Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005571.1 Hibiscus syriacus cultivar Beakdansim tig00012922_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: 68911
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1280 original size:19 final size:19
Alignment explanation
Indices: 1245--1283 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1235 TATTAAAAAG
*
1245 TTATAAAATAATCTTTTAT
1 TTATAAAATAATATTTTAT
1264 TTAT-AAATAATTATTTTAT
1 TTATAAAATAA-TATTTTAT
1283 T
1 T
1284 AAATTTTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATAAAATAATATTTTAT
Found at i:1981 original size:63 final size:60
Alignment explanation
Indices: 1859--1974 Score: 141
Period size: 63 Copynumber: 1.9 Consensus size: 60
1849 GTTGTCAATA
*
1859 ATTAATAAAATTTATATATTCATAGTTAATAAAGTAAGACTTAACTAAAATAAATAAATTG
1 ATTAATAAAATTTATATATTCATAGTTAATAAACTAAGACTTAAC-AAAATAAATAAATTG
1920 ATTAATAAAGATTTTATATATTTC-TAGTTAATAAGACTAA-AC-TAA-AAAAGTAAAT
1 ATTAATAAA-A-TTTATATA-TTCATAGTTAATAA-ACTAAGACTTAACAAAA-TAAAT
1975 TTAAATTATA
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
60 4 0.08
61 14 0.29
62 4 0.08
63 20 0.41
64 7 0.14
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (60 bp):
ATTAATAAAATTTATATATTCATAGTTAATAAACTAAGACTTAACAAAATAAATAAATTG
Found at i:3718 original size:24 final size:24
Alignment explanation
Indices: 3690--3784 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 24
3680 AAACGGAGAT
*
3690 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCATAACAGAATTCAG
* * *
3714 ATCAGATATCATAACAGAATCCCG
1 ATCAGAAATCATAACAGAATTCAG
* * *
3738 ATCAGAAATCAGAACATAATTCTG
1 ATCAGAAATCATAACAGAATTCAG
* * *
3762 ATAAAAAATCATAACATAATTCA
1 ATCAGAAATCATAACAGAATTCA
3785 AATAAAAAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.51, C:0.18, G:0.09, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCATAACAGAATTCAG
Found at i:3789 original size:24 final size:24
Alignment explanation
Indices: 3743--3798 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
3733 TCCCGATCAG
**
3743 AAATCAGAACATAATTCTGATAAA
1 AAATCAGAACATAATTCAAATAAA
*
3767 AAATCATAACATAATTCAAATAAA
1 AAATCAGAACATAATTCAAATAAA
3791 AAATCAGA
1 AAATCAGA
3799 TAAAACATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.59, C:0.12, G:0.05, T:0.23
Consensus pattern (24 bp):
AAATCAGAACATAATTCAAATAAA
Found at i:4170 original size:27 final size:27
Alignment explanation
Indices: 4132--4184 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
4122 TTATCCATAG
*
4132 ATCATCTTCGGAATCATCACTGAATAT
1 ATCATATTCGGAATCATCACTGAATAT
4159 ATCATATTCGGAATCATCACTGAATA
1 ATCATATTCGGAATCATCACTGAATA
4185 AATCTTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (27 bp):
ATCATATTCGGAATCATCACTGAATAT
Found at i:13313 original size:24 final size:24
Alignment explanation
Indices: 13281--13329 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
13271 TTTCTATTAT
13281 CAGAAAAAGAAATGGAAAAAAAGG
1 CAGAAAAAGAAATGGAAAAAAAGG
13305 CAGAAAAAGAAATGGAAAAAAAGG
1 CAGAAAAAGAAATGGAAAAAAAGG
13329 C
1 C
13330 CTGCTTGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.65, C:0.06, G:0.24, T:0.04
Consensus pattern (24 bp):
CAGAAAAAGAAATGGAAAAAAAGG
Found at i:13479 original size:14 final size:15
Alignment explanation
Indices: 13456--13485 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
13446 TAGAAAAGGA
13456 AAAGACAAAAAAATG
1 AAAGACAAAAAAATG
13471 AAAGA-AAAAAAATG
1 AAAGACAAAAAAATG
13485 A
1 A
13486 TCTGCTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.07
Consensus pattern (15 bp):
AAAGACAAAAAAATG
Found at i:16972 original size:29 final size:29
Alignment explanation
Indices: 16877--17128 Score: 269
Period size: 29 Copynumber: 8.6 Consensus size: 29
16867 TTTCGGTTAT
* *
16877 GGTGTTATTTT-GTAATTATTTTTAAAA-
1 GGTGATATTTTGGTAATTATTGTTAAAAC
* * * * *
16904 GTGTGTTATTTTCGTATTTATTTTTAAAAAG
1 G-GTGATATTTTGGTAATTATTGTT-AAAAC
* *
16935 GGTGTTATTTTCGTAATTAATT-TTAAAAC
1 GGTGATATTTTGGTAATT-ATTGTTAAAAC
* *
16964 GGTGATATTCTGGCAATTATTGTT-AAAC
1 GGTGATATTTTGGTAATTATTGTTAAAAC
*
16992 AGTGATATTTTGGTAATTATTGTTAAAAC
1 GGTGATATTTTGGTAATTATTGTTAAAAC
* *
17021 TGTGCTATTTTGGTAATTATTGTTAAAAC
1 GGTGATATTTTGGTAATTATTGTTAAAAC
*
17050 GGTGCTATTTTGGTAATTATTGTTAAAAC
1 GGTGATATTTTGGTAATTATTGTTAAAAC
*
17079 GGTGATATTTTGGTAATTATTATTAAAAAAAC
1 GGTGATATTTTGGTAATTATTGTT---AAAAC
*
17111 AGTGATATTTTGGTAATT
1 GGTGATATTTTGGTAATT
17129 GTTTAAAAAA
Statistics
Matches: 199, Mismatches: 16, Indels: 15
0.87 0.07 0.07
Matches are distributed among these distances:
27 1 0.01
28 38 0.19
29 112 0.56
30 22 0.11
31 4 0.02
32 22 0.11
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (29 bp):
GGTGATATTTTGGTAATTATTGTTAAAAC
Found at i:17084 original size:115 final size:117
Alignment explanation
Indices: 16882--17128 Score: 322
Period size: 115 Copynumber: 2.1 Consensus size: 117
16872 GTTATGGTGT
* * * * * * *
16882 TATTTT-GTAATTATTTTTAAAAGTGTGTTATTTTCGTATTTATTTTTAAAAAGGGTGTTATTTT
1 TATTTTGGTAATTATTGTTAAAACTGTGCTATTTTCGTAATTATTGTTAAAAACGGTGCTATTTT
*
16946 CGTAATTAATTTTAAAACGGTGATATTCTGGCAATTATTGTT-AAACAGTGA
66 CGTAATTAATTTTAAAACGGTGATATTCTGGCAATTATTATTAAAACAGTGA
*
16997 TATTTTGGTAATTATTGTTAAAACTGTGCTATTTTGGTAATTATTGTT-AAAACGGTGCTATTTT
1 TATTTTGGTAATTATTGTTAAAACTGTGCTATTTTCGTAATTATTGTTAAAAACGGTGCTATTTT
* * *
17061 GGTAATT-ATTGTTAAAACGGTGATATTTTGGTAATTATTATTAAAAAAACAGTGA
66 CGTAATTAATT-TTAAAACGGTGATATTCTGGCAATTATTATT---AAAACAGTGA
17116 TATTTTGGTAATT
1 TATTTTGGTAATT
17129 GTTTAAAAAA
Statistics
Matches: 114, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
114 3 0.03
115 54 0.47
116 35 0.31
119 22 0.19
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (117 bp):
TATTTTGGTAATTATTGTTAAAACTGTGCTATTTTCGTAATTATTGTTAAAAACGGTGCTATTTT
CGTAATTAATTTTAAAACGGTGATATTCTGGCAATTATTATTAAAACAGTGA
Found at i:17144 original size:26 final size:28
Alignment explanation
Indices: 16924--17159 Score: 157
Period size: 29 Copynumber: 8.2 Consensus size: 28
16914 TTCGTATTTA
** * *
16924 TTTTTAAAAAGGGTGTTATTTTCGTAAT
1 TTTTTAAAAACAGTGATATTTTGGTAAT
* * *
16952 TAATTTT-AAAACGGTGATATTCTGGCAAT
1 T--TTTTAAAAACAGTGATATTTTGGTAAT
16981 TATTGTT--AAACAGTGATATTTTGGTAAT
1 T-TT-TTAAAAACAGTGATATTTTGGTAAT
* *
17009 TATTGTT-AAAACTGTGCTATTTTGGTAAT
1 T-TT-TTAAAAACAGTGATATTTTGGTAAT
* *
17038 TATTGTT-AAAACGGTGCTATTTTGGTAAT
1 T-TT-TTAAAAACAGTGATATTTTGGTAAT
*
17067 TATTGTT-AAAACGGTGATATTTTGGTAAT
1 T-TT-TTAAAAACAGTGATATTTTGGTAAT
17096 TATTATTAAAAAAACAGTGATATTTTGGTAAT
1 T-TT-TT--AAAAACAGTGATATTTTGGTAAT
*
17128 TGTTTAAAAA-A-TGATATTTCT-GTAAT
1 TTTTTAAAAACAGTGATATTT-TGGTAAT
17154 TTTTTA
1 TTTTTA
17160 CTGTGGACTA
Statistics
Matches: 184, Mismatches: 16, Indels: 18
0.84 0.07 0.08
Matches are distributed among these distances:
26 18 0.10
27 2 0.01
28 34 0.18
29 101 0.55
30 6 0.03
31 1 0.01
32 22 0.12
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.46
Consensus pattern (28 bp):
TTTTTAAAAACAGTGATATTTTGGTAAT
Found at i:23635 original size:21 final size:21
Alignment explanation
Indices: 23607--23711 Score: 137
Period size: 21 Copynumber: 5.1 Consensus size: 21
23597 TATATATATC
*
23607 TAAT-AGCACTATAGATAAAA
1 TAATAAGCACTATAAATAAAA
23627 TAATAAGCACTATAAATAAAA
1 TAATAAGCACTATAAATAAAA
23648 TAATAAGCACTATAAATAAAA
1 TAATAAGCACTATAAATAAAA
* **
23669 TAATAA-CACAATAAATATTA
1 TAATAAGCACTATAAATAAAA
23689 TAAT-AGCACTA-AGAATAAAA
1 TAATAAGCACTATA-AATAAAA
23709 TAA
1 TAA
23712 AATGAAGTGG
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
19 2 0.03
20 31 0.41
21 42 0.56
ACGTcount: A:0.60, C:0.10, G:0.06, T:0.25
Consensus pattern (21 bp):
TAATAAGCACTATAAATAAAA
Found at i:24498 original size:29 final size:29
Alignment explanation
Indices: 24230--24504 Score: 297
Period size: 29 Copynumber: 9.4 Consensus size: 29
24220 GTTATGGTGT
* * ** *
24230 TATTTTCGTAATTATTTTTAAAAGTGTGT
1 TATTTTGGTAATTATTGTTAAAACAGTGA
* * * *
24259 TATTTTCGTATTTATTTTTAAAA-AGGGTGT
1 TATTTTGGTAATTATTGTTAAAACA--GTGA
* *
24289 TATTTTCGTAATTAATT-TTAAAACGGTGA
1 TATTTTGGTAATT-ATTGTTAAAACAGTGA
* * *
24318 TATTTTGGCAATTATTATTAAAACGGTGA
1 TATTTTGGTAATTATTGTTAAAACAGTGA
*
24347 TATTTTGGTAATTATTGTTAAAACAGTGT
1 TATTTTGGTAATTATTGTTAAAACAGTGA
* *
24376 TATTTTGGTAATTATTGTTAAAACAATGC
1 TATTTTGGTAATTATTGTTAAAACAGTGA
*
24405 TATTTTGGTAATTATTGTTAAAAC-GTTGC
1 TATTTTGGTAATTATTGTTAAAACAG-TGA
* *
24434 TATTTTGGTAATTATTGTTAAAGCGGTGA
1 TATTTTGGTAATTATTGTTAAAACAGTGA
24463 TATTTTGGTAATTATTGTTAAAAACAGTGA
1 TATTTTGGTAATTATTGTT-AAAACAGTGA
24493 TA-TTTGGTAATT
1 TATTTTGGTAATT
24505 GTTTAAAAAA
Statistics
Matches: 220, Mismatches: 18, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
28 3 0.01
29 181 0.82
30 33 0.15
31 3 0.01
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (29 bp):
TATTTTGGTAATTATTGTTAAAACAGTGA
Found at i:27546 original size:3 final size:3
Alignment explanation
Indices: 27538--27565 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
27528 TACCGACAGC
27538 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
27566 ACATTTAAGT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:31283 original size:21 final size:21
Alignment explanation
Indices: 31232--31284 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
31222 ATTATGACTA
*
31232 TCGCAATGCAATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
31253 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
31274 TCGCAATGCGA
1 TCGCAATGCGA
31285 ATTTGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:31301 original size:21 final size:21
Alignment explanation
Indices: 31277--31326 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
31267 TCCCAATTCG
31277 CAATGCGAATTTGGAAAATCA
1 CAATGCGAATTTGGAAAATCA
*
31298 CAATGCGAATTTGGAAAATCG
1 CAATGCGAATTTGGAAAATCA
*
31319 CAACGCGA
1 CAATGCGA
31327 TACTGACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (21 bp):
CAATGCGAATTTGGAAAATCA
Found at i:31340 original size:20 final size:20
Alignment explanation
Indices: 31315--31409 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
31305 AATTTGGAAA
31315 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
31335 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
31356 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
31376 TTCGCAACGCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
31396 TTCGCAACGAGATA
1 ATCGCAACGCGATA
31410 ATACATAATC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.70
21 15 0.23
22 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:31624 original size:22 final size:22
Alignment explanation
Indices: 31596--31639 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
31586 CACTCTCTCA
*
31596 CCCATCTCTGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
31618 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
31640 TATCTTCATC
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:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:33301 original size:18 final size:18
Alignment explanation
Indices: 33280--33327 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
33270 TCCACTTCGG
33280 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
33298 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
33316 GAGCCATCACCT
1 GAGCCATCACCT
33328 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:34099 original size:21 final size:21
Alignment explanation
Indices: 34073--34141 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
34063 CTGTCATCCC
34073 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCCAATCGT
* * **
34094 TCAAGAGGCCCCTATC-ATCCC
1 TCAAGAGTCCCCT-CCAATCGT
* *
34115 TCAAGAGTCCCCCCCACT-GT
1 TCAAGAGTCCCCTCCAATCGT
34135 TCAAGAG
1 TCAAGAG
34142 GCCACTGTCA
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
20 8 0.22
21 27 0.75
22 1 0.03
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCAATCGT
Found at i:34153 original size:41 final size:42
Alignment explanation
Indices: 34063--34153 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
34053 CCCGACTCAC
* *
34063 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCCCCAATCGTTCAAGAGGCCA
* *
34105 CTATCATCCCTCAAGAGTCCCCCCCACT-GTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCCCCAATCGTTCAAGAGGCCA
34146 CTGTCATC
1 CTGTCATC
34154 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 19 0.43
42 25 0.57
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCCCCAATCGTTCAAGAGGCCA
Found at i:35597 original size:14 final size:14
Alignment explanation
Indices: 35563--35601 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
35553 TTGATTATTT
35563 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
35577 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
35591 TGTTGATTTGT
1 AATTGATTTGT
35602 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:35762 original size:19 final size:17
Alignment explanation
Indices: 35737--35786 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 17
35727 TATCGTAACG
35737 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCG-A
35755 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
35770 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
35787 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:35774 original size:14 final size:14
Alignment explanation
Indices: 35728--35781 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
35718 GAAACTGACT
*
35728 ATCGTAACGAGAAA
1 ATCGCAACGAGAAA
35742 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
35761 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
35775 ATCGCAA
1 ATCGCAA
35782 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:36180 original size:20 final size:20
Alignment explanation
Indices: 36074--36179 Score: 151
Period size: 20 Copynumber: 5.3 Consensus size: 20
36064 TAGAATCTCA
* * *
36074 TTGCTAAAGTCAGAATCTCG
1 TTGCGAAAGTCAGTATCGCG
*
36094 TTGCGAAAGTCAGAATCGCG
1 TTGCGAAAGTCAGTATCGCG
36114 TTGCGAAAGTCAGTATCGCG
1 TTGCGAAAGTCAGTATCGCG
36134 TTGCGAAAGTCAGTATCGCG
1 TTGCGAAAGTCAGTATCGCG
*
36154 TTGCGATAA-TCAGTATCGCA
1 TTGCGA-AAGTCAGTATCGCG
36174 TTGCGA
1 TTGCGA
36180 TTTTCCAAAT
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 79 0.98
21 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (20 bp):
TTGCGAAAGTCAGTATCGCG
Found at i:36213 original size:20 final size:21
Alignment explanation
Indices: 36169--36220 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
36159 ATAATCAGTA
*
36169 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
36190 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
36210 TCGCATTGCGA
1 TCGCATTGCGA
36221 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:36436 original size:12 final size:12
Alignment explanation
Indices: 36417--36450 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
36407 CTCTTCGGCG
36417 ACATCCGTTCCT
1 ACATCCGTTCCT
*
36429 ATATCCGTTCCT
1 ACATCCGTTCCT
36441 ACATCC-TTCC
1 ACATCCGTTCC
36451 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:37251 original size:12 final size:12
Alignment explanation
Indices: 37234--37258 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37224 ATATAATTCT
37234 GAAGAAGAAAAA
1 GAAGAAGAAAAA
37246 GAAGAAGAAAAA
1 GAAGAAGAAAAA
37258 G
1 G
37259 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:39590 original size:19 final size:19
Alignment explanation
Indices: 39568--39659 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
39558 GGAAATTACT
39568 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
39587 ATCGCAAT--G--A-GATA
1 ATCGCAATGCGAAATGAAA
39601 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
39620 ATCACAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
39634 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
39653 ATCGCAA
1 ATCGCAA
39660 CGAGGGAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.35
15 2 0.04
16 3 0.05
17 3 0.05
18 2 0.04
19 27 0.47
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:39610 original size:33 final size:33
Alignment explanation
Indices: 39568--39694 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
39558 GGAAATTACT
* *
39568 ATCGCAATGCGAAATGAAAATCGCAATGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
39601 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
39634 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
39667 ATCGCAAAACGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
39695 CGAATTTAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:39698 original size:19 final size:18
Alignment explanation
Indices: 39568--39698 Score: 70
Period size: 19 Copynumber: 7.7 Consensus size: 18
39558 GGAAATTACT
39568 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
39587 ATCGCAA-TG--A-GATA
1 ATCGCAAGCGAAATGAAA
39601 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
39620 ATCACAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
39634 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
39653 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
*
39667 ATCGCAAAACGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
39686 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
39699 TTTAGTTTCG
Statistics
Matches: 83, Mismatches: 13, Indels: 32
0.65 0.10 0.25
Matches are distributed among these distances:
14 26 0.31
15 5 0.06
16 5 0.06
17 5 0.06
18 5 0.06
19 37 0.45
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:39729 original size:19 final size:19
Alignment explanation
Indices: 39694--39770 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
39684 AAATCGCAAC
*
39694 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
39713 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
39732 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
*
39746 GCGATTTTCA-TTTCGCATT
1 GCGATTTT-AGTTTCGCGTT
39765 GCGATT
1 GCGATT
39771 CTCTCGTTGC
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.24
16 1 0.02
17 1 0.02
18 1 0.02
19 35 0.70
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:39751 original size:33 final size:33
Alignment explanation
Indices: 39709--39835 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
39699 TTTAGTTTCG
* * *
39709 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTATCT
*
39742 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
39775 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
39808 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
39836 AGTAATTTTT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
33 88 0.99
34 1 0.01
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTATCT
Found at i:39801 original size:19 final size:18
Alignment explanation
Indices: 39704--39835 Score: 92
Period size: 19 Copynumber: 7.7 Consensus size: 18
39694 GCGAATTTAG
39704 TTTCGCGTTGCGATTTT-A
1 TTTCGC-TTGCGATTTTCA
39722 GTTTCGCGTTGCGA-TTT--
1 -TTTCGC-TTGCGATTTTCA
*
39739 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
39756 TTTCGCATTGCGA--TTC-
1 TTTCGC-TTGCGATTTTCA
*
39772 TCTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
39789 TTTCGCATTGCGA--TT-A
1 TTTCGC-TTGCGATTTTCA
*
39805 TCTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
39822 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
39836 AGTAATTTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 30
0.72 0.05 0.23
Matches are distributed among these distances:
14 18 0.20
15 3 0.03
16 18 0.20
17 18 0.20
18 3 0.03
19 32 0.35
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.46
Consensus pattern (18 bp):
TTTCGCTTGCGATTTTCA
Found at i:39961 original size:14 final size:14
Alignment explanation
Indices: 39942--39978 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
39932 CATCAATTAA
39942 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
39956 ACAAATAAACTTTT
1 ACAAATCAACTTTT
39970 ACAAATCAA
1 ACAAATCAA
39979 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:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:41413 original size:42 final size:42
Alignment explanation
Indices: 41328--41421 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
41318 GTGAATCGGG
* *
41328 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
* * *
41370 CTCTTGAACGGTGGGAGGAGA-CTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGG-GACCTCTTCAACG-ATGACAGGGGC
*
41412 CTCTTCAACG
1 CTCTTGAACG
41422 ATAGGAGTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
Found at i:41436 original size:42 final size:42
Alignment explanation
Indices: 41367--41446 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
41357 CGATGACAGT
* * *
41367 GGCCTCTTGAACGGTGGGAGGAGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGAGACTCTCGAGGAATGATAGG
* *
41409 GGCCTCTTCAACGATAGGAGTGA-ACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAG-GAGACTCTCGAGGAATGA
41447 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 30 0.94
43 2 0.06
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGAGACTCTCGAGGAATGATAGG
Found at i:41844 original size:91 final size:90
Alignment explanation
Indices: 41668--41852 Score: 293
Period size: 91 Copynumber: 2.0 Consensus size: 90
41658 ATTTCAAACT
*
41668 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
41733 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
41761 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
41825 -ATATTGGCAGCAACCGAATAAATTTAC
64 GA-ATTGGCAGCAACCGAATAAATTTAC
41852 T
1 T
41853 AAGCAATATA
Statistics
Matches: 88, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
90 1 0.01
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:43526 original size:20 final size:19
Alignment explanation
Indices: 43499--43653 Score: 88
Period size: 14 Copynumber: 8.8 Consensus size: 19
43489 TCTTTTGGTT
43499 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
43518 GATAATGAAAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
43539 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
43558 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
43572 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
43591 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
43605 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
43624 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
43638 GAAATGAAAATTGCAA
1 GAAATGAAAATCGCAA
43654 TGCGATTTTG
Statistics
Matches: 104, Mismatches: 15, Indels: 34
0.68 0.10 0.22
Matches are distributed among these distances:
14 30 0.29
16 6 0.06
17 6 0.06
19 30 0.29
20 30 0.29
21 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:43581 original size:33 final size:33
Alignment explanation
Indices: 43527--43644 Score: 227
Period size: 33 Copynumber: 3.5 Consensus size: 33
43517 AGATAATGAA
43527 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACGAGAG
43561 AATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
43594 AATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
43627 AATCGCAACGCGAAATGA
1 AATCGCAACGCGAAATGA
43645 AAATTGCAAT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
33 73 0.87
34 11 0.13
ACGTcount: A:0.40, C:0.24, G:0.25, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAG
Found at i:44279 original size:20 final size:20
Alignment explanation
Indices: 44238--44349 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
44228 GCTATGTAAA
* *
44238 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
44258 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * *
44278 TCGCATTGCAATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
44299 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
44319 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
44339 TCGCATTGCGA
1 TCGCATTGCGA
44350 ATTATGAAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 57 0.74
21 17 0.22
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:44305 original size:41 final size:40
Alignment explanation
Indices: 44256--44349 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
44246 CGATAGTAAG
* *
44256 ATTCGCATTGCGATTTACGTATTCGCATTGCAATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCAATTTACCT
* * * *
44296 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCAATTTACCT
44337 ATTCGCATTGCGA
1 ATTCGCATTGCGA
44350 ATTATGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCAATTTACCT
Found at i:44403 original size:21 final size:21
Alignment explanation
Indices: 44345--44411 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
44335 GTATTCGCAT
* *
44345 TGCGAATTATGAAAATCGCAA
1 TGCGAATTACGAAAATTGCAA
** *
44366 CACGAA-TACGTAAATTGCAA
1 TGCGAATTACGAAAATTGCAA
* *
44386 TGCGAATTAGGAAAATTGCAT
1 TGCGAATTACGAAAATTGCAA
44407 TGCGA
1 TGCGA
44412 TAGTCAGTAT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
20 15 0.43
21 20 0.57
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (21 bp):
TGCGAATTACGAAAATTGCAA
Found at i:44465 original size:20 final size:21
Alignment explanation
Indices: 44421--44472 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
44411 ATAGTCAGTA
*
44421 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
44442 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
44462 TCGCATTGCGA
1 TCGCATTGCGA
44473 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:44487 original size:41 final size:40
Alignment explanation
Indices: 44317--44487 Score: 112
Period size: 41 Copynumber: 4.2 Consensus size: 40
44307 CGATTTACTT
* * *
44317 AATCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGAA
1 AATCGCATTGCGA-TTACTTATTCGCATTGCGAATTAGGAA
*** * * *
44358 AATCGCAACACGAATACGTAAATT-GCAATGCGAATTAGGAA
1 AATCGCATTGCGATTAC-T-TATTCGCATTGCGAATTAGGAA
* * * * ***
44399 AATTGCATTGCGA-TAGTCAGTATCGCATTGCGATTTTCCAA
1 AATCGCATTGCGATTACTTA-T-TCGCATTGCGAATTAGGAA
* *
44440 ATTCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGAA
1 AATCGCATTGCGA-TTACTTATTCGCATTGCGAATTAGGAA
44481 AATCGCA
1 AATCGCA
44488 ACGCGAAATT
Statistics
Matches: 94, Mismatches: 29, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
38 1 0.01
39 2 0.02
40 6 0.06
41 77 0.82
42 4 0.04
43 4 0.04
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (40 bp):
AATCGCATTGCGATTACTTATTCGCATTGCGAATTAGGAA
Found at i:44514 original size:21 final size:22
Alignment explanation
Indices: 44462--44514 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
44452 ATTTACTTAT
44462 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
44483 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
44504 TCGCATTGCGA
1 TCGCATTGCGA
44515 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:44572 original size:20 final size:20
Alignment explanation
Indices: 44549--44594 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
44539 GGAAACTGAT
*
44549 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
44569 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
44588 TTGCGAT
1 TTGCGAT
44595 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:48505 original size:30 final size:30
Alignment explanation
Indices: 48438--48505 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 30
48428 ATTTAAGATG
48438 TATT-TTTAAGTTAATAAAAGAATAAAATA
1 TATTATTTAAGTTAATAAAAGAATAAAATA
*
48467 TA-TATTTAAGTTAATGAAAGAATAAAATA
1 TATTATTTAAGTTAATAAAAGAATAAAATA
48496 TATTATTTAA
1 TATTATTTAA
48506 TGAGTTGACA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 1 0.03
29 28 0.78
30 7 0.19
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (30 bp):
TATTATTTAAGTTAATAAAAGAATAAAATA
Found at i:51236 original size:15 final size:16
Alignment explanation
Indices: 51208--51237 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51198 TTTTATGTGG
51208 ATTTAAAAATAATATA
1 ATTTAAAAATAATATA
51224 ATTTAAAAA-AATAT
1 ATTTAAAAATAATAT
51238 TAACCAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTTAAAAATAATATA
Done.