Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008062.1 Hibiscus syriacus cultivar Beakdansim tig00110557_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: 2089609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1213378 original size:2 final size:2
Alignment explanation
Indices: 1213371--1213398 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1213361 TCGAAGCAGA
1213371 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1213399 ACTCACTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1224030 original size:37 final size:37
Alignment explanation
Indices: 1223980--1224056 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
1223970 AATTTTATAT
* * *
1223980 TTACAAGATAATATATATTCAAATTTTTTCTTAACTA
1 TTACAAGATAATATATATTCAAAATTTTCCTTAAATA
*
1224017 TTACAAGATAATATATGTTCAAAATTTTCCTTAAATA
1 TTACAAGATAATATATATTCAAAATTTTCCTTAAATA
1224054 TTA
1 TTA
1224057 GCAATGCACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (37 bp):
TTACAAGATAATATATATTCAAAATTTTCCTTAAATA
Found at i:1224188 original size:21 final size:21
Alignment explanation
Indices: 1224150--1224189 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1224140 ACCACTTGAT
*
1224150 AAATTAATATTTAATAAATGA
1 AAATTAATATTAAATAAATGA
1224171 AAATTAAT-TTAAATTAAAT
1 AAATTAATATTAAA-TAAAT
1224190 ATTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
AAATTAATATTAAATAAATGA
Found at i:1224459 original size:2 final size:2
Alignment explanation
Indices: 1224452--1224497 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1224442 ATTTTTAATC
1224452 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
1224494 AT AT
1 AT AT
1224498 CAACATCGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1228619 original size:17 final size:18
Alignment explanation
Indices: 1228597--1228703 Score: 67
Period size: 19 Copynumber: 5.6 Consensus size: 18
1228587 TCATTTTTAA
1228597 TATTTTAATAA-AATTAT
1 TATTTTAATAATAATTAT
* *
1228614 TATTTTTATAAGTAATTAA
1 TATTTTAATAA-TAATTAT
*
1228633 TATAATTAATAATATATTAT
1 TAT-TTTAATAATA-ATTAT
1228653 TATTGTTTTAATAAATAATTAAT
1 TA---TTTTAAT-AATAATT-AT
* *
1228676 ATAATTT-ATAATAAGT-T
1 -TATTTTAATAATAATTAT
1228693 TATTTTAATAA
1 TATTTTAATAA
1228704 ATATCATAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
16 5 0.07
17 15 0.21
19 16 0.23
20 14 0.20
21 3 0.04
22 8 0.11
23 7 0.10
24 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TATTTTAATAATAATTAT
Found at i:1228672 original size:42 final size:42
Alignment explanation
Indices: 1228609--1228688 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
1228599 TTTTAATAAA
* *
1228609 ATTATTATTTTTATAAGTAATTAATATAATTAATAATATATT
1 ATTATTATTTTAATAAATAATTAATATAATTAATAATATATT
* *
1228651 ATTATTGTTTTAATAAATAATTAATATAATTTATAATA
1 ATTATTATTTTAATAAATAATTAATATAATTAATAATA
1228689 AGTTTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (42 bp):
ATTATTATTTTAATAAATAATTAATATAATTAATAATATATT
Found at i:1234581 original size:6 final size:6
Alignment explanation
Indices: 1234572--1234633 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
1234562 AGTTTCTTCT
* * * * * * *
1234572 TCCTCA TCCTCC TCATCG TCATCA TCCTCA TCCTCA TCCTCC TCATCG
1 TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA
*
1234620 TCATCA TCCTCA TC
1 TCCTCA TCCTCA TC
1234634 AATTTCGTCA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.16, C:0.47, G:0.03, T:0.34
Consensus pattern (6 bp):
TCCTCA
Found at i:1234599 original size:15 final size:15
Alignment explanation
Indices: 1234575--1234633 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
1234565 TTCTTCTTCC
*
1234575 TCATCCTCCTCATCG
1 TCATCATCCTCATCG
*
1234590 TCATCATCCTCATCC
1 TCATCATCCTCATCG
*
1234605 TCATCCTCCTCATCG
1 TCATCATCCTCATCG
1234620 TCATCATCCTCATC
1 TCATCATCCTCATC
1234634 AATTTCGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.17, C:0.46, G:0.03, T:0.34
Consensus pattern (15 bp):
TCATCATCCTCATCG
Found at i:1234608 original size:30 final size:30
Alignment explanation
Indices: 1234572--1234633 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1234562 AGTTTCTTCT
1234572 TCCTCATCCTCCTCATCGTCATCATCCTCA
1 TCCTCATCCTCCTCATCGTCATCATCCTCA
1234602 TCCTCATCCTCCTCATCGTCATCATCCTCA
1 TCCTCATCCTCCTCATCGTCATCATCCTCA
1234632 TC
1 TC
1234634 AATTTCGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.16, C:0.47, G:0.03, T:0.34
Consensus pattern (30 bp):
TCCTCATCCTCCTCATCGTCATCATCCTCA
Found at i:1234632 original size:9 final size:9
Alignment explanation
Indices: 1234575--1234666 Score: 58
Period size: 9 Copynumber: 9.6 Consensus size: 9
1234565 TTCTTCTTCC
*
1234575 TCATCCTCC
1 TCATCCTCA
*
1234584 TCATCGTCA
1 TCATCCTCA
1234593 TCATCCTCA
1 TCATCCTCA
*
1234602 TCCTCATCCTCC
1 ---TCATCCTCA
*
1234614 TCATCGTCA
1 TCATCCTCA
1234623 TCATCCTCA
1 TCATCCTCA
*
1234632 TCAATTTCGTCA
1 TC-A--TCCTCA
* *
1234644 TCATCTTCT
1 TCATCCTCA
*
1234653 TCATCATCA
1 TCATCCTCA
1234662 TCATC
1 TCATC
1234667 ATCTTCTAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
9 48 0.74
10 1 0.02
11 1 0.02
12 15 0.23
ACGTcount: A:0.20, C:0.40, G:0.03, T:0.37
Consensus pattern (9 bp):
TCATCCTCA
Found at i:1234664 original size:6 final size:6
Alignment explanation
Indices: 1234584--1234669 Score: 57
Period size: 6 Copynumber: 14.3 Consensus size: 6
1234574 CTCATCCTCC
* * * * * * *
1234584 TCATCG TCATCA TCCTCA TCCTCA TCCTCC TCATCG TCATCA TCCTCA
1 TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA
* * * *
1234632 TCAAT-T TCGTCA TCATCT TCTTCA TCATCA TCATCA TC
1 TC-ATCA TCATCA TCATCA TCATCA TCATCA TCATCA TC
1234670 TTCTAACTCA
Statistics
Matches: 62, Mismatches: 16, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
5 1 0.02
6 60 0.97
7 1 0.02
ACGTcount: A:0.21, C:0.38, G:0.03, T:0.37
Consensus pattern (6 bp):
TCATCA
Found at i:1236975 original size:32 final size:29
Alignment explanation
Indices: 1236889--1236975 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
1236879 TCGCCTATAC
* *
1236889 ATTATAAAATATCATTAAATTTATTATTTT
1 ATTATAAAATA-CATTAAATTTATCATATT
* *
1236919 CTAATAAAAT-CATTAAATTGTATCATATT
1 ATTATAAAATACATTAAATT-TATCATATT
1236948 ATTATAAAATGACCATTAAATATTATCA
1 ATTATAAAAT-A-CATTAAAT-TTATCA
1236976 AAAAATTACA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
28 9 0.20
29 15 0.33
30 8 0.17
32 13 0.28
33 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (29 bp):
ATTATAAAATACATTAAATTTATCATATT
Found at i:1237516 original size:31 final size:31
Alignment explanation
Indices: 1237473--1237550 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
1237463 CAATTACGTC
* * *
1237473 GGGGTCCATATTGCAAATGGACTAAATTTTG
1 GGGGACCATATTGCAAATGAACTAAATATTG
*
1237504 GGGGACCATATTGAAAATGAACTAAATATTG
1 GGGGACCATATTGCAAATGAACTAAATATTG
* **
1237535 GGAGACTGTATTGCAA
1 GGGGACCATATTGCAA
1237551 GTTTTAAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.28
Consensus pattern (31 bp):
GGGGACCATATTGCAAATGAACTAAATATTG
Found at i:1243350 original size:6 final size:6
Alignment explanation
Indices: 1243339--1243366 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1243329 CTTTTAAAGG
1243339 CGGTCC CGGTCC CGGTCC CGGTCC CGGT
1 CGGTCC CGGTCC CGGTCC CGGTCC CGGT
1243367 ATCCATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.46, G:0.36, T:0.18
Consensus pattern (6 bp):
CGGTCC
Found at i:1247239 original size:6 final size:6
Alignment explanation
Indices: 1247223--1247284 Score: 51
Period size: 5 Copynumber: 10.3 Consensus size: 6
1247213 TTAATACTTA
1247223 AATTATT AATTTT AA-TTT -ATTTT AATGTTT AGATTTT -ATTTT -ATTTT
1 AATT-TT AATTTT AATTTT AATTTT AAT-TTT A-ATTTT AATTTT AATTTT
*
1247270 AATGTTA AATTTT AA
1 AAT-TTT AATTTT AA
1247285 ATTGATATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
4 1 0.02
5 16 0.34
6 12 0.26
7 16 0.34
8 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (6 bp):
AATTTT
Found at i:1247281 original size:23 final size:24
Alignment explanation
Indices: 1247230--1247284 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1247220 TTAAATTATT
1247230 AATTTTAATTTATTTTAATGTTTA
1 AATTTTAATTTATTTTAATGTTTA
* *
1247254 GATTTTATTTTATTTTAATG-TTA
1 AATTTTAATTTATTTTAATGTTTA
1247277 AATTTTAA
1 AATTTTAA
1247285 ATTGATATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (24 bp):
AATTTTAATTTATTTTAATGTTTA
Found at i:1248872 original size:2 final size:2
Alignment explanation
Indices: 1248865--1248896 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1248855 AAGATTTTGA
1248865 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
1248897 CGCCGTCGAT
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:1249444 original size:9 final size:9
Alignment explanation
Indices: 1249430--1249562 Score: 62
Period size: 9 Copynumber: 14.3 Consensus size: 9
1249420 TTCAATTCCC
1249430 TTATTTATT
1 TTATTTATT
1249439 TTATTTCATT
1 TTATTT-ATT
* *
1249449 TATTTTTGTT
1 T-TATTTATT
1249459 TCTATTTACTT
1 T-TATTTA-TT
1249470 ATTCATTTTATT
1 -TT-A-TTTATT
*
1249482 ATTA-TTATGC
1 -TTATTTAT-T
*
1249492 TT-TTCATT
1 TTATTTATT
1249500 TTATTTATT
1 TTATTTATT
1249509 TTATTTA--
1 TTATTTATT
*
1249516 TTATTTCTT
1 TTATTTATT
1249525 CTT-TTTATT
1 -TTATTTATT
*
1249534 TTATTTATC
1 TTATTTATT
*
1249543 TCATTTA-T
1 TTATTTATT
*
1249551 TTATTTCTT
1 TTATTTATT
1249560 TTA
1 TTA
1249563 CCTTTTTATT
Statistics
Matches: 94, Mismatches: 16, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
7 6 0.06
8 9 0.10
9 47 0.50
10 13 0.14
11 8 0.09
12 7 0.07
13 4 0.04
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.71
Consensus pattern (9 bp):
TTATTTATT
Found at i:1249487 original size:23 final size:23
Alignment explanation
Indices: 1249461--1249512 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1249451 TTTTTGTTTC
1249461 TATT-TACTTATTCATTTTATTAT
1 TATTATACTT-TTCATTTTATTAT
*
1249484 TATTATGCTTTTCATTTTATTTAT
1 TATTATACTTTTCATTTTA-TTAT
1249508 T-TTAT
1 TATTAT
1249513 TTATTATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (23 bp):
TATTATACTTTTCATTTTATTAT
Found at i:1249540 original size:29 final size:29
Alignment explanation
Indices: 1249474--1249541 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
1249464 TTACTTATTC
1249474 ATTTTA-TTA-TTATTATGCTTTTCATTTT
1 ATTTTATTTATTTATTAT-CTTTTCATTTT
*
1249502 A-TTTATTTTATTTATTAT-TTCTTCTTTTT
1 ATTTTA-TTTATTTATTATCTT-TTCATTTT
1249531 ATTTTATTTAT
1 ATTTTATTTAT
1249542 CTCATTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
27 4 0.12
28 3 0.09
29 16 0.47
30 11 0.32
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.72
Consensus pattern (29 bp):
ATTTTATTTATTTATTATCTTTTCATTTT
Found at i:1249570 original size:34 final size:34
Alignment explanation
Indices: 1249497--1249574 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
1249487 TATGCTTTTC
* * **
1249497 ATTTTATTTATTTTATTTATTATTTCTTCTTTTT
1 ATTTTATTTATCTCATTTATTATTTCTTCTTCCT
1249531 ATTTTATTTATCTCATTTATTTATTTCTT-TTACCT
1 ATTTTATTTATCTCATTTA-TTATTTCTTCTT-CCT
1249566 -TTTTATTTA
1 ATTTTATTTA
1249575 CTTTTCTACT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 28 0.74
35 10 0.26
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (34 bp):
ATTTTATTTATCTCATTTATTATTTCTTCTTCCT
Found at i:1250095 original size:12 final size:12
Alignment explanation
Indices: 1250078--1250114 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1250068 TAGAGTTGAT
1250078 AAGTTGAATTTG
1 AAGTTGAATTTG
1250090 AAGTTGAATTTG
1 AAGTTGAATTTG
*
1250102 AAGTTAAATTTG
1 AAGTTGAATTTG
1250114 A
1 A
1250115 CTTATCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:1251181 original size:37 final size:37
Alignment explanation
Indices: 1251126--1251197 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 37
1251116 AGAGTCGAGG
*
1251126 GTTTACCTATGTCTTTCGGGACATATGGACAATTATA
1 GTTTACCTATGTCTTTCGGAACATATGGACAATTATA
1251163 GTTTACCTATGT-TATTCGGAACATATGGACAATTA
1 GTTTACCTATGTCT-TTCGGAACATATGGACAATTA
1251198 CATAGGTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 1 0.03
37 32 0.97
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (37 bp):
GTTTACCTATGTCTTTCGGAACATATGGACAATTATA
Found at i:1260103 original size:23 final size:21
Alignment explanation
Indices: 1260047--1260107 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
1260037 TTCTGGTGCA
*
1260047 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
* *
1260067 GAGGGAACCAATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
1260088 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
1260108 ACAGGGGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 1 0.03
23 15 0.44
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:1260115 original size:20 final size:20
Alignment explanation
Indices: 1260090--1260127 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1260080 CCCCCTTTGA
*
1260090 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
1260110 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
1260128 TGGGGTTTTG
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:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:1265671 original size:17 final size:17
Alignment explanation
Indices: 1265614--1265671 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
1265604 CAAAAATAGA
*
1265614 ATATTAAGAAAATATAT
1 ATATTAAGAAAAAATAT
* *
1265631 ATATAAACGTATAAAATAT
1 ATATTAA-G-AAAAAATAT
*
1265650 AATATTAAGAAAAAATGT
1 -ATATTAAGAAAAAATAT
1265668 ATAT
1 ATAT
1265672 ACATAGTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
17 10 0.31
18 8 0.25
19 8 0.25
20 6 0.19
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (17 bp):
ATATTAAGAAAAAATAT
Found at i:1265792 original size:21 final size:21
Alignment explanation
Indices: 1265754--1265794 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1265744 TAGTATAATA
*
1265754 TAAATAAAAAAAGGAATATAG
1 TAAATAAAAAAAGAAATATAG
1265775 TAAATAAATAAAA-AAATATA
1 TAAATAAA-AAAAGAAATATA
1265795 ATTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (21 bp):
TAAATAAAAAAAGAAATATAG
Found at i:1267350 original size:21 final size:21
Alignment explanation
Indices: 1267254--1267343 Score: 153
Period size: 21 Copynumber: 4.3 Consensus size: 21
1267244 AGTTTCCAGA
1267254 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
1267275 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
1267296 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* *
1267317 ATCGCAATGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
1267338 ATCGCA
1 ATCGCA
1267344 CTGCGAATAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:1267430 original size:21 final size:20
Alignment explanation
Indices: 1267404--1267507 Score: 59
Period size: 21 Copynumber: 5.0 Consensus size: 20
1267394 GATTTACATA
1267404 TTCGCAGTGCGATAGTCCAAG
1 TTCGC-GTGCGATAGTCCAAG
* * *
1267425 TTCGCATTGCGATTTATTCCAAA
1 TTCGC-GTGCGA--TAGTCCAAG
* *
1267448 TTCG-TTGCGATAGTCGAAG
1 TTCGCGTGCGATAGTCCAAG
* *
1267467 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCG-TGCGA--TAGTCCAAG
*
1267490 TTCG-TTGCGATAGTCCAA
1 TTCGCGTGCGATAGTCCAA
1267508 AATCGCAACG
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
19 17 0.26
21 27 0.42
23 21 0.32
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (20 bp):
TTCGCGTGCGATAGTCCAAG
Found at i:1267468 original size:42 final size:42
Alignment explanation
Indices: 1267411--1267507 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
1267401 ATATTCGCAG
1267411 TGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCGT
1 TGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCGT
* *
1267453 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
1 TGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCGT
1267495 TGCGATAGTCCAA
1 TGCGATAGTCCAA
1267508 AATCGCAACG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.34
Consensus pattern (42 bp):
TGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCGT
Found at i:1268522 original size:27 final size:27
Alignment explanation
Indices: 1268492--1268550 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
1268482 AAATTCTAAA
* *
1268492 TTTTTAGGGG-TGACTTCTCTCTATAGG
1 TTTTTAGGGGCT-ACCTCTCTCCATAGG
*
1268519 TTTTTAGGGGCTACCTCTCTCCCTAGG
1 TTTTTAGGGGCTACCTCTCTCCATAGG
1268546 TTTTT
1 TTTTT
1268551 CCTACTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (27 bp):
TTTTTAGGGGCTACCTCTCTCCATAGG
Found at i:1272832 original size:6 final size:6
Alignment explanation
Indices: 1272818--1272874 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
1272808 ACAATGTAAC
* *
1272818 AAAG-A AAAGGA AAAGAA AAAGAA AAAGAA AATA-AT AAA-AA AAAGTAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAAG-AA
1272865 AAA-AA AAAGA
1 AAAGAA AAAGA
1272875 TAACAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
5 14 0.32
6 24 0.55
7 6 0.14
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:1272859 original size:23 final size:25
Alignment explanation
Indices: 1272833--1272886 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
1272823 AAAGGAAAAG
* *
1272833 AAAAAG-AAAAAGAAA-ATAATAAA
1 AAAAAGAAAAAAAAAAGATAACAAA
1272856 AAAAAGTAAAAAAAAAAGATAACAAA
1 AAAAAG-AAAAAAAAAAGATAACAAA
1272882 AAAAA
1 AAAAA
1272887 TGTAACGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 6 0.23
25 8 0.31
26 12 0.46
ACGTcount: A:0.83, C:0.02, G:0.07, T:0.07
Consensus pattern (25 bp):
AAAAAGAAAAAAAAAAGATAACAAA
Found at i:1272868 original size:26 final size:27
Alignment explanation
Indices: 1272839--1272891 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
1272829 AAAGAAAAAG
* *
1272839 AAAAAGAAA-ATAATAAAAAAAA-GTA
1 AAAAAAAAAGATAACAAAAAAAATGTA
1272864 AAAAAAAAAGATAACAAAAAAAATGTA
1 AAAAAAAAAGATAACAAAAAAAATGTA
1272891 A
1 A
1272892 CGCAGCTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 12 0.50
27 4 0.17
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.11
Consensus pattern (27 bp):
AAAAAAAAAGATAACAAAAAAAATGTA
Found at i:1272892 original size:14 final size:13
Alignment explanation
Indices: 1272813--1272892 Score: 62
Period size: 12 Copynumber: 6.4 Consensus size: 13
1272803 AGAAAACAAT
*
1272813 GTAACAAAGAAAA
1 GTAACAAAAAAAA
* *
1272826 GGAA-AAGAAAAA
1 GTAACAAAAAAAA
*
1272838 G-AA-AAAGAAAA
1 GTAACAAAAAAAA
*
1272849 -TAATAAAAAAAA
1 GTAACAAAAAAAA
1272861 GTAA-AAAAAAAA
1 GTAACAAAAAAAA
1272873 GATAACAAAAAAAA
1 G-TAACAAAAAAAA
1272887 TGTAAC
1 -GTAAC
1272893 GCAGCTACAG
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
11 10 0.18
12 23 0.42
13 9 0.16
14 12 0.22
15 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.12, T:0.09
Consensus pattern (13 bp):
GTAACAAAAAAAA
Found at i:1274333 original size:36 final size:36
Alignment explanation
Indices: 1274286--1274354 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
1274276 AGTAGTACAT
*
1274286 TTTATTGAAATAA-AATATTATAA-ATTATATTAATTA
1 TTTATTAAAATAATAATA-TATAATA-TATATTAATTA
1274322 TTTATTAAAATAATAATATATAATATATATTAA
1 TTTATTAAAATAATAATATATAATATATATTAA
1274355 AAAGTATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 25 0.83
37 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (36 bp):
TTTATTAAAATAATAATATATAATATATATTAATTA
Found at i:1274419 original size:19 final size:20
Alignment explanation
Indices: 1274397--1274446 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
1274387 ATTAAAATGT
*
1274397 TATTATATCATTATATTAA-
1 TATTATATCATTATATAAAG
*
1274416 TATTAAAT-A-TATATAAAG
1 TATTATATCATTATATAAAG
1274434 TATTAT-TCATTAT
1 TATTATATCATTAT
1274447 TAATTATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
17 8 0.32
18 7 0.28
19 10 0.40
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
TATTATATCATTATATAAAG
Found at i:1275597 original size:109 final size:109
Alignment explanation
Indices: 1275424--1275641 Score: 346
Period size: 109 Copynumber: 2.0 Consensus size: 109
1275414 TTTTCAACCA
* * *
1275424 ATTTATAAGCAAATTAATCATATTTACATTTATGTCATTCAATATATTAAGATAAATATAATATT
1 ATTTATAAGCAAATTAATCATATTTACATCTATGTCATCCAATATATTAAGATAAACATAATATT
* *
1275489 AATTAAACTAAACGTCGAACCCAAAGGTGATTTAGGTGTGATCG
66 AATTAAACTAAACGTCAAACCCAAACGTGATTTAGGTGTGATCG
* ** *
1275533 ATTTATATGCAAATTAATCATATTTACATCTATGTCATCCAATATATTATTATAACCATAATATT
1 ATTTATAAGCAAATTAATCATATTTACATCTATGTCATCCAATATATTAAGATAAACATAATATT
*
1275598 AATTAAACTAAACGTCAAATCCAAACGTGATTTAGGTGTGATCG
66 AATTAAACTAAACGTCAAACCCAAACGTGATTTAGGTGTGATCG
1275642 GTCTTCGTAT
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
109 99 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (109 bp):
ATTTATAAGCAAATTAATCATATTTACATCTATGTCATCCAATATATTAAGATAAACATAATATT
AATTAAACTAAACGTCAAACCCAAACGTGATTTAGGTGTGATCG
Found at i:1278884 original size:31 final size:31
Alignment explanation
Indices: 1278848--1278921 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 31
1278838 ATGTACCAAA
* *
1278848 ATTGGATATTTTGTCAAAGGACAAGTACCAC
1 ATTGGATATTTTGTAAAAGGACAAGTACAAC
* * *
1278879 ATTGGACA-TTT-TAAAAGTACAGGTACAAC
1 ATTGGATATTTTGTAAAAGGACAAGTACAAC
1278908 ATTGGATATTTTGT
1 ATTGGATATTTTGT
1278922 TTAAGTACAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 21 0.60
30 6 0.17
31 8 0.23
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (31 bp):
ATTGGATATTTTGTAAAAGGACAAGTACAAC
Found at i:1278931 original size:31 final size:31
Alignment explanation
Indices: 1278848--1278948 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 31
1278838 ATGTACCAAA
* * * *
1278848 ATTGGATATTTTGTCAAAGGACAAGTACCAC
1 ATTGGATATTTTGTAAAAGTACAGGTACAAC
*
1278879 ATTGGACA-TTT-TAAAAGTACAGGTACAAC
1 ATTGGATATTTTGTAAAAGTACAGGTACAAC
** *
1278908 ATTGGATATTTTGTTTAAGTACAGATATCAA-
1 ATTGGATATTTTGTAAAAGTACAGGTA-CAAC
*
1278939 ATTTGATATT
1 ATTGGATATT
1278949 ATCCCTCTAT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 21 0.37
30 6 0.11
31 27 0.47
32 3 0.05
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.36
Consensus pattern (31 bp):
ATTGGATATTTTGTAAAAGTACAGGTACAAC
Found at i:1282507 original size:64 final size:65
Alignment explanation
Indices: 1282433--1282604 Score: 276
Period size: 64 Copynumber: 2.6 Consensus size: 65
1282423 GAGTATGAAA
1282433 TAATATATTTTTTATATAGTCTTGTAATAAATCAACCATCTTCACGTGAATGA-TTTCTTTAATA
1 TAATA-ATTTTTTATATAGTCTTGTAATAAATCAACCATCTTCACGTGAATGAGTTTCTTTAATA
1282497 C
65 C
* *
1282498 TAATAATTTTTTATATAGTCTTGTAATAAATCAACCATCTTCATGTGAATGATGTTTTTTTAATA
1 TAATAATTTTTTATATAGTCTTGTAATAAATCAACCATCTTCACGTGAATGA-GTTTCTTTAATA
*
1282563 T
65 C
*
1282564 TAAT-ATTTTTTATATAGTCTTGTAATAAATCAATCATCTTC
1 TAATAATTTTTTATATAGTCTTGTAATAAATCAACCATCTTC
1282605 GTGGGAATGA
Statistics
Matches: 101, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
64 46 0.46
65 41 0.41
66 14 0.14
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.47
Consensus pattern (65 bp):
TAATAATTTTTTATATAGTCTTGTAATAAATCAACCATCTTCACGTGAATGAGTTTCTTTAATAC
Found at i:1282604 original size:65 final size:65
Alignment explanation
Indices: 1282437--1282621 Score: 293
Period size: 65 Copynumber: 2.9 Consensus size: 65
1282427 ATGAAATAAT
* *
1282437 ATATTTTTTATATAGTCTTGTAATAAATCAACCATCTTCACGTGAATGA--TTTCTTTAATACTA
1 ATATTTTTTATATAGTCTTGTAATAAATCAACCATCTTCATGTGAATGATGTTTTTTTAATACTA
*
1282500 ATAATTTTTTATATAGTCTTGTAATAAATCAACCATCTTCATGTGAATGATGTTTTTTTAATATT
1 AT-ATTTTTTATATAGTCTTGTAATAAATCAACCATCTTCATGTGAATGATGTTTTTTTAATACT
1282565 A
65 A
* * *
1282566 ATATTTTTTATATAGTCTTGTAATAAATCAATCATCTTCGTGGGAATGATGTTTTT
1 ATATTTTTTATATAGTCTTGTAATAAATCAACCATCTTCATGTGAATGATGTTTTT
1282622 ATATAGTCTT
Statistics
Matches: 113, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
63 2 0.02
64 46 0.41
65 51 0.45
66 14 0.12
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (65 bp):
ATATTTTTTATATAGTCTTGTAATAAATCAACCATCTTCATGTGAATGATGTTTTTTTAATACTA
Found at i:1282649 original size:47 final size:47
Alignment explanation
Indices: 1282570--1282673 Score: 136
Period size: 47 Copynumber: 2.2 Consensus size: 47
1282560 ATATTAATAT
* * *
1282570 TTTTTATATAGTCTTGTAATAAATCAATCATCTTCGTGGGAATGATG
1 TTTTTATATAGTCTTGTAATAAATCAACCATCTTCATGGAAATGATG
* ** *
1282617 TTTTTATATAGTCTTGTAGTATTTCAACCATCTTCATGTAAATGATG
1 TTTTTATATAGTCTTGTAATAAATCAACCATCTTCATGGAAATGATG
*
1282664 TTTTTTTATA
1 TTTTTATATA
1282674 TTTTAATCTA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (47 bp):
TTTTTATATAGTCTTGTAATAAATCAACCATCTTCATGGAAATGATG
Found at i:1283114 original size:15 final size:15
Alignment explanation
Indices: 1283094--1283125 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1283084 TCCATGTTTC
1283094 TGTTAGTCCCGAAGG
1 TGTTAGTCCCGAAGG
1283109 TGTTAGTCCCGAAGG
1 TGTTAGTCCCGAAGG
1283124 TG
1 TG
1283126 ATGGTAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (15 bp):
TGTTAGTCCCGAAGG
Found at i:1285139 original size:85 final size:85
Alignment explanation
Indices: 1284960--1285129 Score: 286
Period size: 85 Copynumber: 2.0 Consensus size: 85
1284950 TTTGTGCAAC
* * * *
1284960 ATGCAATCAATTTTGTTTATTGTTCATGTTGTATCCCATGATTACCTGAAAAATGATTCAGAAAG
1 ATGCAATCAACTTTGTTTATCGTTCATGTTGTATCCCATGATTACATGAAAAATGATTAAGAAAG
*
1285025 TTGGTCTGCAGGAAACCTGT
66 TTGATCTGCAGGAAACCTGT
*
1285045 ATGCAATCAACTTTGTTTATCGTTCATGTTGTATCCCATGATTACATGCAAAATGATTAAGAAAG
1 ATGCAATCAACTTTGTTTATCGTTCATGTTGTATCCCATGATTACATGAAAAATGATTAAGAAAG
1285110 TTGATCTGCAGGAAACCTGT
66 TTGATCTGCAGGAAACCTGT
1285130 TTGGCATCAA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (85 bp):
ATGCAATCAACTTTGTTTATCGTTCATGTTGTATCCCATGATTACATGAAAAATGATTAAGAAAG
TTGATCTGCAGGAAACCTGT
Found at i:1287171 original size:18 final size:18
Alignment explanation
Indices: 1287133--1287172 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1287123 TTATAAATTT
*
1287133 AAAATAAAAATATTTAAA
1 AAAATAAAAATATATAAA
* *
1287151 AAAATAAAACTATATATA
1 AAAATAAAAATATATAAA
1287169 AAAA
1 AAAA
1287173 GAGAATATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATAAAAATATATAAA
Found at i:1287610 original size:2 final size:2
Alignment explanation
Indices: 1287598--1287627 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
1287588 ATTTTATAAT
1287598 TA TA TA CTA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA T
1287628 TTGTATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1289302 original size:16 final size:17
Alignment explanation
Indices: 1289281--1289323 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1289271 ATGTAAAAAT
1289281 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
1289297 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
1289314 AAATATTTAA
1 AAATATTTAA
1289324 TCAAATAGGG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:1289733 original size:32 final size:32
Alignment explanation
Indices: 1289692--1289752 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1289682 GTATATGACT
* * *
1289692 ATAATTGAAAGTTTAAAACATTAGACATAGCA
1 ATAATTGAAAATTAAAAACATTAAACATAGCA
*
1289724 ATAATTGAAAATTAAAAATATTAAACATA
1 ATAATTGAAAATTAAAAACATTAAACATA
1289753 ACAAAAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.30
Consensus pattern (32 bp):
ATAATTGAAAATTAAAAACATTAAACATAGCA
Found at i:1289769 original size:32 final size:32
Alignment explanation
Indices: 1289706--1289769 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
1289696 TTGAAAGTTT
* * * *
1289706 AAAACATTAGACATAGCAATAATTGAAAATTA
1 AAAACATTAAACATAACAAAAATAGAAAATTA
* *
1289738 AAAATATTAAACATAACAAAAATAGAGAATTA
1 AAAACATTAAACATAACAAAAATAGAAAATTA
1289770 TTGAGATCGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.23
Consensus pattern (32 bp):
AAAACATTAAACATAACAAAAATAGAAAATTA
Found at i:1297919 original size:30 final size:31
Alignment explanation
Indices: 1297885--1297964 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 31
1297875 ATGATTCAAT
*
1297885 AAGAACAAAAATGGCAAAAA-AA-AAAAAGAA
1 AAGAACAAAAATGGAAAAAATAACAAAAAG-A
1297915 AAGAAGCAAAAA-GGAAAAAATAACAAAAAGA
1 AAGAA-CAAAAATGGAAAAAATAACAAAAAGA
1297946 AAGAACAAAAAT--AAAAAAT
1 AAGAACAAAAATGGAAAAAAT
1297965 GGGACAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
29 7 0.16
30 18 0.40
31 14 0.31
32 6 0.13
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.05
Consensus pattern (31 bp):
AAGAACAAAAATGGAAAAAATAACAAAAAGA
Found at i:1298582 original size:22 final size:22
Alignment explanation
Indices: 1298554--1298604 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1298544 CCCCATCAAT
*
1298554 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATAAAATACCAAA
*
1298576 CCTTTGAGCATAAAATGCCAAA
1 CCTTTGAGCATAAAATACCAAA
1298598 CCTTTGA
1 CCTTTGA
1298605 CCAAACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATAAAATACCAAA
Found at i:1299502 original size:36 final size:36
Alignment explanation
Indices: 1299455--1299559 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
1299445 GTGCTCGCCA
1299455 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
* *
1299491 TTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
1299528 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1299560 TAAACATTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
36 31 0.50
37 31 0.50
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:1299549 original size:37 final size:37
Alignment explanation
Indices: 1299455--1299564 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
1299445 GTGCTCGCCA
1299455 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* *
1299491 TTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
1299528 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
1299565 ATTGAAAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 30 0.46
37 32 0.49
38 3 0.05
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:1299618 original size:15 final size:15
Alignment explanation
Indices: 1299598--1299655 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
1299588 GAGTTTTGTC
1299598 TCTCTTGAGACAGTT
1 TCTCTTGAGACAGTT
* *
1299613 TCTCTTGAAACATTTT
1 TCTCTTGAGACA-GTT
1299629 GTCTCCCTTGAGACAGTTT
1 -TCT--CTTGAGACAG-TT
1299648 TCTCTTGA
1 TCTCTTGA
1299656 AGCATCATCT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
15 11 0.32
16 7 0.21
17 3 0.09
18 3 0.09
19 10 0.29
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (15 bp):
TCTCTTGAGACAGTT
Found at i:1299771 original size:35 final size:36
Alignment explanation
Indices: 1299730--1299800 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 36
1299720 GGAACTAAGT
* * *
1299730 TTTGTCTCTCTTGAGACAGTTT-TCTTAAAACAAAA
1 TTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
1299765 TTTGTCTCCCTTAAGACCGTTTCCCTTGAAACAAAA
1 TTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
1299801 ATATCTTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.37
Consensus pattern (36 bp):
TTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:1300517 original size:106 final size:106
Alignment explanation
Indices: 1300357--1301122 Score: 1039
Period size: 105 Copynumber: 7.3 Consensus size: 106
1300347 GCCATCCGCG
* * * * * *
1300357 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * * *
1300422 GGGACGGTTGATTGTCAACAAACAACTTCTCAATTTCAGAGTCA
63 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1300466 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * **
1300531 ACCGCT-GTTTTCAATAAACAATTTTTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1300571 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1300636 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
1300677 ATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
1300742 ACCGCTGGTTGTCAAC-AA-ATTTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
1300781 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1300846 ACCGCTGCTTGTCAAC-AACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1300886 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
1300951 ACCGCTGCTTGTCAAC-AA-AA-TT-TC-A-TTCAGAATCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * * *
1300986 ATTTCAACTTCACAACGAAAGATGTTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * ** *
1301051 ACGGTTGGTTGTCAACAACCAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
1301092 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
1301123 TGGAACAATG
Statistics
Matches: 593, Mismatches: 56, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
100 80 0.13
101 2 0.00
102 3 0.01
103 4 0.01
104 100 0.17
105 201 0.34
106 178 0.30
107 3 0.01
109 22 0.04
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
Found at i:1310628 original size:2 final size:2
Alignment explanation
Indices: 1310621--1310673 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1310611 CTAATTGATA
1310621 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
1310663 AT AT AT AT AT A
1 AT AT AT AT AT A
1310674 ACGGCTAATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1366000 original size:14 final size:15
Alignment explanation
Indices: 1365973--1366002 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1365963 TCCCCTAATT
1365973 AAATAAATAATATAA
1 AAATAAATAATATAA
1365988 AAATAAA-AATATAA
1 AAATAAATAATATAA
1366002 A
1 A
1366003 CTATACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAATAATATAA
Found at i:1366002 original size:23 final size:23
Alignment explanation
Indices: 1365972--1366028 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
1365962 TTCCCCTAAT
1365972 TAAATAAATAATA-TAAAAATAAA
1 TAAATAAATAATACT-AAAATAAA
1365995 -AATATAAACT-ATACTAAAATAAA
1 TAA-ATAAA-TAATACTAAAATAAA
1366018 TAAATAAATAA
1 TAAATAAATAA
1366029 AACATTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
22 3 0.10
23 22 0.76
24 4 0.14
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (23 bp):
TAAATAAATAATACTAAAATAAA
Found at i:1366069 original size:24 final size:23
Alignment explanation
Indices: 1366015--1366069 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
1366005 ATACTAAAAT
*
1366015 AAATAAAT-AAATAAAACATTCA
1 AAATAATTAAAATAAAACATTCA
* *
1366037 AAATAATTAAAATAACACAATTTA
1 AAATAATTAAAATAAAAC-ATTCA
*
1366061 AAATTATTA
1 AAATAATTA
1366070 TCATATCAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 7 0.26
23 8 0.30
24 12 0.44
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATAATTAAAATAAAACATTCA
Found at i:1367795 original size:18 final size:18
Alignment explanation
Indices: 1367772--1367839 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 18
1367762 ACCCTACCCG
1367772 AAATAATATATTTATTAA
1 AAATAATATATTTATTAA
* * *
1367790 AAATAATTTTATTCAATAA
1 AAATAA-TATATTTATTAA
*
1367809 AAATAAGA-ATTTCATTGAAA
1 AAATAATATATTT-ATT--AA
1367829 AAATAATATAT
1 AAATAATATAT
1367840 AGAGTGACAC
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
17 3 0.08
18 8 0.22
19 15 0.41
20 9 0.24
21 2 0.05
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
AAATAATATATTTATTAA
Found at i:1368764 original size:8 final size:8
Alignment explanation
Indices: 1368751--1368782 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
1368741 AAATGGCGAT
1368751 GGCAATGA
1 GGCAATGA
1368759 GGCAATGA
1 GGCAATGA
1368767 GGCAATGA
1 GGCAATGA
*
1368775 GCCAATGA
1 GGCAATGA
1368783 CCCACCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.38, C:0.16, G:0.34, T:0.12
Consensus pattern (8 bp):
GGCAATGA
Found at i:1369365 original size:37 final size:36
Alignment explanation
Indices: 1369292--1369366 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 36
1369282 GTTGGAAAAT
1369292 ATTTATATATTTTCTTTAAAAAAATTAAATCCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAT-CATAAA
* * *
1369329 ATTTATATAATTTTTTTTACAAAATTTAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAATCATAAA
1369366 A
1 A
1369367 AGTTTAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 15 0.45
39 4 0.12
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAAATTAAATCATAAA
Found at i:1370287 original size:40 final size:41
Alignment explanation
Indices: 1370227--1370306 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 41
1370217 GACAAACTCT
* *
1370227 TTATTCGTGTTCATTCATTTAAT-TAAACGAACATAAAATA
1 TTATTCATGTCCATTCATTTAATATAAACGAACATAAAATA
*
1370267 TTATTCATGTCCATTTATTTAATAAATAAACGAACATAAA
1 TTATTCATGTCCATTCATTTAAT--ATAAACGAACATAAA
1370307 CGAATTTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 20 0.59
43 14 0.41
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (41 bp):
TTATTCATGTCCATTCATTTAATATAAACGAACATAAAATA
Found at i:1371047 original size:16 final size:16
Alignment explanation
Indices: 1371028--1371061 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1371018 CAATATACGA
1371028 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
1371044 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
1371060 AT
1 AT
1371062 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:1371137 original size:14 final size:16
Alignment explanation
Indices: 1371101--1371137 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1371091 TATTAATGTA
1371101 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
1371118 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
1371133 T-AATA
1 TGAATA
1371138 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:1371766 original size:16 final size:16
Alignment explanation
Indices: 1371741--1371800 Score: 111
Period size: 16 Copynumber: 3.8 Consensus size: 16
1371731 AATTAGGTGG
*
1371741 TGACATGTGTCACCAA
1 TGACACGTGTCACCAA
1371757 TGACACGTGTCACCAA
1 TGACACGTGTCACCAA
1371773 TGACACGTGTCACCAA
1 TGACACGTGTCACCAA
1371789 TGACACGTGTCA
1 TGACACGTGTCA
1371801 TGATCATGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (16 bp):
TGACACGTGTCACCAA
Found at i:1372325 original size:35 final size:35
Alignment explanation
Indices: 1372275--1372350 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1372265 AATTGAATTT
* *
1372275 AATTGAATTATTTTGGAATTTAAGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAAGGTTTAGAATGA
**
1372310 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAAGGTTTAGAATGA
1372345 AATTGA
1 AATTGA
1372351 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAAGGTTTAGAATGA
Found at i:1374659 original size:2 final size:2
Alignment explanation
Indices: 1374652--1374676 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1374642 GCTTGTGTAT
1374652 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1374677 TGGATAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1376869 original size:31 final size:31
Alignment explanation
Indices: 1376834--1376914 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
1376824 ATGTATCATG
1376834 TCATTAATTTAAACACGTGTTATGTGCCACA
1 TCATTAATTTAAACACGTGTTATGTGCCACA
*
1376865 TCATTAATTTAAACAAGTGTTATGTGCCACA
1 TCATTAATTTAAACACGTGTTATGTGCCACA
1376896 TCATT-ATTTATATACACGT
1 TCATTAATTTA-A-ACACGT
1376915 TAAATATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 5 0.11
31 36 0.78
32 5 0.11
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.38
Consensus pattern (31 bp):
TCATTAATTTAAACACGTGTTATGTGCCACA
Found at i:1393903 original size:212 final size:212
Alignment explanation
Indices: 1393536--1393958 Score: 837
Period size: 212 Copynumber: 2.0 Consensus size: 212
1393526 ACGGAGATAC
1393536 ACTGCATCCCGTGAAGAAACCCCGAGCGTCTGATTGAACTAGAATTATCATTATTCCTTCCAAAA
1 ACTGCATCCCGTGAAGAAACCCCGAGCGTCTGATTGAACTAGAATTATCATTATTCCTTCCAAAA
*
1393601 ATCAGCGGCATGGTATTTAGTAAATGAAACAAGCAGAGAAAAGATAAGGAGCGTAGAAGCAGTGG
66 ATCAGCGGAATGGTATTTAGTAAATGAAACAAGCAGAGAAAAGATAAGGAGCGTAGAAGCAGTGG
1393666 GTATTAATAATAATATCTGTTGAAGCGCACATGGTAAGGCGATATTTCCGCCATTGTTGAAGAGA
131 GTATTAATAATAATATCTGTTGAAGCGCACATGGTAAGGCGATATTTCCGCCATTGTTGAAGAGA
1393731 GAGAGAGAGAGAGAGAG
196 GAGAGAGAGAGAGAGAG
1393748 ACTGCATCCCGTGAAGAAACCCCGAGCGTCTGATTGAACTAGAATTATCATTATTCCTTCCAAAA
1 ACTGCATCCCGTGAAGAAACCCCGAGCGTCTGATTGAACTAGAATTATCATTATTCCTTCCAAAA
1393813 ATCAGCGGAATGGTATTTAGTAAATGAAACAAGCAGAGAAAAGATAAGGAGCGTAGAAGCAGTGG
66 ATCAGCGGAATGGTATTTAGTAAATGAAACAAGCAGAGAAAAGATAAGGAGCGTAGAAGCAGTGG
1393878 GTATTAATAATAATATCTGTTGAAGCGCACATGGTAAGGCGATATTTCCGCCATTGTTGAAGAGA
131 GTATTAATAATAATATCTGTTGAAGCGCACATGGTAAGGCGATATTTCCGCCATTGTTGAAGAGA
1393943 GAGAGAGAGAGAGAGA
196 GAGAGAGAGAGAGAGA
1393959 ATAAAATAAT
Statistics
Matches: 210, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 210 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (212 bp):
ACTGCATCCCGTGAAGAAACCCCGAGCGTCTGATTGAACTAGAATTATCATTATTCCTTCCAAAA
ATCAGCGGAATGGTATTTAGTAAATGAAACAAGCAGAGAAAAGATAAGGAGCGTAGAAGCAGTGG
GTATTAATAATAATATCTGTTGAAGCGCACATGGTAAGGCGATATTTCCGCCATTGTTGAAGAGA
GAGAGAGAGAGAGAGAG
Found at i:1394955 original size:13 final size:13
Alignment explanation
Indices: 1394931--1394964 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1394921 TATAATTATT
1394931 TTAAAA-TTTTAA
1 TTAAAATTTTTAA
1394943 TTAAAATTTTTAA
1 TTAAAATTTTTAA
*
1394956 TTATAATTT
1 TTAAAATTT
1394965 AATAACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAAATTTTTAA
Found at i:1404299 original size:580 final size:580
Alignment explanation
Indices: 1403199--1404362 Score: 2328
Period size: 580 Copynumber: 2.0 Consensus size: 580
1403189 GAATCGAGCG
1403199 GCTCCATAGATTGTAGTTCTCAATTCCAGTCAGCTGATGCGAGACCAGCACTATCCCCGGCGTAT
1 GCTCCATAGATTGTAGTTCTCAATTCCAGTCAGCTGATGCGAGACCAGCACTATCCCCGGCGTAT
1403264 CCGATGGATGAAGATAAAGGGGATGAGTGAAATCGATGGAATCCATGAAGGAAAAGAGGGGGGAA
66 CCGATGGATGAAGATAAAGGGGATGAGTGAAATCGATGGAATCCATGAAGGAAAAGAGGGGGGAA
1403329 AAAAACGAAACTCTGGAAAGAAAAAAGAAAGGGGAAAAAAATTAGAGAGAGTGATATATCAAACG
131 AAAAACGAAACTCTGGAAAGAAAAAAGAAAGGGGAAAAAAATTAGAGAGAGTGATATATCAAACG
1403394 AGACTTTTCAACTGATACCATGTTAAAACACGTGTGATTAATACTTTGTATCTCTCCATTATACT
196 AGACTTTTCAACTGATACCATGTTAAAACACGTGTGATTAATACTTTGTATCTCTCCATTATACT
1403459 ATCATGTACATCATCCTTTTATACAATTTAAAAACAAACTAATACACTAACTAACTTCTAACTGA
261 ATCATGTACATCATCCTTTTATACAATTTAAAAACAAACTAATACACTAACTAACTTCTAACTGA
1403524 TCATTAACTAAATAACAAACTTTCTAATAAACTTTTATCACCTCAACACACGGTTCCTTTCTCGT
326 TCATTAACTAAATAACAAACTTTCTAATAAACTTTTATCACCTCAACACACGGTTCCTTTCTCGT
1403589 CCGATATGTTGAACACGAACCTCCCAATGATAGTCCAGCATGGCATAGATATGTGCTAATATATT
391 CCGATATGTTGAACACGAACCTCCCAATGATAGTCCAGCATGGCATAGATATGTGCTAATATATT
1403654 AATAGTGCCACCCTTTGGTTTTCTATCCCGCAGCAAATGGATGGCGTGGCAGCTATCGGATTCTA
456 AATAGTGCCACCCTTTGGTTTTCTATCCCGCAGCAAATGGATGGCGTGGCAGCTATCGGATTCTA
1403719 CAACAACTCTCTGCTTCCCTAAATTCCACGCGCATTTCAGCCCGACATAAATTTCCCACA
521 CAACAACTCTCTGCTTCCCTAAATTCCACGCGCATTTCAGCCCGACATAAATTTCCCACA
1403779 GCTCCATAGATTGTAGTTCTCAATTCCAGTCAGCTGATGCGAGACCAGCACTATCCCCGGCGTAT
1 GCTCCATAGATTGTAGTTCTCAATTCCAGTCAGCTGATGCGAGACCAGCACTATCCCCGGCGTAT
1403844 CCGATGGATGAAGATAAAGGGGATGAGTGAAATCGATGGAATCCATGAAGGAAAAGAGGGGGGAA
66 CCGATGGATGAAGATAAAGGGGATGAGTGAAATCGATGGAATCCATGAAGGAAAAGAGGGGGGAA
1403909 AAAAACGAAACTCTGGAAAGAAAAAAGAAAGGGGAAAAAAATTAGAGAGAGTGATATATCAAACG
131 AAAAACGAAACTCTGGAAAGAAAAAAGAAAGGGGAAAAAAATTAGAGAGAGTGATATATCAAACG
1403974 AGACTTTTCAACTGATACCATGTTAAAACACGTGTGATTAATACTTTGTATCTCTCCATTATACT
196 AGACTTTTCAACTGATACCATGTTAAAACACGTGTGATTAATACTTTGTATCTCTCCATTATACT
1404039 ATCATGTACATCATCCTTTTATACAATTTAAAAACAAACTAATACACTAACTAACTTCTAACTGA
261 ATCATGTACATCATCCTTTTATACAATTTAAAAACAAACTAATACACTAACTAACTTCTAACTGA
1404104 TCATTAACTAAATAACAAACTTTCTAATAAACTTTTATCACCTCAACACACGGTTCCTTTCTCGT
326 TCATTAACTAAATAACAAACTTTCTAATAAACTTTTATCACCTCAACACACGGTTCCTTTCTCGT
1404169 CCGATATGTTGAACACGAACCTCCCAATGATAGTCCAGCATGGCATAGATATGTGCTAATATATT
391 CCGATATGTTGAACACGAACCTCCCAATGATAGTCCAGCATGGCATAGATATGTGCTAATATATT
1404234 AATAGTGCCACCCTTTGGTTTTCTATCCCGCAGCAAATGGATGGCGTGGCAGCTATCGGATTCTA
456 AATAGTGCCACCCTTTGGTTTTCTATCCCGCAGCAAATGGATGGCGTGGCAGCTATCGGATTCTA
1404299 CAACAACTCTCTGCTTCCCTAAATTCCACGCGCATTTCAGCCCGACATAAATTTCCCACA
521 CAACAACTCTCTGCTTCCCTAAATTCCACGCGCATTTCAGCCCGACATAAATTTCCCACA
1404359 GCTC
1 GCTC
1404363 AGCTTCAAGC
Statistics
Matches: 584, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
580 584 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (580 bp):
GCTCCATAGATTGTAGTTCTCAATTCCAGTCAGCTGATGCGAGACCAGCACTATCCCCGGCGTAT
CCGATGGATGAAGATAAAGGGGATGAGTGAAATCGATGGAATCCATGAAGGAAAAGAGGGGGGAA
AAAAACGAAACTCTGGAAAGAAAAAAGAAAGGGGAAAAAAATTAGAGAGAGTGATATATCAAACG
AGACTTTTCAACTGATACCATGTTAAAACACGTGTGATTAATACTTTGTATCTCTCCATTATACT
ATCATGTACATCATCCTTTTATACAATTTAAAAACAAACTAATACACTAACTAACTTCTAACTGA
TCATTAACTAAATAACAAACTTTCTAATAAACTTTTATCACCTCAACACACGGTTCCTTTCTCGT
CCGATATGTTGAACACGAACCTCCCAATGATAGTCCAGCATGGCATAGATATGTGCTAATATATT
AATAGTGCCACCCTTTGGTTTTCTATCCCGCAGCAAATGGATGGCGTGGCAGCTATCGGATTCTA
CAACAACTCTCTGCTTCCCTAAATTCCACGCGCATTTCAGCCCGACATAAATTTCCCACA
Found at i:1408927 original size:30 final size:29
Alignment explanation
Indices: 1408891--1408955 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1408881 AAACTATATA
**
1408891 ATATATATT-TCAAAAATATTTTTTAAAACT
1 ATATATATTCTCAAAAA-A-TTTCCAAAACT
*
1408921 ATATATATTCTTAAAAAATTTCCAAAACT
1 ATATATATTCTCAAAAAATTTCCAAAACT
1408950 ATATAT
1 ATATAT
1408956 TATAGTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 15 0.48
30 10 0.32
31 6 0.19
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATATATTCTCAAAAAATTTCCAAAACT
Found at i:1409120 original size:36 final size:36
Alignment explanation
Indices: 1408920--1409242 Score: 193
Period size: 34 Copynumber: 9.2 Consensus size: 36
1408910 TTTTTAAAAC
* *
1408920 TATATATATTCTT-AAAA-AATTTCCAAAACTATATA
1 TATATATATT-TTCAAAATGATTTTCAAAACTATATA
*
1408955 T-TATA-GTTTTCAAAAATGA-TTT-AAGAA-TAT-TA
1 TATATATATTTTC-AAAATGATTTTCAA-AACTATATA
* * *
1408987 TATA-AGA-TTCCAAAAT-ATGTTTTAAAACTATATA
1 TATATATATTTTCAAAATGAT-TTTCAAAACTATATA
* *
1409021 T-TATATAATTTTTCAAAAATGTTTTTTTTAAAACTATAT-
1 TATATAT-A-TTTTC-AAAATG--ATTTTCAAAACTATATA
1409060 TATATATATTTTCAAAATGA-TTTCAAAACTATATA
1 TATATATATTTTCAAAATGATTTTCAAAACTATATA
*
1409095 TATATATATTTTC-AAATGCATTTTCAAAAACTATACA
1 TATATATATTTTCAAAATG-ATTTTC-AAAACTATATA
* ** *
1409132 TTATATATGTTTTC-AAATTTTTTTAAAAACTATATA
1 -TATATATATTTTCAAAATGATTTTCAAAACTATATA
* * **
1409168 -CTATATATTTTCGAAATG-TTTTTGAAACTATATA
1 TATATATATTTTCAAAATGATTTTCAAAACTATATA
* ** *
1409202 GTACATATATTTT-AAAAACATTTTCAAAAAT-TATA
1 -TATATATATTTTCAAAATGATTTTCAAAACTATATA
1409237 T-TATAT
1 TATATAT
1409243 TGCTATAAAA
Statistics
Matches: 229, Mismatches: 30, Indels: 60
0.72 0.09 0.19
Matches are distributed among these distances:
30 1 0.00
31 5 0.02
32 14 0.06
33 20 0.09
34 59 0.26
35 28 0.12
36 31 0.14
37 23 0.10
38 26 0.11
39 2 0.01
40 19 0.08
41 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATATATTTTCAAAATGATTTTCAAAACTATATA
Found at i:1409145 original size:73 final size:71
Alignment explanation
Indices: 1409010--1409185 Score: 192
Period size: 73 Copynumber: 2.4 Consensus size: 71
1409000 AATATGTTTT
** **
1409010 AAAACTATATATTATATAATTTTTCAAAAATGTTTTTTTTAAAACTATATTATATATATTTTCAA
1 AAAACTATATATTATAT-A-TTTTC-AAAATGCATTTTCAAAAACTATATTATATATATTTTCAA
*
1409075 AATGATTTC
63 AATGATTTA
*
1409084 AAAACTATATATATATATATTTTC-AAATGCATTTTCAAAAACTATACATTATATATGTTTTCAA
1 AAAACTATATAT-TATATATTTTCAAAATGCATTTTCAAAAACTAT--ATTATATATATTTTCAA
* **
1409148 ATTTTTTTA
63 AATGATTTA
* *
1409157 AAAACTATATACTATATATTTTCGAAATG
1 AAAACTATATATTATATATTTTCAAAATG
1409186 TTTTTGAAAC
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
71 17 0.19
72 11 0.12
73 42 0.48
74 13 0.15
75 5 0.06
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (71 bp):
AAAACTATATATTATATATTTTCAAAATGCATTTTCAAAAACTATATTATATATATTTTCAAAAT
GATTTA
Found at i:1409174 original size:107 final size:109
Alignment explanation
Indices: 1409010--1409236 Score: 284
Period size: 107 Copynumber: 2.1 Consensus size: 109
1409000 AATATGTTTT
* *
1409010 AAAACTATATATTATATAATTTTTCAAAAATGTTTTTTTTAAAACTATATTATATATATTTTCAA
1 AAAACTATACATTATATAATTTTTC-AAAA-GTTTTTTTAAAAACTATATTATATATATTTTCAA
* **
1409075 AATGATTTCAAAACTATATA-TATATATATTTTCAAATGCATTTTCA
64 AATGATTTCAAAACTATATAGTACATATATTTT-AAAAACATTTTCA
*
1409121 AAAACTATACATTATAT-ATGTTTTC-AAA-TTTTTTTAAAAACTATA-TACTATATATTTTCGA
1 AAAACTATACATTATATAAT-TTTTCAAAAGTTTTTTTAAAAACTATATTA-TATATATTTTCAA
* **
1409182 AATGTTTTTGAAACTATATAGTACATATATTTTAAAAACATTTTCA
64 AATGATTTCAAAACTATATAGTACATATATTTTAAAAACATTTTCA
*
1409228 AAAATTATA
1 AAAACTATA
1409237 TTATATTGCT
Statistics
Matches: 103, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
106 2 0.02
107 64 0.62
108 11 0.11
109 3 0.03
110 2 0.02
111 21 0.20
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (109 bp):
AAAACTATACATTATATAATTTTTCAAAAGTTTTTTTAAAAACTATATTATATATATTTTCAAAA
TGATTTCAAAACTATATAGTACATATATTTTAAAAACATTTTCA
Found at i:1415025 original size:81 final size:82
Alignment explanation
Indices: 1414862--1415013 Score: 254
Period size: 83 Copynumber: 1.9 Consensus size: 82
1414852 TGAGTATATG
1414862 AAACTAAAATATATTTTTATAATTACTAATAGATTATAATATTTTTTAAATTAATCTAGGATAAT
1 AAACTAAAATATATTTTTATAATTACTAATAGATTATAATATTTTTTAAATTAATCTAGGATAAT
1414927 TACATGCGGTAACATTT
66 TACATGCGGTAACATTT
* * *
1414944 AAACTAAAATATATTTTTTATAATTATTAATAGATTATAAT-TTTTTT-AATTAATCTAGTATGA
1 AAACTAAAATATA-TTTTTATAATTACTAATAGATTATAATATTTTTTAAATTAATCTAGGATAA
1415007 TTACATG
65 TTACATG
1415014 TTGTAGTATT
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
81 21 0.32
82 19 0.29
83 26 0.39
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (82 bp):
AAACTAAAATATATTTTTATAATTACTAATAGATTATAATATTTTTTAAATTAATCTAGGATAAT
TACATGCGGTAACATTT
Found at i:1420874 original size:21 final size:21
Alignment explanation
Indices: 1420848--1420897 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1420838 ATACGAACAA
1420848 TATCGATACTGACTCATACAT
1 TATCGATACTGACTCATACAT
**
1420869 TATCGATGTTGACTCATACAT
1 TATCGATACTGACTCATACAT
1420890 TATCGATA
1 TATCGATA
1420898 TTGGCACCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (21 bp):
TATCGATACTGACTCATACAT
Found at i:1424945 original size:183 final size:182
Alignment explanation
Indices: 1424602--1424945 Score: 566
Period size: 182 Copynumber: 1.9 Consensus size: 182
1424592 ATTAAATTTT
* *
1424602 AAATATTAAATATATTATATATAATATATAGGCTCAACCCAAACCATTTAAAACCCAAGTAATAA
1 AAATATTAAATATATTATATATAACATATAGGCTAAACCCAAACCATTTAAAACCCAAGTAATAA
*
1424667 TTTAAGATTCAATAACTTTTAAACTAAATCAATATTAATTAATTAAAAATTTTATATAAATTTTT
66 TTTAAGATCCAATAACTTTTAAACTAAATCAATATTAATTAATTAAAAATTTTATATAAATTTTT
1424732 ATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAA
131 ATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAA
* * * *
1424784 AAATATTATATATATTATATATAACATAT-GAGCTAAACCCAAATCATTTAAAACCTAATTAATA
1 AAATATTAAATATATTATATATAACATATAG-GCTAAACCCAAACCATTTAAAACCCAAGTAATA
* *
1424848 ATTTAATATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAA-TTTATCTGAAATT
65 ATTTAAGATCCAATAACTTTTAAA-CTAAATCAATATTAATTAATTAAAAATTTTATAT-AAATT
1424912 TTTATTTTATAATTATATATTATTTAAATTAATT
128 TTTATTTTATAATTATATATTATTTAAATTAATT
1424946 ATTTTTTTGA
Statistics
Matches: 150, Mismatches: 9, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
181 1 0.01
182 84 0.56
183 65 0.43
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (182 bp):
AAATATTAAATATATTATATATAACATATAGGCTAAACCCAAACCATTTAAAACCCAAGTAATAA
TTTAAGATCCAATAACTTTTAAACTAAATCAATATTAATTAATTAAAAATTTTATATAAATTTTT
ATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAA
Found at i:1425895 original size:29 final size:29
Alignment explanation
Indices: 1425862--1425920 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1425852 CGCCAGAATG
1425862 CATGTCGCTAGGATGCCCTGGCGACCTAC
1 CATGTCGCTAGGATGCCCTGGCGACCTAC
*
1425891 CATGTCGCTTGGATGCCCTGGCGACCTAC
1 CATGTCGCTAGGATGCCCTGGCGACCTAC
1425920 C
1 C
1425921 CATCGGACGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.15, C:0.36, G:0.27, T:0.22
Consensus pattern (29 bp):
CATGTCGCTAGGATGCCCTGGCGACCTAC
Found at i:1426373 original size:20 final size:20
Alignment explanation
Indices: 1426348--1426390 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1426338 TTACACGAAT
1426348 TATATTATACGTATTTGATA
1 TATATTATACGTATTTGATA
1426368 TATATTATACGTATTTGATA
1 TATATTATACGTATTTGATA
1426388 TAT
1 TAT
1426391 CATGGCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (20 bp):
TATATTATACGTATTTGATA
Found at i:1427225 original size:23 final size:23
Alignment explanation
Indices: 1427197--1427240 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1427187 GATTTTTTTT
1427197 AAATATTTTAAATTCAAAATATA
1 AAATATTTTAAATTCAAAATATA
1427220 AAATATTTTAAATTCAAAATA
1 AAATATTTTAAATTCAAAATA
1427241 AATAAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATATTTTAAATTCAAAATATA
Found at i:1434236 original size:5 final size:5
Alignment explanation
Indices: 1434226--1434285 Score: 54
Period size: 5 Copynumber: 12.4 Consensus size: 5
1434216 TAGATATAAA
* * **
1434226 AAAAT AAAAT -AAAT -AAAT AAATT CAACC AAAAT AAAA- ATAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT
1434274 AAAAT AAAAT AA
1 AAAAT AAAAT AA
1434286 TAAATAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
4 9 0.20
5 35 0.78
6 1 0.02
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1434241 original size:4 final size:4
Alignment explanation
Indices: 1434221--1434301 Score: 53
Period size: 4 Copynumber: 19.2 Consensus size: 4
1434211 CATGTTAGAT
*
1434221 ATAA AAAA ATAAA ATAA ATAA ATAA ATTCAA CCA-AA AT-A A-AA ATAA
1 ATAA ATAA AT-AA ATAA ATAA ATAA A-T-AA --ATAA ATAA ATAA ATAA
1434267 ATAAA ATAAA ATAA A-ATA ATAA ATAA ATAA ATAA A
1 AT-AA AT-AA ATAA ATA-A ATAA ATAA ATAA ATAA A
1434302 GCATAGAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 22
0.73 0.02 0.25
Matches are distributed among these distances:
3 6 0.09
4 38 0.59
5 17 0.27
6 2 0.03
8 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:1434269 original size:25 final size:26
Alignment explanation
Indices: 1434233--1434298 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 26
1434223 AAAAAAATAA
* *
1434233 AATAAATAAATAAATTCAACCAAAAT
1 AATAAATAAATAAATTAAAACAAAAT
* *
1434259 AA-AAATAAATAAAATAAAATAAAAT
1 AATAAATAAATAAATTAAAACAAAAT
1434284 AATAAATAAATAAAT
1 AATAAATAAATAAAT
1434299 AAAGCATAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 21 0.62
26 13 0.38
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (26 bp):
AATAAATAAATAAATTAAAACAAAAT
Found at i:1434854 original size:9 final size:9
Alignment explanation
Indices: 1434840--1434865 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1434830 TGCACATGCA
1434840 AAAAAAAAT
1 AAAAAAAAT
1434849 AAAAAAAAT
1 AAAAAAAAT
1434858 AAAAAAAA
1 AAAAAAAA
1434866 AAAGATACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:1435054 original size:37 final size:35
Alignment explanation
Indices: 1435004--1435139 Score: 166
Period size: 37 Copynumber: 3.8 Consensus size: 35
1434994 GTGCTTGTGG
* * * * *
1435004 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAG-A-AAATCT
*
1435041 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT-CT
*
1435078 ATCCTATTTTTAGGAGTTTGAATCCTA-AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAATCT
1435112 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
1435140 CAGGACGAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
34 28 0.32
35 4 0.05
36 3 0.03
37 53 0.60
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (35 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGAAAATCT
Found at i:1435115 original size:34 final size:35
Alignment explanation
Indices: 1435038--1435138 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
1435028 TTAGTAGAAC
1435038 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
1435076 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
1435109 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1435139 GCAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:1435994 original size:105 final size:105
Alignment explanation
Indices: 1435687--1436242 Score: 701
Period size: 105 Copynumber: 5.3 Consensus size: 105
1435677 CATTGTTCCA
* * * * * ** * *
1435687 AGTCCAAAATCCTCCGTCGTGAAGTTGAAATTTGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAG
* ** *
1435752 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTGG
** *
1435793 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
* *
1435853 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTGG
* * *
1435893 AGTCTAATATCCTTCGGTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
*
1435958 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTGG
*
1435998 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
*
1436063 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTGA
66 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTGG
* ** * *
1436103 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTAAGAAGTTGTTTGTTAACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAG
** *
1436168 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAG-CGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTGG
* * *
1436209 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1436243 CGCGGATGGC
Statistics
Matches: 404, Mismatches: 36, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
100 82 0.20
101 1 0.00
102 7 0.02
104 5 0.01
105 203 0.50
106 80 0.20
107 4 0.01
109 22 0.05
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTGG
Found at i:1437010 original size:65 final size:67
Alignment explanation
Indices: 1436846--1437013 Score: 232
Period size: 68 Copynumber: 2.5 Consensus size: 67
1436836 AAGATATCTG
* * * **
1436846 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
1436911 TT
66 TT
* *
1436913 TCTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATT-TGTTTTAGGGGAAATAAATTCAAAGA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
1436977 -TT
65 TTT
* *
1436979 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1437014 CTTAGTTCCA
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
65 31 0.34
66 3 0.03
67 24 0.27
68 32 0.36
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.30
Consensus pattern (67 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
TT
Found at i:1437056 original size:102 final size:101
Alignment explanation
Indices: 1436927--1437169 Score: 351
Period size: 102 Copynumber: 2.4 Consensus size: 101
1436917 TTTCAAGAGT
* * *
1436927 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
1436992 AACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGA
66 AACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGA
* * * * *
1437029 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * **
1437094 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGA
66 AACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGA
*
1437130 AACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAAC
1437170 TATCTCAAGA
Statistics
Matches: 124, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
101 27 0.22
102 97 0.78
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (101 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGA
Found at i:1437170 original size:37 final size:37
Alignment explanation
Indices: 1437073--1437184 Score: 190
Period size: 36 Copynumber: 3.0 Consensus size: 37
1437063 AAAACATATT
1437073 CAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAA-ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
*
1437111 CAAAA-TTTATTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
*
1437147 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1437184 C
1 C
1437185 GAAGGGAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
36 35 0.50
37 31 0.44
38 4 0.06
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
Found at i:1437252 original size:36 final size:36
Alignment explanation
Indices: 1437209--1437278 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
1437199 TCAATGTTTA
1437209 TGTTTCAAGAGAAACTGTCTCAATG-GAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAA-GAGAGACAAAATT
*
1437245 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1437279 CTCTTCTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 1 0.03
36 31 0.97
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1438262 original size:22 final size:22
Alignment explanation
Indices: 1438236--1438290 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1438226 TTGTGTTTGG
1438236 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGGCATTTGATAC
*
1438258 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATAC
1438280 TCAAAGGTTTG
1 TCAAAGGTTTG
1438291 ATGGGATAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATAC
Found at i:1438944 original size:16 final size:15
Alignment explanation
Indices: 1438925--1439005 Score: 78
Period size: 15 Copynumber: 5.3 Consensus size: 15
1438915 TTATCCCTTT
*
1438925 TTCTTTTTTATTTTTG
1 TTCTTTTCT-TTTTTG
1438941 TTC-TTTCTTTTTTTG
1 TTCTTTTC-TTTTTTG
1438956 TT-TTCTTCTTTTTTG
1 TTCTT-TTCTTTTTTG
1438971 CTTCTTTTCTTTTTTG
1 -TTCTTTTCTTTTTTG
*
1438987 TT-TTTGCTCTTTTTG
1 TTCTTTTCT-TTTTTG
1439002 TTCT
1 TTCT
1439006 GATTGAATCT
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
14 5 0.09
15 29 0.52
16 20 0.36
17 2 0.04
ACGTcount: A:0.01, C:0.14, G:0.07, T:0.78
Consensus pattern (15 bp):
TTCTTTTCTTTTTTG
Found at i:1438949 original size:20 final size:20
Alignment explanation
Indices: 1438924--1438966 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1438914 TTTATCCCTT
*
1438924 TTTCTTTTTTAT-TTTTGTTC
1 TTTCTTTTTT-TGTTTTCTTC
1438944 TTTCTTTTTTTGTTTTCTTC
1 TTTCTTTTTTTGTTTTCTTC
1438964 TTT
1 TTT
1438967 TTTGCTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (20 bp):
TTTCTTTTTTTGTTTTCTTC
Found at i:1439000 original size:31 final size:31
Alignment explanation
Indices: 1438935--1439005 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
1438925 TTCTTTTTTA
*
1438935 TTTTTGTTC-TTTCTTTTTTTGTTTTCTTCT
1 TTTTTGTTCTTTTCTTTTTTTGTTTTCTGCT
1438965 TTTTTGCTTCTTTTC-TTTTTTGTTTT-TGCT
1 TTTTTG-TTCTTTTCTTTTTTTGTTTTCTGCT
1438995 CTTTTTGTTCT
1 -TTTTTGTTCT
1439006 GATTGAATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 13 0.35
31 20 0.54
32 4 0.11
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.77
Consensus pattern (31 bp):
TTTTTGTTCTTTTCTTTTTTTGTTTTCTGCT
Found at i:1442016 original size:5 final size:5
Alignment explanation
Indices: 1442006--1442086 Score: 62
Period size: 5 Copynumber: 16.6 Consensus size: 5
1441996 TTAGATATAA
* * **
1442006 AAAAT AAAAT AAAAT -AAAT -AAAT AAATT CAACC AAAAT AAAA- ATAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT
* *
1442054 AAAAT AAAAT AAAAA AATAAA AAAAT -AAAT AAA
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAA
1442087 GCATAAAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
4 13 0.21
5 43 0.69
6 6 0.10
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1442026 original size:4 final size:4
Alignment explanation
Indices: 1442002--1442086 Score: 52
Period size: 4 Copynumber: 20.2 Consensus size: 4
1441992 CATGTTAGAT
1442002 ATAA A-AA ATAAA ATAAA ATAA ATAA ATAA ATTCAA CCA-AA AT-A A-AA
1 ATAA ATAA AT-AA AT-AA ATAA ATAA ATAA A-T-AA --ATAA ATAA ATAA
* *
1442048 ATAA ATAAA ATAAA ATAA AAAA ATAA AAAA ATAA ATAA A
1 ATAA AT-AA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA A
1442087 GCATAAAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
3 8 0.12
4 35 0.52
5 21 0.31
6 2 0.03
8 1 0.01
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.19
Consensus pattern (4 bp):
ATAA
Found at i:1442094 original size:25 final size:25
Alignment explanation
Indices: 1442002--1442095 Score: 75
Period size: 25 Copynumber: 3.5 Consensus size: 25
1441992 CATGTTAGAT
1442002 ATAAAA-AATAAAATAAAATAAATAA
1 ATAAAACAA-AAAATAAAATAAATAA
*
1442027 ATAAATTCAACCAAAATAAAAATAAATAAA
1 ATAAA-ACAA--AAAAT-AAAATAAAT-AA
*
1442057 ATAAAATAAAAAAATAAAA-AAATAA
1 ATAAAA-CAAAAAATAAAATAAATAA
*
1442082 ATAAAGCATAAAAA
1 ATAAAACA-AAAAA
1442096 AATGATAGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
24 1 0.02
25 17 0.30
26 4 0.07
27 6 0.11
28 10 0.18
29 9 0.16
30 9 0.16
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.18
Consensus pattern (25 bp):
ATAAAACAAAAAATAAAATAAATAA
Found at i:1442098 original size:55 final size:56
Alignment explanation
Indices: 1442002--1442133 Score: 137
Period size: 55 Copynumber: 2.4 Consensus size: 56
1441992 CATGTTAGAT
* **
1442002 ATAAAA-AATAAAATAAAATAAATAAATAAATTCAACCAAAATAAAAATAAATAA-A
1 ATAAAATAATAAAATAAAA-AAATAAATAAATGCAAAAAAAATAAAAATAAATAATA
* * * *
1442057 ATAAAATAAAAAAATAAAAAAATAAATAAA-GCATAAAAAAATGATAGTAAATAATA
1 ATAAAATAATAAAATAAAAAAATAAATAAATGCA-AAAAAAATAAAAATAAATAATA
*
1442113 GTATAAAT-ATAAAATAAAAAA
1 ATA-AAATAATAAAATAAAAAA
1442134 TGTAATATAT
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
54 2 0.03
55 32 0.50
56 26 0.41
57 4 0.06
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (56 bp):
ATAAAATAATAAAATAAAAAAATAAATAAATGCAAAAAAAATAAAAATAAATAATA
Found at i:1442159 original size:19 final size:18
Alignment explanation
Indices: 1442000--1442173 Score: 68
Period size: 19 Copynumber: 8.8 Consensus size: 18
1441990 AACATGTTAG
*
1442000 ATATAAAAAATAAAATAAA
1 ATATAATAAAT-AAATAAA
1442019 ATA-AATAAATAAATTCAACCA
1 ATATAATAAATAAA-T-AA--A
*
1442040 AAATAA-AAATAAATAAA
1 ATATAATAAATAAATAAA
* *
1442057 ATAAAATAAAAAAATAAAA
1 ATATAATAAATAAAT-AAA
*
1442076 AAATAAATAAAGCATAAA-AAA
1 ATAT-AAT-AA--ATAAATAAA
*
1442097 ATGATAGTAAATAATAGTATAA
1 AT-ATAATAAATAA-A-TA-AA
**
1442119 ATATAAAATAAA-AAATGTA
1 ATAT--AATAAATAAATAAA
1442138 ATATATATAAATAAATAAA
1 ATATA-ATAAATAAATAAA
*
1442157 ATACACATAAAGTAAAT
1 ATATA-ATAAA-TAAAT
1442174 GAAGCAATAA
Statistics
Matches: 117, Mismatches: 17, Indels: 41
0.67 0.10 0.23
Matches are distributed among these distances:
17 9 0.08
18 23 0.20
19 32 0.27
20 12 0.10
21 22 0.19
22 10 0.09
23 9 0.08
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
ATATAATAAATAAATAAA
Found at i:1442838 original size:37 final size:35
Alignment explanation
Indices: 1442788--1442919 Score: 140
Period size: 37 Copynumber: 3.7 Consensus size: 35
1442778 GTGCTTGTGG
* * * *
1442788 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAATTTGAATCCTAG-A-AAATCT
* *
1442825 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAATTTGAATCCTAG-AAAAT-CT
*
1442862 ATCCTATTTTTAGGAATTTGAATCCTA-AAATTCT
1 ATCCTATTTTTAGGAATTTGAATCCTAGAAAATCT
* *
1442896 ATCATATTTTTAGGAGTTTGAATC
1 ATCCTATTTTTAGGAATTTGAATC
1442920 ATAGCAGGAC
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
34 23 0.28
35 4 0.05
36 3 0.04
37 52 0.63
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (35 bp):
ATCCTATTTTTAGGAATTTGAATCCTAGAAAATCT
Found at i:1442904 original size:34 final size:36
Alignment explanation
Indices: 1442822--1442919 Score: 139
Period size: 34 Copynumber: 2.8 Consensus size: 36
1442812 TTAGTAGAAC
1442822 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA--AAAATG
*
1442860 T-TATCCTATTTTTAGGAATTTGAATCCT-AAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAATG
*
1442893 TCTATCATATTTTTAGGAGTTTGAATC
1 TCTATCCTATTTTTAGGAGTTTGAATC
1442920 ATAGCAGGAC
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
33 1 0.02
34 28 0.50
37 26 0.46
38 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAATG
Found at i:1442911 original size:71 final size:73
Alignment explanation
Indices: 1442788--1442925 Score: 199
Period size: 71 Copynumber: 1.9 Consensus size: 73
1442778 GTGCTTGTGG
* * *
1442788 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATCTTTAGGAATTTAAATCCTAG-AGAACTCTATCATATTTTTAGGAGTTTGAATCATAG
1442853 CAAAATGTT
65 CAAAATGTT
* * *
1442862 ATCCTATTTTTAGGAATTTGAATCCTA-A-AATTCTATCATATTTTTAGGAGTTTGAATCATAGC
1 ATCCTATCTTTAGGAATTTAAATCCTAGAGAACTCTATCATATTTTTAGGAGTTTGAATCATAGC
1442925 A
66 A
1442926 GGACGAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
71 33 0.57
72 1 0.02
74 24 0.41
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (73 bp):
ATCCTATCTTTAGGAATTTAAATCCTAGAGAACTCTATCATATTTTTAGGAGTTTGAATCATAGC
AAAATGTT
Found at i:1446441 original size:24 final size:24
Alignment explanation
Indices: 1446409--1446456 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1446399 AAAATTGGGC
1446409 TGAATATAAACGAACAAACATAAA
1 TGAATATAAACGAACAAACATAAA
* *
1446433 TGAATATAAATGAACGAACATAAA
1 TGAATATAAACGAACAAACATAAA
1446457 CAAACAGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.19
Consensus pattern (24 bp):
TGAATATAAACGAACAAACATAAA
Found at i:1448104 original size:21 final size:21
Alignment explanation
Indices: 1448064--1448104 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1448054 TAAAACGTTC
* **
1448064 AATAATAATATTTTTGATAAA
1 AATAATAATATTATAAATAAA
1448085 AATAATAATATTATAAATAA
1 AATAATAATATTATAAATAA
1448105 TATTTTACGA
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:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AATAATAATATTATAAATAAA
Found at i:1449804 original size:17 final size:17
Alignment explanation
Indices: 1449774--1449814 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1449764 GGTCCTGCAA
*
1449774 TATATTTTTTCTCTT-T
1 TATATTTTTCCTCTTAT
1449790 TATATTTTTACCTCTTAT
1 TATATTTTT-CCTCTTAT
1449808 T-TATTTT
1 TATATTTT
1449815 CGTGGTCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 9 0.41
17 11 0.50
18 2 0.09
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATTTTTCCTCTTAT
Found at i:1450488 original size:15 final size:16
Alignment explanation
Indices: 1450468--1450497 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1450458 CCCATAGAGA
1450468 TTGTTAAAA-GTTATT
1 TTGTTAAAAGGTTATT
1450483 TTGTTAAAAGGTTAT
1 TTGTTAAAAGGTTAT
1450498 AAAATGACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (16 bp):
TTGTTAAAAGGTTATT
Found at i:1464202 original size:20 final size:20
Alignment explanation
Indices: 1464179--1464219 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1464169 ATTAAAATGA
* *
1464179 AAATTGATTAAAATTTTAAT
1 AAATGGATTAAAATCTTAAT
*
1464199 AAATGGTTTAAAATCTTAAT
1 AAATGGATTAAAATCTTAAT
1464219 A
1 A
1464220 TTTAGCAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (20 bp):
AAATGGATTAAAATCTTAAT
Found at i:1469107 original size:31 final size:31
Alignment explanation
Indices: 1469029--1469114 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
1469019 GAATAAATTT
* * *
1469029 TAATAATTATTTTATAATAAATTGATGAAATT
1 TAATAATAATATTATAAT-AATTGATGAAATA
* *
1469061 TAATAATTATTTTATAATAATTGAAT-AAATA
1 TAATAATAATATTATAATAATTG-ATGAAATA
* *
1469092 TAGTAATAATATTATAAGAATTG
1 TAATAATAATATTATAATAATTG
1469115 TACAAAATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 28 0.58
32 20 0.42
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (31 bp):
TAATAATAATATTATAATAATTGATGAAATA
Found at i:1474456 original size:18 final size:18
Alignment explanation
Indices: 1474417--1474459 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
1474407 CCCATTAGTG
1474417 TATT-ATTCGATATAATT
1 TATTAATTCGATATAATT
1474434 TATTAATTC-ATATAATT
1 TATTAATTCGATATAATT
1474451 TCATTAATT
1 T-ATTAATT
1474460 AATGCATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (18 bp):
TATTAATTCGATATAATT
Found at i:1475028 original size:26 final size:26
Alignment explanation
Indices: 1474989--1475038 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1474979 CGGACTGGAG
* *
1474989 TCGAGTGAATGATATATATTTTTTGA
1 TCGAGTGAAGGATATATAATTTTTGA
*
1475015 TCGAGTGAAGGATATGTAATTTTT
1 TCGAGTGAAGGATATATAATTTTT
1475039 CAGTTAGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.44
Consensus pattern (26 bp):
TCGAGTGAAGGATATATAATTTTTGA
Found at i:1481122 original size:6 final size:6
Alignment explanation
Indices: 1481111--1481178 Score: 136
Period size: 6 Copynumber: 11.3 Consensus size: 6
1481101 AAATTACATT
1481111 GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA
1 GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA
1481159 GAGGTA GAGGTA GAGGTA GA
1 GAGGTA GAGGTA GAGGTA GA
1481179 AGTTGATTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.50, T:0.16
Consensus pattern (6 bp):
GAGGTA
Found at i:1486851 original size:29 final size:29
Alignment explanation
Indices: 1486785--1486852 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
1486775 AAAGGTCCAT
*
1486785 TAGTATAATTGAAGTTAAAATCAAAGTTTAG
1 TAGTATAATTGAA--TAAAATAAAAGTTTAG
*
1486816 T-GTTATAATTGAA-AAAATTAAAATTTTAG
1 TAG-TATAATTGAATAAAA-TAAAAGTTTAG
1486845 TAGTATAA
1 TAGTATAA
1486853 ACAATATTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
28 4 0.12
29 15 0.47
30 2 0.06
31 11 0.34
ACGTcount: A:0.47, C:0.01, G:0.13, T:0.38
Consensus pattern (29 bp):
TAGTATAATTGAATAAAATAAAAGTTTAG
Found at i:1487155 original size:10 final size:10
Alignment explanation
Indices: 1487140--1487213 Score: 68
Period size: 10 Copynumber: 7.6 Consensus size: 10
1487130 CATTTAATAA
1487140 ATAAACGAAC
1 ATAAACGAAC
1487150 ATAAACGAAC
1 ATAAACGAAC
1487160 ----ACGAAC
1 ATAAACGAAC
1487166 ATAAACGAAC
1 ATAAACGAAC
* *
1487176 ATGAAC-ATAA
1 ATAAACGA-AC
1487186 ATGAACACGAAC
1 AT-AA-ACGAAC
1487198 ATAAACGAAC
1 ATAAACGAAC
1487208 ATAAAC
1 ATAAAC
1487214 ATTAGAGACC
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 36 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1487215 original size:16 final size:16
Alignment explanation
Indices: 1487144--1487208 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1487134 TAATAAATAA
1487144 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1487160 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
1487176 ATGAACATAAATGAAC
1 ACGAACATAAACGAAC
1487192 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1487208 A
1 A
1487209 TAAACATTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1487575 original size:14 final size:14
Alignment explanation
Indices: 1487558--1487598 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1487548 GATTGAGTTA
*
1487558 AACATAAATAAACG
1 AACATAAACAAACG
* *
1487572 AACATAACCGAACG
1 AACATAAACAAACG
1487586 AACATAAACAAAC
1 AACATAAACAAAC
1487599 ATAACCGAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.61, C:0.22, G:0.07, T:0.10
Consensus pattern (14 bp):
AACATAAACAAACG
Done.