Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 38 of 131
Found at i:12312730 original size:18 final size:18
Alignment explanation
Indices: 12312707--12312748 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
12312697 CTCATAAATA
12312707 TGAAATAATGAAATATAC-
1 TGAAATAATGAAATA-ACT
12312725 TGAAATAATGAAATAACT
1 TGAAATAATGAAATAACT
12312743 TGAAAT
1 TGAAAT
12312749 TCAATAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (18 bp):
TGAAATAATGAAATAACT
Found at i:12312748 original size:10 final size:8
Alignment explanation
Indices: 12312702--12312740 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
12312692 AACAACTCAT
12312702 AAAT-ATG
1 AAATAATG
12312709 AAATAATG
1 AAATAATG
12312717 AAATATACTG
1 AAATA-A-TG
12312727 AAATAATG
1 AAATAATG
12312735 AAATAA
1 AAATAA
12312741 CTTGAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 4 0.14
8 16 0.55
9 2 0.07
10 7 0.24
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (8 bp):
AAATAATG
Found at i:12323226 original size:21 final size:21
Alignment explanation
Indices: 12323200--12323248 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
12323190 TAGGAGTGCA
12323200 GTCGATGTCGTTCATAATCCT
1 GTCGATGTCGTTCATAATCCT
12323221 GTCGATGTCGTTCATAATCCT
1 GTCGATGTCGTTCATAATCCT
*
12323242 TTCGATG
1 GTCGATG
12323249 GCTTCCAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.39
Consensus pattern (21 bp):
GTCGATGTCGTTCATAATCCT
Found at i:12326141 original size:15 final size:16
Alignment explanation
Indices: 12326121--12326150 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12326111 TTAAATCGAT
12326121 AAAAATGA-CTAAATA
1 AAAAATGAGCTAAATA
12326136 AAAAATGAGCTAAAT
1 AAAAATGAGCTAAAT
12326151 TAGAGTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (16 bp):
AAAAATGAGCTAAATA
Found at i:12327926 original size:12 final size:12
Alignment explanation
Indices: 12327909--12327936 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12327899 TTAGGCAGTT
12327909 ACACGGCCTAGC
1 ACACGGCCTAGC
12327921 ACACGGCCTAGC
1 ACACGGCCTAGC
12327933 ACAC
1 ACAC
12327937 AAGCGTGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.43, G:0.21, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:12331433 original size:25 final size:25
Alignment explanation
Indices: 12331405--12331479 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 25
12331395 AGCTGAATAA
12331405 CGGTAAGCTCATATGAGCTGTGAAT
1 CGGTAAGCTCATATGAGCTGTGAAT
* *
12331430 CGGTAAGCTC-TCATGAGCGAGCTAAAAT
1 CGGTAAGCTCAT-ATGAGC-TG-T-GAAT
**
12331458 CGGTAAGCTCATACAAGCTGTG
1 CGGTAAGCTCATATGAGCTGTG
12331480 GTGTCTCCGC
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
24 1 0.03
25 16 0.41
26 2 0.05
27 2 0.05
28 17 0.44
29 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (25 bp):
CGGTAAGCTCATATGAGCTGTGAAT
Found at i:12339143 original size:25 final size:25
Alignment explanation
Indices: 12339115--12339194 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 25
12339105 AAGCTCTTCT
12339115 GAGCTGAATAACGGTAAGCTCATAC
1 GAGCTGAATAACGGTAAGCTCATAC
12339140 GAGCTG--TGAATCGGTAAGCTC-TCAC
1 GAGCTGAAT-AA-CGGTAAGCTCAT-AC
* *
12339165 GAGCTGAA-ATCAGTAAGCTCATAC
1 GAGCTGAATAACGGTAAGCTCATAC
12339189 GAGCTG
1 GAGCTG
12339195 TGGTGTCTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
23 1 0.02
24 20 0.43
25 26 0.55
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (25 bp):
GAGCTGAATAACGGTAAGCTCATAC
Found at i:12339180 original size:24 final size:25
Alignment explanation
Indices: 12339128--12339195 Score: 95
Period size: 24 Copynumber: 2.8 Consensus size: 25
12339118 CTGAATAACG
* *
12339128 GTAAGCTCATACGAGCTGTGAATCG
1 GTAAGCTCATACGAGCTGTAAATCA
12339153 GTAAGCTC-TCACGAGCTG-AAATCA
1 GTAAGCTCAT-ACGAGCTGTAAATCA
12339177 GTAAGCTCATACGAGCTGT
1 GTAAGCTCATACGAGCTGT
12339196 GGTGTCTCCG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
24 21 0.55
25 17 0.45
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (25 bp):
GTAAGCTCATACGAGCTGTAAATCA
Found at i:12342004 original size:27 final size:27
Alignment explanation
Indices: 12341935--12342004 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
12341925 CAATGAGACA
* * *
12341935 TTAAACACGGGGTAGTCTGACAAGATG
1 TTAAACATGAGGTAGTCCGACAAGATG
*
12341962 TTAAAAAT-AGGCTAGTCCGA-AAGGATG
1 TTAAACATGAGG-TAGTCCGACAA-GATG
12341989 TTAAACATGAGGTAGT
1 TTAAACATGAGGTAGT
12342005 TTGATGGGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 4 0.11
27 28 0.80
28 3 0.09
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.24
Consensus pattern (27 bp):
TTAAACATGAGGTAGTCCGACAAGATG
Found at i:12344067 original size:12 final size:12
Alignment explanation
Indices: 12344052--12344076 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12344042 TAACCACGTC
12344052 CACAATTATGGT
1 CACAATTATGGT
12344064 CACAATTATGGT
1 CACAATTATGGT
12344076 C
1 C
12344077 GTGGCTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (12 bp):
CACAATTATGGT
Found at i:12344635 original size:6 final size:6
Alignment explanation
Indices: 12344621--12344661 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
12344611 CTCTACCCCA
*
12344621 CCCTTT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTC
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTC
12344662 CCAACATCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CCCTCT
Found at i:12347425 original size:16 final size:16
Alignment explanation
Indices: 12347404--12347439 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
12347394 GATTTGCTAT
12347404 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12347420 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12347436 TACA
1 TACA
12347440 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:12350713 original size:25 final size:25
Alignment explanation
Indices: 12350646--12350730 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
12350636 AGCTTCCTGA
* *
12350646 ATATGGCTCTTATGAGCTTCCTATT
1 ATATGGCTCATATGAGCTTCCCATT
** * * *
12350671 ATACAGCCCAGATAAGCTTCCCATT
1 ATATGGCTCATATGAGCTTCCCATT
* *
12350696 ACATGGCTCATATGAGCTTCCCGTT
1 ATATGGCTCATATGAGCTTCCCATT
12350721 ATATGGCTCA
1 ATATGGCTCA
12350731 AGTGAGAGCT
Statistics
Matches: 45, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (25 bp):
ATATGGCTCATATGAGCTTCCCATT
Found at i:12351778 original size:34 final size:34
Alignment explanation
Indices: 12351732--12351796 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
12351722 TGTGTCATGG
12351732 CACACGGACGTGTGACTTGG-TCGTGTGACCCCTA
1 CACACGGACGTGTGACTTGGCT-GTGTGACCCCTA
*
12351766 CACACGGGCGTGTGACTTGGCTGTGTGACCC
1 CACACGGACGTGTGACTTGGCTGTGTGACCC
12351797 AAGTTAGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 28 0.97
35 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.32, T:0.23
Consensus pattern (34 bp):
CACACGGACGTGTGACTTGGCTGTGTGACCCCTA
Found at i:12361539 original size:18 final size:17
Alignment explanation
Indices: 12361508--12361541 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12361498 ATAGATTATA
12361508 TTTAAAATTATTAAAAC
1 TTTAAAATTATTAAAAC
*
12361525 TTTAATAATTTTTAAAA
1 TTTAA-AATTATTAAAA
12361542 AATAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAAATTATTAAAAC
Found at i:12362273 original size:25 final size:23
Alignment explanation
Indices: 12362236--12362298 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
12362226 AATCATTATT
12362236 AATA-ATAAATAACAAAAAAATA
1 AATATATAAATAACAAAAAAATA
* * *
12362258 CATTATATAAATTAACTAAAAATTA
1 -AATATATAAA-TAACAAAAAAATA
12362283 AATATATAAAATAACA
1 AATATAT-AAATAACA
12362299 TGTAATACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 3 0.09
24 15 0.47
25 14 0.44
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (23 bp):
AATATATAAATAACAAAAAAATA
Found at i:12362278 original size:24 final size:24
Alignment explanation
Indices: 12362242--12362297 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
12362232 TATTAATAAT
* * *
12362242 AAATAACAAAAAAATACATTATATA
1 AAATAACTAAAAATTA-AATATATA
*
12362267 AATTAACTAAAAATTAAATATATA
1 AAATAACTAAAAATTAAATATATA
12362291 AAATAAC
1 AAATAAC
12362298 ATGTAATACA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (24 bp):
AAATAACTAAAAATTAAATATATA
Found at i:12374419 original size:25 final size:25
Alignment explanation
Indices: 12374377--12374429 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
12374367 TCGGCTTGGG
* *
12374377 CCAATGATGACTCGATCAATCCAGT
1 CCAATGACGACTCAATCAATCCAGT
* *
12374402 CCAATGACGGCTCAATCAGTCCAGT
1 CCAATGACGACTCAATCAATCCAGT
12374427 CCA
1 CCA
12374430 GCCATCGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (25 bp):
CCAATGACGACTCAATCAATCCAGT
Found at i:12389443 original size:44 final size:44
Alignment explanation
Indices: 12389371--12389458 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
12389361 ATTTATGAAC
* * *
12389371 TCACATGTATAAGTCATTAAATCTATGAATCTTCTTCTATGAGT
1 TCACATGTATAAGCCATTAAATCCATGAATCTTATTCTATGAGT
* ** * *
12389415 TCACATGTATGAGCCATTGTATCCATGAATTTTATTTTATGAGT
1 TCACATGTATAAGCCATTAAATCCATGAATCTTATTCTATGAGT
12389459 CCGCATATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.42
Consensus pattern (44 bp):
TCACATGTATAAGCCATTAAATCCATGAATCTTATTCTATGAGT
Found at i:12395256 original size:44 final size:44
Alignment explanation
Indices: 12395193--12395325 Score: 266
Period size: 44 Copynumber: 3.0 Consensus size: 44
12395183 TTCTGATATA
12395193 TTCCAAAGAAGAGTTCAAGCATGCTCAATACTTGAAAATTGTAT
1 TTCCAAAGAAGAGTTCAAGCATGCTCAATACTTGAAAATTGTAT
12395237 TTCCAAAGAAGAGTTCAAGCATGCTCAATACTTGAAAATTGTAT
1 TTCCAAAGAAGAGTTCAAGCATGCTCAATACTTGAAAATTGTAT
12395281 TTCCAAAGAAGAGTTCAAGCATGCTCAATACTTGAAAATTGTAT
1 TTCCAAAGAAGAGTTCAAGCATGCTCAATACTTGAAAATTGTAT
12395325 T
1 T
12395326 ACAGACTTTA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 89 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (44 bp):
TTCCAAAGAAGAGTTCAAGCATGCTCAATACTTGAAAATTGTAT
Found at i:12396083 original size:15 final size:15
Alignment explanation
Indices: 12396063--12396092 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12396053 TGAGTTTAGG
12396063 GGCTAATATGAAACT
1 GGCTAATATGAAACT
12396078 GGCTAATATGAAACT
1 GGCTAATATGAAACT
12396093 ATGTAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
GGCTAATATGAAACT
Found at i:12396798 original size:20 final size:20
Alignment explanation
Indices: 12396773--12396812 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12396763 ACTTGTTTGG
* *
12396773 GATTGCACTTTGGTGCCTCT
1 GATTGCACATTCGTGCCTCT
12396793 GATTGCACATTCGTGCCTCT
1 GATTGCACATTCGTGCCTCT
12396813 TTTTTCACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.28, G:0.23, T:0.38
Consensus pattern (20 bp):
GATTGCACATTCGTGCCTCT
Found at i:12400428 original size:25 final size:25
Alignment explanation
Indices: 12400400--12400452 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
12400390 TGGGCCTAAG
*
12400400 TTTGGTAACTTAGTTCTGATGAAAA
1 TTTGGTAACTAAGTTCTGATGAAAA
12400425 TTTGGTAACTAAGTTCTGATGAAAA
1 TTTGGTAACTAAGTTCTGATGAAAA
12400450 TTT
1 TTT
12400453 CTTGTTACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (25 bp):
TTTGGTAACTAAGTTCTGATGAAAA
Found at i:12401501 original size:7 final size:7
Alignment explanation
Indices: 12401489--12401521 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
12401479 GCCTCTCCAT
12401489 TTTTTCA
1 TTTTTCA
12401496 TTTTTCA
1 TTTTTCA
12401503 -TTTTCA
1 TTTTTCA
12401509 TTTTTCA
1 TTTTTCA
12401516 TCTTTT
1 T-TTTT
12401522 TTTCCCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 14 0.58
8 4 0.17
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:12401508 original size:13 final size:13
Alignment explanation
Indices: 12401490--12401516 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12401480 CCTCTCCATT
12401490 TTTTCATTTTTCA
1 TTTTCATTTTTCA
12401503 TTTTCATTTTTCA
1 TTTTCATTTTTCA
12401516 T
1 T
12401517 CTTTTTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:12402424 original size:14 final size:14
Alignment explanation
Indices: 12402407--12402465 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
12402397 TTTCTTTTTC
12402407 TTTTTTATTTTCAT
1 TTTTTTATTTTCAT
*
12402421 TTTTTTATTTTGA-
1 TTTTTTATTTTCAT
* *
12402434 -TTTTGA--TTGAT
1 TTTTTTATTTTCAT
12402445 TTTTTTCATTTTCAT
1 TTTTTT-ATTTTCAT
12402460 TTTTTT
1 TTTTTT
12402466 GACTTTGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
10 4 0.11
12 9 0.25
13 1 0.03
14 12 0.33
15 10 0.28
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTTTTATTTTCAT
Found at i:12402437 original size:25 final size:25
Alignment explanation
Indices: 12402416--12402462 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
12402406 CTTTTTTATT
*
12402416 TTCATTTTTTT-ATTTTGATTTTGA
1 TTCATTTTTTTCATTTTCATTTTGA
*
12402440 TTGATTTTTTTCATTTTCATTTT
1 TTCATTTTTTTCATTTTCATTTT
12402463 TTTGACTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.72
Consensus pattern (25 bp):
TTCATTTTTTTCATTTTCATTTTGA
Found at i:12407806 original size:21 final size:20
Alignment explanation
Indices: 12407774--12407814 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
12407764 TTATTTTTTT
*
12407774 CAAACAATGAATAGAAAAAA
1 CAAACAAAGAATAGAAAAAA
*
12407794 CAAAGCAAAGAATCGAAAAAA
1 CAAA-CAAAGAATAGAAAAAA
12407815 AGATTGAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.07
Consensus pattern (20 bp):
CAAACAAAGAATAGAAAAAA
Found at i:12418191 original size:20 final size:20
Alignment explanation
Indices: 12418155--12418192 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12418145 TTTATATTCC
*
12418155 AATGATGATATTATGATCCT
1 AATGATGATAATATGATCCT
12418175 AATGAGTGATAAT-TGATC
1 AATGA-TGATAATATGATC
12418193 TTGCTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (20 bp):
AATGATGATAATATGATCCT
Found at i:12431607 original size:16 final size:17
Alignment explanation
Indices: 12431574--12431606 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12431564 ATTAATTAAT
*
12431574 TTTTTAAAATTAAAAAA
1 TTTTAAAAATTAAAAAA
12431591 TTTTAAAAATTAAAAA
1 TTTTAAAAATTAAAAA
12431607 TCATTNNNNN
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTTAAAAATTAAAAAA
Found at i:12438016 original size:26 final size:27
Alignment explanation
Indices: 12437980--12438031 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
12437970 ATTGGGGAAA
*
12437980 CAAAAAGGATT-TACATCAGTTATAAT
1 CAAAAAGGATTCAACATCAGTTATAAT
* *
12438006 CAAAAGGGATTCAACTTCAGTTATAA
1 CAAAAAGGATTCAACATCAGTTATAA
12438032 AGAAAAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (27 bp):
CAAAAAGGATTCAACATCAGTTATAAT
Found at i:12439504 original size:43 final size:42
Alignment explanation
Indices: 12439451--12439568 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 42
12439441 ATATGGGATA
*
12439451 TGGCATCGATATGAGACTTCATGTAAGACCATGTCTAGGACAT
1 TGGCATCGATATGAGA-TTCATGTAAGACCATGGCTAGGACAT
* * **
12439494 TGGCATCGATAT-ATGATTTCGTGTAAGACCATGGCTGGGGTAT
1 TGGCATCGATATGA-GA-TTCATGTAAGACCATGGCTAGGACAT
*
12439537 TGGCATCGATACGAGATTACATGTAAGACCAT
1 TGGCATCGATATGAGATT-CATGTAAGACCAT
12439569 ATCTCAGATA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 3 0.05
43 60 0.94
44 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (42 bp):
TGGCATCGATATGAGATTCATGTAAGACCATGGCTAGGACAT
Found at i:12445328 original size:13 final size:13
Alignment explanation
Indices: 12445310--12445337 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12445300 ATCATTCATA
12445310 GTACATGCATACT
1 GTACATGCATACT
12445323 GTACATGCATACT
1 GTACATGCATACT
12445336 GT
1 GT
12445338 CCCAAAATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (13 bp):
GTACATGCATACT
Found at i:12445522 original size:12 final size:12
Alignment explanation
Indices: 12445505--12445535 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
12445495 GACACATGGT
12445505 TGTGTCCCAGCC
1 TGTGTCCCAGCC
12445517 TGTGTCCCAGCC
1 TGTGTCCCAGCC
*
12445529 CGTGTCC
1 TGTGTCC
12445536 TTACCCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.42, G:0.26, T:0.26
Consensus pattern (12 bp):
TGTGTCCCAGCC
Found at i:12446330 original size:38 final size:38
Alignment explanation
Indices: 12446258--12446416 Score: 228
Period size: 38 Copynumber: 4.2 Consensus size: 38
12446248 ACACCAGCAA
* * *
12446258 TAAGTCTGAATAACACCGGCACCAAGCCTGCTAGGCAC
1 TAAGCCTGAATAACACCGACACTAAGCCTGCTAGGCAC
* * * *
12446296 TAAGCCTGAATAACACTGACACAAAACCTACTAGGCAC
1 TAAGCCTGAATAACACCGACACTAAGCCTGCTAGGCAC
* *
12446334 AAAGCTTGAATAACACCGACACTAAGCCTGCTAGGCAC
1 TAAGCCTGAATAACACCGACACTAAGCCTGCTAGGCAC
*
12446372 TAAGCCTGAATAACACCGGCACTAAGCCTGCTAGGCAC
1 TAAGCCTGAATAACACCGACACTAAGCCTGCTAGGCAC
12446410 TAAGCCT
1 TAAGCCT
12446417 ACTAGGCACA
Statistics
Matches: 106, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 106 1.00
ACGTcount: A:0.35, C:0.30, G:0.18, T:0.16
Consensus pattern (38 bp):
TAAGCCTGAATAACACCGACACTAAGCCTGCTAGGCAC
Found at i:12446374 original size:16 final size:16
Alignment explanation
Indices: 12446353--12446471 Score: 94
Period size: 16 Copynumber: 6.7 Consensus size: 16
12446343 ATAACACCGA
12446353 CACTAAGCCTGCTAGG
1 CACTAAGCCTGCTAGG
*
12446369 CACTAAGCCTGAATAACACCGG
1 CACTAAGCCTG-CT---A--GG
12446391 CACTAAGCCTGCTAGG
1 CACTAAGCCTGCTAGG
*
12446407 CACTAAGCCTACTAGG
1 CACTAAGCCTGCTAGG
* *
12446423 CACAAAGCCTGAATAACAGTG
1 CACTAAGCCTG-CT---AG-G
12446444 ACACTAAGCCTGCTAGG
1 -CACTAAGCCTGCTAGG
12446461 CACTAAGCCTG
1 CACTAAGCCTG
12446472 AATAACACCT
Statistics
Matches: 83, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
16 48 0.58
17 3 0.04
18 3 0.04
20 3 0.04
21 3 0.04
22 23 0.28
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.17
Consensus pattern (16 bp):
CACTAAGCCTGCTAGG
Found at i:12446419 original size:92 final size:92
Alignment explanation
Indices: 12446322--12446508 Score: 329
Period size: 92 Copynumber: 2.0 Consensus size: 92
12446312 TGACACAAAA
*
12446322 CCTACTAGGCACAAAGCTTGAATAACACCGACACTAAGCCTGCTAGGCACTAAGCCTGAATAACA
1 CCTACTAGGCACAAAGCCTGAATAACACCGACACTAAGCCTGCTAGGCACTAAGCCTGAATAACA
12446387 CCGGCACTAAGCCTGCTAGGCACTAAG
66 CCGGCACTAAGCCTGCTAGGCACTAAG
**
12446414 CCTACTAGGCACAAAGCCTGAATAACAGTGACACTAAGCCTGCTAGGCACTAAGCCTGAATAACA
1 CCTACTAGGCACAAAGCCTGAATAACACCGACACTAAGCCTGCTAGGCACTAAGCCTGAATAACA
* *
12446479 CCTGCACTAAGCCTGCTAGGCAGTAAG
66 CCGGCACTAAGCCTGCTAGGCACTAAG
12446506 CCT
1 CCT
12446509 GAATAACACC
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (92 bp):
CCTACTAGGCACAAAGCCTGAATAACACCGACACTAAGCCTGCTAGGCACTAAGCCTGAATAACA
CCGGCACTAAGCCTGCTAGGCACTAAG
Found at i:12446435 original size:54 final size:54
Alignment explanation
Indices: 12446353--12446470 Score: 191
Period size: 54 Copynumber: 2.2 Consensus size: 54
12446343 ATAACACCGA
* * *
12446353 CACTAAGCCTGCTAGGCACTAAGCCTGAATAACACCGGCACTAAGCCTGCTAGG
1 CACTAAGCCTACTAGGCACAAAGCCTGAATAACACCGACACTAAGCCTGCTAGG
**
12446407 CACTAAGCCTACTAGGCACAAAGCCTGAATAACAGTGACACTAAGCCTGCTAGG
1 CACTAAGCCTACTAGGCACAAAGCCTGAATAACACCGACACTAAGCCTGCTAGG
12446461 CACTAAGCCT
1 CACTAAGCCT
12446471 GAATAACACC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.32, C:0.31, G:0.20, T:0.17
Consensus pattern (54 bp):
CACTAAGCCTACTAGGCACAAAGCCTGAATAACACCGACACTAAGCCTGCTAGG
Found at i:12446449 original size:38 final size:37
Alignment explanation
Indices: 12446406--12446552 Score: 213
Period size: 38 Copynumber: 3.9 Consensus size: 37
12446396 AGCCTGCTAG
* *
12446406 GCACTAAGCCTACTAGGCACAAAGCCTGAATAACAGT
1 GCACTAAGCCTGCTAGGCACAAAGCCTGAATAACACT
*
12446443 GACACTAAGCCTGCTAGGCACTAAGCCTGAATAACACCT
1 G-CACTAAGCCTGCTAGGCACAAAGCCTGAATAACA-CT
** *
12446482 GCACTAAGCCTGCTAGGCAGTAAGCCTGAATAACACCG
1 GCACTAAGCCTGCTAGGCACAAAGCCTGAATAACA-CT
12446520 GCACTAAGCCTGCTAGGCACAAAGCCTGAATAA
1 GCACTAAGCCTGCTAGGCACAAAGCCTGAATAA
12446553 TAGTACGATT
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
37 1 0.01
38 98 0.97
39 2 0.02
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.16
Consensus pattern (37 bp):
GCACTAAGCCTGCTAGGCACAAAGCCTGAATAACACT
Found at i:12446455 original size:22 final size:21
Alignment explanation
Indices: 12446422--12446493 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 21
12446412 AGCCTACTAG
*
12446422 GCACAAAGCCTGAATAACAGT
1 GCACTAAGCCTGAATAACAGT
*
12446443 GACACTAAGCCTG-CT---AG-
1 G-CACTAAGCCTGAATAACAGT
*
12446460 GCACTAAGCCTGAATAACACCT
1 GCACTAAGCCTGAATAACA-GT
12446482 GCACTAAGCCTG
1 GCACTAAGCCTG
12446494 CTAGGCAGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
16 11 0.28
17 2 0.05
18 2 0.05
20 1 0.03
21 2 0.05
22 22 0.55
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (21 bp):
GCACTAAGCCTGAATAACAGT
Found at i:12446508 original size:130 final size:130
Alignment explanation
Indices: 12446275--12446546 Score: 429
Period size: 130 Copynumber: 2.1 Consensus size: 130
12446265 GAATAACACC
* * * *
12446275 GGCACCAAGCCTGCTAGGCACTAAGCCTGAATAACACTGACACAAAACCTACTAGGCACAAAGCT
1 GGCACAAAGCCTACTAGGCACAAAGCCTGAATAACACTGACACAAAACCTACTAGGCACAAAGCC
12446340 TGAATAACACCGACACTAAGCCTGCTAGGCACTAAGCCTGAATAACACCGGCACTAAGCCTGCTA
66 TGAATAACACCGACACTAAGCCTGCTAGGCACTAAGCCTGAATAACACCGGCACTAAGCCTGCTA
* * * * * *
12446405 GGCACTAAGCCTACTAGGCACAAAGCCTGAATAACAGTGACACTAAGCCTGCTAGGCACTAAGCC
1 GGCACAAAGCCTACTAGGCACAAAGCCTGAATAACACTGACACAAAACCTACTAGGCACAAAGCC
*
12446470 TGAATAACACCTG-CACTAAGCCTGCTAGGCAGTAAGCCTGAATAACACCGGCACTAAGCCTGCT
66 TGAATAACACC-GACACTAAGCCTGCTAGGCACTAAGCCTGAATAACACCGGCACTAAGCCTGCT
12446534 A
130 A
12446535 GGCACAAAGCCT
1 GGCACAAAGCCT
12446547 GAATAATAGT
Statistics
Matches: 130, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
130 129 0.99
131 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.20, T:0.16
Consensus pattern (130 bp):
GGCACAAAGCCTACTAGGCACAAAGCCTGAATAACACTGACACAAAACCTACTAGGCACAAAGCC
TGAATAACACCGACACTAAGCCTGCTAGGCACTAAGCCTGAATAACACCGGCACTAAGCCTGCTA
Found at i:12446527 original size:22 final size:22
Alignment explanation
Indices: 12446459--12446531 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 22
12446449 AAGCCTGCTA
12446459 GGCACTAAGCCTGAATAACACC
1 GGCACTAAGCCTGAATAACACC
* *
12446481 TGCACTAAGCCTG-CT---A--
1 GGCACTAAGCCTGAATAACACC
*
12446497 GGCAGTAAGCCTGAATAACACC
1 GGCACTAAGCCTGAATAACACC
12446519 GGCACTAAGCCTG
1 GGCACTAAGCCTG
12446532 CTAGGCACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
16 11 0.28
17 1 0.03
18 1 0.03
20 1 0.03
21 1 0.03
22 24 0.62
ACGTcount: A:0.32, C:0.30, G:0.22, T:0.16
Consensus pattern (22 bp):
GGCACTAAGCCTGAATAACACC
Found at i:12457145 original size:20 final size:20
Alignment explanation
Indices: 12457109--12457146 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12457099 TTTATGATTT
*
12457109 TTTTATTTGTTTTATTTTAA
1 TTTTATTTGTTTGATTTTAA
12457129 TTTTATTT-TGTTGATTTT
1 TTTTATTTGT-TTGATTTT
12457147 GGACTGTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (20 bp):
TTTTATTTGTTTGATTTTAA
Found at i:12466567 original size:8 final size:9
Alignment explanation
Indices: 12466551--12466575 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12466541 TTTAAAAATA
12466551 TATTTTTTT
1 TATTTTTTT
12466560 TATTTTTTT
1 TATTTTTTT
12466569 TATTTTT
1 TATTTTT
12466576 AAAATATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:12472752 original size:16 final size:16
Alignment explanation
Indices: 12472731--12472762 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12472721 CACTTATTTA
12472731 AAAATATTCTATTTTT
1 AAAATATTCTATTTTT
*
12472747 AAAATATTTTATTTTT
1 AAAATATTCTATTTTT
12472763 GCTAATGTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
AAAATATTCTATTTTT
Found at i:12476591 original size:20 final size:20
Alignment explanation
Indices: 12476566--12476611 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
12476556 AATTAAACTG
12476566 AGCTCAAACGAGCTGAATTA
1 AGCTCAAACGAGCTGAATTA
***
12476586 AGCTCATGTGAGCTGAATTA
1 AGCTCAAACGAGCTGAATTA
*
12476606 AACTCA
1 AGCTCA
12476612 TGTGAGTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (20 bp):
AGCTCAAACGAGCTGAATTA
Found at i:12476612 original size:20 final size:20
Alignment explanation
Indices: 12476575--12476622 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
12476565 GAGCTCAAAC
*
12476575 GAGCTGAATTAAGCTCATGT
1 GAGCTGAATTAAACTCATGT
12476595 GAGCTGAATTAAACTCATGT
1 GAGCTGAATTAAACTCATGT
*
12476615 GAGTTGAA
1 GAGCTGAA
12476623 CCGAGCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (20 bp):
GAGCTGAATTAAACTCATGT
Found at i:12478411 original size:17 final size:17
Alignment explanation
Indices: 12478391--12478424 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12478381 TTTCAATTTC
*
12478391 TTTTTCAATCTCTTTTT
1 TTTTTCAATCACTTTTT
*
12478408 TTTTTCACTCACTTTTT
1 TTTTTCAATCACTTTTT
12478425 CAATTTCCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTCAATCACTTTTT
Found at i:12478440 original size:18 final size:18
Alignment explanation
Indices: 12478419--12478476 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
12478409 TTTTCACTCA
*
12478419 CTTTTTCAATTTCCTTTT
1 CTTTTTCAATTTCATTTT
** *
12478437 CTTTTGAAATTTCTTTTT
1 CTTTTTCAATTTCATTTT
*
12478455 CTTTTTCAATGTCATTTT
1 CTTTTTCAATTTCATTTT
12478473 CTTT
1 CTTT
12478477 CATTTCTCCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.14, C:0.17, G:0.03, T:0.66
Consensus pattern (18 bp):
CTTTTTCAATTTCATTTT
Found at i:12479631 original size:10 final size:10
Alignment explanation
Indices: 12479616--12479662 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
12479606 AATAAACTTT
12479616 TTTTTTTGAA
1 TTTTTTTGAA
12479626 TTTTTTTGAA
1 TTTTTTTGAA
12479636 TTTTTTTG-A
1 TTTTTTTGAA
*
12479645 TTTTTTTCAA
1 TTTTTTTGAA
12479655 TTTATTTT
1 TTT-TTTT
12479663 CACAATGGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
9 8 0.24
10 22 0.65
11 4 0.12
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.74
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:12479641 original size:19 final size:20
Alignment explanation
Indices: 12479616--12479662 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
12479606 AATAAACTTT
*
12479616 TTTTTTTGAATTTTTTTGAA
1 TTTTTTTGAATTTTTTTCAA
12479636 TTTTTTTG-ATTTTTTTCAA
1 TTTTTTTGAATTTTTTTCAA
12479655 TTTATTTT
1 TTT-TTTT
12479663 CACAATGGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.74
Consensus pattern (20 bp):
TTTTTTTGAATTTTTTTCAA
Found at i:12480685 original size:28 final size:29
Alignment explanation
Indices: 12480627--12480686 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
12480617 GCTAATGGCC
*
12480627 ATGTCCATATTCAGCCACTTGGGATGCCA
1 ATGTCCATATTCAGCCACTTGGGACGCCA
*
12480656 ATGT-CATATTCAGCCACTTGGGACGGCA
1 ATGTCCATATTCAGCCACTTGGGACGCCA
12480684 ATG
1 ATG
12480687 GGTAGCTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (29 bp):
ATGTCCATATTCAGCCACTTGGGACGCCA
Found at i:12493713 original size:25 final size:25
Alignment explanation
Indices: 12493684--12493733 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
12493674 ATTGTTAAAC
12493684 ACAACAAAGAATGAATTGAGTTAAG
1 ACAACAAAGAATGAATTGAGTTAAG
12493709 ACAACAAAGAATGAATTGAGTTAAG
1 ACAACAAAGAATGAATTGAGTTAAG
12493734 TGTTGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.20, T:0.20
Consensus pattern (25 bp):
ACAACAAAGAATGAATTGAGTTAAG
Found at i:12496219 original size:19 final size:19
Alignment explanation
Indices: 12496176--12496220 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
12496166 TCATGCAATT
12496176 GTAT-GAATGAATGTTATG
1 GTATAGAATGAATGTTATG
* *
12496194 G-ATAGAATGCATGTTCTG
1 GTATAGAATGAATGTTATG
12496212 GTATAGAAT
1 GTATAGAAT
12496221 TTGAGAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 14 0.61
19 7 0.30
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (19 bp):
GTATAGAATGAATGTTATG
Found at i:12498051 original size:31 final size:31
Alignment explanation
Indices: 12498013--12498072 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
12498003 AAGTTCTTAC
12498013 GAACTTATATTGG-TGTGTGTTTTGTTATAAT
1 GAACTTATA-TGGATGTGTGTTTTGTTATAAT
12498044 GAACTTATATGGATGTGTGTTTTGTTATA
1 GAACTTATATGGATGTGTGTTTTGTTATA
12498073 GGCAAATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.50
Consensus pattern (31 bp):
GAACTTATATGGATGTGTGTTTTGTTATAAT
Found at i:12502981 original size:23 final size:22
Alignment explanation
Indices: 12502931--12502981 Score: 52
Period size: 23 Copynumber: 2.2 Consensus size: 22
12502921 AAAATTTTAA
12502931 AAAATATATAAAAATTAAAAAT
1 AAAATATATAAAAATTAAAAAT
12502953 ATAAATA-ATAAATAA-TAAAGAACT
1 A-AAATATATAAA-AATTAAA-AA-T
12502977 AAAAT
1 AAAAT
12502982 TTTATGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
22 10 0.40
23 13 0.52
24 2 0.08
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATATATAAAAATTAAAAAT
Found at i:12503163 original size:25 final size:26
Alignment explanation
Indices: 12503130--12503189 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
12503120 ATTTTTTTAC
* *
12503130 TAATT-TATATATTTTATTTTTAAAA
1 TAATTATATATATTTTAATTTCAAAA
12503155 -AATTATATATATTTTAATTTCAAAA
1 TAATTATATATATTTTAATTTCAAAA
*
12503180 TAATAATATA
1 TAATTATATA
12503190 AATAACTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.13
25 18 0.60
26 8 0.27
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TAATTATATATATTTTAATTTCAAAA
Found at i:12505298 original size:7 final size:7
Alignment explanation
Indices: 12505286--12505314 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
12505276 TTAAATTATG
12505286 ATCAATA
1 ATCAATA
12505293 ATCAATA
1 ATCAATA
12505300 ATCAATA
1 ATCAATA
12505307 ATCAATA
1 ATCAATA
12505314 A
1 A
12505315 ATGGCTCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (7 bp):
ATCAATA
Found at i:12508891 original size:12 final size:12
Alignment explanation
Indices: 12508857--12508897 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
12508847 TGCTACAACT
12508857 CCTCCAACTCTAG
1 CCTCCAACTCT-G
12508870 CC-CCAACTCTG
1 CCTCCAACTCTG
*
12508881 CCTCCACCTCTG
1 CCTCCAACTCTG
12508893 CCTCC
1 CCTCC
12508898 TATTCAGCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 3 0.12
12 21 0.81
13 2 0.08
ACGTcount: A:0.15, C:0.56, G:0.07, T:0.22
Consensus pattern (12 bp):
CCTCCAACTCTG
Found at i:12518774 original size:14 final size:14
Alignment explanation
Indices: 12518757--12518783 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12518747 GTTTTCAATT
12518757 TTAACTTTTATTCA
1 TTAACTTTTATTCA
12518771 TTAACTTTTATTC
1 TTAACTTTTATTC
12518784 TTTGTGTTTG
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:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAACTTTTATTCA
Found at i:12524431 original size:14 final size:14
Alignment explanation
Indices: 12524409--12524446 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
12524399 TATAATACAT
*
12524409 GAAAAGTTATCATA
1 GAAAGGTTATCATA
12524423 GAAAGGTTATCATA
1 GAAAGGTTATCATA
12524437 GAAAGGTTAT
1 GAAAGGTTAT
12524447 GTCGAACCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (14 bp):
GAAAGGTTATCATA
Found at i:12526573 original size:33 final size:31
Alignment explanation
Indices: 12526524--12526592 Score: 120
Period size: 33 Copynumber: 2.2 Consensus size: 31
12526514 CTGAATAAGA
12526524 TTGCAAAGAAGCCCTTGAAGAACTTTCAACC
1 TTGCAAAGAAGCCCTTGAAGAACTTTCAACC
12526555 TTGCGAAAGGAAGCCCTTGAAGAACTTTCAACC
1 TTGC-AAA-GAAGCCCTTGAAGAACTTTCAACC
12526588 TTGCA
1 TTGCA
12526593 TTCAAACCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
31 4 0.11
32 4 0.11
33 28 0.78
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (31 bp):
TTGCAAAGAAGCCCTTGAAGAACTTTCAACC
Found at i:12526729 original size:38 final size:38
Alignment explanation
Indices: 12526676--12526750 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
12526666 TTTTCCATAT
* *
12526676 GTGTGGCCAGCCAAGGGGGGTCTCTTTGGCTGATGGAC
1 GTGTGGCCAGACAAGGGGGGTCTCTTTGGATGATGGAC
*
12526714 GTGTGGCCGGACAAGGGGGGTCTCTTTGGATGATGGA
1 GTGTGGCCAGACAAGGGGGGTCTCTTTGGATGATGGA
12526751 ATTTGCTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.15, C:0.17, G:0.44, T:0.24
Consensus pattern (38 bp):
GTGTGGCCAGACAAGGGGGGTCTCTTTGGATGATGGAC
Found at i:12526819 original size:38 final size:38
Alignment explanation
Indices: 12526777--12526851 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
12526767 AGCCACAATC
*
12526777 AGCTATAAAAGCCACCCCTTGCTGATCATTCCACTCAA
1 AGCTATAAAAGCCACCCCTTGCTGATCATTCAACTCAA
* *
12526815 AGCTATAAAATCCACCCCTTGCTGATTATTCAACTCA
1 AGCTATAAAAGCCACCCCTTGCTGATCATTCAACTCA
12526852 TCCCTCACAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.27
Consensus pattern (38 bp):
AGCTATAAAAGCCACCCCTTGCTGATCATTCAACTCAA
Found at i:12528706 original size:21 final size:22
Alignment explanation
Indices: 12528665--12528706 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12528655 GTCCTTTTTT
* *
12528665 ATTTTCTTTATTTTCTTTATTA
1 ATTTTATTAATTTTCTTTATTA
12528687 ATTTTATTAATTTT-TTTATT
1 ATTTTATTAATTTTCTTTATT
12528707 TTTCATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (22 bp):
ATTTTATTAATTTTCTTTATTA
Found at i:12528846 original size:23 final size:22
Alignment explanation
Indices: 12528774--12528863 Score: 58
Period size: 23 Copynumber: 3.9 Consensus size: 22
12528764 TGTAGTATAA
*
12528774 TATAATTAT-TTTTATTTTATT
1 TATAATTATATTTTATTTTCTT
* * * * *
12528795 TTTATTTCTATGTAATTTT-TT
1 TATAATTATATTTTATTTTCTT
12528816 TATCTATATGTATATATTTATTTTCTT
1 TA--TA-AT-TATAT-TTTATTTTCTT
12528843 TATAAATTATATTTTATTTTC
1 TAT-AATTATATTTTATTTTC
12528864 ACAAATGCAT
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
21 9 0.18
22 7 0.14
23 11 0.22
24 6 0.12
25 7 0.14
26 7 0.14
27 4 0.08
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATAATTATATTTTATTTTCTT
Found at i:12547129 original size:18 final size:17
Alignment explanation
Indices: 12547093--12547135 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
12547083 GTGTGAATCC
*
12547093 AAACTAAAATATTAATT
1 AAACTAAAAAATTAATT
*
12547110 AAACTAAGAAAATTACTT
1 AAACTAA-AAAATTAATT
*
12547128 AACCTAAA
1 AAACTAAA
12547136 TTAACCTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (17 bp):
AAACTAAAAAATTAATT
Found at i:12551865 original size:23 final size:23
Alignment explanation
Indices: 12551767--12551886 Score: 100
Period size: 23 Copynumber: 5.2 Consensus size: 23
12551757 TAAACATGTA
*
12551767 ATATTCTATTAAGCCTTTGTGGC
1 ATATTCTGTTAAGCCTTTGTGGC
* * *
12551790 ACATTCT-ATACAACCTTTGTGGC
1 ATATTCTGTTA-AGCCTTTGTGGC
*
12551813 ATAAAT-TGTTAAGCCTTTGTGGC
1 AT-ATTCTGTTAAGCCTTTGTGGC
* *
12551836 ATGTTCTGTTAAGCCTTTGTGGT
1 ATATTCTGTTAAGCCTTTGTGGC
* * * **
12551859 GTATTCTGTAAAGGCTTTGAAGC
1 ATATTCTGTTAAGCCTTTGTGGC
12551882 ATATT
1 ATATT
12551887 TTGTAATGCC
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
22 3 0.04
23 68 0.91
24 4 0.05
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (23 bp):
ATATTCTGTTAAGCCTTTGTGGC
Found at i:12554718 original size:25 final size:26
Alignment explanation
Indices: 12554680--12554769 Score: 82
Period size: 25 Copynumber: 3.6 Consensus size: 26
12554670 GGCTATCGAT
** *
12554680 TTCAGCTCTTATGAGGTTACCGA-TA
1 TTCAGCTCGCATGAGCTTACCGATTA
12554705 CTT-AGCTCGCATGAGCTTACC-ATTA
1 -TTCAGCTCGCATGAGCTTACCGATTA
* *
12554730 TTCAGCTCGGATGAGCTTACCGTTTA
1 TTCAGCTCGCATGAGCTTACCGATTA
*
12554756 -T-AGCTCGTATGAGC
1 TTCAGCTCGCATGAGC
12554770 ATACATGTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
24 15 0.27
25 35 0.64
26 5 0.09
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.33
Consensus pattern (26 bp):
TTCAGCTCGCATGAGCTTACCGATTA
Found at i:12559712 original size:29 final size:29
Alignment explanation
Indices: 12559663--12559719 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
12559653 TTATGGAATA
* *
12559663 GGTGAAGAACTTGTTCGTTGAGAGTTCGC
1 GGTGAAGAACTTGTTCATTGAGAATTCGC
12559692 GGTGAAGAACTTGTGT-ATTGAGAATTCG
1 GGTGAAGAACTTGT-TCATTGAGAATTCG
12559720 TGTCAAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.25, C:0.11, G:0.33, T:0.32
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCATTGAGAATTCGC
Found at i:12561768 original size:5 final size:5
Alignment explanation
Indices: 12561745--12561783 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
12561735 AATTAAAATA
12561745 AATTT AAATTT AA--T AATTT AATTT AATTT AATTT AATTT
1 AATTT -AATTT AATTT AATTT AATTT AATTT AATTT AATTT
12561784 TTAAACCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.10
5 23 0.74
6 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:12565610 original size:6 final size:7
Alignment explanation
Indices: 12565594--12565622 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
12565584 TAAAAATTCC
12565594 AAAAAGA
1 AAAAAGA
12565601 AAAAAGA
1 AAAAAGA
12565608 AAAAAG-
1 AAAAAGA
12565614 AAAAAGA
1 AAAAAGA
12565621 AA
1 AA
12565623 GTTGCAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:12565617 original size:13 final size:14
Alignment explanation
Indices: 12565594--12565622 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12565584 TAAAAATTCC
12565594 AAAAAGAAAAAAGA
1 AAAAAGAAAAAAGA
12565608 AAAAAG-AAAAAGA
1 AAAAAGAAAAAAGA
12565621 AA
1 AA
12565623 GTTGCAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAGA
Found at i:12583920 original size:17 final size:16
Alignment explanation
Indices: 12583890--12583930 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
12583880 ACACCATTCA
12583890 TCATTCACTCATTTCT
1 TCATTCACTCATTTCT
*
12583906 TCTTTCACTTCATTTCT
1 TCATTCAC-TCATTTCT
12583923 TCATTCAC
1 TCATTCAC
12583931 CTTTGCCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (16 bp):
TCATTCACTCATTTCT
Found at i:12584438 original size:30 final size:30
Alignment explanation
Indices: 12584402--12584461 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
12584392 TCTAATTGAT
12584402 GCACATTTAATCTTCTAAGGTAAATGAATG
1 GCACATTTAATCTTCTAAGGTAAATGAATG
*
12584432 GCACATTTAATCTTCTAAGTTAAATGAATG
1 GCACATTTAATCTTCTAAGGTAAATGAATG
12584462 TTAAATTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (30 bp):
GCACATTTAATCTTCTAAGGTAAATGAATG
Found at i:12587299 original size:13 final size:13
Alignment explanation
Indices: 12587283--12587316 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12587273 ATGTGTAAAC
12587283 GAAATGGTAAGAT
1 GAAATGGTAAGAT
* *
12587296 GAAATGTTTAGAT
1 GAAATGGTAAGAT
12587309 GAAATGGT
1 GAAATGGT
12587317 TATACGAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29
Consensus pattern (13 bp):
GAAATGGTAAGAT
Found at i:12591602 original size:35 final size:36
Alignment explanation
Indices: 12591531--12591607 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 36
12591521 TGTGAAAGAG
* * *
12591531 AATATGTTGGTATGATATTCATGCCATGTGAGAGTA
1 AATATGTGGGTATGATATTCATACCATGGGAGAGTA
* *
12591567 AATATGTGGGTATG-TTTTCATACCATGGGATAGTA
1 AATATGTGGGTATGATATTCATACCATGGGAGAGTA
12591602 AATATG
1 AATATG
12591608 CAATGAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 23 0.64
36 13 0.36
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (36 bp):
AATATGTGGGTATGATATTCATACCATGGGAGAGTA
Found at i:12592163 original size:27 final size:27
Alignment explanation
Indices: 12592125--12592195 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
12592115 TATGAATATG
* * *
12592125 TGACATGTTTGCTTAGTTGATGCATAA
1 TGACTTGTTTGCTTAGTCGATACATAA
12592152 TGACTTGTTTGCTTAGTCGATACATAA
1 TGACTTGTTTGCTTAGTCGATACATAA
*
12592179 TGACTTGTTTGCATAGT
1 TGACTTGTTTGCTTAGT
12592196 GGTTGTTCTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (27 bp):
TGACTTGTTTGCTTAGTCGATACATAA
Found at i:12595811 original size:38 final size:38
Alignment explanation
Indices: 12595750--12595891 Score: 144
Period size: 38 Copynumber: 3.7 Consensus size: 38
12595740 TTACACCAGC
* *
12595750 ACGAAGCCTACTAGGCATC-AAGCCAGATGAACA-TCGGT
1 ACGAAGCCTGCTAGGC-TCAAAGCCCGATGAACACT-GGT
** * *
12595788 ACGAAGCCTGCTAGGCTCAAAGCCCGATTGGTCACTAGC
1 ACGAAGCCTGCTAGGCTCAAAGCCCGA-TGAACACTGGT
* * *
12595827 ATGAAGCTTGCTAGGCTCAAAGCCCGATAAACACTGGT
1 ACGAAGCCTGCTAGGCTCAAAGCCCGATGAACACTGGT
* *
12595865 ACGAGGCCTGCTAGGCTCAAGGCCCGA
1 ACGAAGCCTGCTAGGCTCAAAGCCCGA
12595892 CACAATACAC
Statistics
Matches: 84, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
37 2 0.02
38 51 0.61
39 30 0.36
40 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (38 bp):
ACGAAGCCTGCTAGGCTCAAAGCCCGATGAACACTGGT
Found at i:12595927 original size:41 final size:41
Alignment explanation
Indices: 12595873--12595950 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
12595863 GTACGAGGCC
*
12595873 TGCTAGGCTCAAGGCCCGACACAATACACCGACATAAAGCT
1 TGCTAGGCTCAAGGCCCAACACAATACACCGACATAAAGCT
* *
12595914 TGCTAGG-TCCAAGGCCCAATACAATACACCGCCATAA
1 TGCTAGGCT-CAAGGCCCAACACAATACACCGACATAA
12595951 CAACTCAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.03
41 32 0.97
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (41 bp):
TGCTAGGCTCAAGGCCCAACACAATACACCGACATAAAGCT
Found at i:12600698 original size:15 final size:15
Alignment explanation
Indices: 12600669--12600709 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
12600659 TATTCAATTA
12600669 TTTCATTTA-TTAAT
1 TTTCATTTATTTAAT
12600683 TTTCATTTATTTAAT
1 TTTCATTTATTTAAT
* *
12600698 TTGCTTTTATTT
1 TTTCATTTATTT
12600710 CCTTGCTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTCATTTATTTAAT
Found at i:12606370 original size:30 final size:30
Alignment explanation
Indices: 12606329--12606583 Score: 164
Period size: 30 Copynumber: 8.5 Consensus size: 30
12606319 AACCAAAGTT
* * *
12606329 ATCCC-TTTCATAGTTCGATGGGCGAAGCT
1 ATCCCTTTTCATAGTTCGATAGTCGAAGCC
* * *
12606358 ATCCCTTTTCATAATTTGATAGTCGTCA-CC
1 ATCCCTTTTCATAGTTCGATAGTCG-AAGCC
* * *
12606388 ATCCCTTTTCATAGTTCAATGGTCGTCA-CC
1 ATCCCTTTTCATAGTTCGATAGTCG-AAGCC
* * *
12606418 ATCCCTTTTCATAATTTGATAG-CTGAAGCT
1 ATCCCTTTTCATAGTTCGATAGTC-GAAGCC
*
12606448 ATCCCTTTTCATAGATT-GATAGCCGAAGCC
1 ATCCCTTTTCATAG-TTCGATAGTCGAAGCC
* * **
12606478 ATCCCTTTTCATAAATT-GATAGTTGAAGTT
1 ATCCCTTTTCAT-AGTTCGATAGTCGAAGCC
* * * * *
12606508 ATCTCTTTCCATAGTTCAATAGCCGAAACC
1 ATCCCTTTTCATAGTTCGATAGTCGAAGCC
* * * *
12606538 ATCCCTTTTCATAGTCCGATGGTAGTCA-CC
1 ATCCCTTTTCATAGTTCGATAGTCG-AAGCC
*
12606568 ATCCCTTTTAATAGTT
1 ATCCCTTTTCATAGTT
12606584 AGCTGGTCAT
Statistics
Matches: 175, Mismatches: 42, Indels: 17
0.75 0.18 0.07
Matches are distributed among these distances:
29 10 0.06
30 159 0.91
31 6 0.03
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTCGATAGTCGAAGCC
Found at i:12606422 original size:60 final size:60
Alignment explanation
Indices: 12606358--12606550 Score: 189
Period size: 60 Copynumber: 3.2 Consensus size: 60
12606348 GGGCGAAGCT
* * * *
12606358 ATCCCTTTTCATAATTTGATAGTCGTCA-CCATCCCTTTTCATAGTTCAATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATAGTCGTAAGCCATCCCTTTTCATAGTT-AATAGCCGTAACC
* *
12606418 ATCCCTTTTCATAATTTGATAG-C-TGAAGCTATCCCTTTTCATAGATTGATAGCCG-AAGCC
1 ATCCCTTTTCATAATTTGATAGTCGT-AAGCCATCCCTTTTCATAG-TTAATAGCCGTAA-CC
* * ** * * *
12606478 ATCCCTTTTCATAAATTGATAGTTG-AAGTTATCTCTTTCCATAGTTCAATAGCCGAAACC
1 ATCCCTTTTCATAATTTGATAGTCGTAAGCCATCCCTTTTCATAGTT-AATAGCCGTAACC
12606538 ATCCCTTTTCATA
1 ATCCCTTTTCATA
12606551 GTCCGATGGT
Statistics
Matches: 113, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
58 1 0.01
59 5 0.04
60 103 0.91
61 4 0.04
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (60 bp):
ATCCCTTTTCATAATTTGATAGTCGTAAGCCATCCCTTTTCATAGTTAATAGCCGTAACC
Found at i:12606597 original size:30 final size:30
Alignment explanation
Indices: 12606535--12606604 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
12606525 AATAGCCGAA
* *
12606535 ACCATCCCTTTTCATAGTCCGATGGTAGTC
1 ACCATCCCTTTTAATAGTCAGATGGTAGTC
* *
12606565 ACCATCCCTTTTAATAGTTAGCTGGTCA-TC
1 ACCATCCCTTTTAATAGTCAGATGGT-AGTC
12606595 ACC-TCCCTTT
1 ACCATCCCTTT
12606605 ACATAATCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.20
30 27 0.77
31 1 0.03
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.36
Consensus pattern (30 bp):
ACCATCCCTTTTAATAGTCAGATGGTAGTC
Found at i:12609946 original size:27 final size:27
Alignment explanation
Indices: 12609916--12610046 Score: 136
Period size: 27 Copynumber: 4.9 Consensus size: 27
12609906 AGTTAGTCCA
12609916 TTCAGAGTTCGCCACAAAGGCTATTCT
1 TTCAGAGTTCGCCACAAAGGCTATTCT
* * *
12609943 TTCAGAGTTTGCCATAAAGGCTATTAT
1 TTCAGAGTTCGCCACAAAGGCTATTCT
* * *** *
12609970 TTCAAAGCTCGCCACAAATAATATTTT
1 TTCAGAGTTCGCCACAAAGGCTATTCT
* * *
12609997 TTCAAAGTTCACCACAAAGACTATTCT
1 TTCAGAGTTCGCCACAAAGGCTATTCT
* *
12610024 TTCAGAGTTCGTCAAAAAGGCTA
1 TTCAGAGTTCGCCACAAAGGCTA
12610047 ACAAAATGCC
Statistics
Matches: 83, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (27 bp):
TTCAGAGTTCGCCACAAAGGCTATTCT
Found at i:12612837 original size:26 final size:26
Alignment explanation
Indices: 12612808--12612877 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
12612798 CACCAATATT
*
12612808 GCAGCAAAGCTGCCAGTAATAGTATC
1 GCAGCAAAGCTGCCAGTAACAGTATC
12612834 GCAGCAAAGCTGCCAGTAACAGTATC
1 GCAGCAAAGCTGCCAGTAACAGTATC
* * *
12612860 ACAGCAAAGTTACCAGTA
1 GCAGCAAAGCTGCCAGTA
12612878 CAATATATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.17
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAACAGTATC
Found at i:12619365 original size:17 final size:17
Alignment explanation
Indices: 12619343--12619377 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12619333 TGGTACTTAG
12619343 TCCTTGTACTATAGCAT
1 TCCTTGTACTATAGCAT
12619360 TCCTTGTACTATAGCAT
1 TCCTTGTACTATAGCAT
12619377 T
1 T
12619378 TTAGCTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (17 bp):
TCCTTGTACTATAGCAT
Found at i:12623339 original size:28 final size:28
Alignment explanation
Indices: 12623307--12623364 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
12623297 TTAAGAATTG
12623307 AGCAATGTCTTAAATGGATATTAAACCA
1 AGCAATGTCTTAAATGGATATTAAACCA
12623335 AGCAATGTCTTAAATGGATATTAAACCA
1 AGCAATGTCTTAAATGGATATTAAACCA
12623363 AG
1 AG
12623365 GATCAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (28 bp):
AGCAATGTCTTAAATGGATATTAAACCA
Found at i:12629533 original size:24 final size:24
Alignment explanation
Indices: 12629479--12629534 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
12629469 TCCTAGCAGT
* *
12629479 TTGAGTAGGTGCCTCAGCAGCAAG
1 TTGAGTGGGTGCCTCAGCAGCAAC
* * *
12629503 TTGAGTGGGTGCTTTAGTAGCAAC
1 TTGAGTGGGTGCCTCAGCAGCAAC
12629527 TTGAGTGG
1 TTGAGTGG
12629535 ACTCCTTGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (24 bp):
TTGAGTGGGTGCCTCAGCAGCAAC
Found at i:12634411 original size:43 final size:43
Alignment explanation
Indices: 12634341--12634445 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
12634331 AAAACACCAC
* * * * *
12634341 TATAGAACATGATCTTTAGTGGCGCTTTTCCTAAAAATGTCGA
1 TATAGAACATGATCTTTAGCGACGCTTTTACTAAAAACGCCGA
* * *
12634384 TATAGAACATGATCTTTAGCGATGCTTTTATTACAAACGCCGA
1 TATAGAACATGATCTTTAGCGACGCTTTTACTAAAAACGCCGA
* *
12634427 TAAAGAACATGATTTTTAG
1 TATAGAACATGATCTTTAG
12634446 GAACGTTTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (43 bp):
TATAGAACATGATCTTTAGCGACGCTTTTACTAAAAACGCCGA
Found at i:12634949 original size:21 final size:21
Alignment explanation
Indices: 12634911--12634961 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
12634901 TTTCTTGTTG
* *
12634911 CCTCTGCTAACCTTGCTGCTA
1 CCTCTGCTTACCTCGCTGCTA
* *
12634932 CCTCTGCTTCCCTCGCTGCTG
1 CCTCTGCTTACCTCGCTGCTA
*
12634953 CCTCCGCTT
1 CCTCTGCTT
12634962 TAAGTTGTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.45, G:0.16, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTACCTCGCTGCTA
Found at i:12640846 original size:35 final size:35
Alignment explanation
Indices: 12640805--12640874 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
12640795 TTTATATTCT
12640805 TTAAATGTTTATGTAAGTTATGACTATCATCTTTA
1 TTAAATGTTTATGTAAGTTATGACTATCATCTTTA
*
12640840 TTAAATGTTTATGTAAGTTATGATTATCATCTTTA
1 TTAAATGTTTATGTAAGTTATGACTATCATCTTTA
12640875 AATATTGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.50
Consensus pattern (35 bp):
TTAAATGTTTATGTAAGTTATGACTATCATCTTTA
Found at i:12644897 original size:41 final size:41
Alignment explanation
Indices: 12644832--12644919 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
12644822 AAATTCATGG
*
12644832 CGTTTATGGGAAAAACACTACTATTACTTTACCTTTTGTGA
1 CGTTAATGGGAAAAACACTACTATTACTTTACCTTTTGTGA
* * * *
12644873 CGTTAATGGGTAAAACATTGCTATTGCTTTACCTTTTGTGA
1 CGTTAATGGGAAAAACACTACTATTACTTTACCTTTTGTGA
12644914 CGTTAA
1 CGTTAA
12644920 AATGAAAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (41 bp):
CGTTAATGGGAAAAACACTACTATTACTTTACCTTTTGTGA
Found at i:12644929 original size:41 final size:41
Alignment explanation
Indices: 12644840--12644929 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
12644830 GGCGTTTATG
**
12644840 GGAAAAACACTACTATTACTTTACCTTTTGTGACGTTAATG
1 GGAAAAACACTACTATTACTTTACCTTTTGTGACGTTAAAA
* * * *
12644881 GGTAAAACATTGCTATTGCTTTACCTTTTGTGACGTTAAAA
1 GGAAAAACACTACTATTACTTTACCTTTTGTGACGTTAAAA
*
12644922 TGAAAAAC
1 GGAAAAAC
12644930 GCCACTATAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (41 bp):
GGAAAAACACTACTATTACTTTACCTTTTGTGACGTTAAAA
Found at i:12666535 original size:25 final size:25
Alignment explanation
Indices: 12666507--12666680 Score: 179
Period size: 25 Copynumber: 7.0 Consensus size: 25
12666497 AAAGCATTTA
12666507 AGAGAATTCGCCACAAAGGCTTTCT
1 AGAGAATTCGCCACAAAGGCTTTCT
* *
12666532 AGAGAGTTTGCCACAAAGGCTTTCT
1 AGAGAATTCGCCACAAAGGCTTTCT
* * *
12666557 AGAGAGTTTC-CCACAAAGGTTTTCC
1 AGAGA-ATTCGCCACAAAGGCTTTCT
* * *
12666582 AAAGAATTCACCACAAAGGCTTTCC
1 AGAGAATTCGCCACAAAGGCTTTCT
* * * *
12666607 AGATAGTTCACTACAAAGGCTTTCT
1 AGAGAATTCGCCACAAAGGCTTTCT
* **
12666632 AGAGAATTCTCCACAAAATCTTTCT
1 AGAGAATTCGCCACAAAGGCTTTCT
* *
12666657 AGAGAATTTGCAACAAAGGCTTTC
1 AGAGAATTCGCCACAAAGGCTTTC
12666681 CAAAGAAATT
Statistics
Matches: 122, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
24 3 0.02
25 117 0.96
26 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (25 bp):
AGAGAATTCGCCACAAAGGCTTTCT
Found at i:12666663 original size:75 final size:75
Alignment explanation
Indices: 12666507--12666682 Score: 212
Period size: 75 Copynumber: 2.3 Consensus size: 75
12666497 AAAGCATTTA
* ** *
12666507 AGAGAATTCGCCACAAAGGCTTTCTAGAGAGTTTGCCACAAAGGCTTTCTAGAGAGTTTCCCACA
1 AGAGAATTCGCCACAAAGGCTTTCCAGAGAGTTCACCACAAAGGCTTTCTAGAGAATTTCCCACA
*
12666572 AAGGTTTTCC
66 AAGATTTTCC
* * * *
12666582 AAAGAATTCACCACAAAGGCTTTCCAGATAGTTCACTACAAAGGCTTTCTAGAGAA-TTCTCCAC
1 AGAGAATTCGCCACAAAGGCTTTCCAGAGAGTTCACCACAAAGGCTTTCTAGAGAATTTC-CCAC
*
12666646 AAA-ATCTTTCT
65 AAAGAT-TTTCC
* *
12666657 AGAGAATTTGCAACAAAGGCTTTCCA
1 AGAGAATTCGCCACAAAGGCTTTCCA
12666683 AAGAAATTGC
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
74 4 0.05
75 81 0.95
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (75 bp):
AGAGAATTCGCCACAAAGGCTTTCCAGAGAGTTCACCACAAAGGCTTTCTAGAGAATTTCCCACA
AAGATTTTCC
Found at i:12666687 original size:25 final size:25
Alignment explanation
Indices: 12666507--12666704 Score: 173
Period size: 25 Copynumber: 7.9 Consensus size: 25
12666497 AAAGCATTTA
*
12666507 AGAGAATTCGCCACAAAGGCTTTCT
1 AGAGAATTTGCCACAAAGGCTTTCT
*
12666532 AGAGAGTTTGCCACAAAGGCTTTCT
1 AGAGAATTTGCCACAAAGGCTTTCT
* * * *
12666557 AGAGAGTTTCCCACAAAGGTTTTCC
1 AGAGAATTTGCCACAAAGGCTTTCT
* ** *
12666582 AAAGAATTCACCACAAAGGCTTTCC
1 AGAGAATTTGCCACAAAGGCTTTCT
* * ** *
12666607 AGATAGTTCACTACAAAGGCTTTCT
1 AGAGAATTTGCCACAAAGGCTTTCT
**
12666632 AGAGAATTCT-CCACAAAATCTTTCT
1 AGAGAATT-TGCCACAAAGGCTTTCT
* *
12666657 AGAGAATTTGCAACAAAGGCTTTCC
1 AGAGAATTTGCCACAAAGGCTTTCT
* * * *
12666682 AAAGAAATTGCCATAAAAGCTTT
1 AGAGAATTTGCCACAAAGGCTTT
12666705 TCAGGTAATC
Statistics
Matches: 141, Mismatches: 30, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
24 1 0.01
25 140 0.99
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (25 bp):
AGAGAATTTGCCACAAAGGCTTTCT
Found at i:12668221 original size:59 final size:59
Alignment explanation
Indices: 12668143--12668260 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 59
12668133 AATCCAATAG
12668143 CGACTAGAATATTTAATTTT-AAAAAATGAAGTGACTAAATCGAAAAATCCAATAGTTAA
1 CGACTAGAATATTTAATTTTGAAAAAAT-AAGTGACTAAATCGAAAAATCCAATAGTTAA
* * *
12668202 CGACTAGAATATTTAATTTTGAGAAACTAAGTGACTAAATCGAAAAATCCAGTAGTTAA
1 CGACTAGAATATTTAATTTTGAAAAAATAAGTGACTAAATCGAAAAATCCAATAGTTAA
12668261 ATGATGAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 50 0.91
60 5 0.09
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.29
Consensus pattern (59 bp):
CGACTAGAATATTTAATTTTGAAAAAATAAGTGACTAAATCGAAAAATCCAATAGTTAA
Found at i:12673912 original size:43 final size:42
Alignment explanation
Indices: 12673789--12673919 Score: 120
Period size: 43 Copynumber: 3.1 Consensus size: 42
12673779 GTATTCTAGA
* * *
12673789 AAGGAAAGAAATCAACTGAAATAAAATTGCAAT-TGAAACCA
1 AAGGAAAGAAATAAACTGAAATAAAATTGCAATGAGAAACCT
** * * **
12673830 AAAAAAATGAAGTAAAGTGAAATAAAATCACAATTGAGAAACCT
1 AAGGAAA-GAAATAAACTGAAATAAAATTGCAA-TGAGAAACCT
* * *
12673874 AAGGAAAGAAATGAACTGAAATAAGATTGCAATCGAGAAAACT
1 AAGGAAAGAAATAAACTGAAATAAAATTGCAAT-GAGAAACCT
12673917 AAG
1 AAG
12673920 TCTTAAGTAG
Statistics
Matches: 68, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
41 5 0.07
42 21 0.31
43 31 0.46
44 11 0.16
ACGTcount: A:0.56, C:0.10, G:0.17, T:0.17
Consensus pattern (42 bp):
AAGGAAAGAAATAAACTGAAATAAAATTGCAATGAGAAACCT
Found at i:12681125 original size:22 final size:24
Alignment explanation
Indices: 12681089--12681135 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
12681079 TATATTATTT
*
12681089 ATATAAATGATAAAAAT-AAATAG
1 ATATAAATGAAAAAAATAAAATAG
12681112 ATAT-AATGAAAAAAATAAAATAG
1 ATATAAATGAAAAAAATAAAATAG
12681135 A
1 A
12681136 AATACAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (24 bp):
ATATAAATGAAAAAAATAAAATAG
Found at i:12681974 original size:44 final size:45
Alignment explanation
Indices: 12681868--12682165 Score: 168
Period size: 44 Copynumber: 6.9 Consensus size: 45
12681858 GGATTATCGG
* * * *
12681868 CTTTAATCTGCTCCACTACAACTTCATGGA-GATGAGATTTGCCAT
1 CTTTAGTCTGCTCCACTGCAACTTCA-GGAGGATAAGACTTGCCAT
12681913 CTTTAGTCTGC-CTCACTGCAACTTCAGGAGGATAAGACTTGTCCA-
1 CTTTAGTCTGCTC-CACTGCAACTTCAGGAGGATAAGACTTG-CCAT
*
12681958 C-TTAGTCTGCTCCACTGCAACTTCAGG-GAGATAAGACTAG--AT
1 CTTTAGTCTGCTCCACTGCAACTTCAGGAG-GATAAGACTTGCCAT
* * * * ****
12682000 GC--GA-TCTGCT-CTCTGTAACTTCA-GAGAGATAAGATTTAAGGT
1 -CTTTAGTCTGCTCCACTGCAACTTCAGGAG-GATAAGACTTGCCAT
* * * * *
12682042 -TTTAATCCGCT-CACTGCAACTTTAGCGA-GATAGGA-TTACCGA-
1 CTTTAGTCTGCTCCACTGCAACTTCAG-GAGGATAAGACTTGCC-AT
* * * * *
12682084 CTTTAATCTGCTCCACTGTAACTTCAGGA-GATAAAATTTGTCAT
1 CTTTAGTCTGCTCCACTGCAACTTCAGGAGGATAAGACTTGCCAT
12682128 CTTTAGTCTGC-CTCACTGC-ACTTCAGGAGGATAAGACT
1 CTTTAGTCTGCTC-CACTGCAACTTCAGGAGGATAAGACT
12682166 CGATCTGTTA
Statistics
Matches: 199, Mismatches: 32, Indels: 45
0.72 0.12 0.16
Matches are distributed among these distances:
39 1 0.01
40 21 0.11
41 7 0.04
42 6 0.03
43 51 0.26
44 75 0.38
45 35 0.18
46 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (45 bp):
CTTTAGTCTGCTCCACTGCAACTTCAGGAGGATAAGACTTGCCAT
Found at i:12690147 original size:24 final size:24
Alignment explanation
Indices: 12690118--12690163 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
12690108 ATCATCTTTT
*
12690118 GCTGCTCATTCATTTACTTTTGAA
1 GCTGCTCATGCATTTACTTTTGAA
* *
12690142 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTACTTTTG
12690164 GGATTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTACTTTTGAA
Found at i:12694519 original size:22 final size:24
Alignment explanation
Indices: 12694483--12694529 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
12694473 CATATTATTT
*
12694483 ATATAAATGATAAAAAT-AAATAG
1 ATATAAATGAAAAAAATAAAATAG
12694506 ATAT-AATGAAAAAAATAAAATAG
1 ATATAAATGAAAAAAATAAAATAG
12694529 A
1 A
12694530 AATACAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (24 bp):
ATATAAATGAAAAAAATAAAATAG
Found at i:12700327 original size:50 final size:50
Alignment explanation
Indices: 12700214--12700396 Score: 285
Period size: 50 Copynumber: 3.6 Consensus size: 50
12700204 TTTGAGTGCT
* *
12700214 TCTGATTAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGATAAGTGGTAGC-TTAGCTACACTTA
* * *
12700265 TCTGATTAGTGACAAGTGATAGGTGATAAGTGGTAGCTTAGCTACATTTA
1 TCTGATCAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTA
12700315 TCTGATCAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTA
* * *
12700365 TCTGATCAGTGAGAAGAGATAAATGATAAGTG
1 TCTGATCAGTGACAAGTGATAAGTGATAAGTG
12700397 ATTCCGTGTA
Statistics
Matches: 123, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 88 0.72
51 35 0.28
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (50 bp):
TCTGATCAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:12709112 original size:2 final size:2
Alignment explanation
Indices: 12709105--12709131 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12709095 ACAAGCAAAA
12709105 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
12709132 AGAAGCTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12719312 original size:20 final size:21
Alignment explanation
Indices: 12719287--12719326 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12719277 AAACAACATT
*
12719287 AAAT-AATAGCAATTAAAAAG
1 AAATAAATAGAAATTAAAAAG
*
12719307 AAATAAATGGAAATTAAAAA
1 AAATAAATAGAAATTAAAAA
12719327 TAAAAGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.68, C:0.03, G:0.10, T:0.20
Consensus pattern (21 bp):
AAATAAATAGAAATTAAAAAG
Found at i:12731167 original size:21 final size:21
Alignment explanation
Indices: 12731125--12731169 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
12731115 ATTGCTTGTA
*
12731125 TTTGGTACATTTATTTGCATT
1 TTTGGTACATTTATTGGCATT
*
12731146 TTTGG-ACATTTCATTGGTATT
1 TTTGGTACATTT-ATTGGCATT
12731167 TTT
1 TTT
12731170 ATCATTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.18, C:0.09, G:0.16, T:0.58
Consensus pattern (21 bp):
TTTGGTACATTTATTGGCATT
Found at i:12735217 original size:16 final size:16
Alignment explanation
Indices: 12735196--12735226 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12735186 CCAACGAATA
*
12735196 TATATATGAATATATG
1 TATATATGAAAATATG
12735212 TATATATGAAAATAT
1 TATATATGAAAATAT
12735227 CAAAAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
TATATATGAAAATATG
Found at i:12735779 original size:25 final size:25
Alignment explanation
Indices: 12735743--12735793 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
12735733 CCGTTTTAGG
12735743 GCCACTGAGGTAGGCCCTAAACGGT
1 GCCACTGAGGTAGGCCCTAAACGGT
*
12735768 GCCACTGTGGTAGGCCCTAAACGGT
1 GCCACTGAGGTAGGCCCTAAACGGT
12735793 G
1 G
12735794 TCGTTTCATG
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:0.22, C:0.27, G:0.33, T:0.18
Consensus pattern (25 bp):
GCCACTGAGGTAGGCCCTAAACGGT
Found at i:12736889 original size:50 final size:49
Alignment explanation
Indices: 12736808--12737770 Score: 417
Period size: 50 Copynumber: 19.2 Consensus size: 49
12736798 GTGATGTCGA
* * * * * * * *
12736808 GGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTCCACTGCACCGCTAG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACGCT-G
* * ** *
12736858 GGAAGTAAGATTCACCACTGTGGCTTTAATCTTTTTAACTGCAATATCGG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAA-CGCTG
* * * * * *
12736908 GGAAGCAAGATTCACCGATGTGGCTTTCAT-TTATTCCACTGCATCGCCAG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTT-TTCAACTGCAACG-CTG
* * * * ** *
12736958 GGAGGTAAGATTCGCTGCTGTGGCTTTAATCTTTTTAACTGCAATTTCGG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAA-CGCTG
* * ** * * *
12737008 GGAAGTAAGATTCACCGATGTGGCTTTAACCTGCTCTACTGCACCACTAG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACGCT-G
* * * * *
12737058 GGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGCAATGCCGG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACG-CTG
** * * * * **
12737108 GGAAACAAGATTCACTGATGTGGCTTTAATCTGTTCCACTGCAGTGCCT-
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACG-CTG
* ** * * *
12737157 GGAAGGTAAGATTCACTGCTGTACCTTTAACCTTTTTAACTGCAATG-TCG
1 GGAA-GTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACGCT-G
* * ** * *
12737207 GGACA-TCAAAATTCACCGTTGTGGCTTTAATCTGCTCCACTGCATCGCCTG
1 GGA-AGT-AAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACG-CTG
* * * * * * *
12737258 GGGAGTAAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATGCCGG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACG-CTG
** * * * * *
12737308 GGAAACAAGATTCACCGATATGGCTTTAATCTGTTCCACTGCACCGCCTG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACG-CTG
* * * * * *
12737358 GGAGGTAAGATTCACGGCTGTAGCTTTAATCTTTTTAACCGCAATG-TGAG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACGCT--G
* ** * * * *
12737408 GGAGGCGAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACG-CTG
* * * * * ** * *
12737458 GGAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTAAACCACAATGTCAG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACG-CTG
* * *** * * *
12737508 GGAGGCAAGATTCACTATTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACG-CTG
* * * * * *** * *
12737558 GGAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAACCATAATGTCAG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACG-CTG
* * * ** * *
12737608 GGAGGCAAGATTCATCATTGTGGCTTTAATCTATTCCACTGCATCAC-CTG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCA--ACGCTG
* * * * * * * * *
12737658 GGAGGCAAGATTCGCTGTTGTAGCTTTAATCTTTTTGAACTGCAATGTTGG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATC-TTTTCAACTGCAACGCT-G
* * ** * * * *
12737709 GGAAGCAAGATTTACCAATGTGGCTTTAATCTGTTCCACTACATCGCCTG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACG-CTG
*
12737759 GGAGGTAAGATT
1 GGAAGTAAGATT
12737771 TGTAATTCTT
Statistics
Matches: 662, Mismatches: 226, Indels: 50
0.71 0.24 0.05
Matches are distributed among these distances:
48 2 0.00
49 9 0.01
50 604 0.91
51 44 0.07
52 3 0.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (49 bp):
GGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTCAACTGCAACGCTG
Found at i:12736960 original size:100 final size:100
Alignment explanation
Indices: 12736781--12737770 Score: 1132
Period size: 100 Copynumber: 9.9 Consensus size: 100
12736771 TAACTCATAA
** * * * * * * * *
12736781 CTTTAAT-TTGTTTAACTGTGATGTCGAGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTCC
1 CTTTAATCTT-TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCC
* * ** *
12736845 ACTGCACCG-CTAGGGAAGTAAGATTCACCACTGTGG
65 ACTGCACCGCCT-GGGAGGTAAGATTCGCTGCTGTAG
* * * *
12736881 CTTTAATCTTTTTAACTGCAATATCGGGGAAGCAAGATTCACCGATGTGGCTTTCATTTATTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* * *
12736946 CTGCATCGCCAGGGAGGTAAGATTCGCTGCTGTGG
66 CTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAG
* * * * *
12736981 CTTTAATCTTTTTAACTGCAATTTCGGGGAAGTAAGATTCACCGATGTGGCTTTAACCTGCTCTA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* * * * *
12737046 CTGCACC-ACTAGGGAAGTAGGATTCGCCGCTGTGG
66 CTGCACCGCCT-GGGAGGTAAGATTCGCTGCTGTAG
* * *
12737081 CTTTAATCTTTTTAACTGCAATGCCGGGGAAACAAGATTCACTGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
** * * *
12737146 CTGCAGTGCCTGGAAGGTAAGATTCACTGCTGTAC
66 CTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAG
* * * * *
12737181 CTTTAACCTTTTTAACTGCAATGTC-GGGACATCAAAATTCACCGTTGTGGCTTTAATCTGCTCC
1 CTTTAATCTTTTTAACTGCAATGTCGGGGA-AGCAAGATTCACCGATGTGGCTTTAATCTGTTCC
* * *
12737245 ACTGCATCGCCTGGG-GAGTAAGATTCACTGTTGTAG
65 ACTGCACCGCCTGGGAG-GTAAGATTCGCTGCTGTAG
* * *
12737281 CTTTAATCTTTTTAACTGCAATGCCGGGGAAACAAGATTCACCGATATGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* *
12737346 CTGCACCGCCTGGGAGGTAAGATTCACGGCTGTAG
66 CTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAG
* * * *
12737381 CTTTAATCTTTTTAACCGCAATGT-GAGGGAGGCGAGATTCACCGTTGTGGCTTTAATCTGTTCC
1 CTTTAATCTTTTTAACTGCAATGTCG-GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCC
12737445 ACTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAG
65 ACTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAG
* ** * * *
12737481 CTTTAATCTTTTAAACCACAATGTCAGGGAGGCAAGATTCA-CTATTGTGGCTTTAATCTGTTCC
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGTTCC
12737545 ACTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAG
65 ACTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAG
*** * * * *
12737581 CTTTAATCTTTTTAACCATAATGTCAGGGAGGCAAGATTCATC-ATTGTGGCTTTAATCTATTCC
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGTTCC
* * * *
12737645 ACTGCATCACCTGGGAGGCAAGATTCGCTGTTGTAG
65 ACTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAG
* * *
12737681 CTTTAATCTTTTTGAACTGCAATGTTGGGGAAGCAAGATTTACCAATGTGGCTTTAATCTGTTCC
1 CTTTAATCTTTTT-AACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCC
* *
12737746 ACTACATCGCCTGGGAGGTAAGATT
65 ACTGCACCGCCTGGGAGGTAAGATT
12737771 TGTAATTCTT
Statistics
Matches: 770, Mismatches: 106, Indels: 27
0.85 0.12 0.03
Matches are distributed among these distances:
99 8 0.01
100 688 0.89
101 73 0.09
102 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
CTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAG
Found at i:12737932 original size:44 final size:44
Alignment explanation
Indices: 12737873--12738556 Score: 275
Period size: 44 Copynumber: 14.7 Consensus size: 44
12737863 TTTTAATCCC
12737873 GCTCCACTG-AATCTCAGGGAGATAGGATTACTAGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
* * ** *
12737916 GCTCCACTGTATTCTCAGGGAGATAAGATTTTTGGCTTCAATCTGAT
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATC---T
* * * * * * * *
12737963 GCGATCTACTCTACTATAACTTCAGAGAGATAAGATCCT-TTA-TTTTAATCA
1 GC--TCCACTGTA--AT--C-TCAGGGAGATAGGAT--TACTAGCTTCAATCT
* *
12738014 GCTCCACTGTATTCTCAGGGAGATAGGATTACTAGCTTCAATAT
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
* * * *
12738058 GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGT
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATC-----T
* * * * * *
12738107 GATCTACACTACTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTTAATCC
1 G--CT-C-C-ACTGTAATC-TCAGGGAGATAGGAT--TACTAGCTTCAATCT
*
12738156 ACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
* * *
12738200 GCTCCGCTGTAATCTCAGGGAGAT-GAGATTTCTGGCTTCAATCTGAT
1 GCTCCACTGTAATCTCAGGGAGATAG-GATTACTAGCTTCAATC---T
* * * * *
12738247 GCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTTAATCT
1 --G--CT-C-C-ACTGTAATC-TCAGGGAGATAGGAT--TACTAGCTTCAATCT
12738298 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
* * *
12738342 GCTCCACTGTAATCTCAGGAAGAT-GAGATTCCTGGCTTCAATCTAATGT
1 GCTCCACTGTAATCTCAGGGAGATAG-GATTACTAGCTTCAATC-----T
* * * * * * *
12738391 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTTAGTCC
1 G--CT-C-C-ACTGTAATC-TCAGGGAGATAGGAT--TACTAGCTTCAATCT
* * *
12738440 GATCCACTGTAATCTCAAGGAGATAGGATTAATAGCTTC-ATCT
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
* * * ** * *
12738483 ACTCCGCTGTAATCTCAGGGAGAAAATATTTCTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
*
12738527 GCTCCACTGTAA-CATCAGGGAGATAAGATT
1 GCTCCACTGTAATC-TCAGGGAGATAGGATT
12738557 CACCATTTCT
Statistics
Matches: 478, Mismatches: 94, Indels: 137
0.67 0.13 0.19
Matches are distributed among these distances:
42 4 0.01
43 51 0.11
44 260 0.54
45 7 0.01
46 3 0.01
47 10 0.02
49 21 0.04
51 10 0.02
52 3 0.01
53 7 0.01
54 93 0.19
55 5 0.01
56 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
Found at i:12738075 original size:142 final size:142
Alignment explanation
Indices: 12737819--12738527 Score: 1145
Period size: 142 Copynumber: 5.0 Consensus size: 142
12737809 ATAAGACCTT
* *
12737819 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCCGCTCCACTG-A
1 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAT-CAGCTCCACTGTA
* * *
12737883 ATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTATTCTCAGGGAGATAAGATTTT
65 ATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTC
12737948 TGGCTTCAATCTG
130 TGGCTTCAATCTG
* *
12737961 ATGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCAGCTCCACTGTAT
1 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCAGCTCCACTGTAA
*
12738026 TCTCAGGGAGATAGGATTACTAGCTTCAATATGCTCCGCTGTAATCTCAGGGAGATAAGATTTCT
66 TCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCT
12738091 GGCTTCAATCTG
131 GGCTTCAATCTG
* *
12738103 ATGTGATCTACACTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCA-CTCCACTGTA
1 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAT-CAGCTCCACTGTA
*
12738167 ATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATGAGATTTC
65 ATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTC
12738232 TGGCTTCAATCTG
130 TGGCTTCAATCTG
*
12738245 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAA
1 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCAGCTCCACTGTAA
* * * *
12738310 TCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGAAGATGAGATTCCT
66 TCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCT
*
12738375 GGCTTCAATCTA
131 GGCTTCAATCTG
* * * *
12738387 ATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAGTCCGATCCACTGTAA
1 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCAGCTCCACTGTAA
* * * * *
12738452 TCTCAAGGAGATAGGATTAATAGCTTC-ATCTACTCCGCTGTAATCTCAGGGAGAAAATATTTCT
66 TCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCT
12738516 GGCTTCAATCTG
131 GGCTTCAATCTG
12738528 CTCCACTGTA
Statistics
Matches: 529, Mismatches: 35, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
141 52 0.10
142 475 0.90
143 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (142 bp):
ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCAGCTCCACTGTAA
TCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCT
GGCTTCAATCTG
Found at i:12738263 original size:98 final size:97
Alignment explanation
Indices: 12738156--12738342 Score: 227
Period size: 98 Copynumber: 1.9 Consensus size: 97
12738146 ATTTTAATCC
* * *
12738156 ACTCCACTGTAA-TCTCAGGGAGATAGGAT-TACTAGCTTCAATCTGCTCCGCTGTAATCTCAGG
1 ACTCCACTGTAACT-TCAGAGAGATAAGATCT-CTA-CTTCAATCTGCTCCACTGTAATCTCAGG
* *
12738219 GAGAT-GAGATTTCTGGCTTCAATCTGATGCGATCT
63 GAGATAG-GATTACTAGCTTCAATCTGATGCGATCT
* * * *
12738254 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGA
1 ACTCCACTGTAACTTCAGAGAGATAAGAT-CTCTACTTCAATCTGCTCCACTGTAATCTCAGGGA
12738319 GATAGGATTACTAGCTTCAATCTG
65 GATAGGATTACTAGCTTCAATCTG
12738343 CTCCACTGTA
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
98 71 0.93
99 4 0.05
100 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (97 bp):
ACTCCACTGTAACTTCAGAGAGATAAGATCTCTACTTCAATCTGCTCCACTGTAATCTCAGGGAG
ATAGGATTACTAGCTTCAATCTGATGCGATCT
Found at i:12740932 original size:30 final size:30
Alignment explanation
Indices: 12740868--12740961 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 30
12740858 CATATTTTTA
* * * *
12740868 TTTTGACTTTAATTGATTTCTCTTTTTTT-C
1 TTTTGACTTTGATT-TTTTCTTTTTTTTTGT
12740898 TTTTGACTTTGATTTTTTCTTTTTTTTTGT
1 TTTTGACTTTGATTTTTTCTTTTTTTTTGT
* *
12740928 TTTTGATTTTGATTTTGAT-TTTTTTTTTGT
1 TTTTGACTTTGATTTT-TTCTTTTTTTTTGT
12740958 TTTT
1 TTTT
12740962 TTATTGAATC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.21
30 43 0.77
31 1 0.02
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (30 bp):
TTTTGACTTTGATTTTTTCTTTTTTTTTGT
Found at i:12746681 original size:16 final size:16
Alignment explanation
Indices: 12746660--12746697 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
12746650 CAACGAATAT
12746660 ATATATATATATATGA
1 ATATATATATATATGA
*
12746676 ATATATGTATATATGA
1 ATATATATATATATGA
*
12746692 AAATAT
1 ATATAT
12746698 CAAAAATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (16 bp):
ATATATATATATATGA
Found at i:12749925 original size:6 final size:6
Alignment explanation
Indices: 12749841--12749916 Score: 100
Period size: 6 Copynumber: 12.7 Consensus size: 6
12749831 GATTTCTCTT
* * * *
12749841 TTTTGC TTTTGA CTTTGA TTTT-T TTATTTA TTTTGA TTTTGA TTTTGA
1 TTTTGA TTTTGA TTTTGA TTTTGA TT-TTGA TTTTGA TTTTGA TTTTGA
12749889 TTTTGA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTT
12749917 TTTGTTTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
5 2 0.03
6 58 0.94
7 2 0.03
ACGTcount: A:0.14, C:0.03, G:0.13, T:0.70
Consensus pattern (6 bp):
TTTTGA
Found at i:12754831 original size:16 final size:16
Alignment explanation
Indices: 12754810--12754840 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12754800 CCAACGAATA
*
12754810 TATATATGAATATATG
1 TATATATGAAAATATG
12754826 TATATATGAAAATAT
1 TATATATGAAAATAT
12754841 CAAAAATAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
TATATATGAAAATATG
Found at i:12773451 original size:14 final size:14
Alignment explanation
Indices: 12773432--12773463 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
12773422 TTAATTGAAA
12773432 AAATTATTTAAATT
1 AAATTATTTAAATT
12773446 AAATTATTTAAATT
1 AAATTATTTAAATT
12773460 AAAT
1 AAAT
12773464 AAATAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTATTTAAATT
Found at i:12778039 original size:28 final size:28
Alignment explanation
Indices: 12777981--12778040 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
12777971 AAAACCCTTT
* *
12777981 TTTTTTTAAATTTATCGAAATGGGCCGA
1 TTTTTTTAAATTTACCGAAATGAGCCGA
* *
12778009 TTTTTTTATTATTTACCGGAATGAGCC-A
1 TTTTTTTA-AATTTACCGAAATGAGCCGA
12778037 TTTT
1 TTTT
12778041 CTGCGAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (28 bp):
TTTTTTTAAATTTACCGAAATGAGCCGA
Done.