Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 26
Found at i:3597911 original size:35 final size:36
Alignment explanation
Indices: 3597840--3597914 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
3597830 TGTTTCTTTG
* * *
3597840 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCTGTTTACCTT
3597876 GAAACAAAA-TAAACATCTTTGAGATC-GTTTACCTT
1 GAAACAAAATTAAACATCTTTGA-ATCTGTTTACCTT
3597911 GAAA
1 GAAA
3597915 TGAATTTCGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCTGTTTACCTT
Found at i:3598358 original size:43 final size:44
Alignment explanation
Indices: 3598265--3598499 Score: 170
Period size: 40 Copynumber: 5.5 Consensus size: 44
3598255 TGGCCAACCG
* * ** *
3598265 TCCTCATCATGTAGGAACCGTGTCAT-CCCCAG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
*
3598305 TCCTTATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
* * * ** *
3598347 GTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT-ACCAT-AGATAACCAGACC
* * * * * *
3598394 TCTTCATCACGTATGAGCCGTGTCATTCC-CAG---GCCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
*
3598434 TCCTTATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
*
3598476 GTCCTCATCACGTAGGAACCGTGT
1 -TCCTCATCACGTAGGAGCCGTGT
3598500 TATCACCTTT
Statistics
Matches: 152, Mismatches: 29, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
39 2 0.01
40 57 0.38
42 2 0.01
43 54 0.36
45 6 0.04
46 30 0.20
47 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (44 bp):
TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
Found at i:3598406 original size:46 final size:45
Alignment explanation
Indices: 3598268--3598531 Score: 152
Period size: 43 Copynumber: 6.1 Consensus size: 45
3598258 CCAACCGTCC
* * *
3598268 TCATCATGTAGGAACCGTGTCATC-CC---CA-GACCAGATCTCCT
1 TCATCACGTAGGAACCGTGTCATCACCTTAGATGACCAGAACT-CT
* * * * *
3598309 T-ATCACGTAGGAGCCGTGTCA--ACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTCATCACCTTAGATGACCAGAAC-TCT
* *
3598351 TCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTCATCACCTT-AGATGACCAGAACTCT
* * *
3598397 TCATCACGTATGAGCCGTGTCATTC-CC--AG--G-CCAGATCTCCT
1 TCATCACGTAGGAACCGTGTCA-TCACCTTAGATGACCAGAACT-CT
* * * * *
3598438 T-ATCACGTAGGAGCCGTGTCA--ACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTCATCACCTTAGATGACCAGAAC-TCT
* *
3598480 TCATCACGTAGGAACCGTGTTATCACCTTTAGACGACCAGAACTCT
1 TCATCACGTAGGAACCGTGTCATCACC-TTAGATGACCAGAACTCT
3598526 TCATCA
1 TCATCA
3598532 TGTATGAGCA
Statistics
Matches: 170, Mismatches: 28, Indels: 45
0.70 0.12 0.19
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 46 0.27
41 5 0.03
42 7 0.04
43 49 0.29
45 7 0.04
46 48 0.28
47 4 0.02
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (45 bp):
TCATCACGTAGGAACCGTGTCATCACCTTAGATGACCAGAACTCT
Found at i:3598481 original size:129 final size:129
Alignment explanation
Indices: 3598251--3598553 Score: 482
Period size: 129 Copynumber: 2.3 Consensus size: 129
3598241 ATAGCTTCTA
* * * *
3598251 AAGATGGCCA-ACCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTTATCAC
1 AAGATGGCCAGAAC-TCTTCATCATGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTTATCAC
3598315 GTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
65 GTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
* * *
3598380 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGGCCAGATCTCCTTATCACG
1 AAGATGGCCAGAACTCTTCATCATGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTTATCACG
3598445 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
66 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
* * * * *
3598509 TAGACGACCAGAACTCTTCATCATGTATGAGCAGTGTCGTCCCCA
1 AAGATGGCCAGAACTCTTCATCATGTATGAGCCGTGTCATCCCCA
3598554 ACAACCAACA
Statistics
Matches: 159, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
129 157 0.99
130 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (129 bp):
AAGATGGCCAGAACTCTTCATCATGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTTATCACG
TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
Found at i:3598728 original size:3 final size:3
Alignment explanation
Indices: 3598720--3598761 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
3598710 AATTTTAATT
3598720 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
3598762 ATTACATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3598746 original size:22 final size:21
Alignment explanation
Indices: 3598719--3598761 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
3598709 TAATTTTAAT
3598719 TTTATTATTATTATTATTATTA
1 TTTATTATTATTATTA-TATTA
3598741 TTTATTATTATTATTATATTA
1 TTTATTATTATTATTATATTA
3598762 ATTACATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATTATTATTATTATATTA
Found at i:3603066 original size:18 final size:18
Alignment explanation
Indices: 3603024--3603073 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
3603014 ACTATTTTCC
3603024 GAATATGTTTT-TA-A-T
1 GAATATGTTTTATATATT
* *
3603039 GAAGAAGTTTTATATATT
1 GAATATGTTTTATATATT
3603057 GAATATGTTTTAT-TATT
1 GAATATGTTTTATATATT
3603074 TATTATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.32
16 2 0.07
17 5 0.18
18 12 0.43
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (18 bp):
GAATATGTTTTATATATT
Found at i:3606199 original size:18 final size:18
Alignment explanation
Indices: 3606176--3606212 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3606166 TAAGTTATTG
3606176 GCATTTGATATTATTAAT
1 GCATTTGATATTATTAAT
3606194 GCATTTGATATTATTAAT
1 GCATTTGATATTATTAAT
3606212 G
1 G
3606213 TAACACCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (18 bp):
GCATTTGATATTATTAAT
Found at i:3607285 original size:21 final size:19
Alignment explanation
Indices: 3607227--3607285 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 19
3607217 CAAAACAACG
*
3607227 AAGGGATCGATCCTTTATCT
1 AAGGGATTGATCCTTT-TCT
**
3607247 AGAGGGATTGATTATTTTCCCT
1 A-AGGGATTGATCCTTTT--CT
3607269 AAGGGATTGATCCTTTT
1 AAGGGATTGATCCTTTT
3607286 GAAAAAGAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.06
21 26 0.84
22 3 0.10
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (19 bp):
AAGGGATTGATCCTTTTCT
Found at i:3615784 original size:17 final size:17
Alignment explanation
Indices: 3615752--3615783 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3615742 TAAAATATTT
3615752 TCTCTTTTTAATAAAAC
1 TCTCTTTTTAATAAAAC
3615769 TCTCTTTTT-ATAAAA
1 TCTCTTTTTAATAAAA
3615784 AAAAGTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (17 bp):
TCTCTTTTTAATAAAAC
Found at i:3616051 original size:28 final size:28
Alignment explanation
Indices: 3616020--3616073 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3616010 CAAACGTTTA
* *
3616020 GGTTTATGGTTTA-TGATATGGGGTTTGT
1 GGTTTAGGGTTTAGTGAT-TGGAGTTTGT
3616048 GGTTTAGGGTTTAGTGATTGGAGTTT
1 GGTTTAGGGTTTAGTGATTGGAGTTT
3616074 AAGATTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (28 bp):
GGTTTAGGGTTTAGTGATTGGAGTTTGT
Found at i:3617319 original size:60 final size:59
Alignment explanation
Indices: 3617229--3617399 Score: 173
Period size: 60 Copynumber: 2.9 Consensus size: 59
3617219 GGGAGGGTTA
* ** ** * * *
3617229 TTAGAATGTTCAAAATTTTGGGGATTAATTTGGGATGAGGGTCATAGTTTGGGGATGATT
1 TTAGAATGTTCAAAAGTTTAAGGACCAATTTGGAATGAGGATCATAGTTTGGGG-TGAAT
* * * *
3617289 TTGGAATGTTCAAAAGTTTAAGGACCAATTTAGAATGATGATCATAGTTTAAGGGTGAAT
1 TTAGAATGTTCAAAAGTTTAAGGACCAATTTGGAATGAGGATCATAGTTT-GGGGTGAAT
* * *
3617349 TTAAAACT-TTTAAAAGTTTAAGGACCAATTTGGAAGGAGGATCATAGTTTG
1 TTAGAA-TGTTCAAAAGTTTAAGGACCAATTTGGAATGAGGATCATAGTTTG
3617400 AGGACGTACA
Statistics
Matches: 90, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
60 86 0.96
61 4 0.04
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.35
Consensus pattern (59 bp):
TTAGAATGTTCAAAAGTTTAAGGACCAATTTGGAATGAGGATCATAGTTTGGGGTGAAT
Found at i:3617324 original size:29 final size:29
Alignment explanation
Indices: 3617292--3617379 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 29
3617282 GATGATTTTG
3617292 GAATGTTCAAAAGTTTAAGGACCAATTTA
1 GAATGTTCAAAAGTTTAAGGACCAATTTA
* ***
3617321 GAATGATGATC-ATAGTTTAAGGGTGAATTTA
1 GAATG-T--TCAAAAGTTTAAGGACCAATTTA
* *
3617352 AAACT-TTTAAAAGTTTAAGGACCAATTT
1 GAA-TGTTCAAAAGTTTAAGGACCAATTT
3617380 GGAAGGAGGA
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
28 1 0.02
29 20 0.45
30 2 0.05
31 18 0.41
32 3 0.07
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (29 bp):
GAATGTTCAAAAGTTTAAGGACCAATTTA
Found at i:3638505 original size:21 final size:21
Alignment explanation
Indices: 3638481--3638541 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3638471 TTCAAAGAAA
3638481 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
* *
3638502 CATTT-TC-AA----GGAAA-
1 CATTTACCAAACTTTGAAAAC
3638516 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
3638537 CATTT
1 CATTT
3638542 TTTCAAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 5 0.17
15 5 0.17
16 2 0.07
19 2 0.07
20 5 0.17
21 10 0.34
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:3638516 original size:35 final size:34
Alignment explanation
Indices: 3638433--3638542 Score: 157
Period size: 35 Copynumber: 3.1 Consensus size: 34
3638423 CCATTATCAT
* * *
3638433 TTTTCAACAAACATCTACCAAACTTTGAAAAACTAA
1 TTTTCAAGAAACATTTACCAAACTTTG-AAAAC-CA
3638469 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTC-AAGAAACATTTACCAAACTTTGAAAACCA
3638504 TTTTCAAGGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAA-GAAACATTTACCAAACTTTGAAAACCA
3638539 TTTT
1 TTTT
3638543 TTCAAAGTTG
Statistics
Matches: 69, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
34 2 0.03
35 37 0.54
36 10 0.14
37 20 0.29
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (34 bp):
TTTTCAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:3643076 original size:34 final size:34
Alignment explanation
Indices: 3642992--3643099 Score: 162
Period size: 34 Copynumber: 3.1 Consensus size: 34
3642982 CCATTATCAT
* * *
3642992 TTTTCAACAAACATCTACCAAACTTTGAAAAACTA
1 TTTTCAAGAAACATTTACCAAACTTTG-AAAACAA
*
3643027 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTC-AAGAAACATTTACCAAACTTTGAAAACAA
3643062 TTTTCAAGAAACATTTACCAAACTTTGAAAACAA
1 TTTTCAAGAAACATTTACCAAACTTTGAAAACAA
3643096 TTTT
1 TTTT
3643100 TTCAAAGTTG
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
34 32 0.47
35 16 0.24
36 20 0.29
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.31
Consensus pattern (34 bp):
TTTTCAAGAAACATTTACCAAACTTTGAAAACAA
Found at i:3650985 original size:18 final size:18
Alignment explanation
Indices: 3650962--3651057 Score: 85
Period size: 18 Copynumber: 5.4 Consensus size: 18
3650952 AAGTTTACAA
*
3650962 TTATCAAATGATTTTCAG
1 TTATCAGATGATTTTCAG
3650980 TTATCAGAT-ATTTAT-AG
1 TTATCAGATGATTT-TCAG
*
3650997 TTATCAGATGATTTTCAA
1 TTATCAGATGATTTTCAG
* *
3651015 CTATTAGATG-TTTAT-AG
1 TTATCAGATGATTT-TCAG
*
3651032 TTATAAGATG-TTTTACAG
1 TTATCAGATGATTTT-CAG
3651050 TTATCAGA
1 TTATCAGA
3651058 CGTAGCTTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
16 1 0.02
17 31 0.48
18 32 0.50
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (18 bp):
TTATCAGATGATTTTCAG
Found at i:3651001 original size:35 final size:35
Alignment explanation
Indices: 3650962--3651057 Score: 115
Period size: 35 Copynumber: 2.7 Consensus size: 35
3650952 AAGTTTACAA
3650962 TTATCAAATGATTTTCAGTTATCAGATATTTATAG
1 TTATCAAATGATTTTCAGTTATCAGATATTTATAG
* ** * *
3650997 TTATCAGATGATTTTCAACTATTAGATGTTTATAG
1 TTATCAAATGATTTTCAGTTATCAGATATTTATAG
3651032 TTAT-AAGATG-TTTTACAGTTATCAGA
1 TTATCAA-ATGATTTT-CAGTTATCAGA
3651058 CGTAGCTTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
34 5 0.10
35 45 0.90
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (35 bp):
TTATCAAATGATTTTCAGTTATCAGATATTTATAG
Found at i:3654503 original size:10 final size:11
Alignment explanation
Indices: 3654475--3654515 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
3654465 ATTTACTTTA
3654475 TATAAATTCTTT
1 TATAAATT-TTT
3654487 TATAAATTTTT
1 TATAAATTTTT
*
3654498 TA-AAATTTGT
1 TATAAATTTTT
3654508 TATAAATT
1 TATAAATT
3654516 AGAGAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.33
11 10 0.37
12 8 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TATAAATTTTT
Found at i:3661110 original size:2 final size:2
Alignment explanation
Indices: 3661098--3661133 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
3661088 TTCACACCCT
*
3661098 AG AG AG TAG AG AG AG AG AG AG AA AG AG AG AG AG AG A
1 AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3661134 TGGAAAGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (2 bp):
AG
Found at i:3669627 original size:9 final size:9
Alignment explanation
Indices: 3669605--3669647 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
3669595 CTTGAATTTA
*
3669605 AAAAAATCAG
1 AAAAAAT-AC
3669615 AAAAAATAC
1 AAAAAATAC
3669624 AAAAAATTAC
1 AAAAAA-TAC
*
3669634 AAAAATTAC
1 AAAAAATAC
3669643 AAAAA
1 AAAAA
3669648 TTATATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 15 0.50
10 15 0.50
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.14
Consensus pattern (9 bp):
AAAAAATAC
Found at i:3669648 original size:9 final size:9
Alignment explanation
Indices: 3669615--3669650 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
3669605 AAAAAATCAG
*
3669615 AAAAAATAC
1 AAAAATTAC
3669624 AAAAAATTAC
1 -AAAAATTAC
3669634 AAAAATTAC
1 AAAAATTAC
3669643 AAAAATTA
1 AAAAATTA
3669651 TATATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAATTAC
Found at i:3669650 original size:18 final size:19
Alignment explanation
Indices: 3669605--3669647 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3669595 CTTGAATTTA
* *
3669605 AAAAAATCAGAAAAAATAC
1 AAAAAATTACAAAAAATAC
*
3669624 AAAAAATTACAAAAATTAC
1 AAAAAATTACAAAAAATAC
3669643 AAAAA
1 AAAAA
3669648 TTATATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAAAATTACAAAAAATAC
Found at i:3676354 original size:22 final size:22
Alignment explanation
Indices: 3676326--3676368 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3676316 GTATCAGTAA
*
3676326 TAAAA-TTTAAATAACAATTAAC
1 TAAAATTTTAAA-AAAAATTAAC
3676348 TAAAATTTTAAAAAAAATTAA
1 TAAAATTTTAAAAAAAATTAA
3676369 TAGTTGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATTTTAAAAAAAATTAAC
Found at i:3678556 original size:51 final size:53
Alignment explanation
Indices: 3678490--3678617 Score: 197
Period size: 54 Copynumber: 2.4 Consensus size: 53
3678480 ATCGAATAAT
*
3678490 AAAAGCAGCAACGTTTAGCAAAATTT-AAG-AAAAACTAACAATTATTTTGTA
1 AAAAGCAGCAGCGTTTAGCAAAATTTAAAGAAAAAACTAACAATTATTTTGTA
3678541 AAAAGCAGCAGCGTTTAGCAAAATTTAAAAGAAAAAACTAACAATTATTTTGTA
1 AAAAGCAGCAGCGTTTAGCAAAATTT-AAAGAAAAAACTAACAATTATTTTGTA
* * *
3678595 AAAAACATCAGCGTTTAACAAAA
1 AAAAGCAGCAGCGTTTAGCAAAA
3678618 AATCAGAAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 25 0.36
53 3 0.04
54 42 0.60
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (53 bp):
AAAAGCAGCAGCGTTTAGCAAAATTTAAAGAAAAAACTAACAATTATTTTGTA
Found at i:3678882 original size:15 final size:14
Alignment explanation
Indices: 3678862--3678891 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3678852 TTTGTCCGGG
3678862 ATTTTTATTGTTATT
1 ATTTTTATT-TTATT
3678877 ATTTTTATTTTATT
1 ATTTTTATTTTATT
3678891 A
1 A
3678892 ATTATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
ATTTTTATTTTATT
Found at i:3681231 original size:10 final size:11
Alignment explanation
Indices: 3681203--3681243 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
3681193 ATTTACTTTA
3681203 TATAAATTCTTT
1 TATAAATT-TTT
3681215 TATAAATTTTT
1 TATAAATTTTT
*
3681226 TA-AAATTTGT
1 TATAAATTTTT
3681236 TATAAATT
1 TATAAATT
3681244 AGAGAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.33
11 10 0.37
12 8 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TATAAATTTTT
Found at i:3683375 original size:41 final size:42
Alignment explanation
Indices: 3683322--3683400 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
3683312 CACTACCTTG
*
3683322 CGTACTTCAGTGGCCTTT-TATAGAAAACACCGCAATTTCAT
1 CGTACTTCAGTGGCCTTTGTATAAAAAACACCGCAATTTCAT
* * *
3683363 CGTACGTT-AGTGGCGTTTGTTTAAAAAACGCCGCAATT
1 CGTAC-TTCAGTGGCCTTTGTATAAAAAACACCGCAATT
3683401 GTCCAGTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 14 0.44
42 18 0.56
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (42 bp):
CGTACTTCAGTGGCCTTTGTATAAAAAACACCGCAATTTCAT
Found at i:3686630 original size:18 final size:18
Alignment explanation
Indices: 3686588--3686631 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3686578 TTTTTGCCCT
*
3686588 TACTTTTATTAGTTATTA
1 TACTTTTATTAATTATTA
*
3686606 TATTTTTATTAATTATTGA
1 TACTTTTATTAATTATT-A
3686625 -ACTTTTA
1 TACTTTTA
3686632 CTTTTTATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (18 bp):
TACTTTTATTAATTATTA
Found at i:3687682 original size:25 final size:24
Alignment explanation
Indices: 3687653--3687704 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
3687643 AAAAATATGT
**
3687653 CACAAAAGCAGAGATAAATGTGCAA
1 CACAAAA-CAGAGATAAACATGCAA
*
3687678 CAC-AAATAGAGATAAACATGCAA
1 CACAAAACAGAGATAAACATGCAA
3687701 CACA
1 CACA
3687705 GATAGAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 17 0.74
24 3 0.13
25 3 0.13
ACGTcount: A:0.54, C:0.19, G:0.15, T:0.12
Consensus pattern (24 bp):
CACAAAACAGAGATAAACATGCAA
Found at i:3687688 original size:23 final size:23
Alignment explanation
Indices: 3687662--3687714 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
3687652 TCACAAAAGC
**
3687662 AGAGATAAATGTGCAACACAAAT
1 AGAGATAAACATGCAACACAAAT
*
3687685 AGAGATAAACATGCAACACAGAT
1 AGAGATAAACATGCAACACAAAT
3687708 AGA-ATAA
1 AGAGATAA
3687715 TTCTTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.55, C:0.13, G:0.17, T:0.15
Consensus pattern (23 bp):
AGAGATAAACATGCAACACAAAT
Found at i:3690855 original size:2 final size:2
Alignment explanation
Indices: 3690843--3690876 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
3690833 TTCACACCCT
*
3690843 AG AG AG TAG AG AG AG AG AG AG AA AG AG AG AG AG A
1 AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG A
3690877 TATGGAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (2 bp):
AG
Found at i:3693897 original size:16 final size:16
Alignment explanation
Indices: 3693853--3693898 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
3693843 AAAAATAATC
*
3693853 TCTTATTTTTCTCTTT
1 TCTTATTTTTTTCTTT
* *
3693869 TATTATTTCTTTCTTT
1 TCTTATTTTTTTCTTT
*
3693885 TCTTTTTTTTTTCT
1 TCTTATTTTTTTCT
3693899 CTCCCTCCAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (16 bp):
TCTTATTTTTTTCTTT
Found at i:3694471 original size:2 final size:2
Alignment explanation
Indices: 3694464--3694538 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
3694454 TAACAATATC
3694464 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3694506 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3694539 ATTTGCTGAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3694824 original size:2 final size:2
Alignment explanation
Indices: 3694819--3694859 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3694809 ATAAAATCTT
3694819 TA TA TA 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 TA TA TA T
3694860 TGAAGTGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3695248 original size:29 final size:29
Alignment explanation
Indices: 3695204--3695278 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
3695194 TAACGGAGGT
*
3695204 AGGTCGCCATGTACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
3695233 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
3695262 AGGTCGCCATGCACGCC
1 AGGTCGCCATGCACGCC
3695279 ATATACTCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.20, C:0.43, G:0.28, T:0.09
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:3695322 original size:17 final size:18
Alignment explanation
Indices: 3695288--3695323 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3695278 CATATACTCA
3695288 CCATGCAGACGAGCCATAC
1 CCATGCAGAC-AGCCATAC
3695307 CCATGCAGAC-GCCATAC
1 CCATGCAGACAGCCATAC
3695324 AAGCCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.31, C:0.39, G:0.19, T:0.11
Consensus pattern (18 bp):
CCATGCAGACAGCCATAC
Found at i:3695368 original size:28 final size:28
Alignment explanation
Indices: 3695337--3695392 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3695327 CCATATACTC
3695337 ACCATGCAGACGAGCCAGCCAACGGAGA
1 ACCATGCAGACGAGCCAGCCAACGGAGA
3695365 ACCATGCAGACGAGCCAGCCAACGGAGA
1 ACCATGCAGACGAGCCAGCCAACGGAGA
3695393 GGTCGCCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.32, G:0.29, T:0.04
Consensus pattern (28 bp):
ACCATGCAGACGAGCCAGCCAACGGAGA
Found at i:3695406 original size:28 final size:28
Alignment explanation
Indices: 3695375--3695431 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
3695365 ACCATGCAGA
*
3695375 CGAGCCAGCCAACGGAGAGGTCGCCATG
1 CGAGCCAGCCAACAGAGAGGTCGCCATG
*
3695403 CGAGCCAGCCAATAGAGAGGTCGCCATG
1 CGAGCCAGCCAACAGAGAGGTCGCCATG
3695431 C
1 C
3695432 AGTCTGGGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.32, G:0.33, T:0.09
Consensus pattern (28 bp):
CGAGCCAGCCAACAGAGAGGTCGCCATG
Found at i:3695464 original size:29 final size:29
Alignment explanation
Indices: 3695420--3695514 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
3695410 GCCAATAGAG
* **
3695420 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
3695449 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
3695478 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
3695507 AGGTCGCC
1 AGGTCGCC
3695515 CCCTGCGAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:3695547 original size:19 final size:19
Alignment explanation
Indices: 3695523--3695559 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3695513 CCCCCTGCGA
3695523 ACCATGCATGCACCAGCCG
1 ACCATGCATGCACCAGCCG
3695542 ACCATGCATGCACCAGCC
1 ACCATGCATGCACCAGCC
3695560 AAATAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.43, G:0.19, T:0.11
Consensus pattern (19 bp):
ACCATGCATGCACCAGCCG
Found at i:3695619 original size:49 final size:48
Alignment explanation
Indices: 3695557--3695657 Score: 168
Period size: 49 Copynumber: 2.1 Consensus size: 48
3695547 GCATGCACCA
*
3695557 GCCAAATAACTTCACGTGCTCCTGCT-CCCGCTGCATGCCTGCATGCAT
1 GCCAAATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACA-GCAT
3695605 GCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACAGCAT
1 GCCAA-ATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACAGCAT
3695654 GCCA
1 GCCA
3695658 TGTGATCCTA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
48 5 0.10
49 29 0.58
50 16 0.32
ACGTcount: A:0.20, C:0.39, G:0.19, T:0.23
Consensus pattern (48 bp):
GCCAAATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACAGCAT
Found at i:3695890 original size:16 final size:18
Alignment explanation
Indices: 3695869--3695907 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
3695859 GGAGATAAGG
*
3695869 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
3695885 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
3695903 TAAAT
1 TAAAT
3695908 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:3696055 original size:47 final size:47
Alignment explanation
Indices: 3696012--3696102 Score: 127
Period size: 45 Copynumber: 2.0 Consensus size: 47
3696002 TTATATAGTT
3696012 AAAAAA-TAATTAATTAGTTTGTT-TT-GTT-AATAGTTAGTTATATA
1 AAAAAATTAATTAATTAGTTT-TTGTTAGTTAAATAGTTAGTTATATA
*
3696056 AAAAAATTATTTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAATTAATTAATTAGTTTTTGTTAGTTAAATAGTT-AGTTATAT
3696103 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
44 8 0.20
45 15 0.37
46 3 0.07
47 7 0.17
48 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (47 bp):
AAAAAATTAATTAATTAGTTTTTGTTAGTTAAATAGTTAGTTATATA
Found at i:3696147 original size:12 final size:12
Alignment explanation
Indices: 3696132--3696184 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
3696122 TATATAAAAA
3696132 ATTAGTTAGTTT
1 ATTAGTTAGTTT
3696144 ATTAGTTAGTTTT
1 ATTAGTTAG-TTT
*
3696157 AGTTAGTAAGTTT
1 A-TTAGTTAGTTT
*
3696170 ATTAG-TAGTAT
1 ATTAGTTAGTTT
3696181 ATTA
1 ATTA
3696185 TAATGAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 8 0.22
12 13 0.36
13 8 0.22
14 7 0.19
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (12 bp):
ATTAGTTAGTTT
Found at i:3696201 original size:32 final size:32
Alignment explanation
Indices: 3696165--3696240 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
3696155 TTAGTTAGTA
3696165 AGTTTATTAGTAG-TATA-TTATAATGAAAAAAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAAAT
*
3696197 AGTTTATTAGTTAGTTTTAGTTATATAAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAAT
*
3696230 ATTTTATTAGT
1 AGTTTATTAGT
3696241 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.28
33 19 0.49
34 5 0.13
35 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (32 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAAT
Found at i:3698497 original size:17 final size:17
Alignment explanation
Indices: 3698475--3698507 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3698465 CAATGATGTT
3698475 TAGTATCAAATAATTAC
1 TAGTATCAAATAATTAC
3698492 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
3698508 GTATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:3698511 original size:14 final size:14
Alignment explanation
Indices: 3698474--3698524 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
3698464 ACAATGATGT
3698474 TTAGTATCAAATAA
1 TTAGTATCAAATAA
3698488 TTACTAGTATCAAATAA
1 -T--TAGTATCAAATAA
* *
3698505 TTAGTATTAAATCA
1 TTAGTATCAAATAA
3698519 TTAGTA
1 TTAGTA
3698525 ATAATTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 17 0.53
15 1 0.03
16 1 0.03
17 13 0.41
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (14 bp):
TTAGTATCAAATAA
Found at i:3698526 original size:21 final size:21
Alignment explanation
Indices: 3698502--3698545 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3698492 TAGTATCAAA
* *
3698502 TAATTAGTATTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
*
3698523 TAATAATTAGTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
3698544 TA
1 TA
3698546 TCAAATCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (21 bp):
TAATAAGTAGTAAATCATTAG
Found at i:3698544 original size:11 final size:11
Alignment explanation
Indices: 3698512--3698545 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3698502 TAATTAGTAT
3698512 TAAATCATTAG
1 TAAATCATTAG
*
3698523 T-AATAATTAG
1 TAAATCATTAG
3698533 TAAATCATTAG
1 TAAATCATTAG
3698544 TA
1 TA
3698546 TCAAATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (11 bp):
TAAATCATTAG
Found at i:3698553 original size:14 final size:13
Alignment explanation
Indices: 3698492--3698556 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
3698482 AAATAATTAC
*
3698492 TAGTATCAAATAAT
1 TAGTAT-AAATCAT
3698506 TAGTATTAAATCAT
1 TAGTA-TAAATCAT
*
3698520 TAG--T-AATAAT
1 TAGTATAAATCAT
3698530 TAG--TAAATCAT
1 TAGTATAAATCAT
3698541 TAGTATCAAATCAT
1 TAGTAT-AAATCAT
3698555 TA
1 TA
3698557 AATATTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
10 9 0.21
11 9 0.21
13 1 0.02
14 23 0.53
15 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TAGTATAAATCAT
Found at i:3698677 original size:7 final size:7
Alignment explanation
Indices: 3698665--3698691 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3698655 TATTACTAAA
3698665 TCATTGT
1 TCATTGT
3698672 TCATTGT
1 TCATTGT
3698679 TCATTGT
1 TCATTGT
3698686 TCATTG
1 TCATTG
3698692 AACCAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
TCATTGT
Found at i:3698782 original size:14 final size:14
Alignment explanation
Indices: 3698763--3698810 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
3698753 TTCAAGTCGT
3698763 AAATCATTACTATC
1 AAATCATTACTATC
3698777 AAATCATTAC--T-
1 AAATCATTACTATC
*
3698788 AAATCATTAATATC
1 AAATCATTACTATC
3698802 AAATCATTA
1 AAATCATTA
3698811 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:3698840 original size:47 final size:49
Alignment explanation
Indices: 3698782--3698892 Score: 172
Period size: 47 Copynumber: 2.3 Consensus size: 49
3698772 CTATCAAATC
*
3698782 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-A-T
1 ATTACT-AATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
* *
3698830 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
3698879 ATTACTAATCATTA
1 ATTACTAATCATTA
3698893 CTAAATCATT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
47 36 0.62
48 7 0.12
49 15 0.26
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
Found at i:3698903 original size:21 final size:21
Alignment explanation
Indices: 3698879--3698966 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 21
3698869 TAATTTCATT
3698879 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* * *
3698900 ATTACT-ATCA-AATCATACATA
1 ATTACTAATCATTA-C-TAAATC
* * * *
3698921 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
3698939 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
3698960 ATTACTA
1 ATTACTA
3698967 TCAAATCATT
Statistics
Matches: 49, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
18 14 0.29
19 2 0.04
20 6 0.12
21 24 0.49
22 3 0.06
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:3698905 original size:60 final size:60
Alignment explanation
Indices: 3698830--3699019 Score: 339
Period size: 60 Copynumber: 3.2 Consensus size: 60
3698820 AATAAATTAT
3698830 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
3698889 ATTACTAAATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATC
*
3698949 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
3699009 ATTACTAAATC
1 ATTACTAAATC
3699020 TTATAAATAC
Statistics
Matches: 125, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
59 8 0.06
60 115 0.92
61 2 0.02
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:3702115 original size:28 final size:28
Alignment explanation
Indices: 3702084--3702137 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
3702074 ATAATCTAAT
*
3702084 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
3702112 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
3702138 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:3702144 original size:28 final size:28
Alignment explanation
Indices: 3702080--3702144 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
3702070 TTATATAATC
*
3702080 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
3702108 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
3702136 TAATTTATA
1 TAATATATA
3702145 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:3702147 original size:21 final size:21
Alignment explanation
Indices: 3702114--3702162 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3702104 TTAATATAAT
3702114 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
3702135 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
3702156 ATTAACT
1 A-TAACT
3702163 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:3702814 original size:30 final size:30
Alignment explanation
Indices: 3702771--3702873 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
3702761 TTTGGCGAGC
*
3702771 TGGGCGTGTATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
* * *
3702801 TGGCCGTGCATGGAGGTCGTTGGACGTGCC
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
*
3702831 TGGGCATGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
3702861 TGGGCGTGCATGG
1 TGGGCGTGCATGG
3702874 GCGTGCATGG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.11, C:0.17, G:0.48, T:0.24
Consensus pattern (30 bp):
TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
Found at i:3702844 original size:20 final size:20
Alignment explanation
Indices: 3702791--3702884 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
3702781 TGGAGGTCGT
*
3702791 TGGGCGTGCATGGCCGTGCA
1 TGGGCGTGCATGGACGTGCA
* *
3702811 TGGAG-GT-CGTTGGACGTGCC
1 TGG-GCGTGC-ATGGACGTGCA
* * *
3702831 TGGGCATGCATGGAGGT-CGT
1 TGGGCGTGCATGGACGTGC-A
*
3702851 TGGGCGTGCATGGGCGTGCA
1 TGGGCGTGCATGGACGTGCA
3702871 TGGGCGTGCATGGA
1 TGGGCGTGCATGGA
3702885 GGTCGTGGGG
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
19 3 0.05
20 50 0.89
21 3 0.05
ACGTcount: A:0.12, C:0.19, G:0.47, T:0.22
Consensus pattern (20 bp):
TGGGCGTGCATGGACGTGCA
Found at i:3702866 original size:10 final size:10
Alignment explanation
Indices: 3702851--3702883 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
3702841 TGGAGGTCGT
3702851 TGGGCGTGCA
1 TGGGCGTGCA
3702861 TGGGCGTGCA
1 TGGGCGTGCA
3702871 TGGGCGTGCA
1 TGGGCGTGCA
3702881 TGG
1 TGG
3702884 AGGTCGTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.52, T:0.21
Consensus pattern (10 bp):
TGGGCGTGCA
Found at i:3702938 original size:29 final size:29
Alignment explanation
Indices: 3702897--3703008 Score: 206
Period size: 29 Copynumber: 3.9 Consensus size: 29
3702887 TCGTGGGGTA
*
3702897 GGTCGCAGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
3702926 GGTCGCCGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
3702955 GGTCGCCGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
*
3702984 GGTCGCCGGGCGTACATGGCGACCT
1 GGTCGCCGGGCGTGCATGGCGACCT
3703009 ACCTCCGTTA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.20
Consensus pattern (29 bp):
GGTCGCCGGGCGTGCATGGCGACCTGGTT
Found at i:3703268 original size:29 final size:29
Alignment explanation
Indices: 3703224--3703335 Score: 206
Period size: 29 Copynumber: 3.9 Consensus size: 29
3703214 TAACGGAGGT
*
3703224 AGGTCGCCATGTACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
3703253 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
3703282 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
*
3703311 AGGTCGCCATGCACGCCCTGCGACC
1 AGGTCGCCATGCACGCCCGGCGACC
3703336 TACCCCACGA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.20, C:0.44, G:0.28, T:0.09
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:3703364 original size:10 final size:10
Alignment explanation
Indices: 3703349--3703441 Score: 68
Period size: 10 Copynumber: 9.3 Consensus size: 10
3703339 CCCACGACCT
3703349 CCATGCACGC
1 CCATGCACGC
3703359 CCATGCACGC
1 CCATGCACGC
3703369 CCATGCACGC
1 CCATGCACGC
*
3703379 CCA-ACGAC-C
1 CCATGC-ACGC
*
3703388 TCCATGCATGC
1 -CCATGCACGC
* *
3703399 CCAGGCACGT
1 CCATGCACGC
*
3703409 CCA-ACGAC-C
1 CCATGC-ACGC
*
3703418 TCCATGCACGG
1 -CCATGCACGC
3703429 CCATGCACGC
1 CCATGCACGC
3703439 CCA
1 CCA
3703442 ACGACCTCCA
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
9 3 0.05
10 58 0.91
11 3 0.05
ACGTcount: A:0.23, C:0.47, G:0.19, T:0.11
Consensus pattern (10 bp):
CCATGCACGC
Found at i:3703393 original size:30 final size:30
Alignment explanation
Indices: 3703359--3703461 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
3703349 CCATGCACGC
3703359 CCATGCACGCCCATGCACGCCCAACGACCT
1 CCATGCACGCCCATGCACGCCCAACGACCT
* * *
3703389 CCATGCATGCCCAGGCACGTCCAACGACCT
1 CCATGCACGCCCATGCACGCCCAACGACCT
*
3703419 CCATGCACGGCCATGCACGCCCAACGACCT
1 CCATGCACGCCCATGCACGCCCAACGACCT
*
3703449 CCATACACGCCCA
1 CCATGCACGCCCA
3703462 GCTCGCCAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.24, C:0.48, G:0.17, T:0.11
Consensus pattern (30 bp):
CCATGCACGCCCATGCACGCCCAACGACCT
Found at i:3704119 original size:20 final size:21
Alignment explanation
Indices: 3704072--3704119 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
3704062 ACAGAAATTT
3704072 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTTAGTATA
* *
3704094 AATTATTAG-TTGTTAGTTTA
1 AGTTATTAGTTTGTTAGTATA
3704114 AGTTAT
1 AGTTAT
3704120 ATTATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 15 0.65
21 5 0.22
22 3 0.13
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (21 bp):
AGTTATTAGTTTGTTAGTATA
Found at i:3704153 original size:30 final size:28
Alignment explanation
Indices: 3704103--3704158 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 28
3704093 AAATTATTAG
*
3704103 TTGTTAGTTTAAGTTATATTATATTAAT
1 TTGTTAGTTTAAGTTATATTAGATTAAT
3704131 TTGTTAGTTTAAGTTATATATTAGATTA
1 TTGTTAGTTTAAG-T-TATATTAGATTA
3704159 TATAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 13 0.52
29 1 0.04
30 11 0.44
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.55
Consensus pattern (28 bp):
TTGTTAGTTTAAGTTATATTAGATTAAT
Found at i:3707278 original size:60 final size:60
Alignment explanation
Indices: 3707207--3707448 Score: 341
Period size: 60 Copynumber: 4.2 Consensus size: 60
3707197 TGTATTTATA
*
3707207 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
*
3707267 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
3707327 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
* *
3707387 GA-TTAG---T-A--A-TAATAAT----TTATTATTAATATTTAATGA-TTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
3707434 GATTTAGTAATGATT
1 GATTTAGTAATGATT
3707449 TGATAGTAAT
Statistics
Matches: 168, Mismatches: 5, Indels: 24
0.85 0.03 0.12
Matches are distributed among these distances:
47 12 0.07
48 23 0.14
51 1 0.01
52 8 0.05
53 1 0.01
55 1 0.01
56 1 0.01
59 6 0.04
60 113 0.67
61 2 0.01
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
Found at i:3707420 original size:21 final size:21
Alignment explanation
Indices: 3707396--3707444 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3707386 TGATTAGTAA
*
3707396 TAATAATTTATTATTAAT-ATT
1 TAATAATTGA-TATTAATGATT
*
3707417 TAATGATTGATATTAATGATT
1 TAATAATTGATATTAATGATT
*
3707438 TAGTAAT
1 TAATAAT
3707445 GATTTGATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (21 bp):
TAATAATTGATATTAATGATT
Found at i:3707423 original size:48 final size:48
Alignment explanation
Indices: 3707323--3707444 Score: 178
Period size: 48 Copynumber: 2.6 Consensus size: 48
3707313 GATTTGATAG
*
3707323 TAATGATT--TAGTAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
3707369 TAATGATTTGATAGTAATGATTAGTAATAAT-AATTTATTATTAATATT
1 TAATGA-TTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
3707417 TAATGATTGATATTAATGATTTAGTAAT
1 TAATGATTGATAGTAATGA-TTAGTAAT
3707445 GATTTGATAG
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
46 6 0.09
47 14 0.20
48 29 0.42
49 20 0.29
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (48 bp):
TAATGATTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:3707463 original size:14 final size:13
Alignment explanation
Indices: 3707417--3707462 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
3707407 TATTAATATT
*
3707417 TAATGATTGATAT
1 TAATGATTGATAG
3707430 TAATGATT--TAG
1 TAATGATTGATAG
3707441 TAATGATTTGATAG
1 TAATGA-TTGATAG
3707455 TAATGATT
1 TAATGATT
3707463 TACGACTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
13 10 0.34
14 9 0.31
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (13 bp):
TAATGATTGATAG
Found at i:3707548 original size:7 final size:7
Alignment explanation
Indices: 3707536--3707562 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3707526 ATTTTTGGTT
3707536 CAATGAA
1 CAATGAA
3707543 CAATGAA
1 CAATGAA
3707550 CAATGAA
1 CAATGAA
3707557 CAATGA
1 CAATGA
3707563 TTTAGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
CAATGAA
Found at i:3707609 original size:19 final size:22
Alignment explanation
Indices: 3707568--3707612 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3707558 AATGATTTAG
3707568 TAATAATCATTATAAAATGATT
1 TAATAATCATTATAAAATGATT
*
3707590 TAATAATGATT-T-AAAT-ATT
1 TAATAATCATTATAAAATGATT
3707609 TAAT
1 TAAT
3707613 GATTTGATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 1 0.05
22 10 0.45
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
TAATAATCATTATAAAATGATT
Found at i:3707722 original size:23 final size:21
Alignment explanation
Indices: 3707681--3707725 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 21
3707671 AATGATTTGA
3707681 TACTAATGATTTACTAATTAT
1 TACTAATGATTTACTAATTAT
3707702 TACTAATGATTAATACTAATTAT
1 TACTAATGATT--TACTAATTAT
3707725 T
1 T
3707726 TGATACTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 11 0.50
23 11 0.50
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (21 bp):
TACTAATGATTTACTAATTAT
Found at i:3710014 original size:34 final size:31
Alignment explanation
Indices: 3709962--3710039 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 31
3709952 CCAAACCCTT
*
3709962 AAAC-AACTAA-AAA-TATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCAT-T-A-TA
3709993 AAACTAACTAATAAACTATTTTTTCATTATA
1 AAACTAACTAATAAACTATTTTTTCATTATA
*
3710024 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
3710040 TACTAACTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 11 0.26
31 10 0.24
32 7 0.17
33 4 0.10
34 10 0.24
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (31 bp):
AAACTAACTAATAAACTATTTTTTCATTATA
Found at i:3710024 original size:35 final size:31
Alignment explanation
Indices: 3709962--3710024 Score: 81
Period size: 34 Copynumber: 1.9 Consensus size: 31
3709952 CCAAACCCTT
*
3709962 AAACAACTAAAAATATTTTTTTATATAACTA
1 AAACAACTAAAAATATTTTTTCATATAACTA
3709993 AAACTAACTAATAAACTATTTTTTCATTATAA
1 AAAC-AACTAA-AAA-TATTTTTTCA-TATAA
3710025 TACTACTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 6 0.22
33 3 0.11
34 9 0.33
35 5 0.19
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (31 bp):
AAACAACTAAAAATATTTTTTCATATAACTA
Found at i:3710043 original size:12 final size:12
Alignment explanation
Indices: 3710029--3710072 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
3710019 TTATAATACT
*
3710029 ACTAATAAACTT
1 ACTAATAAACTA
3710041 ACTAACTAAAACTA
1 ACTAA-T-AAACTA
3710055 ACTAATAAACTA
1 ACTAATAAACTA
3710067 ACTAAT
1 ACTAAT
3710073 TTTTATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 17 0.59
13 2 0.07
14 10 0.34
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (12 bp):
ACTAATAAACTA
Found at i:3710188 original size:44 final size:47
Alignment explanation
Indices: 3710099--3710189 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 47
3710089 CAACAAACAA
3710099 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
*
3710146 ATATAAC-TAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTT
1 ATATAACTTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT
3710189 A
1 A
3710190 ACTATATAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
43 13 0.31
44 11 0.26
45 5 0.12
46 6 0.14
47 7 0.17
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (47 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
Found at i:3710200 original size:43 final size:45
Alignment explanation
Indices: 3710099--3710229 Score: 125
Period size: 43 Copynumber: 3.0 Consensus size: 45
3710089 CAACAAACAA
3710099 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
1 ATATAAC-TAACTA-TTAACTAACAAAAACTAATTAAATAATTTTTT
*
3710146 ATATAACTAACTATTAAC-AA-AACAAACTAATT-AATTATTTTTT
1 ATATAACTAACTATTAACTAACAA-AAACTAATTAAATAATTTTTT
* * *
3710189 A-ACTATA-TAACTA-T--CAAACATATACTAATTAAATAATTTTT
1 ATA-TA-ACTAACTATTAACTAACAAAAACTAATTAAATAATTTTT
3710230 AATTTATGTA
Statistics
Matches: 74, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
40 1 0.01
41 10 0.14
42 12 0.16
43 21 0.28
44 12 0.16
45 5 0.07
46 6 0.08
47 7 0.09
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (45 bp):
ATATAACTAACTATTAACTAACAAAAACTAATTAAATAATTTTTT
Found at i:3710257 original size:41 final size:40
Alignment explanation
Indices: 3710169--3710257 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
3710159 TTAACAAAAC
* *
3710169 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
3710210 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
3710251 AAACTAA
1 AAACTAA
3710258 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:3710321 original size:16 final size:18
Alignment explanation
Indices: 3710292--3710330 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
3710282 ACTAATTAAC
*
3710292 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
3710310 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
3710326 ATTTA
1 ATTTA
3710331 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:3710593 original size:49 final size:48
Alignment explanation
Indices: 3710539--3710639 Score: 168
Period size: 49 Copynumber: 2.1 Consensus size: 48
3710529 TAGGATCACA
*
3710539 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGC-GGGAGCAGGAGCACGTGAAGTTAT-T
3710588 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
1 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
3710636 TGGC
1 TGGC
3710640 TGGTGCATGC
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
48 5 0.10
49 32 0.64
50 13 0.26
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.20
Consensus pattern (48 bp):
TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
Found at i:3710610 original size:50 final size:47
Alignment explanation
Indices: 3710539--3710652 Score: 167
Period size: 49 Copynumber: 2.4 Consensus size: 47
3710529 TAGGATCACA
*
3710539 TGGCATGCTGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCTGCAGGCATGCAGC-GGGAGCAGGAGCACGTGAAGTTAT-T
3710588 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
1 TGGCATGC-TGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
* *
3710636 TGGC-TGGTGCATGCATG
1 TGGCATGCTGCAGGCATG
3710653 GTCGGCTGGT
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
46 9 0.15
47 2 0.03
48 5 0.08
49 32 0.52
50 13 0.21
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.21
Consensus pattern (47 bp):
TGGCATGCTGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
Found at i:3710661 original size:19 final size:19
Alignment explanation
Indices: 3710637--3710673 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3710627 GAAGTTATTT
3710637 GGCTGGTGCATGCATGGTC
1 GGCTGGTGCATGCATGGTC
3710656 GGCTGGTGCATGCATGGT
1 GGCTGGTGCATGCATGGT
3710674 TCGCAGGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.19, G:0.43, T:0.27
Consensus pattern (19 bp):
GGCTGGTGCATGCATGGTC
Found at i:3710724 original size:29 final size:29
Alignment explanation
Indices: 3710682--3710776 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
3710672 GTTCGCAGGG
3710682 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
3710711 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
3710740 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
3710769 GGCGACCT
1 GGCGACCT
3710777 CTCTATTGGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:3710803 original size:28 final size:28
Alignment explanation
Indices: 3710765--3710821 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
3710755 CGCCCAGACT
*
3710765 GCATGGCGACCTCTCTATTGGCTGGCTC
1 GCATGGCGACCTCTCCATTGGCTGGCTC
*
3710793 GCATGGCGACCTCTCCGTTGGCTGGCTC
1 GCATGGCGACCTCTCCATTGGCTGGCTC
3710821 G
1 G
3710822 TCTGCATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.09, C:0.33, G:0.32, T:0.26
Consensus pattern (28 bp):
GCATGGCGACCTCTCCATTGGCTGGCTC
Found at i:3710835 original size:28 final size:28
Alignment explanation
Indices: 3710804--3710859 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3710794 CATGGCGACC
3710804 TCTCCGTTGGCTGGCTCGTCTGCATGGT
1 TCTCCGTTGGCTGGCTCGTCTGCATGGT
3710832 TCTCCGTTGGCTGGCTCGTCTGCATGGT
1 TCTCCGTTGGCTGGCTCGTCTGCATGGT
3710860 GAGTATATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.04, C:0.29, G:0.32, T:0.36
Consensus pattern (28 bp):
TCTCCGTTGGCTGGCTCGTCTGCATGGT
Found at i:3710895 original size:17 final size:18
Alignment explanation
Indices: 3710873--3710908 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3710863 TATATGGCTT
3710873 GTATGG-CGTCTGCATGG
1 GTATGGCCGTCTGCATGG
3710890 GTATGGCTCGTCTGCATGG
1 GTATGGC-CGTCTGCATGG
3710909 TGAGTATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.11, C:0.19, G:0.39, T:0.31
Consensus pattern (18 bp):
GTATGGCCGTCTGCATGG
Found at i:3710951 original size:29 final size:29
Alignment explanation
Indices: 3710918--3710992 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
3710908 GTGAGTATAT
3710918 GGCGTGCATGGCGACCTGGTTGGTCGCCG
1 GGCGTGCATGGCGACCTGGTTGGTCGCCG
*
3710947 GGCGTGCATGGTGACCTGGTTGGTCGCCG
1 GGCGTGCATGGCGACCTGGTTGGTCGCCG
*
3710976 GGCGTACATGGCGACCT
1 GGCGTGCATGGCGACCT
3710993 ACCTCCGTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.09, C:0.27, G:0.43, T:0.21
Consensus pattern (29 bp):
GGCGTGCATGGCGACCTGGTTGGTCGCCG
Found at i:3715515 original size:93 final size:92
Alignment explanation
Indices: 3715346--3715517 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 92
3715336 GTGCATTTCA
* * *
3715346 AAAAATTAGTATGTTTATTTATCTAATTTTAATGTATTTTTATCAATCTTACAAATTAATCTATT
1 AAAAATTAGTATGTTTATATATCTAATTTTAATATATTTTTATCAATCTTACAAATTAA-CTATA
*
3715411 TGAATTTAAAAAAAATCAGAAAAAATAC
65 CGAATTTAAAAAAAATCAGAAAAAATAC
* * ** *
3715439 AAAAATTAGTATGTTTATATATTTAATTTTAATATATTTTTATCTATCTTGTAATTTAA-TATAC
1 AAAAATTAGTATGTTTATATATCTAATTTTAATATATTTTTATCAATCTTACAAATTAACTATAC
3715503 GAATTTAAAAAAAAT
66 GAATTTAAAAAAAAT
3715518 AAAAAGAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
91 18 0.26
93 52 0.74
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (92 bp):
AAAAATTAGTATGTTTATATATCTAATTTTAATATATTTTTATCAATCTTACAAATTAACTATAC
GAATTTAAAAAAAATCAGAAAAAATAC
Found at i:3722157 original size:22 final size:22
Alignment explanation
Indices: 3722129--3722171 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3722119 GTATCAGTAA
*
3722129 TAAAA-TTTAAATAACAATTAAC
1 TAAAATTTTAAA-AAAAATTAAC
3722151 TAAAATTTTAAAAAAAATTAA
1 TAAAATTTTAAAAAAAATTAA
3722172 TAGTTGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATTTTAAAAAAAATTAAC
Found at i:3724355 original size:51 final size:53
Alignment explanation
Indices: 3724289--3724416 Score: 197
Period size: 54 Copynumber: 2.4 Consensus size: 53
3724279 ATCGAATAAT
*
3724289 AAAAGCAGCAACGTTTAGCAAAATTT-AAG-AAAAACTAACAATTATTTTGTA
1 AAAAGCAGCAGCGTTTAGCAAAATTTAAAGAAAAAACTAACAATTATTTTGTA
3724340 AAAAGCAGCAGCGTTTAGCAAAATTTAAAAGAAAAAACTAACAATTATTTTGTA
1 AAAAGCAGCAGCGTTTAGCAAAATTT-AAAGAAAAAACTAACAATTATTTTGTA
* * *
3724394 AAAAACATCAGCGTTTAACAAAA
1 AAAAGCAGCAGCGTTTAGCAAAA
3724417 AATCAGAAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 25 0.36
53 3 0.04
54 42 0.60
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (53 bp):
AAAAGCAGCAGCGTTTAGCAAAATTTAAAGAAAAAACTAACAATTATTTTGTA
Found at i:3724682 original size:15 final size:14
Alignment explanation
Indices: 3724662--3724691 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3724652 TTTGTCCGGG
3724662 ATTTTTATTGTTATT
1 ATTTTTATT-TTATT
3724677 ATTTTTATTTTATT
1 ATTTTTATTTTATT
3724691 A
1 A
3724692 ATTATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
ATTTTTATTTTATT
Found at i:3728060 original size:20 final size:20
Alignment explanation
Indices: 3728037--3728088 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3728027 AACGCGATCC
3728037 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
3728057 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
3728077 CCAAAATCGCAA
1 CCAGAATCGCAA
3728089 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:3728105 original size:21 final size:20
Alignment explanation
Indices: 3728078--3728176 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
3728068 AATCAGTTTC
3728078 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
3728099 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3728120 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3728140 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3728161 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3728177 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3728205 original size:20 final size:20
Alignment explanation
Indices: 3728143--3728336 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3728133 CGATTTTCCA
* ** *
3728143 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
3728163 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
3728183 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3728203 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
3728223 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
3728243 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3728263 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
3728283 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
3728303 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
3728324 AAATCGCAACGCG
1 AAATCGCAACGCG
3728337 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3728227 original size:60 final size:60
Alignment explanation
Indices: 3728143--3728336 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3728133 CGATTTTCCA
* ** * *
3728143 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
3728203 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
3728263 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
3728324 AAATCGCAACGCG
1 AAATCGCAACGCG
3728337 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:3728758 original size:33 final size:33
Alignment explanation
Indices: 3728719--3728789 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3728709 TTCACTTAGA
*
3728719 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3728752 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3728785 TTTCA
1 TTTCA
3728790 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3728929 original size:14 final size:14
Alignment explanation
Indices: 3728910--3728978 Score: 84
Period size: 14 Copynumber: 4.6 Consensus size: 14
3728900 AGAATGACTG
3728910 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
3728924 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
3728943 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
3728957 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
3728971 TCGCAACG
1 TCGCAACG
3728979 CGAAACCAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
14 30 0.62
15 1 0.02
16 4 0.08
17 4 0.08
18 1 0.02
19 8 0.17
ACGTcount: A:0.41, C:0.23, G:0.28, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:3729012 original size:19 final size:19
Alignment explanation
Indices: 3728990--3729087 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
3728980 GAAACCAAAA
*
3728990 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3729009 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3729023 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3729042 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
3729056 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
3729075 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3729088 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3729031 original size:14 final size:14
Alignment explanation
Indices: 3729012--3729101 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3729002 TTTCATTTCG
3729012 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3729026 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3729045 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3729059 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
3729076 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
3729092 CGTTGCGATT
1 CGTTGCGATT
3729102 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3729037 original size:33 final size:33
Alignment explanation
Indices: 3728995--3729109 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3728985 CAAAATCGCA
3728995 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3729028 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
3729061 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3729094 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3729110 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3731035 original size:185 final size:186
Alignment explanation
Indices: 3730806--3731278 Score: 930
Period size: 185 Copynumber: 2.5 Consensus size: 186
3730796 TAGATTGCTT
3730806 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3730871 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
3730936 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCGTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCGTTGTTTTGTCTTTTGGTTGAA
3730991 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3731056 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
3731121 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCGTTGTTTTGTCTTTTGGTTGAA
3731177 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3731242 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
3731279 ATCCATTCAA
Statistics
Matches: 286, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
185 155 0.54
186 131 0.46
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCGTTGTTTTGTCTTTTGGTTGAA
Found at i:3731120 original size:93 final size:93
Alignment explanation
Indices: 3730806--3731278 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
3730796 TAGATTGCTT
3730806 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3730871 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3730899 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
3730963 TTTGTCGTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3730991 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3731056 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3731084 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3731149 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3731177 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3731242 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3731270 AGTAAATTT
1 AGTAAATTT
3731279 ATCCATTCAA
Statistics
Matches: 377, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 91 0.24
93 286 0.76
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3731362 original size:19 final size:19
Alignment explanation
Indices: 3731322--3731450 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3731312 TAGTTTACTT
* *
3731322 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3731342 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3731361 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3731380 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
3731394 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
3731413 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
3731427 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3731446 TCGCA
1 TCGCA
3731451 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:3731401 original size:33 final size:32
Alignment explanation
Indices: 3731358--3731450 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
3731348 CGCGAAACCA
**
3731358 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
3731390 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
3731423 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
3731451 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:3731448 original size:52 final size:52
Alignment explanation
Indices: 3731322--3731450 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
3731312 TAGTTTACTT
**
3731322 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
3731374 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
3731427 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
3731451 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:3731468 original size:19 final size:19
Alignment explanation
Indices: 3731446--3731580 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3731436 GAAACCAAAA
*
3731446 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3731465 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
3731481 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3731498 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3731514 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3731531 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3731550 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3731570 TCGTGTTGCGA
1 TCGCGTTGCGA
3731581 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3731487 original size:14 final size:14
Alignment explanation
Indices: 3731468--3731524 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3731458 TTTCATTTCG
3731468 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3731482 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3731499 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
3731515 CGTTGCGATT
1 CGTTGCGATT
3731525 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3731493 original size:33 final size:33
Alignment explanation
Indices: 3731451--3731543 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3731441 CAAAATCGCA
*
3731451 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
3731484 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3731517 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3731544 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3732988 original size:14 final size:14
Alignment explanation
Indices: 3732969--3733004 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3732959 ATTGTTTAAT
3732969 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3732983 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3732997 TGATTTGT
1 TGATTTGT
3733005 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:3733127 original size:19 final size:19
Alignment explanation
Indices: 3733111--3733212 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3733101 AAAAATGACT
3733111 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3733130 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3733149 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3733163 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3733182 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3733202 ATCGCAATGCG
1 ATCGCAATGCG
3733213 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3733271 original size:19 final size:19
Alignment explanation
Indices: 3733241--3733544 Score: 338
Period size: 19 Copynumber: 17.4 Consensus size: 19
3733231 GATTATCTCG
3733241 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3733259 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3733278 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
3733292 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3733311 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3733330 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
3733349 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
3733368 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
3733383 TT-CGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
3733400 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3733419 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3733433 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3733452 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3733471 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
3733485 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3733504 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
3733518 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3733537 TTGCGATT
1 TTGCGATT
3733545 GTATTTTCCG
Statistics
Matches: 246, Mismatches: 13, Indels: 53
0.79 0.04 0.17
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 34 0.14
17 29 0.12
18 15 0.06
19 134 0.54
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3733404 original size:141 final size:136
Alignment explanation
Indices: 3733209--3733544 Score: 482
Period size: 141 Copynumber: 2.4 Consensus size: 136
3733199 AAAATCGCAA
3733209 TGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTCATTTCGCATTGCGATTTTCATT
1 TGCGATTT-TAATTTCGCATTGCGATTATCTCGTTGCGATTTCATTTCGCATTGCGATTTTCATT
*
3733273 TCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
65 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
*
3733338 TTCATTTCGTAT
128 TTC-TCTCG--T
*
3733350 TGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCA-TTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTATCTC-GTTGCGA-TTTCATTTCGCATTGCGATTTTCAT
3733413 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
3733478 TCTCTCGT
129 TCTCTCGT
* * * * *
3733486 TGCGATTTTCATTTCGCGTTGCGATTTTCAT-GTTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTAATTTCGCATTGCGATTATC-TCGTTGCGA-TTTCATTTCGCATTGCGATT
3733545 GTATTTTCCG
Statistics
Matches: 180, Mismatches: 9, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
135 3 0.02
136 34 0.19
137 14 0.08
138 4 0.02
139 3 0.02
141 111 0.62
142 11 0.06
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.47
Consensus pattern (136 bp):
TGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTCATTTCGCATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTC
TCTCGT
Found at i:3733479 original size:52 final size:52
Alignment explanation
Indices: 3733241--3733516 Score: 334
Period size: 52 Copynumber: 5.2 Consensus size: 52
3733231 GATTATCTCG
*
3733241 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
3733292 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
3733349 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
3733400 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
3733452 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
3733504 TTGCGATTTTCAT
1 TTGCGATTTTCAT
3733517 GTTGGGATTT
Statistics
Matches: 208, Mismatches: 8, Indels: 17
0.89 0.03 0.07
Matches are distributed among these distances:
50 3 0.01
51 49 0.24
52 116 0.56
53 2 0.01
54 6 0.03
55 8 0.04
57 24 0.12
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:3735860 original size:12 final size:12
Alignment explanation
Indices: 3735843--3735867 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3735833 TCTTCGGGGA
3735843 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3735855 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3735867 C
1 C
3735868 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3736075 original size:24 final size:24
Alignment explanation
Indices: 3736041--3736087 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3736031 CTGAAACATC
3736041 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3736065 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3736088 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:3736783 original size:20 final size:20
Alignment explanation
Indices: 3736755--3737143 Score: 498
Period size: 20 Copynumber: 19.4 Consensus size: 20
3736745 AAATTTCAGT
* * * *
3736755 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3736775 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
3736795 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3736815 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3736835 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3736855 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3736875 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3736895 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3736915 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3736935 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3736955 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
3736975 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3736995 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3737015 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
3737035 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
3737055 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
3737075 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
3737095 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
3737115 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
3737135 GTTGCGATT
1 GTTGCGATT
3737144 ATGGAAAATC
Statistics
Matches: 329, Mismatches: 32, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
19 5 0.02
20 319 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:3753560 original size:23 final size:23
Alignment explanation
Indices: 3753534--3753587 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
3753524 AAAAATTTTA
* *
3753534 AAACGTGCCACAAAGACATATAT
1 AAACGTGCCACAAAGACAGAGAT
3753557 AAACGTGCCACAAAGACAGAGAT
1 AAACGTGCCACAAAGACAGAGAT
3753580 AAACGTGC
1 AAACGTGC
3753588 AACACAAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (23 bp):
AAACGTGCCACAAAGACAGAGAT
Done.