Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 71 of 182
Found at i:22624603 original size:11 final size:10
Alignment explanation
Indices: 22624586--22624624 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
22624576 GTTTATACAC
22624586 CTTAATTAAA
1 CTTAATTAAA
*
22624596 CTTTAATTAAT
1 C-TTAATTAAA
22624607 CTTAATTAAA
1 CTTAATTAAA
22624617 -TTAATTAA
1 CTTAATTAA
22624625 TATAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 8 0.31
10 9 0.35
11 9 0.35
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (10 bp):
CTTAATTAAA
Found at i:22625827 original size:155 final size:154
Alignment explanation
Indices: 22625539--22625838 Score: 564
Period size: 155 Copynumber: 1.9 Consensus size: 154
22625529 AAAAAATTAA
22625539 TTTTTGGGTTTTGGTCATGTGATGATCGACATTAGAGTATTTTTTACTCCGTATTATATTGGTGT
1 TTTTTGGGTTTTGGTCATGTGATGATCGACATTAGAGTATTTTTTACTCCGTATTATATTGGTGT
* * *
22625604 ATAAATATACTAGTTTTTGAAAAAAATAATTTTGAGTCTTGGTCACCTAATGACCAGCACCAAGT
66 ATAAATATACTAGTTTTTGAAAAAAATAATTTTAAGTCTTGGTCACCTAATGACCAGCAACAAAT
22625669 CCCATCACAGATAAAAGTAATATT
131 CCCATCACAGATAAAAGTAATATT
22625693 TTTTTGGGTTTTGGTCATGTGATGATCGACATTAGAGTATTTTTTTACTCCGTATTATATTGGTG
1 TTTTTGGGTTTTGGTCATGTGATGATCGACATTAGAGTA-TTTTTTACTCCGTATTATATTGGTG
22625758 TATAAATATACTAGTTTTTGAAAAAAATAATTTTAAGTCTTGGTCACCTAATGACCAGCAACAAA
65 TATAAATATACTAGTTTTTGAAAAAAATAATTTTAAGTCTTGGTCACCTAATGACCAGCAACAAA
22625823 TCCCATCACAGATAAA
130 TCCCATCACAGATAAA
22625839 TTTTTTTTTT
Statistics
Matches: 142, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
154 39 0.27
155 103 0.73
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (154 bp):
TTTTTGGGTTTTGGTCATGTGATGATCGACATTAGAGTATTTTTTACTCCGTATTATATTGGTGT
ATAAATATACTAGTTTTTGAAAAAAATAATTTTAAGTCTTGGTCACCTAATGACCAGCAACAAAT
CCCATCACAGATAAAAGTAATATT
Found at i:22625916 original size:60 final size:62
Alignment explanation
Indices: 22625839--22625970 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 62
22625829 CACAGATAAA
* * *
22625839 TTTTTT-TTTTGATCATCTAATGGTC-GACACCAAGTCCCATAACAGATAAAAAAAT-A-TTT
1 TTTTTTGTTTTAACCATCTAATGGTCAG-CACCAAATCCCATAACAGATAAAAAAATAACTTT
* * * *
22625898 TTTTTTGTTTTAACCATCTAATTGTCAGCATCAAATCCTATCACAGATAAAAAAATAACTTT
1 TTTTTTGTTTTAACCATCTAATGGTCAGCACCAAATCCCATAACAGATAAAAAAATAACTTT
22625960 TTTTTTGTTTT
1 TTTTTTGTTTT
22625971 GGCCTATAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 6 0.10
60 40 0.65
61 2 0.03
62 14 0.23
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.42
Consensus pattern (62 bp):
TTTTTTGTTTTAACCATCTAATGGTCAGCACCAAATCCCATAACAGATAAAAAAATAACTTT
Found at i:22626340 original size:25 final size:27
Alignment explanation
Indices: 22626312--22626377 Score: 93
Period size: 25 Copynumber: 2.5 Consensus size: 27
22626302 TTGGGGCTTT
22626312 AAGTTTATTTAAAATT-AATTT-TTTA
1 AAGTTTATTTAAAATTAAATTTATTTA
*
22626337 AAGTTTATTTAAAATTAAATTTATTTT
1 AAGTTTATTTAAAATTAAATTTATTTA
22626364 AA-TTCTATTTAAAA
1 AAGTT-TATTTAAAA
22626378 AAATTTCTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
25 16 0.43
26 7 0.19
27 14 0.38
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (27 bp):
AAGTTTATTTAAAATTAAATTTATTTA
Found at i:22626564 original size:41 final size:41
Alignment explanation
Indices: 22626480--22626584 Score: 147
Period size: 41 Copynumber: 2.5 Consensus size: 41
22626470 TAAGAACTTC
* * *
22626480 AAATAGTAACAAAATAAATTTAATTAAAATCGATTTTAAACCG
1 AAATAGTAACAAAATAAA--AAAATGAAATCGATTTTAAACCG
* *
22626523 AAATGGTAACAAAATAAAAAAATGAAATTGATTTTAAACCG
1 AAATAGTAACAAAATAAAAAAATGAAATCGATTTTAAACCG
22626564 AAATAGTAACAAAATAAAAAA
1 AAATAGTAACAAAATAAAAAA
22626585 TAAAAAACAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 39 0.70
43 17 0.30
ACGTcount: A:0.59, C:0.08, G:0.09, T:0.25
Consensus pattern (41 bp):
AAATAGTAACAAAATAAAAAAATGAAATCGATTTTAAACCG
Found at i:22629039 original size:49 final size:49
Alignment explanation
Indices: 22628973--22629070 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
22628963 ATTGTGAGAT
* * *
22628973 TCTTCTATTATCTTGTACAAGCCCCTCATTCACCCTTTTATTTTGTGCC
1 TCTTCTACTATCCTGTACAAGCCCCTCATTCACCCTTTTATTTCGTGCC
* * *
22629022 TCTTCTACTATCCTGTACTAGCCCCTTATTCAGCCTTTTATTTCGTGCC
1 TCTTCTACTATCCTGTACAAGCCCCTCATTCACCCTTTTATTTCGTGCC
22629071 GTCTAGAGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.15, C:0.32, G:0.09, T:0.44
Consensus pattern (49 bp):
TCTTCTACTATCCTGTACAAGCCCCTCATTCACCCTTTTATTTCGTGCC
Found at i:22632639 original size:25 final size:25
Alignment explanation
Indices: 22632611--22632661 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
22632601 TGGTATAACG
22632611 TGATGAAAGTTAATTGCAATAAACA
1 TGATGAAAGTTAATTGCAATAAACA
*
22632636 TGATGAAAGTTAATTGCAATGAACA
1 TGATGAAAGTTAATTGCAATAAACA
22632661 T
1 T
22632662 AGTATATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (25 bp):
TGATGAAAGTTAATTGCAATAAACA
Found at i:22633024 original size:41 final size:42
Alignment explanation
Indices: 22632878--22633110 Score: 281
Period size: 43 Copynumber: 5.5 Consensus size: 42
22632868 TCACTTGGCG
* * *
22632878 TAAATGGAAGACTCATGTCTCGGGATGAGTATGAGATTATGTA
1 TAAA-GGAAGACTCATGACTCGGAATGAGCATGAGATTATGTA
* * * **
22632921 TAAATGGAATACTCATGTCTCGGGACAAGCATGAGATTATGTA
1 TAAA-GGAAGACTCATGACTCGGAATGAGCATGAGATTATGTA
*
22632964 TAAATGGAAGACTCATGACTTGGAATGAGCATGAGATTATGT-
1 TAAA-GGAAGACTCATGACTCGGAATGAGCATGAGATTATGTA
* *
22633006 TTAAGGAAGACTCATGACTCAGAATGAGCATGAGATTATGT-
1 TAAAGGAAGACTCATGACTCGGAATGAGCATGAGATTATGTA
* * *
22633047 TTAAGGAAGACTCGTGACTCGGAATGAGCATGAGATTATGTG
1 TAAAGGAAGACTCATGACTCGGAATGAGCATGAGATTATGTA
* *
22633089 TAAAGGAAGACTTATAACTCGG
1 TAAAGGAAGACTCATGACTCGG
22633111 TAAAGCATAA
Statistics
Matches: 170, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
41 74 0.44
42 21 0.12
43 75 0.44
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (42 bp):
TAAAGGAAGACTCATGACTCGGAATGAGCATGAGATTATGTA
Found at i:22633118 original size:41 final size:40
Alignment explanation
Indices: 22632878--22633124 Score: 246
Period size: 41 Copynumber: 5.9 Consensus size: 40
22632868 TCACTTGGCG
* * *
22632878 TAAATGGAAGACTCATGTCTCGGGATGAGTATGAGATTATGT
1 TAAA-GGAAGACTCATGACTC-GGAAGAGCATGAGATTATGT
* *
22632920 ATAAATGGAATACTCATGTCTCGGGACA-AGCATGAGATTATGT
1 -TAAA-GGAAGACTCATGACTC-GGA-AGAGCATGAGATTATGT
*
22632963 ATAAATGGAAGACTCATGACTTGGAATGAGCATGAGATTATGT
1 -TAAA-GGAAGACTCATGACTCGGAA-GAGCATGAGATTATGT
* *
22633006 TTAAGGAAGACTCATGACTCAGAATGAGCATGAGATTATGT
1 TAAAGGAAGACTCATGACTCGGAA-GAGCATGAGATTATGT
* *
22633047 TTAAGGAAGACTCGTGACTCGGAATGAGCATGAGATTATGT
1 TAAAGGAAGACTCATGACTCGGAA-GAGCATGAGATTATGT
* * *
22633088 GTAAAGGAAGACTTATAACTCGGTAA-AGCATAAGATT
1 -TAAAGGAAGACTCATGACTCGG-AAGAGCATGAGATT
22633125 GTTTAAAAAG
Statistics
Matches: 183, Mismatches: 16, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
41 85 0.46
42 24 0.13
43 74 0.40
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.28
Consensus pattern (40 bp):
TAAAGGAAGACTCATGACTCGGAAGAGCATGAGATTATGT
Found at i:22633118 original size:82 final size:82
Alignment explanation
Indices: 22632878--22633124 Score: 291
Period size: 82 Copynumber: 2.9 Consensus size: 82
22632868 TCACTTGGCG
* * * * *
22632878 TAAATGGAAGACTCATGTCTCGGGATGAGTATGAGATTATGTATAAATGGAATACTCATGTCTCG
1 TAAATGGAAGACTCATGACTCGGAATGAGCATGAGATTATGT-TAAA-GGAAGACTCATGACTC-
22632943 GGACAAGCATGAGATTATGTA
63 GGA-AAGCATGAGATTATGTA
* * *
22632964 TAAATGGAAGACTCATGACTTGGAATGAGCATGAGATTATGTTTAAGGAAGACTCATGACTCAGA
1 TAAATGGAAGACTCATGACTCGGAATGAGCATGAGATTATGTTAAAGGAAGACTCATGACTCGGA
22633029 ATGAGCATGAGATTATGT-
66 A--AGCATGAGATTATGTA
* * * *
22633047 TTAA-GGAAGACTCGTGACTCGGAATGAGCATGAGATTATGTGTAAAGGAAGACTTATAACTCGG
1 TAAATGGAAGACTCATGACTCGGAATGAGCATGAGATTATGT-TAAAGGAAGACTCATGACTCGG
*
22633111 TAAAGCATAAGATT
65 -AAAGCATGAGATT
22633125 GTTTAAAAAG
Statistics
Matches: 141, Mismatches: 16, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
82 46 0.33
83 23 0.16
84 31 0.22
85 3 0.02
86 38 0.27
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.28
Consensus pattern (82 bp):
TAAATGGAAGACTCATGACTCGGAATGAGCATGAGATTATGTTAAAGGAAGACTCATGACTCGGA
AAGCATGAGATTATGTA
Found at i:22639186 original size:44 final size:45
Alignment explanation
Indices: 22639119--22639204 Score: 129
Period size: 44 Copynumber: 1.9 Consensus size: 45
22639109 AAATAACATA
* *
22639119 AAATTTATGATAACTATAAATTTAAAAATAATTATAATTTAATAG
1 AAATTTATGATAACTACAAATTTAAAAATAATTAGAATTTAATAG
* *
22639164 AAATTT-TGATAATTACACATTTAAAAATAATTAGAATTTAA
1 AAATTTATGATAACTACAAATTTAAAAATAATTAGAATTTAA
22639205 ATTACAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 31 0.84
45 6 0.16
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (45 bp):
AAATTTATGATAACTACAAATTTAAAAATAATTAGAATTTAATAG
Found at i:22639204 original size:17 final size:18
Alignment explanation
Indices: 22639172--22639205 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22639162 AGAAATTTTG
22639172 ATAATTACACATTTAAAA
1 ATAATTACACATTTAAAA
*
22639190 ATAATTAGA-ATTTAAA
1 ATAATTACACATTTAAA
22639206 TTACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAATTACACATTTAAAA
Found at i:22640521 original size:13 final size:13
Alignment explanation
Indices: 22640489--22640523 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
22640479 TTAATTACTG
22640489 TAATTAAAAATAC
1 TAATTAAAAATAC
*
22640502 AATATTAAAAATAC
1 TA-ATTAAAAATAC
22640516 TAATTAAA
1 TAATTAAA
22640524 TATTAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATTAAAAATAC
Found at i:22640783 original size:19 final size:19
Alignment explanation
Indices: 22640755--22640794 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
22640745 AAAATTCAAA
*
22640755 AAATACTTTATATTTTTAT
1 AAATACTTTATATTTATAT
* *
22640774 AAATATTTTATCTTTATAT
1 AAATACTTTATATTTATAT
22640793 AA
1 AA
22640795 TTTATAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATACTTTATATTTATAT
Found at i:22640791 original size:17 final size:19
Alignment explanation
Indices: 22640755--22640791 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
22640745 AAAATTCAAA
*
22640755 AAATACTTTATATTTTTAT
1 AAATACTTTATATCTTTAT
22640774 AAATA-TTT-TATCTTTAT
1 AAATACTTTATATCTTTAT
22640791 A
1 A
22640792 TAATTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATACTTTATATCTTTAT
Found at i:22640792 original size:25 final size:26
Alignment explanation
Indices: 22640760--22640808 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
22640750 TCAAAAAATA
*
22640760 CTTTATAT-TTTTATAAATATTTTAT
1 CTTTATATAATTTATAAATATTTTAT
22640785 CTTTATATAATTTATAAATATTTT
1 CTTTATATAATTTATAAATATTTT
22640809 CTATCATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
CTTTATATAATTTATAAATATTTTAT
Found at i:22644319 original size:195 final size:192
Alignment explanation
Indices: 22643866--22644319 Score: 486
Period size: 201 Copynumber: 2.3 Consensus size: 192
22643856 GAAACCGACG
** * * * * *
22643866 CGATGGCTGAGGTACCGCATATATTGCAAGTCCTCGACAGCTCGTGCGAGTAGCATCGTGAGTCA
1 CGATGGCTGAGGTACCGCATACGTTACGAGTCCTCGACAGCTCATGTGAGTAGCATCGTGACTC-
* *
22643931 GGAAATGAGAAAAGAAATATGGATCCTAAATGGATTACAGACCCTACGATGGCTGAGATTTATGC
65 ------GAG-AAAGAAATATGGATCCTAAATGGATCACAGACCCTACGATGGCTGAGATCTATGC
* *
22643996 ATAAGTGCATATTCTCGACAGCTCGTGTGAGCAGCATCATTAAGGAACAGTTATATGCACAGATA
123 ATAAGTGCATACTCTCGACAGCTCGTGTGAGCAGCATCATTAAGGAACAGTTATATACACAGATA
*
22644061 CCGTAT
188 -CGTAC
* * * *
22644067 CGATGGCTGAGGTACTGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGTAGCATCGTGACTCG
1 CGATGGCTGAGGTACCGCATACGTTACGAGTCCTCGACAGCTCATGTGAGTAGCATCGTGACTCG
* * * * * *
22644132 AGAAAGAGATATGGATCCTAAATGGATCACATG-CCTTACGATGGTTGGGA-CTATGC-TTATTG
66 AGAAAGAAATATGGATCCTAAATGGATCACA-GACCCTACGATGGCTGAGATCTATGCATAAGTG
* * *
22644194 CATACTCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACACTTTATAGTACAAACAAGCAT-C
130 CATACTCTCGACAGCTCGTGTGAGCAGCATCATTAAGGAACA-GTTATA-TAC--AC-AG-ATAC
22644258 GTAC
189 GTAC
*
22644262 CGATGGCTGGGGTACCGCATACGTTACGAGTCCTCGACAGCTCATGTGA-TCAGCATCG
1 CGATGGCTGAGGTACCGCATACGTTACGAGTCCTCGACAGCTCATGTGAGT-AGCATCG
22644320 AGTAGTGGTT
Statistics
Matches: 221, Mismatches: 24, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
191 43 0.19
192 10 0.05
193 43 0.19
194 5 0.02
195 57 0.26
196 2 0.01
197 2 0.01
201 59 0.27
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (192 bp):
CGATGGCTGAGGTACCGCATACGTTACGAGTCCTCGACAGCTCATGTGAGTAGCATCGTGACTCG
AGAAAGAAATATGGATCCTAAATGGATCACAGACCCTACGATGGCTGAGATCTATGCATAAGTGC
ATACTCTCGACAGCTCGTGTGAGCAGCATCATTAAGGAACAGTTATATACACAGATACGTAC
Found at i:22644575 original size:6 final size:6
Alignment explanation
Indices: 22644535--22644623 Score: 55
Period size: 6 Copynumber: 15.0 Consensus size: 6
22644525 TTTTGATTTT
* **
22644535 TTTAAA GTTTAAA -TTAATT TTTAAA TTT--A TCTTAAA TTTAAA TTTACTGG
1 TTTAAA -TTTAAA TTTAA-A TTTAAA TTTAAA T-TTAAA TTTAAA TTTA--AA
*
22644585 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
22644624 ATAATATTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 21
0.69 0.09 0.23
Matches are distributed among these distances:
4 4 0.06
5 14 0.22
6 30 0.47
7 12 0.19
8 4 0.06
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:22644632 original size:17 final size:16
Alignment explanation
Indices: 22644597--22644639 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
22644587 TAAATTTATT
* *
22644597 TTAAATTTAAATTTAA
1 TTAAATTTAAAATAAA
22644613 TTAAATTTAAAATAATA
1 TTAAATTTAAAATAA-A
*
22644630 TTAAACTTAA
1 TTAAATTTAA
22644640 TAAATAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Found at i:22645403 original size:3 final size:3
Alignment explanation
Indices: 22645397--22645436 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
22645387 TGAATATTAT
* *
22645397 TAA TAA TAT TAA TAA TAA TTA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
22645437 ATATTTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:22645406 original size:12 final size:12
Alignment explanation
Indices: 22645389--22645453 Score: 64
Period size: 12 Copynumber: 5.4 Consensus size: 12
22645379 CAACTCTTTG
*
22645389 AATATTATTAAT
1 AATATTAATAAT
22645401 AATATTAATAAT
1 AATATTAATAAT
22645413 AAT-TATAATAAT
1 AATAT-TAATAAT
22645425 AA-A-TAATAAT
1 AATATTAATAAT
*
22645435 AAATATTTATAATT
1 -AATATTAATAA-T
22645449 AATAT
1 AATAT
22645454 CATTATTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
10 7 0.16
11 3 0.07
12 24 0.53
13 10 0.22
14 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:22645446 original size:10 final size:10
Alignment explanation
Indices: 22645398--22645439 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
22645388 GAATATTATT
*
22645398 AATAAT-ATT
1 AATAATAATA
22645407 AATAATAAT-
1 AATAATAATA
*
22645416 TATAATAATA
1 AATAATAATA
22645426 AATAATAATA
1 AATAATAATA
22645436 AATA
1 AATA
22645440 TTTATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATAATAATA
Found at i:22646590 original size:117 final size:118
Alignment explanation
Indices: 22646378--22647048 Score: 963
Period size: 117 Copynumber: 5.7 Consensus size: 118
22646368 CTAGACTGTC
** * *
22646378 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTTCATTTTTGACCCC-GATTTCATCAAAA
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAG-TTTCATCAAAA
** *
22646442 ATTACCATTTTACCCCCGAACTTTTCAAAATTCCATTTTTAACCCCGATTTCAT
65 ATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
** * *
22646496 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTAACCCCAGTTTCACCAAAAG
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCATCAAAAA
* * *
22646560 TTACCATTTTACCCCTAAACTTTCCAAAATTCAATTTTTAACCCCAAATTCAT
66 TTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* **
22646613 CAAAAATTACCATTTTACCCCTAAACATTCCAAAATT-TGTTTTTAACCCC-GATTTCATCAAAA
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAG-TTTCATCAAAA
* * *
22646676 ATTACCATTTTACCCCTAAACTTTCCAAAACTCCATTATTAACCCCAATTTCAT
65 ATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
22646730 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCATCAAAAA
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCATCAAAAA
* * *
22646795 TTACCATTTTACCCCTAAACTTTCTAAAATTCCATTATTAACCCCGGTTTCAT
66 TTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * * *
22646848 CAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCTATTTTTAACCCTAGTTTCATCAAAAG
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCATCAAAAA
22646913 TTACCATTTTACCCCTAAACTTTCCAAAATTCCATTATTTTTAACCCCGATTTCAT
66 TTACCATTTTACCCCTAAACTTTCCAAAATTCC---ATTTTTAACCCCGATTTCAT
* * * * * *
22646969 CAAAAGTTACCATTTTACCCCTAAACTTTCCAAAATTCCATTATTAACCTCGGTTTCACCAAAAG
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCATCAAAAA
*
22647034 TTACCATTTTGCCCC
66 TTACCATTTTACCCC
22647049 CGCACATCCA
Statistics
Matches: 501, Mismatches: 44, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
116 1 0.00
117 205 0.41
118 205 0.41
119 1 0.00
121 89 0.18
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (118 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCATCAAAAA
TTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
Found at i:22647069 original size:59 final size:59
Alignment explanation
Indices: 22646378--22647048 Score: 947
Period size: 59 Copynumber: 11.4 Consensus size: 59
22646368 CTAGACTGTC
** * *
22646378 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTTCATTTTTGACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
** *
22646437 CAAAAATTACCATTTTACCCCCGAACTTTTCAAAATTCCATTTTTAACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
** *
22646496 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTAACCCC-AGTTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCAT
* * * *
22646554 CAAAAGTTACCATTTTACCCCTAAACTTTCCAAAATTCAATTTTTAACCCCAAATTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* **
22646613 CAAAAATTACCATTTTACCCCTAAACATTCCAAAATT-TGTTTTTAACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * *
22646671 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAACTCCATTATTAACCCCAATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
22646730 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCC-AGTTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCAT
* * *
22646789 CAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTATTAACCCCGGTTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * *
22646848 CAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCTATTTTTAA-CCCTAGTTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCAT
*
22646907 CAAAAGTTACCATTTTACCCCTAAACTTTCCAAAATTCCATTATTTTTAACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCC---ATTTTTAACCCCGATTTCAT
* * * * *
22646969 CAAAAGTTACCATTTTACCCCTAAACTTTCCAAAATTCCATTATTAACCTCGGTTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* *
22647028 CAAAAGTTACCATTTTGCCCC
1 CAAAAATTACCATTTTACCCC
22647049 CGCACATCCA
Statistics
Matches: 558, Mismatches: 43, Indels: 22
0.90 0.07 0.04
Matches are distributed among these distances:
57 1 0.00
58 107 0.19
59 392 0.70
60 1 0.00
62 53 0.09
63 4 0.01
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
Found at i:22647084 original size:27 final size:29
Alignment explanation
Indices: 22647027--22647090 Score: 114
Period size: 28 Copynumber: 2.3 Consensus size: 29
22647017 CTCGGTTTCA
22647027 CCAAAAGTTACCATTTTGCCCCCGCACAT
1 CCAAAAGTTACCATTTTGCCCCCGCACAT
22647056 CCAAAA-TTACCATTTTGCCCCCG-ACAT
1 CCAAAAGTTACCATTTTGCCCCCGCACAT
22647083 CCAAAAGT
1 CCAAAAGT
22647091 CTCATTTTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 10 0.29
28 18 0.53
29 6 0.18
ACGTcount: A:0.31, C:0.36, G:0.09, T:0.23
Consensus pattern (29 bp):
CCAAAAGTTACCATTTTGCCCCCGCACAT
Found at i:22647096 original size:27 final size:28
Alignment explanation
Indices: 22647027--22647098 Score: 103
Period size: 27 Copynumber: 2.6 Consensus size: 28
22647017 CTCGGTTTCA
22647027 CCAAAAGTTACCATTTTGCCCCCGCACAT
1 CCAAAAG-TACCATTTTGCCCCCGCACAT
*
22647056 CCAAAATTACCATTTTGCCCCCG-ACAT
1 CCAAAAGTACCATTTTGCCCCCGCACAT
22647083 CCAAAAGT-CTCATTTT
1 CCAAAAGTAC-CATTTT
22647099 CGACCCTGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 1 0.03
27 17 0.43
28 16 0.40
29 6 0.15
ACGTcount: A:0.29, C:0.35, G:0.08, T:0.28
Consensus pattern (28 bp):
CCAAAAGTACCATTTTGCCCCCGCACAT
Found at i:22659359 original size:40 final size:40
Alignment explanation
Indices: 22659315--22659459 Score: 112
Period size: 40 Copynumber: 3.3 Consensus size: 40
22659305 CTATCCTTTT
22659315 GAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCA
1 GAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCA
** * * * *
22659355 GAAATTGAAGTAAGAG-TAAAATGAAGCACCAACATCATTTCCCTATCCTCTT
1 GAAATTGAAGTAA-AGCT-GGAT-AA-CA--AGC--C--TT-CGT-CCCTC-A
22659407 GAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCA
1 GAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCA
22659447 GAAATTGAAGTAA
1 GAAATTGAAGTAA
22659460 GAGTAAAATG
Statistics
Matches: 79, Mismatches: 12, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
40 27 0.34
41 8 0.10
42 4 0.05
43 4 0.05
45 3 0.04
47 3 0.04
49 4 0.05
50 4 0.05
51 8 0.10
52 14 0.18
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (40 bp):
GAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCA
Found at i:22659359 original size:92 final size:92
Alignment explanation
Indices: 22659199--22659644 Score: 677
Period size: 92 Copynumber: 4.9 Consensus size: 92
22659189 TCACGTCAAT
22659199 CCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTG
1 CCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTG
* * *
22659264 AAATTGAAGTAAGATTGAGAA-GAAGGA
66 AAATTGAAGTAAGAGT-AAAATGAAGCA
* * *
22659291 CCAACATTATTTTCCTATCCTTTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCAG
1 CCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTG
22659356 AAATTGAAGTAAGAGTAAAATGAAGCA
66 AAATTGAAGTAAGAGTAAAATGAAGCA
* *
22659383 CCAACATCATTTCCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCAG
1 CCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTG
22659448 AAATTGAAGTAAGAGTAAAATGAAGCA
66 AAATTGAAGTAAGAGTAAAATGAAGCA
*
22659475 CCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAA-CTTGGATAACAAGTCTTCGTCCCTCT
1 CCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGC-TGGATAACAAGCCTTCGTCCCTCT
* * *
22659539 GAAATCGAAATAAGAGTAAGAA-GAAGGA
65 GAAATTGAAGTAAGAGTAA-AATGAAGCA
* * ** *
22659567 CCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAATCTTCAT--CTCTG
1 CCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTG
22659630 AAATTGAAGTAAGAG
66 AAATTGAAGTAAGAG
22659645 CAAGATTATT
Statistics
Matches: 329, Mismatches: 21, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
90 18 0.05
91 4 0.01
92 305 0.93
93 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (92 bp):
CCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTG
AAATTGAAGTAAGAGTAAAATGAAGCA
Found at i:22659417 original size:52 final size:51
Alignment explanation
Indices: 22659355--22659511 Score: 149
Period size: 52 Copynumber: 3.3 Consensus size: 51
22659345 TCGTCCCTCA
22659355 GAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCATTTCCCTATCCTCTT
1 GAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCATTT-CCTATCCTCTT
** * * * *
22659407 GAAATTGAAGTAA-AGCT-GGAT-AA-CA--AGC--C--TTCGT-CCCTC-A
1 GAAATTGAAGTAAGAG-TAAAATGAAGCACCAACATCATTTCCTATCCTCTT
22659447 GAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCATTTTCCTATCCTCTT
1 GAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCA-TTTCCTATCCTCTT
22659499 GAAATTGAAGTAA
1 GAAATTGAAGTAA
22659512 ACTTGGATAA
Statistics
Matches: 79, Mismatches: 12, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
40 14 0.18
41 8 0.10
42 4 0.05
43 4 0.05
45 3 0.04
47 3 0.04
49 2 0.03
50 6 0.08
51 8 0.10
52 27 0.34
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (51 bp):
GAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCATTTCCTATCCTCTT
Found at i:22659669 original size:76 final size:76
Alignment explanation
Indices: 22659572--22659951 Score: 581
Period size: 76 Copynumber: 5.0 Consensus size: 76
22659562 AAGGACCAAC
* *
22659572 ATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAATCTTCATCTCTGAAATTGA
1 ATCA-TTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
22659637 AGTAAGAGCAAG
65 AGTAAGAGCAAG
* *
22659649 ATTATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTTTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAA
22659714 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
22659725 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTTCATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAA
22659790 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
22659801 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTAGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAA
* *
22659866 ATAAGAACAAG
66 GTAAGAGCAAG
* *
22659877 ATCATTTCCTATCCTCTTGAAATT---G--AAGTTGGATAGCAAGTCTTTATCTCTCTGGAATTG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTA--TCTCTGAAATTG
22659937 AAGTAAGAGCAAG
64 AAGTAAGAGCAAG
22659950 AT
1 AT
22659952 GAAGCCTCGA
Statistics
Matches: 281, Mismatches: 20, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
71 18 0.06
73 25 0.09
76 235 0.84
77 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (76 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAG
Found at i:22659898 original size:38 final size:38
Alignment explanation
Indices: 22659572--22659905 Score: 251
Period size: 38 Copynumber: 8.8 Consensus size: 38
22659562 AAGGACCAAC
** *
22659572 ATCATTTTCCTATCCTCTTGAAATTGAAGTAA-AGTTGGAT
1 ATCA-TTTCCTATCCTCTTGAAATTGAAGTAAGAG--CAAG
** *
22659612 ATCAAAT-CT-TCATCTCTGAAATTGAAGTAAGAGCAAG
1 ATCATTTCCTATCCTCT-TGAAATTGAAGTAAGAGCAAG
* ** *
22659649 ATTATTTCCTATCCTCTTGAAATTGAAGTAA-AGTTGGAT
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAGAG--CAAG
** *
22659688 ATCAAGTCTTTAT-CT-TTGAAATTGAAGTAAGAGCAAG
1 ATCATTTC-CTATCCTCTTGAAATTGAAGTAAGAGCAAG
* *
22659725 ATCATTTCCTATCCTCTTGAAATTGAAGTAA-AGCTGGAT
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGC--AAG
** *
22659764 ATCAAAT-CT-TCATCTCTGAAATTGAAGTAAGAGCAAG
1 ATCATTTCCTATCCTCT-TGAAATTGAAGTAAGAGCAAG
*
22659801 ATCATTTCCTATCCTCTTGAAATTGAAGTAA-AGCTAGAT
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGC-A-AG
** * * *
22659840 ATCAAGTCTTTAT-CTC-TGAAATTGAAATAAGAACAAG
1 ATCATTTC-CTATCCTCTTGAAATTGAAGTAAGAGCAAG
22659877 ATCATTTCCTATCCTCTTGAAATTGAAGT
1 ATCATTTCCTATCCTCTTGAAATTGAAGT
22659906 TGGATAGCAA
Statistics
Matches: 228, Mismatches: 44, Indels: 46
0.72 0.14 0.14
Matches are distributed among these distances:
36 6 0.03
37 48 0.21
38 120 0.53
39 44 0.19
40 10 0.04
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (38 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGCAAG
Found at i:22660254 original size:6 final size:6
Alignment explanation
Indices: 22660215--22660298 Score: 52
Period size: 6 Copynumber: 14.0 Consensus size: 6
22660205 TTTTGATTTT
* *
22660215 TTTAAA GTTTAAA -TTAAT TTTAAA -TTAATT TTTAAA TTT--A TCTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA T-TTAAA
* *
22660262 TTTAAA TTTACTGA TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA
22660299 ATAATATTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
4 2 0.03
5 14 0.23
6 27 0.45
7 12 0.20
8 5 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:22660271 original size:23 final size:23
Alignment explanation
Indices: 22660215--22660271 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
22660205 TTTTGATTTT
*
22660215 TTTAAAGTTTAAATTAATTTTAAA
1 TTTAAA-TTTAAATTAATCTTAAA
* *
22660239 -TTAATTTTTAAATTTATCTTAAA
1 TTTAA-ATTTAAATTAATCTTAAA
22660262 TTTAAATTTA
1 TTTAAATTTA
22660272 CTGATTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTAAATTTAAATTAATCTTAAA
Found at i:22660292 original size:11 final size:11
Alignment explanation
Indices: 22660222--22660296 Score: 57
Period size: 11 Copynumber: 6.9 Consensus size: 11
22660212 TTTTTTAAAG
*
22660222 TTTAAATTAAT
1 TTTAAATTTAT
*
22660233 TTTAAATTAATT
1 TTTAAATTTA-T
22660245 TTTAAATTTAT
1 TTTAAATTTAT
* *
22660256 CTTAAATTTAAA
1 TTTAAATTT-AT
* *
22660268 TTT--ACTGA-
1 TTTAAATTTAT
22660276 TTTAAATTTAT
1 TTTAAATTTAT
22660287 TTTAAATTTA
1 TTTAAATTTA
22660297 AAATAATATT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
8 3 0.06
9 1 0.02
10 5 0.10
11 29 0.57
12 13 0.25
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:22661070 original size:9 final size:9
Alignment explanation
Indices: 22661058--22661110 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
22661048 TTTGAATATG
22661058 ATTAATAAT
1 ATTAATAAT
22661067 ATTAATAAT
1 ATTAATAAT
*
22661076 AATAATAAT
1 ATTAATAAT
22661085 A--AATAAT
1 ATTAATAAT
*
22661092 AATAAATAAT
1 -ATTAATAAT
*
22661102 ATTTATAAT
1 ATTAATAAT
22661111 TAATATCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
7 6 0.16
8 1 0.03
9 25 0.66
10 6 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATTAATAAT
Found at i:22661075 original size:3 final size:3
Alignment explanation
Indices: 22661060--22661102 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
22661050 TGAATATGAT
*
22661060 TAA TAA TAT TAA TAA TAA TAA TAA TAAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA T-AA TAA TA
22661103 TTTATAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:22661091 original size:10 final size:9
Alignment explanation
Indices: 22661060--22661102 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 9
22661050 TGAATATGAT
*
22661060 TAATAATAT
1 TAATAATAA
22661069 TAATAATAA
1 TAATAATAA
22661078 TAATAATAAA
1 TAATAAT-AA
22661088 TAATAATAAA
1 TAATAAT-AA
22661098 TAATA
1 TAATA
22661103 TTTATAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 15 0.47
10 17 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAATAATAA
Found at i:22661109 original size:13 final size:13
Alignment explanation
Indices: 22661061--22661116 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 13
22661051 GAATATGATT
22661061 AATAATATTAAT-
1 AATAATATTAATA
*
22661073 AATAATAATAATA
1 AATAATATTAATA
22661086 AAT-A-A-TAATA
1 AATAATATTAATA
*
22661096 AATAATATTTATA
1 AATAATATTAATA
*
22661109 ATTAATAT
1 AATAATAT
22661117 CATTATTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 8 0.22
11 2 0.05
12 13 0.35
13 14 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATAATATTAATA
Found at i:22662587 original size:59 final size:59
Alignment explanation
Indices: 22662071--22662564 Score: 774
Period size: 59 Copynumber: 8.4 Consensus size: 59
22662061 CTAGACTATC
** * *
22662071 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCTATTTTTGACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * *
22662130 CAAAAATTACCATTTTACCCCCTGAAGTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTA-CCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * * *
22662190 CAAAAGTTACCATTTTACCCCTAAACTTTCCAAAACTCCATTATTAACCCCGGTTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
22662249 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * *
22662308 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTATTAACCTC-AGTTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCAT
*
22662367 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* *
22662426 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTATTAACCTCGATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * *
22662485 CAAAAATTACCATTTTACCCCCAAACTTTCCAAGATTCCATTTTTAACCCCGGTTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
*
22662544 CAAAAATTACCATTTTTCCCC
1 CAAAAATTACCATTTTACCCC
22662565 CATGCGTCCA
Statistics
Matches: 401, Mismatches: 31, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
58 1 0.00
59 346 0.86
60 54 0.13
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
Found at i:22662622 original size:28 final size:28
Alignment explanation
Indices: 22662546--22662633 Score: 115
Period size: 28 Copynumber: 3.1 Consensus size: 28
22662536 GGTTTCATCA
*
22662546 AAAATTACCATTTTTCCCCC-ATGCGTCC
1 AAAATTACCATTTTGCCCCCGA-GCGTCC
*
22662574 AAAATTACCATTTTGCCCCCGCGCGTCC
1 AAAATTACCATTTTGCCCCCGAGCGTCC
* * *
22662602 AAAATTATCATTTTGCTCCCGAGCATCC
1 AAAATTACCATTTTGCCCCCGAGCGTCC
22662630 AAAA
1 AAAA
22662634 GTCCCGTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.28, C:0.33, G:0.10, T:0.28
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCCGAGCGTCC
Found at i:22668888 original size:195 final size:193
Alignment explanation
Indices: 22668436--22668889 Score: 484
Period size: 201 Copynumber: 2.3 Consensus size: 193
22668426 GAAACCGACA
* * * * ** * *
22668436 CGATGGCTGAGGTACTGCATATGTTGCGAGTCCTCTACAGCTCGTGTGAGCAGCATTGTGAGTCG
1 CGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGACAGCTCATGCAAGCAGCATCGTGACTCG
* *
22668501 GGAAATGAGAAAAGGAATATGGATCCTAAATGGATTACAGGCCCTACGATGGCTGAGATTTATGC
66 GG-AA--AG---A-G-ATATGGATCCTAAATGGATCACAGGCCCTACGATGGCTGAGATCTATGC
* *
22668566 ATAAGTGCATATTCTCGACAGCTCGTGTGAGCAGCATCATTCAGGAACAGTTATATGCACAGATA
123 ATAAGTGCATACTCTCGACAGCTCATGTGAGCAGCATCATTCAGGAACAGTTATATGCACAGATA
* *
22668631 CCGTAT
188 CCATAC
* * ** *
22668637 CGATGGCTGAGGTACTGCATATGTTACGAGTCCTCGACAGCTCGTGTGATCAGCATCGTGACTCG
1 CGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGACAGCTCATGCAAGCAGCATCGTGACTCG
* * * * *
22668702 GGAAAGAGATATGGATCCTAAATGGATCACATGCCCTATGATGGCTGGGA-CTATGC-TTATTGC
66 GGAAAGAGATATGGATCCTAAATGGATCACAGGCCCTACGATGGCTGAGATCTATGCATAAGTGC
* * *
22668765 ATACTCTCGACAGCTCATGTGAGCAGCATCGTT-AGGGAATAGTT-TATTGTACAGATAGGCACC
131 ATACTCTCGACAGCTCATGTGAGCAGCATCATTCA-GGAACAGTTATA-TGCACAGAT----ACC
22668828 ATAC
190 ATAC
* * *
22668832 CGATGGCTGGGGTACCGCATATGTTATGAGTCCTCGATAGCTCATGCAAGCAGCATCG
1 CGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGACAGCTCATGCAAGCAGCATCG
22668890 AGTACTAGTA
Statistics
Matches: 220, Mismatches: 27, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
190 3 0.01
191 51 0.23
192 5 0.02
193 38 0.17
194 1 0.00
195 56 0.25
198 2 0.01
200 2 0.01
201 62 0.28
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (193 bp):
CGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGACAGCTCATGCAAGCAGCATCGTGACTCG
GGAAAGAGATATGGATCCTAAATGGATCACAGGCCCTACGATGGCTGAGATCTATGCATAAGTGC
ATACTCTCGACAGCTCATGTGAGCAGCATCATTCAGGAACAGTTATATGCACAGATACCATAC
Found at i:22669671 original size:21 final size:21
Alignment explanation
Indices: 22669639--22669690 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
22669629 TGAGTTTTTA
*
22669639 GTATCAGTAGAAG-CATTACAT
1 GTATCGGTAGAAGTCA-TACAT
* *
22669660 GTTTCGGTAGAAGTCATACTT
1 GTATCGGTAGAAGTCATACAT
22669681 GTATCGGTAG
1 GTATCGGTAG
22669691 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACAT
Found at i:22670769 original size:24 final size:24
Alignment explanation
Indices: 22670737--22670784 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
22670727 TCACGGTAGG
22670737 AGCAACACTCGGTGAACAATCTTT
1 AGCAACACTCGGTGAACAATCTTT
22670761 AGCAACACTCGGTGAACAATCTTT
1 AGCAACACTCGGTGAACAATCTTT
22670785 CATTCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (24 bp):
AGCAACACTCGGTGAACAATCTTT
Found at i:22676602 original size:2 final size:2
Alignment explanation
Indices: 22676595--22676628 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22676585 GCAGATTTGT
22676595 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
22676629 GGTTTTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22678965 original size:25 final size:26
Alignment explanation
Indices: 22678900--22678954 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
22678890 AAATTTAAAC
* *
22678900 AAAACAAAACAA-TTTATAATAATTA
1 AAAACAAAATAACTTTAAAATAATTA
22678925 AAAACAAAATAACTTTAAAATAATTA
1 AAAACAAAATAACTTTAAAATAATTA
22678951 AAAA
1 AAAA
22678955 AAATTACCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.25
Consensus pattern (26 bp):
AAAACAAAATAACTTTAAAATAATTA
Found at i:22679293 original size:135 final size:136
Alignment explanation
Indices: 22678988--22679435 Score: 591
Period size: 135 Copynumber: 3.2 Consensus size: 136
22678978 AAACAATTTT
*
22678988 TTTAAAACAAATCACATAAACATTAAACTAAACAAATAATTTATAATAATTACTAA-AAAATAAA
1 TTTATAACAAATCACATAAACATTAAACTAAACAAATAATTTATAATAATTACTAACAAAATAAA
** ** *
22679052 TTTAAATTAAATTTAAAAAAAAACTTAACAATTTATCTTTCTTTCCCTTTAATCTACTCTACTAA
66 TTTAAATTAAA-TT-AAAAGCAACAAAACAATTTATCTTTCTTTCCTTTTAATCTACTCTACTAA
*
22679117 ATAAAAAAA
129 A-CAAAAAA
* * * *
22679126 TTAATAACAAATCACAAAAAAATTAAACTAAACAAATAATTTATAATAATTACTAACAAAATAAG
1 TTTATAACAAATCACATAAACATTAAACTAAACAAATAATTTATAATAATTACTAACAAAATAAA
22679191 TTTAAATTAAATTAAAAGCAACAAAACAATTTATCTTTC-TTCCTTTTAATCTACTCTACTAAAC
66 TTTAAATTAAATTAAAAGCAACAAAACAATTTATCTTTCTTTCCTTTTAATCTACTCTACTAAAC
22679255 AAAAAA
131 AAAAAA
* *
22679261 TTTATAACAAATCATATAAACATTAAACTAAACAAATAATTTATAATAATTACTAACAAAATAAT
1 TTTATAACAAATCACATAAACATTAAACTAAACAAATAATTTATAATAATTACTAACAAAATAAA
* **
22679326 TTTAAATTAAATTAAAAGCAACAAAA-AAGTTCTCTCTTTTGGCTTTTTTTTCCATTAATCTACT
66 TTTAAATTAAATTAAAAGCAACAAAACAA-TT-TATC-TTT--C-TTTCCTT---TTAATCTACT
22679390 CTACTAAACAAAAAA
122 CTACTAAACAAAAAA
* *
22679405 TCTATAACATAT--CATAAACATTAAACTAAAC
1 TTTATAACAAATCACATAAACATTAAACTAAAC
22679436 TTTATAATAA
Statistics
Matches: 277, Mismatches: 22, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
134 2 0.01
135 94 0.34
136 26 0.09
137 25 0.09
138 54 0.19
139 19 0.07
141 4 0.01
142 18 0.06
144 35 0.13
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.33
Consensus pattern (136 bp):
TTTATAACAAATCACATAAACATTAAACTAAACAAATAATTTATAATAATTACTAACAAAATAAA
TTTAAATTAAATTAAAAGCAACAAAACAATTTATCTTTCTTTCCTTTTAATCTACTCTACTAAAC
AAAAAA
Found at i:22679469 original size:20 final size:20
Alignment explanation
Indices: 22679444--22679482 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
22679434 ACTTTATAAT
*
22679444 AATTAAAAACAAATAAAATA
1 AATTAAAAACAAAAAAAATA
22679464 AATTAAAAACAAAAAAAAT
1 AATTAAAAACAAAAAAAAT
22679483 CACCTCTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
AATTAAAAACAAAAAAAATA
Found at i:22679545 original size:6 final size:6
Alignment explanation
Indices: 22679500--22679525 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
22679490 CTTTCCCTTT
22679500 CTTCTC CTTCTC CTTCTC CTTCTC CT
1 CTTCTC CTTCTC CTTCTC CTTCTC CT
22679526 CCACTCTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
CTTCTC
Found at i:22680888 original size:16 final size:16
Alignment explanation
Indices: 22680867--22680901 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
22680857 TTAGGAATAA
22680867 AAACATAAGTTTAATG
1 AAACATAAGTTTAATG
* *
22680883 AAACATAATTTTATTG
1 AAACATAAGTTTAATG
22680899 AAA
1 AAA
22680902 AGGAAAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (16 bp):
AAACATAAGTTTAATG
Found at i:22702516 original size:21 final size:21
Alignment explanation
Indices: 22702490--22702540 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 21
22702480 GTTAGTTACA
*
22702490 TGCATTTTATTTAGTTGTCAT
1 TGCATTTTATTTAGTTGTCAC
*
22702511 TGCA--TT-TTTATTTGTCAC
1 TGCATTTTATTTAGTTGTCAC
22702529 TGCATTTTATTT
1 TGCATTTTATTT
22702541 GTTAGTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 14 0.56
19 2 0.08
20 2 0.08
21 7 0.28
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.59
Consensus pattern (21 bp):
TGCATTTTATTTAGTTGTCAC
Found at i:22703150 original size:8 final size:8
Alignment explanation
Indices: 22703122--22703166 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
22703112 AGTTGCCTAT
22703122 AAAAAAAG
1 AAAAAAAG
22703130 AAAGAAAAG
1 AAA-AAAAG
*
22703139 AAAAAGAG
1 AAAAAAAG
*
22703147 AAAAGAATG
1 AAAA-AAAG
22703156 AAAAAAAG
1 AAAAAAAG
22703164 AAA
1 AAA
22703167 TAATTTGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 17 0.55
9 14 0.45
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:22705743 original size:15 final size:15
Alignment explanation
Indices: 22705723--22705754 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
22705713 AACTAGTGAA
22705723 TGCACCTATTGTCGT
1 TGCACCTATTGTCGT
22705738 TGCACCTATTGTCGT
1 TGCACCTATTGTCGT
22705753 TG
1 TG
22705755 TAACAGACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (15 bp):
TGCACCTATTGTCGT
Found at i:22707711 original size:37 final size:37
Alignment explanation
Indices: 22707661--22707734 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
22707651 GCTCTCTTCT
22707661 CCCCCTCTTCAGTTACATATTTGGTGAAATGGCTCCA
1 CCCCCTCTTCAGTTACATATTTGGTGAAATGGCTCCA
22707698 CCCCCTCTTCAGTTACATATTTGGTGAAATGGCTCCA
1 CCCCCTCTTCAGTTACATATTTGGTGAAATGGCTCCA
22707735 ACAAGCTGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (37 bp):
CCCCCTCTTCAGTTACATATTTGGTGAAATGGCTCCA
Found at i:22709144 original size:38 final size:38
Alignment explanation
Indices: 22709063--22709140 Score: 106
Period size: 36 Copynumber: 2.1 Consensus size: 38
22709053 TTGGGAATAA
* *
22709063 TGGCATTTAGGGGAAAAAATAGGGTAAGGTAAAAGGTT
1 TGGCATTTAGGGGAAAAAATAGGGTAAAGTAAAAGATT
*
22709101 TGGCATTT-GGGG-GAAAATAGGGTAAAGTAAAAAGATT
1 TGGCATTTAGGGGAAAAAATAGGGTAAAGT-AAAAGATT
22709138 TGG
1 TGG
22709141 GCATGGGTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 14 0.39
37 14 0.39
38 8 0.22
ACGTcount: A:0.38, C:0.03, G:0.35, T:0.24
Consensus pattern (38 bp):
TGGCATTTAGGGGAAAAAATAGGGTAAAGTAAAAGATT
Found at i:22717237 original size:11 final size:11
Alignment explanation
Indices: 22717223--22717292 Score: 52
Period size: 11 Copynumber: 6.0 Consensus size: 11
22717213 TTTAAATGGG
22717223 TTTTAAATTTA
1 TTTTAAATTTA
22717234 TTTTAAATTTAA
1 TTTTAAATTT-A
* *
22717246 ATTT-ATTTTAA
1 TTTTAAATTT-A
*
22717257 ATTTAAATTTA
1 TTTTAAATTTA
22717268 CTTATTTAAATTTA
1 --T-TTTAAATTTA
*
22717282 CTTTAAATTTA
1 TTTTAAATTTA
22717293 AGTTTAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
11 31 0.63
12 8 0.16
14 10 0.20
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:22717244 original size:6 final size:6
Alignment explanation
Indices: 22717224--22717299 Score: 68
Period size: 6 Copynumber: 12.8 Consensus size: 6
22717214 TTAAATGGGT
* * *
22717224 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTACTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA
* *
22717272 TTTAAA TTT-AC TTTAAA TTTAAG TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
22717300 TCAAATTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
5 12 0.21
6 39 0.70
8 5 0.09
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:22717244 original size:17 final size:17
Alignment explanation
Indices: 22717224--22717298 Score: 102
Period size: 17 Copynumber: 4.6 Consensus size: 17
22717214 TTAAATGGGT
22717224 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
22717241 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
22717258 TTTAAATTTA-CTT--A
1 TTTAAATTTATTTTAAA
*
22717272 TTTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
*
22717289 TTTAAGTTTA
1 TTTAAATTTA
22717299 ATCAAATTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
14 11 0.21
15 2 0.04
16 2 0.04
17 37 0.71
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:22717276 original size:14 final size:14
Alignment explanation
Indices: 22717257--22717284 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22717247 TTTATTTTAA
22717257 ATTTAAATTTACTT
1 ATTTAAATTTACTT
22717271 ATTTAAATTTACTT
1 ATTTAAATTTACTT
22717285 TAAATTTAAG
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:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAAATTTACTT
Found at i:22717278 original size:31 final size:31
Alignment explanation
Indices: 22717240--22717298 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
22717230 TTTATTTTAA
*
22717240 ATTTAAATTTATTTTAAATTTAAATTTACTT
1 ATTTAAATTTACTTTAAATTTAAATTTACTT
*
22717271 ATTTAAATTTACTTTAAATTTAAGTTTA
1 ATTTAAATTTACTTTAAATTTAAATTTA
22717299 ATCAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (31 bp):
ATTTAAATTTACTTTAAATTTAAATTTACTT
Found at i:22719295 original size:30 final size:30
Alignment explanation
Indices: 22719261--22719537 Score: 245
Period size: 30 Copynumber: 9.5 Consensus size: 30
22719251 TAAACTACCC
*
22719261 AAAAATTACATTTTGACCCCAAAACTTTCT
1 AAAAATTACATTTTAACCCCAAAACTTTCT
*
22719291 AAAAATTACATTTTAACCCTAAAACTTTCT
1 AAAAATTACATTTTAACCCCAAAACTTTCT
* * *
22719321 AAAAATTGCATTTTAACCCTAAAA-TTTTT
1 AAAAATTACATTTTAACCCCAAAACTTTCT
* *
22719350 CCAAAATTACATTTTAACCCTAAAACTTT-T
1 -AAAAATTACATTTTAACCCCAAAACTTTCT
* * *
22719380 CCAAAATTACATTTTGACCTCAAAACTTTCT
1 -AAAAATTACATTTTAACCCCAAAACTTTCT
* * *
22719411 AAAAATTACTTTTTGACCCCAAAA-TTTTT
1 AAAAATTACATTTTAACCCCAAAACTTTCT
* *
22719440 CCAAAATTACATTTTAACCCTAAAAACTTT-T
1 -AAAAATTACATTTTAACCC-CAAAACTTTCT
* *
22719471 CCAAAATTATATTTTAACCCC--AA------
1 -AAAAATTACATTTTAACCCCAAAACTTTCT
* *
22719494 AAAAATTACATTTTGACCCTAAAACTTTCT
1 AAAAATTACATTTTAACCCCAAAACTTTCT
*
22719524 AAAAATTGCATTTT
1 AAAAATTACATTTT
22719538 GACCTCGATT
Statistics
Matches: 209, Mismatches: 24, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.08
24 2 0.01
28 2 0.01
29 8 0.04
30 150 0.72
31 28 0.13
32 3 0.01
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCCAAAACTTTCT
Found at i:22719388 original size:90 final size:90
Alignment explanation
Indices: 22719262--22719495 Score: 337
Period size: 90 Copynumber: 2.6 Consensus size: 90
22719252 AAACTACCCA
* * *
22719262 AAAATTACATTTTGACCCCAAAAC-TTTCTAAAAATTACATTTTAACCCTAAAACTTTCTAAAAA
1 AAAATTACATTTTAACCCTAAAACTTTTC-CAAAATTACATTTTAACCCTAAAACTTTCTAAAAA
* *
22719326 TTGCATTTTAACCCTAAAATTTTTCC
65 TTACATTTTAACCCCAAAATTTTTCC
*
22719352 AAAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTGA-CCTCAAAACTTTCTAAAAA
1 AAAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTAACCCT-AAAACTTTCTAAAAA
* *
22719416 TTACTTTTTGACCCCAAAATTTTTCC
65 TTACATTTTAACCCCAAAATTTTTCC
* *
22719442 AAAATTACATTTTAACCCTAAAAACTTTTCCAAAATTATATTTTAACCCCAAAA
1 AAAATTACATTTTAACCCT-AAAACTTTTCCAAAATTACATTTTAACCCTAAAA
22719496 AAATTACATT
Statistics
Matches: 129, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
89 3 0.02
90 92 0.71
91 32 0.25
92 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.02, T:0.36
Consensus pattern (90 bp):
AAAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTTTCTAAAAAT
TACATTTTAACCCCAAAATTTTTCC
Found at i:22719517 original size:21 final size:22
Alignment explanation
Indices: 22719473--22719517 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
22719463 AAACTTTTCC
*
22719473 AAAATTATATTTTAACCCCAAA
1 AAAATTACATTTTAACCCCAAA
* *
22719495 AAAATTACATTTTGACCCTAAA
1 AAAATTACATTTTAACCCCAAA
22719517 A
1 A
22719518 CTTTCTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAATTACATTTTAACCCCAAA
Found at i:22725510 original size:28 final size:28
Alignment explanation
Indices: 22725470--22725523 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
22725460 GGTATCAGGT
*
22725470 ATGACCTTTGGGTCAACAGGGAGTAAGC
1 ATGACCTTTGGGTCAACACGGAGTAAGC
*
22725498 ATGACGTTTGGGTCAACACGGAGTAA
1 ATGACCTTTGGGTCAACACGGAGTAA
22725524 ATCGAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (28 bp):
ATGACCTTTGGGTCAACACGGAGTAAGC
Found at i:22728076 original size:29 final size:29
Alignment explanation
Indices: 22728033--22728290 Score: 267
Period size: 29 Copynumber: 9.3 Consensus size: 29
22728023 GTCAATCCCA
*
22728033 AAATTATTCTTATTGATTTTAAATTGAAT
1 AAATTATTCTGATTGATTTTAAATTGAAT
*
22728062 AAATTATTCTGATTGATTTTAATTTGAAT
1 AAATTATTCTGATTGATTTTAAATTGAAT
* *
22728091 AAATTATTTTGATTGATTTTAATTTGAAT
1 AAATTATTCTGATTGATTTTAAATTGAAT
* * *
22728120 AAATTATTCCGTTTGAATTTAAATTGAAT
1 AAATTATTCTGATTGATTTTAAATTGAAT
22728149 AAATTATTCTGATTG-------ATTGAAT
1 AAATTATTCTGATTGATTTTAAATTGAAT
* *
22728171 AAATTGTTCTGATTGATTTTAAATTCAAT
1 AAATTATTCTGATTGATTTTAAATTGAAT
**
22728200 AAATTATTCT-A---A---TCGATTGAAT
1 AAATTATTCTGATTGATTTTAAATTGAAT
*
22728222 AAATTATTCTGATTAATTTTAAATTGAAAT
1 AAATTATTCTGATTGATTTTAAATTG-AAT
*
22728252 AAATTATTCT-ATTTGAATTTAAAATTGAAT
1 AAATTATTCTGA-TTG-ATTTTAAATTGAAT
22728282 AAATTATTC
1 AAATTATTC
22728291 CGTTTTCTGC
Statistics
Matches: 192, Mismatches: 20, Indels: 33
0.78 0.08 0.13
Matches are distributed among these distances:
22 38 0.20
23 1 0.01
25 1 0.01
26 1 0.01
28 1 0.01
29 113 0.59
30 27 0.14
31 10 0.05
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (29 bp):
AAATTATTCTGATTGATTTTAAATTGAAT
Found at i:22728123 original size:58 final size:56
Alignment explanation
Indices: 22728033--22728290 Score: 266
Period size: 51 Copynumber: 4.6 Consensus size: 56
22728023 GTCAATCCCA
*
22728033 AAATTATTCTTATTGATTTTAAATTGAATAAATTATTCTGATTGATTTTAATTTGAAT
1 AAATTATTC-TATTGATTTT-AATTGAATAAATTATTCTGATTGATTTTAAATTGAAT
* * * *
22728091 AAATTATTTTGATTGATTTTAATTTGAATAAATTATTCCGTTTGAATTTAAATTGAAT
1 AAATTATTCT-ATTGATTTTAA-TTGAATAAATTATTCTGATTGATTTTAAATTGAAT
* * *
22728149 AAATTATTC---TGA--TTGATTGAATAAATTGTTCTGATTGATTTTAAATTCAAT
1 AAATTATTCTATTGATTTTAATTGAATAAATTATTCTGATTGATTTTAAATTGAAT
** *
22728200 AAATTATTCTA---A--TCGATTGAATAAATTATTCTGATTAATTTTAAATTGAAAT
1 AAATTATTCTATTGATTTTAATTGAATAAATTATTCTGATTGATTTTAAATTG-AAT
*
22728252 AAATTATTCTATTTGAATTTAAAATTGAATAAATTATTC
1 AAATTATTCTA-TTG-ATTT-TAATTGAATAAATTATTC
22728291 CGTTTTCTGC
Statistics
Matches: 169, Mismatches: 18, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
51 72 0.43
52 17 0.10
54 3 0.02
57 4 0.02
58 56 0.33
59 1 0.01
60 16 0.09
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (56 bp):
AAATTATTCTATTGATTTTAATTGAATAAATTATTCTGATTGATTTTAAATTGAAT
Found at i:22728170 original size:22 final size:22
Alignment explanation
Indices: 22728142--22728235 Score: 89
Period size: 22 Copynumber: 4.0 Consensus size: 22
22728132 TTGAATTTAA
22728142 ATTGAATAAATTATTCTGATTG
1 ATTGAATAAATTATTCTGATTG
*
22728164 ATTGAATAAATTGTTCTGATTG
1 ATTGAATAAATTATTCTGATTG
* * *
22728186 ATTTTAAATTCAATAAATTATTCTAATCG
1 -------ATTGAATAAATTATTCTGATTG
22728215 ATTGAATAAATTATTCTGATT
1 ATTGAATAAATTATTCTGATT
22728236 AATTTTAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
22 39 0.68
29 18 0.32
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (22 bp):
ATTGAATAAATTATTCTGATTG
Found at i:22728254 original size:30 final size:30
Alignment explanation
Indices: 22728215--22728290 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 30
22728205 ATTCTAATCG
*
22728215 ATTGAATAAATTATTCTGA-TT-AATTTTAA
1 ATTGAATAAATTATTCT-ATTTGAATTTAAA
22728244 ATTGAAATAAATTATTCTATTTGAATTTAAA
1 ATTG-AATAAATTATTCTATTTGAATTTAAA
22728275 ATTGAATAAATTATTC
1 ATTGAATAAATTATTC
22728291 CGTTTTCTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 5 0.12
30 27 0.63
31 11 0.26
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (30 bp):
ATTGAATAAATTATTCTATTTGAATTTAAA
Found at i:22729457 original size:42 final size:43
Alignment explanation
Indices: 22729394--22729501 Score: 128
Period size: 42 Copynumber: 2.5 Consensus size: 43
22729384 GCGAAAAAAC
*
22729394 GCCACTATAGAACATGATCTTTAACGACGCTTTT-CGACAAAT
1 GCCACTATAGAACATGATCTTTAACGACGCTTTTACCACAAAT
* * * * *
22729436 GCCACTATAGAACATGGTCTTTAGCGGCGTTTTTACCATAAAT
1 GCCACTATAGAACATGATCTTTAACGACGCTTTTACCACAAAT
* * *
22729479 GTCGCTATAGAACATGTTCTTTA
1 GCCACTATAGAACATGATCTTTA
22729502 TCGGTATTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
42 30 0.54
43 26 0.46
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (43 bp):
GCCACTATAGAACATGATCTTTAACGACGCTTTTACCACAAAT
Found at i:22729965 original size:66 final size:66
Alignment explanation
Indices: 22729829--22729966 Score: 170
Period size: 66 Copynumber: 2.1 Consensus size: 66
22729819 TCATATTTTG
* * **
22729829 AAGTTGTAGCTACAGTTCGTCATACTTTCTTTGAGACTCTGCTTCCCTCGCTGCTACCTTGGCTT
1 AAGTTGTAGCTACAGTTCATCATACTTTCTTTAAGACTCTGCTTCCCTCGCTGCTACCTCCGCTT
22729894 C
66 C
* * * * *
22729895 AAGTTGTAGCTGA-AGTTCATCATATTTTCTTTAAGCCTCTGGTTCTCTCGCTGCTGCCTCCGCT
1 AAGTTGTAGCT-ACAGTTCATCATACTTTCTTTAAGACTCTGCTTCCCTCGCTGCTACCTCCGCT
*
22729959 TT
65 TC
22729961 AAGTTG
1 AAGTTG
22729967 AGCAATTTGC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
66 60 0.98
67 1 0.02
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (66 bp):
AAGTTGTAGCTACAGTTCATCATACTTTCTTTAAGACTCTGCTTCCCTCGCTGCTACCTCCGCTT
C
Found at i:22735704 original size:6 final size:6
Alignment explanation
Indices: 22735693--22735730 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
22735683 TGTTATATGC
22735693 TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TT
1 TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TT
22735731 TATCATCCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (6 bp):
TTAGAT
Found at i:22736032 original size:34 final size:33
Alignment explanation
Indices: 22735953--22736020 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 33
22735943 ATTTAAACCG
* *
22735953 AATATTT-AAGTTGTTTTTATTAATTAAATAGTT
1 AATATTTGAA-TTGTTTTTAATAATTAAATAATT
22735986 AAATATTTGAATTGTTTTTAATAATTAAATAATT
1 -AATATTTGAATTGTTTTTAATAATTAAATAATT
22736020 A
1 A
22736021 TTTTGTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 1 0.03
34 28 0.90
35 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (33 bp):
AATATTTGAATTGTTTTTAATAATTAAATAATT
Found at i:22739764 original size:18 final size:18
Alignment explanation
Indices: 22739722--22739757 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22739712 TTCTTTTTAT
* *
22739722 TCAAACTCTCTAATTCTC
1 TCAAACTCTCAAACTCTC
22739740 TCAAACTCTCAAACTCTC
1 TCAAACTCTCAAACTCTC
22739758 CACAACTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (18 bp):
TCAAACTCTCAAACTCTC
Found at i:22739959 original size:12 final size:12
Alignment explanation
Indices: 22739944--22739985 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
22739934 TTTAATTTAG
*
22739944 TTTAATTTTTCA
1 TTTAGTTTTTCA
22739956 TTTAGTTTTTCA
1 TTTAGTTTTTCA
*
22739968 CTTAGTTTTTCA
1 TTTAGTTTTTCA
*
22739980 CTTAGT
1 TTTAGT
22739986 GATATATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.62
Consensus pattern (12 bp):
TTTAGTTTTTCA
Found at i:22740304 original size:40 final size:41
Alignment explanation
Indices: 22740226--22740318 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 41
22740216 GCTAATGCTC
* **
22740226 TTTACCTTTTGTGGCATTTTCCCATAAACGCTGTTATTG-A
1 TTTACCTTTTGTGGCATTTTCCCATAAACACTACTATTGCA
* *
22740266 TTTACCTTTTGTGGCATTTTTCCATAAACACTACTATTGCTC
1 TTTACCTTTTGTGGCATTTTCCCATAAACACTACTATTGC-A
22740308 TTTACCTTTTG
1 TTTACCTTTTG
22740319 CGGCGCTTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 35 0.76
42 11 0.24
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (41 bp):
TTTACCTTTTGTGGCATTTTCCCATAAACACTACTATTGCA
Found at i:22740872 original size:20 final size:21
Alignment explanation
Indices: 22740827--22740872 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
22740817 GATGATACCT
22740827 GCAAAAAGGAAAGCAGAAACA
1 GCAAAAAGGAAAGCAGAAACA
* *
22740848 ACAAAAA-GAACAG-AGACACA
1 GCAAAAAGGAA-AGCAGAAACA
22740868 GCAAA
1 GCAAA
22740873 CAATAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.63, C:0.17, G:0.20, T:0.00
Consensus pattern (21 bp):
GCAAAAAGGAAAGCAGAAACA
Found at i:22742306 original size:13 final size:14
Alignment explanation
Indices: 22742288--22742316 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
22742278 ACATTCATTC
22742288 AAATATTCTAG-TA
1 AAATATTCTAGCTA
22742301 AAATATTCTAGCTA
1 AAATATTCTAGCTA
22742315 AA
1 AA
22742317 TTATATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (14 bp):
AAATATTCTAGCTA
Found at i:22742490 original size:79 final size:79
Alignment explanation
Indices: 22742399--22742548 Score: 300
Period size: 79 Copynumber: 1.9 Consensus size: 79
22742389 CCTTAACGAA
22742399 TACTTAGTATAATTTTTATTTATCGTTTATTATTAACACTACATTGTTATTTTGTATGCCATTGT
1 TACTTAGTATAATTTTTATTTATCGTTTATTATTAACACTACATTGTTATTTTGTATGCCATTGT
22742464 TTTATTACTTATTT
66 TTTATTACTTATTT
22742478 TACTTAGTATAATTTTTATTTATCGTTTATTATTAACACTACATTGTTATTTTGTATGCCATTGT
1 TACTTAGTATAATTTTTATTTATCGTTTATTATTAACACTACATTGTTATTTTGTATGCCATTGT
22742543 TTTATT
66 TTTATT
22742549 TATGTTTTTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.57
Consensus pattern (79 bp):
TACTTAGTATAATTTTTATTTATCGTTTATTATTAACACTACATTGTTATTTTGTATGCCATTGT
TTTATTACTTATTT
Found at i:22742524 original size:352 final size:352
Alignment explanation
Indices: 22742111--22742751 Score: 1273
Period size: 352 Copynumber: 1.8 Consensus size: 352
22742101 TTTTTAATTA
22742111 TTTTATTACTTATTTTACTTAGTATAATTTTTATTTATCGTTTATTATTAACACTACATTGTTAT
1 TTTTATTACTTATTTTACTTAGTATAATTTTTATTTATCGTTTATTATTAACACTACATTGTTAT
22742176 TTTGTATGCCATTGTTTTATTTATGTTTTTTTACAGATTATACTTCACGTAATCTATTTTTATTC
66 TTTGTATGCCATTGTTTTATTTATGTTTTTTTACAGATTATACTTCACGTAATCTATTTTTATTC
22742241 ATGTTTTAGTCACTTTCAGTCCTTTCAATTTTAAGGCACATTCATTCAAATATTCTAGTAAAATA
131 ATGTTTTAGTCACTTTCAGTCCTTTCAATTTTAAGGCACATTCATTCAAATATTCTAGTAAAATA
22742306 TTCTAGCTAAATTATATGTTTTGAAAATACATTATCCTTTTTAAGACAAAATGCTTTTGTTTTGG
196 TTCTAGCTAAATTATATGTTTTGAAAATACATTATCCTTTTTAAGACAAAATGCTTTTGTTTTGG
22742371 GGAATTTGGAAGGTAATGCCTTAACGAATACTTAGTATAATTTTTATTTATCGTTTATTATTAAC
261 GGAATTTGGAAGGTAATGCCTTAACGAATACTTAGTATAATTTTTATTTATCGTTTATTATTAAC
22742436 ACTACATTGTTATTTTGTATGCCATTG
326 ACTACATTGTTATTTTGTATGCCATTG
22742463 TTTTATTACTTATTTTACTTAGTATAATTTTTATTTATCGTTTATTATTAACACTACATTGTTAT
1 TTTTATTACTTATTTTACTTAGTATAATTTTTATTTATCGTTTATTATTAACACTACATTGTTAT
22742528 TTTGTATGCCATTGTTTTATTTATGTTTTTTTACAGATTATACTTCACGTAATCTATTTTTATTC
66 TTTGTATGCCATTGTTTTATTTATGTTTTTTTACAGATTATACTTCACGTAATCTATTTTTATTC
22742593 ATGTTTTAGTCACTTTCAGTCCTTTCAATTTTAAGGCACATTCATTCAAATATTCTAGTAAAATA
131 ATGTTTTAGTCACTTTCAGTCCTTTCAATTTTAAGGCACATTCATTCAAATATTCTAGTAAAATA
*
22742658 TTCTAGCTAAATTATATGTTTTGAAAATACATTATCCTTTTTAAGGCAAAATGCTTTTGTTTTGG
196 TTCTAGCTAAATTATATGTTTTGAAAATACATTATCCTTTTTAAGACAAAATGCTTTTGTTTTGG
22742723 GGAATTTGGAAGGTAATGCCTTAACGAAT
261 GGAATTTGGAAGGTAATGCCTTAACGAAT
22742752 TGGGTATTAT
Statistics
Matches: 288, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
352 288 1.00
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (352 bp):
TTTTATTACTTATTTTACTTAGTATAATTTTTATTTATCGTTTATTATTAACACTACATTGTTAT
TTTGTATGCCATTGTTTTATTTATGTTTTTTTACAGATTATACTTCACGTAATCTATTTTTATTC
ATGTTTTAGTCACTTTCAGTCCTTTCAATTTTAAGGCACATTCATTCAAATATTCTAGTAAAATA
TTCTAGCTAAATTATATGTTTTGAAAATACATTATCCTTTTTAAGACAAAATGCTTTTGTTTTGG
GGAATTTGGAAGGTAATGCCTTAACGAATACTTAGTATAATTTTTATTTATCGTTTATTATTAAC
ACTACATTGTTATTTTGTATGCCATTG
Found at i:22742658 original size:13 final size:14
Alignment explanation
Indices: 22742640--22742668 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
22742630 ACATTCATTC
22742640 AAATATTCTAG-TA
1 AAATATTCTAGCTA
22742653 AAATATTCTAGCTA
1 AAATATTCTAGCTA
22742667 AA
1 AA
22742669 TTATATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (14 bp):
AAATATTCTAGCTA
Found at i:22743578 original size:40 final size:40
Alignment explanation
Indices: 22743522--22743915 Score: 237
Period size: 40 Copynumber: 9.7 Consensus size: 40
22743512 TAAAGCACCA
22743522 CTATTG-CTTTACCTTTTGCGGCGTTTTCCCATAACGCCG
1 CTATTGTCTTTACCTTTTGCGGCGTTTTCCCATAACGCCG
* *
22743561 CTATTGCTCTTTACTTTTTGCGGCTTTTTCCCTATAAACGCCG
1 CTATTG-TCTTTACCTTTTGCGGCGTTTTCCC-AT-AACGCCG
* * *** *** * *
22743604 TTTTTG-CTTTACCTTTTAAAGCGTTTAT-GGGTAAGTGCCA
1 CTATTGTCTTTACCTTTTGCGGCGTTT-TCCCATAA-CGCCG
* * * *
22743644 CTATTGTTTTTACCTTTTGCGCCGTTTTCCCATAAATGTCG
1 CTATTGTCTTTACCTTTTGCGGCGTTTTCCCAT-AACGCCG
* * * * *
22743685 CTATTG-GTTTACCTTTTGTGGCGTTTTCTCATAAACACCA
1 CTATTGTCTTTACCTTTTGCGGCGTTTTCCCAT-AACGCCG
* ***
22743725 CTATTGCTCTTTACCTTTTGCGGTGTTTATGGGA-AAGCGCCG
1 CTATTG-TCTTTACCTTTTGCGGCGTTT-TCCCATAA-CGCCG
** *
22743767 CTATTG-CTTTACCTTTTGCGATGTTTTACCATAAACGCCG
1 CTATTGTCTTTACCTTTTGCGGCGTTTTCCCAT-AACGCCG
* * * *** *
22743807 CTATTGCGCTTTACCTTTTGCAGTGTTTATGGTA-AAGCACCG
1 CTATTG-TCTTTACCTTTTGCGGCGTTT-TCCCATAA-CGCCG
* * * *
22743849 CTATTGT-TTTTCCTTTTGTGGCGTTTTCCTATAACGCCA
1 CTATTGTCTTTACCTTTTGCGGCGTTTTCCCATAACGCCG
*
22743888 CTATTGCTCTTTACCTTTTGCAGCGTTT
1 CTATTG-TCTTTACCTTTTGCGGCGTTT
22743916 ATGGGTAAGT
Statistics
Matches: 269, Mismatches: 64, Indels: 42
0.72 0.17 0.11
Matches are distributed among these distances:
39 22 0.08
40 89 0.33
41 84 0.31
42 59 0.22
43 15 0.06
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.43
Consensus pattern (40 bp):
CTATTGTCTTTACCTTTTGCGGCGTTTTCCCATAACGCCG
Found at i:22743615 original size:122 final size:122
Alignment explanation
Indices: 22743436--22743827 Score: 398
Period size: 122 Copynumber: 3.2 Consensus size: 122
22743426 ATGGGAAAGT
* * * *** * *
22743436 GCCGCTATTG-CTTTACCTTTTGTGGCATTTTACCATAAACATGGCTATTACGTTTTACCTTTTG
1 GCCGCTATTGCCTTTACCTTTTGCGGCGTTTTCCCATAAACACCACTATTGC-CTTTACCTTTTG
* *
22743500 CAGTGTTTATGGTAAAGCACCACTATTGCTTTACCTTTTGCGGCGTTTTCCCAT-AAC
65 CAGTGTTTATGGTAAAGCGCCACTATTGCTTTACCTTTTGCGACGTTTTCCCATAAAC
* * * ** *
22743557 GCCGCTATTGCTCTTTACTTTTTGCGGCTTTTTCCCTATAAACGCCGTTTTTG-CTTTACCTTTT
1 GCCGCTATTGC-CTTTACCTTTTGCGGCGTTTTCCC-ATAAACACCACTATTGCCTTTACCTTTT
** * * * * *
22743621 AAAGCGTTTATGGGT-AAGTGCCACTATTGTTTTTACCTTTTGCGCCGTTTTCCCATAAAT
64 GCAGTGTTTAT-GGTAAAGCGCCACTATTG-CTTTACCTTTTGCGACGTTTTCCCATAAAC
* * * *
22743681 GTCGCTATTG-GTTTACCTTTTGTGGCGTTTTCTCATAAACACCACTATTGCTCTTTACCTTTTG
1 GCCGCTATTGCCTTTACCTTTTGCGGCGTTTTCCCATAAACACCACTATTGC-CTTTACCTTTTG
* * * * *
22743745 CGGTGTTTATGGGAAAGCGCCGCTATTGCTTTACCTTTTGCGATGTTTTACCATAAAC
65 CAGTGTTTATGGTAAAGCGCCACTATTGCTTTACCTTTTGCGACGTTTTCCCATAAAC
22743803 GCCGCTATTGCGCTTTACCTTTTGC
1 GCCGCTATTGC-CTTTACCTTTTGC
22743828 AGTGTTTATG
Statistics
Matches: 216, Mismatches: 44, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
121 22 0.10
122 85 0.39
123 77 0.36
124 32 0.15
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (122 bp):
GCCGCTATTGCCTTTACCTTTTGCGGCGTTTTCCCATAAACACCACTATTGCCTTTACCTTTTGC
AGTGTTTATGGTAAAGCGCCACTATTGCTTTACCTTTTGCGACGTTTTCCCATAAAC
Found at i:22743923 original size:82 final size:83
Alignment explanation
Indices: 22743422--22743955 Score: 377
Period size: 82 Copynumber: 6.5 Consensus size: 83
22743412 CGACAGTGGC
** * ****
22743422 GTTTATGGG-AAAGTGCCGCTATTGCTTTACCTTTTGTGGCATTTTACC-ATAAACATGGCTATT
1 GTTTATGGGTAAAGCACCGCTATTGCTTTACCTTTTGTGGCGTTTT-CCTATAAACGCCACTATT
*
22743485 ACGT-TTTACCTTTTGCAGT
65 GC-TCTTTACCTTTTGCAGT
* * * *
22743504 GTTTAT-GGTAAAGCACCACTATTGCTTTACCTTTTGCGGCGTTTTCCCAT-AACGCCGCTATTG
1 GTTTATGGGTAAAGCACCGCTATTGCTTTACCTTTTGTGGCGTTTTCCTATAAACGCCACTATTG
*
22743567 CTCTTTACTTTTTGC-G-
66 CTCTTTACCTTTTGCAGT
* *** * * * * *** *** **
22743583 GCTTTTTCCCTATAAACGCCGTTTTTGCTTTACCTTTTAAAGCGTTTAT-GGGTAAGTGCCACTA
1 G-TTTATGGGTA-AAGCACCGCTATTGCTTTACCTTTTGTGGCGTTT-TCCTATAAACGCCACTA
* *
22743647 TTG-TTTTTACCTTTTGC-GCC
63 TTGCTCTTTACCTTTTGCAG-T
*** * * *
22743667 GTTT-TCCCATAAATG--TCGCTATTGGTTTACCTTTTGTGGCGTTTT-CTCATAAACACCACTA
1 GTTTAT-GGGTAAA-GCACCGCTATTGCTTTACCTTTTGTGGCGTTTTCCT-ATAAACGCCACTA
*
22743728 TTGCTCTTTACCTTTTGCGGT
63 TTGCTCTTTACCTTTTGCAGT
* * ** *
22743749 GTTTATGGG-AAAGCGCCGCTATTGCTTTACCTTTTGCGATGTTTTACC-ATAAACGCCGCTATT
1 GTTTATGGGTAAAGCACCGCTATTGCTTTACCTTTTGTGGCGTTTT-CCTATAAACGCCACTATT
*
22743812 GCGCTTTACCTTTTGCAGT
65 GCTCTTTACCTTTTGCAGT
* *
22743831 GTTTAT-GGTAAAGCACCGCTATTGTTTTTCCTTTTGTGGCGTTTTCCTAT-AACGCCACTATTG
1 GTTTATGGGTAAAGCACCGCTATTGCTTTACCTTTTGTGGCGTTTTCCTATAAACGCCACTATTG
*
22743894 CTCTTTACCTTTTGCAGC
66 CTCTTTACCTTTTGCAGT
*** * *
22743912 GTTTATGGGT-AAGTGTCACTATTGCTTTACCTTTTGCGGCGTTT
1 GTTTATGGGTAAAGCACCGCTATTGCTTTACCTTTTGTGGCGTTT
22743956 ATTGAAAAAC
Statistics
Matches: 355, Mismatches: 74, Indels: 47
0.75 0.16 0.10
Matches are distributed among these distances:
79 1 0.00
80 8 0.02
81 129 0.36
82 195 0.55
83 20 0.06
84 2 0.01
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (83 bp):
GTTTATGGGTAAAGCACCGCTATTGCTTTACCTTTTGTGGCGTTTTCCTATAAACGCCACTATTG
CTCTTTACCTTTTGCAGT
Found at i:22743955 original size:245 final size:244
Alignment explanation
Indices: 22743420--22743955 Score: 566
Period size: 245 Copynumber: 2.2 Consensus size: 244
22743410 TTCGACAGTG
* * * ***
22743420 GCGTTTATGGGAAAGTGCCGCTATTGCTTTACCTTTTGTGGCATTTTACCATAAACATGGCTATT
1 GCGTTTATGGGTAAGTGTCGCTATTGCTTTACCTTTTGTGGCGTTTTACCATAAACACCACTATT
* * *
22743485 ACGTTTTACCTTTTGCAGTGTTTATGGTAAAGCACCACTATTGCTTTACCTTTTGCGGCGTTTTC
66 ACGTTTTACCTTTTGCAGTGTTTATGGGAAAGCACCACTATTGCTTTACCTTTTGCGACGTTTTA
* * * * * *
22743550 CCATAACGCCGCTATTGCTCTTTACTTTTTGCGGCTTTTTCCCTATAAACGCCGTTTTTGCTTTA
131 CCATAACGCCGCTATTGCGCTTTACCTTTTGCGGCTTTATCCCTATAAACACCGCTATTGCTTTA
** ** *
22743615 CCTTTTAAAGCGTTTATGGGTAAGTGCCACTATTGTTTTTACCTTTTGC
196 CCTTTTAAAGCGTTTATGCCTAAACGCCACTATTGTCTTTACCTTTTGC
*** * *
22743664 GCCGTTT-TCCCATAAATGTCGCTATTGGTTTACCTTTTGTGGCGTTTT-CTCATAAACACCACT
1 G-CGTTTAT-GGGTAAGTGTCGCTATTGCTTTACCTTTTGTGGCGTTTTAC-CATAAACACCACT
* * * * *
22743727 ATTGC-TCTTTACCTTTTGCGGTGTTTATGGGAAAGCGCCGCTATTGCTTTACCTTTTGCGATGT
63 ATTACGT-TTTACCTTTTGCAGTGTTTATGGGAAAGCACCACTATTGCTTTACCTTTTGCGACGT
** *
22743791 TTTACCATAAACGCCGCTATTGCGCTTTACCTTTTGCAGTG-TTTAT-GGTA-AAGCACCGCTAT
127 TTTACCAT-AACGCCGCTATTGCGCTTTACCTTTTGC-G-GCTTTATCCCTATAAACACCGCTAT
* * ***
22743853 TGTTTTTCCTTTTGTGGCGTTT-T-CCTATAACGCCACTATTGCTCTTTACCTTTTGC
189 TGCTTTACCTTTTAAAGCGTTTATGCCTA-AACGCCACTATTG-TCTTTACCTTTTGC
* *
22743909 AGCGTTTATGGGTAAGTGTCACTATTGCTTTACCTTTTGCGGCGTTT
1 -GCGTTTATGGGTAAGTGTCGCTATTGCTTTACCTTTTGTGGCGTTT
22743956 ATTGAAAAAC
Statistics
Matches: 236, Mismatches: 45, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
243 2 0.01
244 16 0.07
245 182 0.77
246 30 0.13
247 5 0.02
248 1 0.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (244 bp):
GCGTTTATGGGTAAGTGTCGCTATTGCTTTACCTTTTGTGGCGTTTTACCATAAACACCACTATT
ACGTTTTACCTTTTGCAGTGTTTATGGGAAAGCACCACTATTGCTTTACCTTTTGCGACGTTTTA
CCATAACGCCGCTATTGCGCTTTACCTTTTGCGGCTTTATCCCTATAAACACCGCTATTGCTTTA
CCTTTTAAAGCGTTTATGCCTAAACGCCACTATTGTCTTTACCTTTTGC
Found at i:22743974 original size:40 final size:39
Alignment explanation
Indices: 22743489--22743991 Score: 196
Period size: 40 Copynumber: 12.4 Consensus size: 39
22743479 GCTATTACGT
* * * * * *
22743489 TTTACCTTTTGCAGTGTTTATGGTAAAGCACCACTATTGC
1 TTTACCTTTTGCGGCGTTT-TGGAAAAACGCCGCTATTGC
*** *
22743529 TTTACCTTTTGCGGCGTTTTCCCATAACGCCGCTATTGCTC
1 TTTACCTTTTGCGGCGTTTTGGAAAAACGCCGCTATTG--C
* * ** * * *
22743570 TTTACTTTTTGCGGCTTTTTCCCTATAAACGCCGTTTTTGC
1 TTTACCTTTTGCGGCGTTTT--GGAAAAACGCCGCTATTGC
*** ** ** * *
22743611 TTTACCTTTTAAAGCGTTTATGGGTAAGTGCCACTATTGTT
1 TTTACCTTTTGCGGCGTTT-TGGAAAAACGCCGCTATTG-C
* ** * * * *
22743652 TTTACCTTTTGCGCCGTTTTCCCATAAATGTCGCTATTGG
1 TTTACCTTTTGCGGCGTTTT-GGAAAAACGCCGCTATTGC
* ** * * *
22743692 TTTACCTTTTGTGGCGTTTTCTCATAAACACCACTATTGCTC
1 TTTACCTTTTGCGGCGTTTT-GGAAAAACGCCGCTATTG--C
* * *
22743734 TTTACCTTTTGCGGTGTTTATGGGAAAGCGCCGCTATTGC
1 TTTACCTTTTGCGGCGTTT-TGGAAAAACGCCGCTATTGC
** ** *
22743774 TTTACCTTTTGCGATGTTTTACCATAAACGCCGCTATTGCGC
1 TTTACCTTTTGCGGCGTTTT-GGAAAAACGCCGCTATT--GC
* * * * * *
22743816 TTTACCTTTTGCAGTGTTTATGGTAAAGCACCGCTATTGT
1 TTTACCTTTTGCGGCGTTT-TGGAAAAACGCCGCTATTGC
* * *** * *
22743856 TTTTCCTTTTGTGGCGTTTTCCTATAACGCCACTATTGCTC
1 TTTACCTTTTGCGGCGTTTTGGAAAAACGCCGCTATTG--C
* ** ** * *
22743897 TTTACCTTTTGCAGCGTTTATGGGTAAGTGTCACTATTGC
1 TTTACCTTTTGCGGCGTTT-TGGAAAAACGCCGCTATTGC
*
22743937 TTTACCTTTTGCGGCGTTTATTGAAAAACGCCGCTATTGC
1 TTTACCTTTTGCGGCGTTT-TGGAAAAACGCCGCTATTGC
* *
22743977 TTTACTTTTTACGGC
1 TTTACCTTTTGCGGC
22743992 ATGTTTGATC
Statistics
Matches: 340, Mismatches: 106, Indels: 34
0.71 0.22 0.07
Matches are distributed among these distances:
39 26 0.08
40 153 0.45
41 77 0.23
42 70 0.21
43 14 0.04
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (39 bp):
TTTACCTTTTGCGGCGTTTTGGAAAAACGCCGCTATTGC
Found at i:22743976 original size:163 final size:163
Alignment explanation
Indices: 22743419--22743955 Score: 523
Period size: 163 Copynumber: 3.3 Consensus size: 163
22743409 TTTCGACAGT
* * * ***
22743419 GGCGTTTATGGGAAAGTGCCGCTATTGCTTTACCTTTTGTGGCATTTTACCATAAACATGGCTAT
1 GGCGTTTATGGGAAAGCGCCGCTATTGCTTTACCTTTTGCGGCGTTTTACCATAAACGCCGCTAT
* * *
22743484 TACGTTTTACCTTTTGCAGTGTTTATGGTAAAGCACCACTATTGCTTTACCTTTTGCGGCGTTTT
66 TGCGTTTTACCTTTTGCAGTGTTTATGGTAAAGCACCGCTATTGCTTTACCTTTTGTGGCGTTTT
* * *
22743549 CCCATAACGCCGCTATTGCTCTTTACTTTTTGC
131 CCTATAACGCCACTATTGCTCTTTACCTTTTGC
* *** * * * *** *** ** *
22743582 GGC-TTTTTCCCTATAAACGCCGTTTTTGCTTTACCTTTTAAAGCG-TTTATGGGTAAGTGCCAC
1 GGCGTTTAT-GGGA-AAGCGCCGCTATTGCTTTACCTTTTGCGGCGTTTTA-CCATAAACGCCGC
* * ** * *
22743645 TATTG-TTTTTACCTTTTGC-GCCGTTT-TCCCATAAATG--TCGCTATTGGTTTACCTTTTGTG
63 TATTGCGTTTTACCTTTTGCAG-TGTTTAT--GGTAAA-GCACCGCTATTGCTTTACCTTTTGTG
*
22743705 GCGTTTT-CTCATAAACACCACTATTGCTCTTTACCTTTTGC
124 GCGTTTTCCT-AT-AACGCCACTATTGCTCTTTACCTTTTGC
* **
22743746 GGTGTTTATGGGAAAGCGCCGCTATTGCTTTACCTTTTGCGATGTTTTACCATAAACGCCGCTAT
1 GGCGTTTATGGGAAAGCGCCGCTATTGCTTTACCTTTTGCGGCGTTTTACCATAAACGCCGCTAT
* * *
22743811 TGCGCTTTACCTTTTGCAGTGTTTATGGTAAAGCACCGCTATTGTTTTTCCTTTTGTGGCGTTTT
66 TGCGTTTTACCTTTTGCAGTGTTTATGGTAAAGCACCGCTATTGCTTTACCTTTTGTGGCGTTTT
22743876 CCTATAACGCCACTATTGCTCTTTACCTTTTGC
131 CCTATAACGCCACTATTGCTCTTTACCTTTTGC
* * * * *
22743909 AGCGTTTATGGGTAAGTGTCACTATTGCTTTACCTTTTGCGGCGTTT
1 GGCGTTTATGGGAAAGCGCCGCTATTGCTTTACCTTTTGCGGCGTTT
22743956 ATTGAAAAAC
Statistics
Matches: 287, Mismatches: 70, Indels: 34
0.73 0.18 0.09
Matches are distributed among these distances:
162 8 0.03
163 158 0.55
164 112 0.39
165 9 0.03
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (163 bp):
GGCGTTTATGGGAAAGCGCCGCTATTGCTTTACCTTTTGCGGCGTTTTACCATAAACGCCGCTAT
TGCGTTTTACCTTTTGCAGTGTTTATGGTAAAGCACCGCTATTGCTTTACCTTTTGTGGCGTTTT
CCTATAACGCCACTATTGCTCTTTACCTTTTGC
Found at i:22747076 original size:19 final size:22
Alignment explanation
Indices: 22747052--22747100 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 22
22747042 TACAACTGAC
22747052 AATAATTAC-AAT-CAAAATT-
1 AATAATTACAAATACAAAATTA
*
22747071 AATAATTACAAATACCAAATTA
1 AATAATTACAAATACAAAATTA
22747093 AATAATTA
1 AATAATTA
22747101 GTTCACCGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 9 0.35
20 3 0.12
21 6 0.23
22 8 0.31
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAATTACAAATACAAAATTA
Found at i:22747518 original size:16 final size:17
Alignment explanation
Indices: 22747487--22747520 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
22747477 AACATCATTA
*
22747487 TAAAATGATATGTTTTT
1 TAAAATGATATATTTTT
22747504 TAAAAT-ATATATTTTT
1 TAAAATGATATATTTTT
22747520 T
1 T
22747521 TAAGGGTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TAAAATGATATATTTTT
Found at i:22749198 original size:58 final size:58
Alignment explanation
Indices: 22749094--22749286 Score: 196
Period size: 59 Copynumber: 3.3 Consensus size: 58
22749084 ATTAAGCAAT
* * * * *
22749094 ATTTTGTACCTGAACTTGACATATTTTATTAATTTGATACCT-AACTTTTTTGGACCCA
1 ATTTGGTACCTAAATTTGACAT-TTTTCTTAATTTGGTACCTAAACTTTTTTGGACCCA
*
22749152 ATTTGGTACCTAAATTTGACACTTTTTCTTAATTTGGTA-CTAAACTTTTTTTGGACCAA
1 ATTTGGTACCTAAATTTGACA-TTTTTCTTAATTTGGTACCTAAAC-TTTTTTGGACCCA
* * * **
22749211 ATTTGGTACCTAAACTTGGA-ATTTTTTCCTAATTTGGTACCTAAGA-TTTTTTAGATTCA
1 ATTTGGTACCTAAA-TTTGACA-TTTTTCTTAATTTGGTACCTAA-ACTTTTTTGGACCCA
*
22749270 ATTTGGTACATAAATTT
1 ATTTGGTACCTAAATTT
22749287 ATTAAATATT
Statistics
Matches: 114, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
57 2 0.02
58 37 0.32
59 66 0.58
60 8 0.07
61 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.46
Consensus pattern (58 bp):
ATTTGGTACCTAAATTTGACATTTTTCTTAATTTGGTACCTAAACTTTTTTGGACCCA
Found at i:22749248 original size:31 final size:30
Alignment explanation
Indices: 22749151--22749254 Score: 99
Period size: 31 Copynumber: 3.5 Consensus size: 30
22749141 TTTTGGACCC
* * *
22749151 AATTTGGTACCTAAATTTGACACTTTTTCTT
1 AATTTGGTACCTAAACTTGA-ATTTTTTCCT
* *
22749182 AATTTGGTA-CTAAACTT---TTTTTGGACCA
1 AATTTGGTACCTAAACTTGAATTTTT--TCCT
22749210 AATTTGGTACCTAAACTTGGAATTTTTTCCT
1 AATTTGGTACCTAAACTT-GAATTTTTTCCT
22749241 AATTTGGTACCTAA
1 AATTTGGTACCTAA
22749255 GATTTTTTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
26 4 0.07
28 10 0.17
29 8 0.14
30 7 0.12
31 25 0.42
33 5 0.08
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (30 bp):
AATTTGGTACCTAAACTTGAATTTTTTCCT
Found at i:22749521 original size:30 final size:31
Alignment explanation
Indices: 22749487--22749565 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 31
22749477 GGACCCTAAA
*
22749487 AAGTTTAAGTACCAACTT-AAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
22749517 AAGTTTAAGTACCAAATTAAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATT-AAAAAAAAGTGTC
* *
22749549 AAGTTCAAGTGCCAAAT
1 AAGTTTAAGTACCAAAT
22749566 GTTATATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 17 0.39
32 27 0.61
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
Found at i:22752554 original size:166 final size:166
Alignment explanation
Indices: 22752193--22752646 Score: 616
Period size: 165 Copynumber: 2.7 Consensus size: 166
22752183 AAATAGATGA
* *
22752193 AACTTATAGGGACTAAGTTGGCTA-TTTTTTAGTAAAAGATGA-AAAATGCAATCTGATTTCTAG
1 AACTTATAGGGACTAATTTGACTATTTTTTTAGTAAAAGA-GACAAAATGCAATCTGATTTCTAG
* * *
22752256 TATAAGGGCTTATATGGCACTTTTATCTAATCCTAGTATCCTTAAATTCCATGTCACTTACATAA
65 TATAACGGCTTATATGGTACTTTTATCTAATCCTACTATCCTTAAATTCCATGTCACTTACATAA
22752321 TTTTTTTTAACAAAAAGGTGAGTTTGCTTTTTGATCT
130 TTTTTTTTAACAAAAAGGTGAGTTTGCTTTTTGATCT
* * *
22752358 AACTTACAGGGACTAATTT-ACT-TATTTTTTAGTAAAAGAGACAAAATGCAATCCGATTCCTAG
1 AACTTATAGGGACTAATTTGACTAT-TTTTTTAGTAAAAGAGACAAAATGCAATCTGATTTCTAG
*
22752421 TATAACGGCCTATATGGTACTTTTTATCTAATCCTACTATCCTTAAATTCCATGTCACTTACATA
65 TATAACGGCTTATATGGTAC-TTTTATCTAATCCTACTATCCTTAAATTCCATGTCACTTACATA
*
22752486 A-TTTTTTTAACAAAAAGGTGAGTTT-TTTATTTGATCT
129 ATTTTTTTTAACAAAAAGGTGAGTTTGCTT-TTTGATCT
* * * *
22752523 AACTTATAAGAACTAATTTGTCTATTTTTTTAGTAAAAGA-AGCAAAATGCAATATGATTTCTAG
1 AACTTATAGGGACTAATTTGACTATTTTTTTAGTAAAAGAGA-CAAAATGCAATCTGATTTCTAG
* * * ** * *
22752587 TATAATGACTTCTATAATACTTTTATCTAATCCTACTCATCATTTAATTCCATGTCACTT
65 TATAACGGCTTATATGGTACTTTTATCTAATCCTACT-ATCCTTAAATTCCATGTCACTT
22752647 GCATTTTTTT
Statistics
Matches: 255, Mismatches: 25, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
164 6 0.02
165 134 0.53
166 114 0.45
167 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (166 bp):
AACTTATAGGGACTAATTTGACTATTTTTTTAGTAAAAGAGACAAAATGCAATCTGATTTCTAGT
ATAACGGCTTATATGGTACTTTTATCTAATCCTACTATCCTTAAATTCCATGTCACTTACATAAT
TTTTTTTAACAAAAAGGTGAGTTTGCTTTTTGATCT
Found at i:22753574 original size:19 final size:19
Alignment explanation
Indices: 22753528--22753579 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
22753518 ATATGCCATA
*
22753528 TAAACAAATAATTTAAAAAT
1 TAAA-AAATAATTCAAAAAT
22753548 TATAAAAAT-ATTCAAAAATT
1 TA-AAAAATAATTCAAAAA-T
*
22753568 TAAAAAAAAATT
1 TAAAAAATAATT
22753580 AAGAAAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 13 0.48
20 12 0.44
21 2 0.07
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAAATAATTCAAAAAT
Found at i:22753574 original size:20 final size:20
Alignment explanation
Indices: 22753528--22753579 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
22753518 ATATGCCATA
* *
22753528 TAAACAAATAATTTAAAAAT
1 TAAAAAAATAATTCAAAAAT
*
22753548 TATAAAAAT-ATTCAAAAATT
1 TAAAAAAATAATTCAAAAA-T
22753568 TAAAAAAA-AATT
1 TAAAAAAATAATT
22753580 AAGAAAAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAAAATAATTCAAAAAT
Found at i:22761308 original size:2 final size:2
Alignment explanation
Indices: 22761301--22761336 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
22761291 TTTCTTTTAC
22761301 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22761337 TACTTATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22761365 original size:15 final size:15
Alignment explanation
Indices: 22761326--22761358 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22761316 TATATATATA
*
22761326 TATTATAATATTACT
1 TATTAAAATATTACT
22761341 TATTAAAATATTA-T
1 TATTAAAATATTACT
22761355 TATT
1 TATT
22761359 TTAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTAAAATATTACT
Found at i:22762157 original size:27 final size:27
Alignment explanation
Indices: 22762079--22762157 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
22762069 CTTTAGAATT
*
22762079 GCCTTACATA-CGATTCCTTCAGAGCTC
1 GCCTTACATATC-ATTCCTTCAGAGTTC
* *
22762106 GCCTTACATATCATTCTTTTAGAGTTC
1 GCCTTACATATCATTCCTTCAGAGTTC
* *
22762133 GTCTTACATATTATTCCTTCAGAGT
1 GCCTTACATATCATTCCTTCAGAGT
22762158 GATTGCCACA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 43 0.98
28 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (27 bp):
GCCTTACATATCATTCCTTCAGAGTTC
Found at i:22762251 original size:30 final size:29
Alignment explanation
Indices: 22762210--22762336 Score: 127
Period size: 28 Copynumber: 4.4 Consensus size: 29
22762200 TTCCTTTCGT
22762210 TATTAGCCACAAAGGCTTCCATCTTTATAG
1 TATT-GCCACAAAGGCTTCCATCTTTATAG
*
22762240 ATATTGCCACAAAGGCTTCCATCTTCATAG
1 -TATTGCCACAAAGGCTTCCATCTTTATAG
* ** * * *
22762270 -GTTGCTGCAAATGTTTCCATTTTTATAG
1 TATTGCCACAAAGGCTTCCATCTTTATAG
*
22762298 -ATTACCACAAAGGCTTCCAT-TTTCATAG
1 TATTGCCACAAAGGCTTCCATCTTT-ATAG
22762326 T-TTGCCACAAA
1 TATTGCCACAAA
22762337 AGCTCTTCAT
Statistics
Matches: 79, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
27 3 0.04
28 48 0.61
30 24 0.30
31 4 0.05
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (29 bp):
TATTGCCACAAAGGCTTCCATCTTTATAG
Found at i:22762449 original size:55 final size:54
Alignment explanation
Indices: 22762318--22762449 Score: 122
Period size: 54 Copynumber: 2.4 Consensus size: 54
22762308 AGGCTTCCAT
** * * *
22762318 TTTCATAGTTTGCCACAAAAGCTCTTCATTTAGAGTGCGCCAAAAGGCAATTCC
1 TTTCATAAATTGCCACAAAGGCTCTTCATTTAGAGTACGCCAAAAGACAATTCC
* * * * * * * *
22762372 TTTCATGAATCGTCATAGAGGCTCTTCATTTAGATTATGCCACAAAGACATTTCC
1 TTTCATAAATTGCCACAAAGGCTCTTCATTTAGAGTACGCCA-AAAGACAATTCC
22762427 TTTCA-AAAGTTGCCACAAAGGCT
1 TTTCATAAA-TTGCCACAAAGGCT
22762450 TTCCTTTTAG
Statistics
Matches: 58, Mismatches: 18, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
54 33 0.57
55 25 0.43
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (54 bp):
TTTCATAAATTGCCACAAAGGCTCTTCATTTAGAGTACGCCAAAAGACAATTCC
Found at i:22763074 original size:21 final size:21
Alignment explanation
Indices: 22763049--22763089 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22763039 CTTGATCTCC
22763049 AAATCTAAACAT-CCCTCCACG
1 AAATCTAAA-ATGCCCTCCACG
*
22763070 AAATCTACAATGCCCTCCAC
1 AAATCTAAAATGCCCTCCAC
22763090 TCGACTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.37, C:0.39, G:0.05, T:0.20
Consensus pattern (21 bp):
AAATCTAAAATGCCCTCCACG
Found at i:22765736 original size:6 final size:6
Alignment explanation
Indices: 22765725--22765759 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
22765715 TATTTGCAAC
* *
22765725 AAAATT AAAATT AAAATT AAAATC AAAATC AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT
22765760 CAATTCTCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (6 bp):
AAAATT
Found at i:22765742 original size:12 final size:12
Alignment explanation
Indices: 22765724--22765762 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
22765714 TTATTTGCAA
22765724 CAAAATTAAAAT
1 CAAAATTAAAAT
*
22765736 TAAAATTAAAAT
1 CAAAATTAAAAT
*
22765748 CAAAATCAAAAT
1 CAAAATTAAAAT
22765760 CAA
1 CAA
22765763 TTCTCGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (12 bp):
CAAAATTAAAAT
Found at i:22765760 original size:6 final size:6
Alignment explanation
Indices: 22765724--22765762 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
22765714 TTATTTGCAA
* * *
22765724 CAAAAT TAAAAT TAAAAT TAAAAT CAAAAT CAAAAT CAA
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAA
22765763 TTCTCGTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (6 bp):
CAAAAT
Found at i:22766392 original size:2 final size:2
Alignment explanation
Indices: 22766385--22766418 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22766375 TTAAAGTTTC
22766385 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
22766419 TTGAACCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22768348 original size:9 final size:9
Alignment explanation
Indices: 22768323--22768356 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
22768313 CGGTTGACTC
22768323 TTAAATCAA
1 TTAAATCAA
22768332 TATAAATCAA
1 T-TAAATCAA
22768342 TTAAATCAGA
1 TTAAATCA-A
22768352 TTAAA
1 TTAAA
22768357 AAAGATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (9 bp):
TTAAATCAA
Found at i:22771033 original size:21 final size:20
Alignment explanation
Indices: 22770996--22771087 Score: 109
Period size: 19 Copynumber: 4.5 Consensus size: 20
22770986 ATTATATTGT
22770996 TGTTTTGG-TGCTTTTTTTAC
1 TGTTTTGGTTGC-TTTTTTAC
22771016 TGTTTTGGTTGCTATTTTTTAC
1 TGTTTTGGTTGC--TTTTTTAC
22771038 TGTTTTTGTGTTG-TTTTTTAC
1 TG-TTTTG-GTTGCTTTTTTAC
*
22771059 TGTTTTAG-TGCTTTTTTAC
1 TGTTTTGGTTGCTTTTTTAC
22771078 TGTTTTGGTT
1 TGTTTTGGTT
22771088 ACTGTTTTCG
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
18 2 0.03
19 16 0.25
20 13 0.21
21 13 0.21
22 10 0.16
23 5 0.08
24 4 0.06
ACGTcount: A:0.07, C:0.08, G:0.20, T:0.66
Consensus pattern (20 bp):
TGTTTTGGTTGCTTTTTTAC
Found at i:22771095 original size:21 final size:21
Alignment explanation
Indices: 22770996--22771095 Score: 102
Period size: 21 Copynumber: 4.9 Consensus size: 21
22770986 ATTATATTGT
*
22770996 TGTTTTGG-TGCTTTTTTTAC
1 TGTTTTGGTTGCTGTTTTTAC
*
22771016 TGTTTTGGTTGCTATTTTTTAC
1 TGTTTTGGTTGCT-GTTTTTAC
22771038 TGTTTTTGTGTTG-T-TTTTTAC
1 TG-TTTTG-GTTGCTGTTTTTAC
*
22771059 TGTTTTAG-TGCT-TTTTTAC
1 TGTTTTGGTTGCTGTTTTTAC
*
22771078 TGTTTTGGTTACTGTTTT
1 TGTTTTGGTTGCTGTTTT
22771096 CGTGTTGTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
18 2 0.03
19 16 0.23
20 15 0.21
21 17 0.24
22 10 0.14
23 6 0.09
24 4 0.06
ACGTcount: A:0.07, C:0.08, G:0.19, T:0.66
Consensus pattern (21 bp):
TGTTTTGGTTGCTGTTTTTAC
Found at i:22771128 original size:12 final size:13
Alignment explanation
Indices: 22771112--22771160 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
22771102 GTTTTTACTG
22771112 TTATTTTTGTTGC
1 TTATTTTTGTTGC
*
22771125 -TATTTTTGTTAC
1 TTATTTTTGTTGC
*
22771137 TTTTTTTTGTTG-
1 TTATTTTTGTTGC
22771149 TT-TTTTATGTTG
1 TTATTTT-TGTTG
22771161 TTTTTCCGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 4 0.13
12 18 0.58
13 9 0.29
ACGTcount: A:0.08, C:0.04, G:0.14, T:0.73
Consensus pattern (13 bp):
TTATTTTTGTTGC
Found at i:22772042 original size:5 final size:5
Alignment explanation
Indices: 22772034--22772063 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
22772024 TTTCTTGATC
22772034 TTTTA TTTTA TTTTA TTTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTT
22772064 CTTCTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:22772053 original size:11 final size:11
Alignment explanation
Indices: 22772034--22772063 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
22772024 TTTCTTGATC
22772034 TTTTA-TTTTA
1 TTTTATTTTTA
22772044 TTTTATTTTTA
1 TTTTATTTTTA
22772055 TTTTATTTT
1 TTTTATTTT
22772064 CTTCTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:22772586 original size:109 final size:109
Alignment explanation
Indices: 22772447--22772755 Score: 474
Period size: 109 Copynumber: 2.8 Consensus size: 109
22772437 TAATATTTTT
* * *
22772447 TTTTATTTTAGAGAATTCAAAAAATGGTGCTCAAACGTACTGGGTATGATTTTTTCTTTGAACCT
1 TTTTA-TTTAGAGAATTCGAGAAATTGTGCTCAAACGTACTGGGTATGATTTTTTCTTTGAACCT
*
22772512 AAATAATCGAGTATCCTATTTAAAATCAATAAATGTTCGATGTTC
65 AAATAATCGAGTATCCTATTTAAAATCAATAAATGTTCGATATTC
* * *
22772557 TTTTATTTAGAGAATTCGGGAAATTGTGCTCAAACATACTAGGTATGATTTTTTCTTTGAACCTA
1 TTTTATTTAGAGAATTCGAGAAATTGTGCTCAAACGTACTGGGTATGATTTTTTCTTTGAACCTA
* *
22772622 AATAATCGAGTATACTATTTAAAATCAATAAATGTTCGATATTT
66 AATAATCGAGTATCCTATTTAAAATCAATAAATGTTCGATATTC
* * *
22772666 TTTTATTTAGGGAATTCGAGAAATTGTGCTCAAACGTATTGAGTATGATTTTTTCTTTGAACCTA
1 TTTTATTTAGAGAATTCGAGAAATTGTGCTCAAACGTACTGGGTATGATTTTTTCTTTGAACCTA
* * *
22772731 AGTAGTCGAATATCCTATTTAAAAT
66 AATAATCGAGTATCCTATTTAAAAT
22772756 TGATAAATAT
Statistics
Matches: 180, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
109 175 0.97
110 5 0.03
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (109 bp):
TTTTATTTAGAGAATTCGAGAAATTGTGCTCAAACGTACTGGGTATGATTTTTTCTTTGAACCTA
AATAATCGAGTATCCTATTTAAAATCAATAAATGTTCGATATTC
Found at i:22780016 original size:49 final size:49
Alignment explanation
Indices: 22779960--22780250 Score: 411
Period size: 49 Copynumber: 5.9 Consensus size: 49
22779950 TAGAATTATA
* * *
22779960 AAGGGAAAGGTTGAAGCCGCAATGGCGAGTCTTACACCCTAGAGATGTG
1 AAGGGAAAGATTGAAGCCGCAATGGCGAATCTTACACCCTAGAGATGCG
22780009 AAGGGAAAGATTGAAGCCGCAATGGCGAATCTTACACCCTAGAGATGCG
1 AAGGGAAAGATTGAAGCCGCAATGGCGAATCTTACACCCTAGAGATGCG
* *
22780058 AAGGGAAAGATTGAAGCCGCAATGGCGAGTTTTACACCCTAGAGATGCG
1 AAGGGAAAGATTGAAGCCGCAATGGCGAATCTTACACCCTAGAGATGCG
* * * * *
22780107 AAGGGAAAGATTGAAACTGCAATGACGAGTCTTACACCCAAGAGATGCG
1 AAGGGAAAGATTGAAGCCGCAATGGCGAATCTTACACCCTAGAGATGCG
** * * * * *
22780156 AAGGGAAAGATTGAAATCACAATGGCGAATCTTGCGCCCCAGAGATGTG
1 AAGGGAAAGATTGAAGCCGCAATGGCGAATCTTACACCCTAGAGATGCG
* *
22780205 AAGGGAAAGATTGAAGCCGCAATGGCAAATCTTATACCCTAGAGAT
1 AAGGGAAAGATTGAAGCCGCAATGGCGAATCTTACACCCTAGAGAT
22780251 ATGGAGAAGC
Statistics
Matches: 215, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 215 1.00
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.18
Consensus pattern (49 bp):
AAGGGAAAGATTGAAGCCGCAATGGCGAATCTTACACCCTAGAGATGCG
Found at i:22782974 original size:110 final size:107
Alignment explanation
Indices: 22782774--22783093 Score: 410
Period size: 110 Copynumber: 2.9 Consensus size: 107
22782764 GGAGGCAATA
* ** * *
22782774 TTCTTTTATTTTAGGGAAATCAAAAAATTGTACTCAAACGTATTGGATATGATTTTTTTTTGAAC
1 TTCTTTTA-TTTAGGGAATTGGAGAAATTGTACTCAAACGTACTGG-TATGATTTTTTTTTGAAC
*
22782839 CTAAATAATCGAGTATCCCATTTAAAATCAATAAATGTTCGATG
64 CTAAATAATCGAGTATCCCATTTAAAATTAATAAATGTTCGATG
* *
22782883 TTTTTTTATTTAGGGAAGTT-GAGAAATTGTGCTCAAACGTACTGAGTATGATTTTTTTCTTTGA
1 TTCTTTTATTTAGGGAA-TTGGAGAAATTGTACTCAAACGTACTG-GTATGA-TTTTTT-TTTGA
*
22782947 ACCTAAATAATCGAGTATCCCATTTAAAATTAATAAATGTTTGATG
62 ACCTAAATAATCGAGTATCCCATTTAAAATTAATAAATGTTCGATG
* *
22782993 TTCTTTTATTTAGGGAATTGGAGAAATTGTACTCAAACGTACTGGGCATGA-TATTTTTTGAACC
1 TTCTTTTATTTAGGGAATTGGAGAAATTGTACTCAAACGTACT-GGTATGATTTTTTTTTGAACC
* * * * * *
22783057 TAAGTAGTTGAATATCCTATTTAAAATTGATAAATGT
65 TAAATAATCGAGTATCCCATTTAAAATTAATAAATGT
22783094 CATTGATCTT
Statistics
Matches: 187, Mismatches: 18, Indels: 14
0.85 0.08 0.06
Matches are distributed among these distances:
107 39 0.21
108 38 0.20
109 17 0.09
110 92 0.49
111 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (107 bp):
TTCTTTTATTTAGGGAATTGGAGAAATTGTACTCAAACGTACTGGTATGATTTTTTTTTGAACCT
AAATAATCGAGTATCCCATTTAAAATTAATAAATGTTCGATG
Found at i:22783734 original size:14 final size:13
Alignment explanation
Indices: 22783715--22783749 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
22783705 AAGAAAAACA
*
22783715 AGAAGAAAAATAGT
1 AGAAGAAAAA-AGG
22783729 AGAAGAAAAAAGG
1 AGAAGAAAAAAGG
22783742 AGAAGAAA
1 AGAAGAAA
22783750 GGGAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.06
Consensus pattern (13 bp):
AGAAGAAAAAAGG
Found at i:22786737 original size:7 final size:7
Alignment explanation
Indices: 22786719--22786782 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
22786709 TGGTTCGATT
22786719 TTAAACCC
1 TTAAA-CC
22786727 TTAAACC
1 TTAAACC
*
22786734 TTAAACA
1 TTAAACC
*
22786741 TAAAACC
1 TTAAACC
*
22786748 CTAAACC
1 TTAAACC
*
22786755 CTAAACC
1 TTAAACC
*
22786762 TTAAACA
1 TTAAACC
*
22786769 TAAAACC
1 TTAAACC
*
22786776 CTAAACC
1 TTAAACC
22786783 ATATGTGAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
7 40 0.89
8 5 0.11
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.20
Consensus pattern (7 bp):
TTAAACC
Found at i:22786752 original size:14 final size:14
Alignment explanation
Indices: 22786729--22786781 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
22786719 TTAAACCCTT
*
22786729 AAACCTTAAACATA
1 AAACCCTAAACATA
*
22786743 AAACCCTAAACCCT-
1 AAACCCTAAA-CATA
*
22786757 AAACCTTAAACATA
1 AAACCCTAAACATA
22786771 AAACCCTAAAC
1 AAACCCTAAAC
22786782 CATATGTGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.06
14 28 0.88
15 2 0.06
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (14 bp):
AAACCCTAAACATA
Found at i:22786763 original size:28 final size:29
Alignment explanation
Indices: 22786720--22786782 Score: 119
Period size: 28 Copynumber: 2.2 Consensus size: 29
22786710 GGTTCGATTT
22786720 TAAACCCTTAAACCTTAAACATAAAACCC
1 TAAACCCTTAAACCTTAAACATAAAACCC
22786749 TAAACCC-TAAACCTTAAACATAAAACCC
1 TAAACCCTTAAACCTTAAACATAAAACCC
22786777 TAAACC
1 TAAACC
22786783 ATATGTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 27 0.79
29 7 0.21
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (29 bp):
TAAACCCTTAAACCTTAAACATAAAACCC
Found at i:22786767 original size:21 final size:21
Alignment explanation
Indices: 22786719--22786782 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
22786709 TGGTTCGATT
* *
22786719 TTAAACCCTTAAACCTTAAACA
1 TTAAACCC-TAAACCCTAAACC
*
22786741 TAAAACCCTAAACCCTAAACC
1 TTAAACCCTAAACCCTAAACC
*
22786762 TTAAA-CATAAAACCCTAAACC
1 TTAAACCCT-AAACCCTAAACC
22786783 ATATGTGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.75
22 7 0.19
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.20
Consensus pattern (21 bp):
TTAAACCCTAAACCCTAAACC
Found at i:22796513 original size:14 final size:14
Alignment explanation
Indices: 22796496--22796522 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22796486 TAGTTTACCG
22796496 AAATTATTATAATA
1 AAATTATTATAATA
22796510 AAATTATTATAAT
1 AAATTATTATAAT
22796523 TATTTTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTATTATAATA
Found at i:22798816 original size:27 final size:27
Alignment explanation
Indices: 22798778--22798845 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
22798768 ACACATTTTG
* * * *
22798778 GTTCCTTCAGAGTTCATCATTCTTAAT
1 GTTCTTTCAGAGTTCACCAATCATAAT
* * *
22798805 GTTCTTTTAGAGCTCACCAATCATGAT
1 GTTCTTTCAGAGTTCACCAATCATAAT
22798832 GTTCTTTCAGAGTT
1 GTTCTTTCAGAGTT
22798846 TTTCATTTCT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.43
Consensus pattern (27 bp):
GTTCTTTCAGAGTTCACCAATCATAAT
Found at i:22799823 original size:40 final size:40
Alignment explanation
Indices: 22799768--22799847 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
22799758 ATTCTTGTTA
*
22799768 ATATTACGAATAAATAATTCATATAATCGTTTCATACATC
1 ATATTACAAATAAATAATTCATATAATCGTTTCATACATC
* *
22799808 ATATTACAAATAAATAATTCATATGATTGTTTCATACATC
1 ATATTACAAATAAATAATTCATATAATCGTTTCATACATC
22799848 TACTTTCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (40 bp):
ATATTACAAATAAATAATTCATATAATCGTTTCATACATC
Done.