGCCACAGTG
65 TTCATTCTCTGTCGTGGTGCCACAGTG
* *
31422674 TCTTTCAACCATTGTCATATTTATTCTCGA-CTTGATGCCATAGTGTCTTTCAAACATGGTTTTA
1 TCTTTCAACCATGGTCATATTTATTCTC-ATCTTGATGCCATAGTGTCTTTCAAACATGGTCTTA
* * *
31422738 TTCATTTTCTGTCGTGTTGCCATAGTG
65 TTCATTCTCTGTCGTGGTGCCACAGTG
*
31422765 TCTTTCAACCATGGTCTTATT
1 TCTTTCAACCATGGTCATATT
31422786 CATTTAATTT
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
90 64 0.65
91 35 0.35
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (91 bp):
TCTTTCAACCATGGTCATATTTATTCTCATCTTGATGCCATAGTGTCTTTCAAACATGGTCTTAT
TCATTCTCTGTCGTGGTGCCACAGTG
Found at i:31422824 original size:91 final size:89
Alignment explanation
Indices: 31422573--31422828 Score: 264
Period size: 90 Copynumber: 2.8 Consensus size: 89
31422563 TTATCGGAGT
* * * * *
31422573 GTGCCATGGTATCTTTCAACCATGGTATTATTTATTCTCATCTTGATGCCATAGTGTCTTTCAAC
1 GTGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTAATCTTGATGCCATAGTGTCTTT-AAA
* *
31422638 CATGGTCTTATTTATTCTCGTCTTG
65 CATGGTCTTATTCATTCTCGTCGTG
* * * *
31422663 GTGCCACAGTGTCTTTCAACCATTGTCATATTTATTCTCGA-CTTGATGCCATAGTGTCTTTCAA
1 GTGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCT-AATCTTGATGCCATAGTGTCTTT-AA
* *
31422727 ACATGGTTTTATTCATTTTCTGTCGTG
64 ACATGGTCTTATTCATTCTC-GTCGTG
* * * * * * *
31422754 TTGCCATAGTGTCTTTCAACCATGGTCTTATTCATT-TAATTTGTGATGTCATAGCGTCTTTTAG
1 GTGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTAATCT-TGATGCCATAGTGTCTTTAAA
31422818 CTATGGTCTTA
65 C-ATGGTCTTA
31422829 CTCAATAGAA
Statistics
Matches: 137, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
89 1 0.01
90 75 0.55
91 61 0.45
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (89 bp):
GTGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTAATCTTGATGCCATAGTGTCTTTAAAC
ATGGTCTTATTCATTCTCGTCGTG
Found at i:31432392 original size:20 final size:20
Alignment explanation
Indices: 31432367--31432413 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
31432357 ATAGAGGTAG
*
31432367 TAAAATGTATACAATAAA-AT
1 TAAAATGTATA-AAAAAATAT
*
31432387 TAAAATATATAAAAAAATAT
1 TAAAATGTATAAAAAAATAT
31432407 TAAAATG
1 TAAAATG
31432414 AAGTTGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (20 bp):
TAAAATGTATAAAAAAATAT
Found at i:31432776 original size:2 final size:2
Alignment explanation
Indices: 31432769--31432798 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31432759 GCGAGAAGGG
31432769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31432799 GAGTGAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31451440 original size:958 final size:959
Alignment explanation
Indices: 31449320--31452190 Score: 5636
Period size: 958 Copynumber: 3.0 Consensus size: 959
31449310 TACTAGGAAA
31449320 ACCAAGCAACAACTAATGTAGGAGAGGCTTGAGTGCCCACTTCCATTGACACATTGAGCAATTTT
1 ACCAAGCAACAACTAATGTAGGAGAGGCTTGAGTGCCCACTTCCATTGACACATTGAGCAATTTT
*
31449385 TAAGGATTCAATAAAAGATGATCAATCATCTAACATCATCTATTAAATCTCATGAATGAGTGATT
66 TAAGGATTCAATAAAAGATGATCGATCATCTAACATCATCTATTAAATCTCATGAATGAGTGATT
31449450 TTTAGGATGTGTTCAGAGATTAGGGTTATACAACAGATCTGTGATAGGGAGTAACATTAAGGAAT
131 TTTAGGATGTGTTCAGAGATTAGGGTTATACAACAGATCTGTGATAGGGAGTAACATTAAGGAAT
31449515 GATCTACAACGCAAGTGATCCTTGAAAAGTTGTTCACTTAATCCAGTAATCTTGTACTCCTGATT
196 GATCTACAACGCAAGTGATCCTTGAAAAGTTGTTCACTTAATCCAGTAATCTTGTACTCCTGATT
31449580 TAATAGGCCGACTTACTTCTGATTTGATGGATTGTTTTAATCATCATATTCTTCAACATTTGCTT
261 TAATAGGCCGACTTACTTCTGATTTGATGGATTGTTTTAATCATCATATTCTTCAACATTTGCTT
31449645 TGTCTTAGTCTAGTTAATAGATTAAGGGTTTTTGGCATTCTGATTGGCAAGTTTCTTGAACAAAA
326 TGTCTTAGTCTAGTTAATAGATTAAGGGTTTTTGGCATTCTGATTGGCAAGTTTCTTGAACAAAA
*
31449710 AGAGGAAGTAGAAAAGTATGCTATGGAATCTAAAGTTATGTTGAGTGATGTTGGTTGTTGAATTT
391 AGAGGAAGTAGAAGAGTATGCTATGGAATCTAAAGTTATGTTGAGTGATGTTGGTTGTTGAATTT
31449775 TTGAAGCTCTAATTGTTGTTGTTTTGCTATAGGGGAAGTATATGTCCTTTTGCATTTGAAGCTGC
456 TTGAAGCTCTAATTGTTGTTGTTTTGCTATAGGGGAAGTATATGTCCTTTTGCATTTGAAGCTGC
31449840 TTATGTTTGCTAAATAAGATGTTGAACTGGAGATGGTGCTGACTTTGTGTGGTGATGAATTTTTT
521 TTATGTTTGCTAAATAAGATGTTGAACTGGAGATGGTGCTGACTTTGTGTGGTGATGAA-TTTTT
31449905 TTTTCCTTTTTGAACTTTTATTTTGATGGGTTTGTATAATCTTTGAGATGATGATATTGATTTGA
585 TTTTCCTTTTTGAACTTTTATTTTGATGGGTTTGTATAATCTTTGAGATGATGATATTGATTTGA
31449970 TGATGCTAATGCTACTGTGATATTGAAACTAATATGAAACTATGATATTATGCTAAGGTGATTGT
650 TGATGCTAATGCTACTGTGATATTGAAACTAATATGAAACTATGATATTATGCTAAGGTGATTGT
31450035 TTACTTTCTGCATTTTACCTTATTTTCAACTTACTTAGATATAATCTAGTATTTTGATTATTGGT
715 TTACTTTCTGCATTTTACCTTATTTTCAACTTACTTAGATATAATCTAGTATTTTGATTATTGGT
31450100 GCGAATTCTAGATATGGAGTTAATATTTAAAATTACTATATTATATTCTAATTTGAGTTTAGTAT
780 GCGAATTCTAGATATGGAGTTAATATTTAAAATTACTATATTATATTCTAATTTGAGTTTAGTAT
31450165 GGGGAGGTTTGTACTAAAGGGGAGTTATTGGTGACTATTATGTTTAACTTCTTGTATTGTTTGAT
845 GGGGAGGTTTGTACTAAAGGGGAGTTATTGGTGACTATTATGTTTAACTTCTTGTATTGTTTGAT
31450230 TTTGTTAAATAAATTACCAAAAGGGGAGATTTTTGAGGAAAAATAAGAAG
910 TTTGTTAAATAAATTACCAAAAGGGGAGATTTTTGAGGAAAAATAAGAAG
31450280 ACCAAGCAACAACTAATGTAGGAGAGGCTTGAGTGCCCACTTCCATTGACACATTGAGCAATTTT
1 ACCAAGCAACAACTAATGTAGGAGAGGCTTGAGTGCCCACTTCCATTGACACATTGAGCAATTTT
31450345 TAAGGATTCAATAAAAGATGATCGATCATCTAACATCATCTATTAAATCTCATGAATGAGTGATT
66 TAAGGATTCAATAAAAGATGATCGATCATCTAACATCATCTATTAAATCTCATGAATGAGTGATT
31450410 TTTAGGATGTGTTCAGAGATTAGGGTTATACAACAGATCTGTGATAGGGAGTAACATTAAGGAAT
131 TTTAGGATGTGTTCAGAGATTAGGGTTATACAACAGATCTGTGATAGGGAGTAACATTAAGGAAT
* *
31450475 AATCTACAACGCAAGTGATCCTTGAAAAGTTGTTCACTTAATCCAGTAGTCTTGTACTCCTGATT
196 GATCTACAACGCAAGTGATCCTTGAAAAGTTGTTCACTTAATCCAGTAATCTTGTACTCCTGATT
31450540 TAATAGGCCGACTTACTTCTGATTTGATGGATTGTTTTAATCATCATATTCTTCAACATTTGCTT
261 TAATAGGCCGACTTACTTCTGATTTGATGGATTGTTTTAATCATCATATTCTTCAACATTTGCTT
31450605 TGTCTTAGTCTAGTTAATAGATTAAGGGTTTTTGGCATTCTGATTGGCAAGTTTCTTGAACAAAA
326 TGTCTTAGTCTAGTTAATAGATTAAGGGTTTTTGGCATTCTGATTGGCAAGTTTCTTGAACAAAA
31450670 AGAGGAAGTAGAAGAGTATGCTATGGAATCTAAAGTTATGTTGAGTGATGTTGGTTGTTGAATTT
391 AGAGGAAGTAGAAGAGTATGCTATGGAATCTAAAGTTATGTTGAGTGATGTTGGTTGTTGAATTT
31450735 TTGAAGCTCTAATTGTTGTTGTTTTGCTATAGGGGAAGTATATGTCCTTTTGCATTTGAAGCTGC
456 TTGAAGCTCTAATTGTTGTTGTTTTGCTATAGGGGAAGTATATGTCCTTTTGCATTTGAAGCTGC
31450800 TTATGTTTGCTAAATAAGATGTTGAACTGGAGATGGTGCTGACTTTGTGTGGTGATGAATTTTTT
521 TTATGTTTGCTAAATAAGATGTTGAACTGGAGATGGTGCTGACTTTGTGTGGTGATGAATTTTTT
31450865 TTTCCTTTTTGAACTTTTATTTTGATGGGTTTGTATAATCTTTGAGATGATGATATTGATTTGAT
586 TTTCCTTTTTGAACTTTTATTTTGATGGGTTTGTATAATCTTTGAGATGATGATATTGATTTGAT
31450930 GATGCTAATGCTACTGTGATATTGAAACTAATATGAAACTATGATATTATGCTAAGGTGATT-TT
651 GATGCTAATGCTACTGTGATATTGAAACTAATATGAAACTATGATATTATGCTAAGGTGATTGTT
*
31450994 TACTTTCTGCATTATACCTTATTTTCAACTTACTTAGATATAATCTAGTATTTTGATTATTGGTG
716 TACTTTCTGCATTTTACCTTATTTTCAACTTACTTAGATATAATCTAGTATTTTGATTATTGGTG
31451059 CGAATTCTAGATATGGAGTTAATATTTAAAATTACTATATTATATTCTAATTTGAGTTTAGTATG
781 CGAATTCTAGATATGGAGTTAATATTTAAAATTACTATATTATATTCTAATTTGAGTTTAGTATG
31451124 GGGAGGTTTGTACTAAAGGGGAGTTATTGGTGACTATTATGTTTAACTTCTTGTATTGTTTGATT
846 GGGAGGTTTGTACTAAAGGGGAGTTATTGGTGACTATTATGTTTAACTTCTTGTATTGTTTGATT
*
31451189 TTGTTAAATAAATTACCAAAAGGGGAGATTTTTGAGGAAAAATAAGATG
911 TTGTTAAATAAATTACCAAAAGGGGAGATTTTTGAGGAAAAATAAGAAG
* *
31451238 ACCAAGCAACAACTATTGTAGGAGAGGCTTGAGTGCCCACTTCCATTAACACATTGAGCAATTTT
1 ACCAAGCAACAACTAATGTAGGAGAGGCTTGAGTGCCCACTTCCATTGACACATTGAGCAATTTT
31451303 TAAGGATTCAATAAAAGATGATCGATCATCTAACATCATCTATTAAATCTCATGAATGAGTGATT
66 TAAGGATTCAATAAAAGATGATCGATCATCTAACATCATCTATTAAATCTCATGAATGAGTGATT
31451368 TTTAGGATGTGTTCAGAGATTAGGGTTATACAACAGATCTGTGATAGGGAGTAACATTAAGGAAT
131 TTTAGGATGTGTTCAGAGATTAGGGTTATACAACAGATCTGTGATAGGGAGTAACATTAAGGAAT
31451433 GATCTACAACGCAAGTGATCCTTGAAAAGTTGTTCACTTAATCCAGTAATCTTGTACTCCTGATT
196 GATCTACAACGCAAGTGATCCTTGAAAAGTTGTTCACTTAATCCAGTAATCTTGTACTCCTGATT
31451498 TAATAGGCCGACTTACTTCTGATTTGATGGATTGTTTTAATCATCATATTCTTCAACATTTGCTT
261 TAATAGGCCGACTTACTTCTGATTTGATGGATTGTTTTAATCATCATATTCTTCAACATTTGCTT
*
31451563 TGTCTTAGTCTAGTTAATAGAATAAGGGTTTTTGGCATTCTGATTGGCAAGTTTCTTGAACAAAA
326 TGTCTTAGTCTAGTTAATAGATTAAGGGTTTTTGGCATTCTGATTGGCAAGTTTCTTGAACAAAA
31451628 AGAGGAAGTAGAAGAGTATGCTATGGAATCTAAAGTTATGTTGAGTGATGTTGGTTGTTGAATTT
391 AGAGGAAGTAGAAGAGTATGCTATGGAATCTAAAGTTATGTTGAGTGATGTTGGTTGTTGAATTT
31451693 TTGAAGCTCTAATTGTTGTTGTTTTGCTATAGGGGAAGTATATGTCCTTTTGCATTTGAAGCTGC
456 TTGAAGCTCTAATTGTTGTTGTTTTGCTATAGGGGAAGTATATGTCCTTTTGCATTTGAAGCTGC
31451758 TTATGTTTGCTAAATAAGATGTTGAACTGGAGATGGTGCTGACTTTGTGTGGTGATGAATTTTTT
521 TTATGTTTGCTAAATAAGATGTTGAACTGGAGATGGTGCTGACTTTGTGTGGTGATGAATTTTTT
31451823 TTTCCTTTTTGAACTTTTATTTTGATGGGTTTGTATAATCTTTGAGATGATGATATTGATTTGAT
586 TTTCCTTTTTGAACTTTTATTTTGATGGGTTTGTATAATCTTTGAGATGATGATATTGATTTGAT
31451888 GATGCTAATGCTACTGTGATATTGAAACTAATATGAAACTATGATATTATGCTAAGGTGATTGTT
651 GATGCTAATGCTACTGTGATATTGAAACTAATATGAAACTATGATATTATGCTAAGGTGATTGTT
31451953 TACTTTCTGCATTTTACCTTATTTTCAACTTACTTAGATATAATCTAGTATTTTGATTATTGGTG
716 TACTTTCTGCATTTTACCTTATTTTCAACTTACTTAGATATAATCTAGTATTTTGATTATTGGTG
*
31452018 CGAATTCTAGGTATGGAGTTAATATTTAAAATTACTATATTATATTCTAATTTGAGTTTAGTATG
781 CGAATTCTAGATATGGAGTTAATATTTAAAATTACTATATTATATTCTAATTTGAGTTTAGTATG
31452083 GGGAGGTTTGTACTAAAGGGGAGTTATTGGTGACTATTATGTTTAACTTCTTGTATTGTTTGATT
846 GGGAGGTTTGTACTAAAGGGGAGTTATTGGTGACTATTATGTTTAACTTCTTGTATTGTTTGATT
31452148 TTGTTAAATAAATTACCAAAAGGGGAGATTTTTGAGGAAAAAT
911 TTGTTAAATAAATTACCAAAAGGGGAGATTTTTGAGGAAAAAT
31452191 GCGTTGAATG
Statistics
Matches: 1897, Mismatches: 13, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
958 951 0.50
959 371 0.20
960 575 0.30
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.39
Consensus pattern (959 bp):
ACCAAGCAACAACTAATGTAGGAGAGGCTTGAGTGCCCACTTCCATTGACACATTGAGCAATTTT
TAAGGATTCAATAAAAGATGATCGATCATCTAACATCATCTATTAAATCTCATGAATGAGTGATT
TTTAGGATGTGTTCAGAGATTAGGGTTATACAACAGATCTGTGATAGGGAGTAACATTAAGGAAT
GATCTACAACGCAAGTGATCCTTGAAAAGTTGTTCACTTAATCCAGTAATCTTGTACTCCTGATT
TAATAGGCCGACTTACTTCTGATTTGATGGATTGTTTTAATCATCATATTCTTCAACATTTGCTT
TGTCTTAGTCTAGTTAATAGATTAAGGGTTTTTGGCATTCTGATTGGCAAGTTTCTTGAACAAAA
AGAGGAAGTAGAAGAGTATGCTATGGAATCTAAAGTTATGTTGAGTGATGTTGGTTGTTGAATTT
TTGAAGCTCTAATTGTTGTTGTTTTGCTATAGGGGAAGTATATGTCCTTTTGCATTTGAAGCTGC
TTATGTTTGCTAAATAAGATGTTGAACTGGAGATGGTGCTGACTTTGTGTGGTGATGAATTTTTT
TTTCCTTTTTGAACTTTTATTTTGATGGGTTTGTATAATCTTTGAGATGATGATATTGATTTGAT
GATGCTAATGCTACTGTGATATTGAAACTAATATGAAACTATGATATTATGCTAAGGTGATTGTT
TACTTTCTGCATTTTACCTTATTTTCAACTTACTTAGATATAATCTAGTATTTTGATTATTGGTG
CGAATTCTAGATATGGAGTTAATATTTAAAATTACTATATTATATTCTAATTTGAGTTTAGTATG
GGGAGGTTTGTACTAAAGGGGAGTTATTGGTGACTATTATGTTTAACTTCTTGTATTGTTTGATT
TTGTTAAATAAATTACCAAAAGGGGAGATTTTTGAGGAAAAATAAGAAG
Found at i:31459219 original size:42 final size:42
Alignment explanation
Indices: 31459159--31459242 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
31459149 TCATATGAAG
* *
31459159 CAAATAGCAACGAGAGGTAGAAATAATATATTTATTTGTTAA
1 CAAATAGCAACGACAGGTAGAAACAATATATTTATTTGTTAA
31459201 CAAATAGCAACGACAGGTAGAAACAATATATTTATTTGTTAA
1 CAAATAGCAACGACAGGTAGAAACAATATATTTATTTGTTAA
31459243 AATATTAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (42 bp):
CAAATAGCAACGACAGGTAGAAACAATATATTTATTTGTTAA
Found at i:31474562 original size:22 final size:21
Alignment explanation
Indices: 31474537--31474585 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
31474527 AATTATTAAC
*
31474537 ATATTGAATTTTAATTAATTTT
1 ATATTAAATTTT-ATTAATTTT
*
31474559 ATATCAAAATTTTATTAATTTT
1 ATAT-TAAATTTTATTAATTTT
31474581 -TATTA
1 ATATTA
31474586 TTTTCGACAG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.04
21 3 0.13
22 13 0.57
23 6 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
ATATTAAATTTTATTAATTTT
Found at i:31477493 original size:16 final size:15
Alignment explanation
Indices: 31477466--31477499 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
31477456 ATAACTAGTA
*
31477466 TATAATTATATTTAT
1 TATAATTATATTAAT
31477481 TATAATATATATTAAT
1 TATAAT-TATATTAAT
31477497 TAT
1 TAT
31477500 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:31478270 original size:24 final size:25
Alignment explanation
Indices: 31478225--31478272 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
31478215 CAATTTCAAT
*
31478225 TTTATTTAATTATTTAAAATTTTAG
1 TTTATTGAATTATTTAAAATTTTAG
*
31478250 TTTATTGAATTA-TTAATATTTTA
1 TTTATTGAATTATTTAAAATTTTA
31478273 TACTCATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTATTGAATTATTTAAAATTTTAG
Found at i:31479931 original size:19 final size:19
Alignment explanation
Indices: 31479907--31479945 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
31479897 GTTCGTATGG
*
31479907 TTAAACTTTAAATTTTATA
1 TTAAACTTTAAAGTTTATA
31479926 TTAAACTTTAAAGTTTATA
1 TTAAACTTTAAAGTTTATA
31479945 T
1 T
31479946 ATATGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
TTAAACTTTAAAGTTTATA
Found at i:31480277 original size:42 final size:43
Alignment explanation
Indices: 31480207--31480334 Score: 172
Period size: 42 Copynumber: 3.0 Consensus size: 43
31480197 TGAGTTTTCG
* * * *
31480207 TTCAACCCTTACGGGTTT-TCGTTCAGCTCTTTTGAGCTTCTGT
1 TTCAACCCTTATGGGTTTCT-TTTTAGCTCTTATGAGCTTCTGT
* *
31480250 TT-AACCCTTATGGGTTTCTTTTTAGCTCTTACGAGCTT-TTT
1 TTCAACCCTTATGGGTTTCTTTTTAGCTCTTATGAGCTTCTGT
31480291 TTCAACCCTTATGGGTTTCTTTTTAGCTCTTATGAGCTTCTGT
1 TTCAACCCTTATGGGTTTCTTTTTAGCTCTTATGAGCTTCTGT
31480334 T
1 T
31480335 CAGCCTTCGG
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 4 0.05
42 64 0.86
43 6 0.08
ACGTcount: A:0.13, C:0.22, G:0.16, T:0.48
Consensus pattern (43 bp):
TTCAACCCTTATGGGTTTCTTTTTAGCTCTTATGAGCTTCTGT
Found at i:31480331 original size:21 final size:21
Alignment explanation
Indices: 31480231--31480331 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
31480221 GTTTTCGTTC
* *
31480231 AGCTCTTTTGAGCTTCTGTTT
1 AGCTCTTATGAGCTTCTTTTT
* * * *
31480252 AACCCTTATGGGTTTCTTTTT
1 AGCTCTTATGAGCTTCTTTTT
*
31480273 AGCTCTTACGAGCTT-TTTTT
1 AGCTCTTATGAGCTTCTTTTT
* * * *
31480293 CAACCCTTATGGGTTTCTTTTT
1 -AGCTCTTATGAGCTTCTTTTT
31480315 AGCTCTTATGAGCTTCT
1 AGCTCTTATGAGCTTCT
31480332 GTTCAGCCTT
Statistics
Matches: 58, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
20 5 0.09
21 48 0.83
22 5 0.09
ACGTcount: A:0.14, C:0.21, G:0.16, T:0.50
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTTTTT
Found at i:31481915 original size:25 final size:22
Alignment explanation
Indices: 31481867--31481915 Score: 53
Period size: 25 Copynumber: 2.1 Consensus size: 22
31481857 CATACTTCTA
**
31481867 GAACATAAAAAATTAGAATTTT
1 GAACATAAAAAATTAGAAAATT
31481889 GAACATAATAAAAGTGTAGAAAATT
1 GAACATAA-AAAA-T-TAGAAAATT
31481914 GA
1 GA
31481916 GTAATAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 4 0.18
24 1 0.05
25 9 0.41
ACGTcount: A:0.55, C:0.04, G:0.14, T:0.27
Consensus pattern (22 bp):
GAACATAAAAAATTAGAAAATT
Found at i:31496917 original size:17 final size:17
Alignment explanation
Indices: 31496895--31496927 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31496885 TATAACTTCC
31496895 TTTGAAAGCTT-TAAAAA
1 TTTGAAA-CTTCTAAAAA
31496912 TTTGAAACTTCTAAAA
1 TTTGAAACTTCTAAAA
31496928 GAAGTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (17 bp):
TTTGAAACTTCTAAAAA
Found at i:31506827 original size:15 final size:15
Alignment explanation
Indices: 31506807--31506859 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
31506797 AGCTTCACCT
31506807 TCTATACCTGTTACC
1 TCTATACCTGTTACC
* *
31506822 TCTATATCTCCTTCACCC
1 TCTATACCT-GTT-A-CC
*
31506840 TCTATACCGGTTACC
1 TCTATACCTGTTACC
31506855 TCTAT
1 TCTAT
31506860 TTCACCTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 15 0.50
16 3 0.10
17 3 0.10
18 9 0.30
ACGTcount: A:0.19, C:0.36, G:0.06, T:0.40
Consensus pattern (15 bp):
TCTATACCTGTTACC
Found at i:31506900 original size:33 final size:33
Alignment explanation
Indices: 31506799--31506886 Score: 131
Period size: 33 Copynumber: 2.7 Consensus size: 33
31506789 GAGACTTTAG
* *
31506799 CTTCACCTTCTATACCTGTTACCTCTATATCTC
1 CTTCACCTTCTATACCTGTTACCTCTATTTCAC
* *
31506832 CTTCACCCTCTATACCGGTTACCTCTATTTCAC
1 CTTCACCTTCTATACCTGTTACCTCTATTTCAC
*
31506865 CTTCATCTTCTATACCTGTTAC
1 CTTCACCTTCTATACCTGTTAC
31506887 TCCTTCTTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.18, C:0.36, G:0.05, T:0.41
Consensus pattern (33 bp):
CTTCACCTTCTATACCTGTTACCTCTATTTCAC
Found at i:31510337 original size:43 final size:44
Alignment explanation
Indices: 31510249--31510374 Score: 129
Period size: 43 Copynumber: 2.9 Consensus size: 44
31510239 AGCTCGTACA
* *
31510249 ATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCACATACCG
1 ATGCCAACTGTCCCAGACGTGGTCTTACACGTAAACACATACCG
*
31510292 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACA-AGTCG
1 ATGCCAACTGTCCCAGAC-GTGGTCTTACACGTAAACACATA-CCG
* * *
31510335 ATGCCGACAT-T-CCAGATGTGGTCTTACACGAAAACACATA
1 ATGCCAAC-TGTCCCAGACGTGGTCTTACACGTAAACACATA
31510375 TCGGAGTCCT
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
42 4 0.06
43 61 0.86
44 5 0.07
45 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (44 bp):
ATGCCAACTGTCCCAGACGTGGTCTTACACGTAAACACATACCG
Found at i:31511752 original size:33 final size:33
Alignment explanation
Indices: 31511710--31511776 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
31511700 CGTTGTATTT
31511710 ATAATTTGATAAAGGGCCAAATTTTAAACACCC
1 ATAATTTGATAAAGGGCCAAATTTTAAACACCC
* *
31511743 ATAATTTGATAAGGGGCCAAATTTTAAATACCC
1 ATAATTTGATAAAGGGCCAAATTTTAAACACCC
31511776 A
1 A
31511777 AAACTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (33 bp):
ATAATTTGATAAAGGGCCAAATTTTAAACACCC
Found at i:31512596 original size:21 final size:21
Alignment explanation
Indices: 31512572--31512612 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31512562 AGGGAGTGAC
31512572 ACTTACAATTTCATTATTGAA
1 ACTTACAATTTCATTATTGAA
*
31512593 ACTTACAATTTTATTATTGA
1 ACTTACAATTTCATTATTGA
31512613 TAAAGGTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (21 bp):
ACTTACAATTTCATTATTGAA
Found at i:31515872 original size:88 final size:90
Alignment explanation
Indices: 31515656--31515872 Score: 215
Period size: 90 Copynumber: 2.4 Consensus size: 90
31515646 AACCAAAAAC
* ** * * * * ***
31515656 GTTGCAGGTTAATACGTTGCCAAATGGTTGTGAATACACAACATATTTGCAAATAAGAGCTTTTA
1 GTTGCAGATTAATACACTACCAGATGGTTGTGAATACACAACATATTCGCAAATAAGAACTGCCA
* *
31515721 GATATTGGATGGATGAACCAACGAT
66 GAAAGTGGATGGATGAACCAACGAT
* * * * *
31515746 GTTGCAGGTTAATACACTGCTAGATGGTTGTGAGTACACAACATATTCGCAGATAAGAACTGCCA
1 GTTGCAGATTAATACACTACCAGATGGTTGTGAATACACAACATATTCGCAAATAAGAACTGCCA
* *
31515811 -AAAGTGGGTGGATGAACC-AC-CT
66 GAAAGTGGATGGATGAACCAACGAT
* *
31515833 GTTTTCAGATTTATACACTACCAGATGGTTGTGAATACAC
1 G-TTGCAGATTAATACACTACCAGATGGTTGTGAATACAC
31515873 CATAGGGTTG
Statistics
Matches: 105, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
87 2 0.02
88 34 0.32
89 15 0.14
90 54 0.51
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (90 bp):
GTTGCAGATTAATACACTACCAGATGGTTGTGAATACACAACATATTCGCAAATAAGAACTGCCA
GAAAGTGGATGGATGAACCAACGAT
Found at i:31520006 original size:17 final size:18
Alignment explanation
Indices: 31519968--31520008 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
31519958 AAACATAATG
31519968 AAAATTTTGTATCGATAT
1 AAAATTTTGTATCGATAT
31519986 AAAATTTTGGTATC-A-AT
1 AAAATTTT-GTATCGATAT
31520003 AAAATT
1 AAAATT
31520009 CAATAGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 9 0.41
19 5 0.23
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (18 bp):
AAAATTTTGTATCGATAT
Found at i:31522310 original size:20 final size:20
Alignment explanation
Indices: 31522265--31522314 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
31522255 ATAAAATTTT
31522265 GGTATCGATAAAATTCAATA
1 GGTATCGATAAAATTCAATA
* *
31522285 GATATCGATAAAATTTTAA-A
1 GGTATCGATAAAA-TTCAATA
31522305 GGTATCGATA
1 GGTATCGATA
31522315 CTCAATGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (20 bp):
GGTATCGATAAAATTCAATA
Found at i:31522541 original size:20 final size:19
Alignment explanation
Indices: 31522500--31522541 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 19
31522490 GTCAAAATTA
31522500 TTCTAAGTGTTTAAAGCATT
1 TTCTAAGTGTTTAAAG-ATT
31522520 TTCTAAGCTGTTTGAAAG-TT
1 TTCTAAG-TGTTT-AAAGATT
31522540 TT
1 TT
31522542 GAAATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 11 0.55
21 5 0.25
22 4 0.20
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.48
Consensus pattern (19 bp):
TTCTAAGTGTTTAAAGATT
Found at i:31532900 original size:17 final size:17
Alignment explanation
Indices: 31532878--31532910 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31532868 TTCTACTACA
31532878 AAATATTTATTATTAAT
1 AAATATTTATTATTAAT
*
31532895 AAATATTTTTTATTAA
1 AAATATTTATTATTAA
31532911 AACATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATATTTATTATTAAT
Found at i:31532980 original size:16 final size:16
Alignment explanation
Indices: 31532949--31532985 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
31532939 ATTTGAAGAA
31532949 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
31532965 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
31532981 TATTA
1 TATTA
31532986 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:31532994 original size:18 final size:19
Alignment explanation
Indices: 31532971--31533006 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31532961 TTATTATTTT
*
31532971 TAAAATTTAT-TATTAAAA
1 TAAAATTGATATATTAAAA
31532989 TAAAATTGATATATTAAA
1 TAAAATTGATATATTAAA
31533007 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAATTGATATATTAAAA
Found at i:31533039 original size:31 final size:30
Alignment explanation
Indices: 31532970--31533046 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
31532960 ATTATTATTT
31532970 TTAAAATTTATTATTAAAATAAAATTGATA
1 TTAAAATTTATTATTAAAATAAAATTGATA
*
31533000 TATTAAA-TTATTTATTAAAATAATAAATT-ATA
1 T-TAAAATTTA-TTATTAAAAT-A-AAATTGATA
31533032 TTAAAATTTTATTAT
1 TTAAAA-TTTATTAT
31533047 ATGATTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
30 4 0.10
31 18 0.46
32 9 0.23
33 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
TTAAAATTTATTATTAAAATAAAATTGATA
Found at i:31537821 original size:34 final size:35
Alignment explanation
Indices: 31537777--31537843 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
31537767 CCAGTAAATA
*
31537777 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
31537811 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
31537844 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:31540155 original size:21 final size:22
Alignment explanation
Indices: 31540111--31540166 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
31540101 CTTGTTCAGT
31540111 TCATTTATGTTCATTCACAAGC
1 TCATTTATGTTCATTCACAAGC
* *
31540133 TCATTTATGTTCGTTTA-AAGC
1 TCATTTATGTTCATTCACAAGC
*
31540154 TCTTTTATTGTTC
1 TCATTTA-TGTTC
31540167 CATTAGTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.50
Consensus pattern (22 bp):
TCATTTATGTTCATTCACAAGC
Found at i:31540953 original size:13 final size:13
Alignment explanation
Indices: 31540935--31540963 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
31540925 TGAAAGGAAG
31540935 ACTACCTTAGTTA
1 ACTACCTTAGTTA
31540948 ACTACCTTAGTTA
1 ACTACCTTAGTTA
31540961 ACT
1 ACT
31540964 GGGCTGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (13 bp):
ACTACCTTAGTTA
Found at i:31544480 original size:40 final size:40
Alignment explanation
Indices: 31544357--31544497 Score: 144
Period size: 40 Copynumber: 3.6 Consensus size: 40
31544347 CGACTTTGAG
* *
31544357 TCGATGAGACACTAGGTGTCAAATTATTACTTCCAATATAT
1 TCGATGAGACACTGGGTGTCAAATTATTACTTCGAAT-TAT
* * * ** *
31544398 TCAATGAGGCATTGGGTGTC-AA-T-TTACTTCGGTTTAG
1 TCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTAT
*
31544435 CCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTAT
1 TCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTAT
* * *
31544475 TCGATGAGGCAGTGGGTGCCAAA
1 TCGATGAGACACTGGGTGTCAAA
31544498 CTGGTGTGTA
Statistics
Matches: 78, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 18 0.23
38 10 0.13
39 2 0.03
40 32 0.41
41 16 0.21
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTAT
Found at i:31546443 original size:9 final size:9
Alignment explanation
Indices: 31546426--31546851 Score: 173
Period size: 9 Copynumber: 49.2 Consensus size: 9
31546416 TAAGTATAAT
*
31546426 TAAGCTATG
1 TAAGTTATG
31546435 TAAGTTATG
1 TAAGTTATG
31546444 T-A-TTATG
1 TAAGTTATG
31546451 TAAGTTAT-
1 TAAGTTATG
*
31546459 TTA-TTATG
1 TAAGTTATG
* *
31546467 AAAATTATG
1 TAAGTTATG
*
31546476 TAAGTTGTG
1 TAAGTTATG
31546485 T-A-TTATG
1 TAAGTTATG
*
31546492 -AA--AAT-
1 TAAGTTATG
* *
31546497 TATGCTATG
1 TAAGTTATG
31546506 TAAGTTATG
1 TAAGTTATG
* *
31546515 TAAGTCATA
1 TAAGTTATG
31546524 TAAGTTATG
1 TAAGTTATG
31546533 T-A-TTATG
1 TAAGTTATG
31546540 TAAGTTATG
1 TAAGTTATG
31546549 TAAGTTAT-
1 TAAGTTATG
*
31546557 TTA-TTATG
1 TAAGTTATG
* * *
31546565 AAAATTAAG
1 TAAGTTATG
31546574 TAAGTTATG
1 TAAGTTATG
*
31546583 TAATTTATG
1 TAAGTTATG
*
31546592 -AA-TAAT-
1 TAAGTTATG
***
31546598 TAAAAAAATG
1 T-AAGTTATG
31546608 TAAGTTATG
1 TAAGTTATG
31546617 TAAG-T-TG
1 TAAGTTATG
31546624 TAAGTTATG
1 TAAGTTATG
31546633 TAAGTTATG
1 TAAGTTATG
*
31546642 TAATTTATG
1 TAAGTTATG
*
31546651 TATAATATTAATG
1 --TAA-GTT-ATG
31546664 TAAGTTATG
1 TAAGTTATG
*
31546673 TAATTTATG
1 TAAGTTATG
*
31546682 -AA-TAAT-
1 TAAGTTATG
***
31546688 TAAAAAAATG
1 T-AAGTTATG
31546698 TAAGTTATG
1 TAAGTTATG
31546707 TAAG-T-TG
1 TAAGTTATG
31546714 TAAGTTATG
1 TAAGTTATG
31546723 TAAGTTATG
1 TAAGTTATG
*
31546732 TATAATATTAATG
1 --TAA-GTT-ATG
31546745 TAAGTTATG
1 TAAGTTATG
*
31546754 TAATTTATG
1 TAAGTTATG
31546763 T-A--TAT-
1 TAAGTTATG
31546768 TAA-TTAAT-
1 TAAGTT-ATG
31546776 TAAGTTATG
1 TAAGTTATG
*
31546785 TAATTTATG
1 TAAGTTATG
*
31546794 TATAATATTAATG
1 --TAA-GTT-ATG
31546807 TAAGTTATG
1 TAAGTTATG
*
31546816 TATA-ATAT-
1 TA-AGTTATG
31546824 TAA-TTAAT-
1 TAAGTT-ATG
31546832 TAAGTTATG
1 TAAGTTATG
*
31546841 TAATTTATG
1 TAAGTTATG
31546850 TA
1 TA
31546852 TAATATTAAT
Statistics
Matches: 323, Mismatches: 48, Indels: 92
0.70 0.10 0.20
Matches are distributed among these distances:
5 1 0.00
6 7 0.02
7 46 0.14
8 42 0.13
9 185 0.57
10 9 0.03
11 18 0.06
12 6 0.02
13 9 0.03
ACGTcount: A:0.39, C:0.01, G:0.15, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:31546452 original size:16 final size:16
Alignment explanation
Indices: 31546431--31546550 Score: 96
Period size: 16 Copynumber: 7.9 Consensus size: 16
31546421 ATAATTAAGC
31546431 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
31546447 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
31546463 TATG-AA---A---AT
1 TATGTAAGTTATGTAT
*
31546472 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * *
31546488 TATGAAAATTATG--C
1 TATGTAAGTTATGTAT
31546502 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
31546520 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
31546536 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
31546551 AGTTATTTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
12 1 0.01
14 11 0.14
15 2 0.03
16 45 0.56
17 1 0.01
18 12 0.15
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:31546473 original size:25 final size:25
Alignment explanation
Indices: 31546445--31546599 Score: 129
Period size: 25 Copynumber: 6.2 Consensus size: 25
31546435 TAAGTTATGT
31546445 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
31546470 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
31546495 ATTATGCTATG-TA---AGTTATGTAA
1 ATTATG-TAAGTTATTTA-TTATGAAA
* * * * *
31546518 GTCATATAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATTTATTATGAAA
*
31546543 GTTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
31546568 ATTAAGTAAGTTATGTAATTTATGAATA
1 ATTATGTAAGTTAT-TTA-TTATGAA-A
31546596 ATTA
1 ATTA
31546600 AAAAAATGTA
Statistics
Matches: 105, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
22 4 0.04
23 12 0.11
25 71 0.68
26 6 0.06
27 7 0.07
28 5 0.05
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATTTATTATGAAA
Found at i:31546577 original size:34 final size:35
Alignment explanation
Indices: 31546471--31546652 Score: 119
Period size: 34 Copynumber: 5.2 Consensus size: 35
31546461 ATTATGAAAA
* *
31546471 TTATGTAAGTTGTGTATTATGAAAATTATGCTATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTA----ATGTAAG
*
31546510 TTATGTAAGTCATAT-AAGTTATG--TATT-ATGTAAG
1 TTATGTAAGT--TATGAA-TTATGAAAATTAATGTAAG
**
31546544 TTATGTAAGTTATTTATTATGAAAATTAA-GTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * *
31546578 TTATGTAATTTATGAATAATTAAAA-AAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * *
31546612 TTATGTAAGTTGT-AAGTTATGTAAGTT-ATGTAAT
1 TTATGTAAGTTATGAA-TTATGAAAATTAATGTAAG
31546646 TTATGTA
1 TTATGTA
31546653 TAATATTAAT
Statistics
Matches: 114, Mismatches: 19, Indels: 25
0.72 0.12 0.16
Matches are distributed among these distances:
32 8 0.07
33 5 0.04
34 79 0.69
35 1 0.01
39 13 0.11
40 1 0.01
41 7 0.06
ACGTcount: A:0.38, C:0.01, G:0.17, T:0.44
Consensus pattern (35 bp):
TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
Found at i:31546627 original size:16 final size:18
Alignment explanation
Indices: 31546605--31546851 Score: 114
Period size: 16 Copynumber: 13.8 Consensus size: 18
31546595 AATTAAAAAA
31546605 ATGTAAGTTATGTAAG-T
1 ATGTAAGTTATGTAAGTT
31546622 -TGTAAGTTATGTAAGTT
1 ATGTAAGTTATGTAAGTT
* *
31546639 ATGTAATTTATGTATAATATT
1 ATGTAAGTTATG--TAA-GTT
*
31546660 AATGTAAGTTATGTAATTT
1 -ATGTAAGTTATGTAAGTT
* ***
31546679 ATG-AA-TAAT-TAAAAAA
1 ATGTAAGTTATGT-AAGTT
31546695 ATGTAAGTTATGTAAG-T
1 ATGTAAGTTATGTAAGTT
31546712 -TGTAAGTTATGTAAGTT
1 ATGTAAGTTATGTAAGTT
*
31546729 ATGTATAATATTAATGTAAGTT
1 ATG--TAA-GTT-ATGTAAGTT
*
31546751 ATGTAATTTATGT-A--T
1 ATGTAAGTTATGTAAGTT
31546766 AT-TAA-TTAAT-TAAGTT
1 ATGTAAGTT-ATGTAAGTT
* *
31546782 ATGTAATTTATGTATAATATT
1 ATGTAAGTTATG--TAA-GTT
*
31546803 AATGTAAGTTATGTATA-AT
1 -ATGTAAGTTATGTA-AGTT
31546822 AT-TAA-TTAAT-TAAGTT
1 ATGTAAGTT-ATGTAAGTT
*
31546838 ATGTAATTTATGTA
1 ATGTAAGTTATGTA
31546852 TAATATTAAT
Statistics
Matches: 180, Mismatches: 17, Indels: 65
0.69 0.06 0.25
Matches are distributed among these distances:
13 3 0.02
14 6 0.03
15 5 0.03
16 48 0.27
17 22 0.12
18 32 0.18
19 6 0.03
20 17 0.09
21 7 0.04
22 34 0.19
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (18 bp):
ATGTAAGTTATGTAAGTT
Found at i:31546633 original size:25 final size:25
Alignment explanation
Indices: 31546502--31546644 Score: 91
Period size: 25 Copynumber: 5.6 Consensus size: 25
31546492 AAAATTATGC
*
31546502 TATGTAAGTTATGTAAGTCATATAAGT
1 TATGTAAGTTATGTAAGT--TGTAAGT
31546529 TATGT-A-TTATGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAG-T-TGTAAGT
* * *
31546554 TAT-TTA-TTATGAAAATTAAGTAAGT
1 TATGTAAGTTATGTAAGTT--GTAAGT
* * **
31546579 TATGTAATTTATGAATAA-TT-AAAAA
1 TATGTAAGTTATG--TAAGTTGTAAGT
*
31546604 AATGTAAGTTATGTAAGTTGTAAGT
1 TATGTAAGTTATGTAAGTTGTAAGT
31546629 TATGTAAGTTATGTAA
1 TATGTAAGTTATGTAA
31546645 TTTATGTATA
Statistics
Matches: 92, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
23 4 0.04
24 4 0.04
25 66 0.72
26 4 0.04
27 10 0.11
28 2 0.02
29 2 0.02
ACGTcount: A:0.40, C:0.01, G:0.17, T:0.43
Consensus pattern (25 bp):
TATGTAAGTTATGTAAGTTGTAAGT
Found at i:31546693 original size:90 final size:85
Alignment explanation
Indices: 31546524--31546855 Score: 346
Period size: 90 Copynumber: 3.9 Consensus size: 85
31546514 GTAAGTCATA
* *
31546524 TAAGTTATGT-ATTATGTAAGTTATGTAAGTTAT-TTATTATGAAAATTAAGTAAGTTATGTAAT
1 TAAGTTATGTAAGT-TGTAAGTTATGTAAGTTATGTAATTATGAAAATTAAGTAAGTTATGTAAT
31546587 TTATGAATAATTAAAAAAATG
65 TTATGAATAATTAAAAAAATG
31546608 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATG
1 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTAA-TTATG-A-AA-ATTAA-GTAAGTTATG
31546673 TAATTTATGAATAATTAAAAAAATG
61 TAATTTATGAATAATTAAAAAAATG
*
31546698 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATG----TAT-AATATTAATGTAAGTTATGTAAT
1 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTAATTATGAAAATTAA-GTAAGTTATGTAAT
* **
31546758 TTATGTAT-ATT-AATTAAT-
65 TTATGAATAATTAAAAAAATG
* * * * *
31546776 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGT-ATAAT-ATTAATTAATTAAGTTA
1 TAAGTTATGTAA-GT-TG--TAA-GTT-ATGTAAGTTATGTAATTATGA-AAATTAAGTAAGTTA
*
31546839 TGTAATTTATGTATAAT
59 TGTAATTTATGAATAAT
31546856 ATTAATGTAA
Statistics
Matches: 218, Mismatches: 12, Indels: 32
0.83 0.05 0.12
Matches are distributed among these distances:
78 12 0.06
79 6 0.03
80 5 0.02
81 27 0.12
82 4 0.02
83 3 0.01
84 41 0.19
85 7 0.03
86 5 0.02
87 25 0.11
88 9 0.04
89 5 0.02
90 69 0.32
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (85 bp):
TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTAATTATGAAAATTAAGTAAGTTATGTAATT
TATGAATAATTAAAAAAATG
Found at i:31546699 original size:56 final size:54
Alignment explanation
Indices: 31546604--31546911 Score: 229
Period size: 56 Copynumber: 5.5 Consensus size: 54
31546594 TAATTAAAAA
* * *
31546604 AATGTAAGTTATGTAAGTTGTAAGT-T-ATGTAAGTTATGTAATTTATGTATAATATT
1 AATGTAAGTTATGTAA-TT-TATGTATAAT-TAA-TAATGTAAGTTATGTATAATATT
* * **
31546660 AATGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTT
1 AATGTAAGTTATGTAATTTATGTATAATT--AATAATGTAAGTTATGT-A-TAAT-A-TT
* * * * *
31546720 -ATGTAAGTTATGT-A-TAATAT-TAATGTAAGTTATGTAATTTATGTATATTAATT
1 AATGTAAGTTATGTAATTTATGTATAAT-TAA-TAATGTAAGTTATGTATAAT-ATT
*
31546773 AAT-TAAGTTATGTAATTTATGTATAA-TATTAATGTAAGTTATGTATAATATT
1 AATGTAAGTTATGTAATTTATGTATAATTAATAATGTAAGTTATGTATAATATT
* *
31546825 AATTAATTAAGTTATGTAATTTATGTATAA-TATTAATGTAAGTTATGTATAATATT
1 AA-T--GTAAGTTATGTAATTTATGTATAATTAATAATGTAAGTTATGTATAATATT
* *
31546881 AATTAATTAAGTGATGTAATTTATGTATAAT
1 AA-T--GTAAGTTATGTAATTTATGTATAAT
31546912 ATTAATTAAT
Statistics
Matches: 211, Mismatches: 22, Indels: 37
0.78 0.08 0.14
Matches are distributed among these distances:
52 5 0.02
53 30 0.14
54 12 0.06
55 11 0.05
56 127 0.60
57 7 0.03
58 3 0.01
59 14 0.07
60 2 0.01
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (54 bp):
AATGTAAGTTATGTAATTTATGTATAATTAATAATGTAAGTTATGTATAATATT
Found at i:31546733 original size:34 final size:32
Alignment explanation
Indices: 31546446--31546873 Score: 118
Period size: 34 Copynumber: 13.2 Consensus size: 32
31546436 AAGTTATGTA
* *
31546446 TTATGTAAGTTAT-TTATTATGAAAATTATGTAAG
1 TTATGTAAGTTATGTAATTATG-TAA-T-TGTAAG
* *
31546480 TTGTGT-A-TTATGAAAATTATGCT-A-TGTAAG
1 TTATGTAAGTTATG-TAATTATG-TAATTGTAAG
* * *
31546510 TTATGTAAGTCATATAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTAA-TTATGTAAT-TGTAAG
* *
31546544 TTATGTAAGTTAT-TTATTATGAAAATTAAGTAAG
1 TTATGTAAGTTATGTAATTATG-TAATT--GTAAG
* *** *
31546578 TTATGTAATTTATGAATAATTAAAAAAATGTAAG
1 TTATGTAAGTTATG--TAATTATGTAATTGTAAG
*
31546612 TTATGTAAG-T-TGT-A--A-GTTA-TGTAAG
1 TTATGTAAGTTATGTAATTATGTAATTGTAAG
* *
31546637 TTATGTAATTTATGTATAATAT-TAA-TGTAAG
1 TTATGTAAGTTATGTA-ATTATGTAATTGTAAG
* *** *
31546668 TTATGTAATTTATGAATAATTAAAAAAATGTAAG
1 TTATGTAAGTTATG--TAATTATGTAATTGTAAG
*
31546702 TTATGTAAG-T-TGTAAGTTATGTAAGTTATGTATAATA
1 TTATGTAAGTTATGTAA-TTATGTAA--T-TG--TAA-G
31546739 TTAATGTAAGTTATGTAATTTATGT-ATAT-TAA-
1 TT-ATGTAAGTTATGTAA-TTATGTAAT-TGTAAG
**
31546771 TTAAT-TAAGTTATGTAATTTATGT-ATAAT-A-
1 TT-ATGTAAGTTATGTAA-TTATGTAATTGTAAG
* *
31546801 TTAATGTAAGTTATGTATAATAT-TAATTAATTAAG
1 TT-ATGTAAGTTATGTA-ATTATGTAATT--GTAAG
* *
31546836 TTATGTAATTTATGTATAATAT-TAA-TGTAAG
1 TTATGTAAGTTATGTA-ATTATGTAATTGTAAG
31546867 TTATGTA
1 TTATGTA
31546874 TAATATTAAT
Statistics
Matches: 310, Mismatches: 41, Indels: 89
0.70 0.09 0.20
Matches are distributed among these distances:
25 14 0.05
26 2 0.01
27 4 0.01
29 2 0.01
30 22 0.07
31 81 0.26
32 31 0.10
33 14 0.05
34 101 0.33
35 2 0.01
36 7 0.02
37 10 0.03
38 7 0.02
39 2 0.01
40 11 0.04
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (32 bp):
TTATGTAAGTTATGTAATTATGTAATTGTAAG
Found at i:31546748 original size:22 final size:22
Alignment explanation
Indices: 31546720--31546827 Score: 106
Period size: 22 Copynumber: 5.1 Consensus size: 22
31546710 GTTGTAAGTT
31546720 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
31546742 ATGTAAGTTATG--TAAT-TT-
1 ATGTAAGTTATGTATAATATTA
*
31546760 ATGTATA-TTAAT-TAATTAA-GTT-
1 ATGTA-AGTT-ATGT-A-TAATATTA
*
31546782 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
31546804 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
31546826 AT
1 AT
31546828 TAATTAAGTT
Statistics
Matches: 73, Mismatches: 2, Indels: 22
0.75 0.02 0.23
Matches are distributed among these distances:
18 7 0.10
19 5 0.07
20 7 0.10
21 6 0.08
22 48 0.66
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:31546870 original size:22 final size:22
Alignment explanation
Indices: 31546838--31546883 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
31546828 TAATTAAGTT
*
31546838 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
31546860 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
31546882 AT
1 AT
31546884 TAATTAAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:31546905 original size:34 final size:34
Alignment explanation
Indices: 31546860--31546924 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
31546850 TATAATATTA
31546860 ATGTAAGTTATGTATAATATTAATTAATTAAGTG
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTG
*
31546894 ATGTAATTTATGTATAATATTAATTAATTAA
1 ATGTAAGTTATGTATAATATTAATTAATTAA
31546925 TTAAGTTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (34 bp):
ATGTAAGTTATGTATAATATTAATTAATTAAGTG
Found at i:31546912 original size:56 final size:56
Alignment explanation
Indices: 31546764--31546917 Score: 299
Period size: 56 Copynumber: 2.8 Consensus size: 56
31546754 TAATTTATGT
31546764 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATA
1 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATA
31546820 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATA
1 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATA
*
31546876 ATATTAATTAATTAAGTGATGTAATTTATGTATAATATTAAT
1 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT
31546918 TAATTAATTA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 97 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (56 bp):
ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATA
Found at i:31546924 original size:90 final size:87
Alignment explanation
Indices: 31546534--31546920 Score: 342
Period size: 90 Copynumber: 4.4 Consensus size: 87
31546524 TAAGTTATGT
* * *
31546534 ATTATGTAAGTTATGTAAGTTATTTATTATGA-AAATTAAGTAAGTTATGTAATTTATGAATAAT
1 ATTAT-TAAGTTATGTAAGTTATGTATAAT-ATTAATTAAGTAAGTTATGTAATTTATGAATAAT
31546598 TAAAAAAATGTAAGTTATGTAAGTTGTA
64 T-AAAAAATGTAAGTTATG-AA-TT-TA
*
31546626 AGTTATGTAAGTTATGTAATTTATGTATAATATTAA-T--GTAAGTTATGTAATTTATGAATAAT
1 A-TTAT-TAAGTTATGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTATGAATAAT
31546688 TAAAAAAATGTAAGTTATG----TA
64 T-AAAAAATGTAAGTTATGAATTTA
* *
31546709 AGTT-GTAAGTTATGTAAGTTATGTATAATATTAA-T--GTAAGTTATGTAATTTATGTAT-ATT
1 A-TTATTAAGTTATGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTATGAATAATT
**
31546769 AATTAAT-TAAGTTATGTAATTT-
65 AAAAAATGTAAGTTATG-AATTTA
* * *
31546791 ATGTA-TAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAA
1 AT-TATTAA-GTT-ATGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTATGAATAA
**
31546855 -T-ATTAATGTAAGTTATGTATAATATTA
63 TTAAAAAATGTAAGTTATG---AAT-TTA
* *
31546882 ATTAATTAAGTGATGTAATTTATGTATAATATTAATTAA
1 ATT-ATTAAGTTATGTAAGTTATGTATAATATTAATTAA
31546921 TTAATTAAGT
Statistics
Matches: 259, Mismatches: 14, Indels: 46
0.81 0.04 0.14
Matches are distributed among these distances:
78 9 0.03
79 5 0.02
80 3 0.01
81 51 0.20
82 5 0.02
83 9 0.03
84 23 0.09
85 1 0.00
86 6 0.02
87 31 0.12
88 1 0.00
89 4 0.02
90 73 0.28
91 4 0.02
92 6 0.02
93 28 0.11
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.45
Consensus pattern (87 bp):
ATTATTAAGTTATGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTATGAATAATTA
AAAAATGTAAGTTATGAATTTA
Found at i:31547512 original size:45 final size:39
Alignment explanation
Indices: 31547461--31547556 Score: 129
Period size: 39 Copynumber: 2.3 Consensus size: 39
31547451 AGCTAATTTT
31547461 TATTTAAGTAATGTAATATATATATAAATTTTAAGTAATGTAATA
1 TATTTAAGTAATGT-A-A-AT-TATAAATTTT-AGTAA-GTAATA
*
31547506 TATTTAAGTAATGTAAGTTATAAATTTTAGTAAGTAATA
1 TATTTAAGTAATGTAAATTATAAATTTTAGTAAGTAATA
31547545 TATTTAAGTAAT
1 TATTTAAGTAAT
31547557 TATGTAATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
39 18 0.36
40 5 0.10
41 10 0.20
42 1 0.02
43 1 0.02
44 1 0.02
45 14 0.28
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (39 bp):
TATTTAAGTAATGTAAATTATAAATTTTAGTAAGTAATA
Found at i:31547540 original size:17 final size:17
Alignment explanation
Indices: 31547518--31547559 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
31547508 TTTAAGTAAT
*
31547518 GTAAGTTATAAATTTTA
1 GTAAGTTATAAATTTAA
* *
31547535 GTAAGTAATATATTTAA
1 GTAAGTTATAAATTTAA
31547552 GTAA-TTAT
1 GTAAGTTAT
31547560 GTAATATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (17 bp):
GTAAGTTATAAATTTAA
Found at i:31547576 original size:21 final size:22
Alignment explanation
Indices: 31547465--31547585 Score: 85
Period size: 22 Copynumber: 5.5 Consensus size: 22
31547455 AATTTTTATT
*
31547465 TAAGTAATGTAATATATATATAAATTT
1 TAAGTAATGTAATATAT-T-T-AA--G
31547492 TAAGTAATGTAATATATTTAAG
1 TAAGTAATGTAATATATTTAAG
* *
31547514 TAATGTAA-GTTATAAATTT---
1 TAA-GTAATGTAATATATTTAAG
31547533 T-AGTAA-GTAATATATTTAAG
1 TAAGTAATGTAATATATTTAAG
* **
31547553 TAA-TTATGTAATATATTTTCG
1 TAAGTAATGTAATATATTTAAG
31547574 TAAGTAATGTAA
1 TAAGTAATGTAA
31547586 GTAACGTAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
17 13 0.17
18 1 0.01
19 1 0.01
20 3 0.04
21 16 0.21
22 19 0.24
23 4 0.05
24 2 0.03
25 1 0.01
26 1 0.01
27 17 0.22
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.44
Consensus pattern (22 bp):
TAAGTAATGTAATATATTTAAG
Found at i:31550298 original size:7 final size:7
Alignment explanation
Indices: 31550227--31550301 Score: 51
Period size: 7 Copynumber: 10.0 Consensus size: 7
31550217 AATCCATAAC
31550227 CCCCTAA
1 CCCCTAA
*
31550234 CCCCTTA
1 CCCCTAA
31550241 CCCCTAAA
1 CCCCT-AA
*
31550249 TTCCCTAA
1 -CCCCTAA
31550257 CCCCTAA
1 CCCCTAA
** *
31550264 AGCATAA
1 CCCCTAA
*
31550271 CCCTTAA
1 CCCCTAA
31550278 CCCCTACA
1 CCCCTA-A
31550286 TCCCCCTAA
1 --CCCCTAA
31550295 CCCCTAA
1 CCCCTAA
31550302 ACATTAAATT
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
7 37 0.71
8 4 0.08
9 5 0.10
10 6 0.12
ACGTcount: A:0.29, C:0.49, G:0.01, T:0.20
Consensus pattern (7 bp):
CCCCTAA
Found at i:31551558 original size:14 final size:14
Alignment explanation
Indices: 31551539--31551606 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
31551529 ATGACCGTTG
31551539 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
31551553 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
31551568 TAACCCTTAAAT-T-
1 AAACCC-TAAATCTC
* *
31551581 -AACCTTAAATCCC
1 AAACCCTAAATCTC
*
31551594 AAACCTTAAATCT
1 AAACCCTAAATCT
31551607 ATACCCCGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
11 5 0.12
12 4 0.09
14 18 0.42
15 16 0.37
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:31553448 original size:22 final size:22
Alignment explanation
Indices: 31553271--31553561 Score: 159
Period size: 23 Copynumber: 12.4 Consensus size: 22
31553261 ACACCAAAAT
* *
31553271 TTGGACAGCATATATACAACAAT
1 TTGG-CAGCAAATATACAACAAA
* *
31553294 TTAGGCAGCATATATACAACATA
1 TT-GGCAGCAAATATACAACAAA
** * * *
31553317 TTGAGCAGCATTTTTGCACCAAAA
1 TTG-GCAGCAAATATACAAC-AAA
** *
31553341 TTGGACAGCTTATACACAACAAA
1 TTGG-CAGCAAATATACAACAAA
* *
31553364 TTGGACAGCAATTACACAACAAA
1 TTGG-CAGCAAATATACAACAAA
** * *
31553387 TTGAGCAGCATTTTTACACCAAAAA
1 TTG-GCAGCAAATATACA--ACAAA
** *
31553412 TTGGACAGCTTATATAAAACAAA
1 TTGG-CAGCAAATATACAACAAA
31553435 TTGGCAGCAAATATACAACAAA
1 TTGGCAGCAAATATACAACAAA
** * *
31553457 TTGAGCAGCATTTTTACACCAAAAA
1 TTG-GCAGCAAATATACA--ACAAA
**
31553482 TTGGACAGCTTATATACAACAAA
1 TTGG-CAGCAAATATACAACAAA
*
31553505 TTGGCAACAAATATACAACAAA
1 TTGGCAGCAAATATACAACAAA
*
31553527 TTGAGCAGCATATATATACAAGAAA
1 TTG-GCAGCA-A-ATATACAACAAA
31553552 TTGTGCAGCA
1 TTG-GCAGCA
31553562 TTTAAGCATA
Statistics
Matches: 211, Mismatches: 42, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
22 37 0.18
23 101 0.48
24 20 0.09
25 53 0.25
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (22 bp):
TTGGCAGCAAATATACAACAAA
Found at i:31553499 original size:48 final size:48
Alignment explanation
Indices: 31553286--31553508 Score: 166
Period size: 48 Copynumber: 4.7 Consensus size: 48
31553276 CAGCATATAT
* * * *
31553286 ACAACAATTTAGG-CAGCATATATACAACATATT-GAGCAGCATTTTTGC
1 ACAACAAATT-GGACAGCTTATATACAACAAATTGGA-CAGCATTTTTAC
* * *
31553334 ACCA-AAATTGGACAGCTTATACACAACAAATTGGACAGCA--ATTAC
1 ACAACAAATTGGACAGCTTATATACAACAAATTGGACAGCATTTTTAC
* * *
31553379 ACAACAAATT-GAGCAGCATT-TTTACACCAAAAATTGGACAGC-TTATATA-
1 ACAACAAATTGGA-CAGC-TTATATACA--ACAAATTGGACAGCATT-TTTAC
**
31553428 A-AACAAATTGG-CAGCAAATATACAACAAATT-GAGCAGCATTTTTAC
1 ACAACAAATTGGACAGCTTATATACAACAAATTGGA-CAGCATTTTTAC
31553474 ACCAA-AAATTGGACAGCTTATATACAACAAATTGG
1 A-CAACAAATTGGACAGCTTATATACAACAAATTGG
31553509 CAACAAATAT
Statistics
Matches: 136, Mismatches: 20, Indels: 37
0.70 0.10 0.19
Matches are distributed among these distances:
44 2 0.01
45 21 0.15
46 18 0.13
47 44 0.32
48 46 0.34
49 3 0.02
50 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (48 bp):
ACAACAAATTGGACAGCTTATATACAACAAATTGGACAGCATTTTTAC
Found at i:31553554 original size:70 final size:70
Alignment explanation
Indices: 31553251--31553537 Score: 432
Period size: 70 Copynumber: 4.1 Consensus size: 70
31553241 CCAAACTAAA
* * * * * * *
31553251 CAGCAATTTCACACCAAAATTTGGACAGCATATATACAACAATTTAGGCAGCATATATACAACAT
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATT-GGCAGCAAATATACAACAA
31553316 ATTGAG
65 ATTGAG
* * * *
31553322 CAGCATTTTTGCACC-AAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACACAACAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGG-CAGCAAATATACAACAA
31553386 ATTGAG
65 ATTGAG
*
31553392 CAGCATTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAATATACAACAAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
31553457 TTGAG
66 TTGAG
*
31553462 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAACAAATATACAACAAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
31553527 TTGAG
66 TTGAG
31553532 CAGCAT
1 CAGCAT
31553538 ATATATACAA
Statistics
Matches: 196, Mismatches: 18, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
69 2 0.01
70 153 0.78
71 41 0.21
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.24
Consensus pattern (70 bp):
CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
TTGAG
Found at i:31554117 original size:2 final size:2
Alignment explanation
Indices: 31554110--31554140 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31554100 AGAATCATCT
31554110 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31554141 GATTCCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31554343 original size:28 final size:27
Alignment explanation
Indices: 31554311--31554408 Score: 106
Period size: 28 Copynumber: 3.5 Consensus size: 27
31554301 TTTAATAAGT
* *
31554311 TCGCACACTTAGTGCTCAATAATCAAAC
1 TCGCACACTTAGTGCT-TATAATTAAAC
* * * *
31554339 TCGCACACTTAGAGGTTTTCCATTAAAC
1 TCGCACACTTAGTGCTTAT-AATTAAAC
*
31554367 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGC-TTATAATTAAAC
31554395 TCGCACACTTAGTG
1 TCGCACACTTAGTG
31554409 TCGAAAGTCA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 1 0.02
28 54 0.95
29 2 0.04
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.30
Consensus pattern (27 bp):
TCGCACACTTAGTGCTTATAATTAAAC
Found at i:31554533 original size:2 final size:2
Alignment explanation
Indices: 31554526--31554553 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31554516 AACGATACGA
31554526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31554554 GCTTAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31561697 original size:27 final size:28
Alignment explanation
Indices: 31561637--31561698 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
31561627 CACAAAAAAG
*
31561637 TTCCTTTCATAATTCGCCACAAAGGACT
1 TTCCTTTCATAATTCACCACAAAGGACT
* *
31561665 TT-CTTTCATATTTCACCACAAAGG-GT
1 TTCCTTTCATAATTCACCACAAAGGACT
31561691 TTCCTTTC
1 TTCCTTTC
31561699 CTTATGTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 3 0.10
27 25 0.83
28 2 0.07
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (28 bp):
TTCCTTTCATAATTCACCACAAAGGACT
Found at i:31578827 original size:3 final size:3
Alignment explanation
Indices: 31578821--31578846 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31578811 GTTATTTATT
31578821 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
31578847 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:31578854 original size:6 final size:6
Alignment explanation
Indices: 31578845--31578955 Score: 143
Period size: 6 Copynumber: 18.5 Consensus size: 6
31578835 CATCATCATC
31578845 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
* * * * *
31578893 ATTATT ATTATCT -TTATT TTTATT TTTATT TTTATT TTTATT TTTATT
1 ATTATT ATTAT-T ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
* *
31578941 TTTATT TTTATT ATT
1 ATTATT ATTATT ATT
31578956 CATGCGCATG
Statistics
Matches: 102, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
5 1 0.01
6 100 0.98
7 1 0.01
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (6 bp):
ATTATT
Found at i:31579442 original size:19 final size:20
Alignment explanation
Indices: 31579401--31579442 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
31579391 ATTTCTATGC
* *
31579401 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
31579421 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
31579440 CAT
1 CAT
31579443 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:31579819 original size:23 final size:23
Alignment explanation
Indices: 31579776--31579822 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
31579766 TTTAGTAATA
*
31579776 AATATTTTATAGAATAAAATATG
1 AATATTTTATAAAATAAAATATG
*
31579799 AATATTTTATTAAAAT-GAATATG
1 AATATTTTA-TAAAATAAAATATG
31579822 A
1 A
31579823 GTTTTTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (23 bp):
AATATTTTATAAAATAAAATATG
Found at i:31580164 original size:7 final size:7
Alignment explanation
Indices: 31580152--31580178 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
31580142 AATTCTAAAA
31580152 TTAATAT
1 TTAATAT
31580159 TTAATAT
1 TTAATAT
31580166 TTAATAT
1 TTAATAT
31580173 TTAATA
1 TTAATA
31580179 CTTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAATAT
Found at i:31583348 original size:2 final size:2
Alignment explanation
Indices: 31583331--31583364 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
31583321 GAAAACTAGG
* *
31583331 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31583365 GTATTATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:31586808 original size:3 final size:3
Alignment explanation
Indices: 31586800--31586831 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
31586790 CTGTTGAACT
31586800 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31586832 GGTGTTTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:31587042 original size:44 final size:43
Alignment explanation
Indices: 31586975--31587472 Score: 233
Period size: 44 Copynumber: 11.5 Consensus size: 43
31586965 CAAGTAGCCT
*
31586975 CACTGCAACTTCAAGAGG-G-TAAGACTTGTTTACTTAGTCTGCTC
1 CACTGCAACTTC-AG-GGAGATAAGACTTG-TTACTTAATCTGCTC
* * * *
31587019 CACTGCAACTTCAGGGAGATAAGACTAGATGC--GATCTGCT-
1 CACTGCAACTTCAGGGAGATAAGACTTGTTACTTAATCTGCTC
* * * * ** *
31587059 CTCTACAACTTCAGAGAGATAAAATCCAAGATT--TTAATCCGCTC
1 CACTGCAACTTCAGGGAGATAAGA--CTTG-TTACTTAATCTGCTC
* * * * * *
31587103 CATTGCAACTTCAGGGAAAT-AGAATTATTGGCTTTAACCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTTGTT-AC-TTAATCTGCTC
** * *
31587147 CACTGCAACTTCAGGGAGATAAGGTTTGTCATCTTCAGTCTGC-C
1 CACTGCAACTTCAGGGAGATAAGACTTGTTA-CTT-AATCTGCTC
* *
31587191 TCACTGCAACTTCA-GGAGGATAAGACCTGCTTACTTAGTCTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGACTTG-TTACTTAATCTGCTC
* * **
31587236 TACTGCAACTTCAGGGAGATAAGACTAG--A-TGGGATCTGC-C
1 CACTGCAACTTCAGGGAGATAAGACTTGTTACT-TAATCTGCTC
* * ** **
31587276 CTCTGCAACTTCAGAGAGATAAGATCCAAGATT--TTAATCCACTC
1 CACTGCAACTTCAGGGAGATAAGA--CTTG-TTACTTAATCTGCTC
* * * * * *
31587320 CACTTCAACTTCAGGGAAATAGGA-TTATTGGCTTTAACCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTTGTT-AC-TTAATCTGCTC
* * * *
31587364 CACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCTAC-C
1 CACTGCAACTTCAGGGAGATAAGACTTGTTA-CTT-AATCTGCTC
* *
31587408 TCGCTGTAACTTCA-GGAGGATAAGACTTGCTTACTTAATCTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGACTTG-TTACTTAATCTGCTC
31587453 CACTGCAACTTCAGGGAGAT
1 CACTGCAACTTCAGGGAGAT
31587473 GGGATTATTG
Statistics
Matches: 335, Mismatches: 80, Indels: 78
0.68 0.16 0.16
Matches are distributed among these distances:
40 47 0.14
41 12 0.04
42 8 0.02
43 18 0.05
44 171 0.51
45 75 0.22
46 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
CACTGCAACTTCAGGGAGATAAGACTTGTTACTTAATCTGCTC
Found at i:31587349 original size:217 final size:217
Alignment explanation
Indices: 31586971--31587472 Score: 844
Period size: 217 Copynumber: 2.3 Consensus size: 217
31586961 TCTTCAAGTA
* * *
31586971 GCCTCACTGCAACTTCAAGAGGGTAAGACTTGTTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
1 GCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
* *
31587036 GATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGAGATAAAATCCAAGATTTTAATCCGC
66 GATAAGACTAGATGCGATCTGCCCTCTACAACTTCAGAGAGATAAAATCCAAGATTTTAATCCAC
31587101 TCCATTGCAACTTCAGGGAAATAGAATTATTGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGA
131 TCCATTGCAACTTCAGGGAAATAGAATTATTGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGA
*
31587166 TAAGGTTTGTCATCTTCAGTCT
196 TAAGATTTGTCATCTTCAGTCT
* *
31587188 GCCTCACTGCAACTTCAGGAGGATAAGACCTGCTTACTTAGTCTGCTCTACTGCAACTTCAGGGA
1 GCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
* * *
31587253 GATAAGACTAGATGGGATCTGCCCTCTGCAACTTCAGAGAGATAAGATCCAAGATTTTAATCCAC
66 GATAAGACTAGATGCGATCTGCCCTCTACAACTTCAGAGAGATAAAATCCAAGATTTTAATCCAC
*
31587318 TCCACTT-CAACTTCAGGGAAATAGGATTATTGGCTTTAACCTGCTCCACTGCAACTTCAGGGAG
131 TCCA-TTGCAACTTCAGGGAAATAGAATTATTGGCTTTAACCTGCTCCACTGCAACTTCAGGGAG
31587382 ATAAGATTTGTCATCTTCAGTCT
195 ATAAGATTTGTCATCTTCAGTCT
* * * *
31587405 ACCTCGCTGTAACTTCAGGAGGATAAGACTTGCTTACTTAATCTGCTCCACTGCAACTTCAGGGA
1 GCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
31587470 GAT
66 GAT
31587473 GGGATTATTG
Statistics
Matches: 266, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
217 264 0.99
218 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (217 bp):
GCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
GATAAGACTAGATGCGATCTGCCCTCTACAACTTCAGAGAGATAAAATCCAAGATTTTAATCCAC
TCCATTGCAACTTCAGGGAAATAGAATTATTGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGA
TAAGATTTGTCATCTTCAGTCT
Found at i:31599643 original size:18 final size:18
Alignment explanation
Indices: 31599603--31599644 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
31599593 AAAAAAAGGG
31599603 TATAAATACGTACATAATA
1 TATAAATAC-TACATAATA
31599622 -ATAAATA-TACATATATA
1 TATAAATACTACATA-ATA
31599639 TATAAA
1 TATAAA
31599645 ATAATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.29
17 3 0.14
18 12 0.57
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (18 bp):
TATAAATACTACATAATA
Found at i:31602416 original size:2 final size:2
Alignment explanation
Indices: 31602409--31602435 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31602399 AAAACAAGTT
31602409 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
31602436 TTAAGATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31609306 original size:2 final size:2
Alignment explanation
Indices: 31609295--31609341 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
31609285 TTGCGGCTTT
31609295 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31609336 TA TA TA
1 TA TA TA
31609342 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:31614771 original size:90 final size:93
Alignment explanation
Indices: 31614641--31614824 Score: 232
Period size: 90 Copynumber: 2.0 Consensus size: 93
31614631 TATTTTTAAG
* *
31614641 GCTCGTTGATTTACGATCACAGTCTAAGTTCATTGATTTACAATTATGAACAAGTTT-TCCTGAG
1 GCTCGGTGATTTACGAT-ACAGTCTAAGTTCATTGATTTACAATCATGAACAA-TTTCTCCTGAG
31614705 TTTGCTGACTTACAATCACAACTCCAAATA
64 TTTGCTGACTTACAATCACAACTCCAAATA
* * * *
31614735 GCTCGGTGATTTACGAT-C-G-CTAAGTTTATTGATTTACGATCATGAATAATTTCTCTTGAGTT
1 GCTCGGTGATTTACGATACAGTCTAAGTTCATTGATTTACAATCATGAACAATTTCTCCTGAGTT
* * **
31614797 TGTTGATTTATTATCACAACTCCAAATA
66 TGCTGACTTACAATCACAACTCCAAATA
31614825 ACTCACTAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
89 3 0.04
90 58 0.73
91 1 0.01
92 1 0.01
94 16 0.20
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (93 bp):
GCTCGGTGATTTACGATACAGTCTAAGTTCATTGATTTACAATCATGAACAATTTCTCCTGAGTT
TGCTGACTTACAATCACAACTCCAAATA
Found at i:31614936 original size:63 final size:63
Alignment explanation
Indices: 31614869--31615009 Score: 196
Period size: 63 Copynumber: 2.2 Consensus size: 63
31614859 AGGCCTTTTT
* * *
31614869 ATTTACGATCACAACCTAAGTTCATTAATTAACGATCATGAACAAT-TTCTCCTGAGTTCGCT-G
1 ATTTACGATCACAACCTAAATTCATTAATTAACGATCATGAACAATATT-TCCCGAGTTAG-TGG
* *
31614932 ATTTACGATCACAACCTAAATTCATTAATTTACGATCATGAATAATATTTCCCGAGTTAGTGG
1 ATTTACGATCACAACCTAAATTCATTAATTAACGATCATGAACAATATTTCCCGAGTTAGTGG
*
31614995 ATTCACGATCACAAC
1 ATTTACGATCACAAC
31615010 TTAGGTACGA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
62 1 0.01
63 67 0.96
64 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (63 bp):
ATTTACGATCACAACCTAAATTCATTAATTAACGATCATGAACAATATTTCCCGAGTTAGTGG
Found at i:31620888 original size:5 final size:6
Alignment explanation
Indices: 31620870--31620894 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31620860 AAACTTTCGC
31620870 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
31620895 CGTTTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:31622598 original size:16 final size:16
Alignment explanation
Indices: 31622573--31622606 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
31622563 TAATGAATAT
*
31622573 ATGTGTAAATATGATA
1 ATGTGCAAATATGATA
31622589 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
31622605 AT
1 AT
31622607 TAGATATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:31624436 original size:27 final size:27
Alignment explanation
Indices: 31624406--31624470 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
31624396 CGAGCTAGGT
* *
31624406 TTCGCCAGTCTATTTGGTGAACT-GGGG
1 TTCGCCAGTCTATTTGGCGAA-TAAGGG
* **
31624433 TTCGCTAGTCGGTTTGGCGAATAAGGG
1 TTCGCCAGTCTATTTGGCGAATAAGGG
31624460 TTCGCCAGTCT
1 TTCGCCAGTCT
31624471 TATTGTGGAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.15, C:0.20, G:0.32, T:0.32
Consensus pattern (27 bp):
TTCGCCAGTCTATTTGGCGAATAAGGG
Found at i:31635642 original size:22 final size:22
Alignment explanation
Indices: 31635578--31635644 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
31635568 CCTGGGAGGC
**
31635578 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGTT
31635600 TAACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGTT
*
31635622 TCACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGTT
31635644 T
1 T
31635645 GAACAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGTT
Found at i:31640318 original size:19 final size:21
Alignment explanation
Indices: 31640280--31640319 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
31640270 CTTGTTTTGA
*
31640280 TTAAATAAATTATTTAAAATT
1 TTAAATAAATTATATAAAATT
31640301 TTAAA-AAA-TATATAAAATT
1 TTAAATAAATTATATAAAATT
31640320 GATTAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAATAAATTATATAAAATT
Found at i:31646182 original size:25 final size:25
Alignment explanation
Indices: 31646149--31646216 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
31646139 CGGTAAACAA
* *
31646149 TAAGTTCTTCCGAGCTGAATAACGG
1 TAAGCTCTTCCAAGCTGAATAACGG
* *
31646174 TAAGCTCTTTCAAGCTGCATAACGG
1 TAAGCTCTTCCAAGCTGAATAACGG
* *
31646199 TAAGCTCATACAAGCTGA
1 TAAGCTCTTCCAAGCTGA
31646217 GTATCGATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (25 bp):
TAAGCTCTTCCAAGCTGAATAACGG
Found at i:31651489 original size:15 final size:15
Alignment explanation
Indices: 31651469--31651527 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 15
31651459 TTGACCGAAA
31651469 AATTATAATTACAAT
1 AATTATAATTACAAT
31651484 AATTATAATAATATCCATTAT
1 AATTATAAT--TA--CA--AT
31651505 AAATTATAATTACAAT
1 -AATTATAATTACAAT
31651521 AATTATA
1 AATTATA
31651528 GCAAGGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
15 16 0.43
16 2 0.05
17 2 0.05
18 2 0.05
19 2 0.05
20 2 0.05
21 2 0.05
22 9 0.24
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTATAATTACAAT
Found at i:31662443 original size:66 final size:66
Alignment explanation
Indices: 31662300--31662462 Score: 195
Period size: 66 Copynumber: 2.5 Consensus size: 66
31662290 AACAAATTAC
* * * *
31662300 ACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
31662365 T
66 T
* *
31662366 ACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAG
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAG
31662430 C-
65 CT
* * ** *
31662431 AGTAGCTTAAAGCAGATGTGGCAGCAAGAGAA
1 A-CAACTTAAAGCAGATGCAGCAGCGAGAGAA
31662463 TCAGAGGCGG
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 1 0.01
66 78 0.94
67 4 0.05
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.14
Consensus pattern (66 bp):
ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
T
Found at i:31662533 original size:21 final size:21
Alignment explanation
Indices: 31662451--31662573 Score: 111
Period size: 21 Copynumber: 5.9 Consensus size: 21
31662441 AGCAGATGTG
* * *
31662451 GCAGCAAGAGAATCAGAGGCG
1 GCAGCGAGAGAAGCAGAGGCT
* * *
31662472 GCAACGAGAGAAGTACAGGCT
1 GCAGCGAGAGAAGCAGAGGCT
* *
31662493 GCAGCGAGAGAAGTACAGGCT
1 GCAGCGAGAGAAGCAGAGGCT
* *
31662514 GCAGCAAGGGAAGCAGAGGCT
1 GCAGCGAGAGAAGCAGAGGCT
** *
31662535 AAAGCGAGGGAAGCAGAGGCT
1 GCAGCGAGAGAAGCAGAGGCT
* *
31662556 ACAGCGAGGGAAGCAGAG
1 GCAGCGAGAGAAGCAGAG
31662574 CAGCGTCAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 87 1.00
ACGTcount: A:0.37, C:0.18, G:0.40, T:0.06
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGCT
Found at i:31663023 original size:85 final size:83
Alignment explanation
Indices: 31662881--31663150 Score: 276
Period size: 86 Copynumber: 3.2 Consensus size: 83
31662871 ATCTGCCAAA
* * * **
31662881 TTTAGTGGCGTTTTTTAAAAAA-CGCCACTAAAGGTGTTGGTCTTTAGTGGCGTTTTTGGTCAAA
1 TTTAGCGGCG-TTTTGAAAAAAGCGCCACTAAAGATCATGGTCTTTAGTGGCGTTTTTGG-CAAA
31662945 GCGCCGCTAAAGATAAGGTC
64 GCGCCGCTAAAGATAAGGTC
* * * *
31662965 TTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATAGTCTTTAGTGGTGTTTTTGGGAGAA
1 TTTAGCGGCGTTT-TGAAAAAAGCGCCACTAAAGATCATGGTCTTTAGTGGCGTTTTTGGCA-AA
*
31663030 GCGCTGCTAAAGATAAGGGTC
64 GCGCCGCTAAAGATAA-GGTC
* * * * *
31663051 TTTAGCGGCG-TTTGAAAGAGAAGCGCCGCTAAAGATTAGGGTCTTTAGCGGCGTTTGT-GCAAG
1 TTTAGCGGCGTTTTGAAA-A-AAGCGCCACTAAAGATCATGGTCTTTAGTGGCGTTTTTGGCAA-
*
31663114 ATGCGCCGCTAAAGATCAGGGTC
63 A-GCGCCGCTAAAGAT-AAGGTC
*
31663137 TTTAGCGGTGTTTT
1 TTTAGCGGCGTTTT
31663151 TTTCTAAAAC
Statistics
Matches: 154, Mismatches: 22, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
83 3 0.02
84 21 0.14
85 55 0.36
86 71 0.46
87 4 0.03
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (83 bp):
TTTAGCGGCGTTTTGAAAAAAGCGCCACTAAAGATCATGGTCTTTAGTGGCGTTTTTGGCAAAGC
GCCGCTAAAGATAAGGTC
Found at i:31663032 original size:43 final size:43
Alignment explanation
Indices: 31662919--31663149 Score: 243
Period size: 43 Copynumber: 5.4 Consensus size: 43
31662909 TAAAGGTGTT
* * * *
31662919 GGTCTTTAGTGGCGTTTTTGGTCA-AAGCGCCGCTAAAGAT-AA
1 GGTCTTTAGCGGCGTTTGTGG-AAGAAGCGCCGCTAAAGATCAG
* * *
31662961 GGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCAT
1 GGTCTTTAGCGGCGTTTGTGGAAGAAGCGCCGCTAAAGATCAG
* * * * * * *
31663004 AGTCTTTAGTGGTGTTTTTGGGAGAAGCGCTGCTAAAGATAAG
1 GGTCTTTAGCGGCGTTTGTGGAAGAAGCGCCGCTAAAGATCAG
** *
31663047 GGTCTTTAGCGGCGTTTG-AAAGAGAAGCGCCGCTAAAGATTAG
1 GGTCTTTAGCGGCGTTTGTGGA-AGAAGCGCCGCTAAAGATCAG
* *
31663090 GGTCTTTAGCGGCGTTTGTGCAAGATGCGCCGCTAAAGATCAG
1 GGTCTTTAGCGGCGTTTGTGGAAGAAGCGCCGCTAAAGATCAG
*
31663133 GGTCTTTAGCGGTGTTT
1 GGTCTTTAGCGGCGTTT
31663150 TTTTCTAAAA
Statistics
Matches: 156, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 34 0.22
43 120 0.77
44 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (43 bp):
GGTCTTTAGCGGCGTTTGTGGAAGAAGCGCCGCTAAAGATCAG
Found at i:31667804 original size:20 final size:20
Alignment explanation
Indices: 31667779--31667820 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
31667769 ATCGAGTTTA
31667779 ATCACATCCAAATTCATGAT
1 ATCACATCCAAATTCATGAT
31667799 ATCACATCCAAATTCATGAT
1 ATCACATCCAAATTCATGAT
31667819 AT
1 AT
31667821 TGAAGTCAAA
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:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (20 bp):
ATCACATCCAAATTCATGAT
Found at i:31669794 original size:13 final size:13
Alignment explanation
Indices: 31669776--31669800 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31669766 GTGATTTTTG
31669776 TAAATTTTGAATT
1 TAAATTTTGAATT
31669789 TAAATTTTGAAT
1 TAAATTTTGAAT
31669801 ATTTATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TAAATTTTGAATT
Found at i:31669869 original size:24 final size:24
Alignment explanation
Indices: 31669801--31669871 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
31669791 AATTTTGAAT
* *
31669801 ATTTATATT-ATTAATAAACATTTT
1 ATTTAAATTAATTAATAAA-ATTTA
*
31669825 ATTTAAATTAATATCATAAAATTTA
1 ATTTAAATTAAT-TAATAAAATTTA
* *
31669850 ATTTAATTTAATTAAGAAAATT
1 ATTTAAATTAATTAATAAAATT
31669872 ACGAAAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 16 0.41
25 17 0.44
26 6 0.15
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (24 bp):
ATTTAAATTAATTAATAAAATTTA
Found at i:31672882 original size:22 final size:22
Alignment explanation
Indices: 31672851--31672917 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
31672841 TGCACTAATG
31672851 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* * *
31672873 TATAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
* *
31672895 AACAGAGAGCACTGACGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
31672917 A
1 A
31672918 TAATCAGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:31675351 original size:14 final size:14
Alignment explanation
Indices: 31675304--31675365 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
31675294 TTACCCTATA
31675304 AAAAATAATAAATTT
1 AAAAATAATAAA-TT
* *
31675319 AGTATATAA-AAATT
1 A-AAAATAATAAATT
*
31675333 TAAAATAATAAATT
1 AAAAATAATAAATT
*
31675347 AAAAATAACCAAATT
1 AAAAATAA-TAAATT
31675362 AAAA
1 AAAA
31675366 TAGTCAACTT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
13 5 0.14
14 14 0.38
15 13 0.35
16 5 0.14
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (14 bp):
AAAAATAATAAATT
Found at i:31677914 original size:29 final size:29
Alignment explanation
Indices: 31677881--31677953 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
31677871 AAATTACATT
*
31677881 ATTATATTAATTATGTTAT-AAAAATAATA
1 ATTATATTAATTAT-ATATGAAAAATAATA
**
31677910 ATTATATTAATTATATATGTTAAATAATA
1 ATTATATTAATTATATATGAAAAATAATA
*
31677939 ATTATA-TATTTATAT
1 ATTATATTAATTATAT
31677954 TAAATCACTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 11 0.28
29 28 0.72
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
ATTATATTAATTATATATGAAAAATAATA
Found at i:31678205 original size:15 final size:16
Alignment explanation
Indices: 31678174--31678206 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31678164 TTTAGTGATT
31678174 ATATTTTCTAAAAAAA
1 ATATTTTCTAAAAAAA
31678190 ATATTTT-TAAATAAAA
1 ATATTTTCTAAA-AAAA
31678206 A
1 A
31678207 GTTTATCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATTTTCTAAAAAAA
Found at i:31679943 original size:15 final size:15
Alignment explanation
Indices: 31679925--31679971 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
31679915 ATAAATTTTT
31679925 TTATTTACCAAAATA
1 TTATTTACCAAAATA
* **
31679940 TTA-TAAAAAAAAT-
1 TTATTTACCAAAATA
31679953 TTATTTACCAAAATA
1 TTATTTACCAAAATA
31679968 TTAT
1 TTAT
31679972 AAATTTTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
13 3 0.12
14 14 0.58
15 7 0.29
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (15 bp):
TTATTTACCAAAATA
Found at i:31679983 original size:28 final size:27
Alignment explanation
Indices: 31679904--31679996 Score: 132
Period size: 28 Copynumber: 3.4 Consensus size: 27
31679894 ATAAAAAATA
31679904 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
****
31679931 ACCAAAATATTATAAAAAAAATTTATTT
1 ACCAAAATATTAT-AAATTTTTTTATTT
31679959 ACCAAAATATTATAAATTTTTTTTATTT
1 ACCAAAATATTATAAA-TTTTTTTATTT
31679987 ACCAAAATAT
1 ACCAAAATAT
31679997 ACCCAAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 16 0.29
28 40 0.71
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:31680422 original size:19 final size:19
Alignment explanation
Indices: 31680398--31680463 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
31680388 ATTAAAATAG
31680398 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
31680417 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
31680435 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
31680454 TTTAATTTAA
1 TTTAATTTAA
31680464 AAAAATTAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:31680646 original size:26 final size:26
Alignment explanation
Indices: 31680611--31680664 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
31680601 CACCTTTGGT
31680611 GCCGCCAATGTGATTGGCCTAATCAG
1 GCCGCCAATGTGATTGGCCTAATCAG
31680637 GCCGCCAATGTGATTGGCCTAATCAG
1 GCCGCCAATGTGATTGGCCTAATCAG
31680663 GC
1 GC
31680665 TGATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.22
Consensus pattern (26 bp):
GCCGCCAATGTGATTGGCCTAATCAG
Found at i:31680710 original size:18 final size:19
Alignment explanation
Indices: 31680687--31680725 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
31680677 CATATTTTGG
31680687 TAAATAAAAAAA-TTATAA
1 TAAATAAAAAAAGTTATAA
31680705 TAAATAAAAAAAGTTATAA
1 TAAATAAAAAAAGTTATAA
31680724 TA
1 TA
31680726 TTTTGGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
TAAATAAAAAAAGTTATAA
Found at i:31682268 original size:54 final size:54
Alignment explanation
Indices: 31682181--31682304 Score: 167
Period size: 54 Copynumber: 2.3 Consensus size: 54
31682171 AAGCTTTAAG
* ** * *
31682181 TCAGTGAGTTACACGGCCTAGCACACGGCCTGGCACATGGGCGTGTGTGACAAC
1 TCAGTGAGTTACACGACCTAGCACACAACCTGGCACACGGGCGTGTGGGACAAC
* * * *
31682235 TCAGAGAGTTACACGACCTAGCACACAACCTGGCACACGGGCTTGTGGGGCTAC
1 TCAGTGAGTTACACGACCTAGCACACAACCTGGCACACGGGCGTGTGGGACAAC
31682289 TCAGTGAGTTACACGA
1 TCAGTGAGTTACACGA
31682305 GTGAGGACAC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.19
Consensus pattern (54 bp):
TCAGTGAGTTACACGACCTAGCACACAACCTGGCACACGGGCGTGTGGGACAAC
Found at i:31685218 original size:4 final size:4
Alignment explanation
Indices: 31685209--31685244 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
31685199 TGAGAGGAGA
31685209 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA- AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
31685245 TCAAGAGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:31685966 original size:16 final size:16
Alignment explanation
Indices: 31685945--31685983 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31685935 CCTACTCCCT
31685945 CCCAATTGAAACCCAG
1 CCCAATTGAAACCCAG
* **
31685961 CCCAATTTAAATGCAG
1 CCCAATTGAAACCCAG
31685977 CCCAATT
1 CCCAATT
31685984 TTTTCTTAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (16 bp):
CCCAATTGAAACCCAG
Found at i:31687257 original size:9 final size:9
Alignment explanation
Indices: 31687243--31687279 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31687233 TATAGTTTGA
31687243 TATTCGAAT
1 TATTCGAAT
31687252 TATTCGAAT
1 TATTCGAAT
*
31687261 TATTCGAGT
1 TATTCGAAT
31687270 TATTCGAAT
1 TATTCGAAT
31687279 T
1 T
31687280 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31688416 original size:9 final size:9
Alignment explanation
Indices: 31688398--31688449 Score: 68
Period size: 9 Copynumber: 5.6 Consensus size: 9
31688388 TGTAGTGATT
*
31688398 TAATTTGGG
1 TAATTCGGG
31688407 TAATTCGGG
1 TAATTCGGG
*
31688416 TAATTTGGG
1 TAATTCGGG
31688425 TAATTTTCGGG
1 TAA--TTCGGG
31688436 TAATTCGGG
1 TAATTCGGG
31688445 TAATT
1 TAATT
31688450 TTTAACCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 30 0.79
11 8 0.21
ACGTcount: A:0.23, C:0.06, G:0.29, T:0.42
Consensus pattern (9 bp):
TAATTCGGG
Found at i:31688435 original size:20 final size:20
Alignment explanation
Indices: 31688398--31688451 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
31688388 TGTAGTGATT
31688398 TAATTTGGGTAA--TTCGGG
1 TAATTTGGGTAATTTTCGGG
31688416 TAATTTGGGTAATTTTCGGG
1 TAATTTGGGTAATTTTCGGG
*
31688436 TAATTCGGGTAATTTT
1 TAATTTGGGTAATTTT
31688452 TAACCAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 12 0.36
20 21 0.64
ACGTcount: A:0.22, C:0.06, G:0.28, T:0.44
Consensus pattern (20 bp):
TAATTTGGGTAATTTTCGGG
Done.