Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001543.1 Hibiscus syriacus cultivar Beakdansim tig00003032_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: 51546
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:443 original size:12 final size:12
Alignment explanation
Indices: 426--475 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
416 TTGTTCCCTA
426 AGAGGGAAGGGG
1 AGAGGGAAGGGG
*
438 AGAGGGACGGGG
1 AGAGGGAAGGGG
*
450 AAGAGGGAAAGGG
1 -AGAGGGAAGGGG
*
463 AGAGGGACGGGG
1 AGAGGGAAGGGG
475 A
1 A
476 TAGAGAGAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 22 0.69
13 10 0.31
ACGTcount: A:0.34, C:0.04, G:0.62, T:0.00
Consensus pattern (12 bp):
AGAGGGAAGGGG
Found at i:453 original size:25 final size:25
Alignment explanation
Indices: 425--480 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
415 ATTGTTCCCT
*
425 AAGAGGGAAGGGGAGAGGGACGGGG
1 AAGAGGGAAAGGGAGAGGGACGGGG
450 AAGAGGGAAAGGGAGAGGGACGGGG
1 AAGAGGGAAAGGGAGAGGGACGGGG
475 ATAGAG
1 A-AGAG
481 AGAGAGAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.36, C:0.04, G:0.59, T:0.02
Consensus pattern (25 bp):
AAGAGGGAAAGGGAGAGGGACGGGG
Found at i:493 original size:25 final size:25
Alignment explanation
Indices: 437--494 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
427 GAGGGAAGGG
* *
437 GAGAGGGACGGGGAAGAGGGAAAGG
1 GAGAGGGACGGGGAAGAGAGAAAGA
*
462 GAGAGGGACGGGGATAGAGAGAGAGA
1 GAGAGGGACGGGGA-AGAGAGAAAGA
488 GA-AGGGA
1 GAGAGGGA
495 GAGGGGCGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 19 0.66
26 10 0.34
ACGTcount: A:0.38, C:0.03, G:0.57, T:0.02
Consensus pattern (25 bp):
GAGAGGGACGGGGAAGAGAGAAAGA
Found at i:1332 original size:67 final size:67
Alignment explanation
Indices: 1253--1538 Score: 294
Period size: 69 Copynumber: 4.2 Consensus size: 67
1243 GATTAGGTGT
* * * *
1253 TCCCGTGCGAGTCATCC-GAATTAAATATGATTAGGTGCTCTCGTACGAGTCACTCCAATCTTCG
1 TCCCGTGGGAGTCACCCAGAA-TAAATATGATTAGGTGCTCTCGTGCGAGTCACTCTAATCTTCG
1317 GGC
65 GGC
** * *
1320 TCCCGTGGGAGTCACCTGGAATAAATATGATTAGGTTCTCTCATGCGAGTCACTCTAATCATTCG
1 TCCCGTGGGAGTCACCCAGAATAAATATGATTAGGTGCTCTCGTGCGAGTCACTCTAATC-TTCG
1385 TGGC
65 -GGC
** *
1389 TCTAGTGGGAATCACCCAGAATAAATATGATTAGGTGCTC-CTGTGCGAGTCACTCTAATCCTTC
1 TCCCGTGGGAGTCACCCAGAATAAATATGATTAGGTGCTCTC-GTGCGAGTCACTCTAAT-CTTC
*
1453 AAGGC
64 -GGGC
* * **
1458 TCCCGTGCGG-G-CACCCAGAAAAAATATGATGAGGAACTCTCGTGCGAGTCACTCTAATCCTTC
1 TCCCGTG-GGAGTCACCCAGAATAAATATGATTAGGTGCTCTCGTGCGAGTCACTCTAAT-CTTC
*
1521 AGG-
64 GGGC
* *
1524 ACCCGTGTGAGTCAC
1 TCCCGTGGGAGTCAC
1539 TCCCGTGTGA
Statistics
Matches: 185, Mismatches: 24, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
65 1 0.01
66 7 0.04
67 55 0.30
68 54 0.29
69 65 0.35
70 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.27
Consensus pattern (67 bp):
TCCCGTGGGAGTCACCCAGAATAAATATGATTAGGTGCTCTCGTGCGAGTCACTCTAATCTTCGG
GC
Found at i:1545 original size:15 final size:15
Alignment explanation
Indices: 1525--1553 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1515 TCCTTCAGGA
1525 CCCGTGTGAGTCACT
1 CCCGTGTGAGTCACT
1540 CCCGTGTGAGTCAC
1 CCCGTGTGAGTCAC
1554 CAGGAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (15 bp):
CCCGTGTGAGTCACT
Found at i:3435 original size:24 final size:25
Alignment explanation
Indices: 3389--3444 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
3379 AACCTAATGA
*
3389 ATTTTTTTAATAATTATAGTTTAATTT
1 ATTTTTTTAATAA-TATAGTTT-ATTC
*
3416 ATTTTTTTAATAA-CTA-TTTATTC
1 ATTTTTTTAATAATATAGTTTATTC
3439 ATTTTT
1 ATTTTT
3445 ATTTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 9 0.33
24 3 0.11
25 2 0.07
27 13 0.48
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (25 bp):
ATTTTTTTAATAATATAGTTTATTC
Found at i:5314 original size:22 final size:22
Alignment explanation
Indices: 5250--5305 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
5240 ATGTTTTAAA
5250 ATTTATTTTAAAATATATATTG
1 ATTTATTTTAAAATATATATTG
5272 ATTTATTTTAAAATATATATTG
1 ATTTATTTTAAAATATATATTG
5294 ATTT-TTTTAAAA
1 ATTTATTTTAAAA
5306 AAATTTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 8 0.24
22 26 0.76
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTTATTTTAAAATATATATTG
Found at i:5364 original size:31 final size:31
Alignment explanation
Indices: 5329--5388 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
5319 TAGTTGTATG
*
5329 AATTATTTAAATTTCAGTATTGTAAAATTAA
1 AATTATTTAAATCTCAGTATTGTAAAATTAA
5360 AATTATTTAAATCTCAGTATTGTAAAATT
1 AATTATTTAAATCTCAGTATTGTAAAATT
5389 CTTTTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGTAAAATTAA
Found at i:5407 original size:12 final size:12
Alignment explanation
Indices: 5377--5423 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 12
5367 TAAATCTCAG
*
5377 TATTGTAAAA-T
1 TATTTTAAAATT
*
5388 TCTTTTAAAATT
1 TATTTTAAAATT
5400 TATTTTAAAATAT
1 TATTTTAAAAT-T
5413 TATTTTAAAAT
1 TATTTTAAAAT
5424 ATGGATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
11 8 0.26
12 11 0.35
13 12 0.39
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (12 bp):
TATTTTAAAATT
Found at i:5417 original size:13 final size:13
Alignment explanation
Indices: 5390--5425 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
5380 TGTAAAATTC
5390 TTTTAAAAT-TTA
1 TTTTAAAATATTA
5402 TTTTAAAATATTA
1 TTTTAAAATATTA
5415 TTTTAAAATAT
1 TTTTAAAATAT
5426 GGATTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTAAAATATTA
Found at i:5440 original size:22 final size:22
Alignment explanation
Indices: 5412--5488 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
5402 TTTTAAAATA
*
5412 TTATTTTAAAATATGGATTAAT
1 TTATTTTAAAATATGGATTGAT
*
5434 TTATTTTAAAATATAGATTGAT
1 TTATTTTAAAATATGGATTGAT
5456 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
*
5478 TTATTTAAAAA
1 TTATTTTAAAA
5489 AATTATTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:5567 original size:25 final size:27
Alignment explanation
Indices: 5510--5569 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 27
5500 TAGTTTTATG
5510 AATTATTTAAATTTTAGTATTGTAAAACTAA
1 AATTATTTAAATTTTAGTATTG----ACTAA
5541 AATTATTTAAATTTTAGTATTG-C-AA
1 AATTATTTAAATTTTAGTATTGACTAA
5566 AATT
1 AATT
5570 CTTTTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 6 0.21
26 1 0.03
31 22 0.76
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (27 bp):
AATTATTTAAATTTTAGTATTGACTAA
Found at i:5570 original size:181 final size:182
Alignment explanation
Indices: 5249--5593 Score: 584
Period size: 181 Copynumber: 1.9 Consensus size: 182
5239 TATGTTTTAA
* * *
5249 AATTTATTTTAAAATATATATTGATTTATTTTAAAATATATATTGATTTTTTTAAAAAAATTTAT
1 AATTTATTTTAAAATATAGATTGATTTATTTTAAAATATAGATTGATTTATTTAAAAAAATTTAT
*
5314 TATTATAGTTGTATGAATTATTTAAATTTCAGTATTGTAAAATTAAAATTATTTAAATCTCAGTA
66 TATTATAGTTGTATGAATTATTTAAATTTCAGTATTGTAAAACTAAAATTATTTAAATCTCAGTA
*
5379 TTGTAAAATTCTTTTAAAATTTATTTTAAAATATTATTTTAAAATATGGATT
131 TTGCAAAATTCTTTTAAAATTTATTTTAAAATATTATTTTAAAATATGGATT
*
5431 AATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTGATTTATTTAAAAAAA-TTAT
1 AATTTATTTTAAAATATAGATTGATTTATTTTAAAATATAGATTGATTTATTTAAAAAAATTTAT
* * * * *
5495 TATTGTAGTTTTATGAATTATTTAAATTTTAGTATTGTAAAACTAAAATTATTTAAATTTTAGTA
66 TATTATAGTTGTATGAATTATTTAAATTTCAGTATTGTAAAACTAAAATTATTTAAATCTCAGTA
5560 TTGCAAAATTCTTTTAAAATTTATTTTAAAATAT
131 TTGCAAAATTCTTTTAAAATTTATTTTAAAATAT
5594 GGATTGATTT
Statistics
Matches: 152, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
181 96 0.63
182 56 0.37
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (182 bp):
AATTTATTTTAAAATATAGATTGATTTATTTTAAAATATAGATTGATTTATTTAAAAAAATTTAT
TATTATAGTTGTATGAATTATTTAAATTTCAGTATTGTAAAACTAAAATTATTTAAATCTCAGTA
TTGCAAAATTCTTTTAAAATTTATTTTAAAATATTATTTTAAAATATGGATT
Found at i:5600 original size:146 final size:147
Alignment explanation
Indices: 5431--5723 Score: 464
Period size: 147 Copynumber: 2.0 Consensus size: 147
5421 AATATGGATT
*
5431 AATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTGATTTA-TTTAAAAAAATTAT
1 AATTTATTTTAAAATATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAAAAATTAT
* * * * *
5495 TATTGTAGTTTTAT-GAATTATTTAAATTTTAGTATTGTAAAACTAAAATTATTTAAATTTTAGT
66 TATAGTAGTTGTATAG-ATTATTTAAATTTCAGTATTGTAAAACTAAAATTATTTAAATCTCAGT
* *
5559 ATTGCAAAATTCTTTTAA
130 ATTACAAAACTCTTTTAA
* *
5577 AATTTATTTTAAAATATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAAAATTTAT
1 AATTTATTTTAAAATATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAAAAATTAT
*
5642 TATAGTAGTTGTATAGATTATTTAAATTTCAGTATTGTAAAATTAAAATTATTTAAATCTCAGTA
66 TATAGTAGTTGTATAGATTATTTAAATTTCAGTATTGTAAAACTAAAATTATTTAAATCTCAGTA
5707 TTACAAAACTCTTTTAA
131 TTACAAAACTCTTTTAA
5724 TTTTAAAAAA
Statistics
Matches: 134, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
146 48 0.36
147 85 0.63
148 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (147 bp):
AATTTATTTTAAAATATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAAAAATTAT
TATAGTAGTTGTATAGATTATTTAAATTTCAGTATTGTAAAACTAAAATTATTTAAATCTCAGTA
TTACAAAACTCTTTTAA
Found at i:5606 original size:22 final size:22
Alignment explanation
Indices: 5578--5634 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
5568 TTCTTTTAAA
*
5578 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
5600 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATAGATTG
5622 ATTTATTTTAAAA
1 ATTTATTTTAAAA
5635 AATTTATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
ATTTATTTTAAAATATAGATTG
Found at i:5750 original size:11 final size:11
Alignment explanation
Indices: 5734--5762 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5724 TTTTAAAAAA
5734 ATATTTTATTT
1 ATATTTTATTT
5745 ATATTTTATTT
1 ATATTTTATTT
5756 -TATTTTA
1 ATATTTTA
5763 GTAGTCTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATATTTTATTT
Found at i:6159 original size:3 final size:3
Alignment explanation
Indices: 6136--6331 Score: 80
Period size: 3 Copynumber: 62.7 Consensus size: 3
6126 TAATCACCAT
* * *
6136 TAA TAA TAT TAG TAA TAAA TAA TAA T-A TAA TATA TAA TAA TAGA AAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA
* * *
6183 TAA T-A TAA TAAA TAG TAA TAA -AA -AA TAA TCA TCA TATA TAA TATA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA-A
* * * *
6228 TAA TAA -ATT TAA TAA TAT TTA TAA TTAA TAA AAA T-A TAA TAA TTAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA -TAA
* * * * *
6274 TAA TAG TATA TAG TACG TAG TAA TAA TATA TAA TAT TAA GTAA TAAA
1 TAA TAA TA-A TAA TA-A TAA TAA TAA TA-A TAA TAA TAA -TAA T-AA
*
6321 TAA TAA GAA TA
1 TAA TAA TAA TA
6332 GTTTTTTTAA
Statistics
Matches: 149, Mismatches: 25, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
2 11 0.07
3 100 0.67
4 38 0.26
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:6160 original size:7 final size:7
Alignment explanation
Indices: 6148--6278 Score: 60
Period size: 7 Copynumber: 18.7 Consensus size: 7
6138 ATAATATTAG
6148 TAATAAA
1 TAATAAA
6155 TAATAATA
1 TAATAA-A
*
6163 TAATATA
1 TAATAAA
6170 TAAT-AA
1 TAATAAA
6176 TAGA-AAA
1 TA-ATAAA
6183 TAAT--A
1 TAATAAA
6188 TAATAAA
1 TAATAAA
*
6195 TAGT-AA
1 TAATAAA
*
6201 TAAAAAA
1 TAATAAA
*
6208 TAAT-CA
1 TAATAAA
* *
6214 TCATATA
1 TAATAAA
*
6221 TAATATA
1 TAATAAA
6228 TAATAAA
1 TAATAAA
6235 TTTAATAATA
1 --TAATAA-A
* *
6245 TTTATAAT
1 -TAATAAA
6253 TAATAAA
1 TAATAAA
6260 -AATATAA
1 TAATA-AA
*
6267 TAATTAA
1 TAATAAA
6274 TAATA
1 TAATA
6279 GTATATAGTA
Statistics
Matches: 94, Mismatches: 17, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
5 5 0.05
6 16 0.17
7 51 0.54
8 9 0.10
9 12 0.13
10 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (7 bp):
TAATAAA
Found at i:6176 original size:25 final size:25
Alignment explanation
Indices: 6138--6278 Score: 105
Period size: 25 Copynumber: 5.6 Consensus size: 25
6128 ATCACCATTA
*
6138 ATAATAT-TAGTAATAAATAATAAT
1 ATAATATATAATAATAAATAATAAT
6162 ATAATATATAATAATAGAA-AATAAT
1 ATAATATATAATAATA-AATAATAAT
* * *
6187 ATAATAAATAGTAATAAAAAATAAT
1 ATAATATATAATAATAAATAATAAT
*
6212 CATCATATATAAT-AT--ATAATAAAT
1 -ATAATATATAATAATAAATAAT-AAT
* * * *
6236 TTAATAATATTTATAATTAATAAAAAT
1 ATAAT-ATA-TAATAATAAATAATAAT
6263 ATAATA-ATTAATAATA
1 ATAATATA-TAATAATA
6279 GTATATAGTA
Statistics
Matches: 93, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
23 7 0.08
24 15 0.16
25 46 0.49
26 14 0.15
27 7 0.08
28 4 0.04
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (25 bp):
ATAATATATAATAATAAATAATAAT
Found at i:6229 original size:40 final size:40
Alignment explanation
Indices: 6122--6244 Score: 106
Period size: 40 Copynumber: 3.0 Consensus size: 40
6112 TGGACTTCTG
* *
6122 AAAATAATCACCAT-TAATAATATTAGTAATAAATAATAATAT
1 AAAATAATCATCATAT-ATAATA-TA-TAATAAATAATAATAA
* * * * * *
6164 AATAT-ATAATAATAGAAAATAATATAATAAATAGTAATAA
1 AAAATAATCATCATATATAAT-ATATAATAAATAATAATAA
6204 AAAATAATCATCATATATAATATATAATAAATTTAATAATA
1 AAAATAATCATCATATATAATATATAATAAA--TAATAATA
6245 TTTATAATTA
Statistics
Matches: 62, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
40 28 0.45
41 22 0.35
42 12 0.19
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (40 bp):
AAAATAATCATCATATATAATATATAATAAATAATAATAA
Found at i:9468 original size:7 final size:7
Alignment explanation
Indices: 9456--9545 Score: 54
Period size: 7 Copynumber: 12.7 Consensus size: 7
9446 GTACATGTGA
9456 TTTAGGG
1 TTTAGGG
*
9463 TTTAGGA
1 TTTAGGG
*
9470 TTTAGAG
1 TTTAGGG
*
9477 TTTAGAG
1 TTTAGGG
*
9484 TTTAAGG
1 TTTAGGG
*
9491 TTTAGAG
1 TTTAGGG
***
9498 TTTATTA
1 TTTAGGG
9505 TTTAGGG
1 TTTAGGG
*
9512 TTTTATGG
1 -TTTAGGG
***
9520 TTTATTA
1 TTTAGGG
9527 TTTAGGG
1 TTTAGGG
*
9534 TTTAAGG
1 TTTAGGG
9541 TTTAG
1 TTTAG
9546 TGCTAATTGC
Statistics
Matches: 61, Mismatches: 21, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
7 55 0.90
8 6 0.10
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (7 bp):
TTTAGGG
Found at i:9481 original size:21 final size:21
Alignment explanation
Indices: 9456--9501 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
9446 GTACATGTGA
*
9456 TTTAGGGTTT-AGGATTTAGAG
1 TTTAGAGTTTAAGG-TTTAGAG
9477 TTTAGAGTTTAAGGTTTAGAG
1 TTTAGAGTTTAAGGTTTAGAG
9498 TTTA
1 TTTA
9502 TTATTTAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (21 bp):
TTTAGAGTTTAAGGTTTAGAG
Found at i:9522 original size:22 final size:21
Alignment explanation
Indices: 9484--9544 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 21
9474 GAGTTTAGAG
*
9484 TTTAAGGTTT-AGAGTTTATTA
1 TTTAGGGTTTAAG-GTTTATTA
*
9505 TTTAGGGTTTTATGGTTTATTA
1 TTTAGGG-TTTAAGGTTTATTA
9527 TTTAGGGTTTAAGGTTTA
1 TTTAGGGTTTAAGGTTTA
9545 GTGCTAATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 16 0.46
22 18 0.51
23 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (21 bp):
TTTAGGGTTTAAGGTTTATTA
Found at i:24306 original size:20 final size:20
Alignment explanation
Indices: 24283--24332 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
24273 ACAGGTTCCA
24283 AAATCGCAACGCGAATAGGT
1 AAATCGCAACGCGAATAGGT
*
24303 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATAGGT
24323 AAATCGCAAC
1 AAATCGCAAC
24333 ACAGAAGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (20 bp):
AAATCGCAACGCGAATAGGT
Found at i:24535 original size:20 final size:20
Alignment explanation
Indices: 24507--24579 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
24497 AATTTGGAGA
*
24507 ATTCGCGTTGCGATTTACCT
1 ATTCACGTTGCGATTTACCT
* *
24527 ATTCACGTTTCGATTTACAT
1 ATTCACGTTGCGATTTACCT
24547 ATT-ATCGTTGCGATTTACCT
1 ATTCA-CGTTGCGATTTACCT
24567 ATTCACGTTGCGA
1 ATTCACGTTGCGA
24580 ATTTGGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (20 bp):
ATTCACGTTGCGATTTACCT
Found at i:24615 original size:20 final size:20
Alignment explanation
Indices: 24590--24643 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
24580 ATTTGGAAAA
*
24590 TCGCAACGCGAATTTCGTTT
1 TCGCAACGCGAATTTCATTT
24610 TCGCAACGCGAATTTCATTT
1 TCGCAACGCGAATTTCATTT
* *
24630 TCACAACGCTAATT
1 TCGCAACGCGAATT
24644 ACCGATAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (20 bp):
TCGCAACGCGAATTTCATTT
Found at i:24765 original size:20 final size:20
Alignment explanation
Indices: 24740--24786 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
24730 AGAAATTCGA
*
24740 GTTGCGATTTACATATTATC
1 GTTGCGATTTACATATTAGC
* *
24760 GTTGCGATTTACCTATTCGC
1 GTTGCGATTTACATATTAGC
24780 GTTGCGA
1 GTTGCGA
24787 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACATATTAGC
Found at i:24806 original size:20 final size:20
Alignment explanation
Indices: 24783--24849 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
24773 TATTCGCGTT
24783 GCGAATTTCGTTTTCGCAAC
1 GCGAATTTCGTTTTCGCAAC
****
24803 GCG-ATTCTCCAAATCGCAAC
1 GCGAATT-TCGTTTTCGCAAC
*
24823 GCAAATTTCGTTTTCGCAAC
1 GCGAATTTCGTTTTCGCAAC
*
24843 GCTAATT
1 GCGAATT
24850 ACTTATATCG
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
19 3 0.09
20 29 0.83
21 3 0.09
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (20 bp):
GCGAATTTCGTTTTCGCAAC
Found at i:24933 original size:20 final size:20
Alignment explanation
Indices: 24904--24974 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
24894 GGAGAATTTG
*
24904 CGTTGTGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
* **
24924 TGTTGCGATTTATC-TATTCG
1 CGTTGCGATTTA-CATATTAT
*
24944 CGTTGCGAATTACATATTAT
1 CGTTGCGATTTACATATTAT
24964 CGTTGCGATTT
1 CGTTGCGATTT
24975 TGACTTTCGC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.03
20 38 0.95
21 1 0.03
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Found at i:24957 original size:40 final size:39
Alignment explanation
Indices: 24903--24991 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 39
24893 TGGAGAATTT
* * *
24903 GCGTTGTGATTTACATATTATTGTTGCGA-TTTATCTATTC
1 GCGTTGCGAATTACATATTATCGTTGCGATTTTA-CT-TTC
24943 GCGTTGCGAATTACATATTATCGTTGCGATTTTGACTTTC
1 GCGTTGCGAATTACATATTATCGTTGCGATTTT-ACTTTC
24983 GCGTTGCGA
1 GCGTTGCGA
24992 TTTTGGAACA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 38 0.86
41 5 0.11
42 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (39 bp):
GCGTTGCGAATTACATATTATCGTTGCGATTTTACTTTC
Found at i:26574 original size:19 final size:19
Alignment explanation
Indices: 26550--26588 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
26540 TTGGATAGAG
*
26550 ATAAAATTTAAGATA-AAAA
1 ATAAAATATAA-ATATAAAA
26569 ATAAAATATAAATATAAAA
1 ATAAAATATAAATATAAAA
26588 A
1 A
26589 AGTGAGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (19 bp):
ATAAAATATAAATATAAAA
Found at i:27292 original size:24 final size:26
Alignment explanation
Indices: 27264--27315 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
27254 TAGCATTTTT
* *
27264 AAAATTAAAACTT-AAAATAAAA-TA
1 AAAATGAAAACTTGAAAAGAAAAGTA
27288 AAAATGAAAACTTGAAAAGAAAAGTA
1 AAAATGAAAACTTGAAAAGAAAAGTA
27314 AA
1 AA
27316 CAACTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.50
25 8 0.33
26 4 0.17
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.19
Consensus pattern (26 bp):
AAAATGAAAACTTGAAAAGAAAAGTA
Found at i:34795 original size:43 final size:43
Alignment explanation
Indices: 34649--34796 Score: 235
Period size: 43 Copynumber: 3.4 Consensus size: 43
34639 ATCACGTAAT
34649 TTTATTAATTTAAAGATG-TACTAATTAATCGATAAATTAATAA
1 TTTATTAATTTAAAGA-GATACTAATTAATCGATAAATTAATAA
* * *
34692 TTTATTAATTTACAGAGTTACTAATTAATTGATAAATTAATAA
1 TTTATTAATTTAAAGAGATACTAATTAATCGATAAATTAATAA
* *
34735 TTTATTAATTTAAAGAGATATTAATTAATCGATAAATTAATAT
1 TTTATTAATTTAAAGAGATACTAATTAATCGATAAATTAATAA
34778 TTTATTAATTTAAAGAGAT
1 TTTATTAATTTAAAGAGAT
34797 TTTTTCCGAT
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
42 1 0.01
43 96 0.99
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.44
Consensus pattern (43 bp):
TTTATTAATTTAAAGAGATACTAATTAATCGATAAATTAATAA
Found at i:42458 original size:45 final size:47
Alignment explanation
Indices: 42394--42492 Score: 148
Period size: 51 Copynumber: 2.1 Consensus size: 47
42384 AAATTTAAGA
42394 ATGAGGGTCC-AA-AATTTTAATTTTATTTTCTTAAAAATAATGGGT
1 ATGAGGGTCCAAATAATTTTAATTTTATTTTCTTAAAAATAATGGGT
42439 ATGAGGGTCCAAAATTTTAATTTTAATTTTATTTTCTTAAAAATAATGGGT
1 ATGAGGGTCC-AAA---TAATTTTAATTTTATTTTCTTAAAAATAATGGGT
42490 ATG
1 ATG
42493 CAAAAATTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
45 10 0.21
47 2 0.04
51 36 0.75
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.43
Consensus pattern (47 bp):
ATGAGGGTCCAAATAATTTTAATTTTATTTTCTTAAAAATAATGGGT
Found at i:42497 original size:45 final size:48
Alignment explanation
Indices: 42406--42508 Score: 140
Period size: 51 Copynumber: 2.1 Consensus size: 48
42396 GAGGGTCCAA
*
42406 AATTTTAATTTTATTTTCTTAAAAATAATGGGTATGAGGGTCC-AAAATTTT
1 AATTTTAATTTTATTTTCTTAAAAATAATGGGTAT---GG-CCAAAAATTGT
42457 AATTTTAATTTTATTTTCTTAAAAATAATGGGTAT-G-CAAAAATTGT
1 AATTTTAATTTTATTTTCTTAAAAATAATGGGTATGGCCAAAAATTGT
42503 AATTTT
1 AATTTT
42509 TTTTTCTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
45 1 0.02
46 13 0.26
47 1 0.02
51 35 0.70
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.47
Consensus pattern (48 bp):
AATTTTAATTTTATTTTCTTAAAAATAATGGGTATGGCCAAAAATTGT
Found at i:44007 original size:29 final size:29
Alignment explanation
Indices: 43974--44050 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
43964 AAAAAATCGG
43974 TTAATTTGGTTTGATTAATAATTTCCAAA
1 TTAATTTGGTTTGATTAATAATTTCCAAA
* *
44003 TTAATCTT-G-TTCAGTTAATAATTTTCAAA
1 TTAAT-TTGGTTTGA-TTAATAATTTCCAAA
* *
44032 TAAATTTTGGTTCGATTAA
1 TTAA-TTTGGTTTGATTAA
44051 CGGTGTCAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
28 3 0.08
29 25 0.66
30 8 0.21
31 2 0.05
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (29 bp):
TTAATTTGGTTTGATTAATAATTTCCAAA
Found at i:44430 original size:7 final size:6
Alignment explanation
Indices: 44397--44497 Score: 66
Period size: 6 Copynumber: 16.0 Consensus size: 6
44387 CAAAAGACAA
*
44397 AAAACAT AACAAT AAAAAT AAAAAT AAAATAT AAAAAAT ATAAAA- AATAAAT
1 AAAA-AT AAAAAT AAAAAT AAAAAT AAAA-AT -AAAAAT A-AAAAT AA-AAAT
* *
44449 AAAAGGA- AACAAAT -AAAAT AATAAT AATAAT -AAAAT AATAAAT AAAAAT
1 AAAA--AT AA-AAAT AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT AAAAAT
44498 TAAATAAATC
Statistics
Matches: 78, Mismatches: 4, Indels: 25
0.73 0.04 0.23
Matches are distributed among these distances:
5 9 0.12
6 41 0.53
7 21 0.27
8 7 0.09
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:44432 original size:18 final size:17
Alignment explanation
Indices: 44397--44505 Score: 76
Period size: 19 Copynumber: 5.8 Consensus size: 17
44387 CAAAAGACAA
44397 AAAACATAACAATAAAAAT
1 AAAA-ATAA-AATAAAAAT
44416 AAAAATAAAATATAAAAAAT
1 AAAAAT-AAA-AT-AAAAAT
*
44436 ATAAAAAATAAATAAAAGGA-
1 A-AAAATA-AAATAAAA--AT
*
44456 AACAAATAAAATAATAAT
1 AA-AAATAAAATAAAAAT
*
44474 AATAATAAAATAATAAAT
1 AAAAATAAAATAA-AAAT
*
44492 AAAAATTAAATAAA
1 AAAAATAAAATAAA
44506 TCAAAGGAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 22
0.72 0.07 0.22
Matches are distributed among these distances:
17 12 0.16
18 19 0.26
19 20 0.27
20 15 0.21
21 7 0.10
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAAATAAAATAAAAAT
Found at i:44433 original size:34 final size:34
Alignment explanation
Indices: 44381--44452 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
44371 TGTTAGATAA
44381 AAAAATCAAAAGACAAAAAACATAACAATAA-AAAT
1 AAAAATCAAAAGACAAAAAACATAA-AA-AATAAAT
* * *
44416 AAAAAT-AAAATATAAAAAATATAAAAAATAAAT
1 AAAAATCAAAAGACAAAAAACATAAAAAATAAAT
44449 AAAA
1 AAAA
44453 GGAAACAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 2 0.06
33 10 0.30
34 15 0.45
35 6 0.18
ACGTcount: A:0.78, C:0.06, G:0.01, T:0.15
Consensus pattern (34 bp):
AAAAATCAAAAGACAAAAAACATAAAAAATAAAT
Found at i:44442 original size:58 final size:58
Alignment explanation
Indices: 44380--44519 Score: 135
Period size: 58 Copynumber: 2.3 Consensus size: 58
44370 ATGTTAGATA
*
44380 AAAAAATCAAAAGACAAAAAACATAACAATAAAAATAAAAATAAAAT-ATAAA-AAATA-T
1 AAAAAATCAAAAGA-AAAAAA-ATAA-AATAAAAATAAAAATAAAATAATAAATAAAAATT
* * *
44438 AAAAAAT-AAATAAAAGGAAACAAATAAAATAATAATAATAATAAAATAATAAATAAAAATT
1 AAAAAATCAAA-AGAA--AAA-AAATAAAATAAAAATAAAAATAAAATAATAAATAAAAATT
*
44499 AAATAAATCAAAGGAAAAAAA
1 AAA-AAATCAAAAGAAAAAAA
44520 TATTATTTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
57 4 0.06
58 27 0.40
59 14 0.21
60 9 0.13
61 4 0.06
62 6 0.09
63 3 0.04
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (58 bp):
AAAAAATCAAAAGAAAAAAAATAAAATAAAAATAAAAATAAAATAATAAATAAAAATT
Found at i:44452 original size:9 final size:8
Alignment explanation
Indices: 44377--44495 Score: 55
Period size: 9 Copynumber: 14.1 Consensus size: 8
44367 ATAATGTTAG
44377 ATAAAAAA
1 ATAAAAAA
* *
44385 ATCAAAAG
1 ATAAAAAA
*
44393 ACAAAAAA
1 ATAAAAAA
*
44401 CAT--AACA
1 -ATAAAAAA
44408 ATAAAAATA
1 ATAAAAA-A
44417 A-AAATAAA
1 ATAAA-AAA
44425 ATATAAAAA
1 ATA-AAAAA
44434 ATATAAAAA
1 ATA-AAAAA
44443 ATAAATAAA
1 ATAAA-AAA
* *
44452 AGGAAACAA
1 A-TAAAAAA
*
44461 ATAAAATA
1 ATAAAAAA
*
44469 ATAATAATA
1 ATAA-AAAA
*
44478 ATAAAATA
1 ATAAAAAA
44486 ATAAATAAA
1 ATAAA-AAA
44495 A
1 A
44496 ATTAAATAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
6 2 0.02
7 3 0.03
8 37 0.43
9 39 0.45
10 5 0.06
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.18
Consensus pattern (8 bp):
ATAAAAAA
Found at i:44501 original size:11 final size:12
Alignment explanation
Indices: 44411--44505 Score: 62
Period size: 11 Copynumber: 8.2 Consensus size: 12
44401 CATAACAATA
44411 AAAATAA-AAAT
1 AAAATAATAAAT
44422 AAAAT-ATAAA-
1 AAAATAATAAAT
*
44432 AAATATAAAAAAT
1 AAA-ATAATAAAT
**
44445 -AAATAA-AAGG
1 AAAATAATAAAT
44455 AAACA-AATAAAAT
1 AAA-ATAAT-AAAT
44468 AATAATAAT-AAT
1 AA-AATAATAAAT
44480 AAAATAATAAAT
1 AAAATAATAAAT
*
44492 AAAA-ATTAAAT
1 AAAATAATAAAT
44503 AAA
1 AAA
44506 TCAAAGGAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
10 6 0.09
11 33 0.49
12 19 0.28
13 5 0.07
14 4 0.06
ACGTcount: A:0.76, C:0.01, G:0.02, T:0.21
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:44521 original size:58 final size:59
Alignment explanation
Indices: 44395--44521 Score: 152
Period size: 58 Copynumber: 2.2 Consensus size: 59
44385 ATCAAAAGAC
44395 AAAAAACATAACAATAAAAATAAAAATAAAATATAAAAAATATAAAAAATAAATAAAAGG
1 AAAAAA-ATAACAATAAAAATAAAAATAAAATATAAAAAATATAAAAAATAAATAAAAGG
* * * ** *
44455 AAACAAATAA-AATAATAATAATAATAAAATAATAAATAAA-A-ATTAAATAAATCAAAGG
1 AAAAAAATAACAATAAAAATAAAAATAAAAT-ATAAA-AAATATAAAAAATAAATAAAAGG
44513 AAAAAAATA
1 AAAAAAATA
44522 TTATTTTAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
58 40 0.69
59 10 0.17
60 8 0.14
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (59 bp):
AAAAAAATAACAATAAAAATAAAAATAAAATATAAAAAATATAAAAAATAAATAAAAGG
Found at i:44573 original size:22 final size:22
Alignment explanation
Indices: 44556--44599 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
44546 ACAATATTAG
*
44556 GTAAAAATAATACTAATAATAA
1 GTAAAAATAATAATAATAATAA
*
44578 TTAAAAATAATAATAATAATAA
1 GTAAAAATAATAATAATAATAA
44600 ACAATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
GTAAAAATAATAATAATAATAA
Found at i:44575 original size:3 final size:3
Alignment explanation
Indices: 44561--44599 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
44551 ATTAGGTAAA
* *
44561 AAT AAT ACT AAT AAT AATT AAA AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AA
44600 ACAATAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:44591 original size:19 final size:19
Alignment explanation
Indices: 44564--44611 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
44554 AGGTAAAAAT
*
44564 AATACTAATAATAATTAAA-
1 AATAATAATAATAA-TAAAC
44583 AATAATAATAATAATAAAC
1 AATAATAATAATAATAAAC
44602 AATAA-AATAA
1 AATAATAATAA
44612 ATTTTAGGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAATAATAATAATAAAC
Found at i:44605 original size:16 final size:15
Alignment explanation
Indices: 44570--44612 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
44560 AAATAATACT
*
44570 AATAATAATTAAAAAT
1 AATAATAA-TAAAAAC
44586 AATAATAATAATAAAC
1 AATAATAATAA-AAAC
44602 AATAA-AATAAA
1 AATAATAATAAA
44613 TTTTAGGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 1 0.04
15 8 0.32
16 16 0.64
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAATAATAAAAAC
Found at i:45577 original size:19 final size:18
Alignment explanation
Indices: 45553--45591 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
45543 CGACGCGTGA
*
45553 TGCTTCTGGCCGTTGAGAT
1 TGCTTCTGGCCATTG-GAT
45572 TGCTTCTGGCCATTGGAT
1 TGCTTCTGGCCATTGGAT
45590 TG
1 TG
45592 GGTCAGATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.10, C:0.21, G:0.31, T:0.38
Consensus pattern (18 bp):
TGCTTCTGGCCATTGGAT
Found at i:45835 original size:10 final size:10
Alignment explanation
Indices: 45805--45852 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
45795 GAAATAAAGT
45805 TAATAAATAAAA
1 TAATAAAT--AA
45817 TGAATAAATAA
1 T-AATAAATAA
*
45828 TCATAAATAA
1 TAATAAATAA
45838 TAAT-AATAA
1 TAATAAATAA
45847 TAATAA
1 TAATAA
45853 TAAAACTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 9 0.28
10 12 0.38
11 3 0.09
12 1 0.03
13 7 0.22
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (10 bp):
TAATAAATAA
Found at i:45841 original size:3 final size:3
Alignment explanation
Indices: 45805--45855 Score: 50
Period size: 3 Copynumber: 16.0 Consensus size: 3
45795 GAAATAAAGT
*
45805 TAA TAAA TAA -AA TGAA TAAA TAA TCA TAAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA T-AA T-AA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
45853 TAA
1 TAA
45856 AACTATATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 2 0.05
3 28 0.68
4 11 0.27
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:45867 original size:22 final size:22
Alignment explanation
Indices: 45805--45856 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
45795 GAAATAAAGT
45805 TAATAAATAA-AATGAATAAATAA
1 TAATAAATAATAAT-AAT-AATAA
*
45828 TCATAAATAATAATAATAATAA
1 TAATAAATAATAATAATAATAA
45850 TAATAAA
1 TAATAAA
45857 ACTATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 11 0.42
23 12 0.46
24 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
TAATAAATAATAATAATAATAA
Found at i:45958 original size:34 final size:34
Alignment explanation
Indices: 45854--46264 Score: 255
Period size: 35 Copynumber: 11.5 Consensus size: 34
45844 TAATAATAAT
*
45854 AAAACTATATA-ATATATATTTC-AAAAT-ATTT-
1 AAAACTATATATATATAT-TTTCAAAAATGTTTTA
* * *
45885 -AAACTATATATTATATATTTTTTAAAAATATTTTC
1 AAAACTATATA-TATATA-TTTTCAAAAATGTTTTA
45920 AAAACTATATATATATAGTTTTCAAAAATGTTTT-
1 AAAACTATATATATATA-TTTTCAAAAATGTTTTA
*
45954 AAAACTATTATTATATATTTTTTTC-AAAATGTTTTAA
1 AAAACTA-TA-TATATA-TATTTTCAAAAATGTTTT-A
*
45991 AAAACTATAATATATATATATATATATATAGTTTTCAAATGTTTTA
1 AAAACTAT-ATATATATAT-T-T-T-CA-A------AAATGTTTTA
46037 AAAACTATATATATATATTTTC-AAAATGTTTT-
1 AAAACTATATATATATATTTTCAAAAATGTTTTA
*
46069 AAAACTTTATATTATATATATTTC-AAAATGTTTTA
1 AAAACTATATA-TATATAT-TTTCAAAAATGTTTTA
46104 AAAACTATATATATATATATATATGTTTTC-AAAATGTTTTA
1 AAAAC------TATATATATATA--TTTTCAAAAATGTTTTA
** *
46145 AAAA-TCATATATTATATATTTTCAAATGTTTTTTA
1 AAAACT-ATATA-TATATATTTTCAAAAATGTTTTA
46180 AAAACTATATAT-TATATTTTTCAAAATAT-TTTT-
1 AAAACTATATATATATA-TTTTCAAAA-ATGTTTTA
* *
46213 --AACTATATA-ATATACTTTTCAAAAATAATTTTC
1 AAAACTATATATATATA-TTTTCAAAAAT-GTTTTA
46246 AAAACTATATATATTATAT
1 AAAACTATATATA-TATAT
46265 ATATATTTCA
Statistics
Matches: 313, Mismatches: 17, Indels: 95
0.74 0.04 0.22
Matches are distributed among these distances:
30 12 0.04
31 22 0.07
32 22 0.07
33 26 0.08
34 43 0.14
35 71 0.23
36 38 0.12
37 14 0.04
38 1 0.00
39 1 0.00
40 6 0.02
41 25 0.08
42 2 0.01
43 1 0.00
44 1 0.00
45 10 0.03
46 9 0.03
47 9 0.03
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.47
Consensus pattern (34 bp):
AAAACTATATATATATATTTTCAAAAATGTTTTA
Found at i:46031 original size:47 final size:46
Alignment explanation
Indices: 45965--46054 Score: 137
Period size: 48 Copynumber: 1.9 Consensus size: 46
45955 AAACTATTAT
**
45965 TATATATTTTTTTCAAAATGTTTTAAAAAACTATAATATATATATATA
1 TATATATAGTTTTCAAAATGTTTT-AAAAACTAT-ATATATATATATA
46013 TATATATAGTTTTC-AAATGTTTTAAAAACTATATATATATAT
1 TATATATAGTTTTCAAAATGTTTTAAAAACTATATATATATAT
46055 TTTCAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
45 10 0.25
46 9 0.22
47 9 0.22
48 12 0.30
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (46 bp):
TATATATAGTTTTCAAAATGTTTTAAAAACTATATATATATATATA
Found at i:46155 original size:108 final size:106
Alignment explanation
Indices: 46001--46226 Score: 311
Period size: 108 Copynumber: 2.1 Consensus size: 106
45991 AAAACTATAA
46001 TATATATATATATATATATAGTTTTCAAATGTTTTAAAAACTATATA-TATATATTTTCAAAATG
1 TATATATATATATATATATAGTTTTCAAATGTTTTAAAAACTATATATTATATATTTTC-AAATG
* *
46065 -TTTT-AAAACTTTATATTATATATATTTCAAAATGTTTTAAAAAC
65 TTTTTAAAAACTATATATTATAT-T-TTTCAAAATATTTT--AAAC
46109 TATATATATATATATATAT-GTTTTCAAAATGTTTTAAAAA-TCATATATTATATATTTTCAAAT
1 TATATATATATATATATATAGTTTTC-AAATGTTTTAAAAACT-ATATATTATATATTTTCAAAT
*
46172 GTTTTTTAAAAACTATATATTATATTTTTCAAAATATTTTTAAC
64 G-TTTTTAAAAACTATATATTATATTTTTCAAAATATTTTAAAC
46216 TATATA-ATATA
1 TATATATATATA
46227 CTTTTCAAAA
Statistics
Matches: 109, Mismatches: 3, Indels: 14
0.87 0.02 0.11
Matches are distributed among these distances:
106 5 0.05
107 16 0.15
108 43 0.39
109 24 0.22
110 5 0.05
111 16 0.15
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (106 bp):
TATATATATATATATATATAGTTTTCAAATGTTTTAAAAACTATATATTATATATTTTCAAATGT
TTTTAAAAACTATATATTATATTTTTCAAAATATTTTAAAC
Found at i:46307 original size:41 final size:42
Alignment explanation
Indices: 46229--46312 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 42
46219 ATAATATACT
* *
46229 TTTCAAAAATAATTTTCAAAACTATATATATTATATA-TATA
1 TTTCAAAAATAATTTGCAAAACTATATATAATATATATTATA
* * *
46270 TTTCAAAAATCATTTGC-AATCTATTTATAATATTATATTATA
1 TTTCAAAAATAATTTGCAAAACTATATATAATA-TATATTATA
46312 T
1 T
46313 ATATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 12 0.33
41 19 0.53
42 5 0.14
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.46
Consensus pattern (42 bp):
TTTCAAAAATAATTTGCAAAACTATATATAATATATATTATA
Found at i:46315 original size:2 final size:2
Alignment explanation
Indices: 46295--46331 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
46285 GCAATCTATT
46295 TA TA -A TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46332 ATAATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47224 original size:85 final size:85
Alignment explanation
Indices: 47076--47896 Score: 1016
Period size: 85 Copynumber: 9.7 Consensus size: 85
47066 TCTCGACTGA
* * * * * * * *
47076 AGCTATGCTGTAAATCTGACATGCC--CGAGCTGAATAG-AATCTAACTCGAAGGTATTTGCTGA
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGT-GTAATCGAACTCGAAGGTCTTGGTTGA
**
47138 CAGATAACCCTTCTTTCCTTG
65 CAGATAACCCTTCTCGCCTTG
* *
47159 AGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTATAATCGAACTCGAAGGTCTTGGTTGAC
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGAC
47224 AGATAGA-CCTTCTCGCCTTG
66 AGATA-ACCCTTCTCGCCTTG
* * * * **
47244 AGCTATGTTGTAAATTTGATATGCCTTTAAGCTGAGTGTAATCTAACTCGAAGGTATTTTATTGA
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT-CTTGGTTGA
*
47309 CAG-TAGCCCTTCTCGCCTTG
65 CAGATAACCCTTCTCGCCTTG
* * *
47329 AGCTATGTTGTAAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGAC
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGAC
* *
47394 AGATAACCCTTTTCACCTTG
66 AGATAACCCTTCTCGCCTTG
* * *
47414 AGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGA
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGA
*
47479 CAGATAGCCCTTCTCGCCTTG
65 CAGATAACCCTTCTCGCCTTG
* * *
47500 AGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTATAATCGAACTTGAAGGTCTTGGTTGAC
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGAC
* *
47565 AGATAGCCCTTCTTGCCTTG
66 AGATAACCCTTCTCGCCTTG
* * * * **
47585 AGCTATGCTGTAAATTTGATATGCC-TTAAGTTGAATGTAATCAAACTCGAAGGTCTTTTATTGA
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGA
47649 CAGATAGA-CCTTCTCGCCTTG
65 CAGATA-ACCCTTCTCGCCTTG
* * *
47670 AGCTATGTTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGAT
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGAC
* *
47735 ATATAGCCCTTCTCGCCTTG
66 AGATAACCCTTCTCGCCTTG
* * * *
47755 AGCTATGCTGTAAATTAGATATGTCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTTG-
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGA
*
47819 CAGTTAACCCTTCTCGCC-TG
65 CAGATAACCCTTCTCGCCTTG
* * *
47839 AGTTATG-T-TACGAATTTGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTT
1 AGCTATGCTGTA--AATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTT
47897 TAAAGGTTCT
Statistics
Matches: 638, Mismatches: 85, Indels: 30
0.85 0.11 0.04
Matches are distributed among these distances:
82 2 0.00
83 25 0.04
84 80 0.13
85 413 0.65
86 118 0.18
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (85 bp):
AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGAC
AGATAACCCTTCTCGCCTTG
Found at i:47343 original size:170 final size:171
Alignment explanation
Indices: 47019--47896 Score: 1150
Period size: 170 Copynumber: 5.2 Consensus size: 171
47009 ATATGTTGTC
* * * * * * ** *
47019 GAGCTGAATGGAATCGAACTCGACA-ATTTTTGTTGACAAATAGATTTTCTCGAC-TGAAGCTAT
1 GAGCTGAGTGTAATCGAACTCGA-AGGTCTTGGTTGACAGATAGACCTTCTCGCCTTG-AGCTAT
* * ** * * **
47082 GCTGTAAATCTGACATGCC--CGAGCTGAATAG-AATCTAACTCGAAGGT-ATTTGCTGACAGAT
64 GCTGTAAATTTGATATGCCTTTAAGCTGAAT-GTAATCGAACTCGAAGGTCTTTTATTGACAGAT
* ** *
47143 AACCCTTCTTTCCTTGAGCTATGCTGTAAATTTGATGTGCCTTT
128 AGCCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATGTGCCTTT
* *
47187 GAGCTGAGTATAATCGAACTCGAAGGTCTTGGTTGACAGATAGACCTTCTCGCCTTGAGCTATGT
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGACCTTCTCGCCTTGAGCTATGC
* * *
47252 TGTAAATTTGATATGCCTTTAAGCTGAGTGTAATCTAACTCGAAGGTATTTTATTGACAG-TAGC
66 TGTAAATTTGATATGCCTTTAAGCTGAATGTAATCGAACTCGAAGGTCTTTTATTGACAGATAGC
*
47316 CCTTCTCGCCTTGAGCTATGTTGTAAATTCGATGTGCCTTT
131 CCTTCTCGCCTTGAGCTATGTTGTAAATTTGATGTGCCTTT
* * *
47357 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATA-ACCCTTTTCACCTTGAGTTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGA-CCTTCTCGCCTTGAGCTATG
* *
47421 CTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAG
65 CTGTAAATTTGATATGCCTTTAAGCTGAATGTAATCGAACTCGAAGGTCTTTTATTGACAGATAG
*
47486 CCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTT
130 CCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATGTGCCTTT
* * * *
47528 GAGCTGAGTATAATCGAACTTGAAGGTCTTGGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGC
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGACCTTCTCGCCTTGAGCTATGC
* * *
47593 TGTAAATTTGATATGCC-TTAAGTTGAATGTAATCAAACTCGAAGGTCTTTTATTGACAGATAGA
66 TGTAAATTTGATATGCCTTTAAGCTGAATGTAATCGAACTCGAAGGTCTTTTATTGACAGATAGC
47657 CCTTCTCGCCTTGAGCTATGTTGTAAATTTGATGTGCCTTT
131 CCTTCTCGCCTTGAGCTATGTTGTAAATTTGATGTGCCTTT
* * *
47698 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGATATATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGACCTTCTCGCCTTGAGCTATGC
* * * * *
47763 TGTAAATTAGATATGTCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGT-TTG-CAGTTAA
66 TGTAAATTTGATATGCCTTTAAGCTGAATGTAATCGAACTCGAAGGTCTTT-TATTGACAGATAG
* ***
47826 CCCTTCTCGCC-TGAGTTATGTTACGAATTTGATGTGCCTTT
130 CCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATGTGCCTTT
*
47867 GAGCTGAGTGTAATCAAACTCGAAGGTCTT
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTT
47897 TAAAGGTTCT
Statistics
Matches: 632, Mismatches: 67, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
167 1 0.00
168 64 0.10
169 59 0.09
170 348 0.55
171 159 0.25
172 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (171 bp):
GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGACCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCTTTAAGCTGAATGTAATCGAACTCGAAGGTCTTTTATTGACAGATAGC
CCTTCTCGCCTTGAGCTATGTTGTAAATTTGATGTGCCTTT
Found at i:47517 original size:341 final size:340
Alignment explanation
Indices: 47076--47896 Score: 1253
Period size: 341 Copynumber: 2.4 Consensus size: 340
47066 TCTCGACTGA
* * * * * *
47076 AGCTATGCTGTAAATCTGACATGCC--CGAGCTGAATAG-AATCTAACTCGAAGGTATTTGCTGA
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAAT-GTAATCGAACTCGAAGGTCTTTGTTGA
**
47138 CAGATAACCCTTCTTTCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTATAATCG
65 CAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTATAATCG
*
47203 AACTCGAAGGTCTTGGTTGACAGATAGACCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGC
130 AACTCGAAGGTCTTGGTTGACAGATAGACCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
* * *
47268 CTTTAAGCTGAGTGTAATCTAACTCGAAGGTATTTTATTGACAG-TAGCCCTTCTCGCCTTGAGC
195 C-TTAAGCTGAATGTAATCAAACTCGAAGGTATTTTATTGACAGATAGACCTTCTCGCCTTGAGC
47332 TATGTTGTAAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGA
259 TATGTTGTAAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGA
*
47397 TAACCCTTTTCACCTTG
324 TAACCCTTCTCACCTTG
*
47414 AGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGA
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGA
*
47479 CAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTATAATCG
65 CAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTATAATCG
* * *
47544 AACTTGAAGGTCTTGGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATATGC
130 AACTCGAAGGTCTTGGTTGACAGATAGACCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
* *
47609 CTTAAGTTGAATGTAATCAAACTCGAAGGTCTTTTATTGACAGATAGACCTTCTCGCCTTGAGCT
195 CTTAAGCTGAATGTAATCAAACTCGAAGGTATTTTATTGACAGATAGACCTTCTCGCCTTGAGCT
* * *
47674 ATGTTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGATATAT
260 ATGTTGTAAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGAT
* *
47739 AGCCCTTCTCGCCTTG
325 AACCCTTCTCACCTTG
* *
47755 AGCTATGCTGTAAATTAGATATGTCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTTG-
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTG-TTGA
* * *
47819 CAGTTAACCCTTCTCGCC-TGAGTTATG-T-TACGAATTTGATGTGCCTTTGAGCTGAGTGTAAT
65 CAGATAACCCTTCTCGCCTTGAGCTATGCTGTA--AATTTGATGTGCCTTTGAGCTGAGTATAAT
*
47881 CAAACTCGAAGGTCTT
128 CGAACTCGAAGGTCTT
47897 TAAAGGTTCT
Statistics
Matches: 441, Mismatches: 34, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
337 2 0.00
338 23 0.05
339 52 0.12
340 82 0.19
341 282 0.64
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (340 bp):
AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
AGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTATAATCGA
ACTCGAAGGTCTTGGTTGACAGATAGACCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCC
TTAAGCTGAATGTAATCAAACTCGAAGGTATTTTATTGACAGATAGACCTTCTCGCCTTGAGCTA
TGTTGTAAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATA
ACCCTTCTCACCTTG
Found at i:48827 original size:93 final size:95
Alignment explanation
Indices: 48678--48926 Score: 287
Period size: 93 Copynumber: 2.7 Consensus size: 95
48668 AGCAGGATCT
* *
48678 ATAAAG-CGGGGTGTTTATCCAATTGCTTTAGAGGGACAGCTCAA-CATTATTG-ATATTATATA
1 ATAAAGTCGGGGTGTTTAACCAATTGCTTTAGAGGGA-AACTCAAGCATTATTGTATA-TATATA
* *
48740 ATCACCTTTATCA-GCTAG-TGAATATTATCC
64 ACCACCCTTATCAGGCTAGCTGAATATTATCC
* * * * *
48770 ATAAAGTCGAGGTGTTTAACTAATTGCTCTAGAGGGATA-TCAAGCCTTATTGTATAT-TATAAC
1 ATAAAGTCGGGGTGTTTAACCAATTGCTTTAGAGGGAAACTCAAGCATTATTGTATATATATAAC
* *
48833 CACCCTTGTCAGGCTAGCTGAATCTTATCC
66 CACCCTTATCAGGCTAGCTGAATATTATCC
* * * *
48863 ATAAATTCGGGGCGTTTAACCAATTACTTTAGAGGGACAACTCAAGCTTTATTGTATATATATA
1 ATAAAGTCGGGGTGTTTAACCAATTGCTTTAGAGGGA-AACTCAAGCATTATTGTATATATATA
48927 GATAACATTA
Statistics
Matches: 130, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
91 18 0.14
92 19 0.15
93 71 0.55
94 1 0.01
95 17 0.13
96 4 0.03
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (95 bp):
ATAAAGTCGGGGTGTTTAACCAATTGCTTTAGAGGGAAACTCAAGCATTATTGTATATATATAAC
CACCCTTATCAGGCTAGCTGAATATTATCC
Done.