Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 11 of 25
Found at i:1744868 original size:7 final size:6
Alignment explanation
Indices: 1744840--1744864 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1744830 TTTTTAAAGG
1744840 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
1744865 ATAATTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:1745151 original size:8 final size:8
Alignment explanation
Indices: 1745117--1745213 Score: 56
Period size: 8 Copynumber: 11.4 Consensus size: 8
1745107 TTTTTACACT
1745117 TTTATA-A
1 TTTATATA
*
1745124 TTTATTTA
1 TTTATATA
1745132 TTTATATCATA
1 -TT-TAT-ATA
1745143 TTTATATA
1 TTTATATA
*
1745151 TTATATAAA
1 TT-TATATA
*
1745160 TTTTAAAATA
1 -TTT-ATATA
1745170 TTTATATA
1 TTTATATA
1745178 TTTATATAA
1 TTTATAT-A
1745187 TATTATAT-
1 T-TTATATA
1745195 TTTA-ATTA
1 TTTATA-TA
*
1745203 TTTTTATA
1 TTTATATA
1745211 TTT
1 TTT
1745214 TATTTATGAT
Statistics
Matches: 71, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
6 1 0.01
7 9 0.13
8 26 0.37
9 17 0.24
10 16 0.23
11 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTATATA
Found at i:1745184 original size:33 final size:33
Alignment explanation
Indices: 1745147--1745217 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
1745137 ATCATATTTA
1745147 TATATTATA-TAAATTTTAAAATATTTATATATT
1 TATATTATATTAAATTTT-AAATATTTATATATT
* * * *
1745180 TATATAATATTATATTTTAATTATTTTTATATT
1 TATATTATATTAAATTTTAAATATTTATATATT
1745213 T-TATT
1 TATATT
1745218 TATGATGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.09
33 22 0.69
34 7 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
TATATTATATTAAATTTTAAATATTTATATATT
Found at i:1745725 original size:24 final size:25
Alignment explanation
Indices: 1745692--1745749 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
1745682 GAGGTAAAAT
* * *
1745692 ATAATGAAAAAATATATAT-TTAAA
1 ATAATAAAAAAATAAATATATGAAA
**
1745716 ATAATAAAAATTTAAATATATGAAA
1 ATAATAAAAAAATAAATATATGAAA
1745741 ATAATAAAA
1 ATAATAAAA
1745750 TTAATTGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (25 bp):
ATAATAAAAAAATAAATATATGAAA
Found at i:1745864 original size:22 final size:22
Alignment explanation
Indices: 1745815--1745867 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1745805 TATTTAAGTC
*
1745815 ATAAAATTATAATTTTAATCAT
1 ATAAAATTAAAATTTTAATCAT
* * *
1745837 AAAAAATTAAAATTTTATTTAT
1 ATAAAATTAAAATTTTAATCAT
*
1745859 TTAAAATTA
1 ATAAAATTA
1745868 TATTAATAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAAATTAAAATTTTAATCAT
Found at i:1746318 original size:14 final size:15
Alignment explanation
Indices: 1746277--1746320 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1746267 TTTTATTTTA
*
1746277 TTAAATAAATTAAAAT
1 TTAAATTAATT-AAAT
1746293 TTAAATTAATTAAAT
1 TTAAATTAATTAAAT
*
1746308 TTGAA-TAATTAAA
1 TTAAATTAATTAAA
1746321 ATATAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 8 0.31
15 8 0.31
16 10 0.38
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
TTAAATTAATTAAAT
Found at i:1746322 original size:15 final size:16
Alignment explanation
Indices: 1746277--1746328 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 16
1746267 TTTTATTTTA
*
1746277 TTAAATAAATTAAAAT
1 TTAAATTAATTAAAAT
1746293 TTAAATTAATT-AAAT
1 TTAAATTAATTAAAAT
*
1746308 TTGAA-TAATTAAAAT
1 TTAAATTAATTAAAAT
*
1746323 ATAAAT
1 TTAAAT
1746329 ATAAATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 5 0.17
15 15 0.50
16 10 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
TTAAATTAATTAAAAT
Found at i:1746354 original size:36 final size:31
Alignment explanation
Indices: 1746276--1746354 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 31
1746266 ATTTTATTTT
*
1746276 ATTAAATAAATTAAAATTTAAATTAATTAAA
1 ATTAAATAAATTAAAATATAAATTAATTAAA
* *
1746307 TTTGAAT-AATTAAAATATAAATATAAATTTATTAA
1 ATTAAATAAATTAAAATATAAAT-T-AA-TTA--AA
1746342 ATTAAATAAATTA
1 ATTAAATAAATTA
1746355 TGTAATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
30 14 0.38
31 6 0.16
32 2 0.05
33 3 0.08
35 7 0.19
36 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
ATTAAATAAATTAAAATATAAATTAATTAAA
Found at i:1747383 original size:8 final size:8
Alignment explanation
Indices: 1747370--1747496 Score: 86
Period size: 8 Copynumber: 15.8 Consensus size: 8
1747360 CAATAATTAA
1747370 ATTTATAT
1 ATTTATAT
1747378 ATTTATAT
1 ATTTATAT
1747386 ATTTATAT
1 ATTTATAT
*
1747394 ATATATA-
1 ATTTATAT
*
1747401 ATTAATAT
1 ATTTATAT
*
1747409 ATTAATA-
1 ATTTATAT
1747416 ATTTATAT
1 ATTTATAT
*
1747424 -TATATAT
1 ATTTATAT
1747431 AATTTTAATAT
1 -A-TTT-ATAT
1747442 ATTTATAT
1 ATTTATAT
* *
1747450 -TTTTTAA
1 ATTTATAT
1747457 ATTATATCAT
1 ATT-TAT-AT
*
1747467 ATTTCATTT
1 ATTT-ATAT
1747476 A-TT-TAT
1 ATTTATAT
1747482 ATTTATAT
1 ATTTATAT
1747490 ATCTTAT
1 AT-TTAT
1747497 TTATGACTTT
Statistics
Matches: 94, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
6 3 0.03
7 24 0.26
8 42 0.45
9 12 0.13
10 9 0.10
11 4 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.58
Consensus pattern (8 bp):
ATTTATAT
Found at i:1747428 original size:31 final size:31
Alignment explanation
Indices: 1747369--1747449 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
1747359 TCAATAATTA
* *
1747369 AATTTATATATTTATATATTTATATATATAT
1 AATTAATATATTAATATATTTATATATATAT
1747400 AATTAATATATTAATA-ATTTATAT-TATAT
1 AATTAATATATTAATATATTTATATATATAT
1747429 -A-TAAT-T-TTAATATATTTATAT
1 AATTAATATATTAATATATTTATAT
1747450 TTTTTAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.13
26 9 0.19
27 4 0.09
28 1 0.02
29 5 0.11
30 8 0.17
31 14 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
AATTAATATATTAATATATTTATATATATAT
Found at i:1747463 original size:33 final size:34
Alignment explanation
Indices: 1747374--1747485 Score: 99
Period size: 33 Copynumber: 3.4 Consensus size: 34
1747364 AATTAAATTT
* *
1747374 ATATATTTATA-TATTTATATATATATAA--TTA
1 ATATATTTATATTTTTTAAATATATATAATTTTA
* * * *
1747405 ATATATTAATAATTTAT-ATTATATATAATTTTA
1 ATATATTTATATTTTTTAAATATATATAATTTTA
* *
1747438 ATATATTTATATTTTTTAAAT-TATATCATATTTC
1 ATATATTTATATTTTTTAAATATATATAAT-TTTA
*
1747472 ATTTATTTATATTT
1 ATATATTTATATTT
1747486 ATATATCTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
31 19 0.30
32 3 0.05
33 24 0.38
34 18 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (34 bp):
ATATATTTATATTTTTTAAATATATATAATTTTA
Found at i:1750117 original size:19 final size:19
Alignment explanation
Indices: 1750095--1750132 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1750085 CGATAAAAAT
*
1750095 ATTTATATATTATTA-ATTA
1 ATTTA-ATAATATTATATTA
1750114 ATTTAATAATATTATATTA
1 ATTTAATAATATTATATTA
1750133 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTAATAATATTATATTA
Found at i:1750716 original size:21 final size:21
Alignment explanation
Indices: 1750677--1750717 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1750667 AATACAACGT
*
1750677 TAAAATTTTAATTTTAATAAC
1 TAAAATTTTAATTTCAATAAC
1750698 TAAAA-TTTAATTCTCAATAA
1 TAAAATTTTAATT-TCAATAA
1750718 TTTAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATTTTAATTTCAATAAC
Found at i:1750996 original size:2 final size:2
Alignment explanation
Indices: 1750989--1751014 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1750979 TTGATGCTTT
1750989 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
1751015 CACTCATTGG
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:1753095 original size:14 final size:15
Alignment explanation
Indices: 1753076--1753109 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1753066 TTTATATTTT
*
1753076 AAAATTATAT-ATAA
1 AAAATTAAATAATAA
1753090 AAAATTAAATAATAA
1 AAAATTAAATAATAA
1753105 AAAAT
1 AAAAT
1753110 ACCCGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTAAATAATAA
Found at i:1753289 original size:28 final size:29
Alignment explanation
Indices: 1753222--1753289 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 29
1753212 AATAACAAAA
* *
1753222 AATATTTACTTAAAATTAATTTTATTATTT
1 AATATTTA-TAAAAAATAATTTTATTATTT
* *
1753252 AAAATATATAAAAAAT-ATTTT-TTATATT
1 AATATTTATAAAAAATAATTTTATTAT-TT
1753280 AATATTTATA
1 AATATTTATA
1753290 TATTTTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
27 4 0.13
28 15 0.48
29 6 0.19
30 6 0.19
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
AATATTTATAAAAAATAATTTTATTATTT
Found at i:1753295 original size:21 final size:21
Alignment explanation
Indices: 1753266--1753308 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1753256 TATATAAAAA
*
1753266 ATATTTTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1753287 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1753308 A
1 A
1753309 AATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1755963 original size:10 final size:10
Alignment explanation
Indices: 1755950--1756014 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
1755940 AATAATATAT
1755950 TTTTTATTAA
1 TTTTTATTAA
*
1755960 TTTTTATAAA
1 TTTTTATTAA
*
1755970 TTTTATTAATATAT
1 -TTT-TT-AT-TAA
*
1755984 TTTTTATAAA
1 TTTTTATTAA
1755994 TTTTTA-TAA
1 TTTTTATTAA
*
1756003 ATTTTATTAA
1 TTTTTATTAA
1756013 TT
1 TT
1756015 ACGTTATCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
9 7 0.17
10 20 0.48
11 5 0.12
12 4 0.10
13 5 0.12
14 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTATTAA
Found at i:1755985 original size:34 final size:34
Alignment explanation
Indices: 1755942--1756013 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
1755932 ATATATTAAA
*
1755942 TAATATATTTTTTATTAATTTTTATAAATTTTAT
1 TAATATATTTTTTATAAATTTTTATAAATTTTAT
1755976 TAATATATTTTTTATAAATTTTTATAAATTTTAT
1 TAATATATTTTTTATAAATTTTTATAAATTTTAT
1756010 TAAT
1 TAAT
1756014 TACGTTATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (34 bp):
TAATATATTTTTTATAAATTTTTATAAATTTTAT
Found at i:1757125 original size:12 final size:12
Alignment explanation
Indices: 1757099--1757206 Score: 51
Period size: 12 Copynumber: 8.3 Consensus size: 12
1757089 TTACTAGGAT
1757099 TTTCAT-CATAA
1 TTTCATGCATAA
1757110 TTTCATGCATAA
1 TTTCATGCATAA
*
1757122 TTTCTTGCAACTATAA
1 TTTCATG---C-ATAA
*
1757138 TTTCCAT-CATTA
1 TTT-CATGCATAA
*
1757150 TTCCATGCATAA
1 TTTCATGCATAA
*
1757162 TTTCTTTGCAACCCTAA
1 TTTC-ATGC-A---TAA
1757179 TTTCCAT-CATAA
1 TTT-CATGCATAA
*
1757191 TTCCATGCATAA
1 TTTCATGCATAA
1757203 TTTC
1 TTTC
1757207 TTGGCAAGCC
Statistics
Matches: 73, Mismatches: 10, Indels: 27
0.66 0.09 0.25
Matches are distributed among these distances:
11 12 0.16
12 36 0.49
13 4 0.05
14 1 0.01
15 2 0.03
16 8 0.11
17 9 0.12
18 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.43
Consensus pattern (12 bp):
TTTCATGCATAA
Found at i:1757183 original size:41 final size:41
Alignment explanation
Indices: 1757097--1757213 Score: 173
Period size: 41 Copynumber: 2.9 Consensus size: 41
1757087 TTTTACTAGG
* * *
1757097 ATTTTCATCATAATTTCATGCATAATTTC-TTGCAACTATA
1 ATTTCCATCATAATTCCATGCATAATTTCTTTGCAACCATA
* *
1757137 ATTTCCATCATTATTCCATGCATAATTTCTTTGCAACCCTA
1 ATTTCCATCATAATTCCATGCATAATTTCTTTGCAACCATA
*
1757178 ATTTCCATCATAATTCCATGCATAATTTCTTGGCAA
1 ATTTCCATCATAATTCCATGCATAATTTCTTTGCAA
1757214 GCCTTGCAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 26 0.38
41 43 0.62
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (41 bp):
ATTTCCATCATAATTCCATGCATAATTTCTTTGCAACCATA
Found at i:1757331 original size:13 final size:14
Alignment explanation
Indices: 1757304--1757333 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1757294 ATGTTAAATT
1757304 TTATTAAATATAAA
1 TTATTAAATATAAA
1757318 TTATTAAA-ATAAA
1 TTATTAAATATAAA
1757331 TTA
1 TTA
1757334 AATTTTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTATTAAATATAAA
Found at i:1758224 original size:2 final size:2
Alignment explanation
Indices: 1758214--1758246 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1758204 AAACCAAAAA
*
1758214 AT AT GT 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 A
1758247 CAATTTCTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1759592 original size:7 final size:7
Alignment explanation
Indices: 1759575--1759614 Score: 53
Period size: 7 Copynumber: 5.3 Consensus size: 7
1759565 TACTCTACTC
1759575 AAAATTAT
1 AAAA-TAT
1759583 AAAATAT
1 AAAATAT
1759590 AAAATAT
1 AAAATAT
1759597 AAAATAATT
1 AAAAT-A-T
1759606 AAAATAT
1 AAAATAT
1759613 AA
1 AA
1759615 TATAAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 18 0.60
8 6 0.20
9 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAATAT
Found at i:1759599 original size:14 final size:16
Alignment explanation
Indices: 1759575--1759619 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1759565 TACTCTACTC
1759575 AAAATTATAAAAT-A-T
1 AAAA-TATAAAATAATT
1759590 AAAATATAAAATAATT
1 AAAATATAAAATAATT
*
1759606 AAAATATAATATAA
1 AAAATATAAAATAA
1759620 ATTATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.30
15 5 0.19
16 14 0.52
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATATAAAATAATT
Found at i:1762143 original size:2 final size:2
Alignment explanation
Indices: 1762136--1762161 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1762126 ACAATGATAA
1762136 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
1762162 GTGTATATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1763192 original size:13 final size:13
Alignment explanation
Indices: 1763152--1763201 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
1763142 TAGTGAAGAA
*
1763152 AATATTTAAATTT
1 AATATTTTAATTT
*
1763165 TATATTATATAATTT
1 AATATT-T-TAATTT
1763180 AATATTTTAATTT
1 AATATTTTAATTT
1763193 ATATATTTT
1 A-ATATTTT
1763202 TAAAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 12 0.39
14 9 0.29
15 10 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTTAATTT
Found at i:1763200 original size:21 final size:20
Alignment explanation
Indices: 1763153--1763200 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
1763143 AGTGAAGAAA
1763153 ATATTTAAATTTTATATTAT
1 ATATTTAAATTTTATATTAT
1763173 ATAATTTAATATTTTA-ATTTAT
1 AT-ATTTAA-ATTTTATA-TTAT
1763195 ATATTT
1 ATATTT
1763201 TTAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.08
21 11 0.44
22 12 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTAAATTTTATATTAT
Found at i:1763202 original size:15 final size:15
Alignment explanation
Indices: 1763160--1763204 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1763150 AAAATATTTA
*
1763160 AATTT-TATATTATAT
1 AATTTATATATT-TTT
1763175 AATTTA-ATA-TTTT
1 AATTTATATATTTTT
1763188 AATTTATATATTTTT
1 AATTTATATATTTTT
1763203 AA
1 AA
1763205 AATAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 8 0.31
14 4 0.15
15 14 0.54
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTTATATATTTTT
Found at i:1763210 original size:28 final size:28
Alignment explanation
Indices: 1763152--1763216 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
1763142 TAGTGAAGAA
**
1763152 AATATTTAAATTTTATATTATATAATTT
1 AATATTTAAATTTTATATTATATAAAAT
* *
1763180 AATATTTTAATTTATATATT-TTTAAAAT
1 AATATTTAAATTT-TATATTATATAAAAT
*
1763208 AATAATTAA
1 AATATTTAA
1763217 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AATATTTAAATTTTATATTATATAAAAT
Found at i:1763227 original size:14 final size:15
Alignment explanation
Indices: 1763202--1763233 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1763192 TATATATTTT
1763202 TAAAATAATAATTAA
1 TAAAATAATAATTAA
1763217 TAAAA-AATAATTAA
1 TAAAATAATAATTAA
1763231 TAA
1 TAA
1763234 TATTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAATAATAATTAA
Found at i:1763289 original size:30 final size:30
Alignment explanation
Indices: 1763223--1763281 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1763213 TTAATAAAAA
* * *
1763223 ATAATTAATAATATTAAAATTTTATTTAAAT
1 ATAAATAA-AATATTAAAATGTTATATAAAT
*
1763254 ATAAATAAAATATTAACATGTTATATAA
1 ATAAATAAAATATTAAAATGTTATATAA
1763282 TTTTAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (30 bp):
ATAAATAAAATATTAAAATGTTATATAAAT
Found at i:1765994 original size:15 final size:14
Alignment explanation
Indices: 1765960--1766012 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
1765950 ACTAATATTA
* *
1765960 TATTTTTTAAAATA
1 TATTTTTTATAATT
1765974 TA-TTTTTATAATT
1 TATTTTTTATAATT
*
1765987 TAATTTTTAATAATT
1 T-ATTTTTTATAATT
1766002 TATTTATTTAT
1 TATTT-TTTAT
1766013 TTATTAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 10 0.31
14 7 0.22
15 15 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTTTTTATAATT
Found at i:1766087 original size:23 final size:22
Alignment explanation
Indices: 1766057--1766099 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1766047 ATAATATTAC
1766057 ATATATATTATATAATATAAATT
1 ATATATATTATATAAT-TAAATT
*
1766080 ATATATATTATTTAATTAAA
1 ATATATATTATATAATTAAA
1766100 AAAGAGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATATATTATATAATTAAATT
Found at i:1768964 original size:34 final size:34
Alignment explanation
Indices: 1768900--1769082 Score: 269
Period size: 34 Copynumber: 5.4 Consensus size: 34
1768890 CAACTGTTCC
* *
1768900 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1768933 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1768967 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1769001 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1769035 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1769069 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1769083 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 11 0.08
34 123 0.92
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1769075 original size:102 final size:101
Alignment explanation
Indices: 1768900--1769082 Score: 321
Period size: 102 Copynumber: 1.8 Consensus size: 101
1768890 CAACTGTTCC
1768900 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1768965 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1769001 TGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTAC
1769066 CATTGTTGATTAAATGG
65 CATTGTTGATTAAATGG
1769083 TGGTTTTTAC
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 12 0.16
102 65 0.84
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1769443 original size:19 final size:19
Alignment explanation
Indices: 1769387--1769449 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1769377 TGGTTGTCGA
**
1769387 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1769406 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1769425 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1769444 GTTACT
1 GGTACT
1769450 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1773583 original size:34 final size:34
Alignment explanation
Indices: 1773517--1773701 Score: 273
Period size: 34 Copynumber: 5.5 Consensus size: 34
1773507 AAGTGGGAGA
* *
1773517 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1773550 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1773584 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1773618 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1773652 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1773686 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1773702 TGGTTTTTAC
Statistics
Matches: 136, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 13 0.10
34 123 0.90
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1773692 original size:102 final size:101
Alignment explanation
Indices: 1773517--1773701 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
1773507 AAGTGGGAGA
1773517 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1773582 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1773618 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
*
1773683 GCCATTGTTGATTAAATGG
65 ACCATTGTTGATTAAATGG
1773702 TGGTTTTTAC
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 14 0.18
102 65 0.82
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1774371 original size:18 final size:19
Alignment explanation
Indices: 1774348--1774390 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1774338 AAGAATTATA
1774348 ATTTTTAAAT-TAAAAAAT
1 ATTTTTAAATGTAAAAAAT
*
1774366 ATTTTTAAATGTAAATAAT
1 ATTTTTAAATGTAAAAAAT
1774385 ATTTTT
1 ATTTTT
1774391 TAAAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTTTAAATGTAAAAAAT
Found at i:1774447 original size:44 final size:43
Alignment explanation
Indices: 1774355--1774447 Score: 100
Period size: 44 Copynumber: 2.1 Consensus size: 43
1774345 ATAATTTTTA
**
1774355 AATTA-AAAAATATTTTTAAATGTAAATAATATTTTTTAAAATT
1 AATTATAAAAATATTTTTAAATAAAAATAATATTTTTT-AAATT
* * *
1774398 TATTATAAATATATTTTTAAATAAAAATAAATATATTTTT-TATT
1 AATTATAAAAATATTTTTAAATAAAAAT-AATAT-TTTTTAAATT
1774442 AATTAT
1 AATTAT
1774448 TTAGTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
43 4 0.10
44 27 0.66
45 5 0.12
46 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (43 bp):
AATTATAAAAATATTTTTAAATAAAAATAATATTTTTTAAATT
Found at i:1774798 original size:16 final size:17
Alignment explanation
Indices: 1774777--1774835 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
1774767 AAATAAAATA
1774777 TATTTTTATAT-AATTT
1 TATTTTTATATCAATTT
* * *
1774793 TATTTTTTTTTCATTTT
1 TATTTTTATATCAATTT
1774810 TCATTTTTA-ATCAATTT
1 T-ATTTTTATATCAATTT
*
1774827 TATTATTAT
1 TATTTTTAT
1774836 TAAATTTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
16 15 0.45
17 12 0.36
18 6 0.18
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTTATATCAATTT
Found at i:1774889 original size:24 final size:23
Alignment explanation
Indices: 1774827--1774891 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
1774817 TAATCAATTT
* *
1774827 TATTATTATTAAATTTAAAAAAA
1 TATTATAAATAAATTTAAAAAAA
* *
1774850 TATTAATTAATTAATTTAACTAAAAA
1 TATT-ATAAATAAATTTAA--AAAAA
1774876 TATT-TAAATAAATTTA
1 TATTATAAATAAATTTA
1774892 TTTAATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 4 0.11
24 22 0.63
26 9 0.26
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATAAATAAATTTAAAAAAA
Found at i:1774889 original size:28 final size:24
Alignment explanation
Indices: 1774838--1774896 Score: 64
Period size: 28 Copynumber: 2.3 Consensus size: 24
1774828 ATTATTATTA
*
1774838 AATTTAAAAAAATATTAATTAATT
1 AATTTAAAAAAATATTAATAAATT
1774862 AATTTAACTAAAAATATTTAAATAAATT
1 AATTTAA--AAAAATA-TT-AATAAATT
*
1774890 TATTTAA
1 AATTTAA
1774897 TATATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 7 0.24
26 7 0.24
27 2 0.07
28 13 0.45
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTTAAAAAAATATTAATAAATT
Found at i:1777557 original size:16 final size:16
Alignment explanation
Indices: 1777535--1777573 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1777525 CAGCCATGGG
1777535 TTTTTGTTTTAT-ATT
1 TTTTTGTTTTATCATT
1777550 TGTTTTG-TTTATCATT
1 T-TTTTGTTTTATCATT
1777566 TTTTTGTT
1 TTTTTGTT
1777574 CATCGGTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.77
Consensus pattern (16 bp):
TTTTTGTTTTATCATT
Found at i:1779392 original size:24 final size:24
Alignment explanation
Indices: 1779364--1779411 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1779354 AAATTTAAAT
1779364 AAAT-ATATAAAATATTATAATTAA
1 AAATAATATAAAATATTA-AATTAA
*
1779388 AAATAATATAAATTATTAAATTAA
1 AAATAATATAAAATATTAAATTAA
1779412 TTCAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATAATATAAAATATTAAATTAA
Found at i:1781558 original size:2 final size:2
Alignment explanation
Indices: 1781551--1781577 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1781541 TGTTGGATGA
1781551 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 A
1781578 AGCATTGGTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1782689 original size:18 final size:19
Alignment explanation
Indices: 1782666--1782701 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1782656 AATTCGATAG
1782666 AAAATAATTT-ATTTATTT
1 AAAATAATTTAATTTATTT
*
1782684 AAAATATTTTAATTTATT
1 AAAATAATTTAATTTATT
1782702 AATTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAAATAATTTAATTTATTT
Found at i:1782700 original size:23 final size:23
Alignment explanation
Indices: 1782670--1782716 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1782660 CGATAGAAAA
* *
1782670 TAATTTATTTATTTAAAATATTT
1 TAATTTATTAATTAAAAATATTT
*
1782693 TAATTTATTAATTAAAAATGTTT
1 TAATTTATTAATTAAAAATATTT
1782716 T
1 T
1782717 TGACAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TAATTTATTAATTAAAAATATTT
Found at i:1783359 original size:21 final size:21
Alignment explanation
Indices: 1783325--1783385 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
1783315 ATCAATTGCT
*
1783325 ATTTACTCA-AAAATATTTAA
1 ATTTAATCATAAAATATTTAA
*
1783345 ATTTAATCATAAAATATATAA
1 ATTTAATCATAAAATATTTAA
1783366 ATATTAAT-ATAAAATATTTA
1 AT-TTAATCATAAAATATTTA
1783386 TTTTATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.22
21 23 0.64
22 5 0.14
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTAATCATAAAATATTTAA
Found at i:1783666 original size:23 final size:24
Alignment explanation
Indices: 1783640--1783688 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1783630 ATTATTTTTT
1783640 TAAAAAA-TAAA-ATATAAATTAGA
1 TAAAAAATTAAATATATAAA-TAGA
1783663 TAAAAAATTAAATATATAAATAGA
1 TAAAAAATTAAATATATAAATAGA
1783687 TA
1 TA
1783689 TTGAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.29
24 10 0.42
25 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (24 bp):
TAAAAAATTAAATATATAAATAGA
Found at i:1786110 original size:26 final size:26
Alignment explanation
Indices: 1786081--1786131 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1786071 GTATATTAGT
*
1786081 TTTTTTAAAAAAAATTTTATAATTAA
1 TTTTTTAAAAAAAATTATATAATTAA
* *
1786107 TTTTTTTAAAAAAATTATATCATTA
1 TTTTTTAAAAAAAATTATATAATTA
1786132 TACGATTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTTTTAAAAAAAATTATATAATTAA
Found at i:1787659 original size:26 final size:26
Alignment explanation
Indices: 1787630--1787684 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
1787620 AAACAAATAT
* *
1787630 AAAT-AATAATCATTAAAGTTTATTTG
1 AAATAAATAAACATTAAAATTTA-TTG
1787656 AAATAAATAAACATTAAAATTTATTG
1 AAATAAATAAACATTAAAATTTATTG
1787682 AAA
1 AAA
1787685 CTTCATCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (26 bp):
AAATAAATAAACATTAAAATTTATTG
Found at i:1790247 original size:28 final size:29
Alignment explanation
Indices: 1790192--1790249 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1790182 AACTGACCGA
1790192 TCATCACTACGGCTATTCAAACAGTCAGT
1 TCATCACTACGGCTATTCAAACAGTCAGT
* * *
1790221 TCATTACTAGGGCT-TTCAAACGGTCAGT
1 TCATCACTACGGCTATTCAAACAGTCAGT
1790249 T
1 T
1790250 TGGTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (29 bp):
TCATCACTACGGCTATTCAAACAGTCAGT
Found at i:1793110 original size:1 final size:1
Alignment explanation
Indices: 1793104--1793128 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1793094 GCGTTTTCTC
1793104 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1793129 CAGTTTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1794261 original size:27 final size:27
Alignment explanation
Indices: 1794217--1794294 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
1794207 TTCTATTTAT
* *
1794217 TATTTATAATCATATTTAATTTATTATA
1 TATTTAT-ATAATATTTAATTTATTAAA
* *
1794245 TTTTTATATAA-ATTTTAATATATTAAA
1 TATTTATATAATA-TTTAATTTATTAAA
*
1794272 TATTTATATTATATTTAATTTAT
1 TATTTATATAATATTTAATTTAT
1794295 ATTATTTATA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
26 1 0.02
27 33 0.80
28 7 0.17
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (27 bp):
TATTTATATAATATTTAATTTATTAAA
Found at i:1796167 original size:19 final size:19
Alignment explanation
Indices: 1796145--1796183 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1796135 ATTCGATAAA
*
1796145 AATTTATATATTATTA-ATT
1 AATTTA-ATAATATTATATT
1796164 AATTTAATAATATTATATT
1 AATTTAATAATATTATATT
1796183 A
1 A
1796184 TTAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATTTAATAATATTATATT
Found at i:1796240 original size:3 final size:3
Alignment explanation
Indices: 1796232--1796264 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1796222 ATATATAGTC
1796232 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1796265 TTTTGCTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1796777 original size:21 final size:21
Alignment explanation
Indices: 1796738--1796778 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1796728 AATACAACGT
*
1796738 TAAAATTTTAATTTTAATAAC
1 TAAAATTTTAATTTCAATAAC
1796759 TAAAA-TTTAATTCTCAATAA
1 TAAAATTTTAATT-TCAATAA
1796779 TTTAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATTTTAATTTCAATAAC
Found at i:1798570 original size:15 final size:17
Alignment explanation
Indices: 1798537--1798574 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1798527 TATTATATGA
1798537 ATATCTGATATGAATAT
1 ATATCTGATATGAATAT
1798554 ATATCTGATATGAATAT
1 ATATCTGATATGAATAT
1798571 ATAT
1 ATAT
1798575 AGTTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (17 bp):
ATATCTGATATGAATAT
Found at i:1799359 original size:22 final size:22
Alignment explanation
Indices: 1799334--1799378 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1799324 TATTAAAAAA
1799334 ATATATTTTTAT-ATTAATATTT
1 ATATATTTTTATAATTAA-ATTT
1799356 ATATATTTTTATAATTAAATTT
1 ATATATTTTTATAATTAAATTT
1799378 A
1 A
1799379 AATAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATATTTTTATAATTAAATTT
Found at i:1799683 original size:2 final size:2
Alignment explanation
Indices: 1799645--1799673 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1799635 ATTAATGAAC
1799645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1799674 ACATTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1802000 original size:3 final size:3
Alignment explanation
Indices: 1801992--1802028 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
1801982 GGGTAAAATT
1801992 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1802029 AATAATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1802052 original size:10 final size:10
Alignment explanation
Indices: 1802039--1802103 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
1802029 AATAATATAT
1802039 TTTTTATTAA
1 TTTTTATTAA
*
1802049 TTTTTATAAA
1 TTTTTATTAA
*
1802059 TTTTATTAATATAT
1 -TTT-TT-AT-TAA
*
1802073 TTTTTATAAA
1 TTTTTATTAA
1802083 TTTTTA-TAA
1 TTTTTATTAA
*
1802092 ATTTTATTAA
1 TTTTTATTAA
1802102 TT
1 TT
1802104 ACGTTATCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
9 7 0.17
10 20 0.48
11 5 0.12
12 4 0.10
13 5 0.12
14 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTATTAA
Found at i:1802074 original size:34 final size:34
Alignment explanation
Indices: 1801987--1802102 Score: 137
Period size: 34 Copynumber: 3.4 Consensus size: 34
1801977 TTTCTGGGTA
* *
1801987 AAATTTTATTATTATTATTATTATTATT-ATTATTAT
1 AAATTTTATTAATA-TATT-TT-TTATTAATTTTTAT
* * *
1802023 ATA-TTAAATAATATATTTTTTATTAATTTTTAT
1 AAATTTTATTAATATATTTTTTATTAATTTTTAT
*
1802056 AAATTTTATTAATATATTTTTTATAAATTTTTAT
1 AAATTTTATTAATATATTTTTTATTAATTTTTAT
1802090 AAATTTTATTAAT
1 AAATTTTATTAAT
1802103 TACGTTATCA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
32 5 0.07
33 11 0.16
34 44 0.64
35 7 0.10
36 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (34 bp):
AAATTTTATTAATATATTTTTTATTAATTTTTAT
Found at i:1803218 original size:12 final size:12
Alignment explanation
Indices: 1803192--1803299 Score: 51
Period size: 12 Copynumber: 8.3 Consensus size: 12
1803182 TTACTAGGAT
1803192 TTTCAT-CATAA
1 TTTCATGCATAA
1803203 TTTCATGCATAA
1 TTTCATGCATAA
*
1803215 TTTCTTGCAACTATAA
1 TTTCATG---C-ATAA
*
1803231 TTTCCAT-CATTA
1 TTT-CATGCATAA
*
1803243 TTCCATGCATAA
1 TTTCATGCATAA
*
1803255 TTTCTTTGCAACCCTAA
1 TTTC-ATGC-A---TAA
1803272 TTTCCAT-CATAA
1 TTT-CATGCATAA
*
1803284 TTCCATGCATAA
1 TTTCATGCATAA
1803296 TTTC
1 TTTC
1803300 TTGGCAAGCC
Statistics
Matches: 73, Mismatches: 10, Indels: 27
0.66 0.09 0.25
Matches are distributed among these distances:
11 12 0.16
12 36 0.49
13 4 0.05
14 1 0.01
15 2 0.03
16 8 0.11
17 9 0.12
18 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.43
Consensus pattern (12 bp):
TTTCATGCATAA
Found at i:1803276 original size:41 final size:41
Alignment explanation
Indices: 1803190--1803306 Score: 173
Period size: 41 Copynumber: 2.9 Consensus size: 41
1803180 TTTTACTAGG
* * *
1803190 ATTTTCATCATAATTTCATGCATAATTTC-TTGCAACTATA
1 ATTTCCATCATAATTCCATGCATAATTTCTTTGCAACCATA
* *
1803230 ATTTCCATCATTATTCCATGCATAATTTCTTTGCAACCCTA
1 ATTTCCATCATAATTCCATGCATAATTTCTTTGCAACCATA
*
1803271 ATTTCCATCATAATTCCATGCATAATTTCTTGGCAA
1 ATTTCCATCATAATTCCATGCATAATTTCTTTGCAA
1803307 GCCTTGCAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 26 0.38
41 43 0.62
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (41 bp):
ATTTCCATCATAATTCCATGCATAATTTCTTTGCAACCATA
Found at i:1803413 original size:35 final size:36
Alignment explanation
Indices: 1803374--1803447 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 36
1803364 AAAAAATAGG
** *
1803374 ATAAAAATATAAAAATATGTTAAATTTTA-TTAAAT
1 ATAAAAATATAAAAATAAATTAAATTTTAGATAAAT
* *
1803409 AT-AAATTATTAAAATAAATTAAATTTTAGATAAAT
1 ATAAAAATATAAAAATAAATTAAATTTTAGATAAAT
1803444 ATAA
1 ATAA
1803448 TACTAGATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
34 22 0.69
35 9 0.28
36 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (36 bp):
ATAAAAATATAAAAATAAATTAAATTTTAGATAAAT
Found at i:1803427 original size:13 final size:14
Alignment explanation
Indices: 1803400--1803429 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1803390 ATGTTAAATT
1803400 TTATTAAATATAAA
1 TTATTAAATATAAA
1803414 TTATTAAA-ATAAA
1 TTATTAAATATAAA
1803427 TTA
1 TTA
1803430 AATTTTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTATTAAATATAAA
Found at i:1805653 original size:7 final size:7
Alignment explanation
Indices: 1805636--1805675 Score: 53
Period size: 7 Copynumber: 5.3 Consensus size: 7
1805626 TACTCTACTC
1805636 AAAATTAT
1 AAAA-TAT
1805644 AAAATAT
1 AAAATAT
1805651 AAAATAT
1 AAAATAT
1805658 AAAATAATT
1 AAAAT-A-T
1805667 AAAATAT
1 AAAATAT
1805674 AA
1 AA
1805676 TATAAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 18 0.60
8 6 0.20
9 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAATAT
Found at i:1805660 original size:14 final size:16
Alignment explanation
Indices: 1805636--1805680 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1805626 TACTCTACTC
1805636 AAAATTATAAAAT-A-T
1 AAAA-TATAAAATAATT
1805651 AAAATATAAAATAATT
1 AAAATATAAAATAATT
*
1805667 AAAATATAATATAA
1 AAAATATAAAATAA
1805681 ATTATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.30
15 5 0.19
16 14 0.52
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATATAAAATAATT
Found at i:1808210 original size:2 final size:2
Alignment explanation
Indices: 1808203--1808228 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1808193 ACAATGATAA
1808203 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
1808229 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1809273 original size:13 final size:13
Alignment explanation
Indices: 1809233--1809282 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
1809223 AGTGAAGAAA
*
1809233 AATATTTAAATTT
1 AATATTTTAATTT
*
1809246 TATATTATATAATTT
1 AATATT-T-TAATTT
1809261 AATATTTTAATTT
1 AATATTTTAATTT
1809274 ATATATTTT
1 A-ATATTTT
1809283 TAAAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 12 0.39
14 9 0.29
15 10 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTTAATTT
Found at i:1809281 original size:21 final size:20
Alignment explanation
Indices: 1809234--1809281 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
1809224 GTGAAGAAAA
1809234 ATATTTAAATTTTATATTAT
1 ATATTTAAATTTTATATTAT
1809254 ATAATTTAATATTTTA-ATTTAT
1 AT-ATTTAA-ATTTTATA-TTAT
1809276 ATATTT
1 ATATTT
1809282 TTAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.08
21 11 0.44
22 12 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTAAATTTTATATTAT
Found at i:1809283 original size:15 final size:15
Alignment explanation
Indices: 1809241--1809285 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1809231 AAAATATTTA
*
1809241 AATTT-TATATTATAT
1 AATTTATATATT-TTT
1809256 AATTTA-ATA-TTTT
1 AATTTATATATTTTT
1809269 AATTTATATATTTTT
1 AATTTATATATTTTT
1809284 AA
1 AA
1809286 AATAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 8 0.31
14 4 0.15
15 14 0.54
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTTATATATTTTT
Found at i:1809291 original size:28 final size:28
Alignment explanation
Indices: 1809233--1809297 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
1809223 AGTGAAGAAA
**
1809233 AATATTTAAATTTTATATTATATAATTT
1 AATATTTAAATTTTATATTATATAAAAT
* *
1809261 AATATTTTAATTTATATATT-TTTAAAAT
1 AATATTTAAATTT-TATATTATATAAAAT
*
1809289 AATAATTAA
1 AATATTTAA
1809298 TAAAAAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AATATTTAAATTTTATATTATATAAAAT
Found at i:1809301 original size:15 final size:15
Alignment explanation
Indices: 1809283--1809315 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1809273 TATATATTTT
*
1809283 TAAAATAATAATTAA
1 TAAAAAAATAATTAA
1809298 TAAAAAAATAATTAA
1 TAAAAAAATAATTAA
1809313 TAA
1 TAA
1809316 TATTAAAAAA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAAAATAATTAA
Found at i:1809340 original size:18 final size:19
Alignment explanation
Indices: 1809284--1809340 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
1809274 ATATATTTTT
1809284 AAAATAA-TAATTAATA-AA
1 AAAATAATTAA-TAATATAA
1809302 AAAATAATTAATAATATTAA
1 AAAATAATTAATAATA-TAA
* *
1809322 AAAATTATTTA-AATATAA
1 AAAATAATTAATAATATAA
1809340 A
1 A
1809341 TAAAATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 16 0.47
19 7 0.21
20 11 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATAATTAATAATATAA
Found at i:1812168 original size:23 final size:22
Alignment explanation
Indices: 1812142--1812185 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1812132 TAATATTACA
1812142 TATATATATTATATAATATAAAT
1 TATATATATTATATAAT-TAAAT
*
1812165 TATATATATTATTTAATTAAA
1 TATATATATTATATAATTAAA
1812186 AAAGAGCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATATATATTATATAATTAAAT
Found at i:1815051 original size:34 final size:34
Alignment explanation
Indices: 1814987--1815169 Score: 269
Period size: 34 Copynumber: 5.4 Consensus size: 34
1814977 CAACTGTTCC
* *
1814987 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1815020 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1815054 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1815088 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1815122 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1815156 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1815170 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 11 0.08
34 123 0.92
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1815162 original size:102 final size:101
Alignment explanation
Indices: 1814987--1815169 Score: 321
Period size: 102 Copynumber: 1.8 Consensus size: 101
1814977 CAACTGTTCC
1814987 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1815052 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1815088 TGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTAC
1815153 CATTGTTGATTAAATGG
65 CATTGTTGATTAAATGG
1815170 TGGTTTTTAC
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 12 0.16
102 65 0.84
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1815530 original size:19 final size:19
Alignment explanation
Indices: 1815474--1815536 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1815464 TGGTTGTCGA
**
1815474 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1815493 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1815512 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1815531 GTTACT
1 GGTACT
1815537 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1819668 original size:34 final size:34
Alignment explanation
Indices: 1819602--1819786 Score: 273
Period size: 34 Copynumber: 5.5 Consensus size: 34
1819592 AAGTGGGAGA
* *
1819602 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1819635 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1819669 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1819703 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1819737 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1819771 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1819787 TGGTTTTTAC
Statistics
Matches: 136, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 13 0.10
34 123 0.90
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1819777 original size:102 final size:101
Alignment explanation
Indices: 1819602--1819786 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
1819592 AAGTGGGAGA
1819602 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1819667 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1819703 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
*
1819768 GCCATTGTTGATTAAATGG
65 ACCATTGTTGATTAAATGG
1819787 TGGTTTTTAC
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 14 0.18
102 65 0.82
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1820459 original size:19 final size:20
Alignment explanation
Indices: 1820435--1820483 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1820425 AAGAATTATA
1820435 ATTTTTTAAAT-TAAAAAAT
1 ATTTTTTAAATGTAAAAAAT
*
1820454 ATTTTTTAAATGTAAATAAT
1 ATTTTTTAAATGTAAAAAAT
1820474 ATTTTTTAAA
1 ATTTTTTAAA
1820484 ATTTATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTTTTTAAATGTAAAAAAT
Found at i:1820559 original size:21 final size:20
Alignment explanation
Indices: 1820522--1820560 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1820512 AATAAATATA
*
1820522 TTTTTTATTTAATTATTTAG
1 TTTTTTATTTAAATATTTAG
1820542 TTTTTTATTTAAAATATTT
1 TTTTTTATTT-AAATATTT
1820561 TTAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTTTATTTAAATATTTAG
Found at i:1820897 original size:16 final size:17
Alignment explanation
Indices: 1820876--1820934 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
1820866 AAATAAAATA
1820876 TATTTTTATAT-AATTT
1 TATTTTTATATCAATTT
* * *
1820892 TATTTTTTTTTCATTTT
1 TATTTTTATATCAATTT
1820909 TCATTTTTA-ATCAATTT
1 T-ATTTTTATATCAATTT
*
1820926 TATTATTAT
1 TATTTTTAT
1820935 TAAATTTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
16 15 0.45
17 12 0.36
18 6 0.18
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTTATATCAATTT
Found at i:1820988 original size:24 final size:23
Alignment explanation
Indices: 1820926--1820990 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
1820916 TAATCAATTT
* *
1820926 TATTATTATTAAATTTAAAAAAA
1 TATTATAAATAAATTTAAAAAAA
* *
1820949 TATTAATTAATTAATTTAACTAAAAA
1 TATT-ATAAATAAATTTAA--AAAAA
1820975 TATT-TAAATAAATTTA
1 TATTATAAATAAATTTA
1820991 TTATTAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 4 0.11
24 22 0.63
26 9 0.26
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATAAATAAATTTAAAAAAA
Found at i:1823633 original size:16 final size:17
Alignment explanation
Indices: 1823612--1823650 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1823602 AGCCATGGGT
1823612 TTTTGTTTTAT-ATTTG
1 TTTTGTTTTATCATTTG
*
1823628 TTTTG-TTTATCATTTT
1 TTTTGTTTTATCATTTG
1823644 TTTTGTT
1 TTTTGTT
1823651 CATCGGTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 14 0.70
17 1 0.05
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.77
Consensus pattern (17 bp):
TTTTGTTTTATCATTTG
Found at i:1824177 original size:13 final size:13
Alignment explanation
Indices: 1824161--1824185 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1824151 AATTAATTAT
1824161 AATAAATATTAAC
1 AATAAATATTAAC
1824174 AATAAATATTAA
1 AATAAATATTAA
1824186 TAATTAAAAA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAAATATTAAC
Found at i:1825466 original size:24 final size:24
Alignment explanation
Indices: 1825438--1825485 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1825428 AAATTTAAAT
1825438 AAAT-ATATAAAATATTATAATTAA
1 AAATAATATAAAATATTA-AATTAA
*
1825462 AAATAATATAAATTATTAAATTAA
1 AAATAATATAAAATATTAAATTAA
1825486 TTCAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATAATATAAAATATTAAATTAA
Found at i:1827636 original size:2 final size:2
Alignment explanation
Indices: 1827629--1827661 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1827619 TGTTGGATGA
1827629 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 A
1827662 AGCATTGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1828770 original size:18 final size:19
Alignment explanation
Indices: 1828747--1828782 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1828737 AATTCGATAG
1828747 AAAATAATTT-ATTTATTT
1 AAAATAATTTAATTTATTT
*
1828765 AAAATATTTTAATTTATT
1 AAAATAATTTAATTTATT
1828783 AAATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAAATAATTTAATTTATTT
Found at i:1828791 original size:23 final size:23
Alignment explanation
Indices: 1828751--1828797 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1828741 CGATAGAAAA
* * *
1828751 TAATTTATTTATTTAAAATATTT
1 TAATTTATTAAATAAAAATATTT
*
1828774 TAATTTATTAAATAAAAATGTTT
1 TAATTTATTAAATAAAAATATTT
1828797 T
1 T
1828798 TGACAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TAATTTATTAAATAAAAATATTT
Found at i:1829433 original size:21 final size:21
Alignment explanation
Indices: 1829408--1829458 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1829398 CTATTTACTC
1829408 AAAATATTTAAAT-TTAATCAT
1 AAAATATTTAAATATTAAT-AT
*
1829429 AAAATATATAAATATTAATAT
1 AAAATATTTAAATATTAATAT
1829450 -AAATATTTA
1 AAAATATTTA
1829459 TTTTATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 8 0.30
21 14 0.52
22 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAATATTTAAATATTAATAT
Found at i:1829737 original size:23 final size:24
Alignment explanation
Indices: 1829711--1829759 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1829701 ATTATTTTTT
1829711 TAAAAAA-TAAA-ATATAAATTAGA
1 TAAAAAATTAAATATATAAA-TAGA
1829734 TAAAAAATTAAATATATAAATAGA
1 TAAAAAATTAAATATATAAATAGA
1829758 TA
1 TA
1829760 TTGAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.29
24 10 0.42
25 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (24 bp):
TAAAAAATTAAATATATAAATAGA
Found at i:1831913 original size:2 final size:2
Alignment explanation
Indices: 1831906--1831930 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1831896 AAAGATAAGG
1831906 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1831931 GGTATTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1832178 original size:27 final size:27
Alignment explanation
Indices: 1832148--1832205 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1832138 ATTTAAGTAT
* * *
1832148 ATTAGTTTTTTTAAAAAAAATTTTATA
1 ATTAATTTTTTAAAAAAAAATTATATA
*
1832175 ATTAATTTTTTAAAAAAAAATTATATC
1 ATTAATTTTTTAAAAAAAAATTATATA
1832202 ATTA
1 ATTA
1832206 TACGATTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTAATTTTTTAAAAAAAAATTATATA
Found at i:1832494 original size:2 final size:2
Alignment explanation
Indices: 1832487--1832518 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1832477 CAATGTGATC
1832487 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
1832519 GGAGACAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1833748 original size:26 final size:26
Alignment explanation
Indices: 1833719--1833773 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
1833709 AAACAAATAT
* *
1833719 AAAT-AATAATCATTAAAGTTTATTTG
1 AAATAAATAAACATTAAAATTTA-TTG
1833745 AAATAAATAAACATTAAAATTTATTG
1 AAATAAATAAACATTAAAATTTATTG
1833771 AAA
1 AAA
1833774 CTTCATCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (26 bp):
AAATAAATAAACATTAAAATTTATTG
Found at i:1835417 original size:2 final size:2
Alignment explanation
Indices: 1835410--1835435 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1835400 GTGCCAATAC
1835410 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
1835436 TACGAGTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1836336 original size:28 final size:29
Alignment explanation
Indices: 1836281--1836338 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1836271 AACTGATCGA
1836281 TCATCACTACGGCTATTCAAACAGTCAGT
1 TCATCACTACGGCTATTCAAACAGTCAGT
* * *
1836310 TCATTACTAGGGCT-TTCAAACGGTCAGT
1 TCATCACTACGGCTATTCAAACAGTCAGT
1836338 T
1 T
1836339 TGGTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (29 bp):
TCATCACTACGGCTATTCAAACAGTCAGT
Found at i:1848330 original size:17 final size:17
Alignment explanation
Indices: 1848296--1848350 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
1848286 ATAAATTATT
1848296 TAAATTTTAAATAAATTTAA
1 TAAA-TTTAAAT--ATTTAA
1848316 TAAATTTAAATATTTAA
1 TAAATTTAAATATTTAA
* *
1848333 AAAATATAAATATTTAA
1 TAAATTTAAATATTTAA
1848350 T
1 T
1848351 TTCTTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 21 0.66
19 7 0.22
20 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATATTTAA
Found at i:1849228 original size:39 final size:36
Alignment explanation
Indices: 1849160--1849236 Score: 84
Period size: 39 Copynumber: 2.0 Consensus size: 36
1849150 ATTTGATTTA
1849160 ATTTAAGTTAAAATATTATTTAATAAATATATAATTTTT
1 ATTTAAGTTAAAATATTATTT-AT-AA-ATATAATTTTT
* *
1849199 ATTTAATTTAAAATATTGATATT-TTAATATAATTTTT
1 ATTTAAGTTAAAATATT-AT-TTATAAATATAATTTTT
1849236 A
1 A
1849237 AAATTTTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
37 12 0.35
38 1 0.03
39 17 0.50
40 2 0.06
41 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (36 bp):
ATTTAAGTTAAAATATTATTTATAAATATAATTTTT
Found at i:1849678 original size:26 final size:26
Alignment explanation
Indices: 1849635--1849685 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
1849625 TACTTAATTT
1849635 TTAAACAAATTTATTATTATTTTAATAA
1 TTAAACAAATTTATTA-T-TTTTAATAA
*
1849663 TTAAA-AATTTTA-TATTTTTAATA
1 TTAAACAAATTTATTATTTTTAATA
1849686 TACATATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 8 0.36
25 1 0.05
26 2 0.09
27 6 0.27
28 5 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAAACAAATTTATTATTTTTAATAA
Found at i:1850813 original size:25 final size:28
Alignment explanation
Indices: 1850748--1850813 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
1850738 TATTAAAAAA
* *
1850748 TTATTTTTATATTAATATTTATATATTT
1 TTATTTTTAAATTAATAATTATATATTT
* *
1850776 TTATAATTAAAATTAA-AATT-TAT-TTT
1 TTAT-TTTTAAATTAATAATTATATATTT
1850802 TTATTTTTAAAT
1 TTATTTTTAAAT
1850814 AACAGTTCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
25 6 0.19
26 7 0.23
27 3 0.10
28 7 0.23
29 8 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TTATTTTTAAATTAATAATTATATATTT
Found at i:1853653 original size:4 final size:4
Alignment explanation
Indices: 1853646--1853682 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
1853636 ATTTTCTCTC
*
1853646 TCTT TCTT TCTT TCTT TCGT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1853683 TGGCTTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:1854725 original size:19 final size:18
Alignment explanation
Indices: 1854666--1854738 Score: 53
Period size: 19 Copynumber: 4.1 Consensus size: 18
1854656 ATTGTAAGAA
1854666 AAATTTAAATT-TTAAGTTT
1 AAATTTAAATTATT-A-TTT
* *
1854685 AAATTTGAATT-TGATTT
1 AAATTTAAATTATTATTT
* * *
1854702 -GATTTGATTTATTTATTT
1 AAATTTAAATTA-TTATTT
1854720 AAATTTAAATTATTATTT
1 AAATTTAAATTATTATTT
1854738 A
1 A
1854739 TTATATTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
16 8 0.19
17 3 0.07
18 13 0.30
19 19 0.44
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (18 bp):
AAATTTAAATTATTATTT
Found at i:1854742 original size:29 final size:28
Alignment explanation
Indices: 1854709--1854776 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
1854699 TTTGATTTGA
* *
1854709 TTTAT-TTATTTAAATTTAAATTATTATT
1 TTTATATTATTAAAATTTAAA-AATTATT
*
1854737 TATTATATTA-AAAAATTTAAAAATTATT
1 T-TTATATTATTAAAATTTAAAAATTATT
1854765 TTTATATTATTA
1 TTTATATTATTA
1854777 TTTATATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 8 0.24
28 9 0.27
29 13 0.39
30 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTATATTATTAAAATTTAAAAATTATT
Found at i:1855434 original size:19 final size:19
Alignment explanation
Indices: 1855412--1855450 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1855402 TAAAACAATT
1855412 AAAACATCACAAAAATATA
1 AAAACATCACAAAAATATA
* *
1855431 AAAATATCTCAAAAATATA
1 AAAACATCACAAAAATATA
1855450 A
1 A
1855451 TATAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAACATCACAAAAATATA
Found at i:1855462 original size:16 final size:16
Alignment explanation
Indices: 1855443--1855547 Score: 51
Period size: 16 Copynumber: 6.6 Consensus size: 16
1855433 AATATCTCAA
*
1855443 AAATATAATATAATAT
1 AAATATAATAAAATAT
* *
1855459 AAAT-TACTAATATATT
1 AAATATAATAAAATA-T
* *
1855475 AAATTTTTTATAAAATAT
1 AAA--TATAATAAAATAT
*
1855493 AAA-ATATTTAAAATAT
1 AAATATA-ATAAAATAT
* *
1855509 AAATTATGATATAATA-
1 AAA-TATAATAAAATAT
1855525 AAATAT-ATAAAATA-
1 AAATATAATAAAATAT
1855539 AAAT-TAATA
1 AAATATAATA
1855548 CATAAATTAT
Statistics
Matches: 68, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
13 1 0.01
14 14 0.21
15 11 0.16
16 22 0.32
17 6 0.09
18 7 0.10
19 7 0.10
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (16 bp):
AAATATAATAAAATAT
Found at i:1855495 original size:7 final size:7
Alignment explanation
Indices: 1855483--1855542 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
1855473 TTAAATTTTT
1855483 TATAAAA
1 TATAAAA
1855490 TATAAAA
1 TATAAAA
1855497 TATTTAAAA
1 TA--TAAAA
*
1855506 TATAAAT
1 TATAAAA
* *
1855513 TATGATA
1 TATAAAA
1855520 TAATAAAA
1 T-ATAAAA
1855528 TATATAAA
1 TATA-AAA
1855536 -ATAAAA
1 TATAAAA
1855542 T
1 T
1855543 TAATACATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
6 3 0.07
7 24 0.57
8 8 0.19
9 7 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (7 bp):
TATAAAA
Found at i:1855540 original size:14 final size:14
Alignment explanation
Indices: 1855491--1855542 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
1855481 TTTATAAAAT
*
1855491 ATAAAATATTTAAA
1 ATAAAATATATAAA
*
1855505 ATATAAATTATGATATA
1 ATA-AAA-TAT-ATAAA
1855522 ATAAAATATATAAA
1 ATAAAATATATAAA
1855536 ATAAAAT
1 ATAAAAT
1855543 TAATACATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 14 0.44
15 6 0.19
16 6 0.19
17 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
ATAAAATATATAAA
Found at i:1855781 original size:2 final size:2
Alignment explanation
Indices: 1855774--1855817 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1855764 TAAGAAGTTC
1855774 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1855816 AG
1 AG
1855818 GGTATATACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1862320 original size:21 final size:20
Alignment explanation
Indices: 1862295--1862335 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1862285 AATAAAATGA
*
1862295 TTAATGAAAATTTCATTTAAT
1 TTAATGAAAATCTC-TTTAAT
*
1862316 TTAATGATAATCTCTTTAAT
1 TTAATGAAAATCTCTTTAAT
1862336 ATAAATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAATGAAAATCTCTTTAAT
Found at i:1862439 original size:18 final size:18
Alignment explanation
Indices: 1862416--1862454 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1862406 AACATTTTTT
1862416 TATTATAGATAT-ATCATA
1 TATTATAGATATGATC-TA
*
1862434 TATTATAGGTATGATCTA
1 TATTATAGATATGATCTA
1862452 TAT
1 TAT
1862455 GATTTAGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (18 bp):
TATTATAGATATGATCTA
Found at i:1862778 original size:2 final size:2
Alignment explanation
Indices: 1862771--1862810 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1862761 TTCCTAGTTA
1862771 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
1862811 GAGAGAGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1871301 original size:267 final size:265
Alignment explanation
Indices: 1870808--1871339 Score: 706
Period size: 267 Copynumber: 2.0 Consensus size: 265
1870798 AACTTTTCTA
* * ** * *
1870808 AAAGCAAAGAACACTTTAAGATGAACATATTCACTTATGTGAGTGTCAGTAATAATCCAAGAATA
1 AAAGCAAAGAACAATTTAACATGAACATATTCACGCATGTAAGCGTCAGTAATAATCCAAGAATA
* * * * *
1870873 ACCAACAAATATGCATCATACACCAAGCAAGACGTCTTATATTTGAGCATGTGCAAATCACTGAT
66 ACCAACAAATATGCAACACACACCAAGCAAGACATCTTAAACTTGAGCATGTGCAAATCACTGAT
* * *
1870938 ATATATTAACCTTTTCTGATGATAAACCTGGTCCTAACTCTAGTCCTGAATTAGCATCAAACTTT
131 ATATATTAACATTTTCTGATGATAAACCTGGACCTAACTCTAGTCCTGAAATAGCATCAAACTTT
* * * *
1871003 GATGAAAATATAAGACACCAAAGAAAATCTTTAGATGTTTCCCTCTGGAAGAAAATTAAATTCAT
196 GATGAAAATATAAGACACCAAAGAAAATCTTTAGAAGTTTCCATCTGCAAAAAAATTAAATTCAT
1871068 ACTTT
261 ACTTT
** *
1871073 AAAGCATAA-AACAATTTAACATGAACATATTCACGCATGTAAGCGTTTGTCATAATCCAAGAAT
1 AAAGCA-AAGAACAATTTAACATGAACATATTCACGCATGTAAGCGTCAGTAATAATCCAAGAAT
* * * * *
1871137 GACCAACAGATATGCAACACACATCAAGCAAGACATCTTAAACTTGAGCGTGTGCCAATCACTGC
65 AACCAACAAATATGCAACACACACCAAGCAAGACATCTTAAACTTGAGCATGTGCAAATCACTG-
* * * * **
1871202 AATATATATTAAGATTTTCTGATGATAAACCTGGACCTAATTCTGGTCTTGAAATAGCATCCTAC
129 -ATATATATTAACATTTTCTGATGATAAACCTGGACCTAACTCTAGTCCTGAAATAGCATCAAAC
* * * *
1871267 TTTGATGAAAATGTAAGACACTAACGAAAATCTTTGGAAGTTTCCATCTGCAAAAAAATTAAATT
193 TTTGATGAAAATATAAGACACCAAAGAAAATCTTTAGAAGTTTCCATCTGCAAAAAAATTAAATT
1871332 CATACTTT
258 CATACTTT
1871340 TCTATCCGCT
Statistics
Matches: 228, Mismatches: 36, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
265 106 0.46
266 2 0.01
267 120 0.53
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (265 bp):
AAAGCAAAGAACAATTTAACATGAACATATTCACGCATGTAAGCGTCAGTAATAATCCAAGAATA
ACCAACAAATATGCAACACACACCAAGCAAGACATCTTAAACTTGAGCATGTGCAAATCACTGAT
ATATATTAACATTTTCTGATGATAAACCTGGACCTAACTCTAGTCCTGAAATAGCATCAAACTTT
GATGAAAATATAAGACACCAAAGAAAATCTTTAGAAGTTTCCATCTGCAAAAAAATTAAATTCAT
ACTTT
Found at i:1874012 original size:12 final size:12
Alignment explanation
Indices: 1873997--1874021 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1873987 ATATATATAT
1873997 AAAGAGAGAGAG
1 AAAGAGAGAGAG
1874009 AAAGAGAGAGAG
1 AAAGAGAGAGAG
1874021 A
1 A
1874022 GAGATTTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
AAAGAGAGAGAG
Found at i:1875612 original size:6 final size:6
Alignment explanation
Indices: 1875601--1875626 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1875591 TATATTAGGG
1875601 TTATGA TTATGA TTATGA TTATGA TT
1 TTATGA TTATGA TTATGA TTATGA TT
1875627 TAAAAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (6 bp):
TTATGA
Done.