Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 17 of 216
Found at i:5424786 original size:20 final size:21
Alignment explanation
Indices: 5424751--5424789 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5424741 CTTAATTGAC
*
5424751 TAACTGACATTAACTAACTTT
1 TAACTGACAATAACTAACTTT
5424772 TAACT-ACAATAACTAACT
1 TAACTGACAATAACTAACT
5424790 ACATTGCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.33
Consensus pattern (21 bp):
TAACTGACAATAACTAACTTT
Found at i:5426501 original size:28 final size:28
Alignment explanation
Indices: 5426461--5426518 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
5426451 TAAATTAAAT
5426461 AATTAATCCTATAAATCAACTCAATTCA
1 AATTAATCCTATAAATCAACTCAATTCA
* * *
5426489 AATTAATTCTATAAATTAATTCAATTCA
1 AATTAATCCTATAAATCAACTCAATTCA
5426517 AA
1 AA
5426519 AAAACACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (28 bp):
AATTAATCCTATAAATCAACTCAATTCA
Found at i:5426528 original size:28 final size:28
Alignment explanation
Indices: 5426469--5426528 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
5426459 ATAATTAATC
** **
5426469 CTATAAATCAACTCAATTCAAATTAATT
1 CTATAAATCAACTCAATTCAAAAAAACA
* *
5426497 CTATAAATTAATTCAATTCAAAAAAACA
1 CTATAAATCAACTCAATTCAAAAAAACA
5426525 CTAT
1 CTAT
5426529 GATTTTGGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (28 bp):
CTATAAATCAACTCAATTCAAAAAAACA
Found at i:5430167 original size:43 final size:43
Alignment explanation
Indices: 5430079--5430250 Score: 247
Period size: 43 Copynumber: 4.0 Consensus size: 43
5430069 TTTTCTTTAC
* ***
5430079 AACGCTGCTATAGACCATGGTCTTT-GCGGCGCTTACCCTTGA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* * *
5430121 AACGCCGCGATAGACCATGGTCTTTAGCGGCGCATACCAAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* *
5430164 AACGTCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
*
5430207 AACGCCGCTATAGACCATGGTCTTTTGCGGCGCTTACCCAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
5430250 A
1 A
5430251 TCTATAGCGG
Statistics
Matches: 114, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
42 23 0.20
43 91 0.80
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (43 bp):
AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
Found at i:5430323 original size:43 final size:43
Alignment explanation
Indices: 5430276--5430510 Score: 355
Period size: 43 Copynumber: 5.5 Consensus size: 43
5430266 AGACAAGAAA
* *
5430276 CGCCGCTATAGACCATGGTCTTTAGCGGCGTTTCTTGCGTAAG
1 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTTCTTGCGTAAG
* * *
5430319 CGCCGCTATAGACCATGGTCTATAGCGGCGTTTGTTGGGTAAG
1 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTTCTTGCGTAAG
5430362 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTTCTTGCGTAAG
1 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTTCTTGCGTAAG
* * *
5430405 CGCTGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGTAAG
1 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTTCTTGCGTAAG
* **
5430448 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTTG-GTTTG
1 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTT-CTTGCGTAAG
5430491 CGCCGCTAAAGACCATGGTC
1 CGCCGCTAAAGACCATGGTC
5430511 AAATAAATTA
Statistics
Matches: 178, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
43 175 0.98
44 3 0.02
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (43 bp):
CGCCGCTAAAGACCATGGTCTATAGCGGCGTTTCTTGCGTAAG
Found at i:5430396 original size:86 final size:86
Alignment explanation
Indices: 5430276--5430510 Score: 391
Period size: 86 Copynumber: 2.7 Consensus size: 86
5430266 AGACAAGAAA
* * *
5430276 CGCCGCTATAGACCATGGTCTTTAGCGGCGTTTCTTGCGTAAGCGCCGCTATAGACCATGGTCTA
1 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTTCTTGCGTAAGCGCCGCTAAAGACCATGGTCTA
5430341 TAGCGGCGTTTGTTGGGTAAG
66 TAGCGGCGTTTGTTGGGTAAG
*
5430362 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTTCTTGCGTAAGCGCTGCTAAAGACCATGGTCTA
1 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTTCTTGCGTAAGCGCCGCTAAAGACCATGGTCTA
5430427 TAGCGGCGTTTGTTGGGTAAG
66 TAGCGGCGTTTGTTGGGTAAG
* **
5430448 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTTG-GTTTGCGCCGCTAAAGACCATGGTC
1 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTT-CTTGCGTAAGCGCCGCTAAAGACCATGGTC
5430511 AAATAAATTA
Statistics
Matches: 140, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
86 137 0.98
87 3 0.02
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (86 bp):
CGCCGCTAAAGACCATGGTCTATAGCGGCGTTTCTTGCGTAAGCGCCGCTAAAGACCATGGTCTA
TAGCGGCGTTTGTTGGGTAAG
Found at i:5434466 original size:16 final size:15
Alignment explanation
Indices: 5434445--5434676 Score: 91
Period size: 16 Copynumber: 15.2 Consensus size: 15
5434435 TTATTATGTC
5434445 GTATTATATAAGTTAT
1 GTATTA-ATAAGTTAT
* *
5434461 GTATTAAAAATATTAT
1 GTATTAATAA-GTTAT
5434477 GTATTAATAAGTTAT
1 GTATTAATAAGTTAT
5434492 GTAAGTT-AT--GTATCAT
1 GT-A-TTAATAAGT-T-AT
5434508 -T-TTAA-AA--TAT
1 GTATTAATAAGTTAT
*
5434518 ATATTAATAAGTTAT
1 GTATTAATAAGTTAT
*
5434533 GTAATATTATGTAAGTTAT
1 G---TATTA-ATAAGTTAT
* *
5434552 GAATTAAAAATGTTAT
1 GTATTAATAA-GTTAT
5434568 GTATTAATAAGTTAT
1 GTATTAATAAGTTAT
5434583 GTAAGTT-AT--GTATCAT
1 GT-A-TTAATAAGT-T-AT
5434599 -T-TTAA-AA--TAT
1 GTATTAATAAGTTAT
* *
5434609 ATATTAATAAGCTATGT
1 GTATTAATAAG-T-TAT
5434626 CGTATTATATAAGTTAT
1 -GTATTA-ATAAGTTAT
*
5434643 GTATTAAAAATGTTAT
1 GTATTAATAA-GTTAT
5434659 GTATTAATAAGTTAT
1 GTATTAATAAGTTAT
5434674 GTA
1 GTA
5434677 ATGTATGTAT
Statistics
Matches: 165, Mismatches: 16, Indels: 71
0.65 0.06 0.28
Matches are distributed among these distances:
10 4 0.02
11 4 0.02
12 12 0.07
13 6 0.04
14 4 0.02
15 36 0.22
16 66 0.40
17 8 0.05
18 11 0.07
19 14 0.08
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (15 bp):
GTATTAATAAGTTAT
Found at i:5434498 original size:40 final size:40
Alignment explanation
Indices: 5434448--5434595 Score: 138
Period size: 40 Copynumber: 3.4 Consensus size: 40
5434438 TTATGTCGTA
*
5434448 TTATATAAGTTATGTATTAAAAATATTATGTATTAATAAG
1 TTATGTAAGTTATGTATTAAAAATATTATGTATTAATAAG
5434488 TTATGTAAGTTATGTATCATTTTAAAATATATATTAATAAGTTATGTAAT-A-
1 TTATGTAAGTTATG--T-A--TT-AAA-A-ATATT-AT--G-TAT-TAATAAG
* *
5434539 TTATGTAAGTTATGAATTAAAAATGTTATGTATTAATAAG
1 TTATGTAAGTTATGTATTAAAAATATTATGTATTAATAAG
5434579 TTATGTAAGTTATGTAT
1 TTATGTAAGTTATGTAT
5434596 CATTTTAAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 30
0.72 0.03 0.24
Matches are distributed among these distances:
38 4 0.04
39 4 0.04
40 30 0.34
42 3 0.03
43 5 0.06
44 1 0.01
45 5 0.06
46 5 0.06
47 1 0.01
48 6 0.07
49 2 0.02
51 15 0.17
52 4 0.04
53 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (40 bp):
TTATGTAAGTTATGTATTAAAAATATTATGTATTAATAAG
Found at i:5434530 original size:41 final size:41
Alignment explanation
Indices: 5434478--5434625 Score: 170
Period size: 41 Copynumber: 3.4 Consensus size: 41
5434468 AAATATTATG
5434478 TATTAATAAGTTATGTAAGTTATGTATCATTTTAAAATATA
1 TATTAATAAGTTATGTAAGTTATGTATCATTTTAAAATATA
* * * *
5434519 TATTAATAAGTTATGTAATATTATGTAAGTTATGAATTAAAAATGTTATG
1 TATTAATAAGTTATGTAA-GTTATGT-A-TCAT---TTTAAAA---TATA
5434569 TATTAATAAGTTATGTAAGTTATGTATCATTTTAAAATATA
1 TATTAATAAGTTATGTAAGTTATGTATCATTTTAAAATATA
*
5434610 TATTAATAAGCTATGT
1 TATTAATAAGTTATGT
5434626 CGTATTATAT
Statistics
Matches: 89, Mismatches: 9, Indels: 18
0.77 0.08 0.16
Matches are distributed among these distances:
41 36 0.40
42 6 0.07
43 1 0.01
44 9 0.10
47 9 0.10
48 1 0.01
49 6 0.07
50 21 0.24
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.45
Consensus pattern (41 bp):
TATTAATAAGTTATGTAAGTTATGTATCATTTTAAAATATA
Found at i:5434545 original size:51 final size:51
Alignment explanation
Indices: 5434488--5434646 Score: 160
Period size: 51 Copynumber: 3.3 Consensus size: 51
5434478 TATTAATAAG
5434488 TTATGTAAGTTATGTATCATTTTAAAATATATATTAATAAGTTATGTAATA
1 TTATGTAAGTTATGTATCATTTTAAAATATATATTAATAAGTTATGTAATA
* * * * *
5434539 TTATGTAAGTTATG-A--A-TTAAAAATGT-TA-T-GT-A-TTA-ATAA-G
1 TTATGTAAGTTATGTATCATTTTAAAATATATATTAATAAGTTATGTAATA
* **
5434579 TTATGTAAGTTATGTATCATTTTAAAATATATATTAATAAGCTATGTCGTA
1 TTATGTAAGTTATGTATCATTTTAAAATATATATTAATAAGTTATGTAATA
*
5434630 TTATATAAGTTATGTAT
1 TTATGTAAGTTATGTAT
5434647 TAAAAATGTT
Statistics
Matches: 83, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
40 14 0.17
41 4 0.05
42 3 0.04
43 2 0.02
44 9 0.11
45 3 0.04
46 3 0.04
47 9 0.11
48 2 0.02
49 2 0.02
50 2 0.02
51 30 0.36
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.46
Consensus pattern (51 bp):
TTATGTAAGTTATGTATCATTTTAAAATATATATTAATAAGTTATGTAATA
Found at i:5434549 original size:91 final size:91
Alignment explanation
Indices: 5434446--5434686 Score: 412
Period size: 91 Copynumber: 2.6 Consensus size: 91
5434436 TATTATGTCG
*
5434446 TATTATATAAGTTATGTATTAAAAATATTATGTATTAATAAGTTATGTAAGTTATGTATCATTTT
1 TATTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATTTT
*
5434511 AAAATATATATTAATAAGTTATGTAA
66 AAAATATATATTAATAAGCTATGTAA
* *
5434537 TATTATGTAAGTTATGAATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATTTT
1 TATTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATTTT
**
5434602 AAAATATATATTAATAAGCTATGTCG
66 AAAATATATATTAATAAGCTATGTAA
5434628 TATTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAA-TGTATGTAT
1 TATTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGT-TATGTAT
5434687 TATAAATGGG
Statistics
Matches: 141, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
90 1 0.01
91 140 0.99
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.46
Consensus pattern (91 bp):
TATTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATTTT
AAAATATATATTAATAAGCTATGTAA
Found at i:5434582 original size:50 final size:49
Alignment explanation
Indices: 5434519--5434678 Score: 174
Period size: 50 Copynumber: 3.4 Consensus size: 49
5434509 TTAAAATATA
5434519 TATTAATAAGTTATGTAATATTATGTAAGTTATGAATTAAAAATGTTATG
1 TATTAATAAGTTATGTAATATTATGTAAGTTATG-ATTAAAAATGTTATG
* * * *
5434569 TATTAATAAGTTATGTAA-GTTATGT-A-TCAT--TTTAAAA---TATA
1 TATTAATAAGTTATGTAATATTATGTAAGTTATGATTAAAAATGTTATG
* ** *
5434610 TATTAATAAGCTATGTCGTATTATATAAGTTATGTATTAAAAATGTTATG
1 TATTAATAAGTTATGTAATATTATGTAAGTTATG-ATTAAAAATGTTATG
5434660 TATTAATAAGTTATGTAAT
1 TATTAATAAGTTATGTAAT
5434679 GTATGTATTA
Statistics
Matches: 86, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
41 18 0.21
42 5 0.06
43 1 0.01
44 9 0.10
47 9 0.10
48 1 0.01
49 6 0.07
50 37 0.43
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (49 bp):
TATTAATAAGTTATGTAATATTATGTAAGTTATGATTAAAAATGTTATG
Found at i:5435318 original size:15 final size:15
Alignment explanation
Indices: 5435290--5435325 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
5435280 TTAATAAAAG
*
5435290 GAAAA-AGTAGAAAT
1 GAAAACAGTACAAAT
5435304 GAAAACAGTACAAAT
1 GAAAACAGTACAAAT
5435319 GAAAACA
1 GAAAACA
5435326 AATTGGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (15 bp):
GAAAACAGTACAAAT
Found at i:5438348 original size:74 final size:73
Alignment explanation
Indices: 5438190--5438421 Score: 367
Period size: 73 Copynumber: 3.2 Consensus size: 73
5438180 ATAACTATCA
* * ** *
5438190 TTTGCGGTGTTTGTACCAAAAACGATGCTAATACCAATAAACAGTATAAAAATGAAGTCATTTTG
1 TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCATTTTG
5438255 GTTAAACT
66 GTTAAACT
5438263 TTTGCGGCGTTTG-ATCCAGAAACGCCGCTAATACCAATAAACAGTATACAAAACGAAGTCATTT
1 TTTGCGGCGTTTGTA-CCAGAAACGCCGCTAATACCAATAAACAGTATA-AAAACGAAGTCATTT
5438327 TGGTTAAACT
64 TGGTTAAACT
* * *
5438337 TTTGCGGCGTTTTTACTAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCGTTTTG
1 TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCATTTTG
5438402 GTTAAACT
66 GTTAAACT
5438410 TTTGCGGCGTTT
1 TTTGCGGCGTTT
5438422 TTACAATAAA
Statistics
Matches: 148, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
72 1 0.01
73 78 0.53
74 68 0.46
75 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (73 bp):
TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCATTTTG
GTTAAACT
Found at i:5439607 original size:41 final size:41
Alignment explanation
Indices: 5439514--5439607 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
5439504 GCTAGCTACA
* *
5439514 AAACGCCGCTAATGCTCCGGTCTTTAGCGGCGTTTTCTAAT
1 AAACGCCGCTAATGCTACGGTCTTTAGCGGCGTTTTCTAAG
** * *
5439555 ATGCGCAGCTAATGCTACGGTTTTTAGCGGCGCTTTT-TAAG
1 AAACGCCGCTAATGCTACGGTCTTTAGCGGCG-TTTTCTAAG
5439596 AAACGCCGCTAA
1 AAACGCCGCTAA
5439608 AGACCTGAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
41 39 0.91
42 4 0.09
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.30
Consensus pattern (41 bp):
AAACGCCGCTAATGCTACGGTCTTTAGCGGCGTTTTCTAAG
Found at i:5439623 original size:41 final size:41
Alignment explanation
Indices: 5439578--5439827 Score: 332
Period size: 41 Copynumber: 6.2 Consensus size: 41
5439568 GCTACGGTTT
* *
5439578 TTAGCGGCGCTTTTTAAGAAACGCCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTGAGCA
* *
5439619 TTAGCGGCGCTTGGTAAAAAACGCCGCTAAA-A---GAACA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTGAGCA
* *
5439656 TTAGCGGCGCTTTGTAAAAAACGCCGCTAACGACCTCAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTGAGCA
* * *
5439697 TTAGCGGCGCTTTGTAAAGAACGCTGCGAAAGACCTGAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTGAGCA
5439738 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTGAGCA
* * *
5439779 TTAGCGGCGCATAT-TAGAAAACGCCGCAAAAGACC-GCAGCA
1 TTAGCGGCGC-TTTGTAAAAAACGCCGCTAAAGACCTG-AGCA
5439820 TTAGCGGC
1 TTAGCGGC
5439828 TTTCGTTTTT
Statistics
Matches: 184, Mismatches: 19, Indels: 12
0.86 0.09 0.06
Matches are distributed among these distances:
37 33 0.18
38 1 0.01
40 2 0.01
41 146 0.79
42 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (41 bp):
TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTGAGCA
Found at i:5440581 original size:32 final size:32
Alignment explanation
Indices: 5440544--5440608 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
5440534 AAGACAAAAG
5440544 AGTAAGCTAAAACCTTATTACTGAACCAACAA
1 AGTAAGCTAAAACCTTATTACTGAACCAACAA
5440576 AGTAAGCTAAAACCTTATTACTGAACCAACAA
1 AGTAAGCTAAAACCTTATTACTGAACCAACAA
5440608 A
1 A
5440609 CTCATTCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.22, G:0.09, T:0.22
Consensus pattern (32 bp):
AGTAAGCTAAAACCTTATTACTGAACCAACAA
Found at i:5441092 original size:41 final size:41
Alignment explanation
Indices: 5441033--5441113 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
5441023 TGGCTCAATT
*
5441033 TGGTCGGTTGAGTCGGTTTTAATCGCTAACTATAATAGATG
1 TGGTCGGTTGAGTCGGTTTTAATCACTAACTATAATAGATG
* *
5441074 TGGTCGGTTGATTTGGTTTTAATCACTAACTATAATAGAT
1 TGGTCGGTTGAGTCGGTTTTAATCACTAACTATAATAGAT
5441114 AATATTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (41 bp):
TGGTCGGTTGAGTCGGTTTTAATCACTAACTATAATAGATG
Found at i:5441150 original size:20 final size:20
Alignment explanation
Indices: 5441112--5441150 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5441102 ACTATAATAG
* *
5441112 ATAATATTATATTACATAAT
1 ATAATAATATAGTACATAAT
*
5441132 ATAATAATATAGTATATAA
1 ATAATAATATAGTACATAA
5441151 CTATTACTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
ATAATAATATAGTACATAAT
Found at i:5442715 original size:20 final size:20
Alignment explanation
Indices: 5442686--5442748 Score: 60
Period size: 22 Copynumber: 3.1 Consensus size: 20
5442676 ATTTTGATGG
5442686 TTTT-TAATTTTAAAAATAA
1 TTTTATAATTTTAAAAATAA
* *
5442705 TTTTATAATTTTTTTAAAAT-T
1 TTTTATAA--TTTTAAAAATAA
5442726 TTTTA-AATTTTAAAAATTAA
1 TTTTATAATTTTAAAAA-TAA
5442746 TTT
1 TTT
5442749 AAAACTATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
18 8 0.23
19 5 0.14
20 8 0.23
21 5 0.14
22 9 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATAATTTTAAAAATAA
Found at i:5450606 original size:25 final size:26
Alignment explanation
Indices: 5450537--5450606 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 26
5450527 TTTATCATTA
5450537 TTTATATTATTATTTTATTTGAAATTGT
1 TTTATATTATTA-TTTATTT-AAATTGT
* *
5450565 TTTACATTA-AATTTATTT-AATT-T
1 TTTATATTATTATTTATTTAAATTGT
5450588 TTTATATATATTATTTATT
1 TTTATAT-TATTATTTATT
5450607 ATAAGTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
23 7 0.19
24 6 0.17
25 7 0.19
26 7 0.19
27 1 0.03
28 8 0.22
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (26 bp):
TTTATATTATTATTTATTTAAATTGT
Found at i:5450902 original size:15 final size:17
Alignment explanation
Indices: 5450869--5450903 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5450859 TATTTGGTGT
5450869 GTTGTGTGATTATTGTC
1 GTTGTGTGATTATTGTC
5450886 GTTGTGT-ATTATT-TC
1 GTTGTGTGATTATTGTC
5450901 GTT
1 GTT
5450904 TACCCATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 6 0.33
17 7 0.39
ACGTcount: A:0.11, C:0.06, G:0.26, T:0.57
Consensus pattern (17 bp):
GTTGTGTGATTATTGTC
Found at i:5456135 original size:21 final size:20
Alignment explanation
Indices: 5456109--5456148 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5456099 AATAAACACC
*
5456109 AAAAAATTATTTTAAAAATA
1 AAAAAAATATTTTAAAAATA
5456129 AAAAAAATATTTTAAAAATA
1 AAAAAAATATTTTAAAAATA
5456149 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAAATATTTTAAAAATA
Found at i:5456157 original size:10 final size:11
Alignment explanation
Indices: 5456110--5456156 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
5456100 ATAAACACCA
5456110 AAAAATTATTTT
1 AAAAA-TATTTT
**
5456122 AAAAATA--AA
1 AAAAATATTTT
5456131 AAAAATATTTT
1 AAAAATATTTT
5456142 AAAAATATTTT
1 AAAAATATTTT
5456153 AAAA
1 AAAA
5456157 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
9 7 0.24
11 17 0.59
12 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:5458812 original size:16 final size:15
Alignment explanation
Indices: 5458791--5458838 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
5458781 GATGTGAATA
5458791 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
5458807 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
5458822 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
5458838 A
1 A
5458839 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:5458814 original size:24 final size:24
Alignment explanation
Indices: 5458787--5458842 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
5458777 TAATGATGTG
*
5458787 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
5458811 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
5458835 AATAATAA
1 AATAATAA
5458843 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:5458821 original size:8 final size:8
Alignment explanation
Indices: 5458787--5458838 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
5458777 TAATGATGTG
*
5458787 AATAATAA
1 AATATTAA
5458795 AATATATAA
1 AATAT-TAA
5458804 AATA-TAA
1 AATATTAA
5458811 AATATTAA
1 AATATTAA
*
5458819 AATATCAA
1 AATATTAA
*
5458827 AATATTAG
1 AATATTAA
5458835 AATA
1 AATA
5458839 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:5459021 original size:25 final size:25
Alignment explanation
Indices: 5458993--5459041 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
5458983 CGTGATAATA
**
5458993 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATACATACATAATATAGTG
5459018 TTAAAAATACATACATAATATAGT
1 TTAAAAATACATACATAATATAGT
5459042 TAAGATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (25 bp):
TTAAAAATACATACATAATATAGTG
Found at i:5459090 original size:28 final size:27
Alignment explanation
Indices: 5459046--5459105 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
5459036 TATAGTTAAG
*
5459046 ATATATACATAAGATAACATGTAAATAT
1 ATATATACATAAGATAACAT-TAAAGAT
* *
5459074 ATATATA-AGTAATATAATATTAAAGAT
1 ATATATACA-TAAGATAACATTAAAGAT
5459101 ATATA
1 ATATA
5459106 CATAAAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (27 bp):
ATATATACATAAGATAACATTAAAGAT
Found at i:5459150 original size:25 final size:25
Alignment explanation
Indices: 5459074--5459151 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
5459064 ATGTAAATAT
*
5459074 ATATATAAGTAATAT--AATATTAAA
1 ATATATACGTAATATAGAAT-TTAAA
* * * *
5459098 GATATATACATAAAATAG--TATAAT
1 -ATATATACGTAATATAGAATTTAAA
5459122 ATATATACGTAATATAGAATTTAAA
1 ATATATACGTAATATAGAATTTAAA
5459147 ATATA
1 ATATA
5459152 CCTAATATAT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
23 15 0.38
24 3 0.08
25 22 0.55
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (25 bp):
ATATATACGTAATATAGAATTTAAA
Found at i:5459201 original size:23 final size:24
Alignment explanation
Indices: 5458987--5459203 Score: 96
Period size: 23 Copynumber: 9.0 Consensus size: 24
5458977 TAAATACGTG
5458987 ATAATATTAA-AAATATGTACATAAT
1 ATAATATTAAGAAATA--TACATAAT
* *
5459012 ATAGTGTTAA-AAATACATACATAAT
1 ATAATATTAAGAAAT--ATACATAAT
* * *
5459037 AT-A-GTTAAGATATATACATAAG
1 ATAATATTAAGAAATATACATAAT
* *
5459059 ATAACATGTAA-ATATATATATAAGTAAT
1 ATAATAT-TAAGA-A-ATATA-CA-TAAT
* *
5459087 ATAATATTAAAGATATATACATAAA
1 ATAATATT-AAGAAATATACATAAT
* * * *
5459112 ATAGTA-TAATATATATACGTAAT
1 ATAATATTAAGAAATATACATAAT
* *
5459135 ATAGA-ATTTA-AAATATACCTAAT
1 ATA-ATATTAAGAAATATACATAAT
* * *
5459158 ATATTA-AAAG-AATATATATAAT
1 ATAATATTAAGAAATATACATAAT
5459180 ATAATATTAAGAAATATA-ATAAT
1 ATAATATTAAGAAATATACATAAT
5459203 A
1 A
5459204 ACAAAAAAGG
Statistics
Matches: 146, Mismatches: 28, Indels: 38
0.69 0.13 0.18
Matches are distributed among these distances:
22 26 0.18
23 47 0.32
24 14 0.10
25 33 0.23
26 6 0.04
27 8 0.05
28 11 0.08
29 1 0.01
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (24 bp):
ATAATATTAAGAAATATACATAAT
Found at i:5459729 original size:30 final size:30
Alignment explanation
Indices: 5459694--5459806 Score: 181
Period size: 30 Copynumber: 3.8 Consensus size: 30
5459684 GGTACAAGTA
* *
5459694 GTGGTGGAGAAGGTGTGGCTAGTGGAGTTG
1 GTGGTGGAAAAGGAGTGGCTAGTGGAGTTG
*
5459724 GTGGTGGAAAAAGAGTGGCTAGTGGAGTTG
1 GTGGTGGAAAAGGAGTGGCTAGTGGAGTTG
*
5459754 GTGGTGGAAAAGGTGTGGCTAGTGGAGTTG
1 GTGGTGGAAAAGGAGTGGCTAGTGGAGTTG
*
5459784 GTAGTGGAAAAGGAGTGGCTAGT
1 GTGGTGGAAAAGGAGTGGCTAGT
5459807 TGAGAAAAGT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.23, C:0.04, G:0.49, T:0.25
Consensus pattern (30 bp):
GTGGTGGAAAAGGAGTGGCTAGTGGAGTTG
Found at i:5460572 original size:14 final size:14
Alignment explanation
Indices: 5460553--5460602 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
5460543 GAGTTGATTT
* *
5460553 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
5460567 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
5460582 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
5460596 TT-AAAAA
1 TTGAAAAA
5460603 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:5460741 original size:75 final size:75
Alignment explanation
Indices: 5460625--5460825 Score: 291
Period size: 76 Copynumber: 2.7 Consensus size: 75
5460615 TGAGCCGAGA
* *
5460625 CTCAACTCACCTCTCGCAATATGAGTT-A-ATTTTTGACAAACAGAAATTGAAATTACCTCAGCG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAATACCTCAGCG
5460688 TGTCCCAAGG
66 TGTCCCAAGG
* * * *
5460698 CTTAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAATACCTCAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAA-TTGAAAATACCTCAGC
**
5460763 GTGTCCTGAGG
65 GTGTCCCAAGG
*
5460774 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT-ACGAACAGAAATTGAA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAATTGAA
5460826 GAACAGAAAT
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
73 25 0.22
74 5 0.04
75 25 0.22
76 57 0.51
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (75 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAATACCTCAGCG
TGTCCCAAGG
Found at i:5460848 original size:239 final size:236
Alignment explanation
Indices: 5460574--5461284 Score: 1203
Period size: 239 Copynumber: 3.0 Consensus size: 236
5460564 AAATTGAAAA
5460574 AACAGAAATTGAA-AAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTC
1 AACAGAAATTGAAGAA-CAGAAATTAAAAAGACCTCAGCATGTGAGCCGAG-CTCAACTCACCTC
* *
5460638 TCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCAAGGCTTAA
64 TCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAA
*
5460703 CTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTC
129 CTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTC
*
5460768 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTACG
192 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTACG
5460813 AACAGAAATTGAAGAACAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
1 AACAGAAATTGAAGAACAGAAATTAAAAAGACCTCAGCATGTGAGCCGA-GCTCAACTCACCTCT
*
5460878 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGACTCAAC
65 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
5460943 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTA
130 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTA
5461008 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
195 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTACG
*
5461052 AACAGAAATTGAAGAACAGAAATTCAAAAGACCTCAGCATGTGAGCCGATGCTCAACTCACCTCT
1 AACAGAAATTGAAGAACAGAAATTAAAAAGACCTCAGCATGTGAGCCGA-GCTCAACTCACCTCT
5461117 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
65 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
* *
5461182 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA-TTGAAAATACCTCAGCGTGTGAGC
130 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGT---C
* * *
5461246 C-AAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTT
192 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5461285 GATGAACATA
Statistics
Matches: 452, Mismatches: 13, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
237 73 0.16
238 24 0.05
239 320 0.71
240 33 0.07
241 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (236 bp):
AACAGAAATTGAAGAACAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGCTCAACTCACCTCTC
GCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACT
CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTAA
GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTACG
Found at i:5460884 original size:90 final size:88
Alignment explanation
Indices: 5460732--5460915 Score: 264
Period size: 89 Copynumber: 2.1 Consensus size: 88
5460722 GTTGATTTTT
* *
5460732 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
* * *
5460797 AGTTGATTTTTTTACGAACAGAAA
66 AGTT-AATTTTTGACAAACAGAAA
*
5460821 TTGAAGAACAGAAA-TTAAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAAT
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTCTCGCAAT
5460884 ATGAGTTAATTTTTGACAAACAGAAA
63 ATGAGTTAATTTTTGACAAACAGAAA
5460910 TTGAAA
1 TTGAAA
5460916 TTACCTCAGC
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
88 15 0.18
89 34 0.40
90 34 0.40
91 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (88 bp):
TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTAATTTTTGACAAACAGAAA
Found at i:5460949 original size:73 final size:74
Alignment explanation
Indices: 5460821--5461044 Score: 317
Period size: 74 Copynumber: 3.0 Consensus size: 74
5460811 CGAACAGAAA
* * **
5460821 TTGAAGAACAGAAA-TTAAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTTAAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATA
*
5460885 TGAGTTAATTT
64 TGAGTTGATTT
* * * *
5460896 TTGACAAACAGAAA-TTGAAATTACCTCAGCGTGTCCCGAGACTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
5460960 AGTTGATTT
66 AGTTGATTT
**
5460969 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
5461034 AGTTGATTT
66 AGTTGATTT
5461043 TT
1 TT
5461045 TTTTACGAAC
Statistics
Matches: 133, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
73 52 0.39
74 56 0.42
75 25 0.19
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (74 bp):
TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTT
Found at i:5461036 original size:74 final size:72
Alignment explanation
Indices: 5460821--5461044 Score: 313
Period size: 73 Copynumber: 3.0 Consensus size: 72
5460811 CGAACAGAAA
* * *
5460821 TTGAAGAACAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTAAAAATACCTCAGC--GTG-TCCGAGGCTCAACTCACCTCTCGCAATAT
*
5460886 GAGTTAATTT
63 GAGTTGATTT
* * * *
5460896 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGACTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGCGTGT-CCGAGGCTCAACTCACCTCTCGCAATATGA
5460961 GTTGATTT
65 GTTGATTT
*
5460969 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAA-TTAAAAATACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATG
5461034 AGTTGATTT
64 AGTTGATTT
5461043 TT
1 TT
5461045 TTTTACGAAC
Statistics
Matches: 133, Mismatches: 13, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
73 54 0.41
74 54 0.41
75 25 0.19
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (72 bp):
TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTT
Found at i:5461283 original size:75 final size:73
Alignment explanation
Indices: 5461060--5461372 Score: 360
Period size: 73 Copynumber: 4.2 Consensus size: 73
5461050 CGAACAGAAA
* * * * *
5461060 TTGAAGAACAGAAATTCAAAAGACCTCAGCATGTGAGCCGATGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGC--GTGTGCCGAGGCTCAACTCACCTCTCGCAATAT
5461125 GAGTTAATTT
64 GAGTTAATTT
* * *
5461135 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTGCCGAGGCTCAACTCACCTCTCGCAATATGA
*
5461200 GTTGATTT
66 GTTAATTT
* * *
5461208 TTGAAAAATAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT--GCCGAGGCTCAACTCACCTCTCGCAATAT
*
5461273 GAGCTAATTT
64 GAGTTAATTT
** * * *
5461283 TTGATGAACATAAATT-AAAACCACCTCAGCGTGT-CCTGAGGTTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAA-TACCTCAGCGTGTGCC-GAGGCTCAACTCACCTCTCGCAATAT
*
5461346 GAGTTGATTTTT
64 GAGTT-A-ATTT
*
5461358 TTGAAAATCAGAAAT
1 TTGAAAAACAGAAAT
5461373 AAAAACATTA
Statistics
Matches: 201, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
72 2 0.01
73 97 0.48
74 5 0.02
75 97 0.48
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (73 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTGCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTAATTT
Found at i:5461329 original size:148 final size:148
Alignment explanation
Indices: 5461060--5461372 Score: 446
Period size: 148 Copynumber: 2.1 Consensus size: 148
5461050 CGAACAGAAA
* * *
5461060 TTGAAGAACAGAAATTCAAAAGACCTCAGCATGTGAGCCGATGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTCAAAAGACCTCAGCATGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
* * **
5461125 GAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCT
66 GAGCTAATTTTTGACAAACAGAAATTAAAACCACCTCAGCGTGTCCCGAGGCTCAACTCACCTCT
5461190 CGCAATATGAGTTGATTT
131 CGCAATATGAGTTGATTT
* * * * *
5461208 TTGAAAAATAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATAT
1 TTGAAAAACAGAAATTCAAAAGACCTCAGCATGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
** * * *
5461273 GAGCTAATTTTTGATGAACATAAATTAAAACCACCTCAGCGTGTCCTGAGGTTCAACTCACCTCT
66 GAGCTAATTTTTGACAAACAGAAATTAAAACCACCTCAGCGTGTCCCGAGGCTCAACTCACCTCT
5461338 CGCAATATGAGTTGATTTTT
131 CGCAATATGAGTTGA--TTT
*
5461358 TTGAAAATCAGAAAT
1 TTGAAAAACAGAAAT
5461373 AAAAACATTA
Statistics
Matches: 144, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
148 128 0.89
150 16 0.11
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (148 bp):
TTGAAAAACAGAAATTCAAAAGACCTCAGCATGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
GAGCTAATTTTTGACAAACAGAAATTAAAACCACCTCAGCGTGTCCCGAGGCTCAACTCACCTCT
CGCAATATGAGTTGATTT
Found at i:5471122 original size:16 final size:15
Alignment explanation
Indices: 5471101--5471148 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
5471091 GATGTGAATA
5471101 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
5471117 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
5471132 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
5471148 A
1 A
5471149 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:5471124 original size:24 final size:24
Alignment explanation
Indices: 5471097--5471152 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
5471087 TAATGATGTG
*
5471097 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
5471121 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
5471145 AATAATAA
1 AATAATAA
5471153 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:5471131 original size:8 final size:8
Alignment explanation
Indices: 5471097--5471148 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
5471087 TAATGATGTG
*
5471097 AATAATAA
1 AATATTAA
5471105 AATATATAA
1 AATAT-TAA
5471114 AATA-TAA
1 AATATTAA
5471121 AATATTAA
1 AATATTAA
*
5471129 AATATCAA
1 AATATTAA
*
5471137 AATATTAG
1 AATATTAA
5471145 AATA
1 AATA
5471149 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:5471389 original size:30 final size:29
Alignment explanation
Indices: 5471353--5471420 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
5471343 TATAGTTAAG
*
5471353 ATATATACATAAGATAACATGTAAAAATAT
1 ATATATAAATAAGATAACAT-TAAAAATAT
* * *
5471383 ATATATAAATAATATAATATTAAAGATAT
1 ATATATAAATAAGATAACATTAAAAATAT
*
5471412 ATACATAAA
1 ATATATAAA
5471421 ATAGTATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (29 bp):
ATATATAAATAAGATAACATTAAAAATAT
Found at i:5471411 original size:25 final size:25
Alignment explanation
Indices: 5471295--5471514 Score: 115
Period size: 25 Copynumber: 9.0 Consensus size: 25
5471285 TAAATATGTC
*
5471295 ATAATATTAAA-ATATGTACATAAT
1 ATAATATTAAAGATATATACATAAT
* * * *
5471319 ATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
5471344 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * *
5471366 ATAACATGTAAAAATATATATATAAATAAT
1 ATAATAT-T---AA-AGATATATACATAAT
*
5471396 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAAGATATATACATAAT
* * *
5471421 ATAGTA-TAATATATATATACGTAAT
1 ATAATATTAA-AGATATATACATAAT
* *
5471446 ATAGA-ATTTAA-A-ATATACCTAAT
1 ATA-ATATTAAAGATATATACATAAT
* *
5471469 AT-AT-TAAAAGA-ATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
5471491 ATAATATT-AAGAAATATA-ATAAT
1 ATAATATTAAAGATATATACATAAT
5471514 A
1 A
5471515 ACAAAAAAGG
Statistics
Matches: 151, Mismatches: 28, Indels: 35
0.71 0.13 0.16
Matches are distributed among these distances:
21 4 0.03
22 27 0.18
23 28 0.19
24 20 0.13
25 48 0.32
26 4 0.03
29 2 0.01
30 18 0.12
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:5472038 original size:30 final size:30
Alignment explanation
Indices: 5472003--5472175 Score: 283
Period size: 30 Copynumber: 5.8 Consensus size: 30
5471993 GGTACAAGTA
* *
5472003 GTGGTGGAGAAGGTGTGGCTAGTGGAGTTG
1 GTGGTGGAAAAGGAGTGGCTAGTGGAGTTG
*
5472033 GTGGTGGAAAAAGAGTGGCTAGTGGAGTTG
1 GTGGTGGAAAAGGAGTGGCTAGTGGAGTTG
*
5472063 GTGGTGGAAAAGGTGTGGCTAGTGGAGTTG
1 GTGGTGGAAAAGGAGTGGCTAGTGGAGTTG
* *
5472093 GTGGTGGAAAAAGAGTGGCTAATGGAGTTG
1 GTGGTGGAAAAGGAGTGGCTAGTGGAGTTG
*
5472123 GTGGTGGAAAAGGTGTGGCTAGTGGAGTTG
1 GTGGTGGAAAAGGAGTGGCTAGTGGAGTTG
5472153 GTGGTGGAAAAGGAGTGGCTAGT
1 GTGGTGGAAAAGGAGTGGCTAGT
5472176 TGAGAAAAGT
Statistics
Matches: 131, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 131 1.00
ACGTcount: A:0.23, C:0.03, G:0.49, T:0.25
Consensus pattern (30 bp):
GTGGTGGAAAAGGAGTGGCTAGTGGAGTTG
Found at i:5472094 original size:60 final size:60
Alignment explanation
Indices: 5472003--5472175 Score: 319
Period size: 60 Copynumber: 2.9 Consensus size: 60
5471993 GGTACAAGTA
*
5472003 GTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGTTG
1 GTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGTTG
*
5472063 GTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAATGGAGTTG
1 GTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGTTG
*
5472123 GTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGT
1 GTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGT
5472176 TGAGAAAAGT
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 109 1.00
ACGTcount: A:0.23, C:0.03, G:0.49, T:0.25
Consensus pattern (60 bp):
GTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGTTG
Found at i:5477068 original size:6 final size:6
Alignment explanation
Indices: 5477031--5477064 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5477021 ACCATTTCTG
* *
5477031 AACCTT AACCTT AACCTT AACTTT AACCCT AACC
1 AACCTT AACCTT AACCTT AACCTT AACCTT AACC
5477065 CTAATTTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (6 bp):
AACCTT
Found at i:5478435 original size:3 final size:3
Alignment explanation
Indices: 5478427--5478469 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
5478417 ATATTTTAAC
*
5478427 ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5478470 ATTTGAGGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:5479464 original size:28 final size:28
Alignment explanation
Indices: 5479428--5479481 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5479418 ATCCGTAATT
* *
5479428 AAGTTCAAGTACTAAAA-TAGATTTAAAA
1 AAGTACAAGTACCAAAATTA-ATTTAAAA
5479456 AAGTACAAGTACCAAAATTAATTTAA
1 AAGTACAAGTACCAAAATTAATTTAA
5479482 TTACCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (28 bp):
AAGTACAAGTACCAAAATTAATTTAAAA
Found at i:5500078 original size:14 final size:14
Alignment explanation
Indices: 5500061--5500090 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5500051 CTCTTTTAAC
5500061 TCTTCTTTCCTTTT
1 TCTTCTTTCCTTTT
*
5500075 TCTTCTTTCTTTTT
1 TCTTCTTTCCTTTT
5500089 TC
1 TC
5500091 CATTCCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TCTTCTTTCCTTTT
Found at i:5511999 original size:40 final size:42
Alignment explanation
Indices: 5511909--5512002 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
5511899 CCATTTCCCC
*
5511909 AAAATCGCGTCCACGTCAGCGCGATGTCAGGGGACGTGTCAG
1 AAAATCGCGTCCACGTCAGCGCGATGTCAGCGGACGTGTCAG
* * * * *
5511951 CAAATCGCGTCCACGTCAGCGCGCT-T-TGCTGATGTGTCAG
1 AAAATCGCGTCCACGTCAGCGCGATGTCAGCGGACGTGTCAG
5511991 AAAATCGCGTCC
1 AAAATCGCGTCC
5512003 TCGTAGGCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 21 0.47
41 1 0.02
42 23 0.51
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.20
Consensus pattern (42 bp):
AAAATCGCGTCCACGTCAGCGCGATGTCAGCGGACGTGTCAG
Found at i:5512276 original size:24 final size:23
Alignment explanation
Indices: 5512249--5512299 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
5512239 ATTTTTTTAA
5512249 TTAT-AATTATAATTATAATAAAAT
1 TTATAAATTATAA-TATAA-AAAAT
* *
5512273 TTATAAATTCTTATATAAAAAAT
1 TTATAAATTATAATATAAAAAAT
5512296 TTAT
1 TTAT
5512300 CCTACTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 9 0.38
25 6 0.25
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATAAATTATAATATAAAAAAT
Found at i:5513974 original size:4 final size:4
Alignment explanation
Indices: 5513965--5514034 Score: 54
Period size: 4 Copynumber: 17.8 Consensus size: 4
5513955 TTTTCGCTTG
* * * * *
5513965 TTTA TTTA TTCA TTTTA TTTA TTCA TTTA CTTA TTTA -TGA ATTA TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
5514013 TTCA TTTA TCTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTT
5514035 TAATCCTTCT
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
3 5 0.10
4 42 0.84
5 3 0.06
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:5520496 original size:90 final size:90
Alignment explanation
Indices: 5520204--5520880 Score: 501
Period size: 90 Copynumber: 7.4 Consensus size: 90
5520194 TTGTGATAAG
* * * *
5520204 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCCA-CATACCCTACCTCCCTAAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCA-ACCTTATCTCCCTGAAGTTGC
* * * *
5520268 ATTGGAGTAGATTGAAGACAGAT-AGCAAA
65 AGTGGAGCAGGTT-AA-A-A-ATAAACAAA
* * * * * *
5520297 TCTTATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTCT-TCTCCCTGAAGTTG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCAACCT-TATCTCCCTGAAGTTGC
* *
5520360 AGTGGAGTAGGTTAAAAATAAACGAA
65 AGTGGAGCAGGTTAAAAATAAACAAA
* * * * * *
5520386 TCTTATCTCCCTAAATTTGCAGTGGAGTAGATTGAAGCTATTAATCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCAACCTTATCTCCCTGAAGTTGCA
*
5520451 GTGGAGCAGGTTAAAAATAAACGAA
66 GTGGAGCAGGTTAAAAATAAACAAA
* * * * *
5520476 TATTATCTCCCTGAAGTTGCAATAGAGCAGATTGAAGCCATCAATCTAATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCAACCTTATCTCCCTGAAGTTGCA
*
5520541 GTAGAGCAGGTTAAAAATAAACAAA
66 GTGGAGCAGGTTAAAAATAAACAAA
* * ** * * * * * *
5520566 TCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTGAAGATAACGAATCTTATTTTCCTGAAATTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATC-AACCTTATCTCCCTGAAGTTGC
* * *
5520631 AGTGGAACAGATTAAAGCTATAAGTTACAAA
65 AGTGGAGCAGGTTAAA--AATAA---ACAAA
* * * * * *
5520662 TCTTATTTCCCTGAAGTTACAATGGTGCGGATTGAA-CTCATCATGACAAATCTTATAC-CCTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC-CATCA--AC----CTTAT-CTCCCTG
* * ** * *
5520725 AAGTTGTAGTGGGGCAAATTGAATAT-AACAAA
58 AAGTTGCAGTGGAGCAGGTTAAAAATAAACAAA
* * * * *
5520757 TCTTATCTCCCTGAAGTTACAGTTGAGCAGATTAAAGCCA-CAAACCTTATCTCCCTAAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATC-AACCTTATCTCCCTGAAGTTGC
* * * *
5520821 AGTGGAACAGGTT-AAAGT-TACAAG
65 AGTGGAGCAGGTTAAAAATAAACAAA
* * *
5520845 TCTTATCTCCCTGAAGTTGTAGTAGAGCAGACTGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
5520881 AATAGCAAAT
Statistics
Matches: 470, Mismatches: 92, Indels: 49
0.77 0.15 0.08
Matches are distributed among these distances:
88 42 0.09
89 83 0.18
90 139 0.30
91 32 0.07
92 11 0.02
93 55 0.12
94 3 0.01
95 39 0.08
96 37 0.08
97 1 0.00
98 1 0.00
99 3 0.01
101 24 0.05
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (90 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCAACCTTATCTCCCTGAAGTTGCA
GTGGAGCAGGTTAAAAATAAACAAA
Found at i:5520772 original size:45 final size:45
Alignment explanation
Indices: 5520204--5520959 Score: 399
Period size: 44 Copynumber: 16.6 Consensus size: 45
5520194 TTGTGATAAG
* *** *
5520204 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTG-AAGCCACATA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * * * * * *
5520248 CCCTACCTCCCTAAAGTTGCATTGGAGTAGATTGAAGACAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-A-A-A-ATAACAAA
* * * * *
5520297 TCTTATCTCTCTAAAGTTGCAGTAGAGCAGATT-AAAGCT-ATAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-ATAACAAA
* * * * *
5520341 CCTCT-TCTCCCTGAAGTTG-AGTGGAGTAGGTTAAAAATAAACGAA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAT-AACAAA
* * * ** **
5520386 TCTTATCTCCCTAAATTTGCAGTGGAGTAGATTGAAGCT-ATTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * *
5520430 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAACGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAT-AACAAA
* * * *** *
5520476 TATTATCTCCCTGAAGTTGCAATAGAGCAGATTGAAGCCATC-AA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * * *
5520520 TCTAATCTCCCTGAAGTTGCAGTAGAGCAGGTTAAAAATAAACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAT-AACAAA
* * * *
5520566 TCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTGAAGATAACGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * * * *
5520611 TCTTATTTTCCTGAAATTACAGTGGAACAGATT-AAAGCTATAAGTTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA---AT-A---ACAAA
* * * * * *
5520662 TCTTATTTCCCTGAAGTTACAATGGTGCGGATTGAACTCATCATGACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA---A--ATAACAAA
* * * * *
5520712 TCTTATAC-CCTTGAAGTTGTAGTGGGGCAAATTGAATATAACAAA
1 TCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * ***
5520757 TCTTATCTCCCTGAAGTTACAGTTGAGCAGATT-AAAGCCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * * * * * * *
5520801 CCTTATCTCCCTAAAGTTGTAGTGGAACAGGTT-AAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * * *
5520845 TCTTATCTCCCTGAAGTTGTAGTAGAGCAGACTGAAAATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
** * * * *
5520890 TCTTATCTCTTTGAAGTTGAAGTAGAGCATATT-AAAGCT-ACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-ATAACAAA
*
5520934 -CATTATCTCCTTGAAGTTAG-AGTGGA
1 TC-TTATCTCCCTGAAGTT-GCAGTGGA
5520960 ACAGTAGAGC
Statistics
Matches: 538, Mismatches: 142, Indels: 64
0.72 0.19 0.09
Matches are distributed among these distances:
43 12 0.02
44 214 0.40
45 125 0.23
46 84 0.16
47 4 0.01
48 2 0.00
49 29 0.05
50 32 0.06
51 31 0.06
52 2 0.00
54 2 0.00
55 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
Found at i:5520905 original size:133 final size:133
Alignment explanation
Indices: 5520723--5520963 Score: 324
Period size: 133 Copynumber: 1.8 Consensus size: 133
5520713 CTTATACCCT
* * * * *
5520723 TGAAGTTGTAGTGGGGCAAATTGAATATAACAAATCTTATCTCCCTGAAGTT-ACAGTTGAGCAG
1 TGAAGTTGTAGTAGAGCAAACTGAAAATAACAAATCTTATCTCCCTGAAGTTGA-AGTAGAGCAG
*
5520787 ATTAAAGCCACAAACCTTATCTCCCTAAAGTT-GTAGTGGAACAGGTTAAAGTTACAAGTCTTAT
65 ATTAAAGCCACAAACATTATCTCCCTAAAGTTAG-AGTGGAACAGGTTAAAGTTACAAGTCTTAT
5520851 CTCCC
129 CTCCC
* * ** *
5520856 TGAAGTTGTAGTAGAGCAGACTGAAAATAGCAAATCTTATCTCTTTGAAGTTGAAGTAGAGCATA
1 TGAAGTTGTAGTAGAGCAAACTGAAAATAACAAATCTTATCTCCCTGAAGTTGAAGTAGAGCAGA
* * *
5520921 TTAAAGCTACAAACATTATCTCCTTGAAGTTAGAGTGGAACAG
66 TTAAAGCCACAAACATTATCTCCCTAAAGTTAGAGTGGAACAG
5520964 TAGAGCACAT
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
133 90 0.98
134 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (133 bp):
TGAAGTTGTAGTAGAGCAAACTGAAAATAACAAATCTTATCTCCCTGAAGTTGAAGTAGAGCAGA
TTAAAGCCACAAACATTATCTCCCTAAAGTTAGAGTGGAACAGGTTAAAGTTACAAGTCTTATCT
CCC
Found at i:5522626 original size:4 final size:4
Alignment explanation
Indices: 5522617--5522715 Score: 60
Period size: 4 Copynumber: 24.8 Consensus size: 4
5522607 TTTTCGCTTG
* ** * *
5522617 TTTA TTTA TTCA -TTA TTCC TTTTA TTTTA TTCA TTTTA TTTA TTCA TTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TT-TA TTTA TT-TA TTTA TTTA TTTA
* * * * *
5522667 TTCA TTTA CTTA TTTA TGTA -TTA TTTA TTCA TTTA TCTA TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
5522713 TTT
1 TTT
5522716 TAATCCTTCT
Statistics
Matches: 70, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
3 7 0.10
4 53 0.76
5 10 0.14
ACGTcount: A:0.23, C:0.09, G:0.01, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:5522660 original size:13 final size:14
Alignment explanation
Indices: 5522629--5522665 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
5522619 TATTTATTCA
*
5522629 TTATTCCTTTTATT
1 TTATTCATTTTATT
5522643 TTATTCATTTTA-T
1 TTATTCATTTTATT
5522656 TTATTCATTT
1 TTATTCATTT
5522666 ATTCATTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTCATTTTATT
Found at i:5522691 original size:35 final size:32
Alignment explanation
Indices: 5522617--5522715 Score: 103
Period size: 34 Copynumber: 2.9 Consensus size: 32
5522607 TTTTCGCTTG
* *
5522617 TTTATTTATTCA-TTATTCCTTTTATTTTATTCAT
1 TTTATTTATTCATTTATT-CATTTA--TTATTTAT
5522651 TTTATTTATTCATTTATTCATTTACTTATTTAT
1 TTTATTTATTCATTTATTCATTTA-TTATTTAT
5522684 GTATTATTTATTCATTTA-TCTATTTATTATTT
1 -T-TTATTTATTCATTTATTC-ATTTATTATTT
5522716 TAATCCTTCT
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
33 7 0.12
34 26 0.45
35 25 0.43
ACGTcount: A:0.23, C:0.09, G:0.01, T:0.67
Consensus pattern (32 bp):
TTTATTTATTCATTTATTCATTTATTATTTAT
Found at i:5522714 original size:19 final size:19
Alignment explanation
Indices: 5522652--5522707 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
5522642 TTTATTCATT
5522652 TTATTTATTCATTTA--T-
1 TTATTTATTCATTTATCTA
* *
5522668 TCATTTACTT-ATTTATGTA
1 TTATTTA-TTCATTTATCTA
5522687 TTATTTATTCATTTATCTA
1 TTATTTATTCATTTATCTA
5522706 TT
1 TT
5522708 TATTATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 11 0.34
17 2 0.06
18 3 0.09
19 16 0.50
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATTTATTCATTTATCTA
Found at i:5524469 original size:21 final size:21
Alignment explanation
Indices: 5524430--5524470 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5524420 TTATATATTC
* *
5524430 TTTAGAATTTTTTTTAAAATT
1 TTTAGAATTTTTGTAAAAATT
*
5524451 TTTATAATTTTTGTAAAAAT
1 TTTAGAATTTTTGTAAAAAT
5524471 ATATAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTAGAATTTTTGTAAAAATT
Found at i:5524513 original size:19 final size:20
Alignment explanation
Indices: 5524477--5524528 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
5524467 AAATATATAA
5524477 ATTTGAAATTTTTAAAAATT
1 ATTTGAAATTTTTAAAAATT
5524497 ATTTGAAATTTTT-AAAATT
1 ATTTGAAATTTTTAAAAATT
5524516 ATTTTG-AATTTTT
1 A-TTTGAAATTTTT
5524529 TTTTGTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (20 bp):
ATTTGAAATTTTTAAAAATT
Found at i:5524529 original size:20 final size:20
Alignment explanation
Indices: 5524439--5524529 Score: 71
Period size: 19 Copynumber: 4.3 Consensus size: 20
5524429 CTTTAGAATT
5524439 TTTTTTAAAATT-TTTAT-AA
1 TTTTTTAAAATTATTT-TGAA
5524458 TTTTTGTAAAAATATATAAATTTGAAA
1 TTTTT-T-AAAAT-TAT---TTTG-AA
*
5524485 TTTTTAAAAATTA-TTTGAA
1 TTTTTTAAAATTATTTTGAA
*
5524504 ATTTTTAAAATTATTTTGAA
1 TTTTTTAAAATTATTTTGAA
5524524 TTTTTT
1 TTTTTT
5524530 TTTGTAATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
19 18 0.31
20 16 0.28
21 5 0.09
22 1 0.02
23 1 0.02
24 2 0.03
25 6 0.10
26 2 0.03
27 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTTTAAAATTATTTTGAA
Found at i:5536203 original size:114 final size:114
Alignment explanation
Indices: 5536047--5536812 Score: 1255
Period size: 114 Copynumber: 6.7 Consensus size: 114
5536037 TATTTGCAAG
* * * *
5536047 CGCCACAAAATATCTTAACCAAAACGCAACGTTAGGTCTTGAGGTATATTAGAATTAGTGACGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* *
5536112 TATGCAAAAATGCCGCTAAAGCACAGTATTAGCGGCGCATTGTAAAAAA
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
5536161 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* *
5536226 TATGCAAAAACGCCGCTAAAGCACATTATTAGCGGCGCATTGTAAAAAAA
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTAT-AAAAAA
*
5536276 TGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * **
5536341 TATGCAAAAACGCCACTAAAGTACAGTATTAGCGGCGCATTATAAAAGG
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
5536390 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* *
5536455 TATGGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTGTAAAAAA
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
*
5536504 CGCCGCAAAATATCTTAACCAAAATGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * *
5536569 TATGCAAAAACGCTGCTAAAGCACAGTATTAGTGGCGCATTATAAAAAG
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
** * * *
5536618 CGCCATAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTAAGGTATATTAGGAGTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* *
5536683 TATGGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATACAAAA
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
* *
5536732 CGCCGCAAAATATCTTAACCAAAATGCAGCGTTTGGTCTTGAGGTGTATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
5536797 TATG-AAAAAGCGCCGC
66 TATGCAAAAA-CGCCGC
5536813 AAAATATCTT
Statistics
Matches: 606, Mismatches: 44, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
113 5 0.01
114 492 0.81
115 109 0.18
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (114 bp):
CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
Found at i:5536837 original size:75 final size:75
Alignment explanation
Indices: 5536710--5536849 Score: 221
Period size: 75 Copynumber: 1.9 Consensus size: 75
5536700 AAAGCACAGT
**
5536710 ATTAGCGGCGCATTATACAAAACGCCGCAAAATATCTTAACCAAAATGCAGCGTTTGGTCTTGAG
1 ATTAGCGGCGCATTATACAAAACGCCGCAAAATATCTTAACCAAAACACAGCGTTTGGTCTTGAG
5536775 GTGTATTAGA
66 GTGTATTAGA
*
5536785 ATTAGTGGCGC-TTATGA-AAAAGCGCCGCAAAATATCTTAACCAAAACACAGCGTTTGGTCTTG
1 ATTAGCGGCGCATTAT-ACAAAA-CGCCGCAAAATATCTTAACCAAAACACAGCGTTTGGTCTTG
5536848 AG
64 AG
5536850 TTATAGAGCC
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
74 8 0.13
75 52 0.87
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (75 bp):
ATTAGCGGCGCATTATACAAAACGCCGCAAAATATCTTAACCAAAACACAGCGTTTGGTCTTGAG
GTGTATTAGA
Found at i:5537381 original size:14 final size:13
Alignment explanation
Indices: 5537355--5537417 Score: 63
Period size: 14 Copynumber: 4.5 Consensus size: 13
5537345 TTATGATGTA
*
5537355 GGTTTAGTGTTTGA
1 GGTTTAG-GTTTGG
5537369 GGTTTAGGATTTGG
1 GGTTTAGG-TTTGG
*
5537383 GAGTTTGGGGTTTGG
1 G-GTTT-AGGTTTGG
5537398 GGTTTAAGGTTTGG
1 GGTTT-AGGTTTGG
5537412 GGTTTA
1 GGTTTA
5537418 TGCTGCTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
13 2 0.05
14 28 0.67
15 10 0.24
16 2 0.05
ACGTcount: A:0.13, C:0.00, G:0.43, T:0.44
Consensus pattern (13 bp):
GGTTTAGGTTTGG
Found at i:5537391 original size:8 final size:7
Alignment explanation
Indices: 5537363--5537416 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
5537353 TAGGTTTAGT
*
5537363 GTTTGAG
1 GTTTGGG
*
5537370 GTTTAGG
1 GTTTGGG
*
5537377 ATTTGGG
1 GTTTGGG
5537384 AGTTTGGG
1 -GTTTGGG
5537392 GTTTGGG
1 GTTTGGG
**
5537399 GTTTAAG
1 GTTTGGG
5537406 GTTTGGG
1 GTTTGGG
5537413 GTTT
1 GTTT
5537417 ATGCTGCTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 31 0.84
8 6 0.16
ACGTcount: A:0.11, C:0.00, G:0.44, T:0.44
Consensus pattern (7 bp):
GTTTGGG
Found at i:5539441 original size:16 final size:16
Alignment explanation
Indices: 5539420--5539477 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 16
5539410 ATGTTAAGCT
5539420 ATGTTAAACATTTTGA
1 ATGTTAAACATTTTGA
*
5539436 ATGTTAAGCATAGTTTTGA
1 ATGTTAA--ACA-TTTTGA
*
5539455 ATGTTAAACATTGTGA
1 ATGTTAAACATTTTGA
5539471 ATGTTAA
1 ATGTTAA
5539478 GCATATGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 19 0.53
17 2 0.06
18 2 0.06
19 13 0.36
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.41
Consensus pattern (16 bp):
ATGTTAAACATTTTGA
Found at i:5539454 original size:19 final size:18
Alignment explanation
Indices: 5539429--5539483 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
5539419 TATGTTAAAC
5539429 ATTTTGAATGTTAAGCAT
1 ATTTTGAATGTTAAGCAT
*
5539447 AGTTTTGAATGTTAA--AC
1 A-TTTTGAATGTTAAGCAT
*
5539464 ATTGTGAATGTTAAGCAT
1 ATTTTGAATGTTAAGCAT
5539482 AT
1 AT
5539484 GAGATTCTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 12 0.39
17 2 0.06
18 4 0.13
19 13 0.42
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (18 bp):
ATTTTGAATGTTAAGCAT
Found at i:5539892 original size:21 final size:21
Alignment explanation
Indices: 5539868--5539940 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 21
5539858 GTTTTGGGAC
5539868 TATTTATTTATATTTTTAGCG
1 TATTTATTTATATTTTTAGCG
* *
5539889 TATTTAATATTATTGATATTATA--T
1 TATTT-AT-TTA-T-AT-TTTTAGCG
5539913 TATTTATTTATATTTTTAGCG
1 TATTTATTTATATTTTTAGCG
5539934 TATTTAT
1 TATTTAT
5539941 ATAAACATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 13 0.32
22 5 0.12
23 5 0.12
24 6 0.15
25 2 0.05
26 4 0.10
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.62
Consensus pattern (21 bp):
TATTTATTTATATTTTTAGCG
Found at i:5540647 original size:9 final size:9
Alignment explanation
Indices: 5540633--5541063 Score: 159
Period size: 9 Copynumber: 50.4 Consensus size: 9
5540623 ACTATCACAT
5540633 CTTACATAA
1 CTTACATAA
*
5540642 CTTACATAG
1 CTTACATAA
*
5540651 CTTA-ATTA
1 CTTACATAA
*
5540659 --TACTTAA
1 CTTACATAA
5540666 CTTACATAA
1 CTTACATAA
*
5540675 CTTACATTA
1 CTTACATAA
*
5540684 --TACACAA
1 CTTACATAA
5540691 CTTACATAA
1 CTTACATAA
*
5540700 CTTTCATTATACA
1 C-TT-A-CATA-A
*
5540713 CATACATAA
1 CTTACATAA
5540722 CTTACATATA
1 CTTACATA-A
* *
5540732 -ATACACAA
1 CTTACATAA
*
5540740 CATACATAA
1 CTTACATAA
5540749 CTTACATAA
1 CTTACATAA
* *
5540758 TTTTCAT-A
1 CTTACATAA
*
5540766 -GTACATAA
1 CTTACATAA
5540774 CTTACATAA
1 CTTACATAA
*
5540783 --TA-TTAAA
1 CTTACAT-AA
5540790 CTTACATAA
1 CTTACATAA
* *
5540799 TTTTCATAA
1 CTTACATAA
5540808 --TACATAA
1 CTTACATAA
*
5540815 CTTACTTAA
1 CTTACATAA
* *
5540824 TTTTCATAA
1 CTTACATAA
* *
5540833 --AAAATAA
1 CTTACATAA
5540840 CTTACATAA
1 CTTACATAA
5540849 CTTACATAA
1 CTTACATAA
* *
5540858 TTTTCATAA
1 CTTACATAA
*
5540867 CCTACATAA
1 CTTACATAA
* *
5540876 CTTATACAA
1 CTTACATAA
*
5540885 --TACACAA
1 CTTACATAA
5540892 CTTACATAA
1 CTTACATAA
* *
5540901 TTTTCATAA
1 CTTACATAA
5540910 --TACATAA
1 CTTACATAA
5540917 CTTACATAA
1 CTTACATAA
*
5540926 --TA-TTGAA
1 CTTACAT-AA
5540933 CTTACATAA
1 CTTACATAA
* * *
5540942 TTTTCGTAA
1 CTTACATAA
5540951 --TACATAA
1 CTTACATAA
*
5540958 CTTATATAA
1 CTTACATAA
*
5540967 --TA-TTGAA
1 CTTACAT-AA
5540974 CTTACATAA
1 CTTACATAA
* * *
5540983 TTTTCACAA
1 CTTACATAA
5540992 --TACATAA
1 CTTACATAA
* *
5540999 GTTACTTAA
1 CTTACATAA
* *
5541008 TTTTCATAA
1 CTTACATAA
* *
5541017 --TAAAAAA
1 CTTACATAA
5541024 CTTACATAA
1 CTTACATAA
5541033 CTTACATAA
1 CTTACATAA
* *
5541042 TTTTCATAA
1 CTTACATAA
5541051 CTTACATAA
1 CTTACATAA
5541060 CTTA
1 CTTA
5541064 TACAGTACAC
Statistics
Matches: 305, Mismatches: 78, Indels: 78
0.66 0.17 0.17
Matches are distributed among these distances:
6 5 0.02
7 59 0.19
8 5 0.02
9 219 0.72
10 9 0.03
11 2 0.01
12 4 0.01
13 2 0.01
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.37
Consensus pattern (9 bp):
CTTACATAA
Found at i:5540692 original size:25 final size:25
Alignment explanation
Indices: 5540635--5540925 Score: 227
Period size: 25 Copynumber: 11.6 Consensus size: 25
5540625 TATCACATCT
* *
5540635 TACATAACTTACATAGCTTA-ATTA
1 TACATAACTTACATAACTTACATAA
* *
5540659 TACTTAACTTACATAACTTACATTA
1 TACATAACTTACATAACTTACATAA
* * *
5540684 TACACAACTTACATAACTTTCATTA
1 TACATAACTTACATAACTTACATAA
*
5540709 TAC---ACATACATAACTTACATATAA
1 TACATAACTTACATAACTTAC--ATAA
* *
5540733 TACACAACATACATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
5540758 TTTTCAT-A-GTACATAACTTACATAA
1 --TACATAACTTACATAACTTACATAA
* * *
5540783 TA-TTAAACTTACATAATTTTCATAA
1 TACAT-AACTTACATAACTTACATAA
* * *
5540808 TACATAACTTACTTAATTTTCATAA
1 TACATAACTTACATAACTTACATAA
* *
5540833 AAAATAACTTACATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* * * *
5540858 TTTTCATAACCTACATAACTTATACAA
1 --TACATAACTTACATAACTTACATAA
* * *
5540885 TACACAACTTACATAATTTTCATAA
1 TACATAACTTACATAACTTACATAA
5540910 TACATAACTTACATAA
1 TACATAACTTACATAA
5540926 TATTGAACTT
Statistics
Matches: 216, Mismatches: 37, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
22 14 0.06
23 1 0.00
24 25 0.12
25 137 0.63
26 2 0.01
27 37 0.17
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.36
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:5540782 original size:34 final size:34
Alignment explanation
Indices: 5540729--5541098 Score: 202
Period size: 34 Copynumber: 10.3 Consensus size: 34
5540719 TAACTTACAT
* *
5540729 ATAATACACAACATACATAACTTACATAATTTTC
1 ATAATACATAACTTACATAACTTACATAATTTTC
* * * *
5540763 ATAGTACATAACTTACATAA--TA-TTAAACTTAC
1 ATAATACATAACTTACATAACTTACAT-AATTTTC
* *
5540795 ATAATTTTCATAA--TACATAACTTACTTAATTTTC
1 ATAA--TACATAACTTACATAACTTACATAATTTTC
* *
5540829 ATAAAAAATAACTTACATAACTTACATAATTTTC
1 ATAATACATAACTTACATAACTTACATAATTTTC
5540863 ATAACCTACATAACTTATACAATACACAACTTACATAATTTTC
1 ATAA--TACATAAC-T-TAC-AT----AACTTACATAATTTTC
5540906 ATAATACATAACTTACATAATATTGAACTTACATAATTTTC
1 ATAATACATAACTTAC-----A-T-AACTTACATAATTTTC
* * * * *
5540947 GTAATACATAACTTATATAA--TA-TTGAACTTAC
1 ATAATACATAACTTACATAACTTACAT-AATTTTC
* * * *
5540979 ATAATTTTCACAA--TACATAAGTTACTTAATTTTC
1 ATAA--TACATAACTTACATAACTTACATAATTTTC
* *
5541013 ATAATAAAAAACTTACATAACTTACATAATTTTC
1 ATAATACATAACTTACATAACTTACATAATTTTC
5541047 ATAACTTACATAACTTATACAGTACACAGCTTACATAATTTTC
1 ATAA--TACATAAC-T-TACA-T--A-A-CTTACATAATTTTC
5541090 ATAATACAT
1 ATAATACAT
5541099 GTAATAAGCC
Statistics
Matches: 261, Mismatches: 36, Indels: 71
0.71 0.10 0.19
Matches are distributed among these distances:
31 2 0.01
32 41 0.16
34 99 0.38
35 5 0.02
36 13 0.05
37 2 0.01
38 7 0.03
39 6 0.02
40 1 0.00
41 44 0.17
42 1 0.00
43 39 0.15
44 1 0.00
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (34 bp):
ATAATACATAACTTACATAACTTACATAATTTTC
Found at i:5540848 original size:41 final size:41
Alignment explanation
Indices: 5540741--5541098 Score: 168
Period size: 41 Copynumber: 8.8 Consensus size: 41
5540731 AATACACAAC
*
5540741 ATACATAACTTACATAATTTTCATAGTACATAACTTACATA
1 ATACATAACTTACATAATTTTCATAATACATAACTTACATA
* *
5540782 ATA-TTAAACTTACATAATTTTCATAATACATAACTTACTTA
1 ATACAT-AACTTACATAATTTTCATAATACATAACTTACATA
* * * * * * *
5540823 ATTTTCATAA--AAAATAACTTACATAACTTACATAATTTTCATA
1 A--TACATAACTTACATAATTTTCATAA--TACATAACTTACATA
* * * * * *
5540866 ACCTACATAACTTATACAA--TACACAACTTACATAATTTTCATA
1 A--TACATAACTTACATAATTTTCATAA--TACATAACTTACATA
* * * * * *
5540909 ATACATAACTTACATAATATTGA-ACTTACATAATTTTCGTA
1 ATACATAACTTACATAATTTTCATA-ATACATAACTTACATA
* * * * * * *
5540950 ATACATAACTTATATAATATTGA-ACTTACATAATTTTCACA
1 ATACATAACTTACATAATTTTCATA-ATACATAACTTACATA
* * *
5540991 ATACATAAGTTACTTAATTTTCATAATA-A-AA--AAC-T-
1 ATACATAACTTACATAATTTTCATAATACATAACTTACATA
* *
5541026 -TACATAACTTACATAATTTTCATAACTTACATAACTTATACA
1 ATACATAACTTACATAATTTTCATAA--TACATAACTTACATA
* * *
5541068 GTACACAGCTTACATAATTTTCATAATACAT
1 ATACATAACTTACATAATTTTCATAATACAT
5541099 GTAATAAGCC
Statistics
Matches: 252, Mismatches: 44, Indels: 42
0.75 0.13 0.12
Matches are distributed among these distances:
34 23 0.09
36 2 0.01
37 2 0.01
38 2 0.01
39 2 0.01
40 3 0.01
41 140 0.56
42 2 0.01
43 71 0.28
44 1 0.00
45 4 0.02
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (41 bp):
ATACATAACTTACATAATTTTCATAATACATAACTTACATA
Found at i:5540913 original size:16 final size:16
Alignment explanation
Indices: 5540668--5540942 Score: 101
Period size: 16 Copynumber: 17.1 Consensus size: 16
5540658 ATACTTAACT
*
5540668 TACATAACTTACATTA
1 TACATAACTTACATAA
*
5540684 TACACAACTTACATAA
1 TACATAACTTACATAA
* * *
5540700 CTTTCATTA--TACA-CA
1 --TACATAACTTACATAA
5540715 TACATAACTTACATATAA
1 TACATAACTTAC--ATAA
* *
5540733 TACACAACATACATAA
1 TACATAACTTACATAA
* * *
5540749 CTTACATAATTTTCATAG
1 --TACATAACTTACATAA
5540767 TACATAACTTACATAA
1 TACATAACTTACATAA
*
5540783 TA-TTAAACTTACATAA
1 TACAT-AACTTACATAA
*
5540799 TTTTCATAA--TACATAA
1 --TACATAACTTACATAA
* * *
5540815 CTTACTTAATTTTCATAA
1 --TACATAACTTACATAA
* *
5540833 AAAATAACTTACATAA
1 TACATAACTTACATAA
* *
5540849 CTTACATAATTTTCATAA
1 --TACATAACTTACATAA
* *
5540867 CCTACATAACTTATACAA
1 --TACATAACTTACATAA
*
5540885 TACACAACTTACATAA
1 TACATAACTTACATAA
5540901 T---T---TT-CATAA
1 TACATAACTTACATAA
5540910 TACATAACTTACATAA
1 TACATAACTTACATAA
*
5540926 TA-TTGAACTTACATAA
1 TACAT-AACTTACATAA
5540942 T
1 T
5540943 TTTCGTAATA
Statistics
Matches: 189, Mismatches: 45, Indels: 50
0.67 0.16 0.18
Matches are distributed among these distances:
9 6 0.03
10 2 0.01
12 1 0.01
13 5 0.03
15 8 0.04
16 105 0.56
17 1 0.01
18 60 0.32
19 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.36
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:5541003 original size:25 final size:25
Alignment explanation
Indices: 5540972--5541098 Score: 105
Period size: 25 Copynumber: 5.0 Consensus size: 25
5540962 TATAATATTG
*
5540972 AACTTACATAATTTTCACAATACAT
1 AACTTACATAATTTTCATAATACAT
* * * *
5540997 AAGTTACTTAATTTTCATAATAAAA
1 AACTTACATAATTTTCATAATACAT
* * *
5541022 AACTTACATAACTTACATAATTTTCAT
1 AACTTACATAATTTTCATAA--TACAT
* *
5541049 AACTTACATAA-CTT-ATACAGTACAC
1 AACTTACATAATTTTCATA-A-TACAT
*
5541074 AGCTTACATAATTTTCATAATACAT
1 AACTTACATAATTTTCATAATACAT
5541099 GTAATAAGCC
Statistics
Matches: 77, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
25 56 0.73
26 5 0.06
27 16 0.21
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.37
Consensus pattern (25 bp):
AACTTACATAATTTTCATAATACAT
Found at i:5541059 original size:184 final size:184
Alignment explanation
Indices: 5540747--5541098 Score: 607
Period size: 184 Copynumber: 1.9 Consensus size: 184
5540737 CAACATACAT
* *
5540747 AACTTACATAATTTTCATAGTACATAACTTACATAATATTAAACTTACATAATTTTCATAATACA
1 AACTTACATAATTTTCATAATACATAACTTACATAATATTAAACTTACATAATTTTCACAATACA
5540812 TAACTTACTTAATTTTCATAAAAAATAACTTACATAACTTACATAATTTTCATAACCTACATAAC
66 TAACTTACTTAATTTTCATAAAAAATAACTTACATAACTTACATAATTTTCATAACCTACATAAC
5540877 TTATACAATACACAACTTACATAATTTTCATAATACATAACTTACATAATATTG
131 TTATACAATACACAACTTACATAATTTTCATAATACATAACTTACATAATATTG
* * *
5540931 AACTTACATAATTTTCGTAATACATAACTTATATAATATTGAACTTACATAATTTTCACAATACA
1 AACTTACATAATTTTCATAATACATAACTTACATAATATTAAACTTACATAATTTTCACAATACA
* *
5540996 TAAGTTACTTAATTTTCATAATAAAA-AACTTACATAACTTACATAATTTTCATAACTTACATAA
66 TAACTTACTTAATTTTCATAA-AAAATAACTTACATAACTTACATAATTTTCATAACCTACATAA
* *
5541060 CTTATACAGTACACAGCTTACATAATTTTCATAATACAT
130 CTTATACAATACACAACTTACATAATTTTCATAATACAT
5541099 GTAATAAGCC
Statistics
Matches: 158, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
184 154 0.97
185 4 0.03
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (184 bp):
AACTTACATAATTTTCATAATACATAACTTACATAATATTAAACTTACATAATTTTCACAATACA
TAACTTACTTAATTTTCATAAAAAATAACTTACATAACTTACATAATTTTCATAACCTACATAAC
TTATACAATACACAACTTACATAATTTTCATAATACATAACTTACATAATATTG
Found at i:5542586 original size:26 final size:26
Alignment explanation
Indices: 5542550--5542610 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
5542540 TTCAACAATA
5542550 TTTATATATATATACCTAATCCTATT
1 TTTATATATATATACCTAATCCTATT
5542576 TTTATATATATATACCTAATCCTATT
1 TTTATATATATATACCTAATCCTATT
*
5542602 TTCATATAT
1 TTTATATAT
5542611 CATAGATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTATATATATATACCTAATCCTATT
Found at i:5549126 original size:14 final size:15
Alignment explanation
Indices: 5549095--5549127 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5549085 TTTTAGGGTC
5549095 GAAAATGACTTTTCA
1 GAAAATGACTTTTCA
*
5549110 GAAAATGA-TTTTTA
1 GAAAATGACTTTTCA
5549124 GAAA
1 GAAA
5549128 TAAATTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (15 bp):
GAAAATGACTTTTCA
Found at i:5549699 original size:13 final size:14
Alignment explanation
Indices: 5549666--5549709 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
5549656 ATATGTGAAG
5549666 AATATTATTTTT-A
1 AATATTATTTTTAA
*
5549679 ATTATTATTTTTAA
1 AATATTATTTTTAA
*
5549693 AAT-TTATTATTAA
1 AATATTATTTTTAA
5549706 AATA
1 AATA
5549710 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 23 0.88
14 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATATTATTTTTAA
Found at i:5549737 original size:20 final size:20
Alignment explanation
Indices: 5549712--5549772 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
5549702 TTAAAATAAA
5549712 ATTAAAATATTAAATAATTT
1 ATTAAAATATTAAATAATTT
* *
5549732 ATTAAAATAATAAAT--TAT
1 ATTAAAATATTAAATAATTT
*
5549750 ATTAATATATT-AATAATTT
1 ATTAAAATATTAAATAATTT
5549769 ATTA
1 ATTA
5549773 TATGACTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 3 0.09
18 11 0.32
19 6 0.18
20 14 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTAAAATATTAAATAATTT
Found at i:5549744 original size:34 final size:36
Alignment explanation
Indices: 5549693--5549774 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 36
5549683 TTATTTTTAA
*
5549693 AATTTATTATTAAAATAAAATTA-A-AATAT-TAAAT
1 AATTTATTATAAAAAT-AAATTATATAATATATAAAT
*
5549727 AATTTATTA-AAATAATAAATTATATTAATATATTAAT
1 AATTTATTATAAA-AATAAATTATA-TAATATATAAAT
5549764 AATTTATTATA
1 AATTTATTATA
5549775 TGACTAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
33 8 0.20
34 13 0.32
36 5 0.12
37 13 0.32
38 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
AATTTATTATAAAAATAAATTATATAATATATAAAT
Found at i:5553095 original size:17 final size:16
Alignment explanation
Indices: 5553051--5553098 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
5553041 TATGATGTGA
* *
5553051 GATTATTATGTGCATT
1 GATTATTATTTGTATT
5553067 GTATTAATTATTTGTATT
1 G-ATT-ATTATTTGTATT
5553085 GATTGATTATTTGT
1 GATT-ATTATTTGT
5553099 GTTCATTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 1 0.04
17 15 0.56
18 11 0.41
ACGTcount: A:0.25, C:0.02, G:0.17, T:0.56
Consensus pattern (16 bp):
GATTATTATTTGTATT
Found at i:5555416 original size:33 final size:35
Alignment explanation
Indices: 5555379--5555475 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
5555369 ACAGTTATAT
5555379 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
5555412 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
5555447 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAATATA-ATTT-ATATATT
5555476 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 8 0.16
35 11 0.22
36 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:5567728 original size:15 final size:17
Alignment explanation
Indices: 5567694--5567728 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5567684 AAAAATTCTC
5567694 AAAATAATTTTAAGTAAA
1 AAAATAATTTTAAG-AAA
5567712 AAAAT-ATTTTAAGAAA
1 AAAATAATTTTAAGAAA
5567728 A
1 A
5567729 CAAACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
AAAATAATTTTAAGAAA
Found at i:5571391 original size:17 final size:18
Alignment explanation
Indices: 5571371--5571405 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5571361 CAATTTGATC
5571371 TTAAATT-TAATTTTTTT
1 TTAAATTCTAATTTTTTT
*
5571388 TTAATTTCTAATTTTTTT
1 TTAAATTCTAATTTTTTT
5571406 AAAAAATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTAAATTCTAATTTTTTT
Found at i:5575454 original size:3 final size:3
Alignment explanation
Indices: 5575446--5575486 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5575436 ATTGTACAGT
5575446 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5575487 TTTATAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5583653 original size:18 final size:18
Alignment explanation
Indices: 5583630--5583674 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
5583620 GCCAATATGT
* * *
5583630 GGCCCAATACCATTCTTC
1 GGCCCAATACCACTATTA
*
5583648 GGCCCAACACCACTATTA
1 GGCCCAATACCACTATTA
5583666 GGCCCAATA
1 GGCCCAATA
5583675 GTACCATCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.38, G:0.13, T:0.20
Consensus pattern (18 bp):
GGCCCAATACCACTATTA
Found at i:5583914 original size:21 final size:21
Alignment explanation
Indices: 5583865--5583924 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
5583855 TTTTGACCAG
* *
5583865 CAAAATAATTCTGACCACTTC
1 CAAAATAATTTTGACCATTTC
** *
5583886 CATTATAATTTTGACCATTTT
1 CAAAATAATTTTGACCATTTC
5583907 CAAAATAATTTTGACCAT
1 CAAAATAATTTTGACCAT
5583925 GGTTAGAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (21 bp):
CAAAATAATTTTGACCATTTC
Found at i:5589162 original size:21 final size:22
Alignment explanation
Indices: 5589131--5589172 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
5589121 AATGATATTT
5589131 AAATTTAGAAAAAATTTAAATA
1 AAATTTAGAAAAAATTTAAATA
*
5589153 AAATTT-GAAAAATTTTAAAT
1 AAATTTAGAAAAAATTTAAAT
5589173 GACCCTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
AAATTTAGAAAAAATTTAAATA
Found at i:5589341 original size:5 final size:5
Alignment explanation
Indices: 5589331--5589450 Score: 66
Period size: 5 Copynumber: 22.4 Consensus size: 5
5589321 TGAAAAAATT
* * *
5589331 AATGA AATGA AATGTTA AATGA ATATGA AATGA AATGTA ATTTGT AATAA
1 AATGA AATGA AATG--A AATGA A-ATGA AATGA AATG-A A-ATGA AATGA
*
5589381 ACATGAA AAT-A AACGA AATGTTA AATGA ATATGA AATGA AATGA AATG-
1 A-ATG-A AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA AATGA
* *
5589429 -ATGA TTATGA AATGG AATGA AA
1 AATGA -AATGA AATGA AATGA AA
5589451 GTTTAAATGA
Statistics
Matches: 90, Mismatches: 11, Indels: 28
0.70 0.09 0.22
Matches are distributed among these distances:
3 3 0.03
4 3 0.03
5 49 0.54
6 21 0.23
7 14 0.16
ACGTcount: A:0.53, C:0.02, G:0.17, T:0.28
Consensus pattern (5 bp):
AATGA
Found at i:5589350 original size:12 final size:11
Alignment explanation
Indices: 5589331--5589429 Score: 57
Period size: 11 Copynumber: 9.0 Consensus size: 11
5589321 TGAAAAAATT
5589331 AATG-AAATGA
1 AATGTAAATGA
5589341 AATGTTAAATGA
1 AATG-TAAATGA
5589353 ATATG-AAATGA
1 A-ATGTAAATGA
* *
5589364 AATGTAATTTGT
1 AATGTAA-ATGA
*
5589376 AAT-AAACATGA
1 AATGTAA-ATGA
* *
5589387 AA-ATAAACGA
1 AATGTAAATGA
5589397 AATGTTAAATGA
1 AATG-TAAATGA
5589409 ATATG-AAATGA
1 A-ATGTAAATGA
5589420 AATG-AAATGA
1 AATGTAAATGA
5589430 TGATTATGAA
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
10 21 0.30
11 24 0.34
12 19 0.27
13 6 0.09
ACGTcount: A:0.55, C:0.02, G:0.16, T:0.27
Consensus pattern (11 bp):
AATGTAAATGA
Found at i:5589363 original size:28 final size:28
Alignment explanation
Indices: 5589331--5589461 Score: 123
Period size: 28 Copynumber: 4.8 Consensus size: 28
5589321 TGAAAAAATT
5589331 AATGAAATGAAATGTTAAATGAATATGA
1 AATGAAATGAAATGTTAAATGAATATGA
* * * *
5589359 AATGAAATGTAAT-TTGTAATAAACATGAA
1 AATGAAATGAAATGTT-AAATGAATATG-A
*
5589388 AAT-AAACGAAATGTTAAATGAATATGA
1 AATGAAATGAAATGTTAAATGAATATGA
*
5589415 AATGAAATGAAATG----ATGATTATGA
1 AATGAAATGAAATGTTAAATGAATATGA
*
5589439 AATGGAATGAAA-GTTTAAATGAA
1 AATGAAATGAAATG-TTAAATGAA
5589462 AATAAATTAT
Statistics
Matches: 81, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
23 1 0.01
24 20 0.25
27 6 0.07
28 48 0.59
29 6 0.07
ACGTcount: A:0.53, C:0.02, G:0.18, T:0.28
Consensus pattern (28 bp):
AATGAAATGAAATGTTAAATGAATATGA
Found at i:5589437 original size:24 final size:24
Alignment explanation
Indices: 5589405--5589450 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5589395 GAAATGTTAA
5589405 ATGAATATGAAATGAAATGAAATG
1 ATGAATATGAAATGAAATGAAATG
* *
5589429 ATGATTATGAAATGGAATGAAA
1 ATGAATATGAAATGAAATGAAA
5589451 GTTTAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (24 bp):
ATGAATATGAAATGAAATGAAATG
Found at i:5589524 original size:20 final size:21
Alignment explanation
Indices: 5589490--5589541 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
5589480 ATGAAAACAA
* * *
5589490 AAATTGAAATGAGAAATAATT
1 AAATTTAAATGAGAAAAAAGT
5589511 AAATTTAAAT-AGAAAAAAGT
1 AAATTTAAATGAGAAAAAAGT
5589531 -AATTTAAATGA
1 AAATTTAAATGA
5589542 ATGGAAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.33
20 9 0.33
21 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (21 bp):
AAATTTAAATGAGAAAAAAGT
Found at i:5589540 original size:40 final size:41
Alignment explanation
Indices: 5589452--5589542 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 41
5589442 GGAATGAAAG
5589452 TTTAAATGAAAATAAATTATAAATTCAAATGAAAACAAAAA
1 TTTAAATGAAAATAAATTATAAATTCAAATGAAAACAAAAA
* * *
5589493 TTGAAATGAGAAAT-AA-T-TAAATTTAAATAGAAAA-AAGTAA
1 TTTAAATGA-AAATAAATTATAAATTCAAAT-GAAAACAA-AAA
5589533 TTTAAATGAA
1 TTTAAATGAA
5589543 TGGAAATGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
39 13 0.30
40 16 0.37
41 10 0.23
42 4 0.09
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (41 bp):
TTTAAATGAAAATAAATTATAAATTCAAATGAAAACAAAAA
Found at i:5589556 original size:16 final size:16
Alignment explanation
Indices: 5589535--5589580 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
5589525 AAAAGTAATT
5589535 TAAATGAATGGAAATG
1 TAAATGAATGGAAATG
5589551 TAAATGAAAT-GAAATG
1 TAAATG-AATGGAAATG
* *
5589567 GAAATGAAAGGAAA
1 TAAATGAATGGAAA
5589581 AAAAAAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 2 0.08
16 21 0.81
17 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.20
Consensus pattern (16 bp):
TAAATGAATGGAAATG
Found at i:5589561 original size:11 final size:11
Alignment explanation
Indices: 5589536--5589580 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
5589526 AAAGTAATTT
5589536 AAATG-AATGG
1 AAATGAAATGG
5589546 AAATGTAAAT-G
1 AAATG-AAATGG
5589557 AAATGAAATGG
1 AAATGAAATGG
5589568 AAATGAAA-GG
1 AAATGAAATGG
5589578 AAA
1 AAA
5589581 AAAAAAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 14 0.44
11 15 0.47
12 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (11 bp):
AAATGAAATGG
Found at i:5596376 original size:21 final size:21
Alignment explanation
Indices: 5596352--5596398 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5596342 TATTTAGCAA
*
5596352 CTTTTTAATAATCACATTTTT
1 CTTTTTAACAATCACATTTTT
* * *
5596373 CTTTATGACAATCACTTTTTT
1 CTTTTTAACAATCACATTTTT
5596394 CTTTT
1 CTTTT
5596399 AAATTAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.02, T:0.57
Consensus pattern (21 bp):
CTTTTTAACAATCACATTTTT
Found at i:5597650 original size:17 final size:17
Alignment explanation
Indices: 5597628--5597661 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5597618 AAACTACTTT
5597628 TTTTAAAAAATTTTTAA
1 TTTTAAAAAATTTTTAA
*
5597645 TTTTAAAATATTTTTAA
1 TTTTAAAAAATTTTTAA
5597662 AATACATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAAAAATTTTTAA
Found at i:5602369 original size:3 final size:3
Alignment explanation
Indices: 5602361--5602398 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5602351 CAAAACCTGT
5602361 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5602399 TTCTGGGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5612897 original size:31 final size:31
Alignment explanation
Indices: 5612819--5612897 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
5612809 CCCAAAAAGT
* * *
5612819 TTTAAGTACCAACTTAAGAAAAAGTGTCAAG
1 TTTAGGTACCAAATTAGGAAAAAGTGTCAAG
*
5612850 TTTAGGTACCACATTAGGAAAACA-TGTCAAG
1 TTTAGGTACCAAATTAGGAAAA-AGTGTCAAG
*
5612881 TTTGGGTACCAAATTAG
1 TTTAGGTACCAAATTAG
5612898 ACCGAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (31 bp):
TTTAGGTACCAAATTAGGAAAAAGTGTCAAG
Found at i:5624596 original size:17 final size:19
Alignment explanation
Indices: 5624574--5624615 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
5624564 AACAGTTGTA
5624574 TTCTTTTA-TAAA-ATTAT
1 TTCTTTTACTAAATATTAT
5624591 TTCTTTTACTAAATATTAT
1 TTCTTTTACTAAATATTAT
*
5624610 ATCTTT
1 TTCTTT
5624616 ACATAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (19 bp):
TTCTTTTACTAAATATTAT
Found at i:5624616 original size:18 final size:18
Alignment explanation
Indices: 5624575--5624624 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
5624565 ACAGTTGTAT
*
5624575 TCTTTTA-TAAAATTATT
1 TCTTTTACTAAAATTATA
5624592 TCTTTTACTAAATATTATA
1 TCTTTTACTAAA-ATTATA
5624611 TC-TTTACATAAAAT
1 TCTTTTAC-TAAAAT
5624625 AATCATTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.24
18 11 0.38
19 11 0.38
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (18 bp):
TCTTTTACTAAAATTATA
Found at i:5625105 original size:30 final size:30
Alignment explanation
Indices: 5625071--5625146 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 30
5625061 AATATTTTTT
5625071 AAAAATATTAAAAT-TATTACATTTT-AAATA
1 AAAAATATTAAAATATA-TA-ATTTTAAAATA
* *
5625101 AAAAATAATAGAAATATATATTTTTAAAATA
1 AAAAATATTA-AAATATATAATTTTAAAATA
5625132 AAAGAATAATTAAAA
1 AAA-AAT-ATTAAAA
5625147 ACAATTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 13 0.34
31 14 0.37
32 8 0.21
33 3 0.08
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAAATATTAAAATATATAATTTTAAAATA
Found at i:5626326 original size:5 final size:5
Alignment explanation
Indices: 5626316--5626340 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5626306 ATTCATGATG
5626316 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
5626341 AGCTTAGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:5638628 original size:30 final size:30
Alignment explanation
Indices: 5638582--5638675 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
5638572 ATTTCTTATG
* *
5638582 CCAATATCTCGATACCTATATATTTGATTTT
1 CCAATAT-TTGATACCTATATATTTGACTTT
*
5638613 CCAATATTTGATACCTATATCTTTGACTTT
1 CCAATATTTGATACCTATATATTTGACTTT
*
5638643 CCATTATTTGATAACC-ATATATTTGACTTT
1 CCAATATTTGAT-ACCTATATATTTGACTTT
5638673 CCA
1 CCA
5638676 TAAATATGGA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
30 47 0.82
31 10 0.18
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (30 bp):
CCAATATTTGATACCTATATATTTGACTTT
Found at i:5638652 original size:15 final size:16
Alignment explanation
Indices: 5638599--5638677 Score: 69
Period size: 15 Copynumber: 5.2 Consensus size: 16
5638589 CTCGATACCT
*
5638599 ATATATTTGATTTTCC
1 ATATATTTGACTTTCC
*
5638615 A-ATATTTGA--TACC
1 ATATATTTGACTTTCC
*
5638628 TATATCTTTGACTTTCC
1 -ATATATTTGACTTTCC
**
5638645 AT-TATTTGA-TAACC
1 ATATATTTGACTTTCC
5638659 ATATATTTGACTTTCC
1 ATATATTTGACTTTCC
5638675 ATA
1 ATA
5638678 AATATGGATG
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
13 3 0.06
14 6 0.12
15 28 0.57
16 9 0.18
17 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.48
Consensus pattern (16 bp):
ATATATTTGACTTTCC
Found at i:5647793 original size:15 final size:15
Alignment explanation
Indices: 5647773--5647850 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
5647763 TTTATGGAAA
5647773 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
5647788 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
5647802 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
5647818 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
5647832 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
5647848 ATC
1 ATC
5647851 GAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:5647810 original size:30 final size:30
Alignment explanation
Indices: 5647769--5647850 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
5647759 CATATTTATG
*
5647769 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
5647799 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
5647829 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
5647851 GAGATATTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:5652451 original size:15 final size:15
Alignment explanation
Indices: 5652431--5652538 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
5652421 TTTATGGAAA
5652431 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
5652446 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
5652460 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
5652476 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
5652490 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
5652506 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
5652520 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
5652536 ATC
1 ATC
5652539 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:5652468 original size:30 final size:30
Alignment explanation
Indices: 5652425--5652548 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
5652415 TCCATATTTA
* *
5652425 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
5652455 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
5652485 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
5652515 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
5652546 TGG
1 TGG
5652549 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:5655360 original size:20 final size:19
Alignment explanation
Indices: 5655305--5655364 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
5655295 GCCCGAATTA
5655305 TATATTAAATATATATTTT
1 TATATTAAATATATATTTT
* * *
5655324 TATTTTTAATCAAATATACTTT
1 TA-TATTAA--ATATATATTTT
5655346 T-TATTAAATATATATTTT
1 TATATTAAATATATATTTT
5655364 T
1 T
5655365 TAGACTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
18 10 0.31
19 2 0.06
20 10 0.31
22 10 0.31
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTAAATATATATTTT
Found at i:5655362 original size:40 final size:37
Alignment explanation
Indices: 5655306--5655420 Score: 124
Period size: 40 Copynumber: 2.9 Consensus size: 37
5655296 CCCGAATTAT
*
5655306 ATATTAAATATATATTTTTATTTTTAATCAAATATACTTT
1 ATATTAAATATATATTTTTATTTTTAATCAAATATA---A
* * *
5655346 TTATTAAATATATATTTTTTAGACTTTTAATCTGAAT-TAA
1 ATATTAAATATATA-TTTTT--ATTTTTAATC-AAATATAA
5655386 ATATTAAATATATATTTTTATTTTTAATCAAATAT
1 ATATTAAATATATATTTTTATTTTTAATCAAATAT
5655421 GGGCCGGGCC
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
36 3 0.05
37 10 0.16
39 5 0.08
40 26 0.41
41 5 0.08
43 11 0.17
44 3 0.05
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (37 bp):
ATATTAAATATATATTTTTATTTTTAATCAAATATAA
Found at i:5656071 original size:18 final size:18
Alignment explanation
Indices: 5656015--5656071 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
5656005 TCGAATTATA
*
5656015 TATTAAATATACATTTATT
1 TATTAAATATATATTT-TT
*
5656034 T-TTAATCATATATACTTTT
1 TATTAA--ATATATATTTTT
5656053 TATTAAATATATATTTTT
1 TATTAAATATATATTTTT
5656071 T
1 T
5656072 GGACTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 16 0.50
19 4 0.12
20 12 0.38
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTAAATATATATTTTT
Found at i:5656349 original size:696 final size:694
Alignment explanation
Indices: 5654854--5656945 Score: 3287
Period size: 696 Copynumber: 3.0 Consensus size: 694
5654844 GACACTGTTG
*
5654854 TGGATTATATTTGTTTATGATGAATTAATGTTGCAAGAGAACTTTTGGTGGATATGTCTGAATAG
1 TGGATTATATTTGTTTATGATGAATTAATGTTGCAGGAGAACTTTTGGTGGATATGTCTGAATAG
*
5654919 GTGTAGGATTGATTTAATTAAATTCCAAACCAGCTGCATTGATATGGCACCCTCCTCCGCATGGA
66 GTGTAGGATTGATTTAATTAAATTCCAAACCAGCTGCATTGATATGACACCCTCCTCCGCATGGA
*
5654984 TGCTTAAAGTTCAATGTTTGTGGGATTGAAAACGAGGATAGAGCAGGCTGTGGAGGTGTCTTGAG
131 TGCTTAAAGTTCAATGTTTGTGGGATTGCAAACGAGGATAGAGCAGGCTGTGGAGGTGTCTTGAG
*
5655049 AGATAATGAGGGAGTCGCAAGAGCTTTATTTTTAGGTCCAGTAGCAGCAAATGATATTGATTTGG
196 AGATAAGGAGGGAGTCGCAAGAGCTTTATTTTTAGGTCCAGTAGCAGCAAATGATATTGATTTGG
* *
5655114 CAGAGATTGGCGCGGTGATGTTAGAGGTGATCATGAGTTGGGCTA----CCCGGCC--C-G--C-
261 CAGAGATTGGCGCGGTGATGGTAGAGGTGATCATGGGTTGGGCTACCGGCCCGGCCGACGGCCCG
* * * *
5655169 CCAAAAAATGGGAGGGTTCAAGTAAAAATATAGGCTCGAAATATGGGTTTGGGAAAAAATGAGGC
326 CCAAAAAATAGGAGGGTTCGAGTAAAAATATAGGCCCGAAATATGGGTTTGGGAAAAAAAGAGGC
* *
5655234 CCGTTTAGAAAACAAGCTAGGCCTCGGGTAAGACTTTTTTGGCCTGAGCTGGGCCGTGCCGGCCC
391 CCGTTTAGAAAACAAGCTGGGCCTCGGGTAAGACTTTTTTGGCCTGAGCCGGGCCGTGCCGGCCC
*
5655299 GAATTATATATTAAATATATATTTTTATTTTTAATCAAATATACTTTTTATTAAATATATATTTT
456 GAATTATATATTAAATATA-AATTTTATTTTTAATCAAATATACTTTTTATTAAATATATATTTT
* *
5655364 TTAGACTTTTAATCTGAATTAAATATTAAATATATATTTTTATTTTTAATCAAATATGGGCCGGG
520 TTGGACTTTTAATCTGAATTATATATTAAATATATATTTTTATTTTTAATCAAATATGGGCCGGG
* *
5655429 CCGGGCCGGGTCGGGCTCGAGCTTAGCAATTTTCTTTTGGGCCGGGCTTGGACAAATTTTTAGGC
585 TCGGG-C---T----CTCG-GCTTAGCAATTTTCTTTCGGGCCGGG-TTGGACAAATTTTTAGGC
* * * *
5655494 CCATATTTCAGGTCAGGCCGGACTCAGACCTATAAAATGGGCCTAAAATTTCATC
640 CCATATTTCGGGTCAGGCCGGGCTCGGACCTATAAAACGGGCCTAAAATTTCATC
* *
5655549 TGGATTATATTTGTTTATGATGAATTAATGTTGTAGGAGAAATTTTGGTGGATATGTCTGAATAG
1 TGGATTATATTTGTTTATGATGAATTAATGTTGCAGGAGAACTTTTGGTGGATATGTCTGAATAG
* *
5655614 GTGTAGGATTGATTTAATTAAATTCCAAACTAGCTGCATTGGTATGACACCCTCCTCCGCATGGA
66 GTGTAGGATTGATTTAATTAAATTCCAAACCAGCTGCATTGATATGACACCCTCCTCCGCATGGA
*
5655679 TGCTTAAAGTTCAATGTTTGTGGGATTGCAAACGAGGATAGAGCAGGCTGTGGAGGTGTCTTGAA
131 TGCTTAAAGTTCAATGTTTGTGGGATTGCAAACGAGGATAGAGCAGGCTGTGGAGGTGTCTTGAG
5655744 AGATAAGGAGGGAGTCGCAAGAGCTTTATTTTTAGGTCCAGTAGCAGCAAATGATATTGATTTGG
196 AGATAAGGAGGGAGTCGCAAGAGCTTTATTTTTAGGTCCAGTAGCAGCAAATGATATTGATTTGG
* * *
5655809 TAGAGAGTGGCGCGGTGATGGTAGAGGTGATCATGGGTTAGGCTACCTGGCCCGGCCGACGGCCC
261 CAGAGATTGGCGCGGTGATGGTAGAGGTGATCATGGGTTGGGCTACC-GGCCCGGCCGACGGCCC
5655874 GCCTAAAAAATAGGAGGGTTCGAGTAAAAATATAGGCCCGAAATATGGGTTTGGGAAAAAAACGA
325 GCC-AAAAAATAGGAGGGTTCGAGTAAAAATATAGGCCCGAAATATGGGTTTGGGAAAAAAA-GA
* *
5655939 GGCCTGTTTAAAAAACAAGCTGGGCCTCGGGTAAGACTTTTTTGGCCTGAGCCGGGCCGTGCCGG
388 GGCCCGTTTAGAAAACAAGCTGGGCCTCGGGTAAGACTTTTTTGGCCTGAGCCGGGCCGTGCCGG
* * *
5656004 CTCGAATTATATATTAAATATACA-TTTATTTTTAATCATATATACTTTTTATTAAATATATATT
453 CCCGAATTATATATTAAATATAAATTTTATTTTTAATCAAATATACTTTTTATTAAATATATATT
5656068 TTTTGGACTTTTAATCTGAATTATATATTAAATATATATTTTTATTTTTAATCAAATATGGGCCG
518 TTTTGGACTTTTAATCTGAATTATATATTAAATATATATTTTTATTTTTAATCAAATATGGGCCG
* *
5656133 GGTCGAGCTCT-GGCTTAGTAATTTTCTTTCGGGCCGGGTTTGGACAAATTTTTAGGCCCATATT
583 GGTCGGGCTCTCGGCTTAGCAATTTTCTTTCGGGCCGGG-TTGGACAAATTTTTAGGCCCATATT
*
5656197 TCGGGTCAGGCCGGGCTCGGACCTATAAAACGGGTCTAAAATTTCATC
647 TCGGGTCAGGCCGGGCTCGGACCTATAAAACGGGCCTAAAATTTCATC
*
5656245 TGGATTATATTTGTTTATGATGAATTAATGTTGCAGGAGAACTTTTGGTGGATATGTTTGAATAG
1 TGGATTATATTTGTTTATGATGAATTAATGTTGCAGGAGAACTTTTGGTGGATATGTCTGAATAG
* *
5656310 GTGTAGGATTGATTTAATTAAATTCCAAACCAACTGCATTGATAT-AGCACCCTCCTCTGCATGG
66 GTGTAGGATTGATTTAATTAAATTCCAAACCAGCTGCATTGATATGA-CACCCTCCTCCGCATGG
* * * * *
5656374 ATGCTTAAAGTTCAATGTTTGTAGAATTGCAGACGATGATAGAGCAGACTGTGGAGGTGTCTTGA
130 ATGCTTAAAGTTCAATGTTTGTGGGATTGCAAACGAGGATAGAGCAGGCTGTGGAGGTGTCTTGA
* *
5656439 GAGATAAGGAGGGAGTCGCAAGAGCTTTATTTTCAGGTCTAGTAG-ACGCAAATGATATTGATTT
195 GAGATAAGGAGGGAGTCGCAAGAGCTTTATTTTTAGGTCCAGTAGCA-GCAAATGATATTGATTT
* * * * * *
5656503 GGCATAGATTGCCACGATGATGGTAGAGGTGATTATGGGTTGGGCTACCCGGCTCGGCCCGACGG
259 GGCAGAGATTGGCGCGGTGATGGTAGAGGTGATCATGGGTTGGGCTA-CCGGCCCGG-CCGACGG
* * *
5656568 CCCGCCCAAAAAATAGAAGGGTTCGGGTAAAAATATAGTCCCGAAATATGGGTTTGGGAAAAAAA
322 CCCG-CCAAAAAATAGGAGGGTTCGAGTAAAAATATAGGCCCGAAATATGGGTTTGGGAAAAAAA
* * *
5656633 TAGGCCCGTTTAGAAAACAGGCTGGGCCTCGGGTAAGACTTTTTTGGCCTGAGCCGGGTCGTGCC
386 GAGGCCCGTTTAGAAAACAAGCTGGGCCTCGGGTAAGACTTTTTTGGCCTGAGCCGGGCCGTGCC
5656698 GGCCCGAATTATATATTAAATATATAATTTTATTTTTAATCAAATATACTTTTTATTAAATATAT
451 GGCCCGAATTATATATTAAATATA-AATTTTATTTTTAATCAAATATACTTTTTATTAAATATAT
*
5656763 ATTTTTTGGACTTTTAATCTGAATTATATATTAAATATAAATTTTTTATTTTTAATCAAATATGG
515 ATTTTTTGGACTTTTAATCTGAATTATATATTAAATATATA-TTTTTATTTTTAATCAAATATGG
* * *
5656828 GCCGGGTCGGGCT-TGGGCTTAGCAATTTTCTTTCGAGCCGGGTTGGAAAAATTTTTAGGCCCAT
579 GCCGGGTCGGGCTCTCGGCTTAGCAATTTTCTTTCGGGCCGGGTTGGACAAATTTTTAGGCCCAT
* * *
5656892 ATTTCGAGTCAGACCAGGCTCGGACCTATAAAACGGGCCTAAAATTTCATC
644 ATTTCGGGTCAGGCCGGGCTCGGACCTATAAAACGGGCCTAAAATTTCATC
5656943 TGG
1 TGG
5656946 GCGCAGCCCG
Statistics
Matches: 1293, Mismatches: 82, Indels: 41
0.91 0.06 0.03
Matches are distributed among these distances:
695 293 0.23
696 459 0.35
697 70 0.05
698 152 0.12
699 60 0.05
700 7 0.01
702 2 0.00
703 1 0.00
705 2 0.00
706 109 0.08
707 54 0.04
708 84 0.06
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (694 bp):
TGGATTATATTTGTTTATGATGAATTAATGTTGCAGGAGAACTTTTGGTGGATATGTCTGAATAG
GTGTAGGATTGATTTAATTAAATTCCAAACCAGCTGCATTGATATGACACCCTCCTCCGCATGGA
TGCTTAAAGTTCAATGTTTGTGGGATTGCAAACGAGGATAGAGCAGGCTGTGGAGGTGTCTTGAG
AGATAAGGAGGGAGTCGCAAGAGCTTTATTTTTAGGTCCAGTAGCAGCAAATGATATTGATTTGG
CAGAGATTGGCGCGGTGATGGTAGAGGTGATCATGGGTTGGGCTACCGGCCCGGCCGACGGCCCG
CCAAAAAATAGGAGGGTTCGAGTAAAAATATAGGCCCGAAATATGGGTTTGGGAAAAAAAGAGGC
CCGTTTAGAAAACAAGCTGGGCCTCGGGTAAGACTTTTTTGGCCTGAGCCGGGCCGTGCCGGCCC
GAATTATATATTAAATATAAATTTTATTTTTAATCAAATATACTTTTTATTAAATATATATTTTT
TGGACTTTTAATCTGAATTATATATTAAATATATATTTTTATTTTTAATCAAATATGGGCCGGGT
CGGGCTCTCGGCTTAGCAATTTTCTTTCGGGCCGGGTTGGACAAATTTTTAGGCCCATATTTCGG
GTCAGGCCGGGCTCGGACCTATAAAACGGGCCTAAAATTTCATC
Found at i:5656764 original size:20 final size:20
Alignment explanation
Indices: 5656709--5656768 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
5656699 GCCCGAATTA
5656709 TATATTAAATATATA-ATTT
1 TATATTAAATATATATATTT
* * *
5656728 TATTTTTAATCAAATATACTTT
1 TATATTAAAT-ATATATA-TTT
5656750 T-TATTAAATATATAT-TTT
1 TATATTAAATATATATATTT
5656768 T
1 T
5656769 TGGACTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
18 4 0.12
19 8 0.25
20 9 0.28
21 7 0.22
22 4 0.12
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TATATTAAATATATATATTT
Found at i:5657610 original size:108 final size:111
Alignment explanation
Indices: 5657409--5657630 Score: 360
Period size: 108 Copynumber: 2.0 Consensus size: 111
5657399 CTTTGATAGC
*
5657409 CCCATCTCAAATTTTGTGTTAGGCAATTTGTTTTTGTTTTTATTAGAGGGAAATAAAATTAAAAA
1 CCCATCTCAAATATTGTGTTAGGCAATTTGTTTTTGTTTTTATTAGAGGG--A-AAAA-TAAAAA
*
5657474 AAATGCATGATTAACTGTTAATAATCATTGTCAACTATAGATTTGTAAAG
62 AAATGCATGATTAACTGTTAATAATCATTGTCAACTAAAGATTTGTAAAG
*
5657524 CCCATCTCAAATATTGTGTTAGGCAATTTG-TTTTGTTTTTATTAGAGGG-AAAA-AAAAAACAT
1 CCCATCTCAAATATTGTGTTAGGCAATTTGTTTTTGTTTTTATTAGAGGGAAAAATAAAAAAAAT
5657586 GCATGATTAACTGTTAATAATCATTGTCAACTAAAGATTTGTAAA
66 GCATGATTAACTGTTAATAATCATTGTCAACTAAAGATTTGTAAA
5657631 TTGCCTTGGT
Statistics
Matches: 104, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
108 52 0.50
110 4 0.04
114 19 0.18
115 29 0.28
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (111 bp):
CCCATCTCAAATATTGTGTTAGGCAATTTGTTTTTGTTTTTATTAGAGGGAAAAATAAAAAAAAT
GCATGATTAACTGTTAATAATCATTGTCAACTAAAGATTTGTAAAG
Found at i:5669545 original size:31 final size:29
Alignment explanation
Indices: 5669475--5669548 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
5669465 GGTTCAGGTT
* *
5669475 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
5669504 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
5669535 ACATTTTAGTCACT
1 ACATTTTAGTCACT
5669549 AAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Done.