Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_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: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 19
Found at i:2193945 original size:11 final size:11
Alignment explanation
Indices: 2193929--2193953 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2193919 CATTGCAAAC
2193929 GTTATTTAGGT
1 GTTATTTAGGT
2193940 GTTATTTAGGT
1 GTTATTTAGGT
2193951 GTT
1 GTT
2193954 TGGGTCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (11 bp):
GTTATTTAGGT
Found at i:2194053 original size:6 final size:7
Alignment explanation
Indices: 2194022--2194052 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2194012 TTATAAATTT
2194022 ATTTAAA
1 ATTTAAA
2194029 ATTTAAA
1 ATTTAAA
2194036 ATTTAAA
1 ATTTAAA
*
2194043 AATTAAA
1 ATTTAAA
2194050 ATT
1 ATT
2194053 ATATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTTAAA
Found at i:2194413 original size:21 final size:21
Alignment explanation
Indices: 2194387--2194441 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
2194377 GAATTTTGGG
*
2194387 TTTTTTAAT-AATTTAATATAA
1 TTTTTTAATAAATATAATA-AA
* *
2194408 TTTTTTTATAAATATAATAAT
1 TTTTTTAATAAATATAATAAA
2194429 TTTTTTAA-AAATA
1 TTTTTTAATAAATA
2194442 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 5 0.17
21 16 0.55
22 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTTTAATAAATATAATAAA
Found at i:2194414 original size:22 final size:21
Alignment explanation
Indices: 2194387--2194441 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
2194377 GAATTTTGGG
*
2194387 TTTTTTAAT-AATTTAATATAAT
1 TTTTTTAATAAATAT-A-ATAAT
2194409 TTTTTT-ATAAATATAATAAT
1 TTTTTTAATAAATATAATAAT
2194429 TTTTTTAA-AAATA
1 TTTTTTAATAAATA
2194442 AAATTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 16 0.53
21 4 0.13
22 10 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTTTAATAAATATAATAAT
Found at i:2194427 original size:20 final size:20
Alignment explanation
Indices: 2194404--2194441 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2194394 ATAATTTAAT
*
2194404 ATAATTTTTTTATAAATATA
1 ATAATTTTTTTAAAAATATA
2194424 ATAATTTTTTTAAAAATA
1 ATAATTTTTTTAAAAATA
2194442 AAATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAATTTTTTTAAAAATATA
Found at i:2194446 original size:17 final size:18
Alignment explanation
Indices: 2194401--2194447 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
2194391 TTAATAATTT
*
2194401 AATATAATTTTTTTATAA
1 AATAAAATTTTTTTATAA
2194419 ATATAATAATTTTTTTA-AA
1 A-ATAA-AATTTTTTTATAA
2194438 AATAAAATTT
1 AATAAAATTT
2194448 AAAATCACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 5 0.19
18 5 0.19
19 6 0.23
20 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATAAAATTTTTTTATAA
Found at i:2194719 original size:19 final size:19
Alignment explanation
Indices: 2194695--2194745 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
2194685 GAACTCAAAA
2194695 TAATATTATTTTA-TATATT
1 TAATATTATTTTATTAT-TT
* *
2194714 TAATATTAATATATTATTT
1 TAATATTATTTTATTATTT
*
2194733 TAATATCATTTTA
1 TAATATTATTTTA
2194746 ATAAAAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 23 0.88
20 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TAATATTATTTTATTATTT
Found at i:2194735 original size:13 final size:13
Alignment explanation
Indices: 2194697--2194738 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2194687 ACTCAAAATA
2194697 ATATTATTTT-AT
1 ATATTATTTTAAT
*
2194709 ATATTTAATATTAAT
1 ATA-TT-ATTTTAAT
2194724 ATATTATTTTAAT
1 ATATTATTTTAAT
2194737 AT
1 AT
2194739 CATTTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 11 0.44
14 6 0.24
15 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATTATTTTAAT
Found at i:2194755 original size:30 final size:27
Alignment explanation
Indices: 2194691--2194755 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
2194681 ATAAGAACTC
2194691 AAAATAATATTATTTTATATATTTAATA
1 AAAAT-ATATTATTTTATATATTTAATA
**
2194719 TTAATATATTATTTTAATATCATTTTAATA
1 AAAATATATTATTTT-ATAT-A-TTTAATA
2194749 AAAATAT
1 AAAATAT
2194756 TAATTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 10 0.33
28 7 0.23
29 1 0.03
30 12 0.40
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
AAAATATATTATTTTATATATTTAATA
Found at i:2194811 original size:3 final size:3
Alignment explanation
Indices: 2194805--2194829 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2194795 AATATTATAT
2194805 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2194830 ATAATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2194914 original size:29 final size:30
Alignment explanation
Indices: 2194860--2194923 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
2194850 TTATATTATA
* *
2194860 ATAATATTCTTATTCTAGTAATTAA-TAAT
1 ATAATATTCTTATTCTAATAAATAATTAAT
* * *
2194889 GTAATGTTCTTATTTTAATAAATAATTAAT
1 ATAATATTCTTATTCTAATAAATAATTAAT
2194919 ATAAT
1 ATAAT
2194924 TTATAATATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (30 bp):
ATAATATTCTTATTCTAATAAATAATTAAT
Found at i:2194946 original size:33 final size:35
Alignment explanation
Indices: 2194909--2194981 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 35
2194899 TATTTTAATA
2194909 AATAATTAATATAAT-TT-ATAATATTTTAATTT-T
1 AATAATTAATATAATATTCATAATATTTT-ATTTAT
*
2194942 AATAA--AATATAATATTCCTAATATTTTATTTAT
1 AATAATTAATATAATATTCATAATATTTTATTTAT
2194975 AA-AATTA
1 AATAATTA
2194982 TCAAAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
31 8 0.24
32 8 0.24
33 17 0.50
34 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (35 bp):
AATAATTAATATAATATTCATAATATTTTATTTAT
Found at i:2195059 original size:18 final size:19
Alignment explanation
Indices: 2195038--2195087 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 19
2195028 AAATTAATTT
2195038 TAATATTTAAAA-AAATAA
1 TAATATTTAAAATAAATAA
2195056 TAATAGTTTTTAAAATAAATAA
1 TAATA---TTTAAAATAAATAA
*
2195078 TATTATTTAA
1 TAATATTTAA
2195088 TTTTATAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
21 7 0.26
22 10 0.37
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TAATATTTAAAATAAATAA
Found at i:2195731 original size:38 final size:38
Alignment explanation
Indices: 2195683--2195755 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
2195673 ATATATTAAA
* *
2195683 AATATAAAAAAATCATAATTTAGTGT-TATTTAATTAGC
1 AATATAAAAAAATCATAAATT-CTGTATATTTAATTAGC
* *
2195721 AATATTAAAAATTCATAAATTCTGTATATTTAATT
1 AATATAAAAAAATCATAAATTCTGTATATTTAATT
2195756 TATATGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 3 0.10
38 27 0.90
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (38 bp):
AATATAAAAAAATCATAAATTCTGTATATTTAATTAGC
Found at i:2199098 original size:16 final size:15
Alignment explanation
Indices: 2199077--2199112 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2199067 GGTCTCTTTT
*
2199077 ATTATTATAATCATCA
1 ATTATTATAATAAT-A
2199093 ATTATTATAATAATA
1 ATTATTATAATAATA
2199108 ATTAT
1 ATTAT
2199113 ATATTTCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATTATAATAATA
Found at i:2201329 original size:20 final size:21
Alignment explanation
Indices: 2201292--2201332 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2201282 CCCATAATGG
*
2201292 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2201313 GGGAATCGATA-CCCTTCATA
1 GGGAATCGATACCCCTTCATA
2201333 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:2204638 original size:21 final size:21
Alignment explanation
Indices: 2204612--2204653 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2204602 CCATAATGGG
**
2204612 GGGAATCGGTACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
2204633 GGGAATCAATACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
2204654 ATATTCAAAT
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:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
GGGAATCAATACCCCTTCATA
Found at i:2208068 original size:14 final size:14
Alignment explanation
Indices: 2208049--2208076 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2208039 AGTAACTCGA
2208049 GTATATAGATAATG
1 GTATATAGATAATG
2208063 GTATATAGATAATG
1 GTATATAGATAATG
2208077 CCCGATAAAG
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:0.21, T:0.36
Consensus pattern (14 bp):
GTATATAGATAATG
Found at i:2211878 original size:171 final size:171
Alignment explanation
Indices: 2211593--2211938 Score: 667
Period size: 171 Copynumber: 2.0 Consensus size: 171
2211583 TTTAAGTGGT
2211593 TAAAAGATCAAGATGAATTTTCTTTTCAATTAAACACGTTCAACATTTCACAATGCTCCTCACAA
1 TAAAAGATCAAGATGAATTTTCTTTTCAATTAAACACGTTCAACATTTCACAATGCTCCTCACAA
*
2211658 GAATTACTAGTTCCTAAATCGCACTTAGAAGACTTCATTGATTACTTTCACCCA-CACTTGACAT
66 GAATTACTAGTTCCTAAATCGCACTTAGAAGACTTCATTGATTACTTTCACCAACCACTTGACAT
2211722 GAATTTTAAAACACTTCTTCTCTCCACACACAAGTGAAACCA
131 GAATTTT-AAACACTTCTTCTCTCCACACACAAGTGAAACCA
2211764 TAAAAGATCAAGATGAATTTTCTTTTCAATTAAACACGTTCAACATTTCACAATGCTCCTCACAA
1 TAAAAGATCAAGATGAATTTTCTTTTCAATTAAACACGTTCAACATTTCACAATGCTCCTCACAA
2211829 GAATTACTAGTTCCTAAATCGCACTTAGAAGACTTCATTGATTACTTTCACCAACCACTTGACAT
66 GAATTACTAGTTCCTAAATCGCACTTAGAAGACTTCATTGATTACTTTCACCAACCACTTGACAT
2211894 GAATTTTAAACACTTCTTCTCTCCACACACAAGTGAAACCA
131 GAATTTTAAACACTTCTTCTCTCCACACACAAGTGAAACCA
2211935 TAAA
1 TAAA
2211939 GAAAACATAT
Statistics
Matches: 173, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
171 156 0.90
172 17 0.10
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (171 bp):
TAAAAGATCAAGATGAATTTTCTTTTCAATTAAACACGTTCAACATTTCACAATGCTCCTCACAA
GAATTACTAGTTCCTAAATCGCACTTAGAAGACTTCATTGATTACTTTCACCAACCACTTGACAT
GAATTTTAAACACTTCTTCTCTCCACACACAAGTGAAACCA
Found at i:2212801 original size:25 final size:22
Alignment explanation
Indices: 2212757--2212802 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2212747 AGGATGATGC
2212757 ATTATATTTTAGGATTATATTT
1 ATTATATTTTAGGATTATATTT
*
2212779 ATTATTTTATTAGGAATTAATATT
1 ATTATATT-TTAGG-ATT-ATATT
2212803 GCATTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 3 0.15
25 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (22 bp):
ATTATATTTTAGGATTATATTT
Found at i:2216617 original size:14 final size:14
Alignment explanation
Indices: 2216598--2216630 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2216588 ATCAAAAGAG
2216598 GAAGATGAAGGGAT
1 GAAGATGAAGGGAT
2216612 GAAGATGAAGGGAT
1 GAAGATGAAGGGAT
2216626 GAAGA
1 GAAGA
2216631 AGGACGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.12
Consensus pattern (14 bp):
GAAGATGAAGGGAT
Found at i:2218450 original size:65 final size:64
Alignment explanation
Indices: 2218373--2218515 Score: 191
Period size: 65 Copynumber: 2.2 Consensus size: 64
2218363 AAATTGAACT
* * *
2218373 ATGCATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTTTTATGAAAACATTGAATGCATT
1 ATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTATTT-TG-AAACATCGAATGCACT
*
2218436 TG
63 TC
*
2218438 ATGTATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTTC
1 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTTC
*
2218502 ATGCATTGATGCAC
1 ATGCATCGATGCAC
2218516 TCTTAGTGCA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 28 0.41
65 37 0.54
66 4 0.06
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTTC
Found at i:2219453 original size:20 final size:21
Alignment explanation
Indices: 2219428--2219467 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2219418 TTTACCCCAA
*
2219428 TTCAT-CCAGTATTGATATTG
1 TTCATCCCAATATTGATATTG
2219448 TTCATCCCAATATTGATATT
1 TTCATCCCAATATTGATATT
2219468 TGAACCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (21 bp):
TTCATCCCAATATTGATATTG
Found at i:2220387 original size:15 final size:15
Alignment explanation
Indices: 2220366--2220404 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2220356 GTCTTTATTT
2220366 ATCTTTATTATCTTA
1 ATCTTTATTATCTTA
* *
2220381 GTCTTTATTGTCTTA
1 ATCTTTATTATCTTA
2220396 ATCTTTATT
1 ATCTTTATT
2220405 CTTGATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.62
Consensus pattern (15 bp):
ATCTTTATTATCTTA
Found at i:2225202 original size:28 final size:28
Alignment explanation
Indices: 2225170--2225227 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
2225160 AGTGGAAAGA
*
2225170 AAGTTTTGAACAAAAATTCAAAAGGCAT
1 AAGTTTTGAACAAAAATTCAAAAGACAT
*
2225198 AAGTTTTGAACACAAATTCAAAAGACAT
1 AAGTTTTGAACAAAAATTCAAAAGACAT
2225226 AA
1 AA
2225228 TCAGATGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (28 bp):
AAGTTTTGAACAAAAATTCAAAAGACAT
Found at i:2225770 original size:51 final size:51
Alignment explanation
Indices: 2225698--2225794 Score: 194
Period size: 51 Copynumber: 1.9 Consensus size: 51
2225688 ATTTAACCTT
2225698 TGAATATGACACGTTGCGAATAGGGAATAATTTAGAAAAAGGTTAAATGAA
1 TGAATATGACACGTTGCGAATAGGGAATAATTTAGAAAAAGGTTAAATGAA
2225749 TGAATATGACACGTTGCGAATAGGGAATAATTTAGAAAAAGGTTAA
1 TGAATATGACACGTTGCGAATAGGGAATAATTTAGAAAAAGGTTAA
2225795 GGGAGAGAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (51 bp):
TGAATATGACACGTTGCGAATAGGGAATAATTTAGAAAAAGGTTAAATGAA
Found at i:2226122 original size:24 final size:24
Alignment explanation
Indices: 2226078--2226123 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2226068 AACGGGAATG
* **
2226078 GGAACGGGATAGAGAGCGAGATAT
1 GGAACGGGAAAGAGAAAGAGATAT
2226102 GGAACGGGAAAGAGAAAGAGAT
1 GGAACGGGAAAGAGAAAGAGAT
2226124 CGCTTGAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.07, G:0.41, T:0.09
Consensus pattern (24 bp):
GGAACGGGAAAGAGAAAGAGATAT
Found at i:2229207 original size:13 final size:13
Alignment explanation
Indices: 2229189--2229214 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2229179 ACGATCTAAC
2229189 TCTTCTTCTTCTT
1 TCTTCTTCTTCTT
2229202 TCTTCTTCTTCTT
1 TCTTCTTCTTCTT
2229215 CTTATGGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TCTTCTTCTTCTT
Found at i:2229972 original size:20 final size:20
Alignment explanation
Indices: 2229947--2230004 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
2229937 ATCCTATTTC
2229947 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
2229967 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
2229987 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2230005 GTGAACCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.36
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2232259 original size:27 final size:27
Alignment explanation
Indices: 2232221--2232274 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2232211 TCCCTGGGTA
*
2232221 AGGTCACCTATGCCTTAGCAGTTTAGG
1 AGGTCACCTATGCCTTAGCAATTTAGG
2232248 AGGTCACCTATGCCTTAGCAATTTAGG
1 AGGTCACCTATGCCTTAGCAATTTAGG
2232275 TTAAGGTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (27 bp):
AGGTCACCTATGCCTTAGCAATTTAGG
Found at i:2233028 original size:22 final size:21
Alignment explanation
Indices: 2233001--2233053 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
2232991 CTGACCTTTG
2233001 ACTTTGACCAGAGTTGACTTCA
1 ACTTTGACCAGAGTTGACTT-A
* * *
2233023 ACTTTGACTAGTGTTGACTTG
1 ACTTTGACCAGAGTTGACTTA
2233044 ACTTTGACCA
1 ACTTTGACCA
2233054 AAAAGTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (21 bp):
ACTTTGACCAGAGTTGACTTA
Found at i:2258412 original size:23 final size:23
Alignment explanation
Indices: 2258382--2258434 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
2258372 CGATGTGTAT
* *
2258382 CGATACCCCCTTTGCATGGGTAC
1 CGATACCCCCGTTGAATGGGTAC
*
2258405 CGATACCCTCGTTGAATGGGTAC
1 CGATACCCCCGTTGAATGGGTAC
*
2258428 TGATACC
1 CGATACC
2258435 TCCACATGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (23 bp):
CGATACCCCCGTTGAATGGGTAC
Found at i:2258952 original size:13 final size:14
Alignment explanation
Indices: 2258915--2258951 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
2258905 CATATATTGA
2258915 TTTTTCAAAAATAG
1 TTTTTCAAAAATAG
2258929 -TTTTCAAAAATAG
1 TTTTTCAAAAATAG
2258942 TTTTTCAAAA
1 TTTTTCAAAA
2258952 TTTCTCATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (14 bp):
TTTTTCAAAAATAG
Found at i:2262133 original size:5 final size:5
Alignment explanation
Indices: 2262123--2262326 Score: 408
Period size: 5 Copynumber: 40.8 Consensus size: 5
2262113 ACTATAGTAC
2262123 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
2262173 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
2262223 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
2262273 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
2262323 ATAT
1 ATAT
2262327 ATCAACTATA
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 199 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
ATATG
Found at i:2263474 original size:3 final size:3
Alignment explanation
Indices: 2263468--2263507 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2263458 TCTTCTTTTC
2263468 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2263508 ACATAAGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2267463 original size:22 final size:22
Alignment explanation
Indices: 2267435--2267477 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2267425 AACGGTCAAC
2267435 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
2267457 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
2267478 AGACTGATCA
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:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:2274703 original size:17 final size:17
Alignment explanation
Indices: 2274683--2274721 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
2274673 GAAAGTCAAC
2274683 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
2274700 GGTCAACGGTTGGGTCG
1 GGTCAACGGTCGGGTCG
2274717 GGTCA
1 GGTCA
2274722 GACCGGTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.46, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:2274741 original size:19 final size:19
Alignment explanation
Indices: 2274719--2274780 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
2274709 TTGGGTCGGG
*
2274719 TCAGACCGGTCAAACTGGT
1 TCAGACCGGTCAAACCGGT
2274738 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
2274757 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
2274776 TCAGA
1 TCAGA
2274781 ACCGATTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 1 0.03
19 28 0.74
20 9 0.24
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:2274756 original size:9 final size:9
Alignment explanation
Indices: 2274717--2274784 Score: 55
Period size: 10 Copynumber: 7.1 Consensus size: 9
2274707 GGTTGGGTCG
*
2274717 GGTCAGACC
1 GGTCAAACC
*
2274726 GGTCAAACT
1 GGTCAAACC
*
2274735 GGTTCAGACC
1 GG-TCAAACC
2274745 GGTCAAACC
1 GGTCAAACC
*
2274754 GGTTCGAACC
1 GG-TCAAACC
*
2274764 GGTTGAAACC
1 GG-TCAAACC
2274774 GGTCAGAACC
1 GGTCA-AACC
2274784 G
1 G
2274785 ATTGAAAACC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
9 19 0.40
10 28 0.60
ACGTcount: A:0.26, C:0.28, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2274765 original size:10 final size:10
Alignment explanation
Indices: 2274749--2274807 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
2274739 CAGACCGGTC
2274749 AAACCGGTTCG
1 AAACCGGTT-G
2274760 -AACCGGTTG
1 AAACCGGTTG
*
2274769 AAACCGG-TC
1 AAACCGGTTG
*
2274778 AGAACCGATTG
1 A-AACCGGTTG
2274789 AAAACCGGTT-
1 -AAACCGGTTG
2274799 AAACCGGTT
1 AAACCGGTT
2274808 TCCAGCAGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
9 12 0.30
10 19 0.47
11 8 0.20
12 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (10 bp):
AAACCGGTTG
Found at i:2274774 original size:20 final size:21
Alignment explanation
Indices: 2274749--2274807 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
2274739 CAGACCGGTC
2274749 AAACCGGTTCGAACCGGTTG-
1 AAACCGGTTCGAACCGGTTGA
*
2274769 AAACCGG-TCAGAACCGATTGA
1 AAACCGGTTC-GAACCGGTTGA
*
2274790 AAACCGGTT-AAACCGGTT
1 AAACCGGTTCGAACCGGTT
2274808 TCCAGCAGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.06
20 23 0.70
21 7 0.21
22 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (21 bp):
AAACCGGTTCGAACCGGTTGA
Found at i:2281582 original size:44 final size:44
Alignment explanation
Indices: 2281516--2281601 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
2281506 TCATCAATCA
*
2281516 CATAAGGAGTTGTATAAACATCACCATTTTGCTTAATTCCATTG
1 CATAAGGAGTTGGATAAACATCACCATTTTGCTTAATTCCATTG
* * * * *
2281560 CATAAGGAGTTGGATCAGCATCACCCTTTTGTTTGATTCCAT
1 CATAAGGAGTTGGATAAACATCACCATTTTGCTTAATTCCAT
2281602 CACAGAAGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (44 bp):
CATAAGGAGTTGGATAAACATCACCATTTTGCTTAATTCCATTG
Found at i:2281796 original size:43 final size:43
Alignment explanation
Indices: 2281748--2281840 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 43
2281738 TGTTGTCTCA
* * *
2281748 TCCATCACATAAGAATTTGGATAAGCATCACCATTTTA-TTAAT
1 TCCATCAAATAA-AAGTTGGATAAGAATCACCATTTTATTTAAT
* *
2281791 TCCATCAAATAAAAGTTGGATCAGAATCACCATTTTATTTGAT
1 TCCATCAAATAAAAGTTGGATAAGAATCACCATTTTATTTAAT
2281834 TCCATCA
1 TCCATCA
2281841 TAGAAGAAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 22 0.50
43 22 0.50
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (43 bp):
TCCATCAAATAAAAGTTGGATAAGAATCACCATTTTATTTAAT
Found at i:2281820 original size:42 final size:44
Alignment explanation
Indices: 2281748--2281849 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 44
2281738 TGTTGTCTCA
* * *
2281748 TCCATCACATAAGAATTTGGATAAGCATCACCATTTTA-TTAAT
1 TCCATCAAATAAGAAGTTGGATAAGAATCACCATTTTATTTAAT
* *
2281791 TCCATCAAATAA-AAGTTGGATCAGAATCACCATTTTATTTGAT
1 TCCATCAAATAAGAAGTTGGATAAGAATCACCATTTTATTTAAT
* *
2281834 TCCATCATAGAAGAAG
1 TCCATCAAATAAGAAG
2281850 GTAGATCAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 22 0.44
43 25 0.50
44 3 0.06
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (44 bp):
TCCATCAAATAAGAAGTTGGATAAGAATCACCATTTTATTTAAT
Found at i:2282156 original size:3 final size:3
Alignment explanation
Indices: 2282075--2282137 Score: 74
Period size: 3 Copynumber: 21.3 Consensus size: 3
2282065 ATTTGTCCCT
* * * *
2282075 TTA TTA TCA TTA -CA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2282122 TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA T
2282138 AAATAAGTAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
2 1 0.02
3 48 0.98
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:2283261 original size:15 final size:15
Alignment explanation
Indices: 2283241--2283275 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
2283231 CAGTCCTTTT
2283241 ATTTTTGTAC-TTTAA
1 ATTTTT-TACTTTTAA
2283256 ATTTTTTACTTTTAA
1 ATTTTTTACTTTTAA
2283271 ATTTT
1 ATTTT
2283276 CAACATTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (15 bp):
ATTTTTTACTTTTAA
Found at i:2289721 original size:297 final size:300
Alignment explanation
Indices: 2289163--2289763 Score: 1165
Period size: 297 Copynumber: 2.0 Consensus size: 300
2289153 CTCTGTTCAT
2289163 TTTTGTACTGAATCTCTACTCTTTTTTTGAGGGGAAACCCACTCTAACCTTTGCTTAGATTTACT
1 TTTTGTACTGAATCTCTACTCTTTTTTTGAGGGGAAACCCACTCTAACCTTTGCTTAGATTTACT
2289228 TTTCACAAAAAAAGCATGCAAACTAGAAAAAATGATGTTTAGATTTATTTGATGAGAAAAAACAT
66 TTTCACAAAAAAAGCATGCAAACTAGAAAAAATGATGTTTAGATTTATTTGATGAGAAAAAACAT
2289293 GAGGGTAGAAATCATGTCTAACTAGGATCTATTAAACCATGTTTGGGTAGACAACATGTGAGGAT
131 GAGGGTAGAAATCATGTCTAACTAGGATCTATTAAACCATGTTTGGGTAGACAACATGTGAGGAT
2289358 AGGTTTTTATTTGTTAACAATAGTTCTTACTATTTTATTGATTATCTTATTGATACTAACTTTTT
196 AGGTTTTTATTTGTTAACAATAGTTCTTACTATTTTATTGATTATCTTATTGATACTAACTTTTT
2289423 TTTT-TTTCCGTTCTTTCTTGTATTTGC-TCACCATGACA
261 TTTTATTTCCGTTCTTTCTTGTATTTGCATCACCATGACA
2289461 TTTTGTACTGAATCTCTACTC-TTTTTTGAGGGGAAACCCACTCTAACCTTTGCTTAGATTTACT
1 TTTTGTACTGAATCTCTACTCTTTTTTTGAGGGGAAACCCACTCTAACCTTTGCTTAGATTTACT
2289525 TTTCACAAAAAAAGCATGCAAACTAGAAAAAATGATGTTTAGATTTATTTGATGAGAAAAAACAT
66 TTTCACAAAAAAAGCATGCAAACTAGAAAAAATGATGTTTAGATTTATTTGATGAGAAAAAACAT
2289590 GAGGGTAGAAATCATGTCTAACTAGGATCTATTAAACCATGTTTGGGTAGACAACATGTGAGGAT
131 GAGGGTAGAAATCATGTCTAACTAGGATCTATTAAACCATGTTTGGGTAGACAACATGTGAGGAT
2289655 AGG-TTTTATTTGTTAACAATAGTTCTTACTATTTTATTGATTATCTTATTGATACTAACTTTTT
196 AGGTTTTTATTTGTTAACAATAGTTCTTACTATTTTATTGATTATCTTATTGATACTAAC-TTTT
2289719 TTTTTATTTCCGTTCTTTCTTGTATTTGCATCACCATGACA
260 TTTTTATTTCCGTTCTTTCTTGTATTTGCATCACCATGACA
2289760 TTTT
1 TTTT
2289764 CATCATTATT
Statistics
Matches: 300, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
296 56 0.19
297 185 0.62
298 44 0.15
299 15 0.05
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (300 bp):
TTTTGTACTGAATCTCTACTCTTTTTTTGAGGGGAAACCCACTCTAACCTTTGCTTAGATTTACT
TTTCACAAAAAAAGCATGCAAACTAGAAAAAATGATGTTTAGATTTATTTGATGAGAAAAAACAT
GAGGGTAGAAATCATGTCTAACTAGGATCTATTAAACCATGTTTGGGTAGACAACATGTGAGGAT
AGGTTTTTATTTGTTAACAATAGTTCTTACTATTTTATTGATTATCTTATTGATACTAACTTTTT
TTTTATTTCCGTTCTTTCTTGTATTTGCATCACCATGACA
Found at i:2294929 original size:3 final size:3
Alignment explanation
Indices: 2294921--2294957 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
2294911 TATCTGACCC
* *
2294921 TTA TTA TTA TTA TTA TTA TCA TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2294958 AAATAACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2297974 original size:29 final size:28
Alignment explanation
Indices: 2297932--2298016 Score: 152
Period size: 29 Copynumber: 3.0 Consensus size: 28
2297922 CAGTGACAGC
2297932 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCC-T
2297961 ATAGGTCGCCATGCACGCCCGGCGTCCT
1 ATAGGTCGCCATGCACGCCCGGCGTCCT
2297989 ATAAGGTCGCCATGCACGCCCGGCGTCC
1 AT-AGGTCGCCATGCACGCCCGGCGTCC
2298017 AACATTTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 3 0.05
29 52 0.95
ACGTcount: A:0.15, C:0.39, G:0.28, T:0.18
Consensus pattern (28 bp):
ATAGGTCGCCATGCACGCCCGGCGTCCT
Found at i:2298966 original size:22 final size:22
Alignment explanation
Indices: 2298941--2299017 Score: 84
Period size: 22 Copynumber: 3.3 Consensus size: 22
2298931 AATCATTTAT
*
2298941 TAGTTTAAGTTATATTAAAAAA
1 TAGTTTAAGTTATATTAAAGAA
2298963 TAGTTTATTAGTTGTTATATT-AAGAA
1 TAGTTTA--A---GTTATATTAAAGAA
*
2298989 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
2299011 TAGTTTA
1 TAGTTTA
2299018 TTGGTTGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
21 8 0.17
22 18 0.39
24 2 0.04
26 10 0.22
27 8 0.17
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:2301247 original size:17 final size:17
Alignment explanation
Indices: 2301217--2301327 Score: 69
Period size: 17 Copynumber: 6.1 Consensus size: 17
2301207 AAACCTTAAC
*
2301217 AAATCATTACTAATCATT
1 AAAT-ATTAATAATCATT
*
2301235 AAATATTAATAATAATTT
1 AAATATTAATAATCA-TT
* * *
2301253 CATTATTACTAATCATTACT
1 AAATATTAATAATCA-T--T
*
2301273 AAATCTTAATATCAATCATT
1 AAATATT-A-AT-AATCATT
*
2301293 AAATATTAATAATAATT
1 AAATATTAATAATCATT
* *
2301310 CAATATTACTAATCATT
1 AAATATTAATAATCATT
2301327 A
1 A
2301328 CTAAATCATT
Statistics
Matches: 71, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
17 29 0.41
18 21 0.30
19 1 0.01
20 12 0.17
21 1 0.01
22 2 0.03
23 5 0.07
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTAATAATCATT
Found at i:2301336 original size:11 final size:10
Alignment explanation
Indices: 2301218--2301338 Score: 50
Period size: 10 Copynumber: 12.8 Consensus size: 10
2301208 AACCTTAACA
2301218 AATCATTACT
1 AATCATTACT
2301228 AATCATTA--
1 AATCATTACT
*
2301236 AAT-ATTAAT
1 AATCATTACT
*
2301245 AATAATT--T
1 AATCATTACT
* *
2301253 CATTATTACT
1 AATCATTACT
2301263 AATCATTACT
1 AATCATTACT
*
2301273 AAATC-TTAATAT
1 -AATCATT-A-CT
2301285 CAATCATTA--
1 -AATCATTACT
*
2301294 AAT-ATTAAT
1 AATCATTACT
*
2301303 AATAATT-C-
1 AATCATTACT
2301311 AAT-ATTACT
1 AATCATTACT
2301320 AATCATTACT
1 AATCATTACT
2301330 AAATCATTA
1 -AATCATTA
2301339 TTATAATTTC
Statistics
Matches: 88, Mismatches: 7, Indels: 31
0.70 0.06 0.25
Matches are distributed among these distances:
7 11 0.12
8 16 0.18
9 9 0.10
10 31 0.35
11 13 0.15
12 6 0.07
13 2 0.02
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (10 bp):
AATCATTACT
Found at i:2301585 original size:17 final size:17
Alignment explanation
Indices: 2301534--2301591 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
2301524 AATATAAATA
*
2301534 AAACA-AATATTTTTTA
1 AAACACAATATTTTTTT
* *
2301550 AAACAACACTAAATATTTTT
1 AAAC-ACA--ATATTTTTTT
2301570 AAACACAATATTTTTTT
1 AAACACAATATTTTTTT
2301587 AAACA
1 AAACA
2301592 AAATTATCTC
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.12
17 14 0.42
18 1 0.03
19 3 0.09
20 11 0.33
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
AAACACAATATTTTTTT
Found at i:2301734 original size:17 final size:17
Alignment explanation
Indices: 2301708--2301742 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2301698 ACGTATAGCC
2301708 TTCCTCCTTTCTTTCTT
1 TTCCTCCTTTCTTTCTT
* *
2301725 TTCCTTCTTTGTTTCTT
1 TTCCTCCTTTCTTTCTT
2301742 T
1 T
2301743 CTTCGAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.69
Consensus pattern (17 bp):
TTCCTCCTTTCTTTCTT
Found at i:2302101 original size:21 final size:21
Alignment explanation
Indices: 2302027--2302102 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
2302017 AAACTAATTA
**
2302027 ACTAATTAACTAATTTTTTTAT
1 ACTAATTAACTAA-TAATTTAT
* *
2302049 A-TAATATAA-TATATAACTTAA
1 ACTAAT-TAACTA-ATAATTTAT
**
2302070 ACTAACAAACTAATAATTTAT
1 ACTAATTAACTAATAATTTAT
2302091 ACTAATTAACTA
1 ACTAATTAACTA
2302103 GATTTTAGTT
Statistics
Matches: 40, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
21 30 0.75
22 10 0.25
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (21 bp):
ACTAATTAACTAATAATTTAT
Found at i:2302489 original size:21 final size:21
Alignment explanation
Indices: 2302464--2302503 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2302454 ACGCTGCAAT
**
2302464 CATGCAGCTATGGATGCAACG
1 CATGCAGCTACAGATGCAACG
2302485 CATGCAGCTACAGATGCAA
1 CATGCAGCTACAGATGCAA
2302504 GAATATCCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (21 bp):
CATGCAGCTACAGATGCAACG
Found at i:2302705 original size:29 final size:29
Alignment explanation
Indices: 2302663--2302804 Score: 230
Period size: 29 Copynumber: 4.9 Consensus size: 29
2302653 CCACAGCTTG
* * *
2302663 GTCGCCGGGACTCCATGACAACTTACCAT
1 GTCGCCGGGACTCCATGGCGACCTACCAT
* *
2302692 GTCGTCGAGACTCCATGGCGACCTACCAT
1 GTCGCCGGGACTCCATGGCGACCTACCAT
2302721 GTCGCCGGGACTCCATGGCGACCTACCAT
1 GTCGCCGGGACTCCATGGCGACCTACCAT
*
2302750 GTAGCCGGGACTCCATGGCGACCTACCAT
1 GTCGCCGGGACTCCATGGCGACCTACCAT
2302779 GTCGCCGGGACTCCATGGCGACCTAC
1 GTCGCCGGGACTCCATGGCGACCTAC
2302805 GATCTCCCCA
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 104 1.00
ACGTcount: A:0.20, C:0.36, G:0.26, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGACTCCATGGCGACCTACCAT
Found at i:2302869 original size:36 final size:36
Alignment explanation
Indices: 2302819--2302891 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
2302809 TCCCCAATCT
2302819 CCCCATGCAAGAACCGATCCTTGGTCGCCCCGAGTG
1 CCCCATGCAAGAACCGATCCTTGGTCGCCCCGAGTG
*
2302855 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
1 CCCCATGCAAGAACCGATCCTTGGTCGCCCCGAGTG
2302891 C
1 C
2302892 ATGGCACGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.18, C:0.40, G:0.25, T:0.18
Consensus pattern (36 bp):
CCCCATGCAAGAACCGATCCTTGGTCGCCCCGAGTG
Found at i:2302953 original size:29 final size:29
Alignment explanation
Indices: 2302934--2303015 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
2302924 TGGTCGCCCC
2302934 GAGTGCATGGCGACCTCCTTGGTCGTTGG
1 GAGTGCATGGCGACCTCCTTGGTCGTTGG
* *
2302963 GCGTGCATGGCGACCTCTTTGGTCGTTGG
1 GAGTGCATGGCGACCTCCTTGGTCGTTGG
* *
2302992 GTGTGCATGGCGACCTCTTTGGTC
1 GAGTGCATGGCGACCTCCTTGGTC
2303016 ACTGTACAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.09, C:0.24, G:0.37, T:0.30
Consensus pattern (29 bp):
GAGTGCATGGCGACCTCCTTGGTCGTTGG
Found at i:2303436 original size:92 final size:92
Alignment explanation
Indices: 2303279--2303462 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
2303269 TTAATAAATT
2303279 TTAGGACATCGATCATCGTAATGAGATTGAGATTGCATCTAGAGATTGTAAATCACATTGATTTT
1 TTAGGACATCGATCATCGTAATGAGATTGAGATTGCATCTAGAGATTGTAAATCACATTGATTTT
2303344 ATCAGTGTAGATATATTTTTGCTAAAA
66 ATCAGTGTAGATATATTTTTGCTAAAA
2303371 TTAGGACATCGATCATCGTAATGAGATTGAGATTGCATCTAGAGATTGTAAATCACATTGATTTT
1 TTAGGACATCGATCATCGTAATGAGATTGAGATTGCATCTAGAGATTGTAAATCACATTGATTTT
2303436 ATCAGTGTAGATATATTTTTGCTAAAA
66 ATCAGTGTAGATATATTTTTGCTAAAA
2303463 CTCCTAGAAT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (92 bp):
TTAGGACATCGATCATCGTAATGAGATTGAGATTGCATCTAGAGATTGTAAATCACATTGATTTT
ATCAGTGTAGATATATTTTTGCTAAAA
Found at i:2304686 original size:49 final size:49
Alignment explanation
Indices: 2304614--2304784 Score: 270
Period size: 49 Copynumber: 3.5 Consensus size: 49
2304604 ATCGAGGGTA
* *
2304614 CATTTAGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGATG
1 CATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTG
*
2304663 CATTTCGGCGTAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTG
1 CATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTG
* * *
2304712 CATTTCTGCATAAAAGATACCACTAATGAAAGTTAAATGCATAACGGTG
1 CATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTG
* *
2304761 CATTTCGACATAAAAGGTGTCACT
1 CATTTCGGCATAAAAGGTGCCACT
2304785 CATGGTATTA
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 110 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (49 bp):
CATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTG
Found at i:2305526 original size:83 final size:83
Alignment explanation
Indices: 2305387--2305552 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
2305377 TGACACCAAT
2305387 GACTTGTGTACGGAAACGTATACGGGAAATGAGTGTTATATTTATTGGTATCAGAGCTACAGGTT
1 GACTTGTGTACGGAAACGTATACGGGAAATGAGTGTTATATTTATTGGTATCAGAGCTACAGGTT
2305452 TAGCCGATTCTCGGTCGA
66 TAGCCGATTCTCGGTCGA
2305470 GACTTGTGTACGGAAACGTATACGGGAAATGAGTGTTATATTTATTGGTATCAGAGCTACAGGTT
1 GACTTGTGTACGGAAACGTATACGGGAAATGAGTGTTATATTTATTGGTATCAGAGCTACAGGTT
2305535 TAGCCGATTCTCGGTCGA
66 TAGCCGATTCTCGGTCGA
2305553 AATTGGGTTT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (83 bp):
GACTTGTGTACGGAAACGTATACGGGAAATGAGTGTTATATTTATTGGTATCAGAGCTACAGGTT
TAGCCGATTCTCGGTCGA
Found at i:2315376 original size:25 final size:25
Alignment explanation
Indices: 2315348--2315398 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2315338 CTTCTAAATG
2315348 TTAGCTTCACCGCTAACTAAGTTGT
1 TTAGCTTCACCGCTAACTAAGTTGT
2315373 TTAGCTTCACCGCTAACTAAGTTGT
1 TTAGCTTCACCGCTAACTAAGTTGT
2315398 T
1 T
2315399 ATGGAAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (25 bp):
TTAGCTTCACCGCTAACTAAGTTGT
Found at i:2317749 original size:22 final size:22
Alignment explanation
Indices: 2317724--2317771 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
2317714 GGTTTAAGGA
2317724 AAGTTCAAGGATGCTTAAAACT
1 AAGTTCAAGGATGCTTAAAACT
2317746 AAGTTCAAGGATGCTTAAAACT
1 AAGTTCAAGGATGCTTAAAACT
2317768 AAGT
1 AAGT
2317772 GATTAGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (22 bp):
AAGTTCAAGGATGCTTAAAACT
Found at i:2318595 original size:14 final size:14
Alignment explanation
Indices: 2318576--2318614 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
2318566 AATAAGATCT
2318576 ATAAATTTTAATTC
1 ATAAATTTTAATTC
2318590 ATAAATTTTAATTC
1 ATAAATTTTAATTC
2318604 ATAAATTTTAA
1 ATAAATTTTAA
2318615 AATAACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
ATAAATTTTAATTC
Found at i:2321975 original size:28 final size:28
Alignment explanation
Indices: 2321935--2321994 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
2321925 TTTTCACCCT
* *
2321935 AAACCCGACCCGAATATCACACTTAAAA
1 AAACCCAACCCGAATATCAAACTTAAAA
2321963 AAACCCAACCCGAATATCAAACTTAAAA
1 AAACCCAACCCGAATATCAAACTTAAAA
2321991 AAAC
1 AAAC
2321995 TCGACCTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.52, C:0.30, G:0.05, T:0.13
Consensus pattern (28 bp):
AAACCCAACCCGAATATCAAACTTAAAA
Found at i:2322098 original size:33 final size:32
Alignment explanation
Indices: 2322052--2322130 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 32
2322042 ATTTTTTGAA
* * *
2322052 AAAAATCCGACCCAACCTGAATATCACACTTAT
1 AAAAACCCGACCCAACCCGAATATCAAACTT-T
*
2322085 AAAAACCCAACCCAACCCGAATATCAAACTTT
1 AAAAACCCGACCCAACCCGAATATCAAACTTT
2322117 AAAAAGCCCGACCC
1 AAAAA-CCCGACCC
2322131 GAACTCGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 6 0.15
33 34 0.85
ACGTcount: A:0.44, C:0.34, G:0.06, T:0.15
Consensus pattern (32 bp):
AAAAACCCGACCCAACCCGAATATCAAACTTT
Found at i:2329421 original size:29 final size:29
Alignment explanation
Indices: 2329370--2329542 Score: 242
Period size: 29 Copynumber: 6.0 Consensus size: 29
2329360 ATAGCAATGT
* * *
2329370 TTTTAAAAATATTTA-CACCAATATCA-CT
1 TTTTAAAAATAATTACCA-AAATATCACCG
2329398 TCTTTAAAAATAATTACCAAAATATCACCG
1 T-TTTAAAAATAATTACCAAAATATCACCG
*
2329428 TTTTAAAAATAATTACCAAAATATCATCG
1 TTTTAAAAATAATTACCAAAATATCACCG
* *
2329457 TTTTAAAAATAATTACTAAAATATAACCG
1 TTTTAAAAATAATTACCAAAATATCACCG
*
2329486 TTTTAAAAATAATTATCAAAATATCACCG
1 TTTTAAAAATAATTACCAAAATATCACCG
*
2329515 TTTTAAAAATAATTCCCAAAATATCACC
1 TTTTAAAAATAATTACCAAAATATCACC
2329543 AGGTCGGGTC
Statistics
Matches: 130, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
28 1 0.01
29 125 0.96
30 4 0.03
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.34
Consensus pattern (29 bp):
TTTTAAAAATAATTACCAAAATATCACCG
Found at i:2336727 original size:85 final size:85
Alignment explanation
Indices: 2336637--2336830 Score: 207
Period size: 85 Copynumber: 2.3 Consensus size: 85
2336627 ATTTTTTATT
** *
2336637 TTTATAATTGAGATTTC-TAATTTT-T-TATCTAACTTTATACATTAATAATTGAGGAC-CCTAA
1 TTTATAATTGAG-GCTCATAATTTTCTCTATCTAACTTTATACATTAATAATTAAGG-CTCCTAA
*
2336698 TTCTTTTAAATTTCAATTTTTACC
64 -TCTTTT-AATCTCAATTTTTACC
* * * * *
2336722 TTTATAATTGAGGCTCATGATTTTCTCTATCTTACTTTCTACTTTTATAATTAAGGCTCCTAATC
1 TTTATAATTGAGGCTCATAATTTTCTCTATCTAACTTTATACATTAATAATTAAGGCTCCTAATC
*
2336787 TTTTAATCTCATTTTTTACC
66 TTTTAATCTCAATTTTTACC
* * *
2336807 TTTATAATTTAGGCCCCTAATTTT
1 TTTATAATTGAGGCTCATAATTTT
2336831 TTACCTTTAT
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
84 2 0.02
85 52 0.57
86 8 0.09
87 29 0.32
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (85 bp):
TTTATAATTGAGGCTCATAATTTTCTCTATCTAACTTTATACATTAATAATTAAGGCTCCTAATC
TTTTAATCTCAATTTTTACC
Found at i:2336826 original size:42 final size:43
Alignment explanation
Indices: 2336681--2336833 Score: 130
Period size: 42 Copynumber: 3.6 Consensus size: 43
2336671 TTATACATTA
* *
2336681 ATAATTGAGGACCCTAATTCTTTTAAATTTCAATTTTTACCTTT
1 ATAATTGAGGCCCCTAA-TCTTTTAAATCTCAATTTTTACCTTT
* * * ** * * * *
2336725 ATAATTGAGGCTCATGAT-TTTCTCTATCTTACTTTCTACTTTT
1 ATAATTGAGGCCCCTAATCTTT-TAAATCTCAATTTTTACCTTT
* * *
2336768 ATAATTAAGGCTCCTAATCTTTT-AATCTCATTTTTTACCTTT
1 ATAATTGAGGCCCCTAATCTTTTAAATCTCAATTTTTACCTTT
* *
2336810 ATAATTTAGGCCCCTAATTTTTTA
1 ATAATTGAGGCCCCTAATCTTTTA
2336834 CCTTTATAAT
Statistics
Matches: 84, Mismatches: 22, Indels: 7
0.74 0.19 0.06
Matches are distributed among these distances:
42 37 0.44
43 31 0.37
44 16 0.19
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (43 bp):
ATAATTGAGGCCCCTAATCTTTTAAATCTCAATTTTTACCTTT
Found at i:2336829 original size:29 final size:29
Alignment explanation
Indices: 2336797--2336861 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
2336787 TTTTAATCTC
2336797 ATTTTTTACCTTTATAATTTAGGCCCCTA
1 ATTTTTTACCTTTATAATTTAGGCCCCTA
* *
2336826 ATTTTTTACCTTTATAATTTATGCCCTTA
1 ATTTTTTACCTTTATAATTTAGGCCCCTA
2336855 ATTTTTT
1 ATTTTTT
2336862 TCAACATCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.23, C:0.17, G:0.05, T:0.55
Consensus pattern (29 bp):
ATTTTTTACCTTTATAATTTAGGCCCCTA
Found at i:2336877 original size:44 final size:44
Alignment explanation
Indices: 2336828--2336934 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
2336818 GGCCCCTAAT
* * *
2336828 TTTTTACCTTTATAATTTATGCCCTTAATTTTTTTCAACATCA-C
1 TTTTTACCTTTATAATTGAAGCCCTTAATATTTTT-AACATCACC
* *
2336872 TTTTTACCTTTATAATTGAAGCTCTTAATATTTTTAATATCACC
1 TTTTTACCTTTATAATTGAAGCCCTTAATATTTTTAACATCACC
*
2336916 TTTTTACCTTTACAATTGA
1 TTTTTACCTTTATAATTGA
2336935 GGTTCGTAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 6 0.11
44 50 0.89
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (44 bp):
TTTTTACCTTTATAATTGAAGCCCTTAATATTTTTAACATCACC
Found at i:2340552 original size:118 final size:117
Alignment explanation
Indices: 2340326--2340552 Score: 339
Period size: 117 Copynumber: 1.9 Consensus size: 117
2340316 GAAACAAAGA
* *
2340326 TTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATTGGATGAGTTCTTCTCATTAAAACC
1 TTGAACAAGTTATTCTCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTCATTAAAACC
*
2340391 CTTCCATTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCGGGCAAATG
66 CTTCCATTGGAAATGTTGATCCACCTCATTATGTGATGGAATCGGGCAAATG
* * * **
2340443 TTGAACAAGTTATTCTCATTATGTACTTATTT-TTCTTCATCGGATGAGTTCTTCTCATTGTGAA
1 TTGAACAAGTTATTCTCATTATGAACTT-TTTCTCCCTCATCGGATGAGTTCTTCTCATT-AAAA
* *
2340507 CCCTTCCATTGGAAATGTTGATCCATCTCCTTATGTGATGGAATCG
64 CCCTTCCATTGGAAATGTTGATCCACCTCATTATGTGATGGAATCG
2340553 AGTGAAATGC
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
117 50 0.51
118 48 0.49
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (117 bp):
TTGAACAAGTTATTCTCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTCATTAAAACC
CTTCCATTGGAAATGTTGATCCACCTCATTATGTGATGGAATCGGGCAAATG
Found at i:2340617 original size:44 final size:44
Alignment explanation
Indices: 2340525--2340620 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 44
2340515 TTGGAAATGT
* * * * *
2340525 TGATCCATCTCCTTATGTGATGGAATCGAGTGAAATGCTGATAT
1 TGATCCAACTCCTTATATGATGGAATCGAGTCAAATGATGATAC
* * *
2340569 TGATCCAACTTCTTATATGATGGAATCGAG-CAAAGTGATGGTGC
1 TGATCCAACTCCTTATATGATGGAATCGAGTCAAA-TGATGATAC
2340613 TGATCCAA
1 TGATCCAA
2340621 GAGGTTTAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 3 0.07
44 40 0.93
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (44 bp):
TGATCCAACTCCTTATATGATGGAATCGAGTCAAATGATGATAC
Found at i:2341924 original size:54 final size:52
Alignment explanation
Indices: 2341642--2342574 Score: 838
Period size: 54 Copynumber: 17.1 Consensus size: 52
2341632 ATTTACATTT
* * *
2341642 AACATCAAGAAACCCCTAAAAAATTAGGCTTAGTTTCCTTAAAAATTCATTTGAA
1 AACATCAAGAAA-CCCT-GAAAATTAGGCTTAGCTT-CTTTAAAATTCATTTGAA
* * * * *
2341697 GACATCAAGAAACCCTTGAAAATCAGGATTAACTCCTTTCTAAAATTCATTTGAA
1 AACATCAAGAAACCC-TGAAAATTAGGCTTAGCTTC-TT-TAAAATTCATTTGAA
* * *
2341752 GACATCAAGAAACCCTTGGAAATCAGGCTTAGC-TCATTTCCAAAAATT-ATTTTGAA
1 AACATCAAGAAACCC-TGAAAATTAGGCTTAGCTTC-TTT---AAAATTCA-TTTGAA
* * * * *
2341808 GACATCAAGAAACCCCTAAAAATAAGACTTAGC-TCCTTAGAAATTCATTTGAA
1 AACATCAAGAAA-CCCTGAAAATTAGGCTTAGCTTCTTTA-AAATTCATTTGAA
* *
2341861 AACATCAAGAAACCGCT-AAAAGTTAGGCTTACCTTCTTTAAAAGTTCATTTAAA
1 AACATCAAGAAACC-CTGAAAA-TTAGGCTTAGCTTCTTTAAAA-TTCATTTGAA
* * * *
2341915 AACATCAAGAAACTCTTGAAAATCAAGCTTAGCTCCTTTAAAAATTCATTTGAA
1 AACATCAAGAAAC-CCTGAAAATTAGGCTTAGCTTCTTT-AAAATTCATTTGAA
*
2341969 AACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAA
1 AACATCAAGAAA-CCCTGAAAATTAGGCTTAGCTTCTTT-AAAATTCATTTGAA
* * *
2342023 AACATCAAGAAATCCCTAAAAATTATGCTTAGCTTCTTTCAAAATTCATTTAAA
1 AACATCAAGAAA-CCCTGAAAATTAGGCTTAGCTTCTTT-AAAATTCATTTGAA
* *
2342077 AACATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAATTCATTTGAA
1 AACATCAAGAAA-CCCTGAAAATTAGGCTTAGCTTCTTTAAAATTCATTTGAA
* * * *
2342130 AACATCAAGAAACGCTTGAAAATTAGGCATATCTTCTTTCAAAATTCATTTAAA
1 AACATCAAGAAAC-CCTGAAAATTAGGCTTAGCTTCTTT-AAAATTCATTTGAA
* * * *
2342184 AACATAAAAAAAAACCCTGAAAATCAGGCTTAGC-TCATTTAAAAATTAATTTGAA
1 AACAT--CAAGAAACCCTGAAAATTAGGCTTAGCTTC-TTT-AAAATTCATTTGAA
* *
2342239 AACATCAAGAAACTCCTAAAGAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAG
1 AACATCAAGAAAC-CCTGAA-AATTAGGCTTAGCTTCTTT-AAAATTCATTTGAA
* * * *
2342294 AACATCAAGAAATCCCTAAAAATCAGGCTTAGCTCCTTTAAAAATTAATTTGAA
1 AACATCAAGAAA-CCCTGAAAATTAGGCTTAGCTTCTTT-AAAATTCATTTGAA
* * *
2342348 AACATCAAAAAAACCCCT-AAAAATAGGCTTAGTTTCTTTCAAAATTCATTT-AA
1 AACATC-AAGAAA-CCCTGAAAATTAGGCTTAGCTTCTTT-AAAATTCATTTGAA
* * * * *
2342401 AACAAT-ACGGAACCCTTGAAAATTAGGCTTAACTCCTTTAAAAAAATCATTTGAA
1 AAC-ATCAAGAAACCC-TGAAAATTAGGCTTAGCTTCTTT--AAAATTCATTTGAA
* * *
2342456 AACATCAAGAAGCCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTAAA
1 AACATCAAGAA-ACCCTGAAAATTAGGCTTAGCTTCTTT-AAAATTCATTTGAA
* * *
2342510 AAAATCAAGAAACCCTTAAAAAAATTAGGCTTAGCTTTTTTTTTCAAAATTCATTTGAA
1 AACATCAAGAAACCC-T--GAAAATTAGGCTTAGC---TTCTTT-AAAATTCATTTGAA
*
2342569 GACATC
1 AACATC
2342575 TTATTGTTTG
Statistics
Matches: 733, Mismatches: 104, Indels: 78
0.80 0.11 0.09
Matches are distributed among these distances:
51 3 0.00
52 12 0.02
53 113 0.15
54 326 0.44
55 186 0.25
56 67 0.09
57 3 0.00
59 23 0.03
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (52 bp):
AACATCAAGAAACCCTGAAAATTAGGCTTAGCTTCTTTAAAATTCATTTGAA
Found at i:2341997 original size:108 final size:108
Alignment explanation
Indices: 2341642--2342574 Score: 1011
Period size: 108 Copynumber: 8.6 Consensus size: 108
2341632 ATTTACATTT
* * *
2341642 AACATCAAGAAACCCCTAAAAAATTAGGCTTAGTTTCCTTAAAAATTCATTTGAAGACATCAAGA
1 AACATCAAGAAACCCCT-AAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGA
* * * * * *
2341707 AACCCTTGAAAATCAGGATTAACTCCTTTCTAAAATTCATTTGAA
65 AACCCCTAAAAATTAGGCTTAGCTTCTTTC-AAAATTCATTTGAA
* * ** * *
2341752 GACATCAAGAAACCCTTGGAAATCAGGCTTAGC-TCATTTCCAAAAATT-ATTTTGAAGACATCA
1 AACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTC-TTT--AAAAATTCA-TTTGAAAACATCA
* * *
2341815 AGAAACCCCTAAAAATAAGACTTAGC-TCCTT-AGAAATTCATTTGAA
62 AGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCA-AAATTCATTTGAA
* * * * *
2341861 AACATCAAGAAACCGCTAAAAGTTAGGCTTACCTTCTTTAAAAGTTCATTTAAAAACATCAAGAA
1 AACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * * * * * *
2341926 ACTCTTGAAAATCAAGCTTAGCTCCTTTAAAAATTCATTTGAA
66 ACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAA
2341969 AACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
1 AACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * *
2342034 ATCCCTAAAAATTATGCTTAGCTTCTTTCAAAATTCATTTAAA
66 ACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAA
* * *
2342077 AACATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTT-AAAATTCATTTGAAAACATCAAGAA
1 AACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * * * * *
2342141 ACGCTTGAAAATTAGGCATATCTTCTTTCAAAATTCATTTAAA
66 ACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAA
* * * * * *
2342184 AACATAAAAAAAAACCCTGAAAATCAGGCTTAGC-TCATTTAAAAATTAATTTGAAAACATCAAG
1 AACAT-CAAGAAACCCCTAAAAATTAGGCTTAGCTTC-TTTAAAAATTCATTTGAAAACATCAAG
* *
2342248 AAACTCCTAAAGAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAG
64 AAACCCCTAAA-AATTAGGCTTAGCTTCTTTCAAAATTCATTTGAA
* * * * *
2342294 AACATCAAGAAATCCCTAAAAATCAGGCTTAGCTCCTTTAAAAATTAATTTGAAAACATCAAAAA
1 AACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATC-AAGA
*
2342359 AACCCCTAAAAA-TAGGCTTAGTTTCTTTCAAAATTCATTT-AA
65 AACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAA
* * * * * * *
2342401 AACAAT-ACGGAACCCTTGAAAATTAGGCTTAACTCCTTTAAAAAAATCATTTGAAAACATCAAG
1 AAC-ATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTT-AAAAATTCATTTGAAAACATCAAG
* *
2342465 AAGCCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTAAA
64 AAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAA
* * * * *
2342510 AAAATCAAGAAACCCTTAAAAAAATTAGGCTTAGCTTTTTTTTTCAAAATTCATTTGAAGACATC
1 AACATCAAGAAACCCCT--AAAAATTAGGCTTAGC---TTCTTTAAAAATTCATTTGAAAACATC
2342575 TTATTGTTTG
Statistics
Matches: 697, Mismatches: 101, Indels: 47
0.82 0.12 0.06
Matches are distributed among these distances:
107 148 0.21
108 255 0.37
109 149 0.21
110 69 0.10
111 54 0.08
113 18 0.03
114 4 0.01
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (108 bp):
AACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
ACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAA
Found at i:2342453 original size:433 final size:434
Alignment explanation
Indices: 2341616--2342543 Score: 1178
Period size: 433 Copynumber: 2.1 Consensus size: 434
2341606 AGCAGACTCT
* * *
2341616 GCTTC-TTCAAAAATTCATTTACATTTAACATCAAGAAACCCCTAAAAAATTAGGCTTAGTTTCC
1 GCTTCTTTC-AAAATTCATTTA-A--AAACATCAAGAAACCCCTAAAAAATCAGGCTTAGTCTCC
*
2341680 TTAAAAATTCATTTGAAGACATCAAGAAACCCTTGAAAATCAGGATTAACTCCTTTCTAAAATTC
62 TTAAAAATTCATTTGAAAACATCAAGAAACCCTTGAAAATCAGGATTAACTCCTTTCTAAAATTC
* * * * * * *
2341745 ATTTGAAGACATCAAGAAACCCTTGGAAATCAGGCTTAGCTCATTTCCAAAAATTATTTTGAAGA
127 ATTTAAAAACATAAAAAAACCCTTGAAAATCAGGCTTAGCTCATTT-CAAAAATTAATTTGAAAA
2341810 CATCAAGAAACCCCTAAAAATAAGACTTAGCTCCTTAGAAATTCATTTGAAAACATCAAGAAACC
191 CATCAAGAAACCCCTAAAAATAAGACTTAGCTCCTTAGAAATTCATTTGAAAACATCAAGAAACC
* * * * * * * * *
2341875 GCTAAAAGTTAGGCTTACCTTCTTTAAAAGTTCATTTAAAAACATCAAGAAACTCTTGAAAATCA
256 GCTAAAAATCAGGCTTACCTCCTTTAAAAATTAATTTAAAAACATCAAAAAACCCCTAAAAATCA
* *
2341940 AGCTTAGCTCCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTC
321 AGCTTAGCTCCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAACTCC
* * *
2342005 TTTAAAAATTCATTTGAAAACATCAAGAAATCCCTAAAAATTATGCTTA
386 TTTAAAAAATCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTA
* *
2342054 GCTTCTTTCAAAATTCATTTAAAAACATCAAGAAACCCCT-GAAAATCAGGCTTAG-CTCCTTTA
1 GCTTCTTTCAAAATTCATTTAAAAACATCAAGAAACCCCTAAAAAATCAGGCTTAGTCTCCTTAA
* * * *
2342117 AAATTCATTTGAAAACATCAAGAAACGCTTGAAAATTAGGCA-TATCTTCTTTC-AAAATTCATT
66 AAATTCATTTGAAAACATCAAGAAACCCTTGAAAATCAGG-ATTAACTCCTTTCTAAAATTCATT
2342180 TAAAAACATAAAAAAAAACCC-TGAAAATCAGGCTTAGCTCATTT-AAAAATTAATTTGAAAACA
130 TAAAAACAT--AAAAAAACCCTTGAAAATCAGGCTTAGCTCATTTCAAAAATTAATTTGAAAACA
* * * * *
2342243 TCAAGAAACTCCTAAAGAATTAGGCTTAGCTTCTTTCA-AAATTCATTTGAGAACATCAAGAAAT
193 TCAAGAAACCCCTAAA-AATAAGACTTAGC-TCCTT-AGAAATTCATTTGAAAACATCAAGAAA-
* *
2342307 CC-CTAAAAATCAGGCTTAGCTCCTTTAAAAATTAATTTGAAAACATCAAAAAAACCCCTAAAAA
254 CCGCTAAAAATCAGGCTTACCTCCTTTAAAAATTAATTTAAAAACATC-AAAAAACCCCTAAAAA
* * * * * * * *
2342371 T-AGGCTTAGTTTCTTTCAAAATTCATTT-AAAACAAT-ACGGAACCCTTGAAAATTAGGCTTAA
318 TCAAGCTTAGCTCCTTTAAAAATTCATTTGAAAAC-ATCAAGAAACCCCTAAAAATTAGGCTTAA
*
2342433 CTCCTTTAAAAAAATCATTTGAAAACATCAAGAAGCCCCTAAAAATTAGGCTTA
382 CTCCTTT-AAAAAATCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTA
* * *
2342487 GCTTCTTTCAAAATTCATTTAAAAAAATCAAGAAACCCTTAAAAAAATTAGGCTTAG
1 GCTTCTTTCAAAATTCATTTAAAAACATCAAGAAACCCCT-AAAAAATCAGGCTTAG
2342544 CTTTTTTTTT
Statistics
Matches: 426, Mismatches: 51, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
431 32 0.08
432 60 0.14
433 245 0.58
434 38 0.09
435 30 0.07
437 1 0.00
438 17 0.04
439 3 0.01
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (434 bp):
GCTTCTTTCAAAATTCATTTAAAAACATCAAGAAACCCCTAAAAAATCAGGCTTAGTCTCCTTAA
AAATTCATTTGAAAACATCAAGAAACCCTTGAAAATCAGGATTAACTCCTTTCTAAAATTCATTT
AAAAACATAAAAAAACCCTTGAAAATCAGGCTTAGCTCATTTCAAAAATTAATTTGAAAACATCA
AGAAACCCCTAAAAATAAGACTTAGCTCCTTAGAAATTCATTTGAAAACATCAAGAAACCGCTAA
AAATCAGGCTTACCTCCTTTAAAAATTAATTTAAAAACATCAAAAAACCCCTAAAAATCAAGCTT
AGCTCCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAACTCCTTTAA
AAAATCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTA
Found at i:2344702 original size:22 final size:21
Alignment explanation
Indices: 2344658--2344725 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
2344648 AATTACTTTA
* *
2344658 TTTTCTCTCCCTTTTTTTGCTT
1 TTTTCTCTCTCTTTCTTT-CTT
2344680 TTTTCTCTCTCTCTTCTTTCTT
1 TTTTCTCTCTCT-TTCTTTCTT
*
2344702 TCTTT-TCTCT-TTTCTCTCTT
1 T-TTTCTCTCTCTTTCTTTCTT
2344722 TTTT
1 TTTT
2344726 ATTTTTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 3 0.07
20 9 0.22
21 1 0.02
22 20 0.49
23 8 0.20
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (21 bp):
TTTTCTCTCTCTTTCTTTCTT
Found at i:2344721 original size:24 final size:23
Alignment explanation
Indices: 2344654--2344730 Score: 63
Period size: 24 Copynumber: 3.3 Consensus size: 23
2344644 TTTTAATTAC
2344654 TTTATTTTCTCTC-C-CTT-TTT
1 TTTATTTTCTCTCTCTCTTCTTT
*
2344674 TTGCTTTTTTCTCTCTCTCTTCTTT
1 TT--TATTTTCTCTCTCTCTTCTTT
* *
2344699 CTTTCTTTTCTCT-TTTCTCTCTTT
1 -TTTATTTTCTCTCTCTCT-TCTTT
2344723 TTTATTTT
1 TTTATTTT
2344731 TTATTTTTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
20 2 0.04
22 10 0.22
23 12 0.26
24 17 0.37
25 3 0.07
26 2 0.04
ACGTcount: A:0.03, C:0.25, G:0.01, T:0.71
Consensus pattern (23 bp):
TTTATTTTCTCTCTCTCTTCTTT
Found at i:2348180 original size:29 final size:29
Alignment explanation
Indices: 2348137--2348211 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
2348127 AGCGAAAGCG
2348137 AGGACCAAATTAAGAATTCACCTAATTTA
1 AGGACCAAATTAAGAATTCACCTAATTTA
* *
2348166 CGGACCAAATTAAGAATTCGCCTAATTTA
1 AGGACCAAATTAAGAATTCACCTAATTTA
*
2348195 AGGACTAAATTAAGAAT
1 AGGACCAAATTAAGAAT
2348212 AAAAGTAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (29 bp):
AGGACCAAATTAAGAATTCACCTAATTTA
Found at i:2348560 original size:28 final size:29
Alignment explanation
Indices: 2348486--2348560 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 29
2348476 GACTGAAATG
* *
2348486 TAAAT-ACTGAAAAGTAAATGCATAAATTA
1 TAAATAACAGAAAA-TAAAGGCATAAATTA
* *
2348515 -AAATAAAAGAAATTTAAAGGCA-AAATTA
1 TAAATAACAGAAA-ATAAAGGCATAAATTA
*
2348543 TAAATAACGGAAAATAAA
1 TAAATAACAGAAAATAAA
2348561 TTAATTGAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
28 14 0.39
29 22 0.61
ACGTcount: A:0.61, C:0.05, G:0.11, T:0.23
Consensus pattern (29 bp):
TAAATAACAGAAAATAAAGGCATAAATTA
Found at i:2349341 original size:22 final size:22
Alignment explanation
Indices: 2349313--2349356 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2349303 CCCCAAACTC
*
2349313 CGACTGGGAAGGCAACTTAAGG
1 CGACTGGGAAGACAACTTAAGG
*
2349335 CGACTGGGAAGACGACTTAAGG
1 CGACTGGGAAGACAACTTAAGG
2349357 TAATAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.36, T:0.14
Consensus pattern (22 bp):
CGACTGGGAAGACAACTTAAGG
Found at i:2354406 original size:65 final size:64
Alignment explanation
Indices: 2354273--2354433 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
2354263 GTGCACTAAG
* *
2354273 TGTGCATCGATTCATAAAATGCATTCGATG-TTTCAAACAAGCCCGAGTGCATCGATGCATGGCT
1 TGTGCATCGATGCAT-AAATGCATTCGATGTTTTCAAACAAACCCGAGTGCATCGATGCATGGCT
* *
2354337 TGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAA-AAACCTGAGTGCATCGATGCATGG-
1 TGTGCATCGATGCAT-AAATGCATTCGATGTTTTCA-AACAAACCCGAGTGCATCGATGCATGGC
2354400 T
64 T
2354401 ATGTGCATCGATGCATATAATGCATTCGATGTT
1 -TGTGCATCGATGCATA-AATGCATTCGATGTT
2354434 CAATTTATTC
Statistics
Matches: 87, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
64 29 0.33
65 56 0.64
66 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.32
Consensus pattern (64 bp):
TGTGCATCGATGCATAAATGCATTCGATGTTTTCAAACAAACCCGAGTGCATCGATGCATGGCT
Found at i:2354469 original size:20 final size:20
Alignment explanation
Indices: 2354444--2354481 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2354434 CAATTTATTC
2354444 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
2354464 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2354482 TCCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:2354811 original size:14 final size:15
Alignment explanation
Indices: 2354786--2354815 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2354776 TTTCTAAAAA
2354786 TTTTGAAAAAATTAC
1 TTTTGAAAAAATTAC
2354801 TTTTG-AAAAATTAC
1 TTTTGAAAAAATTAC
2354815 T
1 T
2354816 CCCCCTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (15 bp):
TTTTGAAAAAATTAC
Found at i:2357134 original size:21 final size:22
Alignment explanation
Indices: 2357079--2357134 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
2357069 TTTGTACATT
2357079 GATGCACATTCAAGGAGTGCATC
1 GATGCACATTC-AGGAGTGCATC
* * * *
2357102 GATGAACTTTCATGA-TGTATC
1 GATGCACATTCAGGAGTGCATC
2357123 GATGCACATTCA
1 GATGCACATTCA
2357135 AAGGGATGCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 15 0.56
22 3 0.11
23 9 0.33
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (22 bp):
GATGCACATTCAGGAGTGCATC
Found at i:2357165 original size:44 final size:44
Alignment explanation
Indices: 2357079--2357172 Score: 113
Period size: 44 Copynumber: 2.1 Consensus size: 44
2357069 TTTGTACATT
*
2357079 GATGCACATTCAAGGAGTGCATCGATGAACTTTCATGATGTATC
1 GATGCACATTCAAGGAGTGCATCGATGAACTTTCAAGATGTATC
* *
2357123 GATGCACATTCAAAGG-GATGCATCGATGTACTGTT-AAG-TGTATT
1 GATGCACATTC-AAGGAG-TGCATCGATGAACT-TTCAAGATGTATC
2357167 GATGCA
1 GATGCA
2357173 TTAAGCACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
44 23 0.52
45 19 0.43
46 2 0.05
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (44 bp):
GATGCACATTCAAGGAGTGCATCGATGAACTTTCAAGATGTATC
Found at i:2365941 original size:25 final size:25
Alignment explanation
Indices: 2365907--2365962 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
2365897 CACCATGGAT
2365907 GTTCTTCAAAGCTGTTTCTAAGGGA
1 GTTCTTCAAAGCTGTTTCTAAGGGA
*
2365932 GTTCTTCAAAGTTGTTTCTAAGGGA
1 GTTCTTCAAAGCTGTTTCTAAGGGA
2365957 GTTCTT
1 GTTCTT
2365963 TATTACCCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.41
Consensus pattern (25 bp):
GTTCTTCAAAGCTGTTTCTAAGGGA
Found at i:2372888 original size:64 final size:65
Alignment explanation
Indices: 2372820--2372944 Score: 173
Period size: 64 Copynumber: 1.9 Consensus size: 65
2372810 GGTGCACAAG
* * * *
2372820 TGTGCATCGATGCATAAAATGCATTAGATG-TTTCA-AACAAGCTCGAGTGCATCGATGCATGGC
1 TGTGCATCGATGAATAAAATGCATTAGATGTTTTCATAAAAACCT-AAGTGCATCGATGCATGGC
2372883 T
65 T
* *
2372884 TGTGCATCGATGAATCAAATGCATTCGATGTTTTCATAAAAACCTAAGTGCATCGATGCAT
1 TGTGCATCGATGAATAAAATGCATTAGATGTTTTCATAAAAACCTAAGTGCATCGATGCAT
2372945 ATAATGCATT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 27 0.51
65 20 0.38
66 6 0.11
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (65 bp):
TGTGCATCGATGAATAAAATGCATTAGATGTTTTCATAAAAACCTAAGTGCATCGATGCATGGCT
Found at i:2373341 original size:12 final size:12
Alignment explanation
Indices: 2373324--2373350 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2373314 TGAAGCCCTT
2373324 GAAAAGTTTAAG
1 GAAAAGTTTAAG
2373336 GAAAAGTTTAAG
1 GAAAAGTTTAAG
2373348 GAA
1 GAA
2373351 TTTAAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.26, T:0.22
Consensus pattern (12 bp):
GAAAAGTTTAAG
Found at i:2378655 original size:4 final size:4
Alignment explanation
Indices: 2378646--2378691 Score: 51
Period size: 4 Copynumber: 11.2 Consensus size: 4
2378636 AAAAATAATA
2378646 AAAT AAAT AAAT AAAT ATAATT AAA- AAAT -AAT AAAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT A-AA-T AAAT AAAT AAAT -AAAT AAAT AAAT A
2378692 TAATTAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
3 6 0.16
4 22 0.59
5 7 0.19
6 2 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:2378688 original size:29 final size:29
Alignment explanation
Indices: 2378650--2378705 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
2378640 ATAATAAAAT
2378650 AAATAAATAAATATAATTAAAAAATAATA
1 AAATAAATAAATATAATTAAAAAATAATA
*
2378679 AAATAAATAAATATAATTAAAAGATAA
1 AAATAAATAAATATAATTAAAAAATAA
2378706 AAGGAGGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (29 bp):
AAATAAATAAATATAATTAAAAAATAATA
Found at i:2381061 original size:65 final size:64
Alignment explanation
Indices: 2380939--2381071 Score: 169
Period size: 65 Copynumber: 2.1 Consensus size: 64
2380929 CCCTATTTCA
* * * * *
2380939 AATGCATTTTTTGTACCGATGCATAGCTATGCATCGATGCACTCTTGATTTTATTGAAAAATCG
1 AATGCATTTTATGTACCGATGCACAGCCATGCATCGATGCACTCCTGATCTTATTGAAAAATCG
* * *
2381003 AATGCATTTTATGTACTGATGCACAGACCATGCATCGATGCACTCCTGCCTCTT-TTGAAACATC
1 AATGCATTTTATGTACCGATGCACAG-CCATGCATCGATGCACTCCTG-ATCTTATTGAAAAATC
2381067 G
64 G
2381068 AATG
1 AATG
2381072 TAATTAGTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
64 23 0.39
65 33 0.56
66 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (64 bp):
AATGCATTTTATGTACCGATGCACAGCCATGCATCGATGCACTCCTGATCTTATTGAAAAATCG
Found at i:2381083 original size:65 final size:64
Alignment explanation
Indices: 2380939--2381091 Score: 157
Period size: 65 Copynumber: 2.4 Consensus size: 64
2380929 CCCTATTTCA
* * * * * *
2380939 AATGCATTTTTTGTACCGATGCATAGCTATGCATCGATGCACTCTTGATTTTATTGAAAAATCG
1 AATGCATATTATGTACCGATGCACAGCCATGCATCGATGCACTCCTGATCTTATTGAAAAATCG
* * * *
2381003 AATGCATTTTATGTACTGATGCACAGACCATGCATCGATGCACTCCTGCCTCTT-TTGAAACATC
1 AATGCATATTATGTACCGATGCACAG-CCATGCATCGATGCACTCCTG-ATCTTATTGAAAAATC
2381067 G
64 G
* *
2381068 AATGTA-ATTAGTGTACCCATGCAC
1 AATGCATATTA-TGTACCGATGCAC
2381092 CCCAAGTGTA
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
64 26 0.35
65 45 0.61
66 3 0.04
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (64 bp):
AATGCATATTATGTACCGATGCACAGCCATGCATCGATGCACTCCTGATCTTATTGAAAAATCG
Found at i:2386599 original size:44 final size:44
Alignment explanation
Indices: 2386536--2386655 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 44
2386526 TTTTGTGCAC
*
2386536 TATGCATCGATACACTATGAAAGTGTACCGATGCATCCCTTGAA
1 TATGCATCGATACACTATGAAAGTGTACCGATACATCCCTTGAA
* * * *
2386580 TATGCATCGATACACTATGAAGGTGCATCGATACATTCCTTGAA
1 TATGCATCGATACACTATGAAAGTGTACCGATACATCCCTTGAA
* * * *
2386624 TGTGCAACGATACACTCTG-CAGTGTACCGATA
1 TATGCATCGATACACTATGAAAGTGTACCGATA
2386656 TACTCGTCAG
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
43 9 0.14
44 55 0.86
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (44 bp):
TATGCATCGATACACTATGAAAGTGTACCGATACATCCCTTGAA
Found at i:2386606 original size:21 final size:21
Alignment explanation
Indices: 2386538--2386614 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
2386528 TTGTGCACTA
2386538 TGCATCGATACACTATGAAAG
1 TGCATCGATACACTATGAAAG
* * *
2386559 TGTACCGATGCATCCCT-TGAATA-
1 TGCATCGAT--A-CACTATGAA-AG
*
2386582 TGCATCGATACACTATGAAGG
1 TGCATCGATACACTATGAAAG
2386603 TGCATCGATACA
1 TGCATCGATACA
2386615 TTCCTTGAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
20 3 0.07
21 24 0.56
23 12 0.28
24 4 0.09
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (21 bp):
TGCATCGATACACTATGAAAG
Found at i:2386628 original size:23 final size:22
Alignment explanation
Indices: 2386538--2386637 Score: 73
Period size: 23 Copynumber: 4.5 Consensus size: 22
2386528 TTGTGCACTA
*
2386538 TGCATCGATACA--CTATGAAAG
1 TGCATCGATACATCCT-TGAATG
* * * *
2386559 TGTACCGATGCATCCCTTGAATA
1 TGCATCGATACAT-CCTTGAATG
*
2386582 TGCATCGATACA--CTATGAAGG
1 TGCATCGATACATCCT-TGAATG
2386603 TGCATCGATACATTCCTTGAATG
1 TGCATCGATACA-TCCTTGAATG
*
2386626 TGCAACGATACA
1 TGCATCGATACA
2386638 CTCTGCAGTG
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
20 2 0.03
21 25 0.42
23 29 0.48
24 4 0.07
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (22 bp):
TGCATCGATACATCCTTGAATG
Found at i:2387091 original size:18 final size:20
Alignment explanation
Indices: 2387061--2387105 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
2387051 AAATAAAAAA
2387061 ATTG-TTTTGATTTAATT-T
1 ATTGTTTTTGATTTAATTAT
*
2387079 -TTGTTTTTTATTTAATTAT
1 ATTGTTTTTGATTTAATTAT
2387098 ATTGTTTT
1 ATTGTTTT
2387106 CATGAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
19 1 0.04
20 7 0.30
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (20 bp):
ATTGTTTTTGATTTAATTAT
Found at i:2389378 original size:64 final size:65
Alignment explanation
Indices: 2389257--2389389 Score: 171
Period size: 65 Copynumber: 2.1 Consensus size: 65
2389247 CCCTATTTTG
* ** * *
2389257 AATGCATTTTGGGTACCGATGCACAGCCATGCATTGATGAACTCCTGATTTTATTT-AAACATCA
1 AATGCATTTTAGGTACCGATGCACAGCCATGCATCAATGAACTCCTGACTCTATTTAAAACATCA
* *
2389321 AATGCATTTTATGTACCGATGCACAGACCATGCATCAATGCACTCCTGACTCT-TTTAAAACATC
1 AATGCATTTTAGGTACCGATGCACAG-CCATGCATCAATGAACTCCTGACTCTATTTAAAACATC
*
2389385 G
65 A
2389386 AATG
1 AATG
2389390 TAATTAGTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
64 27 0.46
65 32 0.54
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (65 bp):
AATGCATTTTAGGTACCGATGCACAGCCATGCATCAATGAACTCCTGACTCTATTTAAAACATCA
Found at i:2393198 original size:11 final size:11
Alignment explanation
Indices: 2393156--2393190 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2393146 AAAACAAAGC
*
2393156 GAAATTAAAAT
1 GAAAATAAAAT
*
2393167 GAAAATAAAAG
1 GAAAATAAAAT
2393178 GAAAATAAAAT
1 GAAAATAAAAT
2393189 GA
1 GA
2393191 TATTAAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (11 bp):
GAAAATAAAAT
Found at i:2393203 original size:22 final size:22
Alignment explanation
Indices: 2393146--2393203 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
2393136 AATTTTGCTA
* * *
2393146 AAAACAAAGCGAAATTAAAATG
1 AAAATAAAACGAAAATAAAATG
*
2393168 AAAATAAAAGGAAAATAAAATG
1 AAAATAAAACGAAAATAAAATG
* *
2393190 ATATTAAAACGAAA
1 AAAATAAAACGAAA
2393204 TGGGTTGCCT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.16
Consensus pattern (22 bp):
AAAATAAAACGAAAATAAAATG
Found at i:2397582 original size:10 final size:11
Alignment explanation
Indices: 2397522--2397581 Score: 61
Period size: 10 Copynumber: 5.4 Consensus size: 11
2397512 CAGTTGTATA
*
2397522 GTTATGAGTTA
1 GTTATGAGTTT
2397533 GTTA-GAGTTT
1 GTTATGAGTTT
*
2397543 GTTATGGGTTT
1 GTTATGAGTTT
2397554 GTTGATGTCAGTTT
1 GTT-ATG--AGTTT
2397568 GTTA-GAGTTT
1 GTTATGAGTTT
2397578 GTTA
1 GTTA
2397582 GTCAGCTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
10 18 0.43
11 12 0.29
12 4 0.10
13 1 0.02
14 7 0.17
ACGTcount: A:0.18, C:0.02, G:0.30, T:0.50
Consensus pattern (11 bp):
GTTATGAGTTT
Found at i:2397593 original size:24 final size:25
Alignment explanation
Indices: 2397538--2397596 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
2397528 AGTTAGTTAG
*
2397538 AGTTTGTTATGGGTTTGTTGATGTC
1 AGTTTGTTATGAGTTTGTTGATGTC
2397563 AGTTTGTTA-GAGTTTGTT-A-GTC
1 AGTTTGTTATGAGTTTGTTGATGTC
2397585 AGCTATTGTTAT
1 AG-T-TTGTTAT
2397597 AAATAGCTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.17
23 2 0.07
24 14 0.47
25 9 0.30
ACGTcount: A:0.17, C:0.05, G:0.27, T:0.51
Consensus pattern (25 bp):
AGTTTGTTATGAGTTTGTTGATGTC
Found at i:2402529 original size:35 final size:35
Alignment explanation
Indices: 2402483--2402549 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
2402473 AAGTTGAAGC
* *
2402483 ACAAACGTGAATTGCATGGGGAATGTTAGTGTCTT
1 ACAAACGTGAATTACATGGAGAATGTTAGTGTCTT
2402518 ACAAACGTGAATTACATGGAGAATGTTAGTGT
1 ACAAACGTGAATTACATGGAGAATGTTAGTGT
2402550 ATAGAATGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (35 bp):
ACAAACGTGAATTACATGGAGAATGTTAGTGTCTT
Found at i:2404389 original size:3 final size:3
Alignment explanation
Indices: 2404381--2404406 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2404371 TCTACAAAAA
2404381 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2404407 CATCTATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2406076 original size:2 final size:2
Alignment explanation
Indices: 2406064--2406114 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2406054 TAGTTATTTG
*
2406064 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2406106 TA TA TA TA T
1 TA TA TA TA T
2406115 TGACTCTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2407829 original size:18 final size:18
Alignment explanation
Indices: 2407806--2407843 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2407796 ATTGATTATC
2407806 TTGTTTGTACTAACTCAT
1 TTGTTTGTACTAACTCAT
*
2407824 TTGTTTGTACTAACTTAT
1 TTGTTTGTACTAACTCAT
2407842 TT
1 TT
2407844 CTTTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (18 bp):
TTGTTTGTACTAACTCAT
Found at i:2410847 original size:31 final size:32
Alignment explanation
Indices: 2410789--2410851 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
2410779 AAGAAGTGAT
2410789 GAATGATGGGACATCTTTGAAGATTCAACATC
1 GAATGATGGGACATCTTTGAAGATTCAACATC
* * *
2410821 GAATGTTGGGGCATC-TTGGAGATTCAACATC
1 GAATGATGGGACATCTTTGAAGATTCAACATC
2410852 CTAAAGTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (32 bp):
GAATGATGGGACATCTTTGAAGATTCAACATC
Found at i:2410997 original size:40 final size:36
Alignment explanation
Indices: 2410953--2411078 Score: 105
Period size: 36 Copynumber: 3.4 Consensus size: 36
2410943 ACAAAACGTC
* *
2410953 GTCTCGCTGGAGACAAATTTTCTTGGAAAAACAAAATTTT
1 GTCTCGCTTGAGACAAATGTTC-T--AAAAAC-AAATTTT
* *
2410993 GTCTCGCTTGAGTC-AGTGTTCTAAAAACAAATTTT
1 GTCTCGCTTGAGACAAATGTTCTAAAAACAAATTTT
* *
2411028 GTCTCGCTTGAGAC-AAT-TTCTATCAAAATAAATTTC
1 GTCTCGCTTGAGACAAATGTTCTA--AAAACAAATTTT
* *
2411064 ATCTCACTTGAGACA
1 GTCTCGCTTGAGACA
2411079 TTTCTTCTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
34 5 0.07
35 22 0.30
36 28 0.38
38 1 0.01
39 5 0.07
40 12 0.16
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (36 bp):
GTCTCGCTTGAGACAAATGTTCTAAAAACAAATTTT
Found at i:2411290 original size:65 final size:64
Alignment explanation
Indices: 2411145--2411388 Score: 260
Period size: 65 Copynumber: 3.8 Consensus size: 64
2411135 CTATGAGGTT
* * * ** *
2411145 GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAAACAAAAATCTTTGAGC
1 GTTTCCCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-ATCATCTTTGAGT
2411210 C
64 C
* * * * *
2411211 TTTTCTCTTGAAACACA-TTTTGTCTCTATTGAGACAGTTTCTCTTGAAACACTCATGTTTGGGT
1 GTTTCCCTTGAAACA-AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-TCATCTTTGAGT
2411275 C
64 C
* * * * * *
2411276 GTTTCCCTTTAAACAAGTTTTGTCTTTCTTGAAATAGCTTCTCTTGAAGCATCATCTTTGAGTC
1 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGTC
2411340 TGTTTCCCTTGAAACAAG-TTTGTCTCTCTTGAGAC-GATTTCTCTTGAAA
1 -GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAA
2411389 TCATTATCCT
Statistics
Matches: 147, Mismatches: 26, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
63 1 0.01
64 37 0.25
65 95 0.65
66 14 0.10
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.42
Consensus pattern (64 bp):
GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGTC
Found at i:2411323 original size:130 final size:130
Alignment explanation
Indices: 2411145--2411388 Score: 305
Period size: 130 Copynumber: 1.9 Consensus size: 130
2411135 CTATGAGGTT
* * * *
2411145 GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAAACAAAAATCTTTGAGC
1 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAAACAACTTCTCTTGAAAC-AAAATCTTTGAGC
* *
2411210 CT-TTTCTCTTGAAACACATTTTGTCTCTATTGAGAC-AGTTTCTCTTGAAACACTCATGTTTGG
65 CTGTTTCCCTTGAAACA-AGTTTGTCTCTATTGAGACGA-TTTCTCTTGAAACACTCATGTTTGG
2411273 GTC
128 GTC
* * * * * ** *
2411276 GTTTCCCTTTAAAC-AAGTTTTGTCTTTCTTGAAATAGCTTCTCTTGAAGCATCATCTTTGAGTC
1 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAAACAACTTCTCTTGAAACAAAATCTTTGAGCC
*
2411340 TGTTTCCCTTGAAACAAGTTTGTCTCTCTTGAGACGATTTCTCTTGAAA
66 TGTTTCCCTTGAAACAAGTTTGTCTCTATTGAGACGATTTCTCTTGAAA
2411389 TCATTATCCT
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
129 41 0.43
130 43 0.45
131 12 0.12
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.42
Consensus pattern (130 bp):
GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAAACAACTTCTCTTGAAACAAAATCTTTGAGCC
TGTTTCCCTTGAAACAAGTTTGTCTCTATTGAGACGATTTCTCTTGAAACACTCATGTTTGGGTC
Found at i:2411825 original size:3 final size:3
Alignment explanation
Indices: 2411810--2411880 Score: 99
Period size: 3 Copynumber: 23.7 Consensus size: 3
2411800 CTACAAAAAA
* * *
2411810 TAT TAT TAA TAT TAT TAA TAT TAT TAA T-T TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2411857 TATT TAT TAT TAT TAT TAT TAT TA
1 TA-T TAT TAT TAT TAT TAT TAT TA
2411881 CATCTATTAC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 56 0.93
4 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2420346 original size:24 final size:25
Alignment explanation
Indices: 2420293--2420339 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2420283 GAACTCAAAA
2420293 AAAAATTAGAAGCTTGATTGAAGCC
1 AAAAATTAGAAGCTTGATTGAAGCC
* *
2420318 TAAAATTCG-AGCTTGATTGAAG
1 AAAAATTAGAAGCTTGATTGAAG
2420340 TGAAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (25 bp):
AAAAATTAGAAGCTTGATTGAAGCC
Found at i:2420347 original size:25 final size:25
Alignment explanation
Indices: 2420292--2420348 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
2420282 TGAACTCAAA
2420292 AAAAAATTAGAAGCTTGATTGAAGC
1 AAAAAATTAGAAGCTTGATTGAAGC
** * *
2420317 CTAAAATTCG-AGCTTGATTGAAGTG
1 AAAAAATTAGAAGCTTGATTGAAG-C
2420342 AAAAAAT
1 AAAAAAT
2420349 AGTTCACTCA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (25 bp):
AAAAAATTAGAAGCTTGATTGAAGC
Found at i:2422936 original size:21 final size:21
Alignment explanation
Indices: 2422912--2422958 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2422902 AATATGTAAA
2422912 TCGCATTGCAATTTTCCAAAT
1 TCGCATTGCAATTTTCCAAAT
* *
2422933 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCAATTTTCCAAAT
2422954 TCGCA
1 TCGCA
2422959 ACGCGAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (21 bp):
TCGCATTGCAATTTTCCAAAT
Found at i:2422964 original size:21 final size:20
Alignment explanation
Indices: 2422828--2422964 Score: 73
Period size: 20 Copynumber: 6.8 Consensus size: 20
2422818 AAATGACCAA
*
2422828 CAAATTCGCAACGCGATCT-
1 CAAATTCGCAACGCGATTTC
*
2422847 CAAATTCGCAACGCGAATTC
1 CAAATTCGCAACGCGATTTC
* *
2422867 CAATTTCGCAAC-CCAGTTTC
1 CAAATTCGCAACGCGA-TTTC
* * * * *
2422887 TAATTTCGCAACGTGAATATG
1 CAAATTCGCAACGCG-ATTTC
* ** *
2422908 TAAA-TCGCATTGCAATTTTC
1 CAAATTCGCAACGCGA-TTTC
***
2422928 CAAATTCGCGTTGCGATTTTC
1 CAAATTCGCAACGCGA-TTTC
2422949 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
2422965 AAGTCAAACT
Statistics
Matches: 89, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
19 20 0.22
20 36 0.40
21 32 0.36
22 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTC
Found at i:2423024 original size:20 final size:20
Alignment explanation
Indices: 2422968--2423037 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
2422958 AACGCGAAAG
*
2422968 TCAAACTCG-AAACTGAATT
1 TCAAATTCGCAAACTGAATT
*
2422987 TCAAATTCGGAAACTGAATT
1 TCAAATTCGCAAACTGAATT
2423007 TCAAATTCGCAATA-TGAATT
1 TCAAATTCGCAA-ACTGAATT
*
2423027 T-AATTTCGCAA
1 TCAAATTCGCAA
2423038 CAAGTTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (20 bp):
TCAAATTCGCAAACTGAATT
Found at i:2423803 original size:12 final size:12
Alignment explanation
Indices: 2423782--2423815 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2423772 ACCACATTTT
*
2423782 CAATACCAAACA
1 CAATATCAAACA
2423794 CAATATCAAACA
1 CAATATCAAACA
*
2423806 CAATCTCAAA
1 CAATATCAAA
2423816 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:2426267 original size:18 final size:18
Alignment explanation
Indices: 2426244--2426284 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2426234 AGCAAAAAGG
*
2426244 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
2426262 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
*
2426280 CAATC
1 AAATC
2426285 GGCTTCACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.27, G:0.02, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:2426744 original size:14 final size:14
Alignment explanation
Indices: 2426725--2426784 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
2426715 ATTCTTATTT
2426725 ACAAATCAAATTAA
1 ACAAATCAAATTAA
* **
2426739 ACAAATCAACTTTT
1 ACAAATCAAATTAA
* **
2426753 ACAAATCAACTTTT
1 ACAAATCAAATTAA
2426767 ACAAATC-AATTAA
1 ACAAATCAAATTAA
*
2426780 TCAAA
1 ACAAA
2426785 AAATAAATCT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
13 7 0.18
14 32 0.82
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAAATTAA
Done.