Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 96 of 187
Found at i:28093835 original size:24 final size:25
Alignment explanation
Indices: 28093791--28093837 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
28093781 CCCAAATCTC
*
28093791 AATATTCTCTCCTCAAATCTCTCCA
1 AATATCCTCTCCTCAAATCTCTCCA
*
28093816 AATATCCT-TCCTCAATTCTCTC
1 AATATCCTCTCCTCAAATCTCTC
28093838 TATGACAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.26, C:0.36, G:0.00, T:0.38
Consensus pattern (25 bp):
AATATCCTCTCCTCAAATCTCTCCA
Found at i:28111808 original size:19 final size:20
Alignment explanation
Indices: 28111784--28111826 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
28111774 CTAATGTACA
*
28111784 ATTTTATACA-GAAACTTTG
1 ATTTTATACATGAAAATTTG
*
28111803 ATTTTATGCATGAAAATTTG
1 ATTTTATACATGAAAATTTG
28111823 ATTT
1 ATTT
28111827 GATTCAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.47
Consensus pattern (20 bp):
ATTTTATACATGAAAATTTG
Found at i:28115424 original size:25 final size:25
Alignment explanation
Indices: 28115369--28115416 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28115359 TTGCAAGATA
*
28115369 TATATGTTAAAAGAATTGCAAGCCT
1 TATATGTTAAAAGAATTACAAGCCT
* *
28115394 TATATGTTATAAGCATTACAAGC
1 TATATGTTAAAAGAATTACAAGC
28115417 TTTTTATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (25 bp):
TATATGTTAAAAGAATTACAAGCCT
Found at i:28117108 original size:27 final size:27
Alignment explanation
Indices: 28117076--28117143 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
28117066 TGAGCTATGC
*
28117076 TCGCAAATATGTTTTGGCGAA-TAGTGT
1 TCGCAAATATGTTTTGGCGAACCA-TGT
* * *
28117103 TTGCAAATGTGTTATGGCGAACCATGT
1 TCGCAAATATGTTTTGGCGAACCATGT
28117130 TCGCAAATATGTTT
1 TCGCAAATATGTTT
28117144 GTTAAAATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (27 bp):
TCGCAAATATGTTTTGGCGAACCATGT
Found at i:28131111 original size:22 final size:23
Alignment explanation
Indices: 28131083--28131127 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28131073 ATGCAATCTT
28131083 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
28131105 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
28131128 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:28131797 original size:9 final size:9
Alignment explanation
Indices: 28131785--28131827 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
28131775 TATACACATG
28131785 TTTAATTTA
1 TTTAATTTA
28131794 TTTAATTTA
1 TTTAATTTA
28131803 TTTTAATATTA
1 -TTTAAT-TTA
28131814 TATTAA-TTA
1 T-TTAATTTA
28131823 TTTAA
1 TTTAA
28131828 AACTTATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 4 0.13
9 13 0.42
10 7 0.23
11 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTAATTTA
Found at i:28134012 original size:24 final size:24
Alignment explanation
Indices: 28133985--28134030 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
28133975 AGAACAATCC
*
28133985 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGGAAATGAAGGAGCAGCTT
* *
28134009 CAAAAGTAAATGAATGAGCAGC
1 CAAAAGGAAATGAAGGAGCAGC
28134031 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.26, T:0.13
Consensus pattern (24 bp):
CAAAAGGAAATGAAGGAGCAGCTT
Found at i:28137931 original size:22 final size:22
Alignment explanation
Indices: 28137891--28137932 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28137881 TCTTTGGTTG
* *
28137891 TAGTGGAGCAGGTTAAAGATAA
1 TAGTGGAGCAGATCAAAGATAA
*
28137913 TAGTGGAGCAGATCGAAGAT
1 TAGTGGAGCAGATCAAAGAT
28137933 GGCGGATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.21
Consensus pattern (22 bp):
TAGTGGAGCAGATCAAAGATAA
Found at i:28138150 original size:132 final size:132
Alignment explanation
Indices: 28137913--28138417 Score: 798
Period size: 132 Copynumber: 3.8 Consensus size: 132
28137903 TTAAAGATAA
*
28137913 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCC
* *
28137978 AGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGC
66 AGTAATTCTACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
28138043 AG
131 AG
* * *
28138045 TAGTGGAGCAGATCGGAGATGGCGGATTTTACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCC
*
28138110 AGTAATTCTACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGC
66 AGTAATTCTACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
28138175 AG
131 AG
* * *
28138177 TAGTGGAGCAGATCGAAGTTGGCAGATTTTACCTCCCTGTGGTTATAGTAGAGTACATTGAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCC
* *
28138242 AGTAATTCTACTTCCTTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
66 AGTAATTCTACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
*
28138307 AC
131 AG
** *
28138309 TAGTGGAGTGGATCGAAGATGGCGGATTTTACCTCCATGTGGTTACAGTAGAGTACATTGAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCC
** * *
28138374 AGTAA-TCATA-TCTCCCTATTCAGCAGTGGAATAGGTTGAAGATT
66 AGTAATTC-TACT-TCCCTAGACAACAGTGGAATAGATTGAAGATT
28138418 GTAAGTCCTA
Statistics
Matches: 344, Mismatches: 27, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
131 3 0.01
132 341 0.99
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (132 bp):
TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCC
AGTAATTCTACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
AG
Found at i:28138931 original size:232 final size:232
Alignment explanation
Indices: 28138525--28138987 Score: 917
Period size: 232 Copynumber: 2.0 Consensus size: 232
28138515 AGAAATGCAG
28138525 TAAGATCCAGCGAGACTGGGCAAAAATTGGTCATTTCTAAAGTCTTTGCTCCGTTCCTGTTACAC
1 TAAGATCCAGCGAGACTGGGCAAAAATTGGTCATTTCTAAAGTCTTTGCTCCGTTCCTGTTACAC
28138590 GACAATGAGCAAAGAGGGGCAGCTGTAATACCCAATTTTAGCCCGAGCTCACAAAAAAAAACCCA
66 GACAATGAGCAAAGAGGGGCAGCTGTAATACCCAATTTTAGCCCGAGCTCACAAAAAAAAACCCA
28138655 ATGTAATATCATTTGGCCCGATCAGAATTGCCCATTACTTGAAAAGGTTGAAGGTCCATCTACAA
131 ATGTAATATCATTTGGCCCGATCAGAATTGCCCATTACTTGAAAAGGTTGAAGGTCCATCTACAA
28138720 GCTTATGGAGACATAATCTTCAGGGATATGCAATCTC
196 GCTTATGGAGACATAATCTTCAGGGATATGCAATCTC
*
28138757 TAAGATCCAGCGTGACTGGGCAAAAATTGGTCATTTCTAAAGTCTTTGCTCCGTTCCTGTTACAC
1 TAAGATCCAGCGAGACTGGGCAAAAATTGGTCATTTCTAAAGTCTTTGCTCCGTTCCTGTTACAC
28138822 GACAATGAGCAAAGAGGGGCAGCTGTAATACCCAATTTTAGCCCGAGCTCACAAAAAAAAACCCA
66 GACAATGAGCAAAGAGGGGCAGCTGTAATACCCAATTTTAGCCCGAGCTCACAAAAAAAAACCCA
28138887 ATGTAATATCATTTGGCCCGATCAGAATTGCCCATTACTTGAAAAGGTTGAAGGTCCATCTACAA
131 ATGTAATATCATTTGGCCCGATCAGAATTGCCCATTACTTGAAAAGGTTGAAGGTCCATCTACAA
28138952 GCTTATGGAGACATAATCTTCAGGGATATGCAATCT
196 GCTTATGGAGACATAATCTTCAGGGATATGCAATCT
28138988 TACATATAAT
Statistics
Matches: 230, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
232 230 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (232 bp):
TAAGATCCAGCGAGACTGGGCAAAAATTGGTCATTTCTAAAGTCTTTGCTCCGTTCCTGTTACAC
GACAATGAGCAAAGAGGGGCAGCTGTAATACCCAATTTTAGCCCGAGCTCACAAAAAAAAACCCA
ATGTAATATCATTTGGCCCGATCAGAATTGCCCATTACTTGAAAAGGTTGAAGGTCCATCTACAA
GCTTATGGAGACATAATCTTCAGGGATATGCAATCTC
Found at i:28139005 original size:19 final size:19
Alignment explanation
Indices: 28138983--28139067 Score: 82
Period size: 19 Copynumber: 4.5 Consensus size: 19
28138973 AGGGATATGC
*
28138983 AATCTTACATATAATATAT
1 AATCTTAGATATAATATAT
**
28139002 AATCTTAGATA-AGATATGC
1 AATCTTAGATATA-ATATAT
* *
28139021 AATCTTAGATGTGATATAT
1 AATCTTAGATATAATATAT
* **
28139040 AATCTTAGATATGATATGC
1 AATCTTAGATATAATATAT
28139059 AATCTTAGA
1 AATCTTAGA
28139068 AGATATGATT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
18 1 0.02
19 53 0.98
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (19 bp):
AATCTTAGATATAATATAT
Found at i:28139066 original size:38 final size:38
Alignment explanation
Indices: 28138976--28139067 Score: 148
Period size: 38 Copynumber: 2.4 Consensus size: 38
28138966 AATCTTCAGG
*
28138976 GATATGCAATCTTACATATAATATATAATCTTAGATAA
1 GATATGCAATCTTAGATATAATATATAATCTTAGATAA
* * *
28139014 GATATGCAATCTTAGATGTGATATATAATCTTAGATAT
1 GATATGCAATCTTAGATATAATATATAATCTTAGATAA
28139052 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
28139068 AGATATGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (38 bp):
GATATGCAATCTTAGATATAATATATAATCTTAGATAA
Found at i:28139093 original size:22 final size:21
Alignment explanation
Indices: 28138991--28139093 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 21
28138981 GCAATCTTAC
* *
28138991 ATATAATATATAATCTT--AG
1 ATATGATATGTAATCTTAGAG
* *
28139010 ATAAGATATGCAATCTT--AG
1 ATATGATATGTAATCTTAGAG
* *
28139029 ATGTGATATATAATCTT--AG
1 ATATGATATGTAATCTTAGAG
*
28139048 ATATGATATGCAATCTTAGAAG
1 ATATGATATGTAATCTTAG-AG
*
28139070 ATATGATTTTGTAATCTTAGAG
1 ATATGA-TATGTAATCTTAGAG
28139092 AT
1 AT
28139094 TTAATTTGTA
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
19 44 0.66
22 12 0.18
23 11 0.16
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.39
Consensus pattern (21 bp):
ATATGATATGTAATCTTAGAG
Found at i:28150085 original size:42 final size:41
Alignment explanation
Indices: 28149993--28150089 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 41
28149983 GCTCCCTATC
* *
28149993 TGAGCATAAGTGACAAGCTGTGTATAAGCAAAGCTCCCCACG
1 TGAGCTTAAGTGACAAGCTATGTATAAGCAAAGCT-CCCACG
* * * *
28150035 TGATCTTAAGTGACAAGTTATGTATCAGCAAAGCT-CCTCG
1 TGAGCTTAAGTGACAAGCTATGTATAAGCAAAGCTCCCACG
28150075 TGCAAGCTTAAGTGA
1 TG--AGCTTAAGTGA
28150090 TTGTGCTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 6 0.13
42 40 0.87
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (41 bp):
TGAGCTTAAGTGACAAGCTATGTATAAGCAAAGCTCCCACG
Found at i:28152104 original size:39 final size:39
Alignment explanation
Indices: 28152037--28152114 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
28152027 CATCAACATT
*
28152037 TAATATTTAAAAAAAATTAAATTTTTTTATAATTTTTAAA
1 TAATATTTAAAAAAAATTAAATTCTTTTA-AATTTTTAAA
* *
28152077 TAAT-TTTAATAAAAATTATAA-TCTTTTAATTTTTTAAA
1 TAATATTTAAAAAAAATTA-AATTCTTTTAAATTTTTAAA
28152115 CTTAATACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 9 0.26
39 19 0.56
40 6 0.18
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (39 bp):
TAATATTTAAAAAAAATTAAATTCTTTTAAATTTTTAAA
Found at i:28154278 original size:4 final size:4
Alignment explanation
Indices: 28154269--28154309 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
28154259 CAGGAACACT
**
28154269 TAAA TAAA TAAA TAAA TAAA TAAA TACTC TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA-AA TAAA TAAA TAAA
28154310 CAACGAAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 30 0.94
5 2 0.06
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:28155020 original size:3 final size:3
Alignment explanation
Indices: 28155014--28155092 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
28155004 AAAGATGATG
28155014 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28155062 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28155093 AAGATACCAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28156106 original size:13 final size:14
Alignment explanation
Indices: 28156078--28156111 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
28156068 ATGAGTTGCT
28156078 ATATAATATGATATA
1 ATATAATA-GATATA
28156093 ATATAATA-ATATA
1 ATATAATAGATATA
28156106 ATATAA
1 ATATAA
28156112 ATGGATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
15 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
ATATAATAGATATA
Found at i:28186535 original size:20 final size:18
Alignment explanation
Indices: 28186496--28186533 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
28186486 TTGAGTTGCA
28186496 TGCAAGCCTATATACATG
1 TGCAAGCCTATATACATG
28186514 TGCAAGCCTATATACATG
1 TGCAAGCCTATATACATG
28186532 TG
1 TG
28186534 TGAGCTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (18 bp):
TGCAAGCCTATATACATG
Found at i:28192580 original size:24 final size:27
Alignment explanation
Indices: 28192548--28192599 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 27
28192538 TGATCTTATT
*
28192548 TTATCTCATGGAAA-TC-ATTAC-ATC
1 TTATCTCATGAAAAGTCAATTACTATC
*
28192572 TTATTTCATGAAAAGTCAATTACTATC
1 TTATCTCATGAAAAGTCAATTACTATC
28192599 T
1 T
28192600 CATAGTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 12 0.52
25 2 0.09
26 5 0.22
27 4 0.17
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (27 bp):
TTATCTCATGAAAAGTCAATTACTATC
Found at i:28194015 original size:18 final size:18
Alignment explanation
Indices: 28193992--28194027 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28193982 AGAAAATTTT
28193992 GAAGAAATTTTTAAAATA
1 GAAGAAATTTTTAAAATA
28194010 GAAGAAATTTTTAAAATA
1 GAAGAAATTTTTAAAATA
28194028 CCAATTCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (18 bp):
GAAGAAATTTTTAAAATA
Found at i:28194372 original size:24 final size:24
Alignment explanation
Indices: 28194339--28194387 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
28194329 ATGCAAATGA
28194339 CAAGGAAAATGCCCAATCCAACTT
1 CAAGGAAAATGCCCAATCCAACTT
* * *
28194363 CAAGGCAAATTCTCAATCCAACTT
1 CAAGGAAAATGCCCAATCCAACTT
28194387 C
1 C
28194388 TAGGTTATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.31, G:0.10, T:0.20
Consensus pattern (24 bp):
CAAGGAAAATGCCCAATCCAACTT
Found at i:28199131 original size:8 final size:8
Alignment explanation
Indices: 28199120--28199147 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
28199110 TAAATAGAAT
28199120 AATAATAA
1 AATAATAA
28199128 AATAATAA
1 AATAATAA
28199136 AATAATAA
1 AATAATAA
28199144 AATA
1 AATA
28199148 TCATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AATAATAA
Found at i:28201271 original size:50 final size:50
Alignment explanation
Indices: 28201155--28201690 Score: 653
Period size: 50 Copynumber: 10.6 Consensus size: 50
28201145 ATAATAACAA
* * * ** * * *
28201155 GCCAAAGCCATGTCCTAGACATAGTCTTACATGGGATGTTTCCTGTAC--T
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGGT
* * ** *
28201204 GCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* * *
28201254 GCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTTGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
** * * * *
28201304 GCCAACACCATGTCCTAGACACGGTTTTACATGGGACCTCTCATCTAGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
** *
28201354 GCCAACACCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* *
28201404 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCACATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* * *
28201454 GCCAATGCCATGTCCTAGATATGGTCTTACATGAGACCTCTCATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* * *
28201504 GCCAATGCCATGTCCCAGACATGGTCTTACATAGGACCTCTTATCTCAGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* *
28201554 GCCAATGCCATGTCCCAAACATGGTGTTACATGGGACCTCTCATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* * *
28201604 GCGAATGCCATGTCCCAGACATGATCTTACATGGGACCTCTCATAATCTCAATGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GGT
28201660 GCCAATGCCATGTCCCAGACATGGTCTTACA
1 GCCAATGCCATGTCCCAGACATGGTCTTACA
28201691 CTGGCTCACA
Statistics
Matches: 422, Mismatches: 57, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
48 1 0.00
49 36 0.09
50 349 0.83
53 5 0.01
56 31 0.07
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (50 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
Found at i:28201774 original size:42 final size:41
Alignment explanation
Indices: 28201702--28201783 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 41
28201692 TGGCTCACAT
* * *
28201702 ATCGACGTTGATGCCATGTCCCAAACATGGTCTTATATGAG
1 ATCGACGTCGATGCCATATCCCAAACATGGTCTTACATGAG
* * *
28201743 ATCGCACGTCGATGCCATATCTCAGATATGGTCTTACATGA
1 ATCG-ACGTCGATGCCATATCCCAAACATGGTCTTACATGA
28201784 AAATCACATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 4 0.12
42 30 0.88
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (41 bp):
ATCGACGTCGATGCCATATCCCAAACATGGTCTTACATGAG
Found at i:28214547 original size:51 final size:51
Alignment explanation
Indices: 28214416--28214607 Score: 174
Period size: 51 Copynumber: 3.8 Consensus size: 51
28214406 GAAATTGAAT
* * * * * * *
28214416 GTGATGGTCACGTGTGTAGTCCTATGTGCATGCTACTACGTGTACC--AAA
1 GTGATGATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA
* * *
28214465 ATGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA
1 GTGAT-GATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA
* * * *** *
28214517 G-GTTCGATCACGTGTGTAGTACTATATGCAGGCTACTACATGTATCGGATA
1 GTGAT-GATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA
* *
28214568 GTGATGGTCACATGTGTAGTGCTATGTGCAGGCTACTATG
1 GTGATGATCACATGTGTAGTACTATGTGCAGGCTACTATG
28214608 TGAACCGGTA
Statistics
Matches: 113, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 4 0.04
50 35 0.31
51 70 0.62
52 4 0.04
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (51 bp):
GTGATGATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA
Found at i:28214605 original size:102 final size:101
Alignment explanation
Indices: 28214423--28214607 Score: 264
Period size: 102 Copynumber: 1.8 Consensus size: 101
28214413 AATGTGATGG
* * * * *
28214423 TCACGTGTGTAGTCCTATGTGCATGCTACTACGTGTACCAAAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATATGCAGGCTACTACATGTACCAAAATGATAGGTCACATGTGTAGTAC
28214488 TATGTGCAGGCTACTATGCGTACCGGATAGGTTCGA
66 TATGTGCAGGCTACTATGCGTACCGGATAGGTTCGA
* * *
28214524 TCACGTGTGTAGTACTATATGCAGGCTACTACATGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATATGCAGGCTACTACATGTA-C-CAAAATGATAGGTCACATGTGTAGT
*
28214588 GCTATGTGCAGGCTACTATG
64 ACTATGTGCAGGCTACTATG
28214608 TGAACCGGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
101 33 0.45
102 34 0.47
103 6 0.08
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATATGCAGGCTACTACATGTACCAAAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGGATAGGTTCGA
Found at i:28214854 original size:16 final size:16
Alignment explanation
Indices: 28214833--28214864 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28214823 TGATTGAAAG
*
28214833 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
28214849 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
28214865 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:28228537 original size:64 final size:63
Alignment explanation
Indices: 28228422--28228577 Score: 183
Period size: 64 Copynumber: 2.5 Consensus size: 63
28228412 GCTTTACGGG
* * ** *
28228422 GGTTCGGTGGATGAGAATAGGGTCTTAGT-TTGAATATTGTTAAGTAAATTATGGA-TTTGTAGA
1 GGTTC-GTGGATGAGAATGGGGTTTTAGTATCAAATATTGTTAAGCAAATTAT-GACTTTGTAGA
* *
28228485 GGTTCAGTTGATGAGAATGGGGTTTTAGTATCAAATATTGTTAAGCAAATTATGACTTTGTGGA
1 GGTTC-GTGGATGAGAATGGGGTTTTAGTATCAAATATTGTTAAGCAAATTATGACTTTGTAGA
* *
28228549 GGTT-GTGGATGAGAACGGGGTTTCAGTAT
1 GGTTCGTGGATGAGAATGGGGTTTTAGTAT
28228578 AGGAAGAACA
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
62 22 0.28
63 27 0.34
64 31 0.39
ACGTcount: A:0.28, C:0.05, G:0.31, T:0.37
Consensus pattern (63 bp):
GGTTCGTGGATGAGAATGGGGTTTTAGTATCAAATATTGTTAAGCAAATTATGACTTTGTAGA
Found at i:28236397 original size:20 final size:20
Alignment explanation
Indices: 28236352--28236445 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
28236342 CTCAGAGGGG
* *
28236352 CTTCTACCGATACAACTCCA
1 CTTCTACCCATACAAGTCCA
* *
28236372 CCTCTACCCATACAAGTACA
1 CTTCTACCCATACAAGTCCA
*
28236392 CTTCTACCCATTCAAGTCCA
1 CTTCTACCCATACAAGTCCA
* * *
28236412 TTTCTACCTATGCAAGTCCA
1 CTTCTACCCATACAAGTCCA
*
28236432 GTTCTACCCATACA
1 CTTCTACCCATACA
28236446 TCTTTTGAGT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.29, C:0.37, G:0.06, T:0.28
Consensus pattern (20 bp):
CTTCTACCCATACAAGTCCA
Found at i:28236861 original size:28 final size:29
Alignment explanation
Indices: 28236819--28236882 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
28236809 AAGTAGAGTG
* * *
28236819 TAAAAGGTTTCTAGTTGAGCCACAAAAGC
1 TAAAGGGTTTCTAGTTAAGCCACAAAAAC
*
28236848 TAAAGGGTTT-TAGTTAAGCCATAAAAAC
1 TAAAGGGTTTCTAGTTAAGCCACAAAAAC
*
28236876 TAGAGGG
1 TAAAGGG
28236883 AATGTTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (29 bp):
TAAAGGGTTTCTAGTTAAGCCACAAAAAC
Found at i:28260168 original size:27 final size:27
Alignment explanation
Indices: 28260137--28260314 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28260127 TAAATTGTAC
28260137 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28260164 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28260190 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28260218 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28260246 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28260273 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28260300 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28260315 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28260251 original size:82 final size:81
Alignment explanation
Indices: 28260138--28260293 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28260128 AAATTGTACA
* *
28260138 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28260202 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28260219 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
28260284 TGCGAGTTGA
65 TGCGAATTGA
28260294 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28260305 original size:82 final size:81
Alignment explanation
Indices: 28260134--28260314 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
28260124 GATTAAATTG
* *
28260134 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28260199 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28260215 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28260279 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28260297 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28260315 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28268358 original size:27 final size:27
Alignment explanation
Indices: 28268327--28268504 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28268317 TAAATTGTAC
28268327 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28268354 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28268380 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28268408 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28268436 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28268463 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28268490 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28268505 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28268441 original size:82 final size:81
Alignment explanation
Indices: 28268328--28268483 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28268318 AAATTGTACA
* *
28268328 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28268392 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28268409 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
28268474 TGCGAGTTGA
65 TGCGAATTGA
28268484 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28268495 original size:82 final size:81
Alignment explanation
Indices: 28268324--28268504 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
28268314 GATTAAATTG
* *
28268324 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28268389 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28268405 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28268469 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28268487 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28268505 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28278727 original size:21 final size:20
Alignment explanation
Indices: 28278667--28278727 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
28278657 ATTCGTTTTG
28278667 ACCCTTATGGGTTTCTGTTCA
1 ACCCTTATGGGTTTC-GTTCA
* *
28278688 ACTCC-TATGAGCTTCCGTTCA
1 AC-CCTTATG-GGTTTCGTTCA
28278709 ACCCTTATGGGTTTTCGTT
1 ACCCTTATGGG-TTTCGTT
28278728 TAGCACTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 3 0.09
21 23 0.72
22 6 0.19
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.41
Consensus pattern (20 bp):
ACCCTTATGGGTTTCGTTCA
Found at i:28282148 original size:74 final size:74
Alignment explanation
Indices: 28282027--28282187 Score: 225
Period size: 74 Copynumber: 2.2 Consensus size: 74
28282017 TAATGAGTAT
* * *
28282027 GATTGAAAAGGTGTGTATATGAAATGAGTTATGGCATTGAGCTTATGAAATTTAAA-TTGTAATA
1 GATTGAAAAGGTATGTATATGAAATGAGCTATGGCATTGAGCTTATGAAA-TGAAAGTTGTAATA
* *
28282091 TGTGTAAATG
65 TATATAAATG
* * *
28282101 GATTGAAAAGGTATGTATATGAAATGAGCTATGTCATTGAGTTTATGAAATGAAAGTTGTGATAT
1 GATTGAAAAGGTATGTATATGAAATGAGCTATGGCATTGAGCTTATGAAATGAAAGTTGTAATAT
28282166 ATATAAATG
66 ATATAAATG
*
28282175 GTTTGAAAAGGTA
1 GATTGAAAAGGTA
28282188 ACTAATTGAT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
73 4 0.05
74 73 0.95
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (74 bp):
GATTGAAAAGGTATGTATATGAAATGAGCTATGGCATTGAGCTTATGAAATGAAAGTTGTAATAT
ATATAAATG
Found at i:28282439 original size:21 final size:22
Alignment explanation
Indices: 28282392--28282440 Score: 55
Period size: 26 Copynumber: 2.1 Consensus size: 22
28282382 TTATATGAGC
28282392 TTACTATACACTAGTTGCTTATGTAA
1 TTACTATACACTAGTTGC---T-TAA
28282418 TTACTATACACTAGTTGC-TAA
1 TTACTATACACTAGTTGCTTAA
28282439 TT
1 TT
28282441 TTGGCAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 5 0.22
26 18 0.78
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (22 bp):
TTACTATACACTAGTTGCTTAA
Found at i:28284435 original size:138 final size:138
Alignment explanation
Indices: 28284260--28284530 Score: 366
Period size: 138 Copynumber: 2.0 Consensus size: 138
28284250 ATTTTCTTTC
* * * * * *
28284260 TTTTGATTATCAAGAGTTTCCAATTAGAATAAATTATTATAAGTATTATATTGAATAATTAATTC
1 TTTTGAGTATCAAGAGTTTCCAATCAGAATAAATTATTATAAGTACTAGATTGAATAACTAACTC
* * * * *
28284325 AATTCA-AACTAATTAATCAAAATATATATAATTGAAAATAAAATT-TGAGTATTCCTTAACTAG
66 AACT-ATAACTAACTAATCAAAACATATATAATCGAAAAT-AAATTCGGAGTATTCCTTAACTAG
28284388 CAAACTTGAA
129 CAAACTTGAA
* * * *
28284398 TTTTGAGTATCAAGAGTTTCCTATCAGAATCACTTATTATAAGTACTGGATTGAATAACTAACTC
1 TTTTGAGTATCAAGAGTTTCCAATCAGAATAAATTATTATAAGTACTAGATTGAATAACTAACTC
*
28284463 AACTATAACTAACTAATCAAAACATATATAATCGAAAATCAATTCGGAGTATTCCTTAACTAGCA
66 AACTATAACTAACTAATCAAAACATATATAATCGAAAATAAATTCGGAGTATTCCTTAACTAGCA
28284528 AAC
131 AAC
28284531 CTTAATACTT
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
137 5 0.04
138 110 0.96
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (138 bp):
TTTTGAGTATCAAGAGTTTCCAATCAGAATAAATTATTATAAGTACTAGATTGAATAACTAACTC
AACTATAACTAACTAATCAAAACATATATAATCGAAAATAAATTCGGAGTATTCCTTAACTAGCA
AACTTGAA
Found at i:28284846 original size:3 final size:3
Alignment explanation
Indices: 28284838--28284890 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
28284828 ATAAATACTA
28284838 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28284886 TAT TA
1 TAT TA
28284891 GGGTTAGGGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28285523 original size:22 final size:22
Alignment explanation
Indices: 28285498--28285544 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
28285488 TAGATCATAT
* *
28285498 TATAAAT-ATATTGTATTTATCA
1 TATAAATAAT-TTGTATCTAACA
28285520 TATAAATAATTTGTATCTAACA
1 TATAAATAATTTGTATCTAACA
28285542 TAT
1 TAT
28285545 TAGAAAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (22 bp):
TATAAATAATTTGTATCTAACA
Found at i:28288568 original size:24 final size:25
Alignment explanation
Indices: 28288540--28288599 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
28288530 CATTTTAAGT
28288540 TACTTTTTTACAAA-ATATTTTTTA
1 TACTTTTTTACAAATATATTTTTTA
* *
28288564 TACTTTTTTTATAAATTTATTTTTTA
1 TAC-TTTTTTACAAATATATTTTTTA
* *
28288590 AAATTTTTTA
1 TACTTTTTTA
28288600 TTACGGCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 3 0.10
25 17 0.57
26 10 0.33
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (25 bp):
TACTTTTTTACAAATATATTTTTTA
Found at i:28288571 original size:25 final size:26
Alignment explanation
Indices: 28288543--28288598 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
28288533 TTTAAGTTAC
* *
28288543 TTTTTTACAAA-ATATTTTTTATACT
1 TTTTTTACAAATATATTTTTTAAAAT
* *
28288568 TTTTTTATAAATTTATTTTTTAAAAT
1 TTTTTTACAAATATATTTTTTAAAAT
28288594 TTTTT
1 TTTTT
28288599 ATTACGGCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTTTTACAAATATATTTTTTAAAAT
Found at i:28289197 original size:16 final size:16
Alignment explanation
Indices: 28289162--28289206 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
28289152 ATCTTTATTG
28289162 AATCCCTAAAATCTTCA
1 AATCCCT-AAATCTTCA
* *
28289179 AATCCCTAAATTTTGA
1 AATCCCTAAATCTTCA
28289195 AATCCCTAAATC
1 AATCCCTAAATC
28289207 GTTAGCATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.40, C:0.27, G:0.02, T:0.31
Consensus pattern (16 bp):
AATCCCTAAATCTTCA
Found at i:28293114 original size:27 final size:27
Alignment explanation
Indices: 28293084--28293165 Score: 64
Period size: 26 Copynumber: 3.1 Consensus size: 27
28293074 ACGTGCAGCA
28293084 GCAACATTATCCAGTCTATCTGATGTT
1 GCAACATTATCCAGTCTATCTGATGTT
* * * **
28293111 GCAAAATCA-CCAG-CATAT-TCAT-CA
1 GCAACATTATCCAGTC-TATCTGATGTT
* *
28293135 GCAACATTATCCACTCAATCTGATGTT
1 GCAACATTATCCAGTCTATCTGATGTT
28293162 GCAA
1 GCAA
28293166 AATCACTAGC
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
24 7 0.18
25 9 0.24
26 11 0.29
27 11 0.29
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (27 bp):
GCAACATTATCCAGTCTATCTGATGTT
Found at i:28293138 original size:51 final size:51
Alignment explanation
Indices: 28293082--28293188 Score: 187
Period size: 51 Copynumber: 2.1 Consensus size: 51
28293072 CTACGTGCAG
* *
28293082 CAGCAACATTATCCAGTCTATCTGATGTTGCAAAATCACCAGCATATTCAT
1 CAGCAACATTATCCACTCAATCTGATGTTGCAAAATCACCAGCATATTCAT
*
28293133 CAGCAACATTATCCACTCAATCTGATGTTGCAAAATCACTAGCATATTCAT
1 CAGCAACATTATCCACTCAATCTGATGTTGCAAAATCACCAGCATATTCAT
28293184 CAGCA
1 CAGCA
28293189 GCAACTTCAC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (51 bp):
CAGCAACATTATCCACTCAATCTGATGTTGCAAAATCACCAGCATATTCAT
Found at i:28293925 original size:19 final size:19
Alignment explanation
Indices: 28293873--28293928 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
28293863 CTTTAACATC
28293873 TTTTCTAAGC-AAAAACAA
1 TTTTCTAAGCAAAAAACAA
* ** *
28293891 ATTTCTTTGAATAAAAACAA
1 TTTTCTAAGCA-AAAAACAA
28293911 TTTTCTAAGCAAAAAACA
1 TTTTCTAAGCAAAAAACA
28293929 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
18 6 0.21
19 7 0.25
20 15 0.54
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.30
Consensus pattern (19 bp):
TTTTCTAAGCAAAAAACAA
Found at i:28295520 original size:14 final size:14
Alignment explanation
Indices: 28295492--28295554 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
28295482 AATATATACG
*
28295492 TATATATATATAAA
1 TATATATATAAAAA
28295506 TATATATATAAAAA
1 TATATATATAAAAA
* * * *
28295520 TTTGTTAGAAAAAAA
1 TAT-ATATATAAAAA
* *
28295535 TATATAAATATAAA
1 TATATATATAAAAA
28295549 TATATA
1 TATATA
28295555 CATATATATA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 28 0.74
15 10 0.26
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TATATATATAAAAA
Found at i:28303277 original size:43 final size:42
Alignment explanation
Indices: 28303220--28303443 Score: 222
Period size: 43 Copynumber: 5.3 Consensus size: 42
28303210 TTAGTGGAAG
*
28303220 CGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTCTCCTAAAA
1 CGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCTCC-AAAA
* *
28303263 CGCCGC-AATAGACCCTGATCTATAGCGGCGC-TTCGACCACAAAA
1 CGCCGCTAA-AGACCCTGATCTTTAGCGGCGCTTTC--TC-CAAAA
* * * *
28303307 CGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTC-CCCAAA
1 CGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCTCCAAAA
* * *
28303348 -GCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCATAAA
1 CGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCTCCA-AAA
* * **
28303390 CCCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAAAAA
1 CGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCTCC-AAAA
*
28303433 CGCCACTAAAG
1 CGCCGCTAAAG
28303444 GCCAACACCT
Statistics
Matches: 150, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
40 28 0.19
41 6 0.04
42 9 0.06
43 71 0.47
44 30 0.20
45 6 0.04
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (42 bp):
CGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCTCCAAAA
Found at i:28303341 original size:87 final size:83
Alignment explanation
Indices: 28303220--28303423 Score: 230
Period size: 83 Copynumber: 2.4 Consensus size: 83
28303210 TTAGTGGAAG
* * *
28303220 CGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTCTCCTAAAACGCCGC-AATAGACCCTGATCT
1 CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTTC-CC-AAAA-GCCGCTAA-AGACCATGATCT
28303284 ATAGCGGCGCTTCGACCACAAAA
62 ATAGCGGCGCTTCGACCA-AAAA
* * * *
28303307 CGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCAAAGCCGCTAAAGACCATGATCTTTAG
1 CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTTCCCAAAAGCCGCTAAAGACCATGATCTATAG
* *** *
28303372 TGGCGCTTTTTCCATAAA
66 CGGCGCTTCGACCAAAAA
* *
28303390 CCCCGCTAAAGACCCTTATCTTTAGCGGCGCTTT
1 CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTT
28303424 GACCAAAAAC
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
83 33 0.33
84 29 0.29
85 5 0.05
86 2 0.02
87 31 0.31
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (83 bp):
CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTTCCCAAAAGCCGCTAAAGACCATGATCTATAG
CGGCGCTTCGACCAAAAA
Found at i:28303456 original size:43 final size:42
Alignment explanation
Indices: 28303280--28303462 Score: 138
Period size: 43 Copynumber: 4.3 Consensus size: 42
28303270 ATAGACCCTG
* * *
28303280 ATCTATAGCGGCGCTTCGACCACAAAACGCCACTAAAGAACCTA
1 ATCTTTAGCGGCGCTTTGACCA-AAAACGCCACTAAAG-ACCAA
** * *
28303324 ATCTTTAGCGGCGCTTT--CCCCAAA-GCCGCTAAAGACCATG
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGACCA-A
* ** * * * **
28303364 ATCTTTAGTGGCGCTTTTTCCATAAACCCCGCTAAAGACCCTT
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGA-CCAA
*
28303407 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGGCCAA
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGACCAA
* *
28303449 CACCTTTAGTGGCG
1 -ATCTTTAGCGGCG
28303463 TTTTTTTAAA
Statistics
Matches: 109, Mismatches: 24, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
39 3 0.03
40 25 0.23
41 3 0.03
42 9 0.08
43 52 0.48
44 17 0.16
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (42 bp):
ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGACCAA
Found at i:28303817 original size:21 final size:21
Alignment explanation
Indices: 28303787--28303844 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
28303777 TTTGACGCTG
*
28303787 CTCTGTTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
**
28303808 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
28303829 CTCTGCTTCCCTCGCT
1 CTCTGCTTCCCTCGCT
28303845 NATCCAACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.03, C:0.45, G:0.16, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:28304814 original size:9 final size:9
Alignment explanation
Indices: 28304800--28304919 Score: 121
Period size: 9 Copynumber: 14.2 Consensus size: 9
28304790 TAAGGGATAT
28304800 TTATGTAAG
1 TTATGTAAG
28304809 TTATGTAAG
1 TTATGTAAG
28304818 TTATGT-A-
1 TTATGTAAG
* *
28304825 TTAAGTAAA
1 TTATGTAAG
28304834 TTATGTAAG
1 TTATGTAAG
28304843 TTATGT-A-
1 TTATGTAAG
*
28304850 TTATCTAAG
1 TTATGTAAG
28304859 TTATGTAAG
1 TTATGTAAG
28304868 TTATGT-A-
1 TTATGTAAG
* *
28304875 TTAAGTAGG
1 TTATGTAAG
*
28304884 TTATGTAAT
1 TTATGTAAG
*
28304893 TTATGT--C
1 TTATGTAAG
28304900 TTATGTAAG
1 TTATGTAAG
28304909 TTATGTAAG
1 TTATGTAAG
28304918 TT
1 TT
28304920 TTTGATTTTG
Statistics
Matches: 91, Mismatches: 12, Indels: 16
0.76 0.10 0.13
Matches are distributed among these distances:
7 21 0.23
8 5 0.05
9 65 0.71
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28304832 original size:25 final size:25
Alignment explanation
Indices: 28304804--28304919 Score: 169
Period size: 25 Copynumber: 4.6 Consensus size: 25
28304794 GGATATTTAT
28304804 GTAAGTTATGTAAGTTATGTATTAA
1 GTAAGTTATGTAAGTTATGTATTAA
* *
28304829 GTAAATTATGTAAGTTATGTATTAT
1 GTAAGTTATGTAAGTTATGTATTAA
*
28304854 CTAAGTTATGTAAGTTATGTATTAA
1 GTAAGTTATGTAAGTTATGTATTAA
* * * *
28304879 GTAGGTTATGTAATTTATGTCTTAT
1 GTAAGTTATGTAAGTTATGTATTAA
28304904 GTAAGTTATGTAAGTT
1 GTAAGTTATGTAAGTT
28304920 TTTGATTTTG
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 79 1.00
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (25 bp):
GTAAGTTATGTAAGTTATGTATTAA
Found at i:28304880 original size:50 final size:50
Alignment explanation
Indices: 28304800--28304919 Score: 195
Period size: 50 Copynumber: 2.4 Consensus size: 50
28304790 TAAGGGATAT
28304800 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
* ** * *
28304850 TTATCTAAGTTATGTAAGTTATGTATTAAGTAGGTTATGTAATTTATGTC
1 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
28304900 TTATGTAAGTTATGTAAGTT
1 TTATGTAAGTTATGTAAGTT
28304920 TTTGATTTTG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (50 bp):
TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
Found at i:28304938 original size:50 final size:49
Alignment explanation
Indices: 28304800--28304946 Score: 170
Period size: 50 Copynumber: 2.9 Consensus size: 49
28304790 TAAGGGATAT
* *
28304800 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTATTAAGT-GATTATGTAACTTATGTA
* * * *
28304850 TTATCTAAGTTATGTAAGTTATGTATTAAGTAGGTTATGTAATTTATGTC
1 TTATGTAAGTTATGTAAGTTATGTATTAAGT-GATTATGTAACTTATGTA
* **
28304900 TTATGTAAGTTATGTAAGTT-TTTGATTTTGTGTATTATGTAACTTAT
1 TTATGTAAGTTATGTAAGTTATGT-ATTAAGTG-ATTATGTAACTTAT
28304947 TTAATTTGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
49 3 0.04
50 81 0.96
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.50
Consensus pattern (49 bp):
TTATGTAAGTTATGTAAGTTATGTATTAAGTGATTATGTAACTTATGTA
Found at i:28305009 original size:12 final size:12
Alignment explanation
Indices: 28304968--28305030 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
28304958 TGGTTATGTA
28304968 TTATTATGTAAG
1 TTATTATGTAAG
* * *
28304980 TTACTATTTAGG
1 TTATTATGTAAG
28304992 TTATTATGTAAG
1 TTATTATGTAAG
* * *
28305004 TCATTATATATG
1 TTATTATGTAAG
*
28305016 TTGGTTATGTAAG
1 TT-ATTATGTAAG
28305029 TT
1 TT
28305031 GTGATATGAT
Statistics
Matches: 37, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
12 28 0.76
13 9 0.24
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.51
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:28305232 original size:29 final size:29
Alignment explanation
Indices: 28305199--28305273 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
28305189 ACGTAGGCTA
28305199 TGTATTATGCAAGTTATTTATGTAAGTGG
1 TGTATTATGCAAGTTATTTATGTAAGTGG
28305228 TGTATTATGCAAGTTATTTATGTAAGTGG
1 TGTATTATGCAAGTTATTTATGTAAGTGG
*
28305257 TGTATTATGTAAGTTAT
1 TGTATTATGCAAGTTAT
28305274 GTACGCTATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.47
Consensus pattern (29 bp):
TGTATTATGCAAGTTATTTATGTAAGTGG
Found at i:28305276 original size:16 final size:16
Alignment explanation
Indices: 28305165--28305276 Score: 74
Period size: 16 Copynumber: 7.2 Consensus size: 16
28305155 ACGTAAGTGG
28305165 TGTATTATGTAAGTTA
1 TGTATTATGTAAGTTA
* * * *
28305181 AGTAAGTTACGTAGGCTA
1 TGT-A-TTATGTAAGTTA
*
28305199 TGTATTATGCAAGTTA
1 TGTATTATGTAAGTTA
**
28305215 --T-TTATGTAAGTGG
1 TGTATTATGTAAGTTA
*
28305228 TGTATTATGCAAGTTA
1 TGTATTATGTAAGTTA
**
28305244 --T-TTATGTAAGTGG
1 TGTATTATGTAAGTTA
28305257 TGTATTATGTAAGTTA
1 TGTATTATGTAAGTTA
28305273 TGTA
1 TGTA
28305277 CGCTATGTAT
Statistics
Matches: 68, Mismatches: 20, Indels: 16
0.65 0.19 0.15
Matches are distributed among these distances:
13 18 0.26
14 2 0.03
15 2 0.03
16 33 0.49
17 2 0.03
18 11 0.16
ACGTcount: A:0.29, C:0.04, G:0.23, T:0.44
Consensus pattern (16 bp):
TGTATTATGTAAGTTA
Found at i:28306084 original size:23 final size:20
Alignment explanation
Indices: 28306039--28306079 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
28306029 ATGTTATTCG
28306039 AATTTTAAATATATATA-TA
1 AATTTTAAATATATATATTA
28306058 AATTTTAAATATATATATTA
1 AATTTTAAATATATATATTA
28306078 AA
1 AA
28306080 AAATTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTTTAAATATATATATTA
Found at i:28306769 original size:29 final size:29
Alignment explanation
Indices: 28306698--28306770 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 29
28306688 GCAAATAAAT
*
28306698 CCTCACCGACAAAAAATTAAAAATTGAAA
1 CCTCACCGACAAAACATTAAAAATTGAAA
28306727 CCTCACCGA-AAAACATTAAAAATTGAAA
1 CCTCACCGACAAAACATTAAAAATTGAAA
28306755 CCTCACCGACAAAACA
1 CCTCACCGACAAAACA
28306771 AAAAAGAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
28 27 0.64
29 15 0.36
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.15
Consensus pattern (29 bp):
CCTCACCGACAAAACATTAAAAATTGAAA
Found at i:28307539 original size:47 final size:49
Alignment explanation
Indices: 28307454--28307551 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 49
28307444 CATAGTTTTG
*
28307454 TTAAGTAATATTTATAATATATAGTAGTAAAATTATAAATTTTAGTGTT
1 TTAACTAATATTTATAATATATAGTAGTAAAATTATAAATTTTAGTGTT
*
28307503 TTAACTAATATTTATAA-AT-T-TTAGATAAAATTATAAATTTTAGTGTT
1 TTAACTAATATTTATAATATATAGTAG-TAAAATTATAAATTTTAGTGTT
28307550 TT
1 TT
28307552 TATTTTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
46 3 0.07
47 25 0.54
48 2 0.04
49 16 0.35
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (49 bp):
TTAACTAATATTTATAATATATAGTAGTAAAATTATAAATTTTAGTGTT
Found at i:28308089 original size:13 final size:13
Alignment explanation
Indices: 28308071--28308100 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28308061 AATTAGAAAA
*
28308071 TTTTTTATTTCAT
1 TTTTTTATTCCAT
28308084 TTTTTTATTCCAT
1 TTTTTTATTCCAT
28308097 TTTT
1 TTTT
28308101 ATTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTATTCCAT
Found at i:28308117 original size:19 final size:19
Alignment explanation
Indices: 28308073--28308119 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
28308063 TTAGAAAATT
* *
28308073 TTTTA-TTTCATTTTTTTA
1 TTTTATTTTTATTTTTGTA
**
28308091 TTCCATTTTTATTTTTGTA
1 TTTTATTTTTATTTTTGTA
28308110 TTTTATTTTT
1 TTTTATTTTT
28308120 TCTTATAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTATTTTTATTTTTGTA
Found at i:28308493 original size:23 final size:23
Alignment explanation
Indices: 28308466--28308511 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28308456 AACCCTAAAT
* *
28308466 CCCTAGCTCTTAACCCATAAACC
1 CCCTAACTCCTAACCCATAAACC
*
28308489 CCCTAACTCCTAACCCCTAAACC
1 CCCTAACTCCTAACCCATAAACC
28308512 TTAAACCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.48, G:0.02, T:0.20
Consensus pattern (23 bp):
CCCTAACTCCTAACCCATAAACC
Found at i:28309323 original size:41 final size:41
Alignment explanation
Indices: 28309264--28309417 Score: 211
Period size: 41 Copynumber: 3.8 Consensus size: 41
28309254 TAAAAAAAAT
* **
28309264 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTTAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGATCAGAGC
* **
28309305 ATTAGCGGCGCTTCTTCAAAAATGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGATCAGAGC
* *
28309346 ATTACCGGCGCTTCTTCAAAAACGTCGCTAAAGGAT-AGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAA-GATCAGAGC
*
28309387 ATTAGCGGCGCTTCTTAAAAAACGCCGCTAA
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAA
28309418 GGGCCCCAAA
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 97 0.99
42 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGATCAGAGC
Found at i:28309529 original size:39 final size:38
Alignment explanation
Indices: 28309459--28309532 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
28309449 TGGCTTAGGC
*
28309459 TTTTGCGGCGATTTTCAGAAAACGCCGCTAATGCTAAT
1 TTTTGCGGCGATTTTCAGAAAACGCCACTAATGCTAAT
* *
28309497 TTTTAGCGGCG-TTTTCTGTAAACCGCCACTAATGCT
1 TTTT-GCGGCGATTTTCAG-AAAACGCCACTAATGCT
28309533 CTACCTTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 10 0.32
39 21 0.68
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (38 bp):
TTTTGCGGCGATTTTCAGAAAACGCCACTAATGCTAAT
Found at i:28309582 original size:40 final size:39
Alignment explanation
Indices: 28309459--28309609 Score: 112
Period size: 40 Copynumber: 3.8 Consensus size: 39
28309449 TGGCTTAGGC
28309459 TTTT-GCGGCGATTTTCA-GAAAACGCCGCTAATGCT-AAT
1 TTTTAGCGGCG-TTTT-ATGAAAACGCCGCTAATGCTCAAT
* * * * *
28309497 TTTTAGCGGCGTTTTCTGTAAACCGCCACTAATGCTCTAC
1 TTTTAGCGGCGTTTTATG-AAAACGCCGCTAATGCTCAAT
* * *
28309537 CTTTAGCGGTGTATTTAT-AAAAGCGCCGCTAATGCTCGAT
1 TTTTAGCGGCGT-TTTATGAAAA-CGCCGCTAATGCTCAAT
* * *
28309577 TTTTAGTGGCGTTTTTTGTCCAAACGCCGCTAA
1 TTTTAGCGGCGTTTTATG--AAAACGCCGCTAA
28309610 AAATGCCGCT
Statistics
Matches: 87, Mismatches: 17, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
38 9 0.10
39 28 0.32
40 34 0.39
41 13 0.15
42 3 0.03
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (39 bp):
TTTTAGCGGCGTTTTATGAAAACGCCGCTAATGCTCAAT
Found at i:28310885 original size:47 final size:47
Alignment explanation
Indices: 28310826--28310970 Score: 290
Period size: 47 Copynumber: 3.1 Consensus size: 47
28310816 TTGTTTTTAC
28310826 ATATATTGCAATGATTTATTTATAAATAAATAAATCAAATTAAATAT
1 ATATATTGCAATGATTTATTTATAAATAAATAAATCAAATTAAATAT
28310873 ATATATTGCAATGATTTATTTATAAATAAATAAATCAAATTAAATAT
1 ATATATTGCAATGATTTATTTATAAATAAATAAATCAAATTAAATAT
28310920 ATATATTGCAATGATTTATTTATAAATAAATAAATCAAATTAAATAT
1 ATATATTGCAATGATTTATTTATAAATAAATAAATCAAATTAAATAT
28310967 ATAT
1 ATAT
28310971 TGCAAGGGTT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 98 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (47 bp):
ATATATTGCAATGATTTATTTATAAATAAATAAATCAAATTAAATAT
Found at i:28313704 original size:16 final size:16
Alignment explanation
Indices: 28313680--28313719 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28313670 AAAATTAGAA
* *
28313680 ATATGTAAGCGTGTAT
1 ATATATAAGCATGTAT
*
28313696 ATATATAAGTATGTAT
1 ATATATAAGCATGTAT
28313712 ATATATAA
1 ATATATAA
28313720 AAAAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (16 bp):
ATATATAAGCATGTAT
Found at i:28314682 original size:98 final size:98
Alignment explanation
Indices: 28314488--28314687 Score: 271
Period size: 98 Copynumber: 2.0 Consensus size: 98
28314478 GGGAGATAAG
*
28314488 ATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATGATTTTAATCCATTCCAC
1 ATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATGATTTTAATCCACTCCAC
* *
28314553 TGCAACTTCAGGAAGATAGAATTATCGGCTTCA
66 TACAACTTCAGGAAGATAGAATTATCAGCTTCA
* * *
28314586 ATCTGATGTGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCT-TTATTTTAATCCACTCCA
1 ATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTATGATTTTAATCCACTCCA
* * *
28314650 CTATAACTTCA-GAGAGTTAGGATTA-CTAGCTTCA
65 CTACAACTTCAGGA-AGATAGAATTATC-AGCTTCA
28314684 ATCT
1 ATCT
28314688 ACTCCGTTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
97 3 0.03
98 85 0.94
99 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (98 bp):
ATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATGATTTTAATCCACTCCAC
TACAACTTCAGGAAGATAGAATTATCAGCTTCA
Found at i:28314692 original size:44 final size:44
Alignment explanation
Indices: 28314596--28314980 Score: 142
Period size: 44 Copynumber: 8.8 Consensus size: 44
28314586 ATCTGATGTG
* * * * * *
28314596 ATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTA-TTTTA
1 ATCTACTCCACTATAACTTCAGAGAGATAAGAT-CTCTAGCTTCA
* * *
28314640 ATCCACTCCACTATAACTTCAGAGAGTTAGGAT-TACTAGCTTCA
1 ATCTACTCCACTATAACTTCAGAGAGATAAGATCT-CTAGCTTCA
** * *
28314684 ATCTACTCCGTTATAA-TATCAGGGAGATAAGATCTCTGGCTTCA
1 ATCTACTCCACTATAACT-TCAGAGAGATAAGATCTCTAGCTTCA
* * * * * ** * *
28314728 ATCTGCTCCACTGTAACCTCAGGGATATAAGATCTGAAATTCTTCG
1 ATCTACTCCACTATAACTTCAGAGAGATAAGATCT-CTA-GCTTCA
* * * * * * *
28314774 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGCG
1 ATCTACTCCACTATAACTTCAGAGAGATAAGATCTCTAGCTTCA
* * * * * *
28314815 ATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTA-TTTTA
1 ATCTACTCCACTATAACTTCAGAGAGATAAGAT-CTCTAGCTTCA
** * * * ** **
28314859 ATCCGCTCCACTGTAACTTCAGGGAGATAGGAT-AGT-GTCTTGG
1 ATCTACTCCACTATAACTTCAGAGAGATAAGATCTCTAG-CTTCA
* * * * *
28314902 ATCTGCTCCGCTGTAA-TCTCAGAGAGATAAGATTTCTGGCTTCA
1 ATCTACTCCACTATAACT-TCAGAGAGATAAGATCTCTAGCTTCA
** * * *
28314946 ATCTGTTCCACTGTAACCTCAGGGAGATAAGATCT
1 ATCTACTCCACTATAACTTCAGAGAGATAAGATCT
28314981 GAAATTCTTC
Statistics
Matches: 255, Mismatches: 69, Indels: 34
0.71 0.19 0.09
Matches are distributed among these distances:
41 30 0.12
42 3 0.01
43 33 0.13
44 153 0.60
45 3 0.01
46 33 0.13
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
ATCTACTCCACTATAACTTCAGAGAGATAAGATCTCTAGCTTCA
Found at i:28314990 original size:218 final size:219
Alignment explanation
Indices: 28314588--28314999 Score: 639
Period size: 218 Copynumber: 1.9 Consensus size: 219
28314578 CGGCTTCAAT
* *
28314588 CTGATGTGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTA
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTA
* * *
28314653 TAACTTCAGAGAGTTAGGATTACTAGCTTCAATCTACTCCGTTATAATATCAGGGAGATAAGATC
66 TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTATAATATCAGAGAGATAAGATC
*
28314718 TCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGATATAAGATCTGAAATTCTTCGGTCTACTCC
131 TCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCC
28314783 ACTGTAACCTCAGGGAGATAAGAC
196 ACTGTAACCTCAGGGAGATAAGAC
* * *
28314807 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTA
* * ** * * *
28314872 TAACTTCAGGGAGATAGGA-TAGT-GTCTTGGATCTGCTCCGCTGTAATCTCAGAGAGATAAGAT
66 TAACTTCAGAGAGATAGGATTACTAG-CTTCAATCTACTCCGCTATAATATCAGAGAGATAAGAT
* *
28314935 TTCTGGCTTCAATCTGTTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTC
130 CTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTC
28315000 GTGATTGGAT
Statistics
Matches: 174, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
217 1 0.01
218 96 0.55
219 77 0.44
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (219 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTA
TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTATAATATCAGAGAGATAAGATC
TCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCC
ACTGTAACCTCAGGGAGATAAGAC
Found at i:28316237 original size:16 final size:16
Alignment explanation
Indices: 28316213--28316252 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28316203 AAAATTAGAA
* *
28316213 ATATGTAAGCGTGTAT
1 ATATATAAGCATGTAT
*
28316229 ATATATAAGTATGTAT
1 ATATATAAGCATGTAT
28316245 ATATATAA
1 ATATATAA
28316253 AAAAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (16 bp):
ATATATAAGCATGTAT
Found at i:28317215 original size:98 final size:98
Alignment explanation
Indices: 28317021--28317220 Score: 271
Period size: 98 Copynumber: 2.0 Consensus size: 98
28317011 GGGAGATAAG
*
28317021 ATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATGATTTTAATCCATTCCAC
1 ATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATGATTTTAATCCACTCCAC
* *
28317086 TGCAACTTCAGGAAGATAGAATTATCGGCTTCA
66 TACAACTTCAGGAAGATAGAATTATCAGCTTCA
* * *
28317119 ATCTGATGTGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCT-TTATTTTAATCCACTCCA
1 ATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTATGATTTTAATCCACTCCA
* * *
28317183 CTATAACTTCA-GAGAGTTAGGATTA-CTAGCTTCA
65 CTACAACTTCAGGA-AGATAGAATTATC-AGCTTCA
28317217 ATCT
1 ATCT
28317221 ACTCCGTTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
97 3 0.03
98 85 0.94
99 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (98 bp):
ATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATGATTTTAATCCACTCCAC
TACAACTTCAGGAAGATAGAATTATCAGCTTCA
Found at i:28317448 original size:87 final size:86
Alignment explanation
Indices: 28317330--28318293 Score: 646
Period size: 87 Copynumber: 11.1 Consensus size: 86
28317320 TAACTTTAGA
*
28317330 GAGATAAGATCCTT-TATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGG
1 GAGATAAGAT--TTCTATTTCAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGG
*
28317394 ATCTGCTCCGCTGTAATCTCAGA
64 ATCTGCTCCGCTGTAATCTCAGG
** * * * * *
28317417 GAGATAAGATTTCTGGCTTCAATCTGTTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCT
1 GAGATAAGATTTCT-ATTTCAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTG----TCT
* ** *
28317481 TCGG-TCTACTCTACTGTAACCTCAGG
61 T-GGATCTGCTCCGCTGTAATCTCAGG
* * * ** ** * * * * *
28317507 GAGATAAGA--CCTGA-TGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCA-TTTATTTT
1 GAGATAAGATTTCT-ATTTCAATCCGCTCCACTGTAACTTCAGGGAGATAGGAT-AGTGT-CTTG
* ** *
28317568 AATCCACTCCACTGTAATCTCAGG
63 GATCTGCTCCGCTGTAATCTCAGG
* * * * * * * ** * **
28317592 GAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATTTCAGGGAGATAAGA-CCTG-ATACGA
1 GAGATAAGATTTCTA-TTTCAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGA
* ** *
28317655 TCTACTCTACTGTAA-CTTCAGA
65 TCTGCTCCGCTGTAATC-TCAGG
* *
28317677 GAGATAAGATCCTT-TATTTTAATCCGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTAG-CT
1 GAGATAAGAT--TTCTATTTCAATCCGCTCCACTGTAACT-TCAGGGAGATAGGA-TAGT-GTCT
**
28317739 TCAATCTGCTCCGCTGTAATCTCAGG
61 TGGATCTGCTCCGCTGTAATCTCAGG
* * *
28317765 GAGATAAGATTTTTTATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGA
1 GAGATAAGA-TTTCTATTTCAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGA
28317830 TCTGCTCCGCTGTAATCTCAGG
65 TCTGCTCCGCTGTAATCTCAGG
* * *
28317852 GAGATAAGATTTTTTATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGA
1 GAGATAAGA-TTTCTATTTCAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGA
28317917 TCTGCTCCGCTGTAATCTCAGG
65 TCTGCTCCGCTGTAATCTCAGG
* ** * * * * ** * **
28317939 GAGATAAGATCTCTGGCTTCAATCTGCTCCGCTCTAA-TCTCAGGGAGATAAGA-CCTG-ATACG
1 GAGATAAGATTTCT-ATTTCAATCCGCTCCACTGTAACT-TCAGGGAGATAGGATAGTGTCTTGG
* *** *
28318001 ATCTACTCTAATGTAA-CTTCAGA
64 ATCTGCTCCGCTGTAATC-TCAGG
* *
28318024 GAGATAAGATCCTT-TATTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTGG
1 GAGATAAGAT--TTCTATTTCAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGG
28318088 ATCTGCTCCGCTGTAATCTCAGG
64 ATCTGCTCCGCTGTAATCTCAGG
* * ** ** * * *
28318111 GAGATAAGA-TCCGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTAATG--
1 GAGATAAGATTTC--TA-T-TTCAATCCGCTCCACTGTAACTTCAGGGAGATAGGA--TAGTGTC
* ** *
28318173 -T-GATCTACTCTACTGTAA-CTTCAGA
60 TTGGATCTGCTCCGCTGTAATC-TCAGG
* *
28318198 GAGATGAGATCCTT-TATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGG
1 GAGATAAGAT--TTCTATTTCAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGG
28318262 ATCTGCTCCGCTGTAATCTCAGG
64 ATCTGCTCCGCTGTAATCTCAGG
28318285 GAGATAAGA
1 GAGATAAGA
28318294 CCTGATAAGA
Statistics
Matches: 688, Mismatches: 136, Indels: 106
0.74 0.15 0.11
Matches are distributed among these distances:
83 4 0.01
84 5 0.01
85 174 0.25
86 20 0.03
87 314 0.46
88 103 0.15
89 31 0.05
90 31 0.05
91 6 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (86 bp):
GAGATAAGATTTCTATTTCAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGAT
CTGCTCCGCTGTAATCTCAGG
Found at i:28317503 original size:46 final size:46
Alignment explanation
Indices: 28317266--28317520 Score: 156
Period size: 46 Copynumber: 5.7 Consensus size: 46
28317256 CTTCAATCTG
*
28317266 CTCCACTGTAACCTCAGGGATATAAGATCTGAAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
* * * * ** ** **
28317312 CTCTACTGTAACTTTAGAGAGATAAGATCCT-TTATT-TT-AATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTCGGTCTA
* * * *
28317356 CTCCACTGTAACTTCAGGGAGATAGGA--T--AGTGTCTT-GGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTCGG-TCTA
* * * * ** *
28317399 CTCCGCTGTAATCTCAGAGAGATAAGATTTCTG----GCTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGA--TCTGAAATTCTTCGGTCTA
*
28317443 TTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
* *
28317489 CTCTACTGTAACCTCAGGGAGATAAGACCTGA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGA
28317521 TGCGATCTAC
Statistics
Matches: 156, Mismatches: 39, Indels: 28
0.70 0.17 0.13
Matches are distributed among these distances:
40 1 0.01
41 2 0.01
42 6 0.04
43 25 0.16
44 55 0.35
45 2 0.01
46 62 0.40
47 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (46 bp):
CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
Found at i:28317552 original size:41 final size:42
Alignment explanation
Indices: 28317129--28318814 Score: 367
Period size: 44 Copynumber: 38.8 Consensus size: 42
28317119 ATCTGATGTG
* * * *
28317129 ATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTA
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCC-TGA-TTCA
* * * * * * * *
28317173 ATCCACTCCACTATAACTTCAGAGAGTTAGGATTACTAGCTTCA
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGA-TCCT-GATTCA
*** * *
28317217 ATCTACTCCGTTATAA-TATCAGGGAGATAAGATCTCTGGCTTCA
1 ATCTACTCTACTGTAACT-TCAGGGAGATAAGATC-CT-GATTCA
* * * * *
28317261 ATCTGCTCCACTGTAACCTCAGGGATATAAGAT-CTGAAATTCTTCG
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTG--A---TTCA
* * * * *
28317307 GTCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTA
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCC-TGA-TTCA
** * * ** * **
28317351 ATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGG
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTG-ATTCA
* ** * * *
28317394 ATCTGCTCCGCTGTAA-TCTCAGAGAGATAAGATTTCTGGCTTCA
1 ATCTACTCTACTGTAACT-TCAGGGAGATAAGA-TCCT-GATTCA
** * * *
28317438 ATCTGTTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTCG
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTG--A---TTCA
* * * *
28317484 GTCTACTCTACTGTAACCTCAGGGAGATAAGA-CCTGATGCG
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTGATTCA
* * * * *
28317525 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATCATTTATTTTA
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATC-CTGA-TTCA
* * * * *
28317569 ATCCACTCCACTGTAA-TCTCAGGGAGATAGGATTACTAGCTTCA
1 ATCTACTCTACTGTAACT-TCAGGGAGATAAGA-TCCT-GATTCA
* ** * * *
28317613 ATCTGCTCCGCTGTAATTTCAGGGAGATAAGA-CCTGATACG
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTGATTCA
* * *
28317654 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCC-TGA-TTCA
** * * * *
28317698 ATCCGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTAGCTTCA
1 ATCTACTCTACTGTAACT-TCAGGGAGATAAGA-TCCT-GATTCA
* ** ** * *
28317742 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATTTTTTATTTTA
1 ATCTACTCTACTGTAACT-TCAGGGAGATAAGA-TCCTGA-TTCA
* * * ** * **
28317786 ATCCACTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGG
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTG-ATTCA
* ** ** * *
28317829 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATTTTTTATTTTA
1 ATCTACTCTACTGTAACT-TCAGGGAGATAAGA-TCCTGA-TTCA
* * * ** * **
28317873 ATCCACTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGG
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTG-ATTCA
* ** *
28317916 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCA
1 ATCTACTCTACTGTAACT-TCAGGGAGATAAGATC-CT-GATTCA
* ** * * *
28317960 ATCTGCTCCGCTCTAA-TCTCAGGGAGATAAGA-CCTGATACG
1 ATCTACTCTACTGTAACT-TCAGGGAGATAAGATCCTGATTCA
* * * *
28318001 ATCTACTCTAATGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCC-TGA-TTCA
** * * * ** * **
28318045 ATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTGG
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTG-ATTCA
* ** *
28318088 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCC-GAAATTCTTCG
1 ATCTACTCTACTGTAACT-TCAGGGAGATAAGATCCTG--A---TTCA
* * * * *
28318134 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-CCTAATGT-G
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTGAT-TCA
* * * *
28318175 ATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTA
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCC-TGA-TTCA
** * * ** * **
28318219 ATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGG
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTG-ATTCA
* ** *
28318262 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGA-CCTGA-TAA
1 ATCTACTCTACTGTAACT-TCAGGGAGATAAGATCCTGATTCA
* * *
28318302 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 -ATCTACTCTACTGTAACTTCAGGGAGATAAGATCC-TGA-TTCA
** * ** *
28318347 ATCCGCTCCACTGTAACTTCAGGGAGAT-AGAATAGTG-TCTTA
1 ATCTACTCTACTGTAACTTCAGGGAGATAAG-ATCCTGAT-TCA
* * * *
28318389 GATCTGCTCCACTATAA-TCTCAGGGAGATAAGATCTCTAGCTTCA
1 -ATCTACTCTACTGTAACT-TCAGGGAGATAAGATC-CT-GATTCA
* * * * * *
28318434 ATCTGCTCCACTATAACCTCAGAGAGATAAGAT-CTGAAATTCTTCG
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTG--A---TTCA
* * * * * * *
28318480 GTCTATTCCACTGTAGCTTCAGGGAGATAAGA-CTTGATGCG
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTGATTCA
* * ** * *
28318521 ATCTACT-TGCTGGAACTTCAAAGAGATAAGATCCTTTATTTTA
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCC-TGA-TTCA
** * * * * *
28318564 ATCCGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTAGCTTTA
1 ATCTACTCTACTGTAACT-TCAGGGAGATAAGA-TCCT-GATTCA
* * * * *
28318608 ATCTGCT-TCGCTGTAA-TCTCAGAGAGATAAGA-CCTGATACG
1 ATCTACTCT-ACTGTAACT-TCAGGGAGATAAGATCCTGATTCA
* ** * *
28318649 ATCTACTCTACTGTAACTTTAAAGAGATAAGATCCTTTATTTTA
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATCC-TGA-TTCA
** * * * * * *
28318693 ATCCGCTCCACTATAA-TCTCAGGGAGATAGGGTTACTAGCTTCA
1 ATCTACTCTACTGTAACT-TCAGGGAGATA-AGATCCT-GATTCA
* ** *
28318737 ATCTGCTCCGCTGTAATCTT-AGGGAGATAAGATCTCTGGCTTCA
1 ATCTACTCTACTGTAA-CTTCAGGGAGATAAGATC-CT-GATTCA
* * * *
28318781 ATCTGCTCCACTGTAACCTCAGAGAGATAAGATC
1 ATCTACTCTACTGTAACTTCAGGGAGATAAGATC
28318815 TGAAATTTTT
Statistics
Matches: 1211, Mismatches: 324, Indels: 214
0.69 0.19 0.12
Matches are distributed among these distances:
40 19 0.02
41 182 0.15
42 42 0.03
43 210 0.17
44 607 0.50
45 23 0.02
46 126 0.10
47 1 0.00
48 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (42 bp):
ATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTGATTCA
Found at i:28318228 original size:174 final size:173
Alignment explanation
Indices: 28317124--28318639 Score: 1235
Period size: 174 Copynumber: 8.7 Consensus size: 173
28317114 CTTCAATCTG
* * *
28317124 ATGTGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAA
1 ATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
* * * * * * *
28317189 CTTCAGAGAGTTAGGATTACTAG-CTTCAATCTACTCCGTTATAATATCAGGGAGATAAGATCTC
66 CTTCAGGGAGATAGGA-TACT-GTCTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC-C
* * *
28317253 --TGGCTTCAATCTGCTCCACTGTAACCTCAGGGATATAAGATCTGAA
128 AATGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCT--A
* * *
28317299 ATTCTTCGGTCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 A-T-GT-GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * * *
28317364 TAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGAGAGATAAGATTT
63 TAACTTCAGGGAGATAGGATACTGTCTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-TC
** *
28317429 C--TGGCTTCAATCTGTTCCACTGTAACCTCAGGGAGATAAGATCTGAA
127 CAATGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCT--A
* * * * * *** ** **
28317476 ATTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGA-CC-TGA-TGCGATCTACTCTGCTG
1 A-T-GT-GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * * * * ** * *
28317538 TAACTTCAGAGAGATAAGAT-CATTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGAT
63 TAACTTCAGGGAGATAGGATAC-TGT-CTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
* * * * * ** *
28317602 -TACTAGCTTCAATCTGCTCCGCTGTAATTTCAGGGAGATAAGACCTG
126 CCAATGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTA
**
28317649 ATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
1 ATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
* *
28317714 -TCTCAGGGAGATAGGATTACTAG-CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-T
66 CT-TCAGGGAGATAGGA-TACT-GTCTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCC
** *** * * * *
28317776 TTTTATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGA--TA
128 AATGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTA
* * ** * ** *
28317820 GTGTCTTGGATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATTTTTTATTTTAATCCACTCCAC
1 ATG---T-GATCTACTCTACTGTAACT-TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCAC
* *
28317884 TGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
61 TGTAACTTCAGGGAGATAGGATACTGTCTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
* * * * *
28317949 CTC--TGGCTTCAATCTGCTCCGCTCTAATCTCAGGGAGATAAGACCTG
126 C-CAATGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTA
** *
28317996 ATACGATCTACTCTAATGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
1 ATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
* * *
28318061 CTTCAAGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCGAA
66 CTTCAGGGAGATAGGATACTGTCTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCC--A
* **
28318126 AT-TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTA
129 ATGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTA
*
28318170 ATGTGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAATCCGCTCCACTGTAA
1 ATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
* *
28318235 CTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-CC--T
66 CTTCAGGGAGATAGGATACTGTCTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCAAT
* * * * *
28318297 -G-ATAAGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTA
131 GGCTTCA-ATCTACTCCACTGTAACCTCAGGGAGATAAGA-CC--TA
* * * ** * * ** * * * *
28318342 TTTTAATCCGCTCCACTGTAACTTCAGGGAGAT-AGAAT--AGTGTCTTAGATCTGCTCCACTAT
1 ATGTGATCTACTCTACTGTAACTTCAGAGAGATAAG-ATCCTTTATTTTA-ATCCGCTCCACTGT
* * * * * * *
28318404 AA-TCTCAGGGAGATAAGAT-CTCTAGCTTCAATCTGCTCCACTATAACCTCAGAGAGATAAGAT
64 AACT-TCAGGGAGATAGGATACTGT--CTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
* * ** * * * * *
28318467 CTGAAAT-TCTTCGGTCTATTCCACTGTAGCTTCAGGGAGATAAGACTTG
126 C--CAATGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTA
* * * *
28318516 ATGCGATCTACT-TGCTGGAACTTCAAAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
1 ATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
* * *
28318580 -TCTCAGGGAGATAGGATTACTAG-CTTTAATCTGCTTCGCTGTAATCTCAGAGAGATAAGA
66 CT-TCAGGGAGATAGGA-TACT-GTCTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
28318640 CCTGATACGA
Statistics
Matches: 1089, Mismatches: 199, Indels: 107
0.78 0.14 0.08
Matches are distributed among these distances:
168 1 0.00
169 29 0.03
170 40 0.04
171 35 0.03
172 176 0.16
173 112 0.10
174 325 0.30
175 143 0.13
176 10 0.01
177 144 0.13
178 74 0.07
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (173 bp):
ATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
CTTCAGGGAGATAGGATACTGTCTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCAAT
GGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTA
Found at i:28318580 original size:302 final size:300
Alignment explanation
Indices: 28317939--28318592 Score: 769
Period size: 302 Copynumber: 2.2 Consensus size: 300
28317929 TAATCTCAGG
* * * * *
28317939 GAGATAAGATCTCTGGCTTCAATCTGCTCCGCTCTAATCTCAGGGAGATAAGACCTGATACGATC
1 GAGATAAGAT-ACTGTCTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATAAGATC
28318004 TACTCTAATGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAAGG
65 TACTCTAATGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAAGG
* * * * * *
28318069 AGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCGAAATTCTTCG
130 AGATAGAATAGTGTCTTAGATCTGCTCCACTATAATCTCAGGGAGATAAGATCC-AAATGCTTCA
* * * *
28318134 GTCTACTCCACTGTAACCTCAGGGAGATAAGACCTAATGTGATCTACTCTACTGTAACTTCAGAG
194 ATCTACTCCACTATAACCTCAGAGAGATAAGACCTAATGTGATCTACTCCACTGTAACTTCAGAG
* * ** * * **
28318199 AGATGAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGG
259 AGATAAGA-CCTTGATTGCAATCCACTCCACTGGAACTTCAAA
* * *
28318242 GAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATAAGATCT
1 GAGATAAGATACTGTCTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATAAGATCT
* *
28318307 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGA
66 ACTCTAATGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAAGGA
*
28318372 GATAGAATAGTGTCTTAGATCTGCTCCACTATAATCTCAGGGAGATAAGATCTC-TA-GCTTCAA
131 GATAGAATAGTGTCTTAGATCTGCTCCACTATAATCTCAGGGAGATAAGATC-CAAATGCTTCAA
* * * * * *
28318435 TCTGCTCCACTATAACCTCAGAGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAGCTTC
195 TCTACTCCACTATAACCTCAGAGAGATAAGACCT--AA-T-GT-GATCTACTCCACTGTAACTTC
* * * **
28318500 AGGGAGATAAGA-CTTGA-TGCGATCTACT-TGCTGGAACTTCAAA
255 AGAGAGATAAGACCTTGATTGCAATCCACTCCACTGGAACTTCAAA
* * * * * *
28318543 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATA
1 GAGATAAGATACTGT-CTTGAATCTGCTCCGCTGTAATCTCAGGGAGATA
28318593 GGATTACTAG
Statistics
Matches: 295, Mismatches: 49, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
300 34 0.12
301 22 0.07
302 196 0.66
303 15 0.05
304 1 0.00
305 27 0.09
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (300 bp):
GAGATAAGATACTGTCTTGAATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATAAGATCT
ACTCTAATGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAAGGA
GATAGAATAGTGTCTTAGATCTGCTCCACTATAATCTCAGGGAGATAAGATCCAAATGCTTCAAT
CTACTCCACTATAACCTCAGAGAGATAAGACCTAATGTGATCTACTCCACTGTAACTTCAGAGAG
ATAAGACCTTGATTGCAATCCACTCCACTGGAACTTCAAA
Found at i:28318645 original size:346 final size:347
Alignment explanation
Indices: 28318088--28318835 Score: 1105
Period size: 346 Copynumber: 2.2 Consensus size: 347
28318078 AGTGTCTTGG
* * * * *
28318088 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCGAAATTCTTCGGTCTACTCCACTGTAACCT
1 ATCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAACCT
* * * *
28318153 CAGGGAGATAAGACCTAATGTGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTT
66 CAGGGAGATAAGACCTAATGCGATCTACTCTACTGGAACTTCAAAGAGATAAGATCCTTTATTTT
* *
28318218 AATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCA
131 AATCCGCTCCACTGTAACTTCAGGGAGATAGGATACTGTCTTGAATCTGCTCCGCTGTAATCTCA
* *
28318283 GGGAGATAAGACCTGATAAGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAA
196 GAGAGATAAGACCTGATAAGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTTTATTTTAA
* *
28318348 TCCGCTCCACTGTAA-CTTCAGGGAGATA-GAATAGT-GTCTT-AGATCTGCTCCACTATAATCT
261 TCCGCTCCACTATAATC-TCAGGGAGATAGGAATACTAG-CTTCA-ATCTGCTCCACTATAATCT
28318409 CAGGGAGATAAGATCTCTAGCTTCA
323 CAGGGAGATAAGATCTCTAGCTTCA
* * *
28318434 ATCTGCTCCACTATAACCTCAGAGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAGCTT
1 ATCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAACCT
* * *
28318499 CAGGGAGATAAGACTTGATGCGATCTACT-TGCTGGAACTTCAAAGAGATAAGATCCTTTATTTT
66 CAGGGAGATAAGACCTAATGCGATCTACTCTACTGGAACTTCAAAGAGATAAGATCCTTTATTTT
* *
28318563 AATCCGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTAG-CTTTAATCTGCTTCGCTGTAATC
131 AATCCGCTCCACTGTAACT-TCAGGGAGATAGGA-TACT-GTCTTGAATCTGCTCCGCTGTAATC
* *
28318626 TCAGAGAGATAAGACCTGATACGATCTACTCTACTGTAACTTTAAAGAGATAAGATCCTTTATTT
193 TCAGAGAGATAAGACCTGATAAGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTTTATTT
** * *
28318691 TAATCCGCTCCACTATAATCTCAGGGAGATAGGGTTACTAGCTTCAATCTGCTCCGCTGTAATCT
258 TAATCCGCTCCACTATAATCTCAGGGAGATAGGAATACTAGCTTCAATCTGCTCCACTATAATCT
* *
28318756 TAGGGAGATAAGATCTCTGGCTTCA
323 CAGGGAGATAAGATCTCTAGCTTCA
*
28318781 ATCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGAAATTTTTCGGTCTATTCC
1 ATCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGAAATTCTTCGGTCTATTCC
28318836 CTGGGGAACA
Statistics
Matches: 362, Mismatches: 33, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
344 1 0.00
345 62 0.17
346 195 0.54
347 102 0.28
348 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (347 bp):
ATCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAACCT
CAGGGAGATAAGACCTAATGCGATCTACTCTACTGGAACTTCAAAGAGATAAGATCCTTTATTTT
AATCCGCTCCACTGTAACTTCAGGGAGATAGGATACTGTCTTGAATCTGCTCCGCTGTAATCTCA
GAGAGATAAGACCTGATAAGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTTTATTTTAA
TCCGCTCCACTATAATCTCAGGGAGATAGGAATACTAGCTTCAATCTGCTCCACTATAATCTCAG
GGAGATAAGATCTCTAGCTTCA
Found at i:28318691 original size:129 final size:128
Alignment explanation
Indices: 28318498--28318768 Score: 434
Period size: 129 Copynumber: 2.1 Consensus size: 128
28318488 CACTGTAGCT
* * *
28318498 TCAGGGAGATAAGACTTGATGCGATCTACTTGCTGGAACTTCAAAGAGATAAGATCCTTTATTTT
1 TCAGGGAGATAAGACCTGATACGATCTACTTACTGGAACTTCAAAGAGATAAGATCCTTTATTTT
* * *
28318563 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTTAATCTGCTTCGCTGTAATC
66 AATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
* * *
28318626 TCAGAGAGATAAGACCTGATACGATCTACTCTACTGTAACTTTAAAGAGATAAGATCCTTTATTT
1 TCAGGGAGATAAGACCTGATACGATCTACT-TACTGGAACTTCAAAGAGATAAGATCCTTTATTT
*
28318691 TAATCCGCTCCACTATAATCTCAGGGAGATAGGGTTACTAGCTTCAATCTGCTCCGCTGTAATC
65 TAATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
*
28318755 TTAGGGAGATAAGA
1 TCAGGGAGATAAGA
28318769 TCTCTGGCTT
Statistics
Matches: 130, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
128 27 0.21
129 103 0.79
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (128 bp):
TCAGGGAGATAAGACCTGATACGATCTACTTACTGGAACTTCAAAGAGATAAGATCCTTTATTTT
AATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
Found at i:28320952 original size:15 final size:16
Alignment explanation
Indices: 28320932--28320966 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
28320922 CTCCTTTTTC
28320932 TTTTCTTTTTCTCTT-
1 TTTTCTTTTTCTCTTA
28320947 TTTTCTTTTTCTCTTA
1 TTTTCTTTTTCTCTTA
28320963 TTTT
1 TTTT
28320967 TGACTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCTTTTTCTCTTA
Found at i:28321035 original size:25 final size:26
Alignment explanation
Indices: 28320976--28321043 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 26
28320966 TTGACTTTGA
*
28320976 TTGATTTTTCTTTTTTTGCTTTTGCTT
1 TTGATTTTTC-TTTTTTGCTTTTCCTT
28321003 TTGATTTTTCTTTTTT-CTTTTCCTT
1 TTGATTTTTCTTTTTTGCTTTTCCTT
28321028 CTT--TTTTTACTTTTTT
1 -TTGATTTTT-CTTTTTT
28321044 ATAGAATCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
24 5 0.13
25 15 0.39
26 8 0.21
27 10 0.26
ACGTcount: A:0.04, C:0.13, G:0.06, T:0.76
Consensus pattern (26 bp):
TTGATTTTTCTTTTTTGCTTTTCCTT
Found at i:28325512 original size:16 final size:16
Alignment explanation
Indices: 28325488--28325527 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28325478 AAAATTAGAA
* *
28325488 ATATGTAAGCGTGTAT
1 ATATATAAGCATGTAT
*
28325504 ATATATAAGTATGTAT
1 ATATATAAGCATGTAT
28325520 ATATATAA
1 ATATATAA
28325528 CAAAATCTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (16 bp):
ATATATAAGCATGTAT
Found at i:28325546 original size:23 final size:21
Alignment explanation
Indices: 28325520--28325562 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
28325510 AAGTATGTAT
*
28325520 ATATATAACAAAATCTAGAAA
1 ATATATAACAAAATCTAAAAA
28325541 ATATATAACAAAATCTAAAAA
1 ATATATAACAAAATCTAAAAA
28325562 A
1 A
28325563 CGATATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.23
Consensus pattern (21 bp):
ATATATAACAAAATCTAAAAA
Found at i:28329585 original size:4 final size:4
Alignment explanation
Indices: 28329576--28329633 Score: 107
Period size: 4 Copynumber: 14.5 Consensus size: 4
28329566 ATCCTTTTCT
*
28329576 CATA CATA CATA CATA CATG CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
28329624 CATA CATA CA
1 CATA CATA CA
28329634 CGCATGCATG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:28332009 original size:21 final size:21
Alignment explanation
Indices: 28331984--28332038 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
28331974 GCTTTTGTGG
28331984 TTGTACTTGTTTTTGATGAAC
1 TTGTACTTGTTTTTGATGAAC
28332005 TTGTACTTGTTTTTGATGAAC
1 TTGTACTTGTTTTTGATGAAC
*
28332026 TTGAACTTGTTTT
1 TTGTACTTGTTTT
28332039 CGATTTTACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (21 bp):
TTGTACTTGTTTTTGATGAAC
Found at i:28332075 original size:7 final size:7
Alignment explanation
Indices: 28332065--28332090 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28332055 ATCAAAATCC
28332065 AAAAATA
1 AAAAATA
28332072 AAAAATA
1 AAAAATA
28332079 AAAAATA
1 AAAAATA
28332086 AAAAA
1 AAAAA
28332091 AGACAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:28333047 original size:29 final size:29
Alignment explanation
Indices: 28332983--28333052 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
28332973 ACTACTAAAA
*
28332983 TAGTCACTTTTGTTTGACTCAAGTTACATTT
1 TAGTCACTTATGTTTGA--CAAGTTACATTT
*
28333014 TAGTCACTTATGTTTGA-AATGTTACGTTT
1 TAGTCACTTATGTTTGACAA-GTTACATTT
28333043 TAGTCACTTA
1 TAGTCACTTA
28333053 CGTTATCGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 2 0.06
29 18 0.50
31 16 0.44
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATGTTTGACAAGTTACATTT
Found at i:28334007 original size:27 final size:27
Alignment explanation
Indices: 28333959--28334011 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28333949 GGATTTGGTG
28333959 GTGCCTTCCTGAAAGGTGGCACCAGTT
1 GTGCCTTCCTGAAAGGTGGCACCAGTT
* *
28333986 GTGCCTTCTTGACAGGCT-GCACCAGT
1 GTGCCTTCCTGAAAGG-TGGCACCAGT
28334012 CTGATTAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.26
Consensus pattern (27 bp):
GTGCCTTCCTGAAAGGTGGCACCAGTT
Found at i:28335609 original size:13 final size:13
Alignment explanation
Indices: 28335591--28335615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28335581 TTGGATCTGT
28335591 ACCAAAACAATCC
1 ACCAAAACAATCC
28335604 ACCAAAACAATC
1 ACCAAAACAATC
28335616 ATGAAACATA
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:0.56, C:0.36, G:0.00, T:0.08
Consensus pattern (13 bp):
ACCAAAACAATCC
Found at i:28336475 original size:42 final size:43
Alignment explanation
Indices: 28336375--28336539 Score: 140
Period size: 43 Copynumber: 3.9 Consensus size: 43
28336365 AGCTCGTACA
* * * * *
28336375 ATGCCAACGTCCCAGA-CGAGGTCTTACATGTAATCAAATGTCG
1 ATGCCAACGTCCCAGATAGAGGTCTTACACGAAATCATAT-ACG
***
28336418 ATGCCATTATCCCAGATAG-GGTCTTACACGAAATCATATACG
1 ATGCCAACGTCCCAGATAGAGGTCTTACACGAAATCATATACG
* * * * *
28336460 ATGCCAATGTCCCAGACA-TGGTCTTACACGTAAATCTTAAATCG
1 ATGCCAACGTCCCAGATAGAGGTCTTACACG-AAATCATATA-CG
* *
28336504 ATGCCAACGTCCCAGAT-GTGGTCTTACACAAAATCA
1 ATGCCAACGTCCCAGATAGAGGTCTTACACGAAATCA
28336540 CATATCAGAA
Statistics
Matches: 100, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 28 0.28
43 43 0.43
44 29 0.29
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGATAGAGGTCTTACACGAAATCATATACG
Found at i:28336527 original size:86 final size:84
Alignment explanation
Indices: 28336375--28336539 Score: 201
Period size: 86 Copynumber: 1.9 Consensus size: 84
28336365 AGCTCGTACA
* **
28336375 ATGCCAACGTCCCAGACGAGGTCTTACATGTAATCAAATGTCGATGCCATTATCCCAGATAGGGT
1 ATGCCAACGTCCCAGACGAGGTCTTACACGTAATCAAA-GTCGATGCCAACATCCCAGATAGGGT
*
28336440 CTTACACGAAATCATATACG
65 CTTACACAAAATCATATACG
* *
28336460 ATGCCAATGTCCCAGAC-ATGGTCTTACACGTAAATCTTAAA-TCGATGCCAACGTCCCAGAT-G
1 ATGCCAACGTCCCAGACGA-GGTCTTACACGT-AATC--AAAGTCGATGCCAACATCCCAGATAG
28336522 TGGTCTTACACAAAATCA
62 -GGTCTTACACAAAATCA
28336540 CATATCAGAA
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
84 1 0.01
85 28 0.41
86 37 0.54
88 3 0.04
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACGAGGTCTTACACGTAATCAAAGTCGATGCCAACATCCCAGATAGGGTC
TTACACAAAATCATATACG
Found at i:28337884 original size:22 final size:22
Alignment explanation
Indices: 28337859--28337912 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
28337849 AAACTGTTTA
*
28337859 GTATTTTTTTAATGATATTATT
1 GTATTTTATTAATGATATTATT
* **
28337881 GTATGTTATTAATTTTATTATT
1 GTATTTTATTAATGATATTATT
*
28337903 -TATTGTATTA
1 GTATTTTATTA
28337913 TATTTATGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (22 bp):
GTATTTTATTAATGATATTATT
Found at i:28341216 original size:15 final size:15
Alignment explanation
Indices: 28341198--28341231 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28341188 AATATATAAT
28341198 ATAATAAAAAAAATA
1 ATAATAAAAAAAATA
* *
28341213 ATAATAACAAAATTA
1 ATAATAAAAAAAATA
28341228 ATAA
1 ATAA
28341232 AATAGACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAATAAAAAAAATA
Found at i:28341478 original size:19 final size:21
Alignment explanation
Indices: 28341440--28341480 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
28341430 CCTTTTTTAA
*
28341440 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
28341461 AATCG-AAA-AAGAAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
28341480 A
1 A
28341481 GTAAGCCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 3 0.16
21 5 0.26
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:28341694 original size:19 final size:19
Alignment explanation
Indices: 28341647--28341723 Score: 91
Period size: 19 Copynumber: 3.8 Consensus size: 19
28341637 AAATTAAATC
*
28341647 TCTAAGATTACAAAATCTTATA
1 TCTAAGATTAC-ATATC--ATA
28341669 TTCTAAGATTACATATCATA
1 -TCTAAGATTACATATCATA
*
28341689 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
28341708 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
28341724 CTCGAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
20 3 0.06
22 4 0.08
23 11 0.21
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:28341733 original size:17 final size:18
Alignment explanation
Indices: 28341673--28341733 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
28341663 CTTATATTCT
* *
28341673 AAGATTACATATCATATCT
1 AAGATTGCATATCA-ATCG
*
28341692 AAGATTGCATATCATATCT
1 AAGATTGCATATCA-ATCG
*
28341711 AAGATTGCATATC-CTCG
1 AAGATTGCATATCAATCG
28341728 AAGATT
1 AAGATT
28341734 ATGTTTCCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
17 8 0.21
19 31 0.79
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (18 bp):
AAGATTGCATATCAATCG
Found at i:28342592 original size:44 final size:44
Alignment explanation
Indices: 28342520--28342895 Score: 401
Period size: 44 Copynumber: 8.7 Consensus size: 44
28342510 GTTATTTTCC
* * * * *
28342520 ACCTACTCCACTACT-ACTCAGAGAGATAGGGTTCACGATCTTCA
1 ACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTCA
* * *
28342564 ACCTATTTCACTGTTGACCAGGGAGATAGGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATCTTCA
* * * *
28342608 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* *
28342652 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCATAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* *
28342696 ACCTATTCCACTGCTGTCTAGGGAGATAGGATT--C--T-TT-A
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * *
28342734 ATCTATTCCACTGCT-ACCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGA-CCAGGGAGATAGGATTCACAATCTTCA
* * *
28342778 ACCTATTCCACTACTGACCAGTGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * * *
28342822 ACCTATTCCACTGTTGTCCAGGGAGATAGGATTCACAATATTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
** *
28342866 ACCTATAACACTGTTGACCAGGGAGATAGG
1 ACCTATTCCACTGCTGACCAGGGAGATAGG
28342896 GCTGGGGTCA
Statistics
Matches: 279, Mismatches: 42, Indels: 22
0.81 0.12 0.06
Matches are distributed among these distances:
38 29 0.10
39 2 0.01
40 2 0.01
42 1 0.00
43 3 0.01
44 238 0.85
45 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (44 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
Found at i:28342782 original size:126 final size:126
Alignment explanation
Indices: 28342520--28342855 Score: 467
Period size: 126 Copynumber: 2.6 Consensus size: 126
28342510 GTTATTTTCC
* * * * * * * *
28342520 ACCTACTCCACTACT-ACTCAGAGAGATAGGGTTCACGATCTTCAACCTATTTCACTGTTGACCA
1 ACCTATTCCACTACTGAC-CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCA
*
28342584 GGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCT
65 GGGAGATAGGA--T----TCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTCTCAATCT
28342649 TCA
124 TCA
* * *
28342652 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCATAATCTTTAACCTATTCCACTGCTGTCTAG
1 ACCTATTCCACTACTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
*
28342717 GGAGATAGGATTCTTTAATCTATTCCACTGCTACCCAGGGAGATAGAATTCTCAATCTTCA
66 GGAGATAGGATTCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTCTCAATCTTCA
* *
28342778 ACCTATTCCACTACTGACCAGTGAGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCCAG
1 ACCTATTCCACTACTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
28342843 GGAGATAGGATTC
66 GGAGATAGGATTC
28342856 ACAATATTTA
Statistics
Matches: 185, Mismatches: 18, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
126 121 0.65
130 1 0.01
132 61 0.33
133 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (126 bp):
ACCTATTCCACTACTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
GGAGATAGGATTCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTCTCAATCTTCA
Found at i:28342786 original size:170 final size:170
Alignment explanation
Indices: 28342581--28342895 Score: 452
Period size: 170 Copynumber: 1.9 Consensus size: 170
28342571 TCACTGTTGA
* * * * *
28342581 CCAGGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAA
1 CCAGGGAGATAGAACCTACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGAATTCACAA
* * **
28342646 TCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCATAATCTTTAACCTATTCCACTGCT
66 TCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATATTTAACCTATAACACTGCT
* *
28342711 GTCTAGGGAGATAGGATTCTTTAATCTATTCCACTGCTAC
131 GACCAGGGAGATAGGATTCTTTAATCTATTCCACTGCTAC
* * *
28342751 CCAGGGAGATAGAATTCT-CAATCTTCAACCTATTCCACTACTGACCAGTGAGATAGGATTCACA
1 CCAGGGAGATAGAA-CCTACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGAATTCACA
* * * *
28342815 ATCTTTAACCTATTCCACTGTTGTCCAGGGAGATAGGATTCACAATATTTAACCTATAACACTGT
65 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATATTTAACCTATAACACTGC
28342880 TGACCAGGGAGATAGG
130 TGACCAGGGAGATAGG
28342896 GCTGGGGTCA
Statistics
Matches: 126, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
170 124 0.98
171 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (170 bp):
CCAGGGAGATAGAACCTACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGAATTCACAA
TCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATATTTAACCTATAACACTGCT
GACCAGGGAGATAGGATTCTTTAATCTATTCCACTGCTAC
Found at i:28342975 original size:88 final size:88
Alignment explanation
Indices: 28342895--28343384 Score: 593
Period size: 88 Copynumber: 5.6 Consensus size: 88
28342885 AGGGAGATAG
* * * * * * *
28342895 GGCTGGGGTCATCAATCTACTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTAC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
* *
28342960 TCCATTGTAACCCAGGGAGGCAA
66 TCCACTGCAACCCAGGGAGGCAA
* * * * * *
28342983 AGCTGGTGTCTTCGATCTACTTCGCTGTCAGTGCTGGAAAGAAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
28343048 TCCACTGCAACCCAGGGAGGCAA
66 TCCACTGCAACCCAGGGAGGCAA
* * * *
28343071 GGCTGGTGACTTCGATCTGCTTCGTTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTCAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
* *
28343136 TCCGCTGCAACCCAAGGAGGCAA
66 TCCACTGCAACCCAGGGAGGCAA
* * * * * * *
28343159 GGCTGGTATCTTCGATCTGCTTCGCTGTAGGTGCAAGAAGGCAAGATTTACTATTTTCAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
*
28343224 TCCGCTGCAACCCAGGGAGGCAA
66 TCCACTGCAACCCAGGGAGGCAA
* * * *
28343247 GACTGGTGTCTTCGACCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAGCCTAC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
* * **
28343312 TCCGCTGCCACTAAGGGAGGCAA
66 TCCACTGCAACCCAGGGAGGCAA
* ** * **
28343335 GGCTAGTGTCTTCGATCTGCTTTACTGTCAGTATAGGAAGGCAAGATCTG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
28343385 TTATCTTCAC
Statistics
Matches: 348, Mismatches: 54, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 348 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
TCCACTGCAACCCAGGGAGGCAA
Found at i:28343157 original size:44 final size:44
Alignment explanation
Indices: 28343107--28343319 Score: 137
Period size: 44 Copynumber: 4.8 Consensus size: 44
28343097 GTCAGTGCAG
28343107 GAAGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAA
1 GAAGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAA
* * * * * * * ***
28343151 GGAGGCAAG-GCTGGTATCTTC-GATCTGCTTCGCTGTAGGTGCAA
1 GAAGGCAAGATCTGCTATTTTCAG-CCTGCTCCGCTGCA-ACCCAA
* * * *
28343195 GAAGGCAAGATTTACTATTTTCAACCTGCTCCGCTGCAACCCAG
1 GAAGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAA
* * * * * ****
28343239 GGAGGCAAGA-CTGGTGTCTTC-GACCTGCTTCGCTGTCGGTGCAA
1 GAAGGCAAGATCTGCTATTTTCAG-CCTGCTCCGCTG-CAACCCAA
* *
28343283 GAAGGCAAGATCTGCTATTTTTAGCCTACTCCGCTGC
1 GAAGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGC
28343320 CACTAAGGGA
Statistics
Matches: 117, Mismatches: 44, Indels: 16
0.66 0.25 0.09
Matches are distributed among these distances:
42 1 0.01
43 37 0.32
44 43 0.37
45 35 0.30
46 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.26
Consensus pattern (44 bp):
GAAGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAA
Found at i:28345645 original size:25 final size:25
Alignment explanation
Indices: 28345593--28345645 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
28345583 AAGAAAATCC
*
28345593 AAAAGAATGAAAGAATAATTATTCA
1 AAAAGAATGAAAGAATAATTACTCA
28345618 AAAAGAATGAAA-AAT-ATTAGCTCA
1 AAAAGAATGAAAGAATAATTA-CTCA
28345642 AAAA
1 AAAA
28345646 TAAATGCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 4 0.15
24 10 0.38
25 12 0.46
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:28345651 original size:25 final size:23
Alignment explanation
Indices: 28345593--28345660 Score: 55
Period size: 25 Copynumber: 2.7 Consensus size: 23
28345583 AAGAAAATCC
* *
28345593 AAAAGAATGAAAGAATAATTATTCA
1 AAAAAAATGAAA-AAT-ATTACTCA
*
28345618 AAAAGAATGAAAAATATTAGCTCA
1 AAAAAAATGAAAAATATTA-CTCA
*
28345642 AAAATAAATGCAAAGATAT
1 AAAA-AAATG-AAAAATAT
28345661 ATTTTATTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.11
24 10 0.27
25 16 0.43
26 7 0.19
ACGTcount: A:0.60, C:0.06, G:0.12, T:0.22
Consensus pattern (23 bp):
AAAAAAATGAAAAATATTACTCA
Found at i:28349320 original size:49 final size:49
Alignment explanation
Indices: 28349267--28349382 Score: 121
Period size: 52 Copynumber: 2.3 Consensus size: 49
28349257 TATAAAACTT
* *
28349267 ATATATATATAAAATACATA-ATGCATTTATGAAAACAAGGAAA-ATATAA
1 ATATATATATAAAA-ACATATATGCATTTA-CAAAAAAAGGAAATATATAA
* *
28349316 ATATATACATATAAAACATATTCATGCATTTACAAAAAAATGAAATATATAA
1 ATATATATATA-AAAACATA-T-ATGCATTTACAAAAAAAGGAAATATATAA
*
28349368 GTATA-ATATAAAAAC
1 ATATATATATAAAAAC
28349383 GTGGAAAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
49 15 0.27
50 8 0.14
51 14 0.25
52 19 0.34
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (49 bp):
ATATATATATAAAAACATATATGCATTTACAAAAAAAGGAAATATATAA
Found at i:28349649 original size:3 final size:3
Alignment explanation
Indices: 28349641--28349674 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
28349631 ATATGTAGGT
28349641 ATA ATA ATA ATA TATA AT- ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A
28349675 CAAAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:28349655 original size:21 final size:18
Alignment explanation
Indices: 28349640--28349674 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28349630 TATATGTAGG
28349640 TATAATAATAATATATAA
1 TATAATAATAATATATAA
28349658 TATAATAATAATA-ATAA
1 TATAATAATAATATATAA
28349675 CAAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAATAATAATATATAA
Found at i:28349684 original size:21 final size:21
Alignment explanation
Indices: 28349641--28349690 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
28349631 ATATGTAGGT
* *
28349641 ATAATAATAATATATAATATA
1 ATAATAATAATACAAAATATA
28349662 ATAATAATAATAACAAAAT-TA
1 ATAATAATAAT-ACAAAATATA
28349683 ATAA-AATA
1 ATAATAATA
28349691 GACTAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 17 0.65
22 5 0.19
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAATAATAATACAAAATATA
Found at i:28350132 original size:23 final size:22
Alignment explanation
Indices: 28350089--28350146 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
28350079 AAAGGGTATC
* *
28350089 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
28350110 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
28350133 TACATATCATATCT
1 TACAAATCATATCT
28350147 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:28350149 original size:19 final size:19
Alignment explanation
Indices: 28350102--28350199 Score: 106
Period size: 19 Copynumber: 4.8 Consensus size: 19
28350092 AAATTAAATC
*
28350102 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
28350122 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
28350144 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
28350165 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
28350184 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
28350200 CTCGAAGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
19 33 0.48
21 18 0.26
22 7 0.10
23 11 0.16
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:28350162 original size:21 final size:21
Alignment explanation
Indices: 28350136--28350198 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
28350126 CTAAGATTAC
28350136 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
28350157 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
28350176 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
28350197 AT
1 AT
28350199 CCTCGAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:28351052 original size:7 final size:7
Alignment explanation
Indices: 28351042--28351068 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28351032 TATATTTATT
28351042 TTTTAAA
1 TTTTAAA
28351049 TTTTAAA
1 TTTTAAA
28351056 TTTTAAA
1 TTTTAAA
28351063 TTTTAA
1 TTTTAA
28351069 TATTATTAAT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:28355167 original size:30 final size:29
Alignment explanation
Indices: 28355109--28355185 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 29
28355099 ACAAGACAAC
28355109 AGCAAAAAAAGAAGGAAGAAAAAGAAAAAA-AT
1 AGCAAAAAAA-AA-G-A-AAAAAGAAAAAAGAT
*
28355141 AGCAACAGAAAAAGAAAAAGAGAAAAAAGAT
1 AGCAA-AAAAAAAGAAAAA-AGAAAAAAGAT
28355172 AGCAAAAAAAAAGA
1 AGCAAAAAAAAAGA
28355186 GATGTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 4 0.10
30 17 0.43
31 8 0.20
32 7 0.17
33 4 0.10
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (29 bp):
AGCAAAAAAAAAGAAAAAAGAAAAAAGAT
Found at i:28358427 original size:37 final size:37
Alignment explanation
Indices: 28358372--28358476 Score: 151
Period size: 37 Copynumber: 2.8 Consensus size: 37
28358362 TGTTTTCTAT
* *
28358372 TGGACTAGCTCTTATGAGCATCT-GCTATGTTGTCGGG
1 TGGATTAGCTCTTATGAGCATCTGGC-ATGTTATCGGG
*
28358409 TGGATTAGCTCTTATGAGCATCTGGCGTGTTATCGGG
1 TGGATTAGCTCTTATGAGCATCTGGCATGTTATCGGG
28358446 TGGATTAGCTCTTATGAGCGAT-TGGCATGTT
1 TGGATTAGCTCTTATGAGC-ATCTGGCATGTT
28358477 TTGGTTGGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
37 58 0.94
38 4 0.06
ACGTcount: A:0.17, C:0.16, G:0.30, T:0.36
Consensus pattern (37 bp):
TGGATTAGCTCTTATGAGCATCTGGCATGTTATCGGG
Found at i:28359490 original size:25 final size:25
Alignment explanation
Indices: 28359428--28359490 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
28359418 CCTAACATAC
* * *
28359428 GGGCGTGTGACATAGCTTGGCACAT
1 GGGCGTCTGACACAGCCTGGCACAT
*
28359453 GGGCGTCTAACACAGCCTGGCACAT
1 GGGCGTCTGACACAGCCTGGCACAT
28359478 GGGCG-CATGACAC
1 GGGCGTC-TGACAC
28359491 GGTCTTGTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 1 0.03
25 31 0.97
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.17
Consensus pattern (25 bp):
GGGCGTCTGACACAGCCTGGCACAT
Found at i:28360266 original size:25 final size:25
Alignment explanation
Indices: 28360228--28360281 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
28360218 TCCATATCTT
* * *
28360228 GTGTGAGCATTTACAGTTATAGCTC
1 GTGTGAGCAATTACAATTACAGCTC
* *
28360253 GTGTGATCAATTACAATTACAGCTT
1 GTGTGAGCAATTACAATTACAGCTC
28360278 GTGT
1 GTGT
28360282 TAGTATTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (25 bp):
GTGTGAGCAATTACAATTACAGCTC
Done.