Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008164.1 Hibiscus syriacus cultivar Beakdansim tig00110744_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2577652
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:2260519 original size:32 final size:32
Alignment explanation
Indices: 2260415--2260534 Score: 134
Period size: 32 Copynumber: 3.8 Consensus size: 32
2260405 AGTCACAAAA
* * *
2260415 AGTCAGTATTGCATTCATATAATGGACAGTAG
1 AGTCAGTATTGCATTTAGATAATGCACAGTAG
* * *
2260447 AGCCAGTATTGCATTCAGATAATGCATAGTAG
1 AGTCAGTATTGCATTTAGATAATGCACAGTAG
2260479 AGTCAGTATTGCATTTAGATAATGCACCA-TAG
1 AGTCAGTATTGCATTTAGATAATGCA-CAGTAG
* * **
2260511 TGTTAGTATCACATTTAGATAATG
1 AGTCAGTATTGCATTTAGATAATG
2260535 TGCATCAAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
32 75 0.99
33 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (32 bp):
AGTCAGTATTGCATTTAGATAATGCACAGTAG
Found at i:2285696 original size:14 final size:14
Alignment explanation
Indices: 2285661--2285689 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2285651 TGTTTGGGTA
2285661 ATGAAATCACTCGC
1 ATGAAATCACTCGC
2285675 ATGAAATCACTCGC
1 ATGAAATCACTCGC
2285689 A
1 A
2285690 GTAAATCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.21
Consensus pattern (14 bp):
ATGAAATCACTCGC
Found at i:2290964 original size:8 final size:8
Alignment explanation
Indices: 2290951--2290975 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2290941 ATTTTGAAAA
2290951 ATTGTTTT
1 ATTGTTTT
2290959 ATTGTTTT
1 ATTGTTTT
2290967 ATTGTTTT
1 ATTGTTTT
2290975 A
1 A
2290976 ACATGTGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (8 bp):
ATTGTTTT
Found at i:2297490 original size:17 final size:17
Alignment explanation
Indices: 2297468--2297517 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
2297458 GATATTGGAG
*
2297468 AGTATTGATACTACAAT
1 AGTATTGATACTACAAC
2297485 AGTATTGATACT--AAC
1 AGTATTGATACTACAAC
*
2297500 AGTATTGGTACTACAAC
1 AGTATTGATACTACAAC
2297517 A
1 A
2297518 ATATCGGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 13 0.45
17 16 0.55
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (17 bp):
AGTATTGATACTACAAC
Found at i:2297505 original size:15 final size:15
Alignment explanation
Indices: 2297468--2297512 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2297458 GATATTGGAG
*
2297468 AGTATTGATACTACAAT
1 AGTATTGATACT--AAC
2297485 AGTATTGATACTAAC
1 AGTATTGATACTAAC
*
2297500 AGTATTGGTACTA
1 AGTATTGATACTA
2297513 CAACAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 14 0.54
17 12 0.46
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
AGTATTGATACTAAC
Found at i:2297601 original size:20 final size:19
Alignment explanation
Indices: 2297576--2297643 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
2297566 CAGTACATAC
*
2297576 ACTACAAGAATAATATCGGT
1 ACTACAAGAATAATAT-GAT
* *
2297596 ACTACAAGAACAGTATTGAT
1 ACTACAAGAATAATA-TGAT
*
2297616 ACTATAAGAATAATATGAT
1 ACTACAAGAATAATATGAT
2297635 ACTACAAGA
1 ACTACAAGA
2297644 TCAGTATTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 12 0.30
20 27 0.68
21 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (19 bp):
ACTACAAGAATAATATGAT
Found at i:2297608 original size:40 final size:39
Alignment explanation
Indices: 2297564--2297649 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 39
2297554 TATCGGCACT
*
2297564 AACAGTACAT-ACACTACAAGAATAATATCGGTACTACAAG
1 AACAGTA-ATGACACTACAAGAATAATAT-GATACTACAAG
* * *
2297604 AACAGTATTGATACTATAAGAATAATATGATACTACAAG
1 AACAGTAATGACACTACAAGAATAATATGATACTACAAG
*
2297643 ATCAGTA
1 AACAGTA
2297650 TTTATACTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 17 0.43
40 23 0.57
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (39 bp):
AACAGTAATGACACTACAAGAATAATATGATACTACAAG
Found at i:2297649 original size:39 final size:40
Alignment explanation
Indices: 2297576--2297661 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 40
2297566 CAGTACATAC
*
2297576 ACTACAAGAATAATATCGGTACTACAAGAACAGTATTGAT
1 ACTACAAGAATAATATCGATACTACAAGAACAGTATTGAT
* * *
2297616 ACTATAAGAATAATAT-GATACTACAAGATCAGTATTTAT
1 ACTACAAGAATAATATCGATACTACAAGAACAGTATTGAT
2297655 ACTACAA
1 ACTACAA
2297662 CCCATAAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 26 0.63
40 15 0.37
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (40 bp):
ACTACAAGAATAATATCGATACTACAAGAACAGTATTGAT
Found at i:2297658 original size:20 final size:20
Alignment explanation
Indices: 2297595--2297661 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
2297585 ATAATATCGG
*
2297595 TACTACAAGAACAGTATTGA
1 TACTACAAGATCAGTATTGA
* *
2297615 TACTATAAGAAT-AATA-TGA
1 TACTACAAG-ATCAGTATTGA
*
2297634 TACTACAAGATCAGTATTTA
1 TACTACAAGATCAGTATTGA
2297654 TACTACAA
1 TACTACAA
2297662 CCCATAAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.05
19 14 0.37
20 21 0.55
21 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.30
Consensus pattern (20 bp):
TACTACAAGATCAGTATTGA
Found at i:2298657 original size:23 final size:23
Alignment explanation
Indices: 2298614--2298658 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
2298604 AAGTTACAAA
2298614 TAAAAGTCTAAATTTTTATATAAG
1 TAAAAGTCT-AATTTTTATATAAG
2298638 TAAAAGTCT-ATTTTTAATATA
1 TAAAAGTCTAATTTTT-ATATA
2298659 TTACAATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 9 0.45
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (23 bp):
TAAAAGTCTAATTTTTATATAAG
Found at i:2298810 original size:29 final size:29
Alignment explanation
Indices: 2298765--2298831 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
2298755 TACCAAAAGG
2298765 AATTACAATCAGAGAAAAAACTTATCATA
1 AATTACAATCAGAGAAAAAACTTATCATA
* *
2298794 AATTACAATCAGGGAAAAAACTTCTCATA
1 AATTACAATCAGAGAAAAAACTTATCATA
2298823 AATTACAAT
1 AATTACAAT
2298832 AATAATCTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.25
Consensus pattern (29 bp):
AATTACAATCAGAGAAAAAACTTATCATA
Found at i:2299121 original size:14 final size:15
Alignment explanation
Indices: 2299104--2299137 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2299094 TTATAATTTT
2299104 ATATTTTAAAG-AAA
1 ATATTTTAAAGTAAA
*
2299118 ATATTTTAGAGTAAA
1 ATATTTTAAAGTAAA
2299133 ATATT
1 ATATT
2299138 AACGAGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (15 bp):
ATATTTTAAAGTAAA
Found at i:2299856 original size:3 final size:3
Alignment explanation
Indices: 2299848--2299881 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2299838 CCTCTATTCG
2299848 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2299882 ATAAATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2300927 original size:30 final size:30
Alignment explanation
Indices: 2300867--2301012 Score: 158
Period size: 29 Copynumber: 5.0 Consensus size: 30
2300857 TTTTGAATAC
* * *
2300867 TTTTAAATTAAAATAAAAAT-AAA-CTATT
1 TTTTAAATTAAGATAAGAATAAAATATATT
* *
2300895 TTTTAAAATAAGATAAGAATAACATATATT
1 TTTTAAATTAAGATAAGAATAAAATATATT
* *
2300925 TTTTAAGTTAAGATAAGAGTAAAATA-ATT
1 TTTTAAATTAAGATAAGAATAAAATATATT
* * **
2300954 TTTTAAGTTAAAATAAGAGCAAAATATA-T
1 TTTTAAATTAAGATAAGAATAAAATATATT
2300983 TTTTAAATTAAGATAAGAAT-AAATATATT
1 TTTTAAATTAAGATAAGAATAAAATATATT
2301012 T
1 T
2301013 AGTAATTTAA
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.24
29 48 0.48
30 27 0.27
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (30 bp):
TTTTAAATTAAGATAAGAATAAAATATATT
Found at i:2302129 original size:13 final size:13
Alignment explanation
Indices: 2302111--2302135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2302101 TTTTCGTCCA
2302111 TTTTTTATTTTAT
1 TTTTTTATTTTAT
2302124 TTTTTTATTTTA
1 TTTTTTATTTTA
2302136 CATATATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTATTTTAT
Found at i:2302223 original size:38 final size:37
Alignment explanation
Indices: 2302172--2302400 Score: 349
Period size: 36 Copynumber: 6.2 Consensus size: 37
2302162 TGTAGTATAT
*
2302172 TTTTG-AAAATATATATAATATATAGCTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
*
2302208 TTTTGAAAACT-TATATAATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
*
2302244 TTTTGAAAAAATATATATAATATATAGGTTTTAAAACA
1 TTTTG-AAAAATATATATAATATATAGTTTTTAAAACA
*
2302282 TTTT-AAAAATATATATAATATATAGTTTTAAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
*
2302318 TTTTGAAAATATATATATAATATATAGTTTTTAAAATA
1 TTTTGAAAA-ATATATATAATATATAGTTTTTAAAACA
* *
2302356 TTTTGAAAAATATATATAATATATA-ATTTTAAAATA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
2302392 TTTTGAAAA
1 TTTTGAAAA
2302401 TAATTATTTT
Statistics
Matches: 179, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
36 87 0.49
37 29 0.16
38 63 0.35
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (37 bp):
TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
Found at i:2302276 original size:74 final size:75
Alignment explanation
Indices: 2302177--2302400 Score: 355
Period size: 74 Copynumber: 3.0 Consensus size: 75
2302167 TATATTTTTG
*
2302177 AAAATATATATAATATATAGCTTTTAAAACATTTTGAAAACT-TATATAATATATAGTTTTTAAA
1 AAAATATATATAATATATAGCTTTTAAAACATTTTGAAAAATATATATAATATATAGTTTTTAAA
2302241 ACATTTTGAA
66 ACATTTTGAA
* *
2302251 AAAATATATATAATATATAGGTTTTAAAACATTTT-AAAAATATATATAATATATAGTTTTAAAA
1 AAAATATATATAATATATAGCTTTTAAAACATTTTGAAAAATATATATAATATATAGTTTTTAAA
2302315 ACATTTTGAA
66 ACATTTTGAA
* * * *
2302325 AATATATATATAATATATAGTTTTTAAAATATTTTGAAAAATATATATAATATATA-ATTTTAAA
1 AAAATATATATAATATATAGCTTTTAAAACATTTTGAAAAATATATATAATATATAGTTTTTAAA
*
2302389 ATATTTTGAA
66 ACATTTTGAA
2302399 AA
1 AA
2302401 TAATTATTTT
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
73 5 0.04
74 114 0.82
75 20 0.14
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (75 bp):
AAAATATATATAATATATAGCTTTTAAAACATTTTGAAAAATATATATAATATATAGTTTTTAAA
ACATTTTGAA
Found at i:2303533 original size:3 final size:3
Alignment explanation
Indices: 2303525--2303562 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2303515 AATTTAACCC
2303525 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
2303563 TTTTTTTTTT
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:2303632 original size:15 final size:14
Alignment explanation
Indices: 2303612--2303654 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
2303602 TTTTTACTGA
*
2303612 ATTTTATTTATCTTT
1 ATTTTATTT-TATTT
2303627 ATTTTATTTTATTT
1 ATTTTATTTTATTT
2303641 ATTATTATTATTAT
1 ATT-TTATT-TTAT
2303655 ATTAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 7 0.28
15 14 0.56
16 4 0.16
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTTATTTTATTT
Found at i:2303648 original size:20 final size:21
Alignment explanation
Indices: 2303612--2303654 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2303602 TTTTTACTGA
2303612 ATTTTATTTATCTTTATT-TT
1 ATTTTATTTATCTTTATTATT
2303632 ATTTTATTTAT-TATTATTATT
1 ATTTTATTTATCT-TTATTATT
2303653 AT
1 AT
2303655 ATTAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.05
20 16 0.76
21 4 0.19
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTTATTTATCTTTATTATT
Found at i:2303684 original size:46 final size:46
Alignment explanation
Indices: 2303634--2303723 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 46
2303624 TTTATTTTAT
* *
2303634 TTTATTTATTATTATTATTATATT-A-ATATTTTT-TCCTTTTTTCATG
1 TTTATTT-TTATT-TTATCAT-TTAACATATTTTTGACCTTTTTTCATG
2303680 TTTATTTTTATTTTATCATTTAACATATTTTTGACCTTTTTTCA
1 TTTATTTTTATTTTATCATTTAACATATTTTTGACCTTTTTTCA
2303724 GTAGTAATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
43 2 0.05
44 7 0.18
45 13 0.33
46 17 0.44
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (46 bp):
TTTATTTTTATTTTATCATTTAACATATTTTTGACCTTTTTTCATG
Found at i:2304436 original size:47 final size:47
Alignment explanation
Indices: 2304367--2304463 Score: 167
Period size: 47 Copynumber: 2.1 Consensus size: 47
2304357 ATAGTCATAA
*
2304367 GGGAATATATCCTCTCGAGTTTAACTTAGTCCACATAAGCTTGTAAT
1 GGGAATATATCCTCTCGAGTTTAACTTAGTCCACATAAGATTGTAAT
* *
2304414 GGGAATGTATCCTCTCGAGTTTAACTTAGTCTACATAAGATTGTAAT
1 GGGAATATATCCTCTCGAGTTTAACTTAGTCCACATAAGATTGTAAT
2304461 GGG
1 GGG
2304464 CTTAAGACTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (47 bp):
GGGAATATATCCTCTCGAGTTTAACTTAGTCCACATAAGATTGTAAT
Found at i:2309525 original size:85 final size:85
Alignment explanation
Indices: 2309348--2309601 Score: 357
Period size: 85 Copynumber: 3.0 Consensus size: 85
2309338 CTCCCAGCCT
* * * * * *
2309348 ATTTACAGTATAGCTCAAGGCT-AAAAGGGTTATCTATCAACAACAAACCTTCAAGTTCGATTGC
1 ATTTACAGCATAGCTCAAGG-TGAGAAGGGTTATCTGTCAACAA-AGACCTTCGAGTTCGATTAC
* * *
2309412 ATTCAGCTTAAGGGCATATGAA
64 ATTCAGCTCAAAGGCATATCAA
2309434 ATTTACAGCATAGCTCAAGGTGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAT
1 ATTTACAGCATAGCTCAAGGTGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAT
*
2309499 TCATCTCAAAGGCATATCAA
66 TCAGCTCAAAGGCATATCAA
* * *
2309519 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACATTCGAGTTCGATTACAT
1 ATTTACAGCATAGCTCAAGGTGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAT
*
2309584 TCAGCTGAAAGGCATATC
66 TCAGCTCAAAGGCATATC
2309602 TCAAGGCGAG
Statistics
Matches: 152, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
85 114 0.75
86 38 0.25
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (85 bp):
ATTTACAGCATAGCTCAAGGTGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAT
TCAGCTCAAAGGCATATCAA
Found at i:2309613 original size:69 final size:69
Alignment explanation
Indices: 2309526--2309655 Score: 224
Period size: 69 Copynumber: 1.9 Consensus size: 69
2309516 CAAATTTACA
*
2309526 GCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACATTCGAGTTCGATTACATTCAGCTG
1 GCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACATTCGAGTTCGATTACATTCAGCTG
2309591 AAAG
66 AAAG
* * *
2309595 GCATATCTCAAGGCGAGAAGGGCTATCTGTCAGCAAAGACCTTCGAGTTCGATTACATTCA
1 GCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACATTCGAGTTCGATTACATTCA
2309656 ACTCAAGGAC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (69 bp):
GCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACATTCGAGTTCGATTACATTCAGCTG
AAAG
Found at i:2309691 original size:154 final size:154
Alignment explanation
Indices: 2309441--2309752 Score: 502
Period size: 154 Copynumber: 2.0 Consensus size: 154
2309431 GAAATTTACA
* * *
2309441 GCATAGCTCAAGGTGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCATCTC
1 GCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAACTC
2309506 AAAGGCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGA-CATTC
66 AAAGGCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGATC-TTC
*
2309570 GAGTTCGATTACATTCAGCTGAAAG
130 GAGTTCGATTACATTCAGCTCAAAG
* *
2309595 GCATATCTCAAGGCGAGAAGGGCTATCTGTCAGCAAAGACCTTCGAGTTCGATTACATTCAACTC
1 GCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAACTC
* *
2309660 -AAGGACATATCAAATTTATAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAATATCTTC
66 AAAGG-CATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGATCTTC
* *
2309724 GAGTTCGATTCCATTCAGCTCAAGG
130 GAGTTCGATTACATTCAGCTCAAAG
2309749 GCAT
1 GCAT
2309753 GTCAAATTTA
Statistics
Matches: 146, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
153 4 0.03
154 141 0.97
155 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (154 bp):
GCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAACTC
AAAGGCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGATCTTCG
AGTTCGATTACATTCAGCTCAAAG
Found at i:2309826 original size:85 final size:85
Alignment explanation
Indices: 2309595--2309826 Score: 286
Period size: 85 Copynumber: 2.7 Consensus size: 85
2309585 CAGCTGAAAG
* ** * * * * *
2309595 GCATATCTCAAGGCGAGAAGGGCTATCTGTCAGCAAAGACCTTCGAGTTCGATTACATTCAACTC
1 GCATAACTCAAGGCGAGAAAAGCTATCTGTCAACAAAAATCTTCGAGTTCGATTCCATTCAGCTC
*
2309660 AAGGACATATCAAATTTATA
66 AAGGACATATCAAATTTACA
** * *
2309680 GCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAATATCTTCGAGTTCGATTCCATTCAGCTC
1 GCATAACTCAAGGCGAGAAAAGCTATCTGTCAACAAAAATCTTCGAGTTCGATTCCATTCAGCTC
* *
2309745 AAGGGCATGTCAAATTTACA
66 AAGGACATATCAAATTTACA
* * *
2309765 GCATAGCTTAAGTCGAGAAAAGCTATCTGTCAACAAAAAT-TGTCGAGTTCGATTCCATTCAG
1 GCATAACTCAAGGCGAGAAAAGCTATCTGTCAACAAAAATCT-TCGAGTTCGATTCCATTCAG
2309827 TTCGATGACA
Statistics
Matches: 129, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
84 1 0.01
85 128 0.99
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (85 bp):
GCATAACTCAAGGCGAGAAAAGCTATCTGTCAACAAAAATCTTCGAGTTCGATTCCATTCAGCTC
AAGGACATATCAAATTTACA
Found at i:2309826 original size:239 final size:240
Alignment explanation
Indices: 2309361--2309826 Score: 641
Period size: 239 Copynumber: 1.9 Consensus size: 240
2309351 TACAGTATAG
* * * * * *
2309361 CTCAAGGCTAAAAGGGTTATCTATCAACAACAAACCTTCAAGTTCGATTGCATTCAGCTTAAGGG
1 CTCAAGGCGAAAAGGGCTATCTATCAACAACAAACCTTCAAGTTCGATTACATTCAACTCAAGGA
* * *
2309426 CATATGAAATTTACAGCATAGCTCAAGGTGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTC
66 CATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTC
* ** *
2309491 GATTACATTCATCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGT
131 GATTACATTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAGAAAAGCTATCTGT
2309556 CAACAAAGACATTCGAGTTCGATTACATTCAGCTGAAAGGCATAT
196 CAACAAAGACATTCGAGTTCGATTACATTCAGCTGAAAGGCATAT
* * * * *
2309601 CTCAAGGCGAGAAGGGCTATCTGTCAGCAA-AGACCTTCGAGTTCGATTACATTCAACTCAAGGA
1 CTCAAGGCGAAAAGGGCTATCTATCAACAACAAACCTTCAAGTTCGATTACATTCAACTCAAGGA
* * *
2309665 CATATCAAATTTATAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAATATCTTCGAGTTC
66 CATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTC
* * * * * *
2309730 GATTCCATTCAGCTCAAGGGCATGTCAAATTTACAGCATAGCTTAAGTCGAGAAAAGCTATCTGT
131 GATTACATTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAGAAAAGCTATCTGT
*
2309795 CAACAAA-A-ATTGTCGAGTTCGATTCCATTCAG
196 CAACAAAGACA-T-TCGAGTTCGATTACATTCAG
2309827 TTCGATGACA
Statistics
Matches: 196, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
237 1 0.01
238 2 0.01
239 168 0.86
240 25 0.13
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (240 bp):
CTCAAGGCGAAAAGGGCTATCTATCAACAACAAACCTTCAAGTTCGATTACATTCAACTCAAGGA
CATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTC
GATTACATTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAGAAAAGCTATCTGT
CAACAAAGACATTCGAGTTCGATTACATTCAGCTGAAAGGCATAT
Found at i:2310545 original size:3 final size:3
Alignment explanation
Indices: 2310537--2310564 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2310527 CGGATTTTAT
2310537 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2310565 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2310651 original size:36 final size:37
Alignment explanation
Indices: 2310593--2310885 Score: 433
Period size: 36 Copynumber: 8.1 Consensus size: 37
2310583 GTAGCATAAG
*
2310593 TTTTGAAAAAAATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
**
2310630 TTTTGAAAGCT-TATATAATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
2310666 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
2310703 TTTT-AAAAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
2310739 TTTTGAAAAAATATATATAATATATAG-TTTTAAAACA
1 TTTTG-AAAAATATATATAATATATAGTTTTTAAAACA
* **
2310776 TTTT-AAAAATATATATAATATATAATTTTCGAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
*
2310812 TTTTGAAAATATATATATAATATATAGTTTTTAAAATA
1 TTTTGAAAA-ATATATATAATATATAGTTTTTAAAACA
*
2310850 TTTTG---AAT-TATATAATATATAG-TTTTAAAATA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
2310882 TTTT
1 TTTT
2310886 ATAAATAATT
Statistics
Matches: 238, Mismatches: 12, Indels: 17
0.89 0.04 0.06
Matches are distributed among these distances:
32 14 0.06
33 14 0.06
34 2 0.01
35 21 0.09
36 82 0.34
37 55 0.23
38 50 0.21
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
Found at i:2310687 original size:73 final size:73
Alignment explanation
Indices: 2310593--2310885 Score: 436
Period size: 73 Copynumber: 4.1 Consensus size: 73
2310583 GTAGCATAAG
* **
2310593 TTTTGAAAAAAATATATAATATATAGTTTTTAAAACATTTTGAAAGCT-TATATAATATATAGTT
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTT-AAAAATATATATAATATATAGTT
2310657 TTTAAAACA
65 TTTAAAACA
2310666 TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTAAAAATATATATAATATATAGTTT
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTAAAAATATATATAATATATAGTTT
2310731 TTAAAACA
66 TTAAAACA
*
2310739 TTTTGAAAAAATATATATAATATATAG-TTTTAAAACATTTTAAAAATATATATAATATATAATT
1 TTTTG-AAAAATATATATAATATATAGTTTTTAAAACATTTTAAAAATATATATAATATATAGTT
**
2310803 TTCGAAACA
65 TTTAAAACA
* *
2310812 TTTTGAAAATATATATATAATATATAGTTTTTAAAATATTTT--GAAT-TATATAATATATAG-T
1 TTTTGAAAA-ATATATATAATATATAGTTTTTAAAACATTTTAAAAATATATATAATATATAGTT
*
2310873 TTTAAAATA
65 TTTAAAACA
2310882 TTTT
1 TTTT
2310886 ATAAATAATT
Statistics
Matches: 204, Mismatches: 12, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
70 11 0.05
71 13 0.06
72 11 0.05
73 135 0.66
74 34 0.17
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (73 bp):
TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTAAAAATATATATAATATATAGTTT
TTAAAACA
Found at i:2310724 original size:109 final size:106
Alignment explanation
Indices: 2310593--2310892 Score: 442
Period size: 109 Copynumber: 2.8 Consensus size: 106
2310583 GTAGCATAAG
*
2310593 TTTTGAAAAAAATATATAATATATAGTTTTTAAAACATTTTGAAAGCTTATATAATATATAGTTT
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAA--TTATATAATATATAG-TT
* *
2310658 TTAAAACATTTTGAAAAATATATATAATATATAGTTTTTAAAACA
63 TTAAAACATTTT-AAAAATATATATAATATATAATTTTCAAAACA
2310703 TTTT-AAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAAAATATATATAATATATAGT
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTG---AAAT-TATATAATATATAGT
*
2310767 TTTAAAACATTTTAAAAATATATATAATATATAATTTTCGAAACA
62 TTTAAAACATTTTAAAAATATATATAATATATAATTTTCAAAACA
*
2310812 TTTTGAAAATATATATATAATATATAGTTTTTAAAATATTTTG-AATTATATAATATATAGTTTT
1 TTTTGAAAA-ATATATATAATATATAGTTTTTAAAACATTTTGAAATTATATAATATATAGTTTT
* *
2310876 AAAATATTTTATAAATA
65 AAAACATTTTAAAAATA
2310893 ATTATTTTGA
Statistics
Matches: 177, Mismatches: 7, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
106 33 0.19
107 3 0.02
109 69 0.39
110 23 0.13
111 46 0.26
112 3 0.02
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (106 bp):
TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAATTATATAATATATAGTTTTA
AAACATTTTAAAAATATATATAATATATAATTTTCAAAACA
Found at i:2310998 original size:18 final size:18
Alignment explanation
Indices: 2310957--2311005 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2310947 ATATTAATAT
* *
2310957 TTTTTATATTATTTATTTA
1 TTTTTAT-TTATTTACTCA
*
2310976 ATTTTATTTATTTACTCA
1 TTTTTATTTATTTACTCA
*
2310994 TTTTTCTTTATT
1 TTTTTATTTATT
2311006 GTTTTTTGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATTTATTTACTCA
Found at i:2311807 original size:2 final size:2
Alignment explanation
Indices: 2311800--2311846 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2311790 CTTAAGGGAA
2311800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2311842 AT AT A
1 AT AT A
2311847 GCATAGGCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2312269 original size:3 final size:3
Alignment explanation
Indices: 2312261--2312295 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2312251 TCTTTATTTG
2312261 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2312296 ATAATTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2323474 original size:38 final size:39
Alignment explanation
Indices: 2323432--2323516 Score: 104
Period size: 38 Copynumber: 2.2 Consensus size: 39
2323422 TAAAAAGGGA
*
2323432 AAAAGAATTTAA-ATTAGGATTAAAAT-AAAATA-AAATT
1 AAAAGAA-TTAATACTAGGATTAAAATAAAAATATAAATT
*
2323469 GAAAAGAATTAATACTAGGGTTAAAATAAAAATATTAAATT
1 -AAAAGAATTAATACTAGGATTAAAATAAAAATA-TAAATT
2323510 AAAAGAA
1 AAAAGAA
2323517 AATAAAAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
37 4 0.10
38 19 0.46
39 6 0.15
40 7 0.17
41 5 0.12
ACGTcount: A:0.61, C:0.01, G:0.11, T:0.27
Consensus pattern (39 bp):
AAAAGAATTAATACTAGGATTAAAATAAAAATATAAATT
Found at i:2324911 original size:27 final size:27
Alignment explanation
Indices: 2324848--2324913 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 27
2324838 TTCAAAAACC
2324848 GTTTTAAAAAACTATATATATATATAT
1 GTTTTAAAAAACTATATATATATATAT
*
2324875 GTTTTCAAAATAACTATAT-TATATATGT
1 GTTTT-AAAA-AACTATATATATATATAT
2324903 -TTTTAAAAAAC
1 GTTTTAAAAAAC
2324914 CATTTTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
25 3 0.08
26 4 0.11
27 9 0.25
28 12 0.33
29 8 0.22
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (27 bp):
GTTTTAAAAAACTATATATATATATAT
Found at i:2324920 original size:67 final size:64
Alignment explanation
Indices: 2324798--2324961 Score: 194
Period size: 67 Copynumber: 2.5 Consensus size: 64
2324788 TTCACAAACA
* * *
2324798 ATATA-ATATGTTTTCAAAGATTATAC-ATACTATAGACGTTTTCAAAAACCGTTTTAAAAAACT
1 ATATATATATGTTTTCAAA-A-TA-ACTATACTATATACGTTTTAAAAAACCATTTTAAAAAAC-
2324861 ATAT
62 -TAT
* *
2324865 ATATATATATGTTTTCAAAATAACTATATTATATATGTTTTTAAAAAACCATTTTAAAAAACTAT
1 ATATATATATGTTTTCAAAATAACTATACTATATACG-TTTTAAAAAACCATTTTAAAAAACTAT
2324930 ATAT-TATATGTTTTC-AAA-AACTATACTATATA
1 ATATATATATGTTTTCAAAATAACTATACTATATA
2324962 ACTTCAAAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
62 13 0.15
63 3 0.03
64 11 0.12
65 9 0.10
66 11 0.12
67 28 0.32
68 13 0.15
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.41
Consensus pattern (64 bp):
ATATATATATGTTTTCAAAATAACTATACTATATACGTTTTAAAAAACCATTTTAAAAAACTAT
Found at i:2324948 original size:24 final size:22
Alignment explanation
Indices: 2324915--2324979 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 22
2324905 TTAAAAAACC
*
2324915 ATTTTAAAAAACTATATATTAT
1 ATTTTCAAAAACTATATATTAT
2324937 ATGTTTTCAAAAACTATACTA-TAT
1 A--TTTTCAAAAACTATA-TATTAT
**
2324961 AACTTCAAAAACTATATAT
1 ATTTTCAAAAACTATATAT
2324980 ATTATTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 2 0.06
22 14 0.39
24 18 0.50
25 2 0.06
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTTTCAAAAACTATATATTAT
Found at i:2325005 original size:2 final size:2
Alignment explanation
Indices: 2324998--2325064 Score: 100
Period size: 2 Copynumber: 33.0 Consensus size: 2
2324988 TTTTTGAAAT
2324998 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2325040 TG TA TA T- TA TCA TA TA TA CTA TA TA
1 TA TA TA TA TA T-A TA TA TA -TA TA TA
2325065 ATGTAATAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 1 0.02
2 55 0.92
3 4 0.07
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2327812 original size:62 final size:62
Alignment explanation
Indices: 2327713--2327837 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
2327703 AGGTTCGAGG
* * *
2327713 GTTTACCTATGTTCTTCGCGACATATAGACTGTTTACCTATGTTCTTCGGGA-CATATGGACT
1 GTTTACCTATGTTCTTCGCGACATATAGACTGATTACCTAGGTTCTTCGGAATC-TATGGACT
*
2327775 GTTTACCTATGTTCTTCGGGACATATAGACTGATTACCTAGGTTCTTCGGAATCTATGGACT
1 GTTTACCTATGTTCTTCGCGACATATAGACTGATTACCTAGGTTCTTCGGAATCTATGGACT
2327837 G
1 G
2327838 GTCCTTTGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 57 0.98
63 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGCGACATATAGACTGATTACCTAGGTTCTTCGGAATCTATGGACT
Found at i:2327837 original size:31 final size:31
Alignment explanation
Indices: 2327713--2327824 Score: 188
Period size: 31 Copynumber: 3.6 Consensus size: 31
2327703 AGGTTCGAGG
*
2327713 GTTTACCTATGTTCTTCGCGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACT
*
2327744 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACT
2327775 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACT
* *
2327806 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
2327825 AATCTATGGA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATAGACT
Found at i:2330716 original size:16 final size:18
Alignment explanation
Indices: 2330691--2330727 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
2330681 TAGAAAGGTT
2330691 AAAAGGATAAA-GA-ATG
1 AAAAGGATAAATGATATG
*
2330707 AAAAGTATAAATGATATG
1 AAAAGGATAAATGATATG
2330725 AAA
1 AAA
2330728 GGAATGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (18 bp):
AAAAGGATAAATGATATG
Found at i:2333414 original size:31 final size:31
Alignment explanation
Indices: 2333376--2333485 Score: 184
Period size: 31 Copynumber: 3.5 Consensus size: 31
2333366 AGGGTCGAGG
*
2333376 GTTTACCTATGTTCTTCGAGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
2333407 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
*
2333438 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
* *
2333469 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
2333486 AGAATCTATG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGATT
Found at i:2333496 original size:31 final size:31
Alignment explanation
Indices: 2333378--2333502 Score: 146
Period size: 31 Copynumber: 4.0 Consensus size: 31
2333368 GGTCGAGGGT
* *
2333378 TTACCTATGTTCTTC-GAGACATATGGATTGT
1 TTACCTATGTTCTTCGGA-ACATATGGACTGA
* * *
2333409 TTACCTATGTTCTTCGGGACATATGGATTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGA
*
2333440 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGA
* *
2333471 TTACCTAGGTTCTTCAGAATC-TATGGACTGA
1 TTACCTATGTTCTTCGGAA-CATATGGACTGA
2333502 T
1 T
2333503 CCTTCGGGAC
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
31 84 0.98
32 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGA
Found at i:2334213 original size:12 final size:12
Alignment explanation
Indices: 2334196--2334221 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2334186 TTTTAACATT
2334196 CGGCACTGTTCA
1 CGGCACTGTTCA
2334208 CGGCACTGTTCA
1 CGGCACTGTTCA
2334220 CG
1 CG
2334222 ATACGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.35, G:0.27, T:0.23
Consensus pattern (12 bp):
CGGCACTGTTCA
Found at i:2335049 original size:214 final size:212
Alignment explanation
Indices: 2334681--2335070 Score: 672
Period size: 214 Copynumber: 1.8 Consensus size: 212
2334671 GATAAATGTG
*
2334681 ATGCTCTTTAGTATGTCTAAGATGTAAGAAAAAATGTATTTTTTCTCATTTTATCTCTTGGACGA
1 ATGCTCTTTAGTATGTCTAAGATGCAAGAAAAAATGTATTTTTTCTCATTTTATCTCTTGGACGA
* * *
2334746 AGTCTCATTCTTTGCTTGCTGGTCTTTTCCTTGGAATTGATCATGCCCCAGCACCGATGGCTTCA
66 AGTCTCATTCTTTGCTTGCTGGTCTTGTCCTTGGAATTGATCATGCCCCAACACCGACGGCTTCA
*
2334811 TGGAAAGTATCTAAGCTTTGCTCATTTTGTTGGCTCAATCCAATGATGTATCAATTCTAATCTAA
131 TGGAAAATATCTAAGCTTTGCTCA-TTTGTTGGCTCAATCCAATGATGTATCAATTCTAATCTAA
2334876 AGATTCTTAAGCTCAGAT
195 AGATTCTTAAGCTCAGAT
* * *
2334894 ATGCTCTTTAGTATGTCTAAGATGCATGCAAAAATGTATTTTTTTCTCATTTTATCTCTTGGATG
1 ATGCTCTTTAGTATGTCTAAGATGCAAGAAAAAATGTA-TTTTTTCTCATTTTATCTCTTGGACG
*
2334959 AAGTCTCATTCTTTGCTTGCTGGTCTTGTCCTTGGAATTGATCATGCCCCAACACTGACGGCTTC
65 AAGTCTCATTCTTTGCTTGCTGGTCTTGTCCTTGGAATTGATCATGCCCCAACACCGACGGCTTC
*
2335024 ATGGAAAATATCTAAGCTTTGCTCATTTGTTGGCTCAATCCAGTGAT
130 ATGGAAAATATCTAAGCTTTGCTCATTTGTTGGCTCAATCCAATGAT
2335071 CTTGCACTCT
Statistics
Matches: 166, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
213 56 0.34
214 110 0.66
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.39
Consensus pattern (212 bp):
ATGCTCTTTAGTATGTCTAAGATGCAAGAAAAAATGTATTTTTTCTCATTTTATCTCTTGGACGA
AGTCTCATTCTTTGCTTGCTGGTCTTGTCCTTGGAATTGATCATGCCCCAACACCGACGGCTTCA
TGGAAAATATCTAAGCTTTGCTCATTTGTTGGCTCAATCCAATGATGTATCAATTCTAATCTAAA
GATTCTTAAGCTCAGAT
Found at i:2338381 original size:18 final size:19
Alignment explanation
Indices: 2338354--2338390 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2338344 TGATAAAAAT
*
2338354 ACAAATAAAA-GAAATAAG
1 ACAAAAAAAAGGAAATAAG
2338372 ACAAAAAAAAGGAAATAAG
1 ACAAAAAAAAGGAAATAAG
2338391 TTAGTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.08
Consensus pattern (19 bp):
ACAAAAAAAAGGAAATAAG
Found at i:2339688 original size:21 final size:21
Alignment explanation
Indices: 2339662--2339740 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
2339652 AGGGTGTCAA
2339662 AGTGCATCCATGCACCTCTGC
1 AGTGCATCCATGCACCTCTGC
**
2339683 AGTGCATCCATGCACCTGCCAC
1 AGTGCATCCATGCACCT-CTGC
* * *
2339705 TAGTGCATCGATGCACC-ATGT
1 -AGTGCATCCATGCACCTCTGC
*
2339726 AGTGCATCCAAGCAC
1 AGTGCATCCATGCAC
2339741 TCCATTTCGA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 13 0.28
21 17 0.36
22 2 0.04
23 15 0.32
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCTCTGC
Found at i:2339785 original size:20 final size:20
Alignment explanation
Indices: 2339760--2339872 Score: 190
Period size: 20 Copynumber: 5.7 Consensus size: 20
2339750 AATGCAATTA
*
2339760 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTGCT
2339780 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
2339800 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
**
2339820 GTATATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
2339840 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
2339860 GTGCATCCATGCA
1 GTGCATCGATGCA
2339873 CCAAGGCTGC
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:2345191 original size:14 final size:15
Alignment explanation
Indices: 2345167--2345195 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2345157 AAATAAGAAA
2345167 GAAAGATAAAATATT
1 GAAAGATAAAATATT
2345182 GAAA-ATAAAATATT
1 GAAAGATAAAATATT
2345196 AATCTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (15 bp):
GAAAGATAAAATATT
Found at i:2345277 original size:2 final size:2
Alignment explanation
Indices: 2345270--2345304 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2345260 TTTCAAAGAT
2345270 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2345305 TCAAAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2345361 original size:20 final size:23
Alignment explanation
Indices: 2345313--2345371 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 23
2345303 ATTCAAAATA
*
2345313 ATATGTTTTCAAAAACTATATTAT
1 ATATGTTTTCAAAAAC-ATAGTAT
2345337 ATATGTTTTCAAAAAC-T-GT-T
1 ATATGTTTTCAAAAACATAGTAT
2345357 ATATGTTTTCAAAAA
1 ATATGTTTTCAAAAA
2345372 ATATTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 16 0.47
21 1 0.03
22 1 0.03
24 16 0.47
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (23 bp):
ATATGTTTTCAAAAACATAGTAT
Found at i:2348658 original size:54 final size:55
Alignment explanation
Indices: 2348599--2348705 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
2348589 TTACCGTATA
*
2348599 GCACTATACGTG-AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGG
1 GCACTATACGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGG
**
2348653 GCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 GCACTATACGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
2348706 TGGTAATGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 10 0.20
55 39 0.80
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (55 bp):
GCACTATACGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGG
Found at i:2350233 original size:2 final size:2
Alignment explanation
Indices: 2350226--2350257 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2350216 AACAGACCAA
2350226 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2350258 TAAGTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2352301 original size:22 final size:23
Alignment explanation
Indices: 2352256--2352313 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
2352246 GTAACCTCAA
2352256 GGGGTATCGATACCCACTCAAAG
1 GGGGTATCGATACCCACTCAAAG
* **
2352279 GGGGTATCGATGCCCA-TGTAAG
1 GGGGTATCGATACCCACTCAAAG
2352301 GGGG-ATCGATACC
1 GGGGTATCGATACC
2352314 TAGCCCAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 8 0.26
22 8 0.26
23 15 0.48
ACGTcount: A:0.26, C:0.22, G:0.33, T:0.19
Consensus pattern (23 bp):
GGGGTATCGATACCCACTCAAAG
Found at i:2356142 original size:21 final size:22
Alignment explanation
Indices: 2356118--2356160 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2356108 AAGACTATTT
2356118 TCATTTTTCA-ATTTT-AAAATA
1 TCATTTTT-ATATTTTGAAAATA
2356139 TCATTTTTATATTTTGAAAATA
1 TCATTTTTATATTTTGAAAATA
2356161 AAGTCTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.65
22 6 0.30
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (22 bp):
TCATTTTTATATTTTGAAAATA
Found at i:2360762 original size:23 final size:21
Alignment explanation
Indices: 2360732--2360793 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
2360722 GGTTATATGG
2360732 GTCCTTCGGGACATAGTACAT-AA
1 GTCCTTCGGGACATAG---ATGAA
*
2360755 GTCCTTCGGGACATAGATGAG
1 GTCCTTCGGGACATAGATGAA
2360776 GTCCTTCGGGACATAGAT
1 GTCCTTCGGGACATAGAT
2360794 TTCACATGCC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 2 0.05
21 19 0.51
23 16 0.43
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (21 bp):
GTCCTTCGGGACATAGATGAA
Found at i:2361218 original size:34 final size:34
Alignment explanation
Indices: 2361175--2361247 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
2361165 TGTGTGTTAG
2361175 AATTTTGCTTATGATTTTATATGCCTCACTAAGA
1 AATTTTGCTTATGATTTTATATGCCTCACTAAGA
2361209 AATTTTGCTTATGATTTTATATGCCTCACTAAGA
1 AATTTTGCTTATGATTTTATATGCCTCACTAAGA
2361243 AATTT
1 AATTT
2361248 CTTAGCGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (34 bp):
AATTTTGCTTATGATTTTATATGCCTCACTAAGA
Found at i:2367125 original size:40 final size:40
Alignment explanation
Indices: 2367081--2367161 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
2367071 TTTTTAAAAA
2367081 GTAGATTGTTATATAAATAGACACGAATAATATTGAACAT
1 GTAGATTGTTATATAAATAGACACGAATAATATTGAACAT
** *
2367121 GTAGATTGTTATATAAATAGACATTAATAGTATTGAACAT
1 GTAGATTGTTATATAAATAGACACGAATAATATTGAACAT
2367161 G
1 G
2367162 ACAGTCACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (40 bp):
GTAGATTGTTATATAAATAGACACGAATAATATTGAACAT
Found at i:2376035 original size:20 final size:21
Alignment explanation
Indices: 2375998--2376051 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
2375988 TTATTCAAGG
**
2375998 AGTATCGATACC-TAAAGGGT
1 AGTATCGATACCATAAAGGCA
*
2376018 AGTACCGATACCAT-AAGGCA
1 AGTATCGATACCATAAAGGCA
2376038 AGTATCGATACCAT
1 AGTATCGATACCAT
2376052 TTTGAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTATCGATACCATAAAGGCA
Found at i:2382607 original size:35 final size:32
Alignment explanation
Indices: 2382523--2382608 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 32
2382513 ATTGTGCAGG
* *
2382523 TAATAATACAAACTTACAATAAGTATTAAATGG
1 TAATAA-ACAAAATTACAATAAGTATTAAATGA
*
2382556 TAAGTGATAACCAAATTACAATAACTGATATTAAATGA
1 TAA-T-A-AACAAAATTACAATAA--G-TATTAAATGA
2382594 TAATAAACAAAATTA
1 TAATAAACAAAATTA
2382609 ACTGAAATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
33 3 0.07
34 1 0.02
35 23 0.53
36 2 0.05
37 2 0.05
38 12 0.28
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.29
Consensus pattern (32 bp):
TAATAAACAAAATTACAATAAGTATTAAATGA
Found at i:2384950 original size:25 final size:23
Alignment explanation
Indices: 2384917--2384970 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 23
2384907 TTTATATCTG
*
2384917 TAAAAAAATTAAATAAGTAAAATAT
1 TAAAAAAATTAAAT-A-CAAAATAT
*
2384942 TAAATAAATTAAATACAAAATAT
1 TAAAAAAATTAAATACAAAATAT
2384965 TAAAAA
1 TAAAAA
2384971 TATAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 12 0.46
24 1 0.04
25 13 0.50
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
TAAAAAAATTAAATACAAAATAT
Found at i:2385015 original size:10 final size:10
Alignment explanation
Indices: 2385002--2385041 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2384992 AGAGATTATA
*
2385002 AGAGTATTTG
1 AGAGAATTTG
*
2385012 AGAGAAGTTG
1 AGAGAATTTG
*
2385022 AGAGAAATTG
1 AGAGAATTTG
2385032 AGAGAATTTG
1 AGAGAATTTG
2385042 GTGTGATGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.28
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:2393131 original size:54 final size:54
Alignment explanation
Indices: 2393068--2393191 Score: 167
Period size: 54 Copynumber: 2.3 Consensus size: 54
2393058 CATGGTTTGC
*
2393068 ACACTTAGTGCCTATACGATCATTCATCAACATATGACAAATTCTGTGGGTTGT
1 ACACATAGTGCCTATACGATCATTCATCAACATATGACAAATTCTGTGGGTTGT
* * ** * **
2393122 ACACCTAGTGCCTATACGGTTGTTCATCAACGTATGATGAATTCTGTGGGTTGT
1 ACACATAGTGCCTATACGATCATTCATCAACATATGACAAATTCTGTGGGTTGT
*
2393176 ACACATAGTGCATATA
1 ACACATAGTGCCTATA
2393192 TACAATTGCA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (54 bp):
ACACATAGTGCCTATACGATCATTCATCAACATATGACAAATTCTGTGGGTTGT
Found at i:2398871 original size:54 final size:54
Alignment explanation
Indices: 2398809--2399096 Score: 353
Period size: 54 Copynumber: 5.3 Consensus size: 54
2398799 TTCTCTGGGG
* * * * * * *
2398809 GCACACTTAGTGCCGATATGGTCGTTCATAAACACATTATGAATTTTTTGGTTT
1 GCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTT
*
2398863 GCACACTTAGTGCCTATACGGTCATTCATCAACATATGATGAATTTTGTGGGTT
1 GCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTT
* * * **
2398917 GCACACCTAGTGCTTATACGGTCGTTCATCAATATATGATGAATTCCGTGGGTT
1 GCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTT
* * * * *
2398971 GCACACTTAGTGCCTATACGATTGTTTATCAACATAGGATGAATTCTGTGGGTT
1 GCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTT
* * *
2399025 GCACA-TATAGTGCCTATACGGTCGTTCATCAACATATGATAAAGTCTGTGGGTT
1 GCACACT-TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTT
* *
2399079 GCACACATATTGCCTATA
1 GCACACTTAGTGCCTATA
2399097 TACAATTGCA
Statistics
Matches: 202, Mismatches: 30, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
53 1 0.00
54 201 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (54 bp):
GCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTT
Found at i:2400929 original size:63 final size:65
Alignment explanation
Indices: 2400790--2400908 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 65
2400780 TTGTTCAAGG
* * **
2400790 TGTATCGATGCA-CAGGAAGTGCATCGATGCACTCTTTTAAAATACAAACATCGAATGCCATCAA
1 TGTATCGATGCATAAGGAAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGCCATCAA
* *
2400854 TGCATCGATGCATAAGG-AGTGCATCGATGCACCCCCTT-AAATATAAACATCGAAT
1 TGTATCGATGCATAAGGAAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAAT
2400909 AGGATTTATG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
63 16 0.33
64 29 0.60
65 3 0.06
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (65 bp):
TGTATCGATGCATAAGGAAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGCCATCAA
Found at i:2401611 original size:23 final size:23
Alignment explanation
Indices: 2401585--2401628 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2401575 GTACTACGGT
* *
2401585 GCAATTCTACGCGGTACTTCGTA
1 GCAATTCCACGCGGCACTTCGTA
*
2401608 GCAATTCCACGTGGCACTTCG
1 GCAATTCCACGCGGCACTTCG
2401629 GTGCGTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (23 bp):
GCAATTCCACGCGGCACTTCGTA
Found at i:2408270 original size:31 final size:30
Alignment explanation
Indices: 2408232--2408291 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
2408222 TTATATAAGC
2408232 TATGTGATAAA-GTGATGGAACATGATATGTT
1 TATGTGATAAAGGT-ATGGAA-ATGATATGTT
*
2408263 TATGTGATAAAGGTATGGAAATTATATGT
1 TATGTGATAAAGGTATGGAAATGATATGT
2408292 ATATACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 17 0.63
32 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATGATATGTT
Found at i:2408541 original size:23 final size:23
Alignment explanation
Indices: 2408515--2408573 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
2408505 AATCTTATAT
*
2408515 GGTACTACGGTGCAATTCTACGC
1 GGTACTTCGGTGCAATTCTACGC
*
2408538 GGTACTTC-GTAGCAATTCTACGT
1 GGTACTTCGGT-GCAATTCTACGC
*
2408561 GGCACTTCGGTGC
1 GGTACTTCGGTGC
2408574 GTTTATATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 2 0.06
23 27 0.87
24 2 0.06
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (23 bp):
GGTACTTCGGTGCAATTCTACGC
Found at i:2410010 original size:22 final size:22
Alignment explanation
Indices: 2409985--2410026 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2409975 AAGTGGCCAC
2409985 TCCCATAAGACCATTAACATCA
1 TCCCATAAGACCATTAACATCA
2410007 TCCCATAAGACCATTAACAT
1 TCCCATAAGACCATTAACAT
2410027 TTTGCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.31, G:0.05, T:0.24
Consensus pattern (22 bp):
TCCCATAAGACCATTAACATCA
Found at i:2411276 original size:2 final size:2
Alignment explanation
Indices: 2411269--2411299 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2411259 AGAAAAATCA
2411269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2411300 GATTTAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2414151 original size:20 final size:20
Alignment explanation
Indices: 2414090--2414154 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
2414080 ATAGTAAATA
* *
2414090 AGTATCGATACCAAAAGGTG
1 AGTATCGATACTAAAAGGTC
* * *
2414110 GGTATTGATACT--CAGGTC
1 AGTATCGATACTAAAAGGTC
*
2414128 AGTATCGATACTAAAAGGTT
1 AGTATCGATACTAAAAGGTC
2414148 AGTATCG
1 AGTATCG
2414155 GTACCAACGA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
18 14 0.41
20 20 0.59
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (20 bp):
AGTATCGATACTAAAAGGTC
Found at i:2416535 original size:3 final size:3
Alignment explanation
Indices: 2416527--2416589 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
2416517 TCTAGGTTTG
2416527 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2416575 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
2416590 ACAATTTAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2417527 original size:45 final size:45
Alignment explanation
Indices: 2417454--2417933 Score: 473
Period size: 45 Copynumber: 10.7 Consensus size: 45
2417444 AGTCAGGTTG
* * * * *
2417454 AAGAAAGACATCATTGAAAAG-TTAACTCCTCTCCGCGAGAAATTC
1 AAGAATGACATCACT-AAAAGATTGACTCCTCTTCGCGAGAAAGTC
**
2417499 AAGAATGACATCACTAAAAGATTGACTCCTCTTCATGAGAAAGTC
1 AAGAATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTC
* *
2417544 AAGAAGGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTC
1 AAGAATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTC
* * *
2417589 AAGAATGACATCATTGAAAGATTGACTCCTCTTCGTAC-A-AAAGTA
1 AAGAATGACATCACTAAAAGATTGACTCCTCTTCG--CGAGAAAGTC
* * * *
2417634 AAAAATGACATCACTAAAAGGTTGACTCCTCTTCGCAAGAAATTC
1 AAGAATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTC
* * ** * *
2417679 AATAATGACATCACTAAAAGGTTGACTTATCTTCACGACAAAGTC
1 AAGAATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTC
* * * * **
2417724 AATAATGACATCAGTGAAAGGTTGACTCCTCTTCATGAGAAAGTC
1 AAGAATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTC
* * * * * *
2417769 AATAATGACATCACTGAAAGGTTAACTCCACATT-GGGAGAAAGTC
1 AAGAATGACATCACTAAAAGATTGACTCCTC-TTCGCGAGAAAGTC
* * * * * * *
2417814 AAGAATGACATCACTAAAATATTGAATCCTCTCCGTGATAAATTT
1 AAGAATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTC
* * *
2417859 AAGAATGAAATCACTAAAATATCGACTCCTCTTCGCGAGAAAGTC
1 AAGAATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTC
* * *
2417904 AAGAAAGAAAACACTAAAAGATTGACTCCT
1 AAGAATGACATCACTAAAAGATTGACTCCT
2417934 TGTCATAAGA
Statistics
Matches: 366, Mismatches: 62, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
43 1 0.00
44 7 0.02
45 354 0.97
46 3 0.01
47 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (45 bp):
AAGAATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTC
Found at i:2418007 original size:37 final size:37
Alignment explanation
Indices: 2417966--2418168 Score: 146
Period size: 37 Copynumber: 5.6 Consensus size: 37
2417956 GGTTTCTAGG
* *
2417966 GAAACAATCCTGAGAAGAACTAAAATGAATTTATAGA
1 GAAACAATCCTAAGAAGGACTAAAATGAATTTATAGA
* ** * * *
2418003 GAAACAATACTAAGAAGGACTCTAACGAATTTCTAGT
1 GAAACAATCCTAAGAAGGACTAAAATGAATTTATAGA
* **
2418040 GAAACAATCCTAATAAGGACTAAAATGAATTTCCAGA
1 GAAACAATCCTAAGAAGGACTAAAATGAATTTATAGA
* * *** * *
2418077 TG-----ATCTTAAGAAGGATTCTGACGAATTTCTAGA
1 -GAAACAATCCTAAGAAGGACTAAAATGAATTTATAGA
** * *
2418110 GAAACGGTCCTAAGAAAGACTAAAATGAATTCATAGA
1 GAAACAATCCTAAGAAGGACTAAAATGAATTTATAGA
**
2418147 GAAATGATCCTAAGAAGGACTA
1 GAAACAATCCTAAGAAGGACTA
2418169 GAGTATGGTT
Statistics
Matches: 124, Mismatches: 36, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
32 1 0.01
33 23 0.19
37 99 0.80
38 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (37 bp):
GAAACAATCCTAAGAAGGACTAAAATGAATTTATAGA
Found at i:2418679 original size:24 final size:26
Alignment explanation
Indices: 2418617--2418679 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 26
2418607 TCAAAAGGTG
2418617 AAAA-GTTTGATG-AAGAAGTTTTGA
1 AAAATGTTTGATGAAAGAAGTTTTGA
2418641 AAATAT-TTT-ATGAAAGAA-TTTTGA
1 AAA-ATGTTTGATGAAAGAAGTTTTGA
2418665 AAAATGTTTGA-GAAA
1 AAAATGTTTGATGAAA
2418680 TGTTGACCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
23 2 0.06
24 22 0.65
25 10 0.29
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (26 bp):
AAAATGTTTGATGAAAGAAGTTTTGA
Found at i:2419824 original size:16 final size:16
Alignment explanation
Indices: 2419803--2419839 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
2419793 CCCAGTGTGG
2419803 AGGGTGATCTTTGGTT
1 AGGGTGATCTTTGGTT
2419819 AGGGTGATCTTTGGTT
1 AGGGTGATCTTTGGTT
2419835 AGGGT
1 AGGGT
2419840 TAGATCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.14, C:0.05, G:0.41, T:0.41
Consensus pattern (16 bp):
AGGGTGATCTTTGGTT
Found at i:2421992 original size:20 final size:20
Alignment explanation
Indices: 2421943--2421982 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2421933 CTACGGGAAA
2421943 TAAATTCACCACGACATCAT
1 TAAATTCACCACGACATCAT
2421963 TAAATTCACCACGACATCAT
1 TAAATTCACCACGACATCAT
2421983 AGCATTCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.05, T:0.25
Consensus pattern (20 bp):
TAAATTCACCACGACATCAT
Found at i:2423830 original size:2 final size:2
Alignment explanation
Indices: 2423823--2423851 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2423813 TGTTGTTTAT
2423823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2423852 TTTTGGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2425823 original size:29 final size:29
Alignment explanation
Indices: 2425790--2425847 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
2425780 TAATAATAAC
*
2425790 ACAATTCAATTTTAGTTTAATTAAAAAAA
1 ACAATTCAATTTTAGTGTAATTAAAAAAA
*
2425819 ACAATTCAATTTTAGTGTAATTGAAAAAA
1 ACAATTCAATTTTAGTGTAATTAAAAAAA
2425848 TTAATACAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (29 bp):
ACAATTCAATTTTAGTGTAATTAAAAAAA
Found at i:2433722 original size:59 final size:59
Alignment explanation
Indices: 2433648--2433775 Score: 213
Period size: 59 Copynumber: 2.2 Consensus size: 59
2433638 ATCGATCCAT
2433648 AGGAAATGTTAACCCCT-TGAGTGGGGTATTACTGATTCAAAATGTCGTGAATCGAGAAA
1 AGGAAATGTTAACCCCTCT-AGTGGGGTATTACTGATTCAAAATGTCGTGAATCGAGAAA
* * *
2433707 AGGAAATGTTAACCCCTCTTGTGGGGTATTACTGATTCAAAATGTCGTGAATTGAGCAA
1 AGGAAATGTTAACCCCTCTAGTGGGGTATTACTGATTCAAAATGTCGTGAATCGAGAAA
2433766 AGGAAATGTT
1 AGGAAATGTT
2433776 GAAAACATCC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
59 64 0.98
60 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (59 bp):
AGGAAATGTTAACCCCTCTAGTGGGGTATTACTGATTCAAAATGTCGTGAATCGAGAAA
Found at i:2434000 original size:284 final size:283
Alignment explanation
Indices: 2433409--2434056 Score: 838
Period size: 284 Copynumber: 2.3 Consensus size: 283
2433399 CGAAGTGATG
* * * *
2433409 TGAATCAAGCAAATGAAATGTGAACCCCTCTGGTGGGGCATTGCTGATTCGAAATGTTGTGAATC
1 TGAATCGAGCAAA-GAAATGTTAACCCCTCTTGTGGGGCATTGCTGATTCGAAATGTCGTGAATC
* * * * *
2433474 GAGAAAAGGAAACGTTGAAAATATCCTGCTTGAAGGTCTTATGGATGACCCAAAGGACTTATCGA
65 GAGCAAAGGAAATGTTGAAAACATCCTGCCTGAAGGACTTATGGATGACCCAAAGGACTTATCGA
* *
2433539 TTGCTTGAGAGACTTATAGGAGACCCGAAGAATTTAAGCATCATGCTCGAAAGAATTACTGATGG
130 TTGCTTGAAAGACTTATAGGAGACCCGAAGAATTTAAGCATCATGCTCCAAAGAATTACTGA--G
* * * *
2433604 CCCAAAGGACTTAAGCTGATTCGAAGTGTTGTGAATCGATCCATAGGAAATGTTAACCCCTTGAG
193 CCCAAAGGACTTAAGCTGACTCAAAGTGTTGTGAATCGAGCCATAGAAAATGTTAACCCCTTGAG
* * * *
2433669 TGGGGTATTACTGATTCAAAATGTCG
258 TGAGGAATTACTAATTCAAAATGTCA
* * * * *
2433695 TGAATCGAGAAAAGGAAATGTTAACCCCTCTTGTGGGGTATTACTGATTCAAAATGTCGTGAATT
1 TGAATCGAGCAAA-GAAATGTTAACCCCTCTTGTGGGGCATTGCTGATTCGAAATGTCGTGAATC
* *
2433760 GAGCAAAGGAAATGTTGAAAACATCCTGCCTGAAGGACTTATGGATGGCTCAAAGGACTTATC-A
65 GAGCAAAGGAAATGTTGAAAACATCCTGCCTGAAGGACTTATGGATGACCCAAAGGACTTATCGA
* * * * *
2433824 TCTTGCTTGAAATATTTATA-GATGACCCGAAGGATTTAAGCATCATGTTCCAAAGACTTACTGA
130 --TTGCTTGAAAGACTTATAGGA-GACCCGAAGAATTTAAGCATCATGCTCCAAAGAATTACTGA
* * *
2433888 -CCCGAAGGACTTAAGCTGACTCAAATTGTTGTGAATCGAGCCTTAGAAAATGTTAACCCCTTTG
192 GCCCAAAGGACTTAAGCTGACTCAAAGTGTTGTGAATCGAGCCATAGAAAATGTTAACCCC-TTG
*
2433952 -GTGAGGAATTGCTAATTCAAAATGTCA
256 AGTGAGGAATTACTAATTCAAAATGTCA
*
2433979 TGAATCGAGCAAAGAAAATGTTAACCCCTC-TGATGGGGCATTGCTGATTCGAAATGCCGTGAAT
1 TGAATCGAGCAAAG-AAATGTTAACCCCTCTTG-TGGGGCATTGCTGATTCGAAATGTCGTGAAT
*
2434043 CGAGCAAATGAAAT
64 CGAGCAAAGGAAAT
2434057 ATTAACCCCT
Statistics
Matches: 313, Mismatches: 43, Indels: 14
0.85 0.12 0.04
Matches are distributed among these distances:
283 3 0.01
284 141 0.45
285 4 0.01
286 113 0.36
287 52 0.17
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (283 bp):
TGAATCGAGCAAAGAAATGTTAACCCCTCTTGTGGGGCATTGCTGATTCGAAATGTCGTGAATCG
AGCAAAGGAAATGTTGAAAACATCCTGCCTGAAGGACTTATGGATGACCCAAAGGACTTATCGAT
TGCTTGAAAGACTTATAGGAGACCCGAAGAATTTAAGCATCATGCTCCAAAGAATTACTGAGCCC
AAAGGACTTAAGCTGACTCAAAGTGTTGTGAATCGAGCCATAGAAAATGTTAACCCCTTGAGTGA
GGAATTACTAATTCAAAATGTCA
Found at i:2434005 original size:59 final size:59
Alignment explanation
Indices: 2433932--2434068 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 59
2433922 ATCGAGCCTT
* * *
2433932 AGAAAATGTTAACCCCTTTGGTGAGGAATTGCTAATTCAAAATGTCATGAATCGAGCAA
1 AGAAAATGTTAACCCCTCTGATGAGGAATTGCTAATTCAAAATGCCATGAATCGAGCAA
* * * * *
2433991 AGAAAATGTTAACCCCTCTGATGGGGCATTGCTGATTCGAAATGCCGTGAATCGAGCAA
1 AGAAAATGTTAACCCCTCTGATGAGGAATTGCTAATTCAAAATGCCATGAATCGAGCAA
*
2434050 ATG-AAATATTAACCCCTCT
1 A-GAAAATGTTAACCCCTCT
2434069 TGTGGGTCGT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 67 0.99
60 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Consensus pattern (59 bp):
AGAAAATGTTAACCCCTCTGATGAGGAATTGCTAATTCAAAATGCCATGAATCGAGCAA
Found at i:2434086 original size:59 final size:58
Alignment explanation
Indices: 2433966--2434120 Score: 150
Period size: 59 Copynumber: 2.6 Consensus size: 58
2433956 GGAATTGCTA
* * * **
2433966 ATTCAAAATGTCATGAATCGAGCAAAGAAAATGTTAACCCCTCTGATGGGGCATTGCTG
1 ATTCGAAATGCCATGAATCGAGCAAAG-AAATATTAACCCCTCTGATGGGGCATAACTG
* * * *
2434025 ATTCGAAATGCCGTGAATCGAGCAAATGAAATATTAACCCCTCTTG-TGGGTCGTAATTG
1 ATTCGAAATGCCATGAATCGAGCAAA-GAAATATTAACCCCTC-TGATGGGGCATAACTG
* * * *
2434084 ATTCGAAATGTCATGAATCAAGTGAAGGAAATATTAA
1 ATTCGAAATGCCATGAATCGAG-CAAAGAAATATTAA
2434121 AAACACCTTG
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
59 74 0.94
60 5 0.06
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (58 bp):
ATTCGAAATGCCATGAATCGAGCAAAGAAATATTAACCCCTCTGATGGGGCATAACTG
Found at i:2434232 original size:42 final size:41
Alignment explanation
Indices: 2434139--2434252 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 41
2434129 TGCACGAAGT
* * * * *
2434139 CTTATGGATGGCCTGAAAGACTTATCATCTTACTCGAAAGG
1 CTTATAGATGGCCCGAAGGACTTATCATCATACTCGAAAGA
*
2434180 CTTATAGATGGCCCGAAGGACTTATGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTAT-CATCATACTCGAAAGA
* * *
2434222 CTT-TCTGATGGCCCAAAGGATTTACTCATCA
1 CTTAT-AGATGGCCCGAAGGACTTA-TCATCA
2434253 AAGAAACCCT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 23 0.38
42 37 0.61
43 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATACTCGAAAGA
Found at i:2434303 original size:34 final size:35
Alignment explanation
Indices: 2434247--2434312 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 35
2434237 AAGGATTTAC
* *
2434247 TCATCAAAGAAACCCTTGAAAATCAAGCTTAGTTA
1 TCATCAAAGAAACCCCTAAAAATCAAGCTTAGTTA
* *
2434282 TCATC-AAGAAACCCCTAAAAATTAGGCTTAG
1 TCATCAAAGAAACCCCTAAAAATCAAGCTTAG
2434313 CTTCTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 22 0.81
35 5 0.19
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.24
Consensus pattern (35 bp):
TCATCAAAGAAACCCCTAAAAATCAAGCTTAGTTA
Found at i:2434979 original size:36 final size:36
Alignment explanation
Indices: 2434932--2435002 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
2434922 AGTGCTTCCT
**
2434932 CTCTTGAATTCTTGTTGTGATCAGGTAGATGACTGG
1 CTCTTGAATTCTTGTTGCAATCAGGTAGATGACTGG
2434968 CTCTTGAATTCTTGTTGCAATCAGGTAGATGACTG
1 CTCTTGAATTCTTGTTGCAATCAGGTAGATGACTG
2435003 AGCACCTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.38
Consensus pattern (36 bp):
CTCTTGAATTCTTGTTGCAATCAGGTAGATGACTGG
Found at i:2436519 original size:8 final size:7
Alignment explanation
Indices: 2436508--2436594 Score: 69
Period size: 6 Copynumber: 12.3 Consensus size: 7
2436498 GACTTTTTAC
2436508 TTCTTTAT
1 TTCTTT-T
2436516 TTCTTGTTT
1 TTC-T-TTT
2436525 TTCTTTT
1 TTCTTTT
2436532 TT-TTTT
1 TTCTTTT
2436538 TTC--TT
1 TTCTTTT
2436543 TTC-TTT
1 TTCTTTT
2436549 TTC-TTT
1 TTCTTTT
2436555 TTCTTGTTT
1 TTC-T-TTT
2436564 TTCTTTT
1 TTCTTTT
2436571 TT-TTTCT
1 TTCTTT-T
2436578 TTCTTTT
1 TTCTTTT
2436585 TATCTTTT
1 T-TCTTTT
2436593 TT
1 TT
2436595 TACTATATAT
Statistics
Matches: 69, Mismatches: 0, Indels: 21
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.07
6 20 0.29
7 16 0.23
8 15 0.22
9 11 0.16
10 2 0.03
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (7 bp):
TTCTTTT
Found at i:2436529 original size:9 final size:8
Alignment explanation
Indices: 2436508--2436595 Score: 71
Period size: 8 Copynumber: 11.2 Consensus size: 8
2436498 GACTTTTTAC
*
2436508 TTCTTTAT
1 TTCTTTTT
2436516 TTCTTGTTT
1 TTCTT-TTT
2436525 TTC--TTT
1 TTCTTTTT
2436531 TT-TTTTT
1 TTCTTTTT
2436538 TTCTTTTCT
1 TTCTTTT-T
2436547 TT-TTCTTT
1 TTCTT-TTT
2436555 TTCTTGTTT
1 TTCTT-TTT
2436564 TTC-TTTT
1 TTCTTTTT
*
2436571 TT-TTTCT
1 TTCTTTTT
2436578 TTCTTTTT
1 TTCTTTTT
*
2436586 ATCTTTTT
1 TTCTTTTT
2436594 TT
1 TT
2436596 ACTATATATT
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
6 5 0.08
7 15 0.23
8 27 0.42
9 18 0.28
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (8 bp):
TTCTTTTT
Found at i:2436542 original size:30 final size:29
Alignment explanation
Indices: 2436508--2436595 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 29
2436498 GACTTTTTAC
2436508 TTCTTTATTTCTTGTTTTTCTTTTTTT-TTT
1 TTCTTT-TTTCTT-TTTTTCTTTTTTTCTTT
*
2436538 TTCTTTTCTTTTTCTTTTTCTTGTTTTTCTTT
1 TTCTTTT-TTCTT-TTTTTCTT-TTTTTCTTT
* *
2436570 TTTTTTCTTTCTTTTTATCTTTTTTT
1 TTCTTT-TTTCTTTTTTTCTTTTTTT
2436596 ACTATATATT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
29 1 0.02
30 23 0.47
31 12 0.24
32 12 0.24
33 1 0.02
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (29 bp):
TTCTTTTTTCTTTTTTTCTTTTTTTCTTT
Found at i:2436584 original size:20 final size:19
Alignment explanation
Indices: 2436522--2436595 Score: 87
Period size: 21 Copynumber: 3.7 Consensus size: 19
2436512 TTATTTCTTG
2436522 TTTTTCTTTTTTTTTTTTC
1 TTTTTCTTTTTTTTTTTTC
*
2436541 -TTTTCTTTTTCTTTTTCTTG
1 TTTTTCTTTTT-TTTTT-TTC
2436561 TTTTTCTTTTTTTTTCTTTC
1 TTTTTCTTTTTTTTT-TTTC
2436581 TTTTTATCTTTTTTT
1 -TTTT-TCTTTTTTT
2436596 ACTATATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
18 10 0.21
19 5 0.11
20 8 0.17
21 15 0.32
22 9 0.19
ACGTcount: A:0.01, C:0.12, G:0.01, T:0.85
Consensus pattern (19 bp):
TTTTTCTTTTTTTTTTTTC
Found at i:2436595 original size:39 final size:38
Alignment explanation
Indices: 2436500--2436595 Score: 122
Period size: 39 Copynumber: 2.4 Consensus size: 38
2436490 ATTTGATCGA
*
2436500 CTTTTTACTTCTTTATTTCTTGTTTTTCTTTTTTTTTTTT
1 CTTTTTA--TCTTTTTTTCTTGTTTTTCTTTTTTTTTTTT
*
2436540 CTTTTCT-TTTTCTTTTTCTTGTTTTTCTTTTTTTTTCTTT
1 CTTTT-TATCTT-TTTTTCTTGTTTTTCTTTTTTTTT-TTT
2436580 CTTTTTATCTTTTTTT
1 CTTTTTATCTTTTTTT
2436596 ACTATATATT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
38 3 0.06
39 29 0.59
40 16 0.33
41 1 0.02
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (38 bp):
CTTTTTATCTTTTTTTCTTGTTTTTCTTTTTTTTTTTT
Found at i:2443234 original size:34 final size:34
Alignment explanation
Indices: 2443187--2443252 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
2443177 ACTATGAAAC
** *
2443187 AAAACAATTAATAA-TAAACTTAATTAAAATAATT
1 AAAACAACAAATAATTAAA-TTAATAAAAATAATT
*
2443221 AAAACAACAAATAATTAAATTAGTAAAAATAA
1 AAAACAACAAATAATTAAATTAATAAAAATAA
2443253 AATAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 23 0.85
35 4 0.15
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (34 bp):
AAAACAACAAATAATTAAATTAATAAAAATAATT
Found at i:2443269 original size:12 final size:11
Alignment explanation
Indices: 2443244--2443299 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
2443234 ATTAAATTAG
2443244 TAAAAATAAAA
1 TAAAAATAAAA
2443255 TAAAAATAAACA
1 TAAAAATAAA-A
*
2443267 TAAACATAAAA
1 TAAAAATAAAA
* *
2443278 -AAGGAATAAAT
1 TAA-AAATAAAA
*
2443289 TAAACATAAAA
1 TAAAAATAAAA
2443300 AGGGGCTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 2 0.06
11 21 0.60
12 12 0.34
ACGTcount: A:0.73, C:0.05, G:0.04, T:0.18
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:2443301 original size:21 final size:22
Alignment explanation
Indices: 2443267--2443319 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
2443257 AAAATAAACA
*
2443267 TAAACATAAAAAAGGAATAAAT
1 TAAACATAAAAAGGGAATAAAT
**
2443289 TAAACATAAAAAGGGGCTAAAT
1 TAAACATAAAAAGGGAATAAAT
2443311 TAAA-ATAAA
1 TAAACATAAA
2443320 TTAAAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.64, C:0.06, G:0.11, T:0.19
Consensus pattern (22 bp):
TAAACATAAAAAGGGAATAAAT
Found at i:2446211 original size:33 final size:32
Alignment explanation
Indices: 2446147--2446228 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 32
2446137 GAATTGAAAC
* *
2446147 TGAAATTAACCCGAACCAAAAGTAATCCGAAT
1 TGAAATTAACCCAAACCAAAAGCAATCCGAAT
2446179 TGAAATTAACCCTAAACCAAAAGCAA-CTCGAAT
1 TGAAATTAACCC-AAACCAAAAGCAATC-CGAAT
*
2446212 TGAAATTAACCCGAACC
1 TGAAATTAACCCAAACC
2446229 GAATTTTAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
32 17 0.38
33 28 0.62
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.18
Consensus pattern (32 bp):
TGAAATTAACCCAAACCAAAAGCAATCCGAAT
Found at i:2455507 original size:14 final size:14
Alignment explanation
Indices: 2455488--2455520 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2455478 ATAGCAAAAA
*
2455488 AAATAAAAATATTT
1 AAATAAAAATAATT
2455502 AAAT-AAAATAATT
1 AAATAAAAATAATT
2455515 AAATAA
1 AAATAA
2455521 TTAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAAAAATAATT
Found at i:2455509 original size:21 final size:21
Alignment explanation
Indices: 2455484--2455550 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
2455474 TATAATAGCA
* *
2455484 AAAAAAATAAAAATATTTAAAT
1 AAAATAAT-AAAATAATTAAAT
*
2455506 AAAATAATTAAATAATTAAAT
1 AAAATAATAAAATAATTAAAT
* *
2455527 AAAATACTAACAAAATATTAAAT
1 AAAATAATAA-AATA-ATTAAAT
2455550 A
1 A
2455551 TAACAAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 19 0.51
22 10 0.27
23 8 0.22
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATAATAAAATAATTAAAT
Found at i:2455556 original size:17 final size:18
Alignment explanation
Indices: 2455528--2455561 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2455518 TAATTAAATA
2455528 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
2455546 AAATA-TAACAAAATAT
1 AAATACTAACAAAATAT
2455562 ACCTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:2461889 original size:21 final size:21
Alignment explanation
Indices: 2461861--2461907 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
2461851 ATTAATAAGC
*
2461861 TAAAAAAGGAATAAATTAAACA
1 TAAAAAGGGAATAAATTAAA-A
**
2461883 TAAAAAGGGGCTAAATTAAAA
1 TAAAAAGGGAATAAATTAAAA
2461904 TAAA
1 TAAA
2461908 TTAAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.64, C:0.04, G:0.13, T:0.19
Consensus pattern (21 bp):
TAAAAAGGGAATAAATTAAAA
Found at i:2464783 original size:32 final size:32
Alignment explanation
Indices: 2464747--2464828 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 32
2464737 GAATTGAAAC
*
2464747 TGAAATTAACCCGAACCAAAAGTAA-TCTGAAT
1 TGAAATTAACCCGAACCAAAAGCAACTC-GAAT
*
2464779 TGAAATTAACCCTAAACCAAAAGCAACTCGAAT
1 TGAAATTAACCC-GAACCAAAAGCAACTCGAAT
*
2464812 TAAAATTAACCCGAACC
1 TGAAATTAACCCGAACC
2464829 GAATTTTAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
32 16 0.36
33 26 0.59
34 2 0.05
ACGTcount: A:0.48, C:0.23, G:0.10, T:0.20
Consensus pattern (32 bp):
TGAAATTAACCCGAACCAAAAGCAACTCGAAT
Found at i:2464986 original size:19 final size:18
Alignment explanation
Indices: 2464931--2464986 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
2464921 ATTAATAATT
*
2464931 TAATTTA-AATAAAATTGA
1 TAATTTATAATAAAA-TAA
* *
2464949 TAATTTATTA-AAAACAA
1 TAATTTATAATAAAATAA
2464966 TATATTTATAATAAAATAA
1 TA-ATTTATAATAAAATAA
2464985 TA
1 TA
2464987 GAAAGTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 3 0.10
18 18 0.60
19 9 0.30
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
TAATTTATAATAAAATAA
Found at i:2469974 original size:18 final size:17
Alignment explanation
Indices: 2469935--2469977 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2469925 ATTATATGGA
2469935 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
2469951 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
2469969 TATTATTAT
1 TATTATTAT
2469978 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:2470494 original size:38 final size:40
Alignment explanation
Indices: 2470443--2470521 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
2470433 AGTGAGAGGG
*
2470443 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
2470481 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
2470521 T
1 T
2470522 TTTTTAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 12 0.33
39 7 0.19
40 17 0.47
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:2470597 original size:13 final size:13
Alignment explanation
Indices: 2470576--2470644 Score: 68
Period size: 13 Copynumber: 5.2 Consensus size: 13
2470566 ATTTTTTTCC
*
2470576 TTATCTTATTTAT
1 TTATTTTATTTAT
2470589 TTATTTTATTTATT
1 TTATTTTATTTA-T
*
2470603 TTATTTT-TTTCTT
1 TTATTTTATTT-AT
*
2470616 TTATTTTATTCTCT
1 TTATTTTATT-TAT
*
2470630 TTATCTTATTTAT
1 TTATTTTATTTAT
2470643 TT
1 TT
2470645 TCTTTACCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
13 26 0.55
14 20 0.43
15 1 0.02
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:2470601 original size:22 final size:22
Alignment explanation
Indices: 2470576--2470621 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2470566 ATTTTTTTCC
2470576 TTATCTTATTTATTTATTTTAT
1 TTATCTTATTTATTTATTTTAT
* * *
2470598 TTATTTTATTTTTTTCTTTTAT
1 TTATCTTATTTATTTATTTTAT
2470620 TT
1 TT
2470622 TATTCTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (22 bp):
TTATCTTATTTATTTATTTTAT
Found at i:2470641 original size:18 final size:17
Alignment explanation
Indices: 2470553--2470660 Score: 69
Period size: 18 Copynumber: 6.2 Consensus size: 17
2470543 CTATATATAA
*
2470553 TTATTACTTTA-C-TAT
1 TTATTTCTTTATCTTAT
* *
2470568 TTTTTTCCTTATCTTAT
1 TTATTTCTTTATCTTAT
*
2470585 TTATTTATTTTAT-TTATT
1 TTATTT-CTTTATCTTA-T
* * *
2470603 TTATTTTTTTCTTTTATT
1 TTATTTCTTTATCTTA-T
2470621 TTATTCTCTTTATCTTAT
1 TTATT-TCTTTATCTTAT
* *
2470639 TTATTTTCTTTACCTTGT
1 TTA-TTTCTTTATCTTAT
2470657 TTAT
1 TTAT
2470661 CTAACACATT
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
15 8 0.11
16 1 0.01
17 17 0.23
18 38 0.51
19 10 0.14
ACGTcount: A:0.17, C:0.11, G:0.01, T:0.71
Consensus pattern (17 bp):
TTATTTCTTTATCTTAT
Found at i:2470650 original size:9 final size:9
Alignment explanation
Indices: 2470584--2470625 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
2470574 CCTTATCTTA
2470584 TTTATTTAT
1 TTTATTTAT
2470593 TTTATTTAT
1 TTTATTTAT
2470602 TTTATTT-T
1 TTTATTTAT
*
2470610 TTTCTTTTAT
1 TTT-ATTTAT
2470620 TTTATT
1 TTTATT
2470626 CTCTTTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 4 0.14
9 21 0.72
10 4 0.14
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTAT
Found at i:2474982 original size:18 final size:18
Alignment explanation
Indices: 2474936--2474992 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
2474926 AGATTCAATC
2474936 AAGAACAAAA-AACAAAAG
1 AAGAACAAAAGAA-AAAAG
*
2474954 AAGCAAC-AAAGAAAAAAT
1 AAG-AACAAAAGAAAAAAG
*
2474972 AAGAACAAAAGAGAAAAG
1 AAGAACAAAAGAAAAAAG
2474990 AAG
1 AAG
2474993 CAAAAATCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.09
18 25 0.76
19 5 0.15
ACGTcount: A:0.74, C:0.09, G:0.16, T:0.02
Consensus pattern (18 bp):
AAGAACAAAAGAAAAAAG
Found at i:2476654 original size:36 final size:36
Alignment explanation
Indices: 2476607--2476681 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
2476597 GTGCTCACCA
*
2476607 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-CT
1 TTGTCTCTCTTGAGACAGTTTCCCTT-AAAAAAACCT
2476643 TTGTCTCTCTTGAGACAGTTTCCCTTAAAAAAACCT
1 TTGTCTCTCTTGAGACAGTTTCCCTTAAAAAAACCT
2476679 TTG
1 TTG
2476682 AAATTGTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
35 6 0.16
36 31 0.84
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.37
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTAAAAAAACCT
Found at i:2476923 original size:37 final size:37
Alignment explanation
Indices: 2476853--2476924 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
2476843 TGGAACTAAG
* * *
2476853 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* * *
2476890 TTTTGTCTCCCTTGATACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAA
2476925 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:2477705 original size:106 final size:106
Alignment explanation
Indices: 2477539--2478079 Score: 724
Period size: 106 Copynumber: 5.1 Consensus size: 106
2477529 ATATCGTGTC
*
2477539 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAGCAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * *
2477604 AAATTCAGAGCCAATTTCAACTTCACAACGAATGATATTTG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
2477645 ACTCGAGATAACACAAGTTCAACTTCACAACAAAGGGATGGCTGATTGTCACCAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * * *
2477710 AATTTTAAAACCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2477751 ACTCAAGACAACACAAGTTCAACTTCACAAAGAAGGGACGGCTGGTTGTCAACAAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCC
* *
2477816 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
2477858 ACTCAAGACGACACAAGTTCAAATTCACAATGAAGGGACGACTAGTTGTCAATAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
2477923 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * ** * * *
2477964 ACTCGAGACAATAAAACCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * * * *
2478029 AGTTCCGGAGCCAATTTCAACTTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
2478070 ACTCGA-ACAA
1 ACTCGAGACAA
2478080 TACTACTCAC
Statistics
Matches: 381, Mismatches: 53, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
105 4 0.01
106 281 0.74
107 96 0.25
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:2477917 original size:213 final size:212
Alignment explanation
Indices: 2477539--2478073 Score: 741
Period size: 213 Copynumber: 2.5 Consensus size: 212
2477529 ATATCGTGTC
*
2477539 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAGCAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
** * * * * * *
2477604 AAATTCAGAGCCAATTTCAACTTCACAACGAATGATATTTGACTCGAGATAACACAAGTTCAACT
66 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAAAT
* * * *
2477669 TCACAACAAAGGGATGGCTGATTGTCACCAAACAATTTCCCAATTTTAAAACCAATTTCAACTTC
131 TCACAACAAAGGGACGACTGATTGTCAACAAACAATTTCCCAATTTCAAAACCAATTTCAACTTC
*
2477734 ACAGCGAAGGATATTGG
196 ACAGCGAAGGATATTGA
* *
2477751 ACTCAAGACAACACAAGTTCAACTTCACAAAGAAGGGACGGCTGGTTGTCAACAAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCC
*
2477816 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACGACACAAGTTCAAA
65 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAAA
** * * *
2477881 TTCACAATGAAGGGACGACT-AGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACT
130 TTCACAACAAAGGGACGACTGA-TTGTCAACAAACAATTTCCCAATTTCAAAACCAATTTCAACT
2477945 TCACAGCGAAGGATATTGA
194 TCACAGCGAAGGATATTGA
* * ** * * *
2477964 ACTCGAGACAATAAAACCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * *
2478029 AGTTCCGGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
66 AGTTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
2478074 GAACAATACT
Statistics
Matches: 286, Mismatches: 34, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
211 1 0.00
212 104 0.36
213 181 0.63
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (212 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAAAT
TCACAACAAAGGGACGACTGATTGTCAACAAACAATTTCCCAATTTCAAAACCAATTTCAACTTC
ACAGCGAAGGATATTGA
Found at i:2479402 original size:18 final size:17
Alignment explanation
Indices: 2479363--2479405 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2479353 ATTATATGGA
2479363 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
2479379 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
2479397 TATTATTAT
1 TATTATTAT
2479406 ACGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:2479459 original size:2 final size:2
Alignment explanation
Indices: 2479454--2479478 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2479444 TATATTTTAT
2479454 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2479479 GTTTCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2479933 original size:38 final size:40
Alignment explanation
Indices: 2479882--2479960 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
2479872 AGTGAGAGGG
*
2479882 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
2479920 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
2479960 T
1 T
2479961 TTTTTTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 12 0.33
39 7 0.19
40 17 0.47
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:2480037 original size:9 final size:9
Alignment explanation
Indices: 2480025--2480049 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2480015 CCTTATCTTA
2480025 TTTATTTAT
1 TTTATTTAT
2480034 TTTATTTAT
1 TTTATTTAT
2480043 TTTATTT
1 TTTATTT
2480050 TTTCCCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTAT
Found at i:2484826 original size:17 final size:18
Alignment explanation
Indices: 2484798--2484831 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2484788 TAATTAAATA
2484798 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
2484816 AAATA-TAACAAAATAT
1 AAATACTAACAAAATAT
2484832 ACCTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:2489440 original size:20 final size:20
Alignment explanation
Indices: 2489394--2489434 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2489384 AAAATTAAAC
2489394 ATCATTTTGATCTTTAACTA
1 ATCATTTTGATCTTTAACTA
2489414 ATCATTTTGATCTTTAACTA
1 ATCATTTTGATCTTTAACTA
2489434 A
1 A
2489435 GTATTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.49
Consensus pattern (20 bp):
ATCATTTTGATCTTTAACTA
Found at i:2489755 original size:20 final size:20
Alignment explanation
Indices: 2489730--2489767 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2489720 ACACTTATAT
*
2489730 AATTTCAATTTTTCTTTTAG
1 AATTTCAATTCTTCTTTTAG
2489750 AATTTCAATTCTTCTTTT
1 AATTTCAATTCTTCTTTT
2489768 TGATAACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.13, G:0.03, T:0.61
Consensus pattern (20 bp):
AATTTCAATTCTTCTTTTAG
Done.