Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 90 of 106
Found at i:34299740 original size:28 final size:27
Alignment explanation
Indices: 34299709--34299761 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
34299699 TTTGGAGTAT
*
34299709 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
34299737 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
34299762 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:34299767 original size:28 final size:28
Alignment explanation
Indices: 34299709--34299767 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
34299699 TTTGGAGTAT
* *
34299709 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
34299737 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
34299765 AGG
1 AGG
34299768 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:34303486 original size:28 final size:26
Alignment explanation
Indices: 34303454--34303511 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
34303444 TCTTATTTTC
*
34303454 ATTTCAAATATTGGTATCAAGCTTTAA
1 ATTTCAAA-ATTGATATCAAGCTTTAA
** *
34303481 GATTTCTCAATTGATATCTAGCTTTAA
1 -ATTTCAAAATTGATATCAAGCTTTAA
34303508 ATTT
1 ATTT
34303512 GCATCGAGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 16 0.62
28 6 0.23
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (26 bp):
ATTTCAAAATTGATATCAAGCTTTAA
Found at i:34307623 original size:38 final size:38
Alignment explanation
Indices: 34307569--34307683 Score: 185
Period size: 38 Copynumber: 3.0 Consensus size: 38
34307559 AATTTAGACT
* *
34307569 TAAATCACATGTCAGGTAATTAACTTCTATAAACTTAA
1 TAAATAACATGCCAGGTAATTAACTTCTATAAACTTAA
*
34307607 TAAATAACGTGCCAGGTAATTAACTTCTATAAACTTAA
1 TAAATAACATGCCAGGTAATTAACTTCTATAAACTTAA
* *
34307645 TAACTAACATGTCAGGTAATTAACTTCTATAAACTTAA
1 TAAATAACATGCCAGGTAATTAACTTCTATAAACTTAA
34307683 T
1 T
34307684 TAAAAAGAGT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 71 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.34
Consensus pattern (38 bp):
TAAATAACATGCCAGGTAATTAACTTCTATAAACTTAA
Found at i:34307645 original size:19 final size:19
Alignment explanation
Indices: 34307623--34307686 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
34307613 ACGTGCCAGG
34307623 TAATTAACTTCTATAAACT
1 TAATTAACTTCTATAAACT
* * * **
34307642 TAA-TAACTAACATGTCAGGT
1 TAATTAACT-TC-TATAAACT
34307662 -AATTAACTTCTATAAACT
1 TAATTAACTTCTATAAACT
34307680 TAATTAA
1 TAATTAA
34307687 AAAGAGTTTA
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
18 9 0.29
19 13 0.42
20 9 0.29
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.38
Consensus pattern (19 bp):
TAATTAACTTCTATAAACT
Found at i:34309372 original size:9 final size:9
Alignment explanation
Indices: 34309360--34309403 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
34309350 AATAATTTTC
*
34309360 AAATTTATT
1 AAATTTACT
34309369 AAATTTACT
1 AAATTTACT
*
34309378 -AATTTAAGT
1 AAATTT-ACT
34309387 AAATTTACT
1 AAATTTACT
34309396 AAATTTAC
1 AAATTTAC
34309404 CAATAAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 5 0.17
9 20 0.67
10 5 0.17
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (9 bp):
AAATTTACT
Found at i:34309527 original size:24 final size:25
Alignment explanation
Indices: 34309492--34309549 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 25
34309482 TTATATAAAT
34309492 TTAC-TAATTTATATAACATC-TTA-A
1 TTACTTAA-TTATATAACA-CATTACA
34309516 TTACTTAA-T-TATAACACATTACA
1 TTACTTAATTATATAACACATTACA
34309539 TTACTTAATTA
1 TTACTTAATTA
34309550 ACTAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
21 1 0.03
22 10 0.34
23 10 0.34
24 5 0.17
25 3 0.10
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (25 bp):
TTACTTAATTATATAACACATTACA
Found at i:34309545 original size:23 final size:22
Alignment explanation
Indices: 34309503--34309549 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
34309493 TACTAATTTA
34309503 TATAACATCTTAATTACTTAAT
1 TATAACATCTTAATTACTTAAT
34309525 TATAACA-CATTACATTACTTAAT
1 TATAACATC-TTA-ATTACTTAAT
34309548 TA
1 TA
34309550 ACTAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.04
22 10 0.43
23 12 0.52
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (22 bp):
TATAACATCTTAATTACTTAAT
Found at i:34309705 original size:116 final size:116
Alignment explanation
Indices: 34309585--34309796 Score: 270
Period size: 116 Copynumber: 1.8 Consensus size: 116
34309575 ACACCATAAC
* * *
34309585 TAATTTAAATATTTTTCAAA-ATAAATA-ATATTACTTATTTAATTAATTTATTAATTACTAA-A
1 TAATTTAAATAATTTT-AAACATAAATAGAT-TTACTAATTTAATTAATTGATTAATTACTAATA
* * *
34309647 -ACATTTTTTCATTTGATTAGTTAAATTATTTAATTAATTTATTCAAATCTTAAT
64 CACAATTCTT-A-TTAATTAGTTAAATTATTTAATTAATTTATTCAAATCTTAAT
* * *
34309701 TAATTTAAATAATTTTAAACTTTACTAGATTTACTAATTTAATTAATTGATTAATTACTAATACA
1 TAATTTAAATAATTTTAAACATAAATAGATTTACTAATTTAATTAATTGATTAATTACTAATACA
*
34309766 CAATTCTTATTAATTATTTAAATTATTTAAT
66 CAATTCTTATTAATTAGTTAAATTATTTAAT
34309797 AAATAATTCC
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
115 3 0.04
116 68 0.83
117 4 0.05
118 7 0.09
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.50
Consensus pattern (116 bp):
TAATTTAAATAATTTTAAACATAAATAGATTTACTAATTTAATTAATTGATTAATTACTAATACA
CAATTCTTATTAATTAGTTAAATTATTTAATTAATTTATTCAAATCTTAAT
Found at i:34310473 original size:23 final size:23
Alignment explanation
Indices: 34310441--34310487 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
34310431 GTTTAGAGTT
*
34310441 TGTGAAACGACATGTTGGGAATG
1 TGTGAAACGACATGGTGGGAATG
* *
34310464 TGTGACACGATATGGTGGGAATG
1 TGTGAAACGACATGGTGGGAATG
34310487 T
1 T
34310488 ATGGCAGGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.09, G:0.36, T:0.28
Consensus pattern (23 bp):
TGTGAAACGACATGGTGGGAATG
Found at i:34310562 original size:58 final size:58
Alignment explanation
Indices: 34310500--34310622 Score: 183
Period size: 58 Copynumber: 2.1 Consensus size: 58
34310490 GGCAGGGCTA
* *
34310500 TGACACAGCAGGGTTTAGAGTTTGTGACAAGACATGGTTGGAATGTGTGACACAGTTG
1 TGACACAGCAGGGTTTAGAGTTTGTGACAAGACATGATGGGAATGTGTGACACAGTTG
** * * *
34310558 TGACATGGCAGGGTTTAGAGTTTGTGACATGCCATGATGGGAATGTGTGACACGGTTG
1 TGACACAGCAGGGTTTAGAGTTTGTGACAAGACATGATGGGAATGTGTGACACAGTTG
34310616 TGACACA
1 TGACACA
34310623 CCAACGTTCA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.26, C:0.13, G:0.33, T:0.28
Consensus pattern (58 bp):
TGACACAGCAGGGTTTAGAGTTTGTGACAAGACATGATGGGAATGTGTGACACAGTTG
Found at i:34310636 original size:58 final size:58
Alignment explanation
Indices: 34310516--34310669 Score: 159
Period size: 58 Copynumber: 2.7 Consensus size: 58
34310506 AGCAGGGTTT
* * * * *** ** *
34310516 AGAGTTTGTGACAAGACATGGTTGGAATGTGTGACACAGTTGTGACATGGCAGGGTTT
1 AGAGTTTGTGACAAGCCATGATGGGAATGTGTGACACGGTTGTGACACACCAACGTTC
*
34310574 AGAGTTTGTGACATGCCATGATGGGAATGTGTGACACGGTTGTGACACACCAACGTTC
1 AGAGTTTGTGACAAGCCATGATGGGAATGTGTGACACGGTTGTGACACACCAACGTTC
* *
34310632 AGAG-TTGCTGACACGCCATGGA-GGGAATATGTGACACG
1 AGAGTTTG-TGACAAGCCAT-GATGGGAATGTGTGACACG
34310670 ACAGCGTTCA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
57 3 0.04
58 76 0.94
59 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (58 bp):
AGAGTTTGTGACAAGCCATGATGGGAATGTGTGACACGGTTGTGACACACCAACGTTC
Found at i:34310683 original size:47 final size:47
Alignment explanation
Indices: 34310614--34310824 Score: 237
Period size: 47 Copynumber: 4.5 Consensus size: 47
34310604 GTGACACGGT
* * *
34310614 TGTGACAC-ACCAACGTTCAGAGTTGCTGACACGCCATGGAGGGAATA
1 TGTGACACGA-CAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAATC
*
34310661 TGTGACACGACAGCGTTCAGAGTTGGTAACACGCCATGGAGGGAATC
1 TGTGACACGACAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAATC
* * * * * * *
34310708 CGTGACATGCCAACATTCAGAGTTGGTGACACGCCATGGACGAAATC
1 TGTGACACGACAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAATC
* * * * *
34310755 TGTGAGATGCCAGCGTTTAGAG-TCGTGACACGCCATGGAGGGAATC
1 TGTGACACGACAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAATC
* *
34310801 TGTGACACGTCAGCGTTCAAAGTT
1 TGTGACACGACAGCGTTCAGAGTT
34310825 TGTCAGACTC
Statistics
Matches: 137, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
46 38 0.28
47 98 0.72
48 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (47 bp):
TGTGACACGACAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAATC
Found at i:34311054 original size:7 final size:7
Alignment explanation
Indices: 34311042--34311066 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34311032 GCTTGTGTTC
34311042 TTCCTCA
1 TTCCTCA
34311049 TTCCTCA
1 TTCCTCA
34311056 TTCCTCA
1 TTCCTCA
34311063 TTCC
1 TTCC
34311067 CAAATATAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.44
Consensus pattern (7 bp):
TTCCTCA
Found at i:34311530 original size:31 final size:31
Alignment explanation
Indices: 34311496--34311601 Score: 167
Period size: 31 Copynumber: 3.4 Consensus size: 31
34311486 CAACATTGGT
* * *
34311496 GTGTTACTACATTTTACATTATATGCATGGT
1 GTGTTACCACATTTTACGTTATATGCATGGC
*
34311527 GTGTTACCACATTTTACGTTATATGCATCGC
1 GTGTTACCACATTTTACGTTATATGCATGGC
*
34311558 GTGTTACCACATTTTACGTTACATGCATGGC
1 GTGTTACCACATTTTACGTTATATGCATGGC
34311589 GTGTTACCACATT
1 GTGTTACCACATT
34311602 ATGGGTTAAC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.40
Consensus pattern (31 bp):
GTGTTACCACATTTTACGTTATATGCATGGC
Found at i:34314035 original size:84 final size:84
Alignment explanation
Indices: 34313933--34314131 Score: 317
Period size: 84 Copynumber: 2.4 Consensus size: 84
34313923 TCTCATATGG
* * * *
34313933 AACGGCTTATGCGTACTCCCACTCGCATATAACCGAGTCAGCAACGGCTTATGTGCACTCCCATT
1 AACGGCTTATGTGCACTCCCACTCGCACATAACCGAGTCAGCAACGGCTTATGTGCACTCCCACT
34313998 CGCACATAGCCGGGTCAGC
66 CGCACATAGCCGGGTCAGC
* *
34314017 AATGGCTTATGTGCACTCCCACTCACACATAACCGAGTCAGCAACGGCTTATGTGCACTCCCACT
1 AACGGCTTATGTGCACTCCCACTCGCACATAACCGAGTCAGCAACGGCTTATGTGCACTCCCACT
*
34314082 CGCACATAGCCGGGTTAGC
66 CGCACATAGCCGGGTCAGC
* *
34314101 AACGGCTTATGTGCACTTCTACTCGCACATA
1 AACGGCTTATGTGCACTCCCACTCGCACATA
34314132 GCCTGGTCCA
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 104 1.00
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (84 bp):
AACGGCTTATGTGCACTCCCACTCGCACATAACCGAGTCAGCAACGGCTTATGTGCACTCCCACT
CGCACATAGCCGGGTCAGC
Found at i:34314132 original size:42 final size:42
Alignment explanation
Indices: 34313933--34314134 Score: 287
Period size: 42 Copynumber: 4.8 Consensus size: 42
34313923 TCTCATATGG
* * * *
34313933 AACGGCTTATGCGTACTCCCACTCGCATATAACCGAGTCAGC
1 AACGGCTTATGTGCACTCCCACTCGCACATAGCCGAGTCAGC
* *
34313975 AACGGCTTATGTGCACTCCCATTCGCACATAGCCGGGTCAGC
1 AACGGCTTATGTGCACTCCCACTCGCACATAGCCGAGTCAGC
* * *
34314017 AATGGCTTATGTGCACTCCCACTCACACATAACCGAGTCAGC
1 AACGGCTTATGTGCACTCCCACTCGCACATAGCCGAGTCAGC
* *
34314059 AACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTTAGC
1 AACGGCTTATGTGCACTCCCACTCGCACATAGCCGAGTCAGC
* *
34314101 AACGGCTTATGTGCACTTCTACTCGCACATAGCC
1 AACGGCTTATGTGCACTCCCACTCGCACATAGCC
34314135 TGGTCCACAT
Statistics
Matches: 142, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 142 1.00
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.22
Consensus pattern (42 bp):
AACGGCTTATGTGCACTCCCACTCGCACATAGCCGAGTCAGC
Found at i:34315642 original size:151 final size:146
Alignment explanation
Indices: 34315362--34315644 Score: 320
Period size: 151 Copynumber: 1.9 Consensus size: 146
34315352 GTTGTAAAGG
*
34315362 TTTGTGTTCAACAATTTCATATGTGTGATTATCAAATAACATATCTGTGTTTACAGTTGTACCAT
1 TTTGTGTTCAACAATTCCATA-GTGTGATTATCAAATAACATATCTGTGTTTACAGTTGTACCAT
* * * * ** *
34315427 ACGACGACAGCTCCACAACCACTAATAGATCCTCCTCAAACTCACAGTGTTAATGAGGAGCCGGT
65 ACGACGACAGCTCCACAACCACCAATAGATCCTCCTCAAACGCAAAGTGGTAATGAAAAACCGGT
34315492 AAGGATGCTTATAATGA
130 AAGGATGCTTATAATGA
* *
34315509 TTTGTGTTCAACAATTCCATA-TGTGATTATCGAATAACATATCTGTATCTGTGTTTGCAGTTAG
1 TTTGTGTTCAACAATTCCATAGTGTGATTATCAAATAAC--A----TATCTGTGTTTACAGTT-G
* * * * * *
34315573 -ACGATACGACGACAGCTCCTCAACCACCAATCGGTCCTGCTCAACCGCAAAGTGGTAAT-AAAA
59 TACCATACGACGACAGCTCCACAACCACCAATAGATCCTCCTCAAACGCAAAGTGGTAATGAAAA
34315636 CACCGGTAA
124 -ACCGGTAA
34315645 AGATATTAAA
Statistics
Matches: 112, Mismatches: 16, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
145 16 0.14
147 21 0.19
150 2 0.02
151 72 0.64
152 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (146 bp):
TTTGTGTTCAACAATTCCATAGTGTGATTATCAAATAACATATCTGTGTTTACAGTTGTACCATA
CGACGACAGCTCCACAACCACCAATAGATCCTCCTCAAACGCAAAGTGGTAATGAAAAACCGGTA
AGGATGCTTATAATGA
Found at i:34317841 original size:124 final size:119
Alignment explanation
Indices: 34317608--34318077 Score: 375
Period size: 124 Copynumber: 4.0 Consensus size: 119
34317598 CAAGTCAACG
* * * * *
34317608 TGTCACGCCAAGTATCTGGTTCCATTCAGCGTGTCACCAC-A-ATTGGGGGATGCCGTGTCACCT
1 TGTCACGCCAAGTATCTAGTTCCACTCAGCGTGTCACCACAAGATGGGGGGATACCGTGTCACCC
* * *
34317671 CACAATACAGCAAGAAGTCAGCGGATCACCATAGAAATCTGCATGCACTTAGCA
66 CACAATACAGCAAGAAATCAACGGATCACCACAGAAATCTGCATGCACTTAGCA
**
34317725 TGTCACGCCAAGTATCTAGTTCCACTCAGCGTGTCTGCACAAGATGGGGATAAGGCATACCGTGT
1 TGTCACGCCAAGTATCTAGTTCCACTCAGCGTGTCACCACAAGATGGGG----GG-ATACCGTGT
*** * *
34317790 CACCCCACAATATTTCAAGAAATCAACGTG-TCACCACAGAAATCTGCATGCATTTAGCG
61 CACCCCACAATACAGCAAGAAATCAACG-GATCACCACAGAAATCTGCATGCACTTAGCA
34317849 TGTCACGCCAAGTATCTAGTTCCACTCAGCGTGTCACCAC-A-A------G--A---TGTCACCC
1 TGTCACGCCAAGTATCTAGTTCCACTCAGCGTGTCACCACAAGATGGGGGGATACCGTGTCACCC
* * * * * * * * *
34317901 CACAATACTGTAAGAAGTCAACGTG-TCACCACAAAAATTTGCATGCCCTCAACG
66 CACAATACAGCAAGAAATCAACG-GATCACCACAGAAATCTGCATGCACTTAGCA
* ** * * * * * *
34317955 TGTCATGCCAACAATCTGGTTTCACTCAGCGTGTCACCACAATAT-GGGGCATGCCGTGTCACCT
1 TGTCACGCCAAGTATCTAGTTCCACTCAGCGTGTCACCACAAGATGGGGGGATACCGTGTCACCC
* * * * * * *
34318019 AACAATACTGCAAGAAGTCAGCGTG-TCACCACAGAAATTTGCATGCACTCAGCG
66 CACAATACAGCAAGAAATCAACG-GATCACCACAGAAATCTGCATGCACTTAGCA
34318073 TGTCA
1 TGTCA
34318078 GCTTAGCATA
Statistics
Matches: 292, Mismatches: 41, Indels: 39
0.78 0.11 0.10
Matches are distributed among these distances:
106 87 0.30
107 1 0.00
108 1 0.00
109 1 0.00
112 1 0.00
117 36 0.12
118 61 0.21
119 5 0.02
122 1 0.00
123 3 0.01
124 94 0.32
125 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (119 bp):
TGTCACGCCAAGTATCTAGTTCCACTCAGCGTGTCACCACAAGATGGGGGGATACCGTGTCACCC
CACAATACAGCAAGAAATCAACGGATCACCACAGAAATCTGCATGCACTTAGCA
Found at i:34317889 original size:62 final size:61
Alignment explanation
Indices: 34317688--34317889 Score: 146
Period size: 62 Copynumber: 3.3 Consensus size: 61
34317678 CAGCAAGAAG
* *
34317688 TCAGCG-GATCACCATAGAAATCTGCATGCACTTAGCATGTCACGCCAAGTATCTAGTTCCAC
1 TCAGCGTG-TCACCACAGAAATCTGCATGCA-TTAGCGTGTCACGCCAAGTATCTAGTTCCAC
** * ** * * * * * *
34317750 TCAGCGTGTCTGCACA-AGATGGGGATAAGGCA-TACCGTGTCACCCCACAATATTTCAAG---A
1 TCAGCGTGTCACCACAGAAATCTGCAT---GCATTAGCGTGTCACGCCA-AGTA--TCTAGTTCC
*
34317810 AA
60 AC
*
34317812 TCAACGTGTCACCACAGAAATCTGCATGCATTTAGCGTGTCACGCCAAGTATCTAGTTCCAC
1 TCAGCGTGTCACCACAGAAATCTGCATGCA-TTAGCGTGTCACGCCAAGTATCTAGTTCCAC
34317874 TCAGCGTGTCACCACA
1 TCAGCGTGTCACCACA
34317890 AGATGTCACC
Statistics
Matches: 99, Mismatches: 28, Indels: 26
0.65 0.18 0.17
Matches are distributed among these distances:
59 4 0.04
60 3 0.03
61 9 0.09
62 66 0.67
63 10 0.10
64 3 0.03
65 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (61 bp):
TCAGCGTGTCACCACAGAAATCTGCATGCATTAGCGTGTCACGCCAAGTATCTAGTTCCAC
Found at i:34317981 original size:106 final size:106
Alignment explanation
Indices: 34317787--34317996 Score: 287
Period size: 106 Copynumber: 2.0 Consensus size: 106
34317777 AGGCATACCG
* * * * *
34317787 TGTCACCCCACAATATTTCAAGAAATCAACGTGTCACCACAGAAATCTGCATGCATTTAGCGTGT
1 TGTCACCCCACAATATGTCAAGAAATCAACGTGTCACCACAAAAATCTGCATGCACTCAACGTGT
**
34317852 CACGCCAAGTATCTAGTTCCACTCAGCGTGTCACCACAAGA
66 CACGCCAACAATCTAGTTCCACTCAGCGTGTCACCACAAGA
* * *
34317893 TGTCACCCCACAATACTGT-AAGAAGTCAACGTGTCACCACAAAAATTTGCATGCCCTCAACGTG
1 TGTCACCCCACAATA-TGTCAAGAAATCAACGTGTCACCACAAAAATCTGCATGCACTCAACGTG
* * *
34317957 TCATGCCAACAATCTGGTTTCACTCAGCGTGTCACCACAA
65 TCACGCCAACAATCTAGTTCCACTCAGCGTGTCACCACAA
34317997 TATGGGGCAT
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
106 88 0.98
107 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (106 bp):
TGTCACCCCACAATATGTCAAGAAATCAACGTGTCACCACAAAAATCTGCATGCACTCAACGTGT
CACGCCAACAATCTAGTTCCACTCAGCGTGTCACCACAAGA
Found at i:34321619 original size:31 final size:31
Alignment explanation
Indices: 34321576--34321715 Score: 172
Period size: 31 Copynumber: 4.5 Consensus size: 31
34321566 TTTGTCAGTC
* *
34321576 ATGTTGTAACACGCCATGCATATAACATATA
1 ATGTGGTAACACGCCATGCATATAACATAAA
* * * *
34321607 ATGTGGTAACACGTCATGCGTATAACGTATA
1 ATGTGGTAACACGCCATGCATATAACATAAA
*
34321638 ATGTGCTAACACGCCATGCATATAACATAAA
1 ATGTGGTAACACGCCATGCATATAACATAAA
* ** *
34321669 ATATGGTAACACATCATGCATATAACGTAAA
1 ATGTGGTAACACGCCATGCATATAACATAAA
*
34321700 ATGTTGTAACACGCCA
1 ATGTGGTAACACGCCA
34321716 ATGAGTATAA
Statistics
Matches: 91, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 91 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (31 bp):
ATGTGGTAACACGCCATGCATATAACATAAA
Found at i:34321658 original size:62 final size:62
Alignment explanation
Indices: 34321576--34321715 Score: 219
Period size: 62 Copynumber: 2.3 Consensus size: 62
34321566 TTTGTCAGTC
* * * * *
34321576 ATGTTGTAACACGCCATGCATATAACATATAATGTGGTAACACGTCATGCGTATAACGTATA
1 ATGTTGTAACACGCCATGCATATAACATAAAATATGGTAACACATCATGCATATAACGTAAA
34321638 ATG-TGCTAACACGCCATGCATATAACATAAAATATGGTAACACATCATGCATATAACGTAAA
1 ATGTTG-TAACACGCCATGCATATAACATAAAATATGGTAACACATCATGCATATAACGTAAA
34321700 ATGTTGTAACACGCCA
1 ATGTTGTAACACGCCA
34321716 ATGAGTATAA
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
61 2 0.03
62 67 0.94
63 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (62 bp):
ATGTTGTAACACGCCATGCATATAACATAAAATATGGTAACACATCATGCATATAACGTAAA
Found at i:34322529 original size:15 final size:15
Alignment explanation
Indices: 34322509--34322592 Score: 70
Period size: 15 Copynumber: 5.9 Consensus size: 15
34322499 ATAATTCAAC
34322509 ATTATTCAACAACAG
1 ATTATTCAACAACAG
*
34322524 ATTATTAAACAACAG
1 ATTATTCAACAACAG
*
34322539 ATTACTCAAC-A-A-
1 ATTATTCAACAACAG
*
34322551 A--ATTCAACAACAA
1 ATTATTCAACAACAG
* * *
34322564 ATTATTGAACCACAT
1 ATTATTCAACAACAG
*
34322579 ATAATTCAACAACA
1 ATTATTCAACAACA
34322593 TTCAACAATA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
10 6 0.11
11 1 0.02
12 2 0.04
13 2 0.04
14 1 0.02
15 42 0.78
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.25
Consensus pattern (15 bp):
ATTATTCAACAACAG
Found at i:34322559 original size:40 final size:40
Alignment explanation
Indices: 34322498--34322616 Score: 116
Period size: 40 Copynumber: 3.0 Consensus size: 40
34322488 GGTATGGACT
* ** *
34322498 GATAATTCAACATTATTCAACAACAGATTATTAAACAACA
1 GATAACTCAACAAAATTCAACAACAAATTATTAAACAACA
* * *
34322538 GATTACTCAACAAAATTCAACAACAAATTATTGAACCACA
1 GATAACTCAACAAAATTCAACAACAAATTATTAAACAACA
* * * * *
34322578 TATAATTCAACAACATTCAAC-A-ATATTATTCAACAACA
1 GATAACTCAACAAAATTCAACAACAAATTATTAAACAACA
34322616 G
1 G
34322617 CCAAACCTCA
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
38 13 0.20
39 1 0.02
40 50 0.78
ACGTcount: A:0.50, C:0.20, G:0.04, T:0.26
Consensus pattern (40 bp):
GATAACTCAACAAAATTCAACAACAAATTATTAAACAACA
Found at i:34324157 original size:21 final size:21
Alignment explanation
Indices: 34324110--34324157 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
34324100 TCTGTGTGAA
*
34324110 AGTTTCAAAATTGCTTACATG
1 AGTTTTAAAATTGCTTACATG
*
34324131 AGTTTTAAATTTGCTTGA-ATG
1 AGTTTTAAAATTGCTT-ACATG
34324152 AGTTTT
1 AGTTTT
34324158 TATTTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (21 bp):
AGTTTTAAAATTGCTTACATG
Found at i:34324200 original size:21 final size:21
Alignment explanation
Indices: 34324128--34324205 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
34324118 AATTGCTTAC
* * * *
34324128 ATGAGTTTTAAATTTGCTTGA
1 ATGAGTTTTGAACTTGTTTAA
* **
34324149 ATGAGTTTTTATTTTGTTTAA
1 ATGAGTTTTGAACTTGTTTAA
*
34324170 ATGATTTTTGAACTTGTTTAA
1 ATGAGTTTTGAACTTGTTTAA
*
34324191 GTGAGTTTTGAACTT
1 ATGAGTTTTGAACTT
34324206 TAATTATTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.26, C:0.04, G:0.18, T:0.53
Consensus pattern (21 bp):
ATGAGTTTTGAACTTGTTTAA
Found at i:34325381 original size:15 final size:17
Alignment explanation
Indices: 34325361--34325397 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
34325351 GAAAAGTTGA
34325361 ATTTGTG-GC-AACTTG
1 ATTTGTGTGCAAACTTG
34325376 ATTTGTGTGCAAACTTG
1 ATTTGTGTGCAAACTTG
34325393 ATTTG
1 ATTTG
34325398 CTTACAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.35
16 2 0.10
17 11 0.55
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (17 bp):
ATTTGTGTGCAAACTTG
Found at i:34332193 original size:13 final size:13
Alignment explanation
Indices: 34332175--34332199 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34332165 GGCCAGAGTT
34332175 GAAAAAGAATTAG
1 GAAAAAGAATTAG
34332188 GAAAAAGAATTA
1 GAAAAAGAATTA
34332200 AAATTCTTAG
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:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (13 bp):
GAAAAAGAATTAG
Found at i:34332763 original size:33 final size:33
Alignment explanation
Indices: 34332717--34332817 Score: 157
Period size: 33 Copynumber: 3.1 Consensus size: 33
34332707 CCATAACAAA
**
34332717 AAAAATCGGATGACCAAAATGCTATCCCAAGTG
1 AAAAATCTAATGACCAAAATGCTATCCCAAGTG
34332750 AAAAATCTAATGACCAAAATGCTATCCCAAGTG
1 AAAAATCTAATGACCAAAATGCTATCCCAAGTG
* * *
34332783 AAAAATCTAACGACCAAAATGCTGTCCCCAGTG
1 AAAAATCTAATGACCAAAATGCTATCCCAAGTG
34332816 AA
1 AA
34332818 CTTGATTTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.19
Consensus pattern (33 bp):
AAAAATCTAATGACCAAAATGCTATCCCAAGTG
Found at i:34341424 original size:21 final size:21
Alignment explanation
Indices: 34341399--34341465 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
34341389 AGTAAAAAGA
34341399 AATAACAATTTAAGAGAACTT
1 AATAACAATTTAAGAGAACTT
* * *
34341420 AATAAAAAAATATTAAG-TAA-TAA
1 AAT--AACAAT-TTAAGAGAACT-T
34341443 AATAACAATTTAAGAGAACTT
1 AATAACAATTTAAGAGAACTT
34341464 AA
1 AA
34341466 ATATATCCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
20 5 0.15
21 12 0.35
22 2 0.06
23 10 0.29
24 5 0.15
ACGTcount: A:0.60, C:0.06, G:0.07, T:0.27
Consensus pattern (21 bp):
AATAACAATTTAAGAGAACTT
Found at i:34341466 original size:23 final size:23
Alignment explanation
Indices: 34341398--34341466 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
34341388 AAGTAAAAAG
34341398 AAATAACAATTTAAGAGAACTTA
1 AAATAACAATTTAAGAGAACTTA
* *
34341421 ATAA-AAAAATATTAAG-TAA--TA
1 A-AATAACAAT-TTAAGAGAACTTA
34341442 AAATAACAATTTAAGAGAACTTA
1 AAATAACAATTTAAGAGAACTTA
34341465 AA
1 AA
34341467 TATATCCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
20 7 0.19
21 10 0.28
23 12 0.33
24 7 0.19
ACGTcount: A:0.61, C:0.06, G:0.07, T:0.26
Consensus pattern (23 bp):
AAATAACAATTTAAGAGAACTTA
Found at i:34343811 original size:45 final size:44
Alignment explanation
Indices: 34343704--34343812 Score: 105
Period size: 45 Copynumber: 2.4 Consensus size: 44
34343694 TTCCTTTTTT
* **
34343704 TTTTTTTACTTTTCTTCTTCCTTTTTCTCTTCCAATCACTTTCTTTG
1 TTTTTTT-CTTTT-TTCTTCCTTTCTCTCTTCCAAT-ACTTTCTTCC
* *
34343751 TTTTCTTT-TTATTTCTTCCTTCTCTCTCTTCCCGAT-CTTTCTTCC
1 TTTT-TTTCTTTTTTCTTCCTT-TCTCTCTT-CCAATACTTTCTTCC
34343796 TTTTTTTCTTTTTTCTT
1 TTTTTTTCTTTTTTCTT
34343813 TTCCTTCTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
44 3 0.06
45 28 0.54
46 10 0.19
47 8 0.15
48 3 0.06
ACGTcount: A:0.06, C:0.27, G:0.02, T:0.66
Consensus pattern (44 bp):
TTTTTTTCTTTTTTCTTCCTTTCTCTCTTCCAATACTTTCTTCC
Found at i:34343814 original size:13 final size:13
Alignment explanation
Indices: 34343788--34343846 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
34343778 CTTCCCGATC
*
34343788 TTTCTTCCTT-TT
1 TTTCTTCTTTCTT
*
34343800 TTTCTTTTTTCTT
1 TTTCTTCTTTCTT
*
34343813 TTCCTTCTTTCTT
1 TTTCTTCTTTCTT
* *
34343826 TTTCTCTCTTCCTC
1 TTTCT-TCTTTCTT
34343840 TTTCTTC
1 TTTCTTC
34343847 CTCGGCTTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
12 8 0.21
13 19 0.50
14 11 0.29
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCTTCTTTCTT
Found at i:34343818 original size:21 final size:22
Alignment explanation
Indices: 34343790--34343845 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
34343780 TCCCGATCTT
*
34343790 TCTTCCTTTTTTTCTTTTT-TC
1 TCTTCCTTTCTTTCTTTTTCTC
*
34343811 TTTTCC-TTCTTTCTTTTTCTC
1 TCTTCCTTTCTTTCTTTTTCTC
34343832 TCTTCC--TCTTTCTT
1 TCTTCCTTTCTTTCTT
34343846 CCTCGGCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (22 bp):
TCTTCCTTTCTTTCTTTTTCTC
Found at i:34343825 original size:20 final size:20
Alignment explanation
Indices: 34343800--34343845 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
34343790 TCTTCCTTTT
*
34343800 TTTCTTTTT-TCTTTTCCTTC
1 TTTCTTTTTCTCTCTTCC-TC
34343820 TTTCTTTTTCTCTCTTCCTC
1 TTTCTTTTTCTCTCTTCCTC
34343840 TTTCTT
1 TTTCTT
34343846 CCTCGGCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTCTTTTTCTCTCTTCCTC
Found at i:34343857 original size:24 final size:24
Alignment explanation
Indices: 34343830--34343892 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 24
34343820 TTTCTTTTTC
*
34343830 TCTCTTCCTCTTTCTTCCTCGGCT
1 TCTCTTCCTCTCTCTTCCTCGGCT
*
34343854 TCTC-TCC-CTCTCTTTCTCGGCT
1 TCTCTTCCTCTCTCTTCCTCGGCT
34343876 TCTCTCTCCT-TC-CTTCC
1 TCTCT-TCCTCTCTCTTCC
34343893 CTCTCTCTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 17 0.52
23 7 0.21
24 9 0.27
ACGTcount: A:0.00, C:0.46, G:0.06, T:0.48
Consensus pattern (24 bp):
TCTCTTCCTCTCTCTTCCTCGGCT
Found at i:34343897 original size:18 final size:18
Alignment explanation
Indices: 34343876--34343919 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
34343866 TTTCTCGGCT
34343876 TCTCTCTCCTTCCTTCCC
1 TCTCTCTCCTTCCTTCCC
*
34343894 TCTCTCTCTTTCCTTCCC
1 TCTCTCTCCTTCCTTCCC
*
34343912 TCACTCTC
1 TCTCTCTC
34343920 TCGGCTTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.45
Consensus pattern (18 bp):
TCTCTCTCCTTCCTTCCC
Found at i:34343901 original size:22 final size:22
Alignment explanation
Indices: 34343876--34343921 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
34343866 TTTCTCGGCT
* *
34343876 TCTCTCTCCTTCCTTCCCTCTC
1 TCTCTCTCCTTCCCTCACTCTC
*
34343898 TCTCTTTCCTTCCCTCACTCTC
1 TCTCTCTCCTTCCCTCACTCTC
34343920 TC
1 TC
34343922 GGCTTCTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.46
Consensus pattern (22 bp):
TCTCTCTCCTTCCCTCACTCTC
Found at i:34344437 original size:17 final size:18
Alignment explanation
Indices: 34344417--34344453 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
34344407 CTTTTTAATT
34344417 TTTAATTTTATTTTT-TA
1 TTTAATTTTATTTTTATA
*
34344434 TTTATTTTTATTTTTATA
1 TTTAATTTTATTTTTATA
34344452 TT
1 TT
34344454 ACCATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTAATTTTATTTTTATA
Found at i:34344450 original size:6 final size:6
Alignment explanation
Indices: 34344408--34344450 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
34344398 TTTTCTCTTC
* *
34344408 TTTTTAA TTTTTA ATTTTA TTTTT- TATTTA TTTTTA TTTTTA T
1 TTTTT-A TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
34344451 ATTACCATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
5 4 0.13
6 22 0.71
7 5 0.16
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:34352268 original size:22 final size:22
Alignment explanation
Indices: 34352238--34352282 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
34352228 AAATTTCTTA
*
34352238 ACTCAATCCTTCTTCCTTTTCT
1 ACTCAATCCTTCTTCCTTCTCT
* *
34352260 ACTCGATCCTTCTTTCTTCTCT
1 ACTCAATCCTTCTTCCTTCTCT
34352282 A
1 A
34352283 TACTCTGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.13, C:0.36, G:0.02, T:0.49
Consensus pattern (22 bp):
ACTCAATCCTTCTTCCTTCTCT
Found at i:34356362 original size:17 final size:17
Alignment explanation
Indices: 34356332--34356364 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34356322 TTTTTGATAA
34356332 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
34356349 AATAACAACT-CTTATT
1 AATAA-AACTCCTTATT
34356365 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.36
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:34356553 original size:30 final size:29
Alignment explanation
Indices: 34356507--34356645 Score: 149
Period size: 28 Copynumber: 4.7 Consensus size: 29
34356497 TTAAGACAAC
*
34356507 TCTTGTCTTTAATTAAGACAAAAATATTTT
1 TCTTGTC-TAAATTAAGACAAAAATATTTT
*
34356537 ATCTTGTCTAAATTAAGAC--AAATATGTCT
1 -TCTTGTCTAAATTAAGACAAAAATAT-TTT
*
34356566 TCTTGTCTAGATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAAAATATTTT
* * *
34356596 TCTTGTCTTAATTTAAAACAAATATA-TTT
1 TCTTGTC-TAAATTAAGACAAAAATATTTT
*
34356625 TCTTATCTAAATTAAGACAAA
1 TCTTGTCTAAATTAAGACAAA
34356646 TAGGTTAAAG
Statistics
Matches: 92, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
28 35 0.38
29 11 0.12
30 25 0.27
31 21 0.23
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAAAATATTTT
Found at i:34356617 original size:59 final size:59
Alignment explanation
Indices: 34356517--34356645 Score: 181
Period size: 59 Copynumber: 2.2 Consensus size: 59
34356507 TCTTGTCTTT
* * *
34356517 AATTAAGAC-AAAAATATTTTATCTTGTCTAAATTAAGACAAATATGTCTTCTTGTCTA
1 AATTAAGACAAAAAATATTTTATCTTGTCTAAATTAAAACAAATATATCTTCTTATCTA
* * *
34356575 GATTAAGACAAAAAATATTTT-TCTTGTCTTAATTTAAAACAAATATATTTTCTTATCTA
1 AATTAAGACAAAAAATATTTTATCTTGTC-TAAATTAAAACAAATATATCTTCTTATCTA
34356634 AATTAAGACAAA
1 AATTAAGACAAA
34356646 TAGGTTAAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
58 15 0.24
59 47 0.76
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.40
Consensus pattern (59 bp):
AATTAAGACAAAAAATATTTTATCTTGTCTAAATTAAAACAAATATATCTTCTTATCTA
Found at i:34360723 original size:21 final size:20
Alignment explanation
Indices: 34360693--34360738 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
34360683 AGTCACCAAG
34360693 ACCACATTCACTGCCATGAT
1 ACCACATTCACTGCCATGAT
*
34360713 CCCACAATTCACTGCCATGAT
1 ACCAC-ATTCACTGCCATGAT
34360734 ACCAC
1 ACCAC
34360739 CAGCATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.30, C:0.39, G:0.09, T:0.22
Consensus pattern (20 bp):
ACCACATTCACTGCCATGAT
Found at i:34381531 original size:39 final size:39
Alignment explanation
Indices: 34381479--34381554 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
34381469 CTAGTTACAT
*
34381479 TAACAATTCCTCTACCTTTACCTCTACAATTAGCTGCCG
1 TAACAATTCCTCTACCTTTACCTCTACAATTAACTGCCG
* * *
34381518 TAAC-ATTCACTCTATCTTTGCCTCTACCATTAACTGC
1 TAACAATTC-CTCTACCTTTACCTCTACAATTAACTGC
34381555 ATCAACATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 4 0.12
39 28 0.88
ACGTcount: A:0.25, C:0.33, G:0.07, T:0.36
Consensus pattern (39 bp):
TAACAATTCCTCTACCTTTACCTCTACAATTAACTGCCG
Found at i:34381562 original size:39 final size:38
Alignment explanation
Indices: 34381479--34381565 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 38
34381469 CTAGTTACAT
* *
34381479 TAACAATTCCTCTACCTTTACCTCTACAATTAGCTGCCG
1 TAAC-ATTCCTCTACCTTTACCTCTACAATTAACTGCCA
* * *
34381518 TAACATTCACTCTATCTTTGCCTCTACCATTAACTG-CA
1 TAACATTC-CTCTACCTTTACCTCTACAATTAACTGCCA
34381556 TCAACATTCC
1 T-AACATTCC
34381566 CTCTCACTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
38 7 0.17
39 34 0.83
ACGTcount: A:0.26, C:0.33, G:0.06, T:0.34
Consensus pattern (38 bp):
TAACATTCCTCTACCTTTACCTCTACAATTAACTGCCA
Found at i:34381671 original size:9 final size:9
Alignment explanation
Indices: 34381659--34381684 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
34381649 ATATTTGGCA
34381659 TATTAACAT
1 TATTAACAT
34381668 TATTAACAT
1 TATTAACAT
34381677 TATTAACA
1 TATTAACA
34381685 GAAAAGTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (9 bp):
TATTAACAT
Found at i:34382239 original size:124 final size:124
Alignment explanation
Indices: 34382017--34382246 Score: 347
Period size: 124 Copynumber: 1.9 Consensus size: 124
34382007 CATTGACTAT
* * *
34382017 ATTACAATACAATAATTTTACATTAATAAAGCATGTACAATAATTTACTGTTACATTGAAAATAG
1 ATTACAACAAAATAATTTTACATTAATAAAGCATGTACAATAATCTACTGTTACATTGAAAATAG
*
34382082 AAAACTTTGCAATTAGGATTTGAAAACCCCAAATGACATTCGATTAGAATTTGAGAGCA
66 AAAACTTTGCAATAAGGATTTGAAAACCCCAAATGACATTCGATTAGAATTTGAGAGCA
* *
34382141 ATTACAACAAAATAATTTTACATTAATAAAGCATGTACAATAATCTACTTTTATATTGAAAATAG
1 ATTACAACAAAATAATTTTACATTAATAAAGCATGTACAATAATCTACTGTTACATTGAAAATAG
* * *
34382206 AAAA-TTTTCTAACTAAGG-TTTGAAAACCTCAAATTACATTC
66 AAAACTTTGC-AA-TAAGGATTTGAAAACCCCAAATGACATTC
34382247 TATCAATGTT
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
123 4 0.04
124 87 0.92
125 4 0.04
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (124 bp):
ATTACAACAAAATAATTTTACATTAATAAAGCATGTACAATAATCTACTGTTACATTGAAAATAG
AAAACTTTGCAATAAGGATTTGAAAACCCCAAATGACATTCGATTAGAATTTGAGAGCA
Found at i:34382424 original size:21 final size:22
Alignment explanation
Indices: 34382385--34382426 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
34382375 TTAGTTTCAA
* *
34382385 TTTCAAAAATAGTGTTTTAGGG
1 TTTCAAAAATACTGATTTAGGG
34382407 TTTCAAAAATACT-ATTTAGG
1 TTTCAAAAATACTGATTTAGG
34382427 TTTTAAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (22 bp):
TTTCAAAAATACTGATTTAGGG
Found at i:34382594 original size:20 final size:20
Alignment explanation
Indices: 34382569--34382611 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
34382559 AGAGAATCCT
34382569 AATAGTCAAGCAAAGCATGC
1 AATAGTCAAGCAAAGCATGC
34382589 AATAGTCAAGCAAAGCATGC
1 AATAGTCAAGCAAAGCATGC
34382609 AAT
1 AAT
34382612 CTGGGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (20 bp):
AATAGTCAAGCAAAGCATGC
Found at i:34387638 original size:28 final size:28
Alignment explanation
Indices: 34387588--34387674 Score: 95
Period size: 30 Copynumber: 3.0 Consensus size: 28
34387578 AAACTTGTAA
34387588 TTGGAAAAGCATTTTCC-ACGGAATTCCG
1 TTGGAAAAGCA-TTTCCAACGGAATTCCG
* * *
34387616 TTGGAAAAACATTTCCAATGGAATTTTTCG
1 TTGGAAAAGCATTTCCAACGGAA--TTCCG
* *
34387646 TTGGTAAAGCATTTCTAACGGAATTCCG
1 TTGGAAAAGCATTTCCAACGGAATTCCG
34387674 T
1 T
34387675 AAGAAATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
27 5 0.10
28 20 0.42
30 23 0.48
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (28 bp):
TTGGAAAAGCATTTCCAACGGAATTCCG
Found at i:34388709 original size:19 final size:20
Alignment explanation
Indices: 34388682--34388727 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
34388672 AGGAGACAAG
*
34388682 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
34388701 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
34388720 ATAATATT
1 ATAATATT
34388728 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:34390563 original size:13 final size:13
Alignment explanation
Indices: 34390545--34390569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34390535 AGGGAAATTG
34390545 TGATTTTATAAAA
1 TGATTTTATAAAA
34390558 TGATTTTATAAA
1 TGATTTTATAAA
34390570 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:34393698 original size:20 final size:20
Alignment explanation
Indices: 34393675--34393716 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
34393665 TTCATTCTCA
*
34393675 ATCAATAGATTAACTTCTTC
1 ATCAAGAGATTAACTTCTTC
34393695 ATCAAGAGATTAACTTCTTC
1 ATCAAGAGATTAACTTCTTC
34393715 AT
1 AT
34393717 AATCACCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (20 bp):
ATCAAGAGATTAACTTCTTC
Found at i:34403703 original size:6 final size:6
Alignment explanation
Indices: 34403695--34403768 Score: 85
Period size: 6 Copynumber: 12.3 Consensus size: 6
34403685 GGAGAAGATA
* * * ** *
34403695 ATGAAA ATGATG ATGAAG ATGAAG ATGAAT ATGACT ATGAAG AAGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
*
34403743 ATGAAG ATAAAG ATGAAG ATGAAG AT
1 ATGAAG ATGAAG ATGAAG ATGAAG AT
34403769 CATGTGGAGC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.51, C:0.01, G:0.27, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:34405243 original size:2 final size:2
Alignment explanation
Indices: 34405238--34405273 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34405228 ATATATCAGG
34405238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34405274 TGACTAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34406263 original size:25 final size:25
Alignment explanation
Indices: 34406225--34406273 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
34406215 TAATAGTTTT
*
34406225 CCAACGGAAATTTCCGTTGGAAATG
1 CCAACCGAAATTTCCGTTGGAAATG
*
34406250 CCAACCGAATTTTCCGTTGGAAAT
1 CCAACCGAAATTTCCGTTGGAAAT
34406274 CTATTTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (25 bp):
CCAACCGAAATTTCCGTTGGAAATG
Found at i:34409363 original size:2 final size:2
Alignment explanation
Indices: 34409356--34409397 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
34409346 TATTACATAC
34409356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34409398 TCCATAGCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34413431 original size:96 final size:96
Alignment explanation
Indices: 34413267--34413458 Score: 384
Period size: 96 Copynumber: 2.0 Consensus size: 96
34413257 TTTTCTTGTT
34413267 ACTCAGTAGTTGTTGATGGAATGGTTAATGTTTAATGTTATTAGTAGATCCGAGGATTGCTTATG
1 ACTCAGTAGTTGTTGATGGAATGGTTAATGTTTAATGTTATTAGTAGATCCGAGGATTGCTTATG
34413332 TTTTGGGCTAGTATCATGTTGTAATAGTGTC
66 TTTTGGGCTAGTATCATGTTGTAATAGTGTC
34413363 ACTCAGTAGTTGTTGATGGAATGGTTAATGTTTAATGTTATTAGTAGATCCGAGGATTGCTTATG
1 ACTCAGTAGTTGTTGATGGAATGGTTAATGTTTAATGTTATTAGTAGATCCGAGGATTGCTTATG
34413428 TTTTGGGCTAGTATCATGTTGTAATAGTGTC
66 TTTTGGGCTAGTATCATGTTGTAATAGTGTC
34413459 TTCAGAGAAA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.42
Consensus pattern (96 bp):
ACTCAGTAGTTGTTGATGGAATGGTTAATGTTTAATGTTATTAGTAGATCCGAGGATTGCTTATG
TTTTGGGCTAGTATCATGTTGTAATAGTGTC
Found at i:34430489 original size:111 final size:110
Alignment explanation
Indices: 34430296--34430516 Score: 406
Period size: 111 Copynumber: 2.0 Consensus size: 110
34430286 TTATGAGCCT
* *
34430296 TTGGCTTCTGAATCTTGTCTGAGATGAAATTTTAATTCTCATGGAAATCTGTATACTGACTTTTC
1 TTGGCTTCCGAATCTTGTCTGAGATGAAATTTTAATTCTCATGGAAATCTGTATACTGACTTCTC
34430361 ATTCTCTTTCACACCCTTTTTGGTAGGTGGGGACTGTCAATCATA
66 ATTCTCTTTCACACCCTTTTTGGTAGGTGGGGACTGTCAATCATA
*
34430406 TTGGCTTCCGAATCTTGTCTGAGATGAAAATTTTAATTCTCATGGAAATCTGTATATTGACTTCT
1 TTGGCTTCCGAATCTTGTCTGAGATG-AAATTTTAATTCTCATGGAAATCTGTATACTGACTTCT
34430471 CATTCTCTTTCACACCCTTTTTGGTAGGTGGGGACTGTCAATCATA
65 CATTCTCTTTCACACCCTTTTTGGTAGGTGGGGACTGTCAATCATA
34430517 CGGAGGAAGG
Statistics
Matches: 107, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
110 25 0.23
111 82 0.77
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (110 bp):
TTGGCTTCCGAATCTTGTCTGAGATGAAATTTTAATTCTCATGGAAATCTGTATACTGACTTCTC
ATTCTCTTTCACACCCTTTTTGGTAGGTGGGGACTGTCAATCATA
Found at i:34437248 original size:18 final size:19
Alignment explanation
Indices: 34437225--34437280 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
34437215 ATGTAGACAC
34437225 ATAAATTAAA-AAAATAAT
1 ATAAATTAAATAAAATAAT
*
34437243 ATAAATTAAATTAAATAA-
1 ATAAATTAAATAAAATAAT
34437261 AGTAAA-TAAATAAAATAAT
1 A-TAAATTAAATAAAATAAT
34437280 A
1 A
34437281 ATAATAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 22 0.67
19 11 0.33
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAAATTAAATAAAATAAT
Found at i:34437256 original size:23 final size:23
Alignment explanation
Indices: 34437226--34437288 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
34437216 TGTAGACACA
34437226 TAAATTAAA-AAAATAATATAAAT
1 TAAATTAAATAAAATAA-ATAAAT
*
34437249 TAAATTAAATAAAGTAAATAAA-
1 TAAATTAAATAAAATAAATAAAT
*
34437271 TAAAAT-AATAATAATAAA
1 TAAATTAAATAA-AATAAA
34437289 AAAAATCGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 5 0.14
22 10 0.29
23 14 0.40
24 6 0.17
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
TAAATTAAATAAAATAAATAAAT
Found at i:34437276 original size:9 final size:9
Alignment explanation
Indices: 34437225--34437294 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
34437215 ATGTAGACAC
*
34437225 ATAAATTAA
1 ATAAAATAA
34437234 A-AAAATAA
1 ATAAAATAA
*
34437242 TATAAATTAA
1 -ATAAAATAA
*
34437252 ATTAAATAA
1 ATAAAATAA
34437261 AGT-AAATAA
1 A-TAAAATAA
34437270 ATAAAAT-A
1 ATAAAATAA
34437278 ATAATAATAA
1 ATAA-AATAA
*
34437288 AAAAAAT
1 ATAAAAT
34437295 CGGGATGGCT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
8 12 0.24
9 27 0.54
10 11 0.22
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.27
Consensus pattern (9 bp):
ATAAAATAA
Found at i:34437286 original size:18 final size:19
Alignment explanation
Indices: 34437225--34437294 Score: 67
Period size: 18 Copynumber: 3.8 Consensus size: 19
34437215 ATGTAGACAC
34437225 ATAAATTAAA-AAAATAAT-
1 ATAAA-TAAATAAAATAATA
*
34437243 ATAAATTAAATTAAATAA-A
1 ATAAA-TAAATAAAATAATA
*
34437262 GTAAATAAATAAAATAATA
1 ATAAATAAATAAAATAATA
*
34437281 AT-AATAAAAAAAAT
1 ATAAATAAATAAAAT
34437295 CGGGATGGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 32 0.73
19 12 0.27
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.27
Consensus pattern (19 bp):
ATAAATAAATAAAATAATA
Found at i:34456882 original size:34 final size:34
Alignment explanation
Indices: 34456839--34456906 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
34456829 TAAAATTTCA
*
34456839 TTGGCAATTAAAAAACCTTAGAAGGCTATTATCG
1 TTGGCAATTAAAAAACCTTAGAAGGCTACTATCG
34456873 TTGGCAATTAAAAAACCTTAGAAGGCTACTATCG
1 TTGGCAATTAAAAAACCTTAGAAGGCTACTATCG
34456907 ACGGAAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (34 bp):
TTGGCAATTAAAAAACCTTAGAAGGCTACTATCG
Found at i:34458898 original size:10 final size:10
Alignment explanation
Indices: 34458879--34458917 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
34458869 GGGCTAACAA
34458879 GATA-AAAAC
1 GATATAAAAC
*
34458888 GGTATAAAAC
1 GATATAAAAC
*
34458898 GATATAAAAT
1 GATATAAAAC
34458908 GATATAAAAC
1 GATATAAAAC
34458918 TCATAAGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
9 3 0.12
10 22 0.88
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.21
Consensus pattern (10 bp):
GATATAAAAC
Found at i:34460059 original size:45 final size:45
Alignment explanation
Indices: 34459995--34460084 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
34459985 TCCCTCTCAC
* *
34459995 CATCATGCGCCCACACGCCCCCATTTGCCATTAGACAAAAGTCTT
1 CATCATGCGCCCACACGCCCCCATTGGCCATTAGACAAAAATCTT
* *
34460040 CATCATGCGCCTATACGCCCCCATTGGCCATTAGACAAAAATCTT
1 CATCATGCGCCCACACGCCCCCATTGGCCATTAGACAAAAATCTT
34460085 TGGCTCAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.28, C:0.36, G:0.13, T:0.23
Consensus pattern (45 bp):
CATCATGCGCCCACACGCCCCCATTGGCCATTAGACAAAAATCTT
Found at i:34468577 original size:44 final size:44
Alignment explanation
Indices: 34468514--34468601 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
34468504 TTGCTTCCTG
* *
34468514 AACTCTGGATAGAAAACTTAAGCCGAAATTTCCCCGGAATCTTT
1 AACTCTGAATAGAAAACTTAAGCAGAAATTTCCCCGGAATCTTT
* **
34468558 AACTCTGAATAGAAAACTTAAGCAGGAATTTCTTCGGAATCTTT
1 AACTCTGAATAGAAAACTTAAGCAGAAATTTCCCCGGAATCTTT
34468602 CAGACCCAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (44 bp):
AACTCTGAATAGAAAACTTAAGCAGAAATTTCCCCGGAATCTTT
Found at i:34475785 original size:73 final size:73
Alignment explanation
Indices: 34475705--34475843 Score: 224
Period size: 73 Copynumber: 1.9 Consensus size: 73
34475695 AAACCTATAC
* *
34475705 TTATAAATATATATTCATTAAATGACGATAATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATATATTCATCAAATGACGATAATTAAAATATTTTTTATTATAATTATTAGTAAGAT
34475770 TAAACTTA
66 TAAACTTA
* * * *
34475778 TTATAAATGTGTATTCATCAAATGATGATCATTAAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATATATTCATCAAATGACGATAATTAAAATATTTTTTATTATAATTATTAGTAAGAT
34475843 T
66 T
34475844 TATTTCATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (73 bp):
TTATAAATATATATTCATCAAATGACGATAATTAAAATATTTTTTATTATAATTATTAGTAAGAT
TAAACTTA
Found at i:34481018 original size:22 final size:22
Alignment explanation
Indices: 34480974--34481107 Score: 120
Period size: 22 Copynumber: 6.4 Consensus size: 22
34480964 TTGATTAGAT
* * *
34480974 TGATTTTTAAGTATTGCGAGAC
1 TGATTTTTAGGCATTGCGTGAC
*
34480996 TGATTTTTAGGCATTACGTGAC
1 TGATTTTTAGGCATTGCGTGAC
**
34481018 ------TTAATCATTGCGTGAC
1 TGATTTTTAGGCATTGCGTGAC
* *
34481034 TGATTTTTAGACATTGCGTGAT
1 TGATTTTTAGGCATTGCGTGAC
* *
34481056 TG-GTTTTAGGCATTGCGTGAT
1 TGATTTTTAGGCATTGCGTGAC
*
34481077 TGGTTTTTAGGCATTGCGTGAC
1 TGATTTTTAGGCATTGCGTGAC
34481099 TGATTTTTA
1 TGATTTTTA
34481108 AGTAATACCT
Statistics
Matches: 90, Mismatches: 15, Indels: 14
0.76 0.13 0.12
Matches are distributed among these distances:
16 13 0.14
21 19 0.21
22 58 0.64
ACGTcount: A:0.21, C:0.11, G:0.25, T:0.43
Consensus pattern (22 bp):
TGATTTTTAGGCATTGCGTGAC
Found at i:34481189 original size:26 final size:25
Alignment explanation
Indices: 34481142--34481303 Score: 147
Period size: 26 Copynumber: 6.6 Consensus size: 25
34481132 TTTACTAACA
34481142 AGTCACGCAATG-CTTATC--AACT
1 AGTCACGCAATGCCTTATCAAAACT
*
34481164 AGTTACGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCA-AAACT
*
34481190 ACTCACGCAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATC-AAAACT
* *
34481216 AGTCACGTAATACC-TATC--AACT
1 AGTCACGCAATGCCTTATCAAAACT
*
34481238 AGTCACGCAATGTCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCA-AAACT
* * * * *
34481264 AGTCAAGTAATGTCGTATTAAAAACT
1 AGTCACGCAATGCCTTA-TCAAAACT
*
34481290 AGTTACGCAATGCC
1 AGTCACGCAATGCC
34481304 CAAAATCAGT
Statistics
Matches: 113, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
22 26 0.23
23 10 0.09
25 4 0.04
26 70 0.62
27 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (25 bp):
AGTCACGCAATGCCTTATCAAAACT
Found at i:34481263 original size:74 final size:74
Alignment explanation
Indices: 34481142--34481300 Score: 210
Period size: 74 Copynumber: 2.1 Consensus size: 74
34481132 TTTACTAACA
* * * * *
34481142 AGTCACGCAATGCTTATCAACTAGTTACGCAATGCCTTATCAGAAACTACTCACGCAATGCCTTA
1 AGTCACGCAATACCTATCAACTAGTCACGCAATGCCTTATCAGAAACTACTCAAGCAATGCCGTA
34481207 TCAAAAACT
66 TCAAAAACT
* * * * *
34481216 AGTCACGTAATACCTATCAACTAGTCACGCAATGTCTTATCAGAAACTAGTCAAGTAATGTCGTA
1 AGTCACGCAATACCTATCAACTAGTCACGCAATGCCTTATCAGAAACTACTCAAGCAATGCCGTA
*
34481281 TTAAAAACT
66 TCAAAAACT
*
34481290 AGTTACGCAAT
1 AGTCACGCAAT
34481301 GCCCAAAATC
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (74 bp):
AGTCACGCAATACCTATCAACTAGTCACGCAATGCCTTATCAGAAACTACTCAAGCAATGCCGTA
TCAAAAACT
Found at i:34481347 original size:21 final size:22
Alignment explanation
Indices: 34481318--34481363 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
34481308 ATCAGTACGC
* *
34481318 AATGTCTAAAGTC-AGTCACAT
1 AATGCCTAAAATCTAGTCACAT
*
34481339 AATGCCTAAAATCTAGTCACGT
1 AATGCCTAAAATCTAGTCACAT
34481361 AAT
1 AAT
34481364 TTTCAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (22 bp):
AATGCCTAAAATCTAGTCACAT
Found at i:34484304 original size:33 final size:33
Alignment explanation
Indices: 34484235--34484307 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
34484225 TCTATGCTAT
* * * *
34484235 TGACATGGCATGTTAACATATTATAATCGATAA
1 TGACATAGCATGTTAACATATCAAAATCAATAA
* * *
34484268 TGACATAGCATGTTAATATATCAAAATTAATGA
1 TGACATAGCATGTTAACATATCAAAATCAATAA
34484301 TGACATA
1 TGACATA
34484308 AAATGCTTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (33 bp):
TGACATAGCATGTTAACATATCAAAATCAATAA
Found at i:34492003 original size:49 final size:49
Alignment explanation
Indices: 34491946--34492045 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
34491936 TGAGGTAAGG
34491946 CACTAAATCTTAGCGTTTATTTCTCTTAGTTCAAGTTCAATTGCTGAAT
1 CACTAAATCTTAGCGTTTATTTCTCTTAGTTCAAGTTCAATTGCTGAAT
34491995 CACTAAATCTTAGCGTTTATTTCTCTTAGTTCAAGTTCAATTGCTGAAT
1 CACTAAATCTTAGCGTTTATTTCTCTTAGTTCAAGTTCAATTGCTGAAT
34492044 CA
1 CA
34492046 TACTTCTCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (49 bp):
CACTAAATCTTAGCGTTTATTTCTCTTAGTTCAAGTTCAATTGCTGAAT
Found at i:34496628 original size:13 final size:12
Alignment explanation
Indices: 34496606--34496635 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
34496596 AAACTTATTT
34496606 TATTTATATTAA
1 TATTTATATTAA
34496618 TATTATATATTAA
1 TATT-TATATTAA
34496631 TATTT
1 TATTT
34496636 TTGAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTATATTAA
Found at i:34497708 original size:22 final size:22
Alignment explanation
Indices: 34497677--34497719 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
34497667 TATTAAAATT
*
34497677 GATTTCTTTGAATAATTTTTAA
1 GATTTATTTGAATAATTTTTAA
* *
34497699 GATTTATTTGTATGATTTTTA
1 GATTTATTTGAATAATTTTTA
34497720 TATGACCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (22 bp):
GATTTATTTGAATAATTTTTAA
Found at i:34500817 original size:37 final size:37
Alignment explanation
Indices: 34500748--34500819 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
34500738 ACCTTACGTT
* *
34500748 ATTAATATTTTTCGTTAGAGATAATGACATCAACACC
1 ATTAATATTTTTAGTTAGAGATAATAACATCAACACC
* *
34500785 ATTAATATTTTTAGTTAGAGATGATAATATCAACA
1 ATTAATATTTTTAGTTAGAGATAATAACATCAACA
34500820 TTGACATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (37 bp):
ATTAATATTTTTAGTTAGAGATAATAACATCAACACC
Found at i:34523063 original size:125 final size:126
Alignment explanation
Indices: 34522838--34523068 Score: 351
Period size: 124 Copynumber: 1.9 Consensus size: 126
34522828 TTTCTGAGTT
* * *
34522838 TACCCTGCATTATCTGCTAGTAGTTTATTTAATTCCATTCTCACTGCCATTGAAAAAAAAGAAAT
1 TACCCTGCATTATCTGCTACTAGTTTAGTTAATTCCATTCTCACTGCCATTCAAAAAAAAGAAAT
*
34522903 TAAAGAAAAAACAAATTGTTTCTCTTCCATTCTTTTTTACCAACATGGTGTATTCTTAATC
66 TAAAGAAAAAACAAAGTGTTTCTCTTCCATTCTTTTTTACCAACATGGTGTATTCTTAATC
* * *
34522964 TACCCTGCATTATCTGCTACTAG-TTAGTTAATTCCATTCTCACTGCCA-TCCAGAAAAGGAAAT
1 TACCCTGCATTATCTGCTACTAGTTTAGTTAATTCCATTCTCACTGCCATTCAAAAAAAAGAAAT
* **
34523027 TAAAGAAAAAGCAAAGTGTTTCT-TTCCATTCCCTTTTACCAA
66 TAAAGAAAAAACAAAGTGTTTCTCTTCCATTCTTTTTTACCAA
34523069 TGCGGTACAG
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
123 17 0.18
124 32 0.34
125 24 0.25
126 22 0.23
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.35
Consensus pattern (126 bp):
TACCCTGCATTATCTGCTACTAGTTTAGTTAATTCCATTCTCACTGCCATTCAAAAAAAAGAAAT
TAAAGAAAAAACAAAGTGTTTCTCTTCCATTCTTTTTTACCAACATGGTGTATTCTTAATC
Found at i:34542146 original size:121 final size:122
Alignment explanation
Indices: 34541926--34542152 Score: 366
Period size: 121 Copynumber: 1.9 Consensus size: 122
34541916 TGAACTTGGA
*
34541926 ATCAGAAACAGAAATCTGATGTCACTAGTGAAGTAAGCAAATTGAAATAAAGCTCCTCATTCCCG
1 ATCAGAAACAGAAATCTGATGTCACTAATGAAGTAAGCAAATTGAAATAAAGCTCCTCATTCCCG
*
34541991 GAGAGAAATCATAGATCATAACATGCACAGGACCAGCATGCTTAGAGATAAGATGAC
66 GAGAGAAATCATAGATCATAACATGCACAAGACCAGCATGCTTAGAGATAAGATGAC
* * * *
34542048 ATCAGAACCAGAAATCTGATGTCACTAATGAAGTAAGC-AATTGAAATAAGGCTCCTCATTTCTG
1 ATCAGAAACAGAAATCTGATGTCACTAATGAAGTAAGCAAATTGAAATAAAGCTCCTCATTCCCG
* * *
34542112 GAGAGAAATCCTAGATCATAATATGCACAAGACCAGTATGC
66 GAGAGAAATCATAGATCATAACATGCACAAGACCAGCATGC
34542153 CACAGAGATA
Statistics
Matches: 96, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
121 60 0.62
122 36 0.38
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (122 bp):
ATCAGAAACAGAAATCTGATGTCACTAATGAAGTAAGCAAATTGAAATAAAGCTCCTCATTCCCG
GAGAGAAATCATAGATCATAACATGCACAAGACCAGCATGCTTAGAGATAAGATGAC
Found at i:34550565 original size:2 final size:2
Alignment explanation
Indices: 34550558--34550582 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34550548 CACAAAGACT
34550558 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
34550583 ATATATATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:34557227 original size:33 final size:34
Alignment explanation
Indices: 34557166--34557233 Score: 104
Period size: 33 Copynumber: 2.0 Consensus size: 34
34557156 TCTGTTACAA
*
34557166 TATCTTAGATTAACTTTTGTCACTTTAATATTTC
1 TATCTTAGATTAACTTGTGTCACTTTAATATTTC
34557200 TATCTTCA-ATTAACTTGT-TCACTTTAATATTTC
1 TATCTT-AGATTAACTTGTGTCACTTTAATATTTC
34557233 T
1 T
34557234 CTCTCTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 16 0.50
34 15 0.47
35 1 0.03
ACGTcount: A:0.26, C:0.16, G:0.04, T:0.53
Consensus pattern (34 bp):
TATCTTAGATTAACTTGTGTCACTTTAATATTTC
Found at i:34564588 original size:76 final size:75
Alignment explanation
Indices: 34564491--34564641 Score: 257
Period size: 76 Copynumber: 2.0 Consensus size: 75
34564481 TTAACATTAC
* *
34564491 CAAAATTGTAACTTATAAAATTATTAATTATACTATATATACCTTTATTTATATAAACTTACGAT
1 CAAAATTATAACTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTACGAT
34564556 ATATTTATAT
66 ATATTTATAT
* *
34564566 NCAAAATTATAACTTTTAAAATTATTAATTATAATATATGTACCTTTATTTATATAAACTTACGA
1 -CAAAATTATAACTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTACGA
34564631 TATATTTATAT
65 TATATTTATAT
34564642 ATCTAAAGAG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (75 bp):
CAAAATTATAACTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTACGAT
ATATTTATAT
Found at i:34564691 original size:40 final size:44
Alignment explanation
Indices: 34564614--34564698 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 44
34564604 TGTACCTTTA
34564614 TTTATATAAACTTACGATATATTTATATATCTAAAGAGAA-TTG
1 TTTATATAAACTTACGATATATTTATATATCTAAAGAGAAGTTG
*
34564657 TTTATATAAACTTA-TA-ATA-TTATATA-CTTAAAGAGAAGTTG
1 TTTATATAAACTTACGATATATTTATATATC-TAAAGAGAAGTTG
34564698 T
1 T
34564699 GAGATTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
39 1 0.03
40 16 0.41
41 7 0.18
42 1 0.03
43 14 0.36
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (44 bp):
TTTATATAAACTTACGATATATTTATATATCTAAAGAGAAGTTG
Found at i:34567307 original size:18 final size:18
Alignment explanation
Indices: 34567284--34567325 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
34567274 AAACTTGACA
34567284 AAGACTTGTAAATAAATT
1 AAGACTTGTAAATAAATT
34567302 AAGACTTGTAAATAAATT
1 AAGACTTGTAAATAAATT
34567320 AAGACT
1 AAGACT
34567326 CTAAGTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (18 bp):
AAGACTTGTAAATAAATT
Found at i:34569953 original size:18 final size:18
Alignment explanation
Indices: 34569930--34569965 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
34569920 ATATAATCTT
34569930 TTGTTTTTCATTT-TTAAA
1 TTGTTTTTC-TTTCTTAAA
34569948 TTGTTTTTCTTTCTTAAA
1 TTGTTTTTCTTTCTTAAA
34569966 AAAACCTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (18 bp):
TTGTTTTTCTTTCTTAAA
Found at i:34571431 original size:20 final size:20
Alignment explanation
Indices: 34571406--34571455 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
34571396 ATCGACATGA
*
34571406 ATCGATACAT-TTGAACAAGT
1 ATCGATACATATTGAA-AACT
* *
34571426 ATCGATAGATATTGAAATCT
1 ATCGATACATATTGAAAACT
34571446 ATCGATACAT
1 ATCGATACAT
34571456 GTTCTTAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (20 bp):
ATCGATACATATTGAAAACT
Found at i:34571606 original size:61 final size:60
Alignment explanation
Indices: 34571541--34571660 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
34571531 CAGTAAAATG
** * *
34571541 CTTACTACCTCAAAAGTATCGATACATTTCTTAAATGTATCGATTCATTTTCAACAGAATA
1 CTTACTACCTCAAAAGTATCGATACA-TTAATAAATGTATCAATACATTTTCAACAGAATA
* *
34571602 CTTACTGCCTCAAAAGTATTGATACATTAATAAATGTATCAATACATTTTCAACAGAAT
1 CTTACTACCTCAAAAGTATCGATACATTAATAAATGTATCAATACATTTTCAACAGAAT
34571661 GTTCAAGTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
60 29 0.55
61 24 0.45
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (60 bp):
CTTACTACCTCAAAAGTATCGATACATTAATAAATGTATCAATACATTTTCAACAGAATA
Found at i:34572185 original size:38 final size:37
Alignment explanation
Indices: 34572112--34572185 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 37
34572102 TTGTATTCAC
34572112 TTGAGTGGTTATACCTTAATCAATCGAAAAAGTAGAAA
1 TTGAGTGGTTATACCTTAATCAA-CGAAAAAGTAGAAA
34572150 TTGAGTGGTTATACCTTAATCAA-GATAAAAGGTAGA
1 TTGAGTGGTTATACCTTAATCAACGA-AAAA-GTAGA
34572186 GTAATTGTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 2 0.06
37 4 0.12
38 28 0.82
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (37 bp):
TTGAGTGGTTATACCTTAATCAACGAAAAAGTAGAAA
Found at i:34591028 original size:1 final size:1
Alignment explanation
Indices: 34591022--34591093 Score: 117
Period size: 1 Copynumber: 72.0 Consensus size: 1
34591012 GCCCTCAATT
* * *
34591022 CCCCCCCCCCCCCCCCCGCCCCCCCCCCCCCCCCCACCCCACCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
34591087 CCCCCCC
1 CCCCCCC
34591094 NTACTCCACT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.03, C:0.96, G:0.01, T:0.00
Consensus pattern (1 bp):
C
Found at i:34591385 original size:12 final size:12
Alignment explanation
Indices: 34591365--34591397 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
34591355 AATACTTGTC
*
34591365 TATTAATACGTA
1 TATTTATACGTA
34591377 TATTTATACGTA
1 TATTTATACGTA
34591389 TATTTATAC
1 TATTTATAC
34591398 ACATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (12 bp):
TATTTATACGTA
Found at i:34597535 original size:17 final size:17
Alignment explanation
Indices: 34597513--34597560 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 17
34597503 ATGTAAGATT
34597513 TTTTTTTCTTGAATAAA
1 TTTTTTTCTTGAATAAA
*
34597530 --TTTTT-TTG-ATGAGA
1 TTTTTTTCTTGAAT-AAA
34597544 TTTTTTTCTTGAATAAA
1 TTTTTTTCTTGAATAAA
34597561 AGTAGACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
13 2 0.08
14 5 0.21
15 5 0.21
16 5 0.21
17 5 0.21
18 2 0.08
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.58
Consensus pattern (17 bp):
TTTTTTTCTTGAATAAA
Found at i:34600879 original size:92 final size:92
Alignment explanation
Indices: 34600722--34600906 Score: 352
Period size: 92 Copynumber: 2.0 Consensus size: 92
34600712 ACAACTGGCA
34600722 AGTGAGTCGTTCTGACATTTCATGATACTAGTGGATGCATCCTACAGATGGTCCCATGTTTGCCT
1 AGTGAGTCGTTCTGACATTTCATGATACTAGTGGATGCATCCTACAGATGGTCCCATGTTTGCCT
34600787 GTTATCTATGTGCAACGTCACCTTTGC
66 GTTATCTATGTGCAACGTCACCTTTGC
* *
34600814 AGTGAGTCGTTCTGACATTTCATGATACTAGTGGATGCATCCTGCAGATGGTCTCATGTTTGCCT
1 AGTGAGTCGTTCTGACATTTCATGATACTAGTGGATGCATCCTACAGATGGTCCCATGTTTGCCT
34600879 GTTATCTATGTGCAACGTCACCTTTGC
66 GTTATCTATGTGCAACGTCACCTTTGC
34600906 A
1 A
34600907 TGTTTACTTG
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (92 bp):
AGTGAGTCGTTCTGACATTTCATGATACTAGTGGATGCATCCTACAGATGGTCCCATGTTTGCCT
GTTATCTATGTGCAACGTCACCTTTGC
Found at i:34602902 original size:20 final size:20
Alignment explanation
Indices: 34602877--34602915 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
34602867 TTTGTGTCAA
34602877 AAGTCAAAGTACAAAAACTC
1 AAGTCAAAGTACAAAAACTC
*
34602897 AAGTCAAAGTATAAAAACT
1 AAGTCAAAGTACAAAAACT
34602916 TGTAGTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.18
Consensus pattern (20 bp):
AAGTCAAAGTACAAAAACTC
Found at i:34603875 original size:17 final size:16
Alignment explanation
Indices: 34603820--34603892 Score: 73
Period size: 16 Copynumber: 4.7 Consensus size: 16
34603810 AAATGAAAAT
34603820 AAAA-TATATTATATTA
1 AAAATTATATTATA-TA
34603836 AAAA-TATATT-TA-A
1 AAAATTATATTATATA
*
34603849 AAGATTATATTATATA
1 AAAATTATATTATATA
*
34603865 AAAATTAATATTATATT
1 AAAATT-ATATTATATA
*
34603882 AAACTTATATT
1 AAAATTATATT
34603893 TTAGTAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
13 4 0.08
14 6 0.12
15 4 0.08
16 21 0.43
17 14 0.29
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (16 bp):
AAAATTATATTATATA
Found at i:34613676 original size:30 final size:30
Alignment explanation
Indices: 34613618--34613680 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
34613608 TTAAATAAGA
*
34613618 TTTTATTTTTTTATTAACTTCAACTAAATTT
1 TTTTATTTTTTTATTAAC-TCAAATAAATTT
*
34613649 TTTTATTTTTTATTTTAA-TCAAATAAATTT
1 TTTTATTTTTT-TATTAACTCAAATAAATTT
34613679 TT
1 TT
34613681 ATAATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 13 0.45
31 11 0.38
32 5 0.17
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTATTTTTTTATTAACTCAAATAAATTT
Found at i:34634005 original size:20 final size:20
Alignment explanation
Indices: 34633968--34634010 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
34633958 TTGTTTGTCC
*
34633968 TTTTCTTTTTATGATTTTCT
1 TTTTCTTTTTATGATTTTAT
*
34633988 TTTTCATTTTTGTG-TTTTAT
1 TTTTC-TTTTTATGATTTTAT
34634008 TTT
1 TTT
34634011 ATTCTCTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTTATGATTTTAT
Found at i:34642680 original size:2 final size:2
Alignment explanation
Indices: 34642675--34642706 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34642665 AGCAACATTG
34642675 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34642707 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34642711 original size:2 final size:2
Alignment explanation
Indices: 34642706--34642754 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
34642696 ATATATATAT
34642706 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
34642748 AG AG AG A
1 AG AG AG A
34642755 AGTGTAGCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:34660131 original size:18 final size:18
Alignment explanation
Indices: 34660082--34660150 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
34660072 CCCATCTTTG
*
34660082 AACAGTTAATGTTTATTCA
1 AACAGTTAA-ATTTATTCA
*** * *
34660101 AATTTTTAGATTTGTTCA
1 AACAGTTAAATTTATTCA
*
34660119 AACAGTTATATTTATTCA
1 AACAGTTAAATTTATTCA
*
34660137 AACTGTTAAATTTA
1 AACAGTTAAATTTA
34660151 AATAAAAAGA
Statistics
Matches: 37, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
18 32 0.86
19 5 0.14
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (18 bp):
AACAGTTAAATTTATTCA
Found at i:34661140 original size:20 final size:20
Alignment explanation
Indices: 34661115--34661159 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
34661105 CACCCTTTTC
34661115 TCTTTTTCTCTCAAATCCCA
1 TCTTTTTCTCTCAAATCCCA
34661135 TCTTTTTCTCTCAAATCCCA
1 TCTTTTTCTCTCAAATCCCA
34661155 TCTTT
1 TCTTT
34661160 AACAACATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (20 bp):
TCTTTTTCTCTCAAATCCCA
Found at i:34666144 original size:17 final size:18
Alignment explanation
Indices: 34666112--34666180 Score: 68
Period size: 18 Copynumber: 3.6 Consensus size: 18
34666102 GGAGTCTTAA
34666112 TTTTAAACTTTATATTAT
1 TTTTAAACTTTATATTAT
*
34666130 TTTTAATCTTT-TATTAT
1 TTTTAAACTTTATATTAT
*
34666147 TTTTATAATTTTAATATCTCAT
1 TTTTA-AACTTT-ATAT-T-AT
34666169 TTTTATAACTTT
1 TTTTA-AACTTT
34666181 TTTTTGCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
17 11 0.26
18 14 0.33
20 3 0.07
21 1 0.02
22 13 0.31
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTAAACTTTATATTAT
Found at i:34671057 original size:36 final size:35
Alignment explanation
Indices: 34670986--34671057 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
34670976 TGAATGAAAG
* * * * *
34670986 AAATCTATTGAATAGTTATGTTTGTTCAAATAGTT
1 AAATCTATTGAACAATTATCTTTATTCAAAAAGTT
34671021 AAATCTATTGAAACAATTATCTTTATTCAAAAAGTT
1 AAATCTATTG-AACAATTATCTTTATTCAAAAAGTT
34671057 A
1 A
34671058 TGTTTGCACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 10 0.32
36 21 0.68
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (35 bp):
AAATCTATTGAACAATTATCTTTATTCAAAAAGTT
Found at i:34672278 original size:29 final size:30
Alignment explanation
Indices: 34672246--34672310 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
34672236 TAATTACCAA
*
34672246 AAGTAGTAG-TGGATACCTTT-AACC-ACAAG
1 AAGTAGTAGATGAATA-CTTTCAACCAAC-AG
*
34672275 AAGTGGTAGATGAATACTTTCAACCAACAG
1 AAGTAGTAGATGAATACTTTCAACCAACAG
34672305 AAGTAG
1 AAGTAG
34672311 ATGAATAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 12 0.40
30 16 0.53
31 2 0.07
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (30 bp):
AAGTAGTAGATGAATACTTTCAACCAACAG
Found at i:34674667 original size:18 final size:19
Alignment explanation
Indices: 34674639--34674675 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
34674629 TTTAATTAGT
34674639 TTGACAATACATTAAAAGA
1 TTGACAATACATTAAAAGA
*
34674658 TTGA-AATACATTTAAAGA
1 TTGACAATACATTAAAAGA
34674676 ATGTAGCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (19 bp):
TTGACAATACATTAAAAGA
Found at i:34676290 original size:28 final size:28
Alignment explanation
Indices: 34676258--34676360 Score: 172
Period size: 28 Copynumber: 3.7 Consensus size: 28
34676248 GTATAAGGGT
34676258 AAAATGGTAATTTTACCACCTCAGGGGA
1 AAAATGGTAATTTTACCACCTCAGGGGA
34676286 AAAATGGTAATTTTACCACCTCAGGGGA
1 AAAATGGTAATTTTACCACCTCAGGGGA
* *
34676314 AAAATGGTAATTTTACCACCTCATGGGT
1 AAAATGGTAATTTTACCACCTCAGGGGA
*
34676342 AAAATTGTAATTTT-CCACC
1 AAAATGGTAATTTTACCACC
34676361 ACCAGGATAT
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 5 0.07
28 67 0.93
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (28 bp):
AAAATGGTAATTTTACCACCTCAGGGGA
Found at i:34690033 original size:23 final size:21
Alignment explanation
Indices: 34690004--34690050 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
34689994 TTGTCGGAGT
*
34690004 AGAGAGATG-AGAATGGGAGAG
1 AGAGAGA-GAAGAATGGCAGAG
*
34690025 AGAGAGAGAAGAATTGCAGAG
1 AGAGAGAGAAGAATGGCAGAG
34690046 AGAGA
1 AGAGA
34690051 AAGACGGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.47, C:0.02, G:0.43, T:0.09
Consensus pattern (21 bp):
AGAGAGAGAAGAATGGCAGAG
Found at i:34704180 original size:2 final size:2
Alignment explanation
Indices: 34704173--34704199 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34704163 CCTACCCTCC
34704173 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
34704200 ATCCTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:34711096 original size:3 final size:3
Alignment explanation
Indices: 34711072--34711115 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
34711062 ATTGCTTTTG
* * *
34711072 TTA TTG TTA TTG TTA TTTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
34711116 CAGTCCCTGC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:34724220 original size:228 final size:228
Alignment explanation
Indices: 34723804--34724257 Score: 784
Period size: 228 Copynumber: 2.0 Consensus size: 228
34723794 ACTGTGGGAA
34723804 TGGGACCTGTAAGGTTAGAACCAGCAAGCTTAAGTTGCCTGAGGTTACCGAGATTAAAGAGCCAC
1 TGGGACCTGTAAGGTTAGAACCAGCAAGCTTAAGTTGCCTGAGGTTACCGAGATTAAAGAGCCAC
* * * *
34723869 TGTGGCATTGAAGAGCTGAATCTATTATATGAGAGGTCAAGAGCCTGAAGTGACGTGAAATTTAC
66 TGAGGCACTGAAGACCTGAATCTATTATATGAGAGGTCAAGAGCCTGAAGTGACGAGAAATTTAC
*
34723934 AAATGGAAGAGATTGAGGAAGGTCAAAAAGTTCACAGACAGACAAATCCAATTGCAACAATGAAG
131 AAATGGAAGAGATTGAGGAAGGTCAAAAAGTTCACAGACAGACAAATCCAACTGCAACAATGAAG
34723999 GAAGCATATTAACAGCTTGTAGCCAATTTGTTG
196 GAAGCATATTAACAGCTTGTAGCCAATTTGTTG
* *
34724032 TGGGACCTGTAAGGTTAGAACCAGCAAGCTTAAGTTGCTTGAGGTTACTGAGATTAAAGAGCCAC
1 TGGGACCTGTAAGGTTAGAACCAGCAAGCTTAAGTTGCCTGAGGTTACCGAGATTAAAGAGCCAC
*
34724097 TGAGGTACTGAAGACCTGAAT-TCATTATATGAGAGGTCAAGAGCCTGAAGTGACGAGAAATTTA
66 TGAGGCACTGAAGACCTGAATCT-ATTATATGAGAGGTCAAGAGCCTGAAGTGACGAGAAATTTA
* * * *
34724161 CAAATGGAAGAGATTGAGGAAGGTCAAAAAGTTGACAGCCAGACATATGCAACTGCAACAATGAA
130 CAAATGGAAGAGATTGAGGAAGGTCAAAAAGTTCACAGACAGACAAATCCAACTGCAACAATGAA
34724226 GGAAGCATATTAACAGCTTGTAGCCAATTTGT
195 GGAAGCATATTAACAGCTTGTAGCCAATTTGT
34724258 CGTTGCCTTA
Statistics
Matches: 213, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
227 1 0.00
228 212 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (228 bp):
TGGGACCTGTAAGGTTAGAACCAGCAAGCTTAAGTTGCCTGAGGTTACCGAGATTAAAGAGCCAC
TGAGGCACTGAAGACCTGAATCTATTATATGAGAGGTCAAGAGCCTGAAGTGACGAGAAATTTAC
AAATGGAAGAGATTGAGGAAGGTCAAAAAGTTCACAGACAGACAAATCCAACTGCAACAATGAAG
GAAGCATATTAACAGCTTGTAGCCAATTTGTTG
Found at i:34725908 original size:27 final size:27
Alignment explanation
Indices: 34725865--34726059 Score: 210
Period size: 27 Copynumber: 7.1 Consensus size: 27
34725855 ATAACTGCAT
* * * *
34725865 TTTTCAGCATAACGTGTAATAATTAAA
1 TTTTCAACATGACGTGTAACAACTAAA
** *
34725892 TTTTCAACATGGTGTGTAACAACTATAT
1 TTTTCAACATGACGTGTAACAACTA-AA
* *
34725920 TTTTCTACATGATGTGTAACAACTAAA
1 TTTTCAACATGACGTGTAACAACTAAA
**
34725947 TTTTCAACAAAACGTGTAACAACTAAA
1 TTTTCAACATGACGTGTAACAACTAAA
* * * *
34725974 TTTTTAACATGACGTATAACAATTACAT
1 TTTTCAACATGACGTGTAACAACTA-AA
* *
34726002 TTTTCTACATGACGTGTAACAAATAAA
1 TTTTCAACATGACGTGTAACAACTAAA
*
34726029 TTTTCAACATGACGTGTAACAATTAAA
1 TTTTCAACATGACGTGTAACAACTAAA
34726056 TTTT
1 TTTT
34726060 TATAAACTCA
Statistics
Matches: 139, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
27 93 0.67
28 46 0.33
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (27 bp):
TTTTCAACATGACGTGTAACAACTAAA
Found at i:34725922 original size:55 final size:54
Alignment explanation
Indices: 34725837--34726059 Score: 225
Period size: 55 Copynumber: 4.1 Consensus size: 54
34725827 TGCAACAACT
* * * * * *
34725837 TTTTCAACATG-CTATGTAATAACTGCATTTTTCAGCATAACGTGTAATAATTAAA
1 TTTTCAACATGAC-GTGTAACAACT-AATTTTTCAACATGACGTGTAACAATTAAA
** * * *
34725892 TTTTCAACATGGTGTGTAACAACTATATTTTTCTACATGATGTGTAACAACTAAA
1 TTTTCAACATGACGTGTAACAACTA-ATTTTTCAACATGACGTGTAACAATTAAA
** * *
34725947 TTTTCAACAAAACGTGTAACAACTAAATTTTT-AACATGACGTATAACAATTACAT
1 TTTTCAACATGACGTGTAACAACT-AATTTTTCAACATGACGTGTAACAATTA-AA
* * *
34726002 TTTTCTACATGACGTGTAACAAATAAATTTTCAACATGACGTGTAACAATTAAA
1 TTTTCAACATGACGTGTAACAACTAATTTTTCAACATGACGTGTAACAATTAAA
34726056 TTTT
1 TTTT
34726060 TATAAACTCA
Statistics
Matches: 137, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
54 27 0.20
55 109 0.80
56 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (54 bp):
TTTTCAACATGACGTGTAACAACTAATTTTTCAACATGACGTGTAACAATTAAA
Found at i:34726060 original size:55 final size:54
Alignment explanation
Indices: 34725865--34726059 Score: 228
Period size: 55 Copynumber: 3.6 Consensus size: 54
34725855 ATAACTGCAT
* * * ** *
34725865 TTTTCAGCATAACGTGTAATAATTAAATTTTCAACATGGTGTGTAACAACTATAT
1 TTTTCAACATGACGTGTAACAATTAAATTTTCAACATGACGTGTAACAACTA-AA
* * * **
34725920 TTTTCTACATGATGTGTAACAACTAAATTTTCAACAAAACGTGTAACAACTAAA
1 TTTTCAACATGACGTGTAACAATTAAATTTTCAACATGACGTGTAACAACTAAA
* * * * *
34725974 TTTTTAACATGACGTATAACAATTACATTTTTCTACATGACGTGTAACAAATAAA
1 TTTTCAACATGACGTGTAACAATTA-AATTTTCAACATGACGTGTAACAACTAAA
34726029 TTTTCAACATGACGTGTAACAATTAAATTTT
1 TTTTCAACATGACGTGTAACAATTAAATTTT
34726060 TATAAACTCA
Statistics
Matches: 115, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
54 26 0.23
55 89 0.77
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (54 bp):
TTTTCAACATGACGTGTAACAATTAAATTTTCAACATGACGTGTAACAACTAAA
Found at i:34726060 original size:82 final size:82
Alignment explanation
Indices: 34725865--34726061 Score: 277
Period size: 82 Copynumber: 2.4 Consensus size: 82
34725855 ATAACTGCAT
* * * ** * *
34725865 TTTTCAGCATAACGTGTAATAATTAAATTTTCAACATGGTGTGTAACAACTATATTTTTCTACAT
1 TTTTCAACATAACGTGTAACAATTAAATTTTTAACATGACGTATAACAACTACATTTTTCTACAT
* *
34725930 GATGTGTAACAACTAAA
66 GACGTGTAACAAATAAA
* * *
34725947 TTTTCAACAAAACGTGTAACAACTAAATTTTTAACATGACGTATAACAATTACATTTTTCTACAT
1 TTTTCAACATAACGTGTAACAATTAAATTTTTAACATGACGTATAACAACTACATTTTTCTACAT
34726012 GACGTGTAACAAATAAA
66 GACGTGTAACAAATAAA
*
34726029 TTTTCAACATGACGTGTAACAATTAAATTTTTA
1 TTTTCAACATAACGTGTAACAATTAAATTTTTA
34726062 TAAACTCAAT
Statistics
Matches: 100, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 100 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (82 bp):
TTTTCAACATAACGTGTAACAATTAAATTTTTAACATGACGTATAACAACTACATTTTTCTACAT
GACGTGTAACAAATAAA
Found at i:34726486 original size:18 final size:18
Alignment explanation
Indices: 34726440--34726488 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
34726430 ATGGAAGTTT
* * *
34726440 TTTAAATAGTTATGTTTG
1 TTTAAATAATTATATTTA
* *
34726458 TTCAAACAATTATATTTA
1 TTTAAATAATTATATTTA
34726476 TTTAAATAATTAT
1 TTTAAATAATTAT
34726489 GCATGTTCAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTAAATAATTATATTTA
Found at i:34729270 original size:173 final size:173
Alignment explanation
Indices: 34728968--34731023 Score: 2239
Period size: 173 Copynumber: 12.1 Consensus size: 173
34728958 CATAACACTT
* * * * *
34728968 AATACTTCAATGACTACTCCAATATTTCTTTCCACCACCTCTAGTACA-TATTTTTATTTATTTG
1 AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCGCCTCTAGTACATTTTTTTTATTTATTTG
* *
34729032 CAATACTACATCTTCCTATCACAAAAATCTTTGTAAAATATCTCATAACATTATTGTTGAAAATG
66 CAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAATG
* *
34729097 TCCAACATAAGCAAAGATTAGGTAGAGATGCATTTCCAAAGTC
131 TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
* * *
34729140 AATATTTCAATGACTACTCCAGTCTTCCTTTCTACCGCCTGTAGTACATTTTTTTTATTTATTTG
1 AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCGCCTCTAGTACATTTTTTTTATTTATTTG
* * * * * ***
34729205 CAATACTACATCTTTCTATCACAAAAATTTTTGTACAATATCTCATATCGTTATTGCCAAAAATG
66 CAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAATG
34729270 TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
131 TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
* * * * *
34729313 AACACTTCAATGACTATTCCAGTCTTCATTTCCACCGCCTCTAGCACATCTTTTTTATTTATTTG
1 AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCGCCTCTAGTACATTTTTTTTATTTATTTG
* * * *
34729378 C-A-A-TGCATCTTCCTATCATAAAAATCTCTGTACAATATCTCATAACATTACTGTTGAAAATG
66 CAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAATG
* * *
34729440 TCCTACACAAGCAAGGATTAGGTGGATATGCATTTCCAAAGTC
131 TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
* * * * * * *
34729483 AATATTTCAATAATTACTCCAGTCTTCCTTTCCACTGTCTCCAGTACATCTTCTTTTATTTATTT
1 AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCGCCTCTAGTACAT-TTTTTTTATTTATTT
* * * * * *
34729548 GCAATATTACATCTTCCTATAAAAAAAATCTTTGTACAATATCTCATAACAGTATTGTTAAAAAT
65 GCAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAAT
* * *
34729613 GTCCAACATAAGCAAGGATTATGTGGATATGCATTTCCAAAGTT
130 GTCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
* * ** * ** *
34729657 AATACTTCAATGACTACTTCAGCCTTTTTTTCCACCACCTCTAACACATCTTTTTTATTTATTTG
1 AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCGCCTCTAGTACATTTTTTTTATTTATTTG
* * *
34729722 CAATACTACATTTTCTTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAATT
66 CAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAATG
* * * * * *
34729787 TTCAACGTAAGCAAGGATTAGGTGGTGAGGAATTTCCGAAGTC
131 TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
* ** * * *
34729830 AATACTTCAATAACTACTCCAGTCTTCCTTTCCATTGTCTCCCA-TACATCTTTTTTATTTATTT
1 AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCGCCT-CTAGTACATTTTTTTTATTTATTT
* * * *
34729894 GCAATCCTCCATCTTCCTAT----AAAA---A---A-AATCTCT-GT-ACGA-TA-TGTTGAAAA
65 GCAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAAC-ATTATTGTTGAAAA
* * *
34729944 TGTCCAACATAATCAAAGATTAGGTGGAAATGCATTTCCAAAGTC
129 TGTCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
* * * * ** ** * **
34729989 AATGCTT-AATGACCACTCCAGTTTTCCTTTTCATTGCCTCCGGAACATCATTTTTATTTATTTG
1 AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCGCCTCTAGTACATTTTTTTTATTTATTTG
* *
34730053 CAATAGTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAATT
66 CAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAATG
* ** * * *
34730118 TTCGGCATAAGCAAGGATTAGGTGGTGAGGCATTTCCAAGGTC
131 TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
** * * ** * * * *
34730161 AATACTTCAACAACTACTCTAGTCTTTCTTTCCATTGTCTCTTGTGCA-TCTTTTTATTTATTTG
1 AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCGCCTCTAGTACATTTTTTTTATTTATTTG
* *
34730225 CAATACTACATCTTCCTATCACAAAAA-C---CT-C--TGT-TC---A-A-TA-TGTTGAAAATG
66 CAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAATG
* * * *
34730276 TCCAACACAATCAAAGATTAGGTGGAGATGAATTTCCAAAGTC
131 TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
* * * * * *
34730319 AATGC-TCAATGACTACTCCAGTCTTCTTTTCCACCGCTTTTAGTAGA-TCTTTTTATTTATTTG
1 AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCGCCTCTAGTACATTTTTTTTATTTATTTG
*
34730382 CAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTACTGTTGAAAATG
66 CAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAATG
* * *
34730447 TCCTACACAAGCAAGGATTAGGTGGATATGCATTTCCAAAGTC
131 TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
* * *
34730490 AATATTTCAATGACTACTCCAGTCTTCCTTTCTACCGCCTGTAGTACATTTTTTTTATTTATTTG
1 AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCGCCTCTAGTACATTTTTTTTATTTATTTG
***
34730555 CAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGCCAAAAATG
66 CAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAATG
34730620 TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
131 TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
* * * * * * *
34730663 CATACTTCAATGACTACACCAATCTTCTTTTCCATCGCCTCTAGTATATTGTTTTTATTTATTTG
1 AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCGCCTCTAGTACATTTTTTTTATTTATTTG
*
34730728 CAATACTACATCTTCCTATCACAATAATCTATGTACAATATCTCATAACATTATTGTTGAAAATG
66 CAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAATG
* * * * * * * *
34730793 TTCAGCGTAAGCAAAGATTATGTGGTGAGGCATTTCCAAAATC
131 TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
* * ** * * * * *
34730836 AATACTTCAATAACTACTCTAGTCTTCCTTTCCATTGTCTTTTA-TACATCTTGTTAATTTATTT
1 AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCG-CCTCTAGTACATTTTTTTTATTTATTT
** * * ** * *
34730900 ATAGTATTACATCTAATTCCTATCACAAAAATCCCTATACAATATCTCATAGCATTATTGTTGAA
65 GCAATACTACATC---TTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAA
*** * * *
34730965 AATGTTCC-GTGTAAACAAGGATTCGGTGGAGAGGCATTTCCAAAGTC
127 AATG-TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
*
34731012 AATAATTCAATG
1 AATACTTCAATG
34731024 GTCCATTGCT
Statistics
Matches: 1572, Mismatches: 267, Indels: 86
0.82 0.14 0.04
Matches are distributed among these distances:
157 74 0.05
158 110 0.07
159 52 0.03
160 5 0.00
161 4 0.00
162 11 0.01
163 1 0.00
164 4 0.00
165 5 0.00
166 1 0.00
167 1 0.00
168 3 0.00
169 11 0.01
170 131 0.08
171 73 0.05
172 170 0.11
173 691 0.44
174 133 0.08
176 90 0.06
177 2 0.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (173 bp):
AATACTTCAATGACTACTCCAGTCTTCCTTTCCACCGCCTCTAGTACATTTTTTTTATTTATTTG
CAATACTACATCTTCCTATCACAAAAATCTATGTACAATATCTCATAACATTATTGTTGAAAATG
TCCAACATAAGCAAGGATTAGGTGGAGATGCATTTCCAAAGTC
Found at i:34735113 original size:27 final size:28
Alignment explanation
Indices: 34735083--34735135 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
34735073 AAAAGAAAAT
*
34735083 AATTTT-TTTTATAATTAAAAAAATTTA
1 AATTTTATTTTATAAATAAAAAAATTTA
*
34735110 AATTTTATTTTTTAAATAAAAAAATT
1 AATTTTATTTTATAAATAAAAAAATT
34735136 ATAGATCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AATTTTATTTTATAAATAAAAAAATTTA
Found at i:34737816 original size:56 final size:56
Alignment explanation
Indices: 34737730--34737844 Score: 212
Period size: 56 Copynumber: 2.1 Consensus size: 56
34737720 GTTGGTTCTT
*
34737730 TTGTACAAATTAACAAGTCAAATGATTTGCACTAGTAAGTGTGAGGCATTGACCGA
1 TTGTACAAATTAACAAGCCAAATGATTTGCACTAGTAAGTGTGAGGCATTGACCGA
*
34737786 TTGTACAAATTAACAAGCCAAATGATTTGCACTAGTGAGTGTGAGGCATTGACCGA
1 TTGTACAAATTAACAAGCCAAATGATTTGCACTAGTAAGTGTGAGGCATTGACCGA
34737842 TTG
1 TTG
34737845 CTGGAACTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29
Consensus pattern (56 bp):
TTGTACAAATTAACAAGCCAAATGATTTGCACTAGTAAGTGTGAGGCATTGACCGA
Done.