Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009425.1 Hibiscus syriacus cultivar Beakdansim tig00113400_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: 61791
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:367 original size:2 final size:2
Alignment explanation
Indices: 360--394 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
350 TATAGTATGA
360 AT AT AT AT AT AT AT AT AT -T 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
395 CGTACATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:381 original size:15 final size:15
Alignment explanation
Indices: 363--392 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
353 AGTATGAATA
363 TATATATATATATAT
1 TATATATATATATAT
378 TATATATATATATAT
1 TATATATATATATAT
393 ATCGTACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:381 original size:17 final size:17
Alignment explanation
Indices: 361--394 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
351 ATAGTATGAA
361 TATATATATATATATAT
1 TATATATATATATATAT
378 TATATATATATATATAT
1 TATATATATATATATAT
395 CGTACATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:466 original size:22 final size:22
Alignment explanation
Indices: 438--480 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
428 ATGTGGAATT
438 AAAGTATCGAGACAGATATAAC
1 AAAGTATCGAGACAGATATAAC
* * *
460 AAAGTATTGATACATATATAA
1 AAAGTATCGAGACAGATATAA
481 AAGTTTACGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (22 bp):
AAAGTATCGAGACAGATATAAC
Found at i:3023 original size:449 final size:447
Alignment explanation
Indices: 2174--3469 Score: 2064
Period size: 449 Copynumber: 2.9 Consensus size: 447
2164 ATTGAATACT
* * *
2174 CTTAGTGAAGTATTGATACTTTTGTGTACGATATTGATACTTTCGAGACGTTTCGTTTTTTTAAA
1 CTTACTGAAGTATCGATACTTTTGTGTACGATATCGATACTTTCGAGACGTTTC-TTTTTTTAAA
*
2239 AATC-AGTATCTATTTACCAGTTTTGTCATATTGAAACCGATTTTTATCAA-TTTTAACTTGTTA
65 AA-CGA-TATCTATTTACCAGTTTTGTCATATTGAAA-CGAATTTTATCAATTTTTAACTTGTTA
* *
2302 TATTGTCATGTATCGATACATGTGTAATAGGTATCGATACTTCCTATGTGCATCTAGTTTGAGAA
127 TATTGTCATGTATCGATACATGTGTAATAGGTATCGATACTTCCTACGTGCATCTAGTTTGGGAA
* ** *
2367 GCATACTAGACAAAAAGTATCGATACATATAGTAAAAGTATCAATACTTTATGTAAACATATTTT
192 GCATACTGGACAAAAAGTATCGATACATATACCAAAAGTATCAATACTTTATGTAAACGTATTTT
* *
2432 GTAATTAAACTCG-TATATTTTTAGATCTTACATTGTAAATTTACCTATTACTTTAATGTAATCG
257 GTAATTAAAC-CGATATATTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAATGTAATCG
* * * * *
2496 GTTTCAAAGTTTTAAGAATCGATACTTTTTATATGTGTATCGATACTTTGTAGGCGCAATTATGG
321 GTTTCGAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTATAGGCACAATTATGG
* *
2561 AAACCAATTTTGTCAAAAAGATGAACCTGTTATGTTATTTATATTTAATTGATACCATTACC
386 AAACCGATTTTGTCAAAAAGATGAACCTGTTATGTTATTTATATTTAATCGATACCATTACC
* *
2623 TTTACTGAAGTATCGATACTTTTGTGTACGATATCGATACTTTCCAGACGTTTCATTTTTTTCAA
1 CTTACTGAAGTATCGATACTTTTGTGTACGATATCGATACTTTCGAGACGTTTC-TTTTTTT-AA
* *
2688 AAACGATATCTATTTACCGGTTTTGTCATATTGAAATC-AGTTTTATCAATTTTTAA-TCTGTTA
64 AAACGATATCTATTTACCAGTTTTGTCATATTGAAA-CGAATTTTATCAATTTTTAACT-TGTTA
* *
2751 TATTGTCATGTATCGATACATGTGTAATAGGTATCAATACTTCCTACGTGCATATAGTTTGGGAA
127 TATTGTCATGTATCGATACATGTGTAATAGGTATCGATACTTCCTACGTGCATCTAGTTTGGGAA
2816 GCATACTGGACAAAAAGTATCGATACATATACCAAAAGTATCAATACTTTATGTAAACGTATTTT
192 GCATACTGGACAAAAAGTATCGATACATATACCAAAAGTATCAATACTTTATGTAAACGTATTTT
2881 GTAATTAAACCGATATATTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAATGTAATCGG
257 GTAATTAAACCGATATATTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAATGTAATCGG
*
2946 TTTCGAAGTTTTAAGAATCGATACTTTTCATACGTGTATTGATACTTTATAGGCACAATTATGGA
322 TTTCGAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTATAGGCACAATTATGGA
*
3011 AACCGGTTTTGTCAAAAAGATGAACCTGTTATGTTATTTATATTTAATCGATACCATTACC
387 AACCGATTTTGTCAAAAAGATGAACCTGTTATGTTATTTATATTTAATCGATACCATTACC
* ** *
3072 CTTACTGAAGTATCGATACTTTTGTGTACGGTATCGATACTTTCGAGACACTTCGTTTTTTAAAA
1 CTTACTGAAGTATCGATACTTTTGTGTACGATATCGATACTTTCGAGACGTTTCTTTTTTTAAAA
* * * * * *
3137 CCGGTAGCTATTTACCAGTTTTGTTATATTGAAACTAATTTTATAAATTTTTAACTTGTTATATT
66 ACGATATCTATTTACCAGTTTTGTCATATTGAAACGAATTTTATCAATTTTTAACTTGTTATATT
* *
3202 GTCATGTATCGATAGATGTGTCATAGGTATCGATACTTCCTACGTGCATCTAGTTTGGGAAGCAT
131 GTCATGTATCGATACATGTGTAATAGGTATCGATACTTCCTACGTGCATCTAGTTTGGGAAGCA-
** *
3267 TA-TGGACAAAAAGTATCGATACATATACCAAAAGTATTGATACTTTATGTAAACGTATTTTGTC
195 TACTGGACAAAAAGTATCGATACATATACCAAAAGTATCAATACTTTATGTAAACGTATTTTGTA
* *
3331 ATTAAACCAATATATTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAAAGTAATCGGTTT
260 ATTAAACCGATATATTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAATGTAATCGGTTT
3396 CGAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTATAGGCACAATTATGGAAAC
325 CGAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTATAGGCACAATTATGGAAAC
3461 CGATTTTGT
390 CGATTTTGT
3470 TAATTTTTTA
Statistics
Matches: 787, Mismatches: 52, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
446 1 0.00
447 312 0.40
448 22 0.03
449 446 0.57
450 6 0.01
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (447 bp):
CTTACTGAAGTATCGATACTTTTGTGTACGATATCGATACTTTCGAGACGTTTCTTTTTTTAAAA
ACGATATCTATTTACCAGTTTTGTCATATTGAAACGAATTTTATCAATTTTTAACTTGTTATATT
GTCATGTATCGATACATGTGTAATAGGTATCGATACTTCCTACGTGCATCTAGTTTGGGAAGCAT
ACTGGACAAAAAGTATCGATACATATACCAAAAGTATCAATACTTTATGTAAACGTATTTTGTAA
TTAAACCGATATATTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAATGTAATCGGTTTC
GAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTATAGGCACAATTATGGAAACC
GATTTTGTCAAAAAGATGAACCTGTTATGTTATTTATATTTAATCGATACCATTACC
Found at i:3519 original size:44 final size:44
Alignment explanation
Indices: 3456--3574 Score: 202
Period size: 44 Copynumber: 2.7 Consensus size: 44
3446 CACAATTATG
3456 GAAACCGATTTTGTTAATTTTTTACCTGTTAAGTTATTTATATT
1 GAAACCGATTTTGTTAATTTTTTACCTGTTAAGTTATTTATATT
3500 GAAACCGATTTTGTTAATTTTTTACCTGTTAAGTTATTTATATT
1 GAAACCGATTTTGTTAATTTTTTACCTGTTAAGTTATTTATATT
* * **
3544 GAAACCGGTTTTGTCAATTTTGAACCTGTTA
1 GAAACCGATTTTGTTAATTTTTTACCTGTTA
3575 TATTGTCATG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (44 bp):
GAAACCGATTTTGTTAATTTTTTACCTGTTAAGTTATTTATATT
Found at i:5092 original size:18 final size:18
Alignment explanation
Indices: 5069--5107 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5059 GCCGAAAATG
5069 AAATTGAAATTCAAACTC
1 AAATTGAAATTCAAACTC
* *
5087 AAATTGAAATTTAAATTC
1 AAATTGAAATTCAAACTC
5105 AAA
1 AAA
5108 CTCCAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (18 bp):
AAATTGAAATTCAAACTC
Found at i:5095 original size:24 final size:24
Alignment explanation
Indices: 5067--5126 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
5057 GAGCCGAAAA
*
5067 TGAAATTGAAATTCAAACTCAAAT
1 TGAAATTGAAATTCAAACTCAAAC
* *
5091 TGAAATTTAAATTCAAACTCCAAC
1 TGAAATTGAAATTCAAACTCAAAC
*
5115 TAAAATTGAAAT
1 TGAAATTGAAAT
5127 GAACATGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (24 bp):
TGAAATTGAAATTCAAACTCAAAC
Found at i:7712 original size:18 final size:18
Alignment explanation
Indices: 7673--7715 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
7663 GAATCCCTTA
*
7673 GTTGAGAAGAAGAGATTG
1 GTTGAGAAGAAGAGATTC
*
7691 GTTGAGAAGAAG-GTTTTC
1 GTTGAGAAGAAGAG-ATTC
7709 GTTGAGA
1 GTTGAGA
7716 TACATGCACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.33, C:0.02, G:0.37, T:0.28
Consensus pattern (18 bp):
GTTGAGAAGAAGAGATTC
Found at i:8792 original size:200 final size:200
Alignment explanation
Indices: 8361--10246 Score: 2509
Period size: 200 Copynumber: 9.4 Consensus size: 200
8351 CATTAAACCA
* * *
8361 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTAGATAG-TTTAAGAATGGATACT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGAT-GTTTTAAGGATCGATACT
* *
8425 TATCATACATGTATCGATACTTTATGCGTGCATCTCCTTTGGGATTCATACTGGACAAAAACTAT
65 TATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTAT
* * *
8490 CGATACTACTAAAACAAGTATCGATACTTTATGTTTACTTATTTTCTCATTAAATCGGTATATTT
130 CGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTT
*
8555 TTACTG
195 TTACCG
* *
8561 GTTACATTGTAAATTTACCTAATATTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
* * *
8626 ATCATATATGTATCGATACTTTATGTGTGTATCTCTTTTGGGATTCATACTGGACAAAAACGTAT
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAA-GTAT
* * * * *
8691 CGATACTACTAAAACAAGTATCTATACTTTACGTTTACCTATTTTCTCATTAAACTGGTATATTG
130 CGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTT
**
8756 TTACTA
195 TTACCG
* *
8762 GTTACATTGTAAATTTACCTATT-CTTTATAATAATCGATTTCGATGTTTTAATGATCGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
* * *
8826 CTCATACATGTATCGATACTTTATACGTGCATCTATTTTGGGATTCATACTGGACAAAAAGTATC
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
* * *
8891 GATACTACTAAAACAAGTATTGATACTTTATGTTTACATATTTTCTTATTAAACCGATATATTTT
131 GATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTTT
8956 TACCG
196 TACCG
* *
8961 GTTACATTGTAAATTTACCTATTACTTTATAATAACCGATTTCGATGTTTTAAGGATCGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
** * *
9026 ATCATACATGTATCGATACTTTATGTATGCATCTCGTTTGGGATTCATAATGGACAAAAAGTATC
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
* *
9091 GATACTACTAAAACAAGTATCGACACTTTATGTTTACCTATTTTCTCATTAAACCGATATAATTT
131 GATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTTT
*
9156 TAGCG
196 TACCG
* * *
9161 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTCCAATGTTTTAAGGATGGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
* * *
9226 ATCATATATGTATCGATACTTTATGTGTGCATCTCGTTTGGGATTCATACTGGACAAAAAGTATC
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
* * *
9291 AATACTACTAAAACAAGTATCGATATTTTATGTTTACCTATTTTCTCATTAAATCGATATATTTT
131 GATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTTT
9356 TACCG
196 TACCG
* *
9361 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTTGATGTTTTAAGAATCGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
* * * * *
9426 CTCACACATGTATCTATACTTTATGCGTGCATCTCTTTTGAGATTCATACTGGACAAAAAGTATT
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
* * * *
9491 GATACTACTAAAACAAGTATCGATACTTTATGTTTACATATTTTCTCATTAAGCAGGTATATTTT
131 GATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTTT
9556 TACCG
196 TACCG
*
9561 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTTGATGTTTTAAGGATCGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
* * * * * *
9626 CTCACACATGTATCTATACTTTATGTGTGCATCTCTTTTGGGATTCATACTGGACAAAACGTATT
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
* **
9691 GATACTACTAAAACAAGTATCGATACTTTATGCTTACCTATTTTCAAATTAAA-CGAATATATTT
131 GATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCG-ATATATTT
9755 TTA-CG
195 TTACCG
* * *
9760 GTTATATTGTAAATTTACCTATTACTTTATAATAATCAGATTCGATGTTTTAAGGATCGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
* * * *
9825 ATCATATATGTATCGATACTTTATGCATGTATCTCGTTTGGGATTCATACTGGACAAAAAGTATC
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
* *
9890 GACACTACTAAAACAAGTATCGATACTTTATGTTTGCCTATTTTCTCATTAAACCGATATATTTT
131 GATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTTT
9955 TACCG
196 TACCG
* * * ** * ** *
9960 GTTACATTATAAATTTACCGATTACCTTCA-AATAATCAATTTCGATGTTTTAAGAATTAAAACT
1 GTTACATTGTAAATTTACCTATTA-CTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACT
* * * * * * *** * * * ** * *
10024 TTTAATA-TTTTCTCGATACTTTCTTTTTACTAACT-TAAGTTTGGTAAGCATAATGGACATAAA
65 TATCATACATGTATCGATACTTTATGCGTGC-ATCTCT---TTTGGGATTCATACTGGACAAAAA
* * * * *
10087 GTATCGATACATA-TAAAA-AAGTATCGATACGTTATGTTAACGTATTTTATCA-TAAACCGGTA
126 GTATCGATAC-TACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATA
*
10149 T-TTTTTAACTG
190 TATTTTT-ACCG
* * * * * ** * * *
10160 CTAAAATTGTAAATTTACCTATTACTTTA-AGTTAATTGGTTTTAAAGTTTTAAGAATCTATACT
1 GTTACATTGTAAATTTACCTATTACTTTATA-ATAATCGGTTTCGATGTTTTAAGGATCGATACT
* *
10224 TTTCATACTTGTATCGATACTTT
65 TATCATACATGTATCGATACTTT
10247 CTTTCTTATT
Statistics
Matches: 1500, Mismatches: 171, Indels: 29
0.88 0.10 0.02
Matches are distributed among these distances:
199 291 0.19
200 1039 0.69
201 135 0.09
202 33 0.02
203 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (200 bp):
GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
GATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTTT
TACCG
Found at i:9039 original size:400 final size:398
Alignment explanation
Indices: 8086--10246 Score: 2774
Period size: 400 Copynumber: 5.4 Consensus size: 398
8076 TATCGTTGTT
* *
8086 TTCATACTAGACAAAAAATATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTT
1 TTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTT
* *
8151 TCTCATTAAACCGTTATAGTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAACCG
66 TCTCATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAACCG
* * *
8216 GTTT-GATG-TTTAAGGATCGATACTTATAATACATGTATTGATACTTTATGCGTGCATCACTTT
131 GTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCGTGCATCTCTTT
* * * * *
8279 TGAGATTCATACTTGAC-AAAACTATCAATACTACTAAAACAAGTATCAATACTTTATGTTTACC
196 TGGGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACC
*
8343 TATTCTCTCATTAAACC----------A--GTTACATTGTAAATTTACCTATTACTTTATAATAA
261 TATTTTCTCATTAAACCGATATATTTTACGGTTACATTGTAAATTTACCTATTACTTTATAATAA
* * *
8396 TCGGTTTAGATAG-TTTAAGAATGGATACTTATCATACATGTATCGATACTTTATGCGTGCATCT
326 TCGGTTTCGAT-GTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCGTGCATCT
*
8460 CCTTTGGGA
390 CTTTTGGGA
* *
8469 TTCATACTGGACAAAAACTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACTTATTT
1 TTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTT
* * * * * *
8534 TCTCATTAAATCGGTATATTTTTACTGGTTACATTGTAAATTTACCTAATATTTTATAATAATCG
66 TCTCATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAACCG
* * *
8599 GTTTCGATGTTTTAAGGATCGATACTTATCATATATGTATCGATACTTTATGTGTGTATCTCTTT
131 GTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCGTGCATCTCTTT
* *
8664 TGGGATTCATACTGGACAAAAACGTATCGATACTACTAAAACAAGTATCTATACTTTACGTTTAC
196 TGGGATTCATACTGGACAAAAA-GTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTAC
* * *
8729 CTATTTTCTCATTAAACTGGTATATTGTTACTAGTTACATTGTAAATTTACCTATT-CTTTATAA
260 CTATTTTCTCATTAAACCGATATATT-TTAC-GGTTACATTGTAAATTTACCTATTACTTTATAA
* * * *
8793 TAATCGATTTCGATGTTTTAATGATCGATACTTCTCATACATGTATCGATACTTTATACGTGCAT
323 TAATCGGTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCGTGCAT
*
8858 CTATTTTGGGA
388 CTCTTTTGGGA
* *
8869 TTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATTGATACTTTATGTTTACATATTT
1 TTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTT
*
8934 TCTTATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAACCG
66 TCTCATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAACCG
* ** *
8999 ATTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGTATGCATCTCGTT
131 GTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCGTGCATCTCTTT
* *
9064 TGGGATTCATAATGGACAAAAAGTATCGATACTACTAAAACAAGTATCGACACTTTATGTTTACC
196 TGGGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACC
9129 TATTTTCTCATTAAACCGATATAATTTTAGCGGTTACATTGTAAATTTACCTATTACTTTATAAT
261 TATTTTCTCATTAAACCGATAT-ATTTTA-CGGTTACATTGTAAATTTACCTATTACTTTATAAT
* * * * *
9194 AATCGGTTCCAATGTTTTAAGGATGGATACTTATCATATATGTATCGATACTTTATGTGTGCATC
324 AATCGGTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCGTGCATC
*
9259 TCGTTTGGGA
389 TCTTTTGGGA
* *
9269 TTCATACTGGACAAAAAGTATCAATACTACTAAAACAAGTATCGATATTTTATGTTTACCTATTT
1 TTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTT
* *
9334 TCTCATTAAATCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATCG
66 TCTCATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAACCG
* * * * *
9399 GTTTTGATGTTTTAAGAATCGATACTTCTCACACATGTATCTATACTTTATGCGTGCATCTCTTT
131 GTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCGTGCATCTCTTT
* * *
9464 TGAGATTCATACTGGACAAAAAGTATTGATACTACTAAAACAAGTATCGATACTTTATGTTTACA
196 TGGGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACC
* * *
9529 TATTTTCTCATTAAGCAGGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAAT
261 TATTTTCTCATTAAACCGATATA-TTTTA-CGGTTACATTGTAAATTTACCTATTACTTTATAAT
* * * * *
9594 AATCGGTTTTGATGTTTTAAGGATCGATACTTCTCACACATGTATCTATACTTTATGTGTGCATC
324 AATCGGTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCGTGCATC
9659 TCTTTTGGGA
389 TCTTTTGGGA
* * *
9669 TTCATACTGGACAAAACGTATTGATACTACTAAAACAAGTATCGATACTTTATGCTTACCTATTT
1 TTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTT
** * *
9734 TCAAATTAAA-CGAATATATTTTTA-CGGTTATATTGTAAATTTACCTATTACTTTATAATAATC
66 TCTCATTAAACCG-ATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAACC
* * * * * *
9797 AGATTCGATGTTTTAAGGATCGATACTTATCATATATGTATCGATACTTTATGCATGTATCTCGT
130 GGTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCGTGCATCTCTT
* *
9862 TTGGGATTCATACTGGACAAAAAGTATCGACACTACTAAAACAAGTATCGATACTTTATGTTTGC
195 TTGGGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTAC
* * *
9927 CTATTTTCTCATTAAACCGATATATTTTTACCGGTTACATTATAAATTTACCGATTACCTTCA-A
260 CTATTTTCTCATTAAACCGATATA-TTTTA-CGGTTACATTGTAAATTTACCTATTA-CTTTATA
** * ** * * * * * * * *** *
9991 ATAATCAATTTCGATGTTTTAAGAATTAAAACTTTTAATA-TTTTCTCGATACTTTCTTTTTACT
322 ATAATCGGTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCGTGC-
* *
10055 AACT-TAAGTTTGGTA
386 ATCTCT---TTTGGGA
** * * * * *
10070 AGCATAATGGACATAAAGTATCGATACATA-TAAAA-AAGTATCGATACGTTATGTTAACGTATT
1 TTCATACTGGACAAAAAGTATCGATAC-TACTAAAACAAGTATCGATACTTTATGTTTACCTATT
* * * * * * *
10133 TTATCA-TAAACCGGTAT-TTTTTAACTGCTAAAATTGTAAATTTACCTATTACTTTA-AGTTAA
65 TTCTCATTAAACCGATATATTTTT-ACCGGTTACATTGTAAATTTACCTATTACTTTATA-ATAA
** ** * * * * *
10195 TTGGTTTTAAAGTTTTAAGAATCTATACTTTTCATACTTGTATCGATACTTT
128 CCGGTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTT
10247 CTTTCTTATT
Statistics
Matches: 1564, Mismatches: 180, Indels: 51
0.87 0.10 0.03
Matches are distributed among these distances:
383 124 0.08
384 4 0.00
385 64 0.04
386 4 0.00
387 54 0.03
398 22 0.01
399 337 0.22
400 898 0.57
401 55 0.04
402 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (398 bp):
TTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTT
TCTCATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAACCG
GTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCGTGCATCTCTTT
TGGGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACC
TATTTTCTCATTAAACCGATATATTTTACGGTTACATTGTAAATTTACCTATTACTTTATAATAA
TCGGTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCGTGCATCTC
TTTTGGGA
Found at i:9228 original size:600 final size:595
Alignment explanation
Indices: 8086--10246 Score: 2884
Period size: 600 Copynumber: 3.6 Consensus size: 595
8076 TATCGTTGTT
* *
8086 TTCATACTAGACAAAAAATATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTT
1 TTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTT
* * *
8151 TCTCATTAAACCGTTATAGTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAACCG
66 TCTCATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATCG
* * * *
8216 GTTT-GATG-TTTAAGGATCGATACTTATAATACATGTATTGATACTTTATGCGTGCATC-ACTT
131 ATTTCGATGTTTTAA-GATCGATACTTCTCATACATGTATCGATACTTTATGCGTGCATCTA-TT
* * * *
8278 TTGAGATTCATACTTGAC-AAAACTATCAATACTACTAAAACAAGTATCAATACTTTATGTTTAC
194 TTGAGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTAC
* *
8342 CTATTCTCTCATTAAACC----------A---GTTACATTGTAAATTTACCTATTACTTTATAAT
259 ATATTTTCTCATTAAACCGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAAT
* * *
8394 AATCGGTTTAGATAG-TTTAAGAATGGATACTTATCATACATGTATCGATACTTTATGCGTGCAT
324 AATCGGTTTAGAT-GTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGTGTGCAT
*
8458 CTCCTTTGGGATTCATACTGGACAAAAACTATCGATACTACTAAAACAAGTATCGATACTTTATG
388 CTCCTTTGGGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATG
* * * *
8523 TTTACTTATTTTCTCATTAAATCGGTATATTTTTACTGGTTACATTGTAAATTTACCTAATATTT
453 TTTACCTATTTTCTCATTAAA-CGATATATTTTTAC-GGTTACATTGTAAATTTACCTATTACTT
8588 TATAATAATCGGTTTCGATGTTTTAAGGATCGATACTTATCATATATGTATCGATACTTTATGTG
516 TATAATAATCGG-TTCGATGTTTTAAGGATCGATACTTATCATATATGTATCGATACTTTATGTG
*
8653 TGTATCTCTTTTGGGA
580 TGTATCTCGTTTGGGA
* *
8669 TTCATACTGGACAAAAACGTATCGATACTACTAAAACAAGTATCTATACTTTACGTTTACCTATT
1 TTCATACTGGACAAAAA-GTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATT
* * * **
8734 TTCTCATTAAACTGGTATATTGTTACTAGTTACATTGTAAATTTACCTATT-CTTTATAATAATC
65 TTCTCATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATC
*
8798 GATTTCGATGTTTTAATGATCGATACTTCTCATACATGTATCGATACTTTATACGTGCATCTATT
130 GATTTCGATGTTTTAA-GATCGATACTTCTCATACATGTATCGATACTTTATGCGTGCATCTATT
* *
8863 TTGGGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATTGATACTTTATGTTTAC
194 TTGAGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTAC
*
8928 ATATTTTCTTATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAA
259 ATATTTTCTCATTAAACCG-TATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAA
* * * *
8993 TAACCGATTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGTATGCAT
323 TAATCGGTTTAGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGTGTGCAT
* * *
9058 CTCGTTTGGGATTCATAATGGACAAAAAGTATCGATACTACTAAAACAAGTATCGACACTTTATG
388 CTCCTTTGGGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATG
*
9123 TTTACCTATTTTCTCATTAAACCGATATAATTTTAGCGGTTACATTGTAAATTTACCTATTACTT
453 TTTACCTATTTTCTCATTAAA-CGATATATTTTTA-CGGTTACATTGTAAATTTACCTATTACTT
* *
9188 TATAATAATCGGTTCCAATGTTTTAAGGATGGATACTTATCATATATGTATCGATACTTTATGTG
516 TATAATAATCGGTT-CGATGTTTTAAGGATCGATACTTATCATATATGTATCGATACTTTATGTG
*
9253 TGCATCTCGTTTGGGA
580 TGTATCTCGTTTGGGA
* *
9269 TTCATACTGGACAAAAAGTATCAATACTACTAAAACAAGTATCGATATTTTATGTTTACCTATTT
1 TTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTT
*
9334 TCTCATTAAATCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATCG
66 TCTCATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATCG
* * * * *
9399 GTTTTGATGTTTTAAGAATCGATACTTCTCACACATGTATCTATACTTTATGCGTGCATCTCTTT
131 ATTTCGATGTTTTAAG-ATCGATACTTCTCATACATGTATCGATACTTTATGCGTGCATCTATTT
*
9464 TGAGATTCATACTGGACAAAAAGTATTGATACTACTAAAACAAGTATCGATACTTTATGTTTACA
195 TGAGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACA
* *
9529 TATTTTCTCATTAAGCAGGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAAT
260 TATTTTCTCATTAAAC-CGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAAT
* * * *
9594 AATCGGTTTTGATGTTTTAAGGATCGATACTTCTCACACATGTATCTATACTTTATGTGTGCATC
324 AATCGGTTTAGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGTGTGCATC
* * * *
9659 TCTTTTGGGATTCATACTGGACAAAACGTATTGATACTACTAAAACAAGTATCGATACTTTATGC
389 TCCTTTGGGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGT
** *
9724 TTACCTATTTTCAAATTAAACGAATATATTTTTACGGTTATATTGTAAATTTACCTATTACTTTA
454 TTACCTATTTTCTCATTAAACG-ATATATTTTTACGGTTACATTGTAAATTTACCTATTACTTTA
* **
9789 TAATAATCAGATTCGATGTTTTAAGGATCGATACTTATCATATATGTATCGATACTTTATGCATG
518 TAATAATC-GGTTCGATGTTTTAAGGATCGATACTTATCATATATGTATCGATACTTTATGTGTG
9854 TATCTCGTTTGGGA
582 TATCTCGTTTGGGA
* *
9868 TTCATACTGGACAAAAAGTATCGACACTACTAAAACAAGTATCGATACTTTATGTTTGCCTATTT
1 TTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTT
* * *
9933 TCTCATTAAACCGATATATTTTTACCGGTTACATTATAAATTTACCGATTACCTTCA-AATAATC
66 TCTCATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTA-CTTTATAATAATC
* ** * * * * * * * *** * *
9997 AATTTCGATGTTTTAAGAATTAAAACTTTTAATA-TTTTCTCGATACTTTCTTTTTACTAACTTA
130 GATTTCGATGTTTTAAG-ATCGATACTTCTCATACATGTATCGATACTTTATGCGTGC-ATC-T-
* ** * * *
10061 AGTTTG-GTAAGCATAATGGACATAAAGTATCGATACATA-TAAAA-AAGTATCGATACGTTATG
191 ATTTTGAG-ATTCATACTGGACAAAAAGTATCGATAC-TACTAAAACAAGTATCGATACTTTATG
* * * * * * *
10123 TTAACGTATTTTATCA-TAAACCGGTAT-TTTTTAACTGCTAAAATTGTAAATTTACCTATTACT
254 TTTACATATTTTCTCATTAAACC-GTATATTTTT-ACCGGTTACATTGTAAATTTACCTATTACT
* * * * * * *
10186 TTA-AGTTAATTGGTTTTA-AAGTTTTAAGAATCTATACTTTTCATACTTGTATCGATACTTT
317 TTATA-ATAATCGG-TTTAGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTT
10247 CTTTCTTATT
Statistics
Matches: 1395, Mismatches: 146, Indels: 58
0.87 0.09 0.04
Matches are distributed among these distances:
583 32 0.02
584 93 0.07
585 63 0.05
586 58 0.04
597 1 0.00
598 20 0.01
599 415 0.30
600 677 0.49
601 34 0.02
602 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (595 bp):
TTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTT
TCTCATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATCG
ATTTCGATGTTTTAAGATCGATACTTCTCATACATGTATCGATACTTTATGCGTGCATCTATTTT
GAGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACAT
ATTTTCTCATTAAACCGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAA
TCGGTTTAGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGTGTGCATCTC
CTTTGGGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTT
ACCTATTTTCTCATTAAACGATATATTTTTACGGTTACATTGTAAATTTACCTATTACTTTATAA
TAATCGGTTCGATGTTTTAAGGATCGATACTTATCATATATGTATCGATACTTTATGTGTGTATC
TCGTTTGGGA
Found at i:12846 original size:20 final size:19
Alignment explanation
Indices: 12796--12847 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
12786 ATGTGAGTTA
* *
12796 TTATATATATTTTACAATG
1 TTATTTATAATTTACAATG
*
12815 TTCTATTA-AATTTACAATG
1 TTAT-TTATAATTTACAATG
12834 CTTATTTATAATTT
1 -TTATTTATAATTT
12848 TAATATGTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (19 bp):
TTATTTATAATTTACAATG
Found at i:12908 original size:27 final size:27
Alignment explanation
Indices: 12870--12921 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
12860 TACGTCTTAG
*
12870 GACAACGCTGACATTTGGAATAATGTA
1 GACAACGATGACATTTGGAATAATGTA
12897 GACAACGATGACATTTGGAATAATG
1 GACAACGATGACATTTGGAATAATG
12922 CAAGTCTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (27 bp):
GACAACGATGACATTTGGAATAATGTA
Found at i:19349 original size:3 final size:3
Alignment explanation
Indices: 19343--19388 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
19333 TTTTTTCACC
19343 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19389 TTTTTATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20147 original size:18 final size:18
Alignment explanation
Indices: 20120--20188 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
20110 TTGAATTTTT
20120 TTATTTATTAAAATAATA
1 TTATTTATTAAAATAATA
* *
20138 TTATTAATTAATAATATTTTA
1 TTATTTATTAA-AATA--ATA
20159 TTATTTATTAAAA-AATA
1 TTATTTATTAAAATAATA
*
20176 ATATATTATTAAA
1 TTAT-TTATTAAA
20189 CTTATTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 5 0.12
18 18 0.43
19 5 0.12
20 2 0.05
21 12 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTTATTAAAATAATA
Found at i:20166 original size:25 final size:25
Alignment explanation
Indices: 20138--20186 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
20128 TAAAATAATA
** *
20138 TTATTAATTAATAATATTTTATTAT
1 TTATTAAAAAATAATATATTATTAT
20163 TTATTAAAAAATAATATATTATTA
1 TTATTAAAAAATAATATATTATTA
20187 AACTTATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTATTAAAAAATAATATATTATTAT
Found at i:33340 original size:30 final size:30
Alignment explanation
Indices: 33306--33366 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
33296 AAATCGTTTG
33306 GAAAATCGTAAAATTAC-TTTAACTTAATTT
1 GAAAATCGTAAAA-TACATTTAACTTAATTT
* *
33336 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCGTAAAATACATTTAACTTAATTT
33366 G
1 G
33367 TTATATCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (30 bp):
GAAAATCGTAAAATACATTTAACTTAATTT
Found at i:35850 original size:21 final size:21
Alignment explanation
Indices: 35768--35851 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
35758 CAGAACCCCA
* *
35768 GGGGGGTATCGATTCCC-CTG
1 GGGGGGAATCGATTCCCTCAG
* *
35788 TGGGGGGAATCGGTTCCCCTTCAA
1 -GGGGGGAATCGATT-CCC-TCAG
* *
35812 AGGGGGAATCGGTTCCCTCAG
1 GGGGGGAATCGATTCCCTCAG
35833 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
35852 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
21 32 0.62
22 6 0.12
23 13 0.25
24 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.37, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCTCAG
Found at i:41945 original size:30 final size:30
Alignment explanation
Indices: 41911--41971 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
41901 AAATCGTTTG
*
41911 GAAAATCGTAAAATTAC-TTTAACTTAATTT
1 GAAAATAGTAAAA-TACATTTAACTTAATTT
* *
41941 GAAAATATTAAAATCCATTTAACTTAATTT
1 GAAAATAGTAAAATACATTTAACTTAATTT
41971 G
1 G
41972 TTATATCGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (30 bp):
GAAAATAGTAAAATACATTTAACTTAATTT
Found at i:42290 original size:38 final size:39
Alignment explanation
Indices: 42216--42297 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
42206 ATTAAAAAGG
* *
42216 AAAAAGAATTAAAATTAGGGTTGAAATAAAATAAAATTA
1 AAAAAGAATTAAAACTAGGGTTGAAATAAAATAAAATAA
**
42255 AAAAAGAATTAATGCTAGGGTT-AAGATAAAA-AAAATAA
1 AAAAAGAATTAAAACTAGGGTTGAA-ATAAAATAAAATAA
42293 AAAAA
1 AAAAA
42298 TAAGGTAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 13 0.34
39 25 0.66
ACGTcount: A:0.63, C:0.01, G:0.13, T:0.22
Consensus pattern (39 bp):
AAAAAGAATTAAAACTAGGGTTGAAATAAAATAAAATAA
Found at i:43533 original size:12 final size:11
Alignment explanation
Indices: 43496--43542 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
43486 ATTGGAGCCG
43496 AAAAATAACAA-
1 AAAAATAA-AAT
43507 AATAAAT-AAAT
1 AA-AAATAAAAT
43518 AAAAATAAAAT
1 AAAAATAAAAT
43529 GAAAAATAAAAT
1 -AAAAATAAAAT
43541 AA
1 AA
43543 TATATATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 6 0.19
11 11 0.34
12 15 0.47
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:43571 original size:15 final size:16
Alignment explanation
Indices: 43551--43583 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
43541 AATATATATA
43551 TTTCAAAA-AATATGT
1 TTTCAAAACAATATGT
*
43566 TTTCAAAACTATATGT
1 TTTCAAAACAATATGT
43582 TT
1 TT
43584 AAAAAAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (16 bp):
TTTCAAAACAATATGT
Found at i:43579 original size:30 final size:30
Alignment explanation
Indices: 43545--43612 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
43535 TAAAATAATA
* * *
43545 TATATATTTCAAAAAA-TATGTTTTCAAAAC
1 TATATATTTAAAAAAACCAT-TTTTAAAAAC
*
43575 TATATGTTTAAAAAAACCATTTTTAAAAAC
1 TATATATTTAAAAAAACCATTTTTAAAAAC
43605 TATATATT
1 TATATATT
43613 ATATGTTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (30 bp):
TATATATTTAAAAAAACCATTTTTAAAAAC
Found at i:43616 original size:67 final size:66
Alignment explanation
Indices: 43545--43694 Score: 160
Period size: 67 Copynumber: 2.2 Consensus size: 66
43535 TAAAATAATA
* * *
43545 TATAT-ATTTCAAAAAATATGTTTTCAAAA-CTATATGTTTAAAAAAACCATTTTTAAAAACTAT
1 TATATGATTTCAAAAAACA--TTTTAAAAATATATATGTTTAAAAAAA-CATTTTTAAAAACTAT
43608 ATAT
63 ATAT
* ** * *
43612 TATATGTTTTCAAAAAACATTTTAAAAATTATATATGTTTTCAAAAATATTTTTCAAAACTATAT
1 TATATGATTTCAAAAAACATTTTAAAAA-TATATATGTTTAAAAAAACATTTTTAAAAACTATAT
43677 AT
65 AT
* *
43679 TATATGTTTTCCAAAA
1 TATATGATTTCAAAAA
43695 CTGATTTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
66 8 0.11
67 38 0.54
68 25 0.35
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (66 bp):
TATATGATTTCAAAAAACATTTTAAAAATATATATGTTTAAAAAAACATTTTTAAAAACTATATA
T
Found at i:43645 original size:36 final size:35
Alignment explanation
Indices: 43575--43694 Score: 126
Period size: 31 Copynumber: 3.5 Consensus size: 35
43565 TTTTCAAAAC
*
43575 TATATG-TTTAAAAAAACCATTTTTAAAAACTATATAT
1 TATATGTTTTCAAAAAA-CA-TTTT-AAAACTATATAT
43612 TATATGTTTTCAAAAAACATTTTAAAA--AT-TA-
1 TATATGTTTTCAAAAAACATTTTAAAACTATATAT
*
43643 TATATGTTTTCAAAAATA-TTTTTCAAAACTATATAT
1 TATATGTTTTCAAAAA-ACATTTT-AAAACTATATAT
*
43679 TATATGTTTTCCAAAA
1 TATATGTTTTCAAAAA
43695 CTGATTTTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 15
0.80 0.03 0.16
Matches are distributed among these distances:
31 20 0.27
32 7 0.10
33 2 0.03
34 2 0.03
35 6 0.08
36 19 0.26
37 8 0.11
38 9 0.12
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (35 bp):
TATATGTTTTCAAAAAACATTTTAAAACTATATAT
Found at i:43676 original size:31 final size:31
Alignment explanation
Indices: 43543--43678 Score: 91
Period size: 31 Copynumber: 4.2 Consensus size: 31
43533 AATAAAATAA
* *
43543 TATATAT-ATTTCAAAAAATATGTTTTCAAAAC
1 TATATATGTTTTC-AAAAATAT-TTTTAAAAAC
** *
43575 --TATATGTTTAAAAAAACCATTTTTAAAAAC
1 TATATATGTTTTCAAAAA-TATTTTTAAAAAC
* *
43605 TATATATTATATGTTTTCAAAAA-ACATTTTAAAAAT
1 ----TA-TATATGTTTTCAAAAATA-TTTTTAAAAAC
*
43641 TATATATGTTTTCAAAAATATTTTTCAAAAC
1 TATATATGTTTTCAAAAATATTTTTAAAAAC
43672 TATATAT
1 TATATAT
43679 TATATGTTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
30 19 0.23
31 35 0.43
32 3 0.04
35 1 0.01
36 9 0.11
37 14 0.17
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (31 bp):
TATATATGTTTTCAAAAATATTTTTAAAAAC
Found at i:43719 original size:2 final size:2
Alignment explanation
Indices: 43714--43745 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
43704 TAAAAAAGAA
43714 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
43746 TCAAAAACCA
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:43721 original size:38 final size:35
Alignment explanation
Indices: 43641--43721 Score: 81
Period size: 39 Copynumber: 2.2 Consensus size: 35
43631 TTTTAAAAAT
* ** *
43641 TATATATGTTTTCAAAAATATTTTTCAAAACTATA
1 TATATATGTTTTCAAAAATATTTTTAAAAAAGAAA
*
43676 TATTATATGTTTTCCAAAACTGATTTTTTAAAAAAGAAA
1 TA-TATATGTTTT-CAAAAAT-A-TTTTTAAAAAAGAAA
43715 TATATAT
1 TATATAT
43722 ATATATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
35 2 0.05
36 10 0.27
37 6 0.16
38 6 0.16
39 13 0.35
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.44
Consensus pattern (35 bp):
TATATATGTTTTCAAAAATATTTTTAAAAAAGAAA
Found at i:45541 original size:29 final size:29
Alignment explanation
Indices: 45497--45566 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
45487 AAAAAATCGG
45497 TTAATTC-GTTCCGTTAATAATTTTCAAA
1 TTAATTCGGTTCCGTTAATAATTTTCAAA
* *
45525 TTAATTCGGTTCGGTTACTAATTTTCAAA
1 TTAATTCGGTTCCGTTAATAATTTTCAAA
*
45554 TAAATTCTGGTTC
1 TTAATTC-GGTTC
45567 AATTAACTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 7 0.19
29 25 0.68
30 5 0.14
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (29 bp):
TTAATTCGGTTCCGTTAATAATTTTCAAA
Found at i:45671 original size:29 final size:29
Alignment explanation
Indices: 45638--45709 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 29
45628 AAAAATTCGG
45638 TTAATTCGGTTCGATTAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
45667 TTAATTC-G---GA-TAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
* *
45691 TAAATTTTGGTTCGATTAA
1 TTAA-TTCGGTTCGATTAA
45710 CCGAACCGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
24 17 0.49
25 4 0.11
26 1 0.03
28 1 0.03
29 9 0.26
30 3 0.09
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (29 bp):
TTAATTCGGTTCGATTAATAATTTTCAAA
Found at i:47446 original size:3 final size:3
Alignment explanation
Indices: 47438--47464 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
47428 CAAGTTTTTG
47438 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
47465 AAAATGAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:53255 original size:22 final size:23
Alignment explanation
Indices: 53209--53255 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
53199 AATGCAAGAG
*
53209 ATAAATTTAAATATACCATTAAA
1 ATAAAATTAAATATACCATTAAA
* *
53232 ATAAAATTAAGTAT-CCCTTAAA
1 ATAAAATTAAATATACCATTAAA
53254 AT
1 AT
53256 CAACCCCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (23 bp):
ATAAAATTAAATATACCATTAAA
Found at i:59999 original size:19 final size:19
Alignment explanation
Indices: 59972--60014 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
59962 CCTTATACTG
*
59972 ATACGAAAGTGCATTAGCA
1 ATACTAAAGTGCATTAGCA
*
59991 ATACTAAAGTGCCTTAGCA
1 ATACTAAAGTGCATTAGCA
*
60010 CTACT
1 ATACT
60015 GGGGATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (19 bp):
ATACTAAAGTGCATTAGCA
Done.