Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 21 of 190
Found at i:3251492 original size:54 final size:54
Alignment explanation
Indices: 3251434--3251546 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 54
3251424 ATAAATTTAA
* *
3251434 GAAAAATTAT-GAATCTTTCTAAAAATTTAATTTTCTA-AAATTTTATAATCTTTT
1 GAAAAATTATAGAATCTTTC-AAAAATTT-ATTTTCGAGAAAGTTTATAATCTTTT
* * * *
3251488 GAAAATTTATATAATTTTTCAAAAATTTATTTTCGAGAAAGTTTATAATTTTTT
1 GAAAAATTATAGAATCTTTCAAAAATTTATTTTCGAGAAAGTTTATAATCTTTT
*
3251542 CAAAA
1 GAAAA
3251547 TCTATTTCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 7 0.14
54 36 0.72
55 7 0.14
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (54 bp):
GAAAAATTATAGAATCTTTCAAAAATTTATTTTCGAGAAAGTTTATAATCTTTT
Found at i:3251500 original size:20 final size:20
Alignment explanation
Indices: 3251464--3251517 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
3251454 AAAAATTTAA
*
3251464 TTTTCTAAAATTT-TATAAT
1 TTTTCAAAAATTTATATAAT
*
3251483 CTTTT-GAAAATTTATATAAT
1 -TTTTCAAAAATTTATATAAT
3251503 TTTTCAAAAATTTAT
1 TTTTCAAAAATTTAT
3251518 TTTCGAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTCAAAAATTTATATAAT
Found at i:3251505 original size:18 final size:18
Alignment explanation
Indices: 3251470--3251517 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
3251460 TTAATTTTCT
3251470 AAAATTTTATAATCTTTTG
1 AAAATTTTATAA-CTTTTG
* *
3251489 AAAATTTATATAATTTTTC
1 AAAATTT-TATAACTTTTG
*
3251508 AAAAATTTAT
1 AAAATTTTAT
3251518 TTTCGAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 17 0.68
20 5 0.20
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (18 bp):
AAAATTTTATAACTTTTG
Found at i:3257995 original size:16 final size:16
Alignment explanation
Indices: 3257965--3257994 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3257955 AGAAACACGA
3257965 AATATTAAAATAAAAT
1 AATATTAAAATAAAAT
3257981 AATA-TAAAATAAAA
1 AATATTAAAATAAAA
3257995 ACAGTTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATATTAAAATAAAAT
Found at i:3260965 original size:14 final size:14
Alignment explanation
Indices: 3260946--3260972 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3260936 TTAATTTTTT
3260946 ATTAAATAAATTTA
1 ATTAAATAAATTTA
3260960 ATTAAATAAATTT
1 ATTAAATAAATTT
3260973 GAGTAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAAATAAATTTA
Found at i:3262819 original size:25 final size:24
Alignment explanation
Indices: 3262756--3262831 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 24
3262746 AAAATTTAAT
*
3262756 TTTAATTGATTGAATCAATTTAATTTA
1 TTTAATTGATT-AA--AAATTAATTTA
* *
3262783 ATTAATTGATTATTAAATTAATTTA
1 TTTAATTGATTA-AAAATTAATTTA
3262808 TTTGAATT-ATTAAAAATT-ATTTA
1 TTT-AATTGATTAAAAATTAATTTA
3262831 T
1 T
3262832 AAAATTTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
23 6 0.14
24 5 0.12
25 16 0.38
26 5 0.12
27 10 0.24
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (24 bp):
TTTAATTGATTAAAAATTAATTTA
Found at i:3277104 original size:6 final size:6
Alignment explanation
Indices: 3277093--3277146 Score: 72
Period size: 6 Copynumber: 9.0 Consensus size: 6
3277083 ATACAATCTA
* * * *
3277093 TCTCTG TCTCTG TCTCTC TCTCTC TCTCTC TCTCTC TCTCTG TCTGTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
3277141 TCTCTC
1 TCTCTC
3277147 CTTTGTCTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.00, C:0.43, G:0.07, T:0.50
Consensus pattern (6 bp):
TCTCTC
Found at i:3277112 original size:4 final size:4
Alignment explanation
Indices: 3277093--3277146 Score: 72
Period size: 4 Copynumber: 13.5 Consensus size: 4
3277083 ATACAATCTA
* * * *
3277093 TCTC TGTC TCTG TCTC TCTC TCTC TCTC TCTC TCTC TCTC TGTC TGTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
3277141 TCTC TC
1 TCTC TC
3277147 CTTTGTCTCC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.00, C:0.43, G:0.07, T:0.50
Consensus pattern (4 bp):
TCTC
Found at i:3288441 original size:303 final size:303
Alignment explanation
Indices: 3287894--3288504 Score: 1213
Period size: 303 Copynumber: 2.0 Consensus size: 303
3287884 ATATTTTCGT
3287894 ATCGATATAAATTGTGATATATAATTTTTATATAAAATAATATATAAATATATAAATTATTAATA
1 ATCGATATAAATTGTGATATATAATTTTTATATAAAATAATATATAAATATATAAATTATTAATA
3287959 TTTTATATGATATAAATATACTAATTATCAAATTTATTCACGAGTCTTATTTCTCAGGATAACGA
66 TTTTATATGATATAAATATACTAATTATCAAATTTATTCACGAGTCTTATTTCTCAGGATAACGA
3288024 CAATCTTATGACCTTGATTTTCATTTTCTACTAACCTTGTAAAAACAAAAGTTGTTGGTCTTTAT
131 CAATCTTATGACCTTGATTTTCATTTTCTACTAACCTTGTAAAAACAAAAGTTGTTGGTCTTTAT
3288089 TTATTTTTGGGTCCACATTCCATTTGAAATTAATTCTGACAAGCCAAAACTTTCCAGACACCCTT
196 TTATTTTTGGGTCCACATTCCATTTGAAATTAATTCTGACAAGCCAAAACTTTCCAGACACCCTT
3288154 CCACGTGGTCCTCTCTCAATATCTGAAAATTTGATGAAAGTGA
261 CCACGTGGTCCTCTCTCAATATCTGAAAATTTGATGAAAGTGA
*
3288197 ATCGATATAAATTGTGATATATAATTTTTATATAAAATAATTTATAAATATATAAATTATTAATA
1 ATCGATATAAATTGTGATATATAATTTTTATATAAAATAATATATAAATATATAAATTATTAATA
3288262 TTTTATATGATATAAATATACTAATTATCAAATTTATTCACGAGTCTTATTTCTCAGGATAACGA
66 TTTTATATGATATAAATATACTAATTATCAAATTTATTCACGAGTCTTATTTCTCAGGATAACGA
3288327 CAATCTTATGACCTTGATTTTCATTTTCTACTAACCTTGTAAAAACAAAAGTTGTTGGTCTTTAT
131 CAATCTTATGACCTTGATTTTCATTTTCTACTAACCTTGTAAAAACAAAAGTTGTTGGTCTTTAT
3288392 TTATTTTTGGGTCCACATTCCATTTGAAATTAATTCTGACAAGCCAAAACTTTCCAGACACCCTT
196 TTATTTTTGGGTCCACATTCCATTTGAAATTAATTCTGACAAGCCAAAACTTTCCAGACACCCTT
3288457 CCACGTGGTCCTCTCTCAATATCTGAAAATTTGATGAAAGTGA
261 CCACGTGGTCCTCTCTCAATATCTGAAAATTTGATGAAAGTGA
3288500 ATCGA
1 ATCGA
3288505 GGAATTTGGC
Statistics
Matches: 307, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
303 307 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (303 bp):
ATCGATATAAATTGTGATATATAATTTTTATATAAAATAATATATAAATATATAAATTATTAATA
TTTTATATGATATAAATATACTAATTATCAAATTTATTCACGAGTCTTATTTCTCAGGATAACGA
CAATCTTATGACCTTGATTTTCATTTTCTACTAACCTTGTAAAAACAAAAGTTGTTGGTCTTTAT
TTATTTTTGGGTCCACATTCCATTTGAAATTAATTCTGACAAGCCAAAACTTTCCAGACACCCTT
CCACGTGGTCCTCTCTCAATATCTGAAAATTTGATGAAAGTGA
Found at i:3288985 original size:21 final size:21
Alignment explanation
Indices: 3288959--3289114 Score: 133
Period size: 21 Copynumber: 7.2 Consensus size: 21
3288949 ACTATTAAAA
3288959 TAAAAATTTAAATTAATAGAT
1 TAAAAATTTAAATTAATAGAT
*
3288980 TAAAAAATTAAATTAATAGAT
1 TAAAAATTTAAATTAATAGAT
* *
3289001 T--AAATTAATAGATTAA-AAAT
1 TAAAAATT--TAAATTAATAGAT
* * *
3289021 T-TAAATTAATAGATTAA-AAATT
1 TAAAAATT--TAAATTAATAGA-T
3289043 TAAATTAATAGATTAAATTAATAGAT
1 TAAA--AAT---TTAAATTAATAGAT
3289069 TAAAAATTTAAATTAATAGAT
1 TAAAAATTTAAATTAATAGAT
3289090 TAAAAATTTAAATTAATAGAT
1 TAAAAATTTAAATTAATAGAT
3289111 TAAA
1 TAAA
3289115 TTAATAGATT
Statistics
Matches: 117, Mismatches: 7, Indels: 22
0.80 0.05 0.15
Matches are distributed among these distances:
19 4 0.03
20 4 0.03
21 85 0.73
22 2 0.02
23 1 0.01
24 3 0.03
25 3 0.03
26 12 0.10
27 2 0.02
28 1 0.01
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
TAAAAATTTAAATTAATAGAT
Found at i:3289004 original size:34 final size:35
Alignment explanation
Indices: 3288964--3289132 Score: 193
Period size: 34 Copynumber: 4.7 Consensus size: 35
3288954 TAAAATAAAA
3288964 ATTTAAATTAATAGATTAAAAAATTAAATTAATAG
1 ATTTAAATTAATAGATTAAAAAATTAAATTAATAG
*
3288999 A-TTAAATTAATAGATTAAAAATTTAAATTAATAG
1 ATTTAAATTAATAGATTAAAAAATTAAATTAATAG
* * *
3289033 ATTAAAAATTTAAATTAATAGATTAAATTAA-TAGATTAA-AA
1 -------ATTTAAATTAATAGATTAAA-AAATTAAATTAATAG
*
3289074 ATTTAAATTAATAGATTAAAAATTTAAATTAATAG
1 ATTTAAATTAATAGATTAAAAAATTAAATTAATAG
3289109 A-TTAAATTAATAGATTAAAAAATT
1 ATTTAAATTAATAGATTAAAAAATT
3289133 TAACTATAAT
Statistics
Matches: 113, Mismatches: 10, Indels: 23
0.77 0.07 0.16
Matches are distributed among these distances:
33 1 0.01
34 81 0.72
35 3 0.03
41 2 0.02
42 25 0.22
43 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (35 bp):
ATTTAAATTAATAGATTAAAAAATTAAATTAATAG
Found at i:3289025 original size:55 final size:55
Alignment explanation
Indices: 3288959--3289150 Score: 327
Period size: 55 Copynumber: 3.5 Consensus size: 55
3288949 ACTATTAAAA
3288959 TAAAAATTTAAATTAATAGATTAAAAAATTAAATTAATAGATTAAATTAATAGAT
1 TAAAAATTTAAATTAATAGATTAAAAAATTAAATTAATAGATTAAATTAATAGAT
*
3289014 TAAAAATTTAAATTAATAGATTAAAAATTTAAATTAATAGATTAAATTAATAGAT
1 TAAAAATTTAAATTAATAGATTAAAAAATTAAATTAATAGATTAAATTAATAGAT
*
3289069 TAAAAATTTAAATTAATAGATTAAAAATTTAAATTAATAGATTAAATTAATAGAT
1 TAAAAATTTAAATTAATAGATTAAAAAATTAAATTAATAGATTAAATTAATAGAT
*
3289124 TAAAAAATTT-AACT-ATA-ATTAAAAAAT
1 T-AAAAATTTAAATTAATAGATTAAAAAAT
3289151 ATGAAACCTT
Statistics
Matches: 133, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
53 9 0.07
54 3 0.02
55 113 0.85
56 8 0.06
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.37
Consensus pattern (55 bp):
TAAAAATTTAAATTAATAGATTAAAAAATTAAATTAATAGATTAAATTAATAGAT
Found at i:3290726 original size:29 final size:29
Alignment explanation
Indices: 3290661--3290728 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
3290651 TTATCTTTTA
*
3290661 AAAAAATTTATGTAAGATATTAAAAATTC
1 AAAAATTTTATGTAAGATATTAAAAATTC
* * *
3290690 AAGTAATTTTATGTAAGATTTTGAAAATTC
1 AA-AAATTTTATGTAAGATATTAAAAATTC
3290720 AAAAATTTT
1 AAAAATTTT
3290729 TAATCTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.40
Consensus pattern (29 bp):
AAAAATTTTATGTAAGATATTAAAAATTC
Found at i:3294288 original size:7 final size:7
Alignment explanation
Indices: 3294273--3294303 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3294263 TTTGAAAGTA
*
3294273 AAATTTT
1 AAATCTT
3294280 AAATCTT
1 AAATCTT
3294287 AAATCTT
1 AAATCTT
3294294 AAATCTT
1 AAATCTT
3294301 AAA
1 AAA
3294304 CAAAATCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATCTT
Found at i:3294904 original size:2 final size:2
Alignment explanation
Indices: 3294897--3294923 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3294887 AATTTAAATT
3294897 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3294924 CATAATAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3296296 original size:3 final size:3
Alignment explanation
Indices: 3296288--3296329 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3296278 CAACCACTCC
3296288 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3296330 TTGGATTTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3298943 original size:28 final size:27
Alignment explanation
Indices: 3298902--3298962 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
3298892 TTTATGCTAG
**
3298902 TATTTTTTAAATTTTTTAATTGTTTTT
1 TATTTTTTAAATTTAATAATTGTTTTT
* *
3298929 TATTTTTATATATTTAATAATTTTTTTT
1 TATTTTT-TAAATTTAATAATTGTTTTT
3298957 TATTTT
1 TATTTT
3298963 AAATTCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (27 bp):
TATTTTTTAAATTTAATAATTGTTTTT
Found at i:3299820 original size:21 final size:21
Alignment explanation
Indices: 3299779--3299820 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3299769 GACGTGTTAC
* *
3299779 TTTTTTATTTTTCTTATTTTA
1 TTTTTTATTTTTCTAAATTTA
3299800 TTTTTTATTTTT-TAAAATTTA
1 TTTTTTATTTTTCT-AAATTTA
3299821 AATAAATGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTATTTTTCTAAATTTA
Found at i:3300521 original size:21 final size:21
Alignment explanation
Indices: 3300491--3300533 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3300481 TTTTTTTAAT
* * *
3300491 TTTTTCTTTTTTTAATATTTA
1 TTTTTATTTTTATAAAATTTA
3300512 TTTTTATTTTTATAAAATTTA
1 TTTTTATTTTTATAAAATTTA
3300533 T
1 T
3300534 GAGAAAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTATTTTTATAAAATTTA
Found at i:3304550 original size:15 final size:15
Alignment explanation
Indices: 3304520--3304561 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3304510 TTGTTCAATA
3304520 TAATTTTT-TTTAAAT
1 TAATTTTTATTT-AAT
3304535 TAATTTTTATTTAAT
1 TAATTTTTATTTAAT
*
3304550 T-ATTATTATTTA
1 TAATTTTTATTTA
3304562 TGAGCGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 10 0.40
15 12 0.48
16 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTATTTAAT
Found at i:3309107 original size:13 final size:13
Alignment explanation
Indices: 3309089--3309113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3309079 TTAAAAACCT
3309089 AATCTATAGGAAA
1 AATCTATAGGAAA
3309102 AATCTATAGGAA
1 AATCTATAGGAA
3309114 TCGGGGATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (13 bp):
AATCTATAGGAAA
Found at i:3309440 original size:19 final size:19
Alignment explanation
Indices: 3309410--3309466 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
3309400 TGAGTTACGC
* *
3309410 ATTAACTTTATTGATTTGAT
1 ATTAA-TTTATTGATATAAT
* *
3309430 GTTAATTTATTTATATAAT
1 ATTAATTTATTGATATAAT
3309449 ATTAATTTATTGATATAA
1 ATTAATTTATTGATATAA
3309467 AAATTTATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 27 0.87
20 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (19 bp):
ATTAATTTATTGATATAAT
Found at i:3309757 original size:24 final size:22
Alignment explanation
Indices: 3309730--3309792 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 22
3309720 TTTTTTTTCA
3309730 ATATTTTAATTTTTTTAAAAAATC
1 ATATTTTAATTTTTTT--AAAATC
**
3309754 ATATTTTTAAAAATTTTTAAAATC
1 ATA-TTTT-AATTTTTTTAAAATC
3309778 ATATTTTAATTTTTT
1 ATATTTTAATTTTTT
3309793 ATTTAAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 6 0.18
23 4 0.12
24 12 0.36
25 4 0.12
26 7 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTTTAATTTTTTTAAAATC
Found at i:3310395 original size:18 final size:20
Alignment explanation
Indices: 3310360--3310401 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
3310350 GAAATCTTTC
3310360 TAAAAAATACATTAAAAAAA
1 TAAAAAATACATTAAAAAAA
*
3310380 TAAAAAA-A-ATTGAAAAAA
1 TAAAAAATACATTAAAAAAA
3310398 TAAA
1 TAAA
3310402 TTTAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
19 1 0.05
20 7 0.33
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (20 bp):
TAAAAAATACATTAAAAAAA
Found at i:3310736 original size:14 final size:14
Alignment explanation
Indices: 3310696--3310736 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3310686 ATAATTTGAG
3310696 AATTAAATTTGTATA
1 AATTAAATTT-TATA
* *
3310711 AATTATAGTTTATA
1 AATTAAATTTTATA
3310725 AATTAAATTTTA
1 AATTAAATTTTA
3310737 AATTTTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (14 bp):
AATTAAATTTTATA
Found at i:3311276 original size:22 final size:23
Alignment explanation
Indices: 3311250--3311299 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3311240 ATCATATTTG
*
3311250 AAATTGCT-AATTTA-ATATTAAA
1 AAATT-CTAAATTTATAGATTAAA
*
3311272 AAATTTTAAATTTATAGATTAAA
1 AAATTCTAAATTTATAGATTAAA
3311295 AAATT
1 AAATT
3311300 TTATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 11 0.46
23 12 0.50
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
AAATTCTAAATTTATAGATTAAA
Found at i:3311296 original size:23 final size:22
Alignment explanation
Indices: 3311258--3311302 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
3311248 TGAAATTGCT
*
3311258 AATTTAATATTAAAAAATTTTA
1 AATTTAAGATTAAAAAATTTTA
3311280 AATTTATAGATTAAAAAATTTTA
1 AATTTA-AGATTAAAAAATTTTA
3311303 TAAAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTTAAGATTAAAAAATTTTA
Found at i:3311314 original size:22 final size:22
Alignment explanation
Indices: 3311266--3311316 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
3311256 CTAATTTAAT
* *
3311266 ATTAAAAAATTTTAAATTTATAG
1 ATTAAAAAATTTTAAA-TAATAA
3311289 ATTAAAAAATTTTATAA-AATAA
1 ATTAAAAAATTTTA-AATAATAA
3311311 ATTAAA
1 ATTAAA
3311317 TGCGTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.36
23 14 0.56
24 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTAAAAAATTTTAAATAATAA
Found at i:3311350 original size:21 final size:21
Alignment explanation
Indices: 3311326--3311366 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3311316 ATGCGTAAAA
3311326 TTTTAAA-AAAAATTTGTTATC
1 TTTTAAATAAAAATTT-TTATC
*
3311347 TTTTAAATAAATATTTTTAT
1 TTTTAAATAAAAATTTTTAT
3311367 TAAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTAAATAAAAATTTTTATC
Found at i:3313933 original size:21 final size:21
Alignment explanation
Indices: 3313907--3313946 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3313897 ACTTAAAATT
3313907 GAATGTAAATAATAATTTATA
1 GAATGTAAATAATAATTTATA
* *
3313928 GAATGTAACTAATATTTTA
1 GAATGTAAATAATAATTTA
3313947 AAGGTGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (21 bp):
GAATGTAAATAATAATTTATA
Found at i:3318495 original size:20 final size:20
Alignment explanation
Indices: 3318472--3318509 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3318462 TTCTTTTTTT
*
3318472 TTTTCATTT-TTTGATTTTGA
1 TTTTAATTTATTT-ATTTTGA
3318492 TTTTAATTTATTTATTTT
1 TTTTAATTTATTTATTTT
3318510 ACCCATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTAATTTATTTATTTTGA
Found at i:3318617 original size:17 final size:17
Alignment explanation
Indices: 3318595--3318643 Score: 75
Period size: 16 Copynumber: 3.0 Consensus size: 17
3318585 TCTGTCTTTT
3318595 TATAAAAAAAATGAAAA
1 TATAAAAAAAATGAAAA
*
3318612 TAT-AAAAATAT-AAAA
1 TATAAAAAAAATGAAAA
3318627 TATAAAAAAAATGAAAA
1 TATAAAAAAAATGAAAA
3318644 AAAAAGGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 7 0.25
16 14 0.50
17 7 0.25
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (17 bp):
TATAAAAAAAATGAAAA
Found at i:3325056 original size:19 final size:18
Alignment explanation
Indices: 3325016--3325081 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 18
3325006 GGTAAAATTT
*
3325016 TTTTTTTTA-ATTTTTTA
1 TTTTTTTTATATTTATTA
*
3325033 ATTTTTTTATATATTATTA
1 TTTTTTTTATAT-TTATTA
* *
3325052 TTTTTGTTAT-TTTGAGT-
1 TTTTTTTTATATTT-ATTA
3325069 TTTTTTTTATATT
1 TTTTTTTTATATT
3325082 CCTGCATGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
17 19 0.49
18 7 0.18
19 13 0.33
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTTTTTATATTTATTA
Found at i:3325618 original size:58 final size:57
Alignment explanation
Indices: 3325525--3325741 Score: 167
Period size: 58 Copynumber: 3.8 Consensus size: 57
3325515 ACCCTAAAAT
* ** *
3325525 CCAAACCTTAAATTTCAAAACCCAAAAGTTGAAACCCTAAAATCAAACTCCAAACAC-C
1 CCAAACCTTAAA-ATCAAAACCCAAACCTTCAAACCCTAAAATCAAACTCCAAAC-CTC
* * *
3325583 CCAAACCTTAAAATCAAAAGTCCAAACCTTTAAACCCTAAAA-CTAAACCCCAAACCTC
1 CCAAACCTTAAAATCAAAA-CCCAAACCTTCAAACCCTAAAATC-AAACTCCAAACCTC
* * * * *
3325641 CC-AACCCTAAAA-CTAAACCCCAAACCTCCAAACCCTAAAACTAAAACTTCAAACCT-
1 CCAAACCTTAAAATC-AAAACCCAAACCTTCAAACCCTAAAA-TCAAACTCCAAACCTC
* * * * *
3325697 -AAAACCCTAAAATCAAATCCCTAAAACATCAAAACCCTAAAATCA
1 CCAAACCTTAAAATCAAAACCC-AAACCTTC-AAACCCTAAAATCA
3325742 TAACCCTAAA
Statistics
Matches: 129, Mismatches: 20, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
56 36 0.28
57 39 0.30
58 54 0.42
ACGTcount: A:0.49, C:0.34, G:0.01, T:0.16
Consensus pattern (57 bp):
CCAAACCTTAAAATCAAAACCCAAACCTTCAAACCCTAAAATCAAACTCCAAACCTC
Found at i:3325646 original size:28 final size:28
Alignment explanation
Indices: 3325556--3325708 Score: 148
Period size: 28 Copynumber: 5.4 Consensus size: 28
3325546 CCAAAAGTTG
* *
3325556 AAACCCTAAAA-TCAAACTCCAAACACCCC
1 AAACCCTAAAACT-AAACCCCAAAC-CTCC
* * ** **
3325585 AAACCTTAAAATCAAAAGTCCAAACCTTT
1 AAACCCTAAAA-CTAAACCCCAAACCTCC
3325614 AAACCCTAAAACTAAACCCCAAACCTCC
1 AAACCCTAAAACTAAACCCCAAACCTCC
*
3325642 CAACCCTAAAACTAAACCCCAAACCTCC
1 AAACCCTAAAACTAAACCCCAAACCTCC
** *
3325670 AAACCCTAAAACTAAAACTTCAAACCT-A
1 AAACCCTAAAACT-AAACCCCAAACCTCC
3325698 AAACCCTAAAA
1 AAACCCTAAAA
3325709 TCAAATCCCT
Statistics
Matches: 104, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
28 62 0.60
29 32 0.31
30 10 0.10
ACGTcount: A:0.49, C:0.36, G:0.01, T:0.14
Consensus pattern (28 bp):
AAACCCTAAAACTAAACCCCAAACCTCC
Found at i:3325675 original size:15 final size:15
Alignment explanation
Indices: 3325627--3325675 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
3325617 CCCTAAAACT
3325627 AAACCCCAAACCTCC
1 AAACCCCAAACCTCC
* * *
3325642 CAACCCTAAAACT--
1 AAACCCCAAACCTCC
3325655 AAACCCCAAACCTCC
1 AAACCCCAAACCTCC
3325670 AAACCC
1 AAACCC
3325676 TAAAACTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
13 10 0.38
15 16 0.62
ACGTcount: A:0.43, C:0.49, G:0.00, T:0.08
Consensus pattern (15 bp):
AAACCCCAAACCTCC
Found at i:3325729 original size:16 final size:16
Alignment explanation
Indices: 3325697--3325751 Score: 64
Period size: 14 Copynumber: 3.7 Consensus size: 16
3325687 CTTCAAACCT
3325697 AAAACCCT-AAA-ATC
1 AAAACCCTAAAACATC
*
3325711 AAATCCCTAAAACATC
1 AAAACCCTAAAACATC
3325727 AAAACCCT-AAA-ATC
1 AAAACCCTAAAACATC
*
3325741 ATAACCCTAAA
1 AAAACCCTAAA
3325752 TCTTTTAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 17 0.49
15 8 0.23
16 10 0.29
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAACCCTAAAACATC
Found at i:3325891 original size:22 final size:22
Alignment explanation
Indices: 3325864--3325962 Score: 79
Period size: 22 Copynumber: 4.7 Consensus size: 22
3325854 GAAACCCTAC
3325864 CCCTAAAATCCAAAATCTCAAA
1 CCCTAAAATCCAAAATCTCAAA
*
3325886 CCCTAAAATCCAAAAACT---A
1 CCCTAAAATCCAAAATCTCAAA
* *
3325905 ----AAAATCCAAATTTCTAAAA
1 CCCTAAAATCCAAA-ATCTCAAA
3325924 CCTCATAAAATCCAAAATC-CTAAA
1 CC-C-TAAAATCCAAAATCTC-AAA
3325948 CCCTAAAATCCAAAA
1 CCCTAAAATCCAAAA
3325963 CCTAAAAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
15 10 0.16
16 2 0.03
19 2 0.03
22 29 0.48
23 1 0.02
24 7 0.11
25 10 0.16
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (22 bp):
CCCTAAAATCCAAAATCTCAAA
Found at i:3325934 original size:25 final size:22
Alignment explanation
Indices: 3325905--3325968 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 22
3325895 CCAAAAACTA
* *
3325905 AAAATCCAAATTTCTAAAACCTCAT
1 AAAATCCAAAATCCT-AAACC-C-T
3325930 AAAATCCAAAATCCTAAACCCT
1 AAAATCCAAAATCCTAAACCCT
3325952 AAAATCCAAAA-CCTAAA
1 AAAATCCAAAATCCTAAA
3325969 AATCCAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.16
22 12 0.32
23 1 0.03
24 5 0.14
25 13 0.35
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAATCCAAAATCCTAAACCCT
Found at i:3325955 original size:15 final size:14
Alignment explanation
Indices: 3325937--3325977 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
3325927 CATAAAATCC
*
3325937 AAAATCCTAAACCCT
1 AAAATCC-AAAACCT
3325952 AAAATCCAAAACCT
1 AAAATCCAAAACCT
3325966 AAAAATCCAAAA
1 -AAAATCCAAAA
3325978 GTCTAAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAATCCAAAACCT
Found at i:3325983 original size:62 final size:62
Alignment explanation
Indices: 3325867--3325984 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 62
3325857 ACCCTACCCC
**
3325867 TAAAATCCAAAATCTCAAACCCTAAAATCCAAAAACTAAAAATCCAAATTTCTAAAACCTCA
1 TAAAATCCAAAATCTCAAACCCTAAAATCCAAAAACTAAAAATCCAAAAGTCTAAAACCTCA
*
3325929 TAAAATCCAAAATC-CTAAACCCTAAAATCCAAAACCTAAAAATCCAAAAGTCTAAA
1 TAAAATCCAAAATCTC-AAACCCTAAAATCCAAAAACTAAAAATCCAAAAGTCTAAA
3325985 TACCCAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
61 1 0.02
62 51 0.98
ACGTcount: A:0.54, C:0.25, G:0.01, T:0.19
Consensus pattern (62 bp):
TAAAATCCAAAATCTCAAACCCTAAAATCCAAAAACTAAAAATCCAAAAGTCTAAAACCTCA
Found at i:3327179 original size:26 final size:26
Alignment explanation
Indices: 3327146--3327198 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3327136 CAATGGTTGG
3327146 ATTTAATTGATTTTATTTGATATTTA
1 ATTTAATTGATTTTATTTGATATTTA
** * *
3327172 ATTTAATTTCTTTTATTTTATTTTTA
1 ATTTAATTGATTTTATTTGATATTTA
3327198 A
1 A
3327199 AAAATATAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (26 bp):
ATTTAATTGATTTTATTTGATATTTA
Found at i:3334630 original size:128 final size:127
Alignment explanation
Indices: 3334402--3334631 Score: 354
Period size: 128 Copynumber: 1.8 Consensus size: 127
3334392 AATATTTTAA
* * * *
3334402 AATTTTTAAAGTTTCATTACCTCTGATTAATATGAGTATTCAAAGATTTTGAGATTTGTAAGACC
1 AATTTTTAAAGTTTCATTACCTCTAATTAAGAGGAGTATTCAAAGATTTTGAGATTTGTAAAACC
* * *
3334467 TCCGGGCATTATCTCCAATACTTTCGAGCATAATTTTCAAGATTTCTGGGCAAAAGATTTTC
66 TCCGGGCATAATCTCCAATACTTTAGAGCAAAATTTTCAAGATTTCTGGGCAAAAGATTTTC
*
3334529 AATTTCTTAAAGTTTCATTGCCTCTAATTAAGAGGAGTATTCAAAGATTTTGAGATTTGTAAAAC
1 AATTT-TTAAAGTTTCATTACCTCTAATTAAGAGGAGTATTCAAAGATTTTGAGATTTGTAAAAC
*
3334594 CTCCGGGCATAATCTCTAATACTTCTAG-GCAAAATTTT
65 CTCCGGGCATAATCTCCAATACTT-TAGAGCAAAATTTT
3334632 TTTAAATTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
127 5 0.05
128 85 0.92
129 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (127 bp):
AATTTTTAAAGTTTCATTACCTCTAATTAAGAGGAGTATTCAAAGATTTTGAGATTTGTAAAACC
TCCGGGCATAATCTCCAATACTTTAGAGCAAAATTTTCAAGATTTCTGGGCAAAAGATTTTC
Found at i:3334679 original size:107 final size:107
Alignment explanation
Indices: 3334524--3334719 Score: 288
Period size: 107 Copynumber: 1.8 Consensus size: 107
3334514 GGGCAAAAGA
* * *
3334524 TTTTCAATTTCTTAAAGTTTCATTGCCTCTAATTAAGAGGAGTATTCAAAGATTTTGAGATTTGT
1 TTTTAAATTTCTTAAAGTTTCATTGCCTCTAATTAAGAGGAGCATTCAAAGATTTTGAGATTTAT
3334589 AAAACCTCCGGGCATAATCTCTAATACTTCTAGGCAAAATTT
66 AAAACCTCCGGGCATAATCTCTAATACTTCTAGGCAAAATTT
*
3334631 TTTTAAATTT-TTAAAAGTTTCATTGCCTCTAATTATGAGG-GACATTCAAAGATTTTGAGATTT
1 TTTTAAATTTCTT-AAAGTTTCATTGCCTCTAATTAAGAGGAG-CATTCAAAGATTTTGAGATTT
* * * *
3334694 ATAAGACCTCTGGGCGTAATTTCTAA
64 ATAAAACCTCCGGGCATAATCTCTAA
3334720 AGCCTTTGGG
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
106 3 0.04
107 76 0.96
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (107 bp):
TTTTAAATTTCTTAAAGTTTCATTGCCTCTAATTAAGAGGAGCATTCAAAGATTTTGAGATTTAT
AAAACCTCCGGGCATAATCTCTAATACTTCTAGGCAAAATTT
Found at i:3335111 original size:110 final size:110
Alignment explanation
Indices: 3334916--3335155 Score: 299
Period size: 110 Copynumber: 2.2 Consensus size: 110
3334906 ATCGATTCTA
** * *
3334916 TAAGACCTCCGAACATAATTTTGATTAACGATGTTGTCTTGATTCAATTCTTAATTTTTTGACTT
1 TAAGACCTCCGGGCATAATTTCGATT-ACGATGTTGTCTCGATTCAATTCTTAATTTTTTGACTT
* * *
3334981 GTGATGTTATCTTGATCGATTCTGTAAGACCTCTAGA-TATGATTTT
65 GCGATGTTATCTCGATCGATTCTGTAAGACCTC-AGAGCATGATTTT
* *
3335027 TAAGACCTCCGGGCATAATTTCGATT-CGCAGTGTTGTCTCGATT-GATTTTTAATTTTTTGACT
1 TAAGACCTCCGGGCATAATTTCGATTACG-A-TGTTGTCTCGATTCAATTCTTAATTTTTTGACT
*
3335090 TGCGATGTTAT-TCCGATCGATTCTGTAAGACCTCCGAGCATGATTTT
64 TGCGATGTTATCT-CGATCGATTCTGTAAGACCTCAGAGCATGATTTT
**
3335137 TAAGACCTCTAGGCATAAT
1 TAAGACCTCCGGGCATAAT
3335156 CTTCAAGACT
Statistics
Matches: 113, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
109 5 0.04
110 73 0.65
111 35 0.31
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (110 bp):
TAAGACCTCCGGGCATAATTTCGATTACGATGTTGTCTCGATTCAATTCTTAATTTTTTGACTTG
CGATGTTATCTCGATCGATTCTGTAAGACCTCAGAGCATGATTTT
Found at i:3335325 original size:132 final size:132
Alignment explanation
Indices: 3335036--3335352 Score: 351
Period size: 132 Copynumber: 2.4 Consensus size: 132
3335026 TTAAGACCTC
3335036 CGGGCATAATTTCGATTCGCAGTGTTGT-CTCGATTGATT-TTTAATTTTTTGACTTGCGATGTT
1 CGGGCATAATTTCGATTCGCAGTGTTGTCCT-GATTGATTCTTT-ATTTTTTGACTTGCGATGTT
* *
3335099 ATTCCGATCGATTCTGTAAGACCTCCGAGCATGATTTTTAAGACCTCTAGGCATAATCTTCAAGA
64 ATTCAGATCGATACTGTAAGACCTCCGAGCATGATTTTTAAGACCTCTAGGCATAATCTTCAAGA
3335164 CTTT
129 CTTT
* * * *
3335168 CGAGCATAATTTCGATTCGTAGTGTTGTCCTAATTGATTCTTTATTTTTTGACTTAG-GGTGTTA
1 CGGGCATAATTTCGATTCGCAGTGTTGTCCTGATTGATTCTTTATTTTTTGACTT-GCGATGTTA
* * * * * *
3335232 TCTTAG-TCGATACTGTAAGACCTTCGCA-TATGATTTTTAGGACCT-TTGCGCATAATCTTTAA
65 T-TCAGATCGATACTGTAAGACCTCCG-AGCATGATTTTTAAGACCTCTAG-GCATAATCTTCAA
*
3335294 GATTTT
127 GACTTT
* * * * * * *
3335300 CGGGCATAATTTTGATTCACGGTGTTATCCCGATCGATTCTTTA-ATTTTGACT
1 CGGGCATAATTTCGATTCGCAGTGTTGTCCTGATTGATTCTTTATTTTTTGACT
3335353 CGTGGTTTGT
Statistics
Matches: 156, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
131 10 0.06
132 137 0.88
133 9 0.06
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (132 bp):
CGGGCATAATTTCGATTCGCAGTGTTGTCCTGATTGATTCTTTATTTTTTGACTTGCGATGTTAT
TCAGATCGATACTGTAAGACCTCCGAGCATGATTTTTAAGACCTCTAGGCATAATCTTCAAGACT
TT
Found at i:3335700 original size:29 final size:27
Alignment explanation
Indices: 3335633--3335759 Score: 110
Period size: 28 Copynumber: 4.4 Consensus size: 27
3335623 TATACTATTT
* **
3335633 TCAAACCCTAAAACTAAACCCCAAACC
1 TCAAACCCTAAAATTAAACCATAAACC
*
3335660 TCCAAACTCTAAAATTAAACCATAAATCC
1 T-CAAACCCTAAAATTAAACCATAAA-CC
* *
3335689 TCTAAACCCTAAAATTAAAACTTCAAACC
1 TC-AAACCCTAAAATTAAACCAT-AAACC
* * *
3335718 TCAAACCCTAAAATCAAATCCCTAAAACA
1 TCAAACCCTAAAATTAAA-CCAT-AAACC
3335747 TCAGAACCCTAAA
1 TCA-AACCCTAAA
3335760 TCCTCTAAAC
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
27 1 0.01
28 36 0.44
29 33 0.40
30 12 0.15
ACGTcount: A:0.49, C:0.31, G:0.01, T:0.19
Consensus pattern (27 bp):
TCAAACCCTAAAATTAAACCATAAACC
Found at i:3335740 original size:14 final size:13
Alignment explanation
Indices: 3335633--3335809 Score: 50
Period size: 13 Copynumber: 12.4 Consensus size: 13
3335623 TATACTATTT
3335633 TCAAACCCTAAAA
1 TCAAACCCTAAAA
* *
3335646 -CTAAACCCCAAACC
1 TC-AAACCCTAAA-A
*
3335660 TCCAAACTCTAAAA
1 T-CAAACCCTAAAA
* * *
3335674 TTAAACCATAAATCC
1 TCAAACCCTAAA--A
3335689 TCTAAACCCTAAAA
1 TC-AAACCCTAAAA
* * * *
3335703 TTAAAACTTCAAACC
1 TCAAACCCT-AAA-A
3335718 TCAAACCCTAAAA
1 TCAAACCCTAAAA
3335731 TCAAATCCCTAAAACA
1 TCAAA-CCCT-AAA-A
*
3335747 TCAGAACCCTAAATCC
1 TCA-AACCCTAAA--A
3335763 TCTAAACCCTAAAA
1 TC-AAACCCTAAAA
* * * *
3335777 CCAAAACTTCAAACC
1 TCAAACCCT-AAA-A
*
3335792 TTAAACCCTAAAA
1 TCAAACCCTAAAA
3335805 TCAAA
1 TCAAA
3335810 ACGACAAATC
Statistics
Matches: 115, Mismatches: 32, Indels: 34
0.64 0.18 0.19
Matches are distributed among these distances:
12 1 0.01
13 36 0.31
14 19 0.17
15 26 0.23
16 30 0.26
17 3 0.03
ACGTcount: A:0.49, C:0.32, G:0.01, T:0.19
Consensus pattern (13 bp):
TCAAACCCTAAAA
Found at i:3335756 original size:16 final size:15
Alignment explanation
Indices: 3335713--3335777 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 15
3335703 TTAAAACTTC
*
3335713 AAACCTCAAACCCT-
1 AAACATCAAACCCTA
3335727 AAA-ATCAAATCCCTA
1 AAACATCAAA-CCCTA
3335742 AAACATCAGAACCCTA
1 AAACATCA-AACCCTA
* *
3335758 AATCCTCTAAACCCTA
1 AAACATC-AAACCCTA
3335774 AAAC
1 AAAC
3335778 CAAAACTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
13 5 0.12
14 7 0.17
15 3 0.07
16 24 0.57
17 3 0.07
ACGTcount: A:0.48, C:0.34, G:0.02, T:0.17
Consensus pattern (15 bp):
AAACATCAAACCCTA
Found at i:3335759 original size:58 final size:57
Alignment explanation
Indices: 3335635--3335759 Score: 137
Period size: 58 Copynumber: 2.2 Consensus size: 57
3335625 TACTATTTTC
* * * *
3335635 AAACCCTAAAACTAAACCCCAAACCTCCAAACTCTAAAATTAAACCATAAATCCTCT
1 AAACCCTAAAACTAAACCCCAAACCTCCAAACCCTAAAATCAAACCATAAAACATCT
* ** *
3335692 AAACCCTAAAATTAAAACTTCAAACCT-CAAACCCTAAAATCAAATCCCTAAAACATC-
1 AAACCCTAAAACT-AAACCCCAAACCTCCAAACCCTAAAATCAAA-CCATAAAACATCT
3335749 AGAACCCTAAA
1 A-AACCCTAAA
3335760 TCCTCTAAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
57 28 0.49
58 29 0.51
ACGTcount: A:0.50, C:0.31, G:0.01, T:0.18
Consensus pattern (57 bp):
AAACCCTAAAACTAAACCCCAAACCTCCAAACCCTAAAATCAAACCATAAAACATCT
Found at i:3335809 original size:28 final size:28
Alignment explanation
Indices: 3335765--3335838 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
3335755 CTAAATCCTC
* **
3335765 TAAACCCTAAAACCAAAACTTCAAACCT
1 TAAACCCTAAAATCAAAACGACAAACCT
*
3335793 TAAACCCTAAAATCAAAACGACAAATCT
1 TAAACCCTAAAATCAAAACGACAAACCT
* *
3335821 CAAACTCTAAAATCAAAA
1 TAAACCCTAAAATCAAAA
3335839 ACCTAAACCC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.54, C:0.27, G:0.01, T:0.18
Consensus pattern (28 bp):
TAAACCCTAAAATCAAAACGACAAACCT
Found at i:3335898 original size:15 final size:15
Alignment explanation
Indices: 3335878--3335964 Score: 77
Period size: 15 Copynumber: 5.7 Consensus size: 15
3335868 TCCTACCCCT
3335878 AAAATCCAAAACCTA
1 AAAATCCAAAACCTA
**
3335893 AAAATCCAAATTTCTA
1 AAAATCCAAA-ACCTA
* *
3335909 AAAACCCTTAAAATCT-
1 AAAATCC--AAAACCTA
* *
3335925 AAAATCCCAAACCTT
1 AAAATCCAAAACCTA
3335940 AAAATCCAAAACCTA
1 AAAATCCAAAACCTA
*
3335955 AAAATTCAAA
1 AAAATCCAAA
3335965 TGTCTAAAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
14 5 0.09
15 32 0.55
16 15 0.26
17 3 0.05
18 3 0.05
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATCCAAAACCTA
Found at i:3343384 original size:3 final size:3
Alignment explanation
Indices: 3343376--3343446 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
3343366 TTAGGTGCTC
3343376 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3343424 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
3343447 TCTTTTTCTG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3343885 original size:20 final size:21
Alignment explanation
Indices: 3343857--3343895 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3343847 GACAACCTAG
*
3343857 AAAT-TTTTTTGAATTTTTCA
1 AAATGTTTTTGGAATTTTTCA
3343877 AAATGTTTTTGGAATTTTT
1 AAATGTTTTTGGAATTTTT
3343896 TTGGGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (21 bp):
AAATGTTTTTGGAATTTTTCA
Found at i:3343963 original size:13 final size:13
Alignment explanation
Indices: 3343945--3343969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3343935 CGACGAATGA
3343945 TGAATTTTTTGGT
1 TGAATTTTTTGGT
3343958 TGAATTTTTTGG
1 TGAATTTTTTGG
3343970 CAGTGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (13 bp):
TGAATTTTTTGGT
Found at i:3344307 original size:8 final size:8
Alignment explanation
Indices: 3344289--3344326 Score: 58
Period size: 8 Copynumber: 4.5 Consensus size: 8
3344279 CCGTAGGTTT
3344289 TTTTTTCTA
1 TTTTTT-TA
3344298 TTTTTTTA
1 TTTTTTTA
3344306 TTTTTTTTA
1 -TTTTTTTA
3344315 TTTTTTTA
1 TTTTTTTA
3344323 TTTT
1 TTTT
3344327 ACCCATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 14 0.50
9 14 0.50
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3344311 original size:17 final size:17
Alignment explanation
Indices: 3344289--3344326 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
3344279 CCGTAGGTTT
3344289 TTTTTTCTATTTTTTTA
1 TTTTTTCTATTTTTTTA
*
3344306 TTTTTTTTATTTTTTTA
1 TTTTTTCTATTTTTTTA
3344323 TTTT
1 TTTT
3344327 ACCCATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTTTCTATTTTTTTA
Found at i:3344396 original size:31 final size:30
Alignment explanation
Indices: 3344347--3344422 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
3344337 ATTTTTTGAT
* * *
3344347 TTTTTTTAAAAAGGAAAAATTGTTATTCTATC
1 TTTTTATAAAAA--AAAAATTATTATTATATC
* *
3344379 TTTTTGTCAAAAAAAAAATTATTATTATGTC
1 TTTTTAT-AAAAAAAAAATTATTATTATATC
3344410 TTTTTATAAAAAA
1 TTTTTATAAAAAA
3344423 TGAAAATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 6 0.16
31 21 0.55
32 6 0.16
33 5 0.13
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (30 bp):
TTTTTATAAAAAAAAAATTATTATTATATC
Found at i:3345961 original size:10 final size:11
Alignment explanation
Indices: 3345930--3345962 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3345920 ATCTTGGCCT
*
3345930 TTGATTAAGTC
1 TTGATTAAATC
3345941 TTGATTAAATC
1 TTGATTAAATC
3345952 TTGA-TAAATC
1 TTGATTAAATC
3345962 T
1 T
3345963 CCTCTTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (11 bp):
TTGATTAAATC
Found at i:3349599 original size:27 final size:27
Alignment explanation
Indices: 3349567--3349622 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3349557 AGAAACTAAG
3349567 TCTATTGTCAGTTAAATCAAGGAAACT
1 TCTATTGTCAGTTAAATCAAGGAAACT
3349594 TCTATTGTCAGTTAAATCAAGGAAACT
1 TCTATTGTCAGTTAAATCAAGGAAACT
3349621 TC
1 TC
3349623 CTTGACCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (27 bp):
TCTATTGTCAGTTAAATCAAGGAAACT
Found at i:3356964 original size:30 final size:31
Alignment explanation
Indices: 3356903--3356965 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
3356893 TGTAATATTG
* * * *
3356903 TTTTTTAAAAATTTTAATTATTATAATATTA
1 TTTTTTAAAAAATTTAATCATTAGAACATTA
*
3356934 TTTTTTAAAAAATTTAATCGTT-GAACATTA
1 TTTTTTAAAAAATTTAATCATTAGAACATTA
3356964 TT
1 TT
3356966 ATCGATTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTTTTAAAAAATTTAATCATTAGAACATTA
Found at i:3366563 original size:128 final size:127
Alignment explanation
Indices: 3366330--3366588 Score: 401
Period size: 128 Copynumber: 2.0 Consensus size: 127
3366320 CATCCACGAC
* * *
3366330 TCAACATTGCTTTAATTTTTTTCTTCTTTTGTGTATTGGTGTTAAATCTTAATGTCACGGGTCGA
1 TCAACATTGCTTTAATTTTTTTCTTCTTTTGTGTATTGGTGTTAAATCCTAATGTCACGGGCCAA
* * * *
3366395 GACTTAAATTTTGAATTCACACGATTTTGAAATCCAAACATCCATTCATTCGACATCTTAGA
66 GACTTAAATTTCGAATTCACACGATTTTGAAACCCAAACATCCAGTCATCCGACATCTTAGA
* * *
3366457 TCAACATTGCTTTAATTTTTTTTCTTCTTTTGTGTGTTGGTGTTGAGTCCTAATGTCACGGGCCA
1 TCAACATTGCTTTAA-TTTTTTTCTTCTTTTGTGTATTGGTGTTAAATCCTAATGTCACGGGCCA
* *
3366522 AGATTTAAATTTCGAATTCACACGATTTTGAAACCCGAACATCCAGTCATCCGACATCTTAGA
65 AGACTTAAATTTCGAATTCACACGATTTTGAAACCCAAACATCCAGTCATCCGACATCTTAGA
3366585 TCAA
1 TCAA
3366589 TCTACCTATC
Statistics
Matches: 119, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
127 15 0.13
128 104 0.87
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (127 bp):
TCAACATTGCTTTAATTTTTTTCTTCTTTTGTGTATTGGTGTTAAATCCTAATGTCACGGGCCAA
GACTTAAATTTCGAATTCACACGATTTTGAAACCCAAACATCCAGTCATCCGACATCTTAGA
Found at i:3367002 original size:74 final size:74
Alignment explanation
Indices: 3366881--3367030 Score: 275
Period size: 74 Copynumber: 2.0 Consensus size: 74
3366871 TTGTCACGGG
*
3366881 TCGAAACTTAAGCTCCGAATTCGCATGGCTCCGAGATCAGGGCATCCACTCATTCGGCATCCTAG
1 TCGAAACTTAAGCTCCGAATTCGCATGGCTCCGAGATCAGGGCATCCACTCATCCGGCATCCTAG
3366946 ATCAACCTA
66 ATCAACCTA
3366955 TCGAAACTTAAGCTCCGAATTCGCATGGCTCC-AGGATCAGGGCATCCACTCATCCGGCATCCTA
1 TCGAAACTTAAGCTCCGAATTCGCATGGCTCCGA-GATCAGGGCATCCACTCATCCGGCATCCTA
3367019 GATCAACCTA
65 GATCAACCTA
3367029 TC
1 TC
3367031 TGTCATGGTT
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
73 1 0.01
74 73 0.99
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.23
Consensus pattern (74 bp):
TCGAAACTTAAGCTCCGAATTCGCATGGCTCCGAGATCAGGGCATCCACTCATCCGGCATCCTAG
ATCAACCTA
Found at i:3367199 original size:17 final size:17
Alignment explanation
Indices: 3367177--3367210 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3367167 ATCTGGTATC
3367177 CCAGATCAACCTATCTG
1 CCAGATCAACCTATCTG
3367194 CCAGATCAACCTATCTG
1 CCAGATCAACCTATCTG
3367211 TCATGGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.24
Consensus pattern (17 bp):
CCAGATCAACCTATCTG
Found at i:3367318 original size:177 final size:178
Alignment explanation
Indices: 3367018--3367337 Score: 536
Period size: 177 Copynumber: 1.8 Consensus size: 178
3367008 CCGGCATCCT
*
3367018 AGATCAACCTATCTGTCATGGTTCACATCCTTGTGAGGTATTATTCGCTTTAGTCCCCTGACCTC
1 AGATCAACCTATCTGTCATGGTTCACATCCTTGTGAGATATTATTCGCTTTAGTCCCCTGACCTC
* * * * *
3367083 ACGATTTTATCTTACAAAAGGTATCTAACAAAAAAGAGATTGTGTGAACCCTTTTATATCCTAGT
66 ACGATTTTATCCTACAAAAGGCATCTAACAAAAAAAAAATTGTGTGAACCCTTTTATATCCTAAT
3367148 GACCTCTTTTTATTCGCTCATCTGGTATCCCAGATCAACCTATCTGCC
131 GACCTCTTTTTATTCGCTCATCTGGTATCCCAGATCAACCTATCTGCC
3367196 AGATCAACCTATCTGTCATGGTTCACATCCTTGTGAGATATTATTCG-TTCTAGT-CCCTGACCT
1 AGATCAACCTATCTGTCATGGTTCACATCCTTGTGAGATATTATTCGCTT-TAGTCCCCTGACCT
* * *
3367259 CATGATTTTATCCTACCAAAGGCGTCTAACAAAAAAAAAATTGTGTGAACCCTTTTATATCCTAA
65 CACGATTTTATCCTACAAAAGGCATCTAACAAAAAAAAAATTGTGTGAACCCTTTTATATCCTAA
3367324 TGACCTCTTTTTAT
130 TGACCTCTTTTTAT
3367338 GTTCGATATG
Statistics
Matches: 132, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
177 82 0.62
178 50 0.38
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (178 bp):
AGATCAACCTATCTGTCATGGTTCACATCCTTGTGAGATATTATTCGCTTTAGTCCCCTGACCTC
ACGATTTTATCCTACAAAAGGCATCTAACAAAAAAAAAATTGTGTGAACCCTTTTATATCCTAAT
GACCTCTTTTTATTCGCTCATCTGGTATCCCAGATCAACCTATCTGCC
Found at i:3372009 original size:2 final size:2
Alignment explanation
Indices: 3372004--3372073 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
3371994 ATATGACCAC
*
3372004 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3372046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3372074 GGGAGAGAGA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3373512 original size:20 final size:20
Alignment explanation
Indices: 3373483--3373521 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3373473 TAAACTCAGG
*
3373483 TAGAATATGTTTTTCTGATT
1 TAGAACATGTTTTTCTGATT
3373503 TAGAACATGTTTTTCTGAT
1 TAGAACATGTTTTTCTGAT
3373522 GTTAACTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (20 bp):
TAGAACATGTTTTTCTGATT
Found at i:3376220 original size:4 final size:4
Alignment explanation
Indices: 3376213--3376240 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3376203 TATATATATA
3376213 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
3376241 AACTTCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:3377161 original size:33 final size:33
Alignment explanation
Indices: 3377117--3377191 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
3377107 ATCACGTGGG
*
3377117 AAAAGCTATCATAGTATCTAAGGACCACCCATA
1 AAAAGCCATCATAGTATCTAAGGACCACCCATA
*
3377150 AAAAGCCATCATAGTATCTGAGGACCACCCATA
1 AAAAGCCATCATAGTATCTAAGGACCACCCATA
3377183 AAAAGCCAT
1 AAAAGCCAT
3377192 GAAAGCTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.43, C:0.25, G:0.13, T:0.19
Consensus pattern (33 bp):
AAAAGCCATCATAGTATCTAAGGACCACCCATA
Found at i:3380609 original size:14 final size:13
Alignment explanation
Indices: 3380556--3380616 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 13
3380546 TTTTAAATAT
3380556 AAATATAAAATTA
1 AAATATAAAATTA
3380569 AATATATATAAA--A
1 AA-ATATA-AAATTA
* *
3380582 ATATATATAATTA
1 AAATATAAAATTA
3380595 AAATATAAAATTTA
1 AAATATAAAA-TTA
*
3380609 AAAAATAA
1 AAATATAA
3380617 TTTTTTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
11 2 0.05
12 5 0.13
13 13 0.34
14 15 0.39
15 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATATAAAATTA
Found at i:3381908 original size:3 final size:3
Alignment explanation
Indices: 3381895--3381936 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
3381885 AAAATATATA
3381895 TAT TCAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3381937 AATAAGAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3383270 original size:40 final size:40
Alignment explanation
Indices: 3383215--3383338 Score: 239
Period size: 40 Copynumber: 3.1 Consensus size: 40
3383205 ATTTGAGTGA
3383215 AAAAGAAAATAGAAGGGATTAATGAATGGATAGTTGTTAT
1 AAAAGAAAATAGAAGGGATTAATGAATGGATAGTTGTTAT
3383255 AAAAGAAAATAGAAGGGATTAATGAATGGATAGTTGTTAT
1 AAAAGAAAATAGAAGGGATTAATGAATGGATAGTTGTTAT
*
3383295 AAAAGAAAATAGAAGGGATTAATGAATGGATATTTGTTAT
1 AAAAGAAAATAGAAGGGATTAATGAATGGATAGTTGTTAT
3383335 AAAA
1 AAAA
3383339 AGTGTTTGTT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.27
Consensus pattern (40 bp):
AAAAGAAAATAGAAGGGATTAATGAATGGATAGTTGTTAT
Found at i:3390233 original size:30 final size:30
Alignment explanation
Indices: 3390197--3390257 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3390187 AAAAAAAACT
** *
3390197 TTTAATTTGTATTTAAATAAATTTTTAATA
1 TTTAATTTGTACATAAATAAAATTTTAATA
*
3390227 TTTAATTTGTACATAAGTAAAATTTTAATA
1 TTTAATTTGTACATAAATAAAATTTTAATA
3390257 T
1 T
3390258 AAATTAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (30 bp):
TTTAATTTGTACATAAATAAAATTTTAATA
Found at i:3395929 original size:26 final size:24
Alignment explanation
Indices: 3395887--3395940 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
3395877 CTGGGAGTGA
3395887 GAAAAATTTTTTAGAAATTTTTGG
1 GAAAAATTTTTTAGAAATTTTTGG
* *
3395911 CGAAAATTTTTTCTGGAAATTTTTGG
1 -GAAAAATTTTT-TAGAAATTTTTGG
3395937 GAAA
1 GAAA
3395941 TTTCCAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.43
Consensus pattern (24 bp):
GAAAAATTTTTTAGAAATTTTTGG
Found at i:3396084 original size:20 final size:19
Alignment explanation
Indices: 3396042--3396084 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
3396032 CCGGCCAACT
* *
3396042 TCCGGCAAAATTTCCAGAT
1 TCCGACAAAATTTCCAGAA
*
3396061 TCCGACAAAATTTTCTAGAA
1 TCCGACAAAA-TTTCCAGAA
3396081 TCCG
1 TCCG
3396085 GCACCGGTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (19 bp):
TCCGACAAAATTTCCAGAA
Found at i:3396440 original size:23 final size:23
Alignment explanation
Indices: 3396397--3396440 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3396387 TCCAGGTTTT
* * *
3396397 TTTTTTTTTTTTTTTTCTTTGAA
1 TTTTTTTTCTTTGTTTATTTGAA
3396420 TTTTTTTTCTTTGTTTATTTG
1 TTTTTTTTCTTTGTTTATTTG
3396441 TTTATTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.82
Consensus pattern (23 bp):
TTTTTTTTCTTTGTTTATTTGAA
Found at i:3399235 original size:14 final size:14
Alignment explanation
Indices: 3399184--3399237 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
3399174 TAAACCCTCC
3399184 AAACCCTAAAATCA
1 AAACCCTAAAATCA
* *
3399198 AATCCTTAAAACATCA
1 AAACCCT-AAA-ATCA
**
3399214 AATTCCTAAAATCA
1 AAACCCTAAAATCA
3399228 AAACCCTAAA
1 AAACCCTAAA
3399238 CCCTTCAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 17 0.53
15 6 0.19
16 9 0.28
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:3399249 original size:16 final size:16
Alignment explanation
Indices: 3399228--3399283 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
3399218 CCTAAAATCA
*
3399228 AAACCCTAAACCCTTC
1 AAACCCTAAACCATTC
* *
3399244 AAACCCTAAA--AATG
1 AAACCCTAAACCATTC
*
3399258 AAACCCTAAACCTTTC
1 AAACCCTAAACCATTC
3399274 AAACCCTAAA
1 AAACCCTAAA
3399284 ATCCAAAACC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 11 0.34
16 21 0.66
ACGTcount: A:0.46, C:0.34, G:0.02, T:0.18
Consensus pattern (16 bp):
AAACCCTAAACCATTC
Found at i:3399282 original size:60 final size:58
Alignment explanation
Indices: 3399108--3399298 Score: 186
Period size: 60 Copynumber: 3.2 Consensus size: 58
3399098 TTCAAACCCT
* * * * *
3399108 AAAACCCTAAACCC-TCTGAACCTTAAAATTAAACCCTAAACCCTTCGAACCCTAAAAAC
1 AAAACCCTAAACCCTTC-AAACCCTAAAATCAAACCCTAAA-CCTTCAAACCCTAAAATC
* * * * * * *
3399167 GAAACCTTAAACCCTCCAAACCCTAAAATCAAATCCTTAAAACATCAAATTCCTAAAATC
1 AAAACCCTAAACCCTTCAAACCCTAAAATCAAA-CCCTAAACCTTCAAA-CCCTAAAATC
*
3399227 AAAACCCTAAACCCTTCAAACCCTAAAAATGAAACCCTAAACCTTTCAAACCCTAAAATCC
1 AAAACCCTAAACCCTTCAAACCCT-AAAATCAAACCCTAAACC-TTCAAACCCTAAAAT-C
*
3399288 AAAACCTTAAA
1 AAAACCCTAAA
3399299 ATTTAAAATT
Statistics
Matches: 105, Mismatches: 21, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
59 30 0.29
60 51 0.49
61 24 0.23
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.19
Consensus pattern (58 bp):
AAAACCCTAAACCCTTCAAACCCTAAAATCAAACCCTAAACCTTCAAACCCTAAAATC
Found at i:3399285 original size:29 final size:29
Alignment explanation
Indices: 3399109--3399285 Score: 160
Period size: 30 Copynumber: 6.0 Consensus size: 29
3399099 TCAAACCCTA
* * *
3399109 AAACCCTAAACCC-TCTGAACCTTAAAATT
1 AAACCCTAAACCCTTC-AAACCCTAAAATG
* *
3399138 AAACCCTAAACCCTTCGAACCCTAAAAACG
1 AAACCCTAAACCCTTCAAACCCT-AAAATG
* * *
3399168 AAACCTTAAACCCTCCAAACCCTAAAATC
1 AAACCCTAAACCCTTCAAACCCTAAAATG
* * * * *
3399197 AAATCCTTAAA-ACATCAAATTCCTAAAATCA
1 AAA-CCCTAAACCCTTCAAA-CCCTAAAAT-G
3399228 AAACCCTAAACCCTTCAAACCCTAAAAATG
1 AAACCCTAAACCCTTCAAACCCT-AAAATG
*
3399258 AAACCCTAAACCTTTCAAACCCTAAAAT
1 AAACCCTAAACCCTTCAAACCCTAAAAT
3399286 CCAAAACCTT
Statistics
Matches: 122, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
29 36 0.30
30 72 0.59
31 14 0.11
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.20
Consensus pattern (29 bp):
AAACCCTAAACCCTTCAAACCCTAAAATG
Found at i:3399313 original size:90 final size:90
Alignment explanation
Indices: 3399138--3399314 Score: 257
Period size: 90 Copynumber: 2.0 Consensus size: 90
3399128 CCTTAAAATT
* * *
3399138 AAACCCTAAACCCTTCGAACCCTAAAAACGAAACCTTAAACCCTCCAAACCCTAAAATCAAATCC
1 AAACCCTAAACCCTTCAAACCCTAAAAACGAAACCCTAAACCCTCCAAACCCTAAAATCAAAACC
*
3399203 TTAAAACATCAAATTCCTAAAATCA
66 TTAAAACATAAAATTCCTAAAATCA
* * *
3399228 AAACCCTAAACCCTTCAAACCCTAAAAATGAAACCCTAAACCTTTCAAACCCTAAAATCCAAAAC
1 AAACCCTAAACCCTTCAAACCCTAAAAACGAAACCCTAAACCCTCCAAACCCTAAAAT-CAAAAC
**
3399293 CTTAAAATTTAAAATT-CTAAAA
65 CTTAAAACATAAAATTCCTAAAA
3399315 ACCCCAAATT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 59 0.77
91 18 0.23
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.20
Consensus pattern (90 bp):
AAACCCTAAACCCTTCAAACCCTAAAAACGAAACCCTAAACCCTCCAAACCCTAAAATCAAAACC
TTAAAACATAAAATTCCTAAAATCA
Found at i:3407355 original size:15 final size:15
Alignment explanation
Indices: 3407335--3407370 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3407325 AAGAAGAGTT
*
3407335 TTGCATTTGCATTGC
1 TTGCATTTGCATTAC
3407350 TTGCATTTGCATTAC
1 TTGCATTTGCATTAC
3407365 TTGCAT
1 TTGCAT
3407371 CTACATCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (15 bp):
TTGCATTTGCATTAC
Found at i:3407737 original size:40 final size:41
Alignment explanation
Indices: 3407660--3407754 Score: 156
Period size: 40 Copynumber: 2.3 Consensus size: 41
3407650 TTAAAGTTTT
* * *
3407660 AAAGTCTCTGTTTAAGAGGAACCATTTTCAATCAAGATTTC
1 AAAGCCTCTGTTTAAGAGGAAACAATTTCAATCAAGATTTC
3407701 AAAGCCTCTGTTTAAGA-GAAACAATTTCAATCAAGATTTC
1 AAAGCCTCTGTTTAAGAGGAAACAATTTCAATCAAGATTTC
3407741 AAAGCCTCTGTTTA
1 AAAGCCTCTGTTTA
3407755 GAAGGAACCT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 35 0.69
41 16 0.31
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.33
Consensus pattern (41 bp):
AAAGCCTCTGTTTAAGAGGAAACAATTTCAATCAAGATTTC
Found at i:3407950 original size:22 final size:23
Alignment explanation
Indices: 3407894--3407951 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
3407884 TGAGATTTAT
* *
3407894 AAGACCTTCGGACATAATCTCTA
1 AAGACCTTCGGGCACAATCTCTA
* * *
3407917 AAG-CCTTTGGGCACAA-CTTTC
1 AAGACCTTCGGGCACAATCTCTA
3407938 AAGACCTTCGGGCA
1 AAGACCTTCGGGCA
3407952 AAAGATTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 6 0.21
22 19 0.68
23 3 0.11
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (23 bp):
AAGACCTTCGGGCACAATCTCTA
Found at i:3408241 original size:110 final size:109
Alignment explanation
Indices: 3408047--3408270 Score: 286
Period size: 110 Copynumber: 2.0 Consensus size: 109
3408037 AATCCCAATC
* * * * *
3408047 GATTTTTAAGACCTCTGGGCATAATTTGATTCATGGTGTTATCCCAATCGATTTCTTATTTTTCA
1 GATTTTTAAAACCTCCGAGCATAATTTGATTCACGGTGTTATCCCAATCAATTTCTTATTTTTCA
* ** * *
3408112 ACTTGATGTGTTATTCCAGTCGATTCTGTAAGACCTTCGAGCAT
66 ACTTAAAATGTTATCCCAGTCGATTCTGTAAGACCTTCGAACAT
** ** * *
3408156 GATTTTTAAAACCTCCGAGCATAATTTTGATTTGCGGTGTTATCTGAATCAATTTTTTATTTTTT
1 GATTTTTAAAACCTCCGAGCATAA-TTTGATTCACGGTGTTATCCCAATCAATTTCTTATTTTTC
*
3408221 GACTTAAAATGTTATCCCAGTCGATTCTGTAAGACCTTCGAACAT
65 AACTTAAAATGTTATCCCAGTCGATTCTGTAAGACCTTCGAACAT
3408266 GATTT
1 GATTT
3408271 CTAAGACTTA
Statistics
Matches: 97, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
109 21 0.22
110 76 0.78
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (109 bp):
GATTTTTAAAACCTCCGAGCATAATTTGATTCACGGTGTTATCCCAATCAATTTCTTATTTTTCA
ACTTAAAATGTTATCCCAGTCGATTCTGTAAGACCTTCGAACAT
Found at i:3408411 original size:22 final size:22
Alignment explanation
Indices: 3408386--3408447 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
3408376 ATTCTGTAAA
* *
3408386 ACCTCCGTGCATAATTTTTAAT
1 ACCTCCGAGCATAATTTTTAAG
* * * *
3408408 ACCTCTGGGCATCATTTCTAAG
1 ACCTCCGAGCATAATTTTTAAG
*
3408430 ACCTACGAGCATAATTTT
1 ACCTCCGAGCATAATTTT
3408448 GATTCACGGT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35
Consensus pattern (22 bp):
ACCTCCGAGCATAATTTTTAAG
Found at i:3408523 original size:132 final size:131
Alignment explanation
Indices: 3408140--3408535 Score: 445
Period size: 132 Copynumber: 3.0 Consensus size: 131
3408130 GTCGATTCTG
* * * * * * * * *
3408140 TAAGACCTTCGAGCATGATTTTTAAAACCTCCGAGCATAATTTTGATTTGCGGTGTTATCTGAAT
1 TAAGACCTACGGGCATCATTTCTAAGACCTACGAGCATAATTTTGATTTACGGTGTTACCCG-AT
* * ** * * *
3408205 CAATTTTTTATTTTTTGACTTAAAATGTTATCCCAGTCGATTCTGTAAGACCTTCGAACATGATT
65 CGATTTCTTATTTTTTGACTTGCAATGTTATCCCAGTCGATTCTGTAAGACCTCCGAGCATAATT
3408270 TC
130 TC
* * * *
3408272 TAAGACTTACGGGCATCATTTCTAAGA-TTTCAAAGCATAATTTTGATTTACGGTGTTATCCCGA
1 TAAGACCTACGGGCATCATTTCTAAGACCTAC-GAGCATAATTTTGATTTACGGTGTTA-CCCGA
* * * *
3408336 TCGATTTCTTATTTTTTGACCTGCAATGTTATCCCAGTCAATTCTGTAAAACCTCCGTGCATAAT
64 TCGATTTCTTATTTTTTGACTTGCAATGTTATCCCAGTCGATTCTGTAAGACCTCCGAGCATAAT
*
3408401 TTT
129 TTC
* *
3408404 TAATACCT-CTGGGCATCATTTCTAAGACCTACGAGCATAATTTTGATTCACGGTGTTAGCCCGA
1 TAAGACCTAC-GGGCATCATTTCTAAGACCTACGAGCATAATTTTGATTTACGGTGTTA-CCCGA
* * * * *
3408468 TCGATTTCTTATTTTTTGACTTGCAGTGTTATCCCAGTCGATTTTTTAAGTCCTCCAAGCATAAT
64 TCGATTTCTTATTTTTTGACTTGCAATGTTATCCCAGTCGATTCTGTAAGACCTCCGAGCATAAT
3408533 TTC
129 TTC
3408536 GATTCGCAGT
Statistics
Matches: 219, Mismatches: 41, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
131 3 0.01
132 212 0.97
133 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (131 bp):
TAAGACCTACGGGCATCATTTCTAAGACCTACGAGCATAATTTTGATTTACGGTGTTACCCGATC
GATTTCTTATTTTTTGACTTGCAATGTTATCCCAGTCGATTCTGTAAGACCTCCGAGCATAATTT
C
Found at i:3408815 original size:20 final size:20
Alignment explanation
Indices: 3408776--3408817 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3408766 TCAATTATTG
**
3408776 ATAATAATAATATTTTTTTA
1 ATAATAATAATATTGGTTTA
3408796 ATAATAATAATATTGGTTTA
1 ATAATAATAATATTGGTTTA
3408816 AT
1 AT
3408818 TAAAACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
ATAATAATAATATTGGTTTA
Found at i:3408857 original size:16 final size:16
Alignment explanation
Indices: 3408838--3408868 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3408828 AATTAATTAT
*
3408838 AAAAAAACCAAAACAA
1 AAAAAAAACAAAACAA
3408854 AAAAAAAACAAAACA
1 AAAAAAAACAAAACA
3408869 TGGTAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAACAA
Found at i:3410226 original size:29 final size:29
Alignment explanation
Indices: 3410194--3410427 Score: 170
Period size: 29 Copynumber: 8.0 Consensus size: 29
3410184 TCAAAAATTT
*
3410194 TTAAACTCTAAAACCTCCAAACCCTAATA
1 TTAAACTCTAAAACCTCCAAACCCTAAAA
* * *
3410223 TTAAA-TCTCAAACTTTCAAACCCTAAAA
1 TTAAACTCTAAAACCTCCAAACCCTAAAA
* * * *
3410251 TTAAACCCTAAACCCTCTAAACCTTAAAA
1 TTAAACTCTAAAACCTCCAAACCCTAAAA
* * *
3410280 TTAAACTTTAAACCCTTCAAACCCTAAAAA
1 TTAAACTCTAAAACCTCCAAACCCT-AAAA
** * *
3410310 CGAAACT-TTAAACCTTTCAAACCCTAAAA
1 TTAAACTCTAAAACC-TCCAAACCCTAAAA
* * * *
3410339 TCAAATCCCTAAAACATCCAAATCCTAAAA
1 TTAAA-CTCTAAAACCTCCAAACCCTAAAA
* * *
3410369 TCAAAACCCTAAACCCTCCAAACCCTAAAAA
1 T-TAAACTCTAAAACCTCCAAACCCT-AAAA
* * *
3410400 TGAAACCCT-AAACCT-CAAACTCTAAAA
1 TTAAACTCTAAAACCTCCAAACCCTAAAA
3410427 T
1 T
3410428 CAAAACCTCA
Statistics
Matches: 164, Mismatches: 34, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
27 5 0.03
28 31 0.19
29 58 0.35
30 57 0.35
31 13 0.08
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.23
Consensus pattern (29 bp):
TTAAACTCTAAAACCTCCAAACCCTAAAA
Found at i:3410318 original size:30 final size:30
Alignment explanation
Indices: 3410237--3410497 Score: 141
Period size: 30 Copynumber: 8.9 Consensus size: 30
3410227 ATCTCAAACT
**
3410237 TTCAAACCCT-AAAATTAAACCCTAAACCC
1 TTCAAACCCTAAAAACGAAACCCTAAACCC
* ** **
3410266 -TCTAAA-CCTTAAAATTAAACTTTAAACCC
1 TTC-AAACCCTAAAAACGAAACCCTAAACCC
** *
3410295 TTCAAACCCTAAAAACGAAACTTTAAACCT
1 TTCAAACCCTAAAAACGAAACCCTAAACCC
* * *
3410325 TTCAAACCCTAAAATC-AAATCCCTAAAACA
1 TTCAAACCCTAAAAACGAAA-CCCTAAACCC
* * * *
3410355 TCCAAATCCTAAAATCAAAACCCTAAACCC
1 TTCAAACCCTAAAAACGAAACCCTAAACCC
* *
3410385 TCCAAACCCTAAAAATGAAACCCTAAA-CC
1 TTCAAACCCTAAAAACGAAACCCTAAACCC
* * * * **
3410414 -TCAAACTCTAAAATC-AAAACCTCAATTC
1 TTCAAACCCTAAAAACGAAACCCTAAACCC
*
3410442 -TCAAACCCTAAAAATCAAAACTCC-AAA--C
1 TTCAAACCCTAAAAA-CGAAAC-CCTAAACCC
*
3410470 ATCAAAACCCT-AAAACTGAAACCCTAAA
1 TTC-AAACCCTAAAAAC-GAAACCCTAAA
3410498 ATCCAAAACC
Statistics
Matches: 187, Mismatches: 31, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
27 8 0.04
28 33 0.18
29 42 0.22
30 99 0.53
31 5 0.03
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.20
Consensus pattern (30 bp):
TTCAAACCCTAAAAACGAAACCCTAAACCC
Found at i:3410350 original size:14 final size:13
Alignment explanation
Indices: 3410326--3410514 Score: 101
Period size: 14 Copynumber: 13.1 Consensus size: 13
3410316 TTTAAACCTT
3410326 TCAAACCCTAAAA
1 TCAAACCCTAAAA
3410339 TCAAATCCCTAAAACA
1 TCAAA-CCCT-AAA-A
*
3410355 TCCAAATCCTAAAA
1 T-CAAACCCTAAAA
*
3410369 TCAAAACCCTAAACCC
1 TC-AAACCCTAAA--A
3410385 TCCAAACCCTAAAAA
1 T-CAAACCCT-AAAA
* *
3410400 TGAAACCCTAAACC
1 TCAAACCCTAAA-A
*
3410414 TCAAACTCTAAAA
1 TCAAACCCTAAAA
* **
3410427 TCAAAACCTCAATTC
1 TCAAACCCT-AA-AA
3410442 TCAAACCCTAAAAA
1 TCAAACCCT-AAAA
3410456 TCAAAACTCC-AAACA
1 TC-AAAC-CCTAAA-A
3410471 TCAAAACCCTAAAA
1 TC-AAACCCTAAAA
*
3410485 CTGAAACCCTAAAA
1 -TCAAACCCTAAAA
*
3410499 TCCAAAACCTTAAAA
1 T-C-AAACCCTAAAA
3410514 T
1 T
3410515 TTAAAATTTT
Statistics
Matches: 137, Mismatches: 20, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
13 17 0.12
14 53 0.39
15 44 0.32
16 15 0.11
17 8 0.06
ACGTcount: A:0.50, C:0.31, G:0.01, T:0.17
Consensus pattern (13 bp):
TCAAACCCTAAAA
Found at i:3410362 original size:17 final size:17
Alignment explanation
Indices: 3410340--3410398 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 17
3410330 ACCCTAAAAT
3410340 CAAATCCCTAAAACATC
1 CAAATCCCTAAAACATC
3410357 CAAAT-CCT-AAA-AT-
1 CAAATCCCTAAAACATC
* * *
3410370 CAAAACCCTAAACCCTC
1 CAAATCCCTAAAACATC
3410387 CAAA-CCCTAAAA
1 CAAATCCCTAAAA
3410399 ATGAAACCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
13 4 0.12
14 5 0.15
15 5 0.15
16 11 0.32
17 9 0.26
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (17 bp):
CAAATCCCTAAAACATC
Found at i:3410759 original size:68 final size:68
Alignment explanation
Indices: 3410672--3410805 Score: 232
Period size: 68 Copynumber: 2.0 Consensus size: 68
3410662 GTTCTTGAAC
* *
3410672 GCCACCTAAATGATGGGGTATTTAAAGAAATCTTGTTCTATTAAGTTTTTTCTCATGAGTCCTTA
1 GCCACCTAAATGATGGGGTATTTAAAGAAATCTTATTCCATTAAGTTTTTTCTCATGAGTCCTTA
3410737 AAT
66 AAT
* *
3410740 GCCATCTAGATGATGGGGTATTTAAAGAAATCTTATTCCATTAAGTTTTTTCTCATGAGTCCTTA
1 GCCACCTAAATGATGGGGTATTTAAAGAAATCTTATTCCATTAAGTTTTTTCTCATGAGTCCTTA
3410805 A
66 A
3410806 TACGTCTTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (68 bp):
GCCACCTAAATGATGGGGTATTTAAAGAAATCTTATTCCATTAAGTTTTTTCTCATGAGTCCTTA
AAT
Found at i:3416731 original size:2 final size:2
Alignment explanation
Indices: 3416724--3416753 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3416714 AATGTAAGTC
3416724 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
3416754 TGATTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3417052 original size:22 final size:22
Alignment explanation
Indices: 3417024--3417069 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3417014 TGATTACGAC
*
3417024 TTAATTTGATTTAAATTTCTTT
1 TTAATTTGATGTAAATTTCTTT
*
3417046 TTAATTTGATGTACATTTCTTT
1 TTAATTTGATGTAAATTTCTTT
3417068 TT
1 TT
3417070 TTGTTCCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.63
Consensus pattern (22 bp):
TTAATTTGATGTAAATTTCTTT
Found at i:3417355 original size:13 final size:14
Alignment explanation
Indices: 3417334--3417366 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3417324 TAATACTTAA
*
3417334 TTATGATTATAA-T
1 TTATAATTATAATT
3417347 TTATAATTATAATT
1 TTATAATTATAATT
3417361 TTATAA
1 TTATAA
3417367 AAATAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TTATAATTATAATT
Found at i:3419274 original size:2 final size:2
Alignment explanation
Indices: 3419269--3419303 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3419259 AAAAAAAAAA
3419269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3419304 AGACAGCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3419723 original size:2 final size:2
Alignment explanation
Indices: 3419716--3419741 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3419706 AGAGTCAGCC
3419716 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3419742 AGTAATCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3425730 original size:18 final size:18
Alignment explanation
Indices: 3425707--3425744 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3425697 CATAGGACAA
3425707 AGAACTAGTACATAACAG
1 AGAACTAGTACATAACAG
*
3425725 AGAACTAGTACATGACAG
1 AGAACTAGTACATAACAG
3425743 AG
1 AG
3425745 CTGCAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (18 bp):
AGAACTAGTACATAACAG
Found at i:3427699 original size:27 final size:28
Alignment explanation
Indices: 3427641--3427696 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
3427631 TTTTACTTTC
*
3427641 TTAAATAAATTTTTATATTTTTATTGTA
1 TTAAATAAAGTTTTATATTTTTATTGTA
3427669 TTAAA-AAAGTTTTAT-TTTATTATT-TA
1 TTAAATAAAGTTTTATATTT-TTATTGTA
3427695 TT
1 TT
3427697 TAAGTACAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 7 0.27
27 14 0.54
28 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (28 bp):
TTAAATAAAGTTTTATATTTTTATTGTA
Found at i:3428298 original size:20 final size:20
Alignment explanation
Indices: 3428233--3428298 Score: 50
Period size: 20 Copynumber: 3.5 Consensus size: 20
3428223 CTTAGTAACA
*
3428233 AATA-ATAA-AAAAA-TTAT
1 AATACATAAGAAAAATTTGT
* *
3428250 AAAACATAAG-AAAATATGAT
1 AATACATAAGAAAAATTTG-T
* *
3428270 AACATATAAGAAAAATTTGT
1 AATACATAAGAAAAATTTGT
3428290 AATACATAA
1 AATACATAA
3428299 TAGAAAGTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
17 3 0.08
18 8 0.22
19 1 0.03
20 17 0.47
21 7 0.19
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.26
Consensus pattern (20 bp):
AATACATAAGAAAAATTTGT
Found at i:3428361 original size:20 final size:20
Alignment explanation
Indices: 3428334--3428384 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3428324 TAATTGCCAC
*
3428334 ACATAATAAAAAGTGGTAAA
1 ACATAATAAAAAGTGATAAA
* *
3428354 ATATAATACAAAGTGATAAA
1 ACATAATAAAAAGTGATAAA
*
3428374 ACATAAGAAAA
1 ACATAATAAAA
3428385 TTTTGATAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.63, C:0.06, G:0.12, T:0.20
Consensus pattern (20 bp):
ACATAATAAAAAGTGATAAA
Found at i:3428507 original size:18 final size:18
Alignment explanation
Indices: 3428486--3428537 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
3428476 ATAAACTATA
3428486 AAAAAATTAGTAACACAT
1 AAAAAATTAGTAACACAT
*
3428504 AAAAAA-TAGTAACA-TT
1 AAAAAATTAGTAACACAT
*
3428520 AAACAAATTTGTAACACA
1 AAA-AAATTAGTAACACA
3428538 ATTAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 4 0.14
17 11 0.39
18 13 0.46
ACGTcount: A:0.60, C:0.12, G:0.06, T:0.23
Consensus pattern (18 bp):
AAAAAATTAGTAACACAT
Found at i:3428992 original size:19 final size:18
Alignment explanation
Indices: 3428964--3429002 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
3428954 TCTTATTTGC
3428964 TTTTTTACTTTATT-TATT
1 TTTTTTACTTT-TTATATT
3428982 TTTTGTTACTTTTTATATT
1 TTTT-TTACTTTTTATATT
3429001 TT
1 TT
3429003 ACTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTTTACTTTTTATATT
Found at i:3429438 original size:22 final size:23
Alignment explanation
Indices: 3429408--3429456 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
3429398 ATAATTTAAA
* * *
3429408 ATTTTATAAAATTTATAAA-TAT
1 ATTTAATAAAATTAAAAAATTAT
3429430 ATTTAATAAAATTAAAAAATTAT
1 ATTTAATAAAATTAAAAAATTAT
3429453 ATTT
1 ATTT
3429457 TATATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAATAAAATTAAAAAATTAT
Found at i:3429507 original size:16 final size:16
Alignment explanation
Indices: 3429474--3429523 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
3429464 TTATATCGAT
*
3429474 ATAAATTATA-AT-AA
1 ATAATTTATACATAAA
3429488 ATAATTTATACATAAA
1 ATAATTTATACATAAA
*
3429504 ATAATATA-ACATAATA
1 ATAATTTATACATAA-A
3429520 ATAA
1 ATAA
3429524 ATACGAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 9 0.29
15 8 0.26
16 14 0.45
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAATTTATACATAAA
Found at i:3429717 original size:6 final size:6
Alignment explanation
Indices: 3429706--3429732 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3429696 CAACACCTAG
3429706 AAATTA AAATTA AAATTA AAATTA AAA
1 AAATTA AAATTA AAATTA AAATTA AAA
3429733 AAAAAGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTA
Found at i:3431399 original size:15 final size:16
Alignment explanation
Indices: 3431358--3431419 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 16
3431348 TAAATCCCAT
**
3431358 AAAATAATA-TATTTA
1 AAAATAATATTATAAA
3431373 AAAATAATATTATAAA
1 AAAATAATATTATAAA
3431389 AAAATAA-ATTAATTAAA
1 AAAATAATATT-A-TAAA
3431406 AAAGATAATATTAT
1 AAA-ATAATATTAT
3431420 TTATCAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 12 0.30
16 12 0.30
17 8 0.20
18 5 0.12
19 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AAAATAATATTATAAA
Found at i:3431501 original size:17 final size:16
Alignment explanation
Indices: 3431453--3431503 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 16
3431443 AAAAATGAAA
3431453 TAACAAAATAT-TAAC
1 TAACAAAATATATAAC
*
3431468 -AA-ATAATATATAA-
1 TAACAAAATATATAAC
3431481 TAACAAAATATAATAAC
1 TAACAAAATAT-ATAAC
3431498 TAACAA
1 TAACAA
3431504 CATGCTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 6 0.21
14 7 0.24
15 6 0.21
16 4 0.14
17 6 0.21
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (16 bp):
TAACAAAATATATAAC
Found at i:3441023 original size:25 final size:27
Alignment explanation
Indices: 3440987--3441036 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
3440977 TTTTGAATTT
3440987 AAATTTTATTG-ATG-ATAATTTATTA
1 AAATTTTATTGAATGTATAATTTATTA
3441012 AAATTATT-TTGAATGTATAATTTAT
1 AAATT-TTATTGAATGTATAATTTAT
3441037 AATTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 8 0.36
26 5 0.23
27 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (27 bp):
AAATTTTATTGAATGTATAATTTATTA
Found at i:3442254 original size:33 final size:33
Alignment explanation
Indices: 3442210--3442285 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 33
3442200 TGCTATAATT
**
3442210 TTGATA-AATTTTTTTAGAATTTTGACAATCTA
1 TTGATATAATTTTAATAGAATTTTGACAATCTA
* * *
3442242 TTGATATAATTTTAATATAATTTTGATAATTTA
1 TTGATATAATTTTAATAGAATTTTGACAATCTA
*
3442275 -TGTTATAATTT
1 TTGATATAATTT
3442286 GATAATAATC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
32 16 0.43
33 21 0.57
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.54
Consensus pattern (33 bp):
TTGATATAATTTTAATAGAATTTTGACAATCTA
Found at i:3442283 original size:21 final size:20
Alignment explanation
Indices: 3442135--3442417 Score: 136
Period size: 21 Copynumber: 13.9 Consensus size: 20
3442125 GTTTTAAAAG
*
3442135 TTTGATAAAATTTTGATAATT
1 TTTGATATAATTTTGATAA-T
* ** *
3442156 TTTAATATTGTTTTAATAAT
1 TTTGATATAATTTTGATAAT
3442176 TTATGATATAATTTT-AGTAAT
1 TT-TGATATAATTTTGA-TAAT
*
3442197 TATTGCTATAATTTTGATAAAT
1 T-TTGATATAATTTTGAT-AAT
** * *
3442219 TTTTTTAGAATTTTGACAA-
1 TTTGATATAATTTTGATAAT
* *
3442238 TCT-AT-TGA---T-ATAAT
1 TTTGATATAATTTTGATAAT
*
3442252 TTTAATATAATTTTGATAAT
1 TTTGATATAATTTTGATAAT
*
3442272 TTATGTTATAA-TTTGATAAT
1 TT-TGATATAATTTTGATAAT
* *
3442292 AATCGATATAATTTTGATAAT
1 -TTTGATATAATTTTGATAAT
* * *
3442313 ATTTGATAAAATTTTTATATT
1 -TTTGATATAATTTTGATAAT
* *
3442334 TTTTATATAATTTTGATACT
1 TTTGATATAATTTTGATAAT
* * *
3442354 ATTTGATATATTTTTTAATAACCA
1 -TTTGATATA-ATTTTGATAA--T
3442378 TTT-ATATAATTTTGATAACT
1 TTTGATATAATTTTGATAA-T
* *
3442398 TCTGATAATAGTTTTGATAA
1 TTTGAT-ATAATTTTGATAA
3442418 CCTTTTATAA
Statistics
Matches: 197, Mismatches: 44, Indels: 41
0.70 0.16 0.15
Matches are distributed among these distances:
13 3 0.02
14 3 0.02
15 2 0.01
16 2 0.01
17 1 0.01
18 1 0.01
19 3 0.02
20 47 0.24
21 102 0.52
22 30 0.15
23 3 0.02
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTGATATAATTTTGATAAT
Found at i:3442326 original size:41 final size:41
Alignment explanation
Indices: 3442256--3442361 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
3442246 TATAATTTTA
* *
3442256 ATATAATTTTGATAAT-TTATGTTATAATTTGATA-ATAATCG
1 ATATAATTTTGATAATATT-TGATAAAATTT-ATATATAATCG
* ** **
3442297 ATATAATTTTGATAATATTTGATAAAATTTTTATATTTTTT
1 ATATAATTTTGATAATATTTGATAAAATTTATATATAATCG
*
3442338 ATATAATTTTGATACTATTTGATA
1 ATATAATTTTGATAATATTTGATA
3442362 TATTTTTTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 2 0.04
41 51 0.93
42 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (41 bp):
ATATAATTTTGATAATATTTGATAAAATTTATATATAATCG
Found at i:3442369 original size:41 final size:43
Alignment explanation
Indices: 3442297--3442477 Score: 145
Period size: 43 Copynumber: 4.3 Consensus size: 43
3442287 ATAATAATCG
***
3442297 ATATAATTTTGATAATATTTGATAAAATTTTT-AT-ATTTTTT
1 ATATAATTTTGATAATATTTGATAAAATTTTTAATAACCATTT
* * *
3442338 ATATAATTTTGATACTATTTGATATATTTTTTAATAACCATTT
1 ATATAATTTTGATAATATTTGATAAAATTTTTAATAACCATTT
* * * * *
3442381 ATATAATTTTGATAACT-TCTGATAATAGTTTTGATAACCTTTT
1 ATATAATTTTGATAA-TATTTGATAAAATTTTTAATAACCATTT
* * * * * * * *
3442424 ATAAAAGTTTGGTAATATTTAATACAA-TTTTATTAATCTTTT
1 ATATAATTTTGATAATATTTGATAAAATTTTTAATAACCATTT
3442466 ATATAATCTTTG
1 ATATAAT-TTTG
3442478 CCACTTTTAT
Statistics
Matches: 109, Mismatches: 26, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
41 29 0.27
42 20 0.18
43 59 0.54
44 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (43 bp):
ATATAATTTTGATAATATTTGATAAAATTTTTAATAACCATTT
Found at i:3442427 original size:22 final size:22
Alignment explanation
Indices: 3442366--3442433 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
3442356 TTGATATATT
* * *
3442366 TTTTAATAACCATTTAT-ATAA
1 TTTTGATAACCTTTTATAATAG
*
3442387 TTTTGATAA-CTTCTGATAATAG
1 TTTTGATAACCTT-TTATAATAG
*
3442409 TTTTGATAACCTTTTATAAAAG
1 TTTTGATAACCTTTTATAATAG
3442431 TTT
1 TTT
3442434 GGTAATATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 2 0.05
21 11 0.29
22 22 0.58
23 3 0.08
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (22 bp):
TTTTGATAACCTTTTATAATAG
Found at i:3443078 original size:16 final size:14
Alignment explanation
Indices: 3443059--3443100 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
3443049 TTTTTTTAAT
*
3443059 TTTAAATTATTTTA
1 TTTATATTATTTTA
3443073 TCTTTATATT-TTTTA
1 --TTTATATTATTTTA
3443088 TTTATATTATTTT
1 TTTATATTATTTT
3443101 CGTATCGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 8 0.33
14 4 0.17
15 5 0.21
16 7 0.29
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATATTATTTTA
Found at i:3449607 original size:2 final size:2
Alignment explanation
Indices: 3449600--3449635 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3449590 CATGAACATG
*
3449600 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3449636 ATTTTTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3449840 original size:27 final size:27
Alignment explanation
Indices: 3449810--3449861 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3449800 AATTAATATC
* * *
3449810 TATTTTTTTTATAAAACTTAAAATTAA
1 TATTTTATTTAAAAAAATTAAAATTAA
3449837 TATTTTATTTAAAAAAATTAAAATT
1 TATTTTATTTAAAAAAATTAAAATT
3449862 TTAATCACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TATTTTATTTAAAAAAATTAAAATTAA
Found at i:3450749 original size:20 final size:21
Alignment explanation
Indices: 3450713--3450764 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3450703 ACCCGAATTA
3450713 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
3450735 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
3450756 AT-AAATATT
1 ATAAAATATT
3450765 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Done.