Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold114
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: 3219552
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 36736 characters in sequence are not A, C, G, or T
File 12 of 13
Found at i:2988174 original size:2 final size:2
Alignment explanation
Indices: 2988167--2988192 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2988157 TTTGTAAGGC
2988167 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
2988193 TTTCGGGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2989773 original size:2 final size:2
Alignment explanation
Indices: 2989766--2989816 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2989756 CTTTGAAAAG
2989766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2989808 AT AT AT AT A
1 AT AT AT AT A
2989817 AAGACTTACT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3001655 original size:28 final size:28
Alignment explanation
Indices: 3001613--3001670 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
3001603 GCTATGAGTT
3001613 CAATTAAGGCTACAGGATCAGCAAATAA
1 CAATTAAGGCTACAGGATCAGCAAATAA
*
3001641 CAATTAAGG-TAACAGGATTAGCAAATAA
1 CAATTAAGGCT-ACAGGATCAGCAAATAA
3001669 CA
1 CA
3001671 TGGTAAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.19
Consensus pattern (28 bp):
CAATTAAGGCTACAGGATCAGCAAATAA
Found at i:3002829 original size:35 final size:35
Alignment explanation
Indices: 3002789--3002856 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
3002779 CGAAATAATC
3002789 ATTTTCTGTTATAACAAACAAATATGATTTCATTA
1 ATTTTCTGTTATAACAAACAAATATGATTTCATTA
* *
3002824 ATTTTCTGTTATAACGAACAGATATGATTTCAT
1 ATTTTCTGTTATAACAAACAAATATGATTTCAT
3002857 AATGAATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.43
Consensus pattern (35 bp):
ATTTTCTGTTATAACAAACAAATATGATTTCATTA
Found at i:3004846 original size:4 final size:4
Alignment explanation
Indices: 3004837--3004866 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
3004827 TCCTTTAACT
*
3004837 TAGA TAGA TATA TAGA TAGA TAGA TAGA TA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
3004867 TAGGTATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (4 bp):
TAGA
Found at i:3017156 original size:25 final size:25
Alignment explanation
Indices: 3017128--3017175 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
3017118 ATGCACATTG
3017128 ATTTTTCTTAACTCCCAATTTTTTT
1 ATTTTTCTTAACTCCCAATTTTTTT
3017153 ATTTTTCTTAACTCCCAATTTTT
1 ATTTTTCTTAACTCCCAATTTTT
3017176 CCCCACTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTTTTCTTAACTCCCAATTTTTTT
Found at i:3027765 original size:3 final size:3
Alignment explanation
Indices: 3027757--3027793 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3027747 TGAAATTCAA
*
3027757 TAT TAT TAT TCT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3027794 GTAGTTTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3029650 original size:17 final size:17
Alignment explanation
Indices: 3029630--3029681 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
3029620 TTTTTAATGT
3029630 TTATGCATTTCAACTGA
1 TTATGCATTTCAACTGA
*
3029647 TTAT-C-CTTCATA-T-A
1 TTATGCATTTCA-ACTGA
3029661 TTATGCATTTCAACTGA
1 TTATGCATTTCAACTGA
3029678 TTAT
1 TTAT
3029682 CTTTCTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
14 5 0.18
15 7 0.25
16 7 0.25
17 9 0.32
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (17 bp):
TTATGCATTTCAACTGA
Found at i:3029665 original size:31 final size:31
Alignment explanation
Indices: 3029630--3029692 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
3029620 TTTTTAATGT
3029630 TTATGCATTTCAACTGATTATCCTTCATATA
1 TTATGCATTTCAACTGATTATCCTTCATATA
* *
3029661 TTATGCATTTCAACTGATTATCTTTCTTATA
1 TTATGCATTTCAACTGATTATCCTTCATATA
3029692 T
1 T
3029693 ACCTTCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.49
Consensus pattern (31 bp):
TTATGCATTTCAACTGATTATCCTTCATATA
Found at i:3034818 original size:6 final size:6
Alignment explanation
Indices: 3034807--3034833 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3034797 GAATGTAATA
3034807 TATGTG TATGTG TATGTG TATGTG TAT
1 TATGTG TATGTG TATGTG TATGTG TAT
3034834 ATATATGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.52
Consensus pattern (6 bp):
TATGTG
Found at i:3035442 original size:16 final size:18
Alignment explanation
Indices: 3035411--3035452 Score: 70
Period size: 16 Copynumber: 2.4 Consensus size: 18
3035401 GCCTACATAC
3035411 ATATATCATATAATATAA
1 ATATATCATATAATATAA
3035429 ATATAT-ATAT-ATATAA
1 ATATATCATATAATATAA
3035445 ATATATCA
1 ATATATCA
3035453 CTCAAAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.52
17 5 0.22
18 6 0.26
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATCATATAATATAA
Found at i:3037630 original size:16 final size:17
Alignment explanation
Indices: 3037609--3037646 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3037599 TAATATGATA
3037609 TAATTC-CA-TTTCATCT
1 TAATTCTCATTTTCAT-T
3037625 TAATTCTCATTTTCATT
1 TAATTCTCATTTTCATT
3037642 TAATT
1 TAATT
3037647 ATATCCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 8 0.40
18 6 0.30
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.55
Consensus pattern (17 bp):
TAATTCTCATTTTCATT
Found at i:3038369 original size:3 final size:3
Alignment explanation
Indices: 3038351--3038411 Score: 104
Period size: 3 Copynumber: 20.0 Consensus size: 3
3038341 ATCCAATAAT
*
3038351 TTC TAC TTC TTCC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3038397 TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC
3038412 ATCCTTACAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:3038880 original size:2 final size:2
Alignment explanation
Indices: 3038873--3038902 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3038863 AAGAGGACTG
*
3038873 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3038903 CCATGTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3039371 original size:2 final size:2
Alignment explanation
Indices: 3039358--3039391 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
3039348 AAAATTTAAT
3039358 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
3039392 GTATGGCGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3041000 original size:2 final size:2
Alignment explanation
Indices: 3040995--3041019 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3040985 TTATATATAT
3040995 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
3041020 TATATACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3049962 original size:24 final size:24
Alignment explanation
Indices: 3049935--3049991 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
3049925 AATTATTTAA
3049935 AGAAATCTTCACTGTATCACTGGT
1 AGAAATCTTCACTGTATCACTGGT
3049959 AGAAATCATT-ACTGTATCACTGGT
1 AGAAATC-TTCACTGTATCACTGGT
3049983 A-AAAT-TTCA
1 AGAAATCTTCA
3049992 TATTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.06
22 1 0.03
23 4 0.13
24 22 0.71
25 2 0.06
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (24 bp):
AGAAATCTTCACTGTATCACTGGT
Found at i:3050942 original size:15 final size:16
Alignment explanation
Indices: 3050924--3050957 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3050914 TGGTATGTGC
3050924 TATTTTA-ATATGATT
1 TATTTTACATATGATT
*
3050939 TATTTTACATCTGATT
1 TATTTTACATATGATT
3050955 TAT
1 TAT
3050958 GTAATTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (16 bp):
TATTTTACATATGATT
Found at i:3058603 original size:19 final size:20
Alignment explanation
Indices: 3058553--3058596 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
3058543 TTATATTTAA
*
3058553 ATTTAAATA-AAAATATATT
1 ATTTTAATATAAAATATATT
3058572 ATTTTAATATAAAA-ATATT
1 ATTTTAATATAAAATATATT
3058591 ATTTTA
1 ATTTTA
3058597 GATTAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTTAATATAAAATATATT
Found at i:3059522 original size:2 final size:2
Alignment explanation
Indices: 3059515--3059550 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3059505 GTAGGTCTGG
*
3059515 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3059551 ATCCGCATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3061558 original size:2 final size:2
Alignment explanation
Indices: 3061553--3061578 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3061543 TTTGCATTGC
3061553 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3061579 GCACTGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3061864 original size:2 final size:2
Alignment explanation
Indices: 3061857--3061890 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3061847 AAAGGAGGGG
3061857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3061891 AAAATATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3062915 original size:3 final size:3
Alignment explanation
Indices: 3062907--3062968 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
3062897 AGTTTCTACA
* *
3062907 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT CCT TCT TCA
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
3062955 TCT TGT TCT TCT TC
1 TCT TCT TCT TCT TC
3062969 AGCTTCAGCT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.02, C:0.34, G:0.02, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:3062988 original size:6 final size:6
Alignment explanation
Indices: 3062905--3063001 Score: 50
Period size: 6 Copynumber: 15.7 Consensus size: 6
3062895 TCAGTTTCTA
* * * * * * * *
3062905 CATCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTC CTTCTT
1 CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT
* * * * *
3062953 CATCTTGTT CTTCTT CAGCTT CAGCTT CATCTT CATCAT CATCAT CATC
1 CATC---TT CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT CATC
3063002 CGATGCGTCG
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
6 74 0.94
9 5 0.06
ACGTcount: A:0.10, C:0.34, G:0.03, T:0.53
Consensus pattern (6 bp):
CATCTT
Found at i:3064128 original size:5 final size:5
Alignment explanation
Indices: 3064118--3064143 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3064108 AGTGAAAGGG
3064118 AACAC AACAC AACAC AACAC AACAC A
1 AACAC AACAC AACAC AACAC AACAC A
3064144 CAAATGGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAC
Found at i:3064282 original size:3 final size:3
Alignment explanation
Indices: 3064274--3064310 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3064264 TTTTTCACAT
3064274 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3064311 GCTTCTACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3065741 original size:2 final size:2
Alignment explanation
Indices: 3065734--3065768 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3065724 CACGACTCAG
3065734 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3065769 TTATTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3067395 original size:16 final size:16
Alignment explanation
Indices: 3067374--3067412 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3067364 GATTTATTGA
3067374 TAAATAAGTA-TTTTTT
1 TAAATAA-TACTTTTTT
3067390 TAAATAATACTTTTTT
1 TAAATAATACTTTTTT
3067406 T-AATAAT
1 TAAATAAT
3067413 CTCGACTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (16 bp):
TAAATAATACTTTTTT
Found at i:3067405 original size:15 final size:15
Alignment explanation
Indices: 3067374--3067412 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3067364 GATTTATTGA
*
3067374 TAAATAAGTATTTTTT
1 TAAATAA-TACTTTTT
3067390 TAAATAATACTTTTT
1 TAAATAATACTTTTT
*
3067405 TTAATAAT
1 TAAATAAT
3067413 CTCGACTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (15 bp):
TAAATAATACTTTTT
Found at i:3069161 original size:2 final size:2
Alignment explanation
Indices: 3069154--3069193 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3069144 ATTATGTTTC
*
3069154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3069194 ATTTGACATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3070035 original size:2 final size:2
Alignment explanation
Indices: 3070028--3070067 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3070018 TTGCCAATTT
3070028 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
3070068 CACATATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3072745 original size:2 final size:2
Alignment explanation
Indices: 3072738--3072773 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3072728 AAACAAGTGA
3072738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3072774 GGGTTAAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3073816 original size:15 final size:15
Alignment explanation
Indices: 3073792--3073822 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3073782 TTTTGTGACC
*
3073792 AAAAAGAAAATTAAA
1 AAAAAAAAAATTAAA
3073807 AAAAAAAAAATTAAA
1 AAAAAAAAAATTAAA
3073822 A
1 A
3073823 GGCTTGCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAAAAAAAATTAAA
Found at i:3076929 original size:2 final size:2
Alignment explanation
Indices: 3076922--3076952 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3076912 GAAATAATCT
3076922 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 T
3076953 CATTCGTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3077809 original size:14 final size:14
Alignment explanation
Indices: 3077790--3077820 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3077780 ATTTTAATGG
*
3077790 ATACATATATATAT
1 ATACATATATACAT
3077804 ATACATATATACAT
1 ATACATATATACAT
3077818 ATA
1 ATA
3077821 TAAATGCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (14 bp):
ATACATATATACAT
Found at i:3077811 original size:8 final size:8
Alignment explanation
Indices: 3077790--3077822 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
3077780 ATTTTAATGG
3077790 ATACATAT
1 ATACATAT
3077798 AT--ATAT
1 ATACATAT
3077804 ATACATAT
1 ATACATAT
3077812 ATACATAT
1 ATACATAT
3077820 ATA
1 ATA
3077823 AATGCTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.26
8 17 0.74
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (8 bp):
ATACATAT
Found at i:3083912 original size:39 final size:39
Alignment explanation
Indices: 3083857--3083935 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
3083847 CATTAAATAG
3083857 TTGTTTGTTTGAATCTTTTCAGTGTGAAAGGCCTGCTGA
1 TTGTTTGTTTGAATCTTTTCAGTGTGAAAGGCCTGCTGA
*
3083896 TTGTTTGTTTGCATCTTTTCAGTGTGAAAGGCCTGCTGA
1 TTGTTTGTTTGAATCTTTTCAGTGTGAAAGGCCTGCTGA
3083935 T
1 T
3083936 AAATAAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.16, C:0.14, G:0.25, T:0.44
Consensus pattern (39 bp):
TTGTTTGTTTGAATCTTTTCAGTGTGAAAGGCCTGCTGA
Found at i:3088665 original size:2 final size:2
Alignment explanation
Indices: 3088658--3088700 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3088648 AGGTTTGGAT
3088658 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3088700 T
1 T
3088701 ATATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3088705 original size:2 final size:2
Alignment explanation
Indices: 3088700--3088742 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3088690 TCTCTCTCTC
3088700 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
3088742 T
1 T
3088743 CAGTTGAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3089694 original size:2 final size:2
Alignment explanation
Indices: 3089687--3089714 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3089677 TGATAAATGA
3089687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3089715 TCCCTCCCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3093975 original size:67 final size:67
Alignment explanation
Indices: 3093864--3093995 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 67
3093854 TGATTTACAC
* *
3093864 GATATAGTACTTGTATGATACTGGATCCTGCTTCACCCAAGGCAACTATAATAAGAAGTTGATTG
1 GATATAGTACTTGTATAAAACTGGATCCTGCTTCACCCAAGGCAACTATAATAAGAAGTTGATTG
3093929 AT
66 AT
** * *
3093931 GATATAGTACTTGTATAAAACTGGATCCTGCTTCAGGCATGGCAACTATTATAAGAAGTTGATTG
1 GATATAGTACTTGTATAAAACTGGATCCTGCTTCACCCAAGGCAACTATAATAAGAAGTTGATTG
3093996 CTTTGGGCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (67 bp):
GATATAGTACTTGTATAAAACTGGATCCTGCTTCACCCAAGGCAACTATAATAAGAAGTTGATTG
AT
Found at i:3094863 original size:5 final size:5
Alignment explanation
Indices: 3094853--3094877 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3094843 CATACATCCA
3094853 TTCTC TTCTC TTCTC TTCTC TTCTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC
3094878 GTGTCCACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TTCTC
Found at i:3097577 original size:2 final size:2
Alignment explanation
Indices: 3097570--3097605 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3097560 CTGTCGCCTC
3097570 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
3097606 TTCAAATTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3098598 original size:2 final size:2
Alignment explanation
Indices: 3098591--3098631 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3098581 TTGTGTTTTC
3098591 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3098632 CACACACACA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3101452 original size:2 final size:2
Alignment explanation
Indices: 3101445--3101486 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3101435 TTTGTGTTGA
3101445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3101487 TCATTCTCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3106488 original size:15 final size:15
Alignment explanation
Indices: 3106468--3106499 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3106458 TAAGAATTAA
*
3106468 TATTTTTTATTTTTT
1 TATTTTTTAATTTTT
3106483 TATTTTTTAATTTTT
1 TATTTTTTAATTTTT
3106498 TA
1 TA
3106500 AATTGTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TATTTTTTAATTTTT
Found at i:3107076 original size:5 final size:5
Alignment explanation
Indices: 3107068--3107092 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3107058 AACACAACAT
3107068 AACCA AACCA AACCA AACCA AACCA
1 AACCA AACCA AACCA AACCA AACCA
3107093 TTGGCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCA
Found at i:3112144 original size:16 final size:16
Alignment explanation
Indices: 3112104--3112147 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
3112094 TATTTTTAGA
*
3112104 TTTAAATTATTTAGAT
1 TTTAAATTATTTAAAT
** *
3112120 TACATATTATTTAAAT
1 TTTAAATTATTTAAAT
3112136 TTTAAATTATTT
1 TTTAAATTATTT
3112148 TAGGCTTAAT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (16 bp):
TTTAAATTATTTAAAT
Found at i:3133317 original size:2 final size:2
Alignment explanation
Indices: 3133310--3133363 Score: 78
Period size: 2 Copynumber: 28.0 Consensus size: 2
3133300 GAGGAACGTT
3133310 TA TA TA TA -A T- TA GTA TA T- 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
3133350 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
3133364 AATAACCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.06
2 43 0.90
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3133773 original size:3 final size:3
Alignment explanation
Indices: 3133765--3133798 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3133755 ACTAATGAAT
3133765 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3133799 TTTGAACCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3133943 original size:2 final size:2
Alignment explanation
Indices: 3133936--3133970 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3133926 GCCAATTTTG
3133936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3133971 GTGAGGACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3134125 original size:2 final size:2
Alignment explanation
Indices: 3134118--3134157 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3134108 ACGTTCACAA
3134118 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3134158 TCAATGACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3134455 original size:5 final size:5
Alignment explanation
Indices: 3134445--3134469 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3134435 AATTAGAGAG
3134445 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
3134470 CAATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:3134479 original size:2 final size:2
Alignment explanation
Indices: 3134472--3134500 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3134462 AATAAAATCA
3134472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3134501 GAAGATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3141322 original size:21 final size:21
Alignment explanation
Indices: 3141298--3141345 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3141288 GTTGTATTTT
3141298 TTTCATCCAAAAAATGCATTC-
1 TTTCATCCAAAAAATGCA-TCA
**
3141319 TTTCATCCAACCAATGCATCA
1 TTTCATCCAAAAAATGCATCA
3141340 TTTCAT
1 TTTCAT
3141346 TTAAAGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (21 bp):
TTTCATCCAAAAAATGCATCA
Found at i:3144700 original size:21 final size:22
Alignment explanation
Indices: 3144651--3144692 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3144641 TTTTGTTATT
*
3144651 AAAAATTATATTTTTTTCATCC
1 AAAAAATATATTTTTTTCATCC
3144673 AAAAAATATA-TTTTTTCATC
1 AAAAAATATATTTTTTTCATC
3144693 TAATAAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAAAATATATTTTTTTCATCC
Found at i:3144852 original size:2 final size:2
Alignment explanation
Indices: 3144845--3144878 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3144835 TGGGGCTTAC
3144845 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3144879 TTTACTTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3146220 original size:24 final size:24
Alignment explanation
Indices: 3146170--3146220 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
3146160 ATTTTTAAAA
*
3146170 ATAAAAATATTAATAATTGATAAT
1 ATAAAAATATTAATAAATGATAAT
* *
3146194 ATAAAAATA-TATTAAATGTTAAGT
1 ATAAAAATATTAATAAATGATAA-T
3146218 ATA
1 ATA
3146221 TATTTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATAAAAATATTAATAAATGATAAT
Found at i:3146543 original size:2 final size:2
Alignment explanation
Indices: 3146538--3146563 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3146528 GCGCGCGCTC
3146538 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3146564 GATGTGCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3146959 original size:2 final size:2
Alignment explanation
Indices: 3146952--3146976 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3146942 ACCACTGGAG
3146952 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3146977 GTTATTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3147421 original size:18 final size:17
Alignment explanation
Indices: 3147390--3147448 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
3147380 TAAAAATTTT
* *
3147390 ATATTACAACTTATTAA
1 ATATTAAAATTTATTAA
3147407 CATATTAAAATTTATATAA
1 -ATATTAAAATTTAT-TAA
3147426 A-ATATAAAATATT-TTAA
1 ATAT-TAAAAT-TTATTAA
3147443 ATATTA
1 ATATTA
3147449 TTATCATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 8 0.23
18 22 0.63
19 5 0.14
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTAAAATTTATTAA
Found at i:3148059 original size:20 final size:20
Alignment explanation
Indices: 3148036--3148073 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3148026 GTATTACTGC
3148036 TTAAAGGGATTCAAATATGT
1 TTAAAGGGATTCAAATATGT
3148056 TTAAAGGGATTCAAATAT
1 TTAAAGGGATTCAAATAT
3148074 CAAGTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.34
Consensus pattern (20 bp):
TTAAAGGGATTCAAATATGT
Found at i:3148740 original size:13 final size:14
Alignment explanation
Indices: 3148713--3148742 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3148703 AGCCGGAATG
3148713 GAAGCTGATGAGCT
1 GAAGCTGATGAGCT
3148727 GAAGCTGA-GAGCT
1 GAAGCTGATGAGCT
3148740 GAA
1 GAA
3148743 ATCTAAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.33, C:0.13, G:0.37, T:0.17
Consensus pattern (14 bp):
GAAGCTGATGAGCT
Found at i:3151356 original size:20 final size:20
Alignment explanation
Indices: 3151324--3151382 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
3151314 TATTAATTAT
*
3151324 TTTATATT-TATAAAAAAAA
1 TTTATATTAAATAAAAAAAA
3151343 TTTATATTAAATAATTAAAAAA
1 TTTATATTAAATAA--AAAAAA
* *
3151365 TATCATATTACATAAAAA
1 T-TTATATTAAATAAAAA
3151383 TATATTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.24
20 4 0.12
21 3 0.09
22 7 0.21
23 11 0.33
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTATATTAAATAAAAAAAA
Found at i:3151372 original size:23 final size:22
Alignment explanation
Indices: 3151337--3151379 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3151327 ATATTTATAA
*
3151337 AAAAAATTTATATTAAATAATT
1 AAAAAATTCATATTAAATAATT
*
3151359 AAAAAATATCATATTACATAA
1 AAAAAAT-TCATATTAAATAA
3151380 AAATATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAAATTCATATTAAATAATT
Found at i:3151400 original size:16 final size:15
Alignment explanation
Indices: 3151351--3151397 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
3151341 AATTTATATT
3151351 AAATA-ATTAAA-AA
1 AAATATATTAAATAA
* *
3151364 ATATCATATTACATAA
1 AAAT-ATATTAAATAA
3151380 AAATATATTAAATAA
1 AAATATATTAAATAA
3151395 AAA
1 AAA
3151398 ATAGTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 3 0.11
14 1 0.04
15 18 0.67
16 5 0.19
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATATTAAATAA
Found at i:3151898 original size:16 final size:17
Alignment explanation
Indices: 3151874--3151919 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
3151864 TTAATACTTA
*
3151874 TATAATATAAAA-TATT
1 TATATTATAAAATTATT
3151890 TATATTATAAAAAATTATT
1 TATATTAT--AAAATTATT
3151909 TAT-TTATAAAA
1 TATATTATAAAA
3151920 GTTTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 11 0.42
18 8 0.31
19 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATATTATAAAATTATT
Found at i:3151915 original size:18 final size:18
Alignment explanation
Indices: 3151866--3151919 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
3151856 AAATCCCATT
* * *
3151866 AATACTTATATAATATAA
1 AATATTTATATTATAAAA
3151884 AATATTTATATTATAAAA
1 AATATTTATATTATAAAA
3151902 AATTATTTAT-TTATAAAA
1 AA-TATTTATATTATAAAA
3151920 GTTTATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 25 0.78
19 7 0.22
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATTTATATTATAAAA
Found at i:3151930 original size:18 final size:18
Alignment explanation
Indices: 3151879--3151930 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
3151869 ACTTATATAA
*
3151879 TATAAAATATT-TATA-T
1 TATAAAAAATTATATATT
*
3151895 TATAAAAAATTATTTATT
1 TATAAAAAATTATATATT
**
3151913 TATAAAAGTTTATATATT
1 TATAAAAAATTATATATT
3151931 GAACGTAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 10 0.34
17 3 0.10
18 16 0.55
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TATAAAAAATTATATATT
Found at i:3152372 original size:19 final size:22
Alignment explanation
Indices: 3152348--3152387 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
3152338 TATATGTATA
3152348 AATACG-AAA-TATC-TATATC
1 AATACGTAAATTATCATATATC
3152367 AATACGTAAATTATCATATAT
1 AATACGTAAATTATCATATAT
3152388 AGATATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 4 0.22
22 5 0.28
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (22 bp):
AATACGTAAATTATCATATATC
Found at i:3154086 original size:12 final size:12
Alignment explanation
Indices: 3154071--3154137 Score: 57
Period size: 12 Copynumber: 5.5 Consensus size: 12
3154061 ATAGTAAAGA
3154071 TATATATTATTT
1 TATATATTATTT
*
3154083 TATATATTATGT
1 TATATATTATTT
*
3154095 TA-AAATTATTT
1 TATATATTATTT
*
3154106 TAATATATAATATT
1 T-ATATATTAT-TT
*
3154120 TATTTA-TATATT
1 TATATATTAT-TT
3154132 TATATA
1 TATATA
3154138 AAAATGGAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
11 8 0.18
12 24 0.55
13 9 0.20
14 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (12 bp):
TATATATTATTT
Found at i:3154253 original size:22 final size:24
Alignment explanation
Indices: 3154198--3154260 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 24
3154188 CAAGGATATT
3154198 TTTTATTGAATTTAAAATGATTCAAA
1 TTTTATT-AATTT-AAATGATTCAAA
*
3154224 ATTTATTAATTTAAAT-ATT-AAA
1 TTTTATTAATTTAAATGATTCAAA
3154246 TTTTATTAATTTAAA
1 TTTTATTAATTTAAA
3154261 AAAAAATAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 17 0.49
23 3 0.09
24 4 0.11
25 5 0.14
26 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (24 bp):
TTTTATTAATTTAAATGATTCAAA
Found at i:3154267 original size:21 final size:22
Alignment explanation
Indices: 3154221--3154267 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3154211 AAAATGATTC
*
3154221 AAAA-TTTATTAATTTAAATAT
1 AAAATTTTATTAATTTAAATAA
*
3154242 TAAATTTTATTAATTTAAA-AA
1 AAAATTTTATTAATTTAAATAA
3154263 AAAAT
1 AAAAT
3154268 AGTAAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAATTTTATTAATTTAAATAA
Found at i:3154799 original size:37 final size:36
Alignment explanation
Indices: 3154745--3154818 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 36
3154735 GTTATTTTAA
3154745 ATTTTAATTAATTAAATTTAATA-CTTAATTTAATTG
1 ATTTTAATTAATTAAATTTAATATCTTAATTT-ATTG
*
3154781 ATTTTGAATTAATTAAATTTAATATTTTAATTTATTG
1 ATTTT-AATTAATTAAATTTAATATCTTAATTTATTG
3154818 A
1 A
3154819 ATGTGATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
36 5 0.14
37 23 0.66
38 7 0.20
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (36 bp):
ATTTTAATTAATTAAATTTAATATCTTAATTTATTG
Found at i:3155128 original size:2 final size:2
Alignment explanation
Indices: 3155121--3155160 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3155111 ATCCTTTGTT
3155121 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
3155161 AATTGTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3155233 original size:3 final size:3
Alignment explanation
Indices: 3155220--3155266 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
3155210 GGATTTATAT
3155220 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3155266 T
1 T
3155267 GAAATTTAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3160433 original size:3 final size:3
Alignment explanation
Indices: 3160415--3160455 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
3160405 GCGTAGACTG
*
3160415 CTT CTCT CTCT CTT CTT CTT CTT CTT CTT CTT CTC CTT CTT
1 CTT CT-T CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3160456 GCTCTTGCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 28 0.80
4 7 0.20
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:3167859 original size:20 final size:20
Alignment explanation
Indices: 3167831--3167870 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3167821 AATCCGTTTT
* *
3167831 TTTTTTTTTTTAAATTTTAG
1 TTTTATTTTTAAAATTTTAG
3167851 TTTTATTTTTAAAATTTTAG
1 TTTTATTTTTAAAATTTTAG
3167871 AATTTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTATTTTTAAAATTTTAG
Found at i:3167879 original size:20 final size:19
Alignment explanation
Indices: 3167833--3167879 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3167823 TCCGTTTTTT
* *
3167833 TTTTTTTTTAAATTTTAGT
1 TTTTTTTTAAAATTTTAGA
3167852 TTTATTTTTAAAATTTTAGA
1 TTT-TTTTTAAAATTTTAGA
*
3167872 ATTTTTTT
1 TTTTTTTT
3167880 CAACCTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTTTTTTAAAATTTTAGA
Found at i:3168938 original size:12 final size:13
Alignment explanation
Indices: 3168921--3168950 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3168911 TTAATCTAAA
3168921 AAAAAATT-AATT
1 AAAAAATTAAATT
3168933 AAAAAATTAAATT
1 AAAAAATTAAATT
3168946 AAAAA
1 AAAAA
3168951 TAAAACGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAAATTAAATT
Found at i:3168942 original size:28 final size:26
Alignment explanation
Indices: 3168895--3168955 Score: 61
Period size: 29 Copynumber: 2.2 Consensus size: 26
3168885 TTTTAAATTC
* *
3168895 AAAAAATTTT-AAAAGTTTAATCTAAA
1 AAAAAATTTTAAAAAATTAAAT-TAAA
3168921 AAAAAATTAATTAAAAAATTAAATTAAA
1 AAAAAATT--TTAAAAAATTAAATTAAA
3168949 AATAAAA
1 AA-AAAA
3168956 CGTTTCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 8 0.28
28 8 0.28
29 13 0.45
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (26 bp):
AAAAAATTTTAAAAAATTAAATTAAA
Found at i:3170270 original size:32 final size:33
Alignment explanation
Indices: 3170206--3170272 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
3170196 AAGTTAATAT
* *
3170206 TTTTATCTATTAATCTATTTTTATTTTATTTCA
1 TTTTATCCAATAATCTATTTTTATTTTATTTCA
*
3170239 TTTTATCCAATAAT-TATTTCTT-TTTTTTTTCA
1 TTTTATCCAATAATCTATTT-TTATTTTATTTCA
3170271 TT
1 TT
3170273 CAATTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.67
Consensus pattern (33 bp):
TTTTATCCAATAATCTATTTTTATTTTATTTCA
Found at i:3170627 original size:6 final size:6
Alignment explanation
Indices: 3170616--3170650 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3170606 GATGCCAACC
*
3170616 ATTCCA ATTCCA ATTCCA ATTCCG ATTCC- ATTCCA
1 ATTCCA ATTCCA ATTCCA ATTCCA ATTCCA ATTCCA
3170651 TGATCTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (6 bp):
ATTCCA
Found at i:3173176 original size:14 final size:14
Alignment explanation
Indices: 3173159--3173188 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3173149 CATGCACAAT
3173159 AAAAGAAAAAAAGA
1 AAAAGAAAAAAAGA
*
3173173 AAAAGAAAAAGAGA
1 AAAAGAAAAAAAGA
3173187 AA
1 AA
3173189 GAAAACAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAGA
Found at i:3175829 original size:2 final size:2
Alignment explanation
Indices: 3175822--3175879 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
3175812 CAAACTCAAC
*
3175822 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3175864 AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT
3175880 TGCGTTTTGG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3176571 original size:39 final size:39
Alignment explanation
Indices: 3176462--3176578 Score: 110
Period size: 39 Copynumber: 3.0 Consensus size: 39
3176452 GATCACCTAC
* * * * *
3176462 TTCAACTTCACTGCTCAACAATGCTAAGCCAGACCCTAC
1 TTCAAATTCACTGGTTAACAATGCTAAGCCAGACTCTAA
* * *
3176501 TTCAAATTCACTGGTTAAAAATACTAGGCCAGACTCTAA
1 TTCAAATTCACTGGTTAACAATGCTAAGCCAGACTCTAA
* * * *
3176540 TTTAACTTCA-TGGGTTACCAATGCTAAGCCAGAATCTAA
1 TTCAAATTCACT-GGTTAACAATGCTAAGCCAGACTCTAA
3176579 AGTTAGTCCG
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
38 1 0.02
39 61 0.98
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (39 bp):
TTCAAATTCACTGGTTAACAATGCTAAGCCAGACTCTAA
Found at i:3182560 original size:6 final size:6
Alignment explanation
Indices: 3182542--3182575 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3182532 ACCCGTATTG
* *
3182542 CGTGTC AGTGTC CGCGTC CGTGTC CGTGTC CGTG
1 CGTGTC CGTGTC CGTGTC CGTGTC CGTGTC CGTG
3182576 CTTCCTTGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.32, G:0.35, T:0.29
Consensus pattern (6 bp):
CGTGTC
Found at i:3185967 original size:86 final size:86
Alignment explanation
Indices: 3185819--3185992 Score: 339
Period size: 86 Copynumber: 2.0 Consensus size: 86
3185809 TTAATGGTTC
3185819 TGTCAGAACTCTGAAACTTTTGAAAAATATTCTTAAGGGATATGGTATCATTGGTCTCATTGTTA
1 TGTCAGAACTCTGAAACTTTTGAAAAATATTCTTAAGGGATATGGTATCATTGGTCTCATTGTTA
3185884 AGGATAACTTCTTGTTTAATA
66 AGGATAACTTCTTGTTTAATA
*
3185905 TGTCAGAACTCTGAAACTTTTGAAAAATATTCTTAAGGGATATGGTATCATTGGTCTTATTGTTA
1 TGTCAGAACTCTGAAACTTTTGAAAAATATTCTTAAGGGATATGGTATCATTGGTCTCATTGTTA
3185970 AGGATAACTTCTTGTTTAATA
66 AGGATAACTTCTTGTTTAATA
3185991 TG
1 TG
3185993 ATATTTTTCC
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (86 bp):
TGTCAGAACTCTGAAACTTTTGAAAAATATTCTTAAGGGATATGGTATCATTGGTCTCATTGTTA
AGGATAACTTCTTGTTTAATA
Found at i:3187118 original size:2 final size:2
Alignment explanation
Indices: 3187111--3187142 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3187101 CTGTGCATGC
3187111 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
3187143 ATATATATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:3190094 original size:15 final size:15
Alignment explanation
Indices: 3190070--3190124 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
3190060 TTTGGATTAG
3190070 GTTTTAGGGTTTTAA
1 GTTTTAGGGTTTTAA
*
3190085 GTTTTTGGGTTTT-A
1 GTTTTAGGGTTTTAA
* * *
3190099 GATTTA-GGATTTAT
1 GTTTTAGGGTTTTAA
*
3190113 GTTTTAAGGTTT
1 GTTTTAGGGTTT
3190125 AGGTTCTAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 16 0.52
ACGTcount: A:0.18, C:0.00, G:0.25, T:0.56
Consensus pattern (15 bp):
GTTTTAGGGTTTTAA
Found at i:3190387 original size:21 final size:21
Alignment explanation
Indices: 3190363--3190414 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
3190353 AGGTTTTGAA
* *
3190363 TTAGTGTTTAGTGTTTAAGGT
1 TTAGGGTTTAGAGTTTAAGGT
*
3190384 TTAGGGTTTAGAGTTTAAGGA
1 TTAGGGTTTAGAGTTTAAGGT
*
3190405 TTAAGGTTTA
1 TTAGGGTTTA
3190415 AGGCTTAACG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTAGAGTTTAAGGT
Found at i:3190544 original size:18 final size:18
Alignment explanation
Indices: 3190479--3190545 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
3190469 AGTTTTTAGG
3190479 TTTAAGGTTTTAAGG-TTT
1 TTTAAGG-TTTAAGGTTTT
* **
3190497 TTTAAGGTTTAAAATGTAGGT
1 TTTAAGGTTT--AAGGT-TTT
3190518 TTT-AGGTTTAAGGTTTT
1 TTTAAGGTTTAAGGTTTT
3190535 TTTAAGGTTTA
1 TTTAAGGTTTA
3190546 TGGGTTATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
17 7 0.18
18 18 0.47
19 3 0.08
20 6 0.16
21 4 0.11
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.52
Consensus pattern (18 bp):
TTTAAGGTTTAAGGTTTT
Found at i:3190625 original size:7 final size:7
Alignment explanation
Indices: 3190613--3190704 Score: 75
Period size: 7 Copynumber: 13.3 Consensus size: 7
3190603 GGTGTAAAGC
3190613 TTAAGGT
1 TTAAGGT
3190620 TTAAGGT
1 TTAAGGT
*
3190627 TTAAAGT
1 TTAAGGT
3190634 TTAAAGG-
1 TT-AAGGT
3190641 TTAAGGT
1 TTAAGGT
3190648 TTAAAGG-
1 TT-AAGGT
**
3190655 TTAAGAA
1 TTAAGGT
3190662 TTAAGGT
1 TTAAGGT
3190669 TTAAAGG-
1 TT-AAGGT
*
3190676 TTAAAG-
1 TTAAGGT
*
3190682 TTAAAGT
1 TTAAGGT
*
3190689 TTGAGGT
1 TTAAGGT
3190696 TTAAGGT
1 TTAAGGT
3190703 TT
1 TT
3190705 GGGATTTGAG
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
6 16 0.23
7 43 0.61
8 11 0.16
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (7 bp):
TTAAGGT
Found at i:3190631 original size:21 final size:20
Alignment explanation
Indices: 3190607--3190703 Score: 97
Period size: 21 Copynumber: 4.7 Consensus size: 20
3190597 GGCTAGGGTG
*
3190607 TAAAGCTTAAGGTTTAAGGTT
1 TAAAGGTTAAGG-TTAAGGTT
*
3190628 TAAAGTTTAAAGGTTAAGGTT
1 TAAAGGTT-AAGGTTAAGGTT
*
3190649 TAAAGGTTAAGAATTAAGGTT
1 TAAAGGTTAAG-GTTAAGGTT
* *
3190670 TAAAGGTTAAAGTTAAAGTT
1 TAAAGGTTAAGGTTAAGGTT
*
3190690 T-GAGGTTTAAGGTT
1 TAAAGG-TTAAGGTT
3190704 TGGGATTTGA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
19 3 0.05
20 18 0.28
21 40 0.62
22 4 0.06
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (20 bp):
TAAAGGTTAAGGTTAAGGTT
Found at i:3190713 original size:21 final size:21
Alignment explanation
Indices: 3190688--3190786 Score: 60
Period size: 22 Copynumber: 4.7 Consensus size: 21
3190678 AAAGTTAAAG
3190688 TTTGAGGTTTAAGGTTTGGGA
1 TTTGAGGTTTAAGGTTTGGGA
*
3190709 TTTGAGATTT--GGATTTGAGG-
1 TTTGAGGTTTAAGG-TTTG-GGA
* * * *
3190729 TTTGGGGTTGAGGGTTTAGGGT
1 TTTGAGGTTTAAGGTTT-GGGA
* * *
3190751 TTTTAAGTTTTAGGTTTGGAGA
1 TTTGAGGTTTAAGGTTTGG-GA
*
3190773 TTTTAGGTTTAAGG
1 TTTGAGGTTTAAGG
3190787 GTGGGGTTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
19 2 0.03
20 11 0.19
21 18 0.31
22 27 0.47
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.45
Consensus pattern (21 bp):
TTTGAGGTTTAAGGTTTGGGA
Found at i:3190958 original size:21 final size:21
Alignment explanation
Indices: 3190934--3190987 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
3190924 TCAAGGTTTA
*
3190934 AAGTTTAAAATTTATAATTTG
1 AAGTTTAAAATTTAGAATTTG
* **
3190955 AAGTTTAAGATTTAGGGTTTG
1 AAGTTTAAAATTTAGAATTTG
*
3190976 AGGTTTAAAATT
1 AAGTTTAAAATT
3190988 AAAATTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (21 bp):
AAGTTTAAAATTTAGAATTTG
Found at i:3191026 original size:27 final size:27
Alignment explanation
Indices: 3190995--3191284 Score: 76
Period size: 27 Copynumber: 10.4 Consensus size: 27
3190985 ATTAAAATTT
3190995 TTTAAGGTTTAGGGTTAGAGGTTTAGG
1 TTTAAGGTTTAGGGTTAGAGGTTTAGG
* * *
3191022 TTTAAAGTTTAAAGGATTGAGTTTAAGGTTTATG
1 TTTAAGGTTT--AGGGTT-AG----AGGTTTAGG
* * * *
3191056 TTAAAGATTTAGGGTTTAAAGGTTTAAAAG
1 TTTAAGGTTTAGGG-TTAGAGGTTT--AGG
* *
3191086 -TT-AGAGTTTAGGATTTAG-GGTCTAAGG
1 TTTAAG-GTTTAGG-GTTAGAGGT-TTAGG
* *
3191113 TTTAAGGTCTAGGTTTA-AGG-TTAGGG
1 TTTAAGGTTTAGGGTTAGAGGTTTA-GG
* * *
3191139 TCTAAGGTTTAAGGTTTGAGGTTT-GG
1 TTTAAGGTTTAGGGTTAGAGGTTTAGG
* * *
3191165 ATTTAAGGTTTTGAGTTTA-AGGTTTCAGA
1 -TTTAAGGTTTAG-GGTTAGAGGTTT-AGG
* * * *
3191194 TTTAAAGTTTAAGGTTTG-GGCTTAGG
1 TTTAAGGTTTAGGGTTAGAGGTTTAGG
* * * * *
3191220 GTTAAGGTTTAAAGGTTAAAGGTTAAAG
1 TTTAAGGTTT-AGGGTTAGAGGTTTAGG
** * *
3191248 TTTAAGGTAGAAGGTTA-AGGGTTAAGG
1 TTTAAGGTTTAGGGTTAGA-GGTTTAGG
3191275 TTTAAGGTTT
1 TTTAAGGTTT
3191285 GTGATTTAAA
Statistics
Matches: 188, Mismatches: 48, Indels: 54
0.65 0.17 0.19
Matches are distributed among these distances:
25 2 0.01
26 27 0.14
27 70 0.37
28 45 0.24
29 19 0.10
30 4 0.02
32 4 0.02
33 2 0.01
34 15 0.08
ACGTcount: A:0.29, C:0.02, G:0.30, T:0.40
Consensus pattern (27 bp):
TTTAAGGTTTAGGGTTAGAGGTTTAGG
Found at i:3191052 original size:7 final size:7
Alignment explanation
Indices: 3190995--3192209 Score: 271
Period size: 7 Copynumber: 175.3 Consensus size: 7
3190985 ATTAAAATTT
3190995 TTTAAGG
1 TTTAAGG
3191002 TTT-AGG
1 TTTAAGG
*
3191008 GTTAGAGG
1 TTTA-AGG
3191016 TTT-AGG
1 TTTAAGG
*
3191022 TTTAAAG
1 TTTAAGG
3191029 TTTAAAGG
1 TTT-AAGG
* *
3191037 ATTGA-G
1 TTTAAGG
3191043 TTTAAGG
1 TTTAAGG
*
3191050 TTT-ATG
1 TTTAAGG
* *
3191056 TTAAAGA
1 TTTAAGG
*
3191063 TTTAGGG
1 TTTAAGG
3191070 TTTAAAGG
1 TTT-AAGG
*
3191078 TTTAAAAG
1 TTT-AAGG
3191086 -TT-AGAG
1 TTTAAG-G
3191092 TTT-AGG
1 TTTAAGG
*
3191098 ATTTAGGG
1 -TTTAAGG
*
3191106 TCTAAGG
1 TTTAAGG
3191113 TTTAAGG
1 TTTAAGG
*
3191120 TCT-AGG
1 TTTAAGG
3191126 TTTAAGG
1 TTTAAGG
*
3191133 -TTAGGG
1 TTTAAGG
*
3191139 TCTAAGG
1 TTTAAGG
3191146 TTTAAGG
1 TTTAAGG
*
3191153 TTTGAGG
1 TTTAAGG
3191160 TTT--GG
1 TTTAAGG
3191165 ATTTAAGG
1 -TTTAAGG
*
3191173 TTT-TGAG
1 TTTAAG-G
3191180 TTTAAGG
1 TTTAAGG
* *
3191187 TTTCAGA
1 TTTAAGG
*
3191194 TTTAAAG
1 TTTAAGG
3191201 TTTAAGG
1 TTTAAGG
*
3191208 TTT-GGG
1 TTTAAGG
*
3191214 CTT-AGG
1 TTTAAGG
*
3191220 GTTAAGG
1 TTTAAGG
3191227 TTTAAAGG
1 TTT-AAGG
*
3191235 TTAAAGG
1 TTTAAGG
*
3191242 -TTAAAG
1 TTTAAGG
3191248 TTTAAGG
1 TTTAAGG
**
3191255 TAGAAGG
1 TTTAAGG
3191262 -TTAAGG
1 TTTAAGG
*
3191268 GTTAAGG
1 TTTAAGG
3191275 TTTAAGG
1 TTTAAGG
** *
3191282 TTTGTGA
1 TTTAAGG
*
3191289 TTTAAAG
1 TTTAAGG
3191296 TTTAAGG
1 TTTAAGG
3191303 TTTGAA-G
1 TTT-AAGG
**
3191310 TTTAAAA
1 TTTAAGG
*
3191317 TTTAAAG
1 TTTAAGG
**
3191324 TTTGGGG
1 TTTAAGG
*
3191331 TTTAAGA
1 TTTAAGG
*
3191338 TTTAAGA
1 TTTAAGG
*
3191345 TTTAAGA
1 TTTAAGG
*
3191352 TTT-AGTA
1 TTTAAG-G
3191359 TTTAAGG
1 TTTAAGG
** *
3191366 GCTAAAG
1 TTTAAGG
3191373 TTTAAGG
1 TTTAAGG
**
3191380 TTTTTGG
1 TTTAAGG
*
3191387 TTTGAGG
1 TTTAAGG
3191394 TTTGAA-G
1 TTT-AAGG
*
3191401 -TTAAGT
1 TTTAAGG
*
3191407 TTTAGGG
1 TTTAAGG
*
3191414 TTTAAAG
1 TTTAAGG
*
3191421 TTT-GGTG
1 TTTAAG-G
3191428 TTTAAGG
1 TTTAAGG
*
3191435 TTTGAGG
1 TTTAAGG
*
3191442 TTTAAGA
1 TTTAAGG
*
3191449 TTTAAGA
1 TTTAAGG
*
3191456 TTTAAGA
1 TTTAAGG
*
3191463 TTAAAGG
1 TTTAAGG
*
3191470 TTT-AGCA
1 TTTAAG-G
*
3191477 TTTAGGG
1 TTTAAGG
*
3191484 TTTAGGG
1 TTTAAGG
3191491 TTTAAGG
1 TTTAAGG
*
3191498 -TTAAAG
1 TTTAAGG
3191504 -TTAAGG
1 TTTAAGG
**
3191510 TTTGGGG
1 TTTAAGG
* *
3191517 GTTAAAG
1 TTTAAGG
*
3191524 TTTAGGGG
1 TTTA-AGG
**
3191532 CTAAAAGG
1 -TTTAAGG
3191540 -TTAAGAG
1 TTTAAG-G
3191547 -TTAAGG
1 TTTAAGG
**
3191553 TTTGGGG
1 TTTAAGG
* *
3191560 GTTAAAG
1 TTTAAGG
3191567 TTTAAGGG
1 TTTAA-GG
**
3191575 CTAAAAGG
1 -TTTAAGG
3191583 -TTAAGAG
1 TTTAAG-G
*
3191590 -TTAAGA
1 TTTAAGG
3191596 TTTAAGG
1 TTTAAGG
*
3191603 TTTAAAGT
1 TTT-AAGG
3191611 TTTAA-G
1 TTTAAGG
3191617 TTTAAGG
1 TTTAAGG
*
3191624 TATCAA-G
1 T-TTAAGG
*
3191631 TTTAGGG
1 TTTAAGG
3191638 TTTTAA-G
1 -TTTAAGG
3191645 TTTAAGG
1 TTTAAGG
**
3191652 TTTAATTT
1 TTTAA-GG
3191660 TTTAA-G
1 TTTAAGG
*
3191666 TTTGAAGT
1 TTT-AAGG
* *
3191674 TTTGAGA
1 TTTAAGG
3191681 TTT-AGG
1 TTTAAGG
**
3191687 TTTTTGG
1 TTTAAGG
**
3191694 TTTTTGGG
1 -TTTAAGG
*
3191702 TTT-TGAG
1 TTTAAG-G
*
3191709 TTTAGGG
1 TTTAAGG
3191716 TTTCAA-G
1 TTT-AAGG
3191723 TTTCAA-G
1 TTT-AAGG
*
3191730 TTTTAGG
1 TTTAAGG
3191737 TTTCAA-G
1 TTT-AAGG
*
3191744 TTTCAAGT
1 TTT-AAGG
3191752 TTTAA-G
1 TTTAAGG
3191758 TTTAAGG
1 TTTAAGG
**
3191765 TTTTGGG
1 TTTAAGG
3191772 CATTT--GTG
1 --TTTAAG-G
**
3191780 TTTTGGG
1 TTTAAGG
*
3191787 TTTGAGG
1 TTTAAGG
3191794 TTCT-AGG
1 TT-TAAGG
3191801 TTTAAGG
1 TTTAAGG
*
3191808 TTTAAAAG
1 TTT-AAGG
*
3191816 -TTAAAG
1 TTTAAGG
3191822 -TTAGAGG
1 TTTA-AGG
3191829 TTT-AGG
1 TTTAAGG
* *
3191835 GTTGAGG
1 TTTAAGG
**
3191842 TAAAAGG
1 TTTAAGG
3191849 TTTAAGG
1 TTTAAGG
*
3191856 TTGAAGG
1 TTTAAGG
* *
3191863 GTTATGG
1 TTTAAGG
3191870 TTTAAAGG
1 TTT-AAGG
* *
3191878 TTAAATG
1 TTTAAGG
*
3191885 TTTAGGG
1 TTTAAGG
*
3191892 TTTAAGA
1 TTTAAGG
*
3191899 TTTAATG
1 TTTAAGG
* **
3191906 ATTAAAA
1 TTTAAGG
*
3191913 ATTAAGG
1 TTTAAGG
3191920 TTTAAGG
1 TTTAAGG
*
3191927 TTTAAAG
1 TTTAAGG
*
3191934 -TTAGCGG
1 TTTA-AGG
*
3191941 TTTAAGA
1 TTTAAGG
*
3191948 TTTAAAG
1 TTTAAGG
3191955 TTTAAGG
1 TTTAAGG
3191962 TTT-AGAG
1 TTTAAG-G
**
3191969 TTTGGGG
1 TTTAAGG
*
3191976 TTGAA-G
1 TTTAAGG
* *
3191982 ATTAAGA
1 TTTAAGG
*
3191989 TTTAAAG
1 TTTAAGG
*
3191996 TTT-TGTG
1 TTTAAG-G
*
3192003 TTTAAAG
1 TTTAAGG
*
3192010 TTTAGGG
1 TTTAAGG
*
3192017 TTTAAAG
1 TTTAAGG
3192024 TTT-AGG
1 TTTAAGG
3192030 ATTT-AGAG
1 -TTTAAG-G
*
3192038 TTTAAAG
1 TTTAAGG
*
3192045 TTTCAGG
1 TTTAAGG
*
3192052 TTTAAAGC
1 TTT-AAGG
*
3192060 TTT-GGG
1 TTTAAGG
*
3192066 TTTCAGG
1 TTTAAGG
**
3192073 TTTGGGG
1 TTTAAGG
*
3192080 TTTCAGG
1 TTTAAGG
*
3192087 TTTAAAG
1 TTTAAGG
3192094 TTT-AGG
1 TTTAAGG
*
3192100 -TTAGGG
1 TTTAAGG
3192106 TTT-AGG
1 TTTAAGG
3192112 -TTAAGG
1 TTTAAGG
**
3192118 TTTAAAA
1 TTTAAGG
3192125 TTT-AGAG
1 TTTAAG-G
*
3192132 TTTAAGT
1 TTTAAGG
* *
3192139 TTTGAGA
1 TTTAAGG
*
3192146 TTTAAGA
1 TTTAAGG
3192153 TTTAAAGG
1 TTT-AAGG
*
3192161 -TTAGGG
1 TTTAAGG
*
3192167 CTTAAGG
1 TTTAAGG
*
3192174 TTT-AGA
1 TTTAAGG
3192180 TTTAAGG
1 TTTAAGG
3192187 TTTTAAGG
1 -TTTAAGG
*
3192195 -TTAGGG
1 TTTAAGG
*
3192201 TTTATGG
1 TTTAAGG
3192208 TT
1 TT
3192210 GTTCTTTTCT
Statistics
Matches: 870, Mismatches: 243, Indels: 190
0.67 0.19 0.15
Matches are distributed among these distances:
5 9 0.01
6 157 0.18
7 583 0.67
8 113 0.13
9 8 0.01
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.42
Consensus pattern (7 bp):
TTTAAGG
Found at i:3191133 original size:20 final size:20
Alignment explanation
Indices: 3191108--3191175 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
3191098 ATTTAGGGTC
3191108 TAAGGTTTAAGGTCTAGGTT
1 TAAGGTTTAAGGTCTAGGTT
*
3191128 TAAGG-TTAGGGTCTAAGGTT
1 TAAGGTTTAAGGTCT-AGGTT
* *
3191148 TAAGGTTTGAGGT-TTGGATT
1 TAAGGTTTAAGGTCTAGG-TT
3191168 TAAGGTTT
1 TAAGGTTT
3191176 TGAGTTTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 10 0.24
20 26 0.63
21 5 0.12
ACGTcount: A:0.24, C:0.03, G:0.32, T:0.41
Consensus pattern (20 bp):
TAAGGTTTAAGGTCTAGGTT
Found at i:3191188 original size:14 final size:14
Alignment explanation
Indices: 3191112--3191189 Score: 56
Period size: 13 Copynumber: 5.8 Consensus size: 14
3191102 AGGGTCTAAG
* *
3191112 GTTTAAGGTCTAG-
1 GTTTAAGGTTTGGA
*
3191125 GTTTAAGGTTAGG-
1 GTTTAAGGTTTGGA
* *
3191138 GTCTAAGGTTT-AA
1 GTTTAAGGTTTGGA
*
3191151 GGTTTGAGGTTTGGA
1 -GTTTAAGGTTTGGA
*
3191166 -TTTAAGGTTTTGA
1 GTTTAAGGTTTGGA
3191179 GTTTAAGGTTT
1 GTTTAAGGTTT
3191190 CAGATTTAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
13 30 0.60
14 19 0.38
15 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.32, T:0.44
Consensus pattern (14 bp):
GTTTAAGGTTTGGA
Found at i:3191261 original size:20 final size:19
Alignment explanation
Indices: 3191219--3191275 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
3191209 TTGGGCTTAG
3191219 GGTTAAGGTTTAAAGGTTAAA
1 GGTTAAGGTTT-AAGG-TAAA
*
3191240 GGTTAAAGTTTAAGGTAGAA
1 GGTTAAGGTTTAAGGTA-AA
*
3191260 GGTTAAGGGTTAAGGT
1 GGTTAAGGTTTAAGGT
3191276 TTAAGGTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.06
20 20 0.62
21 10 0.31
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.32
Consensus pattern (19 bp):
GGTTAAGGTTTAAGGTAAA
Found at i:3191265 original size:13 final size:13
Alignment explanation
Indices: 3191219--3191283 Score: 62
Period size: 13 Copynumber: 4.8 Consensus size: 13
3191209 TTGGGCTTAG
3191219 GGTTAAGGTTTAAA
1 GGTTAAGG-TTAAA
3191233 GGTTAAAGGTTAAA
1 GGTT-AAGGTTAAA
*
3191247 GTTTAAGG-TAGAA
1 GGTTAAGGTTA-AA
3191260 GGTTAAGGGTT-AA
1 GGTTAA-GGTTAAA
3191273 GGTTTAAGGTT
1 GG-TTAAGGTT
3191284 TGTGATTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
12 2 0.05
13 19 0.43
14 18 0.41
15 5 0.11
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (13 bp):
GGTTAAGGTTAAA
Found at i:3191555 original size:43 final size:43
Alignment explanation
Indices: 3191494--3191612 Score: 186
Period size: 43 Copynumber: 2.8 Consensus size: 43
3191484 TTTAGGGTTT
*
3191494 AAGGTTAA-AGTTAAGGTTTGGGGGTTAAAGTTTAGGGGCTAA
1 AAGGTTAAGAGTTAAGGTTTGGGGGTTAAAGTTTAAGGGCTAA
3191536 AAGGTTAAGAGTTAAGGTTTGGGGGTTAAAGTTTAAGGGCTAA
1 AAGGTTAAGAGTTAAGGTTTGGGGGTTAAAGTTTAAGGGCTAA
* ** *
3191579 AAGGTTAAGAGTTAAGATTTAAGGTTTAAAGTTT
1 AAGGTTAAGAGTTAAGGTTTGGGGGTTAAAGTTT
3191613 TAAGTTTAAG
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
42 8 0.11
43 63 0.89
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.33
Consensus pattern (43 bp):
AAGGTTAAGAGTTAAGGTTTGGGGGTTAAAGTTTAAGGGCTAA
Found at i:3192110 original size:12 final size:12
Alignment explanation
Indices: 3192078--3192121 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
3192068 TCAGGTTTGG
3192078 GGTTTCAGGTTTAA
1 GGTTT-AGG-TTAA
* *
3192092 AGTTTAGGTTAG
1 GGTTTAGGTTAA
3192104 GGTTTAGGTTAA
1 GGTTTAGGTTAA
3192116 GGTTTA
1 GGTTTA
3192122 AAATTTAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 19 0.73
13 3 0.12
14 4 0.15
ACGTcount: A:0.23, C:0.02, G:0.32, T:0.43
Consensus pattern (12 bp):
GGTTTAGGTTAA
Found at i:3192195 original size:34 final size:35
Alignment explanation
Indices: 3192133--3192209 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 35
3192123 AATTTAGAGT
*
3192133 TTAAGTTTTGAGATTTAAGATTTAAAGGTTAGGGC
1 TTAAGGTTTGAGATTTAAGATTTAAAGGTTAGGGC
* * *
3192168 TTAAGGTTT-AGATTTAAGGTTTTAAGGTTAGGGT
1 TTAAGGTTTGAGATTTAAGATTTAAAGGTTAGGGC
*
3192202 TTATGGTT
1 TTAAGGTT
3192210 GTTCTTTTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 29 0.78
35 8 0.22
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.44
Consensus pattern (35 bp):
TTAAGGTTTGAGATTTAAGATTTAAAGGTTAGGGC
Found at i:3192744 original size:14 final size:15
Alignment explanation
Indices: 3192727--3192755 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3192717 AGAATATATA
3192727 GTTTAT-GGGTTAGT
1 GTTTATGGGGTTAGT
3192741 GTTTATGGGGTTAGT
1 GTTTATGGGGTTAGT
3192756 TTAAGGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.48
Consensus pattern (15 bp):
GTTTATGGGGTTAGT
Found at i:3192782 original size:20 final size:20
Alignment explanation
Indices: 3192741--3192783 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3192731 ATGGGTTAGT
* *
3192741 GTTTATGGGGTTAGTTTAAG
1 GTTTATGGGATTAGGTTAAG
3192761 GTTTAT-GGATTAGGTTAGAG
1 GTTTATGGGATTAGGTTA-AG
3192781 GTT
1 GTT
3192784 ATGATTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (20 bp):
GTTTATGGGATTAGGTTAAG
Found at i:3194734 original size:25 final size:25
Alignment explanation
Indices: 3194676--3194728 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
3194666 CAAACATGTA
3194676 TTTAAAA-ACTATTTTGTTCAAAATT
1 TTTAAAATA-TATTTTGTTCAAAATT
*
3194701 TTTAAAATATATTTTTTTC-AAATT
1 TTTAAAATATATTTTGTTCAAAATT
3194725 TTTA
1 TTTA
3194729 TCAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 9 0.35
25 16 0.62
26 1 0.04
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTAAAATATATTTTGTTCAAAATT
Found at i:3195488 original size:28 final size:29
Alignment explanation
Indices: 3195408--3195488 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 29
3195398 CCACAATCAC
** *
3195408 TAAACCTT-AATCCCAAATCCT-AATCTT
1 TAAACCTTAAATCATAAATCATAAATCTT
* * *
3195435 TAAAGCCTTAATTCATAACTCTTAAAT-TT
1 TAAA-CCTTAAATCATAAATCATAAATCTT
*
3195464 TAAACCTTAAATCTTAAATCATAAA
1 TAAACCTTAAATCATAAATCATAAA
3195489 CCCCAAAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
27 4 0.10
28 21 0.50
29 14 0.33
30 3 0.07
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (29 bp):
TAAACCTTAAATCATAAATCATAAATCTT
Found at i:3195704 original size:16 final size:16
Alignment explanation
Indices: 3195680--3195726 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
3195670 GCTCAAACTT
*
3195680 GAAAAAACTTGAACCC
1 GAAAAAACTCGAACCC
* *
3195696 GAAAGAACTCGAATCC
1 GAAAAAACTCGAACCC
3195712 GAAAAAACTCGAACC
1 GAAAAAACTCGAACC
3195727 TGAGACTAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.49, C:0.26, G:0.15, T:0.11
Consensus pattern (16 bp):
GAAAAAACTCGAACCC
Found at i:3197575 original size:14 final size:14
Alignment explanation
Indices: 3197556--3197589 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
3197546 CTACACATAT
3197556 ATTCAATTTTTTAA
1 ATTCAATTTTTTAA
3197570 ATTCAATTTTTTAA
1 ATTCAATTTTTTAA
3197584 ATTCAA
1 ATTCAA
3197590 AGTGTAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTCAATTTTTTAA
Found at i:3198371 original size:19 final size:19
Alignment explanation
Indices: 3198340--3198381 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3198330 TTCAATAAAT
*
3198340 AAATAATTAAATATATTAA
1 AAATAATTAAATATAATAA
3198359 AAATATATT-AATATAATAA
1 AAATA-ATTAAATATAATAA
3198378 AAAT
1 AAAT
3198382 TTACTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAATTAAATATAATAA
Found at i:3198579 original size:16 final size:16
Alignment explanation
Indices: 3198555--3198587 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3198545 GGCCTGAACT
*
3198555 CAAATAAGCCCAAACC
1 CAAACAAGCCCAAACC
3198571 CAAACAAGCCCAAACC
1 CAAACAAGCCCAAACC
3198587 C
1 C
3198588 GAATGAGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.42, G:0.06, T:0.03
Consensus pattern (16 bp):
CAAACAAGCCCAAACC
Found at i:3198848 original size:16 final size:17
Alignment explanation
Indices: 3198821--3198852 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3198811 AACTCCAAAA
3198821 TTTATGTCATATATATT
1 TTTATGTCATATATATT
3198838 TTTAT-TCATATATAT
1 TTTATGTCATATATAT
3198853 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTATGTCATATATATT
Found at i:3198850 original size:2 final size:2
Alignment explanation
Indices: 3198845--3198887 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3198835 ATTTTTATTC
3198845 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3198887 A
1 A
3198888 AAGTTTAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3198992 original size:10 final size:10
Alignment explanation
Indices: 3198977--3199001 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3198967 TGTATGTCAC
3198977 ATTTTAATTT
1 ATTTTAATTT
3198987 ATTTTAATTT
1 ATTTTAATTT
3198997 ATTTT
1 ATTTT
3199002 TCTCATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
ATTTTAATTT
Found at i:3199701 original size:12 final size:12
Alignment explanation
Indices: 3199684--3199708 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3199674 TTACTTTTGC
3199684 ACCTTATTTGTT
1 ACCTTATTTGTT
3199696 ACCTTATTTGTT
1 ACCTTATTTGTT
3199708 A
1 A
3199709 GTAGTAAAAG
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:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (12 bp):
ACCTTATTTGTT
Found at i:3199934 original size:14 final size:14
Alignment explanation
Indices: 3199900--3199938 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3199890 GATAAAATAA
*
3199900 TATTTAGTATCTATT
1 TATTTATTAT-TATT
3199915 TATTTATTATTATT
1 TATTTATTATTATT
*
3199929 TTTTTATTAT
1 TATTTATTAT
3199939 CAAAAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (14 bp):
TATTTATTATTATT
Found at i:3200973 original size:12 final size:11
Alignment explanation
Indices: 3200952--3200994 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
3200942 TTGACTTAAT
*
3200952 TTTTTTTTTCTC
1 TTTTTCTTT-TC
3200964 TTTTTC-TTTC
1 TTTTTCTTTTC
3200974 TTTTTCTTTTC
1 TTTTTCTTTTC
3200985 TTTTTTCTTT
1 -TTTTTCTTT
3200995 CACTTGCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 8 0.29
11 6 0.21
12 14 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:3200979 original size:18 final size:18
Alignment explanation
Indices: 3200956--3200994 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3200946 CTTAATTTTT
3200956 TTTTTCTCTTT-TTCTTTC
1 TTTTTCT-TTTCTTCTTTC
*
3200974 TTTTTCTTTTCTTTTTTC
1 TTTTTCTTTTCTTCTTTC
3200992 TTT
1 TTT
3200995 CACTTGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTCTTCTTTC
Done.