Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008959.1 Hibiscus syriacus cultivar Beakdansim tig00112293_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4521124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 21
Found at i:2832636 original size:31 final size:33
Alignment explanation
Indices: 2832575--2832637 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 33
2832565 TGGAGGCTCA
2832575 TCGGCTTTGTGCTCAGGGACTTACTTACTGGATCC
1 TCGGCTTTGTGCTCAGGGAC-T-CTTACTGGATCC
2832610 TCGGCTTTGTGCTCAGGG-C-CTTACTGGA
1 TCGGCTTTGTGCTCAGGGACTCTTACTGGA
2832638 CTTGACGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 9 0.32
34 1 0.04
35 18 0.64
ACGTcount: A:0.13, C:0.25, G:0.29, T:0.33
Consensus pattern (33 bp):
TCGGCTTTGTGCTCAGGGACTCTTACTGGATCC
Found at i:2838463 original size:168 final size:169
Alignment explanation
Indices: 2838273--2838611 Score: 662
Period size: 168 Copynumber: 2.0 Consensus size: 169
2838263 AACAATTCTG
2838273 TTAGTACAAAAAGAAAAACGAAAGATTATATGAGATTGTTATAAAACTTACTACTGTTACGGTTC
1 TTAGTACAAAAAGAAAAACGAAAGATTATATGAGATTGTTATAAAACTTACTACTGTTACGGTTC
2838338 CATTTAAGATGTAAAGATTTAGAAGTATAAACTTATTGATACGTTAAGATGCTGAGCTTT-AATT
66 CATTTAAGATGTAAAGATTTAGAAGTATAAACTTATTGATACGTTAAGATGCTGAGCTTTAAATT
*
2838402 ACGGTTATGTTATGTTTATCCCGAACATAATAGGTGTTA
131 ACGGTTATGTTATGTTTATCACGAACATAATAGGTGTTA
2838441 TTAGTACAAAAAGAAAAACGAAAGATTATATGAGATTGTTATAAAACTTACTACTGTTACGGTTC
1 TTAGTACAAAAAGAAAAACGAAAGATTATATGAGATTGTTATAAAACTTACTACTGTTACGGTTC
2838506 CATTTAAGATGTAAAGATTTAGAAGTATAAACTTATTGATACGTTAAGATGCTGAGCTTTAAATT
66 CATTTAAGATGTAAAGATTTAGAAGTATAAACTTATTGATACGTTAAGATGCTGAGCTTTAAATT
2838571 ACGGTTATGTTATGTTTATCACGAACATAATAGGTGTTA
131 ACGGTTATGTTATGTTTATCACGAACATAATAGGTGTTA
2838610 TT
1 TT
2838612 GTGGTCATTG
Statistics
Matches: 169, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
168 125 0.74
169 44 0.26
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (169 bp):
TTAGTACAAAAAGAAAAACGAAAGATTATATGAGATTGTTATAAAACTTACTACTGTTACGGTTC
CATTTAAGATGTAAAGATTTAGAAGTATAAACTTATTGATACGTTAAGATGCTGAGCTTTAAATT
ACGGTTATGTTATGTTTATCACGAACATAATAGGTGTTA
Found at i:2861197 original size:29 final size:29
Alignment explanation
Indices: 2861118--2861187 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
2861108 CACCTAACTA
2861118 AATTGATGTAAGCAATGTCATCTTCACCT
1 AATTGATGTAAGCAATGTCATCTTCACCT
2861147 AATTGATGTAAGCAATGTCATCTTCACCT
1 AATTGATGTAAGCAATGTCATCTTCACCT
2861176 AATTGATGTAAG
1 AATTGATGTAAG
2861188 TAATAACATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (29 bp):
AATTGATGTAAGCAATGTCATCTTCACCT
Found at i:2861697 original size:41 final size:41
Alignment explanation
Indices: 2861652--2861738 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
2861642 TAATTGCTGG
* * *
2861652 AATAGGGTTATTTATAGTTGTATTTTTCTAACAAATATCGT
1 AATAGGGTTATTTATAGTGGTATTTTCCCAACAAATATCGT
* * *
2861693 AATAGGGTTGTTTATAGTGGTGTTTTCCCATCAAATATCGT
1 AATAGGGTTATTTATAGTGGTATTTTCCCAACAAATATCGT
2861734 AATAG
1 AATAG
2861739 AGTAGTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (41 bp):
AATAGGGTTATTTATAGTGGTATTTTCCCAACAAATATCGT
Found at i:2863477 original size:41 final size:41
Alignment explanation
Indices: 2863420--2863562 Score: 141
Period size: 41 Copynumber: 3.5 Consensus size: 41
2863410 ATTTTTAAAC
* *
2863420 ACAAACACCGCAATAGAGTTGAATTATAGAGGCGTTTTTGT
1 ACAAACGCCGCTATAGAGTTGAATTATAGAGGCGTTTTTGT
* * **
2863461 ACAAATGCCGTTATAGAGTTGGACATT-T-CTGGCGTTTTTAGT
1 ACAAACGCCGCTATAGAGTT-GA-ATTATAGAGGCGTTTTT-GT
* * * *
2863503 --AAACGCCGCGATAGAGTTGCACTATAGAGGCGTTTTTCT
1 ACAAACGCCGCTATAGAGTTGAATTATAGAGGCGTTTTTGT
2863542 ACAAACGCCGCTATAGAGTTG
1 ACAAACGCCGCTATAGAGTTG
2863563 GACAGTAGTG
Statistics
Matches: 80, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
38 2 0.03
39 3 0.04
40 24 0.30
41 43 0.54
42 5 0.06
43 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (41 bp):
ACAAACGCCGCTATAGAGTTGAATTATAGAGGCGTTTTTGT
Found at i:2863532 original size:81 final size:82
Alignment explanation
Indices: 2863422--2863634 Score: 261
Period size: 81 Copynumber: 2.6 Consensus size: 82
2863412 TTTTAAACAC
* * * * *
2863422 AAACACCGCAATAGAGTTGAATTATAGAGGCGTTTTTGTACAAATGCCGTTATAGAGTTGGACAT
1 AAACACCGCGATAGAGTTGCACTATAGAGGCGTTTTT-TACAAATGCCGCTATAGAGTTGGACAG
*
2863487 TTCTGGC-GTTTTT-AGT
65 TACTGGCAGTTTTTAAGT
* *
2863503 AAACGCCGCGATAGAGTTGCACTATAGAGGCGTTTTTCTACAAACGCCGCTATAGAGTTGGACAG
1 AAACACCGCGATAGAGTTGCACTATAGAGGCGTTTTT-TACAAATGCCGCTATAGAGTTGGACAG
* *
2863568 TAGTGGCATTTTTTAAGT
65 TACTGGCAGTTTTTAAGT
*
2863586 AAACACCGCGATATA-TTAGCACTATAGAGGCGCTTTTATTACAAATGCC
1 AAACACCGCGATAGAGTT-GCACTATAGAGGCG-TTTT-TTACAAATGCC
2863635 ACAAACTTTG
Statistics
Matches: 113, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
81 62 0.55
82 7 0.06
83 30 0.27
84 13 0.12
85 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (82 bp):
AAACACCGCGATAGAGTTGCACTATAGAGGCGTTTTTTACAAATGCCGCTATAGAGTTGGACAGT
ACTGGCAGTTTTTAAGT
Found at i:2863580 original size:41 final size:38
Alignment explanation
Indices: 2863420--2863582 Score: 110
Period size: 41 Copynumber: 4.0 Consensus size: 38
2863410 ATTTTTAAAC
* * * * *
2863420 ACAAACACCGCAATAGAGTTGAATTATAGAGGCGTTTTTGT
1 ACAAACGCCGCTATAGAGTTGGA-CATAGTGGC-TTTTT-T
* * ** *
2863461 ACAAATGCCGTTATAGAGTTGGACATTTCTGGCGTTTTT
1 ACAAACGCCGCTATAGAGTTGGACA-TAGTGGCTTTTTT
* * * *
2863500 AGTAAACGCCGCGATAGAGTTGCACTATAGAGGCGTTTTTCT
1 A-CAAACGCCGCTATAGAGTTGGAC-ATAGTGGC-TTTTT-T
2863542 ACAAACGCCGCTATAGAGTTGGACAGTAGTGGCATTTTTT
1 ACAAACGCCGCTATAGAGTTGGACA-TAGTGGC-TTTTTT
2863582 A
1 A
2863583 AGTAAACACC
Statistics
Matches: 92, Mismatches: 24, Indels: 13
0.71 0.19 0.10
Matches are distributed among these distances:
39 2 0.02
40 30 0.33
41 58 0.63
42 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (38 bp):
ACAAACGCCGCTATAGAGTTGGACATAGTGGCTTTTTT
Found at i:2869026 original size:38 final size:38
Alignment explanation
Indices: 2868975--2869051 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
2868965 CTGAAGCTGC
*
2868975 TTAAATTATGGTACATTTATTGGATAGAGAATTTGAAT
1 TTAAATTATGGTACATTTATTGGATAAAGAATTTGAAT
*
2869013 TTAAATTATGGTACGTTTATTGGATAAAGAATTTGAAT
1 TTAAATTATGGTACATTTATTGGATAAAGAATTTGAAT
2869051 T
1 T
2869052 ATGTTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (38 bp):
TTAAATTATGGTACATTTATTGGATAAAGAATTTGAAT
Found at i:2869199 original size:24 final size:23
Alignment explanation
Indices: 2869157--2869204 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2869147 AGCTACATCT
**
2869157 TTTTAGTTTATTTTTATAAAACA
1 TTTTAGTTTATTTAAATAAAACA
2869180 TTTTAGTTTATTTAAAATAAAACA
1 TTTTAGTTTATTT-AAATAAAACA
2869204 T
1 T
2869205 GCATTACACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTTAGTTTATTTAAATAAAACA
Found at i:2869611 original size:54 final size:54
Alignment explanation
Indices: 2869552--2869726 Score: 253
Period size: 54 Copynumber: 3.2 Consensus size: 54
2869542 TTCTTTGTAA
* * *
2869552 TGCACACATAGTGCCGAAACGGTTTTTCAACAACATATGATGAATTTCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGAAT
* *
2869606 TGCACACTTAGTGCC-AATATGGTTATTCATCAACATGTGATGAATTTCGTGAAT
1 TGCACACTTAGTGCCGAA-ACGGTTATTCATCAACATATGATGAATTTCGTGAAT
* * *
2869660 TGCACACTTAGTGTCGAAACTGTTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGAAT
*
2869714 TGCACTCTTAGTG
1 TGCACACTTAGTG
2869727 TAAAAACATT
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
53 2 0.02
54 104 0.96
55 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGAAT
Found at i:2869727 original size:54 final size:54
Alignment explanation
Indices: 2869552--2869747 Score: 245
Period size: 54 Copynumber: 3.6 Consensus size: 54
2869542 TTCTTTGTAA
* * * * *
2869552 TGCACACATAGTGCCGAAACGGTTTTTCAACAACATATGATGAATTTCGTGAAT
1 TGCACACTTAGTGTCGAAACTGTTATTCATCAACATATGATGAATTTCGTGAAT
* *
2869606 TGCACACTTAGTG-CCAATA-TGGTTATTCATCAACATGTGATGAATTTCGTGAAT
1 TGCACACTTAGTGTCGAA-ACT-GTTATTCATCAACATATGATGAATTTCGTGAAT
*
2869660 TGCACACTTAGTGTCGAAACTGTTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGTCGAAACTGTTATTCATCAACATATGATGAATTTCGTGAAT
* **
2869714 TGCACTCTTAGTGTAAAAACAT-TTATTCATCAAC
1 TGCACACTTAGTGTCGAAAC-TGTTATTCATCAAC
2869748 GTTTTAGTTT
Statistics
Matches: 125, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
53 3 0.02
54 117 0.94
55 5 0.04
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (54 bp):
TGCACACTTAGTGTCGAAACTGTTATTCATCAACATATGATGAATTTCGTGAAT
Found at i:2869741 original size:108 final size:108
Alignment explanation
Indices: 2869552--2869747 Score: 275
Period size: 108 Copynumber: 1.8 Consensus size: 108
2869542 TTCTTTGTAA
* *
2869552 TGCACACATAGTGCCGAAACGGTTTTTCAACAACATATGATGAATTTCGTGAATTGCACACTTAG
1 TGCACACATAGTGCCGAAACGGTTATTCAACAACATATGATGAATTCCGTGAATTGCACACTTAG
* * **
2869617 TGCCAATATGGTTATTCATCAACATGTGATGAATTTCGTGAAT
66 TGCAAAAACAGTTATTCATCAACATGTGATGAATTTCGTGAAT
* * * * *
2869660 TGCACACTTAGTGTCGAAACTGTTATTCATCAACATATGATGAATTCCGTGAATTGCACTCTTAG
1 TGCACACATAGTGCCGAAACGGTTATTCAACAACATATGATGAATTCCGTGAATTGCACACTTAG
* *
2869725 TGTAAAAACATTTATTCATCAAC
66 TGCAAAAACAGTTATTCATCAAC
2869748 GTTTTAGTTT
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
108 75 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (108 bp):
TGCACACATAGTGCCGAAACGGTTATTCAACAACATATGATGAATTCCGTGAATTGCACACTTAG
TGCAAAAACAGTTATTCATCAACATGTGATGAATTTCGTGAAT
Found at i:2870202 original size:54 final size:54
Alignment explanation
Indices: 2870143--2870643 Score: 670
Period size: 54 Copynumber: 9.3 Consensus size: 54
2870133 TTCTTTGTAA
* * * * *
2870143 TGCACACATAGTGTCGAAACGGTTATTCAACAACATATGATGAATTTCATGAAT
1 TGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATGAATTTCGTGAAT
*
2870197 TGCACACTTAGTGCC-AATATGGTTATTCATCAACATGTGATGAATTTCGTGAAT
1 TGCACACTTAGTGCCGAA-ATGGTTATTCATCAACATATGATGAATTTCGTGAAT
* *
2870251 TGCACACTTAGTGTCGAAACT-ATTATTCATCAACATATGATGAA-TTCTGTGAAT
1 TGCACACTTAGTGCCGAAA-TGGTTATTCATCAACATATGATGAATTTC-GTGAAT
* *
2870305 TGCACACTTAGTGCCGAAATGGTTATTCATCAATATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATGAATTTCGTGAAT
* **
2870359 TGCACACTTAGTGCCTAAAAAGTTATTCATCAACATATGATGAA-TTCTGTGAAT
1 TGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATGAATTTC-GTGAAT
**
2870413 TATACACTTAGTGCCGAAATGGTTATTCATCAACATATGATGAATTAT-GTGAAT
1 TGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATGAATT-TCGTGAAT
* ** * *
2870467 TGCACACTTAGTGCCTAAACAGTTATTCATCGACATATGATAAATTTCGTGAAT
1 TGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATGAATTTCGTGAAT
* * * *
2870521 TGCACACTTAGTGCCGAAAGGGTTATTCATCAAGATATGATAAATTTCATGAAT
1 TGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATGAATTTCGTGAAT
* **
2870575 TGCACACTTAGTGTCGAAATAATTATTCATCAACATATGATGAATTTCGTGAAT
1 TGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATGAATTTCGTGAAT
*
2870629 TACACACTTAGTGCC
1 TGCACACTTAGTGCC
2870644 AATTTTTTAA
Statistics
Matches: 392, Mismatches: 45, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
53 9 0.02
54 376 0.96
55 6 0.02
56 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATGAATTTCGTGAAT
Found at i:2870307 original size:591 final size:592
Alignment explanation
Indices: 2869157--2870317 Score: 2198
Period size: 591 Copynumber: 2.0 Consensus size: 592
2869147 AGCTACATCT
2869157 TTTTAGTTTATTTTTATAAAACATTTTAGTTTATTTAAAATAAAACATGCATTACACCTAAATAG
1 TTTTAGTTTATTTTTATAAAACATTTTAGTTTATTTAAAATAAAACATGCATTACACCTAAATAG
*
2869222 ACAAACAAAAAGAAATGTTCAAACACTTCACAGTTTTACAACAGTTTAATTCAAATGCTTTTCAG
66 ACAAACAAAAAGAAATGATCAAACACTTCACAGTTTTACAACAGTTTAATTCAAATGCTTTTCAG
*
2869287 AGCCTTCTTACTAAACCTATTACATGTCAACTAAAATACATCAAAAGTAGACATGTATGTCATAC
131 AGCCTTCTTACTAAACCTATTACATGTCAACTAAAATACATCAAAAGTAGACACGTATGTCATAC
*
2869352 TGTTAGTGATGAGACAACTCTGCCATTGATGTCCATAATCTCTTTACTCAGCTTTTATTAAACCT
196 TGTTAGTGACGAGACAACTCTGCCATTGATGTCCATAATCTCTTTACTCAGCTTTTATTAAACCT
2869417 ACGCTTGAAATAAACACACATTAAGTATTACTTAGTGAGGCAAAGACTAATCATACAATGAAAAC
261 ACGCTTGAAATAAACACACATTAAGTATTACTTAGTGAGGCAAAGACTAATCATACAATGAAAAC
*
2869482 ATTATATCATTATTTCTTATCGATCAAATACCAATTCTTTATTTTCCCATCATTTTTCATTTCTT
326 ATTATATCATTATTTCTTATCGATCAAATACCAATTCTTTATTTTCCAATCATTTTTCATTTCTT
* *
2869547 TGTAATGCACACATAGTGCCGAAACGGTTTTTCAACAACATATGATGAATTTCGTGAATTGCACA
391 TGTAATGCACACATAGTGCCGAAACGGTTATTCAACAACATATGATGAATTTCATGAATTGCACA
2869612 CTTAGTGCCAATATGGTTATTCATCAACATGTGATGAATTTCGTGAATTGCACACTTAGTGTCGA
456 CTTAGTGCCAATATGGTTATTCATCAACATGTGATGAATTTCGTGAATTGCACACTTAGTGTCGA
* *
2869677 AACTGTTATTCATCAACATATGATGAATTCCGTGAATTGCACTCTTAGTGTAAAAACATTTATTC
521 AACTATTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGTAAAAACATTTATTC
2869742 ATCAACG
586 ATCAACG
2869749 TTTTAGTTTATTTTTATAAAACATTTTA-TTTATTTAAAATAAAACATGCATTACACCTAAATAG
1 TTTTAGTTTATTTTTATAAAACATTTTAGTTTATTTAAAATAAAACATGCATTACACCTAAATAG
*
2869813 ACAAACAAAAAGAGATGATCAAACACTTCACAGTTTTACAACAGTTTAATTCAAATGCTTTTCAG
66 ACAAACAAAAAGAAATGATCAAACACTTCACAGTTTTACAACAGTTTAATTCAAATGCTTTTCAG
2869878 AGCCTTCTTACTAAACCTATTACATGTCAACTAAAATACATCAAAAGTAGACACGTATGTCATAC
131 AGCCTTCTTACTAAACCTATTACATGTCAACTAAAATACATCAAAAGTAGACACGTATGTCATAC
*
2869943 TGTTAGTGACGAGACAACTCTGCCTTTGATGTCCATAATCTCTTTACTCAGCTTTTATTAAACCT
196 TGTTAGTGACGAGACAACTCTGCCATTGATGTCCATAATCTCTTTACTCAGCTTTTATTAAACCT
*
2870008 ACGCTTGAAATAAACACACATTAAGTATTACTTAGTGAGGCAAATACTAATCATACAATGAAAAC
261 ACGCTTGAAATAAACACACATTAAGTATTACTTAGTGAGGCAAAGACTAATCATACAATGAAAAC
2870073 ATTATATCATTATTTCTTATCGATCAAATACCAATTCTTTATTTTCCAATCATTTTTCATTTCTT
326 ATTATATCATTATTTCTTATCGATCAAATACCAATTCTTTATTTTCCAATCATTTTTCATTTCTT
*
2870138 TGTAATGCACACATAGTGTCGAAACGGTTATTCAACAACATATGATGAATTTCATGAATTGCACA
391 TGTAATGCACACATAGTGCCGAAACGGTTATTCAACAACATATGATGAATTTCATGAATTGCACA
2870203 CTTAGTGCCAATATGGTTATTCATCAACATGTGATGAATTTCGTGAATTGCACACTTAGTGTCGA
456 CTTAGTGCCAATATGGTTATTCATCAACATGTGATGAATTTCGTGAATTGCACACTTAGTGTCGA
*
2870268 AACTATTATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTG
521 AACTATTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTG
2870318 CCGAAATGGT
Statistics
Matches: 556, Mismatches: 13, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
591 528 0.95
592 28 0.05
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (592 bp):
TTTTAGTTTATTTTTATAAAACATTTTAGTTTATTTAAAATAAAACATGCATTACACCTAAATAG
ACAAACAAAAAGAAATGATCAAACACTTCACAGTTTTACAACAGTTTAATTCAAATGCTTTTCAG
AGCCTTCTTACTAAACCTATTACATGTCAACTAAAATACATCAAAAGTAGACACGTATGTCATAC
TGTTAGTGACGAGACAACTCTGCCATTGATGTCCATAATCTCTTTACTCAGCTTTTATTAAACCT
ACGCTTGAAATAAACACACATTAAGTATTACTTAGTGAGGCAAAGACTAATCATACAATGAAAAC
ATTATATCATTATTTCTTATCGATCAAATACCAATTCTTTATTTTCCAATCATTTTTCATTTCTT
TGTAATGCACACATAGTGCCGAAACGGTTATTCAACAACATATGATGAATTTCATGAATTGCACA
CTTAGTGCCAATATGGTTATTCATCAACATGTGATGAATTTCGTGAATTGCACACTTAGTGTCGA
AACTATTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGTAAAAACATTTATTC
ATCAACG
Found at i:2871029 original size:19 final size:22
Alignment explanation
Indices: 2870993--2871039 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 22
2870983 ACCACAATAT
2870993 CGATACTACTATATTATGGTAC
1 CGATACTACTATATTATGGTAC
*
2871015 CGATACT-CTA-A-TATGGTAT
1 CGATACTACTATATTATGGTAC
2871034 CGATAC
1 CGATAC
2871040 CATTTTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 13 0.54
20 1 0.04
21 3 0.12
22 7 0.29
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (22 bp):
CGATACTACTATATTATGGTAC
Found at i:2874096 original size:16 final size:15
Alignment explanation
Indices: 2874059--2874096 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 15
2874049 ACAAATGAAG
2874059 AAAATGATAAATGGAA
1 AAAAT-ATAAATGGAA
2874075 AAAATATAAATGGAA
1 AAAATATAAATGGAA
2874090 AATAATA
1 AA-AATA
2874097 AATAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (15 bp):
AAAATATAAATGGAA
Found at i:2882959 original size:24 final size:23
Alignment explanation
Indices: 2882923--2883018 Score: 88
Period size: 24 Copynumber: 4.0 Consensus size: 23
2882913 ATTTCCTGAA
*
2882923 TGCACA-AATAGTGTCTCGTAGAAT
1 TGCACATAA-AGTGTC-CATAGAAT
* *
2882947 TTCACATAAAGTGCCACATAGAAT
1 TGCACATAAAGTGTC-CATAGAAT
2882971 TGCACATAAAGT-TCCATATAGAAT
1 TGCACATAAAGTGTCC--ATAGAAT
*
2882995 TGCACATAAAGTGTCGCGTAGAAT
1 TGCACATAAAGTGTC-CATAGAAT
2883019 GTACACAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
22 1 0.02
23 1 0.02
24 53 0.88
25 4 0.07
26 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (23 bp):
TGCACATAAAGTGTCCATAGAAT
Found at i:2887778 original size:16 final size:16
Alignment explanation
Indices: 2887737--2887788 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
2887727 AATAAAATAT
2887737 AAAACATGTATCATAATAA
1 AAAACAT-TAT-AT-ATAA
2887756 GAAAACATTATATATAA
1 -AAAACATTATATATAA
2887773 AAAACATT-TA-ATAA
1 AAAACATTATATATAA
2887787 AA
1 AA
2887789 TCAATCTGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.19
15 2 0.06
16 8 0.25
17 4 0.12
18 2 0.06
19 3 0.09
20 7 0.22
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.27
Consensus pattern (16 bp):
AAAACATTATATATAA
Found at i:2887786 original size:14 final size:15
Alignment explanation
Indices: 2887749--2887788 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
2887739 AACATGTATC
2887749 ATAATAAGAAAACATT
1 ATAATAA-AAAACATT
2887765 ATATATAAAAAACATT
1 ATA-ATAAAAAACATT
2887781 -TAATAAAA
1 ATAATAAAA
2887789 TCAATCTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
16 11 0.48
17 4 0.17
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (15 bp):
ATAATAAAAAACATT
Found at i:2888496 original size:19 final size:19
Alignment explanation
Indices: 2888472--2888523 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
2888462 ATGCACTTGA
2888472 TGCACCGATTCACTCTTAG
1 TGCACCGATTCACTCTTAG
*
2888491 TGCACCGATTCCCTCTTAG
1 TGCACCGATTCACTCTTAG
*
2888510 TGCACCGATGCACT
1 TGCACCGATTCACT
2888524 AAGGGTCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.19, C:0.35, G:0.17, T:0.29
Consensus pattern (19 bp):
TGCACCGATTCACTCTTAG
Found at i:2894209 original size:24 final size:24
Alignment explanation
Indices: 2894182--2894260 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
2894172 ACACTTAACA
2894182 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
2894206 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
2894228 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
2894250 GTGCATCGATG
1 GTGCATCGATG
2894261 GACGGGGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
20 3 0.07
21 11 0.26
22 1 0.02
23 12 0.28
24 16 0.37
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:2895846 original size:21 final size:21
Alignment explanation
Indices: 2895804--2895847 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2895794 ACTCCGGGAG
* *
2895804 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
2895825 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
2895846 CT
1 CT
2895848 CCGGCTCTGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:2897095 original size:17 final size:19
Alignment explanation
Indices: 2897067--2897115 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2897057 TATTTTGAAA
2897067 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
2897085 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
2897104 CACCGATGCACT
1 CATCGATGCACT
2897116 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:2897894 original size:12 final size:11
Alignment explanation
Indices: 2897875--2897958 Score: 78
Period size: 12 Copynumber: 7.1 Consensus size: 11
2897865 TCCGTAGAAT
2897875 TGCACATAAAG
1 TGCACATAAAG
*
2897886 TGCCACATATAAT
1 TG-CACATA-AAG
2897899 TGCACATAAAG
1 TGCACATAAAG
*
2897910 TGCCACATAGAAT
1 TG-CACATA-AAG
2897923 TGCACATAAAG
1 TGCACATAAAG
* *
2897934 TGCCACTTAGAAT
1 TG-CACATA-AAG
2897947 TGCACATAAAG
1 TGCACATAAAG
2897958 T
1 T
2897959 ACCGCGTAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
11 13 0.22
12 34 0.58
13 12 0.20
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.24
Consensus pattern (11 bp):
TGCACATAAAG
Found at i:2897969 original size:48 final size:48
Alignment explanation
Indices: 2897867--2897970 Score: 163
Period size: 48 Copynumber: 2.2 Consensus size: 48
2897857 AATAGTGTTC
* *
2897867 CGTAGAATTGCACATAAAGTGCCACATATAATTGCACATAAAGTGCCA
1 CGTAGAATTGCACATAAAGTGCCACATAGAATTGCACATAAAGTACCA
* * *
2897915 CATAGAATTGCACATAAAGTGCCACTTAGAATTGCACATAAAGTACCG
1 CGTAGAATTGCACATAAAGTGCCACATAGAATTGCACATAAAGTACCA
2897963 CGTAGAAT
1 CGTAGAAT
2897971 GTACACGAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.23
Consensus pattern (48 bp):
CGTAGAATTGCACATAAAGTGCCACATAGAATTGCACATAAAGTACCA
Found at i:2897970 original size:24 final size:24
Alignment explanation
Indices: 2897869--2897958 Score: 162
Period size: 24 Copynumber: 3.8 Consensus size: 24
2897859 TAGTGTTCCG
2897869 TAGAATTGCACATAAAGTGCCACA
1 TAGAATTGCACATAAAGTGCCACA
*
2897893 TATAATTGCACATAAAGTGCCACA
1 TAGAATTGCACATAAAGTGCCACA
*
2897917 TAGAATTGCACATAAAGTGCCACT
1 TAGAATTGCACATAAAGTGCCACA
2897941 TAGAATTGCACATAAAGT
1 TAGAATTGCACATAAAGT
2897959 ACCGCGTAGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
TAGAATTGCACATAAAGTGCCACA
Found at i:2903837 original size:24 final size:24
Alignment explanation
Indices: 2903780--2903827 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2903770 TATTTTCAAA
2903780 ACATCAAAAGAAATTTTGGTATTG
1 ACATCAAAAGAAATTTTGGTATTG
2903804 ACATCAAAAGAAATTTTGGTATTG
1 ACATCAAAAGAAATTTTGGTATTG
2903828 GTACTCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (24 bp):
ACATCAAAAGAAATTTTGGTATTG
Found at i:2903861 original size:21 final size:20
Alignment explanation
Indices: 2903836--2903887 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
2903826 TGGTACTCAA
2903836 AGGAGTATCAATAC-CTAAG
1 AGGAGTATCAATACTCTAAG
* *
2903855 ATGGGAGTATCGATACTCTTAG
1 A--GGAGTATCAATACTCTAAG
2903877 AGGAGTATCAA
1 AGGAGTATCAA
2903888 CATTGAGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.04
20 9 0.33
21 12 0.44
22 5 0.19
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (20 bp):
AGGAGTATCAATACTCTAAG
Found at i:2916129 original size:21 final size:20
Alignment explanation
Indices: 2916104--2916142 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2916094 CATCAAGGTC
*
2916104 TTTGTGGAGGCCATGAAATCT
1 TTTGTGGAAGCCAT-AAATCT
*
2916125 TTTGTTGAAGCCATAAAT
1 TTTGTGGAAGCCATAAAT
2916143 TCCTACAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (20 bp):
TTTGTGGAAGCCATAAATCT
Found at i:2918934 original size:26 final size:27
Alignment explanation
Indices: 2918877--2918935 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 27
2918867 TTTCATCATA
2918877 CTTG-CTTCAAACTTCTTCAGATAAAC
1 CTTGCCTTCAAACTTCTTCAGATAAAC
2918903 CTTGCCTT-AAACTTCTTCAGATAAAC
1 CTTGCCTTCAAACTTCTTCAGATAAAC
2918929 CTTGCCT
1 CTTGCCT
2918936 CGGCGAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 29 0.91
27 3 0.09
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.36
Consensus pattern (27 bp):
CTTGCCTTCAAACTTCTTCAGATAAAC
Found at i:2922136 original size:18 final size:20
Alignment explanation
Indices: 2922091--2922143 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 20
2922081 ATTCCTCTAA
2922091 GAGTATCGATACTCTCCCTCTT
1 GAGTATCGATA--CTCCCTCTT
*
2922113 GTGTATCGATACT-CC-CTT
1 GAGTATCGATACTCCCTCTT
2922131 GAGTATCGATACT
1 GAGTATCGATACT
2922144 AAAATTGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 15 0.52
19 2 0.07
20 2 0.07
22 10 0.34
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (20 bp):
GAGTATCGATACTCCCTCTT
Found at i:2929543 original size:19 final size:19
Alignment explanation
Indices: 2929519--2929564 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2929509 ACAGATGTTT
* *
2929519 TCTCTGATTTCTGTTATGA
1 TCTCTGATCTCTGCTATGA
*
2929538 TCTCTGATCTCTGCTCTGA
1 TCTCTGATCTCTGCTATGA
*
2929557 TTTCTGAT
1 TCTCTGAT
2929565 ATCTCTGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.13, C:0.22, G:0.15, T:0.50
Consensus pattern (19 bp):
TCTCTGATCTCTGCTATGA
Found at i:2943464 original size:2 final size:2
Alignment explanation
Indices: 2943459--2943507 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2943449 TGTGTGTGTG
2943459 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2943501 TA TA TA T
1 TA TA TA T
2943508 TTCTCTCTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2944425 original size:2 final size:2
Alignment explanation
Indices: 2944418--2944475 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
2944408 GGATGGCAAA
2944418 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
2944460 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2944476 TTAATAAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2946528 original size:30 final size:30
Alignment explanation
Indices: 2946494--2946560 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
2946484 TTTTTATATA
* * *
2946494 AGCTCATCTCATGCATATCATCATTTCTCT
1 AGCTCATCTCATGCATATAATCACTTATCT
*
2946524 AGCTCAACTCATGCATATAATCACTTATCT
1 AGCTCATCTCATGCATATAATCACTTATCT
2946554 AGCTCAT
1 AGCTCAT
2946561 TCTTAGCTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.36
Consensus pattern (30 bp):
AGCTCATCTCATGCATATAATCACTTATCT
Found at i:2947476 original size:14 final size:15
Alignment explanation
Indices: 2947448--2947476 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2947438 CACAATTACT
2947448 TATATTTTTTGTGAC
1 TATATTTTTTGTGAC
2947463 TATATTTTTT-TGAC
1 TATATTTTTTGTGAC
2947477 ACAATTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (15 bp):
TATATTTTTTGTGAC
Found at i:2947480 original size:38 final size:38
Alignment explanation
Indices: 2947432--2947504 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
2947422 ATTTATTGAA
* *
2947432 TTTTGTCACAATTACTTATATTTTTTGTGACTATATTT
1 TTTTGACACAATTACTTATAGTTTTTGTGACTATATTT
*
2947470 TTTTGACACAATTACTTATGGTTTTTGTGACTATA
1 TTTTGACACAATTACTTATAGTTTTTGTGACTATA
2947505 ATTGTAACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (38 bp):
TTTTGACACAATTACTTATAGTTTTTGTGACTATATTT
Found at i:2948196 original size:23 final size:23
Alignment explanation
Indices: 2948170--2948214 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2948160 CACCACAGCT
*
2948170 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
2948193 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2948215 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2948435 original size:149 final size:149
Alignment explanation
Indices: 2948194--2948490 Score: 533
Period size: 149 Copynumber: 2.0 Consensus size: 149
2948184 GAAGTGCCGC
2948194 GTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAAGACCACATAGAATTCCTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAAGACCACATAGAATTCCTTAAGAATC
** *
2948259 ATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATATAT
66 ATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATAT
2948324 ATATATCCCGAAGGACCGT
131 ATATATCCCGAAGGACCGT
*
2948343 GTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAAGACCACATAGAATTCCTTAAGAATC
*
2948408 ATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATATA
66 ATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATA
2948472 TATATATCCCGAAGGACCG
130 TATATATCCCGAAGGACCG
2948491 CATAGACCCT
Statistics
Matches: 142, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
149 141 0.99
150 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
GTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAAGACCACATAGAATTCCTTAAGAATC
ATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATAT
ATATATCCCGAAGGACCGT
Found at i:2949416 original size:18 final size:18
Alignment explanation
Indices: 2949395--2949429 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2949385 TCCCATCTAG
2949395 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
2949413 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
2949430 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:2950036 original size:21 final size:21
Alignment explanation
Indices: 2950012--2950056 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2950002 TGTTGTTCGT
* *
2950012 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2950033 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2950054 TTG
1 TTG
2950057 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2953343 original size:23 final size:23
Alignment explanation
Indices: 2953317--2953361 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2953307 CACCACAGCT
*
2953317 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
2953340 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2953362 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2953582 original size:149 final size:149
Alignment explanation
Indices: 2953329--2953643 Score: 553
Period size: 149 Copynumber: 2.1 Consensus size: 149
2953319 TATAATTGCA
2953329 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCACAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCACAAGGACCACATAGAA
**
2953393 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
2953458 CCACAGAATATATATATATC
130 CCAAAGAATATATATATATC
*
2953478 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCACAAGGACCACATAGAAT
*
2953543 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTT
2953607 CCAAAGAATATATATATATC
130 CCAAAGAATATATATATATC
2953627 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
2953644 CCCTCGACTC
Statistics
Matches: 159, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
150 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCACAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:2955190 original size:21 final size:21
Alignment explanation
Indices: 2955160--2955204 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2955150 TGTTGTTTGT
* *
2955160 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2955181 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2955202 TTG
1 TTG
2955205 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2957587 original size:30 final size:30
Alignment explanation
Indices: 2957549--2957646 Score: 117
Period size: 30 Copynumber: 3.3 Consensus size: 30
2957539 CATTCATACT
* * *
2957549 TAGCTCATCTTTTGCTTAAGATCATTTATC
1 TAGCTCATCTTATGCATAACATCATTTATC
*
2957579 TAAG-TCATCTTATGCATATCATCATTTATC
1 T-AGCTCATCTTATGCATAACATCATTTATC
* * *
2957609 TAGCTCATCTCATGCATATCATCACTTATC
1 TAGCTCATCTTATGCATAACATCATTTATC
2957639 TAGCTCAT
1 TAGCTCAT
2957647 AAATATGCGA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
29 2 0.03
30 56 0.93
31 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (30 bp):
TAGCTCATCTTATGCATAACATCATTTATC
Found at i:2957997 original size:21 final size:21
Alignment explanation
Indices: 2957973--2958029 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
2957963 TGACACTATT
2957973 TACCTAGCTAGCTACCTACA-C
1 TACCTAGCTAGCTACCTA-ATC
*
2957994 TACCTAGCTACCTACCTAATC
1 TACCTAGCTAGCTACCTAATC
*
2958015 TTCCTAGCTAGCTAC
1 TACCTAGCTAGCTAC
2958030 TAGCCTACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.26, C:0.37, G:0.09, T:0.28
Consensus pattern (21 bp):
TACCTAGCTAGCTACCTAATC
Found at i:2967612 original size:3 final size:3
Alignment explanation
Indices: 2967604--2967684 Score: 162
Period size: 3 Copynumber: 27.0 Consensus size: 3
2967594 TTTAATCAAA
2967604 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2967652 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2967685 TTAACACTGC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2969657 original size:24 final size:24
Alignment explanation
Indices: 2969625--2969676 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
2969615 AGGAAGGTTC
2969625 TCAATCACTTCCACGTTGACCTTA
1 TCAATCACTTCCACGTTGACCTTA
*
2969649 TCAATCACTTCCACGTTGAGCTTA
1 TCAATCACTTCCACGTTGACCTTA
2969673 TCAA
1 TCAA
2969677 CCTTGATGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.33
Consensus pattern (24 bp):
TCAATCACTTCCACGTTGACCTTA
Found at i:2973329 original size:21 final size:21
Alignment explanation
Indices: 2973242--2973330 Score: 58
Period size: 21 Copynumber: 4.2 Consensus size: 21
2973232 CTCTTCATTA
* *
2973242 AAAGATTAAATCCTTTCAT-G
1 AAAGATTAAGTCCTTTTATCG
* *
2973262 AAAAGGTTAAG-CACTTTTCATCA
1 -AAAGATTAAGTC-CTTTT-ATCG
* * *
2973285 AAAGGA-TAAGTCATTTAATTG
1 AAA-GATTAAGTCCTTTTATCG
2973306 AAAGATTAAGTCCTTTTATCG
1 AAAGATTAAGTCCTTTTATCG
2973327 AAAG
1 AAAG
2973331 GCCTTAATCC
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
20 3 0.06
21 33 0.66
22 12 0.24
23 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (21 bp):
AAAGATTAAGTCCTTTTATCG
Found at i:2995733 original size:18 final size:18
Alignment explanation
Indices: 2995710--2995767 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
2995700 ACCGGTTACA
2995710 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2995728 ACCCGATCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
2995746 ACCCGACCCGGCCTGTTG
1 ACCCGACCCGACCCGTTG
2995764 ACCC
1 ACCC
2995768 TATCCGTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.16, C:0.48, G:0.22, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2995813 original size:29 final size:29
Alignment explanation
Indices: 2995780--2995849 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
2995770 TCCGTTGATC
2995780 GGGTGCTATTTTGATAATTATTTAGAAAA
1 GGGTGCTATTTTGATAATTATTTAGAAAA
* * *
2995809 GGGTGCTATTCTGGTAATTATTTTGAAAA
1 GGGTGCTATTTTGATAATTATTTAGAAAA
*
2995838 GGGTTCTATTTT
1 GGGTGCTATTTT
2995850 CGTAATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (29 bp):
GGGTGCTATTTTGATAATTATTTAGAAAA
Found at i:2995854 original size:29 final size:28
Alignment explanation
Indices: 2995780--2995866 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 28
2995770 TCCGTTGATC
*
2995780 GGGTGCTATTTTGATAATTATTTAGAAAA
1 GGGTGCTATTTTG-TAATTATTTTGAAAA
*
2995809 GGGTGCTATTCTGGTAATTATTTTGAAAA
1 GGGTGCTATT-TTGTAATTATTTTGAAAA
* * *
2995838 GGGTTCTATTTTCGTAATTTTTTTTAAAA
1 GGGTGCTATTTT-GTAATTATTTTGAAAA
2995867 AAAAATTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.02
29 47 0.94
30 2 0.04
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.46
Consensus pattern (28 bp):
GGGTGCTATTTTGTAATTATTTTGAAAA
Found at i:2995884 original size:25 final size:24
Alignment explanation
Indices: 2995845--2995893 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
2995835 AAAGGGTTCT
2995845 ATTTTCGTAATTTTTTTTAAAAAAAA
1 ATTTTCGTAA--TTTTTTAAAAAAAA
2995871 ATTTT-GTAATTTTTTAAAAAAAA
1 ATTTTCGTAATTTTTTAAAAAAAA
2995894 TGATATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 14 0.61
25 4 0.17
26 5 0.22
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
ATTTTCGTAATTTTTTAAAAAAAA
Found at i:2995926 original size:29 final size:28
Alignment explanation
Indices: 2995780--2995932 Score: 98
Period size: 29 Copynumber: 5.5 Consensus size: 28
2995770 TCCGTTGATC
* *
2995780 GGGTGCTATTTTGATAATTATTTAGAAAA
1 GGGTGATATTTTG-TAATTATTTTGAAAA
* *
2995809 GGGTGCTATTCTGGTAATTATTTTGAAAA
1 GGGTGATATT-TTGTAATTATTTTGAAAA
** * *
2995838 GGGTTCTATTTTCGTAATTTTTTTTAAAA
1 GGGTGATATTTT-GTAATTATTTTGAAAA
** * *
2995867 ---AAAAATTTTGTAATT-TTTTAAAAA
1 GGGTGATATTTTGTAATTATTTTGAAAA
***
2995891 AAATGATATTTTAGTAATTATTTTGAAAA
1 GGGTGATATTTT-GTAATTATTTTGAAAA
*
2995920 TGGTGATATTTTG
1 GGGTGATATTTTG
2995933 GTACTTTTTT
Statistics
Matches: 99, Mismatches: 18, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
24 8 0.08
25 6 0.06
26 5 0.05
27 6 0.06
28 8 0.08
29 64 0.65
30 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.46
Consensus pattern (28 bp):
GGGTGATATTTTGTAATTATTTTGAAAA
Found at i:2995943 original size:29 final size:28
Alignment explanation
Indices: 2995871--2995964 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 28
2995861 TTAAAAAAAA
**
2995871 ATTTT-GTAATT-TTTTAAAAAAAATGAT
1 ATTTTAGTAATTATTTT-AAAATGATGAT
*
2995898 ATTTTAGTAATTATTTTGAAAATGGTGAT
1 ATTTTAGTAATTATTTT-AAAATGATGAT
* * * *
2995927 ATTTTGGTACTTTTTTTAAAATGATGTT
1 ATTTTAGTAATTATTTTAAAATGATGAT
*
2995955 ATTTTCGTAA
1 ATTTTAGTAA
2995965 AATGGTTGTT
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
27 5 0.09
28 23 0.43
29 26 0.48
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.51
Consensus pattern (28 bp):
ATTTTAGTAATTATTTTAAAATGATGAT
Found at i:2996156 original size:6 final size:6
Alignment explanation
Indices: 2996145--2996169 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2996135 CAGTCAAACC
2996145 CTTTGA CTTTGA CTTTGA CTTTGA C
1 CTTTGA CTTTGA CTTTGA CTTTGA C
2996170 CAAGAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (6 bp):
CTTTGA
Found at i:2998186 original size:2 final size:2
Alignment explanation
Indices: 2998179--2998244 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
2998169 AAACGAGAAA
2998179 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
2998221 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
2998245 CCATTTTACT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3012921 original size:122 final size:122
Alignment explanation
Indices: 3012698--3012941 Score: 373
Period size: 122 Copynumber: 2.0 Consensus size: 122
3012688 AGTGGAAGCA
**
3012698 AATTAACCTCGAATCTGATCTTCACGGAAGAGTAGTGAAACAGATTCTTCTCAAGCAAATCCAGC
1 AATTAACCTCGAATCTGATCTTCACGGAAGAGTAGTGAAACAGATTCTAATCAAGCAAATCCAGC
* * *
3012763 CTTCACAAAAGAGTAGTGAAGTAGGAAAAGACCAAAAGTTCGATCTCCACGGAAGAG
66 CTTCACAAAAGAGTAGTGAAGCAGGAAAAGACCAAAAGTTCAATCTCCACAGAAGAG
* * *
3012820 AATTAATCTCGAATCTGATTTTCTCGGAAGAGTAGTGAAACAGATTCTAATCAAGCAAATCCAGC
1 AATTAACCTCGAATCTGATCTTCACGGAAGAGTAGTGAAACAGATTCTAATCAAGCAAATCCAGC
* * *
3012885 CTTCACAAAAGAGTAGTGAAGCAGGAACATG-TCAAAAGTTCAATTTCCACAGAAGAG
66 CTTCACAAAAGAGTAGTGAAGCAGGAA-AAGACCAAAAGTTCAATCTCCACAGAAGAG
3012942 TAGTGAAACA
Statistics
Matches: 110, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
122 108 0.98
123 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (122 bp):
AATTAACCTCGAATCTGATCTTCACGGAAGAGTAGTGAAACAGATTCTAATCAAGCAAATCCAGC
CTTCACAAAAGAGTAGTGAAGCAGGAAAAGACCAAAAGTTCAATCTCCACAGAAGAG
Found at i:3013088 original size:3 final size:3
Alignment explanation
Indices: 3013080--3013113 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3013070 GTTTTAGTTA
*
3013080 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT AAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3013114 ATAATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3015684 original size:15 final size:15
Alignment explanation
Indices: 3015664--3015693 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3015654 TTGCCGGTCG
*
3015664 AAAAGAAATAAAAAA
1 AAAAGAAAGAAAAAA
3015679 AAAAGAAAGAAAAAA
1 AAAAGAAAGAAAAAA
3015694 GTAAATAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (15 bp):
AAAAGAAAGAAAAAA
Found at i:3015884 original size:35 final size:35
Alignment explanation
Indices: 3015838--3015907 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
3015828 TTCCTATGTG
* *
3015838 TCGAAAATATTTGAGTTGATTCAATGAGTTGTTAA
1 TCGAAAATATTTGAGTTGATGCAATGAGCTGTTAA
3015873 TCGAAAATATTTGAGTTGATGCAATGAGCTGTTAA
1 TCGAAAATATTTGAGTTGATGCAATGAGCTGTTAA
3015908 AACCCTAGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.37
Consensus pattern (35 bp):
TCGAAAATATTTGAGTTGATGCAATGAGCTGTTAA
Found at i:3020239 original size:20 final size:21
Alignment explanation
Indices: 3020210--3020259 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
3020200 TTAACAATGT
* *
3020210 TATCGGTACCTCACCCCTT-G
1 TATCGATACCTAACCCCTTGG
3020230 TATCGATACCTAACCCCTTGG
1 TATCGATACCTAACCCCTTGG
3020251 TATCGATAC
1 TATCGATAC
3020260 TTGAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.22, C:0.34, G:0.14, T:0.30
Consensus pattern (21 bp):
TATCGATACCTAACCCCTTGG
Found at i:3020665 original size:20 final size:19
Alignment explanation
Indices: 3020622--3020709 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 19
3020612 CACTGTTATT
* *
3020622 GATACCAAACATTCAGTATT
1 GATACCAAGC-TTCAGTATC
3020642 GATACCAAGCTTCCAGTATC
1 GATACCAAGCTT-CAGTATC
3020662 GATACTACAAGCCTT-AGTATC
1 GATAC--CAAG-CTTCAGTATC
**
3020683 GATACCAAGGGATCAGTATC
1 GATACCAA-GCTTCAGTATC
3020703 GATACCA
1 GATACCA
3020710 TTCCATCCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
19 6 0.10
20 34 0.59
21 11 0.19
22 4 0.07
23 3 0.05
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (19 bp):
GATACCAAGCTTCAGTATC
Found at i:3023463 original size:17 final size:16
Alignment explanation
Indices: 3023435--3023466 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3023425 TTTTAGAATT
3023435 TAATAAAAAATATATA
1 TAATAAAAAATATATA
3023451 TAATAAGAAAATATAT
1 TAATAA-AAAATATAT
3023467 GAATTTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
TAATAAAAAATATATA
Found at i:3035210 original size:156 final size:158
Alignment explanation
Indices: 3034919--3035233 Score: 616
Period size: 156 Copynumber: 2.0 Consensus size: 158
3034909 AGCTACTGAA
3034919 TCTTTACCCACAATTTCATATGCTCCAAATACTTTTCTAACGGTTCTTAGCCTTGTAGTTAGGAA
1 TCTTTACCCACAATTTCATATGCTCCAAATACTTTTCTAACGGTTCTTAGCCTTGTAGTTAGGAA
3034984 TTGATAGTCATTATTGGCTATCCTGTTAAGGATATCGAAGGCTTCCTTGGGTGATTTATCAAGCA
66 TTGATAGTCATTATTGGCTATCCTGTTAAGGATATCGAAGGCTTCCTTGGGTGATTTATCAAGCA
3035049 AAGTACCG-TTACCGAGGCATCCAACAT
131 AAGTACCGTTTACCGAGGCATCCAACAT
3035076 TCTTTA-CCACAATTTCATATGCTCCAAATACTTTTCTAACGGTTCTTAGCCTTGTAGTTAGGAA
1 TCTTTACCCACAATTTCATATGCTCCAAATACTTTTCTAACGGTTCTTAGCCTTGTAGTTAGGAA
3035140 TTGATAGTCATTATTGGCTATCCTGTTAAGGATATCGAAGGCTTCCTTGGGTGATTTATCAAGCA
66 TTGATAGTCATTATTGGCTATCCTGTTAAGGATATCGAAGGCTTCCTTGGGTGATTTATCAAGCA
3035205 AAGTACCGTTTACCGAGGCATCCAACAT
131 AAGTACCGTTTACCGAGGCATCCAACAT
3035233 T
1 T
3035234 ATTCGAGTAG
Statistics
Matches: 157, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
156 131 0.83
157 26 0.17
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (158 bp):
TCTTTACCCACAATTTCATATGCTCCAAATACTTTTCTAACGGTTCTTAGCCTTGTAGTTAGGAA
TTGATAGTCATTATTGGCTATCCTGTTAAGGATATCGAAGGCTTCCTTGGGTGATTTATCAAGCA
AAGTACCGTTTACCGAGGCATCCAACAT
Found at i:3040220 original size:30 final size:30
Alignment explanation
Indices: 3040186--3040242 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
3040176 TTTTTTGTAA
*
3040186 AAACGCTGTAATAGAGTGGTTTATTACAAT
1 AAACGCCGTAATAGAGTGGTTTATTACAAT
*
3040216 AAACGCCGTAATAGGGTGGTTTATTAC
1 AAACGCCGTAATAGAGTGGTTTATTAC
3040243 GGCGTTTAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (30 bp):
AAACGCCGTAATAGAGTGGTTTATTACAAT
Found at i:3040453 original size:83 final size:82
Alignment explanation
Indices: 3040366--3040536 Score: 193
Period size: 83 Copynumber: 2.1 Consensus size: 82
3040356 GATTACACAT
** * * *
3040366 ATAGTGGCATTTATT-CTTAAAATGCCGCAATAGTGATAATAAATAGTGGTG-TTTTTAGACAAA
1 ATAGTGGCATTT-TTACAAAAAACGCCGCAATAGTGATAATAAATAGTGGCGTTTTTTA-AAAAA
*
3040429 TTCCACAATAGTGTTAATCA
64 CTCCACAATAGTG-TAATCA
* * ** *
3040449 ATAGTGGCGTTTTTAGAAAAAACGCCGCAATAGTTTTAATCAATAGTGGCGTTTTTTAAAAAACT
1 ATAGTGGCATTTTTACAAAAAACGCCGCAATAGTGATAATAAATAGTGGCGTTTTTTAAAAAACT
*
3040514 CCTCAATAGTGTAATCA
66 CCACAATAGTGTAATCA
3040531 ATAGTG
1 ATAGTG
3040537 TCTTTTTTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
82 14 0.19
83 54 0.73
84 6 0.08
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (82 bp):
ATAGTGGCATTTTTACAAAAAACGCCGCAATAGTGATAATAAATAGTGGCGTTTTTTAAAAAACT
CCACAATAGTGTAATCA
Found at i:3040493 original size:42 final size:42
Alignment explanation
Indices: 3040384--3040536 Score: 177
Period size: 41 Copynumber: 3.7 Consensus size: 42
3040374 ATTTATTCTT
* * * *
3040384 AAAATGCCGCAATAGTGATAATAAATAGTGGTGTTTTTAG-A
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAA
* ** *
3040425 CAAATTCCACAATAGTGTTAATCAATAGTGGCGTTTTTAGAA
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAA
* *
3040467 AAAACGCCGCAATAGTTTTAATCAATAGTGGCGTTTTT-TAA
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAA
* *
3040508 AAAACTCCTCAATAGTG-TAATCAATAGTG
1 AAAACGCCGCAATAGTGTTAATCAATAGTG
3040537 TCTTTTTTTT
Statistics
Matches: 96, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
40 12 0.12
41 50 0.52
42 34 0.35
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (42 bp):
AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAA
Found at i:3040557 original size:83 final size:83
Alignment explanation
Indices: 3040384--3040536 Score: 211
Period size: 83 Copynumber: 1.9 Consensus size: 83
3040374 ATTTATTCTT
* * * *
3040384 AAAATGCCGCAATAGTGATAATAAATAGTGGTGTTTTTAGACAAATTCCACAATAGTGTTAATCA
1 AAAACGCCGCAATAGTGATAATAAATAGTGGCGTTTTTAGAAAAACTCCACAATAGTGTTAATCA
3040449 ATAGTGGCGTTTTTAGAA
66 ATAGTGGCGTTTTTAGAA
** * *
3040467 AAAACGCCGCAATAGTTTTAATCAATAGTGGCGTTTTTTA-AAAAACTCCTCAATAGTG-TAATC
1 AAAACGCCGCAATAGTGATAATAAATAGTGGCG-TTTTTAGAAAAACTCCACAATAGTGTTAATC
3040530 AATAGTG
65 AATAGTG
3040537 TCTTTTTTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
82 12 0.20
83 43 0.70
84 6 0.10
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (83 bp):
AAAACGCCGCAATAGTGATAATAAATAGTGGCGTTTTTAGAAAAACTCCACAATAGTGTTAATCA
ATAGTGGCGTTTTTAGAA
Found at i:3042010 original size:41 final size:41
Alignment explanation
Indices: 3041951--3042313 Score: 377
Period size: 42 Copynumber: 8.8 Consensus size: 41
3041941 TCCAATAAAT
* * *
3041951 GCCGCTATAG-GTACGTACTATAGTGGTGTTTTTATACAAAC
1 GCCGCTATAGACT-CGTACTTTAGTGGCGTTTTTATACAAAC
* * *
3041992 GCCGTTATAGAATCGTACTTTAATGGCGTTTTTATACAAAC
1 GCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAAC
* *
3042033 GCCGCTATATACTAGTACTTTAGTGGCGTTTTCTATACAAAC
1 GCCGCTATAGACTCGTACTTTAGTGGCGTTTT-TATACAAAC
* * * ** * *
3042075 ACCGCGATATACTTATACTTTAGTGGCGTTTTGAATCCAAAC
1 GCCGCTATAGACTCGTACTTTAGTGGCGTTTT-TATACAAAC
* * * * * * *
3042117 ACCTCCATAAACTTGTACTTTAGTGGCGTTTTGAATGCAAAC
1 GCCGCTATAGACTCGTACTTTAGTGGCGTTTT-TATACAAAC
* * *
3042159 GCCGCTAAAGACTCGTACTTTAGTAGCGTTTTTATATAAAC
1 GCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAAC
* *
3042200 GCCGCTATAGAGTAGTACTTTAGTGGCGTTTTTATACAAAC
1 GCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAAC
* * *
3042241 GCCGCTATAGACTCGTACTTTAGTGGCATTTTGAATGCAAAC
1 GCCGCTATAGACTCGTACTTTAGTGGCGTTTT-TATACAAAC
* * *
3042283 GCTGCTATAGACTCATACTTTAATGGCGTTT
1 GCCGCTATAGACTCGTACTTTAGTGGCGTTT
3042314 GTATTTCCAA
Statistics
Matches: 273, Mismatches: 46, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
41 132 0.48
42 141 0.52
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
GCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAAC
Found at i:3042602 original size:41 final size:41
Alignment explanation
Indices: 3042557--3042788 Score: 152
Period size: 41 Copynumber: 5.7 Consensus size: 41
3042547 CTTTAGCAGT
* *
3042557 GTTTTTAAATAAACGCCGTAATAGAGTTCATCTATAGTGGC
1 GTTTTTAAACAAACGCCGCAATAGAGTTCATCTATAGTGGC
* * * **
3042598 GTTTTTCAACAAACGTCGTAATAGAGTAGTCAT-T-T-GCAGC
1 GTTTTTAAACAAACGCCGCAATAGAGT--TCATCTATAGTGGC
* * * * *
3042638 ATTTTTTATACAAATGCCGCAATAGGGTTCAACTATAGTGGC
1 -GTTTTTAAACAAACGCCGCAATAGAGTTCATCTATAGTGGC
** * * * * *
3042680 AATTTTCAACAAACGTCGTAATAGAG-T-AGTACTTTAGCGGC
1 GTTTTTAAACAAACGCCGCAATAGAGTTCA-T-CTATAGTGGC
* * * *
3042721 ATTTTTATACAAATGCCGCAATAGGGTTCATCTATAGTGGC
1 GTTTTTAAACAAACGCCGCAATAGAGTTCATCTATAGTGGC
*
3042762 GTTTTTCAAA-AAACGTCGCAATAGAGT
1 GTTTTT-AAACAAACGCCGCAATAGAGT
3042789 AGTACTTTAG
Statistics
Matches: 140, Mismatches: 40, Indels: 22
0.69 0.20 0.11
Matches are distributed among these distances:
39 4 0.03
40 5 0.04
41 118 0.84
42 8 0.06
43 5 0.04
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (41 bp):
GTTTTTAAACAAACGCCGCAATAGAGTTCATCTATAGTGGC
Found at i:3042674 original size:82 final size:82
Alignment explanation
Indices: 3042536--3042860 Score: 381
Period size: 82 Copynumber: 3.9 Consensus size: 82
3042526 AATGAGGTGG
** * * * * *
3042536 ATAGAGTAGTACTTTAGCAGTGTTTTTAAATAAACGCCGTAATAGAGTTCATCTATAGTGGCGTT
1 ATAGAGTAGTACTTTAGCAGCATTTTTATACAAATGCCGCAATAGGGTTCATCTATAGTGGCGTT
3042601 TTTCAACAAACGTCGTA
66 TTTCAACAAACGTCGTA
* *
3042618 ATAGAGTAGT-CATTT-GCAGCATTTTTTATACAAATGCCGCAATAGGGTTCAACTATAGTGGCA
1 ATAGAGTAGTAC-TTTAGCAGCA-TTTTTATACAAATGCCGCAATAGGGTTCATCTATAGTGGCG
*
3042681 ATTTTCAACAAACGTCGTA
64 TTTTTCAACAAACGTCGTA
*
3042700 ATAGAGTAGTACTTTAGCGGCATTTTTATACAAATGCCGCAATAGGGTTCATCTATAGTGGCGTT
1 ATAGAGTAGTACTTTAGCAGCATTTTTATACAAATGCCGCAATAGGGTTCATCTATAGTGGCGTT
* *
3042765 TTTCAAAAAACGTCGCA
66 TTTCAACAAACGTCGTA
* * * * * *
3042782 ATAGAGTAGTACTTTAGCA-C-TGTTTATAGAAAAACGCCGCAATA-GATATAATCTTTAGTGGC
1 ATAGAGTAGTACTTTAGCAGCAT-TTT-TATACAAATGCCGCAATAGGGT-TCATCTATAGTGGC
3042844 GTTTGTTTCAACAAACG
63 G-TT-TTTCAACAAACG
3042861 CCACAACATA
Statistics
Matches: 210, Mismatches: 24, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
80 1 0.00
81 11 0.05
82 179 0.85
83 8 0.04
84 11 0.05
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (82 bp):
ATAGAGTAGTACTTTAGCAGCATTTTTATACAAATGCCGCAATAGGGTTCATCTATAGTGGCGTT
TTTCAACAAACGTCGTA
Found at i:3046646 original size:14 final size:14
Alignment explanation
Indices: 3046627--3046654 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3046617 CGAGATAGAG
3046627 TATTTAGTAAAGAA
1 TATTTAGTAAAGAA
3046641 TATTTAGTAAAGAA
1 TATTTAGTAAAGAA
3046655 AAGTTAGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
TATTTAGTAAAGAA
Found at i:3052250 original size:21 final size:21
Alignment explanation
Indices: 3052224--3052297 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
3052214 AGAAGCAATC
* *
3052224 AGAGAAGCAGCGGAAGCAGAG
1 AGAGAAGCAGCGGCAGCACAG
* *
3052245 AAAGAAGCAGCGGCAGTACAG
1 AGAGAAGCAGCGGCAGCACAG
*
3052266 AGAGAAGTAGCGGCAGCACAG
1 AGAGAAGCAGCGGCAGCACAG
3052287 AGAGAAGCAGC
1 AGAGAAGCAGC
3052298 ATATCAGCAG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.42, C:0.18, G:0.38, T:0.03
Consensus pattern (21 bp):
AGAGAAGCAGCGGCAGCACAG
Found at i:3052779 original size:43 final size:43
Alignment explanation
Indices: 3052712--3053042 Score: 330
Period size: 43 Copynumber: 7.7 Consensus size: 43
3052702 TTTTAGCAAC
* ** *
3052712 AACGCCGCAAAACATCAATGCCTACTGCGGCGTTTGTGAGAAA
1 AACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTGAGAAA
* * * *
3052755 AACGCCGCAAAACATCAAAACCTACTGCGGCGTTTGTG-GGAA
1 AACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTGAGAAA
* * * *
3052797 AATGCCGCAAAACATCAACACCTACTGCGGCGTTT-TAGATAAA
1 AACGCCGCTAAACATCAACACCTATTGCGGCGTTTGT-GAGAAA
* *
3052840 AACGCCGCTAAACATCATA-ACCTATTGCGGCGTTTATCTA-AAA
1 AACGCCGCTAAACATCA-ACACCTATTGCGGCGTTTGT-GAGAAA
** * *
3052883 AACGCCGCTAAATTTCAACACCTATTGCGGCGTTTGTCAAAAA
1 AACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTGAGAAA
* * * *
3052926 AACACCGCTAAATATCAATACCTATTGCGGCGTTTGTCTA-AAA
1 AACGCCGCTAAACATCAACACCTATTGCGGCGTTTGT-GAGAAA
* * * * *
3052969 AACCCCGCTAAATATCAACACCTATTGTGGCGTTTGTGTGACA
1 AACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTGAGAAA
* *
3053012 AACGCCGCTAAATATCAATACCTATTGCGGC
1 AACGCCGCTAAACATCAACACCTATTGCGGC
3053043 ATTTTTTGTT
Statistics
Matches: 251, Mismatches: 29, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.00
42 39 0.16
43 207 0.82
44 4 0.02
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (43 bp):
AACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTGAGAAA
Found at i:3052934 original size:86 final size:86
Alignment explanation
Indices: 3052712--3053042 Score: 371
Period size: 86 Copynumber: 3.9 Consensus size: 86
3052702 TTTTAGCAAC
* * ** * * *
3052712 AACGCCGCAAAACATCAATGCCTACTGCGGCGTTTGTGAGAAAAACGCCGCAAAACATCAAAACC
1 AACGCCGCTAAATATCAACACCTACTGCGGCGTTTGTGAAAAAAACGCCGCTAAACATCAATACC
* ***
3052777 TACTGCGGCGTTTGT-GGGAA
66 TATTGCGGCGTTTGTCTAAAA
* * * *
3052797 AATGCCGCAAAACATCAACACCTACTGCGGCGTTT-TAGATAAAAACGCCGCTAAACATC-ATAA
1 AACGCCGCTAAATATCAACACCTACTGCGGCGTTTGT-GAAAAAAACGCCGCTAAACATCAAT-A
*
3052860 CCTATTGCGGCGTTTATCTAAAA
64 CCTATTGCGGCGTTTGTCTAAAA
* * * * *
3052883 AACGCCGCTAAATTTCAACACCTATTGCGGCGTTTGTCAAAAAAACACCGCTAAATATCAATACC
1 AACGCCGCTAAATATCAACACCTACTGCGGCGTTTGTGAAAAAAACGCCGCTAAACATCAATACC
3052948 TATTGCGGCGTTTGTCTAAAA
66 TATTGCGGCGTTTGTCTAAAA
* * * ** * *
3052969 AACCCCGCTAAATATCAACACCTATTGTGGCGTTTGTGTGACAAACGCCGCTAAATATCAATACC
1 AACGCCGCTAAATATCAACACCTACTGCGGCGTTTGTGAAAAAAACGCCGCTAAACATCAATACC
3053034 TATTGCGGC
66 TATTGCGGC
3053043 ATTTTTTGTT
Statistics
Matches: 212, Mismatches: 29, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
84 2 0.01
85 68 0.32
86 139 0.66
87 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (86 bp):
AACGCCGCTAAATATCAACACCTACTGCGGCGTTTGTGAAAAAAACGCCGCTAAACATCAATACC
TATTGCGGCGTTTGTCTAAAA
Found at i:3054202 original size:2 final size:2
Alignment explanation
Indices: 3054195--3054226 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3054185 CGGGTATCGG
3054195 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
3054227 TAGGACAATA
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):
AT
Found at i:3058893 original size:12 final size:12
Alignment explanation
Indices: 3058876--3058900 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3058866 ATCTTTGAAC
3058876 ACAAACCAAATT
1 ACAAACCAAATT
3058888 ACAAACCAAATT
1 ACAAACCAAATT
3058900 A
1 A
3058901 GCAAGCAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (12 bp):
ACAAACCAAATT
Found at i:3065151 original size:24 final size:24
Alignment explanation
Indices: 3065123--3065172 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
3065113 ATAATCAAAC
*
3065123 TAAAAATCCAAAATTAAAATGGTT
1 TAAAAATCCAAAATTAAAAAGGTT
3065147 TAAAAATCCAAAATTAAAAAGGTT
1 TAAAAATCCAAAATTAAAAAGGTT
3065171 TA
1 TA
3065173 TCACAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (24 bp):
TAAAAATCCAAAATTAAAAAGGTT
Found at i:3072766 original size:19 final size:21
Alignment explanation
Indices: 3072729--3072771 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3072719 TCCTTTCTTG
*
3072729 AAAGGGATCGATTCTTTTG-A
1 AAAGGGATCGATTCCTTTGCA
*
3072749 AAAGGGATTGA-TCCTTTGCA
1 AAAGGGATCGATTCCTTTGCA
3072769 AAA
1 AAA
3072772 CATAAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
AAAGGGATCGATTCCTTTGCA
Found at i:3074831 original size:17 final size:18
Alignment explanation
Indices: 3074795--3074836 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
3074785 GTTATTTTTA
3074795 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
3074813 AAATAAAAGA-AATAATT
1 AAATAAAAGATAAGAATT
3074830 AAATAAA
1 AAATAAA
3074837 TAATTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:3075560 original size:76 final size:76
Alignment explanation
Indices: 3075455--3075670 Score: 355
Period size: 76 Copynumber: 2.8 Consensus size: 76
3075445 TAAAACATCT
* *
3075455 TAAATCTTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
1 TAAAACTTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
3075519 AAAATAATATCC
65 AAAATAATATCC
*
3075531 TGAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
*
3075596 AAATAATATCT
66 AAATAATATCC
*
3075607 TAAAACTTAATT-AAATAACTAAAACTTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
1 TAAAACTTAATTAAAAT-ACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
3075671 TTATTTAAAA
Statistics
Matches: 132, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
75 9 0.07
76 123 0.93
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (76 bp):
TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAATAATATCC
Found at i:3088394 original size:21 final size:22
Alignment explanation
Indices: 3088368--3088420 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
3088358 AAACCATTCA
3088368 GGGGGGAATCAGTACCCCCTTG
1 GGGGGGAATCAGTACCCCCTTG
3088390 GGGGGGAATCAGTACCCCCTT-
1 GGGGGGAATCAGTACCCCCTTG
3088411 GGGGGGAATC
1 GGGGGGAATC
3088421 GGTTTCCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 10 0.32
22 21 0.68
ACGTcount: A:0.19, C:0.25, G:0.40, T:0.17
Consensus pattern (22 bp):
GGGGGGAATCAGTACCCCCTTG
Found at i:3097122 original size:116 final size:118
Alignment explanation
Indices: 3096927--3097151 Score: 305
Period size: 117 Copynumber: 1.9 Consensus size: 118
3096917 AAATGATTAG
** * *
3096927 ATTTAATTAAAAATTGAATGAATAAATAAGAGAAATGAAAAAAGATGGTAAAACACTAAACATTT
1 ATTTAATTAAAAATAAAATGAATAAATAAGAGAAATGAAAAAAGAGGGTAAAACACTAAAAATTT
* *
3096992 TATGGAATTAT-AAAATTAAGGG-TCCTAATTATAAATATAAAAAATTGGTTAA
66 TATGAAATTATAAAAATT-AGGGACCCTAATTATAAATATAAAAAATTGGTTAA
* * **
3097044 ATTTAATTCAAAATAAAATGAATTAATAAGAGAAA-GGGAAAAGAGGGTCAAAA-ACTAAAAATT
1 ATTTAATTAAAAATAAAATGAATAAATAAGAGAAATGAAAAAAGAGGGT-AAAACACTAAAAATT
*
3097107 TTATGAAATTATAAAAATTAGGGACCCTGATTATAAATATAAAAA
65 TTATGAAATTATAAAAATTAGGGACCCTAATTATAAATATAAAAA
3097152 TAAGGGCCTT
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
116 34 0.36
117 60 0.64
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.28
Consensus pattern (118 bp):
ATTTAATTAAAAATAAAATGAATAAATAAGAGAAATGAAAAAAGAGGGTAAAACACTAAAAATTT
TATGAAATTATAAAAATTAGGGACCCTAATTATAAATATAAAAAATTGGTTAA
Found at i:3097166 original size:27 final size:28
Alignment explanation
Indices: 3097107--3097178 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 28
3097097 ACTAAAAATT
* *
3097107 TTATGAAATTATAAAAATTAGGGACCCTGA
1 TTAT-AAA-TATAAAAATAAGGGACCCTAA
*
3097137 TTATAAATATAAAAATAAGGG-CCTTAA
1 TTATAAATATAAAAATAAGGGACCCTAA
*
3097164 TTATAAATACAAAAA
1 TTATAAATATAAAAA
3097179 AATTGGGGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 18 0.47
28 13 0.34
29 3 0.08
30 4 0.11
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.29
Consensus pattern (28 bp):
TTATAAATATAAAAATAAGGGACCCTAA
Found at i:3098357 original size:25 final size:25
Alignment explanation
Indices: 3098329--3098410 Score: 83
Period size: 25 Copynumber: 3.1 Consensus size: 25
3098319 TTCCGAGAGT
3098329 TTATAATTTTGAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
* *
3098354 TTATAAGTTTGGGAATATTTTTTATTTAA
1 TTATAA-TTT-TGAA-A-TTTTAATTTAA
* * *
3098383 TCACAATTTTAAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
3098408 TTA
1 TTA
3098411 ATATTATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
25 18 0.40
26 4 0.09
27 5 0.11
28 4 0.09
29 14 0.31
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (25 bp):
TTATAATTTTGAAATTTTAATTTAA
Found at i:3100687 original size:28 final size:28
Alignment explanation
Indices: 3100655--3100711 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
3100645 TTGAAATTAG
* *
3100655 AAATTTAT-AAAATTTTGGGTTTTTTTAA
1 AAATTT-TCAAAATCTTGGGGTTTTTTAA
3100683 AAATTTTCAAAATCTTGGGGTTTTTTAA
1 AAATTTTCAAAATCTTGGGGTTTTTTAA
3100711 A
1 A
3100712 TATAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (28 bp):
AAATTTTCAAAATCTTGGGGTTTTTTAA
Found at i:3101467 original size:123 final size:122
Alignment explanation
Indices: 3101265--3101485 Score: 345
Period size: 123 Copynumber: 1.8 Consensus size: 122
3101255 GCCAAGATAT
* * *
3101265 ATGATTATATATGATGTCATATTATCATATATCATTTTGACATTATTATTTAACTAACCTTGTCT
1 ATGATTATATATGATATCATATTATCATATATCATTTTGACATTATTATATAACTAAACTTGTCT
* *
3101330 ATTTAAAGTATAAAAAATTTCATATTGCATGATATAGAGGCAAATTTAGCTGAGAAAG
66 ATTTAAAGTAT-AAAAATTTAATATTACATGATATAGAGGCAAATTTAGCTGAGAAAG
* *
3101388 ATGATTATATATGATATCATATTATCATATATCAATTTT-AGATTATTATATAACTAAATTTGTC
1 ATGATTATATATGATATCATATTATCATATATC-ATTTTGACATTATTATATAACTAAACTTGTC
*
3101452 TATTTAAAGTATAAAATTTTAATATTACATGATA
65 TATTTAAAGTATAAAAATTTAATATTACATGATA
3101486 AAATGAAATA
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
122 19 0.21
123 65 0.73
124 5 0.06
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.43
Consensus pattern (122 bp):
ATGATTATATATGATATCATATTATCATATATCATTTTGACATTATTATATAACTAAACTTGTCT
ATTTAAAGTATAAAAATTTAATATTACATGATATAGAGGCAAATTTAGCTGAGAAAG
Found at i:3103415 original size:923 final size:920
Alignment explanation
Indices: 3101620--3103415 Score: 2812
Period size: 923 Copynumber: 1.9 Consensus size: 920
3101610 ATTCTTCTTG
*
3101620 ATTGGTTCATATTGAAGTTGAATATTCAAAGAATCTTATTATTTGTATCACTCAAAATTTTATTG
1 ATTGGTTCATATTGAAGTTGAACATTCAAAGAATCTTATTATTTGTATCACTCAAAATTTTATTG
*
3101685 AATGTAAAGAATTTTGAAGTGACACTTAATACATGAAATACTGATGATGAATACTCTTTGGTGTT
66 AATGTAAAGAATTTTGAAGTGACACTTAATACATAAAATACTGATGATGAATACTCTTTGGTGTT
* * *
3101750 TACATTGCATGAATTGTTCTTATTACTTGACTATAAAACTAAAAAAACATGTATATCTTTTCATT
131 TACATTGCATAAATTGTTCTTATTAATTGACTATAAAACTAAAAAAACATGTATATATTTTCATT
*
3101815 TAAAAAATTACGCTTTACTTCAATAAGGCATGTGTGTTACGTCTTGGCTATAAAACCTCTATCAC
196 TAAAAAATTACGCTTTACTTCAATAAGGCATGTGTCTTACGTCTTGGCTATAAAACCTCTATCAC
* * * * * *
3101880 CTCAGTGTGTCTTACGTCTTTTTTAACATTTTTTGCACCTTGAGATATTGTATTTTGATGAAATA
261 CTCAGTGCGTCTTACATCTTTTTTAAAAGTTTTTACACCTTGAGATAGTGTATTTTGATGAAATA
* *
3101945 GGGCATTGGTTTCAAAACTCATGAGAAATGTAACACCCTCATACCGATGCAGGTGACCTAATCCA
326 GGGCATTGGTTTCAAAACTCATGAGAAATGTAACACCCTCAGACCGATGCAGGTGACCCAATCCA
* **
3102010 ATCTGAGGTGTCATATTAGGGACATCAGAGTGACCCAGACTGAAAATCCTGGAAATTTTTAAAAT
391 ATCTGAGGTGTCACATTAGGGACATCAGAGCAACCCAGACTGAAAATCCTGGAAATTTTTAAAAT
*
3102075 TTTCATTTATCCATTTAAAACTGTAAAATAATTTATAGATAAAATACAAGTTCATAACAACATTA
456 TTTCATTTATCCATTTAAAACTGTAAAATAATTCATAGATAAAATACAAGTTCATAACAACATTA
* * * * *
3102140 TTTTATTAAAAGTAAAATTCAATAATATCCAATAATAAACCAAATTTTAGACTCTAATATAAAAA
521 TTATATTAAAAGTAAAATTCAATAATATCCAATAATAAAACAAATTTCAAACTCGAATATAAAAA
*
3102205 CATAATACAACCTACATGTCCCCTAATCACATACACCATACTCCGCAAGCAACGCTGGTGGAACT
586 CATAATACAACCTACATGTCCCCTAATCACATACACCATACTCCGCAAACAACGCTGGTGGAACT
*
3102270 CCTTTATTGATGTCGATAGCTACACTCGATCAATTTTTTTAACCTGAAATGGTGAGTAAAGAGTG
651 CCTTTATTGATGTCGATAGCTACACTAGATCAATTTTTTTAACCTGAAATGGTGAGTAAAGAGTG
* *
3102335 AGCTTAGGGAAGCTCAGTAATACAGAACTACTAGATGAATGCAATAGGTCATCGGGTATATGGTA
716 AGCTTAGGGAAGCTCAGTAATACAGAACTACCAGATGAATGCAATAAGTCATCGGGTATATGGTA
*
3102400 AAGCATAAATTCCTTAGCGGGACAGTCATCATCAGATTCTAGCGATGAATTCAAATTCCATTAGC
781 AAGCATAAATTCCTTAGCGGGACAATCATCATCAGATTCTAGCGATGAATTCAAATTCCATTAGC
*
3102465 TAAGTCTTCAATTAAAAACATGAATTTACAGTATGAATGAAGTATTTAGAGAGAGAGACAAGTTC
846 TAAGTCTTCAATTAAAAACAGGAATTTACAGTATGAATGAAGTATTTAGAGAGAGAGACAAGTTC
3102530 AAAAGATTGA
911 AAAAGATTGA
* *
3102540 ATTGGTTCATGTTGAAGTTGAACATTCGAAGAATCTTATTATTTGTATCACTCAAAATTTTATTG
1 ATTGGTTCATATTGAAGTTGAACATTCAAAGAATCTTATTATTTGTATCACTCAAAATTTTATTG
*
3102605 AATGTAAAGAATTTTGAAGTGACACTTAATACATAAAATATTGATGATGAATACTCTTTGGTGTT
66 AATGTAAAGAATTTTGAAGTGACACTTAATACATAAAATACTGATGATGAATACTCTTTGGTGTT
* *
3102670 TACATTGCATAAATTGTTCTTTTTAATTGACTATACAACTGGAAAAAAAACATGTATATATTTTC
131 TACATTGCATAAATTGTTCTTATTAATTGACTATAAAACT---AAAAAAACATGTATATATTTTC
* * * * ** *
3102735 ATTTCAAAGATTACGTTTTACTTCAATAAGTCATGTGTCTTACGTCTTTTCTTTAAAACCTCTAT
193 ATTTAAAAAATTACGCTTTACTTCAATAAGGCATGTGTCTTACGTCTTGGCTATAAAACCTCTAT
** *
3102800 C-GTTGTAGTGCGTCTTACATCTTTTTTAAAAGTTTTTACACCTTGAGATAGTGTATTTTGATGA
258 CACCT-CAGTGCGTCTTACATCTTTTTTAAAAGTTTTTACACCTTGAGATAGTGTATTTTGATGA
* * *
3102864 AATAGTGCCTTGGTTTCAAAACTCATGAGAAATGTAACACCCTCAGACTGATGCAGGTGACCCAA
322 AATAGGGCATTGGTTTCAAAACTCATGAGAAATGTAACACCCTCAGACCGATGCAGGTGACCCAA
* * * *
3102929 TTCGATTTGAGGTGTCACATTAGGG-CTATC-GAAGCAACCCAGCCTGAAAATCCTGGAAATTTT
387 TCCAATCTGAGGTGTCACATTAGGGAC-ATCAG-AGCAACCCAGACTGAAAATCCTGGAAATTTT
3102992 TAAAATTTTCATTTATCCATTTAAAACTGTAAAATAATTCATAGATAAAATACAAGTTCATAACA
450 TAAAATTTTCATTTATCCATTTAAAACTGTAAAATAATTCATAGATAAAATACAAGTTCATAACA
* * * *
3103057 TCATT-TATATATTAAAAGTAGAATTCAATAATATCCAGTAATAAAACAAGTTTCAAACTCGAAT
515 ACATTAT-TATATTAAAAGTAAAATTCAATAATATCCAATAATAAAACAAATTTCAAACTCGAAT
* * *
3103121 ATAAAAACATAATACAACCTACATGTCCCCTAATCACGTGCACCGTACTCCGCAAACAACGAC-G
579 ATAAAAACATAATACAACCTACATGTCCCCTAATCACATACACCATACTCCGCAAACAACG-CTG
* * * * * *
3103185 GTTGAACTCTTTTACTT-ATTTCGGTAGTTGCACTAGATCAATTTTTTTAACCTGAAATGGTGAG
643 GTGGAACTCCTTTA-TTGATGTCGATAGCTACACTAGATCAATTTTTTTAACCTGAAATGGTGAG
*
3103249 TAAAGAGTGAGCTTTGGGAAGCTCAGTAATACAGAACTACCAGATGAATGCAATAAGTCATCGGG
707 TAAAGAGTGAGCTTAGGGAAGCTCAGTAATACAGAACTACCAGATGAATGCAATAAGTCATCGGG
** * *
3103314 TATATGGTAAAGCATAAATTCCTTATTGGGACAATCATCGTCAGATTCTAGCGGTGAATTCAAAT
772 TATATGGTAAAGCATAAATTCCTTAGCGGGACAATCATCATCAGATTCTAGCGATGAATTCAAAT
* * * *
3103379 TCTATTAGCTAAGTCTTTAATTACAAAGAGGAATTTA
837 TCCATTAGCTAAGTCTTCAATTAAAAACAGGAATTTA
3103416 TGGTCTGAAG
Statistics
Matches: 794, Mismatches: 73, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
920 161 0.20
922 4 0.01
923 626 0.79
924 3 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (920 bp):
ATTGGTTCATATTGAAGTTGAACATTCAAAGAATCTTATTATTTGTATCACTCAAAATTTTATTG
AATGTAAAGAATTTTGAAGTGACACTTAATACATAAAATACTGATGATGAATACTCTTTGGTGTT
TACATTGCATAAATTGTTCTTATTAATTGACTATAAAACTAAAAAAACATGTATATATTTTCATT
TAAAAAATTACGCTTTACTTCAATAAGGCATGTGTCTTACGTCTTGGCTATAAAACCTCTATCAC
CTCAGTGCGTCTTACATCTTTTTTAAAAGTTTTTACACCTTGAGATAGTGTATTTTGATGAAATA
GGGCATTGGTTTCAAAACTCATGAGAAATGTAACACCCTCAGACCGATGCAGGTGACCCAATCCA
ATCTGAGGTGTCACATTAGGGACATCAGAGCAACCCAGACTGAAAATCCTGGAAATTTTTAAAAT
TTTCATTTATCCATTTAAAACTGTAAAATAATTCATAGATAAAATACAAGTTCATAACAACATTA
TTATATTAAAAGTAAAATTCAATAATATCCAATAATAAAACAAATTTCAAACTCGAATATAAAAA
CATAATACAACCTACATGTCCCCTAATCACATACACCATACTCCGCAAACAACGCTGGTGGAACT
CCTTTATTGATGTCGATAGCTACACTAGATCAATTTTTTTAACCTGAAATGGTGAGTAAAGAGTG
AGCTTAGGGAAGCTCAGTAATACAGAACTACCAGATGAATGCAATAAGTCATCGGGTATATGGTA
AAGCATAAATTCCTTAGCGGGACAATCATCATCAGATTCTAGCGATGAATTCAAATTCCATTAGC
TAAGTCTTCAATTAAAAACAGGAATTTACAGTATGAATGAAGTATTTAGAGAGAGAGACAAGTTC
AAAAGATTGA
Found at i:3106177 original size:24 final size:24
Alignment explanation
Indices: 3106126--3106177 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3106116 AACGTCTCAC
* *
3106126 CCCTCTCGTTTCATAGCCTTCTAT
1 CCCTCTCGTTTCACAGCCTTCTAA
3106150 CCCTCTCGTTTCACAGCCTAT-TAA
1 CCCTCTCGTTTCACAGCCT-TCTAA
3106174 CCCT
1 CCCT
3106178 TTCTTCACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.15, C:0.40, G:0.08, T:0.37
Consensus pattern (24 bp):
CCCTCTCGTTTCACAGCCTTCTAA
Found at i:3107551 original size:173 final size:177
Alignment explanation
Indices: 3107262--3107613 Score: 658
Period size: 173 Copynumber: 2.0 Consensus size: 177
3107252 GATGATGTTG
3107262 TCATTGAACTTTAATGCAAAGAAAAGGAATGCTTTGTTCTTCCTTGGAATAAATGTACAACATAA
1 TCATTGAACTTTAATGCAAAGAAAAGGAATGCTTTGTTCTTCCTTGGAATAAATGTACAACATAA
3107327 CTCGCATCATTTTCTAGTGTTTATGTTGTGAGCTCTGTTTTTGTGCAAC-AAGGTTGGTGGTC-T
66 CTCGCATCATTTTCTAGTGTTTATGTTGTGAGCTCTGTTTTTGTGCAACAAAGGTTGGTGGTCTT
3107390 ATTTATG-ATTTTACTATCAAAAGCAA-TGTGGCAACTTCATATGGA
131 ATTTATGAATTTTACTATCAAAAGCAATTGTGGCAACTTCATATGGA
3107435 TCATTGAACTTTAATGCAAAGAAAAGGAATGCTTTGTTCTTCCTTGGAATAAATGTACAACATAA
1 TCATTGAACTTTAATGCAAAGAAAAGGAATGCTTTGTTCTTCCTTGGAATAAATGTACAACATAA
3107500 CTCGCATCATTTTCTAGTGTTTATGTTGTGAGCTCTGTTTTTGTGCAACAAGAAGGTTGGTGGTC
66 CTCGCATCATTTTCTAGTGTTTATGTTGTGAGCTCTGTTTTTGTGCAAC-A-AAGGTTGGTGGTC
3107565 TTATTTATGAATTTTACTATCAAAAGCAATTGTGGCAACTTCATATGGA
129 TTATTTATGAATTTTACTATCAAAAGCAATTGTGGCAACTTCATATGGA
3107614 ATATGATAAG
Statistics
Matches: 173, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
173 114 0.66
176 13 0.08
177 8 0.05
178 19 0.11
179 19 0.11
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (177 bp):
TCATTGAACTTTAATGCAAAGAAAAGGAATGCTTTGTTCTTCCTTGGAATAAATGTACAACATAA
CTCGCATCATTTTCTAGTGTTTATGTTGTGAGCTCTGTTTTTGTGCAACAAAGGTTGGTGGTCTT
ATTTATGAATTTTACTATCAAAAGCAATTGTGGCAACTTCATATGGA
Found at i:3108140 original size:13 final size:13
Alignment explanation
Indices: 3108122--3108146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3108112 CCAAACAACA
3108122 GAAAATGTTTTCT
1 GAAAATGTTTTCT
3108135 GAAAATGTTTTC
1 GAAAATGTTTTC
3108147 CATAAATGTA
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
GAAAATGTTTTCT
Found at i:3110885 original size:208 final size:208
Alignment explanation
Indices: 3110527--3110946 Score: 741
Period size: 208 Copynumber: 2.0 Consensus size: 208
3110517 CATGAGAAAA
*
3110527 GCAATGTGCTGATATAATGCAAATATAAATGGAATCCTTTTAGGTTTTGTATGAACACATGTACT
1 GCAATGTGCTGATATAATGCAAATATAAATGGAACCCTTTTAGGTTTTGTATGAACACATGTACT
*
3110592 ATCAATTCCGAGTAGAGTTTTAAAAAACATAAAAATTAAGGAACACTTCACAGAGGCACTCATCT
66 ATCAATTCCGAGTAGAGTTTTAAAAAACATAAAAATAAAGGAACACTTCACAGAGGCACTCATCT
* *
3110657 GTCAAAACAATGTGCCTAAGCATCAAGGCCTTATCTTATGTAAATGCTCTTTTCAGCATTATTCT
131 GTCAAAACAATGTGCCTAAGCATCAAGGCCTTATCTTAGGTAAACGCTCTTTTCAGCATTATTCT
*
3110722 AAGGAACAAGGAG
196 AAGGAACAAAGAG
*
3110735 GCAATGTGCTGATATAATGCAAATATAAATGGAACCCTTTTAGGTTTTGTATGAACACATGTATT
1 GCAATGTGCTGATATAATGCAAATATAAATGGAACCCTTTTAGGTTTTGTATGAACACATGTACT
* * *
3110800 ATCAATTCCGAGTAGAGTTTTCAAAAACTTAAAAATAAAGGAATACTTCACAGAGGCACTCATCT
66 ATCAATTCCGAGTAGAGTTTTAAAAAACATAAAAATAAAGGAACACTTCACAGAGGCACTCATCT
* *
3110865 TTCAAAACAATGTGCCTAAGCATCAAGGGCTTATCTTAGGTAAACGCTCTTTTCAGCATTATTCT
131 GTCAAAACAATGTGCCTAAGCATCAAGGCCTTATCTTAGGTAAACGCTCTTTTCAGCATTATTCT
3110930 AAGGAACAAAGAG
196 AAGGAACAAAGAG
3110943 GCAA
1 GCAA
3110947 GGATGCCTTA
Statistics
Matches: 201, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
208 201 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (208 bp):
GCAATGTGCTGATATAATGCAAATATAAATGGAACCCTTTTAGGTTTTGTATGAACACATGTACT
ATCAATTCCGAGTAGAGTTTTAAAAAACATAAAAATAAAGGAACACTTCACAGAGGCACTCATCT
GTCAAAACAATGTGCCTAAGCATCAAGGCCTTATCTTAGGTAAACGCTCTTTTCAGCATTATTCT
AAGGAACAAAGAG
Found at i:3112895 original size:16 final size:17
Alignment explanation
Indices: 3112874--3112906 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3112864 TTACTGTTCA
3112874 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
3112890 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
3112907 TGTCGACGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:3121669 original size:3 final size:3
Alignment explanation
Indices: 3121661--3121749 Score: 88
Period size: 3 Copynumber: 28.7 Consensus size: 3
3121651 ATTTTATTTA
* * * *
3121661 TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT GAT TAT AAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
3121709 TAT AAT TAT TAT TAA TAT ATAT TATT TATT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TA-T TA-T TAT TAT TAT TA
3121750 CAAAACCCAG
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
3 60 0.86
4 10 0.14
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:3123139 original size:17 final size:17
Alignment explanation
Indices: 3123117--3123156 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3123107 TTATGTAGCC
3123117 ATAAATATATATAATAA
1 ATAAATATATATAATAA
* **
3123134 ATAAATATTTATTTTAA
1 ATAAATATATATAATAA
3123151 ATAAAT
1 ATAAAT
3123157 TATTTTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATATATAATAA
Found at i:3123151 original size:13 final size:13
Alignment explanation
Indices: 3123135--3123174 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
3123125 ATATAATAAA
3123135 TAAATATTTATTT
1 TAAATATTTATTT
*
3123148 TAAATAAATTATTT
1 TAAAT-ATTTATTT
3123162 T-AATATTTATTT
1 TAAATATTTATTT
3123174 T
1 T
3123175 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:3123345 original size:11 final size:11
Alignment explanation
Indices: 3123331--3123357 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3123321 CTTTTCTGAT
3123331 ATTTTTATATA
1 ATTTTTATATA
3123342 ATTTTTATATA
1 ATTTTTATATA
3123353 ATTTT
1 ATTTT
3123358 GAAATAGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTTATATA
Found at i:3134327 original size:16 final size:16
Alignment explanation
Indices: 3134306--3134400 Score: 117
Period size: 16 Copynumber: 5.9 Consensus size: 16
3134296 ATTATGCTTG
3134306 AAGAAAAAAAGAAAAA
1 AAGAAAAAAAGAAAAA
3134322 AAGAAAGAAAAG-AAAA
1 AAGAAA-AAAAGAAAAA
3134338 AAG-AAAAAAGAAAAA
1 AAGAAAAAAAGAAAAA
3134353 AA-AGAAAAAAGAAAAA
1 AAGA-AAAAAAGAAAAA
*
3134369 AA-AAAAAAAAAAAAA
1 AAGAAAAAAAGAAAAA
3134384 GAAGAAAAAAAAGAAAA
1 -AAG-AAAAAAAGAAAA
3134401 CGGGGGAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
14 5 0.07
15 19 0.27
16 30 0.43
17 5 0.07
18 11 0.16
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAGAAAAA
Found at i:3134344 original size:23 final size:23
Alignment explanation
Indices: 3134310--3134400 Score: 123
Period size: 23 Copynumber: 4.0 Consensus size: 23
3134300 TGCTTGAAGA
3134310 AAAAAAGAAAAAAAGAAAGAAAAG
1 AAAAAAG-AAAAAAGAAAGAAAAG
*
3134334 AAAAAAGAAAAAAGAAAAAAAAG
1 AAAAAAGAAAAAAGAAAGAAAAG
*
3134357 AAAAAAGAAAAAA-AAA-AAAAA
1 AAAAAAGAAAAAAGAAAGAAAAG
*
3134378 AAAAAAGAAGAAAAAAAAGAAAA
1 AAAAAAGAA-AAAAGAAAGAAAA
3134401 CGGGGGAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
21 13 0.21
22 7 0.11
23 31 0.50
24 11 0.18
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAAAAAGAAAGAAAAG
Found at i:3134359 original size:40 final size:41
Alignment explanation
Indices: 3134305--3134400 Score: 144
Period size: 39 Copynumber: 2.4 Consensus size: 41
3134295 TATTATGCTT
* * *
3134305 GAAG-AAAAAAAGAAAAAAAGAAAGAAAAGAAAAAAGAAAA
1 GAAGAAAAAAAAGAAAAAAAGAAAAAAAAAAAAAAAAAAAA
3134345 -AAGAAAAAAAAG-AAAAAAGAAAAAAAAAAAAAAAAAAAA
1 GAAGAAAAAAAAGAAAAAAAGAAAAAAAAAAAAAAAAAAAA
3134384 GAAGAAAAAAAAGAAAA
1 GAAGAAAAAAAAGAAAA
3134401 CGGGGGAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
39 27 0.54
40 20 0.40
41 3 0.06
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (41 bp):
GAAGAAAAAAAAGAAAAAAAGAAAAAAAAAAAAAAAAAAAA
Found at i:3134415 original size:1 final size:1
Alignment explanation
Indices: 3134309--3134400 Score: 85
Period size: 1 Copynumber: 92.0 Consensus size: 1
3134299 ATGCTTGAAG
* * * * * * * *
3134309 AAAAAAAGAAAAAAAGAAAGAAAAGAAAAAAGAAAAAAGAAAAAAAAGAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
3134374 AAAAAAAAAAGAAGAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
3134401 CGGGGGAAAA
Statistics
Matches: 69, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:3134415 original size:40 final size:39
Alignment explanation
Indices: 3134309--3134400 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 39
3134299 ATGCTTGAAG
3134309 AAAAAAAG-AAAAA-AAGAAAGAAAAGAAAAAAGAAAAAAGA
1 AAAAAAAGAAAAAAGAAGAAA-AAAA-AAAAAA-AAAAAAGA
*
3134349 AAAAAAAGAAAAAAGAAAAAAAAAAAAAAAAAAAAGAAGA
1 AAAAAAAGAAAAAAGAAGAAAAAAAAAAAAAAAAA-AAGA
3134389 AAAAAAAGAAAA
1 AAAAAAAGAAAA
3134401 CGGGGGAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
39 4 0.08
40 30 0.62
41 9 0.19
42 5 0.10
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (39 bp):
AAAAAAAGAAAAAAGAAGAAAAAAAAAAAAAAAAAAAGA
Found at i:3134427 original size:21 final size:20
Alignment explanation
Indices: 3134388--3134426 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3134378 AAAAAAGAAG
3134388 AAAAAAAAGAAAACGGGGGA
1 AAAAAAAAGAAAACGGGGGA
*
3134408 AAAAAAAAGAAAAAGGGGG
1 AAAAAAAAGAAAACGGGGG
3134427 GGGTCAAGGT
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:0.67, C:0.03, G:0.31, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAAAACGGGGGA
Found at i:3135370 original size:41 final size:40
Alignment explanation
Indices: 3135313--3135393 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 40
3135303 TGTCAATTTG
3135313 GCACTTCTTGTACATATTTATAAACAGTTCAACTTTGTTCT
1 GCACTTCTTGTACATATTTATAAACAGTTCAACTTT-TTCT
3135354 GCACTTCTTGTACATATTTATAAACAGTTCAACTTTTTCT
1 GCACTTCTTGTACATATTTATAAACAGTTCAACTTTTTCT
3135394 TAGATTCCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 4 0.10
41 36 0.90
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (40 bp):
GCACTTCTTGTACATATTTATAAACAGTTCAACTTTTTCT
Found at i:3135740 original size:83 final size:83
Alignment explanation
Indices: 3135601--3135862 Score: 422
Period size: 83 Copynumber: 3.2 Consensus size: 83
3135591 ACTGGAACAA
* * *
3135601 ATGAATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
3135666 AATCATTGAAATTGAAAG
66 AATCATTGAAATTGAAAG
* * *
3135684 ATGAATGTACTCACACCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
*
3135749 AATCATTGAATTTGAAAG
66 AATCATTGAAATTGAAAG
*
3135767 ATGAATGTGCTCATAGCGTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
*
3135832 -ATCATTG-AATTAAAAG
66 AATCATTGAAATTGAAAG
3135848 ATGAAT-TGCTCATAG
1 ATGAATGTGCTCATAG
3135863 TAGAAATAAG
Statistics
Matches: 166, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
80 9 0.05
81 13 0.08
82 7 0.04
83 137 0.83
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
AATCATTGAAATTGAAAG
Found at i:3136999 original size:113 final size:112
Alignment explanation
Indices: 3136694--3137560 Score: 964
Period size: 113 Copynumber: 7.8 Consensus size: 112
3136684 TAGCAAAGAT
* *
3136694 AAATCCATCA-TTCGATGGAT-AGCTTTTCCAGAGGAAGTTC---ATGAGAAGAACTCATCTG--
1 AAAT-CATCACTT-GATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
3136752 GAAGGAAGAAGAA-TTCATAATGAGAAGAATTTGTTCAA-CTTTTG--C
64 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
** * *
3136797 ---T-ATCACTTGATGGATCCGCTTTTCCAGAGGAAGATCATAATGAGAAGAA-TC-TCTGAAGA
1 AAATCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
3136856 AGGCTGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
** *
3136903 AAATACATCACTTGATGGATCCGCTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAAT-CATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
3136968 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
65 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
3137016 AAATCTATCACTTGATGGATTATCTTTTCCAGGAGAAAGTTC-TAATGAGAAGAACTCAT-TGAA
1 AAATC-ATCACTTGATGGATCAACTTTTCCA-GAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* * * * * *
3137079 GAAGGAAGAAG-AGTTCATAATGAGAAGAACTTCTTCAACTTTTTGTTTG
64 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CTC
* * * * * *
3137128 AATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAAGAAACTCATCTTA
1 AAATCATCACTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAG-AAG-AACTCATCTGA
3137192 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
63 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
3137242 AAATCATTCACTTGAGGGATCAAC-TTTCCAGTTCGAGTTAAAGTTCATAATGAGAAG-ACTCAT
1 AAATCA-TCACTTGATGGATCAACTTTTCCA----GAG--AAAGTTCATAATGAGAAGAACTCAT
* * * * * *
3137305 CTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTCTTCAACTTTTTGTTTG
59 CTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CTC
* * * * * *
3137359 AATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTTAAG
1 AAATCATCACTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
3137423 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
****
3137471 AAACTCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAA-TCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
3137536 AA--AAG-A-AAGTTCATAATGAGAAGAA
65 AAGGATGAAGAAGTTCATAATGAGAAGAA
3137561 CTCATTTGAA
Statistics
Matches: 659, Mismatches: 65, Indels: 74
0.83 0.08 0.09
Matches are distributed among these distances:
98 11 0.02
99 20 0.03
100 5 0.01
101 2 0.00
102 21 0.03
103 25 0.04
104 6 0.01
106 1 0.00
109 21 0.03
110 8 0.01
111 123 0.19
112 42 0.06
113 197 0.30
114 34 0.05
115 46 0.07
116 53 0.08
117 24 0.04
118 1 0.00
119 4 0.01
120 15 0.02
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (112 bp):
AAATCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:3137147 original size:224 final size:226
Alignment explanation
Indices: 3136734--3137562 Score: 1082
Period size: 224 Copynumber: 3.7 Consensus size: 226
3136724 GAGGAAGTTC
*
3136734 ATGAGAAGAACTCATCTG--GAAGGAAGAAGAA-TTCATAATGAGAAGAATTTGTTCAA-CTTTT
1 ATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
** * *
3136795 G------CTATCACTTGATGGATCCGCTTTTCCA--GAGGAAGATCATAATGAGAAGAA-TC-TC
66 GCTCAAACTATCACTTGATGGATCAACTTTTCCAGTGAGAAAGTTCATAATGAGAAGAACTCATC
** * * * * ** * *
3136850 TGAAGAAGGCTGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATACATCACT
131 TGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTCTTCAACTTTTTGTTTGAATTCATCATT
** * * *
3136915 TGATGGATCCGCTTTTCTAGAG-AAAGTTCATA
195 TGATGGATCAACATTGCCAG-GTAAAGTTCATA
3136947 ATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
1 ATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
* * *
3137012 GCTTAAATCTATCACTTGATGGATTATCTTTTCCAG-GAGAAAGTTC-TAATGAGAAGAACTCAT
66 GCTCAAA-CTATCACTTGATGGATCAACTTTTCCAGTGAGAAAGTTCATAATGAGAAGAACTCAT
3137075 -TGAAGAAGGAAGAAG-AGTTCATAATGAGAAGAACTTCTTCAACTTTTTGTTTGAATTCATCAT
130 CTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTCTTCAACTTTTTGTTTGAATTCATCAT
*
3137138 TTGATGGATCAACATTGCCAGGTAGAGTTCATA
194 TTGATGGATCAACATTGCCAGGTAAAGTTCATA
*
3137171 ATGAGAAAGAAACTCATCTTAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
1 ATGAG-AAG-AACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
*
3137236 TTGCTCAAA-TCATTCACTTGAGGGATCAAC-TTTCCAGTTCGAGTTAAAGTTCATAATGAGAAG
64 TTGCTCAAACT-A-TCACTTGATGGATCAACTTTTCCAG-T-GAG--AAAGTTCATAATGAGAAG
3137299 -ACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTCTTCAACTTTTTGTTTGAATT
123 AACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTCTTCAACTTTTTGTTTGAATT
*
3137363 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATA
188 CATCATTTGATGGATCAACATTGCCAGGTAAAGTTCATA
*
3137402 ATGAGAAGAACTCATCTTAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
1 ATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
**
3137467 GCTCAAACTCATCACTTGATGGATCAACTTTTCCAGTTCG--AGTTCATAATGAGAAGAACTCAT
66 GCTCAAACT-ATCACTTGATGGATCAACTTTTCCAGTGAGAAAGTTCATAATGAGAAGAACTCAT
3137530 CTGAAGAA-AAG-A-AAGTTCATAATGAGAAGAACT
130 CTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACT
3137563 CATTTGAAGA
Statistics
Matches: 556, Mismatches: 30, Indels: 51
0.87 0.05 0.08
Matches are distributed among these distances:
213 18 0.03
215 12 0.02
216 25 0.04
217 6 0.01
222 21 0.04
223 2 0.00
224 126 0.23
225 48 0.09
226 77 0.14
228 4 0.01
229 81 0.15
230 33 0.06
231 103 0.19
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (226 bp):
ATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
GCTCAAACTATCACTTGATGGATCAACTTTTCCAGTGAGAAAGTTCATAATGAGAAGAACTCATC
TGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTCTTCAACTTTTTGTTTGAATTCATCATTT
GATGGATCAACATTGCCAGGTAAAGTTCATA
Found at i:3137554 original size:36 final size:36
Alignment explanation
Indices: 3137507--3137595 Score: 160
Period size: 36 Copynumber: 2.5 Consensus size: 36
3137497 TTCCAGTTCG
3137507 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAGAA
*
3137543 AGTTCATAATGAGAAGAACTCATTTGAAGAAAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAGAA
*
3137579 AGTTCATAATAAGAAGA
1 AGTTCATAATGAGAAGA
3137596 GCTTATGCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (36 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAAGAA
Found at i:3137851 original size:3 final size:3
Alignment explanation
Indices: 3137843--3137924 Score: 76
Period size: 3 Copynumber: 26.7 Consensus size: 3
3137833 ATTTTATTTA
* * * *
3137843 TAT TAT TAT TAT TAT TAT TA- TAT TAT AAT AAT TAT TAT AAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
3137890 TAT TAT TAA TAT ATAT TATT TATT TAT TAA TAT TA
1 TAT TAT TAT TAT -TAT TA-T TA-T TAT TAT TAT TA
3137925 CAAAACCCGG
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.03
3 56 0.82
4 10 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3137851 original size:12 final size:12
Alignment explanation
Indices: 3137836--3137918 Score: 53
Period size: 14 Copynumber: 6.2 Consensus size: 12
3137826 CATTTTAATT
3137836 TTATTTATATTA
1 TTATTTATATTA
3137848 TTA-TTATTATTA
1 TTATTTA-TATTA
*
3137860 TTATATTATAATAA
1 TTAT-TTAT-ATTA
3137874 TTATTATAATAATTA
1 TTATT-T-AT-ATTA
3137889 TTATTATTAATATATA
1 TTA-T-TT-ATAT-TA
3137905 TTATTTAT-TTA
1 TTATTTATATTA
3137916 TTA
1 TTA
3137919 ATATTACAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 19
0.74 0.02 0.23
Matches are distributed among these distances:
11 8 0.13
12 12 0.20
13 4 0.07
14 13 0.22
15 12 0.20
16 10 0.17
17 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTTATATTA
Found at i:3139297 original size:16 final size:17
Alignment explanation
Indices: 3139276--3139314 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3139266 TTATGTAGCC
3139276 ATAAATATATA-TATAA
1 ATAAATATATATTATAA
* *
3139292 ATAAATATTTATTTTAA
1 ATAAATATATATTATAA
3139309 ATAAAT
1 ATAAAT
3139315 TATTTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAATATATATTATAA
Found at i:3139311 original size:13 final size:13
Alignment explanation
Indices: 3139293--3139338 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
3139283 TATATATAAA
3139293 TAAATATTTATTT
1 TAAATATTTATTT
*
3139306 TAAATAAATTATTT
1 TAAAT-ATTTATTT
3139320 T-AATATTTATTT
1 TAAATATTTATTT
*
3139332 TCAATAT
1 TAAATAT
3139339 CGAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:3149623 original size:48 final size:48
Alignment explanation
Indices: 3149571--3149671 Score: 157
Period size: 48 Copynumber: 2.1 Consensus size: 48
3149561 ACATACTTTG
* * *
3149571 TGTATGATGTTTATCGATCGATTTTGTTTAATGTATAAGTTGTATTTT
1 TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTT
*
3149619 TGTATGATGGTTATCGATCGATTTTGTTTAATGCATATGTTGCATTTT
1 TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTT
*
3149667 CGTAT
1 TGTAT
3149672 CAGTACTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.51
Consensus pattern (48 bp):
TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTT
Found at i:3149751 original size:53 final size:53
Alignment explanation
Indices: 3149687--3149802 Score: 178
Period size: 53 Copynumber: 2.2 Consensus size: 53
3149677 CTATATGTAC
* * *
3149687 TTTCGACACTATGTGTGCACCCTTGGCATTCATAATGAGTTTATGAATGACCA
1 TTTCGGCACTATGTGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCA
* * *
3149740 TTTCGGCACTATGTGTGCATCCATGGAATTCATAATGAGTTTGTGAATTACCA
1 TTTCGGCACTATGTGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCA
3149793 TTTCGGCACT
1 TTTCGGCACT
3149803 TAGGTGCAAC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (53 bp):
TTTCGGCACTATGTGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCA
Found at i:3156701 original size:48 final size:48
Alignment explanation
Indices: 3156640--3156739 Score: 137
Period size: 48 Copynumber: 2.1 Consensus size: 48
3156630 CATACTTTGT
* * *
3156640 GTATGATGTTTATCGATCGATATTATTTAATGCATAAGCTGCATTTTC
1 GTATGACGGTTATCAATCGATATTATTTAATGCATAAGCTGCATTTTC
* * * *
3156688 GTATGACGGTTATCAATCGATTTTGTTTAATGCATATGTTGCATTTTC
1 GTATGACGGTTATCAATCGATATTATTTAATGCATAAGCTGCATTTTC
3156736 GTAT
1 GTAT
3156740 CAGTATTATA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (48 bp):
GTATGACGGTTATCAATCGATATTATTTAATGCATAAGCTGCATTTTC
Found at i:3165457 original size:18 final size:19
Alignment explanation
Indices: 3165422--3165458 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3165412 CACGGAATGT
3165422 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
3165442 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
3165459 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:3167365 original size:160 final size:161
Alignment explanation
Indices: 3167101--3167421 Score: 635
Period size: 160 Copynumber: 2.0 Consensus size: 161
3167091 AAAATCGATG
3167101 GAATACTCTACTACCTTTTGTATGTTTTATGGAACTCATTGATAATTGGTAAATGCATGAATATA
1 GAATACTCTACTACCTTTTGTATGTTTTATGGAACTCATTGATAATTGGTAAATGCATGAATATA
3167166 AATGATTGGTCAATTATGAGTAGATAATTATTACTAGACCCAAACT-AATACAATATAAAGTTAG
66 AATGATTGGTCAATTATGAGTAGATAATTATTACTAGACCCAAACTAAATACAATATAAAGTTAG
3167230 CAAATCGAATAAGACTTGGATGAATTGCATA
131 CAAATCGAATAAGACTTGGATGAATTGCATA
3167261 GAATACTCTACTACCTTTTGTATGTTTTATGGAACTCATTGATAATTGGTAAATGCATGAATATA
1 GAATACTCTACTACCTTTTGTATGTTTTATGGAACTCATTGATAATTGGTAAATGCATGAATATA
3167326 AATGATTGGTCAATTATGAGTAGATAATTATTACTAGACCCAAACTAAATACAATATAAAGTTAG
66 AATGATTGGTCAATTATGAGTAGATAATTATTACTAGACCCAAACTAAATACAATATAAAGTTAG
3167391 CAAATCGAATAAGACTTGGATGAATTGCATA
131 CAAATCGAATAAGACTTGGATGAATTGCATA
3167422 AGGAATTGAA
Statistics
Matches: 160, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
160 111 0.69
161 49 0.31
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (161 bp):
GAATACTCTACTACCTTTTGTATGTTTTATGGAACTCATTGATAATTGGTAAATGCATGAATATA
AATGATTGGTCAATTATGAGTAGATAATTATTACTAGACCCAAACTAAATACAATATAAAGTTAG
CAAATCGAATAAGACTTGGATGAATTGCATA
Found at i:3167976 original size:19 final size:19
Alignment explanation
Indices: 3167948--3168041 Score: 64
Period size: 19 Copynumber: 4.8 Consensus size: 19
3167938 TGTATTTTAG
*
3167948 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
3167967 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* *
3167986 ATTATATTA-TTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
* * *
3168006 TTTAGTTTAAGTTTTAAGTGT
1 TTTA-ATTAGGTTTT-AGTAT
*
3168027 TTTAATTAGGATTTA
1 TTTAATTAGGTTTTA
3168042 AGATGTTTTA
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
19 24 0.43
20 20 0.36
21 11 0.20
22 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:3168721 original size:16 final size:16
Alignment explanation
Indices: 3168702--3168742 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3168692 ACTATTAATA
3168702 TTTATTATTATT-TTTT
1 TTTATT-TTATTATTTT
*
3168718 TTTATTTTTTTATTTT
1 TTTATTTTATTATTTT
3168734 TTTATTTTA
1 TTTATTTTA
3168743 ATATCTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTATTTTATTATTTT
Done.