Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008685.1 Hibiscus syriacus cultivar Beakdansim tig00111708_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: 3669133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 19
Found at i:3324707 original size:20 final size:20
Alignment explanation
Indices: 3324684--3324756 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
3324674 CGATAGTCAG
3324684 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3324704 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
3324724 ATTCGCATTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
*
3324744 ATTCGTATTGCGA
1 ATTCGCATTGCGA
3324757 ATTAGGAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:3324777 original size:21 final size:21
Alignment explanation
Indices: 3324753--3324798 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
3324743 TATTCGTATT
3324753 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
3324774 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
3324795 GCGA
1 GCGA
3324799 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:3325179 original size:3 final size:3
Alignment explanation
Indices: 3325171--3325209 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3325161 AATATATTTA
3325171 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3325210 TAATCATGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3325473 original size:28 final size:28
Alignment explanation
Indices: 3325398--3325480 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 28
3325388 TTAAATAAAA
* * * *
3325398 ATAAATATTTTATTTTTATAAATTATAT
1 ATAAATATTTTATTATTATTATTTATAG
*
3325426 ATAAATCTATTTT-TTA-TATTATTTTTAG
1 ATAAA--TATTTTATTATTATTATTTATAG
*
3325454 ATAAATGTTTTATTATTATTTATTTAT
1 ATAAATATTTTATTATTA-TTATTTAT
3325481 TTTTTTATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
26 5 0.12
27 3 0.07
28 20 0.47
29 9 0.21
30 6 0.14
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (28 bp):
ATAAATATTTTATTATTATTATTTATAG
Found at i:3327476 original size:12 final size:12
Alignment explanation
Indices: 3327459--3327487 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3327449 GCTAGGAGGT
3327459 GGATGATTTTCG
1 GGATGATTTTCG
3327471 GGATGATTTTCG
1 GGATGATTTTCG
3327483 GGATG
1 GGATG
3327488 TGCACCACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.38, T:0.38
Consensus pattern (12 bp):
GGATGATTTTCG
Found at i:3335501 original size:112 final size:115
Alignment explanation
Indices: 3335320--3335865 Score: 520
Period size: 121 Copynumber: 4.6 Consensus size: 115
3335310 ATTCCCAAAG
* *
3335320 AAGTTCGTAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
3335385 CAACCTTTTGATCAAATTCATCAC-TAGAT-GA-ATCAACTTTTCTAGAGA
66 CAACCTTTTG-TCAAATTCATCACATAGATCAACATCAACTTTTCCAGAGA
** *
3335433 AAGTTCATAATGAGAAGAACTTGTCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
3335497 CAACCTTTTG-CATGACTCTATCACAGAAAGAGATATATCAATATCAACATTTCCAGA-A
66 CAACCTTTTGTCA-AATTC-ATCAC--------ATAGATCAACATCAACTTTTCCAGAGA
** *
3335555 GTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAATAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
3335620 CAACCTTTTGCTCGAATTCATCAATCGATGGATCAACATCAACTTTTCCATAGA
66 CAACCTTTTG-TCAAATTCATC-A-C-ATAGATCAACATCAACTTTTCCAGAGA
* * *
3335674 AAGTTCATAATAAGAAGAACTTATCTAAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
3335738 CAACC-TTTG-CATGACTCTATCACAGAAGGATATAAATCAACATCCACATTTCCAGA-A
66 CAACCTTTTGTCA-AATTC-ATCAC--------ATAGATCAACATCAACTTTTCCAGAGA
** * *
3335795 GTGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATAATAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
3335859 CAACCTT
66 CAACCTT
3335866 GCCTTAATTC
Statistics
Matches: 356, Mismatches: 47, Indels: 51
0.78 0.10 0.11
Matches are distributed among these distances:
110 2 0.01
111 3 0.01
112 48 0.13
113 26 0.07
115 2 0.01
116 4 0.01
117 7 0.02
118 59 0.17
119 26 0.07
121 63 0.18
122 52 0.15
123 58 0.16
124 4 0.01
125 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (115 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTGTCAAATTCATCACATAGATCAACATCAACTTTTCCAGAGA
Found at i:3335738 original size:20 final size:20
Alignment explanation
Indices: 3335676--3335739 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
3335666 TCCATAGAAA
*
3335676 GTTCATAATAAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * ***
3335696 -ATC-TAAAGAGGAAGAAGAA
1 GTTCATAATGA-GAAGAACTT
3335715 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
3335735 GTTCA
1 GTTCA
3335740 ACCTTTGCAT
Statistics
Matches: 30, Mismatches: 11, Indels: 6
0.64 0.23 0.13
Matches are distributed among these distances:
18 4 0.13
19 8 0.27
20 13 0.43
21 5 0.17
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:3335852 original size:121 final size:120
Alignment explanation
Indices: 3335435--3335865 Score: 536
Period size: 121 Copynumber: 3.6 Consensus size: 120
3335425 TCTAGAGAAA
** *
3335435 GTTCATAATGAGAAGAACTTGTCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* *
3335500 CCTTTTGCATGACTCTATCACAGAAAGAGATATATCAATATCAACATTTCCAGAAGT
66 CC-TTTGCATGACTCTATCACAGAAAGA-ATAAATCAACATCAACATTTCCAGAAGT
*
3335557 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* ** ** * *
3335622 ACCTTT---TG-CTCGAATTCATCA-ATCG-ATGGATCAACATCAACTTTTCCATAGAA-A
65 ACCTTTGCATGACTC-TA-TCA-CAGAAAGAATAAATCAACATCAACATTTCC--AGAAGT
* * *
3335676 GTTCATAATAAGAAGAACTTATCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* *
3335741 CCTTTGCATGACTCTATCACAGAAGGATATAAATCAACATCCACATTTCCAGAAGT
66 CCTTTGCATGACTCTATCACAGAAAGA-ATAAATCAACATCAACATTTCCAGAAGT
* *
3335797 GTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATAATAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
3335861 ACCTT
65 ACCTT
3335866 GCCTTAATTC
Statistics
Matches: 265, Mismatches: 29, Indels: 31
0.82 0.09 0.10
Matches are distributed among these distances:
118 62 0.23
119 30 0.11
120 18 0.07
121 65 0.25
122 53 0.20
123 37 0.14
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (120 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTTGCATGACTCTATCACAGAAAGAATAAATCAACATCAACATTTCCAGAAGT
Found at i:3336213 original size:3 final size:3
Alignment explanation
Indices: 3336205--3336280 Score: 68
Period size: 3 Copynumber: 26.0 Consensus size: 3
3336195 CTATTTGTTT
* * *
3336205 TTA TTA TTA TTA TT- TTA ATA TTA ATA TT- TTA TTTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * *
3336249 TTA TT- TTA TAA TAA TAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3336281 ATAAAAAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
2 6 0.10
3 52 0.85
4 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3336234 original size:29 final size:30
Alignment explanation
Indices: 3336202--3336280 Score: 79
Period size: 35 Copynumber: 2.5 Consensus size: 30
3336192 CATCTATTTG
* *
3336202 TTTTTATTATTATTATTTTAATATTAATATT
1 TTTTTATTATTATTATTTT-ATAATAATAAT
3336233 TTATTTATTACTATTATTATTTTATAATAATAA-
1 TT-TTTA-T--TATTATTATTTTATAATAATAAT
*
3336266 TTATTATTATTATTA
1 TTTTTATTATTATTA
3336281 ATAAAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
29 8 0.20
31 3 0.07
32 7 0.17
33 3 0.07
34 8 0.20
35 12 0.29
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTTATTATTATTATTTTATAATAATAAT
Found at i:3336255 original size:35 final size:35
Alignment explanation
Indices: 3336209--3336277 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
3336199 TTGTTTTTAT
*
3336209 TATTATTATTTTAATATTAAT-ATT-TTATTTATTAC
1 TATTATTATTTT-ATAATAATAATTATTA-TTATTAC
3336244 TATTATTATTTTATAATAATAATTATTATTATTA
1 TATTATTATTTTATAATAATAATTATTATTATTA
3336278 TTAATAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 7 0.23
35 21 0.68
36 3 0.10
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (35 bp):
TATTATTATTTTATAATAATAATTATTATTATTAC
Found at i:3342018 original size:65 final size:64
Alignment explanation
Indices: 3341914--3342045 Score: 228
Period size: 65 Copynumber: 2.0 Consensus size: 64
3341904 TCAGCCAAAG
* *
3341914 AACTTTAGCCTTTTTCTTATAAAACAAAGCCTCAGCCTTTTCTAGCTCAACAAGTTCCCCCTCTC
1 AACTTTAGCCTTTTGCTTATAAAACAAAGCCTCAGCCTTTTCCAGCTCAACAAGTT-CCCCTCTC
*
3341979 AACTTTAGCCTTTTGCTTATAAATCAAAGCCTCAGCCTTTTCCAGCTCAACAAGTTCCCCTCTC
1 AACTTTAGCCTTTTGCTTATAAAACAAAGCCTCAGCCTTTTCCAGCTCAACAAGTTCCCCTCTC
3342043 AAC
1 AAC
3342046 CGAATTTTAC
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
64 11 0.17
65 53 0.83
ACGTcount: A:0.27, C:0.33, G:0.08, T:0.33
Consensus pattern (64 bp):
AACTTTAGCCTTTTGCTTATAAAACAAAGCCTCAGCCTTTTCCAGCTCAACAAGTTCCCCTCTC
Found at i:3344808 original size:25 final size:25
Alignment explanation
Indices: 3344780--3344840 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
3344770 TTGATGATCT
*
3344780 AATTTCGCACCACATGAAAATTTGC
1 AATTTCACACCACATGAAAATTTGC
3344805 AATTTCACACCACATGAAAATTTGC
1 AATTTCACACCACATGAAAATTTGC
3344830 AATTTCACACC
1 AATTTCACACC
3344841 CCCTAGATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.38, C:0.26, G:0.08, T:0.28
Consensus pattern (25 bp):
AATTTCACACCACATGAAAATTTGC
Found at i:3348673 original size:26 final size:26
Alignment explanation
Indices: 3348624--3348674 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
3348614 CTTCATCACT
**
3348624 CTTTAAGAGGAAGCATATGGCAAGTG
1 CTTTAAGAGGAAGCATATCCCAAGTG
3348650 CTTTAAGAGGAAGCATATCCCAAGT
1 CTTTAAGAGGAAGCATATCCCAAGT
3348675 ATTTGTGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (26 bp):
CTTTAAGAGGAAGCATATCCCAAGTG
Found at i:3349576 original size:21 final size:22
Alignment explanation
Indices: 3349547--3349598 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
3349537 GTGAGTTTGA
*
3349547 GATCGATCCCTTTA-CAAAAAG
1 GATCGATCCCTTCACCAAAAAG
*
3349568 GATCTATCCCTTCACCAAAAAG
1 GATCGATCCCTTCACCAAAAAG
3349590 GATCGATCC
1 GATCGATCC
3349599 TCTTGTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (22 bp):
GATCGATCCCTTCACCAAAAAG
Found at i:3353469 original size:2 final size:2
Alignment explanation
Indices: 3353462--3353511 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3353452 CATGTTACAG
3353462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3353504 TA TA TA TA
1 TA TA TA TA
3353512 AATGTGATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3353962 original size:32 final size:32
Alignment explanation
Indices: 3353892--3354141 Score: 407
Period size: 32 Copynumber: 7.8 Consensus size: 32
3353882 GAGTCGAGGG
* *
3353892 TTACCTATG-TCTTTC-GAGACATGTGGATA-GA
1 TTACCTATGTTC-TTCGGA-ACATATGGACATGA
3353923 TTACCTATGTTCTTCGGAACATATGGACATGA
1 TTACCTATGTTCTTCGGAACATATGGACATGA
3353955 TTACCTATGTTCTTCGGAACATATGGACATGA
1 TTACCTATGTTCTTCGGAACATATGGACATGA
3353987 TTACCTATGTTCTTCGGAACATATGGACATGA
1 TTACCTATGTTCTTCGGAACATATGGACATGA
* *
3354019 TTACCTATGTTCTCCGGAACATATGGACAGGA
1 TTACCTATGTTCTTCGGAACATATGGACATGA
*
3354051 TTACCTATGTTATTCGGAACATATGGACATGA
1 TTACCTATGTTCTTCGGAACATATGGACATGA
*
3354083 TTACCTATGTTCTCCGGAACATATGGACATGA
1 TTACCTATGTTCTTCGGAACATATGGACATGA
3354115 TTACCTATGTTCTTCGGAACATATGGA
1 TTACCTATGTTCTTCGGAACATATGGA
3354142 TAGGTCCTTC
Statistics
Matches: 206, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
31 21 0.10
32 185 0.90
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (32 bp):
TTACCTATGTTCTTCGGAACATATGGACATGA
Found at i:3354641 original size:64 final size:64
Alignment explanation
Indices: 3354526--3354687 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 64
3354516 AATTAAATTG
* * *
3354526 AACATCGAATGTATTTCATGCATCGAATGCACTTACCATGCACCGATGCACT-AGGAT-TTTATA
1 AACATCGAATGCATTTGATGCATC-AATGCACTCACCATGCACCGATGCACTCAGGATATTT-T-
3354589 AA
63 AA
* * * *
3354591 AACATCGAATGCATTTGATGCATCAATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCAATGCACTCA-CCATGCACCGATGCACTCAGGATATTTTAA
* *
3354655 AACATCGAATGCACTTGATGCATCGATGCACTC
1 AACATCGAATGCATTTGATGCATCAATGCACTC
3354688 TTAGTGCACT
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
63 1 0.01
64 53 0.63
65 27 0.32
66 3 0.04
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCAATGCACTCACCATGCACCGATGCACTCAGGATATTTTAA
Found at i:3363281 original size:64 final size:65
Alignment explanation
Indices: 3363122--3363301 Score: 201
Period size: 65 Copynumber: 2.8 Consensus size: 65
3363112 AATTAAATTG
* *
3363122 AACATCGAATGCATTTCATGCATCGATGCACTTACCATGCACCGATGCACTGAGGATTTTATAAA
1 AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCACCGATGCACTGAGGATTTTATAAA
* * * *
3363187 AACATCAAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTA-GCTATTT-T
1 AACATCGAATGCATTTGATGCATCGATGCACTCA-CCATGCACCGATGCACT-GAGGAT-TTTAT
*
3363249 -GA
63 AAA
*
3363251 AACATCGAATGCACTTGATGCATCGATGCACTCTTA-C-TGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACTC--ACCATGCACCGATGCACT
3363302 AAGGGTCCAA
Statistics
Matches: 99, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
64 44 0.44
65 50 0.51
66 4 0.04
67 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCACCGATGCACTGAGGATTTTATAAA
Found at i:3367322 original size:18 final size:20
Alignment explanation
Indices: 3367299--3367341 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
3367289 AATAATTAAA
3367299 CATCGAAAGCA-AT-TAGTG
1 CATCGAAAGCACATGTAGTG
*
3367317 CATCG-ATGCACATGTAGTG
1 CATCGAAAGCACATGTAGTG
3367336 CATCGA
1 CATCGA
3367342 TACAACCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.19
18 7 0.33
19 10 0.48
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (20 bp):
CATCGAAAGCACATGTAGTG
Found at i:3368470 original size:32 final size:32
Alignment explanation
Indices: 3368400--3368681 Score: 394
Period size: 32 Copynumber: 8.8 Consensus size: 32
3368390 GAGTTGAGGG
*
3368400 TTACCTATG-TCTTTC-GAGACATATGGATA-GA
1 TTACCTATGTTC-TTCGGA-ACATATGGACAGGA
*
3368431 TTACCTATGTTCTTCGGAACATATGGACATGA
1 TTACCTATGTTCTTCGGAACATATGGACAGGA
*
3368463 TTACCTATGTTCTTCGGAACATATGGACAAGA
1 TTACCTATGTTCTTCGGAACATATGGACAGGA
3368495 TTACCTATGTTCTTCGGAACATATGGACAGGA
1 TTACCTATGTTCTTCGGAACATATGGACAGGA
* *
3368527 TTACCTATGTGCTTCGGAACATA-GTGACATGA
1 TTACCTATGTTCTTCGGAACATATG-GACAGGA
*
3368559 TTACCTATGTTCTCCGGAACATATGGACAGGA
1 TTACCTATGTTCTTCGGAACATATGGACAGGA
*
3368591 TTACCTATGTTCTTGGGAACATATGGACAGGA
1 TTACCTATGTTCTTCGGAACATATGGACAGGA
* * *
3368623 TTACTTATTTTC-TCTGGAACATATGGACATGA
1 TTACCTATGTTCTTC-GGAACATATGGACAGGA
*
3368655 TTACCTATGTTCTTCGGAACGTATGGA
1 TTACCTATGTTCTTCGGAACATATGGA
3368682 TAGGTCCTTC
Statistics
Matches: 227, Mismatches: 17, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
31 24 0.11
32 200 0.88
33 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (32 bp):
TTACCTATGTTCTTCGGAACATATGGACAGGA
Found at i:3369410 original size:43 final size:41
Alignment explanation
Indices: 3369330--3369410 Score: 101
Period size: 44 Copynumber: 1.9 Consensus size: 41
3369320 TTGCTACATT
* *
3369330 TTGGATATTTGAGTTTATATGTTTGGTATTTTGAACTTTTA
1 TTGGATATTTGAGTTTATATGTTGGGTACTTTGAACTTTTA
*
3369371 TTGGATATTTGGATGTTTATTTTGTTGGGTACTTT-AACTT
1 TTGGATATTT-GA-GTTTA-TATGTTGGGTACTTTGAACTT
3369411 ATATATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 10 0.29
42 2 0.06
43 10 0.29
44 12 0.35
ACGTcount: A:0.20, C:0.04, G:0.21, T:0.56
Consensus pattern (41 bp):
TTGGATATTTGAGTTTATATGTTGGGTACTTTGAACTTTTA
Found at i:3370030 original size:30 final size:24
Alignment explanation
Indices: 3369964--3370012 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3369954 TTTACCAAAT
3369964 GATCGATCCCTTTGATTCCAGTGA
1 GATCGATCCCTTTGATTCCAGTGA
3369988 GATCGATCCCTTTGATTCCAGTGA
1 GATCGATCCCTTTGATTCCAGTGA
3370012 G
1 G
3370013 TTTGGGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.33
Consensus pattern (24 bp):
GATCGATCCCTTTGATTCCAGTGA
Found at i:3370043 original size:21 final size:21
Alignment explanation
Indices: 3370017--3370092 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
3370007 AGTGAGTTTG
*
3370017 GGATCGATCCCTTTATAAAAA
1 GGATCGATCCCTTAATAAAAA
* **
3370038 GGATCGATCCCTTCACCAAAA
1 GGATCGATCCCTTAATAAAAA
*
3370059 GGATCGATCCCTTAATGAAAA
1 GGATCGATCCCTTAATAAAAA
* *
3370080 TGATTGATCCCTT
1 GGATCGATCCCTT
3370093 CCCTTAAAGG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (21 bp):
GGATCGATCCCTTAATAAAAA
Found at i:3370089 original size:42 final size:42
Alignment explanation
Indices: 3370017--3370111 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
3370007 AGTGAGTTTG
*
3370017 GGATCGATCCCTTTATAAAAAGGATCGATCCCTTCACC-AAAA
1 GGATCGATCCCTTAATAAAAAGGATCGATCCCTTC-CCTAAAA
* * * *
3370059 GGATCGATCCCTTAATGAAAATGATTGATCCCTTCCCTTAAA
1 GGATCGATCCCTTAATAAAAAGGATCGATCCCTTCCCTAAAA
3370101 GGATCGATCCC
1 GGATCGATCCC
3370112 CTTGTTACAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 2 0.04
42 45 0.96
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (42 bp):
GGATCGATCCCTTAATAAAAAGGATCGATCCCTTCCCTAAAA
Found at i:3370109 original size:21 final size:21
Alignment explanation
Indices: 3370017--3370111 Score: 79
Period size: 21 Copynumber: 4.5 Consensus size: 21
3370007 AGTGAGTTTG
**
3370017 GGATCGATCCCTT-TATAAAAA
1 GGATCGATCCCTTCCCT-AAAA
3370038 GGATCGATCCCTTCACC-AAAA
1 GGATCGATCCCTTC-CCTAAAA
**
3370059 GGATCGATCCCTT-AATGAAAA
1 GGATCGATCCCTTCCCT-AAAA
* * *
3370080 TGATTGATCCCTTCCCTTAAA
1 GGATCGATCCCTTCCCTAAAA
3370101 GGATCGATCCC
1 GGATCGATCCC
3370112 CTTGTTACAA
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
21 57 0.98
22 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (21 bp):
GGATCGATCCCTTCCCTAAAA
Found at i:3373169 original size:24 final size:24
Alignment explanation
Indices: 3373142--3373200 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
3373132 TTTGGGTAAG
*
3373142 AATTTTTCAAAACCCTAAATTTTT
1 AATTTTTCAAAACACTAAATTTTT
*
3373166 AATTTTTCAAAACACTAACTTTTT
1 AATTTTTCAAAACACTAAATTTTT
3373190 AATTTTTCAAA
1 AATTTTTCAAA
3373201 TTTAGATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTTTTCAAAACACTAAATTTTT
Found at i:3374807 original size:17 final size:17
Alignment explanation
Indices: 3374785--3374824 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
3374775 CCTTAATATA
3374785 CTTATTGATGATTCTAG
1 CTTATTGATGATTCTAG
3374802 CTTATTGATGATTCTAG
1 CTTATTGATGATTCTAG
3374819 CTTATT
1 CTTATT
3374825 TTTAATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (17 bp):
CTTATTGATGATTCTAG
Found at i:3375269 original size:20 final size:21
Alignment explanation
Indices: 3375244--3375302 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
3375234 TTTTTAACTT
3375244 AAAGGATCGATCCCCTAGA-A
1 AAAGGATCGATCCCCTAGACA
* * * *
3375264 AAAGGATTGATCCCTTTGACC
1 AAAGGATCGATCCCCTAGACA
*
3375285 AAATGATCGATCCCCTAG
1 AAAGGATCGATCCCCTAG
3375303 TGAGTTTGGG
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (21 bp):
AAAGGATCGATCCCCTAGACA
Found at i:3379653 original size:16 final size:15
Alignment explanation
Indices: 3379632--3379663 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
3379622 CGCGACAAAA
3379632 TTTAATAAAAATATAT
1 TTTAATAAAAA-ATAT
3379648 TTTAATAAAAAATAT
1 TTTAATAAAAAATAT
3379663 T
1 T
3379664 ATTTAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTAATAAAAAATAT
Found at i:3379660 original size:17 final size:17
Alignment explanation
Indices: 3379632--3379667 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
3379622 CGCGACAAAA
3379632 TTTAATAAAAATA-TAT
1 TTTAATAAAAATATTAT
3379648 TTTAATAAAAAATATTAT
1 TTTAAT-AAAAATATTAT
3379666 TT
1 TT
3379668 AAACAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAATAAAAATATTAT
Found at i:3381503 original size:19 final size:19
Alignment explanation
Indices: 3381479--3381517 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3381469 CGCCGGCGTG
3381479 ACGAATTCCATGGTCATAA
1 ACGAATTCCATGGTCATAA
3381498 ACGAATTCCATGGTCATAA
1 ACGAATTCCATGGTCATAA
3381517 A
1 A
3381518 ATATTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (19 bp):
ACGAATTCCATGGTCATAA
Found at i:3382864 original size:15 final size:15
Alignment explanation
Indices: 3382844--3382873 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3382834 ACTGGGTGGA
3382844 CGGATGCGGGACGGG
1 CGGATGCGGGACGGG
*
3382859 CGGATGCGGGGCGGG
1 CGGATGCGGGACGGG
3382874 TAATGTCTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.20, G:0.63, T:0.07
Consensus pattern (15 bp):
CGGATGCGGGACGGG
Found at i:3386960 original size:16 final size:16
Alignment explanation
Indices: 3386936--3386973 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3386926 ACTTAACTCA
3386936 ATTAATATTA-TATATT
1 ATTAATATTATTAT-TT
*
3386952 ATTATTATTATTATTT
1 ATTAATATTATTATTT
3386968 ATTAAT
1 ATTAAT
3386974 CTAGGATGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTAATATTATTATTT
Found at i:3389825 original size:23 final size:23
Alignment explanation
Indices: 3389799--3389864 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 23
3389789 TTTAAATTCA
3389799 AAATATAAAAATATTCAAAAATT
1 AAATATAAAAATATTCAAAAATT
*
3389822 AAATATAATAATA-TCAAAAA-T
1 AAATATAAAAATATTCAAAAATT
* * *
3389843 AAAAATTAAATTATTCAAAAAT
1 AAATATAAAAATATTCAAAAAT
3389865 ATTATTTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 10 0.28
22 14 0.39
23 12 0.33
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATATAAAAATATTCAAAAATT
Found at i:3390070 original size:15 final size:15
Alignment explanation
Indices: 3390050--3390087 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3390040 TACAAAAAGT
3390050 AAAATT-TAAAATTTA
1 AAAATTATAAAA-TTA
*
3390065 AAAATTATGAAATTA
1 AAAATTATAAAATTA
3390080 AAAATTAT
1 AAAATTAT
3390088 TTATAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
AAAATTATAAAATTA
Found at i:3397874 original size:17 final size:16
Alignment explanation
Indices: 3397854--3397896 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3397844 TAACTACGAG
*
3397854 AATTAAACAAATGACTA
1 AATTAAACAAAT-ACAA
*
3397871 AATTGAAATAAATACAA
1 AATT-AAACAAATACAA
3397888 AATTAAACA
1 AATTAAACA
3397897 TACAATTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 11 0.50
18 7 0.32
ACGTcount: A:0.63, C:0.09, G:0.05, T:0.23
Consensus pattern (16 bp):
AATTAAACAAATACAA
Found at i:3397895 original size:34 final size:36
Alignment explanation
Indices: 3397830--3397896 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 36
3397820 AATGTTTAGA
* * *
3397830 GACTAAATATTAAATAACTACGAGAATTAAACAAAT
1 GACTAAATATGAAATAAATACGAAAATTAAACAAAT
3397866 GACTAAAT-TGAAATAAATAC-AAAATTAAACA
1 GACTAAATATGAAATAAATACGAAAATTAAACA
3397897 TACAATTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 10 0.36
35 10 0.36
36 8 0.29
ACGTcount: A:0.58, C:0.10, G:0.07, T:0.24
Consensus pattern (36 bp):
GACTAAATATGAAATAAATACGAAAATTAAACAAAT
Found at i:3398123 original size:117 final size:117
Alignment explanation
Indices: 3397989--3398208 Score: 440
Period size: 117 Copynumber: 1.9 Consensus size: 117
3397979 TAGTATTAAA
3397989 ACATAAAAATGGTAAATAAAAAATAAAGATAAAAATTCAAATTAATTAAGAAAATAACATAAAAT
1 ACATAAAAATGGTAAATAAAAAATAAAGATAAAAATTCAAATTAATTAAGAAAATAACATAAAAT
3398054 TGGTGACCAAATTGTAATCCTAAAAGAGGTACGGTGGATAGAGGGATACCTT
66 TGGTGACCAAATTGTAATCCTAAAAGAGGTACGGTGGATAGAGGGATACCTT
3398106 ACATAAAAATGGTAAATAAAAAATAAAGATAAAAATTCAAATTAATTAAGAAAATAACATAAAAT
1 ACATAAAAATGGTAAATAAAAAATAAAGATAAAAATTCAAATTAATTAAGAAAATAACATAAAAT
3398171 TGGTGACCAAATTGTAATCCTAAAAGAGGTACGGTGGA
66 TGGTGACCAAATTGTAATCCTAAAAGAGGTACGGTGGA
3398209 CATGGAAGGG
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 103 1.00
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.24
Consensus pattern (117 bp):
ACATAAAAATGGTAAATAAAAAATAAAGATAAAAATTCAAATTAATTAAGAAAATAACATAAAAT
TGGTGACCAAATTGTAATCCTAAAAGAGGTACGGTGGATAGAGGGATACCTT
Found at i:3414244 original size:16 final size:17
Alignment explanation
Indices: 3414219--3414257 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
3414209 AATAATATAT
*
3414219 ATTTAGTTTTTTA-TTA
1 ATTTATTTTTTTATTTA
3414235 ATTTATTTTTTTATTTA
1 ATTTATTTTTTTATTTA
3414252 ATTTAT
1 ATTTAT
3414258 ATAATCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
ATTTATTTTTTTATTTA
Found at i:3414268 original size:25 final size:23
Alignment explanation
Indices: 3414238--3414299 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 23
3414228 TTTATTAATT
3414238 TATTTTTTTATTTAA-TTT-ATA
1 TATTTTTTTATTTAATTTTCATA
3414259 TAATCTTTTTATATTTTAATTTTCATA
1 T-AT-TTTTT-TA-TTTAATTTTCATA
3414286 TATTTTTTTTATTT
1 TA-TTTTTTTATTT
3414300 TTTTTAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
21 1 0.03
22 2 0.06
23 5 0.15
24 5 0.15
25 7 0.21
26 9 0.26
27 5 0.15
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (23 bp):
TATTTTTTTATTTAATTTTCATA
Found at i:3414300 original size:25 final size:25
Alignment explanation
Indices: 3414240--3414300 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
3414230 TATTAATTTA
3414240 TTTTTTTA-TTTAATTTATATAATC
1 TTTTTTTATTTTAATTTATATAATC
*
3414264 TTTTTATATTTTAATTT-TCATATAT-
1 TTTTTTTATTTTAATTTAT-ATA-ATC
3414289 TTTTTTTATTTT
1 TTTTTTTATTTT
3414301 TTTTAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 8 0.25
25 22 0.69
26 2 0.06
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTTTTATTTTAATTTATATAATC
Found at i:3417065 original size:18 final size:18
Alignment explanation
Indices: 3417042--3417080 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3417032 AGGAAAGGGA
3417042 AGTTAATCTTCCCTGTTT
1 AGTTAATCTTCCCTGTTT
3417060 AGTTAATCTTCCCTGTTT
1 AGTTAATCTTCCCTGTTT
3417078 AGT
1 AGT
3417081 GAATGTAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.49
Consensus pattern (18 bp):
AGTTAATCTTCCCTGTTT
Found at i:3418855 original size:24 final size:24
Alignment explanation
Indices: 3418778--3418860 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
3418768 AGGGTGTCGG
*
3418778 GATAAAGACAATGACTGAGGCTGC
1 GATAAAGACAATGACTGAGGCTGA
** * *
3418802 GA-ATTG-CGATGACGGAGGCTGA
1 GATAAAGACAATGACTGAGGCTGA
*
3418824 GATGAAGACAATGACTGAGGCT-A
1 GATAAAGACAATGACTGAGGCTGA
*
3418847 GGATAAAGAGAATG
1 -GATAAAGACAATG
3418861 CTAATTCTGA
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
22 15 0.34
23 4 0.09
24 25 0.57
ACGTcount: A:0.37, C:0.12, G:0.34, T:0.17
Consensus pattern (24 bp):
GATAAAGACAATGACTGAGGCTGA
Found at i:3430866 original size:12 final size:12
Alignment explanation
Indices: 3430841--3430899 Score: 73
Period size: 12 Copynumber: 4.9 Consensus size: 12
3430831 TCATTTCATT
* *
3430841 TTATTACTAGTA
1 TTATTAATATTA
*
3430853 TTATTAAAATTA
1 TTATTAATATTA
3430865 TTATTAATATTA
1 TTATTAATATTA
*
3430877 ATATTAATATTA
1 TTATTAATATTA
*
3430889 TTATTATTATT
1 TTATTAATATT
3430900 TAATAAATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATTAATATTA
Found at i:3430867 original size:3 final size:3
Alignment explanation
Indices: 3430841--3430899 Score: 55
Period size: 3 Copynumber: 19.7 Consensus size: 3
3430831 TCATTTCATT
* * ** * * *
3430841 TTA TTA CTA GTA TTA TTA AAA TTA TTA TTA ATA TTA ATA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3430889 TTA TTA TTA TT
1 TTA TTA TTA TT
3430900 TAATAAATAA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:3431116 original size:26 final size:26
Alignment explanation
Indices: 3431030--3431096 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
3431020 AGCTCCCAAT
*
3431030 CGCCGCTGCTTCCAGAATATCTCAGC
1 CGCCGCTGCTTCCAAAATATCTCAGC
3431056 CGCCGCTGCTTCCAAAATATCTCAGC
1 CGCCGCTGCTTCCAAAATATCTCAGC
3431082 CGCCGCTGCTTCCAA
1 CGCCGCTGCTTCCAA
3431097 GGGATTCCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.19, C:0.40, G:0.18, T:0.22
Consensus pattern (26 bp):
CGCCGCTGCTTCCAAAATATCTCAGC
Found at i:3433107 original size:30 final size:30
Alignment explanation
Indices: 3433060--3433158 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 30
3433050 AATTAAAAAT
* * *
3433060 TAATATATTTAATATATAATTCTTTCTTTTCA
1 TAATAT-TTTTATATATAATT-ATTATTTTCA
* *
3433092 -AATTTTTTTATATATACTTATTATTTTCA
1 TAATATTTTTATATATAATTATTATTTTCA
*
3433121 TAATATTTTTATATAT-ATTATT-TTAT--
1 TAATATTTTTATATATAATTATTATTTTCA
3433147 TAATATTTTTAT
1 TAATATTTTTAT
3433159 TTTATTTTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
26 12 0.21
28 3 0.05
29 13 0.22
30 26 0.45
31 4 0.07
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (30 bp):
TAATATTTTTATATATAATTATTATTTTCA
Found at i:3435826 original size:21 final size:21
Alignment explanation
Indices: 3435800--3435840 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3435790 GACTATCGCA
3435800 TTGCGATTTTCCAAATTCACG
1 TTGCGATTTTCCAAATTCACG
*
3435821 TTGCGATTTTCCTAATTCAC
1 TTGCGATTTTCCAAATTCAC
3435841 AATGCGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCACG
Found at i:3435846 original size:21 final size:21
Alignment explanation
Indices: 3435801--3435847 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3435791 ACTATCGCAT
**
3435801 TGCGATTTTCCAAATTCACGT
1 TGCGATTTTCCAAATTCACAA
*
3435822 TGCGATTTTCCTAATTCACAA
1 TGCGATTTTCCAAATTCACAA
3435843 TGCGA
1 TGCGA
3435848 AAACATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (21 bp):
TGCGATTTTCCAAATTCACAA
Found at i:3435865 original size:20 final size:20
Alignment explanation
Indices: 3435840--3435929 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
3435830 TCCTAATTCA
* *
3435840 CAATGCGAAAACATAAATCG
1 CAATGCGAATACGTAAATCG
3435860 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
3435880 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
3435900 CAATGTGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
3435920 CAACGCGAAT
1 CAATGCGAAT
3435930 CTGACTATCG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:3436063 original size:20 final size:20
Alignment explanation
Indices: 3435916--3436062 Score: 231
Period size: 20 Copynumber: 7.3 Consensus size: 20
3435906 GAATACGTAA
*
3435916 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
3435936 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
3435956 ATCGCAATGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
3435976 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
3435996 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
3436016 ATCGCAACATGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
3436036 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
3436056 ATCGCAA
1 ATCGCAA
3436063 TACTAAATTT
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 116 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:3436248 original size:22 final size:22
Alignment explanation
Indices: 3436220--3436275 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
3436210 CTCTCTTCGG
3436220 CGACATCCGTTCCTATATCCAA
1 CGACATCCGTTCCTATATCCAA
3436242 CGACATCCGTTCCTATATCCAA
1 CGACATCCGTTCCTATATCCAA
3436264 CGACATCC-TTCC
1 CGACATCCGTTCC
3436276 CCATCCGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.25, C:0.39, G:0.09, T:0.27
Consensus pattern (22 bp):
CGACATCCGTTCCTATATCCAA
Found at i:3436954 original size:24 final size:24
Alignment explanation
Indices: 3436927--3436979 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
3436917 GTATTCGAAA
*
3436927 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCAGAC
*
3436951 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACTCAGAC
3436975 TTTGA
1 TTTGA
3436980 GGATTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCAGAC
Found at i:3437192 original size:15 final size:14
Alignment explanation
Indices: 3437174--3437209 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
3437164 GAAAAAGAAG
3437174 AAGAAGAAATCCCCA
1 AAGAA-AAATCCCCA
*
3437189 AAGAAAAGTCCCCA
1 AAGAAAAATCCCCA
3437203 AAGAAAA
1 AAGAAAA
3437210 TACCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.58, C:0.22, G:0.14, T:0.06
Consensus pattern (14 bp):
AAGAAAAATCCCCA
Found at i:3439440 original size:34 final size:34
Alignment explanation
Indices: 3439397--3439525 Score: 120
Period size: 34 Copynumber: 3.7 Consensus size: 34
3439387 GACATTCATT
3439397 TGACTATCGCAACGCGGA-AATCGCAACGCGAATA
1 TGACTATCGCAACGCGGAGAATCGCAACGCGAA-A
*
3439431 TGACTATCGCAACACGGAAATGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGG--A-GA--ATCGCAACGC-GAAA
* *
3439471 TGACTATCGCAACG-AGAGAATCGCAATGCGAAA
1 TGACTATCGCAACGCGGAGAATCGCAACGCGAAA
** *
3439504 TGAAAATCGCAACG-AGAGAATC
1 TGACTATCGCAACGCGGAGAATC
3439526 ACAGTGCAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 15
0.80 0.06 0.15
Matches are distributed among these distances:
33 24 0.29
34 25 0.30
36 3 0.04
37 1 0.01
38 1 0.01
39 1 0.01
40 24 0.29
41 3 0.04
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15
Consensus pattern (34 bp):
TGACTATCGCAACGCGGAGAATCGCAACGCGAAA
Found at i:3439441 original size:20 final size:20
Alignment explanation
Indices: 3439416--3439484 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
3439406 CAACGCGGAA
3439416 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
3439436 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
3439456 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
3439476 ATCGCAACG
1 ATCGCAACG
3439485 AGAGAATCGC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 43 0.93
21 3 0.07
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:3439544 original size:34 final size:33
Alignment explanation
Indices: 3439476--3439549 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
3439466 GGAAATGACT
* *
3439476 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCACAATGCAAAATGAAA
*
3439509 ATCGCAACGAGAGAATCACAGTGCAAAAATGAAA
1 ATCGCAACGAGAGAATCACAATGC-AAAATGAAA
3439543 ATCGCAA
1 ATCGCAA
3439550 TGCGAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 22 0.59
34 15 0.41
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCACAATGCAAAATGAAA
Found at i:3439623 original size:33 final size:33
Alignment explanation
Indices: 3439568--3439661 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
3439558 TAGTTTTGCG
3439568 TTGCGATTTTCATTTTCGCATTGCGATTCTCTCA
1 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCA
*
3439602 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCA
** *
3439635 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTT-CGCATTGCGAT
3439662 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 33 0.60
34 22 0.40
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCA
Found at i:3439786 original size:14 final size:14
Alignment explanation
Indices: 3439767--3439803 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3439757 CATCAATTAA
3439767 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3439781 ACAAATCATCTTTT
1 ACAAATCAACATTT
3439795 ACAAATCAA
1 ACAAATCAA
3439804 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3441240 original size:21 final size:21
Alignment explanation
Indices: 3441185--3441291 Score: 99
Period size: 21 Copynumber: 5.1 Consensus size: 21
3441175 TCTAGAATGT
* *
3441185 TGGGAGGGACCTCTTCAACGA
1 TGGGAGGGGCCTCTTGAACGA
** *
3441206 TGACAGTGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
* **
3441227 TGGGAGGGGACTCTTGAGGGA
1 TGGGAGGGGCCTCTTGAACGA
**
3441248 TGATAGGGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
*
3441269 TAGGG-GAGGCCTCTTGAACGA
1 T-GGGAGGGGCCTCTTGAACGA
3441290 TG
1 TG
3441292 ACAGGTGAGT
Statistics
Matches: 66, Mismatches: 19, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
20 1 0.02
21 64 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.21
Consensus pattern (21 bp):
TGGGAGGGGCCTCTTGAACGA
Found at i:3441250 original size:42 final size:42
Alignment explanation
Indices: 3441186--3441296 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
3441176 CTAGAATGTT
* *
3441186 GGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGAT-G
1 GGGA-GGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
* ** *
3441229 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAG
1 GG-GAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
*
3441272 GGGAGGCCTCTTGAACGATGACAGG
1 GGGAGGACTCTTGAACGATGACAGG
3441297 TGAGTCGGAC
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
42 46 0.84
43 8 0.15
44 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.20
Consensus pattern (42 bp):
GGGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
Found at i:3441802 original size:20 final size:20
Alignment explanation
Indices: 3441776--3441844 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
3441766 GAAACTTAAA
**
3441776 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAATTTGACT
* *
3441796 ATTGCAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
3441816 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
3441836 ATCGCAACG
1 ATCGCAACG
3441845 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:3441970 original size:87 final size:87
Alignment explanation
Indices: 3441857--3442022 Score: 251
Period size: 87 Copynumber: 1.9 Consensus size: 87
3441847 AGAATCGCAA
* * * *
3441857 TGCGATTTTCATTTTGCATTGTGATTCTTTCATTACGATAGTCAAATTCGTATTGCGATAGTCAT
1 TGCGATTTTCATTTAGCATTGCGATTCTCTCATTACGATAGTCAAATTCGCATTGCGATAGTCAT
*
3441922 TTTCGCGTTGCGATTTTGTTGT
66 TTTCGCATTGCGATTTTGTTGT
* ** *
3441944 TGCGATTTTCATTTAGCATTGCGATTCTCTCATTGCGATAGTCATTTTCGCGTTGCGATAGTCAT
1 TGCGATTTTCATTTAGCATTGCGATTCTCTCATTACGATAGTCAAATTCGCATTGCGATAGTCAT
3442009 TTTCGCATTGCGAT
66 TTTCGCATTGCGAT
3442023 AGTAAACTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.45
Consensus pattern (87 bp):
TGCGATTTTCATTTAGCATTGCGATTCTCTCATTACGATAGTCAAATTCGCATTGCGATAGTCAT
TTTCGCATTGCGATTTTGTTGT
Found at i:3441989 original size:33 final size:33
Alignment explanation
Indices: 3441908--3441990 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 33
3441898 TCAAATTCGT
* * * * *
3441908 ATTGCGATAGTCATTTTCGCGTTGCGATTTTGTT
1 ATTGCGATAGTCA-TTTAGCATTGCGATTCTCTC
* **
3441942 GTTGCGATTTTCATTTAGCATTGCGATTCTCTC
1 ATTGCGATAGTCATTTAGCATTGCGATTCTCTC
3441975 ATTGCGATAGTCATTT
1 ATTGCGATAGTCATTT
3441991 TCGCGTTGCG
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
33 28 0.74
34 10 0.26
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (33 bp):
ATTGCGATAGTCATTTAGCATTGCGATTCTCTC
Found at i:3442001 original size:20 final size:20
Alignment explanation
Indices: 3441974--3442025 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3441964 GCGATTCTCT
3441974 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
3441994 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
3442014 CATTGCGATAGT
1 CATTGCGATAGT
3442026 AAACTATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:3443923 original size:20 final size:20
Alignment explanation
Indices: 3443908--3443950 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3443898 TTAAAATCTT
*
3443908 AACACGAAAATGAAAATCGC
1 AACACAAAAATGAAAATCGC
**
3443928 AACACAAAAATGACTATCGC
1 AACACAAAAATGAAAATCGC
3443948 AAC
1 AAC
3443951 GCAAGAATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.23, G:0.12, T:0.12
Consensus pattern (20 bp):
AACACAAAAATGAAAATCGC
Found at i:3444383 original size:22 final size:22
Alignment explanation
Indices: 3444333--3444386 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
3444323 ATTTCGCCGA
* *
3444333 AGATGGAGACTGATATCGTCGG
1 AGATGGGGACTGATATCATCGG
* *
3444355 AGATGGGGATTGATTTCATCGG
1 AGATGGGGACTGATATCATCGG
3444377 AGATGGGGAC
1 AGATGGGGAC
3444387 GGATGTCGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.39, T:0.24
Consensus pattern (22 bp):
AGATGGGGACTGATATCATCGG
Found at i:3444607 original size:20 final size:20
Alignment explanation
Indices: 3444584--3444796 Score: 354
Period size: 20 Copynumber: 10.7 Consensus size: 20
3444574 CGATAGTCAG
*
3444584 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3444604 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
3444624 ATTCACATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
3444644 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3444664 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3444684 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
3444704 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
3444724 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
3444744 ATTCGCATTACGATTTACAT
1 ATTCGCATTGCGATTTACGT
* *
3444764 ATTCTCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
3444784 ATTCGCATTGCGA
1 ATTCGCATTGCGA
3444797 ATTAGGAAAA
Statistics
Matches: 179, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 179 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:3444817 original size:21 final size:21
Alignment explanation
Indices: 3444793--3444833 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3444783 TATTCGCATT
3444793 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
3444814 GCGAATTTGGAAAATTGCAA
1 GCGAATTAGGAAAATCGCAA
3444834 TGCAATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:3453775 original size:54 final size:53
Alignment explanation
Indices: 3453624--3453778 Score: 175
Period size: 54 Copynumber: 2.9 Consensus size: 53
3453614 AGAAATCTGT
* * * * *
3453624 GCAGAAACCACAGAAAATGATGAATGTGTTGTCAAATGCTTTATGAACATCTGG
1 GCAGAAGCCACAGAAAA-GATGAATGTGTTATCAAATGCTTTACGAAAATCCGG
* * *
3453678 CCAGAAGCCACAAGAAAGGATGAATGTGTTATCAAAAGCTTTACGAAAATCCGG
1 GCAGAAGCCAC-AGAAAAGATGAATGTGTTATCAAATGCTTTACGAAAATCCGG
* * * *
3453732 GCAGAAGCCACGAGAAAAGATGAATGTATTTTCACATGTTTTACGAA
1 GCAGAAGCCAC-AGAAAAGATGAATGTGTTATCAAATGCTTTACGAA
3453779 CCAGTGATTA
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
54 79 0.94
55 5 0.06
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (53 bp):
GCAGAAGCCACAGAAAAGATGAATGTGTTATCAAATGCTTTACGAAAATCCGG
Found at i:3454200 original size:22 final size:21
Alignment explanation
Indices: 3454146--3454185 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3454136 TATCTACACT
3454146 CTTCAAAGATGATAAATTCAC
1 CTTCAAAGATGATAAATTCAC
3454167 CTTCAAAGATGATAAATTC
1 CTTCAAAGATGATAAATTC
3454186 TCTTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.30
Consensus pattern (21 bp):
CTTCAAAGATGATAAATTCAC
Found at i:3455046 original size:73 final size:74
Alignment explanation
Indices: 3454869--3455785 Score: 1250
Period size: 74 Copynumber: 12.4 Consensus size: 74
3454859 CTATCTCCCA
* * *
3454869 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
1 CATCTGTAAGACCTACAGTGCATGATG-TTTC-AAAAAGCCTTCGGGAGCTTTTTGAT-ATTTTA
* *
3454934 AAGCCTCTGGGA
63 AAGCCTCCGGGT
*
3454946 CATCTGTAAGACCTACATTGCATGATG-TTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTAAAG
3455010 CCTCCGGGT
66 CCTCCGGGT
* *
3455019 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAG-TTTTTGATATTTTTAA
1 CATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTCGGGAGCTTTTTGATA-TTTTAA
3455083 AGCCTCCGGGT
64 AGCCTCCGGGT
* * *
3455094 CATCTGTAAGACCTACAGTGAATTATGTTT-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTCGGGAGCTTTTTGAT-ATTTTAAA
3455158 GCCTCCGGGT
65 GCCTCCGGGT
* * * * *
3455168 CAT-TCATAAGCCCTACGGTGTAAGATGTTTTCAAAAAGCCTTCGGGAG-TTTTTGAT-TTTTAA
1 CATCT-GTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTAA
3455230 AGCCTCCGGGT
64 AGCCTCCGGGT
*
3455241 CATCTGTAAGACCTACAGTGCATGATG-TTCAAAAAGCCTTCGGGAGCTTTTTGATATTTCAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTAAAG
3455305 CCTCCGGGT
66 CCTCCGGGT
*
3455314 CATCTGTAAGACCTACAGTGCATGATG-TTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTCGGGAGCTTTTTGAT-ATTTTAAA
3455378 GCCTCCGGGT
65 GCCTCCGGGT
** * * *
3455388 CATCCATAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTAT-TTTTAAA
1 CATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTAAA
3455452 GCCTCCGGGT
65 GCCTCCGGGT
*
3455462 CATCTGTAAGACCTACAGTGCATGATG-TTCAAAAAAGCCTTC-GGAGCTTTTTGATA-TTCAAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTC-AAAAAGCCTTCGGGAGCTTTTTGATATTTTAAA
3455524 GCCTCCGGGT
65 GCCTCCGGGT
* * *
3455534 CATATGTAAGACCTACAGTGCATGATGTTTTCAAAAAAGCTTTCGGGAGCTTTTTTA-ATTTTAA
1 CATCTGTAAGACCTACAGTGCATGATG-TTTC-AAAAAGCCTTCGGGAGCTTTTTGATATTTTAA
*
3455598 AGCCTCTGGGT
64 AGCCTCCGGGT
* *
3455609 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTCGGGAGCTTTTTGAT-ATTTTAA
*
3455674 AGCCTCCGAGT
64 AGCCTCCGGGT
** * * *
3455685 CATCCATAAGCCCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGATTTTTGATA-TTTAAA
1 CATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTAAA
*
3455749 GCCTTCGGGT
65 GCCTCCGGGT
*
3455759 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
3455786 ATAAGACTTC
Statistics
Matches: 754, Mismatches: 64, Indels: 47
0.87 0.07 0.05
Matches are distributed among these distances:
71 19 0.03
72 64 0.08
73 175 0.23
74 234 0.31
75 129 0.17
76 109 0.14
77 24 0.03
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (74 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTAAAG
CCTCCGGGT
Found at i:3455368 original size:220 final size:224
Alignment explanation
Indices: 3454869--3455785 Score: 1326
Period size: 220 Copynumber: 4.1 Consensus size: 224
3454859 CTATCTCCCA
* *
3454869 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
1 CATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
* * * *
3454934 AAGCCTCTGGGACATCTGTAAGACCTACATTGCATGATG--TTCAAAAAGCCTTCGGGAGCTTTT
65 AAGCCTCCGGGTCATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
*
3454997 TGATATTTTAAAGCCTCCGGGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTC
130 TGAT-TTTTAAAGCCTCCGGGTCATCCGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTC
*
3455062 GGGAG-TTTTTGATATTTTTAAAGCCTCCGGGT
193 GGGAGCTTTTTGATA-TTTCAAAGCCTCCGGGT
* *
3455094 CATCTGTAAGACCTACAGTGAATTATGTTT--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
* * * *
3455157 AGCCTCCGGGTCAT-TCATAAGCCCTACGGTGTAAGATGTTTTCAAAAAGCCTTCGGGAG-TTTT
66 AGCCTCCGGGTCATCT-ATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
*
3455220 TGATTTTTAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCATGATG-TTCAAAAAGCCTTCGG
130 TGATTTTTAAAGCCTCCGGGTCATCCGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTCGG
3455284 GAGCTTTTTGATATTTCAAAGCCTCCGGGT
195 GAGCTTTTTGATATTTCAAAGCCTCCGGGT
3455314 CATCTGTAAGACCTACAGTGCATGATG-TTC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
* * *
3455377 AGCCTCCGGGTCATCCATAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTCCGGGTCATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTT
* *
3455442 TATTTTTAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCATGATG-TTCAAAAAAGCCTTC-G
131 GATTTTTAAAGCCTCCGGGTCATCCGTAAGACCTACAGTGCATGATGTTTC-AAAAAGCCTTCGG
3455505 GAGCTTTTTGATA-TTCAAAGCCTCCGGGT
195 GAGCTTTTTGATATTTCAAAGCCTCCGGGT
* * **
3455534 CATATGTAAGACCTACAGTGCATGATGTTTTCAAAAAAGCTTTCGGGAGCTTTTT--TAATTTTA
1 CATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
* * *
3455597 AAGCCTCTGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTT
65 AAGCCTCCGGGTCATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
* * *
3455662 TGATGTTTTTAAAGCCTCCGAGTCATCCATAAGCCCTACAGTGCATGATGTTTTCAAAAAGCCTT
130 TGA--TTTTTAAAGCCTCCGGGTCATCCGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTT
* * *
3455727 TGGGAGATTTTTGATATTT-AAAGCCTTCGGGT
192 CGGGAGCTTTTTGATATTTCAAAGCCTCCGGGT
*
3455759 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
3455786 ATAAGACTTC
Statistics
Matches: 632, Mismatches: 43, Indels: 34
0.89 0.06 0.05
Matches are distributed among these distances:
219 2 0.00
220 188 0.30
221 145 0.23
222 117 0.19
223 70 0.11
224 32 0.05
225 76 0.12
226 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (224 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
AGCCTCCGGGTCATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTT
GATTTTTAAAGCCTCCGGGTCATCCGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTCGGG
AGCTTTTTGATATTTCAAAGCCTCCGGGT
Found at i:3455968 original size:3 final size:3
Alignment explanation
Indices: 3455962--3456012 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
3455952 TCATTTCATT
**
3455962 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA -TA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
3456007 TTA TTA
1 TTA TTA
3456013 ATAAATAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:3457464 original size:18 final size:20
Alignment explanation
Indices: 3457430--3457469 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
3457420 ATTAGTCATA
*
3457430 TAAATATATATATATTTGTT
1 TAAATATATATATATTTATT
3457450 TAAATA-ATA-ATATTTATT
1 TAAATATATATATATTTATT
3457468 TA
1 TA
3457470 TTTTTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TAAATATATATATATTTATT
Found at i:3457471 original size:26 final size:25
Alignment explanation
Indices: 3457432--3457480 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
3457422 TAGTCATATA
*
3457432 AATATATATATATTTGTTTAAATAAT
1 AATATATATATATTT-TTCAAATAAT
* *
3457458 AATATTTATTTATTTTTCAAATA
1 AATATATATATATTTTTCAAATA
3457481 TTCAGAAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
AATATATATATATTTTTCAAATAAT
Found at i:3459380 original size:20 final size:20
Alignment explanation
Indices: 3459317--3459380 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
3459307 TATATATATG
*
3459317 AAATGT-TTTTAAGTTAATTA
1 AAATGTGTTTTAAGTT-TTTA
* * *
3459337 AAACGTGTTTAAAGTGTTTA
1 AAATGTGTTTTAAGTTTTTA
*
3459357 AAATGTGTTTTAAGTTTTTT
1 AAATGTGTTTTAAGTTTTTA
3459377 AAAT
1 AAAT
3459381 ATGAAAAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 28 0.80
21 7 0.20
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (20 bp):
AAATGTGTTTTAAGTTTTTA
Found at i:3459473 original size:19 final size:20
Alignment explanation
Indices: 3459449--3459503 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
3459439 TATTGTTCAT
3459449 AGTTTAGAAACTTT-GTAAG
1 AGTTTAGAAACTTTAGTAAG
*
3459468 AGTTTAGAAACTTTTATTAAG
1 AGTTTAGAAAC-TTTAGTAAG
*
3459489 AGTTTTGAAACTTTA
1 AGTTTAGAAACTTTA
3459504 CAAAAGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 11 0.34
20 7 0.22
21 14 0.44
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.42
Consensus pattern (20 bp):
AGTTTAGAAACTTTAGTAAG
Found at i:3461357 original size:14 final size:14
Alignment explanation
Indices: 3461334--3461398 Score: 69
Period size: 14 Copynumber: 4.7 Consensus size: 14
3461324 TGGGCTAAAT
* *
3461334 ATAAATGAACGCAC
1 ATAAACGAACGAAC
*
3461348 ATAAACGAACTAAC
1 ATAAACGAACGAAC
*
3461362 ATAAA-GAATGAAC
1 ATAAACGAACGAAC
* *
3461375 ATAAATGAGCGAAC
1 ATAAACGAACGAAC
3461389 ATAAACGAAC
1 ATAAACGAAC
3461399 ATATTACCTA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
13 11 0.27
14 30 0.73
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.14
Consensus pattern (14 bp):
ATAAACGAACGAAC
Found at i:3462547 original size:23 final size:23
Alignment explanation
Indices: 3462460--3462549 Score: 81
Period size: 23 Copynumber: 3.9 Consensus size: 23
3462450 CATATAAATT
* * *
3462460 AACATCAAACGAACAGGTTCATG
1 AACATTAAACGAACATGTTCGTG
** * *
3462483 AACGCTAAATGAACATGTTTGTG
1 AACATTAAACGAACATGTTCGTG
* * *
3462506 GACATATAAATGAATATGTTCGTG
1 AACAT-TAAACGAACATGTTCGTG
3462530 AACATTAAACGAACATGTTC
1 AACATTAAACGAACATGTTC
3462550 ACGAACAATA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
23 31 0.61
24 20 0.39
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (23 bp):
AACATTAAACGAACATGTTCGTG
Found at i:3462555 original size:23 final size:23
Alignment explanation
Indices: 3462460--3462561 Score: 78
Period size: 23 Copynumber: 4.4 Consensus size: 23
3462450 CATATAAATT
* *
3462460 AACATCAAACGAACAGGTTCATG
1 AACATTAAACGAACATGTTCATG
** * **
3462483 AACGCTAAATGAACATGTTTGTG
1 AACATTAAACGAACATGTTCATG
* * * *
3462506 GACATATAAATGAATATGTTCGTG
1 AACAT-TAAACGAACATGTTCATG
*
3462530 AACATTAAACGAACATGTTCACG
1 AACATTAAACGAACATGTTCATG
*
3462553 AACAATAAA
1 AACATTAAA
3462562 TAAACGAATA
Statistics
Matches: 60, Mismatches: 18, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
23 40 0.67
24 20 0.33
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.25
Consensus pattern (23 bp):
AACATTAAACGAACATGTTCATG
Found at i:3470145 original size:37 final size:37
Alignment explanation
Indices: 3470095--3470166 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
3470085 TAGTCCTCCA
3470095 ATCCGGAGATGTCATGTGTCACTATATGATTGGAGTG
1 ATCCGGAGATGTCATGTGTCACTATATGATTGGAGTG
3470132 ATCCGGAGATGTCATGTGTCACTATATGATTGGAG
1 ATCCGGAGATGTCATGTGTCACTATATGATTGGAG
3470167 GGTGAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (37 bp):
ATCCGGAGATGTCATGTGTCACTATATGATTGGAGTG
Found at i:3470591 original size:17 final size:18
Alignment explanation
Indices: 3470552--3470596 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
3470542 ACTAAACTTT
*
3470552 TTTAAATGATTAATTAAG
1 TTTAAATTATTAATTAAG
*
3470570 TTTAAATTATTAATT-TG
1 TTTAAATTATTAATTAAG
3470587 TTTAAATTAT
1 TTTAAATTAT
3470597 CCTTCAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (18 bp):
TTTAAATTATTAATTAAG
Found at i:3477398 original size:45 final size:45
Alignment explanation
Indices: 3477348--3477435 Score: 176
Period size: 45 Copynumber: 2.0 Consensus size: 45
3477338 CGATGTATTG
3477348 TGAAGCTCCAATGGAAGGCGAGCACACCCGGGGGATCAAGGAAGT
1 TGAAGCTCCAATGGAAGGCGAGCACACCCGGGGGATCAAGGAAGT
3477393 TGAAGCTCCAATGGAAGGCGAGCACACCCGGGGGATCAAGGAA
1 TGAAGCTCCAATGGAAGGCGAGCACACCCGGGGGATCAAGGAA
3477436 AGGAATCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.23, G:0.35, T:0.10
Consensus pattern (45 bp):
TGAAGCTCCAATGGAAGGCGAGCACACCCGGGGGATCAAGGAAGT
Found at i:3481026 original size:17 final size:17
Alignment explanation
Indices: 3480996--3481028 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3480986 TCAAATCTCT
3480996 TAGTTTTATATTCTTTA
1 TAGTTTTATATTCTTTA
3481013 TAGTCTTTAT-TTCTTT
1 TAGT-TTTATATTCTTT
3481029 GTCAAGACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.67
Consensus pattern (17 bp):
TAGTTTTATATTCTTTA
Found at i:3487101 original size:27 final size:27
Alignment explanation
Indices: 3487068--3487123 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3487058 GCCCTCTTAA
3487068 CTGCCACTTATTTGATTAATCGTCTTC
1 CTGCCACTTATTTGATTAATCGTCTTC
3487095 CTGCCACTTATTTGATTAATCGTCTTC
1 CTGCCACTTATTTGATTAATCGTCTTC
3487122 CT
1 CT
3487124 AGCAAACCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.27, G:0.11, T:0.45
Consensus pattern (27 bp):
CTGCCACTTATTTGATTAATCGTCTTC
Found at i:3490995 original size:21 final size:22
Alignment explanation
Indices: 3490949--3490995 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
3490939 TTTTGTTTCT
*
3490949 TTGTTTAGGCAATCTTTTGTAA
1 TTGTTTAGGCAATCTTATGTAA
*
3490971 -TGTTT-GGTAATCTTATGTAA
1 TTGTTTAGGCAATCTTATGTAA
3490991 TTGTT
1 TTGTT
3490996 GGTTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.53
Consensus pattern (22 bp):
TTGTTTAGGCAATCTTATGTAA
Found at i:3508904 original size:25 final size:27
Alignment explanation
Indices: 3508845--3508894 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
3508835 TGAGGGGGGT
*
3508845 GAGCAGCTGTGGCAGTGGTCCCCTCCA
1 GAGCAGCTGTGGCAGTGATCCCCTCCA
3508872 GAGCAGCTG-GGCA-TGATCCCCTC
1 GAGCAGCTGTGGCAGTGATCCCCTC
3508895 ATGGGCAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 4 0.18
27 9 0.41
ACGTcount: A:0.16, C:0.34, G:0.32, T:0.18
Consensus pattern (27 bp):
GAGCAGCTGTGGCAGTGATCCCCTCCA
Found at i:3520603 original size:24 final size:24
Alignment explanation
Indices: 3520575--3520627 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
3520565 AAACTGATAG
3520575 TTTAAGTACTAAATGCGTTAAGTT
1 TTTAAGTACTAAATGCGTTAAGTT
3520599 TTTAAGTACTAAATGCGTTAAGTT
1 TTTAAGTACTAAATGCGTTAAGTT
3520623 TTTAA
1 TTTAA
3520628 CGGTGGGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (24 bp):
TTTAAGTACTAAATGCGTTAAGTT
Found at i:3526097 original size:21 final size:20
Alignment explanation
Indices: 3526012--3526168 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
3526002 AATGACCAAT
** *
3526012 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
3526031 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
3526051 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
3526071 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
3526092 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
3526113 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
3526134 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
3526154 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
3526169 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:3526197 original size:20 final size:20
Alignment explanation
Indices: 3526135--3526327 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
3526125 CGATTTTCCA
* ** *
3526135 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
3526155 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
3526175 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3526195 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
3526215 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
3526235 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3526255 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3526275 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
3526295 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
3526315 AAATCGCAACGCG
1 AAATCGCAACGCG
3526328 ATATTTAAAG
Statistics
Matches: 148, Mismatches: 21, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 144 0.97
21 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3526499 original size:22 final size:22
Alignment explanation
Indices: 3526474--3526528 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
3526464 CTCTCTACGG
*
3526474 CGAAGAAATCTGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
* **
3526496 CGAATATTTCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
3526518 CGGCGAAATCC
1 CGAAGAAATCC
3526529 CTCACAACCA
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.24
Consensus pattern (22 bp):
CGAAGAAATCCGTCCCCATCTC
Found at i:3526842 original size:20 final size:20
Alignment explanation
Indices: 3526816--3526873 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 20
3526806 TTTGCAGAAG
*
3526816 AGTCGCAACGAGAGAATGAT
1 AGTCGCAACGAGAGAATGAA
*
3526836 TGTCGCAACGAGAGAAATGAA
1 AGTCGCAACGAGAG-AATGAA
*
3526857 AATCGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
3526874 CGCAACGCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.43, C:0.16, G:0.28, T:0.14
Consensus pattern (20 bp):
AGTCGCAACGAGAGAATGAA
Found at i:3526876 original size:14 final size:14
Alignment explanation
Indices: 3526857--3526913 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3526847 GAGAAATGAA
3526857 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3526871 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3526890 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3526904 AATCGCAACG
1 AATCGCAACG
3526914 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3526889 original size:33 final size:33
Alignment explanation
Indices: 3526849--3526929 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
3526839 CGCAACGAGA
3526849 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3526882 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
3526915 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
3526930 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3526947 original size:19 final size:19
Alignment explanation
Indices: 3526925--3527022 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
3526915 GAAACCAAAA
*
3526925 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3526944 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3526958 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3526977 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
3526991 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
3527010 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3527023 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:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3526966 original size:14 final size:14
Alignment explanation
Indices: 3526947--3527036 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
3526937 TTTCATTTCG
3526947 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3526961 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3526980 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3526994 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
3527013 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3527027 CGTTGCGATT
1 CGTTGCGATT
3527037 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3526972 original size:33 final size:33
Alignment explanation
Indices: 3526930--3527044 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
3526920 CAAAATCGCA
3526930 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3526963 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
3526996 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3527029 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3527045 AACCCAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3529010 original size:19 final size:19
Alignment explanation
Indices: 3528970--3529098 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3528960 TAGTTTACTT
* *
3528970 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3528990 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3529009 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3529028 TCGCAA--CG-AA--AGAA
1 TCGCAACGCGAAACCAAAA
3529042 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
3529061 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
3529075 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3529094 TCGCA
1 TCGCA
3529099 TTGCGATTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 19 0.21
15 1 0.01
16 6 0.07
17 6 0.07
18 1 0.01
19 45 0.49
20 13 0.14
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3529044 original size:33 final size:34
Alignment explanation
Indices: 3529007--3529098 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 34
3528997 GCGAAACCAA
**
3529007 AATCGCAACGCGAAATGAAAATCGCAACGA-AAG
1 AATCGCAACGCGAAACCAAAATCGCAACGACAAG
3529040 AATCGCAACGCGAAACCAAAATCGCAACGACAAG
1 AATCGCAACGCGAAACCAAAATCGCAACGACAAG
3529074 -ATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAACCAAAATCGCA
3529099 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 53 0.95
34 3 0.05
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.08
Consensus pattern (34 bp):
AATCGCAACGCGAAACCAAAATCGCAACGACAAG
Found at i:3529096 original size:52 final size:52
Alignment explanation
Indices: 3528970--3529098 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
3528960 TAGTTTACTT
**
3528970 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACGAAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* *
3529022 T-G-AAAATCGCAACGAAAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAACGAAA-AATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
* *
3529075 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACGAAAAATCGCA
3529099 TTGCGATTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
50 3 0.05
51 8 0.13
52 39 0.62
53 5 0.08
54 6 0.10
55 2 0.03
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACGAAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:3529135 original size:14 final size:14
Alignment explanation
Indices: 3529116--3529172 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3529106 TTTCATTTCG
3529116 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
3529130 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
3529147 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
3529163 CGTTGCGATT
1 CGTTGCGATT
3529173 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3529141 original size:33 final size:33
Alignment explanation
Indices: 3529099--3529228 Score: 161
Period size: 33 Copynumber: 3.8 Consensus size: 33
3529089 CAAAATCGCA
3529099 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
** *
3529132 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
3529165 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC-TTT--CG
* *
3529203 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
3529229 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
33 53 0.64
35 3 0.04
36 2 0.02
38 13 0.16
39 12 0.14
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:3529225 original size:20 final size:19
Alignment explanation
Indices: 3529094--3529228 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
3529084 GAAACCAAAA
*
3529094 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3529113 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
**
3529129 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3529146 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3529162 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3529179 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3529198 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3529218 TCGTGTTGCGA
1 TCGCGTTGCGA
3529229 AAGTAAACTA
Statistics
Matches: 98, Mismatches: 7, Indels: 21
0.78 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 10 0.10
17 10 0.10
19 50 0.51
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3531158 original size:14 final size:14
Alignment explanation
Indices: 3531139--3531174 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3531129 ATTGTTTAAT
3531139 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3531153 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3531167 TGATTTGT
1 TGATTTGT
3531175 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:3531293 original size:19 final size:19
Alignment explanation
Indices: 3531277--3531374 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
3531267 AAAAATGACT
3531277 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3531296 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3531315 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3531329 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3531348 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3531368 ATCGCAA
1 ATCGCAA
3531375 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3531406 original size:53 final size:53
Alignment explanation
Indices: 3531277--3531393 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
3531267 AAAAATGACT
3531277 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
3531329 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
3531382 ATCGCAATGCGA
1 ATCGCAATGCGA
3531394 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:3531411 original size:19 final size:19
Alignment explanation
Indices: 3531383--3531585 Score: 212
Period size: 19 Copynumber: 11.7 Consensus size: 19
3531373 AACGAGAGAA
*
3531383 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3531402 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3531421 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
3531437 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3531454 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3531473 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
3531489 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3531506 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
3531522 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
3531539 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
3531557 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
3531573 TCGCATTGCGATT
1 TCGCATTGCGATT
3531586 CTCTCGTTGC
Statistics
Matches: 154, Mismatches: 9, Indels: 42
0.75 0.04 0.20
Matches are distributed among these distances:
14 33 0.21
16 19 0.12
17 16 0.10
18 3 0.02
19 72 0.47
20 11 0.07
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3531446 original size:52 final size:52
Alignment explanation
Indices: 3531389--3531599 Score: 262
Period size: 52 Copynumber: 4.1 Consensus size: 52
3531379 AGAATCGCAA
3531389 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
3531441 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
3531493 TGCGATTTTCATTTCGCATTGCGATTTTC---TCG--TTGCGATTTTTATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA---TTATCT-CG--T
* *
3531546 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
3531593 TGCGATT
1 TGCGATT
3531600 GTAATTCCGT
Statistics
Matches: 142, Mismatches: 6, Indels: 27
0.81 0.03 0.15
Matches are distributed among these distances:
47 14 0.10
48 10 0.07
49 5 0.04
50 9 0.06
51 6 0.04
52 80 0.56
53 18 0.13
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
Found at i:3531496 original size:33 final size:33
Alignment explanation
Indices: 3531459--3531599 Score: 221
Period size: 33 Copynumber: 4.2 Consensus size: 33
3531449 TCATTTCGCA
3531459 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
3531492 TTGCGATTTTCATTTCGCATTGCGATTTTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
3531525 TTGCGATTTTTATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
3531559 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
3531592 TTGCGATT
1 TTGCGATT
3531600 GTAATTCCGT
Statistics
Matches: 99, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
32 1 0.01
33 68 0.69
34 29 0.29
35 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:3533899 original size:12 final size:12
Alignment explanation
Indices: 3533882--3533906 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3533872 TCTTCGGGGA
3533882 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3533894 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3533906 C
1 C
3533907 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:3534115 original size:24 final size:24
Alignment explanation
Indices: 3534081--3534127 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3534071 CTGAAACATC
3534081 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3534105 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3534128 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:3534863 original size:20 final size:20
Alignment explanation
Indices: 3534838--3535082 Score: 258
Period size: 20 Copynumber: 12.2 Consensus size: 20
3534828 TGCCCTACCG
* *
3534838 GATTTACAGATTCTCGTTGC
1 GATTTACGGATTCGCGTTGC
**
3534858 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
**
3534878 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
* *
3534898 GATTTACAGATTCTCGTTGC
1 GATTTACGGATTCGCGTTGC
**
3534918 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
*
3534938 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
* * *
3534958 GATATACGGATACGCATTGC
1 GATTTACGGATTCGCGTTGC
** *
3534978 GATTTACCCATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
* *
3534998 GATTTACGGATACACGTTGC
1 GATTTACGGATTCGCGTTGC
*
3535018 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
*
3535038 GATTTATGTG-TTCGCGTTGC
1 GATTTACG-GATTCGCGTTGC
* **
3535058 GATTTTCATATTCGCGTTGC
1 GATTTACGGATTCGCGTTGC
3535078 GATTT
1 GATTT
3535083 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GATTTACGGATTCGCGTTGC
Found at i:3535099 original size:21 final size:21
Alignment explanation
Indices: 3535069--3535151 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
3535059 ATTTTCATAT
*
3535069 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
3535090 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3535111 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
* *
3535132 TCACGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3535152 CTGATTTGCG
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3536466 original size:21 final size:21
Alignment explanation
Indices: 3536430--3536493 Score: 51
Period size: 23 Copynumber: 3.0 Consensus size: 21
3536420 TATCTAAAGT
*
3536430 ATATTTTAT-TAT-ATTTTTA
1 ATATTTTATATTTAATTTTTA
3536449 ATATTTTATATTTAATTTATTTA
1 ATATTTTATATTTAA-TT-TTTA
* *
3536472 ATAATTTACTTAATTAATTTTT
1 ATATTTTA--TATTTAATTTTT
3536494 TTACAGATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 9 0.25
20 2 0.06
21 1 0.03
22 2 0.06
23 14 0.39
24 2 0.06
25 6 0.17
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATTTTATATTTAATTTTTA
Found at i:3537080 original size:11 final size:11
Alignment explanation
Indices: 3537061--3537156 Score: 50
Period size: 11 Copynumber: 8.0 Consensus size: 11
3537051 ACACCAACGC
*
3537061 TAAACAAATAT
1 TAAATAAATAT
*
3537072 TAAATAAATAC
1 TAAATAAATAT
*
3537083 TAAACAAATAT
1 TAAATAAATAT
3537094 TAAATGAACATATTCAT
1 TAAAT--A-A-A-T-AT
*
3537111 TAAACAAATAT
1 TAAATAAATAT
3537122 TAAATGAACATAT
1 TAAAT-AA-ATAT
* *
3537135 T-CAGAAATAT
1 TAAATAAATAT
3537145 ATAAATAAATAT
1 -TAAATAAATAT
3537157 ATTCACGAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
10 4 0.06
11 31 0.48
12 11 0.17
13 7 0.11
14 2 0.03
15 2 0.03
16 1 0.02
17 6 0.09
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.30
Consensus pattern (11 bp):
TAAATAAATAT
Found at i:3537103 original size:15 final size:15
Alignment explanation
Indices: 3537085--3537131 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
3537075 ATAAATACTA
3537085 AACAAATATTAAATG
1 AACAAATATTAAATG
* * *
3537100 AAC--ATATTCATTA
1 AACAAATATTAAATG
3537113 AACAAATATTAAATG
1 AACAAATATTAAATG
3537128 AACA
1 AACA
3537132 TATTCAGAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
13 10 0.42
15 14 0.58
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.28
Consensus pattern (15 bp):
AACAAATATTAAATG
Found at i:3537115 original size:28 final size:27
Alignment explanation
Indices: 3537061--3537137 Score: 110
Period size: 28 Copynumber: 3.0 Consensus size: 27
3537051 ACACCAACGC
3537061 TAAACAAATATTAAAT-AA-ATA--C-
1 TAAACAAATATTAAATGAACATATTCA
3537083 TAAACAAATATTAAATGAACATATTCA
1 TAAACAAATATTAAATGAACATATTCA
3537110 TTAAACAAATATTAAATGAACATATTCA
1 -TAAACAAATATTAAATGAACATATTCA
3537138 GAAATATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
22 16 0.33
23 2 0.04
24 3 0.06
26 1 0.02
28 27 0.55
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (27 bp):
TAAACAAATATTAAATGAACATATTCA
Found at i:3537158 original size:24 final size:24
Alignment explanation
Indices: 3537116--3537170 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
3537106 TTCATTAAAC
*
3537116 AAATATTAAATGAACATATTCA-G
1 AAATATTAAATAAACATATTCACG
*
3537139 AAATATATAAATAAATATATTCACG
1 AAATAT-TAAATAAACATATTCACG
3537164 AACATAT
1 AA-ATAT
3537171 CTATTAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 6 0.22
24 14 0.52
25 3 0.11
26 4 0.15
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (24 bp):
AAATATTAAATAAACATATTCACG
Done.