Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 98 of 168
Found at i:28903262 original size:2 final size:2
Alignment explanation
Indices: 28903255--28903291 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28903245 TAATTTACAA
28903255 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
28903292 ATAATGTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28903483 original size:30 final size:30
Alignment explanation
Indices: 28903447--28903529 Score: 148
Period size: 30 Copynumber: 2.8 Consensus size: 30
28903437 CAATATCTCA
28903447 ATACCCATATCTTTGACTTTCCAATATTTG
1 ATACCCATATCTTTGACTTTCCAATATTTG
* *
28903477 ATACCCATATCTTTGACTTTCTATTATTTG
1 ATACCCATATCTTTGACTTTCCAATATTTG
28903507 ATACCCATATCTTTGACTTTCCA
1 ATACCCATATCTTTGACTTTCCA
28903530 TAAATATGGA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.25, C:0.24, G:0.06, T:0.45
Consensus pattern (30 bp):
ATACCCATATCTTTGACTTTCCAATATTTG
Found at i:28903491 original size:15 final size:15
Alignment explanation
Indices: 28903447--28903522 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
28903437 CAATATCTCA
28903447 ATACCCATATCTTTG
1 ATACCCATATCTTTG
** *
28903462 ACTTTCCA-ATATTTG
1 A-TACCCATATCTTTG
28903477 ATACCCATATCTTTG
1 ATACCCATATCTTTG
** * *
28903492 ACTTTCTAT-TATTTG
1 A-TACCCATATCTTTG
28903507 ATACCCATATCTTTG
1 ATACCCATATCTTTG
28903522 A
1 A
28903523 CTTTCCATAA
Statistics
Matches: 43, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
14 8 0.19
15 27 0.63
16 8 0.19
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.45
Consensus pattern (15 bp):
ATACCCATATCTTTG
Found at i:28904608 original size:43 final size:43
Alignment explanation
Indices: 28904556--28904650 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 43
28904546 TTTTAAAGGT
* *
28904556 TTCTTTAGCGGCGTTTCTGAAAAAAGTGCCGCTTAAGGTCATG
1 TTCTTTAGCGGCGTTTCTGAAAAAAGCGCCGCTAAAGGTCATG
* ** *
28904599 TTCTTTAGCGGCGTTTGTGATGAATGCGCCGCTAAAGGTCATG
1 TTCTTTAGCGGCGTTTCTGAAAAAAGCGCCGCTAAAGGTCATG
28904642 TTCTTTAGC
1 TTCTTTAGC
28904651 AGTGTTTATG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (43 bp):
TTCTTTAGCGGCGTTTCTGAAAAAAGCGCCGCTAAAGGTCATG
Found at i:28905763 original size:11 final size:11
Alignment explanation
Indices: 28905749--28905824 Score: 86
Period size: 11 Copynumber: 6.9 Consensus size: 11
28905739 TTTAAATAGA
28905749 AATTTGAGAGG
1 AATTTGAGAGG
28905760 AATTTGAGAGG
1 AATTTGAGAGG
28905771 AAATTT-AGAGG
1 -AATTTGAGAGG
*
28905782 AATTTGAAAGG
1 AATTTGAGAGG
28905793 AATTTGAGA-G
1 AATTTGAGAGG
28905803 AATATT-AGAGAG
1 AAT-TTGAGAG-G
*
28905815 AAATTGAGAG
1 AATTTGAGAG
28905825 AAAGGATTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
10 12 0.21
11 32 0.57
12 12 0.21
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.26
Consensus pattern (11 bp):
AATTTGAGAGG
Found at i:28905786 original size:33 final size:33
Alignment explanation
Indices: 28905749--28905824 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
28905739 TTTAAATAGA
28905749 AATTTGAGAGGAATTTGAGAGGAA-ATTTAGAG-G
1 AATTTGAGAGGAATTTGAGA-GAATA-TTAGAGAG
*
28905782 AATTTGAAAGGAATTTGAGAGAATATTAGAGAG
1 AATTTGAGAGGAATTTGAGAGAATATTAGAGAG
*
28905815 AAATTGAGAG
1 AATTTGAGAG
28905825 AAAGGATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 9 0.24
33 29 0.76
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.26
Consensus pattern (33 bp):
AATTTGAGAGGAATTTGAGAGAATATTAGAGAG
Found at i:28909545 original size:124 final size:124
Alignment explanation
Indices: 28909325--28909674 Score: 580
Period size: 124 Copynumber: 2.8 Consensus size: 124
28909315 TTATTTCGAG
* *
28909325 TTGACGTTTCTG-GTCAAATAGTATAAAATCAG-CTCTACCAGGATGCTATTTGAGAATAAAATG
1 TTGACGTTTCTGAG-CAAATAGTATAAAATC-GCCTCTACCAGGATGCTATTTGAGAAGAAATTG
28909388 TGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
64 TGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
*
28909449 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACTAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* **
28909514 AAATCGCACCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
*
28909573 TTGACGTTTCTGAGGAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTG-GTAAGAAATTGT
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAG-AAGAAATTGT
*
28909637 GAAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAG
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
28909675 CAAGTTTGGG
Statistics
Matches: 213, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
123 2 0.01
124 210 0.99
125 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
Found at i:28912796 original size:10 final size:10
Alignment explanation
Indices: 28912781--28912805 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28912771 CAAATCTAAC
28912781 ATTATGTAAA
1 ATTATGTAAA
28912791 ATTATGTAAA
1 ATTATGTAAA
28912801 ATTAT
1 ATTAT
28912806 TAAGTCCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:28912856 original size:65 final size:64
Alignment explanation
Indices: 28912781--28912981 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 64
28912771 CAAATCTAAC
* *
28912781 ATTATGTAAAATTATGTAAAATTATTAAGTCCCAAAATTTTGTCAATGGTTAGTAAAATTTTCAA
1 ATTATGTAAAATTATGTAAAATTATTAAGTCCAAAAATTTTGT-AATGGTTAGTAAAATTATCAA
* *
28912846 ATTATGTAAAATTATGTAAAATTATTAAG-CCAAAAAAATTT-TAA----T--T-AAATTAGGTA
1 ATTATGTAAAATTATGTAAAATTATTAAGTCC-AAAAATTTTGTAATGGTTAGTAAAATTA--TC
28912902 AA
63 AA
* *
28912904 ATTA--TCAAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAA
1 ATTATGTAAAATTATGTAAAATTATTAAGTCCAAAAATTTTG-TAATGGTTAGTAAAATTATCAA
28912967 ATTATGTAAAATTAT
1 ATTATGTAAAATTAT
28912982 TAAGTCCAAC
Statistics
Matches: 112, Mismatches: 9, Indels: 30
0.74 0.06 0.20
Matches are distributed among these distances:
56 34 0.30
57 3 0.03
58 10 0.09
59 1 0.01
62 1 0.01
63 9 0.08
64 4 0.04
65 50 0.45
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (64 bp):
ATTATGTAAAATTATGTAAAATTATTAAGTCCAAAAATTTTGTAATGGTTAGTAAAATTATCAA
Found at i:28912859 original size:10 final size:10
Alignment explanation
Indices: 28912844--28912870 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
28912834 TAAAATTTTC
28912844 AAATTATGTA
1 AAATTATGTA
28912854 AAATTATGTA
1 AAATTATGTA
28912864 AAATTAT
1 AAATTAT
28912871 TAAGCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
AAATTATGTA
Found at i:28912915 original size:18 final size:18
Alignment explanation
Indices: 28912892--28912926 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28912882 AATTTTAATT
28912892 AAATTAGGTAAAATTATC
1 AAATTAGGTAAAATTATC
*
28912910 AAATTATGTAAAATTAT
1 AAATTAGGTAAAATTAT
28912927 TAAGTCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (18 bp):
AAATTAGGTAAAATTATC
Found at i:28912963 original size:55 final size:55
Alignment explanation
Indices: 28912854--28913035 Score: 271
Period size: 55 Copynumber: 3.3 Consensus size: 55
28912844 AAATTATGTA
* **
28912854 AAATTATGTAAAATTATTAAG-CCAAAAAAAT-T-TTAATTAAATTAGGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCC-AAAAATTGTGTTAA-T-GGTTA-GTAAAATTATC
28912910 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
*
28912965 AAATTATGTAAAATTATTAAGTCCAACAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
28913020 AAATTATGTAAAATTA
1 AAATTATGTAAAATTA
28913036 GGTTAGGGTT
Statistics
Matches: 119, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
55 81 0.68
56 30 0.25
57 4 0.03
58 4 0.03
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.37
Consensus pattern (55 bp):
AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:28913066 original size:18 final size:18
Alignment explanation
Indices: 28913043--28913205 Score: 140
Period size: 18 Copynumber: 9.7 Consensus size: 18
28913033 TTAGGTTAGG
28913043 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
28913061 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
**
28913079 GTTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
*
28913090 GTTAGGGTTTTTAACTAA
1 GTTAGGGTTTTTAATTAA
28913108 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
28913126 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
**
28913144 GTTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
28913155 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
28913173 GTTAGGGTTTAATTAAATTAA
1 GTTAGGGTTT--TT-AATTAA
*
28913194 -ATAGGGTTTTTA
1 GTTAGGGTTTTTA
28913206 TTACATCAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 35
0.72 0.06 0.21
Matches are distributed among these distances:
11 8 0.07
12 4 0.03
13 2 0.02
14 4 0.03
15 4 0.03
16 2 0.02
17 5 0.04
18 73 0.62
20 10 0.08
21 6 0.05
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.47
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:28913102 original size:47 final size:47
Alignment explanation
Indices: 28913033--28913131 Score: 189
Period size: 47 Copynumber: 2.1 Consensus size: 47
28913023 TTATGTAAAA
*
28913033 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAG
1 TTAGGTTAGGGTTAGGGTTTTTAACTAAGTTAGGGTTTTTAATTAAG
28913080 TTAGGTTAGGGTTAGGGTTTTTAACTAAGTTAGGGTTTTTAATTAAG
1 TTAGGTTAGGGTTAGGGTTTTTAACTAAGTTAGGGTTTTTAATTAAG
28913127 TTAGG
1 TTAGG
28913132 GTTTTTAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.25, C:0.01, G:0.28, T:0.45
Consensus pattern (47 bp):
TTAGGTTAGGGTTAGGGTTTTTAACTAAGTTAGGGTTTTTAATTAAG
Found at i:28913124 original size:65 final size:65
Alignment explanation
Indices: 28913043--28913205 Score: 274
Period size: 65 Copynumber: 2.5 Consensus size: 65
28913033 TTAGGTTAGG
28913043 GTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAACTAA
1 GTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAACTAA
*
28913108 GTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAACTAA
*
28913173 GTTAGGGTTTAATTAAATTAA-ATAGGGTTTTTA
1 GTTAGGGTTT--TT-AATTAAGTTAGGGTTTTTA
28913206 TTACATCAAA
Statistics
Matches: 93, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
65 74 0.80
67 13 0.14
68 6 0.06
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.47
Consensus pattern (65 bp):
GTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAACTAA
Found at i:28913208 original size:21 final size:20
Alignment explanation
Indices: 28913175--28913218 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
28913165 TTAATTAAGT
*
28913175 TAGGGTTTAATTAAATTAAA
1 TAGGGTTTAATTAAATCAAA
* *
28913195 TAGGGTTTTTATTACATCAAA
1 TAGGG-TTTAATTAAATCAAA
28913216 TAG
1 TAG
28913219 AACTTCTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.41
Consensus pattern (20 bp):
TAGGGTTTAATTAAATCAAA
Found at i:28913253 original size:25 final size:26
Alignment explanation
Indices: 28913201--28913264 Score: 103
Period size: 25 Copynumber: 2.5 Consensus size: 26
28913191 TAAATAGGGT
28913201 TTTTATTACATCAAATAGAACTTCTA
1 TTTTATTACATCAAATAGAACTTCTA
* *
28913227 TTTTATTATATTAAATA-AACTTCTA
1 TTTTATTACATCAAATAGAACTTCTA
28913252 TTTTATTACATCA
1 TTTTATTACATCA
28913265 GATAATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTATTACATCAAATAGAACTTCTA
Found at i:28913700 original size:18 final size:18
Alignment explanation
Indices: 28913673--28913707 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28913663 CTGAAAAGGA
* *
28913673 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
28913691 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
28913708 AAACACACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:28916219 original size:31 final size:32
Alignment explanation
Indices: 28916184--28916249 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
28916174 GCCATTGATG
28916184 AAAATATAAAAAAAA-TTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTTAAAATTATTTTAAA
28916215 AAAATATAAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTTAAAATTATTTTAAA
28916247 AAA
1 AAA
28916250 TGAAATTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 15 0.44
32 19 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (32 bp):
AAAATATAAAAAAAATTTAAAATTATTTTAAA
Found at i:28916233 original size:21 final size:20
Alignment explanation
Indices: 28916192--28916236 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
28916182 TGAAAATATA
** *
28916192 AAAAAAATTAAAATTATTTT
1 AAAAAAATTAAAAAAAATTT
28916212 AAAAAAATATAAAAAAAATTT
1 AAAAAAAT-TAAAAAAAATTT
28916233 AAAA
1 AAAA
28916237 TTATTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAAATTAAAAAAAATTT
Found at i:28916306 original size:29 final size:29
Alignment explanation
Indices: 28916274--28916357 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 29
28916264 AATTGAAATT
28916274 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
* * **
28916303 AAAT-T-GA---GAG-GAA-ATTGAAATT
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
28916325 AAATATGGGTTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
28916354 AAAT
1 AAAT
28916358 TGAGAGAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 14
0.63 0.15 0.23
Matches are distributed among these distances:
22 9 0.23
23 4 0.10
24 4 0.10
27 5 0.13
28 4 0.10
29 13 0.33
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.30
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGGAAGG
Found at i:28916306 original size:51 final size:51
Alignment explanation
Indices: 28916251--28916363 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 51
28916241 TTTAAAAAAT
*
28916251 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
28916302 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
28916353 GAAATTGAGAG
1 GAAATTGAGAG
28916364 AATTTAGGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:28916360 original size:22 final size:22
Alignment explanation
Indices: 28916335--28916399 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
28916325 AAATATGGGT
*
28916335 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTAGGAAGGAAA
28916357 TTGAGAGAATTTAGGAAGGAAA
1 TTGAGAGAATTTAGGAAGGAAA
* *
28916379 TTGAGAGGA-TTAGAAAGGAAA
1 TTGAGAGAATTTAGGAAGGAAA
28916400 AATTAGATAG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 11 0.28
22 29 0.73
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (22 bp):
TTGAGAGAATTTAGGAAGGAAA
Found at i:28917649 original size:146 final size:150
Alignment explanation
Indices: 28917322--28917792 Score: 499
Period size: 158 Copynumber: 3.1 Consensus size: 150
28917312 TAACCTTACA
* * * * *
28917322 AATATATTATATTTTAAAAACTTAAGTATATTTTTTTAATTTGGTTATATATTTTAAATATTTTT
1 AATATATTATATTTCAAAAACTTAAGTATA----TTT-ATTTTGATATATCTTTTAAATATTATT
* * ** * ** *
28917387 TTATTAATAA-TTTATTTAATATATCGCTATTTAAATAA-AAAATTATAAAACATATGAGTAACC
61 TTATCAATAATTTTATTTAATATATCGTTATTTAAATAATAATTTTATAAAACAAACAAGCAACC
** * *
28917450 TGTGCATTACACGGGATAAAAAATT
126 CATGCATCACACGAGATAAAAAATT
* *
28917475 AGTATATTATATTTCAAAAATTTAAGTATA-TT-TTTT-A-ATATCTTTTAAATATTATTTTATC
1 AATATATTATATTTCAAAAACTTAAGTATATTTATTTTGATATATCTTTTAAATATTATTTTATC
* *
28917536 AATAATTTTATTTAATATATCGTTATTTAAATAATAATTTTATAAAACACACAAGCAACCCATGA
66 AATAATTTTATTTAATATATCGTTATTTAAATAATAATTTTATAAAACAAACAAGCAACCCATGC
* *
28917601 ATCACACGAGATAGAAAACT
131 ATCACACGAGATAAAAAATT
*
28917621 AATATATTATATTTCAAAAACTTGAGTATATTTTAAATTTTGATTATATCTTAATTTTAAATATT
1 AATATATTATATTTCAAAAACTTAAGTATA-TTT--ATTTTGA-TATATC----TTTTAAATATT
* * * *
28917686 GTTTAATCAAAAATTTTATTTAATATATCATTATTTAAATAATAATTTTATAAAACAAACTAA-C
58 ATTTTATCAATAATTTTATTTAATATATCGTTATTTAAATAATAATTTTATAAAACAAAC-AAGC
28917750 AACCCATGCATCACACGAGATAAAAAATT
122 AACCCATGCATCACACGAGATAAAAAATT
28917779 AAT-TATTTATATTT
1 AATATA-TTATATTT
28917793 GAAGCTTTGA
Statistics
Matches: 269, Mismatches: 33, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
144 26 0.10
145 27 0.10
146 67 0.25
148 4 0.01
151 4 0.01
152 1 0.00
153 27 0.10
154 5 0.02
157 2 0.01
158 104 0.39
159 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (150 bp):
AATATATTATATTTCAAAAACTTAAGTATATTTATTTTGATATATCTTTTAAATATTATTTTATC
AATAATTTTATTTAATATATCGTTATTTAAATAATAATTTTATAAAACAAACAAGCAACCCATGC
ATCACACGAGATAAAAAATT
Found at i:28918371 original size:24 final size:24
Alignment explanation
Indices: 28918339--28918389 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
28918329 GATTTAGTAT
* *
28918339 TTAGTATAATATATTTAACATTTA
1 TTAGCATAATATATTTAACATTGA
*
28918363 TTAGCATAATATATTTGACATTGA
1 TTAGCATAATATATTTAACATTGA
28918387 TTA
1 TTA
28918390 AAATTAGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (24 bp):
TTAGCATAATATATTTAACATTGA
Found at i:28920949 original size:25 final size:25
Alignment explanation
Indices: 28920903--28920965 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
28920893 TATAAATATC
*
28920903 AATAAA-TTAAATATAATAATTAAT
1 AATAAATTTAAATAGAATAATTAAT
*
28920927 AATAAATTTAAATAGAATCATTAAT
1 AATAAATTTAAATAGAATAATTAAT
28920952 AATAAATTTAAATA
1 AATAAATTTAAATA
28920966 TGTGTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 6 0.17
25 30 0.83
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
AATAAATTTAAATAGAATAATTAAT
Found at i:28924836 original size:46 final size:46
Alignment explanation
Indices: 28924767--28924941 Score: 237
Period size: 46 Copynumber: 3.8 Consensus size: 46
28924757 AGTGTGGAAC
* * *
28924767 GTAGGTATGG--TTTCAGTAAAGAAAACCATACTAACTTTTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* * *
28924811 GTAGGTATGATATTTCGGTAAAGAAAACCATGCTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
28924857 GTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* * *
28924903 GTAGGTATGGTATTTCCGTGAAGAAAACCATATTGAGTT
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
28924942 ATAGCATTGT
Statistics
Matches: 115, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
44 9 0.08
46 106 0.92
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.30
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
Found at i:28935661 original size:15 final size:15
Alignment explanation
Indices: 28935641--28935670 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28935631 GAGTATGGTA
28935641 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
28935656 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
28935671 TACTAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:28937310 original size:27 final size:31
Alignment explanation
Indices: 28937246--28937311 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 31
28937236 TCTCTTTCAA
*
28937246 CAAATATTACAAAATAATTCAAAATAACATT
1 CAAAAATTACAAAATAATTCAAAATAACATT
*
28937277 CAAAAATTA-AAAAT-ATTCATAA-AA-ATT
1 CAAAAATTACAAAATAATTCAAAATAACATT
*
28937304 CTAAAATT
1 CAAAAATT
28937312 TATCTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 10 0.31
28 2 0.06
29 7 0.22
30 5 0.16
31 8 0.25
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (31 bp):
CAAAAATTACAAAATAATTCAAAATAACATT
Found at i:28937948 original size:17 final size:18
Alignment explanation
Indices: 28937916--28937950 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28937906 GAAAATCTAA
*
28937916 TTTACATGCTTTAATTAG
1 TTTACATGCATTAATTAG
28937934 TTTACATG-ATTAATTAG
1 TTTACATGCATTAATTAG
28937951 AGCATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTACATGCATTAATTAG
Found at i:28938652 original size:23 final size:23
Alignment explanation
Indices: 28938626--28938679 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
28938616 CAAACTAATC
28938626 CTCTCAAATTTCC-TCTC-AATTT
1 CTCTCAAATTTCCTTC-CAAATTT
28938648 GCTCTCAAA-TTCCTTCCAAATTT
1 -CTCTCAAATTTCCTTCCAAATTT
28938671 CTCTCAAAT
1 CTCTCAAAT
28938680 CCATATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.26, C:0.31, G:0.02, T:0.41
Consensus pattern (23 bp):
CTCTCAAATTTCCTTCCAAATTT
Found at i:28938678 original size:11 final size:12
Alignment explanation
Indices: 28938624--28938679 Score: 66
Period size: 11 Copynumber: 4.9 Consensus size: 12
28938614 CACAAACTAA
28938624 TCCTCTCAAATT
1 TCCTCTCAAATT
28938636 TCCTCTC-AATT
1 TCCTCTCAAATT
*
28938647 TGCTCTCAAA-T
1 TCCTCTCAAATT
28938658 TCCT-TCCAAATT
1 TCCTCT-CAAATT
28938670 T-CTCTCAAAT
1 TCCTCTCAAAT
28938680 CCATATTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 1 0.03
11 25 0.66
12 12 0.32
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (12 bp):
TCCTCTCAAATT
Found at i:28938702 original size:51 final size:51
Alignment explanation
Indices: 28938639--28938738 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
28938629 TCAAATTTCC
28938639 TCTCAATTTGCTCTCAAATTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* * *
28938690 TCTCAATTTGCTCTCAAATTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCATATTT
28938739 TTAAATAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.44
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:28940574 original size:18 final size:18
Alignment explanation
Indices: 28940547--28940586 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28940537 TAGGTGCGTT
* *
28940547 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
28940565 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
28940583 TCCT
1 TCCT
28940587 TTTCTGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:28941170 original size:21 final size:21
Alignment explanation
Indices: 28941167--28941402 Score: 316
Period size: 21 Copynumber: 11.0 Consensus size: 21
28941157 TAAAAACCCT
*
28941167 AACCCTAACCCTTAATCTAAA
1 AACCCTAACCCTTAACCTAAA
*
28941188 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACCTAAA
*
28941209 AACCCTAAACCCTTAACATAAA
1 AACCCT-AACCCTTAACCTAAA
28941231 AACCCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACCTAAA
*
28941252 AACCCTAACCCTT-ATCTAAAA
1 AACCCTAACCCTTAACCT-AAA
*
28941273 CCCTAACACTAACCCTTAACCTAAA
1 ----AACCCTAACCCTTAACCTAAA
*
28941298 AACCCTAACCATTAACCTAAA
1 AACCCTAACCCTTAACCTAAA
*
28941319 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACCTAAA
*
28941340 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACCTAAA
28941362 AACCCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACCTAAA
28941383 AACCCTAACCC-TAACC-AAA
1 AACCCTAACCCTTAACCTAAA
28941402 A
1 A
28941403 TGCATATTTA
Statistics
Matches: 195, Mismatches: 12, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
19 4 0.02
20 8 0.04
21 124 0.64
22 41 0.21
25 15 0.08
26 3 0.02
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCCTAACCCTTAACCTAAA
Found at i:28941178 original size:43 final size:41
Alignment explanation
Indices: 28941167--28941402 Score: 285
Period size: 43 Copynumber: 5.5 Consensus size: 41
28941157 TAAAAACCCT
* *
28941167 AACCCTAACCCTTAATCTAAAAACCCTAACCCTTAACTTAAA
1 AACCCTAACCC-TAACCTAAAAACCCTAACCCTTAACCTAAA
*
28941209 AACCCTAAACCCTTAACATAAAAACCCTAACCCTTAACCTAAA
1 AACCCT-AACCC-TAACCTAAAAACCCTAACCCTTAACCTAAA
* * *
28941252 AACCCTAACCCTTATCTAAAACCCTAACACTAACCCTTAACCTAAA
1 AACCCTAACCCTAACCT-AAA----AACCCTAACCCTTAACCTAAA
* *
28941298 AACCCTAACCATTAACCTAAAAACCCTAACCCTTAACTTAAA
1 AACCCTAACC-CTAACCTAAAAACCCTAACCCTTAACCTAAA
*
28941340 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAA
1 AACCCT-AACCC-TAACCTAAAAACCCTAACCCTTAACCTAAA
28941383 AACCCTAACCCTAACC-AAAA
1 AACCCTAACCCTAACCTAAAA
28941403 TGCATATTTA
Statistics
Matches: 169, Mismatches: 16, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
40 4 0.02
41 7 0.04
42 44 0.26
43 77 0.46
46 33 0.20
47 4 0.02
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.20
Consensus pattern (41 bp):
AACCCTAACCCTAACCTAAAAACCCTAACCCTTAACCTAAA
Found at i:28941186 original size:27 final size:27
Alignment explanation
Indices: 28941146--28941330 Score: 99
Period size: 21 Copynumber: 8.0 Consensus size: 27
28941136 TAAATCCTTA
28941146 AACCCTTAACCTAAAAACCCTAACCCT
1 AACCCTTAACCTAAAAACCCTAACCCT
*
28941173 AACCCTTAATCT--AAA----AACCCT
1 AACCCTTAACCTAAAAACCCTAACCCT
* *
28941194 AACCCTTAACTTAAAAACCCTAA--A-
1 AACCCTTAACCTAAAAACCCTAACCCT
*
28941218 --CCCTTAACATAAAAACCCT------
1 AACCCTTAACCTAAAAACCCTAACCCT
28941237 AACCCTTAACCTAAAAACCCT------
1 AACCCTTAACCTAAAAACCCTAACCCT
* *
28941258 AACCCTT-ATCT-AAAACCCTAACACT
1 AACCCTTAACCTAAAAACCCTAACCCT
28941283 AACCCTTAACCTAAAAACCCTAA-CC-
1 AACCCTTAACCTAAAAACCCTAACCCT
28941308 -A---TTAACCTAAAAACCCTAACCCT
1 AACCCTTAACCTAAAAACCCTAACCCT
28941331 TAACTTAAAA
Statistics
Matches: 131, Mismatches: 9, Indels: 40
0.73 0.05 0.22
Matches are distributed among these distances:
19 8 0.06
20 3 0.02
21 59 0.45
22 20 0.15
23 3 0.02
24 1 0.01
25 10 0.08
26 4 0.03
27 23 0.18
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (27 bp):
AACCCTTAACCTAAAAACCCTAACCCT
Found at i:28941202 original size:64 final size:64
Alignment explanation
Indices: 28941130--28941394 Score: 247
Period size: 64 Copynumber: 4.1 Consensus size: 64
28941120 TTAATTGACA
* *** *
28941130 AACCCTTAAATCCTT-AAACCCTTAA-CCTAAAAACCCTAACCCTAACCCTTAATCTAAAAACCC
1 AACCCTTAAA--CTTAAAACCCTAAACCCTAAAAACAAAAACCCTAACCCTTAACCTAAAAACCC
28941193 T
64 T
* * *
28941194 AACCCTT-AACTTAAAAACCCTAAACCCTTAACATAAAAACCCTAACCCTTAACCTAAAAACCCT
1 AACCCTTAAACTT-AAAACCCTAAACCCTAAAAACAAAAACCCTAACCCTTAACCTAAAAACCCT
* * * *
28941258 AACCCTT-ATC-TAAAACCCTAACACTAACCCT-TAACCTAAAAACCCTAACCATTAACCTAAAA
1 AACCCTTAAACTTAAAACCCT---A--AACCCTAAAAAC-AAAAACCCTAACCCTTAACCTAAAA
28941320 ACCCT
60 ACCCT
* ***
28941325 AACCCTT-AACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAAAACCCT
1 AACCCTTAAACTT-AAAACCCTAAACCCTAAAAACAAAAACCCTAACCCTTAACCTAAAAACCCT
28941389 AACCCT
1 AACCCT
28941395 AACCAAAATG
Statistics
Matches: 169, Mismatches: 20, Indels: 24
0.79 0.09 0.11
Matches are distributed among these distances:
61 3 0.02
62 8 0.05
63 12 0.07
64 89 0.53
65 2 0.01
66 2 0.01
67 44 0.26
68 1 0.01
69 8 0.05
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (64 bp):
AACCCTTAAACTTAAAACCCTAAACCCTAAAAACAAAAACCCTAACCCTTAACCTAAAAACCCT
Found at i:28941285 original size:110 final size:112
Alignment explanation
Indices: 28941146--28941398 Score: 413
Period size: 110 Copynumber: 2.3 Consensus size: 112
28941136 TAAATCCTTA
* * *
28941146 AACCCTTAACCTAAAAACCCTAACCCTAACCCTTAATCTAAAAACCCTAACCCTTAACTTAAAAA
1 AACCCTTAACCTAAAAACCCTAACCCTAACCCTTAACCTAAAAACCCTAACCATTAACCTAAAAA
28941211 CCCTAAACCCTTAACATAAAAACCCT-AACCCTTAACCTAAAAACCCT
66 CCCT-AACCCTTAACATAAAAACCCTAAACCCTTAACCTAAAAACCCT
* *
28941258 AACCCTT-ATCT-AAAACCCTAACACTAACCCTTAACCTAAAAACCCTAACCATTAACCTAAAAA
1 AACCCTTAACCTAAAAACCCTAACCCTAACCCTTAACCTAAAAACCCTAACCATTAACCTAAAAA
* *
28941321 CCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCT
66 CCCTAACCCTTAACATAAAAACCCTAAACCCTTAACCTAAAAACCCT
28941368 AACCCTTAACCTAAAAACCCTAACCCTAACC
1 AACCCTTAACCTAAAAACCCTAACCCTAACC
28941399 AAAATGCATA
Statistics
Matches: 129, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
109 20 0.16
110 79 0.61
111 6 0.05
112 24 0.19
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (112 bp):
AACCCTTAACCTAAAAACCCTAACCCTAACCCTTAACCTAAAAACCCTAACCATTAACCTAAAAA
CCCTAACCCTTAACATAAAAACCCTAAACCCTTAACCTAAAAACCCT
Found at i:28941422 original size:131 final size:131
Alignment explanation
Indices: 28941167--28941402 Score: 411
Period size: 131 Copynumber: 1.8 Consensus size: 131
28941157 TAAAAACCCT
* *
28941167 AACCCTAACCCTTAATCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACATAAAA
1 AACCCTAACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACATAAAA
* * *
28941232 ACCCTAACCCTTAACCTAAAAACCCTAACCCTTATCTAAAACCCTAACACTAACCCTTAACCTAA
66 ACCCTAACCCTTAACCTAAAAACCCTAACCCTTAACCAAAACCATAACACTAACCCTTAACCTAA
28941297 A
131 A
*
28941298 AACCCTAACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAA
1 AACCCTAACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACATAAAA
28941363 ACCCTAACCCTTAACCTAAAAACCCTAACCC-TAACCAAAA
66 ACCCTAACCCTTAACCTAAAAACCCTAACCCTTAACCAAAA
28941403 TGCATATTTA
Statistics
Matches: 100, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
130 7 0.07
131 93 0.93
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.20
Consensus pattern (131 bp):
AACCCTAACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACATAAAA
ACCCTAACCCTTAACCTAAAAACCCTAACCCTTAACCAAAACCATAACACTAACCCTTAACCTAA
A
Found at i:28952160 original size:77 final size:76
Alignment explanation
Indices: 28951991--28952538 Score: 726
Period size: 74 Copynumber: 7.2 Consensus size: 76
28951981 TTGCAAAAAT
* *
28951991 TATTTTTCAATTTCTGTTTTCTGAAAAAATCAACTCATAATGCGAGATGTGAGTTGGGCCTCGGG
1 TATTTTTCAATTTCTGTTTT-TGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
* *
28952056 TCACACACTGAGG
65 -CACACGCCGAGG
*
28952069 TATTTTTCAATTTCTGTTTTCTGAAAAAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGTTTT-TGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
*
28952134 CACACGCCAAGG
65 CACACGCCGAGG
* * * *
28952146 TATTTTTTAATTTCTATTTTTGTCAAAAATTAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGTTTTTG-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
*
28952211 TCACACGTCGAGG
65 -CACACGCCGAGG
*
28952224 TATTTTTCAATTTCTGTTTTTTGAAAAAATAAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTG-TTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
*
28952289 CACACGCCGATG
65 CACACGCCGAGG
* * *
28952301 TATTTTTTAATTTCTATTTTT--AAAAATCAGCTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
1 TATTTTTCAATTTCTGTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
***
28952364 ACATTTCGAGG
66 ACACGCCGAGG
* *
28952375 TACTTTTCAATTTCTGTTTTT--AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGC
1 TATTTTTCAATTTCTGTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
* *
28952438 ACATGCCAAGG
66 ACACGCCGAGG
** * ** *
28952449 TACATTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTAGGG
1 TATTTTTCAATTTCTGTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCC-TCGGG
*
28952514 CACATGCCGAGG
65 CACACGCCGAGG
*
28952526 TATCTTTCAATTT
1 TATTTTTCAATTT
28952539 ATATTTAAAA
Statistics
Matches: 422, Mismatches: 42, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
74 132 0.31
76 42 0.10
77 116 0.27
78 126 0.30
79 6 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (76 bp):
TATTTTTCAATTTCTGTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
ACACGCCGAGG
Found at i:28952274 original size:155 final size:153
Alignment explanation
Indices: 28951991--28952538 Score: 766
Period size: 155 Copynumber: 3.6 Consensus size: 153
28951981 TTGCAAAAAT
* ** * *
28951991 TATTTTTCAATTTCTGTTTTCTGAAAAAATCAACTCATAATGCGAGATGTGAGTTGGGCCTCGGG
1 TATTTTTCAATTTCTATTTT-TTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
* * *
28952056 TCACAC-ACTGAGGTATTTTTCAATTTCTGTTTTCTGAAAAAATCAACTCATAATGCGATAGGTG
65 -CACACGTC-GAGGTATTTTTCAATTTCTGTTTTTTGAAAAAATCAACTCATAATGCGAGAGGTG
28952120 AGTTGAGCCTCGGGCACACGCCAAGG
128 AGTTGAGCCTCGGGCACACGCCAAGG
* *
28952146 TATTTTTTAATTTCTATTTTTGTCAAAAATTAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTATTTTT-TCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
*
28952211 TCACACGTCGAGGTATTTTTCAATTTCTGTTTTTTGAAAAAATAAACTCATAATGCGAGAGGTGA
65 -CACACGTCGAGGTATTTTTCAATTTCTGTTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGA
* *
28952276 GTTGAGCCTCGGGCACACGCCGATG
129 GTTGAGCCTCGGGCACACGCCAAGG
* *
28952301 TATTTTTTAATTTCTA-TTTTT-AAAAATCAGCTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
1 TATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
** * *
28952364 ACATTTCGAGGTACTTTTCAATTTCTG-TTTTT--AAAAATCAACTCATAATGCGAGAAGTGAGT
66 ACACGTCGAGGTATTTTTCAATTTCTGTTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGT
*
28952426 TGAGCCTCGGGCACATGCCAAGG
131 TGAGCCTCGGGCACACGCCAAGG
** *
28952449 TACATTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTAGGG
1 TATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCC-TCGGG
* * *
28952514 CACATGCCGAGGTATCTTTCAATTT
65 CACACGTCGAGGTATTTTTCAATTT
28952539 ATATTTAAAA
Statistics
Matches: 356, Mismatches: 32, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
148 61 0.17
149 5 0.01
150 40 0.11
151 50 0.14
152 39 0.11
153 1 0.00
154 5 0.01
155 154 0.43
156 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (153 bp):
TATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
ACACGTCGAGGTATTTTTCAATTTCTGTTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGT
TGAGCCTCGGGCACACGCCAAGG
Found at i:28952719 original size:30 final size:30
Alignment explanation
Indices: 28952688--28952841 Score: 143
Period size: 30 Copynumber: 5.2 Consensus size: 30
28952678 TTCGTTTTTT
*
28952688 TCAAAATTATATTTTAACCCCCTAAACTTT-
1 TCAAAATTACATTTTAA-CCCCTAAACTTTC
* * ** *
28952718 TCAAAATTACAATTTGACCATTAAAATTTC
1 TCAAAATTACATTTTAACCCCTAAACTTTC
*
28952748 TTAAAATTACATTTTAACCCCTAAACTTTC
1 TCAAAATTACATTTTAACCCCTAAACTTTC
**
28952778 TTTAAATTACATTTTAA-CCCTAAACTTTC
1 TCAAAATTACATTTTAACCCCTAAACTTTC
** * * * *
28952807 TTGAAATTACTTTTTAGCACCTAAAATTT-
1 TCAAAATTACATTTTAACCCCTAAACTTTC
28952836 TCAAAA
1 TCAAAA
28952842 ATTGCATATT
Statistics
Matches: 102, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
29 39 0.38
30 63 0.62
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.40
Consensus pattern (30 bp):
TCAAAATTACATTTTAACCCCTAAACTTTC
Found at i:28952814 original size:59 final size:59
Alignment explanation
Indices: 28952690--28952841 Score: 171
Period size: 59 Copynumber: 2.6 Consensus size: 59
28952680 CGTTTTTTTC
* * *
28952690 AAAATTATATTTTAACCCCCTAAACTTTTCAAAATTACAATTTGACCATTAAAATTTCTT
1 AAAATTACATTTTAA-CCCCTAAACTTTTCAAAATTACAATTTAACCACTAAAATTTCTT
** * *
28952750 AAAATTACATTTTAACCCCTAAACTTTCTTTAAATTACATTTTAACC-CTAAACTTTCTT
1 AAAATTACATTTTAACCCCTAAACTTT-TCAAAATTACAATTTAACCACTAAAATTTCTT
* * * * *
28952809 GAAATTACTTTTTAGCACCTAAAATTTTCAAAA
1 AAAATTACATTTTAACCCCTAAACTTTTCAAAA
28952842 ATTGCATATT
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
58 4 0.05
59 44 0.57
60 29 0.38
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.40
Consensus pattern (59 bp):
AAAATTACATTTTAACCCCTAAACTTTTCAAAATTACAATTTAACCACTAAAATTTCTT
Found at i:28953417 original size:25 final size:24
Alignment explanation
Indices: 28953387--28953458 Score: 92
Period size: 25 Copynumber: 3.0 Consensus size: 24
28953377 GGGCCGAACG
28953387 AAGAAGAAATGAGAGAAAAAAAATA
1 AAGAAGAAA-GAGAGAAAAAAAATA
* *
28953412 AAGAAGAAAGAAAGAAAAAAAAGGA
1 AAGAAGAAAGAGAGAAAAAAAA-TA
*
28953437 AAGAAGAAAAAGA-AAAAAAAAT
1 AAGAAGAAAGAGAGAAAAAAAAT
28953459 TAAAAACAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 20 0.49
25 21 0.51
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (24 bp):
AAGAAGAAAGAGAGAAAAAAAATA
Found at i:28953440 original size:14 final size:13
Alignment explanation
Indices: 28953400--28953457 Score: 59
Period size: 14 Copynumber: 4.6 Consensus size: 13
28953390 AAGAAATGAG
*
28953400 AGAAAAAAAATAA
1 AGAAAAAAAAGAA
*
28953413 AG--AAGAAAGAA
1 AGAAAAAAAAGAA
28953424 AGAAAAAAAAGGAA
1 AGAAAAAAAA-GAA
*
28953438 AGAAGAAAAAGAA
1 AGAAAAAAAAGAA
28953451 A-AAAAAA
1 AGAAAAAA
28953458 TTAAAAACAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 9 0.24
12 5 0.14
13 11 0.30
14 12 0.32
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (13 bp):
AGAAAAAAAAGAA
Found at i:28953740 original size:15 final size:17
Alignment explanation
Indices: 28953720--28953757 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
28953710 CAGCAGGCCA
28953720 AAAAAAGGAAAAA-G-G
1 AAAAAAGGAAAAATGAG
28953735 AAAAAA-GAAAAATGAG
1 AAAAAAGGAAAAATGAG
28953751 AAAAAAG
1 AAAAAAG
28953758 AAGAAGGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
15 7 0.35
16 7 0.35
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
AAAAAAGGAAAAATGAG
Found at i:28953758 original size:16 final size:14
Alignment explanation
Indices: 28953720--28953764 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 14
28953710 CAGCAGGCCA
28953720 AAAAAAGGAAAAAGG
1 AAAAAA-GAAAAAGG
28953735 AAAAAAGAAAAATGAG
1 AAAAAAGAAAAA-G-G
*
28953751 AAAAAAGAAGAAGG
1 AAAAAAGAAAAAGG
28953765 CTCGTTCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.26
15 8 0.30
16 12 0.44
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAAAAGG
Found at i:28953887 original size:6 final size:6
Alignment explanation
Indices: 28953878--28953924 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
28953868 TATTTTTAGC
* * *
28953878 ATTTTT ATTTTT ATTTAT ATGTTT AATTTT A-TTTT A-TTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
28953924 A
1 A
28953925 ATTTAGATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:28953929 original size:5 final size:5
Alignment explanation
Indices: 28953880--28953922 Score: 50
Period size: 5 Copynumber: 7.8 Consensus size: 5
28953870 TTTTTAGCAT
28953880 TTTTA TTTTTA TTTATA TGTTTAA TTTTA TTTTA TTTTA TTTT
1 TTTTA -TTTTA TTT-TA T-TTT-A TTTTA TTTTA TTTTA TTTT
28953923 TAATTTAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 18 0.53
6 12 0.35
7 4 0.12
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:28954967 original size:36 final size:34
Alignment explanation
Indices: 28954886--28954954 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
28954876 TGATTATTAC
28954886 AATTATAATTTAATTTAGAATTATTAGTTAAAAAT
1 AATTATAATTTAATTTAGAATTATTAG-TAAAAAT
*
28954921 AATTATAATTTAATTTTGAAATTATTA-TAAAAAT
1 AATTATAATTTAATTTAG-AATTATTAGTAAAAAT
28954955 GATTTTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 7 0.22
35 17 0.53
36 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (34 bp):
AATTATAATTTAATTTAGAATTATTAGTAAAAAT
Found at i:28955661 original size:22 final size:22
Alignment explanation
Indices: 28955633--28955687 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
28955623 CAATGAGTAC
28955633 AAATATATA-TT-AGAAATTATAA
1 AAATATATATTTAAG-AATTA-AA
28955655 AAATATATTATTTAATGAATTAAA
1 AAATATA-TATTTAA-GAATTAAA
28955679 AAATATATA
1 AAATATATA
28955688 AAATCACGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 7 0.24
23 4 0.14
24 11 0.38
25 6 0.21
26 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
AAATATATATTTAAGAATTAAA
Found at i:28961055 original size:37 final size:36
Alignment explanation
Indices: 28960959--28961068 Score: 104
Period size: 37 Copynumber: 3.0 Consensus size: 36
28960949 TACAACATAA
*
28960959 AAATTAAATTGAAT-TT-AA-TATTAAGATAATCATTTT
1 AAATTAAATTTAATATTAAACTATTAAGATAAT-A--TT
*
28960995 AATATTAAA-TTAATA-AAATACTATTAAGATAAGTATT
1 AA-ATTAAATTTAATATTAA-ACTATTAAGATAA-TATT
*
28961032 AAATTAAATTTAATATTAAACTATTAAAATAATATT
1 AAATTAAATTTAATATTAAACTATTAAGATAATATT
28961068 A
1 A
28961069 TTTTTGGAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
36 17 0.27
37 29 0.47
38 3 0.05
39 12 0.19
40 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (36 bp):
AAATTAAATTTAATATTAAACTATTAAGATAATATT
Found at i:28962751 original size:177 final size:178
Alignment explanation
Indices: 28962454--28962808 Score: 595
Period size: 177 Copynumber: 2.0 Consensus size: 178
28962444 CGACATAATA
* * *
28962454 ATCATTCTCAGTATTTGAATCAAATGCTCACTTTGATTTTTTTTACGGGATTACAGACTTATTTA
1 ATCATTCTCAGTATTTGAATCAAATGCTCACTTTGATTTCTTTTACGGGACTACAGACTCATTTA
*
28962519 GATTATCTATTGAAGTAAGTTGTCTTTCTAGCAATGCAAACGTTCTTACAATGTCACTTATCTTT
66 GATTATCTATTGAAGTAAGTTGCCTTTCTAGCAATGCAAACGTTCTTACAATGTCACTTATCTTT
* * * *
28962584 AGTTTGAACTTTGATAATCAATGAGCTAATATTTGCTTGTCACAATTT
131 AGTTTGAACTTAGACAATCAATGAACTAATATTTGCTTATCACAATTT
28962632 ATCATTCTCAGTATTTGAATCAAATGCTCACTTTGA-TTCTTTTACGGGACTACAGACTCATTTA
1 ATCATTCTCAGTATTTGAATCAAATGCTCACTTTGATTTCTTTTACGGGACTACAGACTCATTTA
* * * *
28962696 GATTATCTATTGAAGTAAGTTGCCTTTCTCGCAATGTAAACTTTCTTACAATGTCACTTGTCTTT
66 GATTATCTATTGAAGTAAGTTGCCTTTCTAGCAATGCAAACGTTCTTACAATGTCACTTATCTTT
28962761 AGTTTGAACTTAGACAATCAATGAACTAATATTTGCTTATCACAATTT
131 AGTTTGAACTTAGACAATCAATGAACTAATATTTGCTTATCACAATTT
28962809 CGCTATGTAT
Statistics
Matches: 165, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
177 129 0.78
178 36 0.22
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (178 bp):
ATCATTCTCAGTATTTGAATCAAATGCTCACTTTGATTTCTTTTACGGGACTACAGACTCATTTA
GATTATCTATTGAAGTAAGTTGCCTTTCTAGCAATGCAAACGTTCTTACAATGTCACTTATCTTT
AGTTTGAACTTAGACAATCAATGAACTAATATTTGCTTATCACAATTT
Found at i:28965863 original size:21 final size:21
Alignment explanation
Indices: 28965833--28965874 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28965823 CTATCACTTA
28965833 GGGACAATCAATGGAAACTGT
1 GGGACAATCAATGGAAACTGT
* *
28965854 GGGACCATCAATGGAAGCTGT
1 GGGACAATCAATGGAAACTGT
28965875 AGGTCTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (21 bp):
GGGACAATCAATGGAAACTGT
Found at i:28967184 original size:29 final size:29
Alignment explanation
Indices: 28967152--28967291 Score: 101
Period size: 29 Copynumber: 4.8 Consensus size: 29
28967142 ATAAAAATCA
*
28967152 ATAAAATTTATTAAATTTAATAAATAAAT
1 ATAAAATTTATAAAATTTAATAAATAAAT
* ** *
28967181 ATAAAATTTATTAAAA-ATCGTAAAAAAAT
1 ATAAAATTTA-TAAAATTTAATAAATAAAT
* *
28967210 ATAAAAATTTGTAAAATTTTAT-AAT-AAT
1 AT-AAAATTTATAAAATTTAATAAATAAAT
* * *
28967238 CATAAAAATTATAAAATATATAGAAATATAA-
1 -ATAAAATTTATAAAATTTA-ATAAATA-AAT
*
28967269 A-AAAATTTATAAAATTTTATAAA
1 ATAAAATTTATAAAATTTAATAAA
28967292 GTCGTAAGAA
Statistics
Matches: 84, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
28 20 0.24
29 45 0.54
30 17 0.20
32 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (29 bp):
ATAAAATTTATAAAATTTAATAAATAAAT
Found at i:28967206 original size:20 final size:19
Alignment explanation
Indices: 28967183--28967338 Score: 72
Period size: 19 Copynumber: 8.2 Consensus size: 19
28967173 AAATAAATAT
28967183 AAAATTTATTAAAAATCGTA
1 AAAATTTA-TAAAAATCGTA
** *
28967203 AAAAAATATAAAAATTTGTA
1 AAAATTTATAAAAA-TCGTA
* * *
28967223 AAATTTTATAATAATCATA
1 AAAATTTATAAAAATCGTA
*
28967242 AAAA-TTATAAAATAT-ATA
1 AAAATTTATAAAA-ATCGTA
* * * *
28967260 GAAATATAAAAAAAT-TTA
1 AAAATTTATAAAAATCGTA
*
28967278 TAAAATTT-TATAAAGTCGTA
1 -AAAATTTATA-AAAATCGTA
* *
28967298 AGAAAATTATAAAAAT-ATA
1 A-AAATTTATAAAAATCGTA
* *
28967317 AAAA-ATATAAAATTCGTA
1 AAAATTTATAAAAATCGTA
28967335 AAAA
1 AAAA
28967339 AATTACAAAA
Statistics
Matches: 101, Mismatches: 26, Indels: 20
0.69 0.18 0.14
Matches are distributed among these distances:
17 8 0.08
18 27 0.27
19 33 0.33
20 31 0.31
21 2 0.02
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (19 bp):
AAAATTTATAAAAATCGTA
Found at i:28967251 original size:9 final size:9
Alignment explanation
Indices: 28967142--28967353 Score: 65
Period size: 9 Copynumber: 22.2 Consensus size: 9
28967132 AATGATAAAA
*
28967142 ATAAAAATCA
1 ATAAAAAT-T
*
28967152 ATAAAATTT
1 ATAAAAATT
* *
28967161 ATTAAATTT
1 ATAAAAATT
*
28967170 AATAAATAAAT
1 -ATAAA-AATT
*
28967181 ATAAAATTT
1 ATAAAAATT
28967190 ATTAAAAATCGT
1 A-TAAAAAT--T
*
28967202 A-AAAAAAT
1 ATAAAAATT
28967210 ATAAAAATTT
1 ATAAAAA-TT
* *
28967220 GTAAAATTTT
1 ATAAAA-ATT
* *
28967230 ATAATAATC
1 ATAAAAATT
28967239 ATAAAAATT
1 ATAAAAATT
28967248 AT-AAAATAT
1 ATAAAAAT-T
*
28967257 ATAGAAATAT
1 ATAAAAAT-T
*
28967267 AAAAAAATT
1 ATAAAAATT
28967276 -TATAAAATT
1 ATA-AAAATT
* *
28967285 TTATAAAGTCGT
1 ATA-AAAAT--T
28967297 A-AGAAAATT
1 ATA-AAAATT
28967306 ATAAAAA-T
1 ATAAAAATT
*
28967314 ATAAAAAAT
1 ATAAAAATT
*
28967323 ATAAAATTCGT
1 ATAAAAAT--T
*
28967334 AAAAAAATT
1 ATAAAAATT
*
28967343 ACAAAAATT
1 ATAAAAATT
28967352 AT
1 AT
28967354 CGTAATACCA
Statistics
Matches: 151, Mismatches: 33, Indels: 37
0.68 0.15 0.17
Matches are distributed among these distances:
8 16 0.11
9 59 0.39
10 59 0.39
11 14 0.09
12 3 0.02
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:28967266 original size:10 final size:9
Alignment explanation
Indices: 28967205--28967329 Score: 53
Period size: 10 Copynumber: 13.6 Consensus size: 9
28967195 AAATCGTAAA
28967205 AAAATATA-
1 AAAATATAT
* *
28967213 AAAATTTGT
1 AAAATATAT
*
28967222 AAAATTTTAT
1 AAAA-TATAT
28967232 AATAATCATA-
1 AA-AAT-ATAT
28967242 AAAAT-TAT
1 AAAATATAT
28967250 AAAATATAT
1 AAAATATAT
*
28967259 AGAAATATAAA
1 A-AAATAT-AT
*
28967270 AAAATTTAT
1 AAAATATAT
*
28967279 AAAATTTTAT
1 AAAA-TATAT
* * *
28967289 AAAGTCGTAAG
1 AAAAT-AT-AT
28967300 AAAAT-TAT
1 AAAATATAT
28967308 AAAA-ATAT
1 AAAATATAT
*
28967316 AAAAAATAT
1 AAAATATAT
28967325 AAAAT
1 AAAAT
28967330 TCGTAAAAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
7 2 0.02
8 23 0.25
9 26 0.29
10 29 0.32
11 11 0.12
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (9 bp):
AAAATATAT
Found at i:28967893 original size:21 final size:21
Alignment explanation
Indices: 28967869--28967913 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28967859 AAATTACAAA
28967869 AAAAAATTCAAAATAATTTTT
1 AAAAAATTCAAAATAATTTTT
* * *
28967890 AAAAGATTTAAATTAATTTTT
1 AAAAAATTCAAAATAATTTTT
28967911 AAA
1 AAA
28967914 TTTCAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAAAATTCAAAATAATTTTT
Found at i:28967936 original size:20 final size:20
Alignment explanation
Indices: 28967875--28967940 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
28967865 CAAAAAAAAA
28967875 TTCAAAATAATTTTTAAAAGAT
1 TTCAAAATAA-TTTT-AAAGAT
* *
28967897 TT-AAATTAATTTTTAA-AT
1 TTCAAAATAATTTTAAAGAT
28967915 TTCAAAAT-ATTTATAAAGAT
1 TTCAAAATAATTT-TAAAGAT
28967935 TTCAAA
1 TTCAAA
28967941 TTTTATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 8 0.22
19 9 0.24
20 12 0.32
21 6 0.16
22 2 0.05
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (20 bp):
TTCAAAATAATTTTAAAGAT
Found at i:28967994 original size:16 final size:17
Alignment explanation
Indices: 28967966--28967997 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28967956 AAATTTATAT
28967966 AAATTCTTAAAAAATAA
1 AAATTCTTAAAAAATAA
28967983 AAATTC-TAAAAAATA
1 AAATTCTTAAAAAATA
28967998 TATAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATTCTTAAAAAATAA
Found at i:28973712 original size:9 final size:9
Alignment explanation
Indices: 28973698--28973764 Score: 98
Period size: 9 Copynumber: 7.2 Consensus size: 9
28973688 CCAATTTATT
28973698 TTCGGGTAA
1 TTCGGGTAA
28973707 TTCGGGTAA
1 TTCGGGTAA
*
28973716 TTTTCTGGTAA
1 --TTCGGGTAA
28973727 TTCGGGTAA
1 TTCGGGTAA
28973736 TTCGGGTAA
1 TTCGGGTAA
*
28973745 TTCGGATAA
1 TTCGGGTAA
28973754 TTCGGGTAA
1 TTCGGGTAA
28973763 TT
1 TT
28973765 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
9 44 0.85
11 8 0.15
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.39
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:28973740 original size:29 final size:27
Alignment explanation
Indices: 28973698--28973764 Score: 100
Period size: 29 Copynumber: 2.4 Consensus size: 27
28973688 CCAATTTATT
28973698 TTCGGGTAATTCGGGTAATTTTCTGG-TAA
1 TTCGGGTAATTCGGGTAA--TTC-GGATAA
28973727 TTCGGGTAATTCGGGTAATTCGGATAA
1 TTCGGGTAATTCGGGTAATTCGGATAA
28973754 TTCGGGTAATT
1 TTCGGGTAATT
28973765 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
26 2 0.05
27 17 0.46
29 18 0.49
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.39
Consensus pattern (27 bp):
TTCGGGTAATTCGGGTAATTCGGATAA
Found at i:28974863 original size:6 final size:6
Alignment explanation
Indices: 28974816--28974851 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
28974806 GATTTTTTCC
28974816 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
28974852 GGAGAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:28975359 original size:20 final size:20
Alignment explanation
Indices: 28975336--28975381 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
28975326 AATAAACACC
28975336 AAAAATTTATTTTAAAAATA
1 AAAAATTTATTTTAAAAATA
* *
28975356 AAAAAATTATTTTAAAATTA
1 AAAAATTTATTTTAAAAATA
28975376 AAAAAT
1 AAAAAT
28975382 AAAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTTATTTTAAAAATA
Found at i:28980227 original size:29 final size:29
Alignment explanation
Indices: 28980195--28980279 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 29
28980185 TTTAATGTGT
28980195 AATTGTATACATGAACTTTAATTTGGTGC
1 AATTGTATACATGAACTTTAATTTGGTGC
* * * *
28980224 AATTATATGCATGAAACTCTAATTGTGGTTC
1 AATTGTATACATG-AACTTTAATT-TGGTGC
* * *
28980255 AAATGTATACTTAAAACTTTAATTT
1 AATTGTATACAT-GAACTTTAATTT
28980280 TGATTTAATC
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
29 11 0.26
30 10 0.23
31 22 0.51
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (29 bp):
AATTGTATACATGAACTTTAATTTGGTGC
Found at i:28981439 original size:3 final size:3
Alignment explanation
Indices: 28981431--28981481 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
28981421 CATCAAACAA
28981431 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28981479 AAT
1 AAT
28981482 TCTAAGTGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28982843 original size:27 final size:27
Alignment explanation
Indices: 28982813--28982883 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
28982803 AGGCCAATGG
*
28982813 CATTGGCGGCACCAATGGTGCCAAAGC
1 CATTGGCGGCACCAATGGTGCCAAAAC
28982840 CATTGGCGGCACCAATGGTGCCAAAAC
1 CATTGGCGGCACCAATGGTGCCAAAAC
*
28982867 CATTGGCAGCACCAATG
1 CATTGGCGGCACCAATG
28982884 CCATAATAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (27 bp):
CATTGGCGGCACCAATGGTGCCAAAAC
Found at i:28982939 original size:27 final size:27
Alignment explanation
Indices: 28982909--28982966 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
28982899 TGGTGGTGGG
*
28982909 GGAAGGAGAGGGAAAGAAAGAAAGA-AA
1 GGAAGGAGA-GGAAAGAAAGAAAAAGAA
28982936 GGAAGGAGAGGAAAGAAAGAAAAAGAA
1 GGAAGGAGAGGAAAGAAAGAAAAAGAA
28982963 GGAA
1 GGAA
28982967 AGAAAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (27 bp):
GGAAGGAGAGGAAAGAAAGAAAAAGAA
Found at i:28982965 original size:18 final size:18
Alignment explanation
Indices: 28982924--28983026 Score: 69
Period size: 16 Copynumber: 5.8 Consensus size: 18
28982914 GAGAGGGAAA
28982924 GAAAGAAAGAAAGGAAGGAGAG
1 GAAAGAAAGAAA--AA-GA-AG
28982946 GAAAGAAAGAAAAAGAAG
1 GAAAGAAAGAAAAAGAAG
*
28982964 GAAAG-AA-AAAGA-AAG
1 GAAAGAAAGAAAAAGAAG
28982979 G--AGAAGAGAAAAA-AAG
1 GAAAGAA-AGAAAAAGAAG
*
28982995 GAAAG-AAGAATAAG-AG
1 GAAAGAAAGAAAAAGAAG
28983011 GAAATGAGAAGAAAAA
1 GAAA-GA-AAGAAAAA
28983027 ATAAAGAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
13 2 0.03
14 1 0.01
15 5 0.07
16 24 0.35
17 4 0.06
18 9 0.13
19 9 0.13
20 2 0.03
22 12 0.18
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (18 bp):
GAAAGAAAGAAAAAGAAG
Found at i:28983023 original size:47 final size:48
Alignment explanation
Indices: 28982921--28983108 Score: 124
Period size: 47 Copynumber: 3.9 Consensus size: 48
28982911 AAGGAGAGGG
* *
28982921 AAAGAAAGAAAGAAAG-GAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAA
1 AAAGAAA-AAAGAAAGAAAAAGA-AGGAAAG-AAGAAAAAGAAGGAAAGAA
** *
28982971 AAAGAAAGGAGAAGAGAAAAA-AAGGAAAGAAGAATAAG-AGGAAATG-A
1 AAAGAAAAAAGAA-AGAAAAAGAAGGAAAGAAGAAAAAGAAGGAAA-GAA
* * **
28983018 GAAGAAAAAATAAAGAAAAAGAAGGAAAGAA-AAGGA-AAGGAGAAGAGA
1 AAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAGAAAAAGAAGGA-AAGA-A
** * *
28983066 AAA-AAAAAAGAAGAGGGAATGAAGGAAGGAA-AAAAA-AAGGAAA
1 AAAGAAAAAAGAA-AGAAAAAGAAGGAAAGAAGAAAAAGAAGGAAA
28983109 AAAGGTAATT
Statistics
Matches: 110, Mismatches: 19, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
46 15 0.14
47 38 0.35
48 34 0.31
49 11 0.10
50 10 0.09
51 2 0.02
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (48 bp):
AAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAGAAAAAGAAGGAAAGAA
Found at i:28983072 original size:46 final size:46
Alignment explanation
Indices: 28982985--28983073 Score: 112
Period size: 46 Copynumber: 1.9 Consensus size: 46
28982975 AAAGGAGAAG
* *
28982985 AGAAAAAAAGGAAAGAAGAATAAGAGGAAATGAGAAGAAAAAATAA
1 AGAAAAAAAGGAAAGAAGAAGAAGAGGAAATGAGAAAAAAAAATAA
28983031 AGAAAAAGAAGGAAAGAA-AAGGAA-AGGAGAA-GAGAAAAAAAAA
1 AGAAAAA-AAGGAAAGAAGAA-GAAGAGGA-AATGAGAAAAAAAAA
28983074 AGAAGAGGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
46 24 0.63
47 14 0.37
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (46 bp):
AGAAAAAAAGGAAAGAAGAAGAAGAGGAAATGAGAAAAAAAAATAA
Found at i:28986426 original size:11 final size:11
Alignment explanation
Indices: 28986406--28986445 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
28986396 TTAAAAATAC
28986406 CTTCTTTTTCT
1 CTTCTTTTTCT
*
28986417 CTTCTCTTTCT
1 CTTCTTTTTCT
28986428 C-TCTTTTTCT
1 CTTCTTTTTCT
28986438 CTTCTTTT
1 CTTCTTTT
28986446 CCACAACACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:28986433 original size:21 final size:20
Alignment explanation
Indices: 28986408--28986446 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
28986398 AAAAATACCT
28986408 TCTTTTTCTCTTCTCTTTCTC
1 TCTTTTTCTCTTCT-TTTCTC
28986429 TCTTTTTCTCTTCTTTTC
1 TCTTTTTCTCTTCTTTTC
28986447 CACAACACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TCTTTTTCTCTTCTTTTCTC
Found at i:28986652 original size:27 final size:27
Alignment explanation
Indices: 28986622--28986689 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 27
28986612 GTTTTTTTTA
28986622 TATATTTTGGTAAATAATAAAAA-TAAT
1 TATATTTTGGTAAATAA-AAAAATTAAT
*
28986649 TATAATAATTTGGTAAATAAAAAAATTTAT
1 TAT-AT--TTTGGTAAATAAAAAAATTAAT
*
28986679 AATATTTTGGT
1 TATATTTTGGT
28986690 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
27 9 0.26
28 2 0.06
29 7 0.20
30 17 0.49
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (27 bp):
TATATTTTGGTAAATAAAAAAATTAAT
Found at i:28986661 original size:30 final size:27
Alignment explanation
Indices: 28986618--28986689 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 27
28986608 TTTTGTTTTT
28986618 TTTAT-ATATTTTGGTAAATAATAAAAA
1 TTTATAATATTTTGGTAAATAA-AAAAA
*
28986645 TAATTATAATAATTTGGTAAATAAAAAAA
1 T--TTATAATATTTTGGTAAATAAAAAAA
28986674 TTTATAATATTTTGGT
1 TTTATAATATTTTGGT
28986690 TATTTTTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 15 0.38
29 10 0.25
30 15 0.38
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (27 bp):
TTTATAATATTTTGGTAAATAAAAAAA
Found at i:28987832 original size:32 final size:30
Alignment explanation
Indices: 28987796--28987856 Score: 104
Period size: 32 Copynumber: 2.0 Consensus size: 30
28987786 AATTTTTTTA
28987796 ATTTTAAAAATTCAAAAAAAATTATAAAAAAT
1 ATTTTAAAAATTC-AAAAAAATTA-AAAAAAT
28987828 ATTTTAAAAATTCAAAAAAATTAAAAAAA
1 ATTTTAAAAATTCAAAAAAATTAAAAAAA
28987857 GTGTAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 6 0.21
31 10 0.34
32 13 0.45
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (30 bp):
ATTTTAAAAATTCAAAAAAATTAAAAAAAT
Found at i:28988039 original size:22 final size:22
Alignment explanation
Indices: 28988011--28988053 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
28988001 TTTATTGTTC
28988011 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
28988033 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
28988054 TAGCCATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:28991129 original size:2 final size:2
Alignment explanation
Indices: 28991122--28991161 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
28991112 CTGAGGTAGA
28991122 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
28991162 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29005757 original size:3 final size:3
Alignment explanation
Indices: 29005701--29005745 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
29005691 ATTATAATAC
* ** *
29005701 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TCC TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29005746 AGGTGTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:29006002 original size:51 final size:48
Alignment explanation
Indices: 29005899--29006009 Score: 113
Period size: 51 Copynumber: 2.2 Consensus size: 48
29005889 CACATTTTTA
* *
29005899 TAATTTTATTT-TACAATATATTCATAAATTCCATTTTTATATATTTC
1 TAATTTTATTTATACAATATATTCATAAATTCCATTTTCATATATTAC
29005946 TAATTTTATTTATACAATAATATTTTCAT-AATTCCA-TTTCATGCATATATAC
1 TAATTTTATTTATACAAT-ATA--TTCATAAATTCCATTTTCAT--ATAT-TAC
29005998 -AATTTATATTTA
1 TAATTT-TATTTA
29006010 ATTATTTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
47 11 0.20
48 6 0.11
49 8 0.15
50 7 0.13
51 14 0.26
52 8 0.15
ACGTcount: A:0.36, C:0.11, G:0.01, T:0.52
Consensus pattern (48 bp):
TAATTTTATTTATACAATATATTCATAAATTCCATTTTCATATATTAC
Found at i:29009403 original size:17 final size:18
Alignment explanation
Indices: 29009373--29009406 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29009363 AATTTAGCCA
*
29009373 TTTTTTATATATTTTTAT
1 TTTTTTATAAATTTTTAT
29009391 TTTTTTA-AAATTTTTA
1 TTTTTTATAAATTTTTA
29009407 CATTCTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTATAAATTTTTAT
Found at i:29009611 original size:18 final size:18
Alignment explanation
Indices: 29009588--29009624 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29009578 TACTGAGGAG
29009588 ATGGACGATAATCAGAAT
1 ATGGACGATAATCAGAAT
29009606 ATGGACGATAATCAGAAT
1 ATGGACGATAATCAGAAT
29009624 A
1 A
29009625 CTAAGTTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (18 bp):
ATGGACGATAATCAGAAT
Found at i:29011676 original size:12 final size:12
Alignment explanation
Indices: 29011655--29011779 Score: 54
Period size: 12 Copynumber: 9.8 Consensus size: 12
29011645 AAAAACGAAA
*
29011655 TGATTAAAAACT
1 TGATGAAAAACT
* *
29011667 TGATGGAAAATT
1 TGATGAAAAACT
*
29011679 TTATGAAAAGACT
1 TGATGAAAA-ACT
*
29011692 CGATGAAAAACT
1 TGATGAAAAACT
* *
29011704 TTA-AAAAGAACT
1 TGATGAAA-AACT
* *
29011716 TGCTGCAAAACT
1 TGATGAAAAACT
*
29011728 TGATAAAAAAAACT
1 TGAT--GAAAAACT
*
29011742 TGGTAATTAAAAACT
1 T-G--ATGAAAAACT
*
29011757 TGATAAAAGAACT
1 TGATGAAA-AACT
*
29011770 AGATGAAAAA
1 TGATGAAAAA
29011780 TACTTGAAGA
Statistics
Matches: 82, Mismatches: 22, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
11 3 0.04
12 39 0.48
13 21 0.26
14 8 0.10
15 9 0.11
17 2 0.02
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:29011706 original size:25 final size:24
Alignment explanation
Indices: 29011660--29011706 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
29011650 CGAAATGATT
* * *
29011660 AAAAACTTGATGGAAAATTTTATG
1 AAAAACTCGATGAAAAACTTTATG
29011684 AAAAGACTCGATGAAAAACTTTA
1 AAAA-ACTCGATGAAAAACTTTA
29011707 AAAAGAACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAAACTCGATGAAAAACTTTATG
Found at i:29011755 original size:15 final size:14
Alignment explanation
Indices: 29011722--29011786 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
29011712 AACTTGCTGC
29011722 AAAACTTGATAAAA
1 AAAACTTGATAAAA
* *
29011736 AAAACTTGGTAATTA
1 AAAACTTGATAA-AA
29011751 AAAACTTGAT-AAA
1 AAAACTTGATAAAA
* * *
29011764 AGAACTAGATGAAA
1 AAAACTTGATAAAA
*
29011778 AATACTTGA
1 AAAACTTGA
29011787 AGAAAGAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
13 9 0.22
14 21 0.52
15 10 0.25
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.25
Consensus pattern (14 bp):
AAAACTTGATAAAA
Found at i:29011797 original size:18 final size:18
Alignment explanation
Indices: 29011774--29011811 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
29011764 AGAACTAGAT
*
29011774 GAAAAATACTTGAA-GAAA
1 GAAAAACACTT-AATGAAA
29011792 GAAAAACACTTAATGAAA
1 GAAAAACACTTAATGAAA
29011810 GA
1 GA
29011812 CTTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (18 bp):
GAAAAACACTTAATGAAA
Found at i:29012693 original size:12 final size:12
Alignment explanation
Indices: 29012669--29012715 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
29012659 ACCAGAGGAG
29012669 TATTTTTAT-TTT
1 TATTTTT-TGTTT
29012681 TATTTTTTGTTT
1 TATTTTTTGTTT
*
29012693 TGTTTTTTGTTT
1 TATTTTTTGTTT
*
29012705 TTTTTTTTGTT
1 TATTTTTTGTT
29012716 GAAAAGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 1 0.03
12 31 0.97
ACGTcount: A:0.06, C:0.00, G:0.09, T:0.85
Consensus pattern (12 bp):
TATTTTTTGTTT
Found at i:29012699 original size:19 final size:19
Alignment explanation
Indices: 29012677--29012715 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
29012667 AGTATTTTTA
29012677 TTTTTATTTTTTGTTTTGT
1 TTTTTATTTTTTGTTTTGT
* *
29012696 TTTTTGTTTTTTTTTTTGT
1 TTTTTATTTTTTGTTTTGT
29012715 T
1 T
29012716 GAAAAGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (19 bp):
TTTTTATTTTTTGTTTTGT
Found at i:29013161 original size:7 final size:6
Alignment explanation
Indices: 29013144--29013220 Score: 57
Period size: 6 Copynumber: 12.2 Consensus size: 6
29013134 ATGTTTCCTG
* * *
29013144 TAAAAA TAAAAA TGAAAA T-AAAA TAAAATA GTAAAAA TAATAA TAATAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA-A -TAAAAA TAAAAA TAAAAA
* *
29013193 TAATAA TAATAATA TAGAAAA TTAAAA T
1 TAAAAA TAA-AA-A TA-AAAA TAAAAA T
29013221 GTTTTTTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
5 5 0.08
6 40 0.66
7 5 0.08
8 10 0.16
9 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (6 bp):
TAAAAA
Found at i:29013187 original size:3 final size:3
Alignment explanation
Indices: 29013160--29013206 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
29013150 TAAAAATGAA
* *
29013160 AAT AA- AAT AA- AAT AGT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29013206 A
1 A
29013207 TAGAAAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:29017497 original size:12 final size:12
Alignment explanation
Indices: 29017476--29017598 Score: 61
Period size: 12 Copynumber: 9.8 Consensus size: 12
29017466 TAAAACGAAA
*
29017476 TGATTAAAAACT
1 TGATGAAAAACT
* *
29017488 TGATGGAAAATT
1 TGATGAAAAACT
*
29017500 TTATGAAAAGACT
1 TGATGAAAA-ACT
*
29017513 AGATGAAAAACT
1 TGATGAAAAACT
* *
29017525 TTA-AAAAGAACT
1 TGATGAAA-AACT
* *
29017537 TGCTGCAAAACT
1 TGATGAAAAACT
29017549 TGAT-AGAAAACT
1 TGATGA-AAAACT
*
29017561 TGGTAATTAAAAACT
1 T-G--ATGAAAAACT
*
29017576 TGATAAAAGAACT
1 TGATGAAA-AACT
*
29017589 AGATGAAAAA
1 TGATGAAAAA
29017599 TACTTGAAGA
Statistics
Matches: 82, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
11 3 0.04
12 46 0.56
13 22 0.27
14 1 0.01
15 9 0.11
16 1 0.01
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.26
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:29017527 original size:25 final size:24
Alignment explanation
Indices: 29017481--29017527 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
29017471 CGAAATGATT
* * *
29017481 AAAAACTTGATGGAAAATTTTATG
1 AAAAACTAGATGAAAAACTTTATG
29017505 AAAAGACTAGATGAAAAACTTTA
1 AAAA-ACTAGATGAAAAACTTTA
29017528 AAAAGAACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAAACTAGATGAAAAACTTTATG
Found at i:29017616 original size:18 final size:18
Alignment explanation
Indices: 29017593--29017630 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
29017583 AGAACTAGAT
*
29017593 GAAAAATACTTGAA-GAAA
1 GAAAAACACTT-AATGAAA
29017611 GAAAAACACTTAATGAAA
1 GAAAAACACTTAATGAAA
29017629 GA
1 GA
29017631 CTTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (18 bp):
GAAAAACACTTAATGAAA
Found at i:29020432 original size:8 final size:8
Alignment explanation
Indices: 29020421--29020455 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
29020411 TTTTTAATTC
29020421 TTTATTAT
1 TTTATTAT
29020429 TTTATTAT
1 TTTATTAT
*
29020437 TTTATCAT
1 TTTATTAT
29020445 TTTATTAT
1 TTTATTAT
29020453 TTT
1 TTT
29020456 CTTTAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTATTAT
Found at i:29022433 original size:90 final size:89
Alignment explanation
Indices: 29022272--29022450 Score: 270
Period size: 90 Copynumber: 2.0 Consensus size: 89
29022262 CATTTTGTTT
* *
29022272 AGTGAATTTAGCTAAACAATTAAATGAAAAGAAAGTCAAATATATGTTTGTTTCATTTAAAATAA
1 AGTGAATTTAGCTAAACAATTAAAAGAAAAAAAAGTCAAATATATGTTTGTTTCATTTAAAATAA
29022337 CTTTTTTGAAATATTTTCA-AGAA
66 CTTTTTTGAAATATTTTCAGAGAA
* * * *
29022360 AGTGAATTTAGCTAAACAATTAAAAGACAAGAAAAATTCAAATGTATGTTTGTTTCGTTTATAAT
1 AGTGAATTTAGCTAAACAATTAAAAGA-AA-AAAAAGTCAAATATATGTTTGTTTCATTTAAAAT
*
29022425 AGCTTTTTTGAAATATTTTCAGAGAA
64 AACTTTTTTGAAATATTTTCAGAGAA
29022451 TCTACCAAAC
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
88 26 0.32
89 2 0.02
90 49 0.60
91 4 0.05
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.37
Consensus pattern (89 bp):
AGTGAATTTAGCTAAACAATTAAAAGAAAAAAAAGTCAAATATATGTTTGTTTCATTTAAAATAA
CTTTTTTGAAATATTTTCAGAGAA
Found at i:29025941 original size:11 final size:10
Alignment explanation
Indices: 29025924--29025952 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
29025914 GTTTTAGAAA
29025924 GAAAAAAATC
1 GAAAAAAATC
29025934 GAAAAAAATC
1 GAAAAAAATC
29025944 GAAAAAAAT
1 GAAAAAAAT
29025953 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.07, G:0.10, T:0.10
Consensus pattern (10 bp):
GAAAAAAATC
Found at i:29026425 original size:20 final size:20
Alignment explanation
Indices: 29026402--29026454 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
29026392 TGATTTCGGG
29026402 AAAATGTTTTACTTTTCTGT
1 AAAATGTTTTACTTTTCTGT
29026422 AAAATGTTTTACTTTTCTGT
1 AAAATGTTTTACTTTTCTGT
*
29026442 AAAATGATTTACT
1 AAAATGTTTTACT
29026455 GGAAAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (20 bp):
AAAATGTTTTACTTTTCTGT
Found at i:29029456 original size:13 final size:13
Alignment explanation
Indices: 29029438--29029464 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29029428 TCATTATTTC
29029438 TTTTATTTTTTAT
1 TTTTATTTTTTAT
29029451 TTTTATTTTTTAT
1 TTTTATTTTTTAT
29029464 T
1 T
29029465 GTTGAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:29030496 original size:71 final size:70
Alignment explanation
Indices: 29030358--29030527 Score: 175
Period size: 71 Copynumber: 2.4 Consensus size: 70
29030348 CAATCAAGTG
* *
29030358 CTACTGATACCTTGAAGGCTTCTATCGAAACAAGTCAACTCAATAGGCAAAGTTCAGCATCTCCT
1 CTACTAATACCTTGAAGGCTTCTATCGAAACAAGTCAACTCAATAGCCAAAGTTCA-CATCTCCT
*
29030423 GCATTT
65 GCACTT
* * *
29030429 CTACTAATACCTTG-AGGACTTCTA-CTGAAACAAGTCAAGTCAGTAGCCAAAGTTCA-ATTTCC
1 CTACTAATACCTTGAAGG-CTTCTATC-GAAACAAGTCAACTCAATAGCCAAAGTTCACATCT-C
29030491 TCTGCACTT
63 -CTGCACTT
** * * *
29030500 CTACCGATACTTTGATGGGTTCTATCGA
1 CTACTAATACCTTGAAGGCTTCTATCGA
29030528 TACCAAATGA
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
69 3 0.04
70 5 0.06
71 71 0.87
72 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (70 bp):
CTACTAATACCTTGAAGGCTTCTATCGAAACAAGTCAACTCAATAGCCAAAGTTCACATCTCCTG
CACTT
Found at i:29030700 original size:34 final size:34
Alignment explanation
Indices: 29030656--29030733 Score: 147
Period size: 34 Copynumber: 2.3 Consensus size: 34
29030646 CGAAGCTGCA
*
29030656 GACTACATTTAATGCTGATTTTTATTGCTGCAAT
1 GACTCCATTTAATGCTGATTTTTATTGCTGCAAT
29030690 GACTCCATTTAATGCTGATTTTTATTGCTGCAAT
1 GACTCCATTTAATGCTGATTTTTATTGCTGCAAT
29030724 GACTCCATTT
1 GACTCCATTT
29030734 TGTTTCTAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (34 bp):
GACTCCATTTAATGCTGATTTTTATTGCTGCAAT
Found at i:29034660 original size:16 final size:15
Alignment explanation
Indices: 29034630--29034702 Score: 58
Period size: 16 Copynumber: 4.5 Consensus size: 15
29034620 CAAAACTTTC
29034630 CCCAAATAC-TAAAAT
1 CCCAAAT-CGTAAAAT
*
29034645 CCCAAATTCGTCAAATT
1 CCCAAA-TCGT-AAAAT
*
29034662 CCCTAAATCGTAAAAC
1 CCC-AAATCGTAAAAT
*
29034678 CTCCAAATCGTGAAAT
1 C-CCAAATCGTAAAAT
29034694 CCCCAAATC
1 -CCCAAATC
29034703 CATAACATCC
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
15 7 0.15
16 23 0.49
17 14 0.30
18 3 0.06
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (15 bp):
CCCAAATCGTAAAAT
Found at i:29034664 original size:33 final size:33
Alignment explanation
Indices: 29034627--29034702 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
29034617 ATTCAAAACT
*
29034627 TTCCCCAAATAC-TAAAATC-CCAAATTCGTCAAA
1 TTCCCCAAAT-CGTAAAACCTCCAAA-TCGTCAAA
* *
29034660 TTCCCTAAATCGTAAAACCTCCAAATCGTGAAA
1 TTCCCCAAATCGTAAAACCTCCAAATCGTCAAA
29034693 -TCCCCAAATC
1 TTCCCCAAATC
29034703 CATAACATCC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 10 0.27
33 22 0.59
34 5 0.14
ACGTcount: A:0.39, C:0.32, G:0.05, T:0.24
Consensus pattern (33 bp):
TTCCCCAAATCGTAAAACCTCCAAATCGTCAAA
Found at i:29036042 original size:14 final size:15
Alignment explanation
Indices: 29036010--29036042 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
29036000 CCAAAACCAG
29036010 AATGTTGTAGGCTCAA
1 AATGTTGTAGGC-CAA
29036026 AATGTTGTAGG-CAA
1 AATGTTGTAGGCCAA
29036040 AAT
1 AAT
29036043 ACCTTACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
16 11 0.65
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (15 bp):
AATGTTGTAGGCCAA
Found at i:29039226 original size:33 final size:33
Alignment explanation
Indices: 29039152--29039229 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
29039142 TCTTTCTAGT
* * *
29039152 TCACCTTCACCATCAGATTCTACCCATTTATCA
1 TCACCCTCCCCATCAGATTCTACCCATTTAACA
*
29039185 TCACCCTCCCCATCA-ATTTCTACCCTTTTAACA
1 TCACCCTCCCCATCAGA-TTCTACCCATTTAACA
29039218 TCACCCTCCCCA
1 TCACCCTCCCCA
29039230 ACAGTCAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 1 0.03
33 39 0.98
ACGTcount: A:0.24, C:0.44, G:0.01, T:0.31
Consensus pattern (33 bp):
TCACCCTCCCCATCAGATTCTACCCATTTAACA
Found at i:29041415 original size:13 final size:13
Alignment explanation
Indices: 29041397--29041423 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29041387 ATATGAATAC
29041397 AAGTAATAGTAAA
1 AAGTAATAGTAAA
29041410 AAGTAATAGTAAA
1 AAGTAATAGTAAA
29041423 A
1 A
29041424 TAAAGTGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (13 bp):
AAGTAATAGTAAA
Found at i:29042051 original size:17 final size:18
Alignment explanation
Indices: 29042029--29042063 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29042019 ATCCATATTC
29042029 AATAA-TAAATATATAAA
1 AATAATTAAATATATAAA
*
29042046 AATAATTAAATTTATAAA
1 AATAATTAAATATATAAA
29042064 TATTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAATTAAATATATAAA
Found at i:29042404 original size:50 final size:50
Alignment explanation
Indices: 29042338--29042482 Score: 166
Period size: 53 Copynumber: 2.8 Consensus size: 50
29042328 ATACTAATAT
*
29042338 CACCCATCTCTTTCCCTCCACCCTTAAAAAATATTTTTTTATACTGGTGC
1 CACCCATCTCTCTCCCTCCACCCTTAAAAAATATTTTTTTATACTGGTGC
** * * * *
29042388 TGCCCATCTCTCTCCCTCGACCATCAAAAAATAATTTTTTGTTATACTGGTTC
1 CACCCATCTCTCTCCCTCCACCCTTAAAAAAT-A-TTTTT-TTATACTGGTGC
*
29042441 CACCCATCTCTC-CCTCTCCACCCTTAAAAACATTTTTTTTTA
1 CACCCATCTCTCTCC-CTCCACCCTTAAAAA-ATATTTTTTTA
29042483 AAAAAACACA
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
50 26 0.34
51 4 0.05
52 12 0.16
53 33 0.43
54 2 0.03
ACGTcount: A:0.24, C:0.32, G:0.06, T:0.38
Consensus pattern (50 bp):
CACCCATCTCTCTCCCTCCACCCTTAAAAAATATTTTTTTATACTGGTGC
Found at i:29043706 original size:11 final size:11
Alignment explanation
Indices: 29043684--29043719 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
29043674 AACTAATCCT
29043684 CTCTCAAATTTC
1 CTCTC-AATTTC
29043696 CTCTCAATTTC
1 CTCTCAATTTC
29043707 CTCTCAATTTC
1 CTCTCAATTTC
29043718 CT
1 CT
29043720 TCCAAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.19, C:0.36, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:29043822 original size:10 final size:10
Alignment explanation
Indices: 29043792--29043830 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
29043782 CATAACTCCC
29043792 TTTTTTTAAA
1 TTTTTTTAAA
**
29043802 TAATTTT-AA
1 TTTTTTTAAA
29043811 TTTTTTTAAA
1 TTTTTTTAAA
29043821 TTTTTTTAAA
1 TTTTTTTAAA
29043831 CTGTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:29044925 original size:7 final size:7
Alignment explanation
Indices: 29044913--29044937 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29044903 TTTCTCATGT
29044913 TATTTAG
1 TATTTAG
29044920 TATTTAG
1 TATTTAG
29044927 TATTTAG
1 TATTTAG
29044934 TATT
1 TATT
29044938 ATGTATATAA
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:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:29045852 original size:21 final size:21
Alignment explanation
Indices: 29045810--29045854 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29045800 AAATGCCGTA
* *
29045810 CCGGAAGAACTAGAATCCCCG
1 CCGGAAGAACAACAATCCCCG
29045831 CCGGAAGAACAACAA-CCACCG
1 CCGGAAGAACAACAATCC-CCG
29045852 CCG
1 CCG
29045855 AAAGCTAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.36, C:0.38, G:0.22, T:0.04
Consensus pattern (21 bp):
CCGGAAGAACAACAATCCCCG
Found at i:29046034 original size:21 final size:21
Alignment explanation
Indices: 29046010--29046082 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
29046000 ATAGAAATTT
*
29046010 TTAAGTTAAAAACCTTAACCC
1 TTAACTTAAAAACCTTAACCC
* * *
29046031 TTAACTTTAAAACTTTAA-AC
1 TTAACTTAAAAACCTTAACCC
* *
29046051 TAAAACTTAAAAACCGTAACCC
1 T-TAACTTAAAAACCTTAACCC
29046073 TTAACTTAAA
1 TTAACTTAAA
29046083 TATAATTTGA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.05
21 36 0.90
22 2 0.05
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.30
Consensus pattern (21 bp):
TTAACTTAAAAACCTTAACCC
Found at i:29046212 original size:104 final size:103
Alignment explanation
Indices: 29046085--29046295 Score: 386
Period size: 104 Copynumber: 2.0 Consensus size: 103
29046075 AACTTAAATA
29046085 TAATTTGATAAATTTACTAACCATTAATACAATTTTTTGAGTTAATAATTTTACATTCACATAAT
1 TAATTTGATAAATTTACTAACCATTAATACAATTTTTTGAGTTAATAATTTTACATTCACATAAT
**
29046150 GTTAGATTTGGAAAAATGTTTTTTCCTGGTACTAACAAT
66 GTTAGATTTGGAAAAATG-TTTTAACTGGTACTAACAAT
*
29046189 TAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAGTTAATAATTTTACATTCACATAAT
1 TAATTTGATAAATTTACTAACCATTAATACAATTTTTTGAGTTAATAATTTTACATTCACATAAT
29046254 GTTAGATTTGGAAAAATGTTTTAACTGGTACTAACAAT
66 GTTAGATTTGGAAAAATGTTTTAACTGGTACTAACAAT
29046292 TAAT
1 TAAT
29046296 AATTTTATAT
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
103 22 0.21
104 82 0.79
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.43
Consensus pattern (103 bp):
TAATTTGATAAATTTACTAACCATTAATACAATTTTTTGAGTTAATAATTTTACATTCACATAAT
GTTAGATTTGGAAAAATGTTTTAACTGGTACTAACAAT
Found at i:29046309 original size:17 final size:16
Alignment explanation
Indices: 29046289--29046369 Score: 58
Period size: 18 Copynumber: 4.8 Consensus size: 16
29046279 TGGTACTAAC
29046289 AATTAATAATTTTATA
1 AATTAATAATTTTATA
*
29046305 TAATTTGATAATTTTACTA
1 -AA-TTAATAATTTTA-TA
* *
29046324 ACCATTAATACAATTTATC
1 A--ATTAATA-ATTTTATA
*
29046343 AATTAATAATTTTACA
1 AATTAATAATTTTATA
29046359 AA-T-ATAATTTT
1 AATTAATAATTTT
29046370 TTTACAATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
14 8 0.15
15 1 0.02
16 7 0.13
17 9 0.17
18 12 0.23
19 9 0.17
20 6 0.12
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.47
Consensus pattern (16 bp):
AATTAATAATTTTATA
Found at i:29049522 original size:124 final size:124
Alignment explanation
Indices: 29049360--29049611 Score: 398
Period size: 124 Copynumber: 2.0 Consensus size: 124
29049350 CCCAAACATG
* * * * * *
29049360 CTACTGTAGTAAAAGCTCGTCCACGAGGGCGCGCTTTCACAAATTCTTTTCAATTAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
*
29049425 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAATTTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACAAAAA-TTATTTCTTCCAAGAC
29049484 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
**
29049549 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAAGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAC-AAAAATTATTTCTTCCAAGAC
29049609 CTA
1 CTA
29049612 AAAACCCTAA
Statistics
Matches: 117, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
124 96 0.82
125 18 0.15
126 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACAAAAATTATTTCTTCCAAGAC
Found at i:29053305 original size:12 final size:12
Alignment explanation
Indices: 29053288--29053312 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29053278 GATGAAGCTA
29053288 CTACAGTTTGTG
1 CTACAGTTTGTG
29053300 CTACAGTTTGTG
1 CTACAGTTTGTG
29053312 C
1 C
29053313 AGTCTGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (12 bp):
CTACAGTTTGTG
Found at i:29063458 original size:34 final size:36
Alignment explanation
Indices: 29063392--29063481 Score: 123
Period size: 34 Copynumber: 2.6 Consensus size: 36
29063382 TATGAGATTT
**
29063392 GGTGTTATATATATAATA-ATATATATGTGTGCATG
1 GGTGTTATATATATAATATATATATATACGTGCATG
29063427 GGTGTTATATATATAATATATAT-TA-ACGTGCATG
1 GGTGTTATATATATAATATATATATATACGTGCATG
* *
29063461 GGTGTTATATGTATAAAATAT
1 GGTGTTATATATATAATATAT
29063482 TTGCGTGGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 26 0.52
35 20 0.40
36 4 0.08
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (36 bp):
GGTGTTATATATATAATATATATATATACGTGCATG
Found at i:29063563 original size:2 final size:2
Alignment explanation
Indices: 29063558--29063591 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29063548 TGGGTTTTAT
29063558 TA TA TA -A 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 TA TA TA T
29063592 GCAGTTATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.