Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 19 of 25
Found at i:2952457 original size:16 final size:16
Alignment explanation
Indices: 2952434--2952507 Score: 87
Period size: 16 Copynumber: 4.6 Consensus size: 16
2952424 TTTCATGATG
*
2952434 ATTTTAAATGTTTTTAA
1 ATTTAAAAT-TTTTTAA
* *
2952451 ATTTAAATTTTTTTAT
1 ATTTAAAATTTTTTAA
2952467 ATTTAAAATTTTTT-A
1 ATTTAAAATTTTTTAA
2952482 ATTTAAAATTTTTTAA
1 ATTTAAAATTTTTTAA
* *
2952498 CTTTTAAATT
1 ATTTAAAATT
2952508 AATATAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
15 14 0.29
16 28 0.57
17 7 0.14
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (16 bp):
ATTTAAAATTTTTTAA
Found at i:2952478 original size:15 final size:15
Alignment explanation
Indices: 2952444--2952494 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
2952434 ATTTTAAATG
* *
2952444 TTTTTAAATTTAAATT
1 TTTTTATATTTAAA-A
2952460 TTTTTATATTTAAAA
1 TTTTTATATTTAAAA
2952475 TTTTT-TAATTTAAAA
1 TTTTTAT-ATTTAAAA
2952490 TTTTT
1 TTTTT
2952495 TAACTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 1 0.03
15 18 0.56
16 13 0.41
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTATATTTAAAA
Found at i:2952480 original size:32 final size:32
Alignment explanation
Indices: 2952434--2952496 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
2952424 TTTCATGATG
* *
2952434 ATTTTAAATGTTTTTAAATTTAAATTTTTTTAT
1 ATTTAAAATGTTTTT-AATTTAAAATTTTTTAT
2952467 ATTTAAAAT-TTTTTAATTTAAAATTTTTTA
1 ATTTAAAATGTTTTTAATTTAAAATTTTTTA
2952497 ACTTTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 15 0.54
32 5 0.18
33 8 0.29
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (32 bp):
ATTTAAAATGTTTTTAATTTAAAATTTTTTAT
Found at i:2953096 original size:16 final size:17
Alignment explanation
Indices: 2953071--2953108 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2953061 TAAATGTATA
*
2953071 ATTAATATTTTAAT-AT
1 ATTAAAATTTTAATAAT
*
2953087 ATTAAAATTTTTATAAT
1 ATTAAAATTTTAATAAT
2953104 ATTAA
1 ATTAA
2953109 TTATTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAAAATTTTAATAAT
Found at i:2953108 original size:33 final size:34
Alignment explanation
Indices: 2953071--2953156 Score: 88
Period size: 32 Copynumber: 2.6 Consensus size: 34
2953061 TAAATGTATA
* **
2953071 ATTAATATTTTAATATATTAAAATTTTTAT-AAT
1 ATTAATATTTTAATATATAAAAATTTACATAAAT
* *
2953104 ATTAAT-TATTAATTTATAAAAATTTACATAAAT
1 ATTAATATTTTAATATATAAAAATTTACATAAAT
*
2953137 ATATATTATTTTAA-ATATAA
1 AT-TAATATTTTAATATATAA
2953157 TTATAATAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
32 18 0.43
33 11 0.26
34 8 0.19
35 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (34 bp):
ATTAATATTTTAATATATAAAAATTTACATAAAT
Found at i:2953179 original size:11 final size:11
Alignment explanation
Indices: 2953159--2953189 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2953149 AAATATAATT
2953159 ATAATA-AAAA
1 ATAATATAAAA
2953169 ATAATATAAAA
1 ATAATATAAAA
2953180 ATAATATAAA
1 ATAATATAAA
2953190 TACCTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:2953714 original size:117 final size:115
Alignment explanation
Indices: 2953530--2953951 Score: 465
Period size: 117 Copynumber: 3.6 Consensus size: 115
2953520 TTAATTCAAT
* * * * *
2953530 ATTAAATACTAAATATATATTTTCTTGCCGTATAAACTCATAGAAGACGAAATTAATCGAGTAAA
1 ATTAAATAGT-AATATATATTTTCTTACCATATAAACTCATAGAAGACAAAATTAATTGAGTAAA
* * *
2953595 ATATTTCAATACTTTACATTAGATCTATTTAATAATCAATTTTATCTGCTTA
65 ATATTTCAATA-TTTACATTAGATCTATTCAATGATCAATTTTATCTACTTA
* *
2953647 ATTAAATAGTAA-ATTTATTTTCTTACCATATAAACTGATAGAAAAGACAAAATTAATTGAGTAA
1 ATTAAATAGTAATATATATTTTCTTACCATATAAACTCATAG--AAGACAAAATTAATTGAGTAA
* * * ** * *
2953711 AATATTTCATTATATTACGTCAGATCTATTCAATGGCCAATGTTATTTACTTA
64 AATATTTCAATAT-TTACATTAGATCTATTCAATGATCAATTTTATCTACTTA
* * *
2953764 ATTAAATAGTTAATATATATTTTCTTATCATATAAACTCATAGAAGACAAAATTGATTAAGTAAA
1 ATTAAATAG-TAATATATATTTTCTTACCATATAAACTCATAGAAGACAAAATTAATTGAGTAAA
* * * * *
2953829 ATACTTT-ACTATTTTATATTAGATCTATTCAATGATTAATTTTATCAACTTG
65 ATA-TTTCAATA-TTTACATTAGATCTATTCAATGATCAATTTTATCTACTTA
* * *
2953881 ATTAAATACAG-AATATATATTTTCTTATCATATAAACTTATAGAAGACGAAATTAATT-ACGTA
1 ATTAAAT--AGTAATATATATTTTCTTACCATATAAACTCATAGAAGACAAAATTAATTGA-GTA
2953944 AAATATTT
63 AAATATTT
2953952 TGTTATTTTA
Statistics
Matches: 259, Mismatches: 36, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
115 25 0.10
116 7 0.03
117 192 0.74
118 7 0.03
119 28 0.11
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.40
Consensus pattern (115 bp):
ATTAAATAGTAATATATATTTTCTTACCATATAAACTCATAGAAGACAAAATTAATTGAGTAAAA
TATTTCAATATTTACATTAGATCTATTCAATGATCAATTTTATCTACTTA
Found at i:2953947 original size:234 final size:233
Alignment explanation
Indices: 2953530--2953951 Score: 564
Period size: 234 Copynumber: 1.8 Consensus size: 233
2953520 TTAATTCAAT
* * * *
2953530 ATTAAATACTAAATATATATTTTCTTGCCGTATAAACTCATAGAAGACGAAATTAATCGAGTAAA
1 ATTAAATACTAAATATATATTTTCTTACCATATAAACTCATAGAAGACAAAATTAATCAAGTAAA
* **
2953595 ATATTTCAATACTTTACATTAGATCTATTTAATAATCAATTTTATCTGCTTAATTAAATAGTAAA
66 ATATTTCAATACTTTACATTAGATCTATTCAATAATCAATTTTATCAACTTAATTAAATAGTAAA
*
2953660 TTTATTTTCTTACCATATAAACTGATAGAAAAGACAAAATTAATTGAGTAAAATATTTCATTATA
131 TATATTTTCTTACCATATAAACTGATAG-AAAGACAAAATTAATTGAGTAAAATATTTCATTATA
2953725 TTACGTCAGATCTATTCAATGGCCAATGTTATTTACTTA
195 TTACGTCAGATCTATTCAATGGCCAATGTTATTTACTTA
* * * * *
2953764 ATTAAATAGTTAATATATATTTTCTTATCATATAAACTCATAGAAGACAAAATTGATTAAGTAAA
1 ATTAAATACTAAATATATATTTTCTTACCATATAAACTCATAGAAGACAAAATTAATCAAGTAAA
* * * * * *
2953829 ATACTTT-ACTATTTTATATTAGATCTATTCAATGATTAATTTTATCAACTTGATTAAATACAG-
66 ATA-TTTCAATACTTTACATTAGATCTATTCAATAATCAATTTTATCAACTTAATTAAAT--AGT
* * *
2953892 AATATATATTTTCTTATCATATAAACTTATAG-AAGACGAAATTAATT-ACGTAAAATATTT
128 AA-ATATATTTTCTTACCATATAAACTGATAGAAAGACAAAATTAATTGA-GTAAAATATTT
2953952 TGTTATTTTA
Statistics
Matches: 161, Mismatches: 22, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
233 1 0.01
234 127 0.79
235 5 0.03
236 28 0.17
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.40
Consensus pattern (233 bp):
ATTAAATACTAAATATATATTTTCTTACCATATAAACTCATAGAAGACAAAATTAATCAAGTAAA
ATATTTCAATACTTTACATTAGATCTATTCAATAATCAATTTTATCAACTTAATTAAATAGTAAA
TATATTTTCTTACCATATAAACTGATAGAAAGACAAAATTAATTGAGTAAAATATTTCATTATAT
TACGTCAGATCTATTCAATGGCCAATGTTATTTACTTA
Found at i:2953959 original size:117 final size:116
Alignment explanation
Indices: 2953530--2953998 Score: 453
Period size: 117 Copynumber: 4.0 Consensus size: 116
2953520 TTAATTCAAT
* * * *
2953530 ATTAAATACTA-AATATATATTTTCTTGCCGTATAAACTCATAGAAGACGAAATTAATCGAGTAA
1 ATTAAATAC-AGAATATATATTTTCTTACCATATAAACTCATAGAAGACAAAATTAAT-TAGTAA
* * * * *
2953594 AATATTTCAATACTTTACATTAGATCTATTTAATAATCAATTTTATCTGCTTA
64 AATATTTCATTATTTTACATTAGATCTATTCAATGATCAATTTTATCTACTTA
* *
2953647 ATTAAAT--AGTAA-ATTTATTTTCTTACCATATAAACTGATAGAAAAGACAAAATTAATTGAGT
1 ATTAAATACAG-AATATATATTTTCTTACCATATAAACTCATAG--AAGACAAAATTAATT-AGT
* * * ** * *
2953709 AAAATATTTCATTATATTACGTCAGATCTATTCAATGGCCAATGTTATTTACTTA
62 AAAATATTTCATTATTTTACATTAGATCTATTCAATGATCAATTTTATCTACTTA
*** * *
2953764 ATTAAATAGTTAATATATATTTTCTTATCATATAAACTCATAGAAGACAAAATTGATTAAGTAAA
1 ATTAAATACAGAATATATATTTTCTTACCATATAAACTCATAGAAGACAAAATTAATT-AGTAAA
* * * * *
2953829 ATACTTT-ACTATTTTATATTAGATCTATTCAATGATTAATTTTATCAACTTG
65 ATA-TTTCATTATTTTACATTAGATCTATTCAATGATCAATTTTATCTACTTA
* * *
2953881 ATTAAATACAGAATATATATTTTCTTATCATATAAACTTATAGAAGACGAAATTAATTACGTAAA
1 ATTAAATACAGAATATATATTTTCTTACCATATAAACTCATAGAAGACAAAATTAATTA-GTAAA
** ** * ** * * *
2953946 ATATTTTGTTATTTTATTTTAAATCTATTCGGTTATAAATTTTATTTACTTA
65 ATATTTCATTATTTTACATTAGATCTATTCAATGATCAATTTTATCTACTTA
2953998 A
1 A
2953999 ATTTAAAAGT
Statistics
Matches: 287, Mismatches: 54, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
114 1 0.00
115 25 0.09
116 6 0.02
117 224 0.78
118 5 0.02
119 26 0.09
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.42
Consensus pattern (116 bp):
ATTAAATACAGAATATATATTTTCTTACCATATAAACTCATAGAAGACAAAATTAATTAGTAAAA
TATTTCATTATTTTACATTAGATCTATTCAATGATCAATTTTATCTACTTA
Found at i:2954164 original size:20 final size:20
Alignment explanation
Indices: 2954118--2954164 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
2954108 TATTTAAATT
*
2954118 TATTTTTAAAATATATTTAA
1 TATTATTAAAATATATTTAA
* *
2954138 AAATATTAATAATAT-TTTAA
1 TATTATTAA-AATATATTTAA
2954158 TATTATT
1 TATTATT
2954165 TACTAAATCA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTATTAAAATATATTTAA
Found at i:2954693 original size:22 final size:23
Alignment explanation
Indices: 2954667--2954710 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2954657 ATAAAAATTT
2954667 TATATTTA-ATATATTA-ATAATA
1 TATATTTATATA-ATTAGATAATA
2954689 TATATTTATATAATTAGATAAT
1 TATATTTATATAATTAGATAAT
2954711 TTTATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATTTATATAATTAGATAATA
Found at i:2955508 original size:22 final size:22
Alignment explanation
Indices: 2955483--2955528 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2955473 TCGTGCTTTG
* *
2955483 TTTTGAATTAATT-TTTATATAA
1 TTTTAAATT-ATTATTTATAAAA
2955505 TTTTAAATTATTATTTATAAAA
1 TTTTAAATTATTATTTATAAAA
2955527 TT
1 TT
2955529 AATTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTAAATTATTATTTATAAAA
Found at i:2955871 original size:12 final size:12
Alignment explanation
Indices: 2955837--2955929 Score: 53
Period size: 10 Copynumber: 8.5 Consensus size: 12
2955827 TAAAGTATTT
2955837 TATATTTATATA
1 TATATTTATATA
*
2955849 -A-AATT-TA-A
1 TATATTTATATA
2955857 TATATTTATATA
1 TATATTTATATA
*
2955869 TATA--TATATC
1 TATATTTATATA
2955879 TATATTTATATTA
1 TATATTTATA-TA
* * *
2955892 TTTGTTTGTAT-
1 TATATTTATATA
*
2955903 TATATTAAT-TA
1 TATATTTATATA
2955914 TAT-TTTATAT-
1 TATATTTATATA
2955924 TATATT
1 TATATT
2955930 ATAATTTTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 21
0.64 0.13 0.23
Matches are distributed among these distances:
8 1 0.02
9 3 0.05
10 23 0.39
11 14 0.24
12 10 0.17
13 8 0.14
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (12 bp):
TATATTTATATA
Found at i:2955906 original size:24 final size:22
Alignment explanation
Indices: 2955857--2955935 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
2955847 TAAAATTTAA
*
2955857 TATATTT-A-TATATATATATAT
1 TATATTTAATTATAT-TTTATAT
* *
2955878 CTATATTTATATTATTTGTTTGTAT
1 -TATATTTA-ATTATAT-TTTATAT
2955903 TATA-TTAATTATATTTTATAT
1 TATATTTAATTATATTTTATAT
2955924 TATATTATAATT
1 TATATT-TAATT
2955936 TTTTATATGG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 10 0.22
22 14 0.30
23 8 0.17
24 5 0.11
25 9 0.20
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (22 bp):
TATATTTAATTATATTTTATAT
Found at i:2955913 original size:4 final size:5
Alignment explanation
Indices: 2955857--2955932 Score: 52
Period size: 5 Copynumber: 14.8 Consensus size: 5
2955847 TAAAATTTAA
* *
2955857 TATAT T-TAT ATATAT ATATAT CTATATT TATAT TAT-T TGT-T TGTAT
1 TATAT TATAT -TATAT -TATAT -TATA-T TATAT TATAT TATAT TATAT
2955903 TATAT TA-AT TATATTT TATAT TATAT TATA
1 TATAT TATAT TATA--T TATAT TATAT TATA
2955933 ATTTTTTATA
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
4 14 0.23
5 24 0.39
6 17 0.28
7 6 0.10
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:2956259 original size:20 final size:19
Alignment explanation
Indices: 2956208--2956262 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
2956198 ATTAATTAAC
*
2956208 ATTATTAACATATAAAA-AT
1 ATTATTAA-ATATAAAATAA
2956227 A-TATATAAA-ATAAAATAA
1 ATTAT-TAAATATAAAATAA
2956245 ATTATTAATATATAAAAT
1 ATTATTAA-ATATAAAAT
2956263 TTTTTATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
17 6 0.20
18 9 0.30
19 8 0.27
20 7 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTATTAAATATAAAATAA
Found at i:2956269 original size:20 final size:20
Alignment explanation
Indices: 2956254--2956298 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2956244 AATTATTAAT
2956254 ATATAAAATTTTTTATAAAA
1 ATATAAAATTTTTTATAAAA
* * *
2956274 ATATAATATTTTATGTAAAA
1 ATATAAAATTTTTTATAAAA
2956294 A-ATAA
1 ATATAA
2956299 TACAAATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATATAAAATTTTTTATAAAA
Found at i:2956325 original size:4 final size:4
Alignment explanation
Indices: 2956316--2956357 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
2956306 ATGATTATAA
* * *
2956316 TTTC TTTC TTTC TTTC TTTT TTTT TTTC -TCC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
2956358 TTTTTTTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 2 0.06
4 31 0.94
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:2957519 original size:14 final size:14
Alignment explanation
Indices: 2957470--2957520 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
2957460 TTTATATTTT
2957470 TATATAAATTTTAA
1 TATATAAATTTTAA
*
2957484 TATATTGATAATTTATAT
1 TATA-T-A-AATTT-TAA
2957502 TATATAAATTTTAA
1 TATATAAATTTTAA
2957516 TATAT
1 TATAT
2957521 TTTTGTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 11 0.35
15 6 0.19
16 2 0.06
17 6 0.19
18 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:2957798 original size:2 final size:2
Alignment explanation
Indices: 2957786--2957829 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2957776 GCTAATTTGC
*
2957786 TA TA TA CA 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
2957828 TA
1 TA
2957830 AAATACAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2959771 original size:7 final size:7
Alignment explanation
Indices: 2959761--2959785 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2959751 CGTAATATAT
2959761 AAATTTA
1 AAATTTA
2959768 AAATTTA
1 AAATTTA
2959775 AAATTTA
1 AAATTTA
2959782 AAAT
1 AAAT
2959786 AAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:2961692 original size:2 final size:2
Alignment explanation
Indices: 2961685--2961721 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2961675 GGCTTGTTTG
2961685 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 A
2961722 CACACATACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2961739 original size:4 final size:4
Alignment explanation
Indices: 2961719--2961758 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
2961709 ATATATATAT
* * *
2961719 ATAC ACAC ATAC CTAC ATAC ATAC AAAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2961759 TAATCATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (4 bp):
ATAC
Found at i:2964060 original size:21 final size:20
Alignment explanation
Indices: 2964036--2964082 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2964026 ATTTTTATTT
* *
2964036 ATTAAATAATTATTATTTTAA
1 ATTAAAAAATTAATA-TTTAA
2964057 ATTAAAAAAATTAATATTTAA
1 ATT-AAAAAATTAATATTTAA
2964078 ATTAA
1 ATTAA
2964083 TTTATTTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 11 0.48
22 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAAAAAATTAATATTTAA
Found at i:2964915 original size:28 final size:24
Alignment explanation
Indices: 2964863--2964936 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 24
2964853 ACAAATATAG
*
2964863 TAAAATTTATATAATATAAATTTT
1 TAAAATTTATATAATATAAAATTT
2964887 TAAAATTTATATAAATTATATAACATTT
1 TAAAATTTATAT-AA-TATA-AA-ATTT
*
2964915 TAAACA-TAATTATAATATAAAA
1 TAAA-ATTTA-TATAATATAAAA
2964937 AAACCTAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
24 12 0.29
25 3 0.07
26 6 0.14
27 6 0.14
28 11 0.26
29 4 0.10
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAAATTTATATAATATAAAATTT
Found at i:2967873 original size:16 final size:16
Alignment explanation
Indices: 2967840--2967896 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
2967830 ATCGCAAAAC
2967840 TAAAA-TAATCGAAA-T
1 TAAAATTAATC-AAATT
2967855 TAAAATTAATCAAATT
1 TAAAATTAATCAAATT
* * *
2967871 TAAAATGATTTAAATT
1 TAAAATTAATCAAATT
*
2967887 TAAAAATAAT
1 TAAAATTAAT
2967897 TTAAAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 8 0.24
16 26 0.76
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (16 bp):
TAAAATTAATCAAATT
Found at i:2967898 original size:17 final size:18
Alignment explanation
Indices: 2967866--2967912 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
2967856 AAAATTAATC
*
2967866 AAATTT-AAAATGATTT-
1 AAATTTAAAAATAATTTA
2967882 AAATTTAAAAATAATTTA
1 AAATTTAAAAATAATTTA
2967900 AAATTTTAAAAAT
1 AAA-TTTAAAAAT
2967913 TTAAAAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.22
17 9 0.33
18 3 0.11
19 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAATTTAAAAATAATTTA
Found at i:2967902 original size:27 final size:26
Alignment explanation
Indices: 2967867--2967920 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
2967857 AAATTAATCA
2967867 AATTTAAAATGATTT-AAATTTAAAAAT
1 AATTTAAAAT--TTTAAAATTTAAAAAT
2967894 AATTTAAAATTTTAAAAATTTAAAAAT
1 AATTTAAAATTTT-AAAATTTAAAAAT
2967921 CAATCTGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 3 0.12
27 22 0.88
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
AATTTAAAATTTTAAAATTTAAAAAT
Found at i:2971539 original size:374 final size:374
Alignment explanation
Indices: 2970850--2971599 Score: 1439
Period size: 374 Copynumber: 2.0 Consensus size: 374
2970840 ATCATCAACA
2970850 TACAAGAGGAGATAAATGAAAGATCCATCTTGTAACTTACACAAATACACACAATGGTCGTATTT
1 TACAAGAGGAGATAAATGAAAGATCCATCTTGTAACTTACACAAATACACACAATGGTCGTATTT
2970915 GCTTCTGGTGTACTTCTGCCTTTTCATAAAGCTATCAAATCGCTTGTACCACTGCCTCGAAGATT
66 GCTTCTGGTGTACTTCTGCCTTTTCATAAAGCTATCAAATCGCTTGTACCACTGCCTCGAAGATT
2970980 GCTTCAATCCATATAATGATTTGTTCAGCTTACAAACCCATTTTTCACCACCAGCATCCTTGTAT
131 GCTTCAATCCATATAATGATTTGTTCAGCTTACAAACCCATTTTTCACCACCAGCATCCTTGTAT
2971045 CCTTCTGGCTGAGTCATATAGATCTCCTCTTCTAAATCACCGTGCAAGAAAGCCGCTTTACATCA
196 CCTTCTGGCTGAGTCATATAGATCTCCTCTTCTAAATCACCGTGCAAGAAAGCCGCTTTACATCA
2971110 AATTGAGCTAGCTCCAAATTCAACTGTGCTACCACGACCAACAATATTCTAATAGAGGAATGCTT
261 AATTGAGCTAGCTCCAAATTCAACTGTGCTACCACGACCAACAATATTCTAATAGAGGAATGCTT
*
2971175 TACAATCGGAGAAAATACTTCATTGTAGTCGATTCTTTCCTTTTGAGCG
326 TACAATCGGAGAAAATACTTCATTGTAGTCGATTCCTTCCTTTTGAGCG
*
2971224 TACAAGAGGAGATAAATGAAAGATCCATCTTGTAACTTACGCAAATACACACAATGGTCGTATTT
1 TACAAGAGGAGATAAATGAAAGATCCATCTTGTAACTTACACAAATACACACAATGGTCGTATTT
* *
2971289 GCTTCTGGTTTACTTCTGCCTTTTCATAAAGCTATCAAATCGCTTGTACCACTGCCTCGGAGATT
66 GCTTCTGGTGTACTTCTGCCTTTTCATAAAGCTATCAAATCGCTTGTACCACTGCCTCGAAGATT
2971354 GCTTCAATCCATATAATGATTTGTTCAGCTTACAAACCCATTTTTCACCACCAGCATCCTTGTAT
131 GCTTCAATCCATATAATGATTTGTTCAGCTTACAAACCCATTTTTCACCACCAGCATCCTTGTAT
2971419 CCTTCTGGCTGAGTCA-ATAGATCTCCTCTTCTAAATCACCGTGCAAGAAAGCCGTCTTTACATC
196 CCTTCTGGCTGAGTCATATAGATCTCCTCTTCTAAATCACCGTGCAAGAAAGCCG-CTTTACATC
*
2971483 AAATTGAGCTAGCTCCAAATTCAACTGTGCTACCACGACTAACAATATTCTAATAGAGGAATGCT
260 AAATTGAGCTAGCTCCAAATTCAACTGTGCTACCACGACCAACAATATTCTAATAGAGGAATGCT
2971548 TTACAATCGGAGAAAATACTTCATTGTAGTCGATTCCTTCCTTTTGAGCG
325 TTACAATCGGAGAAAATACTTCATTGTAGTCGATTCCTTCCTTTTGAGCG
2971598 TA
1 TA
2971600 GCCTTTAGCT
Statistics
Matches: 370, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
373 38 0.10
374 332 0.90
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (374 bp):
TACAAGAGGAGATAAATGAAAGATCCATCTTGTAACTTACACAAATACACACAATGGTCGTATTT
GCTTCTGGTGTACTTCTGCCTTTTCATAAAGCTATCAAATCGCTTGTACCACTGCCTCGAAGATT
GCTTCAATCCATATAATGATTTGTTCAGCTTACAAACCCATTTTTCACCACCAGCATCCTTGTAT
CCTTCTGGCTGAGTCATATAGATCTCCTCTTCTAAATCACCGTGCAAGAAAGCCGCTTTACATCA
AATTGAGCTAGCTCCAAATTCAACTGTGCTACCACGACCAACAATATTCTAATAGAGGAATGCTT
TACAATCGGAGAAAATACTTCATTGTAGTCGATTCCTTCCTTTTGAGCG
Found at i:2971956 original size:28 final size:26
Alignment explanation
Indices: 2971920--2971976 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 26
2971910 TATAAATATA
*
2971920 ATACGAAAAATAT-GAATATGATATTAAT
1 ATAC-AAAAATATCAAATAT-ATA-TAAT
2971948 ATACAAAAATATCAAATATATATAAT
1 ATACAAAAATATCAAATATATATAAT
2971974 ATA
1 ATA
2971977 AATTTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 7 0.26
27 11 0.41
28 9 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (26 bp):
ATACAAAAATATCAAATATATATAAT
Found at i:2974834 original size:12 final size:11
Alignment explanation
Indices: 2974778--2974838 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 11
2974768 TTTTTAAAAT
2974778 ATAATTTTAAA
1 ATAATTTTAAA
**
2974789 A-AATAACTAAA
1 ATAAT-TTTAAA
2974800 ATAATTTTAAA
1 ATAATTTTAAA
2974811 AT--TTTTAAAA
1 ATAATTTT-AAA
2974821 ATAATTTTAGAA
1 ATAATTTTA-AA
2974833 ATAATT
1 ATAATT
2974839 ATTGATTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
9 4 0.10
10 8 0.20
11 13 0.32
12 15 0.38
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:2977636 original size:23 final size:20
Alignment explanation
Indices: 2977610--2977658 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
2977600 TATCATATCA
*
2977610 TATTTTAATTATTTTTTATTAT
1 TATTTTAA-AATTTTTTATT-T
2977632 T-TATTTAAAATTTTTTATTT
1 TAT-TTTAAAATTTTTTATTT
2977652 TATTTTA
1 TATTTTA
2977659 TTTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 6 0.25
21 12 0.50
22 6 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTTAAAATTTTTTATTT
Found at i:2978208 original size:35 final size:31
Alignment explanation
Indices: 2978168--2978231 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 31
2978158 AAAATTTATG
2978168 TTTAATTTTAAATATATAATTATTATTTAATAAAA
1 TTTAA-TTTAAA-AT-TAATTATTA-TTAATAAAA
*
2978203 TTTAATTTAAAATTAATTTTTATTAATAA
1 TTTAATTTAAAATTAATTATTATTAATAA
2978232 TGACAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 7 0.25
32 8 0.29
33 2 0.07
34 6 0.21
35 5 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTAATTTAAAATTAATTATTATTAATAAAA
Found at i:2979817 original size:2 final size:2
Alignment explanation
Indices: 2979810--2979844 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2979800 GGCTTGTTTG
2979810 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
2979845 CTGATCATGA
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:2981393 original size:15 final size:15
Alignment explanation
Indices: 2981373--2981404 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2981363 TTAAAATACA
2981373 TATAATTTATAATTT
1 TATAATTTATAATTT
*
2981388 TATAATTTGTAATTT
1 TATAATTTATAATTT
2981403 TA
1 TA
2981405 AAAAATAGAT
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:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TATAATTTATAATTT
Found at i:2985727 original size:24 final size:26
Alignment explanation
Indices: 2985676--2985733 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
2985666 TGGGTGGCTA
*
2985676 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
2985702 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
2985726 GTCAACAA
1 GTCAACAA
2985734 TGGTGGTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:2988366 original size:21 final size:22
Alignment explanation
Indices: 2988337--2988382 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2988327 TGTTCAGACA
** *
2988337 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2988359 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2988380 AGT
1 AGT
2988383 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2990297 original size:24 final size:26
Alignment explanation
Indices: 2990246--2990303 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
2990236 TGGGTGGCTA
*
2990246 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
2990272 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
2990296 GTCAACAA
1 GTCAACAA
2990304 TGGTGATTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:2990856 original size:14 final size:15
Alignment explanation
Indices: 2990837--2990871 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2990827 GGATGAAAAT
2990837 AATTAAT-AATTCAA
1 AATTAATCAATTCAA
*
2990851 AATTAATCAATTTAA
1 AATTAATCAATTCAA
2990866 AATTAA
1 AATTAA
2990872 AAATAACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTAATCAATTCAA
Found at i:2991985 original size:11 final size:11
Alignment explanation
Indices: 2991969--2991999 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
2991959 TAATTATGTA
2991969 AATATAAATAC
1 AATATAAATAC
2991980 AATATAAATAC
1 AATATAAATAC
2991991 AATATAAAT
1 AATATAAAT
2992000 TATTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (11 bp):
AATATAAATAC
Found at i:2993410 original size:27 final size:26
Alignment explanation
Indices: 2993360--2993431 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
2993350 CAAAAGTCAC
*
2993360 CTTTTGTTTGTAAAAAATAATGGTTA
1 CTTTTGTTTGTCAAAAATAATGGTTA
** *
2993386 CTTTGTGTTTGTCAAAAATTTTGGTTT
1 CTTT-TGTTTGTCAAAAATAATGGTTA
*
2993413 CTTTTTTATTTGTCAAAAA
1 C--TTTTGTTTGTCAAAAA
2993432 AAGTGACATG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 4 0.11
27 19 0.50
28 12 0.32
29 3 0.08
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (26 bp):
CTTTTGTTTGTCAAAAATAATGGTTA
Found at i:2997970 original size:27 final size:27
Alignment explanation
Indices: 2997932--2998019 Score: 92
Period size: 28 Copynumber: 3.3 Consensus size: 27
2997922 TACCCTTTAA
*
2997932 TTGTCAAAAATGGTGGTTATTTTGTGT
1 TTGTCAAAAATGGTGGTTATTTTGTAT
* * *
2997959 TTGTCAAAAATGATGGTTTCTTTTTTAT
1 TTGTCAAAAATGGTGG-TTATTTTGTAT
* *
2997987 TTGTAAAAAATGGTGG-TA-TGT-TAT
1 TTGTCAAAAATGGTGGTTATTTTGTAT
2998011 TTGTCAAAA
1 TTGTCAAAA
2998020 TTTGTAGCTA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
24 11 0.22
25 2 0.04
26 1 0.02
27 15 0.29
28 22 0.43
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (27 bp):
TTGTCAAAAATGGTGGTTATTTTGTAT
Found at i:2997989 original size:28 final size:28
Alignment explanation
Indices: 2997927--2998003 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
2997917 AAAGCTACCC
*
2997927 TTTAATTGTCAAAAATGGTGG-TTATTT
1 TTTATTTGTCAAAAATGGTGGTTTATTT
* * * *
2997954 TGTGTTTGTCAAAAATGATGGTTTCTTT
1 TTTATTTGTCAAAAATGGTGGTTTATTT
*
2997982 TTTATTTGTAAAAAATGGTGGT
1 TTTATTTGTCAAAAATGGTGGT
2998004 ATGTTATTTG
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 17 0.43
28 23 0.57
ACGTcount: A:0.27, C:0.04, G:0.21, T:0.48
Consensus pattern (28 bp):
TTTATTTGTCAAAAATGGTGGTTTATTT
Found at i:2998718 original size:20 final size:20
Alignment explanation
Indices: 2998695--2998757 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 20
2998685 ATTTTTATAA
2998695 ATATTTTAATATATAATT-T
1 ATATTTTAATATATAATTAT
*
2998714 -TATATTAA-A-ATAATTAT
1 ATATTTTAATATATAATTAT
* *
2998731 AT-TTTTAATATAAAAATTAA
1 ATATTTTAATAT-ATAATTAT
2998751 ATATTTT
1 ATATTTT
2998758 TAAGTTACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
16 6 0.18
17 7 0.21
18 9 0.26
20 8 0.24
21 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTTTAATATATAATTAT
Found at i:2998736 original size:22 final size:23
Alignment explanation
Indices: 2998683--2998759 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 23
2998673 ATTTATTTAA
**
2998683 ATATTTTTATA-AATATTTTAATAT
1 ATATTTTTATATAA-AAATTAAT-T
* *
2998707 ATAATTTTATATTAAAA-TAATT
1 ATATTTTTATATAAAAATTAATT
2998729 ATATTTTTAATATAAAAATTAA--
1 ATATTTTT-ATATAAAAATTAATT
2998751 ATATTTTTA
1 ATATTTTTA
2998760 AGTTACATCT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 1 0.02
22 16 0.36
23 12 0.27
24 14 0.32
25 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTTTATATAAAAATTAATT
Found at i:2998741 original size:23 final size:24
Alignment explanation
Indices: 2998700--2998760 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 24
2998690 TATAAATATT
* *
2998700 TTAATATATAATTTT-ATATTAAAA
1 TTAAT-TATATTTTTAATATAAAAA
2998724 -TAATTATATTTTTAATATAAAAA
1 TTAATTATATTTTTAATATAAAAA
2998747 TTAA--ATATTTTTAA
1 TTAATTATATTTTTAA
2998761 GTTACATCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 18 0.55
23 12 0.36
24 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAATTATATTTTTAATATAAAAA
Found at i:2999109 original size:79 final size:77
Alignment explanation
Indices: 2999026--2999179 Score: 200
Period size: 79 Copynumber: 2.0 Consensus size: 77
2999016 ATTTGATTAT
* * ** *
2999026 TAATAATTATTTATTGTAATAATAGTAGGTAAAAAATATTTTTAATTTAATGGTGTTAATTTTGT
1 TAATAATTATTTATTATAATAATAATAAATAAAAAATATTTTTAATTTAAT-GT-TTAATTTTAT
2999091 AATTCTTTCAAATC
64 AATTCTTTCAAATC
* * ** *
2999105 TAATAATTATTTATTATAATGATAATAAATAACAAATATTTTTTGTTTAGTGTTTAATTTTATAA
1 TAATAATTATTTATTATAATAATAATAAATAAAAAATATTTTTAATTTAATGTTTAATTTTATAA
2999170 TTCTTTCAAA
66 TTCTTTCAAA
2999180 AAATTTCTGA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 21 0.32
78 2 0.03
79 42 0.65
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (77 bp):
TAATAATTATTTATTATAATAATAATAAATAAAAAATATTTTTAATTTAATGTTTAATTTTATAA
TTCTTTCAAATC
Found at i:3000657 original size:34 final size:33
Alignment explanation
Indices: 3000609--3000829 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 33
3000599 TGGTAAAAAC
*
3000609 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
3000642 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
3000676 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
3000710 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * **
3000744 CTCCCATTTAGTCAACAATGACAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATG-GTAACCTACCAAAT
*
3000778 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
3000812 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
3000830 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 23 0.14
34 131 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:3000725 original size:68 final size:67
Alignment explanation
Indices: 3000611--3000829 Score: 287
Period size: 68 Copynumber: 3.2 Consensus size: 67
3000601 GTAAAAACCA
* * *
3000611 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
3000676 CAC
65 CAC
* * * *
3000679 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
3000744 CTC
65 CAC
* * * * *
3000747 CCATTTAGTCAACAATGACAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
3000812 CA-
65 CAC
3000814 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
3000830 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 17 0.13
68 113 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:3000753 original size:102 final size:101
Alignment explanation
Indices: 3000609--3000829 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 101
3000599 TGGTAAAAAC
** *
3000609 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAA
* *
3000674 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
3000710 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGACAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCA
3000775 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
3000812 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
3000830 TCTCCCACTT
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:3005289 original size:34 final size:33
Alignment explanation
Indices: 3005236--3005455 Score: 255
Period size: 34 Copynumber: 6.5 Consensus size: 33
3005226 TGGTAAAAAC
* *
3005236 CACCATTTAATCAATAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
3005269 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
3005303 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
3005337 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
3005371 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
3005405 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
3005439 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
3005456 AATCAAAAGA
Statistics
Matches: 160, Mismatches: 18, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 22 0.14
34 132 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:3005352 original size:68 final size:67
Alignment explanation
Indices: 3005238--3005452 Score: 288
Period size: 68 Copynumber: 3.2 Consensus size: 67
3005228 GTAAAAACCA
* * *
3005238 CCATTTAATCAATAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAATAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
3005303 CAC
65 CAC
* * *
3005306 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAATAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
3005371 CTC
65 CAC
* * * * *
3005374 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAATAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
3005439 CA-
65 CAC
3005441 CCATTTAATCAA
1 CCATTTAATCAA
3005453 CAAAATCAAA
Statistics
Matches: 129, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
67 13 0.10
68 115 0.89
69 1 0.01
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAATAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:3005380 original size:102 final size:101
Alignment explanation
Indices: 3005236--3005455 Score: 341
Period size: 102 Copynumber: 2.2 Consensus size: 101
3005226 TGGTAAAAAC
* * *
3005236 CACCATTTAATCAATAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
3005301 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
3005337 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
3005402 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
3005439 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
3005456 AATCAAAAGA
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 15 0.14
102 91 0.86
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:3009562 original size:28 final size:28
Alignment explanation
Indices: 3009501--3009563 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
3009491 CAAATGCCAC
*
3009501 CTTTTGTATTTGTCAAATATGGTGGTTT
1 CTTTTGTATTTGTCAAATATGATGGTTT
*
3009529 CCTTTGTATTTGTCAAATATGATGGTTAT
1 CTTTTGTATTTGTCAAATATGATGGTT-T
3009558 -TTTTGT
1 CTTTTGT
3009564 TTGTAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (28 bp):
CTTTTGTATTTGTCAAATATGATGGTTT
Found at i:3009584 original size:27 final size:27
Alignment explanation
Indices: 3009554--3009612 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 27
3009544 AATATGATGG
*
3009554 TTATTTTTGTTTGTAAAAATTGGTGGC
1 TTATTTTTGTTTGTAAAAATTGGTAGC
*
3009581 TTA---TTGTTTGTCAAAATTGGTAGC
1 TTATTTTTGTTTGTAAAAATTGGTAGC
*
3009605 TAATTTTT
1 TTATTTTT
3009613 ATTAGAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
24 21 0.81
27 5 0.19
ACGTcount: A:0.24, C:0.05, G:0.19, T:0.53
Consensus pattern (27 bp):
TTATTTTTGTTTGTAAAAATTGGTAGC
Found at i:3014180 original size:26 final size:26
Alignment explanation
Indices: 3014146--3014215 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 26
3014136 TGTATTTGTC
3014146 AAATATGGTGGCTATTTTTTTTTGTAA
1 AAAT-TGGTGGCTATTTTTTTTTGTAA
* * *
3014173 AAATTGGTGGC--TTGTTGTTTGTCA
1 AAATTGGTGGCTATTTTTTTTTGTAA
*
3014197 AAATTGGTGGCTAATTTTT
1 AAATTGGTGGCTATTTTTT
3014216 ATTAGAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 21 0.60
26 10 0.29
27 4 0.11
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.49
Consensus pattern (26 bp):
AAATTGGTGGCTATTTTTTTTTGTAA
Found at i:3014827 original size:186 final size:186
Alignment explanation
Indices: 3014494--3014879 Score: 596
Period size: 186 Copynumber: 2.1 Consensus size: 186
3014484 TCATAGTATC
* * *
3014494 AATTAA-AAGATAGTACGTATTAATTTCATGTTATCTTTATTTTGAAAAAATATTTTTAACTTTA
1 AATTAAGAAG-TAATACATATTAATTTCATGTTATCTTTATTTTGAAAAAATAATTTTAACTTTA
*
3014558 ATATCCAAAATAATTCACTTAATGCATTTTACTAGAAACATTATTATATTTCTCGTAATGTCTTT
65 ATATCCAAAATAATTCACTTAATACATTTTACTAGAAACATTATTATATTTCTCGTAATGTCTTT
* * *
3014623 TTATTTGAAAACTTTTAACATCAAAGACTTCATCTAAATTTCCAAACATTTAAGTGG
130 TTATTTGAAAACTTTTAACATCAAAGACTTCATCTAAATTCCCAAACATTCAAGTGA
3014680 AATTAAGAAGTAATACATATTAATTTCATGTTATCTTTATTTTGAAAAAATAATTTTAACTTTAA
1 AATTAAGAAGTAATACATATTAATTTCATGTTATCTTTATTTTGAAAAAATAATTTTAACTTTAA
* * *
3014745 TA-CCTAAAATAATTTACTTAATACATTTTATTAGAAATATTATTATATTTCTCGTAATGTCTTT
66 TATCC-AAAATAATTCACTTAATACATTTTACTAGAAACATTATTATATTTCTCGTAATGTCTTT
** * * *
3014809 TTATTTGAAAGTTTTTAACGTCGAAGACTTCATCTAAATTCCCAACCATTCAAGTGA
130 TTATTTGAAAACTTTTAACATCAAAGACTTCATCTAAATTCCCAAACATTCAAGTGA
*
3014866 AATTCAGAAGTAAT
1 AATTAAGAAGTAAT
3014880 TCTCCCTTGC
Statistics
Matches: 182, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
185 2 0.01
186 177 0.97
187 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (186 bp):
AATTAAGAAGTAATACATATTAATTTCATGTTATCTTTATTTTGAAAAAATAATTTTAACTTTAA
TATCCAAAATAATTCACTTAATACATTTTACTAGAAACATTATTATATTTCTCGTAATGTCTTTT
TATTTGAAAACTTTTAACATCAAAGACTTCATCTAAATTCCCAAACATTCAAGTGA
Found at i:3015011 original size:97 final size:97
Alignment explanation
Indices: 3014840--3015032 Score: 269
Period size: 97 Copynumber: 2.0 Consensus size: 97
3014830 CGAAGACTTC
* *
3014840 ATCTAAATTCCCAACCATTCAAGTGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTCCGTAA
1 ATCTAAATCCCCAACCATTCAAGTGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTCCATAA
3014905 CAATCCCTTGAATTTGAGATGGAGCACCCTTA
66 CAATCCCTTGAATTTGAGATGGAGCACCCTTA
* * * * * * **
3014937 ATCTAAATCCCCCAGCATTCAAGTGAAATTCAGAAGTAATTTTCCTTTGTAAGGAAATTTTATAA
1 ATCTAAATCCCCAACCATTCAAGTGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTCCATAA
* * *
3015002 TAATTCCTTGAATTTGAGATGGAGCATCCTT
66 CAATCCCTTGAATTTGAGATGGAGCACCCTT
3015033 CGTAGAAAAT
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
97 83 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (97 bp):
ATCTAAATCCCCAACCATTCAAGTGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTCCATAA
CAATCCCTTGAATTTGAGATGGAGCACCCTTA
Found at i:3015730 original size:22 final size:22
Alignment explanation
Indices: 3015697--3015747 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
3015687 AATTAGTTAA
*
3015697 TAATA-AAAAATATTTAAAT-T
1 TAATATAAAAATATATAAATAT
3015717 TAATGATAAAAATATATAAATAT
1 TAAT-ATAAAAATATATAAATAT
3015740 TAATATAA
1 TAATATAA
3015748 TATTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 4 0.15
21 1 0.04
22 17 0.63
23 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TAATATAAAAATATATAAATAT
Found at i:3020691 original size:17 final size:17
Alignment explanation
Indices: 3020666--3020713 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
3020656 GTCATTTTAA
*
3020666 TTATTTTTTATATAATT
1 TTATATTTTATATAATT
* *
3020683 TTATATTTTATTTTATT
1 TTATATTTTATATAATT
3020700 TTATATTTT-TATAA
1 TTATATTTTATATAA
3020714 AATATAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 3 0.12
17 23 0.88
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATATTTTATATAATT
Found at i:3021070 original size:13 final size:12
Alignment explanation
Indices: 3021044--3021082 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
3021034 CTTTAGTTAA
3021044 AATTTTTTTAATT
1 AATTTTTTT-ATT
3021057 AATTTGTTTTATT
1 AATTT-TTTTATT
3021070 AATTATTTTTATT
1 AATT-TTTTTATT
3021083 TTATTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (12 bp):
AATTTTTTTATT
Found at i:3021200 original size:16 final size:18
Alignment explanation
Indices: 3021176--3021216 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
3021166 AATATTATTT
3021176 AATATAA-TTTAATTAAA
1 AATATAATTTTAATTAAA
*
3021193 AATA-AATTTTTATTAAA
1 AATATAATTTTAATTAAA
3021210 AATATAA
1 AATATAA
3021217 AAAATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 17 0.81
18 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATAATTTTAATTAAA
Found at i:3023869 original size:18 final size:18
Alignment explanation
Indices: 3023848--3023884 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3023838 ATTTTTTATT
3023848 TAAAT-TTAATTATAAAAA
1 TAAATATTAA-TATAAAAA
3023866 TAAATATTAATATAAAAA
1 TAAATATTAATATAAAAA
3023884 T
1 T
3023885 TATTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATATTAATATAAAAA
Found at i:3023951 original size:18 final size:19
Alignment explanation
Indices: 3023896--3023951 Score: 51
Period size: 24 Copynumber: 2.7 Consensus size: 19
3023886 ATTTTTTATT
*
3023896 TTTTAAATAATAATTTAAA
1 TTTTAAATAAAAATTTAAA
3023915 TTTATAAATCAAATTAAATTTAAA
1 TTT-TAAAT--AA--AAATTTAAA
3023939 -TTTAAATAAAAAT
1 TTTTAAATAAAAAT
3023952 ATTTAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
18 4 0.13
19 3 0.10
20 7 0.23
22 7 0.23
23 2 0.06
24 8 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTAAATAAAAATTTAAA
Found at i:3027974 original size:63 final size:63
Alignment explanation
Indices: 3027894--3028025 Score: 237
Period size: 63 Copynumber: 2.1 Consensus size: 63
3027884 CATAACACAC
3027894 TTAGATCAGCACAAGTCGTTTTTCAATGTCATTAATCACGCTAGTACAACTTGCAATCACTAA
1 TTAGATCAGCACAAGTCGTTTTTCAATGTCATTAATCACGCTAGTACAACTTGCAATCACTAA
* * *
3027957 TTAGATCAGCACAAGTCGTTTTTCAATGTCCTTAATCATGCTAGTACAAGTTGCAATCACTAA
1 TTAGATCAGCACAAGTCGTTTTTCAATGTCATTAATCACGCTAGTACAACTTGCAATCACTAA
3028020 TTAGAT
1 TTAGAT
3028026 ATGCTGATGG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (63 bp):
TTAGATCAGCACAAGTCGTTTTTCAATGTCATTAATCACGCTAGTACAACTTGCAATCACTAA
Found at i:3029218 original size:13 final size:13
Alignment explanation
Indices: 3029200--3029226 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3029190 TTGTTTGTAA
3029200 ACCTATTATGCTT
1 ACCTATTATGCTT
3029213 ACCTATTATGCTT
1 ACCTATTATGCTT
3029226 A
1 A
3029227 TTAGCTTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (13 bp):
ACCTATTATGCTT
Found at i:3031666 original size:2 final size:2
Alignment explanation
Indices: 3031659--3031683 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3031649 GGCTTGTTTG
3031659 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
3031684 CCTACATACA
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:3034017 original size:21 final size:20
Alignment explanation
Indices: 3033961--3034038 Score: 58
Period size: 20 Copynumber: 3.9 Consensus size: 20
3033951 ATATATCTTT
*
3033961 ATAATTAATTTAAA-TAAAA
1 ATAATTATTTTAAATTAAAA
*
3033980 AT-ATT-TTTTATTTATTAAATA
1 ATAATTATTTTA--AATTAAA-A
3034001 ATAATTATTTTAAATT-AAA
1 ATAATTATTTTAAATTAAAA
3034020 A-AATTAATATTTAAATTAA
1 ATAATT-AT-TTTAAATTAA
3034039 TTTGTTTCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
17 4 0.09
18 7 0.15
19 7 0.15
20 14 0.30
21 7 0.15
22 3 0.06
23 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATTATTTTAAATTAAAA
Found at i:3035047 original size:16 final size:16
Alignment explanation
Indices: 3035005--3035049 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
3034995 AATATTAAAA
3035005 TAAAA-AATAATTTTT
1 TAAAATAATAATTTTT
* **
3035020 TAATATTTTAATTTTT
1 TAAAATAATAATTTTT
3035036 TAAAATAATAATTT
1 TAAAATAATAATTT
3035050 AAATTTATAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAAATAATAATTTTT
Found at i:3035050 original size:21 final size:21
Alignment explanation
Indices: 3035020--3035096 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
3035010 AATAATTTTT
* * *
3035020 TAATATTTTAATTTTTTAAAA
1 TAATAATTTAAATTTATAAAA
*
3035041 TAATAATTTAAATTTATAAAT
1 TAATAATTTAAATTTATAAAA
3035062 TAAATTAAATTTAAATTTA-AACAA
1 T-AA-T-AATTTAAATTTATAA-AA
*
3035086 AAAT-ATTTAAA
1 TAATAATTTAAA
3035097 AATTTTTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 7 0.15
21 18 0.39
22 3 0.07
23 5 0.11
24 13 0.28
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATAATTTAAATTTATAAAA
Found at i:3035056 original size:6 final size:6
Alignment explanation
Indices: 3035045--3035082 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
3035035 TTAAAATAAT
*
3035045 AATTTA AATTTA TAAATTA AA-TTA AATTTA AATTTA AA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AA
3035083 CAAAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 5 0.17
6 19 0.66
7 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:3035782 original size:245 final size:246
Alignment explanation
Indices: 3035351--3035841 Score: 779
Period size: 245 Copynumber: 2.0 Consensus size: 246
3035341 ATGGTGACTG
* * * *
3035351 GTATAGTTGACTTCTCAACTTTGGAGTAATCTATGCTTTTTTTGATTTGAGTTGTTTTTTTATAT
1 GTATAGTTGACTTCTCAACTTTGGAGTAATCTATGCCTTCTTTGATTTAAGTCGTTTTTTTATAT
* * * *
3035416 AGAGGTTACCAAGGCGGTCCTCAGTATCATGATTGACTTGCAGAAAGCCAAGTCTACCTCTCAAT
66 AAAGGTTACCAAGGCGATCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTACCTCTCAAT
* *
3035481 CACCCGTTCCACAAGTTAATGTCTACCATTCAATCCTCTCATTCCACAAGTTGATGTCTGCCTCT
131 CACCCGTTCCACAAGTTAATGTCTACCACTCAATCCTCTCATTCCACAAGTTGATGTCTACCTCT
* * * *
3035546 CAATCACACCCCATTCTACAAGGTAATGTTTACCTCTCAATCTCAACCCAT
196 CAATCACACCCCATTCCACAAGGTAATATCTACCTCTCAATCCCAACCCAT
* *
3035597 GTATAGTTGACTTCTCAACTTTGGGGTGATCTATGCCTTCTTTGATTTAAGTCGTTTTTTTATAT
1 GTATAGTTGACTTCTCAACTTTGGAGTAATCTATGCCTTCTTTGATTTAAGTCGTTTTTTTATAT
3035662 AAAGGTTA-CAAGGCGATCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTACCTCTCAAT
66 AAAGGTTACCAAGGCGATCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTACCTCTCAAT
*
3035726 CCCCCGTTCCACAAGTTAATGTCTACCACTCAATCACTC-CATTCCACAAGTTGATGTCTACCTC
131 CACCCGTTCCACAAGTTAATGTCTACCACTCAATC-CTCTCATTCCACAAGTTGATGTCTACCTC
* * *
3035790 TCAATCATACTCCATTCCACAAGGTAATATCTACCTCTCAATCCCACCCCAT
195 TCAATCACACCCCATTCCACAAGGTAATATCTACCTCTCAATCCCAACCCAT
3035842 TCCACAAGTT
Statistics
Matches: 224, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
245 155 0.69
246 69 0.31
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (246 bp):
GTATAGTTGACTTCTCAACTTTGGAGTAATCTATGCCTTCTTTGATTTAAGTCGTTTTTTTATAT
AAAGGTTACCAAGGCGATCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTACCTCTCAAT
CACCCGTTCCACAAGTTAATGTCTACCACTCAATCCTCTCATTCCACAAGTTGATGTCTACCTCT
CAATCACACCCCATTCCACAAGGTAATATCTACCTCTCAATCCCAACCCAT
Found at i:3035811 original size:37 final size:35
Alignment explanation
Indices: 3035712--3035856 Score: 184
Period size: 37 Copynumber: 4.1 Consensus size: 35
3035702 AAAAAGCCAA
*
3035712 GTCTACCTCTCAATC-CCCCGTTCCACAAGTTAAT
1 GTCTACCTCTCAATCACCCCATTCCACAAGTTAAT
* * *
3035746 GTCTACCACTCAATCACTCCATTCCACAAGTTGAT
1 GTCTACCTCTCAATCACCCCATTCCACAAGTTAAT
* *
3035781 GTCTACCTCTCAATCATACTCCATTCCACAAGGTAAT
1 GTCTACCTCTCAATC--ACCCCATTCCACAAGTTAAT
*
3035818 ATCTACCTCTCAATCCCACCCCATTCCACAAGTTAAT
1 GTCTACCTCTCAAT--CACCCCATTCCACAAGTTAAT
3035855 GT
1 GT
3035857 ATGACACTTG
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
34 14 0.15
35 30 0.32
37 50 0.53
39 1 0.01
ACGTcount: A:0.28, C:0.36, G:0.08, T:0.29
Consensus pattern (35 bp):
GTCTACCTCTCAATCACCCCATTCCACAAGTTAAT
Found at i:3035824 original size:72 final size:70
Alignment explanation
Indices: 3035712--3035856 Score: 184
Period size: 72 Copynumber: 2.0 Consensus size: 70
3035702 AAAAAGCCAA
* * * *
3035712 GTCTACCTCTCAATCCCCCGTTCCACAAGTTAATGTCTACCACTCAAT-CACTCCATTCCACAAG
1 GTCTACCTCTCAATCCCCCATTCCACAAGGTAATATCTACCACTCAATCCACCCCATTCCACAAG
*
3035776 TTGAT
66 TTAAT
* *
3035781 GTCTACCTCTCAATCATACTCCATTCCACAAGGTAATATCTACCTCTCAATCCCACCCCATTCCA
1 GTCTACCTCTCAATC---CCCCATTCCACAAGGTAATATCTACCACTCAAT-CCACCCCATTCCA
3035846 CAAGTTAAT
62 CAAGTTAAT
3035855 GT
1 GT
3035857 ATGACACTTG
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
69 15 0.23
72 28 0.44
74 21 0.33
ACGTcount: A:0.28, C:0.36, G:0.08, T:0.29
Consensus pattern (70 bp):
GTCTACCTCTCAATCCCCCATTCCACAAGGTAATATCTACCACTCAATCCACCCCATTCCACAAG
TTAAT
Found at i:3036371 original size:2 final size:2
Alignment explanation
Indices: 3036364--3036406 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
3036354 ACCATTCTTT
3036364 TA TA TA TA TA TA TA T- TA TA TA TA TA T- 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
3036404 TA T
1 TA T
3036407 TGCAATGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3036383 original size:15 final size:15
Alignment explanation
Indices: 3036363--3036407 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
3036353 CACCATTCTT
3036363 TTATATATATATATA
1 TTATATATATATATA
3036378 TTATATATATAT-TA
1 TTATATATATATATA
3036392 -TATATATATATATA
1 TTATATATATATATA
3036406 TT
1 TT
3036408 GCAATGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.39
14 4 0.14
15 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATATATATATATA
Found at i:3037155 original size:12 final size:12
Alignment explanation
Indices: 3037140--3037177 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3037130 AAAATTTTTT
3037140 ATTTAAATTTGA
1 ATTTAAATTTGA
3037152 ATTT-AATTT-A
1 ATTTAAATTTGA
3037162 ATTTATAATTTGA
1 ATTTA-AATTTGA
3037175 ATT
1 ATT
3037178 ATTATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.22
11 5 0.22
12 9 0.39
13 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (12 bp):
ATTTAAATTTGA
Found at i:3037794 original size:15 final size:15
Alignment explanation
Indices: 3037776--3037811 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3037766 TGTAAATTTT
*
3037776 ATTTTTTATAATTAA
1 ATTTTTTACAATTAA
*
3037791 ATTTTTTACGATTAA
1 ATTTTTTACAATTAA
3037806 ATTTTT
1 ATTTTT
3037812 ATTTATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTTTTTACAATTAA
Found at i:3038265 original size:17 final size:17
Alignment explanation
Indices: 3038222--3038266 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
3038212 TTTTAATTAG
3038222 TATT-AATAA-AAATTT
1 TATTAAATAATAAATTT
*
3038237 AATTATAA-AATAAATTT
1 TATTA-AATAATAAATTT
3038254 TATTAAATAATAA
1 TATTAAATAATAA
3038267 TTATGTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.12
16 4 0.17
17 17 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATTAAATAATAAATTT
Found at i:3038312 original size:36 final size:35
Alignment explanation
Indices: 3038196--3038312 Score: 84
Period size: 32 Copynumber: 3.3 Consensus size: 35
3038186 GGGGTTTTTT
* * *
3038196 ATTT-TTATTTTATAAATTTTAATTAGTATTAATAAAA
1 ATTTATTATTTAAAAAATTTTAATTA-TAAT-AT-AAA
* *
3038233 ATTTAATTA-TAAAATAAATTTT-ATTA-AATA-ATA
1 ATTT-ATTATTTAAA-AAATTTTAATTATAATATAAA
3038266 A-TTATGTATTTAAAAAATTTTAATTATAATATGAAA
1 ATTTAT-TATTTAAAAAATTTTAATTATAATAT-AAA
3038302 ATTTATTATTT
1 ATTTATTATTT
3038313 TAAATATATT
Statistics
Matches: 63, Mismatches: 7, Indels: 21
0.69 0.08 0.23
Matches are distributed among these distances:
31 2 0.03
32 11 0.17
33 11 0.17
34 4 0.06
35 1 0.02
36 10 0.16
37 8 0.13
38 6 0.10
39 10 0.16
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (35 bp):
ATTTATTATTTAAAAAATTTTAATTATAATATAAA
Found at i:3038600 original size:22 final size:21
Alignment explanation
Indices: 3038554--3038624 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 21
3038544 TAAATATACG
* *
3038554 AAAAATAA-AAAATATGATAT
1 AAAAATAATAAAACATAATAT
3038574 AAAAAATAATTAAAACATAATAT
1 -AAAAATAA-TAAAACATAATAT
**
3038597 AAAAATAAATATGACATAAATAT
1 AAAAAT-AATAAAACAT-AATAT
3038620 AAAAA
1 AAAAA
3038625 CATATAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
21 8 0.19
22 12 0.29
23 22 0.52
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (21 bp):
AAAAATAATAAAACATAATAT
Found at i:3038618 original size:23 final size:22
Alignment explanation
Indices: 3038556--3038624 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
3038546 AATATACGAA
*
3038556 AAATAAAAAATATGATATAAAAAAT
1 AAATAAAACATA--ATAT-AAAAAT
*
3038581 AATTAAAACATAATATAAAAAT
1 AAATAAAACATAATATAAAAAT
**
3038603 AAATATGACATAAATATAAAAA
1 AAATAAAACAT-AATATAAAAA
3038625 CATATAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 14 0.37
23 14 0.37
25 10 0.26
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (22 bp):
AAATAAAACATAATATAAAAAT
Found at i:3038900 original size:18 final size:20
Alignment explanation
Indices: 3038857--3038901 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
3038847 TTATGTAGTT
3038857 AATTTTATATTATTAATAAA
1 AATTTTATATTATTAATAAA
3038877 AA-TTTA-ATTA-TAA-AATA
1 AATTTTATATTATTAATAA-A
3038894 AATTTTAT
1 AATTTTAT
3038902 TAAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.09
17 6 0.27
18 8 0.36
19 4 0.18
20 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTTATATTATTAATAAA
Found at i:3038910 original size:17 final size:17
Alignment explanation
Indices: 3038866--3038911 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
3038856 TAATTTTATA
3038866 TTATT-AATAA-AAATT
1 TTATTAAATAATAAATT
*
3038881 TAATTATAA-AATAAATT
1 TTATTA-AATAATAAATT
3038898 TTATTAAATAATAA
1 TTATTAAATAATAA
3038912 TTATGTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.16
16 4 0.16
17 17 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTATTAAATAATAAATT
Found at i:3039031 original size:16 final size:17
Alignment explanation
Indices: 3039010--3039042 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3039000 ATAAATAATG
3039010 ATATTTTTAATT-TTTT
1 ATATTTTTAATTATTTT
3039026 ATATTTTTAATTATTTT
1 ATATTTTTAATTATTTT
3039043 CAATAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATATTTTTAATTATTTT
Found at i:3039284 original size:24 final size:21
Alignment explanation
Indices: 3039241--3039298 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 21
3039231 TTATATTATT
3039241 TTAAATATATAAAAAATAAAGACA
1 TTAAATA-A-AAAAAATAAA-ACA
3039265 TTAAATAAAAAATAATTAAAACA
1 TTAAATAAAAAA-AA-TAAAACA
3039288 -TAATATAAAAA
1 TTAA-ATAAAAA
3039299 TCAATATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 7 0.23
23 13 0.42
24 11 0.35
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (21 bp):
TTAAATAAAAAAAATAAAACA
Found at i:3039528 original size:2 final size:2
Alignment explanation
Indices: 3039521--3039556 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3039511 TGTAGTTAAT
*
3039521 TA TA TA TA TA TA TA TA TG 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
3039557 AATTAATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3039892 original size:18 final size:19
Alignment explanation
Indices: 3039869--3039905 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3039859 CACGTAAATT
3039869 TTTTTTTCTTTTTC-TTTC
1 TTTTTTTCTTTTTCATTTC
*
3039887 TTTTTTTTTTTTTCATTTC
1 TTTTTTTCTTTTTCATTTC
3039906 AAATCTCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTCTTTTTCATTTC
Found at i:3039892 original size:19 final size:19
Alignment explanation
Indices: 3039868--3039905 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3039858 GCACGTAAAT
3039868 TTTTTTTTCTTTTTC-TTTC
1 TTTTTTTT-TTTTTCATTTC
3039887 TTTTTTTTTTTTTCATTTC
1 TTTTTTTTTTTTTCATTTC
3039906 AAATCTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTTTTTCATTTC
Found at i:3040029 original size:16 final size:17
Alignment explanation
Indices: 3039995--3040041 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
3039985 ATATTAGTAG
*
3039995 ATATAATATAAATATATTT
1 ATATAATATTAA-A-ATTT
3040014 ATAT-ATATTAAAATTT
1 ATATAATATTAAAATTT
3040030 ATATAATATTAA
1 ATATAATATTAA
3040042 TATAAGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 8 0.31
17 8 0.31
18 6 0.23
19 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAATATTAAAATTT
Found at i:3040271 original size:23 final size:23
Alignment explanation
Indices: 3040245--3040307 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
3040235 TTTATTAATT
3040245 AATTTTAAATTTAAAATTTAAAA
1 AATTTTAAATTTAAAATTTAAAA
*
3040268 AATTATT-AATTTATAATTTTAAAA
1 AATT-TTAAATTTA-AAATTTAAAA
* *
3040292 ATTTTTATATTTAAAA
1 AATTTTAAATTTAAAA
3040308 ATAAATTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTTTAAATTTAAAATTTAAAA
Found at i:3040697 original size:21 final size:23
Alignment explanation
Indices: 3040664--3040728 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 23
3040654 TAATAATTAT
3040664 ATAATATAAATAAGATATAAAAA
1 ATAATATAAATAAGATATAAAAA
*
3040687 A-ATTA-AAATAA-ATTATAAAAA
1 ATAATATAAATAAGA-TATAAAAA
*
3040708 ATAATATAAATATGATATAAA
1 ATAATATAAATAAGATATAAA
3040729 TATTTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
20 1 0.03
21 15 0.43
22 6 0.17
23 12 0.34
24 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (23 bp):
ATAATATAAATAAGATATAAAAA
Found at i:3040741 original size:16 final size:16
Alignment explanation
Indices: 3040722--3040808 Score: 52
Period size: 16 Copynumber: 5.2 Consensus size: 16
3040712 TATAAATATG
3040722 ATATAAATATTTAAAT
1 ATATAAATATTTAAAT
*
3040738 ATATTAAA-ATTTATAT
1 ATA-TAAATATTTAAAT
* * **
3040754 AAATAAAAATTATTATTT
1 ATATAAATA-T-TTAAAT
*
3040772 ATAAAAATATATATAAAT
1 ATATAAATAT-T-TAAAT
3040790 ATAT-AATATTTTAAAT
1 ATATAAATA-TTTAAAT
3040806 ATA
1 ATA
3040809 ATTATAAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
15 4 0.07
16 21 0.38
17 13 0.23
18 18 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAAATATTTAAAT
Found at i:3040804 original size:28 final size:28
Alignment explanation
Indices: 3040715--3040804 Score: 74
Period size: 32 Copynumber: 3.0 Consensus size: 28
3040705 AAAATAATAT
* *
3040715 AAATATGATATAAATATTTAAATATATT-A
1 AAATAT-ATATAAATATAT-AATATTTTAA
* * *
3040744 AAATTTATATAAATAAAAATTATTATTTATAA
1 AAATATATATAAAT--ATA-TAATATTT-TAA
3040776 AAATATATATAAATATATAATATTTTAA
1 AAATATATATAAATATATAATATTTTAA
3040804 A
1 A
3040805 TATAATTATA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
28 12 0.25
29 12 0.25
30 8 0.17
31 2 0.04
32 14 0.29
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
AAATATATATAAATATATAATATTTTAA
Found at i:3041244 original size:12 final size:12
Alignment explanation
Indices: 3041197--3041257 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
3041187 TAAGACACAT
3041197 ATATAATA-AAA
1 ATATAATATAAA
*
3041208 ATAATTAATATATA
1 AT-A-TAATATAAA
* *
3041222 ATTTAAAATAAA
1 ATATAATATAAA
3041234 ATATAATATAAAA
1 ATATAATAT-AAA
3041247 ATATAA-ATAAA
1 ATATAATATAAA
3041258 TAAATTTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
11 5 0.12
12 17 0.43
13 14 0.35
14 4 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:3041272 original size:10 final size:10
Alignment explanation
Indices: 3041259--3041313 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
3041249 ATAAATAAAT
3041259 AAATTTATTA
1 AAATTTATTA
3041269 AAATTTATATA
1 AAATTTAT-TA
*
3041280 AAATTAATTA
1 AAATTTATTA
*
3041290 TTAATTTATTA
1 -AAATTTATTA
*
3041301 TAATTTATATA
1 AAATTTAT-TA
3041312 AA
1 AA
3041314 TATATAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
10 18 0.47
11 20 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
AAATTTATTA
Found at i:3041290 original size:24 final size:24
Alignment explanation
Indices: 3041201--3041293 Score: 73
Period size: 24 Copynumber: 3.8 Consensus size: 24
3041191 ACACATATAT
* *
3041201 AATAAAAATAATTAATATATAATTTAA
1 AATAAAATTAATT-AT-TAAAATTT-A
* *
3041228 AATAAAATATAA-TATAAAAATATA
1 AATAAAAT-TAATTATTAAAATTTA
*
3041252 AAT-AAATAAATTTATTAAAATTTA
1 AATAAAATTAA-TTATTAAAATTTA
*
3041276 TATAAAATTAATTATTAA
1 AATAAAATTAATTATTAA
3041294 TTTATTATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
22 2 0.04
23 4 0.08
24 23 0.43
25 11 0.21
26 2 0.04
27 8 0.15
28 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AATAAAATTAATTATTAAAATTTA
Found at i:3042969 original size:15 final size:17
Alignment explanation
Indices: 3042951--3042988 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
3042941 TATTTCATGT
3042951 TAATTTATA-TAT-TAA
1 TAATTTATATTATATAA
3042966 TAATTTATATTATATAA
1 TAATTTATATTATATAA
3042983 -AATTTA
1 TAATTTA
3042989 AAATATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 9 0.43
17 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTTATATTATATAA
Found at i:3051524 original size:27 final size:27
Alignment explanation
Indices: 3051470--3051565 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 27
3051460 ATCCACCAAA
*
3051470 TTTGACAAACAACAA-G--TCACAATT
1 TTTGACAAACAAAAAGGAATCACAATT
*
3051494 TTTGACAAACAAAAAGGAATCACTATT
1 TTTGACAAACAAAAAGGAATCACAATT
* * * * *
3051521 TTTGACAAATATAAAGTAACCACCATT
1 TTTGACAAACAAAAAGGAATCACAATT
* *
3051548 TTTTATAAACACAAAAGG
1 TTTGACAAACA-AAAAGG
3051566 TGACTTTTGT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
24 14 0.25
25 1 0.02
27 37 0.66
28 4 0.07
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.27
Consensus pattern (27 bp):
TTTGACAAACAAAAAGGAATCACAATT
Found at i:3052418 original size:8 final size:8
Alignment explanation
Indices: 3052405--3052429 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3052395 ATATAATTAT
3052405 AATATAAA
1 AATATAAA
3052413 AATATAAA
1 AATATAAA
3052421 AATATAAA
1 AATATAAA
3052429 A
1 A
3052430 TATTTACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATATAAA
Found at i:3053550 original size:15 final size:15
Alignment explanation
Indices: 3053520--3053548 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3053510 TTGTGAATAA
3053520 ATTTAATAATATTTT
1 ATTTAATAATATTTT
3053535 ATTTAATAA-ATTTT
1 ATTTAATAATATTTT
3053549 TAATATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTAATAATATTTT
Found at i:3053556 original size:23 final size:24
Alignment explanation
Indices: 3053515--3053564 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
3053505 TTGATTTGTG
*
3053515 AATAAATTTAATAATATTTTATTT
1 AATAAATTTAATAATATTTAATTT
*
3053539 AATAAATTT-TTAATATTTAATTT
1 AATAAATTTAATAATATTTAATTT
3053562 AAT
1 AAT
3053565 TTTTAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATAAATTTAATAATATTTAATTT
Found at i:3053557 original size:18 final size:19
Alignment explanation
Indices: 3053534--3053575 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3053524 AATAATATTT
3053534 TATTTAA-TAAATTTTTAA
1 TATTTAATTAAATTTTTAA
*
3053552 TATTTAATTTAATTTTTAA
1 TATTTAATTAAATTTTTAA
3053571 TATTT
1 TATTT
3053576 TTTATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTAATTAAATTTTTAA
Found at i:3053566 original size:28 final size:28
Alignment explanation
Indices: 3053530--3053583 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
3053520 ATTTAATAAT
*
3053530 ATTTTATTTAATAA-ATTTTTAATATTTA
1 ATTTAATTT-ATAATATTTTTAATATTTA
* *
3053558 ATTTAATTTTTAATATTTTTTATATT
1 ATTTAATTTATAATATTTTTAATATT
3053584 AAAGTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 3 0.14
28 19 0.86
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
ATTTAATTTATAATATTTTTAATATTTA
Found at i:3056014 original size:2 final size:2
Alignment explanation
Indices: 3056009--3056033 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3055999 CCACCATTCT
3056009 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 T
3056034 TACAATGATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3056638 original size:18 final size:18
Alignment explanation
Indices: 3056614--3056654 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3056604 TTTTATAAAT
3056614 AATATTATATAA-ATATTA
1 AATATTA-ATAATATATTA
*
3056632 TATATTAATAATATATTA
1 AATATTAATAATATATTA
3056650 AATAT
1 AATAT
3056655 AAATTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATTAATAATATATTA
Found at i:3056663 original size:24 final size:27
Alignment explanation
Indices: 3056611--3056666 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 27
3056601 TTTTTTTATA
*
3056611 AATAATATTATATAAATATTATATATT
1 AATAATATTATATAAATATTAAATATT
*
3056638 AATAATA-TAT-TAAATA-TAAATTTT
1 AATAATATTATATAAATATTAAATATT
3056662 AATAA
1 AATAA
3056667 AAATATTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 11 0.41
25 6 0.22
26 3 0.11
27 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AATAATATTATATAAATATTAAATATT
Found at i:3056756 original size:17 final size:18
Alignment explanation
Indices: 3056726--3056773 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
3056716 AAATTTTTTG
* *
3056726 TTTAAGTTAAAATTT-AA
1 TTTAATTTATAATTTAAA
3056743 TTTAATTTATAATTTAAA
1 TTTAATTTATAATTTAAA
*
3056761 TTATTATTTATAA
1 TT-TAATTTATAA
3056774 AATATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 13 0.50
18 4 0.15
19 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TTTAATTTATAATTTAAA
Found at i:3057448 original size:17 final size:17
Alignment explanation
Indices: 3057409--3057451 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3057399 ATAATATAAA
* *
3057409 AATAATTTTTTTAATAT
1 AATAATTTTTTAAAAAT
**
3057426 TTTAATTTTTTAAAAAT
1 AATAATTTTTTAAAAAT
3057443 AATAATTTT
1 AATAATTTT
3057452 AATTTATAAA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATAATTTTTTAAAAAT
Found at i:3057461 original size:22 final size:22
Alignment explanation
Indices: 3057420--3057461 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3057410 ATAATTTTTT
*
3057420 TAATATTTTAATTTTTTAAAAA
1 TAATATTTTAATTTTATAAAAA
3057442 TAATAATTTTAA-TTTATAAA
1 TAAT-ATTTTAATTTTATAAA
3057462 TTAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATTTTAATTTTATAAAAA
Found at i:3057716 original size:13 final size:13
Alignment explanation
Indices: 3057683--3057755 Score: 59
Period size: 13 Copynumber: 5.9 Consensus size: 13
3057673 ATAATAATTT
3057683 AAATATAATATAA
1 AAATATAATATAA
*
3057696 TTAA-ATAATATAA
1 -AAATATAATATAA
3057709 AAATATAATAT--
1 AAATATAATATAA
*
3057720 -GATATAATATAA
1 AAATATAATATAA
3057732 AAATA-AA-ATAA
1 AAATATAATATAA
*
3057743 ATATATAAATATA
1 AAATAT-AATATA
3057756 TATCAAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
10 9 0.19
11 8 0.17
12 4 0.09
13 21 0.45
14 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:3057743 original size:34 final size:35
Alignment explanation
Indices: 3057685--3057758 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
3057675 AATAATTTAA
*
3057685 ATATAATATAATTAAATAATATAAAAATAT-AATAT
1 ATATAATATAA-TAAATAAAATAAAAATATAAATAT
*
3057720 GATATAATATAA-AAATAAAATAAATATATAAATAT
1 -ATATAATATAATAAATAAAATAAAAATATAAATAT
3057755 ATAT
1 ATAT
3057759 CAAAATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 19 0.54
35 5 0.14
36 11 0.31
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (35 bp):
ATATAATATAATAAATAAAATAAAAATATAAATAT
Found at i:3057756 original size:8 final size:8
Alignment explanation
Indices: 3057697--3057757 Score: 52
Period size: 8 Copynumber: 7.2 Consensus size: 8
3057687 ATAATATAAT
3057697 TAAATAATA
1 TAAAT-ATA
*
3057706 TAAAAATA
1 TAAATATA
3057714 T-AATATGA
1 TAAATAT-A
3057722 TATAATATA
1 TA-AATATA
* *
3057731 AAAATAAAA
1 TAAAT-ATA
3057740 TAAATATA
1 TAAATATA
3057748 TAAATATA
1 TAAATATA
3057756 TA
1 TA
3057758 TCAAAATTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
7 4 0.10
8 21 0.50
9 12 0.29
10 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (8 bp):
TAAATATA
Found at i:3057758 original size:29 final size:30
Alignment explanation
Indices: 3057668--3057764 Score: 81
Period size: 32 Copynumber: 3.1 Consensus size: 30
3057658 TTACTTACGT
*
3057668 ATAAAAT-AATAATTTAAATATAATATAATTAA
1 ATAAAATAAAT-ATATAAATATAATATAA--AA
* *
3057700 ATAATATAAAAATATAATATGATATAATATAAAA
1 ATAA-A-ATAAATAT-ATA-AATATAATATAAAA
*
3057734 ATAAAATAAATATATAAATAT-ATATCAAA
1 ATAAAATAAATATATAAATATAATATAAAA
3057763 AT
1 AT
3057765 TTATATAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
29 9 0.17
30 4 0.07
31 3 0.06
32 11 0.20
33 2 0.04
34 9 0.17
35 5 0.09
36 11 0.20
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (30 bp):
ATAAAATAAATATATAAATATAATATAAAA
Found at i:3058884 original size:12 final size:11
Alignment explanation
Indices: 3058852--3058955 Score: 57
Period size: 11 Copynumber: 9.8 Consensus size: 11
3058842 TAAGACAGAT
3058852 ATATAA-TAAA
1 ATATAATTAAA
3058862 A-ATAATTAAA
1 ATATAATTAAA
3058872 ATATAATTTAAA
1 ATATAA-TTAAA
* *
3058884 ATA-AAATATA
1 ATATAATTAAA
3058894 ATAT-A--AAA
1 ATATAATTAAA
3058902 ATATTAA-TAAA
1 ATA-TAATTAAA
3058913 ATATTAATATATAA
1 ATA-TAAT-TA-AA
*
3058927 AT-TTATTAAA
1 ATATAATTAAA
3058937 AT-TAATATAAA
1 ATATAAT-TAAA
3058948 AT-TAATTA
1 ATATAATTA
3058956 TTAATTTATC
Statistics
Matches: 78, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
8 5 0.06
9 5 0.06
10 23 0.29
11 28 0.36
12 11 0.14
13 2 0.03
14 4 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATAATTAAA
Found at i:3058888 original size:17 final size:17
Alignment explanation
Indices: 3058868--3058901 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3058858 TAAAAATAAT
*
3058868 TAAAATATAATTTAAAA
1 TAAAATATAATATAAAA
3058885 TAAAATATAATATAAAA
1 TAAAATATAATATAAAA
3058902 ATATTAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATATAATATAAAA
Found at i:3058915 original size:24 final size:23
Alignment explanation
Indices: 3058883--3058948 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 23
3058873 TATAATTTAA
3058883 AATAAAATATAATATAAAAATATT
1 AATAAAATATAATATAAAAAT-TT
*
3058907 AATAAAATATTAATATATAAATTT
1 AATAAAATA-TAATATAAAAATTT
*
3058931 ATTAAAAT-TAATATAAAA
1 AATAAAATATAATATAAAA
3058949 TTAATTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 9 0.24
24 18 0.47
25 11 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AATAAAATATAATATAAAAATTT
Found at i:3058933 original size:27 final size:27
Alignment explanation
Indices: 3058855--3058935 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 27
3058845 GACAGATATA
*
3058855 TAATAAAAATAATTAAAATAT-AATTTA-
1 TAAT-AAAAT-ATTAATATATAAATTTAT
* *
3058882 AAATAAAATA-TAATATA-AAA-ATAT
1 TAATAAAATATTAATATATAAATTTAT
3058906 TAATAAAATATTAATATATAAATTTAT
1 TAATAAAATATTAATATATAAATTTAT
3058933 TAA
1 TAA
3058936 AATTAATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
23 2 0.05
24 17 0.39
25 8 0.18
26 8 0.18
27 9 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
TAATAAAATATTAATATATAAATTTAT
Found at i:3058961 original size:22 final size:22
Alignment explanation
Indices: 3058865--3058955 Score: 76
Period size: 25 Copynumber: 4.0 Consensus size: 22
3058855 TAATAAAAAT
* * *
3058865 AATTAAAATATAATTTAAAATAA
1 AATTAATATATAAATT-AATTAA
* *
3058888 AATATAATATAAAAATATTAATAAA
1 AAT-TAATAT-ATAA-ATTAATTAA
*
3058913 ATATTAATATATAAATTTATTAA
1 A-ATTAATATATAAATTAATTAA
3058936 AATTAATATA-AAATTAATTA
1 AATTAATATATAAATTAATTA
3058956 TTAATTTATC
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
21 9 0.16
22 9 0.16
23 11 0.20
24 8 0.15
25 14 0.25
26 4 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTAATATATAAATTAATTAA
Found at i:3058977 original size:32 final size:33
Alignment explanation
Indices: 3058904--3058979 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 33
3058894 ATATAAAAAT
*
3058904 ATTAATA-AAATATTAATATATAAATTTATTAAA
1 ATTAATATAAA-ATTAATATATAAATTTATCAAA
* *
3058937 ATTAATATAAAATTAAT-TATTAATTTATCATA
1 ATTAATATAAAATTAATATATAAATTTATCAAA
*
3058969 ATTTATATAAA
1 ATTAATATAAA
3058980 TTTATAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 22 0.58
33 13 0.34
34 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (33 bp):
ATTAATATAAAATTAATATATAAATTTATCAAA
Done.