Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 33
Found at i:2605831 original size:17 final size:16
Alignment explanation
Indices: 2605797--2605888 Score: 66
Period size: 17 Copynumber: 5.7 Consensus size: 16
2605787 TGGTTATAAA
2605797 TATTATATTATAATTAT
1 TATTATATTAT-ATTAT
*
2605814 TACTAT-TATATTATTAT
1 TATTATAT-TA-TATTAT
2605831 TATTATTATTATATTAT
1 TATTA-TATTATATTAT
**
2605848 TATTATAACA-ATTA-
1 TATTATATTATATTAT
*
2605862 TATTATAATA-ATTAT
1 TATTATATTATATTAT
*
2605877 TAATATTATTAT
1 TATTA-TATTAT
2605889 TAATATCATT
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
14 13 0.21
15 8 0.13
16 8 0.13
17 27 0.44
18 4 0.07
19 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATATTATATTAT
Found at i:2605835 original size:23 final size:22
Alignment explanation
Indices: 2605802--2605890 Score: 78
Period size: 20 Copynumber: 4.1 Consensus size: 22
2605792 ATAAATATTA
2605802 TATTATAATTATTACTATTATAT
1 TATTATAATTA-TACTATTATAT
*
2605825 TATTATTATTAT--TATTATAT
1 TATTATAATTATACTATTATAT
* *
2605845 TATTATTA-TA-ACAATTATAT
1 TATTATAATTATACTATTATAT
* *
2605865 TATAATAATTATTAATATTATTAT
1 TATTATAATTA-TACTATTA-TAT
2605889 TA
1 TA
2605891 ATATCATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
19 2 0.04
20 29 0.54
21 2 0.04
22 1 0.02
23 15 0.28
24 5 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTATAATTATACTATTATAT
Found at i:2613861 original size:113 final size:113
Alignment explanation
Indices: 2613657--2613965 Score: 478
Period size: 113 Copynumber: 2.7 Consensus size: 113
2613647 CCGAGACTTT
* * * * * *
2613657 CAGATATGATCTTTCCTTTAGAGTAAGCGGAATAGGTCTTTCTTTTCCAAGATTTGATATTCCCT
1 CAGATCTGATCTTACCTTCAGAGTAAGCGGAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCT
*
2613722 TCAGAGTAAGTGAAACAAGTCTGCCTCGATTCAATGAAT-AAGCTC-CC
66 TCAGAGTAAGTGAAACAAATCTGCCTCGATTCAATGAATCAA-CTCTCC
* *
2613769 CTAGATCTGATCTTACCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCTAAGATTTGATATTCCC
1 C-AGATCTGATCTTACCTTCAGAGTAAGCGGAACAAGTCTCTCTTTTCCAAGATTTGATATTCCC
*
2613834 TTCAGAGTAAGTGGAACAAATCTGCCTCGATTCAATGAATCAACTCTCC
65 TTCAGAGTAAGTGAAACAAATCTGCCTCGATTCAATGAATCAACTCTCC
* *
2613883 CAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCT
1 CAGATCTGATCTTACCTTCAGAGTAAGCGGAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCT
2613948 TCAGAGTAAGTGAAACAA
66 TCAGAGTAAGTGAAACAA
2613966 GTCTCTCTTT
Statistics
Matches: 180, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
112 1 0.01
113 174 0.97
114 5 0.03
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (113 bp):
CAGATCTGATCTTACCTTCAGAGTAAGCGGAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCT
TCAGAGTAAGTGAAACAAATCTGCCTCGATTCAATGAATCAACTCTCC
Found at i:2613945 original size:48 final size:48
Alignment explanation
Indices: 2613884--2614017 Score: 241
Period size: 48 Copynumber: 2.8 Consensus size: 48
2613874 CAACTCTCCC
* *
2613884 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTTTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTTTCCA
*
2613932 AGATTTGATATTCCCTTCAGAGTAAGTGAAACAAGTCTCTCTTTTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTTTCCA
2613980 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
2614018 GCCTCGATTT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 82 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTTTCCA
Found at i:2613985 original size:161 final size:161
Alignment explanation
Indices: 2613784--2614106 Score: 556
Period size: 161 Copynumber: 2.0 Consensus size: 161
2613774 TCTGATCTTA
* * *
2613784 CCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCTAAGATTTGATATTCCCTTCAGAGTAAGTGGA
1 CCTTCAGAGTAAGCGAAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGA
2613849 ACAAATCTGCCTCGATTCAATGAATCAACTCTCCCAGATCTGATATTCCCTTCAGAGTAAGCGGA
66 ACAAATCTGCCTCGATTCAATGAATCAACTCTCCCAGATCTGATATTCCCTTCAGAGTAAGCGGA
2613914 ACAAGTCTCTCTTTTCCAAGATTTGATATTC
131 ACAAGTCTCTCTTTTCCAAGATTTGATATTC
*
2613945 CCTTCAGAGTAAGTGAAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGA
1 CCTTCAGAGTAAGCGAAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGA
* * * * *
2614010 ACAAGTCTGCCTCGATTTATTGAATCAACTTTCCCATATCTGATATTCCCTTCAGAGTAAGCGGA
66 ACAAATCTGCCTCGATTCAATGAATCAACTCTCCCAGATCTGATATTCCCTTCAGAGTAAGCGGA
*
2614075 ACAGGTCTCTCTTTTCCAAGATTTGATATTC
131 ACAAGTCTCTCTTTTCCAAGATTTGATATTC
2614106 C
1 C
2614107 ATGAGTGACA
Statistics
Matches: 152, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
161 152 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (161 bp):
CCTTCAGAGTAAGCGAAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGA
ACAAATCTGCCTCGATTCAATGAATCAACTCTCCCAGATCTGATATTCCCTTCAGAGTAAGCGGA
ACAAGTCTCTCTTTTCCAAGATTTGATATTC
Found at i:2614401 original size:12 final size:12
Alignment explanation
Indices: 2614384--2614412 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2614374 TATATTATTA
2614384 TATTATAACAAT
1 TATTATAACAAT
2614396 TATTATAACAAT
1 TATTATAACAAT
2614408 TATTA
1 TATTA
2614413 GTATTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (12 bp):
TATTATAACAAT
Found at i:2616326 original size:18 final size:17
Alignment explanation
Indices: 2616303--2616336 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2616293 TAAGTTCCAT
2616303 TATTTTATAATATATTTA
1 TATTTTATAAT-TATTTA
*
2616321 TATTTTTTAATTATTT
1 TATTTTATAATTATTT
2616337 TTTTACATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTTATAATTATTTA
Found at i:2618758 original size:12 final size:12
Alignment explanation
Indices: 2618741--2618765 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2618731 GTCAAATAAT
2618741 TTAGGCACCAAA
1 TTAGGCACCAAA
2618753 TTAGGCACCAAA
1 TTAGGCACCAAA
2618765 T
1 T
2618766 AGTGCTTTGT
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:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:2627089 original size:3 final size:3
Alignment explanation
Indices: 2627081--2627140 Score: 111
Period size: 3 Copynumber: 19.7 Consensus size: 3
2627071 AATCTCCATT
2627081 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2627129 TTC TTC TGTC TT
1 TTC TTC T-TC TT
2627141 TGATGTTGGA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2632093 original size:105 final size:106
Alignment explanation
Indices: 2631882--2632186 Score: 458
Period size: 105 Copynumber: 2.9 Consensus size: 106
2631872 CTGAATGAAT
* * * * * * *
2631882 TTGACAATCAGCCGTCCCTTCGTCGTAAAGTTGAGCTTGTGTTGTCTAGGGTCCAATATCCTTCG
1 TTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCG
* * *
2631947 -T-TGAAGTT-AAATTGGCTCTGAAATTGGGAAGTTGTTTG
66 CTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTG
2631985 TTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGC-TGTGCTGTCTTGAGTCCAATATCCTTCG
1 TTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCG
*
2632049 CTGTGAAGTTGAGATTGGCTCTGAAGTTGGGAAATTATTTG
66 CTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTG
* *
2632090 TTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTATCTTGAGTTCAATATCCTTCG
1 TTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCG
2632155 CTGTGAAGTTGAAATTGGCTCT-AAGTTGGGAA
66 CTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAA
2632187 GCCCCTTCGT
Statistics
Matches: 184, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
102 25 0.14
103 33 0.18
104 7 0.04
105 72 0.39
106 47 0.26
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (106 bp):
TTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCG
CTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTG
Found at i:2633274 original size:8 final size:7
Alignment explanation
Indices: 2633253--2633298 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
2633243 CTTATTTTTC
2633253 TTTTC-T
1 TTTTCTT
2633259 TTTTCTT
1 TTTTCTT
2633266 TTGTTCTT
1 TT-TTCTT
*
2633274 TTTTCTC
1 TTTTCTT
*
2633281 TTTTC-C
1 TTTTCTT
2633287 TTTTCTT
1 TTTTCTT
2633294 TTTTC
1 TTTTC
2633299 AATTTAGGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 11 0.31
7 17 0.49
8 7 0.20
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTTCTT
Found at i:2633362 original size:56 final size:56
Alignment explanation
Indices: 2633281--2633388 Score: 164
Period size: 56 Copynumber: 1.9 Consensus size: 56
2633271 CTTTTTTCTC
* *
2633281 TTTTCCTTTTCTTTTTTCAATTTAGGGCGT-CCTTTCGGGTTTTCACCCTAAATTTT
1 TTTTCCTTTTCTTTTTTCAACTTAGGAC-TCCCTTTCGGGTTTTCACCCTAAATTTT
* *
2633337 TTTTCTTTTTCTTTTTTCAACTTAGGACTCCCTTTCGGGTTTTCATCCTAAA
1 TTTTCCTTTTCTTTTTTCAACTTAGGACTCCCTTTCGGGTTTTCACCCTAAA
2633389 CGAAGTATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
55 1 0.02
56 46 0.98
ACGTcount: A:0.14, C:0.22, G:0.11, T:0.53
Consensus pattern (56 bp):
TTTTCCTTTTCTTTTTTCAACTTAGGACTCCCTTTCGGGTTTTCACCCTAAATTTT
Found at i:2640059 original size:170 final size:171
Alignment explanation
Indices: 2639777--2640117 Score: 639
Period size: 170 Copynumber: 2.0 Consensus size: 171
2639767 TTTGTACTGC
2639777 TCTAAGAAATACTTGGCTAAGTCTTTCCACGTCTTGACATGAGTTCAGCTGAGCTGGTTGTACCA
1 TCTAAGAAATACTTGGCTAAGTCTTTCCACGTCTTGACATGAGTTCAGCTGAGCTGGTTGTACCA
2639842 CCAGATAGCTGAACCGGACAGGCTCTCCTGAAAGTAGTGGATTAAGAGTTGGTCATTTCCCCCGT
66 CCAGATAGCTGAACCGGACAGGCTCTCCTGAAAGTAGTGGATTAAGAGTTGGTCATTTCCCCCGT
2639907 ACCCTGTCATCTCCCGACAGAA-ATAGTGATATGGGCTGAA
131 ACCCTGTCATCTCCCGACAGAACATAGTGATATGGGCTGAA
*
2639947 TCTAAGAAATACTTGGCTAAGTCTTTCCACGTCTTGACATGAGTTCGGCTGAGCTGGTTGTACCA
1 TCTAAGAAATACTTGGCTAAGTCTTTCCACGTCTTGACATGAGTTCAGCTGAGCTGGTTGTACCA
*
2640012 CCGGATAGCTGAACCGGACAGGCTCTCCTGAAAGTAGTGGATTAAGAGTTGGTCATTTCCCCCGT
66 CCAGATAGCTGAACCGGACAGGCTCTCCTGAAAGTAGTGGATTAAGAGTTGGTCATTTCCCCCGT
* *
2640077 ACCCTGTCATCTTCCGACATAACATAGTGATATGGGCTGAA
131 ACCCTGTCATCTCCCGACAGAACATAGTGATATGGGCTGAA
2640118 GGGCAGCTGT
Statistics
Matches: 166, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
170 148 0.89
171 18 0.11
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (171 bp):
TCTAAGAAATACTTGGCTAAGTCTTTCCACGTCTTGACATGAGTTCAGCTGAGCTGGTTGTACCA
CCAGATAGCTGAACCGGACAGGCTCTCCTGAAAGTAGTGGATTAAGAGTTGGTCATTTCCCCCGT
ACCCTGTCATCTCCCGACAGAACATAGTGATATGGGCTGAA
Found at i:2648860 original size:36 final size:35
Alignment explanation
Indices: 2648813--2648881 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
2648803 TAACCAGTTT
*
2648813 AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
1 AGGTTTCATAAGAAATTTGAG-AATTTTCTTATTAA
* *
2648849 AGGTTTTATAAGAAATTTGTGAATTTTCTTATT
1 AGGTTTCATAAGAAATTTGAGAATTTTCTTATT
2648882 GAAGTTGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.49
Consensus pattern (35 bp):
AGGTTTCATAAGAAATTTGAGAATTTTCTTATTAA
Found at i:2652372 original size:16 final size:18
Alignment explanation
Indices: 2652351--2652386 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
2652341 TAGTTTATGC
2652351 ACTTGAGCA-TGA-AATG
1 ACTTGAGCATTGATAATG
2652367 ACTTGAGCATTGATAATG
1 ACTTGAGCATTGATAATG
2652385 AC
1 AC
2652387 CCAGTCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 3 0.17
18 6 0.33
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (18 bp):
ACTTGAGCATTGATAATG
Found at i:2654088 original size:14 final size:15
Alignment explanation
Indices: 2654060--2654088 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2654050 ATCTATGAAT
2654060 CATATTTTAGTTATG
1 CATATTTTAGTTATG
2654075 CATATTTT-GTTATG
1 CATATTTTAGTTATG
2654089 ATTATAGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (15 bp):
CATATTTTAGTTATG
Found at i:2656326 original size:63 final size:63
Alignment explanation
Indices: 2656248--2656851 Score: 976
Period size: 63 Copynumber: 9.6 Consensus size: 63
2656238 TCGAAGAACC
* * * *
2656248 TAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTATATTGTCCATATGTCACGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
* * *
2656310 TAGGTAATTATGTCCATATGTTCCTTAGAACATATGTATACTGTCCATATGTCCCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
* *
2656373 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTATTCATATGTCCCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
* *
2656436 TAGATAATTCTGTCCATATGTTCCGTAAAACATAGGTATACTGTCCATATGTCCCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
* *
2656499 TAGGTAATTCTGTCCATATGTTCCGTAGAACATATGTATACTGTACATATGTCCCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
* *
2656562 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATGCTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
*
2656625 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTATCCATATGTCCCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
* * **
2656688 TAGGTAATTTTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATATCCTAAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
* * **
2656751 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTATCCATATATCCTAAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
*
2656814 TAGGTAATTCAGTCCATATGTTCCGTAGAACATAGGTA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTA
2656852 ATTCTTTGAC
Statistics
Matches: 508, Mismatches: 33, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
62 7 0.01
63 501 0.99
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
Found at i:2660640 original size:31 final size:31
Alignment explanation
Indices: 2660584--2660678 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 31
2660574 AACATAGTTA
* * * *
2660584 AGGGACTAAAACCGAACGAACCGATAATGTT
1 AGGGACTGAAATCGGACGGACCGATAATGTT
* * * *
2660615 AGGGACTGAAATCGGATGGATCGATAACGTC
1 AGGGACTGAAATCGGACGGACCGATAATGTT
* *
2660646 AGGGACTTAAATCGGACGGACCGATAGTGTT
1 AGGGACTGAAATCGGACGGACCGATAATGTT
2660677 AG
1 AG
2660679 TGACCATTTC
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (31 bp):
AGGGACTGAAATCGGACGGACCGATAATGTT
Found at i:2661167 original size:2 final size:2
Alignment explanation
Indices: 2661160--2661204 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
2661150 ATCCTATTAC
2661160 AT AT AT AT AT AT AT AT AT AT AT -T 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
2661201 AT AT
1 AT AT
2661205 GGATAGGATC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2661790 original size:17 final size:18
Alignment explanation
Indices: 2661755--2661793 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2661745 AAATTTGTAT
*
2661755 ATTATTTTCATTTCATTC
1 ATTATTTTCATTGCATTC
2661773 ATTATTTT-ATTGCATTC
1 ATTATTTTCATTGCATTC
2661790 ATTA
1 ATTA
2661794 CTCATTCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.59
Consensus pattern (18 bp):
ATTATTTTCATTGCATTC
Found at i:2663879 original size:26 final size:26
Alignment explanation
Indices: 2663835--2663889 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
2663825 AAAGTACATC
* * *
2663835 CAAGCCCTGAATGACTAAAT-ACCCT
1 CAAGCCCTAAATGAATAAATCAACCT
2663860 CAAGCTCCTAAATGAATAAATCAACCT
1 CAAGC-CCTAAATGAATAAATCAACCT
2663887 CAA
1 CAA
2663890 ATACCAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.20
26 13 0.52
27 7 0.28
ACGTcount: A:0.42, C:0.29, G:0.09, T:0.20
Consensus pattern (26 bp):
CAAGCCCTAAATGAATAAATCAACCT
Found at i:2667871 original size:29 final size:28
Alignment explanation
Indices: 2667839--2667927 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 28
2667829 TATTTTTGCT
2667839 TTAGGTATCTAAACTATTTTTTAGTCAAA
1 TTAGGTA-CTAAACTATTTTTTAGTCAAA
* * **
2667868 TTAGGTACTTAAACTATTATATATAATCACT
1 TTAGGTAC-TAAACTATT-T-TTTAGTCAAA
* *
2667899 TTAGGTAGCTCAACTATTTTTTTGTCAAA
1 TTAGGTA-CTAAACTATTTTTTAGTCAAA
2667928 ATAAGTCCCT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
28 1 0.02
29 21 0.46
30 2 0.04
31 21 0.46
32 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (28 bp):
TTAGGTACTAAACTATTTTTTAGTCAAA
Found at i:2668566 original size:2 final size:2
Alignment explanation
Indices: 2668561--2668594 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2668551 AAATTTTTTG
2668561 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
2668595 CCACACAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2668961 original size:41 final size:41
Alignment explanation
Indices: 2668916--2669046 Score: 99
Period size: 41 Copynumber: 3.1 Consensus size: 41
2668906 CGTCACAACA
2668916 TAAATAAACATCTATTATTCTTTTAAGATTTATGAAATAAT
1 TAAATAAACATCTATTATTCTTTTAAGATTTATGAAATAAT
* * * * *
2668957 TAAATTAAGC-TTTATAATT-TTAATTTAGAATTTTACTTAACA-AA-
1 TAAA-TAAACATCTATTATTCTT--TTAAG-A-TTTA-TGAA-ATAAT
* * *
2669001 TAAATAACCATCTATTATTCTTTTAAGGTTTGTGAAATAAT
1 TAAATAAACATCTATTATTCTTTTAAGATTTATGAAATAAT
2669042 TAAAT
1 TAAAT
2669047 TATTTTTTAT
Statistics
Matches: 67, Mismatches: 12, Indels: 22
0.66 0.12 0.22
Matches are distributed among these distances:
39 1 0.01
40 7 0.10
41 19 0.28
42 8 0.12
43 9 0.13
44 15 0.22
45 7 0.10
46 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (41 bp):
TAAATAAACATCTATTATTCTTTTAAGATTTATGAAATAAT
Found at i:2669061 original size:85 final size:86
Alignment explanation
Indices: 2668887--2669048 Score: 254
Period size: 85 Copynumber: 1.9 Consensus size: 86
2668877 CAACTGACTT
* * *
2668887 ATTTTCATTTATAATTTTACGTCACAACATAAATAAACATCTATTATTCTTTTAAGATTTATGAA
1 ATTTTAATTTAGAATTTTACGTAACAACATAAATAAACATCTATTATTCTTTTAAGATTTATGAA
2668952 ATAATTAAATTAAGCTTTATA
66 ATAATTAAATTAAGCTTTATA
* * * *
2668973 ATTTTAATTTAGAATTTTACTTAACAA-ATAAATAACCATCTATTATTCTTTTAAGGTTTGTGAA
1 ATTTTAATTTAGAATTTTACGTAACAACATAAATAAACATCTATTATTCTTTTAAGATTTATGAA
2669037 ATAATTAAATTA
66 ATAATTAAATTA
2669049 TTTTTTATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
85 46 0.67
86 23 0.33
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (86 bp):
ATTTTAATTTAGAATTTTACGTAACAACATAAATAAACATCTATTATTCTTTTAAGATTTATGAA
ATAATTAAATTAAGCTTTATA
Found at i:2680585 original size:37 final size:36
Alignment explanation
Indices: 2680544--2680617 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
2680534 GTTGGAAAAT
*
2680544 ATTTATAT-ATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATAATTTT-TTTAAAAAAATTAAAAT-ATAAA
* *
2680581 ATTTATATAATTTTTTTACAAAATTTAAAATATAAA
1 ATTTATATAATTTTTTTAAAAAAATTAAAATATAAA
2680617 A
1 A
2680618 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 6 0.18
37 22 0.67
38 5 0.15
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (36 bp):
ATTTATATAATTTTTTTAAAAAAATTAAAATATAAA
Found at i:2681889 original size:21 final size:22
Alignment explanation
Indices: 2681852--2681896 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2681842 CGGGGCAAAA
*
2681852 CAATTAACTGAATAACAAA-TT
1 CAATTAACTGAAGAACAAACTT
2681873 CAATTAACCT-AAGAACAAACTT
1 CAATTAA-CTGAAGAACAAACTT
2681895 CA
1 CA
2681897 TCCAGCTGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.24
Consensus pattern (22 bp):
CAATTAACTGAAGAACAAACTT
Found at i:2682217 original size:43 final size:43
Alignment explanation
Indices: 2682167--2682604 Score: 474
Period size: 43 Copynumber: 10.2 Consensus size: 43
2682157 TGAGAACAAA
* * * *
2682167 AAACGCCGCAATAGGTCAATATCTATTA-CGGCATTTTTTGA-AC
1 AAACGCCGCAAAAGGTC-AGATCTA-TAGCGGCGTTTTTGGACAC
* * * *
2682210 AAACGCCGCAAAAAGTCGATATCTATAGCGGCGTTTCTGGA-AT
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGACAC
* * * * * *
2682253 AAACGCCGCAAAAAGTTATGATATATAGCGGCGTTTCTAGA-AA
1 AAACGCCGCAAAAGGTCA-GATCTATAGCGGCGTTTTTGGACAC
* * *
2682296 AAACGCCGCAAAATGTCAGATCTATAGCGACGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGACAC
* * * * *
2682339 AAACGCCGCAAAAGATAAGACCTATA-CTGGCATTTTTAGA-AC
1 AAACGCCGCAAAAGGTCAGATCTATAGC-GGCGTTTTTGGACAC
* *
2682381 AAACGCCGCAAAAGGTCAGACCTATAGTGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGACAC
* *
2682424 AAACGCCGCAAAATGTCAGACCTATAGCGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGACAC
* * * *
2682467 AAACGCCGCAAAAGGTCAGATATATAGCGGCATTTTTTGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGACAC
2682510 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGACAC
* * * * *
2682553 AAACGTCGCAAAAGGTCGGATATATAGCGGCGTTTTTTGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGACAC
2682596 AAACGCCGC
1 AAACGCCGC
2682605 TAATTACCAT
Statistics
Matches: 340, Mismatches: 49, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
42 58 0.17
43 282 0.83
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGACAC
Found at i:2685258 original size:41 final size:41
Alignment explanation
Indices: 2685213--2685717 Score: 436
Period size: 41 Copynumber: 12.3 Consensus size: 41
2685203 TTTGCGGTAC
* *
2685213 AAACGCCACTAAAGTACAAGTCTTTTGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
** * *
2685254 AAACGCCACTAGCGTATGAGTCTTTTGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
** * * *
2685295 AAACGCCACTAGCGTACGAGTCTTTTGCGGCATTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * *
2685336 AAACGCCACTAAAGTACAAGTCTATAGCGACGTTTGTAAACAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT--ATAA
* *
2685379 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAAACAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT--ATAA
* * * * *
2685422 AAACGCCACTAAAGTATGAGT-TATAGCAGTGTTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * **
2685462 AAACGCCAGTAAAGTATGAGT-TATAGCATCGCTTT-TATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCG-TTTGTATAA
* *
2685502 AAACGCCACTAAAGTACGAGTCTTTAGCGACATTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
2685543 AAACGCCCCTAAAGAACGA-TTTTATACCGGCGTTTGTGTAA
1 AAACGCCACTAAAGTACGAGTCTT-TAGCGGCGTTTGTATAA
* * * * *
2685584 AAATGCCACTACAA-TACTAATCTTTAGCAGCGTTTGTATAC
1 AAACGCCACTA-AAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
2685625 AAACGCCACTAAAGTAAGA-TCTTTTGCGGCGTTT-TATAC
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
2685664 AAACGCCTCTAAAGTTA-G-GTTTTTTGCGGCGTTTGT-TCAAA
1 AAACGCCACTAAAG-TACGAGTCTTTAGCGGCGTTTGTAT--AA
*
2685705 AAACGCCGCTAAA
1 AAACGCCACTAAA
2685718 ATTGCAACCC
Statistics
Matches: 393, Mismatches: 57, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
39 34 0.09
40 79 0.20
41 199 0.51
42 17 0.04
43 64 0.16
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
Found at i:2685500 original size:166 final size:164
Alignment explanation
Indices: 2685213--2685640 Score: 450
Period size: 166 Copynumber: 2.6 Consensus size: 164
2685203 TTTGCGGTAC
* * * * ** *
2685213 AAACGCCACTAAAGTACAAGTCTTTTGCGGCGTTTGTATAAAAACGCCACTAGCGTATGAGTCTT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTACAAAAACGCCACTAAAGTATGAGTCTA
* * ** * * * *
2685278 TTGCGGCGTTTGTATAAAAACGCCACTAGCGTACGAGTCTTTTGCGGCATTTTTATAAAAACGCC
66 TAGCAGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCAGCACTTTTATAAAAACGCC
*
2685343 ACTAAAGTACAAGTCTATAGCGACGTTTGTAAACAA
131 ACTAAAGTACAAGTCTATAGCGACATTTGT--ACAA
2685379 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAAACAAAAACGCCACTAAAGTATGAGT-
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT--ACAAAAACGCCACTAAAGTATGAGTC
* * * * * *
2685443 TATAGCAGTGTTTTTATAAAAACGCCAGTAAAGTATGAGT-TATAGCATCGCTTTTATAAAAACG
64 TATAGCAGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCAGCACTTTTATAAAAACG
* * *
2685507 CCACTAAAGTACGAGTCTTTAGCGACATTTGTATAA
129 CCACTAAAGTACAAGTCTATAGCGACATTTGTACAA
* * * * * ** * *
2685543 AAACGCCCCTAAAGAACGATTTTATACCGGCGTTTGTGTAAAAATGCCACTACAA-TACT-AATC
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTACAAAAACGCCACTA-AAGTA-TGAGTC
* *
2685606 TTTAGCAGCGTTTGTATACAAACGCCACTAAAGTA
64 TATAGCAGCGTTTGTATAAAAACGCCACTAAAGTA
2685641 AGATCTTTTG
Statistics
Matches: 218, Mismatches: 39, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
162 16 0.07
163 33 0.15
164 35 0.16
166 81 0.37
167 31 0.14
168 22 0.10
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (164 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTACAAAAACGCCACTAAAGTATGAGTCTA
TAGCAGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCAGCACTTTTATAAAAACGCC
ACTAAAGTACAAGTCTATAGCGACATTTGTACAA
Found at i:2686588 original size:22 final size:21
Alignment explanation
Indices: 2686548--2686605 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
2686538 TATTATAGAA
* * *
2686548 ATATATATTTTTATAGTTTTT
1 ATATATATATATATTGTTTTT
2686569 CATATATATATATATTGTTTTT
1 -ATATATATATATATTGTTTTT
* *
2686591 AAAAATATATATATT
1 ATATATATATATATT
2686606 ATATTTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (21 bp):
ATATATATATATATTGTTTTT
Found at i:2686598 original size:21 final size:21
Alignment explanation
Indices: 2686574--2686641 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
2686564 TTTTTCATAT
2686574 ATATATATATTGTTTTTAAAA
1 ATATATATATTGTTTTTAAAA
*
2686595 ATATATATATTATATTTTTAAAA
1 ATATATATA-T-TGTTTTTAAAA
* **
2686618 A-ATATATATAGTTTTGGAAA
1 ATATATATATTGTTTTTAAAA
2686638 ATAT
1 ATAT
2686642 TTACAGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 8 0.21
21 12 0.31
22 8 0.21
23 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (21 bp):
ATATATATATTGTTTTTAAAA
Found at i:2686598 original size:23 final size:24
Alignment explanation
Indices: 2686570--2686627 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
2686560 ATAGTTTTTC
*
2686570 ATATATATATATATTGTTTTTAAAA
1 ATATATATATATA-TATTTTTAAAA
2686595 ATATATATAT-TATATTTTTAAAA
1 ATATATATATATATATTTTTAAAA
2686618 A-ATATATATA
1 ATATATATATA
2686628 GTTTTGGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 8 0.26
23 11 0.35
24 2 0.06
25 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATATATATATATATATTTTTAAAA
Found at i:2686618 original size:24 final size:25
Alignment explanation
Indices: 2686570--2686627 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
2686560 ATAGTTTTTC
*
2686570 ATATATATATATATTGTTTTTAAAA
1 ATATATATATATATTGTTTTAAAAA
2686595 ATATATATAT-TATAT-TTTTAAAAA
1 ATATATATATATAT-TGTTTTAAAAA
2686619 ATATATATA
1 ATATATATA
2686628 GTTTTGGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 20 0.65
25 11 0.35
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
ATATATATATATATTGTTTTAAAAA
Found at i:2686638 original size:19 final size:19
Alignment explanation
Indices: 2686616--2686665 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
2686606 ATATTTTTAA
*
2686616 AAAATATATATAGTTTTGG
1 AAAATATATATAGTTTTGC
* * *
2686635 AAAATATTTACAGTTTTTC
1 AAAATATATATAGTTTTGC
2686654 AATAATATATAT
1 AA-AATATATAT
2686666 TATTATATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (19 bp):
AAAATATATATAGTTTTGC
Found at i:2686703 original size:19 final size:18
Alignment explanation
Indices: 2686669--2686752 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 18
2686659 TATATATTAT
** *
2686669 TATATATTTTTCAATACA
1 TATATATTTTAAAATATA
*
2686687 TATATAGTTTTGAAATATA
1 TATATA-TTTTAAAATATA
2686706 TATTATATTTTAAAATATA
1 TA-TATATTTTAAAATATA
* *
2686725 TATGTTTTATTGAAAATATA
1 TATATATT-TT-AAAATATA
2686745 TATTATAT
1 TA-TATAT
2686753 GTTTTGAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
18 10 0.19
19 26 0.49
20 14 0.26
21 3 0.06
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATATTTTAAAATATA
Found at i:2686703 original size:63 final size:62
Alignment explanation
Indices: 2686585--2686727 Score: 159
Period size: 65 Copynumber: 2.3 Consensus size: 62
2686575 TATATATATT
*
2686585 GTTTTTAAAAATATATATATTATATTTTTAAAAAATATATATAGTTTTGGAAAATATTTACA
1 GTTTTTAAAAATATATATATTATATTTTTAAAAAACATATATAGTTTTGGAAAATATTTACA
* ** *
2686647 GTTTTTCAATAATATATATTATTATATATTTTTCAATACATATATAGTTTT-GAAATATATATTA
1 GTTTTT-AAAAATATATA-TATTATAT-TTTTAAAAAACATATATAGTTTTGGAAA-ATAT-TTA
*
2686711 TA
61 CA
2686713 --TTTT-AAAATATATAT
1 GTTTTTAAAAATATATAT
2686728 GTTTTATTGA
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
61 1 0.01
62 15 0.22
63 10 0.14
64 16 0.23
65 23 0.33
66 4 0.06
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (62 bp):
GTTTTTAAAAATATATATATTATATTTTTAAAAAACATATATAGTTTTGGAAAATATTTACA
Found at i:2686708 original size:17 final size:17
Alignment explanation
Indices: 2686686--2686733 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
2686676 TTTTCAATAC
2686686 ATATATAGTTTTGAAATAT
1 ATATATAGTTTT-AAA-AT
2686705 ATATTATA-TTTTAAAAT
1 ATA-TATAGTTTTAAAAT
2686722 ATATAT-GTTTTA
1 ATATATAGTTTTA
2686734 TTGAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 8 0.30
17 5 0.19
18 3 0.11
19 7 0.26
20 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
ATATATAGTTTTAAAAT
Found at i:2686751 original size:39 final size:40
Alignment explanation
Indices: 2686699--2686775 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 40
2686689 TATAGTTTTG
2686699 AAATATATATTATAT-TTTAAAATATATATGTT-TTATTGA
1 AAATATATATTATATGTTTAAAATA-ATATGTTATTATTGA
**
2686738 AAATATATATTATATGTTTTGAATAATATGTTATTATT
1 AAATATATATTATATGTTTAAAATAATATGTTATTATT
2686776 ATTTTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 22 0.65
40 12 0.35
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (40 bp):
AAATATATATTATATGTTTAAAATAATATGTTATTATTGA
Found at i:2686762 original size:20 final size:19
Alignment explanation
Indices: 2686671--2686766 Score: 65
Period size: 19 Copynumber: 5.0 Consensus size: 19
2686661 TATATTATTA
* *
2686671 TATATTTTTCAATACATA-
1 TATATTTTTGAATATATAT
*
2686689 TATAGTTTTGAAATATATAT
1 TATATTTTTG-AATATATAT
**
2686709 TATATTTTAAAATATATAT
1 TATATTTTTGAATATATAT
*
2686728 GT-T-TTATTGAAAATATATAT
1 -TATATTTTTG--AATATATAT
2686748 TATATGTTTTGAATA-ATAT
1 TATAT-TTTTGAATATATAT
2686767 GTTATTATTA
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
18 11 0.18
19 22 0.37
20 22 0.37
21 1 0.02
22 4 0.07
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (19 bp):
TATATTTTTGAATATATAT
Found at i:2686801 original size:21 final size:20
Alignment explanation
Indices: 2686768--2686807 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2686758 GAATAATATG
2686768 TTATTATTATTTTTTATTTTT
1 TTATTATTA-TTTTTATTTTT
* *
2686789 TTATTTTTCTTTTTATTTT
1 TTATTATTATTTTTATTTT
2686808 AATTTTCAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (20 bp):
TTATTATTATTTTTATTTTT
Found at i:2688113 original size:12 final size:13
Alignment explanation
Indices: 2688085--2688112 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2688075 ATTTATTTAC
2688085 TTTATTATTTGTT
1 TTTATTATTTGTT
2688098 TTTATTATTTGTT
1 TTTATTATTTGTT
2688111 TT
1 TT
2688113 ACTACTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTATTATTTGTT
Found at i:2688561 original size:21 final size:23
Alignment explanation
Indices: 2688514--2688562 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
2688504 TGTAAGTTTA
2688514 AATTTTTAATTTATTTTAGATCT
1 AATTTTTAATTTATTTTAGATCT
2688537 -ATTTTT-ATTTATCTTT-GAT-T
1 AATTTTTAATTTAT-TTTAGATCT
2688557 AATTTT
1 AATTTT
2688563 CAAATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 1 0.04
21 14 0.58
22 9 0.38
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (23 bp):
AATTTTTAATTTATTTTAGATCT
Found at i:2691460 original size:22 final size:22
Alignment explanation
Indices: 2691435--2691484 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
2691425 TGTATGTGAT
* *
2691435 TATAGGAAAATGTTATATGAGC
1 TATAGGAAAATGTGATATAAGC
* * *
2691457 TATATGAACATGTGATATAAGT
1 TATAGGAAAATGTGATATAAGC
2691479 TATAGG
1 TATAGG
2691485 GTCACGAACT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (22 bp):
TATAGGAAAATGTGATATAAGC
Found at i:2692278 original size:20 final size:20
Alignment explanation
Indices: 2692253--2692303 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2692243 GGATAATGGC
*
2692253 CCTTCGCGACATACATAGGT
1 CCTTCGGGACATACATAGGT
2692273 CCTTCGGGACATACATAGGT
1 CCTTCGGGACATACATAGGT
*
2692293 CATTCGGGACA
1 CCTTCGGGACA
2692304 ATTTCACATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (20 bp):
CCTTCGGGACATACATAGGT
Found at i:2699253 original size:41 final size:40
Alignment explanation
Indices: 2699123--2699270 Score: 136
Period size: 41 Copynumber: 3.6 Consensus size: 40
2699113 TCGTCTCACT
* * * *
2699123 TGACTTAGACCCACGAAGGGGAGTCAACTGAAGTATCAAGAA
1 TGACTTA-AACCATGAAGGGGAGTCAAC-AAAGTATCAAGAC
* * *
2699165 TGACTTAAACCATGAA-GGGTGTCAACCAAAGTATTAATAC
1 TGACTTAAACCATGAAGGGGAGTCAA-CAAAGTATCAAGAC
* * *
2699205 TGACTTAAATCGTGAAGGGGAGTCAATCAAAGAATCAAGAC
1 TGACTTAAACCATGAAGGGGAGTCAA-CAAAGTATCAAGAC
* * *
2699246 TGGCTTAAACCACGAAGGGAAGTCA
1 TGACTTAAACCATGAAGGGGAGTCA
2699271 TATTGTTTAG
Statistics
Matches: 85, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
40 31 0.36
41 47 0.55
42 7 0.08
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.20
Consensus pattern (40 bp):
TGACTTAAACCATGAAGGGGAGTCAACAAAGTATCAAGAC
Found at i:2699719 original size:199 final size:200
Alignment explanation
Indices: 2699372--2699919 Score: 579
Period size: 199 Copynumber: 2.7 Consensus size: 200
2699362 TATTTGTTTG
* * ** ** * *
2699372 AGAGCGCATTGACCACATAATAGC-ATCGAGGAACTAAATTTTGGTTAAAATTCCAAA-TGAGGT
1 AGAGTGCATTGACCGCATAATAGCAAT-GAAAAACTACCTTCTGGCTAAAATT-CAAATTGAGGT
* * ** * * * *
2699435 CTTCAAGCCTATAAGGAA-ACTTAAATCGGCTGGGACTTAGCAAAAAGGAACTA-TTTCCCAACC
64 CTTCAAGTCTA-AAAGAATACCAAAATCAGATGTGATTTAGC-AAAAGGAACTACTTT-CCAACC
* ** * *
2699498 TAAATTTCAATGTAGCTTAAGTCAAGAAGAGTTATTTGTTGACCAAAGCTTTCAATTTTGATTCC
126 CAAATTTCAACATAGCTTAAGTCAAGAAGAGCTATTTGTTGACCAAAGCTTTCAAGTTTGATTCC
2699563 ACTCAACTCA
191 ACTCAACTCA
*
2699573 AGAGTGCATTGACCGCATAATAGCAATGAAAAACTACCTTC-GG-TCAAAATTCCAATTGAGG-C
1 AGAGTGCATTGACCGCATAATAGCAATGAAAAACTACCTTCTGGCT-AAAATTCAAATTGAGGTC
* * * *
2699635 TTCAAGTCTAAAAGAATGCCAAAATTAGTTGTGATTTAGCAACGAGGAACTACTTTCCAACCCAA
65 TTCAAGTCTAAAAGAATACCAAAATCAGATGTGATTTAGCAA-AAGGAACTACTTTCCAACCCAA
* *
2699700 ATTTCGACATAGCTTAAGTCGAGAAGAGCTATTTGTTGACCAAAGCTTTCAAGTTTGATTCCACT
129 ATTTCAACATAGCTTAAGTCAAGAAGAGCTATTTGTTGACCAAAGCTTTCAAGTTTGATTCCACT
2699765 CAACTCA
194 CAACTCA
* ** * ** *
2699772 AGAGTGCATTGACTGCATGGTAGCAATTAGGAACTACCTTCTGGCTAAAATTTAAATTGAGGTCT
1 AGAGTGCATTGACCGCATAATAGCAATGAAAAACTACCTTCTGGCTAAAATTCAAATTGAGGTCT
* * * * * * *
2699837 TCAAGTCTAGAAGAATACCCAAATCGGATGTGATTTAGCAAAATGAAACTACTTCCCAGCCCGAA
66 TCAAGTCTAAAAGAATACCAAAATCAGATGTGATTTAGCAAAA-GGAACTACTTTCCAACCCAAA
**
2699902 TTTTTACATAGCTTAAGT
130 TTTCAACATAGCTTAAGT
2699920 TGAGCTTTCA
Statistics
Matches: 290, Mismatches: 47, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
198 7 0.02
199 146 0.50
200 33 0.11
201 102 0.35
202 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (200 bp):
AGAGTGCATTGACCGCATAATAGCAATGAAAAACTACCTTCTGGCTAAAATTCAAATTGAGGTCT
TCAAGTCTAAAAGAATACCAAAATCAGATGTGATTTAGCAAAAGGAACTACTTTCCAACCCAAAT
TTCAACATAGCTTAAGTCAAGAAGAGCTATTTGTTGACCAAAGCTTTCAAGTTTGATTCCACTCA
ACTCA
Found at i:2700593 original size:16 final size:16
Alignment explanation
Indices: 2700559--2700603 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2700549 TATATATTAT
* * *
2700559 TATGGTTTTTAATATA
1 TATGGTTTTGAAAACA
2700575 TATGGTTTTGAAAACA
1 TATGGTTTTGAAAACA
*
2700591 TATAGTTTTGAAA
1 TATGGTTTTGAAA
2700604 TATATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (16 bp):
TATGGTTTTGAAAACA
Found at i:2700637 original size:19 final size:18
Alignment explanation
Indices: 2700603--2700645 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
2700593 TAGTTTTGAA
2700603 ATATATATTTTAAAAAAT
1 ATATATATTTTAAAAAAT
* *
2700621 ATATATAGTTTTTAAAACT
1 ATATATA-TTTTAAAAAAT
2700640 ATATAT
1 ATATAT
2700646 TATATGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATATATTTTAAAAAAT
Found at i:2701905 original size:38 final size:37
Alignment explanation
Indices: 2701674--2702025 Score: 299
Period size: 38 Copynumber: 9.7 Consensus size: 37
2701664 CCATTTTTTT
* *
2701674 TATATATATTATATAG-TTTG-AAATCATTTTGAAAA
1 TATATATATTATATAGTTTTGAAAATTATTTTTAAAA
* * * * *
2701709 T-TATATAATATATGGTTTTTATAAAATATTTTGAAAA
1 TATATATATTATATAGTTTTGA-AAATTATTTTTAAAA
2701746 TATATA-A-TATATAGTTTTTG--AATT-TTTTCT-AAA
1 TATATATATTATATAG-TTTTGAAAATTATTTT-TAAAA
**
2701779 TATATATCA-TATATAGCTTTT-AAAAACATTTTTGAAAA
1 TATATAT-ATTATATAG-TTTTGAAAATTATTTTT-AAAA
* *
2701817 TCATATATATTATATAATTTTGAAAATTAGTTTCT--AA
1 T-ATATATATTATATAGTTTTGAAAATTA-TTTTTAAAA
2701854 -ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
1 TATATATATTATATAGTTTTGAAAATTA-TTTTTAAAA
2701891 TATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
1 TATATATATTATATAGTTTTGAAAATTA-TTTTTAAAA
* *
2701929 TATATATATTATATAG-TTTG-AAATCATTTTGAAAA
1 TATATATATTATATAGTTTTGAAAATTATTTTTAAAA
* * * * *
2701964 T-TATATAATATATGGTTTTTATAAAATATTTTGAAAA
1 TATATATATTATATAGTTTTGA-AAATTATTTTTAAAA
*
2702001 TATATATGA-TATATAGTTTTTAAAA
1 TATATAT-ATTATATAGTTTTGAAAA
2702026 CATTTTCGAA
Statistics
Matches: 266, Mismatches: 26, Indels: 48
0.78 0.08 0.14
Matches are distributed among these distances:
33 13 0.05
34 27 0.10
35 59 0.22
36 14 0.05
37 48 0.18
38 83 0.31
39 18 0.07
40 4 0.02
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.48
Consensus pattern (37 bp):
TATATATATTATATAGTTTTGAAAATTATTTTTAAAA
Found at i:2702059 original size:63 final size:63
Alignment explanation
Indices: 2701992--2702111 Score: 181
Period size: 63 Copynumber: 1.9 Consensus size: 63
2701982 TTATAAAATA
*
2701992 TTTTG-AAAATATATATGATATATAGTTTTTAAAAC-ATTTTCGAAAACATGTATATATTATAGT
1 TTTTGAAAAATATATAT-ATATA-AGTTTTTAAAACAATTTTCGAAAACATATATATATTATAGT
* *
2702055 TTTTGAAAAATATATATATATAAGTTTTTAAAACAATTTTTGAAAATATATATATAT
1 TTTTGAAAAATATATATATATAAGTTTTTAAAACAATTTTCGAAAACATATATATAT
2702112 AATTTTGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
62 12 0.23
63 29 0.56
64 11 0.21
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (63 bp):
TTTTGAAAAATATATATATATAAGTTTTTAAAACAATTTTCGAAAACATATATATATTATAGT
Found at i:2702087 original size:23 final size:22
Alignment explanation
Indices: 2702042--2702087 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
2702032 CGAAAACATG
2702042 TATATATTATAGTTTTTGAAAAA
1 TATATATTATAGTTTTT-AAAAA
2702065 TATATATATATAAGTTTTTAAAA
1 TATATAT-TAT-AGTTTTTAAAA
2702088 CAATTTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TATATATTATAGTTTTTAAAAA
Found at i:2702106 original size:36 final size:35
Alignment explanation
Indices: 2702054--2702167 Score: 129
Period size: 36 Copynumber: 3.1 Consensus size: 35
2702044 TATATTATAG
* *
2702054 TTTTTGAAAAATATATATATATAAGTTTTTAAAACAA
1 TTTTTG-AAAATATATATATATAA-TTTTAAAAAAAA
* **
2702091 TTTTTGAAAATATATATATATAATTTTGAAAATTA
1 TTTTTGAAAATATATATATATAATTTTAAAAAAAA
* *
2702126 TTTTTTAACATATATATTATATAATTTTAAAAAAAA
1 TTTTTGAAAATATATA-TATATAATTTTAAAAAAAA
2702162 TATTTT
1 T-TTTT
2702168 TTTATTATAT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
35 23 0.34
36 34 0.51
37 10 0.15
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (35 bp):
TTTTTGAAAATATATATATATAATTTTAAAAAAAA
Found at i:2702175 original size:3 final size:3
Alignment explanation
Indices: 2702169--2702228 Score: 54
Period size: 3 Copynumber: 19.7 Consensus size: 3
2702159 AAATATTTTT
2702169 TTA TTA -TA TTAA TTA TTA TTA TTA TTTA TT- TTA TT- TTA TTA TTTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA
*
2702214 TTA CTTA TTT TTA TT
1 TTA -TTA TTA TTA TT
2702229 TTTTCTTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
2 6 0.12
3 30 0.62
4 12 0.25
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2702198 original size:20 final size:18
Alignment explanation
Indices: 2702162--2702224 Score: 74
Period size: 17 Copynumber: 3.3 Consensus size: 18
2702152 TTAAAAAAAA
*
2702162 TATTTTTTTATTATATTAAT
1 TATTTTATTATT-TATT-AT
2702182 TATTATTATTATTTATT-T
1 TATT-TTATTATTTATTAT
2702200 TATTTTATTATTTATTACT
1 TATTTTATTATTTATTA-T
2702219 TATTTT
1 TATTTT
2702225 TATTTTTTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 12 0.31
18 5 0.13
19 7 0.18
20 8 0.21
21 7 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTTATTATTTATTAT
Found at i:2702201 original size:30 final size:31
Alignment explanation
Indices: 2702162--2702230 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
2702152 TTAAAAAAAA
2702162 TATTT-TTTTATTATATTAATTATTA-TTAT
1 TATTTATTTTATTATATTAATTATTACTTAT
* *
2702191 TATTTATTTTATTTTATTATTTATTACTTAT
1 TATTTATTTTATTATATTAATTATTACTTAT
2702222 T-TTTATTTT
1 TATTTATTTT
2702231 TTCTTTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 5 0.14
30 26 0.72
31 5 0.14
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (31 bp):
TATTTATTTTATTATATTAATTATTACTTAT
Found at i:2702225 original size:20 final size:19
Alignment explanation
Indices: 2702162--2702228 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
2702152 TTAAAAAAAA
2702162 TATTTTT-TTATTATATTAAT
1 TATTTTTATTATT-TATT-AT
*
2702182 TATTATTATTATTTATT-T
1 TATTTTTATTATTTATTAT
2702200 TA-TTTTATTATTTATTACT
1 TATTTTTATTATTTATTA-T
2702219 TATTTTTATT
1 TATTTTTATT
2702229 TTTTCTTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 13 0.32
18 3 0.07
19 3 0.07
20 17 0.41
21 5 0.12
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTTATTATTTATTAT
Found at i:2703584 original size:22 final size:23
Alignment explanation
Indices: 2703559--2703601 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2703549 TTTTCCCTTC
2703559 ATATTAT-TATTATTT-TTTATAT
1 ATATTATAT-TTATTTATTTATAT
2703581 ATATTATATTTATTTATTTAT
1 ATATTATATTTATTTATTTAT
2703602 TTTCACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
ATATTATATTTATTTATTTATAT
Found at i:2703587 original size:19 final size:18
Alignment explanation
Indices: 2703559--2703602 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
2703549 TTTTCCCTTC
2703559 ATATTATTATTATTT-TTT
1 ATATTATTA-TATTTATTT
2703577 ATATATATTATATTTATTT
1 ATAT-TATTATATTTATTT
2703596 AT-TTATT
1 ATATTATT
2703603 TTCACTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.17
18 10 0.42
19 10 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATATTATTATATTTATTT
Found at i:2704451 original size:18 final size:18
Alignment explanation
Indices: 2704409--2704451 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2704399 TTGCAGCATT
* *
2704409 TTATTTACTTTCTTTTAT
1 TTATTTACTTTATTTTAA
2704427 TTATTTACTTTATTATTAA
1 TTATTTACTTTATT-TTAA
2704446 TT-TTTA
1 TTATTTA
2704452 TTATTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTTACTTTATTTTAA
Found at i:2704474 original size:25 final size:26
Alignment explanation
Indices: 2704421--2704475 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
2704411 ATTTACTTTC
* *
2704421 TTTTATTTATTTACTTTATTATTAAT
1 TTTTATTTATTTACTTTACTACTAAT
* *
2704447 TTTTA-TTATTTATTTTACTACTAGT
1 TTTTATTTATTTACTTTACTACTAAT
2704472 TTTT
1 TTTT
2704476 TTCTTTAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTTATTTATTTACTTTACTACTAAT
Found at i:2704978 original size:40 final size:42
Alignment explanation
Indices: 2704921--2705022 Score: 127
Period size: 40 Copynumber: 2.5 Consensus size: 42
2704911 TTGATATCCT
*
2704921 TATTTTTAAAAGAATATTAATAATAAATTTAATATTATAAT-
1 TATTTTTAAAAGAATATTAATAATAAAGTTAATATTATAATA
** * *
2704962 T-TTTTTAAAATTATATTAATTATAAAGTTATTATTATAATA
1 TATTTTTAAAAGAATATTAATAATAAAGTTAATATTATAATA
* *
2705003 TATTTTTAAAGGAATTTTAA
1 TATTTTTAAAAGAATATTAA
2705023 GAGTTTGAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
40 34 0.68
41 2 0.04
42 14 0.28
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (42 bp):
TATTTTTAAAAGAATATTAATAATAAAGTTAATATTATAATA
Found at i:2705279 original size:31 final size:30
Alignment explanation
Indices: 2705204--2705292 Score: 92
Period size: 31 Copynumber: 3.0 Consensus size: 30
2705194 ACTTAGATTG
** *
2705204 AATTC-ATGGTTAGTTTGATATTTTATTTA
1 AATTCAATGGTTAAATTAATATTTTATTTA
* * *
2705233 AGTTTAAGGGTTAAATTAATATTTTATCTTA
1 AATTCAATGGTTAAATTAATATTTTAT-TTA
*
2705264 AATTCAATGGTTAAATTAGTATTTT-TTTA
1 AATTCAATGGTTAAATTAATATTTTATTTA
2705293 TGAAATTTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
29 6 0.12
30 18 0.38
31 24 0.50
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (30 bp):
AATTCAATGGTTAAATTAATATTTTATTTA
Found at i:2706501 original size:21 final size:20
Alignment explanation
Indices: 2706472--2706511 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2706462 CACTTCTTGA
* *
2706472 ACACTCTTTTATTTAATATAT
1 ACACCCTTTTAATT-ATATAT
2706493 ACACCCTTTTAATTATATA
1 ACACCCTTTTAATTATATA
2706512 AAAACATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.47
Consensus pattern (20 bp):
ACACCCTTTTAATTATATAT
Found at i:2706530 original size:2 final size:2
Alignment explanation
Indices: 2706525--2706554 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2706515 ACATACATAC
2706525 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
2706555 GTATTTGTTG
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:2706870 original size:17 final size:17
Alignment explanation
Indices: 2706843--2706881 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2706833 AATTTACAAT
2706843 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
2706859 TAATTATAAATAATATC
1 TAATTATAAATAATATC
2706876 TAATTA
1 TAATTA
2706882 ATTTTGCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:2713083 original size:20 final size:20
Alignment explanation
Indices: 2713058--2713125 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
2713048 TCCAAAGTTA
2713058 GTAGTATCGATACTCTACTT
1 GTAGTATCGATACTCTACTT
* * **
2713078 GTAGTATTGATACCCTA-GA
1 GTAGTATCGATACTCTACTT
2713097 GTCAAGTATCGATACTCTACTT
1 GT--AGTATCGATACTCTACTT
2713119 GTAGTAT
1 GTAGTAT
2713126 TAATAACTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 2 0.05
20 20 0.54
21 13 0.35
22 2 0.05
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (20 bp):
GTAGTATCGATACTCTACTT
Found at i:2714591 original size:33 final size:33
Alignment explanation
Indices: 2714554--2714626 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
2714544 TTTTCCATTA
*
2714554 TAAAAATAGAAATTAAGGATTATTTTATAAAAT
1 TAAAAATAGAAAGTAAGGATTATTTTATAAAAT
2714587 TAAAAATAGAAAGTAAGGATTATTTTATAAAAT
1 TAAAAATAGAAAGTAAGGATTATTTTATAAAAT
*
2714620 TGAAAAT
1 TAAAAAT
2714627 TAAGAATCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (33 bp):
TAAAAATAGAAAGTAAGGATTATTTTATAAAAT
Found at i:2714675 original size:55 final size:57
Alignment explanation
Indices: 2714587--2714712 Score: 211
Period size: 56 Copynumber: 2.2 Consensus size: 57
2714577 TTTATAAAAT
* *
2714587 TAAAAATAGAAAGTAAGGATTATTTTATAAAATT-GAAAATTAAGAATCCTTAGCTA
1 TAAAAATAGAAAGTAAGGATTATTTTATAAAATTCAAAAATTAAGAATCCTTAACTA
2714643 TAAAAATAGAAAGTAA-GATTATTTTATAAAATTCAAAAATTAAGAATCCTTAACTA
1 TAAAAATAGAAAGTAAGGATTATTTTATAAAATTCAAAAATTAAGAATCCTTAACTA
*
2714699 TAAAAATAAAAAGT
1 TAAAAATAGAAAGT
2714713 GGAGCCTATA
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
55 17 0.26
56 49 0.74
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.31
Consensus pattern (57 bp):
TAAAAATAGAAAGTAAGGATTATTTTATAAAATTCAAAAATTAAGAATCCTTAACTA
Found at i:2714702 original size:30 final size:28
Alignment explanation
Indices: 2714612--2714710 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 28
2714602 AGGATTATTT
*
2714612 TATAAAATTGAAAATTAAGAATCCTTAGC
1 TATAAAATTAAAAATTAAGAATCCTTA-C
* * * ** *
2714641 TATAAAAATAGAAAGTAAG-ATTATT-T
1 TATAAAATTAAAAATTAAGAATCCTTAC
2714667 TATAAAATTCAAAAATTAAGAATCCTTAAC
1 TATAAAATT-AAAAATTAAGAATCCTT-AC
*
2714697 TATAAAAATAAAAA
1 TATAAAATTAAAAA
2714711 GTGGAGCCTA
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
26 8 0.15
27 8 0.15
28 8 0.15
29 20 0.38
30 8 0.15
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (28 bp):
TATAAAATTAAAAATTAAGAATCCTTAC
Found at i:2714951 original size:31 final size:30
Alignment explanation
Indices: 2714898--2714974 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
2714888 TCAAAATACA
* *
2714898 TAAGTTATGGTCACCTTTGTTTTTATTTAAT
1 TAAGATATGATCACCTTTGTTTTTATTT-AT
*
2714929 TAAGATATGATCACTTTTGTTTTTATTTAT
1 TAAGATATGATCACCTTTGTTTTTATTTAT
* *
2714959 TGAAGATGTGGTCACC
1 T-AAGATATGATCACC
2714975 ACGGGTTAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 3 0.08
31 36 0.92
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (30 bp):
TAAGATATGATCACCTTTGTTTTTATTTAT
Found at i:2716024 original size:182 final size:184
Alignment explanation
Indices: 2715804--2716171 Score: 722
Period size: 182 Copynumber: 2.0 Consensus size: 184
2715794 CCAATGTTTA
2715804 AAAAGGGCGTATTTTTGTTTGACTTAATAAAAATAAATATTTTTATTTTCTTTCTAAAGGAAAAA
1 AAAAGGGCGTATTTTTGTTTGACTTAATAAAAATAAATATTTTTATTTTCTTTCTAAAGGAAAAA
2715869 AAGGGGAAATTGTGACTGAGAAATACATTTGTTTTCTTGTTAAACTGA-TTTCTGATACGATGTT
66 AAGGGGAAATTGTGACTGAGAAATACATTTGTTTTCTTGTTAAACTGATTTTCTGATACGATGTT
2715933 ATGAAATATATGTTGGAGTAGTGGACATCTAAATCATAATTTCCACATGTGGAT
131 ATGAAATATATGTTGGAGTAGTGGACATCTAAATCATAATTTCCACATGTGGAT
2715987 AAAAGGGCGTA-TTTTGTTTGACTTAATAAAAATAAATATTTTTATTTTCTTTCTAAAGGAAAAA
1 AAAAGGGCGTATTTTTGTTTGACTTAATAAAAATAAATATTTTTATTTTCTTTCTAAAGGAAAAA
2716051 AAGGGGAAATTGTGACTGAGAAATACATTTGTTTTCTTGTTAAACTGATTTTCTGATACGATGTT
66 AAGGGGAAATTGTGACTGAGAAATACATTTGTTTTCTTGTTAAACTGATTTTCTGATACGATGTT
2716116 ATGAAATATATGTTGGAGTAGTGGACATCTAAATCATAATTTCCACATGTGGAT
131 ATGAAATATATGTTGGAGTAGTGGACATCTAAATCATAATTTCCACATGTGGAT
2716170 AA
1 AA
2716172 TACAATAAAA
Statistics
Matches: 184, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
182 101 0.55
183 83 0.45
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (184 bp):
AAAAGGGCGTATTTTTGTTTGACTTAATAAAAATAAATATTTTTATTTTCTTTCTAAAGGAAAAA
AAGGGGAAATTGTGACTGAGAAATACATTTGTTTTCTTGTTAAACTGATTTTCTGATACGATGTT
ATGAAATATATGTTGGAGTAGTGGACATCTAAATCATAATTTCCACATGTGGAT
Found at i:2717820 original size:19 final size:20
Alignment explanation
Indices: 2717731--2717821 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 20
2717721 AACGCGATTT
2717731 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* * *
2717751 T-TAAAATGTGTTGCAAGAG
1 TGAAAAATGTGTTGCGATAG
2717770 TTTGAAAAACGTGTTGTTGCGATAG
1 --TGAAAAA--TG-TGTTGCGATAG
2717795 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
2717814 TGAAAAAT
1 TGAAAAAT
2717822 CCAAAATAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 33 0.57
20 2 0.03
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.03
25 9 0.16
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.31
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:2718148 original size:18 final size:18
Alignment explanation
Indices: 2718125--2718160 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2718115 CGTCTCGGGC
2718125 CGTGGTCGGGGCCGTGGT
1 CGTGGTCGGGGCCGTGGT
2718143 CGTGGTCGGGGCCGTGGT
1 CGTGGTCGGGGCCGTGGT
2718161 TGGTGTGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.22, G:0.56, T:0.22
Consensus pattern (18 bp):
CGTGGTCGGGGCCGTGGT
Found at i:2719305 original size:29 final size:30
Alignment explanation
Indices: 2719248--2719320 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 30
2719238 AAAACCGAAT
*
2719248 TAAACGTGGACGGGAAAAAACCGTTTATGC
1 TAAACGGGGACGGGAAAAAACCGTTTATGC
2719278 TAAACGGGGACGGG-AAAAACCGTTTATGC
1 TAAACGGGGACGGGAAAAAACCGTTTATGC
*
2719307 TAAACGGGGTCGGG
1 TAAACGGGGACGGG
2719321 TTTGGTAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 28 0.68
30 13 0.32
ACGTcount: A:0.33, C:0.16, G:0.33, T:0.18
Consensus pattern (30 bp):
TAAACGGGGACGGGAAAAAACCGTTTATGC
Found at i:2719441 original size:37 final size:37
Alignment explanation
Indices: 2719408--2719490 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
2719398 ATAATTATTT
*
2719408 TATATATATAATATTAATA-AATTAAATTAAATTAAAA
1 TATATATATAATATTAATATAATTAAATTAAATT-ATA
* * *
2719445 TATATATATAATATTTATATATTTAATTTAAA-TATA
1 TATATATATAATATTAATATAATTAAATTAAATTATA
2719481 TATATATATA
1 TATATATATA
2719491 CCCGGCCCGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
36 12 0.29
37 19 0.46
38 10 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
TATATATATAATATTAATATAATTAAATTAAATTATA
Found at i:2730139 original size:20 final size:20
Alignment explanation
Indices: 2730114--2730153 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2730104 GACTTTTTGG
*
2730114 GTCAAAGTCAACGGTGAACT
1 GTCAAAGTCAACGGTCAACT
2730134 GTCAAAGTCAACGGTCAACT
1 GTCAAAGTCAACGGTCAACT
2730154 CTGGTCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (20 bp):
GTCAAAGTCAACGGTCAACT
Found at i:2730180 original size:19 final size:19
Alignment explanation
Indices: 2730156--2730215 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
2730146 GGTCAACTCT
2730156 GGTCAAAGAT-AACGGGTCG
1 GGTCAAAG-TCAACGGGTCG
* *
2730175 GGTCAAAGTCAACGTGTCA
1 GGTCAAAGTCAACGGGTCG
*
2730194 GGTCAAAGTCAACAGGTCG
1 GGTCAAAGTCAACGGGTCG
2730213 GGT
1 GGT
2730216 TGGGTTGAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 1 0.03
19 34 0.97
ACGTcount: A:0.30, C:0.18, G:0.33, T:0.18
Consensus pattern (19 bp):
GGTCAAAGTCAACGGGTCG
Found at i:2734605 original size:14 final size:14
Alignment explanation
Indices: 2734586--2734613 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2734576 AAGTGAAAGA
2734586 ATAGTTATATAATT
1 ATAGTTATATAATT
2734600 ATAGTTATATAATT
1 ATAGTTATATAATT
2734614 TTATTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:2736638 original size:18 final size:17
Alignment explanation
Indices: 2736617--2736677 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
2736607 TAATGATTTG
2736617 ATTTTATAGTATTTTTAT
1 ATTTTATA-TATTTTTAT
* *
2736635 ATTTAATATA-TTTAAT
1 ATTTTATATATTTTTAT
*
2736651 ATCTTA-ATGATTGTTTAT
1 ATTTTATAT-ATT-TTTAT
2736669 ATTTTATAT
1 ATTTTATAT
2736678 TTAAAATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
15 2 0.06
16 10 0.30
17 3 0.09
18 16 0.48
19 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.61
Consensus pattern (17 bp):
ATTTTATATATTTTTAT
Found at i:2739139 original size:31 final size:31
Alignment explanation
Indices: 2739104--2739181 Score: 156
Period size: 31 Copynumber: 2.5 Consensus size: 31
2739094 ATATCTAATT
2739104 TTTGCTGTTGTTTGCATAGAAACCCATTTCG
1 TTTGCTGTTGTTTGCATAGAAACCCATTTCG
2739135 TTTGCTGTTGTTTGCATAGAAACCCATTTCG
1 TTTGCTGTTGTTTGCATAGAAACCCATTTCG
2739166 TTTGCTGTTGTTTGCA
1 TTTGCTGTTGTTTGCA
2739182 GACAACAACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.45
Consensus pattern (31 bp):
TTTGCTGTTGTTTGCATAGAAACCCATTTCG
Found at i:2740069 original size:25 final size:26
Alignment explanation
Indices: 2740014--2740071 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 26
2740004 CTAGTGTTTA
2740014 AACTATATTACATTTCACTTGAATGTTG
1 AACTATATTACATTTCAC-T-AATGTTG
*
2740042 AACTATATTATATTTCAC-AATGTTG
1 AACTATATTACATTTCACTAATGTTG
2740067 AACTA
1 AACTA
2740072 CATTTCTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 12 0.41
28 17 0.59
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (26 bp):
AACTATATTACATTTCACTAATGTTG
Found at i:2740330 original size:43 final size:42
Alignment explanation
Indices: 2740276--2740400 Score: 142
Period size: 43 Copynumber: 2.9 Consensus size: 42
2740266 CATTGCGGCA
* * *
2740276 TTTGAAAAAGAAATGTCGCTAAATGTCCTAACATATTGCGGTG
1 TTTGTAAAAGAAACG-CGCTAAATGTCCTAACATATTGCGATG
* * * *
2740319 TTTGTATAAGAAACGCTGCTAAATGTCCGAACTTGTTGCGATG
1 TTTGTAAAAGAAACGC-GCTAAATGTCCTAACATATTGCGATG
* *
2740362 TTTGTAAAAAAAACGCCGCTAAATGTCCTAACCTATTGC
1 TTTGTAAAAGAAACG-CGCTAAATGTCCTAACATATTGC
2740401 AACGTTTTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.01
43 66 0.97
44 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (42 bp):
TTTGTAAAAGAAACGCGCTAAATGTCCTAACATATTGCGATG
Found at i:2743079 original size:29 final size:29
Alignment explanation
Indices: 2743045--2743100 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
2743035 AAGTATACCG
*
2743045 AATTCTTAGTTTCATACATAATGTTTTAA
1 AATTCTTAATTTCATACATAATGTTTTAA
*
2743074 AATTCTTAATTTCATACATGATGTTTT
1 AATTCTTAATTTCATACATAATGTTTT
2743101 CTGCCATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (29 bp):
AATTCTTAATTTCATACATAATGTTTTAA
Found at i:2748543 original size:18 final size:17
Alignment explanation
Indices: 2748520--2748562 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2748510 ATATATACAT
2748520 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
2748538 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
2748555 ATAA-AATA
1 ATAATAATA
2748563 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:2749901 original size:105 final size:105
Alignment explanation
Indices: 2749714--2750163 Score: 696
Period size: 105 Copynumber: 4.3 Consensus size: 105
2749704 GCATTGTTCA
* ** *
2749714 GAGTCCAATATCC-TCCTTCGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAA
1 GAGTCCAATATCCTTCGTT-GTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAA
2749773 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2749814 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
2749879 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2749919 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
2749984 CAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2750024 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
2750089 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2750129 GAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 GAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
2750164 CGCGGATGGC
Statistics
Matches: 323, Mismatches: 18, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
100 33 0.10
101 5 0.02
102 1 0.00
104 5 0.02
105 254 0.79
106 3 0.01
108 22 0.07
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2750939 original size:65 final size:66
Alignment explanation
Indices: 2750731--2751221 Score: 262
Period size: 65 Copynumber: 7.2 Consensus size: 66
2750721 AAAGAGATAG
* * * * *
2750731 AATTCGTTTCAAGGGAAAT-GATCTCAAAGATATATGTTGTTTCATGAGAAACGGTCTCAAGGGA
1 AATTTGTTTTAAGGGAAATAAAT-TCAAAGAT-T-T-TTGTTTCAAGAGAAACTGTCTCAAGGGA
*
2750795 AACAA
62 GACAA
** *
2750800 AATTATGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGA
1 AATT-TGTTTTAAGGGAAATAAATTCAAAGATTTT-TGTTTCAAGAGAAACTGTCTCAAGGGAGA
2750865 CAA
64 CAA
* * ** *
2750868 AATTTGTTTTAGGGGAAATAAATTCAAAGA-TTTTGTTTCAAGGGAAACTGTCTCAAGATAGACG
1 AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACA
2750932 A
66 A
* * * ** * * *
2750933 AATTTGTTTCAAGAGAAACT--GTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCA
1 AATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-AG----ATTTTTGTTTCAAGAGAAACTGTCTCA
2750996 AGGGAGACAA
57 AGGGAGACAA
* * * * * * * *
2751006 AATTTGTTTCAAAGAAAACATATTCAAATA-TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
1 AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACA
2751070 A
66 A
* * * * * * *
2751071 AATTTATTTCAAGAGAAACT--GTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCA
1 AATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-AG----ATTTTTGTTTCAAGAGAAACTGTCTCA
* *
2751134 AGAGAGACGA
57 AGGGAGACAA
* * *** * * * *
2751144 AATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC-
1 AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACA
2751207 A
66 A
2751208 AATCTTGTTTTAAG
1 AAT-TTGTTTTAAG
2751222 AAAAACAATC
Statistics
Matches: 336, Mismatches: 58, Indels: 60
0.74 0.13 0.13
Matches are distributed among these distances:
64 6 0.02
65 128 0.38
66 7 0.02
67 26 0.08
68 36 0.11
69 5 0.01
70 21 0.06
71 4 0.01
72 5 0.01
73 96 0.29
74 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (66 bp):
AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACA
A
Found at i:2750951 original size:36 final size:36
Alignment explanation
Indices: 2750899--2751161 Score: 274
Period size: 36 Copynumber: 7.4 Consensus size: 36
2750889 ATTCAAAGAT
* * *
2750899 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
2750935 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
2750971 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
2751008 TTTGTTTCAA-AGAAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
2751037 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
2751073 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
2751109 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
2751146 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGAGAAA
2751162 TGTTTTCAAT
Statistics
Matches: 191, Mismatches: 23, Indels: 26
0.80 0.10 0.11
Matches are distributed among these distances:
28 2 0.01
29 18 0.09
30 2 0.01
31 1 0.01
34 1 0.01
35 3 0.02
36 98 0.51
37 66 0.35
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:2751011 original size:138 final size:137
Alignment explanation
Indices: 2750848--2751227 Score: 492
Period size: 138 Copynumber: 2.8 Consensus size: 137
2750838 TTTCAAGAGT
* * *
2750848 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
*
2750913 AACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
66 AACTGTCTCAAGAGAGAC-AAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
2750978 CCAAAAGA
130 CCAAAAGA
* * * *
2750986 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
* * *
2751051 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTT
66 AACTGTCTCAAGAGAGAC-AAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
* **
2751116 TCAAGGGA
130 CCAAAAGA
* * * * * * * *
2751124 AACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAG
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATATATTCAAAGATTT-TGTTTCAAGGG
* * *
2751188 AAACTATCTCAAGAGAGACAAATCTTGTTTTAAGAAAAAC
65 AAACTGTCTCAAGAGAGACAAAT-TTGTTTCAAGAGAAAC
2751228 AATCATGAGT
Statistics
Matches: 209, Mismatches: 31, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
137 7 0.03
138 202 0.97
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTC
CAAAAGA
Found at i:2751058 original size:102 final size:102
Alignment explanation
Indices: 2750935--2751119 Score: 309
Period size: 102 Copynumber: 1.8 Consensus size: 102
2750925 ATAGACGAAA
*
2750935 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAG
2751000 AGACAAAA-TTTGTTTCAAAGAAAACATATTCAAATAT
65 AGACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
* * * *
2751037 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
2751102 GACAAAATTTTGTTTCAA
66 GACAAAATTTTGTTTCAA
2751120 GGGAAACTAT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
101 29 0.38
102 48 0.62
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
Found at i:2752153 original size:22 final size:22
Alignment explanation
Indices: 2752128--2752171 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2752118 ATTTTTTGTT
2752128 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAA-GGTTTGA
2752150 CATTTGATGCTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
2752172 TGGGGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:2752785 original size:12 final size:12
Alignment explanation
Indices: 2752770--2752808 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2752760 TTTTTGTCCC
2752770 TTTTTCTTTTTT
1 TTTTTCTTTTTT
*
2752782 TTTTTGTTCTTTT
1 TTTTTCTT-TTTT
*
2752795 TTTTGCTTTTTT
1 TTTTTCTTTTTT
2752807 TT
1 TT
2752809 GCCCTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:2752787 original size:22 final size:22
Alignment explanation
Indices: 2752759--2752822 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
2752749 TTTGCATGTG
2752759 TTTTTTGTCCCTTTTTCTTT-TT
1 TTTTTTGTCCCTTTTT-TTTCTT
*
2752781 TTTTTTGT-TCTTTTTTTTGCTT
1 TTTTTTGTCCCTTTTTTTT-CTT
*
2752803 TTTTTTG-CCCTTTTTATTCT
1 TTTTTTGTCCCTTTTTTTTCT
2752823 GATTAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 3 0.08
21 8 0.22
22 25 0.69
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.77
Consensus pattern (22 bp):
TTTTTTGTCCCTTTTTTTTCTT
Found at i:2754010 original size:8 final size:8
Alignment explanation
Indices: 2753994--2754032 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2753984 ATTGTAGATG
2753994 AAAATGCA
1 AAAATGCA
*
2754002 AAAAGGCA
1 AAAATGCA
2754010 AAAATGC-
1 AAAATGCA
2754017 AAAATGCA
1 AAAATGCA
*
2754025 AGAATGCA
1 AAAATGCA
2754033 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:2754020 original size:15 final size:15
Alignment explanation
Indices: 2753994--2754032 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2753984 ATTGTAGATG
2753994 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
2754010 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
2754025 AGAATGCA
1 AAAATGCA
2754033 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:2757178 original size:18 final size:17
Alignment explanation
Indices: 2757155--2757197 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2757145 ATATATACAT
2757155 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
2757173 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
2757190 ATAA-AATA
1 ATAATAATA
2757198 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:2760672 original size:2 final size:2
Alignment explanation
Indices: 2760667--2760691 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2760657 TTAGTCTAGT
2760667 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 T
2760692 CTTTTAAATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2762145 original size:116 final size:116
Alignment explanation
Indices: 2761929--2762339 Score: 504
Period size: 116 Copynumber: 3.5 Consensus size: 116
2761919 CATAATTTCA
* * * * * *
2761929 ATGAGGGAGAAGGAA-TTCATAATAAGAAGAACTTGTTCAACGTTAGCTCATCCATCACATAAAG
1 ATGAGAGAGAA-GAAGTTCCTAATGAGAAGAACTTGTTTAACCTTAGCTCATCCATCACATAAGG
* * *
2761993 AGTTGGATTAGCATTT-TCAATGGAATGATTCGTAATGAGAAGAACTCGTCCG
65 AGTTGGATCAGCATTTCT-AATGGAAGGGTTCGTAATGAGAAGAACTCGTCCG
* * * *
2762045 ATGAGAGAGAAGAAGCTCCTAATGAGAATAACTTGTTTGACCTTAGCTAATCCATCACATAAGGA
1 ATGAGAGAGAAGAAGTTCCTAATGAGAAGAACTTGTTTAACCTTAGCTCATCCATCACATAAGGA
** * * *
2762110 GTTATATCAGCATTTCTAGTGAAAGGGTTCATAATGAGAAGAACTCGTCCG
66 GTTGGATCAGCATTTCTAATGGAAGGGTTCGTAATGAGAAGAACTCGTCCG
* * *
2762161 ATGA-AGGAGAAGAAGTTCCTAATGAAAAGAATTTGTTTGACCTTAGCTCATCCATCACATAAGG
1 ATGAGA-GAGAAGAAGTTCCTAATGAGAAGAACTTGTTTAACCTTAGCTCATCCATCACATAAGG
* * * *
2762225 AGTTGGATCAGCATTTCCAATGGAAGGGTTCGTAATAAGAAGAACTCATTCG
65 AGTTGGATCAGCATTTCTAATGGAAGGGTTCGTAATGAGAAGAACTCGTCCG
* * * *
2762277 ATGAGGGAGAAGATGTTCCTAATGAGAAGAACTTGTTCAAACCTTGGCTCATCCATCACATAA
1 ATGAGAGAGAAGAAGTTCCTAATGAGAAGAACTTGTT-TAACCTTAGCTCATCCATCACATAA
2762340 TGAGAAGGAT
Statistics
Matches: 251, Mismatches: 39, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
115 4 0.02
116 224 0.89
117 23 0.09
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (116 bp):
ATGAGAGAGAAGAAGTTCCTAATGAGAAGAACTTGTTTAACCTTAGCTCATCCATCACATAAGGA
GTTGGATCAGCATTTCTAATGGAAGGGTTCGTAATGAGAAGAACTCGTCCG
Found at i:2762395 original size:44 final size:43
Alignment explanation
Indices: 2762328--2762622 Score: 186
Period size: 44 Copynumber: 6.7 Consensus size: 43
2762318 CCTTGGCTCA
* * *
2762328 TCCATCACATAATGAG-AAGGATCAACATTAAATTTTTGTTCAAT
1 TCCATCACATAAGGAGTTA-GATCAACATCAAA-TTTTGTTCAAT
* * * *
2762372 TTCATCACATAAGGAGTTAGATCATCATCAACATTTCGCTT-TAT
1 TCCATCACATAAGGAGTTAGATCAACATCAA-ATTTTG-TTCAAT
* * * *
2762416 TCCATCACATAAGGAGTTGGATCAACATCACCATTTTGCTCGAT
1 TCCATCACATAAGGAGTTAGATCAACATCA-AATTTTGTTCAAT
* * * * *
2762460 TCCATCACATAAGGAGTTGGATCATCAT-AACTATTTCGCTCTAT
1 TCCATCACATAAGGAGTTAGATCAACATCAA--ATTTTGTTCAAT
* * * * ** *
2762504 TCCATCATATAAGGAGTTGGATTAGCATCAATATTTCCCTT-GAT
1 TCCATCACATAAGGAGTTAGATCAACATCAA-ATTT-TGTTCAAT
* * * **
2762548 TCCATCACATAAGGACTTGGATCAACATCACCATTTT-TCTCGTT
1 TCCATCACATAAGGAGTTAGATCAACATCA-AATTTTGT-TCAAT
* *
2762592 TCCATCACATAAGGAGTTGGAACAACATCAA
1 TCCATCACATAAGGAGTTAGATCAACATCAA
2762623 TATCATTTTT
Statistics
Matches: 205, Mismatches: 34, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 193 0.94
45 8 0.04
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (43 bp):
TCCATCACATAAGGAGTTAGATCAACATCAAATTTTGTTCAAT
Found at i:2762477 original size:88 final size:87
Alignment explanation
Indices: 2762328--2762622 Score: 333
Period size: 88 Copynumber: 3.4 Consensus size: 87
2762318 CCTTGGCTCA
* ** * * * * *
2762328 TCCATCACATAATGAGAAGGATCAACATTAAATTTTTGTTCAATTTCATCACATAAGGAGTTAGA
1 TCCATCACATAAGGAGTTGGATCAACATCAAA-TTTTGCTCGATTCCATCACATAAGGAGTTGGA
*
2762393 TCATCATCAACATTTCGCTTTAT
65 TCATCATCAACATTTCGCTCTAT
*
2762416 TCCATCACATAAGGAGTTGGATCAACATCACCATTTTGCTCGATTCCATCACATAAGGAGTTGGA
1 TCCATCACATAAGGAGTTGGATCAACATCA-AATTTTGCTCGATTCCATCACATAAGGAGTTGGA
2762481 TCATCAT-AACTATTTCGCTCTAT
65 TCATCATCAAC-ATTTCGCTCTAT
* * * ** * *
2762504 TCCATCATATAAGGAGTTGGATTAGCATCAATATTTCCCTTGATTCCATCACATAAGGACTTGGA
1 TCCATCACATAAGGAGTTGGATCAACATCAA-ATTTTGCTCGATTCCATCACATAAGGAGTTGGA
* * **
2762569 TCAACATCACCATTTTTCTCGT-T
65 TCATCATCAACATTTCGCTC-TAT
*
2762592 TCCATCACATAAGGAGTTGGAACAACATCAA
1 TCCATCACATAAGGAGTTGGATCAACATCAA
2762623 TATCATTTTT
Statistics
Matches: 176, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
87 3 0.02
88 169 0.96
89 4 0.02
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (87 bp):
TCCATCACATAAGGAGTTGGATCAACATCAAATTTTGCTCGATTCCATCACATAAGGAGTTGGAT
CATCATCAACATTTCGCTCTAT
Found at i:2762568 original size:132 final size:132
Alignment explanation
Indices: 2762374--2762612 Score: 388
Period size: 132 Copynumber: 1.8 Consensus size: 132
2762364 TGTTCAATTT
* * * *
2762374 CATCACATAAGGAGTTAGATCATCATCAACATTTCGCTTTATTCCATCACATAAGGAGTTGGATC
1 CATCACATAAGGAGTTAGATCAGCATCAACATTTCCCTTGATTCCATCACATAAGGACTTGGATC
2762439 AACATCACCATTTTGCTCGATTCCATCACATAAGGAGTTGGATCATCATAACTATTTCGCTCTAT
66 AACATCACCATTTTGCTCGATTCCATCACATAAGGAGTTGGATCATCATAACTATTTCGCTCTAT
2762504 TC
131 TC
* * * *
2762506 CATCATATAAGGAGTTGGATTAGCATCAATATTTCCCTTGATTCCATCACATAAGGACTTGGATC
1 CATCACATAAGGAGTTAGATCAGCATCAACATTTCCCTTGATTCCATCACATAAGGACTTGGATC
* *
2762571 AACATCACCATTTTTCTCGTTTCCATCACATAAGGAGTTGGA
66 AACATCACCATTTTGCTCGATTCCATCACATAAGGAGTTGGA
2762613 ACAACATCAA
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 97 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (132 bp):
CATCACATAAGGAGTTAGATCAGCATCAACATTTCCCTTGATTCCATCACATAAGGACTTGGATC
AACATCACCATTTTGCTCGATTCCATCACATAAGGAGTTGGATCATCATAACTATTTCGCTCTAT
TC
Found at i:2762957 original size:74 final size:75
Alignment explanation
Indices: 2762827--2762972 Score: 188
Period size: 74 Copynumber: 2.0 Consensus size: 75
2762817 TTGAAAATAC
* ** *
2762827 CAACATGTGAGATTAGGGCAAATCAAGTGGGAGGATTTTCAGATATAGAGAAGCAGATCAATTGA
1 CAACATGTGAGATTAGGGCAAACCAAGTGGGAAAATTTTCAAATATAGAGAAGCAGATCAATTGA
2762892 TTGAAAGGAA
66 TTGAAAGGAA
* * ** *
2762902 CAACATGTGATATT-GGGCAAACCAAGTGGGAAAATTTTCAAATAT-GTTGGGGCAGATCATTTG
1 CAACATGTGAGATTAGGGCAAACCAAGTGGGAAAATTTTCAAATATAG-AGAAGCAGATCAATTG
2762965 ATTGAAAG
65 ATTGAAAG
2762973 ATGGAGAAGT
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
73 1 0.02
74 47 0.77
75 13 0.21
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (75 bp):
CAACATGTGAGATTAGGGCAAACCAAGTGGGAAAATTTTCAAATATAGAGAAGCAGATCAATTGA
TTGAAAGGAA
Found at i:2764303 original size:30 final size:32
Alignment explanation
Indices: 2764269--2764338 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 32
2764259 TATATTTCCT
2764269 TTATTTATATTTACGCAC-TTTAT-TTTTATG
1 TTATTTATATTTACGCACTTTTATATTTTATG
* * * * *
2764299 TTATTTACATTTATGCTCTTTTTTATTTTATT
1 TTATTTATATTTACGCACTTTTATATTTTATG
2764331 TTATTTAT
1 TTATTTAT
2764339 GTTCTTTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 15 0.47
31 4 0.12
32 13 0.41
ACGTcount: A:0.21, C:0.09, G:0.04, T:0.66
Consensus pattern (32 bp):
TTATTTATATTTACGCACTTTTATATTTTATG
Found at i:2764329 original size:27 final size:26
Alignment explanation
Indices: 2764291--2764345 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
2764281 ACGCACTTTA
2764291 TTTTTATGTTATTTACATTTATGCTCT
1 TTTTTATGTTATTT-CATTTATGCTCT
* * *
2764318 TTTTTATTTTATTTTATTTATGTTCT
1 TTTTTATGTTATTTCATTTATGCTCT
2764344 TT
1 TT
2764346 CATTTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.71
Consensus pattern (26 bp):
TTTTTATGTTATTTCATTTATGCTCT
Found at i:2764409 original size:15 final size:15
Alignment explanation
Indices: 2764386--2764438 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
2764376 TTTTCTATTG
* *
2764386 TTTATATTTTTGTCC
1 TTTAAATTTATGTCC
*
2764401 TTTAAATTTATGTAC
1 TTTAAATTTATGTCC
2764416 TTT-AATTTATGTCC
1 TTTAAATTTATGTCC
2764430 TTTAAATTT
1 TTTAAATTT
2764439 CTAGCATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.60
Consensus pattern (15 bp):
TTTAAATTTATGTCC
Found at i:2764424 original size:14 final size:14
Alignment explanation
Indices: 2764386--2764434 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
2764376 TTTTCTATTG
*
2764386 TTTATATTTTTGTCC
1 TTTA-ATTTATGTCC
*
2764401 TTTAAATTTATGTAC
1 TTT-AATTTATGTCC
2764416 TTTAATTTATGTCC
1 TTTAATTTATGTCC
2764430 TTTAA
1 TTTAA
2764435 ATTTCTAGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 15 0.50
15 14 0.47
16 1 0.03
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.59
Consensus pattern (14 bp):
TTTAATTTATGTCC
Found at i:2764448 original size:29 final size:30
Alignment explanation
Indices: 2764386--2764462 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
2764376 TTTTCTATTG
* *
2764386 TTTATATTTTTGTCCTTTAAATTTATGTAC
1 TTTATATTTATGTCCTTTAAATTTATGCAC
*
2764416 TTTA-ATTTATGTCCTTTAAATTTCTAGCA-
1 TTTATATTTATGTCCTTTAAATTTAT-GCAC
2764445 TTTATATTTGA-GTCCTTT
1 TTTATATTT-ATGTCCTTT
2764463 TTATGTTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 23 0.56
30 17 0.41
31 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.57
Consensus pattern (30 bp):
TTTATATTTATGTCCTTTAAATTTATGCAC
Found at i:2771975 original size:19 final size:20
Alignment explanation
Indices: 2771951--2771999 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
2771941 AAACGATTTT
2771951 ATTTTGAAAACAAAAATAG-
1 ATTTTGAAAACAAAAATAGA
* * *
2771970 ATTTTGAAAGCCAAAATGGA
1 ATTTTGAAAACAAAAATAGA
2771990 ATTTTGAAAA
1 ATTTTGAAAA
2772000 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (20 bp):
ATTTTGAAAACAAAAATAGA
Found at i:2773054 original size:21 final size:21
Alignment explanation
Indices: 2773025--2773065 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2773015 TGGTATGTTT
*
2773025 TTAATAATTGATATCATTTTG
1 TTAACAATTGATATCATTTTG
* *
2773046 TTAACAATTGGTATCTTTTT
1 TTAACAATTGATATCATTTT
2773066 CATAAACTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (21 bp):
TTAACAATTGATATCATTTTG
Found at i:2773412 original size:20 final size:22
Alignment explanation
Indices: 2773374--2773413 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2773364 TTTTAGTAGA
2773374 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
2773396 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
2773414 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:2773670 original size:34 final size:34
Alignment explanation
Indices: 2773630--2773716 Score: 174
Period size: 34 Copynumber: 2.6 Consensus size: 34
2773620 TTGTAAAGGG
2773630 GAAAGGTTCTAGTTTATCCTGTGTAAAAGCTAGA
1 GAAAGGTTCTAGTTTATCCTGTGTAAAAGCTAGA
2773664 GAAAGGTTCTAGTTTATCCTGTGTAAAAGCTAGA
1 GAAAGGTTCTAGTTTATCCTGTGTAAAAGCTAGA
2773698 GAAAGGTTCTAGTTTATCC
1 GAAAGGTTCTAGTTTATCC
2773717 CAAAAAAACT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (34 bp):
GAAAGGTTCTAGTTTATCCTGTGTAAAAGCTAGA
Found at i:2775117 original size:20 final size:19
Alignment explanation
Indices: 2775074--2775121 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2775064 CAAGGATTAA
* **
2775074 TATCGATACTGATATTGGG
1 TATCGATACTGAGAAGGGG
2775093 TATCGATACTGAGAAGGGAG
1 TATCGATACTGAGAAGGG-G
2775113 TATCGATAC
1 TATCGATAC
2775122 CAAGAGTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (19 bp):
TATCGATACTGAGAAGGGG
Found at i:2775827 original size:23 final size:23
Alignment explanation
Indices: 2775801--2775879 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 23
2775791 TCTATGTAAA
*
2775801 CATTCAGGATATTTCTATGTGGT
1 CATTCGGGATATTTCTATGTGGT
* * *
2775824 CATTCGGGACA-ATCTATGTGAT
1 CATTCGGGATATTTCTATGTGGT
* * *
2775846 CCTTCGAGATATTTCTACGTGGT
1 CATTCGGGATATTTCTATGTGGT
*
2775869 CCTTCGGGATA
1 CATTCGGGATA
2775880 AATTCTACGT
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 17 0.39
23 27 0.61
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.37
Consensus pattern (23 bp):
CATTCGGGATATTTCTATGTGGT
Found at i:2775842 original size:22 final size:22
Alignment explanation
Indices: 2775771--2775843 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
2775761 GTCGAGGGTT
* *
2775771 TATGCGGTCCTTCGGGACAATC
1 TATGTGGTCATTCGGGACAATC
*** * * *
2775793 TATGTAAACATTCAGGATATTTC
1 TATGTGGTCATTCGGGACA-ATC
2775816 TATGTGGTCATTCGGGACAATC
1 TATGTGGTCATTCGGGACAATC
2775838 TATGTG
1 TATGTG
2775844 ATCCTTCGAG
Statistics
Matches: 36, Mismatches: 14, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (22 bp):
TATGTGGTCATTCGGGACAATC
Found at i:2775851 original size:22 final size:22
Alignment explanation
Indices: 2775781--2775851 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
2775771 TATGCGGTCC
* *
2775781 TTCGGGACAATCTATGTAAACA
1 TTCGGGACAATCTATGTGATCA
* * * *
2775803 TTCAGGATATTTCTATGTGGTCA
1 TTCGGGACA-ATCTATGTGATCA
*
2775826 TTCGGGACAATCTATGTGATCC
1 TTCGGGACAATCTATGTGATCA
2775848 TTCG
1 TTCG
2775852 AGATATTTCT
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
22 21 0.57
23 16 0.43
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (22 bp):
TTCGGGACAATCTATGTGATCA
Found at i:2775857 original size:45 final size:45
Alignment explanation
Indices: 2775771--2775877 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
2775761 GTCGAGGGTT
*
2775771 TATGCGGTCCTTCGGGACAATCTATGTAAACATTCAGGATATTTC
1 TATGTGGTCCTTCGGGACAATCTATGTAAACATTCAGGATATTTC
* * * *
2775816 TATGTGGTCATTCGGGACAATCTATGTGATCCTTC-GAGATATTTC
1 TATGTGGTCCTTCGGGACAATCTATGTAAACATTCAG-GATATTTC
*
2775861 TACGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
2775878 TAAATTCTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.02
45 53 0.98
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (45 bp):
TATGTGGTCCTTCGGGACAATCTATGTAAACATTCAGGATATTTC
Found at i:2779974 original size:16 final size:17
Alignment explanation
Indices: 2779942--2779975 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2779932 AGAATCAAAT
*
2779942 AATATTATACTATTAAA
1 AATATTATACAATTAAA
2779959 AATATT-TACAATTAAA
1 AATATTATACAATTAAA
2779975 A
1 A
2779976 TTAAATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
AATATTATACAATTAAA
Found at i:2780448 original size:3 final size:3
Alignment explanation
Indices: 2780428--2780468 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
2780418 ATTAAAGAAC
2780428 ATA A-A ATA ATA AGT- ATA ATA ATA ATA AT- ATA ATA ATA ATA A
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2780469 ACATCTGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 5 0.15
3 28 0.82
4 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2780458 original size:14 final size:15
Alignment explanation
Indices: 2780428--2780468 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
2780418 ATTAAAGAAC
2780428 ATAA-AATAATAAGT
1 ATAATAATAATAAGT
2780442 ATAATAATAATAA-T
1 ATAATAATAATAAGT
2780456 ATAATAATAATAA
1 ATAATAATAATAA
2780469 ACATCTGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
ATAATAATAATAAGT
Found at i:2782143 original size:21 final size:21
Alignment explanation
Indices: 2782119--2782253 Score: 243
Period size: 21 Copynumber: 6.4 Consensus size: 21
2782109 AAAATCGCAA
2782119 TGCGATAGCACTGTTCACCGT
1 TGCGATAGCACTGTTCACCGT
2782140 TGCGATAGCACTGTTCACCGT
1 TGCGATAGCACTGTTCACCGT
2782161 TGCGATAGCACTGTTCACCGTT
1 TGCGATAGCACTGTTCACCG-T
2782183 TGCGATAGCACTGTTCACCGT
1 TGCGATAGCACTGTTCACCGT
*
2782204 TGCGATAGCACTGTTCACTGT
1 TGCGATAGCACTGTTCACCGT
*
2782225 TGCGATAGCACTGTTCACCAT
1 TGCGATAGCACTGTTCACCGT
2782246 TGCGATAG
1 TGCGATAG
2782254 TGATCAAAAT
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
21 89 0.81
22 21 0.19
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.30
Consensus pattern (21 bp):
TGCGATAGCACTGTTCACCGT
Done.