Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004664.1 Hibiscus syriacus cultivar Beakdansim tig00010458_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 132823
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3753 original size:14 final size:14
Alignment explanation
Indices: 3734--3765 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3724 ATTGATAATT
3734 ATAAATTTTTAAAA
1 ATAAATTTTTAAAA
*
3748 ATAAATTTTTAAAT
1 ATAAATTTTTAAAA
3762 ATAA
1 ATAA
3766 TATAAGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAAATTTTTAAAA
Found at i:8965 original size:18 final size:19
Alignment explanation
Indices: 8938--8983 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
8928 GATTCTTATG
*
8938 AACTTAAGTTAT-AGTTTA
1 AACTTGAGTTATGAGTTTA
*
8956 AACTTGAGTT-TGAGTTTC
1 AACTTGAGTTATGAGTTTA
8974 AA-TTGAGTTA
1 AACTTGAGTTA
8984 AGTCTGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (19 bp):
AACTTGAGTTATGAGTTTA
Found at i:16252 original size:15 final size:16
Alignment explanation
Indices: 16232--16262 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
16222 TATTCGTTTG
16232 TATATGAAT-TGTATT
1 TATATGAATGTGTATT
16247 TATATGAATGTGTATT
1 TATATGAATGTGTATT
16263 AATTGTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (16 bp):
TATATGAATGTGTATT
Found at i:21750 original size:34 final size:33
Alignment explanation
Indices: 21674--21750 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 33
21664 GTGGTAAGAA
* * *
21674 ATTTATTTTTATGTTAGTATTTTTTTAAATAGTT
1 ATTT-TTTTTATATTAATATTTTTGTAAATAGTT
21708 ATTATTTTTTATATTAATATATTTATGTAAATA-TT
1 ATT-TTTTTTATATTAATAT-TTT-TGTAAATAGTT
21743 ATTTTTTT
1 ATTTTTTT
21751 ATTAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
34 21 0.57
35 9 0.24
36 7 0.19
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (33 bp):
ATTTTTTTTATATTAATATTTTTGTAAATAGTT
Found at i:21774 original size:31 final size:31
Alignment explanation
Indices: 21706--21782 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
21696 TTTTAAATAG
* *
21706 TTATTATTTTTTATATTAATATATTTATGTAA
1 TTATTATTTTTT-TATTAAAATATATATGTAA
* *
21738 ATATTATTTTTTTATTAAAATA-ATATTTATA
1 TTATTATTTTTTTATTAAAATATATATGTA-A
*
21769 TTATTATTTATTTA
1 TTATTATTTTTTTA
21783 GAATTATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 5 0.13
31 22 0.58
32 11 0.29
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (31 bp):
TTATTATTTTTTTATTAAAATATATATGTAA
Found at i:21943 original size:17 final size:17
Alignment explanation
Indices: 21921--21974 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
21911 AATGTTCATA
21921 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
21938 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
21955 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
21972 TTT
1 TTT
21975 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:23533 original size:21 final size:21
Alignment explanation
Indices: 23503--23550 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
23493 GTAGGGGTAC
* *
23503 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
23524 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
23545 ATGCCA
1 ATGCCA
23551 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:23580 original size:21 final size:21
Alignment explanation
Indices: 23554--23605 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
23544 TATGCCATCT
23554 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
23575 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
23596 CCGCAGGGTT
1 CCGCAGGGTT
23606 TTATACCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:24163 original size:32 final size:33
Alignment explanation
Indices: 24127--24222 Score: 122
Period size: 32 Copynumber: 2.9 Consensus size: 33
24117 TAAATGCTTT
*
24127 TAAAATACAAATTATATTATTCAAATTTAAA-A
1 TAAAATAAAAATTATATTATTCAAATTTAAATA
* *
24159 TAAAATAAAAATAATATTATTCAAAATTTAAATT
1 TAAAATAAAAATTATATTATTC-AAATTTAAATA
* * *
24193 TAAAATATAAATTATAGTATTCGAATTTAA
1 TAAAATAAAAATTATATTATTCAAATTTAA
24223 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
32 20 0.36
33 16 0.29
34 19 0.35
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (33 bp):
TAAAATAAAAATTATATTATTCAAATTTAAATA
Found at i:25226 original size:128 final size:128
Alignment explanation
Indices: 24621--25369 Score: 1207
Period size: 127 Copynumber: 5.9 Consensus size: 128
24611 TTACCTGATT
24621 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* *** *
24686 TGACAAAATAAT-GAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCT-GAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
24748 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
* *** *
24812 ATGACAAAATAATGGAAGGCGCG-CCCCGGGAACGCG-CTTCAAGTCCCCT-GAGAAATAATAGG
65 ATGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
24874 TACTGATATGA-ATAATGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
24937 ATGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
65 ATGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
25001 TACT-ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
*
25065 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGTGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
25128 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
*
25193 TGACAAAATAATGGAAGGCGCGCCCCCGAGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
25256 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
*
25321 TG---AAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
25370 ACTCCGATTA
Statistics
Matches: 599, Mismatches: 15, Indels: 18
0.95 0.02 0.03
Matches are distributed among these distances:
125 114 0.19
126 67 0.11
127 221 0.37
128 197 0.33
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:25329 original size:380 final size:378
Alignment explanation
Indices: 24621--25369 Score: 1195
Period size: 380 Copynumber: 2.0 Consensus size: 378
24611 TTACCTGATT
24621 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
**
24686 TGACAAAATAATGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAC
66 TGACAAAATAATGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCAATGAGAAATAATAGGTAC
24751 TGATATGAATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGA
131 TGATATGAATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGA
* **
24816 CAAAATAATGGAAGGCGCGCCCCGGGAACGCGCTTCAAGTCCCCTGAGAAATAATAGGTACTGAT
196 CAAAATAATGGAAGGCGCGCCCCGAGAACGCGCTTCAAGTCCAATGAGAAATAATAGGTACTGAT
24881 ATGAATAATGTCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGACAAAA
261 ATGAATAATGTCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATG--AAAA
*
24946 TAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
324 TAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
25001 TACT-ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* * * *
25065 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGTGCCTTCATGT-GAATAGTGAAATAATAGGT
66 TGACAAAATAAT-GAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCAAT-GAGAAATAATAGGT
* * *
25129 ACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
129 ACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* * *
25193 TGACAAAATAATGGAAGGCGCGCCCCCGAGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGT
193 TGACAAAATAATGGAAGGCGCG-CCCCGAGAACGCG-CTTCAAGTCCAAT-GAGAAATAATAGGT
* * *
25257 ACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
255 ACTGATATGA-ATAATGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
25321 TG-AAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
318 TGAAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
25370 ACTCCGATTA
Statistics
Matches: 342, Mismatches: 19, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
379 74 0.22
380 174 0.51
381 14 0.04
382 33 0.10
383 47 0.14
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (378 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCAATGAGAAATAATAGGTAC
TGATATGAATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGA
CAAAATAATGGAAGGCGCGCCCCGAGAACGCGCTTCAAGTCCAATGAGAAATAATAGGTACTGAT
ATGAATAATGTCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGAAAATA
ATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:25468 original size:8 final size:8
Alignment explanation
Indices: 25440--25472 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
25430 TCACAAGCTT
25440 TCAAATTC
1 TCAAATTC
*
25448 TCAAACTC
1 TCAAATTC
25456 T-AAATTC
1 TCAAATTC
25463 TCAAATTC
1 TCAAATTC
25471 TC
1 TC
25473 TGAAAATGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (8 bp):
TCAAATTC
Found at i:31502 original size:20 final size:20
Alignment explanation
Indices: 31477--31527 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
31467 ATCCTTTTCT
31477 CTGGTAATCTTTTATTCCAA
1 CTGGTAATCTTTTATTCCAA
*
31497 CTGGTAATCTTTTATTTCAA
1 CTGGTAATCTTTTATTCCAA
31517 CTGGTAATCTT
1 CTGGTAATCTT
31528 ACATTCCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.47
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCAA
Found at i:32609 original size:13 final size:14
Alignment explanation
Indices: 32586--32625 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
32576 TTGATAATGC
32586 GTTCGTTTATGTTA
1 GTTCGTTTATGTTA
**
32600 GTTC-TTTATGTCG
1 GTTCGTTTATGTTA
32613 GTTCGTTTATGTT
1 GTTCGTTTATGTT
32626 TGTTGAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.10, C:0.10, G:0.23, T:0.57
Consensus pattern (14 bp):
GTTCGTTTATGTTA
Found at i:35988 original size:12 final size:12
Alignment explanation
Indices: 35973--36017 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
35963 TATATTTTTT
35973 AAAAATAATATA
1 AAAAATAATATA
35985 AAAAATAATATA
1 AAAAATAATATA
*
35997 AAAAATAATATT
1 AAAAATAATATA
*
36009 GAAAATAAT
1 AAAAATAAT
36018 TTAATGATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
AAAAATAATATA
Found at i:41995 original size:34 final size:34
Alignment explanation
Indices: 41937--42010 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
41927 AAAATAATGA
* *
41937 AAAATATTTTTAAATTATTTAATATTATTGTTTG
1 AAAATATTTTTAAATTAATCAATATTATTGTTTG
* *
41971 AAAATATTTTTAAA-TAGATCAATATTATTTTTTT
1 AAAATATTTTTAAATTA-ATCAATATTATTGTTTG
42005 AAAATA
1 AAAATA
42011 GAAAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 2 0.06
34 33 0.94
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (34 bp):
AAAATATTTTTAAATTAATCAATATTATTGTTTG
Found at i:47640 original size:34 final size:34
Alignment explanation
Indices: 47602--47675 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
47592 ACTGTTATGG
*
47602 TGTTATTTATTTTAGATTTATTGAGACTTAATGA
1 TGTTATTTATTTTAGACTTATTGAGACTTAATGA
* *
47636 TGTTATTTATTTTAGACTTATTGTGATTTAATGA
1 TGTTATTTATTTTAGACTTATTGAGACTTAATGA
47670 TGTTAT
1 TGTTAT
47676 GGTGTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.55
Consensus pattern (34 bp):
TGTTATTTATTTTAGACTTATTGAGACTTAATGA
Found at i:47640 original size:42 final size:40
Alignment explanation
Indices: 47570--47689 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 40
47560 GTTGATTTTG
47570 TTTAGACTTATTGAGACTTATTACTGTTATGGTGTTATTTAT
1 TTTAGACTTATTGAGACTTA-TA-TGTTATGGTGTTATTTAT
*
47612 TTTAGATTTATTGAGACTTA-ATG--A---TGTTATTTAT
1 TTTAGACTTATTGAGACTTATATGTTATGGTGTTATTTAT
* * *
47646 TTTAGACTTATTGTGATTTAATGATGTTATGGTGTTTTTTAT
1 TTTAGACTTATTGAGACTT-AT-ATGTTATGGTGTTATTTAT
47688 TT
1 TT
47690 ATTTGTTTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
34 26 0.40
35 1 0.02
37 4 0.06
39 3 0.05
40 1 0.02
42 30 0.46
ACGTcount: A:0.24, C:0.04, G:0.17, T:0.55
Consensus pattern (40 bp):
TTTAGACTTATTGAGACTTATATGTTATGGTGTTATTTAT
Found at i:47809 original size:65 final size:67
Alignment explanation
Indices: 47738--47892 Score: 163
Period size: 73 Copynumber: 2.3 Consensus size: 67
47728 AATGAACTTT
47738 TGGTGTTATGGTGTTATT-TAGC-AAC-TTCAGTTTCAAATTAATAGTGTAATTGACTTTTGATG
1 TGGTGTTATGGTGTTATTGTAGCTAACTTTC-GTTTCAAATTAATAGTGTAATTGACTTTTGATG
47800 TTA
65 TTA
* * * *
47803 TGGTGTTATTGTGGATCATTTTTTGTTGCTAACTTTCGTTTCAGATTAATAGTGTAATTGACTTT
1 TGGTGTTA---TGG-T--GTTATTGTAGCTAACTTTCGTTTCAAATTAATAGTGTAATTGACTTT
*
47868 TGGTGTTA
60 TGATGTTA
* *
47876 TAGTGTTATTGTGTTAT
1 TGGTGTTATGGTGTTAT
47893 GGTTGTTATT
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
65 8 0.11
67 3 0.04
68 3 0.04
69 2 0.03
70 2 0.03
71 4 0.06
72 3 0.04
73 44 0.61
74 3 0.04
ACGTcount: A:0.22, C:0.07, G:0.21, T:0.50
Consensus pattern (67 bp):
TGGTGTTATGGTGTTATTGTAGCTAACTTTCGTTTCAAATTAATAGTGTAATTGACTTTTGATGT
TA
Found at i:47889 original size:16 final size:17
Alignment explanation
Indices: 47870--47902 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
47860 TTGACTTTTG
47870 GTGTTATAG-TGTTATT
1 GTGTTATAGTTGTTATT
*
47886 GTGTTATGGTTGTTATT
1 GTGTTATAGTTGTTATT
47903 TAAAAATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (17 bp):
GTGTTATAGTTGTTATT
Found at i:49073 original size:21 final size:21
Alignment explanation
Indices: 49035--49074 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
49025 ACATATAATT
* *
49035 ATTTTGTTAATTATGACCTGC
1 ATTTTGTTAATAACGACCTGC
*
49056 ATTTTTTTAATAACGACCT
1 ATTTTGTTAATAACGACCT
49075 TCGAGAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (21 bp):
ATTTTGTTAATAACGACCTGC
Found at i:51417 original size:2 final size:2
Alignment explanation
Indices: 51379--51403 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51369 CAAACTCATA
51379 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
51404 TCGATTCACT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:58558 original size:18 final size:18
Alignment explanation
Indices: 58535--58576 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
58525 TTAATATACT
58535 ATTTGAGATATAATAGTC
1 ATTTGAGATATAATAGTC
*
58553 ATTTGAGATATAATAGTT
1 ATTTGAGATATAATAGTC
58571 ATTTGA
1 ATTTGA
58577 TATTATGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (18 bp):
ATTTGAGATATAATAGTC
Found at i:59655 original size:155 final size:155
Alignment explanation
Indices: 59368--59671 Score: 493
Period size: 155 Copynumber: 2.0 Consensus size: 155
59358 ATATTTATAT
*
59368 ATTCTTTCAATTTGGTCATAGTTTTAATTCAATTTAATAAATTTGATTTTCAAATTAGATGGTGA
1 ATTCTTTCAATTTGGTCATAGTTTTAATTCAATTTAATAAATTTGATTTTCAAATTAGATGGCGA
* * * *
59433 CACGTGTCACTACCAGATTGGAGGCTATTTTATTCATTTTAATTATTTATTTTATTTTATTTTGT
66 CACGGGTCACTACCAGATTGAAGGATATTTTATTCATTTTAATTATTTATTTTATTTTATTTCGT
*
59498 ATCCAATCCGGTGGTGACACAACAC
131 ATCCAATCCAGTGGTGACACAACAC
* * *
59523 ATTCTTTTAATTTGGTCATAGTTTTAATTCAATTTAATAAATTTGATTTTCCAATTAGGTGGCGA
1 ATTCTTTCAATTTGGTCATAGTTTTAATTCAATTTAATAAATTTGATTTTCAAATTAGATGGCGA
* *
59588 CATGGGTCACTACCATATTGAAGGATATTTTATTCATTTTAATTATTTGA-TTTATTTTATTTCG
66 CACGGGTCACTACCAGATTGAAGGATATTTTATTCATTTTAATTATTT-ATTTTATTTTATTTCG
59652 TATCCAATCCAGTGGTGACA
130 TATCCAATCCAGTGGTGACA
59672 TGTGTAACAC
Statistics
Matches: 137, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
155 136 0.99
156 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (155 bp):
ATTCTTTCAATTTGGTCATAGTTTTAATTCAATTTAATAAATTTGATTTTCAAATTAGATGGCGA
CACGGGTCACTACCAGATTGAAGGATATTTTATTCATTTTAATTATTTATTTTATTTTATTTCGT
ATCCAATCCAGTGGTGACACAACAC
Found at i:69193 original size:75 final size:75
Alignment explanation
Indices: 69025--69210 Score: 250
Period size: 74 Copynumber: 2.5 Consensus size: 75
69015 CGTTGAACAT
* * * *
69025 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
** *
69089 AAAATGTTTA
66 AAAACATTCA
* * *
69099 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
*
69163 AAACCATTCA
66 AAAACATTCA
69173 GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCC
1 -GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCC
69211 TCCTATGGGG
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
74 61 0.62
75 22 0.22
76 15 0.15
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.23
Consensus pattern (75 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
AAAACATTCA
Found at i:69201 original size:22 final size:22
Alignment explanation
Indices: 69173--69254 Score: 164
Period size: 22 Copynumber: 3.7 Consensus size: 22
69163 AAACCATTCA
69173 GGGGGGAATCGGTTCCTCCTAT
1 GGGGGGAATCGGTTCCTCCTAT
69195 GGGGGGAATCGGTTCCTCCTAT
1 GGGGGGAATCGGTTCCTCCTAT
69217 GGGGGGAATCGGTTCCTCCTAT
1 GGGGGGAATCGGTTCCTCCTAT
69239 GGGGGGAATCGGTTCC
1 GGGGGGAATCGGTTCC
69255 CTCTGAGCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.13, C:0.22, G:0.39, T:0.26
Consensus pattern (22 bp):
GGGGGGAATCGGTTCCTCCTAT
Found at i:71875 original size:20 final size:21
Alignment explanation
Indices: 71851--71932 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
71841 AGAACCCCAT
*
71851 GGGGGTATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCTGTG
* *
71872 GGGGGAATCGGTTCCCCT-TCAAA
1 GGGGGAATCGATTCCCCTGT---G
* * **
71895 TGGGGAATCGGTT-CCCTCAG
1 GGGGGAATCGATTCCCCTGTG
71915 GGGGGAATCGATTCCCCT
1 GGGGGAATCGATTCCCCT
71933 ATGCACCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
20 12 0.25
21 20 0.42
22 4 0.08
23 12 0.25
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTGTG
Found at i:75777 original size:22 final size:21
Alignment explanation
Indices: 75735--75774 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
75725 GAGTTTGTTT
*
75735 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
75756 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
75775 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:78639 original size:21 final size:20
Alignment explanation
Indices: 78585--78641 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
78575 TAATAAAAAA
*
78585 TTAATATTTTAAAATTAAAT
1 TTAATATTTTAAAAATAAAT
* * *
78605 TTGATAAGTATAAAAATAAAT
1 TTAAT-ATTTTAAAAATAAAT
*
78626 TTAATATTTTTAAAAT
1 TTAATATTTTAAAAAT
78642 GATTTTAAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
TTAATATTTTAAAAATAAAT
Found at i:78807 original size:25 final size:26
Alignment explanation
Indices: 78760--78834 Score: 71
Period size: 28 Copynumber: 2.8 Consensus size: 26
78750 CTATATATAT
* * *
78760 ATTTATTTATATATATCATAAAA-TTA
1 ATTTATTAAT-TATATTAAAAAAGTTA
78786 ATTTATTAATTATATTAAAAAAAAGTTA
1 ATTTATTAATTATATT--AAAAAAGTTA
* *
78814 ATTTAATGATTATATTAAAAA
1 ATTTATTAATTATATTAAAAA
78835 TAAATATAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
25 5 0.12
26 14 0.34
27 5 0.12
28 17 0.41
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (26 bp):
ATTTATTAATTATATTAAAAAAGTTA
Found at i:78825 original size:28 final size:27
Alignment explanation
Indices: 78779--78839 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
78769 TATATATCAT
*
78779 AAAATTAATTTATTAATTATATTAAAA
1 AAAATTAATTTAATAATTATATTAAAA
*
78806 AAAAGTTAATTTAATGATTATATTAAAA
1 AAAA-TTAATTTAATAATTATATTAAAA
78834 ATAAAT
1 A-AAAT
78840 ATAGGTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 4 0.13
28 23 0.77
29 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
AAAATTAATTTAATAATTATATTAAAA
Found at i:79221 original size:5 final size:5
Alignment explanation
Indices: 79206--79246 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
79196 GATAAGAAGA
*
79206 TATTT TA-TT TATTT TA-AT TA-TT TATTT TATTT TATTT TATT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATT
79247 AAAACTACGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 10 0.31
5 22 0.69
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:79228 original size:13 final size:13
Alignment explanation
Indices: 79210--79234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
79200 AGAAGATATT
79210 TTATTTATTTTAA
1 TTATTTATTTTAA
79223 TTATTTATTTTA
1 TTATTTATTTTA
79235 TTTTATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTATTTTAA
Found at i:79896 original size:16 final size:16
Alignment explanation
Indices: 79877--79909 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
79867 TTAAGACAAA
79877 TATAATTAAAAAAAAT
1 TATAATTAAAAAAAAT
*
79893 TATAATTAAAGAAAAT
1 TATAATTAAAAAAAAT
79909 T
1 T
79910 TAAACTTTAG
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:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
TATAATTAAAAAAAAT
Found at i:80118 original size:7 final size:7
Alignment explanation
Indices: 80108--80132 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
80098 AAACTCTAAG
80108 TTAGTGT
1 TTAGTGT
80115 TTAGTGT
1 TTAGTGT
80122 TTAGTGT
1 TTAGTGT
80129 TTAG
1 TTAG
80133 ATGTAATTAG
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:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (7 bp):
TTAGTGT
Found at i:83628 original size:12 final size:12
Alignment explanation
Indices: 83613--83687 Score: 53
Period size: 13 Copynumber: 5.9 Consensus size: 12
83603 ATAAAATAGT
83613 AAATAAAAAAAC
1 AAATAAAAAAAC
* *
83625 AAATAATAAAAT
1 AAATAAAAAAAC
* *
83637 ATATATAAAAAAG
1 AAATA-AAAAAAC
*
83650 AAA-AAGAAAAAGA
1 AAATAA-AAAAA-C
83663 AAATAAATAAAAC
1 AAATAAA-AAAAC
83676 AAATAAACAAAA
1 AAATAAA-AAAA
83688 TAATAATAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
11 1 0.02
12 20 0.41
13 22 0.45
14 6 0.12
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (12 bp):
AAATAAAAAAAC
Found at i:83959 original size:52 final size:51
Alignment explanation
Indices: 83870--83968 Score: 114
Period size: 52 Copynumber: 1.9 Consensus size: 51
83860 AAAGAAATAT
*
83870 ATATATATATATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTTA
1 ATATATATATATAATAATAAAATATAGTAAAAAAAT-AATAAAAATAATTTA
**
83922 ATATATATATATACAT-ATAATAATA-A-TAACATGAATAATAAAAATAA
1 ATATATATATATA-ATAATAA-AATATAGTAA-AAAAATAATAAAAATAA
83969 ATGAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
51 13 0.32
52 22 0.54
53 6 0.15
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (51 bp):
ATATATATATATAATAATAAAATATAGTAAAAAAATAATAAAAATAATTTA
Found at i:83961 original size:18 final size:17
Alignment explanation
Indices: 83938--83980 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
83928 ATATATACAT
83938 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
83956 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
83973 ATAA-AATA
1 ATAATAATA
83981 TCTATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:83981 original size:56 final size:55
Alignment explanation
Indices: 83866--83988 Score: 142
Period size: 58 Copynumber: 2.2 Consensus size: 55
83856 TATTAAAGAA
* * *
83866 ATATATATATATATATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTTAAT
1 ATATATATATACATATAATAATAAAACATAATAAAAAAATAAATG-AAATAA--TAAT
83924 ATATATATATACATATAATAATAATAACATGAATAATAAAAATAAATG-AATAA-AAT
1 ATATATATATACATATAATAATAA-AACAT-AATAA-AAAAATAAATGAAATAATAAT
*
83980 ATCTATATA
1 ATATATATA
83989 ATAAATAAAG
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
56 11 0.19
58 23 0.40
59 9 0.16
60 4 0.07
61 11 0.19
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.33
Consensus pattern (55 bp):
ATATATATATACATATAATAATAAAACATAATAAAAAAATAAATGAAATAATAAT
Found at i:85288 original size:105 final size:105
Alignment explanation
Indices: 84984--85614 Score: 887
Period size: 105 Copynumber: 6.0 Consensus size: 105
84974 GCATTGTTCC
* * ** *
84984 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
85048 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
85090 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTTA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
** *
85150 CAGCGGTCCCTTCAACGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
85190 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
85255 CAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
85295 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTGTGAGATTGGGAAGTTATTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
85360 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
85400 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
85465 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
85505 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
85570 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
85611 GAGT
1 GAGT
85615 GTCACGATAT
Statistics
Matches: 478, Mismatches: 40, Indels: 14
0.90 0.08 0.03
Matches are distributed among these distances:
100 81 0.17
101 1 0.00
102 7 0.01
104 5 0.01
105 298 0.62
106 86 0.18
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:85874 original size:36 final size:36
Alignment explanation
Indices: 85814--85889 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
85804 TGTTTGGAGA
* * *
85814 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
* *
85850 GAAACTATCTTAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
85886 GAAA
1 GAAA
85890 TGTTTTCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:86010 original size:105 final size:104
Alignment explanation
Indices: 85789--86107 Score: 491
Period size: 105 Copynumber: 3.1 Consensus size: 104
85779 TTCGTTAAAT
* ** *
85789 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * *
85851 AAACTATCTTAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
85890 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
85955 AAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAATTCATTTCAAGGGAAA
* *
85995 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTCTGTTTAGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * *
86060 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGCGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
86099 TGTTTTCAA
1 TGTTTTCAA
86108 GAGAAACTGT
Statistics
Matches: 200, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
101 46 0.23
103 3 0.01
104 52 0.26
105 99 0.50
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:86262 original size:36 final size:36
Alignment explanation
Indices: 86222--86336 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
86212 CTTTCGAGTG
* *
86222 AAAACGATCTCAAGCGAGACAAATCTTGTTTTAAGA
1 AAAACAATCTCAAGTGAGACAAATCTTGTTTTAAGA
** * * * **
86258 AAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGA
1 AAAACAATCTCAAGTGAGACAAATCTTGTTTTAAGA
* * *
86294 AAAATAGTCTCAAGTGAGACAAAGT-ATGTTTTAAGA
1 AAAACAATCTCAAGTGAGACAAA-TCTTGTTTTAAGA
86330 AAAACAA
1 AAAACAA
86337 ATTTGAGTGA
Statistics
Matches: 57, Mismatches: 21, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
36 56 0.98
37 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (36 bp):
AAAACAATCTCAAGTGAGACAAATCTTGTTTTAAGA
Found at i:86324 original size:72 final size:74
Alignment explanation
Indices: 86181--86351 Score: 199
Period size: 72 Copynumber: 2.3 Consensus size: 74
86171 AATATTCTTA
** * *
86181 AAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGATCTCAAGCGAGACAAAT
1 AAAAACAATCTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAAAGATCTCAAGCGAGACAAAT
*
86246 CTTGTTTTAAG
64 CATGTTTTAAG
*
86257 AAAAACAATCTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAATAG-TCTCAAGTGAGACAAAGT
1 AAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAA-AGATCTCAAGCGAGACAAA-T
86319 -ATGTTTTAAG
64 CATGTTTTAAG
*
86329 AAAAACAAAT-TTGAGTGAGATAA
1 AAAAAC-AATCTTGAGTGAAATAA
86352 TCATCTGCAT
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
72 46 0.54
73 16 0.19
75 4 0.05
76 19 0.22
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (74 bp):
AAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAAAGATCTCAAGCGAGACAAATCA
TGTTTTAAG
Found at i:87800 original size:183 final size:183
Alignment explanation
Indices: 87492--88028 Score: 932
Period size: 183 Copynumber: 2.9 Consensus size: 183
87482 ATCAGGTTTA
*
87492 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* ** *
87557 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCTAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
87621 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
87675 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAATGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
87740 GTCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
87805 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAACTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
87858 ACTGAAGGATTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
87923 GCCAAGTGTCTGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
* * *
87988 TTCTCTATAACCAATTTCCTTAGTGAAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
88029 CGGATTTAAT
Statistics
Matches: 335, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
183 334 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:91995 original size:26 final size:25
Alignment explanation
Indices: 91913--92018 Score: 67
Period size: 24 Copynumber: 4.0 Consensus size: 25
91903 AAATGAAAAG
91913 AAAACAAATTAAGTAAAATGATAAAATAAA
1 AAAACAAA-TAA-TAAAAT-AT--AATAAA
* *
91943 GAAAGCAAA-GATAAAATAGTAAGTAAA
1 -AAAACAAATAATAAAATA-TAA-TAAA
91970 AAAACAAATAATAAAATAT-ATATAA
1 AAAACAAATAATAAAATATAATA-AA
* *
91995 AAAAGAAA-AAGAAAATA-AATAAA
1 AAAACAAATAATAAAATATAATAAA
92018 A
1 A
92019 CAAATAAACA
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
23 3 0.05
24 13 0.20
25 10 0.16
26 10 0.16
27 13 0.20
28 7 0.11
29 1 0.02
31 7 0.11
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (25 bp):
AAAACAAATAATAAAATATAATAAA
Found at i:92031 original size:22 final size:21
Alignment explanation
Indices: 91966--92044 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 21
91956 AAATAGTAAG
91966 TAAA-AAAACAAATAATAAAATA
1 TAAATAAAACAAATAA-AAAA-A
* *
91988 TATATAAAA-AAGAAAAAGAAAA
1 TAAATAAAACAA-ATAAA-AAAA
92010 TAAATAAAACAAATAAACAAAA
1 TAAATAAAACAAATAAA-AAAA
92032 T-AATAATAACAAA
1 TAAATAA-AACAAA
92045 GTACGAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
21 5 0.11
22 30 0.64
23 12 0.26
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (21 bp):
TAAATAAAACAAATAAAAAAA
Found at i:92303 original size:18 final size:17
Alignment explanation
Indices: 92280--92322 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
92270 ATATATACAT
92280 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
92298 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
92315 ATAA-AATA
1 ATAATAATA
92323 TCTATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:92756 original size:37 final size:37
Alignment explanation
Indices: 92679--92780 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
92669 GTGCTTGTGG
* * * * * *
92679 ATCCTATCTTTAAGAATTTAAATCTTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* *
92716 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
92753 ATCCTATTTTTAGGAGTTTGAATTCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
92781 TATGACGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:93589 original size:15 final size:15
Alignment explanation
Indices: 93560--93600 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 15
93550 ACCAGTTCCA
93560 GATGATGATGGTGAT
1 GATGATGATGGTGAT
93575 G--G-TGATGGTGAT
1 GATGATGATGGTGAT
93587 GATGATGATGGTGA
1 GATGATGATGGTGA
93601 AAGTCTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 11 0.48
13 1 0.04
14 1 0.04
15 10 0.43
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (15 bp):
GATGATGATGGTGAT
Found at i:95127 original size:108 final size:103
Alignment explanation
Indices: 94952--95150 Score: 265
Period size: 108 Copynumber: 1.9 Consensus size: 103
94942 TCCTGAAGTC
* *
94952 TTATGCTGACTCATTGATTCTCTCATTTCCACTCTTGGGATTAGCTTGGTCGAAGGTGATAACGA
1 TTATGCTGACACATTGATTCTCTCATTTCCACTCTTGGGATTAGCTTGGTCCAAGGTGATAACGA
95017 AAGCAG-TTATATCATCTATTTAAATATTTCCCAAGGCT
66 AAGC-GTTTATATCATCTATTTAAATATTTCCCAAGGCT
* * *
95055 TTATGCTGACACATTGGTTCTCTCTTTTTCCATTCTTTCTTGTGATTAGCTTGGTCCAAGGTGAT
1 TTATGCTGACACATTGATTCTCTC-ATTTCCA--C--TCTTGGGATTAGCTTGGTCCAAGGTGAT
** *
95120 ATTGAAAGCGTTTTTATCATCTATTTAAATA
61 AACGAAAGCGTTTATATCATCTATTTAAATA
95151 AAAACAAATA
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
103 22 0.27
104 6 0.07
106 1 0.01
107 1 0.01
108 52 0.63
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (103 bp):
TTATGCTGACACATTGATTCTCTCATTTCCACTCTTGGGATTAGCTTGGTCCAAGGTGATAACGA
AAGCGTTTATATCATCTATTTAAATATTTCCCAAGGCT
Found at i:98858 original size:2 final size:2
Alignment explanation
Indices: 98853--98887 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
98843 CTTGGGATTC
98853 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
98888 CCTGCTGTTC
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:100413 original size:2 final size:2
Alignment explanation
Indices: 100408--100433 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
100398 AAATATATTC
100408 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
100434 CCTCGAGTTG
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:101888 original size:14 final size:14
Alignment explanation
Indices: 101869--101924 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
101859 CGTTCGTGAA
101869 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
101883 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
101896 --TT-GTTTATGTT
1 CGTTCGATTATGTT
101907 CGTTCGATTATGTT
1 CGTTCGATTATGTT
101921 CGTT
1 CGTT
101925 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:101903 original size:24 final size:24
Alignment explanation
Indices: 101876--101945 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
101866 GAACGTTCGA
*
101876 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
101900 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
101924 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
101946 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:102685 original size:10 final size:10
Alignment explanation
Indices: 102670--102744 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
102660 GGGTCTCTAA
102670 CGTTTATGTT
1 CGTTTATGTT
102680 CGTTTATGTT
1 CGTTTATGTT
102690 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
102701 ATGTTCGTGTT
1 -CGTTTATGTT
102712 CGTTTATGTT
1 CGTTTATGTT
102722 CG----TGTT
1 CGTTTATGTT
102728 CGTTTATGTT
1 CGTTTATGTT
102738 CGTTTAT
1 CGTTTAT
102745 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:102701 original size:16 final size:16
Alignment explanation
Indices: 102676--102740 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
102666 CTAACGTTTA
102676 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
102692 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
102708 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
102724 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
102740 T
1 T
102741 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:103691 original size:12 final size:12
Alignment explanation
Indices: 103674--103717 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
103664 TCCTTTCCAA
103674 CTTGTTTATTAG
1 CTTGTTTATTAG
** *
103686 CTTGTTTACCAA
1 CTTGTTTATTAG
*
103698 CTAGTTTATTAG
1 CTTGTTTATTAG
103710 CTTGTTTA
1 CTTGTTTA
103718 CCGATTAGTT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.52
Consensus pattern (12 bp):
CTTGTTTATTAG
Found at i:103697 original size:24 final size:24
Alignment explanation
Indices: 103670--103735 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
103660 TTCATCCTTT
*
103670 CCAACTTGTTTATTAGCTTGTTTA
1 CCAACTAGTTTATTAGCTTGTTTA
103694 CCAACTAGTTTATTAGCTTGTTTA
1 CCAACTAGTTTATTAGCTTGTTTA
* * *
103718 CCGATTAGTTTATAAGCT
1 CCAACTAGTTTATTAGCT
103736 CATTTACTCG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (24 bp):
CCAACTAGTTTATTAGCTTGTTTA
Found at i:103741 original size:24 final size:24
Alignment explanation
Indices: 103690--103749 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
103680 TATTAGCTTG
* * * **
103690 TTTACCAACTAGTTTATTAGCTTG
1 TTTACCGATTAGTTTATAAGCTCA
103714 TTTACCGATTAGTTTATAAGCTCA
1 TTTACCGATTAGTTTATAAGCTCA
103738 TTTACTCGATTA
1 TTTAC-CGATTA
103750 TCATTTTCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 24 0.80
25 6 0.20
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.45
Consensus pattern (24 bp):
TTTACCGATTAGTTTATAAGCTCA
Found at i:104593 original size:20 final size:20
Alignment explanation
Indices: 104570--104621 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
104560 AACGCGATCC
104570 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
104590 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
104610 CCAAAATCGCAA
1 CCAGAATCGCAA
104622 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:104638 original size:21 final size:20
Alignment explanation
Indices: 104612--104709 Score: 65
Period size: 21 Copynumber: 4.8 Consensus size: 20
104602 ATCAGTTTCC
104612 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * **
104633 AAAATCGCGATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
104652 ACAAATTCGCATTGCGATTTT-
1 A-AAA-TCGCAACGCGATTTTG
* *
104673 ACATAATCGCAACGCGAATATG
1 A-A-AATCGCAACGCGATTTTG
104695 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
104710 ACACATAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.28
21 40 0.66
22 3 0.05
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:104771 original size:20 final size:20
Alignment explanation
Indices: 104677--105045 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
104667 GATTTTACAT
* ** *
104677 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
104697 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
104717 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104737 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
104757 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
104777 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104797 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
104817 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
104837 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
104857 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104877 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
104897 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104917 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
104937 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104957 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
104977 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
104997 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
105017 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
105037 AATCACAAC
1 AATCGCAAC
105046 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:105772 original size:24 final size:24
Alignment explanation
Indices: 105728--105774 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
105718 AAATTTGGTC
*
105728 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCAGACTTTGATA
*
105752 TTGGTCAATA-CACAGATTTTGAT
1 TTGGTCAATATC-CAGACTTTGAT
105775 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCAGACTTTGATA
Found at i:105966 original size:12 final size:12
Alignment explanation
Indices: 105949--105973 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
105939 ATATAATCCT
105949 GAAGAAGAAAAA
1 GAAGAAGAAAAA
105961 GAAGAAGAAAAA
1 GAAGAAGAAAAA
105973 G
1 G
105974 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:108278 original size:19 final size:19
Alignment explanation
Indices: 108256--108581 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
108246 CGGAAAATAC
*
108256 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
108275 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
108289 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
108309 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
108323 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
108342 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
108361 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
108380 AATCGCAA--CGACAT---
1 AATCGCAATGCGAAATGAA
*
108394 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
108413 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
108432 AATCGCAA--CGACAT---
1 AATCGCAATGCGAAATGAA
*
108446 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
108465 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
108484 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
108503 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
108522 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
108536 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
108555 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
108574 AATCGCAA
1 AATCGCAA
108582 CGAGATAATC
Statistics
Matches: 271, Mismatches: 10, Indels: 52
0.81 0.03 0.16
Matches are distributed among these distances:
14 46 0.17
15 1 0.00
16 19 0.07
17 18 0.07
18 2 0.01
19 172 0.63
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:108398 original size:71 final size:71
Alignment explanation
Indices: 108256--108581 Score: 456
Period size: 71 Copynumber: 4.6 Consensus size: 71
108246 CGGAAAATAC
* *
108256 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
*
108316 ACGAGAG
65 ACGAAAG
108323 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
* *
108388 CGACAT
66 CGAAAG
* *
108394 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA--CGACAT---AATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
*
108454 TGCGAAATTAA
66 --CG-AA--AG
108465 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
108530 CGAAAG
66 CGAAAG
108536 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
108582 CGAGATAATC
Statistics
Matches: 233, Mismatches: 11, Indels: 26
0.86 0.04 0.10
Matches are distributed among these distances:
66 8 0.03
67 25 0.11
68 2 0.01
69 7 0.03
71 158 0.68
72 16 0.07
73 7 0.03
74 2 0.01
76 8 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
CGAAAG
Found at i:108508 original size:142 final size:143
Alignment explanation
Indices: 108323--108619 Score: 535
Period size: 142 Copynumber: 2.1 Consensus size: 143
108313 GCAACGAGAG
108323 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
* * *
108388 CGACATAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAACGACATAATCGCA
66 CGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACATAATCGCA
108453 ATGCGAAATTA-A
131 ATGCGAAATTATA
108465 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
*
108530 CGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCA
66 CGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACATAATCGCA
108595 ATGCGAAATTATA
131 ATGCGAAATTATA
*
108608 AA-CGCATTGCGA
1 AATCGCAATGCGA
108620 TTTTCATTTC
Statistics
Matches: 149, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
142 146 0.98
143 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (143 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
CGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACATAATCGCA
ATGCGAAATTATA
Found at i:108582 original size:52 final size:55
Alignment explanation
Indices: 108284--108603 Score: 390
Period size: 52 Copynumber: 6.0 Consensus size: 55
108274 AAATCCCAAC
*
108284 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGA-G-AATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAA
*
108337 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAC
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAA
* *
108392 AT---AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA--CGAC
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAA
*
108444 AT---AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAA
108498 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAA
*
108550 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAA
108602 AT
1 AT
108604 TATAAACGCA
Statistics
Matches: 250, Mismatches: 6, Indels: 23
0.90 0.02 0.08
Matches are distributed among these distances:
52 179 0.72
53 16 0.06
54 10 0.04
55 11 0.04
57 34 0.14
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (55 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAA
Found at i:108719 original size:19 final size:19
Alignment explanation
Indices: 108610--108711 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
108600 AAATTATAAA
108610 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
*
108629 CCGCATTGCGA--TTC-TCT
1 -CGCATTGCGATTTTCATTT
108646 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
108663 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
108682 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
108701 CGCATTGCGAT
1 CGCATTGCGAT
108712 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 5 0.07
17 6 0.08
18 3 0.04
19 45 0.60
20 10 0.13
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:108837 original size:14 final size:14
Alignment explanation
Indices: 108818--108854 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
108808 CATCAATTAC
108818 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
108832 ACAAATCATCTTTT
1 ACAAATCAACTTTT
108846 ACAAATCAA
1 ACAAATCAA
108855 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:108958 original size:22 final size:22
Alignment explanation
Indices: 108906--108960 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
108896 TGGTTGTGAG
**
108906 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
108928 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
108950 GGATTTCTTCG
1 GGATTTCTTCG
108961 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:109131 original size:20 final size:20
Alignment explanation
Indices: 109106--109298 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
109096 CTTTAAATAT
109106 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
109126 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
109148 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
109167 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
109187 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
109207 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
109227 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
109247 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
109267 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
109287 CGCGTTGCGATT
1 CGCGTTGCGATT
109299 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:109293 original size:60 final size:60
Alignment explanation
Indices: 109106--109298 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
109096 CTTTAAATAT
**
109106 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
109167 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
109227 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
109287 CGCGTTGCGATT
1 CGCGTTGCGATT
109299 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:109379 original size:20 final size:20
Alignment explanation
Indices: 109354--109405 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
109344 AAGAATCGCG
*
109354 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
109374 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
109394 TTGCGATTCTGG
1 TTGCGATTCTGG
109406 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:113643 original size:2 final size:2
Alignment explanation
Indices: 113636--113735 Score: 65
Period size: 2 Copynumber: 54.5 Consensus size: 2
113626 CAGGCCGGGG
* * * *
113636 AT AT AT AT AT AT AT TT AA AT -T AA AT AT AT AA AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
113676 AT AT AT AT AT AT AT -T A- AT TT AA AT -T AA AT TT AT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
113713 AT -T AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
113736 AAAATAATTA
Statistics
Matches: 73, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
1 9 0.12
2 64 0.88
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:113696 original size:44 final size:43
Alignment explanation
Indices: 113636--113734 Score: 155
Period size: 44 Copynumber: 2.3 Consensus size: 43
113626 CAGGCCGGGG
113636 ATATATATATA-TATTTAAATTAAATATATAAATATTATATAT
1 ATATATATATATTATTTAAATTAAATATATAAATATTATATAT
* *
113678 ATATATATATATTAATTTAAATTAAATTTATTAATATTATATAT
1 ATATATATATATT-ATTTAAATTAAATATATAAATATTATATAT
113722 ATATATTATATAT
1 ATATA-TATATAT
113735 AAAAATAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
42 11 0.21
43 1 0.02
44 33 0.63
45 7 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (43 bp):
ATATATATATATTATTTAAATTAAATATATAAATATTATATAT
Found at i:113729 original size:38 final size:39
Alignment explanation
Indices: 113638--113729 Score: 120
Period size: 38 Copynumber: 2.4 Consensus size: 39
113628 GGCCGGGGAT
113638 ATATATATATAT-TTAAATTAAATATATAAATATTATAT
1 ATATATATATATATTAAATTAAATATATAAATATTATAT
* *
113676 ATATATATATATATTAATTTAAAT-TA-AATTTATTA-AT
1 ATATATATATATATTAAATTAAATATATAA-ATATTATAT
113713 ATTATATATATATATTA
1 A-TATATATATATATTA
113730 TATATAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
37 5 0.10
38 34 0.69
39 10 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (39 bp):
ATATATATATATATTAAATTAAATATATAAATATTATAT
Found at i:113745 original size:44 final size:44
Alignment explanation
Indices: 113636--113756 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 44
113626 CAGGCCGGGG
* ** * *
113636 ATATATATATATATTTAAATTAAATATATAAATATTATATATAT
1 ATATATATATAAAAATAAATTAAATTTATTAATATTATATATAT
* **
113680 ATATATATATTAATTTAAATTAAATTTATTAATATTATATATAT
1 ATATATATATAAAAATAAATTAAATTTATTAATATTATATATAT
113724 ATATTATATATAAAAAT-AATT--ATTT-TTAATATT
1 ATA-TATATATAAAAATAAATTAAATTTATTAATATT
113757 TATCGGGCCG
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 8 0.12
42 4 0.06
44 47 0.68
45 10 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (44 bp):
ATATATATATAAAAATAAATTAAATTTATTAATATTATATATAT
Found at i:113747 original size:38 final size:39
Alignment explanation
Indices: 113636--113747 Score: 119
Period size: 38 Copynumber: 2.9 Consensus size: 39
113626 CAGGCCGGGG
* *
113636 ATATATATATATAT-TTAAAT-TAAATATATAAATATTAT
1 ATATATATATATATATTATATATAAATA-ATAATTATTAT
* *
113674 ATATATATATATATATTA-ATTTAAATTAA-ATTTATTA-
1 ATATATATATATATATTATATATAAA-TAATAATTATTAT
113711 ATATTATATATATATATTATATATAAA-AATAATTATT
1 ATA-TATATATATATATTATATATAAATAATAATTATT
113748 TTTAATATTT
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
37 5 0.08
38 43 0.67
39 14 0.22
40 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (39 bp):
ATATATATATATATATTATATATAAATAATAATTATTAT
Found at i:114394 original size:12 final size:12
Alignment explanation
Indices: 114379--114459 Score: 56
Period size: 12 Copynumber: 6.3 Consensus size: 12
114369 TACTAAAGTG
114379 AAAATTAAATAA
1 AAAATTAAATAA
*
114391 AAAA-TAAAAAA
1 AAAATTAAATAA
*
114402 AACAATTAAATAG
1 AA-AATTAAATAA
*
114415 AAACTTAAATATA
1 AAAATTAAATA-A
*
114428 AACATTACAATTCAA
1 AAAATTA-AA-T-AA
*
114443 ACAATTAAATAA
1 AAAATTAAATAA
114455 TAAAA
1 -AAAA
114460 AAAATTTAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
11 8 0.15
12 16 0.31
13 16 0.31
14 4 0.08
15 7 0.13
16 1 0.02
ACGTcount: A:0.68, C:0.07, G:0.01, T:0.23
Consensus pattern (12 bp):
AAAATTAAATAA
Found at i:114508 original size:22 final size:22
Alignment explanation
Indices: 114475--114552 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
114465 TTAAAAAACA
*
114475 AAATAAATAAAAGTTTCATAATT
1 AAATAAATAAAA-ATTCATAATT
* * *
114498 AAAT-AATAAAACATTAAGAA-A
1 AAATAAATAAAA-ATTCATAATT
*
114519 AAATAAATAAAAATCCATAATT
1 AAATAAATAAAAATTCATAATT
114541 AAAT-AATAAAAA
1 AAATAAATAAAAA
114553 CATTAAGAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
21 17 0.39
22 23 0.52
23 4 0.09
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (22 bp):
AAATAAATAAAAATTCATAATT
Found at i:114524 original size:21 final size:21
Alignment explanation
Indices: 114498--114571 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 21
114488 TTTCATAATT
114498 AAATAATAAAACATTAAGAAA
1 AAATAATAAAACATTAAGAAA
** * *
114519 AAATAAATAAAA-ATCCATAATT
1 AAAT-AATAAAACATTAAGAA-A
114541 AAATAATAAAAACATTAAGAAA
1 AAATAAT-AAAACATTAAGAAA
*
114563 CAA-AATAAA
1 AAATAATAAA
114572 TAAATAAAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 9
0.69 0.16 0.16
Matches are distributed among these distances:
20 3 0.08
21 15 0.38
22 17 0.43
23 5 0.12
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (21 bp):
AAATAATAAAACATTAAGAAA
Found at i:114545 original size:92 final size:92
Alignment explanation
Indices: 114445--114624 Score: 251
Period size: 92 Copynumber: 2.0 Consensus size: 92
114435 CAATTCAAAC
** *
114445 AATTAAATAATAAAAAAAATTTAAAAAACAAAATAAAT-AA-AAGTTTCATAATTAAATAATAAA
1 AATTAAATAAT-AAAAAAA-TTAAAAAACAAAATAAATAAATAAAATCCATAATTAAAT-A-AAA
114508 ACATTAAGAAA-AA-ATAAATAAAAATCCAT
62 ACATTAAGAAACAAGATAAATAAAAATCCAT
* *
114537 AATTAAATAATAAAAACATTAAGAAACAAAATAAATAAATAAAATCCATAATTAAATAAAAACAT
1 AATTAAATAATAAAAAAATTAAAAAACAAAATAAATAAATAAAATCCATAATTAAATAAAAACAT
114602 TAAGAAACAAGATAAATAAAAAT
66 TAAGAAACAAGATAAATAAAAAT
114625 AAGTTTATTG
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
90 31 0.39
91 11 0.14
92 37 0.47
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.23
Consensus pattern (92 bp):
AATTAAATAATAAAAAAATTAAAAAACAAAATAAATAAATAAAATCCATAATTAAATAAAAACAT
TAAGAAACAAGATAAATAAAAATCCAT
Found at i:114573 original size:25 final size:25
Alignment explanation
Indices: 114541--114623 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 25
114531 ATCCATAATT
114541 AAAT-AATAAAAACATTAAGAAACA
1 AAATAAATAAAAACATTAAGAAACA
*
114565 AAATAAAT---AA-A-TAA-AATCCA
1 AAATAAATAAAAACATTAAGAA-ACA
*
114585 TAATTAAATAAAAACATTAAGAAACA
1 -AAATAAATAAAAACATTAAGAAACA
*
114611 AGATAAATAAAAA
1 AAATAAATAAAAA
114624 TAAGTTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 17
0.67 0.07 0.25
Matches are distributed among these distances:
19 2 0.04
20 5 0.11
21 8 0.18
22 2 0.04
24 6 0.13
25 15 0.33
26 5 0.11
27 2 0.04
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.19
Consensus pattern (25 bp):
AAATAAATAAAAACATTAAGAAACA
Found at i:114593 original size:49 final size:47
Alignment explanation
Indices: 114445--114623 Score: 219
Period size: 46 Copynumber: 3.9 Consensus size: 47
114435 CAATTCAAAC
* * ** *
114445 AATTAAATAATAAAAAAAATTTAAAAAACAAAATAAATAAAAGTTTCAT
1 AATTAAATAAT-AAAAACA-TTAAGAAACAAAATAAATAAAAAATCCAT
114494 AATTAAATAAT-AAAACATTAAG-AA-AAAATAAAT-AAAAATCCAT
1 AATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAATCCAT
114537 AATTAAATAATAAAAACATTAAGAAACAAAATAAATAAATAAAATCCAT
1 AATTAAATAATAAAAACATTAAGAAACAAAATAAAT-AA-AAAATCCAT
*
114586 AATT--A-AATAAAAACATTAAGAAACAAGATAAATAAAAA
1 AATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAA
114624 TAAGTTTATT
Statistics
Matches: 118, Mismatches: 6, Indels: 17
0.84 0.04 0.12
Matches are distributed among these distances:
43 18 0.15
44 23 0.19
45 6 0.05
46 40 0.34
47 6 0.05
48 1 0.01
49 24 0.20
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.23
Consensus pattern (47 bp):
AATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAATCCAT
Found at i:115851 original size:21 final size:22
Alignment explanation
Indices: 115821--115861 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
115811 ATTTAGTTTA
115821 AAAACAAATTCA-TTATATACTC
1 AAAACAAATT-ATTTATATACTC
115843 AAAA-AAATTATTTATATAC
1 AAAACAAATTATTTATATAC
115862 AAACTCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 13 0.72
22 4 0.22
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAACAAATTATTTATATACTC
Found at i:116770 original size:16 final size:16
Alignment explanation
Indices: 116723--116770 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
116713 TGCAAAAAGT
* *
116723 AATAAAAAATTAGTAC
1 AATAAAAAATTAATAA
*
116739 AATAAAATA-TAATAA
1 AATAAAAAATTAATAA
*
116754 AATAAAAAATTATTAA
1 AATAAAAAATTAATAA
116770 A
1 A
116771 TGATTATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (16 bp):
AATAAAAAATTAATAA
Found at i:116771 original size:15 final size:15
Alignment explanation
Indices: 116723--116771 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
116713 TGCAAAAAGT
*
116723 AATAAAAAATTAGTA
1 AATAAAAAATTATTA
* * *
116738 CAATAAAATATAATAA
1 -AATAAAAAATTATTA
116754 AATAAAAAATTATTA
1 AATAAAAAATTATTA
116769 AAT
1 AAT
116772 GATTATAATA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
AATAAAAAATTATTA
Found at i:116786 original size:29 final size:31
Alignment explanation
Indices: 116722--116795 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 31
116712 CTGCAAAAAG
116722 TAATAAAAAATTAGTACAATAAAATATAATA
1 TAATAAAAAATTAGTACAATAAAATATAATA
* * * *
116753 AAATAAAAAATTATTA-AAT-GATTATAATA
1 TAATAAAAAATTAGTACAATAAAATATAATA
116782 TAATAAAAAATTAG
1 TAATAAAAAATTAG
116796 CTTCTAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 20 0.54
30 3 0.08
31 14 0.38
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (31 bp):
TAATAAAAAATTAGTACAATAAAATATAATA
Found at i:118129 original size:2 final size:2
Alignment explanation
Indices: 118124--118174 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
118114 TTATTTTTTT
118124 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
118166 AG AG AG AG A
1 AG AG AG AG A
118175 AGCAAAGAAA
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:118899 original size:274 final size:274
Alignment explanation
Indices: 118410--118959 Score: 1082
Period size: 274 Copynumber: 2.0 Consensus size: 274
118400 ATTCTTCGAT
118410 TTTTTTCATTCTCAAATATTTATAGTTCACCGTCCGACAGGCTTGAAATTGGACTATGTTGGTTA
1 TTTTTTCATTCTCAAATATTTATAGTTCACCGTCCGACAGGCTTGAAATTGGACTATGTTGGTTA
118475 ACTCGTCATTCTCTAGCGATTCACCCTTCGTATCGATCGTCCAACCACCAGAGCTATATCACGGC
66 ACTCGTCATTCTCTAGCGATTCACCCTTCGTATCGATCGTCCAACCACCAGAGCTATATCACGGC
118540 AGCTCGTCCGCTAAGTTTTTAATGACGAAATACTAAAATCAAACAAAAACTAAATGTTAAGTAAT
131 AGCTCGTCCGCTAAGTTTTTAATGACGAAATACTAAAATCAAACAAAAACTAAATGTTAAGTAAT
118605 TTTTTTTAAAAAAAATGAAAGTTTATATACTAAAACATACCAAAATTGATAGTTTAAATACTAAA
196 TTTTTTTAAAAAAAATGAAAGTTTATATACTAAAACATACCAAAATTGATAGTTTAAATACTAAA
118670 CGCATAATTTACCA
261 CGCATAATTTACCA
118684 TTTTTTCATTCTCAAATATTTATAGTTCACCGTCCGACAGGCTTGAAATTGGACTATGTTGGTTA
1 TTTTTTCATTCTCAAATATTTATAGTTCACCGTCCGACAGGCTTGAAATTGGACTATGTTGGTTA
118749 ACTCGTCATTCTCTAGCGATTCACCCTTCGTATCGATCGTCCAACCACCAGAGCTATATCACGGC
66 ACTCGTCATTCTCTAGCGATTCACCCTTCGTATCGATCGTCCAACCACCAGAGCTATATCACGGC
118814 AGCTCGTCCGCTAAGTTTTTAATGACGAAATACTAAAATCAAACAAAAACTAAATGTTAAGTAAT
131 AGCTCGTCCGCTAAGTTTTTAATGACGAAATACTAAAATCAAACAAAAACTAAATGTTAAGTAAT
* *
118879 TTTTTTTTAAAAAAATGAAAGTTTATATACTAAAACGTACCAAAATTGATAGTTTAAATACTAAA
196 TTTTTTTAAAAAAAATGAAAGTTTATATACTAAAACATACCAAAATTGATAGTTTAAATACTAAA
118944 CGCATAATTTACCA
261 CGCATAATTTACCA
118958 TT
1 TT
118960 AATATTAATT
Statistics
Matches: 274, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
274 274 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (274 bp):
TTTTTTCATTCTCAAATATTTATAGTTCACCGTCCGACAGGCTTGAAATTGGACTATGTTGGTTA
ACTCGTCATTCTCTAGCGATTCACCCTTCGTATCGATCGTCCAACCACCAGAGCTATATCACGGC
AGCTCGTCCGCTAAGTTTTTAATGACGAAATACTAAAATCAAACAAAAACTAAATGTTAAGTAAT
TTTTTTTAAAAAAAATGAAAGTTTATATACTAAAACATACCAAAATTGATAGTTTAAATACTAAA
CGCATAATTTACCA
Found at i:119705 original size:10 final size:10
Alignment explanation
Indices: 119690--119715 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
119680 TATCATTTAA
119690 ATGAACGAAC
1 ATGAACGAAC
119700 ATGAACGAAC
1 ATGAACGAAC
119710 ATGAAC
1 ATGAAC
119716 AAGTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (10 bp):
ATGAACGAAC
Found at i:125203 original size:15 final size:15
Alignment explanation
Indices: 125183--125234 Score: 95
Period size: 15 Copynumber: 3.5 Consensus size: 15
125173 ATATTTAGCT
*
125183 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
125198 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
125213 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
125228 GGGCGGG
1 GGGCGGG
125235 TAATGTCTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.06, C:0.17, G:0.69, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:126133 original size:17 final size:17
Alignment explanation
Indices: 126113--126145 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
126103 TTATTAAAAT
126113 AAAAATATTTAAATTTA
1 AAAAATATTTAAATTTA
*
126130 AAAAATATTTATATTT
1 AAAAATATTTAAATTT
126146 TAACGACCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAAATATTTAAATTTA
Found at i:127085 original size:23 final size:23
Alignment explanation
Indices: 127035--127079 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
127025 CCGAGACAAT
* *
127035 CCGAACGAGCTATGCGAGGGCAG
1 CCGAGCGAGCTATGCGAGGGAAG
127058 CCGAGCGAGCTATGCGAGGGAA
1 CCGAGCGAGCTATGCGAGGGAA
127080 TTCGAGGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.40, T:0.09
Consensus pattern (23 bp):
CCGAGCGAGCTATGCGAGGGAAG
Found at i:127136 original size:29 final size:29
Alignment explanation
Indices: 127103--127158 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
127093 GAGCGAGGGT
*
127103 AGGTCGCCCGGAGTGCATGGCGACCTAAA
1 AGGTCGCCCGGAGGGCATGGCGACCTAAA
127132 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
127159 TGTGTTGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.29, G:0.38, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTAAA
Found at i:127263 original size:29 final size:29
Alignment explanation
Indices: 127217--127273 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
127207 GAGCAAGGGT
127217 AGGTCACCCGGAGTGCATGACGACCTACA
1 AGGTCACCCGGAGTGCATGACGACCTACA
* *
127246 AGGTCGCCCGGAAG-GCATGGCGACCTAC
1 AGGTCACCCGG-AGTGCATGACGACCTAC
127274 GGCAAATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.25, C:0.32, G:0.32, T:0.12
Consensus pattern (29 bp):
AGGTCACCCGGAGTGCATGACGACCTACA
Found at i:127526 original size:2 final size:2
Alignment explanation
Indices: 127519--127551 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
127509 TTTACATAAT
127519 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 T
127552 GTATGTGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.