Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 29
Found at i:3750061 original size:12 final size:12
Alignment explanation
Indices: 3750046--3750104 Score: 68
Period size: 12 Copynumber: 4.9 Consensus size: 12
3750036 GAATCCAAAT
3750046 CAGAAATCAGAA
1 CAGAAATCAGAA
* *
3750058 CAGAATTCAGAT
1 CAGAAATCAGAA
3750070 CAGAAATCAGAA
1 CAGAAATCAGAA
3750082 CA-AAATTCA-AA
1 CAGAAA-TCAGAA
3750093 TCAGAAATCAGA
1 -CAGAAATCAGA
3750105 TAAAATATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.13
12 30 0.77
13 4 0.10
ACGTcount: A:0.54, C:0.17, G:0.14, T:0.15
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:3750067 original size:48 final size:48
Alignment explanation
Indices: 3750011--3750104 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
3750001 AAAACAAAAT
* *
3750011 AGAATTCAGATAAGATATCA-AGACAGAATCCAAATCAGAAATCAGAAC
1 AGAATTCAGATAAGAAATCAGA-ACAAAATCCAAATCAGAAATCAGAAC
* *
3750059 AGAATTCAGATCAGAAATCAGAACAAAATTCAAATCAGAAATCAGA
1 AGAATTCAGATAAGAAATCAGAACAAAATCCAAATCAGAAATCAGA
3750105 TAAAATATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 40 0.98
49 1 0.02
ACGTcount: A:0.53, C:0.16, G:0.14, T:0.17
Consensus pattern (48 bp):
AGAATTCAGATAAGAAATCAGAACAAAATCCAAATCAGAAATCAGAAC
Found at i:3750103 original size:24 final size:24
Alignment explanation
Indices: 3750041--3750104 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
3750031 AGACAGAATC
*
3750041 CAAATCAGAAATCAGAACAGAATT
1 CAAATCAGAAATCAGAACAAAATT
*
3750065 CAGATCAGAAATCAGAACAAAATT
1 CAAATCAGAAATCAGAACAAAATT
3750089 CAAATCAGAAATCAGA
1 CAAATCAGAAATCAGA
3750105 TAAAATATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.55, C:0.17, G:0.12, T:0.16
Consensus pattern (24 bp):
CAAATCAGAAATCAGAACAAAATT
Found at i:3757370 original size:19 final size:19
Alignment explanation
Indices: 3757346--3757383 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3757336 ATACGGCTTA
*
3757346 ACAATAATGAATATATATT
1 ACAATAATCAATATATATT
3757365 ACAATAATCAATATATATT
1 ACAATAATCAATATATATT
3757384 TATATTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (19 bp):
ACAATAATCAATATATATT
Found at i:3768076 original size:27 final size:27
Alignment explanation
Indices: 3768045--3768109 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
3768035 CAGTGTAATT
3768045 TGGTGGAATTTGCACTATAAAGTGGAA
1 TGGTGGAATTTGCACTATAAAGTGGAA
3768072 TGGTGGAATTTGCACTATAAAGTGGAA
1 TGGTGGAATTTGCACTATAAAGTGGAA
* *
3768099 TAGTGCAATTT
1 TGGTGGAATTT
3768110 AGTGACTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (27 bp):
TGGTGGAATTTGCACTATAAAGTGGAA
Found at i:3769396 original size:14 final size:14
Alignment explanation
Indices: 3769377--3769407 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3769367 TCGATAGCAT
3769377 TTTTAGCATTTTTA
1 TTTTAGCATTTTTA
3769391 TTTTAGCATTTTTA
1 TTTTAGCATTTTTA
3769405 TTT
1 TTT
3769408 GAATTTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTAGCATTTTTA
Found at i:3770240 original size:29 final size:30
Alignment explanation
Indices: 3770184--3770241 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
3770174 TTATGCATGA
*
3770184 TTCATTTTAATAAAGTTATTTGTATAATTG
1 TTCATTTTAATAAAGTTATTTATATAATTG
* * *
3770214 TTCATTTTTAT-ATGTTATTTATTTAATT
1 TTCATTTTAATAAAGTTATTTATATAATT
3770242 ATGTTGCCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.60
Consensus pattern (30 bp):
TTCATTTTAATAAAGTTATTTATATAATTG
Found at i:3771241 original size:16 final size:16
Alignment explanation
Indices: 3771220--3771252 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3771210 AATTTTTCCT
3771220 TTGAGTTTCTTTGACA
1 TTGAGTTTCTTTGACA
3771236 TTGAGTTTCTTTGACA
1 TTGAGTTTCTTTGACA
3771252 T
1 T
3771253 GTTGGTATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (16 bp):
TTGAGTTTCTTTGACA
Found at i:3773115 original size:94 final size:94
Alignment explanation
Indices: 3772954--3773144 Score: 364
Period size: 94 Copynumber: 2.0 Consensus size: 94
3772944 CGCAAGGTCA
*
3772954 TTAATTGAAATATTAAATTTCATTCTCTGAAAAGTGTATCCACGTTGGGAAAAATCTCGCGCCCC
1 TTAATTGAAATATTAAATTTCATTCTCTGAAAAGTGTATCCACGTTGGGAAAAATCTCACGCCCC
*
3773019 GTGTAACGTGAGGCCTTTACTCACTTTTC
66 GTGTAACGCGAGGCCTTTACTCACTTTTC
3773048 TTAATTGAAATATTAAATTTCATTCTCTGAAAAGTGTATCCACGTTGGGAAAAATCTCACGCCCC
1 TTAATTGAAATATTAAATTTCATTCTCTGAAAAGTGTATCCACGTTGGGAAAAATCTCACGCCCC
3773113 GTGTAACGCGAGGCCTTTACTCACTTTTC
66 GTGTAACGCGAGGCCTTTACTCACTTTTC
3773142 TTA
1 TTA
3773145 TTTTTCTAAC
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Consensus pattern (94 bp):
TTAATTGAAATATTAAATTTCATTCTCTGAAAAGTGTATCCACGTTGGGAAAAATCTCACGCCCC
GTGTAACGCGAGGCCTTTACTCACTTTTC
Found at i:3776770 original size:93 final size:94
Alignment explanation
Indices: 3776610--3776793 Score: 343
Period size: 93 Copynumber: 2.0 Consensus size: 94
3776600 CAATTGCAGT
3776610 ATCCTAGAAAGATAAAAAAAAATATCAAATAAAGAACTAAAGAATTAGAAGAAAATTGCATAATG
1 ATCCTAGAAAGATAAAAAAAAATATCAAATAAAGAACTAAAGAATTAGAAGAAAATTGCATAATG
3776675 ATTAACCTTAGAAAATTAATGAAAAAGGA
66 ATTAACCTTAGAAAATTAATGAAAAAGGA
* *
3776704 ATCCTAGAAAGAT-AAAATATATATCAAATAAAGAACTAAAGAATTAGAAGAAAATTGCATAATG
1 ATCCTAGAAAGATAAAAAAAAATATCAAATAAAGAACTAAAGAATTAGAAGAAAATTGCATAATG
3776768 ATTAACCTTAGAAAATTAATGAAAAA
66 ATTAACCTTAGAAAATTAATGAAAAA
3776794 AGACAACTAA
Statistics
Matches: 88, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
93 75 0.85
94 13 0.15
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.23
Consensus pattern (94 bp):
ATCCTAGAAAGATAAAAAAAAATATCAAATAAAGAACTAAAGAATTAGAAGAAAATTGCATAATG
ATTAACCTTAGAAAATTAATGAAAAAGGA
Found at i:3778837 original size:45 final size:46
Alignment explanation
Indices: 3778788--3778878 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
3778778 GAACATCGAA
* *
3778788 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
*
3778833 TGCATTTGATGCATCGATGCACAAGACTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
3778879 GTTTTTTCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.50
46 21 0.50
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:3786631 original size:30 final size:30
Alignment explanation
Indices: 3786595--3786659 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
3786585 TGCTATTCAC
3786595 GAAGCAGTAAATCAACTCTTAGACACTTTG
1 GAAGCAGTAAATCAACTCTTAGACACTTTG
3786625 GAAGCAGTAAATCAACTCTTAGACACTTTG
1 GAAGCAGTAAATCAACTCTTAGACACTTTG
3786655 GAAGC
1 GAAGC
3786660 TCGTCAGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (30 bp):
GAAGCAGTAAATCAACTCTTAGACACTTTG
Found at i:3787547 original size:20 final size:20
Alignment explanation
Indices: 3787522--3787560 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3787512 TTTTCAAGGG
3787522 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
3787542 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
3787561 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:3787628 original size:28 final size:27
Alignment explanation
Indices: 3787597--3787658 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 27
3787587 TATGCATCGA
3787597 TGCACATGCCATGCATCGATGCACTC-AG
1 TGCACATG--ATGCATCGATGCACTCTAG
**
3787625 TGCATTTGATGCATCGATGCACTCTTAG
1 TGCACATGATGCATCGATGCACTC-TAG
3787653 TGCACA
1 TGCACA
3787659 CCGATGCACT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 16 0.57
28 12 0.43
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (27 bp):
TGCACATGATGCATCGATGCACTCTAG
Found at i:3788429 original size:19 final size:20
Alignment explanation
Indices: 3788405--3788442 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3788395 ATACCTTATA
*
3788405 AAGGAA-AGTATCGATACCC
1 AAGGAAGAGTATCAATACCC
3788424 AAGGAAGAGTATCAATACC
1 AAGGAAGAGTATCAATACC
3788443 AGCATGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (20 bp):
AAGGAAGAGTATCAATACCC
Found at i:3798867 original size:59 final size:60
Alignment explanation
Indices: 3798804--3798951 Score: 174
Period size: 59 Copynumber: 2.5 Consensus size: 60
3798794 ATGAATTTGT
* ** ** *
3798804 GGATGAAATTGGAATATTTGAAAGTTTGTGAACCAATTTAGAAAG-ATGTCATA-ATTTA
1 GGATGAAATTAGAATATTCAAAAGTTTAAGAACCAATTTAGAAAGAAAGTCATAGATTTA
* * * * *
3798862 GGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAAAGTCATAGTTTTA
1 -GGATGAAATTAGAATATTCAAAAGTTTAAGAACCAATTTAGAAAGAAAGTCATAGATTTA
3798923 GGATGAAATTAGAATATTCAAAAGTTTAA
1 GGATGAAATTAGAATATTCAAAAGTTTAA
3798952 AGACCAAGTT
Statistics
Matches: 75, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
59 36 0.48
60 35 0.47
61 4 0.05
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (60 bp):
GGATGAAATTAGAATATTCAAAAGTTTAAGAACCAATTTAGAAAGAAAGTCATAGATTTA
Found at i:3798980 original size:60 final size:61
Alignment explanation
Indices: 3798858--3798972 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 61
3798848 GATGTCATAA
* * * * *
3798858 TTTAGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAAAGTCATAGT
1 TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAAGACCAATTGAGAATAAAAGTCATAGT
3798919 TTTA-GGATGAAATTAGAATATTCAAAAGTTTAAAGACCAAGTTGA-AATAAAAGT
1 TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAAGACCAA-TTGAGAATAAAAGT
3798973 TGTAGTTTGG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 41 0.85
61 7 0.15
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.31
Consensus pattern (61 bp):
TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAAGACCAATTGAGAATAAAAGTCATAGT
Found at i:3801090 original size:18 final size:18
Alignment explanation
Indices: 3801056--3801109 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
3801046 AAAAATATAA
*
3801056 AATAAGAATCAAG-TAAAT
1 AATAA-AATAAAGATAAAT
*
3801074 AATAAAATAAAGATAAAA
1 AATAAAATAAAGATAAAT
*
3801092 AATGAAATAAAGA-AAAT
1 AATAAAATAAAGATAAAT
3801109 A
1 A
3801110 TTTAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 10 0.32
18 21 0.68
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (18 bp):
AATAAAATAAAGATAAAT
Found at i:3802310 original size:23 final size:22
Alignment explanation
Indices: 3802267--3802310 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
3802257 TTGGACCTAA
* *
3802267 AAATAAAAACATTATTCAAAAC
1 AAATAAAAACATTAATAAAAAC
*
3802289 AAATAAATAATATTAATAAAAA
1 AAATAAA-AACATTAATAAAAA
3802311 ATAATATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (22 bp):
AAATAAAAACATTAATAAAAAC
Found at i:3802321 original size:5 final size:5
Alignment explanation
Indices: 3802291--3802568 Score: 145
Period size: 5 Copynumber: 54.6 Consensus size: 5
3802281 TTCAAAACAA
* *
3802291 ATAA- ATAAT ATTAAT AAAAA ATAAT ATAAT ATAAT ATATAT ATATAT
1 ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATA-AT
* * *
3802338 ATATAT ATATAT ATAAT ATAAT ATAAT ATATAT GTAAT A-CAT ATTAT
1 ATA-AT ATA-AT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT
* *
3802385 ATAAC ATAAT AT-AT ATACTAT ATAAT GTAAT AT-AT ATATAT ATAAT
1 ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT ATAAT ATA-AT ATAAT
* * *
3802431 ATAAT ACT-AT CACATAT ATAAT ACT--T ATTAT ATAATAT ATAAT ATAAC
1 ATAAT A-TAAT -ATA-AT ATAAT A-TAAT ATAAT AT-A-AT ATAAT ATAAT
* *
3802479 ATAAT AT-AT AT-AT ATACTAT ATAAT ACAA- AT-AT ATAAT AT-AT GCT-AT
1 ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT
* *
3802526 ATAAT ATAAT AT-AT A-ATT ATAATAT ATAAT ATACT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATA
3802569 TAATACTATA
Statistics
Matches: 218, Mismatches: 26, Indels: 59
0.72 0.09 0.19
Matches are distributed among these distances:
3 2 0.01
4 36 0.17
5 116 0.53
6 45 0.21
7 19 0.09
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:3802329 original size:7 final size:7
Alignment explanation
Indices: 3802290--3802671 Score: 192
Period size: 7 Copynumber: 51.3 Consensus size: 7
3802280 ATTCAAAACA
*
3802290 AATAAAT
1 AATATAT
3802297 AATAT-T
1 AATATAT
* *
3802303 AATAAAA
1 AATATAT
3802310 AATAATAT
1 AAT-ATAT
3802318 AATATA-
1 AATATAT
3802324 ATATATAT
1 A-ATATAT
3802332 ATATATAT
1 A-ATATAT
3802340 ATATATAT
1 A-ATATAT
3802348 ATATAATAT
1 A-AT-ATAT
3802357 AATATAAT
1 AATAT-AT
*
3802365 ATATATGT
1 A-ATATAT
*
3802373 AATACAT
1 AATATAT
*
3802380 ATTATAT
1 AATATAT
*
3802387 AACATA-
1 AATATAT
3802393 ATATATAT
1 A-ATATAT
*
3802401 ACTATAT
1 AATATAT
*
3802408 AATGTAAT
1 AATAT-AT
3802416 ATATATAT
1 A-ATATAT
3802424 ATATAATAT
1 A-AT-ATAT
3802433 AATACTAT
1 AATA-TAT
3802441 CACATATAT
1 -A-ATATAT
3802450 AATACT-T
1 AATA-TAT
*
3802457 ATTATAT
1 AATATAT
3802464 AATATAT
1 AATATAT
3802471 AATATA-
1 AATATAT
3802477 ACATAATAT
1 A-AT-ATAT
3802486 ATATATAT
1 A-ATATAT
*
3802494 ACTATAT
1 AATATAT
*
3802501 AATACA-
1 AATATAT
3802507 AATATAT
1 AATATAT
3802514 AATATAT
1 AATATAT
**
3802521 GCTATAT
1 AATATAT
3802528 -A-ATAT
1 AATATAT
3802533 AATATAT
1 AATATAT
3802540 AAT-TAT
1 AATATAT
3802546 AATATAT
1 AATATAT
3802553 AATATACTAT
1 -A-ATA-TAT
3802563 AATATAT
1 AATATAT
3802570 AATACTAT
1 AATA-TAT
3802578 ACACTATAT
1 A-A-TATAT
*
3802587 AAAGACTAT
1 -AATA-TAT
3802596 AACATATAT
1 -A-ATATAT
*
3802605 ACTATAT
1 AATATAT
3802612 AATATACCAT
1 AATAT---AT
*
3802622 ACTATAT
1 AATATAT
3802629 AATATAT
1 AATATAT
* *
3802636 ACTATGT
1 AATATAT
3802643 AA-A-AT
1 AATATAT
3802648 AATATAT
1 AATATAT
* *
3802655 ACTACAT
1 AATATAT
3802662 AATAATAT
1 AAT-ATAT
3802670 AA
1 AA
3802672 AAAGAAATCC
Statistics
Matches: 295, Mismatches: 41, Indels: 77
0.71 0.10 0.19
Matches are distributed among these distances:
5 7 0.02
6 23 0.08
7 135 0.46
8 72 0.24
9 41 0.14
10 17 0.06
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.39
Consensus pattern (7 bp):
AATATAT
Found at i:3802579 original size:84 final size:85
Alignment explanation
Indices: 3802332--3802676 Score: 272
Period size: 84 Copynumber: 4.0 Consensus size: 85
3802322 TAATATATAT
* * *
3802332 ATATATATATATATA-TATATAATATAATATAATATATATGTAATACATATTATATAACATAATA
1 ATATATACATATATACTATATAATATAATAT-ATA-ATATATAAT--ATATAATATAACATAATA
* *
3802396 TATATACTATA-TAATGTAATATATAT
62 TATATACTATACT-ATATAATA-A-AG
* *
3802422 ATATATA-ATATAATACTATCACATATATAATACT-TATTATATAATATATAATATAACATAATA
1 ATATATACATAT-ATACTAT-ATA-ATATAATA-TATAATATATAATATATAATATAACATAATA
3802485 TATATA-TATACTATATAATACAA-
62 TATATACTATACTATATAATA-AAG
*
3802508 ATATATA-ATATATGCTATATAATATAATATATAAT-TATAATATATAATAT-ACTATAATATAT
1 ATATATACATATATACTATATAATATAATATATAATATATAATATATAATATAAC-ATAATATAT
3802570 AATACTATAC-ACTAT-ATAAAG
65 -ATACTATACTA-TATAATAAAG
** * * *
3802591 ACTATA-ACATATATACTATATAATAT-A-CCATACTATATAATATATACTATGTAAAATAATAT
1 A-TATATACATATATACTATATAATATAATATATAATATATAATATATA--ATATAACATAATAT
*
3802653 ATACTAC-ATAATAATATAA-AAAG
63 ATA-TACTATACT-ATATAATAAAG
3802676 A
1 A
3802677 AATCCTGACG
Statistics
Matches: 217, Mismatches: 16, Indels: 49
0.77 0.06 0.17
Matches are distributed among these distances:
81 2 0.01
82 31 0.14
83 32 0.15
84 35 0.16
85 29 0.13
86 14 0.06
87 1 0.00
88 12 0.06
89 28 0.13
90 10 0.05
91 10 0.05
92 4 0.02
93 8 0.04
94 1 0.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (85 bp):
ATATATACATATATACTATATAATATAATATATAATATATAATATATAATATAACATAATATATA
TACTATACTATATAATAAAG
Found at i:3802611 original size:59 final size:58
Alignment explanation
Indices: 3802319--3802637 Score: 192
Period size: 59 Copynumber: 5.5 Consensus size: 58
3802309 AAATAATATA
* * * *
3802319 ATATAATATATATATATATATATATATATATA-TAATATAATATAATATAT-ATGTAATAC-
1 ATATAATATACATA-ATATATA-ATATATACACT-ATATAATAGAATATATAATAT-ATACT
* * *
3802378 ATATTATATAACATAATATATATACTATATA-A-TGTAATATATA-TATATATAATATAATACT
1 ATATAATAT-ACATAATATATA-A-TATATACACTAT-ATA-ATAGAATATATAATAT-ATACT
* *
3802439 ATCACATATATAATACTTATTATATAATATATA-A-TATA-ACAT--AATATAT-ATATATACT
1 AT---ATA-AT-ATACATAATATATAATATATACACTATATA-ATAGAATATATAATATATACT
* * *
3802497 ATAT-A-ATACA-AATATATAATATAT--GCTATATAATATAATATATAAT-TATAAT
1 ATATAATATACATAATATATAATATATACACTATATAATAGAATATATAATATATACT
*
3802549 ATATAATATACTATAATATATAATACTATACACTATATAA-AGACTATA-ACATATATACT
1 ATATAATATAC-ATAATATATAATA-TATACACTATATAATAGAATATATA-ATATATACT
*
3802608 ATATAATATACCATACTATATAATATATAC
1 ATATAATATA-CATAATATATAATATATAC
3802638 TATGTAAAAT
Statistics
Matches: 214, Mismatches: 20, Indels: 53
0.75 0.07 0.18
Matches are distributed among these distances:
50 19 0.09
51 5 0.02
52 16 0.07
53 4 0.02
54 4 0.02
55 3 0.01
56 11 0.05
57 4 0.02
58 21 0.10
59 67 0.31
60 28 0.13
61 5 0.02
62 1 0.00
63 9 0.04
64 3 0.01
65 12 0.06
66 2 0.01
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.40
Consensus pattern (58 bp):
ATATAATATACATAATATATAATATATACACTATATAATAGAATATATAATATATACT
Found at i:3802655 original size:2 final size:2
Alignment explanation
Indices: 3802314--3802636 Score: 172
Period size: 2 Copynumber: 171.5 Consensus size: 2
3802304 ATAAAAAATA
3802314 AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
3802353 AT AT A- AT AT A- AT AT AT AT GT A- AT AC AT AT -T AT AT A- AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3802390 AT A- AT AT AT AT ACT AT AT A- AT GT A- AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3802429 AT AT A- AT ACT AT CAC AT AT AT A- AT ACT -T AT -T AT AT A- AT
1 AT AT AT AT A-T AT -AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
3802467 AT AT A- AT AT A- AC AT A- AT AT AT AT AT AT ACT AT AT A- AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
3802506 AA AT AT AT A- AT AT AT GCT AT AT A- AT AT A- AT AT AT A- AT -T
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3802544 AT A- AT AT AT A- AT AT ACT AT A- AT AT AT A- AT ACT AT AC ACT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T
* * * *
3802583 AT AT AA AG ACT AT A- AC AT AT AT ACT AT AT A- AT AT ACC AT ACT
1 AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT A-T
3802625 AT AT A- AT AT AT A
1 AT AT AT AT AT AT A
3802637 CTATGTAAAA
Statistics
Matches: 252, Mismatches: 23, Indels: 92
0.69 0.06 0.25
Matches are distributed among these distances:
1 33 0.13
2 199 0.79
3 20 0.08
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:3803032 original size:81 final size:79
Alignment explanation
Indices: 3802924--3803073 Score: 185
Period size: 79 Copynumber: 1.9 Consensus size: 79
3802914 ACAGATGACT
* * * * *
3802924 CCTTTGTCGTGAGGTTGAGTCGATCTTGAGATGTCTTTGCGCACAATATCCTTCGTCATGAAGTT
1 CCTTCGTCGTGAAGTAGAGTCGATCTTG-GAGGT-TTTGAGCACAATATCCTTCGTCATGAAGTT
3802989 GAAATCATGGTTAACC
64 GAAATCATGGTTAACC
** **
3803005 CCTTCGTCGTGAAGTAGAGTC-AGTCTTGGAGGTTTTGAGCATGATATCCTTCGTTGTGAAGTTG
1 CCTTCGTCGTGAAGTAGAGTCGA-TCTTGGAGGTTTTGAGCACAATATCCTTCGTCATGAAGTTG
3803069 AAATC
65 AAATC
3803074 TAGTTCGATG
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
79 31 0.53
80 5 0.08
81 23 0.39
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (79 bp):
CCTTCGTCGTGAAGTAGAGTCGATCTTGGAGGTTTTGAGCACAATATCCTTCGTCATGAAGTTGA
AATCATGGTTAACC
Found at i:3812334 original size:20 final size:21
Alignment explanation
Indices: 3812309--3812360 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
3812299 GATCAAAGTA
* *
3812309 GTATCGATACTGATGTGG-AG
1 GTATCGATACTGAAGAGGAAG
*
3812329 GTATCGATAC-CAAGAGGAAG
1 GTATCGATACTGAAGAGGAAG
3812349 GTATCGATACTG
1 GTATCGATACTG
3812361 TAATTGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (21 bp):
GTATCGATACTGAAGAGGAAG
Found at i:3813060 original size:53 final size:52
Alignment explanation
Indices: 3812981--3813088 Score: 146
Period size: 53 Copynumber: 2.1 Consensus size: 52
3812971 CTATGTGTAC
*
3812981 TTTCAAACTATGTGTACACCCATGGTACTCATAACGAGTTTATGAATGACCA
1 TTTCAAACTATGTGTACACCCATGGTACTCATAACGAGTTTATAAATGACCA
* * * *
3813033 TTTCAACACTATGTGTGA-ACCCATGGTATTCATAATGAGTTTGTAAATTACCA
1 TTTCAA-ACTATGTGT-ACACCCATGGTACTCATAACGAGTTTATAAATGACCA
3813086 TTT
1 TTT
3813089 TGTTTCCTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
52 6 0.12
53 42 0.86
54 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (52 bp):
TTTCAAACTATGTGTACACCCATGGTACTCATAACGAGTTTATAAATGACCA
Found at i:3822275 original size:12 final size:12
Alignment explanation
Indices: 3822258--3822284 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3822248 GTAAAATAGT
3822258 AATAATAATCAA
1 AATAATAATCAA
3822270 AATAATAATCAA
1 AATAATAATCAA
3822282 AAT
1 AAT
3822285 TCCTTCCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAATAATCAA
Found at i:3824551 original size:18 final size:19
Alignment explanation
Indices: 3824520--3824565 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
3824510 AACTTGGACC
3824520 TAAAAAATAAAAATATTAT
1 TAAAAAATAAAAATATTAT
*
3824539 TAAAAAA-ATAAATATTAT
1 TAAAAAATAAAAATATTAT
*
3824557 TAATAAATA
1 TAAAAAATA
3824566 TAATATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAAATAAAAATATTAT
Found at i:3824557 original size:21 final size:20
Alignment explanation
Indices: 3824521--3824563 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3824511 ACTTGGACCT
*
3824521 AAAAAATAAAAATATTATTA
1 AAAAAATAAAAATATTAATA
*
3824541 AAAAAATAAATATTATTAATA
1 AAAAAATAAA-AATATTAATA
3824562 AA
1 AA
3824564 TATAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAAATAAAAATATTAATA
Found at i:3824580 original size:2 final size:2
Alignment explanation
Indices: 3824563--3824781 Score: 122
Period size: 2 Copynumber: 116.5 Consensus size: 2
3824553 TTATTAATAA
* *
3824563 AT AT A- AT AT A- AT AT AT AT GT A- AT AC AT ACT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
3824602 AT AT GT A- AT AC AT ACT AT AT A- AT AT AT AT AT AT AT A- AT ACT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
3824643 AT CAC AT AT AT A- AT -T CT -T AT -T AT AT A- AT AT AT AT A- AC
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3824680 AT A- AT AT AT AT AT AT AT AT AT AT A- AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3824718 AT A- AT ACT AT AT ACT AT AT A- AT AT A- AC AT ACT AT AT A- AT
1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT
* *
3824757 AT AT ACT AT AT A- AA AT AA AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT A
3824782 CTACATAATA
Statistics
Matches: 172, Mismatches: 15, Indels: 60
0.70 0.06 0.24
Matches are distributed among these distances:
1 22 0.13
2 135 0.78
3 15 0.09
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:3824585 original size:25 final size:25
Alignment explanation
Indices: 3824568--3824742 Score: 133
Period size: 25 Copynumber: 7.4 Consensus size: 25
3824558 AATAAATATA
3824568 ATATAATATATATGTAATACATACT
1 ATATAATATATATGTAATACATACT
3824593 ATATAATATATATGTAATACATACT
1 ATATAATATATATGTAATACATACT
*
3824618 ATATAATATATATATATATA-ATAC-
1 ATATAATATATATGTA-ATACATACT
* * * * *
3824642 -TATCACATATA--TAATTCTTATT
1 ATATAATATATATGTAATACATACT
*
3824664 ATATAATATATA--T-A-ACATAAT
1 ATATAATATATATGTAATACATACT
*
3824685 ATAT-ATATATATATATATA-ATA-T
1 ATATAATATATATGTA-ATACATACT
* * *
3824708 ATTATAATATATA-ATACTATATACT
1 A-TATAATATATATGTAATACATACT
3824733 ATATAATATA
1 ATATAATATA
3824743 ACATACTATA
Statistics
Matches: 125, Mismatches: 12, Indels: 27
0.76 0.07 0.16
Matches are distributed among these distances:
20 9 0.07
21 12 0.10
22 2 0.02
23 23 0.18
24 22 0.18
25 54 0.43
26 3 0.02
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (25 bp):
ATATAATATATATGTAATACATACT
Found at i:3824604 original size:7 final size:7
Alignment explanation
Indices: 3824559--3824792 Score: 128
Period size: 7 Copynumber: 33.0 Consensus size: 7
3824549 AATATTATTA
3824559 ATAA-AT
1 ATAATAT
3824565 ATAATAT
1 ATAATAT
3824572 AATATATAT
1 -ATA-ATAT
* *
3824581 GTAATAC
1 ATAATAT
*
3824588 ATACTAT
1 ATAATAT
3824595 AT-A-AT
1 ATAATAT
3824600 AT-ATAT
1 ATAATAT
* *
3824606 GTAATAC
1 ATAATAT
*
3824613 ATACTAT
1 ATAATAT
3824620 ATAATAT
1 ATAATAT
3824627 ATATATAT
1 ATA-ATAT
3824635 ATAATACT
1 ATAATA-T
3824643 ATCACATAT
1 AT-A-ATAT
3824652 ATAAT-T
1 ATAATAT
* *
3824658 CTTATTAT
1 -ATAATAT
3824666 ATAATAT
1 ATAATAT
*
3824673 AT-ATAAC
1 ATAAT-AT
3824680 ATAATAT
1 ATAATAT
3824687 AT-ATAT
1 ATAATAT
3824693 ATATATAT
1 ATA-ATAT
3824701 ATAATAT
1 ATAATAT
*
3824708 ATTATA-
1 ATAATAT
3824714 AT-ATAT
1 ATAATAT
*
3824720 AATACTAT
1 -ATAATAT
*
3824728 ATACTAT
1 ATAATAT
3824735 ATAATAT
1 ATAATAT
*
3824742 AACATACTAT
1 ---ATAATAT
3824752 ATAATAT
1 ATAATAT
*
3824759 ATACTAT
1 ATAATAT
*
3824766 ATAAAAT
1 ATAATAT
3824773 A-AATAT
1 ATAATAT
* *
3824779 ATACTAC
1 ATAATAT
3824786 ATAATAT
1 ATAATAT
3824793 GAAAAGAAAT
Statistics
Matches: 175, Mismatches: 31, Indels: 43
0.70 0.12 0.17
Matches are distributed among these distances:
5 8 0.05
6 23 0.13
7 98 0.56
8 29 0.17
9 8 0.05
10 9 0.05
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (7 bp):
ATAATAT
Found at i:3824651 original size:17 final size:15
Alignment explanation
Indices: 3824545--3824781 Score: 156
Period size: 14 Copynumber: 15.8 Consensus size: 15
3824535 TTATTAAAAA
*
3824545 AATAAATAT-TAT-T
1 AATATATATATATAT
*
3824558 AATAAATATA-ATAT
1 AATATATATATATAT
*
3824572 AATATATATGTA-AT
1 AATATATATATATAT
3824586 ACATACTATATAATATAT
1 A-ATA-TATAT-ATATAT
* *
3824604 ATGTAATACATACTATAT
1 A-AT-ATATATA-TATAT
3824622 AATATATATATATAT
1 AATATATATATATAT
*
3824637 AATACTATCACATATAT
1 AATA-TAT-ATATATAT
*
3824654 AAT-TCT-TATTATAT
1 AATATATATA-TATAT
*
3824668 AATATATATA-ACAT
1 AATATATATATATAT
3824682 AATATATATATATAT
1 AATATATATATATAT
3824697 -ATATATA-ATATAT
1 AATATATATATATAT
*
3824710 TATA-ATATATA-AT
1 AATATATATATATAT
* *
3824723 ACTATATA-CTATAT
1 AATATATATATATAT
*
3824737 AATATAACATACTATAT
1 AATAT-ATATA-TATAT
*
3824754 AATATATACTATATAA
1 AATATATA-TATATAT
*
3824770 AATAAATATATA
1 AATATATATATA
3824782 CTACATAATA
Statistics
Matches: 178, Mismatches: 23, Indels: 44
0.73 0.09 0.18
Matches are distributed among these distances:
13 27 0.15
14 55 0.31
15 26 0.15
16 29 0.16
17 26 0.15
18 14 0.08
19 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:3824671 original size:60 final size:55
Alignment explanation
Indices: 3824563--3824792 Score: 210
Period size: 55 Copynumber: 4.2 Consensus size: 55
3824553 TTATTAATAA
* * * *
3824563 ATATAATATAATATATATGTAATACATACTATATAATATATATGTAATACATACT
1 ATATAATATAATATATATATAATATATACTATATAATATATATATAATATATACT
*
3824618 ATATAATAT-ATATATATATAATACTATCACATATATAATTCTTATTATATAATATATA-T
1 ATATAATATAATATATATATAATA-TAT-AC-TATATAA-T-ATA-TATATAATATATACT
* *
3824677 AACATAATAT-ATATATATATATATATAATA-TATTATAATATATA-ATACTATATACT
1 -ATATAATATAATATATATATA-ATAT-ATACTA-TATAATATATATATAATATATACT
*
3824733 ATATAATATAACATACTATATAATATATACTATAT-A-A-A-ATA-AATATATACT
1 ATATAATATAATATA-TATATAATATATACTATATAATATATATATAATATATACT
*
3824784 ACATAATAT
1 ATATAATAT
3824793 GAAAAGAAAT
Statistics
Matches: 148, Mismatches: 12, Indels: 34
0.76 0.06 0.18
Matches are distributed among these distances:
51 18 0.12
52 2 0.01
53 1 0.01
54 14 0.09
55 34 0.23
56 15 0.10
57 15 0.10
58 4 0.03
59 8 0.05
60 32 0.22
61 5 0.03
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (55 bp):
ATATAATATAATATATATATAATATATACTATATAATATATATATAATATATACT
Found at i:3824955 original size:17 final size:16
Alignment explanation
Indices: 3824926--3824964 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
3824916 AAAAAAATAT
3824926 TTATTTATTATTATAA
1 TTATTTATTATTATAA
*
3824942 TTATTTATTTATTATTA
1 TTATTTA-TTATTATAA
3824959 TTATTT
1 TTATTT
3824965 TTGTAGGCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTTATTATTATAA
Found at i:3826412 original size:20 final size:20
Alignment explanation
Indices: 3826387--3826427 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3826377 ATTTTATTAC
*
3826387 TTTTAAAATTTTAATTTATT
1 TTTTAAAATTGTAATTTATT
3826407 TTTTAAAATTGTAATTTATT
1 TTTTAAAATTGTAATTTATT
3826427 T
1 T
3826428 AATATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTAAAATTGTAATTTATT
Found at i:3829032 original size:21 final size:21
Alignment explanation
Indices: 3828984--3829035 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
3828974 CACCATTGTC
* *
3828984 TTTTTAGACTCAAAATTGACA
1 TTTTTATACCCAAAATTGACA
3829005 TTTTTATACCCAAAATTGACA
1 TTTTTATACCCAAAATTGACA
3829026 TTTTTATACC
1 TTTTTATACC
3829036 ATTAAAACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (21 bp):
TTTTTATACCCAAAATTGACA
Found at i:3829522 original size:15 final size:15
Alignment explanation
Indices: 3829502--3829533 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3829492 AATCAAGAAC
*
3829502 AAAAAGAGAAGAAGA
1 AAAAAGAGAAAAAGA
3829517 AAAAAGAGAAAAAGA
1 AAAAAGAGAAAAAGA
3829532 AA
1 AA
3829534 GAAAAAAAGA
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:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAAGAGAAAAAGA
Found at i:3829538 original size:18 final size:17
Alignment explanation
Indices: 3829517--3829581 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 17
3829507 GAGAAGAAGA
3829517 AAAAAGAGAAAAAGAAAG
1 AAAAAGAGAAAAA-AAAG
* *
3829535 AAAAAAAGAAAAAACAAA
1 AAAAAGAGAAAAAA-AAG
3829553 AACAAAG-GAAAAATAAAG
1 AA-AAAGAGAAAAA-AAAG
3829571 AAAAA-AGAAAA
1 AAAAAGAGAAAA
3829582 CAAGACGCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 9 0.23
18 26 0.67
19 4 0.10
ACGTcount: A:0.82, C:0.03, G:0.14, T:0.02
Consensus pattern (17 bp):
AAAAAGAGAAAAAAAAG
Found at i:3829543 original size:27 final size:26
Alignment explanation
Indices: 3829504--3829586 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 26
3829494 TCAAGAACAA
* *
3829504 AAAGAGAAGAAGAAAAAAGAGAAAAAG
1 AAAGAAAAAAAGAAAAAAGA-AAAAAG
*
3829531 AAAGAAAAAAAGAAAAAACAAAAACA-
1 AAAGAAAAAAAGAAAAAAGAAAAA-AG
*
3829557 AAGGAAAAATAAAGAAAAAAGAAAACAAG
1 AAAG-AAAA-AAAGAAAAAAGAAAA-AAG
3829586 A
1 A
3829587 CGCATATGCA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
26 7 0.15
27 22 0.48
28 15 0.33
29 2 0.04
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.01
Consensus pattern (26 bp):
AAAGAAAAAAAGAAAAAAGAAAAAAG
Found at i:3830674 original size:32 final size:32
Alignment explanation
Indices: 3830604--3830675 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
3830594 GCACATTTGA
* * *
3830604 AGATTCAACATCAAATGTTGGGGCATTTTTGG
1 AGATTCAACATCAAATATTGGGGCATCTTCGG
* *
3830636 AAATTCAACATCGAATATTGGGGCATCTTCGG
1 AGATTCAACATCAAATATTGGGGCATCTTCGG
*
3830668 GGATTCAA
1 AGATTCAA
3830676 AATCCTGATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGGCATCTTCGG
Found at i:3831332 original size:110 final size:110
Alignment explanation
Indices: 3831194--3831702 Score: 778
Period size: 110 Copynumber: 4.7 Consensus size: 110
3831184 TCGAGAAAAG
* * *
3831194 CTGACTGTCAACAAACAAATTTTCAGTTTCATTTAGAGTCAATTTCAACTTCACAGCGAATGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
* *
3831259 TTGGACTCGAGACAACATAAGCTCAACTTCACAACAAAGGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGA
*
3831304 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTAACAGCGAAGGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
* * *
3831369 TTGGACTCGAGACAACACAAGCTCAAATTCACAGCGAAGGGGAGA
66 TTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGA
* * * *
3831414 CTGACTGTCAACAAACAACTTTTTAGTTTCATTCAGATTCAATTTCAACTTCACATCGAAGAATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
* *
3831479 TTGGAATCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGA
* * *
3831524 CTGACTGTCAACAAACAATTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAATGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
*
3831589 TTGGACTCGAGGCAACACAAGCTCAACTTCACAACGAAGGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGA
* *
3831634 CTGACTGTCAACAAACAAC---T---TTTCATTCAGAGTCAATTTCAAATTTACAGCGAAGGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
*
3831693 TTGAACTCGA
66 TTGGACTCGA
3831703 AGCGACACAA
Statistics
Matches: 367, Mismatches: 32, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
104 44 0.12
107 1 0.00
110 322 0.88
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (110 bp):
CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
TTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGA
Found at i:3832666 original size:3 final size:3
Alignment explanation
Indices: 3832658--3832711 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
3832648 AAATATTTAT
*
3832658 TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
3832704 TTT TTA TT
1 TTA TTA TT
3832712 TTTGTAGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3834162 original size:20 final size:20
Alignment explanation
Indices: 3834137--3834177 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3834127 ATTTTATTAC
*
3834137 TTTTAAAATTTTAATTTATT
1 TTTTAAAATTGTAATTTATT
3834157 TTTTAAAATTGTAATTTATT
1 TTTTAAAATTGTAATTTATT
3834177 T
1 T
3834178 AATATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTAAAATTGTAATTTATT
Found at i:3834284 original size:13 final size:13
Alignment explanation
Indices: 3834266--3834295 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3834256 TGAATCAGAT
3834266 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
3834279 TTTTAATTTTTAA
1 TTTTAAATTTTAA
3834292 TTTT
1 TTTT
3834296 TTGAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:3834296 original size:7 final size:7
Alignment explanation
Indices: 3834264--3834296 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
3834254 TTTGAATCAG
3834264 ATTTTTA
1 ATTTTTA
*
3834271 AATTTTA
1 ATTTTTA
3834278 A-TTTTA
1 ATTTTTA
3834284 ATTTTTA
1 ATTTTTA
3834291 ATTTTT
1 ATTTTT
3834297 TGAATTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTTTA
Found at i:3845642 original size:20 final size:20
Alignment explanation
Indices: 3845576--3845649 Score: 82
Period size: 22 Copynumber: 3.6 Consensus size: 20
3845566 ATCTAATTTT
3845576 GGTATCGATACC-TA-ATAGG
1 GGTATCGATACCATATATA-G
3845595 GGTATCGATACCATAATATAG
1 GGTATCGATACCAT-ATATAG
*
3845616 TGGTATCGATACCAT-TGTGAG
1 -GGTATCGATACCATATAT-AG
3845637 GGTATCGATACCA
1 GGTATCGATACCA
3845650 AACTACATCA
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
19 12 0.24
20 16 0.33
21 4 0.08
22 17 0.35
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (20 bp):
GGTATCGATACCATATATAG
Found at i:3845667 original size:95 final size:93
Alignment explanation
Indices: 3845520--3845746 Score: 269
Period size: 95 Copynumber: 2.4 Consensus size: 93
3845510 CCCAAGCGAT
* *
3845520 GTGGTATCGATACCATGGTAAGGGTATCGATACCAGTAAACATCGAATCTAATTTTGGTATCGAT
1 GTGGTATCGATACCATGGTAAGGGTATCGATACCAG-AAACATCAAAGCTAATTTTGGTATCGAT
*
3845585 ACCT-AATAGGGGTATCGATACCATAATATA
65 A-CTGAA-AGGGGTATCGATACCATAATAGA
* * *
3845615 GTGGTATCGATACCATTGTGAGGGTATCGATACCA-AACTACATCAAAGCTAATTTTGGTATTGA
1 GTGGTATCGATACCATGGTAAGGGTATCGATACCAGAA--ACATCAAAGCTAATTTTGGTATCGA
* *
3845679 TACTGGAAGGGGGTATCGATACCATAATAGG
64 TACT-GAAAGGGGTATCGATACCATAATAGA
* **
3845710 GTAGTATCGATACCATAATAAGGTAGTATCGATACCA
1 GTGGTATCGATACCATGGTAAGG--GTATCGATACCA
3845747 TAGTAGGGGT
Statistics
Matches: 114, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
93 2 0.02
94 2 0.02
95 96 0.84
96 2 0.02
97 12 0.11
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (93 bp):
GTGGTATCGATACCATGGTAAGGGTATCGATACCAGAAACATCAAAGCTAATTTTGGTATCGATA
CTGAAAGGGGTATCGATACCATAATAGA
Found at i:3845719 original size:22 final size:22
Alignment explanation
Indices: 3845691--3845764 Score: 116
Period size: 22 Copynumber: 3.5 Consensus size: 22
3845681 CTGGAAGGGG
3845691 GTATCGATACCATAATAGGGTA
1 GTATCGATACCATAATAGGGTA
*
3845713 GTATCGATACCATAATAAGGTA
1 GTATCGATACCATAATAGGGTA
*
3845735 GTATCGATACCATAGTAGGG--
1 GTATCGATACCATAATAGGGTA
3845755 GTATCGATAC
1 GTATCGATAC
3845765 TGAAGGGTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 10 0.20
22 39 0.80
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (22 bp):
GTATCGATACCATAATAGGGTA
Found at i:3846282 original size:79 final size:79
Alignment explanation
Indices: 3846151--3846506 Score: 606
Period size: 79 Copynumber: 4.5 Consensus size: 79
3846141 TGAATAAAAG
* *
3846151 AATAATGCATATGGATGCA-TATTTGGCATGAAAGGATGTCTTAGCTGAAATGTATATGGGTACA
1 AATAATGCATATGGGTGCATTA-TTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACA
*
3846215 TTCTCAGCATAACAA
65 TTCTCGGCATAACAA
3846230 AATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACAT
1 AATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACAT
*
3846295 TCTCGGCATAAAAA
66 TCTCGGCATAACAA
*
3846309 AATAAGGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACAT
1 AATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACAT
*
3846374 TCTCGGCATAACAG
66 TCTCGGCATAACAA
* *
3846388 AATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTACCTGAAATTTATATGGGTACAT
1 AATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACAT
* *
3846453 TCTCGACATAACAG
66 TCTCGGCATAACAA
3846467 AATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCC
1 AATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCC
3846507 AAAGTTGAAA
Statistics
Matches: 265, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
79 263 0.99
80 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (79 bp):
AATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATATGGGTACAT
TCTCGGCATAACAA
Found at i:3846303 original size:45 final size:45
Alignment explanation
Indices: 3846233--3846580 Score: 154
Period size: 45 Copynumber: 8.5 Consensus size: 45
3846223 ATAACAAAAT
* *
3846233 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGA
1 AATGCATATGGGTACATTATCGGCATGAAAGGATGCCTTAGCTGA
* * **
3846278 AATGTATATGGGTACATTCTCGGCAT-AAA--A------AAAT--
1 AATGCATATGGGTACATTATCGGCATGAAAGGATGCCTTAGCTGA
* * *
3846312 AAGGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGA
1 AATGCATATGGGTACATTATCGGCATGAAAGGATGCCTTAGCTGA
* *
3846357 AATGTATATGGGTACATTCTCGGCAT-AACA-GA------A--T--
1 AATGCATATGGGTACATTATCGGCATGAA-AGGATGCCTTAGCTGA
* * *
3846391 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTACCTGA
1 AATGCATATGGGTACATTATCGGCATGAAAGGATGCCTTAGCTGA
** * *
3846436 AATTTATATGGGTACATTCTCGACAT-AACA-GA------A--T--
1 AATGCATATGGGTACATTATCGGCATGAA-AGGATGCCTTAGCTGA
* * ** *
3846470 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTGA
1 AATGCATATGGGTACATTATCGGCATGAAAGGATGCCTTAGCTGA
* * * ** *
3846515 AACGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTGA
1 AATGCATATGGGTACATTATCGGCATGAAAGGATGCCTTAGCTGA
* *
3846560 AATACATATGGGTGCATTATC
1 AATGCATATGGGTACATTATC
3846581 AATATAAAAG
Statistics
Matches: 228, Mismatches: 38, Indels: 74
0.67 0.11 0.22
Matches are distributed among these distances:
34 65 0.29
35 11 0.05
36 4 0.02
37 1 0.00
38 2 0.01
41 2 0.01
42 1 0.00
43 4 0.02
44 11 0.05
45 127 0.56
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (45 bp):
AATGCATATGGGTACATTATCGGCATGAAAGGATGCCTTAGCTGA
Found at i:3847193 original size:68 final size:68
Alignment explanation
Indices: 3847065--3847193 Score: 161
Period size: 68 Copynumber: 1.9 Consensus size: 68
3847055 AAGACCTAGC
* * ** *
3847065 TGTGCATTTGGCAGAAAGGTGTAAATTATGCCAGTTAGATGAAAGACTAAGTGTCTTTGAGGCAT
1 TGTGCAATTGGCAGAAAGGTATAAATTATGCCAGTTAGATGAAAGACTAAGTACCGTTGAGGCAT
3847130 AGT
66 AGT
* * * *
3847133 TGTGCAATTGGTAGAAAGGTATCAATTATGCTAGTTAGATGAACAG-TTAAGTACCGTTGAG
1 TGTGCAATTGGCAGAAAGGTATAAATTATGCCAGTTAGATGAA-AGACTAAGTACCGTTGAG
3847194 AGAAAGAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
68 49 0.96
69 2 0.04
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (68 bp):
TGTGCAATTGGCAGAAAGGTATAAATTATGCCAGTTAGATGAAAGACTAAGTACCGTTGAGGCAT
AGT
Found at i:3847473 original size:45 final size:45
Alignment explanation
Indices: 3847447--3847568 Score: 217
Period size: 45 Copynumber: 2.7 Consensus size: 45
3847437 TAAACAGTAC
3847447 ATAAAAGGCATGAAAGGATGCCATAAATGAAAGGTATAATAGAGT
1 ATAAAAGGCATGAAAGGATGCCATAAATGAAAGGTATAATAGAGT
3847492 ATAAAAGGCATGAAAGGATGCCATAAATGAAAGGTATAATAGAGT
1 ATAAAAGGCATGAAAGGATGCCATAAATGAAAGGTATAATAGAGT
* * *
3847537 ATAAAAGGAATGAAAGGATGACATAATTGAAA
1 ATAAAAGGCATGAAAGGATGCCATAAATGAAA
3847569 CATATAGGTA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.51, C:0.06, G:0.24, T:0.20
Consensus pattern (45 bp):
ATAAAAGGCATGAAAGGATGCCATAAATGAAAGGTATAATAGAGT
Found at i:3848229 original size:71 final size:70
Alignment explanation
Indices: 3848113--3848248 Score: 238
Period size: 71 Copynumber: 1.9 Consensus size: 70
3848103 ATGATAAACA
*
3848113 TTATTTAAAAATGATGTGACATCCATATCTCGGGTACGAATGGGTATACGGGAGATGGGTGTTAC
1 TTATTTAAAAATGATGTGACATCCATATCTCGAGTACGAATGGGTATACGGG-GATGGGTGTTAC
3848178 ATTTAT
65 ATTTAT
3848184 TTATTTAAAAATGATGTGACATCCATATCTCGAGTACAGAA-GGGTATACGGGGATGGGTGTTAC
1 TTATTTAAAAATGATGTGACATCCATATCTCGAGTAC-GAATGGGTATACGGGGATGGGTGTTAC
3848248 A
65 A
3848249 AAGATAATTT
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
70 13 0.21
71 47 0.75
72 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.32
Consensus pattern (70 bp):
TTATTTAAAAATGATGTGACATCCATATCTCGAGTACGAATGGGTATACGGGGATGGGTGTTACA
TTTAT
Found at i:3850788 original size:17 final size:17
Alignment explanation
Indices: 3850766--3850810 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3850756 TTAATAAAGT
3850766 TAGTTCATTGA-TTACAC
1 TAGTTCATTGATTTA-AC
*
3850783 TAGTTCATTCATTTAAC
1 TAGTTCATTGATTTAAC
*
3850800 TAGTTAATTGA
1 TAGTTCATTGA
3850811 ACAAACTAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (17 bp):
TAGTTCATTGATTTAAC
Found at i:3868503 original size:44 final size:45
Alignment explanation
Indices: 3868440--3868551 Score: 190
Period size: 45 Copynumber: 2.5 Consensus size: 45
3868430 TGGTAGTATG
3868440 AAAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTATGTTGGT
*
3868484 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTATGTTGGT
* *
3868529 AAAGTAAGCTTACAAGCTTATGG
1 AAAATAAGCTTACGAGCTTATGG
3868552 GATTAAATTG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
44 26 0.41
45 38 0.59
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTATGTTGGT
Found at i:3874342 original size:34 final size:35
Alignment explanation
Indices: 3874304--3874378 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 35
3874294 AGGGAAGTAG
* * *
3874304 TTCATTTATGCATTTAGATCATTTAATAA-GTTAC
1 TTCATTCATGCATCTAGACCATTTAATAATGTTAC
* * *
3874338 TTCATTCATGCATCTAGCCCTTTTAATAATGTTAG
1 TTCATTCATGCATCTAGACCATTTAATAATGTTAC
3874373 TTCATT
1 TTCATT
3874379 AATTACACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 24 0.71
35 10 0.29
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (35 bp):
TTCATTCATGCATCTAGACCATTTAATAATGTTAC
Found at i:3874390 original size:17 final size:16
Alignment explanation
Indices: 3874370--3874412 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3874360 TTAATAATGT
3874370 TAGTTCATTAATTACAC
1 TAGTTCATTAATTA-AC
* *
3874387 TAGTTCACTCATTTAAC
1 TAGTTCA-TTAATTAAC
3874404 TAGTTCATT
1 TAGTTCATT
3874413 GAACAAAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 16 0.73
18 5 0.23
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (16 bp):
TAGTTCATTAATTAAC
Found at i:3886595 original size:7 final size:7
Alignment explanation
Indices: 3886583--3886672 Score: 86
Period size: 7 Copynumber: 13.7 Consensus size: 7
3886573 ATACTACACT
3886583 TAAAAAA
1 TAAAAAA
3886590 TAAAAAAA
1 T-AAAAAA
*
3886598 TAAAGAA
1 TAAAAAA
3886605 T--AAAA
1 TAAAAAA
*
3886610 TAAAGAA
1 TAAAAAA
*
3886617 TAAAATA
1 TAAAAAA
3886624 -AAAAAA
1 TAAAAAA
*
3886630 T-GAAAA
1 TAAAAAA
3886636 TAAAAAA
1 TAAAAAA
3886643 TAAAAAA
1 TAAAAAA
3886650 T-AAAAA
1 TAAAAAA
3886656 T-AAAAA
1 TAAAAAA
3886662 T-AAAAA
1 TAAAAAA
3886668 TAAAA
1 TAAAA
3886673 GAGAATAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
5 4 0.06
6 28 0.41
7 30 0.43
8 7 0.10
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:3886621 original size:26 final size:26
Alignment explanation
Indices: 3886583--3886672 Score: 114
Period size: 26 Copynumber: 3.5 Consensus size: 26
3886573 ATACTACACT
3886583 TAAAAAATAAAAAAATAAAGAAT-AAAA
1 TAAAAAAT-AAAAAATAAA-AATAAAAA
* *
3886610 TAAAGAATAAAATAA-AAAAATGAAAA
1 TAAAAAATAAAA-AATAAAAATAAAAA
3886636 TAAAAAATAAAAAATAAAAATAAAAA
1 TAAAAAATAAAAAATAAAAATAAAAA
3886662 T-AAAAATAAAA
1 TAAAAAATAAAA
3886673 GAGAATAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
25 15 0.26
26 33 0.58
27 9 0.16
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (26 bp):
TAAAAAATAAAAAATAAAAATAAAAA
Found at i:3886635 original size:6 final size:6
Alignment explanation
Indices: 3886593--3886672 Score: 90
Period size: 6 Copynumber: 12.7 Consensus size: 6
3886583 TAAAAAATAA
* *
3886593 AAAAAT AAAGAAT -AAAAT AAAGAAT AAAATAA AAAAAT GAAAAT AAAAAAT
1 AAAAAT AAA-AAT AAAAAT AAA-AAT AAAA-AT AAAAAT AAAAAT -AAAAAT
3886644 AAAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 -AAAAAT AAAAAT AAAAAT AAAAAT AAAA
3886673 GAGAATAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
5 3 0.05
6 36 0.55
7 26 0.40
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:3889597 original size:37 final size:37
Alignment explanation
Indices: 3889550--3889621 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
3889540 TTTAATATAA
*
3889550 ATATAATATTTTACATATT-TATGCCTTATTTTTTATT
1 ATATAATATTTTACATATTCT-TACCTTATTTTTTATT
* *
3889587 ATATACTATTTTATATATTCTTACCTTATTTTTTA
1 ATATAATATTTTACATATTCTTACCTTATTTTTTA
3889622 CGTAGTTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 30 0.97
38 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.01, T:0.60
Consensus pattern (37 bp):
ATATAATATTTTACATATTCTTACCTTATTTTTTATT
Found at i:3905384 original size:25 final size:25
Alignment explanation
Indices: 3905350--3905403 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
3905340 AAAGCGCACT
*
3905350 AGGCAAGGAGCTGCTAGCACCTCCA
1 AGGCAAGGAGCTACTAGCACCTCCA
*
3905375 AGGCGAGGAGCTACTAGCACCTCCA
1 AGGCAAGGAGCTACTAGCACCTCCA
3905400 AGGC
1 AGGC
3905404 CACGCCACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.31, G:0.30, T:0.11
Consensus pattern (25 bp):
AGGCAAGGAGCTACTAGCACCTCCA
Found at i:3907162 original size:14 final size:14
Alignment explanation
Indices: 3907143--3907170 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3907133 GAGAACCGCG
3907143 AGATAAGATCCTCA
1 AGATAAGATCCTCA
3907157 AGATAAGATCCTCA
1 AGATAAGATCCTCA
3907171 TAAGCAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
AGATAAGATCCTCA
Found at i:3912372 original size:24 final size:24
Alignment explanation
Indices: 3912324--3912372 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3912314 CATTCTTGAA
* **
3912324 GAGAGAGAAAAATAAAATGGGAAT
1 GAGAGAGAAAAAGAAAATGAAAAT
3912348 GAGAGAGAAAAAGAAAATGAAAAT
1 GAGAGAGAAAAAGAAAATGAAAAT
3912372 G
1 G
3912373 GGTTTCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.29, T:0.10
Consensus pattern (24 bp):
GAGAGAGAAAAAGAAAATGAAAAT
Found at i:3919966 original size:15 final size:15
Alignment explanation
Indices: 3919947--3920002 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
3919937 TTCATGGGGT
* *
3919947 AAGAAGACAACGTCT
1 AAGAAGAAAACGTCA
*
3919962 AAGAAGAAAACGGCA
1 AAGAAGAAAACGTCA
3919977 AAGAAGAAAACGTCA
1 AAGAAGAAAACGTCA
3919992 AAGAAGGAAAA
1 AAGAA-GAAAA
3920003 AAGAAAGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 31 0.86
16 5 0.14
ACGTcount: A:0.59, C:0.12, G:0.23, T:0.05
Consensus pattern (15 bp):
AAGAAGAAAACGTCA
Found at i:3925801 original size:2 final size:2
Alignment explanation
Indices: 3925794--3925900 Score: 214
Period size: 2 Copynumber: 53.5 Consensus size: 2
3925784 TCAATCTACA
3925794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3925836 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3925878 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
3925901 ATTTCCGAAA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 105 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3926174 original size:88 final size:86
Alignment explanation
Indices: 3925970--3926224 Score: 363
Period size: 88 Copynumber: 3.0 Consensus size: 86
3925960 TCAATGACAT
* * * * **
3925970 GCAATGTAAGTAATATATGCGTTTCATAAATTTATGAAACACAAATGTATGTCA-AGTAGATTTA
1 GCAATGTAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTGTGTCATCTTA-ATTTA
3926034 TGAC-GGGGCTTTAATGA-CGC
65 TGACGGGGGCTTTAATGACCGC
* * *
3926054 GCAATGTAAGTCATACATGCGTGTCATAAATTTATGACTCACAAATGTGTGTTATCTTAATTTAT
1 GCAATGTAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTGTGTCATCTTAATTTAT
3926119 GACGGGGGCTTTAATGACGCGCC
66 GACGGGGGCTTTAATGAC-CG-C
*
3926142 GCAATGTAAGTCATATATGCGTGTCATAAATTTATGACGCACAAATGTGTGTCATCTTAATTTAT
1 GCAATGTAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTGTGTCATCTTAATTTAT
*
3926207 GACGGGGGCTTCAATGAC
66 GACGGGGGCTTTAATGAC
3926225 ACTCAAAGAA
Statistics
Matches: 153, Mismatches: 13, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
84 56 0.37
85 15 0.10
87 2 0.01
88 80 0.52
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (86 bp):
GCAATGTAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTGTGTCATCTTAATTTAT
GACGGGGGCTTTAATGACCGC
Found at i:3927828 original size:2 final size:2
Alignment explanation
Indices: 3927821--3927880 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
3927811 ATTAAAGAGA
3927821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3927863 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
3927881 GAAGCAATGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3928124 original size:18 final size:18
Alignment explanation
Indices: 3928101--3928141 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3928091 TATGGAACAC
3928101 TTAATATATT-TTTAAAAT
1 TTAATA-ATTATTTAAAAT
*
3928119 TTAATAATTATTTATAAT
1 TTAATAATTATTTAAAAT
3928137 TTAAT
1 TTAAT
3928142 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATAATTATTTAAAAT
Found at i:3928304 original size:18 final size:18
Alignment explanation
Indices: 3928281--3928321 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3928271 AATCGAACAC
3928281 TTAATATATT-TTTAAAAT
1 TTAATA-ATTATTTAAAAT
*
3928299 TTAATAATTATTTATAAT
1 TTAATAATTATTTAAAAT
3928317 TTAAT
1 TTAAT
3928322 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATAATTATTTAAAAT
Found at i:3928397 original size:180 final size:180
Alignment explanation
Indices: 3928095--3928456 Score: 724
Period size: 180 Copynumber: 2.0 Consensus size: 180
3928085 TGAAATTATG
3928095 GAACACTTAATATATTTTTAAAATTTAATAATTATTTATAATTTAATTTAAAAAATAAAAATTTT
1 GAACACTTAATATATTTTTAAAATTTAATAATTATTTATAATTTAATTTAAAAAATAAAAATTTT
3928160 AATATATTATATGTTTGAGTTGCTCGTTAACTTTTGGATTTGAATATCAAGTAACTTGTTTCGCC
66 AATATATTATATGTTTGAGTTGCTCGTTAACTTTTGGATTTGAATATCAAGTAACTTGTTTCGCC
3928225 TCGTTAAGGATTTCACTTAAGTTTGAACTTAAGTTAAACTTATTCGAATC
131 TCGTTAAGGATTTCACTTAAGTTTGAACTTAAGTTAAACTTATTCGAATC
3928275 GAACACTTAATATATTTTTAAAATTTAATAATTATTTATAATTTAATTTAAAAAATAAAAATTTT
1 GAACACTTAATATATTTTTAAAATTTAATAATTATTTATAATTTAATTTAAAAAATAAAAATTTT
3928340 AATATATTATATGTTTGAGTTGCTCGTTAACTTTTGGATTTGAATATCAAGTAACTTGTTTCGCC
66 AATATATTATATGTTTGAGTTGCTCGTTAACTTTTGGATTTGAATATCAAGTAACTTGTTTCGCC
3928405 TCGTTAAGGATTTCACTTAAGTTTGAACTTAAGTTAAACTTATTCGAATC
131 TCGTTAAGGATTTCACTTAAGTTTGAACTTAAGTTAAACTTATTCGAATC
3928455 GA
1 GA
3928457 GTGTTGATCG
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 182 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (180 bp):
GAACACTTAATATATTTTTAAAATTTAATAATTATTTATAATTTAATTTAAAAAATAAAAATTTT
AATATATTATATGTTTGAGTTGCTCGTTAACTTTTGGATTTGAATATCAAGTAACTTGTTTCGCC
TCGTTAAGGATTTCACTTAAGTTTGAACTTAAGTTAAACTTATTCGAATC
Found at i:3929239 original size:23 final size:23
Alignment explanation
Indices: 3929204--3929249 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3929194 TTTTTAATAA
*
3929204 TTATATTTCTATGACACGTTTTC
1 TTATATTTCTATGACACATTTTC
3929227 TTATATCTT-TATGACACATTTTC
1 TTATAT-TTCTATGACACATTTTC
3929250 ATCGTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (23 bp):
TTATATTTCTATGACACATTTTC
Found at i:3930186 original size:37 final size:38
Alignment explanation
Indices: 3930145--3930217 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
3930135 ATTATTTTAA
* *
3930145 TAATATAATTGATAATA-TATTATTTTTATTAAATAAT
1 TAATATAATTGATAATACTATTATTTTAATAAAATAAT
* *
3930182 TAATATAATTTATAATACTTTTATTTTAATAAAATA
1 TAATATAATTGATAATACTATTATTTTAATAAAATA
3930218 TAATAATCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (38 bp):
TAATATAATTGATAATACTATTATTTTAATAAAATAAT
Found at i:3931058 original size:183 final size:183
Alignment explanation
Indices: 3930849--3931267 Score: 730
Period size: 183 Copynumber: 2.3 Consensus size: 183
3930839 GATACAAATA
*
3930849 AAAAATATATCGATCCATATCAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
1 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
* *
3930914 AAATCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATTAGATTGAAATAAGTATCGACATTT
66 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATTAGATTGAAATAAGTATCGACACTT
* *
3930979 TTGGAATTTAAAAGAGAAGAAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
131 TTGGAATTTAAAAGAGAAGAAGTAATAGCACCTATAAAGTGTCGACACTTTAT
* * *
3931032 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGATCTTAAAATGACA
1 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
3931097 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATTAGATTGAAATAAGTATCGACACTT
66 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATTAGATTGAAATAAGTATCGACACTT
3931162 TTGGAATTTAAAAGAGAAGAAGTAATAGCACCTATAAAGTGTCGACACTTTAT
131 TTGGAATTTAAAAGAGAAGAAGTAATAGCACCTATAAAGTGTCGACACTTTAT
* ** *
3931215 AAAAATATATTGATTTATAACAATATAACAGGGAAAAATATGACAAAACCGGT
1 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
3931268 AAAGCGCTAC
Statistics
Matches: 222, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
183 222 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (183 bp):
AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATTAGATTGAAATAAGTATCGACACTT
TTGGAATTTAAAAGAGAAGAAGTAATAGCACCTATAAAGTGTCGACACTTTAT
Found at i:3931361 original size:162 final size:163
Alignment explanation
Indices: 3931091--3931589 Score: 538
Period size: 162 Copynumber: 3.1 Consensus size: 163
3931081 CGATCTTAAA
*
3931091 ATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTATCGATTAGATTGAAATAAGTATCG
1 ATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTAGATTGAAATAAGTATCG
*
3931156 ACACTTTTGGAATTTAAAAGAGAAGAAGTAATAGCACCTATAAAGTGTCGACACTTTATAAAAAT
66 ACACTTTTGGAATTTAAAAGAGAAGAAGTAACAGCACCTATAAAGTGTCGACACTTTATAAAAAT
* **
3931221 ATATTGATTTATAACAATATAACAGGGAAAAAT
131 ATATCGATCCATAACAATATAACAGGGAAAAAT
* * *
3931254 ATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGA-TA-CTTTAATATAAGTATC
1 ATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTAGATTGAA-ATAAGTATC
*
3931317 GACACTTTTGGAATTTAAAAGAGAATAAGTAACAGCGA-CTATAAAGTGTCGACACTTTATAAAA
65 GACACTTTTGGAATTTAAAAGAGAAGAAGTAACAGC-ACCTATAAAGTGTCGACACTTTATAAAA
* * *
3931381 ATGTGTCGATCCATAACAATATAACAGGTAAAAAT
129 ATATATCGATCCATAACAATATAACAGGGAAAAAT
*** *** * * * *
3931416 ATGAC--AACCGGTCTCGAAATGA-CA-AAACCGGT-AAAGCGATATCGAATATG-TTG--A-AA
1 ATGACAAAACCGGTAAAGCGCT-ACCAGATA-TGTTGAAA--G-TATCGATTA-GATTGAAATAA
* * * * * * *
3931472 GTGTCGACACTTTTGGAATTTAAAAGGGAAGCAGTAATAGCGCCTATAAAGTGTCAATACTTTAT
60 GTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTAACAGCACCTATAAAGTGTCGACACTTTAT
* *
3931537 AAAAATGA-ATCGCTCCATAACAATATAACAGGTAAAAAT
125 AAAAAT-ATATCGATCCATAACAATATAACAGGGAAAAAT
*
3931576 ATGATAAAACCGGT
1 ATGACAAAACCGGT
3931590 TTCGAAAAGA
Statistics
Matches: 287, Mismatches: 35, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
159 5 0.02
160 110 0.38
161 7 0.02
162 117 0.41
163 46 0.16
164 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (163 bp):
ATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTAGATTGAAATAAGTATCG
ACACTTTTGGAATTTAAAAGAGAAGAAGTAACAGCACCTATAAAGTGTCGACACTTTATAAAAAT
ATATCGATCCATAACAATATAACAGGGAAAAAT
Found at i:3931606 original size:20 final size:20
Alignment explanation
Indices: 3931581--3931626 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3931571 AAAATATGAT
* *
3931581 AAAACCGGTTTCGAAAAGAC
1 AAAACCGATCTCGAAAAGAC
*
3931601 AAAACCGATCTCGAAATGAC
1 AAAACCGATCTCGAAAAGAC
3931621 AAAACC
1 AAAACC
3931627 AGTAAAGCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.24, G:0.15, T:0.13
Consensus pattern (20 bp):
AAAACCGATCTCGAAAAGAC
Found at i:3938239 original size:73 final size:74
Alignment explanation
Indices: 3938108--3938254 Score: 176
Period size: 74 Copynumber: 2.0 Consensus size: 74
3938098 TGAATAAATC
** *
3938108 TTCATGAATGTATCTTCATGGCTGAATCCTTCCTCCCATGTGTGAACATGTTTGATTTGTCTTCT
1 TTCATGAATGTATCTT-ATGGCTGAATCCTTCCTCCCATGTGTGAACATGACTGATTTGGCTTCT
*
3938173 ATGGATGAATG
65 -TGCATGAATG
* *
3938184 TTCATGAATGTATC-T-TGGCTGAAATTCTT-CTCCCCTTGTGTGAACATGACT-ATTTGGCTTC
1 TTCATGAATGTATCTTATGGCTG-AATCCTTCCT-CCCATGTGTGAACATGACTGATTTGGCTTC
3938245 TTGCATGAAT
64 TTGCATGAAT
3938255 AGATGAACTT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
72 8 0.13
73 18 0.29
74 22 0.35
75 1 0.02
76 14 0.22
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (74 bp):
TTCATGAATGTATCTTATGGCTGAATCCTTCCTCCCATGTGTGAACATGACTGATTTGGCTTCTT
GCATGAATG
Found at i:3939429 original size:18 final size:18
Alignment explanation
Indices: 3939406--3939444 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3939396 GAAAAAATAT
3939406 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
*
3939424 GAAGAAGAAAATATGGAG
1 GAAGAAGAAAAGATGGAG
3939442 GAA
1 GAA
3939445 TTAGGAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:3941035 original size:19 final size:19
Alignment explanation
Indices: 3940990--3941038 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
3940980 AATGTAGGGT
*
3940990 TAATTTTCTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
3941009 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
3941028 TAATTTTGTAT
1 TAATTTTGTAT
3941039 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3941871 original size:200 final size:201
Alignment explanation
Indices: 3941472--3942636 Score: 1505
Period size: 200 Copynumber: 5.8 Consensus size: 201
3941462 ATAAACAGAT
* * * *
3941472 GTGTCGATACATTTGCT-AAAAGTATGGACCCCAAAAACATCAAAACCAATAATTATAATGTAAT
1 GTGTCGATACATTT-ATAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAAT
* * **
3941536 AGGTAAATTAACAATGTAACCGGTATAAATATACCAG-TTAATTAGAAAATAGGTCAACATAATG
65 AGGTAAATTTACAATATAACCGGTATAAATATA-CAGTTTAATTAGAAAAGCGGTCAACATAATG
*
3941600 TATCGATACTTGTGGAATTTGTGTCGATA-TTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCA
129 TATCGACACTTGTGGAATTTGTGTCGATACTTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCA
3941664 CGCATAAA
194 CGCATAAA
*
3941672 GTGTCGATACATTTATAAAAAGTATCTAT-CCAAAAACATCAAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
* * *
3941736 GGTAAATTTAAAATATAA-TGGTATAAATATACTAGTTTAATTAGAAAAGCGGTCAACAAAATGT
66 GGTAAATTTACAATATAACCGGTATAAATATAC-AGTTTAATTAGAAAAGCGGTCAACATAATGT
* * * *
3941800 ATCAACACATGTGGAATTTGTGTCGATACTTTTTTGTCCAGAATGAATGCCCAAGCGAGGTGCAA
130 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCAC
3941865 GCATAAA
195 GCATAAA
**
3941872 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACATATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
* * *
3941937 GGTAAATTTACAATATAACCGGTATAAATATACCGGCTTAATTATAAAAGCGGTCAACATAATGT
66 GGTAAATTTACAATATAACCGGTATAAATATA-CAGTTTAATTAGAAAAGCGGTCAACATAATGT
* * ** * * * * *
3942002 ATCGACATTTTTTTAATTTGTGTCGATAC-TTTTTGTCCATAATCAATGGCCAAACAAGGTGTAC
130 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCAC
3942066 GCA-ATAA
195 GCATA-AA
** * *
3942073 GTGTCGATACATTTA-AAATTGTATCGATCCCAAAAATATCAAAACTGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
* * * * * * ** *
3942137 GGTAAATTTACAATGTAACCGGTAGATATAAACCGATTTTATGT-GAAAATAGGTCTACATAATG
66 GGTAAATTTACAATATAACCGGTATAAATATACAG-TTTAAT-TAGAAAAGCGGTCAACATAATG
* *
3942201 TATCGACACATGTGGAATTTGTGTCGATAC-TTTTTGTCCAAAATGAATGCCCAAACGAGGTGCA
129 TATCGACACTTGTGGAATTTGTGTCGATACTTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCA
*
3942265 AGCATAAA
194 CGCATAAA
* ** *
3942273 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATTGAAACCGATAATTATAATTTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
* *
3942338 GGTAAATTTACAATGTAACCGGTATAAATATACAGGTTTAATTAGAAAAACGGTCAACATAATGT
66 GGTAAATTTACAATATAACCGGTATAAATATACA-GTTTAATTAGAAAAGCGGTCAACATAATGT
* ** ** * * *
3942403 ATCAACACTT-TTAAATTTGTGTCGA-AAATTTTTGTCCAGAATCAAAGCCCAAACGAGGTGTAC
130 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCAC
3942466 GCATAAA
195 GCATAAA
** *
3942473 GTGTCGATACATTTA-AAATTGTATAGATCCCAAAAACAT-AGAAACCGATAATTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCA-AAACCGATAATTATAATGTAAT
* *
3942536 AGGTAAATTTATAATATAACCGGTATAAATATATCGGTTTAATTAGAAAAGCGGTCAACATAATG
65 AGGTAAATTTACAATATAACCGGTATAAATATA-CAGTTTAATTAGAAAAGCGGTCAACATAATG
* **
3942601 TATCGACACTTTTTATAATTT-TGTCGATACTTTTTT
129 TATCGACAC-TTGTGGAATTTGTGTCGATACTTTTTT
3942637 AAATTTCGCG
Statistics
Matches: 838, Mismatches: 107, Indels: 39
0.85 0.11 0.04
Matches are distributed among these distances:
197 1 0.00
198 14 0.02
199 211 0.25
200 334 0.40
201 214 0.26
202 63 0.08
203 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (201 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
GGTAAATTTACAATATAACCGGTATAAATATACAGTTTAATTAGAAAAGCGGTCAACATAATGTA
TCGACACTTGTGGAATTTGTGTCGATACTTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCACG
CATAAA
Found at i:3942237 original size:401 final size:397
Alignment explanation
Indices: 3941472--3942635 Score: 1597
Period size: 401 Copynumber: 2.9 Consensus size: 397
3941462 ATAAACAGAT
* * *
3941472 GTGTCGATACATTTGCT-AAAAGTATGGACCCCAAAAACATCAAAACCAATAATTATAATGTAAT
1 GTGTCGATACATTT-ATAAAAAGTATCGATCCCAAAAACATCAAAA-CAATAATTATAATGTAAT
* *
3941536 AGGTAAATTAACAATGTAACCGGTATAAATATACCAGTTAATTAGAAAATA-GGTCAACATAATG
64 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTAATTAGAAAA-ACGGTCAACATAATG
* * ** * * *
3941600 TATCGATACTTGTGGAATTTGTGTCGATATTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCAC
128 TATCGACA-TTTTTAAATTTGTGTCGATAATTTTTGTCCAGAATCAATGCCCAAACGAGGTGTAC
** *
3941665 GCATAAAGTGTCGATACATTTATAAAAAGTATCTAT-CCAAAAACATCAAAACCGATAATTATAA
192 GCATAAAGTGTCGATACATTTA-AAATTGTATCGATCCCAAAAACATCAAAACCGATAATTATAA
* *
3941729 TGTAATAGGTAAATTTAAAATATAA-TGGTATAAATATACTAGTTTAATTAGAAAAGCGGTCAAC
256 TGTAATAGGTAAATTTAAAATATAACCGGTATAAATATACGA-TTTAATTAGAAAAGCGGTCAAC
* * * *
3941793 AAAATGTATCAACACATGTGGAATTTGTGTCGATACTTTTTTGTCCAGAATGAATGCCCAAGCGA
320 ATAATGTATCGACACATGTGGAATTTGTGTCGATAC-TTTTTGTCCAAAATGAATGCCCAAACGA
3941858 GGTGCAAGCATAAA
384 GGTGCAAGCATAAA
3941872 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACATATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACA-ATAATTATAATGTAATA
* * *
3941937 GGTAAATTTACAATATAACCGGTATAAATATACCGGCTTAATTATAAAAGCGGTCAACATAATGT
65 GGTAAATTTACAATGTAACCGGTATAAATATACCGG-TTAATTAGAAAAACGGTCAACATAATGT
* * * * *
3942002 ATCGACATTTTTTTAATTTGTGTCGATACTTTTTGTCCATAATCAATGGCCAAACAAGGTGTACG
129 ATCGACA-TTTTTAAATTTGTGTCGATAATTTTTGTCCAGAATCAATGCCCAAACGAGGTGTACG
* *
3942067 CA-ATAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAATATCAAAACTGATAATTATAAT
193 CATA-AAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCAAAACCGATAATTATAAT
* * * * * * ** *
3942131 GTAATAGGTAAATTTACAATGTAACCGGTAGATATAAACCGATTTTATGT-GAAAATAGGTCTAC
257 GTAATAGGTAAATTTAAAATATAACCGGTATAAATATA-CGATTTAAT-TAGAAAAGCGGTCAAC
3942195 ATAATGTATCGACACATGTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACGAG
320 ATAATGTATCGACACATGTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACGAG
3942260 GTGCAAGCATAAA
385 GTGCAAGCATAAA
* * * * *
3942273 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATTGAAACCGATAATTATAATTTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACA-TCAAAACAATAATTATAATGTAATA
*
3942338 GGTAAATTTACAATGTAACCGGTATAAATATACAGGTTTAATTAGAAAAACGGTCAACATAATGT
65 GGTAAATTTACAATGTAACCGGTATAAATATACCGG-TTAATTAGAAAAACGGTCAACATAATGT
* * * *
3942403 ATCAACACTTTTAAATTTGTGTCGAAAATTTTTGTCCAGAATCAAAGCCCAAACGAGGTGTACGC
129 ATCGACATTTTTAAATTTGTGTCGATAATTTTTGTCCAGAATCAATGCCCAAACGAGGTGTACGC
*
3942468 ATAAAGTGTCGATACATTTAAAATTGTATAGATCCCAAAAACAT-AGAAACCGATAATTATAATG
194 ATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCA-AAACCGATAATTATAATG
* *
3942532 TAATAGGTAAATTTATAATATAACCGGTATAAATATATCGGTTTAATTAGAAAAGCGGTCAACAT
258 TAATAGGTAAATTTAAAATATAACCGGTATAAATATA-CGATTTAATTAGAAAAGCGGTCAACAT
* * **
3942597 AATGTATCGACACTTTTTATAATTT-TGTCGATACTTTTT
322 AATGTATCGACAC-ATGTGGAATTTGTGTCGATACTTTTT
3942636 TAAATTTCGC
Statistics
Matches: 674, Mismatches: 76, Indels: 28
0.87 0.10 0.04
Matches are distributed among these distances:
399 5 0.01
400 287 0.43
401 315 0.47
402 64 0.09
403 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (397 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACAATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGTATAAATATACCGGTTAATTAGAAAAACGGTCAACATAATGTAT
CGACATTTTTAAATTTGTGTCGATAATTTTTGTCCAGAATCAATGCCCAAACGAGGTGTACGCAT
AAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAA
TAGGTAAATTTAAAATATAACCGGTATAAATATACGATTTAATTAGAAAAGCGGTCAACATAATG
TATCGACACATGTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACGAGGTGCAA
GCATAAA
Found at i:3942873 original size:23 final size:23
Alignment explanation
Indices: 3942843--3942890 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3942833 GATTAGACTC
3942843 TTTTTTTCCTTAATGTGTTTGTG
1 TTTTTTTCCTTAATGTGTTTGTG
3942866 TTTTTTTCCTTAATGTGTTTGTG
1 TTTTTTTCCTTAATGTGTTTGTG
3942889 TT
1 TT
3942891 CCAATTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.08, C:0.08, G:0.17, T:0.67
Consensus pattern (23 bp):
TTTTTTTCCTTAATGTGTTTGTG
Found at i:3944476 original size:18 final size:18
Alignment explanation
Indices: 3944427--3944479 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
3944417 ACTATAGCGA
* *
3944427 AAATCGTTAATATACAATT
1 AAAT-GTTAACATTCAATT
3944446 AAATGTTAACATTCAATT
1 AAATGTTAACATTCAATT
3944464 AAATGTTAACATTCAA
1 AAATGTTAACATTCAA
3944480 ACTTGATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (18 bp):
AAATGTTAACATTCAATT
Found at i:3945855 original size:15 final size:15
Alignment explanation
Indices: 3945837--3945867 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3945827 GAAGATTGGA
3945837 TATCTGAAGAATGCC
1 TATCTGAAGAATGCC
3945852 TATCTGAAGAATGCC
1 TATCTGAAGAATGCC
3945867 T
1 T
3945868 TTCGGATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (15 bp):
TATCTGAAGAATGCC
Found at i:3947519 original size:197 final size:199
Alignment explanation
Indices: 3947147--3947885 Score: 991
Period size: 197 Copynumber: 3.7 Consensus size: 199
3947137 TTTATTAAAA
* * ** *
3947147 GTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAATAGGTAAATACACAAGGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * * * *
3947212 ATAGATATATACTGGTTTTAA-GAGAAAATAAGTCTACATAAAGTATCAACACTTTATAAATTTG
66 ATAGAAATATACCGG-TTTAATGAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTG
* *
3947276 TGTCGATACTTATTGTCCAGAATGAATGCCCAACTAGGTGCACGCATAAAGTGTCGATACATTTA
130 TGTCGATACTTTTTGTCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTA
3947341 AAATT
195 AAATT
* * *
3947346 GTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTTATATGTAACTTTACAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * *
3947411 GTAGAAATATACCGG-TTAATTAGAAAATAGGTCAACATAATGTATCGATACTTTTTAAA-TTGT
66 ATAGAAATATACCGGTTTAATGAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGT
* *
3947474 GCCGATACTTTTTGTCCAGAATGAATGACAAACTAGGTGCACGCATAAAGTGTCGATACATTTAA
131 GTCGATACTTTTTGTCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTAA
3947539 AATT
196 AATT
* ** * *
3947543 GTATCGATCCCAAAAACATCGATACTGATAATTACAATGTAATAGGTAAATTAACAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * *
3947608 GTAGAAATATATCGGTTTTATGACAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGT
66 ATAGAAATATACCGGTTTAATGAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGT
* * * *
3947673 GTCGATACTTTTTGTCCAGAATGAAAGCCAAACGAGGTACACACATAAAGTGTCGATACATTTAT
131 GTCGATACTTTTTGTCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTA-
3947738 TAAATT
195 -AAATT
* * * *
3947744 -TATCGATCCCAAAGACATCGAAACTCATAATTATAATGTAATATGTAAATTTATAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * * *
3947808 ATAGAAACATACCGGTATAATTAGAATATAGGTTAATATAATGTATCGACACTTTTTAAATTTGT
66 ATAGAAATATACCGGTTTAATGAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGT
* *
3947873 ATCGATATTTTTT
131 GTCGATACTTTTT
3947886 TAAATTACGC
Statistics
Matches: 473, Mismatches: 62, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
197 144 0.30
198 71 0.15
199 131 0.28
200 122 0.26
201 5 0.01
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (199 bp):
GTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
ATAGAAATATACCGGTTTAATGAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGT
GTCGATACTTTTTGTCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTAA
AATT
Found at i:3947610 original size:20 final size:19
Alignment explanation
Indices: 3947572--3947610 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3947562 CGATACTGAT
*
3947572 AATTACAATGTAATAGGTA
1 AATTACAATGTAACAGGTA
*
3947591 AATTAACAATGTAACCGGTA
1 AATT-ACAATGTAACAGGTA
3947611 GAAATATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (19 bp):
AATTACAATGTAACAGGTA
Found at i:3947873 original size:21 final size:22
Alignment explanation
Indices: 3947849--3947891 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3947839 GTTAATATAA
3947849 TGTATCGACA-CTTTTTAAATT
1 TGTATCGACATCTTTTTAAATT
* *
3947870 TGTATCGATATTTTTTTAAATT
1 TGTATCGACATCTTTTTAAATT
3947892 ACGCATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (22 bp):
TGTATCGACATCTTTTTAAATT
Found at i:3949528 original size:19 final size:19
Alignment explanation
Indices: 3949504--3949547 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
3949494 ATGTAGGGGA
3949504 AATTTTGTATACGATTCAT
1 AATTTTGTATACGATTCAT
*
3949523 AATTTTGTATACGATTTAT
1 AATTTTGTATACGATTCAT
3949542 AATTTT
1 AATTTT
3949548 TTTATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (19 bp):
AATTTTGTATACGATTCAT
Found at i:3950053 original size:27 final size:27
Alignment explanation
Indices: 3950033--3950095 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
3950023 AGCATAACTA
*
3950033 CTTGACGTTGCACGTAGAGCAGTGAAC
1 CTTGACATTGCACGTAGAGCAGTGAAC
* *
3950060 CTTGCCATTGCACGTAGAGCAGCGAAC
1 CTTGACATTGCACGTAGAGCAGTGAAC
*
3950087 CTTGCCATT
1 CTTGACATT
3950096 TGTATTACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (27 bp):
CTTGACATTGCACGTAGAGCAGTGAAC
Found at i:3952686 original size:200 final size:199
Alignment explanation
Indices: 3952339--3952857 Score: 690
Period size: 200 Copynumber: 2.6 Consensus size: 199
3952329 CATATGTGTC
* * *
3952339 GATACATTTATTAAAAGTATCAATCCCAAAAACATCGAAACCGATAATTATAATATAATAGGTAA
1 GATACATTTATTAAAAGTATCGATCCCAAAAACATTGAAACCGATAATTATAATGTAATAGGTAA
* * * * *
3952404 ATTTACAATGTGACCAGTATAAATATATCGGTTTTATGAGAGAATATGTCAACATAATGTATATA
66 ATTTACAATGTGACCGGTATAAATATACCGGTTTTATGAGAAAATAAGTCAACATAATGTATAGA
*
3952469 CACTTTTTCAATTTGTGTCGATACATTTTGTCCAGAATGAATGCCAAATGAGGTGCACGCATAAA
131 CACTTTTTCAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCATAAA
3952534 ATGTA
195 ATGTA
* * * *
3952539 GATACATTTATTAAAAGTATCGATCTCAAAAACATTGAAACCGCTAATTACAATGTAATAGGCAA
1 GATACATTTATTAAAAGTATCGATCCCAAAAACATTGAAACCGATAATTATAATGTAATAGGTAA
* * * * * * *
3952604 ATTTACAATATGCCCGGTAGAAATATACCAGTTTTATGATAAAATAAGTCTACATAATGTATCGA
66 ATTTACAATGTGACCGGTATAAATATACCGGTTTTATGAGAAAATAAGTCAACATAATGTATAGA
* *
3952669 CACTTTTT-AAGTTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAACGAGGTGCACGCATAAA
131 CACTTTTTCAA-TTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCATAAA
* *
3952733 GTGTC
195 ATGTA
3952738 GATACATTTA--AAATTA-TAT-GATCCCAAAAACATTGAAACCGATAATTATAATGTAATAGGT
1 GATACATTTATTAAA--AGTATCGATCCCAAAAACATTGAAACCGATAATTATAATGTAATAGGT
* * * * *
3952799 AAATTTGCAATGTTACCGGTATAAATATACCGGTTTAGAT-AGAAAATAGGTCAATATAA
64 AAATTTACAATGTGACCGGTATAAATATACCGGTTT-TATGAGAAAATAAGTCAACATAA
3952858 GCGCTACATA
Statistics
Matches: 276, Mismatches: 39, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
197 86 0.31
198 5 0.02
199 53 0.19
200 132 0.48
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (199 bp):
GATACATTTATTAAAAGTATCGATCCCAAAAACATTGAAACCGATAATTATAATGTAATAGGTAA
ATTTACAATGTGACCGGTATAAATATACCGGTTTTATGAGAAAATAAGTCAACATAATGTATAGA
CACTTTTTCAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCATAAAA
TGTA
Found at i:3952953 original size:87 final size:87
Alignment explanation
Indices: 3952852--3953013 Score: 270
Period size: 87 Copynumber: 1.9 Consensus size: 87
3952842 AAATAGGTCA
* * **
3952852 ATATAAGCGCTACATATTACATTATATAAGTGATACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGATACATATTACATTATATAAGCGATACCTAATATGTTATTACACTTGATAATATTT
3952917 TCGGTTAAATGCTTATTTTATT
66 TCGGTTAAATGCTTATTTTATT
* *
3952939 ATATAAGCGATACATATTACATTATATAAGCGCTACCTAATATGTTATTACATTTGATAATATTT
1 ATATAAGCGATACATATTACATTATATAAGCGATACCTAATATGTTATTACACTTGATAATATTT
3953004 TCGGTTAAAT
66 TCGGTTAAAT
3953014 AATATAACAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (87 bp):
ATATAAGCGATACATATTACATTATATAAGCGATACCTAATATGTTATTACACTTGATAATATTT
TCGGTTAAATGCTTATTTTATT
Found at i:3952986 original size:23 final size:23
Alignment explanation
Indices: 3952936--3952980 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3952926 TGCTTATTTT
*
3952936 ATTATATAAGCGATACATATTAC
1 ATTATATAAGCGATACATAATAC
* *
3952959 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGATACATAATA
3952981 TGTTATTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGATACATAATAC
Found at i:3957870 original size:15 final size:15
Alignment explanation
Indices: 3957850--3957882 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3957840 AATAGACCAA
*
3957850 ACTAGGGAGTATCGG
1 ACTAGGGAGTATCAG
3957865 ACTAGGGAGTATCAG
1 ACTAGGGAGTATCAG
3957880 ACT
1 ACT
3957883 CGGACTAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.21
Consensus pattern (15 bp):
ACTAGGGAGTATCAG
Found at i:3957887 original size:21 final size:21
Alignment explanation
Indices: 3957861--3957903 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
3957851 CTAGGGAGTA
3957861 TCGGACTAGGGAGTATC-AGAC
1 TCGGACTA-GGAGTATCGAGAC
3957882 TCGGACTAGGAGTATCGAGAC
1 TCGGACTAGGAGTATCGAGAC
3957903 T
1 T
3957904 TCCTTTGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.21
Consensus pattern (21 bp):
TCGGACTAGGAGTATCGAGAC
Found at i:3961033 original size:9 final size:9
Alignment explanation
Indices: 3961021--3961052 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3961011 CACTTTTTTT
3961021 TTTTTTGCA
1 TTTTTTGCA
3961030 TTTTTTGCA
1 TTTTTTGCA
*
3961039 TTTTTTGTA
1 TTTTTTGCA
3961048 TTTTT
1 TTTTT
3961053 GATAATCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.75
Consensus pattern (9 bp):
TTTTTTGCA
Found at i:3962886 original size:18 final size:18
Alignment explanation
Indices: 3962850--3962891 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3962840 TATTTTAAAA
*
3962850 ACTTTATTTGTATATTGG
1 ACTTTATTTGTATAATGG
3962868 ACTTATATTTGTA-AATGG
1 ACTT-TATTTGTATAATGG
3962886 ACTTTA
1 ACTTTA
3962892 CTTATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 12 0.55
19 8 0.36
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (18 bp):
ACTTTATTTGTATAATGG
Found at i:3965432 original size:21 final size:21
Alignment explanation
Indices: 3965403--3965453 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
3965393 TGAACCCTCC
3965403 TTTTCTTTTTT-TTATTT-ATT
1 TTTTCTTTTTTATT-TTTGATT
3965423 TTTCTCTTTTTTATTTTTGATT
1 TTT-TCTTTTTTATTTTTGATT
3965445 TTTTCTTTT
1 TTTTCTTTT
3965454 CTTCAAGCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.11
21 17 0.61
22 8 0.29
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.82
Consensus pattern (21 bp):
TTTTCTTTTTTATTTTTGATT
Found at i:3965453 original size:19 final size:20
Alignment explanation
Indices: 3965403--3965453 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 20
3965393 TGAACCCTCC
* *
3965403 TTTTCTTTTTTTTATTTATT
1 TTTTCTTTTATTTATTGATT
3965423 TTTCTCTTTTTTATTT-TTGATT
1 TTT-TC--TTTTATTTATTGATT
3965445 TTTTCTTTT
1 TTTTCTTTT
3965454 CTTCAAGCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
19 4 0.15
20 3 0.12
21 4 0.15
22 8 0.31
23 7 0.27
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTCTTTTATTTATTGATT
Found at i:3969837 original size:19 final size:19
Alignment explanation
Indices: 3969813--3969860 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
3969803 TTCAAATTCA
*
3969813 AGGTGATTGAATTTAGTCT
1 AGGTGATTGAATGTAGTCT
3969832 AGGTGATTGAATGTAGTCT
1 AGGTGATTGAATGTAGTCT
*
3969851 AGATGATTGA
1 AGGTGATTGA
3969861 TCATCATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.38
Consensus pattern (19 bp):
AGGTGATTGAATGTAGTCT
Found at i:3978821 original size:23 final size:23
Alignment explanation
Indices: 3978791--3978838 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
3978781 CCCTTGTCTG
3978791 AAGTAGCAGCTAATAGAAAAGCA
1 AAGTAGCAGCTAATAGAAAAGCA
*
3978814 AAGTAGCAGCTAATAGGAAAGCA
1 AAGTAGCAGCTAATAGAAAAGCA
3978837 AA
1 AA
3978839 CTTGTTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.12, G:0.23, T:0.12
Consensus pattern (23 bp):
AAGTAGCAGCTAATAGAAAAGCA
Found at i:3979686 original size:30 final size:30
Alignment explanation
Indices: 3979641--3979781 Score: 117
Period size: 30 Copynumber: 4.7 Consensus size: 30
3979631 GTCTTATGCA
*
3979641 TGCTCTCTTTCCTTTTCATCAAACAAT-GG
1 TGCTCTCTTTCCTTTTCATCAAACAATACG
* * *
3979670 TTGCTCTATTTTCTTTTCATCAAACACTACG
1 -TGCTCTCTTTCCTTTTCATCAAACAATACG
**
3979701 TGCTCTCTTTCCTTTTCATCAAACGCTA-G
1 TGCTCTCTTTCCTTTTCATCAAACAATACG
* * * * **
3979730 T-TTCTCTTTTCCCTATTCATCAATCATTGGG
1 TGCTCTC-TTT-CCTTTTCATCAAACAATACG
*
3979761 TGCTCTCTTCCCTTTTCATCA
1 TGCTCTCTTTCCTTTTCATCA
3979782 TACATTTTTT
Statistics
Matches: 90, Mismatches: 16, Indels: 10
0.78 0.14 0.09
Matches are distributed among these distances:
28 4 0.04
29 5 0.06
30 72 0.80
31 5 0.06
32 4 0.04
ACGTcount: A:0.18, C:0.29, G:0.09, T:0.45
Consensus pattern (30 bp):
TGCTCTCTTTCCTTTTCATCAAACAATACG
Found at i:3979749 original size:60 final size:60
Alignment explanation
Indices: 3979641--3979781 Score: 167
Period size: 60 Copynumber: 2.4 Consensus size: 60
3979631 GTCTTATGCA
* * *
3979641 TGCTCTCTTTCCTTTTCATCAAACAATGGTTGCTCTATTTTCTTTTCATCAAACACTACG
1 TGCTCTCTTTCCTTTTCATCAAACAATAGTTGCTCTATTTCCTATTCATCAAACACTACG
** * * * **
3979701 TGCTCTCTTTCCTTTTCATCAAACGCTAGTTTCTCT-TTTCCCTATTCATCAATCATTGGG
1 TGCTCTCTTTCCTTTTCATCAAACAATAGTTGCTCTATTT-CCTATTCATCAAACACTACG
*
3979761 TGCTCTCTTCCCTTTTCATCA
1 TGCTCTCTTTCCTTTTCATCA
3979782 TACATTTTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
59 3 0.04
60 66 0.96
ACGTcount: A:0.18, C:0.29, G:0.09, T:0.45
Consensus pattern (60 bp):
TGCTCTCTTTCCTTTTCATCAAACAATAGTTGCTCTATTTCCTATTCATCAAACACTACG
Found at i:3980557 original size:13 final size:14
Alignment explanation
Indices: 3980521--3980578 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
3980511 TCATCAAACG
*
3980521 TTTGCTCTCTTTCA
1 TTTGCTCTCTTCCA
*
3980535 TTTTCTCTCTTCCA
1 TTTGCTCTCTTCCA
3980549 -TTGCTCTCTTCACA
1 TTTGCTCTCTTC-CA
3980563 CCTTGTGCTCTCTTCC
1 --TT-TGCTCTCTTCC
3980579 GTTGCTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
13 10 0.28
14 14 0.39
17 2 0.06
18 10 0.28
ACGTcount: A:0.07, C:0.36, G:0.07, T:0.50
Consensus pattern (14 bp):
TTTGCTCTCTTCCA
Found at i:3980577 original size:31 final size:31
Alignment explanation
Indices: 3980539--3980687 Score: 112
Period size: 31 Copynumber: 4.8 Consensus size: 31
3980529 CTTTCATTTT
3980539 CTCTCTTCCATTGCTCTCTTCACACCTTGTG
1 CTCTCTTCCATTGCTCTCTTCACACCTTGTG
* * *
3980570 CTCTCTTCCGTTGCTTTTTTCACA--TTGGTTG
1 CTCTCTTCCATTGCTCTCTTCACACCTT-G-TG
* * *
3980601 CTTTCATCAAACACTTGCTCTCTT--CA-CTT-TT
1 CTCTCTTC---CA-TTGCTCTCTTCACACCTTGTG
* *
3980632 CTCTTTTCCTTTGCTCTCTTCACACCTTGTG
1 CTCTCTTCCATTGCTCTCTTCACACCTTGTG
* *
3980663 CTCTTTTCCGTTGCTCTCTTCACAC
1 CTCTCTTCCATTGCTCTCTTCACAC
3980688 TGGTTGATTT
Statistics
Matches: 92, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
27 10 0.11
28 1 0.01
29 4 0.04
30 4 0.04
31 60 0.65
33 2 0.02
34 3 0.03
35 8 0.09
ACGTcount: A:0.10, C:0.34, G:0.09, T:0.46
Consensus pattern (31 bp):
CTCTCTTCCATTGCTCTCTTCACACCTTGTG
Found at i:3980660 original size:93 final size:93
Alignment explanation
Indices: 3980501--3980725 Score: 335
Period size: 93 Copynumber: 2.4 Consensus size: 93
3980491 AAACAAATGG
**
3980501 TTGGTTGCTTTCATCAAACGTTTGCTCTCTTTCA-TTTTCTCTCTTCCATTGCTCTCTTCACACC
1 TTGGTTGCTTTCATCAAACACTTGCTCTC-TTCACTTTTCTCTCTTCCATTGCTCTCTTCACACC
* *
3980565 TTGTGCTCTCTTCCGTTGCTTTTTTCACA
65 TTGTGCTCTCTTCCGTTGCTCTCTTCACA
* *
3980594 TTGGTTGCTTTCATCAAACACTTGCTCTCTTCACTTTTCTCTTTTCCTTTGCTCTCTTCACACCT
1 TTGGTTGCTTTCATCAAACACTTGCTCTCTTCACTTTTCTCTCTTCCATTGCTCTCTTCACACCT
*
3980659 TGTGCTCTTTTCCGTTGCTCTCTTCACA
66 TGTGCTCTCTTCCGTTGCTCTCTTCACA
* * * *
3980687 CTGGTTGATTTCATCAAACACTTGCCCTATTCACTTTTC
1 TTGGTTGCTTTCATCAAACACTTGCTCTCTTCACTTTTC
3980726 AAAAATGACT
Statistics
Matches: 120, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 4 0.03
93 116 0.97
ACGTcount: A:0.12, C:0.31, G:0.10, T:0.47
Consensus pattern (93 bp):
TTGGTTGCTTTCATCAAACACTTGCTCTCTTCACTTTTCTCTCTTCCATTGCTCTCTTCACACCT
TGTGCTCTCTTCCGTTGCTCTCTTCACA
Found at i:3981091 original size:30 final size:30
Alignment explanation
Indices: 3981015--3981316 Score: 254
Period size: 30 Copynumber: 10.1 Consensus size: 30
3981005 AAACAATGCG
*
3981015 TGCTTTCTTCCATTTTCATCAAAC-TATGGT
1 TGCTCTCTTCCATTTTCATCAAACAT-TGGT
* * * * *
3981045 TGATATATTTCTTTTTCATCAAACATTGAG-
1 TGCTCTCTTCCATTTTCATCAAACATTG-GT
* *
3981075 TGCTCTCTTCCCTTTTCATCAAACACTGGT
1 TGCTCTCTTCCATTTTCATCAAACATTGGT
3981105 TGCTCTCTTCCATTTTCATCAAACATTGGT
1 TGCTCTCTTCCATTTTCATCAAACATTGGT
* * * **
3981135 TACTCTCTTCCATTTTCATAAAATACAGGT
1 TGCTCTCTTCCATTTTCATCAAACATTGGT
** * * * *
3981165 TATTCTATTCCCTTTTCATGAAACACTGGT
1 TGCTCTCTTCCATTTTCATCAAACATTGGT
* * *
3981195 TGCTTTCTTCCTTTTTGATCAAACATTGCG-
1 TGCTCTCTTCCATTTTCATCAAACATTG-GT
* * *
3981225 TGCACTCTTCCTTTTTCATCAAACAATGGT
1 TGCTCTCTTCCATTTTCATCAAACATTGGT
* * * *
3981255 TGTTCTATTTCATTTTCATCAAACACTGCG-
1 TGCTCTCTTCCATTTTCATCAAACATTG-GT
*
3981285 TGCTCTCTTTCC-TTTTCATCAAACACTGGT
1 TGCTCTC-TTCCATTTTCATCAAACATTGGT
3981315 TG
1 TG
3981317 TGCAAAAGAC
Statistics
Matches: 219, Mismatches: 45, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
29 3 0.01
30 209 0.95
31 7 0.03
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.43
Consensus pattern (30 bp):
TGCTCTCTTCCATTTTCATCAAACATTGGT
Found at i:3981151 original size:90 final size:91
Alignment explanation
Indices: 3980992--3981315 Score: 308
Period size: 90 Copynumber: 3.6 Consensus size: 91
3980982 TGGTTACTTT
** * * * * *
3980992 TTCCCTTTTTTTCAAACAATGCGTGCTTTCTTCCATTTTCATCAAAC-TATGGTTGA-TATATTT
1 TTCCCTTTTCATCAAACACTGCGTGCTCTCTTCCATTTTCATCAAACAT-TGGTT-ACTCTCTTC
* *
3981055 CTTTTTCATCAAACATTGAG-TGCTCTC
64 CTTTTTCATCAAACATTGAGTTGTTCTA
3981082 TTCCCTTTTCATCAAACACTG-GTTGCTCTCTTCCATTTTCATCAAACATTGGTTACTCTCTTCC
1 TTCCCTTTTCATCAAACACTGCG-TGCTCTCTTCCATTTTCATCAAACATTGGTTACTCTCTTCC
* ** *
3981146 ATTTTCAT-AAA-ATACAGGTTATTCTA
65 TTTTTCATCAAACATTGA-GTTGTTCTA
* * * * * *
3981172 TTCCCTTTTCATGAAACACTG-GTTGCTTTCTTCCTTTTTGATCAAACATTGCG-TGCACTCTTC
1 TTCCCTTTTCATCAAACACTGCG-TGCTCTCTTCCATTTTCATCAAACATTG-GTTACTCTCTTC
*
3981235 CTTTTTCATCAAACAATG-GTTGTTCTA
64 CTTTTTCATCAAACATTGAGTTGTTCTA
* * *
3981262 TTTCATTTTCATCAAACACTGCGTGCTCTCTTTCC-TTTTCATCAAACACTGGTT
1 TTCCCTTTTCATCAAACACTGCGTGCTCTC-TTCCATTTTCATCAAACATTGGTT
3981316 GTGCAAAAGA
Statistics
Matches: 193, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
88 3 0.02
89 7 0.04
90 172 0.89
91 10 0.05
92 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.44
Consensus pattern (91 bp):
TTCCCTTTTCATCAAACACTGCGTGCTCTCTTCCATTTTCATCAAACATTGGTTACTCTCTTCCT
TTTTCATCAAACATTGAGTTGTTCTA
Found at i:3981779 original size:30 final size:27
Alignment explanation
Indices: 3981715--3981779 Score: 67
Period size: 30 Copynumber: 2.3 Consensus size: 27
3981705 ATAAATACTT
3981715 AAAATAATATTATTTTATATATTTAATA
1 AAAAT-ATATTATTTTATATATTTAATA
** *
3981743 TTAATATATTATTTTAGTCTCATTTTAATA
1 AAAATATATTATTTTA-TAT-A-TTTAATA
3981773 AAAATAT
1 AAAATAT
3981780 TAATTATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 11 0.38
28 5 0.17
29 1 0.03
30 12 0.41
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (27 bp):
AAAATATATTATTTTATATATTTAATA
Found at i:3981827 original size:21 final size:20
Alignment explanation
Indices: 3981794--3981848 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
3981784 TATAAAAATG
3981794 TATTAATAATAATTTTAATT
1 TATTAATAATAATTTTAATT
* *
3981814 TATTATATTATAATTTTATTT
1 TATTA-ATAATAATTTTAATT
*
3981835 TAATAATATATAAT
1 TATTAATA-ATAAT
3981849 AAATTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTAATAATAATTTTAATT
Found at i:3981861 original size:11 final size:12
Alignment explanation
Indices: 3981794--3981867 Score: 50
Period size: 12 Copynumber: 6.2 Consensus size: 12
3981784 TATAAAAATG
3981794 TATTAATAATAAT
1 TATTAATAAT-AT
*
3981807 T-TTAAT-TTAT
1 TATTAATAATAT
* *
3981817 TATATTATAATTT
1 TAT-TAATAATAT
3981830 TATTTTAATAATA-
1 TA--TTAATAATAT
3981843 TA-TAATAA-AT
1 TATTAATAATAT
3981853 TATTAATAATAT
1 TATTAATAATAT
3981865 TAT
1 TAT
3981868 CAAACATTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 17
0.67 0.09 0.24
Matches are distributed among these distances:
9 1 0.02
10 11 0.23
11 8 0.17
12 13 0.28
13 7 0.15
14 6 0.13
15 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTAATAATAT
Found at i:3981945 original size:30 final size:30
Alignment explanation
Indices: 3981866--3981997 Score: 122
Period size: 30 Copynumber: 4.4 Consensus size: 30
3981856 TAATAATATT
** * *
3981866 ATCAAACATTGGGTGCCCGCTTCCTTTTTC
1 ATCAAACATTGGGTGTTCTCTTCCCTTTTC
* ** *
3981896 ATCAAACACTGGGCATTCTCTTCAAC-TTTC
1 ATCAAACATTGGGTGTTCTCTTC-CCTTTTC
* *
3981926 ATCAAATATTGGGTGTTCTCTCCCCTTTTC
1 ATCAAACATTGGGTGTTCTCTTCCCTTTTC
* * **
3981956 ATTAAATATTGCATGTTCTCTTCCCTTTTC
1 ATCAAACATTGGGTGTTCTCTTCCCTTTTC
3981986 ATCAAACATTGG
1 ATCAAACATTGG
3981998 TTGCTCTAAC
Statistics
Matches: 79, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
29 1 0.01
30 78 0.99
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (30 bp):
ATCAAACATTGGGTGTTCTCTTCCCTTTTC
Found at i:3982041 original size:30 final size:30
Alignment explanation
Indices: 3982005--3982068 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
3981995 TGGTTGCTCT
3982005 AACACTGGTT-TCTCTCTT-CACTTTTCATCA
1 AACACTGGTTGT-TCTCTTCCA-TTTTCATCA
*
3982035 AACACTGGTTGTTCTCTTCCATTTTCGTCA
1 AACACTGGTTGTTCTCTTCCATTTTCATCA
3982065 AACA
1 AACA
3982069 TTTTGTACTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.22, C:0.28, G:0.09, T:0.41
Consensus pattern (30 bp):
AACACTGGTTGTTCTCTTCCATTTTCATCA
Found at i:3982247 original size:61 final size:60
Alignment explanation
Indices: 3982178--3982353 Score: 167
Period size: 60 Copynumber: 2.9 Consensus size: 60
3982168 CATGAAACTG
* * *
3982178 TGGTTGCTCTCTTCCCTTTCGATCAAACACTGCGTGCTCTCTTTCTTTTTTCATCAAAAAA
1 TGGTTGCTCTATTTCCTTTC-ATCAAACACTGCGTGCTCTCTTTCTCTTTTCATCAAAAAA
** * ** * * **
3982239 TGGTTGCTCTATTTTTTTTTTATCAAACACTATGTGTTCCCTTT-TCTTTTCATCAAATGA
1 TGGTTGCTCTA-TTTCCTTTCATCAAACACTGCGTGCTCTCTTTCTCTTTTCATCAAAAAA
* * * *
3982299 TGGTTTCTCTATTTCCTATTCATCAAACATTGGGTGCTCT-TTTCCCTTTTCATCA
1 TGGTTGCTCTATTTCCT-TTCATCAAACACTGCGTGCTCTCTTTCTCTTTTCATCA
3982354 TACATGTTTT
Statistics
Matches: 90, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
59 7 0.08
60 49 0.54
61 29 0.32
62 5 0.06
ACGTcount: A:0.19, C:0.24, G:0.11, T:0.47
Consensus pattern (60 bp):
TGGTTGCTCTATTTCCTTTCATCAAACACTGCGTGCTCTCTTTCTCTTTTCATCAAAAAA
Found at i:3982351 original size:30 final size:30
Alignment explanation
Indices: 3982164--3982358 Score: 87
Period size: 30 Copynumber: 6.5 Consensus size: 30
3982154 TTCTCCTCGT
* * *
3982164 TTTTCATGAAAC-TGTGGTTGCTCT-CTTCC
1 TTTTCATCAAACAT-TGGGTGCTCTATTTCC
* * * * *
3982193 CTTTCGATCAAACACTGCGTGCTCTCTTTCTT
1 TTTTC-ATCAAACATTGGGTGCTCTATTTC-C
* * * **
3982225 TTTTCATCAAAAAATGGTTGCTCTATTTTT
1 TTTTCATCAAACATTGGGTGCTCTATTTCC
* * * *
3982255 TTTTTATCAAACACTATGTGTTCCCT-TTT-C
1 TTTTCATCAAACA-T-TGGGTGCTCTATTTCC
* * *
3982285 TTTTCATCAAATGA-TGGTTTCTCTATTTCC
1 TTTTCATCAAA-CATTGGGTGCTCTATTTCC
*
3982315 TATTCATCAAACATTGGGTGCTCT-TTTCCC
1 TTTTCATCAAACATTGGGTGCTCTATTT-CC
*
3982345 TTTTCATCATACAT
1 TTTTCATCAAACAT
3982359 GTTTTTTAAT
Statistics
Matches: 122, Mismatches: 33, Indels: 21
0.69 0.19 0.12
Matches are distributed among these distances:
28 7 0.06
29 11 0.09
30 69 0.57
31 25 0.20
32 10 0.08
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.46
Consensus pattern (30 bp):
TTTTCATCAAACATTGGGTGCTCTATTTCC
Found at i:3983607 original size:30 final size:29
Alignment explanation
Indices: 3983567--3984208 Score: 437
Period size: 30 Copynumber: 21.3 Consensus size: 29
3983557 TACTTCTTTT
* *
3983567 CTTTTTATCAAACACTGCGTGCTTTCTTCC
1 CTTTTCATCAAACACTG-GTGCTCTCTTCC
* ** * *
3983597 GTTTTCATCAAACTA-TGGTTTTAATCTTTC
1 CTTTTCATCAAAC-ACTGGTGCT-CTCTTCC
*
3983627 CTTTTCATCAAACATTGAGTGCTCTCTTCC
1 CTTTTCATCAAACACTG-GTGCTCTCTTCC
* *
3983657 TTTTTCATCAAACACTGGTTGATCTCTTCC
1 CTTTTCATCAAACACTGG-TGCTCTCTTCC
* *
3983687 ATTTTCATCAAACACTGGTTACTCTCTTCC
1 CTTTTCATCAAACACTGG-TGCTCTCTTCC
* * ** *
3983717 CTTTTCATCAAATACTAGTTATTCTATTCC
1 CTTTTCATCAAACACT-GGTGCTCTCTTCC
* * * *
3983747 CTTTTCATGAAACACTGCTTGTTTTCTTCC
1 CTTTTCATCAAACACTG-GTGCTCTCTTCC
* *
3983777 GTTTTGATCAAACACTGCGTGCTCTCTTCC
1 CTTTTCATCAAACACTG-GTGCTCTCTTCC
* * * *
3983807 CTTTTTATCAAACAATGGTTGCTCTATTTC
1 CTTTTCATCAAACACTGG-TGCTCTCTTCC
* *
3983837 CTTTTCATCAAACATTGGTTACTCTCTTCC
1 CTTTTCATCAAACACTGG-TGCTCTCTTCC
* *
3983867 CTTTTCATTAAACACTGGTAGCTCTCTTAC
1 CTTTTCATCAAACACTGGT-GCTCTCTTCC
* *
3983897 GTTTTCATCAAACACTGGTAACTCTCTTCC
1 CTTTTCATCAAACACTGGT-GCTCTCTTCC
* *
3983927 CTTTTCATTAAACATTGGTTGCTCTCTT-C
1 CTTTTCATCAAACACTGG-TGCTCTCTTCC
* * *
3983956 CTTTCTCATCAAACATTATGTGTTCTCTTCC
1 CTTT-TCATCAAACACT-GGTGCTCTCTTCC
* * * *
3983987 CTTTTCCTCAAATACTGGTTGTTCTCCTCC
1 CTTTTCATCAAACACTGG-TGCTCTCTTCC
* * *
3984017 TTTTTCATGAAACAGTGGTTGCTCTCTTCC
1 CTTTTCATCAAACACTGG-TGCTCTCTTCC
* *
3984047 C-TTTCGATCAAAAACTGCGTGCTCTCTTTCT
1 CTTTTC-ATCAAACACTG-GTGCTCTC-TTCC
* * * * *
3984078 TTTTTCATCAAAAAATGATTGCTCTATTTCC
1 CTTTTCATCAAACACTG-GTGCTCT-CTTCC
* * * * *
3984109 TTTTTTATCAAACACTACGTGTTCTCTTTC
1 CTTTTCATCAAACACT-GGTGCTCTCTTCC
* ** * *
3984139 CTTTTCATCAAATGA-TGGTTTTTCTATTTC
1 CTTTTCATCAAA-CACTGG-TGCTCTCTTCC
* *
3984169 CTATTCATCAAACATTGGGTGCTCTCTTCC
1 CTTTTCATCAAACACT-GGTGCTCTCTTCC
3984199 CTTTTCATCA
1 CTTTTCATCA
3984209 TACATAATTT
Statistics
Matches: 486, Mismatches: 102, Indels: 48
0.76 0.16 0.08
Matches are distributed among these distances:
29 20 0.04
30 406 0.84
31 56 0.12
32 4 0.01
ACGTcount: A:0.20, C:0.26, G:0.10, T:0.44
Consensus pattern (29 bp):
CTTTTCATCAAACACTGGTGCTCTCTTCC
Found at i:3984091 original size:31 final size:31
Alignment explanation
Indices: 3984048--3984150 Score: 102
Period size: 31 Copynumber: 3.3 Consensus size: 31
3984038 CTCTCTTCCC
3984048 TTTCGATCAAAAACTGCGTGCTCTCTTTCTTT
1 TTTC-ATCAAAAACTGCGTGCTCTCTTTCTTT
* ** *
3984080 TTTCATCAAAAAATGATTGCTCTATTTCCTTT
1 TTTCATCAAAAACTGCGTGCTCTCTTT-CTTT
* * * *
3984112 TTT-ATCAAACACTACGTGTTCTCTTTC-CT
1 TTTCATCAAAAACTGCGTGCTCTCTTTCTTT
3984141 TTTCATCAAA
1 TTTCATCAAA
3984151 TGATGGTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
29 4 0.07
30 7 0.12
31 35 0.61
32 11 0.19
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.45
Consensus pattern (31 bp):
TTTCATCAAAAACTGCGTGCTCTCTTTCTTT
Found at i:3985096 original size:93 final size:93
Alignment explanation
Indices: 3984927--3985143 Score: 249
Period size: 93 Copynumber: 2.3 Consensus size: 93
3984917 GAACAAATGG
* ** * * * * *
3984927 CTGGTTACTTTCATCAAATTCTTGCTCTCTTATATTTTCTCTCTTTTATTGGTCTCTTTACTCCT
1 CTGGTTGCTTTCATCAAACACTTGCTCTCTTACATTTTCTATCTTTTATTGCTCTCTTCACACCT
*
3984992 TGTTCTCTATTTCGATGCTCTCTTCAAA
66 TGTTCTATATTTCGATGCTCTCTTCAAA
* * *
3985020 CTGGTTGCTTTCATCAAACACTTGCTCTCTTCCCTTTTCTAT-TTTCTGTTGCTCTCTTCACACC
1 CTGGTTGCTTTCATCAAACACTTGCTCTCTTACATTTTCTATCTTT-TATTGCTCTCTTCACACC
* *
3985084 TT-TTCTTATATTTCGTTGCTCTCTTCACA
65 TTGTTC-TATATTTCGATGCTCTCTTCAAA
* * *
3985113 CTAGTTGCTTTCATCAAACATTTTCTCTCTT
1 CTGGTTGCTTTCATCAAACACTTGCTCTCTT
3985144 TACTTTTAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
92 6 0.06
93 99 0.94
ACGTcount: A:0.15, C:0.27, G:0.08, T:0.50
Consensus pattern (93 bp):
CTGGTTGCTTTCATCAAACACTTGCTCTCTTACATTTTCTATCTTTTATTGCTCTCTTCACACCT
TGTTCTATATTTCGATGCTCTCTTCAAA
Found at i:3985105 original size:31 final size:30
Alignment explanation
Indices: 3985041--3985113 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
3985031 CATCAAACAC
3985041 TTGCTCTCTT--C-CCTTTTCTATTTTCTG
1 TTGCTCTCTTCACACCTTTTCTATTTTCTG
3985068 TTGCTCTCTTCACACCTTTTCTTATATTTC-G
1 TTGCTCTCTTCACACCTTTTC-TAT-TTTCTG
3985099 TTGCTCTCTTCACAC
1 TTGCTCTCTTCACAC
3985114 TAGTTGCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
27 10 0.24
29 1 0.02
30 7 0.17
31 19 0.46
32 4 0.10
ACGTcount: A:0.10, C:0.32, G:0.07, T:0.52
Consensus pattern (30 bp):
TTGCTCTCTTCACACCTTTTCTATTTTCTG
Done.