Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006644.1 Hibiscus syriacus cultivar Beakdansim tig00016360_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: 51084
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Found at i:603 original size:45 final size:43
Alignment explanation
Indices: 551--655 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 43
541 GGCGTAGATT
551 TGTCCCGAAGGACCACGTAGATGTCCC-GGACCACATATAACACATA
1 TGTCCCGAAGGACCAC-T---TGTCCCAGGACCACATATAACACATA
597 -GTCCCGAAGGACCACTTGTCCCGAAGGACCACATATAACACATA
1 TGTCCCGAAGGACCACTTGTCCC--AGGACCACATATAACACATA
641 TGTCCCG-AGGACCAC
1 TGTCCCGAAGGACCAC
656 ATATAACACA
Statistics
Matches: 55, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
41 6 0.11
44 28 0.51
45 21 0.38
ACGTcount: A:0.31, C:0.32, G:0.20, T:0.16
Consensus pattern (43 bp):
TGTCCCGAAGGACCACTTGTCCCAGGACCACATATAACACATA
Found at i:655 original size:27 final size:28
Alignment explanation
Indices: 613--680 Score: 129
Period size: 27 Copynumber: 2.5 Consensus size: 28
603 AAGGACCACT
613 TGTCCCGAAGGACCACATATAACACATA
1 TGTCCCGAAGGACCACATATAACACATA
641 TGTCCCG-AGGACCACATATAACACATA
1 TGTCCCGAAGGACCACATATAACACATA
668 TGTCCCGAAGGAC
1 TGTCCCGAAGGAC
681 TACTATGTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 27 0.69
28 12 0.31
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.18
Consensus pattern (28 bp):
TGTCCCGAAGGACCACATATAACACATA
Found at i:1493 original size:24 final size:20
Alignment explanation
Indices: 1444--1501 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1434 TTTCTCTTGA
*
1444 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1464 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1487 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
1502 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1619 original size:62 final size:59
Alignment explanation
Indices: 1489--1626 Score: 145
Period size: 62 Copynumber: 2.2 Consensus size: 59
1479 TCTTTAACAG
* *
1489 GTGCATCGATGCACTACCATGCATCGATACACAATTTACATTCGATGTTTCCATTTTAAGG
1 GTGCATCGATGCACTACCATGCATCGATACACAATGTACA-TCGATGTTT-CATTTTAAGA
* * *
1550 GATGCATCGATGCACTCCTCATGCATCGATGCACCAACTGTAC-TCGATGTTT-ATTTATTGAGA
1 G-TGCATCGATGCACTAC-CATGCATCGATACA-CAA-TGTACATCGATGTTTCA-TT-TTAAGA
1613 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1627 ACAACCCAGA
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
61 2 0.03
62 30 0.45
63 27 0.41
64 3 0.05
65 4 0.06
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (59 bp):
GTGCATCGATGCACTACCATGCATCGATACACAATGTACATCGATGTTTCATTTTAAGA
Found at i:7047 original size:14 final size:16
Alignment explanation
Indices: 7012--7055 Score: 74
Period size: 14 Copynumber: 2.9 Consensus size: 16
7002 TCTAATACCA
7012 TGTAGAAAACAGACTG
1 TGTAGAAAACAGACTG
7028 TGTAGAAAACAGA-T-
1 TGTAGAAAACAGACTG
7042 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
7056 AAGTCTGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.48
15 1 0.04
16 13 0.48
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (16 bp):
TGTAGAAAACAGACTG
Found at i:18975 original size:28 final size:30
Alignment explanation
Indices: 18944--18999 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
18934 CAAAAATAAC
*
18944 ATACAGAAGA-AA-ACACACTCCTACAAAA
1 ATACAGAAGACAAGAAACACTCCTACAAAA
**
18972 ATACTTAAGACAAGAAACACTCCTACAA
1 ATACAGAAGACAAGAAACACTCCTACAA
19000 TACCTCACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 2 0.09
30 13 0.57
ACGTcount: A:0.54, C:0.25, G:0.07, T:0.14
Consensus pattern (30 bp):
ATACAGAAGACAAGAAACACTCCTACAAAA
Found at i:26535 original size:98 final size:98
Alignment explanation
Indices: 26366--26561 Score: 374
Period size: 98 Copynumber: 2.0 Consensus size: 98
26356 TTGTTTGTAC
26366 AATGCTTCCCTCCCACTTCCTACTGCCTGAATAATATCTACTGATGCAGTCCATGGTTTCATGTC
1 AATGCTTCCCTCCCACTTCCTACTGCCTGAATAATATCTACTGATGCAGTCCATGGTTTCATGTC
26431 AATGAAATATTATTCTCCTCTATCGTATGATCT
66 AATGAAATATTATTCTCCTCTATCGTATGATCT
*
26464 AATGCTTCCCTCCCACTTCCTACTGCCTGAATAATTTCTACTGATGCAGTCCATGGTTTCATGTC
1 AATGCTTCCCTCCCACTTCCTACTGCCTGAATAATATCTACTGATGCAGTCCATGGTTTCATGTC
*
26529 CATGAAATATTATTCTCCTCTATCGTATGATCT
66 AATGAAATATTATTCTCCTCTATCGTATGATCT
26562 CTGTAGATGT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.37
Consensus pattern (98 bp):
AATGCTTCCCTCCCACTTCCTACTGCCTGAATAATATCTACTGATGCAGTCCATGGTTTCATGTC
AATGAAATATTATTCTCCTCTATCGTATGATCT
Found at i:29804 original size:2 final size:2
Alignment explanation
Indices: 29799--29825 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29789 TGACAACAAC
29799 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 A
29826 ATAAGCGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31171 original size:16 final size:16
Alignment explanation
Indices: 31150--31183 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31140 TTATATAAAA
31150 ATATTTAAAAAAGAAT
1 ATATTTAAAAAAGAAT
**
31166 ATATTTTTAAAAGAAT
1 ATATTTAAAAAAGAAT
31182 AT
1 AT
31184 TGACACCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
ATATTTAAAAAAGAAT
Found at i:33436 original size:15 final size:15
Alignment explanation
Indices: 33416--33447 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
33406 AATAAAATTT
*
33416 ATTTTAAATTTAAAA
1 ATTTTAAATATAAAA
33431 ATTTTAAATATAAAA
1 ATTTTAAATATAAAA
33446 AT
1 AT
33448 AGTCAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTTAAATATAAAA
Found at i:33448 original size:8 final size:8
Alignment explanation
Indices: 33436--33554 Score: 52
Period size: 8 Copynumber: 14.8 Consensus size: 8
33426 TAAAAATTTT
33436 AAATATAA
1 AAATATAA
33444 AAATAGTCAA
1 AAATA-T-AA
* *
33454 ATATTTAA
1 AAATATAA
*
33462 AAAAATAA
1 AAATATAA
33470 AAA-A-AA
1 AAATATAA
*
33476 AACTA-AA
1 AAATATAA
33483 AATATTATTAA
1 AA-A-TA-TAA
*
33494 AAATAAAA
1 AAATATAA
* *
33502 AAAAATCAT
1 AAATAT-AA
33511 AAATAT-A
1 AAATATAA
33518 AAATGAT-A
1 AAAT-ATAA
33526 AAATAT-A
1 AAATATAA
*
33533 AAATATTA
1 AAATATAA
*
33541 AAACATAA
1 AAATATAA
33549 AAATAT
1 AAATAT
33555 TTTTTAAAAA
Statistics
Matches: 85, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
6 4 0.05
7 19 0.22
8 40 0.47
9 12 0.14
10 6 0.07
11 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (8 bp):
AAATATAA
Found at i:33526 original size:14 final size:15
Alignment explanation
Indices: 33503--33550 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
33493 AAAATAAAAA
33503 AAAATCAT-AAATAT
1 AAAATCATAAAATAT
*
33517 AAAATGATAAAATAT
1 AAAATCATAAAATAT
*
33532 AAAAT-ATTAAAACAT
1 AAAATCA-TAAAATAT
33547 AAAA
1 AAAA
33551 ATATTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (15 bp):
AAAATCATAAAATAT
Found at i:33529 original size:15 final size:15
Alignment explanation
Indices: 33511--33555 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
33501 AAAAAATCAT
33511 AAATATAAAATGA-TA
1 AAATATAAAAT-ATTA
33526 AAATATAAAATATTA
1 AAATATAAAATATTA
*
33541 AAACATAAAAATATT
1 AAATAT-AAAATATT
33556 TTTTAAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.67
16 8 0.30
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
AAATATAAAATATTA
Found at i:33571 original size:2 final size:2
Alignment explanation
Indices: 33566--33608 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
33556 TTTTAAAAAC
*
33566 AT AT AT -T AT AC AT A- 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
33606 AT A
1 AT A
33609 ATTTATAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39097 original size:15 final size:17
Alignment explanation
Indices: 39066--39097 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
39056 GTCTTTTTAA
39066 TAATATATTTATTTTTT
1 TAATATATTTATTTTTT
39083 TAATA-ATTT-TTTTTT
1 TAATATATTTATTTTTT
39098 ATTTTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TAATATATTTATTTTTT
Found at i:39101 original size:22 final size:23
Alignment explanation
Indices: 39073--39116 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
39063 TAATAATATA
39073 TTTATTTTTT-TAATAATTTTTT
1 TTTATTTTTTATAATAATTTTTT
*
39095 TTTATTTTTTATATTAATTTTT
1 TTTATTTTTTATAATAATTTTT
39117 ATGAATATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTATTTTTTATAATAATTTTTT
Found at i:39103 original size:23 final size:22
Alignment explanation
Indices: 39073--39116 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
39063 TAATAATATA
*
39073 TTTATTTTTTTAATAATTTTTT
1 TTTATTTTTATAATAATTTTTT
*
39095 TTTATTTTTTATATTAATTTTT
1 TTTA-TTTTTATAATAATTTTT
39117 ATGAATATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTATTTTTATAATAATTTTTT
Found at i:40080 original size:2 final size:2
Alignment explanation
Indices: 40073--40127 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
40063 CTTATTGAGC
40073 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
40115 AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT
40128 TAGGTCATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41285 original size:20 final size:20
Alignment explanation
Indices: 41262--41313 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
41252 AACGCGATCC
41262 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
41282 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
41302 CCAAAATCGCAA
1 CCAGAATCGCAA
41314 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:41394 original size:20 final size:20
Alignment explanation
Indices: 41369--41562 Score: 138
Period size: 20 Copynumber: 9.7 Consensus size: 20
41359 GATTTTCCAT
*
41369 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAATA-CATA
41389 AATCGCAACGCGAATACATA
1 AATCGCAACGCGAATACATA
* * *
41409 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACATA
* * * *
41429 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACATA
* ***
41449 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAATACATA
* * * *
41469 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACATA
* * * *
41489 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACATA
**
41509 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAATACAT-A
* * *
41530 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACATA
41550 AATCGCAACGCGA
1 AATCGCAACGCGA
41563 TATTTAAAGC
Statistics
Matches: 147, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
19 1 0.01
20 131 0.89
21 15 0.10
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACATA
Found at i:41414 original size:40 final size:40
Alignment explanation
Indices: 41369--41562 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
41359 GATTTTCCAT
* ** *
41369 AATCGCAACGCGAATATGAAAATCGCAACGCGAATACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATA
* * * *
41409 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATA
** * * * *
41449 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATA
* **
41489 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-A
41530 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
41563 TATTTAAAGC
Statistics
Matches: 129, Mismatches: 24, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
40 98 0.76
41 31 0.24
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATA
Found at i:41452 original size:60 final size:60
Alignment explanation
Indices: 41369--41561 Score: 260
Period size: 60 Copynumber: 3.2 Consensus size: 60
41359 GATTTTCCAT
* ** *
41369 AATCGCAACGCGAATATGAAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
41429 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
41489 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
41550 AATCGCAACGCG
1 AATCGCAACGCG
41562 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:41976 original size:33 final size:33
Alignment explanation
Indices: 41937--42006 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
41927 TTCACTTAGA
*
41937 TTCATTTCGCGTTACGATTCTGTCGTTGCGATT
1 TTCATTTCGCGTTACGATTCTCTCGTTGCGATT
* *
41970 TTCATTTCGCGTTGCTATTCTCTCGTTGCGATT
1 TTCATTTCGCGTTACGATTCTCTCGTTGCGATT
42003 TTCA
1 TTCA
42007 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (33 bp):
TTCATTTCGCGTTACGATTCTCTCGTTGCGATT
Found at i:42146 original size:14 final size:14
Alignment explanation
Indices: 42127--42181 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
42117 AGAATGACTG
42127 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
42141 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
42160 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
42174 TCGCAACG
1 TCGCAACG
42182 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:42164 original size:33 final size:33
Alignment explanation
Indices: 42127--42197 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
42117 AGAATGACTG
**
42127 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
42160 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
42193 TCGCA
1 TCGCA
42198 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:42215 original size:19 final size:19
Alignment explanation
Indices: 42193--42289 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
42183 GAAACCAAAA
*
42193 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42212 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
42226 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42245 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
42259 TCTCGTTGCGA-TTTCATC
1 TCGCGTTGCGATTTTCATT
42277 TCGCGTTGCGATT
1 TCGCGTTGCGATT
42290 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 3 0.05
16 3 0.05
17 6 0.10
18 10 0.16
19 21 0.33
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:42234 original size:14 final size:14
Alignment explanation
Indices: 42215--42303 Score: 88
Period size: 14 Copynumber: 5.7 Consensus size: 14
42205 TTTCATTTCG
42215 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
42229 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
42248 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
42262 CGTTGCGATTTCATCT
1 CGTTGCGA-TTC-TCT
42278 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
42294 CGTTGCGATT
1 CGTTGCGATT
42304 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
14 28 0.44
15 3 0.05
16 9 0.14
17 6 0.09
18 8 0.12
19 10 0.16
ACGTcount: A:0.09, C:0.26, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:42240 original size:33 final size:33
Alignment explanation
Indices: 42198--42311 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
42188 CAAAATCGCA
42198 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
42231 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
42264 TTGCGA-TTTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
42296 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
42312 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
32 31 0.40
33 47 0.60
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:42432 original size:25 final size:26
Alignment explanation
Indices: 42378--42432 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
42368 TTATGTTTAT
*
42378 TGTTTTTGGTATATCTTCACATTGTA
1 TGTTTTTGGTATATCTTAACATTGTA
42404 -GTTTTTGGTATATC-TAAC-TTGGTA
1 TGTTTTTGGTATATCTTAACATT-GTA
42428 TGTTT
1 TGTTT
42433 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 2 0.08
24 6 0.23
25 18 0.69
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (26 bp):
TGTTTTTGGTATATCTTAACATTGTA
Found at i:44237 original size:91 final size:92
Alignment explanation
Indices: 44000--44462 Score: 816
Period size: 91 Copynumber: 5.1 Consensus size: 92
43990 TTAGATGCTT
*
44000 AGTAAATTTATTCGGTTGCTGCCAA-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
44064 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
44092 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTATATTCTTTACACTGTGAAATA-TAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
44155 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
44182 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
44247 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
44274 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
44335 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
44363 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATT-TTAACACTGTGAAATAGTAG
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
44427 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
44454 AGTAAATTT
1 AGTAAATTT
44463 ATCCATTCAA
Statistics
Matches: 357, Mismatches: 6, Indels: 17
0.94 0.02 0.04
Matches are distributed among these distances:
88 11 0.03
89 35 0.10
90 104 0.29
91 122 0.34
92 79 0.22
93 6 0.02
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:44378 original size:181 final size:181
Alignment explanation
Indices: 44000--44458 Score: 827
Period size: 181 Copynumber: 2.5 Consensus size: 181
43990 TTAGATGCTT
*
44000 AGTAAATTTATTCGGTTGCTGCCAA-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
44064 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAACTG
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAACTG
44129 TATATTCTTTACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
129 TATATTCTTTACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
44182 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
44247 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGT
*
44312 GTATTCTTTAACACTGTG-AA-ATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 ATATTCTTT-ACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
44363 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATT-TTAACACTGTGAAATAGTAG
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
44427 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
44459 ATTTATCCAT
Statistics
Matches: 271, Mismatches: 3, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
180 51 0.19
181 103 0.38
182 90 0.33
183 27 0.10
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (181 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAACTGTA
TATTCTTTACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:44546 original size:19 final size:19
Alignment explanation
Indices: 44506--44634 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
44496 TAGTTTACTT
* *
44506 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
44526 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
44545 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
44564 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
44578 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
44597 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
44611 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
44630 TCGCA
1 TCGCA
44635 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:44585 original size:33 final size:32
Alignment explanation
Indices: 44542--44634 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
44532 CGCGAAACCA
**
44542 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
44574 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
44607 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
44635 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:44632 original size:52 final size:52
Alignment explanation
Indices: 44506--44634 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
44496 TAGTTTACTT
**
44506 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
44558 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
44611 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
44635 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:44652 original size:19 final size:19
Alignment explanation
Indices: 44630--44762 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
44620 GAAACCAAAA
*
44630 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
44649 TCGCGTTGCGA---TC-TT
1 TCGCGTTGCGATTTTCATT
44664 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
* *
44680 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
44696 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
44713 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
44732 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
44752 TCGTGTTGCGA
1 TCGCGTTGCGA
44763 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
13 8 0.09
14 7 0.08
15 5 0.05
16 10 0.11
17 5 0.05
18 7 0.08
19 39 0.42
20 12 0.13
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:44670 original size:13 final size:14
Alignment explanation
Indices: 44652--44706 Score: 58
Period size: 16 Copynumber: 3.7 Consensus size: 14
44642 TTTCATTTCG
44652 CGTTGCGA-TCTTT
1 CGTTGCGATTCTTT
44665 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TTT
*
44681 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
44697 CGTTGCGATT
1 CGTTGCGATT
44707 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.22
14 8 0.22
15 2 0.06
16 9 0.25
17 3 0.08
18 6 0.17
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:44715 original size:33 final size:33
Alignment explanation
Indices: 44635--44725 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
44625 CAAAATCGCA
*
44635 TTGCGATTTTCATTTCGCGTTGCGA-TCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
44667 TTGCGA-TTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
44699 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
44726 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
31 17 0.31
32 18 0.33
33 19 0.35
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:46669 original size:14 final size:14
Alignment explanation
Indices: 46650--46685 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
46640 GATTGTTAAT
46650 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
46664 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
46678 TGATTTGT
1 TGATTTGT
46686 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:46806 original size:19 final size:19
Alignment explanation
Indices: 46790--46891 Score: 160
Period size: 19 Copynumber: 5.6 Consensus size: 19
46780 AAAAATGACT
46790 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
46809 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
46828 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
46842 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
46861 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
46881 ATCGCAATGCG
1 ATCGCAATGCG
46892 TTTATAATTT
Statistics
Matches: 77, Mismatches: 0, Indels: 12
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 41 0.53
20 19 0.25
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:46847 original size:33 final size:33
Alignment explanation
Indices: 46805--46867 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
46795 AATGCGAAAT
46805 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
46838 GAAAATCGCAATGCGAAATGAAAATCGCAA
1 GAAAATCGCAATGCGAAATGAAAATCGCAA
46868 TGCGGAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.13
Consensus pattern (33 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAACGA
Found at i:46950 original size:19 final size:19
Alignment explanation
Indices: 46920--47202 Score: 409
Period size: 19 Copynumber: 15.7 Consensus size: 19
46910 GATTATCTCG
46920 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
46938 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
46957 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
46976 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
46990 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
47009 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
47028 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
47047 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
47066 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
47085 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
47104 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
*
47118 TTGCGATTTTCATTTCGCT
1 TTGCGATTTTCATTTCGCA
47137 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
47156 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
47170 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
47190 TTGCGATTTTCAT
1 TTGCGATTTTCAT
47203 GTTGGGATTT
Statistics
Matches: 241, Mismatches: 7, Indels: 32
0.86 0.03 0.11
Matches are distributed among these distances:
14 18 0.07
16 22 0.09
17 19 0.08
18 8 0.03
19 161 0.67
20 13 0.05
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:47005 original size:52 final size:55
Alignment explanation
Indices: 46898--47229 Score: 359
Period size: 52 Copynumber: 6.3 Consensus size: 55
46888 TGCGTTTATA
*
46898 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCG-ATTGCGATTTTC
46949 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
47001 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
47058 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
* *
47113 -TGTCG--TTGCGATTTTCATTTCGCTTTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
* *
47165 -TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCA--T-G-TTGGGATTTTC
1 ATTTCGCATTGCGATTTTCATTT-CGCATTGCGA-TTTCATTTCGATTGCGATTTTC
*
47215 ATTT-GCGTTGCGATT
1 ATTTCGCATTGCGATT
47230 GTATTTTCCG
Statistics
Matches: 256, Mismatches: 9, Indels: 31
0.86 0.03 0.10
Matches are distributed among these distances:
48 5 0.02
50 5 0.02
51 17 0.07
52 116 0.45
53 17 0.07
54 17 0.07
55 11 0.04
56 6 0.02
57 62 0.24
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (55 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
Found at i:50414 original size:20 final size:20
Alignment explanation
Indices: 50397--50722 Score: 402
Period size: 20 Copynumber: 16.6 Consensus size: 20
50387 TACAGATTCT
*
50397 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
* *
50417 CGTTGCGATTTACAGAT-CT
1 CGTTGCGATTTACGGATACG
*
50436 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
50456 CGTTGCGATTT-CGGATACG
1 CGTTGCGATTTACGGATACG
*
50475 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
50495 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
50515 CGTT--GATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
50533 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
50553 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
*
50573 CGTTGC-AGTTACGGATACG
1 CGTTGCGATTTACGGATACG
50592 CGTTGCGA-TTACGGATACG
1 CGTTGCGATTTACGGATACG
*
50611 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
* **
50631 CATTGCGATTTTACCCATACG
1 CGTTGCGA-TTTACGGATACG
*
50652 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
50672 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
50692 CGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
50712 CGTTGCGATTT
1 CGTTGCGATTT
50723 TTCATATTCG
Statistics
Matches: 271, Mismatches: 22, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
18 19 0.07
19 70 0.26
20 163 0.60
21 19 0.07
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:50441 original size:39 final size:40
Alignment explanation
Indices: 50397--50722 Score: 402
Period size: 39 Copynumber: 8.3 Consensus size: 40
50387 TACAGATTCT
* * *
50397 CGTTGCGATTTACGGATTA-TCGTTGCGATTTACAGAT-CT
1 CGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACG
*
50436 CGTTGCGATTTACGGATTA-TCGTTGCGATTT-CGGATACG
1 CGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACG
*
50475 CGTTGCGATTTACGGATTA-TCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACG
*
50515 CGTT--GATTTACGGATACGCATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACG
* *
50553 CGTTGCGATTTACGGATACACGTTGC-AGTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACG
*
50592 CGTTGCGA-TTACGGATACGCGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACG
* ** *
50631 CATTGCGATTTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGA-TTTACGGATACGCGTTGCGATTTACGGATACG
* *
50672 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACG-GATACG
50712 CGTTGCGATTT
1 CGTTGCGATTT
50723 TTCATATTCG
Statistics
Matches: 257, Mismatches: 21, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
37 2 0.01
38 53 0.21
39 101 0.39
40 66 0.26
41 35 0.14
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACG
Found at i:50734 original size:21 final size:20
Alignment explanation
Indices: 50690--50742 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
50680 TTTACGGATA
* *
50690 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTTATATATT
*
50710 CGCGTTGCGATTTTTCATATT
1 CGCGTTGCGATTTAT-ATATT
50731 CGCGTTGCGATT
1 CGCGTTGCGATT
50743 ATGGAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.43
Consensus pattern (20 bp):
CGCGTTGCGATTTATATATT
Done.