Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008011.1 Hibiscus syriacus cultivar Beakdansim tig00110474_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: 1648842
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:590963 original size:20 final size:20
Alignment explanation
Indices: 590940--591033 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
590930 TGATAGTCAG
590940 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
590960 ATTCGCATTGCGATTTTTC-T
1 ATTCGCATTGCGA-TTTACGT
590980 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* *
591001 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
591021 ATTCGCATTGCGA
1 ATTCGCATTGCGA
591034 ATTAGGAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
20 47 0.72
21 18 0.28
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:590988 original size:41 final size:40
Alignment explanation
Indices: 590940--591033 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 40
590930 TGATAGTCAG
* *
590940 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTTC-T
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGA-TTTACGT
*
590980 AATTCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
591021 ATTCGCATTGCGA
1 ATTCGCATTGCGA
591034 ATTAGGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
40 17 0.35
41 32 0.65
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
Found at i:597498 original size:20 final size:21
Alignment explanation
Indices: 597473--597565 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
597463 TTTTCCCAAT
*
597473 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
597493 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
597514 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
597534 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
597555 TCGCAATGCGA
1 TCGCAATGCGA
597566 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:597579 original size:20 final size:20
Alignment explanation
Indices: 597554--597688 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
597544 AATTGGGAAA
597554 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
597574 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
597595 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
*
597615 TTCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
597635 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
597655 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
597675 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
597689 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 64 0.68
21 24 0.26
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:597580 original size:41 final size:41
Alignment explanation
Indices: 597473--597565 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
597463 TTTTCCCAAT
597473 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
597514 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
597555 TCGCAATGCGA
1 TCGCAATGCGA
597566 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:597884 original size:22 final size:22
Alignment explanation
Indices: 597856--597899 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
597846 CACTCTCTCA
597856 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
597878 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
597900 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:598216 original size:20 final size:20
Alignment explanation
Indices: 598162--598220 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
598152 GCGATTATCT
**
598162 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
598182 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
598202 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
598221 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:599560 original size:18 final size:18
Alignment explanation
Indices: 599539--599583 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
599529 TCCACTTCGG
*
599539 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
599557 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
599575 GAGCCATCA
1 GAGCCATCA
599584 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:600125 original size:19 final size:20
Alignment explanation
Indices: 600071--600137 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
600061 TAGTTTACTT
* *
600071 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
600091 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
600111 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
600130 TCGCAACG
1 TCGCAACG
600138 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:600145 original size:14 final size:14
Alignment explanation
Indices: 600126--600189 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 14
600116 ATGCGAAATG
600126 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
600140 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
600156 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
600172 AAAATCGCAACG-C
1 AAAATCGCAACGAC
600185 AAAAT
1 AAAAT
600190 GAAAATCGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 6 0.14
14 21 0.48
16 8 0.18
18 9 0.20
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:600168 original size:32 final size:33
Alignment explanation
Indices: 600110--600200 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
600100 GGAAATGGCT
600110 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
600143 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
600175 ATCGCAACGCAAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
600201 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:600236 original size:14 final size:14
Alignment explanation
Indices: 600217--600274 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
600207 TTGTGTTTCG
600217 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
600231 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
600247 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
600263 CGTTGCGATTTT
1 CGTTGCGATTTT
600275 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:600251 original size:32 final size:33
Alignment explanation
Indices: 600212--600290 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
600202 GCGATTTGTG
600212 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
600244 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
600277 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
600291 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:600289 original size:19 final size:19
Alignment explanation
Indices: 600231--600348 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
600221 GCGATTTTGT
600231 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
600249 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
600263 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
600282 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
600302 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
600321 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
600341 TGTTGCGA
1 CGTTGCGA
600349 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:602193 original size:14 final size:14
Alignment explanation
Indices: 602174--602209 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
602164 ATTGTTTAAT
602174 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
602188 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
602202 TGATTTGT
1 TGATTTGT
602210 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:602340 original size:19 final size:17
Alignment explanation
Indices: 602317--602366 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 17
602307 TATCGTAACG
602317 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCG-A
602335 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
602350 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
602367 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (17 bp):
AGAAAATCGCAATGCGA
Found at i:602354 original size:14 final size:14
Alignment explanation
Indices: 602308--602361 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
602298 CGAAATGGCT
*
602308 ATCGTAACGAGAAA
1 ATCGCAACGAGAAA
602322 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
602341 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
602355 ATCGCAA
1 ATCGCAA
602362 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 17 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:602379 original size:33 final size:33
Alignment explanation
Indices: 602289--602366 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
602279 AAAACAGACT
* *** *
602289 ATCGCAACGCGAAATGGCTATCGTAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
602322 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
602355 ATCGCAATGCGA
1 ATCGCAATGCGA
602367 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:602410 original size:20 final size:20
Alignment explanation
Indices: 602385--602442 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
602375 TCGCATTGCG
*
602385 ATTTTCTCGTTGCAATAGCC
1 ATTTTCTCGTTGCGATAGCC
*
602405 ATTTTCGCGTTGCGATAGCC
1 ATTTTCTCGTTGCGATAGCC
602425 ATTTTCTCGTTGCGATAG
1 ATTTTCTCGTTGCGATAG
602443 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTTTCTCGTTGCGATAGCC
Found at i:603545 original size:24 final size:24
Alignment explanation
Indices: 603489--603547 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
603479 AGTCAGTATT
* *
603489 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
603513 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
603537 CGAATTTTGAT
1 CGAAATTTGAT
603548 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:606066 original size:33 final size:33
Alignment explanation
Indices: 606008--606132 Score: 182
Period size: 32 Copynumber: 3.8 Consensus size: 33
605998 GGAAATTACT
606008 ATCGCAATGCGAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * **
606040 ATCGTAATGCAAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
606072 TTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
606105 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
606133 CGATTTAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
32 40 0.50
33 40 0.50
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:606114 original size:65 final size:64
Alignment explanation
Indices: 606009--606133 Score: 214
Period size: 65 Copynumber: 1.9 Consensus size: 64
605999 GAAATTACTA
*
606009 TCGCAATGCGAAATGAAATCGCAACGAGAGAATCGTAATGCAAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGCTAAT
* *
606073 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGC
1 TCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGC
606134 GATTTAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
64 15 0.26
65 42 0.74
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.15
Consensus pattern (64 bp):
TCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGCTAAT
Found at i:606155 original size:18 final size:19
Alignment explanation
Indices: 606132--606175 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
606122 AAATCGCAAC
606132 GCGATTT-AATTTCGCGTT
1 GCGATTTCAATTTCGCGTT
* *
606150 GTGATTTTCATTTTCGCGTT
1 GCGA-TTTCAATTTCGCGTT
606170 GCGATT
1 GCGATT
606176 CTCTCGTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.14
19 5 0.24
20 13 0.62
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.48
Consensus pattern (19 bp):
GCGATTTCAATTTCGCGTT
Found at i:606330 original size:14 final size:14
Alignment explanation
Indices: 606311--606347 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
606301 CATCAATTAA
606311 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
606325 ACAAATCACCTTTT
1 ACAAATCAACTTTT
606339 ACAAATCAA
1 ACAAATCAA
606348 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:607760 original size:21 final size:21
Alignment explanation
Indices: 607694--607763 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
607684 GTGAATCGGG
*
607694 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
607714 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
607736 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
607757 CTCTTGA
1 CTCTTGA
607764 GGAATGATAG
Statistics
Matches: 35, Mismatches: 13, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 33 0.94
22 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:607779 original size:42 final size:41
Alignment explanation
Indices: 607694--607816 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 41
607684 GTGAATCGGG
* * * *
607694 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTT-GAGGATGACAGGGGC
*
607736 CTCTTGAACGGTGGGAGGGGACTCTTGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTGAGG-ATGACAGGGGC
* * * *
607778 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTTGA-GGATGACAGG
607817 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 2 0.03
42 60 0.88
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTTGAGGATGACAGGGGC
Found at i:609900 original size:20 final size:19
Alignment explanation
Indices: 609813--609930 Score: 130
Period size: 19 Copynumber: 6.1 Consensus size: 19
609803 TCTTTTGGTT
*
609813 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
609832 GATAATGAGAGTCGCAACGC
1 GA-AATGAAAATCGCAACGC
* * *
609852 GACCA-GACAATCGCAACGA
1 GA-AATGAAAATCGCAACGC
609871 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
609891 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
609910 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
609929 GA
1 GA
609931 TTTTTGTTTC
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
18 1 0.01
19 47 0.57
20 34 0.41
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:609903 original size:39 final size:38
Alignment explanation
Indices: 609813--609930 Score: 139
Period size: 39 Copynumber: 3.1 Consensus size: 38
609803 TCTTTTGGTT
* *
609813 GAAATGAAAATCGCAACGAGATAATGAGAGTCGCAACGC
1 GAAATGAAAATCGCAACGAGA-AATGAAAATCGCAACGC
* *
609852 GACCA-GACAATCGCAACGAGAAATGAAAATCGCAACCGC
1 GA-AATGAAAATCGCAACGAGAAATGAAAATCGCAA-CGC
* * *
609891 GAAATAAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGC
609929 GA
1 GA
609931 TTTTTGTTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
38 17 0.25
39 49 0.73
40 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGC
Found at i:609922 original size:58 final size:58
Alignment explanation
Indices: 609813--609925 Score: 140
Period size: 58 Copynumber: 1.9 Consensus size: 58
609803 TCTTTTGGTT
* * * * *
609813 GAAATGAAAATCGCAACGAGATAATGAGAGTCGCAACGCGACCAGACAATCGCAACGA
1 GAAATGAAAATCGCAACGAGATAATAAAAATCGCAACGCGACAAGAAAATCGCAACGA
*
609871 GAAATGAAAATCGCAACCGCGA-AATAAAAATCGCAACGCGA-AATGAAAATCGCAA
1 GAAATGAAAATCGCAA-CGAGATAATAAAAATCGCAACGCGACAA-GAAAATCGCAA
609926 TGCGATTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.02
58 42 0.89
59 4 0.09
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (58 bp):
GAAATGAAAATCGCAACGAGATAATAAAAATCGCAACGCGACAAGAAAATCGCAACGA
Found at i:609962 original size:19 final size:19
Alignment explanation
Indices: 609926--609992 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
609916 AAAATCGCAA
*
609926 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
609945 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
609964 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
609984 TGCGATTTT
1 TGCGATTTT
609993 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:610532 original size:20 final size:20
Alignment explanation
Indices: 610507--610559 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
610497 GCGCTATGTA
610507 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
610527 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
610547 TATCTCGTTGCGA
1 AATCGCGTTGCGA
610560 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:610593 original size:20 final size:20
Alignment explanation
Indices: 610568--610621 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
610558 GATTTTGTAT
610568 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
610588 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
610608 TATCGCATTGCGAT
1 TATCGCATTGCGAT
610622 TTTCCCATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:610606 original size:61 final size:61
Alignment explanation
Indices: 610508--610624 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
610498 CGCTATGTAA
* * * * *
610508 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
610569 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
610625 CCCATTCGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:610633 original size:20 final size:20
Alignment explanation
Indices: 610610--610660 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
610600 ATAGTCAGTA
*
610610 TCGCATTGCGATTTTCCCAT
1 TCGCATTGCGATTTACCCAT
* **
610630 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCCAT
610650 TCGCATTGCGA
1 TCGCATTGCGA
610661 ATTGGAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACCCAT
Found at i:611433 original size:21 final size:21
Alignment explanation
Indices: 611407--611451 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
611397 GATTTCTGGG
* *
611407 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
611428 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
611449 CAA
1 CAA
611452 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:612318 original size:31 final size:31
Alignment explanation
Indices: 612260--612337 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
612250 AGAGTTGAGG
*
612260 GTTTACCTATGTCTTTCGAGACATATGGAAA
1 GTTTACCTAGGTCTTTCGAGACATATGGAAA
* * *
612291 GTTTACCTAGGT-TCTTCGGGACCTATGGACA
1 GTTTACCTAGGTCT-TTCGAGACATATGGAAA
*
612322 G-TTACCGAGGATCTTT
1 GTTTACCTAGG-TCTTT
612338 ATGACCTCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 9 0.23
31 29 0.74
32 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATGGAAA
Found at i:612344 original size:30 final size:30
Alignment explanation
Indices: 612310--612528 Score: 395
Period size: 30 Copynumber: 7.3 Consensus size: 30
612300 GGTTCTTCGG
*
612310 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
612340 GACCTCTGGACAGTTACCGAGGATCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
612370 GACCTCTGGACAGTTACCGAGGATC-TTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
612399 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
612429 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
612459 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* *
612489 GACCTCTAGACAGTTACCGAGGATCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
612519 GACCTCTGGA
1 GACCTCTGGA
612529 TAGGTCCTTC
Statistics
Matches: 182, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
29 28 0.15
30 154 0.85
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:612462 original size:89 final size:90
Alignment explanation
Indices: 612310--612528 Score: 395
Period size: 89 Copynumber: 2.4 Consensus size: 90
612300 GGTTCTTCGG
* *
612310 GACCTATGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTGTGACCT
1 GACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCT
612375 CTGGACAGTTACCGAGGATC-TTAT
66 CTGGACAGTTACCGAGGATCTTTAT
612399 GACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCT
1 GACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCT
612464 CTGGACAGTTACCGAGGATCTTTAT
66 CTGGACAGTTACCGAGGATCTTTAT
* *
612489 GACCTCTAGACAGTTACCGAGGATCTTTGTGACCTCTGGA
1 GACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGA
612529 TAGGTCCTTC
Statistics
Matches: 125, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 83 0.66
90 42 0.34
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (90 bp):
GACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCT
CTGGACAGTTACCGAGGATCTTTAT
Found at i:612812 original size:2 final size:2
Alignment explanation
Indices: 612805--612839 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
612795 CGTGGATAGG
612805 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
612840 GAAATGTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:615722 original size:21 final size:21
Alignment explanation
Indices: 615696--615740 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
615686 GATTTCTGGG
* *
615696 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
615717 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
615738 CAA
1 CAA
615741 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:615788 original size:20 final size:20
Alignment explanation
Indices: 615763--615800 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
615753 CAGAATGTCA
615763 GAGGGAACCGATACCCCCAG
1 GAGGGAACCGATACCCCCAG
*
615783 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
615801 CTAAAGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.37, G:0.29, T:0.08
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAG
Found at i:616626 original size:31 final size:31
Alignment explanation
Indices: 616568--616645 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
616558 AGAGTTGAGG
*
616568 GTTTACCTATGTCTTTCGAGACATATGGAAA
1 GTTTACCTAGGTCTTTCGAGACATATGGAAA
* * *
616599 GTTTACCTAGGT-TCTTCGGGACCTATGGACA
1 GTTTACCTAGGTCT-TTCGAGACATATGGAAA
*
616630 G-TTACCGAGGATCTTT
1 GTTTACCTAGG-TCTTT
616646 ATGACCTCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 9 0.23
31 29 0.74
32 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATGGAAA
Found at i:616652 original size:30 final size:30
Alignment explanation
Indices: 616618--616837 Score: 395
Period size: 30 Copynumber: 7.3 Consensus size: 30
616608 GGTTCTTCGG
*
616618 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
616648 GACCTCTGGACAGTTACCGAGGATCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
616678 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
616708 GACCTCTGGACAGTTATCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
616738 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
616768 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* *
616798 GACCTCTGGACAGTTAACGAGGATCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
616828 GACCTCTGGA
1 GACCTCTGGA
616838 TAGGTCCTTC
Statistics
Matches: 183, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 183 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:617115 original size:2 final size:2
Alignment explanation
Indices: 617108--617150 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
617098 CGTGGATAGG
617108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
617150 T
1 T
617151 GAAAGGTGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:619041 original size:30 final size:32
Alignment explanation
Indices: 619001--619072 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
618991 AATAATCATC
* * *
619001 ATTTTGTAATACTTTGAT-AAGTGTAATGA-T
1 ATTTTATAATACTTTAATAAAATGTAATGATT
* *
619031 ATTTTATAATAGTTTAATAAAATTTAATGATT
1 ATTTTATAATACTTTAATAAAATGTAATGATT
619063 ATTTTATAAT
1 ATTTTATAAT
619073 TATTTGGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 15 0.43
31 9 0.26
32 11 0.31
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.50
Consensus pattern (32 bp):
ATTTTATAATACTTTAATAAAATGTAATGATT
Found at i:619088 original size:31 final size:31
Alignment explanation
Indices: 619019--619089 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
619009 ATACTTTGAT
* *
619019 AAGTGTAATGATATTTTATAATAGTTTAATA
1 AAGTTTAATGATATTTTATAATAGTTTAAGA
* *
619050 AAATTTAATGATTATTTTATAATTA-TTT-GGA
1 AAGTTTAATGA-TATTTTATAA-TAGTTTAAGA
619081 AAGTTTAAT
1 AAGTTTAAT
619090 AACCATTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
31 18 0.55
32 13 0.39
33 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (31 bp):
AAGTTTAATGATATTTTATAATAGTTTAAGA
Found at i:622404 original size:19 final size:20
Alignment explanation
Indices: 622380--622418 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
622370 TAATATAGAA
*
622380 TATTTTTATT-TTATAATAT
1 TATTTTTATTATTAAAATAT
622399 TATTTTTATTATTAAAATAT
1 TATTTTTATTATTAAAATAT
622419 GTTTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTTTATTATTAAAATAT
Found at i:626563 original size:12 final size:12
Alignment explanation
Indices: 626548--626593 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
626538 CGGTTTTTTT
*
626548 ACCGGATAAAAA
1 ACCGGTTAAAAA
626560 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
626575 ACCGGTTAAAAA
1 ACCGGTTAAAAA
626587 ACCGGTT
1 ACCGGTT
626594 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:626575 original size:15 final size:13
Alignment explanation
Indices: 626554--626594 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
626544 TTTTACCGGA
626554 TAAAAAACCGGTT
1 TAAAAAACCGGTT
626567 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
626581 TAAAAAACCGGTT
1 TAAAAAACCGGTT
626594 T
1 T
626595 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:628492 original size:2 final size:2
Alignment explanation
Indices: 628485--628510 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
628475 TGAAAGTGAA
628485 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
628511 GAATATGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:628770 original size:32 final size:31
Alignment explanation
Indices: 628728--628855 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
628718 AGAGTCGAGG
628728 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
628759 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
628791 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* ** * *
628822 GTTTACCTAGGTTCTTTGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
628853 GTT
1 GTT
628856 GACGAGGTTC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
31 54 0.66
32 28 0.34
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:628838 original size:63 final size:62
Alignment explanation
Indices: 628731--628854 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 62
628721 GTCGAGGGTT
* *
628731 TACCTATGTTCTACGGAACATATGGACAGTTTTACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTT-GAGACATATGGACAGTA
* *
628794 TACCTATGTTCTAAGGAACATATGGACAG-TTTACCTAGGTTCTTTGGGACCTATGGACAGT
1 TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGG-TCTTTGAGACATATGGACAGT
628855 TGACGAGGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
62 23 0.41
63 33 0.59
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (62 bp):
TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTTGAGACATATGGACAGTA
Found at i:628875 original size:30 final size:31
Alignment explanation
Indices: 628814--628889 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
628804 CTAAGGAACA
* * *
628814 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTGACCGAGGTTCTTTAGGACC
*
628845 TATGGACAGTTGA-CGAGGTTCTTTATGACC
1 TATGGACAGTTGACCGAGGTTCTTTAGGACC
* *
628875 TCTGGATAGTT-ACCG
1 TATGGACAGTTGACCG
628890 GGGTCTGTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 1 0.03
30 25 0.66
31 12 0.32
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.34
Consensus pattern (31 bp):
TATGGACAGTTGACCGAGGTTCTTTAGGACC
Found at i:631573 original size:21 final size:21
Alignment explanation
Indices: 631549--631588 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
631539 TTTATTTTAT
631549 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
631570 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
631589 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:631624 original size:32 final size:33
Alignment explanation
Indices: 631583--631681 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
631573 TTTGTTTCAA
631583 TTATCGAACTTG-AAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
*
631615 TTATCGAACTTGTAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
* * *
631648 TTATCAAACTTGAAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
631681 T
1 T
631682 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 12 0.19
33 50 0.81
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
Found at i:631710 original size:13 final size:13
Alignment explanation
Indices: 631667--631721 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
631657 TTGAAAGTAT
631667 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
631680 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
631694 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
631707 TTAAGTATTTGAA
1 TTAAGTATTTCAA
631720 TT
1 TT
631722 TATCAAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:631943 original size:21 final size:21
Alignment explanation
Indices: 631917--631994 Score: 147
Period size: 21 Copynumber: 3.7 Consensus size: 21
631907 TGGAGCGTGG
631917 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTACCCTCTCATA
631938 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTACCCTCTCATA
631959 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTACCCTCTCATA
*
631980 GGGAATCGGTTCCCT
1 GGGAATCGGTACCCT
631995 AAGTGTAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (21 bp):
GGGAATCGGTACCCTCTCATA
Found at i:632186 original size:15 final size:15
Alignment explanation
Indices: 632161--632216 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
632151 ATCTGGAATA
*
632161 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
632176 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
632191 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
632208 TTAAAACCG
1 TTAAAACCG
632217 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:632225 original size:21 final size:18
Alignment explanation
Indices: 632180--632213 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
632170 GTTTTTTTAT
632180 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
632197 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
632214 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:632333 original size:15 final size:17
Alignment explanation
Indices: 632307--632338 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
632297 TTCTATGAGA
632307 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
632323 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
632339 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:634575 original size:28 final size:29
Alignment explanation
Indices: 634532--634588 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
634522 GGATTGATAG
* *
634532 TTCAGATCATCCAAGGG-GGCTGAAACCT
1 TTCAGATCATCAAAGGGAGACTGAAACCT
*
634560 TTCAGCTCATCAAAGGGAGACTGAAACCT
1 TTCAGATCATCAAAGGGAGACTGAAACCT
634589 AAGGACTCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.21
Consensus pattern (29 bp):
TTCAGATCATCAAAGGGAGACTGAAACCT
Found at i:637528 original size:53 final size:53
Alignment explanation
Indices: 637382--637536 Score: 208
Period size: 53 Copynumber: 3.0 Consensus size: 53
637372 ACATTTCTAT
* * * * *
637382 ATGTGAATAAATAAAGCTAAATGGTCGAAGAACTCAGAAAACCAACAAG--AC
1 ATGTGAATAAATAAAGCTAAATGGTCGTAGAACTTACAAAGCCAAAAAGACAC
* *
637433 ATGTGAATAAATAAAGCTAAACGCT-GTAGAACTTACAAAGCCAAAAAGACAC
1 ATGTGAATAAATAAAGCTAAATGGTCGTAGAACTTACAAAGCCAAAAAGACAC
* *
637485 ATGTGAATAAATAAAGTTAAATGGTCGTAGAACTTACAAAGCCAATAAGACA
1 ATGTGAATAAATAAAGCTAAATGGTCGTAGAACTTACAAAGCCAAAAAGACA
637537 AGCATTATCC
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
50 18 0.20
51 23 0.26
52 24 0.27
53 25 0.28
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.19
Consensus pattern (53 bp):
ATGTGAATAAATAAAGCTAAATGGTCGTAGAACTTACAAAGCCAAAAAGACAC
Found at i:638683 original size:2 final size:2
Alignment explanation
Indices: 638676--638706 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
638666 TCAACTATCA
638676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
638707 ATTGTAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:639692 original size:41 final size:41
Alignment explanation
Indices: 639635--639719 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
639625 CAGGACATAA
639635 AAGAAAACTCACCATTGTAACCATCACTATAAATATGACCT
1 AAGAAAACTCACCATTGTAACCATCACTATAAATATGACCT
639676 AAGAAAACTCACCATTGTAACCATCACTATAAATATGACCT
1 AAGAAAACTCACCATTGTAACCATCACTATAAATATGACCT
639717 AAG
1 AAG
639720 CAACAACAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.24
Consensus pattern (41 bp):
AAGAAAACTCACCATTGTAACCATCACTATAAATATGACCT
Found at i:644759 original size:14 final size:14
Alignment explanation
Indices: 644740--644767 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
644730 GAAAAGAAGC
644740 TATGTGATACGTGA
1 TATGTGATACGTGA
644754 TATGTGATACGTGA
1 TATGTGATACGTGA
644768 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:645138 original size:149 final size:149
Alignment explanation
Indices: 644868--645182 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
644858 GAGTCGAGGG
644868 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
644933 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
*
644998 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTACAAT
*
645017 TCTACGCGGTCTTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* **
645082 ATTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTTTTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
645147 TATGGCACTACGGTACAAT
131 TATGGCACTACGGTACAAT
645166 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
645183 TGCAATTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTACAAT
Found at i:645183 original size:23 final size:23
Alignment explanation
Indices: 645150--645194 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
645140 ATTTTTATAT
*
645150 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTATACGC
* *
645173 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTACAATTATACG
645195 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGC
Found at i:648753 original size:16 final size:16
Alignment explanation
Indices: 648732--648763 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
648722 TTTAGTTGGT
648732 ATTATTTTAAAATTTA
1 ATTATTTTAAAATTTA
648748 ATTATTTTAAAATTTA
1 ATTATTTTAAAATTTA
648764 TCATGTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATTTTAAAATTTA
Found at i:650906 original size:22 final size:21
Alignment explanation
Indices: 650881--650925 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
650871 ATAAAAATAG
650881 AATAAAATGTAATAAATAATTA
1 AATAAAATGTAAT-AATAATTA
* * *
650903 AATATAATTTAATAATATTTA
1 AATAAAATGTAATAATAATTA
650924 AA
1 AA
650926 ATCGAGATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AATAAAATGTAATAATAATTA
Found at i:652686 original size:2 final size:2
Alignment explanation
Indices: 652679--652714 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
652669 CTTATGCAAT
652679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
652715 CTTTCTTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:655616 original size:31 final size:31
Alignment explanation
Indices: 655581--655664 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
655571 GAGTACCTTG
* *
655581 GGGCCTGTAAGCCTACCCAAGAATATTCTCA
1 GGGCCTGTAAGCCTACCCAAGAAAAATCTCA
**
655612 GGGCCT-TCCTGGCCTACCCAAGAAAAATCTCA
1 GGGCCTGT--AAGCCTACCCAAGAAAAATCTCA
*
655644 GGGCC-GCAGAGCCTACCCAAG
1 GGGCCTGTA-AGCCTACCCAAG
655665 GGTCGCCTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
30 1 0.02
31 17 0.40
32 24 0.57
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.17
Consensus pattern (31 bp):
GGGCCTGTAAGCCTACCCAAGAAAAATCTCA
Found at i:655832 original size:12 final size:12
Alignment explanation
Indices: 655809--655912 Score: 77
Period size: 12 Copynumber: 8.7 Consensus size: 12
655799 GATATATAAA
*
655809 AAATCTGAACAG
1 AAATCAGAACAG
*
655821 AACTCAGAACAG
1 AAATCAGAACAG
*
655833 AAATCA-AAGCAT
1 AAATCAGAA-CAG
655845 AAATCAGAACAG
1 AAATCAGAACAG
*
655857 AAATCACAACAG
1 AAATCAGAACAG
* * * *
655869 AATTTAGACCAT
1 AAATCAGAACAG
*
655881 AAATCA-AAGAAG
1 AAATCAGAA-CAG
* *
655893 AATTTAGAACAG
1 AAATCAGAACAG
655905 AAATCAGA
1 AAATCAGA
655913 TAAAATATTA
Statistics
Matches: 67, Mismatches: 21, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
11 3 0.04
12 60 0.90
13 4 0.06
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.15
Consensus pattern (12 bp):
AAATCAGAACAG
Found at i:655855 original size:36 final size:36
Alignment explanation
Indices: 655809--655910 Score: 98
Period size: 36 Copynumber: 2.8 Consensus size: 36
655799 GATATATAAA
* * *
655809 AAATCTGAACAGAACTCAGAACAGAAATCAAAGCAT
1 AAATCAGAACAGAAATCAGAACAGAAATCAAACCAT
* * * *
655845 AAATCAGAACAGAAATCACAACAGAATTTAGACCAT
1 AAATCAGAACAGAAATCAGAACAGAAATCAAACCAT
* * *
655881 AAATCA-AAGAAGAATTTAGAACAGAAATCA
1 AAATCAGAA-CAGAAATCAGAACAGAAATCA
655911 GATAAAATAT
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
35 2 0.04
36 50 0.96
ACGTcount: A:0.55, C:0.17, G:0.13, T:0.16
Consensus pattern (36 bp):
AAATCAGAACAGAAATCAGAACAGAAATCAAACCAT
Found at i:655884 original size:24 final size:24
Alignment explanation
Indices: 655826--655910 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
655816 AACAGAACTC
* * * *
655826 AGAACAGAAATCAAAGCATAAATC
1 AGAACAGAAATCAAAGAAGAATTT
*
655850 AGAACAGAAATCACAA-CAGAATTT
1 AGAACAGAAATCA-AAGAAGAATTT
* *
655874 AGACCATAAATCAAAGAAGAATTT
1 AGAACAGAAATCAAAGAAGAATTT
655898 AGAACAGAAATCA
1 AGAACAGAAATCA
655911 GATAAAATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 2 0.04
24 47 0.92
25 2 0.04
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (24 bp):
AGAACAGAAATCAAAGAAGAATTT
Found at i:660838 original size:44 final size:45
Alignment explanation
Indices: 660789--660941 Score: 118
Period size: 44 Copynumber: 3.5 Consensus size: 45
660779 CTAGAGGTCT
* * *
660789 CAATTATAAATGTAAAAAGTGAAATTAAAAAAAATTAAGAGC-CC
1 CAATTATAAAAGTAAAAAGTGAAATTAAAAAAAATTAAGAACTCA
** * * * *
660833 CAATTATAAAAACAAAATGTGAAATTAGAAGAAACT-AGAACTCA
1 CAATTATAAAAGTAAAAAGTGAAATTAAAAAAAATTAAGAACTCA
* * * *
660877 CAATTATAAAGGTAGAAAA-TAAAATT-AAAAAAATTAAGGA-TCT
1 CAATTATAAAAGTA-AAAAGTGAAATTAAAAAAAATTAAGAACTCA
* * *
660920 TATTTATAAAGGTAAAAAGTGA
1 CAATTATAAAAGTAAAAAGTGA
660942 GATGAATAAA
Statistics
Matches: 83, Mismatches: 22, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
42 4 0.05
43 26 0.31
44 50 0.60
45 3 0.04
ACGTcount: A:0.56, C:0.07, G:0.12, T:0.24
Consensus pattern (45 bp):
CAATTATAAAAGTAAAAAGTGAAATTAAAAAAAATTAAGAACTCA
Found at i:661582 original size:37 final size:37
Alignment explanation
Indices: 661510--661582 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
661500 TTATATTTTT
*
661510 ATTTTTGTAAAAAAATTATATAAATATTATGAATTTA
1 ATTTTTGTAAAAAAATTATATAAATATTATCAATTTA
*
661547 ATTTTT-TAAAGAAAA-TATATAAATATTTTACAATTT
1 ATTTTTGTAAA-AAAATTATATAAATATTAT-CAATTT
661583 GTAATATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
ATTTTTGTAAAAAAATTATATAAATATTATCAATTTA
Found at i:666098 original size:24 final size:24
Alignment explanation
Indices: 666063--666109 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
666053 TGGAAGAGGT
666063 GGAAGGAGTGGTGGATGGA-GTGGC
1 GGAAGGAGTGGTGG-TGGACGTGGC
666087 GGAAGG-GATGGTGGTGGACGTGG
1 GGAAGGAG-TGGTGGTGGACGTGG
666110 AGGTCGTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.19, C:0.04, G:0.60, T:0.17
Consensus pattern (24 bp):
GGAAGGAGTGGTGGTGGACGTGGC
Found at i:666133 original size:15 final size:15
Alignment explanation
Indices: 666082--666134 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
666072 GGTGGATGGA
666082 GTGGCGGAAGGGATG
1 GTGGCGGAAGGGATG
* * *
666097 GTGGTGGACGTGGAGGTC
1 GTGGCGGAAG-GGA--TG
666115 GTGGCGGAAGGGATG
1 GTGGCGGAAGGGATG
666130 GTGGC
1 GTGGC
666135 CGAGGCGGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 14 0.48
16 3 0.10
17 3 0.10
18 9 0.31
ACGTcount: A:0.15, C:0.09, G:0.58, T:0.17
Consensus pattern (15 bp):
GTGGCGGAAGGGATG
Found at i:666151 original size:33 final size:33
Alignment explanation
Indices: 666082--666151 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
666072 GGTGGATGGA
** *
666082 GTGGCGGAAGGGATGGTGGTGGACGTGGAGGTC
1 GTGGCGGAAGGGATGGTGGCCGACGCGGAGGTC
*
666115 GTGGCGGAAGGGATGGTGGCCGAGGCGGTAGG-C
1 GTGGCGGAAGGGATGGTGGCCGACGCGG-AGGTC
666148 GTGG
1 GTGG
666152 AGGTGGCCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.14, C:0.11, G:0.59, T:0.16
Consensus pattern (33 bp):
GTGGCGGAAGGGATGGTGGCCGACGCGGAGGTC
Found at i:669335 original size:772 final size:762
Alignment explanation
Indices: 667817--669350 Score: 1930
Period size: 772 Copynumber: 2.0 Consensus size: 762
667807 GGCTAAAGAA
* * *
667817 ACTCATGAGAAACAAGTGGCTGCCAAAAGGCAGAAGAAAAGCGACGATGTTGCACAGGCTATTGT
1 ACTCATGAGAAACAAGTGGCTGCAAAAAGGCAGAAGAAAAACGACGATGTAGCACAGGCTATTGT
* *
667882 AAAGAAGAAGGTTGAAGCTAAGACGAAGAGGAAATATGAAACTAGTAGTTCATCTAATGACTTTT
66 AAAGAAGAAGGTTGAAGCTAAGACGAAGAGGAAATACGAAACTAGTAGTTCATCTAATGACTCTT
667947 CTGATTCCGATTACATATGCGAAAGCCCACTACTGGTTGATGACTCTTCTAACTCCGATTATGTA
131 CTGATTCCGATTACATATGCGAAAGCCCACTACTGGTTGATGACTCTTCTAACTCCGATTATGTA
* *
668012 TTCACAAACCCACTACTGGTTTACTTATGATGCTACATTTGTTGCTCTCGACATCCATGTATGCT
196 TTCACAAACCCACTACTGGTTTACTTATGATGCTAAATTTGTTGCTCTC-ACA-CCATGCATGCT
* * * *
668077 GATAGTTCACTTTTCATTACATGTTCTGCTTTGAATGGGTTCCTTATATCATTTAAGCTCTTAGT
259 GATAATTCACTTTTCATTACATGTTCTGCTTTGAATAGGTTCCTTACATCATTTAAGCTCTAAGT
* * *
668142 ACTCTTTAAGTATCGAGGCAATACATTCGTGTGATTGTAAAAATGGAGTAGATGAACGCATGTTT
324 ACTCTTTAAGTAACGAGGCAATACATTCGTGTGATTGTAAAAATGAAGCAGATGAACGCATGTTT
* ** * *
668207 GTATATGTTTTGCTTCTTTATGGTTATTTGTTTTTCATCCAGAAACCTGCTCCTGTGAAGCAACA
389 GTATATGTTTCGCCACTTTATGGTTAATTGTTTTTCATCCAGAAACCCGCTCCTGTGAAGCAACA
* *
668272 GCCGGCCGTTGTGAAGAATGGTTCTGTACCTGCAAAGAAAGCAAAACAAGCTAGATATTCAGATT
454 GCC-GCCGTTGCGAAGAATGGCTCTGTACCTGCAAAGAAAGCAAAACAAGCTAGATATTCAGATT
* * *
668337 CTTCAGACTCTAGCAGTGACGAAGATTTATCCTCCGATGAAATGAATATTACTCTTATGCTTGTA
518 CTTCAGAC-CTAGCAGTGACGAAGATTTATCCTCCAATGAAATGAATATTACGCTCATGCTTGTA
* *
668402 ACATTGTATGGTTGCAGATGTTAATTTTATGATTGTTAATGTTCAATGTTTTTGGCTTTCCAGGA
582 ACATTATATGGTTGCAGATGTTAATTTTATGATTGTTAATGTTCAATGTTTTTGACTTTCCAGGA
668467 AGCTCCTGCTCGGAATAAAAAACCTACAGTAGCTACAAAAGCCTCTGATCCAGCTGCAAAGACAG
647 AGCTCCTGCTCGGAATAAAAAACCTACAGTAGCTACAAAAGCCTCTGATCCAGCTGCAAAGACAG
* *
668532 TGAAATCTGATAGCAGTTCAGATTCTTCTTCTGACAATTATGTGTGTTTTGAG
712 TGAAAGCTGATAACAGTTCAGA-T-TTCTTCTGACAATTATGTGTGTTTTGAG
* * ** *
668585 ACTCCTGAGAAACAAGTGGCTGCAAAAAGGCAGATGAAAAACGGTGGTGTAGCACAGGCTATTGT
1 ACTCATGAGAAACAAGTGGCTGCAAAAAGGCAGAAGAAAAACGACGATGTAGCACAGGCTATTGT
* * * *
668650 AAAGATGAAGGTTGAAGCTAAGACGACGACGAAGACGAATAAATACGGAACTAGTAGTTCTTCTG
66 AAAGAAGAAGGTTGAAGCTAAGACGA--A-G-AG--G---AAATACGAAACTAGTAGTTCATCTA
* * * * * *
668715 ATGACTCTTCTGATTTCGATTACATATGTGAAAGCTCAGC-ACTGGTTGATGATTCTTCTGATTC
122 ATGACTCTTCTGATTCCGATTACATATGCGAAAGCCCA-CTACTGGTTGATGACTCTTCTAACTC
* * * * *
668779 TGATTATGTATGTGAC-AACCTACTATTGGTTTACTTAT-ATGCTAAATTTGTTGCTCT-AC-CG
186 CGATTATGTAT-TCACAAACCCACTACTGGTTTACTTATGATGCTAAATTTGTTGCTCTCACACC
* * * *
668840 ATGCCTGCTGATAATTCACTTTTCATTATATGTTTTGCTTTGAATAGGTTCCTTACATGATTTAA
250 ATGCATGCTGATAATTCACTTTTCATTACATGTTCTGCTTTGAATAGGTTCCTTACATCATTTAA
* * * * *
668905 GCTCTAAGTTCTCTTTAAGTAACTAGTCAGTACATTTGTGTGATTGTAAAAATGAAGCAGATGAA
315 GCTCTAAGTACTCTTTAAGTAACGAGGCAATACATTCGTGTGATTGTAAAAATGAAGCAGATGAA
* ** *
668970 -GCCATGTTTGTATCTGTTTCGCCCACTTTATGG-TAATTG-TTTTGGTCCAGGAACCACG-TCC
380 CG-CATGTTTGTATATGTTTCG-CCACTTTATGGTTAATTGTTTTTCATCCAGAAACC-CGCTCC
669031 TGTGAAG-AA-ATGCC-CCATTGTTGCGAAGAATGGCTCTGTACCTGCAAAGAAAGCAAAACAAG
442 TGTGAAGCAACA-GCCGCC---GTTGCGAAGAATGGCTCTGTACCTGCAAAGAAAGCAAAACAAG
* * * * * * *
669093 CTAGCA-ATTCGGGTTCTTCAGA-GTAGTAGTGAC-AGATATTTATCCTCCAATGTAGTGAATAT
503 CTAG-ATATTCAGATTCTTCAGACCTAGCAGTGACGA-AGATTTATCCTCCAATGAAATGAATAT
* * * * *
669155 TTCGCTCATTCTTGTAACTATTTTATATGGTTGCAGATGTTATTTTTATGATTTTTTATCGTTCA
566 TACGCTCATGCTTGTAAC-A--TTATATGGTTGCAGATGTTAATTTTATGATTGTTAAT-GTTCA
* *
669220 ATG-TTTTGACTTTCCCGCAGGAAGCTCCTGCTCGGAATAAAAAACCTGCAGTTGCTACAAAAGC
627 ATGTTTTTGACTTT--C-CAGGAAGCTCCTGCTCGGAATAAAAAACCTACAGTAGCTACAAAAGC
* * * *
669284 CTCTGTTCCAGCTGCTAAGACAGTGAGAGCTGATAACAGTTCAGATTCTTCTTCTGACAATGATG
689 CTCTGATCCAGCTGCAAAGACAGTGAAAGCTGATAACAGTTCAGA-T-TTCTTCTGACAATTATG
669349 TG
752 TG
669351 AGTATTGGGA
Statistics
Matches: 660, Mismatches: 79, Indels: 47
0.84 0.10 0.06
Matches are distributed among these distances:
768 85 0.13
769 47 0.07
770 7 0.01
771 84 0.13
772 182 0.28
773 17 0.03
774 4 0.01
775 106 0.16
776 18 0.03
777 106 0.16
778 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (762 bp):
ACTCATGAGAAACAAGTGGCTGCAAAAAGGCAGAAGAAAAACGACGATGTAGCACAGGCTATTGT
AAAGAAGAAGGTTGAAGCTAAGACGAAGAGGAAATACGAAACTAGTAGTTCATCTAATGACTCTT
CTGATTCCGATTACATATGCGAAAGCCCACTACTGGTTGATGACTCTTCTAACTCCGATTATGTA
TTCACAAACCCACTACTGGTTTACTTATGATGCTAAATTTGTTGCTCTCACACCATGCATGCTGA
TAATTCACTTTTCATTACATGTTCTGCTTTGAATAGGTTCCTTACATCATTTAAGCTCTAAGTAC
TCTTTAAGTAACGAGGCAATACATTCGTGTGATTGTAAAAATGAAGCAGATGAACGCATGTTTGT
ATATGTTTCGCCACTTTATGGTTAATTGTTTTTCATCCAGAAACCCGCTCCTGTGAAGCAACAGC
CGCCGTTGCGAAGAATGGCTCTGTACCTGCAAAGAAAGCAAAACAAGCTAGATATTCAGATTCTT
CAGACCTAGCAGTGACGAAGATTTATCCTCCAATGAAATGAATATTACGCTCATGCTTGTAACAT
TATATGGTTGCAGATGTTAATTTTATGATTGTTAATGTTCAATGTTTTTGACTTTCCAGGAAGCT
CCTGCTCGGAATAAAAAACCTACAGTAGCTACAAAAGCCTCTGATCCAGCTGCAAAGACAGTGAA
AGCTGATAACAGTTCAGATTTCTTCTGACAATTATGTGTGTTTTGAG
Found at i:672760 original size:2 final size:2
Alignment explanation
Indices: 672753--672806 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
672743 TGTGTTGTTA
672753 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
672795 AT AT AT AT AT AT
1 AT AT AT AT AT AT
672807 GCTCACCCTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:682920 original size:10 final size:10
Alignment explanation
Indices: 682905--682930 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
682895 CAAAGAAGGG
682905 CAAGAACCTC
1 CAAGAACCTC
682915 CAAGAACCTC
1 CAAGAACCTC
682925 CAAGAA
1 CAAGAA
682931 AAGAGGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.35, G:0.12, T:0.08
Consensus pattern (10 bp):
CAAGAACCTC
Found at i:687881 original size:3 final size:3
Alignment explanation
Indices: 687875--687902 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
687865 ATCTTCCCCC
687875 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
687903 GGAGATCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:689007 original size:23 final size:23
Alignment explanation
Indices: 688964--689009 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
688954 TATTAGTTTA
*
688964 TGTGAATTATTATTTTACTTATT
1 TGTGAATTATTATATTACTTATT
*
688987 TGTGAATTGTTAATATT-CTTATT
1 TGTGAATTATT-ATATTACTTATT
689010 ATTAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59
Consensus pattern (23 bp):
TGTGAATTATTATATTACTTATT
Found at i:692150 original size:24 final size:25
Alignment explanation
Indices: 692123--692172 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
692113 TGCATGACAT
692123 TGTACATAGAT-ATTTTATACATCA
1 TGTACATAGATGATTTTATACATCA
*
692147 TGTACATAGATGTTTTTATACATCA
1 TGTACATAGATGATTTTATACATCA
692172 T
1 T
692173 CAGGAAGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (25 bp):
TGTACATAGATGATTTTATACATCA
Found at i:692443 original size:21 final size:21
Alignment explanation
Indices: 692414--692467 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
692404 TCATTGAGGG
* *
692414 ACAGGGTATAGTTGGCACGCC
1 ACAGAGTATAGCTGGCACGCC
* *
692435 ACAGAGTATAACTGGCATGCC
1 ACAGAGTATAGCTGGCACGCC
*
692456 ATAGAGTATAGC
1 ACAGAGTATAGC
692468 AGCTGTAGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.20
Consensus pattern (21 bp):
ACAGAGTATAGCTGGCACGCC
Found at i:692626 original size:60 final size:60
Alignment explanation
Indices: 692549--692661 Score: 181
Period size: 60 Copynumber: 1.9 Consensus size: 60
692539 ATCATGTCTG
* * *
692549 GATTAACACTATAGCGTAAGCTTAGTGTAGGTGGTGGGCACGACCTTATGTGTATATCCA
1 GATTAACACTATAGCGTAAACTTAATGTAGGTGGTGGGCACGACCTTAGGTGTATATCCA
* *
692609 GATTAGCACTATGGCGTAAACTTAATGTAGGTGGTGGGCACGACCTTAGGTGT
1 GATTAACACTATAGCGTAAACTTAATGTAGGTGGTGGGCACGACCTTAGGTGT
692662 TGGTATTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (60 bp):
GATTAACACTATAGCGTAAACTTAATGTAGGTGGTGGGCACGACCTTAGGTGTATATCCA
Found at i:692714 original size:18 final size:18
Alignment explanation
Indices: 692691--692734 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
692681 ACAGGGTTCT
692691 TAGGGTTTTAAATTAGGC
1 TAGGGTTTTAAATTAGGC
*
692709 TAGGGTTTTAAATTGGGC
1 TAGGGTTTTAAATTAGGC
*
692727 TATGGTTT
1 TAGGGTTT
692735 ATGGTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.30, T:0.43
Consensus pattern (18 bp):
TAGGGTTTTAAATTAGGC
Found at i:693544 original size:46 final size:46
Alignment explanation
Indices: 693492--693584 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
693482 AAGACAGTGG
693492 AGAGATTTCATTGGAAGATGAATTGGGTGTTGGATA-ATATATATAT
1 AGAGATTTCATTGGAAGATGAATT-GGTGTTGGATATATATATATAT
693538 AGAGATTTCATTGGAAGATGAATTGGTGTTGGATATATATATATAT
1 AGAGATTTCATTGGAAGATGAATTGGTGTTGGATATATATATATAT
693584 A
1 A
693585 TATATATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 11 0.24
46 35 0.76
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (46 bp):
AGAGATTTCATTGGAAGATGAATTGGTGTTGGATATATATATATAT
Found at i:704710 original size:35 final size:36
Alignment explanation
Indices: 704665--704767 Score: 138
Period size: 35 Copynumber: 2.9 Consensus size: 36
704655 TCAACTTTGA
704665 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTAT-TTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTT-TCTTG
* * *
704701 -AAAACGGTTTTTAAAGTTTAGTAAATGTTTTCTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTTCTTG
*
704736 AAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 AAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
704768 GTTAAATATT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
34 1 0.02
35 30 0.53
36 6 0.11
37 20 0.35
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (36 bp):
AAAAATGGTTTTCAAAGTTTGGTAAATGTTTTCTTG
Found at i:709309 original size:21 final size:21
Alignment explanation
Indices: 709285--709345 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
709275 AACTTTGAAA
709285 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
709306 AAAT-G-TTT---A-TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
709320 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
709341 AAATG
1 AAATG
709346 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:709376 original size:37 final size:36
Alignment explanation
Indices: 709277--709385 Score: 175
Period size: 35 Copynumber: 3.0 Consensus size: 36
709267 TGGCAACCAA
709277 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
709314 ATTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
709349 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
709386 GTTGAAATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 34 0.51
36 7 0.10
37 26 0.39
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:718590 original size:2 final size:2
Alignment explanation
Indices: 718583--718613 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
718573 TATTAAAATA
718583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
718614 AATGATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:731004 original size:17 final size:17
Alignment explanation
Indices: 730983--731021 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
730973 AACTAACACA
*
730983 AAAATTAGGAAAACTAC
1 AAAATCAGGAAAACTAC
* *
731000 GAAATCAGGACAACTAC
1 AAAATCAGGAAAACTAC
731017 AAAAT
1 AAAAT
731022 GGCAGAATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (17 bp):
AAAATCAGGAAAACTAC
Found at i:732545 original size:51 final size:51
Alignment explanation
Indices: 732434--732994 Score: 653
Period size: 51 Copynumber: 10.8 Consensus size: 51
732424 AACGTGTCTT
* * * * *
732434 CTCCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACGTGTCTG
1 CTCCCTATTCCTTCAGAGAGTATAAGACT----CAATCTTCAACGAACTTGTCCG
* * * ** *
732489 CTCCCTATTCGTTCAGGGAGTATAAGACTCGATCTTCAATAAACATGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAACTTGTCCG
* * **
732540 CTCCCTATTCCTTCAGAGAG--CAGGACTCAAACAATCTTCAACGAACGGGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAAGACT----CAATCTTCAACGAACTTGTCCG
* * **
732593 CTCTCTATT-CTATCAGAGAGTAT-AGAACTCGAACAATCTTCAACAAAACGGGTCCG
1 CTCCCTATTCCT-TCAGAGAGTATAAG-ACT----CAATCTTCAAC-GAACTTGTCCG
* *
732649 CTCTCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAACTTGTCCG
* * *
732700 CTCCCTATTCCTTTAGAGAGTATAGGACTCAATCTTCAACGAACTTGTTCG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAACTTGTCCG
* * *
732751 CTCTCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAACTTGTCCG
* * *
732802 CTCTCTATTCATTCAGAGAGTATATGACTCAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAACTTGTCCG
732853 CTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAACTTGTCCG
* * *
732904 CTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAACTTGTCCG
*
732955 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAAC
732995 AAACGAATTT
Statistics
Matches: 456, Mismatches: 39, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
49 5 0.01
51 323 0.71
52 13 0.03
53 33 0.07
54 1 0.00
55 45 0.10
56 33 0.07
57 3 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (51 bp):
CTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAACTTGTCCG
Found at i:732831 original size:153 final size:154
Alignment explanation
Indices: 732438--732994 Score: 719
Period size: 153 Copynumber: 3.6 Consensus size: 154
732428 TGTCTTCTCC
* * * *
732438 CTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACGTGTCTGCTCCCTATTCGTTC
1 CTATTCATTCAGAGAGTATAGGACT---ACAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTC
* * * ** * *
732503 AGGGAGTATAAGACTCGATCTTCAATAAACATGTCCGCTCCCTATTCCTTCAGAGAG--CAGGAC
63 AGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGAC
**
732566 TCAAACAATCTTCAACGAACGGGTCCGCTCT
128 T----CAATCTTCAACGAACTTGTCCGCTCT
* * *
732597 CTATTC-TATCAGAGAGTATAGAACTCGAACAATCTTCAACAAAACGGGTCCGCTCTCTATTCCT
1 CTATTCAT-TCAGAGAGTATAGGACT---ACAATCTTCAAC-AAACGTGTCCGCTCCCTATTCCT
*
732661 TCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTTAGAGAGTATAGG
61 TCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGG
*
732726 ACTCAATCTTCAACGAACTTGTTCGCTCT
126 ACTCAATCTTCAACGAACTTGTCCGCTCT
* * * *
732755 CTATTCATTCAGAGAGTATAGGACT-CAATCTTCAACGAACTTGTCCGCTCTCTATTCATTCAGA
1 CTATTCATTCAGAGAGTATAGGACTACAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGA
* *
732819 GAGTATATGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCA
66 GAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCA
*
732884 ATCTTCAACGAACTTGTCCGCTCC
131 ATCTTCAACGAACTTGTCCGCTCT
** *
732908 CTATTCATTCAGAGAGTATAGGACT-CAATCTTCAATGAACTTGTCCGCTCCCTATTCCTTCAGA
1 CTATTCATTCAGAGAGTATAGGACTACAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGA
732972 GAGTATAGGACTCAATCTTCAAC
66 GAGTATAGGACTCAATCTTCAAC
732995 AAACGAATTT
Statistics
Matches: 360, Mismatches: 33, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
153 191 0.53
154 11 0.03
158 46 0.13
159 35 0.10
160 71 0.20
162 6 0.02
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (154 bp):
CTATTCATTCAGAGAGTATAGGACTACAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGA
GAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCA
ATCTTCAACGAACTTGTCCGCTCT
Found at i:734176 original size:27 final size:28
Alignment explanation
Indices: 734137--734245 Score: 77
Period size: 27 Copynumber: 4.0 Consensus size: 28
734127 CTTTATTTCT
*
734137 CTTTTTTCA-TTTTTC-TCTTTTTCTTC
1 CTTTTTCCATTTTTTCATCTTTTTCTTC
* *
734163 CTTTTTCCATTTTTTC-TCTTCTTTTTTT
1 CTTTTTCCATTTTTTCATCTT-TTTCTTC
* *
734191 C-TTTT-CGTTTTTTCCATCATTTT-TTC
1 CTTTTTCCATTTTTT-CATCTTTTTCTTC
* *
734217 TTTTTTCTCATTTTTTCTTCTTTTCTCTT
1 CTTTTTC-CATTTTTTCATCTTTT-TCTT
734246 TTATTTCTTC
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
26 17 0.27
27 22 0.34
28 15 0.23
29 8 0.12
30 2 0.03
ACGTcount: A:0.05, C:0.22, G:0.01, T:0.72
Consensus pattern (28 bp):
CTTTTTCCATTTTTTCATCTTTTTCTTC
Found at i:734190 original size:13 final size:13
Alignment explanation
Indices: 734170--734217 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
734160 TTCCTTTTTC
734170 CATTTTTTCTCTT
1 CATTTTTTCTCTT
* *
734183 CTTTTTTTCTTTT
1 CATTTTTTCTCTT
* *
734196 CGTTTTTTC-CAT
1 CATTTTTTCTCTT
734208 CATTTTTTCT
1 CATTTTTTCT
734218 TTTTTCTCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.06, C:0.21, G:0.02, T:0.71
Consensus pattern (13 bp):
CATTTTTTCTCTT
Found at i:734203 original size:45 final size:45
Alignment explanation
Indices: 734126--734241 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 45
734116 TTGAACCCTC
* * *
734126 CCTTTATTTCTC-TTTTTTCAT-TTTTC-TCTTTTT-CTTCCTTTTT
1 CCTTT-TTTCTCATTTTTTCTTCTTTTCGT-TTTTTCCATCATTTTT
*
734169 CCATTTTTTCTC-TTCTTTTTTTCTTTTCGTTTTTTCCATCATTTTT
1 CC-TTTTTTCTCATT-TTTTCTTCTTTTCGTTTTTTCCATCATTTTT
*
734215 TCTTTTTTCTCATTTTTTCTTCTTTTC
1 CCTTTTTTCTCATTTTTTCTTCTTTTC
734242 TCTTTTATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
43 10 0.16
44 8 0.13
45 31 0.51
46 12 0.20
ACGTcount: A:0.05, C:0.22, G:0.01, T:0.72
Consensus pattern (45 bp):
CCTTTTTTCTCATTTTTTCTTCTTTTCGTTTTTTCCATCATTTTT
Found at i:734252 original size:19 final size:18
Alignment explanation
Indices: 734132--734257 Score: 83
Period size: 17 Copynumber: 7.1 Consensus size: 18
734122 CCTCCCTTTA
*
734132 TTTCTC-TTTTTTCAT-T
1 TTTCTCATTTTTTCTTCT
734148 TTTCTC--TTTTTCTTCCT
1 TTTCTCATTTTTTCTT-CT
734165 TTT-TCCATTTTTTCTCTTCT
1 TTTCT-CA-TTTTT-TCTTCT
734185 TTT-T--TTCTTTTCGTT-T
1 TTTCTCATT-TTTTC-TTCT
734201 TTTCCATCATTTTTTCTT-T
1 TTT-C-TCATTTTTTCTTCT
734220 TTTCTCATTTTTTCTTCT
1 TTTCTCATTTTTTCTTCT
*
734238 TTTCTCTTTTATTTCTTCT
1 TTTCTCATTT-TTTCTTCT
734257 T
1 T
734258 CAAGCAAAAT
Statistics
Matches: 92, Mismatches: 2, Indels: 29
0.75 0.02 0.24
Matches are distributed among these distances:
15 7 0.08
16 15 0.16
17 22 0.24
18 11 0.12
19 16 0.17
20 15 0.16
21 6 0.07
ACGTcount: A:0.05, C:0.21, G:0.01, T:0.73
Consensus pattern (18 bp):
TTTCTCATTTTTTCTTCT
Found at i:744422 original size:13 final size:13
Alignment explanation
Indices: 744406--744430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
744396 AAGCGAAAGA
744406 AAAAACACTCAAT
1 AAAAACACTCAAT
744419 AAAAACACTCAA
1 AAAAACACTCAA
744431 AATCAATTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.24, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAACACTCAAT
Found at i:745832 original size:17 final size:17
Alignment explanation
Indices: 745811--745849 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
745801 AACTAACACA
*
745811 AAAATTAGGAAAACTAC
1 AAAATCAGGAAAACTAC
* *
745828 GAAATCAGGACAACTAC
1 AAAATCAGGAAAACTAC
745845 AAAAT
1 AAAAT
745850 GGCAGAATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (17 bp):
AAAATCAGGAAAACTAC
Found at i:748090 original size:20 final size:20
Alignment explanation
Indices: 748006--748138 Score: 110
Period size: 20 Copynumber: 6.6 Consensus size: 20
747996 AAATGACCAA
*
748006 CAAATTCGCAACGCGA-ATT
1 CAAATTCGCAACGCGATAGT
* *
748025 CCAATTTCGCAATGCGAATATGT
1 -CAAATTCGCAACGCG-ATA-GT
** **
748048 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGATAGT
748066 CCAAATTCGCAACGCGATAGT
1 -CAAATTCGCAACGCGATAGT
* *
748087 CAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGT
* *
748107 CAAATTCGCAACACGAAAGT
1 CAAATTCGCAACGCGATAGT
748127 CAAATTCGCAAC
1 CAAATTCGCAAC
748139 AGAATTTCAA
Statistics
Matches: 92, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 73 0.79
21 14 0.15
22 1 0.01
23 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:748139 original size:20 final size:20
Alignment explanation
Indices: 748067--748177 Score: 127
Period size: 20 Copynumber: 5.7 Consensus size: 20
748057 TGCGATTTTC
* *
748067 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACACGAAAGT
* *
748087 CAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACACGAAAGT
748107 CAAATTCGCAACACGAAAGT
1 CAAATTCGCAACACGAAAGT
**
748127 CAAATTCGCAACA-GAATTT
1 CAAATTCGCAACACGAAAGT
* **
748146 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAAAGT
748165 CAAATTCGCAACA
1 CAAATTCGCAACA
748178 GGTTTTAGTT
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
19 34 0.41
20 49 0.59
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.22
Consensus pattern (20 bp):
CAAATTCGCAACACGAAAGT
Found at i:748150 original size:19 final size:19
Alignment explanation
Indices: 748106--748178 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
748096 AACGCGAAAG
**
748106 TCAAATTCGCAACACGAAAG
1 TCAAATTCGCAACA-GAATT
748126 TCAAATTCGCAACAGAATT
1 TCAAATTCGCAACAGAATT
*
748145 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACAGAATT
748164 TCAAATTCGCAACAG
1 TCAAATTCGCAACAG
748179 GTTTTAGTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 35 0.71
20 14 0.29
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (19 bp):
TCAAATTCGCAACAGAATT
Found at i:748942 original size:12 final size:12
Alignment explanation
Indices: 748922--748955 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
748912 CCACATTTCT
*
748922 AATACCAAACAC
1 AATATCAAACAC
748934 AATATCAAACAC
1 AATATCAAACAC
*
748946 AATCTCAAAC
1 AATATCAAAC
748956 CCCACAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
AATATCAAACAC
Found at i:751411 original size:18 final size:18
Alignment explanation
Indices: 751388--751423 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
751378 AAGCAAAAGG
*
751388 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
751406 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
751424 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:751997 original size:61 final size:63
Alignment explanation
Indices: 751866--752006 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 63
751856 TTTTTGAAAC
*
751866 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACAAATCAAATT
751931 A
63 A
* * ** *
751932 AACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATT-A
751993 AACAAATCAACTTT
1 AACAAATCAACTTT
752007 CGATGTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
60 4 0.06
61 35 0.51
62 3 0.04
66 26 0.38
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.31
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:753299 original size:21 final size:21
Alignment explanation
Indices: 753262--753326 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
753252 GAACGGTGGG
*
753262 AGGGGCTTCTTCG-ATGATGAT
1 AGGGGCCTCTT-GAATGATGAT
*
753283 AGGGGCCTCTTGAATGAT-AGG
1 AGGGGCCTCTTGAATGATGA-T
**
753304 AGGCACCTCTTGAATGATGAT
1 AGGGGCCTCTTGAATGATGAT
753325 AG
1 AG
753327 ATACATCAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 2 0.06
21 33 0.92
22 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (21 bp):
AGGGGCCTCTTGAATGATGAT
Found at i:753301 original size:18 final size:20
Alignment explanation
Indices: 753278--753321 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
753268 TTCTTCGATG
753278 ATGATAGG-GG-CCTCTTGA
1 ATGATAGGAGGACCTCTTGA
753296 ATGATAGGAGGCACCTCTTGA
1 ATGATAGGAGG-ACCTCTTGA
753317 ATGAT
1 ATGAT
753322 GATAGATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
21 13 0.57
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (20 bp):
ATGATAGGAGGACCTCTTGA
Found at i:755827 original size:22 final size:22
Alignment explanation
Indices: 755799--755845 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
755789 GAGATAGACA
755799 GATTTCGTCGGAAATGAGGACG
1 GATTTCGTCGGAAATGAGGACG
* *
755821 GATTTCGTCGGAGATGGGGACG
1 GATTTCGTCGGAAATGAGGACG
755843 GAT
1 GAT
755846 GTCGCCGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.13, G:0.40, T:0.23
Consensus pattern (22 bp):
GATTTCGTCGGAAATGAGGACG
Found at i:755998 original size:20 final size:20
Alignment explanation
Indices: 755973--756036 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
755963 GCATAAAAAC
755973 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
755993 ATTTGACTATT-GCTTTGAGA
1 ATTTGACT-TTCGCGTTGCGA
* *
756013 ATTTGACTATCGCGTTACGA
1 ATTTGACTTTCGCGTTGCGA
756033 ATTT
1 ATTT
756037 AGAAAATTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.92
21 2 0.06
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:761426 original size:20 final size:20
Alignment explanation
Indices: 761401--761451 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
761391 AAATTCAGTG
761401 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* *
761421 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
761441 TTGCGATAGTC
1 TTGCGATAGTC
761452 GGAAAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:780018 original size:21 final size:21
Alignment explanation
Indices: 779976--780019 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
779966 TTGGGATCAG
*
779976 TTTAGTGTATATGATAATAAT
1 TTTAGTGTATATGATAAAAAT
*
779997 TTTA-TGTATATGCTCAAAAAT
1 TTTAGTGTATATGAT-AAAAAT
780018 TT
1 TT
780020 AAGAGAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (21 bp):
TTTAGTGTATATGATAAAAAT
Found at i:780249 original size:33 final size:34
Alignment explanation
Indices: 780197--780263 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
780187 TAAAAACATT
* *
780197 GTAATTGGTTTTCTGGAATTGGTTTTCCAGAAAA
1 GTAATTGGTTTTCTAGAATTGATTTTCCAGAAAA
780231 GTAATTGG-TTTCTAGAATTGATTTTCCAGAAAA
1 GTAATTGGTTTTCTAGAATTGATTTTCCAGAAAA
780264 CCAATTACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 23 0.74
34 8 0.26
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (34 bp):
GTAATTGGTTTTCTAGAATTGATTTTCCAGAAAA
Found at i:780297 original size:6 final size:6
Alignment explanation
Indices: 780286--780326 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
780276 AAACAAATAG
780286 ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC ACTTT
1 ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC ACTTT
780327 TTCTTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (6 bp):
ACTTTC
Found at i:786182 original size:149 final size:149
Alignment explanation
Indices: 785991--786305 Score: 587
Period size: 149 Copynumber: 2.1 Consensus size: 149
785981 GAGTCGAGGG
* *
785991 TCTACGTGGTCTTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
786056 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
786121 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
786140 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
786205 ACTTGATCCCTAGTATATGTATATGTTTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
786270 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
786289 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
786306 TGCAATTATA
Statistics
Matches: 162, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 161 0.99
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:786306 original size:23 final size:23
Alignment explanation
Indices: 786273--786317 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
786263 ATTATTATAT
*
786273 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
786296 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
786318 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:805289 original size:16 final size:16
Alignment explanation
Indices: 805225--805290 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 16
805215 CCATTCCCCA
*
805225 TCTTCTT-TTTCTTCAC
1 TCTTCTTCTTTCTT-TC
*
805241 TTTTCTTC-TTCTTTC
1 TCTTCTTCTTTCTTTC
*
805256 T-TTC-TCTTCACTTT-
1 TCTTCTTCTT-TCTTTC
805270 TCTTCTTCTTTCTTTC
1 TCTTCTTCTTTCTTTC
805286 TCTTC
1 TCTTC
805291 ACTTTTCTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
13 2 0.05
14 5 0.12
15 13 0.32
16 20 0.50
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (16 bp):
TCTTCTTCTTTCTTTC
Found at i:805297 original size:16 final size:16
Alignment explanation
Indices: 805252--805299 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
805242 TTTCTTCTTC
805252 TTTCTTTCTCTTCACT
1 TTTCTTTCTCTTCACT
805268 TTTC--T-TCTT--C-
1 TTTCTTTCTCTTCACT
805278 TTTCTTTCTCTTCACT
1 TTTCTTTCTCTTCACT
805294 TTTCTT
1 TTTCTT
805300 CACTTTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
10 4 0.15
11 1 0.04
12 1 0.04
13 8 0.31
14 1 0.04
15 1 0.04
16 10 0.38
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTCTTTCTCTTCACT
Done.