Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009331.1 Hibiscus syriacus cultivar Beakdansim tig00113098_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: 375911
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:260251 original size:24 final size:24
Alignment explanation
Indices: 260223--260309 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
260213 GAATGTTTTA
* *
260223 TCTGATTTCCGATTTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* *
260247 TCTGATTTCTAATATGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* * *
260271 TCTAATATATGATATGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
260295 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
260310 CTCCGTTTAT
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:261614 original size:71 final size:71
Alignment explanation
Indices: 261539--261758 Score: 163
Period size: 71 Copynumber: 3.1 Consensus size: 71
261529 ATTGATATTA
261539 ATTTTAAGTAACCCATTAAATTTATGAATACTCGTCAAAGGTAAATAGTTTGGATCGAACATAAA
1 ATTTTAAGTAACCCATTAAATTTATGAATACTCGTCAAAGGTAAATAGTTTGGATCGAACATAAA
261604 TGTTAT
66 TGTTAT
** * * * * *
261610 ATTTTTTATTTAA---ATTTATATTTTTGTAAT--TAAGAT-AACCGGGT-AATCA-ATT-GATA
1 A--TTTTAAGTAACCCA-TTAAATTTATG-AATACT-CG-TCAA--AGGTAAAT-AGTTTGGAT-
** *
261666 CTGAAACATTGATATTA-
56 C-G-AACATAAATGTTAT
*
261683 ATTTTAAGGAACCCATTAAATTTATGAATACTCGTCAAAGGTAAATAGTTTGGATCGAACATAAA
1 ATTTTAAGTAACCCATTAAATTTATGAATACTCGTCAAAGGTAAATAGTTTGGATCGAACATAAA
261748 TGTTAT
66 TGTTAT
261754 ATTTT
1 ATTTT
261759 TTATTTAAAT
Statistics
Matches: 106, Mismatches: 21, Indels: 44
0.62 0.12 0.26
Matches are distributed among these distances:
70 12 0.11
71 33 0.31
72 20 0.19
73 29 0.27
74 12 0.11
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (71 bp):
ATTTTAAGTAACCCATTAAATTTATGAATACTCGTCAAAGGTAAATAGTTTGGATCGAACATAAA
TGTTAT
Found at i:261642 original size:20 final size:20
Alignment explanation
Indices: 261600--261642 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
261590 GGATCGAACA
*
261600 TAAATGTTATATTTTTTATT
1 TAAATGTTATATTTTTTAAT
261620 TAAAT-TTATATTTTTGTAAT
1 TAAATGTTATATTTTT-TAAT
261640 TAA
1 TAA
261643 GATAACCGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TAAATGTTATATTTTTTAAT
Found at i:261655 original size:73 final size:73
Alignment explanation
Indices: 261578--261799 Score: 171
Period size: 73 Copynumber: 3.1 Consensus size: 73
261568 ACTCGTCAAA
261578 GGTAAATAGTTTGGATCGAACATAAATGTTATATTTTTTATTTAAATTTATATTTTTGTAATTAA
1 GGTAAATAGTTTGGATCGAACATAAATGTTATATTTTTTATTTAAATTTATATTTTTGTAATTAA
261643 GATAACCG
66 GATAACCG
* ** * *** * *
261651 GGT-AATCA-ATT-GATACTGAAACATTGATATTA-A--TTTTAAGGAACCCA-TTAAATTTATG
1 GGTAAAT-AGTTTGGAT-C-G-AACATAAATGTTATATTTTTTATTTAA---ATTTATATTTTTG
* *
261709 -AA-TACTCG-TCAA--A
59 TAATTA--AGAT-AACCG
261722 GGTAAATAGTTTGGATCGAACATAAATGTTATATTTTTTATTTAAATTTATATTTTTGTAATTAA
1 GGTAAATAGTTTGGATCGAACATAAATGTTATATTTTTTATTTAAATTTATATTTTTGTAATTAA
261787 GATAACCG
66 GATAACCG
261795 GGTAA
1 GGTAA
261800 TCAATTGATA
Statistics
Matches: 105, Mismatches: 22, Indels: 44
0.61 0.13 0.26
Matches are distributed among these distances:
70 11 0.10
71 30 0.29
72 18 0.17
73 35 0.33
74 11 0.10
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (73 bp):
GGTAAATAGTTTGGATCGAACATAAATGTTATATTTTTTATTTAAATTTATATTTTTGTAATTAA
GATAACCG
Found at i:261786 original size:20 final size:20
Alignment explanation
Indices: 261744--261786 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
261734 GGATCGAACA
*
261744 TAAATGTTATATTTTTTATT
1 TAAATGTTATATTTTTTAAT
261764 TAAAT-TTATATTTTTGTAAT
1 TAAATGTTATATTTTT-TAAT
261784 TAA
1 TAA
261787 GATAACCGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TAAATGTTATATTTTTTAAT
Found at i:261786 original size:144 final size:144
Alignment explanation
Indices: 261526--261815 Score: 571
Period size: 144 Copynumber: 2.0 Consensus size: 144
261516 TTTATACCCT
*
261526 AACATTGATATTAATTTTAAGTAACCCATTAAATTTATGAATACTCGTCAAAGGTAAATAGTTTG
1 AACATTGATATTAATTTTAAGGAACCCATTAAATTTATGAATACTCGTCAAAGGTAAATAGTTTG
261591 GATCGAACATAAATGTTATATTTTTTATTTAAATTTATATTTTTGTAATTAAGATAACCGGGTAA
66 GATCGAACATAAATGTTATATTTTTTATTTAAATTTATATTTTTGTAATTAAGATAACCGGGTAA
261656 TCAATTGATACTGA
131 TCAATTGATACTGA
261670 AACATTGATATTAATTTTAAGGAACCCATTAAATTTATGAATACTCGTCAAAGGTAAATAGTTTG
1 AACATTGATATTAATTTTAAGGAACCCATTAAATTTATGAATACTCGTCAAAGGTAAATAGTTTG
261735 GATCGAACATAAATGTTATATTTTTTATTTAAATTTATATTTTTGTAATTAAGATAACCGGGTAA
66 GATCGAACATAAATGTTATATTTTTTATTTAAATTTATATTTTTGTAATTAAGATAACCGGGTAA
261800 TCAATTGATACTGA
131 TCAATTGATACTGA
261814 AA
1 AA
261816 GGGAGACTTG
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 145 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.40
Consensus pattern (144 bp):
AACATTGATATTAATTTTAAGGAACCCATTAAATTTATGAATACTCGTCAAAGGTAAATAGTTTG
GATCGAACATAAATGTTATATTTTTTATTTAAATTTATATTTTTGTAATTAAGATAACCGGGTAA
TCAATTGATACTGA
Found at i:278166 original size:564 final size:566
Alignment explanation
Indices: 277066--278196 Score: 1717
Period size: 564 Copynumber: 2.0 Consensus size: 566
277056 AGCATAGTGA
*
277066 CCTTAGATGTTCTTTTAGGGCTTGGGTTATGATCGCATGTAAATGTGTGTGATGTGGCATGCAAA
1 CCTTAGATGTTCTTTTAGGGCTTGGGTTATGATCCCATGTAAATGTGTGTGATGTGGCATGCAAA
*
277131 TATGTGCAAGTATACACAATCAAAGAAAGTAATACCATAGTGAACGAGTATTGTCTCCATAGGGA
66 TATGTGCAAGTATACACAATCAAAGAAAGTAATACCATAGTGAACGAGTATCGTCTCCATAGGGA
*
277196 TTGGGGAATTTTTTAAAGATTGCTACAACTAGGAATAAGTGTCACTAACTAATCCTAAATGCCTA
131 TTGGGGAATTTTTTAAAGATTGCTACAACTAGGAATAAGCGTCACTAACTAATCCTAAATGCCTA
* *
277261 AATCTAATTATATAAACAAATGAGGAAAGAGATATGGCATATGGTATGAACAGATGGAAAACATT
196 AATCAAATTATATAAACAAATGAGGAAAGAGATATGGCAGATGGTATGAACAGATGGAAAACATT
* *
277326 TTTCGAGGTAAGAATCGTGTAAAGTGATATGAGCAGATATTTTTTGTCGTGGAAAAAATATTTAA
261 TTTCAAGGTAAGAATCGTGTAAAGTGATATGA-CAGATAATTTTTGTCGTGGAAAAAATATTTAA
* * *
277391 GGCAAAAATTAATTGCAAGAGTAAGTAAATAAAAGTTTATACGGAGAAAAATGTTTGAGTTATGA
325 GGCAAAAATTAATTACAAGAGTAAGTAAATAAAAGTTTATAAGGAGAAAAATGTTCGAGTTATGA
* * * * *
277456 ATATAGATTAACAACCTCAGACAATCAGACTTCTAACGGAGCACTTTGGTTGGATTTACTATGGC
390 ATATAGACTAACAACCTCACACAATCAGACTTCTAACAGAGCACTTGGGTTGGATTTACTATAGC
* *
277521 GAGAAATTATTCTATGCCTAAGATGAACTAAGTATGCTATGCCTATGTTACCCGATATGATTTAC
455 GAGAAATTATTCTATGCCTAAGATGAACTAAGTATGCTATGCCTATGTTACCCGAAAGGATTTAC
* **
277586 TAAAGTGTTTCTAAGCTATCTCTAGTAAGGATCCTGATACAACTATT
520 TAAAGTGTTCCTAAGCTATCTCTAGTAAGGAAACTGATACAACTATT
*
277633 CCTTAGATGTTCTTTTAGGGCTTGGGTTATGATCCCATGTAAATGTGTGTGTTGTGGCATGCAAA
1 CCTTAGATGTTCTTTTAGGGCTTGGGTTATGATCCCATGTAAATGTGTGTGATGTGGCATGCAAA
* * * * * *
277698 TCTGTGCAAGTATACACAATCGATAG-TAGTAATACCGTAGTGAGCGAGTATCGTCTCTATAGGG
66 TATGTGCAAGTATACACAATC-AAAGAAAGTAATACCATAGTGAACGAGTATCGTCTCCATAGGG
* * *
277762 ATTGGGGGAATTTTTTAAAGATTGCTATAGCTAGGAATATGCGTCACTAACTAATCCTAAA-GCC
130 ATT-GGGGAATTTTTTAAAGATTGCTACAACTAGGAATAAGCGTCACTAACTAATCCTAAATGCC
* * *
277826 TAAATCAAATTATTTAAACAAATGAGGAAAGAGCTATGGTAGATGGTATGAACAGATGGAAAA-A
194 TAAATCAAATTATATAAACAAATGAGGAAAGAGATATGGCAGATGGTATGAACAGATGGAAAACA
* * *
277890 GTTTGTT-AAGGTAAGAATCGTGTGAAGTGA-GT-A-A-ATAATTTTTGTTGTGGCAAAAAAATA
259 -TTT-TTCAAGGTAAGAATCGTGTAAAGTGATATGACAGATAATTTTTGTCGTGG--AAAAAATA
* * *
277950 TGTT-AGGTAAAAATTAATTACAAGAGTAAGTAAATAAAAG-TTACTAAGGATAAGAATGTTCGA
320 T-TTAAGGCAAAAATTAATTACAAGAGTAAGTAAATAAAAGTTTA-TAAGGAGAAAAATGTTCGA
*
278013 GTTCTGAATATAGACTAACAACCTCACACAATCAGACTTCTAACAGAGCACTTGGGTTGGATTTT
383 GTTATGAATATAGACTAACAACCTCACACAATCAGACTTCTAACAGAGCACTTGGGTTGGA-TTT
*
278078 A-TATAGCGAGAAATTATTCTATGCCTAGGATGAACTAAGTATGCTATGCCTATGTTACCCGAAA
447 ACTATAGCGAGAAATTATTCTATGCCTAAGATGAACTAAGTATGCTATGCCTATGTTACCCGAAA
*
278142 GGATTTACTAAAGTGTTCCTAAGCTATCTCTAGTAAGGAAACTTATACAACTATT
512 GGATTTACTAAAGTGTTCCTAAGCTATCTCTAGTAAGGAAACTGATACAACTATT
278197 TCCACGGCAA
Statistics
Matches: 513, Mismatches: 42, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
562 14 0.03
563 4 0.01
564 224 0.44
565 7 0.01
566 2 0.00
567 204 0.40
568 58 0.11
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (566 bp):
CCTTAGATGTTCTTTTAGGGCTTGGGTTATGATCCCATGTAAATGTGTGTGATGTGGCATGCAAA
TATGTGCAAGTATACACAATCAAAGAAAGTAATACCATAGTGAACGAGTATCGTCTCCATAGGGA
TTGGGGAATTTTTTAAAGATTGCTACAACTAGGAATAAGCGTCACTAACTAATCCTAAATGCCTA
AATCAAATTATATAAACAAATGAGGAAAGAGATATGGCAGATGGTATGAACAGATGGAAAACATT
TTTCAAGGTAAGAATCGTGTAAAGTGATATGACAGATAATTTTTGTCGTGGAAAAAATATTTAAG
GCAAAAATTAATTACAAGAGTAAGTAAATAAAAGTTTATAAGGAGAAAAATGTTCGAGTTATGAA
TATAGACTAACAACCTCACACAATCAGACTTCTAACAGAGCACTTGGGTTGGATTTACTATAGCG
AGAAATTATTCTATGCCTAAGATGAACTAAGTATGCTATGCCTATGTTACCCGAAAGGATTTACT
AAAGTGTTCCTAAGCTATCTCTAGTAAGGAAACTGATACAACTATT
Found at i:285140 original size:36 final size:36
Alignment explanation
Indices: 285087--285161 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
285077 AGCTTATGAC
*
285087 TTATGGAATATATCCATGGGTCAAGTTGCCTCCACT
1 TTATGGAATATACCCATGGGTCAAGTTGCCTCCACT
* *
285123 TTATGGAATTTACCCATGGGTCAAGTTGCCTCTACT
1 TTATGGAATATACCCATGGGTCAAGTTGCCTCCACT
285159 TTA
1 TTA
285162 GTAATAGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (36 bp):
TTATGGAATATACCCATGGGTCAAGTTGCCTCCACT
Found at i:287796 original size:39 final size:40
Alignment explanation
Indices: 287752--287847 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 40
287742 ATATTTTAAA
287752 AATAATTTAGAGTGTTAACGTG-AAATAATTTAAG-AAATT
1 AATAATTTAGAGTGTTAACGTGTAAA-AATTTAAGAAAATT
* ** *
287791 AATAATTTAGAATGTTATGGTGTTAAAATTTAAGAAAATT
1 AATAATTTAGAGTGTTAACGTGTAAAAATTTAAGAAAATT
**
287831 AGGAATTTAGAGTGTTA
1 AATAATTTAGAGTGTTA
287848 GAGCGAAACA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 27 0.56
40 21 0.44
ACGTcount: A:0.44, C:0.01, G:0.18, T:0.38
Consensus pattern (40 bp):
AATAATTTAGAGTGTTAACGTGTAAAAATTTAAGAAAATT
Found at i:288501 original size:20 final size:20
Alignment explanation
Indices: 288476--288542 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
288466 TTTTCCCAAT
288476 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
288496 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
288517 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
288537 TCGCAA
1 TCGCAA
288543 CACGAATTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:288519 original size:21 final size:21
Alignment explanation
Indices: 288493--288568 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
288483 GCGAATAAGT
288493 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
288514 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
*
288534 AAATCGCAACACGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
288555 AAATCGCAATGCGA
1 AAATCGCAACGCGA
288569 TACTGACTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:288582 original size:20 final size:20
Alignment explanation
Indices: 288557--288651 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
288547 AATTGGGAAA
*
288557 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
288577 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
288598 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
288618 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
288638 TTCGCAACGCGATA
1 ATCGCAACGCGATA
288652 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:288583 original size:41 final size:41
Alignment explanation
Indices: 288476--288568 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
288466 TTTTCCCAAT
*
288476 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
288517 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
288558 TCGCAATGCGA
1 TCGCAATGCGA
288569 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
Found at i:288599 original size:41 final size:41
Alignment explanation
Indices: 288554--288631 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
288544 ACGAATTGGG
* * *
288554 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
288595 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
288632 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:289109 original size:19 final size:19
Alignment explanation
Indices: 289085--289135 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
289075 ATCAACCAAG
289085 AATCGCAACGCGAAATGCA
1 AATCGCAACGCGAAATGCA
289104 AATCGCAACGCGAAATGCA
1 AATCGCAACGCGAAATGCA
289123 AATCGCAACGCGA
1 AATCGCAACGCGA
289136 TTTTAGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.41, C:0.27, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGCA
Found at i:289187 original size:20 final size:20
Alignment explanation
Indices: 289162--289199 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
289152 CGATTCTCTC
289162 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
289182 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
289200 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:290529 original size:18 final size:18
Alignment explanation
Indices: 290508--290552 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
290498 TCCACTTCGG
*
290508 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
290526 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
290544 GAGCCATCA
1 GAGCCATCA
290553 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:290969 original size:17 final size:17
Alignment explanation
Indices: 290935--290979 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
290925 ACTGCTAAAC
290935 TGTTTTT-GTTAGTATT
1 TGTTTTTGGTTAGTATT
* *
290951 TGTTTTTGGTTTGTTTT
1 TGTTTTTGGTTAGTATT
290968 TGTCTTTTGGTT
1 TGT-TTTTGGTT
290980 GAAGTAATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 7 0.28
17 10 0.40
18 8 0.32
ACGTcount: A:0.04, C:0.02, G:0.22, T:0.71
Consensus pattern (17 bp):
TGTTTTTGGTTAGTATT
Found at i:291087 original size:19 final size:20
Alignment explanation
Indices: 291033--291088 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
291023 TAGTTTACTT
* *
291033 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
291053 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
291073 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
291089 AAATCGTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:291094 original size:19 final size:19
Alignment explanation
Indices: 291072--291135 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
291062 GGAAATGGCT
291072 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
291091 ATCGTAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
291105 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
291124 ATTGCAATGCGA
1 ATCGCAATGCGA
291136 TTTGTGTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.56
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:291166 original size:14 final size:14
Alignment explanation
Indices: 291147--291204 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
291137 TTGTGTTTCG
291147 CGTTGCGATTTTAT
1 CGTTGCGATTTTAT
*
291161 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TAT
*
291177 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTAT
291193 CGTTGCGATTTT
1 CGTTGCGATTTT
291205 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTAT
Found at i:291181 original size:32 final size:33
Alignment explanation
Indices: 291142--291220 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
291132 GCGATTTGTG
291142 TTTCGCGTTGCGATTTTATCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTATCGTTGCGATTTTCA
*
291174 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTATCGTTGCGATTTTCA
*
291207 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
291221 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTATCGTTGCGATTTTCA
Found at i:291219 original size:19 final size:19
Alignment explanation
Indices: 291142--291278 Score: 98
Period size: 20 Copynumber: 7.7 Consensus size: 19
291132 GCGATTTGTG
291142 TTTCGCGTTGCGATTTT-A
1 TTTCGCGTTGCGATTTTCA
291160 --T--CGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
291174 TTTCGCGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
291190 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
291207 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
291226 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
291246 TTTCGCGTTGCGATTTTAA
1 TTTCGCGTTGCGATTTTCA
*
291265 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
291279 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
13 3 0.03
14 17 0.18
15 3 0.03
16 4 0.04
17 2 0.02
18 11 0.12
19 26 0.27
20 29 0.31
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:293144 original size:14 final size:14
Alignment explanation
Indices: 293125--293160 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
293115 ATTGTTTAAT
293125 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
293139 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
293153 TGATTTGT
1 TGATTTGT
293161 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:293382 original size:20 final size:20
Alignment explanation
Indices: 293325--293382 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
293315 TCGCATTGCG
* *
293325 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
293345 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
293365 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
293383 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:294685 original size:12 final size:12
Alignment explanation
Indices: 294668--294692 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
294658 ATATAATCCT
294668 GAAGAAGAAAAA
1 GAAGAAGAAAAA
294680 GAAGAAGAAAAA
1 GAAGAAGAAAAA
294692 G
1 G
294693 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:297023 original size:33 final size:33
Alignment explanation
Indices: 296981--297107 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
296971 GGAAATTACT
*
296981 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
297014 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
297046 TTTCGCAATGCGAAATGAAAATCGTAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
297080 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
297108 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:297088 original size:66 final size:66
Alignment explanation
Indices: 296982--297114 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
296972 GAAATTACTA
*
296982 TCGCAATGCGAAATGAAAATCGTAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGTAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
297047 T
66 T
*
297048 TCGCAATGCGAAATGAAAATCGTAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGTAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
297113 T
66 T
297114 T
1 T
297115 AATTTTGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGTAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:297129 original size:19 final size:20
Alignment explanation
Indices: 297107--297149 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
297097 AAATCGCAAC
297107 GCGAATTTAATTTT-GCGTT
1 GCGAATTTAATTTTCGCGTT
* *
297126 GCGATTTTCATTTTCGCGTT
1 GCGAATTTAATTTTCGCGTT
297146 GCGA
1 GCGA
297150 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44
Consensus pattern (20 bp):
GCGAATTTAATTTTCGCGTT
Found at i:297309 original size:14 final size:14
Alignment explanation
Indices: 297290--297340 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
297280 CATCAATTAA
297290 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
297304 ACAAATCACCTTTT
1 ACAAATCAACTTTT
*
297318 ACAAATCACCTTTT
1 ACAAATCAACTTTT
297332 ACAAATCAA
1 ACAAATCAA
297341 TTAAACAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:298766 original size:21 final size:21
Alignment explanation
Indices: 298700--298766 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
298690 GTGAATCGGG
*
298700 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
298720 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
298742 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
298763 CTCT
1 CTCT
298767 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:298785 original size:42 final size:41
Alignment explanation
Indices: 298700--298822 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
298690 GTGAATCGGG
* * * * *
298700 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
298742 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
298784 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
298823 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:300907 original size:33 final size:33
Alignment explanation
Indices: 300849--300947 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
300839 ACGAGATAAT
* *
300849 GAGAATCGCAACGCGGAAATTACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
* *
300883 GAGAATCGCAACGCGAAATGACTATCACGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
300916 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
300948 GCGAAATAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
33 42 0.75
34 14 0.25
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:300943 original size:19 final size:19
Alignment explanation
Indices: 300919--300989 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
300909 ACGACCAGAC
300919 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
300938 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
300958 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
300977 AATCGCAATGCGA
1 AATCGCAACGCGA
300990 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 30 0.62
20 18 0.38
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:300952 original size:20 final size:19
Alignment explanation
Indices: 300824--300989 Score: 118
Period size: 20 Copynumber: 9.1 Consensus size: 19
300814 TCTTTTGGTT
*
300824 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
300843 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
* **
300863 GGAAATTACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
300881 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** * *
300897 GAAATGACTATCACGAC-C
1 GAAATGAAAATCGCAACGC
*
300915 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
300930 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
300950 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
300969 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
300988 GA
1 GA
300990 TTTTGGTTTC
Statistics
Matches: 115, Mismatches: 19, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
14 17 0.15
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 42 0.37
20 44 0.38
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:301018 original size:19 final size:19
Alignment explanation
Indices: 300985--301065 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
300975 AAAATCGCAA
**
300985 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
301004 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
301023 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
301037 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
301057 TGCGATTTT
1 TGCGATTTT
301066 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:301607 original size:20 final size:20
Alignment explanation
Indices: 301582--301634 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
301572 GCGCTATGTA
301582 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
301602 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
301622 TATCTCGTTGCGA
1 AATCGCGTTGCGA
301635 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:301787 original size:21 final size:21
Alignment explanation
Indices: 301747--301787 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
301737 ATTGTATACC
**
301747 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
301768 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
301788 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:302046 original size:26 final size:27
Alignment explanation
Indices: 301997--302051 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
301987 TAAAAGTATG
*
301997 TTTAATTTTTTTATATTTTAAATT-AA
1 TTTAATATTTTTATATTTTAAATTCAA
302023 TTTAATATTTTTATA-TTTATAATTCAA
1 TTTAATATTTTTATATTTTA-AATTCAA
302050 TT
1 TT
302052 ATATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 18 0.69
27 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTAATATTTTTATATTTTAAATTCAA
Found at i:302480 original size:23 final size:24
Alignment explanation
Indices: 302436--302480 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
302426 ATTTTATATT
* *
302436 AAATATTATATTAACTACATTTTA
1 AAATATTATATAAAATACATTTTA
*
302460 AAAT-TTATATAAAATATATTT
1 AAATATTATATAAAATACATTT
302481 AATTAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATATTATATAAAATACATTTTA
Found at i:304044 original size:17 final size:17
Alignment explanation
Indices: 304018--304053 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
304008 GGCAATGACC
*
304018 AAATCGGGAAGAGGACA
1 AAATCAGGAAGAGGACA
304035 AAATCAGGAAGAGGACA
1 AAATCAGGAAGAGGACA
304052 AA
1 AA
304054 CTGGGAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.11, G:0.31, T:0.06
Consensus pattern (17 bp):
AAATCAGGAAGAGGACA
Found at i:304075 original size:16 final size:16
Alignment explanation
Indices: 304017--304078 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
304007 AGGCAATGAC
*
304017 CAAATCGGGAAGAGGA
1 CAAACCGGGAAGAGGA
* *
304033 CAAAATCAGGAAGAGGA
1 C-AAACCGGGAAGAGGA
* *
304050 CAAACTGGGAAGGGGA
1 CAAACCGGGAAGAGGA
*
304066 CAAGCCGGGAAGA
1 CAAACCGGGAAGA
304079 AGTTGAGCTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
16 22 0.59
17 15 0.41
ACGTcount: A:0.44, C:0.15, G:0.37, T:0.05
Consensus pattern (16 bp):
CAAACCGGGAAGAGGA
Found at i:304856 original size:30 final size:30
Alignment explanation
Indices: 304817--304885 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
304807 AAAACCGTTT
304817 AATATTAACGGTTCAATGAATTAACATATTA
1 AATA-TAACGGTTCAATGAATTAACATATTA
* *
304848 AATATAACGTTTCAATGAATTAACCTATTA
1 AATATAACGGTTCAATGAATTAACATATTA
304878 AATATAAC
1 AATATAAC
304886 ATTTACGGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (30 bp):
AATATAACGGTTCAATGAATTAACATATTA
Found at i:306622 original size:40 final size:40
Alignment explanation
Indices: 306527--306640 Score: 174
Period size: 40 Copynumber: 2.8 Consensus size: 40
306517 CAATTAATCA
* *
306527 ATTAATAGATTAAATATTAATGATTATATAAAAAATAATTG
1 ATTAATAGATCAAATATTAATGATTATAT-AAGAATAATTG
* *
306568 ATTAATAAATCAAATATTAATGATTATATAAGATTAATTG
1 ATTAATAGATCAAATATTAATGATTATATAAGAATAATTG
*
306608 ATTAATAGACCAAATATTAATGATTATATAAGA
1 ATTAATAGATCAAATATTAATGATTATATAAGA
306641 GTATGAAATG
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 40 0.60
41 27 0.40
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (40 bp):
ATTAATAGATCAAATATTAATGATTATATAAGAATAATTG
Found at i:307729 original size:2 final size:2
Alignment explanation
Indices: 307722--307771 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
307712 TATCTAAATG
307722 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
307764 AT AT AT AT
1 AT AT AT AT
307772 TGTTAATAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:309977 original size:26 final size:26
Alignment explanation
Indices: 309941--310029 Score: 133
Period size: 26 Copynumber: 3.4 Consensus size: 26
309931 CACTACAGTT
*
309941 TAGAAAAAAATGAGAGGGTAGACATC
1 TAGAGAAAAATGAGAGGGTAGACATC
*
309967 TAGAGAAAAATGAGAGGATAGACATC
1 TAGAGAAAAATGAGAGGGTAGACATC
* *
309993 TAGAGAAAAATGAGATGGTAGGCATC
1 TAGAGAAAAATGAGAGGGTAGACATC
310019 TAGAGATAAAA
1 TAGAGA-AAAA
310030 CGAAGCTCGG
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 53 0.93
27 4 0.07
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.17
Consensus pattern (26 bp):
TAGAGAAAAATGAGAGGGTAGACATC
Found at i:312683 original size:27 final size:27
Alignment explanation
Indices: 312645--312702 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
312635 TCAAGTATTG
* *
312645 AAATAATCAAAATACCATCGAGC-ACTA
1 AAATAATCAAAATAACATAGA-CTACTA
312672 AAATAA-CTAAAATAACATAGACTACTA
1 AAATAATC-AAAATAACATAGACTACTA
312699 AAAT
1 AAAT
312703 GACCTAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.57, C:0.17, G:0.05, T:0.21
Consensus pattern (27 bp):
AAATAATCAAAATAACATAGACTACTA
Found at i:314995 original size:23 final size:23
Alignment explanation
Indices: 314969--315046 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
314959 CACCATAGCT
314969 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
314992 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
315015 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
315038 TATAATAAT
1 CAT-ATAAT
315047 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:315224 original size:103 final size:103
Alignment explanation
Indices: 315053--315373 Score: 615
Period size: 103 Copynumber: 3.1 Consensus size: 103
315043 TAATGTCCAT
*
315053 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
315118 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
315156 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
315221 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
315259 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
315324 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
315362 AAGGACCACATA
1 AAGGACCACATA
315374 GACCCTCGAC
Statistics
Matches: 215, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 215 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:321052 original size:23 final size:22
Alignment explanation
Indices: 321026--321102 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 22
321016 ACCACAGCTA
321026 ATATAATTGCATCGAAGTGCCAC
1 ATATAATTGCA-CGAAGTGCCAC
*
321049 ATATAATTGCACCAGAGTGCCAC
1 ATATAATTGCACGA-AGTGCCAC
* * * *
321072 GTAGAATTGCACCGTAGTGCCAT
1 ATATAATTGCA-CGAAGTGCCAC
321095 ATAATAAT
1 AT-ATAAT
321103 GTCCATAAGG
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
22 2 0.05
23 36 0.84
24 5 0.12
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (22 bp):
ATATAATTGCACGAAGTGCCAC
Found at i:321280 original size:103 final size:103
Alignment explanation
Indices: 321109--321429 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
321099 TAATGTCCAT
*
321109 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
321174 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
321212 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
321277 GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
321315 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
321380 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
321418 AATGACCACATA
1 AAGGACCACATA
321430 GACCCTCGAC
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:326465 original size:24 final size:22
Alignment explanation
Indices: 326440--326497 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
326430 AAATACCCCA
*
326440 AAATATCAAATGAATATAATTTC
1 AAATATCAAATGAAAATAA-TTC
*
326463 AAATATCCAACATGAAAATCATTC
1 AAATAT-CAA-ATGAAAATAATTC
326487 AAATATCAAAT
1 AAATATCAAAT
326498 AAACATAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 2 0.06
23 9 0.29
24 12 0.39
25 8 0.26
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.29
Consensus pattern (22 bp):
AAATATCAAATGAAAATAATTC
Found at i:331368 original size:42 final size:42
Alignment explanation
Indices: 331317--331414 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
331307 GTTACAAGAA
* *
331317 AGAGATCGATCCTTTAGGGGAGAGG-ATCGATCATTTACATCG
1 AGAGATCGATCATTTAGGGGA-AGGAATCAATCATTTACATCG
* * * * *
331359 AGGGATCGATCATTTTGGTGAAGGAATCAATCATTTTCCTCG
1 AGAGATCGATCATTTAGGGGAAGGAATCAATCATTTACATCG
331401 AGAGATCGAT-ATTT
1 AGAGATCGATCATTT
331415 TTTATGAAGG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 7 0.15
42 40 0.85
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (42 bp):
AGAGATCGATCATTTAGGGGAAGGAATCAATCATTTACATCG
Found at i:331423 original size:42 final size:42
Alignment explanation
Indices: 331346--331431 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
331336 GAGAGGATCG
* *
331346 ATCATTTACATCGAGGGATCGATCATTTTGGTGAAGGAATCA
1 ATCATTTACATCGAGAGATCGATCATTTTGATGAAGGAATCA
* * * *
331388 ATCATTTTCCTCGAGAGATCGAT-ATTTTTTATGAAGGGATCA
1 ATCATTTACATCGAGAGATCGATCA-TTTTGATGAAGGAATCA
331430 AT
1 AT
331432 ACAAAACCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
41 1 0.03
42 36 0.97
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
ATCATTTACATCGAGAGATCGATCATTTTGATGAAGGAATCA
Found at i:331477 original size:21 final size:20
Alignment explanation
Indices: 331451--331508 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
331441 AATGGAATCC
331451 AAGGGATCGATCCTTTGGTCA
1 AAGGGATCGATCCTTT-GTCA
* *
331472 AAGGGAT-TAGTCCATTT-TCT
1 AAGGGATCGA-TCC-TTTGTCA
331492 AAGGGATCGATCCTTTG
1 AAGGGATCGATCCTTTG
331509 AGCCAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
19 3 0.10
20 13 0.43
21 11 0.37
22 3 0.10
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
AAGGGATCGATCCTTTGTCA
Found at i:336148 original size:31 final size:31
Alignment explanation
Indices: 336082--336154 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
336072 AAAGTATTTT
** *
336082 AAATTTGTGTTGGAATATGTCGACCCATCAT
1 AAATTTGTGACGGAATATGTCGACCCATCAC
* * *
336113 AAATTTGTGACGGAATATGTGGATCCGTCAC
1 AAATTTGTGACGGAATATGTCGACCCATCAC
*
336144 AAATTTCTGAC
1 AAATTTGTGAC
336155 AGATTCACCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (31 bp):
AAATTTGTGACGGAATATGTCGACCCATCAC
Found at i:336171 original size:31 final size:31
Alignment explanation
Indices: 336136--336208 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
336126 AATATGTGGA
*
336136 TCCGTCACAAATTTCTGACAGATTCACCTAT
1 TCCGTCACAAATTTCTGACAGATTCACATAT
* * * *
336167 TCCGTCACAAATTTCTGACGGGTTCATATGT
1 TCCGTCACAAATTTCTGACAGATTCACATAT
336198 TCCGTCACAAA
1 TCCGTCACAAA
336209 GTTTAGAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (31 bp):
TCCGTCACAAATTTCTGACAGATTCACATAT
Found at i:337269 original size:12 final size:12
Alignment explanation
Indices: 337252--337295 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
337242 TTACTAAACT
337252 TAAATTCCGTCA
1 TAAATTCCGTCA
*
337264 TAAATTCCTTCA
1 TAAATTCCGTCA
*
337276 GT-AATTCTGTCA
1 -TAAATTCCGTCA
337288 TAAATTCC
1 TAAATTCC
337296 CTCAGTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 1 0.04
12 24 0.92
13 1 0.04
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (12 bp):
TAAATTCCGTCA
Found at i:337287 original size:24 final size:24
Alignment explanation
Indices: 337254--337307 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
337244 ACTAAACTTA
*
337254 AATTCCGTCATAAATTCCTTCAGT
1 AATTCCGTCATAAATTCCCTCAGT
*
337278 AATTCTGTCATAAATTCCCTCAGT
1 AATTCCGTCATAAATTCCCTCAGT
337302 AATTCC
1 AATTCC
337308 ATCAACAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (24 bp):
AATTCCGTCATAAATTCCCTCAGT
Found at i:346045 original size:20 final size:19
Alignment explanation
Indices: 346020--346091 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
346010 AGTGGCTGAA
*
346020 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GATTTG
*
346040 AACCGGTTTTGACCGATTTC
1 AACCGG-TTTGACCGATTTG
* *
346060 AATCGGTTTGACCGATCTG
1 AACCGGTTTGACCGATTTG
*
346079 AACCGGTCTGACC
1 AACCGGTTTGACC
346092 CGACCCGACC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 22 0.50
20 15 0.34
21 7 0.16
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (19 bp):
AACCGGTTTGACCGATTTG
Found at i:346133 original size:19 final size:17
Alignment explanation
Indices: 346102--346141 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 17
346092 CGACCCGACC
346102 GACCCGACCTGACCGTT
1 GACCCGACCTGACCGTT
346119 GACCCGACCGTTGACCGTT
1 GACCCGACC--TGACCGTT
346138 GACC
1 GACC
346142 GTTGACTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.43
19 12 0.57
ACGTcount: A:0.17, C:0.40, G:0.25, T:0.17
Consensus pattern (17 bp):
GACCCGACCTGACCGTT
Found at i:346134 original size:7 final size:7
Alignment explanation
Indices: 346111--346147 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
346101 CGACCCGACC
346111 TGACCGT
1 TGACCGT
346118 TGACC--
1 TGACCGT
*
346123 CGACCGT
1 TGACCGT
346130 TGACCGT
1 TGACCGT
346137 TGACCGT
1 TGACCGT
346144 TGAC
1 TGAC
346148 TTCCTTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
5 4 0.15
7 22 0.85
ACGTcount: A:0.16, C:0.32, G:0.27, T:0.24
Consensus pattern (7 bp):
TGACCGT
Found at i:348940 original size:21 final size:20
Alignment explanation
Indices: 348855--349011 Score: 75
Period size: 21 Copynumber: 7.8 Consensus size: 20
348845 AATGACCAAT
** *
348855 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
348874 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
348894 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
348914 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * * *
348935 AAAATCGCGATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
348956 AAATTCGCATTGCGATTTTC
1 AAAATCGCAACGCGATTTTC
* * *
348976 AATAATCGCAACGCGAATATG
1 AA-AATCGCAACGCGATTTTC
348997 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
349012 ACACATAAAT
Statistics
Matches: 102, Mismatches: 30, Indels: 11
0.71 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:349004 original size:20 final size:20
Alignment explanation
Indices: 348979--349172 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
348969 GATTTTCAAT
* *
348979 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
348999 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
349019 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
349039 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
349059 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
349079 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
349099 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
349119 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
349140 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
349160 AATCGCAACGCGA
1 AATCGCAACGCGA
349173 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:349024 original size:40 final size:39
Alignment explanation
Indices: 348979--349172 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
348969 GATTTTCAAT
* ** *
348979 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
349019 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
349059 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
349099 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
349140 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
349173 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:349062 original size:60 final size:60
Alignment explanation
Indices: 348979--349171 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
348969 GATTTTCAAT
* ** * *
348979 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
349039 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
349099 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
349160 AATCGCAACGCG
1 AATCGCAACGCG
349172 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:349591 original size:33 final size:33
Alignment explanation
Indices: 349552--349622 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
349542 TTCACTTAGA
*
349552 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
349585 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
349618 TTTCA
1 TTTCA
349623 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:349762 original size:14 final size:14
Alignment explanation
Indices: 349743--349797 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
349733 AGAATGACTG
349743 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
349757 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
349776 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
349790 TCGCAACG
1 TCGCAACG
349798 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:349780 original size:33 final size:33
Alignment explanation
Indices: 349743--349813 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
349733 AGAATGACTG
**
349743 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
349776 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
349809 TCGCA
1 TCGCA
349814 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:349831 original size:19 final size:19
Alignment explanation
Indices: 349809--349906 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
349799 GAAACCAAAA
*
349809 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
349828 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
349842 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
349861 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
349875 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
349894 TCGCGTTGCGATT
1 TCGCGTTGCGATT
349907 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:349850 original size:14 final size:14
Alignment explanation
Indices: 349831--349920 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
349821 TTTCATTTCG
349831 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
349845 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
349864 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
349878 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
349895 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
349911 CGTTGCGATT
1 CGTTGCGATT
349921 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:349856 original size:33 final size:33
Alignment explanation
Indices: 349814--349928 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
349804 CAAAATCGCA
349814 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
349847 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
349880 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
349913 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
349929 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:351829 original size:92 final size:93
Alignment explanation
Indices: 351623--352001 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
351613 TAGATTGCTT
*
351623 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
351688 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
351716 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
351780 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
351808 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
351872 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
351900 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
351965 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
351993 AGTAAATTT
1 AGTAAATTT
352002 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 100 0.35
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:351853 original size:185 final size:185
Alignment explanation
Indices: 351623--352003 Score: 737
Period size: 185 Copynumber: 2.1 Consensus size: 185
351613 TAGATTGCTT
351623 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
351688 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
351753 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
351808 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
351873 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
351938 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
351993 AGTAAATTTAT
1 AGTAAATTTAT
352004 CCATTCAAGT
Statistics
Matches: 193, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 92 0.48
185 101 0.52
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:352085 original size:19 final size:19
Alignment explanation
Indices: 352045--352173 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
352035 TAGTTTACTT
* *
352045 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
352065 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
352084 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
352103 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
352117 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
352136 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
352150 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
352169 TCGCA
1 TCGCA
352174 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:352124 original size:33 final size:32
Alignment explanation
Indices: 352081--352173 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
352071 CGCGAAACCA
**
352081 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
352113 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
352146 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
352174 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:352171 original size:52 final size:52
Alignment explanation
Indices: 352045--352173 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
352035 TAGTTTACTT
**
352045 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
352097 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
352150 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
352174 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:352191 original size:19 final size:19
Alignment explanation
Indices: 352169--352303 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
352159 GAAACCAAAA
*
352169 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
352188 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
352204 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
352221 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
352237 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
352254 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
352273 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
352293 TCGTGTTGCGA
1 TCGCGTTGCGA
352304 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:352210 original size:14 final size:14
Alignment explanation
Indices: 352191--352247 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
352181 TTTCATTTCG
352191 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
352205 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
352222 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
352238 CGTTGCGATT
1 CGTTGCGATT
352248 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:352216 original size:33 final size:33
Alignment explanation
Indices: 352174--352266 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
352164 CAAAATCGCA
*
352174 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
352207 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
352240 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
352267 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:354215 original size:14 final size:14
Alignment explanation
Indices: 354196--354231 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
354186 ATTGTTTAAT
354196 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
354210 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
354224 TGATTTGT
1 TGATTTGT
354232 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:354354 original size:19 final size:18
Alignment explanation
Indices: 354338--354419 Score: 100
Period size: 19 Copynumber: 4.6 Consensus size: 18
354328 AAAAATGACT
354338 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
354357 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
354371 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
354390 ATCGCAATGCGGAAATGAA
1 ATCGCAATGC-GAAATGAA
354409 ATCGCAATGCG
1 ATCGCAATGCG
354420 TTTATAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
14 8 0.15
16 5 0.09
17 5 0.09
18 1 0.02
19 30 0.55
20 6 0.11
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:354466 original size:52 final size:52
Alignment explanation
Indices: 354426--354692 Score: 446
Period size: 52 Copynumber: 5.0 Consensus size: 52
354416 TGCGTTTATA
*
354426 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
354478 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
354530 ATTTCGCATTGCGATTTCCATTTCGCATTGCGA-TTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
354586 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
354638 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
354691 AT
1 AT
354693 GTTGGGATTT
Statistics
Matches: 205, Mismatches: 3, Indels: 13
0.93 0.01 0.06
Matches are distributed among these distances:
51 6 0.03
52 124 0.60
53 23 0.11
54 2 0.01
55 7 0.03
56 37 0.18
57 6 0.03
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:354472 original size:19 final size:19
Alignment explanation
Indices: 354448--354720 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
354438 GATTATCTCG
354448 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
354467 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
354486 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
354500 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
354519 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
354538 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
354557 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
354575 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
354594 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
354608 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
354627 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
354646 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
354660 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
354680 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
354694 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
354713 TTGCGATT
1 TTGCGATT
354721 GTATTTTCCG
Statistics
Matches: 224, Mismatches: 8, Indels: 44
0.81 0.03 0.16
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 21 0.09
18 20 0.09
19 118 0.53
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:354634 original size:108 final size:102
Alignment explanation
Indices: 354448--354690 Score: 165
Period size: 108 Copynumber: 2.3 Consensus size: 102
354438 GATTATCTCG
* ** *
354448 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTC-GTTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTC-TTTCG--TTGCGATTATCGCAATTGCGATTTTCA
* * *
354512 TTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCA
63 TTTCGCATTGCGA---TCCTCTCG--TTGCGATTTTCATTTCGCA
* * *
354557 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTC-TTTCG--TTGCGATTATCGCAATTGCGATTTTCA
* * * * * *
354620 TTTCGCATTGCGAT--TTTCATTTCGCA-TTGCGATTCTCTCG
63 TTTCGCATTGCGATCCTCTCGTTGCG-ATTTTC-ATT-TCGCA
354660 TTGCGATTTTCATTTCCGCATTGCGATTTTC
1 TTGCGATTTTCATTT-CGCATTGCGATTTTC
354691 ATGTTGGGAT
Statistics
Matches: 123, Mismatches: 6, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
101 7 0.06
102 4 0.03
103 13 0.11
104 8 0.07
105 16 0.13
108 69 0.56
109 6 0.05
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.47
Consensus pattern (102 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCTTTCGTTGCGATTATCGCAATTGCGATTTTCATTT
CGCATTGCGATCCTCTCGTTGCGATTTTCATTTCGCA
Found at i:357017 original size:12 final size:12
Alignment explanation
Indices: 357000--357024 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
356990 TCTTCGGGGA
357000 CTTTTTCTTCTT
1 CTTTTTCTTCTT
357012 CTTTTTCTTCTT
1 CTTTTTCTTCTT
357024 C
1 C
357025 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:357233 original size:24 final size:24
Alignment explanation
Indices: 357199--357245 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
357189 CTGAAACATC
357199 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
357223 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
357246 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:357949 original size:20 final size:20
Alignment explanation
Indices: 357921--358310 Score: 464
Period size: 20 Copynumber: 19.4 Consensus size: 20
357911 AAATTTCAGT
* * * *
357921 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
* *
357941 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATACGC
* * *
357961 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
357981 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
358001 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
358021 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
358041 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
358061 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
358081 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
358101 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
358121 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
358141 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
358162 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
358182 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
358202 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
358222 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
358242 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
358262 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
358282 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
358302 GTTGCGATT
1 GTTGCGATT
358311 ATTGAAAATC
Statistics
Matches: 327, Mismatches: 34, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.02
20 301 0.92
21 18 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:360099 original size:15 final size:15
Alignment explanation
Indices: 360076--360105 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
360066 ATGAGGCTGG
360076 AATTACAACAACAAC
1 AATTACAACAACAAC
*
360091 AATTCCAACAACAAC
1 AATTACAACAACAAC
360106 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:372562 original size:11 final size:11
Alignment explanation
Indices: 372546--372579 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
372536 GTAATAATGT
372546 TGTCGCAAAGG
1 TGTCGCAAAGG
372557 TGTCGCAAAGG
1 TGTCGCAAAGG
*
372568 TGTTGCAAAGG
1 TGTCGCAAAGG
372579 T
1 T
372580 ATTGAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (11 bp):
TGTCGCAAAGG
Found at i:375383 original size:13 final size:13
Alignment explanation
Indices: 375365--375403 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
375355 CGAATTTGAA
375365 GAAACGGACTTCG
1 GAAACGGACTTCG
375378 GAAACGGACTTCG
1 GAAACGGACTTCG
375391 GAAACGGA-TTCG
1 GAAACGGACTTCG
375403 G
1 G
375404 GACGTCGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (13 bp):
GAAACGGACTTCG
Found at i:375538 original size:5 final size:5
Alignment explanation
Indices: 375528--375566 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
375518 AACGGCCAAC
*
375528 GGTCG GGTC- GGTC- AGTCG GGTCG GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG G
375567 TCAGACCGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 7 0.23
5 24 0.77
ACGTcount: A:0.03, C:0.21, G:0.56, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:375576 original size:9 final size:9
Alignment explanation
Indices: 375564--375597 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
375554 CGGGTCGGGT
375564 CGGTCAGAC
1 CGGTCAGAC
*
375573 CGGTCAAAC
1 CGGTCAGAC
375582 CGGTTCAGAC
1 CGG-TCAGAC
375592 CGGTCA
1 CGGTCA
375598 AACTGGTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.24, C:0.32, G:0.29, T:0.15
Consensus pattern (9 bp):
CGGTCAGAC
Found at i:375591 original size:19 final size:19
Alignment explanation
Indices: 375567--375620 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
375557 GTCGGGTCGG
375567 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
375586 TCAGACCGGTCAAACTGGT
1 TCAGACCGGTCAAACCGGT
*
375605 TC-GAACGGTCAAACCG
1 TCAGACCGGTCAAACCG
375621 ATTTCCAGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 12 0.38
19 20 0.62
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Done.