Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 21 of 100
Found at i:4049375 original size:18 final size:17
Alignment explanation
Indices: 4049305--4049393 Score: 72
Period size: 17 Copynumber: 4.9 Consensus size: 17
4049295 GGATTTTATT
* *
4049305 TAAAGAAAATAAAATAA
1 TAAAAAAAATAAAAAAA
4049322 TAAAACAAAATAAAAGAGAAAA
1 TAAAA-AAAAT--AA-A-AAAA
*
4049344 TAAAAAAATTAAAAAAA
1 TAAAAAAAATAAAAAAA
*
4049361 TAAAGAAAATAAAAACAA
1 TAAAAAAAATAAAAA-AA
4049379 -AAATAAAAATAAAAA
1 TAAA-AAAAATAAAAA
4049394 TAAAGATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
17 24 0.41
18 18 0.31
19 2 0.03
20 2 0.03
21 5 0.08
22 8 0.14
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (17 bp):
TAAAAAAAATAAAAAAA
Found at i:4049402 original size:18 final size:18
Alignment explanation
Indices: 4049366--4049405 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
4049356 AAAAATAAAG
4049366 AAAATAAAAACAAAAATA
1 AAAATAAAAACAAAAATA
* *
4049384 AAAATAAAAATAAAGATA
1 AAAATAAAAACAAAAATA
4049402 AAAA
1 AAAA
4049406 AATATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (18 bp):
AAAATAAAAACAAAAATA
Found at i:4050343 original size:12 final size:12
Alignment explanation
Indices: 4050326--4050365 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
4050316 TAAATAAAAA
4050326 AAATTAACAGAT
1 AAATTAACAGAT
4050338 AAATTAA-A-ATT
1 AAATTAACAGA-T
4050349 AAA-TAACAGAT
1 AAATTAACAGAT
4050360 AAATTA
1 AAATTA
4050366 TAACATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (12 bp):
AAATTAACAGAT
Found at i:4050364 original size:22 final size:22
Alignment explanation
Indices: 4050303--4050365 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
4050293 AATATTAATG
*
4050303 AAAATAAATCAGATAAA-TAAAA
1 AAAATTAA-CAGATAAATTAAAA
4050325 AAAATTAACAGATAAATTAAAA
1 AAAATTAACAGATAAATTAAAA
*
4050347 TTAAA-TAACAGATAAATTA
1 -AAAATTAACAGATAAATTA
4050366 TAACATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.22
22 26 0.70
23 3 0.08
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (22 bp):
AAAATTAACAGATAAATTAAAA
Found at i:4050479 original size:6 final size:6
Alignment explanation
Indices: 4050468--4050564 Score: 56
Period size: 6 Copynumber: 16.2 Consensus size: 6
4050458 AATACATAAG
* * * * * * *
4050468 ATAAAA AT-AAA AGAAAA ATATAT ATAAAA ACAATA ATAATA ATAATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
* * *
4050515 ATAATA ATGAAA AT-AAA ATAAAA ATGTAAA ATACAAA A-ATAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA AT-AAAA ATA-AAA ATA-AAA ATAAAA
4050564 A
1 A
4050565 AAATAGACTT
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
5 9 0.12
6 53 0.74
7 10 0.14
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (6 bp):
ATAAAA
Found at i:4050507 original size:3 final size:3
Alignment explanation
Indices: 4050499--4050535 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
4050489 ATATAAAAAC
4050499 AAT AAT AAT AAT AAT AAT AAT AAT GAA- AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
4050536 AAATGTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 25 0.81
4 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:4050546 original size:13 final size:12
Alignment explanation
Indices: 4050470--4050565 Score: 61
Period size: 13 Copynumber: 7.4 Consensus size: 12
4050460 TACATAAGAT
*
4050470 AAAAATAAAAGA
1 AAAAATAAAATA
4050482 AAAATATATATAA-A
1 AAAA-ATA-A-AATA
*
4050496 AACAATAATAATA
1 AAAAATAA-AATA
4050509 ATAATAATAATAAT-
1 A-AA-AATAA-AATA
*
4050523 GAAAATAAAATA
1 AAAAATAAAATA
*
4050535 AAAATGTAAAATA
1 AAAA-ATAAAATA
4050548 CAAAAATAAAATA
1 -AAAAATAAAATA
4050561 AAAAA
1 AAAAA
4050566 AATAGACTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
11 3 0.04
12 21 0.30
13 24 0.35
14 10 0.14
15 11 0.16
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:4050901 original size:1 final size:1
Alignment explanation
Indices: 4050897--4050956 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
4050887 ATTTTTTTAC
* * * * * * *
4050897 TTTTTTTGTTTTTTTTTGTTTTGTTGTTTTTTTTTTTTGTTTTCTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4050957 AATTTGATCA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (1 bp):
T
Found at i:4050911 original size:18 final size:18
Alignment explanation
Indices: 4050888--4050930 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4050878 ACAGAAGCAA
*
4050888 TTTTTTTACTTTTTTTGT
1 TTTTTTTACTTTTGTTGT
**
4050906 TTTTTTTTGTTTTGTTGT
1 TTTTTTTACTTTTGTTGT
4050924 TTTTTTT
1 TTTTTTT
4050931 TTTTGTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.86
Consensus pattern (18 bp):
TTTTTTTACTTTTGTTGT
Found at i:4050926 original size:25 final size:22
Alignment explanation
Indices: 4050891--4050956 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
4050881 GAAGCAATTT
*
4050891 TTTTACTTTTTTTGTTTTTTTTTG
1 TTTT-CTTTGTTT-TTTTTTTTTG
*
4050915 TTTT-GTTGTTTTTTTTTTTTG
1 TTTTCTTTGTTTTTTTTTTTTG
4050936 TTTTCTTTGTTTTTTTTTTTT
1 TTTTCTTTGTTTTTTTTTTTT
4050957 AATTTGATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 14 0.37
22 20 0.53
24 4 0.11
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.86
Consensus pattern (22 bp):
TTTTCTTTGTTTTTTTTTTTTG
Found at i:4050930 original size:22 final size:23
Alignment explanation
Indices: 4050900--4050956 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 23
4050890 TTTTTACTTT
4050900 TTTTGTTTTTTTTTGTTTT-GTTG
1 TTTT-TTTTTTTTTGTTTTCGTTG
*
4050923 -TTTTTTTTTTTTGTTTTCTTTG
1 TTTTTTTTTTTTTGTTTTCGTTG
4050945 TTTTTTTTTTTT
1 TTTTTTTTTTTT
4050957 AATTTGATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 14 0.45
22 6 0.19
23 11 0.35
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (23 bp):
TTTTTTTTTTTTTGTTTTCGTTG
Found at i:4051027 original size:41 final size:41
Alignment explanation
Indices: 4050966--4051133 Score: 207
Period size: 41 Copynumber: 4.1 Consensus size: 41
4050956 TAATTTGATC
* * * *
4050966 AATGCTCCTCTAAGCAGAGGCTCAACAACTTTGGAAAA-TA
1 AATGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTA
* * *
4051006 AATGACTCCTCTAACCAGAGGCACTATGACTTT-GAAAAGTA
1 AATG-CTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTA
*
4051047 AATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTA
1 AA-TGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTA
4051089 AATTGCTCCTCTAAACAGAGGCACCACGACTTTTGG-AAAGTA
1 AA-TGCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAAGTA
4051131 AAT
1 AAT
4051134 TACTCCTTAA
Statistics
Matches: 114, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
40 9 0.08
41 53 0.46
42 48 0.42
43 4 0.04
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (41 bp):
AATGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTA
Found at i:4051095 original size:42 final size:42
Alignment explanation
Indices: 4050968--4051140 Score: 226
Period size: 42 Copynumber: 4.2 Consensus size: 42
4050958 ATTTGATCAA
* * * * *
4050968 TGCTCCTCTAAGCAGAGGCTCAACAACTTTGGAAAA-TAAA-
1 TGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAAT
* * *
4051008 TGACTCCTCTAACCAGAGGCACTATGAC-TTTGAAAAGTAAAT
1 TG-CTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAAT
4051050 TGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAAT
1 TGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAAT
*
4051092 TGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAGTAAAT
1 TGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAAT
*
4051134 TACTCCT
1 TGCTCCT
4051141 TAACAATCAT
Statistics
Matches: 118, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
40 9 0.08
41 46 0.39
42 63 0.53
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (42 bp):
TGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAAT
Found at i:4052160 original size:23 final size:21
Alignment explanation
Indices: 4052129--4052194 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 21
4052119 TCGCCTTGAG
*
4052129 TCTTCTTTTTTTATTCACTTTTT
1 TCTTTTTTTTTTATT-A-TTTTT
4052152 TCTTTTTTTCACTTT-TTATTTTT
1 TCTTTTTTT---TTTATTATTTTT
4052175 TCTTTTTTTTCTTATT-TTTT
1 TCTTTTTTTT-TTATTATTTT
4052195 AAGCATAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
20 1 0.03
21 6 0.16
22 2 0.05
23 22 0.59
24 1 0.03
25 2 0.05
26 3 0.08
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.79
Consensus pattern (21 bp):
TCTTTTTTTTTTATTATTTTT
Found at i:4052174 original size:17 final size:17
Alignment explanation
Indices: 4052134--4052175 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
4052124 TTGAGTCTTC
4052134 TTTTTTTATTCACTTTT
1 TTTTTTTATTCACTTTT
4052151 TTCTTTTT-TTCACTTTT
1 TT-TTTTTATTCACTTTT
4052168 TATTTTTT
1 T-TTTTTT
4052176 CTTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTTATTCACTTTT
Found at i:4062797 original size:57 final size:58
Alignment explanation
Indices: 4062545--4062815 Score: 273
Period size: 57 Copynumber: 4.7 Consensus size: 58
4062535 TTTGTGCAGA
* * * * * * **
4062545 AAAAATTGATACTTTCAAC-TTTTCCCCAAAATATTTTTTAAAAATTTTAATCTCGAG
1 AAAAATTGATACTTTCAACTTTTTCCCAAAAATTTTTTTTGAAAAGTTTATTTTTAAG
* * * *** *
4062602 AAAAATTAATACTTTTAAC-TTTTCCTTAAAAACCGTTTTAG-AAA-TTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCC-CAAAAATTTTTTTTGAAAAGTTTATTTTTAAG
* * * **
4062658 GAAAATTGATACTTTCAACTTTTCCCCAAAAATATATTTAGGAAAAGTTTATTTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCCCAAAAAT-TTTTTTTGAAAAGTTTA-TTTTTAAG
*
4062718 AAAAATTGATACTTTCAACTTTTTCTCAAAAATTTTTTTTGAAAA-TTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCCCAAAAATTTTTTTTGAAAAGTTTATTTTTAAG
*
4062775 AAAAATTGATACTTTCAGCTTTTTCCCAAAAATATTTTTTT
1 AAAAATTGATACTTTCAACTTTTTCCCAAAAAT-TTTTTTT
4062816 TGGATTTTAT
Statistics
Matches: 176, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
56 29 0.16
57 74 0.42
58 22 0.12
59 13 0.07
60 38 0.22
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (58 bp):
AAAAATTGATACTTTCAACTTTTTCCCAAAAATTTTTTTTGAAAAGTTTATTTTTAAG
Found at i:4062865 original size:30 final size:28
Alignment explanation
Indices: 4062830--4062918 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 28
4062820 TTTTATTTAA
4062830 AGAAAATAAAATAATAAAACAAAATAAAAG
1 AGAAAATAAAA-AATAAAA-AAAATAAAAG
* *
4062860 AGAAAATAAAAAAATAAAGAAAAGTAAAAC
1 AGAAAAT-AAAAAATAAA-AAAAATAAAAG
4062890 A-AAAAT-AAAAATAAAATAAAGATAAAAG
1 AGAAAATAAAAAATAAAA-AAA-ATAAAAG
4062918 A
1 A
4062919 ATATTTAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
26 1 0.02
27 12 0.24
28 6 0.12
29 5 0.10
30 22 0.43
31 5 0.10
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (28 bp):
AGAAAATAAAAAATAAAAAAAATAAAAG
Found at i:4062880 original size:17 final size:17
Alignment explanation
Indices: 4062827--4062905 Score: 53
Period size: 17 Copynumber: 4.8 Consensus size: 17
4062817 GGATTTTATT
*
4062827 TAAAGAAAATAAAATAA
1 TAAAGAAAATAAAAAAA
* *
4062844 T-AA-AACA-AAATAAA
1 TAAAGAAAATAAAAAAA
*
4062858 -AGAGAAAATAAAAAAA
1 TAAAGAAAATAAAAAAA
4062874 TAAAGAAAAGTAAAACAAA
1 TAAAGAAAA-TAAAA-AAA
4062893 -AATA-AAAATAAAA
1 TAA-AGAAAATAAAA
4062906 TAAAGATAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
14 6 0.12
15 6 0.12
16 8 0.17
17 13 0.27
18 11 0.23
19 4 0.08
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.13
Consensus pattern (17 bp):
TAAAGAAAATAAAAAAA
Found at i:4062914 original size:17 final size:17
Alignment explanation
Indices: 4062870--4062916 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
4062860 AGAAAATAAA
*
4062870 AAAATAAAG--AAAAGT
1 AAAATAAAGATAAAAAT
* *
4062885 AAAACAAAAATAAAAAT
1 AAAATAAAGATAAAAAT
4062902 AAAATAAAGATAAAA
1 AAAATAAAGATAAAA
4062917 GAATATTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 7 0.28
17 18 0.72
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (17 bp):
AAAATAAAGATAAAAAT
Found at i:4063497 original size:16 final size:17
Alignment explanation
Indices: 4063443--4063494 Score: 97
Period size: 17 Copynumber: 3.1 Consensus size: 17
4063433 AATTTTTTAG
4063443 AAATTTC-CAGAAAAAA
1 AAATTTCACAGAAAAAA
4063459 AAATTTCACAGAAAAAA
1 AAATTTCACAGAAAAAA
4063476 AAATTTCACAGAAAAAA
1 AAATTTCACAGAAAAAA
4063493 AA
1 AA
4063495 TTTTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 7 0.20
17 28 0.80
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.17
Consensus pattern (17 bp):
AAATTTCACAGAAAAAA
Found at i:4071872 original size:16 final size:16
Alignment explanation
Indices: 4071835--4071865 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4071825 TTGATTTGTC
*
4071835 AATTTTTAAAAATTAA
1 AATTTTTAAAATTTAA
4071851 AATTTTTAAAATTTA
1 AATTTTTAAAATTTA
4071866 TGATTTTAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTTTAAAATTTAA
Found at i:4079263 original size:16 final size:16
Alignment explanation
Indices: 4079244--4079276 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4079234 GTTTAATTTA
4079244 TTTATCTTTT-ATCATT
1 TTTAT-TTTTAATCATT
4079260 TTTATTTTTAATCATT
1 TTTATTTTTAATCATT
4079276 T
1 T
4079277 AGAATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTTTTAATCATT
Found at i:4079668 original size:101 final size:98
Alignment explanation
Indices: 4079553--4079742 Score: 227
Period size: 98 Copynumber: 1.9 Consensus size: 98
4079543 AGATTTAGAG
* * * * *
4079553 TTGTGTAGTCTCAAATTTAAATAGATCTAATATTTATAAAATAATGTAAGTAAATAATTTGATTT
1 TTGTGTAATCTCAAATCTAAATAGATCCAA-A-AT-TAAAATAATGTAAGCAAATAATTTGATTT
* *
4079618 AGAGTTTGTAAAATTTTTGAATAAATAGATCTTGAT
63 AGAATTTATAAAATTTTTGAATAAATAGATCTTGAT
* * * * * *
4079654 TTGTGTAATTTCAAATCTAGATAGATCCAAAATTCAAGTAATGTAGGCAAATGATTTGATTTAGA
1 TTGTGTAATCTCAAATCTAAATAGATCCAAAATTAAAATAATGTAAGCAAATAATTTGATTTAGA
*
4079719 ATTTATAAAATTTTTTAATAAATA
66 ATTTATAAAATTTTTGAATAAATA
4079743 AATTTAAAAT
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
98 48 0.64
99 1 0.01
100 1 0.01
101 25 0.33
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (98 bp):
TTGTGTAATCTCAAATCTAAATAGATCCAAAATTAAAATAATGTAAGCAAATAATTTGATTTAGA
ATTTATAAAATTTTTGAATAAATAGATCTTGAT
Found at i:4082013 original size:30 final size:30
Alignment explanation
Indices: 4081977--4082035 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
4081967 CTTTTAAAAC
*
4081977 ATGATATTTAATAAATTTAGAGTAAAAATT
1 ATGATATTTAATAAATTTAAAGTAAAAATT
*
4082007 ATGATATTTAATAAATTTAAAGTATAAAT
1 ATGATATTTAATAAATTTAAAGTAAAAAT
4082036 CTTAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (30 bp):
ATGATATTTAATAAATTTAAAGTAAAAATT
Found at i:4082044 original size:30 final size:30
Alignment explanation
Indices: 4081980--4082046 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
4081970 TTAAAACATG
* *
4081980 ATATTTAATAAATTTAGAGTAAAAATTATG
1 ATATTTAATAAATTTAAAGTAAAAATTATA
*
4082010 ATATTTAATAAATTTAAAGTATAAATCT-TA
1 ATATTTAATAAATTTAAAGTAAAAAT-TATA
4082040 ATATTTA
1 ATATTTA
4082047 TAATTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.43
Consensus pattern (30 bp):
ATATTTAATAAATTTAAAGTAAAAATTATA
Found at i:4088480 original size:164 final size:164
Alignment explanation
Indices: 4088209--4088535 Score: 566
Period size: 164 Copynumber: 2.0 Consensus size: 164
4088199 GCCCGGTACT
* **
4088209 TAGCTCATTAATTCATGTAGCTTAATATCTAGTAGGTTTGAAATTCACATCTCAATACGTATAAT
1 TAGCTCATTAATTCATGTAACTTAATATCTAGTAAATTTGAAATTCACATCTCAATACGTATAAT
*
4088274 CTTTTCTCTTATCCCAAATTGCAGCCACTTATGCAAAAGAAATGGCTAGGCTAAGTTCCAAGTTT
66 CTTTTCTCTTATCCCAAATTGCAGCCACTTATGCAAAAGAAATGGCTAGGCTAAGTTACAAGTTT
4088339 GCAAAATTTCAAGAAAATGGTTTGTTATGGTTCA
131 GCAAAATTTCAAGAAAATGGTTTGTTATGGTTCA
*
4088373 TAGCTCATTAATTCATGTAACTTAATATCTAGTAAATTTGAAATTCACATTTCAATACGTATAAT
1 TAGCTCATTAATTCATGTAACTTAATATCTAGTAAATTTGAAATTCACATCTCAATACGTATAAT
* *
4088438 CTTTTCTCTTATCCC-AATCTGCGGCCACTTATGTAAAAGAAATGGCTAGGCTAAGTTACAAGTT
66 CTTTTCTCTTATCCCAAAT-TGCAGCCACTTATGCAAAAGAAATGGCTAGGCTAAGTTACAAGTT
*
4088502 TGCAAAGTTTCAAGAAAATGGTTTGTTATGGTTC
130 TGCAAAATTTCAAGAAAATGGTTTGTTATGGTTC
4088536 GTAATTCTTA
Statistics
Matches: 154, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
163 3 0.02
164 151 0.98
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (164 bp):
TAGCTCATTAATTCATGTAACTTAATATCTAGTAAATTTGAAATTCACATCTCAATACGTATAAT
CTTTTCTCTTATCCCAAATTGCAGCCACTTATGCAAAAGAAATGGCTAGGCTAAGTTACAAGTTT
GCAAAATTTCAAGAAAATGGTTTGTTATGGTTCA
Found at i:4095115 original size:20 final size:20
Alignment explanation
Indices: 4095090--4095145 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
4095080 TGTAAGAATG
*
4095090 TCATGCAAATATATTAATTA
1 TCATGCAAATATATTAAATA
*
4095110 TCATGCAACA-ATATAAAATA
1 TCATGCAA-ATATATTAAATA
*
4095130 GCATGCAAATATATTA
1 TCATGCAAATATATTA
4095146 GTAGCCATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.32
Consensus pattern (20 bp):
TCATGCAAATATATTAAATA
Found at i:4095465 original size:40 final size:41
Alignment explanation
Indices: 4095404--4095503 Score: 150
Period size: 40 Copynumber: 2.5 Consensus size: 41
4095394 ATGCTAAGAG
*
4095404 ACATGAAATTAAATATATAATCACACAATTAA-AATGTAA-
1 ACATGCAATTAAATATATAATCACACAATTAACAATGTAAT
**
4095443 AGCATGCAATTAAATATATAATCATGCAATTAACAATGTAAT
1 A-CATGCAATTAAATATATAATCACACAATTAACAATGTAAT
4095485 ACATGCAATTAAATATATA
1 ACATGCAATTAAATATATA
4095504 TTCATAATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
39 1 0.02
40 28 0.51
41 25 0.45
42 1 0.02
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (41 bp):
ACATGCAATTAAATATATAATCACACAATTAACAATGTAAT
Found at i:4095493 original size:41 final size:39
Alignment explanation
Indices: 4095404--4095509 Score: 149
Period size: 41 Copynumber: 2.6 Consensus size: 39
4095394 ATGCTAAGAG
* *
4095404 ACATGAAATTAAATATATAATCACACAATTAAAATGTAA
1 ACATGCAATTAAATATATAATCATACAATTAAAATGTAA
*
4095443 AGCATGCAATTAAATATATAATCATGCAATTAACAATGTAA
1 A-CATGCAATTAAATATATAATCATACAATTAA-AATGTAA
*
4095484 TACATGCAATTAAATATATATTCATA
1 -ACATGCAATTAAATATATAATCATA
4095510 ATAATAATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
39 1 0.02
40 28 0.47
41 29 0.49
42 1 0.02
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (39 bp):
ACATGCAATTAAATATATAATCATACAATTAAAATGTAA
Found at i:4095581 original size:19 final size:20
Alignment explanation
Indices: 4095405--4095664 Score: 129
Period size: 20 Copynumber: 13.4 Consensus size: 20
4095395 TGCTAAGAGA
* *
4095405 CATGAAATTAAATATATAAT
1 CATGCAATTAAATATAAAAT
** * *
4095425 CACACAATTAAA-ATGTAAAG
1 CATGCAATTAAATAT-AAAAT
*
4095445 CATGCAATTAAATATATAAT
1 CATGCAATTAAATATAAAAT
**
4095465 CATGCAATTAACA-ATGTAAT
1 CATGCAATTAA-ATATAAAAT
* *
4095485 ACATGCAATTAAATATATATT
1 -CATGCAATTAAATATAAAAT
*
4095506 CAT--AA-T-AATAATATAA-
1 CATGCAATTAAAT-ATAAAAT
*
4095522 -A-GC-ATGAAA-AT-AAA-
1 CATGCAATTAAATATAAAAT
* *
4095536 CATGAAATTAAATATATAAT
1 CATGCAATTAAATATAAAAT
*
4095556 TATGCAATTAAAT-TAAAAT
1 CATGCAATTAAATATAAAAT
* *
4095575 CATGCAAATAAAATATATAA-
1 CATGC-AATTAAATATAAAAT
**
4095595 CATGCAATTAAATATATGAT
1 CATGCAATTAAATATAAAAT
* *
4095615 CATGCAAATAACAATATATAAAA
1 CATGC-AATTA-AATATA-AAAT
*
4095638 CATGCAATTGAAT-TAAAAT
1 CATGCAATTAAATATAAAAT
4095657 CATGCAAT
1 CATGCAAT
4095665 ATATTATAAT
Statistics
Matches: 183, Mismatches: 35, Indels: 45
0.70 0.13 0.17
Matches are distributed among these distances:
14 2 0.01
15 5 0.03
16 4 0.02
17 13 0.07
18 4 0.02
19 36 0.20
20 74 0.40
21 30 0.16
22 9 0.05
23 6 0.03
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (20 bp):
CATGCAATTAAATATAAAAT
Found at i:4095709 original size:42 final size:46
Alignment explanation
Indices: 4095658--4095741 Score: 115
Period size: 43 Copynumber: 1.9 Consensus size: 46
4095648 AATTAAAATC
*
4095658 ATGCAATAT-ATTATAATTAAA-TCTTGC-AAA-AAAAAAAAACTAA
1 ATGCAATATAATTA-AATTAAATTCATGCTAAAGAAAAAAAAACTAA
4095701 ATGC-ATATAATTAAATTAAATTCATGCTAAAGAAAAAAAAA
1 ATGCAATATAATTAAATTAAATTCATGCTAAAGAAAAAAAAA
4095742 TGTCATGTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
42 11 0.31
43 13 0.36
44 3 0.08
45 9 0.25
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.27
Consensus pattern (46 bp):
ATGCAATATAATTAAATTAAATTCATGCTAAAGAAAAAAAAACTAA
Found at i:4096591 original size:6 final size:6
Alignment explanation
Indices: 4096575--4096641 Score: 57
Period size: 6 Copynumber: 11.5 Consensus size: 6
4096565 ACAAACTAAC
* * * * *
4096575 TAAAA- TAAAAT TAAAAT CAAAA- TCAAAC TAAAAT CAAAAC TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
* *
4096621 TAAAGT TAAAAT CAAAAT TAA
1 TAAAAT TAAAAT TAAAAT TAA
4096642 GATAAGATTT
Statistics
Matches: 47, Mismatches: 13, Indels: 3
0.75 0.21 0.05
Matches are distributed among these distances:
5 8 0.17
6 39 0.83
ACGTcount: A:0.66, C:0.09, G:0.01, T:0.24
Consensus pattern (6 bp):
TAAAAT
Found at i:4096606 original size:17 final size:17
Alignment explanation
Indices: 4096576--4096641 Score: 78
Period size: 18 Copynumber: 3.8 Consensus size: 17
4096566 CAAACTAACT
4096576 AAAATAAAATTAAAATC
1 AAAATAAAATTAAAATC
* *
4096593 AAAATCAAACTAAAATC
1 AAAATAAAATTAAAATC
* *
4096610 AAAACTAAAATTAAAGTT
1 AAAA-TAAAATTAAAATC
4096628 AAAATCAAAATTAA
1 AAAAT-AAAATTAA
4096642 GATAAGATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
17 20 0.49
18 21 0.51
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.23
Consensus pattern (17 bp):
AAAATAAAATTAAAATC
Found at i:4096641 original size:12 final size:12
Alignment explanation
Indices: 4096576--4096641 Score: 64
Period size: 12 Copynumber: 5.7 Consensus size: 12
4096566 CAAACTAACT
*
4096576 AAAA-TAAAATT
1 AAAATTAAAATC
*
4096587 AAAATCAAAATC
1 AAAATTAAAATC
*
4096599 -AAACTAAAATC
1 AAAATTAAAATC
* *
4096610 AAAACTAAAATT
1 AAAATTAAAATC
*
4096622 AAAGTTAAAATC
1 AAAATTAAAATC
4096634 AAAATTAA
1 AAAATTAA
4096642 GATAAGATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
11 13 0.30
12 31 0.70
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.23
Consensus pattern (12 bp):
AAAATTAAAATC
Found at i:4097370 original size:7 final size:7
Alignment explanation
Indices: 4097358--4097382 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4097348 AAAATCAAAT
4097358 TTTTATA
1 TTTTATA
4097365 TTTTATA
1 TTTTATA
4097372 TTTTATA
1 TTTTATA
4097379 TTTT
1 TTTT
4097383 CGTATCGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:4099178 original size:62 final size:63
Alignment explanation
Indices: 4099102--4099227 Score: 200
Period size: 62 Copynumber: 2.0 Consensus size: 63
4099092 GAAATAATTC
* * *
4099102 TCAAAATACTCCAATACGTTGGTAATATTAGAAGAACTCTTTTTCACCTAGAGA-TTCTTAGG
1 TCAAAATACTCCAATACGTTGGTAATATCAGAAGAACTCTTTCTCACCTAAAGATTTCTTAGG
* *
4099164 TCAAAATACTCCAATTCGTTGGTAATATCAGAAGAACTCTTTCTCACTTAAAGATTTCTTAGG
1 TCAAAATACTCCAATACGTTGGTAATATCAGAAGAACTCTTTCTCACCTAAAGATTTCTTAGG
4099227 T
1 T
4099228 ATTGTTTCTC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
62 49 0.84
63 9 0.16
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.35
Consensus pattern (63 bp):
TCAAAATACTCCAATACGTTGGTAATATCAGAAGAACTCTTTCTCACCTAAAGATTTCTTAGG
Found at i:4099781 original size:10 final size:10
Alignment explanation
Indices: 4099756--4099790 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
4099746 AAAAATTTAT
*
4099756 TTTTTTCTTA
1 TTTTTTATTA
4099766 TCTTTTTATTA
1 T-TTTTTATTA
4099777 TTTTTTATTA
1 TTTTTTATTA
4099787 TTTT
1 TTTT
4099791 AGAAGATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:4100053 original size:31 final size:31
Alignment explanation
Indices: 4099992--4100063 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
4099982 GGTCAAGGCA
* **
4099992 CGATTCGGTTTGACAGTTCAGTCGGGTTCAG
1 CGATTCGGTTTGACAGTTCAATCGCATTCAG
* *
4100023 CGATTCTGTTTGGCAGTTCAATCGCATTCAG
1 CGATTCGGTTTGACAGTTCAATCGCATTCAG
* *
4100054 TGGTTCGGTT
1 CGATTCGGTT
4100064 GCAGTCCGGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.15, C:0.19, G:0.29, T:0.36
Consensus pattern (31 bp):
CGATTCGGTTTGACAGTTCAATCGCATTCAG
Found at i:4101583 original size:16 final size:16
Alignment explanation
Indices: 4101564--4101618 Score: 74
Period size: 17 Copynumber: 3.3 Consensus size: 16
4101554 TCTTTTTTTT
4101564 TTTTTTGTATTTTGTA
1 TTTTTTGTATTTTGTA
*
4101580 TTTTTTTGATATTTTATA
1 -TTTTTTG-TATTTTGTA
*
4101598 TTTTTTGTATTATGTA
1 TTTTTTGTATTTTGTA
4101614 TTTTT
1 TTTTT
4101619 GTTAAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 12 0.35
17 14 0.41
18 8 0.24
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.75
Consensus pattern (16 bp):
TTTTTTGTATTTTGTA
Found at i:4101628 original size:34 final size:33
Alignment explanation
Indices: 4101558--4101640 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 33
4101548 CCATCCTCTT
* * *
4101558 TTTTTTTTTTTTGTATTTTGTATTTTTTTGATA
1 TTTTTATTTTTTGTATTATGTATTTTTTTGAAA
4101591 TTTTATATTTTTTGTATTATGTATTTTTGTT-AAA
1 TTTT-TATTTTTTGTATTATGTATTTTT-TTGAAA
*
4101625 TTTTTA-TTATTGTATT
1 TTTTTATTTTTTGTATT
4101641 TAATAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
32 9 0.20
33 6 0.14
34 27 0.61
35 2 0.05
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.73
Consensus pattern (33 bp):
TTTTTATTTTTTGTATTATGTATTTTTTTGAAA
Found at i:4110067 original size:4 final size:4
Alignment explanation
Indices: 4110048--4110114 Score: 59
Period size: 4 Copynumber: 16.2 Consensus size: 4
4110038 GTACCAAAGT
*
4110048 TTTA TTTTA TTTTA TTTA TTTA -TT- TTTA CTTA TTTA TTCTA TTTA TTTA
1 TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA
4110097 TTT- TGCTTA TTTA TTTA T
1 TTTA T--TTA TTTA TTTA T
4110115 AGGTTAAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
3 5 0.09
4 33 0.61
5 15 0.28
6 1 0.02
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:4110067 original size:9 final size:9
Alignment explanation
Indices: 4110048--4110114 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
4110038 GTACCAAAGT
4110048 TTTATTTTA
1 TTTATTTTA
4110057 TTT-TATTTA
1 TTTAT-TTTA
4110066 TTTATTTTTA
1 TTTA-TTTTA
*
4110076 CTTA-TTTA
1 TTTATTTTA
4110084 TTCTA-TTTA
1 TT-TATTTTA
*
4110093 TTTATTTTG
1 TTTATTTTA
*
4110102 CTTA-TTTA
1 TTTATTTTA
4110110 TTTAT
1 TTTAT
4110115 AGGTTAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
8 14 0.30
9 24 0.52
10 7 0.15
11 1 0.02
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.73
Consensus pattern (9 bp):
TTTATTTTA
Found at i:4110071 original size:13 final size:13
Alignment explanation
Indices: 4110048--4110112 Score: 76
Period size: 13 Copynumber: 4.8 Consensus size: 13
4110038 GTACCAAAGT
4110048 TTTATTTTATTTTA
1 TTTA-TTTATTTTA
4110062 TTTATTTATTTTTA
1 TTTATTTA-TTTTA
* *
4110076 CTTATTTATTCTA
1 TTTATTTATTTTA
*
4110089 TTTATTTATTTTG
1 TTTATTTATTTTA
*
4110102 CTTATTTATTT
1 TTTATTTATTT
4110113 ATAGGTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
13 28 0.64
14 16 0.36
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:4110085 original size:27 final size:26
Alignment explanation
Indices: 4110053--4110112 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
4110043 AAAGTTTTAT
4110053 TTTATTTTATTTATTTATTTTTACTTA
1 TTTATTTTATTTATTTA-TTTTACTTA
* *
4110080 TTTATTCTATTTATTTATTTTGCTTA
1 TTTATTTTATTTATTTATTTTACTTA
4110106 TTTATTT
1 TTTATTT
4110113 ATAGGTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (26 bp):
TTTATTTTATTTATTTATTTTACTTA
Found at i:4110169 original size:30 final size:26
Alignment explanation
Indices: 4110103--4110166 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
4110093 TTTATTTTGC
4110103 TTATTTATTTATAGGTTAAATTGTTA
1 TTATTTATTTATAGGTTAAATTGTTA
*
4110129 TTATTTATTTATAGGTTAAATTGATA
1 TTATTTATTTATAGGTTAAATTGTTA
4110155 TTATTTATTTAT
1 TTATTTATTTAT
4110167 TTAATTTGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (26 bp):
TTATTTATTTATAGGTTAAATTGTTA
Found at i:4110288 original size:28 final size:27
Alignment explanation
Indices: 4110219--4110289 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 27
4110209 TTTAAAATGA
4110219 TAAAAAA-AT-ATTTTTTAAAAAAAAT
1 TAAAAAATATAATTTTTTAAAAAAAAT
* * *
4110244 T-GAAAGTATCAATTTTTTTAAAAAAATT
1 TAAAAAATAT-AA-TTTTTTAAAAAAAAT
4110272 TCAAAAAATATAATTTTT
1 T-AAAAAATATAATTTTT
4110290 ATAATAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
24 3 0.09
25 3 0.09
27 1 0.03
28 20 0.57
29 2 0.06
30 6 0.17
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (27 bp):
TAAAAAATATAATTTTTTAAAAAAAAT
Found at i:4110562 original size:56 final size:56
Alignment explanation
Indices: 4110275--4110563 Score: 218
Period size: 56 Copynumber: 5.1 Consensus size: 56
4110265 AAAAATTTCA
* * *
4110275 AAAAATATAATTTTTATAATAAACATTTTAATGAAAAA-TTAAAAATATCAATTTTTCTT
1 AAAAATAAAATTTTTA-AA-AAATATTTTAA-GAAAAAGTTAAAAGTATCAATTTTT-TT
* * ** * *
4110334 GAAAACA-AAAATTTTGAGAATGT-TTTTAGGAAAAA-TTAAAAATATCAATTTTCTTT
1 -AAAA-ATAAAATTTTTAAAAAATATTTTAAGAAAAAGTTAAAAGTATCAATTTT-TTT
* * * * **
4110390 GAAAATAAAAATTTT-AAAAATATTTTTTA-AAAAAGTTGAAAGTATCAATATTCCTT
1 AAAAATAAAATTTTTAAAAAATA-TTTTAAGAAAAAGTTAAAAGTATCAAT-TTTTTT
* ** * *
4110446 ATACACGAAAA-TTTT-AAAAATGTTTTAA-AGAAAAGTTGAAAGTATCAATTTTTCTT
1 A-AAAATAAAATTTTTAAAAAATATTTTAAGA-AAAAGTTAAAAGTATCAATTTTT-TT
*
4110502 AAAAATAAAATTTTTAAAAAATACTTTAAGAAAAAGTTAAAAGTATCAATTTTTTT
1 AAAAATAAAATTTTTAAAAAATATTTTAAGAAAAAGTTAAAAGTATCAATTTTTTT
4110558 AAAAAT
1 AAAAAT
4110564 GAGAACTTCA
Statistics
Matches: 183, Mismatches: 33, Indels: 30
0.74 0.13 0.12
Matches are distributed among these distances:
54 4 0.02
55 29 0.16
56 87 0.48
57 47 0.26
58 2 0.01
59 1 0.01
60 12 0.07
61 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (56 bp):
AAAAATAAAATTTTTAAAAAATATTTTAAGAAAAAGTTAAAAGTATCAATTTTTTT
Found at i:4110577 original size:112 final size:112
Alignment explanation
Indices: 4110275--4110562 Score: 296
Period size: 112 Copynumber: 2.5 Consensus size: 112
4110265 AAAAATTTCA
* * * *
4110275 AAAAATATAATTTTTATAATAAACATTTTAATGAAAAA-TTAAAAATATCAATTTTTCTTGAAAA
1 AAAAATAAAATTTTTA-AA-AAATATTTTAA-GAAAAAGTTAAAAGTATCAATTTTT-TTAAAAA
* * * * *
4110339 CAAAAATTTTGAGAATGTTTTTAGGAAAAATTAAAAATATCAATTTTCTTT
62 CGAAAATTTTAAAAATGTTTTAAAGAAAAATTAAAAATATCAATTTTCTTT
* * * * ** * *
4110390 GAAAATAAAAATTTT-AAAAATATTTTTTA-AAAAAGTTGAAAGTATCAATATTCCTTATACACG
1 AAAAATAAAATTTTTAAAAAATA-TTTTAAGAAAAAGTTAAAAGTATCAAT-TTTTTTAAAAACG
* * *
4110453 AAAATTTTAAAAATGTTTTAAAGAAAAGTTGAAAGTATCAATTTT-TCTT
64 AAAATTTTAAAAATGTTTTAAAGAAAAATTAAAAATATCAATTTTCT-TT
*
4110502 AAAAATAAAATTTTTAAAAAATACTTTAAGAAAAAGTTAAAAGTATCAATTTTTTTAAAAA
1 AAAAATAAAATTTTTAAAAAATATTTTAAGAAAAAGTTAAAAGTATCAATTTTTTTAAAAA
4110563 TGAGAACTTC
Statistics
Matches: 138, Mismatches: 29, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
111 6 0.04
112 85 0.62
113 35 0.25
115 12 0.09
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (112 bp):
AAAAATAAAATTTTTAAAAAATATTTTAAGAAAAAGTTAAAAGTATCAATTTTTTTAAAAACGAA
AATTTTAAAAATGTTTTAAAGAAAAATTAAAAATATCAATTTTCTTT
Found at i:4110578 original size:57 final size:57
Alignment explanation
Indices: 4110357--4110628 Score: 166
Period size: 56 Copynumber: 4.8 Consensus size: 57
4110347 TTGAGAATGT
* * * * * ** *
4110357 TTTTAGGAAAAA-TTAAAAATATCAATTTTCTTTGAAAATAAAAATTTTAAAAATA-T
1 TTTTAAGAAAAAGTTGAAAGTATCAATTTT-TTTAAAAATAAAACTTCAAAAAATACC
* ** * ** ** *
4110413 TTTTTA-AAAAAGTTGAAAGTATCAATATTCCTTATACACGAAAA-TTTTAAAAAT--G
1 TTTTAAGAAAAAGTTGAAAGTATCAAT-TTTTTTA-AAAATAAAACTTCAAAAAATACC
* *
4110468 TTTTAA-AGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTTAAAAAATA-C
1 TTTTAAGA-AAAAGTTGAAAGTATCAATTTTT-TTAAAAATAAAA-CTTCAAAAAATACC
* *
4110526 -TTTAAGAAAAAGTTAAAAGTATCAATTTTTTTAAAAATGAGAACTTCAAAAAATACC
1 TTTTAAGAAAAAGTTGAAAGTATCAATTTTTTTAAAAAT-AAAACTTCAAAAAATACC
* * * *
4110583 TTTTTTGAGAAAAAGTTGAGAGTATCGATTTTTTAAAAAAATAAAA
1 --TTTTAAGAAAAAGTTGAAAGTATCAATTTTTT-TAAAAATAAAA
4110629 ACCCAAAAAA
Statistics
Matches: 172, Mismatches: 29, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
55 19 0.11
56 68 0.40
57 48 0.28
58 1 0.01
60 30 0.17
61 6 0.03
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (57 bp):
TTTTAAGAAAAAGTTGAAAGTATCAATTTTTTTAAAAATAAAACTTCAAAAAATACC
Found at i:4110636 original size:60 final size:60
Alignment explanation
Indices: 4110476--4110674 Score: 176
Period size: 60 Copynumber: 3.4 Consensus size: 60
4110466 TGTTTTAAAG
* * ** ** *
4110476 AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTTAAAAAATAC---T-TTAAGA
1 AAAAGTTAAAAGTATCAATTTTT-TAAAAAATAAAAACTCCAAAAAATACTTTTCTTGAGA
* * * *
4110533 AAAAGTTAAAAGTATCAATTTTTTTAAAAATGAGAACTTCAAAAAATACCTTTT-TTGAGA
1 AAAAGTTAAAAGTATCAATTTTTTAAAAAATAAAAACTCCAAAAAATA-CTTTTCTTGAGA
* * * * *
4110593 AAAAGTTGAGAGTATCGATTTTTTAAAAAAATAAAAAC-CCAAAAAATATTTTTCTTGAGG
1 AAAAGTTAAAAGTATCAATTTTTT-AAAAAATAAAAACTCCAAAAAATACTTTTCTTGAGA
*
4110653 AAAAGTTAAAAATATCAATTTT
1 AAAAGTTAAAAGTATCAATTTT
4110675 CATTGAATAA
Statistics
Matches: 116, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
56 20 0.17
57 23 0.20
59 4 0.03
60 59 0.51
61 10 0.09
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.35
Consensus pattern (60 bp):
AAAAGTTAAAAGTATCAATTTTTTAAAAAATAAAAACTCCAAAAAATACTTTTCTTGAGA
Found at i:4111234 original size:433 final size:425
Alignment explanation
Indices: 4110665--4111478 Score: 1062
Period size: 426 Copynumber: 1.9 Consensus size: 425
4110655 AAGTTAAAAA
* *
4110665 TATCAATTTTCATTGAATAAAGGCATTGATCTTTCAAAAAATAAAATAAAAAAAAATCTCAAAAA
1 TATCAATTTTCATTGAATAAAGGCATTGACCTTTCAAAAAATAAAAAAAAAAAAAATCTCAAAAA
* *
4110730 AAAGTTGAAGTACTAATTTTTTCTCATTGAAATTTTTTATGTTAAATAATTAAACGAAAAAGCCT
66 AAAGTTAAAGTACTAATTTTTTCTCATTGAAATTTTTTATGTTAAATAATTAAACGAAAAAGCCC
*
4110795 TTACAAGAGAAATAGTAATTTTTTTGTATACTTTTGAGGTGAAATAATTTTTTTTAATTTTTTAT
131 TTACAAGAGAAATAGTAA--TTTTT-T-T-CTCTTGAGGTGAAA-AATTTTTTTTAATTTTTTAT
* * * * *
4110860 AAAAAATATTGGAGTCAATTAATAATAATTTTTAATAATTAATTACTTGATACGATTTTTAAGGT
190 -AAAAAGATTGGAGTCAATTAAGAATAATTTTTAAAAATTAATTACTTGATAAGATTTTTAAAGT
** * * * *
4110925 TTAATAGATAACACGAAATGAAGCTAATACTATTTTTTGATGGGTGTTGT-AGGAGTGTTATAAC
254 TTAATAGATAACACGAAATGAAAATAATACTATCTTTTGATAGGTGTTGTGA-GAATATTATAAC
* * *
4110989 CTTCCTCATATGTAATTATACTC-CTAGATCTAATTTTGATTTCGTAAACATTGAATTTTTCTTA
318 CTTCCTCATATATAATTATACTCTC-AGATCTAATTTTGATTTCGTAAACATTGAAGTTATCTTA
4111053 AAAATAAAAACAAATAAATGTCTTTTTTAAGAAAAAATTGAAAG
382 AAAATAAAAACAAATAAATGTCTTTTTTAAGAAAAAATTGAAAG
* *
4111097 TATCAATTTTTC-TTGAATAAAGGCATTGACCTTTTAAAAAATAAAAAAGAAAAAAAATCTCCAA
1 TATCAA-TTTTCATTGAATAAAGGCATTGACCTTTCAAAAAATAAAAAA-AAAAAAAATCTCAAA
* * * **
4111161 AAAAAGTTAAAGTATTAATTTTTT-TCATTGAATTTTTTTTATGTTAAATAATCT-AATGATGAA
64 AAAAAGTTAAAGTACTAATTTTTTCTCATTGAA-ATTTTTTATGTTAAATAAT-TAAACGAAAAA
* * *
4111224 GCCCTTACAAGAGAAATAGTAATTTTTTTCTCTTGATGTGAGAAATTTTTTTTAATTTTTTATCA
127 GCCCTTACAAGAGAAATAGTAATTTTTTTCTCTTGAGGTGAAAAATTTTTTTTAATTTTTTATAA
* * *
4111289 AAAGATTGGTGTCAATTAAGAATAATTTTTAAAAATTAATTATTTGGTAAGATTTTTAAAGTTTA
192 AAAGATTGGAGTCAATTAAGAATAATTTTTAAAAATTAATTACTTGATAAGATTTTTAAAGTTTA
* * * * * * * *
4111354 ATGGATAATATGAAATTAAAATGATATTATCTTTTGATAGGTGTTGTGAGAATATTATAATCTTT
257 ATAGATAACACGAAATGAAAATAATACTATCTTTTGATAGGTGTTGTGAGAATATTATAACCTTC
* * * * * *
4111419 TTCATATATAATTGTACTCTCATATTTAATTTTGGTTTCGTAAATATTGAAGTTATCTTA
322 CTCATATATAATTATACTCTCAGATCTAATTTTGATTTCGTAAACATTGAAGTTATCTTA
4111479 TAAAGATATC
Statistics
Matches: 330, Mismatches: 46, Indels: 18
0.84 0.12 0.05
Matches are distributed among these distances:
426 156 0.47
427 22 0.07
428 11 0.03
429 1 0.00
430 1 0.00
431 5 0.02
432 47 0.14
433 86 0.26
434 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (425 bp):
TATCAATTTTCATTGAATAAAGGCATTGACCTTTCAAAAAATAAAAAAAAAAAAAATCTCAAAAA
AAAGTTAAAGTACTAATTTTTTCTCATTGAAATTTTTTATGTTAAATAATTAAACGAAAAAGCCC
TTACAAGAGAAATAGTAATTTTTTTCTCTTGAGGTGAAAAATTTTTTTTAATTTTTTATAAAAAG
ATTGGAGTCAATTAAGAATAATTTTTAAAAATTAATTACTTGATAAGATTTTTAAAGTTTAATAG
ATAACACGAAATGAAAATAATACTATCTTTTGATAGGTGTTGTGAGAATATTATAACCTTCCTCA
TATATAATTATACTCTCAGATCTAATTTTGATTTCGTAAACATTGAAGTTATCTTAAAAATAAAA
ACAAATAAATGTCTTTTTTAAGAAAAAATTGAAAG
Found at i:4113013 original size:2 final size:2
Alignment explanation
Indices: 4113006--4113032 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4112996 TTAAATGTGT
4113006 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
4113033 GTACATTTGT
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:4123532 original size:29 final size:30
Alignment explanation
Indices: 4123500--4123557 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
4123490 CTAAACTTAA
* *
4123500 TATTAAATTTTGTTGTTGTATTT-TAGTTT
1 TATTAAATTTTGTCGTTGCATTTGTAGTTT
*
4123529 TATTGAATTTTGTCGTTGCATTTGTAGTT
1 TATTAAATTTTGTCGTTGCATTTGTAGTT
4123558 ATGTTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.19, C:0.03, G:0.17, T:0.60
Consensus pattern (30 bp):
TATTAAATTTTGTCGTTGCATTTGTAGTTT
Found at i:4123570 original size:30 final size:29
Alignment explanation
Indices: 4123499--4123570 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
4123489 ACTAAACTTA
* * *
4123499 ATATTAAATTTTGTTGTTGTATTTTAGTT
1 ATATTGAATTTTGTCGTTGCATTTTAGTT
*
4123528 TTATTGAATTTTGTCGTTGCATTTGTAGTT
1 ATATTGAATTTTGTCGTTGCATTT-TAGTT
* *
4123558 ATGTTGATTTTTG
1 ATATTGAATTTTG
4123571 AAAAAAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.19, C:0.03, G:0.18, T:0.60
Consensus pattern (29 bp):
ATATTGAATTTTGTCGTTGCATTTTAGTT
Found at i:4131435 original size:22 final size:23
Alignment explanation
Indices: 4131410--4131459 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
4131400 AAAAGCTTTA
4131410 ATTAAGAAATA-TTTGATACATT
1 ATTAAGAAATATTTTGATACATT
* * * *
4131432 ATTAATATATATTTTTATATATT
1 ATTAAGAAATATTTTGATACATT
4131455 ATTAA
1 ATTAA
4131460 TAAACAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (23 bp):
ATTAAGAAATATTTTGATACATT
Found at i:4132107 original size:15 final size:16
Alignment explanation
Indices: 4132087--4132116 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4132077 AATTTTTCAT
4132087 ATATATAATA-TATAA
1 ATATATAATACTATAA
4132102 ATATATAATACTATA
1 ATATATAATACTATA
4132117 TTACTAACCC
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:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATATAATACTATAA
Found at i:4135186 original size:25 final size:23
Alignment explanation
Indices: 4135141--4135186 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
4135131 AAAATAATTG
* *
4135141 AATTCAGCTCATTCGATAATACA
1 AATTCAGCTCATTCAACAATACA
4135164 AATTCAAGCTCGATTCAACAATA
1 AATTC-AGCTC-ATTCAACAATA
4135187 ATTAAAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 5 0.26
25 9 0.47
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (23 bp):
AATTCAGCTCATTCAACAATACA
Found at i:4136121 original size:19 final size:19
Alignment explanation
Indices: 4136097--4136133 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4136087 AATTGACATT
4136097 ATTTACTTAATGTATCATC
1 ATTTACTTAATGTATCATC
4136116 ATTTACTTAATGTATCAT
1 ATTTACTTAATGTATCAT
4136134 TCTTTATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (19 bp):
ATTTACTTAATGTATCATC
Found at i:4136139 original size:19 final size:19
Alignment explanation
Indices: 4136093--4136139 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
4136083 TTGAAATTGA
*
4136093 CATTATTTACTTAATGTAT
1 CATTCTTTACTTAATGTAT
4136112 CA-TCATTTACTTAATGTAT
1 CATTC-TTTACTTAATGTAT
4136131 CATTCTTTA
1 CATTCTTTA
4136140 TCTTCCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 22 0.88
20 2 0.08
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (19 bp):
CATTCTTTACTTAATGTAT
Found at i:4137244 original size:2 final size:2
Alignment explanation
Indices: 4137239--4137268 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4137229 TTCTGCTAAT
*
4137239 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4137269 ATTCATGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4139797 original size:1 final size:1
Alignment explanation
Indices: 4139793--4139817 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4139783 TTTGAAACCC
4139793 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
4139818 GGAAGATAAA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4142883 original size:3 final size:3
Alignment explanation
Indices: 4142877--4142902 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4142867 AATAATAAGA
4142877 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
4142903 TAGTGAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:4149583 original size:28 final size:27
Alignment explanation
Indices: 4149551--4149603 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
4149541 ACATTTCGTA
4149551 AATTCATAAATCAATATAAAAATATGTC
1 AATTCATAAATCAATAT-AAAATATGTC
*
4149579 AATTCATAAATCATTATAAAATATG
1 AATTCATAAATCAATATAAAATATG
4149604 CTACCATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (27 bp):
AATTCATAAATCAATATAAAATATGTC
Found at i:4154366 original size:24 final size:23
Alignment explanation
Indices: 4154339--4154383 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
4154329 ATATAGTCTG
4154339 TCAAGTAA-AATTCATATCTTTAAT
1 TCAAGTAATAA-T-ATATCTTTAAT
*
4154363 TCAATTAATAATATATCTTTA
1 TCAAGTAATAATATATCTTTA
4154384 TATATCTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 8 0.42
25 2 0.11
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.44
Consensus pattern (23 bp):
TCAAGTAATAATATATCTTTAAT
Found at i:4154861 original size:23 final size:23
Alignment explanation
Indices: 4154787--4154861 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
4154777 CAAATCATGG
* * *
4154787 ATCAATCATTAAAAATCATCGTAA
1 ATCAATC-TTTAAAATAATCATAA
**
4154811 AT-AATCTTTATATACA-AATCATGG
1 ATCAATCTTTA-A-A-ATAATCATAA
4154835 ATCAATCTTTAAAATAATCATAA
1 ATCAATCTTTAAAATAATCATAA
4154858 ATCA
1 ATCA
4154862 TCATTATCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 11
0.68 0.12 0.19
Matches are distributed among these distances:
22 4 0.10
23 16 0.41
24 10 0.26
25 9 0.23
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (23 bp):
ATCAATCTTTAAAATAATCATAA
Found at i:4166814 original size:15 final size:15
Alignment explanation
Indices: 4166767--4166818 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
4166757 GTCATATAAC
*
4166767 TTTTCAAAAATAAAA
1 TTTTCAAAAATAAAT
*
4166782 TTTTGAAATATTATAAAT
1 TTTTCAAA-A--ATAAAT
4166800 TTTTCAAAAATAAAT
1 TTTTCAAAAATAAAT
4166815 TTTT
1 TTTT
4166819 TGAAAGTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 17 0.55
16 1 0.03
17 1 0.03
18 12 0.39
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (15 bp):
TTTTCAAAAATAAAT
Found at i:4166838 original size:34 final size:34
Alignment explanation
Indices: 4166732--4166843 Score: 104
Period size: 33 Copynumber: 3.3 Consensus size: 34
4166722 TTCACACAAG
* **
4166732 TTTTCAGAAATAGAATTTTTAAAAAGTCATATAAC
1 TTTTCAAAAATA-AATTTTTTGAAAGTCATATAAC
* *
4166767 TTTTCAAAAATAAA-ATTTTGAAA-T-ATTATAAAT
1 TTTTCAAAAATAAATTTTTTGAAAGTCA-TAT-AAC
* *
4166800 TTTTCAAAAATAAATTTTTTGAAAGTCAAATGAC
1 TTTTCAAAAATAAATTTTTTGAAAGTCATATAAC
*
4166834 TTTTCGAAAA
1 TTTTCAAAAA
4166844 CCTATTTTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
31 1 0.02
32 4 0.06
33 22 0.35
34 20 0.32
35 14 0.23
36 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (34 bp):
TTTTCAAAAATAAATTTTTTGAAAGTCATATAAC
Found at i:4171358 original size:12 final size:12
Alignment explanation
Indices: 4171341--4171376 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
4171331 TTATATTTCA
*
4171341 AATATCTATTTT
1 AATATCTATCTT
4171353 AATATCTATCTT
1 AATATCTATCTT
4171365 AATATCTATCTT
1 AATATCTATCTT
4171377 TTAAAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (12 bp):
AATATCTATCTT
Found at i:4175924 original size:2 final size:2
Alignment explanation
Indices: 4175912--4175942 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4175902 CCCAAAAGTG
4175912 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4175943 CTAGTTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4177239 original size:3 final size:3
Alignment explanation
Indices: 4177231--4177277 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
4177221 GAATTCATGC
4177231 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4177278 AATCATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4178075 original size:22 final size:22
Alignment explanation
Indices: 4178050--4178226 Score: 110
Period size: 22 Copynumber: 8.0 Consensus size: 22
4178040 TCAATTGACA
* *
4178050 ACTAAGTTATCACTGATTTATT
1 ACTAAGTTATCAATGATTTACT
* * *
4178072 ACTATGTTATCAATGATGTATT
1 ACTAAGTTATCAATGATTTACT
* *
4178094 AATAAATTATCAATGATTTACT
1 ACTAAGTTATCAATGATTTACT
* * *
4178116 ATTAAGTTATGAATTATTTACT
1 ACTAAGTTATCAATGATTTACT
** * *
4178138 ACTAAGTTATTGATAATTTATT
1 ACTAAGTTATCAATGATTTACT
* *
4178160 A-TAAAGTTAT-AATTAATTTTCT
1 ACT-AAGTTATCAA-TGATTTACT
*
4178182 A-TGAAGTTGTCAATGATTTACT
1 ACT-AAGTTATCAATGATTTACT
* * *
4178204 A-TAAAATTATCCATGATTAACT
1 ACT-AAGTTATCAATGATTTACT
4178226 A
1 A
4178227 ATTTACTACT
Statistics
Matches: 123, Mismatches: 29, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
21 2 0.02
22 119 0.97
23 2 0.02
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (22 bp):
ACTAAGTTATCAATGATTTACT
Found at i:4178201 original size:44 final size:44
Alignment explanation
Indices: 4178050--4178213 Score: 127
Period size: 44 Copynumber: 3.7 Consensus size: 44
4178040 TCAATTGACA
* * * * * * *
4178050 ACTAAGTTATCACTGATTTATTACT-ATGTTATCAATGATGTATT
1 ACTAAGTTATCAATGATTTACTA-TAAAGTTATGAATTATTTACT
* * *
4178094 AATAAATTATCAATGATTTACTATTAAGTTATGAATTATTTACT
1 ACTAAGTTATCAATGATTTACTATAAAGTTATGAATTATTTACT
** * * *
4178138 ACTAAGTTATTGATAATTTATTATAAAGTTAT-AATTAATTTTCT
1 ACTAAGTTATCAATGATTTACTATAAAGTTATGAATT-ATTTACT
* *
4178182 A-TGAAGTTGTCAATGATTTACTATAAAATTAT
1 ACT-AAGTTATCAATGATTTACTATAAAGTTAT
4178214 CCATGATTAA
Statistics
Matches: 94, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
43 6 0.06
44 88 0.94
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (44 bp):
ACTAAGTTATCAATGATTTACTATAAAGTTATGAATTATTTACT
Found at i:4178410 original size:22 final size:22
Alignment explanation
Indices: 4178384--4178439 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4178374 AATTAGCTAT
*
4178384 TAAGTTATCAATTATTTACTAC
1 TAAGTTATCAATGATTTACTAC
** *
4178406 TAAGTTATTTATGATTTACTAT
1 TAAGTTATCAATGATTTACTAC
*
4178428 TAATTTATCAAT
1 TAAGTTATCAAT
4178440 AAATTACAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (22 bp):
TAAGTTATCAATGATTTACTAC
Found at i:4178446 original size:22 final size:22
Alignment explanation
Indices: 4178374--4178446 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
4178364 ACTTTTTAAT
*
4178374 AATTAGCTATTAAGTTATCAATT
1 AATTA-CTATTAAGTTATCAATA
* * ** *
4178397 ATTTACTACTAAGTTATTTATG
1 AATTACTATTAAGTTATCAATA
* *
4178419 ATTTACTATTAATTTATCAATA
1 AATTACTATTAAGTTATCAATA
4178441 AATTAC
1 AATTAC
4178447 AATATATGAG
Statistics
Matches: 39, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (22 bp):
AATTACTATTAAGTTATCAATA
Found at i:4178762 original size:22 final size:22
Alignment explanation
Indices: 4178719--4178772 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
4178709 TCAATTTATC
* * *
4178719 ACTAAGTTATAGATGATTTACT
1 ACTAAGTTATAAACGATATACT
4178741 ACTAAGTTATAAACGATATACT
1 ACTAAGTTATAAACGATATACT
*
4178763 ACTAAATTAT
1 ACTAAGTTAT
4178773 TGATAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (22 bp):
ACTAAGTTATAAACGATATACT
Found at i:4178784 original size:22 final size:22
Alignment explanation
Indices: 4178711--4178785 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
4178701 AATCATTATC
*
4178711 AATTTA-TCACTAAGTTATAGAT
1 AATTTACT-ACTAAATTATAGAT
* * * *
4178733 GATTTACTACTAAGTTATAAAC
1 AATTTACTACTAAATTATAGAT
* * *
4178755 GATATACTACTAAATTATTGAT
1 AATTTACTACTAAATTATAGAT
4178777 AATTTACTA
1 AATTTACTA
4178786 TGAAGTTGTT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
22 41 0.98
23 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (22 bp):
AATTTACTACTAAATTATAGAT
Found at i:4178818 original size:11 final size:11
Alignment explanation
Indices: 4178804--4178870 Score: 64
Period size: 11 Copynumber: 6.1 Consensus size: 11
4178794 TTAATAATTA
*
4178804 ACTAATTTATG
1 ACTAATTTATC
*
4178815 ACTAAATTATC
1 ACTAATTTATC
* *
4178826 ATTAATTTATA
1 ACTAATTTATC
*
4178837 ACTAAATTATC
1 ACTAATTTATC
4178848 ACTAATTTA-C
1 ACTAATTTATC
*
4178858 AGCTAAGTTATC
1 A-CTAATTTATC
4178870 A
1 A
4178871 ATGATTTACC
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
10 2 0.05
11 40 0.91
12 2 0.05
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (11 bp):
ACTAATTTATC
Found at i:4178832 original size:22 final size:22
Alignment explanation
Indices: 4178804--4178870 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
4178794 TTAATAATTA
*
4178804 ACTAATTTATGACTAAATTATC
1 ACTAATTTATAACTAAATTATC
*
4178826 ATTAATTTATAACTAAATTATC
1 ACTAATTTATAACTAAATTATC
* * *
4178848 ACTAATTTACAGCTAAGTTATC
1 ACTAATTTATAACTAAATTATC
4178870 A
1 A
4178871 ATGATTTACC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (22 bp):
ACTAATTTATAACTAAATTATC
Found at i:4178877 original size:22 final size:22
Alignment explanation
Indices: 4178816--4178879 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
4178806 TAATTTATGA
* * *
4178816 CTAAATTATCATTAATTTATAA
1 CTAAATTATCAATAATTTACAG
*
4178838 CTAAATTATCACTAATTTACAG
1 CTAAATTATCAATAATTTACAG
* *
4178860 CTAAGTTATCAATGATTTAC
1 CTAAATTATCAATAATTTAC
4178880 CATGATGTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
CTAAATTATCAATAATTTACAG
Found at i:4178940 original size:22 final size:22
Alignment explanation
Indices: 4178901--4178948 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
4178891 TAGTGATTTG
* **
4178901 CTATTAAATTGTTGATAATTGA
1 CTATTAAATTATCAATAATTGA
*
4178923 CTATTAAATTATCAATAATTTA
1 CTATTAAATTATCAATAATTGA
4178945 CTAT
1 CTAT
4178949 ATATTATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (22 bp):
CTATTAAATTATCAATAATTGA
Found at i:4179059 original size:22 final size:23
Alignment explanation
Indices: 4178997--4179059 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 23
4178987 ACTATTGAGT
*
4178997 TTTAGTGATTAACTACTAAATTA
1 TTTAGTGATTTACTACTAAATTA
* * * * *
4179020 -TCATTGTTTTATTGCTAAATTA
1 TTTAGTGATTTACTACTAAATTA
4179042 TTTA-TGATTTACTACTAA
1 TTTAGTGATTTACTACTAA
4179060 GTTTATAATT
Statistics
Matches: 29, Mismatches: 10, Indels: 3
0.69 0.24 0.07
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (23 bp):
TTTAGTGATTTACTACTAAATTA
Found at i:4179291 original size:66 final size:67
Alignment explanation
Indices: 4179187--4179341 Score: 185
Period size: 66 Copynumber: 2.4 Consensus size: 67
4179177 CTTTTTTTAA
* * * *
4179187 AAATTATCATT-CATTTACTACTATGCTATTTTGCATTTACAATTATGTTAT-AATTGATTTACT
1 AAATTATTATTGCATTTACTATTATACTATTTTGCATTTACAATTAAGTTATCAATT-ATTTACT
*
4179250 ATT
65 ATG
* *
4179253 AAGTTATTA-TGCATTTACTATTATATTATTATTG-ATTTACAATTAAGTTATCAATTATTTACT
1 AAATTATTATTGCATTTACTATTATACTATT-TTGCATTTACAATTAAGTTATCAATTATTTACT
4179316 ATG
65 ATG
*
4179319 AAATTATTATTG-ATATACTATTA
1 AAATTATTATTGCATTTACTATTA
4179342 AGTTATCACT
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
65 1 0.01
66 66 0.87
67 9 0.12
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (67 bp):
AAATTATTATTGCATTTACTATTATACTATTTTGCATTTACAATTAAGTTATCAATTATTTACTA
TG
Found at i:4179312 original size:22 final size:22
Alignment explanation
Indices: 4179046--4179430 Score: 141
Period size: 22 Copynumber: 17.6 Consensus size: 22
4179036 AAATTATTTA
*
4179046 TGATTTACTACTAAGTTTATAAT
1 TGATTTACTATTAAG-TTATAAT
* * ** *
4179069 TTACTTACTATTAAACTAAAAT
1 TGATTTACTATTAAGTTATAAT
* *
4179091 AGATTTGCTATTAAGTTAT--T
1 TGATTTACTATTAAGTTATAAT
* * * *
4179111 TGTAATTTACTACTAAATTTTCAT
1 TG--ATTTACTATTAAGTTATAAT
* *
4179135 TGATTTAATATTAAATTATCAA-
1 TGATTTACTATTAAGTTAT-AAT
* * **
4179157 TAATTAACTATTAAGTTATCCT
1 TGATTTACTATTAAGTTATAAT
* * * *
4179179 T--TTT-TTA-AAAATTATCAT
1 TGATTTACTATTAAGTTATAAT
* * * * *
4179197 TCATTTACTACTATGCTAT-TT
1 TGATTTACTATTAAGTTATAAT
* *
4179218 TGCATTTACAATTATGTTATAAT
1 TG-ATTTACTATTAAGTTATAAT
*
4179241 TGATTTACTATTAAGTTATTA-
1 TGATTTACTATTAAGTTATAAT
*
4179262 TGCATTTACTATTATA-TTATTAT
1 TG-ATTTACTATTA-AGTTATAAT
*
4179285 TGATTTACAATTAAGTTATCAAT
1 TGATTTACTATTAAGTTAT-AAT
* * *
4179308 T-ATTTACTATGAAATTATTAT
1 TGATTTACTATTAAGTTATAAT
* * *
4179329 TGATATACTATTAAGTTATCAC
1 TGATTTACTATTAAGTTATAAT
* * *
4179351 TAATTTACTATACTGAA-TTATCAC
1 TGATTTACTAT--T-AAGTTATAAT
* * * * *
4179375 TAATTAACTATTAATTTATCAG
1 TGATTTACTATTAAGTTATAAT
*
4179397 TGA-TTACTATTAAATTAT-AT
1 TGATTTACTATTAAGTTATAAT
*
4179417 TGATTTACTTTTAA
1 TGATTTACTATTAA
4179431 TTTTCAATTA
Statistics
Matches: 272, Mismatches: 67, Indels: 48
0.70 0.17 0.12
Matches are distributed among these distances:
18 9 0.03
19 2 0.01
20 11 0.04
21 34 0.12
22 172 0.63
23 21 0.08
24 21 0.08
25 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (22 bp):
TGATTTACTATTAAGTTATAAT
Found at i:4179348 original size:44 final size:44
Alignment explanation
Indices: 4179234--4179539 Score: 194
Period size: 44 Copynumber: 6.9 Consensus size: 44
4179224 TACAATTATG
* * * *
4179234 TTATAATTGATTTACTATTAAGTTAT-TATGCATTTACTATTATA
1 TTATTATTGATTTACTATTAAGTTATCAAT-TATTTACTATTAAA
* *
4179278 TTATTATTGATTTACAATTAAGTTATCAATTATTTACTATGAAA
1 TTATTATTGATTTACTATTAAGTTATCAATTATTTACTATTAAA
* * * *
4179322 TTATTATTGATATACTATTAAGTTATCACTAATTTACTATACTGAA
1 TTATTATTGATTTACTATTAAGTTATCAATTATTTACTAT--TAAA
* * * * * * *
4179368 TTATCACTAATTAACTATTAATTTATCAGTGA-TTACTATTAAA
1 TTATTATTGATTTACTATTAAGTTATCAATTATTTACTATTAAA
* * * *
4179411 TTA-TATTGATTTACTTTTAA-TTTTCAATTATTAATTACTACTAAG
1 TTATTATTGATTTACTATTAAGTTATCAATTA-T--TTACTATTAAA
* * * * * *
4179456 TTCTAAATT-ATTTACTACTAAATTATC-ATTAATTTATTGTTAAA
1 TTAT-TATTGATTTACTATTAAGTTATCAATT-ATTTACTATTAAA
* * * *
4179500 TTATT-TATGATTTATTGTTAAATTTATCAATTAATTACTA
1 TTATTAT-TGATTTACTATT-AAGTTATCAATTATTTACTA
4179540 CTTCCTCTAT
Statistics
Matches: 198, Mismatches: 49, Indels: 29
0.72 0.18 0.11
Matches are distributed among these distances:
41 7 0.04
42 13 0.07
43 7 0.04
44 88 0.44
45 32 0.16
46 43 0.22
47 8 0.04
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (44 bp):
TTATTATTGATTTACTATTAAGTTATCAATTATTTACTATTAAA
Found at i:4179490 original size:22 final size:22
Alignment explanation
Indices: 4179113--4179503 Score: 154
Period size: 22 Copynumber: 17.9 Consensus size: 22
4179103 AAGTTATTTG
* *
4179113 TAATTTACTACTAAATTTTCAT
1 TAATTTACTATTAAATTATCAT
* * *
4179135 TGATTTAATATTAAATTATCAA
1 TAATTTACTATTAAATTATCAT
* * *
4179157 TAATTAACTATTAAGTTATCCT
1 TAATTTACTATTAAATTATCAT
* *
4179179 T--TTT-TTA-AAAATTATCAT
1 TAATTTACTATTAAATTATCAT
* * *** *
4179197 TCATTTACTACTATGCTAT-TT
1 TAATTTACTATTAAATTATCAT
* * ** *
4179218 TGCATTTACAATTATGTTATAAT
1 T-AATTTACTATTAAATTATCAT
* * *
4179241 TGATTTACTATTAAGTTATTAT
1 TAATTTACTATTAAATTATCAT
** * *
4179263 GCATTTACTATTATATTATTAT
1 TAATTTACTATTAAATTATCAT
* * *
4179285 TGATTTACAATTAAGTTATCAAT
1 TAATTTACTATTAAATTATC-AT
* *
4179308 T-ATTTACTATGAAATTATTAT
1 TAATTTACTATTAAATTATCAT
* * * *
4179329 TGATATACTATTAAGTTATCAC
1 TAATTTACTATTAAATTATCAT
* *
4179351 TAATTTACTATACTGAATTATCAC
1 TAATTTACTAT--TAAATTATCAT
* * *
4179375 TAATTAACTATTAATTTATCAG
1 TAATTTACTATTAAATTATCAT
*
4179397 TGA-TTACTATTAAATTAT-AT
1 TAATTTACTATTAAATTATCAT
* * *
4179417 TGATTTACT-TTTAATTTTCAAT
1 TAATTTACTATTAAATTATC-AT
* * * * *
4179439 TATTAATTACTACTAAGTTCTAAAT
1 TA--ATTTACTATTAAATTAT-CAT
*
4179464 T-ATTTACTACTAAATTATCAT
1 TAATTTACTATTAAATTATCAT
* *
4179485 TAATTTATTGTTAAATTAT
1 TAATTTACTATTAAATTAT
4179504 TTATGATTTA
Statistics
Matches: 274, Mismatches: 77, Indels: 36
0.71 0.20 0.09
Matches are distributed among these distances:
18 9 0.03
19 2 0.01
20 16 0.06
21 28 0.10
22 181 0.66
23 5 0.02
24 25 0.09
25 8 0.03
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (22 bp):
TAATTTACTATTAAATTATCAT
Found at i:4180707 original size:2 final size:2
Alignment explanation
Indices: 4180700--4180728 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4180690 TATCACATTT
4180700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4180729 TAAACATCTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4183225 original size:13 final size:13
Alignment explanation
Indices: 4183207--4183231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4183197 TTATTTTTAG
4183207 AAAAATAAAAATA
1 AAAAATAAAAATA
4183220 AAAAATAAAAAT
1 AAAAATAAAAAT
4183232 TTTGGAATTA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:4197127 original size:23 final size:23
Alignment explanation
Indices: 4197097--4197143 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4197087 CTGTGCAAGA
4197097 GTTCTTCTTGTTCTCGATGATGT
1 GTTCTTCTTGTTCTCGATGATGT
4197120 GTTCTTCTTGTTCTCGATGATGT
1 GTTCTTCTTGTTCTCGATGATGT
4197143 G
1 G
4197144 GATGATTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.09, C:0.17, G:0.23, T:0.51
Consensus pattern (23 bp):
GTTCTTCTTGTTCTCGATGATGT
Found at i:4199496 original size:75 final size:75
Alignment explanation
Indices: 4199373--4199524 Score: 277
Period size: 75 Copynumber: 2.0 Consensus size: 75
4199363 CATTTTGACA
*
4199373 AACCATATTGTCTACTCAGCAAAAAAAGATTGTTTAACCGCCTAAGGAAGAGGTAGTATACATCA
1 AACCATATTGTCTACTCAGCAAAAAAAGATTGTTTAACCACCTAAGGAAGAGGTAGTATACATCA
4199438 TCAAATCCAC
66 TCAAATCCAC
* *
4199448 AACCATATTGTCTACTCAGCATAAAAAGATTGTTTAACCACCTAAGGAAGAGGTAGTATATATCA
1 AACCATATTGTCTACTCAGCAAAAAAAGATTGTTTAACCACCTAAGGAAGAGGTAGTATACATCA
4199513 TCAAATCCAC
66 TCAAATCCAC
4199523 AA
1 AA
4199525 AACAGCTTGC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (75 bp):
AACCATATTGTCTACTCAGCAAAAAAAGATTGTTTAACCACCTAAGGAAGAGGTAGTATACATCA
TCAAATCCAC
Found at i:4201610 original size:17 final size:18
Alignment explanation
Indices: 4201590--4201629 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
4201580 ATTTTCATTT
4201590 TTTTTTATTTTTT-TCTC
1 TTTTTTATTTTTTCTCTC
* *
4201607 TTTTTTCTTTTTTCTTTC
1 TTTTTTATTTTTTCTCTC
4201625 TTTTT
1 TTTTT
4201630 CCTTATCCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTATTTTTTCTCTC
Found at i:4203101 original size:12 final size:12
Alignment explanation
Indices: 4203086--4203116 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4203076 CAAAATTAAA
4203086 AATAAAAAAATT
1 AATAAAAAAATT
*
4203098 AATAAAACAATT
1 AATAAAAAAATT
4203110 AATAAAA
1 AATAAAA
4203117 TTTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAAAAAAATT
Found at i:4207817 original size:112 final size:112
Alignment explanation
Indices: 4207620--4207846 Score: 427
Period size: 112 Copynumber: 2.0 Consensus size: 112
4207610 TGAGGAGCTT
4207620 CTTACAGTATTATGAGCTTTAAACACGACTACCAAAGTCTCCATAGGGGAGAGTCCTTTCAATTT
1 CTTACAGTATTATGAGCTTTAAACACGACTACCAAAGTCTCCATAGGGGAGAGTCCTTTCAATTT
*
4207685 GGCTTTTGGAATAAAAGTCATGGTCCTAGTTGAAATTGACCTCTAAA
66 GGCTTTTGGAATAAAAGTCATGGTCCTAGTTGAAATTGACCTCCAAA
* *
4207732 CTTACAGTATTATGAGTTTTAAACATGACTACCAAAGTCTCCATAGGGGAGAGTCCTTTCAATTT
1 CTTACAGTATTATGAGCTTTAAACACGACTACCAAAGTCTCCATAGGGGAGAGTCCTTTCAATTT
4207797 GGCTTTTGGAATAAAAGTCATGGTCCTAGTTGAAATTGACCTCCAAA
66 GGCTTTTGGAATAAAAGTCATGGTCCTAGTTGAAATTGACCTCCAAA
4207844 CTT
1 CTT
4207847 CCTAGTTGAG
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (112 bp):
CTTACAGTATTATGAGCTTTAAACACGACTACCAAAGTCTCCATAGGGGAGAGTCCTTTCAATTT
GGCTTTTGGAATAAAAGTCATGGTCCTAGTTGAAATTGACCTCCAAA
Found at i:4208785 original size:4 final size:4
Alignment explanation
Indices: 4208768--4208907 Score: 67
Period size: 4 Copynumber: 33.5 Consensus size: 4
4208758 TTTAGTTTGT
*
4208768 TTTA TTTTA TTTTA TTTA TTTA CTTA TTTA TTCTA TATT- TTGTA TTT-
1 TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TT-TA T-TTA TT-TA TTTA
4208815 TTGTA TTTTA TTTA TTTA TTTA TTTA TTT- TTCTA -TTA TTACTA TTTA
1 TT-TA -TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TT--TA TTTA
* * * * * *
4208862 TTAA TATA TATA -TT- TTTA TTTG TTTA TATA TCTA TTATA TATTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA T-TTA TT
4208908 GTCATAACGT
Statistics
Matches: 108, Mismatches: 11, Indels: 33
0.71 0.07 0.22
Matches are distributed among these distances:
3 10 0.09
4 67 0.62
5 23 0.21
6 8 0.07
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:4208850 original size:29 final size:30
Alignment explanation
Indices: 4208791--4208863 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 30
4208781 ATTTATTTAC
*
4208791 TTATTTATTCTATATTTTGTATTTTTGTATT-
1 TTATTTATT-TAT-TTTTGTATTTTTCTATTA
4208822 TTATTTATTTATTTATT-TATTTTTCTATTA
1 TTATTTATTTATTT-TTGTATTTTTCTATTA
*
4208852 TTA-CTATTTATT
1 TTATTTATTTATT
4208864 AATATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 21 0.55
30 8 0.21
31 9 0.24
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.71
Consensus pattern (30 bp):
TTATTTATTTATTTTTGTATTTTTCTATTA
Found at i:4208881 original size:22 final size:22
Alignment explanation
Indices: 4208856--4208897 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4208846 CTATTATTAC
4208856 TATTTATTAATATATATATTTT
1 TATTTATTAATATATATATTTT
* * *
4208878 TATTTGTTTATATATCTATT
1 TATTTATTAATATATATATT
4208898 ATATATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTTATTAATATATATATTTT
Found at i:4209666 original size:59 final size:59
Alignment explanation
Indices: 4209385--4209744 Score: 449
Period size: 59 Copynumber: 5.9 Consensus size: 59
4209375 TTTTTTGTAG
* *
4209385 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTCGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTTGATTTTCAA
* * * * *
4209444 GAAAAATTGATACTTTCAATTTTTCCTCAAAAATCCCTTTTTTTG-AAATTTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT---ATTTTTTGAAAATTTTGATTTTCAA
* * *
4209504 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTTTGAAAA-TTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-----TATTTTTTGAAAATTTTGATTTTCAA
*
4209566 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGAAAATTTTGATTTTCAA
*
4209627 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTTGATTTTCAA
* *
4209686 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAAAATTTGATTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA---TTTTTTGAAAATTTTGATTTT
4209745 TATTTAAAGA
Statistics
Matches: 268, Mismatches: 17, Indels: 29
0.85 0.05 0.09
Matches are distributed among these distances:
57 1 0.00
59 99 0.37
60 41 0.15
61 47 0.18
62 76 0.28
63 3 0.01
65 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.46
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTTGATTTTCAA
Found at i:4209798 original size:17 final size:17
Alignment explanation
Indices: 4209754--4209816 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
4209744 TTATTTAAAG
4209754 AAAATAGAATAATAAAA-A
1 AAAATA-AA-AATAAAACA
* *
4209772 ATAAAGAAAAGTAAAACA
1 A-AAATAAAAATAAAACA
*
4209790 AAAATAAAAATAAAACT
1 AAAATAAAAATAAAACA
*
4209807 AAGATAAAAA
1 AAAATAAAAA
4209817 GAATATTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
17 28 0.76
18 5 0.14
19 4 0.11
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAATAAAAATAAAACA
Found at i:4209857 original size:13 final size:14
Alignment explanation
Indices: 4209839--4209867 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4209829 AATCTAATAT
4209839 AATAAATAAA-AAA
1 AATAAATAAACAAA
4209852 AATAAATAAACAAA
1 AATAAATAAACAAA
4209866 AA
1 AA
4209868 AAAACATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (14 bp):
AATAAATAAACAAA
Found at i:4209861 original size:17 final size:17
Alignment explanation
Indices: 4209764--4209870 Score: 60
Period size: 17 Copynumber: 6.1 Consensus size: 17
4209754 AAAATAGAAT
4209764 AATAAA-AAATAAAGAAA
1 AATAAATAAATAAA-AAA
*
4209781 AGTAAA-ACAA-AAATAAA
1 AATAAATA-AATAAA-AAA
*
4209798 AATAAAACTAAGATAAAAAG
1 AAT-AAA-TAA-ATAAAAAA
* ***
4209818 AAT-ATTAAATAAATCT
1 AATAAATAAATAAAAAA
4209834 AATATAATAAATAAAAAA
1 AATA-AATAAATAAAAAA
*
4209852 AATAAATAAACAAAAAA
1 AATAAATAAATAAAAAA
4209869 AA
1 AA
4209871 ACATTCAAAG
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
16 8 0.12
17 31 0.45
18 19 0.28
19 1 0.01
20 7 0.10
21 3 0.04
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (17 bp):
AATAAATAAATAAAAAA
Found at i:4209981 original size:23 final size:23
Alignment explanation
Indices: 4209954--4210001 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
4209944 TCAGGGGGAG
* *
4209954 CGGCTTGGCGGCTTGGCGCGGCT
1 CGGCTTGACGGCTTGGCACGGCT
4209977 CGGCTTGACGGCTTGGCACGGCT
1 CGGCTTGACGGCTTGGCACGGCT
4210000 CG
1 CG
4210002 ACTCAGCTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.04, C:0.31, G:0.44, T:0.21
Consensus pattern (23 bp):
CGGCTTGACGGCTTGGCACGGCT
Found at i:4210064 original size:22 final size:23
Alignment explanation
Indices: 4210024--4210066 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4210014 GGGGGCAAGC
4210024 ACGCGCGGGTCAGAATCGGGTCG
1 ACGCGCGGGTCAGAATCGGGTCG
*
4210047 ACGCTCGGGTC-GAATCGGGT
1 ACGCGCGGGTCAGAATCGGGT
4210067 TTCGGCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.16, C:0.26, G:0.42, T:0.16
Consensus pattern (23 bp):
ACGCGCGGGTCAGAATCGGGTCG
Found at i:4210974 original size:16 final size:14
Alignment explanation
Indices: 4210886--4210975 Score: 56
Period size: 13 Copynumber: 7.0 Consensus size: 14
4210876 TACATATTAG
4210886 TAATAATACATAAA
1 TAATAATACATAAA
*
4210900 T-ATTA-ACA-AAA
1 TAATAATACATAAA
* *
4210911 -AAAAATAAATAAA
1 TAATAATACATAAA
4210924 T-AT-ATACAT--A
1 TAATAATACATAAA
*
4210934 TATTAATACAT-AA
1 TAATAATACATAAA
4210947 TAATAATA-ATAAA
1 TAATAATACATAAA
4210960 TAATACAATACATAAA
1 TAAT--AATACATAAA
4210976 ATACAAAAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
10 2 0.04
11 6 0.11
12 18 0.32
13 21 0.37
14 1 0.02
15 4 0.07
16 5 0.09
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATAATACATAAA
Found at i:4211102 original size:11 final size:11
Alignment explanation
Indices: 4211086--4211134 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
4211076 TGTCTACAAT
4211086 TATTATATATC
1 TATTATATATC
*
4211097 TATTATTTATC
1 TATTATATATC
4211108 TATTATTATTAT-
1 TATTA-TA-TATC
*
4211120 TATTATTTATC
1 TATTATATATC
4211131 TATT
1 TATT
4211135 TACATAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 3 0.09
11 20 0.62
12 6 0.19
13 3 0.09
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTATATATC
Found at i:4211103 original size:3 final size:3
Alignment explanation
Indices: 4211084--4211126 Score: 50
Period size: 3 Copynumber: 13.0 Consensus size: 3
4211074 GGTGTCTACA
4211084 ATT ATT ATAT ATCT ATT ATTT ATCT ATT ATT ATT ATT ATT ATT
1 ATT ATT AT-T AT-T ATT A-TT AT-T ATT ATT ATT ATT ATT ATT
4211127 TATCTATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
3 24 0.67
4 12 0.33
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:4211173 original size:22 final size:22
Alignment explanation
Indices: 4211086--4211170 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 22
4211076 TGTCTACAAT
* *
4211086 TATTATATATCTATTATTTATC
1 TATTACATATATATTATTTATC
*
4211108 TATTA-TTATTATTATTATTTATC
1 TATTACATA-TA-TATTATTTATC
*
4211131 TATTTACATA-ATATCATTTATC
1 TA-TTACATATATATTATTTATC
4211153 TATTA-ATATATATTATTT
1 TATTACATATATATTATTT
4211171 TATTTTATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
20 3 0.06
21 13 0.25
22 18 0.34
23 14 0.26
24 3 0.06
25 2 0.04
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTACATATATATTATTTATC
Found at i:4211493 original size:26 final size:24
Alignment explanation
Indices: 4211445--4211495 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
4211435 TCGGTGGAAA
**
4211445 TTTTTTAGAATTTTTGGTGAATTT
1 TTTTTTAGAATTTTTGGAAAATTT
4211469 TTTTTCTAGAAATTTTTGGAAAATTT
1 TTTTT-TAG-AATTTTTGGAAAATTT
4211495 T
1 T
4211496 CAAATTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 3 0.13
26 15 0.65
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (24 bp):
TTTTTTAGAATTTTTGGAAAATTT
Found at i:4212009 original size:3 final size:3
Alignment explanation
Indices: 4211998--4212046 Score: 55
Period size: 3 Copynumber: 15.3 Consensus size: 3
4211988 TTTTTTTTCC
4211998 ATT ATTT ATT ATTT ATT ATT ATT ATT ATT ATT ATTT ATT GATT A-T ATT
1 ATT A-TT ATT A-TT ATT ATT ATT ATT ATT ATT A-TT ATT -ATT ATT ATT
4212046 A
1 A
4212047 GAATTGTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 2 0.05
3 27 0.66
4 12 0.29
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4212010 original size:7 final size:7
Alignment explanation
Indices: 4211998--4212046 Score: 55
Period size: 7 Copynumber: 6.6 Consensus size: 7
4211988 TTTTTTTTCC
4211998 ATTATTT
1 ATTATTT
4212005 ATTATTT
1 ATTATTT
4212012 ATTA-TT
1 ATTATTT
4212018 ATTATTATT
1 ATTA-T-TT
4212027 ATTATTT
1 ATTATTT
4212034 ATTGATTAT
1 ATT-ATT-T
4212043 ATTA
1 ATTA
4212047 GAATTGTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
6 6 0.16
7 16 0.43
8 5 0.14
9 10 0.27
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (7 bp):
ATTATTT
Found at i:4212031 original size:22 final size:23
Alignment explanation
Indices: 4211998--4212046 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
4211988 TTTTTTTTCC
4211998 ATTATTTATTATTTATT-ATTATT
1 ATTATTTATTATTTATTGATTA-T
4212021 ATTA-TTATTATTTATTGATTAT
1 ATTATTTATTATTTATTGATTAT
4212043 ATTA
1 ATTA
4212047 GAATTGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
ATTATTTATTATTTATTGATTAT
Found at i:4212204 original size:116 final size:115
Alignment explanation
Indices: 4212084--4212308 Score: 330
Period size: 116 Copynumber: 1.9 Consensus size: 115
4212074 TTATTTTTTT
*
4212084 AAATAA-AATTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAACTTTT-CTTGAAAAT-
1 AAATAAGAATTC-AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTGAAAATA
4212146 AAGCTTTCTAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAA
64 AAG-TTTCTAAAAAATA-TTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAA
** ** *
4212200 AAATAAGTTTTCAAAAATGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAA
1 AAATAAGAATTCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAA
*
4212265 GTTTCTAAAAAATATTTTGGGGAAAAGTTGAAAGTATCAATTTT
66 GTTTCTAAAAAATATTTTGGGAAAAAGTTGAAAGTATCAATTTT
4212309 CTCTGTACAA
Statistics
Matches: 99, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
115 33 0.33
116 60 0.61
117 6 0.06
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (115 bp):
AAATAAGAATTCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAA
GTTTCTAAAAAATATTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAA
Found at i:4212292 original size:57 final size:57
Alignment explanation
Indices: 4212097--4212309 Score: 299
Period size: 58 Copynumber: 3.7 Consensus size: 57
4212087 TAAAATTCAA
4212097 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAACTTTT-CTTGAAAATAAGCTTTCT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTGAAAATAAG-TTTCT
* *
4212155 AAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTT-T
1 AAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTCT
* *
4212211 CAAAAATGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTTTCT
1 AAAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGTTTCT
*
4212271 AAAAAATA-TTTTGGGGAAAAGTTGAAAGTATCAATTTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
4212310 TCTGTACAAA
Statistics
Matches: 141, Mismatches: 7, Indels: 15
0.87 0.04 0.09
Matches are distributed among these distances:
56 7 0.05
57 39 0.28
58 80 0.57
59 8 0.06
60 7 0.05
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.37
Consensus pattern (57 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTCT
Found at i:4215522 original size:15 final size:15
Alignment explanation
Indices: 4215504--4215534 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4215494 GCATACATGT
4215504 ATTCTCATTCATTGC
1 ATTCTCATTCATTGC
4215519 ATTCTCATTCATTGC
1 ATTCTCATTCATTGC
4215534 A
1 A
4215535 CTTAATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.26, G:0.06, T:0.45
Consensus pattern (15 bp):
ATTCTCATTCATTGC
Found at i:4222761 original size:12 final size:11
Alignment explanation
Indices: 4222741--4222792 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
4222731 ATACTATACT
4222741 TGAATAAAAAAA
1 TGAA-AAAAAAA
4222753 TGAAGAAAAAAA
1 TGAA-AAAAAAA
*
4222765 -GAAAAATAAA
1 TGAAAAAAAAA
4222775 TGAAAAAAGAAA
1 TGAAAAAA-AAA
*
4222787 AGAAAA
1 TGAAAA
4222793 GTGAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
10 6 0.18
11 9 0.26
12 19 0.56
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (11 bp):
TGAAAAAAAAA
Found at i:4222791 original size:23 final size:22
Alignment explanation
Indices: 4222746--4222804 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
4222736 ATACTTGAAT
*
4222746 AAAA-AAATGAAGAAAAAAAGA
1 AAAATAAATGAAAAAAAAAAGA
4222767 AAAATAAATGAAAAAAGAAAAGA
1 AAAATAAATGAAAAAA-AAAAGA
* *
4222790 AAAGTGAATGAAAAA
1 AAAATAAATGAAAAA
4222805 TGAGGACTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 4 0.12
22 10 0.30
23 19 0.58
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.08
Consensus pattern (22 bp):
AAAATAAATGAAAAAAAAAAGA
Found at i:4223849 original size:43 final size:42
Alignment explanation
Indices: 4223796--4224329 Score: 605
Period size: 43 Copynumber: 12.5 Consensus size: 42
4223786 CCAAAGTTGC
* *
4223796 GAGCCTCTGATTAGAGGAGCTTTGTTTATCTTTCAAAGTCATA
1 GAGCCTCTGATTAGAGGAGCTTTATTTAT-TTTCAAAGTCATT
* * **
4223839 GAGCCTCTGATTAAAGGAGC-TTGTTTA-TTTCAAAAGTTGTT
1 GAGCCTCTGATTAGAGGAGCTTTATTTATTTTC-AAAGTCATT
* * * * *
4223880 GAGCCTTTAATTAGAAGAGCCTTT-TATT-TTTTAAAAGTCGTT
1 GAGCCTCTGATTAGAGGAG-CTTTAT-TTATTTTCAAAGTCATT
* * *
4223922 AAGCATCTGATTAGAGAAGCTTTATTTATTTTTCAAAGTCATT
1 GAGCCTCTGATTAGAGGAGCTTTATTTA-TTTTCAAAGTCATT
**
4223965 GAGCCTCTGATTAGAGGAGCTTTATTTATCTTTCAAAAGTTGTT
1 GAGCCTCTGATTAGAGGAGCTTTATTTAT-TTTC-AAAGTCATT
* * *
4224009 GAGCCTCTAATTAGAGGAGC--CATTTATTTTCAAAGTCATA
1 GAGCCTCTGATTAGAGGAGCTTTATTTATTTTCAAAGTCATT
* *
4224049 GAGCCTCTGATTAGAGGAGCTTTATTTATCTTTCAAAGTCGTA
1 GAGCCTCTGATTAGAGGAGCTTTATTTAT-TTTCAAAGTCATT
* *
4224092 AAGCCTCTGATTAGAGGAGCTTTGTTTATCTTTCAAAGTCATT
1 GAGCCTCTGATTAGAGGAGCTTTATTTAT-TTTCAAAGTCATT
*
4224135 GAGCCTCTGATTAGAGGAGCTTTGTTTATCTTTCAAAGTCATT
1 GAGCCTCTGATTAGAGGAGCTTTATTTAT-TTTCAAAGTCATT
* *
4224178 GAGCCTCTGATTAGAGGAGCTTTATTTATTTGTTAAAGTCACT
1 GAGCCTCTGATTAGAGGAGCTTTATTTATTT-TCAAAGTCATT
* *
4224221 GAGCCTCTGATTAGAGGAGCTTTATTCATTTTCAAAGTCGTT
1 GAGCCTCTGATTAGAGGAGCTTTATTTATTTTCAAAGTCATT
* *
4224263 GA-CCTCTGATTAGAGGAGCTTTGTTTATGTTTTTCAAAGTCGTT
1 GAGCCTCTGATTAGAGGAGCTTTATTTA---TTTTCAAAGTCATT
* *
4224307 GAGCCTCTGTTTAGAGAAGCTTT
1 GAGCCTCTGATTAGAGGAGCTTT
4224330 GATCAAAATT
Statistics
Matches: 426, Mismatches: 47, Indels: 34
0.84 0.09 0.07
Matches are distributed among these distances:
40 29 0.07
41 54 0.13
42 56 0.13
43 227 0.53
44 42 0.10
45 18 0.04
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (42 bp):
GAGCCTCTGATTAGAGGAGCTTTATTTATTTTCAAAGTCATT
Found at i:4224511 original size:7 final size:7
Alignment explanation
Indices: 4224484--4224562 Score: 61
Period size: 7 Copynumber: 10.9 Consensus size: 7
4224474 TTTCAGTTTG
4224484 TTTTATT
1 TTTTATT
*
4224491 TTATTTTAT
1 TT-TTAT-T
4224500 TTTTATT
1 TTTTATT
4224507 TTTTATT
1 TTTTATT
* *
4224514 CTATATT
1 TTTTATT
*
4224521 TTGTA-T
1 TTTTATT
*
4224527 TTTTATA
1 TTTTATT
4224534 TTTTATT
1 TTTTATT
4224541 TATTTATT
1 T-TTTATT
*
4224549 TATTATT
1 TTTTATT
4224556 TATTTAT
1 T-TTTAT
4224563 CTATTATTAC
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
6 5 0.09
7 31 0.55
8 17 0.30
9 3 0.05
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.76
Consensus pattern (7 bp):
TTTTATT
Found at i:4224522 original size:20 final size:19
Alignment explanation
Indices: 4224489--4224558 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 19
4224479 GTTTGTTTTA
4224489 TTTTATTT-TATTTTTATT
1 TTTTATTTATATTTTTATT
4224507 TTTTATTCTATATTTTGTATT
1 TTTTATT-TATATTTT-TATT
4224528 TTTATATTT-TATTTATTTATT
1 TTT-TATTTATA-TT-TTTATT
*
4224549 TATTATTTAT
1 TTTTATTTAT
4224559 TTATCTATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
18 7 0.16
19 1 0.02
20 13 0.30
21 17 0.39
22 6 0.14
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (19 bp):
TTTTATTTATATTTTTATT
Found at i:4224544 original size:4 final size:4
Alignment explanation
Indices: 4224501--4224580 Score: 53
Period size: 4 Copynumber: 19.5 Consensus size: 4
4224491 TTATTTTATT
4224501 TTTA TTT- TTTA TTCTA TATT- TTGTA TTT- TTATA TTTTA TTTA TTTA
1 TTTA TTTA TTTA TT-TA T-TTA TT-TA TTTA TT-TA -TTTA TTTA TTTA
*
4224547 TTTA -TTA TTTA TTTA TCTA -TTA TTACTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TT
4224581 AATATATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 24
0.70 0.02 0.27
Matches are distributed among these distances:
3 11 0.18
4 36 0.58
5 8 0.13
6 7 0.11
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:4224569 original size:7 final size:7
Alignment explanation
Indices: 4224496--4224701 Score: 65
Period size: 7 Copynumber: 27.9 Consensus size: 7
4224486 TTATTTTATT
4224496 TTATTT-
1 TTATTTA
*
4224502 TTATTTT
1 TTATTTA
4224509 TTATTCTA
1 TTATT-TA
4224517 -TATTT-
1 TTATTTA
4224522 TGTATTT-
1 T-TATTTA
4224529 TTATATT-
1 TTAT-TTA
4224536 TTATTTA
1 TTATTTA
4224543 TTTATTTA
1 -TTATTTA
4224551 TTATTTA
1 TTATTTA
*
4224558 TTTATCTA
1 -TTATTTA
4224566 TTA-TTA
1 TTATTTA
*
4224572 CTATTTA
1 TTATTTA
4224579 TTAATATATA
1 TT-AT-T-TA
4224589 TT-TTTA
1 TTATTTA
*
4224595 TCTGTTTA
1 T-TATTTA
4224603 -TATGTCTA
1 TTAT-T-TA
4224611 TTATATATTA
1 -T-TAT-TTA
4224621 TTATTTA
1 TTATTTA
*
4224628 TCT-GTTA
1 T-TATTTA
4224635 TTA-TTA
1 TTATTTA
4224641 TTATTTA
1 TTATTTA
4224648 TCTATTTA
1 T-TATTTA
*
4224656 -CATATTA
1 TTAT-TTA
*
4224663 TCATTTA
1 TTATTTA
4224670 TCTATTAATA
1 T-TATT--TA
*
4224680 TATATTTT
1 T-TATTTA
4224688 TTATTTTA
1 TTA-TTTA
4224696 TTATTT
1 TTATTT
4224702 TTTTTCTTGG
Statistics
Matches: 158, Mismatches: 13, Indels: 57
0.69 0.06 0.25
Matches are distributed among these distances:
6 30 0.19
7 62 0.39
8 47 0.30
9 2 0.01
10 13 0.08
11 4 0.03
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (7 bp):
TTATTTA
Found at i:4224577 original size:49 final size:49
Alignment explanation
Indices: 4224535--4224701 Score: 94
Period size: 52 Copynumber: 3.2 Consensus size: 49
4224525 ATTTTTATAT
4224535 TTTATTTATTTATTTATTATT-TATTTATCTATTATTACTATTTATTAATAT
1 TTTATTTATTTATTTATTATTATATTTATCTATTATTA-TATTT-TT-ATAT
* * * * *
4224586 ATATT-TTTATCTGTTTA-TATGTCTA-TTATATATTATTATTTATCTGTTATTAT
1 -T-TTATTTATTTATTTATTAT-TATATTTATCTATTATTA--TAT-TTTTA-TAT
* *
4224639 TATTATTTATCTATTTACATATTATCATTTATCTATTAATATATATTTTT-TAT
1 T-TTATTTATTTATTTA-TTATTAT-ATTTATCTATT-AT-TATATTTTTATAT
4224692 TTTA-TTATTT
1 TTTATTTATTT
4224702 TTTTTCTTGG
Statistics
Matches: 92, Mismatches: 10, Indels: 27
0.71 0.08 0.21
Matches are distributed among these distances:
51 8 0.09
52 32 0.35
53 27 0.29
54 3 0.03
55 7 0.08
56 11 0.12
57 2 0.02
58 2 0.02
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (49 bp):
TTTATTTATTTATTTATTATTATATTTATCTATTATTATATTTTTATAT
Done.