Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold226
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: 1170647
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 1 of 8
Found at i:668 original size:8 final size:9
Alignment explanation
Indices: 645--700 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
635 AAAGATGTCA
645 TTAAAAAAT
1 TTAAAAAAT
654 TTAAAAAAT
1 TTAAAAAAT
663 TTAAAAATAATT
1 TT-AAAA-AA-T
*
675 TTTAAAAAT
1 TTAAAAAAT
*
684 TTTAAAAA-
1 TTAAAAAAT
692 -TAAAAAAT
1 TTAAAAAAT
700 T
1 T
701 ATTTTTAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
7 6 0.15
9 20 0.50
10 6 0.15
11 5 0.12
12 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
TTAAAAAAT
Found at i:678 original size:22 final size:22
Alignment explanation
Indices: 653--694 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
643 CATTAAAAAA
653 TTTAAAAAATTTAAAAATAATT
1 TTTAAAAAATTTAAAAATAATT
*
675 TTTAAAAATTTTAAAAATAA
1 TTTAAAAAATTTAAAAATAA
695 AAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAAAATTTAAAAATAATT
Found at i:684 original size:30 final size:29
Alignment explanation
Indices: 648--713 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
638 GATGTCATTA
*
648 AAAAATTTAAAAAATTTAAAAATAATTTTT
1 AAAAATTTAAAAAA-TAAAAAATAATTTTT
* *
678 AAAAATTTTAAAAATAAAAAATTATTTTT
1 AAAAATTTAAAAAATAAAAAATAATTTTT
*
707 AATAATT
1 AAAAATT
714 ATTTTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 19 0.59
30 13 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAAATTTAAAAAATAAAAAATAATTTTT
Found at i:715 original size:13 final size:12
Alignment explanation
Indices: 695--768 Score: 71
Period size: 13 Copynumber: 6.0 Consensus size: 12
685 TTAAAAATAA
695 AAAATTATTTTT
1 AAAATTATTTTT
707 AATAATTATTTTT
1 AA-AATTATTTTT
* **
720 AAAATCA--TAA
1 AAAATTATTTTT
730 AAAATTATTTTT
1 AAAATTATTTTT
742 AATAATTATTTTTT
1 AA-AATTA-TTTTT
756 AAAATTATATTTT
1 AAAATTAT-TTTT
769 TGATAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 7 0.14
12 10 0.20
13 26 0.52
14 7 0.14
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (12 bp):
AAAATTATTTTT
Found at i:735 original size:35 final size:35
Alignment explanation
Indices: 683--760 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
673 TTTTTAAAAA
683 TTTTAAAA-ATAAAAAATTATTTTTAATAATTA-T
1 TTTTAAAATATAAAAAATTATTTTTAATAATTATT
716 TTTTAAAATCATAAAAAATTATTTTTAATAATTATT
1 TTTTAAAAT-ATAAAAAATTATTTTTAATAATTATT
752 TTTTAAAAT
1 TTTTAAAAT
761 TATATTTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
33 8 0.19
35 24 0.57
36 10 0.24
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (35 bp):
TTTTAAAATATAAAAAATTATTTTTAATAATTATT
Found at i:820 original size:33 final size:34
Alignment explanation
Indices: 781--850 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 34
771 ATAAATTTTT
*
781 AAAATAATATTTATTTTTAATATTAAT-AAATTA
1 AAAATAATATTTATTTATAATATTAATAAAATTA
*
814 AAAATAATATTTATTTATAATATTATTAAAATTA
1 AAAATAATATTTATTTATAATATTAATAAAATTA
848 AAA
1 AAA
851 TAAATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 25 0.74
34 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
AAAATAATATTTATTTATAATATTAATAAAATTA
Found at i:845 original size:27 final size:27
Alignment explanation
Indices: 754--845 Score: 80
Period size: 33 Copynumber: 3.3 Consensus size: 27
744 TAATTATTTT
* * *
754 TTAAAATTATATTT-TTGATAA-ATTT
1 TTAAAATAATATTTATTTATAATATTA
*
779 TTAAAATAATATTTATTTTTAATATTAATAAA
1 TTAAAATAATATTTATTTATAATA-T--T--A
811 TTAAAAATAATATTTATTTATAATATTA
1 TT-AAAATAATATTTATTTATAATATTA
839 TTAAAAT
1 TTAAAAT
846 TAAAATAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
25 13 0.24
26 5 0.09
27 6 0.11
28 4 0.07
30 2 0.04
32 3 0.06
33 21 0.39
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TTAAAATAATATTTATTTATAATATTA
Found at i:899 original size:20 final size:20
Alignment explanation
Indices: 859--899 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
849 AATAAATAAT
*
859 TTTTTAAAATTTTAATTTTA
1 TTTTTAAAATTTTAATATTA
* *
879 TTTTTATAATTTTTATATTA
1 TTTTTAAAATTTTAATATTA
899 T
1 T
900 AATATATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTAAAATTTTAATATTA
Found at i:955 original size:28 final size:28
Alignment explanation
Indices: 902--955 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
892 TATATTATAA
* * *
902 TATATTTAAAATTAAATTTATTAAATTT
1 TATATTTAAAAATAAATATATAAAATTT
930 TATATTTAAAGAATAAATATA-AAAAT
1 TATATTTAAA-AATAAATATATAAAAT
956 AAATTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 14 0.64
29 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
TATATTTAAAAATAAATATATAAAATTT
Found at i:1320 original size:22 final size:22
Alignment explanation
Indices: 1294--1340 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1284 ATTTCATTAA
1294 TTTTGTACCAGATATATGTATT
1 TTTTGTACCAGATATATGTATT
*
1316 TTTTGTACTAGATATATGTATT
1 TTTTGTACCAGATATATGTATT
1338 TTT
1 TTT
1341 ACATCAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (22 bp):
TTTTGTACCAGATATATGTATT
Found at i:2122 original size:2 final size:2
Alignment explanation
Indices: 2117--2145 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2107 TATATAACTT
2117 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
2146 CACGTAGATT
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:2182 original size:2 final size:2
Alignment explanation
Indices: 2175--2203 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2165 AAGATTGTGA
2175 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
2204 GTGTAGCCAT
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:3598 original size:2 final size:2
Alignment explanation
Indices: 3593--3625 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3583 CTCTTGCAGA
3593 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
3626 GATAAAGAAA
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:3717 original size:14 final size:14
Alignment explanation
Indices: 3689--3723 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
3679 TAATATAGTG
3689 ATATAATTTTTAAA
1 ATATAATTTTTAAA
3703 ATAT-ATTTTTAAA
1 ATATAATTTTTAAA
*
3716 AAATAATT
1 ATATAATT
3724 AACAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATAATTTTTAAA
Found at i:3787 original size:2 final size:2
Alignment explanation
Indices: 3782--3816 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3772 TATATCGTTA
3782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3817 AAATTGTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4031 original size:19 final size:19
Alignment explanation
Indices: 4009--4052 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3999 ATGAATAATA
*
4009 AATTTTGATA-TCTAAATTT
1 AATTTTCATATTC-AAATTT
*
4028 AATTTTCATATTCATATTT
1 AATTTTCATATTCAAATTT
4047 AATTTT
1 AATTTT
4053 AGTTTGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (19 bp):
AATTTTCATATTCAAATTT
Found at i:4209 original size:27 final size:26
Alignment explanation
Indices: 4148--4212 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
4138 ATAATATATG
* *
4148 AATAATATATAATTTAAATTTTAAATT
1 AATAAAATAT-ATTTAAATTTAAAATT
*
4175 AATTAAATATATTTAAATTTAAATATTT
1 AATAAAATATATTTAAATTTAAA-A-TT
4203 AA-AAAATATA
1 AATAAAATATA
4213 AATATTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 12 0.38
27 16 0.50
28 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AATAAAATATATTTAAATTTAAAATT
Found at i:4211 original size:25 final size:26
Alignment explanation
Indices: 4159--4221 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
4149 ATAATATATA
*
4159 ATTTAAATTTTAAATTAATTAAATAT
1 ATTTAAATTTTAAATTAATTAAAAAT
*
4185 ATTTAAA-TTTAAA-TATTTAAAAA-
1 ATTTAAATTTTAAATTAATTAAAAAT
*
4208 ATATAAATATTTAA
1 ATTTAAAT-TTTAA
4222 TCCGTTATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 6 0.19
24 8 0.25
25 11 0.34
26 7 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTAAATTTTAAATTAATTAAAAAT
Found at i:4214 original size:17 final size:17
Alignment explanation
Indices: 4189--4221 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4179 AAATATATTT
*
4189 AAATTTAAATATTTAAA
1 AAATATAAATATTTAAA
4206 AAATATAAATATTTAA
1 AAATATAAATATTTAA
4222 TCCGTTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATAAATATTTAAA
Found at i:4312 original size:34 final size:35
Alignment explanation
Indices: 4248--4317 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 35
4238 CTCTAGGCCC
*
4248 ATGCATGATATAATAAAAGAATAAAAAGGAATGGTG
1 ATGCATGAAATAATAAAAG-ATAAAAAGGAATGGTG
4284 ATGCATGAAATAATAAAAG-TAAAAAGGAATGGTG
1 ATGCATGAAATAATAAAAGATAAAAAGGAATGGTG
4318 TGAAATTGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 15 0.45
36 18 0.55
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.21
Consensus pattern (35 bp):
ATGCATGAAATAATAAAAGATAAAAAGGAATGGTG
Found at i:8235 original size:2 final size:2
Alignment explanation
Indices: 8228--8259 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8218 AAAAATTTTC
8228 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
8260 GAGATTCAAT
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:8591 original size:23 final size:24
Alignment explanation
Indices: 8547--8597 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
8537 TGATAGTTAG
* *
8547 AAAAAAATAAATATAAAT-TATA-T
1 AAAAAAAT-TATACAAATATATACT
8570 AAAAAAATTATACAAATATATACT
1 AAAAAAATTATACAAATATATACT
8594 AAAA
1 AAAA
8598 TATGATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 12 0.50
24 5 0.21
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (24 bp):
AAAAAAATTATACAAATATATACT
Found at i:11301 original size:30 final size:28
Alignment explanation
Indices: 11270--11329 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 28
11260 ATTATTTTTA
11270 AAATA-TAATATTTAATAAATTTTAAATTT
1 AAATATTAATATTT-AT-AATTTTAAATTT
*
11299 AAATATTAATATTTATAATTTT-ATTTT
1 AAATATTAATATTTATAATTTTAAATTT
11326 AAAT
1 AAAT
11330 TGTGACCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 8 0.28
28 6 0.21
29 7 0.24
30 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AAATATTAATATTTATAATTTTAAATTT
Found at i:11959 original size:28 final size:28
Alignment explanation
Indices: 11900--11960 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
11890 TACTAGGTTT
* * * *
11900 TTTTATTTATTTAAGTAATATTATTTAT
1 TTTTATTAATTTAAGTAAAATTATATAA
11928 TTTTATTAATTTAAGTTAAAATTA-ATAA
1 TTTTATTAATTTAAG-TAAAATTATATAA
11956 TTTTA
1 TTTTA
11961 AATATATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTTATTAATTTAAGTAAAATTATATAA
Found at i:12015 original size:24 final size:24
Alignment explanation
Indices: 11986--12119 Score: 75
Period size: 24 Copynumber: 5.7 Consensus size: 24
11976 TATGAAATAA
*
11986 ATATAATATAAA-ATATATTTATATT
1 ATATAATATAAATATA-ATATA-ATT
* *
12011 A-ATAATTTTAGATATAATATAATT
1 ATATAA-TATAAATATAATATAATT
* **
12035 ATATAATATAAATATAATAAAAGA
1 ATATAATATAAATATAATATAATT
* * *
12059 AAATAA-ATAAA-AAAATATAA-A
1 ATATAATATAAATATAATATAATT
* *
12080 ATATAATGATAAAAAATTATATAA--
1 ATATAAT-AT-AAATATAATATAATT
12104 ATATAATATAAATATA
1 ATATAATATAAATATA
12120 TGAATAAATT
Statistics
Matches: 86, Mismatches: 16, Indels: 17
0.72 0.13 0.14
Matches are distributed among these distances:
21 6 0.07
22 12 0.14
23 9 0.10
24 36 0.42
25 20 0.23
26 3 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
ATATAATATAAATATAATATAATT
Found at i:12040 original size:13 final size:11
Alignment explanation
Indices: 12022--12158 Score: 84
Period size: 11 Copynumber: 11.9 Consensus size: 11
12012 ATAATTTTAG
12022 ATATAATATAA
1 ATATAATATAA
12033 TTATATAATATAA
1 --ATATAATATAA
12046 ATATAATA-AA
1 ATATAATATAA
* *
12056 AGAAAATAAATAA
1 ATATAAT--ATAA
*
12069 A-AAAATATAAA
1 ATATAATAT-AA
12080 ATATAATGATAAA
1 ATATAAT-AT-AA
* *
12093 AAATTATATAA
1 ATATAATATAA
12104 ATATAATATAA
1 ATATAATATAA
12115 ATAT-ATGAATAA
1 ATATAAT--ATAA
* **
12127 ATTTAA-ATTT
1 ATATAATATAA
12137 ATATAATATAA
1 ATATAATATAA
12148 ATTATAATATA
1 A-TATAATATA
12159 TCAAAATTTA
Statistics
Matches: 100, Mismatches: 13, Indels: 23
0.74 0.10 0.17
Matches are distributed among these distances:
10 18 0.18
11 29 0.29
12 28 0.28
13 25 0.25
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
ATATAATATAA
Found at i:12091 original size:23 final size:23
Alignment explanation
Indices: 12035--12115 Score: 78
Period size: 23 Copynumber: 3.5 Consensus size: 23
12025 TAATATAATT
* *
12035 ATATAATATAAATATAATA-AAAGA
1 ATATAATATAAA-AAAATATATA-A
*
12059 AAATAA-ATAAAAAAATATA-AA
1 ATATAATATAAAAAAATATATAA
*
12080 ATATAATGATAAAAAATTATATAA
1 ATATAAT-ATAAAAAAATATATAA
12104 ATATAATATAAA
1 ATATAATATAAA
12116 TATATGAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.12
22 6 0.12
23 23 0.47
24 14 0.29
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
ATATAATATAAAAAAATATATAA
Found at i:12109 original size:31 final size:31
Alignment explanation
Indices: 12071--12178 Score: 85
Period size: 38 Copynumber: 3.2 Consensus size: 31
12061 ATAAATAAAA
12071 AAATATAAAATATAATGATAAAAAATTATAT
1 AAATATAAAATATAATGATAAAAAATTATAT
*
12102 AAATATAATATAAATATATGAATAAATTTAAATT-TAT
1 AAATATAA-A-ATATA-ATG-ATAAA---AAATTATAT
* *
12139 ATAATATAAATTATAAT-ATATCAAAATTTATAT
1 A-AATATAAAATATAATGATA--AAAAATTATAT
12172 AAATATA
1 AAATATA
12179 TTATATTTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 21
0.71 0.05 0.24
Matches are distributed among these distances:
31 8 0.13
32 11 0.18
33 11 0.18
34 3 0.05
35 9 0.15
36 3 0.05
37 5 0.08
38 12 0.19
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (31 bp):
AAATATAAAATATAATGATAAAAAATTATAT
Found at i:12490 original size:23 final size:23
Alignment explanation
Indices: 12464--12532 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 23
12454 GTATTCGTAT
12464 ATATGTTATTTTTTATATATAA-A
1 ATAT-TTATTTTTTATATATAATA
12487 ATATTATATTTTTGTATAT-TAATA
1 ATATT-TATTTTT-TATATATAATA
*
12511 ATTTATTTTATTTTATATATAT
1 A--TA-TTTATTTTTTATATAT
12533 TTTTATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
22 1 0.03
23 14 0.37
24 7 0.18
25 5 0.13
26 9 0.24
27 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (23 bp):
ATATTTATTTTTTATATATAATA
Found at i:12498 original size:21 final size:23
Alignment explanation
Indices: 12469--12531 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
12459 CGTATATATG
*
12469 TTATTTTTTATATATAA-AA-TA
1 TTATATTTTATATATAATAATTA
*
12490 TTATATTTTTGTATATTAATAATTTA
1 TTATA-TTTTATATA-TAATAA-TTA
*
12516 TTTTATTTTATATATA
1 TTATATTTTATATATA
12532 TTTTTATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 4 0.12
22 8 0.24
23 3 0.09
24 4 0.12
25 8 0.24
26 6 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTATATTTTATATATAATAATTA
Found at i:12981 original size:21 final size:23
Alignment explanation
Indices: 12950--12991 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
12940 TCCGCTCCCT
*
12950 CGTCTTTTTTTTC-TTCTGTTTC
1 CGTCTTTTTTTCCTTTCTGTTTC
12972 CGTC-TTTTTTCCTTTCTGTT
1 CGTCTTTTTTTCCTTTCTGTT
12992 ATTGTTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.00, C:0.24, G:0.10, T:0.67
Consensus pattern (23 bp):
CGTCTTTTTTTCCTTTCTGTTTC
Found at i:13763 original size:162 final size:161
Alignment explanation
Indices: 13431--13778 Score: 502
Period size: 162 Copynumber: 2.1 Consensus size: 161
13421 CCGTATTTAT
* * *
13431 ATTATTTTTCATGTTGTGTTTTAATTTTTTATAGAGATCTTAAGTTTGTATTATATCTCAATTCA
1 ATTATTTTTTATATTGTG-TTT-ATTTTTTATAGAGATCTTAAGTTTATATTATATCTCAATTCA
*
13496 TGTTATATTTTGCATAGCTAATTACCGTGATTTATATAAAATCAGCTAGATAAATTCACCCAGTA
64 TGTTATATTTTGCATAGCTAATTACCGTGATTTATATAAAATCAACTAGATAAATTCACCCAGTA
*
13561 CTGACACGTAGTATTTTTTTTACGTTTAGCAAG
129 CTGACACGTAGTATTTTTTTTACATTTAGCAAG
* * *
13594 ATTATTTTTTAATATTGTGTTTATGTTTTTATATAGATGTTATGTTTATATTATATCTCAATTCA
1 ATTATTTTTT-ATATTGTGTTTAT-TTTTTATAGAGATCTTAAGTTTATATTATATCTCAATTCA
* ***
13659 TGTTATATTTTGCATAGCT-ATTACTGTGATTTATATAAAATCAACTAGATAAATTCACTTGGTA
64 TGTTATATTTTGCATAGCTAATTACCGTGATTTATATAAAATCAACTAGATAAATTCACCCAGTA
* * *
13723 TTGACACGT-GATATTTTTTTTGCATTTAGTAAG
129 CTGACACGTAG-TATTTTTTTTACATTTAGCAAG
13756 ATTATTTTTTATATTGTGTTTAT
1 ATTATTTTTTATATTGTGTTTAT
13779 ATTATATCTT
Statistics
Matches: 167, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
161 14 0.08
162 79 0.47
163 67 0.40
164 7 0.04
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.49
Consensus pattern (161 bp):
ATTATTTTTTATATTGTGTTTATTTTTTATAGAGATCTTAAGTTTATATTATATCTCAATTCATG
TTATATTTTGCATAGCTAATTACCGTGATTTATATAAAATCAACTAGATAAATTCACCCAGTACT
GACACGTAGTATTTTTTTTACATTTAGCAAG
Found at i:13802 original size:17 final size:18
Alignment explanation
Indices: 13780--13833 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 18
13770 TGTGTTTATA
*
13780 TTATATCTTA-ATATATT
1 TTATATCTTATATAAATT
*
13797 TTATATTTTATATAAATT
1 TTATATCTTATATAAATT
* *
13815 TTTTAT-ATAT-TAAATT
1 TTATATCTTATATAAATT
13831 TTA
1 TTA
13834 ACTTTAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 8 0.26
17 12 0.39
18 11 0.35
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATCTTATATAAATT
Found at i:14269 original size:17 final size:16
Alignment explanation
Indices: 14243--14289 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
14233 AAATTTATTT
*
14243 AAATTCAATTTAATAAA
1 AAATTAAATTTAA-AAA
14260 AAATTAAATTT-AAAA
1 AAATTAAATTTAAAAA
* *
14275 AATTTAAACTTAAAA
1 AAATTAAATTTAAAA
14290 TAATATCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 12 0.46
16 4 0.15
17 10 0.38
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATTAAATTTAAAAA
Found at i:14273 original size:14 final size:15
Alignment explanation
Indices: 14256--14289 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
14246 TTCAATTTAA
*
14256 TAAAAAA-TTAAATT
1 TAAAAAATTTAAACT
14270 TAAAAAATTTAAACT
1 TAAAAAATTTAAACT
14285 TAAAA
1 TAAAA
14290 TAATATCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAAAATTTAAACT
Found at i:14301 original size:23 final size:22
Alignment explanation
Indices: 14275--14317 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
14265 AAATTTAAAA
14275 AATTTAAACTTAAAATAATATCC
1 AATTTAAACTTAAAA-AATATCC
14298 AATTTAAACTTAAAAAATAT
1 AATTTAAACTTAAAAAATAT
14318 AATAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (22 bp):
AATTTAAACTTAAAAAATATCC
Found at i:16569 original size:15 final size:15
Alignment explanation
Indices: 16545--16576 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16535 CAGAAAGATG
16545 AATTTATCTTACGTT
1 AATTTATCTTACGTT
*
16560 AATTTGTCTTACGTT
1 AATTTATCTTACGTT
16575 AA
1 AA
16577 ACCTTTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.50
Consensus pattern (15 bp):
AATTTATCTTACGTT
Found at i:24632 original size:2 final size:2
Alignment explanation
Indices: 24625--24660 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24615 ATGGGGATTG
24625 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
24661 TTTGATTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29049 original size:15 final size:16
Alignment explanation
Indices: 29020--29049 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29010 ATGTTACACT
29020 TAAAATAGCAATATAG
1 TAAAATAGCAATATAG
29036 TAAAATAG-AATATA
1 TAAAATAGCAATATA
29050 AATTTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.27
Consensus pattern (16 bp):
TAAAATAGCAATATAG
Found at i:30050 original size:32 final size:32
Alignment explanation
Indices: 29958--30075 Score: 94
Period size: 32 Copynumber: 3.7 Consensus size: 32
29948 GAATAAACTC
* * * *
29958 AAACTCAAATAAGCCCGAACCCAAATAAACCT
1 AAACTCGAATAAGCTCGAACCCAAAAAAATCT
* * ** * **
29990 GAACTCGAAAAAATTCAAACCCGTAAAAATCT
1 AAACTCGAATAAGCTCGAACCCAAAAAAATCT
*
30022 AAAC-CTGAATAAGCTCGAACCCAAAAAAATTT
1 AAACTC-GAATAAGCTCGAACCCAAAAAAATCT
* *
30054 AAATTCGAATAAGCTTGAACCC
1 AAACTCGAATAAGCTCGAACCC
30076 GAACCTGTCC
Statistics
Matches: 63, Mismatches: 21, Indels: 4
0.72 0.24 0.05
Matches are distributed among these distances:
31 1 0.02
32 61 0.97
33 1 0.02
ACGTcount: A:0.48, C:0.25, G:0.09, T:0.18
Consensus pattern (32 bp):
AAACTCGAATAAGCTCGAACCCAAAAAAATCT
Found at i:37213 original size:23 final size:25
Alignment explanation
Indices: 37187--37241 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 25
37177 CAAGAAAAAA
37187 TTTTAAAATTTA-TTTT-AATTA-AT
1 TTTTAAAA-TTACTTTTAAATTATAT
*
37210 TTTTATAATTACTTTTAAATTATAT
1 TTTTAAAATTACTTTTAAATTATAT
37235 TATTTAA
1 T-TTTAA
37242 TAAACTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 3 0.12
23 11 0.42
24 5 0.19
25 3 0.12
26 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTAAAATTACTTTTAAATTATAT
Found at i:37471 original size:22 final size:22
Alignment explanation
Indices: 37428--37471 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
37418 TTTAATTATT
*
37428 ATTTATAAACATAATTTTTATA
1 ATTTATAAACATAATTTATATA
*
37450 ATTTATAAATA-AATTATATATA
1 ATTTATAAACATAATT-TATATA
37472 TATATATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTATAAACATAATTTATATA
Found at i:37907 original size:16 final size:16
Alignment explanation
Indices: 37869--37907 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
37859 ATATGAAAAA
*
37869 ATAATTAAAATTTAAT
1 ATAATTAAAAATTAAT
*
37885 AT-GTTAAAAATTAAT
1 ATAATTAAAAATTAAT
37900 ATAATTAA
1 ATAATTAA
37908 TGTATTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
ATAATTAAAAATTAAT
Found at i:37907 original size:24 final size:23
Alignment explanation
Indices: 37880--37926 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
37870 TAATTAAAAT
*
37880 TTAATATGTTAAAAATTAATATAA
1 TTAATATATT-AAAATTAATATAA
* *
37904 TTAATGTATTAAAATTTATATAA
1 TTAATATATTAAAATTAATATAA
37927 ATATATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAATATATTAAAATTAATATAA
Found at i:38443 original size:16 final size:15
Alignment explanation
Indices: 38421--38485 Score: 78
Period size: 16 Copynumber: 4.2 Consensus size: 15
38411 AATAAAAAAT
38421 AAAAATTTAAATTTA
1 AAAAATTTAAATTTA
*
38436 AGAAAATTTGAATTTA
1 A-AAAATTTAAATTTA
*
38452 AAAAATTTAAACTTA
1 AAAAATTTAAATTTA
38467 AAATAATATT-AATTTA
1 AAA-AAT-TTAAATTTA
38483 AAA
1 AAA
38486 TAATCGAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
15 16 0.37
16 25 0.58
17 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (15 bp):
AAAAATTTAAATTTA
Found at i:38443 original size:39 final size:41
Alignment explanation
Indices: 38373--38456 Score: 102
Period size: 39 Copynumber: 2.1 Consensus size: 41
38363 ATAAATTTGT
* ***
38373 TAAAAATATATAAATATAAATTTATTTAAATTT-AATTTAA
1 TAAAAATATAAAAATATAAATTTAAGAAAATTTGAATTTAA
*
38413 TAAAAA-ATAAAAATTTAAATTTAAGAAAATTTGAATTTAA
1 TAAAAATATAAAAATATAAATTTAAGAAAATTTGAATTTAA
38453 -AAAA
1 TAAAA
38457 TTTAAACTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
39 25 0.66
40 13 0.34
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (41 bp):
TAAAAATATAAAAATATAAATTTAAGAAAATTTGAATTTAA
Found at i:38459 original size:31 final size:31
Alignment explanation
Indices: 38421--38503 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 31
38411 AATAAAAAAT
*
38421 AAAAATTTAAATTTAAGAA-AAT-TTGAATTTA
1 AAAAATTTAAACTTAA-AATAATATT-AATTTA
38452 AAAAATTTAAACTTAAAATAATATTAATTTA
1 AAAAATTTAAACTTAAAATAATATTAATTTA
** *
38483 AAATAATCGAATCTTAAAATA
1 AAA-AATTTAAACTTAAAATA
38504 TTTAAATCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
30 2 0.04
31 27 0.60
32 16 0.36
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (31 bp):
AAAAATTTAAACTTAAAATAATATTAATTTA
Found at i:38486 original size:16 final size:16
Alignment explanation
Indices: 38424--38510 Score: 76
Period size: 16 Copynumber: 5.6 Consensus size: 16
38414 AAAAAATAAA
38424 AATTTAAATTTAAGAA-
1 AATTTAAATTTAA-AAT
*
38440 AATTTGAATTTAAAA-
1 AATTTAAATTTAAAAT
*
38455 AATTTAAACTTAAAAT
1 AATTTAAATTTAAAAT
38471 AATATT-AATTTAAAAT
1 AAT-TTAAATTTAAAAT
**
38487 AA-TCGAATCTTAAAAT
1 AATTTAAAT-TTAAAAT
38503 -ATTTAAAT
1 AATTTAAAT
38511 CTAATTTTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
14 1 0.02
15 19 0.32
16 37 0.63
17 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:38647 original size:16 final size:16
Alignment explanation
Indices: 38600--38654 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
38590 TTTAAATCTA
*
38600 AATTTAAAATAAAAAT
1 AATTTAAAATTAAAAT
* * *
38616 -A-TTATATTTAATAT
1 AATTTAAAATTAAAAT
38630 AATTTAAAATTAAAAT
1 AATTTAAAATTAAAAT
38646 AATTTAAAA
1 AATTTAAAA
38655 ATTATTTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 9 0.30
15 2 0.07
16 19 0.63
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTAAAATTAAAAT
Found at i:39408 original size:2 final size:2
Alignment explanation
Indices: 39403--39428 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39393 GTCTATTTTC
39403 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
39429 TGCAATTTAT
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:40039 original size:70 final size:70
Alignment explanation
Indices: 39926--40066 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
39916 CTTTACCTGT
39926 TACTTGTTTACTTTGACTAAATGCTTCTGCACTTGAAGCTACGCTCATCTTATTAAAAAGCTACC
1 TACTTGTTTACTTTGACTAAATGCTTCTGCACTTGAAGCTACGCTCATCTTATTAAAAAGCTACC
39991 AAAAA
66 AAAAA
*
39996 TACTTGTTTACTTTGACTAAATGCTTCTGCACTTGAAGCTACGCTCATCTTATTAAAAAGCTGCC
1 TACTTGTTTACTTTGACTAAATGCTTCTGCACTTGAAGCTACGCTCATCTTATTAAAAAGCTACC
40061 AAAAA
66 AAAAA
40066 T
1 T
40067 CCAGCACATA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (70 bp):
TACTTGTTTACTTTGACTAAATGCTTCTGCACTTGAAGCTACGCTCATCTTATTAAAAAGCTACC
AAAAA
Found at i:40771 original size:15 final size:15
Alignment explanation
Indices: 40753--40783 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40743 ATAGATGAAT
40753 ATTTATCTTACGTTA
1 ATTTATCTTACGTTA
*
40768 ATTTGTCTTACGTTA
1 ATTTATCTTACGTTA
40783 A
1 A
40784 ACCTTTAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.52
Consensus pattern (15 bp):
ATTTATCTTACGTTA
Found at i:42818 original size:16 final size:16
Alignment explanation
Indices: 42768--42822 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
42758 AATTTTAAAT
*
42768 TTTTAAATTATTTTTAA
1 TTTTAAATTA-TTTTGA
* * * *
42785 GTTTGAATCATTTCGA
1 TTTTAAATTATTTTGA
42801 TTTTAAATTATTTTGA
1 TTTTAAATTATTTTGA
42817 TTTTAA
1 TTTTAA
42823 GTTTAAGTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
16 22 0.76
17 7 0.24
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (16 bp):
TTTTAAATTATTTTGA
Found at i:42819 original size:22 final size:23
Alignment explanation
Indices: 42794--42846 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
42784 AGTTTGAATC
42794 ATTTCGATTTTAAATTATT-TTG
1 ATTTCGATTTTAAATTATTCTTG
** * * *
42816 ATTTTAAGTTTAAGTTATTCTTT
1 ATTTCGATTTTAAATTATTCTTG
42839 ATTTCGAT
1 ATTTCGAT
42847 CATTTTAATT
Statistics
Matches: 22, Mismatches: 8, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.58
Consensus pattern (23 bp):
ATTTCGATTTTAAATTATTCTTG
Found at i:42880 original size:16 final size:16
Alignment explanation
Indices: 42816--42890 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 16
42806 AATTATTTTG
42816 ATTTTAAGTTTA-AGTT
1 ATTTTAAGTTTAGA-TT
* * *
42832 ATTCTTTA-TTTCGATC
1 ATT-TTAAGTTTAGATT
*
42848 ATTTTAA-TTTCGAATT
1 ATTTTAAGTTTAG-ATT
42864 ATTTTAAGTTTAGATT
1 ATTTTAAGTTTAGATT
*
42880 A-ATTAAGTTTA
1 ATTTTAAGTTTA
42891 ACATCAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
15 17 0.35
16 23 0.48
17 8 0.17
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (16 bp):
ATTTTAAGTTTAGATT
Found at i:42967 original size:16 final size:15
Alignment explanation
Indices: 42941--42974 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
42931 AGGTTTATCG
*
42941 AATTTGATCATTTTA
1 AATTTGATCATTTCA
42956 AATTTAGATCATTTCA
1 AATTT-GATCATTTCA
42972 AAT
1 AAT
42975 AAAAATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (15 bp):
AATTTGATCATTTCA
Found at i:47348 original size:2 final size:2
Alignment explanation
Indices: 47343--47367 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47333 TATATATATA
47343 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
47368 AAAATTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:49956 original size:16 final size:16
Alignment explanation
Indices: 49937--49974 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
49927 ATATAATTAA
49937 TTATATTTATTAT-CTT
1 TTATATTTATT-TCCTT
49953 TTATATTTATTTCCTT
1 TTATATTTATTTCCTT
49969 TTATAT
1 TTATAT
49975 AAAATATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATATTTATTTCCTT
Found at i:50417 original size:16 final size:16
Alignment explanation
Indices: 50396--50433 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
50386 AAATAATTAA
*
50396 TTATATTTATTTTCTT
1 TTATATTTATTTCCTT
50412 TTATATTTATTTCCTT
1 TTATATTTATTTCCTT
*
50428 TAATAT
1 TTATAT
50434 AAAATATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATATTTATTTCCTT
Found at i:51832 original size:40 final size:41
Alignment explanation
Indices: 51755--51837 Score: 98
Period size: 40 Copynumber: 2.0 Consensus size: 41
51745 TTTAATATTT
***
51755 AAAATATTTTATATAATTAATTATATTTATTTTTTTATATA
1 AAAATATTTTATATAATTAATTATATTTATACATTTATATA
* *
51796 AAAAT-TTTTATTTAATTAACTTATATTT-TACATTTATCTA
1 AAAATATTTTATATAATTAA-TTATATTTATACATTTATATA
51836 AA
1 AA
51838 TAAATAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 23 0.64
41 13 0.36
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (41 bp):
AAAATATTTTATATAATTAATTATATTTATACATTTATATA
Found at i:52108 original size:3 final size:3
Alignment explanation
Indices: 52100--52149 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
52090 TTTATTTCTA
52100 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
52148 AT
1 AT
52150 ATGCCATGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:52887 original size:54 final size:54
Alignment explanation
Indices: 52828--52936 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
52818 TTTGCATTAC
52828 TAATATAAAACCTAAAGATTTAATGTTAGAACAATTGCTTGAGCCTATGTTTAA
1 TAATATAAAACCTAAAGATTTAATGTTAGAACAATTGCTTGAGCCTATGTTTAA
52882 TAATATAAAACCTAAAGATTTAATGTTAGAACAATTGCTTGAGCCTATGTTTAA
1 TAATATAAAACCTAAAGATTTAATGTTAGAACAATTGCTTGAGCCTATGTTTAA
52936 T
1 T
52937 GATGTGAAGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (54 bp):
TAATATAAAACCTAAAGATTTAATGTTAGAACAATTGCTTGAGCCTATGTTTAA
Found at i:53465 original size:2 final size:2
Alignment explanation
Indices: 53458--53487 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53448 TAATTATCCA
53458 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
53488 TGATTGATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55091 original size:2 final size:2
Alignment explanation
Indices: 55084--55127 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
55074 GATACAAGCG
55084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55126 AT
1 AT
55128 CTGTCGGACA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56465 original size:19 final size:20
Alignment explanation
Indices: 56443--56497 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
56433 AATATATACC
56443 TATTATATTTTATTATATT-
1 TATTATATTTTATTATATTA
* **
56462 TATTTTATTAAATTATATTA
1 TATTATATTTTATTATATTA
56482 TATATATATTTT-TTAT
1 TAT-TATATTTTATTAT
56498 GTCATGTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 16 0.57
20 7 0.25
21 5 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTATATTTTATTATATTA
Found at i:56480 original size:24 final size:26
Alignment explanation
Indices: 56443--56493 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
56433 AATATATACC
* *
56443 TATTATATTTTATTATAT-T-TATTT
1 TATTAAATTATATTATATATATATTT
56467 TATTAAATTATATTATATATATATTT
1 TATTAAATTATATTATATATATATTT
56493 T
1 T
56494 TTATGTCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 1 0.04
26 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TATTAAATTATATTATATATATATTT
Found at i:56482 original size:5 final size:5
Alignment explanation
Indices: 56443--56491 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
56433 AATATATACC
* * *
56443 TATTA TATTT TATTA TATT- TATTT TATTA AATTA TATTA TATATA TATT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT-TA TATT
56492 TTTTATGTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
4 4 0.11
5 28 0.76
6 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TATTA
Found at i:56614 original size:32 final size:33
Alignment explanation
Indices: 56573--56634 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
56563 TATTTTAATT
* *
56573 AATATTAAAAAATTTAATTTAAATTTAAATTCA
1 AATATTAAAAAATTAAATTTAAAATTAAATTCA
56606 AATA-TAAAAAATTAAATTTAAAATTAAAT
1 AATATTAAAAAATTAAATTTAAAATTAAAT
56635 ATAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (33 bp):
AATATTAAAAAATTAAATTTAAAATTAAATTCA
Found at i:56620 original size:26 final size:25
Alignment explanation
Indices: 56591--56648 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
56581 AAAATTTAAT
56591 TTAAATTT-AAATTCAAATATAAAAAA
1 TTAAATTTAAAATT-AAATAT-AAAAA
56617 TTAAATTTAAAATTAAATATAAAAA
1 TTAAATTTAAAATTAAATATAAAAA
56642 TTAAATT
1 TTAAATT
56649 ACATTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 12 0.39
26 14 0.45
27 5 0.16
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
TTAAATTTAAAATTAAATATAAAAA
Found at i:56628 original size:12 final size:12
Alignment explanation
Indices: 56582--56648 Score: 57
Period size: 12 Copynumber: 5.4 Consensus size: 12
56572 TAATATTAAA
*
56582 AAATTT-AATTT
1 AAATTTAAAATT
56593 AAATTT-AAATT
1 AAATTTAAAATT
*
56604 CAAATATAAAAAATT
1 -AAAT-T-TAAAATT
56619 AAATTTAAAATT
1 AAATTTAAAATT
*
56631 AAATATAAAAATT
1 AAAT-TTAAAATT
56644 AAATT
1 AAATT
56649 ACATTTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
11 10 0.21
12 15 0.32
13 13 0.28
14 4 0.09
15 5 0.11
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATTTAAAATT
Found at i:56752 original size:6 final size:6
Alignment explanation
Indices: 56741--56811 Score: 90
Period size: 6 Copynumber: 11.7 Consensus size: 6
56731 TGAAAATTAA
* * *
56741 TAAATTT TAATTT TAATTT TAATTT TAAATTT TAAA-T TAAATT TAAATT
1 TAAA-TT TAAATT TAAATT TAAATT TAAA-TT TAAATT TAAATT TAAATT
56790 TAAATT TAAATT TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAA
56812 CTTTCTTTTG
Statistics
Matches: 60, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.08
6 46 0.77
7 9 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TAAATT
Found at i:68563 original size:24 final size:25
Alignment explanation
Indices: 68514--68563 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
68504 GATACGGATA
* *
68514 TGTTAAATTTTTTTTCAAAAATTTT
1 TGTTAAATTTGTTTACAAAAATTTT
68539 TGTTAAATTTGTTTAC-AAAATTTT
1 TGTTAAATTTGTTTACAAAAATTTT
68563 T
1 T
68564 ATGTAATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (25 bp):
TGTTAAATTTGTTTACAAAAATTTT
Found at i:70315 original size:19 final size:19
Alignment explanation
Indices: 70291--70330 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
70281 ACTTAGTAAA
*
70291 TAATTAAGAA-ATATCACTT
1 TAATTAA-AAGATATAACTT
70310 TAATTAAAAGATATAACTT
1 TAATTAAAAGATATAACTT
70329 TA
1 TA
70331 TGATTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (19 bp):
TAATTAAAAGATATAACTT
Found at i:70538 original size:20 final size:19
Alignment explanation
Indices: 70502--70541 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
70492 AGTTTTTATT
70502 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
70521 TAAATATTAA-TATAAAA-A
1 TAAAT-TTAATTATAAAATA
70539 TAA
1 TAA
70542 TTTTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:71977 original size:23 final size:22
Alignment explanation
Indices: 71912--71977 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 22
71902 ATAACCGTTT
*
71912 ATTTAATA-AAAAATTATATGTAA
1 ATTTAATATAAAAA-TA-ATATAA
*
71935 ATTTAATTATAAAAA-CATATAA
1 ATTTAA-TATAAAAATAATATAA
71957 ATATTAATATAAAAATAATAT
1 AT-TTAATATAAAAATAATAT
71978 TTTAATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 15 0.42
23 14 0.39
24 2 0.06
25 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTTAATATAAAAATAATATAA
Found at i:73000 original size:3 final size:3
Alignment explanation
Indices: 72994--73020 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
72984 AAAGGAAAGA
72994 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
73021 CTTACTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:73294 original size:2 final size:2
Alignment explanation
Indices: 73287--73325 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
73277 GATGATGAGA
73287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73326 AAAGAAGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:75301 original size:27 final size:26
Alignment explanation
Indices: 75270--75334 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
75260 TAACTCGATT
75270 TATATTATTATTTAAATAATAAAAATA
1 TATATTATTATTT-AATAATAAAAATA
* *
75297 TATATT-TTAAATTTAATTATAAAATTA
1 TATATTATT--ATTTAATAATAAAAATA
75324 TATAATTATTA
1 TAT-ATTATTA
75335 ATATAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
26 2 0.06
27 21 0.66
28 7 0.22
29 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATATTATTATTTAATAATAAAAATA
Found at i:75354 original size:19 final size:23
Alignment explanation
Indices: 75308--75354 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 23
75298 ATATTTTAAA
75308 TTTAATTATAAAATTATATAATT
1 TTTAATTATAAAATTATATAATT
*
75331 ATTAA-TATAAAA-TAT-T-ATT
1 TTTAATTATAAAATTATATAATT
75350 TTTAA
1 TTTAA
75355 AATTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 7 0.32
20 1 0.05
21 3 0.14
22 7 0.32
23 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTAATTATAAAATTATATAATT
Found at i:76054 original size:27 final size:25
Alignment explanation
Indices: 76022--76071 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
76012 ATCATATCTT
76022 TTATAATTAAAAATATAATAAATATTA
1 TTATAATT--AAATATAATAAATATTA
*
76049 TTATAATTAATTATAATAAATAT
1 TTATAATTAAATATAATAAATAT
76072 CAATCGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.64
27 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TTATAATTAAATATAATAAATATTA
Found at i:76964 original size:16 final size:17
Alignment explanation
Indices: 76928--76969 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
76918 TGAAATTGAT
*
76928 TAATTCGAATCTAATAA
1 TAATTCAAATCTAATAA
*
76945 TAATTCAAATTTAA-AA
1 TAATTCAAATCTAATAA
76961 TAATTCAAA
1 TAATTCAAA
76970 CTCAACATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATTCAAATCTAATAA
Found at i:77793 original size:15 final size:15
Alignment explanation
Indices: 77769--77805 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
77759 TTTTTAAAAT
77769 TTAAAATAATCTAAC
1 TTAAAATAATCTAAC
* *
77784 TTAAACTAATCTAAT
1 TTAAAATAATCTAAC
77799 TTAAAAT
1 TTAAAAT
77806 TAACTCTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAAAATAATCTAAC
Found at i:85210 original size:36 final size:37
Alignment explanation
Indices: 85140--85226 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 37
85130 ATATGTAATA
* *
85140 TTATAAAAAAATATGTTAAGTTATATAAATTTTAAACT
1 TTATAAAAAAATATGTTAAATTATATAAAATTTAAA-T
*
85178 TTATAAAAAAAT-T-TTAAATTATTTAAAATTTAAAT
1 TTATAAAAAAATATGTTAAATTATATAAAATTTAAAT
* *
85213 TTTTAAAAATATAT
1 TTATAAAAAAATAT
85227 ATTTTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
35 11 0.26
36 19 0.44
37 1 0.02
38 12 0.28
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (37 bp):
TTATAAAAAAATATGTTAAATTATATAAAATTTAAAT
Found at i:85221 original size:16 final size:16
Alignment explanation
Indices: 85184--85238 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
85174 AACTTTATAA
85184 AAAAATTTTAAATTATTT
1 AAAAA-TTTAAATT-TTT
85202 -AAAATTTAAATTTTT
1 AAAAATTTAAATTTTT
* *
85217 AAAAATATATATTTTT
1 AAAAATTTAAATTTTT
*
85233 TAAAAT
1 AAAAAT
85239 AACATACATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 3 0.09
16 26 0.79
17 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAAATTTAAATTTTT
Found at i:85239 original size:16 final size:16
Alignment explanation
Indices: 85192--85239 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
85182 AAAAAAATTT
* *
85192 TAAATTATTTAAAATT
1 TAAATTTTTTAAAATA
*
85208 TAAATTTTTAAAAATA
1 TAAATTTTTTAAAATA
*
85224 TATATTTTTTAAAATA
1 TAAATTTTTTAAAATA
85240 ACATACATAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATTTTTTAAAATA
Found at i:89444 original size:19 final size:18
Alignment explanation
Indices: 89402--89447 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
89392 TAATTAAAAA
*
89402 TATATATAAATATAAATT
1 TATAAATAAATATAAATT
*
89420 TATAAATAAATATTTAATT
1 TATAAATAAATA-TAAATT
*
89439 TTTAAATAA
1 TATAAATAA
89448 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATAAATAAATATAAATT
Found at i:94600 original size:16 final size:16
Alignment explanation
Indices: 94579--94614 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
94569 ATTTAATTTA
*
94579 AGTTCGCATCATTTGG
1 AGTTCGCATCATTTCG
*
94595 AGTTCGGATCATTTCG
1 AGTTCGCATCATTTCG
94611 AGTT
1 AGTT
94615 AAGATCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (16 bp):
AGTTCGCATCATTTCG
Found at i:94620 original size:16 final size:16
Alignment explanation
Indices: 94586--94625 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
94576 TTAAGTTCGC
* **
94586 ATCATTTGGAGTTCGG
1 ATCATTTCGAGTTAAG
94602 ATCATTTCGAGTTAAG
1 ATCATTTCGAGTTAAG
94618 ATCATTTC
1 ATCATTTC
94626 AGATTCGAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (16 bp):
ATCATTTCGAGTTAAG
Found at i:94752 original size:15 final size:14
Alignment explanation
Indices: 94712--94759 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
94702 TAACTTTTTT
94712 ATCAAATTGAGTTAG
1 ATCAAATTGA-TTAG
94727 ATCAAA-T--TTAG
1 ATCAAATTGATTAG
94738 ATTCAAATTGATTAG
1 A-TCAAATTGATTAG
94753 -TCAAATT
1 ATCAAATT
94760 TTTTGAGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
13 8 0.28
14 1 0.03
15 10 0.34
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (14 bp):
ATCAAATTGATTAG
Found at i:95580 original size:31 final size:32
Alignment explanation
Indices: 95542--95609 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 32
95532 GGGATTTATA
*
95542 TCTTTTACATTATAAAAAA-AAAAAAACATGT
1 TCTTTTACATTAAAAAAAATAAAAAAACATGT
*
95573 TCTTTTACCTTAAAAAAAATAAAAAAACATGT
1 TCTTTTACATTAAAAAAAATAAAAAAACATGT
95605 TCTTT
1 TCTTT
95610 CACCTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 17 0.50
32 17 0.50
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (32 bp):
TCTTTTACATTAAAAAAAATAAAAAAACATGT
Found at i:95597 original size:32 final size:31
Alignment explanation
Indices: 95542--95621 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 31
95532 GGGATTTATA
* *
95542 TCTTTTACATTATAAAAAAAAAAAAACATGT
1 TCTTTTACCTTAAAAAAAAAAAAAAACATGT
95573 TCTTTTACCTTAAAAAAAATAAAAAAACATGT
1 TCTTTTACCTTAAAAAAAA-AAAAAAACATGT
* *
95605 TCTTTCACCTTTAAAAA
1 TCTTTTACCTTAAAAAA
95622 CTGGTAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 17 0.39
32 27 0.61
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.34
Consensus pattern (31 bp):
TCTTTTACCTTAAAAAAAAAAAAAAACATGT
Found at i:97966 original size:28 final size:31
Alignment explanation
Indices: 97926--97984 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
97916 GTTTAGATTA
97926 TTATTTAATAAATAAATTA-AAAATA-ATAT
1 TTATTTAATAAATAAATTATAAAATATATAT
* *
97955 TTATTTTA-AAATTAATTATAAAATATATAT
1 TTATTTAATAAATAAATTATAAAATATATAT
97985 ATTAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 9 0.35
29 13 0.50
30 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TTATTTAATAAATAAATTATAAAATATATAT
Found at i:98010 original size:19 final size:20
Alignment explanation
Indices: 97965--98011 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
97955 TTATTTTAAA
*
97965 ATTAATTATAAAATATATAT
1 ATTAAATATAAAATATATAT
*
97985 ATT-AATATAAAA-ATATTT
1 ATTAAATATAAAATATATAT
*
98003 TTTAAATAT
1 ATTAAATAT
98012 TTTAATGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 7 0.30
19 13 0.57
20 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTAAATATAAAATATATAT
Found at i:98336 original size:11 final size:10
Alignment explanation
Indices: 98328--98441 Score: 90
Period size: 11 Copynumber: 11.1 Consensus size: 10
98318 AATATATTCG
98328 TATTATATTTA
1 TATTATA-TTA
98339 TATATATATTA
1 TAT-TATATTA
98350 TATTATATTA
1 TATTATATTA
**
98360 TTATATATAAAA
1 -TAT-TATATTA
98372 TATTATA-TA
1 TATTATATTA
98381 T-TTATATTA
1 TATTATATTA
* *
98390 TATCATATCA
1 TATTATATTA
* *
98400 TATAATATTT
1 TATTATATTA
*
98410 TAATTATTTTA
1 T-ATTATATTA
98421 T-TTATATTA
1 TATTATATTA
98430 TATTTATATTA
1 TA-TTATATTA
98441 T
1 T
98442 TAAATTTTTG
Statistics
Matches: 83, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
8 5 0.06
9 13 0.16
10 25 0.30
11 31 0.37
12 9 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
TATTATATTA
Found at i:98342 original size:2 final size:2
Alignment explanation
Indices: 98331--98407 Score: 53
Period size: 2 Copynumber: 41.5 Consensus size: 2
98321 ATATTCGTAT
*
98331 TA TA TT TA TA TA TA TA T- TA TA T- TA TA T- TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
98369 -A AA TA T- TA TA TA TT TA TA T- TA TA TCA TA TCA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA TA TA TA T
98408 TTTAATTATT
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
1 8 0.13
2 48 0.80
3 4 0.07
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:98351 original size:5 final size:5
Alignment explanation
Indices: 98328--98441 Score: 90
Period size: 5 Copynumber: 22.2 Consensus size: 5
98318 AATATATTCG
**
98328 TATTA TATTTA TATATA TATTA TATTA TATTA TTATATA TAAAA TATTA
1 TATTA TA-TTA TAT-TA TATTA TATTA TATTA -TAT-TA TATTA TATTA
* * * * *
98377 TA-TA T-TTA TATTA TATCA TATCA TATAA TATTT TAATTA TTTTA T-TTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA T-ATTA TATTA TATTA
98425 TATTA TATTTA TATTA T
1 TATTA TA-TTA TATTA T
98442 TAAATTTTTG
Statistics
Matches: 90, Mismatches: 10, Indels: 18
0.76 0.08 0.15
Matches are distributed among these distances:
4 10 0.11
5 54 0.60
6 24 0.27
7 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:98387 original size:40 final size:39
Alignment explanation
Indices: 98332--98443 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 39
98322 TATTCGTATT
*
98332 ATATTTATATATATATTATATTATATTATTATATATAAA
1 ATATTTATATTTATATTATATTATATTATTATATATAAA
* * * *
98371 ATATTATATATTTATATTATATCATATCATATAATATTTTAA
1 ATATT-TATATTTATATTATATTATAT--TATTATATATAAA
*
98413 TTATTT-TATTTATATTATATTTATATTATTA
1 ATATTTATATTTATATTATA-TTATATTATTA
98444 AATTTTTGAG
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
39 9 0.15
40 32 0.52
41 6 0.10
42 14 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (39 bp):
ATATTTATATTTATATTATATTATATTATTATATATAAA
Found at i:98391 original size:35 final size:36
Alignment explanation
Indices: 98339--98430 Score: 102
Period size: 35 Copynumber: 2.6 Consensus size: 36
98329 ATTATATTTA
98339 TATATATATTATATTATATTATTAT-ATATAAAATAT
1 TATATAT-TTATATTATATTATTATCATATAAAATAT
* * *
98375 TATATATTTATATTATATCA-TATCATATAATATTT
1 TATATATTTATATTATATTATTATCATATAAAATAT
98410 TA-ATTATTT-TATTTATATTAT
1 TATA-TATTTATA-TTATATTAT
98431 ATTTATATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
34 6 0.12
35 35 0.73
36 7 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (36 bp):
TATATATTTATATTATATTATTATCATATAAAATAT
Found at i:99026 original size:2 final size:2
Alignment explanation
Indices: 99021--99072 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
99011 TTTATATGTG
* * * *
99021 TA TA TA TA TA TA TA TA TA TA TT TA TA TG TG TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
99063 TA -A TA TA TA T
1 TA TA TA TA TA T
99073 TTTTTTATTG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (2 bp):
TA
Found at i:99553 original size:2 final size:2
Alignment explanation
Indices: 99546--99583 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
99536 CTTACCATTA
99546 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
99584 CATCAATCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:100526 original size:3 final size:3
Alignment explanation
Indices: 100518--100543 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
100508 ATGGCATTTA
100518 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
100544 ACTTGTTTGA
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:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:101879 original size:24 final size:25
Alignment explanation
Indices: 101839--101888 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
101829 ATGTTAATCG
101839 ATTTATTTAAACGTAGAGT-AATTT
1 ATTTATTTAAACGTAGAGTAAATTT
* *
101863 ATTTGATTTAAA-TTAGATTAAATTT
1 ATTT-ATTTAAACGTAGAGTAAATTT
101888 A
1 A
101889 AAATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (25 bp):
ATTTATTTAAACGTAGAGTAAATTT
Found at i:104821 original size:48 final size:48
Alignment explanation
Indices: 104750--104849 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 48
104740 AACAAAGGAA
*
104750 AATGAAAACTTTCATCGTAAGTAAGAGATCAACATGCAAAATGACATC
1 AATGAAAACTTTCATCGTAAGTAAGAGATCAACATGCAAAATGACAAC
* *
104798 AATGAAAGCTTTCATTGTAAGTAAGAGATCAACATGCAAAATGACAAC
1 AATGAAAACTTTCATCGTAAGTAAGAGATCAACATGCAAAATGACAAC
104846 AATG
1 AATG
104850 TACACCTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (48 bp):
AATGAAAACTTTCATCGTAAGTAAGAGATCAACATGCAAAATGACAAC
Found at i:106285 original size:150 final size:149
Alignment explanation
Indices: 106097--106528 Score: 684
Period size: 150 Copynumber: 2.9 Consensus size: 149
106087 GGAAGAGAAA
*
106097 GAAAAATTAAAGTGTTTGAAGCACTTAATTTTAGTAGTTGCTATGTAAAAACGACGTTGAACGTT
1 GAAAAATTAAAGTGTTTGAAGCACTTAATTTTAGTAGTTGCTATGTAAAAACGAAGTTGAACGTT
106162 AAAAATTATGTTTTTTCGTAATTTTAATATTAAAAAAGTAAAAAAAAAGTTATTCTTTTATT-AA
66 AAAAATTATGTTTTTTCGTAATTTTAATATTAAAAAAGT-AAAAAAAA-TTATTCTTTTATTAAA
106226 AAATAGATTTAGGAAAGGAAG
129 AAATAGATTTAGGAAAGGAAG
* *
106247 GAAAAATTAAAGTATTTGAAGCACTTAATTTTAATAGTTGCTATGTAAAAACGAAGTTGAACGTT
1 GAAAAATTAAAGTGTTTGAAGCACTTAATTTTAGTAGTTGCTATGTAAAAACGAAGTTGAACGTT
* *
106312 AAAAATTATATTTTATCGTAATTTTAATATTAAAAAAGTAAAAAAAATTATTCTTTTATTAAAAA
66 AAAAATTATGTTTTTTCGTAATTTTAATATTAAAAAAGTAAAAAAAATTATTCTTTTATT-AAAA
106377 AATAGATTTAGGAAAGGAAG
130 AATAGATTTAGGAAAGGAAG
*
106397 GAAAAATTAAAGTGTTTGAAGCACTTAATTTTAGTAGTTGCTATGTAAAAATGAAGTTGAACG-T
1 GAAAAATTAAAGTGTTTGAAGCACTTAATTTTAGTAGTTGCTATGTAAAAACGAAGTTGAACGTT
* *
106461 AAAAAGTTATG----TT--TAATTTTAATATTAAATAAGTAAATAAAATTA-TCTTTTTATTAAA
66 AAAAA-TTATGTTTTTTCGTAATTTTAATATTAAAAAAGTAAAAAAAATTATTC-TTTTATTAAA
106519 AAATAGATTT
129 AAATAGATTT
106529 TTAAACTAAA
Statistics
Matches: 266, Mismatches: 12, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
143 15 0.06
144 37 0.14
146 1 0.00
148 13 0.05
149 14 0.05
150 186 0.70
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.37
Consensus pattern (149 bp):
GAAAAATTAAAGTGTTTGAAGCACTTAATTTTAGTAGTTGCTATGTAAAAACGAAGTTGAACGTT
AAAAATTATGTTTTTTCGTAATTTTAATATTAAAAAAGTAAAAAAAATTATTCTTTTATTAAAAA
ATAGATTTAGGAAAGGAAG
Found at i:107151 original size:12 final size:12
Alignment explanation
Indices: 107134--107164 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
107124 ACCAAACTTC
107134 AATATATATATA
1 AATATATATATA
*
107146 AATATAGATATA
1 AATATATATATA
107158 AATATAT
1 AATATAT
107165 TTCTCGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
AATATATATATA
Found at i:108371 original size:12 final size:12
Alignment explanation
Indices: 108354--108386 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
108344 AACATTAAAA
108354 TTATTTAAAACT
1 TTATTTAAAACT
108366 TTATTTAAAACT
1 TTATTTAAAACT
108378 TTATTTAAA
1 TTATTTAAA
108387 TAAATTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATTTAAAACT
Found at i:109191 original size:11 final size:11
Alignment explanation
Indices: 109149--109200 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
109139 AAAAATTTTA
109149 AAATTTACA-TT
1 AAATTTA-ATTT
109160 AAA-TTAA-TT
1 AAATTTAATTT
*
109169 AAAATTATATTT
1 AAATTTA-ATTT
109181 AAATTTAATTT
1 AAATTTAATTT
109192 AAATTTAAT
1 AAATTTAAT
109201 CCAATATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
9 6 0.16
10 6 0.16
11 17 0.46
12 8 0.22
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:109342 original size:5 final size:5
Alignment explanation
Indices: 109328--109363 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
109318 AATTCGCACA
*
109328 TTTTC TTTTC CTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
109364 CGCTAGAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:112141 original size:2 final size:2
Alignment explanation
Indices: 112134--112176 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
112124 ATGATTTCTA
112134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112176 A
1 A
112177 AACCTTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:115994 original size:15 final size:14
Alignment explanation
Indices: 115974--116004 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
115964 AATGTTACAA
115974 AAACAATAAATATAT
1 AAACAATAAATA-AT
115989 AAACAATAAATAAT
1 AAACAATAAATAAT
116003 AA
1 AA
116005 TAATTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACAATAAATAAT
Found at i:116264 original size:43 final size:43
Alignment explanation
Indices: 116217--116301 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
116207 TTTATTGTTA
*
116217 AAAATATATTAAAA-T-AATAAA-ATAAAATTTATATTAATATTTT
1 AAAAT-TATTAAAATTAAATAAATAAAAAATTT-TA-TAATATTTT
*
116260 AAAATTTTTAAAATTAAATAAATAAAAAATTTTATAATATTT
1 AAAATTATTAAAATTAAATAAATAAAAAATTTTATAATATTT
116302 AAATGATAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
42 7 0.19
43 14 0.38
44 8 0.22
45 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (43 bp):
AAAATTATTAAAATTAAATAAATAAAAAATTTTATAATATTTT
Found at i:116378 original size:32 final size:31
Alignment explanation
Indices: 116316--116378 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
116306 GATAAGACAA
* *
116316 AATAAATTAATTTAAATTATTAAAATTTTAT
1 AATAAATTAATTTAAATTATAAAAAATTTAT
*
116347 AATAAATTCAATTTAATTTA-AAATAAATTTAT
1 AATAAATT-AATTTAAATTATAAA-AAATTTAT
116379 CAAATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 10 0.37
32 17 0.63
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (31 bp):
AATAAATTAATTTAAATTATAAAAAATTTAT
Found at i:116484 original size:14 final size:15
Alignment explanation
Indices: 116465--116499 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
116455 TATAATTAAA
116465 AAATA-AAAATATAT
1 AAATACAAAATATAT
116479 AAATAACAAAATATAT
1 AAAT-ACAAAATATAT
116495 AAATA
1 AAATA
116500 TAATTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 2 0.11
16 13 0.68
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATACAAAATATAT
Found at i:116570 original size:20 final size:19
Alignment explanation
Indices: 116523--116571 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
116513 ATTTTTTGAA
116523 TTAATTTAAAATAATATTT
1 TTAATTTAAAATAATATTT
*
116542 TTAAATTAAAATAATATATT
1 TTAATTTAAAATAATAT-TT
*
116562 TTTATTTAAA
1 TTAATTTAAA
116572 TTTAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAATTTAAAATAATATTT
Found at i:121839 original size:8 final size:8
Alignment explanation
Indices: 121816--121889 Score: 55
Period size: 8 Copynumber: 9.5 Consensus size: 8
121806 TAAATATTAA
121816 ATATATTT
1 ATATATTT
*
121824 AT-TTTTT
1 ATATATTT
*
121831 ATATTTTT
1 ATATATTT
*
121839 ATAAATTT
1 ATATATTT
121847 ATATA-TT
1 ATATATTT
*
121854 -TATATTA
1 ATATATTT
121861 ATATATTT
1 ATATATTT
* *
121869 AAATATAT
1 ATATATTT
*
121877 ATCAAATTT
1 AT-ATATTT
121886 ATAT
1 ATAT
121890 GGGATATGGA
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
6 4 0.08
7 9 0.18
8 31 0.62
9 6 0.12
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (8 bp):
ATATATTT
Found at i:126175 original size:22 final size:22
Alignment explanation
Indices: 126133--126181 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
126123 TAAAAAATAT
126133 TAAAATTTATATTAATATTT-A
1 TAAAATTTATATTAATATTTAA
*
126154 TAAATTTTATAATTAA-ATTTTAA
1 TAAAATTTAT-ATTAATA-TTTAA
126177 TAAAA
1 TAAAA
126182 AAATCTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 10 0.43
22 8 0.35
23 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAAAATTTATATTAATATTTAA
Found at i:126762 original size:21 final size:22
Alignment explanation
Indices: 126724--126765 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
126714 AATTATAACG
126724 TAATATTAAATTTATTATTATA
1 TAATATTAAATTTATTATTATA
* *
126746 TAAT-TTAATTTTTTTATTAT
1 TAATATTAAATTTATTATTAT
126766 TGATATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TAATATTAAATTTATTATTATA
Found at i:130160 original size:120 final size:120
Alignment explanation
Indices: 129947--130178 Score: 428
Period size: 120 Copynumber: 1.9 Consensus size: 120
129937 CTCTTGATTG
* *
129947 GCTAGAAACCATGGGAGGAAAGCATTTGGGAAAGATCAGAATGTTCCTTAGGGGTCTACCACCAT
1 GCTAGAAACCATGGGAGGAAAGCATTTGGGAAAGATCAGAATGTTCCTTAGGAGTCTACCACCAA
*
130012 TAGTCAGAAAATTGACAAACCAATAGGGGAAAGGAATATTTGCAAGACAACATTA
66 TAGTCAGAAAATTGACAAACAAATAGGGGAAAGGAATATTTGCAAGACAACATTA
*
130067 GCTAGAAACCATGGGAGGAAAGCATTTTGGAAAGATCAGAATGTTCCTTAGGAGTCTACCACCAA
1 GCTAGAAACCATGGGAGGAAAGCATTTGGGAAAGATCAGAATGTTCCTTAGGAGTCTACCACCAA
130132 TAGTCAGAAAATTGACAAACAAATAGGGGAAAGGAATATTTGCAAGA
66 TAGTCAGAAAATTGACAAACAAATAGGGGAAAGGAATATTTGCAAGA
130179 AGACTGAATA
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (120 bp):
GCTAGAAACCATGGGAGGAAAGCATTTGGGAAAGATCAGAATGTTCCTTAGGAGTCTACCACCAA
TAGTCAGAAAATTGACAAACAAATAGGGGAAAGGAATATTTGCAAGACAACATTA
Found at i:131993 original size:4 final size:4
Alignment explanation
Indices: 131984--132011 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
131974 TTTTTTAAAA
131984 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
132012 GAAAAGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:134449 original size:15 final size:16
Alignment explanation
Indices: 134421--134453 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
134411 TTTTTTAAAA
134421 TTTTAAACATATATTT
1 TTTTAAACATATATTT
*
134437 TTTTAAATA-ATATTT
1 TTTTAAACATATATTT
134452 TT
1 TT
134454 AAATTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAAACATATATTT
Done.