Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 92 of 144
Found at i:21357807 original size:23 final size:23
Alignment explanation
Indices: 21357781--21357825 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
21357771 GTAATTCATG
21357781 GTATGAGAATAGTAGAAAAGATC
1 GTATGAGAATAGTAGAAAAGATC
*
21357804 GTATGAGAATAGTAGAGAAGAT
1 GTATGAGAATAGTAGAAAAGAT
21357826 TGTTTGGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.29, T:0.22
Consensus pattern (23 bp):
GTATGAGAATAGTAGAAAAGATC
Found at i:21361510 original size:17 final size:17
Alignment explanation
Indices: 21361469--21361511 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
21361459 CTTGTTTAAT
*
21361469 AATACTTTTATCTCAAA
1 AATATTTTTATCTCAAA
* *
21361486 AGTGTTTTTATCTCAAA
1 AATATTTTTATCTCAAA
21361503 AATATTTTT
1 AATATTTTT
21361512 GAGAAATAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (17 bp):
AATATTTTTATCTCAAA
Found at i:21362899 original size:19 final size:20
Alignment explanation
Indices: 21362858--21362897 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21362848 TTTAATGACT
*
21362858 ATTTATTTGTTTGTTTTTAA
1 ATTTATTAGTTTGTTTTTAA
21362878 ATTTATTAGTGTT-TTTTTAA
1 ATTTATTAGT-TTGTTTTTAA
21362898 TTACAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (20 bp):
ATTTATTAGTTTGTTTTTAA
Found at i:21363051 original size:27 final size:28
Alignment explanation
Indices: 21363021--21363081 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
21363011 CATTAAGAAT
21363021 TTTAAAATCTATGT-T-TTTATTAATTTA
1 TTTAAAAT-TATGTGTGTTTATTAATTTA
* *
21363048 TTTAAAATTATGTGTGTTTATTCATTTG
1 TTTAAAATTATGTGTGTTTATTAATTTA
21363076 TTTAAA
1 TTTAAA
21363082 TTGAATTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 5 0.17
27 9 0.30
28 16 0.53
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.57
Consensus pattern (28 bp):
TTTAAAATTATGTGTGTTTATTAATTTA
Found at i:21363981 original size:19 final size:19
Alignment explanation
Indices: 21363951--21364001 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
21363941 AATAATTTTA
*
21363951 AAAATCTTAAAATAGATA-T
1 AAAATATTAAAA-AGATATT
* *
21363970 AAATTATTAAAAATATATT
1 AAAATATTAAAAAGATATT
21363989 AAAATATTAAAAA
1 AAAATATTAAAAA
21364002 TTATGTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATATTAAAAAGATATT
Found at i:21363982 original size:20 final size:19
Alignment explanation
Indices: 21363959--21364002 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
21363949 TAAAAATCTT
*
21363959 AAAATAGATATAAATTATTA
1 AAAATAGAT-TAAAATATTA
*
21363979 AAAATATATTAAAATATTA
1 AAAATAGATTAAAATATTA
21363998 AAAAT
1 AAAAT
21364003 TATGTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATAGATTAAAATATTA
Found at i:21363983 original size:10 final size:10
Alignment explanation
Indices: 21363970--21364013 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
21363960 AAATAGATAT
21363970 AAATTATTAA
1 AAATTATTAA
21363980 AAATATATT-A
1 AAAT-TATTAA
21363990 AAA-TATTAA
1 AAATTATTAA
21363999 AAATTATGTAA
1 AAATTAT-TAA
21364010 AAAT
1 AAAT
21364014 ATTTTTAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 4 0.13
9 4 0.13
10 11 0.37
11 11 0.37
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
AAATTATTAA
Found at i:21364002 original size:19 final size:20
Alignment explanation
Indices: 21363959--21364016 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
21363949 TAAAAATCTT
* *
21363959 AAAATAGATATAAATTATTA
1 AAAATATATATAAAATATTA
21363979 AAAATATAT-TAAAATATTA
1 AAAATATATATAAAATATTA
*
21363998 AAAAT-TATGTAAAAATATT
1 AAAATATATAT-AAAATATT
21364017 TTTAAGATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.09
19 15 0.44
20 16 0.47
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAATATATATAAAATATTA
Found at i:21377580 original size:20 final size:19
Alignment explanation
Indices: 21377531--21377582 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
21377521 TTTATTTTAT
*
21377531 AATTCATAAAA-AAAATTA
1 AATTCATAAAATAAAATCA
* *
21377549 AATTTATTAAATATAAATCA
1 AATTCATAAAATA-AAATCA
*
21377569 AATTGATAAAATAA
1 AATTCATAAAATAA
21377583 GTAAATATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 9 0.33
19 2 0.07
20 16 0.59
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (19 bp):
AATTCATAAAATAAAATCA
Found at i:21380248 original size:10 final size:11
Alignment explanation
Indices: 21380224--21380259 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
21380214 TTTTGATACG
21380224 TATTTTTTATA
1 TATTTTTTATA
21380235 TATTTTTTAT-
1 TATTTTTTATA
21380245 TA-TTTTTATA
1 TATTTTTTATA
21380255 TATTT
1 TATTT
21380260 AAAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 7 0.30
10 4 0.17
11 12 0.52
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TATTTTTTATA
Found at i:21380250 original size:9 final size:10
Alignment explanation
Indices: 21380227--21380259 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
21380217 TGATACGTAT
21380227 TTTTTATATA
1 TTTTTATATA
21380237 TTTTT-TATTA
1 TTTTTATA-TA
21380247 TTTTTATATA
1 TTTTTATATA
21380257 TTT
1 TTT
21380260 AAAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.10
10 17 0.81
11 2 0.10
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTATATA
Found at i:21380587 original size:4 final size:4
Alignment explanation
Indices: 21380578--21380630 Score: 63
Period size: 4 Copynumber: 13.2 Consensus size: 4
21380568 AAATAAACGG
* * *
21380578 GAAA GAAA GAAA GAAA GAAA GAAG GAGAG GAAA GAAA -AAA GAAG GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA
21380626 GAAA G
1 GAAA G
21380631 GTAATGTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 3 0.07
4 36 0.84
5 4 0.09
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:21383753 original size:13 final size:13
Alignment explanation
Indices: 21383735--21383760 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21383725 ATCAAATAGG
21383735 TTAAAATTCATCA
1 TTAAAATTCATCA
21383748 TTAAAATTCATCA
1 TTAAAATTCATCA
21383761 ATAGTCAAAT
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:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAATTCATCA
Found at i:21385953 original size:16 final size:16
Alignment explanation
Indices: 21385932--21385981 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
21385922 TGATGGAGGT
21385932 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
21385948 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
21385963 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
21385978 ATTA
1 ATTA
21385982 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:21386284 original size:95 final size:93
Alignment explanation
Indices: 21386173--21386433 Score: 402
Period size: 95 Copynumber: 2.8 Consensus size: 93
21386163 TTATATTATT
21386173 TTTTAAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAA
1 TTTT-AAATCAATAAATATGAACAATATTTTTTACTTACTACTAC-TA-TAACAACAAAATAAAA
***
21386238 TTACTAACTA-ATTTTTTTAAACATTATTAAA
63 TTACTAACTACA-AAATTTAAACATTATTAAA
* *
21386269 TTTTAAATCAATAAATATGAACAATGTTTTTTACTTACTACCACTATTAACAACAAAATAAAATT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTA-TAACAACAAAATAAAATT
21386334 ACTAACTAGCAAAATTTAAACATTATTAAA
65 ACTAACTA-CAAAATTTAAACATTATTAAA
21386364 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTA-T-TAACAACAAAATAAAATTA
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTATAACAACAAAATAAAATTA
21386427 CTAACTA
66 CTAACTA
21386434 GTAAAATTAA
Statistics
Matches: 155, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
92 26 0.17
94 29 0.19
95 95 0.61
96 5 0.03
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (93 bp):
TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTATAACAACAAAATAAAATTA
CTAACTACAAAATTTAAACATTATTAAA
Found at i:21386836 original size:13 final size:12
Alignment explanation
Indices: 21386820--21386857 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
21386810 TTCCTTCTTC
21386820 TTCTTTTCTTTCT
1 TTCTTTTCTTT-T
21386833 TTCTTTCTCTTTT
1 TTCTTT-TCTTTT
21386846 TTCTTTT-TTTT
1 TTCTTTTCTTTT
21386857 T
1 T
21386858 CCCTCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.21
12 1 0.04
13 13 0.54
14 5 0.21
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTTTTCTTTT
Found at i:21386843 original size:22 final size:22
Alignment explanation
Indices: 21386777--21386858 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 22
21386767 TAAAACATTT
* *
21386777 TTTTCTTTCTCCTTCTTCCCCTTC
1 TTTTCTTTCT--TTCTTTCTCTTC
* * *
21386801 TTCTCATTC-TTCCTTCTTCTTC
1 TTTTCTTTCTTTCTTTC-TCTTC
21386823 TTTTCTTTCTTTCTTTCTCTT-
1 TTTTCTTTCTTTCTTTCTCTTC
21386844 TTTTCTTT-TTT-TTTC
1 TTTTCTTTCTTTCTTTC
21386859 CCTCAATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
19 4 0.08
20 3 0.06
21 13 0.27
22 15 0.31
23 6 0.12
24 7 0.15
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTCTTTCTTTCTTTCTCTTC
Found at i:21388577 original size:101 final size:102
Alignment explanation
Indices: 21388273--21388583 Score: 245
Period size: 109 Copynumber: 3.0 Consensus size: 102
21388263 TTCAAACGAA
* * * * * * * * * *
21388273 ATATTCAATTACTTAGGTTCAAGGCAAAATCATACCCACCACGTTAGGGCACAATTTTTTGAGTC
1 ATATTCAATT-CTTAGGTTCAAAGAAAAATCACACCCAACACGTTATGACACAATTTCTCGACTT
* * * ** *
21388338 CCCTAAAATAACAGAATATTGAGCATTAATTGGTTCCGAATAGG
65 CCCTAAAATAAAAGAACATT--GCCTCGATT--TT--GAAAAGG
*
21388382 ATATTCAATTGTTCAGGTTCAAAGAAAAATCACACCCAACACGTTATGACACAATTTCTCGACTT
1 ATATTCAATTCTT-AGGTTCAAAGAAAAATCACACCCAACACGTTATGACACAATTTCTCGACTT
* * *
21388447 CCTTAAAATAAAAGAATATTGTCTCGATTTTTGAAAAGG
65 CCCTAAAATAAAAGAACATTGCCTCGA-TTTTGAAAAGG
* * ** * *
21388486 ATATTCAATTACTT-GGTTCGAAGAAAAATCGCA-CCAGTACGTT-TGAGCATAATTTCTCGAGT
1 ATATTCAATT-CTTAGGTTCAAAGAAAAATCACACCCAACACGTTATGA-CACAATTTCTCGACT
21388548 TCCCT-AAAT-AAAGAAACATTGCCTCGATTTTGAAAA
64 TCCCTAAAATAAAAG-AACATTGCCTCGATTTTGAAAA
21388584 TATTTGTCTT
Statistics
Matches: 169, Mismatches: 28, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
100 13 0.08
101 18 0.11
102 25 0.15
103 17 0.10
104 16 0.09
105 2 0.01
106 2 0.01
107 3 0.02
108 4 0.02
109 69 0.41
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (102 bp):
ATATTCAATTCTTAGGTTCAAAGAAAAATCACACCCAACACGTTATGACACAATTTCTCGACTTC
CCTAAAATAAAAGAACATTGCCTCGATTTTGAAAAGG
Found at i:21388960 original size:30 final size:30
Alignment explanation
Indices: 21388909--21389096 Score: 168
Period size: 30 Copynumber: 6.3 Consensus size: 30
21388899 AAGGAAAAAT
* * *
21388909 AGGGTCAAA-ACAAAATTTTGGAAAGTTCG
1 AGGGTCAAATTCAAATTTTTGGAAAGTTTG
* * *
21388938 ATGGCCAAATTCAAATTTTTGGAAAG-TTA
1 AGGGTCAAATTCAAATTTTTGGAAAGTTTG
* * *
21388967 ATGGTCAAATTTAAATTTTTAGAAAGTTTG
1 AGGGTCAAATTCAAATTTTTGGAAAGTTTG
*
21388997 -GGGTTCAAATTCAAATTTTTGAAAAGTTTG
1 AGGG-TCAAATTCAAATTTTTGGAAAGTTTG
*
21389027 AGGGGTCAAATTCAAATTTTTGGAAAATTTG
1 A-GGGTCAAATTCAAATTTTTGGAAAGTTTG
** * * * *
21389058 TTGGTCAAAAATGAAA-TTTTAGAAAGTTCG
1 AGGGTC-AAATTCAAATTTTTGGAAAGTTTG
21389088 AGGGTCAAA
1 AGGGTCAAA
21389097 ATATCATTTT
Statistics
Matches: 128, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
29 36 0.28
30 58 0.45
31 31 0.24
32 3 0.02
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (30 bp):
AGGGTCAAATTCAAATTTTTGGAAAGTTTG
Found at i:21390894 original size:45 final size:45
Alignment explanation
Indices: 21390817--21391435 Score: 610
Period size: 45 Copynumber: 13.9 Consensus size: 45
21390807 GAGATAGTAA
* *
21390817 CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGAATGGTAG
1 CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
* * ** *
21390862 CTTTAGTCTACCCCTCTTGATTATATGG-AAAAGATTGGATTGTGG
1 CTTCAATCTACCCCTCTTGATTA-GGGGTAAAAGATTGGATGGTGG
*
21390907 GTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
1 CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
** * * * ***
21390952 CTTCAATCTGTCCCTCTTGATTAAGGCTAAAAGTTTGGACCATGG
1 CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
* * * * *
21390997 TTTCAATCTGCCCCTCTTGACTAAGGGTAAAAGATTGGACGGTGG
1 CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
* *
21391042 CTTCAATCTACCTCTCTTAATTAGGGGTAAAAGATTGGATGGTGG
1 CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
*
21391087 CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATAGTGG
1 CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
* ** * * * **
21391132 CTTCAATTTGTCCCTTTTAACTAGGGGTAAAAGATTAAATGGTGG
1 CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
* * * * * *
21391177 CTTCAAACTGCCTCTCTTGACTTAGGAGAAAAAGATTGGA---TGA
1 CTTCAATCTACCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTGG
* * * * *
21391220 CTTCAATCTGCCCCTCTTAATTAGAGGTAAAAGATTGGACGGTAG
1 CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
* * * *
21391265 CTTCAATCTGCCCCTCTTGATTAGAGGTAAAAGATTGGATGATGA
1 CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
* * *
21391310 CTTCAATCTGCCCCTTTTGACTT-GGGGTAAAAGATTTGATGGT--
1 CTTCAATCTACCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTGG
* * * * *
21391353 TTTCAATTTGCCCCTTTTGACTT-GGGGTAAAAGATTTGATGGT--
1 CTTCAATCTACCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTGG
* *
21391396 CTTCAATCTTCCCCTCTTAACTTAGGGGTAAAAGATTGGA
1 CTTCAATCTACCCCTCTTGA-TTAGGGGTAAAAGATTGGA
21391436 CGATGATGTA
Statistics
Matches: 481, Mismatches: 85, Indels: 17
0.83 0.15 0.03
Matches are distributed among these distances:
42 16 0.03
43 78 0.16
44 17 0.04
45 352 0.73
46 18 0.04
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (45 bp):
CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
Found at i:21392475 original size:112 final size:115
Alignment explanation
Indices: 21392273--21392496 Score: 337
Period size: 112 Copynumber: 2.0 Consensus size: 115
21392263 TATTTCTTAT
21392273 ATCATTAGACCACTAACCATTATTTCAAATGCAAAAAATGCTTGAATCAAGGTTGTAAGGTGGAT
1 ATCATTAGACCACTAACCATTATTTCAAATGCAAAAAATGCTTGAATCAAGGTTGTAAGGTGGAT
* * * *
21392338 GAAATTGAGTTTTATTGGAGACAAAGCTCGTCTGAATGAAAAGATTACGA
66 AAAATTGAATTTTATTAGAGACAAAGCTCGTATGAATGAAAAGATTACGA
* * * * *
21392388 ATCATTGGTCCACTAACCGTTATTTC-GATGC-AAAAATGCTTGAA-CAATGTTGTAAGGTGGAT
1 ATCATTAGACCACTAACCATTATTTCAAATGCAAAAAATGCTTGAATCAAGGTTGTAAGGTGGAT
*
21392450 AAAATTGAATTTTATTAGAGGCAAAGCTCGTATGAATGAAAAGATTA
66 AAAATTGAATTTTATTAGAGACAAAGCTCGTATGAATGAAAAGATTA
21392497 AAAAAGATAA
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
112 59 0.60
113 13 0.13
114 4 0.04
115 23 0.23
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (115 bp):
ATCATTAGACCACTAACCATTATTTCAAATGCAAAAAATGCTTGAATCAAGGTTGTAAGGTGGAT
AAAATTGAATTTTATTAGAGACAAAGCTCGTATGAATGAAAAGATTACGA
Found at i:21395473 original size:29 final size:29
Alignment explanation
Indices: 21395382--21395550 Score: 117
Period size: 30 Copynumber: 5.7 Consensus size: 29
21395372 GACTCTTAAA
* * *
21395382 TTTTCCAAAAATTAGATTTTAACCCCTAAAC
1 TTTT-CAAAAATTACATTTTAACCTC-GAAC
* * * *
21395413 -TTTCTAAAAATCATATTTTAACCCCCAAAC
1 TTTTC-AAAAATTACATTTTAA-CCTCGAAC
*
21395443 TTTTCAAAAATTACACTTTAACCTCGAAC
1 TTTTCAAAAATTACATTTTAACCTCGAAC
* * * * * *
21395472 TTTTTAAAAATCACTTTTTTACCCTTGGA-
1 TTTTCAAAAATTAC-ATTTTAACCTCGAAC
* * *
21395501 TGTCCAAAAATTACATTTTAACCTCAAAC
1 TTTTCAAAAATTACATTTTAACCTCGAAC
21395530 TTTTCAAAAATTACCATTTTA
1 TTTTCAAAAATTA-CATTTTA
21395551 CCCCTGAGTG
Statistics
Matches: 107, Mismatches: 25, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
28 9 0.08
29 40 0.37
30 50 0.47
31 8 0.07
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (29 bp):
TTTTCAAAAATTACATTTTAACCTCGAAC
Found at i:21395521 original size:58 final size:58
Alignment explanation
Indices: 21395447--21395572 Score: 173
Period size: 58 Copynumber: 2.2 Consensus size: 58
21395437 CCAAACTTTT
* * ** *
21395447 CAAAAATTACACTTTAACCTCGAACTTTTTAAAAATCACTTTTTTACCCTTG-GATGTC
1 CAAAAATTACACTTTAACCTCAAACTTTTCAAAAATCACCATTTTACCCCTGAG-TGTC
* *
21395505 CAAAAATTACATTTTAACCTCAAACTTTTCAAAAATTACCATTTTACCCCTGAGTGTC
1 CAAAAATTACACTTTAACCTCAAACTTTTCAAAAATCACCATTTTACCCCTGAGTGTC
21395563 CAAAAATTAC
1 CAAAAATTAC
21395573 CGTTTTACCC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 59 0.98
59 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.35
Consensus pattern (58 bp):
CAAAAATTACACTTTAACCTCAAACTTTTCAAAAATCACCATTTTACCCCTGAGTGTC
Found at i:21395566 original size:29 final size:29
Alignment explanation
Indices: 21395534--21395628 Score: 120
Period size: 29 Copynumber: 3.3 Consensus size: 29
21395524 TCAAACTTTT
*
21395534 CAAAAATTACCATTTTACCCCTGAGTGTC
1 CAAAAATTACCATTTTACCCCTGAGTATC
* *
21395563 CAAAAATTACCGTTTTACCCCTGATTATC
1 CAAAAATTACCATTTTACCCCTGAGTATC
* * *
21395592 CCAAAATTACCATTTTA-CCCTCGGGCATC
1 CAAAAATTACCATTTTACCCCT-GAGTATC
21395621 CAAAAATT
1 CAAAAATT
21395629 GCATTTTTGA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 4 0.07
29 52 0.93
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCTGAGTATC
Found at i:21397010 original size:632 final size:633
Alignment explanation
Indices: 21396091--21397351 Score: 2186
Period size: 632 Copynumber: 2.0 Consensus size: 633
21396081 GTCATGTGTC
* **
21396091 CGAGGATCGTATTTTAAACTCAGTACAAAATTTCGAGTTCTCAAAATTATATATATGTATACAAA
1 CGAGGATCGTATTTTAAACTCAATACAAAATTTCGAGTTCTCAAAAAAATATATATGTATACAAA
21396156 TAATTTTAAAACAAAACGAGGCAATATCCTTTCGTGTGAAAACTTCGAAAGACCATGCCCTAACG
66 TAATTTTAAAACAAAACGAGGCAATATCCTTTCGTGTGAAAACTTCGAAAGACCATGCCCTAACG
21396221 TGCTGGGTGTGATTTTCGTATAATTCACACTATCGAATATCCCCTTTAAAGTCTTTCAAAATGTC
131 TGCTGGGTGTGATTTTCGTATAATTCACACTATCGAATATCCCCTTTAAAGTCTTTCAAAATGTC
* *
21396286 TTTCAGTATCGAAAGTCCGAGAACATAGTACCCTAAAGTGTTGGACATGATCTCCAGTTCTCTTA
196 TTTCAGTATCGAAAGTCCGAGAACATAGTACCCTAAAGTGTTGGACACGACCTCCAGTTCTCTTA
* *
21396351 AAAATTCGAAACGCGCGGACCATTTTTCTCAAATATGATTTTTGAAAATCTTGTAAAATTGTCTA
261 AAAATTCGAAACGCACGGACCATTTTTCTCAAATATGATTTTTGAAAATCTTGTAAAATTATCTA
* *
21396416 AAGACAAAGATCGTATCTTAATTTTTACTCGAGATTTCAAAGTTTTAACAAACCAAGACCCGAAA
326 AAGACAAAGATCGTATCTTAAGTTTTACTCGAGATTTCAAAGTTTTAACAAACCAAAACCCGAAA
* * *
21396481 GTAATCAATGTGGTACCAATTTTGGGTGTGTAAGGGTGTTAATCCTTCCTTACGCGTAACCGACT
391 GTAATCAATGTGGTACCAATTTTGGGCGTGTAAGGGTGCTAATCCTTCCTTACGAGTAACCGACT
* *
21396546 CCCGAACCCATTTTCTGGATTTTTGAAGACCAACAA-ATATTTCAAAACGGATTTTAAACGTTTT
456 CCCGAACCCATTTTCTGGATTTTCGAAAACCAA-AATATATTTCAAAACGGATTTTAAACGTTTT
* * *
21396610 GTTG-TGATCCAATCACACCATATAAAAAGATTGGTGGCGACTCCC-TTTTTTTGATCATTTAAA
520 G-CGATGATCCAATCACACCATATAAAAAGATTGGTGGCAACTCCCAATTTTTTGATCATTTAAA
*
21396673 ATACCTATTTTCTTGATTTTAAATATTGTTTGAGACTTATTTGTTTCACT
584 ATACCTATTTTCTTGATTTTAAATATTGTTCGAGACTTATTTGTTTCACT
*
21396723 CGAGGATCGTATTTTAAACTCAATACGAAATTTCGAGTTCTCAAAAAAATATATATGTATACAAA
1 CGAGGATCGTATTTTAAACTCAATACAAAATTTCGAGTTCTCAAAAAAATATATATGTATACAAA
*
21396788 TAATTTTAAAACAAAATGAGGCAATATCCTTTCGTGTGAAAACTTCGAAAGACCATGCCCTAACG
66 TAATTTTAAAACAAAACGAGGCAATATCCTTTCGTGTGAAAACTTCGAAAGACCATGCCCTAACG
* *
21396853 TGCTGGGTGTGATTTTCGTATAGTTCACACTATCGAATATCCTCTTTAAAGTCTTTCAAAATGTC
131 TGCTGGGTGTGATTTTCGTATAATTCACACTATCGAATATCCCCTTTAAAGTCTTTCAAAATGTC
* * *
21396918 TTTCAGTTTCGAAAGTCCGAGAACATAGTGCCCTAATGTGTTGGACACGACCTCCAGTTCTCTTA
196 TTTCAGTATCGAAAGTCCGAGAACATAGTACCCTAAAGTGTTGGACACGACCTCCAGTTCTCTTA
* *
21396983 AAAATTCGAAATGCACGGACGATTTTTCTCAAATATGATTTTTGAAAATCTTGTAAAATTATCTA
261 AAAATTCGAAACGCACGGACCATTTTTCTCAAATATGATTTTTGAAAATCTTGTAAAATTATCTA
* *
21397048 GAGACAAAGATCGTATTTTAAGTTTTACTCGAGATTTCAAAGTTTTAACAAACCAAAACCCGAAA
326 AAGACAAAGATCGTATCTTAAGTTTTACTCGAGATTTCAAAGTTTTAACAAACCAAAACCCGAAA
*
21397113 GTAATCAATGTGGTACCAATTTTGGGCGTGTAAGGGTGCTAATCCTTCCTTACGAGTAACTGACT
391 GTAATCAATGTGGTACCAATTTTGGGCGTGTAAGGGTGCTAATCCTTCCTTACGAGTAACCGACT
* *
21397178 CCCGAACCCATTTTCTGGATTTTCGAAAACCAAAATATTTTTCAAAATGGATTTTAAACGTTTTG
456 CCCGAACCCATTTTCTGGATTTTCGAAAACCAAAATATATTTCAAAACGGATTTTAAACGTTTTG
21397243 CGATGATCCAATCACACCATATAAAAAGATTGGTGGCAACTCCCAATTTTTTGATCATTTAAAAT
521 CGATGATCCAATCACACCATATAAAAAGATTGGTGGCAACTCCCAATTTTTTGATCATTTAAAAT
*
21397308 ACCTATTTTCTTGATTTTAAATATTGTTCGAGACTTGTTTGTTT
586 ACCTATTTTCTTGATTTTAAATATTGTTCGAGACTTATTTGTTT
21397352 TCTCCGAAAA
Statistics
Matches: 593, Mismatches: 33, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
631 3 0.01
632 529 0.89
633 61 0.10
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (633 bp):
CGAGGATCGTATTTTAAACTCAATACAAAATTTCGAGTTCTCAAAAAAATATATATGTATACAAA
TAATTTTAAAACAAAACGAGGCAATATCCTTTCGTGTGAAAACTTCGAAAGACCATGCCCTAACG
TGCTGGGTGTGATTTTCGTATAATTCACACTATCGAATATCCCCTTTAAAGTCTTTCAAAATGTC
TTTCAGTATCGAAAGTCCGAGAACATAGTACCCTAAAGTGTTGGACACGACCTCCAGTTCTCTTA
AAAATTCGAAACGCACGGACCATTTTTCTCAAATATGATTTTTGAAAATCTTGTAAAATTATCTA
AAGACAAAGATCGTATCTTAAGTTTTACTCGAGATTTCAAAGTTTTAACAAACCAAAACCCGAAA
GTAATCAATGTGGTACCAATTTTGGGCGTGTAAGGGTGCTAATCCTTCCTTACGAGTAACCGACT
CCCGAACCCATTTTCTGGATTTTCGAAAACCAAAATATATTTCAAAACGGATTTTAAACGTTTTG
CGATGATCCAATCACACCATATAAAAAGATTGGTGGCAACTCCCAATTTTTTGATCATTTAAAAT
ACCTATTTTCTTGATTTTAAATATTGTTCGAGACTTATTTGTTTCACT
Found at i:21397592 original size:12 final size:12
Alignment explanation
Indices: 21397557--21397592 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
21397547 TTTTCTTCCT
21397557 TTTTCTTTTTTTC
1 TTTT-TTTTTTTC
*
21397570 TTTTGTTTTTTC
1 TTTTTTTTTTTC
21397582 TTTTTTTTTTT
1 TTTTTTTTTTT
21397593 AAAAAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:21401880 original size:24 final size:23
Alignment explanation
Indices: 21401848--21401908 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
21401838 CATATAAAAT
*
21401848 AAAATAAATAAAATACGCAATA-CG
1 AAAA-AAATAAAAT-CGAAATATCG
*
21401872 AAAGAAAATTCAAATCGAAATATCG
1 AAA-AAAA-TAAAATCGAAATATCG
21401897 AAAAAAATAAAA
1 AAAAAAATAAAA
21401909 AGACAAGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 4 0.13
24 16 0.52
25 11 0.35
ACGTcount: A:0.66, C:0.10, G:0.08, T:0.16
Consensus pattern (23 bp):
AAAAAAATAAAATCGAAATATCG
Found at i:21402054 original size:30 final size:29
Alignment explanation
Indices: 21402018--21402250 Score: 146
Period size: 30 Copynumber: 7.8 Consensus size: 29
21402008 AAAAATGAAA
*
21402018 TTTTGGAAAGTTCGAGGGCCAAATTCAATT
1 TTTTGGAAAGTTCGAGGGTCAAATTCAA-T
* *
21402048 TTTTGGAAAGTT-TAGGGGTCAAATTTAAAT
1 TTTTGGAAAGTTCGA-GGGTCAAA-TTCAAT
* *
21402078 TTTTGAAAAGTTCGAGAGTCAAATTCGAAT
1 TTTTGGAAAGTTCGAGGGTCAAATTC-AAT
* * * *
21402108 TTTTGGAAAGTTTGGGGGTTAAATTTAAAT
1 TTTTGGAAAGTTCGAGGGTCAAA-TTCAAT
* * * * * *
21402138 TTTTAGAGAGTTCAAGGGTCAAAAATGAAA
1 TTTTGGAAAGTTCGAGGGTC-AAATTCAAT
* * *
21402168 TTTTGAAAAGTTTGAGGGGTAAAATTCAAAT
1 TTTTGGAAAGTTCGA-GGGTCAAATTC-AAT
** * * *
21402199 TTTTTAAAAGTTTGGGGGTCAAATTCAAAA
1 TTTTGGAAAGTTCGAGGGTCAAATTC-AAT
* *
21402229 TTTTGGAAAATTTG-GGGTCAAA
1 TTTTGGAAAGTTCGAGGGTCAAA
21402251 ATATCATTTT
Statistics
Matches: 157, Mismatches: 38, Indels: 17
0.74 0.18 0.08
Matches are distributed among these distances:
29 11 0.07
30 117 0.75
31 29 0.18
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (29 bp):
TTTTGGAAAGTTCGAGGGTCAAATTCAAT
Found at i:21402101 original size:60 final size:59
Alignment explanation
Indices: 21402001--21402250 Score: 236
Period size: 60 Copynumber: 4.2 Consensus size: 59
21401991 ATAAGGAAAA
* * * * *
21402001 AGGGGTCAAAAATGAAA-TTTTGGAAAGTTCGAGGGCCAAATTCAATTTTTTGGAAAGTTT
1 AGGGGTC-AAATTTAAATTTTTGAAAAGTTCGAGGGTCAAATTCAA-ATTTTGGAAAGTTT
* *
21402061 AGGGGTCAAATTTAAATTTTTGAAAAGTTCGAGAGTCAAATTCGAATTTTTGGAAAGTTT
1 AGGGGTCAAATTTAAATTTTTGAAAAGTTCGAGGGTCAAATTC-AAATTTTGGAAAGTTT
* * * * * * *
21402121 GGGGGTTAAATTTAAATTTTT-AGAGAGTTCAAGGGTCAAAAATGAAATTTTGAAAAGTTT
1 AGGGGTCAAATTTAAATTTTTGA-AAAGTTCGAGGGTC-AAATTCAAATTTTGGAAAGTTT
* * * * * *
21402181 GAGGGGTAAAATTCAAATTTTTTAAAAGTTTGGGGGTCAAATTCAAAATTTTGGAAAATTT
1 -AGGGGTCAAATTTAAATTTTTGAAAAGTTCGAGGGTCAAATTC-AAATTTTGGAAAGTTT
21402242 -GGGGTCAAA
1 AGGGGTCAAA
21402251 ATATCATTTT
Statistics
Matches: 157, Mismatches: 26, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
59 16 0.10
60 92 0.59
61 48 0.31
62 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (59 bp):
AGGGGTCAAATTTAAATTTTTGAAAAGTTCGAGGGTCAAATTCAAATTTTGGAAAGTTT
Found at i:21402112 original size:90 final size:90
Alignment explanation
Indices: 21402018--21402252 Score: 258
Period size: 90 Copynumber: 2.6 Consensus size: 90
21402008 AAAAATGAAA
* * * * * *
21402018 TTTTGGAAAGTTCGAGGGCCAAATTCAATTTTTTGGAAAGTTTAGGGGTCAAATTTAAATTTTTG
1 TTTTGGAAAGTTTGGGGGTCAAATTCAAATTTTTGGAAAGTTTAGGGGTCAAAATGAAA-TTTTG
* *
21402083 AAAAGTTCGA-GAGTCAAATTCGAAT
65 AAAAGTTCGAGGAGTAAAATTCAAAT
* * * * * *
21402108 TTTTGGAAAGTTTGGGGGTTAAATTTAAATTTTTAGAGAGTTCAAGGGTCAAAAATGAAATTTTG
1 TTTTGGAAAGTTTGGGGGTCAAATTCAAATTTTTGGAAAGTTTAGGGGTC-AAAATGAAATTTTG
* *
21402173 AAAAGTTTGAGGGGTAAAATTCAAAT
65 AAAAGTTCGAGGAGTAAAATTCAAAT
** * *
21402199 TTTTTAAAAGTTTGGGGGTCAAATTCAAAATTTTGGAAAATTT-GGGGTCAAAAT
1 TTTTGGAAAGTTTGGGGGTCAAATTCAAATTTTTGGAAAGTTTAGGGGTCAAAAT
21402253 ATCATTTTTA
Statistics
Matches: 117, Mismatches: 26, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
89 5 0.04
90 59 0.50
91 53 0.45
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (90 bp):
TTTTGGAAAGTTTGGGGGTCAAATTCAAATTTTTGGAAAGTTTAGGGGTCAAAATGAAATTTTGA
AAAGTTCGAGGAGTAAAATTCAAAT
Found at i:21403685 original size:16 final size:16
Alignment explanation
Indices: 21403640--21403686 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
21403630 CCTCTACAAG
21403640 ATAATTACATGTAAA-AA
1 ATAA-TACAT-TAAATAA
* *
21403657 ATAATAAAATAAATAA
1 ATAATACATTAAATAA
21403673 ATAATACATTAAAT
1 ATAATACATTAAAT
21403687 TAAAAAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 4 0.16
16 17 0.68
17 4 0.16
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (16 bp):
ATAATACATTAAATAA
Found at i:21408592 original size:33 final size:33
Alignment explanation
Indices: 21408548--21408610 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
21408538 TAATTGAATG
*
21408548 ATTGTTATTTTAAGGGAAATTTGTATTTTTTTT
1 ATTGTTATTTTAAGGGAAATTAGTATTTTTTTT
*
21408581 ATTGTTTTTTTAAGGGAAATTAGTATTTTT
1 ATTGTTATTTTAAGGGAAATTAGTATTTTT
21408611 AATAGAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.16, T:0.59
Consensus pattern (33 bp):
ATTGTTATTTTAAGGGAAATTAGTATTTTTTTT
Found at i:21408735 original size:44 final size:44
Alignment explanation
Indices: 21408667--21408756 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
21408657 GATTCTAAAG
*
21408667 ATAGATTTTGAAAAAGAATTTGTGTTGGAGGATCTCAATGATTA
1 ATAGATTTTGAAAAAGAATCTGTGTTGGAGGATCTCAATGATTA
21408711 ATAGATTTTGAAAAAGAATCTGTGTTGGAGGATCTCAATGATTA
1 ATAGATTTTGAAAAAGAATCTGTGTTGGAGGATCTCAATGATTA
21408755 AT
1 AT
21408757 TTTAATCCTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.36
Consensus pattern (44 bp):
ATAGATTTTGAAAAAGAATCTGTGTTGGAGGATCTCAATGATTA
Found at i:21416182 original size:16 final size:16
Alignment explanation
Indices: 21416161--21416191 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21416151 AAAATTAATT
*
21416161 ATTTTTTTAAAATATA
1 ATTTTTTAAAAATATA
21416177 ATTTTTTAAAAATAT
1 ATTTTTTAAAAATAT
21416192 TTTAAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTTTAAAAATATA
Found at i:21416196 original size:11 final size:11
Alignment explanation
Indices: 21416176--21416221 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
21416166 TTTAAAATAT
21416176 AATT-TTTTAA
1 AATTATTTTAA
*
21416186 AAATATTTTAA
1 AATTATTTTAA
*
21416197 AATTAATTTAA
1 AATTATTTTAA
*
21416208 AATTATTTTTA
1 AATTATTTTAA
21416219 AAT
1 AAT
21416222 ATAAAATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 3 0.10
11 27 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTATTTTAA
Found at i:21416205 original size:12 final size:12
Alignment explanation
Indices: 21416165--21416220 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 12
21416155 TTAATTATTT
21416165 TTTTAAAATATAA
1 TTTTAAAAT-TAA
*
21416178 TTTTTTAAAAAT-A
1 --TTTTAAAATTAA
21416191 TTTTAAAATTAA
1 TTTTAAAATTAA
*
21416203 -TTTAAAATTAT
1 TTTTAAAATTAA
21416214 TTTTAAA
1 TTTTAAA
21416221 TATAAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 19 0.53
12 7 0.19
13 1 0.03
14 1 0.03
15 8 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTAAAATTAA
Found at i:21417156 original size:23 final size:25
Alignment explanation
Indices: 21417126--21417172 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
21417116 TAATTTTATA
21417126 TTTAAAAAA-TA-ATTTTAAAAAAT
1 TTTAAAAAATTATATTTTAAAAAAT
21417149 TTTAAAAAATTATATTTTAAAAAA
1 TTTAAAAAATTATATTTTAAAAAA
21417173 AATAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 9 0.41
24 2 0.09
25 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TTTAAAAAATTATATTTTAAAAAAT
Found at i:21418433 original size:2 final size:2
Alignment explanation
Indices: 21418426--21418457 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
21418416 TGCATACATT
*
21418426 CA CA CA CA CA CA CA TA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
21418458 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:21419860 original size:53 final size:53
Alignment explanation
Indices: 21419746--21419875 Score: 208
Period size: 53 Copynumber: 2.4 Consensus size: 53
21419736 TGGTTCACTT
*
21419746 GGTTTGGGTCAAATGTTTGGGTTTAAGTTTATTGGGTTGGTTTTGGGTAATAAG
1 GGTTTGGGTCAAA-GTTTGGGTTTAAGTTTATTGGGTTGGTTTTAGGTAATAAG
21419800 GGTTTGGGTCAAAGGTTTGGGTTTAAGTTTATT-GGTTGGTTTTAGGTAATAAG
1 GGTTTGGGTCAAA-GTTTGGGTTTAAGTTTATTGGGTTGGTTTTAGGTAATAAG
*
21419853 GGTTTGGGTTTAAAGTTTGGGTT
1 GGTTTGGG-TCAAAGTTTGGGTT
21419876 AGATATAAAG
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
53 36 0.50
54 36 0.50
ACGTcount: A:0.18, C:0.02, G:0.35, T:0.45
Consensus pattern (53 bp):
GGTTTGGGTCAAAGTTTGGGTTTAAGTTTATTGGGTTGGTTTTAGGTAATAAG
Found at i:21425607 original size:10 final size:10
Alignment explanation
Indices: 21425594--21425619 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
21425584 CGCATACTTT
21425594 CACATACACA
1 CACATACACA
21425604 CACATACACA
1 CACATACACA
21425614 CACATA
1 CACATA
21425620 TATATATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (10 bp):
CACATACACA
Found at i:21425765 original size:13 final size:13
Alignment explanation
Indices: 21425740--21425776 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
21425730 TAAAAACCCA
*
21425740 AAAATATAATAAT
1 AAAATAAAATAAT
*
21425753 AAGATAAAATAAT
1 AAAATAAAATAAT
21425766 AAAATAAAATA
1 AAAATAAAATA
21425777 TCCATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:21426829 original size:14 final size:14
Alignment explanation
Indices: 21426810--21426910 Score: 73
Period size: 14 Copynumber: 7.4 Consensus size: 14
21426800 GAAAAAAGAT
*
21426810 AACGATTAACGGTC
1 AACGATCAACGGTC
*
21426824 AACGATCATA--GTT
1 AACGATCA-ACGGTC
* *
21426837 AACGGTCAATGGTC
1 AACGATCAACGGTC
* * *
21426851 AAAG-TTAACAGTC
1 AACGATCAACGGTC
* *
21426864 AACGATCTACGATC
1 AACGATCAACGGTC
*
21426878 AACGATCAATGGTC
1 AACGATCAACGGTC
*
21426892 AACGATCAACGATC
1 AACGATCAACGGTC
21426906 AACGA
1 AACGA
21426911 GTCGGGTCGG
Statistics
Matches: 65, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
12 1 0.02
13 18 0.28
14 45 0.69
15 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (14 bp):
AACGATCAACGGTC
Found at i:21426840 original size:20 final size:20
Alignment explanation
Indices: 21426815--21426870 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
21426805 AAGATAACGA
*
21426815 TTAACGGTCAACGATCATAG
1 TTAACGGTCAACGATCAAAG
* *
21426835 TTAACGGTCAATGGTCAAAG
1 TTAACGGTCAACGATCAAAG
*
21426855 TTAACAGTCAACGATC
1 TTAACGGTCAACGATC
21426871 TACGATCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
TTAACGGTCAACGATCAAAG
Found at i:21426877 original size:7 final size:7
Alignment explanation
Indices: 21426862--21426910 Score: 71
Period size: 7 Copynumber: 7.0 Consensus size: 7
21426852 AAGTTAACAG
21426862 TCAACGA
1 TCAACGA
*
21426869 TCTACGA
1 TCAACGA
21426876 TCAACGA
1 TCAACGA
* *
21426883 TCAATGG
1 TCAACGA
21426890 TCAACGA
1 TCAACGA
21426897 TCAACGA
1 TCAACGA
21426904 TCAACGA
1 TCAACGA
21426911 GTCGGGTCGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (7 bp):
TCAACGA
Found at i:21429968 original size:28 final size:28
Alignment explanation
Indices: 21429895--21429972 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
21429885 TTTAAAGGTC
*
21429895 AATTTTTTTACCAACTTTTAAGGAGCCCT
1 AATTTTTTTACCAACTTTTTA-GAGCCCT
** *
21429924 AATTTTTTT-TTATCTTTTTAGAGCCC-
1 AATTTTTTTACCAACTTTTTAGAGCCCT
21429950 AAGTTTTTTTACCAACTTTTTAG
1 AA-TTTTTTTACCAACTTTTTAG
21429973 GGGCTTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
26 2 0.05
27 13 0.32
28 16 0.40
29 9 0.22
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (28 bp):
AATTTTTTTACCAACTTTTTAGAGCCCT
Found at i:21431619 original size:31 final size:30
Alignment explanation
Indices: 21431576--21431642 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
21431566 TAAATTTTTT
21431576 TTTTGTCCAATTT-GATACTCAAACTTGACAC
1 TTTT-TCCAATTTAGA-ACTCAAACTTGACAC
*
21431607 TTTTTCCTAATTTAGAACTTAAACTTGACAC
1 TTTTTCC-AATTTAGAACTCAAACTTGACAC
21431638 TTTTT
1 TTTTT
21431643 TTAAGTTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 3 0.09
31 28 0.85
32 2 0.06
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.45
Consensus pattern (30 bp):
TTTTTCCAATTTAGAACTCAAACTTGACAC
Found at i:21431948 original size:58 final size:58
Alignment explanation
Indices: 21431867--21432029 Score: 213
Period size: 58 Copynumber: 2.8 Consensus size: 58
21431857 TAATAAATTT
*
21431867 AAGTACCAAATTGAATCTAAAAAAAGTTTAAGTGCCAAATTAA-AAAAAATGCCAAGTTC
1 AAGTACCAAATTGAATC-AAAAAAA-TTTAAGTACCAAATTAAGAAAAAATGCCAAGTTC
* * *
21431926 AAGTATCAAATT-AGATCAAAAAAATTTAAGTACTAAATTAAGAAAAAATGTCAAGTTC
1 AAGTACCAAATTGA-ATCAAAAAAATTTAAGTACCAAATTAAGAAAAAATGCCAAGTTC
* * * *
21431984 ACGTACCAAATTGAATAAAAAAAATTTAAGAACAAAATTAAGAAAA
1 AAGTACCAAATTGAATCAAAAAAATTTAAGTACCAAATTAAGAAAA
21432030 TGTGTCAAAT
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
57 15 0.16
58 62 0.67
59 15 0.16
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.24
Consensus pattern (58 bp):
AAGTACCAAATTGAATCAAAAAAATTTAAGTACCAAATTAAGAAAAAATGCCAAGTTC
Found at i:21450808 original size:18 final size:16
Alignment explanation
Indices: 21450787--21450861 Score: 69
Period size: 18 Copynumber: 4.3 Consensus size: 16
21450777 TAATAAAAAA
21450787 TAAATTTATTCTAAAATT
1 TAAATTTATT-T-AAATT
*
21450805 TAAATTTAATTTAAGTT
1 TAAATTT-ATTTAAATT
*
21450822 TAAATTTATATTTATATT
1 TAAA-TT-TATTTAAATT
*
21450840 TAAAATTATTATAAATT
1 TAAATTTATT-TAAATT
21450857 TAAAT
1 TAAAT
21450862 AATAAATGTC
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
16 4 0.09
17 18 0.38
18 21 0.45
19 4 0.09
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (16 bp):
TAAATTTATTTAAATT
Found at i:21450811 original size:6 final size:6
Alignment explanation
Indices: 21450800--21450861 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
21450790 ATTTATTCTA
* * * *
21450800 AAATTT AAATTT -AATTT AAGTTT AAATTT ATATTT ATATTT AAAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
21450847 --ATTAT AAATTT AAAT
1 AAATT-T AAATTT AAAT
21450862 AATAAATGTC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 2 0.04
5 6 0.13
6 35 0.76
7 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:21450825 original size:17 final size:16
Alignment explanation
Indices: 21450801--21450861 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
21450791 TTTATTCTAA
21450801 AATTTAAATTTAATTT
1 AATTTAAATTTAATTT
21450817 AAGTTTAAATTTATATTT
1 AA-TTTAAATTTA-ATTT
*
21450835 ATATTTAAAATT-ATTAT
1 A-ATTTAAATTTAATT-T
21450852 AAATTTAAAT
1 -AATTTAAAT
21450862 AATAAATGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 5 0.13
17 18 0.47
18 14 0.37
19 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AATTTAAATTTAATTT
Found at i:21451656 original size:3 final size:3
Alignment explanation
Indices: 21451650--21451685 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
21451640 AATAAGTCTT
*
21451650 TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21451686 CATTTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:21452761 original size:29 final size:28
Alignment explanation
Indices: 21452708--21452850 Score: 146
Period size: 29 Copynumber: 5.0 Consensus size: 28
21452698 ATATTTAGAC
* *
21452708 CCCTGAACTTTTCCAAAATTCCATTTTTAA
1 CCCTAAAC-TTTCCAAAATTACATTTTT-A
* *
21452738 CCCTGAAC-TTCCAAAAATTACATTTTTT
1 CCCTAAACTTTCC-AAAATTACATTTTTA
*
21452766 CCCTTAAACTTTCCAAAATTACATTTTGA
1 CCC-TAAACTTTCCAAAATTACATTTTTA
*
21452795 CCAC-AAAATTTCCAAAAATTACATTTTTA
1 CC-CTAAACTTTCC-AAAATTACATTTTTA
* *
21452824 CCCCAAACTTTCCAAAATTTCATTTTT
1 CCCTAAACTTTCCAAAATTACATTTTT
21452851 GACCTCGATT
Statistics
Matches: 98, Mismatches: 9, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
28 29 0.30
29 56 0.57
30 13 0.13
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.38
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAATTACATTTTTA
Found at i:21452851 original size:58 final size:58
Alignment explanation
Indices: 21452717--21452854 Score: 181
Period size: 58 Copynumber: 2.4 Consensus size: 58
21452707 CCCCTGAACT
* * ** * *
21452717 TTTCCAAAATTCCATTTTTAACCCTGAACTTCCAAAAATTACATTTTTTCCCTTAAAC
1 TTTCCAAAATTACATTTTTGACCCAAAACTTCCAAAAATTACATTTTTACCCTCAAAC
*
21452775 TTTCCAAAATTACA-TTTTGACCACAAAATTTCCAAAAATTACATTTTTACCC-CAAAC
1 TTTCCAAAATTACATTTTTGACC-CAAAACTTCCAAAAATTACATTTTTACCCTCAAAC
*
21452832 TTTCCAAAATTTCATTTTTGACC
1 TTTCCAAAATTACATTTTTGACC
21452855 TCGATTTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
57 24 0.34
58 46 0.66
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (58 bp):
TTTCCAAAATTACATTTTTGACCCAAAACTTCCAAAAATTACATTTTTACCCTCAAAC
Found at i:21452930 original size:30 final size:28
Alignment explanation
Indices: 21452868--21452939 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
21452858 ATTTTTTTCC
21452868 AAAATTACCATTTTACCCCTGAGTGACCA
1 AAAATTA-CATTTTACCCCTGAGTGACCA
* *
21452897 AAAATTATCATTTTGCCCCTCGGGT-ATCCA
1 AAAATTA-CATTTTACCCCT-GAGTGA-CCA
*
21452927 AAAATCACATTTT
1 AAAATTACATTTT
21452940 CAACTCCGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.32
Consensus pattern (28 bp):
AAAATTACATTTTACCCCTGAGTGACCA
Found at i:21455407 original size:30 final size:30
Alignment explanation
Indices: 21455371--21455667 Score: 309
Period size: 30 Copynumber: 9.9 Consensus size: 30
21455361 TAAGTTGTCC
*
21455371 AAAAATTACATTTTAACCCCAAAACTTTCT
1 AAAAATTACATTTTGACCCCAAAACTTTCT
*
21455401 AAAAATTTCATTTTGACCCCAAAACTTTCCT
1 AAAAATTACATTTTGACCCCAAAACTTT-CT
* *
21455432 -AAAATTATATTTTGACCCTAAAACTTTCT
1 AAAAATTACATTTTGACCCCAAAACTTTCT
* **
21455461 AAAAATTATATTTTGACCTTAAAACTTT-T
1 AAAAATTACATTTTGACCCCAAAACTTTCT
* *
21455490 CCAAAATTATATTTTGACCCCAAAACTTTCT
1 -AAAAATTACATTTTGACCCCAAAACTTTCT
*
21455521 AAAAATTACATTTTGACCCTAAAACTTT-T
1 AAAAATTACATTTTGACCCCAAAACTTTCT
* * *
21455550 CCAAAATTACATTTTAACCCTAAAACTTT-T
1 -AAAAATTACATTTTGACCCCAAAACTTTCT
* * *
21455580 CCAAAATTACATTTTGACTCCAAAAATTT-T
1 -AAAAATTACATTTTGACCCCAAAACTTTCT
* * *
21455610 CCAAAATTATACTTTGACCCCAAAACTTTC-
1 -AAAAATTACATTTTGACCCCAAAACTTTCT
* *
21455640 AAAAATTACCATTTTTACCCCCAAACTT
1 AAAAATTA-CATTTTGACCCCAAAACTT
21455668 CCTTAAATCC
Statistics
Matches: 233, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
29 11 0.05
30 219 0.94
31 3 0.01
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCCAAAACTTTCT
Found at i:21455465 original size:60 final size:59
Alignment explanation
Indices: 21455372--21455667 Score: 371
Period size: 60 Copynumber: 4.9 Consensus size: 59
21455362 AAGTTGTCCA
* * *
21455372 AAAATTACATTTTAACCCCAAAACTTTCTAAAAATTTCATTTTGACCCCAAAACTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTCC
* * **
21455431 TAAAATTATATTTTGACCCTAAAACTTTCTAAAAATTATATTTTGACCTTAAAACTTTTCC
1 -AAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCCAAAAC-TTTCC
*
21455492 AAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCCAAAAC-TTTCC
* * * * * *
21455552 AAAATTACATTTTAACCCTAAAACTTT-TCCAAAATTACATTTTGACTCCAAAAATTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTCT-AAAAATTACATTTTGAC-CCCAAAACTTTCC
* * *
21455612 AAAATTATACTTTGACCCCAAAACTTTC-AAAAATTACCATTTTTACCCCCAAACTT
1 AAAATTATATTTTGACCCCAAAACTTTCTAAAAATTA-CATTTTGACCCCAAAACTT
21455668 CCTTAAATCC
Statistics
Matches: 206, Mismatches: 25, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
59 15 0.07
60 180 0.87
61 11 0.05
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.36
Consensus pattern (59 bp):
AAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTCC
Found at i:21455666 original size:90 final size:88
Alignment explanation
Indices: 21455370--21455667 Score: 373
Period size: 90 Copynumber: 3.3 Consensus size: 88
21455360 CTAAGTTGTC
* *
21455370 CAAAAATTACATTTTAACCCCAAAAC-TTTCTAAAAATTTCATTTTGACCCCAAAACTTTCCTAA
1 CAAAAATTACATTTTAACCCCAAAACTTTTC-CAAAATTACATTTTGACCCCAAAACTTTCC-AA
21455434 AATTATATTTTGACCCTAAAACTTT
64 AATTATATTTTGACCCTAAAACTTT
* * ** * *
21455459 CTAAAAATTATATTTTGACCTTAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTCTAAA
1 C-AAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTC-CAA
*
21455524 AATTACATTTTGACCCTAAAACTTTT
64 AATTATATTTTGACCCTAAAAC-TTT
* * * *
21455550 CCAAAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTGACTCCAAAAATTTTCCAAA
1 CAAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGAC-CCCAAAACTTTCCAAA
* *
21455615 ATTATACTTTGACCCCAAAACTTT
65 ATTATATTTTGACCCTAAAACTTT
* *
21455639 CAAAAATTACCATTTTTACCCCCAAACTT
1 CAAAAATTA-CATTTTAACCCCAAAACTT
21455668 CCTTAAATCC
Statistics
Matches: 179, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
89 12 0.07
90 149 0.83
91 18 0.10
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.36
Consensus pattern (88 bp):
CAAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTCCAAAA
TTATATTTTGACCCTAAAACTTT
Found at i:21455822 original size:59 final size:57
Alignment explanation
Indices: 21455639--21455831 Score: 158
Period size: 59 Copynumber: 3.3 Consensus size: 57
21455629 CCAAAACTTT
* * *
21455639 CAAAAATTACCATTTTTACCCCCAAAC-TTCCTTAAATCCCATTTTTAACCCCGATTTCA
1 CAAAAATTACCATTTTT-CCCTCAAACTTTCC--AAATTCCATTTTTAGCCCCGATTTCA
* * * * * ** * *
21455698 CCAAAACTTACC-GTTTTGCCTCCGAACTTTCCAAATTTTCATTTTT-GACCTTGTTTTTA
1 -CAAAAATTACCATTTTTCCCT-CAAACTTTCCAAA-TTCCATTTTTAG-CCCCGATTTCA
* *
21455757 CCAAAATTTACCATTTTATTCCTCAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA
1 -CAAAAATTACCATTTT-TCCCTCAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA
21455816 CAAAAATTACCATTTT
1 CAAAAATTACCATTTT
21455832 ACCCCTAAAA
Statistics
Matches: 104, Mismatches: 22, Indels: 16
0.73 0.15 0.11
Matches are distributed among these distances:
58 20 0.19
59 50 0.48
60 30 0.29
61 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.04, T:0.39
Consensus pattern (57 bp):
CAAAAATTACCATTTTTCCCTCAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA
Found at i:21472373 original size:28 final size:28
Alignment explanation
Indices: 21472341--21472398 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
21472331 CTAGCCTTTA
*
21472341 AATCAAAATTGTATAATACAACAAGCGC
1 AATCAAAATTATATAATACAACAAGCGC
21472369 AATCAAAATTATATAATACAACAAGCGC
1 AATCAAAATTATATAATACAACAAGCGC
21472397 AA
1 AA
21472399 GTTACTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.53, C:0.17, G:0.09, T:0.21
Consensus pattern (28 bp):
AATCAAAATTATATAATACAACAAGCGC
Found at i:21472842 original size:46 final size:46
Alignment explanation
Indices: 21472724--21472865 Score: 164
Period size: 46 Copynumber: 3.1 Consensus size: 46
21472714 CAAATTGATT
* * *
21472724 TTAAATTAGGTTTTGATTGCTTCCAATTACTTGTTTTA--T-ATAGAT
1 TTAAATTAGG-TTAGATTGCTT-CAATTACCTGTTTTATTTAATAGAC
* * *
21472769 TTAAAGTAGGTTGGATTGCTTCTATTACCTGTTTTATTTAATAGAC
1 TTAAATTAGGTTAGATTGCTTCAATTACCTGTTTTATTTAATAGAC
* * *
21472815 TTAAATTAGGCTAGATTTCTTCAATTACCTGTTTTATTTAATAGAG
1 TTAAATTAGGTTAGATTGCTTCAATTACCTGTTTTATTTAATAGAC
21472861 TTAAA
1 TTAAA
21472866 GTCAGCAATA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
43 13 0.16
44 10 0.12
45 10 0.12
46 50 0.60
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (46 bp):
TTAAATTAGGTTAGATTGCTTCAATTACCTGTTTTATTTAATAGAC
Found at i:21473948 original size:15 final size:16
Alignment explanation
Indices: 21473928--21473979 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
21473918 CTAATAAAAT
*
21473928 ATAAAATAAAT-GGAA
1 ATAAAAAAAATAGGAA
21473943 ATAAAAAAAATAGGAA
1 ATAAAAAAAATAGGAA
*
21473959 AAAGAAAAAGAATA-GAA
1 ATA-AAAAA-AATAGGAA
21473976 ATAA
1 ATAA
21473980 TATTTTGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 10 0.32
16 7 0.23
17 10 0.32
18 4 0.13
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (16 bp):
ATAAAAAAAATAGGAA
Found at i:21474391 original size:20 final size:20
Alignment explanation
Indices: 21474347--21474411 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 20
21474337 AAAATTGGAT
*
21474347 ATATCTATATAAT--TAATCT
1 ATATCTATATAATAATAAT-A
21474366 ATATCTATATAATAATAATA
1 ATATCTATATAATAATAATA
21474386 ATATCTATATCTAGATAATAATA
1 ATATCTATA--TA-ATAATAATA
21474409 ATA
1 ATA
21474412 AAATTTAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 13 0.32
20 9 0.22
21 4 0.10
22 2 0.05
23 12 0.30
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (20 bp):
ATATCTATATAATAATAATA
Found at i:21474397 original size:26 final size:26
Alignment explanation
Indices: 21474362--21474412 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
21474352 TATATAATTA
*
21474362 ATCTATATCTATATAATAATAATAAT
1 ATCTATATCTAGATAATAATAATAAT
21474388 ATCTATATCTAGATAATAATAATAA
1 ATCTATATCTAGATAATAATAATAA
21474413 AATTTAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (26 bp):
ATCTATATCTAGATAATAATAATAAT
Found at i:21475590 original size:23 final size:23
Alignment explanation
Indices: 21475559--21475603 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21475549 TTCTTTGGGG
*
21475559 GCCAAAATAAAATTATAATTTTT
1 GCCAAAATAAAAATATAATTTTT
* *
21475582 GCCATAATAAAAATGTAATTTT
1 GCCAAAATAAAAATATAATTTT
21475604 ATCATTGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (23 bp):
GCCAAAATAAAAATATAATTTTT
Found at i:21476540 original size:25 final size:25
Alignment explanation
Indices: 21476512--21476566 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
21476502 TATCATATAA
21476512 AAAATT-TTAATAAATAAAA-ATAAAT
1 AAAATTATTAA-AAATAAAATA-AAAT
*
21476537 AAAATTATTAAACATAAAATAAAAT
1 AAAATTATTAAAAATAAAATAAAAT
21476562 AAAAT
1 AAAAT
21476567 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAATTATTAAAAATAAAATAAAAT
Found at i:21486114 original size:20 final size:20
Alignment explanation
Indices: 21486091--21486277 Score: 114
Period size: 20 Copynumber: 8.8 Consensus size: 20
21486081 AAAACGCATA
21486091 AAAAATAACATCAAAACAAC
1 AAAAATAACATCAAAACAAC
*
21486111 AAAAATAACATCCAAACAAC
1 AAAAATAACATCAAAACAAC
*
21486131 AAAAATAACAACCAAAACAGCAGC
1 AAAAATAAC-ATCAAAACA--A-C
*
21486155 AAAAATAACAGC-AAACAAC
1 AAAAATAACATCAAAACAAC
* *
21486174 ATTAAAAACAACA-AAAATAGCAAC
1 ---AAAAATAACATCAAA-A-CAAC
*
21486198 AAAAATAACAGTAAAAACAAC
1 AAAAATAACA-TCAAAACAAC
21486219 ACGAAAATAACAATCAAAACAGTA-
1 A--AAAATAAC-ATCAAAACA--AC
* * *
21486243 AAAAAAAAGCACCAAAACAAT
1 AAAAATAA-CATCAAAACAAC
21486264 AAAAA-AACA-CAAAA
1 AAAAATAACATCAAAA
21486278 ACAGTAAAAA
Statistics
Matches: 138, Mismatches: 10, Indels: 40
0.73 0.05 0.21
Matches are distributed among these distances:
18 5 0.04
19 3 0.02
20 32 0.23
21 26 0.19
22 31 0.22
23 24 0.17
24 16 0.12
25 1 0.01
ACGTcount: A:0.68, C:0.19, G:0.04, T:0.08
Consensus pattern (20 bp):
AAAAATAACATCAAAACAAC
Found at i:21486142 original size:12 final size:12
Alignment explanation
Indices: 21486125--21486237 Score: 60
Period size: 12 Copynumber: 9.8 Consensus size: 12
21486115 ATAACATCCA
21486125 AACAACAAAAAT
1 AACAACAAAAAT
* *
21486137 AACAACCAAAAC
1 AACAACAAAAAT
* *
21486149 AGCAGCAAAAAT
1 AACAACAAAAAT
*
21486161 AACAGC----A-
1 AACAACAAAAAT
*
21486168 AACAACATTAAA-
1 AACAACA-AAAAT
21486180 AACAACAAAAAT
1 AACAACAAAAAT
*
21486192 AGCAACAAAAAT
1 AACAACAAAAAT
** *
21486204 AACAGTAAAAAC
1 AACAACAAAAAT
*
21486216 AAC-ACGAAAAT
1 AACAACAAAAAT
21486227 AACAATCAAAA
1 AACAA-CAAAA
21486238 CAGTAAAAAA
Statistics
Matches: 74, Mismatches: 19, Indels: 15
0.69 0.18 0.14
Matches are distributed among these distances:
7 5 0.07
8 1 0.01
11 10 0.14
12 54 0.73
13 4 0.05
ACGTcount: A:0.67, C:0.19, G:0.05, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:21486184 original size:43 final size:43
Alignment explanation
Indices: 21486107--21486289 Score: 146
Period size: 43 Copynumber: 4.2 Consensus size: 43
21486097 AACATCAAAA
* *
21486107 CAACAAAAATAACATCCAAACAACAAAAATAACAACCAAAACAG
1 CAACAAAAATAACA-GCAAACAACAAAAATAACAACAAAAACAG
* * *
21486151 CAGCAAAAATAACAGCAAACAACATTAAA-AACAACAAAAATAG
1 CAACAAAAATAACAGCAAACAACA-AAAATAACAACAAAAACAG
*
21486194 CAACAAAAATAACAGTAAAAACAACACGAAAATAACAATC-AAAACAG
1 CAACAAAAATAACAG--CAAACAACA--AAAATAACAA-CAAAAACAG
* * *
21486241 TAA-AAAAA-AAGCACCAAAACAATAAAAA-AAC-ACAAAAACAG
1 CAACAAAAATAA-CAGC-AAACAACAAAAATAACAACAAAAACAG
*
21486282 TAA-AAAAA
1 CAACAAAAA
21486290 CAGCAACCAA
Statistics
Matches: 116, Mismatches: 14, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
40 1 0.01
41 16 0.14
42 3 0.03
43 39 0.34
44 16 0.14
45 17 0.15
46 10 0.09
47 13 0.11
48 1 0.01
ACGTcount: A:0.68, C:0.19, G:0.05, T:0.08
Consensus pattern (43 bp):
CAACAAAAATAACAGCAAACAACAAAAATAACAACAAAAACAG
Found at i:21486216 original size:33 final size:35
Alignment explanation
Indices: 21486171--21486237 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 35
21486161 AACAGCAAAC
* *
21486171 AACATTAAAAACAACA-AAAATAGCAA-CAAAAAT
1 AACAGTAAAAACAACACAAAATAACAATCAAAAAT
21486204 AACAGTAAAAACAACACGAAAATAACAATCAAAA
1 AACAGTAAAAACAACAC-AAAATAACAATCAAAA
21486238 CAGTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 15 0.52
35 9 0.31
36 5 0.17
ACGTcount: A:0.69, C:0.16, G:0.04, T:0.10
Consensus pattern (35 bp):
AACAGTAAAAACAACACAAAATAACAATCAAAAAT
Found at i:21486269 original size:19 final size:19
Alignment explanation
Indices: 21486245--21486324 Score: 79
Period size: 19 Copynumber: 3.9 Consensus size: 19
21486235 AAACAGTAAA
21486245 AAAAAAGCACCAAAACAAT
1 AAAAAAGCACCAAAACAAT
* * *
21486264 AAAAAAACACAAAAACAGTAA
1 AAAAAAGCACCAAAACA--AT
*
21486285 AAAAACAGCAACCAAAACAGT
1 AAAAA-AGC-ACCAAAACAAT
21486306 AAAAAAAGCACCAAAACAA
1 -AAAAAAGCACCAAAACAA
21486325 CAATATAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
19 15 0.31
20 9 0.19
21 9 0.19
22 7 0.15
23 8 0.17
ACGTcount: A:0.70, C:0.20, G:0.06, T:0.04
Consensus pattern (19 bp):
AAAAAAGCACCAAAACAAT
Found at i:21486286 original size:41 final size:43
Alignment explanation
Indices: 21486234--21486323 Score: 139
Period size: 41 Copynumber: 2.1 Consensus size: 43
21486224 AATAACAATC
21486234 AAAACAGTAAAAAAAAAGC-ACCAAAACAATAAAAAAA-CACA
1 AAAACAGTAAAAAAAAAGCAACCAAAACAATAAAAAAAGCACA
* * *
21486275 AAAACAGTAAAAAAACAGCAACCAAAACAGTAAAAAAAGCACC
1 AAAACAGTAAAAAAAAAGCAACCAAAACAATAAAAAAAGCACA
21486318 AAAACA
1 AAAACA
21486324 ACAATATAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 18 0.41
42 17 0.39
43 9 0.20
ACGTcount: A:0.70, C:0.19, G:0.07, T:0.04
Consensus pattern (43 bp):
AAAACAGTAAAAAAAAAGCAACCAAAACAATAAAAAAAGCACA
Found at i:21498141 original size:23 final size:22
Alignment explanation
Indices: 21498084--21498141 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
21498074 ATTCTCATTT
*
21498084 AATTAATAAATATATATTTTTAAA
1 AATT-ATAAA-ATATATTATTAAA
21498108 AATTATAAAAATATATTAATTAATA
1 AATTAT-AAAATATATT-ATTAA-A
21498133 AATT-TAAAA
1 AATTATAAAA
21498142 AATAAACACA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 13 0.43
24 12 0.40
25 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTATAAAATATATTATTAAA
Found at i:21500008 original size:20 final size:21
Alignment explanation
Indices: 21499974--21500014 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
21499964 ATTTCATAAA
**
21499974 TTAAATTTTTTAATTT-ATTT
1 TTAAATTTTCAAATTTGATTT
21499994 TTAAATTTTCAAATTTGATTT
1 TTAAATTTTCAAATTTGATTT
21500015 CGATTCGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTAAATTTTCAAATTTGATTT
Found at i:21501618 original size:11 final size:11
Alignment explanation
Indices: 21501585--21501705 Score: 66
Period size: 11 Copynumber: 10.6 Consensus size: 11
21501575 CAAAATCAGC
*
21501585 TATTTTATTAT
1 TATTTTATTGT
*
21501596 TGTTTTGA-TGT
1 TATTTT-ATTGT
*
21501607 TATTTCATTGT
1 TATTTTATTGT
* * *
21501618 TGTTTTGTTAT
1 TATTTTATTGT
*
21501629 TATATTATTGT
1 TATTTTATTGT
*
21501640 TATTTTATTAT
1 TATTTTATTGT
*
21501651 TATTGTT-TTGA
1 TATT-TTATTGT
* *
21501662 TATTGTATAACTCT
1 TATT-T-T-ATTGT
21501676 TATTTTATTGT
1 TATTTTATTGT
*
21501687 TAATTTTATTAT
1 T-ATTTTATTGT
21501699 TATTTTA
1 TATTTTA
21501706 GAAACATAAA
Statistics
Matches: 81, Mismatches: 22, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
10 1 0.01
11 59 0.73
12 15 0.19
13 1 0.01
14 5 0.06
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.66
Consensus pattern (11 bp):
TATTTTATTGT
Found at i:21501639 original size:14 final size:14
Alignment explanation
Indices: 21501622--21501651 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21501612 CATTGTTGTT
21501622 TTGTTATTATATTA
1 TTGTTATTATATTA
*
21501636 TTGTTATTTTATTA
1 TTGTTATTATATTA
21501650 TT
1 TT
21501652 ATTGTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
TTGTTATTATATTA
Found at i:21503234 original size:21 final size:22
Alignment explanation
Indices: 21503208--21503253 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
21503198 ATAAACAATA
21503208 TAATGGTTTTG-TCTTTTAA-TT
1 TAATGGTTTTGAT-TTTTAACTT
21503229 TAATGGTTTTGATTTTTAACTT
1 TAATGGTTTTGATTTTTAACTT
21503251 TAA
1 TAA
21503254 AAAGTGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.24, C:0.04, G:0.13, T:0.59
Consensus pattern (22 bp):
TAATGGTTTTGATTTTTAACTT
Found at i:21504667 original size:52 final size:52
Alignment explanation
Indices: 21504585--21504878 Score: 462
Period size: 52 Copynumber: 5.7 Consensus size: 52
21504575 ATTCCATTTA
* * * * * * *
21504585 ATACTCACGATGACACATAATCATTGGACCTCTTAAACCGTGAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
21504637 ATACTCACGATGACACATAGTCATCAGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
** *
21504689 ATACTCACGATGACACATAGTCATCAAACCTTTTAATCCATAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
21504741 ATACTCACGATGACGCATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
21504793 ATACTCACGATGACACATAGTCATCGGACTTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
21504845 ATACTCACGATGATACATAGTCATCGGACCTTTT
1 ATACTCACGATGACACATAGTCATCGGACCTTTT
21504879 CTTTATTTAC
Statistics
Matches: 224, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 224 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
Found at i:21510844 original size:2 final size:2
Alignment explanation
Indices: 21510837--21510866 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21510827 ACAAAAGAGA
21510837 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
21510867 TAAAACAGCC
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:21511236 original size:18 final size:20
Alignment explanation
Indices: 21511194--21511237 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
21511184 TGGCTCATGT
21511194 AAAAGTTAAGAAAAACATAA
1 AAAAGTTAAGAAAAACATAA
* *
21511214 GAAAGTTAA-ATAAA-ATAA
1 AAAAGTTAAGAAAAACATAA
21511232 AAAAGT
1 AAAAGT
21511238 ACTGTATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 9 0.43
19 4 0.19
20 8 0.38
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.18
Consensus pattern (20 bp):
AAAAGTTAAGAAAAACATAA
Found at i:21514076 original size:26 final size:26
Alignment explanation
Indices: 21514025--21514078 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
21514015 CTCACATTGC
21514025 GAGCTTGATACACAAGCTCAATGTGT
1 GAGCTTGATACACAAGCTCAATGTGT
**
21514051 GAGCTTGATATGCAAGCTCAATGTGT
1 GAGCTTGATACACAAGCTCAATGTGT
21514077 GA
1 GA
21514079 ACCGTGTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (26 bp):
GAGCTTGATACACAAGCTCAATGTGT
Found at i:21515085 original size:14 final size:13
Alignment explanation
Indices: 21515062--21515110 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
21515052 TGATAAGTAC
21515062 TTTTAAAAAAAAA
1 TTTTAAAAAAAAA
21515075 TTTTAAAAAAAAA
1 TTTTAAAAAAAAA
* ** *
21515088 TTTTGAAAAGCAT
1 TTTTAAAAAAAAA
21515101 TTTTAAAAAA
1 TTTTAAAAAA
21515111 TTTGAGTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (13 bp):
TTTTAAAAAAAAA
Found at i:21522058 original size:90 final size:91
Alignment explanation
Indices: 21521905--21522115 Score: 248
Period size: 90 Copynumber: 2.3 Consensus size: 91
21521895 GTATTGTACT
* * * * *
21521905 TTAAAAATG-TCTAATATTATACCTGAATTATCAATTTGTGTATTATTTGATACTTTTATTTTCA
1 TTAAAAATGTTC-AATATGATACCTGAACTATCAATTTATGTATTATTTGATACTTGTACTTTCA
* * * *
21521969 TAAAATGTCTACTGTGGTACTTATAAA
65 TAAAATATCCAATGTGATACTTATAAA
* *
21521996 TTAAAAATGTTCAATATGATACTTGAACTATCAATTTATGTGTTATTTG-TACTTGTACTTTCAT
1 TTAAAAATGTTCAATATGATACCTGAACTATCAATTTATGTATTATTTGATACTTGTACTTTCAT
**
21522060 AAAATATCCAATGTGATACTTATACT
66 AAAATATCCAATGTGATACTTATAAA
* *
21522086 TTGAAAATGTTCAATAT-AGTACCTAAACTA
1 TTAAAAATGTTCAATATGA-TACCTGAACTA
21522116 CCAGTGTGTG
Statistics
Matches: 102, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
89 1 0.01
90 58 0.57
91 41 0.40
92 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (91 bp):
TTAAAAATGTTCAATATGATACCTGAACTATCAATTTATGTATTATTTGATACTTGTACTTTCAT
AAAATATCCAATGTGATACTTATAAA
Found at i:21523802 original size:79 final size:79
Alignment explanation
Indices: 21523585--21523813 Score: 332
Period size: 79 Copynumber: 2.9 Consensus size: 79
21523575 ACATGGAAGT
* * *
21523585 GGATTTGATGGACATTGTTGGTTAATCCAACTAGAGTTGGGCTCACATTTACGGTTTATCCGTTA
1 GGATTTGACGGACATTGTTGGTTAATCCAACTAGAGTTGGGCTCACATTTGCGGTTTATCCGCTA
*
21523650 GGCACTGGGTGTTA
66 GGCACTGGGTGTCA
* * * * *
21523664 GGATTTGACGGACATTGTTGGTTAGTCCAACTAGAATTGGGCTCGCATCTGCGGGTTATCCGCTA
1 GGATTTGACGGACATTGTTGGTTAATCCAACTAGAGTTGGGCTCACATTTGCGGTTTATCCGCTA
*
21523729 GGCATTGGGTGTCA
66 GGCACTGGGTGTCA
* * * *
21523743 GGATTTGACGGACATTGTTGGTTAATCCAACTAGAGCTGGGCTCACATTTGTGATTTATCCACTA
1 GGATTTGACGGACATTGTTGGTTAATCCAACTAGAGTTGGGCTCACATTTGCGGTTTATCCGCTA
21523808 GGCACT
66 GGCACT
21523814 AGGTTCCATA
Statistics
Matches: 130, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 130 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (79 bp):
GGATTTGACGGACATTGTTGGTTAATCCAACTAGAGTTGGGCTCACATTTGCGGTTTATCCGCTA
GGCACTGGGTGTCA
Found at i:21525836 original size:62 final size:62
Alignment explanation
Indices: 21525713--21525836 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 62
21525703 TTTCAAAATA
* * * *
21525713 TAAATATCACTTTGAACATTTTATAACAATATAAATACCAAATAATACACAAATTAATAATT
1 TAAATATCACATTAAACATTTTATAACAATACAAATACCAAATAATACACAAATGAATAATT
* * *
21525775 TAAATATCACATTAAACATTTTATGAA-AGA-ACAAATATCAAATAATACATAAATGACTAATT
1 TAAATATCACATTAAACATTTTAT-AACA-ATACAAATACCAAATAATACACAAATGAATAATT
21525837 CTGATTCCAC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 50 0.94
63 3 0.06
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.32
Consensus pattern (62 bp):
TAAATATCACATTAAACATTTTATAACAATACAAATACCAAATAATACACAAATGAATAATT
Found at i:21532785 original size:24 final size:24
Alignment explanation
Indices: 21532758--21532813 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
21532748 CTCTTATACA
* *
21532758 TTATTTAAGTTTA-AAAAATTATAT
1 TTATATAAGTCTATAAAAATTAT-T
*
21532782 TTATATAAGTCTATAAAAGTTATT
1 TTATATAAGTCTATAAAAATTATT
21532806 TTATATAA
1 TTATATAA
21532814 TGATAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (24 bp):
TTATATAAGTCTATAAAAATTATT
Found at i:21533398 original size:10 final size:10
Alignment explanation
Indices: 21533383--21533429 Score: 60
Period size: 10 Copynumber: 4.5 Consensus size: 10
21533373 TGGTTATCTT
21533383 AATTCAAGTA
1 AATTCAAGTA
21533393 AATTCAAGTA
1 AATTCAAGTA
21533403 AATTGTGCAAG-A
1 AA-T-T-CAAGTA
21533415 AATTCAAGTA
1 AATTCAAGTA
21533425 AATTC
1 AATTC
21533430 GAGTCAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 4 0.12
10 19 0.58
11 2 0.06
12 4 0.12
13 4 0.12
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.30
Consensus pattern (10 bp):
AATTCAAGTA
Found at i:21536537 original size:2 final size:2
Alignment explanation
Indices: 21536530--21536578 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
21536520 TTAAAAATTA
21536530 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21536572 AT AT AT A
1 AT AT AT A
21536579 GCATTTTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 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):
AT
Found at i:21540733 original size:23 final size:23
Alignment explanation
Indices: 21540690--21540733 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
21540680 CAATTATTTA
* *
21540690 ATGTCATTGCATTATCTTTTTTT
1 ATGTCATTGCATCATCATTTTTT
21540713 ATGTCATTGACA-CATCATTTT
1 ATGTCATTG-CATCATCATTTT
21540734 GATGATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (23 bp):
ATGTCATTGCATCATCATTTTTT
Found at i:21540932 original size:19 final size:19
Alignment explanation
Indices: 21540908--21540945 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21540898 ATGACGTGTT
21540908 AATAACATAAAAAAATTGA
1 AATAACATAAAAAAATTGA
* *
21540927 AATAACATTAAATAATTGA
1 AATAACATAAAAAAATTGA
21540946 TAAGGGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
AATAACATAAAAAAATTGA
Found at i:21544662 original size:23 final size:23
Alignment explanation
Indices: 21544636--21544717 Score: 146
Period size: 23 Copynumber: 3.6 Consensus size: 23
21544626 CGAACTTGAA
*
21544636 ACTCGAATTACTTATTCGAGTTG
1 ACTCGAATAACTTATTCGAGTTG
21544659 ACTCGAATAACTTATTCGAGTTG
1 ACTCGAATAACTTATTCGAGTTG
21544682 ACTCGAATAACTTATTCGAGTTG
1 ACTCGAATAACTTATTCGAGTTG
*
21544705 ACTCAAATAACTT
1 ACTCGAATAACTT
21544718 GAAATTCAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (23 bp):
ACTCGAATAACTTATTCGAGTTG
Found at i:21555679 original size:18 final size:18
Alignment explanation
Indices: 21555656--21555698 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
21555646 GAATAGATTT
21555656 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
21555674 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
21555692 TTAATTA
1 TTAATTA
21555699 CACTTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:21563200 original size:17 final size:17
Alignment explanation
Indices: 21563180--21563212 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21563170 TTATCCAAAT
21563180 AATTT-AATGTTATTTTC
1 AATTTAAAT-TTATTTTC
21563197 AATTTAAATTTATTTT
1 AATTTAAATTTATTTT
21563213 GATCATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTAAATTTATTTTC
Found at i:21566664 original size:30 final size:30
Alignment explanation
Indices: 21566520--21567057 Score: 524
Period size: 30 Copynumber: 17.9 Consensus size: 30
21566510 GAATGTGGAG
* * * *
21566520 CTTCTACGGGCGACGGTGCCGGTGATGGCA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
* * * *
21566550 CTTTTACAGGTGAC-GCTTCTGGTGTTGACA
1 CTTCTACAGGTGACAG-TGCTGGTGATGGCA
* * *
21566580 ATTCTACAGGTGAC-GCTGTTGGTGATGACA
1 CTTCTACAGGTGACAG-TGCTGGTGATGGCA
* *
21566610 CTTCTACAGGTGAC-GATGCTGGTAATGGAA
1 CTTCTACAGGTGACAG-TGCTGGTGATGGCA
* * *
21566640 ATTCTACAGGTGACAGTGCAGGTAATGGCA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
* ** * *
21566670 CTTCTACAGATGATGGTGCTAGTGATGGTA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
* *
21566700 CTTCAACAGGTGAAAGTGCTGGTGATGGCA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
* *
21566730 CTTCTACAGGTGACAGTGCTGGTAATGGAA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
* *
21566760 ATTCTACAGGTGACAGTGCTGGTAATGGCA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
** ** * *
21566790 CTTCTACAAATGATGGTGCAGGTGATGGTA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
* *
21566820 CTTGTACAGGTGAAAGTGCTGGTGATGGCA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
* *
21566850 CTTCTACAGGTGACGGTGTTGGTGATGGCA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
* * **
21566880 CTTCTACAGGTGACAATGCTGGTAATGAAA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
*
21566910 ATTCTACAGGTGACAGTGCTGGTGATGGCA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
* * * *
21566940 CTTCTACGGGTGACAATGCTAGTGATGGTA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
* ** *
21566970 CTTCTACAGGTGACGGACCTAGTGATGGCA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
* * *
21567000 CTTCTACAAGTAACGGTGCTGGTGATGGCA
1 CTTCTACAGGTGACAGTGCTGGTGATGGCA
* **
21567030 CTTCTACAAGTGATGGTGCTGGTGATGG
1 CTTCTACAGGTGACAGTGCTGGTGATGG
21567058 AGGTGGTGAT
Statistics
Matches: 417, Mismatches: 89, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
29 1 0.00
30 415 1.00
31 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (30 bp):
CTTCTACAGGTGACAGTGCTGGTGATGGCA
Found at i:21570190 original size:30 final size:30
Alignment explanation
Indices: 21570156--21570213 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
21570146 GGAGGTGGAG
*
21570156 CTTCTACAGGCGACGGTGCCGGTGATGGCA
1 CTTCTACAGGCAACGGTGCCGGTGATGGCA
* *
21570186 CTTCTACAGGTAATGGTGCCGGTGATGG
1 CTTCTACAGGCAACGGTGCCGGTGATGG
21570214 AGATGGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.17, C:0.22, G:0.36, T:0.24
Consensus pattern (30 bp):
CTTCTACAGGCAACGGTGCCGGTGATGGCA
Found at i:21574889 original size:189 final size:188
Alignment explanation
Indices: 21574482--21574917 Score: 470
Period size: 189 Copynumber: 2.3 Consensus size: 188
21574472 TTGGATTTTG
* * *
21574482 ATGAAGATTAT-ATTCGTTTTTGTTTAAGTTTATAGCTTTCTGTCACTTTTTAAAGCTCTTCTTC
1 ATGAAGATGATGA-TCGTTTTTGTTTAAGTTTATAGCTTTCTGTCACCTTTTCAAGCTCTTCTTC
* * ** * *
21574546 GAGTTTACCGGTGTTTTTTTTTCAGGTTTCGATGAAGATGATGGCCGCTTTCATTTAAGTTTTAC
65 GAGTTTACC-G-GATCTCCTTTCAGGTTTCAATGAAGATGATAGCCGCTTTCATTTAAGTTTTAC
** * * * *
21574611 CTTTCTATTACCTTTTTAAGCTCTTATTCTTCATGTTTATCAATCTCTTTTTCGGGTTCCG
128 CTTTCTATTACCTTTCCAAGCTCTTATTCTTCAGGTTTATCAATATCCTTTTCGGGTTCCA
* * * * *
21574672 ATGAAGATGATGGTTGTTTCTGTTTAAGTTTATAACTTTTTGTCACCTTTTCAAGCTCTTCTTCG
1 ATGAAGATGATGATCGTTTTTGTTTAAGTTTATAGCTTTCTGTCACCTTTTCAAGCTCTTCTTCG
* * ** *
21574737 AGTTTACC-GATCTCCTTTC-GGGTTCTAATGAATATGATAGCCGCTTTTTGTTTACGTTTATAC
66 AGTTTACCGGATCTCCTTTCAGGTTTC-AATGAAGATGATAGCCGC-TTTCATTTAAGTTT-TAC
* * * * **
21574800 CTTTTTGTTACCTTTCCAGGCTCTTCTTCTTC-GGATTTATTGATATCCTTTTCGGGTTCCA
128 CTTTCTATTACCTTTCCAAGCTCTTATTCTTCAGG-TTTATCAATATCCTTTTCGGGTTCCA
21574861 ATGACA-ATGATGATCGTTTTTGTTTAAGTTTATAGCTTTCTGTCA-CTTTTGCAAGCT
1 ATGA-AGATGATGATCGTTTTTGTTTAAGTTTATAGCTTTCTGTCACCTTTT-CAAGCT
21574918 ACTCTTTAGG
Statistics
Matches: 203, Mismatches: 36, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
186 5 0.02
187 22 0.11
188 17 0.08
189 94 0.46
190 65 0.32
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.48
Consensus pattern (188 bp):
ATGAAGATGATGATCGTTTTTGTTTAAGTTTATAGCTTTCTGTCACCTTTTCAAGCTCTTCTTCG
AGTTTACCGGATCTCCTTTCAGGTTTCAATGAAGATGATAGCCGCTTTCATTTAAGTTTTACCTT
TCTATTACCTTTCCAAGCTCTTATTCTTCAGGTTTATCAATATCCTTTTCGGGTTCCA
Found at i:21577967 original size:18 final size:18
Alignment explanation
Indices: 21577944--21577986 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
21577934 TTTAAAGGTA
21577944 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
21577962 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
21577980 TAATTAA
1 TAATTAA
21577987 AAGTGTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:21596565 original size:14 final size:14
Alignment explanation
Indices: 21596527--21596570 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
21596517 ATTTATTGTA
* *
21596527 TGTGTCATATTTATC
1 TGTGT-ATATATATT
*
21596542 TGTGTGTATATATT
1 TGTGTATATATATT
21596556 TGTGTATATATATT
1 TGTGTATATATATT
21596570 T
1 T
21596571 TTGTTTTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.23, C:0.05, G:0.16, T:0.57
Consensus pattern (14 bp):
TGTGTATATATATT
Found at i:21599086 original size:18 final size:19
Alignment explanation
Indices: 21599054--21599089 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
21599044 TCCAATTTTG
21599054 TTTATTTATTTATTTTATT
1 TTTATTTATTTATTTTATT
21599073 TTTATTTA-TTATTTTAT
1 TTTATTTATTTATTTTAT
21599090 AAATAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTATTTATTTATTTTATT
Found at i:21603989 original size:25 final size:27
Alignment explanation
Indices: 21603939--21603992 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
21603929 AAACCAACCT
*
21603939 AACCCAAAACTCTTATTACCCATTTAA
1 AACCCAAAACTCTTATAACCCATTTAA
21603966 AACCC-AAA-TCTTATAAACCC-TTTAA
1 AACCCAAAACTCTTAT-AACCCATTTAA
21603991 AA
1 AA
21603993 ATCTTTAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 13 0.52
26 7 0.28
27 5 0.20
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (27 bp):
AACCCAAAACTCTTATAACCCATTTAA
Found at i:21604042 original size:16 final size:16
Alignment explanation
Indices: 21604017--21604048 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21604007 ACCTAGACCC
*
21604017 AATAACCCAAACCCAA
1 AATAAACCAAACCCAA
21604033 AATAAACCAAACCCAA
1 AATAAACCAAACCCAA
21604049 TTGAACCATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.34, G:0.00, T:0.06
Consensus pattern (16 bp):
AATAAACCAAACCCAA
Found at i:21604119 original size:14 final size:14
Alignment explanation
Indices: 21604100--21604145 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
21604090 TGATCGGCTA
21604100 TTGACCGTTGACAG
1 TTGACCGTTGACAG
21604114 TTGACCGTTGACA-
1 TTGACCGTTGACAG
*
21604127 TTGA-CTTTGACCAG
1 TTGACCGTTGA-CAG
21604141 TTGAC
1 TTGAC
21604146 TTTTTCCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 5 0.18
13 6 0.21
14 17 0.61
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (14 bp):
TTGACCGTTGACAG
Found at i:21606264 original size:79 final size:79
Alignment explanation
Indices: 21606133--21606286 Score: 299
Period size: 79 Copynumber: 1.9 Consensus size: 79
21606123 AGAGATAAAC
*
21606133 TACCCTGCTGGATAGAAGGTTACAGTTGATGTTTCTTTAATGAGGGGTGAGGCCCAAAATTGGTG
1 TACCCTGCTGGATAGAAGGTTACAATTGATGTTTCTTTAATGAGGGGTGAGGCCCAAAATTGGTG
21606198 AGAAACTGTGAAAT
66 AGAAACTGTGAAAT
21606212 TACCCTGCTGGATAGAAGGTTACAATTGATGTTTCTTTAATGAGGGGTGAGGCCCAAAATTGGTG
1 TACCCTGCTGGATAGAAGGTTACAATTGATGTTTCTTTAATGAGGGGTGAGGCCCAAAATTGGTG
21606277 AGAAACTGTG
66 AGAAACTGTG
21606287 GAAGAGTCTA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (79 bp):
TACCCTGCTGGATAGAAGGTTACAATTGATGTTTCTTTAATGAGGGGTGAGGCCCAAAATTGGTG
AGAAACTGTGAAAT
Found at i:21609557 original size:14 final size:14
Alignment explanation
Indices: 21609538--21609566 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21609528 ATCCTTTGAG
21609538 TAAGTTAGGTCGAC
1 TAAGTTAGGTCGAC
21609552 TAAGTTAGGTCGAC
1 TAAGTTAGGTCGAC
21609566 T
1 T
21609567 CTATATCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (14 bp):
TAAGTTAGGTCGAC
Found at i:21611351 original size:15 final size:16
Alignment explanation
Indices: 21611319--21611353 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
21611309 ACCCAATAAC
21611319 CCAAACCCAAAATGAA
1 CCAAACCCAAAATGAA
*
21611335 CCAAACCC-AATTGAA
1 CCAAACCCAAAATGAA
21611350 CCAA
1 CCAA
21611354 GTCAAACCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.34, G:0.06, T:0.09
Consensus pattern (16 bp):
CCAAACCCAAAATGAA
Found at i:21611392 original size:7 final size:7
Alignment explanation
Indices: 21611382--21611416 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
21611372 CGTTGATCGG
*
21611382 CCGTTGG
1 CCGTTGA
21611389 CCGTTGA
1 CCGTTGA
21611396 CCGTTGA
1 CCGTTGA
21611403 CCGTTGA
1 CCGTTGA
21611410 CC-TTGA
1 CCGTTGA
21611416 C
1 C
21611417 TTTGACCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.11, C:0.31, G:0.29, T:0.29
Consensus pattern (7 bp):
CCGTTGA
Found at i:21614381 original size:19 final size:19
Alignment explanation
Indices: 21614353--21614398 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
21614343 TTAGATTTTA
* *
21614353 AAATTTAATTACATTTAGT
1 AAATTAAATTACATTGAGT
**
21614372 AAATTAAATTTTATTGAGT
1 AAATTAAATTACATTGAGT
21614391 AAATTAAA
1 AAATTAAA
21614399 GTCATAAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (19 bp):
AAATTAAATTACATTGAGT
Found at i:21615360 original size:21 final size:21
Alignment explanation
Indices: 21615336--21615389 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
21615326 TGTGTCTAGT
21615336 AGGCTTTGTGCCAGTGTTATC
1 AGGCTTTGTGCCAGTGTTATC
21615357 AGGCTTTGTGCCAGTGTTATC
1 AGGCTTTGTGCCAGTGTTATC
21615378 AGGCTTTGTGCC
1 AGGCTTTGTGCC
21615390 TAATAGGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.13, C:0.20, G:0.30, T:0.37
Consensus pattern (21 bp):
AGGCTTTGTGCCAGTGTTATC
Found at i:21623864 original size:65 final size:65
Alignment explanation
Indices: 21623755--21623883 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
21623745 AAATCAATAT
* *
21623755 AAAATCACTTTTGACAACTTTTCATGCATAATCATTCATGCGCATTTAGATAGGAGCATTTGATA
1 AAAACCACTTTTGACAACTTTGCATGCATAATCATTCATGCGCATTTAGATAGGAGCATTTGATA
21623820 AAAACCACTTTTGACATA-TTTGCATGCATAATCATTCATGCGCATTTAGATAGGAGCATTTGAT
1 AAAACCACTTTTGACA-ACTTTGCATGCATAATCATTCATGCGCATTTAGATAGGAGCATTTGAT
21623884 TCATTCAAAC
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 60 0.98
66 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (65 bp):
AAAACCACTTTTGACAACTTTGCATGCATAATCATTCATGCGCATTTAGATAGGAGCATTTGATA
Found at i:21624095 original size:49 final size:50
Alignment explanation
Indices: 21623992--21624087 Score: 131
Period size: 49 Copynumber: 1.9 Consensus size: 50
21623982 ATCTTTTATT
* * * *
21623992 CCTAAAGCTGTGGAGGTGCAGATTGAAGCCGCAATGGCAAATCTCATACA
1 CCTAAAGCTGTGAAGGGGCAGAATGAAGCCGCAATGACAAATCTCATACA
* *
21624042 CCTAAAGCTGT-AAGGGGCAGAATGAAGCTGCAATGACGAATCTCAT
1 CCTAAAGCTGTGAAGGGGCAGAATGAAGCCGCAATGACAAATCTCAT
21624088 TCCCCTAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 29 0.73
50 11 0.28
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (50 bp):
CCTAAAGCTGTGAAGGGGCAGAATGAAGCCGCAATGACAAATCTCATACA
Found at i:21626968 original size:40 final size:40
Alignment explanation
Indices: 21626912--21627039 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 40
21626902 CGGATGTTAC
* * *
21626912 ATTGAAGACCATCCGATCTCTTACCTCGATCATGGGGTAG
1 ATTGAAGATCACCCGATCTCTTACCTCGATCATGGGGCAG
** * **
21626952 ATTG-AGAATCACCCGATCTCTTACCTTAACCAAAGGGCAG
1 ATTGAAG-ATCACCCGATCTCTTACCTCGATCATGGGGCAG
* * *
21626992 ATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGCAG
1 ATTGAAGATCACCCGATCTCTTACCTCGATCATGGGGCAG
21627032 ATTGAAGA
1 ATTGAAGA
21627040 AATCCAATCT
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 66 0.94
41 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (40 bp):
ATTGAAGATCACCCGATCTCTTACCTCGATCATGGGGCAG
Found at i:21627069 original size:39 final size:41
Alignment explanation
Indices: 21626967--21627139 Score: 155
Period size: 40 Copynumber: 4.3 Consensus size: 41
21626957 GAATCACCCG
* * * *
21626967 ATCTCTTACCTTAACCA-AAGGGCAGATTGAAGATC-ATCCG
1 ATCTTTTACCCTAACCATGAGGGCAGATTGAAGA-CAATCCA
** *
21627007 ATCTTTTACCCCGATCATG-GGGCAGATTGAAGA-AATCCA
1 ATCTTTTACCCTAACCATGAGGGCAGATTGAAGACAATCCA
* * *
21627046 ATCTTTTACCCTAACCA-GAGGGCAAATTGAAGACCATCAA
1 ATCTTTTACCCTAACCATGAGGGCAGATTGAAGACAATCCA
* *
21627086 ATCTCTTATCCC-GACCATGA-GGCAGATTGAA-ACAATCCA
1 ATCTTTTA-CCCTAACCATGAGGGCAGATTGAAGACAATCCA
21627125 ATCTTTTACCTCTAA
1 ATCTTTTACC-CTAA
21627140 AGCTATAGAG
Statistics
Matches: 105, Mismatches: 20, Indels: 16
0.74 0.14 0.11
Matches are distributed among these distances:
38 3 0.03
39 45 0.43
40 52 0.50
41 5 0.05
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (41 bp):
ATCTTTTACCCTAACCATGAGGGCAGATTGAAGACAATCCA
Found at i:21627099 original size:79 final size:78
Alignment explanation
Indices: 21626912--21627139 Score: 262
Period size: 79 Copynumber: 2.9 Consensus size: 78
21626902 CGGATGTTAC
* * * *
21626912 ATTGAAGACCATCCGATCTCTTACCTCGATCATGGGGTAGATTG-AGAATCACCCGATCTCTTAC
1 ATTGAAGACCATCCGATCTCTTACC-CGATCATGGGGCAGATTGAAGAA--ATCCAATCTTTTAC
* *
21626976 CTTAACCAAAGGGCAG
63 CCTAACCAAAGGGCAA
* *
21626992 ATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCC
1 ATTGAAGACCATCCGATCTCTTA-CCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCC
*
21627057 TAACCAGAGGGCAA
65 TAACCAAAGGGCAA
** * *
21627071 ATTGAAGACCATCAAATCTCTTATCCCGACCATGAGGCAGATTGAA-ACAATCCAATCTTTTACC
1 ATTGAAGACCATCCGATCTCTTA-CCCGATCATGGGGCAGATTGAAGA-AATCCAATCTTTTACC
21627135 TCTAA
64 -CTAA
21627140 AGCTATAGAG
Statistics
Matches: 128, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
78 1 0.01
79 79 0.62
80 42 0.33
81 6 0.05
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (78 bp):
ATTGAAGACCATCCGATCTCTTACCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCT
AACCAAAGGGCAA
Found at i:21627115 original size:40 final size:38
Alignment explanation
Indices: 21626987--21627134 Score: 147
Period size: 39 Copynumber: 3.8 Consensus size: 38
21626977 TTAACCAAAG
* * *
21626987 GGCAGATTGAAGATCATCCGATCTTTTACCCCGATCATGG
1 GGCAGATTGAAGA-CATCCAATCTTTTA-CCCGACCATGA
* *
21627027 GGCAGATTGAAGAAATCCAATCTTTTACCCTAACCA-GA
1 GGCAGATTGAAGACATCCAATCTTTTACCC-GACCATGA
* * *
21627065 GGGCAAATTGAAGACCATCAAATCTCTTATCCCGACCATGA
1 -GGCAGATTGAAGA-CATCCAATCTTTTA-CCCGACCATGA
21627106 GGCAGATTGAA-ACAATCCAATCTTTTACC
1 GGCAGATTGAAGAC-ATCCAATCTTTTACC
21627135 TCTAAAGCTA
Statistics
Matches: 89, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
38 7 0.08
39 39 0.44
40 38 0.43
41 5 0.06
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (38 bp):
GGCAGATTGAAGACATCCAATCTTTTACCCGACCATGA
Found at i:21627708 original size:18 final size:18
Alignment explanation
Indices: 21627687--21627722 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
21627677 TCCAATTTTG
21627687 TTTT-TTTATTTATTTTAT
1 TTTTATTTA-TTATTTTAT
21627705 TTTTATTTATTATTTTAT
1 TTTTATTTATTATTTTAT
21627723 AAATAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTATTTATTATTTTAT
Found at i:21632545 original size:134 final size:134
Alignment explanation
Indices: 21632296--21632567 Score: 370
Period size: 134 Copynumber: 2.0 Consensus size: 134
21632286 TCTTACAAAC
*
21632296 TTTCTTTTTTCACAACAGAGCAGAAAACATTTAAAAACTTAACCCCACACCTAATACTCCCCCTA
1 TTTCTTTTTTCACAACAGAGCAGAAAACATTT----ACATAACCCCACACCTAATACTCCCCCTA
* *
21632361 ATATTATATATCAACCCCATTAACTTTCCCTTCTTTTCATAATCATCCCCATAATTAAAACACAG
62 ATATTATATATCAACCCCACTAACTTTCCCTTCTTTTCATAATCATCCCCATAATAAAAACACAG
21632426 CTTTTTAG
127 CTTTTTAG
* * * *
21632434 TTTCTTTTTTTCACAACAGAGTAGAAAACATTT-CATAGCGCCCATACCTAATA-TTCCCCTAAT
1 TTTC-TTTTTTCACAACAGAGCAGAAAACATTTACATAAC-CCCACACCTAATACTCCCCCTAAT
* * *
21632497 ATTTTTATATCAACCCC-CTGATTTTCCCTTCTTTTCATAATCATCCCCATAATAAAAACACAGC
64 A-TTATATATCAACCCCACTAACTTTCCCTTCTTTTCATAATCATCCCCATAATAAAAACACAGC
21632561 TTTTTAG
128 TTTTTAG
21632568 CTTCGTACTA
Statistics
Matches: 121, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
134 64 0.53
135 26 0.21
138 4 0.03
139 27 0.22
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (134 bp):
TTTCTTTTTTCACAACAGAGCAGAAAACATTTACATAACCCCACACCTAATACTCCCCCTAATAT
TATATATCAACCCCACTAACTTTCCCTTCTTTTCATAATCATCCCCATAATAAAAACACAGCTTT
TTAG
Found at i:21635274 original size:22 final size:22
Alignment explanation
Indices: 21635244--21635291 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
21635234 CATATTAATA
21635244 TAAAATATAAT-AAATTAAAAAT
1 TAAAATATAATCAAA-TAAAAAT
* * *
21635266 TAAATTATATTCAAATAAAATT
1 TAAAATATAATCAAATAAAAAT
21635288 TAAA
1 TAAA
21635292 CCCGAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATATAATCAAATAAAAAT
Found at i:21635890 original size:22 final size:22
Alignment explanation
Indices: 21635865--21635908 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
21635855 AAAAAATAAA
21635865 AAAAATATTTATAATA-ATATAT
1 AAAAATATTTA-AATATATATAT
* *
21635887 AAAACTGTTTAAATATATATAT
1 AAAAATATTTAAATATATATAT
21635909 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
AAAAATATTTAAATATATATAT
Found at i:21645663 original size:2 final size:2
Alignment explanation
Indices: 21645656--21645730 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
21645646 TTCTAAAATT
21645656 TA TA TA 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
21645698 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21645731 TGTAAAACTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21645793 original size:20 final size:21
Alignment explanation
Indices: 21645761--21645799 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
21645751 CAATTTCTAG
21645761 AATTTATATTTTTT-AGTTAA
1 AATTTATATTTTTTGAGTTAA
21645781 AATTT-TATGTTTTTGAGTT
1 AATTTATAT-TTTTTGAGTT
21645800 TTTTATTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (21 bp):
AATTTATATTTTTTGAGTTAA
Found at i:21648836 original size:16 final size:16
Alignment explanation
Indices: 21648815--21648847 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21648805 TAGTCCAACG
21648815 ACTTTATGAATTTCTT
1 ACTTTATGAATTTCTT
21648831 ACTTTATGAATTTCTT
1 ACTTTATGAATTTCTT
21648847 A
1 A
21648848 TACTCTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (16 bp):
ACTTTATGAATTTCTT
Done.